Optimized protein family-specific gap penalties for the VTML200 and BLOSUM50 matrices derived for the SUP groups from the SABmark database.
Group N reference
alignments		 Average
length		 SCOP sunid SCOP description VTML200
Gap INIT		 VTML200
Gap EXT		 BLOSUM50
Gap INIT		 BLOSUM50
Gap EXT
1 300 149 46458 Globin-like 14 2 17 2
2 6 146 46548 alpha-helical ferredoxin 22 1 21 1
3 10 84 46566 Chaperone J-domain 12 2 14 2
4 6 80 46589 tRNA-binding arm 31 1 22 6
5 28 89 46610 "Fe,Mn superoxide dismutase (SOD), N-terminal domain" 23 2 34 5
6 300 124 46627 monodomain cytochrome c 15 1 12 1
7 300 68 46689 Homeodomain-like 11 2 12 2
8 3 85 46771 O6-alkylguanine-DNA alkyltransferase 15 5 18 5
9 3 112 46775 ARID domain 11 1 14 1
10 300 111 46785 Winged helix DNA-binding domain 13 1 19 1
11 15 91 46894 C-terminal effector domain of the bipartite response regulators 13 3 16 4
12 10 51 46934 UBA-like 23 1 18 2
13 21 92 46946 S13-like H2TH domain 25 1 24 1
14 36 77 46955 Putative DNA-binding domain 17 2 19 2
15 21 115 46966 Spectrin repeat 26 2 24 2
16 10 144 46978 Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain 34 1 18 1
17 3 56 46997 Bacterial immunoglobulin/albumin-binding domains 5 5 3 2
18 6 39 47015 Protozoan pheromone proteins 15 2 19 1
19 3 110 47032 Second domain of FERM 10 4 16 2
20 3 71 47060 S15/NS1 RNA-binding domain 12 2 14 5
21 21 80 47097 "HMG1, domains A and B" 25 4 17 3
22 45 99 47113 Histone-fold 24 1 26 1
23 21 125 47180 Cytochrome c' 12 4 20 9
24 3 158 47196 TMV-like viral coat proteins 10 2 12 2
25 10 166 47203 Acyl-CoA dehydrogenase C-terminal domain-like 21 3 21 3
26 120 240 47240 Ferritin-like 31 1 28 1
27 105 147 47305 Interferons/interleukin-10 (IL-10) 31 3 17 5
28 28 165 47325 Methionyl-tRNA synthetase (MetRS) 19 1 17 1
29 15 85 47336 ACP-like 16 3 10 6
30 3 80 47354 Retrovirus capsid protein C-terminal domain 18 2 18 3
31 3 85 47365 Domain of the SRP/SRP receptor G-proteins 7 3 7 4
32 6 123 47370 Bromodomain 18 1 17 1
33 66 70 47413 lambda repressor-like DNA-binding domains 22 1 10 1
34 21 75 47460 Helix-loop-helix DNA-binding domain 14 1 24 1
35 300 140 47473 EF-hand 15 1 27 1
36 21 116 47576 "Calponin-homology domain, CH-domain" 20 2 23 1
37 10 62 47598 Met repressor-like 12 10 10 6
38 231 133 47617 "Glutathione S-transferase (GST), C-terminal domain" 18 2 20 1
39 6 70 47649 Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain 11 7 12 8
40 3 109 47662 t-snare proteins 11 10 18 1
41 6 88 47699 Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin 13 1 12 1
42 6 86 47729 IHF-like DNA-binding proteins 7 2 8 2
43 3 89 47742 CO dehydrogenase ISP C-domain like 12 1 13 1
44 10 75 47773 SAM (sterile alpha motif) domain 42 25 36 8
45 6 97 47781 RuvA domain 2-like 9 2 9 1
46 10 114 47815 Flap endonuclease-1 (Fen-1 nuclease) 17 1 20 1
47 10 110 47836 Retroviral matrix proteins 13 1 13 1
48 6 79 47863 NKL-like 9 1 10 1
49 15 282 47875 Annexin 23 2 26 3
50 3 126 47918 C-terminal domain of alpha and beta subunits of F1 ATP synthase 19 1 13 2
