Query 011878
Match_columns 475
No_of_seqs 139 out of 1485
Neff 8.6
Searched_HMMs 46136
Date Fri Mar 29 06:13:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011878.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011878hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00578 ku70 ATP-dependent D 100.0 1.5E-83 3.3E-88 677.5 43.1 432 3-474 8-472 (584)
2 KOG2326 DNA-binding subunit of 100.0 2.9E-52 6.3E-57 413.9 31.9 455 4-473 3-475 (669)
3 KOG2327 DNA-binding subunit of 100.0 3.8E-52 8.2E-57 416.5 26.7 439 3-475 16-489 (602)
4 cd00873 KU80 Ku-core domain, K 100.0 8.4E-52 1.8E-56 405.5 25.4 250 217-474 2-257 (300)
5 cd00788 KU70 Ku-core domain, K 100.0 1.8E-50 3.9E-55 393.7 24.9 244 216-474 1-254 (287)
6 cd00594 KU Ku-core domain; inc 100.0 1.4E-49 3E-54 386.7 24.6 239 216-474 1-239 (272)
7 cd00789 KU_like Ku-core domain 100.0 3E-46 6.5E-51 353.8 23.1 223 216-473 1-224 (256)
8 TIGR02772 Ku_bact Ku protein, 100.0 2.4E-45 5.1E-50 348.1 22.5 223 215-473 1-225 (258)
9 PF02735 Ku: Ku70/Ku80 beta-ba 100.0 7.3E-43 1.6E-47 323.5 18.4 199 223-433 1-200 (200)
10 smart00559 Ku78 Ku70 and Ku80 100.0 1.3E-35 2.8E-40 257.8 12.9 136 279-417 2-138 (140)
11 COG1273 Ku-homolog [Replicatio 100.0 9.2E-33 2E-37 251.6 15.5 220 215-471 3-225 (278)
12 PF03731 Ku_N: Ku70/Ku80 N-ter 100.0 1.8E-29 3.9E-34 238.6 18.7 201 7-217 1-223 (224)
13 cd01458 vWA_ku Ku70/Ku80 N-ter 99.9 5.6E-26 1.2E-30 213.6 15.5 153 5-166 1-172 (218)
14 cd01453 vWA_transcription_fact 99.5 1.4E-12 2.9E-17 119.1 16.9 164 7-208 5-175 (183)
15 COG1240 ChlD Mg-chelatase subu 99.4 2.1E-11 4.5E-16 112.9 17.2 168 6-202 79-248 (261)
16 cd01451 vWA_Magnesium_chelatas 99.4 3E-11 6.5E-16 109.9 18.2 163 7-201 2-167 (178)
17 PRK13685 hypothetical protein; 99.3 6.4E-11 1.4E-15 118.1 18.6 178 6-204 89-279 (326)
18 cd01452 VWA_26S_proteasome_sub 99.3 9.6E-11 2.1E-15 106.1 17.2 152 5-191 3-161 (187)
19 cd01480 vWA_collagen_alpha_1-V 99.3 2.3E-10 4.9E-15 104.9 17.8 152 8-194 5-166 (186)
20 cd01465 vWA_subgroup VWA subgr 99.3 5.7E-10 1.2E-14 100.4 19.3 161 8-204 3-166 (170)
21 PRK13406 bchD magnesium chelat 99.3 2.4E-10 5.1E-15 121.1 18.9 165 6-201 402-570 (584)
22 cd01474 vWA_ATR ATR (Anthrax T 99.2 5.3E-10 1.2E-14 102.3 17.1 152 6-193 5-159 (185)
23 cd01467 vWA_BatA_type VWA BatA 99.2 8.8E-10 1.9E-14 100.2 17.9 165 7-201 4-177 (180)
24 cd01470 vWA_complement_factors 99.2 8.2E-10 1.8E-14 102.2 17.6 167 8-205 3-194 (198)
25 cd01472 vWA_collagen von Wille 99.2 6.8E-10 1.5E-14 99.5 16.1 151 8-195 3-157 (164)
26 TIGR03436 acidobact_VWFA VWFA- 99.2 1.2E-09 2.6E-14 107.7 17.0 168 6-198 54-238 (296)
27 cd01456 vWA_ywmD_type VWA ywmD 99.2 1.3E-09 2.7E-14 101.6 16.3 162 5-201 20-203 (206)
28 cd01482 vWA_collagen_alphaI-XI 99.2 1.6E-09 3.6E-14 97.0 16.2 147 8-191 3-153 (164)
29 TIGR02031 BchD-ChlD magnesium 99.1 2E-09 4.3E-14 115.1 18.2 166 7-201 409-583 (589)
30 cd01471 vWA_micronemal_protein 99.1 1.9E-09 4E-14 98.7 15.5 136 8-166 3-147 (186)
31 cd01469 vWA_integrins_alpha_su 99.1 3.3E-09 7.2E-14 96.3 16.6 164 8-201 3-171 (177)
32 cd01473 vWA_CTRP CTRP for CS 99.1 1E-09 2.2E-14 100.9 13.1 138 8-166 3-149 (192)
33 PF13519 VWA_2: von Willebrand 99.1 8.6E-10 1.9E-14 98.8 11.8 148 8-198 2-158 (172)
34 cd01463 vWA_VGCC_like VWA Volt 99.1 2.6E-09 5.7E-14 98.1 14.8 167 5-200 13-188 (190)
35 cd01476 VWA_integrin_invertebr 99.1 3.3E-09 7.1E-14 94.9 14.8 152 8-191 3-157 (163)
36 TIGR02442 Cob-chelat-sub cobal 99.1 6E-09 1.3E-13 112.6 19.5 165 6-198 466-632 (633)
37 cd01461 vWA_interalpha_trypsin 99.0 1.6E-08 3.6E-13 90.8 17.0 163 7-207 4-168 (171)
38 cd01454 vWA_norD_type norD typ 99.0 1.8E-08 4E-13 91.2 17.3 144 7-166 2-152 (174)
39 cd01475 vWA_Matrilin VWA_Matri 99.0 1.5E-08 3.4E-13 95.6 17.1 155 7-198 4-166 (224)
40 cd01450 vWFA_subfamily_ECM Von 99.0 9.4E-09 2E-13 91.1 14.6 149 8-191 3-155 (161)
41 cd01466 vWA_C3HC4_type VWA C3H 99.0 8.8E-09 1.9E-13 91.4 14.2 146 8-197 3-153 (155)
42 TIGR00868 hCaCC calcium-activa 99.0 1.8E-08 4E-13 109.8 18.6 151 7-199 306-461 (863)
43 cd01455 vWA_F11C1-5a_type Von 99.0 1.6E-08 3.4E-13 91.3 14.6 163 7-205 2-179 (191)
44 cd01477 vWA_F09G8-8_type VWA F 99.0 2.2E-08 4.8E-13 92.0 15.4 137 8-166 22-171 (193)
45 cd01464 vWA_subfamily VWA subf 98.9 6.6E-08 1.4E-12 87.7 15.1 147 6-189 4-159 (176)
46 PTZ00441 sporozoite surface pr 98.9 7.7E-08 1.7E-12 99.7 17.1 137 6-166 43-188 (576)
47 cd00198 vWFA Von Willebrand fa 98.9 9.1E-08 2E-12 84.0 15.0 150 7-191 2-155 (161)
48 PF13768 VWA_3: von Willebrand 98.8 1.7E-07 3.6E-12 83.1 14.9 147 8-195 3-153 (155)
49 smart00327 VWA von Willebrand 98.8 3.4E-07 7.4E-12 82.3 16.8 156 7-196 3-163 (177)
50 cd01460 vWA_midasin VWA_Midasi 98.8 1.9E-07 4.2E-12 89.2 15.5 136 5-166 60-204 (266)
51 cd01481 vWA_collagen_alpha3-VI 98.8 2.2E-07 4.7E-12 83.3 14.3 147 8-191 3-156 (165)
52 PF00092 VWA: von Willebrand f 98.7 2.5E-07 5.5E-12 83.4 13.4 150 8-191 2-156 (178)
53 cd01462 VWA_YIEM_type VWA YIEM 98.7 1.2E-06 2.5E-11 77.4 16.2 132 7-166 2-134 (152)
54 TIGR03788 marine_srt_targ mari 98.6 3.2E-06 7E-11 91.3 18.9 154 6-201 272-431 (596)
55 PF04056 Ssl1: Ssl1-like; Int 98.3 1.6E-05 3.4E-10 72.2 13.4 149 11-196 1-157 (193)
56 KOG2884 26S proteasome regulat 98.2 7E-05 1.5E-09 67.4 15.3 138 5-166 3-146 (259)
57 COG5148 RPN10 26S proteasome r 98.1 0.00014 3.1E-09 63.9 14.5 135 5-166 3-146 (243)
58 cd01457 vWA_ORF176_type VWA OR 98.1 0.00014 2.9E-09 67.3 14.7 136 7-166 4-151 (199)
59 PRK10997 yieM hypothetical pro 97.5 0.0022 4.7E-08 66.5 14.7 132 3-165 321-456 (487)
60 COG4867 Uncharacterized protei 97.5 0.0036 7.8E-08 62.0 14.5 151 4-196 462-631 (652)
61 PF11265 Med25_VWA: Mediator c 97.3 0.0074 1.6E-07 56.0 14.3 148 6-164 14-185 (226)
62 KOG2807 RNA polymerase II tran 97.2 0.0087 1.9E-07 57.4 13.5 154 7-197 62-221 (378)
63 COG4245 TerY Uncharacterized p 97.0 0.012 2.7E-07 52.3 11.9 106 5-131 3-119 (207)
