Query 014440
Match_columns 424
No_of_seqs 266 out of 1197
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 05:08:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014440.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014440hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2807 RNA polymerase II tran 100.0 1E-121 3E-126 887.0 28.7 369 26-414 9-377 (378)
2 COG5151 SSL1 RNA polymerase II 100.0 8E-106 2E-110 772.1 22.5 375 26-414 36-420 (421)
3 PF04056 Ssl1: Ssl1-like; Int 100.0 2.9E-54 6.3E-59 401.7 21.5 191 91-281 1-193 (193)
4 TIGR00622 ssl1 transcription f 100.0 2.6E-48 5.7E-53 329.3 7.5 105 303-412 1-111 (112)
5 TIGR00627 tfb4 transcription f 100.0 6.9E-41 1.5E-45 328.1 23.7 233 87-327 4-279 (279)
6 cd01453 vWA_transcription_fact 100.0 4.9E-40 1.1E-44 305.0 23.5 183 83-265 1-183 (183)
7 PF03850 Tfb4: Transcription f 100.0 6E-36 1.3E-40 293.8 22.2 229 87-324 3-276 (276)
8 KOG2487 RNA polymerase II tran 100.0 6.4E-34 1.4E-38 271.2 15.5 234 86-328 24-298 (314)
9 cd01452 VWA_26S_proteasome_sub 100.0 2.1E-31 4.6E-36 248.0 21.8 155 87-242 5-163 (187)
10 COG5242 TFB4 RNA polymerase II 100.0 1.4E-27 3.1E-32 222.6 19.8 233 87-328 22-285 (296)
11 PRK13685 hypothetical protein; 99.9 7.5E-24 1.6E-28 213.1 21.7 170 87-261 90-287 (326)
12 cd01467 vWA_BatA_type VWA BatA 99.9 3.9E-20 8.5E-25 168.7 20.2 159 87-252 4-179 (180)
13 cd01455 vWA_F11C1-5a_type Von 99.9 1.8E-20 3.8E-25 174.7 17.8 167 87-262 2-187 (191)
14 PF13519 VWA_2: von Willebrand 99.9 3.3E-20 7.1E-25 165.2 18.1 165 87-260 1-172 (172)
15 PF07975 C1_4: TFIIH C1-like d 99.8 9.8E-22 2.1E-26 145.0 1.3 49 364-412 1-51 (51)
16 TIGR03436 acidobact_VWFA VWFA- 99.8 7.6E-18 1.6E-22 166.5 18.3 166 87-262 55-252 (296)
17 cd01456 vWA_ywmD_type VWA ywmD 99.8 1.6E-17 3.4E-22 156.0 17.8 155 87-249 22-202 (206)
18 cd01466 vWA_C3HC4_type VWA C3H 99.8 1E-17 2.2E-22 150.9 15.7 146 87-247 2-154 (155)
19 cd01451 vWA_Magnesium_chelatas 99.8 3E-17 6.6E-22 150.9 19.1 158 88-252 3-169 (178)
20 TIGR00868 hCaCC calcium-activa 99.8 3.7E-17 8.1E-22 180.7 20.6 160 86-256 305-469 (863)
21 cd01465 vWA_subgroup VWA subgr 99.8 9.1E-17 2E-21 144.6 19.4 161 87-257 2-170 (170)
22 cd01461 vWA_interalpha_trypsin 99.7 1E-16 2.2E-21 144.2 17.8 161 85-257 2-169 (171)
23 cd01472 vWA_collagen von Wille 99.7 1.7E-16 3.7E-21 143.3 17.9 154 87-248 2-161 (164)
24 cd01470 vWA_complement_factors 99.7 2.5E-16 5.4E-21 146.9 17.3 165 87-257 2-197 (198)
25 cd01480 vWA_collagen_alpha_1-V 99.7 2.4E-16 5.3E-21 145.9 16.4 166 87-262 4-181 (186)
26 cd01463 vWA_VGCC_like VWA Volt 99.7 2.8E-16 6E-21 145.8 15.4 151 86-250 14-189 (190)
27 cd01474 vWA_ATR ATR (Anthrax T 99.7 1.2E-15 2.6E-20 141.0 19.5 166 87-261 6-178 (185)
28 smart00327 VWA von Willebrand 99.7 1.9E-15 4.2E-20 135.0 19.4 155 86-246 2-164 (177)
29 KOG2884 26S proteasome regulat 99.7 1.1E-15 2.4E-20 142.8 17.6 156 87-243 5-164 (259)
30 cd01477 vWA_F09G8-8_type VWA F 99.7 2.3E-15 5.1E-20 141.2 18.3 157 82-246 18-191 (193)
31 cd01469 vWA_integrins_alpha_su 99.7 3.2E-15 6.9E-20 137.5 17.8 162 87-254 2-175 (177)
32 cd01450 vWFA_subfamily_ECM Von 99.7 3E-15 6.4E-20 132.2 16.9 152 87-244 2-159 (161)
33 cd01460 vWA_midasin VWA_Midasi 99.6 3.2E-15 6.9E-20 146.6 14.8 145 76-229 53-205 (266)
34 cd01475 vWA_Matrilin VWA_Matri 99.6 1.9E-14 4E-19 137.2 19.1 169 87-263 4-182 (224)
35 cd00198 vWFA Von Willebrand fa 99.6 2.3E-14 5E-19 124.3 17.2 152 87-244 2-160 (161)
36 cd01471 vWA_micronemal_protein 99.6 4.1E-14 9E-19 130.2 18.4 166 87-258 2-183 (186)
37 PRK13406 bchD magnesium chelat 99.6 3.5E-14 7.6E-19 152.9 20.1 165 86-258 402-580 (584)
38 cd01482 vWA_collagen_alphaI-XI 99.6 7.1E-14 1.5E-18 126.6 17.8 151 87-245 2-158 (164)
39 PTZ00441 sporozoite surface pr 99.6 1.1E-13 2.5E-18 146.7 19.4 175 79-260 38-226 (576)
40 COG5148 RPN10 26S proteasome r 99.6 1.2E-13 2.6E-18 126.8 16.6 156 86-242 4-162 (243)
41 PF00092 VWA: von Willebrand f 99.5 1.6E-13 3.6E-18 123.3 15.4 167 87-259 1-177 (178)
42 cd01473 vWA_CTRP CTRP for CS 99.5 1.8E-13 3.8E-18 128.1 16.1 167 87-258 2-184 (192)
43 TIGR03788 marine_srt_targ mari 99.5 4.2E-13 9E-18 145.4 18.4 164 84-259 270-440 (596)
44 PF13768 VWA_3: von Willebrand 99.5 5.5E-13 1.2E-17 119.1 15.1 143 87-245 2-154 (155)
45 cd01476 VWA_integrin_invertebr 99.5 1.6E-12 3.5E-17 116.8 17.8 142 87-237 2-154 (163)
46 cd01458 vWA_ku Ku70/Ku80 N-ter 99.5 5E-13 1.1E-17 126.9 14.8 144 87-230 3-174 (218)
47 cd01464 vWA_subfamily VWA subf 99.5 2.7E-13 5.9E-18 124.1 12.4 142 87-238 5-159 (176)
48 TIGR02442 Cob-chelat-sub cobal 99.5 1E-12 2.3E-17 143.3 19.0 154 87-247 467-632 (633)
49 COG1240 ChlD Mg-chelatase subu 99.5 1.7E-12 3.6E-17 125.3 17.1 158 87-251 80-248 (261)
50 TIGR02031 BchD-ChlD magnesium 99.5 1.5E-12 3.2E-17 141.0 18.7 155 87-249 409-582 (589)
51 cd01454 vWA_norD_type norD typ 99.4 6.7E-12 1.4E-16 114.6 17.3 135 87-230 2-154 (174)
52 cd01462 VWA_YIEM_type VWA YIEM 99.4 2.8E-11 6E-16 107.8 16.8 134 87-229 2-135 (152)
53 cd01481 vWA_collagen_alpha3-VI 99.4 3.6E-11 7.9E-16 109.9 17.2 147 86-240 1-156 (165)
54 cd01457 vWA_ORF176_type VWA OR 99.3 2.8E-11 6.1E-16 113.3 15.3 149 86-239 3-165 (199)
55 COG4245 TerY Uncharacterized p 98.8 1.2E-07 2.6E-12 87.8 13.2 159 87-261 5-181 (207)
56 PF10138 vWA-TerF-like: vWA fo 98.6 1.3E-06 2.9E-11 82.4 15.4 150 87-241 3-157 (200)
57 PF03731 Ku_N: Ku70/Ku80 N-ter 98.6 1.1E-06 2.5E-11 83.4 14.1 139 88-226 2-172 (224)
58 cd01479 Sec24-like Sec24-like: 98.4 1.6E-05 3.5E-10 77.4 18.6 152 87-248 5-219 (244)
59 PF05762 VWA_CoxE: VWA domain 98.4 4.4E-06 9.6E-11 80.0 13.4 125 86-225 58-186 (222)
60 cd01468 trunk_domain trunk dom 98.4 2.5E-05 5.4E-10 75.5 18.5 154 87-249 5-223 (239)
61 PRK10997 yieM hypothetical pro 98.4 9.3E-06 2E-10 86.1 15.6 139 87-238 325-468 (487)
62 PF04811 Sec23_trunk: Sec23/Se 98.4 1.4E-05 2.9E-10 77.3 15.5 154 87-249 5-225 (243)
63 COG2425 Uncharacterized protei 98.2 8.4E-06 1.8E-10 85.1 11.9 155 87-257 274-432 (437)
64 TIGR00578 ku70 ATP-dependent D 98.1 7E-05 1.5E-09 81.6 16.3 142 87-228 12-183 (584)
65 PF06707 DUF1194: Protein of u 98.0 4.4E-05 9.6E-10 72.4 11.4 142 87-230 5-158 (205)
66 COG4867 Uncharacterized protei 98.0 0.00012 2.6E-09 75.4 15.1 156 87-260 465-646 (652)
67 smart00187 INB Integrin beta s 98.0 0.00022 4.8E-09 74.2 16.9 165 87-261 101-335 (423)
68 cd01478 Sec23-like Sec23-like: 97.9 0.00084 1.8E-08 66.3 17.1 92 166-257 139-265 (267)
69 PLN00162 transport protein sec 97.6 0.005 1.1E-07 69.2 19.9 96 167-262 261-391 (761)
70 KOG2353 L-type voltage-depende 97.3 0.0016 3.4E-08 75.1 12.2 152 86-251 226-399 (1104)
71 PTZ00395 Sec24-related protein 97.3 0.0045 9.7E-08 71.7 14.8 158 79-245 946-1176(1560)
72 PF11265 Med25_VWA: Mediator c 97.3 0.028 6E-07 54.3 17.9 162 80-245 8-203 (226)
73 KOG1984 Vesicle coat complex C 96.9 0.019 4.1E-07 64.0 15.1 152 87-247 419-634 (1007)
74 COG2304 Uncharacterized protei 96.9 0.019 4E-07 58.5 13.8 153 86-247 38-198 (399)
75 PF00362 Integrin_beta: Integr 96.8 0.042 9.1E-07 57.9 16.2 160 87-257 104-334 (426)
76 KOG3768 DEAD box RNA helicase 96.5 0.056 1.2E-06 58.2 14.2 186 87-281 3-259 (888)
77 PF09967 DUF2201: VWA-like dom 96.4 0.016 3.4E-07 51.0 8.2 78 88-180 1-79 (126)
78 cd01459 vWA_copine_like VWA Co 96.2 0.14 3.1E-06 50.4 14.5 155 81-238 27-206 (254)
79 COG5028 Vesicle coat complex C 95.9 0.13 2.9E-06 56.9 13.5 149 87-245 278-482 (861)
80 KOG1985 Vesicle coat complex C 95.9 0.16 3.5E-06 56.7 14.1 148 87-245 296-506 (887)
81 KOG1986 Vesicle coat complex C 95.8 0.58 1.3E-05 51.6 17.8 163 88-262 124-378 (745)
82 TIGR01651 CobT cobaltochelatas 95.2 0.41 9E-06 52.1 14.4 78 171-257 499-589 (600)
83 COG3552 CoxE Protein containin 95.2 0.15 3.3E-06 52.4 10.3 118 86-217 219-340 (395)
84 COG4548 NorD Nitric oxide redu 95.1 0.11 2.5E-06 55.5 9.5 91 163-257 528-628 (637)
85 PF11775 CobT_C: Cobalamin bio 95.0 0.81 1.7E-05 44.1 14.2 59 170-230 118-189 (219)
86 KOG2326 DNA-binding subunit of 95.0 0.58 1.3E-05 50.7 14.3 171 88-265 7-215 (669)
87 COG1721 Uncharacterized conser 94.9 0.53 1.1E-05 49.3 14.0 71 87-160 226-296 (416)
88 KOG2462 C2H2-type Zn-finger pr 94.4 0.044 9.5E-07 54.1 4.0 40 303-342 130-187 (279)
89 PF07002 Copine: Copine; Inte 94.1 0.93 2E-05 41.0 11.7 118 104-227 9-146 (146)
90 PF01363 FYVE: FYVE zinc finge 91.4 0.12 2.5E-06 40.2 1.8 40 356-399 3-42 (69)
91 KOG2462 C2H2-type Zn-finger pr 91.1 0.16 3.5E-06 50.2 2.8 77 303-396 161-257 (279)
92 PRK04023 DNA polymerase II lar 90.9 0.18 3.9E-06 57.5 3.3 69 338-416 595-675 (1121)
93 TIGR00373 conserved hypothetic 89.8 0.21 4.5E-06 45.7 2.2 26 303-328 109-139 (158)
94 smart00064 FYVE Protein presen 89.8 0.22 4.7E-06 38.6 2.0 40 356-399 4-43 (68)
95 KOG1226 Integrin beta subunit 89.1 3.1 6.8E-05 46.5 10.8 164 87-259 134-365 (783)
96 PRK06266 transcription initiat 88.6 0.27 5.9E-06 45.9 2.1 27 303-329 117-148 (178)
97 KOG1327 Copine [Signal transdu 88.2 5.5 0.00012 43.1 11.8 156 83-241 283-466 (529)
98 cd00729 rubredoxin_SM Rubredox 88.1 0.38 8.3E-06 32.8 2.0 24 303-326 2-27 (34)
99 PF11443 DUF2828: Domain of un 85.7 13 0.00029 40.4 13.1 134 82-226 337-482 (534)
100 PF09538 FYDLN_acid: Protein o 85.2 0.41 9E-06 41.2 1.2 28 303-330 9-39 (108)
101 COG3864 Uncharacterized protei 84.7 3 6.5E-05 42.3 7.1 79 87-181 263-341 (396)
102 cd00065 FYVE FYVE domain; Zinc 84.5 0.54 1.2E-05 34.9 1.4 34 363-400 3-36 (57)
103 cd00350 rubredoxin_like Rubred 84.0 0.87 1.9E-05 30.6 2.1 22 304-325 2-25 (33)
104 TIGR02300 FYDLN_acid conserved 83.2 0.64 1.4E-05 41.0 1.5 32 303-334 9-43 (129)
105 PRK12496 hypothetical protein; 83.0 4.9 0.00011 37.0 7.3 98 206-332 59-158 (164)
106 COG1592 Rubrerythrin [Energy p 82.5 0.86 1.9E-05 42.1 2.2 24 303-326 134-158 (166)
107 smart00531 TFIIE Transcription 82.3 0.73 1.6E-05 41.5 1.6 27 303-329 99-135 (147)
108 PF09723 Zn-ribbon_8: Zinc rib 81.4 1.1 2.3E-05 31.9 1.8 30 382-412 5-34 (42)
109 PRK00398 rpoP DNA-directed RNA 81.1 1.2 2.5E-05 32.1 2.0 26 303-328 3-32 (46)
110 PF03833 PolC_DP2: DNA polymer 80.7 0.51 1.1E-05 53.2 0.0 68 337-414 622-702 (900)
111 TIGR01384 TFS_arch transcripti 79.8 1.8 3.8E-05 36.4 3.0 31 362-392 62-100 (104)
112 TIGR02605 CxxC_CxxC_SSSS putat 79.8 1 2.3E-05 33.0 1.4 30 303-332 5-45 (52)
113 PF01485 IBR: IBR domain; Int 79.8 1.1 2.4E-05 33.5 1.6 42 363-404 19-62 (64)
114 PF13639 zf-RING_2: Ring finge 79.7 0.79 1.7E-05 32.4 0.7 42 364-410 2-43 (44)
115 cd06167 LabA_like LabA_like pr 79.5 5.2 0.00011 35.1 6.1 62 167-238 82-144 (149)
116 PF07754 DUF1610: Domain of un 78.9 1.6 3.4E-05 27.6 1.8 24 365-390 1-24 (24)
117 PF10571 UPF0547: Uncharacteri 77.9 1.3 2.9E-05 28.4 1.3 23 305-327 2-24 (26)
118 PRK14890 putative Zn-ribbon RN 77.7 2.4 5.2E-05 32.6 2.8 47 362-412 7-56 (59)
119 PF01936 NYN: NYN domain; Int 77.3 3.1 6.8E-05 36.0 4.0 61 168-238 79-140 (146)
120 PF04438 zf-HIT: HIT zinc fing 77.2 0.98 2.1E-05 29.9 0.5 14 303-316 13-26 (30)
121 COG5271 MDN1 AAA ATPase contai 76.8 39 0.00085 42.3 13.2 174 77-261 4386-4590(4600)
122 COG0528 PyrH Uridylate kinase 76.3 19 0.00041 35.3 9.2 45 85-135 3-51 (238)
123 PRK14714 DNA polymerase II lar 76.3 2.3 5E-05 50.1 3.5 23 303-327 667-689 (1337)
124 PF04285 DUF444: Protein of un 76.1 22 0.00047 37.7 10.4 109 88-215 249-360 (421)
125 PF12760 Zn_Tnp_IS1595: Transp 76.1 1.3 2.7E-05 32.0 0.9 23 303-325 18-45 (46)
126 TIGR01206 lysW lysine biosynth 76.0 1.6 3.6E-05 32.9 1.5 24 303-327 2-32 (54)
127 PF08271 TF_Zn_Ribbon: TFIIB z 75.9 1 2.2E-05 32.0 0.3 24 304-327 1-29 (43)
128 PF13923 zf-C3HC4_2: Zinc fing 75.9 1.1 2.4E-05 30.8 0.6 29 382-410 11-39 (39)
129 PRK05325 hypothetical protein; 75.8 21 0.00045 37.7 10.0 109 88-215 225-336 (401)
130 PF13240 zinc_ribbon_2: zinc-r 75.6 1.5 3.2E-05 27.3 1.0 22 306-327 2-23 (23)
131 PF05191 ADK_lid: Adenylate ki 75.5 2.6 5.7E-05 29.1 2.3 26 304-329 2-33 (36)
132 PRK14714 DNA polymerase II lar 75.3 2.1 4.6E-05 50.4 2.9 45 363-415 668-720 (1337)
133 PF13719 zinc_ribbon_5: zinc-r 74.7 1.7 3.7E-05 30.0 1.2 29 364-392 4-35 (37)
134 cd02340 ZZ_NBR1_like Zinc fing 74.0 2 4.4E-05 30.7 1.5 28 364-397 2-30 (43)
135 smart00647 IBR In Between Ring 74.0 3.4 7.3E-05 30.9 2.9 43 362-404 18-62 (64)
136 TIGR02877 spore_yhbH sporulati 73.9 31 0.00068 35.9 10.6 110 88-216 205-317 (371)
137 TIGR00599 rad18 DNA repair pro 73.4 2.9 6.4E-05 43.8 3.2 45 362-414 26-70 (397)
138 KOG0320 Predicted E3 ubiquitin 72.5 2.3 5E-05 39.7 1.8 28 385-412 148-175 (187)
139 PRK14559 putative protein seri 72.2 2.9 6.3E-05 46.5 3.0 6 364-369 17-22 (645)
140 smart00834 CxxC_CXXC_SSSS Puta 72.2 2.9 6.3E-05 28.8 2.0 30 382-412 5-34 (41)
141 KOG2932 E3 ubiquitin ligase in 72.0 2.1 4.6E-05 43.1 1.6 41 362-412 90-131 (389)
142 PF09538 FYDLN_acid: Protein o 71.8 2.8 6.1E-05 36.1 2.1 34 359-395 6-39 (108)
143 PF01927 Mut7-C: Mut7-C RNAse 71.7 3.8 8.3E-05 36.8 3.1 11 382-392 124-134 (147)
144 KOG0978 E3 ubiquitin ligase in 71.5 1 2.3E-05 50.0 -0.7 49 363-419 644-693 (698)
145 KOG4465 Uncharacterized conser 70.3 22 0.00047 36.9 8.4 125 87-228 429-563 (598)
146 PF01882 DUF58: Protein of unk 69.9 8.6 0.00019 30.6 4.5 41 86-126 41-81 (86)
147 PF03853 YjeF_N: YjeF-related 69.3 20 0.00042 32.8 7.3 66 186-253 22-93 (169)
148 KOG4317 Predicted Zn-finger pr 69.0 2.2 4.7E-05 43.1 1.0 28 290-317 6-33 (383)
149 PLN03086 PRLI-interacting fact 68.1 6.5 0.00014 43.1 4.5 23 305-327 435-463 (567)
150 COG2888 Predicted Zn-ribbon RN 67.0 4.8 0.0001 31.0 2.3 47 362-412 9-58 (61)
151 COG1675 TFA1 Transcription ini 66.9 3.1 6.7E-05 38.9 1.5 27 303-329 113-144 (176)
152 TIGR02098 MJ0042_CXXC MJ0042 f 66.6 3 6.6E-05 28.5 1.1 25 304-328 3-36 (38)
153 PRK04023 DNA polymerase II lar 66.1 4.3 9.2E-05 46.9 2.6 23 302-326 625-647 (1121)
154 PRK00415 rps27e 30S ribosomal 65.7 2.8 6.2E-05 32.2 0.8 27 305-331 13-44 (59)
155 cd00730 rubredoxin Rubredoxin; 65.7 4 8.6E-05 30.3 1.6 22 304-325 2-42 (50)
156 PHA02929 N1R/p28-like protein; 65.3 5.8 0.00013 38.8 3.1 51 362-412 174-224 (238)
157 TIGR00288 conserved hypothetic 64.3 24 0.00052 32.5 6.8 76 153-238 70-150 (160)
158 PRK14892 putative transcriptio 64.2 3.6 7.8E-05 34.9 1.3 25 303-327 21-52 (99)
159 cd05017 SIS_PGI_PMI_1 The memb 63.8 12 0.00026 31.8 4.5 55 191-251 45-100 (119)
160 PF13717 zinc_ribbon_4: zinc-r 63.4 5.2 0.00011 27.5 1.7 29 364-392 4-35 (36)
161 TIGR00627 tfb4 transcription f 62.0 9.7 0.00021 38.1 4.1 36 363-413 243-278 (279)
162 KOG1819 FYVE finger-containing 61.9 2.4 5.2E-05 45.3 -0.2 33 361-397 900-932 (990)
163 cd00162 RING RING-finger (Real 61.1 5.6 0.00012 26.7 1.6 41 365-412 2-43 (45)
164 PF12773 DZR: Double zinc ribb 60.1 9 0.0002 27.6 2.6 23 306-328 1-23 (50)
165 cd02335 ZZ_ADA2 Zinc finger, Z 59.4 5.8 0.00013 29.0 1.5 30 364-398 2-32 (49)
166 PRK07418 acetolactate synthase 58.2 1E+02 0.0022 34.0 11.6 89 168-262 434-547 (616)
167 PRK02842 light-independent pro 57.9 67 0.0015 33.8 9.7 79 207-286 302-385 (427)
168 PF02318 FYVE_2: FYVE-type zin 57.8 2.5 5.3E-05 36.7 -0.9 47 361-410 53-100 (118)
169 PF10221 DUF2151: Cell cycle a 57.7 1.6E+02 0.0035 33.3 12.8 113 87-199 7-163 (695)
170 PF14369 zf-RING_3: zinc-finge 57.4 7.7 0.00017 26.6 1.7 28 364-392 4-31 (35)
171 cd02249 ZZ Zinc finger, ZZ typ 57.2 6.4 0.00014 28.3 1.4 29 364-398 2-31 (46)
172 cd02004 TPP_BZL_OCoD_HPCL Thia 57.1 68 0.0015 28.9 8.5 90 166-261 46-159 (172)
173 KOG2593 Transcription initiati 57.1 3.2 7E-05 43.6 -0.3 26 303-328 128-164 (436)
174 PRK13130 H/ACA RNA-protein com 56.8 7.3 0.00016 29.7 1.6 25 304-330 6-30 (56)
175 KOG2660 Locus-specific chromos 56.5 2.9 6.2E-05 42.5 -0.8 21 390-410 50-72 (331)
176 KOG0317 Predicted E3 ubiquitin 55.8 11 0.00023 37.8 3.1 49 361-417 238-286 (293)
177 smart00154 ZnF_AN1 AN1-like Zi 55.8 7.5 0.00016 27.2 1.5 25 382-409 12-36 (39)
178 smart00661 RPOL9 RNA polymeras 55.5 11 0.00023 27.3 2.4 29 364-392 2-30 (52)
179 TIGR02300 FYDLN_acid conserved 54.8 8.7 0.00019 34.0 2.0 34 359-395 6-39 (129)
180 PF00643 zf-B_box: B-box zinc 54.5 6.6 0.00014 27.2 1.1 34 362-403 3-36 (42)
181 PRK14559 putative protein seri 54.3 11 0.00024 42.0 3.3 22 392-413 29-50 (645)
182 COG1432 Uncharacterized conser 53.2 34 0.00073 31.8 5.9 65 164-238 90-155 (181)
183 PF09237 GAGA: GAGA factor; I 52.6 6.1 0.00013 29.7 0.6 24 315-338 22-45 (54)
184 COG3958 Transketolase, C-termi 52.4 66 0.0014 32.6 8.0 67 206-283 206-283 (312)
185 cd02010 TPP_ALS Thiamine pyrop 52.2 1.3E+02 0.0029 27.4 9.6 92 165-262 45-158 (177)
186 TIGR00622 ssl1 transcription f 51.7 24 0.00052 30.7 4.2 69 249-324 27-110 (112)
187 PF02775 TPP_enzyme_C: Thiamin 51.6 54 0.0012 28.9 6.8 88 168-261 28-143 (153)
188 COG4547 CobT Cobalamin biosynt 50.7 1.1E+02 0.0024 33.0 9.6 58 171-230 520-590 (620)
189 PF00096 zf-C2H2: Zinc finger, 50.5 6.6 0.00014 23.4 0.5 13 383-395 1-13 (23)
190 cd02341 ZZ_ZZZ3 Zinc finger, Z 50.3 9.3 0.0002 28.1 1.3 28 364-397 2-33 (48)
191 PF14570 zf-RING_4: RING/Ubox 49.8 8.8 0.00019 28.4 1.1 44 365-412 1-45 (48)
192 cd02339 ZZ_Mind_bomb Zinc fing 49.6 10 0.00022 27.5 1.4 29 364-398 2-32 (45)
193 cd02008 TPP_IOR_alpha Thiamine 49.4 58 0.0013 29.7 6.8 71 189-261 69-164 (178)
194 PTZ00260 dolichyl-phosphate be 49.4 1.6E+02 0.0035 29.8 10.7 97 106-216 83-189 (333)
195 PRK12726 flagellar biosynthesi 49.2 2.3E+02 0.0051 30.0 11.8 92 166-260 176-280 (407)
196 smart00291 ZnF_ZZ Zinc-binding 48.9 11 0.00025 26.8 1.5 29 362-396 4-33 (44)
197 PF13920 zf-C3HC4_3: Zinc fing 48.7 5.9 0.00013 28.7 0.0 44 363-414 3-47 (50)
198 PF03850 Tfb4: Transcription f 48.6 15 0.00033 36.6 2.9 36 363-411 241-276 (276)
199 PF13248 zf-ribbon_3: zinc-rib 48.2 9.4 0.0002 24.2 0.9 20 392-411 4-23 (26)
200 cd02003 TPP_IolD Thiamine pyro 48.2 2.3E+02 0.005 26.4 10.8 92 164-261 44-171 (205)
201 PLN02948 phosphoribosylaminoim 48.1 2.1E+02 0.0045 31.6 11.9 78 186-265 407-491 (577)
202 PF15227 zf-C3HC4_4: zinc fing 48.0 6.3 0.00014 27.9 0.1 11 387-397 15-25 (42)
203 cd02013 TPP_Xsc_like Thiamine 47.7 1.7E+02 0.0036 27.2 9.7 91 166-262 51-164 (196)
204 PRK00420 hypothetical protein; 47.6 10 0.00022 32.9 1.4 26 303-328 23-51 (112)
205 COG3183 Predicted restriction 47.4 4.7 0.0001 39.9 -0.9 32 318-349 196-232 (272)
206 COG5574 PEX10 RING-finger-cont 47.3 9.6 0.00021 37.8 1.2 49 361-417 214-264 (271)
207 COG1198 PriA Primosomal protei 46.9 34 0.00074 38.8 5.7 130 210-391 341-484 (730)
208 PF00301 Rubredoxin: Rubredoxi 46.5 14 0.0003 27.1 1.7 10 304-313 2-11 (47)
209 TIGR01279 DPOR_bchN light-inde 46.5 1E+02 0.0023 32.2 8.9 80 206-286 285-368 (407)
210 cd04192 GT_2_like_e Subfamily 46.2 2E+02 0.0043 25.9 9.9 69 190-262 29-109 (229)
211 PRK08611 pyruvate oxidase; Pro 45.0 1E+02 0.0022 33.7 8.9 89 168-262 408-518 (576)
212 COG2051 RPS27A Ribosomal prote 44.6 8.9 0.00019 30.2 0.5 27 305-331 21-52 (67)
213 PRK05978 hypothetical protein; 44.5 13 0.00028 33.9 1.5 23 305-327 35-62 (148)
214 PF06220 zf-U1: U1 zinc finger 44.3 9 0.0002 26.7 0.4 14 390-403 3-17 (38)
215 COG1533 SplB DNA repair photol 44.3 98 0.0021 31.2 8.0 108 170-283 65-186 (297)
216 cd02006 TPP_Gcl Thiamine pyrop 44.1 2.4E+02 0.0052 26.2 10.2 88 168-261 57-177 (202)
217 PRK06260 threonine synthase; V 44.0 15 0.00032 38.3 2.2 42 303-344 3-57 (397)
218 COG2718 Uncharacterized conser 43.5 65 0.0014 33.8 6.5 90 88-196 249-341 (423)
219 PF00097 zf-C3HC4: Zinc finger 43.4 11 0.00024 25.7 0.8 26 385-410 14-41 (41)
220 COG0062 Uncharacterized conser 42.7 89 0.0019 29.9 7.0 56 173-230 33-88 (203)
221 PF14634 zf-RING_5: zinc-RING 41.6 17 0.00036 25.7 1.5 42 365-411 2-43 (44)
222 PF07649 C1_3: C1-like domain; 41.6 10 0.00022 24.7 0.4 28 364-396 2-29 (30)
223 TIGR03472 HpnI hopanoid biosyn 41.2 1.7E+02 0.0037 29.8 9.5 69 189-261 70-152 (373)
224 smart00355 ZnF_C2H2 zinc finge 40.9 7.4 0.00016 23.0 -0.4 23 383-405 1-23 (26)
225 smart00659 RPOLCX RNA polymera 40.5 21 0.00046 25.7 1.9 26 303-328 2-30 (44)
226 KOG1818 Membrane trafficking a 40.0 13 0.00028 41.2 0.9 45 362-410 165-217 (634)
227 KOG2272 Focal adhesion protein 39.6 16 0.00035 36.0 1.5 90 289-392 120-231 (332)
228 PHA02768 hypothetical protein; 39.6 21 0.00046 27.1 1.8 19 319-337 7-25 (55)
229 COG1645 Uncharacterized Zn-fin 39.0 13 0.00028 33.2 0.6 24 303-326 28-53 (131)
230 PF03604 DNA_RNApol_7kD: DNA d 38.9 25 0.00053 23.7 1.9 24 304-327 1-27 (32)
231 PF01428 zf-AN1: AN1-like Zinc 38.7 16 0.00035 25.9 1.0 25 382-409 13-37 (43)
232 cd02005 TPP_PDC_IPDC Thiamine 38.6 1.7E+02 0.0038 26.8 8.2 91 166-262 48-161 (183)
233 PHA00733 hypothetical protein 38.5 24 0.00052 31.1 2.3 33 303-335 73-117 (128)
234 PF13824 zf-Mss51: Zinc-finger 38.4 21 0.00047 27.1 1.7 23 305-327 1-24 (55)
235 PRK07525 sulfoacetaldehyde ace 38.0 1.5E+02 0.0034 32.3 9.0 91 166-262 433-547 (588)
236 PF07191 zinc-ribbons_6: zinc- 37.8 12 0.00026 29.8 0.2 33 294-327 7-40 (70)
237 PRK12380 hydrogenase nickel in 37.7 17 0.00036 31.4 1.1 9 382-390 70-78 (113)
238 cd02001 TPP_ComE_PpyrDC Thiami 37.5 1.2E+02 0.0026 27.2 6.8 70 190-262 60-143 (157)
239 cd02014 TPP_POX Thiamine pyrop 37.4 2.1E+02 0.0046 25.9 8.5 90 166-261 49-160 (178)
240 PF09186 DUF1949: Domain of un 37.3 84 0.0018 22.5 4.8 41 203-243 4-56 (56)
241 KOG1356 Putative transcription 36.9 15 0.00032 41.8 0.9 43 362-410 229-277 (889)
242 KOG2879 Predicted E3 ubiquitin 36.8 18 0.0004 36.0 1.4 48 315-390 237-284 (298)
243 cd04196 GT_2_like_d Subfamily 36.8 3E+02 0.0066 24.4 10.5 86 174-264 13-108 (214)
244 TIGR00100 hypA hydrogenase nic 36.7 18 0.00038 31.3 1.1 10 364-373 72-81 (115)
245 PTZ00303 phosphatidylinositol 36.5 23 0.00049 40.2 2.1 37 362-398 460-497 (1374)
246 TIGR00595 priA primosomal prot 36.4 24 0.00052 38.1 2.4 49 304-391 214-262 (505)
247 CHL00073 chlN photochlorophyll 36.2 3.3E+02 0.0072 29.3 10.8 91 189-286 314-416 (457)
248 PF08274 PhnA_Zn_Ribbon: PhnA 36.2 9.7 0.00021 25.3 -0.4 8 382-389 19-26 (30)
249 PF00535 Glycos_transf_2: Glyc 36.1 1.1E+02 0.0024 25.5 6.2 73 189-265 27-108 (169)
250 TIGR00570 cdk7 CDK-activating 36.1 16 0.00034 37.2 0.8 26 387-412 25-51 (309)
251 TIGR00595 priA primosomal prot 35.9 22 0.00047 38.4 2.0 40 361-412 212-261 (505)
252 cd00568 TPP_enzymes Thiamine p 35.9 3E+02 0.0065 24.0 9.4 90 166-261 44-156 (168)
253 TIGR00686 phnA alkylphosphonat 35.9 23 0.00049 30.6 1.6 23 385-412 5-27 (109)
254 PRK05580 primosome assembly pr 35.8 32 0.0007 38.5 3.3 63 289-391 368-430 (679)
255 cd02012 TPP_TK Thiamine pyroph 35.7 3.8E+02 0.0082 25.9 10.5 72 189-261 127-213 (255)
256 cd02015 TPP_AHAS Thiamine pyro 35.5 3.4E+02 0.0075 24.7 10.1 88 168-261 50-161 (186)
257 PF06750 DiS_P_DiS: Bacterial 35.4 12 0.00026 31.1 -0.1 37 317-373 33-69 (92)
258 KOG2327 DNA-binding subunit of 35.2 5.8E+02 0.013 28.4 12.4 112 87-198 20-154 (602)
259 PF05290 Baculo_IE-1: Baculovi 35.1 19 0.00042 32.2 1.1 29 303-331 103-135 (140)
260 KOG3576 Ovo and related transc 35.0 11 0.00024 36.1 -0.4 23 382-404 212-234 (267)
261 PRK06450 threonine synthase; V 35.0 25 0.00054 36.0 2.1 42 303-344 3-48 (338)
262 KOG2858 Uncharacterized conser 34.8 13 0.00029 38.2 0.1 15 303-317 29-43 (390)
263 PLN03208 E3 ubiquitin-protein 34.6 25 0.00053 33.4 1.8 46 361-414 17-78 (193)
264 PF11181 YflT: Heat induced st 34.5 71 0.0015 26.7 4.5 74 206-283 11-85 (103)
265 cd06370 PBP1_Speract_GC_like L 34.3 2.5E+02 0.0055 28.7 9.5 54 167-221 18-72 (404)
266 cd02002 TPP_BFDC Thiamine pyro 34.3 3.4E+02 0.0074 24.3 9.6 88 168-261 49-166 (178)
267 KOG4275 Predicted E3 ubiquitin 34.2 7.7 0.00017 39.0 -1.7 44 363-411 45-88 (350)
268 PLN00209 ribosomal protein S27 34.0 18 0.0004 29.9 0.8 27 305-331 38-69 (86)
269 TIGR01504 glyox_carbo_lig glyo 33.9 2.2E+02 0.0048 31.2 9.4 88 168-261 418-538 (588)
270 PF01667 Ribosomal_S27e: Ribos 33.9 19 0.0004 27.4 0.7 27 305-331 9-40 (55)
271 PF09862 DUF2089: Protein of u 33.8 17 0.00037 31.6 0.6 22 306-327 1-22 (113)
272 PF13894 zf-C2H2_4: C2H2-type 33.8 21 0.00045 20.7 0.8 19 383-401 1-19 (24)
273 PRK00448 polC DNA polymerase I 33.7 19 0.00041 43.9 1.1 24 303-328 908-944 (1437)
274 COG0375 HybF Zn finger protein 33.7 23 0.00049 30.9 1.3 26 362-391 70-95 (115)
275 cd06326 PBP1_STKc_like Type I 33.4 2.8E+02 0.0061 26.9 9.3 59 168-227 18-77 (336)
276 COG2176 PolC DNA polymerase II 33.1 19 0.00042 42.6 1.0 39 303-348 914-963 (1444)
277 cd02009 TPP_SHCHC_synthase Thi 33.0 1.6E+02 0.0034 26.8 6.9 70 189-261 68-162 (175)
278 PRK14571 D-alanyl-alanine synt 32.9 1.8E+02 0.004 28.5 7.9 37 191-227 2-41 (299)
279 KOG2228 Origin recognition com 32.8 6.1E+02 0.013 26.7 14.0 97 169-265 116-223 (408)
280 PF02670 DXP_reductoisom: 1-de 32.7 3.3E+02 0.0072 24.1 8.6 62 193-259 1-65 (129)
281 cd02520 Glucosylceramide_synth 32.6 1.7E+02 0.0037 26.3 7.2 59 189-251 30-96 (196)
282 PF01155 HypA: Hydrogenase exp 32.6 12 0.00026 32.2 -0.5 10 364-373 72-81 (113)
283 cd02525 Succinoglycan_BP_ExoA 32.5 3.2E+02 0.0068 24.9 9.1 91 115-219 15-111 (249)
284 smart00504 Ubox Modified RING 32.5 32 0.00069 25.5 1.8 44 364-415 3-46 (63)
285 COG1996 RPC10 DNA-directed RNA 32.4 26 0.00056 26.0 1.2 27 382-412 6-32 (49)
286 PF13453 zf-TFIIB: Transcripti 32.2 23 0.0005 24.7 0.9 28 365-392 2-29 (41)
287 TIGR02720 pyruv_oxi_spxB pyruv 32.1 2.6E+02 0.0057 30.5 9.6 88 168-261 408-517 (575)
288 TIGR01285 nifN nitrogenase mol 32.1 3.3E+02 0.0071 28.8 10.0 75 206-285 322-404 (432)
289 PF00569 ZZ: Zinc finger, ZZ t 32.0 24 0.00053 25.3 1.1 31 362-398 4-36 (46)
290 PTZ00083 40S ribosomal protein 32.0 21 0.00046 29.4 0.8 27 305-331 37-68 (85)
291 TIGR01405 polC_Gram_pos DNA po 32.0 21 0.00045 42.8 1.1 24 303-328 683-719 (1213)
292 KOG4317 Predicted Zn-finger pr 31.9 24 0.00052 35.9 1.3 25 362-394 7-31 (383)
293 COG1182 AcpD Acyl carrier prot 31.7 4.7E+02 0.01 25.1 9.9 117 89-222 4-121 (202)
294 PF15135 UPF0515: Uncharacteri 31.6 34 0.00073 33.8 2.2 31 363-393 133-166 (278)
295 PRK11788 tetratricopeptide rep 31.6 26 0.00055 35.2 1.5 24 303-326 354-377 (389)
296 cd01407 SIR2-fam SIR2 family o 31.3 1.1E+02 0.0024 29.0 5.7 35 290-327 99-143 (218)
297 PRK03681 hypA hydrogenase nick 31.2 25 0.00055 30.3 1.2 9 382-390 70-78 (114)
298 PLN02470 acetolactate synthase 31.2 2.1E+02 0.0045 31.3 8.6 89 168-262 426-545 (585)
299 KOG4399 C2HC-type Zn-finger pr 31.0 12 0.00025 37.1 -1.0 28 384-412 251-282 (325)
300 KOG1813 Predicted E3 ubiquitin 30.7 19 0.00041 36.3 0.4 50 363-420 242-291 (313)
301 PRK06457 pyruvate dehydrogenas 30.6 2.9E+02 0.0064 29.9 9.6 90 168-262 396-507 (549)
302 cd01840 SGNH_hydrolase_yrhL_li 30.6 3.6E+02 0.0078 23.5 8.6 74 170-247 34-115 (150)
303 PRK08978 acetolactate synthase 30.5 2.4E+02 0.0051 30.5 8.8 88 168-261 401-512 (548)
304 PRK00564 hypA hydrogenase nick 30.5 24 0.00053 30.6 1.0 10 382-391 71-80 (117)
305 PF13912 zf-C2H2_6: C2H2-type 30.5 22 0.00048 22.0 0.6 23 383-405 2-24 (27)
306 PRK06112 acetolactate synthase 30.3 2.2E+02 0.0048 31.0 8.6 90 166-261 435-547 (578)
307 PRK15404 leucine ABC transport 30.2 2.8E+02 0.0062 28.1 8.9 52 169-221 44-95 (369)
308 PRK10220 hypothetical protein; 30.1 33 0.00071 29.7 1.7 24 385-413 6-29 (111)
309 PF14205 Cys_rich_KTR: Cystein 30.1 39 0.00084 25.7 1.9 23 304-326 5-37 (55)
310 PF03660 PHF5: PHF5-like prote 30.0 14 0.00031 31.5 -0.5 27 291-325 8-35 (106)
311 TIGR03669 urea_ABC_arch urea A 30.0 2.9E+02 0.0062 28.3 9.0 61 167-228 17-78 (374)
312 PF02591 DUF164: Putative zinc 29.7 23 0.00049 26.4 0.6 30 362-391 22-55 (56)
313 COG1579 Zn-ribbon protein, pos 29.7 19 0.00042 35.2 0.3 55 329-391 172-230 (239)
314 PRK12286 rpmF 50S ribosomal pr 29.5 53 0.0012 25.0 2.6 21 303-325 27-48 (57)
315 PF14835 zf-RING_6: zf-RING of 29.4 50 0.0011 26.0 2.4 47 364-420 9-56 (65)
316 cd02338 ZZ_PCMF_like Zinc fing 29.3 31 0.00067 25.2 1.3 29 364-398 2-32 (49)
317 PRK00432 30S ribosomal protein 29.3 33 0.0007 25.4 1.4 25 303-327 20-47 (50)
318 PRK00481 NAD-dependent deacety 29.2 46 0.00099 32.2 2.8 39 382-422 122-160 (242)
319 KOG2041 WD40 repeat protein [G 29.2 56 0.0012 37.0 3.6 27 381-413 1155-1183(1189)
320 PF14353 CpXC: CpXC protein 29.0 35 0.00077 29.5 1.8 21 382-402 38-58 (128)
321 PHA00616 hypothetical protein 28.8 17 0.00036 26.4 -0.3 17 383-399 2-18 (44)
322 PRK08322 acetolactate synthase 28.4 2.1E+02 0.0045 30.8 8.0 91 166-262 404-516 (547)
323 PF13842 Tnp_zf-ribbon_2: DDE_ 28.2 59 0.0013 21.8 2.3 28 364-395 2-29 (32)
324 PRK09545 znuA high-affinity zi 28.1 1.6E+02 0.0034 29.7 6.5 43 204-246 238-280 (311)
325 cd04195 GT2_AmsE_like GT2_AmsE 28.1 3.8E+02 0.0081 23.7 8.5 82 175-260 16-105 (201)
326 PF13465 zf-H2C2_2: Zinc-finge 28.1 31 0.00067 21.6 0.9 11 382-392 14-24 (26)
327 PRK06965 acetolactate synthase 27.9 2.5E+02 0.0054 30.8 8.5 88 168-261 437-548 (587)
328 PF14803 Nudix_N_2: Nudix N-te 27.9 27 0.00059 23.8 0.7 28 364-391 2-31 (34)
329 PF14206 Cys_rich_CPCC: Cystei 27.8 33 0.00072 27.9 1.3 21 304-324 2-27 (78)
330 cd06349 PBP1_ABC_ligand_bindin 27.7 2.4E+02 0.0052 27.7 7.7 30 168-197 17-46 (340)
331 TIGR03863 PQQ_ABC_bind ABC tra 27.7 3.3E+02 0.007 27.7 8.8 78 166-245 9-87 (347)
332 cd03466 Nitrogenase_NifN_2 Nit 27.7 7.3E+02 0.016 26.0 14.8 78 206-284 311-402 (429)
333 PF14949 ARF7EP_C: ARF7 effect 27.7 28 0.00061 29.8 0.9 19 363-394 68-86 (103)
334 PRK06882 acetolactate synthase 27.6 3.3E+02 0.0072 29.6 9.4 88 168-261 421-532 (574)
335 cd04919 ACT_AK-Hom3_2 ACT doma 27.4 1.6E+02 0.0035 21.6 5.0 36 193-228 4-39 (66)
336 cd03376 TPP_PFOR_porB_like Thi 27.3 3.9E+02 0.0085 25.7 8.9 89 168-261 62-187 (235)
337 COG1656 Uncharacterized conser 27.3 28 0.0006 32.3 0.8 30 363-392 98-140 (165)
338 PRK08979 acetolactate synthase 27.2 2.7E+02 0.0059 30.3 8.6 88 168-261 421-532 (572)
339 PRK08527 acetolactate synthase 27.1 4.3E+02 0.0093 28.7 10.1 88 168-261 414-525 (563)
340 cd02344 ZZ_HERC2 Zinc finger, 27.0 42 0.00092 24.3 1.6 29 364-398 2-32 (45)
341 COG4888 Uncharacterized Zn rib 27.0 28 0.00061 29.7 0.7 25 303-327 22-56 (104)
342 cd06355 PBP1_FmdD_like Peripla 26.9 3.7E+02 0.0081 26.7 9.1 75 167-242 16-92 (348)
343 cd06335 PBP1_ABC_ligand_bindin 26.9 3E+02 0.0065 27.3 8.3 51 168-219 17-68 (347)
344 PF12646 DUF3783: Domain of un 26.7 1.4E+02 0.0031 22.5 4.5 44 193-239 3-53 (58)
345 COG1198 PriA Primosomal protei 26.7 42 0.00092 38.1 2.3 39 363-413 436-484 (730)
346 PRK09124 pyruvate dehydrogenas 26.6 3E+02 0.0065 29.9 8.8 89 168-262 408-518 (574)
347 PRK07789 acetolactate synthase 26.6 3.1E+02 0.0067 30.2 9.0 89 168-262 447-563 (612)
348 COG1439 Predicted nucleic acid 26.5 39 0.00085 31.6 1.7 24 362-391 139-162 (177)
349 KOG1812 Predicted E3 ubiquitin 26.4 40 0.00087 35.2 2.0 90 303-411 258-352 (384)
350 PHA02926 zinc finger-like prot 26.2 43 0.00094 32.6 1.9 52 361-412 169-227 (242)
351 PRK03564 formate dehydrogenase 25.8 47 0.001 33.8 2.2 41 364-412 214-260 (309)
352 PF01155 HypA: Hydrogenase exp 25.6 33 0.00072 29.4 1.0 27 381-413 69-95 (113)
353 TIGR03457 sulphoacet_xsc sulfo 25.4 2.6E+02 0.0056 30.5 8.1 89 168-262 430-542 (579)
354 PF07295 DUF1451: Protein of u 25.4 50 0.0011 29.9 2.1 29 381-413 111-139 (146)
355 PRK05858 hypothetical protein; 25.4 3.1E+02 0.0066 29.7 8.6 89 168-262 407-518 (542)
356 COG1545 Predicted nucleic-acid 25.3 47 0.001 29.7 1.9 24 303-326 29-52 (140)
357 PRK14873 primosome assembly pr 25.3 46 0.001 37.4 2.3 39 362-413 383-431 (665)
358 KOG0804 Cytoplasmic Zn-finger 25.2 22 0.00047 37.9 -0.3 64 315-394 174-252 (493)
359 PF02780 Transketolase_C: Tran 25.2 88 0.0019 26.6 3.6 49 190-241 10-62 (124)
360 PF05621 TniB: Bacterial TniB 25.1 5.1E+02 0.011 26.4 9.4 126 81-230 57-190 (302)
361 cd01979 Pchlide_reductase_N Pc 25.1 4.7E+02 0.01 27.1 9.6 79 207-286 288-370 (396)
362 KOG2858 Uncharacterized conser 25.1 34 0.00073 35.4 1.1 40 362-410 17-57 (390)
363 cd01973 Nitrogenase_VFe_beta_l 25.1 8.5E+02 0.018 25.9 12.1 78 207-284 317-411 (454)
364 cd04922 ACT_AKi-HSDH-ThrA_2 AC 25.0 1.9E+02 0.004 21.1 5.0 36 193-228 4-39 (66)
365 PRK09107 acetolactate synthase 25.0 3.7E+02 0.008 29.5 9.2 90 166-261 428-541 (595)
366 PRK03815 murD UDP-N-acetylmura 25.0 6.6E+02 0.014 26.2 10.7 44 190-237 299-342 (401)
367 TIGR00375 conserved hypothetic 25.0 22 0.00047 37.2 -0.4 10 334-343 290-299 (374)
368 COG4530 Uncharacterized protei 25.0 38 0.00082 29.4 1.2 25 303-327 9-36 (129)
369 cd01017 AdcA Metal binding pro 24.9 3.1E+02 0.0067 26.9 7.8 43 204-246 206-248 (282)
370 PRK07119 2-ketoisovalerate fer 24.8 2.9E+02 0.0063 28.4 7.9 69 190-261 247-319 (352)
371 PF06221 zf-C2HC5: Putative zi 24.7 55 0.0012 25.0 1.9 46 289-334 2-52 (57)
372 cd06433 GT_2_WfgS_like WfgS an 24.7 4.6E+02 0.01 22.7 8.5 59 190-252 28-86 (202)
373 PRK07524 hypothetical protein; 24.6 2.6E+02 0.0056 30.1 7.8 89 168-262 407-517 (535)
374 PF05596 Taeniidae_ag: Taeniid 24.5 72 0.0016 25.0 2.6 27 104-130 4-30 (64)
375 smart00547 ZnF_RBZ Zinc finger 24.5 40 0.00087 20.8 1.0 24 303-326 2-25 (26)
376 PF08459 UvrC_HhH_N: UvrC Heli 24.4 68 0.0015 29.4 2.8 33 193-229 82-114 (155)
377 cd01407 SIR2-fam SIR2 family o 24.4 55 0.0012 31.1 2.3 40 383-423 110-152 (218)
378 PLN03049 pyridoxine (pyridoxam 23.9 1.8E+02 0.0039 31.2 6.3 37 190-228 60-96 (462)
379 PRK11823 DNA repair protein Ra 23.9 44 0.00096 35.5 1.7 24 303-326 7-30 (446)
380 TIGR03111 glyc2_xrt_Gpos1 puta 23.9 4.9E+02 0.011 27.3 9.6 70 191-264 82-160 (439)
381 PRK03681 hypA hydrogenase nick 23.8 36 0.00078 29.4 0.8 28 361-391 69-96 (114)
382 cd04924 ACT_AK-Arch_2 ACT doma 23.7 2.1E+02 0.0046 20.7 5.0 36 193-228 4-39 (66)
383 PF07282 OrfB_Zn_ribbon: Putat 23.7 68 0.0015 24.5 2.3 31 360-392 26-56 (69)
384 PF13458 Peripla_BP_6: Peripla 23.6 2.7E+02 0.0058 27.1 7.2 79 168-247 19-99 (343)
385 PF06957 COPI_C: Coatomer (COP 23.5 45 0.00097 35.4 1.6 43 289-331 362-410 (422)
386 PF07693 KAP_NTPase: KAP famil 23.4 4.4E+02 0.0096 25.7 8.7 54 188-242 170-226 (325)
387 PRK07591 threonine synthase; V 23.4 69 0.0015 33.7 3.0 28 303-330 18-46 (421)
388 cd06342 PBP1_ABC_LIVBP_like Ty 23.4 4.2E+02 0.0091 25.6 8.5 50 169-219 18-67 (334)
389 smart00184 RING Ring finger. E 23.4 31 0.00068 21.9 0.3 26 385-410 13-39 (39)
390 TIGR03844 cysteate_syn cysteat 23.4 52 0.0011 34.5 2.1 22 303-324 2-24 (398)
391 PF10122 Mu-like_Com: Mu-like 23.3 40 0.00088 25.2 0.9 31 362-392 4-34 (51)
392 PF14446 Prok-RING_1: Prokaryo 23.3 58 0.0013 24.7 1.8 32 362-397 5-36 (54)
393 cd01019 ZnuA Zinc binding prot 23.1 2.2E+02 0.0048 28.1 6.5 43 203-245 213-255 (286)
394 PF12675 DUF3795: Protein of u 23.0 47 0.001 26.5 1.4 24 391-414 7-44 (78)
395 PRK03824 hypA hydrogenase nick 23.0 54 0.0012 29.1 1.8 12 303-314 70-81 (135)
396 PRK12496 hypothetical protein; 23.0 45 0.00097 30.7 1.4 25 363-391 128-152 (164)
397 CHL00099 ilvB acetohydroxyacid 23.0 4.2E+02 0.009 29.0 9.1 90 166-261 428-542 (585)
398 PF02875 Mur_ligase_C: Mur lig 22.9 1E+02 0.0022 24.7 3.3 49 174-224 27-78 (91)
399 PF03854 zf-P11: P-11 zinc fin 22.9 25 0.00054 26.0 -0.2 25 303-327 21-45 (50)
400 PF13911 AhpC-TSA_2: AhpC/TSA 22.9 1.4E+02 0.003 24.9 4.3 41 209-250 4-44 (115)
401 PRK08329 threonine synthase; V 22.9 44 0.00095 34.2 1.4 41 304-345 2-54 (347)
402 KOG4602 Nanos and related prot 22.8 42 0.0009 33.3 1.1 25 274-298 216-243 (318)
403 cd06345 PBP1_ABC_ligand_bindin 22.7 4.9E+02 0.011 25.6 9.0 53 168-221 17-70 (344)
404 COG1779 C4-type Zn-finger prot 22.6 32 0.00069 32.8 0.3 42 318-375 15-56 (201)
405 PF03833 PolC_DP2: DNA polymer 22.6 29 0.00062 39.8 0.0 42 287-332 665-707 (900)
406 KOG2177 Predicted E3 ubiquitin 22.5 32 0.0007 32.3 0.4 43 361-411 12-54 (386)
407 cd02522 GT_2_like_a GT_2_like_ 22.4 5.7E+02 0.012 22.9 9.7 48 169-223 59-106 (221)
408 PRK08617 acetolactate synthase 22.4 2.4E+02 0.0051 30.5 7.0 70 189-261 432-523 (552)
409 cd02345 ZZ_dah Zinc finger, ZZ 22.2 54 0.0012 23.9 1.4 29 364-398 2-32 (49)
410 PRK07710 acetolactate synthase 22.2 4.8E+02 0.01 28.3 9.4 88 169-262 425-536 (571)
411 cd06438 EpsO_like EpsO protein 22.2 5.5E+02 0.012 22.6 10.2 47 168-216 62-108 (183)
412 PRK06048 acetolactate synthase 22.2 3.6E+02 0.0077 29.3 8.3 88 168-261 414-525 (561)
413 cd01018 ZntC Metal binding pro 22.1 3.2E+02 0.007 26.5 7.3 43 204-246 203-245 (266)
414 COG1439 Predicted nucleic acid 22.1 52 0.0011 30.8 1.6 28 303-330 139-166 (177)
415 TIGR03469 HonB hopene-associat 22.0 8.6E+02 0.019 24.8 12.0 53 166-220 112-164 (384)
416 PRK06027 purU formyltetrahydro 22.0 6.2E+02 0.013 25.2 9.4 54 189-246 89-142 (286)
417 KOG1940 Zn-finger protein [Gen 22.0 39 0.00084 33.9 0.8 114 276-412 31-166 (276)
418 KOG2813 Predicted molecular ch 21.9 80 0.0017 32.4 3.0 69 291-397 187-263 (406)
419 TIGR01053 LSD1 zinc finger dom 21.9 83 0.0018 21.0 2.1 25 364-390 3-27 (31)
420 PF06676 DUF1178: Protein of u 21.9 34 0.00074 31.2 0.3 21 319-339 34-58 (148)
421 cd06352 PBP1_NPR_GC_like Ligan 21.9 2.9E+02 0.0063 27.7 7.2 17 168-184 17-33 (389)
422 smart00440 ZnF_C2C2 C2C2 Zinc 21.8 60 0.0013 22.7 1.5 15 378-392 24-38 (40)
423 cd03371 TPP_PpyrDC Thiamine py 21.8 6.2E+02 0.014 23.3 8.8 71 189-262 66-151 (188)
424 KOG1812 Predicted E3 ubiquitin 21.7 35 0.00076 35.7 0.4 40 364-403 240-279 (384)
425 cd06348 PBP1_ABC_ligand_bindin 21.6 3.3E+02 0.0071 26.8 7.4 7 144-150 5-11 (344)
426 cd06334 PBP1_ABC_ligand_bindin 21.6 4.6E+02 0.0099 26.3 8.5 60 167-228 16-76 (351)
427 KOG2857 Predicted MYND Zn-fing 21.5 39 0.00084 30.6 0.6 14 304-317 18-31 (157)
428 TIGR01556 rhamnosyltran L-rham 21.4 4.6E+02 0.01 25.0 8.3 52 169-224 57-108 (281)
429 PF03119 DNA_ligase_ZBD: NAD-d 21.4 42 0.00092 21.8 0.6 13 319-331 1-13 (28)
430 PRK06466 acetolactate synthase 21.3 4.3E+02 0.0093 28.8 8.8 88 168-261 423-534 (574)
431 cd04476 RPA1_DBD_C RPA1_DBD_C: 21.2 59 0.0013 29.4 1.8 26 364-392 36-61 (166)
432 PRK06456 acetolactate synthase 21.1 4.2E+02 0.0092 28.7 8.7 88 168-261 421-532 (572)
433 TIGR00197 yjeF_nterm yjeF N-te 21.1 3.1E+02 0.0066 25.9 6.7 38 189-228 45-82 (205)
434 PF00641 zf-RanBP: Zn-finger i 21.1 79 0.0017 20.4 1.9 24 303-326 4-27 (30)
435 PRK14093 UDP-N-acetylmuramoyla 20.9 4.2E+02 0.0091 28.2 8.4 16 248-263 428-443 (479)
436 PRK11269 glyoxylate carboligas 20.9 5.1E+02 0.011 28.3 9.3 88 168-261 419-539 (591)
437 PRK11869 2-oxoacid ferredoxin 20.9 3.7E+02 0.0081 26.9 7.5 56 168-229 60-116 (280)
438 PF10825 DUF2752: Protein of u 20.8 31 0.00068 25.6 -0.1 15 319-341 11-25 (52)
439 cd02511 Beta4Glucosyltransfera 20.8 5.8E+02 0.013 23.6 8.6 67 191-264 28-100 (229)
440 cd04916 ACT_AKiii-YclM-BS_2 AC 20.8 2.4E+02 0.0052 20.4 4.9 36 193-228 4-39 (66)
441 KOG3576 Ovo and related transc 20.8 16 0.00034 35.2 -2.1 76 319-412 119-220 (267)
442 PRK08266 hypothetical protein; 20.8 4.5E+02 0.0097 28.3 8.7 88 168-261 402-512 (542)
443 PRK08659 2-oxoglutarate ferred 20.7 3.4E+02 0.0075 28.2 7.5 69 190-261 274-346 (376)
444 PHA00626 hypothetical protein 20.7 53 0.0012 25.1 1.1 14 381-394 22-35 (59)
445 cd07041 STAS_RsbR_RsbS_like Su 20.7 3.1E+02 0.0066 22.4 5.9 41 190-230 42-85 (109)
446 PF00731 AIRC: AIR carboxylase 20.6 5.3E+02 0.012 23.5 7.8 73 191-265 2-81 (150)
447 PLN02235 ATP citrate (pro-S)-l 20.6 4.6E+02 0.0099 28.0 8.4 127 125-260 266-415 (423)
448 cd06331 PBP1_AmiC_like Type I 20.5 7.1E+02 0.015 24.3 9.5 53 168-221 17-70 (333)
449 PRK11204 N-glycosyltransferase 20.4 6.2E+02 0.014 25.9 9.4 68 189-260 83-159 (420)
450 TIGR01562 FdhE formate dehydro 20.3 45 0.00098 33.9 0.9 42 320-390 187-232 (305)
451 KOG3362 Predicted BBOX Zn-fing 20.3 54 0.0012 29.8 1.2 76 233-317 68-143 (156)
452 PRK06546 pyruvate dehydrogenas 20.3 3.5E+02 0.0077 29.5 7.9 88 168-261 408-517 (578)
453 cd06330 PBP1_Arsenic_SBP_like 20.1 6.6E+02 0.014 24.6 9.2 54 168-222 17-71 (346)
454 PF02887 PK_C: Pyruvate kinase 20.1 2.5E+02 0.0054 23.6 5.4 48 190-247 18-65 (117)
455 PF01488 Shikimate_DH: Shikima 20.1 2.4E+02 0.0053 24.4 5.4 74 176-260 2-76 (135)
456 COG0603 Predicted PP-loop supe 20.0 3.2E+02 0.0069 26.6 6.6 58 191-255 4-68 (222)
No 1
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=100.00 E-value=1.3e-121 Score=887.04 Aligned_cols=369 Identities=59% Similarity=1.013 Sum_probs=351.6
Q ss_pred ccccccccccccccccceeeCCCccccccchHHHHHHhHhhhhcccccccchhhhhccccceEEEEEeCCHhhhcCCCCC
Q 014440 26 GLEAWERSYADDRSWEALQEDESGFLRPIDNSAIYHAQYRRRLRGRSLTVATARIQKGLIRYLYIVIDLSRAAAEMDFRP 105 (424)
Q Consensus 26 ~~~~We~~y~~~~sW~~l~ed~~g~l~~~~~~~~~~~kr~~~~~~~~~~~~~~~~r~GiiR~lvlvLD~S~SM~~~D~~P 105 (424)
++|+||++| +||||.|+||++|+|..+++++++.+||||+++ ..++.|+|||||++||||.|++|.++|++|
T Consensus 9 ~~y~WE~eY--~RsWe~l~ede~Gsl~~~ia~~v~~~krk~~~~------~~t~~r~GiiRhl~iviD~S~am~e~Df~P 80 (378)
T KOG2807|consen 9 KGYTWEGEY--KRSWEILKEDESGSLEKSIASIVNEAKRKRRLR------YSTRIRKGIIRHLYIVIDCSRAMEEKDFRP 80 (378)
T ss_pred cccchhhhh--hhhHHHhhcccccchHHHHHHHHHHHHHhhhhh------ccchhhhhhheeEEEEEEhhhhhhhccCCc
Confidence 479999999 999999999999999999999999999999985 668999999999999999999999999999
Q ss_pred ChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCHHHHHHHHhhhhCCCCcchHHHHHHHHHHHHcCCC
Q 014440 106 SRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSPESHIKALMGKLGCSGDSSIQNALDLVHGLLNQIP 185 (424)
Q Consensus 106 ~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~~~~~~G~tsL~~AL~~Al~~L~~~p 185 (424)
+|+..+.++++.||.+||+|||++|||||+++||.|++++.+|+|++.|+++|+.+.++.|++||||||++|.+.|+++|
T Consensus 81 ~r~a~~~K~le~Fv~eFFdQNPiSQigii~~k~g~A~~lt~ltgnp~~hI~aL~~~~~~~g~fSLqNaLe~a~~~Lk~~p 160 (378)
T KOG2807|consen 81 SRFANVIKYLEGFVPEFFDQNPISQIGIISIKDGKADRLTDLTGNPRIHIHALKGLTECSGDFSLQNALELAREVLKHMP 160 (378)
T ss_pred hHHHHHHHHHHHHHHHHhccCchhheeEEEEecchhhHHHHhcCCHHHHHHHHhcccccCCChHHHHHHHHHHHHhcCCC
Confidence 99999999999999999999999999999999999999999999999999999988789999999999999999999999
Q ss_pred CCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchHHHHHHHHHHhCCEEEEecChhhHHHHHHhcCCCCc
Q 014440 186 SYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEMFICKHLCQETGGTYSVALDESHSKELILEHAPPPP 265 (424)
Q Consensus 186 ~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~~pp~ 265 (424)
+|.+||||||++++.|+||+||+++|+++++.+|||++|||++|+.++|+||++|||.|.|+.|++||++||.++.+|||
T Consensus 161 ~H~sREVLii~sslsT~DPgdi~~tI~~lk~~kIRvsvIgLsaEv~icK~l~kaT~G~Y~V~lDe~HlkeLl~e~~~Pp~ 240 (378)
T KOG2807|consen 161 GHVSREVLIIFSSLSTCDPGDIYETIDKLKAYKIRVSVIGLSAEVFICKELCKATGGRYSVALDEGHLKELLLEHTHPPP 240 (378)
T ss_pred cccceEEEEEEeeecccCcccHHHHHHHHHhhCeEEEEEeechhHHHHHHHHHhhCCeEEEEeCHHHHHHHHHhcCCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cchhhhhhheeeecCCCCCCCCCcceeeecCCccccCeEEcCCCCccccCCCCCCCCCCceecCchhHHhhhcccCCCCC
Q 014440 266 AIAEFAIASLIKMGFPQRAGEGSISICSCHKEVKIGVGYTCPRCKARVCELPTECRICGLQLVSSPHLARSYHHLFPIAP 345 (424)
Q Consensus 266 ~~~~~~~~~Li~mGFP~~~~~~~~a~C~CH~~~~~~~Gy~Cp~C~s~~C~lP~~C~~C~l~Lvs~phLarsyhhl~p~~~ 345 (424)
+.+. .+.+||+||||++...+.|++|+||..++.. ||.||||++++|+||++||+|+|+|||||||||||||||||++
T Consensus 241 ~~~~-~~~sLvkmGFP~~~~e~~ps~C~CH~~~~~~-Gy~CP~CkakvCsLP~eCpiC~ltLVss~hLARSyhhL~PL~~ 318 (378)
T KOG2807|consen 241 ANKS-KECSLVKMGFPSRSPEDTPSFCACHSELSGG-GYFCPQCKAKVCSLPIECPICSLTLVSSPHLARSYHHLFPLKP 318 (378)
T ss_pred cccc-cCCceEEecCCCcccccCcchheeccccccC-ceeCCcccCeeecCCccCCccceeEecchHHHHHHHhhcCCcc
Confidence 8844 4899999999999999999999999888888 9999999999999999999999999999999999999999999
Q ss_pred CcccCccccccccCCCCCceeecccccccCCCCCCceeeCCCcCcccccccchhhhccCCCCCCCCCCC
Q 014440 346 FDEATPSRLNDLHNISRSTCFGCQQSLLASGNKAGLCVACPKCKKHFCLECDIYIHESLHNCPGCESLR 414 (424)
Q Consensus 346 f~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~dCd~fihe~lh~CPgC~~~~ 414 (424)
|.|+++ .+..+++.||+|+..+. .+.+|+|+.|+++||.|||+||||+||+||||++++
T Consensus 319 F~Eip~-----~~~~~~~~Cf~C~~~~~-----~~~~y~C~~Ck~~FCldCDv~iHesLh~CpgCeh~~ 377 (378)
T KOG2807|consen 319 FVEIPE-----TEYNGSRFCFACQGELL-----SSGRYRCESCKNVFCLDCDVFIHESLHNCPGCEHKP 377 (378)
T ss_pred hhhccc-----cccCCCcceeeeccccC-----CCCcEEchhccceeeccchHHHHhhhhcCCCcCCCC
Confidence 999964 45556788999964443 346899999999999999999999999999999654
No 2
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=100.00 E-value=8.4e-106 Score=772.10 Aligned_cols=375 Identities=43% Similarity=0.750 Sum_probs=356.4
Q ss_pred ccccccccccccccccceeeCCCccccccchHHHHHHhHhhhhcccccccchhhhhccccceEEEEEeCCHhhhcCCCCC
Q 014440 26 GLEAWERSYADDRSWEALQEDESGFLRPIDNSAIYHAQYRRRLRGRSLTVATARIQKGLIRYLYIVIDLSRAAAEMDFRP 105 (424)
Q Consensus 26 ~~~~We~~y~~~~sW~~l~ed~~g~l~~~~~~~~~~~kr~~~~~~~~~~~~~~~~r~GiiR~lvlvLD~S~SM~~~D~~P 105 (424)
++|+||++| +||||.+.+|..|+|...|+++.+.+|+++.. .++++.|||||||++|+||+|++|.+.|+.|
T Consensus 36 ~gysWE~Ey--kRsWd~v~~d~eg~l~~vva~~~~~~k~~~~~------~~~tp~qrGIiRhl~l~lD~Seam~e~Df~p 107 (421)
T COG5151 36 KGYSWEQEY--KRSWDDVNDDKEGSLVGVVAEFNLETKAPYSN------NRTTPLQRGIIRHLHLILDVSEAMDESDFLP 107 (421)
T ss_pred cCcchHHhh--hhhhhhhcccccccHHHHHHHHHHhccccccc------cCCChhhhhhhheeEEEEEhhhhhhhhhccc
Confidence 469999999 99999999999999999999999999988766 4899999999999999999999999999999
Q ss_pred ChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCHHHHHHHHhhhhCCCCcchHHHHHHHHHHHHcCCC
Q 014440 106 SRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSPESHIKALMGKLGCSGDSSIQNALDLVHGLLNQIP 185 (424)
Q Consensus 106 ~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~~~~~~G~tsL~~AL~~Al~~L~~~p 185 (424)
+|...+.+++.+||.+||+|||++|++||.++||-|.+++.+.+|+++|+.+|+.+.++.|++||+||||||+..|.+.+
T Consensus 108 ~r~a~vikya~~Fv~eFf~qNPiSqlsii~irdg~a~~~s~~~gnpq~hi~~lkS~rd~~gnfSLqNaLEmar~~l~~~~ 187 (421)
T COG5151 108 TRRANVIKYAEGFVPEFFSQNPISQLSIISIRDGCAKYTSSMDGNPQAHIGQLKSKRDCSGNFSLQNALEMARIELMKNT 187 (421)
T ss_pred hHHHHHHHHHHHHhHHHhccCCchheeeeehhhhHHHHhhhcCCCHHHHHHHhhcccccCCChhHHhHHHHhhhhhcccc
Confidence 99999999999999999999999999999999999999999999999999999988899999999999999999998888
Q ss_pred CCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchHHHHHHHHHHh----CCEEEEecChhhHHHHHHhcC
Q 014440 186 SYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEMFICKHLCQET----GGTYSVALDESHSKELILEHA 261 (424)
Q Consensus 186 ~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~~iLq~iA~~T----GG~Y~~~~d~~~L~~lL~~~~ 261 (424)
.|++||||||++|..+.||++|.++|+.|...+|||.+|||.+++.++|+|++.| .|.|+++.|+.||++|+.+..
T Consensus 188 ~H~trEvLiifgS~st~DPgdi~~tid~Lv~~~IrV~~igL~aevaicKeickaTn~~~e~~y~v~vde~Hl~el~~E~~ 267 (421)
T COG5151 188 MHGTREVLIIFGSTSTRDPGDIAETIDKLVAYNIRVHFIGLCAEVAICKEICKATNSSTEGRYYVPVDEGHLSELMRELS 267 (421)
T ss_pred cccceEEEEEEeecccCCCccHHHHHHHHHhhceEEEEEeehhHHHHHHHHHhhcCcCcCceeEeeecHHHHHHHHHhcC
Confidence 9999999999999999999999999999999999999999999999999999999 699999999999999999999
Q ss_pred CCCccchhhhhhheeeecCCCCCCCCCcceeeecCCccccCeEEcCCCCccccCCCCCCCCCCceecCchhHHhhhcccC
Q 014440 262 PPPPAIAEFAIASLIKMGFPQRAGEGSISICSCHKEVKIGVGYTCPRCKARVCELPTECRICGLQLVSSPHLARSYHHLF 341 (424)
Q Consensus 262 ~pp~~~~~~~~~~Li~mGFP~~~~~~~~a~C~CH~~~~~~~Gy~Cp~C~s~~C~lP~~C~~C~l~Lvs~phLarsyhhl~ 341 (424)
.||+........+||+||||.+.-++.|++|+||.+++.+ ||.||+|++++|+||..||+|.|+||+++||||||||||
T Consensus 268 ~P~~~n~~k~~~sLVkmGFPs~~~E~~Ps~CaCHs~~~~g-Gy~CP~CktkVCsLPi~CP~Csl~LilsthLarSyhhL~ 346 (421)
T COG5151 268 HPTDFNGTKTDLSLVKMGFPSPMMEQLPSVCACHSEVKGG-GYECPVCKTKVCSLPISCPICSLQLILSTHLARSYHHLY 346 (421)
T ss_pred CCCCCCccccCceEEEecCCchhhhcCccceeeeeeeccC-ceeCCcccceeecCCccCcchhHHHHHHHHHHHHHHhhc
Confidence 9999876667789999999999999999999999999999 999999999999999999999999999999999999999
Q ss_pred CCCCCcccCccccccccCCCCCceeecccccccCCC------CCCceeeCCCcCcccccccchhhhccCCCCCCCCCCC
Q 014440 342 PIAPFDEATPSRLNDLHNISRSTCFGCQQSLLASGN------KAGLCVACPKCKKHFCLECDIYIHESLHNCPGCESLR 414 (424)
Q Consensus 342 p~~~f~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~------~~~~~~~C~~C~~~fC~dCd~fihe~lh~CPgC~~~~ 414 (424)
||++|.|+++ .+...+..||.||.+||.+.. ..+++|+|+.|++.||.|||+||||+||+||||+...
T Consensus 347 PLk~f~E~p~-----~~~~ks~~Cf~CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe~Lh~C~gCe~~~ 420 (421)
T COG5151 347 PLKPFVEKPE-----GTNPKSTHCFVCQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVFIHETLHFCIGCELPH 420 (421)
T ss_pred cCcccccccC-----CCCCCCccceeccCCCCCCCCCcccccccccceechhhhhhhhhhhHHHHHHHHhhCCCCcCCC
Confidence 9999999964 445567899999999997752 2467999999999999999999999999999998754
No 3
>PF04056 Ssl1: Ssl1-like; InterPro: IPR007198 Ssl1-like proteins are 40 kDa subunits of the transcription factor II H complex. This domain is often found associated with the C2H2 type Zn-finger (IPR007087 from INTERPRO).; GO: 0008270 zinc ion binding, 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent
Probab=100.00 E-value=2.9e-54 Score=401.73 Aligned_cols=191 Identities=53% Similarity=0.940 Sum_probs=185.5
Q ss_pred EEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCHHHHHHHHhhhh--CCCCcc
Q 014440 91 VIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSPESHIKALMGKL--GCSGDS 168 (424)
Q Consensus 91 vLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~~~--~~~G~t 168 (424)
|||+|.+|.++|++||||.++++++++||++||+|||++|||||+++||.|+++++|++|+++|+++|.+.. .+.|++
T Consensus 1 viD~S~~m~~~D~~PtRl~~~~~~l~~Fv~eff~qNPiSqlgii~~~~~~a~~ls~lsgn~~~h~~~L~~~~~~~~~G~~ 80 (193)
T PF04056_consen 1 VIDMSEAMREKDLKPTRLQCVLKALEEFVREFFDQNPISQLGIIVMRDGRAERLSELSGNPQEHIEALKKLRKLEPSGEP 80 (193)
T ss_pred CeechHhHHhCcCCccHHHHHHHHHHHHHHHHHhcCChhheeeeeeecceeEEeeecCCCHHHHHHHHHHhccCCCCCCh
Confidence 699999999999999999999999999999999999999999999999999999999999999999998764 799999
Q ss_pred hHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchHHHHHHHHHHhCCEEEEec
Q 014440 169 SIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEMFICKHLCQETGGTYSVAL 248 (424)
Q Consensus 169 sL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~~iLq~iA~~TGG~Y~~~~ 248 (424)
||||||++|+..|++.|+|++||||||+|++.++||+||+++++.+++++|||++|||++|+++||+||++|||+|.+++
T Consensus 81 SLqN~Le~A~~~L~~~p~~~srEIlvi~gSl~t~Dp~di~~ti~~l~~~~IrvsvI~laaEv~I~k~i~~~T~G~y~V~l 160 (193)
T PF04056_consen 81 SLQNGLEMARSSLKHMPSHGSREILVIFGSLTTCDPGDIHETIESLKKENIRVSVISLAAEVYICKKICKETGGTYGVIL 160 (193)
T ss_pred hHHHHHHHHHHHHhhCccccceEEEEEEeecccCCchhHHHHHHHHHHcCCEEEEEEEhHHHHHHHHHHHhhCCEEEEec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ChhhHHHHHHhcCCCCccchhhhhhheeeecCC
Q 014440 249 DESHSKELILEHAPPPPAIAEFAIASLIKMGFP 281 (424)
Q Consensus 249 d~~~L~~lL~~~~~pp~~~~~~~~~~Li~mGFP 281 (424)
|++||+++|+++.+||++.....+++||+||||
T Consensus 161 de~H~~~lL~~~~~PP~~~~~~~~~~Li~mGFP 193 (193)
T PF04056_consen 161 DEDHFKELLMEHVPPPPTSSSKSEASLIKMGFP 193 (193)
T ss_pred CHHHHHHHHHhhCCCCcccccCCCCCEEEecCC
Confidence 999999999999999999844458999999999
No 4
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=2.6e-48 Score=329.34 Aligned_cols=105 Identities=51% Similarity=1.113 Sum_probs=94.7
Q ss_pred eEEcCCCCccccCCCCCCCCCCceecCchhHHhhhcccCCCCCCcccCccccccccCCCCCceeecccccccCCC-----
Q 014440 303 GYTCPRCKARVCELPTECRICGLQLVSSPHLARSYHHLFPIAPFDEATPSRLNDLHNISRSTCFGCQQSLLASGN----- 377 (424)
Q Consensus 303 Gy~Cp~C~s~~C~lP~~C~~C~l~Lvs~phLarsyhhl~p~~~f~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~----- 377 (424)
||+||||+||||+||++|++|||||||||||||||||||||++|+||++ .+...+..||||+++|+.++.
T Consensus 1 GY~CPrC~skvC~LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~-----~~~~~~~~C~~C~~~f~~~~~~~~~~ 75 (112)
T TIGR00622 1 GYFCPQCRAKVCELPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPL-----EEYNGSRFCFGCQGPFPKPPVSPFDE 75 (112)
T ss_pred CccCCCCCCCccCCCCcCCcCCCEEeccchHHHhhhccCCCcccccccc-----cccCCCCcccCcCCCCCCcccccccc
Confidence 7999999999999999999999999999999999999999999999965 234456789999999986531
Q ss_pred -CCCceeeCCCcCcccccccchhhhccCCCCCCCCC
Q 014440 378 -KAGLCVACPKCKKHFCLECDIYIHESLHNCPGCES 412 (424)
Q Consensus 378 -~~~~~~~C~~C~~~fC~dCd~fihe~lh~CPgC~~ 412 (424)
..+++|+|++|+++||+|||+||||+|||||||++
T Consensus 76 ~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~~ 111 (112)
T TIGR00622 76 LKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGCIH 111 (112)
T ss_pred cccccceeCCCCCCccccccchhhhhhccCCcCCCC
Confidence 24569999999999999999999999999999984
No 5
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=6.9e-41 Score=328.07 Aligned_cols=233 Identities=15% Similarity=0.306 Sum_probs=195.6
Q ss_pred eEEEEEeCCHhhh---cCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCC----C-----H---
Q 014440 87 YLYIVIDLSRAAA---EMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGG----S-----P--- 151 (424)
Q Consensus 87 ~lvlvLD~S~SM~---~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~----d-----~--- 151 (424)
-++||||+++--+ +.+-.+.-|..+++.+..|+|.|+..|+.|||+||+.+.+.+..++|-+. + .
T Consensus 4 lL~vvlD~np~~W~~~~~~~~~~~l~~~l~sllvF~NahL~l~~~N~vaVIAs~~~~~~~LYps~~~~~~~~~~~~~~~~ 83 (279)
T TIGR00627 4 LLVVIIEANPCSWGMLALAHGKRTISKVLRAIVVFLNAHLAFNANNKLAVIASHSQDNKYLYPSTRCEDRNASELDPKRL 83 (279)
T ss_pred EEEEEEeCCHHHHHHHhhccCCCcHHHHHHHHHHHHHHHHhcCccCCEEEEEecCCcceEEecCCccccccccccccccc
Confidence 5899999999876 22223668999999999999999999999999999999999999999741 0 0
Q ss_pred ------------HHHHHHHhhhh---C----CCCcchHHHHHHHHHHHHcCCC------CCCCcEEEEEEcCCC-CCCcc
Q 014440 152 ------------ESHIKALMGKL---G----CSGDSSIQNALDLVHGLLNQIP------SYGHREVLILYSALS-TCDPG 205 (424)
Q Consensus 152 ------------~~~~~~L~~~~---~----~~G~tsL~~AL~~Al~~L~~~p------~~~~reILvI~ss~~-t~dp~ 205 (424)
+.+++.|.+++ . ..+.+.|..||.+|++++++.. ....+|||||.++.+ ..++.
T Consensus 84 ~~~~y~~f~~v~~~v~~~l~~l~~~~~~~~~~~~~s~lagals~ALcyinr~~~~~~~~~~~~~RIlii~~s~~~~~qYi 163 (279)
T TIGR00627 84 RELLYRDFRTVDETIVEEIKPLMAHADKHMKKDSRTVLAGALSDALGYINRSEQSETASEKLKSRILVISITPDMALQYI 163 (279)
T ss_pred cchhccchhHHHHHHHHHHHHHHhhchhcccccccccchhHHHhhhhhhcccccccccCcCCcceEEEEECCCCchHHHH
Confidence 11344444332 1 1256789999999999998741 234678999987654 36777
Q ss_pred CHHHHHHHHHhCCcEEEEEEecch--HHHHHHHHHHhCCEEEEecChhhHHHHHHhcCCCCccchhhhhhheeeecCCCC
Q 014440 206 DIMETIQKCKESKIRCSVIGLSAE--MFICKHLCQETGGTYSVALDESHSKELILEHAPPPPAIAEFAIASLIKMGFPQR 283 (424)
Q Consensus 206 ~i~~~i~~akk~~IrV~vIgLg~e--~~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~~pp~~~~~~~~~~Li~mGFP~~ 283 (424)
.+|++|+.||+.+|+||+|+|+++ +.+|||+|++|||.|+++.+++||.++|+.++.||+.. +..|++ |.+
T Consensus 164 ~~mn~Ifaaqk~~I~Idv~~L~~e~~~~~lqQa~~~TgG~Y~~~~~~~~L~q~L~~~~~pp~~~----r~~Li~---P~~ 236 (279)
T TIGR00627 164 PLMNCIFSAQKQNIPIDVVSIGGDFTSGFLQQAADITGGSYLHVKKPQGLLQYLMTNMLPDPTL----RAVLSK---PNH 236 (279)
T ss_pred HHHHHHHHHHHcCceEEEEEeCCccccHHHHHHHHHhCCEEeccCCHhHHHHHHHHhcCCChhh----hHhhcC---CCC
Confidence 899999999999999999999987 99999999999999999999999999998888777754 345765 999
Q ss_pred CCCCCcceeeecCCccccCeEEcCCCCccccCCCCCCCCCCcee
Q 014440 284 AGEGSISICSCHKEVKIGVGYTCPRCKARVCELPTECRICGLQL 327 (424)
Q Consensus 284 ~~~~~~a~C~CH~~~~~~~Gy~Cp~C~s~~C~lP~~C~~C~l~L 327 (424)
..+|++++||||++++++ ||+||+|+||||++|++|++||+.|
T Consensus 237 ~~vd~ra~CfCh~k~v~~-GyvCs~Clsi~C~~p~~C~~Cgt~f 279 (279)
T TIGR00627 237 NSVDYRASCFCHHQLVSI-GFVCSVCLSVLCQYTPICKTCKTAF 279 (279)
T ss_pred CCCCCcceeeecCccccc-eEECCCccCCcCCCCCCCCCCCCCC
Confidence 999999999999999999 9999999999999999999999864
No 6
>cd01453 vWA_transcription_factor_IIH_type Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme. Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins contain a VWA domain. The p44 subunit of TFIIH functions as a DNA helicase in RNA polymerase II transcription initiation and DNA repair, and its transcriptional activity is dependent on its C-terminal Zn-binding domains. The function of the vWA domain is unclear, but may be involved in complex assembly. The MIDAS motif is not conserved in this sub-group.
Probab=100.00 E-value=4.9e-40 Score=304.99 Aligned_cols=183 Identities=57% Similarity=0.966 Sum_probs=170.5
Q ss_pred cccceEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCHHHHHHHHhhhh
Q 014440 83 GLIRYLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSPESHIKALMGKL 162 (424)
Q Consensus 83 GiiR~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~~~ 162 (424)
||||++||+||+|+||.+.|+.||||+++++.+.+|++.++++||.+|+|||+|+++.|++++|||.|.+.++..|....
T Consensus 1 ~~~r~ivi~lD~S~SM~a~D~~ptRl~~ak~~~~~fi~~~~~~~~~~~vglv~f~~~~a~~~~PlT~D~~~~~~~L~~~~ 80 (183)
T cd01453 1 GIMRHLIIVIDCSRSMEEQDLKPSRLAVVLKLLELFIEEFFDQNPISQLGIISIKNGRAEKLTDLTGNPRKHIQALKTAR 80 (183)
T ss_pred CceeEEEEEEECcHHHhcCCCCchHHHHHHHHHHHHHHHHhhcCccccEEEEEEcCCccEEEECCCCCHHHHHHHhhccc
Confidence 89999999999999999999999999999999999999999999999999999977999999999999998888887654
Q ss_pred CCCCcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchHHHHHHHHHHhCC
Q 014440 163 GCSGDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEMFICKHLCQETGG 242 (424)
Q Consensus 163 ~~~G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~~iLq~iA~~TGG 242 (424)
.+.|+|+|..||++|+..|++.+....++||||+++.++++++++.++++.+++++|+|++||+|+++.+|++||+.|||
T Consensus 81 ~~~G~t~l~~aL~~A~~~l~~~~~~~~~~iiil~sd~~~~~~~~~~~~~~~l~~~~I~v~~IgiG~~~~~L~~ia~~tgG 160 (183)
T cd01453 81 ECSGEPSLQNGLEMALESLKHMPSHGSREVLIIFSSLSTCDPGNIYETIDKLKKENIRVSVIGLSAEMHICKEICKATNG 160 (183)
T ss_pred CCCCchhHHHHHHHHHHHHhcCCccCceEEEEEEcCCCcCChhhHHHHHHHHHHcCcEEEEEEechHHHHHHHHHHHhCC
Confidence 56788999999999999998765556788999988777777878888999999999999999999999999999999999
Q ss_pred EEEEecChhhHHHHHHhcCCCCc
Q 014440 243 TYSVALDESHSKELILEHAPPPP 265 (424)
Q Consensus 243 ~Y~~~~d~~~L~~lL~~~~~pp~ 265 (424)
+||.+.|.++|.++|..+..||+
T Consensus 161 ~~~~~~~~~~l~~~~~~~~~p~~ 183 (183)
T cd01453 161 TYKVILDETHLKELLLEHVTPPP 183 (183)
T ss_pred eeEeeCCHHHHHHHHHhcCCCCC
Confidence 99999999999999999999986
No 7
>PF03850 Tfb4: Transcription factor Tfb4; InterPro: IPR004600 Members of this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. The core-TFIIH basal transcription factor complex has six subunits, this is the p34 subunit.; GO: 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent, 0000439 core TFIIH complex
Probab=100.00 E-value=6e-36 Score=293.77 Aligned_cols=229 Identities=21% Similarity=0.340 Sum_probs=187.6
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCC--------C--------
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGG--------S-------- 150 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~--------d-------- 150 (424)
-|+||||+|+.-+..--.+.-|..+++.+..|+|.|+..|..|+|+||+.+.+.++.++|... +
T Consensus 3 LLvIILD~nP~~W~~~~~~~~l~~~l~~llvFlNahL~l~~~N~vaVIAs~~~~s~~LYP~~~~~~~~~~~~~~~~~~~~ 82 (276)
T PF03850_consen 3 LLVIILDTNPLAWGQLSDQLSLSQFLDSLLVFLNAHLALNHSNQVAVIASHSNSSKFLYPSPSSSESSNSGDVEMNSSDS 82 (276)
T ss_pred EEEEEEECCHHHHhhccccccHHHHHHHHHHHHHHHHhhCccCCEEEEEEcCCccEEEeCCCccccccCCCccccccccc
Confidence 589999999998866555689999999999999999999999999999999999999999876 0
Q ss_pred -H--------HHHHHHHhhhhC-------CCCcchHHHHHHHHHHHHcCC----C---CCCCcEEEE-EEcCC-CCCCcc
Q 014440 151 -P--------ESHIKALMGKLG-------CSGDSSIQNALDLVHGLLNQI----P---SYGHREVLI-LYSAL-STCDPG 205 (424)
Q Consensus 151 -~--------~~~~~~L~~~~~-------~~G~tsL~~AL~~Al~~L~~~----p---~~~~reILv-I~ss~-~t~dp~ 205 (424)
. +.+.+.|+.++. ....+.|..||.+|++++++. + ..-++|||| +..+. ...++.
T Consensus 83 ~~y~~f~~v~~~v~~~l~~l~~~~~~~~~~~~~s~LagALS~ALCyINR~~~~~~~~~~~~~~RILv~~s~s~d~~~QYi 162 (276)
T PF03850_consen 83 NKYRQFRNVDETVLEELKKLMSETSESSDSTTSSLLAGALSMALCYINRISRESPSGGTSLKSRILVIVSGSPDSSSQYI 162 (276)
T ss_pred chhHHHHHHHHHHHHHHHHHHhhcccccccccchhhHHHHHHHHHHHhhhhhcccCCCCCcCccEEEEEecCCCccHHHH
Confidence 0 112333333321 112379999999999999986 1 134568999 66544 346777
Q ss_pred CHHHHHHHHHhCCcEEEEEEecc-hHHHHHHHHHHhCCEEEEecChhh-HHHHHHhcCCCCccchhhhhhheeeecCCCC
Q 014440 206 DIMETIQKCKESKIRCSVIGLSA-EMFICKHLCQETGGTYSVALDESH-SKELILEHAPPPPAIAEFAIASLIKMGFPQR 283 (424)
Q Consensus 206 ~i~~~i~~akk~~IrV~vIgLg~-e~~iLq~iA~~TGG~Y~~~~d~~~-L~~lL~~~~~pp~~~~~~~~~~Li~mGFP~~ 283 (424)
.+||+|+.|+|.+|.||++.|+. +..+|||+|++|||.|+.+.+.+. +++|++.++++|..| ..|+ .|.+
T Consensus 163 ~~MN~iFaAqk~~v~IDv~~L~~~~s~fLqQa~d~T~G~y~~~~~~~~l~q~L~~~fl~~~~~R-----~~l~---~p~~ 234 (276)
T PF03850_consen 163 PLMNCIFAAQKQKVPIDVCKLGGKDSTFLQQASDITGGIYLKVSKPEGLLQYLLTAFLPDPSSR-----SFLI---LPTQ 234 (276)
T ss_pred HHHHHHHHHhcCCceeEEEEecCCchHHHHHHHHHhCceeeccCccccHHHHHHHhhcCCHHHH-----hhcc---CCCC
Confidence 89999999999999999999999 899999999999999998877555 555666666555544 4554 7999
Q ss_pred CCCCCcceeeecCCccccCeEEcCCCCccccCCCC--CCCCCC
Q 014440 284 AGEGSISICSCHKEVKIGVGYTCPRCKARVCELPT--ECRICG 324 (424)
Q Consensus 284 ~~~~~~a~C~CH~~~~~~~Gy~Cp~C~s~~C~lP~--~C~~C~ 324 (424)
..+||||.||||++.+++ |||||+|+|+||++|. +|++||
T Consensus 235 ~~vd~ra~Cfch~k~vd~-g~vCsvCLsIfc~~p~~~~C~tC~ 276 (276)
T PF03850_consen 235 SSVDFRASCFCHRKVVDI-GYVCSVCLSIFCEFPDGGICPTCG 276 (276)
T ss_pred CCCCcceeeeecCCcccc-eeEchhhhhhhhCCCCCCCCCCCC
Confidence 999999999999999999 9999999999999984 999997
No 8
>KOG2487 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 [Transcription; Replication, recombination and repair]
Probab=100.00 E-value=6.4e-34 Score=271.18 Aligned_cols=234 Identities=16% Similarity=0.265 Sum_probs=190.9
Q ss_pred ceEEEEEeCCH---hhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeC--------------CC
Q 014440 86 RYLYIVIDLSR---AAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTD--------------LG 148 (424)
Q Consensus 86 R~lvlvLD~S~---SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lsp--------------LT 148 (424)
.-++++||.++ .|.+.--.---+..+++++..|+|+|+.+|..||++||+.+...-..++| +|
T Consensus 24 slL~vlId~~p~~Wg~~as~~~~~ti~kvl~aivVFlNAHL~~~~~NrvaViA~~~q~~~~lyp~st~~e~~n~~~~~~t 103 (314)
T KOG2487|consen 24 SLLVVLIDANPCSWGMLASAENWETISKVLNAIVVFLNAHLAFSRNNRVAVIASHSQVDNYLYPSSTRCEDRNASELDPT 103 (314)
T ss_pred eeEEEEEecCcchhhhhhhhcCceeHHHHHHHHHHHHHHHHhhccCCcEEEEEecccccceeccccccCCccCccccCch
Confidence 36899999999 66544333347788999999999999999999999999998777888888 22
Q ss_pred C----CH-------HHHHHHHhhhhC-----CCC-cchHHHHHHHHHHHHcCCCCC-----CCcEEEEEEcCC-CCCCcc
Q 014440 149 G----SP-------ESHIKALMGKLG-----CSG-DSSIQNALDLVHGLLNQIPSY-----GHREVLILYSAL-STCDPG 205 (424)
Q Consensus 149 ~----d~-------~~~~~~L~~~~~-----~~G-~tsL~~AL~~Al~~L~~~p~~-----~~reILvI~ss~-~t~dp~ 205 (424)
. ++ +.+++.|..+++ ..| .|-|.+||..|+.++.+.... ...|||||+-+. ...+++
T Consensus 104 ~~~~~~y~~~~~~d~tiv~ei~~lm~~~~~~~~~~rt~lagals~~L~yi~~~~ke~~~~~lkSRilV~t~t~d~~~qyi 183 (314)
T KOG2487|consen 104 RLVLFDYSEFRTVDDTIVEEIYRLMEHPDKYDVGDRTVLAGALSDALGYINRLHKEEASEKLKSRILVFTLTRDRALQYI 183 (314)
T ss_pred hhhcchhhhhcccchHHHHHHHHHHhCccccccccceeeccchhhccchHhhhhhhhhhhhhhceEEEEEechHHHhhhh
Confidence 1 11 223444544431 122 678999999999999875322 256799987543 336788
Q ss_pred CHHHHHHHHHhCCcEEEEEEecchHHHHHHHHHHhCCEEEEecCh-hhHHHHHHhcCCCCccchhhhhhheeeecCCCCC
Q 014440 206 DIMETIQKCKESKIRCSVIGLSAEMFICKHLCQETGGTYSVALDE-SHSKELILEHAPPPPAIAEFAIASLIKMGFPQRA 284 (424)
Q Consensus 206 ~i~~~i~~akk~~IrV~vIgLg~e~~iLq~iA~~TGG~Y~~~~d~-~~L~~lL~~~~~pp~~~~~~~~~~Li~mGFP~~~ 284 (424)
++|+.|+.|+|.+|+|+++.||.+..+|||.|++|||.|..+.+. +.|++|++.+++.|..| +.|+ -|.+.
T Consensus 184 ~~MNciFaAqKq~I~Idv~~l~~~s~~LqQa~D~TGG~YL~v~~~~gLLqyLlt~~~~D~~~R-----~~l~---kpnh~ 255 (314)
T KOG2487|consen 184 PYMNCIFAAQKQNIPIDVVSLGGDSGFLQQACDITGGDYLHVEKPDGLLQYLLTLLLTDPELR-----AVLS---KPNHN 255 (314)
T ss_pred hHHHHHHHHHhcCceeEEEEecCCchHHHHHHhhcCCeeEecCCcchHHHHHHHHhcCCcchh-----hhcc---CCCCC
Confidence 999999999999999999999999999999999999999987655 56778888888888766 6676 49999
Q ss_pred CCCCcceeeecCCccccCeEEcCCCCccccCCCCCCCCCCceec
Q 014440 285 GEGSISICSCHKEVKIGVGYTCPRCKARVCELPTECRICGLQLV 328 (424)
Q Consensus 285 ~~~~~a~C~CH~~~~~~~Gy~Cp~C~s~~C~lP~~C~~C~l~Lv 328 (424)
.+||||.|+||++++.+ |||||+|+|+||.++++|++|...+-
T Consensus 256 ~VDfRAtC~CH~~lv~i-G~VCSVCLSVfC~~~PiC~~C~s~F~ 298 (314)
T KOG2487|consen 256 SVDFRATCYCHNRLVLI-GFVCSVCLSVFCRFVPICKTCKSKFS 298 (314)
T ss_pred CcCcceeeeeecceeee-eeehHHHHHHhhCCCCccchhhhhcc
Confidence 99999999999999999 99999999999999999999999874
No 9
>cd01452 VWA_26S_proteasome_subunit 26S proteasome plays a major role in eukaryotic protein breakdown, especially for ubiquitin-tagged proteins. It is an ATP-dependent protease responsible for the bulk of non-lysosomal proteolysis in eukaryotes, often using covalent modification of proteins by ubiquitylation. It consists of a 20S proteolytic core particle (CP) and a 19S regulatory particle (RP). The CP is an ATP independent peptidase consisting of hydrolyzing activities. One or both ends of CP carry the RP that confers both ubiquitin and ATP dependence to the 26S proteosome. The RP's proposed functions include recognition of substrates and translocation of these to CP for proteolysis. The RP can dissociate into a stable lid and base subcomplexes. The base is composed of three non-ATPase subunits (Rpn 1, 2 and 10). A single residue in the vWA domain of Rpn10 has been implicated to be responsible for stabilizing the lid-base association.
Probab=100.00 E-value=2.1e-31 Score=248.01 Aligned_cols=155 Identities=15% Similarity=0.236 Sum_probs=144.3
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCHHHHHHHHhhhhCCCC
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSPESHIKALMGKLGCSG 166 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~~~~~~G 166 (424)
-+||+||+|.||.+.|++||||+++++++..|+.+|+++||.+|+|||+|+++.|++++|||+|+..++..|... .+.|
T Consensus 5 a~vi~lD~S~sM~a~D~~PnRL~aak~~i~~~~~~f~~~np~~~vGlv~fag~~a~v~~plT~D~~~~~~~L~~i-~~~g 83 (187)
T cd01452 5 ATMICIDNSEYMRNGDYPPTRFQAQADAVNLICQAKTRSNPENNVGLMTMAGNSPEVLVTLTNDQGKILSKLHDV-QPKG 83 (187)
T ss_pred EEEEEEECCHHHHcCCCCCCHHHHHHHHHHHHHHHHHhcCCCccEEEEEecCCceEEEECCCCCHHHHHHHHHhC-CCCC
Confidence 579999999999999999999999999999999999999999999999998779999999999999999999764 6789
Q ss_pred cchHHHHHHHHHHHHcCCCCCCCc-EEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecch---HHHHHHHHHHhCC
Q 014440 167 DSSIQNALDLVHGLLNQIPSYGHR-EVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAE---MFICKHLCQETGG 242 (424)
Q Consensus 167 ~tsL~~AL~~Al~~L~~~p~~~~r-eILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e---~~iLq~iA~~TGG 242 (424)
+++|++||++|...|++.+.++++ ||||+++|+.++|++++.++++.++++||+|++||||.+ ...|+.+.+..++
T Consensus 84 ~~~l~~AL~~A~~~L~~~~~~~~~~rivi~v~S~~~~d~~~i~~~~~~lkk~~I~v~vI~~G~~~~~~~~l~~~~~~~~~ 163 (187)
T cd01452 84 KANFITGIQIAQLALKHRQNKNQKQRIVAFVGSPIEEDEKDLVKLAKRLKKNNVSVDIINFGEIDDNTEKLTAFIDAVNG 163 (187)
T ss_pred cchHHHHHHHHHHHHhcCCCcCCcceEEEEEecCCcCCHHHHHHHHHHHHHcCCeEEEEEeCCCCCCHHHHHHHHHHhcC
Confidence 999999999999999999888875 999999998888999999999999999999999999975 5788888888853
No 10
>COG5242 TFB4 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 [Transcription / DNA replication, recombination, and repair]
Probab=99.96 E-value=1.4e-27 Score=222.62 Aligned_cols=233 Identities=17% Similarity=0.222 Sum_probs=185.0
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCH---------------
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSP--------------- 151 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~--------------- 151 (424)
-++++||+.+.-+..--+.--...++..+..|+|+++.-+..++++||+-.+..-+.++|-+...