51 3 141 47944 "Retrovirus capsid protein, N-terminal core domain" 9 3 15 2
52 91 122 47954 Cyclin-like 14 1 16 1
53 55 104 47986 DEATH domain 16 3 15 3
54 3 116 48020 "DNA polymerase III clamp loader subunits, C-terminal domain" 17 4 19 1
55 3 209 48066 DBL homology domain (DH-domain) 18 1 15 1
56 10 150 48098 "Regulator of G-protein signalling, RGS" 10 1 12 1
57 36 346 48114 CCP-like 24 1 18 1
58 28 196 48150 DNA-glycosylase 21 1 21 1
59 6 266 48175 C-terminal domain of DNA photolyase 22 1 21 1
60 36 179 48179 6-phosphogluconate dehydrogenase C-terminal domain-like 20 2 20 1
61 55 448 48208 Six-hairpin glycosyltransferases 27 1 14 1
62 10 355 48234 "Hyaluronate lyase-like catalytic, N-terminal domain" 20 2 14 1
63 10 300 48239 Terpenoid cylases/Protein prenyltransferases 14 1 16 5
64 15 392 48258 Citrate synthase 27 1 23 1
65 36 410 48265 Cytochrome P450 24 1 21 1
67 3 235 48351 BCR-homology GTPase activation domain (BH-domain) 7 2 31 1
68 36 246 48371 ARM repeat 11 5 4 1
69 28 153 48404 Ankyrin repeat 35 1 35 2
70 28 179 48453 Tetratricopeptide repeat (TPR) 24 1 30 1
71 3 147 48468 VHS domain 12 5 10 5
72 28 245 48509 Nuclear receptor ligand-binding domain 16 3 22 1
73 3 253 48537 Phospholipase C/P1 nuclease 34 3 29 3
74 10 168 48552 Serum albumin-like 23 1 21 1
75 6 456 48558 L-aspartase/fumarase 40 1 49 1
76 45 123 48624 Snake phospholipase A2 15 1 17 1
77 171 206 48696 Cytochrome c3-like 14 1 16 1
78 300 124 48727 V set domains (antibody variable domain-like) 13 2 16 2
79 300 102 49266 Fibronectin type III 11 2 11 4
80 3 107 49304 beta-Galactosidase/glucuronidase domain 8 1 10 1
81 21 107 49309 "Transglutaminase, two C-terminal domains" 13 3 17 4
82 6 110 49314 Cadherin 10 2 11 3
83 6 112 49320 Actinoxanthin-like 11 1 11 3
84 6 150 49341 "Copper chaperone for superoxide dismutase, C-terminal domain" 8 3 9 1
85 6 130 49348 Clathrin adaptor appendage domain 16 3 13 4
86 15 95 49373 Invasin/intimin cell-adhesion fragments 23 2 17 5
87 28 140 49384 Carbohydrate-binding domain 13 2 13 1
88 21 149 49401 Bacterial adhesins 22 4 19 2
89 21 192 81315 "Rel/Dorsal transcription factors, DNA-binding domain" 11 1 14 1
90 6 105 49453 Starch-binding domain 24 6 24 13
91 3 250 49483 Aromatic compound dioxygenase 9 1 14 1
92 300 165 49503 Cupredoxins 15 1 16 1
93 10 136 49575 Synaptotagmin-like (S variant) 14 1 17 2
94 3 166 49599 TRAF domain-like 23 1 20 5
95 36 88 49695 gamma-Crystallin-like 21 5 9 4
96 3 156 49742 PHM/PNGase F 6 3 15 4
97 10 219 49749 Group II dsDNA viruses VP 20 1 8 3
98 3 125 49764 HSP20-like chaperones 28 1 19 1
99 300 165 49785 Galactose-binding domain-like 8 2 21 7
100 21 223 49820 "Virus capsid protein vp7 (BTV-10 vp7), central (top) domain" 21 2 23 2
101 6 159 49837 "Adenovirus fiber protein ""knob"" domain" 13 3 11 2
102 10 143 49843 TNF-like 20 2 20 3
103 3 104 49864 "Hyaluronate lyase-like, C-terminal domain" 23 1 22 1
104 6 129 49879 SMAD/FHA domain 30 1 15 1