64 COG2425 Uncharacterized protei 96.8 0.018 3.8E-07 58.8 12.9 130 6-166 273-406 (437)
65 PF05762 VWA_CoxE: VWA domain 96.7 0.018 3.8E-07 54.2 11.2 128 5-163 56-186 (222)
66 PF10138 vWA-TerF-like: vWA fo 96.6 0.093 2E-06 47.9 14.8 136 6-166 2-143 (200)
67 cd01479 Sec24-like Sec24-like: 96.3 0.1 2.2E-06 49.8 14.0 172 6-196 4-216 (244)
68 TIGR00627 tfb4 transcription f 96.3 0.059 1.3E-06 52.1 12.3 179 6-201 3-210 (279)
69 cd01468 trunk_domain trunk dom 96.0 0.49 1.1E-05 45.0 17.0 175 6-198 4-221 (239)
70 PF04811 Sec23_trunk: Sec23/Se 95.6 0.13 2.7E-06 49.1 11.2 176 5-197 3-222 (243)
71 KOG3768 DEAD box RNA helicase 95.6 0.24 5.3E-06 51.5 13.4 109 7-129 3-132 (888)
72 COG4548 NorD Nitric oxide redu 95.2 0.082 1.8E-06 54.4 8.4 151 7-166 448-600 (637)
73 cd01478 Sec23-like Sec23-like: 94.7 1.5 3.2E-05 42.5 15.5 175 6-199 4-254 (267)
74 PF03850 Tfb4: Transcription f 94.7 0.35 7.6E-06 46.9 11.0 180 7-204 3-211 (276)
75 KOG2487 RNA polymerase II tran 94.4 0.78 1.7E-05 43.3 12.0 174 7-201 25-228 (314)
76 COG5242 TFB4 RNA polymerase II 94.4 2.8 6E-05 38.6 15.1 173 7-202 22-216 (296)
77 KOG1984 Vesicle coat complex C 94.3 1.8 3.9E-05 47.4 15.9 210 6-237 418-678 (1007)
78 PLN00162 transport protein sec 94.1 1.5 3.3E-05 48.9 15.7 126 97-236 263-419 (761)
79 PF11775 CobT_C: Cobalamin bio 93.7 1.1 2.3E-05 41.5 11.3 154 6-166 13-187 (219)
80 KOG2353 L-type voltage-depende 93.6 0.88 1.9E-05 52.0 12.9 141 2-166 222-373 (1104)
81 TIGR01651 CobT cobaltochelatas 93.3 1.7 3.7E-05 46.0 13.5 63 99-166 499-567 (600)
82 PTZ00395 Sec24-related protein 93.2 3.6 7.8E-05 47.5 16.5 216 6-236 953-1222(1560)
83 PF12257 DUF3608: Protein of u 93.0 1.1 2.3E-05 43.4 10.7 154 7-166 72-270 (281)
84 PF09967 DUF2201: VWA-like dom 92.4 1.2 2.5E-05 37.9 9.1 41 8-53 1-42 (126)
85 cd01459 vWA_copine_like VWA Co 91.5 5.9 0.00013 37.9 13.8 139 7-166 33-195 (254)
86 smart00187 INB Integrin beta s 90.5 6.2 0.00014 40.3 13.4 152 8-164 102-297 (423)
87 KOG2326 DNA-binding subunit of 89.8 0.0036 7.8E-08 64.6 -10.2 135 281-416 325-469 (669)
88 KOG1986 Vesicle coat complex C 88.8 22 0.00049 38.4 16.3 147 8-164 124-337 (745)
89 COG5151 SSL1 RNA polymerase II 88.6 6.1 0.00013 38.1 11.0 145 7-191 89-242 (421)
90 PF07002 Copine: Copine; Inte 86.1 22 0.00048 30.9 12.9 133 15-165 6-146 (146)
91 TIGR02877 spore_yhbH sporulati 83.5 20 0.00042 36.1 12.2 36 97-133 270-305 (371)
92 PF04285 DUF444: Protein of un 83.1 18 0.00038 37.3 12.0 36 97-133 314-349 (421)
93 PRK05325 hypothetical protein; 79.5 32 0.00069 35.2 12.3 36 97-133 290-325 (401)
94 COG1721 Uncharacterized conser 75.4 5.8 0.00013 41.0 6.0 47 5-53 224-276 (416)
95 COG2718 Uncharacterized conser 75.3 47 0.001 33.5 11.6 38 97-135 314-351 (423)
96 COG5028 Vesicle coat complex C 73.0 49 0.0011 36.3 12.0 151 6-165 277-461 (861)
97 PF00362 Integrin_beta: Integr 66.7 23 0.0005 36.7 7.9 121 8-132 105-245 (426)
98 COG4902 Uncharacterized protei 59.8 18 0.00039 31.0 4.6 42 426-469 87-128 (189)
99 KOG1985 Vesicle coat complex C 59.3 2.4E+02 0.0052 31.6 13.9 152 6-166 295-486 (887)
100 COG2304 Uncharacterized protei 56.0 2.3E+02 0.0049 28.6 13.2 139 5-166 37-177 (399)
101 PF06707 DUF1194: Protein of u 55.9 1.7E+02 0.0037 27.0 14.0 140 6-166 4-156 (205)
102 PF11443 DUF2828: Domain of un 55.4 1.8E+02 0.004 31.0 12.2 136 6-160 341-478 (534)
103 PF09968 DUF2202: Uncharacteri 53.2 24 0.00052 31.2 4.5 43 427-471 39-81 (162)
104 COG3552 CoxE Protein containin 50.9 18 0.00039 36.2 3.8 47 5-57 218-264 (395)
105 cd03364 TOPRIM_DnaG_primases T 49.7 29 0.00063 26.3 4.1 35 120-162 43-77 (79)
106 COG5047 SEC23 Vesicle coat com 49.6 1.1E+02 0.0023 32.8 9.1 33 99-134 260-292 (755)
107 KOG0071 GTP-binding ADP-ribosy 47.8 87 0.0019 27.1 6.8 47 4-55 84-130 (180)
108 PF13662 Toprim_4: Toprim doma 42.3 16 0.00035 28.0 1.6 35 120-162 46-80 (81)
109 PF01882 DUF58: Protein of unk 40.8 34 0.00075 26.3 3.3 41 5-47 40-86 (86)
110 COG4547 CobT Cobalamin biosynt 39.3 1.6E+02 0.0034 30.6 8.3 151 6-165 414-587 (620)
111 KOG1327 Copine [Signal transdu 38.9 4.3E+02 0.0093 28.2 11.7 143 6-166 286-452 (529)
112 PF07744 SPOC: SPOC domain; I 37.6 61 0.0013 26.5 4.6 41 344-385 79-119 (119)
113 PF13344 Hydrolase_6: Haloacid 26.0 1.1E+02 0.0024 24.5 4.1 29 120-159 30-58 (101)
114 PF01975 SurE: Survival protei 25.6 1.8E+02 0.0039 26.6 5.9 34 124-165 3-36 (196)
115 PRK14465 ribosomal RNA large s 24.0 5.6E+02 0.012 25.7 9.5 56 100-166 239-294 (342)
116 cd05006 SIS_GmhA Phosphoheptos 24.0 1.9E+02 0.0041 25.6 5.7 75 281-360 99-173 (177)
117 PF00025 Arf: ADP-ribosylation 21.1 1.7E+02 0.0037 25.8 4.8 47 4-55 81-127 (175)
No 1
>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=100.00 E-value=1.5e-83 Score=677.49 Aligned_cols=432 Identities=19% Similarity=0.257 Sum_probs=369.7
Q ss_pred CCceEEEEEEecCCCcCC---------CchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEe
Q 011878 3 RTREALLLLLDVSPSMHS---------VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQ 73 (475)
Q Consensus 3 ~~ke~~vflID~s~sM~~---------~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~ 73 (475)
.+||++|||||||++||+ +|..|++||..+|++|||++++|+||||||||++++|++ +|+|||+++
T Consensus 8 ~~keailflIDvs~sM~~~~~~~~~~s~~~~al~~i~~l~q~kIis~~~D~vGivlfgT~~t~n~~-----~~~~i~v~~ 82 (584)
T TIGR00578 8 SGRDSLIFLVDASKAMFEESQGEDELTPFDMSIQCIQSVYTSKIISSDKDLLAVVFYGTEKDKNSV-----NFKNIYVLQ 82 (584)
T ss_pred cceeEEEEEEECCHHHcCCCcCcCcCChHHHHHHHHHHHHHhcCCCCCCCeEEEEEEeccCCCCcc-----CCCceEEEe
Confidence 469999999999999996 367899999999999999999999999999999999987 799999999
Q ss_pred ecCCCCHHHHHHhhcCCCCC------------CCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCc
Q 011878 74 DIKVVDGHLVQSLKHLPQGT------------CAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTK 141 (475)
Q Consensus 74 ~l~~~~~~~i~~L~~l~~~~------------~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~ 141 (475)
+|+.|+++.++.|++|..+. ..++++||||+|.++|.+ + +++..+||||||||+++|++. +...