T Consensus 22 lL~viid~~p~~W~~~~ek~~~~kvl~di~VFLNAhlaf~~~NrVaVva~~s~~~~yLypss~s~~k~se~e~tr~sd~y 101 (296)
T COG5242 22 LLFVIIDLEPENWELTTEKGSRDKVLNDIVVFLNAHLAFSRNNRVAVVAGYSQGKTYLYPSSESALKASESENTRNSDMY 101 (296)
T ss_pred eEEEEEecChhhcccccccccHHHHHHHHHHHHHHHHhhccCCeEEEEEeccCceEEeccCcchhhhhhcccCccchhhh
Confidence 47899999988765433334456688899999999999999999999997667778888875431
Q ss_pred -------HHHHHHHhhhhC-CC---CcchHHHHHHHHHHHHcCCCCCC--CcEEEEEEcCC--CCCCccCHHHHHHHHHh
Q 014440 152 -------ESHIKALMGKLG-CS---GDSSIQNALDLVHGLLNQIPSYG--HREVLILYSAL--STCDPGDIMETIQKCKE 216 (424)
Q Consensus 152 -------~~~~~~L~~~~~-~~---G~tsL~~AL~~Al~~L~~~p~~~--~reILvI~ss~--~t~dp~~i~~~i~~akk 216 (424)
+..+..+..+.+ +. .-+.+++|+..++.+.++..... ..+|||++-++ .-.++..+|+.|+.|++
T Consensus 102 rrfr~vde~~i~eiyrl~e~~~k~sqr~~v~gams~glay~n~~~~e~slkSriliftlsG~d~~~qYip~mnCiF~Aqk 181 (296)
T COG5242 102 RRFRNVDETDITEIYRLIEHPHKNSQRYDVGGAMSLGLAYCNHRDEETSLKSRILIFTLSGRDRKDQYIPYMNCIFAAQK 181 (296)
T ss_pred hhhcccchHHHHHHHHHHhCcccccceeehhhhhhhhHHHHhhhcccccccceEEEEEecCchhhhhhchhhhheeehhh
Confidence 112334444332 32 24789999999999998864332 35788887433 22566788999999999
Q ss_pred CCcEEEEEEecchHHHHHHHHHHhCCEEEEecCh-hhHHHHHHhcCCCCccchhhhhhheeeecCCCCCCCCCcceeeec
Q 014440 217 SKIRCSVIGLSAEMFICKHLCQETGGTYSVALDE-SHSKELILEHAPPPPAIAEFAIASLIKMGFPQRAGEGSISICSCH 295 (424)
Q Consensus 217 ~~IrV~vIgLg~e~~iLq~iA~~TGG~Y~~~~d~-~~L~~lL~~~~~pp~~~~~~~~~~Li~mGFP~~~~~~~~a~C~CH 295 (424)
.||+|+++.++....+|+|.|+.|||.|..+.|. +.|++|++.+.+.|..+ +.++ =|.+..+|||+.|+||
T Consensus 182 ~~ipI~v~~i~g~s~fl~Q~~daTgG~Yl~ve~~eGllqyL~~~lf~d~~lr-----p~~~---~pn~~svdFratCych 253 (296)
T COG5242 182 FGIPISVFSIFGNSKFLLQCCDATGGDYLTVEDTEGLLQYLLSLLFTDGELR-----PLGV---KPNHGSVDFRATCYCH 253 (296)
T ss_pred cCCceEEEEecCccHHHHHHhhccCCeeEeecCchhHHHHHHHHhcCCCCcc-----cccc---CCCcccccccceeEEe
Confidence 9999999999999999999999999999988775 45677777777766655 4444 4999999999999999
Q ss_pred CCccccCeEEcCCCCccccCCCCCCCCCCceec
Q 014440 296 KEVKIGVGYTCPRCKARVCELPTECRICGLQLV 328 (424)
Q Consensus 296 ~~~~~~~Gy~Cp~C~s~~C~lP~~C~~C~l~Lv 328 (424)
++.+.. ||+||+|+|+||+.-+.|+.|...+-
T Consensus 254 ~rvv~~-GfvCsVCLsvfc~p~~~C~~C~skF~ 285 (296)
T COG5242 254 NRVVLL-GFVCSVCLSVFCRPVPVCKKCKSKFS 285 (296)
T ss_pred ccEEEE-eeehhhhheeecCCcCcCcccccccc
Confidence 999999 99999999999999999999999873
No 11
>PRK13685 hypothetical protein; Provisional
Probab=99.92 E-value=7.5e-24 Score=213.06 Aligned_cols=170 Identities=16% Similarity=0.252 Sum_probs=143.0
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCHHHHHHHHhhhhCCCC
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSPESHIKALMGKLGCSG 166 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~~~~~~G 166 (424)
++|+|||+|+||.+.|..|+||+.+++.+.+|++.+ +|.+++|+|+| ++.++++.|+|.|.+.+...|..+ .+.|
T Consensus 90 ~vvlvlD~S~SM~~~D~~p~RL~~ak~~~~~~l~~l---~~~d~vglv~F-a~~a~~~~p~t~d~~~l~~~l~~l-~~~~ 164 (326)
T PRK13685 90 VVMLVIDVSQSMRATDVEPNRLAAAQEAAKQFADEL---TPGINLGLIAF-AGTATVLVSPTTNREATKNAIDKL-QLAD 164 (326)
T ss_pred eEEEEEECCccccCCCCCCCHHHHHHHHHHHHHHhC---CCCCeEEEEEE-cCceeecCCCCCCHHHHHHHHHhC-CCCC
Confidence 899999999999999999999999999999999864 46789999999 589999999999999998888764 6778
Q ss_pred cchHHHHHHHHHHHHcCC-------CCCCCcEEEEEEcCCCCCC-----ccCHHHHHHHHHhCCcEEEEEEecch-----
Q 014440 167 DSSIQNALDLVHGLLNQI-------PSYGHREVLILYSALSTCD-----PGDIMETIQKCKESKIRCSVIGLSAE----- 229 (424)
Q Consensus 167 ~tsL~~AL~~Al~~L~~~-------p~~~~reILvI~ss~~t~d-----p~~i~~~i~~akk~~IrV~vIgLg~e----- 229 (424)
+|+++.+|..|++.+... .....+.||+|+++.++.. +....++++.+++.||+|++||+|++
T Consensus 165 ~T~~g~al~~A~~~l~~~~~~~~~~~~~~~~~IILlTDG~~~~~~~~~~~~~~~~aa~~a~~~gi~i~~Ig~G~~~g~~~ 244 (326)
T PRK13685 165 RTATGEAIFTALQAIATVGAVIGGGDTPPPARIVLMSDGKETVPTNPDNPRGAYTAARTAKDQGVPISTISFGTPYGSVE 244 (326)
T ss_pred CcchHHHHHHHHHHHHhhhcccccccCCCCCEEEEEcCCCCCCCCCCCCcccHHHHHHHHHHcCCeEEEEEECCCCCCcC
Confidence 999999999999998632 1123456776666654422 12345678899999999999999973
Q ss_pred -----------HHHHHHHHHHhCCEEEEecChhhHHHHHHhcC
Q 014440 230 -----------MFICKHLCQETGGTYSVALDESHSKELILEHA 261 (424)
Q Consensus 230 -----------~~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~ 261 (424)
...|++||+.|||+|+.+.+.++|.+++.++.
T Consensus 245 ~~g~~~~~~~d~~~L~~iA~~tgG~~~~~~~~~~L~~if~~I~ 287 (326)
T PRK13685 245 INGQRQPVPVDDESLKKIAQLSGGEFYTAASLEELRAVYATLQ 287 (326)
T ss_pred cCCceeeecCCHHHHHHHHHhcCCEEEEcCCHHHHHHHHHHHH
Confidence 47899999999999999999999999988875
No 12
>cd01467 vWA_BatA_type VWA BatA type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses. In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if
Probab=99.86 E-value=3.9e-20 Score=168.68 Aligned_cols=159 Identities=23% Similarity=0.275 Sum_probs=126.7
Q ss_pred eEEEEEeCCHhhhcCCC-CCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCHHHHHHHHhhhh--C
Q 014440 87 YLYIVIDLSRAAAEMDF-RPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSPESHIKALMGKL--G 163 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~-~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~~~--~ 163 (424)
+++|+||+|+||...|+ .++|++.++..+..|+. ..|.+++|||+| ++.+..+.|++.+...+.+.|..+. .
T Consensus 4 ~vv~vlD~S~SM~~~~~~~~~r~~~a~~~~~~~~~----~~~~~~v~lv~f-~~~~~~~~~~~~~~~~~~~~l~~l~~~~ 78 (180)
T cd01467 4 DIMIALDVSGSMLAQDFVKPSRLEAAKEVLSDFID----RRENDRIGLVVF-AGAAFTQAPLTLDRESLKELLEDIKIGL 78 (180)
T ss_pred eEEEEEECCcccccccCCCCCHHHHHHHHHHHHHH----hCCCCeEEEEEE-cCCeeeccCCCccHHHHHHHHHHhhhcc
Confidence 99999999999999888 68999999998887776 457789999999 5788999999988776666665442 3
Q ss_pred CCCcchHHHHHHHHHHHHcCCCCCCCcEEEEEE-cCCCCCCccCHHHHHHHHHhCCcEEEEEEecc-------------h
Q 014440 164 CSGDSSIQNALDLVHGLLNQIPSYGHREVLILY-SALSTCDPGDIMETIQKCKESKIRCSVIGLSA-------------E 229 (424)
Q Consensus 164 ~~G~tsL~~AL~~Al~~L~~~p~~~~reILvI~-ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~-------------e 229 (424)
+.|+|++..||..|+..|...+ ..+.+|||+ ++..+..+....++++.+++.||+|++|++|. +
T Consensus 79 ~~g~T~l~~al~~a~~~l~~~~--~~~~~iiliTDG~~~~g~~~~~~~~~~~~~~gi~i~~i~ig~~~~~~~~~~~~~~~ 156 (180)
T cd01467 79 AGQGTAIGDAIGLAIKRLKNSE--AKERVIVLLTDGENNAGEIDPATAAELAKNKGVRIYTIGVGKSGSGPKPDGSTILD 156 (180)
T ss_pred cCCCCcHHHHHHHHHHHHHhcC--CCCCEEEEEeCCCCCCCCCCHHHHHHHHHHCCCEEEEEEecCCCCCcCCCCcccCC
Confidence 5788999999999999997753 233445555 44343333345567788888999999999997 4
Q ss_pred HHHHHHHHHHhCCEEEEecChhh
Q 014440 230 MFICKHLCQETGGTYSVALDESH 252 (424)
Q Consensus 230 ~~iLq~iA~~TGG~Y~~~~d~~~ 252 (424)
...|++||+.|||.|+.+.+...
T Consensus 157 ~~~l~~la~~tgG~~~~~~~~~~ 179 (180)
T cd01467 157 EDSLVEIADKTGGRIFRALDGFE 179 (180)
T ss_pred HHHHHHHHHhcCCEEEEecCccc
Confidence 57999999999999999887654
No 13
>cd01455 vWA_F11C1-5a_type Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A
Probab=99.86 E-value=1.8e-20 Score=174.71 Aligned_cols=167 Identities=17% Similarity=0.147 Sum_probs=125.7
Q ss_pred eEEEEEeCCHhhhcCC-C--C-CChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCH---------HH
Q 014440 87 YLYIVIDLSRAAAEMD-F--R-PSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSP---------ES 153 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D-~--~-P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~---------~~ 153 (424)
+|+|+||+|+||...+ + + .+||++++..++.|+ +|.++.+.+++| | .|.+..+.|+|.+. +.
T Consensus 2 ~l~lavDlSgSM~~~~~~dg~~~~RL~a~k~v~~~f~-~f~~~r~~DriG---~-~g~~~~~~~lt~d~p~t~d~~~~~~ 76 (191)
T cd01455 2 RLKLVVDVSGSMYRFNGYDGRLDRSLEAVVMVMEAFD-GFEDKIQYDIIG---H-SGDGPCVPFVKTNHPPKNNKERLET 76 (191)
T ss_pred ceEEEEECcHhHHHHhccCCccccHHHHHHHHHHHHH-HHHHhCccceee---e-cCcccccCccccccCcccchhHHHH
Confidence 6899999999997544 2 3 599999999999997 456678889999 3 46777677766544 33
Q ss_pred HHHHHhhhh-CCCC-cchHHHHHHHHHHHHc-CCCCCCCcEEEEEEcCCC-CCCccCHHH-HHHHHHhCCcEEEEEEecc
Q 014440 154 HIKALMGKL-GCSG-DSSIQNALDLVHGLLN-QIPSYGHREVLILYSALS-TCDPGDIME-TIQKCKESKIRCSVIGLSA 228 (424)
Q Consensus 154 ~~~~L~~~~-~~~G-~tsL~~AL~~Al~~L~-~~p~~~~reILvI~ss~~-t~dp~~i~~-~i~~akk~~IrV~vIgLg~ 228 (424)
+...|.... ...| +|+ .||.+|++.|+ ..+ ...+||||+++.. +....+..+ ++..+++.||+||+||+|+
T Consensus 77 l~~~l~~~q~g~ag~~Ta--dAi~~av~rl~~~~~--a~~kvvILLTDG~n~~~~i~P~~aAa~lA~~~gV~iytIgiG~ 152 (191)
T cd01455 77 LKMMHAHSQFCWSGDHTV--EATEFAIKELAAKED--FDEAIVIVLSDANLERYGIQPKKLADALAREPNVNAFVIFIGS 152 (191)
T ss_pred HHHHHHhcccCccCccHH--HHHHHHHHHHHhcCc--CCCcEEEEEeCCCcCCCCCChHHHHHHHHHhCCCEEEEEEecC
Confidence 333443322 2334 566 99999999997 653 3345666665443 333335566 4788999999999999998
Q ss_pred -hHHHHHHHHHHhCCEEEEecChhhHHHHHHhcCC
Q 014440 229 -EMFICKHLCQETGGTYSVALDESHSKELILEHAP 262 (424)
Q Consensus 229 -e~~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~~ 262 (424)
+...|+.+|+.|||+||.+.|.+.|.+++.++++
T Consensus 153 ~d~~~l~~iA~~tgG~~F~A~d~~~L~~iy~~I~~ 187 (191)
T cd01455 153 LSDEADQLQRELPAGKAFVCMDTSELPHIMQQIFT 187 (191)
T ss_pred CCHHHHHHHHhCCCCcEEEeCCHHHHHHHHHHHHH
Confidence 6788999999999999999999999999998874
No 14
>PF13519 VWA_2: von Willebrand factor type A domain; PDB: 3IBS_B 3RAG_B 2X5N_A.
Probab=99.85 E-value=3.3e-20 Score=165.17 Aligned_cols=165 Identities=18% Similarity=0.244 Sum_probs=131.3
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCHHHHHHHHhhhh---C
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSPESHIKALMGKL---G 163 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~~~---~ 163 (424)
++||+||.|+||...|..++|+..++..+..|++.+ |.+++||+.|. +.+.+..|+|.+...+.+.|.++. .
T Consensus 1 dvv~v~D~SgSM~~~~~~~~~~~~~~~~~~~~~~~~----~~~~v~l~~f~-~~~~~~~~~t~~~~~~~~~l~~~~~~~~ 75 (172)
T PF13519_consen 1 DVVFVLDNSGSMNGYDGNRTRIDQAKDALNELLANL----PGDRVGLVSFS-DSSRTLSPLTSDKDELKNALNKLSPQGM 75 (172)
T ss_dssp EEEEEEE-SGGGGTTTSSS-HHHHHHHHHHHHHHHH----TTSEEEEEEES-TSCEEEEEEESSHHHHHHHHHTHHHHG-
T ss_pred CEEEEEECCcccCCCCCCCcHHHHHHHHHHHHHHHC----CCCEEEEEEec-ccccccccccccHHHHHHHhhccccccc
Confidence 689999999999999989999999999999999874 56799999995 678999999999999988887653 4
Q ss_pred CCCcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH---HHHHHHHHHh
Q 014440 164 CSGDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM---FICKHLCQET 240 (424)
Q Consensus 164 ~~G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~---~iLq~iA~~T 240 (424)
+.|++.+..||..|.++|...+ ..+++||++++... ..+..++++.+++.+|+|++|+++.+. ..|+++|+.|
T Consensus 76 ~~~~t~~~~al~~a~~~~~~~~--~~~~~iv~iTDG~~--~~~~~~~~~~~~~~~i~i~~v~~~~~~~~~~~l~~la~~t 151 (172)
T PF13519_consen 76 PGGGTNLYDALQEAAKMLASSD--NRRRAIVLITDGED--NSSDIEAAKALKQQGITIYTVGIGSDSDANEFLQRLAEAT 151 (172)
T ss_dssp -SSS--HHHHHHHHHHHHHC-S--SEEEEEEEEES-TT--HCHHHHHHHHHHCTTEEEEEEEES-TT-EHHHHHHHHHHT
T ss_pred CccCCcHHHHHHHHHHHHHhCC--CCceEEEEecCCCC--CcchhHHHHHHHHcCCeEEEEEECCCccHHHHHHHHHHhc
Confidence 6788999999999999998763 33444555444322 134457899999999999999999764 5899999999
Q ss_pred CCEEEEe-cChhhHHHHHHhc
Q 014440 241 GGTYSVA-LDESHSKELILEH 260 (424)
Q Consensus 241 GG~Y~~~-~d~~~L~~lL~~~ 260 (424)
||.|+.+ .+.+.|.++|.++
T Consensus 152 gG~~~~~~~~~~~l~~~~~~I 172 (172)
T PF13519_consen 152 GGRYFHVDNDPEDLDDAFQQI 172 (172)
T ss_dssp EEEEEEE-SSSHHHHHHHHH-
T ss_pred CCEEEEecCCHHHHHHHHhcC
Confidence 9999998 7889999998765
No 15
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=99.83 E-value=9.8e-22 Score=145.02 Aligned_cols=49 Identities=55% Similarity=1.333 Sum_probs=33.2
Q ss_pred ceeecccccccCCC--CCCceeeCCCcCcccccccchhhhccCCCCCCCCC
Q 014440 364 TCFGCQQSLLASGN--KAGLCVACPKCKKHFCLECDIYIHESLHNCPGCES 412 (424)
Q Consensus 364 ~C~~C~~~~~~~~~--~~~~~~~C~~C~~~fC~dCd~fihe~lh~CPgC~~ 412 (424)
+||||+++|+.+.. ..+.+|+||+|+++||+|||+||||+||+||||++
T Consensus 1 ~CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHE~LH~CPGC~s 51 (51)
T PF07975_consen 1 YCFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFIHETLHNCPGCES 51 (51)
T ss_dssp EETTTTEE-TTS-------EEE--TTTT--B-HHHHHTTTTTS-SSSTT--
T ss_pred CCccCCCCCCCcccccccCCeEECCCCCCccccCcChhhhccccCCcCCCC
Confidence 59999999987642 13578999999999999999999999999999974
No 16
>TIGR03436 acidobact_VWFA VWFA-related Acidobacterial domain. Members of this family are bacterial domains that include a region related to the von Willebrand factor type A (VWFA) domain (pfam00092). These domains are restricted to, and have undergone a large paralogous family expansion in, the Acidobacteria, including Solibacter usitatus and Acidobacterium capsulatum ATCC 51196.
Probab=99.78 E-value=7.6e-18 Score=166.55 Aligned_cols=166 Identities=16% Similarity=0.183 Sum_probs=131.0
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCHHHHHHHHhhhhC---
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSPESHIKALMGKLG--- 163 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~~~~--- 163 (424)
+++|+||+|+||. .++..+++++..|++..+ .|.+++|||.| ++.+..+.|+|.+...+.++|..+..
T Consensus 55 ~vvlvlD~SgSM~------~~~~~a~~a~~~~l~~~l--~~~d~v~lv~f-~~~~~~~~~~t~~~~~l~~~l~~l~~~~~ 125 (296)
T TIGR03436 55 TVGLVIDTSGSMR------NDLDRARAAAIRFLKTVL--RPNDRVFVVTF-NTRLRLLQDFTSDPRLLEAALNRLKPPLR 125 (296)
T ss_pred eEEEEEECCCCch------HHHHHHHHHHHHHHHhhC--CCCCEEEEEEe-CCceeEeecCCCCHHHHHHHHHhccCCCc
Confidence 8999999999997 368899999999998754 57899999999 58899999999999998888876522
Q ss_pred -----------CCCcchHHHHHHHHH-HHHcCCCC--CCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecc-
Q 014440 164 -----------CSGDSSIQNALDLVH-GLLNQIPS--YGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSA- 228 (424)
Q Consensus 164 -----------~~G~tsL~~AL~~Al-~~L~~~p~--~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~- 228 (424)
+.|+|+|.+||.+|. ..+..... .+.+.||+|+++.++....++.++++.+++.+|.|++|+++.
T Consensus 126 ~~~~~~~~~~~~~g~T~l~~al~~aa~~~~~~~~~~~p~rk~iIllTDG~~~~~~~~~~~~~~~~~~~~v~vy~I~~~~~ 205 (296)
T TIGR03436 126 TDYNSSGAFVRDGGGTALYDAITLAALEQLANALAGIPGRKALIVISDGGDNRSRDTLERAIDAAQRADVAIYSIDARGL 205 (296)
T ss_pred cccccccccccCCCcchhHHHHHHHHHHHHHHhhcCCCCCeEEEEEecCCCcchHHHHHHHHHHHHHcCCEEEEeccCcc
Confidence 278999999998775 44443211 134444444555444334457788999999999999999983
Q ss_pred --------------hHHHHHHHHHHhCCEEEEecChhhHHHHHHhcCC
Q 014440 229 --------------EMFICKHLCQETGGTYSVALDESHSKELILEHAP 262 (424)
Q Consensus 229 --------------e~~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~~ 262 (424)
....|++||+.|||+|+.+ +.+.|...+..+..
T Consensus 206 ~~~~~~~~~~~~~~~~~~L~~iA~~TGG~~~~~-~~~~l~~~f~~i~~ 252 (296)
T TIGR03436 206 RAPDLGAGAKAGLGGPEALERLAEETGGRAFYV-NSNDLDGAFAQIAE 252 (296)
T ss_pred ccCCcccccccCCCcHHHHHHHHHHhCCeEecc-cCccHHHHHHHHHH
Confidence 3579999999999999998 88888888877774
No 17
>cd01456 vWA_ywmD_type VWA ywmD type:Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if
Probab=99.77 E-value=1.6e-17 Score=156.03 Aligned_cols=155 Identities=21% Similarity=0.246 Sum_probs=114.0
Q ss_pred eEEEEEeCCHhhhc-CCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCce------EEee---CCC--------
Q 014440 87 YLYIVIDLSRAAAE-MDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVA------NCLT---DLG-------- 148 (424)
Q Consensus 87 ~lvlvLD~S~SM~~-~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A------~~ls---pLT-------- 148 (424)
+++||||.|+||.. .+-.++||+.++..+..|++.+ .|.+++|||+|. +.+ ..+. |++
T Consensus 22 ~vv~vlD~SgSM~~~~~~~~~rl~~ak~a~~~~l~~l---~~~~~v~lv~F~-~~~~~~~~~~~~~p~~~~~~~~~~~~~ 97 (206)
T cd01456 22 NVAIVLDNSGSMREVDGGGETRLDNAKAALDETANAL---PDGTRLGLWTFS-GDGDNPLDVRVLVPKGCLTAPVNGFPS 97 (206)
T ss_pred cEEEEEeCCCCCcCCCCCcchHHHHHHHHHHHHHHhC---CCCceEEEEEec-CCCCCCccccccccccccccccCCCCc
Confidence 89999999999984 3446899999999999999864 456899999995 422 2232 332
Q ss_pred CCHHHHHHHHhhhhCCCCcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHh-----CCcEEEE
Q 014440 149 GSPESHIKALMGKLGCSGDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKE-----SKIRCSV 223 (424)
Q Consensus 149 ~d~~~~~~~L~~~~~~~G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk-----~~IrV~v 223 (424)
.+.+.+.+.|..+..+.|+|+|..||+.|.+.|. + ...+.||||+++..++++ +..+.+..+.+ .+|+|++
T Consensus 98 ~~~~~l~~~i~~i~~~~G~T~l~~aL~~a~~~l~--~-~~~~~iillTDG~~~~~~-~~~~~~~~~~~~~~~~~~i~i~~ 173 (206)
T cd01456 98 AQRSALDAALNSLQTPTGWTPLAAALAEAAAYVD--P-GRVNVVVLITDGEDTCGP-DPCEVARELAKRRTPAPPIKVNV 173 (206)
T ss_pred ccHHHHHHHHHhhcCCCCcChHHHHHHHHHHHhC--C-CCcceEEEEcCCCccCCC-CHHHHHHHHHHhcCCCCCceEEE
Confidence 2445555566554237899999999999999996 1 122567777776555433 44455554444 4999999
Q ss_pred EEecch--HHHHHHHHHHhCCEE-EEecC
Q 014440 224 IGLSAE--MFICKHLCQETGGTY-SVALD 249 (424)
Q Consensus 224 IgLg~e--~~iLq~iA~~TGG~Y-~~~~d 249 (424)
||||.+ ...|++||+.|||.| +.+.+
T Consensus 174 igiG~~~~~~~l~~iA~~tgG~~~~~~~~ 202 (206)
T cd01456 174 IDFGGDADRAELEAIAEATGGTYAYNQSD 202 (206)
T ss_pred EEecCcccHHHHHHHHHhcCCeEeccccc
Confidence 999986 689999999999999 65544
No 18
>cd01466 vWA_C3HC4_type VWA C3HC4-type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most,
Probab=99.77 E-value=1e-17 Score=150.88 Aligned_cols=146 Identities=18% Similarity=0.288 Sum_probs=109.8
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCC----HHHHHHHHhhhh
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGS----PESHIKALMGKL 162 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d----~~~~~~~L~~~~ 162 (424)
+++||||.|+||.. +||+.++.++..+++.+. +.+++|||+| ++.++.+.|++.. ...+...|.. +
T Consensus 2 ~v~~vlD~S~SM~~-----~rl~~ak~a~~~l~~~l~---~~~~~~li~F-~~~~~~~~~~~~~~~~~~~~~~~~i~~-~ 71 (155)
T cd01466 2 DLVAVLDVSGSMAG-----DKLQLVKHALRFVISSLG---DADRLSIVTF-STSAKRLSPLRRMTAKGKRSAKRVVDG-L 71 (155)
T ss_pred cEEEEEECCCCCCc-----HHHHHHHHHHHHHHHhCC---CcceEEEEEe-cCCccccCCCcccCHHHHHHHHHHHHh-c
Confidence 78999999999975 399999999987776543 4579999999 5789999998742 2333344443 4
Q ss_pred CCCCcchHHHHHHHHHHHHcCCCCCC-CcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEec--chHHHHHHHHHH
Q 014440 163 GCSGDSSIQNALDLVHGLLNQIPSYG-HREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLS--AEMFICKHLCQE 239 (424)
Q Consensus 163 ~~~G~tsL~~AL~~Al~~L~~~p~~~-~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg--~e~~iLq~iA~~ 239 (424)
.+.|+|++..||..|.+.+....... .+.||+|+++..+. + .....+++.+|+|++||+| .+...|++||..
T Consensus 72 ~~~g~T~~~~al~~a~~~~~~~~~~~~~~~iillTDG~~~~--~---~~~~~~~~~~v~v~~igig~~~~~~~l~~iA~~ 146 (155)
T cd01466 72 QAGGGTNVVGGLKKALKVLGDRRQKNPVASIMLLSDGQDNH--G---AVVLRADNAPIPIHTFGLGASHDPALLAFIAEI 146 (155)
T ss_pred cCCCCccHHHHHHHHHHHHhhcccCCCceEEEEEcCCCCCc--c---hhhhcccCCCceEEEEecCCCCCHHHHHHHHhc
Confidence 68899999999999999997542222 34455555543332 2 2334566789999999999 567899999999
Q ss_pred hCCEEEEe
Q 014440 240 TGGTYSVA 247 (424)
Q Consensus 240 TGG~Y~~~ 247 (424)
|||+|+.+
T Consensus 147 t~G~~~~~ 154 (155)
T cd01466 147 TGGTFSYV 154 (155)
T ss_pred cCceEEEe
Confidence 99999976
No 19
>cd01451 vWA_Magnesium_chelatase Magnesium chelatase: Mg-chelatase catalyses the insertion of Mg into protoporphyrin IX (Proto). In chlorophyll biosynthesis, insertion of Mg2+ into protoporphyrin IX is catalysed by magnesium chelatase in an ATP-dependent reaction. Magnesium chelatase is a three sub-unit (BchI, BchD and BchH) enzyme with a novel arrangement of domains: the C-terminal helical domain is located behind the nucleotide binding site. The BchD domain contains a AAA domain at its N-terminus and a VWA domain at its C-terminus. The VWA domain has been speculated to be involved in mediating protein-protein interactions.
Probab=99.77 E-value=3e-17 Score=150.85 Aligned_cols=158 Identities=21% Similarity=0.270 Sum_probs=120.5
Q ss_pred EEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCHHHHHHHHhhhhCCCCc
Q 014440 88 LYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSPESHIKALMGKLGCSGD 167 (424)
Q Consensus 88 lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~~~~~~G~ 167 (424)
++|+||.|+||... +||+.++..+..|+...+ ++.+++|||+|.++.++.+.|+|.+...+...|..+ .+.|+
T Consensus 3 v~lvlD~SgSM~~~----~rl~~ak~a~~~~~~~~~--~~~d~v~lv~F~~~~~~~~~~~t~~~~~~~~~l~~l-~~~G~ 75 (178)
T cd01451 3 VIFVVDASGSMAAR----HRMAAAKGAVLSLLRDAY--QRRDKVALIAFRGTEAEVLLPPTRSVELAKRRLARL-PTGGG 75 (178)
T ss_pred EEEEEECCccCCCc----cHHHHHHHHHHHHHHHhh--cCCCEEEEEEECCCCceEEeCCCCCHHHHHHHHHhC-CCCCC
Confidence 78999999999753 699999999999997654 356899999995445888999999887776666653 67889
Q ss_pred chHHHHHHHHHHHH-cCCCCCCCcEEEEEE-cCCCCC--CccC-H-HHHHHHHHhCCcEEEEEEecch---HHHHHHHHH
Q 014440 168 SSIQNALDLVHGLL-NQIPSYGHREVLILY-SALSTC--DPGD-I-METIQKCKESKIRCSVIGLSAE---MFICKHLCQ 238 (424)
Q Consensus 168 tsL~~AL~~Al~~L-~~~p~~~~reILvI~-ss~~t~--dp~~-i-~~~i~~akk~~IrV~vIgLg~e---~~iLq~iA~ 238 (424)
|+|..||..|...+ ...+..+.+.+|||+ ++..+. +|.. . .+.++.+++.+|.|++|+++.. ...|++||+
T Consensus 76 T~l~~aL~~a~~~l~~~~~~~~~~~~ivliTDG~~~~g~~~~~~~~~~~~~~l~~~gi~v~~I~~~~~~~~~~~l~~iA~ 155 (178)
T cd01451 76 TPLAAGLLAAYELAAEQARDPGQRPLIVVITDGRANVGPDPTADRALAAARKLRARGISALVIDTEGRPVRRGLAKDLAR 155 (178)
T ss_pred CcHHHHHHHHHHHHHHHhcCCCCceEEEEECCCCCCCCCCchhHHHHHHHHHHHhcCCcEEEEeCCCCccCccHHHHHHH
Confidence 99999999999998 222222333455555 443332 2221 2 4567889999999999999864 579999999
Q ss_pred HhCCEEEEecChhh
Q 014440 239 ETGGTYSVALDESH 252 (424)
Q Consensus 239 ~TGG~Y~~~~d~~~ 252 (424)
.|||+|+.+.|.++
T Consensus 156 ~tgG~~~~~~d~~~ 169 (178)
T cd01451 156 ALGGQYVRLPDLSA 169 (178)
T ss_pred HcCCeEEEcCcCCH
Confidence 99999998866543
No 20
>TIGR00868 hCaCC calcium-activated chloride channel protein 1. distributions. found a row in 1A13.INFO that was not parsed out
Probab=99.75 E-value=3.7e-17 Score=180.71 Aligned_cols=160 Identities=23% Similarity=0.272 Sum_probs=123.1
Q ss_pred ceEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCC-CHHHHHHHHhhhh--
Q 014440 86 RYLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGG-SPESHIKALMGKL-- 162 (424)
Q Consensus 86 R~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~-d~~~~~~~L~~~~-- 162 (424)
|.++||||+|+||...| ||.+++++++.|+...+ +|.+++|||+| ++.|+++.||+. +.....++|...+
T Consensus 305 r~VVLVLDvSGSM~g~d----RL~~lkqAA~~fL~~~l--~~~DrVGLVtF-sssA~vl~pLt~Its~~dr~aL~~~L~~ 377 (863)
T TIGR00868 305 RIVCLVLDKSGSMTVED----RLKRMNQAAKLFLLQTV--EKGSWVGMVTF-DSAAYIKNELIQITSSAERDALTANLPT 377 (863)
T ss_pred ceEEEEEECCccccccC----HHHHHHHHHHHHHHHhC--CCCCEEEEEEE-CCceeEeeccccCCcHHHHHHHHHhhcc
Confidence 57999999999998754 99999999999998775 46799999999 689999999873 1112233333322
Q ss_pred CCCCcchHHHHHHHHHHHHcCCCC-CCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecch-HHHHHHHHHHh
Q 014440 163 GCSGDSSIQNALDLVHGLLNQIPS-YGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAE-MFICKHLCQET 240 (424)
Q Consensus 163 ~~~G~tsL~~AL~~Al~~L~~~p~-~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e-~~iLq~iA~~T 240 (424)
.+.|+|+|..||.+|++.|.+... ...+.||+|+++..+ ++..++..+++.+|+|++||+|.. ...|++||+.|
T Consensus 378 ~A~GGT~I~~GL~~Alq~L~~~~~~~~~~~IILLTDGedn----~~~~~l~~lk~~gVtI~TIg~G~dad~~L~~IA~~T 453 (863)
T TIGR00868 378 AASGGTSICSGLKAAFQVIKKSYQSTDGSEIVLLTDGEDN----TISSCFEEVKQSGAIIHTIALGPSAAKELEELSDMT 453 (863)
T ss_pred ccCCCCcHHHHHHHHHHHHHhcccccCCCEEEEEeCCCCC----CHHHHHHHHHHcCCEEEEEEeCCChHHHHHHHHHhc
Confidence 468999999999999999987532 234556666655432 345778889999999999999964 45799999999
Q ss_pred CCEEEEecChhhHHHH
Q 014440 241 GGTYSVALDESHSKEL 256 (424)
Q Consensus 241 GG~Y~~~~d~~~L~~l 256 (424)
||+|+.+.+..++..|
T Consensus 454 GG~~f~asd~~dl~~L 469 (863)
T TIGR00868 454 GGLRFYASDQADNNGL 469 (863)
T ss_pred CCEEEEeCCHHHHHHH
Confidence 9999999877654444
No 21
>cd01465 vWA_subgroup VWA subgroup: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if n
Probab=99.75 E-value=9.1e-17 Score=144.56 Aligned_cols=161 Identities=16% Similarity=0.202 Sum_probs=123.3
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCC--CHHHHHHHHhhhhCC
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGG--SPESHIKALMGKLGC 164 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~--d~~~~~~~L~~~~~~ 164 (424)
+++++||+|+||... +++.+++.+..++..+ ++.+++|||+|. +.+..+.|++. +.+.+.+.|.+ +.+
T Consensus 2 ~~~~vlD~S~SM~~~-----~~~~~k~a~~~~~~~l---~~~~~v~li~f~-~~~~~~~~~~~~~~~~~l~~~l~~-~~~ 71 (170)
T cd01465 2 NLVFVIDRSGSMDGP-----KLPLVKSALKLLVDQL---RPDDRLAIVTYD-GAAETVLPATPVRDKAAILAAIDR-LTA 71 (170)
T ss_pred cEEEEEECCCCCCCh-----hHHHHHHHHHHHHHhC---CCCCEEEEEEec-CCccEEecCcccchHHHHHHHHHc-CCC
Confidence 789999999999742 5899999888888754 566899999995 77888888764 45555555554 357
Q ss_pred CCcchHHHHHHHHHHHHcCCCC-CCCcEEEEEEcCCCCCCccC---HHHHHHHHHhCCcEEEEEEecc--hHHHHHHHHH
Q 014440 165 SGDSSIQNALDLVHGLLNQIPS-YGHREVLILYSALSTCDPGD---IMETIQKCKESKIRCSVIGLSA--EMFICKHLCQ 238 (424)
Q Consensus 165 ~G~tsL~~AL~~Al~~L~~~p~-~~~reILvI~ss~~t~dp~~---i~~~i~~akk~~IrV~vIgLg~--e~~iLq~iA~ 238 (424)
.|+|.+..||..|+..+.+... ...+.||+++++..+.++.+ +.+.++.+++.+|+|++||+|. +...|++||+
T Consensus 72 ~g~T~~~~al~~a~~~~~~~~~~~~~~~ivl~TDG~~~~~~~~~~~~~~~~~~~~~~~v~i~~i~~g~~~~~~~l~~ia~ 151 (170)
T cd01465 72 GGSTAGGAGIQLGYQEAQKHFVPGGVNRILLATDGDFNVGETDPDELARLVAQKRESGITLSTLGFGDNYNEDLMEAIAD 151 (170)
T ss_pred CCCCCHHHHHHHHHHHHHhhcCCCCeeEEEEEeCCCCCCCCCCHHHHHHHHHHhhcCCeEEEEEEeCCCcCHHHHHHHHh
Confidence 8899999999999999976422 22355666666554444433 3345566677999999999995 4689999999
Q ss_pred HhCCEEEEecChhhHHHHH
Q 014440 239 ETGGTYSVALDESHSKELI 257 (424)
Q Consensus 239 ~TGG~Y~~~~d~~~L~~lL 257 (424)
.++|.|+.+.+...+.+++
T Consensus 152 ~~~g~~~~~~~~~~~~~~~ 170 (170)
T cd01465 152 AGNGNTAYIDNLAEARKVF 170 (170)
T ss_pred cCCceEEEeCCHHHHHhhC
Confidence 9999999999998888763
No 22
>cd01461 vWA_interalpha_trypsin_inhibitor vWA_interalpha trypsin inhibitor (ITI): ITI is a glycoprotein composed of three polypeptides- two heavy chains and one light chain (bikunin). Bikunin confers the protease-inhibitor function while the heavy chains are involved in rendering stability to the extracellular matrix by binding to hyaluronic acid. The heavy chains carry the VWA domain with a conserved MIDAS motif. Although the exact role of the VWA domains remains unknown, it has been speculated to be involved in mediating protein-protein interactions with the components of the extracellular matrix.
Probab=99.74 E-value=1e-16 Score=144.20 Aligned_cols=161 Identities=14% Similarity=0.282 Sum_probs=118.3
Q ss_pred cceEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCC--CCHHH---HHHHHh
Q 014440 85 IRYLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLG--GSPES---HIKALM 159 (424)
Q Consensus 85 iR~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT--~d~~~---~~~~L~ 159 (424)
-|+++|+||.|+||.. .+++.++..+..|+..+ ++.++++||+|. +.+..+.|.+ .+... .++.|.
T Consensus 2 ~~~v~~vlD~S~SM~~-----~~~~~~~~al~~~l~~l---~~~~~~~l~~Fs-~~~~~~~~~~~~~~~~~~~~~~~~l~ 72 (171)
T cd01461 2 PKEVVFVIDTSGSMSG-----TKIEQTKEALLTALKDL---PPGDYFNIIGFS-DTVEEFSPSSVSATAENVAAAIEYVN 72 (171)
T ss_pred CceEEEEEECCCCCCC-----hhHHHHHHHHHHHHHhC---CCCCEEEEEEeC-CCceeecCcceeCCHHHHHHHHHHHH
Confidence 3689999999999963 57999999999998764 345789999994 6677766543 23222 223333
Q ss_pred hhhCCCCcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecc--hHHHHHHHH
Q 014440 160 GKLGCSGDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSA--EMFICKHLC 237 (424)
Q Consensus 160 ~~~~~~G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~--e~~iLq~iA 237 (424)
. +.+.|+|++..||..|...+...+ ...+.||+|+++. ..++..+.+.++.+.+.+|+|++||+|. +...|+++|
T Consensus 73 ~-~~~~g~T~l~~al~~a~~~l~~~~-~~~~~iillTDG~-~~~~~~~~~~~~~~~~~~i~i~~i~~g~~~~~~~l~~ia 149 (171)
T cd01461 73 R-LQALGGTNMNDALEAALELLNSSP-GSVPQIILLTDGE-VTNESQILKNVREALSGRIRLFTFGIGSDVNTYLLERLA 149 (171)
T ss_pred h-cCCCCCcCHHHHHHHHHHhhccCC-CCccEEEEEeCCC-CCCHHHHHHHHHHhcCCCceEEEEEeCCccCHHHHHHHH
Confidence 2 356889999999999999997632 2334455555543 3333345566666666799999999995 578999999
Q ss_pred HHhCCEEEEecChhhHHHHH
Q 014440 238 QETGGTYSVALDESHSKELI 257 (424)
Q Consensus 238 ~~TGG~Y~~~~d~~~L~~lL 257 (424)
+.|||.|+.+.+.+.+.+-+
T Consensus 150 ~~~gG~~~~~~~~~~~~~~~ 169 (171)
T cd01461 150 REGRGIARRIYETDDIESQL 169 (171)
T ss_pred HcCCCeEEEecChHHHHHHh
Confidence 99999999999988877654
No 23
>cd01472 vWA_collagen von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form heterodimers while in vWF it forms homodimers and multimers. There are different interaction surfaces of this domain as seen by its complexes with collagen with either integrin or human vWFA. In integrins collagen binding occurs via the metal ion-dependent adhesion site (MIDAS) and involves three surface loops located on the upper surface of the molecule. In human vWFA, collagen binding is thought to occur on the bottom of the molecule and does not involve the vestigial MIDAS motif.
Probab=99.73 E-value=1.7e-16 Score=143.28 Aligned_cols=154 Identities=17% Similarity=0.156 Sum_probs=122.7
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCC--CCHHHHHHHHhhhhCC
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLG--GSPESHIKALMGKLGC 164 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT--~d~~~~~~~L~~~~~~ 164 (424)
++|++||.|+||.. .+++.+++.+..+++.+...+...++|||.| ++.+..+.|++ .|.+.+.+.|..+...
T Consensus 2 Dvv~vlD~SgSm~~-----~~~~~~k~~~~~~~~~l~~~~~~~~~giv~F-s~~~~~~~~~~~~~~~~~~~~~l~~l~~~ 75 (164)
T cd01472 2 DIVFLVDGSESIGL-----SNFNLVKDFVKRVVERLDIGPDGVRVGVVQY-SDDPRTEFYLNTYRSKDDVLEAVKNLRYI 75 (164)
T ss_pred CEEEEEeCCCCCCH-----HHHHHHHHHHHHHHhhcccCCCCeEEEEEEE-cCceeEEEecCCCCCHHHHHHHHHhCcCC
Confidence 79999999999975 5889999999999988765556679999999 58899999999 7888888888765333
Q ss_pred CCcchHHHHHHHHHHHHcCC---CCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecc-hHHHHHHHHHHh
Q 014440 165 SGDSSIQNALDLVHGLLNQI---PSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSA-EMFICKHLCQET 240 (424)
Q Consensus 165 ~G~tsL~~AL~~Al~~L~~~---p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~-e~~iLq~iA~~T 240 (424)
.|+|+++.||..|.+.|... +....++++|+++++.+. .+....+..+++.||+|++||+|. +...|++||..+
T Consensus 76 ~g~T~~~~al~~a~~~l~~~~~~~~~~~~~~iiliTDG~~~--~~~~~~~~~l~~~gv~i~~ig~g~~~~~~L~~ia~~~ 153 (164)
T cd01472 76 GGGTNTGKALKYVRENLFTEASGSREGVPKVLVVITDGKSQ--DDVEEPAVELKQAGIEVFAVGVKNADEEELKQIASDP 153 (164)
T ss_pred CCCchHHHHHHHHHHHhCCcccCCCCCCCEEEEEEcCCCCC--chHHHHHHHHHHCCCEEEEEECCcCCHHHHHHHHCCC
Confidence 67899999999999999863 223445565665544332 234556778889999999999997 789999999999
Q ss_pred CCEEEEec
Q 014440 241 GGTYSVAL 248 (424)
Q Consensus 241 GG~Y~~~~ 248 (424)
+|.|....
T Consensus 154 ~~~~~~~~ 161 (164)
T cd01472 154 KELYVFNV 161 (164)
T ss_pred chheEEec
Confidence 99998654
No 24
>cd01470 vWA_complement_factors Complement factors B and C2 are two critical proteases for complement activation. They both contain three CCP or Sushi domains, a trypsin-type serine protease domain and a single VWA domain with a conserved metal ion dependent adhesion site referred commonly as the MIDAS motif. Orthologues of these molecules are found from echinoderms to chordates. During complement activation, the CCP domains are cleaved off, resulting in the formation of an active protease that cleaves and activates complement C3. Complement C2 is in the classical pathway and complement B is in the alternative pathway. The interaction of C2 with C4 and of factor B with C3b are both dependent on Mg2+ binding sites within the VWA domains and the VWA domain of factor B has been shown to mediate the binding of C3. This is consistent with the common inferred function of VWA domains as magnesium-dependent protein interaction domains.
Probab=99.72 E-value=2.5e-16 Score=146.88 Aligned_cols=165 Identities=15% Similarity=0.184 Sum_probs=119.3
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCC----CHHHHHHHHhhhh
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGG----SPESHIKALMGKL 162 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~----d~~~~~~~L~~~~ 162 (424)
+++|+||.|+||. ++||..++..+..|++.+....+..++|||+| ++.+..+.|++. +...++..|..+.
T Consensus 2 di~~vlD~SgSM~-----~~~~~~~k~~~~~l~~~l~~~~~~~~v~li~F-s~~~~~~~~~~~~~~~~~~~~~~~l~~~~ 75 (198)
T cd01470 2 NIYIALDASDSIG-----EEDFDEAKNAIKTLIEKISSYEVSPRYEIISY-ASDPKEIVSIRDFNSNDADDVIKRLEDFN 75 (198)
T ss_pred cEEEEEECCCCcc-----HHHHHHHHHHHHHHHHHccccCCCceEEEEEe-cCCceEEEecccCCCCCHHHHHHHHHhCC
Confidence 6899999999995 46999999999999988754456789999999 488888888763 4566767776542
Q ss_pred ----CCCCcchHHHHHHHHHHHHcCC---CC---CCCcEEEEE-EcCCCCC--CccCHHHHHHHH----------HhCCc
Q 014440 163 ----GCSGDSSIQNALDLVHGLLNQI---PS---YGHREVLIL-YSALSTC--DPGDIMETIQKC----------KESKI 219 (424)
Q Consensus 163 ----~~~G~tsL~~AL~~Al~~L~~~---p~---~~~reILvI-~ss~~t~--dp~~i~~~i~~a----------kk~~I 219 (424)
...|+|.+..||.++.+.+... +. ...+++||| +++..+. +|....+.++.+ ++.+|
T Consensus 76 ~~~~~~~ggT~~~~Al~~~~~~l~~~~~~~~~~~~~~~~~iillTDG~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~v 155 (198)
T cd01470 76 YDDHGDKTGTNTAAALKKVYERMALEKVRNKEAFNETRHVIILFTDGKSNMGGSPLPTVDKIKNLVYKNNKSDNPREDYL 155 (198)
T ss_pred cccccCccchhHHHHHHHHHHHHHHHHhcCccchhhcceEEEEEcCCCcCCCCChhHHHHHHHHHHhcccccccchhcce
Confidence 1347899999999999887321 11 112445554 5443332 222222233333 45589
Q ss_pred EEEEEEecc--hHHHHHHHHHHhCC--EEEEecChhhHHHHH
Q 014440 220 RCSVIGLSA--EMFICKHLCQETGG--TYSVALDESHSKELI 257 (424)
Q Consensus 220 rV~vIgLg~--e~~iLq~iA~~TGG--~Y~~~~d~~~L~~lL 257 (424)
.|++||+|. +...|++||..||| .||.+.+.+.|++++
T Consensus 156 ~i~~iGvG~~~~~~~L~~iA~~~~g~~~~f~~~~~~~l~~v~ 197 (198)
T cd01470 156 DVYVFGVGDDVNKEELNDLASKKDNERHFFKLKDYEDLQEVF 197 (198)
T ss_pred eEEEEecCcccCHHHHHHHhcCCCCCceEEEeCCHHHHHHhc
Confidence 999999996 47899999999999 467888888888875
No 25
>cd01480 vWA_collagen_alpha_1-VI-type VWA_collagen alpha(VI) type: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.
Probab=99.71 E-value=2.4e-16 Score=145.94 Aligned_cols=166 Identities=12% Similarity=0.096 Sum_probs=126.7
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhcc------CCCCcEEEEEecCCceEEeeCCC---CCHHHHHHH
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQ------NPLSQIGLVTVKDGVANCLTDLG---GSPESHIKA 157 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~q------nP~sqlGII~~~~g~A~~lspLT---~d~~~~~~~ 157 (424)
+|+|+||.|+||.. ++++.+++.++.|++.+..+ +...++|||.| ++.+.+..|++ .+...+.++
T Consensus 4 dvv~vlD~S~Sm~~-----~~~~~~k~~~~~~~~~l~~~~~~~i~~~~~rvglv~f-s~~~~~~~~l~~~~~~~~~l~~~ 77 (186)
T cd01480 4 DITFVLDSSESVGL-----QNFDITKNFVKRVAERFLKDYYRKDPAGSWRVGVVQY-SDQQEVEAGFLRDIRNYTSLKEA 77 (186)
T ss_pred eEEEEEeCCCccch-----hhHHHHHHHHHHHHHHHhhhhccCCCCCceEEEEEEe-cCCceeeEecccccCCHHHHHHH
Confidence 79999999999975 47888888888888888542 44589999999 48899999998 567777778
Q ss_pred HhhhhCCCCcchHHHHHHHHHHHHcCCCCCCCcEEEEEE-cCCCC-CCccCHHHHHHHHHhCCcEEEEEEecc-hHHHHH
Q 014440 158 LMGKLGCSGDSSIQNALDLVHGLLNQIPSYGHREVLILY-SALST-CDPGDIMETIQKCKESKIRCSVIGLSA-EMFICK 234 (424)
Q Consensus 158 L~~~~~~~G~tsL~~AL~~Al~~L~~~p~~~~reILvI~-ss~~t-~dp~~i~~~i~~akk~~IrV~vIgLg~-e~~iLq 234 (424)
|.++.-..|+|.++.||..|...+...+....+++|||+ ++..+ .+..++.++++.+++.||.|++||+|. +...|+
T Consensus 78 i~~l~~~gg~T~~~~AL~~a~~~l~~~~~~~~~~~iillTDG~~~~~~~~~~~~~~~~~~~~gi~i~~vgig~~~~~~L~ 157 (186)
T cd01480 78 VDNLEYIGGGTFTDCALKYATEQLLEGSHQKENKFLLVITDGHSDGSPDGGIEKAVNEADHLGIKIFFVAVGSQNEEPLS 157 (186)
T ss_pred HHhCccCCCCccHHHHHHHHHHHHhccCCCCCceEEEEEeCCCcCCCcchhHHHHHHHHHHCCCEEEEEecCccchHHHH
Confidence 876533578899999999999999863223344455555 44322 122356788999999999999999996 457899
Q ss_pred HHHHHhCCEEEEecChhhHHHHHHhcCC
Q 014440 235 HLCQETGGTYSVALDESHSKELILEHAP 262 (424)
Q Consensus 235 ~iA~~TGG~Y~~~~d~~~L~~lL~~~~~ 262 (424)
+||...+|.|+.. .+.+++++++.
T Consensus 158 ~IA~~~~~~~~~~----~~~~l~~~~~~ 181 (186)
T cd01480 158 RIACDGKSALYRE----NFAELLWSFFI 181 (186)
T ss_pred HHHcCCcchhhhc----chhhhcccccc
Confidence 9999999987765 36666666654
No 26
>cd01463 vWA_VGCC_like VWA Voltage gated Calcium channel like: Voltage-gated calcium channels are a complex of five proteins: alpha 1, beta 1, gamma, alpha 2 and delta. The alpha 2 and delta subunits result from proteolytic processing of a single gene product and carries at its N-terminus the VWA and cache domains, The alpha 2 delta gene family has orthologues in D. melanogaster and C. elegans but none have been detected in aither A. thaliana or yeast. The exact biochemical function of the VWA domain is not known but the alpha 2 delta complex has been shown to regulate various functional properties of the channel complex.
Probab=99.70 E-value=2.8e-16 Score=145.81 Aligned_cols=151 Identities=16% Similarity=0.192 Sum_probs=110.8
Q ss_pred ceEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCC---------CHHHHHH
Q 014440 86 RYLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGG---------SPESHIK 156 (424)
Q Consensus 86 R~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~---------d~~~~~~ 156 (424)
++++|+||.|+||.. +||+.++..+..|++.+ ++.+++|||+| ++.+..+.|++. +.+.+..
T Consensus 14 ~~vv~llD~SgSM~~-----~~l~~ak~~~~~ll~~l---~~~d~v~lv~F-~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 84 (190)
T cd01463 14 KDIVILLDVSGSMTG-----QRLHLAKQTVSSILDTL---SDNDFFNIITF-SNEVNPVVPCFNDTLVQATTSNKKVLKE 84 (190)
T ss_pred ceEEEEEECCCCCCc-----HHHHHHHHHHHHHHHhC---CCCCEEEEEEe-CCCeeEEeeecccceEecCHHHHHHHHH
Confidence 499999999999974 69999999999998864 56689999999 588888887653 2344445
Q ss_pred HHhhhhCCCCcchHHHHHHHHHHHHcC---C--C---CCCCcEEEEEEcCCCCCCccCHHHHHHHHHh-C----CcEEEE
Q 014440 157 ALMGKLGCSGDSSIQNALDLVHGLLNQ---I--P---SYGHREVLILYSALSTCDPGDIMETIQKCKE-S----KIRCSV 223 (424)
Q Consensus 157 ~L~~~~~~~G~tsL~~AL~~Al~~L~~---~--p---~~~~reILvI~ss~~t~dp~~i~~~i~~akk-~----~IrV~v 223 (424)
.|.. +.+.|+|.+..||..|++.|.. . + +...+.||||+++..+ + ..+.+..+++ . +|+|++
T Consensus 85 ~l~~-l~~~G~T~~~~al~~a~~~l~~~~~~~~~~~~~~~~~~iillTDG~~~-~---~~~~~~~~~~~~~~~~~v~i~t 159 (190)
T cd01463 85 ALDM-LEAKGIANYTKALEFAFSLLLKNLQSNHSGSRSQCNQAIMLITDGVPE-N---YKEIFDKYNWDKNSEIPVRVFT 159 (190)
T ss_pred HHhh-CCCCCcchHHHHHHHHHHHHHHhhhcccccccCCceeEEEEEeCCCCC-c---HhHHHHHhcccccCCCcEEEEE
Confidence 5543 3567889999999999999975 1 1 1222345555555332 2 2334444322 2 599999
Q ss_pred EEecch---HHHHHHHHHHhCCEEEEecCh
Q 014440 224 IGLSAE---MFICKHLCQETGGTYSVALDE 250 (424)
Q Consensus 224 IgLg~e---~~iLq~iA~~TGG~Y~~~~d~ 250 (424)
||+|.+ ...|++||..+||.|+.+.|.
T Consensus 160 igiG~~~~d~~~L~~lA~~~~G~~~~i~~~ 189 (190)
T cd01463 160 YLIGREVTDRREIQWMACENKGYYSHIQSL 189 (190)
T ss_pred EecCCccccchHHHHHHhhcCCeEEEcccC
Confidence 999965 579999999999999988663
No 27
>cd01474 vWA_ATR ATR (Anthrax Toxin Receptor): Anthrax toxin is a key virulence factor for Bacillus anthracis, the causative agent of anthrax. ATR is the cellular receptor for the anthrax protective antigen and facilitates entry of the toxin into cells. The VWA domain in ATR contains the toxin binding site and mediates interaction with protective antigen. The binding is mediated by divalent cations that binds to the MIDAS motif. These proteins are a family of vertebrate ECM receptors expressed by endothelial cells.
Probab=99.70 E-value=1.2e-15 Score=140.98 Aligned_cols=166 Identities=15% Similarity=0.089 Sum_probs=120.2
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCHHHHHHHHhhh--hCC
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSPESHIKALMGK--LGC 164 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~~--~~~ 164 (424)
+++|+||.|+||.... +. .++.++.+++.|. +|..|+|||.| ++.+..+.||+.+.....+.|..+ +.+
T Consensus 6 Dvv~llD~SgSm~~~~--~~----~~~~~~~l~~~~~--~~~~rvglv~F-s~~~~~~~~l~~~~~~~~~~l~~l~~~~~ 76 (185)
T cd01474 6 DLYFVLDKSGSVAANW--IE----IYDFVEQLVDRFN--SPGLRFSFITF-STRATKILPLTDDSSAIIKGLEVLKKVTP 76 (185)
T ss_pred eEEEEEeCcCchhhhH--HH----HHHHHHHHHHHcC--CCCcEEEEEEe-cCCceEEEeccccHHHHHHHHHHHhccCC
Confidence 8999999999997532 22 3355666665553 46799999999 588999999998876665555322 246
Q ss_pred CCcchHHHHHHHHHHHHcCC--CCC-CCcEEEEEEcCCCC-CCccCHHHHHHHHHhCCcEEEEEEecc-hHHHHHHHHHH
Q 014440 165 SGDSSIQNALDLVHGLLNQI--PSY-GHREVLILYSALST-CDPGDIMETIQKCKESKIRCSVIGLSA-EMFICKHLCQE 239 (424)
Q Consensus 165 ~G~tsL~~AL~~Al~~L~~~--p~~-~~reILvI~ss~~t-~dp~~i~~~i~~akk~~IrV~vIgLg~-e~~iLq~iA~~ 239 (424)
.|+|.++.||+.|.+.|... .+. ..+.||+|+++..+ .+..+....++.+++.||.|++||++. +...|++||..
T Consensus 77 ~g~T~~~~aL~~a~~~l~~~~~~~r~~~~~villTDG~~~~~~~~~~~~~a~~l~~~gv~i~~vgv~~~~~~~L~~iA~~ 156 (185)
T cd01474 77 SGQTYIHEGLENANEQIFNRNGGGRETVSVIIALTDGQLLLNGHKYPEHEAKLSRKLGAIVYCVGVTDFLKSQLINIADS 156 (185)
T ss_pred CCCCcHHHHHHHHHHHHHhhccCCCCCCeEEEEEcCCCcCCCCCcchHHHHHHHHHcCCEEEEEeechhhHHHHHHHhCC
Confidence 78999999999999988532 111 12334444444332 223355677889999999999999963 45789999999
Q ss_pred hCCEEEEecChhhHHHHHHhcC
Q 014440 240 TGGTYSVALDESHSKELILEHA 261 (424)
Q Consensus 240 TGG~Y~~~~d~~~L~~lL~~~~ 261 (424)
+++.|.+..+-+.|+.++..+.
T Consensus 157 ~~~~f~~~~~~~~l~~~~~~~~ 178 (185)
T cd01474 157 KEYVFPVTSGFQALSGIIESVV 178 (185)
T ss_pred CCeeEecCccHHHHHHHHHHHH
Confidence 9877777788889988887765
No 28
>smart00327 VWA von Willebrand factor (vWF) type A domain. VWA domains in extracellular eukaryotic proteins mediate adhesion via metal ion-dependent adhesion sites (MIDAS). Intracellular VWA domains and homologues in prokaryotes have recently been identified. The proposed VWA domains in integrin beta subunits have recently been substantiated using sequence-based methods.
Probab=99.70 E-value=1.9e-15 Score=134.98 Aligned_cols=155 Identities=24% Similarity=0.285 Sum_probs=128.2
Q ss_pred ceEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCC--CCCHHHHHHHHhhhhC
Q 014440 86 RYLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDL--GGSPESHIKALMGKLG 163 (424)
Q Consensus 86 R~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspL--T~d~~~~~~~L~~~~~ 163 (424)
.+++|+||.|+||. ++++..++..+..|+..+..+++..++||+.|. +......|+ +.+...+...+..+..
T Consensus 2 ~~v~l~vD~S~SM~-----~~~~~~~~~~~~~~~~~~~~~~~~~~i~ii~f~-~~~~~~~~~~~~~~~~~~~~~i~~~~~ 75 (177)
T smart00327 2 LDVVFLLDGSGSMG-----PNRFEKAKEFVLKLVEQLDIGPDGDRVGLVTFS-DDATVLFPLNDSRSKDALLEALASLSY 75 (177)
T ss_pred ccEEEEEeCCCccc-----hHHHHHHHHHHHHHHHhcCCCCCCcEEEEEEeC-CCceEEEcccccCCHHHHHHHHHhcCC
Confidence 47999999999996 579999999999999999988889999999995 677788888 6677777777776432
Q ss_pred -CCCcchHHHHHHHHHHHHcCCC---CCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecc--hHHHHHHHH
Q 014440 164 -CSGDSSIQNALDLVHGLLNQIP---SYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSA--EMFICKHLC 237 (424)
Q Consensus 164 -~~G~tsL~~AL~~Al~~L~~~p---~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~--e~~iLq~iA 237 (424)
..|.+++..||..|...+.... ....+++|||+++....++.++.+.++.+++.+|.|++|++|. ....|++++
T Consensus 76 ~~~~~~~~~~al~~~~~~~~~~~~~~~~~~~~~iviitDg~~~~~~~~~~~~~~~~~~~i~i~~i~~~~~~~~~~l~~~~ 155 (177)
T smart00327 76 KLGGGTNLGAALQYALENLFSKSAGSRRGAPKVLILITDGESNDGGDLLKAAKELKRSGVKVFVVGVGNDVDEEELKKLA 155 (177)
T ss_pred CCCCCchHHHHHHHHHHHhcCcCCCCCCCCCeEEEEEcCCCCCCCccHHHHHHHHHHCCCEEEEEEccCccCHHHHHHHh
Confidence 5788999999999999986321 1222567777766555454578899999999999999999998 689999999
Q ss_pred HHhCCEEEE
Q 014440 238 QETGGTYSV 246 (424)
Q Consensus 238 ~~TGG~Y~~ 246 (424)
..++|.|..
T Consensus 156 ~~~~~~~~~ 164 (177)
T smart00327 156 SAPGGVYVF 164 (177)
T ss_pred CCCcceEEe
Confidence 999999987
No 29
>KOG2884 consensus 26S proteasome regulatory complex, subunit RPN10/PSMD4 [Posttranslational modification, protein turnover, chaperones]
Probab=99.69 E-value=1.1e-15 Score=142.83 Aligned_cols=156 Identities=14% Similarity=0.248 Sum_probs=137.7
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCHHHHHHHHhhhhCCCC
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSPESHIKALMGKLGCSG 166 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~~~~~~G 166 (424)
.+||+||.|..|+..||.|+||.+.++++.-.+..-+..||.|.+|||++.+....+++.+|.+.-.++..|... .+.|
T Consensus 5 atmi~iDNse~mrNgDy~PtRf~aQ~daVn~v~~~K~~snpEntvGiitla~a~~~vLsT~T~d~gkils~lh~i-~~~g 83 (259)
T KOG2884|consen 5 ATMICIDNSEYMRNGDYLPTRFQAQKDAVNLVCQAKLRSNPENTVGIITLANASVQVLSTLTSDRGKILSKLHGI-QPHG 83 (259)
T ss_pred eEEEEEeChHHhhcCCCChHHHHHHHHHHHHHHHhhhcCCcccceeeEeccCCCceeeeeccccchHHHHHhcCC-CcCC
Confidence 579999999999999999999999999999999999999999999999998779999999999988888877653 7889
Q ss_pred cchHHHHHHHHHHHHcCCCCCCCc-EEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecch---HHHHHHHHHHhCC
Q 014440 167 DSSIQNALDLVHGLLNQIPSYGHR-EVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAE---MFICKHLCQETGG 242 (424)
Q Consensus 167 ~tsL~~AL~~Al~~L~~~p~~~~r-eILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e---~~iLq~iA~~TGG 242 (424)
+..+..+|..|.-.|++..+...| +||++++|.-..+..++...++.+||++|-|++|.+|.. ...|.+.-+.++|
T Consensus 84 ~~~~~~~i~iA~lalkhRqnk~~~~riVvFvGSpi~e~ekeLv~~akrlkk~~Vaidii~FGE~~~~~e~l~~fida~N~ 163 (259)
T KOG2884|consen 84 KANFMTGIQIAQLALKHRQNKNQKQRIVVFVGSPIEESEKELVKLAKRLKKNKVAIDIINFGEAENNTEKLFEFIDALNG 163 (259)
T ss_pred cccHHHHHHHHHHHHHhhcCCCcceEEEEEecCcchhhHHHHHHHHHHHHhcCeeEEEEEeccccccHHHHHHHHHHhcC
Confidence 999999999999999998665544 688888887655566788899999999999999999953 3678888888887
Q ss_pred E
Q 014440 243 T 243 (424)
Q Consensus 243 ~ 243 (424)
.
T Consensus 164 ~ 164 (259)
T KOG2884|consen 164 K 164 (259)
T ss_pred C
Confidence 5
No 30
>cd01477 vWA_F09G8-8_type VWA F09G8.8 type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of mo
Probab=99.68 E-value=2.3e-15 Score=141.17 Aligned_cols=157 Identities=16% Similarity=0.204 Sum_probs=115.8
Q ss_pred ccccceEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhcc--CC----CCcEEEEEecCCceEEeeCCCC--CHHH
Q 014440 82 KGLIRYLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQ--NP----LSQIGLVTVKDGVANCLTDLGG--SPES 153 (424)
Q Consensus 82 ~GiiR~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~q--nP----~sqlGII~~~~g~A~~lspLT~--d~~~ 153 (424)
.|+ +||++||.|.||. ++||+.+++.+..|+..+..- +| ..|+|||+| ++.+++..||+. +..+
T Consensus 18 ~~~--DivfvlD~S~Sm~-----~~~f~~~k~fi~~~~~~~~~~~~~~~~~~~~rVGlV~f-s~~a~~~~~L~d~~~~~~ 89 (193)
T cd01477 18 LWL--DIVFVVDNSKGMT-----QGGLWQVRATISSLFGSSSQIGTDYDDPRSTRVGLVTY-NSNATVVADLNDLQSFDD 89 (193)
T ss_pred cee--eEEEEEeCCCCcc-----hhhHHHHHHHHHHHHhhccccccccCCCCCcEEEEEEc-cCceEEEEecccccCHHH
Confidence 466 9999999999996 568999888888877765431 22 369999999 699999999984 4466
Q ss_pred HHHHHhhhh---CCCCcchHHHHHHHHHHHHcCC---CCCCCcEEEEEE-cCCCCCCccCHHHHHHHHHhCCcEEEEEEe
Q 014440 154 HIKALMGKL---GCSGDSSIQNALDLVHGLLNQI---PSYGHREVLILY-SALSTCDPGDIMETIQKCKESKIRCSVIGL 226 (424)
Q Consensus 154 ~~~~L~~~~---~~~G~tsL~~AL~~Al~~L~~~---p~~~~reILvI~-ss~~t~dp~~i~~~i~~akk~~IrV~vIgL 226 (424)
+..+|...+ ...|+|.++.||.+|.+.|... ......+||||+ ++..+....+....++.|++.||+|++||+
T Consensus 90 ~~~ai~~~~~~~~~~ggT~ig~aL~~A~~~l~~~~~~~R~~v~kvvIllTDg~~~~~~~~~~~~a~~l~~~GI~i~tVGi 169 (193)
T cd01477 90 LYSQIQGSLTDVSSTNASYLDTGLQAAEQMLAAGKRTSRENYKKVVIVFASDYNDEGSNDPRPIAARLKSTGIAIITVAF 169 (193)
T ss_pred HHHHHHHHhhccccCCcchHHHHHHHHHHHHHhhhccccCCCCeEEEEEecCccCCCCCCHHHHHHHHHHCCCEEEEEEe
Confidence 667777532 2457899999999999999742 112234555555 432221224567789999999999999999
Q ss_pred cch--HHHHHHHHHHhCCEEEE
Q 014440 227 SAE--MFICKHLCQETGGTYSV 246 (424)
Q Consensus 227 g~e--~~iLq~iA~~TGG~Y~~ 246 (424)
|.. ...+++|+++..+.|+.
T Consensus 170 G~~~d~~~~~~L~~ias~~~~~ 191 (193)
T cd01477 170 TQDESSNLLDKLGKIASPGMNF 191 (193)
T ss_pred CCCCCHHHHHHHHHhcCCCCCC
Confidence 974 46789999988776653
No 31
>cd01469 vWA_integrins_alpha_subunit Integrins are a class of adhesion receptors that link the extracellular matrix to the cytoskeleton and cooperate with growth factor receptors to promote celll survival, cell cycle progression and cell migration. Integrins consist of an alpha and a beta sub-unit. Each sub-unit has a large extracellular portion, a single transmembrane segment and a short cytoplasmic domain. The N-terminal domains of the alpha and beta subunits associate to form the integrin headpiece, which contains the ligand binding site, whereas the C-terminal segments traverse the plasma membrane and mediate interaction with the cytoskeleton and with signalling proteins.The VWA domains present in the alpha subunits of integrins seem to be a chordate specific radiation of the gene family being found only in vertebrates. They mediate protein-protein interactions.
Probab=99.67 E-value=3.2e-15 Score=137.55 Aligned_cols=162 Identities=15% Similarity=0.090 Sum_probs=123.8
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCC--CHHHHHHHHhhhhCC
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGG--SPESHIKALMGKLGC 164 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~--d~~~~~~~L~~~~~~ 164 (424)
+|+++||.|+||. |.+++.+++.++.|++.+....+..|+|||.| ++.+.+..||+. +..++.+++......
T Consensus 2 Di~fvlD~S~S~~-----~~~f~~~k~fi~~~i~~l~~~~~~~rvgvv~f-s~~~~~~~~l~~~~~~~~~~~~i~~~~~~ 75 (177)
T cd01469 2 DIVFVLDGSGSIY-----PDDFQKVKNFLSTVMKKLDIGPTKTQFGLVQY-SESFRTEFTLNEYRTKEEPLSLVKHISQL 75 (177)
T ss_pred cEEEEEeCCCCCC-----HHHHHHHHHHHHHHHHHcCcCCCCcEEEEEEE-CCceeEEEecCccCCHHHHHHHHHhCccC
Confidence 7999999999996 57899999999999998877667899999999 488999999983 345566666654345
Q ss_pred CCcchHHHHHHHHHHHHcCCC---CCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecch------HHHHHH
Q 014440 165 SGDSSIQNALDLVHGLLNQIP---SYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAE------MFICKH 235 (424)
Q Consensus 165 ~G~tsL~~AL~~Al~~L~~~p---~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e------~~iLq~ 235 (424)
.|.|.++.||+.|.+.+.... ....++|+||++++.+.++....++++.+++.||.|++||+|.. ...|+.
T Consensus 76 ~g~T~~~~AL~~a~~~l~~~~~g~R~~~~kv~illTDG~~~~~~~~~~~~~~~k~~gv~v~~Vgvg~~~~~~~~~~~L~~ 155 (177)
T cd01469 76 LGLTNTATAIQYVVTELFSESNGARKDATKVLVVITDGESHDDPLLKDVIPQAEREGIIRYAIGVGGHFQRENSREELKT 155 (177)
T ss_pred CCCccHHHHHHHHHHHhcCcccCCCCCCCeEEEEEeCCCCCCccccHHHHHHHHHCCcEEEEEEecccccccccHHHHHH
Confidence 677999999999999884321 12345566666554444444446778899999999999999974 488999
Q ss_pred HHHHhCCEEE-EecChhhHH
Q 014440 236 LCQETGGTYS-VALDESHSK 254 (424)
Q Consensus 236 iA~~TGG~Y~-~~~d~~~L~ 254 (424)
||..+++.|+ ...|.+.|+
T Consensus 156 ias~p~~~h~f~~~~~~~l~ 175 (177)
T cd01469 156 IASKPPEEHFFNVTDFAALK 175 (177)
T ss_pred HhcCCcHHhEEEecCHHHhc
Confidence 9999987555 456655554
No 32
>cd01450 vWFA_subfamily_ECM Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A
Probab=99.67 E-value=3e-15 Score=132.25 Aligned_cols=152 Identities=17% Similarity=0.160 Sum_probs=122.6
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCC--HHHHHHHHhhhhCC
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGS--PESHIKALMGKLGC 164 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d--~~~~~~~L~~~~~~ 164 (424)
+|+|+||.|+||.. .++..++..+..|+..+...++..++|||+|. +.+....+++.+ ...+.+.|..+...
T Consensus 2 di~~llD~S~Sm~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~li~f~-~~~~~~~~~~~~~~~~~~~~~i~~~~~~ 75 (161)
T cd01450 2 DIVFLLDGSESVGP-----ENFEKVKDFIEKLVEKLDIGPDKTRVGLVQYS-DDVRVEFSLNDYKSKDDLLKAVKNLKYL 75 (161)
T ss_pred cEEEEEeCCCCcCH-----HHHHHHHHHHHHHHHheeeCCCceEEEEEEEc-CCceEEEECCCCCCHHHHHHHHHhcccC
Confidence 78999999999974 38899999999999998877788999999995 678888998876 67777777654333
Q ss_pred C-CcchHHHHHHHHHHHHcCCC--CCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecc-hHHHHHHHHHHh
Q 014440 165 S-GDSSIQNALDLVHGLLNQIP--SYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSA-EMFICKHLCQET 240 (424)
Q Consensus 165 ~-G~tsL~~AL~~Al~~L~~~p--~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~-e~~iLq~iA~~T 240 (424)
. |+|++..||..|...+.... ....+.+||+++++...++.++.++++.+++.+|+|++||+|. ....|+++|..|
T Consensus 76 ~~~~t~~~~al~~a~~~~~~~~~~~~~~~~~iiliTDG~~~~~~~~~~~~~~~~~~~v~v~~i~~g~~~~~~l~~la~~~ 155 (161)
T cd01450 76 GGGGTNTGKALQYALEQLFSESNARENVPKVIIVLTDGRSDDGGDPKEAAAKLKDEGIKVFVVGVGPADEEELREIASCP 155 (161)
T ss_pred CCCCccHHHHHHHHHHHhcccccccCCCCeEEEEECCCCCCCCcchHHHHHHHHHCCCEEEEEeccccCHHHHHHHhCCC
Confidence 4 38999999999999998763 1345566666655444344468899999999999999999997 789999999999
Q ss_pred CCEE
Q 014440 241 GGTY 244 (424)
Q Consensus 241 GG~Y 244 (424)
|+.|
T Consensus 156 ~~~~ 159 (161)
T cd01450 156 SERH 159 (161)
T ss_pred CCCc
Confidence 5544
No 33
>cd01460 vWA_midasin VWA_Midasin: Midasin is a member of the AAA ATPase family. The proteins of this family are unified by their common archetectural organization that is based upon a conserved ATPase domain. The AAA domain of midasin contains six tandem AAA protomers. The AAA domains in midasin is followed by a D/E rich domain that is following by a VWA domain. The members of this subgroup have a conserved MIDAS motif. The function of this domain is not exactly known although it has been speculated to play a crucial role in midasin function.
Probab=99.64 E-value=3.2e-15 Score=146.55 Aligned_cols=145 Identities=14% Similarity=0.119 Sum_probs=112.6
Q ss_pred chhhhhccccceEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCHHHHH
Q 014440 76 ATARIQKGLIRYLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSPESHI 155 (424)
Q Consensus 76 ~~~~~r~GiiR~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~~~~~ 155 (424)
.+.+.+|+. +++|+||.|.||.+.|..|+||+ ++..+.+|+. +.+.+++||++| ++.+.++.|+|.+... .
T Consensus 53 Rtkpskr~~--qIvlaID~S~SM~~~~~~~~ale-ak~lIs~al~----~Le~g~vgVv~F-g~~~~~v~Plt~d~~~-~ 123 (266)
T cd01460 53 RTKPAKRDY--QILIAIDDSKSMSENNSKKLALE-SLCLVSKALT----LLEVGQLGVCSF-GEDVQILHPFDEQFSS-Q 123 (266)
T ss_pred eccCCccCc--eEEEEEecchhcccccccccHHH-HHHHHHHHHH----hCcCCcEEEEEe-CCCceEeCCCCCCchh-h
Confidence 677889999 99999999999999999999998 7777776665 667799999999 4899999999998766 3
Q ss_pred HHHh---hhhCCCCcchHHHHHHHHHHHHcCC--CCCCC--cEEEEEEcCCCC-CCccCHHHHHHHHHhCCcEEEEEEec
Q 014440 156 KALM---GKLGCSGDSSIQNALDLVHGLLNQI--PSYGH--REVLILYSALST-CDPGDIMETIQKCKESKIRCSVIGLS 227 (424)
Q Consensus 156 ~~L~---~~~~~~G~tsL~~AL~~Al~~L~~~--p~~~~--reILvI~ss~~t-~dp~~i~~~i~~akk~~IrV~vIgLg 227 (424)
..+. ......++|++..+|.+|+..+... +.++. .+++||++++.. .+.+.....++.+++.||.|++|+|.
T Consensus 124 a~~~~l~~~~f~~~~Tni~~aL~~a~~~f~~~~~~~~s~~~~qlilLISDG~~~~~e~~~~~~~r~a~e~~i~l~~I~ld 203 (266)
T cd01460 124 SGPRILNQFTFQQDKTDIANLLKFTAQIFEDARTQSSSGSLWQLLLIISDGRGEFSEGAQKVRLREAREQNVFVVFIIID 203 (266)
T ss_pred HHHHHhCcccCCCCCCcHHHHHHHHHHHHHhhhccccccccccEEEEEECCCcccCccHHHHHHHHHHHcCCeEEEEEEc
Confidence 3333 2223567899999999999999865 22222 256666655442 23444446689999999999999998
Q ss_pred ch
Q 014440 228 AE 229 (424)
Q Consensus 228 ~e 229 (424)
+.
T Consensus 204 ~~ 205 (266)
T cd01460 204 NP 205 (266)
T ss_pred CC
Confidence 74
No 34
>cd01475 vWA_Matrilin VWA_Matrilin: In cartilaginous plate, extracellular matrix molecules mediate cell-matrix and matrix-matrix interactions thereby providing tissue integrity. Some members of the matrilin family are expressed specifically in developing cartilage rudiments. The matrilin family consists of at least four members. All the members of the matrilin family contain VWA domains, EGF-like domains and a heptad repeat coiled-coiled domain at the carboxy terminus which is responsible for the oligomerization of the matrilins. The VWA domains have been shown to be essential for matrilin network formation by interacting with matrix ligands.
Probab=99.63 E-value=1.9e-14 Score=137.23 Aligned_cols=169 Identities=17% Similarity=0.106 Sum_probs=129.8
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCC--CHHHHHHHHhhhhCC
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGG--SPESHIKALMGKLGC 164 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~--d~~~~~~~L~~~~~~ 164 (424)
+|+|+||.|+||. +++++.+++.++.|++.+.-.....++|||.| +..+.+..||+. +..++..+|..+.-.
T Consensus 4 DlvfllD~S~Sm~-----~~~~~~~k~f~~~l~~~l~~~~~~~rvglv~f-s~~~~~~~~l~~~~~~~~l~~~i~~i~~~ 77 (224)
T cd01475 4 DLVFLIDSSRSVR-----PENFELVKQFLNQIIDSLDVGPDATRVGLVQY-SSTVKQEFPLGRFKSKADLKRAVRRMEYL 77 (224)
T ss_pred cEEEEEeCCCCCC-----HHHHHHHHHHHHHHHHhcccCCCccEEEEEEe-cCceeEEecccccCCHHHHHHHHHhCcCC
Confidence 8999999999996 46899999999999987654445679999999 588999999983 456676777654334
Q ss_pred CCcchHHHHHHHHHHHHcCC-----CCC-CCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecc-hHHHHHHHH
Q 014440 165 SGDSSIQNALDLVHGLLNQI-----PSY-GHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSA-EMFICKHLC 237 (424)
Q Consensus 165 ~G~tsL~~AL~~Al~~L~~~-----p~~-~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~-e~~iLq~iA 237 (424)
.|+|.++.||..|+..+... |.. ..++||||++++.+. .++.+.++.+++.||+|++||+|. +...|++||
T Consensus 78 ~~~t~tg~AL~~a~~~~~~~~~g~r~~~~~~~kvvillTDG~s~--~~~~~~a~~lk~~gv~i~~VgvG~~~~~~L~~ia 155 (224)
T cd01475 78 ETGTMTGLAIQYAMNNAFSEAEGARPGSERVPRVGIVVTDGRPQ--DDVSEVAAKARALGIEMFAVGVGRADEEELREIA 155 (224)
T ss_pred CCCChHHHHHHHHHHHhCChhcCCCCCCCCCCeEEEEEcCCCCc--ccHHHHHHHHHHCCcEEEEEeCCcCCHHHHHHHh
Confidence 57789999999998765321 111 125676666554442 357788999999999999999996 467899999
Q ss_pred HHhCC-EEEEecChhhHHHHHHhcCCC
Q 014440 238 QETGG-TYSVALDESHSKELILEHAPP 263 (424)
Q Consensus 238 ~~TGG-~Y~~~~d~~~L~~lL~~~~~p 263 (424)
..+++ .|+.+.|.+.|..+...+...
T Consensus 156 s~~~~~~~f~~~~~~~l~~~~~~l~~~ 182 (224)
T cd01475 156 SEPLADHVFYVEDFSTIEELTKKFQGK 182 (224)
T ss_pred CCCcHhcEEEeCCHHHHHHHhhhcccc
Confidence 88765 567788888899888877643
No 35
>cd00198 vWFA Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains.
Probab=99.62 E-value=2.3e-14 Score=124.28 Aligned_cols=152 Identities=21% Similarity=0.261 Sum_probs=120.9
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCC--CHHHHHHHHhhhhC-
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGG--SPESHIKALMGKLG- 163 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~--d~~~~~~~L~~~~~- 163 (424)
+++++||.|.|| .++++..++..+..++..+...++..+++|+.|. +......+++. +.+.+.+.+.....
T Consensus 2 ~v~~viD~S~Sm-----~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~~f~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 75 (161)
T cd00198 2 DIVFLLDVSGSM-----GGEKLDKAKEALKALVSSLSASPPGDRVGLVTFG-SNARVVLPLTTDTDKADLLEAIDALKKG 75 (161)
T ss_pred cEEEEEeCCCCc-----CcchHHHHHHHHHHHHHhcccCCCCcEEEEEEec-CccceeecccccCCHHHHHHHHHhcccC
Confidence 789999999999 5689999999999999999887788999999995 67788888876 66777777765433
Q ss_pred CCCcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCcc-CHHHHHHHHHhCCcEEEEEEecc--hHHHHHHHHHHh
Q 014440 164 CSGDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPG-DIMETIQKCKESKIRCSVIGLSA--EMFICKHLCQET 240 (424)
Q Consensus 164 ~~G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~-~i~~~i~~akk~~IrV~vIgLg~--e~~iLq~iA~~T 240 (424)
..|++++..||..|...+........+++||++++....++. ++.++++.+++.+|+|++|++|. ....|+.++..|
T Consensus 76 ~~~~t~~~~al~~~~~~~~~~~~~~~~~~lvvitDg~~~~~~~~~~~~~~~~~~~~v~v~~v~~g~~~~~~~l~~l~~~~ 155 (161)
T cd00198 76 LGGGTNIGAALRLALELLKSAKRPNARRVIILLTDGEPNDGPELLAEAARELRKLGITVYTIGIGDDANEDELKEIADKT 155 (161)
T ss_pred CCCCccHHHHHHHHHHHhcccCCCCCceEEEEEeCCCCCCCcchhHHHHHHHHHcCCEEEEEEcCCCCCHHHHHHHhccc
Confidence 678899999999999999875222344455555443332322 67789999999999999999995 679999999998
Q ss_pred -CCEE
Q 014440 241 -GGTY 244 (424)
Q Consensus 241 -GG~Y 244 (424)
+|.|
T Consensus 156 ~~~~~ 160 (161)
T cd00198 156 TGGAV 160 (161)
T ss_pred ccccc
Confidence 5554
No 36
>cd01471 vWA_micronemal_protein Micronemal proteins: The Toxoplasma lytic cycle begins when the parasite actively invades a target cell. In association with invasion, T. gondii sequentially discharges three sets of secretory organelles beginning with the micronemes, which contain adhesive proteins involved in parasite attachment to a host cell. Deployed as protein complexes, several micronemal proteins possess vertebrate-derived adhesive sequences that function in binding receptors. The VWA domain likely mediates the protein-protein interactions of these with their interacting partners.
Probab=99.61 E-value=4.1e-14 Score=130.25 Aligned_cols=166 Identities=18% Similarity=0.162 Sum_probs=117.4
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCC----CHHH---HHHHHh
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGG----SPES---HIKALM 159 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~----d~~~---~~~~L~ 159 (424)
+++|+||.|+||... +|+..+++.+..|++.+--.++..++|||+| ++.+..+.|++. +.+. .++.|.
T Consensus 2 Dv~~vlD~SgSm~~~----~~~~~~k~~~~~~~~~~~~~~~~~~vglv~F-s~~~~~~~~l~~~~~~~~~~~~~~i~~l~ 76 (186)
T cd01471 2 DLYLLVDGSGSIGYS----NWVTHVVPFLHTFVQNLNISPDEINLYLVTF-STNAKELIRLSSPNSTNKDLALNAIRALL 76 (186)
T ss_pred cEEEEEeCCCCccch----hhHHHHHHHHHHHHHhcccCCCceEEEEEEe-cCCceEEEECCCccccchHHHHHHHHHHH
Confidence 799999999999764 4799999999999988754555679999999 588999888875 3333 333343
Q ss_pred hhhCCCCcchHHHHHHHHHHHHcCC---CCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecc--hHHHHH
Q 014440 160 GKLGCSGDSSIQNALDLVHGLLNQI---PSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSA--EMFICK 234 (424)
Q Consensus 160 ~~~~~~G~tsL~~AL~~Al~~L~~~---p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~--e~~iLq 234 (424)
....+.|+|.+..||..|.+.+... .....+.||+|+++. ..++....+.++.+++.||.|++||+|. +...|+
T Consensus 77 ~~~~~~G~T~l~~aL~~a~~~l~~~~~~r~~~~~~villTDG~-~~~~~~~~~~a~~l~~~gv~v~~igiG~~~d~~~l~ 155 (186)
T cd01471 77 SLYYPNGSTNTTSALLVVEKHLFDTRGNRENAPQLVIIMTDGI-PDSKFRTLKEARKLRERGVIIAVLGVGQGVNHEENR 155 (186)
T ss_pred hCcCCCCCccHHHHHHHHHHHhhccCCCcccCceEEEEEccCC-CCCCcchhHHHHHHHHCCCEEEEEEeehhhCHHHHH
Confidence 3334678999999999999999762 112334455555544 3344445577889999999999999986 468899
Q ss_pred HHHHHhC-C---EEEEecChhhHHHHHH
Q 014440 235 HLCQETG-G---TYSVALDESHSKELIL 258 (424)
Q Consensus 235 ~iA~~TG-G---~Y~~~~d~~~L~~lL~ 258 (424)
.||..-+ . ..+...+-++++..+.
T Consensus 156 ~ia~~~~~~~~~~~~~~~~~~~~~~~~~ 183 (186)
T cd01471 156 SLVGCDPDDSPCPLYLQSSWSEVQNVIK 183 (186)
T ss_pred HhcCCCCCCCCCCeeecCCHHHHHHHhh
Confidence 9887541 1 2333445555555544
No 37
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=99.60 E-value=3.5e-14 Score=152.92 Aligned_cols=165 Identities=20% Similarity=0.217 Sum_probs=127.1
Q ss_pred ceEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCHHHHHHHHhhhhCCC
Q 014440 86 RYLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSPESHIKALMGKLGCS 165 (424)
Q Consensus 86 R~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~~~~~~ 165 (424)
..++|+||.|+||.. +||..+|.++..|+.+-+ .+.++||||+|++..++++.|+|.+.......|..+ .+.
T Consensus 402 ~~vvfvvD~SGSM~~-----~rl~~aK~a~~~ll~~ay--~~rD~v~lI~F~g~~a~~~lppT~~~~~~~~~L~~l-~~g 473 (584)
T PRK13406 402 TTTIFVVDASGSAAL-----HRLAEAKGAVELLLAEAY--VRRDQVALVAFRGRGAELLLPPTRSLVRAKRSLAGL-PGG 473 (584)
T ss_pred ccEEEEEECCCCCcH-----hHHHHHHHHHHHHHHhhc--CCCCEEEEEEECCCceeEEcCCCcCHHHHHHHHhcC-CCC
Confidence 499999999999953 599999999999997643 356899999997567999999999988887777653 677
Q ss_pred CcchHHHHHHHHHHHHcCCCCCC-CcEEEEEEcCCCCCCc----------cCHHHHHHHHHhCCcEEEEEEecchH-HHH
Q 014440 166 GDSSIQNALDLVHGLLNQIPSYG-HREVLILYSALSTCDP----------GDIMETIQKCKESKIRCSVIGLSAEM-FIC 233 (424)
Q Consensus 166 G~tsL~~AL~~Al~~L~~~p~~~-~reILvI~ss~~t~dp----------~~i~~~i~~akk~~IrV~vIgLg~e~-~iL 233 (424)
|+|.|..||.+|++.+.+....+ .+.||+|+++..+..- .+..+++..+++.+|++++|..+... ..+
T Consensus 474 GgTpL~~gL~~A~~~l~~~~~~~~~~~iVLlTDG~~n~~~~~~~~~~~~~~~~~~~a~~~~~~gi~~~vId~g~~~~~~~ 553 (584)
T PRK13406 474 GGTPLAAGLDAAAALALQVRRKGMTPTVVLLTDGRANIARDGTAGRAQAEEDALAAARALRAAGLPALVIDTSPRPQPQA 553 (584)
T ss_pred CCChHHHHHHHHHHHHHHhccCCCceEEEEEeCCCCCCCccccccccchhhHHHHHHHHHHhcCCeEEEEecCCCCcHHH
Confidence 99999999999999987653333 3445555555443211 12345688889999999999998654 589
Q ss_pred HHHHHHhCCEEEEe--cChhhHHHHHH
Q 014440 234 KHLCQETGGTYSVA--LDESHSKELIL 258 (424)
Q Consensus 234 q~iA~~TGG~Y~~~--~d~~~L~~lL~ 258 (424)
++||+.|||.|+.. .+.+.+..+..
T Consensus 554 ~~LA~~~gg~y~~l~~~~a~~~~~~v~ 580 (584)
T PRK13406 554 RALAEAMGARYLPLPRADAGRLSQAVR 580 (584)
T ss_pred HHHHHhcCCeEEECCCCCHHHHHHHHH
Confidence 99999999999975 44555655543
No 38
>cd01482 vWA_collagen_alphaI-XII-like Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.
Probab=99.59 E-value=7.1e-14 Score=126.59 Aligned_cols=151 Identities=18% Similarity=0.122 Sum_probs=115.7
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCC--CCHHHHHHHHhhhhCC
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLG--GSPESHIKALMGKLGC 164 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT--~d~~~~~~~L~~~~~~ 164 (424)
+++++||.|+||.. .++..+++.++.+++.+--.++..++|||.| ++.+....|++ .+.+.+.+.|.++..+
T Consensus 2 Dv~~vlD~S~Sm~~-----~~~~~~k~~~~~l~~~~~~~~~~~rvgli~f-s~~~~~~~~l~~~~~~~~l~~~l~~~~~~ 75 (164)
T cd01482 2 DIVFLVDGSWSIGR-----SNFNLVRSFLSSVVEAFEIGPDGVQVGLVQY-SDDPRTEFDLNAYTSKEDVLAAIKNLPYK 75 (164)
T ss_pred CEEEEEeCCCCcCh-----hhHHHHHHHHHHHHhheeeCCCceEEEEEEE-CCCeeEEEecCCCCCHHHHHHHHHhCcCC
Confidence 78999999999964 4788999999999988744556799999999 48899999997 4566677777665446
Q ss_pred CCcchHHHHHHHHHHHHcCC-C--CCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecch-HHHHHHHHHHh
Q 014440 165 SGDSSIQNALDLVHGLLNQI-P--SYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAE-MFICKHLCQET 240 (424)
Q Consensus 165 ~G~tsL~~AL~~Al~~L~~~-p--~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e-~~iLq~iA~~T 240 (424)
.|+|.++.||..|...+... . ....+++|||++++.+. .++.++++.+++.||.|++||+|.. ...|++||..+
T Consensus 76 ~g~T~~~~aL~~a~~~~~~~~~~~r~~~~k~iillTDG~~~--~~~~~~a~~lk~~gi~i~~ig~g~~~~~~L~~ia~~~ 153 (164)
T cd01482 76 GGNTRTGKALTHVREKNFTPDAGARPGVPKVVILITDGKSQ--DDVELPARVLRNLGVNVFAVGVKDADESELKMIASKP 153 (164)
T ss_pred CCCChHHHHHHHHHHHhcccccCCCCCCCEEEEEEcCCCCC--chHHHHHHHHHHCCCEEEEEecCcCCHHHHHHHhCCC
Confidence 78999999999998765432 1 12234566666544432 3567889999999999999999854 67899999887
Q ss_pred CCEEE
Q 014440 241 GGTYS 245 (424)
Q Consensus 241 GG~Y~ 245 (424)
.+.+.
T Consensus 154 ~~~~~ 158 (164)
T cd01482 154 SETHV 158 (164)
T ss_pred chheE
Confidence 76444
No 39
>PTZ00441 sporozoite surface protein 2 (SSP2); Provisional
Probab=99.57 E-value=1.1e-13 Score=146.67 Aligned_cols=175 Identities=17% Similarity=0.165 Sum_probs=128.7
Q ss_pred hhhccccceEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCC----HHHH
Q 014440 79 RIQKGLIRYLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGS----PESH 154 (424)
Q Consensus 79 ~~r~GiiR~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d----~~~~ 154 (424)
..++.+ +|+|+||.|.||. .+++++.++..+..||..+.-+.-..+||||+| ++.+..+.+++.. .+.+
T Consensus 38 vC~~~l--DIvFLLD~SgSMg----~~Nfle~AK~Fa~~LV~~l~Is~D~V~VgiV~F-Sd~~r~vfpL~s~~s~Dk~~a 110 (576)
T PTZ00441 38 VCNEEV--DLYLLVDGSGSIG----YHNWITHVIPMLMGLIQQLNLSDDAINLYMSLF-SNNTTELIRLGSGASKDKEQA 110 (576)
T ss_pred cccCCc--eEEEEEeCCCccC----CccHHHHHHHHHHHHHHHhccCCCceEEEEEEe-CCCceEEEecCCCccccHHHH
Confidence 345666 9999999999996 357889999999999988765444456777888 5888888888653 2355
Q ss_pred HHHHhhhh---CCCCcchHHHHHHHHHHHHcCCC-CCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecc--
Q 014440 155 IKALMGKL---GCSGDSSIQNALDLVHGLLNQIP-SYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSA-- 228 (424)
Q Consensus 155 ~~~L~~~~---~~~G~tsL~~AL~~Al~~L~~~p-~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~-- 228 (424)
+..|.++. .+.|+|.++.||..|...|.+.. .....++|||++++...+..+..++++.|++.||.|++||||.
T Consensus 111 L~~I~sL~~~~~pgGgTnig~AL~~Aae~L~sr~~R~nvpKVVILLTDG~sns~~dvleaAq~LR~~GVeI~vIGVG~g~ 190 (576)
T PTZ00441 111 LIIVKSLRKTYLPYGKTNMTDALLEVRKHLNDRVNRENAIQLVILMTDGIPNSKYRALEESRKLKDRNVKLAVIGIGQGI 190 (576)
T ss_pred HHHHHHHHhhccCCCCccHHHHHHHHHHHHhhcccccCCceEEEEEecCCCCCcccHHHHHHHHHHCCCEEEEEEeCCCc
Confidence 55555442 47799999999999999987531 1223346666554443344556678899999999999999996
Q ss_pred hHHHHHHHH----HHhCCEEEEecChhhHHHHHHhc
Q 014440 229 EMFICKHLC----QETGGTYSVALDESHSKELILEH 260 (424)
Q Consensus 229 e~~iLq~iA----~~TGG~Y~~~~d~~~L~~lL~~~ 260 (424)
...+|+.|| ..++|.||...+-+.|+.+...+
T Consensus 191 n~e~LrlIAgC~p~~g~c~~Y~vadf~eL~~ivk~L 226 (576)
T PTZ00441 191 NHQFNRLLAGCRPREGKCKFYSDADWEEAKNLIKPF 226 (576)
T ss_pred CHHHHHHHhccCCCCCCCceEEeCCHHHHHHHHHHH
Confidence 467889898 45677899888877776665443
No 40
>COG5148 RPN10 26S proteasome regulatory complex, subunit RPN10/PSMD4 [Posttranslational modification, protein turnover, chaperones]
Probab=99.57 E-value=1.2e-13 Score=126.82 Aligned_cols=156 Identities=18% Similarity=0.260 Sum_probs=135.2
Q ss_pred ceEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCHHHHHHHHhhhhCCC
Q 014440 86 RYLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSPESHIKALMGKLGCS 165 (424)
Q Consensus 86 R~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~~~~~~ 165 (424)
-.+|++||.|..|...|+.|+||++.++.+.-.++.-+++||.+.+|+|........+++.+|.+...++..|... ...
T Consensus 4 EatvvliDNse~s~NgDy~ptRFeAQkd~ve~if~~K~ndnpEntiGli~~~~a~p~vlsT~T~~~gkilt~lhd~-~~~ 82 (243)
T COG5148 4 EATVVLIDNSEASQNGDYLPTRFEAQKDAVESIFSKKFNDNPENTIGLIPLVQAQPNVLSTPTKQRGKILTFLHDI-RLH 82 (243)
T ss_pred ceEEEEEeChhhhhcCCCCcHHHHHHHHHHHHHHHHHhcCCccceeeeeecccCCcchhccchhhhhHHHHHhccc-ccc
Confidence 3679999999999999999999999999999999999999999999999998888999999999988888888754 557
Q ss_pred CcchHHHHHHHHHHHHcCCCCCCCc-EEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecc--hHHHHHHHHHHhCC
Q 014440 166 GDSSIQNALDLVHGLLNQIPSYGHR-EVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSA--EMFICKHLCQETGG 242 (424)
Q Consensus 166 G~tsL~~AL~~Al~~L~~~p~~~~r-eILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~--e~~iLq~iA~~TGG 242 (424)
|+..+..+|..|.-.|++..+.+.+ +|+++++|.-..+..++...++.++++||.|++|-+|. +...|.+.-+.|+-
T Consensus 83 g~a~~~~~lqiaql~lkhR~nk~q~qriVaFvgSpi~esedeLirlak~lkknnVAidii~fGE~~n~~~l~efIda~N~ 162 (243)
T COG5148 83 GGADIMRCLQIAQLILKHRDNKGQRQRIVAFVGSPIQESEDELIRLAKQLKKNNVAIDIIFFGEAANMAGLFEFIDATNF 162 (243)
T ss_pred CcchHHHHHHHHHHHHhcccCCccceEEEEEecCcccccHHHHHHHHHHHHhcCeeEEEEehhhhhhhhHHHHHHHhhcc
Confidence 8899999999999999998666654 57777787655555667788999999999999999994 46778887778876
No 41
>PF00092 VWA: von Willebrand factor type A domain; InterPro: IPR002035 The von Willebrand factor is a large multimeric glycoprotein found in blood plasma. Mutant forms are involved in the aetiology of bleeding disorders []. In von Willebrand factor, the type A domain (vWF) is the prototype for a protein superfamily. The vWF domain is found in various plasma proteins: complement factors B, C2, CR3 and CR4; the integrins (I-domains); collagen types VI, VII, XII and XIV; and other extracellular proteins [, , ]. Although the majority of VWA-containing proteins are extracellular, the most ancient ones present in all eukaryotes are all intracellular proteins involved in functions such as transcription, DNA repair, ribosomal and membrane transport and the proteasome. A common feature appears to be involvement in multiprotein complexes. Proteins that incorporate vWF domains participate in numerous biological events (e.g. cell adhesion, migration, homing, pattern formation, and signal transduction), involving interaction with a large array of ligands []. A number of human diseases arise from mutations in VWA domains. Secondary structure prediction from 75 aligned vWF sequences has revealed a largely alternating sequence of alpha-helices and beta-strands []. Fold recognition algorithms were used to score sequence compatibility with a library of known structures: the vWF domain fold was predicted to be a doubly-wound, open, twisted beta-sheet flanked by alpha-helices []. 3D structures have been determined for the I-domains of integrins CD11b (with bound magnesium) [] and CD11a (with bound manganese) []. The domain adopts a classic alpha/beta Rossmann fold and contains an unusual metal ion coordination site at its surface. It has been suggested that this site represents a general metal ion-dependent adhesion site (MIDAS) for binding protein ligands []. The residues constituting the MIDAS motif in the CD11b and CD11a I-domains are completely conserved, but the manner in which the metal ion is coordinated differs slightly [].; GO: 0005515 protein binding; PDB: 2XGG_B 3ZQK_B 3GXB_A 3PPV_A 3PPX_A 3PPW_A 3PPY_A 1CQP_B 3TCX_B 2ICA_A ....
Probab=99.54 E-value=1.6e-13 Score=123.26 Aligned_cols=167 Identities=19% Similarity=0.207 Sum_probs=129.6
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCC--CHHHHHHHH-hhhhC
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGG--SPESHIKAL-MGKLG 163 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~--d~~~~~~~L-~~~~~ 163 (424)
+|+|+||.|+||.. +++..+++.+..|++.+...++..++|||.| +..+..+.+++. +..+....+ .....
T Consensus 1 DivflvD~S~sm~~-----~~~~~~~~~v~~~i~~~~~~~~~~rv~iv~f-~~~~~~~~~~~~~~~~~~~~~~i~~~~~~ 74 (178)
T PF00092_consen 1 DIVFLVDTSGSMSG-----DNFEKAKQFVKSIISRLSISNNGTRVGIVTF-SDSARVLFSLTDYQSKNDLLNAINDSIPS 74 (178)
T ss_dssp EEEEEEE-STTSCH-----HHHHHHHHHHHHHHHHSTBSTTSEEEEEEEE-SSSEEEEEETTSHSSHHHHHHHHHTTGGC
T ss_pred CEEEEEeCCCCCch-----HHHHHHHHHHHHHHHhhhccccccccceeee-ecccccccccccccccccccccccccccc
Confidence 68999999999986 5799999999999998867888999999999 588888888875 356677776 44445
Q ss_pred CCCcchHHHHHHHHHHHHcCC---CCCCCcEEEEEEcCCCCCCccCHHHHHHHHHh-CCcEEEEEEe-cchHHHHHHHHH
Q 014440 164 CSGDSSIQNALDLVHGLLNQI---PSYGHREVLILYSALSTCDPGDIMETIQKCKE-SKIRCSVIGL-SAEMFICKHLCQ 238 (424)
Q Consensus 164 ~~G~tsL~~AL~~Al~~L~~~---p~~~~reILvI~ss~~t~dp~~i~~~i~~akk-~~IrV~vIgL-g~e~~iLq~iA~ 238 (424)
..|+|+++.||..|...|... .....+++||+++++...+..........+++ .+|.+.+||+ +.+...|+.|+.
T Consensus 75 ~~g~t~~~~aL~~a~~~l~~~~~~~r~~~~~~iiliTDG~~~~~~~~~~~~~~~~~~~~i~~~~ig~~~~~~~~l~~la~ 154 (178)
T PF00092_consen 75 SGGGTNLGAALKFAREQLFSSNNGGRPNSPKVIILITDGNSNDSDSPSEEAANLKKSNGIKVIAIGIDNADNEELRELAS 154 (178)
T ss_dssp CBSSB-HHHHHHHHHHHTTSGGGTTGTTSEEEEEEEESSSSSSHSGHHHHHHHHHHHCTEEEEEEEESCCHHHHHHHHSH
T ss_pred cchhhhHHHHHhhhhhcccccccccccccccceEEEEeecccCCcchHHHHHHHHHhcCcEEEEEecCcCCHHHHHHHhC
Confidence 778999999999999999764 22345677777765555454445555555555 5999999999 788999999997
Q ss_pred Hh--CCEEEEecChhhHHHHHHh
Q 014440 239 ET--GGTYSVALDESHSKELILE 259 (424)
Q Consensus 239 ~T--GG~Y~~~~d~~~L~~lL~~ 259 (424)
.+ ++.++...+...+.++..+
T Consensus 155 ~~~~~~~~~~~~~~~~l~~~~~~ 177 (178)
T PF00092_consen 155 CPTSEGHVFYLADFSDLSQIIQQ 177 (178)
T ss_dssp SSTCHHHEEEESSHHHHHHHHHH
T ss_pred CCCCCCcEEEcCCHHHHHHHHhc
Confidence 75 3677788898888887654
No 42
>cd01473 vWA_CTRP CTRP for CS protein-TRAP-related protein: Adhesion of Plasmodium to host cells is an important phenomenon in parasite invasion and in malaria associated pathology.CTRP encodes a protein containing a putative signal sequence followed by a long extracellular region of 1990 amino acids, a transmembrane domain, and a short cytoplasmic segment. The extracellular region of CTRP contains two separated adhesive domains. The first domain contains six 210-amino acid-long homologous VWA domain repeats. The second domain contains seven repeats of 87-60 amino acids in length, which share similarities with the thrombospondin type 1 domain found in a variety of adhesive molecules. Finally, CTRP also contains consensus motifs found in the superfamily of haematopoietin receptors. The VWA domains in these proteins likely mediate protein-protein interactions.
Probab=99.54 E-value=1.8e-13 Score=128.13 Aligned_cols=167 Identities=12% Similarity=0.135 Sum_probs=115.2
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCC----HHHHHHHHhhhh
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGS----PESHIKALMGKL 162 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d----~~~~~~~L~~~~ 162 (424)
+|+++||.|.||...++.+.+... ++.+++.+.-.....|+|||.|. +.+++..|++.+ ..+++.+|.++.
T Consensus 2 Di~fllD~S~Si~~~~f~~~~~~f----~~~lv~~l~i~~~~~rvgvv~fs-~~~~~~~~~~~~~~~~~~~l~~~i~~l~ 76 (192)
T cd01473 2 DLTLILDESASIGYSNWRKDVIPF----TEKIINNLNISKDKVHVGILLFA-EKNRDVVPFSDEERYDKNELLKKINDLK 76 (192)
T ss_pred cEEEEEeCCCcccHHHHHHHHHHH----HHHHHHhCccCCCccEEEEEEec-CCceeEEecCcccccCHHHHHHHHHHHH
Confidence 799999999999887776555555 44455555445567899999994 899999999853 345666665442
Q ss_pred ---CCCCcchHHHHHHHHHHHHcCCCC--CCCcEEEEEEcCCCCCCc--cCHHHHHHHHHhCCcEEEEEEecch-HHHHH
Q 014440 163 ---GCSGDSSIQNALDLVHGLLNQIPS--YGHREVLILYSALSTCDP--GDIMETIQKCKESKIRCSVIGLSAE-MFICK 234 (424)
Q Consensus 163 ---~~~G~tsL~~AL~~Al~~L~~~p~--~~~reILvI~ss~~t~dp--~~i~~~i~~akk~~IrV~vIgLg~e-~~iLq 234 (424)
.+.|+|.++.||+.|++.+....+ ...++|+||++++.+.++ .++.++++.|++.||+|++||+|.. ...|+
T Consensus 77 ~~~~~~g~T~~~~AL~~a~~~~~~~~~~r~~~~kv~IllTDG~s~~~~~~~~~~~a~~lk~~gV~i~~vGiG~~~~~el~ 156 (192)
T cd01473 77 NSYRSGGETYIVEALKYGLKNYTKHGNRRKDAPKVTMLFTDGNDTSASKKELQDISLLYKEENVKLLVVGVGAASENKLK 156 (192)
T ss_pred hccCCCCcCcHHHHHHHHHHHhccCCCCcccCCeEEEEEecCCCCCcchhhHHHHHHHHHHCCCEEEEEEeccccHHHHH
Confidence 357899999999999999865321 222456666655554343 3467889999999999999999964 45688
Q ss_pred HHHHH--hCCE--EEEecChhhHHHHHH
Q 014440 235 HLCQE--TGGT--YSVALDESHSKELIL 258 (424)
Q Consensus 235 ~iA~~--TGG~--Y~~~~d~~~L~~lL~ 258 (424)
.||.- ..+. |+...+-+.|..+-.