105 300 199 49899 Concanavalin A-like lectins/glucanases 14 1 28 1
106 21 144 50023 Rieske iron-sulfur protein (ISP) 20 2 17 1
107 3 62 50037 C-terminal domain of transcriptional repressors 14 5 11 6
108 231 70 50045 SH3-domain 18 1 18 1
109 10 128 50090 Electron transport accessory proteins 17 1 16 1
110 15 95 50104 Translation proteins SH3-like domain 16 1 16 1
111 3 101 50130 GroES 23 7 17 1
112 120 99 50157 PDZ domain 15 1 14 1
113 45 72 50183 "Sm motif of small nuclear ribonucleoproteins, SNRNP" 17 1 18 1
114 66 100 50203 Bacterial enterotoxins 30 1 18 1
115 6 155 50242 TIMP-like 10 1 12 2
116 300 145 50249 Nucleic acid-binding proteins 15 1 15 3
117 3 211 50326 Inorganic pyrophosphatase 16 1 34 1
118 36 73 50331 MOP-like 13 2 19 1
119 15 138 50354 Fibroblast growth factors (FGF) 26 2 14 3
120 28 130 50370 Ricin B-like lectins 13 2 15 1
121 21 191 50386 STI-like 13 2 11 1
122 3 116 50405 Actin-crosslinking proteins 9 5 12 4
123 10 157 50448 Elongation factors 17 2 12 1
124 3 101 50467 Elongation factor Tu (EF-Tu) 21 1 24 1
125 10 179 50475 FMN-binding split barrel 18 3 17 1
126 300 239 50495 Prokaryotic proteases 15 1 21 1
127 3 76 50616 N-terminal domain of alpha and beta subunits of F1 ATP synthase 17 1 24 1
128 55 235 50646 Pepsin-like 27 2 18 2
129 6 182 50678 ValRS/IleRS/LeuRS editing domain 26 2 20 1
130 36 131 50708 Cdc48 N-terminal domain-like 13 2 16 2
131 171 118 50729 PH domain-like 13 3 13 2
132 3 100 50802 Pyruvate kinase (PK) 8 4 14 1
133 300 151 50814 Lipocalins 16 2 15 4
134 3 167 50892 Cyclophilin (peptidylprolyl isomerase) 9 2 9 2
135 6 196 50924 Hemopexin-like domain 14 5 13 10
136 28 405 50940 Sialidases (neuraminidases) 14 1 20 1
137 6 311 50978 WD40 repeat-like 13 2 15 4
138 300 82 51012 "alpha-Amylases, C-terminal beta-sheet domain" 12 2 13 2
139 10 43 51046 WW domain 13 1 17 6
140 3 246 51071 Carbonic anhydrase 12 2 11 2
141 3 209 51098 "delta-Endotoxin (insectocide), middle domain" 10 3 12 2
142 3 112 51112 Lectin (agglutinin) 10 1 10 1
143 66 374 51126 Pectin lyase-like 12 1 6 3
144 28 219 51161 Trimeric LpxA-like enzymes 13 1 10 1
145 78 190 51182 RmlC-like cupins 19 3 22 3
146 6 320 51197 Clavaminate synthase-like 10 1 12 2
147 21 135 51206 cAMP-binding domain-like 20 1 19 1
148 28 90 51231 Biotinyl/lipoyl-carrier proteins and domains 20 2 16 2
149 10 79 51247 BC C-terminal domain-like 15 3 18 3
150 3 154 51262 Glucose permease-like 16 2 21 1
151 3 119 51280 "Urease, beta-subunit" 17 1 16 1
152 10 137 51285 Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase) 20 1 21 1
153 3 240 51353 Triosephosphate isomerase 10 3 14 3
154 66 233 51366 Ribulose-phoshate binding barrel 15 2 18 1
155 10 345 51396 FMN-linked oxidoreductases 11 1 12 1
156 10 329 51431 Aldo-keto reductases (NADP) 17 1 15 1
157 300 445 51445 (Trans)glycosidases 19 1 19 1
158 28 344 51556 Metallo-dependent hydrolases 18 3 16 2
159 171 286 51570 Class I aldolase 12 1 17 4
160 28 256 51604 Enolase C-terminal domain-like 15 1 15 1