T Consensus 83 ~L~~p~a~~i~~L~~l~~~~~~~~~~~~~~~~~~~~l~daL~~~~~~f~~-~-~~k~~~kRI~lfTd~D~P~~~--~~~~ 158 (584)
T TIGR00578 83 ELDNPGAKRILELDQFKGDQGPKKFRDTYGHGSDYSLSEVLWVCANLFSD-V-QFRMSHKRIMLFTNEDNPHGN--DSAK 158 (584)
T ss_pred eCCCCCHHHHHHHHHHhhccCccchhhccCCCCCCcHHHHHHHHHHHHHh-c-chhhcCcEEEEECCCCCCCCC--chhH
Confidence 99999999999999875531 124789999999999985 3 346789999999999999985 3344
Q ss_pred hhhHHHHHHHHhhcCcEEEEEEeccCCCCCCCccccccchHHHHHHhhcCCCe----Eee-hhhHHHhhccCccccCCCc
Q 011878 142 EDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAK----TLF-VDSTTSLRGARKTRDISPV 216 (475)
Q Consensus 142 ~~~~~~~~~~l~~~~I~l~~i~i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~----~~~-~~~~~~ll~~~~~r~~~~r 216 (475)
.+++.++|++|++.||.|++|+++. +++|+. ..++..+....++. ... .....++++.++.|++++|
T Consensus 159 ~~~a~~~a~dl~~~gi~ielf~l~~--~~~Fd~------s~Fy~dii~~~~~~~~~~~~~~~~~l~~l~~~l~~k~~~kR 230 (584)
T TIGR00578 159 ASRARTKAGDLRDTGIFLDLMHLKK--PGGFDI------SLFYRDIITDAEDEDLGVHPEESSKLEDLLRKVRAKETRKR 230 (584)
T ss_pred HHHHHHHHHHHHhcCeEEEEEecCC--CCCCCh------hhhhHhhhccccccccccCcchhHHHHHHHHHHhhccccee
Confidence 4667889999999999999999953 333333 23444433211110 111 1234577788999999999
Q ss_pred eeeeeeEeecCCeEEEEEEEeeccccCCCc-ceEecccCCCCccccccceeEEEEEeccCCCCCCCCcccccccceeCCc
Q 011878 217 TIFRGDLELSEKMKIKVWVYKKTGEEKFPT-LKKYSDKAPSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYGPQ 295 (475)
Q Consensus 217 ~~~~~~l~ig~~~~I~V~~y~~~~~~~~p~-~~~~~~~~~~~~~~~~~~v~~~~~y~~~~d~~~~v~~~~~~k~y~yG~~ 295 (475)
+.|+++|+||++++|+|++|.+++++++|. .|++..+ +..|+.+|+|++ .+++++|+++|++|||+|||+
T Consensus 231 ~~~~~~L~lg~~~~I~V~~Y~~~~~~~~~~~~~l~~~~--------~~~v~~~~~~~~-~dtg~~V~~~~i~Kgy~yGg~ 301 (584)
T TIGR00578 231 ALSRLKLKLNKDVVMSVGIYNLVQKAGKPAPVKLYRET--------NEPVKTKTRTFN-MDTGSLLLPSDTKRSQTYGGR 301 (584)
T ss_pred eEEeccEEECCCCEEEEEEEEEEEeecCCceEEEecCC--------ceeeEEEEEEEe-cCCccccCHHHceeeeeECCE
Confidence 999999999999999999999999987665 5666654 357899998984 678889999999999999999
Q ss_pred eEeCChhhHHhhccCCCccEEEEeEeeCCCcccccccCceEEEEcCCC-ChhhHHHHHHHHHHHHhcCeEEEEEEEecCC
Q 011878 296 VVPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPG-NSRATVAVSALARAMKEMNKVAIVRCVWRQG 374 (475)
Q Consensus 296 ~V~~~~~e~~~~k~~~~~~l~llGF~~~~~i~~~~~~~~~~~i~p~~~-~~~s~~~f~aL~~am~~~~~vai~r~v~r~~ 374 (475)
+|+|+++|++++|..++|+|+||||+++++|+++|++++++||+|+++ ..||.++|+||+++|.++++|||||||+|+|
T Consensus 302 ~V~~t~ee~~~lk~~~~~~l~ilGF~~~s~l~~~~~~~~s~fi~Pde~~~~gs~~afsaL~~~l~~~~kvAI~~~v~r~~ 381 (584)
T TIGR00578 302 QIYLEKEETEELKRFDPPGLQLMGFKPLSMLKKHHHLRPSLFVYPEESLVRGSTTLFSALLQKCLEKEVAALCRYISRRN 381 (584)
T ss_pred EEecCHHHHHHHhccCCCceEEEeeccHHHCCchhhcCCceEEecCCcccccHHHHHHHHHHHHHhcCcEEEEEEEecCC
Confidence 999999999999999999999999999999999999999999999986 4589999999999999999999999999999
Q ss_pred CCceEEEEecccccCCC-----CCCCeEEEecCCCccccccCCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCCCCCc
Q 011878 375 QQSVVVGVLTPNVSEKI-----NIPDSFYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLVKMLDLAPSGKGE 449 (475)
Q Consensus 375 ~~~~~v~~L~P~~~~~~-----~~~~gl~~~~LPf~dDiR~~~f~~l~~~~~~~~~~~~q~~~~~~lI~~l~l~~~~~~~ 449 (475)
+.|++ ++|+|+.+..+ ..|+|||+++|||+||||+++|++ ...++++|+++|++||++|+++
T Consensus 382 ~~P~l-vaL~P~~~~~d~~~~q~~p~G~~l~~LPfadDIR~~~~~~------~~~~~~e~~~~a~~LI~~l~~~------ 448 (584)
T TIGR00578 382 QPPYF-VALVPQEEELDDQKIQVTPPGFHLVFLPFADDKRKVPFTE------KVKATPEQVDKMKAIVEKLRFT------ 448 (584)
T ss_pred CCCEE-EEEeCCcccccccCCccCCCeEEEEecCchhhccCCCCcc------cCCCCHHHHHHHHHHHHhcCCC------
Confidence 87665 57889875422 257899999999999999998742 2469999999999999999997
Q ss_pred CCCCCCCCChhhHHHHHHhhhcccc
Q 011878 450 ILQPELTPNPALEVLNICGYFGFLD 474 (475)
Q Consensus 450 ~~~p~~~~NP~lq~~y~~l~~~a~~ 474 (475)
|+|+.|+||+|||||+||+|+|||
T Consensus 449 -y~P~~~~NP~LQ~hY~~LealAL~ 472 (584)
T TIGR00578 449 -YRSDSFENPVLQQHFRNLEALALD 472 (584)
T ss_pred -CCcccCCChHHHHHHHHHHHHhCC
Confidence 999999999999999999999998
No 2
>KOG2326 consensus DNA-binding subunit of a DNA-dependent protein kinase (Ku80 autoantigen) [Replication, recombination and repair]
Probab=100.00 E-value=2.9e-52 Score=413.94 Aligned_cols=455 Identities=20% Similarity=0.239 Sum_probs=372.1
Q ss_pred CceEEEEEEecCCCcCC-------CchHHHHHHHHHHHHHHhcC-CccEEEEEEEccCCcCccccccCCCcccEEEEeec
Q 011878 4 TREALLLLLDVSPSMHS-------VLPDVEKLCSRLIQKKLIYG-KNHEVGVILFGTEETENELTKEVGGYEHVKVLQDI 75 (475)
Q Consensus 4 ~ke~~vflID~s~sM~~-------~~~~a~~~~~~l~~~ki~~~-~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l 75 (475)
+++|++|++|+|++|.. .++.|+.++..++++|.+.+ ++|.||||+|||+.|+|++. ++..|+||+++.|+
T Consensus 3 ~se~ttfilDvG~~Ms~~~~~~~S~fE~a~~y~~~~lsrK~fa~rktD~is~vlyncD~ten~le-gg~~fqnisvl~p~ 81 (669)
T KOG2326|consen 3 SSESTTFILDVGPSMSKNNETGKSNFEKAMAYLEYTLSRKSFASRKTDWISCVLYNCDVTENSLE-GGNVFQNISVLAPV 81 (669)
T ss_pred CCcceEEEEecCccccccCCCccccHHHHHHHHHHHHHHHHhhccCCceEEEEEecCCCccCccc-cccccceeEEeecc
Confidence 57899999999999986 37889999999999999987 99999999999999999985 55689999999998
Q ss_pred CCCCH-HHHHHhhc-CCCCCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHh
Q 011878 76 KVVDG-HLVQSLKH-LPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMV 153 (475)
Q Consensus 76 ~~~~~-~~i~~L~~-l~~~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~ 153 (475)
..|.. ..++.+.. ++.++..+|+.+||.+..+++.+++..++...+|+++++++-.--- ..+.. ++++|.