T Consensus 157 ~ia~~~~~~~~~~~~~~~~f~~l~~~~~ 184 (192)
T cd01473 157 LLAGCDINNDNCPNVIKTEWNNLNGISK 184 (192)
T ss_pred HhcCCCCCCCCCCeEEecchhhHHHHHH
Confidence 88853 2221 333334555555543
No 43
>TIGR03788 marine_srt_targ marine proteobacterial sortase target protein. Members of this protein family are restricted to the Proteobacteria. Each contains a C-terminal sortase-recognition motif, transmembrane domain, and basic residues cluster at the the C-terminus, and is encoded adjacent to a sortase gene. This protein is frequently the only sortase target in its genome, which is as unusual its occurrence in Gram-negative rather than Gram-positive genomes. Many bacteria with this system are marine. In addition to the LPXTG signal, members carry a vault protein inter-alpha-trypsin inhibitor domain (pfam08487) and a von Willebrand factor type A domain (pfam00092).
Probab=99.51 E-value=4.2e-13 Score=145.41 Aligned_cols=164 Identities=16% Similarity=0.189 Sum_probs=117.2
Q ss_pred ccceEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCC--CHH---HHHHHH
Q 014440 84 LIRYLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGG--SPE---SHIKAL 158 (424)
Q Consensus 84 iiR~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~--d~~---~~~~~L 158 (424)
+-++++||||.|+||.. +++..++.++..+++. .+|.++++||+| ++.+..+.|.+. +.. .....|
T Consensus 270 ~p~~vvfvlD~SgSM~g-----~~i~~ak~al~~~l~~---L~~~d~~~ii~F-~~~~~~~~~~~~~~~~~~~~~a~~~i 340 (596)
T TIGR03788 270 LPRELVFVIDTSGSMAG-----ESIEQAKSALLLALDQ---LRPGDRFNIIQF-DSDVTLLFPVPVPATAHNLARARQFV 340 (596)
T ss_pred CCceEEEEEECCCCCCC-----ccHHHHHHHHHHHHHh---CCCCCEEEEEEE-CCcceEeccccccCCHHHHHHHHHHH
Confidence 34689999999999985 4688899998888875 467789999999 578888877643 222 223334
Q ss_pred hhhhCCCCcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecch--HHHHHHH
Q 014440 159 MGKLGCSGDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAE--MFICKHL 236 (424)
Q Consensus 159 ~~~~~~~G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e--~~iLq~i 236 (424)
.. +.+.|+|+|..||..|+...........+.||+|+++.. .+...+.+.++. +..+++|++||+|.. ..+|++|
T Consensus 341 ~~-l~a~GgT~l~~aL~~a~~~~~~~~~~~~~~iillTDG~~-~~~~~~~~~~~~-~~~~~ri~tvGiG~~~n~~lL~~l 417 (596)
T TIGR03788 341 AG-LQADGGTEMAGALSAALRDDGPESSGALRQVVFLTDGAV-GNEDALFQLIRT-KLGDSRLFTVGIGSAPNSYFMRKA 417 (596)
T ss_pred hh-CCCCCCccHHHHHHHHHHhhcccCCCceeEEEEEeCCCC-CCHHHHHHHHHH-hcCCceEEEEEeCCCcCHHHHHHH
Confidence 33 357799999999999998754332233456777776542 233333333322 234699999999974 6899999
Q ss_pred HHHhCCEEEEecChhhHHHHHHh
Q 014440 237 CQETGGTYSVALDESHSKELILE 259 (424)
Q Consensus 237 A~~TGG~Y~~~~d~~~L~~lL~~ 259 (424)
|+.+||.|..+.+.+.+...+..
T Consensus 418 A~~g~G~~~~i~~~~~~~~~~~~ 440 (596)
T TIGR03788 418 AQFGRGSFTFIGSTDEVQRKMSQ 440 (596)
T ss_pred HHcCCCEEEECCCHHHHHHHHHH
Confidence 99999999998888776544433
No 44
>PF13768 VWA_3: von Willebrand factor type A domain
Probab=99.50 E-value=5.5e-13 Score=119.11 Aligned_cols=143 Identities=17% Similarity=0.282 Sum_probs=102.3
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCC--CCH---HHHHHHHhhh
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLG--GSP---ESHIKALMGK 161 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT--~d~---~~~~~~L~~~ 161 (424)
++||+||+|.||... . ..+++++..+++. ..|.+++.||.|. ..+..+.|-. .+. +...+.|++
T Consensus 2 ~vvilvD~S~Sm~g~-----~-~~~k~al~~~l~~---L~~~d~fnii~f~-~~~~~~~~~~~~~~~~~~~~a~~~I~~- 70 (155)
T PF13768_consen 2 DVVILVDTSGSMSGE-----K-ELVKDALRAILRS---LPPGDRFNIIAFG-SSVRPLFPGLVPATEENRQEALQWIKS- 70 (155)
T ss_pred eEEEEEeCCCCCCCc-----H-HHHHHHHHHHHHh---CCCCCEEEEEEeC-CEeeEcchhHHHHhHHHHHHHHHHHHH-
Confidence 689999999999753 3 7888889888887 5678999999994 6766666542 111 222333433
Q ss_pred hCC-CCcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHh--CCcEEEEEEecch--HHHHHHH
Q 014440 162 LGC-SGDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKE--SKIRCSVIGLSAE--MFICKHL 236 (424)
Q Consensus 162 ~~~-~G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk--~~IrV~vIgLg~e--~~iLq~i 236 (424)
+.+ .|+|.+..||+.|+..+.. ....+.|++|+++..+..+ .++++.+++ .+|+|+++|+|.. ..+|++|
T Consensus 71 ~~~~~G~t~l~~aL~~a~~~~~~--~~~~~~IilltDG~~~~~~---~~i~~~v~~~~~~~~i~~~~~g~~~~~~~L~~L 145 (155)
T PF13768_consen 71 LEANSGGTDLLAALRAALALLQR--PGCVRAIILLTDGQPVSGE---EEILDLVRRARGHIRIFTFGIGSDADADFLREL 145 (155)
T ss_pred hcccCCCccHHHHHHHHHHhccc--CCCccEEEEEEeccCCCCH---HHHHHHHHhcCCCceEEEEEECChhHHHHHHHH
Confidence 355 8999999999999988722 2345567777755432222 344444433 5799999999974 5899999
Q ss_pred HHHhCCEEE
Q 014440 237 CQETGGTYS 245 (424)
Q Consensus 237 A~~TGG~Y~ 245 (424)
|+.|||.|.
T Consensus 146 A~~~~G~~~ 154 (155)
T PF13768_consen 146 ARATGGSFH 154 (155)
T ss_pred HHcCCCEEE
Confidence 999999995
No 45
>cd01476 VWA_integrin_invertebrates VWA_integrin (invertebrates): Integrins are a family of cell surface receptors that have diverse functions in cell-cell and cell-extracellular matrix interactions. Because of their involvement in many biologically important adhesion processes, integrins are conserved across a wide range of multicellular animals. Integrins from invertebrates have been identified from six phyla. There are no data to date to suggest any immunological functions for the invertebrate integrins. The members of this sub-group have the conserved MIDAS motif that is charateristic of this domain suggesting the involvement of the integrins in the recognition and binding of multi-ligands.
Probab=99.50 E-value=1.6e-12 Score=116.78 Aligned_cols=142 Identities=14% Similarity=0.136 Sum_probs=103.5
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCC--ceEEeeCCCC--CHHHHHHHHhhhh
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDG--VANCLTDLGG--SPESHIKALMGKL 162 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g--~A~~lspLT~--d~~~~~~~L~~~~ 162 (424)
+++++||.|+||.. ++..+++.++.++..+....+..++|||.|. + .+.+..|++. +...+.+.|..+.
T Consensus 2 dv~~llD~S~Sm~~------~~~~~~~~~~~~~~~l~~~~~~~~v~lv~f~-~~~~~~~~~~l~~~~~~~~l~~~i~~l~ 74 (163)
T cd01476 2 DLLFVLDSSGSVRG------KFEKYKKYIERIVEGLEIGPTATRVALITYS-GRGRQRVRFNLPKHNDGEELLEKVDNLR 74 (163)
T ss_pred CEEEEEeCCcchhh------hHHHHHHHHHHHHHhcCCCCCCcEEEEEEEc-CCCceEEEecCCCCCCHHHHHHHHHhCc
Confidence 68999999999963 5777888899999887766667999999995 5 6787888874 5666777776643
Q ss_pred CCCCcchHHHHHHHHHHHHcCCC--CCCCcEEEEEEcCCCCCCccCHHHHHHHHHh-CCcEEEEEEecch----HHHHHH
Q 014440 163 GCSGDSSIQNALDLVHGLLNQIP--SYGHREVLILYSALSTCDPGDIMETIQKCKE-SKIRCSVIGLSAE----MFICKH 235 (424)
Q Consensus 163 ~~~G~tsL~~AL~~Al~~L~~~p--~~~~reILvI~ss~~t~dp~~i~~~i~~akk-~~IrV~vIgLg~e----~~iLq~ 235 (424)
.+.|+|+++.||..|...|.... ....++++||++++.+. .+....++.+++ .+|.|++||+|.. ...|++
T Consensus 75 ~~gg~T~l~~aL~~a~~~l~~~~~~r~~~~~~villTDG~~~--~~~~~~~~~l~~~~~v~v~~vg~g~~~~~~~~~L~~ 152 (163)
T cd01476 75 FIGGTTATGAAIEVALQQLDPSEGRREGIPKVVVVLTDGRSH--DDPEKQARILRAVPNIETFAVGTGDPGTVDTEELHS 152 (163)
T ss_pred cCCCCccHHHHHHHHHHHhccccCCCCCCCeEEEEECCCCCC--CchHHHHHHHhhcCCCEEEEEECCCccccCHHHHHH
Confidence 34677999999999999996321 11233555555544332 235566788888 9999999999975 344444
Q ss_pred HH
Q 014440 236 LC 237 (424)
Q Consensus 236 iA 237 (424)
||
T Consensus 153 ia 154 (163)
T cd01476 153 IT 154 (163)
T ss_pred Hh
Confidence 44
No 46
>cd01458 vWA_ku Ku70/Ku80 N-terminal domain. The Ku78 heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks (DSB) in a preferred orientation. DSB's are repaired by either homologues recombination or non-homologues end joining and facilitate repair by the non-homologous end-joining pathway (NHEJ). The Ku heterodimer is required for accurate process that tends to preserve the sequence at the junction. Ku78 is found in all three kingdoms of life. However, only the eukaryotic proteins have a vWA domain fused to them at their N-termini. The vWA domain is not involved in DNA binding but may very likey mediate Ku78's interactions with other proteins. Members of this subgroup lack the conserved MIDAS motif.
Probab=99.49 E-value=5e-13 Score=126.89 Aligned_cols=144 Identities=17% Similarity=0.182 Sum_probs=103.9
Q ss_pred eEEEEEeCCHhhhcC-CC-CCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCc---------eEEeeCCCCCHHHHH
Q 014440 87 YLYIVIDLSRAAAEM-DF-RPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGV---------ANCLTDLGGSPESHI 155 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~-D~-~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~---------A~~lspLT~d~~~~~ 155 (424)
.++++||+|+||... |. .|+||+.+++++..|+.+..-.+|.+++|||.|+... .+++.|+.......+
T Consensus 3 ~ivf~iDvS~SM~~~~~~~~~s~l~~a~~~i~~~~~~ki~~~~~D~vGlilf~t~~~~~~~~~~~i~v~~~l~~~~~~~l 82 (218)
T cd01458 3 SVVFLVDVSPSMFESKDGEYESPFEEALKCIRQLMKSKIISSPKDLVGVVFYGTEESKNPVGYENIYVLLDLDTPGAERV 82 (218)
T ss_pred EEEEEEeCCHHHcCCCCCCCCChHHHHHHHHHHHHHhceeCCCCCeEEEEEEcccCCCCcCCCCceEEeecCCCCCHHHH
Confidence 579999999999855 33 4999999999999999976667999999999995332 135677744333444
Q ss_pred HHHhhhhC-----------CCCcchHHHHHHHHHHHHcCC-CCCCCcEEEEEEcCCCCCC-----ccCHHHHHHHHHhCC
Q 014440 156 KALMGKLG-----------CSGDSSIQNALDLVHGLLNQI-PSYGHREVLILYSALSTCD-----PGDIMETIQKCKESK 218 (424)
Q Consensus 156 ~~L~~~~~-----------~~G~tsL~~AL~~Al~~L~~~-p~~~~reILvI~ss~~t~d-----p~~i~~~i~~akk~~ 218 (424)
+.|.+.+. ..++++|.+||..|+.+|.+. +....|+|++|+++.+... +..+...++.+++.|
T Consensus 83 ~~l~~~~~~~~~~~~~~~~~~~~~~l~~aL~~a~~~~~~~~~~~~~k~IvL~TDg~~p~~~~~~~~~~~~~~a~~l~~~g 162 (218)
T cd01458 83 EDLKELIEPGGLSFAGQVGDSGQVSLSDALWVCLDLFSKGKKKKSHKRIFLFTNNDDPHGGDSIKDSQAAVKAEDLKDKG 162 (218)
T ss_pred HHHHHHhhcchhhhcccCCCCCCccHHHHHHHHHHHHHhccccccccEEEEECCCCCCCCCCHHHHHHHHHHHHHHHhCC
Confidence 55544321 245789999999999999873 2345667777776543321 122345678888899
Q ss_pred cEEEEEEecchH
Q 014440 219 IRCSVIGLSAEM 230 (424)
Q Consensus 219 IrV~vIgLg~e~ 230 (424)
|.|++|+++.+.
T Consensus 163 I~i~~i~i~~~~ 174 (218)
T cd01458 163 IELELFPLSSPG 174 (218)
T ss_pred cEEEEEecCCCC
Confidence 999999998764
No 47
>cd01464 vWA_subfamily VWA subfamily: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if
Probab=99.49 E-value=2.7e-13 Score=124.14 Aligned_cols=142 Identities=19% Similarity=0.246 Sum_probs=100.4
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccC---CCCcEEEEEecCCceEEeeCCCCCHHHHHHHHhhhhC
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQN---PLSQIGLVTVKDGVANCLTDLGGSPESHIKALMGKLG 163 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qn---P~sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~~~~ 163 (424)
.++++||.|+||.. .++..+++.+..|++.+.... +..++|||+| ++.++.+.|++...... + ..+.
T Consensus 5 ~v~~llD~SgSM~~-----~~~~~~k~a~~~~~~~l~~~~~~~~~~~v~ii~F-~~~a~~~~~l~~~~~~~---~-~~l~ 74 (176)
T cd01464 5 PIYLLLDTSGSMAG-----EPIEALNQGLQMLQSELRQDPYALESVEISVITF-DSAARVIVPLTPLESFQ---P-PRLT 74 (176)
T ss_pred CEEEEEECCCCCCC-----hHHHHHHHHHHHHHHHHhcChhhccccEEEEEEe-cCCceEecCCccHHhcC---C-Cccc
Confidence 68999999999965 468888899999988765422 4678999999 57899999998632211 1 1235
Q ss_pred CCCcchHHHHHHHHHHHHcCCC--------CCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecc--hHHHH
Q 014440 164 CSGDSSIQNALDLVHGLLNQIP--------SYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSA--EMFIC 233 (424)
Q Consensus 164 ~~G~tsL~~AL~~Al~~L~~~p--------~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~--e~~iL 233 (424)
+.|+|++..||..|++.|.... ....+.||+|+++..+.++....+.++.+++.+++|++||+|. +...|
T Consensus 75 ~~GgT~l~~aL~~a~~~l~~~~~~~~~~~~~~~~~~iillTDG~~~~~~~~~~~~~~~~~~~~~~i~~igiG~~~~~~~L 154 (176)
T cd01464 75 ASGGTSMGAALELALDCIDRRVQRYRADQKGDWRPWVFLLTDGEPTDDLTAAIERIKEARDSKGRIVACAVGPKADLDTL 154 (176)
T ss_pred CCCCCcHHHHHHHHHHHHHHHHHHhcccCcCCcCcEEEEEcCCCCCchHHHHHHHHHhhcccCCcEEEEEeccccCHHHH
Confidence 6789999999999999996531 1112345555555433222222355677777789999999996 46778
Q ss_pred HHHHH
Q 014440 234 KHLCQ 238 (424)
Q Consensus 234 q~iA~ 238 (424)
++||.
T Consensus 155 ~~ia~ 159 (176)
T cd01464 155 KQITE 159 (176)
T ss_pred HHHHC
Confidence 88884
No 48
>TIGR02442 Cob-chelat-sub cobaltochelatase subunit. A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis.
Probab=99.49 E-value=1e-12 Score=143.27 Aligned_cols=154 Identities=19% Similarity=0.245 Sum_probs=116.8
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCHHHHHHHHhhhhCCCC
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSPESHIKALMGKLGCSG 166 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~~~~~~G 166 (424)
.++|+||+|+||.. .+|+..++.++..|+...+. +.+++|||+|.+..++++.|+|.+.......|.. +.+.|
T Consensus 467 ~vv~vvD~SgSM~~----~~rl~~ak~a~~~ll~~a~~--~~D~v~lI~F~g~~a~~~~p~t~~~~~~~~~L~~-l~~gG 539 (633)
T TIGR02442 467 LVIFVVDASGSMAA----RGRMAAAKGAVLSLLRDAYQ--KRDKVALITFRGEEAEVLLPPTSSVELAARRLEE-LPTGG 539 (633)
T ss_pred eEEEEEECCccCCC----ccHHHHHHHHHHHHHHHhhc--CCCEEEEEEECCCCceEEcCCCCCHHHHHHHHHh-CCCCC
Confidence 89999999999974 36999999999999876543 3589999999655799999999887776666655 36778
Q ss_pred cchHHHHHHHHHHHHcCC--CCCCCcEEEEEEc-CCCCCC---cc---CHHHHHHHHHhCCcEEEEEEecch---HHHHH
Q 014440 167 DSSIQNALDLVHGLLNQI--PSYGHREVLILYS-ALSTCD---PG---DIMETIQKCKESKIRCSVIGLSAE---MFICK 234 (424)
Q Consensus 167 ~tsL~~AL~~Al~~L~~~--p~~~~reILvI~s-s~~t~d---p~---~i~~~i~~akk~~IrV~vIgLg~e---~~iLq 234 (424)
+|.|..||.+|...+.+. .....+.+|||++ +..+.. +. +...++..+++.+|.+.+|..+.. ...++
T Consensus 540 ~Tpl~~aL~~A~~~l~~~~~~~~~~~~~vvliTDG~~n~~~~~~~~~~~~~~~a~~l~~~~i~~~vIdt~~~~~~~~~~~ 619 (633)
T TIGR02442 540 RTPLAAGLLKAAEVLSNELLRDDDGRPLLVVITDGRANVADGGEPPTDDARTIAAKLAARGILFVVIDTESGFVRLGLAE 619 (633)
T ss_pred CCCHHHHHHHHHHHHHHhhccCCCCceEEEEECCCCCCCCCCCCChHHHHHHHHHHHHhcCCeEEEEeCCCCCcchhHHH
Confidence 999999999999999831 1223344555554 433321 11 234567788889999999988653 57899
Q ss_pred HHHHHhCCEEEEe
Q 014440 235 HLCQETGGTYSVA 247 (424)
Q Consensus 235 ~iA~~TGG~Y~~~ 247 (424)
+||+.+||+|+..
T Consensus 620 ~lA~~~gg~y~~l 632 (633)
T TIGR02442 620 DLARALGGEYVRL 632 (633)
T ss_pred HHHHhhCCeEEec
Confidence 9999999999863
No 49
>COG1240 ChlD Mg-chelatase subunit ChlD [Coenzyme metabolism]
Probab=99.47 E-value=1.7e-12 Score=125.33 Aligned_cols=158 Identities=19% Similarity=0.249 Sum_probs=123.8
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCHHHHHHHHhhhhCCCC
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSPESHIKALMGKLGCSG 166 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~~~~~~G 166 (424)
-+|+|+|.|+||... .|+.+++-.+..|+++-.... ++|+||+|+..+|+++.|+|.+.+...+.|..+ .+.|
T Consensus 80 lvvfvVDASgSM~~~----~Rm~aaKG~~~~lL~dAYq~R--dkvavI~F~G~~A~lll~pT~sv~~~~~~L~~l-~~GG 152 (261)
T COG1240 80 LIVFVVDASGSMAAR----RRMAAAKGAALSLLRDAYQRR--DKVAVIAFRGEKAELLLPPTSSVELAERALERL-PTGG 152 (261)
T ss_pred cEEEEEeCcccchhH----HHHHHHHHHHHHHHHHHHHcc--ceEEEEEecCCcceEEeCCcccHHHHHHHHHhC-CCCC
Confidence 789999999999874 499999999999998876544 999999999899999999999998888888764 7788
Q ss_pred cchHHHHHHHHHHHHcCCCC--CCCcEEEEEEcCCCCCCc--cC----HHHHHHHHHhCCcEEEEEEecch---HHHHHH
Q 014440 167 DSSIQNALDLVHGLLNQIPS--YGHREVLILYSALSTCDP--GD----IMETIQKCKESKIRCSVIGLSAE---MFICKH 235 (424)
Q Consensus 167 ~tsL~~AL~~Al~~L~~~p~--~~~reILvI~ss~~t~dp--~~----i~~~i~~akk~~IrV~vIgLg~e---~~iLq~ 235 (424)
.|.|..||.+|.+.+.+..- ...+-++|+++++...++ .+ ..++...+...++.+-||..... ..+.++
T Consensus 153 ~TPL~~aL~~a~ev~~r~~r~~p~~~~~~vviTDGr~n~~~~~~~~~e~~~~a~~~~~~g~~~lvid~e~~~~~~g~~~~ 232 (261)
T COG1240 153 KTPLADALRQAYEVLAREKRRGPDRRPVMVVITDGRANVPIPLGPKAETLEAASKLRLRGIQLLVIDTEGSEVRLGLAEE 232 (261)
T ss_pred CCchHHHHHHHHHHHHHhhccCCCcceEEEEEeCCccCCCCCCchHHHHHHHHHHHhhcCCcEEEEecCCccccccHHHH
Confidence 99999999999999987521 123334444443333222 23 22456667788899999888764 368999
Q ss_pred HHHHhCCEEEEecChh
Q 014440 236 LCQETGGTYSVALDES 251 (424)
Q Consensus 236 iA~~TGG~Y~~~~d~~ 251 (424)
||...||.|+...+..
T Consensus 233 iA~~~Gg~~~~L~~l~ 248 (261)
T COG1240 233 IARASGGEYYHLDDLS 248 (261)
T ss_pred HHHHhCCeEEeccccc
Confidence 9999999999864433
No 50
>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. Unlike subunit I (TIGR02030), this subunit is not found in archaea.
Probab=99.47 E-value=1.5e-12 Score=140.97 Aligned_cols=155 Identities=20% Similarity=0.228 Sum_probs=118.6
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCHHHHHHHHhhhhCCCC
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSPESHIKALMGKLGCSG 166 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~~~~~~G 166 (424)
.++|+||.|+||. .+||..++.++..|+...+. +.+++|||+|.++.++++.|+|.+.......|..+ .+.|
T Consensus 409 ~v~fvvD~SGSM~-----~~rl~~aK~av~~Ll~~~~~--~~D~v~Li~F~~~~a~~~lp~t~~~~~~~~~L~~l-~~gG 480 (589)
T TIGR02031 409 LLIFVVDASGSAA-----VARMSEAKGAVELLLGEAYV--HRDQVSLIAFRGTAAEVLLPPSRSVEQAKRRLDVL-PGGG 480 (589)
T ss_pred eEEEEEECCCCCC-----hHHHHHHHHHHHHHHHhhcc--CCCEEEEEEECCCCceEECCCCCCHHHHHHHHhcC-CCCC
Confidence 6899999999995 36999999999999986543 45899999997566788889998877776666653 6788
Q ss_pred cchHHHHHHHHHHHHcCCCCCCC-cEEEEEEcCCCCC--Cc-------------cCHHHHHHHHHhCCcEEEEEEecch-
Q 014440 167 DSSIQNALDLVHGLLNQIPSYGH-REVLILYSALSTC--DP-------------GDIMETIQKCKESKIRCSVIGLSAE- 229 (424)
Q Consensus 167 ~tsL~~AL~~Al~~L~~~p~~~~-reILvI~ss~~t~--dp-------------~~i~~~i~~akk~~IrV~vIgLg~e- 229 (424)
+|.|..||.+|++.+.+...... ..||+|+++..+. +. .++...+..+++.||.+.+|+++..
T Consensus 481 gTpL~~gL~~A~~~~~~~~~~~~~~~ivllTDG~~nv~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~gi~~~vid~~~~~ 560 (589)
T TIGR02031 481 GTPLAAGLAAAFQTALQARSSGGTPTIVLITDGRGNIPLDGDPESIKADREQAAEEALALARKIREAGMPALVIDTAMRF 560 (589)
T ss_pred CCcHHHHHHHHHHHHHHhcccCCceEEEEECCCCCCCCCCcccccccccchhHHHHHHHHHHHHHhcCCeEEEEeCCCCC
Confidence 99999999999999976422233 3455555544331 11 1234557888999999999999854
Q ss_pred --HHHHHHHHHHhCCEEEEecC
Q 014440 230 --MFICKHLCQETGGTYSVALD 249 (424)
Q Consensus 230 --~~iLq~iA~~TGG~Y~~~~d 249 (424)
..++++||+..||.|+...+
T Consensus 561 ~~~~~~~~lA~~~~g~y~~l~~ 582 (589)
T TIGR02031 561 VSTGFAQKLARKMGAHYIYLPN 582 (589)
T ss_pred ccchHHHHHHHhcCCcEEeCCC
Confidence 46799999999999998654
No 51
>cd01454 vWA_norD_type norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases. Denitrification plays a major role in completing the nitrogen cycle by converting nitrate or nitrite to nitrogen gas. The pathway for microbial denitrification has been established as NO3- ------ NO2- ------ NO ------- N2O --------- N2. This reaction generally occurs under oxygen limiting conditions. Genetic and biochemical studies have shown that the first srep of the biochemical pathway is catalyzed by periplasmic nitrate reductases. This family is widely present in proteobacteria and firmicutes. This version of the domain is also present in some archaeal members. The function of the vWA domain in this sub-group is not known. Members of this subgroup have a conserved MIDAS motif.
Probab=99.43 E-value=6.7e-12 Score=114.63 Aligned_cols=135 Identities=17% Similarity=0.179 Sum_probs=93.3
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCC---c--eEEee--CCCCCH-HHHHHHH
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDG---V--ANCLT--DLGGSP-ESHIKAL 158 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g---~--A~~ls--pLT~d~-~~~~~~L 158 (424)
.++|+||+|+||... +|++.+++++..|+..+.. +.+++||++|.++ . ...+. +++.+. ......|
T Consensus 2 ~v~~llD~SgSM~~~----~kl~~ak~a~~~l~~~l~~--~~d~~~l~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 75 (174)
T cd01454 2 AVTLLLDLSGSMRSD----RRIDVAKKAAVLLAEALEA--CGVPHAILGFTTDAGGRERVRWIKIKDFDESLHERARKRL 75 (174)
T ss_pred EEEEEEECCCCCCCC----cHHHHHHHHHHHHHHHHHH--cCCcEEEEEecCCCCCccceEEEEecCcccccchhHHHHH
Confidence 478999999999753 7999999999999877654 5689999999643 1 13334 222221 2333444
Q ss_pred hhhhCCCCcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCc----cC---HHHH---HHHHHhCCcEEEEEEecc
Q 014440 159 MGKLGCSGDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDP----GD---IMET---IQKCKESKIRCSVIGLSA 228 (424)
Q Consensus 159 ~~~~~~~G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp----~~---i~~~---i~~akk~~IrV~vIgLg~ 228 (424)
.. +.+.|+|.++.||..|.+.|...+ ..+++||+++++...+. ++ +.++ ++.+++.||+|++||+|.
T Consensus 76 ~~-~~~~g~T~~~~al~~a~~~l~~~~--~~~~~iiliTDG~~~~~~~~~~~~~~~~~~~~~~~~~~~~gi~v~~igig~ 152 (174)
T cd01454 76 AA-LSPGGNTRDGAAIRHAAERLLARP--EKRKILLVISDGEPNDLDYYEGNVFATEDALRAVIEARKLGIEVFGITIDR 152 (174)
T ss_pred Hc-cCCCCCCcHHHHHHHHHHHHhcCC--CcCcEEEEEeCCCcCcccccCcchhHHHHHHHHHHHHHhCCcEEEEEEecC
Confidence 43 356778999999999999998753 23455555544333221 12 3344 788899999999999998
Q ss_pred hH
Q 014440 229 EM 230 (424)
Q Consensus 229 e~ 230 (424)
+.
T Consensus 153 ~~ 154 (174)
T cd01454 153 DA 154 (174)
T ss_pred cc
Confidence 64
No 52
>cd01462 VWA_YIEM_type VWA YIEM type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if
Probab=99.37 E-value=2.8e-11 Score=107.79 Aligned_cols=134 Identities=13% Similarity=0.172 Sum_probs=91.8
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCHHHHHHHHhhhhCCCC
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSPESHIKALMGKLGCSG 166 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~~~~~~G 166 (424)
+++|+||+|+||.. .|+..++..+..++..... +.++++||.|.++......+...+....++.|.. +.+.|
T Consensus 2 ~v~illD~SgSM~~-----~k~~~a~~~~~~l~~~~~~--~~~~v~li~F~~~~~~~~~~~~~~~~~~~~~l~~-~~~~g 73 (152)
T cd01462 2 PVILLVDQSGSMYG-----APEEVAKAVALALLRIALA--ENRDTYLILFDSEFQTKIVDKTDDLEEPVEFLSG-VQLGG 73 (152)
T ss_pred CEEEEEECCCCCCC-----CHHHHHHHHHHHHHHHHHH--cCCcEEEEEeCCCceEEecCCcccHHHHHHHHhc-CCCCC
Confidence 68999999999963 4888999999989887764 3478999999644222222333455555555543 25678
Q ss_pred cchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecch
Q 014440 167 DSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAE 229 (424)
Q Consensus 167 ~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e 229 (424)
+|++..||..+...+.+.. ...+.||||+++.+..++..+.+..+.+++.+++|++||+|..
T Consensus 74 gT~l~~al~~a~~~l~~~~-~~~~~ivliTDG~~~~~~~~~~~~~~~~~~~~~~v~~~~~g~~ 135 (152)
T cd01462 74 GTDINKALRYALELIERRD-PRKADIVLITDGYEGGVSDELLREVELKRSRVARFVALALGDH 135 (152)
T ss_pred CcCHHHHHHHHHHHHHhcC-CCCceEEEECCCCCCCCCHHHHHHHHHHHhcCcEEEEEEecCC
Confidence 9999999999999997641 2223344444443333343444446666777899999999964
No 53
>cd01481 vWA_collagen_alpha3-VI-like VWA_collagen alpha 3(VI) like: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.
Probab=99.36 E-value=3.6e-11 Score=109.89 Aligned_cols=147 Identities=16% Similarity=0.120 Sum_probs=111.5
Q ss_pred ceEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCC--CHHHHHHHHhhhhC
Q 014440 86 RYLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGG--SPESHIKALMGKLG 163 (424)
Q Consensus 86 R~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~--d~~~~~~~L~~~~~ 163 (424)
++|+++||.|.||. +..++.+++.++.+++.|--.+...|+|||.| ++.+....+|.. +.++++++|.++.-
T Consensus 1 ~DivfllD~S~Si~-----~~~f~~~k~fi~~lv~~f~i~~~~~rVgvv~y-s~~~~~~~~l~~~~~~~~l~~~i~~i~~ 74 (165)
T cd01481 1 KDIVFLIDGSDNVG-----SGNFPAIRDFIERIVQSLDVGPDKIRVAVVQF-SDTPRPEFYLNTHSTKADVLGAVRRLRL 74 (165)
T ss_pred CCEEEEEeCCCCcC-----HHHHHHHHHHHHHHHhhccCCCCCcEEEEEEe-cCCeeEEEeccccCCHHHHHHHHHhccc
Confidence 48999999999995 46889999999999988765555689999999 488888888864 45677777776432
Q ss_pred CCC-cchHHHHHHHHHHHHcCCCC-----CCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEec-chHHHHHHH
Q 014440 164 CSG-DSSIQNALDLVHGLLNQIPS-----YGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLS-AEMFICKHL 236 (424)
Q Consensus 164 ~~G-~tsL~~AL~~Al~~L~~~p~-----~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg-~e~~iLq~i 236 (424)
..| +|..+.||..+...+...+. .+.+++|||++++.+. .++.+.++.|++.||.|++||+| .+..-|++|
T Consensus 75 ~~g~~t~t~~AL~~~~~~~f~~~~g~R~~~~~~kv~vviTdG~s~--d~~~~~a~~lr~~gv~i~~vG~~~~~~~eL~~i 152 (165)
T cd01481 75 RGGSQLNTGSALDYVVKNLFTKSAGSRIEEGVPQFLVLITGGKSQ--DDVERPAVALKRAGIVPFAIGARNADLAELQQI 152 (165)
T ss_pred CCCCcccHHHHHHHHHHhhcCccccCCccCCCCeEEEEEeCCCCc--chHHHHHHHHHHCCcEEEEEeCCcCCHHHHHHH
Confidence 334 47999999999887654321 1223566666554443 35788899999999999999999 677888888
Q ss_pred HHHh
Q 014440 237 CQET 240 (424)
Q Consensus 237 A~~T 240 (424)
|..-
T Consensus 153 as~p 156 (165)
T cd01481 153 AFDP 156 (165)
T ss_pred hCCC
Confidence 8544
No 54
>cd01457 vWA_ORF176_type VWA ORF176 type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses. In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most
Probab=99.34 E-value=2.8e-11 Score=113.28 Aligned_cols=149 Identities=15% Similarity=0.136 Sum_probs=102.0
Q ss_pred ceEEEEEeCCHhhhcCC--CCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCHHHHHHHHhhhhC
Q 014440 86 RYLYIVIDLSRAAAEMD--FRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSPESHIKALMGKLG 163 (424)
Q Consensus 86 R~lvlvLD~S~SM~~~D--~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~~~~ 163 (424)
|+++|+||.|+||...+ ..|+|+..+++.+..++.... +...+.++++.| ++.+..+.|++ ...+.+.+.+ +.
T Consensus 3 ~dvv~~ID~SgSM~~~~~~~~~~k~~~ak~~~~~l~~~~~-~~D~d~i~l~~f-~~~~~~~~~~~--~~~v~~~~~~-~~ 77 (199)
T cd01457 3 RDYTLLIDKSGSMAEADEAKERSRWEEAQESTRALARKCE-EYDSDGITVYLF-SGDFRRYDNVN--SSKVDQLFAE-NS 77 (199)
T ss_pred cCEEEEEECCCcCCCCCCCCCchHHHHHHHHHHHHHHHHH-hcCCCCeEEEEe-cCCccccCCcC--HHHHHHHHhc-CC
Confidence 68999999999999876 678999999999999986543 333467999998 47777777776 4444444433 35
Q ss_pred CCCcchHHHHHHHHHHHHcCC-CC---CCCcEEEEEEcCCCCCCccCHHHHH-HHHHh----CCcEEEEEEecch---HH
Q 014440 164 CSGDSSIQNALDLVHGLLNQI-PS---YGHREVLILYSALSTCDPGDIMETI-QKCKE----SKIRCSVIGLSAE---MF 231 (424)
Q Consensus 164 ~~G~tsL~~AL~~Al~~L~~~-p~---~~~reILvI~ss~~t~dp~~i~~~i-~~akk----~~IrV~vIgLg~e---~~ 231 (424)
+.|+|.+..+|+.|+..+... +. ...+.+|||++++...+...+.++| +.+++ .+|.+++|++|.+ ..
T Consensus 78 p~G~T~l~~~l~~a~~~~~~~~~~~~~~p~~~~vIiiTDG~~~d~~~~~~~i~~a~~~l~~~~~i~i~~v~vG~~~~~~~ 157 (199)
T cd01457 78 PDGGTNLAAVLQDALNNYFQRKENGATCPEGETFLVITDGAPDDKDAVERVIIKASDELDADNELAISFLQIGRDPAATA 157 (199)
T ss_pred CCCcCcHHHHHHHHHHHHHHHHhhccCCCCceEEEEEcCCCCCcHHHHHHHHHHHHHhhccccCceEEEEEeCCcHHHHH
Confidence 789999999999998654321 11 1113455555444433443433332 33222 4799999999975 45
Q ss_pred HHHHHHHH
Q 014440 232 ICKHLCQE 239 (424)
Q Consensus 232 iLq~iA~~ 239 (424)
.|+++++.
T Consensus 158 ~L~~ld~~ 165 (199)
T cd01457 158 FLKALDDQ 165 (199)
T ss_pred HHHHHhHH
Confidence 69999876
No 55
>COG4245 TerY Uncharacterized protein encoded in toxicity protection region of plasmid R478, contains von Willebrand factor (vWF) domain [General function prediction only]
Probab=98.77 E-value=1.2e-07 Score=87.81 Aligned_cols=159 Identities=13% Similarity=0.197 Sum_probs=101.5
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCC----CcEEEEEecCCceEEeeCCCCCHHHHHHHHh-hh
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPL----SQIGLVTVKDGVANCLTDLGGSPESHIKALM-GK 161 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~----sqlGII~~~~g~A~~lspLT~d~~~~~~~L~-~~ 161 (424)
-++|+||+|+||.. .++++...-++.+++++ .|+|. ..++||+| +|.|.++.|||.- ..+. ..
T Consensus 5 P~~lllDtSgSM~G-----e~IealN~Glq~m~~~L-kqdp~Ale~v~lsIVTF-~~~a~~~~pf~~~-----~nF~~p~ 72 (207)
T COG4245 5 PCYLLLDTSGSMIG-----EPIEALNAGLQMMIDTL-KQDPYALERVELSIVTF-GGPARVIQPFTDA-----ANFNPPI 72 (207)
T ss_pred CEEEEEecCccccc-----ccHHHHHHHHHHHHHHH-HhChhhhheeEEEEEEe-cCcceEEechhhH-----hhcCCCc
Confidence 57999999999986 58999999999999876 46775 46899999 5899999999742 1111 12
Q ss_pred hCCCCcchHHHHHHHHHHHHcCC-------CCCCCcEEEEEEcCCCCCCccCHHHHHH-HHHh--CCcEEEEEEecc---
Q 014440 162 LGCSGDSSIQNALDLVHGLLNQI-------PSYGHREVLILYSALSTCDPGDIMETIQ-KCKE--SKIRCSVIGLSA--- 228 (424)
Q Consensus 162 ~~~~G~tsL~~AL~~Al~~L~~~-------p~~~~reILvI~ss~~t~dp~~i~~~i~-~akk--~~IrV~vIgLg~--- 228 (424)
+...|+|+++.||..|+.++... +..--|-.++|+++++-.| +..+.+. ..++ ...+|-.+++|.
T Consensus 73 L~a~GgT~lGaAl~~a~d~Ie~~~~~~~a~~kgdyrP~vfLiTDG~PtD--~w~~~~~~~~~~~~~~k~v~a~~~G~~~a 150 (207)
T COG4245 73 LTAQGGTPLGAALTLALDMIEERKRKYDANGKGDYRPWVFLITDGEPTD--DWQAGAALVFQGERRAKSVAAFSVGVQGA 150 (207)
T ss_pred eecCCCCchHHHHHHHHHHHHHHHhhcccCCccccceEEEEecCCCcch--HHHhHHHHhhhcccccceEEEEEeccccc
Confidence 35679999999999999999753 1111234555554433222 1222211 1111 223455556654
Q ss_pred hHHHHHHHHHHhCCEEEEecChhhHHHHHHhcC
Q 014440 229 EMFICKHLCQETGGTYSVALDESHSKELILEHA 261 (424)
Q Consensus 229 e~~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~ 261 (424)
+...|+||++.-+ . +...+...|.+++.=+.
T Consensus 151 d~~~L~qit~~V~-~-~~t~d~~~f~~fFkW~S 181 (207)
T COG4245 151 DNKTLNQITEKVR-Q-FLTLDGLQFREFFKWLS 181 (207)
T ss_pred ccHHHHHHHHhhc-c-ccccchHHHHHHHHHHH
Confidence 4677777775542 2 23456677777764433
No 56
>PF10138 vWA-TerF-like: vWA found in TerF C terminus ; InterPro: IPR019303 This entry represents the N-terminal domain of a family of proteins that confer resistance to the metalloid element tellurium and its salts.
Probab=98.61 E-value=1.3e-06 Score=82.39 Aligned_cols=150 Identities=16% Similarity=0.216 Sum_probs=110.0
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCC-CHHHHHHHHhhhh---
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGG-SPESHIKALMGKL--- 162 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~-d~~~~~~~L~~~~--- 162 (424)
.++||||.|+||.. -++--+.+.+.+.+.-+.-. |+. ...|=++.| +.....+-++|. |.+..++.+....
T Consensus 3 rV~LVLD~SGSM~~-~yk~G~vQ~~~Er~lalA~~-~Dd--DG~i~v~~F-s~~~~~~~~vt~~~~~~~v~~~~~~~~~~ 77 (200)
T PF10138_consen 3 RVYLVLDISGSMRP-LYKDGTVQRVVERILALAAQ-FDD--DGEIDVWFF-STEFDRLPDVTLDNYEGYVDELHAGLPDW 77 (200)
T ss_pred EEEEEEeCCCCCch-hhhCccHHHHHHHHHHHHhh-cCC--CCceEEEEe-CCCCCcCCCcCHHHHHHHHHHHhcccccc
Confidence 58999999999974 34556788888777777754 443 467999999 588888889885 4566666664332
Q ss_pred CCCCcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecch-HHHHHHHHHHhC
Q 014440 163 GCSGDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAE-MFICKHLCQETG 241 (424)
Q Consensus 163 ~~~G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e-~~iLq~iA~~TG 241 (424)
.+-|+|+...+|+.++.......+......||+++++...+...+.+++..+.+..|-...||+|.+ -.+|+++.++.|
T Consensus 78 ~~~G~t~y~~vm~~v~~~y~~~~~~~~P~~VlFiTDG~~~~~~~~~~~i~~as~~pifwqFVgiG~~~f~fL~kLD~l~g 157 (200)
T PF10138_consen 78 GRMGGTNYAPVMEDVLDHYFKREPSDAPALVLFITDGGPDDRRAIEKLIREASDEPIFWQFVGIGDSNFGFLEKLDDLAG 157 (200)
T ss_pred CCCCCcchHHHHHHHHHHHhhcCCCCCCeEEEEEecCCccchHHHHHHHHhccCCCeeEEEEEecCCcchHHHHhhccCC
Confidence 4558899999999999998854222223444444444444666788999999999999999999975 589999999633
No 57
>PF03731 Ku_N: Ku70/Ku80 N-terminal alpha/beta domain; InterPro: IPR005161 The Ku heterodimer (composed of Ku70 P12956 from SWISSPROT and Ku80 P13010 from SWISSPROT) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the N-terminal alpha/beta domain. This domain only makes a small contribution to the dimer interface. The domain comprises a six stranded beta sheet of the Rossman fold [].; PDB: 1JEQ_A 1JEY_A.
Probab=98.57 E-value=1.1e-06 Score=83.37 Aligned_cols=139 Identities=17% Similarity=0.234 Sum_probs=92.4
Q ss_pred EEEEEeCCHhhhcCCCCC-ChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCc------------eEEeeCCCCCHHHH
Q 014440 88 LYIVIDLSRAAAEMDFRP-SRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGV------------ANCLTDLGGSPESH 154 (424)
Q Consensus 88 lvlvLD~S~SM~~~D~~P-~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~------------A~~lspLT~d~~~~ 154 (424)
++++||+|+||....-.. ..|..+++++..++.+..-.+|.+.+|||.|+... .+++.||+.-..+.
T Consensus 2 ~vflID~s~sM~~~~~~~~~~l~~al~~i~~~~~~ki~~~~kD~vgvvl~gt~~t~n~~~~~~~~~i~~l~~l~~~~~~~ 81 (224)
T PF03731_consen 2 TVFLIDVSPSMFEPSSESESPLEEALKAIEDLMQQKIISSPKDEVGVVLFGTDETNNPDEDSGYENIFVLQPLDPPSAER 81 (224)
T ss_dssp EEEEEE-SCGGGS-BTTCS-HHHHHHHHHHHHHHHHHHTT---EEEEEEES-SS-BST-TTT-STTEEEEEECC--BHHH
T ss_pred EEEEEECCHHHCCCCCCcchhHHHHHHHHHHHHHHHHcCCCCCeEEEEEEcCCCCCCcccccCCCceEEeecCCccCHHH
Confidence 799999999998554321 28999999999999999999999999999996222 23456666544455
Q ss_pred HHHHhhhhC----------CCCcchHHHHHHHHHHHHcC---CCCCCCcEEEEEEcCCCCC-CccCHHHHHHH-----HH
Q 014440 155 IKALMGKLG----------CSGDSSIQNALDLVHGLLNQ---IPSYGHREVLILYSALSTC-DPGDIMETIQK-----CK 215 (424)
Q Consensus 155 ~~~L~~~~~----------~~G~tsL~~AL~~Al~~L~~---~p~~~~reILvI~ss~~t~-dp~~i~~~i~~-----ak 215 (424)
+..|.+... .....++.+||-.|..+|.. ......|+|++++....-. +...+..++.. ++
T Consensus 82 l~~L~~~~~~~~~~~~~~~~~~~~~l~~al~v~~~~~~~~~~~~k~~~krI~l~Td~d~p~~~~~~~~~~~~~l~~~Dl~ 161 (224)
T PF03731_consen 82 LKELEELLKPGDKFENFFSGSDEGDLSDALWVASDMFRERTCKKKKNKKRIFLFTDNDGPHEDDDELERIIQKLKAKDLQ 161 (224)
T ss_dssp HHHHHTTSHHHHHHHHHC-SSS---HHHHHHHHHHHHHCHCTTS-ECEEEEEEEES-SSTTT-CCCHHHHHHHHHHHHHH
T ss_pred HHHHHHhhcccccccccCCCCCccCHHHHHHHHHHHHHHHhhcccCCCcEEEEEeCCCCCCCCHHHHHHHHHhhccccch
Confidence 566654332 24456899999999999985 2344567788887543323 45566666555 88
Q ss_pred hCCcEEEEEEe
Q 014440 216 ESKIRCSVIGL 226 (424)
Q Consensus 216 k~~IrV~vIgL 226 (424)
..+|.+.++.|
T Consensus 162 ~~~i~~~~~~l 172 (224)
T PF03731_consen 162 DNGIEIELFFL 172 (224)
T ss_dssp HHTEEEEEEEC
T ss_pred hcCcceeEeec
Confidence 99999999999
No 58
>cd01479 Sec24-like Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes of vesicular carriers within the endocytic and the biosynthetic pathways are COP- and clathrin-coated vesicles. Formation of COPII vesicles requires the ordered assembly of the coat built from several cytosolic components GTPase Sar1, complexes of Sec23-Sec24 and Sec13-Sec31. The process is initiated by the conversion of GDP to GTP by the GTPase Sar1 which then recruits the heterodimeric complex of Sec23 and Sec24. This heterodimeric complex generates the pre-budding complex. The final step leading to membrane deformation and budding of COPII-coated vesicles is carried by the heterodimeric complex Sec13-Sec31. The members of this CD belong to the Sec23-like family. Sec 24 is very similar to Sec23. The Sec23 and Sec24
Probab=98.45 E-value=1.6e-05 Score=77.35 Aligned_cols=152 Identities=17% Similarity=0.234 Sum_probs=101.6
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCC------------------
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLG------------------ 148 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT------------------ 148 (424)
..++|||+|..-.+. .=++.+++.++..++.+.+..|..+||||+|. ...+ ++.+.
T Consensus 5 ~~~FvIDvs~~a~~~----g~~~~~~~si~~~L~~lp~~~~~~~VgiITfd-~~v~-~y~l~~~~~~~q~~vv~dl~d~f 78 (244)
T cd01479 5 VYVFLIDVSYNAIKS----GLLATACEALLSNLDNLPGDDPRTRVGFITFD-STLH-FFNLKSSLEQPQMMVVSDLDDPF 78 (244)
T ss_pred EEEEEEEccHHHHhh----ChHHHHHHHHHHHHHhcCCCCCCeEEEEEEEC-CeEE-EEECCCCCCCCeEEEeeCccccc
Confidence 679999998765332 24678888899888876655477999999994 4332 22121
Q ss_pred ----C----CHH----HHHHHHhhh---h--CCCCcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccC-----
Q 014440 149 ----G----SPE----SHIKALMGK---L--GCSGDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGD----- 206 (424)
Q Consensus 149 ----~----d~~----~~~~~L~~~---~--~~~G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~----- 206 (424)
. +.. .+.+.|.++ . ....+.+++.||+.|..+|++. .++|++++++.-+..||.
T Consensus 79 ~P~~~~~lv~l~e~~~~i~~lL~~L~~~~~~~~~~~~c~G~Al~~A~~lL~~~----GGkIi~f~s~~pt~GpG~l~~~~ 154 (244)
T cd01479 79 LPLPDGLLVNLKESRQVIEDLLDQIPEMFQDTKETESALGPALQAAFLLLKET----GGKIIVFQSSLPTLGAGKLKSRE 154 (244)
T ss_pred CCCCcceeecHHHHHHHHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHhc----CCEEEEEeCCCCCcCCcccccCc
Confidence 0 111 111222222 1 1234689999999999999954 356777776543322221
Q ss_pred -------------------H-HHHHHHHHhCCcEEEEEEecc---hHHHHHHHHHHhCCEEEEec
Q 014440 207 -------------------I-METIQKCKESKIRCSVIGLSA---EMFICKHLCQETGGTYSVAL 248 (424)
Q Consensus 207 -------------------i-~~~i~~akk~~IrV~vIgLg~---e~~iLq~iA~~TGG~Y~~~~ 248 (424)
+ .+.+..+.+.+|-|++...+. +...+..+|+.|||..+...
T Consensus 155 ~~~~~~~~~e~~~~~p~~~fY~~la~~~~~~~isvDlF~~~~~~~dla~l~~l~~~TGG~v~~y~ 219 (244)
T cd01479 155 DPKLLSTDKEKQLLQPQTDFYKKLALECVKSQISVDLFLFSNQYVDVATLGCLSRLTGGQVYYYP 219 (244)
T ss_pred cccccCchhhhhhcCcchHHHHHHHHHHHHcCeEEEEEEccCcccChhhhhhhhhhcCceEEEEC
Confidence 2 257888999999999998875 46889999999999777544
No 59
>PF05762 VWA_CoxE: VWA domain containing CoxE-like protein; InterPro: IPR008912 This group of proteins contains a VWA type domain and the function of this family is unknown. It is found as part of a CO oxidising (Cox) system operon in several bacteria [].
Probab=98.41 E-value=4.4e-06 Score=80.04 Aligned_cols=125 Identities=19% Similarity=0.236 Sum_probs=84.2
Q ss_pred ceEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCC--CHHHHHHHHhhhh-
Q 014440 86 RYLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGG--SPESHIKALMGKL- 162 (424)
Q Consensus 86 R~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~--d~~~~~~~L~~~~- 162 (424)
+.+|+++|+|+||.. + ...+..|+..+..+.+ ++.++.|. .....+++.-. ++.+.+..+....
T Consensus 58 ~~lvvl~DvSGSM~~-------~---s~~~l~~~~~l~~~~~--~~~~f~F~-~~l~~vT~~l~~~~~~~~l~~~~~~~~ 124 (222)
T PF05762_consen 58 RRLVVLCDVSGSMAG-------Y---SEFMLAFLYALQRQFR--RVRVFVFS-TRLTEVTPLLRRRDPEEALARLSALVQ 124 (222)
T ss_pred ccEEEEEeCCCChHH-------H---HHHHHHHHHHHHHhCC--CEEEEEEe-eehhhhhhhhccCCHHHHHHHHHhhcc
Confidence 389999999999974 2 2234457777766665 89999995 44444444332 5555555554222
Q ss_pred CCCCcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCC-CCCCccCHHHHHHHHHhCCcEEEEEE
Q 014440 163 GCSGDSSIQNALDLVHGLLNQIPSYGHREVLILYSAL-STCDPGDIMETIQKCKESKIRCSVIG 225 (424)
Q Consensus 163 ~~~G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~-~t~dp~~i~~~i~~akk~~IrV~vIg 225 (424)
.-.|+|+|+.||+.+...+... .. .+.+|||+|+. .+.++....+.++.+++.+.+|..+.
T Consensus 125 ~~~GgTdi~~aL~~~~~~~~~~-~~-~~t~vvIiSDg~~~~~~~~~~~~l~~l~~r~~rviwLn 186 (222)
T PF05762_consen 125 SFGGGTDIGQALREFLRQYARP-DL-RRTTVVIISDGWDTNDPEPLAEELRRLRRRGRRVIWLN 186 (222)
T ss_pred CCCCccHHHHHHHHHHHHhhcc-cc-cCcEEEEEecccccCChHHHHHHHHHHHHhCCEEEEEC
Confidence 4679999999999999998742 23 44456665554 56566666678888999888775553
No 60
>cd01468 trunk_domain trunk domain. COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is known as the trunk domain and has an alpha/beta vWA fold and forms the dimer interface. Some members of this family possess a partial MIDAS motif that is a characteristic feature of most vWA domain proteins.
Probab=98.40 E-value=2.5e-05 Score=75.51 Aligned_cols=154 Identities=19% Similarity=0.283 Sum_probs=103.6
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCC-----------------
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGG----------------- 149 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~----------------- 149 (424)
..++|||+|..- ++..-++.+++.+...+..+.. ++..+||||+|. +.-+ +..+..
T Consensus 5 ~~vFvID~s~~a----i~~~~l~~~~~sl~~~l~~lp~-~~~~~igiITf~-~~V~-~~~~~~~~~~~~~~v~~dl~d~f 77 (239)
T cd01468 5 VFVFVIDVSYEA----IKEGLLQALKESLLASLDLLPG-DPRARVGLITYD-STVH-FYNLSSDLAQPKMYVVSDLKDVF 77 (239)
T ss_pred EEEEEEEcchHh----ccccHHHHHHHHHHHHHHhCCC-CCCcEEEEEEeC-CeEE-EEECCCCCCCCeEEEeCCCccCc
Confidence 679999999753 2245688899999999986542 577899999993 4332 222211
Q ss_pred -----C----HH----HHHHHHhhh---hC----CCCcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccC---
Q 014440 150 -----S----PE----SHIKALMGK---LG----CSGDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGD--- 206 (424)
Q Consensus 150 -----d----~~----~~~~~L~~~---~~----~~G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~--- 206 (424)
+ .. .+.+.|.++ .. ...+.+++.||+.|..+|+.. ....+|++++++.-+..||.
T Consensus 78 ~p~~~~~l~~~~e~~~~i~~~l~~l~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~--~~gGkI~~f~sg~pt~GpG~l~~ 155 (239)
T cd01468 78 LPLPDRFLVPLSECKKVIHDLLEQLPPMFWPVPTHRPERCLGPALQAAFLLLKGT--FAGGRIIVFQGGLPTVGPGKLKS 155 (239)
T ss_pred CCCcCceeeeHHHHHHHHHHHHHhhhhhccccCCCCCcccHHHHHHHHHHHHhhc--CCCceEEEEECCCCCCCCCcccc
Confidence 0 01 122222222 11 123579999999999999875 23567888886644433332
Q ss_pred ---------------------H-HHHHHHHHhCCcEEEEEEecch---HHHHHHHHHHhCCEEEEecC
Q 014440 207 ---------------------I-METIQKCKESKIRCSVIGLSAE---MFICKHLCQETGGTYSVALD 249 (424)
Q Consensus 207 ---------------------i-~~~i~~akk~~IrV~vIgLg~e---~~iLq~iA~~TGG~Y~~~~d 249 (424)
+ .+.+..+.+.+|-|++...+.+ ...++.+++.|||..+...+
T Consensus 156 ~~~~~~~~~~~e~~~~~~a~~fY~~la~~~~~~~isvdlF~~~~~~~dl~~l~~l~~~TGG~v~~y~~ 223 (239)
T cd01468 156 REDKEPIRSHDEAQLLKPATKFYKSLAKECVKSGICVDLFAFSLDYVDVATLKQLAKSTGGQVYLYDS 223 (239)
T ss_pred CcccccCCCccchhcccccHHHHHHHHHHHHHcCeEEEEEeccccccCHHHhhhhhhcCCceEEEeCC
Confidence 2 2567888999999999988864 68899999999998776543
No 61
>PRK10997 yieM hypothetical protein; Provisional
Probab=98.36 E-value=9.3e-06 Score=86.06 Aligned_cols=139 Identities=12% Similarity=0.144 Sum_probs=90.2
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCC--CHHHHHHHHhhhhCC
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGG--SPESHIKALMGKLGC 164 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~--d~~~~~~~L~~~~~~ 164 (424)
.++|+||+|+||... +...|+..+-.+..--. ....++++|.|.++. .. .++++ ....++..|.. ..
T Consensus 325 piII~VDtSGSM~G~-----ke~~AkalAaAL~~iAl--~q~dr~~li~Fs~~i-~~-~~l~~~~gl~~ll~fL~~--~f 393 (487)
T PRK10997 325 PFIVCVDTSGSMGGF-----NEQCAKAFCLALMRIAL--AENRRCYIMLFSTEV-VT-YELTGPDGLEQAIRFLSQ--SF 393 (487)
T ss_pred cEEEEEECCCCCCCC-----HHHHHHHHHHHHHHHHH--hcCCCEEEEEecCCc-ee-eccCCccCHHHHHHHHHH--hc
Confidence 799999999999622 33455554444443333 334789999996433 32 24443 34555566643 24
Q ss_pred CCcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCC-CCccCHHHHHHHHHh-CCcEEEEEEecc-hHHHHHHHHH
Q 014440 165 SGDSSIQNALDLVHGLLNQIPSYGHREVLILYSALST-CDPGDIMETIQKCKE-SKIRCSVIGLSA-EMFICKHLCQ 238 (424)
Q Consensus 165 ~G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t-~dp~~i~~~i~~akk-~~IrV~vIgLg~-e~~iLq~iA~ 238 (424)
.|+|++..+|..|+..+.+. .. .+..|||+|+... ..|..+.+.++.+++ .+.+++.+.||. ...-+.++.+
T Consensus 394 ~GGTDl~~aL~~al~~l~~~-~~-r~adIVVISDF~~~~~~eel~~~L~~Lk~~~~~rf~~l~i~~~~~p~l~~ifD 468 (487)
T PRK10997 394 RGGTDLAPCLRAIIEKMQGR-EW-FDADAVVISDFIAQRLPDELVAKVKELQRQHQHRFHAVAMSAHGKPGIMRIFD 468 (487)
T ss_pred CCCCcHHHHHHHHHHHHccc-cc-CCceEEEECCCCCCCChHHHHHHHHHHHHhcCcEEEEEEeCCCCCchHHHhcC
Confidence 78999999999999999764 22 3345555555432 224557788889887 899999999985 2334455554
No 62
>PF04811 Sec23_trunk: Sec23/Sec24 trunk domain; InterPro: IPR006896 COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger (IPR006895 from INTERPRO), an alpha/beta trunk domain, an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes the Sec23/24 alpha/beta trunk domain, which is formed from a single, approximately 250-residue segment plugged into the beta-barrel between strands beta-1 and beta-19. The trunk has an alpha/beta fold with a vWA topology, and it forms the dimer interface, primarily involving strand beta-14 on Sec23 and Sec24; in addition, the trunk domain of Sec23 contacts Sar1.; GO: 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EGD_A 2NUP_A 3EG9_A 3EFO_A 3EGX_A 2NUT_A 1PD0_A 1PD1_A 1M2V_B 1PCX_A ....
Probab=98.35 E-value=1.4e-05 Score=77.32 Aligned_cols=154 Identities=17% Similarity=0.267 Sum_probs=98.9
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCC-----------------
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGG----------------- 149 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~----------------- 149 (424)
..+++||+|..--+. ..++.+++.++..++.+. .++..+||||+| +..-+ +..|..
T Consensus 5 ~y~FvID~s~~av~~----g~~~~~~~sl~~~l~~l~-~~~~~~vgiitf-d~~V~-~y~l~~~~~~~~~~v~~dl~~~~ 77 (243)
T PF04811_consen 5 VYVFVIDVSYEAVQS----GLLQSLIESLKSALDSLP-GDERTRVGIITF-DSSVH-FYNLSSSLSQPQMIVVSDLDDPF 77 (243)
T ss_dssp EEEEEEE-SHHHHHH----THHHHHHHHHHHHGCTSS-TSTT-EEEEEEE-SSSEE-EEETTTTSSSTEEEEEHHTTSHH
T ss_pred EEEEEEECchhhhhc----cHHHHHHHHHHHHHHhcc-CCCCcEEEEEEe-CCEEE-EEECCCCcCCCcccchHHHhhcc
Confidence 679999999663222 478899999999997655 567899999999 44333 222221
Q ss_pred -------------CHHHH---HHHHhhhhC----CCCcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCcc----
Q 014440 150 -------------SPESH---IKALMGKLG----CSGDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPG---- 205 (424)
Q Consensus 150 -------------d~~~~---~~~L~~~~~----~~G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~---- 205 (424)
....+ ++.|..... ...+.+++.||+.|..+|+.. ....+|++++++.-+..||
T Consensus 78 ~p~~~~llv~~~e~~~~i~~ll~~L~~~~~~~~~~~~~~c~G~Al~~A~~ll~~~--~~gGkI~~F~s~~pt~G~Gg~l~ 155 (243)
T PF04811_consen 78 IPLPDGLLVPLSECRDAIEELLESLPSIFPETAGKRPERCLGSALSAALSLLSSR--NTGGKILVFTSGPPTYGPGGSLK 155 (243)
T ss_dssp SSTSSSSSEETTTCHHHHHHHHHHHHHHSTT-TTB-----HHHHHHHHHHHHHHH--TS-EEEEEEESS---SSSTTSS-
T ss_pred cCCcccEEEEhHHhHHHHHHHHHHhhhhcccccccCccccHHHHHHHHHHHHhcc--ccCCEEEEEeccCCCCCCCceec
Confidence 11122 233332211 224679999999999999943 2356788888764433331
Q ss_pred -----------------------CHHHHHHHHHhCCcEEEEEEecch---HHHHHHHHHHhCCEEEEecC
Q 014440 206 -----------------------DIMETIQKCKESKIRCSVIGLSAE---MFICKHLCQETGGTYSVALD 249 (424)
Q Consensus 206 -----------------------~i~~~i~~akk~~IrV~vIgLg~e---~~iLq~iA~~TGG~Y~~~~d 249 (424)
-+.+.+..+.+.+|.|++...+.+ ...|..+++.|||.-+...+
T Consensus 156 ~~~~~~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~~~~l~tl~~l~~~TGG~l~~y~~ 225 (243)
T PF04811_consen 156 KREDSSHYDTEKEKALLLPPANEFYKKLAEECSKQGISVDLFVFSSDYVDLATLGPLARYTGGSLYYYPN 225 (243)
T ss_dssp SBTTSCCCCHCTTHHCHSHSSSHHHHHHHHHHHHCTEEEEEEEECSS--SHHHHTHHHHCTT-EEEEETT
T ss_pred ccccccccccccchhhhccccchHHHHHHHHHHhcCCEEEEEeecCCCCCcHhHHHHHHhCceeEEEeCC
Confidence 134778899999999999999875 68999999999998776544
No 63
>COG2425 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=98.25 E-value=8.4e-06 Score=85.09 Aligned_cols=155 Identities=12% Similarity=0.066 Sum_probs=112.7
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceE--EeeCCCCCHHHHHHHHhhhhCC
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVAN--CLTDLGGSPESHIKALMGKLGC 164 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~--~lspLT~d~~~~~~~L~~~~~~ 164 (424)
.+++.||.|+||.. +..+.|+..+...++--+.+|. ++.++.|.+ ... .+++-..+.+++++.|.. ..
T Consensus 274 pvilllD~SGSM~G-----~~e~~AKAvalAl~~~alaenR--~~~~~lF~s-~~~~~el~~k~~~~~e~i~fL~~--~f 343 (437)
T COG2425 274 PVILLLDKSGSMSG-----FKEQWAKAVALALMRIALAENR--DCYVILFDS-EVIEYELYEKKIDIEELIEFLSY--VF 343 (437)
T ss_pred CEEEEEeCCCCcCC-----cHHHHHHHHHHHHHHHHHHhcc--ceEEEEecc-cceeeeecCCccCHHHHHHHHhh--hc
Confidence 68999999999975 5888888888888888777773 699999954 322 234444566666666654 35
Q ss_pred CCcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCH-HHHHHHHHhCCcEEEEEEecchH-HHHHHHHHHhCC
Q 014440 165 SGDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDI-METIQKCKESKIRCSVIGLSAEM-FICKHLCQETGG 242 (424)
Q Consensus 165 ~G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i-~~~i~~akk~~IrV~vIgLg~e~-~iLq~iA~~TGG 242 (424)
.|||++..||..|+..++..+-.. ..||+|+++....+ .++ ..+-+..++.+.++++|.+++.. +-|.+|.+.+
T Consensus 344 ~GGTD~~~~l~~al~~~k~~~~~~-adiv~ITDg~~~~~-~~~~~~v~e~~k~~~~rl~aV~I~~~~~~~l~~Isd~~-- 419 (437)
T COG2425 344 GGGTDITKALRSALEDLKSRELFK-ADIVVITDGEDERL-DDFLRKVKELKKRRNARLHAVLIGGYGKPGLMRISDHI-- 419 (437)
T ss_pred CCCCChHHHHHHHHHHhhcccccC-CCEEEEeccHhhhh-hHHHHHHHHHHHHhhceEEEEEecCCCCcccceeeeee--
Confidence 566999999999999999875444 67899988754322 233 35566667999999999999876 8888888876
Q ss_pred EEEEecChhhHHHHH
Q 014440 243 TYSVALDESHSKELI 257 (424)
Q Consensus 243 ~Y~~~~d~~~L~~lL 257 (424)
.|-+ ++.....++
T Consensus 420 i~~~--~~~~~~kv~ 432 (437)
T COG2425 420 IYRV--EPRDRVKVV 432 (437)
T ss_pred EEee--CcHHHhHHH
Confidence 4433 444444444
No 64
>TIGR00578 ku70 ATP-dependent DNA helicase ii, 70 kDa subunit (ku70). Proteins in this family are involved in non-homologous end joining, a process used for the repair of double stranded DNA breaks. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Cutoff does not detect the putative ku70 homologs in yeast.
Probab=98.12 E-value=7e-05 Score=81.56 Aligned_cols=142 Identities=13% Similarity=0.135 Sum_probs=102.3
Q ss_pred eEEEEEeCCHhhhcCCC---CCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCC---------ceEEeeCCCCCHHHH
Q 014440 87 YLYIVIDLSRAAAEMDF---RPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDG---------VANCLTDLGGSPESH 154 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~---~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g---------~A~~lspLT~d~~~~ 154 (424)
-|+++||+|+||..... ..++|..+++.+..++.+..-.+|.+.||||.|.-. ..+++.+|..-..+.
T Consensus 12 ailflIDvs~sM~~~~~~~~~~s~~~~al~~i~~l~q~kIis~~~D~vGivlfgT~~t~n~~~~~~i~v~~~L~~p~a~~ 91 (584)
T TIGR00578 12 SLIFLVDASKAMFEESQGEDELTPFDMSIQCIQSVYTSKIISSDKDLLAVVFYGTEKDKNSVNFKNIYVLQELDNPGAKR 91 (584)
T ss_pred EEEEEEECCHHHcCCCcCcCcCChHHHHHHHHHHHHHhcCCCCCCCeEEEEEEeccCCCCccCCCceEEEeeCCCCCHHH
Confidence 46999999999985321 258999999999999999999999999999999522 234567776544555
Q ss_pred HHHHhhhhCC-----------CCc-chHHHHHHHHHHHHcCC-CCCCCcEEEEEEcCCCCC-CccCH----HHHHHHHHh
Q 014440 155 IKALMGKLGC-----------SGD-SSIQNALDLVHGLLNQI-PSYGHREVLILYSALSTC-DPGDI----METIQKCKE 216 (424)
Q Consensus 155 ~~~L~~~~~~-----------~G~-tsL~~AL~~Al~~L~~~-p~~~~reILvI~ss~~t~-dp~~i----~~~i~~akk 216 (424)
+..|.++... .++ .+|.++|-.|..+|... +..++|+|+++++...-. +..+. ...++.+++
T Consensus 92 i~~L~~l~~~~~~~~~~~~~~~~~~~~l~daL~~~~~~f~~~~~k~~~kRI~lfTd~D~P~~~~~~~~~~a~~~a~dl~~ 171 (584)
T TIGR00578 92 ILELDQFKGDQGPKKFRDTYGHGSDYSLSEVLWVCANLFSDVQFRMSHKRIMLFTNEDNPHGNDSAKASRARTKAGDLRD 171 (584)
T ss_pred HHHHHHHhhccCccchhhccCCCCCCcHHHHHHHHHHHHHhcchhhcCcEEEEECCCCCCCCCchhHHHHHHHHHHHHHh
Confidence 5666544211 122 48999999999999863 345678888888643221 11111 224888999
Q ss_pred CCcEEEEEEecc
Q 014440 217 SKIRCSVIGLSA 228 (424)
Q Consensus 217 ~~IrV~vIgLg~ 228 (424)
.||.|..+.|..
T Consensus 172 ~gi~ielf~l~~ 183 (584)
T TIGR00578 172 TGIFLDLMHLKK 183 (584)
T ss_pred cCeEEEEEecCC
Confidence 999999998875
No 65
>PF06707 DUF1194: Protein of unknown function (DUF1194); InterPro: IPR010607 This family consists of several hypothetical Rhizobiales specific proteins of around 270 residues in length. The function of this family is unknown.
Probab=98.05 E-value=4.4e-05 Score=72.41 Aligned_cols=142 Identities=18% Similarity=0.262 Sum_probs=94.6
Q ss_pred eEEEEEeCCHhhhcCCCCCCh--HHHHHHHHHHHHHHHhccCCCCcEEEEEec-CC--ceEEeeCCC--CCH---HHHHH
Q 014440 87 YLYIVIDLSRAAAEMDFRPSR--MVVVAKQVEAFVREFFDQNPLSQIGLVTVK-DG--VANCLTDLG--GSP---ESHIK 156 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~R--L~~a~~~l~~Fi~~~~~qnP~sqlGII~~~-~g--~A~~lspLT--~d~---~~~~~ 156 (424)
.|||++|+|.||...++.=.| +..++.. .++++.++ ..|..+|+|-.|- +| ...++.|-| .+. +.+..
T Consensus 5 aLvLavDvS~SVD~~E~~lQ~~G~A~Al~d-p~V~~Ai~-~g~~g~Iav~~~eWsg~~~q~~~v~Wt~i~~~~da~a~A~ 82 (205)
T PF06707_consen 5 ALVLAVDVSGSVDADEYRLQREGYAAALRD-PEVIAAIL-SGPIGRIAVAVVEWSGPGRQRVVVPWTRIDSPADAEAFAA 82 (205)
T ss_pred eeeeeeeccCCCCHHHHHHHHHHHHHHHCC-HHHHHHHh-cCCCCeEEEEEEEecCCCCceEEeCCEEeCCHHHHHHHHH
Confidence 589999999999876652111 1111111 23444444 4677777766552 23 566677766 233 33445
Q ss_pred HHhhhh-CCCCcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCc-cCHHHHHHHHHhCCcEEEEEEecchH
Q 014440 157 ALMGKL-GCSGDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDP-GDIMETIQKCKESKIRCSVIGLSAEM 230 (424)
Q Consensus 157 ~L~~~~-~~~G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp-~~i~~~i~~akk~~IrV~vIgLg~e~ 230 (424)
.|...- ...+.|+|+.||..|..+|.+.|..+.|+||=|.|+..+++- .....+-..+...||.|+-+.++.+.
T Consensus 83 ~l~~~~r~~~~~Taig~Al~~a~~ll~~~~~~~~RrVIDvSGDG~~N~G~~p~~~ard~~~~~GitINgL~I~~~~ 158 (205)
T PF06707_consen 83 RLRAAPRRFGGRTAIGSALDFAAALLAQNPFECWRRVIDVSGDGPNNQGPRPVTSARDAAVAAGITINGLAILDDD 158 (205)
T ss_pred HHHhCCCCCCCCchHHHHHHHHHHHHHhCCCCCceEEEEECCCCCCCCCCCccHHHHHHHHHCCeEEeeeEecCCC
Confidence 554431 234569999999999999999987799999999986554332 33347788889999999999998653
No 66
>COG4867 Uncharacterized protein with a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=98.04 E-value=0.00012 Score=75.37 Aligned_cols=156 Identities=14% Similarity=0.170 Sum_probs=104.2
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHH---HHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCHHHHHHHHhhhh-
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQ---VEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSPESHIKALMGKL- 162 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~---l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~~~- 162 (424)
.+++.+|+|-||.... |+.-+|+. +-.+|.. +-|.+.+.+|+|+ ..|..+. +..|..+.
T Consensus 465 AvallvDtS~SM~~eG----Rw~PmKQtALALhHLv~T---rfrGD~l~~i~Fg-r~A~~v~---------v~eLt~l~~ 527 (652)
T COG4867 465 AVALLVDTSFSMVMEG----RWLPMKQTALALHHLVCT---RFRGDALQIIAFG-RYARTVT---------AAELTGLAG 527 (652)
T ss_pred ceeeeeeccHHHHHhc----cCCchHHHHHHHHHHHHh---cCCCcceEEEecc-chhcccC---------HHHHhcCCC
Confidence 6899999999997654 55555554 4445554 6678999999995 4444321 23333321
Q ss_pred CCCCcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCC---C-------------CccCHHHH---HHHHHhCCcEEEE
Q 014440 163 GCSGDSSIQNALDLVHGLLNQIPSYGHREVLILYSALST---C-------------DPGDIMET---IQKCKESKIRCSV 223 (424)
Q Consensus 163 ~~~G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t---~-------------dp~~i~~~---i~~akk~~IrV~v 223 (424)
.-..+|++..||.+|-..|++-++ ..+.||||+++..+ . ||..+..| +....+.||.|.+
T Consensus 528 v~eqgTNlhhaL~LA~r~l~Rh~~-~~~~il~vTDGePtAhle~~DG~~~~f~yp~DP~t~~~Tvr~~d~~~r~G~q~t~ 606 (652)
T COG4867 528 VYEQGTNLHHALALAGRHLRRHAG-AQPVVLVVTDGEPTAHLEDGDGTSVFFDYPPDPRTIAHTVRGFDDMARLGAQVTI 606 (652)
T ss_pred ccccccchHHHHHHHHHHHHhCcc-cCceEEEEeCCCccccccCCCCceEecCCCCChhHHHHHHHHHHHHHhccceeeE
Confidence 112369999999999999998643 34567777765322 1 22223333 5667889999999
Q ss_pred EEecch---HHHHHHHHHHhCCEEEEecChhhHHHHHHhc
Q 014440 224 IGLSAE---MFICKHLCQETGGTYSVALDESHSKELILEH 260 (424)
Q Consensus 224 IgLg~e---~~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~ 260 (424)
.-||.+ +.+++++|+.|+|+-+++.-..-=+.++.++
T Consensus 607 FrLg~DpgL~~Fv~qva~rv~G~vv~pdldglGaaVvgdy 646 (652)
T COG4867 607 FRLGSDPGLARFIDQVARRVQGRVVVPDLDGLGAAVVGDY 646 (652)
T ss_pred EeecCCHhHHHHHHHHHHHhCCeEEecCcchhhHHHHHHH
Confidence 999987 5799999999999988764333333444433
No 67
>smart00187 INB Integrin beta subunits (N-terminal portion of extracellular region). Portion of beta integrins that lies N-terminal to their EGF-like repeats. Integrins are cell adhesion molecules that mediate cell-extracellular matrix and cell-cell interactions. They contain both alpha and beta subunits. Beta integrins are proposed to have a von Willebrand factor type-A "insert" or "I" -like domain (although this remains to be confirmed).
Probab=98.02 E-value=0.00022 Score=74.17 Aligned_cols=165 Identities=18% Similarity=0.166 Sum_probs=111.6
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCce-------------------------
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVA------------------------- 141 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A------------------------- 141 (424)
+|++++|+|.||.. -|+..+.....+.+++-.-.+.-|+|+=+|-++..
T Consensus 101 DLYyLMDlS~SM~d------dl~~lk~lg~~L~~~m~~it~n~rlGfGsFVDK~v~P~~~t~p~~l~~PC~~~~~~c~p~ 174 (423)
T smart00187 101 DLYYLMDLSYSMKD------DLDNLKSLGDDLAREMKGLTSNFRLGFGSFVDKTVSPFVSTRPEKLENPCPNYNLTCEPP 174 (423)
T ss_pred ceEEEEeCCccHHH------HHHHHHHHHHHHHHHHHhcccCceeeEEEeecCccCCcccCCHHHhcCCCcCCCCCcCCC
Confidence 99999999999974 68888888888888888777888999988765421
Q ss_pred ---EEeeCCCCCHHHHHHHHhhhh------CCCCcchHHHHHHHHHHHHcCCC-CCCCcEEEEEEcCCCC----------
Q 014440 142 ---NCLTDLGGSPESHIKALMGKL------GCSGDSSIQNALDLVHGLLNQIP-SYGHREVLILYSALST---------- 201 (424)
Q Consensus 142 ---~~lspLT~d~~~~~~~L~~~~------~~~G~tsL~~AL~~Al~~L~~~p-~~~~reILvI~ss~~t---------- 201 (424)
.-+.|||.|...+.+.+.+.. .|.|+. .||..|.--=+... ...++++||++++...
T Consensus 175 f~f~~~L~LT~~~~~F~~~V~~~~iSgN~D~PEgG~---DAimQaaVC~~~IGWR~~a~rllv~~TDa~fH~AGDGkLaG 251 (423)
T smart00187 175 YGFKHVLSLTDDTDEFNEEVKKQRISGNLDAPEGGF---DAIMQAAVCTEQIGWREDARRLLVFSTDAGFHFAGDGKLAG 251 (423)
T ss_pred cceeeeccCCCCHHHHHHHHhhceeecCCcCCcccH---HHHHHHHhhccccccCCCceEEEEEEcCCCccccCCcceee
Confidence 134678889888888877542 244442 23433331112221 1346778888754221
Q ss_pred ----------------------CCccCHHHHHHHHHhCCcEEEEEEecc-hHHHHHHHHHHhCCEEEEe--cChhhHHHH
Q 014440 202 ----------------------CDPGDIMETIQKCKESKIRCSVIGLSA-EMFICKHLCQETGGTYSVA--LDESHSKEL 256 (424)
Q Consensus 202 ----------------------~dp~~i~~~i~~akk~~IrV~vIgLg~-e~~iLq~iA~~TGG~Y~~~--~d~~~L~~l 256 (424)
-|+..+-+..+.|++++|.+- .++.. ...+.+++++.-.|...-. .|.+.+-+|
T Consensus 252 Iv~PNDg~CHL~~~g~Yt~s~~~DYPSi~ql~~kL~e~nI~~I-FAVT~~~~~~Y~~Ls~lipgs~vg~Ls~DSsNIv~L 330 (423)
T smart00187 252 IVQPNDGQCHLDNNGEYTMSTTQDYPSIGQLNQKLAENNINPI-FAVTKKQVSLYKELSALIPGSSVGVLSEDSSNVVEL 330 (423)
T ss_pred EecCCCCcceeCCCCCcCccCcCCCCCHHHHHHHHHhcCceEE-EEEcccchhHHHHHHHhcCcceeeecccCcchHHHH
Confidence 266678899999999999643 33333 3578999999999988743 455555555
Q ss_pred HHhcC
Q 014440 257 ILEHA 261 (424)
Q Consensus 257 L~~~~ 261 (424)
+.+..
T Consensus 331 I~~aY 335 (423)
T smart00187 331 IKDAY 335 (423)
T ss_pred HHHHH
Confidence 54443
No 68
>cd01478 Sec23-like Sec23-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes of vesicular carriers within the endocytic and the biosynthetic pathways are COP- and clathrin-coated vesicles. Formation of COPII vesicles requires the ordered assembly of the coat built from several cytosolic components GTPase Sar1, complexes of Sec23-Sec24 and Sec13-Sec31. The process is initiated by the conversion of GDP to GTP by the GTPase Sar1 which then recruits the heterodimeric complex of Sec23 and Sec24. This heterodimeric complex generates the pre-budding complex. The final step leading to membrane deformation and budding of COPII-coated vesicles is carried by the heterodimeric complex Sec13-Sec31. The members of this CD belong to the Sec23-like family. Sec 23 is very similar to Sec24. The Sec23 and Sec24
Probab=97.86 E-value=0.00084 Score=66.34 Aligned_cols=92 Identities=16% Similarity=0.188 Sum_probs=63.4
Q ss_pred CcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCH------------------------------HHHHHHHH
Q 014440 166 GDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDI------------------------------METIQKCK 215 (424)
Q Consensus 166 G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i------------------------------~~~i~~ak 215 (424)
...+++.||..|..+|+..-.+...+|++++++.-|..||.+ .+.+..+.
T Consensus 139 ~~r~~G~Al~~A~~ll~~~~~~~gGki~~F~sg~pT~GpG~l~~r~~~~~~r~~~d~~~~~~~~~~~a~~fY~~la~~~~ 218 (267)
T cd01478 139 PLRCTGVALSIAVGLLEACFPNTGARIMLFAGGPCTVGPGAVVSTELKDPIRSHHDIDKDNAKYYKKAVKFYDSLAKRLA 218 (267)
T ss_pred CCCchHHHHHHHHHHHHhhcCCCCcEEEEEECCCCCCCCceeeccccccccccccccccchhhhhhhHHHHHHHHHHHHH
Confidence 357899999999999985422335678888876443333211 12455567
Q ss_pred hCCcEEEEEEecc---hHHHHHHHHHHhCCEEEEe--cChhhHHHHH
Q 014440 216 ESKIRCSVIGLSA---EMFICKHLCQETGGTYSVA--LDESHSKELI 257 (424)
Q Consensus 216 k~~IrV~vIgLg~---e~~iLq~iA~~TGG~Y~~~--~d~~~L~~lL 257 (424)
+.+|-|++...+. ++..++.+++.|||.-+.. -+..-|++-+
T Consensus 219 ~~~vsvDlF~~s~d~vglaem~~l~~~TGG~v~~~~~f~~~~f~~s~ 265 (267)
T cd01478 219 ANGHAVDIFAGCLDQVGLLEMKVLVNSTGGHVVLSDSFTTSIFKQSF 265 (267)
T ss_pred hCCeEEEEEeccccccCHHHHHHHHHhcCcEEEEeCCcchHHHHHHh
Confidence 8999999998875 4789999999999977754 3444455433
No 69
>PLN00162 transport protein sec23; Provisional
Probab=97.58 E-value=0.005 Score=69.23 Aligned_cols=96 Identities=19% Similarity=0.141 Sum_probs=69.1
Q ss_pred cchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCH------------------------------HHHHHHHHh
Q 014440 167 DSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDI------------------------------METIQKCKE 216 (424)
Q Consensus 167 ~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i------------------------------~~~i~~akk 216 (424)
..+++.||..|..+|...-.....+|++++++.-|..||.+ .+.+..+.+
T Consensus 261 ~r~tG~AL~vA~~lL~~~~~~~gGrI~~F~sgppT~GpG~v~~r~~~~~~rsh~di~k~~~~~~~~a~~fY~~la~~~~~ 340 (761)
T PLN00162 261 ARCTGAALSVAAGLLGACVPGTGARIMAFVGGPCTEGPGAIVSKDLSEPIRSHKDLDKDAAPYYKKAVKFYEGLAKQLVA 340 (761)
T ss_pred CccHHHHHHHHHHHHhhccCCCceEEEEEeCCCCCCCCceeecccccccccCccccccchhhhcchHHHHHHHHHHHHHH
Confidence 46899999999999986433345678888876543333321 135667888
Q ss_pred CCcEEEEEEecc---hHHHHHHHHHHhCCEEEEe--cChhhHHHHHHhcCC
Q 014440 217 SKIRCSVIGLSA---EMFICKHLCQETGGTYSVA--LDESHSKELILEHAP 262 (424)
Q Consensus 217 ~~IrV~vIgLg~---e~~iLq~iA~~TGG~Y~~~--~d~~~L~~lL~~~~~ 262 (424)
.||.|++...+. ++..++.+++.|||.-+.. -+...|++-|..++.
T Consensus 341 ~gisvDlF~~s~dqvglaem~~l~~~TGG~v~~~~sF~~~~f~~~l~r~~~ 391 (761)
T PLN00162 341 QGHVLDVFACSLDQVGVAEMKVAVERTGGLVVLAESFGHSVFKDSLRRVFE 391 (761)
T ss_pred cCceEEEEEccccccCHHHHhhhHhhcCcEEEEeCCcChHHHHHHHHHHhc
Confidence 999999998875 4789999999999977754 344457776666665
No 70
>KOG2353 consensus L-type voltage-dependent Ca2+ channel, alpha2/delta subunit [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=97.34 E-value=0.0016 Score=75.13 Aligned_cols=152 Identities=14% Similarity=0.216 Sum_probs=107.4
Q ss_pred ceEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCC---------CHHHHHH
Q 014440 86 RYLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGG---------SPESHIK 156 (424)
Q Consensus 86 R~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~---------d~~~~~~ 156 (424)
++++|++|+|+||.. .||..++..+...+..+.+ .+-+-|++| +..+..+.|-.. |.+.+.+
T Consensus 226 KdiviLlD~SgSm~g-----~~~~lak~tv~~iLdtLs~---~Dfvni~tf-~~~~~~v~pc~~~~lvqAt~~nk~~~~~ 296 (1104)
T KOG2353|consen 226 KDIVILLDVSGSMSG-----LRLDLAKQTVNEILDTLSD---NDFVNILTF-NSEVNPVSPCFNGTLVQATMRNKKVFKE 296 (1104)
T ss_pred cceEEEEeccccccc-----hhhHHHHHHHHHHHHhccc---CCeEEEEee-ccccCcccccccCceeecchHHHHHHHH
Confidence 389999999999975 5999999999988877644 378899998 588888876632 2233444
Q ss_pred HHhhhhCCCCcchHHHHHHHHHHHHcCCC--------CCCCcEEEEEEcCCCCCCccCHHHHHHHHH--hCCcEEEEEEe
Q 014440 157 ALMGKLGCSGDSSIQNALDLVHGLLNQIP--------SYGHREVLILYSALSTCDPGDIMETIQKCK--ESKIRCSVIGL 226 (424)
Q Consensus 157 ~L~~~~~~~G~tsL~~AL~~Al~~L~~~p--------~~~~reILvI~ss~~t~dp~~i~~~i~~ak--k~~IrV~vIgL 226 (424)
.+..+ .+.|.+.+..||+.|.+.|.... +.....|++|+++. +.+..++++.-. ...|||++..|
T Consensus 297 ~i~~l-~~k~~a~~~~~~e~aF~lL~~~n~s~~~~~~~~C~~~iml~tdG~----~~~~~~If~~yn~~~~~Vrvftfli 371 (1104)
T KOG2353|consen 297 AIETL-DAKGIANYTAALEYAFSLLRDYNDSRANTQRSPCNQAIMLITDGV----DENAKEIFEKYNWPDKKVRVFTFLI 371 (1104)
T ss_pred HHhhh-ccccccchhhhHHHHHHHHHHhccccccccccccceeeEEeecCC----cccHHHHHHhhccCCCceEEEEEEe
Confidence 44443 58899999999999999997531 12334456666332 234555555543 47799999999
Q ss_pred cchH---HHHHHHHHHhCCEEEEecChh
Q 014440 227 SAEM---FICKHLCQETGGTYSVALDES 251 (424)
Q Consensus 227 g~e~---~iLq~iA~~TGG~Y~~~~d~~ 251 (424)
|.+. .-+|-.|=.-.|-|..+.+-+
T Consensus 372 g~~~~~~~~~~wmac~n~gyy~~I~~~~ 399 (1104)
T KOG2353|consen 372 GDEVYDLDEIQWMACANKGYYVHIISIA 399 (1104)
T ss_pred cccccccccchhhhhhCCCceEeccchh
Confidence 9875 346667777778777665544
No 71
>PTZ00395 Sec24-related protein; Provisional
Probab=97.28 E-value=0.0045 Score=71.74 Aligned_cols=158 Identities=16% Similarity=0.209 Sum_probs=101.0
Q ss_pred hhhccccceEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEE---------------
Q 014440 79 RIQKGLIRYLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANC--------------- 143 (424)
Q Consensus 79 ~~r~GiiR~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~--------------- 143 (424)
+++.=+--+.+++||+|..--..- -+..+.+.|+.-+..+. .|..+||||+| |..-+.
T Consensus 946 ~~~~p~PP~YvFLIDVS~~AVkSG----Ll~tacesIK~sLDsL~--dpRTRVGIITF-DSsLHFYNLks~l~~~~~~~~ 1018 (1560)
T PTZ00395 946 QVKNMLPPYFVFVVECSYNAIYNN----ITYTILEGIRYAVQNVK--CPQTKIAIITF-NSSIYFYHCKGGKGVSGEEGD 1018 (1560)
T ss_pred cccCCCCCEEEEEEECCHHHHhhC----hHHHHHHHHHHHHhcCC--CCCcEEEEEEe-cCcEEEEecCccccccccccc
Confidence 444444458999999997765543 35566666776666643 46689999999 343321
Q ss_pred ------------e-------eCCC-C----CHH---HHHHH----Hhhhh--CCCCcchHHHHHHHHHHHHcCCCCCCCc
Q 014440 144 ------------L-------TDLG-G----SPE---SHIKA----LMGKL--GCSGDSSIQNALDLVHGLLNQIPSYGHR 190 (424)
Q Consensus 144 ------------l-------spLT-~----d~~---~~~~~----L~~~~--~~~G~tsL~~AL~~Al~~L~~~p~~~~r 190 (424)
+ .|+. . +.. +.++. |.+.. ....+++++.||+.|..+|+.. .+.+
T Consensus 1019 ~~~~l~qPQMLVVSDLDDPFLPlP~ddLLVnL~ESRevIe~LLDkLPemFt~t~~~esCLGSALqAA~~aLk~~--GGGG 1096 (1560)
T PTZ00395 1019 GGGGSGNHQVIVMSDVDDPFLPLPLEDLFFGCVEEIDKINTLIDTIKSVSTTMQSYGSCGNSALKIAMDMLKER--NGLG 1096 (1560)
T ss_pred ccccCCCceEEeecCCccCcCCCCccCeeechHHHHHHHHHHHHHHHHHhhccCCCcccHHHHHHHHHHHHHhc--CCCc
Confidence 1 1221 1 111 12222 22211 1235689999999999999975 2245
Q ss_pred EEEEEEcCCCCCCccC-------------------H-HHHHHHHHhCCcEEEEEEecch-----HHHHHHHHHHhCCEEE
Q 014440 191 EVLILYSALSTCDPGD-------------------I-METIQKCKESKIRCSVIGLSAE-----MFICKHLCQETGGTYS 245 (424)
Q Consensus 191 eILvI~ss~~t~dp~~-------------------i-~~~i~~akk~~IrV~vIgLg~e-----~~iLq~iA~~TGG~Y~ 245 (424)
+|+++.+++-+.-+|. + .+.+..+.+.+|-|++..++.. +..|..|++.|||.-+
T Consensus 1097 KIiVF~SSLPniGpGaLK~Re~~~KEk~Ll~pqd~FYK~LA~ECsk~qISVDLFLfSsqYvDVDVATLg~Lsr~TGGqly 1176 (1560)
T PTZ00395 1097 SICMFYTTTPNCGIGAIKELKKDLQENFLEVKQKIFYDSLLLDLYAFNISVDIFIISSNNVRVCVPSLQYVAQNTGGKIL 1176 (1560)
T ss_pred eEEEEEcCCCCCCCCcccccccccccccccccchHHHHHHHHHHHhcCCceEEEEccCcccccccccccchhcccceeEE
Confidence 7888877554333332 2 2467788899999999988753 4679999999999544
No 72
>PF11265 Med25_VWA: Mediator complex subunit 25 von Willebrand factor type A; InterPro: IPR021419 The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA domain which is this one, an SD2 domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This VWA or von Willebrand factor type A domain when bound to RAR and the histone acetyltransferase CBP is responsible for recruiting Med1 to the rest of the Mediator complex [].
Probab=97.26 E-value=0.028 Score=54.32 Aligned_cols=162 Identities=12% Similarity=0.105 Sum_probs=100.8
Q ss_pred hhccccceEEEEEeCCHhhhc--CCCCCChHHHHHHHHHHHHH------HHhccCCCCcEEEEEecCCceE-----EeeC
Q 014440 80 IQKGLIRYLYIVIDLSRAAAE--MDFRPSRMVVVAKQVEAFVR------EFFDQNPLSQIGLVTVKDGVAN-----CLTD 146 (424)
Q Consensus 80 ~r~GiiR~lvlvLD~S~SM~~--~D~~P~RL~~a~~~l~~Fi~------~~~~qnP~sqlGII~~~~g~A~-----~lsp 146 (424)
.+.+..++||+|||.+.+|.. .+++-+=|.- .++.|-. ++..++...++|||+|+....+ .-++
T Consensus 8 ~~~~~~~~vVfvvEgTAalgpy~~~Lkt~Yl~P---~le~f~~g~~~e~~~~~~~~~t~y~LVvf~t~d~~~~~~v~~~g 84 (226)
T PF11265_consen 8 ADQPPQAQVVFVVEGTAALGPYWNTLKTNYLDP---ILEYFNGGPIAERDFGGDYSNTEYGLVVFNTADCYPEPIVQRSG 84 (226)
T ss_pred cccCccceEEEEEecchhhhhhHHHHHHHHHHH---HHHHhcCCCcccccccccCCCceEEEEEEeccCCCcccceeccC
Confidence 344677899999999999953 1221112221 2222211 1112346688999999744222 2356
Q ss_pred CCCCHHHHHHHHhhhhCCCCc----chHHHHHHHHHHHHcCCC-------C-CCCcEEEEEEcCCCCC-------Cc--c
Q 014440 147 LGGSPESHIKALMGKLGCSGD----SSIQNALDLVHGLLNQIP-------S-YGHREVLILYSALSTC-------DP--G 205 (424)
Q Consensus 147 LT~d~~~~~~~L~~~~~~~G~----tsL~~AL~~Al~~L~~~p-------~-~~~reILvI~ss~~t~-------dp--~ 205 (424)
.|.|+..+++.|.++.-..|+ +.+..||..|+.++.... . ...|..|+|..|.-.. .+ .
T Consensus 85 ~T~~~~~fl~~L~~I~f~GGG~e~~a~iaEGLa~AL~~fd~~~~~r~~~~~~~~~khcILI~nSpP~~~p~~~~~~~~~~ 164 (226)
T PF11265_consen 85 PTSSPQKFLQWLDAIQFSGGGFESCAAIAEGLAEALQCFDDFKQMRQQQQQTDVQKHCILICNSPPYRLPVNECPQYSGK 164 (226)
T ss_pred CcCCHHHHHHHHHccCcCCCCcccchhHHHHHHHHHHHhcchhhhccccCcccccceEEEEeCCCCccccccCCCcccCC
Confidence 688999999999876322222 359999999999997421 1 1346777776542110 11 1
Q ss_pred CHHHHHHHHHhCCcEEEEEEecchHHHHHHHHHHhCCEEE
Q 014440 206 DIMETIQKCKESKIRCSVIGLSAEMFICKHLCQETGGTYS 245 (424)
Q Consensus 206 ~i~~~i~~akk~~IrV~vIgLg~e~~iLq~iA~~TGG~Y~ 245 (424)
.....+....+.+|.+++|+- -....|++|-+..+|.-.
T Consensus 165 ~~d~la~~~~~~~I~LSiisP-rklP~l~~Lfeka~~~~~ 203 (226)
T PF11265_consen 165 TCDQLAVLISERNISLSIISP-RKLPSLRSLFEKAKGNPR 203 (226)
T ss_pred CHHHHHHHHHhcCceEEEEcC-ccCHHHHHHHHhcCCCcc
Confidence 455667777899999999987 355677777777776433
No 73
>KOG1984 consensus Vesicle coat complex COPII, subunit SFB3 [Intracellular trafficking, secretion, and vesicular transport]
Probab=96.95 E-value=0.019 Score=64.03 Aligned_cols=152 Identities=16% Similarity=0.198 Sum_probs=101.5
Q ss_pred eEEEEEeCCHhhhcCCCCCChHH-HHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEee--------------------
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMV-VVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLT-------------------- 145 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~-~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~ls-------------------- 145 (424)
+.|+.||+|-.-.. |++. ++-+.++.-+..+....|.-+||||+| |..-+..-
T Consensus 419 afvFmIDVSy~Ai~-----~G~~~a~ce~ik~~l~~lp~~~p~~~Vgivtf-d~tvhFfnl~s~L~qp~mliVsdv~dvf 492 (1007)
T KOG1984|consen 419 AFVFMIDVSYNAIS-----NGAVKAACEAIKSVLEDLPREEPNIRVGIVTF-DKTVHFFNLSSNLAQPQMLIVSDVDDVF 492 (1007)
T ss_pred eEEEEEEeehhhhh-----cchHHHHHHHHHHHHhhcCccCCceEEEEEEe-cceeEeeccCccccCceEEEeecccccc
Confidence 88999999866543 3444 555677777776666778899999999 45444321
Q ss_pred -CCCC-------CHHHHHHHHhhhh----C--CCCcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCcc------
Q 014440 146 -DLGG-------SPESHIKALMGKL----G--CSGDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPG------ 205 (424)
Q Consensus 146 -pLT~-------d~~~~~~~L~~~~----~--~~G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~------ 205 (424)
||.. ..+.+++.|.... . -.-++.+++||+.|+..|+.. . .++++|+.+++.+.+-+
T Consensus 493 vPf~~g~~V~~~es~~~i~~lLd~Ip~mf~~sk~pes~~g~alqaa~lalk~~--~-gGKl~vF~s~Lpt~g~g~kl~~r 569 (1007)
T KOG1984|consen 493 VPFLDGLFVNPNESRKVIELLLDSIPTMFQDSKIPESVFGSALQAAKLALKAA--D-GGKLFVFHSVLPTAGAGGKLSNR 569 (1007)
T ss_pred cccccCeeccchHHHHHHHHHHHHhhhhhccCCCCchhHHHHHHHHHHHHhcc--C-CceEEEEecccccccCccccccc
Confidence 1111 1133444443221 1 234789999999999999986 2 34566666665543322
Q ss_pred --------------------CHHHHHHHHHhCCcEEEEEEecc---hHHHHHHHHHHhCCEEEEe
Q 014440 206 --------------------DIMETIQKCKESKIRCSVIGLSA---EMFICKHLCQETGGTYSVA 247 (424)
Q Consensus 206 --------------------~i~~~i~~akk~~IrV~vIgLg~---e~~iLq~iA~~TGG~Y~~~ 247 (424)
.+.+.++.+.+.+|.|++....+ ++..|-.+++.|||+-|+-
T Consensus 570 ~D~~l~~t~kek~l~~pq~~~y~~LA~e~v~~g~svDlF~t~~ayvDvAtlg~v~~~TgG~vy~Y 634 (1007)
T KOG1984|consen 570 DDRRLIGTDKEKNLLQPQDKTYTTLAKEFVESGCSVDLFLTPNAYVDVATLGVVPALTGGQVYKY 634 (1007)
T ss_pred chhhhhcccchhhccCcchhHHHHHHHHHHHhCceEEEEEcccceeeeeeecccccccCceeEEe
Confidence 13356888899999999888754 5788999999999976643
No 74
>COG2304 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=96.88 E-value=0.019 Score=58.55 Aligned_cols=153 Identities=19% Similarity=0.231 Sum_probs=110.5
Q ss_pred ceEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCC--CCHHHHHHHHhhhhC
Q 014440 86 RYLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLG--GSPESHIKALMGKLG 163 (424)
Q Consensus 86 R~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT--~d~~~~~~~L~~~~~ 163 (424)
.++.+++|.|.||.... +..++.....++.. .++.+.+.++++. +.+..+.|.+ .+...+..++.....
T Consensus 38 ~~~~~~~~~~~s~~~~~-----~~~~~~~~~~~v~~---~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~i~~~~~ 108 (399)
T COG2304 38 ANLTLAIDTSGSMTGAL-----LELAKSAAIELVNG---LNPGDLLSIVTFA-GSADVLIPPTGATNKESITAAIDQSLQ 108 (399)
T ss_pred cceEEEeccCCCccchh-----HHHHHHHHHHHhcc---cCCCCceEEEEec-CCcceecCcccccCHHHHHHHHhhhhc
Confidence 48999999999997643 55566666666765 4667889999996 5888888887 566777777877667
Q ss_pred CCCcchHHHHHHHHHHHHcCC-CCCCCcEEEEEEcCCCCC---CccCHHHHHHHHHhCCcEEEEEEecch--HHHHHHHH
Q 014440 164 CSGDSSIQNALDLVHGLLNQI-PSYGHREVLILYSALSTC---DPGDIMETIQKCKESKIRCSVIGLSAE--MFICKHLC 237 (424)
Q Consensus 164 ~~G~tsL~~AL~~Al~~L~~~-p~~~~reILvI~ss~~t~---dp~~i~~~i~~akk~~IrV~vIgLg~e--~~iLq~iA 237 (424)
+.|.+.+..++..+...+... +......+++++++.... |+..+....+...+.+|.++++|++.+ ...+..+.
T Consensus 109 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~tdg~~~~~~~d~~~~~~~~~~~~~~~i~~~~~g~~~~~n~~~~~~~~ 188 (399)
T COG2304 109 AGGATAVEASLSLAVELAAKALPRGTLNRILLLTDGENNLGLVDPSRLSALAKLAAGKGIVLDTLGLGDDVNEDELTGIA 188 (399)
T ss_pred cccccHHHHHHHHHHHHhhhcCCccceeeEeeeccCccccCCCCHHHHHHHhcccccCceEEEEEecccccchhhhhhhh
Confidence 888999999999999988763 223344566666654433 333334445555556999999999976 35566788
Q ss_pred HHhCCEEEEe
Q 014440 238 QETGGTYSVA 247 (424)
Q Consensus 238 ~~TGG~Y~~~ 247 (424)
..++|.+...
T Consensus 189 ~~~~g~l~~~ 198 (399)
T COG2304 189 AAANGNLAFI 198 (399)
T ss_pred hccCcccccc
Confidence 8887777654
No 75
>PF00362 Integrin_beta: Integrin, beta chain; InterPro: IPR002369 Integrins are the major metazoan receptors for cell adhesion to extracellular matrix proteins and, in vertebrates, also play important roles in certain cell-cell adhesions, make transmembrane connections to the cytoskeleton and activate many intracellular signalling pathways [, ]. The integrin receptors are composed of alpha and beta subunit heterodimers. Each subunit crosses the membrane once, with most of the polypeptide residing in the extracellular space, and has two short cytoplasmic domains. Some members of this family have EGF repeats at the C terminus and also have a vWA domain inserted within the integrin domain at the N terminus. Most integrins recognise relatively short peptide motifs, and in general require an acidic amino acid to be present. Ligand specificity depends upon both the alpha and beta subunits []. There are at least 18 types of alpha and 8 types of beta subunits recognised in humans []. Each alpha subunit tends to associate only with one type of beta subunit, but there are exceptions to this rule []. Each association of alpha and beta subunits has its own binding specificity and signalling properties. Many integrins require activation on the cell surface before they can bind ligands. Integrins frequently intercommunicate, and binding at one integrin receptor activate or inhibit another. The structure of unliganded alphaV beta3 showed the molecule to be folded, with the head bent over towards the C termini of the legs which would normally be inserted into the membrane []. The head comprises a beta propeller domain at the end terminus of the alphaV subunit and an I/A domain inserted into a loop on the top of the hybrid domain in the beta subunit. The I/A domain consists of a Rossman fold with a core of beta parallel sheets surrounded by amphipathic alpha helices. Integrins are important therapeutic targets in conditions such as atherosclerosis, thrombosis, cancer and asthma []. At the N terminus of the beta subunit is a cysteine-containing domain reminiscent of that found in presenillins and semaphorins, which has hence been termed the PSI domain. C-terminal to the PSI domain is an A-domain, which has been predicted to adopt a Rossmann fold similar to that of the alpha subunit, but with additional loops between the second and third beta strands []. The murine gene Pactolus shares significant similarity with the beta subunit [], but lacks either one or both of the inserted loops. The C-terminal portion of the beta subunit extracellular domain contains an internally disulphide-bonded cysteine-rich region, while the intracellular tail contains putative sites of interaction with a variety of intracellular signalling and cytoskeletal proteins, such as focal adhesion kinase and alpha-actinin respectively []. Integrin cytoplasmic domains are normally less than 50 amino acids in length, with the beta-subunit sequences exhibiting greater homology to each other than the alpha-subunit sequences. This is consistent with current evidence that the beta subunit is the principal site for binding of cytoskeletal and signalling molecules, whereas the alpha subunit has a regulatory role. The first 20 amino acids of the beta-subunit cytoplasmic domain are also alpha helical, but the final 25 residues are disordered and, apart from a turn that follows a conserved NPxY motif, appear to lack defined structure, suggesting that this is adopted on effector binding. The two membrane-proximal helices mediate the link between the subunits via a series of hydrophobic and electrostatic contacts. This entry represents the N-terminal portion of the extracellular region of integrin beta subunits.; GO: 0005488 binding, 0007155 cell adhesion, 0007160 cell-matrix adhesion; PDB: 3VI4_B 3VI3_B 2VDQ_B 3IJE_B 1M1X_B 2VDR_B 3NIF_B 3NID_D 1TYE_F 2Q6W_F ....