161 15 316 51621 Phosphoenolpyruvate/pyruvate domain 11 4 12 5
162 3 369 51666 D-xylose isomerase 17 6 16 2
163 3 298 51679 Bacterial luciferase-like 17 1 16 2
164 3 265 51695 PLC-like phosphodiesterases 20 3 24 3
165 6 513 51703 Cobalamin (vitamin B12)-dependent enzymes 20 1 24 1
166 300 281 51735 NAD(P)-binding Rossmann-fold domains 15 1 22 1
167 210 131 51905 FAD/NAD(P)-binding domain 13 2 12 2
168 3 332 51993 Cellobiohydrolase II (Cel6) 12 4 18 3
170 10 284 52047 RNI-like 32 1 31 3
171 91 208 52058 L domain-like 14 2 12 4
172 21 251 52103 Crotonase-like 14 1 12 1
173 6 94 52113 BRCT domain 14 2 12 2
174 15 155 52123 Lumazine synthase 16 4 15 3
175 10 211 52141 DNA glycosylase 12 1 13 1
176 55 132 52173 CheY-related 22 2 23 2
177 55 177 52219 Flavodoxin-related 15 1 18 2
178 6 156 52243 Cobalamin (vitamin B12)-binding domain 44 1 24 1
179 3 249 52266 SGHN hydrolase 9 4 8 1
180 3 149 52306 Type II 3-dehydroquinate dehydratase 18 6 17 5
181 36 202 52317 Class I glutamine amidotransferase-like 12 1 9 1
182 91 148 52343 "Ferredoxin reductase-like, C-terminal NADP-linked domain" 17 1 21 1
183 78 256 52374 Nucleotidylyl transferase 15 1 19 1
184 36 199 81393 "Large, alpha subunit of electron transfer flavoprotein ETFP, N-terminal domain" 19 2 19 1
185 6 195 52427 DNA photolyase 16 2 22 2
186 66 111 52440 PreATP-grasp domain 10 2 11 2
187 66 185 52467 DHS-like NAD/FAD-binding domain 20 1 19 1
188 10 211 52492 Cell-division protein FtsZ 14 2 14 2
189 6 211 52499 Cysteine hydrolase 34 1 25 2
190 136 218 52518 Thiamin diphosphate-binding fold (THDP-binding) 18 1 18 1
191 300 301 52540 P-loop containing nucleoside triphosphate hydrolases 19 1 21 1
192 28 317 52743 Subtilisin-like 13 2 11 1
193 3 326 52768 Arginase/deacetylase 8 3 7 4
194 15 223 52782 Dihydrolipoamide acetyltransferase 17 4 17 1
195 3 148 52789 Low-molecular-weight phosphotyrosine protein phosphatases 13 1 11 1
196 55 219 52799 (Phosphotyrosine protein) phosphatases II 15 2 17 2
197 3 146 52821 Rhodanese/Cell cycle control phosphatase 5 2 6 5
198 300 124 52833 Thioredoxin-like 10 2 14 2
199 15 150 52922 TK C-terminal domain-like 17 1 23 1
200 3 129 52937 "Pyruvate kinase, C-terminal domain" 15 1 18 1
201 3 176 52949 Macro domain-like 17 1 16 1
202 28 111 52955 Anticodon-binding domain of Class II aaRS 20 1 21 1
203 91 205 52980 Restriction endonuclease-like 10 2 10 2
204 6 209 53058 beta-carbonic anhydrase 14 1 15 1
205 153 212 53067 Actin-like ATPase domain 16 1 11 1
206 55 211 53098 Ribonuclease H-like 20 1 13 1
207 6 132 53137 Translational machinery components 22 1 23 1
208 3 260 53169 "Purine nucleoside phosphorylase, PNP" 11 4 21 10
209 28 312 53187 Zn-dependent exopeptidases 12 3 21 1
210 78 151 53236 Tetrahydrofolate dehydrogenase/cyclohydrolase 19 1 24 1
211 15 243 53254 Phosphoglycerate mutase-like 19 2 20 2
212 55 217 53272 Phosphoribosyltransferases (PRTases) 19 1 21 1
213 15 200 53301 Integrin A (or I) domain 18 1 17 1