T Consensus 82 ~tpaf~~l~k~~~~~~qqns~q~Df~gal~vs~dL~~qhe~~~k~~~kr~Il~~~~l~~df------sd~~~--ive~l~ 153 (669)
T KOG2326|consen 82 TTPAFIGLIKRLKQYCQQNSHQSDFEGALSVSQDLLVQHEDIKKQFQKRKILKQIVLFTDF------SDDLF--IVEDLT 153 (669)
T ss_pred cchhhHHHHHHHHHhcCCCccccchhhhHHHHHHHHHHHHhccchhhceEEEEeecccccc------hhhHH--HHHHHh
Confidence 76654 45666664 5677788999999999999888887666677788777777654211 11222 899999
Q ss_pred hcCcEEEEEEeccCC-----CCCCCccccccchHHHHHHhhcCCCeEeehhhHHHhhccCccccCCCceeeeeeEeec-C
Q 011878 154 AFGLRMKNIVVRASL-----SGEPHMRVIIENDNLLNIFSKKSSAKTLFVDSTTSLRGARKTRDISPVTIFRGDLELS-E 227 (475)
Q Consensus 154 ~~~I~l~~i~i~~~~-----~~~~~~~~~~~n~~~l~~~~~~~~g~~~~~~~~~~ll~~~~~r~~~~r~~~~~~l~ig-~ 227 (475)
+.+|.|-++|++... +++.+...+..|+-+++....-..++++.+++...-+..++.+-++|..+|+|.|+|| +
T Consensus 154 ~~didL~~~gldf~~e~id~s~dl~e~~kk~n~~~~q~~e~l~~~q~~~~~eiYn~i~spa~~~v~pv~if~g~l~ig~~ 233 (669)
T KOG2326|consen 154 DEDIDLLTEGLDFRIELIDCSKDLQEERKKSNYTWLQLVEALPNSQIYNMNEIYNEITSPATSVVKPVRIFSGELRIGAD 233 (669)
T ss_pred hcCcceeEeeccCCccccccCccccccccccchHHHHHHHhcchhhHHhHHHHHHhhcCcccccccceEEEeeeEeeccc
Confidence 999999999996421 1222333455666677776666678889999999988999999999988999999999 7
Q ss_pred CeEEEEEEEeeccccCCCcceEecccCCCCccccccceeEEEEEeccCCCCCCCCcccccccceeCCceEeCChhhHHhh
Q 011878 228 KMKIKVWVYKKTGEEKFPTLKKYSDKAPSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYGPQVVPISSAEWEAV 307 (475)
Q Consensus 228 ~~~I~V~~y~~~~~~~~p~~~~~~~~~~~~~~~~~~~v~~~~~y~~~~d~~~~v~~~~~~k~y~yG~~~V~~~~~e~~~~ 307 (475)
.++|.+.-|+-+.-.+++..+......+++- ...+...+|.|...++.+.+|-+|+++.||.||...||++..+.+.+
T Consensus 234 ~Lsiq~a~y~g~~q~r~~~~~~~vea~~etk--~ke~~n~ktV~~~~d~d~~evlKed~~sGysyG~~iIp~s~nDenv~ 311 (669)
T KOG2326|consen 234 ILSIQTANYSGSMQDRNECLCIKVEAFPETK--AKEGLNRKTVVEVEDSDKLEVLKEDYVSGYSYGEYIIPNSGNDENVS 311 (669)
T ss_pred eeEEeccCCCccccccccceeEEeecchhhc--cchhcccceeEEeecCCchhhHHHhhhhhcccceeEeccCCcchhhc
Confidence 7999999999999999887665443221100 11223334555533444468889999999999999999999999999
Q ss_pred ccCCCccEEEEeEeeCCCcccccccCceEEEEcCCCChhhHHHHHHHHHHHHhcCeEEEEEEEecCCCCceEEEEecccc
Q 011878 308 KFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQGQQSVVVGVLTPNV 387 (475)
Q Consensus 308 k~~~~~~l~llGF~~~~~i~~~~~~~~~~~i~p~~~~~~s~~~f~aL~~am~~~~~vai~r~v~r~~~~~~~v~~L~P~~ 387 (475)
+..+.+++.||||+++++|+.+|++|..+.|+|.-...++..++++|++||...+++|||||++.+++.| .+++|.|+.
T Consensus 312 e~dt~g~~~ilgFikkssv~~~Y~~g~~~~Vlpa~dd~~a~~a~ssli~al~~l~r~Al~Ry~~~~ks~p-ql~vl~Ph~ 390 (669)
T KOG2326|consen 312 EDDTSGSSYILGFIKKSSVTKAYRYGADYVVLPAVDDDQAVYASSSLIDALGFLNREALPRYFLTSKSSP-QLAVLRPHC 390 (669)
T ss_pred ccccCCceEEeeeeccccccceeeecCceEEecccCchHhHHhhhHHHHHHhhhhHHHhhhhhhccCCCc-eEeeecccc
Confidence 9999999999999999999999999999999998666789999999999999999999999999999875 577899998
Q ss_pred cCCCCCCCeEEEecCCCccccccCCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCC--CCCcCCCCCCCCChhhHHHH
Q 011878 388 SEKINIPDSFYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLVKMLDLAPS--GKGEILQPELTPNPALEVLN 465 (475)
Q Consensus 388 ~~~~~~~~gl~~~~LPf~dDiR~~~f~~l~~~~~~~~~~~~q~~~~~~lI~~l~l~~~--~~~~~~~p~~~~NP~lq~~y 465 (475)
..+-. -.+|+-++|||+||+|.+.|++++.. ....|+..|+.|+++||+.|+|..+ +.++.|.|.. +||..||+.
T Consensus 391 ~~~~~-~~yLvdVqLPF~eD~R~y~Fskf~~~-~n~~pt~aql~AVsnlID~M~L~ksdtl~~~pf~p~~-~~mr~hrL~ 467 (669)
T KOG2326|consen 391 QSDLA-FSYLVDVQLPFREDARAYYFSKFDSE-VNMCPTCAQLIAVSNLIDEMKLVKSDTLCRLPFAPPK-LDMRVHRLP 467 (669)
T ss_pred ccccc-eeeEEEeeccchhhhHHhhcccccch-hccCchHHHHHHHHHHhhhhhhhhhccccCCCCCCCC-ccchhhhHH
Confidence 76532 25788899999999999999998764 4578999999999999999999754 3466777777 899999999
Q ss_pred HHhhhccc
Q 011878 466 ICGYFGFL 473 (475)
Q Consensus 466 ~~l~~~a~ 473 (475)
+||-+.|+
T Consensus 468 qlllh~a~ 475 (669)
T KOG2326|consen 468 QLLLHTAT 475 (669)
T ss_pred HHhccccC
Confidence 99998875
No 3
>KOG2327 consensus DNA-binding subunit of a DNA-dependent protein kinase (Ku70 autoantigen) [Replication, recombination and repair]
Probab=100.00 E-value=3.8e-52 Score=416.53 Aligned_cols=439 Identities=21% Similarity=0.228 Sum_probs=322.9
Q ss_pred CCceEEEEEEecCCCcCC---------CchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEe
Q 011878 3 RTREALLLLLDVSPSMHS---------VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQ 73 (475)
Q Consensus 3 ~~ke~~vflID~s~sM~~---------~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~ 73 (475)
++|++++|+||++++|.. +|..++.|+..+.-+++++++.|.+|+++++|.++.+. .+.+.++
T Consensus 16 ~~~~~ilfvi~~~~s~~~~~~~e~~lspl~~~L~~~~~l~~~~vitn~~~~~~v~~y~~~~~~~~--------~~~~~l~ 87 (602)
T KOG2327|consen 16 AGKEAILFVIDVNPSMKAEEPDEFKLSPLKMILDCIDRLCIQLVITNPIDSVGVLFYGTEETEGL--------ENNTLLF 87 (602)
T ss_pred ccccceEEEEecCHHhhccCcccchhhhHHHHHHHHHHHHhheeecCCCCccceEeecccccccC--------ccceEEe
Confidence 579999999999999875 26678999999999999999999999999999987764 3555667
Q ss_pred ecCCCCHHHHHHhhcC-CCC------------CCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCC
Q 011878 74 DIKVVDGHLVQSLKHL-PQG------------TCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGT 140 (475)
Q Consensus 74 ~l~~~~~~~i~~L~~l-~~~------------~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~ 140 (475)
++..+...-+.++..+ ..+ .+.++++..||.|.+++..- .++..++||++|||+++|+.. ++.
T Consensus 88 ~l~d~~~~~~~k~~~~~e~~~q~~~~~~~~~~~~~s~ls~vl~~c~~~~~~~--~~~~~~krv~l~Td~d~P~~~--~~~ 163 (602)
T KOG2327|consen 88 PLGDLGQEEVKKILELFEEENQLSAVNFYGGMHQKSDLSNVLNYCKRMVFAS--QKKLSNKRVFLFTDNDNPHER--DDF 163 (602)
T ss_pred eccccChHHHHHHHHHhhhhhhhhhhhccCcccccccHHHHHHHHHHHHHHH--hhhcccceEEEEecCCCcccc--cch
Confidence 7665555545554443 211 12357999999999987762 346889999999999999964 233
Q ss_pred chhhHHHHHHHHhhcCcEEEEEEeccCCCCCCCccccccchHHHHHHhhcCCCeEee--hhhHHHhhccCccccCCCcee
Q 011878 141 KEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLF--VDSTTSLRGARKTRDISPVTI 218 (475)
Q Consensus 141 ~~~~~~~~~~~l~~~~I~l~~i~i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~~~--~~~~~~ll~~~~~r~~~~r~~ 218 (475)
......+++.++....|.+...+++.+++.........+-. .-..+...++.+.+ ......+++.+..+...+|+.
T Consensus 164 ~~~a~l~r~k~~~~~~i~~~~~~l~~~~~~~~~~~~y~~f~--~i~~~~~~d~~~~~~~~~~~e~~~~ri~~k~~~kR~~ 241 (602)
T KOG2327|consen 164 LESAHLQRAKDLVTKDIGFHHKTLDEPSDIFLYEDFYKPFD--KISKAKELDSDLDTEVQSTLEDLLARILAKITAKRAH 241 (602)
T ss_pred HHHhhhhhhhhcccceeeeeecccCcccccccccccccccc--hheeeccccccccChhhhhHHHHHHHHHHHHHHHHhh
Confidence 33334445555555544444223322111101110000000 00011122232222 124466777788888899999
Q ss_pred eeeeEeecCCeEEEEEEEeeccccCCC-cceEecccCCCCccccccceeEEEE---EeccCCCCCCCCcccccccceeCC
Q 011878 219 FRGDLELSEKMKIKVWVYKKTGEEKFP-TLKKYSDKAPSTDKFATHEVKVDYE---YKSVEDPSKVVPPEQRIKGYRYGP 294 (475)
Q Consensus 219 ~~~~l~ig~~~~I~V~~y~~~~~~~~p-~~~~~~~~~~~~~~~~~~~v~~~~~---y~~~~d~~~~v~~~~~~k~y~yG~ 294 (475)
|++.|.+|+++.|+|++|.++++++.+ ..|++...++ .|+..+. .++ -++|.+.-+.+..+.|.||+
T Consensus 242 f~l~l~lg~~v~i~V~~y~~~~~~~~~~~~~~y~~~~~--------~v~tk~~~~~~f~-~~tg~~~~~~~~~~s~~yG~ 312 (602)
T KOG2327|consen 242 FHLKLNLGPDVTIGVSVYNMVQRAKPADHSQLYRRDEE--------EVITKPSGYKFFS-CETGEELKRRDTKKSYEYGG 312 (602)
T ss_pred heeeeccCCCeEEEEEEeeeeeccccCccceeEecccc--------eeeeecccceEec-cccCCccccccceEEeccCC
Confidence 999999999999999999999998765 5667776542 3333333 453 45666777888999999999
Q ss_pred ceEeCChhhHHhhccCCCccEEEEeEeeCCCcccccccCceEEEEcCCC-ChhhHHHHHHHHHHHHhcCeEEEEEEEecC
Q 011878 295 QVVPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPG-NSRATVAVSALARAMKEMNKVAIVRCVWRQ 373 (475)
Q Consensus 295 ~~V~~~~~e~~~~k~~~~~~l~llGF~~~~~i~~~~~~~~~~~i~p~~~-~~~s~~~f~aL~~am~~~~~vai~r~v~r~ 373 (475)
+.|+|+.++.+.++...+|+|.|+||++.+++++|+++.++.||+|++. ..||.+.|+||+..|++++++|||||+.|.