Probab=96.84 E-value=0.042 Score=57.94 Aligned_cols=160 Identities=14% Similarity=0.141 Sum_probs=96.6
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCc--------------------------
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGV-------------------------- 140 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~-------------------------- 140 (424)
+|++++|+|.||.. -|+..+....++++++-..-..-|+|+=+|-++.
T Consensus 104 DLYyLmDlS~Sm~d------dl~~l~~lg~~l~~~~~~it~~~~~GfGsfvdK~~~P~~~~~p~~l~~pc~~~~~~c~~~ 177 (426)
T PF00362_consen 104 DLYYLMDLSYSMKD------DLENLKSLGQDLAEEMRNITSNFRLGFGSFVDKPVMPFVSTTPEKLKNPCPSKNPNCQPP 177 (426)
T ss_dssp EEEEEEE-SGGGHH------HHHHHCCCCHHHHHHHHTT-SSEEEEEEEESSSSSTTTST-SSHCHHSTSCCTTS--B--
T ss_pred eEEEEeechhhhhh------hHHHHHHHHHHHHHHHHhcCccceEechhhcccccCCcccCChhhhcCcccccCCCCCCC
Confidence 99999999999974 5566666666666666666666889988886542
Q ss_pred --eEEeeCCCCCHHHHHHHHhhhh------CCCCcchHHHHHHHHHH--HHcCCCCCCCcEEEEEEcCCC----------
Q 014440 141 --ANCLTDLGGSPESHIKALMGKL------GCSGDSSIQNALDLVHG--LLNQIPSYGHREVLILYSALS---------- 200 (424)
Q Consensus 141 --A~~lspLT~d~~~~~~~L~~~~------~~~G~tsL~~AL~~Al~--~L~~~p~~~~reILvI~ss~~---------- 200 (424)
-.-+.|||.|...+.+.+.+.. .|.|+ |..-|..|++ .+.=. ...|++||++++..
T Consensus 178 ~~f~~~l~Lt~~~~~F~~~v~~~~is~n~D~PEgg--~dal~Qa~vC~~~igWr--~~a~~llv~~TD~~fH~agDg~l~ 253 (426)
T PF00362_consen 178 FSFRHVLSLTDDITEFNEEVNKQKISGNLDAPEGG--LDALMQAAVCQEEIGWR--NEARRLLVFSTDAGFHFAGDGKLA 253 (426)
T ss_dssp -SEEEEEEEES-HHHHHHHHHTS--B--SSSSBSH--HHHHHHHHH-HHHHT----STSEEEEEEEESS-B--TTGGGGG
T ss_pred eeeEEeecccchHHHHHHhhhhccccCCCCCCccc--cchheeeeecccccCcc--cCceEEEEEEcCCccccccccccc
Confidence 1234466778888888887542 24554 3333333444 23312 34677887764311
Q ss_pred ----------------------CCCccCHHHHHHHHHhCCcE-EEEEEecchHHHHHHHHHHhCCEEEEecCh--hhHHH
Q 014440 201 ----------------------TCDPGDIMETIQKCKESKIR-CSVIGLSAEMFICKHLCQETGGTYSVALDE--SHSKE 255 (424)
Q Consensus 201 ----------------------t~dp~~i~~~i~~akk~~Ir-V~vIgLg~e~~iLq~iA~~TGG~Y~~~~d~--~~L~~ 255 (424)
.-|+..+-+..+.+.+++|. |++| -.....+.+++++.-+|.....+.. +.+-+
T Consensus 254 gi~~pnd~~Chl~~~~~y~~~~~~DYPSv~ql~~~l~e~~i~~IFAV-t~~~~~~Y~~L~~~i~~s~vg~L~~dSsNIv~ 332 (426)
T PF00362_consen 254 GIVKPNDGKCHLDDNGMYTASTEQDYPSVGQLVRKLSENNINPIFAV-TKDVYSIYEELSNLIPGSSVGELSSDSSNIVQ 332 (426)
T ss_dssp T--S---SS--BSTTSBBGGGGCS----HHHHHHHHHHTTEEEEEEE-EGGGHHHHHHHHHHSTTEEEEEESTTSHTHHH
T ss_pred eeeecCCCceEECCCCcccccccccCCCHHHHHHHHHHcCCEEEEEE-chhhhhHHHHHhhcCCCceecccccCchhHHH
Confidence 12455667889999999986 4443 2334578999999999998865443 34444
Q ss_pred HH
Q 014440 256 LI 257 (424)
Q Consensus 256 lL 257 (424)
|+
T Consensus 333 LI 334 (426)
T PF00362_consen 333 LI 334 (426)
T ss_dssp HH
T ss_pred HH
Confidence 43
No 76
>KOG3768 consensus DEAD box RNA helicase [General function prediction only]
Probab=96.50 E-value=0.056 Score=58.21 Aligned_cols=186 Identities=18% Similarity=0.263 Sum_probs=104.7
Q ss_pred eEEEEEeCCHhhhcCCC-CCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCC-----------HHHH
Q 014440 87 YLYIVIDLSRAAAEMDF-RPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGS-----------PESH 154 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~-~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d-----------~~~~ 154 (424)
-+.++||+|.||..+-. .-+-|+.||.+++.|++..-. +| .. -|.-++++.+..- ...+
T Consensus 3 i~lFllDTS~SM~qrah~~~tylD~AKgaVEtFiK~R~r------~~--~~-~gdryml~TfeepP~~vk~~~~~~~a~~ 73 (888)
T KOG3768|consen 3 IFLFLLDTSGSMSQRAHPQFTYLDLAKGAVETFIKQRTR------VG--RE-TGDRYMLTTFEEPPKNVKVACEKLGAVV 73 (888)
T ss_pred eEEEEEecccchhhhccCCchhhHHHHHHHHHHHHHHhc------cc--cc-cCceEEEEecccCchhhhhHHhhcccHH
Confidence 47899999999986654 456788888888888875422 22 11 2444555444322 2446
Q ss_pred HHHHhhhhCCCCcchHHHHHHHHHHHHcC--C----CCCCCcE---------EEEEEcCCC-CCCcc---CH--------
Q 014440 155 IKALMGKLGCSGDSSIQNALDLVHGLLNQ--I----PSYGHRE---------VLILYSALS-TCDPG---DI-------- 207 (424)
Q Consensus 155 ~~~L~~~~~~~G~tsL~~AL~~Al~~L~~--~----p~~~~re---------ILvI~ss~~-t~dp~---~i-------- 207 (424)
++.|+++..+.|.+-+++++..|...|+- + ..++.+| ||+|+++.. +.-.| ++
T Consensus 74 ~~eik~l~a~~~s~~~~~~~t~AFdlLnlnR~qtGID~yGqGR~pf~lEP~~iI~iTDG~r~s~~~GV~~e~~Lpl~~p~ 153 (888)
T KOG3768|consen 74 IEEIKKLHAPYGSCQLHHAITEAFDLLNLNRVQTGIDGYGQGRLPFNLEPVTIILITDGGRYSGVAGVPIEFRLPLDPPF 153 (888)
T ss_pred HHHHHhhcCccchhhhhHHHHHHhhhhhhhhhhhcccccccccCccccCceEEEEEecCCccccccCCceeEEeccCCCC
Confidence 67777664566667788888889888852 1 2344332 455554411 10000 00
Q ss_pred --HHHHHHHHhCCcEEEEEEec---c-------------hHHHHHHHHHHhCCEEEEecChhhHHHHHHhcC--------
Q 014440 208 --METIQKCKESKIRCSVIGLS---A-------------EMFICKHLCQETGGTYSVALDESHSKELILEHA-------- 261 (424)
Q Consensus 208 --~~~i~~akk~~IrV~vIgLg---~-------------e~~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~-------- 261 (424)
.+.-+..-+..=|.+++.|- + +...+..+|+.|||+-|.+.+...|++-+..++
T Consensus 154 pGse~TkepFRWDQrlftlVlRiPgt~~~~~~qlt~Vp~Dds~IermCevTGGRSysV~Spr~lnqciesLvqkvQ~gVv 233 (888)
T KOG3768|consen 154 PGSEMTKEPFRWDQRLFTLVLRIPGTPYPTISQLTAVPIDDSVIERMCEVTGGRSYSVVSPRQLNQCIESLVQKVQYGVV 233 (888)
T ss_pred CccccccccchhhhhhheeeEecCCCCCccHhhhcCCCCCchhhHHhhhhcCCceeeeeCHHHHHHHHHHHHHhhccCeE
Confidence 01111111222344444442 1 236899999999999998877776665544332
Q ss_pred ------CCCccchhhhhhheeeecCC
Q 014440 262 ------PPPPAIAEFAIASLIKMGFP 281 (424)
Q Consensus 262 ------~pp~~~~~~~~~~Li~mGFP 281 (424)
.|-|+...+.+..+|.|-|-
T Consensus 234 v~FE~~~p~papi~s~~~~~Is~~fg 259 (888)
T KOG3768|consen 234 VRFECLPPIPAPITSDEVNLISMKFG 259 (888)
T ss_pred EEeeecCCCCCCcccCcccccccccc
Confidence 23222212334678887773
No 77
>PF09967 DUF2201: VWA-like domain (DUF2201); InterPro: IPR018698 This family of various hypothetical bacterial proteins has no known function.
Probab=96.42 E-value=0.016 Score=50.96 Aligned_cols=78 Identities=13% Similarity=0.241 Sum_probs=51.8
Q ss_pred EEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCHHHHHHHHhhh-hCCCC
Q 014440 88 LYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSPESHIKALMGK-LGCSG 166 (424)
Q Consensus 88 lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~~-~~~~G 166 (424)
|+++||+|+||...+ |.+.+..+..+.+.+ ..++-||.+ |........+.. ....+... ....|
T Consensus 1 i~vaiDtSGSis~~~-----l~~fl~ev~~i~~~~-----~~~v~vi~~-D~~v~~~~~~~~----~~~~~~~~~~~GgG 65 (126)
T PF09967_consen 1 IVVAIDTSGSISDEE-----LRRFLSEVAGILRRF-----PAEVHVIQF-DAEVQDVQVFRS----LEDELRDIKLKGGG 65 (126)
T ss_pred CEEEEECCCCCCHHH-----HHHHHHHHHHHHHhC-----CCCEEEEEE-CCEeeeeeEEec----ccccccccccCCCC
Confidence 589999999997643 555666666666554 256888887 666666666554 11112221 25678
Q ss_pred cchHHHHHHHHHHH
Q 014440 167 DSSIQNALDLVHGL 180 (424)
Q Consensus 167 ~tsL~~AL~~Al~~ 180 (424)
+|+++-+++-+.+.
T Consensus 66 GTdf~pvf~~~~~~ 79 (126)
T PF09967_consen 66 GTDFRPVFEYLEEN 79 (126)
T ss_pred CCcchHHHHHHHhc
Confidence 99999999987653
No 78
>cd01459 vWA_copine_like VWA Copine: Copines are phospholipid-binding proteins originally identified in paramecium. They are found in human and orthologues have been found in C. elegans and Arabidopsis Thaliana. None have been found in D. Melanogaster or S. Cereviciae. Phylogenetic distribution suggests that copines have been lost in some eukaryotes. No functional properties have been assigned to the VWA domains present in copines. The members of this subgroup contain a functional MIDAS motif based on their preferential binding to magnesium and manganese. However, the MIDAS motif is not totally conserved, in most cases the MIDAS consists of the sequence DxTxS instead of the motif DxSxS that is found in most cases. The C2 domains present in copines mediate phospholipid binding.
Probab=96.22 E-value=0.14 Score=50.40 Aligned_cols=155 Identities=13% Similarity=0.153 Sum_probs=97.0
Q ss_pred hccccceEEEEEeCCHhhhcC----------CCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCce--EEeeCCC
Q 014440 81 QKGLIRYLYIVIDLSRAAAEM----------DFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVA--NCLTDLG 148 (424)
Q Consensus 81 r~GiiR~lvlvLD~S~SM~~~----------D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A--~~lspLT 148 (424)
+-|.--+++++||.+.|=... --.||-.+.|+..+-.-+..|-++ .++-+..|++... ..++++-
T Consensus 27 ~~G~~~nl~vaIDfT~SNg~p~~~~SLHy~~~~~~N~Yq~aI~~vg~il~~yD~D---~~ip~~GFGa~~~~~~~v~~~f 103 (254)
T cd01459 27 SAGLESNLIVAIDFTKSNGWPGEKRSLHYISPGRLNPYQKAIRIVGEVLQPYDSD---KLIPAFGFGAIVTKDQSVFSFF 103 (254)
T ss_pred hCCCeeeEEEEEEeCCCCCCCCCCCCcccCCCCCccHHHHHHHHHHHHHHhcCCC---CceeeEeecccCCCCCcccccc
Confidence 445555999999999983211 114688889999988888877554 5788998864211 1123331
Q ss_pred -CC--------HHHHHHHHhhh---hCCCCcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHh
Q 014440 149 -GS--------PESHIKALMGK---LGCSGDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKE 216 (424)
Q Consensus 149 -~d--------~~~~~~~L~~~---~~~~G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk 216 (424)
++ .+.++++-+.. ....|.|.+.-.|..|.+.-++....+.--||+|++++.-.|.....++|-.|.+
T Consensus 104 ~~~~~~p~~~Gi~gvl~aY~~~l~~v~lsGpT~fapvI~~a~~~a~~~~~~~~Y~VLLIiTDG~i~D~~~t~~aIv~AS~ 183 (254)
T cd01459 104 PGYSESPECQGFEGVLRAYREALPNVSLSGPTNFAPVIRAAANIAKASNSQSKYHILLIITDGEITDMNETIKAIVEASK 183 (254)
T ss_pred CCCCCCCcccCHHHHHHHHHHHhceeeecCcchHHHHHHHHHHHHHHhcCCCceEEEEEECCCCcccHHHHHHHHHHHhc
Confidence 11 13444443322 2467889999988888887765422222356777665544444444566666777
Q ss_pred CCcEEEEEEecch-HHHHHHHHH
Q 014440 217 SKIRCSVIGLSAE-MFICKHLCQ 238 (424)
Q Consensus 217 ~~IrV~vIgLg~e-~~iLq~iA~ 238 (424)
.-|-|-+||+|.. -..|+++-.
T Consensus 184 ~PlSIiiVGVGd~~F~~M~~LD~ 206 (254)
T cd01459 184 YPLSIVIVGVGDGPFDAMERLDD 206 (254)
T ss_pred CCeEEEEEEeCCCChHHHHHhcC
Confidence 7788888888854 456777664
No 79
>COG5028 Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]
Probab=95.86 E-value=0.13 Score=56.91 Aligned_cols=149 Identities=18% Similarity=0.280 Sum_probs=94.5
Q ss_pred eEEEEEeCCHhhhcCCCCCChH-HHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCH--------------
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRM-VVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSP-------------- 151 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL-~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~-------------- 151 (424)
+.|+.||+|-.-.. +|+ .++.+.+.+=+..+.+-.|..+||||.| |..-+.+.+..+..
T Consensus 278 ~yvFlIDVS~~a~~-----~g~~~a~~r~Il~~l~~~~~~dpr~kIaii~f-D~sl~ffk~s~d~~~~~~~vsdld~pFl 351 (861)
T COG5028 278 VYVFLIDVSFEAIK-----NGLVKAAIRAILENLDQIPNFDPRTKIAIICF-DSSLHFFKLSPDLDEQMLIVSDLDEPFL 351 (861)
T ss_pred EEEEEEEeehHhhh-----cchHHHHHHHHHhhccCCCCCCCcceEEEEEE-cceeeEEecCCCCccceeeecccccccc
Confidence 89999999954332 344 3556666666655556668899999999 45555444322220
Q ss_pred -----------HHH---HHHHhh----hhCC--CCcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCC----------
Q 014440 152 -----------ESH---IKALMG----KLGC--SGDSSIQNALDLVHGLLNQIPSYGHREVLILYSALST---------- 201 (424)
Q Consensus 152 -----------~~~---~~~L~~----~~~~--~G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t---------- 201 (424)
+.. ++.|-. .... .-...++.||+.|...+... .++|+++++++-+
T Consensus 352 Pf~s~~fv~pl~~~k~~~etLl~~~~~If~d~~~pk~~~G~aLk~a~~l~g~~----GGkii~~~stlPn~G~Gkl~~r~ 427 (861)
T COG5028 352 PFPSGLFVLPLKSCKQIIETLLDRVPRIFQDNKSPKNALGPALKAAKSLIGGT----GGKIIVFLSTLPNMGIGKLQLRE 427 (861)
T ss_pred cCCcchhcccHHHHHHHHHHHHHHhhhhhcccCCCccccCHHHHHHHHHhhcc----CceEEEEeecCCCcccccccccc
Confidence 011 111111 1111 23468999999999988764 4456777654222
Q ss_pred --------CCccCHHHHHHHHHhCCcEEEEEEecc---hHHHHHHHHHHhCCEEE
Q 014440 202 --------CDPGDIMETIQKCKESKIRCSVIGLSA---EMFICKHLCQETGGTYS 245 (424)
Q Consensus 202 --------~dp~~i~~~i~~akk~~IrV~vIgLg~---e~~iLq~iA~~TGG~Y~ 245 (424)
|+.+=+.+....+.|.+|.|++-...+ ++..|-.+++.|||+-+
T Consensus 428 d~e~~ll~c~d~fYk~~a~e~~k~gIsvd~Flt~~~yidvaTls~l~~~T~G~~~ 482 (861)
T COG5028 428 DKESSLLSCKDSFYKEFAIECSKVGISVDLFLTSEDYIDVATLSHLCRYTGGQTY 482 (861)
T ss_pred cchhhhccccchHHHHHHHHHHHhcceEEEEeccccccchhhhcchhhccCcceE
Confidence 221112355778889999999888765 58899999999999654
No 80
>KOG1985 consensus Vesicle coat complex COPII, subunit SEC24/subunit SFB2 [Intracellular trafficking, secretion, and vesicular transport]
Probab=95.86 E-value=0.16 Score=56.67 Aligned_cols=148 Identities=22% Similarity=0.326 Sum_probs=96.1
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCH---------------
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSP--------------- 151 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~--------------- 151 (424)
-.+++||+|-+-.+. --|+.+.+.+.+=++.+. .+|..|||+|+| |..-+... +.++.
T Consensus 296 vy~FliDVS~~a~ks----G~L~~~~~slL~~LD~lp-gd~Rt~igfi~f-Ds~ihfy~-~~~~~~qp~mm~vsdl~d~f 368 (887)
T KOG1985|consen 296 VYVFLIDVSISAIKS----GYLETVARSLLENLDALP-GDPRTRIGFITF-DSTIHFYS-VQGDLNQPQMMIVSDLDDPF 368 (887)
T ss_pred eEEEEEEeehHhhhh----hHHHHHHHHHHHhhhcCC-CCCcceEEEEEe-eceeeEEe-cCCCcCCCceeeeccccccc
Confidence 679999999775442 257778888887777666 678899999999 44443321 11110
Q ss_pred ------------------HHHHHHHhhhhC--CCCcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCC--------C-
Q 014440 152 ------------------ESHIKALMGKLG--CSGDSSIQNALDLVHGLLNQIPSYGHREVLILYSALST--------C- 202 (424)
Q Consensus 152 ------------------~~~~~~L~~~~~--~~G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t--------~- 202 (424)
++.++.|..... -.-+.+|+.||+.|..+|... .++|+++.+++-+ .
T Consensus 369 lp~pd~lLv~L~~ck~~i~~lL~~lp~~F~~~~~t~~alGpALkaaf~li~~~----GGri~vf~s~lPnlG~G~L~~rE 444 (887)
T KOG1985|consen 369 LPMPDSLLVPLKECKDLIETLLKTLPEMFQDTRSTGSALGPALKAAFNLIGST----GGRISVFQSTLPNLGAGKLKPRE 444 (887)
T ss_pred cCCchhheeeHHHHHHHHHHHHHHHHHHHhhccCcccccCHHHHHHHHHHhhc----CCeEEEEeccCCCCCcccccccc
Confidence 112222222221 223579999999999999875 3467777764321 1
Q ss_pred Ccc---------------CHH-HHHHHHHhCCcEEEEEEecc---hHHHHHHHHHHhCCEEE
Q 014440 203 DPG---------------DIM-ETIQKCKESKIRCSVIGLSA---EMFICKHLCQETGGTYS 245 (424)
Q Consensus 203 dp~---------------~i~-~~i~~akk~~IrV~vIgLg~---e~~iLq~iA~~TGG~Y~ 245 (424)
||. ++. +-+-.+.+.+|.|+.-.+.. ++..|..|++-|||.-+
T Consensus 445 dp~~~~s~~~~qlL~~~t~FYK~~a~~cs~~qI~VDlFl~s~qY~DlAsLs~LskySgG~~y 506 (887)
T KOG1985|consen 445 DPNVRSSDEDSQLLSPATDFYKDLALECSKSQICVDLFLFSEQYTDLASLSCLSKYSGGQVY 506 (887)
T ss_pred ccccccchhhhhccCCCchHHHHHHHHhccCceEEEEEeecccccchhhhhccccccCceeE
Confidence 110 122 33455678999999999975 58999999999999533
No 81
>KOG1986 consensus Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking, secretion, and vesicular transport]
Probab=95.79 E-value=0.58 Score=51.56 Aligned_cols=163 Identities=16% Similarity=0.203 Sum_probs=102.1
Q ss_pred EEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCC-----------C----HH
Q 014440 88 LYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGG-----------S----PE 152 (424)
Q Consensus 88 lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~-----------d----~~ 152 (424)
.++|||. -| .+.+|+..++.+..++.-+ .+...||+|+| |+--.+..|+. + .+
T Consensus 124 f~fVvDt--c~-----~eeeL~~LkssL~~~l~lL---P~~alvGlItf--g~~v~v~el~~~~~sk~~VF~G~ke~s~~ 191 (745)
T KOG1986|consen 124 FVFVVDT--CM-----DEEELQALKSSLKQSLSLL---PENALVGLITF--GTMVQVHELGFEECSKSYVFSGNKEYSAK 191 (745)
T ss_pred EEEEEee--cc-----ChHHHHHHHHHHHHHHhhC---CCcceEEEEEe--cceEEEEEcCCCcccceeEEeccccccHH
Confidence 3677776 33 2479999999999988653 34477999999 44444555521 1 00
Q ss_pred HHHHH------------------------------Hhhh---hC------CCCc---chHHHHHHHHHHHHcCCCCCCCc
Q 014440 153 SHIKA------------------------------LMGK---LG------CSGD---SSIQNALDLVHGLLNQIPSYGHR 190 (424)
Q Consensus 153 ~~~~~------------------------------L~~~---~~------~~G~---tsL~~AL~~Al~~L~~~p~~~~r 190 (424)
.+.+. |.++ +. +.|- -+.+.||..|..+|...-.....
T Consensus 192 q~~~~L~~~~~~~~~~~~~~~~~rFL~P~~~c~~~L~~lle~L~~d~wpV~~g~Rp~RcTG~Al~iA~~Ll~~c~p~~g~ 271 (745)
T KOG1986|consen 192 QLLDLLGLSGGAGKGSENQSASNRFLLPAQECEFKLTNLLEELQPDPWPVPPGHRPLRCTGVALSIASGLLEGCFPNTGA 271 (745)
T ss_pred HHHHHhcCCcccccCCcccccchhhhccHHHHHHHHHHHHHHhcCCCCCCCCCCCcccchhHHHHHHHHHhcccCCCCcc
Confidence 01000 1111 11 2231 47889999999999875334455
Q ss_pred EEEEEEcCCCCCCccC------------------------------HHHHHHHHHhCCcEEEEEEecch---HHHHHHHH
Q 014440 191 EVLILYSALSTCDPGD------------------------------IMETIQKCKESKIRCSVIGLSAE---MFICKHLC 237 (424)
Q Consensus 191 eILvI~ss~~t~dp~~------------------------------i~~~i~~akk~~IrV~vIgLg~e---~~iLq~iA 237 (424)
+|+.++++.-|.-||- +...++.+..+|..|++.+=+-+ +..+|.++
T Consensus 272 rIv~f~gGPcT~GpG~vv~~el~~piRshhdi~~d~a~y~kKa~KfY~~La~r~~~~ghvlDifa~~lDQvGi~EMk~l~ 351 (745)
T KOG1986|consen 272 RIVLFAGGPCTRGPGTVVSRELKEPIRSHHDIEKDNAPYYKKAIKFYEKLAERLANQGHVLDIFAAALDQVGILEMKPLV 351 (745)
T ss_pred eEEEeccCCCCcCCceecchhhcCCCcCcccccCcchHHHHHHHHHHHHHHHHHHhCCceEeeeeeeccccchHHHHHHh
Confidence 6777777644333331 12456777788888777766543 57899999
Q ss_pred HHhCCEEEEecCh--hhHHHHHHhcCC
Q 014440 238 QETGGTYSVALDE--SHSKELILEHAP 262 (424)
Q Consensus 238 ~~TGG~Y~~~~d~--~~L~~lL~~~~~ 262 (424)
+.|||.-....+- +-|+.-+..++.
T Consensus 352 ~~TGG~lvl~dsF~~s~Fk~sfqR~f~ 378 (745)
T KOG1986|consen 352 ESTGGVLVLGDSFNTSIFKQSFQRIFT 378 (745)
T ss_pred hcCCcEEEEecccchHHHHHHHHHHhc
Confidence 9999987765443 457777777765
No 82
>TIGR01651 CobT cobaltochelatase, CobT subunit. This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit, with a MW ~70 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobS (TIGR01650) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobT gene product, the P. denitrificans gene symbol is not used in the name of this model.
Probab=95.25 E-value=0.41 Score=52.13 Aligned_cols=78 Identities=18% Similarity=0.229 Sum_probs=51.0
Q ss_pred HHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCC-------ccC-----HHHHHHHHHhC-CcEEEEEEecchHHHHHHHH
Q 014440 171 QNALDLVHGLLNQIPSYGHREVLILYSALSTCD-------PGD-----IMETIQKCKES-KIRCSVIGLSAEMFICKHLC 237 (424)
Q Consensus 171 ~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~d-------p~~-----i~~~i~~akk~-~IrV~vIgLg~e~~iLq~iA 237 (424)
+.||.-|...|... ...++||+++|++.-.| +++ +..+|+...+. +|.+-.||||.++.-
T Consensus 499 GeAl~wa~~rL~~R--~e~rKiL~ViSDG~P~D~~TlsvN~~~~l~~hLr~vi~~~e~~~~vel~aigIg~Dv~r----- 571 (600)
T TIGR01651 499 GEALMWAHQRLIAR--PEQRRILMMISDGAPVDDSTLSVNPGNYLERHLRAVIEEIETRSPVELLAIGIGHDVTR----- 571 (600)
T ss_pred hHHHHHHHHHHhcC--cccceEEEEEeCCCcCCccccccCchhHHHHHHHHHHHHHhccCCceEEEeeccccHHH-----
Confidence 67899999888876 34678998887643322 232 33678888775 899999999988421
Q ss_pred HHhCCEEEEecChhhHHHHH
Q 014440 238 QETGGTYSVALDESHSKELI 257 (424)
Q Consensus 238 ~~TGG~Y~~~~d~~~L~~lL 257 (424)
.- ..++.+.+.+.|...+
T Consensus 572 -~Y-~~~v~i~~~~eL~~~~ 589 (600)
T TIGR01651 572 -YY-RRAVTIVDAEELAGAM 589 (600)
T ss_pred -Hc-cccceecCHHHHHHHH
Confidence 11 2344555655554443
No 83
>COG3552 CoxE Protein containing von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=95.17 E-value=0.15 Score=52.41 Aligned_cols=118 Identities=12% Similarity=0.138 Sum_probs=65.8
Q ss_pred ceEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCC--CCHHHHHHHHhhhh-
Q 014440 86 RYLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLG--GSPESHIKALMGKL- 162 (424)
Q Consensus 86 R~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT--~d~~~~~~~L~~~~- 162 (424)
+.+|+++|+|+||. .+.. ....|++..-.+.+.++ +..|. ..-..++++- .|++.-++.+....
T Consensus 219 ~~lvvL~DVSGSm~-------~ys~---~~L~l~hAl~q~~~R~~--~F~F~-TRLt~vT~~l~~rD~~~Al~~~~a~v~ 285 (395)
T COG3552 219 PPLVVLCDVSGSMS-------GYSR---IFLHLLHALRQQRSRVH--VFLFG-TRLTRVTHMLRERDLEDALRRLSAQVK 285 (395)
T ss_pred CCeEEEEecccchh-------hhHH---HHHHHHHHHHhccccee--EEEee-chHHHHHHHhccCCHHHHHHHHHhhcc
Confidence 48999999999996 3332 23345556555665555 66663 2222223221 35555556665433
Q ss_pred CCCCcchHHHHHHHHHHHHcCCCCCCCcEEEEE-EcCCCCCCccCHHHHHHHHHhC
Q 014440 163 GCSGDSSIQNALDLVHGLLNQIPSYGHREVLIL-YSALSTCDPGDIMETIQKCKES 217 (424)
Q Consensus 163 ~~~G~tsL~~AL~~Al~~L~~~p~~~~reILvI-~ss~~t~dp~~i~~~i~~akk~ 217 (424)
.-.|+|.++++|.-=+...... .-+.+-+||| +++.+..|.......+..+.+.
T Consensus 286 dw~ggTrig~tl~aF~~~~~~~-~L~~gA~VlilsDg~drd~~~~l~~~~~rl~rr 340 (395)
T COG3552 286 DWDGGTRIGNTLAAFLRRWHGN-VLSGGAVVLILSDGLDRDDIPELVTAMARLRRR 340 (395)
T ss_pred cccCCcchhHHHHHHHcccccc-ccCCceEEEEEecccccCCchHHHHHHHHHHHh
Confidence 4579999999998755553332 2233344444 4555543433344455555543
No 84
>COG4548 NorD Nitric oxide reductase activation protein [Inorganic ion transport and metabolism]
Probab=95.11 E-value=0.11 Score=55.47 Aligned_cols=91 Identities=18% Similarity=0.131 Sum_probs=61.5
Q ss_pred CCCCcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCC--CC-cc------CHHHHHHHHHhCCcEEEEEEecchHHHH
Q 014440 163 GCSGDSSIQNALDLVHGLLNQIPSYGHREVLILYSALST--CD-PG------DIMETIQKCKESKIRCSVIGLSAEMFIC 233 (424)
Q Consensus 163 ~~~G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t--~d-p~------~i~~~i~~akk~~IrV~vIgLg~e~~iL 233 (424)
+|.-.|..+.||..|-+.|.+.| ..++.||+++++.- .| +. |-.+++..+.+.||.|.-|-|..+..
T Consensus 528 ePg~ytR~G~AIR~As~kL~~rp--q~qklLivlSDGkPnd~d~YEgr~gIeDTr~AV~eaRk~Gi~VF~Vtld~ea~-- 603 (637)
T COG4548 528 EPGYYTRDGAAIRHASAKLMERP--QRQKLLIVLSDGKPNDFDHYEGRFGIEDTREAVIEARKSGIEVFNVTLDREAI-- 603 (637)
T ss_pred CccccccccHHHHHHHHHHhcCc--ccceEEEEecCCCcccccccccccchhhHHHHHHHHHhcCceEEEEEecchhh--
Confidence 56678999999999999998874 35667888765433 22 21 22367788899999999999986532
Q ss_pred HHHHHHhC-CEEEEecChhhHHHHH
Q 014440 234 KHLCQETG-GTYSVALDESHSKELI 257 (424)
Q Consensus 234 q~iA~~TG-G~Y~~~~d~~~L~~lL 257 (424)
..+-..|| +.|..+.+.++|-..|
T Consensus 604 ~y~p~~fgqngYa~V~~v~~LP~~L 628 (637)
T COG4548 604 SYLPALFGQNGYAFVERVAQLPGAL 628 (637)
T ss_pred hhhHHHhccCceEEccchhhcchhH
Confidence 22333343 5677776766654444
No 85
>PF11775 CobT_C: Cobalamin biosynthesis protein CobT VWA domain
Probab=95.00 E-value=0.81 Score=44.10 Aligned_cols=59 Identities=22% Similarity=0.274 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCC-------CccCH-----HHHHHHHHh-CCcEEEEEEecchH
Q 014440 170 IQNALDLVHGLLNQIPSYGHREVLILYSALSTC-------DPGDI-----METIQKCKE-SKIRCSVIGLSAEM 230 (424)
Q Consensus 170 L~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~-------dp~~i-----~~~i~~akk-~~IrV~vIgLg~e~ 230 (424)
=+.||.-|...|... ...++||+++|++.-. .++++ .++++.... .+|.+-.||+|.++
T Consensus 118 DGeAl~~a~~rL~~r--~e~rkiLiViSDG~P~d~st~~~n~~~~L~~HLr~vi~~ie~~~~Vel~aiGIg~D~ 189 (219)
T PF11775_consen 118 DGEALRWAAERLLAR--PEQRKILIVISDGAPADDSTLSANDGDYLDAHLRQVIAEIETRSDVELIAIGIGHDV 189 (219)
T ss_pred cHHHHHHHHHHHHcC--CccceEEEEEeCCCcCcccccccCChHHHHHHHHHHHHHHhccCCcEEEEEEcCCCc
Confidence 356888888888765 3467788888754322 22223 356766654 47999999999773
No 86
>KOG2326 consensus DNA-binding subunit of a DNA-dependent protein kinase (Ku80 autoantigen) [Replication, recombination and repair]
Probab=94.95 E-value=0.58 Score=50.75 Aligned_cols=171 Identities=17% Similarity=0.124 Sum_probs=107.6
Q ss_pred EEEEEeCCHhhhcCCC-CCChHHHHHHHHHHHHHH-HhccCCCCcEEEEEec---------CCceE----EeeCCCC-CH
Q 014440 88 LYIVIDLSRAAAEMDF-RPSRMVVVAKQVEAFVRE-FFDQNPLSQIGLVTVK---------DGVAN----CLTDLGG-SP 151 (424)
Q Consensus 88 lvlvLD~S~SM~~~D~-~P~RL~~a~~~l~~Fi~~-~~~qnP~sqlGII~~~---------~g~A~----~lspLT~-d~ 151 (424)
+++|+|++.+|...+- .-+-++.++.++..|+.. +|..+-.+-+|+|++. .|.++ ++.|++. +.
T Consensus 7 ttfilDvG~~Ms~~~~~~~S~fE~a~~y~~~~lsrK~fa~rktD~is~vlyncD~ten~legg~~fqnisvl~p~~tpaf 86 (669)
T KOG2326|consen 7 TTFILDVGPSMSKNNETGKSNFEKAMAYLEYTLSRKSFASRKTDWISCVLYNCDVTENSLEGGNVFQNISVLAPVTTPAF 86 (669)
T ss_pred eEEEEecCccccccCCCccccHHHHHHHHHHHHHHHHhhccCCceEEEEEecCCCccCccccccccceeEEeecccchhh
Confidence 4677799999998872 146899999999988854 4454366889999986 12222 3344432 33
Q ss_pred HHHHHHHhhhhCC-CCcchHHHHHHHHHHHHcC---CCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEec
Q 014440 152 ESHIKALMGKLGC-SGDSSIQNALDLVHGLLNQ---IPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLS 227 (424)
Q Consensus 152 ~~~~~~L~~~~~~-~G~tsL~~AL~~Al~~L~~---~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg 227 (424)
-.++..+.+...+ .-..++-.||.+...++.+ .+....+++|+++..+.+ |-.+-.-+++.+.+.+|-.-++||.
T Consensus 87 ~~l~k~~~~~~qqns~q~Df~gal~vs~dL~~qhe~~~k~~~kr~Il~~~~l~~-dfsd~~~ive~l~~~didL~~~gld 165 (669)
T KOG2326|consen 87 IGLIKRLKQYCQQNSHQSDFEGALSVSQDLLVQHEDIKKQFQKRKILKQIVLFT-DFSDDLFIVEDLTDEDIDLLTEGLD 165 (669)
T ss_pred HHHHHHHHHhcCCCccccchhhhHHHHHHHHHHHHhccchhhceEEEEeecccc-cchhhHHHHHHHhhcCcceeEeecc
Confidence 3455555543322 2234688888888886643 233445566666655443 2222223889999999999999997
Q ss_pred chH-----------------H-HHHHHHHHhCCEEEEecChhhHHHHHHhcCCCCc
Q 014440 228 AEM-----------------F-ICKHLCQETGGTYSVALDESHSKELILEHAPPPP 265 (424)
Q Consensus 228 ~e~-----------------~-iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~~pp~ 265 (424)
... + .+|+.-..-.|+|+. +.++|..+..|-+
T Consensus 166 f~~e~id~s~dl~e~~kk~n~~~~q~~e~l~~~q~~~------~~eiYn~i~spa~ 215 (669)
T KOG2326|consen 166 FRIELIDCSKDLQEERKKSNYTWLQLVEALPNSQIYN------MNEIYNEITSPAT 215 (669)
T ss_pred CCccccccCccccccccccchHHHHHHHhcchhhHHh------HHHHHHhhcCccc
Confidence 531 2 445555555666664 4788888776543
No 87
>COG1721 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]
Probab=94.92 E-value=0.53 Score=49.32 Aligned_cols=71 Identities=13% Similarity=0.165 Sum_probs=53.5
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCHHHHHHHHhh
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSPESHIKALMG 160 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~ 160 (424)
+++|+||.|.+|.-.|...++++.+...+..+.-..+.++ +++|+.++.++.-..+.| ....+.....|..
T Consensus 226 ~v~l~lD~~~~m~~~~~~~~~~e~av~~a~~la~~~l~~g--d~vg~~~~~~~~~~~~~p-~~G~~~l~~~l~~ 296 (416)
T COG1721 226 TVVLVLDASRSMLFGSGVASKFEEAVRAAASLAYAALKNG--DRVGLLIFGGGGPKWIPP-SRGRRHLARILKA 296 (416)
T ss_pred eEEEEEeCCccccCCCCCccHHHHHHHHHHHHHHHHHhCC--CeeEEEEECCCcceeeCC-CcchHHHHHHHHH
Confidence 9999999999999888889999999999998888887766 799999995333344444 4443433334443
No 88
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=94.36 E-value=0.044 Score=54.05 Aligned_cols=40 Identities=33% Similarity=0.719 Sum_probs=33.7
Q ss_pred eEEcCCCCccccCCC-----------------CCCCCCCceecCchhHHhhhc-ccCC
Q 014440 303 GYTCPRCKARVCELP-----------------TECRICGLQLVSSPHLARSYH-HLFP 342 (424)
Q Consensus 303 Gy~Cp~C~s~~C~lP-----------------~~C~~C~l~Lvs~phLarsyh-hl~p 342 (424)
-|.|+.|+..|-... -.|++|+...||-|-|+.-.. |-.|
T Consensus 130 r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~ 187 (279)
T KOG2462|consen 130 RYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLP 187 (279)
T ss_pred ceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCCC
Confidence 799999999888765 489999999999999988765 6544
No 89
>PF07002 Copine: Copine; InterPro: IPR010734 This represents a conserved region approximately 180 residues long within eukaryotic copines. Copines are Ca2+-dependent phospholipid-binding proteins that are thought to be involved in membrane-trafficking, and may also be involved in cell division and growth [].
Probab=94.06 E-value=0.93 Score=40.96 Aligned_cols=118 Identities=14% Similarity=0.228 Sum_probs=70.0
Q ss_pred CCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCce--EE---eeCCCCCH--------HHHHHHHhhh---hCCCCc
Q 014440 104 RPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVA--NC---LTDLGGSP--------ESHIKALMGK---LGCSGD 167 (424)
Q Consensus 104 ~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A--~~---lspLT~d~--------~~~~~~L~~~---~~~~G~ 167 (424)
.+|-.+.|+..+.+.+..|-.++ ++-+..|.+... .. -.||++++ +.++++-++. +...|.
T Consensus 9 ~~N~Y~~ai~~vg~il~~Yd~dk---~~p~~GFGa~~~~~~~vsh~F~ln~~~~~p~~~Gi~gvl~~Y~~~~~~v~l~GP 85 (146)
T PF07002_consen 9 QPNPYQQAIRAVGEILQDYDSDK---MIPAYGFGAKIPPDYSVSHCFPLNGNPQNPECQGIDGVLEAYRKALPKVQLSGP 85 (146)
T ss_pred CCCHHHHHHHHHHHHHHhhccCC---ccceeccCCcCCCCcccccceeeecCCCCCcccCHHHHHHHHHHHhhheEECCC
Confidence 48999999999999999885544 577777753322 12 25666543 3344433322 256788
Q ss_pred chHHHHHHHHHHHHcCC-CCCCCcEEEEEEcCCCCCCccCHHHHHHH---HHhCCcEEEEEEec
Q 014440 168 SSIQNALDLVHGLLNQI-PSYGHREVLILYSALSTCDPGDIMETIQK---CKESKIRCSVIGLS 227 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~-p~~~~reILvI~ss~~t~dp~~i~~~i~~---akk~~IrV~vIgLg 227 (424)
|.+.--|..|.+.-+.. .....=-||+|++++.-. |..+|+++ |.+.-+.|-+||+|
T Consensus 86 T~fapiI~~a~~~a~~~~~~~~~Y~iLlIlTDG~i~---D~~~T~~aIv~AS~~PlSIIiVGVG 146 (146)
T PF07002_consen 86 TNFAPIINHAAKIAKQSNQNGQQYFILLILTDGQIT---DMEETIDAIVEASKLPLSIIIVGVG 146 (146)
T ss_pred ccHHHHHHHHHHHHhhhccCCceEEEEEEecccccc---cHHHHHHHHHHHccCCeEEEEEEeC
Confidence 88888888888777631 111122477777654433 44555444 44444555555554
No 90
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=91.43 E-value=0.12 Score=40.22 Aligned_cols=40 Identities=18% Similarity=0.399 Sum_probs=21.9
Q ss_pred cccCCCCCceeecccccccCCCCCCceeeCCCcCcccccccchh
Q 014440 356 DLHNISRSTCFGCQQSLLASGNKAGLCVACPKCKKHFCLECDIY 399 (424)
Q Consensus 356 ~~~~~~~~~C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~dCd~f 399 (424)
|........|..|.+.|.- ...++.|..|+..||.+|-.+
T Consensus 3 W~~d~~~~~C~~C~~~F~~----~~rrhhCr~CG~~vC~~Cs~~ 42 (69)
T PF01363_consen 3 WVPDSEASNCMICGKKFSL----FRRRHHCRNCGRVVCSSCSSQ 42 (69)
T ss_dssp SSSGGG-SB-TTT--B-BS----SS-EEE-TTT--EEECCCS-E
T ss_pred cCCCCCCCcCcCcCCcCCC----ceeeEccCCCCCEECCchhCC
Confidence 3333456789999999952 234789999999999999753
No 91
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=91.13 E-value=0.16 Score=50.16 Aligned_cols=77 Identities=26% Similarity=0.570 Sum_probs=47.9
Q ss_pred eEEcCCCCccccC------------CCCCCCCCCceecCchhHHhhhcccCCCCCCcccCccccccccCCCCCceeeccc
Q 014440 303 GYTCPRCKARVCE------------LPTECRICGLQLVSSPHLARSYHHLFPIAPFDEATPSRLNDLHNISRSTCFGCQQ 370 (424)
Q Consensus 303 Gy~Cp~C~s~~C~------------lP~~C~~C~l~Lvs~phLarsyhhl~p~~~f~~~~~~~~~~~~~~~~~~C~~C~~ 370 (424)
.+.|+.|...|=+ ||-+|.+||..|--+=-|-- |+ .-- .-...-.|.-|.+
T Consensus 161 a~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQG---Hi-------RTH-------TGEKPF~C~hC~k 223 (279)
T KOG2462|consen 161 AFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQG---HI-------RTH-------TGEKPFSCPHCGK 223 (279)
T ss_pred cccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhc---cc-------ccc-------cCCCCccCCcccc
Confidence 7899999988775 57799999987632111100 11 000 0002346999999
Q ss_pred ccccCCC--------CCCceeeCCCcCccccccc
Q 014440 371 SLLASGN--------KAGLCVACPKCKKHFCLEC 396 (424)
Q Consensus 371 ~~~~~~~--------~~~~~~~C~~C~~~fC~dC 396 (424)
.|.+..+ .....|+|++|++.|=.-=
T Consensus 224 AFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~S 257 (279)
T KOG2462|consen 224 AFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKS 257 (279)
T ss_pred hhcchHHHHHHHHhhcCCccccCcchhhHHHHHH
Confidence 9976521 1123699999999986543
No 92
>PRK04023 DNA polymerase II large subunit; Validated
Probab=90.86 E-value=0.18 Score=57.52 Aligned_cols=69 Identities=29% Similarity=0.596 Sum_probs=44.3
Q ss_pred cccCCCCCCcccCccccccc-------cCCCCCceeecccccccCCCCCCceeeCCCcCcc-----cccccchhhhccCC
Q 014440 338 HHLFPIAPFDEATPSRLNDL-------HNISRSTCFGCQQSLLASGNKAGLCVACPKCKKH-----FCLECDIYIHESLH 405 (424)
Q Consensus 338 hhl~p~~~f~~~~~~~~~~~-------~~~~~~~C~~C~~~~~~~~~~~~~~~~C~~C~~~-----fC~dCd~fihe~lh 405 (424)
|-|||+...--...++..+. -..+..+|..|.... ..+.||+|+.. ||.+|-.-... -
T Consensus 595 h~LFPiG~~GG~~R~i~~A~~~~g~~eVEVg~RfCpsCG~~t--------~~frCP~CG~~Te~i~fCP~CG~~~~~--y 664 (1121)
T PRK04023 595 HVLFPIGNAGGSTRDINKAAKYKGTIEVEIGRRKCPSCGKET--------FYRRCPFCGTHTEPVYRCPRCGIEVEE--D 664 (1121)
T ss_pred cccccccccCcccccHHHHHhcCCceeecccCccCCCCCCcC--------CcccCCCCCCCCCcceeCccccCcCCC--C
Confidence 77999877643322110111 112456999998553 24789999975 99999765543 4
Q ss_pred CCCCCCCCCCC
Q 014440 406 NCPGCESLRQS 416 (424)
Q Consensus 406 ~CPgC~~~~~~ 416 (424)
.||.|.....+
T Consensus 665 ~CPKCG~El~~ 675 (1121)
T PRK04023 665 ECEKCGREPTP 675 (1121)
T ss_pred cCCCCCCCCCc
Confidence 49999875543
No 93
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=89.85 E-value=0.21 Score=45.70 Aligned_cols=26 Identities=31% Similarity=0.533 Sum_probs=22.2
Q ss_pred eEEcCCCCccccC-----CCCCCCCCCceec
Q 014440 303 GYTCPRCKARVCE-----LPTECRICGLQLV 328 (424)
Q Consensus 303 Gy~Cp~C~s~~C~-----lP~~C~~C~l~Lv 328 (424)
+|+||+|+.+|-. .--.||.||.+|+
T Consensus 109 ~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 109 FFICPNMCVRFTFNEAMELNFTCPRCGAMLD 139 (158)
T ss_pred eEECCCCCcEeeHHHHHHcCCcCCCCCCEee
Confidence 9999999998863 4569999999986
No 94
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the KOG1226 consensus Integrin beta subunit (N-terminal portion of extracellular region) [Signal transduction mechanisms; Extracellular structures]
Probab=89.06 E-value=3.1 Score=46.52 Aligned_cols=164 Identities=17% Similarity=0.173 Sum_probs=89.3
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCce-------------------------
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVA------------------------- 141 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A------------------------- 141 (424)
+|+.++|+|-||.. -|+..++.=.++.+++-..-..-+||+=.|-++..
T Consensus 134 DLYyLMDlS~SM~D------Dl~~l~~LG~~L~~~m~~lT~nfrlGFGSFVDK~v~P~i~~~pekl~npc~~~~~C~ppf 207 (783)
T KOG1226|consen 134 DLYYLMDLSYSMKD------DLENLKSLGTDLAREMRKLTSNFRLGFGSFVDKTVSPYISTTPEKLRNPCPNYKNCAPPF 207 (783)
T ss_pred eEEEEeecchhhhh------hHHHHHHHHHHHHHHHHHHhccCCccccchhccccccccccCcHHhcCCCCCcccCCCCc
Confidence 99999999999974 34444444334433333333334566555432211
Q ss_pred --EEeeCCCCCHHHHHHHHhhh-----h-CCCCcchHHHHHHHHHHHHcCCC-CCCCcEEEEEEcCC-------------
Q 014440 142 --NCLTDLGGSPESHIKALMGK-----L-GCSGDSSIQNALDLVHGLLNQIP-SYGHREVLILYSAL------------- 199 (424)
Q Consensus 142 --~~lspLT~d~~~~~~~L~~~-----~-~~~G~tsL~~AL~~Al~~L~~~p-~~~~reILvI~ss~------------- 199 (424)
.-+-+||.|.+.+.+++.+. + .|.||++ .-|..|++- .... .+..+++||++.+.
T Consensus 208 gfkhvLsLT~~~~~F~~~V~~q~ISgNlDaPEGGfD--AimQaavC~-~~IGWR~~a~~lLVF~td~~~H~a~DgkLaGi 284 (783)
T KOG1226|consen 208 GFKHVLSLTNDAEEFNEEVGKQRISGNLDAPEGGFD--AIMQAAVCT-EKIGWRNDATRLLVFSTDAGFHFAGDGKLAGI 284 (783)
T ss_pred ccceeeecCCChHHHHHHHhhceeccCCCCCCchHH--HHHhhhhcc-ccccccccceeEEEEEcCcceeeecccceeeE
Confidence 12335677777777776643 1 3666643 122222221 1110 02234455554320
Q ss_pred -------------------CCCCccCHHHHHHHHHhCCcEEEEEEecchHHHHHHHHHHhCCEEEEe--cChhhHHHHHH
Q 014440 200 -------------------STCDPGDIMETIQKCKESKIRCSVIGLSAEMFICKHLCQETGGTYSVA--LDESHSKELIL 258 (424)
Q Consensus 200 -------------------~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~~iLq~iA~~TGG~Y~~~--~d~~~L~~lL~ 258 (424)
.+-|+..+-.....+.+++|.+..---.....+.++++..--|.+.-. .|...+.+|+.
T Consensus 285 v~pnDG~CHL~~~g~Yt~S~~qdyPSia~l~~kl~~~ni~~IFAVt~~~~~~Y~~l~~lip~s~vg~l~~DSsNi~qLI~ 364 (783)
T KOG1226|consen 285 VQPNDGQCHLDKNGEYTQSTTQDYPSIAQLAQKLADNNINTIFAVTKNSQSLYEELSNLIPGSAVGVLSEDSSNIVQLII 364 (783)
T ss_pred ecCCCCccccCCCCccceecCCCCCcHHHHHHHHhhhcchhHHHHhhhhhhHHHhhhhhCCcccccccccchhhHHHHHH
Confidence 012334566778889999987654444445678899998888888743 44555666654
Q ss_pred h
Q 014440 259 E 259 (424)
Q Consensus 259 ~ 259 (424)
.
T Consensus 365 ~ 365 (783)
T KOG1226|consen 365 E 365 (783)
T ss_pred H
Confidence 3
No 96
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=88.57 E-value=0.27 Score=45.86 Aligned_cols=27 Identities=30% Similarity=0.626 Sum_probs=22.9
Q ss_pred eEEcCCCCccccC-----CCCCCCCCCceecC
Q 014440 303 GYTCPRCKARVCE-----LPTECRICGLQLVS 329 (424)
Q Consensus 303 Gy~Cp~C~s~~C~-----lP~~C~~C~l~Lvs 329 (424)
+|+||+|+.+|-. .--.||.||..|+-
T Consensus 117 ~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 117 FFFCPNCHIRFTFDEAMEYGFRCPQCGEMLEE 148 (178)
T ss_pred EEECCCCCcEEeHHHHhhcCCcCCCCCCCCee
Confidence 9999999999863 45699999999874
No 97
>KOG1327 consensus Copine [Signal transduction mechanisms]
Probab=88.21 E-value=5.5 Score=43.09 Aligned_cols=156 Identities=12% Similarity=0.152 Sum_probs=91.0
Q ss_pred cccceEEEEEeCCHhh---------hcCC-CCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCC--c---eEEeeCC
Q 014440 83 GLIRYLYIVIDLSRAA---------AEMD-FRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDG--V---ANCLTDL 147 (424)
Q Consensus 83 GiiR~lvlvLD~S~SM---------~~~D-~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g--~---A~~lspL 147 (424)
|.--++.+.||.+.|= ...| -.||-++.|+..+-.-+..|..+ .++.-..|++. . ..-...|
T Consensus 283 g~~lnf~vgIDfTaSNg~p~~~sSLHyi~p~~~N~Y~~Ai~~vG~~lq~ydsd---k~fpa~GFGakip~~~~vs~~f~l 359 (529)
T KOG1327|consen 283 GEQLNFTVGIDFTASNGDPRNPSSLHYIDPHQPNPYEQAIRSVGETLQDYDSD---KLFPAFGFGAKIPPDGQVSHEFVL 359 (529)
T ss_pred CceeeeEEEEEEeccCCCCCCCCcceecCCCCCCHHHHHHHHHhhhhcccCCC---CccccccccccCCCCcccccceee
Confidence 3334899999999882 2233 56899999999999999887544 56666667533 1 1111233
Q ss_pred CCCH--------HHHHHHHhhh---hCCCCcchHHHHHHHHHHHHcCCCCCC-CcEEEEEEcCCCCCCccCHHHHHHHHH
Q 014440 148 GGSP--------ESHIKALMGK---LGCSGDSSIQNALDLVHGLLNQIPSYG-HREVLILYSALSTCDPGDIMETIQKCK 215 (424)
Q Consensus 148 T~d~--------~~~~~~L~~~---~~~~G~tsL~~AL~~Al~~L~~~p~~~-~reILvI~ss~~t~dp~~i~~~i~~ak 215 (424)
.+++ +.++++-+.. +.+.|.|++.--|..|...-++...++ .=.||+|++++.-.|-....++|-.|-
T Consensus 360 n~~~~~~~c~Gi~gVl~aY~~~lp~v~l~GPTnFaPII~~va~~a~~~~~~~~qY~VLlIitDG~vTdm~~T~~AIV~AS 439 (529)
T KOG1327|consen 360 NFNPEDPECRGIEGVLEAYRKALPNVQLYGPTNFSPIINHVARIAQQSGNTAGQYHVLLIITDGVVTDMKETRDAIVSAS 439 (529)
T ss_pred cCCCCCCccccHHHHHHHHHhhcccccccCCCccHHHHHHHHHHHHHhccCCcceEEEEEEeCCccccHHHHHHHHHhhc
Confidence 3332 3344444333 256788888877777777665542111 225888876554334222234444555
Q ss_pred hCCcEEEEEEecch-HHHHHHHHHHhC
Q 014440 216 ESKIRCSVIGLSAE-MFICKHLCQETG 241 (424)
Q Consensus 216 k~~IrV~vIgLg~e-~~iLq~iA~~TG 241 (424)
+.-..|-+||+|.. -..++++-...+
T Consensus 440 ~lPlSIIiVGVGd~df~~M~~lD~d~~ 466 (529)
T KOG1327|consen 440 DLPLSIIIVGVGDADFDMMRELDGDDP 466 (529)
T ss_pred cCCeEEEEEEeCCCCHHHHHHhhcCCc
Confidence 55566677777743 345565554443
No 98
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=88.13 E-value=0.38 Score=32.75 Aligned_cols=24 Identities=33% Similarity=0.787 Sum_probs=19.8
Q ss_pred eEEcCCCCccccC--CCCCCCCCCce
Q 014440 303 GYTCPRCKARVCE--LPTECRICGLQ 326 (424)
Q Consensus 303 Gy~Cp~C~s~~C~--lP~~C~~C~l~ 326 (424)
-|+|+.|+-++=. .|..||+||..
T Consensus 2 ~~~C~~CG~i~~g~~~p~~CP~Cg~~ 27 (34)
T cd00729 2 VWVCPVCGYIHEGEEAPEKCPICGAP 27 (34)
T ss_pred eEECCCCCCEeECCcCCCcCcCCCCc
Confidence 4899999998654 57899999963
No 99
>PF11443 DUF2828: Domain of unknown function (DUF2828); InterPro: IPR024553 This uncharacterised domain is found in eukaryotic, bacterial and viral proteins.
Probab=85.67 E-value=13 Score=40.43 Aligned_cols=134 Identities=12% Similarity=0.156 Sum_probs=77.4
Q ss_pred ccccceEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCC-HHHHHHHHhh
Q 014440 82 KGLIRYLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGS-PESHIKALMG 160 (424)
Q Consensus 82 ~GiiR~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d-~~~~~~~L~~ 160 (424)
.|-+.+.+.|.|+|+||... -+..+..... ++.+. .+.| =+=.+|+|. ..... ..++++ ..+-++.+..
T Consensus 337 ~g~l~n~iav~DvSGSM~~~-----pm~vaiaLgl-l~ae~-~~~p-f~~~~ITFs-~~P~~-~~i~g~~l~ekv~~~~~ 406 (534)
T PF11443_consen 337 SGSLENCIAVCDVSGSMSGP-----PMDVAIALGL-LIAEL-NKGP-FKGRFITFS-ENPQL-HKIKGDTLREKVRFIRR 406 (534)
T ss_pred cCCccceEEEEecCCccCcc-----HHHHHHHHHH-HHHHh-cccc-cCCeEEeec-CCceE-EEecCCCHHHHHHHHHh
Confidence 46678999999999999865 5555555444 44444 2333 334678884 54443 333444 3444444433
Q ss_pred hhCCCCcchHHHHHHHHHHHHcC--C-CCCCCcEEEEEEc-CCC--CCC-----ccCHHHHHHHHHhCCcEEEEEEe
Q 014440 161 KLGCSGDSSIQNALDLVHGLLNQ--I-PSYGHREVLILYS-ALS--TCD-----PGDIMETIQKCKESKIRCSVIGL 226 (424)
Q Consensus 161 ~~~~~G~tsL~~AL~~Al~~L~~--~-p~~~~reILvI~s-s~~--t~d-----p~~i~~~i~~akk~~IrV~vIgL 226 (424)
. .-.++|+|+...++-+..-.. . |..--++|+||++ ..+ +.. ..++..+.+..++.|-.+=-|-+
T Consensus 407 ~-~wg~nTn~~aVFdlIL~~Av~~~l~~e~M~k~lfV~SDMeFD~a~~~~~~~w~T~~e~i~~~f~~aGY~~P~iVF 482 (534)
T PF11443_consen 407 M-DWGMNTNFQAVFDLILETAVKNKLKQEDMPKRLFVFSDMEFDQASNSSDRPWETNFEAIKRKFEEAGYELPEIVF 482 (534)
T ss_pred C-CcccCCcHHHHHHHHHHHHHHcCCChHHCCceEEEEeccccccccccccCccccHHHHHHHHHHHhCCCCCceEE
Confidence 2 456789999999887776432 2 1223456777764 111 111 12344567777888876544443
No 100
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=85.20 E-value=0.41 Score=41.18 Aligned_cols=28 Identities=36% Similarity=0.871 Sum_probs=24.3
Q ss_pred eEEcCCCCccccCC---CCCCCCCCceecCc
Q 014440 303 GYTCPRCKARVCEL---PTECRICGLQLVSS 330 (424)
Q Consensus 303 Gy~Cp~C~s~~C~l---P~~C~~C~l~Lvs~ 330 (424)
-.+||-|++||=.| |..||-||..+...
T Consensus 9 KR~Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 9 KRTCPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cccCCCCcchhccCCCCCccCCCCCCccCcc
Confidence 47899999999876 68899999998766
No 101
>COG3864 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=84.72 E-value=3 Score=42.32 Aligned_cols=79 Identities=10% Similarity=0.221 Sum_probs=47.4
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCHHHHHHHHhhhhCCCC
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSPESHIKALMGKLGCSG 166 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~~~~~~G 166 (424)
.+++++|+|+||.+. -+.++...+.+.+ .||.-++-||-. |..+.....+..- ..+...+...|
T Consensus 263 ~i~vaVDtSGS~~d~-----ei~a~~~Ei~~Il-----~~~~~eltli~~-D~~v~~~~~~r~g-----~~~~~~~~ggG 326 (396)
T COG3864 263 KIVVAVDTSGSMTDA-----EIDAAMTEIFDIL-----KNKNYELTLIEC-DNIVRRMYRVRKG-----RDMKKKLDGGG 326 (396)
T ss_pred heEEEEecCCCccHH-----HHHHHHHHHHHHH-----hCCCcEEEEEEe-cchhhhhhccCCc-----ccCCcccCCCC
Confidence 488999999999753 3344444444333 577788888876 5555544333211 00111234567
Q ss_pred cchHHHHHHHHHHHH
Q 014440 167 DSSIQNALDLVHGLL 181 (424)
Q Consensus 167 ~tsL~~AL~~Al~~L 181 (424)
+|+++-+++..-+.+
T Consensus 327 ~Tdf~Pvfeylek~~ 341 (396)
T COG3864 327 GTDFSPVFEYLEKNR 341 (396)
T ss_pred CccccHHHHHHHhhc
Confidence 799999888755443
No 102
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=84.55 E-value=0.54 Score=34.91 Aligned_cols=34 Identities=26% Similarity=0.734 Sum_probs=27.5
Q ss_pred CceeecccccccCCCCCCceeeCCCcCcccccccchhh
Q 014440 363 STCFGCQQSLLASGNKAGLCVACPKCKKHFCLECDIYI 400 (424)
Q Consensus 363 ~~C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~dCd~fi 400 (424)
..|..|.+.|... ...+.|..|+..||.+|..+-
T Consensus 3 ~~C~~C~~~F~~~----~rk~~Cr~Cg~~~C~~C~~~~ 36 (57)
T cd00065 3 SSCMGCGKPFTLT----RRRHHCRNCGRIFCSKCSSNR 36 (57)
T ss_pred CcCcccCccccCC----ccccccCcCcCCcChHHcCCe
Confidence 4699999998642 235889999999999998754
No 103
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=84.04 E-value=0.87 Score=30.63 Aligned_cols=22 Identities=36% Similarity=0.842 Sum_probs=18.5
Q ss_pred EEcCCCCccccCC--CCCCCCCCc
Q 014440 304 YTCPRCKARVCEL--PTECRICGL 325 (424)
Q Consensus 304 y~Cp~C~s~~C~l--P~~C~~C~l 325 (424)
|+|+.|+-++=.- |-.||+||.
T Consensus 2 ~~C~~CGy~y~~~~~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEEAPWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCcCCCcCcCCCC
Confidence 8999999887654 679999986
No 104
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=83.24 E-value=0.64 Score=41.02 Aligned_cols=32 Identities=22% Similarity=0.400 Sum_probs=26.1
Q ss_pred eEEcCCCCccccCC---CCCCCCCCceecCchhHH
Q 014440 303 GYTCPRCKARVCEL---PTECRICGLQLVSSPHLA 334 (424)
Q Consensus 303 Gy~Cp~C~s~~C~l---P~~C~~C~l~Lvs~phLa 334 (424)
-.+||-|++||=.| |+.||-||...-.+|-+.
T Consensus 9 Kr~Cp~cg~kFYDLnk~p~vcP~cg~~~~~~~~~~ 43 (129)
T TIGR02300 9 KRICPNTGSKFYDLNRRPAVSPYTGEQFPPEEALK 43 (129)
T ss_pred cccCCCcCccccccCCCCccCCCcCCccCcchhhc
Confidence 57999999999876 899999999976654443
No 105
>PRK12496 hypothetical protein; Provisional
Probab=82.99 E-value=4.9 Score=37.01 Aligned_cols=98 Identities=19% Similarity=0.189 Sum_probs=54.9
Q ss_pred CHHHHHHHHHhCCcEEEEEEecchHHHHHHHHHHhCCEEEEecChhhHHHHHHhcCCCCccchhhhhhheeeecCCCCCC
Q 014440 206 DIMETIQKCKESKIRCSVIGLSAEMFICKHLCQETGGTYSVALDESHSKELILEHAPPPPAIAEFAIASLIKMGFPQRAG 285 (424)
Q Consensus 206 ~i~~~i~~akk~~IrV~vIgLg~e~~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~~pp~~~~~~~~~~Li~mGFP~~~~ 285 (424)
.+..+.+.|++.| +.-.|+...--+..+|.+.+| .+..|+-.++.+...+-.+.... ...| .
T Consensus 59 ~i~~v~~~a~~tg---d~~~Ls~~D~~~iaLA~el~~--~lvtDD~~~~~vA~~lgi~v~~~--------~~~~-----i 120 (164)
T PRK12496 59 SIEKVEEAAIKTG---DLMRLSNTDIEVLALALELNG--TLYTDDYGIQNVAKKLNIKFENI--------KTKG-----I 120 (164)
T ss_pred HHHHHHHHHHhcC---CccccchhhHHHHHHHHHhCC--cEECcHHHHHHHHHHcCCeEecc--------cccc-----c
Confidence 4556666666665 222244333333446777776 35567667777765555332111 0000 0
Q ss_pred CCCcceeeecCCccccCeEEcCCCCccccCCC--CCCCCCCceecCchh
Q 014440 286 EGSISICSCHKEVKIGVGYTCPRCKARVCELP--TECRICGLQLVSSPH 332 (424)
Q Consensus 286 ~~~~a~C~CH~~~~~~~Gy~Cp~C~s~~C~lP--~~C~~C~l~Lvs~ph 332 (424)
.+.... .|.|+-|+..|=+-+ -.||+||..|.--+.
T Consensus 121 ----------~~~~~w-~~~C~gC~~~~~~~~~~~~C~~CG~~~~r~~~ 158 (164)
T PRK12496 121 ----------KKVIKW-RKVCKGCKKKYPEDYPDDVCEICGSPVKRKMV 158 (164)
T ss_pred ----------hhheee-eEECCCCCccccCCCCCCcCCCCCChhhhcch
Confidence 112234 799999999986544 469999988754443
No 106
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=82.50 E-value=0.86 Score=42.14 Aligned_cols=24 Identities=38% Similarity=0.836 Sum_probs=19.1
Q ss_pred eEEcCCCCcccc-CCCCCCCCCCce
Q 014440 303 GYTCPRCKARVC-ELPTECRICGLQ 326 (424)
Q Consensus 303 Gy~Cp~C~s~~C-~lP~~C~~C~l~ 326 (424)
-|+||+|+-.+= +-|-.||+||.+
T Consensus 134 ~~vC~vCGy~~~ge~P~~CPiCga~ 158 (166)
T COG1592 134 VWVCPVCGYTHEGEAPEVCPICGAP 158 (166)
T ss_pred EEEcCCCCCcccCCCCCcCCCCCCh
Confidence 599999997654 456689999964
No 107
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=82.28 E-value=0.73 Score=41.48 Aligned_cols=27 Identities=33% Similarity=0.759 Sum_probs=22.4
Q ss_pred eEEcCCCCccccC-----CC-----CCCCCCCceecC
Q 014440 303 GYTCPRCKARVCE-----LP-----TECRICGLQLVS 329 (424)
Q Consensus 303 Gy~Cp~C~s~~C~-----lP-----~~C~~C~l~Lvs 329 (424)
+|+||.|+.+|-. +. -.||.||..|+.
T Consensus 99 ~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 99 YYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEE 135 (147)
T ss_pred EEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEE
Confidence 8999999998874 43 689999999863
No 108
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=81.41 E-value=1.1 Score=31.89 Aligned_cols=30 Identities=27% Similarity=0.541 Sum_probs=24.4
Q ss_pred eeeCCCcCcccccccchhhhccCCCCCCCCC
Q 014440 382 CVACPKCKKHFCLECDIYIHESLHNCPGCES 412 (424)
Q Consensus 382 ~~~C~~C~~~fC~dCd~fihe~lh~CPgC~~ 412 (424)
-|+|++|++.|=.---+-= +....||.|..
T Consensus 5 ey~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISE-DDPVPCPECGS 34 (42)
T ss_pred EEEeCCCCCEEEEEEEcCC-CCCCcCCCCCC
Confidence 5899999999988765544 58889999976
No 109
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=81.06 E-value=1.2 Score=32.15 Aligned_cols=26 Identities=31% Similarity=0.773 Sum_probs=20.5
Q ss_pred eEEcCCCCccccCC----CCCCCCCCceec
Q 014440 303 GYTCPRCKARVCEL----PTECRICGLQLV 328 (424)
Q Consensus 303 Gy~Cp~C~s~~C~l----P~~C~~C~l~Lv 328 (424)
-|.||.|++.+=.- ...||-||..++
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCeEE
Confidence 59999999976322 568999998776
No 110
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=80.72 E-value=0.51 Score=53.19 Aligned_cols=68 Identities=29% Similarity=0.680 Sum_probs=0.0
Q ss_pred hcccCCCCCCcccCcccccccc--------CCCCCceeecccccccCCCCCCceeeCCCcCcc-----cccccchhhhcc
Q 014440 337 YHHLFPIAPFDEATPSRLNDLH--------NISRSTCFGCQQSLLASGNKAGLCVACPKCKKH-----FCLECDIYIHES 403 (424)
Q Consensus 337 yhhl~p~~~f~~~~~~~~~~~~--------~~~~~~C~~C~~~~~~~~~~~~~~~~C~~C~~~-----fC~dCd~fihe~ 403 (424)
-|-|||+...--...+...+.. .-+.+.|-.|... +....||.|+.+ +|.+|..-+-+.
T Consensus 622 ~h~LFPIG~~GG~~R~i~~A~~~~~g~i~vei~~r~Cp~Cg~~--------t~~~~Cp~CG~~T~~~~~Cp~C~~~~~~~ 693 (900)
T PF03833_consen 622 PHVLFPIGEAGGSRRDIQKAAKKGKGTIEVEIGRRRCPKCGKE--------TFYNRCPECGSHTEPVYVCPDCGIEVEED 693 (900)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred CceeccccccCcccccHHHHHhcCCCeeEEeeecccCcccCCc--------chhhcCcccCCccccceeccccccccCcc
Confidence 4779998765322111101100 1134689999732 235689999988 999999877666
Q ss_pred CCCCCCCCCCC
Q 014440 404 LHNCPGCESLR 414 (424)
Q Consensus 404 lh~CPgC~~~~ 414 (424)
.||-|...+
T Consensus 694 --~C~~C~~~~ 702 (900)
T PF03833_consen 694 --ECPKCGRET 702 (900)
T ss_dssp -----------
T ss_pred --ccccccccC
Confidence 999997543
No 111
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=79.83 E-value=1.8 Score=36.42 Aligned_cols=31 Identities=19% Similarity=0.415 Sum_probs=18.6
Q ss_pred CCceeecccc--------cccCCCCCCceeeCCCcCccc
Q 014440 362 RSTCFGCQQS--------LLASGNKAGLCVACPKCKKHF 392 (424)
Q Consensus 362 ~~~C~~C~~~--------~~~~~~~~~~~~~C~~C~~~f 392 (424)
...|.-|... ..+.+......|.|.+|++.+
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w 100 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVW 100 (104)
T ss_pred cCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCee
Confidence 4678888422 112222345579999998753
No 112
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=79.76 E-value=1 Score=32.96 Aligned_cols=30 Identities=33% Similarity=0.650 Sum_probs=21.9
Q ss_pred eEEcCCCCccccCC-------CCCCCCCCc----eecCchh
Q 014440 303 GYTCPRCKARVCEL-------PTECRICGL----QLVSSPH 332 (424)
Q Consensus 303 Gy~Cp~C~s~~C~l-------P~~C~~C~l----~Lvs~ph 332 (424)
-|.|+.|+..|=.+ ++.||.||. .++|+|.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r~~s~~~ 45 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGGEKLRRLLSAVG 45 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCCCceeEEecccc
Confidence 58999999855443 457999997 3666664
No 113
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=79.75 E-value=1.1 Score=33.53 Aligned_cols=42 Identities=26% Similarity=0.637 Sum_probs=25.7
Q ss_pred Cceee--cccccccCCCCCCceeeCCCcCcccccccchhhhccC
Q 014440 363 STCFG--CQQSLLASGNKAGLCVACPKCKKHFCLECDIYIHESL 404 (424)
Q Consensus 363 ~~C~~--C~~~~~~~~~~~~~~~~C~~C~~~fC~dCd~fihe~l 404 (424)
..|.. |...+............|+.|+..||..|..-.|+.+
T Consensus 19 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~H~~~ 62 (64)
T PF01485_consen 19 RWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPWHEGV 62 (64)
T ss_dssp C--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSESCTTS
T ss_pred cCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcccCCCC
Confidence 58966 9877765432222236899999999999998888754
No 114
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=79.71 E-value=0.79 Score=32.36 Aligned_cols=42 Identities=24% Similarity=0.475 Sum_probs=29.1
Q ss_pred ceeecccccccCCCCCCceeeCCCcCcccccccchhhhccCCCCCCC
Q 014440 364 TCFGCQQSLLASGNKAGLCVACPKCKKHFCLECDIYIHESLHNCPGC 410 (424)
Q Consensus 364 ~C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~dCd~fihe~lh~CPgC 410 (424)
.|.-|+..|... ......+ |++.||.+|=.-.=+.-..||.|
T Consensus 2 ~C~IC~~~~~~~----~~~~~l~-C~H~fh~~Ci~~~~~~~~~CP~C 43 (44)
T PF13639_consen 2 ECPICLEEFEDG----EKVVKLP-CGHVFHRSCIKEWLKRNNSCPVC 43 (44)
T ss_dssp CETTTTCBHHTT----SCEEEET-TSEEEEHHHHHHHHHHSSB-TTT
T ss_pred CCcCCChhhcCC----CeEEEcc-CCCeeCHHHHHHHHHhCCcCCcc
Confidence 488898888532 2356677 99999999964433445699988
No 115
>cd06167 LabA_like LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression.
Probab=79.46 E-value=5.2 Score=35.07 Aligned_cols=62 Identities=11% Similarity=0.198 Sum_probs=40.8
Q ss_pred cchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEec-chHHHHHHHHH
Q 014440 167 DSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLS-AEMFICKHLCQ 238 (424)
Q Consensus 167 ~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg-~e~~iLq~iA~ 238 (424)
+.++.-++++......+ .-..|++++++ +|+..+++.+++.|.+|-+++.. ....-|+..|+
T Consensus 82 ~~D~~l~~d~~~~~~~~----~~d~ivLvSgD------~Df~~~i~~lr~~G~~V~v~~~~~~~s~~L~~~~d 144 (149)
T cd06167 82 GVDVALAIDALELAYKR----RIDTIVLVSGD------SDFVPLVERLRELGKRVIVVGFEAKTSRELRKAAD 144 (149)
T ss_pred CccHHHHHHHHHHhhhc----CCCEEEEEECC------ccHHHHHHHHHHcCCEEEEEccCccChHHHHHhCC
Confidence 45666555544333333 22344444443 36788999999999999999998 45667777665
No 116
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=78.91 E-value=1.6 Score=27.64 Aligned_cols=24 Identities=21% Similarity=0.714 Sum_probs=16.1
Q ss_pred eeecccccccCCCCCCceeeCCCcCc
Q 014440 365 CFGCQQSLLASGNKAGLCVACPKCKK 390 (424)
Q Consensus 365 C~~C~~~~~~~~~~~~~~~~C~~C~~ 390 (424)
|..|...+... +....|.||+|+.
T Consensus 1 C~sC~~~i~~r--~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPR--EQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCc--ccCceEeCCCCCC
Confidence 66787666432 2245799999984
No 117
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=77.86 E-value=1.3 Score=28.37 Aligned_cols=23 Identities=43% Similarity=0.911 Sum_probs=19.5
Q ss_pred EcCCCCccccCCCCCCCCCCcee
Q 014440 305 TCPRCKARVCELPTECRICGLQL 327 (424)
Q Consensus 305 ~Cp~C~s~~C~lP~~C~~C~l~L 327 (424)
.||.|.+.+=.--..||.||-.|
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCC
Confidence 49999999877778999999765
No 118
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=77.68 E-value=2.4 Score=32.60 Aligned_cols=47 Identities=21% Similarity=0.579 Sum_probs=35.6
Q ss_pred CCceeecccccccCCCCCCceeeCCCcCcc---cccccchhhhccCCCCCCCCC
Q 014440 362 RSTCFGCQQSLLASGNKAGLCVACPKCKKH---FCLECDIYIHESLHNCPGCES 412 (424)
Q Consensus 362 ~~~C~~C~~~~~~~~~~~~~~~~C~~C~~~---fC~dCd~fihe~lh~CPgC~~ 412 (424)
...|..|...+...+ ....|.||+|+.. .|..|-.+- ....||-|..
T Consensus 7 ~~~CtSCg~~i~~~~--~~~~F~CPnCG~~~I~RC~~CRk~~--~~Y~CP~CGF 56 (59)
T PRK14890 7 PPKCTSCGIEIAPRE--KAVKFLCPNCGEVIIYRCEKCRKQS--NPYTCPKCGF 56 (59)
T ss_pred CccccCCCCcccCCC--ccCEeeCCCCCCeeEeechhHHhcC--CceECCCCCC
Confidence 457999998885332 2357999999977 899998854 5678999864
No 119
>PF01936 NYN: NYN domain; InterPro: IPR021139 This highly conserved domain has no known function. However it contains many conserved aspartates, suggesting an enzymatic function such as an endonuclease or glycosyl hydrolase.; PDB: 2QIP_A.
Probab=77.33 E-value=3.1 Score=35.98 Aligned_cols=61 Identities=13% Similarity=0.194 Sum_probs=33.4
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEe-cchHHHHHHHHH
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGL-SAEMFICKHLCQ 238 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgL-g~e~~iLq~iA~ 238 (424)
..+.-++++....+.+. + ..++|++|+ +|+..+++.+++.|++|.+++. ......|++.|+
T Consensus 79 ~D~~l~~d~~~~~~~~~--~--d~ivLvSgD------~Df~~~v~~l~~~g~~V~v~~~~~~~s~~L~~~ad 140 (146)
T PF01936_consen 79 VDVALAVDILELAYENP--P--DTIVLVSGD------SDFAPLVRKLRERGKRVIVVGAEDSASEALRSAAD 140 (146)
T ss_dssp -HHHHHHHHHHHG--GG-----SEEEEE---------GGGHHHHHHHHHH--EEEEEE-GGGS-HHHHHHSS
T ss_pred cHHHHHHHHHHHhhccC--C--CEEEEEECc------HHHHHHHHHHHHcCCEEEEEEeCCCCCHHHHHhcC
Confidence 34444444443333332 2 445555553 4678899999999999999995 344677887775
No 120
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=77.18 E-value=0.98 Score=29.95 Aligned_cols=14 Identities=64% Similarity=1.483 Sum_probs=10.1
Q ss_pred eEEcCCCCccccCC
Q 014440 303 GYTCPRCKARVCEL 316 (424)
Q Consensus 303 Gy~Cp~C~s~~C~l 316 (424)
-|.||+|+.++|++
T Consensus 13 kY~Cp~C~~~~CSl 26 (30)
T PF04438_consen 13 KYRCPRCGARYCSL 26 (30)
T ss_dssp SEE-TTT--EESSH
T ss_pred EEECCCcCCceeCc
Confidence 69999999999986
No 121
>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=76.76 E-value=39 Score=42.32 Aligned_cols=174 Identities=16% Similarity=0.143 Sum_probs=93.4
Q ss_pred hhhhhccccceEEEEEeCCHhhhcCCCC---CChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCC--H
Q 014440 77 TARIQKGLIRYLYIVIDLSRAAAEMDFR---PSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGS--P 151 (424)
Q Consensus 77 ~~~~r~GiiR~lvlvLD~S~SM~~~D~~---P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d--~ 151 (424)
+.|.+|-- .++|.||=|.||.+..-. -.-|..+-+++. +--..||+|+-|+ ...+.+.|+... .
T Consensus 4386 ~kpskr~y--qvmisiddsksmses~~~~la~etl~lvtkals--------~le~g~iav~kfg-e~~~~lh~fdkqfs~ 4454 (4600)
T COG5271 4386 VKPSKRTY--QVMISIDDSKSMSESGSTVLALETLALVTKALS--------LLEVGQIAVMKFG-EQPELLHPFDKQFSS 4454 (4600)
T ss_pred cCCcccee--EEEEEecccccccccCceeeehHHHHHHHHHHH--------HHhhccEEEEecC-CChhhhCchhhhhcc
Confidence 34444444 899999999999865421 223333333322 2224789999994 778888887532 1
Q ss_pred HHHHHHHhhhhCCCCcchHHHHHHHHHHHHcC---CCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecc
Q 014440 152 ESHIKALMGKLGCSGDSSIQNALDLVHGLLNQ---IPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSA 228 (424)
Q Consensus 152 ~~~~~~L~~~~~~~G~tsL~~AL~~Al~~L~~---~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~ 228 (424)
+.-.++..-..-.+..|....-...+++.+.. +.-|-.+..=||++++--.|-..|...+..|++++|-+-.|-+..
T Consensus 4455 esg~~~f~~f~feqs~tnv~~l~~~s~k~f~~a~t~~h~d~~qleiiisdgicedhdsi~kllrra~e~kvmivfvild~ 4534 (4600)
T COG5271 4455 ESGVQMFSHFTFEQSNTNVLALADASMKCFNYANTASHHDIRQLEIIISDGICEDHDSIRKLLRRAQEEKVMIVFVILDN 4534 (4600)
T ss_pred hHHHHHHHhhchhcccccHHHHHHHHHHHHHHhhhhcccchheeEEEeecCcccchHHHHHHHHHhhhcceEEEEEEecC
Confidence 22223332211112234333222233333333 212334444455554333355567888899999999755555542
Q ss_pred ---hHHH--HHHHHHHhC------------------CEEEEecChhhHHHHHHhcC
Q 014440 229 ---EMFI--CKHLCQETG------------------GTYSVALDESHSKELILEHA 261 (424)
Q Consensus 229 ---e~~i--Lq~iA~~TG------------------G~Y~~~~d~~~L~~lL~~~~ 261 (424)
...+ ++++-..|. --|.|+.|-+.|-++|..++
T Consensus 4535 v~t~~sildi~kv~y~~~e~g~~~lki~~yid~f~fd~ylvv~ni~elpqlls~~l 4590 (4600)
T COG5271 4535 VNTQKSILDIKKVYYDTKEDGTMDLKIQPYIDEFAFDYYLVVRNIEELPQLLSSAL 4590 (4600)
T ss_pred CccchhhhhhHhhccccccCCCcceeeeechhcccceeEEEeccHHHHHHHHHHHH
Confidence 2222 233333332 24557888888888876654
No 122
>COG0528 PyrH Uridylate kinase [Nucleotide transport and metabolism]
Probab=76.34 E-value=19 Score=35.28 Aligned_cols=45 Identities=20% Similarity=0.355 Sum_probs=35.0
Q ss_pred cceEEEEEeCCHhhhcCC----CCCChHHHHHHHHHHHHHHHhccCCCCcEEEEE
Q 014440 85 IRYLYIVIDLSRAAAEMD----FRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVT 135 (424)
Q Consensus 85 iR~lvlvLD~S~SM~~~D----~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~ 135 (424)
++..-++|.+|++....| +.|+++....+.+++.++. .-++|||+
T Consensus 3 ~~~~rillkLsGe~l~g~~~~gid~~~i~~~a~~i~~~~~~------g~eV~iVv 51 (238)
T COG0528 3 PKYMRILLKLSGEALAGEQGFGIDPEVLDRIANEIKELVDL------GVEVAVVV 51 (238)
T ss_pred cceEEEEEEeecceecCCCCCCCCHHHHHHHHHHHHHHHhc------CcEEEEEE
Confidence 346678999999987764 6788999888888877763 24799998
No 123
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=76.30 E-value=2.3 Score=50.06 Aligned_cols=23 Identities=26% Similarity=0.742 Sum_probs=18.0
Q ss_pred eEEcCCCCccccCCCCCCCCCCcee
Q 014440 303 GYTCPRCKARVCELPTECRICGLQL 327 (424)
Q Consensus 303 Gy~Cp~C~s~~C~lP~~C~~C~l~L 327 (424)
-+.||.|++.. +...|+.||..+
T Consensus 667 ~rkCPkCG~~t--~~~fCP~CGs~t 689 (1337)
T PRK14714 667 RRRCPSCGTET--YENRCPDCGTHT 689 (1337)
T ss_pred EEECCCCCCcc--ccccCcccCCcC
Confidence 47899999964 335999999874
No 124
>PF04285 DUF444: Protein of unknown function (DUF444); InterPro: IPR006698 This entry is represented by Thermus phage phiYS40, Orf56. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches [].
Probab=76.11 E-value=22 Score=37.72 Aligned_cols=109 Identities=14% Similarity=0.233 Sum_probs=59.4
Q ss_pred EEEEEeCCHhhhcCCCCCChHH-HHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCHHHHHHHHhhhhCCCC
Q 014440 88 LYIVIDLSRAAAEMDFRPSRMV-VVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSPESHIKALMGKLGCSG 166 (424)
Q Consensus 88 lvlvLD~S~SM~~~D~~P~RL~-~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~~~~~~G 166 (424)
++.++|+|+||...- .-|. .....+..|+....+ .-.+-.|+. +..|.-+.. +++ . . ...+|
T Consensus 249 v~~lmDvSGSM~~~~---K~lak~ff~~l~~fL~~~Y~---~Ve~vfI~H-~t~A~EVdE-----e~F---F-~-~~esG 311 (421)
T PF04285_consen 249 VFCLMDVSGSMGEFK---KDLAKRFFFWLYLFLRRKYE---NVEIVFIRH-HTEAKEVDE-----EEF---F-H-SRESG 311 (421)
T ss_pred EEEEEeCCCCCchHH---HHHHHHHHHHHHHHHHhccC---ceEEEEEee-cCceEEecH-----HHh---c-c-cCCCC
Confidence 567799999997520 1122 122245566665443 234455553 456655442 111 1 1 14679
Q ss_pred cchHHHHHHHHHHHHcC-CCCCCCcEEEEEE-cCCCCCCccCHHHHHHHHH
Q 014440 167 DSSIQNALDLVHGLLNQ-IPSYGHREVLILY-SALSTCDPGDIMETIQKCK 215 (424)
Q Consensus 167 ~tsL~~AL~~Al~~L~~-~p~~~~reILvI~-ss~~t~dp~~i~~~i~~ak 215 (424)
||-+..|+++|++++.. .|.. .=.|-++- |++++-+ .|-..+++.|+
T Consensus 312 GT~vSSA~~l~~~ii~erypp~-~wNiY~~~~SDGDN~~-~D~~~~~~ll~ 360 (421)
T PF04285_consen 312 GTRVSSAYELALEIIEERYPPS-DWNIYVFHASDGDNWS-SDNERCVELLE 360 (421)
T ss_pred CeEehHHHHHHHHHHHhhCChh-hceeeeEEcccCcccc-CCCHHHHHHHH
Confidence 99999999999999986 4322 22455553 4444422 22234454444
No 125
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=76.11 E-value=1.3 Score=32.01 Aligned_cols=23 Identities=35% Similarity=1.037 Sum_probs=17.0
Q ss_pred eEEcCCCCc-cccCCCC----CCCCCCc
Q 014440 303 GYTCPRCKA-RVCELPT----ECRICGL 325 (424)
Q Consensus 303 Gy~Cp~C~s-~~C~lP~----~C~~C~l 325 (424)
|++||.|++ ++..+.. .|.-|+-
T Consensus 18 g~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 18 GFVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 899999999 5555555 6777753
No 126
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=75.96 E-value=1.6 Score=32.91 Aligned_cols=24 Identities=42% Similarity=1.035 Sum_probs=18.8
Q ss_pred eEEcCCCCccccCCC-------CCCCCCCcee
Q 014440 303 GYTCPRCKARVCELP-------TECRICGLQL 327 (424)
Q Consensus 303 Gy~Cp~C~s~~C~lP-------~~C~~C~l~L 327 (424)
-|.||.|++.+ ++| +.|+.||..|
T Consensus 2 ~~~CP~CG~~i-ev~~~~~GeiV~Cp~CGael 32 (54)
T TIGR01206 2 QFECPDCGAEI-ELENPELGELVICDECGAEL 32 (54)
T ss_pred ccCCCCCCCEE-ecCCCccCCEEeCCCCCCEE
Confidence 36899999866 554 4899999876
No 127
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=75.89 E-value=1 Score=32.03 Aligned_cols=24 Identities=33% Similarity=0.798 Sum_probs=14.7
Q ss_pred EEcCCCCcccc--C---CCCCCCCCCcee
Q 014440 304 YTCPRCKARVC--E---LPTECRICGLQL 327 (424)
Q Consensus 304 y~Cp~C~s~~C--~---lP~~C~~C~l~L 327 (424)
|.||.|++..= . --..|+.||+.|
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGLVL 29 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-BBE
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCCEe
Confidence 67888888651 1 113788888765
No 128
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=75.86 E-value=1.1 Score=30.84 Aligned_cols=29 Identities=34% Similarity=0.675 Sum_probs=22.3
Q ss_pred eeeCCCcCcccccccchhhhccCCCCCCC
Q 014440 382 CVACPKCKKHFCLECDIYIHESLHNCPGC 410 (424)
Q Consensus 382 ~~~C~~C~~~fC~dCd~fihe~lh~CPgC 410 (424)
...-..|++.||.+|=.-..+.-..||.|
T Consensus 11 ~~~~~~CGH~fC~~C~~~~~~~~~~CP~C 39 (39)
T PF13923_consen 11 PVVVTPCGHSFCKECIEKYLEKNPKCPVC 39 (39)
T ss_dssp EEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred cCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence 35678999999999976666667788877
No 129
>PRK05325 hypothetical protein; Provisional
Probab=75.76 E-value=21 Score=37.66 Aligned_cols=109 Identities=14% Similarity=0.228 Sum_probs=58.8
Q ss_pred EEEEEeCCHhhhcCCCCCChHHHHH-HHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCHHHHHHHHhhhhCCCC
Q 014440 88 LYIVIDLSRAAAEMDFRPSRMVVVA-KQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSPESHIKALMGKLGCSG 166 (424)
Q Consensus 88 lvlvLD~S~SM~~~D~~P~RL~~a~-~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~~~~~~G 166 (424)
++.++|+|+||... .-.|.+.. -.+-.|+..-++ | -.+-.|. ++..|.-+.. +++ . . ..-+|
T Consensus 225 mfclMDvSGSM~~~---~K~lakrff~lly~fL~r~Y~-~--vEvvFI~-H~t~AkEVdE-----eeF---F-~-~~esG 287 (401)
T PRK05325 225 MFCLMDVSGSMDEA---EKDLAKRFFFLLYLFLRRKYE-N--VEVVFIR-HHTEAKEVDE-----EEF---F-Y-SRESG 287 (401)
T ss_pred EEEEEeCCCCCchH---HHHHHHHHHHHHHHHHHhccC-c--eEEEEEe-ecCceeEcCH-----HHc---c-c-cCCCC
Confidence 56789999999742 11222211 235566665442 1 3344444 3455655443 111 1 1 14579
Q ss_pred cchHHHHHHHHHHHHcC-CCCCCCcEEEEEE-cCCCCCCccCHHHHHHHHH
Q 014440 167 DSSIQNALDLVHGLLNQ-IPSYGHREVLILY-SALSTCDPGDIMETIQKCK 215 (424)
Q Consensus 167 ~tsL~~AL~~Al~~L~~-~p~~~~reILvI~-ss~~t~dp~~i~~~i~~ak 215 (424)
||-+..|+++|++.+.. .|. ..=.|-+.- |++++-+ .|-..+++.++
T Consensus 288 GT~vSSA~~l~~eIi~~rYpp-~~wNIY~f~aSDGDNw~-~D~~~~~~ll~ 336 (401)
T PRK05325 288 GTIVSSAYKLALEIIEERYPP-AEWNIYAFQASDGDNWS-SDNPRCVELLR 336 (401)
T ss_pred CeEehHHHHHHHHHHHhhCCH-hHCeeEEEEcccCCCcC-CCCHHHHHHHH
Confidence 99999999999999986 332 222455554 3444422 23344555554
No 130
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=75.55 E-value=1.5 Score=27.31 Aligned_cols=22 Identities=36% Similarity=0.853 Sum_probs=15.3
Q ss_pred cCCCCccccCCCCCCCCCCcee
Q 014440 306 CPRCKARVCELPTECRICGLQL 327 (424)
Q Consensus 306 Cp~C~s~~C~lP~~C~~C~l~L 327 (424)
||.|++..=+=-..|+.||..|
T Consensus 2 Cp~CG~~~~~~~~fC~~CG~~l 23 (23)
T PF13240_consen 2 CPNCGAEIEDDAKFCPNCGTPL 23 (23)
T ss_pred CcccCCCCCCcCcchhhhCCcC
Confidence 7777777666666777777654
No 131
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=75.51 E-value=2.6 Score=29.11 Aligned_cols=26 Identities=31% Similarity=0.659 Sum_probs=20.3
Q ss_pred EEcCCCCccccC------CCCCCCCCCceecC
Q 014440 304 YTCPRCKARVCE------LPTECRICGLQLVS 329 (424)
Q Consensus 304 y~Cp~C~s~~C~------lP~~C~~C~l~Lvs 329 (424)
++||.|+++|=. .+..|..||..||.
T Consensus 2 r~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L~q 33 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPPKVEGVCDNCGGELVQ 33 (36)
T ss_dssp EEETTTTEEEETTTB--SSTTBCTTTTEBEBE
T ss_pred cCcCCCCCccccccCCCCCCCccCCCCCeeEe
Confidence 589999998753 34689999998873
No 132
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=75.32 E-value=2.1 Score=50.35 Aligned_cols=45 Identities=24% Similarity=0.668 Sum_probs=31.1
Q ss_pred CceeecccccccCCCCCCceeeCCCcCccc-----ccccchhhhcc---CCCCCCCCCCCC
Q 014440 363 STCFGCQQSLLASGNKAGLCVACPKCKKHF-----CLECDIYIHES---LHNCPGCESLRQ 415 (424)
Q Consensus 363 ~~C~~C~~~~~~~~~~~~~~~~C~~C~~~f-----C~dCd~fihe~---lh~CPgC~~~~~ 415 (424)
..|-.|....+ ...||+|+.+. |.+|..-+... --.||.|.....
T Consensus 668 rkCPkCG~~t~--------~~fCP~CGs~te~vy~CPsCGaev~~des~a~~CP~CGtplv 720 (1337)
T PRK14714 668 RRCPSCGTETY--------ENRCPDCGTHTEPVYVCPDCGAEVPPDESGRVECPRCDVELT 720 (1337)
T ss_pred EECCCCCCccc--------cccCcccCCcCCCceeCccCCCccCCCccccccCCCCCCccc
Confidence 57999975432 24699999774 99998866533 236999976443
No 133
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=74.75 E-value=1.7 Score=30.03 Aligned_cols=29 Identities=38% Similarity=0.804 Sum_probs=21.0
Q ss_pred ceeecccccccCCC---CCCceeeCCCcCccc
Q 014440 364 TCFGCQQSLLASGN---KAGLCVACPKCKKHF 392 (424)
Q Consensus 364 ~C~~C~~~~~~~~~---~~~~~~~C~~C~~~f 392 (424)
.|-.|+..|.-+++ ......+|++|++.|
T Consensus 4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred ECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 68899888864432 234468999999987
No 134
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=74.03 E-value=2 Score=30.70 Aligned_cols=28 Identities=29% Similarity=0.865 Sum_probs=21.6
Q ss_pred ceeecccccccCCCCCCceeeCCCc-Ccccccccc
Q 014440 364 TCFGCQQSLLASGNKAGLCVACPKC-KKHFCLECD 397 (424)
Q Consensus 364 ~C~~C~~~~~~~~~~~~~~~~C~~C-~~~fC~dCd 397 (424)
.|-+|..++.. .+|+|..| .-.+|.+|-
T Consensus 2 ~Cd~C~~~i~G------~ry~C~~C~d~dLC~~C~ 30 (43)
T cd02340 2 ICDGCQGPIVG------VRYKCLVCPDYDLCESCE 30 (43)
T ss_pred CCCCCCCcCcC------CeEECCCCCCccchHHhh
Confidence 59999975532 58999999 567888883
No 135
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=74.03 E-value=3.4 Score=30.91 Aligned_cols=43 Identities=26% Similarity=0.692 Sum_probs=31.2
Q ss_pred CCcee--ecccccccCCCCCCceeeCCCcCcccccccchhhhccC
Q 014440 362 RSTCF--GCQQSLLASGNKAGLCVACPKCKKHFCLECDIYIHESL 404 (424)
Q Consensus 362 ~~~C~--~C~~~~~~~~~~~~~~~~C~~C~~~fC~dCd~fihe~l 404 (424)
-..|- +|...+....+.......|+.|+..||..|-.--|+-.
T Consensus 18 ~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~H~~~ 62 (64)
T smart00647 18 LKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHSPV 62 (64)
T ss_pred ccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcCCCCC
Confidence 45788 89776655421223467899999999999998888654
No 136
>TIGR02877 spore_yhbH sporulation protein YhbH. This protein family, typified by YhbH in Bacillus subtilis, is found in nearly every endospore-forming bacterium and in no other genome (but note that the trusted cutoff score is set high to exclude a single high-scoring sequence from Nitrosococcus oceani ATCC 19707, which is classified in the Gammaproteobacteria). The gene in Bacillus subtilis was shown to be in the regulon of the sporulation sigma factor, sigma-E, and its mutation was shown to create a sporulation defect.
Probab=73.88 E-value=31 Score=35.91 Aligned_cols=110 Identities=13% Similarity=0.195 Sum_probs=59.6
Q ss_pred EEEEEeCCHhhhcCCCCCChHHHH-HHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCHHHHHHHHhhhhCCCC
Q 014440 88 LYIVIDLSRAAAEMDFRPSRMVVV-AKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSPESHIKALMGKLGCSG 166 (424)
Q Consensus 88 lvlvLD~S~SM~~~D~~P~RL~~a-~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~~~~~~G 166 (424)
++.++|+|+||.+. .-.|.+. --.+-.|+..-++ | -.+-.|. +...|.-+.. +++ .. ..-+|
T Consensus 205 ~fc~MDvSGSM~~~---~K~lak~ff~~ly~FL~~~Y~-~--VeivFI~-H~t~AkEVdE-----eeF---F~--~~EsG 267 (371)
T TIGR02877 205 VIAMMDTSGSMGQF---KKYIARSFFFWMVKFLRTKYE-N--VEICFIS-HHTEAKEVTE-----EEF---FH--KGESG 267 (371)
T ss_pred EEEEEeCCCCCCHH---HHHHHHHHHHHHHHHHHhccC-c--eEEEEEe-ecCeeEEcCH-----HHh---cc--cCCCC
Confidence 56679999999642 1122211 1235566665442 1 3344444 3455555442 111 11 14579
Q ss_pred cchHHHHHHHHHHHHcC-CCCCCCcEEEEEE-cCCCCCCccCHHHHHHHHHh
Q 014440 167 DSSIQNALDLVHGLLNQ-IPSYGHREVLILY-SALSTCDPGDIMETIQKCKE 216 (424)
Q Consensus 167 ~tsL~~AL~~Al~~L~~-~p~~~~reILvI~-ss~~t~dp~~i~~~i~~akk 216 (424)
||-+..|+++|++.+.. .|+ ..=.|-..- |++++-+ .|-..+++.|++
T Consensus 268 GT~vSSA~~l~~eII~~rYpp-~~wNIY~f~aSDGDNw~-~D~~~c~~ll~~ 317 (371)
T TIGR02877 268 GTYCSSGYKKALEIIDERYNP-ARYNIYAFHFSDGDNLT-SDNERAVKLVRK 317 (371)
T ss_pred CeEehHHHHHHHHHHHhhCCh-hhCeeEEEEcccCCCcc-CCcHHHHHHHHH
Confidence 99999999999999985 332 222455554 4444322 233456666654
No 137
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=73.40 E-value=2.9 Score=43.79 Aligned_cols=45 Identities=20% Similarity=0.465 Sum_probs=32.3
Q ss_pred CCceeecccccccCCCCCCceeeCCCcCcccccccchhhhccCCCCCCCCCCC
Q 014440 362 RSTCFGCQQSLLASGNKAGLCVACPKCKKHFCLECDIYIHESLHNCPGCESLR 414 (424)
Q Consensus 362 ~~~C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~dCd~fihe~lh~CPgC~~~~ 414 (424)
...|..|...|..+ .-..|++.||..|-...=+.-..||.|....
T Consensus 26 ~l~C~IC~d~~~~P--------vitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~ 70 (397)
T TIGR00599 26 SLRCHICKDFFDVP--------VLTSCSHTFCSLCIRRCLSNQPKCPLCRAED 70 (397)
T ss_pred ccCCCcCchhhhCc--------cCCCCCCchhHHHHHHHHhCCCCCCCCCCcc
Confidence 45899999776532 1358999999999764334445899997643
No 138
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=72.45 E-value=2.3 Score=39.74 Aligned_cols=28 Identities=29% Similarity=0.755 Sum_probs=25.4
Q ss_pred CCCcCcccccccchhhhccCCCCCCCCC
Q 014440 385 CPKCKKHFCLECDIYIHESLHNCPGCES 412 (424)
Q Consensus 385 C~~C~~~fC~dCd~fihe~lh~CPgC~~ 412 (424)
=.+|+++||..|=.=.-..-|.||-|-.
T Consensus 148 sTkCGHvFC~~Cik~alk~~~~CP~C~k 175 (187)
T KOG0320|consen 148 STKCGHVFCSQCIKDALKNTNKCPTCRK 175 (187)
T ss_pred ccccchhHHHHHHHHHHHhCCCCCCccc
Confidence 4699999999999988899999999975
No 139
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=72.22 E-value=2.9 Score=46.50 Aligned_cols=6 Identities=33% Similarity=0.894 Sum_probs=2.4
Q ss_pred ceeecc
Q 014440 364 TCFGCQ 369 (424)
Q Consensus 364 ~C~~C~ 369 (424)
+|.-|.
T Consensus 17 FC~~CG 22 (645)
T PRK14559 17 FCQKCG 22 (645)
T ss_pred cccccC
Confidence 344443
No 140
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=72.21 E-value=2.9 Score=28.75 Aligned_cols=30 Identities=27% Similarity=0.590 Sum_probs=21.5
Q ss_pred eeeCCCcCcccccccchhhhccCCCCCCCCC
Q 014440 382 CVACPKCKKHFCLECDIYIHESLHNCPGCES 412 (424)
Q Consensus 382 ~~~C~~C~~~fC~dCd~fihe~lh~CPgC~~ 412 (424)
.|+|+.|++.|=..-..-. +.+..||.|..
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISD-DPLATCPECGG 34 (41)
T ss_pred EEEcCCCCCEEEEEEecCC-CCCCCCCCCCC
Confidence 5899999998754433322 66788999976
No 141
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=72.00 E-value=2.1 Score=43.14 Aligned_cols=41 Identities=32% Similarity=0.672 Sum_probs=31.6
Q ss_pred CCceeecccccccCCCCCCcee-eCCCcCcccccccchhhhccCCCCCCCCC
Q 014440 362 RSTCFGCQQSLLASGNKAGLCV-ACPKCKKHFCLECDIYIHESLHNCPGCES 412 (424)
Q Consensus 362 ~~~C~~C~~~~~~~~~~~~~~~-~C~~C~~~fC~dCd~fihe~lh~CPgC~~ 412 (424)
-.+|--|..++. .| +=--|+++||++|-. -|+...||+|-.