214 300 271 53335 S-adenosyl-L-methionine-dependent methyltransferases 12 1 23 1
215 300 407 53383 PLP-dependent transferases 14 1 18 1
216 28 251 53448 Nucleotide-diphospho-sugar transferases 13 2 15 5
217 300 360 53474 alpha/beta-Hydrolases 18 1 20 1
218 21 171 53598 Dihydrofolate reductases 14 2 14 3
219 3 322 53614 Ribokinase-like 8 4 7 4
220 3 293 53635 Carbamate kinase 14 1 16 2
221 3 234 53640 AraD-like aldolase/epimerase 14 2 20 1
222 3 468 53651 Alkaline phosphatase 18 1 16 1
223 6 465 53659 Isocitrate/Isopropylmalate dehydrogenases 10 1 13 1
224 45 161 53676 Ornithine transcarbamoylase 14 2 13 3
225 6 120 53681 Aspartate/glutamate racemase 15 1 16 1
226 10 336 53694 1-aminocyclopropane-1-carboxylate deaminase 15 2 16 3
227 3 455 53702 "Phosphoglucose isomerase, PGI" 22 4 16 3
228 3 634 53707 "Formate dehydrogenase/DMSO reductase, domains 1-3" 19 1 21 1
229 15 487 53722 "Aldehyde reductase (dehydrogenase), ALDH" 28 2 18 1
230 21 141 53738 "Phosphoglucomutase, first 3 domains" 20 2 9 1
231 3 407 53750 Phosphoglycerate kinase 24 2 27 1
232 3 499 53756 UDP-Glycosyltransferase/glycogen phosphorylase 9 1 5 4
233 3 327 53776 Asparaginase type II 14 1 15 1
234 6 320 53802 Ferrochelatase 17 2 16 3
235 21 361 53807 Helical backbone metal receptor 39 1 14 1
236 45 317 53823 L-arabinose binding protein-like 15 2 18 3
237 153 328 53850 Periplasmic binding protein-like II 17 1 45 27
238 153 182 53901 Thiolase-like 24 1 18 1
239 6 144 53927 Cytidine deaminase-like 20 2 10 2
240 3 103 53933 Microbial ribonucleases 8 4 12 3
241 55 179 53955 Lysozyme-like 10 1 12 1
242 190 278 54001 Cysteine proteinases 16 1 46 1
243 6 159 54060 His-Me finger endonucleases 1 1 2 1
244 3 127 54077 Ribonuclease A-like 10 2 11 1
245 66 70 54118 Interleukin 8-like chemokines 15 1 16 1
246 10 63 54160 Chromo domain-like 10 2 14 1
247 10 70 54171 DNA-binding domain 21 1 15 6
248 3 124 54189 Ribosomal proteins L23 and L15e 12 1 6 1
249 3 153 54197 HIT-like 11 2 13 3
250 105 140 54211 Ribosomal protein S5 domain 2-like 6 1 12 6
251 105 90 54236 Ubiquitin-like 11 2 17 1
252 10 94 54278 CAD domain 15 1 21 1
253 3 72 54285 MoaD/ThiS 10 1 12 1
254 171 101 54293 2Fe-2S ferredoxin-related 12 1 15 1
255 3 116 54328 Staphylokinase/streptokinase 8 4 9 4
256 28 110 54335 "Superantigen toxins, C-terminal domain" 9 4 15 1
257 91 119 54373 "FAD-linked reductases, C-terminal domain" 14 3 12 2
258 10 103 54407 Cystatins 20 1 22 1
259 28 104 54416 Amine oxidase N-terminal region 9 2 13 1
260 45 137 54432 Nuclear transport factor-2 (NTF2) 12 2 16 2
261 105 146 54453 MHC antigen-recognition domain 25 3 28 2
262 36 149 54497 "Ubiquitin conjugating enzyme, UBC" 17 1 14 1
263 3 140 54525 Pilin 7 3 6 4
264 91 120 54535 FKBP immunophilin/proline isomerase 17 1 15 1
265 21 74 54557 Chitinase insertion domain 15 3 15 2
266 55 147 54593 Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase 22 1 20 1
267 10 146 54637 Thioesterase/thiol ester dehydrase-isomerase 15 1 12 3