T Consensus 313 ~~i~l~~dq~e~v~~~~~p~L~liGFk~~ssl~~~~~i~ps~fi~Pddq~~iGS~~~f~all~rcl~rdkiaic~~~~r~ 392 (602)
T KOG2327|consen 313 EDIILSMDQLEYVREFNKPGLMLIGFKSMSSLKREHYIKPSKFIYPDDQTIIGSTRLFRALLKRCLARDKIAICWFQSRS 392 (602)
T ss_pred cccccChhHHHHhhccCCcceEEEeeccccccCcccccCchhccCcchhhccchHHHHHHHHHHHHhhhhhhheeecccc
Confidence 9999999999999999999999999999999999999999999999987 789999999999999999999999999999
Q ss_pred CCCceEEEEecccccC-----CCCCCCeEEEe-cCCCccccccCCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCCCC
Q 011878 374 GQQSVVVGVLTPNVSE-----KINIPDSFYFN-VLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLVKMLDLAPSGK 447 (475)
Q Consensus 374 ~~~~~~v~~L~P~~~~-----~~~~~~gl~~~-~LPf~dDiR~~~f~~l~~~~~~~~~~~~q~~~~~~lI~~l~l~~~~~ 447 (475)
|+.|+.| ||+++... ....++||.++ +||||||+|.++++. ....+++|.+.|++++.++.+.--
T Consensus 393 n~~p~~v-Alv~~p~~~~d~~~~~l~~GF~LV~flp~aDdirk~p~~~------~v~~~p~~~eqmk~i~Qki~f~~r-- 463 (602)
T KOG2327|consen 393 NQKPRFV-ALVLQPQRGQDDSSESLPCGFQLVGFLPFADDIRKFPLQD------KVSTEPEQEEQMKAIVQKIRFKLR-- 463 (602)
T ss_pred cCCccee-eeecCccccccCcccccccceEEEEeecccchhccCCCcc------cccCCcchHHHHHHHHHHHHHHhh--
Confidence 9988877 57776432 12457899999 599999999988643 223445555556666655554310
Q ss_pred CcCCCCCCCCChhhHHHHHHhhhccccC
Q 011878 448 GEILQPELTPNPALEVLNICGYFGFLDV 475 (475)
Q Consensus 448 ~~~~~p~~~~NP~lq~~y~~l~~~a~~~ 475 (475)
..|.| .|.||.||.||++|+|+|||.
T Consensus 464 -sd~~p-~feNP~Lq~h~knL~alaLd~ 489 (602)
T KOG2327|consen 464 -SDYPP-FFENPSLQQHYKNLEALALDE 489 (602)
T ss_pred -cCCcc-cccChHHHHHHHHHHHHhccc
Confidence 12666 899999999999999999994
No 4
>cd00873 KU80 Ku-core domain, Ku80 subfamily; Ku80 is a subunit of the Ku protein, which plays a key role in multiple nuclear processes such as DNA repair, chromosome maintenance, transcription regulation, and V(D)J recombination. The mechanism underlying the regulation of all the diverse functions of Ku is still unclear, although it seems that Ku is a multifunctional protein that works in nuclei. In mammalian cells, the Ku heterodimer recruits the catalytic subunit of DNA-dependent protein kinase (DNA-PK), which is dependent on its association with the Ku70/80 heterodimer bound to DNA for its protein kinase activity.
Probab=100.00 E-value=8.4e-52 Score=405.48 Aligned_cols=250 Identities=39% Similarity=0.611 Sum_probs=222.0
Q ss_pred eeeeeeEeecCCeEEEEEEEeeccccCCCcceEeccc---CCCCccccccceeEEEEEeccCCCCCCCCcccccccceeC
Q 011878 217 TIFRGDLELSEKMKIKVWVYKKTGEEKFPTLKKYSDK---APSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYG 293 (475)
Q Consensus 217 ~~~~~~l~ig~~~~I~V~~y~~~~~~~~p~~~~~~~~---~~~~~~~~~~~v~~~~~y~~~~d~~~~v~~~~~~k~y~yG 293 (475)
+.|+|.|+||.+++|+|++|++++++++|..+++... ++. ....|+.++.|..+++++++|+++|++|||+||
T Consensus 2 ~~~~g~L~~g~~v~I~V~~y~at~~~~~~~~~~~~~~~~~~e~----~~~~v~~~~~~~~~~~~~~eV~~~~ivkgY~yg 77 (300)
T cd00873 2 AAFKGQLTLGSPLSIAVELYKKTKEERPPKLKKVSDAEKTGED----AFEDVKSERSYDVNDDDKTEVEKEDLIKGYRYG 77 (300)
T ss_pred CcccceeEecCceEEEEEEEEeeeeccCCceEEEEecccCCcc----ccccceEEEEEEccCCCCcccCHHHhhhheecC
Confidence 5799999999999999999999999998776666541 211 115688899997667888899999999999999
Q ss_pred CceEeCChhhHHhhccCCCccEEEEeEeeCCCcccccccCceEEEEcCCCChhhHHHHHHHHHHHHhcCeEEEEEEEecC
Q 011878 294 PQVVPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQ 373 (475)
Q Consensus 294 ~~~V~~~~~e~~~~k~~~~~~l~llGF~~~~~i~~~~~~~~~~~i~p~~~~~~s~~~f~aL~~am~~~~~vai~r~v~r~ 373 (475)
+++|+|+++|++.++..+++||+|+||+++++|+++|+++++|||+|++++.++.++|+||++||.+++++||||||+|+
T Consensus 78 ~~~V~~~~~e~~~~~~~~~~~l~ilgF~~~~~i~~~~~~~~s~~l~P~~~~~~~~~a~~aL~~am~~~~k~aI~r~v~r~ 157 (300)
T cd00873 78 RDIVPLSEEDEEATKLSTSKGLDILGFIKASNVPRYYLMGESSYVVPQQDDEAAALAFSALVRALAELDKYAIARYVYKD 157 (300)
T ss_pred CcEEecCHHHHHHHhcCCCCceEEEeeccHHHCChhheeCCcEEEEcCCCChhHHHHHHHHHHHHHhCCCEEEEEEEEcC
Confidence 99999999999999999999999999999999999999999999999998889999999999999999999999999999
Q ss_pred CCCceEEEEecccccCCCCCCCeEEEecCCCccccccCCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCCC---CCcC
Q 011878 374 GQQSVVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLVKMLDLAPSG---KGEI 450 (475)
Q Consensus 374 ~~~~~~v~~L~P~~~~~~~~~~gl~~~~LPf~dDiR~~~f~~l~~~~~~~~~~~~q~~~~~~lI~~l~l~~~~---~~~~ 450 (475)
++. |.+++|+|+.... +.||++++|||+||||+++||++....+...++++|+++|++||++|++++.+ ..++
T Consensus 158 ~~~-p~l~aL~P~~~~~---~~~l~l~~LPf~eDvR~~~f~~l~~~~~~~~~~~e~~~~a~~lId~m~l~~~~~~~~~~~ 233 (300)
T cd00873 158 NSE-PQLGVLFPRIKED---YECLVLVRLPFAEDVRQYRFPSLDKLKTPNLPTEEQLEAMDDLVDSMDLDDDEEDDPEEA 233 (300)
T ss_pred CCC-cEEEEEeccccCC---CCEEEEEecCchhhhhccCCCCCCcccCCCCCCHHHHHHHHHHHHhcCCCcccccccccc
Confidence 985 5577899997664 57999999999999999999987543212479999999999999999998533 3578
Q ss_pred CCCCCCCChhhHHHHHHhhhcccc
Q 011878 451 LQPELTPNPALEVLNICGYFGFLD 474 (475)
Q Consensus 451 ~~p~~~~NP~lq~~y~~l~~~a~~ 474 (475)
|+|+.++||++||||++|++.||+
T Consensus 234 f~p~~~~nP~~q~~~~~i~~~al~ 257 (300)
T cd00873 234 LKPDETPNPVLQRIYQALRHRALH 257 (300)
T ss_pred cCcccCCChHHHHHHHHHHHHhcC
Confidence 999999999999999999999986
No 5
>cd00788 KU70 Ku-core domain, Ku70 subfamily; Ku70 is a subunit of the Ku protein, which plays a key role in multiple nuclear processes such as DNA repair, chromosome maintenance, transcription regulation, and V(D)J recombination. The mechanism underlying the regulation of all the diverse functions of Ku is still unclear, although it seems that Ku is a multifunctional protein that works in the nuclei. In mammalian cells, the Ku heterodimer recruits the catalytic subunit of DNA-dependent protein kinase (DNA-PK), which is dependent on its association with the Ku70/80 heterodimer bound to DNA for its protein kinase activity.