T Consensus 90 VHfCd~Cd~PI~--------IYGRmIPCkHvFCl~CAr--~~~dK~Cp~C~d 131 (389)
T KOG2932|consen 90 VHFCDRCDFPIA--------IYGRMIPCKHVFCLECAR--SDSDKICPLCDD 131 (389)
T ss_pred eEeecccCCcce--------eeecccccchhhhhhhhh--cCccccCcCccc
Confidence 348999987764 34 555799999999976 355889999953
No 142
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=71.78 E-value=2.8 Score=36.09 Aligned_cols=34 Identities=26% Similarity=0.562 Sum_probs=25.2
Q ss_pred CCCCCceeecccccccCCCCCCceeeCCCcCcccccc
Q 014440 359 NISRSTCFGCQQSLLASGNKAGLCVACPKCKKHFCLE 395 (424)
Q Consensus 359 ~~~~~~C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~d 395 (424)
.+.++.|..|.++|..-... .-.||+|+..|=.+
T Consensus 6 lGtKR~Cp~CG~kFYDLnk~---PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 6 LGTKRTCPSCGAKFYDLNKD---PIVCPKCGTEFPPE 39 (108)
T ss_pred cCCcccCCCCcchhccCCCC---CccCCCCCCccCcc
Confidence 35688999999999865432 24599999987554
No 143
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=71.73 E-value=3.8 Score=36.79 Aligned_cols=11 Identities=36% Similarity=0.924 Sum_probs=8.6
Q ss_pred eeeCCCcCccc
Q 014440 382 CVACPKCKKHF 392 (424)
Q Consensus 382 ~~~C~~C~~~f 392 (424)
.|+||.|+++|
T Consensus 124 f~~C~~C~kiy 134 (147)
T PF01927_consen 124 FWRCPGCGKIY 134 (147)
T ss_pred EEECCCCCCEe
Confidence 57888888876
No 144
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=71.47 E-value=1 Score=50.01 Aligned_cols=49 Identities=29% Similarity=0.564 Sum_probs=36.0
Q ss_pred CceeecccccccCCCCCCceeeCCCcCcccccccchhhhcc-CCCCCCCCCCCCCCCc
Q 014440 363 STCFGCQQSLLASGNKAGLCVACPKCKKHFCLECDIYIHES-LHNCPGCESLRQSNPV 419 (424)
Q Consensus 363 ~~C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~dCd~fihe~-lh~CPgC~~~~~~~~~ 419 (424)
-+|..|+....+. .=++|.+.||..|-----|+ -.-||+|......+.+
T Consensus 644 LkCs~Cn~R~Kd~--------vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganDv 693 (698)
T KOG0978|consen 644 LKCSVCNTRWKDA--------VITKCGHVFCEECVQTRYETRQRKCPKCNAAFGANDV 693 (698)
T ss_pred eeCCCccCchhhH--------HHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCcccc
Confidence 4799999766532 24599999999998555555 4589999887666554
No 145
>KOG4465 consensus Uncharacterized conserved protein [Function unknown]
Probab=70.31 E-value=22 Score=36.94 Aligned_cols=125 Identities=16% Similarity=0.194 Sum_probs=65.4
Q ss_pred eEEEEEeCCHhhhcCCCCCChHHHHHH--HHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCH--HHHHHHHhhhh
Q 014440 87 YLYIVIDLSRAAAEMDFRPSRMVVVAK--QVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSP--ESHIKALMGKL 162 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D~~P~RL~~a~~--~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~--~~~~~~L~~~~ 162 (424)
...|+||+|.||...-+ -+-|. +.. ...-+|+ .+-....-.|+|.+. .+-.|+|.|. ..++.++.+
T Consensus 429 r~~laldvs~sm~~rv~-~s~ln-~reaaa~m~lin----lhnead~~~vaf~d~--lte~pftkd~kigqv~~~~nn-- 498 (598)
T KOG4465|consen 429 RFCLALDVSASMNQRVL-GSILN-AREAAAAMCLIN----LHNEADSRCVAFCDE--LTECPFTKDMKIGQVLDAMNN-- 498 (598)
T ss_pred eEEEEEecchhhhhhhh-ccccc-hHHHHhhhheee----eccccceeEEEeccc--cccCCCcccccHHHHHHHHhc--
Confidence 67999999999985432 22222 122 1222333 233345677888543 3346888774 334444443
Q ss_pred CCCCcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHH--HHHHHHHh-CCcE---EEEEEecc
Q 014440 163 GCSGDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIM--ETIQKCKE-SKIR---CSVIGLSA 228 (424)
Q Consensus 163 ~~~G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~--~~i~~akk-~~Ir---V~vIgLg~ 228 (424)
.+.|+|.-+ |-|.-..=.+ ..-.|.||+.+.+|- .|.|+ ++++..++ .+|. +-|+++.+
T Consensus 499 i~~g~tdcg--lpm~wa~enn----lk~dvfii~tdndt~-ageihp~~aik~yrea~~i~dakliv~amqa 563 (598)
T KOG4465|consen 499 IDAGGTDCG--LPMIWAQENN----LKADVFIIFTDNDTF-AGEIHPAEAIKEYREAMDIHDAKLIVCAMQA 563 (598)
T ss_pred CCCCCCccC--CceeehhhcC----CCccEEEEEecCccc-ccccCHHHHHHHHHHhcCCCcceEEEEEeec
Confidence 255666432 2221111111 233578888776663 34554 56666544 4554 66777654
No 146
>PF01882 DUF58: Protein of unknown function DUF58; InterPro: IPR002881 This domain is found in a family of prokaryotic proteins that have no known function. Proteins belonging to this family include hypothetical proteins from eubacteria and archaebacteria. Some of these proteins also contain the Von Willebrand factor, type A domain (see IPR002035 from INTERPRO).
Probab=69.88 E-value=8.6 Score=30.65 Aligned_cols=41 Identities=17% Similarity=0.165 Sum_probs=35.0
Q ss_pred ceEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccC
Q 014440 86 RYLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQN 126 (424)
Q Consensus 86 R~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qn 126 (424)
..++|+||.+.+|....-....++.++..+..++..+..++
T Consensus 41 ~~~~i~ld~~~~~~~~~~~~~~~e~~l~~a~~l~~~~~~~g 81 (86)
T PF01882_consen 41 QPVWIVLDLSPSMYFGSNGRSKFERALSAAASLANQALRQG 81 (86)
T ss_pred CcEEEEEECCCccccCcCCCCHHHHHHHHHHHHHHHHHhcC
Confidence 38999999999998777667899999999998888877654
No 147
>PF03853 YjeF_N: YjeF-related protein N-terminus; InterPro: IPR004443 The YjeF N-terminal domains occur either as single proteins or fusions with other domains and are commonly associated with enzymes. In bacteria and archaea, YjeF N-terminal domains are often fused to a YjeF C-terminal domain with high structural homology to the members of a ribokinase-like superfamily (see PDOC00806 from PROSITEDOC)and/or belong to operons that encode enzymes of diverse functions: pyridoxal phosphate biosynthetic protein PdxJ; phosphopanteine-protein transferase; ATP/GTP hydrolase; and pyruvate-formate lyase 1-activating enzyme. In plants, the YjeF N-terminal domain is fused to a C-terminal putative pyridoxamine 5'-phosphate oxidase. In eukaryotes, proteins that consist of (Sm)-FDF-YjeF N-terminal domains may be involved in RNA processing [, ]. The YjeF N-terminal domains represent a novel version of the Rossmann fold, one of the most common protein folds in nature observed in numerous enzyme families, that has acquired a set of catalytic residues and structural features that distinguish them from the conventional dehydrogenases. The YjeF N-terminal domain is comprised of a three-layer alpha-beta-alpha sandwich with a central beta-sheet surrounded by helices. The conservation of the acidic residues in the predicted active site of the YjeF N-terminal domains is reminiscent of the presence of such residues in the active sites of diverse hydrolases [, ].; PDB: 3K5W_A 2O8N_A 2DG2_F 3RNO_A 1JZT_B 3D3K_A 3D3J_A 3RSG_A 3RT9_A 3RRF_A ....
Probab=69.28 E-value=20 Score=32.81 Aligned_cols=66 Identities=14% Similarity=0.036 Sum_probs=46.7
Q ss_pred CCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecc------hHHHHHHHHHHhCCEEEEecChhhH
Q 014440 186 SYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSA------EMFICKHLCQETGGTYSVALDESHS 253 (424)
Q Consensus 186 ~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~------e~~iLq~iA~~TGG~Y~~~~d~~~L 253 (424)
.+..++|+||.|+..+ -+|-..++..|.+.|++|.++.+.. +...-.++++.+|+.+....+...+
T Consensus 22 ~~~~~~v~il~G~GnN--GgDgl~~AR~L~~~G~~V~v~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~ 93 (169)
T PF03853_consen 22 SPKGPRVLILCGPGNN--GGDGLVAARHLANRGYNVTVYLVGPPEKLSEDAKQQLEILKKMGIKIIELDSDEDL 93 (169)
T ss_dssp CCTT-EEEEEE-SSHH--HHHHHHHHHHHHHTTCEEEEEEEESSSSTSHHHHHHHHHHHHTT-EEESSCCGSGG
T ss_pred ccCCCeEEEEECCCCC--hHHHHHHHHHHHHCCCeEEEEEEeccccCCHHHHHHHHHHHhcCCcEeeccccchh
Confidence 3556789999987543 4566788999999999999977764 2467778888899888865554443
No 148
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=69.02 E-value=2.2 Score=43.14 Aligned_cols=28 Identities=36% Similarity=0.643 Sum_probs=21.6
Q ss_pred ceeeecCCccccCeEEcCCCCccccCCC
Q 014440 290 SICSCHKEVKIGVGYTCPRCKARVCELP 317 (424)
Q Consensus 290 a~C~CH~~~~~~~Gy~Cp~C~s~~C~lP 317 (424)
++=+||--.+...-|.||||...||+|+
T Consensus 6 ~~~~C~ic~vq~~~YtCPRCn~~YCsl~ 33 (383)
T KOG4317|consen 6 SFLACGICGVQKREYTCPRCNLLYCSLK 33 (383)
T ss_pred ceeeccccccccccccCCCCCccceeee
Confidence 3457886555544799999999999997
No 149
>PLN03086 PRLI-interacting factor K; Provisional
Probab=68.13 E-value=6.5 Score=43.06 Aligned_cols=23 Identities=26% Similarity=0.716 Sum_probs=12.2
Q ss_pred EcCC--CCccccC----CCCCCCCCCcee
Q 014440 305 TCPR--CKARVCE----LPTECRICGLQL 327 (424)
Q Consensus 305 ~Cp~--C~s~~C~----lP~~C~~C~l~L 327 (424)
.||. |+.++-. =+..|+.|+..+
T Consensus 435 ~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f 463 (567)
T PLN03086 435 VCPHDGCGIVLRVEEAKNHVHCEKCGQAF 463 (567)
T ss_pred eCCcccccceeeccccccCccCCCCCCcc
Confidence 4663 6655532 123566776655
No 150
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=66.98 E-value=4.8 Score=31.02 Aligned_cols=47 Identities=21% Similarity=0.653 Sum_probs=34.7
Q ss_pred CCceeecccccccCCCCCCceeeCCCcCc---ccccccchhhhccCCCCCCCCC
Q 014440 362 RSTCFGCQQSLLASGNKAGLCVACPKCKK---HFCLECDIYIHESLHNCPGCES 412 (424)
Q Consensus 362 ~~~C~~C~~~~~~~~~~~~~~~~C~~C~~---~fC~dCd~fihe~lh~CPgC~~ 412 (424)
...|..|...+... .....|.||+|++ ..|.-|-. |-+...||-|..
T Consensus 9 ~~~CtSCg~~i~p~--e~~v~F~CPnCGe~~I~Rc~~CRk--~g~~Y~Cp~CGF 58 (61)
T COG2888 9 PPVCTSCGREIAPG--ETAVKFPCPNCGEVEIYRCAKCRK--LGNPYRCPKCGF 58 (61)
T ss_pred CceeccCCCEeccC--CceeEeeCCCCCceeeehhhhHHH--cCCceECCCcCc
Confidence 45899999888321 2234799999994 57888876 567788999864
No 151
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=66.94 E-value=3.1 Score=38.88 Aligned_cols=27 Identities=37% Similarity=0.837 Sum_probs=22.8
Q ss_pred eEEcCCCCcccc-----CCCCCCCCCCceecC
Q 014440 303 GYTCPRCKARVC-----ELPTECRICGLQLVS 329 (424)
Q Consensus 303 Gy~Cp~C~s~~C-----~lP~~C~~C~l~Lvs 329 (424)
+|+||+|..+|- ++--.||.||-.|+-
T Consensus 113 ~y~C~~~~~r~sfdeA~~~~F~Cp~Cg~~L~~ 144 (176)
T COG1675 113 YYVCPNCHVKYSFDEAMELGFTCPKCGEDLEE 144 (176)
T ss_pred ceeCCCCCCcccHHHHHHhCCCCCCCCchhhh
Confidence 999999999885 566789999988863
No 152
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=66.65 E-value=3 Score=28.50 Aligned_cols=25 Identities=32% Similarity=0.719 Sum_probs=17.7
Q ss_pred EEcCCCCccccC----CC-----CCCCCCCceec
Q 014440 304 YTCPRCKARVCE----LP-----TECRICGLQLV 328 (424)
Q Consensus 304 y~Cp~C~s~~C~----lP-----~~C~~C~l~Lv 328 (424)
+.||.|++.|-- ++ +.|+.||..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 679999986642 21 57999988763
No 153
>PRK04023 DNA polymerase II large subunit; Validated
Probab=66.15 E-value=4.3 Score=46.93 Aligned_cols=23 Identities=26% Similarity=0.753 Sum_probs=19.0
Q ss_pred CeEEcCCCCccccCCCCCCCCCCce
Q 014440 302 VGYTCPRCKARVCELPTECRICGLQ 326 (424)
Q Consensus 302 ~Gy~Cp~C~s~~C~lP~~C~~C~l~ 326 (424)
+...||.|+... .-..||.||..
T Consensus 625 g~RfCpsCG~~t--~~frCP~CG~~ 647 (1121)
T PRK04023 625 GRRKCPSCGKET--FYRRCPFCGTH 647 (1121)
T ss_pred cCccCCCCCCcC--CcccCCCCCCC
Confidence 467899999985 55689999986
No 154
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=65.72 E-value=2.8 Score=32.22 Aligned_cols=27 Identities=26% Similarity=0.730 Sum_probs=22.4
Q ss_pred EcCCCCccc-----cCCCCCCCCCCceecCch
Q 014440 305 TCPRCKARV-----CELPTECRICGLQLVSSP 331 (424)
Q Consensus 305 ~Cp~C~s~~-----C~lP~~C~~C~l~Lvs~p 331 (424)
.||.|.... -..++.|.+||.+|.-+.
T Consensus 13 kCp~C~n~q~vFsha~t~V~C~~Cg~~L~~Pt 44 (59)
T PRK00415 13 KCPDCGNEQVVFSHASTVVRCLVCGKTLAEPT 44 (59)
T ss_pred ECCCCCCeEEEEecCCcEEECcccCCCcccCC
Confidence 599999887 567789999999987553
No 155
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=65.66 E-value=4 Score=30.32 Aligned_cols=22 Identities=36% Similarity=0.866 Sum_probs=16.6
Q ss_pred EEcCCCCccccC-----------------CCC--CCCCCCc
Q 014440 304 YTCPRCKARVCE-----------------LPT--ECRICGL 325 (424)
Q Consensus 304 y~Cp~C~s~~C~-----------------lP~--~C~~C~l 325 (424)
|+|+.|+-+|=+ ||. .||+|+.
T Consensus 2 y~C~~CgyiYd~~~Gd~~~~i~pGt~f~~Lp~~w~CP~C~a 42 (50)
T cd00730 2 YECRICGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGA 42 (50)
T ss_pred cCCCCCCeEECCCCCCcccCcCCCCCHhHCCCCCCCCCCCC
Confidence 778888877763 675 7888875
No 156
>PHA02929 N1R/p28-like protein; Provisional
Probab=65.27 E-value=5.8 Score=38.81 Aligned_cols=51 Identities=22% Similarity=0.503 Sum_probs=35.4
Q ss_pred CCceeecccccccCCCCCCceeeCCCcCcccccccchhhhccCCCCCCCCC
Q 014440 362 RSTCFGCQQSLLASGNKAGLCVACPKCKKHFCLECDIYIHESLHNCPGCES 412 (424)
Q Consensus 362 ~~~C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~dCd~fihe~lh~CPgC~~ 412 (424)
...|.-|...+..+.......-.=+.|++.||.+|=.--.+.-..||-|-.
T Consensus 174 ~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~ 224 (238)
T PHA02929 174 DKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRT 224 (238)
T ss_pred CCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCC
Confidence 457999997765321100001134689999999998777788889999964
No 157
>TIGR00288 conserved hypothetical protein TIGR00288. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.
Probab=64.34 E-value=24 Score=32.49 Aligned_cols=76 Identities=21% Similarity=0.298 Sum_probs=48.2
Q ss_pred HHHHHHhhh-h---CCCCcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecc
Q 014440 153 SHIKALMGK-L---GCSGDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSA 228 (424)
Q Consensus 153 ~~~~~L~~~-~---~~~G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~ 228 (424)
.+.+.|... . ...|.+.++-++.. +.++.. + .=..++|.+|. +|+...+..+++.|.+|.++|...
T Consensus 70 ~l~~~l~~~Gf~pv~~kG~~Dv~laIDa-me~~~~-~---~iD~~vLvSgD-----~DF~~Lv~~lre~G~~V~v~g~~~ 139 (160)
T TIGR00288 70 KLIEAVVNQGFEPIIVAGDVDVRMAVEA-MELIYN-P---NIDAVALVTRD-----ADFLPVINKAKENGKETIVIGAEP 139 (160)
T ss_pred HHHHHHHHCCceEEEecCcccHHHHHHH-HHHhcc-C---CCCEEEEEecc-----HhHHHHHHHHHHCCCEEEEEeCCC
Confidence 344555443 1 24677777766664 444421 1 11345565542 467889999999999999999753
Q ss_pred -hHHHHHHHHH
Q 014440 229 -EMFICKHLCQ 238 (424)
Q Consensus 229 -e~~iLq~iA~ 238 (424)
-..-|++.|+
T Consensus 140 ~ts~~L~~acd 150 (160)
T TIGR00288 140 GFSTALQNSAD 150 (160)
T ss_pred CChHHHHHhcC
Confidence 3567888885
No 158
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=64.16 E-value=3.6 Score=34.92 Aligned_cols=25 Identities=32% Similarity=0.703 Sum_probs=19.4
Q ss_pred eEEcCCCCccccC-------CCCCCCCCCcee
Q 014440 303 GYTCPRCKARVCE-------LPTECRICGLQL 327 (424)
Q Consensus 303 Gy~Cp~C~s~~C~-------lP~~C~~C~l~L 327 (424)
-|.||+|++..-. .-..|+.||...
T Consensus 21 ~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~ 52 (99)
T PRK14892 21 IFECPRCGKVSISVKIKKNIAIITCGNCGLYT 52 (99)
T ss_pred EeECCCCCCeEeeeecCCCcceEECCCCCCcc
Confidence 6999999976443 257999999873
No 159
>cd05017 SIS_PGI_PMI_1 The members of this protein family contain the SIS (Sugar ISomerase) domain and have both the phosphoglucose isomerase (PGI) and the phosphomannose isomerase (PMI) functions. These functions catalyze the reversible reactions of glucose 6-phosphate to fructose 6-phosphate, and mannose 6-phosphate to fructose 6-phosphate, respectively at an equal rate. This protein contains two SIS domains. This alignment is based on the first SIS domain.
Probab=63.76 E-value=12 Score=31.84 Aligned_cols=55 Identities=15% Similarity=0.155 Sum_probs=36.7
Q ss_pred EEEEEEc-CCCCCCccCHHHHHHHHHhCCcEEEEEEecchHHHHHHHHHHhCCEEEEecChh
Q 014440 191 EVLILYS-ALSTCDPGDIMETIQKCKESKIRCSVIGLSAEMFICKHLCQETGGTYSVALDES 251 (424)
Q Consensus 191 eILvI~s-s~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~~iLq~iA~~TGG~Y~~~~d~~ 251 (424)
-++|+++ ++++ .++.++++.+++.|++|-+|- ... -|.++|+..|+.-+...+..
T Consensus 45 dl~I~iS~SG~t---~e~i~~~~~a~~~g~~iI~IT--~~~-~l~~~~~~~~~~~~~~p~~~ 100 (119)
T cd05017 45 TLVIAVSYSGNT---EETLSAVEQAKERGAKIVAIT--SGG-KLLEMAREHGVPVIIIPKGL 100 (119)
T ss_pred CEEEEEECCCCC---HHHHHHHHHHHHCCCEEEEEe--CCc-hHHHHHHHcCCcEEECCCCC
Confidence 4555554 4333 457789999999998664444 333 38889998887777654444
No 160
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=63.42 E-value=5.2 Score=27.49 Aligned_cols=29 Identities=34% Similarity=0.657 Sum_probs=20.4
Q ss_pred ceeecccccccCCC---CCCceeeCCCcCccc
Q 014440 364 TCFGCQQSLLASGN---KAGLCVACPKCKKHF 392 (424)
Q Consensus 364 ~C~~C~~~~~~~~~---~~~~~~~C~~C~~~f 392 (424)
.|-.|+..|.-++. ......+|++|++.|
T Consensus 4 ~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 58899888864431 223457999999876
No 161
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=62.04 E-value=9.7 Score=38.12 Aligned_cols=36 Identities=25% Similarity=0.818 Sum_probs=26.1
Q ss_pred CceeecccccccCCCCCCceeeCCCcCcccccccchhhhccCCCCCCCCCC
Q 014440 363 STCFGCQQSLLASGNKAGLCVACPKCKKHFCLECDIYIHESLHNCPGCESL 413 (424)
Q Consensus 363 ~~C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~dCd~fihe~lh~CPgC~~~ 413 (424)
..|| |-+.+.. ..|.||.|...||.-- -.||.|.+.
T Consensus 243 a~Cf-Ch~k~v~------~GyvCs~Clsi~C~~p--------~~C~~Cgt~ 278 (279)
T TIGR00627 243 ASCF-CHHQLVS------IGFVCSVCLSVLCQYT--------PICKTCKTA 278 (279)
T ss_pred ceee-ecCcccc------ceEECCCccCCcCCCC--------CCCCCCCCC
Confidence 4798 5544432 3599999999999654 389999753
No 162
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=61.91 E-value=2.4 Score=45.25 Aligned_cols=33 Identities=27% Similarity=0.642 Sum_probs=26.1
Q ss_pred CCCceeecccccccCCCCCCceeeCCCcCcccccccc
Q 014440 361 SRSTCFGCQQSLLASGNKAGLCVACPKCKKHFCLECD 397 (424)
Q Consensus 361 ~~~~C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~dCd 397 (424)
....|-+|+.+|..- ..+.-|-.|+.+||..|.
T Consensus 900 ~a~~cmacq~pf~af----rrrhhcrncggifcg~cs 932 (990)
T KOG1819|consen 900 DAEQCMACQMPFNAF----RRRHHCRNCGGIFCGKCS 932 (990)
T ss_pred cchhhhhccCcHHHH----HHhhhhcccCceeecccc
Confidence 345799999999632 125679999999999996
No 163
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=61.14 E-value=5.6 Score=26.73 Aligned_cols=41 Identities=27% Similarity=0.510 Sum_probs=27.8
Q ss_pred eeecccccccCCCCCCceeeCCCcCcccccccchhhhcc-CCCCCCCCC
Q 014440 365 CFGCQQSLLASGNKAGLCVACPKCKKHFCLECDIYIHES-LHNCPGCES 412 (424)
Q Consensus 365 C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~dCd~fihe~-lh~CPgC~~ 412 (424)
|..|...+. ..+.-+.|++.||.+|-.-.-+. --.||.|..
T Consensus 2 C~iC~~~~~-------~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~ 43 (45)
T cd00162 2 CPICLEEFR-------EPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRT 43 (45)
T ss_pred CCcCchhhh-------CceEecCCCChhcHHHHHHHHHhCcCCCCCCCC
Confidence 667775552 13556779999999997544443 456999964
No 164
>PF12773 DZR: Double zinc ribbon
Probab=60.06 E-value=9 Score=27.61 Aligned_cols=23 Identities=30% Similarity=0.680 Sum_probs=10.3
Q ss_pred cCCCCccccCCCCCCCCCCceec
Q 014440 306 CPRCKARVCELPTECRICGLQLV 328 (424)
Q Consensus 306 Cp~C~s~~C~lP~~C~~C~l~Lv 328 (424)
||.|+...=.=-..|+.||..|.
T Consensus 1 Cp~Cg~~~~~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 1 CPHCGTPNPDDAKFCPHCGTPLP 23 (50)
T ss_pred CCCcCCcCCccccCChhhcCChh
Confidence 44444443333334555555543
No 165
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=59.37 E-value=5.8 Score=28.98 Aligned_cols=30 Identities=27% Similarity=0.766 Sum_probs=22.3
Q ss_pred ceeecccccccCCCCCCceeeCCCc-Ccccccccch
Q 014440 364 TCFGCQQSLLASGNKAGLCVACPKC-KKHFCLECDI 398 (424)
Q Consensus 364 ~C~~C~~~~~~~~~~~~~~~~C~~C-~~~fC~dCd~ 398 (424)
.|.+|.+.+.. +.+|+|..| .-..|.+|=.
T Consensus 2 ~Cd~C~~~~~~-----g~r~~C~~C~d~dLC~~Cf~ 32 (49)
T cd02335 2 HCDYCSKDITG-----TIRIKCAECPDFDLCLECFS 32 (49)
T ss_pred CCCCcCCCCCC-----CcEEECCCCCCcchhHHhhh
Confidence 58999876642 258999999 6667887754
No 166
>PRK07418 acetolactate synthase 3 catalytic subunit; Reviewed
Probab=58.24 E-value=1e+02 Score=34.03 Aligned_cols=89 Identities=13% Similarity=0.081 Sum_probs=59.3
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH----H------------
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM----F------------ 231 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~----~------------ 231 (424)
.+++.||-.|+..=-. +..|.|+.|.|++.- . .++ ..+.++++.+++|-+|-+.... .
T Consensus 434 g~mG~glpaAiGA~lA---~p~r~Vv~i~GDG~f-~-m~~-~eL~Ta~r~~lpvi~vV~NN~~~g~i~~~q~~~~~~~~~ 507 (616)
T PRK07418 434 GTMGFGMPAAMGVKVA---LPDEEVICIAGDASF-L-MNI-QELGTLAQYGINVKTVIINNGWQGMVRQWQESFYGERYS 507 (616)
T ss_pred cccccHHHHHHHHHHh---CCCCcEEEEEcchHh-h-hhH-HHHHHHHHhCCCeEEEEEECCcchHHHHHHHHhcCCCce
Confidence 3455555555443222 225678888886432 1 222 3467889999999888886421 1
Q ss_pred ---------HHHHHHHHhCCEEEEecChhhHHHHHHhcCC
Q 014440 232 ---------ICKHLCQETGGTYSVALDESHSKELILEHAP 262 (424)
Q Consensus 232 ---------iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~~ 262 (424)
-+.++|+.-|+.++.+.+.++|.+.|.....
T Consensus 508 ~~~~~~~~~d~~~~A~a~G~~g~~V~~~~el~~al~~a~~ 547 (616)
T PRK07418 508 ASNMEPGMPDFVKLAEAFGVKGMVISERDQLKDAIAEALA 547 (616)
T ss_pred eecCCCCCCCHHHHHHHCCCeEEEeCCHHHHHHHHHHHHh
Confidence 1447889999999999999999999877653
No 167
>PRK02842 light-independent protochlorophyllide reductase subunit N; Provisional
Probab=57.91 E-value=67 Score=33.80 Aligned_cols=79 Identities=11% Similarity=0.005 Sum_probs=44.9
Q ss_pred HHHHHHHHHh-CCcEEEEEEecchH-HH-HHHHHHHhCCEEEE-ecChhhHHHHHHhcCCCCccc-hhhhhhheeeecCC
Q 014440 207 IMETIQKCKE-SKIRCSVIGLSAEM-FI-CKHLCQETGGTYSV-ALDESHSKELILEHAPPPPAI-AEFAIASLIKMGFP 281 (424)
Q Consensus 207 i~~~i~~akk-~~IrV~vIgLg~e~-~i-Lq~iA~~TGG~Y~~-~~d~~~L~~lL~~~~~pp~~~-~~~~~~~Li~mGFP 281 (424)
....+..+.+ .|+.+-.++.+... .. -+.+.....|.-.+ -.|..++.+++...- |.-.- .......|+++|||
T Consensus 302 ~~~la~~L~eelGm~~v~v~t~~~~~~~~~~~~~~l~~~~~v~~~~D~~~l~~~i~~~~-pDllig~~~~~~pl~r~GfP 380 (427)
T PRK02842 302 EIPLARFLSRECGMELVEVGTPYLNRRFLAAELALLPDGVRIVEGQDVERQLDRIRALR-PDLVVCGLGLANPLEAEGIT 380 (427)
T ss_pred HHHHHHHHHHhCCCEEEEeCCCCCCHHHHHHHHHhccCCCEEEECCCHHHHHHHHHHcC-CCEEEccCccCCchhhcCCc
Confidence 3456777887 99999777775432 22 22344444454332 245556666665532 22221 12334689999999
Q ss_pred CCCCC
Q 014440 282 QRAGE 286 (424)
Q Consensus 282 ~~~~~ 286 (424)
.....
T Consensus 381 ~~dr~ 385 (427)
T PRK02842 381 TKWSI 385 (427)
T ss_pred eeEEE
Confidence 96543
No 168
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=57.81 E-value=2.5 Score=36.66 Aligned_cols=47 Identities=26% Similarity=0.616 Sum_probs=32.1
Q ss_pred CCCceeecccccccCCCCCCceeeCCCcCcccccccchhh-hccCCCCCCC
Q 014440 361 SRSTCFGCQQSLLASGNKAGLCVACPKCKKHFCLECDIYI-HESLHNCPGC 410 (424)
Q Consensus 361 ~~~~C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~dCd~fi-he~lh~CPgC 410 (424)
+...|.-|..+|.-.++ ..-.|..|+..+|..|-++. .+..-.|.-|
T Consensus 53 ~~~~C~~C~~~fg~l~~---~~~~C~~C~~~VC~~C~~~~~~~~~WlC~vC 100 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFN---RGRVCVDCKHRVCKKCGVYSKKEPIWLCKVC 100 (118)
T ss_dssp CCSB-TTTS-BCSCTST---TCEEETTTTEEEETTSEEETSSSCCEEEHHH
T ss_pred CCcchhhhCCcccccCC---CCCcCCcCCccccCccCCcCCCCCCEEChhh
Confidence 56799999988753322 23689999999999999993 3444455544
No 169
>PF10221 DUF2151: Cell cycle and development regulator; InterPro: IPR019355 This entry represents the cell cycle regulator Mat89b, which plays an evolutionarily conserved role as a crucial regulator of both cell cycle and development []. Mat89Bb is a PNG kinase substrate that is essential for S-M cycles of early Drosophila embryogenesis, Xenopus embryonic cell cycles and morphogenesis, and cell division in cultured mammalian cells.
Probab=57.75 E-value=1.6e+02 Score=33.35 Aligned_cols=113 Identities=20% Similarity=0.139 Sum_probs=74.1
Q ss_pred eEEEEEeCCHhhhcC-------CC-----------CCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCC
Q 014440 87 YLYIVIDLSRAAAEM-------DF-----------RPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLG 148 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~-------D~-----------~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT 148 (424)
-.|||||=|+-|... |+ .++=-+++.+++.+|-+=.+|.-|..++=-+++.|..|..+..-+
T Consensus 7 KTVfVLDh~p~f~~ss~~~i~~d~~~~~~~~~~~i~KSLWTc~vEa~~EYcRIV~DlFP~~k~IrfivsD~~a~~lntW~ 86 (695)
T PF10221_consen 7 KTVFVLDHSPYFAESSNQPIDFDIVKKSRQQKAPISKSLWTCAVEASIEYCRIVWDLFPDGKLIRFIVSDTAAHILNTWS 86 (695)
T ss_pred cEEEEEcCCchhhhhccCcEEEeeecCCCCCcCcccchHHHHHHHHHHHHHHHHhhccCCCceEEEEEEccccccccCcC
Confidence 579999999998531 22 245667888888888887777777776643444588888887754
Q ss_pred C---CHHHHHHHHhhhhCC------CCcchHHHHHHHHHHHHcCC------------C-----CCCCcEEEEEEcCC
Q 014440 149 G---SPESHIKALMGKLGC------SGDSSIQNALDLVHGLLNQI------------P-----SYGHREVLILYSAL 199 (424)
Q Consensus 149 ~---d~~~~~~~L~~~~~~------~G~tsL~~AL~~Al~~L~~~------------p-----~~~~reILvI~ss~ 199 (424)
. +...+++.|.....| .++.++-.||.+|++.|... + -...++||+|+..-
T Consensus 87 ~~~Qsl~~L~~~la~vG~P~~~~~~~~d~svi~GL~~AIEaL~e~td~Q~e~~~~~~~~~~~~~~N~GrIIciT~~k 163 (695)
T PF10221_consen 87 TSQQSLSHLMNALATVGPPPRSDPENSDYSVIHGLRMAIEALAEPTDSQKEQRASRVNEELKKVENRGRIICITSAK 163 (695)
T ss_pred hhhccHHHHHHHHHhcCCCCCCCcccccchhHHHHHHHHHHHhcCCHHHHHHhhcccchhhhhccCCccEEEEEeec
Confidence 3 233444455443223 12347889999999988532 0 13456899998643
No 170
>PF14369 zf-RING_3: zinc-finger
Probab=57.37 E-value=7.7 Score=26.58 Aligned_cols=28 Identities=29% Similarity=0.685 Sum_probs=12.9
Q ss_pred ceeecccccccCCCCCCceeeCCCcCccc
Q 014440 364 TCFGCQQSLLASGNKAGLCVACPKCKKHF 392 (424)
Q Consensus 364 ~C~~C~~~~~~~~~~~~~~~~C~~C~~~f 392 (424)
.|+.|++.+.-...... .-.||.|+.-|
T Consensus 4 wCh~C~~~V~~~~~~~~-~~~CP~C~~gF 31 (35)
T PF14369_consen 4 WCHQCNRFVRIAPSPDS-DVACPRCHGGF 31 (35)
T ss_pred eCccCCCEeEeCcCCCC-CcCCcCCCCcE
Confidence 57777655532211111 11466666554
No 171
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=57.15 E-value=6.4 Score=28.28 Aligned_cols=29 Identities=24% Similarity=0.764 Sum_probs=21.5
Q ss_pred ceeecccccccCCCCCCceeeCCCcC-cccccccch
Q 014440 364 TCFGCQQSLLASGNKAGLCVACPKCK-KHFCLECDI 398 (424)
Q Consensus 364 ~C~~C~~~~~~~~~~~~~~~~C~~C~-~~fC~dCd~ 398 (424)
.|.+|.+++.. .+|+|..|. -..|.+|=.
T Consensus 2 ~C~~C~~~i~g------~r~~C~~C~d~dLC~~Cf~ 31 (46)
T cd02249 2 SCDGCLKPIVG------VRYHCLVCEDFDLCSSCYA 31 (46)
T ss_pred CCcCCCCCCcC------CEEECCCCCCCcCHHHHHC
Confidence 59999986542 489999998 566777743
No 172
>cd02004 TPP_BZL_OCoD_HPCL Thiamine pyrophosphate (TPP) family, BZL_OCoD_HPCL subfamily, TPP-binding module; composed of proteins similar to benzaldehyde lyase (BZL), oxalyl-CoA decarboxylase (OCoD) and 2-hydroxyphytanoyl-CoA lyase (2-HPCL). Pseudomonas fluorescens biovar I BZL cleaves the acyloin linkage of benzoin producing 2 molecules of benzaldehyde and enabling the Pseudomonas to grow on benzoin as the sole carbon and energy source. OCoD has a role in the detoxification of oxalate, catalyzing the decarboxylation of oxalyl-CoA to formate. 2-HPCL is a peroxisomal enzyme which plays a role in the alpha-oxidation of 3-methyl-branched fatty acids, catalyzing the cleavage of 2-hydroxy-3-methylacyl-CoA into formyl-CoA and a 2-methyl-branched fatty aldehyde. All these enzymes depend on Mg2+ and TPP for activity.
Probab=57.14 E-value=68 Score=28.90 Aligned_cols=90 Identities=8% Similarity=-0.027 Sum_probs=60.1
Q ss_pred CcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH---------------
Q 014440 166 GDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM--------------- 230 (424)
Q Consensus 166 G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~--------------- 230 (424)
+..+++.+|-.|+..-...| .++|+.|+|+..-. ... +.+.++.+.++++-+|-+....
T Consensus 46 ~~g~mG~~lp~AiGa~la~~---~~~vv~i~GDG~f~--~~~-~el~ta~~~~lpv~ivv~NN~~~~~~~~~~~~~~~~~ 119 (172)
T cd02004 46 TFGTLGVGLGYAIAAALARP---DKRVVLVEGDGAFG--FSG-MELETAVRYNLPIVVVVGNNGGWYQGLDGQQLSYGLG 119 (172)
T ss_pred CCCcccchHHHHHHHHHhCC---CCeEEEEEcchhhc--CCH-HHHHHHHHcCCCEEEEEEECcccccchhhhhhhccCC
Confidence 33456666666655432222 56788888865431 222 4567888999998888775320
Q ss_pred ---------HHHHHHHHHhCCEEEEecChhhHHHHHHhcC
Q 014440 231 ---------FICKHLCQETGGTYSVALDESHSKELILEHA 261 (424)
Q Consensus 231 ---------~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~ 261 (424)
.-+.++|+.-|..+..+.+.++|++.|.+..
T Consensus 120 ~~~~~~~~~~d~~~la~a~G~~~~~v~~~~el~~al~~a~ 159 (172)
T cd02004 120 LPVTTLLPDTRYDLVAEAFGGKGELVTTPEELKPALKRAL 159 (172)
T ss_pred CceeccCCCCCHHHHHHHCCCeEEEECCHHHHHHHHHHHH
Confidence 1356788888999998888888888887765
No 173
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=57.13 E-value=3.2 Score=43.59 Aligned_cols=26 Identities=42% Similarity=1.041 Sum_probs=22.4
Q ss_pred eEEcCCCCccccCCC-----------CCCCCCCceec
Q 014440 303 GYTCPRCKARVCELP-----------TECRICGLQLV 328 (424)
Q Consensus 303 Gy~Cp~C~s~~C~lP-----------~~C~~C~l~Lv 328 (424)
||+||.|+++|-.|- -.|..|+.-||
T Consensus 128 ~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelv 164 (436)
T KOG2593|consen 128 GYVCPNCQKKYTSLEALQLLDNETGEFHCENCGGELV 164 (436)
T ss_pred cccCCccccchhhhHHHHhhcccCceEEEecCCCchh
Confidence 999999999987642 37999999998
No 174
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=56.78 E-value=7.3 Score=29.70 Aligned_cols=25 Identities=28% Similarity=0.753 Sum_probs=20.2
Q ss_pred EEcCCCCccccCCCCCCCCCCceecCc
Q 014440 304 YTCPRCKARVCELPTECRICGLQLVSS 330 (424)
Q Consensus 304 y~Cp~C~s~~C~lP~~C~~C~l~Lvs~ 330 (424)
-.||.|+.. .|-..||.||..+.++
T Consensus 6 r~C~~CgvY--TLk~~CP~CG~~t~~~ 30 (56)
T PRK13130 6 RKCPKCGVY--TLKEICPVCGGKTKNP 30 (56)
T ss_pred eECCCCCCE--EccccCcCCCCCCCCC
Confidence 579999988 4578999999986654
No 175
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=56.52 E-value=2.9 Score=42.52 Aligned_cols=21 Identities=38% Similarity=0.759 Sum_probs=17.4
Q ss_pred cccccccchhhhcc--CCCCCCC
Q 014440 390 KHFCLECDIYIHES--LHNCPGC 410 (424)
Q Consensus 390 ~~fC~dCd~fihe~--lh~CPgC 410 (424)
+.+|.-||++||.+ |++++.+
T Consensus 50 ~~~CP~C~i~ih~t~pl~ni~~D 72 (331)
T KOG2660|consen 50 SKYCPTCDIVIHKTHPLLNIRSD 72 (331)
T ss_pred hccCCccceeccCccccccCCcc
Confidence 56788888999988 8888877
No 176
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=55.80 E-value=11 Score=37.85 Aligned_cols=49 Identities=20% Similarity=0.462 Sum_probs=36.8
Q ss_pred CCCceeecccccccCCCCCCceeeCCCcCcccccccchhhhccCCCCCCCCCCCCCC
Q 014440 361 SRSTCFGCQQSLLASGNKAGLCVACPKCKKHFCLECDIYIHESLHNCPGCESLRQSN 417 (424)
Q Consensus 361 ~~~~C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~dCd~fihe~lh~CPgC~~~~~~~ 417 (424)
....|..|...-.. -.|.-|++.||..|=.=--..---||=|-....++
T Consensus 238 a~~kC~LCLe~~~~--------pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~ps 286 (293)
T KOG0317|consen 238 ATRKCSLCLENRSN--------PSATPCGHIFCWSCILEWCSEKAECPLCREKFQPS 286 (293)
T ss_pred CCCceEEEecCCCC--------CCcCcCcchHHHHHHHHHHccccCCCcccccCCCc
Confidence 45789999844322 23889999999999887777778899997644443
No 177
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=55.75 E-value=7.5 Score=27.23 Aligned_cols=25 Identities=36% Similarity=0.786 Sum_probs=17.1
Q ss_pred eeeCCCcCcccccccchhhhccCCCCCC
Q 014440 382 CVACPKCKKHFCLECDIYIHESLHNCPG 409 (424)
Q Consensus 382 ~~~C~~C~~~fC~dCd~fihe~lh~CPg 409 (424)
.+.|..|++.||.+ =-+-..|.|++
T Consensus 12 ~f~C~~C~~~FC~~---HR~~e~H~C~~ 36 (39)
T smart00154 12 GFKCRHCGNLFCGE---HRLPEDHDCPG 36 (39)
T ss_pred CeECCccCCccccc---cCCccccCCcc
Confidence 58999999999975 11224566653
No 178
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=55.55 E-value=11 Score=27.31 Aligned_cols=29 Identities=24% Similarity=0.432 Sum_probs=16.2
Q ss_pred ceeecccccccCCCCCCceeeCCCcCccc
Q 014440 364 TCFGCQQSLLASGNKAGLCVACPKCKKHF 392 (424)
Q Consensus 364 ~C~~C~~~~~~~~~~~~~~~~C~~C~~~f 392 (424)
+|--|...+.........+|.|+.|+.++
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeE
Confidence 56677655543221111368888888654
No 179
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=54.80 E-value=8.7 Score=34.05 Aligned_cols=34 Identities=12% Similarity=0.144 Sum_probs=24.6
Q ss_pred CCCCCceeecccccccCCCCCCceeeCCCcCcccccc
Q 014440 359 NISRSTCFGCQQSLLASGNKAGLCVACPKCKKHFCLE 395 (424)
Q Consensus 359 ~~~~~~C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~d 395 (424)
.+.++.|..|.++|..-... .-.||+|+..|=.+
T Consensus 6 lGtKr~Cp~cg~kFYDLnk~---p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 6 LGTKRICPNTGSKFYDLNRR---PAVSPYTGEQFPPE 39 (129)
T ss_pred hCccccCCCcCccccccCCC---CccCCCcCCccCcc
Confidence 35678999999999865432 34699999887443
No 180
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=54.52 E-value=6.6 Score=27.19 Aligned_cols=34 Identities=24% Similarity=0.630 Sum_probs=25.7
Q ss_pred CCceeecccccccCCCCCCceeeCCCcCcccccccchhhhcc
Q 014440 362 RSTCFGCQQSLLASGNKAGLCVACPKCKKHFCLECDIYIHES 403 (424)
Q Consensus 362 ~~~C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~dCd~fihe~ 403 (424)
...|.-|..+. ..|-|..|+..+|.+|....|..
T Consensus 3 ~~~C~~H~~~~--------~~~~C~~C~~~~C~~C~~~~H~~ 36 (42)
T PF00643_consen 3 EPKCPEHPEEP--------LSLFCEDCNEPLCSECTVSGHKG 36 (42)
T ss_dssp SSB-SSTTTSB--------EEEEETTTTEEEEHHHHHTSTTT
T ss_pred CccCccCCccc--------eEEEecCCCCccCccCCCCCCCC
Confidence 34677776432 35789999999999999998865
No 181
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=54.25 E-value=11 Score=42.01 Aligned_cols=22 Identities=23% Similarity=0.638 Sum_probs=19.2
Q ss_pred cccccchhhhccCCCCCCCCCC
Q 014440 392 FCLECDIYIHESLHNCPGCESL 413 (424)
Q Consensus 392 fC~dCd~fihe~lh~CPgC~~~ 413 (424)
+|..|..-+.+.-.+||.|...
T Consensus 29 ~Cp~CG~~~~~~~~fC~~CG~~ 50 (645)
T PRK14559 29 PCPQCGTEVPVDEAHCPNCGAE 50 (645)
T ss_pred cCCCCCCCCCcccccccccCCc
Confidence 6999999999999999999753
No 182
>COG1432 Uncharacterized conserved protein [Function unknown]
Probab=53.17 E-value=34 Score=31.82 Aligned_cols=65 Identities=17% Similarity=0.275 Sum_probs=45.7
Q ss_pred CCCcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecch-HHHHHHHHH
Q 014440 164 CSGDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAE-MFICKHLCQ 238 (424)
Q Consensus 164 ~~G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e-~~iLq~iA~ 238 (424)
..|+.++..|+++.....+.. -.. ++|++++ +|+.-+++.++..|.+|.+++++.- ..-|+..|+
T Consensus 90 ~k~~vDv~la~D~~~l~~~~~----~D~-ivl~SgD-----~DF~p~v~~~~~~G~rv~v~~~~~~~s~~L~~~aD 155 (181)
T COG1432 90 TKGDVDVELAVDAMELADKKN----VDT-IVLFSGD-----GDFIPLVEAARDKGKRVEVAGIEPMTSSDLRNAAD 155 (181)
T ss_pred cccCcchhhHHHHHHhhcccC----CCE-EEEEcCC-----ccHHHHHHHHHHcCCEEEEEecCCcCHHHHHHhhc
Confidence 357778888888776665432 333 5555442 4677789999999999999999973 356777773
No 183
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=52.65 E-value=6.1 Score=29.65 Aligned_cols=24 Identities=38% Similarity=0.721 Sum_probs=16.4
Q ss_pred CCCCCCCCCCceecCchhHHhhhc
Q 014440 315 ELPTECRICGLQLVSSPHLARSYH 338 (424)
Q Consensus 315 ~lP~~C~~C~l~Lvs~phLarsyh 338 (424)
+-|..||+|+.++-++=.|.|-.+
T Consensus 22 ~~PatCP~C~a~~~~srnLrRHle 45 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSRNLRRHLE 45 (54)
T ss_dssp S--EE-TTT--EESSHHHHHHHHH
T ss_pred CCCCCCCcchhhccchhhHHHHHH
Confidence 457899999999999999999763
No 184
>COG3958 Transketolase, C-terminal subunit [Carbohydrate transport and metabolism]
Probab=52.37 E-value=66 Score=32.63 Aligned_cols=67 Identities=24% Similarity=0.398 Sum_probs=48.8
Q ss_pred CHHHHHHHHHhCCcEEEEEEecc----hHHHHHHHHHHhCCEEEEecCh-------hhHHHHHHhcCCCCccchhhhhhh
Q 014440 206 DIMETIQKCKESKIRCSVIGLSA----EMFICKHLCQETGGTYSVALDE-------SHSKELILEHAPPPPAIAEFAIAS 274 (424)
Q Consensus 206 ~i~~~i~~akk~~IrV~vIgLg~----e~~iLq~iA~~TGG~Y~~~~d~-------~~L~~lL~~~~~pp~~~~~~~~~~ 274 (424)
...++++.|+++||.+-||-+.+ +..++...|++| |.-..+.+- +...++|.+..+ ++
T Consensus 206 ~al~AA~~L~~~GIsa~Vi~m~tIKPiD~~~i~~~A~~t-~~IvT~EeHsi~GGlGsaVAEvlse~~p-~~--------- 274 (312)
T COG3958 206 EALEAAEILKKEGISAAVINMFTIKPIDEQAILKAARET-GRIVTAEEHSIIGGLGSAVAEVLSENGP-TP--------- 274 (312)
T ss_pred HHHHHHHHHHhcCCCEEEEecCccCCCCHHHHHHHHhhc-CcEEEEecceeecchhHHHHHHHHhcCC-cc---------
Confidence 34588999999999999999986 568899999999 544444322 246777777775 33
Q ss_pred eeeecCCCC
Q 014440 275 LIKMGFPQR 283 (424)
Q Consensus 275 Li~mGFP~~ 283 (424)
+.+||.|..
T Consensus 275 ~~riGvp~~ 283 (312)
T COG3958 275 MRRIGVPDT 283 (312)
T ss_pred eEEecCCch
Confidence 347888854
No 185
>cd02010 TPP_ALS Thiamine pyrophosphate (TPP) family, Acetolactate synthase (ALS) subfamily, TPP-binding module; composed of proteins similar to Klebsiella pneumoniae ALS, a catabolic enzyme required for butanediol fermentation. ALS catalyzes the conversion of 2 molecules of pyruvate to acetolactate and carbon dioxide. ALS does not contain FAD, and requires TPP and a divalent metal cation for activity.
Probab=52.24 E-value=1.3e+02 Score=27.43 Aligned_cols=92 Identities=11% Similarity=-0.036 Sum_probs=60.8
Q ss_pred CCcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH--------------
Q 014440 165 SGDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM-------------- 230 (424)
Q Consensus 165 ~G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~-------------- 230 (424)
.|..+++-+|-.|+..=-.. ..++|+.|+|+..- . ... ..+.++++.+++|-+|-+....
T Consensus 45 ~~~g~mG~~lp~aiGa~la~---~~~~vv~i~GDG~f-~-m~~-~eL~ta~~~~l~vi~vV~NN~~~g~~~~~~~~~~~~ 118 (177)
T cd02010 45 NGLATMGVALPGAIGAKLVY---PDRKVVAVSGDGGF-M-MNS-QELETAVRLKIPLVVLIWNDNGYGLIKWKQEKEYGR 118 (177)
T ss_pred CCChhhhhHHHHHHHHHHhC---CCCcEEEEEcchHH-H-hHH-HHHHHHHHHCCCeEEEEEECCcchHHHHHHHHhcCC
Confidence 34456666666665533222 24678888876421 0 111 4466788889988888775320
Q ss_pred --------HHHHHHHHHhCCEEEEecChhhHHHHHHhcCC
Q 014440 231 --------FICKHLCQETGGTYSVALDESHSKELILEHAP 262 (424)
Q Consensus 231 --------~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~~ 262 (424)
.-+.++|+.-|+.++.+.+.++|+..|.+...
T Consensus 119 ~~~~~~~~~d~~~~a~a~G~~~~~v~~~~el~~al~~a~~ 158 (177)
T cd02010 119 DSGVDFGNPDFVKYAESFGAKGYRIESADDLLPVLERALA 158 (177)
T ss_pred cccCcCCCCCHHHHHHHCCCEEEEECCHHHHHHHHHHHHh
Confidence 13457899999999999999999999887764
No 186
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=51.72 E-value=24 Score=30.66 Aligned_cols=69 Identities=20% Similarity=0.143 Sum_probs=36.1
Q ss_pred ChhhHHHHHHhcCCCCccchhhhh-------hheeeecCCCCCCCCCcceeeecCCccccCeEEcCCCCcccc-------
Q 014440 249 DESHSKELILEHAPPPPAIAEFAI-------ASLIKMGFPQRAGEGSISICSCHKEVKIGVGYTCPRCKARVC------- 314 (424)
Q Consensus 249 d~~~L~~lL~~~~~pp~~~~~~~~-------~~Li~mGFP~~~~~~~~a~C~CH~~~~~~~Gy~Cp~C~s~~C------- 314 (424)
...||.+.+-.+.+.++..+...+ ..-=...||.....+.. ++...+.|.|++|+..||
T Consensus 27 ss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~~-------~~~~~~~y~C~~C~~~FC~dCD~fi 99 (112)
T TIGR00622 27 LSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPFD-------ELKDSHRYVCAVCKNVFCVDCDVFV 99 (112)
T ss_pred ccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCccccccc-------ccccccceeCCCCCCccccccchhh
Confidence 445888888888877766421000 00001123332111000 012233899999999999
Q ss_pred -CCCCCCCCCC
Q 014440 315 -ELPTECRICG 324 (424)
Q Consensus 315 -~lP~~C~~C~ 324 (424)
+.--.||.|.
T Consensus 100 He~Lh~CPGC~ 110 (112)
T TIGR00622 100 HESLHCCPGCI 110 (112)
T ss_pred hhhccCCcCCC
Confidence 2223577765
No 187
>PF02775 TPP_enzyme_C: Thiamine pyrophosphate enzyme, C-terminal TPP binding domain; InterPro: IPR011766 A number of enzymes require thiamine pyrophosphate (TPP) (vitamin B1) as a cofactor. It has been shown [] that some of these enzymes are structurally related. This represents the C-terminal TPP binding domain of TPP enzymes.; GO: 0003824 catalytic activity, 0030976 thiamine pyrophosphate binding; PDB: 2WVA_V 1ZPD_F 2WVG_B 2WVH_B 3OE1_D 2NXW_A 2Q5L_B 2Q5Q_B 2Q5J_A 2Q5O_A ....
Probab=51.64 E-value=54 Score=28.89 Aligned_cols=88 Identities=15% Similarity=0.038 Sum_probs=59.0
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH-----------------
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM----------------- 230 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~----------------- 230 (424)
.+++.++-.|+..=...| .++|++|+|+..- .-....+.++.+.+++|-+|-+..+.
T Consensus 28 g~mG~~~~~aiGa~~a~p---~~~vv~i~GDG~f---~~~~~el~ta~~~~~~v~~vv~nN~~~~~~~~~~~~~~~~~~~ 101 (153)
T PF02775_consen 28 GSMGYALPAAIGAALARP---DRPVVAITGDGSF---LMSLQELATAVRYGLPVVIVVLNNGGYGMTGGQQTPFGGGRFS 101 (153)
T ss_dssp T-TTTHHHHHHHHHHHST---TSEEEEEEEHHHH---HHHGGGHHHHHHTTSSEEEEEEESSBSHHHHHHHHHTTSTCHH
T ss_pred cccCCHHHhhhHHHhhcC---cceeEEecCCcce---eeccchhHHHhhccceEEEEEEeCCcceEeccccccCcCcccc
Confidence 344444444443322232 5789999886321 01125578889999999999886420
Q ss_pred ---------HHHHHHHHHhCCEEEEecCh--hhHHHHHHhcC
Q 014440 231 ---------FICKHLCQETGGTYSVALDE--SHSKELILEHA 261 (424)
Q Consensus 231 ---------~iLq~iA~~TGG~Y~~~~d~--~~L~~lL~~~~ 261 (424)
.-+.++|+.-|+.+..+.+. ++|++.|.+..
T Consensus 102 ~~~~~~~~~~d~~~~a~a~G~~~~~v~~~~~~el~~al~~a~ 143 (153)
T PF02775_consen 102 GVDGKTFPNPDFAALAEAFGIKGARVTTPDPEELEEALREAL 143 (153)
T ss_dssp STBTTTSTTCGHHHHHHHTTSEEEEESCHSHHHHHHHHHHHH
T ss_pred cccccccccCCHHHHHHHcCCcEEEEccCCHHHHHHHHHHHH
Confidence 13889999999998888777 99999988776
No 188
>COG4547 CobT Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]
Probab=50.73 E-value=1.1e+02 Score=33.02 Aligned_cols=58 Identities=24% Similarity=0.430 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHcCCCCCCCcEEEEEEcCCCC-------CCccCHH-----HHHHHHH-hCCcEEEEEEecchH
Q 014440 171 QNALDLVHGLLNQIPSYGHREVLILYSALST-------CDPGDIM-----ETIQKCK-ESKIRCSVIGLSAEM 230 (424)
Q Consensus 171 ~~AL~~Al~~L~~~p~~~~reILvI~ss~~t-------~dp~~i~-----~~i~~ak-k~~IrV~vIgLg~e~ 230 (424)
+.||.-|.+.|-..| -.|+|+.+++++.- .+||++. .+|+... ..-|-+-.||||.++
T Consensus 520 GEal~wah~rl~gRp--EqrkIlmmiSDGAPvddstlsvnpGnylerHLRaVieeIEtrSpveLlAIGighDv 590 (620)
T COG4547 520 GEALMWAHQRLIGRP--EQRKILMMISDGAPVDDSTLSVNPGNYLERHLRAVIEEIETRSPVELLAIGIGHDV 590 (620)
T ss_pred hHHHHHHHHHHhcCh--hhceEEEEecCCCcccccccccCCchHHHHHHHHHHHHHhcCCchhheeeeccccc
Confidence 457788888877653 46788888875432 3457764 3455443 345778888888875
No 189
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=50.51 E-value=6.6 Score=23.43 Aligned_cols=13 Identities=38% Similarity=0.899 Sum_probs=9.7
Q ss_pred eeCCCcCcccccc
Q 014440 383 VACPKCKKHFCLE 395 (424)
Q Consensus 383 ~~C~~C~~~fC~d 395 (424)
|+|+.|+..|=.-
T Consensus 1 y~C~~C~~~f~~~ 13 (23)
T PF00096_consen 1 YKCPICGKSFSSK 13 (23)
T ss_dssp EEETTTTEEESSH
T ss_pred CCCCCCCCccCCH
Confidence 6799998887443
No 190
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=50.32 E-value=9.3 Score=28.07 Aligned_cols=28 Identities=25% Similarity=0.757 Sum_probs=21.3
Q ss_pred ceeeccc-ccccCCCCCCceeeCCCcC---cccccccc
Q 014440 364 TCFGCQQ-SLLASGNKAGLCVACPKCK---KHFCLECD 397 (424)
Q Consensus 364 ~C~~C~~-~~~~~~~~~~~~~~C~~C~---~~fC~dCd 397 (424)
.|-+|.. ++. +.||.|..|. -.+|.+|-
T Consensus 2 ~Cd~C~~~pI~------G~R~~C~~C~~~d~DlC~~C~ 33 (48)
T cd02341 2 KCDSCGIEPIP------GTRYHCSECDDGDFDLCQDCV 33 (48)
T ss_pred CCCCCCCCccc------cceEECCCCCCCCCccCHHHH
Confidence 4889986 443 2589999998 67888883
No 191
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=49.76 E-value=8.8 Score=28.35 Aligned_cols=44 Identities=30% Similarity=0.606 Sum_probs=21.4
Q ss_pred eeecccccccCCCCCCceeeCCCcCcccccccchhhhc-cCCCCCCCCC
Q 014440 365 CFGCQQSLLASGNKAGLCVACPKCKKHFCLECDIYIHE-SLHNCPGCES 412 (424)
Q Consensus 365 C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~dCd~fihe-~lh~CPgC~~ 412 (424)
|-+|...+.. .....+-| .|+-..|.+|-.-|-+ .-..||||..
T Consensus 1 cp~C~e~~d~---~d~~~~PC-~Cgf~IC~~C~~~i~~~~~g~CPgCr~ 45 (48)
T PF14570_consen 1 CPLCDEELDE---TDKDFYPC-ECGFQICRFCYHDILENEGGRCPGCRE 45 (48)
T ss_dssp -TTTS-B--C---CCTT--SS-TTS----HHHHHHHTTSS-SB-TTT--
T ss_pred CCCccccccc---CCCccccC-cCCCcHHHHHHHHHHhccCCCCCCCCC
Confidence 4566655522 22245778 7999999999877776 5789999953
No 192
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=49.64 E-value=10 Score=27.47 Aligned_cols=29 Identities=24% Similarity=0.830 Sum_probs=21.4
Q ss_pred ceeeccc-ccccCCCCCCceeeCCCc-Ccccccccch
Q 014440 364 TCFGCQQ-SLLASGNKAGLCVACPKC-KKHFCLECDI 398 (424)
Q Consensus 364 ~C~~C~~-~~~~~~~~~~~~~~C~~C-~~~fC~dCd~ 398 (424)
.|-+|.+ ++. +.+|+|..| .-..|.+|-.
T Consensus 2 ~Cd~C~~~~i~------G~RykC~~C~dyDLC~~C~~ 32 (45)
T cd02339 2 ICDTCRKQGII------GIRWKCAECPNYDLCTTCYH 32 (45)
T ss_pred CCCCCCCCCcc------cCeEECCCCCCccchHHHhC
Confidence 5889983 332 258999999 5778888854
No 193
>cd02008 TPP_IOR_alpha Thiamine pyrophosphate (TPP) family, IOR-alpha subfamily, TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as indolepyruvate or phenylpyruvate, which are generated by the transamination of aromatic amino acids, to the corresponding aryl acetyl-CoA.
Probab=49.42 E-value=58 Score=29.73 Aligned_cols=71 Identities=14% Similarity=0.086 Sum_probs=49.2
Q ss_pred CcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH----------------------HHHHHHHHHhCCEEEE
Q 014440 189 HREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM----------------------FICKHLCQETGGTYSV 246 (424)
Q Consensus 189 ~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~----------------------~iLq~iA~~TGG~Y~~ 246 (424)
.++|+.|+|+..-. .+..+.+.++.+.++.+-+|-+.... .-+.++|+.-|..|..
T Consensus 69 ~~~Vv~i~GDG~f~--~~g~~eL~ta~~~~l~i~vvV~nN~~~g~~~~~~~~~~~~~~~~~~~~~d~~~~a~a~G~~~~~ 146 (178)
T cd02008 69 DKKVVAVIGDSTFF--HSGILGLINAVYNKANITVVILDNRTTAMTGGQPHPGTGKTLTEPTTVIDIEALVRAIGVKRVV 146 (178)
T ss_pred CCCEEEEecChHHh--hccHHHHHHHHHcCCCEEEEEECCcceeccCCCCCCCCcccccCCCCccCHHHHHHHCCCCEEE
Confidence 46788888865421 12135567788899988888775321 2478899999999999
Q ss_pred ecChhhHHH---HHHhcC
Q 014440 247 ALDESHSKE---LILEHA 261 (424)
Q Consensus 247 ~~d~~~L~~---lL~~~~ 261 (424)
+.+.++|.+ .|.+..
T Consensus 147 v~~~~~l~~~~~al~~a~ 164 (178)
T cd02008 147 VVDPYDLKAIREELKEAL 164 (178)
T ss_pred ecCccCHHHHHHHHHHHH
Confidence 988888874 445443
No 194
>PTZ00260 dolichyl-phosphate beta-glucosyltransferase; Provisional
Probab=49.36 E-value=1.6e+02 Score=29.76 Aligned_cols=97 Identities=12% Similarity=0.120 Sum_probs=59.5
Q ss_pred ChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCHHHHHHHHhhh----------hCCCCcchHHHHHH
Q 014440 106 SRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSPESHIKALMGK----------LGCSGDSSIQNALD 175 (424)
Q Consensus 106 ~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~~----------~~~~G~tsL~~AL~ 175 (424)
.++..+++.+...+.+...++|....=||+.-||. +.+..++++.+... +....+...+.|+.
T Consensus 83 ~~i~~~L~~l~~~~~~~~~~~~~~~~EIIVVDDgS-------tD~T~~i~~~~~~~~~~~~~~i~vi~~~~N~G~~~A~~ 155 (333)
T PTZ00260 83 DRLPKMLKETIKYLESRSRKDPKFKYEIIIVNDGS-------KDKTLKVAKDFWRQNINPNIDIRLLSLLRNKGKGGAVR 155 (333)
T ss_pred HHHHHHHHHHHHHHHhhhccCCCCCEEEEEEeCCC-------CCchHHHHHHHHHhcCCCCCcEEEEEcCCCCChHHHHH
Confidence 36777888777777777777776667777776664 33444454444211 11122233566666
Q ss_pred HHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHh
Q 014440 176 LVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKE 216 (424)
Q Consensus 176 ~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk 216 (424)
.++.. +..++|++++++...++.++...++.+.+
T Consensus 156 ~Gi~~-------a~gd~I~~~DaD~~~~~~~l~~l~~~l~~ 189 (333)
T PTZ00260 156 IGMLA-------SRGKYILMVDADGATDIDDFDKLEDIMLK 189 (333)
T ss_pred HHHHH-------ccCCEEEEEeCCCCCCHHHHHHHHHHHHH
Confidence 66552 13468888887777778777777776654
No 195
>PRK12726 flagellar biosynthesis regulator FlhF; Provisional
Probab=49.24 E-value=2.3e+02 Score=30.00 Aligned_cols=92 Identities=9% Similarity=0.052 Sum_probs=60.6
Q ss_pred CcchHHHHHHHHHHHHcCC-C-----CCCCcEEEEEEcCCCCCCccC---HHHHHHHHHhCCcEEEEEEecch----HHH
Q 014440 166 GDSSIQNALDLVHGLLNQI-P-----SYGHREVLILYSALSTCDPGD---IMETIQKCKESKIRCSVIGLSAE----MFI 232 (424)
Q Consensus 166 G~tsL~~AL~~Al~~L~~~-p-----~~~~reILvI~ss~~t~dp~~---i~~~i~~akk~~IrV~vIgLg~e----~~i 232 (424)
+..++.......+..|... | ....++|++|+|.... |. +...+..+.+.+.+|-+|...+- ...
T Consensus 176 ~~~~~~~v~~~~~~~L~~~l~~~~~~~~~~~~ii~lvGptGv---GKTTt~akLA~~l~~~g~~V~lItaDtyR~gAveQ 252 (407)
T PRK12726 176 ETAHLDDITDWFVPYLSGKLAVEDSFDLSNHRIISLIGQTGV---GKTTTLVKLGWQLLKQNRTVGFITTDTFRSGAVEQ 252 (407)
T ss_pred ccccHHHHHHHHHHHhcCcEeeCCCceecCCeEEEEECCCCC---CHHHHHHHHHHHHHHcCCeEEEEeCCccCccHHHH
Confidence 3345677777777777653 1 1234678888874221 32 22334455677888888888643 568
Q ss_pred HHHHHHHhCCEEEEecChhhHHHHHHhc
Q 014440 233 CKHLCQETGGTYSVALDESHSKELILEH 260 (424)
Q Consensus 233 Lq~iA~~TGG~Y~~~~d~~~L~~lL~~~ 260 (424)
|+..++..|=-++++.+..++.+.+..+
T Consensus 253 Lk~yae~lgvpv~~~~dp~dL~~al~~l 280 (407)
T PRK12726 253 FQGYADKLDVELIVATSPAELEEAVQYM 280 (407)
T ss_pred HHHHhhcCCCCEEecCCHHHHHHHHHHH
Confidence 9999999886677788888888776544
No 196
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=48.94 E-value=11 Score=26.77 Aligned_cols=29 Identities=21% Similarity=0.699 Sum_probs=19.9
Q ss_pred CCceeecccccccCCCCCCceeeCCCcC-ccccccc
Q 014440 362 RSTCFGCQQSLLASGNKAGLCVACPKCK-KHFCLEC 396 (424)
Q Consensus 362 ~~~C~~C~~~~~~~~~~~~~~~~C~~C~-~~fC~dC 396 (424)
...|.+|.+++.. .+|+|..|. -..|.+|
T Consensus 4 ~~~C~~C~~~i~g------~ry~C~~C~d~dlC~~C 33 (44)
T smart00291 4 SYSCDTCGKPIVG------VRYHCLVCPDYDLCQSC 33 (44)
T ss_pred CcCCCCCCCCCcC------CEEECCCCCCccchHHH
Confidence 4479999976542 489999983 3455555
No 197
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=48.70 E-value=5.9 Score=28.66 Aligned_cols=44 Identities=25% Similarity=0.511 Sum_probs=32.2
Q ss_pred CceeecccccccCCCCCCceeeCCCcCcc-cccccchhhhccCCCCCCCCCCC
Q 014440 363 STCFGCQQSLLASGNKAGLCVACPKCKKH-FCLECDIYIHESLHNCPGCESLR 414 (424)
Q Consensus 363 ~~C~~C~~~~~~~~~~~~~~~~C~~C~~~-fC~dCd~fihe~lh~CPgC~~~~ 414 (424)
..|.-|...... ..--.|++. ||.+|-.-+...-..||.|....
T Consensus 3 ~~C~iC~~~~~~--------~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i 47 (50)
T PF13920_consen 3 EECPICFENPRD--------VVLLPCGHLCFCEECAERLLKRKKKCPICRQPI 47 (50)
T ss_dssp SB-TTTSSSBSS--------EEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-
T ss_pred CCCccCCccCCc--------eEEeCCCChHHHHHHhHHhcccCCCCCcCChhh
Confidence 368888855431 223368999 99999999999999999997643
No 198
>PF03850 Tfb4: Transcription factor Tfb4; InterPro: IPR004600 Members of this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. The core-TFIIH basal transcription factor complex has six subunits, this is the p34 subunit.; GO: 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent, 0000439 core TFIIH complex
Probab=48.56 E-value=15 Score=36.63 Aligned_cols=36 Identities=28% Similarity=0.633 Sum_probs=27.4
Q ss_pred CceeecccccccCCCCCCceeeCCCcCcccccccchhhhccCCCCCCCC
Q 014440 363 STCFGCQQSLLASGNKAGLCVACPKCKKHFCLECDIYIHESLHNCPGCE 411 (424)
Q Consensus 363 ~~C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~dCd~fihe~lh~CPgC~ 411 (424)
..||-..+.+. ..|.|+.|.++||.-++. ..||.|.
T Consensus 241 a~Cfch~k~vd-------~g~vCsvCLsIfc~~p~~------~~C~tC~ 276 (276)
T PF03850_consen 241 ASCFCHRKVVD-------IGYVCSVCLSIFCEFPDG------GICPTCG 276 (276)
T ss_pred eeeeecCCccc-------ceeEchhhhhhhhCCCCC------CCCCCCC
Confidence 47998886664 369999999999987652 1299884
No 199
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=48.24 E-value=9.4 Score=24.19 Aligned_cols=20 Identities=35% Similarity=0.934 Sum_probs=10.1
Q ss_pred cccccchhhhccCCCCCCCC
Q 014440 392 FCLECDIYIHESLHNCPGCE 411 (424)
Q Consensus 392 fC~dCd~fihe~lh~CPgC~ 411 (424)
+|..|...+.+.-.+||.|.
T Consensus 4 ~Cp~Cg~~~~~~~~fC~~CG 23 (26)
T PF13248_consen 4 FCPNCGAEIDPDAKFCPNCG 23 (26)
T ss_pred CCcccCCcCCcccccChhhC
Confidence 34444444455555555554
No 200
>cd02003 TPP_IolD Thiamine pyrophosphate (TPP) family, IolD subfamily, TPP-binding module; composed of proteins similar to Rhizobium leguminosarum bv. viciae IolD. IolD plays an important role in myo-inositol catabolism.
Probab=48.18 E-value=2.3e+02 Score=26.42 Aligned_cols=92 Identities=13% Similarity=-0.005 Sum_probs=59.7
Q ss_pred CCCcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH-H-----------
Q 014440 164 CSGDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM-F----------- 231 (424)
Q Consensus 164 ~~G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~-~----------- 231 (424)
+.|..+++-||-.|+..=-..| .++|+.|+|+..- . ... ..+.++.+.+++|-+|-+.... .
T Consensus 44 ~~~~gsmG~~lpaAiGa~la~p---~~~vv~i~GDGsf-~-m~~-~eL~Ta~~~~lpv~ivV~NN~~~g~~~~~q~~~~~ 117 (205)
T cd02003 44 EYGYSCMGYEIAAGLGAKLAKP---DREVYVLVGDGSY-L-MLH-SEIVTAVQEGLKIIIVLFDNHGFGCINNLQESTGS 117 (205)
T ss_pred CCCcchhhhHHHHHHHHHHhCC---CCeEEEEEccchh-h-ccH-HHHHHHHHcCCCCEEEEEECCccHHHHHHHHHhcC
Confidence 3444567777777766532222 4678888876432 1 122 4567788899998888876431 1
Q ss_pred ------------------------HHHHHHHHhCCEEEEecChhhHHHHHHhcC
Q 014440 232 ------------------------ICKHLCQETGGTYSVALDESHSKELILEHA 261 (424)
Q Consensus 232 ------------------------iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~ 261 (424)
-+.++|+.-|..+..+.+.++|+..|.+..
T Consensus 118 ~~~~~~~~~~~~~~~~~~~~~~~~d~~~~A~a~G~~~~~v~~~~el~~al~~a~ 171 (205)
T cd02003 118 GSFGTEFRDRDQESGQLDGALLPVDFAANARSLGARVEKVKTIEELKAALAKAK 171 (205)
T ss_pred ccccchhcccccccccccCCCCCCCHHHHHHhCCCEEEEECCHHHHHHHHHHHH
Confidence 234577777788888888888888887765
No 201
>PLN02948 phosphoribosylaminoimidazole carboxylase
Probab=48.09 E-value=2.1e+02 Score=31.60 Aligned_cols=78 Identities=17% Similarity=0.094 Sum_probs=49.2
Q ss_pred CCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecch--HHHHHHHHH---HhC-CEEEE-ecChhhHHHHHH
Q 014440 186 SYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAE--MFICKHLCQ---ETG-GTYSV-ALDESHSKELIL 258 (424)
Q Consensus 186 ~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e--~~iLq~iA~---~TG-G~Y~~-~~d~~~L~~lL~ 258 (424)
++....|.||++|.+ |-.-..+++..|++.||...+--.++. ..-+.++++ .-| -.+.. +--..||-.++.
T Consensus 407 ~~~~~~v~i~~gs~s--d~~~~~~~~~~l~~~g~~~~~~v~sahr~~~~~~~~~~~~~~~~~~v~i~~ag~~~~l~~~~a 484 (577)
T PLN02948 407 PKGTPLVGIIMGSDS--DLPTMKDAAEILDSFGVPYEVTIVSAHRTPERMFSYARSAHSRGLQVIIAGAGGAAHLPGMVA 484 (577)
T ss_pred CCCCCeEEEEECchh--hHHHHHHHHHHHHHcCCCeEEEEECCccCHHHHHHHHHHHHHCCCCEEEEEcCccccchHHHh
Confidence 455667999998743 443445889999999999664444443 233333322 223 34443 566779999998
Q ss_pred hcCCCCc
Q 014440 259 EHAPPPP 265 (424)
Q Consensus 259 ~~~~pp~ 265 (424)
.+++-|.
T Consensus 485 ~~t~~pv 491 (577)
T PLN02948 485 SMTPLPV 491 (577)
T ss_pred hccCCCE
Confidence 8887664
No 202
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=47.96 E-value=6.3 Score=27.87 Aligned_cols=11 Identities=36% Similarity=1.035 Sum_probs=6.9
Q ss_pred CcCcccccccc
Q 014440 387 KCKKHFCLECD 397 (424)
Q Consensus 387 ~C~~~fC~dCd 397 (424)
.|++.||..|=
T Consensus 15 ~CGH~FC~~Cl 25 (42)
T PF15227_consen 15 PCGHSFCRSCL 25 (42)
T ss_dssp SSSSEEEHHHH
T ss_pred CCcCHHHHHHH
Confidence 46666666664
No 203
>cd02013 TPP_Xsc_like Thiamine pyrophosphate (TPP) family, Xsc-like subfamily, TPP-binding module; composed of proteins similar to Alcaligenes defragrans sulfoacetaldehyde acetyltransferase (Xsc). Xsc plays a key role in the degradation of taurine, catalyzing the desulfonation of 2-sulfoacetaldehyde into sulfite and acetyl phosphate. This enzyme requires TPP and divalent metal ions for activity.
Probab=47.70 E-value=1.7e+02 Score=27.17 Aligned_cols=91 Identities=9% Similarity=0.007 Sum_probs=58.4
Q ss_pred CcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH---------------
Q 014440 166 GDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM--------------- 230 (424)
Q Consensus 166 G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~--------------- 230 (424)
+..+++-+|-.|+..=-.. ..|+|++|+|+..- -.++ ..+.++++.+++|-+|-+....
T Consensus 51 ~~g~mG~~lpaaiGa~la~---p~r~vv~i~GDG~f--~m~~-~eL~Ta~~~~lpvi~vV~NN~~yg~~~~~q~~~~~~~ 124 (196)
T cd02013 51 SFGNCGYALPAIIGAKAAA---PDRPVVAIAGDGAW--GMSM-MEIMTAVRHKLPVTAVVFRNRQWGAEKKNQVDFYNNR 124 (196)
T ss_pred CCcccccHHHHHHHHHHhC---CCCcEEEEEcchHH--hccH-HHHHHHHHhCCCeEEEEEECchhHHHHHHHHHHcCCC
Confidence 3345555555555532222 24678888876432 1223 3456788889998877765321
Q ss_pred --------HHHHHHHHHhCCEEEEecChhhHHHHHHhcCC
Q 014440 231 --------FICKHLCQETGGTYSVALDESHSKELILEHAP 262 (424)
Q Consensus 231 --------~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~~ 262 (424)
.-+.++|+..|..+..+.+.++|...|.+...
T Consensus 125 ~~~~~~~~~d~~~lA~a~G~~~~~v~~~~el~~al~~a~~ 164 (196)
T cd02013 125 FVGTELESESFAKIAEACGAKGITVDKPEDVGPALQKAIA 164 (196)
T ss_pred cccccCCCCCHHHHHHHCCCEEEEECCHHHHHHHHHHHHh
Confidence 12467888889999999999999988887763
No 204
>PRK00420 hypothetical protein; Validated
Probab=47.65 E-value=10 Score=32.89 Aligned_cols=26 Identities=27% Similarity=0.617 Sum_probs=19.2
Q ss_pred eEEcCCCCccccCC---CCCCCCCCceec
Q 014440 303 GYTCPRCKARVCEL---PTECRICGLQLV 328 (424)
Q Consensus 303 Gy~Cp~C~s~~C~l---P~~C~~C~l~Lv 328 (424)
+..||+|++..=.+ ...||.||-.++
T Consensus 23 ~~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 23 SKHCPVCGLPLFELKDGEVVCPVHGKVYI 51 (112)
T ss_pred cCCCCCCCCcceecCCCceECCCCCCeee
Confidence 56799999876653 358999998654
No 205
>COG3183 Predicted restriction endonuclease [Defense mechanisms]
Probab=47.36 E-value=4.7 Score=39.85 Aligned_cols=32 Identities=34% Similarity=0.788 Sum_probs=21.0
Q ss_pred CCCCCCCceecC-chhHHhhh---cccCCCCCCc-cc
Q 014440 318 TECRICGLQLVS-SPHLARSY---HHLFPIAPFD-EA 349 (424)
Q Consensus 318 ~~C~~C~l~Lvs-~phLarsy---hhl~p~~~f~-~~ 349 (424)
+.|.+|+..|.- .=.++|-| ||..|+.-|+ +.
T Consensus 196 ~vC~vC~fdF~k~YGe~gKgyIeVHH~~piae~e~~~ 232 (272)
T COG3183 196 TVCDVCEFDFQKKYGEIGKGYIEVHHKIPIAEFEGEY 232 (272)
T ss_pred ceeeecCccHHHHhhhhccCeEEEeeccchhhhcCcc
Confidence 345667766543 23356665 8999999998 44
No 206
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=47.25 E-value=9.6 Score=37.75 Aligned_cols=49 Identities=24% Similarity=0.634 Sum_probs=35.1
Q ss_pred CCCceeecccccccCCCCCCceeeCCCcCcccccccchh--hhccCCCCCCCCCCCCCC
Q 014440 361 SRSTCFGCQQSLLASGNKAGLCVACPKCKKHFCLECDIY--IHESLHNCPGCESLRQSN 417 (424)
Q Consensus 361 ~~~~C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~dCd~f--ihe~lh~CPgC~~~~~~~ 417 (424)
+...|+.|..... ...|.-|++.||.-|=.- --+.-..||=|-..-.+.
T Consensus 214 ~d~kC~lC~e~~~--------~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~pk 264 (271)
T COG5574 214 ADYKCFLCLEEPE--------VPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPK 264 (271)
T ss_pred cccceeeeecccC--------CcccccccchhhHHHHHHHHHhhccccCchhhhhccch
Confidence 3668999984432 356999999999999654 345666799997644433
No 207
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=46.91 E-value=34 Score=38.78 Aligned_cols=130 Identities=17% Similarity=0.307 Sum_probs=71.7
Q ss_pred HHHHHHhCCcEEEEEEecchHHHHHHHHHHhCCEEEEecChhhHHHHHHhcCCCCccchhhhhhheeeec--CCCCC---
Q 014440 210 TIQKCKESKIRCSVIGLSAEMFICKHLCQETGGTYSVALDESHSKELILEHAPPPPAIAEFAIASLIKMG--FPQRA--- 284 (424)
Q Consensus 210 ~i~~akk~~IrV~vIgLg~e~~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~~pp~~~~~~~~~~Li~mG--FP~~~--- 284 (424)
++..+++.+++ |.||+...-|+..+..-.|.|-... |..=.. ...+|...--.++.....-| |+...
T Consensus 341 A~~Ra~~~~~p---vvLgSATPSLES~~~~~~g~y~~~~----L~~R~~-~a~~p~v~iiDmr~e~~~~~~~lS~~Ll~~ 412 (730)
T COG1198 341 AVLRAKKENAP---VVLGSATPSLESYANAESGKYKLLR----LTNRAG-RARLPRVEIIDMRKEPLETGRSLSPALLEA 412 (730)
T ss_pred HHHHHHHhCCC---EEEecCCCCHHHHHhhhcCceEEEE----cccccc-ccCCCcceEEeccccccccCccCCHHHHHH
Confidence 47777888876 4677777888888888889777431 111112 12233322112222222222 33221
Q ss_pred -----CCCCcceeeecCCccccCeEE----cCCCCccccCCCCCCCCCCceecCchhHHhhhcccCCCCCCcccCccccc
Q 014440 285 -----GEGSISICSCHKEVKIGVGYT----CPRCKARVCELPTECRICGLQLVSSPHLARSYHHLFPIAPFDEATPSRLN 355 (424)
Q Consensus 285 -----~~~~~a~C~CH~~~~~~~Gy~----Cp~C~s~~C~lP~~C~~C~l~Lvs~phLarsyhhl~p~~~f~~~~~~~~~ 355 (424)
..+-+++=|=.+ +||. |..|+.+ .+||-|...|+ ||--
T Consensus 413 i~~~l~~geQ~llflnR-----RGys~~l~C~~Cg~v-----~~Cp~Cd~~lt--------~H~~--------------- 459 (730)
T COG1198 413 IRKTLERGEQVLLFLNR-----RGYAPLLLCRDCGYI-----AECPNCDSPLT--------LHKA--------------- 459 (730)
T ss_pred HHHHHhcCCeEEEEEcc-----CCccceeecccCCCc-----ccCCCCCcceE--------EecC---------------
Confidence 123334433332 2664 9988877 56999998863 3311
Q ss_pred cccCCCCCceeecccccccCCCCCCceeeCCCcCcc
Q 014440 356 DLHNISRSTCFGCQQSLLASGNKAGLCVACPKCKKH 391 (424)
Q Consensus 356 ~~~~~~~~~C~~C~~~~~~~~~~~~~~~~C~~C~~~ 391 (424)
...-.|--|..+-+ ....||.|++.
T Consensus 460 ----~~~L~CH~Cg~~~~-------~p~~Cp~Cgs~ 484 (730)
T COG1198 460 ----TGQLRCHYCGYQEP-------IPQSCPECGSE 484 (730)
T ss_pred ----CCeeEeCCCCCCCC-------CCCCCCCCCCC
Confidence 13447999975532 23679999875
No 208
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=46.50 E-value=14 Score=27.09 Aligned_cols=10 Identities=40% Similarity=0.999 Sum_probs=6.1
Q ss_pred EEcCCCCccc
Q 014440 304 YTCPRCKARV 313 (424)
Q Consensus 304 y~Cp~C~s~~ 313 (424)
|.|++|+.+|
T Consensus 2 y~C~~CgyvY 11 (47)
T PF00301_consen 2 YQCPVCGYVY 11 (47)
T ss_dssp EEETTTSBEE
T ss_pred cCCCCCCEEE
Confidence 5666666554
No 209
>TIGR01279 DPOR_bchN light-independent protochlorophyllide reductase, N subunit. This enzyme describes the N subunit of the dark form protochlorophyllide reductase, a nitrogenase-like enzyme involved in bacteriochlorophyll biosynthesis. This subunit shows homology to the nitrogenase molybdenum-iron protein NifN.
Probab=46.47 E-value=1e+02 Score=32.16 Aligned_cols=80 Identities=13% Similarity=-0.019 Sum_probs=43.3
Q ss_pred CHHHHHHHHHhCCcEEEEEEecchH-HHHHHH-HHHhCCEEE-EecChhhHHHHHHhcCCCCccc-hhhhhhheeeecCC
Q 014440 206 DIMETIQKCKESKIRCSVIGLSAEM-FICKHL-CQETGGTYS-VALDESHSKELILEHAPPPPAI-AEFAIASLIKMGFP 281 (424)
Q Consensus 206 ~i~~~i~~akk~~IrV~vIgLg~e~-~iLq~i-A~~TGG~Y~-~~~d~~~L~~lL~~~~~pp~~~-~~~~~~~Li~mGFP 281 (424)
-....++.+.+.|+.+-.++-+... ...++. ....++.-. ...|..++.+++.+. .|.-.- .......|+++|||
T Consensus 285 ~~~~l~~~L~elGm~~v~~~t~~~~~~~~~~~~~~l~~~~~v~~~~d~~~l~~~i~~~-~pDllig~~~~~~pl~r~GfP 363 (407)
T TIGR01279 285 LELPLARFLKRCGMEVVECGTPYIHRRFHAAELALLEGGVRIVEQPDFHRQLQRIRAT-RPDLVVTGLGTANPLEAQGFT 363 (407)
T ss_pred HHHHHHHHHHHCCCEEEEecCCCCChHHHHHHHhhcCCCCeEEeCCCHHHHHHHHHhc-CCCEEecCccCCCcHhhCCcc
Confidence 3456788889999998777765432 121222 222233222 224444555555443 222222 12345689999999
Q ss_pred CCCCC
Q 014440 282 QRAGE 286 (424)
Q Consensus 282 ~~~~~ 286 (424)
.+...
T Consensus 364 ~~dr~ 368 (407)
T TIGR01279 364 TKWSI 368 (407)
T ss_pred eeEee
Confidence 87543
No 210
>cd04192 GT_2_like_e Subfamily of Glycosyltransferase Family GT2 of unknown function. GT-2 includes diverse families of glycosyltransferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. Glycosyltransferases have been classified into more than 90 distinct sequence based families.
Probab=46.21 E-value=2e+02 Score=25.94 Aligned_cols=69 Identities=13% Similarity=0.169 Sum_probs=39.2
Q ss_pred cEEEEEEcCCCCCCccCHHHHHH-HHHhCCcEEEEEEec-----chHHHHHHHHHHhCCEEEEecChhh------HHHHH
Q 014440 190 REVLILYSALSTCDPGDIMETIQ-KCKESKIRCSVIGLS-----AEMFICKHLCQETGGTYSVALDESH------SKELI 257 (424)
Q Consensus 190 reILvI~ss~~t~dp~~i~~~i~-~akk~~IrV~vIgLg-----~e~~iLq~iA~~TGG~Y~~~~d~~~------L~~lL 257 (424)
-||||+-++ ++ | +..+.++ .++..+.+|.++-.. .....+....+..+|.|+...|.+. |+.++
T Consensus 29 ~eiivvdd~-s~-d--~t~~~~~~~~~~~~~~v~~~~~~~~~~~g~~~a~n~g~~~~~~d~i~~~D~D~~~~~~~l~~l~ 104 (229)
T cd04192 29 FEVILVDDH-ST-D--GTVQILEFAAAKPNFQLKILNNSRVSISGKKNALTTAIKAAKGDWIVTTDADCVVPSNWLLTFV 104 (229)
T ss_pred eEEEEEcCC-CC-c--ChHHHHHHHHhCCCcceEEeeccCcccchhHHHHHHHHHHhcCCEEEEECCCcccCHHHHHHHH
Confidence 467766543 22 2 2334444 444555666666443 1234567777788899998776653 55555
Q ss_pred HhcCC
Q 014440 258 LEHAP 262 (424)
Q Consensus 258 ~~~~~ 262 (424)
..+..
T Consensus 105 ~~~~~ 109 (229)
T cd04192 105 AFIQK 109 (229)
T ss_pred HHhhc
Confidence 54443
No 211
>PRK08611 pyruvate oxidase; Provisional
Probab=45.04 E-value=1e+02 Score=33.74 Aligned_cols=89 Identities=9% Similarity=0.028 Sum_probs=61.3
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH-----------------
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM----------------- 230 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~----------------- 230 (424)
-+++.||-.|+..=-.. ..|+||.|+|++.- -.++ +.+.++.+.++++-+|-+....
T Consensus 408 g~mG~glpaaiGa~la~---p~~~Vv~i~GDGsf--~m~~-~eL~Ta~r~~l~~iivV~NN~~~g~i~~~q~~~~~~~~~ 481 (576)
T PRK08611 408 GTMGCGLPGAIAAKIAF---PDRQAIAICGDGGF--SMVM-QDFVTAVKYKLPIVVVVLNNQQLAFIKYEQQAAGELEYA 481 (576)
T ss_pred hhhhhhHHHHHHHHHhC---CCCcEEEEEcccHH--hhhH-HHHHHHHHhCCCeEEEEEeCCcchHHHHHHHHhcCCccc
Confidence 45666666555533222 25678999886432 1222 4567899999998888875320
Q ss_pred -----HHHHHHHHHhCCEEEEecChhhHHHHHHhcCC
Q 014440 231 -----FICKHLCQETGGTYSVALDESHSKELILEHAP 262 (424)
Q Consensus 231 -----~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~~ 262 (424)
.-+.++|+..|+.|..+.+.++|...|.+...
T Consensus 482 ~~~~~~d~~~lA~a~G~~~~~v~~~~eL~~al~~a~~ 518 (576)
T PRK08611 482 IDLSDMDYAKFAEACGGKGYRVEKAEELDPAFEEALA 518 (576)
T ss_pred ccCCCCCHHHHHHHCCCeEEEeCCHHHHHHHHHHHHh
Confidence 13677999999999999999999999987763
No 212
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=44.65 E-value=8.9 Score=30.20 Aligned_cols=27 Identities=30% Similarity=0.753 Sum_probs=21.4
Q ss_pred EcCCCCccccCC-----CCCCCCCCceecCch
Q 014440 305 TCPRCKARVCEL-----PTECRICGLQLVSSP 331 (424)
Q Consensus 305 ~Cp~C~s~~C~l-----P~~C~~C~l~Lvs~p 331 (424)
.||-|+-..+=| .+.|.+||.+|+-|+
T Consensus 21 kCpdC~N~q~vFshast~V~C~~CG~~l~~PT 52 (67)
T COG2051 21 KCPDCGNEQVVFSHASTVVTCLICGTTLAEPT 52 (67)
T ss_pred ECCCCCCEEEEeccCceEEEecccccEEEecC
Confidence 599999887744 469999999998653
No 213
>PRK05978 hypothetical protein; Provisional
Probab=44.46 E-value=13 Score=33.89 Aligned_cols=23 Identities=26% Similarity=0.761 Sum_probs=19.3
Q ss_pred EcCCCCc-----cccCCCCCCCCCCcee
Q 014440 305 TCPRCKA-----RVCELPTECRICGLQL 327 (424)
Q Consensus 305 ~Cp~C~s-----~~C~lP~~C~~C~l~L 327 (424)
-||+|+. .|=++...|+.||+.+
T Consensus 35 rCP~CG~G~LF~g~Lkv~~~C~~CG~~~ 62 (148)
T PRK05978 35 RCPACGEGKLFRAFLKPVDHCAACGEDF 62 (148)
T ss_pred cCCCCCCCcccccccccCCCccccCCcc
Confidence 6999986 4558889999999886
No 214
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=44.30 E-value=9 Score=26.71 Aligned_cols=14 Identities=36% Similarity=0.994 Sum_probs=6.0
Q ss_pred cccccccchhh-hcc
Q 014440 390 KHFCLECDIYI-HES 403 (424)
Q Consensus 390 ~~fC~dCd~fi-he~ 403 (424)
..||.-||+|+ |++
T Consensus 3 ryyCdyC~~~~~~d~ 17 (38)
T PF06220_consen 3 RYYCDYCKKYLTHDS 17 (38)
T ss_dssp S-B-TTT--B-S--S
T ss_pred CeecccccceecCCC
Confidence 57999999999 876
No 215
>COG1533 SplB DNA repair photolyase [DNA replication, recombination, and repair]
Probab=44.28 E-value=98 Score=31.24 Aligned_cols=108 Identities=19% Similarity=0.254 Sum_probs=71.0
Q ss_pred HHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCH-------H-HHHHHHHhCCcEEEEEEecc----hHHHHHHHH
Q 014440 170 IQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDI-------M-ETIQKCKESKIRCSVIGLSA----EMFICKHLC 237 (424)
Q Consensus 170 L~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i-------~-~~i~~akk~~IrV~vIgLg~----e~~iLq~iA 237 (424)
-.|+++.+-+.|... ..+..+|-+|+. +||-.. . .+++.+.+.+.+|.+.-=++ +..+|++++
T Consensus 65 k~n~~e~l~~el~~~---~~k~~~i~is~~--TDpyqp~E~~~~ltR~ilei~~~~~~~v~I~TKS~lv~RDld~l~~~~ 139 (297)
T COG1533 65 KENLLELLERELRKP---GPKRTVIAISSV--TDPYQPIEKEYRLTRKILEILLKYGFPVSIVTKSALVLRDLDLLLELA 139 (297)
T ss_pred chhHHHHHHHHHhhc---cCCceEEEEecC--CCCCCcchHHHHHHHHHHHHHHHcCCcEEEEECCcchhhhHHHHHhhh
Confidence 356777777777642 233445555543 255433 2 56788889999988877666 789999999
Q ss_pred HH--hCCEEEEecChhhHHHHHHhcCCCCccchhhhhhheeeecCCCC
Q 014440 238 QE--TGGTYSVALDESHSKELILEHAPPPPAIAEFAIASLIKMGFPQR 283 (424)
Q Consensus 238 ~~--TGG~Y~~~~d~~~L~~lL~~~~~pp~~~~~~~~~~Li~mGFP~~ 283 (424)
.. +.-.+.+..++..+...+.-.+++|..| -..-..|..-|.|..
T Consensus 140 ~~~~v~V~~Sitt~d~~l~k~~EP~apsp~~R-i~al~~l~eaGi~~~ 186 (297)
T COG1533 140 ERGKVRVAVSITTLDEELAKILEPRAPSPEER-LEALKELSEAGIPVG 186 (297)
T ss_pred hccceEEEEEeecCcHHHHHhcCCCCcCHHHH-HHHHHHHHHCCCeEE
Confidence 99 5556666666667888888888777665 222334555566554
No 216
>cd02006 TPP_Gcl Thiamine pyrophosphate (TPP) family, Gcl subfamily, TPP-binding module; composed of proteins similar to Escherichia coli glyoxylate carboligase (Gcl). E. coli glyoxylate carboligase, plays a key role in glyoxylate metabolism where it catalyzes the condensation of two molecules of glyoxylate to give tartronic semialdehyde and carbon dioxide. This enzyme requires TPP, magnesium ion and FAD as cofactors.
Probab=44.14 E-value=2.4e+02 Score=26.16 Aligned_cols=88 Identities=9% Similarity=-0.006 Sum_probs=57.0
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH----H------------
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM----F------------ 231 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~----~------------ 231 (424)
-+++-+|-.|+..=-.. ..|+|+.|+|+..- -.++ ..+.++++.+++|-+|-+.... .
T Consensus 57 GsmG~~lpaaiGa~la~---p~~~vv~i~GDG~f--~m~~-~eL~Ta~~~~lpviivV~NN~~yg~~~~~q~~~~~~~~~ 130 (202)
T cd02006 57 GPLGWTVPAALGVAAAD---PDRQVVALSGDYDF--QFMI-EELAVGAQHRIPYIHVLVNNAYLGLIRQAQRAFDMDYQV 130 (202)
T ss_pred cchhhhhHHHHhHHhhC---CCCeEEEEEeChHh--hccH-HHHHHHHHhCCCeEEEEEeCchHHHHHHHHHHhcCcccc
Confidence 34555555555432111 25678888876432 1222 4466789999999888886431 1
Q ss_pred -----------------HHHHHHHHhCCEEEEecChhhHHHHHHhcC
Q 014440 232 -----------------ICKHLCQETGGTYSVALDESHSKELILEHA 261 (424)
Q Consensus 232 -----------------iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~ 261 (424)
-+.++|+.-|..+..+.+.++|...|.+..
T Consensus 131 ~~~~~~~~~~~~~~~~~d~~~lA~a~G~~~~~v~~~~el~~al~~a~ 177 (202)
T cd02006 131 NLAFENINSSELGGYGVDHVKVAEGLGCKAIRVTKPEELAAAFEQAK 177 (202)
T ss_pred ccccccccccccCCCCCCHHHHHHHCCCEEEEECCHHHHHHHHHHHH
Confidence 134578888888888888899988887765
No 217
>PRK06260 threonine synthase; Validated
Probab=44.05 E-value=15 Score=38.29 Aligned_cols=42 Identities=24% Similarity=0.420 Sum_probs=29.9
Q ss_pred eEEcCCCCccccC--CCCCCCCCCceecCchhHH-----------hhhcccCCCC
Q 014440 303 GYTCPRCKARVCE--LPTECRICGLQLVSSPHLA-----------RSYHHLFPIA 344 (424)
Q Consensus 303 Gy~Cp~C~s~~C~--lP~~C~~C~l~Lvs~phLa-----------rsyhhl~p~~ 344 (424)
.|.|++|+..|=. ++..||.||-.|-....+. +.|++++|+.
T Consensus 3 ~~~C~~cg~~~~~~~~~~~Cp~cg~~l~~~y~~~~~~~~~~~~~~wry~~~lp~~ 57 (397)
T PRK06260 3 WLKCIECGKEYDPDEIIYTCPECGGLLEVIYDLDKIFDKLRGRGVWRYKELLPVK 57 (397)
T ss_pred EEEECCCCCCCCCCCccccCCCCCCeEEEEecchhhhhccCCcceeeehhhcCCC
Confidence 5899999998743 4467999987765554332 2378888884
No 218
>COG2718 Uncharacterized conserved protein [Function unknown]
Probab=43.49 E-value=65 Score=33.83 Aligned_cols=90 Identities=16% Similarity=0.282 Sum_probs=47.5
Q ss_pred EEEEEeCCHhhhc--CCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCHHHHHHHHhhhhCCC
Q 014440 88 LYIVIDLSRAAAE--MDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSPESHIKALMGKLGCS 165 (424)
Q Consensus 88 lvlvLD~S~SM~~--~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~~~~~~ 165 (424)
++=++|+|+||.. +|+. ....-.+.-|+..-.+ | -.|..|.- ...|..+..- ++ .- ....
T Consensus 249 mfclMDvSGSM~~~~KdlA----krFF~lL~~FL~~kYe-n--veivfIrH-ht~A~EVdE~-----dF---F~--~~es 310 (423)
T COG2718 249 MFCLMDVSGSMDQSEKDLA----KRFFFLLYLFLRRKYE-N--VEIVFIRH-HTEAKEVDET-----DF---FY--SQES 310 (423)
T ss_pred EEEEEecCCCcchHHHHHH----HHHHHHHHHHHhcccc-e--eEEEEEee-cCcceecchh-----hc---ee--ecCC
Confidence 4557899999964 2221 1112234445544332 1 22344442 2344433321 11 10 1457
Q ss_pred CcchHHHHHHHHHHHHcC-CCCCCCcEEEEEE
Q 014440 166 GDSSIQNALDLVHGLLNQ-IPSYGHREVLILY 196 (424)
Q Consensus 166 G~tsL~~AL~~Al~~L~~-~p~~~~reILvI~ 196 (424)
|||-+..||++++..|+. .|. +.=.|-...
T Consensus 311 GGTivSSAl~~m~evi~ErYp~-aeWNIY~fq 341 (423)
T COG2718 311 GGTIVSSALKLMLEVIKERYPP-AEWNIYAFQ 341 (423)
T ss_pred CCeEeHHHHHHHHHHHHhhCCh-hheeeeeee
Confidence 999999999999999987 332 222345554
No 219
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=43.43 E-value=11 Score=25.73 Aligned_cols=26 Identities=31% Similarity=0.662 Sum_probs=19.2
Q ss_pred CCCcCcccccccchhhhc--cCCCCCCC
Q 014440 385 CPKCKKHFCLECDIYIHE--SLHNCPGC 410 (424)
Q Consensus 385 C~~C~~~fC~dCd~fihe--~lh~CPgC 410 (424)
=..|++.||.+|=.-.-+ .-..||.|
T Consensus 14 ~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 14 LLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred EecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 558999999999765544 56667776
No 220
>COG0062 Uncharacterized conserved protein [Function unknown]
Probab=42.65 E-value=89 Score=29.91 Aligned_cols=56 Identities=21% Similarity=0.274 Sum_probs=40.8
Q ss_pred HHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH
Q 014440 173 ALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM 230 (424)
Q Consensus 173 AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~ 230 (424)
|...|...++..|.-..++|+|+-|..++ -||=.-++..|+..|..|.++-++.+.
T Consensus 33 G~aVa~~i~~~~~~~~~~~v~vlcG~GnN--GGDG~VaAR~L~~~G~~V~v~~~~~~~ 88 (203)
T COG0062 33 GLAVARAILREYPLGRARRVLVLCGPGNN--GGDGLVAARHLKAAGYAVTVLLLGDPK 88 (203)
T ss_pred HHHHHHHHHHHcCcccCCEEEEEECCCCc--cHHHHHHHHHHHhCCCceEEEEeCCCC
Confidence 34445555555543326779999886553 567788999999999999999999654
No 221
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=41.63 E-value=17 Score=25.67 Aligned_cols=42 Identities=21% Similarity=0.473 Sum_probs=29.7
Q ss_pred eeecccccccCCCCCCceeeCCCcCcccccccchhhhccCCCCCCCC
Q 014440 365 CFGCQQSLLASGNKAGLCVACPKCKKHFCLECDIYIHESLHNCPGCE 411 (424)
Q Consensus 365 C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~dCd~fihe~lh~CPgC~ 411 (424)
|..|..++... ..+.=..|++.||..|=.-....-..||.|.
T Consensus 2 C~~C~~~~~~~-----~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~ 43 (44)
T PF14634_consen 2 CNICFEKYSEE-----RRPRLTSCGHIFCEKCLKKLKGKSVKCPICR 43 (44)
T ss_pred CcCcCccccCC-----CCeEEcccCCHHHHHHHHhhcCCCCCCcCCC
Confidence 66777776211 1244568999999999876667778999885
No 222
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=41.62 E-value=10 Score=24.66 Aligned_cols=28 Identities=25% Similarity=0.686 Sum_probs=9.5
Q ss_pred ceeecccccccCCCCCCceeeCCCcCccccccc
Q 014440 364 TCFGCQQSLLASGNKAGLCVACPKCKKHFCLEC 396 (424)
Q Consensus 364 ~C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~dC 396 (424)
.|.+|..+... ...|.|+.|+-.+..+|
T Consensus 2 ~C~~C~~~~~~-----~~~Y~C~~Cdf~lH~~C 29 (30)
T PF07649_consen 2 RCDACGKPIDG-----GWFYRCSECDFDLHEEC 29 (30)
T ss_dssp --TTTS----S-------EEE-TTT-----HHH
T ss_pred cCCcCCCcCCC-----CceEECccCCCccChhc
Confidence 48889866642 24688777665554444
No 223
>TIGR03472 HpnI hopanoid biosynthesis associated glycosyl transferase protein HpnI. This family of genes include a glycosyl transferase, group 2 domain (pfam00535) which are responsible, generally for the transfer of nucleotide-diphosphate sugars to substrates such as polysaccharides and lipids. The member of this clade from Acidithiobacillus ferrooxidans ATCC 23270 (AFE_0974) is found in the same locus as squalene-hopene cyclase (SHC, TIGR01507) and other genes associated with the biosynthesis of hopanoid natural products. Similarly, in Ralstonia eutropha JMP134 (Reut_B4902) this gene is adjacent to HpnAB, IspH and HpnH (TIGR03470), although SHC itself is elsewhere in the genome. Notably, this gene (here named HpnI) and three others form a conserved set (HpnIJKL) which occur in a subset of all genomes containing the SHC enzyme. This relationship was discerned using the method of partial phylogenetic profiling. This group includes Zymomonas mobilis, the organism where the initial hopano
Probab=41.21 E-value=1.7e+02 Score=29.85 Aligned_cols=69 Identities=9% Similarity=0.081 Sum_probs=40.3
Q ss_pred CcEEEEEEcCCCCCCccCHHHHHHHHHhC--CcEEEEEEec------chHHHHHHHHHHhCCEEEEecChhh------HH
Q 014440 189 HREVLILYSALSTCDPGDIMETIQKCKES--KIRCSVIGLS------AEMFICKHLCQETGGTYSVALDESH------SK 254 (424)
Q Consensus 189 ~reILvI~ss~~t~dp~~i~~~i~~akk~--~IrV~vIgLg------~e~~iLq~iA~~TGG~Y~~~~d~~~------L~ 254 (424)
.-||||+.++ +.|+ ..++++.+++. +++|.+|.-+ .....+.++.+...|.|++..|.+. |+
T Consensus 70 ~~EIivvdd~--s~D~--t~~iv~~~~~~~p~~~i~~v~~~~~~G~~~K~~~l~~~~~~a~ge~i~~~DaD~~~~p~~L~ 145 (373)
T TIGR03472 70 GFQMLFGVQD--PDDP--ALAVVRRLRADFPDADIDLVIDARRHGPNRKVSNLINMLPHARHDILVIADSDISVGPDYLR 145 (373)
T ss_pred CeEEEEEeCC--CCCc--HHHHHHHHHHhCCCCceEEEECCCCCCCChHHHHHHHHHHhccCCEEEEECCCCCcChhHHH
Confidence 4588775443 2232 23455555543 4566666322 2345677778889999998777653 55
Q ss_pred HHHHhcC
Q 014440 255 ELILEHA 261 (424)
Q Consensus 255 ~lL~~~~ 261 (424)
.+...+.
T Consensus 146 ~lv~~~~ 152 (373)
T TIGR03472 146 QVVAPLA 152 (373)
T ss_pred HHHHHhc
Confidence 5554443
No 224
>smart00355 ZnF_C2H2 zinc finger.