268 3 65 54655 CI-2 family of serine protease inhibitors 9 5 11 4
269 6 135 54666 CO dehydrogenase molybdoprotein N-domain-like 15 1 18 1
270 3 113 54677 "Quinolinic acid phosphoribosyltransferase (NadC), N-terminal domain" 11 4 15 3
271 15 98 54696 BTB/POZ domain 25 1 30 2
272 3 123 54713 "Elongation factor Ts (EF-Ts), dimerisation domain" 23 1 20 1
273 45 114 54720 "Fe,Mn superoxide dismutase (SOD), C-terminal domain" 22 1 15 2
274 28 89 54768 dsRNA-binding domain-like 23 2 19 2
275 21 81 54792 Eukaryotic type KH-domain (KH-domain type I) 14 1 24 1
276 10 88 54815 Prokaryotic type KH domain (KH-domain type II) 13 1 19 1
277 6 131 54827 Enolase N-terminal domain-like 14 4 15 2
278 91 107 54862 4Fe-4S ferredoxins 14 1 12 1
279 15 84 54897 Protease propeptides/inhibitors 26 1 15 4
280 3 101 54909 Dimeric alpha+beta barrel 13 6 15 3
281 6 98 54913 GlnB-like 18 6 23 4
282 6 143 54921 Nucleoside diphosphate kinases 18 1 22 1
283 231 89 54929 Canonical RBD 20 1 18 1
284 3 83 54980 EF-G C-terminal domain-like 21 2 12 1
285 36 72 55009 Metal-binding domain 11 1 8 5
286 3 90 55021 Regulatory domain in the aminoacid metabolism 10 2 12 2
287 6 140 55060 "GHMP Kinase, C-terminal domain" 15 3 15 5
288 3 206 55099 Beta chain 5 2 5 2
289 6 127 55120 Pseudouridine synthase 4 1 27 7
290 6 123 55174 Alpha-L RNA-binding motif 33 1 30 1
291 6 185 55196 "Ribosome recycling factor, RRF" 17 1 17 1
292 3 124 55241 "Ribulose 1,5-bisphosphate carboxylase-oxygenase" 12 1 7 1
293 3 78 55288 RPB5 1 1 17 1
294 10 127 55298 YjgF-like 5 1 8 1
295 6 153 55309 Cell-division protein FtsZ 16 3 17 3
296 3 116 55316 L30e/L7ae ribosomal proteins 33 1 34 1
297 15 101 55339 MIF-related 44 9 37 11
298 66 160 55349 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) 9 2 11 2
299 66 119 55425 "FAD/NAD-linked reductases, dimerisation (C-terminal) domain" 15 5 18 2
300 3 114 55448 CO dehydrogenase flavoprotein C-terminal domain-like 6 3 11 1
301 6 148 55464 "Origin of replication-binding domain, RBD-like" 15 1 34 1
302 6 218 55476 Oxygen-insensitive NAD(P)H nitroreductase 16 1 14 2
303 231 292 55486 "Metalloproteases (""zincins""), catalytic domain" 14 1 22 1
304 3 142 55545 beta-N-acetylhexosaminidase-like domain 10 2 10 2
305 120 116 55551 SH2 domain 18 1 20 1
306 6 86 55595 HPr-like 11 2 12 2
307 6 130 55608 Homing endonucleases 34 1 17 1
308 15 149 55620 Tetrahydrobiopterin biosynthesis enzymes-like 24 2 14 1
309 28 294 55682 "Class II aminoacyl-tRNA synthetase (aaRS)-like, catalyic domain" 14 1 18 1
310 66 185 55730 "N-acetyl transferase, NAT" 16 1 19 1
311 55 129 55762 Cofilin-like 18 1 22 1
312 3 130 55772 Profilin (actin-binding protein) 14 1 7 2
313 6 172 55782 GAF domain 27 1 10 1
314 21 116 55785 PYP-like sensor domain (PAS domain) 25 1 27 1
315 3 196 55805 IIA domain of mannitol-specific and ntr phosphotransferase EII 24 1 29 1
316 10 147 55811 Nudix 20 1 18 1
317 6 275 55832 Thymidylate synthase/dCMP hydroxymethylase 16 1 25 1
318 3 89 55857 Cytochrome b5 7 1 7 1