Probab=100.00 E-value=1.8e-50 Score=393.67 Aligned_cols=244 Identities=25% Similarity=0.334 Sum_probs=211.8
Q ss_pred ceeeeeeEeecCC--eEEEEEEEeeccccCCCc-ceEecccCCCCccccccceeEEEEEeccCCCCCCCCccccccccee
Q 011878 216 VTIFRGDLELSEK--MKIKVWVYKKTGEEKFPT-LKKYSDKAPSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRY 292 (475)
Q Consensus 216 r~~~~~~l~ig~~--~~I~V~~y~~~~~~~~p~-~~~~~~~~~~~~~~~~~~v~~~~~y~~~~d~~~~v~~~~~~k~y~y 292 (475)
|+.|+++|+||++ ++|+|++|+++++++.|. .+.+..++.. ...|+.++.|++ .+++++|+++|++|||+|
T Consensus 1 R~~~~~~l~ig~~~~v~I~V~~Y~~~~~~~~~~~~~l~~~~~~~-----~~~v~~~~~~v~-~~~~~~v~~~di~kgy~~ 74 (287)
T cd00788 1 RALFRLPLELGPGNKLVISVKGYSLVSHAKKPRKYKLDREKNEE-----RREVKSKRKFFD-VESGKTLEKADIKKGYKI 74 (287)
T ss_pred CccEeeeEEECCCCCeEEEEEEEEEeecccCCceEEEecCCCcc-----ceeeEEEEEEEe-cCCCcccChhheEEeEEe
Confidence 4679999999999 999999999999988765 5666544321 114888899995 667889999999999999
Q ss_pred CCceEeCChhhHHhhccCCCccEEEEeEeeCCCcccccccCceEEEEcCCC-ChhhHHHHHHHHHHHHhcCeEEEEEEEe
Q 011878 293 GPQVVPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPG-NSRATVAVSALARAMKEMNKVAIVRCVW 371 (475)
Q Consensus 293 G~~~V~~~~~e~~~~k~~~~~~l~llGF~~~~~i~~~~~~~~~~~i~p~~~-~~~s~~~f~aL~~am~~~~~vai~r~v~ 371 (475)
|+++|+|+++|+++++..+++||+||||+++++|+++|+++++|||+|+++ ..+|.++|+||++||.++++|||||||+
T Consensus 75 g~~~V~~~~~e~~~i~~~~~~~l~ilgF~~~~~i~~~~~~~~s~fl~P~~~~~~gs~~af~aL~~am~~~~kvaIa~~v~ 154 (287)
T cd00788 75 GGEKIIFTKEELKKIKSFGEPGLRLIGFKPRSTLKPYHNIKKSYFIYPDESDYKGSTRLFAALLRSCLKKNKVAICWYIL 154 (287)
T ss_pred CCEEEEeCHHHHHHHhccCCCceEEEeeccHHHCChhhccCCceeEecCcccccCcHHHHHHHHHHHHhcCcEEEEEEEe
Confidence 999999999999999999999999999999999999999999999999986 4679999999999999999999999999
Q ss_pred cCCCCceEEEEecccccCCCC-----CCCeEEEecCCCccccccCCCCCCCCCC-CCCCCCHHHHHHHHHHHHhcCCCCC
Q 011878 372 RQGQQSVVVGVLTPNVSEKIN-----IPDSFYFNVLPFAEDVREFQFPSFSKFP-VSWQPNEQQQEAADNLVKMLDLAPS 445 (475)
Q Consensus 372 r~~~~~~~v~~L~P~~~~~~~-----~~~gl~~~~LPf~dDiR~~~f~~l~~~~-~~~~~~~~q~~~~~~lI~~l~l~~~ 445 (475)
|+++.| .+++|+|+.+...+ .++|||+++|||+||||++ |++...+ ....++++|+++|++||++|++.
T Consensus 155 r~~~~p-~l~aL~P~~~~~~~~~~~~~~~gl~l~~LPfadDiR~~--p~~~~~~~~~~~~~~~~l~~a~~LI~~l~~~-- 229 (287)
T cd00788 155 RKNSPP-RLVALVPQEEELDEPDGQVLPPGFHLVPLPFADDIRKL--PSLLEENASAESASDELVDKAKQIIKKLRLL-- 229 (287)
T ss_pred cCCCCC-EEEEEeccccccCCCCCccCCCcEEEEecCchhhhccC--CcccccccCCCCCCHHHHHHHHHHHHHhcCC--
Confidence 999875 56689999765422 3689999999999999995 3332211 24579999999999999999994
Q ss_pred CCCcCCCCCCCCChhhHHHHHHhhhcccc
Q 011878 446 GKGEILQPELTPNPALEVLNICGYFGFLD 474 (475)
Q Consensus 446 ~~~~~~~p~~~~NP~lq~~y~~l~~~a~~ 474 (475)
.|+|+.|+||++|+||++|++.||+
T Consensus 230 ----~f~p~~~~NP~lq~~~~~l~a~al~ 254 (287)
T cd00788 230 ----SYDPDKFPNPSLQKHYKILEALALD 254 (287)
T ss_pred ----CCCcccCCChHHHHHHHHHHHHHhC
Confidence 1999999999999999999999996
No 6
>cd00594 KU Ku-core domain; includes the central DNA-binding beta-barrels, polypeptide rings, and the C-terminal arm of Ku proteins. The Ku protein consists of two tightly associated homologous subunits, Ku70 and Ku80, and was originally identified as an autoantigen recognized by the sera of patients with an autoimmunity disease. In eukaryotes, the Ku heterodimer contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by non-homologous end-joining. The bacterial Ku homologs does not contain the conserved N-terminal extension that is present in the eukaryotic Ku protein.
Probab=100.00 E-value=1.4e-49 Score=386.70 Aligned_cols=239 Identities=34% Similarity=0.513 Sum_probs=209.5
Q ss_pred ceeeeeeEeecCCeEEEEEEEeeccccCCCcceEecccCCCCccccccceeEEEEEeccCCCCCCCCcccccccceeCCc
Q 011878 216 VTIFRGDLELSEKMKIKVWVYKKTGEEKFPTLKKYSDKAPSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYGPQ 295 (475)
Q Consensus 216 r~~~~~~l~ig~~~~I~V~~y~~~~~~~~p~~~~~~~~~~~~~~~~~~~v~~~~~y~~~~d~~~~v~~~~~~k~y~yG~~ 295 (475)
|+.|+|.|.||++++|+|++|+++++++.+..+++.... +..++.++.+.... +++|+++|++|||+||++
T Consensus 1 r~~~~~~l~lg~~~~i~V~~y~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~--~~~v~~~~i~kgy~~G~~ 71 (272)
T cd00594 1 RAIWKGALSLGLDVSIPVKLYSAATEEKPPSFKQLDRKT-------GERVKVKRVCKYTG--GKEVEKEDIVKGYEYGGD 71 (272)
T ss_pred CcceeeeEEECCCCEEEEEEEeeeccccCCccEEeccCC-------CceeeEEEEEEeec--CcEeCHHHhhhheeeCCe
Confidence 468999999999999999999999999888644444311 12355555554211 578999999999999999
Q ss_pred eEeCChhhHHhhccCCCccEEEEeEeeCCCcccccccCceEEEEcCCCChhhHHHHHHHHHHHHhcCeEEEEEEEecCCC
Q 011878 296 VVPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQGQ 375 (475)
Q Consensus 296 ~V~~~~~e~~~~k~~~~~~l~llGF~~~~~i~~~~~~~~~~~i~p~~~~~~s~~~f~aL~~am~~~~~vai~r~v~r~~~ 375 (475)
+|+|+++|+++++..+++||+||||+++++|+++|++++++||+|+++..+|.++|+||++||.++++|||||||+|+|+
T Consensus 72 ~V~~~~~e~~~~~~~~~~~l~ilgF~~~~~i~~~~~~~~s~~l~P~~~~~~s~~af~aL~~am~~~~kvai~r~v~r~~~ 151 (272)
T cd00594 72 YVPLTEEELEQLKLETSKGLDILGFVPASEIPPYYFDKESYYLVPDDSDKGSEKAFSALRRALLEKDKVAIARYVLRRNS 151 (272)
T ss_pred EEecCHHHHHHhhcCCCCeEEEEeEechHhCCcceecCCcEEEEcCCCCcccHHHHHHHHHHHHHcCcEEEEEEEEcCCC
Confidence 99999999999999999999999999999999999999999999999878999999999999999999999999999997
Q ss_pred CceEEEEecccccCCCCCCCeEEEecCCCccccccCCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCCCCCcCCCCCC
Q 011878 376 QSVVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLVKMLDLAPSGKGEILQPEL 455 (475)
Q Consensus 376 ~~~~v~~L~P~~~~~~~~~~gl~~~~LPf~dDiR~~~f~~l~~~~~~~~~~~~q~~~~~~lI~~l~l~~~~~~~~~~p~~ 455 (475)
.| .+++|+|+.++ .+.||++++|||+||||+++|+.+... ....++++|+++|++||++|+++ .|+|+.
T Consensus 152 ~p-~l~aL~P~~~~---~~~gl~l~~LPfadDvR~~~~~~~~~~-~~~~~~~~~~~~a~~lI~~~~~~------~~~p~~ 220 (272)
T cd00594 152 RP-RLVALRPQEEE---DPEGLVLVTLPFADDVRSYPFPLLLDI-KTEKPTDEELELAKQLIDSLDLD------DFDPEK 220 (272)
T ss_pred Cc-EEEEEeccccC---CCCEEEEEccCCchhhhccCCcccccc-cccCCCHHHHHHHHHHHHhccCC------CCCccc
Confidence 64 56689999766 368999999999999999999876542 22579999999999999999994 299999
Q ss_pred CCChhhHHHHHHhhhcccc
Q 011878 456 TPNPALEVLNICGYFGFLD 474 (475)
Q Consensus 456 ~~NP~lq~~y~~l~~~a~~ 474 (475)
++||++|+||++|++.||+
T Consensus 221 ~~NP~lq~~~~~l~~~al~ 239 (272)
T cd00594 221 FPNPYLQRLYALLEAKALG 239 (272)
T ss_pred CCCHHHHHHHHHHHHHhcC
Confidence 9999999999999999986
No 7
>cd00789 KU_like Ku-core domain, Ku-like subfamily; composed of prokaryotic homologs of the eukaryotic DNA binding protein Ku. The alignment includes the core domain shared by the prokaryotic YkoV-like proteins and the eukaryotic Ku70 and Ku80. The prokaryotic Ku homologs are predicted to form homodimers. It is proposed that the Ku homologs are functionally associated with ATP-dependent DNA ligase and the eukaryotic-type primase, probably as components of a double-strand break repair system.