Probab=40.94 E-value=7.4 Score=22.98 Aligned_cols=23 Identities=30% Similarity=0.577 Sum_probs=17.6
Q ss_pred eeCCCcCcccccccchhhhccCC
Q 014440 383 VACPKCKKHFCLECDIYIHESLH 405 (424)
Q Consensus 383 ~~C~~C~~~fC~dCd~fihe~lh 405 (424)
|+|+.|+..|-..-+...|...|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H 23 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTH 23 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHh
Confidence 56888988888888777776544
No 225
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=40.49 E-value=21 Score=25.68 Aligned_cols=26 Identities=27% Similarity=0.611 Sum_probs=19.5
Q ss_pred eEEcCCCCccccC---CCCCCCCCCceec
Q 014440 303 GYTCPRCKARVCE---LPTECRICGLQLV 328 (424)
Q Consensus 303 Gy~Cp~C~s~~C~---lP~~C~~C~l~Lv 328 (424)
-|+|..|+..+=. -+..||-||-.++
T Consensus 2 ~Y~C~~Cg~~~~~~~~~~irC~~CG~rIl 30 (44)
T smart00659 2 IYICGECGRENEIKSKDVVRCRECGYRIL 30 (44)
T ss_pred EEECCCCCCEeecCCCCceECCCCCceEE
Confidence 4899999986653 3578999986553
No 226
>KOG1818 consensus Membrane trafficking and cell signaling protein HRS, contains VHS and FYVE domains [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=40.01 E-value=13 Score=41.22 Aligned_cols=45 Identities=22% Similarity=0.675 Sum_probs=34.4
Q ss_pred CCceeecccccccCCCCCCceeeCCCcCcccccccchh--------hhccCCCCCCC
Q 014440 362 RSTCFGCQQSLLASGNKAGLCVACPKCKKHFCLECDIY--------IHESLHNCPGC 410 (424)
Q Consensus 362 ~~~C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~dCd~f--------ihe~lh~CPgC 410 (424)
+..|+.|...|..... -+-|-.|+.+||..|-.+ |-+-...|-.|
T Consensus 165 ~~~C~rCr~~F~~~~r----kHHCr~CG~vFC~qcss~s~~lP~~Gi~~~VRVCd~C 217 (634)
T KOG1818|consen 165 SEECLRCRVKFGLTNR----KHHCRNCGQVFCGQCSSKSLTLPKLGIEKPVRVCDSC 217 (634)
T ss_pred ccccceeeeeeeeccc----cccccccchhhccCccccccCcccccccccceehhhh
Confidence 4579999999964432 367999999999999743 44455788888
No 227
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=39.64 E-value=16 Score=36.01 Aligned_cols=90 Identities=29% Similarity=0.629 Sum_probs=59.9
Q ss_pred cceee-ecCCccc--cCeEEcCCCCccccCCC------------CCCCCCCceecCchhHHhhhc-ccCCCCCCcccCcc
Q 014440 289 ISICS-CHKEVKI--GVGYTCPRCKARVCELP------------TECRICGLQLVSSPHLARSYH-HLFPIAPFDEATPS 352 (424)
Q Consensus 289 ~a~C~-CH~~~~~--~~Gy~Cp~C~s~~C~lP------------~~C~~C~l~Lvs~phLarsyh-hl~p~~~f~~~~~~ 352 (424)
+++|+ ||.+.+. .|-|+|-.|+..+=+=| -.|++||..|-|. ||..- -||=|+=+...
T Consensus 120 r~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~~l~fr~d~yH~yHFkCt~C~keL~sd---aRevk~eLyClrChD~m--- 193 (332)
T KOG2272|consen 120 RALCRECNQKEKAKGRGRYVCQKCHAHIDEQPLTFRGDPYHPYHFKCTTCGKELTSD---AREVKGELYCLRCHDKM--- 193 (332)
T ss_pred hHHhhhhhhhhcccccceeehhhhhhhcccccccccCCCCCccceecccccccccch---hhhhccceecccccccc---
Confidence 55654 6655332 24799999999876533 4799999999876 44444 57767666653
Q ss_pred ccccccCCCCCceeecccccccCC----CC--CCceeeCCCcCccc
Q 014440 353 RLNDLHNISRSTCFGCQQSLLASG----NK--AGLCVACPKCKKHF 392 (424)
Q Consensus 353 ~~~~~~~~~~~~C~~C~~~~~~~~----~~--~~~~~~C~~C~~~f 392 (424)
+-..|++|.+++.... ++ -.-.|+|.+|.+.|
T Consensus 194 --------gipiCgaC~rpIeervi~amgKhWHveHFvCa~CekPF 231 (332)
T KOG2272|consen 194 --------GIPICGACRRPIEERVIFAMGKHWHVEHFVCAKCEKPF 231 (332)
T ss_pred --------CCcccccccCchHHHHHHHhccccchhheeehhcCCcc
Confidence 3457999998886321 00 01158999998877
No 228
>PHA02768 hypothetical protein; Provisional
Probab=39.59 E-value=21 Score=27.10 Aligned_cols=19 Identities=26% Similarity=0.621 Sum_probs=15.1
Q ss_pred CCCCCCceecCchhHHhhh
Q 014440 319 ECRICGLQLVSSPHLARSY 337 (424)
Q Consensus 319 ~C~~C~l~Lvs~phLarsy 337 (424)
+|+.||..+..+.||.+..
T Consensus 7 ~C~~CGK~Fs~~~~L~~H~ 25 (55)
T PHA02768 7 ECPICGEIYIKRKSMITHL 25 (55)
T ss_pred CcchhCCeeccHHHHHHHH
Confidence 5667888999999997653
No 229
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=39.03 E-value=13 Score=33.19 Aligned_cols=24 Identities=25% Similarity=0.805 Sum_probs=18.1
Q ss_pred eEEcCCCCccccCCC--CCCCCCCce
Q 014440 303 GYTCPRCKARVCELP--TECRICGLQ 326 (424)
Q Consensus 303 Gy~Cp~C~s~~C~lP--~~C~~C~l~ 326 (424)
++.||.|++..=+-- +.||+||.+
T Consensus 28 ~~hCp~Cg~PLF~KdG~v~CPvC~~~ 53 (131)
T COG1645 28 AKHCPKCGTPLFRKDGEVFCPVCGYR 53 (131)
T ss_pred HhhCcccCCcceeeCCeEECCCCCce
Confidence 899999998655422 589999953
No 230
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=38.91 E-value=25 Score=23.73 Aligned_cols=24 Identities=38% Similarity=0.834 Sum_probs=16.9
Q ss_pred EEcCCCCccccC---CCCCCCCCCcee
Q 014440 304 YTCPRCKARVCE---LPTECRICGLQL 327 (424)
Q Consensus 304 y~Cp~C~s~~C~---lP~~C~~C~l~L 327 (424)
|+|..|++.+=- -|+.|+-||-..
T Consensus 1 Y~C~~Cg~~~~~~~~~~irC~~CG~RI 27 (32)
T PF03604_consen 1 YICGECGAEVELKPGDPIRCPECGHRI 27 (32)
T ss_dssp EBESSSSSSE-BSTSSTSSBSSSS-SE
T ss_pred CCCCcCCCeeEcCCCCcEECCcCCCeE
Confidence 889999987752 346899998654
No 231
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=38.70 E-value=16 Score=25.86 Aligned_cols=25 Identities=36% Similarity=0.745 Sum_probs=15.3
Q ss_pred eeeCCCcCcccccccchhhhccCCCCCC
Q 014440 382 CVACPKCKKHFCLECDIYIHESLHNCPG 409 (424)
Q Consensus 382 ~~~C~~C~~~fC~dCd~fihe~lh~CPg 409 (424)
.+.|+.|+..||..- .+-.-|.|++
T Consensus 13 ~~~C~~C~~~FC~~H---r~~e~H~C~~ 37 (43)
T PF01428_consen 13 PFKCKHCGKSFCLKH---RLPEDHNCSK 37 (43)
T ss_dssp HEE-TTTS-EE-TTT---HSTTTCT-SS
T ss_pred CeECCCCCcccCccc---cCccccCCcc
Confidence 589999999999864 3455677764
No 232
>cd02005 TPP_PDC_IPDC Thiamine pyrophosphate (TPP) family, PDC_IPDC subfamily, TPP-binding module; composed of proteins similar to pyruvate decarboxylase (PDC) and indolepyruvate decarboxylase (IPDC). PDC, a key enzyme in alcoholic fermentation, catalyzes the conversion of pyruvate to acetaldehyde and CO2. It is able to utilize other 2-oxo acids as substrates. In plants and various plant-associated bacteria, IPDC plays a role in the indole-3-pyruvic acid (IPA) pathway, a tryptophan-dependent biosynthetic route to indole-3-acetaldehyde (IAA). IPDC catalyzes the decarboxylation of IPA to IAA. Both PDC and IPDC depend on TPP and Mg2+ as cofactors.
Probab=38.55 E-value=1.7e+02 Score=26.79 Aligned_cols=91 Identities=15% Similarity=0.081 Sum_probs=60.9
Q ss_pred CcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecch----------------
Q 014440 166 GDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAE---------------- 229 (424)
Q Consensus 166 G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e---------------- 229 (424)
+..+++.+|-.|+..=-..| .+.+++|+|+..- -.+.++ +.++++.++++-+|-+-..
T Consensus 48 ~~g~mG~~l~~aiGaala~~---~~~vv~i~GDG~f--~~~~~e-l~ta~~~~~p~~ivV~nN~~~~~~~~~~~~~~~~~ 121 (183)
T cd02005 48 LWGSIGYSVPAALGAALAAP---DRRVILLVGDGSF--QMTVQE-LSTMIRYGLNPIIFLINNDGYTIERAIHGPEASYN 121 (183)
T ss_pred chhhHhhhHHHHHHHHHhCC---CCeEEEEECCchh--hccHHH-HHHHHHhCCCCEEEEEECCCcEEEEEeccCCcCcc
Confidence 44566666666665422222 3678888886543 234444 5578888888777766421
Q ss_pred ---HHHHHHHHHHhC----CEEEEecChhhHHHHHHhcCC
Q 014440 230 ---MFICKHLCQETG----GTYSVALDESHSKELILEHAP 262 (424)
Q Consensus 230 ---~~iLq~iA~~TG----G~Y~~~~d~~~L~~lL~~~~~ 262 (424)
..-+.++|+..| +.|..+.+.++|.+.|.+...
T Consensus 122 ~~~~~d~~~ia~a~G~~~~~~~~~v~~~~el~~al~~a~~ 161 (183)
T cd02005 122 DIANWNYTKLPEVFGGGGGGLSFRVKTEGELDEALKDALF 161 (183)
T ss_pred cCCCCCHHHHHHHhCCCccccEEEecCHHHHHHHHHHHHh
Confidence 124678999998 588889999999999988764
No 233
>PHA00733 hypothetical protein
Probab=38.49 E-value=24 Score=31.10 Aligned_cols=33 Identities=24% Similarity=0.622 Sum_probs=26.4
Q ss_pred eEEcCCCCcccc------------CCCCCCCCCCceecCchhHHh
Q 014440 303 GYTCPRCKARVC------------ELPTECRICGLQLVSSPHLAR 335 (424)
Q Consensus 303 Gy~Cp~C~s~~C------------~lP~~C~~C~l~Lvs~phLar 335 (424)
-|.|++|+..|- +-|-.|+.|+..+..+.+|.+
T Consensus 73 Py~C~~Cgk~Fss~s~L~~H~r~h~~~~~C~~CgK~F~~~~sL~~ 117 (128)
T PHA00733 73 PYVCPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKEFRNTDSTLD 117 (128)
T ss_pred CccCCCCCCcCCCHHHHHHHHhcCCcCccCCCCCCccCCHHHHHH
Confidence 689999987655 235699999999999888865
No 234
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=38.37 E-value=21 Score=27.09 Aligned_cols=23 Identities=35% Similarity=0.826 Sum_probs=17.1
Q ss_pred EcCCCCccccC-CCCCCCCCCcee
Q 014440 305 TCPRCKARVCE-LPTECRICGLQL 327 (424)
Q Consensus 305 ~Cp~C~s~~C~-lP~~C~~C~l~L 327 (424)
.||+|.++.|. ..-+||-||+..
T Consensus 1 ~Cpv~~~~~~~~v~~~Cp~cGipt 24 (55)
T PF13824_consen 1 LCPVCKKDLPAHVNFECPDCGIPT 24 (55)
T ss_pred CCCCCccccccccCCcCCCCCCcC
Confidence 38888888774 345899999864
No 235
>PRK07525 sulfoacetaldehyde acetyltransferase; Validated
Probab=38.02 E-value=1.5e+02 Score=32.33 Aligned_cols=91 Identities=7% Similarity=-0.037 Sum_probs=62.0
Q ss_pred CcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH---------------
Q 014440 166 GDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM--------------- 230 (424)
Q Consensus 166 G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~--------------- 230 (424)
+..+++-||-.|+..--.. ..|+||+|+|++.- . .++ ..+.++.+.+++|-+|-+....
T Consensus 433 ~~g~mG~glp~aiGa~la~---p~r~vv~i~GDG~f-~-~~~-~el~Ta~~~~lpv~ivV~NN~~y~~~~~~~~~~~~~~ 506 (588)
T PRK07525 433 SFGNCGYAFPAIIGAKIAC---PDRPVVGFAGDGAW-G-ISM-NEVMTAVRHNWPVTAVVFRNYQWGAEKKNQVDFYNNR 506 (588)
T ss_pred cccccccHHHHHHHHHHhC---CCCcEEEEEcCchH-h-ccH-HHHHHHHHhCCCeEEEEEeCchhHHHHHHHHHHhCCC
Confidence 3356666666666543322 24678888886432 1 233 4466899999998888775321
Q ss_pred ---------HHHHHHHHHhCCEEEEecChhhHHHHHHhcCC
Q 014440 231 ---------FICKHLCQETGGTYSVALDESHSKELILEHAP 262 (424)
Q Consensus 231 ---------~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~~ 262 (424)
.-+.++|+..|+.+..+.+.++|+..|...+.
T Consensus 507 ~~~~~~~~~~d~~~lA~a~G~~~~~v~~~~el~~al~~a~~ 547 (588)
T PRK07525 507 FVGTELDNNVSYAGIAEAMGAEGVVVDTQEELGPALKRAID 547 (588)
T ss_pred cccccCCCCCCHHHHHHHCCCeEEEECCHHHHHHHHHHHHh
Confidence 13466999999999999999999988877664
No 236
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=37.81 E-value=12 Score=29.84 Aligned_cols=33 Identities=27% Similarity=0.648 Sum_probs=19.6
Q ss_pred ecCCccccC-eEEcCCCCccccCCCCCCCCCCcee
Q 014440 294 CHKEVKIGV-GYTCPRCKARVCELPTECRICGLQL 327 (424)
Q Consensus 294 CH~~~~~~~-Gy~Cp~C~s~~C~lP~~C~~C~l~L 327 (424)
||..+...+ .|.|+.|..-|=. -..||.|+-.|
T Consensus 7 C~~~L~~~~~~~~C~~C~~~~~~-~a~CPdC~~~L 40 (70)
T PF07191_consen 7 CQQELEWQGGHYHCEACQKDYKK-EAFCPDCGQPL 40 (70)
T ss_dssp S-SBEEEETTEEEETTT--EEEE-EEE-TTT-SB-
T ss_pred CCCccEEeCCEEECcccccccee-cccCCCcccHH
Confidence 777766543 8999999997643 46799998754
No 237
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=37.74 E-value=17 Score=31.41 Aligned_cols=9 Identities=22% Similarity=0.527 Sum_probs=4.3
Q ss_pred eeeCCCcCc
Q 014440 382 CVACPKCKK 390 (424)
Q Consensus 382 ~~~C~~C~~ 390 (424)
+.+|+.|++
T Consensus 70 ~~~C~~Cg~ 78 (113)
T PRK12380 70 QAWCWDCSQ 78 (113)
T ss_pred EEEcccCCC
Confidence 344555553
No 238
>cd02001 TPP_ComE_PpyrDC Thiamine pyrophosphate (TPP) family, ComE and PpyrDC subfamily, TPP-binding module; composed of proteins similar to sulfopyruvate decarboxylase beta subunit (ComE) and phosphonopyruvate decarboxylase (Ppyr decarboxylase). Methanococcus jannaschii sulfopyruvate decarboxylase (ComDE) is a dodecamer of six alpha (D) subunits and six (E) beta subunits which, catalyzes the decarboxylation of sulfopyruvic acid to sulfoacetaldehyde in the coenzyme M pathway. Ppyr decarboxylase is a homotrimeric enzyme which functions in the biosynthesis of C-P compounds such as bialaphos tripeptide in Streptomyces hygroscopicus. Ppyr decarboxylase and ComDE require TPP and divalent metal cation cofactors.
Probab=37.53 E-value=1.2e+02 Score=27.20 Aligned_cols=70 Identities=10% Similarity=-0.075 Sum_probs=47.9
Q ss_pred cEEEEEEcCCCCCCccCHHHHHHHHHhC-CcEEEEEEecch-------------HHHHHHHHHHhCCEEEEecChhhHHH
Q 014440 190 REVLILYSALSTCDPGDIMETIQKCKES-KIRCSVIGLSAE-------------MFICKHLCQETGGTYSVALDESHSKE 255 (424)
Q Consensus 190 reILvI~ss~~t~dp~~i~~~i~~akk~-~IrV~vIgLg~e-------------~~iLq~iA~~TGG~Y~~~~d~~~L~~ 255 (424)
++|++|+|+..- -.++ ..+.++.+. +++|-+|-+... ..-+.++|+.-|..+..+.+.++|.+
T Consensus 60 ~~Vv~i~GDG~f--~m~~-~el~t~~~~~~~~i~~vV~nN~~~g~~~~~~~~~~~~d~~~lA~a~G~~~~~v~~~~el~~ 136 (157)
T cd02001 60 RKVIVVDGDGSL--LMNP-GVLLTAGEFTPLNLILVVLDNRAYGSTGGQPTPSSNVNLEAWAAACGYLVLSAPLLGGLGS 136 (157)
T ss_pred CcEEEEECchHH--Hhcc-cHHHHHHHhcCCCEEEEEEeCccccccCCcCCCCCCCCHHHHHHHCCCceEEcCCHHHHHH
Confidence 678888886432 0122 234555555 577766665432 23578999999999999999999999
Q ss_pred HHHhcCC
Q 014440 256 LILEHAP 262 (424)
Q Consensus 256 lL~~~~~ 262 (424)
.|.+...
T Consensus 137 al~~a~~ 143 (157)
T cd02001 137 EFAGLLA 143 (157)
T ss_pred HHHHHHh
Confidence 9888763
No 239
>cd02014 TPP_POX Thiamine pyrophosphate (TPP) family, Pyruvate oxidase (POX) subfamily, TPP-binding module; composed of proteins similar to Lactobacillus plantarum POX, which plays a key role in controlling acetate production under aerobic conditions. POX decarboxylates pyruvate, producing hydrogen peroxide and the energy-storage metabolite acetylphosphate. It requires FAD in addition to TPP and a divalent cation as cofactors.
Probab=37.43 E-value=2.1e+02 Score=25.92 Aligned_cols=90 Identities=10% Similarity=-0.053 Sum_probs=56.8
Q ss_pred CcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH---------------
Q 014440 166 GDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM--------------- 230 (424)
Q Consensus 166 G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~--------------- 230 (424)
+..+++.||-.|+..=-.. ..+++|+|+|+... . .+. ..+..+.+.++.+-+|-+-...
T Consensus 49 ~~g~mG~~~~~aiGa~~a~---~~~~vv~i~GDG~f-~-~~~-~el~t~~~~~lp~~~iv~NN~~~~~~~~~~~~~~~~~ 122 (178)
T cd02014 49 LLATMGNGLPGAIAAKLAY---PDRQVIALSGDGGF-A-MLM-GDLITAVKYNLPVIVVVFNNSDLGFIKWEQEVMGQPE 122 (178)
T ss_pred CCchhhhHHHHHHHHHHhC---CCCcEEEEEcchHH-H-hhH-HHHHHHHHhCCCcEEEEEECCchhHHHHHHHHhcCCc
Confidence 3346666666665532211 24678888876432 1 122 3356678888887777664321
Q ss_pred -------HHHHHHHHHhCCEEEEecChhhHHHHHHhcC
Q 014440 231 -------FICKHLCQETGGTYSVALDESHSKELILEHA 261 (424)
Q Consensus 231 -------~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~ 261 (424)
.-+.++|+..|+.++.+.+.+.+++.+.+..
T Consensus 123 ~~~~~~~~d~~~la~a~G~~~~~v~~~~el~~~l~~a~ 160 (178)
T cd02014 123 FGVDLPNPDFAKIAEAMGIKGIRVEDPDELEAALDEAL 160 (178)
T ss_pred eeccCCCCCHHHHHHHCCCeEEEeCCHHHHHHHHHHHH
Confidence 1356788888888888888888888777654
No 240
>PF09186 DUF1949: Domain of unknown function (DUF1949); InterPro: IPR015269 Members of this entry are a set of functionally uncharacterised hypothetical bacterial proteins. They adopt a ferredoxin-like fold, with a beta-alpha-beta-beta-alpha-beta arrangement []. This entry contains the protein Impact, which is a translational regulator that ensures constant high levels of translation under amino acid starvation. It acts by interacting with Gcn1/Gcn1L1, thereby preventing activation of Gcn2 protein kinases (EIF2AK1 to 4) and subsequent down-regulation of protein synthesis. It is evolutionary conserved from eukaryotes to archaea []. ; PDB: 2CVE_A 1VI7_A.
Probab=37.34 E-value=84 Score=22.51 Aligned_cols=41 Identities=12% Similarity=0.023 Sum_probs=30.0
Q ss_pred CccCHHHHHHHHHhCCcEEEEEEecch------------HHHHHHHHHHhCCE
Q 014440 203 DPGDIMETIQKCKESKIRCSVIGLSAE------------MFICKHLCQETGGT 243 (424)
Q Consensus 203 dp~~i~~~i~~akk~~IrV~vIgLg~e------------~~iLq~iA~~TGG~ 243 (424)
++..+..+-..+.+.++.|.-..++.. ..+.++|++.|+|+
T Consensus 4 ~Y~~~~~v~~~l~~~~~~i~~~~y~~~V~~~v~v~~~~~~~f~~~l~~~t~G~ 56 (56)
T PF09186_consen 4 DYSQYGKVERLLEQNGIEIVDEDYTDDVTLTVAVPEEEVEEFKAQLTDLTSGR 56 (56)
T ss_dssp -CCCHHHHHHHHHHTTTEEEEEEECTTEEEEEEEECCCHHHHHHHHHHHTTT-
T ss_pred chhhHHHHHHHHHHCCCEEEcceecceEEEEEEECHHHHHHHHHHHHHHcCCC
Confidence 445556667778888898876666654 47999999999995
No 241
>KOG1356 consensus Putative transcription factor 5qNCA, contains JmjC domain [Transcription]
Probab=36.92 E-value=15 Score=41.79 Aligned_cols=43 Identities=28% Similarity=0.668 Sum_probs=30.6
Q ss_pred CCceeecccccccCCCCCCceeeCCCcCcccccccchhh------hccCCCCCCC
Q 014440 362 RSTCFGCQQSLLASGNKAGLCVACPKCKKHFCLECDIYI------HESLHNCPGC 410 (424)
Q Consensus 362 ~~~C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~dCd~fi------he~lh~CPgC 410 (424)
...|..|.+.+-. ..|+|++|+..+|.+|---- -|..-.|++|
T Consensus 229 ~~mC~~C~~tlfn------~hw~C~~C~~~~Cl~C~r~~~p~~~~~e~a~k~~~~ 277 (889)
T KOG1356|consen 229 REMCDRCETTLFN------IHWRCPRCGFGVCLDCYRKWYPRLSKEEVAEKCEFS 277 (889)
T ss_pred chhhhhhcccccc------eeEEccccCCeeeecchhhccccchHhHhhhhhhHH
Confidence 4589999865531 47999999999999996433 2444555555
No 242
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=36.78 E-value=18 Score=36.04 Aligned_cols=48 Identities=27% Similarity=0.586 Sum_probs=0.0
Q ss_pred CCCCCCCCCCceecCchhHHhhhcccCCCCCCcccCccccccccCCCCCceeecccccccCCCCCCceeeCCCcCc
Q 014440 315 ELPTECRICGLQLVSSPHLARSYHHLFPIAPFDEATPSRLNDLHNISRSTCFGCQQSLLASGNKAGLCVACPKCKK 390 (424)
Q Consensus 315 ~lP~~C~~C~l~Lvs~phLarsyhhl~p~~~f~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~~~~~~~~C~~C~~ 390 (424)
+.-++|++||-. |.-|+.-.+= +..+||-|. ...-.-...|.||.|+.
T Consensus 237 t~~~~C~~Cg~~---------------PtiP~~~~~C---------~HiyCY~Ci----~ts~~~~asf~Cp~Cg~ 284 (298)
T KOG2879|consen 237 TSDTECPVCGEP---------------PTIPHVIGKC---------GHIYCYYCI----ATSRLWDASFTCPLCGE 284 (298)
T ss_pred cCCceeeccCCC---------------CCCCeeeccc---------cceeehhhh----hhhhcchhhcccCccCC
No 243
>cd04196 GT_2_like_d Subfamily of Glycosyltransferase Family GT2 of unknown function. GT-2 includes diverse families of glycosyltransferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. Glycosyltransferases have been classified into more than 90 distinct sequence based families.
Probab=36.76 E-value=3e+02 Score=24.38 Aligned_cols=86 Identities=19% Similarity=0.175 Sum_probs=46.1
Q ss_pred HHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCC-cEEEEEEecc---hHHHHHHHHHHhCCEEEEecC
Q 014440 174 LDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESK-IRCSVIGLSA---EMFICKHLCQETGGTYSVALD 249 (424)
Q Consensus 174 L~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~-IrV~vIgLg~---e~~iLq~iA~~TGG~Y~~~~d 249 (424)
|..++..+.+. .+..-||||+-++ ++ | +..++++.+.+.. ..+..+-... -..-+.......+|.|+...|
T Consensus 13 l~~~l~sl~~q-~~~~~eiiVvddg-S~-d--~t~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~n~g~~~~~g~~v~~ld 87 (214)
T cd04196 13 LREQLDSILAQ-TYKNDELIISDDG-ST-D--GTVEIIKEYIDKDPFIIILIRNGKNLGVARNFESLLQAADGDYVFFCD 87 (214)
T ss_pred HHHHHHHHHhC-cCCCeEEEEEeCC-CC-C--CcHHHHHHHHhcCCceEEEEeCCCCccHHHHHHHHHHhCCCCEEEEEC
Confidence 44455555443 1224477777543 22 2 2345555555443 3444443332 235556667788999998777
Q ss_pred hh------hHHHHHHhcCCCC
Q 014440 250 ES------HSKELILEHAPPP 264 (424)
Q Consensus 250 ~~------~L~~lL~~~~~pp 264 (424)
.+ .|..++..+...|
T Consensus 88 ~Dd~~~~~~l~~~~~~~~~~~ 108 (214)
T cd04196 88 QDDIWLPDKLERLLKAFLKDD 108 (214)
T ss_pred CCcccChhHHHHHHHHHhcCC
Confidence 55 3666666644333
No 244
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=36.71 E-value=18 Score=31.33 Aligned_cols=10 Identities=20% Similarity=0.697 Sum_probs=5.0
Q ss_pred ceeecccccc
Q 014440 364 TCFGCQQSLL 373 (424)
Q Consensus 364 ~C~~C~~~~~ 373 (424)
.|..|...++
T Consensus 72 ~C~~Cg~~~~ 81 (115)
T TIGR00100 72 ECEDCSEEVS 81 (115)
T ss_pred EcccCCCEEe
Confidence 4555554443
No 245
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=36.48 E-value=23 Score=40.24 Aligned_cols=37 Identities=16% Similarity=0.540 Sum_probs=25.8
Q ss_pred CCceeecccccccCCCC-CCceeeCCCcCcccccccch
Q 014440 362 RSTCFGCQQSLLASGNK-AGLCVACPKCKKHFCLECDI 398 (424)
Q Consensus 362 ~~~C~~C~~~~~~~~~~-~~~~~~C~~C~~~fC~dCd~ 398 (424)
...|..|.+.|..-... ..-++-|-+|+..||..|--
T Consensus 460 SdtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~CSS 497 (1374)
T PTZ00303 460 SDSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFCIT 497 (1374)
T ss_pred CCcccCcCCcccccccccccccccccCCccccCccccC
Confidence 35799999999521000 01246799999999999973
No 246
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=36.38 E-value=24 Score=38.11 Aligned_cols=49 Identities=24% Similarity=0.573 Sum_probs=32.2
Q ss_pred EEcCCCCccccCCCCCCCCCCceecCchhHHhhhcccCCCCCCcccCccccccccCCCCCceeecccccccCCCCCCcee
Q 014440 304 YTCPRCKARVCELPTECRICGLQLVSSPHLARSYHHLFPIAPFDEATPSRLNDLHNISRSTCFGCQQSLLASGNKAGLCV 383 (424)
Q Consensus 304 y~Cp~C~s~~C~lP~~C~~C~l~Lvs~phLarsyhhl~p~~~f~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~~~~~~~ 383 (424)
..|..|+.. ..|+-|+..|+ ||.- ...-.|.-|....+- ..
T Consensus 214 ~~C~~Cg~~-----~~C~~C~~~l~--------~h~~-------------------~~~l~Ch~Cg~~~~~-------~~ 254 (505)
T TIGR00595 214 LLCRSCGYI-----LCCPNCDVSLT--------YHKK-------------------EGKLRCHYCGYQEPI-------PK 254 (505)
T ss_pred eEhhhCcCc-----cCCCCCCCceE--------EecC-------------------CCeEEcCCCcCcCCC-------CC
Confidence 379988765 78999998763 4421 023468888754432 35
Q ss_pred eCCCcCcc
Q 014440 384 ACPKCKKH 391 (424)
Q Consensus 384 ~C~~C~~~ 391 (424)
.||.|++.
T Consensus 255 ~Cp~C~s~ 262 (505)
T TIGR00595 255 TCPQCGSE 262 (505)
T ss_pred CCCCCCCC
Confidence 79999874
No 247
>CHL00073 chlN photochlorophyllide reductase subunit N
Probab=36.24 E-value=3.3e+02 Score=29.27 Aligned_cols=91 Identities=14% Similarity=-0.017 Sum_probs=50.5
Q ss_pred CcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH-----HHHHHHHHHhC-----CEEEE-ecChhhHHHHH
Q 014440 189 HREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM-----FICKHLCQETG-----GTYSV-ALDESHSKELI 257 (424)
Q Consensus 189 ~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~-----~iLq~iA~~TG-----G~Y~~-~~d~~~L~~lL 257 (424)
.|++. ++++ |.-....++.+.+.|+.+-.+|-.... ...+.+.+..+ |...+ -.|..++.+.+
T Consensus 314 GKrva-i~Gd-----p~~~i~LarfL~elGmevV~vgt~~~~~~~~~~d~~~l~~~~~~~~~~~~vive~~D~~el~~~i 387 (457)
T CHL00073 314 GKSVF-FMGD-----NLLEISLARFLIRCGMIVYEIGIPYMDKRYQAAELALLEDTCRKMNVPMPRIVEKPDNYNQIQRI 387 (457)
T ss_pred CCEEE-EECC-----CcHHHHHHHHHHHCCCEEEEEEeCCCChhhhHHHHHHHHHHhhhcCCCCcEEEeCCCHHHHHHHH
Confidence 34565 6664 334456789999999998888776321 12333433333 44433 34545555554
Q ss_pred HhcCCCCccch-hhhhhheeeecCCCCCCC
Q 014440 258 LEHAPPPPAIA-EFAIASLIKMGFPQRAGE 286 (424)
Q Consensus 258 ~~~~~pp~~~~-~~~~~~Li~mGFP~~~~~ 286 (424)
.+. .|.-.-. -...-.|++.|||.+...
T Consensus 388 ~~~-~pDLlIgG~~~~~Pl~~~G~p~~d~~ 416 (457)
T CHL00073 388 REL-QPDLAITGMAHANPLEARGINTKWSV 416 (457)
T ss_pred hhC-CCCEEEccccccCchhhcCCcceEec
Confidence 432 2222211 123457999999998644
No 248
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=36.22 E-value=9.7 Score=25.34 Aligned_cols=8 Identities=38% Similarity=1.294 Sum_probs=3.8
Q ss_pred eeeCCCcC
Q 014440 382 CVACPKCK 389 (424)
Q Consensus 382 ~~~C~~C~ 389 (424)
.|.||.|+
T Consensus 19 ~~vCp~C~ 26 (30)
T PF08274_consen 19 LLVCPECG 26 (30)
T ss_dssp SEEETTTT
T ss_pred EEeCCccc
Confidence 34455444
No 249
>PF00535 Glycos_transf_2: Glycosyl transferase family 2; InterPro: IPR001173 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. This domain is found in a diverse family of glycosyl transferases that transfer the sugar from UDP-glucose, UDP-N-acetyl-galactosamine, GDP-mannose or CDP-abequose, to a range of substrates including cellulose, dolichol phosphate and teichoic acids.; PDB: 2Z87_A 2Z86_B 2D7R_A 2D7I_A 3CKN_A 3CKQ_A 3CKJ_A 3CKV_A 3CKO_A 2FFU_A ....
Probab=36.12 E-value=1.1e+02 Score=25.51 Aligned_cols=73 Identities=19% Similarity=0.247 Sum_probs=47.1
Q ss_pred CcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecch---HHHHHHHHHHhCCEEEEecChh------hHHHHHHh
Q 014440 189 HREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAE---MFICKHLCQETGGTYSVALDES------HSKELILE 259 (424)
Q Consensus 189 ~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e---~~iLq~iA~~TGG~Y~~~~d~~------~L~~lL~~ 259 (424)
.-||||+-++. + .+..+.++.+.+.+.++.+|-.... ...+....+...|.|+...|.+ .|..++..
T Consensus 27 ~~eiivvdd~s-~---d~~~~~~~~~~~~~~~i~~i~~~~n~g~~~~~n~~~~~a~~~~i~~ld~D~~~~~~~l~~l~~~ 102 (169)
T PF00535_consen 27 DFEIIVVDDGS-T---DETEEILEEYAESDPNIRYIRNPENLGFSAARNRGIKHAKGEYILFLDDDDIISPDWLEELVEA 102 (169)
T ss_dssp EEEEEEEECS--S---SSHHHHHHHHHCCSTTEEEEEHCCCSHHHHHHHHHHHH--SSEEEEEETTEEE-TTHHHHHHHH
T ss_pred CEEEEEecccc-c---cccccccccccccccccccccccccccccccccccccccceeEEEEeCCCceEcHHHHHHHHHH
Confidence 45777765542 2 3456777887777778888877754 4677788888889899766655 46777666
Q ss_pred cCCCCc
Q 014440 260 HAPPPP 265 (424)
Q Consensus 260 ~~~pp~ 265 (424)
+..+|+
T Consensus 103 ~~~~~~ 108 (169)
T PF00535_consen 103 LEKNPP 108 (169)
T ss_dssp HHHCTT
T ss_pred HHhCCC
Confidence 665443
No 250
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=36.07 E-value=16 Score=37.19 Aligned_cols=26 Identities=23% Similarity=0.764 Sum_probs=16.0
Q ss_pred CcCcccccccchhhh-ccCCCCCCCCC
Q 014440 387 KCKKHFCLECDIYIH-ESLHNCPGCES 412 (424)
Q Consensus 387 ~C~~~fC~dCd~fih-e~lh~CPgC~~ 412 (424)
.|++.||..|=.-+. ..-..||.|..
T Consensus 25 ~CGH~~C~sCv~~l~~~~~~~CP~C~~ 51 (309)
T TIGR00570 25 VCGHTLCESCVDLLFVRGSGSCPECDT 51 (309)
T ss_pred CCCCcccHHHHHHHhcCCCCCCCCCCC
Confidence 578888888854332 22246888854
No 251
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=35.94 E-value=22 Score=38.44 Aligned_cols=40 Identities=33% Similarity=0.816 Sum_probs=29.7
Q ss_pred CCCceeecccccccCCCCCCceeeCCCcC----------cccccccchhhhccCCCCCCCCC
Q 014440 361 SRSTCFGCQQSLLASGNKAGLCVACPKCK----------KHFCLECDIYIHESLHNCPGCES 412 (424)
Q Consensus 361 ~~~~C~~C~~~~~~~~~~~~~~~~C~~C~----------~~fC~dCd~fihe~lh~CPgC~~ 412 (424)
....|..|.. ..+||.|. ...|..|. |....-..||.|.+
T Consensus 212 ~~~~C~~Cg~-----------~~~C~~C~~~l~~h~~~~~l~Ch~Cg-~~~~~~~~Cp~C~s 261 (505)
T TIGR00595 212 KNLLCRSCGY-----------ILCCPNCDVSLTYHKKEGKLRCHYCG-YQEPIPKTCPQCGS 261 (505)
T ss_pred CeeEhhhCcC-----------ccCCCCCCCceEEecCCCeEEcCCCc-CcCCCCCCCCCCCC
Confidence 3457999972 34699998 45688888 55666789999976
No 252
>cd00568 TPP_enzymes Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and the branched chain alpha-keto acid dehydrogenase complexes.
Probab=35.88 E-value=3e+02 Score=24.03 Aligned_cols=90 Identities=12% Similarity=0.030 Sum_probs=58.0
Q ss_pred CcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH---------------
Q 014440 166 GDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM--------------- 230 (424)
Q Consensus 166 G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~--------------- 230 (424)
+..+++.++..|+..=...| .+++++++|+..-. .. .+.+..+.+.++++-+|-+....
T Consensus 44 ~~g~~G~~~~~a~Gaa~a~~---~~~vv~~~GDG~~~--~~-~~~l~ta~~~~~~~~~iv~nN~~~~~~~~~~~~~~~~~ 117 (168)
T cd00568 44 GFGAMGYGLPAAIGAALAAP---DRPVVCIAGDGGFM--MT-GQELATAVRYGLPVIVVVFNNGGYGTIRMHQEAFYGGR 117 (168)
T ss_pred CchhhhhhHHHHHHHHHhCC---CCcEEEEEcCcHHh--cc-HHHHHHHHHcCCCcEEEEEECCccHHHHHHHHHHcCCC
Confidence 34466666666655433322 45688888765431 12 36677788889988888876431
Q ss_pred --------HHHHHHHHHhCCEEEEecChhhHHHHHHhcC
Q 014440 231 --------FICKHLCQETGGTYSVALDESHSKELILEHA 261 (424)
Q Consensus 231 --------~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~ 261 (424)
.-+.++++.-|..|..+.+.+++++.+.+..
T Consensus 118 ~~~~~~~~~d~~~~a~~~G~~~~~v~~~~~l~~a~~~a~ 156 (168)
T cd00568 118 VSGTDLSNPDFAALAEAYGAKGVRVEDPEDLEAALAEAL 156 (168)
T ss_pred cccccCCCCCHHHHHHHCCCeEEEECCHHHHHHHHHHHH
Confidence 1255677777888887777778877776654
No 253
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=35.88 E-value=23 Score=30.59 Aligned_cols=23 Identities=30% Similarity=0.849 Sum_probs=17.0
Q ss_pred CCCcCcccccccchhhhccCCCCCCCCC
Q 014440 385 CPKCKKHFCLECDIYIHESLHNCPGCES 412 (424)
Q Consensus 385 C~~C~~~fC~dCd~fihe~lh~CPgC~~ 412 (424)
||+|.+.|.. -...+..||-|..
T Consensus 5 CP~C~seytY-----~dg~~~iCpeC~~ 27 (109)
T TIGR00686 5 CPKCNSEYTY-----HDGTQLICPSCLY 27 (109)
T ss_pred CCcCCCcceE-----ecCCeeECccccc
Confidence 8888887754 4666788888875
No 254
>PRK05580 primosome assembly protein PriA; Validated
Probab=35.83 E-value=32 Score=38.55 Aligned_cols=63 Identities=22% Similarity=0.428 Sum_probs=40.4
Q ss_pred cceeeecCCccccCeEEcCCCCccccCCCCCCCCCCceecCchhHHhhhcccCCCCCCcccCccccccccCCCCCceeec
Q 014440 289 ISICSCHKEVKIGVGYTCPRCKARVCELPTECRICGLQLVSSPHLARSYHHLFPIAPFDEATPSRLNDLHNISRSTCFGC 368 (424)
Q Consensus 289 ~a~C~CH~~~~~~~Gy~Cp~C~s~~C~lP~~C~~C~l~Lvs~phLarsyhhl~p~~~f~~~~~~~~~~~~~~~~~~C~~C 368 (424)
+++-+..++.-.. ...|..|+.. ..|+-|+..| +||.- . ..-.|.-|
T Consensus 368 qvll~~nrrGy~~-~~~C~~Cg~~-----~~C~~C~~~l--------~~h~~------~-------------~~l~Ch~C 414 (679)
T PRK05580 368 QVLLFLNRRGYAP-FLLCRDCGWV-----AECPHCDASL--------TLHRF------Q-------------RRLRCHHC 414 (679)
T ss_pred eEEEEEcCCCCCC-ceEhhhCcCc-----cCCCCCCCce--------eEECC------C-------------CeEECCCC
Confidence 5566666553333 5579888765 6899999887 34421 0 23369999
Q ss_pred ccccccCCCCCCceeeCCCcCcc
Q 014440 369 QQSLLASGNKAGLCVACPKCKKH 391 (424)
Q Consensus 369 ~~~~~~~~~~~~~~~~C~~C~~~ 391 (424)
....+. ...||.|++.
T Consensus 415 g~~~~~-------~~~Cp~Cg~~ 430 (679)
T PRK05580 415 GYQEPI-------PKACPECGST 430 (679)
T ss_pred cCCCCC-------CCCCCCCcCC
Confidence 755432 3579999875
No 255
>cd02012 TPP_TK Thiamine pyrophosphate (TPP) family, Transketolase (TK) subfamily, TPP-binding module; TK catalyzes the transfer of a two-carbon unit from ketose phosphates to aldose phosphates. In heterotrophic organisms, TK provides a link between glycolysis and the pentose phosphate pathway and provides precursors for nucleotide, aromatic amino acid and vitamin biosynthesis. In addition, the enzyme plays a central role in the Calvin cycle in plants. Typically, TKs are homodimers. They require TPP and divalent cations, such as magnesium ions, for activity.
Probab=35.72 E-value=3.8e+02 Score=25.89 Aligned_cols=72 Identities=11% Similarity=-0.008 Sum_probs=48.9
Q ss_pred CcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecch-------------HHHHHHHHHHhCCEEEEec--ChhhH
Q 014440 189 HREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAE-------------MFICKHLCQETGGTYSVAL--DESHS 253 (424)
Q Consensus 189 ~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e-------------~~iLq~iA~~TGG~Y~~~~--d~~~L 253 (424)
.++|++|+|+.+ ...+...+++..+...++..-++-+... ..-+.++++.-|..++.+. |.+.+
T Consensus 127 ~~~v~~i~GDG~-~~~G~~~eal~~a~~~~l~~li~vvdnN~~~~~~~~~~~~~~~~~~~~~~a~G~~~~~v~G~d~~~l 205 (255)
T cd02012 127 DYRVYVLLGDGE-LQEGSVWEAASFAGHYKLDNLIAIVDSNRIQIDGPTDDILFTEDLAKKFEAFGWNVIEVDGHDVEEI 205 (255)
T ss_pred CCEEEEEECccc-ccccHHHHHHHHHHHcCCCcEEEEEECCCccccCcHhhccCchhHHHHHHHcCCeEEEECCCCHHHH
Confidence 567888888654 3556677888889888886333333311 2456788888888888776 77777
Q ss_pred HHHHHhcC
Q 014440 254 KELILEHA 261 (424)
Q Consensus 254 ~~lL~~~~ 261 (424)
.+.+.+..
T Consensus 206 ~~al~~a~ 213 (255)
T cd02012 206 LAALEEAK 213 (255)
T ss_pred HHHHHHHH
Confidence 77776543
No 256
>cd02015 TPP_AHAS Thiamine pyrophosphate (TPP) family, Acetohydroxyacid synthase (AHAS) subfamily, TPP-binding module; composed of proteins similar to the large catalytic subunit of AHAS. AHAS catalyzes the condensation of two molecules of pyruvate to give the acetohydroxyacid, 2-acetolactate. 2-Acetolactate is the precursor of the branched chain amino acids, valine and leucine. AHAS also catalyzes the condensation of pyruvate and 2-ketobutyrate to form 2-aceto-2-hydroxybutyrate in isoleucine biosynthesis. In addition to requiring TPP and a divalent metal ion as cofactors, AHAS requires FAD.
Probab=35.53 E-value=3.4e+02 Score=24.66 Aligned_cols=88 Identities=10% Similarity=0.015 Sum_probs=54.9
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH-----------------
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM----------------- 230 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~----------------- 230 (424)
.+++-+|-.|+..=-.. ..++|++|+|+..- . .++ +.+.++.+.++++-+|-+....
T Consensus 50 g~mG~~lp~aiGa~la~---~~~~vv~i~GDG~f-~-~~~-~eL~ta~~~~lpi~ivV~nN~~~~~~~~~~~~~~~~~~~ 123 (186)
T cd02015 50 GTMGFGLPAAIGAKVAR---PDKTVICIDGDGSF-Q-MNI-QELATAAQYNLPVKIVILNNGSLGMVRQWQELFYEGRYS 123 (186)
T ss_pred cchhchHHHHHHHHHhC---CCCeEEEEEcccHH-h-ccH-HHHHHHHHhCCCeEEEEEECCccHHHHHHHHHHcCCcee
Confidence 35555555555432222 24678888876432 1 233 3477788889988888775321
Q ss_pred -------HHHHHHHHHhCCEEEEecChhhHHHHHHhcC
Q 014440 231 -------FICKHLCQETGGTYSVALDESHSKELILEHA 261 (424)
Q Consensus 231 -------~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~ 261 (424)
.-+.++|+.-|+.+..+.+.++|++.+....
T Consensus 124 ~~~~~~~~d~~~~a~a~G~~~~~v~~~~el~~al~~a~ 161 (186)
T cd02015 124 HTTLDSNPDFVKLAEAYGIKGLRVEKPEELEAALKEAL 161 (186)
T ss_pred eccCCCCCCHHHHHHHCCCceEEeCCHHHHHHHHHHHH
Confidence 1245677777888888888888888776654
No 257
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=35.36 E-value=12 Score=31.14 Aligned_cols=37 Identities=30% Similarity=0.618 Sum_probs=26.2
Q ss_pred CCCCCCCCceecCchhHHhhhcccCCCCCCcccCccccccccCCCCCceeecccccc
Q 014440 317 PTECRICGLQLVSSPHLARSYHHLFPIAPFDEATPSRLNDLHNISRSTCFGCQQSLL 373 (424)
Q Consensus 317 P~~C~~C~l~Lvs~phLarsyhhl~p~~~f~~~~~~~~~~~~~~~~~~C~~C~~~~~ 373 (424)
++.|+.|+.+| ++.+|.|+-.|.-. .+.|.-|..+++
T Consensus 33 rS~C~~C~~~L--------~~~~lIPi~S~l~l------------rGrCr~C~~~I~ 69 (92)
T PF06750_consen 33 RSHCPHCGHPL--------SWWDLIPILSYLLL------------RGRCRYCGAPIP 69 (92)
T ss_pred CCcCcCCCCcC--------cccccchHHHHHHh------------CCCCcccCCCCC
Confidence 46788898876 45667676655532 568999987775
No 258
>KOG2327 consensus DNA-binding subunit of a DNA-dependent protein kinase (Ku70 autoantigen) [Replication, recombination and repair]
Probab=35.22 E-value=5.8e+02 Score=28.40 Aligned_cols=112 Identities=15% Similarity=0.320 Sum_probs=64.9
Q ss_pred eEEEEEeCCHhhhcCC---CCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCce------EEeeCCCCCHHHHHHH
Q 014440 87 YLYIVIDLSRAAAEMD---FRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVA------NCLTDLGGSPESHIKA 157 (424)
Q Consensus 87 ~lvlvLD~S~SM~~~D---~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A------~~lspLT~d~~~~~~~ 157 (424)
.+.+|+|+|+||...+ +.++-|..++..+....-...-.||...+|++-+..... ..+.|+-.-++..+..
T Consensus 20 ~ilfvi~~~~s~~~~~~~e~~lspl~~~L~~~~~l~~~~vitn~~~~~~v~~y~~~~~~~~~~~~~l~~l~d~~~~~~~k 99 (602)
T KOG2327|consen 20 AILFVIDVNPSMKAEEPDEFKLSPLKMILDCIDRLCIQLVITNPIDSVGVLFYGTEETEGLENNTLLFPLGDLGQEEVKK 99 (602)
T ss_pred ceEEEEecCHHhhccCcccchhhhHHHHHHHHHHHHhheeecCCCCccceEeecccccccCccceEEeeccccChHHHHH
Confidence 4689999999997644 357777777877777776777789999899887642211 2344544323332222
Q ss_pred Hhhhh------------C-CCCcchHHHHHHHHHHHHcCCC-CCCCcEEEEEEcC
Q 014440 158 LMGKL------------G-CSGDSSIQNALDLVHGLLNQIP-SYGHREVLILYSA 198 (424)
Q Consensus 158 L~~~~------------~-~~G~tsL~~AL~~Al~~L~~~p-~~~~reILvI~ss 198 (424)
+..+. . ....++|.+-|.....++.... ....++|.+++.-
T Consensus 100 ~~~~~e~~~q~~~~~~~~~~~~~s~ls~vl~~c~~~~~~~~~~~~~krv~l~Td~ 154 (602)
T KOG2327|consen 100 ILELFEEENQLSAVNFYGGMHQKSDLSNVLNYCKRMVFASQKKLSNKRVFLFTDN 154 (602)
T ss_pred HHHHhhhhhhhhhhhccCcccccccHHHHHHHHHHHHHHHhhhcccceEEEEecC
Confidence 22111 1 1112367777776666443321 2334566666653
No 259
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=35.08 E-value=19 Score=32.20 Aligned_cols=29 Identities=38% Similarity=0.896 Sum_probs=24.5
Q ss_pred eE-EcCCCCc---cccCCCCCCCCCCceecCch
Q 014440 303 GY-TCPRCKA---RVCELPTECRICGLQLVSSP 331 (424)
Q Consensus 303 Gy-~Cp~C~s---~~C~lP~~C~~C~l~Lvs~p 331 (424)
|| +|--|-+ ++|.+-+.||+|.+.+.||-
T Consensus 103 gY~iCn~Cya~LWK~~~~ypvCPvCkTSFKss~ 135 (140)
T PF05290_consen 103 GYSICNACYANLWKFCNLYPVCPVCKTSFKSSS 135 (140)
T ss_pred chHHHHHHHHHHHHHcccCCCCCcccccccccc
Confidence 66 6777766 89999999999999998874
No 260
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=34.98 E-value=11 Score=36.11 Aligned_cols=23 Identities=22% Similarity=0.288 Sum_probs=11.1
Q ss_pred eeeCCCcCcccccccchhhhccC
Q 014440 382 CVACPKCKKHFCLECDIYIHESL 404 (424)
Q Consensus 382 ~~~C~~C~~~fC~dCd~fihe~l 404 (424)
.|.|+.|+..-|.-=+.|.|-.+
T Consensus 212 l~vcedcg~t~~~~e~~~~h~~~ 234 (267)
T KOG3576|consen 212 LYVCEDCGYTSERPEVYYLHLKL 234 (267)
T ss_pred eeeecccCCCCCChhHHHHHHHh
Confidence 35566555544444444444433
No 261
>PRK06450 threonine synthase; Validated
Probab=34.95 E-value=25 Score=35.98 Aligned_cols=42 Identities=17% Similarity=0.324 Sum_probs=28.4
Q ss_pred eEEcCCCCccccCC-CCCCCCCCceecCchhHHh---hhcccCCCC
Q 014440 303 GYTCPRCKARVCEL-PTECRICGLQLVSSPHLAR---SYHHLFPIA 344 (424)
Q Consensus 303 Gy~Cp~C~s~~C~l-P~~C~~C~l~Lvs~phLar---syhhl~p~~ 344 (424)
+|.|++|+..|=.. +..|+-||-.|.....+.+ -.+.++|+.
T Consensus 3 ~~~C~~Cg~~~~~~~~~~C~~cg~~l~~~~d~~~~~~~~~~~lp~~ 48 (338)
T PRK06450 3 KEVCMKCGKERESIYEIRCKKCGGPFEILIDFEFDKNLERKNFPYI 48 (338)
T ss_pred eeEECCcCCcCCCcccccCCcCCCEeEEeecccccchhhHhhCCCC
Confidence 79999999988432 2469999988876654431 113566664
No 262
>KOG2858 consensus Uncharacterized conserved protein [General function prediction only]
Probab=34.75 E-value=13 Score=38.19 Aligned_cols=15 Identities=60% Similarity=1.382 Sum_probs=14.0
Q ss_pred eEEcCCCCccccCCC
Q 014440 303 GYTCPRCKARVCELP 317 (424)
Q Consensus 303 Gy~Cp~C~s~~C~lP 317 (424)
+|-||||++.+|+|-
T Consensus 29 KYkCPRCl~rtCsLe 43 (390)
T KOG2858|consen 29 KYKCPRCLARTCSLE 43 (390)
T ss_pred cccCcchhhhheecc
Confidence 899999999999984
No 263
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=34.60 E-value=25 Score=33.44 Aligned_cols=46 Identities=22% Similarity=0.431 Sum_probs=31.0
Q ss_pred CCCceeecccccccCCCCCCceeeCCCcCcccccccchh-hhc---------------cCCCCCCCCCCC
Q 014440 361 SRSTCFGCQQSLLASGNKAGLCVACPKCKKHFCLECDIY-IHE---------------SLHNCPGCESLR 414 (424)
Q Consensus 361 ~~~~C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~dCd~f-ihe---------------~lh~CPgC~~~~ 414 (424)
+...|.-|...+.++ .-..|++.||..|=.- .+- .-..||-|....
T Consensus 17 ~~~~CpICld~~~dP--------VvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~I 78 (193)
T PLN03208 17 GDFDCNICLDQVRDP--------VVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDV 78 (193)
T ss_pred CccCCccCCCcCCCc--------EEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcC
Confidence 456899998666432 2367999999999742 221 135899997644
No 264
>PF11181 YflT: Heat induced stress protein YflT
Probab=34.54 E-value=71 Score=26.69 Aligned_cols=74 Identities=16% Similarity=0.124 Sum_probs=47.0
Q ss_pred CHHHHHHHHHhCCcEEEEEEecc-hHHHHHHHHHHhCCEEEEecChhhHHHHHHhcCCCCccchhhhhhheeeecCCCC
Q 014440 206 DIMETIQKCKESKIRCSVIGLSA-EMFICKHLCQETGGTYSVALDESHSKELILEHAPPPPAIAEFAIASLIKMGFPQR 283 (424)
Q Consensus 206 ~i~~~i~~akk~~IrV~vIgLg~-e~~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~~pp~~~~~~~~~~Li~mGFP~~ 283 (424)
.+..+|+.|+..|..-+=|.+=+ +..-+..|++.|+ ..-+...+..+-+-+..+++. .....+..|..||||..
T Consensus 11 E~~~~I~~L~~~Gy~~ddI~Vva~d~~~~~~l~~~t~-~~~~~~~~~~~~d~~~~~f~~---~~d~~~~~l~~lGl~~~ 85 (103)
T PF11181_consen 11 EALSAIEELKAQGYSEDDIYVVAKDKDRTERLADQTD-TNTVGASEESFWDKIKNFFTS---GGDELRSKLESLGLSED 85 (103)
T ss_pred HHHHHHHHHHHcCCCcccEEEEEcCchHHHHHHHhcC-CceeccccccHHHHHHHhccC---CcHHHHHHHHHcCCCHH
Confidence 46678999999998744333333 5566788888883 333334445666666666651 11335578889999864
No 265
>cd06370 PBP1_Speract_GC_like Ligand-binding domain of membrane bound guanylyl cyclases. Ligand-binding domain of membrane bound guanylyl cyclases (GCs), which are known to be activated by sperm-activating peptides (SAPs), such as speract or resact. These ligand peptides are released by a range of invertebrates to stimulate the metabolism and motility of spermatozoa and are also potent chemoattractants. These GCs contain a single transmembrane segment, an extracellular ligand binding domain, and intracellular protein kinase-like and cyclase catalytic domains. GCs of insect and nematodes, which exhibit high sequence similarity to the speract receptor are also included in this model.
Probab=34.28 E-value=2.5e+02 Score=28.70 Aligned_cols=54 Identities=13% Similarity=0.065 Sum_probs=32.7
Q ss_pred cchHHHHHHHHHHHHcCCCCC-CCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEE
Q 014440 167 DSSIQNALDLVHGLLNQIPSY-GHREVLILYSALSTCDPGDIMETIQKCKESKIRC 221 (424)
Q Consensus 167 ~tsL~~AL~~Al~~L~~~p~~-~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV 221 (424)
+....+|+++|++.++..+.- ..++|-+++-+. .+||..-.+++..+.+.+|..
T Consensus 18 G~~~~~a~~lAv~~IN~~ggil~g~~l~l~~~D~-~~~~~~a~~~~~~li~~~v~a 72 (404)
T cd06370 18 GLPISGALTLAVEDVNADPNLLPGYKLQFEWVDT-HGDEVLSIRAVSDWWKRGVVA 72 (404)
T ss_pred cccHHHHHHHHHHHHhCCCCCCCCCEEEEEEEec-CCChHHHHHHHHHHHhcCceE
Confidence 356779999999999876433 245555555432 256655555555555555543
No 266
>cd02002 TPP_BFDC Thiamine pyrophosphate (TPP) family, BFDC subfamily, TPP-binding module; composed of proteins similar to Pseudomonas putida benzoylformate decarboxylase (BFDC). P. putida BFDC plays a role in the mandelate pathway, catalyzing the conversion of benzoylformate to benzaldehyde and carbon dioxide. This enzyme is dependent on TPP and a divalent metal cation as cofactors.
Probab=34.28 E-value=3.4e+02 Score=24.25 Aligned_cols=88 Identities=14% Similarity=0.037 Sum_probs=55.1
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH-H---------------
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM-F--------------- 231 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~-~--------------- 231 (424)
.+++.+|-.|+..--..| .+++++++|+..- . ... +.+..+.+.++++-+|-+.... .
T Consensus 49 g~mG~~lp~aiGaala~~---~~~vv~i~GDG~f-~-~~~-~el~ta~~~~~p~~~iV~nN~~~~~~~~~~~~~~~~~~~ 122 (178)
T cd02002 49 GGLGWGLPAAVGAALANP---DRKVVAIIGDGSF-M-YTI-QALWTAARYGLPVTVVILNNRGYGALRSFLKRVGPEGPG 122 (178)
T ss_pred ccccchHHHHHHHHhcCC---CCeEEEEEcCchh-h-ccH-HHHHHHHHhCCCeEEEEEcCccHHHHHHHHHHHcCCCcc
Confidence 556666665555432222 4678888886542 1 223 4667778889988888775431 1
Q ss_pred --------------HHHHHHHHhCCEEEEecChhhHHHHHHhcC
Q 014440 232 --------------ICKHLCQETGGTYSVALDESHSKELILEHA 261 (424)
Q Consensus 232 --------------iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~ 261 (424)
-+.++|+.-|..|..+.+.++|.+.+.+..
T Consensus 123 ~~~~~~~~~~~~~~d~~~~a~a~G~~~~~v~~~~el~~al~~a~ 166 (178)
T cd02002 123 ENAPDGLDLLDPGIDFAAIAKAFGVEAERVETPEELDEALREAL 166 (178)
T ss_pred cccccccccCCCCCCHHHHHHHcCCceEEeCCHHHHHHHHHHHH
Confidence 144577777777777777777777776654
No 267
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=34.18 E-value=7.7 Score=38.99 Aligned_cols=44 Identities=30% Similarity=0.800 Sum_probs=37.3
Q ss_pred CceeecccccccCCCCCCceeeCCCcCcccccccchhhhccCCCCCCCC
Q 014440 363 STCFGCQQSLLASGNKAGLCVACPKCKKHFCLECDIYIHESLHNCPGCE 411 (424)
Q Consensus 363 ~~C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~dCd~fihe~lh~CPgC~ 411 (424)
..|-+|...|..... ...|..|++.||.-|- -+-++|..|--|.
T Consensus 45 p~ckacg~~f~~~~~----k~~c~dckk~fc~tcs-~v~~~lr~c~~c~ 88 (350)
T KOG4275|consen 45 PHCKACGEEFEDAQS----KSDCEDCKKEFCATCS-RVSISLRTCTSCR 88 (350)
T ss_pred chhhhhchhHhhhhh----hhhhhhhhHHHHHHHH-HhcccchhhhHHH
Confidence 389999988864322 3579999999999999 8999999999995
No 268
>PLN00209 ribosomal protein S27; Provisional
Probab=34.01 E-value=18 Score=29.86 Aligned_cols=27 Identities=19% Similarity=0.411 Sum_probs=21.1
Q ss_pred EcCCCCcccc-----CCCCCCCCCCceecCch
Q 014440 305 TCPRCKARVC-----ELPTECRICGLQLVSSP 331 (424)
Q Consensus 305 ~Cp~C~s~~C-----~lP~~C~~C~l~Lvs~p 331 (424)
.||.|..+.. ..++.|..||.+|.-+.
T Consensus 38 kCp~C~n~q~VFShA~t~V~C~~Cg~~L~~PT 69 (86)
T PLN00209 38 KCQGCFNITTVFSHSQTVVVCGSCQTVLCQPT 69 (86)
T ss_pred ECCCCCCeeEEEecCceEEEccccCCEeeccC
Confidence 5999998765 35589999999986543
No 269
>TIGR01504 glyox_carbo_lig glyoxylate carboligase. Glyoxylate carboligase, also called tartronate-semialdehyde synthase, releases CO2 while synthesizing a single molecule of tartronate semialdehyde from two molecules of glyoxylate. It is a thiamine pyrophosphate-dependent enzyme, closely related in sequence to the large subunit of acetolactate synthase. In the D-glycerate pathway, part of allantoin degradation in the Enterobacteriaceae, tartronate semialdehyde is converted to D-glycerate and then 3-phosphoglycerate, a product of glycolysis and entry point in the general metabolism.
Probab=33.91 E-value=2.2e+02 Score=31.25 Aligned_cols=88 Identities=8% Similarity=-0.002 Sum_probs=59.7
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH----H------------
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM----F------------ 231 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~----~------------ 231 (424)
.+|+-||-.|+..=-.. ..|+|+.|+|++.- . .. ...+.++++.|++|-+|-+.... +
T Consensus 418 gsmG~glpaaiGa~lA~---pdr~Vv~i~GDG~f-~-m~-~~EL~Ta~r~~lpvv~iV~NN~~yg~i~~~q~~~~~~~~~ 491 (588)
T TIGR01504 418 GPLGWTIPAALGVCAAD---PKRNVVALSGDYDF-Q-FM-IEELAVGAQHNIPYIHVLVNNAYLGLIRQAQRAFDMDYCV 491 (588)
T ss_pred ccccchHhHHHhhhhhC---CCCcEEEEEcchHh-h-cc-HHHHHHHHHhCCCeEEEEEeCCchHHHHHHHHHhcccccc
Confidence 45666666555543222 25678888886431 1 12 24578999999999888886321 0
Q ss_pred -----------------HHHHHHHHhCCEEEEecChhhHHHHHHhcC
Q 014440 232 -----------------ICKHLCQETGGTYSVALDESHSKELILEHA 261 (424)
Q Consensus 232 -----------------iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~ 261 (424)
-+.++|+.-|+.+..+.+.++|+..|...+
T Consensus 492 ~~~~~~~~~~~~~~~~~d~~~lA~a~G~~~~~V~~~~eL~~al~~a~ 538 (588)
T TIGR01504 492 QLAFENINSSEVNGYGVDHVKVAEGLGCKAIRVFKPEEIAPAFEQAK 538 (588)
T ss_pred eeeccccccccccCCCCCHHHHHHHCCCEEEEECCHHHHHHHHHHHH
Confidence 145688888899888999999988888775
No 270
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=33.90 E-value=19 Score=27.40 Aligned_cols=27 Identities=26% Similarity=0.684 Sum_probs=16.9
Q ss_pred EcCCCCcccc-----CCCCCCCCCCceecCch
Q 014440 305 TCPRCKARVC-----ELPTECRICGLQLVSSP 331 (424)
Q Consensus 305 ~Cp~C~s~~C-----~lP~~C~~C~l~Lvs~p 331 (424)
.||.|..+.- ..++.|..||.+|.-+.
T Consensus 9 kCp~C~~~q~vFSha~t~V~C~~Cg~~L~~Pt 40 (55)
T PF01667_consen 9 KCPGCYNIQTVFSHAQTVVKCVVCGTVLAQPT 40 (55)
T ss_dssp E-TTT-SEEEEETT-SS-EE-SSSTSEEEEE-
T ss_pred ECCCCCCeeEEEecCCeEEEcccCCCEecCCC
Confidence 5999988654 35679999999987553
No 271
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=33.84 E-value=17 Score=31.63 Aligned_cols=22 Identities=27% Similarity=0.850 Sum_probs=10.1
Q ss_pred cCCCCccccCCCCCCCCCCcee
Q 014440 306 CPRCKARVCELPTECRICGLQL 327 (424)
Q Consensus 306 Cp~C~s~~C~lP~~C~~C~l~L 327 (424)
||+|+...=----.|+.|++++
T Consensus 1 CPvCg~~l~vt~l~C~~C~t~i 22 (113)
T PF09862_consen 1 CPVCGGELVVTRLKCPSCGTEI 22 (113)
T ss_pred CCCCCCceEEEEEEcCCCCCEE
Confidence 5555543322223555555554
No 272
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=33.78 E-value=21 Score=20.74 Aligned_cols=19 Identities=32% Similarity=0.738 Sum_probs=10.9
Q ss_pred eeCCCcCcccccccchhhh
Q 014440 383 VACPKCKKHFCLECDIYIH 401 (424)
Q Consensus 383 ~~C~~C~~~fC~dCd~fih 401 (424)
|.|+.|+..|=.--+.--|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H 19 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQH 19 (24)
T ss_dssp EE-SSTS-EESSHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHH
Confidence 6788888877555444444
No 273
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=33.74 E-value=19 Score=43.86 Aligned_cols=24 Identities=42% Similarity=1.016 Sum_probs=18.8
Q ss_pred eEEcCCCCccccCCC-------------CCCCCCCceec
Q 014440 303 GYTCPRCKARVCELP-------------TECRICGLQLV 328 (424)
Q Consensus 303 Gy~Cp~C~s~~C~lP-------------~~C~~C~l~Lv 328 (424)
.|+||.|+ +.++. -.||.||..|.
T Consensus 908 hy~C~~C~--~~ef~~~~~~~sG~Dlpdk~Cp~Cg~~~~ 944 (1437)
T PRK00448 908 HYVCPNCK--YSEFFTDGSVGSGFDLPDKDCPKCGTKLK 944 (1437)
T ss_pred cccCcccc--cccccccccccccccCccccCcccccccc
Confidence 89999994 66654 36999999853
No 274
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=33.74 E-value=23 Score=30.94 Aligned_cols=26 Identities=31% Similarity=0.650 Sum_probs=15.3
Q ss_pred CCceeecccccccCCCCCCceeeCCCcCcc
Q 014440 362 RSTCFGCQQSLLASGNKAGLCVACPKCKKH 391 (424)
Q Consensus 362 ~~~C~~C~~~~~~~~~~~~~~~~C~~C~~~ 391 (424)
.-.|.-|+..+.. +...|.||+|++.
T Consensus 70 ~~~C~~C~~~~~~----e~~~~~CP~C~s~ 95 (115)
T COG0375 70 ECWCLDCGQEVEL----EELDYRCPKCGSI 95 (115)
T ss_pred EEEeccCCCeecc----hhheeECCCCCCC
Confidence 4467777655542 2234667777754
No 275
>cd06326 PBP1_STKc_like Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins. The type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins, some of which contain a conserved catalytic serine/threonine protein kinase (STKc) domain in the N-terminal region. Members of this group are sequence-similar to the branched-chain amino acid ABC transporter leucine-isoleucine-valine-binding protein (LIVBP); their ligand specificity has not been determined experimentally, however.
Probab=33.37 E-value=2.8e+02 Score=26.93 Aligned_cols=59 Identities=10% Similarity=0.089 Sum_probs=36.1
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhC-CcEEEEEEec
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKES-KIRCSVIGLS 227 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~-~IrV~vIgLg 227 (424)
..+.+|+++|++.++...+-..+.|.++..+ +..||....+.++.+.+. +|..-+...+
T Consensus 18 ~~~~~~~~~a~~~iN~~ggi~G~~v~l~~~D-~~~d~~~~~~~~~~l~~~~~v~avig~~~ 77 (336)
T cd06326 18 RAYRAGAQAYFDAVNAAGGVNGRKIELVTLD-DGYEPERTVANTRKLIEDDKVFALFGYVG 77 (336)
T ss_pred HHHHHHHHHHHHHHHhcCCcCCceEEEEEeC-CCCChHHHHHHHHHHHhhcCcEEEEeCCC
Confidence 4577888999999887544445566666644 223555555667777764 6654433343
No 276
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=33.11 E-value=19 Score=42.59 Aligned_cols=39 Identities=36% Similarity=0.756 Sum_probs=26.7
Q ss_pred eEEcCCCCcccc----------CCC-CCCCCCCceecCchhHHhhhcccCCCCCCcc
Q 014440 303 GYTCPRCKARVC----------ELP-TECRICGLQLVSSPHLARSYHHLFPIAPFDE 348 (424)
Q Consensus 303 Gy~Cp~C~s~~C----------~lP-~~C~~C~l~Lvs~phLarsyhhl~p~~~f~~ 348 (424)
.|+||.|+---+ .|| -.||.||..|. ---|-.|-..|.-
T Consensus 914 HY~Cp~Cky~Ef~~d~svgsGfDLpdK~CPkCg~pl~-------kDG~dIPFETFlG 963 (1444)
T COG2176 914 HYLCPECKYSEFIDDGSVGSGFDLPDKDCPKCGTPLK-------KDGHDIPFETFLG 963 (1444)
T ss_pred cccCCCCceeeeecCCCcCCCCCCCCCCCCcCCCccc-------cCCCCCChhhhcC
Confidence 899999963222 244 38999999863 3346778777754
No 277
>cd02009 TPP_SHCHC_synthase Thiamine pyrophosphate (TPP) family, SHCHC synthase subfamily, TPP-binding module; composed of proteins similar to Escherichia coli 2-succinyl-6-hydroxyl-2,4-cyclohexadiene-1-carboxylic acid (SHCHC) synthase (also called MenD). SHCHC synthase plays a key role in the menaquinone biosynthetic pathway, converting isochorismate and 2-oxoglutarate to SHCHC, pyruvate and carbon dioxide. The enzyme requires TPP and a divalent metal cation for activity.
Probab=33.01 E-value=1.6e+02 Score=26.76 Aligned_cols=70 Identities=13% Similarity=0.174 Sum_probs=46.5
Q ss_pred CcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecch-------------------------HHHHHHHHHHhCCE
Q 014440 189 HREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAE-------------------------MFICKHLCQETGGT 243 (424)
Q Consensus 189 ~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e-------------------------~~iLq~iA~~TGG~ 243 (424)
.|+|+.|+|+..- -.+ ...+.++.+.+++|-+|-+... ..-..++|+.-|+.
T Consensus 68 ~~~Vv~i~GDGsf--~m~-~~eL~ta~~~~l~v~ivVlNN~~~g~~~~~~~~~~~~~~~~~~~~~~~~d~~~lA~a~G~~ 144 (175)
T cd02009 68 DKPTVLLTGDLSF--LHD-LNGLLLGKQEPLNLTIVVINNNGGGIFSLLPQASFEDEFERLFGTPQGLDFEHLAKAYGLE 144 (175)
T ss_pred CCCEEEEEehHHH--HHh-HHHHHhccccCCCeEEEEEECCCCchheeccCCcccchhhhhhcCCCCCCHHHHHHHcCCC
Confidence 3567777765321 011 1445566777777777766421 01256788999999
Q ss_pred EEEecChhhHHHHHHhcC
Q 014440 244 YSVALDESHSKELILEHA 261 (424)
Q Consensus 244 Y~~~~d~~~L~~lL~~~~ 261 (424)
+..+.+.++|+..|.+..
T Consensus 145 ~~~v~~~~el~~al~~a~ 162 (175)
T cd02009 145 YRRVSSLDELEQALESAL 162 (175)
T ss_pred eeeCCCHHHHHHHHHHHH
Confidence 999999999999888775
No 278
>PRK14571 D-alanyl-alanine synthetase A; Provisional
Probab=32.88 E-value=1.8e+02 Score=28.54 Aligned_cols=37 Identities=11% Similarity=0.113 Sum_probs=20.1
Q ss_pred EEEEEEcCCCCCCccCHH---HHHHHHHhCCcEEEEEEec
Q 014440 191 EVLILYSALSTCDPGDIM---ETIQKCKESKIRCSVIGLS 227 (424)
Q Consensus 191 eILvI~ss~~t~dp~~i~---~~i~~akk~~IrV~vIgLg 227 (424)
+|.||+|+.++....++. .+++.+++.|.+|..|...
T Consensus 2 ~v~v~~gg~s~e~~~sl~s~~~i~~al~~~g~~~~~i~~~ 41 (299)
T PRK14571 2 RVALLMGGVSREREISLRSGERVKKALEKLGYEVTVFDVD 41 (299)
T ss_pred eEEEEeCCCCCCccchHHHHHHHHHHHHHcCCeEEEEccC
Confidence 466666655443223332 4566666666666666544
No 279
>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]
Probab=32.78 E-value=6.1e+02 Score=26.69 Aligned_cols=97 Identities=12% Similarity=0.175 Sum_probs=72.2
Q ss_pred hHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCC-CCcc---CHHHHHHHHHhCCcEEEEEEecchHHHHHHHHHHhCCEE
Q 014440 169 SIQNALDLVHGLLNQIPSYGHREVLILYSALST-CDPG---DIMETIQKCKESKIRCSVIGLSAEMFICKHLCQETGGTY 244 (424)
Q Consensus 169 sL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t-~dp~---~i~~~i~~akk~~IrV~vIgLg~e~~iLq~iA~~TGG~Y 244 (424)
++..-|+.-+..|++...+.+..|++|++..+. +.+. =+.+-++..+....+|-+||+.+...+|.-+-+.-..+|
T Consensus 116 sfte~l~~lL~~L~~~~~~t~~~ViFIldEfDlf~~h~rQtllYnlfDisqs~r~Piciig~Ttrld~lE~LEKRVKSRF 195 (408)
T KOG2228|consen 116 SFTENLSKLLEALKKGDETTSGKVIFILDEFDLFAPHSRQTLLYNLFDISQSARAPICIIGVTTRLDILELLEKRVKSRF 195 (408)
T ss_pred ccchhHHHHHHHHhcCCCCCCceEEEEeehhhccccchhhHHHHHHHHHHhhcCCCeEEEEeeccccHHHHHHHHHHhhc
Confidence 667778888888887655666778888864443 2221 234788899999999999999999888888888888766
Q ss_pred E------E-ecChhhHHHHHHhcCCCCc
Q 014440 245 S------V-ALDESHSKELILEHAPPPP 265 (424)
Q Consensus 245 ~------~-~~d~~~L~~lL~~~~~pp~ 265 (424)
. . ...-+++.+++.+.+.-|.
T Consensus 196 shr~I~m~~~~~l~~yv~l~r~ll~v~~ 223 (408)
T KOG2228|consen 196 SHRVIFMLPSLPLGDYVDLYRKLLSVPA 223 (408)
T ss_pred ccceeeccCCCChHHHHHHHHHHhcCCc
Confidence 5 1 3556788999988885554
No 280
>PF02670 DXP_reductoisom: 1-deoxy-D-xylulose 5-phosphate reductoisomerase; InterPro: IPR013512 1-deoxy-D-xylulose 5-phosphate reductoisomerase synthesises 2-C-methyl-D-erythritol 4-phosphate from 1-deoxy-D-xylulose 5-phosphate in a single step by intramolecular rearrangement and reduction and is responsible for terpenoid biosynthesis in some organisms []. In Arabidopsis thaliana 1-deoxy-D-xylulose 5-phosphate reductoisomerase is the first committed enzyme of the non-mevalonate pathway for isoprenoid biosynthesis. The enzyme requires Mn2+, Co2+ or Mg2+ for activity, with the first being most effective. This domain is found at the N terminus of bacterial and plant 1-deoxy-D-xylulose 5-phosphate reductoisomerases.; GO: 0070402 NADPH binding, 0055114 oxidation-reduction process; PDB: 1R0K_D 1R0L_C 3A14_A 3A06_A 3AUA_A 3AU9_B 3AU8_B 3IIE_A 2Y1D_B 4AIC_A ....
Probab=32.75 E-value=3.3e+02 Score=24.11 Aligned_cols=62 Identities=16% Similarity=0.209 Sum_probs=44.2
Q ss_pred EEEEcCCCCCCccCHH-HHHHHHHhCC--cEEEEEEecchHHHHHHHHHHhCCEEEEecChhhHHHHHHh
Q 014440 193 LILYSALSTCDPGDIM-ETIQKCKESK--IRCSVIGLSAEMFICKHLCQETGGTYSVALDESHSKELILE 259 (424)
Q Consensus 193 LvI~ss~~t~dp~~i~-~~i~~akk~~--IrV~vIgLg~e~~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~ 259 (424)
|.|+|+- |+|= +|++-+++.. ++|..++-+.....|.+.+++-+=.|.+..|++.+..+-..
T Consensus 1 i~ILGsT-----GSIG~qtLdVi~~~~d~f~v~~Lsa~~n~~~L~~q~~~f~p~~v~i~~~~~~~~l~~~ 65 (129)
T PF02670_consen 1 IAILGST-----GSIGTQTLDVIRKHPDKFEVVALSAGSNIEKLAEQAREFKPKYVVIADEEAYEELKKA 65 (129)
T ss_dssp EEEESTT-----SHHHHHHHHHHHHCTTTEEEEEEEESSTHHHHHHHHHHHT-SEEEESSHHHHHHHHHH
T ss_pred CEEEcCC-----cHHHHHHHHHHHhCCCceEEEEEEcCCCHHHHHHHHHHhCCCEEEEcCHHHHHHHHHH
Confidence 4566652 4453 6777777776 66766666778899999999999999999888766555443
No 281
>cd02520 Glucosylceramide_synthase Glucosylceramide synthase catalyzes the first glycosylation step of glycosphingolipid synthesis. UDP-glucose:N-acylsphingosine D-glucosyltransferase (glucosylceramide synthase or ceramide glucosyltransferase) catalyzes the first glycosylation step of glycosphingolipid synthesis. Its product, glucosylceramide, serves as the core of more than 300 glycosphingolipids (GSL). GSLs are a group of membrane components that have the lipid portion embedded in the outer plasma membrane leaflet and the sugar chains extended to the outer environment. Several lines of evidence suggest the importance of GSLs in various cellular processes such as differentiation, adhesion, proliferation, and cell-cell recognition. In pathogenic fungus Cryptococcus neoformans, glucosylceramide serves as an antigen that elicits an antibody response in patients and it is essential for fungal growth in host extracellular environment.
Probab=32.64 E-value=1.7e+02 Score=26.32 Aligned_cols=59 Identities=12% Similarity=0.052 Sum_probs=31.5
Q ss_pred CcEEEEEEcCCCCCCccCHHHHHHHHHhC--CcEEEEEEe------cchHHHHHHHHHHhCCEEEEecChh
Q 014440 189 HREVLILYSALSTCDPGDIMETIQKCKES--KIRCSVIGL------SAEMFICKHLCQETGGTYSVALDES 251 (424)
Q Consensus 189 ~reILvI~ss~~t~dp~~i~~~i~~akk~--~IrV~vIgL------g~e~~iLq~iA~~TGG~Y~~~~d~~ 251 (424)
.-||||+.++.+ | +..+.++.+.+. ++++.++-. +.....+....+...|.|++..|.+
T Consensus 30 ~~eiivVdd~s~--d--~t~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~n~g~~~a~~d~i~~~D~D 96 (196)
T cd02520 30 KYEILFCVQDED--D--PAIPVVRKLIAKYPNVDARLLIGGEKVGINPKVNNLIKGYEEARYDILVISDSD 96 (196)
T ss_pred CeEEEEEeCCCc--c--hHHHHHHHHHHHCCCCcEEEEecCCcCCCCHhHHHHHHHHHhCCCCEEEEECCC
Confidence 457777765422 2 223444444332 244433322 2223456677777889999877655
No 282
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=32.61 E-value=12 Score=32.17 Aligned_cols=10 Identities=20% Similarity=0.644 Sum_probs=4.5
Q ss_pred ceeecccccc
Q 014440 364 TCFGCQQSLL 373 (424)
Q Consensus 364 ~C~~C~~~~~ 373 (424)
.|..|...|+
T Consensus 72 ~C~~Cg~~~~ 81 (113)
T PF01155_consen 72 RCRDCGHEFE 81 (113)
T ss_dssp EETTTS-EEE
T ss_pred ECCCCCCEEe
Confidence 4555554443
No 283
>cd02525 Succinoglycan_BP_ExoA ExoA is involved in the biosynthesis of succinoglycan. Succinoglycan Biosynthesis Protein ExoA catalyzes the formation of a beta-1,3 linkage of the second sugar (glucose) of the succinoglycan with the galactose on the lipid carrie. Succinoglycan is an acidic exopolysaccharide that is important for invasion of the nodules. Succinoglycan is a high-molecular-weight polymer composed of repeating octasaccharide units. These units are synthesized on membrane-bound isoprenoid lipid carriers, beginning with galactose followed by seven glucose molecules, and modified by the addition of acetate, succinate, and pyruvate. ExoA is a membrane protein with a transmembrance domain at c-terminus.
Probab=32.54 E-value=3.2e+02 Score=24.94 Aligned_cols=91 Identities=14% Similarity=0.186 Sum_probs=48.5
Q ss_pred HHHHHHHHhccCCC-CcEEEEEecCCceEEeeCCCCCHHHHHHHHhhh-----hCCCCcchHHHHHHHHHHHHcCCCCCC
Q 014440 115 VEAFVREFFDQNPL-SQIGLVTVKDGVANCLTDLGGSPESHIKALMGK-----LGCSGDSSIQNALDLVHGLLNQIPSYG 188 (424)
Q Consensus 115 l~~Fi~~~~~qnP~-sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~~-----~~~~G~tsL~~AL~~Al~~L~~~p~~~ 188 (424)
+...++++..|... ...-||+.-++. +.+..+.++.+... +....+.....|+..|++..
T Consensus 15 l~~~l~sl~~q~~~~~~~evivvd~~s-------~d~~~~~~~~~~~~~~~v~~i~~~~~~~~~a~N~g~~~a------- 80 (249)
T cd02525 15 IEELLESLLNQSYPKDLIEIIVVDGGS-------TDGTREIVQEYAAKDPRIRLIDNPKRIQSAGLNIGIRNS------- 80 (249)
T ss_pred HHHHHHHHHhccCCCCccEEEEEeCCC-------CccHHHHHHHHHhcCCeEEEEeCCCCCchHHHHHHHHHh-------
Confidence 34444455545432 445566654443 23345555555431 11111223556677766643
Q ss_pred CcEEEEEEcCCCCCCccCHHHHHHHHHhCCc
Q 014440 189 HREVLILYSALSTCDPGDIMETIQKCKESKI 219 (424)
Q Consensus 189 ~reILvI~ss~~t~dp~~i~~~i~~akk~~I 219 (424)
+.++|++++++...+|+-+.+.++.+.+.++
T Consensus 81 ~~d~v~~lD~D~~~~~~~l~~~~~~~~~~~~ 111 (249)
T cd02525 81 RGDIIIRVDAHAVYPKDYILELVEALKRTGA 111 (249)
T ss_pred CCCEEEEECCCccCCHHHHHHHHHHHhcCCC
Confidence 2368888887666677767777766666554
No 284
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=32.53 E-value=32 Score=25.50 Aligned_cols=44 Identities=7% Similarity=-0.158 Sum_probs=29.8
Q ss_pred ceeecccccccCCCCCCceeeCCCcCcccccccchhhhccCCCCCCCCCCCC
Q 014440 364 TCFGCQQSLLASGNKAGLCVACPKCKKHFCLECDIYIHESLHNCPGCESLRQ 415 (424)
Q Consensus 364 ~C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~dCd~fihe~lh~CPgC~~~~~ 415 (424)
.|.-|...+..+ ....|++.||..|=.-.-+.-..||-|.....
T Consensus 3 ~Cpi~~~~~~~P--------v~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~ 46 (63)
T smart00504 3 LCPISLEVMKDP--------VILPSGQTYERRAIEKWLLSHGTDPVTGQPLT 46 (63)
T ss_pred CCcCCCCcCCCC--------EECCCCCEEeHHHHHHHHHHCCCCCCCcCCCC
Confidence 477777666532 13467899999997644444678999976443
No 285
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=32.43 E-value=26 Score=26.04 Aligned_cols=27 Identities=22% Similarity=0.571 Sum_probs=17.4
Q ss_pred eeeCCCcCcccccccchhhhccCCCCCCCCC
Q 014440 382 CVACPKCKKHFCLECDIYIHESLHNCPGCES 412 (424)
Q Consensus 382 ~~~C~~C~~~fC~dCd~fihe~lh~CPgC~~ 412 (424)
.|.|-.|+..| +.---...--||.|.+
T Consensus 6 ~Y~C~~Cg~~~----~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 6 EYKCARCGREV----ELDQETRGIRCPYCGS 32 (49)
T ss_pred EEEhhhcCCee----ehhhccCceeCCCCCc
Confidence 47788888777 3333444557888765
No 286
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=32.23 E-value=23 Score=24.72 Aligned_cols=28 Identities=21% Similarity=0.387 Sum_probs=14.7
Q ss_pred eeecccccccCCCCCCceeeCCCcCccc
Q 014440 365 CFGCQQSLLASGNKAGLCVACPKCKKHF 392 (424)
Q Consensus 365 C~~C~~~~~~~~~~~~~~~~C~~C~~~f 392 (424)
|-.|...+..........+.|+.|+-.+
T Consensus 2 CP~C~~~l~~~~~~~~~id~C~~C~G~W 29 (41)
T PF13453_consen 2 CPRCGTELEPVRLGDVEIDVCPSCGGIW 29 (41)
T ss_pred cCCCCcccceEEECCEEEEECCCCCeEE
Confidence 5666655433222222356788887543
No 287
>TIGR02720 pyruv_oxi_spxB pyruvate oxidase. Members of this family are examples of pyruvate oxidase (EC 1.2.3.3), an enzyme with FAD and TPP as cofactors that catalyzes the reaction pyruvate + phosphate + O2 + H2O = acetyl phosphate + CO2 + H2O2. It should not be confused with pyruvate dehydrogenase [cytochrome] (EC 1.2.2.2) as in E. coli PoxB, although the E. coli enzyme is closely homologous and has pyruvate oxidase as an alternate name.
Probab=32.13 E-value=2.6e+02 Score=30.46 Aligned_cols=88 Identities=8% Similarity=-0.030 Sum_probs=58.5
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH-----------------
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM----------------- 230 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~----------------- 230 (424)
-+|+-||-.|+..=-. ...|+|++|+|++.- . .++ ..+.++.+.+++|-+|-+-...
T Consensus 408 gsmG~glpaAiGa~la---~p~r~Vv~i~GDGsf-~-m~~-~eL~Tavr~~lpi~~VV~NN~~yg~i~~~~~~~~~~~~~ 481 (575)
T TIGR02720 408 ATMGVGVPGAIAAKLN---YPDRQVFNLAGDGAF-S-MTM-QDLLTQVQYHLPVINIVFSNCTYGFIKDEQEDTNQPLIG 481 (575)
T ss_pred chhhchHHHHHHHHHh---CCCCcEEEEEcccHH-H-hhH-HHHHHHHHhCCCeEEEEEeCCccHHHHHHHHHhCCCccc
Confidence 4566666655553222 225678888886432 1 122 4578889999999888664321
Q ss_pred -----HHHHHHHHHhCCEEEEecChhhHHHHHHhcC
Q 014440 231 -----FICKHLCQETGGTYSVALDESHSKELILEHA 261 (424)
Q Consensus 231 -----~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~ 261 (424)
.-...+|+..|+.+..+.+.++|.+.+.+.+
T Consensus 482 ~~~~~~df~~iA~a~G~~~~~v~~~~el~~al~~a~ 517 (575)
T TIGR02720 482 VDFNDADFAKIAEGVGAVGFRVNKIEQLPAVFEQAK 517 (575)
T ss_pred ccCCCCCHHHHHHHCCCEEEEeCCHHHHHHHHHHHH
Confidence 1156788888888888888888888887766
No 288
>TIGR01285 nifN nitrogenase molybdenum-iron cofactor biosynthesis protein NifN. This protein forms a complex with NifE, and appears as a NifEN in some species. NifEN is a required for producing the molybdenum-iron cofactor of molybdenum-requiring nitrogenases. NifN is closely related to the nitrogenase molybdenum-iron protein beta chain NifK. This model describes most examples of NifN but excludes some cases, such as the putative NifN of Chlorobium tepidum, for which a separate model may be created.
Probab=32.10 E-value=3.3e+02 Score=28.78 Aligned_cols=75 Identities=15% Similarity=0.038 Sum_probs=48.4
Q ss_pred CHHHHHHHHHhCCcEEEEEEecchHHHHHHHHHHhCCEEEEecChhhHHHHHHhcCCCCccc--------hhhhhhheee
Q 014440 206 DIMETIQKCKESKIRCSVIGLSAEMFICKHLCQETGGTYSVALDESHSKELILEHAPPPPAI--------AEFAIASLIK 277 (424)
Q Consensus 206 ~i~~~i~~akk~~IrV~vIgLg~e~~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~~pp~~~--------~~~~~~~Li~ 277 (424)
.....++.+.+.|+.|..+..+.....++++ ..+.. ...|..++.+++.+.- |...- +....-.|++
T Consensus 322 ~~~~l~~~l~elGm~v~~~~~~~~~~~~~~~---~~~~~-~~~D~~~l~~~i~~~~-~dliig~s~~k~~A~~l~ip~ir 396 (432)
T TIGR01285 322 LLAAWATFFTSMGAQIVAAVTTTGSPLLQKL---PVETV-VIGDLEDLEDLACAAG-ADLLITNSHGRALAQRLALPLVR 396 (432)
T ss_pred HHHHHHHHHHHCCCEEEEEEeCCCCHHHHhC---CcCcE-EeCCHHHHHHHHhhcC-CCEEEECcchHHHHHHcCCCEEE
Confidence 3466788899999999999998776655443 23333 3466667777665542 33221 1223457999
Q ss_pred ecCCCCCC
Q 014440 278 MGFPQRAG 285 (424)
Q Consensus 278 mGFP~~~~ 285 (424)
+|||....
T Consensus 397 ~g~Pi~dr 404 (432)
T TIGR01285 397 AGFPLFDQ 404 (432)
T ss_pred ecCCcccc
Confidence 99998654
No 289
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=32.05 E-value=24 Score=25.31 Aligned_cols=31 Identities=29% Similarity=0.745 Sum_probs=20.0
Q ss_pred CCceeeccc-ccccCCCCCCceeeCCCcC-cccccccch
Q 014440 362 RSTCFGCQQ-SLLASGNKAGLCVACPKCK-KHFCLECDI 398 (424)
Q Consensus 362 ~~~C~~C~~-~~~~~~~~~~~~~~C~~C~-~~fC~dCd~ 398 (424)
...|-+|.. ++. ..+|.|..|. -.+|.+|-.
T Consensus 4 ~~~C~~C~~~~i~------g~Ry~C~~C~d~dLC~~C~~ 36 (46)
T PF00569_consen 4 GYTCDGCGTDPII------GVRYHCLVCPDYDLCEDCFS 36 (46)
T ss_dssp SCE-SSS-SSSEE------SSEEEESSSSS-EEEHHHHH
T ss_pred CeECcCCCCCcCc------CCeEECCCCCCCchhhHHHh
Confidence 457999986 443 2589999998 457777743
No 290
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=32.03 E-value=21 Score=29.44 Aligned_cols=27 Identities=26% Similarity=0.520 Sum_probs=21.1
Q ss_pred EcCCCCccccC-----CCCCCCCCCceecCch
Q 014440 305 TCPRCKARVCE-----LPTECRICGLQLVSSP 331 (424)
Q Consensus 305 ~Cp~C~s~~C~-----lP~~C~~C~l~Lvs~p 331 (424)
.||.|..+..= .++.|..||.+|.-++
T Consensus 37 kCp~C~n~q~VFShA~t~V~C~~Cg~~L~~PT 68 (85)
T PTZ00083 37 KCPGCSQITTVFSHAQTVVLCGGCSSQLCQPT 68 (85)
T ss_pred ECCCCCCeeEEEecCceEEEccccCCEeeccC
Confidence 59999987653 4579999999987553
No 291
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=32.03 E-value=21 Score=42.77 Aligned_cols=24 Identities=46% Similarity=1.025 Sum_probs=18.4
Q ss_pred eEEcCCCCccccCCCC-------------CCCCCCceec
Q 014440 303 GYTCPRCKARVCELPT-------------ECRICGLQLV 328 (424)
Q Consensus 303 Gy~Cp~C~s~~C~lP~-------------~C~~C~l~Lv 328 (424)
.|+||.|+ +.++.. .||.||..|.
T Consensus 683 hy~c~~c~--~~ef~~~~~~~sg~dlp~k~cp~c~~~~~ 719 (1213)
T TIGR01405 683 HYLCPNCK--YSEFITDGSVGSGFDLPDKDCPKCGAPLK 719 (1213)
T ss_pred cccCcccc--cccccccccccccccCccccCcccccccc
Confidence 89999994 655433 6999998864
No 292
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=31.86 E-value=24 Score=35.90 Aligned_cols=25 Identities=24% Similarity=0.575 Sum_probs=20.2
Q ss_pred CCceeecccccccCCCCCCceeeCCCcCccccc
Q 014440 362 RSTCFGCQQSLLASGNKAGLCVACPKCKKHFCL 394 (424)
Q Consensus 362 ~~~C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~ 394 (424)
-..|-.|.+++. .|.||+|+-.||.
T Consensus 7 ~~~C~ic~vq~~--------~YtCPRCn~~YCs 31 (383)
T KOG4317|consen 7 FLACGICGVQKR--------EYTCPRCNLLYCS 31 (383)
T ss_pred eeeccccccccc--------cccCCCCCcccee
Confidence 347888887763 5999999999994
No 293
>COG1182 AcpD Acyl carrier protein phosphodiesterase [Lipid metabolism]
Probab=31.65 E-value=4.7e+02 Score=25.08 Aligned_cols=117 Identities=15% Similarity=0.210 Sum_probs=67.9
Q ss_pred EEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCHHHHHHHHhhhhCCCCcc
Q 014440 89 YIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSPESHIKALMGKLGCSGDS 168 (424)
Q Consensus 89 vlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~~~~~~G~t 168 (424)
||+||.|+. . | ..........||.+|-++||.++|-..-.. .+.+--|+ .+.+.+......+.+.+
T Consensus 4 vL~I~as~~-~--~-----~S~S~~l~~~Fi~~yk~~~P~dev~~~DL~---~e~iP~ld---~~~~~a~~~~~~~~~t~ 69 (202)
T COG1182 4 VLVIKASPL-G--E-----NSVSRKLADEFIETYKEKHPNDEVIERDLA---AEPIPHLD---EELLAAWFKPQAGEGTA 69 (202)
T ss_pred EEEEecCCC-c--c-----ccHHHHHHHHHHHHHHHhCCCCeEEEeecc---cCCCcccC---HHHHhcccCCccCCCCH
Confidence 788888766 2 1 234566789999999999999998766543 12222222 12222222211222346
Q ss_pred hHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCC-CccCHHHHHHHHHhCCcEEE
Q 014440 169 SIQNALDLVHGLLNQIPSYGHREVLILYSALSTC-DPGDIMETIQKCKESKIRCS 222 (424)
Q Consensus 169 sL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~-dp~~i~~~i~~akk~~IrV~ 222 (424)
+.+..++.+-.++...- ..- .+||.....+. =|..+.+-|+.+...|....
T Consensus 70 ~~~~~~~~sd~l~~ef~--aAD-~vVi~~PM~Nf~iPa~LK~yiD~i~~aGkTFk 121 (202)
T COG1182 70 EEKEALARSDKLLEEFL--AAD-KVVIAAPMYNFNIPAQLKAYIDHIAVAGKTFK 121 (202)
T ss_pred HHHHHHHHHHHHHHHHH--hcC-eEEEEecccccCCCHHHHHHHHHHhcCCceEE
Confidence 78888888888887641 122 34554444331 23334455888888887665
No 294
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=31.59 E-value=34 Score=33.78 Aligned_cols=31 Identities=29% Similarity=0.611 Sum_probs=21.8
Q ss_pred CceeecccccccCC-CC--CCceeeCCCcCcccc
Q 014440 363 STCFGCQQSLLASG-NK--AGLCVACPKCKKHFC 393 (424)
Q Consensus 363 ~~C~~C~~~~~~~~-~~--~~~~~~C~~C~~~fC 393 (424)
..|.+|.+.+...+ ++ ...-|.||+|++.|=
T Consensus 133 SRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~ 166 (278)
T PF15135_consen 133 SRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFR 166 (278)
T ss_pred ccccccccccCCCccccccceeeeecccccccch
Confidence 47999998875433 11 123599999999994
No 295
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=31.57 E-value=26 Score=35.18 Aligned_cols=24 Identities=25% Similarity=0.505 Sum_probs=21.5
Q ss_pred eEEcCCCCccccCCCCCCCCCCce
Q 014440 303 GYTCPRCKARVCELPTECRICGLQ 326 (424)
Q Consensus 303 Gy~Cp~C~s~~C~lP~~C~~C~l~ 326 (424)
.|+|+.|+.+.=+.-..||.||..
T Consensus 354 ~~~c~~cg~~~~~~~~~c~~c~~~ 377 (389)
T PRK11788 354 RYRCRNCGFTARTLYWHCPSCKAW 377 (389)
T ss_pred CEECCCCCCCCccceeECcCCCCc
Confidence 799999999999999999999854
No 296
>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.
Probab=31.26 E-value=1.1e+02 Score=29.04 Aligned_cols=35 Identities=23% Similarity=0.432 Sum_probs=23.9
Q ss_pred ceeeecCCccccCeEEcCCCCcccc----------CCCCCCCCCCcee
Q 014440 290 SICSCHKEVKIGVGYTCPRCKARVC----------ELPTECRICGLQL 327 (424)
Q Consensus 290 a~C~CH~~~~~~~Gy~Cp~C~s~~C----------~lP~~C~~C~l~L 327 (424)
...-+|..+.. ..|+.|...+- ...+.|+.||-.|
T Consensus 99 ~v~elHG~~~~---~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~l 143 (218)
T cd01407 99 KVIELHGSLFR---VRCTKCGKEYPRDELQADIDREEVPRCPKCGGLL 143 (218)
T ss_pred CEEECcCCcCc---ceeCCCcCCCcHHHHhHhhccCCCCcCCCCCCcc
Confidence 36778876643 46888887653 2457899998653
No 297
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=31.23 E-value=25 Score=30.30 Aligned_cols=9 Identities=22% Similarity=0.704 Sum_probs=4.9
Q ss_pred eeeCCCcCc
Q 014440 382 CVACPKCKK 390 (424)
Q Consensus 382 ~~~C~~C~~ 390 (424)
+..|+.|++
T Consensus 70 ~~~C~~Cg~ 78 (114)
T PRK03681 70 ECWCETCQQ 78 (114)
T ss_pred EEEcccCCC
Confidence 455555554
No 298
>PLN02470 acetolactate synthase
Probab=31.15 E-value=2.1e+02 Score=31.29 Aligned_cols=89 Identities=10% Similarity=0.013 Sum_probs=59.0
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH-----------------
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM----------------- 230 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~----------------- 230 (424)
-+++-||-.|+..=-..| .|+|++|+|++.- . .+ .+.+.++.+.+++|-+|-+....
T Consensus 426 g~mG~glpaaiGa~la~p---~~~Vv~i~GDG~f-~-m~-~~eL~Ta~~~~l~v~ivV~NN~~yg~i~~~~~~~~~~~~~ 499 (585)
T PLN02470 426 GAMGFGLPAAIGAAAANP---DAIVVDIDGDGSF-I-MN-IQELATIHVENLPVKIMVLNNQHLGMVVQWEDRFYKANRA 499 (585)
T ss_pred ccccchHHHHHHHHHhCC---CCcEEEEEccchh-h-cc-HHHHHHHHHhCCCeEEEEEeCCcchHHHHHHHHHhCCcee
Confidence 345555555544322222 4678888886431 1 12 25678889999998888775321
Q ss_pred --------------HHHHHHHHHhCCEEEEecChhhHHHHHHhcCC
Q 014440 231 --------------FICKHLCQETGGTYSVALDESHSKELILEHAP 262 (424)
Q Consensus 231 --------------~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~~ 262 (424)
.-+.++|+..|+.+..+.+.++|...|.....
T Consensus 500 ~~~~~~~~~~~~~~~d~~~iA~a~G~~~~~v~~~~el~~al~~a~~ 545 (585)
T PLN02470 500 HTYLGDPDAEAEIFPDFLKFAEGCKIPAARVTRKSDLREAIQKMLD 545 (585)
T ss_pred eeecCccccccCCCCCHHHHHHHCCCeEEEECCHHHHHHHHHHHHh
Confidence 13577899999999999999999988877753
No 299
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=30.99 E-value=12 Score=37.14 Aligned_cols=28 Identities=32% Similarity=0.823 Sum_probs=23.3
Q ss_pred eCCCcC----cccccccchhhhccCCCCCCCCC
Q 014440 384 ACPKCK----KHFCLECDIYIHESLHNCPGCES 412 (424)
Q Consensus 384 ~C~~C~----~~fC~dCd~fihe~lh~CPgC~~ 412 (424)
.|..|+ .+||.-||-|+|+- ..||.|.+
T Consensus 251 ~C~~~~~~A~~~~C~iC~~~~~~R-~~C~~~kA 282 (325)
T KOG4399|consen 251 HCSICNHCAVKHGCFICGELDHKR-STCPNIKA 282 (325)
T ss_pred eeecccchhhhcceeecccccccc-ccCccHHH
Confidence 455554 57999999999999 88999975
No 300
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=30.74 E-value=19 Score=36.31 Aligned_cols=50 Identities=22% Similarity=0.461 Sum_probs=39.4
Q ss_pred CceeecccccccCCCCCCceeeCCCcCcccccccchhhhccCCCCCCCCCCCCCCCcc
Q 014440 363 STCFGCQQSLLASGNKAGLCVACPKCKKHFCLECDIYIHESLHNCPGCESLRQSNPVV 420 (424)
Q Consensus 363 ~~C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~dCd~fihe~lh~CPgC~~~~~~~~~~ 420 (424)
-.|+-|...|..+. =.+|+++||--|-+--+..---|+-|...+.++--+
T Consensus 242 f~c~icr~~f~~pV--------vt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g~~~~ 291 (313)
T KOG1813|consen 242 FKCFICRKYFYRPV--------VTKCGHYFCEVCALKPYQKGEKCYVCSQQTHGSFNV 291 (313)
T ss_pred ccccccccccccch--------hhcCCceeehhhhccccccCCcceecccccccccch
Confidence 36999998887543 348999999999998888888999998776655433
No 301
>PRK06457 pyruvate dehydrogenase; Provisional
Probab=30.65 E-value=2.9e+02 Score=29.86 Aligned_cols=90 Identities=11% Similarity=0.038 Sum_probs=61.2
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH-----------------
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM----------------- 230 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~----------------- 230 (424)
.+++-||-.|+..=-..| ..|+||+|+|++.- . .++ +.+.++++.++++-+|-+....
T Consensus 396 g~mG~glpaaiGa~la~p--~~~~Vv~i~GDGsf-~-~~~-~eL~Ta~~~~lpi~ivV~NN~~~g~i~~~q~~~~~~~~~ 470 (549)
T PRK06457 396 GSMGIGVPGSVGASFAVE--NKRQVISFVGDGGF-T-MTM-MELITAKKYDLPVKIIIYNNSKLGMIKFEQEVMGYPEWG 470 (549)
T ss_pred chhhhhHHHHHHHHhcCC--CCCeEEEEEcccHH-h-hhH-HHHHHHHHHCCCeEEEEEECCccchHHHHHHHhcCCccc
Confidence 456666665555432222 15789999986432 1 122 4567889999988888775320
Q ss_pred -----HHHHHHHHHhCCEEEEecChhhHHHHHHhcCC
Q 014440 231 -----FICKHLCQETGGTYSVALDESHSKELILEHAP 262 (424)
Q Consensus 231 -----~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~~ 262 (424)
.-+.++|+.-|+.|..+.+.++|+..+...+.
T Consensus 471 ~~~~~~d~~~lA~a~G~~~~~v~~~~el~~al~~a~~ 507 (549)
T PRK06457 471 VDLYNPDFTKIAESIGFKGFRLEEPKEAEEIIEEFLN 507 (549)
T ss_pred ccCCCCCHHHHHHHCCCeEEEeCCHHHHHHHHHHHHh
Confidence 12678999999999999999999999887763
No 302
>cd01840 SGNH_hydrolase_yrhL_like yrhL-like subfamily of SGNH-hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases. Most members of this sub-family appear to co-occur with N-terminal acyltransferase domains. Might be involved in lipid metabolism.