319 28 187 55874 ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 12 1 14 1
320 10 203 55896 Ribonuclease Rh-like 11 1 14 1
321 10 282 55909 Pentein 33 2 14 2
322 6 255 55921 Creatinase/aminopeptidase 31 1 37 1
323 3 303 55931 Glutamine synthase/guanido kinase 11 1 10 1
324 15 97 55945 TATA-box binding protein-like 17 1 9 1
325 3 122 55958 "Phosphoglucomutase, C-terminal domain" 8 1 8 1
326 10 194 55962 Pathogenesis-related protein 10 (PR10)-like 9 2 14 1
327 3 133 55973 S-adenosylmethionine synthetase 14 1 11 1
328 45 123 55979 DNA clamp 10 1 13 2
329 3 633 56004 Molybdemum cofactor-binding domain 21 5 21 3
330 3 111 56030 Monooxygenase (hydroxylase) regulatory protein 11 1 13 1
331 6 84 56053 Ribosomal protein L6 16 1 9 4
332 45 243 56059 Glutathione synthetase ATP-binding domain-like 19 1 13 1
333 78 308 88854 "Protein kinases, catalytic subunit" 20 1 18 1
334 28 210 56177 "FAD-linked oxidases, N-terminal domain" 12 1 21 1
335 6 116 64419 Holo-(acyl carrier protein) synthase ACPS 17 1 21 2
336 300 233 56236 Class II glutamine amidotransferases 20 1 25 1
337 21 243 56281 Metallo-hydrolase/oxidoreductase 18 1 20 1
338 15 285 56300 Metallo-dependent phosphatases 14 1 11 1
339 66 171 56328 "Lactate & malate dehydrogenases, C-terminal domain" 15 2 12 3
340 28 251 56372 Plant cytotoxins 17 1 12 3
341 28 206 56399 ADP-ribosylation 16 1 14 1
342 21 132 56426 "Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain" 13 1 14 1
343 276 120 56437 C-type lectin domain 12 2 16 2
344 3 225 56498 Fibrinogen C-terminal domains 12 1 10 1
345 3 376 56575 Serpins 10 2 11 3
346 78 285 56606 "beta-Lactamase, class A" 11 1 17 1
347 10 508 56635 Heme-linked catalases 21 1 21 1
348 10 239 56645 Acyl-CoA dehydrogenase NM domain-like 20 1 17 2
349 10 306 56656 "Inositol monophosphatase/fructose-1,6-bisphosphatase-like" 14 1 11 2
350 15 447 56672 DNA/RNA polymerases 31 1 21 1
351 3 315 56753 D-aminoacid aminotransferase-like PLP-dependent enzymes 20 4 20 4
352 21 220 56784 HAD-like 17 1 20 1
354 3 223 56838 Colicin 12 2 14 2
355 3 238 56851 "delta-Endotoxin (insectocide), N-terminal domain" 20 1 34 1
356 6 180 56855 Bcl-2 inhibitors of programmed cell death 17 2 18 2
358 3 158 56925 OMPA-like 17 8 16 9
359 21 446 56935 Porins 31 2 29 3
360 6 37 57017 Hevein-like agglutinin (lectin) domain 28 1 28 1
361 210 37 57072 Spider toxins 10 2 11 3
362 231 48 57097 Scorpion toxin 11 1 14 1
363 28 110 57185 Growth factor receptor domain 12 1 15 2
364 6 41 57190 Colipase-like 9 1 7 1
365 300 47 57196 EGF/Laminin 14 1 16 2
366 10 50 57262 Leech antihemostatic proteins 4 4 4 2
367 45 68 57303 Snake venom toxins 22 2 16 2
368 78 59 57363 Small Kunitz-type ihibitors & BPTI-like toxins 12 2 12 2
369 78 40 57393 Defensin 18 2 15 2
370 3 89 57414 Hairpin loop containing domain-like 15 9 9 2
371 36 43 57424 LDL receptor-like module 19 1 18 1
372 3 46 57430 Crambin-like 7 1 7 1
373 66 73 57440 Kringle-like 12 1 15 2
374 55 53 57467 Ovomucoid/PCI-1 like inhibitors 23 1 25 1