Probab=100.00 E-value=3e-46 Score=353.80 Aligned_cols=223 Identities=20% Similarity=0.309 Sum_probs=199.5
Q ss_pred ceeeeeeEeecCCeEEEEEEEeeccccCCCcceEecccCCCCccccccceeEEEEEeccCCCCCCCCcccccccceeC-C
Q 011878 216 VTIFRGDLELSEKMKIKVWVYKKTGEEKFPTLKKYSDKAPSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYG-P 294 (475)
Q Consensus 216 r~~~~~~l~ig~~~~I~V~~y~~~~~~~~p~~~~~~~~~~~~~~~~~~~v~~~~~y~~~~d~~~~v~~~~~~k~y~yG-~ 294 (475)
|++|+|.|+|| .++|||++|++++..++++++.+..++ ..| ++.|+ +++++++|+++|++|||+|| +
T Consensus 1 r~~wkG~l~fg-lV~ipV~ly~at~~~~i~f~~l~~~~~--------~~v--~~~~v-~~~~g~eV~~~divKgYeyg~~ 68 (256)
T cd00789 1 RAIWKGAISFG-LVNIPVKLYSATESEDISFHQLHKKDG--------ARI--RYQRV-CPETGKEVPRDDIVKGYEYEKG 68 (256)
T ss_pred CCceEEEEEEC-cEEEEEEEEEeeccCCcccEEEecCCC--------CEe--eEEEE-CCCCCCCCCHHHceeeEEeCCC
Confidence 57999999999 799999999988888888888887653 234 46666 58899999999999999999 8
Q ss_pred ceEeCChhhHHhhccCCCccEEEEeEeeCCCcccccccCceEEEEcCCCChhhHHHHHHHHHHHHhcCeEEEEEEEecCC
Q 011878 295 QVVPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQG 374 (475)
Q Consensus 295 ~~V~~~~~e~~~~k~~~~~~l~llGF~~~~~i~~~~~~~~~~~i~p~~~~~~s~~~f~aL~~am~~~~~vai~r~v~r~~ 374 (475)
++|+|+++|+++++..+.++|+|+||++.++|+++|+ +++|||+|++ ++..+|++|++||.+.++|||||||+|.+
T Consensus 69 ~~V~~~~eel~~~~~~~~~~i~IlgFv~~~~I~~~y~-~~syyl~P~~---~~~kaf~~L~~Al~~~~kvaIar~V~r~~ 144 (256)
T cd00789 69 EYVILTDEELEALPPESTRTIEIVDFVPLDEIDPIYF-DKPYYLAPDK---GGEKAYALLREALRDTGKVAIAKVVLRTR 144 (256)
T ss_pred CEEEcCHHHHHhhccCCCCeEEEEeEeCHHHCCHhHc-CCCEEEecCC---CcchHHHHHHHHHHHcCCEEEEEEEEcCC
Confidence 9999999999999999999999999999999999888 4679999998 56679999999999999999999999986
Q ss_pred CCceEEEEecccccCCCCCCCeEEEecCCCccccccCCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCCCCCcCCCCC
Q 011878 375 QQSVVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLVKMLDLAPSGKGEILQPE 454 (475)
Q Consensus 375 ~~~~~v~~L~P~~~~~~~~~~gl~~~~LPf~dDiR~~~f~~l~~~~~~~~~~~~q~~~~~~lI~~l~l~~~~~~~~~~p~ 454 (475)
. .+|+|.|+ ..||++++|||+||||+++|+++.. ....++++|+++|++||++|+.+ |+|+
T Consensus 145 ~---~l~aL~P~-------~~gL~l~~LpfaddvR~~~~~~~~~--~~~~~~~~el~~A~~LI~~m~~~-------fdp~ 205 (256)
T cd00789 145 E---RLAALRPR-------GKGLVLNTLRYPDEVRSPEELFLPI--KAVKVDPKELEMAKQLIEQLTGD-------FDPE 205 (256)
T ss_pred c---eEEEEEEC-------CCEEEEEECCChhhccCccccCccc--ccCCCCHHHHHHHHHHHHHccCC-------CCcc
Confidence 3 37789998 3699999999999999999877542 34579999999999999999986 9999
Q ss_pred CCCChhhHHHHHHhhhccc
Q 011878 455 LTPNPALEVLNICGYFGFL 473 (475)
Q Consensus 455 ~~~NP~lq~~y~~l~~~a~ 473 (475)
.|.||+.++++++|++.+.
T Consensus 206 ~~~d~y~~~l~~li~~K~~ 224 (256)
T cd00789 206 KYEDEYREALMELIEAKIE 224 (256)
T ss_pred ccCCHHHHHHHHHHHHHHc
Confidence 9999999999999998764
No 8
>TIGR02772 Ku_bact Ku protein, prokaryotic. Members of this protein family are Ku proteins of non-homologous end joining (NHEJ) DNA repair in bacteria and in at least one member of the archaea (Archaeoglobus fulgidus). Most members are encoded by a gene adjacent to the gene for the DNA ligase that completes the repair. The NHEJ system is broadly but rather sparsely distributed, being present in about one fifth of the first 250 completed prokarytotic genomes. A few species (e.g. Archaeoglobus fulgidus and Bradyrhizobium japonicum) have multiple copies that appear to represent recent paralogous family expansion.
Probab=100.00 E-value=2.4e-45 Score=348.07 Aligned_cols=223 Identities=20% Similarity=0.295 Sum_probs=197.5
Q ss_pred CceeeeeeEeecCCeEEEEEEEeeccccCCCcceEecccCCCCccccccceeEEEEEeccCCCCCCCCcccccccceeCC
Q 011878 215 PVTIFRGDLELSEKMKIKVWVYKKTGEEKFPTLKKYSDKAPSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYGP 294 (475)
Q Consensus 215 ~r~~~~~~l~ig~~~~I~V~~y~~~~~~~~p~~~~~~~~~~~~~~~~~~~v~~~~~y~~~~d~~~~v~~~~~~k~y~yG~ 294 (475)
+|++|+|.|+|| .++|||++|++++..++++++.+..++ ..|+ +.++ +++++++|+++|++|||+||+
T Consensus 1 ~r~~wkG~l~fg-lV~ipV~lY~at~~~~i~f~~l~~~~~--------~~v~--~~~v-~~~~g~eV~~~divKgYeyg~ 68 (258)
T TIGR02772 1 ARAIWKGAISFG-LVNCPVKLYPATESEDISFHQLHREDG--------NRVR--YQKV-CSETGKEVEREEIVKGYEYDK 68 (258)
T ss_pred CCCceEEEEEEc-cEEEEEEEEEeeecCCCccEEEEcCCC--------Ceee--EEEE-cCCCCCCCCHHHeeeeEEeCC
Confidence 478999999999 799999999999988888888877653 3454 5566 588999999999999999995
Q ss_pred -ceEeCChhhHHhhccCCCccEEEEeEeeCCCcccccccCceEEEEcCCCChhhHHHHHHHHHHHHhcCeEEEEEEEecC
Q 011878 295 -QVVPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQ 373 (475)
Q Consensus 295 -~~V~~~~~e~~~~k~~~~~~l~llGF~~~~~i~~~~~~~~~~~i~p~~~~~~s~~~f~aL~~am~~~~~vai~r~v~r~ 373 (475)
++|+|+++|+++++..++++|+|+||++.++|+++|+ +.+|||+|+ .++..+|++|++||.++++|||||||+|.
T Consensus 69 g~~V~~~~eel~~~~~~~~~~i~I~gFv~~~~i~~~y~-~~syyl~P~---~~~~~a~~~L~~Al~~~~kvaIar~v~r~ 144 (258)
T TIGR02772 69 GKYVIIEDEDIESLPPESTKTIEIEAFVDADEIDPIYF-DTPYYLAPD---KGGEKAYALLREALEDTGKVGIAKVVLRG 144 (258)
T ss_pred CCEEEcCHHHHHhhcccCCCeEEEEEEeCHHHCChhee-CCCEEEccC---CCchHHHHHHHHHHHHcCCEEEEEEEEcC
Confidence 9999999999999999999999999999999998876 557999998 46778999999999999999999999998
Q ss_pred CCCceEEEEecccccCCCCCCCeEEEecCCCccccccC-CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCCCCCcCCC
Q 011878 374 GQQSVVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREF-QFPSFSKFPVSWQPNEQQQEAADNLVKMLDLAPSGKGEILQ 452 (475)
Q Consensus 374 ~~~~~~v~~L~P~~~~~~~~~~gl~~~~LPf~dDiR~~-~f~~l~~~~~~~~~~~~q~~~~~~lI~~l~l~~~~~~~~~~ 452 (475)
+. . +++|.|+ ..||++++|||+||||++ +|++. .....++++|+++|++||++|+.+ |+
T Consensus 145 r~--~-l~aL~P~-------~~gL~l~~LpfadEvR~~~~~~~~---~~~~~~~~~el~~A~~LI~~mt~~-------fd 204 (258)
T TIGR02772 145 RE--R-LAALRPV-------GKGLVLTTLRYPDEVRSPDEFFGP---IKDVEVDPEELELAGQLIDKMTGK-------FD 204 (258)
T ss_pred Cc--E-EEEEEEC-------CCeEEEEECCChhhccChhhcccc---cccCCCCHHHHHHHHHHHHHhccC-------CC
Confidence 63 4 7789998 369999999999999998 46543 234579999999999999999976 99
Q ss_pred CCCCCChhhHHHHHHhhhccc
Q 011878 453 PELTPNPALEVLNICGYFGFL 473 (475)
Q Consensus 453 p~~~~NP~lq~~y~~l~~~a~ 473 (475)
|+.|.||+.|+++++|++.+.