Probab=30.57 E-value=3.6e+02 Score=23.46 Aligned_cols=74 Identities=8% Similarity=0.081 Sum_probs=44.6
Q ss_pred HHHHHHHHHHHHcCCCCCCCcEEEEE-EcCCCCCCccCHHHHHHHHHhCCcEEEEEEecch-------HHHHHHHHHHhC
Q 014440 170 IQNALDLVHGLLNQIPSYGHREVLIL-YSALSTCDPGDIMETIQKCKESKIRCSVIGLSAE-------MFICKHLCQETG 241 (424)
Q Consensus 170 L~~AL~~Al~~L~~~p~~~~reILvI-~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e-------~~iLq~iA~~TG 241 (424)
...|+.....++.. .....++|| +|+.+..-..++.+.++.++ .+.+|..++.-.. ...++++|+...
T Consensus 34 ~~~~~~~l~~~~~~---~~~~d~vvi~lGtNd~~~~~nl~~ii~~~~-~~~~ivlv~~~~~~~~~~~~n~~~~~~a~~~~ 109 (150)
T cd01840 34 MSEAPDLIRQLKDS---GKLRKTVVIGLGTNGPFTKDQLDELLDALG-PDRQVYLVNPHVPRPWEPDVNAYLLDAAKKYK 109 (150)
T ss_pred HHHHHHHHHHHHHc---CCCCCeEEEEecCCCCCCHHHHHHHHHHcC-CCCEEEEEECCCCcchHHHHHHHHHHHHHHCC
Confidence 35666655554442 123344554 56554433456667777774 4678888777532 267888998887
Q ss_pred CEEEEe
Q 014440 242 GTYSVA 247 (424)
Q Consensus 242 G~Y~~~ 247 (424)
+..++.
T Consensus 110 ~v~~id 115 (150)
T cd01840 110 NVTIID 115 (150)
T ss_pred CcEEec
Confidence 766654
No 303
>PRK08978 acetolactate synthase 2 catalytic subunit; Reviewed
Probab=30.55 E-value=2.4e+02 Score=30.51 Aligned_cols=88 Identities=9% Similarity=-0.011 Sum_probs=60.3
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH-----------------
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM----------------- 230 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~----------------- 230 (424)
.+++-||-.|+..=-.. ..+.||+|+|++.- . .+ .+.+.++++.+++|-+|-+-...
T Consensus 401 g~mG~glpaAiGa~la~---p~~~vv~i~GDG~f-~-~~-~~eL~ta~~~~l~v~ivV~NN~~~~~~~~~~~~~~~~~~~ 474 (548)
T PRK08978 401 GTMGFGLPAAIGAQVAR---PDDTVICVSGDGSF-M-MN-VQELGTIKRKQLPVKIVLLDNQRLGMVRQWQQLFFDERYS 474 (548)
T ss_pred hhhhchHHHHHHHHHhC---CCCcEEEEEccchh-h-cc-HHHHHHHHHhCCCeEEEEEeCCccHHHHHHHHHHhCCcce
Confidence 45666666665543222 25678999886431 1 12 25577888999998888875320
Q ss_pred -------HHHHHHHHHhCCEEEEecChhhHHHHHHhcC
Q 014440 231 -------FICKHLCQETGGTYSVALDESHSKELILEHA 261 (424)
Q Consensus 231 -------~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~ 261 (424)
.-+.++|+.-|+.|+.+.+.++|+..|....
T Consensus 475 ~~~~~~~~d~~~la~a~G~~~~~v~~~~el~~al~~a~ 512 (548)
T PRK08978 475 ETDLSDNPDFVMLASAFGIPGQTITRKDQVEAALDTLL 512 (548)
T ss_pred ecCCCCCCCHHHHHHHCCCeEEEECCHHHHHHHHHHHH
Confidence 1267788888999999999999999987775
No 304
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=30.52 E-value=24 Score=30.55 Aligned_cols=10 Identities=20% Similarity=0.680 Sum_probs=4.6
Q ss_pred eeeCCCcCcc
Q 014440 382 CVACPKCKKH 391 (424)
Q Consensus 382 ~~~C~~C~~~ 391 (424)
+..|..|++.
T Consensus 71 ~~~C~~Cg~~ 80 (117)
T PRK00564 71 ELECKDCSHV 80 (117)
T ss_pred EEEhhhCCCc
Confidence 3445555533
No 305
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=30.50 E-value=22 Score=21.95 Aligned_cols=23 Identities=26% Similarity=0.531 Sum_probs=18.8
Q ss_pred eeCCCcCcccccccchhhhccCC
Q 014440 383 VACPKCKKHFCLECDIYIHESLH 405 (424)
Q Consensus 383 ~~C~~C~~~fC~dCd~fihe~lh 405 (424)
|+|..|++.|-..=+..-|-..|
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCccCCccCChhHHHHHhHHh
Confidence 78999999998888777777555
No 306
>PRK06112 acetolactate synthase catalytic subunit; Validated
Probab=30.31 E-value=2.2e+02 Score=30.98 Aligned_cols=90 Identities=8% Similarity=0.044 Sum_probs=61.3
Q ss_pred CcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH---------------
Q 014440 166 GDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM--------------- 230 (424)
Q Consensus 166 G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~--------------- 230 (424)
|..+|+.+|-.|+..=.. ...++|++|+|++.- . .. .+.+.++++.|++|-+|-+....
T Consensus 435 g~gsmG~~l~~aiGa~la---~~~~~vv~i~GDGsf-~-~~-~~el~ta~~~~l~~~~vv~NN~~~g~~~~~~~~~~~~~ 508 (578)
T PRK06112 435 GLAGLGWGVPMAIGAKVA---RPGAPVICLVGDGGF-A-HV-WAELETARRMGVPVTIVVLNNGILGFQKHAETVKFGTH 508 (578)
T ss_pred CccccccHHHHHHHHHhh---CCCCcEEEEEcchHH-H-hH-HHHHHHHHHhCCCeEEEEEeCCccCCEEeccccccCCc
Confidence 334566666666654222 224678888886532 1 12 25577788989988877775320
Q ss_pred --------HHHHHHHHHhCCEEEEecChhhHHHHHHhcC
Q 014440 231 --------FICKHLCQETGGTYSVALDESHSKELILEHA 261 (424)
Q Consensus 231 --------~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~ 261 (424)
.-+.++|+.-|+.+..+.+.++|+..|.+..
T Consensus 509 ~~~~~~~~~d~~~~A~a~G~~~~~v~~~~el~~al~~a~ 547 (578)
T PRK06112 509 TDACHFAAVDHAAIARACGCDGVRVEDPAELAQALAAAM 547 (578)
T ss_pred cccCcCCCCCHHHHHHHCCCeEEEeCCHHHHHHHHHHHH
Confidence 1257899999999999999999999988765
No 307
>PRK15404 leucine ABC transporter subunit substrate-binding protein LivK; Provisional
Probab=30.18 E-value=2.8e+02 Score=28.07 Aligned_cols=52 Identities=12% Similarity=0.037 Sum_probs=24.9
Q ss_pred hHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEE
Q 014440 169 SIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRC 221 (424)
Q Consensus 169 sL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV 221 (424)
...++.++|++.++...+-..++|=+++-+. ..+|..-.+.++.|.+.+|.+
T Consensus 44 ~~~~g~~~av~~iNa~GGi~G~~ielv~~D~-~~~p~~a~~~~~~Li~~~V~~ 95 (369)
T PRK15404 44 MEFTGARQAIEDINAKGGIKGDKLEGVEYDD-ACDPKQAVAVANKVVNDGIKY 95 (369)
T ss_pred hHHHHHHHHHHHHHhcCCCCCeEEEEEeecC-CCCHHHHHHHHHHHHhCCceE
Confidence 4556666666666543333334444444321 124444444455555555443
No 308
>PRK10220 hypothetical protein; Provisional
Probab=30.13 E-value=33 Score=29.69 Aligned_cols=24 Identities=33% Similarity=0.987 Sum_probs=16.7
Q ss_pred CCCcCcccccccchhhhccCCCCCCCCCC
Q 014440 385 CPKCKKHFCLECDIYIHESLHNCPGCESL 413 (424)
Q Consensus 385 C~~C~~~fC~dCd~fihe~lh~CPgC~~~ 413 (424)
||+|.+.|- |-...+..||-|...
T Consensus 6 CP~C~seyt-----Y~d~~~~vCpeC~hE 29 (111)
T PRK10220 6 CPKCNSEYT-----YEDNGMYICPECAHE 29 (111)
T ss_pred CCCCCCcce-----EcCCCeEECCcccCc
Confidence 777777764 445667788888653
No 309
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=30.12 E-value=39 Score=25.68 Aligned_cols=23 Identities=26% Similarity=0.728 Sum_probs=17.8
Q ss_pred EEcCCCCccc----------cCCCCCCCCCCce
Q 014440 304 YTCPRCKARV----------CELPTECRICGLQ 326 (424)
Q Consensus 304 y~Cp~C~s~~----------C~lP~~C~~C~l~ 326 (424)
..||.|+.+- =.||.-||-|...
T Consensus 5 i~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~E 37 (55)
T PF14205_consen 5 ILCPICGNKTRLKIREDTVLKNFPLYCPKCKQE 37 (55)
T ss_pred EECCCCCCccceeeecCceeccccccCCCCCce
Confidence 5799999653 3589999999753
No 310
>PF03660 PHF5: PHF5-like protein; InterPro: IPR005345 Phf5 is a member of a novel murine multigene family that is highly conserved during evolution and belongs to the superfamily of PHD-finger proteins. At least one example, from Mus musculus (Mouse), may act as a chromatin-associated protein []. The Schizosaccharomyces pombe (Fission yeast) ini1 gene is essential, required for splicing []. It is localised in the nucleus, but not detected in the nucleolus and can be complemented by human ini1 []. The proteins of this family contain five CXXC motifs.; PDB: 2K0A_A.
Probab=30.04 E-value=14 Score=31.53 Aligned_cols=27 Identities=30% Similarity=0.823 Sum_probs=11.7
Q ss_pred eeeecCCcc-ccCeEEcCCCCccccCCCCCCCCCCc
Q 014440 291 ICSCHKEVK-IGVGYTCPRCKARVCELPTECRICGL 325 (424)
Q Consensus 291 ~C~CH~~~~-~~~Gy~Cp~C~s~~C~lP~~C~~C~l 325 (424)
+=+|.+... .+ |++|..|--+ |++|..
T Consensus 8 LvmC~KqpG~~i-G~lC~kCdGk-------CpiCDS 35 (106)
T PF03660_consen 8 LVMCRKQPGTAI-GRLCEKCDGK-------CPICDS 35 (106)
T ss_dssp --B----EEEEE--EE-GGGTT---------TTT--
T ss_pred HhhhccCCcchh-hhhhhhcCCc-------ccccCC
Confidence 345666553 45 9999999876 999994
No 311
>TIGR03669 urea_ABC_arch urea ABC transporter, substrate-binding protein, archaeal type. Members of this protein family are identified as the substrate-binding protein of a urea ABC transport system by similarity to a known urea transporter from Corynebacterium glutamicum, operon structure, proximity of its operons to urease (urea-utilization protein) operons, and by Partial Phylogenetic Profiling vs. urea utilization.
Probab=30.03 E-value=2.9e+02 Score=28.30 Aligned_cols=61 Identities=15% Similarity=0.107 Sum_probs=36.0
Q ss_pred cchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHH-hCCcEEEEEEecc
Q 014440 167 DSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCK-ESKIRCSVIGLSA 228 (424)
Q Consensus 167 ~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~ak-k~~IrV~vIgLg~ 228 (424)
+....+|.++|++.++...+-..|+|-++..+.. .+|..-.+.++.|. +.+|.+-+=++++
T Consensus 17 G~~~~~G~~lAv~~iNa~GGi~Gr~ielv~~D~~-~~p~~a~~~a~~li~~d~v~~viG~~~S 78 (374)
T TIGR03669 17 GTPKWHASQLAIEEINKSGGILGRQIELIDPDPQ-SDNERYQELTRRLLNRDKVDALWAGYSS 78 (374)
T ss_pred cHHHHHHHHHHHHHHHhcCCCCCceeEEEEeCCC-CCHHHHHHHHHHHHHhCCCCEEEcCCch
Confidence 3567889999999998654444566776665422 34543334444444 5677664333443
No 312
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=29.74 E-value=23 Score=26.41 Aligned_cols=30 Identities=33% Similarity=0.696 Sum_probs=19.6
Q ss_pred CCceeecccccccCC----CCCCceeeCCCcCcc
Q 014440 362 RSTCFGCQQSLLASG----NKAGLCVACPKCKKH 391 (424)
Q Consensus 362 ~~~C~~C~~~~~~~~----~~~~~~~~C~~C~~~ 391 (424)
.+.|.||...++... ........||.|+..
T Consensus 22 ~~~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 22 GGTCSGCHMELPPQELNEIRKGDEIVFCPNCGRI 55 (56)
T ss_pred CCccCCCCEEcCHHHHHHHHcCCCeEECcCCCcc
Confidence 568999998887542 111235678888753
No 313
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=29.65 E-value=19 Score=35.23 Aligned_cols=55 Identities=22% Similarity=0.387 Sum_probs=32.6
Q ss_pred CchhHHhhhcccCCCCCCcccCccccccccCCCCCceeecccccccCC----CCCCceeeCCCcCcc
Q 014440 329 SSPHLARSYHHLFPIAPFDEATPSRLNDLHNISRSTCFGCQQSLLASG----NKAGLCVACPKCKKH 391 (424)
Q Consensus 329 s~phLarsyhhl~p~~~f~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~----~~~~~~~~C~~C~~~ 391 (424)
.+|+|.--|+++- ..++-+.. -.-....|.||...+|... ......-.||.|+.+
T Consensus 172 l~~ell~~yeri~--~~~kg~gv------vpl~g~~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRI 230 (239)
T COG1579 172 LDPELLSEYERIR--KNKKGVGV------VPLEGRVCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRI 230 (239)
T ss_pred cCHHHHHHHHHHH--hcCCCceE------EeecCCcccCCeeeecHHHHHHHhcCCCCccCCccchH
Confidence 5789999999873 33322100 1113568999999998653 112223458887754
No 314
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=29.55 E-value=53 Score=24.99 Aligned_cols=21 Identities=38% Similarity=0.966 Sum_probs=13.4
Q ss_pred eEEcCCCCccccCCC-CCCCCCCc
Q 014440 303 GYTCPRCKARVCELP-TECRICGL 325 (424)
Q Consensus 303 Gy~Cp~C~s~~C~lP-~~C~~C~l 325 (424)
-..||.|++. .+| ..|+.||.
T Consensus 27 l~~C~~CG~~--~~~H~vC~~CG~ 48 (57)
T PRK12286 27 LVECPNCGEP--KLPHRVCPSCGY 48 (57)
T ss_pred ceECCCCCCc--cCCeEECCCCCc
Confidence 4568888776 333 46777774
No 315
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=29.44 E-value=50 Score=25.99 Aligned_cols=47 Identities=23% Similarity=0.521 Sum_probs=18.1
Q ss_pred ceeecccccccCCCCCCceeeC-CCcCcccccccchhhhccCCCCCCCCCCCCCCCcc
Q 014440 364 TCFGCQQSLLASGNKAGLCVAC-PKCKKHFCLECDIYIHESLHNCPGCESLRQSNPVV 420 (424)
Q Consensus 364 ~C~~C~~~~~~~~~~~~~~~~C-~~C~~~fC~dCd~fihe~lh~CPgC~~~~~~~~~~ 420 (424)
.|.-|...+..+ .| ..|.+.||..|--=--. -.||-|....--.+++
T Consensus 9 rCs~C~~~l~~p--------v~l~~CeH~fCs~Ci~~~~~--~~CPvC~~Paw~qD~~ 56 (65)
T PF14835_consen 9 RCSICFDILKEP--------VCLGGCEHIFCSSCIRDCIG--SECPVCHTPAWIQDIQ 56 (65)
T ss_dssp S-SSS-S--SS---------B---SSS--B-TTTGGGGTT--TB-SSS--B-S-SS--
T ss_pred CCcHHHHHhcCC--------ceeccCccHHHHHHhHHhcC--CCCCCcCChHHHHHHH
Confidence 588887666533 24 57999999999532111 2499997644333333
No 316
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=29.33 E-value=31 Score=25.21 Aligned_cols=29 Identities=28% Similarity=0.752 Sum_probs=20.3
Q ss_pred ceeecc-cccccCCCCCCceeeCCCcCc-ccccccch
Q 014440 364 TCFGCQ-QSLLASGNKAGLCVACPKCKK-HFCLECDI 398 (424)
Q Consensus 364 ~C~~C~-~~~~~~~~~~~~~~~C~~C~~-~fC~dCd~ 398 (424)
.|.+|. .++. +.+|+|..|.. ..|.+|-.
T Consensus 2 ~C~~C~~~~i~------g~R~~C~~C~d~dlC~~Cf~ 32 (49)
T cd02338 2 SCDGCGKSNFT------GRRYKCLICYDYDLCADCYD 32 (49)
T ss_pred CCCCCcCCCcE------EeeEEeCCCCCCccchhHHh
Confidence 589998 4554 25899999965 46777743
No 317
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=29.26 E-value=33 Score=25.41 Aligned_cols=25 Identities=28% Similarity=0.604 Sum_probs=14.4
Q ss_pred eEEcCCCCccccC---CCCCCCCCCcee
Q 014440 303 GYTCPRCKARVCE---LPTECRICGLQL 327 (424)
Q Consensus 303 Gy~Cp~C~s~~C~---lP~~C~~C~l~L 327 (424)
.=.||+|++-+-. ---.|..||.+.
T Consensus 20 ~~fCP~Cg~~~m~~~~~r~~C~~Cgyt~ 47 (50)
T PRK00432 20 NKFCPRCGSGFMAEHLDRWHCGKCGYTE 47 (50)
T ss_pred cCcCcCCCcchheccCCcEECCCcCCEE
Confidence 3478888872111 123688888764
No 318
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=29.22 E-value=46 Score=32.20 Aligned_cols=39 Identities=26% Similarity=0.639 Sum_probs=26.0
Q ss_pred eeeCCCcCcccccccchhhhccCCCCCCCCCCCCCCCcccC
Q 014440 382 CVACPKCKKHFCLECDIYIHESLHNCPGCESLRQSNPVVAN 422 (424)
Q Consensus 382 ~~~C~~C~~~fC~dCd~fihe~lh~CPgC~~~~~~~~~~~~ 422 (424)
.++|.+|+..+-. +.++...+..||.|.....++++--+
T Consensus 122 ~~~C~~C~~~~~~--~~~~~~~~p~C~~Cgg~lrP~Vv~fg 160 (242)
T PRK00481 122 RARCTKCGQTYDL--DEYLKPEPPRCPKCGGILRPDVVLFG 160 (242)
T ss_pred ceeeCCCCCCcCh--hhhccCCCCCCCCCCCccCCCeEECC
Confidence 3568788776643 34555567779999887777766443
No 319
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=29.19 E-value=56 Score=37.00 Aligned_cols=27 Identities=37% Similarity=0.828 Sum_probs=18.8
Q ss_pred ceeeCCCcCcccccccchhhhccCC--CCCCCCCC
Q 014440 381 LCVACPKCKKHFCLECDIYIHESLH--NCPGCESL 413 (424)
Q Consensus 381 ~~~~C~~C~~~fC~dCd~fihe~lh--~CPgC~~~ 413 (424)
..|.||.|++- +.-||--| +||-|-+.
T Consensus 1155 ~fWlC~~CkH~------a~~~EIs~y~~CPLCHs~ 1183 (1189)
T KOG2041|consen 1155 IFWLCPRCKHR------AHQHEISKYNCCPLCHSM 1183 (1189)
T ss_pred eEEEccccccc------cccccccccccCccccCh
Confidence 37899999873 45566543 78988653
No 320
>PF14353 CpXC: CpXC protein
Probab=29.01 E-value=35 Score=29.53 Aligned_cols=21 Identities=33% Similarity=0.850 Sum_probs=14.6
Q ss_pred eeeCCCcCcccccccchhhhc
Q 014440 382 CVACPKCKKHFCLECDIYIHE 402 (424)
Q Consensus 382 ~~~C~~C~~~fC~dCd~fihe 402 (424)
.|.||.|+..|=++=....|+
T Consensus 38 ~~~CP~Cg~~~~~~~p~lY~D 58 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEYPLLYHD 58 (128)
T ss_pred EEECCCCCCceecCCCEEEEc
Confidence 689999998875554444444
No 321
>PHA00616 hypothetical protein
Probab=28.83 E-value=17 Score=26.43 Aligned_cols=17 Identities=18% Similarity=0.470 Sum_probs=12.9
Q ss_pred eeCCCcCcccccccchh
Q 014440 383 VACPKCKKHFCLECDIY 399 (424)
Q Consensus 383 ~~C~~C~~~fC~dCd~f 399 (424)
|+|+.|+..|..-=++-
T Consensus 2 YqC~~CG~~F~~~s~l~ 18 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVI 18 (44)
T ss_pred CccchhhHHHhhHHHHH
Confidence 89999999997654433
No 322
>PRK08322 acetolactate synthase; Reviewed
Probab=28.36 E-value=2.1e+02 Score=30.83 Aligned_cols=91 Identities=9% Similarity=-0.057 Sum_probs=61.7
Q ss_pred CcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH---------------
Q 014440 166 GDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM--------------- 230 (424)
Q Consensus 166 G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~--------------- 230 (424)
|..+|+.||-.|+..=-.. ..|+|+.|+|++.- . .++ ..+.++++.+++|-+|-+....
T Consensus 404 ~~g~mG~~lpaaiGa~la~---p~~~vv~i~GDGsf-~-m~~-~eL~Ta~~~~lpv~iiV~NN~~~g~~~~~~~~~~~~~ 477 (547)
T PRK08322 404 ALATMGAGLPSAIAAKLVH---PDRKVLAVCGDGGF-M-MNS-QELETAVRLGLPLVVLILNDNAYGMIRWKQENMGFED 477 (547)
T ss_pred CcccccchhHHHHHHHHhC---CCCcEEEEEcchhH-h-ccH-HHHHHHHHhCCCeEEEEEeCCCcchHHHHHHhhcCCc
Confidence 3346666666666542222 24678888886432 1 222 4466788999998888775320
Q ss_pred -------HHHHHHHHHhCCEEEEecChhhHHHHHHhcCC
Q 014440 231 -------FICKHLCQETGGTYSVALDESHSKELILEHAP 262 (424)
Q Consensus 231 -------~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~~ 262 (424)
.-+.++|+.-|..|..+.+.++|.+.|.+...
T Consensus 478 ~~~~~~~~df~~lA~a~G~~~~~v~~~~eL~~al~~a~~ 516 (547)
T PRK08322 478 FGLDFGNPDFVKYAESYGAKGYRVESADDLLPTLEEALA 516 (547)
T ss_pred ccccCCCCCHHHHHHHCCCeEEEeCCHHHHHHHHHHHHh
Confidence 12567899999999999999999999988763
No 323
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=28.18 E-value=59 Score=21.76 Aligned_cols=28 Identities=25% Similarity=0.673 Sum_probs=17.6
Q ss_pred ceeecccccccCCCCCCceeeCCCcCcccccc
Q 014440 364 TCFGCQQSLLASGNKAGLCVACPKCKKHFCLE 395 (424)
Q Consensus 364 ~C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~d 395 (424)
.|.-|.+.- ......|.|..|+...|.+
T Consensus 2 rC~vC~~~k----~rk~T~~~C~~C~v~lC~~ 29 (32)
T PF13842_consen 2 RCKVCSKKK----RRKDTRYMCSKCDVPLCVE 29 (32)
T ss_pred CCeECCcCC----ccceeEEEccCCCCcccCC
Confidence 466676411 1122579999998887765
No 324
>PRK09545 znuA high-affinity zinc transporter periplasmic component; Reviewed
Probab=28.12 E-value=1.6e+02 Score=29.72 Aligned_cols=43 Identities=12% Similarity=0.090 Sum_probs=36.7
Q ss_pred ccCHHHHHHHHHhCCcEEEEEEecchHHHHHHHHHHhCCEEEE
Q 014440 204 PGDIMETIQKCKESKIRCSVIGLSAEMFICKHLCQETGGTYSV 246 (424)
Q Consensus 204 p~~i~~~i~~akk~~IrV~vIgLg~e~~iLq~iA~~TGG~Y~~ 246 (424)
+.++.++++.+++.+|++-..--.......+.|++.||.+...
T Consensus 238 ~~~l~~l~~~ik~~~v~~If~e~~~~~~~~~~la~e~g~~v~~ 280 (311)
T PRK09545 238 AQRLHEIRTQLVEQKATCVFAEPQFRPAVIESVAKGTSVRMGT 280 (311)
T ss_pred HHHHHHHHHHHHHcCCCEEEecCCCChHHHHHHHHhcCCeEEE
Confidence 4578899999999999987777767789999999999988654
No 325
>cd04195 GT2_AmsE_like GT2_AmsE_like is involved in exopolysaccharide amylovora biosynthesis. AmsE is a glycosyltransferase involved in exopolysaccharide amylovora biosynthesis in Erwinia amylovora. Amylovara is one of the three exopolysaccharide produced by E. amylovora. Amylovara-deficient mutants are non-pathogenic. It is a subfamily of Glycosyltransferase Family GT2, which includes diverse families of glycosyltransferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds.
Probab=28.12 E-value=3.8e+02 Score=23.72 Aligned_cols=82 Identities=7% Similarity=-0.009 Sum_probs=41.9
Q ss_pred HHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHH-hCCcEEEEEEec-chHHHHHHHHHHhCCEEEEecChhh
Q 014440 175 DLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCK-ESKIRCSVIGLS-AEMFICKHLCQETGGTYSVALDESH 252 (424)
Q Consensus 175 ~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~ak-k~~IrV~vIgLg-~e~~iLq~iA~~TGG~Y~~~~d~~~ 252 (424)
+.++..+... .+...+|||+-++..+ ....++++.+. +.+|++....-. .-..-+........|.|+...|.++
T Consensus 16 ~~~l~Sl~~q-~~~~~eiiivdd~ss~---d~t~~~~~~~~~~~~i~~i~~~~n~G~~~a~N~g~~~a~gd~i~~lD~Dd 91 (201)
T cd04195 16 REALESILKQ-TLPPDEVVLVKDGPVT---QSLNEVLEEFKRKLPLKVVPLEKNRGLGKALNEGLKHCTYDWVARMDTDD 91 (201)
T ss_pred HHHHHHHHhc-CCCCcEEEEEECCCCc---hhHHHHHHHHHhcCCeEEEEcCccccHHHHHHHHHHhcCCCEEEEeCCcc
Confidence 3344444333 2334577776653222 23445555443 345555443211 1134566667777899998777664
Q ss_pred ------HHHHHHhc
Q 014440 253 ------SKELILEH 260 (424)
Q Consensus 253 ------L~~lL~~~ 260 (424)
++.++..+
T Consensus 92 ~~~~~~l~~~~~~~ 105 (201)
T cd04195 92 ISLPDRFEKQLDFI 105 (201)
T ss_pred ccCcHHHHHHHHHH
Confidence 45555444
No 326
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=28.10 E-value=31 Score=21.64 Aligned_cols=11 Identities=45% Similarity=0.993 Sum_probs=9.2
Q ss_pred eeeCCCcCccc
Q 014440 382 CVACPKCKKHF 392 (424)
Q Consensus 382 ~~~C~~C~~~f 392 (424)
.|.|+.|++.|
T Consensus 14 ~~~C~~C~k~F 24 (26)
T PF13465_consen 14 PYKCPYCGKSF 24 (26)
T ss_dssp SEEESSSSEEE
T ss_pred CCCCCCCcCee
Confidence 58999998876
No 327
>PRK06965 acetolactate synthase 3 catalytic subunit; Validated
Probab=27.94 E-value=2.5e+02 Score=30.76 Aligned_cols=88 Identities=15% Similarity=0.137 Sum_probs=61.2
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH-----------------
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM----------------- 230 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~----------------- 230 (424)
-+++.||-.|+..--..| .|+|+.|+|++.- . .++ ..+.++.+.+++|-+|-+....
T Consensus 437 gsmG~glpaaiGa~lA~p---~r~Vv~i~GDGsf-~-m~~-~eL~Ta~r~~lpviivV~NN~~~~~i~~~q~~~~~~~~~ 510 (587)
T PRK06965 437 GTMGVGLPYAMGIKMAHP---DDDVVCITGEGSI-Q-MCI-QELSTCLQYDTPVKIISLNNRYLGMVRQWQEIEYSKRYS 510 (587)
T ss_pred ccccchHHHHHHHHHhCC---CCcEEEEEcchhh-h-cCH-HHHHHHHHcCCCeEEEEEECCcchHHHHHHHHhcCCCcc
Confidence 466666666665433222 5678888886432 1 122 4577888999999888885320
Q ss_pred -------HHHHHHHHHhCCEEEEecChhhHHHHHHhcC
Q 014440 231 -------FICKHLCQETGGTYSVALDESHSKELILEHA 261 (424)
Q Consensus 231 -------~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~ 261 (424)
.-+.++|+..|+.++.+.+.++|...|...+
T Consensus 511 ~~~~~~~~d~~~iA~a~G~~~~~v~~~~eL~~al~~a~ 548 (587)
T PRK06965 511 HSYMDALPDFVKLAEAYGHVGMRIEKTSDVEPALREAL 548 (587)
T ss_pred ccCCCCCCCHHHHHHHCCCEEEEECCHHHHHHHHHHHH
Confidence 1245799999999999999999999888775
No 328
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=27.86 E-value=27 Score=23.82 Aligned_cols=28 Identities=21% Similarity=0.407 Sum_probs=14.5
Q ss_pred ceeecccccccC--CCCCCceeeCCCcCcc
Q 014440 364 TCFGCQQSLLAS--GNKAGLCVACPKCKKH 391 (424)
Q Consensus 364 ~C~~C~~~~~~~--~~~~~~~~~C~~C~~~ 391 (424)
+|..|..++... .+..-.|+.|+.|+.+
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred ccccccChhhhhcCCCCCccceECCCCCCE
Confidence 677886665421 1233458999999865
No 329
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=27.79 E-value=33 Score=27.89 Aligned_cols=21 Identities=33% Similarity=0.744 Sum_probs=13.9
Q ss_pred EEcCCCCccccCCC-----CCCCCCC
Q 014440 304 YTCPRCKARVCELP-----TECRICG 324 (424)
Q Consensus 304 y~Cp~C~s~~C~lP-----~~C~~C~ 324 (424)
|.||-|+...=+-. -+|++|+
T Consensus 2 ~~CPCCg~~Tl~~~~~~~ydIC~VC~ 27 (78)
T PF14206_consen 2 YPCPCCGYYTLEERGEGTYDICPVCF 27 (78)
T ss_pred ccCCCCCcEEeccCCCcCceECCCCC
Confidence 67888887754322 2688886
No 330
>cd06349 PBP1_ABC_ligand_binding_like_14 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=27.74 E-value=2.4e+02 Score=27.73 Aligned_cols=30 Identities=23% Similarity=0.367 Sum_probs=16.4
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEc
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYS 197 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~s 197 (424)
....+++++|.+.++...+...++|-+++-
T Consensus 17 ~~~~~g~~~a~~~iN~~ggi~G~~i~l~~~ 46 (340)
T cd06349 17 TQWKRAFDLALDEINAAGGVGGRPLNIVFE 46 (340)
T ss_pred ccHHHHHHHHHHHHHhhCCcCCeEEEEEEe
Confidence 455566666666666543333455555543
No 331
>TIGR03863 PQQ_ABC_bind ABC transporter, substrate binding protein, PQQ-dependent alcohol dehydrogenase system. Members of this protein family are putative substrate-binding proteins of an ABC transporter family that associates, in gene neighborhood and phylogenomic profile, with pyrroloquinoline-quinone (PQQ)-dependent degradation of certain alcohols, such as 2-phenylethanol in Pseudomonas putida U.
Probab=27.70 E-value=3.3e+02 Score=27.72 Aligned_cols=78 Identities=13% Similarity=0.100 Sum_probs=46.8
Q ss_pred CcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH-HHHHHHHHHhCCEE
Q 014440 166 GDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM-FICKHLCQETGGTY 244 (424)
Q Consensus 166 G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~-~iLq~iA~~TGG~Y 244 (424)
.+.+..+|.++|++.++...+-..++|-++..+ ..+|....+.++.+.+.+|.+-+-++++.+ .-+.++++..+--|
T Consensus 9 ~~~~~~~ga~lAveeiNaaGGv~G~~ielv~~D--~~~p~~a~~~a~~Li~~~V~~vvG~~~S~~~~Av~~~a~~~~vp~ 86 (347)
T TIGR03863 9 PEDRGLDGARLAIEDNNTTGRFLGQTFTLDEVA--VRTPEDLVAALKALLAQGVRFFVLDLPAAALLALADAAKAKGALL 86 (347)
T ss_pred CcchHHHHHHHHHHHHHhhCCcCCceEEEEEcc--CCCHHHHHHHHHHHHHCCCCEEEecCChHHHHHHHHHHHhCCcEE
Confidence 356888999999999986534444566555443 235666666677777778655444455533 22445555444333
Q ss_pred E
Q 014440 245 S 245 (424)
Q Consensus 245 ~ 245 (424)
+
T Consensus 87 i 87 (347)
T TIGR03863 87 F 87 (347)
T ss_pred E
Confidence 3
No 332
>cd03466 Nitrogenase_NifN_2 Nitrogenase_nifN_2: A subgroup of the NifN subunit of the NifEN complex: NifN forms an alpha2beta2 tetramer with NifE. NifN and nifE are structurally homologous to nitrogenase MoFe protein beta and alpha subunits respectively. NifEN participates in the synthesis of the iron-molybdenum cofactor (FeMoco) of the MoFe protein. NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to the NifEN complex where it is further processed to FeMoco. The nifEN bound precursor of FeMoco has been identified as a molybdenum-free, iron- and sulfur- containing analog of FeMoco. It has been suggested that this nifEN bound precursor also acts as a cofactor precursor in nitrogenase systems which require a cofactor other than FeMoco: i.e. iron-vanadium cofactor (FeVco) or iron only cofactor (FeFeco). This group also contains the Clostidium fused NifN-NifB protein.
Probab=27.67 E-value=7.3e+02 Score=26.02 Aligned_cols=78 Identities=17% Similarity=0.060 Sum_probs=44.6
Q ss_pred CHHHHHHHHHhCCcEEEEEEecchHH----HHHHHHHHh-CCEEEE-ecChhhHHHHHHhcCCCCccch--------hhh
Q 014440 206 DIMETIQKCKESKIRCSVIGLSAEMF----ICKHLCQET-GGTYSV-ALDESHSKELILEHAPPPPAIA--------EFA 271 (424)
Q Consensus 206 ~i~~~i~~akk~~IrV~vIgLg~e~~----iLq~iA~~T-GG~Y~~-~~d~~~L~~lL~~~~~pp~~~~--------~~~ 271 (424)
-.....+.+.+.|+.+-+++.+.... .|++....- .....+ ..|..++.+++...- |.-.-. ...
T Consensus 311 ~~~~l~~~L~elG~~~~~v~~~~~~~~~~~~l~~~~~~~~~~~~v~~~~d~~e~~~~l~~~~-~dliiG~s~~~~~a~~~ 389 (429)
T cd03466 311 FVVAITRFVLENGMVPVLIATGSESKKLKEKLEEDLKEYVEKCVILDGADFFDIESYAKELK-IDVLIGNSYGRRIAEKL 389 (429)
T ss_pred HHHHHHHHHHHCCCEEEEEEeCCCChHHHHHHHHHHHhcCCceEEEeCCCHHHHHHHHHhcC-CCEEEECchhHHHHHHc
Confidence 44567888899999996666654322 333333322 233332 346667777776653 332211 123
Q ss_pred hhheeeecCCCCC
Q 014440 272 IASLIKMGFPQRA 284 (424)
Q Consensus 272 ~~~Li~mGFP~~~ 284 (424)
.-.++++|||...
T Consensus 390 ~ip~~~~~~P~~d 402 (429)
T cd03466 390 GIPLIRIGFPIHD 402 (429)
T ss_pred CCCEEEecCCcee
Confidence 4478899999764
No 333
>PF14949 ARF7EP_C: ARF7 effector protein C-terminus
Probab=27.65 E-value=28 Score=29.78 Aligned_cols=19 Identities=42% Similarity=1.114 Sum_probs=15.8
Q ss_pred CceeecccccccCCCCCCceeeCCCcCccccc
Q 014440 363 STCFGCQQSLLASGNKAGLCVACPKCKKHFCL 394 (424)
Q Consensus 363 ~~C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~ 394 (424)
..|-||- |-||+|++..|.
T Consensus 68 ~~C~GC~-------------~PC~~C~S~KCG 86 (103)
T PF14949_consen 68 EDCPGCH-------------YPCPKCGSRKCG 86 (103)
T ss_pred CCCCCcc-------------ccCCCCCCCccC
Confidence 3588885 789999999995
No 334
>PRK06882 acetolactate synthase 3 catalytic subunit; Validated
Probab=27.56 E-value=3.3e+02 Score=29.58 Aligned_cols=88 Identities=14% Similarity=0.109 Sum_probs=59.1
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH-----------------
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM----------------- 230 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~----------------- 230 (424)
.+++.+|-.|+..--..| .++|++|+|++.- . .++ +.+.++.+.+++|-+|-+....
T Consensus 421 g~mG~~lp~aiGa~la~p---~~~vv~i~GDG~f-~-~~~-~eL~ta~~~~lpv~~vV~NN~~~~~i~~~q~~~~~~~~~ 494 (574)
T PRK06882 421 GTMGFGLPAAIGVKFAHP---EATVVCVTGDGSI-Q-MNI-QELSTAKQYDIPVVIVSLNNRFLGMVKQWQDLIYSGRHS 494 (574)
T ss_pred ccccchhHHHHHHHhhcC---CCcEEEEEcchhh-h-ccH-HHHHHHHHhCCCeEEEEEECchhHHHHHHHHHhcCCccc
Confidence 345555555555322222 4678888886432 1 222 5577788999998888775321
Q ss_pred -------HHHHHHHHHhCCEEEEecChhhHHHHHHhcC
Q 014440 231 -------FICKHLCQETGGTYSVALDESHSKELILEHA 261 (424)
Q Consensus 231 -------~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~ 261 (424)
.-+.++|+.-|+.++.+.+.++|+..|....
T Consensus 495 ~~~~~~~~d~~~la~a~G~~~~~v~~~~eL~~al~~a~ 532 (574)
T PRK06882 495 QVYMNSLPDFAKLAEAYGHVGIQIDTPDELEEKLTQAF 532 (574)
T ss_pred ccCCCCCCCHHHHHHHCCCeEEEeCCHHHHHHHHHHHH
Confidence 1256789999999999999999999988775
No 335
>cd04919 ACT_AK-Hom3_2 ACT domains located C-terminal to the catalytic domain of the aspartokinase (AK) HOM3. This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the aspartokinase (AK) HOM3, a monofunctional class enzyme found in Saccharomyces cerevisiae, and other related ACT domains. AK is the first enzyme in the aspartate metabolic pathway, catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP, and in fungi, is responsible for the production of threonine, isoleucine and methionine. S. cerevisiae has a single AK, which is regulated by feedback, allosteric inhibition by L-threonine. Recent studies shown that the allosteric transition triggered by binding of threonine to AK involves a large change in the conformation of the native hexameric enzyme that is converted to an inactive one of different shape and substantially smaller hydrodynamic size. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=27.44 E-value=1.6e+02 Score=21.57 Aligned_cols=36 Identities=17% Similarity=0.075 Sum_probs=25.8
Q ss_pred EEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecc
Q 014440 193 LILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSA 228 (424)
Q Consensus 193 LvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~ 228 (424)
|-+.|..-..+++-..+.++.+.+.||+|+.|+-++
T Consensus 4 isvvg~~~~~~~~~~~~if~~L~~~~I~v~~i~q~~ 39 (66)
T cd04919 4 LSLVGKHMKNMIGIAGRMFTTLADHRINIEMISQGA 39 (66)
T ss_pred EEEECCCCCCCcCHHHHHHHHHHHCCCCEEEEEecC
Confidence 444554443456666788999999999999997654
No 336
>cd03376 TPP_PFOR_porB_like Thiamine pyrophosphate (TPP family), PFOR porB-like subfamily, TPP-binding module; composed of proteins similar to the beta subunit (porB) of the Helicobacter pylori four-subunit pyruvate ferredoxin oxidoreductase (PFOR), which are also found in archaea and some hyperthermophilic bacteria. PFOR catalyzes the oxidative decarboxylation of pyruvate to form acetyl-CoA, a crucial step in many metabolic pathways. Archaea, anaerobic bacteria and eukaryotes that lack mitochondria (and therefore pyruvate dehydrogenase) use PFOR to oxidatively decarboxylate pyruvate, with ferredoxin or flavodoxin as the electron acceptor. The 36-kDa porB subunit contains the binding sites for the cofactors, TPP and a divalent metal cation, which are required for activity.
Probab=27.34 E-value=3.9e+02 Score=25.74 Aligned_cols=89 Identities=9% Similarity=-0.004 Sum_probs=58.9
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH-----------------
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM----------------- 230 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~----------------- 230 (424)
.+++-+|-.|+......| .|.||.|.|+...-+ ..+ +.+..+.+.+++|-+|-+....
T Consensus 62 gsmG~GlpaAiGa~~a~p---~r~VV~i~GDG~~~~-m~~-~eL~ta~~~~~pv~~vVlNN~~yg~tg~q~~~~~~~~~~ 136 (235)
T cd03376 62 AAVASGIEAALKALGRGK---DITVVAFAGDGGTAD-IGF-QALSGAAERGHDILYICYDNEAYMNTGIQRSGSTPYGAW 136 (235)
T ss_pred HHHHHHHHHHHHHhccCC---CCeEEEEEcCchHHh-hHH-HHHHHHHHcCCCeEEEEECCcccccCCCCCCCCCCCCCE
Confidence 388888888887644322 567888887643111 222 4566788999999888775321
Q ss_pred -----------------HHHHHHHHHhCCEEE---EecChhhHHHHHHhcC
Q 014440 231 -----------------FICKHLCQETGGTYS---VALDESHSKELILEHA 261 (424)
Q Consensus 231 -----------------~iLq~iA~~TGG~Y~---~~~d~~~L~~lL~~~~ 261 (424)
.-+.+||+..|..|. .+.+.++|.+.|.+..
T Consensus 137 ~~~~~~g~~~~~~~~~~~d~~~iA~a~G~~~~~~~~v~~~~el~~al~~a~ 187 (235)
T cd03376 137 TTTTPVGKVSFGKKQPKKDLPLIMAAHNIPYVATASVAYPEDLYKKVKKAL 187 (235)
T ss_pred eecCCCCccccccccccCCHHHHHHHcCCcEEEEEcCCCHHHHHHHHHHHH
Confidence 135678888887775 3677778877777665
No 337
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=27.32 E-value=28 Score=32.26 Aligned_cols=30 Identities=30% Similarity=0.584 Sum_probs=20.6
Q ss_pred CceeecccccccCCCC-------------CCceeeCCCcCccc
Q 014440 363 STCFGCQQSLLASGNK-------------AGLCVACPKCKKHF 392 (424)
Q Consensus 363 ~~C~~C~~~~~~~~~~-------------~~~~~~C~~C~~~f 392 (424)
..|--|+.++...... ....|+||+|++.|
T Consensus 98 ~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiY 140 (165)
T COG1656 98 SRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIY 140 (165)
T ss_pred ccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccc
Confidence 3699999888654311 12258999999876
No 338
>PRK08979 acetolactate synthase 3 catalytic subunit; Validated
Probab=27.25 E-value=2.7e+02 Score=30.32 Aligned_cols=88 Identities=10% Similarity=0.074 Sum_probs=60.6
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecch----H-------------
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAE----M------------- 230 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e----~------------- 230 (424)
.+|+.||-.|+..=-.. ..|+|+.|+|++.- . .. ...+.++.+.|++|-+|-+... .
T Consensus 421 g~mG~glpaaiGa~la~---p~~~vv~i~GDG~f-~-m~-~~EL~Ta~r~~lpv~~vV~NN~~y~~i~~~q~~~~~~~~~ 494 (572)
T PRK08979 421 GTMGFGLPAAMGVKFAM---PDETVVCVTGDGSI-Q-MN-IQELSTALQYDIPVKIINLNNRFLGMVKQWQDMIYQGRHS 494 (572)
T ss_pred ccccchhhHHHhhhhhC---CCCeEEEEEcchHh-h-cc-HHHHHHHHHcCCCeEEEEEeCCccHHHHHHHHHHhCCccc
Confidence 46666666666543322 24688888886421 0 12 2558899999999988887532 0
Q ss_pred -------HHHHHHHHHhCCEEEEecChhhHHHHHHhcC
Q 014440 231 -------FICKHLCQETGGTYSVALDESHSKELILEHA 261 (424)
Q Consensus 231 -------~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~ 261 (424)
.-+.++|+..|+.+..+.+.++|...|...+
T Consensus 495 ~~~~~~~~d~~~~A~a~G~~~~~v~~~~eL~~al~~a~ 532 (572)
T PRK08979 495 HSYMDSVPDFAKIAEAYGHVGIRISDPDELESGLEKAL 532 (572)
T ss_pred ccCCCCCCCHHHHHHHCCCeEEEECCHHHHHHHHHHHH
Confidence 1245688889999999999999999888765
No 339
>PRK08527 acetolactate synthase 3 catalytic subunit; Validated
Probab=27.07 E-value=4.3e+02 Score=28.68 Aligned_cols=88 Identities=18% Similarity=0.106 Sum_probs=58.6
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecch----H-------------
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAE----M------------- 230 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e----~------------- 230 (424)
-+++.||-.|+..=...| .++|++|+|++.- . .++++ +.++.+.|++|-+|-+... .
T Consensus 414 g~mG~~l~~aiGa~la~p---~~~vv~i~GDG~f-~-m~~~e-L~Ta~~~~lpvi~vV~NN~~~~~i~~~~~~~~~~~~~ 487 (563)
T PRK08527 414 GTMGYGLPAALGAKLAVP---DKVVINFTGDGSI-L-MNIQE-LMTAVEYKIPVINIILNNNFLGMVRQWQTFFYEERYS 487 (563)
T ss_pred ccccchHHHHHHHHHhCC---CCcEEEEecCchh-c-ccHHH-HHHHHHhCCCeEEEEEECCcchhHHHHHHhhcCCcee
Confidence 455555555554322222 4678888886532 1 34444 6778889999887777532 0
Q ss_pred -------HHHHHHHHHhCCEEEEecChhhHHHHHHhcC
Q 014440 231 -------FICKHLCQETGGTYSVALDESHSKELILEHA 261 (424)
Q Consensus 231 -------~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~ 261 (424)
.-+.++|+.-|+.++.+.+.++|...|....
T Consensus 488 ~~~~~~~~d~~~~a~a~G~~~~~v~~~~el~~al~~a~ 525 (563)
T PRK08527 488 ETDLSTQPDFVKLAESFGGIGFRVTTKEEFDKALKEAL 525 (563)
T ss_pred eccCCCCCCHHHHHHHCCCeEEEECCHHHHHHHHHHHH
Confidence 0246799999999999999999999987765
No 340
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=27.04 E-value=42 Score=24.35 Aligned_cols=29 Identities=38% Similarity=0.886 Sum_probs=20.3
Q ss_pred ceeeccc-ccccCCCCCCceeeCCCcCc-ccccccch
Q 014440 364 TCFGCQQ-SLLASGNKAGLCVACPKCKK-HFCLECDI 398 (424)
Q Consensus 364 ~C~~C~~-~~~~~~~~~~~~~~C~~C~~-~fC~dCd~ 398 (424)
.|-+|.. ++. +.+|.|..|.. ..|..|-.
T Consensus 2 ~Cd~C~~~pI~------G~RykC~~C~dyDLC~~Cf~ 32 (45)
T cd02344 2 TCDGCQMFPIN------GPRFKCRNCDDFDFCENCFK 32 (45)
T ss_pred CCCCCCCCCCc------cCeEECCCCCCccchHHhhC
Confidence 5889974 332 25899999984 56777743
No 341
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=27.03 E-value=28 Score=29.67 Aligned_cols=25 Identities=40% Similarity=1.100 Sum_probs=17.8
Q ss_pred eEEcCCCCccc---cCC-------CCCCCCCCcee
Q 014440 303 GYTCPRCKARV---CEL-------PTECRICGLQL 327 (424)
Q Consensus 303 Gy~Cp~C~s~~---C~l-------P~~C~~C~l~L 327 (424)
-|.||+|++-- |.+ -..|.+||+.+
T Consensus 22 ~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~ 56 (104)
T COG4888 22 TFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSF 56 (104)
T ss_pred eEecCccCCeeeeEEEEEecCceeEEEcccCcceE
Confidence 69999998742 322 24799999863
No 342
>cd06355 PBP1_FmdD_like Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF). This group includes the periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF), found in Methylophilus methylotrophus, and its homologs from other bacteria. FmdD, a type I periplasmic binding protein, is induced by short-chain amides and urea and repressed by excess ammonia, while FmdE and FmdF are hydrophobic transmembrane proteins. FmdDEF is predicted to be an ATP-dependent transporter and closely resembles the periplasmic binding protein and the two transmembrane proteins present in various hydrophobic amino acid-binding transport systems.
Probab=26.94 E-value=3.7e+02 Score=26.71 Aligned_cols=75 Identities=12% Similarity=0.058 Sum_probs=42.6
Q ss_pred cchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHH-hCCcEEEEEEecch-HHHHHHHHHHhCC
Q 014440 167 DSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCK-ESKIRCSVIGLSAE-MFICKHLCQETGG 242 (424)
Q Consensus 167 ~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~ak-k~~IrV~vIgLg~e-~~iLq~iA~~TGG 242 (424)
+....+|+++|.+.++...+-..++|=++.-+.. .+|....+.++.|. +.+|.+-+=.+++. ..-+..+++..+.
T Consensus 16 G~~~~~g~~la~~~iN~~GGi~G~~ielv~~D~~-~~p~~a~~~a~~Li~~~~V~~iiG~~~S~~~~a~~~~~~~~~~ 92 (348)
T cd06355 16 ETTLKDAELLAIEEINAAGGVLGRKIEAVVEDGA-SDWPTFAEKARKLLTQDKVAAVFGCWTSASRKAVLPVFERHNG 92 (348)
T ss_pred chhHHHHHHHHHHHHHhcCCCCCcEEEEEEeCCC-CCHHHHHHHHHHHHHhCCCcEEEeccchhhHHHHHHHHhccCC
Confidence 4678899999999998754444566766664322 35544445555555 45665443234432 2234445555443
No 343
>cd06335 PBP1_ABC_ligand_binding_like_2 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=26.89 E-value=3e+02 Score=27.31 Aligned_cols=51 Identities=16% Similarity=0.141 Sum_probs=31.1
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhC-Cc
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKES-KI 219 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~-~I 219 (424)
..+.+|+++|++.++...+-..++|-++.-+.. .||....+.++.|.+. +|
T Consensus 17 ~~~~~g~~la~~~iN~~gGi~G~~i~lv~~D~~-~~p~~a~~~a~~Li~~~~V 68 (347)
T cd06335 17 VSIRRGARLAIDEINAAGGVLGRKLELVERDDR-GNPARGLQNAQELAADEKV 68 (347)
T ss_pred HHHHHHHHHHHHHHHhcCCcCCeEEEEEeccCC-CCcHHHHHHHHHHhccCCe
Confidence 457788888888887653334456666654322 3555555666666654 66
No 344
>PF12646 DUF3783: Domain of unknown function (DUF3783); InterPro: IPR016621 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=26.74 E-value=1.4e+02 Score=22.46 Aligned_cols=44 Identities=14% Similarity=0.240 Sum_probs=30.8
Q ss_pred EEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecch-------HHHHHHHHHH
Q 014440 193 LILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAE-------MFICKHLCQE 239 (424)
Q Consensus 193 LvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e-------~~iLq~iA~~ 239 (424)
++|+++.+ ...+...++.+++.||++-.-++-++ ..+++++.++
T Consensus 3 ~ll~~g~~---~~el~~~l~~~r~~~~~~~~kAvlT~tN~~Wt~~~L~~El~~E 53 (58)
T PF12646_consen 3 FLLFSGFS---GEELDKFLDALRKAGIPIPLKAVLTPTNINWTLKDLLEELKEE 53 (58)
T ss_pred EEEECCCC---HHHHHHHHHHHHHcCCCcceEEEECCCcccCcHHHHHHHHHHH
Confidence 34555543 24678899999999998777777765 3667777654
No 345
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=26.68 E-value=42 Score=38.07 Aligned_cols=39 Identities=28% Similarity=0.714 Sum_probs=26.1
Q ss_pred CceeecccccccCCCCCCceeeCCCcC----------cccccccchhhhccCCCCCCCCCC
Q 014440 363 STCFGCQQSLLASGNKAGLCVACPKCK----------KHFCLECDIYIHESLHNCPGCESL 413 (424)
Q Consensus 363 ~~C~~C~~~~~~~~~~~~~~~~C~~C~----------~~fC~dCd~fihe~lh~CPgC~~~ 413 (424)
..|..|.. ..+||.|. ..+|.-|+-= -..-+.||-|.+.
T Consensus 436 l~C~~Cg~-----------v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~-~~~p~~Cp~Cgs~ 484 (730)
T COG1198 436 LLCRDCGY-----------IAECPNCDSPLTLHKATGQLRCHYCGYQ-EPIPQSCPECGSE 484 (730)
T ss_pred eecccCCC-----------cccCCCCCcceEEecCCCeeEeCCCCCC-CCCCCCCCCCCCC
Confidence 35777752 34577775 5578888753 3556789999764
No 346
>PRK09124 pyruvate dehydrogenase; Provisional
Probab=26.59 E-value=3e+02 Score=29.92 Aligned_cols=89 Identities=12% Similarity=0.021 Sum_probs=59.0
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH-----------------
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM----------------- 230 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~----------------- 230 (424)
-+|+.+|-.|+..--.. ..|+|++|+|++.- -.++ ..+.++++.+++|-+|-+....
T Consensus 408 G~mG~~lpaAiGa~la~---p~r~vv~i~GDGsf--~m~~-~eL~Ta~~~~lpv~ivV~NN~~~g~i~~~~~~~~~~~~~ 481 (574)
T PRK09124 408 GSMANAMPQALGAQAAH---PGRQVVALSGDGGF--SMLM-GDFLSLVQLKLPVKIVVFNNSVLGFVAMEMKAGGYLTDG 481 (574)
T ss_pred ccccchHHHHHHHHHhC---CCCeEEEEecCcHH--hccH-HHHHHHHHhCCCeEEEEEeCCccccHHHHHHhcCCcccc
Confidence 34555555555433222 24678989886432 1233 3467789999998888775320
Q ss_pred -----HHHHHHHHHhCCEEEEecChhhHHHHHHhcCC
Q 014440 231 -----FICKHLCQETGGTYSVALDESHSKELILEHAP 262 (424)
Q Consensus 231 -----~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~~ 262 (424)
.-+.++|+.-|..++.+.+.++|...|.+...
T Consensus 482 ~~~~~~d~~~lA~a~G~~~~~v~~~~eL~~al~~a~~ 518 (574)
T PRK09124 482 TDLHNPDFAAIAEACGITGIRVEKASELDGALQRAFA 518 (574)
T ss_pred CcCCCCCHHHHHHHCCCeEEEeCCHHHHHHHHHHHHh
Confidence 12567888889999999999999999887653
No 347
>PRK07789 acetolactate synthase 1 catalytic subunit; Validated
Probab=26.57 E-value=3.1e+02 Score=30.19 Aligned_cols=89 Identities=12% Similarity=0.020 Sum_probs=60.8
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH-----------------
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM----------------- 230 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~----------------- 230 (424)
-+++-||-.|+..--.. ..|+|+.|+|++.- . .+ .+.+.++.+.+++|-+|-+....
T Consensus 447 G~mG~glpaaiGa~la~---p~~~Vv~i~GDG~f-~-m~-~~eL~Ta~~~~lpv~ivV~NN~~~g~i~~~q~~~~~~~~~ 520 (612)
T PRK07789 447 GTMGYAVPAAMGAKVGR---PDKEVWAIDGDGCF-Q-MT-NQELATCAIEGIPIKVALINNGNLGMVRQWQTLFYEERYS 520 (612)
T ss_pred ccccchhhhHHhhhccC---CCCcEEEEEcchhh-h-cc-HHHHHHHHHcCCCeEEEEEECCchHHHHHHHHHhhCCCcc
Confidence 45666666666433222 24678888876421 1 12 25578889999998888775320
Q ss_pred -----------HHHHHHHHHhCCEEEEecChhhHHHHHHhcCC
Q 014440 231 -----------FICKHLCQETGGTYSVALDESHSKELILEHAP 262 (424)
Q Consensus 231 -----------~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~~ 262 (424)
.-+.++|+.-|+.|+.+.+.++|...|...+.
T Consensus 521 ~~~~~~~~~~~~d~~~lA~a~G~~~~~V~~~~eL~~al~~a~~ 563 (612)
T PRK07789 521 NTDLHTHSHRIPDFVKLAEAYGCVGLRCEREEDVDAVIEKARA 563 (612)
T ss_pred eeecCcCCCCCCCHHHHHHHCCCeEEEECCHHHHHHHHHHHHh
Confidence 02577999999999999999999998877763
No 348
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=26.52 E-value=39 Score=31.64 Aligned_cols=24 Identities=29% Similarity=0.740 Sum_probs=15.4
Q ss_pred CCceeecccccccCCCCCCceeeCCCcCcc
Q 014440 362 RSTCFGCQQSLLASGNKAGLCVACPKCKKH 391 (424)
Q Consensus 362 ~~~C~~C~~~~~~~~~~~~~~~~C~~C~~~ 391 (424)
...|.||-+.|+.+. -.||.|++.
T Consensus 139 ~~rC~GC~~~f~~~~------~~Cp~CG~~ 162 (177)
T COG1439 139 RLRCHGCKRIFPEPK------DFCPICGSP 162 (177)
T ss_pred eEEEecCceecCCCC------CcCCCCCCc
Confidence 346888888887321 247777764
No 349
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=26.44 E-value=40 Score=35.24 Aligned_cols=90 Identities=19% Similarity=0.473 Sum_probs=49.6
Q ss_pred eEEcCCCCccccCCCCCCCCCCceecCchhHHhhhcccCCCCCCcccCcc-cccc----ccCCCCCceeecccccccCCC
Q 014440 303 GYTCPRCKARVCELPTECRICGLQLVSSPHLARSYHHLFPIAPFDEATPS-RLND----LHNISRSTCFGCQQSLLASGN 377 (424)
Q Consensus 303 Gy~Cp~C~s~~C~lP~~C~~C~l~Lvs~phLarsyhhl~p~~~f~~~~~~-~~~~----~~~~~~~~C~~C~~~~~~~~~ 377 (424)
--.|+.|+..| |--|+.. ||-..-...|++..+. ..+. ..++.-+.|.-|...+....
T Consensus 258 ~~~C~~C~~~f------Cv~C~~~----------wh~~~sC~eykk~~~~~~~d~~~~~~la~~wr~CpkC~~~ie~~~- 320 (384)
T KOG1812|consen 258 RRPCVKCHELF------CVKCKVP----------WHANLSCEEYKKLNPEEYVDDITLKYLAKRWRQCPKCKFMIELSE- 320 (384)
T ss_pred ccccccCCCce------eecCCCc----------CCCCCCHHHHHHhCCcccccHHHHHHHHHhcCcCcccceeeeecC-
Confidence 34688888887 5556665 5533333334333211 0000 00123457888875553221
Q ss_pred CCCceeeCCCcCcccccccchhhhccCCCCCCCC
Q 014440 378 KAGLCVACPKCKKHFCLECDIYIHESLHNCPGCE 411 (424)
Q Consensus 378 ~~~~~~~C~~C~~~fC~dCd~fihe~lh~CPgC~ 411 (424)
.=....|. |++.||..|-.=.+.--+.|..|.
T Consensus 321 -GCnhm~Cr-C~~~fcy~C~~~~~~~~~~~~~~~ 352 (384)
T KOG1812|consen 321 -GCNHMTCR-CGHQFCYMCGGDWKTHNGECYECC 352 (384)
T ss_pred -CcceEEee-ccccchhhcCcchhhCCccccCcc
Confidence 12367999 999999999854444445555443
No 350
>PHA02926 zinc finger-like protein; Provisional
Probab=26.24 E-value=43 Score=32.63 Aligned_cols=52 Identities=21% Similarity=0.508 Sum_probs=31.6
Q ss_pred CCCceeecccccccCCCCCCcee-eCCCcCcccccccchhhhcc------CCCCCCCCC
Q 014440 361 SRSTCFGCQQSLLASGNKAGLCV-ACPKCKKHFCLECDIYIHES------LHNCPGCES 412 (424)
Q Consensus 361 ~~~~C~~C~~~~~~~~~~~~~~~-~C~~C~~~fC~dCd~fihe~------lh~CPgC~~ 412 (424)
....|.-|.-....+......+| .=+.|++.||+.|=.--.++ ...||-|-.
T Consensus 169 kE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~ 227 (242)
T PHA02926 169 KEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRT 227 (242)
T ss_pred CCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcc
Confidence 35689999854422110000011 24589999999997654443 567999965
No 351
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=25.82 E-value=47 Score=33.85 Aligned_cols=41 Identities=20% Similarity=0.540 Sum_probs=24.7
Q ss_pred ceeecccccccCCCCCCceeeCCCcCcccccccchh-h-----hccCCCCCCCCC
Q 014440 364 TCFGCQQSLLASGNKAGLCVACPKCKKHFCLECDIY-I-----HESLHNCPGCES 412 (424)
Q Consensus 364 ~C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~dCd~f-i-----he~lh~CPgC~~ 412 (424)
+|..|...-.- .+-.|+.|++.-=+ +.| + +..+..|-.|..
T Consensus 214 ~CslC~teW~~------~R~~C~~Cg~~~~l--~y~~~~~~~~~~r~e~C~~C~~ 260 (309)
T PRK03564 214 HCNLCESEWHV------VRVKCSNCEQSGKL--HYWSLDSEQAAVKAESCGDCGT 260 (309)
T ss_pred EcCCCCCcccc------cCccCCCCCCCCce--eeeeecCCCcceEeeecccccc
Confidence 78899755532 25679999885311 112 1 234578888865
No 352
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=25.56 E-value=33 Score=29.43 Aligned_cols=27 Identities=26% Similarity=0.540 Sum_probs=17.9
Q ss_pred ceeeCCCcCcccccccchhhhccCCCCCCCCCC
Q 014440 381 LCVACPKCKKHFCLECDIYIHESLHNCPGCESL 413 (424)
Q Consensus 381 ~~~~C~~C~~~fC~dCd~fihe~lh~CPgC~~~ 413 (424)
.+.+|..|+..|=.+=..|. ||.|.+.
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~------CP~Cgs~ 95 (113)
T PF01155_consen 69 ARARCRDCGHEFEPDEFDFS------CPRCGSP 95 (113)
T ss_dssp -EEEETTTS-EEECHHCCHH-------SSSSSS
T ss_pred CcEECCCCCCEEecCCCCCC------CcCCcCC
Confidence 46889999999876654443 9999764
No 353
>TIGR03457 sulphoacet_xsc sulfoacetaldehyde acetyltransferase. Members of this protein family are sulfoacetaldehyde acetyltransferase, an enzyme of taurine utilization. Taurine, or 2-aminoethanesulfonate, can be used by bacteria as a source of carbon, nitrogen, and sulfur.
Probab=25.42 E-value=2.6e+02 Score=30.50 Aligned_cols=89 Identities=10% Similarity=0.038 Sum_probs=60.9
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH-----------------
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM----------------- 230 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~----------------- 230 (424)
.+++-||-.|+..=-.. ..+.||.|+|++.- . .+ ...+.++++.+++|-+|-+....
T Consensus 430 g~mG~~lpaaiGa~la~---p~~~Vv~i~GDG~f-~-m~-~~eL~Tavr~~lpvi~vV~NN~~yg~i~~~~~~~~~~~~~ 503 (579)
T TIGR03457 430 GNCGYAFPTIIGAKIAA---PDRPVVAYAGDGAW-G-MS-MNEIMTAVRHDIPVTAVVFRNRQWGAEKKNQVDFYNNRFV 503 (579)
T ss_pred ccccchHHHHHhhhhhC---CCCcEEEEEcchHH-h-cc-HHHHHHHHHhCCCeEEEEEECcchHHHHHHHHHhhCCcce
Confidence 45666666655533222 24678888886432 1 12 25678899999998888774320
Q ss_pred -------HHHHHHHHHhCCEEEEecChhhHHHHHHhcCC
Q 014440 231 -------FICKHLCQETGGTYSVALDESHSKELILEHAP 262 (424)
Q Consensus 231 -------~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~~ 262 (424)
.-+.++|+.-|+.+..+.+.++|...|.+...
T Consensus 504 ~~~~~~~~d~~~lA~a~G~~g~~v~~~~el~~al~~a~~ 542 (579)
T TIGR03457 504 GTELESELSFAGIADAMGAKGVVVDKPEDVGPALKKAIA 542 (579)
T ss_pred eccCCCCCCHHHHHHHCCCeEEEECCHHHHHHHHHHHHh
Confidence 13577899999999999999999999888763
No 354
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=25.37 E-value=50 Score=29.93 Aligned_cols=29 Identities=28% Similarity=0.581 Sum_probs=22.3
Q ss_pred ceeeCCCcCcccccccchhhhccCCCCCCCCCC
Q 014440 381 LCVACPKCKKHFCLECDIYIHESLHNCPGCESL 413 (424)
Q Consensus 381 ~~~~C~~C~~~fC~dCd~fihe~lh~CPgC~~~ 413 (424)
+.|+|.+|+....+. . =+.|.-||.|...
T Consensus 111 G~l~C~~Cg~~~~~~---~-~~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 111 GTLVCENCGHEVELT---H-PERLPPCPKCGHT 139 (146)
T ss_pred ceEecccCCCEEEec---C-CCcCCCCCCCCCC
Confidence 468999999988875 1 3678999999753
No 355
>PRK05858 hypothetical protein; Provisional
Probab=25.35 E-value=3.1e+02 Score=29.67 Aligned_cols=89 Identities=6% Similarity=-0.023 Sum_probs=59.7
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH-----------------
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM----------------- 230 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~----------------- 230 (424)
-+++.||-.|+..--.. ..|+||.|+|++.- . ..+ ..+.++.+.+++|-+|-+-...
T Consensus 407 gsmG~~lp~aiGa~la~---p~r~vv~i~GDG~f-~-~~~-~eL~Ta~~~~lpi~ivV~NN~~y~~~~~~~~~~~~~~~~ 480 (542)
T PRK05858 407 GCLGTGPGYALAARLAR---PSRQVVLLQGDGAF-G-FSL-MDVDTLVRHNLPVVSVIGNNGIWGLEKHPMEALYGYDVA 480 (542)
T ss_pred cccccchhHHHHHHHhC---CCCcEEEEEcCchh-c-CcH-HHHHHHHHcCCCEEEEEEeCCchhhHHHHHHHhcCCccc
Confidence 45555555554432222 25678888886432 1 223 3466777899999888886421
Q ss_pred ------HHHHHHHHHhCCEEEEecChhhHHHHHHhcCC
Q 014440 231 ------FICKHLCQETGGTYSVALDESHSKELILEHAP 262 (424)
Q Consensus 231 ------~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~~ 262 (424)
.-+.++|+.-|+.+..+.+.++|...|.+.+.
T Consensus 481 ~~~~~~~d~~~lA~a~G~~~~~v~~~~eL~~al~~a~~ 518 (542)
T PRK05858 481 ADLRPGTRYDEVVRALGGHGELVTVPAELGPALERAFA 518 (542)
T ss_pred cccCCCCCHHHHHHHCCCeEEEeCCHHHHHHHHHHHHh
Confidence 12357999999999999999999999987653
No 356
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=25.31 E-value=47 Score=29.70 Aligned_cols=24 Identities=25% Similarity=0.621 Sum_probs=21.8
Q ss_pred eEEcCCCCccccCCCCCCCCCCce
Q 014440 303 GYTCPRCKARVCELPTECRICGLQ 326 (424)
Q Consensus 303 Gy~Cp~C~s~~C~lP~~C~~C~l~ 326 (424)
|=-|+.|+++|.-.-..|+.|+..
T Consensus 29 g~kC~~CG~v~~PPr~~Cp~C~~~ 52 (140)
T COG1545 29 GTKCKKCGRVYFPPRAYCPKCGSE 52 (140)
T ss_pred EEEcCCCCeEEcCCcccCCCCCCC
Confidence 778999999998888899999976
No 357
>PRK14873 primosome assembly protein PriA; Provisional
Probab=25.27 E-value=46 Score=37.36 Aligned_cols=39 Identities=26% Similarity=0.606 Sum_probs=28.7
Q ss_pred CCceeecccccccCCCCCCceeeCCCcC----------cccccccchhhhccCCCCCCCCCC
Q 014440 362 RSTCFGCQQSLLASGNKAGLCVACPKCK----------KHFCLECDIYIHESLHNCPGCESL 413 (424)
Q Consensus 362 ~~~C~~C~~~~~~~~~~~~~~~~C~~C~----------~~fC~dCd~fihe~lh~CPgC~~~ 413 (424)
...|..|.. ..+||.|. ...|.-|.. +..-..||.|.+.
T Consensus 383 ~l~C~~Cg~-----------~~~C~~C~~~L~~h~~~~~l~Ch~CG~--~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 383 SLACARCRT-----------PARCRHCTGPLGLPSAGGTPRCRWCGR--AAPDWRCPRCGSD 431 (665)
T ss_pred eeEhhhCcC-----------eeECCCCCCceeEecCCCeeECCCCcC--CCcCccCCCCcCC
Confidence 447999972 35699997 356999986 3467899999763
No 358
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=25.16 E-value=22 Score=37.85 Aligned_cols=64 Identities=23% Similarity=0.446 Sum_probs=34.3
Q ss_pred CCCCCCCCCC------ceecCchhHHhhhccc---------CCCCCCcccCccccccccCCCCCceeecccccccCCCCC
Q 014440 315 ELPTECRICG------LQLVSSPHLARSYHHL---------FPIAPFDEATPSRLNDLHNISRSTCFGCQQSLLASGNKA 379 (424)
Q Consensus 315 ~lP~~C~~C~------l~Lvs~phLarsyhhl---------~p~~~f~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~~~ 379 (424)
+||+ ||+|= ++-|.+.|--.||||- +||--|-.-+ ....+..|..|...+
T Consensus 174 ELPT-CpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~~scpvcR~~q~p-------~~ve~~~c~~c~~~~------- 238 (493)
T KOG0804|consen 174 ELPT-CPVCLERMDSSTTGILTILCNHSFHCSCLMKWWDSSCPVCRYCQSP-------SVVESSLCLACGCTE------- 238 (493)
T ss_pred cCCC-cchhHhhcCccccceeeeecccccchHHHhhcccCcChhhhhhcCc-------chhhhhhhhhhcccc-------
Confidence 4433 66664 3444555667788873 3433333221 011244566665333
Q ss_pred CceeeCCCcCccccc
Q 014440 380 GLCVACPKCKKHFCL 394 (424)
Q Consensus 380 ~~~~~C~~C~~~fC~ 394 (424)
..|.|=.|+++-|.
T Consensus 239 -~LwicliCg~vgcg 252 (493)
T KOG0804|consen 239 -DLWICLICGNVGCG 252 (493)
T ss_pred -cEEEEEEccceecc
Confidence 25888888887764
No 359
>PF02780 Transketolase_C: Transketolase, C-terminal domain; InterPro: IPR005476 Transketolase 2.2.1.1 from EC (TK) catalyzes the reversible transfer of a two-carbon ketol unit from xylulose 5-phosphate to an aldose receptor, such as ribose 5-phosphate, to form sedoheptulose 7-phosphate and glyceraldehyde 3- phosphate. This enzyme, together with transaldolase, provides a link between the glycolytic and pentose-phosphate pathways. TK requires thiamine pyrophosphate as a cofactor. In most sources where TK has been purified, it is a homodimer of approximately 70 Kd subunits. TK sequences from a variety of eukaryotic and prokaryotic sources [, ] show that the enzyme has been evolutionarily conserved. In the peroxisomes of methylotrophic yeast Pichia angusta (Yeast) (Hansenula polymorpha), there is a highly related enzyme, dihydroxy-acetone synthase (DHAS) 2.2.1.3 from EC (also known as formaldehyde transketolase), which exhibits a very unusual specificity by including formaldehyde amongst its substrates. 1-deoxyxylulose-5-phosphate synthase (DXP synthase) [] is an enzyme so far found in bacteria (gene dxs) and plants (gene CLA1) which catalyzes the thiamine pyrophosphoate-dependent acyloin condensation reaction between carbon atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D- xylulose-5-phosphate (dxp), a precursor in the biosynthetic pathway to isoprenoids, thiamine (vitamin B1), and pyridoxol (vitamin B6). DXP synthase is evolutionary related to TK. The N-terminal section, contains a histidine residue which appears to function in proton transfer during catalysis []. In the central section there are conserved acidic residues that are part of the active cleft and may participate in substrate-binding []. This family includes transketolase enzymes 2.2.1.1 from EC and also partially matches to 2-oxoisovalerate dehydrogenase beta subunit P37941 from SWISSPROT 1.2.4.4 from EC. Both these enzymes utilise thiamine pyrophosphate as a cofactor, suggesting there may be common aspects in their mechanism of catalysis.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 1NGS_B 1TKA_A 1TRK_B 1TKB_A 1GPU_B 1AY0_B 1TKC_B 2E6K_A 3JU3_A 2R8P_B ....
Probab=25.15 E-value=88 Score=26.59 Aligned_cols=49 Identities=18% Similarity=0.239 Sum_probs=34.5
Q ss_pred cEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecc----hHHHHHHHHHHhC
Q 014440 190 REVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSA----EMFICKHLCQETG 241 (424)
Q Consensus 190 reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~----e~~iLq~iA~~TG 241 (424)
++|+||.-+.. -....++++.|++.||.+.+|.+-. +...|.+++..++
T Consensus 10 ~di~iia~G~~---~~~al~A~~~L~~~Gi~~~vi~~~~i~P~d~~~l~~~~~~~~ 62 (124)
T PF02780_consen 10 ADITIIAYGSM---VEEALEAAEELEEEGIKAGVIDLRTIKPFDEEALLESLKKTG 62 (124)
T ss_dssp SSEEEEEETTH---HHHHHHHHHHHHHTTCEEEEEEEEEEESSBHHHHHHHSHHHH
T ss_pred CCEEEEeehHH---HHHHHHHHHHHHHcCCceeEEeeEEEecccccchHHHHHHhc
Confidence 35677754322 1345789999999999999999874 4566777666665
No 360
>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins. TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].
Probab=25.13 E-value=5.1e+02 Score=26.35 Aligned_cols=126 Identities=15% Similarity=0.180 Sum_probs=68.6
Q ss_pred hccccceEEEEEeCCHhhhcCCCCCChHHHHHHHHHHHHHHHhccCCCCcEEEEEecCCceEEeeCCCCCHHHHHHHHhh
Q 014440 81 QKGLIRYLYIVIDLSRAAAEMDFRPSRMVVVAKQVEAFVREFFDQNPLSQIGLVTVKDGVANCLTDLGGSPESHIKALMG 160 (424)
Q Consensus 81 r~GiiR~lvlvLD~S~SM~~~D~~P~RL~~a~~~l~~Fi~~~~~qnP~sqlGII~~~~g~A~~lspLT~d~~~~~~~L~~ 160 (424)
++.-|..+.||=|.. .-++. .++.|.+.|......++.- + -.-.+..|.+.+...+...|-.
T Consensus 57 ~~~Rmp~lLivG~sn------------nGKT~-Ii~rF~~~hp~~~d~~~~~---~--PVv~vq~P~~p~~~~~Y~~IL~ 118 (302)
T PF05621_consen 57 KRHRMPNLLIVGDSN------------NGKTM-IIERFRRLHPPQSDEDAER---I--PVVYVQMPPEPDERRFYSAILE 118 (302)
T ss_pred cccCCCceEEecCCC------------CcHHH-HHHHHHHHCCCCCCCCCcc---c--cEEEEecCCCCChHHHHHHHHH
Confidence 445566777765543 11121 3567777654332222110 0 1224557778887777666655
Q ss_pred hh-CCCC-cchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCC------CCccCHHHHHHHHHhCCcEEEEEEecchH
Q 014440 161 KL-GCSG-DSSIQNALDLVHGLLNQIPSYGHREVLILYSALST------CDPGDIMETIQKCKESKIRCSVIGLSAEM 230 (424)
Q Consensus 161 ~~-~~~G-~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t------~dp~~i~~~i~~akk~~IrV~vIgLg~e~ 230 (424)
.+ .|.. ..++..--.+++..|+.. +.| +||| +...+ .....+.++++.+ .+.-+|.+|++|+..
T Consensus 119 ~lgaP~~~~~~~~~~~~~~~~llr~~---~vr-mLII-DE~H~lLaGs~~~qr~~Ln~LK~L-~NeL~ipiV~vGt~~ 190 (302)
T PF05621_consen 119 ALGAPYRPRDRVAKLEQQVLRLLRRL---GVR-MLII-DEFHNLLAGSYRKQREFLNALKFL-GNELQIPIVGVGTRE 190 (302)
T ss_pred HhCcccCCCCCHHHHHHHHHHHHHHc---CCc-EEEe-echHHHhcccHHHHHHHHHHHHHH-hhccCCCeEEeccHH
Confidence 44 3432 345665556777888765 344 5554 32211 1223455777776 566789999999764
No 361
>cd01979 Pchlide_reductase_N Pchlide_reductase_N: N protein of the NB protein complex of Protochlorophyllide (Pchlide)_reductase. Pchlide reductase catalyzes the reductive formation of chlorophyllide (chlide) from protochlorophyllide (pchlide) during biosynthesis of chlorophylls and bacteriochlorophylls. This group contains both the light-independent Pchlide reductase (DPOR) and light-dependent Pchlide reductase (LPOR). Angiosperms contain only LPOR, cyanobacteria, algae and gymnosperms contain both DPOR and LPOR, primitive anoxygenic photosynthetic bacteria contain only DPOR. NB is structurally similar to the FeMo protein of nitrogenase, forming an N2B2 heterotetramer. N and B are homologous to the FeMo alpha and beta subunits respectively. Also in common with nitrogenase in vitro DPOR activity requires ATP hydrolysis and dithoionite or ferredoxin as electron donor. The NB protein complex may serve as a catalytic site for Pchlide reduction similar to MoFe for nitrogen reduction.
Probab=25.12 E-value=4.7e+02 Score=27.08 Aligned_cols=79 Identities=11% Similarity=-0.037 Sum_probs=40.9
Q ss_pred HHHHHHHHHhCCcEEEEEEecc-hHHHHH-HHHHHhCCEEEE-ecChhhHHHHHHhcCCCCccc-hhhhhhheeeecCCC
Q 014440 207 IMETIQKCKESKIRCSVIGLSA-EMFICK-HLCQETGGTYSV-ALDESHSKELILEHAPPPPAI-AEFAIASLIKMGFPQ 282 (424)
Q Consensus 207 i~~~i~~akk~~IrV~vIgLg~-e~~iLq-~iA~~TGG~Y~~-~~d~~~L~~lL~~~~~pp~~~-~~~~~~~Li~mGFP~ 282 (424)
....++.+.+.|+.|-.+|-.. .....+ .+....++.... ..|..++.+++.+.- |.-.- .....-.|+++|||.
T Consensus 288 ~~~la~~L~elGm~vv~~~t~~~~~~~~~~~~~~l~~~~~v~~~~d~~~l~~~i~~~~-pDlli~~~~~a~pl~r~G~P~ 366 (396)
T cd01979 288 EIPLARFLTRCGMIVVEVGTPYLDKRFQAAELELLPPMVRIVEKPDNYRQLDRIRELR-PDLVVTGLGLANPLEARGITT 366 (396)
T ss_pred HHHHHHHHHHCCCEEEeeCCCcCChHHHHHHHHhcCCCCeEEECCCHHHHHHHHHhcC-CCEEEecccccCcHHhCCCcc
Confidence 4567888889999887765432 111112 222222343222 234444455554432 32221 112335799999999
Q ss_pred CCCC
Q 014440 283 RAGE 286 (424)
Q Consensus 283 ~~~~ 286 (424)
+...
T Consensus 367 ~dr~ 370 (396)
T cd01979 367 KWSI 370 (396)
T ss_pred eeec
Confidence 8654
No 362
>KOG2858 consensus Uncharacterized conserved protein [General function prediction only]
Probab=25.12 E-value=34 Score=35.37 Aligned_cols=40 Identities=33% Similarity=0.711 Sum_probs=32.5
Q ss_pred CCceeecccccccCCCCCCceeeCCCcCcccc-cccchhhhccCCCCCCC
Q 014440 362 RSTCFGCQQSLLASGNKAGLCVACPKCKKHFC-LECDIYIHESLHNCPGC 410 (424)
Q Consensus 362 ~~~C~~C~~~~~~~~~~~~~~~~C~~C~~~fC-~dCd~fihe~lh~CPgC 410 (424)
...|--|++. ...|.||+|...|| ++|.. .|..+.+|-|=
T Consensus 17 ~vlCgVClkn--------E~KYkCPRCl~rtCsLeCsk-kHK~~dnCsG~ 57 (390)
T KOG2858|consen 17 SVLCGVCLKN--------EPKYKCPRCLARTCSLECSK-KHKIGDNCSGS 57 (390)
T ss_pred hhhhhhcccC--------cccccCcchhhhheeccccc-cccccCCCcCC
Confidence 5689999833 23599999999997 68865 79999999886
No 363
>cd01973 Nitrogenase_VFe_beta_like Nitrogenase_VFe_beta -like: Nitrogenase VFe protein, beta subunit like. This group contains proteins similar to the beta subunits of the VFe protein of the vanadium-dependent (V-) nitrogenase. Nitrogenase catalyzes the ATP-dependent reduction of dinitrogen (N2) to ammonia. In addition to V-nitrogenase there is a molybdenum (Mo)-dependent nitrogenase and an iron only (Fe-) nitrogenase. The Mo-nitrogenase is the most widespread and best characterized of these systems. These systems consist of component 1 (VFe protein, FeFe protein or, MoFe protein respectively) and, component 2 (Fe protein). MoFe is an alpha2beta2 tetramer, V-and Fe- nitrogenases are alpha2beta2delta2 hexamers. The alpha and beta subunits of VFe and FeFe are similar to the alpha and beta subunits of MoFe. For MoFe each alphabeta pair contains one P-cluster (at the alphabeta interface) and, one molecule of iron molybdenum cofactor (FeMoco) contained within the alpha subunit. The Fe p
Probab=25.12 E-value=8.5e+02 Score=25.92 Aligned_cols=78 Identities=13% Similarity=0.112 Sum_probs=50.5
Q ss_pred HHHHHHHHHhCCcEEEEEEecch------HHHHHHHHHHhC--CEEEEecChhhHHHHHHhc-CCCCccch--------h
Q 014440 207 IMETIQKCKESKIRCSVIGLSAE------MFICKHLCQETG--GTYSVALDESHSKELILEH-APPPPAIA--------E 269 (424)
Q Consensus 207 i~~~i~~akk~~IrV~vIgLg~e------~~iLq~iA~~TG--G~Y~~~~d~~~L~~lL~~~-~~pp~~~~--------~ 269 (424)
.....+.+.+.|+.+-.+.++++ ...++++.+..+ ..-+...|..++.+++... ..|+-.-. .
T Consensus 317 ~~~l~~fl~elGm~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~vi~~~d~~e~~~~i~~~~~~~dliig~s~~~~~A~ 396 (454)
T cd01973 317 VIGLAEFCLEVEMKPVLLLLGDDNSKYKKDPRIKALKEKADYDMEIVTNADLWELEKRIKNKGLELDLILGHSKGRYIAI 396 (454)
T ss_pred HHHHHHHHHHCCCeEEEEEECCCCcccchhHHHHHHHhhcCCCceEEECCCHHHHHHHHHhcCCCCCEEEECCccHHHHH
Confidence 34556677789999888888763 456777755443 3444556777888887765 33443321 1
Q ss_pred hhhhheeeecCCCCC
Q 014440 270 FAIASLIKMGFPQRA 284 (424)
Q Consensus 270 ~~~~~Li~mGFP~~~ 284 (424)
...-.++++|||...
T Consensus 397 ~~gip~~~~g~Pv~d 411 (454)
T cd01973 397 DNNIPMVRVGFPTFD 411 (454)
T ss_pred HcCCCEEEecCCeee
Confidence 234478999999864
No 364
>cd04922 ACT_AKi-HSDH-ThrA_2 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH). This CD includes the second of two ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH). The ACT domains are positioned between the N-terminal catalytic domain of AK and the C-terminal HSDH domain found in bacteria (Escherichia coli (EC) ThrA) and higher plants (Zea mays AK-HSDH). AK and HSDH are the first and third enzymes in the biosynthetic pathway of the aspartate family of amino acids. AK catalyzes the phosphorylation of Asp to P-aspartyl phosphate. HSDH catalyzes the NADPH-dependent conversion of Asp 3-semialdehyde to homoserine. HSDH is the first committed reaction in the branch of the pathway that leads to Thr and Met. In E. coli, ThrA is subject to allosteric regulation by the end product L-threonine and the native enzyme is reported to be tetrameric. As with bacteria, plant AK and HSDH are feedback inhibited by pathwa
Probab=25.05 E-value=1.9e+02 Score=21.06 Aligned_cols=36 Identities=14% Similarity=0.142 Sum_probs=25.0
Q ss_pred EEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecc
Q 014440 193 LILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSA 228 (424)
Q Consensus 193 LvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~ 228 (424)
|=+.|..-..+++-..++++.+.+.||+|+.|+-++
T Consensus 4 isvvg~~~~~~~~~~~~i~~~l~~~~I~v~~i~~~~ 39 (66)
T cd04922 4 LALVGDGMAGTPGVAATFFSALAKANVNIRAIAQGS 39 (66)
T ss_pred EEEECCCCCCCccHHHHHHHHHHHCCCCEEEEEecC
Confidence 334454333345556688999999999999997653
No 365
>PRK09107 acetolactate synthase 3 catalytic subunit; Validated
Probab=25.04 E-value=3.7e+02 Score=29.55 Aligned_cols=90 Identities=13% Similarity=0.077 Sum_probs=61.1
Q ss_pred CcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH---------------
Q 014440 166 GDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM--------------- 230 (424)
Q Consensus 166 G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~--------------- 230 (424)
|..+++-||-.|+..=-..| .|+|+.|.|++.- -..+ ..+.++.+.+++|-+|-+....
T Consensus 428 ~~gsmG~glpaaiGa~lA~p---~r~Vv~i~GDG~f--~m~~-~EL~Ta~r~~lpvi~vV~NN~~y~~i~~~q~~~~~~~ 501 (595)
T PRK09107 428 GLGTMGYGLPAALGVQIAHP---DALVIDIAGDASI--QMCI-QEMSTAVQYNLPVKIFILNNQYMGMVRQWQQLLHGNR 501 (595)
T ss_pred CchhhhhhHHHHHHHHHhCC---CCeEEEEEcCchh--hccH-HHHHHHHHhCCCeEEEEEeCCccHHHHHHHHHHhCCc
Confidence 33566666666665433322 5678888886431 1122 4588999999999988886321
Q ss_pred ---------HHHHHHHHHhCCEEEEecChhhHHHHHHhcC
Q 014440 231 ---------FICKHLCQETGGTYSVALDESHSKELILEHA 261 (424)
Q Consensus 231 ---------~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~ 261 (424)
.-+.++|+..|+.++.+.+.++|...|....
T Consensus 502 ~~~~~~~~~~d~~~lA~a~G~~~~~v~~~~el~~al~~a~ 541 (595)
T PRK09107 502 LSHSYTEAMPDFVKLAEAYGAVGIRCEKPGDLDDAIQEMI 541 (595)
T ss_pred cccccCCCCCCHHHHHHHCCCeEEEECCHHHHHHHHHHHH
Confidence 1245788888888888888888888887765
No 366
>PRK03815 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=24.99 E-value=6.6e+02 Score=26.20 Aligned_cols=44 Identities=9% Similarity=0.141 Sum_probs=22.5
Q ss_pred cEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchHHHHHHHH
Q 014440 190 REVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEMFICKHLC 237 (424)
Q Consensus 190 reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~~iLq~iA 237 (424)
++|++|+|+... ..+.++.++.+++..+. ++-+|.....+++..
T Consensus 299 ~~ii~IlGG~~k--~~~~~~l~~~~~~~~~~--v~~~G~~~~~~~~~~ 342 (401)
T PRK03815 299 KKIHLILGGDDK--GVDLTPLFEFMKNLNIE--LYAIGSNTEKIQALA 342 (401)
T ss_pred CCEEEEECCCCC--CCCHHHHHHHHHhhCcE--EEEECCCHHHHHHHH
Confidence 356667765321 23445666666666553 444555443444443
No 367
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=24.97 E-value=22 Score=37.17 Aligned_cols=10 Identities=40% Similarity=0.869 Sum_probs=8.3
Q ss_pred HhhhcccCCC
Q 014440 334 ARSYHHLFPI 343 (424)
Q Consensus 334 arsyhhl~p~ 343 (424)
+--|+|+.||
T Consensus 290 rppy~~~iPL 299 (374)
T TIGR00375 290 RPPYVHLIPL 299 (374)
T ss_pred CCCeeeeCCH
Confidence 5569999998
No 368
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.96 E-value=38 Score=29.41 Aligned_cols=25 Identities=16% Similarity=0.216 Sum_probs=21.3
Q ss_pred eEEcCCCCccccCC---CCCCCCCCcee
Q 014440 303 GYTCPRCKARVCEL---PTECRICGLQL 327 (424)
Q Consensus 303 Gy~Cp~C~s~~C~l---P~~C~~C~l~L 327 (424)
--+||-|++||=.| |..||-||.+.
T Consensus 9 KridPetg~KFYDLNrdPiVsPytG~s~ 36 (129)
T COG4530 9 KRIDPETGKKFYDLNRDPIVSPYTGKSY 36 (129)
T ss_pred cccCccccchhhccCCCccccCcccccc
Confidence 35899999999876 78999999874
No 369
>cd01017 AdcA Metal binding protein AcdA. These proteins have been shown to function in the ABC uptake of Zn2+ and Mn2+ and in competence for genetic transformation and adhesion. The AcdA proteins belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and they bind their ligand in the cleft between these domains. In addition, many of these proteins have a low complexity region containing metal binding histidine-rich motif (repetitive HDH sequence).
Probab=24.87 E-value=3.1e+02 Score=26.90 Aligned_cols=43 Identities=26% Similarity=0.359 Sum_probs=36.3
Q ss_pred ccCHHHHHHHHHhCCcEEEEEEecchHHHHHHHHHHhCCEEEE
Q 014440 204 PGDIMETIQKCKESKIRCSVIGLSAEMFICKHLCQETGGTYSV 246 (424)
Q Consensus 204 p~~i~~~i~~akk~~IrV~vIgLg~e~~iLq~iA~~TGG~Y~~ 246 (424)
+.++.++++.+++.+|++-.+--.......+.||+.||.....
T Consensus 206 ~~~l~~l~~~ik~~~v~~if~e~~~~~~~~~~la~~~g~~v~~ 248 (282)
T cd01017 206 PKQLAELVEFVKKSDVKYIFFEENASSKIAETLAKETGAKLLV 248 (282)
T ss_pred HHHHHHHHHHHHHcCCCEEEEeCCCChHHHHHHHHHcCCcEEE
Confidence 4477899999999999987777777789999999999987653
No 370
>PRK07119 2-ketoisovalerate ferredoxin reductase; Validated
Probab=24.79 E-value=2.9e+02 Score=28.42 Aligned_cols=69 Identities=13% Similarity=0.105 Sum_probs=47.2
Q ss_pred cEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecc----hHHHHHHHHHHhCCEEEEecChhhHHHHHHhcC
Q 014440 190 REVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSA----EMFICKHLCQETGGTYSVALDESHSKELILEHA 261 (424)
Q Consensus 190 reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~----e~~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~ 261 (424)
.+++||..+.. .....++++.|++.||++.+|.+.. +...++++.+.++-...+-.+...|...+...+
T Consensus 247 ad~~iva~Gs~---~~~a~eA~~~L~~~Gi~v~vi~~~~l~Pfp~~~i~~~l~~~k~VivvE~n~g~l~~ei~~~~ 319 (352)
T PRK07119 247 AELVLVAYGTS---ARIAKSAVDMAREEGIKVGLFRPITLWPFPEKALEELADKGKGFLSVEMSMGQMVEDVRLAV 319 (352)
T ss_pred CCEEEEEcCcc---HHHHHHHHHHHHHcCCeEEEEeeceecCCCHHHHHHHHhCCCEEEEEeCCccHHHHHHHHHh
Confidence 45676664422 2456789999999999999999875 345677777777766666566555655555443
No 371
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=24.72 E-value=55 Score=25.04 Aligned_cols=46 Identities=28% Similarity=0.621 Sum_probs=31.9
Q ss_pred cceeeecCCccccC--eEEcCCCCccccCC--C-CCCCCCCceecCchhHH
Q 014440 289 ISICSCHKEVKIGV--GYTCPRCKARVCEL--P-TECRICGLQLVSSPHLA 334 (424)
Q Consensus 289 ~a~C~CH~~~~~~~--Gy~Cp~C~s~~C~l--P-~~C~~C~l~Lvs~phLa 334 (424)
+..|+|..+.=... .=.|..|+-|+|+. | ..|+-||..|+++....
T Consensus 2 r~~C~C~a~~H~L~~~~~NCl~CGkIiC~~Eg~~~pC~fCg~~l~~~~~~~ 52 (57)
T PF06221_consen 2 RRKCNCQARRHPLFPYAPNCLNCGKIICEQEGPLGPCPFCGTPLLSSEERQ 52 (57)
T ss_pred CcccccccccCCCccccccccccChhhcccccCcCcCCCCCCcccCHHHHH
Confidence 34688876432221 33699999999974 3 68999998888766544
No 372
>cd06433 GT_2_WfgS_like WfgS and WfeV are involved in O-antigen biosynthesis. Escherichia coli WfgS and Shigella dysenteriae WfeV are glycosyltransferase 2 family enzymes involved in O-antigen biosynthesis. GT-2 enzymes have GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. Glycosyltransferases have been classified into more than 90 distinct sequence based families.
Probab=24.68 E-value=4.6e+02 Score=22.67 Aligned_cols=59 Identities=14% Similarity=0.030 Sum_probs=30.8
Q ss_pred cEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchHHHHHHHHHHhCCEEEEecChhh
Q 014440 190 REVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEMFICKHLCQETGGTYSVALDESH 252 (424)
Q Consensus 190 reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~~iLq~iA~~TGG~Y~~~~d~~~ 252 (424)
-||||+-++ .+ | +..+.++.+.+..+.+..-.=..-..-+....+...|.|....|.++
T Consensus 28 ~evivvDd~-s~-d--~~~~~~~~~~~~~~~~~~~~~~g~~~a~n~~~~~a~~~~v~~ld~D~ 86 (202)
T cd06433 28 IEYIVIDGG-ST-D--GTVDIIKKYEDKITYWISEPDKGIYDAMNKGIALATGDIIGFLNSDD 86 (202)
T ss_pred ceEEEEeCC-CC-c--cHHHHHHHhHhhcEEEEecCCcCHHHHHHHHHHHcCCCEEEEeCCCc
Confidence 467666432 22 2 23455555554423322211112245566666777899998777653
No 373
>PRK07524 hypothetical protein; Provisional
Probab=24.63 E-value=2.6e+02 Score=30.12 Aligned_cols=89 Identities=12% Similarity=0.016 Sum_probs=58.5
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH-----------------
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM----------------- 230 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~----------------- 230 (424)
.+++-||-.|+..--.. ..++|++|+|++.- -.++++ +.++.+.|++|-+|-+....
T Consensus 407 g~mG~~lp~aiGa~lA~---p~~~vv~i~GDG~f--~~~~~e-l~ta~~~~lpi~~vV~NN~~~g~i~~~~~~~~~~~~~ 480 (535)
T PRK07524 407 GTLGYGLPAAIGAALGA---PERPVVCLVGDGGL--QFTLPE-LASAVEADLPLIVLLWNNDGYGEIRRYMVARDIEPVG 480 (535)
T ss_pred ccccchHHHHHHHHHhC---CCCcEEEEEcchHH--hhhHHH-HHHHHHhCCCeEEEEEECCchHHHHHHHHHhcCCccc
Confidence 34555555554432222 25678888886532 133444 66888999998887775421
Q ss_pred -----HHHHHHHHHhCCEEEEecChhhHHHHHHhcCC
Q 014440 231 -----FICKHLCQETGGTYSVALDESHSKELILEHAP 262 (424)
Q Consensus 231 -----~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~~ 262 (424)
.-+.++|+.-|+.+..+.+.++|++.+.+...
T Consensus 481 ~~~~~~d~~~~A~a~G~~~~~v~~~~el~~al~~a~~ 517 (535)
T PRK07524 481 VDPYTPDFIALARAFGCAAERVADLEQLQAALRAAFA 517 (535)
T ss_pred cCCCCCCHHHHHHHCCCcEEEeCCHHHHHHHHHHHHh
Confidence 12467888888888888888999988887764
No 374
>PF05596 Taeniidae_ag: Taeniidae antigen; InterPro: IPR008860 This family consists of several antigen proteins from Taenia and Echinococcus (tapeworm) species.
Probab=24.54 E-value=72 Score=24.98 Aligned_cols=27 Identities=33% Similarity=0.460 Sum_probs=20.2
Q ss_pred CCChHHHHHHHHHHHHHHHhccCCCCc
Q 014440 104 RPSRMVVVAKQVEAFVREFFDQNPLSQ 130 (424)
Q Consensus 104 ~P~RL~~a~~~l~~Fi~~~~~qnP~sq 130 (424)
.|+........-..|++.||..+|++|
T Consensus 4 ~~~~~~k~~kK~i~~v~~FF~~DPlGq 30 (64)
T PF05596_consen 4 KPEDDKKSVKKWIEEVRNFFYEDPLGQ 30 (64)
T ss_pred chhhhHHhHHHHHHHHHHHhccCchHH
Confidence 466666666667789999999998553
No 375
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=24.52 E-value=40 Score=20.81 Aligned_cols=24 Identities=25% Similarity=0.703 Sum_probs=17.1
Q ss_pred eEEcCCCCccccCCCCCCCCCCce
Q 014440 303 GYTCPRCKARVCELPTECRICGLQ 326 (424)
Q Consensus 303 Gy~Cp~C~s~~C~lP~~C~~C~l~ 326 (424)
.+.|+.|....=.--..|..|++.
T Consensus 2 ~W~C~~C~~~N~~~~~~C~~C~~p 25 (26)
T smart00547 2 DWECPACTFLNFASRSKCFACGAP 25 (26)
T ss_pred cccCCCCCCcChhhhccccccCCc
Confidence 467888877665666788888764
No 376
>PF08459 UvrC_HhH_N: UvrC Helix-hairpin-helix N-terminal; InterPro: IPR001162 During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products []. The UvrC proteins contain 4 conserved regions: a central region which interacts with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases. Proteins that contain the UvrC homology region 1, IPR000305 from INTERPRO, are listed below: Prokaryotic UvrC proteins. Bacteriophage T4 END2 protein. Small subunit of ribonucleotide reductase enzyme. T4 TEV1 protein. Endonuclease specific to the thymidylate synthase (td) gene splice junction. Found in putative intron-homing endonucleases encoded by group I introns of fungi and phage. Mycobacterium hypothetical protein Y002. Exonuclease by similarity. Bacillus subtilis hypothetical protein YURQ. ; GO: 0003677 DNA binding, 0004518 nuclease activity, 0006289 nucleotide-excision repair; PDB: 3C65_A 2NRZ_A 2NRR_A 2NRX_A 2NRV_A 2NRT_A 2NRW_A.
Probab=24.41 E-value=68 Score=29.37 Aligned_cols=33 Identities=30% Similarity=0.385 Sum_probs=23.2
Q ss_pred EEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecch
Q 014440 193 LILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAE 229 (424)
Q Consensus 193 LvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e 229 (424)
|||++++ .+.+..+.+.+++.|+.|.+|||+.+
T Consensus 82 LilIDGG----~gQl~aa~~~l~~lgl~i~viglaK~ 114 (155)
T PF08459_consen 82 LILIDGG----KGQLNAAKEVLKELGLNIPVIGLAKN 114 (155)
T ss_dssp EEEESSS----HHHHHHHHHHHHCTT----EEEEESS
T ss_pred EEEEcCC----HHHHHHHHHHHHHcCCCeEEEEEEec
Confidence 6666553 46788999999999999999999864
No 377
>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.
Probab=24.37 E-value=55 Score=31.09 Aligned_cols=40 Identities=30% Similarity=0.603 Sum_probs=25.9
Q ss_pred eeCCCcCcccccccc---hhhhccCCCCCCCCCCCCCCCcccCC
Q 014440 383 VACPKCKKHFCLECD---IYIHESLHNCPGCESLRQSNPVVANE 423 (424)
Q Consensus 383 ~~C~~C~~~fC~dCd---~fihe~lh~CPgC~~~~~~~~~~~~~ 423 (424)
.+|..|+..+-.+ + .+-+..+..||.|.....++++--.|
T Consensus 110 ~~C~~C~~~~~~~-~~~~~~~~~~~p~C~~Cg~~lrP~Vv~fgE 152 (218)
T cd01407 110 VRCTKCGKEYPRD-ELQADIDREEVPRCPKCGGLLRPDVVFFGE 152 (218)
T ss_pred ceeCCCcCCCcHH-HHhHhhccCCCCcCCCCCCccCCCeEECCC
Confidence 5677777765433 1 12355678999998877777765443
No 378
>PLN03049 pyridoxine (pyridoxamine) 5'-phosphate oxidase; Provisional
Probab=23.95 E-value=1.8e+02 Score=31.24 Aligned_cols=37 Identities=19% Similarity=0.117 Sum_probs=29.7
Q ss_pred cEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecc
Q 014440 190 REVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSA 228 (424)
Q Consensus 190 reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~ 228 (424)
++|+|+.|.+.+ .||=.-++..|.+.|+.|.++-++.
T Consensus 60 ~~VlVlcG~GNN--GGDGlv~AR~L~~~G~~V~v~~~~~ 96 (462)
T PLN03049 60 RRVLALCGPGNN--GGDGLVAARHLHHFGYKPSICYPKR 96 (462)
T ss_pred CEEEEEECCCCC--HHHHHHHHHHHHHCCCceEEEEECC
Confidence 578888886543 5677888999999999999998864
No 379
>PRK11823 DNA repair protein RadA; Provisional
Probab=23.89 E-value=44 Score=35.51 Aligned_cols=24 Identities=29% Similarity=0.677 Sum_probs=22.3
Q ss_pred eEEcCCCCccccCCCCCCCCCCce
Q 014440 303 GYTCPRCKARVCELPTECRICGLQ 326 (424)
Q Consensus 303 Gy~Cp~C~s~~C~lP~~C~~C~l~ 326 (424)
.|+|..|+...=+.--.||.|+.+
T Consensus 7 ~y~C~~Cg~~~~~~~g~Cp~C~~w 30 (446)
T PRK11823 7 AYVCQECGAESPKWLGRCPECGAW 30 (446)
T ss_pred eEECCcCCCCCcccCeeCcCCCCc
Confidence 799999999999999999999964
No 380
>TIGR03111 glyc2_xrt_Gpos1 putative glycosyltransferase TIGR03111. Members of this protein family probable glycosyltransferases of family 2, whose genes are near those for Gram-positive proteins (TIGR03110) related to the proposed exosortase (TIGR02602).
Probab=23.88 E-value=4.9e+02 Score=27.26 Aligned_cols=70 Identities=14% Similarity=0.223 Sum_probs=38.8
Q ss_pred EEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEec---chHHHHHHHHHHhCCEEEEecChhh------HHHHHHhcC
Q 014440 191 EVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLS---AEMFICKHLCQETGGTYSVALDESH------SKELILEHA 261 (424)
Q Consensus 191 eILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg---~e~~iLq~iA~~TGG~Y~~~~d~~~------L~~lL~~~~ 261 (424)
+|+|+-++ ++ | +..+.++.+++..-++.++-+. +...-|....+.+.|.|++..|.++ |++++..+.
T Consensus 82 eIiVVDd~-St-D--~T~~il~~~~~~~~~v~v~~~~~~~Gka~AlN~gl~~s~g~~v~~~DaD~~~~~d~L~~l~~~f~ 157 (439)
T TIGR03111 82 DIILANNQ-ST-D--DSFQVFCRAQNEFPGLSLRYMNSDQGKAKALNAAIYNSIGKYIIHIDSDGKLHKDAIKNMVTRFE 157 (439)
T ss_pred EEEEEECC-CC-h--hHHHHHHHHHHhCCCeEEEEeCCCCCHHHHHHHHHHHccCCEEEEECCCCCcChHHHHHHHHHHH
Confidence 56555432 22 2 2344555555543233443332 2356777778888999998766653 666665554
Q ss_pred CCC
Q 014440 262 PPP 264 (424)
Q Consensus 262 ~pp 264 (424)
..|
T Consensus 158 ~~~ 160 (439)
T TIGR03111 158 NNP 160 (439)
T ss_pred hCC
Confidence 333
No 381
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=23.80 E-value=36 Score=29.38 Aligned_cols=28 Identities=25% Similarity=0.500 Sum_probs=18.1
Q ss_pred CCCceeecccccccCCCCCCceeeCCCcCcc
Q 014440 361 SRSTCFGCQQSLLASGNKAGLCVACPKCKKH 391 (424)
Q Consensus 361 ~~~~C~~C~~~~~~~~~~~~~~~~C~~C~~~ 391 (424)
...+|..|...|+... ...+.||.|++.