375 3 57 57493 Trefoil 5 1 6 1
376 36 113 57501 Cystine-knot cytokines 17 1 17 1
377 231 64 57535 Complement control module/SCR domain 11 2 14 2
378 3 53 57553 Blood coagulation inhibitor (disintegrin) 1 1 1 1
379 10 65 57568 ATI-like 7 1 17 1
380 36 45 57586 TNF receptor-like 14 1 10 1
381 15 46 57603 FnI-like domain 10 3 10 2
382 10 72 57654 HIPIP (high potential iron protein) 14 1 12 5
383 171 35 57667 C2H2 and C2HC zinc fingers 12 1 13 1
384 10 45 57702 Zn2/Cys6 DNA-binding domain 12 1 14 1
385 300 51 57716 Glucocorticoid receptor-like (DNA-binding domain) 13 1 22 1
386 3 38 57757 Retrovirus zinc finger-like domains 10 1 19 1
387 3 35 57776 "Microbial and mitochondrial ADK, insert ""zinc finger"" domain" 6 1 6 1
388 36 62 57783 Zinc beta-ribbon 20 1 22 1
389 10 58 57802 Rubredoxin-like 11 1 10 1
390 6 70 57829 Zn-binding ribosomal proteins 3 2 24 1
391 55 76 57851 "RING finger domain, C3HC4" 19 1 14 2
392 15 42 57870 Metallothionein 20 2 23 1
393 6 53 57889 Cysteine-rich domain 16 2 14 4
394 15 64 57903 FYVE/PHD zinc finger 13 3 12 4
395 10 108 57925 Inhibitor of apoptosis (IAP) repeat 20 1 19 1
396 136 139 63381 Ferredoxin reductase FAD-binding domain-like 14 1 18 1
397 66 212 63411 LuxS/MPP-like metallohydrolase 16 1 17 3
398 3 49 63451 LEM domain 11 3 14 2
399 3 84 63571 PABC (PABP) domain 6 3 7 4
400 6 94 63748 Tudor/PWWP/MBT 12 1 17 1
401 6 89 88852 SirA-like 7 2 8 3
402 6 141 75521 Clathrin coat assembly domain 9 3 10 5
403 3 69 64588 C-terminal domain of ProRS 9 1 10 2
404 3 44 68907 SAP domain 8 1 10 1
405 3 225 68925 Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-liase) 16 1 37 1
406 3 102 69697 SRP19 14 5 10 4
407 28 284 50006 "Hyaluronate lyase-like, central domain" 10 6 11 2
408 300 121 81296 E set domains 10 2 14 3
409 6 173 81588 "Poly(A) polymerase N-terminal, catalytic domain" 19 2 16 4
410 3 175 81319 Bacteriorhodopsin-like 9 7 7 6
411 6 108 81323 Voltage-gated potassium channels 14 5 18 3
412 10 149 81373 Succinate dehydrogenase/Fumarate reductase transmembrane subunits (SdhC/FrdC and SdhD/FrdD) 21 2 28 2
413 3 237 81451 Cytochrome c oxidase subunit III-like 47 16 47 15
414 6 80 81463 "Cytochrome c oxidase subunit II-like, transmembrane region" 21 2 24 1
415 3 302 81482 "Bacterial photosystem II reaction centre, L and M subunits" 16 4 40 1
416 10 127 81623 N-terminal domain of MutM-like DNA repair proteins 20 2 14 2
417 3 80 82057 Prokaryotic SH3-related domain 34 1 36 1
418 3 180 82200 Histone lysine methyltransferases 36 1 29 1
419 300 248 88633 Positive stranded ssRNA viruses 13 1 17 1
420 21 350 88645 ssDNA viruses 18 7 24 2
421 3 363 88648 Group I dsDNA viruses 10 1 12 1
422 3 157 88650 Satellite viruses 12 5 9 5
423 6 62 88659 Sigma3 and sigma4 domains of RNA polymerase sigma factors 12 3 20 3
424 3 139 88697 PUA domain-like 8 8 10 6
425 3 124 88947 Sigma2 domain of RNA polymerase sigma factors 19 1 37 1
Development of this resource was supported by NIH grant R15GM090228