T Consensus 69 ~~~~C~~Cg~~~~~~~---~~~~~CP~Cgs~ 96 (114)
T PRK03681 69 AECWCETCQQYVTLLT---QRVRRCPQCHGD 96 (114)
T ss_pred cEEEcccCCCeeecCC---ccCCcCcCcCCC
Confidence 3568999987776421 112568888865
No 382
>cd04924 ACT_AK-Arch_2 ACT domains of a monofunctional aspartokinase found mostly in Archaea species (ACT_AK-Arch_2). Included in this CD is the second of two ACT domains of a monofunctional aspartokinase found mostly in Archaea species (ACT_AK-Arch_2). The first or N-terminal ACT domain of these proteins cluster with the ThrA-like ACT 1 domains (ACT_AKi-HSDH-ThrA-like_1) which includes the threonine-sensitive archaeal Methanococcus jannaschii aspartokinase ACT 1 domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=23.73 E-value=2.1e+02 Score=20.69 Aligned_cols=36 Identities=11% Similarity=0.087 Sum_probs=25.2
Q ss_pred EEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecc
Q 014440 193 LILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSA 228 (424)
Q Consensus 193 LvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~ 228 (424)
|=+.|..-..+++-..++++.+.+.+|+|+.|+-+.
T Consensus 4 isivg~~~~~~~~~~~~i~~~L~~~~I~v~~i~q~~ 39 (66)
T cd04924 4 VAVVGSGMRGTPGVAGRVFGALGKAGINVIMISQGS 39 (66)
T ss_pred EEEECCCCCCCccHHHHHHHHHHHCCCCEEEEEecC
Confidence 344554333345555688999999999999998653
No 383
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=23.67 E-value=68 Score=24.54 Aligned_cols=31 Identities=23% Similarity=0.578 Sum_probs=21.6
Q ss_pred CCCCceeecccccccCCCCCCceeeCCCcCccc
Q 014440 360 ISRSTCFGCQQSLLASGNKAGLCVACPKCKKHF 392 (424)
Q Consensus 360 ~~~~~C~~C~~~~~~~~~~~~~~~~C~~C~~~f 392 (424)
..+..|..|....... .....|.||.|+..+
T Consensus 26 ~TSq~C~~CG~~~~~~--~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 26 YTSQTCPRCGHRNKKR--RSGRVFTCPNCGFEM 56 (69)
T ss_pred CCccCccCcccccccc--cccceEEcCCCCCEE
Confidence 3677899998666541 123468999998764
No 384
>PF13458 Peripla_BP_6: Periplasmic binding protein; PDB: 4EVS_A 4EY3_A 4EYG_B 4EYK_A 3H5L_B 3TD9_A 3EAF_A 1Z18_A 1Z17_A 2LIV_A ....
Probab=23.57 E-value=2.7e+02 Score=27.08 Aligned_cols=79 Identities=15% Similarity=0.193 Sum_probs=46.9
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHh-CCcEEEEEEecch-HHHHHHHHHHhCCEEE
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKE-SKIRCSVIGLSAE-MFICKHLCQETGGTYS 245 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk-~~IrV~vIgLg~e-~~iLq~iA~~TGG~Y~ 245 (424)
..+.+++++|.+.++...+-..++|-++.-+ +..|+....+.++.+.. .+|.+-+=.++.+ ...+..+++..|--++
T Consensus 19 ~~~~~g~~~a~~~~N~~ggi~G~~i~l~~~D-~~~~~~~a~~~~~~l~~~~~v~~vvg~~~s~~~~~~~~~~~~~~ip~i 97 (343)
T PF13458_consen 19 QDFLRGAELAVDEINAAGGINGRKIELVVYD-DGGDPAQAVQAARKLIDDDGVDAVVGPLSSAQAEAVAPIAEEAGIPYI 97 (343)
T ss_dssp HHHHHHHHHHHHHHHHTTEETTEEEEEEEEE--TT-HHHHHHHHHHHHHTSTESEEEESSSHHHHHHHHHHHHHHT-EEE
T ss_pred HHHHHHHHHHHHHHHHhCCcCCccceeeecc-CCCChHHHHHHHHHhhhhcCcEEEEecCCcHHHHHHHHHHHhcCcEEE
Confidence 4677889999999987532234555555432 22355555667777766 7766554444433 4566667777776666
Q ss_pred Ee
Q 014440 246 VA 247 (424)
Q Consensus 246 ~~ 247 (424)
.+
T Consensus 98 ~~ 99 (343)
T PF13458_consen 98 SP 99 (343)
T ss_dssp ES
T ss_pred Ee
Confidence 54
No 385
>PF06957 COPI_C: Coatomer (COPI) alpha subunit C-terminus; InterPro: IPR010714 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the C terminus (approximately 500 residues) of the eukaryotic coatomer alpha subunit [, ]. This domain is found along with the IPR006692 from INTERPRO domain. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0005515 protein binding, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030126 COPI vesicle coat; PDB: 3MKR_B 3MV2_E 3MKQ_B 3MV3_A.
Probab=23.51 E-value=45 Score=35.43 Aligned_cols=43 Identities=19% Similarity=0.369 Sum_probs=24.4
Q ss_pred cceeeecCCcccc---C-eEEcCCCCccccC--CCCCCCCCCceecCch
Q 014440 289 ISICSCHKEVKIG---V-GYTCPRCKARVCE--LPTECRICGLQLVSSP 331 (424)
Q Consensus 289 ~a~C~CH~~~~~~---~-Gy~Cp~C~s~~C~--lP~~C~~C~l~Lvs~p 331 (424)
..+-.|....+.+ . .-.||-|+|+|.. --..|++|++.-|-.+
T Consensus 362 npF~ICa~s~tPIY~G~~~v~CP~cgA~y~~~~kG~lC~vC~l~~IG~~ 410 (422)
T PF06957_consen 362 NPFDICAASYTPIYRGSPSVKCPYCGAKYHPEYKGQLCPVCELSEIGAD 410 (422)
T ss_dssp S-EEEBTTT--EEETTS-EEE-TTT--EEEGGGTTSB-TTTTTBBTT--
T ss_pred CCceeeecccccccCCCCCeeCCCCCCccChhhCCCCCCCCcceeeCCc
Confidence 4567777765532 1 3459999999994 3479999999877544
No 386
>PF07693 KAP_NTPase: KAP family P-loop domain; InterPro: IPR011646 The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals. Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side [].
Probab=23.42 E-value=4.4e+02 Score=25.75 Aligned_cols=54 Identities=15% Similarity=0.346 Sum_probs=34.5
Q ss_pred CCcEEEEEEcCCCCCCccCHHHHHHHH---HhCCcEEEEEEecchHHHHHHHHHHhCC
Q 014440 188 GHREVLILYSALSTCDPGDIMETIQKC---KESKIRCSVIGLSAEMFICKHLCQETGG 242 (424)
Q Consensus 188 ~~reILvI~ss~~t~dp~~i~~~i~~a---kk~~IrV~vIgLg~e~~iLq~iA~~TGG 242 (424)
..++|||++++++-|+|..+.++++.. -...=-++++++. +..+.+.+....|+
T Consensus 170 ~~~~iViiIDdLDR~~~~~i~~~l~~ik~~~~~~~i~~Il~~D-~~~l~~ai~~~~~~ 226 (325)
T PF07693_consen 170 SKKRIVIIIDDLDRCSPEEIVELLEAIKLLLDFPNIIFILAFD-PEILEKAIEKNYGE 226 (325)
T ss_pred CCceEEEEEcchhcCCcHHHHHHHHHHHHhcCCCCeEEEEEec-HHHHHHHHHhhcCc
Confidence 567899999999989988776554444 3433336666664 33445555555544
No 387
>PRK07591 threonine synthase; Validated
Probab=23.37 E-value=69 Score=33.73 Aligned_cols=28 Identities=21% Similarity=0.309 Sum_probs=20.2
Q ss_pred eEEcCCCCcccc-CCCCCCCCCCceecCc
Q 014440 303 GYTCPRCKARVC-ELPTECRICGLQLVSS 330 (424)
Q Consensus 303 Gy~Cp~C~s~~C-~lP~~C~~C~l~Lvs~ 330 (424)
+|.|++|+..|= +....||.||-.|-..
T Consensus 18 ~l~C~~Cg~~~~~~~~~~C~~cg~~l~~~ 46 (421)
T PRK07591 18 ALKCRECGAEYPLGPIHVCEECFGPLEVA 46 (421)
T ss_pred EEEeCCCCCcCCCCCCccCCCCCCeEEEE
Confidence 799999998773 3336799997665443
No 388
>cd06342 PBP1_ABC_LIVBP_like Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine). This subgroup includes the type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine). This subgroup also includes a leucine-specific binding protein (or LivK), which is very similar in sequence and structure to leucine-isoleucine-valine binding protein (LIVBP). ABC-type active transport systems are transmembrane proteins that function in the transport of diverse sets of substrates across extra- and intracellular membranes, including carbohydrates, amino acids, inorganic ions, dipeptides and oligopeptides, metabolic products, lipids and sterols, and heme, to name a few.
Probab=23.36 E-value=4.2e+02 Score=25.61 Aligned_cols=50 Identities=16% Similarity=0.179 Sum_probs=26.4
Q ss_pred hHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCc
Q 014440 169 SIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKI 219 (424)
Q Consensus 169 sL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~I 219 (424)
....|+++|.+.++....-..++|-+++-+ +.++|....+++..+.+.+|
T Consensus 18 ~~~~g~~~a~~~iN~~ggi~g~~i~~~~~D-~~~~~~~~~~~~~~li~~~v 67 (334)
T cd06342 18 DIKNGAQLAVEDINAKGGGKGVKLELVVED-DQADPKQAVAVAQKLVDDGV 67 (334)
T ss_pred HHHHHHHHHHHHHHhcCCCCCeEEEEEEec-CCCChHHHHHHHHHHHhCCc
Confidence 455677777777776422234455555533 22345444455555555543
No 389
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=23.36 E-value=31 Score=21.93 Aligned_cols=26 Identities=27% Similarity=0.644 Sum_probs=16.8
Q ss_pred CCCcCcccccccchhhhc-cCCCCCCC
Q 014440 385 CPKCKKHFCLECDIYIHE-SLHNCPGC 410 (424)
Q Consensus 385 C~~C~~~fC~dCd~fihe-~lh~CPgC 410 (424)
-..|++.||..|=.-.-+ .-..||.|
T Consensus 13 ~~~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 13 VLPCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred EecCCChHHHHHHHHHHHhCcCCCCCC
Confidence 346999999999543322 34458876
No 390
>TIGR03844 cysteate_syn cysteate synthase. Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M.
Probab=23.35 E-value=52 Score=34.50 Aligned_cols=22 Identities=18% Similarity=0.478 Sum_probs=15.7
Q ss_pred eEEcCCCCcccc-CCCCCCCCCC
Q 014440 303 GYTCPRCKARVC-ELPTECRICG 324 (424)
Q Consensus 303 Gy~Cp~C~s~~C-~lP~~C~~C~ 324 (424)
-|.|++|+..|= +....|+.|+
T Consensus 2 ~l~C~~Cg~~~~~~~~~~C~~c~ 24 (398)
T TIGR03844 2 TLRCPGCGEVLPDHYTLSCPLDC 24 (398)
T ss_pred EEEeCCCCCccCCccccCCCCCC
Confidence 378999998884 2345798655
No 391
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=23.33 E-value=40 Score=25.22 Aligned_cols=31 Identities=29% Similarity=0.620 Sum_probs=19.4
Q ss_pred CCceeecccccccCCCCCCceeeCCCcCccc
Q 014440 362 RSTCFGCQQSLLASGNKAGLCVACPKCKKHF 392 (424)
Q Consensus 362 ~~~C~~C~~~~~~~~~~~~~~~~C~~C~~~f 392 (424)
...|-.|++-|...+.....--.||+|+..+
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~tiN 34 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKTIN 34 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCccc
Confidence 3468888877765332222345799888653
No 392
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=23.33 E-value=58 Score=24.68 Aligned_cols=32 Identities=22% Similarity=0.563 Sum_probs=24.4
Q ss_pred CCceeecccccccCCCCCCceeeCCCcCcccccccc
Q 014440 362 RSTCFGCQQSLLASGNKAGLCVACPKCKKHFCLECD 397 (424)
Q Consensus 362 ~~~C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~dCd 397 (424)
...|..|..+|...+ ...+||.|+..+=.+|-
T Consensus 5 ~~~C~~Cg~~~~~~d----DiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGD----DIVVCPECGAPYHRDCW 36 (54)
T ss_pred CccChhhCCcccCCC----CEEECCCCCCcccHHHH
Confidence 458999999996433 25789999998866665
No 393
>cd01019 ZnuA Zinc binding protein ZnuA. These proteins have been shown to function as initial receptors in the ABC uptake of Zn2+. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a single helix and bind their specific ligands in the cleft between these domains. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=23.12 E-value=2.2e+02 Score=28.12 Aligned_cols=43 Identities=16% Similarity=0.194 Sum_probs=35.6
Q ss_pred CccCHHHHHHHHHhCCcEEEEEEecchHHHHHHHHHHhCCEEE
Q 014440 203 DPGDIMETIQKCKESKIRCSVIGLSAEMFICKHLCQETGGTYS 245 (424)
Q Consensus 203 dp~~i~~~i~~akk~~IrV~vIgLg~e~~iLq~iA~~TGG~Y~ 245 (424)
.+.++.++++.+++.+|++-..--.....+.+.|++.||..-.
T Consensus 213 s~~~l~~l~~~ik~~~v~~If~e~~~~~~~~~~ia~~~g~~v~ 255 (286)
T cd01019 213 GAKRLAKIRKEIKEKGATCVFAEPQFHPKIAETLAEGTGAKVG 255 (286)
T ss_pred CHHHHHHHHHHHHHcCCcEEEecCCCChHHHHHHHHhcCceEE
Confidence 4557789999999999998777666778999999999997544
No 394
>PF12675 DUF3795: Protein of unknown function (DUF3795); InterPro: IPR024227 This family of proteins is functionally uncharacterised and is found in bacteria and archaea. Proteins in this family are typically between 99 and 171 amino acids in length. These proteins are likely to be zinc binding given the conserved cysteines.
Probab=23.05 E-value=47 Score=26.52 Aligned_cols=24 Identities=33% Similarity=0.729 Sum_probs=17.3
Q ss_pred ccccccchhhhccCC--------------CCCCCCCCC
Q 014440 391 HFCLECDIYIHESLH--------------NCPGCESLR 414 (424)
Q Consensus 391 ~fC~dCd~fihe~lh--------------~CPgC~~~~ 414 (424)
.+|..|..|.+.... .||||....
T Consensus 7 l~C~~C~~y~~~~~~~~~~~~~~~~~~~~~C~GCr~~~ 44 (78)
T PF12675_consen 7 LDCGNCPAYEAGKISDASLRLKEASPEKIRCPGCRSGG 44 (78)
T ss_pred CccccchhhhcCCccHHHHHHhhccCCCCcCcCCcCCC
Confidence 467788888777655 699997643
No 395
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=22.96 E-value=54 Score=29.14 Aligned_cols=12 Identities=17% Similarity=0.437 Sum_probs=8.3
Q ss_pred eEEcCCCCcccc
Q 014440 303 GYTCPRCKARVC 314 (424)
Q Consensus 303 Gy~Cp~C~s~~C 314 (424)
-|.|+.|+..+=
T Consensus 70 ~~~C~~CG~~~~ 81 (135)
T PRK03824 70 VLKCRNCGNEWS 81 (135)
T ss_pred EEECCCCCCEEe
Confidence 577888886553
No 396
>PRK12496 hypothetical protein; Provisional
Probab=22.96 E-value=45 Score=30.66 Aligned_cols=25 Identities=20% Similarity=0.450 Sum_probs=16.0
Q ss_pred CceeecccccccCCCCCCceeeCCCcCcc
Q 014440 363 STCFGCQQSLLASGNKAGLCVACPKCKKH 391 (424)
Q Consensus 363 ~~C~~C~~~~~~~~~~~~~~~~C~~C~~~ 391 (424)
..|.||.+.|+... ..-.||.|++.
T Consensus 128 ~~C~gC~~~~~~~~----~~~~C~~CG~~ 152 (164)
T PRK12496 128 KVCKGCKKKYPEDY----PDDVCEICGSP 152 (164)
T ss_pred EECCCCCccccCCC----CCCcCCCCCCh
Confidence 46999988885321 11348888864
No 397
>CHL00099 ilvB acetohydroxyacid synthase large subunit
Probab=22.96 E-value=4.2e+02 Score=29.01 Aligned_cols=90 Identities=11% Similarity=0.028 Sum_probs=59.9
Q ss_pred CcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH---------------
Q 014440 166 GDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM--------------- 230 (424)
Q Consensus 166 G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~--------------- 230 (424)
+.-+++-+|-.|+..--.. ..|+|+.|+|++.- . .++ ..+.++.+.+++|-+|-+....
T Consensus 428 ~~g~mG~glpaaiGaala~---p~~~vv~i~GDG~f-~-m~~-~eL~Ta~~~~l~~~~vV~NN~~y~~i~~~q~~~~~~~ 501 (585)
T CHL00099 428 GLGTMGYGLPAAIGAQIAH---PNELVICISGDASF-Q-MNL-QELGTIAQYNLPIKIIIINNKWQGMVRQWQQAFYGER 501 (585)
T ss_pred cccchhhhHHHHHHHHHhC---CCCeEEEEEcchhh-h-hhH-HHHHHHHHhCCCeEEEEEECCcchHHHHHHHHhcCCC
Confidence 3345666666665543322 24678888876432 1 122 4577888999998777775320
Q ss_pred ----------HHHHHHHHHhCCEEEEecChhhHHHHHHhcC
Q 014440 231 ----------FICKHLCQETGGTYSVALDESHSKELILEHA 261 (424)
Q Consensus 231 ----------~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~ 261 (424)
.-+.++|+..|+.+..+.+.++|.+.|....
T Consensus 502 ~~~~~~~~~~~d~~~la~a~G~~~~~v~~~~el~~al~~a~ 542 (585)
T CHL00099 502 YSHSNMEEGAPDFVKLAEAYGIKGLRIKSRKDLKSSLKEAL 542 (585)
T ss_pred cccccCCCCCCCHHHHHHHCCCeEEEeCCHHHHHHHHHHHH
Confidence 1256788888999999999999988887765
No 398
>PF02875 Mur_ligase_C: Mur ligase family, glutamate ligase domain This Prosite entry is a subset of the Pfam family.; InterPro: IPR004101 The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment. The peptidoglycan layer gives the cell wall its strength, and helps maintain the overall shape of the cell. The basic peptidoglycan structure of both Gram-positive and Gram-negative bacteria is comprised of a sheet of glycan chains connected by short cross-linking polypeptides. Biosynthesis of peptidoglycan is a multi-step (11-12 steps) process comprising three main stages: (1) formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc). (2) addition of a short polypeptide chain to the UDPMurNAc. (3) addition of a second GlcNAc to the disaccharide-pentapeptide building block and transport of this unit through the cytoplasmic membrane and incorporation into the growing peptidoglycan layer. Stage two involves four key Mur ligase enzymes: MurC (6.3.2.8 from EC) [], MurD (6.3.2.9 from EC) [], MurE (6.3.2.13 from EC) [] and MurF (6.3.2.10 from EC) []. These four Mur ligases are responsible for the successive additions of L-alanine, D-glutamate, meso-diaminopimelate or L-lysine, and D-alanyl-D-alanine to UDP-N-acetylmuramic acid. All four Mur ligases are topologically similar to one another, even though they display low sequence identity. They are each composed of three domains: an N-terminal Rossmann-fold domain responsible for binding the UDPMurNAc substrate; a central domain (similar to ATP-binding domains of several ATPases and GTPases); and a C-terminal domain (similar to dihydrofolate reductase fold) that appears to be associated with binding the incoming amino acid. The conserved sequence motifs found in the four Mur enzymes also map to other members of the Mur ligase family, including folylpolyglutamate synthetase, cyanophycin synthetase and the capB enzyme from Bacillales []. This entry represents the C-terminal domain from all four stage 2 Mur enzymes: UDP-N-acetylmuramate-L-alanine ligase (MurC), UDP-N-acetylmuramoylalanine-D-glutamate ligase (MurD), UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase (MurE), and UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase (MurF). This entry also includes the C-terminal domain of folylpolyglutamate synthase that transfers glutamate to folylpolyglutamate and cyanophycin synthetase that catalyses the biosynthesis of the cyanobacterial reserve material multi-L-arginyl-poly-L-aspartate (cyanophycin) []. The C-terminal domain is almost always associated with the cytoplasmic peptidoglycan synthetases, N-terminal domain (see IPR000713 from INTERPRO).; GO: 0005524 ATP binding, 0016874 ligase activity, 0009058 biosynthetic process; PDB: 2Y68_A 3UAG_A 4UAG_A 2UAG_A 1E0D_A 2XPC_A 2WJP_A 2VTE_A 2Y67_A 1EEH_A ....
Probab=22.90 E-value=1e+02 Score=24.69 Aligned_cols=49 Identities=10% Similarity=0.114 Sum_probs=20.8
Q ss_pred HHHHHHHHcCCCCCCCcEEEEEEcCCCC---CCccCHHHHHHHHHhCCcEEEEE
Q 014440 174 LDLVHGLLNQIPSYGHREVLILYSALST---CDPGDIMETIQKCKESKIRCSVI 224 (424)
Q Consensus 174 L~~Al~~L~~~p~~~~reILvI~ss~~t---~dp~~i~~~i~~akk~~IrV~vI 224 (424)
+..+++.|+.. +..+++++|++.... .+........+.+.+....|.+.
T Consensus 27 ~~a~l~~l~~~--~~~~~~i~V~G~~~d~g~~~~~~~~~~~~~~~~~~d~vi~~ 78 (91)
T PF02875_consen 27 IRALLEALKEL--YPKGRIIAVFGAMGDLGSKDKDFHEEIGELAAQLADVVILT 78 (91)
T ss_dssp HHHHHHHHHHH--CTTSEEEEEEEEBTT-HTSHHHCHHHHHHHHTTCSSEEEEE
T ss_pred HHHHHHHHHHh--ccCCcEEEEEccccccccccHHHHHHHHHHHHhcCCEEEEc
Confidence 33344444433 224566666663221 22212224444444445554443
No 399
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=22.86 E-value=25 Score=26.01 Aligned_cols=25 Identities=32% Similarity=0.743 Sum_probs=21.0
Q ss_pred eEEcCCCCccccCCCCCCCCCCcee
Q 014440 303 GYTCPRCKARVCELPTECRICGLQL 327 (424)
Q Consensus 303 Gy~Cp~C~s~~C~lP~~C~~C~l~L 327 (424)
.|.|=.|++..=.....|++|+..|
T Consensus 21 HYLCl~CLt~ml~~s~~C~iC~~~L 45 (50)
T PF03854_consen 21 HYLCLNCLTLMLSRSDRCPICGKPL 45 (50)
T ss_dssp -EEEHHHHHHT-SSSSEETTTTEE-
T ss_pred hhHHHHHHHHHhccccCCCcccCcC
Confidence 8999999999999999999999876
No 400
>PF13911 AhpC-TSA_2: AhpC/TSA antioxidant enzyme
Probab=22.86 E-value=1.4e+02 Score=24.89 Aligned_cols=41 Identities=17% Similarity=0.299 Sum_probs=29.6
Q ss_pred HHHHHHHhCCcEEEEEEecchHHHHHHHHHHhCCEEEEecCh
Q 014440 209 ETIQKCKESKIRCSVIGLSAEMFICKHLCQETGGTYSVALDE 250 (424)
Q Consensus 209 ~~i~~akk~~IrV~vIgLg~e~~iLq~iA~~TGG~Y~~~~d~ 250 (424)
+....+++.||++-+|+.|+... +++-++.|+=.|=+..|+
T Consensus 4 ~~~~~l~~~gv~lv~I~~g~~~~-~~~f~~~~~~p~~ly~D~ 44 (115)
T PF13911_consen 4 RRKPELEAAGVKLVVIGCGSPEG-IEKFCELTGFPFPLYVDP 44 (115)
T ss_pred HhHHHHHHcCCeEEEEEcCCHHH-HHHHHhccCCCCcEEEeC
Confidence 34677889999999999998866 788887776433333333
No 401
>PRK08329 threonine synthase; Validated
Probab=22.86 E-value=44 Score=34.16 Aligned_cols=41 Identities=22% Similarity=0.570 Sum_probs=26.2
Q ss_pred EEcCCCCcccc-CCCCCCCCCCceecCchhHH-----------hhhcccCCCCC
Q 014440 304 YTCPRCKARVC-ELPTECRICGLQLVSSPHLA-----------RSYHHLFPIAP 345 (424)
Q Consensus 304 y~Cp~C~s~~C-~lP~~C~~C~l~Lvs~phLa-----------rsyhhl~p~~~ 345 (424)
|.|++|+..|= +.+..| .||-.|....++. +-|+.++|+..
T Consensus 2 l~C~~Cg~~~~~~~~~~C-~c~~~l~~~~~~~~~~~~~~~~~~wry~~~lP~~~ 54 (347)
T PRK08329 2 LRCTKCGRTYEEKFKLRC-DCGGTLLVEREYGSFDSPREYLDMRRYIDYLPVDE 54 (347)
T ss_pred cCcCCCCCCcCCCCceec-CCCCcEEEEeccccccccccccchhhhHHhCCCCC
Confidence 67999998773 233468 5876665553322 34888888754
No 402
>KOG4602 consensus Nanos and related proteins [General function prediction only]
Probab=22.78 E-value=42 Score=33.30 Aligned_cols=25 Identities=4% Similarity=0.081 Sum_probs=12.1
Q ss_pred heeeecCCCCCCC-CCcce--eeecCCc
Q 014440 274 SLIKMGFPQRAGE-GSISI--CSCHKEV 298 (424)
Q Consensus 274 ~Li~mGFP~~~~~-~~~a~--C~CH~~~ 298 (424)
-...|+.|.+... ..+.+ |||-++.
T Consensus 216 ~~~~~~l~~P~pg~Q~r~l~CvFC~nN~ 243 (318)
T KOG4602|consen 216 REQRNNLTSPPPGNQPRPLCCVFCFNNA 243 (318)
T ss_pred cccccCCCCCCCCCCCCceeEEeecCCC
Confidence 3445555554332 22333 6786653
No 403
>cd06345 PBP1_ABC_ligand_binding_like_10 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=22.74 E-value=4.9e+02 Score=25.55 Aligned_cols=53 Identities=15% Similarity=0.271 Sum_probs=24.8
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhC-CcEE
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKES-KIRC 221 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~-~IrV 221 (424)
....+|+++|++.++....-..++|-++.-+ +.+||....+.+..+.+. +|.+
T Consensus 17 ~~~~~g~~~A~~~iN~~ggi~g~~v~l~~~D-~~~~~~~a~~~~~~li~~~~v~a 70 (344)
T cd06345 17 EAMWNGAELAAEEINAAGGILGRKVELVFED-TEGSPEDAVRAFERLVSQDKVDA 70 (344)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCceEEEEEec-CCCCHHHHHHHHHHHhccCCceE
Confidence 4566777777777765433233444444322 122443333444444433 5544
No 404
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=22.64 E-value=32 Score=32.80 Aligned_cols=42 Identities=26% Similarity=0.466 Sum_probs=28.7
Q ss_pred CCCCCCCceecCchhHHhhhcccCCCCCCcccCccccccccCCCCCceeecccccccC
Q 014440 318 TECRICGLQLVSSPHLARSYHHLFPIAPFDEATPSRLNDLHNISRSTCFGCQQSLLAS 375 (424)
Q Consensus 318 ~~C~~C~l~Lvs~phLarsyhhl~p~~~f~~~~~~~~~~~~~~~~~~C~~C~~~~~~~ 375 (424)
..||+||-+|... -+++-+|-|-+|-- ....|-.|..++.+.
T Consensus 15 ~~CPvCg~~l~~~-------~~~~~IPyFG~V~i---------~t~~C~~CgYR~~DV 56 (201)
T COG1779 15 IDCPVCGGTLKAH-------MYLYDIPYFGEVLI---------STGVCERCGYRSTDV 56 (201)
T ss_pred ecCCcccceeeEE-------EeeecCCccceEEE---------EEEEccccCCcccce
Confidence 4677777766432 26677888998742 356899998777643
No 405
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=22.61 E-value=29 Score=39.80 Aligned_cols=42 Identities=29% Similarity=0.625 Sum_probs=0.0
Q ss_pred CCccee-eecCCccccCeEEcCCCCccccCCCCCCCCCCceecCchh
Q 014440 287 GSISIC-SCHKEVKIGVGYTCPRCKARVCELPTECRICGLQLVSSPH 332 (424)
Q Consensus 287 ~~~a~C-~CH~~~~~~~Gy~Cp~C~s~~C~lP~~C~~C~l~Lvs~ph 332 (424)
.+...| .|-.... . -|.||+|+..+= +..|+-|+....++-.
T Consensus 665 t~~~~Cp~CG~~T~-~-~~~Cp~C~~~~~--~~~C~~C~~~~~~~~~ 707 (900)
T PF03833_consen 665 TFYNRCPECGSHTE-P-VYVCPDCGIEVE--EDECPKCGRETTSYSK 707 (900)
T ss_dssp -----------------------------------------------
T ss_pred chhhcCcccCCccc-c-ceeccccccccC--ccccccccccCcccce
Confidence 455556 4554332 2 477888877643 3489999988665543
No 406
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.49 E-value=32 Score=32.31 Aligned_cols=43 Identities=26% Similarity=0.537 Sum_probs=34.5
Q ss_pred CCCceeecccccccCCCCCCceeeCCCcCcccccccchhhhccCCCCCCCC
Q 014440 361 SRSTCFGCQQSLLASGNKAGLCVACPKCKKHFCLECDIYIHESLHNCPGCE 411 (424)
Q Consensus 361 ~~~~C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~dCd~fihe~lh~CPgC~ 411 (424)
....|..|...|..+ ..-.|++.||..|..-+-+....||.|.
T Consensus 12 ~~~~C~iC~~~~~~p--------~~l~C~H~~c~~C~~~~~~~~~~Cp~cr 54 (386)
T KOG2177|consen 12 EELTCPICLEYFREP--------VLLPCGHNFCRACLTRSWEGPLSCPVCR 54 (386)
T ss_pred ccccChhhHHHhhcC--------ccccccchHhHHHHHHhcCCCcCCcccC
Confidence 356899999777543 3457999999999977777778999998
No 407
>cd02522 GT_2_like_a GT_2_like_a represents a glycosyltransferase family-2 subfamily with unknown function. Glycosyltransferase family 2 (GT-2) subfamily of unknown function. GT-2 includes diverse families of glycosyltransferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. Glycosyltransferases have been classified into more than 90 distinct sequence based families.
Probab=22.40 E-value=5.7e+02 Score=22.88 Aligned_cols=48 Identities=8% Similarity=0.025 Sum_probs=28.4
Q ss_pred hHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEE
Q 014440 169 SIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSV 223 (424)
Q Consensus 169 sL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~v 223 (424)
..+.|+.+|+...+ .++|++++++..-+|+.+.+.+....+.+..+..
T Consensus 59 g~~~a~n~g~~~a~-------~~~i~~~D~D~~~~~~~l~~l~~~~~~~~~~~~~ 106 (221)
T cd02522 59 GRARQMNAGAAAAR-------GDWLLFLHADTRLPPDWDAAIIETLRADGAVAGA 106 (221)
T ss_pred CHHHHHHHHHHhcc-------CCEEEEEcCCCCCChhHHHHHHHHhhcCCcEEEE
Confidence 45667776665432 3678888766555665555555555555554433
No 408
>PRK08617 acetolactate synthase; Reviewed
Probab=22.37 E-value=2.4e+02 Score=30.54 Aligned_cols=70 Identities=7% Similarity=-0.059 Sum_probs=51.7
Q ss_pred CcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH----------------------HHHHHHHHHhCCEEEE
Q 014440 189 HREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM----------------------FICKHLCQETGGTYSV 246 (424)
Q Consensus 189 ~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~----------------------~iLq~iA~~TGG~Y~~ 246 (424)
.++|++|+|++.- -.++ +.+.++.+.|++|-+|-+.... .-+.++|+..|+.|..
T Consensus 432 ~~~vv~i~GDGsf--~m~~-~eL~Ta~~~~lpv~~vV~NN~~~~~~~~~~~~~~~~~~~~~~~~~d~~~lA~a~G~~~~~ 508 (552)
T PRK08617 432 GKKVVSVSGDGGF--LFSA-MELETAVRLKLNIVHIIWNDGHYNMVEFQEEMKYGRSSGVDFGPVDFVKYAESFGAKGLR 508 (552)
T ss_pred CCcEEEEEechHH--hhhH-HHHHHHHHhCCCeEEEEEECCccchHHHHHHhhcCCcccCCCCCCCHHHHHHHCCCeEEE
Confidence 4678888886432 1222 4567789999998877775320 1256799999999999
Q ss_pred ecChhhHHHHHHhcC
Q 014440 247 ALDESHSKELILEHA 261 (424)
Q Consensus 247 ~~d~~~L~~lL~~~~ 261 (424)
+.+.++|+..|....
T Consensus 509 v~~~~eL~~al~~a~ 523 (552)
T PRK08617 509 VTSPDELEPVLREAL 523 (552)
T ss_pred ECCHHHHHHHHHHHH
Confidence 999999999998876
No 409
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=22.22 E-value=54 Score=23.94 Aligned_cols=29 Identities=28% Similarity=0.929 Sum_probs=21.1
Q ss_pred ceeeccc-ccccCCCCCCceeeCCCcCcc-cccccch
Q 014440 364 TCFGCQQ-SLLASGNKAGLCVACPKCKKH-FCLECDI 398 (424)
Q Consensus 364 ~C~~C~~-~~~~~~~~~~~~~~C~~C~~~-fC~dCd~ 398 (424)
.|.+|.+ ++. +.+|+|..|..+ .|.+|-.
T Consensus 2 ~C~~C~~~~i~------g~R~~C~~C~dydLC~~Cf~ 32 (49)
T cd02345 2 SCSACRKQDIS------GIRFPCQVCRDYSLCLGCYT 32 (49)
T ss_pred cCCCCCCCCce------EeeEECCCCCCcCchHHHHh
Confidence 5999987 664 258999999763 5777744
No 410
>PRK07710 acetolactate synthase catalytic subunit; Reviewed
Probab=22.19 E-value=4.8e+02 Score=28.34 Aligned_cols=88 Identities=17% Similarity=0.075 Sum_probs=58.8
Q ss_pred hHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH------------------
Q 014440 169 SIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM------------------ 230 (424)
Q Consensus 169 sL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~------------------ 230 (424)
+++-+|-.|+..-...| .+++++|+|++.- -.+++ .+.++.+.++++-+|-+....
T Consensus 425 ~mG~glpaAiGaala~p---~~~vv~i~GDGsf--~m~~~-eL~ta~r~~lpi~ivV~NN~~~~~i~~~~~~~~~~~~~~ 498 (571)
T PRK07710 425 TMGFGLPAAIGAQLAKP---DETVVAIVGDGGF--QMTLQ-ELSVIKELSLPVKVVILNNEALGMVRQWQEEFYNQRYSH 498 (571)
T ss_pred cccchHHHHHHHHHhCC---CCcEEEEEcchHH--hhhHH-HHHHHHHhCCCeEEEEEECchHHHHHHHHHHHhCCccee
Confidence 45555555544332222 4678888886432 12333 478899999998888875321
Q ss_pred ------HHHHHHHHHhCCEEEEecChhhHHHHHHhcCC
Q 014440 231 ------FICKHLCQETGGTYSVALDESHSKELILEHAP 262 (424)
Q Consensus 231 ------~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~~ 262 (424)
.-+.++|+..|+.|..+.+.++|...+.....
T Consensus 499 ~~~~~~~d~~~~A~a~G~~~~~v~~~~el~~al~~a~~ 536 (571)
T PRK07710 499 SLLSCQPDFVKLAEAYGIKGVRIDDELEAKEQLQHAIE 536 (571)
T ss_pred ccCCCCCCHHHHHHHCCCeEEEECCHHHHHHHHHHHHh
Confidence 12567889999999999999999888877653
No 411
>cd06438 EpsO_like EpsO protein participates in the methanolan synthesis. The Methylobacillus sp EpsO protein is predicted to participate in the methanolan synthesis. Methanolan is an exopolysaccharide (EPS), composed of glucose, mannose and galactose. A 21 genes cluster was predicted to participate in the methanolan synthesis. Gene disruption analysis revealed that EpsO is one of the glycosyltransferase enzymes involved in the synthesis of repeating sugar units onto the lipid carrier.
Probab=22.16 E-value=5.5e+02 Score=22.62 Aligned_cols=47 Identities=17% Similarity=0.225 Sum_probs=31.4
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHh
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKE 216 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk 216 (424)
...+.||..++...... ....++|++++++..-+|..+......+.+
T Consensus 62 ~gk~~aln~g~~~a~~~--~~~~d~v~~~DaD~~~~p~~l~~l~~~~~~ 108 (183)
T cd06438 62 RGKGYALDFGFRHLLNL--ADDPDAVVVFDADNLVDPNALEELNARFAA 108 (183)
T ss_pred CCHHHHHHHHHHHHHhc--CCCCCEEEEEcCCCCCChhHHHHHHHHHhh
Confidence 34677777777776432 234578999987666667666677777654
No 412
>PRK06048 acetolactate synthase 3 catalytic subunit; Reviewed
Probab=22.15 E-value=3.6e+02 Score=29.30 Aligned_cols=88 Identities=13% Similarity=0.032 Sum_probs=60.2
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecch----H-------------
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAE----M------------- 230 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e----~------------- 230 (424)
.+++.||-.|+..=-.. ..|+|+.|+|++.- . .++ ..+.++.+.|+++-+|-+... .
T Consensus 414 g~mG~glpaaiGa~la~---p~~~Vv~i~GDG~f-~-m~~-~eL~Ta~~~~l~i~~vV~NN~~y~~i~~~~~~~~~~~~~ 487 (561)
T PRK06048 414 GTMGYGFPAAIGAKVGK---PDKTVIDIAGDGSF-Q-MNS-QELATAVQNDIPVIVAILNNGYLGMVRQWQELFYDKRYS 487 (561)
T ss_pred cccccHHHHHHHHHHhC---CCCcEEEEEeCchh-h-ccH-HHHHHHHHcCCCeEEEEEECCccHHHHHHHHHHcCCccc
Confidence 45666666655543222 24678888886432 1 222 456888999999888887532 0
Q ss_pred -------HHHHHHHHHhCCEEEEecChhhHHHHHHhcC
Q 014440 231 -------FICKHLCQETGGTYSVALDESHSKELILEHA 261 (424)
Q Consensus 231 -------~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~ 261 (424)
.-+.++|+.-|+.|..+.+.++|...|.+..
T Consensus 488 ~~~~~~~~d~~~lA~a~G~~~~~v~t~~el~~al~~a~ 525 (561)
T PRK06048 488 HTCIKGSVDFVKLAEAYGALGLRVEKPSEVRPAIEEAV 525 (561)
T ss_pred ccCCCCCCCHHHHHHHCCCeEEEECCHHHHHHHHHHHH
Confidence 1256788999999999999999999988776
No 413
>cd01018 ZntC Metal binding protein ZntC. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and bind their specific ligands in the cleft between these domains. In addition, many of these proteins possess a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=22.10 E-value=3.2e+02 Score=26.52 Aligned_cols=43 Identities=19% Similarity=0.275 Sum_probs=35.8
Q ss_pred ccCHHHHHHHHHhCCcEEEEEEecchHHHHHHHHHHhCCEEEE
Q 014440 204 PGDIMETIQKCKESKIRCSVIGLSAEMFICKHLCQETGGTYSV 246 (424)
Q Consensus 204 p~~i~~~i~~akk~~IrV~vIgLg~e~~iLq~iA~~TGG~Y~~ 246 (424)
+.++.++++.+++.+|++-+.--.......+.||+.||-....
T Consensus 203 ~~~l~~l~~~ik~~~v~~if~e~~~~~~~~~~la~~~g~~v~~ 245 (266)
T cd01018 203 PADLKRLIDLAKEKGVRVVFVQPQFSTKSAEAIAREIGAKVVT 245 (266)
T ss_pred HHHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHcCCeEEE
Confidence 4478899999999999977776666789999999999976654
No 414
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=22.05 E-value=52 Score=30.84 Aligned_cols=28 Identities=32% Similarity=0.552 Sum_probs=22.5
Q ss_pred eEEcCCCCccccCCCCCCCCCCceecCc
Q 014440 303 GYTCPRCKARVCELPTECRICGLQLVSS 330 (424)
Q Consensus 303 Gy~Cp~C~s~~C~lP~~C~~C~l~Lvs~ 330 (424)
.|.|--|..+|=.---+||.||-.++--
T Consensus 139 ~~rC~GC~~~f~~~~~~Cp~CG~~~~~~ 166 (177)
T COG1439 139 RLRCHGCKRIFPEPKDFCPICGSPLKRK 166 (177)
T ss_pred eEEEecCceecCCCCCcCCCCCCceEEe
Confidence 7899999999985556899999876543
No 415
>TIGR03469 HonB hopene-associated glycosyltransferase HpnB. This family of genes include a glycosyl transferase, group 2 domain (pfam00535) which are responsible, generally for the transfer of nucleotide-diphosphate sugars to substrates such as polysaccharides and lipids. The genes of this family are often found in the same genetic locus with squalene-hopene cyclase genes, and are never associated with genes for the metabolism of phytoene. Indeed, the members of this family appear to never be found in a genome lacking squalene-hopene cyclase (SHC), although not all genomes encoding SHC have this glycosyl transferase. In the organism Zymomonas mobilis the linkage of this gene to hopanoid biosynthesis has been noted and the gene named HpnB. Hopanoids are known to feature polar glycosyl head groups in many organisms.
Probab=22.01 E-value=8.6e+02 Score=24.84 Aligned_cols=53 Identities=13% Similarity=0.119 Sum_probs=33.5
Q ss_pred CcchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcE
Q 014440 166 GDSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIR 220 (424)
Q Consensus 166 G~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~Ir 220 (424)
|...-..|+..+++.-+.. ....++|++++++...+|..+.+.+..+.+.++.
T Consensus 112 g~~Gk~~A~n~g~~~A~~~--~~~gd~llflDaD~~~~p~~l~~lv~~~~~~~~~ 164 (384)
T TIGR03469 112 GWSGKLWAVSQGIAAARTL--APPADYLLLTDADIAHGPDNLARLVARARAEGLD 164 (384)
T ss_pred CCcchHHHHHHHHHHHhcc--CCCCCEEEEECCCCCCChhHHHHHHHHHHhCCCC
Confidence 4334445566665544322 1135789999877666777778888888877753
No 416
>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed
Probab=22.01 E-value=6.2e+02 Score=25.24 Aligned_cols=54 Identities=11% Similarity=0.156 Sum_probs=37.8
Q ss_pred CcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchHHHHHHHHHHhCCEEEE
Q 014440 189 HREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEMFICKHLCQETGGTYSV 246 (424)
Q Consensus 189 ~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~~iLq~iA~~TGG~Y~~ 246 (424)
..+|.|+.++.. .++.+.++..+...+...++.+-++-.-++.+|+..|=.+++
T Consensus 89 ~~ri~vl~Sg~g----snl~al~~~~~~~~~~~~i~~visn~~~~~~lA~~~gIp~~~ 142 (286)
T PRK06027 89 RKRVVILVSKED----HCLGDLLWRWRSGELPVEIAAVISNHDDLRSLVERFGIPFHH 142 (286)
T ss_pred CcEEEEEEcCCC----CCHHHHHHHHHcCCCCcEEEEEEEcChhHHHHHHHhCCCEEE
Confidence 346777766543 356677877777777778888877766777888888766665
No 417
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=21.98 E-value=39 Score=33.86 Aligned_cols=114 Identities=23% Similarity=0.380 Sum_probs=60.9
Q ss_pred eeecCCCCCCCCCcceeeecCCccccCeEEcCCCCcccc--------CCCCCCCCCCcee-----cCchhHHhhhcccCC
Q 014440 276 IKMGFPQRAGEGSISICSCHKEVKIGVGYTCPRCKARVC--------ELPTECRICGLQL-----VSSPHLARSYHHLFP 342 (424)
Q Consensus 276 i~mGFP~~~~~~~~a~C~CH~~~~~~~Gy~Cp~C~s~~C--------~lP~~C~~C~l~L-----vs~phLarsyhhl~p 342 (424)
..+|+|+.... |.=+....+. -|.|=.|..... ..+..|..|.+.+ -+..|..=+.|+.-.
T Consensus 31 ~~~~c~hy~r~-----~~~~a~ccd~-~~~C~hCH~~s~~h~~~r~~v~~~~C~~C~~~q~~~~~c~~c~~~~g~~~c~~ 104 (276)
T KOG1940|consen 31 FPYGCPHYRRN-----CKSRAPCCDR-EITCRHCHNESEDHDLDRKTVYELLCMKCRKIQPVGQICSNCHVELGEYYCLI 104 (276)
T ss_pred cccCCchhhhc-----cccccccccc-eeeeEEecChhhhcccchhhhhhhhhhhHHhhhhhhhccccchhhhhhhcCcc
Confidence 35677876432 1112222233 567777777766 6677788887776 355566666677666
Q ss_pred CCCCcccCccccccccCCCCCceeecccccccCCCCCCceeeCCCcCc---------ccccccchhhhccCCCCCCCCC
Q 014440 343 IAPFDEATPSRLNDLHNISRSTCFGCQQSLLASGNKAGLCVACPKCKK---------HFCLECDIYIHESLHNCPGCES 412 (424)
Q Consensus 343 ~~~f~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~~~~~~~~C~~C~~---------~fC~dCd~fihe~lh~CPgC~~ 412 (424)
-..|.--+ . ....|-+|..- ..+... ..|.|-.|+. ++|.++-. -+|||.|.-
T Consensus 105 C~l~dd~~--------~-~~~hC~~C~ic--r~g~~~-~~fhc~~c~~c~~~~~~~~H~c~e~~~-----~~ncPic~e 166 (276)
T KOG1940|consen 105 CKLFDDDP--------S-KQYHCDLCGIC--REGLGL-DFFHCKKCKACLSAYLSNWHKCVERSS-----EFNCPICKE 166 (276)
T ss_pred cccccccc--------c-ceecccccccc--cccccc-chhHHhhhHhHHhhhcccccchhhhcc-----cCCCchhHH
Confidence 66665321 1 23455555311 111111 3455555542 56666543 356888864
No 418
>KOG2813 consensus Predicted molecular chaperone, contains DnaJ domain [Posttranslational modification, protein turnover, chaperones]
Probab=21.94 E-value=80 Score=32.40 Aligned_cols=69 Identities=25% Similarity=0.596 Sum_probs=43.5
Q ss_pred eeeecCCccccCeEEcCCCCcccc-----CCCCCCCCCCceecCchhHHhhhcccCCCCCCcccCccccccccCCCCCce
Q 014440 291 ICSCHKEVKIGVGYTCPRCKARVC-----ELPTECRICGLQLVSSPHLARSYHHLFPIAPFDEATPSRLNDLHNISRSTC 365 (424)
Q Consensus 291 ~C~CH~~~~~~~Gy~Cp~C~s~~C-----~lP~~C~~C~l~Lvs~phLarsyhhl~p~~~f~~~~~~~~~~~~~~~~~~C 365 (424)
.=+||.-+.++ .|+||-|..-=- .-|..|++|-= .+|| ..+....|
T Consensus 187 v~~ch~c~gRG-~~vc~gc~g~G~~~y~~~~~m~c~sc~G---~~~~-------------------------k~gt~~~C 237 (406)
T KOG2813|consen 187 VTFCHACLGRG-AMVCHGCSGSGSNSYGIGTPMHCMSCTG---VPPP-------------------------KIGTHDLC 237 (406)
T ss_pred hhhhhcccCCC-ceeccCcCCCCccccccCcceecccccC---CCCC-------------------------CCCccchh
Confidence 35788887777 999999976321 23677877732 1111 12356789
Q ss_pred eecccccccCCCCCCceeeCCCcC---cccccccc
Q 014440 366 FGCQQSLLASGNKAGLCVACPKCK---KHFCLECD 397 (424)
Q Consensus 366 ~~C~~~~~~~~~~~~~~~~C~~C~---~~fC~dCd 397 (424)
+-|. .. +.-.|+.|+ +.-|-.||
T Consensus 238 ~~C~----G~-----G~~~C~tC~grG~k~C~TC~ 263 (406)
T KOG2813|consen 238 YMCH----GR-----GIKECHTCKGRGKKPCTTCS 263 (406)
T ss_pred hhcc----CC-----CcccCCcccCCCCccccccc
Confidence 9997 21 235677775 55677776
No 419
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=21.94 E-value=83 Score=21.03 Aligned_cols=25 Identities=28% Similarity=0.685 Sum_probs=17.5
Q ss_pred ceeecccccccCCCCCCceeeCCCcCc
Q 014440 364 TCFGCQQSLLASGNKAGLCVACPKCKK 390 (424)
Q Consensus 364 ~C~~C~~~~~~~~~~~~~~~~C~~C~~ 390 (424)
.|.+|...|.-+.+. ..++|..|+.
T Consensus 3 ~C~~C~t~L~yP~gA--~~vrCs~C~~ 27 (31)
T TIGR01053 3 VCGGCRTLLMYPRGA--SSVRCALCQT 27 (31)
T ss_pred CcCCCCcEeecCCCC--CeEECCCCCe
Confidence 699998777644322 3589999974
No 420
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=21.85 E-value=34 Score=31.15 Aligned_cols=21 Identities=29% Similarity=0.664 Sum_probs=14.3
Q ss_pred CCCCCCce----ecCchhHHhhhcc
Q 014440 319 ECRICGLQ----LVSSPHLARSYHH 339 (424)
Q Consensus 319 ~C~~C~l~----Lvs~phLarsyhh 339 (424)
.||+||.+ .+|+|+|+++=..
T Consensus 34 ~CP~Cgs~~V~K~lmAP~v~~~~~~ 58 (148)
T PF06676_consen 34 SCPVCGSTEVSKALMAPAVATSRSK 58 (148)
T ss_pred cCCCCCCCeEeeecCCCeecCCCCC
Confidence 45555554 5589999888664
No 421
>cd06352 PBP1_NPR_GC_like Ligand-binding domain of membrane guanylyl-cyclase receptors. Ligand-binding domain of membrane guanylyl-cyclase receptors. Membrane guanylyl cyclases (GC) have a single membrane-spanning region and are activated by endogenous and exogenous peptides. This family can be divided into three major subfamilies: the natriuretic peptide receptors (NPRs), sensory organ-specific membrane GCs, and the enterotoxin/guanylin receptors. The binding of peptide ligands to the receptor results in the activation of the cytosolic catalytic domain. Three types of NPRs have been cloned from mammalian tissues: NPR-A/GC-A, NPR-B/ GC-B, and NPR-C. In addition, two of the GCs, GC-D and GC-G, appear to be pseudogenes in humans. Atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) are produced in the heart, and both bind to the NPR-A. NPR-C, also termed the clearance receptor, binds each of the natriuretic peptides and can alter circulating levels of these peptides. The l
Probab=21.85 E-value=2.9e+02 Score=27.72 Aligned_cols=17 Identities=18% Similarity=0.176 Sum_probs=10.0
Q ss_pred chHHHHHHHHHHHHcCC
Q 014440 168 SSIQNALDLVHGLLNQI 184 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~ 184 (424)
..+.+|+.+|++.++..
T Consensus 17 ~~~~~a~~lAve~iN~~ 33 (389)
T cd06352 17 ARVGPAIQLAVERVNAD 33 (389)
T ss_pred hcchHHHHHHHHHHhcC
Confidence 45555666666666554
No 422
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=21.79 E-value=60 Score=22.73 Aligned_cols=15 Identities=20% Similarity=0.614 Sum_probs=11.1
Q ss_pred CCCceeeCCCcCccc
Q 014440 378 KAGLCVACPKCKKHF 392 (424)
Q Consensus 378 ~~~~~~~C~~C~~~f 392 (424)
.....|.|.+|++.|
T Consensus 24 ~mT~fy~C~~C~~~w 38 (40)
T smart00440 24 PMTVFYVCTKCGHRW 38 (40)
T ss_pred CCeEEEEeCCCCCEe
Confidence 345679999998754
No 423
>cd03371 TPP_PpyrDC Thiamine pyrophosphate (TPP) family, PpyrDC subfamily, TPP-binding module; composed of proteins similar to phosphonopyruvate decarboxylase (PpyrDC) proteins. PpyrDC is a homotrimeric enzyme which functions in the biosynthesis of C-P compounds such as bialaphos tripeptide in Streptomyces hygroscopicus. These proteins require TPP and divalent metal cation cofactors.
Probab=21.77 E-value=6.2e+02 Score=23.32 Aligned_cols=71 Identities=7% Similarity=-0.072 Sum_probs=45.7
Q ss_pred CcEEEEEEcCCCCCCccCHHHHHHHHHhCCc-EEEEEEecch-------------HHHHHHHHHHhCCEEE-EecChhhH
Q 014440 189 HREVLILYSALSTCDPGDIMETIQKCKESKI-RCSVIGLSAE-------------MFICKHLCQETGGTYS-VALDESHS 253 (424)
Q Consensus 189 ~reILvI~ss~~t~dp~~i~~~i~~akk~~I-rV~vIgLg~e-------------~~iLq~iA~~TGG~Y~-~~~d~~~L 253 (424)
.++|++|+|+..-. .++ +.+.++.+.++ .|-+|-+... ..-+.++|+..|..|. .+.+.++|
T Consensus 66 ~~~Vv~i~GDG~f~--m~~-~eL~ta~~~~l~~i~ivV~NN~~yg~~~~~~~~~~~~d~~~~A~a~G~~~~~~v~~~~el 142 (188)
T cd03371 66 DRKVVCIDGDGAAL--MHM-GGLATIGGLAPANLIHIVLNNGAHDSVGGQPTVSFDVSLPAIAKACGYRAVYEVPSLEEL 142 (188)
T ss_pred CCcEEEEeCCcHHH--hhc-cHHHHHHHcCCCCcEEEEEeCchhhccCCcCCCCCCCCHHHHHHHcCCceEEecCCHHHH
Confidence 45788888864320 111 34556666665 4555555422 1247889999998874 67889999
Q ss_pred HHHHHhcCC
Q 014440 254 KELILEHAP 262 (424)
Q Consensus 254 ~~lL~~~~~ 262 (424)
.+.+.+...
T Consensus 143 ~~al~~a~~ 151 (188)
T cd03371 143 VAALAKALA 151 (188)
T ss_pred HHHHHHHHh
Confidence 998877653
No 424
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.74 E-value=35 Score=35.68 Aligned_cols=40 Identities=23% Similarity=0.502 Sum_probs=25.6
Q ss_pred ceeecccccccCCCCCCceeeCCCcCcccccccchhhhcc
Q 014440 364 TCFGCQQSLLASGNKAGLCVACPKCKKHFCLECDIYIHES 403 (424)
Q Consensus 364 ~C~~C~~~~~~~~~~~~~~~~C~~C~~~fC~dCd~fihe~ 403 (424)
.|..|.....-.....+.+..|+.|+..||++|.+-=|..
T Consensus 240 ~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~~wh~~ 279 (384)
T KOG1812|consen 240 RCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKVPWHAN 279 (384)
T ss_pred CchHhhhhhhhccchhhcccccccCCCceeecCCCcCCCC
Confidence 4666653332111122335679999999999999877774
No 425
>cd06348 PBP1_ABC_ligand_binding_like_13 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=21.56 E-value=3.3e+02 Score=26.77 Aligned_cols=7 Identities=29% Similarity=0.363 Sum_probs=3.9
Q ss_pred eeCCCCC
Q 014440 144 LTDLGGS 150 (424)
Q Consensus 144 lspLT~d 150 (424)
+.|||+.
T Consensus 5 ~~plsG~ 11 (344)
T cd06348 5 ALALTGN 11 (344)
T ss_pred EEeccCc
Confidence 4566654
No 426
>cd06334 PBP1_ABC_ligand_binding_like_1 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=21.55 E-value=4.6e+02 Score=26.35 Aligned_cols=60 Identities=8% Similarity=-0.051 Sum_probs=37.5
Q ss_pred cchHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhC-CcEEEEEEecc
Q 014440 167 DSSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKES-KIRCSVIGLSA 228 (424)
Q Consensus 167 ~tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~-~IrV~vIgLg~ 228 (424)
+....+|.++|++.++...+-..|+|=+++-+. ..||....+.++.|... +|.+ ++++++
T Consensus 16 G~~~~~g~~la~~~iNa~GGI~Gr~ielv~~D~-~~~p~~a~~~a~~Li~~~~V~~-i~~~~S 76 (351)
T cd06334 16 GIPYAAGFADYFKYINEDGGINGVKLEWEECDT-GYEVPRGVECYERLKGEDGAVA-FQGWST 76 (351)
T ss_pred ChhHHHHHHHHHHHHHHcCCcCCeEEEEEEecC-CCCcHHHHHHHHHHhccCCcEE-EecCcH
Confidence 356888999999999876444456666665432 23565555666666655 5554 445543
No 427
>KOG2857 consensus Predicted MYND Zn-finger protein/hormone receptor interactor [Transcription]
Probab=21.51 E-value=39 Score=30.59 Aligned_cols=14 Identities=50% Similarity=1.490 Sum_probs=0.0
Q ss_pred EEcCCCCccccCCC
Q 014440 304 YTCPRCKARVCELP 317 (424)
Q Consensus 304 y~Cp~C~s~~C~lP 317 (424)
|-||.|..-||++|
T Consensus 18 YKCpkC~vPYCSl~ 31 (157)
T KOG2857|consen 18 YKCPKCSVPYCSLP 31 (157)
T ss_pred ccCCCCCCccccch
No 428
>TIGR01556 rhamnosyltran L-rhamnosyltransferase. Rhamnolipids are glycolipids containing mono- or di- L-rhamnose molecules. Rhamnolipid synthesis occurs by sequential glycosyltransferase reactions involving two distinct rhamnosyltransferase enzymes. In P.aeruginosa, the synthesis of mono-rhamnolipids is catalyzed by rhamnosyltransferase 1, and proceeds by a glycosyltransfer reaction catalyzed by rhamnosyltransferase 2 to yield di-rhamnolipids.
Probab=21.38 E-value=4.6e+02 Score=25.03 Aligned_cols=52 Identities=8% Similarity=-0.078 Sum_probs=30.6
Q ss_pred hHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEE
Q 014440 169 SIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVI 224 (424)
Q Consensus 169 sL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vI 224 (424)
-++.|+..+++..... ..+.|++++++..-+++.+.+.++.+.+.+..+.++
T Consensus 57 G~a~a~N~Gi~~a~~~----~~d~i~~lD~D~~~~~~~l~~l~~~~~~~~~~~~~~ 108 (281)
T TIGR01556 57 GIAGAQNQGLDASFRR----GVQGVLLLDQDSRPGNAFLAAQWKLLSAENGQACAL 108 (281)
T ss_pred chHHHHHHHHHHHHHC----CCCEEEEECCCCCCCHHHHHHHHHHHHhcCCceEEE
Confidence 4555666555554321 337888888766666666666676666654444444
No 429
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=21.37 E-value=42 Score=21.76 Aligned_cols=13 Identities=38% Similarity=0.974 Sum_probs=6.2
Q ss_pred CCCCCCceecCch
Q 014440 319 ECRICGLQLVSSP 331 (424)
Q Consensus 319 ~C~~C~l~Lvs~p 331 (424)
.||+||..|+-.+
T Consensus 1 ~CP~C~s~l~~~~ 13 (28)
T PF03119_consen 1 TCPVCGSKLVREE 13 (28)
T ss_dssp B-TTT--BEEE-C
T ss_pred CcCCCCCEeEcCC
Confidence 4888888876544
No 430
>PRK06466 acetolactate synthase 3 catalytic subunit; Validated
Probab=21.29 E-value=4.3e+02 Score=28.77 Aligned_cols=88 Identities=15% Similarity=0.108 Sum_probs=59.7
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH-----------------
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM----------------- 230 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~----------------- 230 (424)
.+++-||-.|+..=-.. ..|+||.|+|++.- . .++ +.+.++.+.|+++-+|-+....
T Consensus 423 gsmG~glpaAiGa~la~---p~r~Vv~i~GDG~f-~-m~~-~eL~Ta~r~~lpv~ivV~NN~~y~~i~~~q~~~~~~~~~ 496 (574)
T PRK06466 423 GTMGFGLPAAMGVKLAF---PDQDVACVTGEGSI-Q-MNI-QELSTCLQYGLPVKIINLNNGALGMVRQWQDMQYEGRHS 496 (574)
T ss_pred chhhchHHHHHHHHHhC---CCCeEEEEEcchhh-h-ccH-HHHHHHHHhCCCeEEEEEeCCccHHHHHHHHHhcCCcee
Confidence 46666666666543322 25678888886431 1 222 4567889999999888875321
Q ss_pred -------HHHHHHHHHhCCEEEEecChhhHHHHHHhcC
Q 014440 231 -------FICKHLCQETGGTYSVALDESHSKELILEHA 261 (424)
Q Consensus 231 -------~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~ 261 (424)
.-+.++|+.-|+.+..+.+.++|...|...+
T Consensus 497 ~~~~~~~~d~~~lA~a~G~~~~~v~~~~el~~al~~a~ 534 (574)
T PRK06466 497 HSYMESLPDFVKLAEAYGHVGIRITDLKDLKPKLEEAF 534 (574)
T ss_pred ecCCCCCCCHHHHHHHCCCeEEEECCHHHHHHHHHHHH
Confidence 1245678888888889999999988887765
No 431
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=21.21 E-value=59 Score=29.36 Aligned_cols=26 Identities=31% Similarity=0.801 Sum_probs=18.6
Q ss_pred ceeecccccccCCCCCCceeeCCCcCccc
Q 014440 364 TCFGCQQSLLASGNKAGLCVACPKCKKHF 392 (424)
Q Consensus 364 ~C~~C~~~~~~~~~~~~~~~~C~~C~~~f 392 (424)
.|..|.+.+...+ ...|.|++|++.+
T Consensus 36 aC~~C~kkv~~~~---~~~~~C~~C~~~~ 61 (166)
T cd04476 36 ACPGCNKKVVEEG---NGTYRCEKCNKSV 61 (166)
T ss_pred cccccCcccEeCC---CCcEECCCCCCcC
Confidence 5889998876432 1469999998763
No 432
>PRK06456 acetolactate synthase catalytic subunit; Reviewed
Probab=21.10 E-value=4.2e+02 Score=28.72 Aligned_cols=88 Identities=9% Similarity=-0.076 Sum_probs=58.9
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH-----------------
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM----------------- 230 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~----------------- 230 (424)
-+++-||-.|+..=-.. ..++|+.|+|++.- -.++ +.+.++.+.+++|-+|-+....
T Consensus 421 g~mG~glpaAiGa~la~---p~~~vv~i~GDG~f--~m~~-~eL~Ta~~~~l~i~ivV~NN~~yg~i~~~q~~~~~~~~~ 494 (572)
T PRK06456 421 GTMGFGLPAAMGAKLAR---PDKVVVDLDGDGSF--LMTG-TNLATAVDEHIPVISVIFDNRTLGLVRQVQDLFFGKRIV 494 (572)
T ss_pred ccccchhHHHHHHHHhC---CCCeEEEEEccchH--hcch-HHHHHHHHhCCCeEEEEEECCchHHHHHHHHHhhCCCcc
Confidence 45666666555543222 24678888886432 1222 4567889999999888775320
Q ss_pred -------HHHHHHHHHhCCEEEEecChhhHHHHHHhcC
Q 014440 231 -------FICKHLCQETGGTYSVALDESHSKELILEHA 261 (424)
Q Consensus 231 -------~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~ 261 (424)
.-+.++|+..|..++.+.+.++|++.|....
T Consensus 495 ~~~~~~~~d~~~~A~a~G~~~~~v~~~~eL~~al~~a~ 532 (572)
T PRK06456 495 GVDYGPSPDFVKLAEAFGALGFNVTTYEDIEKSLKSAI 532 (572)
T ss_pred cccCCCCCCHHHHHHHCCCeeEEeCCHHHHHHHHHHHH
Confidence 1267788888888888889999988887765
No 433
>TIGR00197 yjeF_nterm yjeF N-terminal region. This model is built on yeast protein YNL200C and the N-terminal regions of E. coli yjeF and its orthologs in various species. The C-terminal region of yjeF and its orthologs shows similarity to hydroxyethylthiazole kinase (thiM) and other enzymes involved in thiamine biosynthesis. Yeast YKL151C and B. subtilis yxkO match the yjeF C-terminal domain but lack this region.
Probab=21.08 E-value=3.1e+02 Score=25.85 Aligned_cols=38 Identities=13% Similarity=0.117 Sum_probs=28.6
Q ss_pred CcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecc
Q 014440 189 HREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSA 228 (424)
Q Consensus 189 ~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~ 228 (424)
.++|+|+.|...+ -+|=..++..|.+.++.|++++...
T Consensus 45 ~~~v~vl~G~GNN--GGDGlv~AR~L~~~~v~V~~~~~~~ 82 (205)
T TIGR00197 45 AGHVIIFCGPGNN--GGDGFVVARHLKGFGVEVFLLKKEK 82 (205)
T ss_pred CCeEEEEECCCCC--ccHHHHHHHHHHhCCCEEEEEccCC
Confidence 4568888886543 5677788888888999999987654
No 434
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=21.06 E-value=79 Score=20.36 Aligned_cols=24 Identities=25% Similarity=0.703 Sum_probs=17.9
Q ss_pred eEEcCCCCccccCCCCCCCCCCce
Q 014440 303 GYTCPRCKARVCELPTECRICGLQ 326 (424)
Q Consensus 303 Gy~Cp~C~s~~C~lP~~C~~C~l~ 326 (424)
.+.|+.|.-.-=.-...|..|+..
T Consensus 4 ~W~C~~C~~~N~~~~~~C~~C~~~ 27 (30)
T PF00641_consen 4 DWKCPSCTFMNPASRSKCVACGAP 27 (30)
T ss_dssp SEEETTTTEEEESSSSB-TTT--B
T ss_pred CccCCCCcCCchHHhhhhhCcCCC
Confidence 678999999888888899999863
No 435
>PRK14093 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D-alanine ligase; Provisional
Probab=20.92 E-value=4.2e+02 Score=28.17 Aligned_cols=16 Identities=6% Similarity=0.057 Sum_probs=9.0
Q ss_pred cChhhHHHHHHhcCCC
Q 014440 248 LDESHSKELILEHAPP 263 (424)
Q Consensus 248 ~d~~~L~~lL~~~~~p 263 (424)
.|.+.+.+.|...+.|
T Consensus 428 ~~~~~~~~~l~~~~~~ 443 (479)
T PRK14093 428 EDAAALESQVVAAIRA 443 (479)
T ss_pred CCHHHHHHHHHHhcCC
Confidence 4555666666555544
No 436
>PRK11269 glyoxylate carboligase; Provisional
Probab=20.89 E-value=5.1e+02 Score=28.30 Aligned_cols=88 Identities=8% Similarity=-0.003 Sum_probs=58.9
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH-----------------
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM----------------- 230 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~----------------- 230 (424)
.+++-||-.|+..=-.. ..|+||.|+|++.- -.++ ..+.++.+.+++|-+|-+-...
T Consensus 419 G~mG~glpaAiGa~la~---p~r~Vv~i~GDG~f--~m~~-~eL~Ta~~~~lpv~~vV~NN~~~g~i~~~~~~~~~~~~~ 492 (591)
T PRK11269 419 GPLGWTIPAALGVRAAD---PDRNVVALSGDYDF--QFLI-EELAVGAQFNLPYIHVLVNNAYLGLIRQAQRAFDMDYCV 492 (591)
T ss_pred ccccchhhhHHhhhhhC---CCCcEEEEEccchh--hcCH-HHHHHHHHhCCCeEEEEEeCCchhHHHHHHHHhccCccc
Confidence 35555555555533222 24678999886432 1222 4567789999998888775320
Q ss_pred ----------------HHHHHHHHHhCCEEEEecChhhHHHHHHhcC
Q 014440 231 ----------------FICKHLCQETGGTYSVALDESHSKELILEHA 261 (424)
Q Consensus 231 ----------------~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~ 261 (424)
.-+.++|+.-|+.+..+.+.++|+..|...+
T Consensus 493 ~~~~~~~~~~~~~~~~~df~~lA~a~G~~~~~v~~~~eL~~al~~a~ 539 (591)
T PRK11269 493 QLAFENINSPELNGYGVDHVKVAEGLGCKAIRVFKPEDIAPALEQAK 539 (591)
T ss_pred eeeccccccccccCCCCCHHHHHHHCCCeEEEECCHHHHHHHHHHHH
Confidence 0146788888999999999999999887765
No 437
>PRK11869 2-oxoacid ferredoxin oxidoreductase subunit beta; Provisional
Probab=20.88 E-value=3.7e+02 Score=26.90 Aligned_cols=56 Identities=7% Similarity=-0.066 Sum_probs=35.0
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCH-HHHHHHHHhCCcEEEEEEecch
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDI-METIQKCKESKIRCSVIGLSAE 229 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i-~~~i~~akk~~IrV~vIgLg~e 229 (424)
+.++.||-.|+..=...| .+.||.+.|+.+. ..+ .+-+..+.+.|+.|-+|-+..+
T Consensus 60 ~~mG~alp~AiGaklA~p---d~~VVai~GDG~~---~~iG~~eL~tA~r~nl~i~~IV~NN~ 116 (280)
T PRK11869 60 TLHGRAIPAATAVKATNP---ELTVIAEGGDGDM---YAEGGNHLIHAIRRNPDITVLVHNNQ 116 (280)
T ss_pred cccccHHHHHHHHHHHCC---CCcEEEEECchHH---hhCcHHHHHHHHHhCcCcEEEEEECH
Confidence 345556655555422222 4678888886543 222 4567788889999999888644
No 438
>PF10825 DUF2752: Protein of unknown function (DUF2752); InterPro: IPR021215 This family is conserved in bacteria. Many members are annotated as being putative membrane proteins.
Probab=20.84 E-value=31 Score=25.59 Aligned_cols=15 Identities=33% Similarity=0.897 Sum_probs=10.1
Q ss_pred CCCCCCceecCchhHHhhhcccC
Q 014440 319 ECRICGLQLVSSPHLARSYHHLF 341 (424)
Q Consensus 319 ~C~~C~l~Lvs~phLarsyhhl~ 341 (424)
.||.||+| ||+++|.
T Consensus 11 ~CPgCG~t--------Ra~~~ll 25 (52)
T PF10825_consen 11 PCPGCGMT--------RAFIALL 25 (52)
T ss_pred CCCCCcHH--------HHHHHHH
Confidence 57788866 6666653
No 439
>cd02511 Beta4Glucosyltransferase UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide. UDP-glucose: lipooligosaccharide (LOS) beta-1-4-glucosyltransferase catalyzes the addition of the first residue, glucose, of the lacto-N-neotetrase structure to HepI of the LOS inner core. LOS is the major constituent of the outer leaflet of the outer membrane of gram-positive bacteria. It consists of a short oligosaccharide chain of variable composition (alpha chain) attached to a branched inner core which is lined in turn to lipid A. Beta 1,4 glucosyltransferase is required to attach the alpha chain to the inner core.
Probab=20.81 E-value=5.8e+02 Score=23.63 Aligned_cols=67 Identities=18% Similarity=0.143 Sum_probs=38.1
Q ss_pred EEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchHHHHHHHHHHhCCEEEEecChh------hHHHHHHhcCCCC
Q 014440 191 EVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEMFICKHLCQETGGTYSVALDES------HSKELILEHAPPP 264 (424)
Q Consensus 191 eILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~~iLq~iA~~TGG~Y~~~~d~~------~L~~lL~~~~~pp 264 (424)
||||+-++ ++ | .|.+.+++.+++|....-..-........+...|.|....|.+ .+..++..+..+|
T Consensus 28 eiivvD~g-St-D-----~t~~i~~~~~~~v~~~~~~g~~~~~n~~~~~a~~d~vl~lDaD~~~~~~~~~~l~~~~~~~~ 100 (229)
T cd02511 28 EIIVVDSG-ST-D-----RTVEIAKEYGAKVYQRWWDGFGAQRNFALELATNDWVLSLDADERLTPELADEILALLATDD 100 (229)
T ss_pred EEEEEeCC-CC-c-----cHHHHHHHcCCEEEECCCCChHHHHHHHHHhCCCCEEEEEeCCcCcCHHHHHHHHHHHhCCC
Confidence 67766543 22 2 2455666788887655222233555666666778888776655 3455555444444
No 440
>cd04916 ACT_AKiii-YclM-BS_2 ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII. This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) YclM) and Clostridia species. Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. B. subtilis YclM is reported to be a single polypeptide of 50 kD. AKIII from B. subtilis strain 168 is induced by lysine and repressed by threonine and it is synergistically inhibited by lysine and threonine. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=20.81 E-value=2.4e+02 Score=20.41 Aligned_cols=36 Identities=8% Similarity=0.061 Sum_probs=25.2
Q ss_pred EEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecc
Q 014440 193 LILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSA 228 (424)
Q Consensus 193 LvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~ 228 (424)
|=+.|..-..+++-....+..+.+.||.|+.|+-+.
T Consensus 4 isivg~~~~~~~~~~~~i~~~L~~~~i~v~~i~~~~ 39 (66)
T cd04916 4 IMVVGEGMKNTVGVSARATAALAKAGINIRMINQGS 39 (66)
T ss_pred EEEEcCCCCCCccHHHHHHHHHHHCCCCEEEEEecC
Confidence 334454333355556678899999999999998764
No 441
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=20.81 E-value=16 Score=35.17 Aligned_cols=76 Identities=25% Similarity=0.527 Sum_probs=49.9
Q ss_pred CCCCCCceecCchhHHhhhc-ccCCCCCCcccCccccccccCCCCCceeecccccccCCC--------CCCceeeCCCcC
Q 014440 319 ECRICGLQLVSSPHLARSYH-HLFPIAPFDEATPSRLNDLHNISRSTCFGCQQSLLASGN--------KAGLCVACPKCK 389 (424)
Q Consensus 319 ~C~~C~l~Lvs~phLarsyh-hl~p~~~f~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~--------~~~~~~~C~~C~ 389 (424)
.|.+||..+-.--.|.|-.- |. ++ ....|..|.+.|.+..+ ...-.|.|..|.
T Consensus 119 tCrvCgK~F~lQRmlnrh~kch~-~v-----------------kr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~ 180 (267)
T KOG3576|consen 119 TCRVCGKKFGLQRMLNRHLKCHS-DV-----------------KRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCE 180 (267)
T ss_pred eeehhhhhhhHHHHHHHHhhhcc-HH-----------------HHHHHhhccCcccchhhhhhhhccccCccccchhhhh
Confidence 46667777765555555332 21 11 12369999999976531 122359999999
Q ss_pred cccccccchhhh-----------------ccCCCCCCCCC
Q 014440 390 KHFCLECDIYIH-----------------ESLHNCPGCES 412 (424)
Q Consensus 390 ~~fC~dCd~fih-----------------e~lh~CPgC~~ 412 (424)
+.|=.-|.+--| +.|+.|--|..
T Consensus 181 kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~ 220 (267)
T KOG3576|consen 181 KAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGY 220 (267)
T ss_pred HHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCC
Confidence 999999986544 45788888864
No 442
>PRK08266 hypothetical protein; Provisional
Probab=20.80 E-value=4.5e+02 Score=28.30 Aligned_cols=88 Identities=7% Similarity=-0.031 Sum_probs=59.5
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH-----------------
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM----------------- 230 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~----------------- 230 (424)
.+++.+|-.|+..-... ..+.|++|+|++.- . .++ +.+.++.+.+++|-+|-+....
T Consensus 402 GsmG~~lp~aiGa~la~---p~~~vv~v~GDG~f-~-~~~-~eL~ta~~~~lpv~ivv~NN~~y~~~~~~~~~~~~~~~~ 475 (542)
T PRK08266 402 GTLGYGFPTALGAKVAN---PDRPVVSITGDGGF-M-FGV-QELATAVQHNIGVVTVVFNNNAYGNVRRDQKRRFGGRVV 475 (542)
T ss_pred cccccHHHHHHHHHHhC---CCCcEEEEEcchhh-h-ccH-HHHHHHHHhCCCeEEEEEeCCcchHHHHHHHHhcCCCcc
Confidence 45666666666543222 24678888886532 1 233 4567788999988887665321
Q ss_pred ------HHHHHHHHHhCCEEEEecChhhHHHHHHhcC
Q 014440 231 ------FICKHLCQETGGTYSVALDESHSKELILEHA 261 (424)
Q Consensus 231 ------~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~ 261 (424)
.-+.++|+.-|..|+.+.+.++|++.+....
T Consensus 476 ~~~~~~~d~~~la~a~G~~~~~v~~~~el~~al~~a~ 512 (542)
T PRK08266 476 ASDLVNPDFVKLAESFGVAAFRVDSPEELRAALEAAL 512 (542)
T ss_pred cCCCCCCCHHHHHHHcCCeEEEeCCHHHHHHHHHHHH
Confidence 1256788888999999999999999987765
No 443
>PRK08659 2-oxoglutarate ferredoxin oxidoreductase subunit alpha; Validated
Probab=20.71 E-value=3.4e+02 Score=28.18 Aligned_cols=69 Identities=9% Similarity=0.102 Sum_probs=45.9
Q ss_pred cEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecc----hHHHHHHHHHHhCCEEEEecChhhHHHHHHhcC
Q 014440 190 REVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSA----EMFICKHLCQETGGTYSVALDESHSKELILEHA 261 (424)
Q Consensus 190 reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~----e~~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~ 261 (424)
.+++||..+.. .+...++++.|++.|++|.++.+.. ....++++++.......+-.+...|...+...+
T Consensus 274 ad~~iv~~Gs~---~~~a~eAv~~Lr~~G~~v~~l~~~~l~Pfp~~~i~~~~~~~k~VivvEe~~g~l~~el~~~~ 346 (376)
T PRK08659 274 AEVVVVAYGSV---ARSARRAVKEAREEGIKVGLFRLITVWPFPEEAIRELAKKVKAIVVPEMNLGQMSLEVERVV 346 (376)
T ss_pred CCEEEEEeCcc---HHHHHHHHHHHHhcCCceEEEEeCeecCCCHHHHHHHHhcCCEEEEEeCCHHHHHHHHHHHh
Confidence 45677664322 3567899999999999999999985 345667777655555555555555555554444
No 444
>PHA00626 hypothetical protein
Probab=20.66 E-value=53 Score=25.13 Aligned_cols=14 Identities=14% Similarity=0.090 Sum_probs=11.3
Q ss_pred ceeeCCCcCccccc
Q 014440 381 LCVACPKCKKHFCL 394 (424)
Q Consensus 381 ~~~~C~~C~~~fC~ 394 (424)
.+|.|++|+-.|=.
T Consensus 22 nrYkCkdCGY~ft~ 35 (59)
T PHA00626 22 DDYVCCDCGYNDSK 35 (59)
T ss_pred cceEcCCCCCeech
Confidence 47999999988754
No 445
>cd07041 STAS_RsbR_RsbS_like Sulphate Transporter and Anti-Sigma factor antagonist domain of the "stressosome" complex proteins RsbS and RsbR, regulators of the bacterial stress activated alternative sigma factor sigma-B by phosphorylation. The STAS (Sulphate Transporter and Anti-Sigma factor antagonist) domain of proteins related to RsbS and RsbR which are part of the "stressosome" complex that plays an important role in the regulation of the bacterial stress activated alternative sigma factor sigma-B. During stress conditions RsbS and RsbR are phosphorylated which leads to the release of RsbT, an activator of of the RsbU phosphatase, which in turn activates RsbV which leads to the release and activation of sigma factor B. RsbS is a single domain protein (STAS domain), while RsbR-like proteins have a well-conserved C-terminal STATS domain and a variable N-terminal domain. The STAS domain is also found in the C- terminal region of sulphate transporters and anti-anti-sigma factors.
Probab=20.65 E-value=3.1e+02 Score=22.37 Aligned_cols=41 Identities=17% Similarity=0.275 Sum_probs=27.3
Q ss_pred cEEEEEEcCCCCCCccC---HHHHHHHHHhCCcEEEEEEecchH
Q 014440 190 REVLILYSALSTCDPGD---IMETIQKCKESKIRCSVIGLSAEM 230 (424)
Q Consensus 190 reILvI~ss~~t~dp~~---i~~~i~~akk~~IrV~vIgLg~e~ 230 (424)
+.||+=+++....|... +.+..+.+++.|+++.++|+..++
T Consensus 42 ~~vvlDls~v~~iDssg~~~l~~~~~~~~~~g~~l~l~g~~~~v 85 (109)
T cd07041 42 RGVIIDLTGVPVIDSAVARHLLRLARALRLLGARTILTGIRPEV 85 (109)
T ss_pred CEEEEECCCCchhcHHHHHHHHHHHHHHHHcCCeEEEEeCCHHH
Confidence 33444455554444332 346788888999999999998654
No 446
>PF00731 AIRC: AIR carboxylase; InterPro: IPR000031 Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. PurK, N5-carboxyaminoimidazole ribonucleotide (N5_CAIR) synthetase, catalyzes the conversion of 5-aminoimidazole ribonucleotide (AIR), ATP, and bicarbonate to N5-CAIR, ADP, and Pi. PurE converts N5-CAIR to CAIR, the sixth step of de novo purine biosynthesis. In the presence of high concentrations of bicarbonate, PurE is reported able to convert AIR to CAIR directly and without ATP. Some members of this family contain two copies of this domain []. The crystal structure of PurE indicates a unique quaternary structure that confirms the octameric nature of the enzyme [].; GO: 0004638 phosphoribosylaminoimidazole carboxylase activity, 0006189 'de novo' IMP biosynthetic process; PDB: 3TRH_O 2YWX_A 2NSL_A 1D7A_A 2NSJ_A 1QCZ_A 2ATE_A 2NSH_A 3RG8_C 3RGG_D ....
Probab=20.63 E-value=5.3e+02 Score=23.46 Aligned_cols=73 Identities=21% Similarity=0.064 Sum_probs=43.8
Q ss_pred EEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecch--HHHHHHHHHHhC--C--EEE-EecChhhHHHHHHhcCCC
Q 014440 191 EVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAE--MFICKHLCQETG--G--TYS-VALDESHSKELILEHAPP 263 (424)
Q Consensus 191 eILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e--~~iLq~iA~~TG--G--~Y~-~~~d~~~L~~lL~~~~~p 263 (424)
+|.||++|.+ |-.-..++.+.|++.||..++=-.++. ..-+.++.+... | .|. ++--+.||-.++..+++-
T Consensus 2 ~V~Ii~gs~S--D~~~~~~a~~~L~~~gi~~~~~V~saHR~p~~l~~~~~~~~~~~~~viIa~AG~~a~Lpgvva~~t~~ 79 (150)
T PF00731_consen 2 KVAIIMGSTS--DLPIAEEAAKTLEEFGIPYEVRVASAHRTPERLLEFVKEYEARGADVIIAVAGMSAALPGVVASLTTL 79 (150)
T ss_dssp EEEEEESSGG--GHHHHHHHHHHHHHTT-EEEEEE--TTTSHHHHHHHHHHTTTTTESEEEEEEESS--HHHHHHHHSSS
T ss_pred eEEEEeCCHH--HHHHHHHHHHHHHHcCCCEEEEEEeccCCHHHHHHHHHHhccCCCEEEEEECCCcccchhhheeccCC
Confidence 5888888743 433345889999999998876555532 333444443332 3 555 356788999999999876
Q ss_pred Cc
Q 014440 264 PP 265 (424)
Q Consensus 264 p~ 265 (424)
|.
T Consensus 80 PV 81 (150)
T PF00731_consen 80 PV 81 (150)
T ss_dssp -E
T ss_pred CE
Confidence 64
No 447
>PLN02235 ATP citrate (pro-S)-lyase
Probab=20.61 E-value=4.6e+02 Score=28.01 Aligned_cols=127 Identities=15% Similarity=0.139 Sum_probs=66.9
Q ss_pred cCCCCcEEEEEecCCceEEeeCCCCCHHHHHHHH------hhhhCCCCcc---hHHHHHHHHHHHHcCCCCCCCcEEEEE
Q 014440 125 QNPLSQIGLVTVKDGVANCLTDLGGSPESHIKAL------MGKLGCSGDS---SIQNALDLVHGLLNQIPSYGHREVLIL 195 (424)
Q Consensus 125 qnP~sqlGII~~~~g~A~~lspLT~d~~~~~~~L------~~~~~~~G~t---sL~~AL~~Al~~L~~~p~~~~reILvI 195 (424)
-++..+||.++..+|-+.. .-+.+... .+.++-.|++ .+..|+.+-+.++.+.| ....-+|.|
T Consensus 266 v~ldG~Ig~mvnGAGlama-------TmD~I~~~G~~g~pANFlDvGG~a~~e~v~~a~~iil~~~~~~~-~vk~ilvnI 337 (423)
T PLN02235 266 LNPKGRIWTMVAGGGASVI-------YADTVGDLGYASELGNYAEYSGAPNEEEVLQYARVVIDCATANP-DGRKRALLI 337 (423)
T ss_pred eCCCCeEEEEecCcHHHHH-------HHHHHHHcCCCCCCceeeecCCCCCHHHHHHHHHHHHhhhhcCC-CCcEEEEEE
Confidence 4677889999976554432 11122221 1223344544 34455555444444442 223334556
Q ss_pred EcCCCCCCccCH--HHHHHHHHhC-------CcEEEEEEec-ch----HHHHHHHHHHhCCEEEEecChhhHHHHHHhc
Q 014440 196 YSALSTCDPGDI--METIQKCKES-------KIRCSVIGLS-AE----MFICKHLCQETGGTYSVALDESHSKELILEH 260 (424)
Q Consensus 196 ~ss~~t~dp~~i--~~~i~~akk~-------~IrV~vIgLg-~e----~~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~ 260 (424)
+|+...||..-. .-+++.+++. +|+|.| -++ +. ..+|+++.+.+|=...+...+.++.+.....
T Consensus 338 fGGI~rcd~VA~tf~GIi~A~~e~~~kl~~~~vpivV-Rl~GtN~eeG~~il~e~~~~~gl~i~~~~~~~~m~~a~~~a 415 (423)
T PLN02235 338 GGGIANFTDVAATFNGIIRALREKESKLKAARMHIFV-RRGGPNYQKGLAKMRALGEEIGVPIEVYGPEATMTGICKQA 415 (423)
T ss_pred ecccccchhhhhhhhHHHHHHHHhhhccccCCccEEE-ECCCCCHHHHHHHHHHhHHhcCCcEEEeCCCCCHHHHHHHH
Confidence 677777774321 2345555553 578744 555 33 4788888878875455554444565554443
No 448
>cd06331 PBP1_AmiC_like Type I periplasmic components of amide-binding protein (AmiC) and the active transport system for short-chain and urea (FmdDEF). This group includes the type I periplasmic components of amide-binding protein (AmiC) and the active transport system for short-chain and urea (FmdDEF), found in bacteria and Archaea. AmiC controls expression of the amidase operon by a ligand-triggered conformational switch. In the absence of ligand or presence of butyramide (repressor), AmiC (the ligand sensor and negative regulator) adopts an open conformation and inhibits the transcription antitermination function of AmiR by direct protein-protein interaction. In the presence of inducing ligands such as acetamide, AmiC adopts a closed conformation which disrupts a silencing AmiC-AmiR complex and the expression of amidase and other genes of the operon is induced. FmdDEF is predicted to be an ATP-dependent transporter and closely resembles the periplasmic binding protein and the two t
Probab=20.46 E-value=7.1e+02 Score=24.26 Aligned_cols=53 Identities=17% Similarity=0.162 Sum_probs=29.7
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhC-CcEE
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKES-KIRC 221 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~-~IrV 221 (424)
..+.+++++|++.++...+-..++|=+++-+.. .||..-.++++.|.+. +|.+
T Consensus 17 ~~~~~g~~~a~~~iN~~gGi~G~~i~l~~~D~~-~~p~~a~~~a~~Li~~~~V~a 70 (333)
T cd06331 17 PSLRNAALLAIEEINAAGGILGRPLELVVEDPA-SDPAFAAKAARRLIRDDKVDA 70 (333)
T ss_pred HHHHHHHHHHHHHHHhcCCCCCeEEEEEEECCC-CCHHHHHHHHHHHHhccCCcE
Confidence 466778888888887653333455555554322 2444444455555544 6543
No 449
>PRK11204 N-glycosyltransferase; Provisional
Probab=20.43 E-value=6.2e+02 Score=25.86 Aligned_cols=68 Identities=18% Similarity=0.214 Sum_probs=42.0
Q ss_pred CcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecc---hHHHHHHHHHHhCCEEEEecChh------hHHHHHHh
Q 014440 189 HREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSA---EMFICKHLCQETGGTYSVALDES------HSKELILE 259 (424)
Q Consensus 189 ~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~---e~~iLq~iA~~TGG~Y~~~~d~~------~L~~lL~~ 259 (424)
.-||+|+-++ ++ | +..+.++.+.+...++.++-... ...-+....+...|.|+...|.+ -|.+++..
T Consensus 83 ~~eiiVvdD~-s~-d--~t~~~l~~~~~~~~~v~~i~~~~n~Gka~aln~g~~~a~~d~i~~lDaD~~~~~d~L~~l~~~ 158 (420)
T PRK11204 83 NYEVIAINDG-SS-D--NTGEILDRLAAQIPRLRVIHLAENQGKANALNTGAAAARSEYLVCIDGDALLDPDAAAYMVEH 158 (420)
T ss_pred CeEEEEEECC-CC-c--cHHHHHHHHHHhCCcEEEEEcCCCCCHHHHHHHHHHHcCCCEEEEECCCCCCChhHHHHHHHH
Confidence 4577777553 22 2 33455666666555666666432 34567777778899999877766 35666555
Q ss_pred c
Q 014440 260 H 260 (424)
Q Consensus 260 ~ 260 (424)
+
T Consensus 159 ~ 159 (420)
T PRK11204 159 F 159 (420)
T ss_pred H
Confidence 5
No 450
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=20.33 E-value=45 Score=33.86 Aligned_cols=42 Identities=26% Similarity=0.544 Sum_probs=0.0
Q ss_pred CCCCCceecCc-hhH---HhhhcccCCCCCCcccCccccccccCCCCCceeecccccccCCCCCCceeeCCCcCc
Q 014440 320 CRICGLQLVSS-PHL---ARSYHHLFPIAPFDEATPSRLNDLHNISRSTCFGCQQSLLASGNKAGLCVACPKCKK 390 (424)
Q Consensus 320 C~~C~l~Lvs~-phL---arsyhhl~p~~~f~~~~~~~~~~~~~~~~~~C~~C~~~~~~~~~~~~~~~~C~~C~~ 390 (424)
||+||..=+.+ -+. .....|| +|..|...-.-. +-.|+.|++
T Consensus 187 CPvCGs~P~~s~~~~~~~~~G~RyL-----------------------~CslC~teW~~~------R~~C~~Cg~ 232 (305)
T TIGR01562 187 CPACGSPPVASMVRQGGKETGLRYL-----------------------SCSLCATEWHYV------RVKCSHCEE 232 (305)
T ss_pred CCCCCChhhhhhhcccCCCCCceEE-----------------------EcCCCCCccccc------CccCCCCCC
No 451
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=20.33 E-value=54 Score=29.80 Aligned_cols=76 Identities=9% Similarity=0.117 Sum_probs=0.0
Q ss_pred HHHHHHHhCCEEEEecChhhHHHHHHhcCCCCccchhhhhhheeeecCCCCCCCCCcceeeecCCccccCeEEcCCCCcc
Q 014440 233 CKHLCQETGGTYSVALDESHSKELILEHAPPPPAIAEFAIASLIKMGFPQRAGEGSISICSCHKEVKIGVGYTCPRCKAR 312 (424)
Q Consensus 233 Lq~iA~~TGG~Y~~~~d~~~L~~lL~~~~~pp~~~~~~~~~~Li~mGFP~~~~~~~~a~C~CH~~~~~~~Gy~Cp~C~s~ 312 (424)
++++-..-++.|+...-...++.+|.+... .-++..--.-..-.+..-..+.+|+--+ ... -|.|-.|+++
T Consensus 68 kr~~~~~~~~~~~~~~~RKnf~~~Ldea~~------~~~k~~~Y~~~~a~p~~KP~r~fCaVCG--~~S-~ysC~~CG~k 138 (156)
T KOG3362|consen 68 KRKKQKSYKSEKFKLRFRKNFQALLDEALL------NLMKNPNYHTAYAKPSFKPLRKFCAVCG--YDS-KYSCVNCGTK 138 (156)
T ss_pred hhhhccccccchhhhhHHHHHHHHHHccch------hhhhccchhhcccCCCCCCcchhhhhcC--CCc-hhHHHhcCCc
Q ss_pred ccCCC
Q 014440 313 VCELP 317 (424)
Q Consensus 313 ~C~lP 317 (424)
||+++
T Consensus 139 yCsv~ 143 (156)
T KOG3362|consen 139 YCSVR 143 (156)
T ss_pred eeech
No 452
>PRK06546 pyruvate dehydrogenase; Provisional
Probab=20.29 E-value=3.5e+02 Score=29.54 Aligned_cols=88 Identities=15% Similarity=0.072 Sum_probs=58.1
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchH-----------------
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEM----------------- 230 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~----------------- 230 (424)
.+++.+|-.|+..--..| .++||+|+|++.- . ..+ ..+.++.+.+++|-+|-+....
T Consensus 408 gsmG~~~paAiGa~la~p---~~~vv~i~GDGsf-~-~~~-~el~Ta~~~~lpv~~vV~NN~~~g~i~~~q~~~~~~~~~ 481 (578)
T PRK06546 408 GSMANALPHAIGAQLADP---GRQVISMSGDGGL-S-MLL-GELLTVKLYDLPVKVVVFNNSTLGMVKLEMLVDGLPDFG 481 (578)
T ss_pred ccccchhHHHHHHHHhCC---CCcEEEEEcCchH-h-hhH-HHHHHHHHhCCCeEEEEEECCccccHHHHHHhcCCCccc
Confidence 456666666655433222 4678888886432 1 233 3467889999998888775321
Q ss_pred -----HHHHHHHHHhCCEEEEecChhhHHHHHHhcC
Q 014440 231 -----FICKHLCQETGGTYSVALDESHSKELILEHA 261 (424)
Q Consensus 231 -----~iLq~iA~~TGG~Y~~~~d~~~L~~lL~~~~ 261 (424)
.-+-++|+..|..+..+.+.++|++.+.+..
T Consensus 482 ~~~~~~df~~lA~a~G~~~~~v~~~~el~~al~~a~ 517 (578)
T PRK06546 482 TDHPPVDYAAIAAALGIHAVRVEDPKDVRGALREAF 517 (578)
T ss_pred ccCCCCCHHHHHHHCCCeeEEeCCHHHHHHHHHHHH
Confidence 1245788888888888888888888887765
No 453
>cd06330 PBP1_Arsenic_SBP_like Periplasmic solute-binding domain of active transport proteins. Periplasmic solute-binding domain of active transport proteins found in bacteria and Archaea that is predicted to be involved in the efflux of toxic compounds. Members of this subgroup include proteins from Herminiimonas arsenicoxydans, which is resistant to arsenic and various heavy metals such as cadmium and zinc. Moreover, they show significant sequence similarity to the cluster of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa.
Probab=20.12 E-value=6.6e+02 Score=24.55 Aligned_cols=54 Identities=13% Similarity=0.214 Sum_probs=25.9
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhC-CcEEE
Q 014440 168 SSIQNALDLVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKES-KIRCS 222 (424)
Q Consensus 168 tsL~~AL~~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~-~IrV~ 222 (424)
.....|+++|++.++....-..++|=+++.+. ..|+....+.++.+.+. +|.+-
T Consensus 17 ~~~~~g~~~a~~~iN~~ggi~G~~v~~~~~D~-~~~~~~a~~~a~~li~~~~v~ai 71 (346)
T cd06330 17 EPARNGAELAVEEINAAGGIGGRKIELVVRDE-AGKPDEAIREARELVENEGVDML 71 (346)
T ss_pred HHHHHHHHHHHHHHhhcCCcCCeEEEEEEecC-CCCHHHHHHHHHHHHhccCCcEE
Confidence 34566777777777654333334444444321 12343333444444443 55433
No 454
>PF02887 PK_C: Pyruvate kinase, alpha/beta domain; InterPro: IPR015795 Pyruvate kinase (2.7.1.40 from EC) (PK) catalyses the final step in glycolysis [], the conversion of phosphoenolpyruvate to pyruvate with concomitant phosphorylation of ADP to ATP: ADP + phosphoenolpyruvate = ATP + pyruvate The enzyme, which is found in all living organisms, requires both magnesium and potassium ions for its activity. In vertebrates, there are four tissue-specific isozymes: L (liver), R (red cells), M1 (muscle, heart and brain), and M2 (early foetal tissue). In plants, PK exists as cytoplasmic and plastid isozymes, while most bacteria and lower eukaryotes have one form, except in certain bacteria, such as Escherichia coli, that have two isozymes. All isozymes appear to be tetramers of identical subunits of ~500 residues. PK helps control the rate of glycolysis, along with phosphofructokinase (IPR000023 from INTERPRO) and hexokinase (IPR001312 from INTERPRO). PK possesses allosteric sites for numerous effectors, yet the isozymes respond differently, in keeping with their different tissue distributions []. The activity of L-type (liver) PK is increased by fructose-1,6-bisphosphate (F1,6BP) and lowered by ATP and alanine (gluconeogenic precursor), therefore when glucose levels are high, glycolysis is promoted, and when levels are low, gluconeogenesis is promoted. L-type PK is also hormonally regulated, being activated by insulin and inhibited by glucagon, which covalently modifies the PK enzyme. M1-type (muscle, brain) PK is inhibited by ATP, but F1,6BP and alanine have no effect, which correlates with the function of muscle and brain, as opposed to the liver. The structure of several pyruvate kinases from various organisms have been determined [, ]. The protein comprises three-four domains: a small N-terminal helical domain (absent in bacterial PK), a beta/alpha-barrel domain, a beta-barrel domain (inserted within the beta/alpha-barrel domain), and a 3-layer alpha/beta/alpha sandwich domain. This entry represents the 3-layer alpha/beta/alpha sandwich domain. This domain has a similar topology to the archaeal hypothetical protein, MTH1675 from Methanobacterium thermoautotrophicum.; PDB: 3QTG_B 1VP8_A 1T57_C 3N25_A 1AQF_C 2G50_B 1F3X_G 1A5U_F 1A49_E 1F3W_C ....
Probab=20.08 E-value=2.5e+02 Score=23.64 Aligned_cols=48 Identities=13% Similarity=0.265 Sum_probs=36.9
Q ss_pred cEEEEEEcCCCCCCccCHHHHHHHHHhCCcEEEEEEecchHHHHHHHHHHhCCEEEEe
Q 014440 190 REVLILYSALSTCDPGDIMETIQKCKESKIRCSVIGLSAEMFICKHLCQETGGTYSVA 247 (424)
Q Consensus 190 reILvI~ss~~t~dp~~i~~~i~~akk~~IrV~vIgLg~e~~iLq~iA~~TGG~Y~~~ 247 (424)
+-|++++.++ .++..+.+..-.+-+|++..+..+.++++ ..-|.|-+.
T Consensus 18 k~Ivv~T~sG---------~ta~~isk~RP~~pIiavt~~~~~~r~l~-l~~GV~p~~ 65 (117)
T PF02887_consen 18 KAIVVFTESG---------RTARLISKYRPKVPIIAVTPNESVARQLS-LYWGVYPVL 65 (117)
T ss_dssp SEEEEE-SSS---------HHHHHHHHT-TSSEEEEEESSHHHHHHGG-GSTTEEEEE
T ss_pred CEEEEECCCc---------hHHHHHHhhCCCCeEEEEcCcHHHHhhhh-cccceEEEE
Confidence 4566665543 36788888888899999999999999999 899998854
No 455
>PF01488 Shikimate_DH: Shikimate / quinate 5-dehydrogenase; InterPro: IPR006151 This entry represents a domain found in shikimate and quinate dehydrogenases, as well as glutamyl-tRNA reductases. Shikimate 5-dehydrogenase (1.1.1.25 from EC) catalyses the conversion of shikimate to 5-dehydroshikimate [, ]. This reaction is part of the shikimate pathway which is involved in the biosynthesis of aromatic amino acids []. Quinate 5-dehydrogenase catalyses the conversion of quinate to 5-dehydroquinate. This reaction is part of the quinate pathway where quinic acid is exploited as a source of carbon in prokaryotes and microbial eukaryotes. Both the shikimate and quinate pathways share two common pathway metabolites, 3-dehydroquinate and dehydroshikimate. Glutamyl-tRNA reductase (1.2.1.70 from EC) catalyzes the first step of tetrapyrrole biosynthesis in plants, archaea and most bacteria. The dimeric enzyme has an unusual V-shaped architecture where each monomer consists of three domains linked by a long 'spinal' alpha-helix. The central catalytic domain specifically recognises the glutamate moiety of the substrate []. ; PDB: 2EV9_B 2CY0_B 1WXD_A 2D5C_A 1NVT_B 2EGG_A 3PWZ_A 3DOO_A 3DON_A 3FBT_C ....
Probab=20.06 E-value=2.4e+02 Score=24.41 Aligned_cols=74 Identities=16% Similarity=0.180 Sum_probs=44.0
Q ss_pred HHHHHHcCCCCCCCcEEEEEEcCCCCCCccCHHHHHHHHHhCCcE-EEEEEecchHHHHHHHHHHhCCEEEEecChhhHH
Q 014440 176 LVHGLLNQIPSYGHREVLILYSALSTCDPGDIMETIQKCKESKIR-CSVIGLSAEMFICKHLCQETGGTYSVALDESHSK 254 (424)
Q Consensus 176 ~Al~~L~~~p~~~~reILvI~ss~~t~dp~~i~~~i~~akk~~Ir-V~vIgLg~e~~iLq~iA~~TGG~Y~~~~d~~~L~ 254 (424)
+|.+.+... ..++++|| |.+ +--..++..+.+.|++ |.+++= ...-.+++++..+|.-+.+.+-+++.
T Consensus 2 la~~~~~~l---~~~~vlvi-GaG-----g~ar~v~~~L~~~g~~~i~i~nR--t~~ra~~l~~~~~~~~~~~~~~~~~~ 70 (135)
T PF01488_consen 2 LAKKKFGDL---KGKRVLVI-GAG-----GAARAVAAALAALGAKEITIVNR--TPERAEALAEEFGGVNIEAIPLEDLE 70 (135)
T ss_dssp HHCTHHSTG---TTSEEEEE-SSS-----HHHHHHHHHHHHTTSSEEEEEES--SHHHHHHHHHHHTGCSEEEEEGGGHC
T ss_pred hhHHhcCCc---CCCEEEEE-CCH-----HHHHHHHHHHHHcCCCEEEEEEC--CHHHHHHHHHHcCccccceeeHHHHH
Confidence 455555433 24445555 432 2234678999999998 877764 34556788888776644443444566
Q ss_pred HHHHhc
Q 014440 255 ELILEH 260 (424)
Q Consensus 255 ~lL~~~ 260 (424)
+.+...
T Consensus 71 ~~~~~~ 76 (135)
T PF01488_consen 71 EALQEA 76 (135)
T ss_dssp HHHHTE
T ss_pred HHHhhC
Confidence 666554
No 456
>COG0603 Predicted PP-loop superfamily ATPase [General function prediction only]
Probab=20.04 E-value=3.2e+02 Score=26.58 Aligned_cols=58 Identities=17% Similarity=0.258 Sum_probs=43.0
Q ss_pred EEEEEEc-CCCCCCccCHHHHHHHHHhCCcEEEEEEec------chHHHHHHHHHHhCCEEEEecChhhHHH
Q 014440 191 EVLILYS-ALSTCDPGDIMETIQKCKESKIRCSVIGLS------AEMFICKHLCQETGGTYSVALDESHSKE 255 (424)
Q Consensus 191 eILvI~s-s~~t~dp~~i~~~i~~akk~~IrV~vIgLg------~e~~iLq~iA~~TGG~Y~~~~d~~~L~~ 255 (424)
+.|||+| +.++ ...+..|++.+-.|+.|++. .|...=|++|+.-|-.+.+ .|-+.+.+
T Consensus 4 kavvl~SGG~DS------tt~l~~a~~~~~ev~alsfdYGQrh~~Ele~A~~iak~lgv~~~i-id~~~~~~ 68 (222)
T COG0603 4 KAVVLLSGGLDS------TTCLAWAKKEGYEVHALTFDYGQRHRKELEAAKELAKKLGVPHHI-IDVDLLGE 68 (222)
T ss_pred eEEEEccCChhH------HHHHHHHHhcCCEEEEEEeeCCCCcHHHHHHHHHHHHHcCCCeEE-echhHHhh
Confidence 4555554 4432 45688899999999999997 3578889999999999884 46555555
Done!