T Consensus 205 p~~y~d~y~~~l~~~i~~K~~ 225 (258)
T TIGR02772 205 PEDYHDEYREALLELVDAKLE 225 (258)
T ss_pred hhhCCCHHHHHHHHHHHHHHh
Confidence 999999999999999999875
No 9
>PF02735 Ku: Ku70/Ku80 beta-barrel domain; InterPro: IPR006164 The Ku heterodimer is composed of Ku70 and Ku80 (or Ku86), 70 kDa and 80 kDa subunits of an ATP-dependent DNA helicase, which contributes to genomic integrity through its ability to bind DNA double-stranded breaks and facilitate repair by the non-homologous end-joining pathway. This is the central DNA-binding beta-barrel domain and is found in both the Ku70 and Ku80 proteins. Ku makes only a few contacts with the sugar-phosphate backbone, and none with the DNA bases, but it fits sterically to major and minor groove contours forming a ring that encircles duplex DNA, cradling two full turns of the DNA molecule. By forming a bridge between the broken DNA ends, Ku acts to structurally support and align the DNA ends, to protect them from degradation, and to prevent promiscuous binding to unbroken DNA. Ku effectively aligns the DNA, while still allowing access of polymerases, nucleases and ligases to the broken DNA ends to promote end joining [].; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0006303 double-strand break repair via nonhomologous end joining; PDB: 1JEY_B 1JEQ_B.
Probab=100.00 E-value=7.3e-43 Score=323.52 Aligned_cols=199 Identities=39% Similarity=0.606 Sum_probs=146.7
Q ss_pred EeecCCeEEEEEEEeeccccCCCcceEecccCCCCccccccceeEEEEEeccCCCCCCCCcccccccceeCCceEeCChh
Q 011878 223 LELSEKMKIKVWVYKKTGEEKFPTLKKYSDKAPSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYGPQVVPISSA 302 (475)
Q Consensus 223 l~ig~~~~I~V~~y~~~~~~~~p~~~~~~~~~~~~~~~~~~~v~~~~~y~~~~d~~~~v~~~~~~k~y~yG~~~V~~~~~ 302 (475)
|+||++++|+|++|++++++++|+.+++.... +..++.++.|+ +++++.+|+++|++|||+||+++|+|+++
T Consensus 1 ~~ig~~v~I~V~~y~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~-~~~~~~~v~~~d~~kgy~~g~~~V~~~~~ 72 (200)
T PF02735_consen 1 LSIGPDVSIPVKLYKATKEAKPPFFKKLSRDT-------NEEVRSRTKYV-CPDTGEEVPPEDIIKGYRYGGEYVPFTDE 72 (200)
T ss_dssp EECTTTEEEEEEEEECE-----S--EEEETTT-------TTEEEEEEEEE-CTTT--EE-GGGEEEEEEECTEEEEE-HH
T ss_pred CEeCCCeEEEEEEEEeEeeccCCCcEEEEecC-------CcCceEEEEEE-cCCCCCccCHHHeEEEEEeCCEEEEeCHH
Confidence 68999999999999999999999887777541 34677777777 57888899999999999999999999999
Q ss_pred hHHhhccCCCccEEEEeEeeCCCcccccccCceEEEEcCCCCh-hhHHHHHHHHHHHHhcCeEEEEEEEecCCCCceEEE
Q 011878 303 EWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPGNS-RATVAVSALARAMKEMNKVAIVRCVWRQGQQSVVVG 381 (475)
Q Consensus 303 e~~~~k~~~~~~l~llGF~~~~~i~~~~~~~~~~~i~p~~~~~-~s~~~f~aL~~am~~~~~vai~r~v~r~~~~~~~v~ 381 (475)
|++.++..++++|+||||+++++|+++|++++++||+|+++.. +|..+|+||++||.++++|||||||+|.++.|. ++
T Consensus 73 e~~~~~~~~~~~l~ilGF~~~~~i~~~~~~~~~~~i~p~~~~~~~s~~~f~aL~~am~~~~~vaI~r~v~r~~~~p~-l~ 151 (200)
T PF02735_consen 73 ELEAIKPETSPGLEILGFVPRSNIPPYYFMGESYFIVPDEKSGEGSAKAFSALVQAMLEKNKVAIARYVLRSNSRPR-LV 151 (200)
T ss_dssp HHHHCT--S-SEEEEEEEEEGGGS-CCG-ECEEEEEEEETTTECCHHHHHHHHHHHHHHCTEEEEEEEESSTTS--E-EE
T ss_pred HHHhhhhcCCCeEEEEEEEcchhCCceEEeCCcEEEEECCCCcchhHHHHHHHHHHHHhcCcEEEEEEEEcCCCCcE-EE
Confidence 9999999999999999999999999999999999999998754 899999999999999999999999999998655 67
Q ss_pred EecccccCCCCCCCeEEEecCCCccccccCCCCCCCCCCCCCCCCHHHHHHH
Q 011878 382 VLTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAA 433 (475)
Q Consensus 382 ~L~P~~~~~~~~~~gl~~~~LPf~dDiR~~~f~~l~~~~~~~~~~~~q~~~~ 433 (475)
+|+|+.+.. ..+.||++++|||+||+|.++||++... +..++++|+++|
T Consensus 152 aL~P~~~~~-~~~~gl~~~~Lpf~dDvR~~~~~~~~~~--~~~~~~eql~~a 200 (200)
T PF02735_consen 152 ALIPQIEES-DTPEGLVLIRLPFADDVRSFPFPSLSSA--KTKPTEEQLDAA 200 (200)
T ss_dssp EEEEEE-CE-EC-CEEEEEE---GGGB-------STT---TT---HHHHHH-
T ss_pred EEEEecccc-CCCCeEEEEEcCChhhccCccccCcCcC--CCCCCHHHhhcC
Confidence 899998653 2258999999999999999999998653 447999999987
No 10
>smart00559 Ku78 Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen. This is a single stranded DNA- and ATP-depedent helicase that has a role in chromosome translocation. This is a domain of unknown function C-terminal to its von Willebrand factor A domain, that also occurs in bacterial hypothetical proteins.
Probab=100.00 E-value=1.3e-35 Score=257.78 Aligned_cols=136 Identities=35% Similarity=0.574 Sum_probs=126.3
Q ss_pred CCCCcccccccceeCCceEeCChhhHHhhccCCCccEEEEeEeeCCCcccccccCceEEEEcCCC-ChhhHHHHHHHHHH
Q 011878 279 KVVPPEQRIKGYRYGPQVVPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPG-NSRATVAVSALARA 357 (475)
Q Consensus 279 ~~v~~~~~~k~y~yG~~~V~~~~~e~~~~k~~~~~~l~llGF~~~~~i~~~~~~~~~~~i~p~~~-~~~s~~~f~aL~~a 357 (475)
++|+++|++|||+||+++|+|+++|++++|..++++|+||||+++++|+++|+++++|||+|++. ..+|+++|+||++|
T Consensus 2 ~~v~~~~~~kgy~yG~~~V~~~~ee~~~~k~~~~~~l~ilgF~~~~~i~~~~~~~~s~~i~P~~~~~~~s~~a~~aL~~a 81 (140)
T smart00559 2 KEVKPEDIVKGYEYGGRYVPLSDEELEQLKYKSEPGLELLGFKPLSSLPPYYFLRPSYFLVPDDKSVIGSTKAFSALVEA 81 (140)
T ss_pred cccChHHceEeeEeCCEEeccCHHHHHHhhccCCCeEEEEeecChHHCCHhHccCCcEEEeeCCcccchhHHHHHHHHHH
Confidence 47899999999999999999999999999999999999999999999999999999999999986 67899999999999
Q ss_pred HHhcCeEEEEEEEecCCCCceEEEEecccccCCCCCCCeEEEecCCCccccccCCCCCCC
Q 011878 358 MKEMNKVAIVRCVWRQGQQSVVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFS 417 (475)
Q Consensus 358 m~~~~~vai~r~v~r~~~~~~~v~~L~P~~~~~~~~~~gl~~~~LPf~dDiR~~~f~~l~ 417 (475)
|.+++++||||||+|+++. +.+++|+|+.++.+ +.||++++|||+||||+++||++.
T Consensus 82 m~~~~~~aiar~v~r~~~~-p~l~aL~P~~~~~~--~~~l~~~~LpfaedvR~~~~~~l~ 138 (140)
T smart00559 82 LLETDKIAIARYTLRTKSN-PRLVALRPYDEEDD--GEGLVLVQLPFADDVRKLDFPELN 138 (140)
T ss_pred HHhcCCEEEEEEEEcCCCC-CEEEEEEeeecccC--CCcEEEEecCCchhccCCCCcCcc
Confidence 9999999999999999986 55778999977543 469999999999999999998874
No 11
>COG1273 Ku-homolog [Replication, recombination, and repair]
Probab=100.00 E-value=9.2e-33 Score=251.62 Aligned_cols=220 Identities=23% Similarity=0.326 Sum_probs=196.4
Q ss_pred CceeeeeeEeecCCeEEEEEEEeeccccCCCcceEecccCCCCccccccceeEEEEEeccCCCCCCCCcccccccceeCC
Q 011878 215 PVTIFRGDLELSEKMKIKVWVYKKTGEEKFPTLKKYSDKAPSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYGP 294 (475)
Q Consensus 215 ~r~~~~~~l~ig~~~~I~V~~y~~~~~~~~p~~~~~~~~~~~~~~~~~~~v~~~~~y~~~~d~~~~v~~~~~~k~y~yG~ 294 (475)
+|+.|+|.+.||- ++|||++|++|+..-+.+++++..++ -+..+.|+ +..+|++|+++|++|||+||+
T Consensus 3 ~Ra~WKG~ikfgL-V~~PV~ly~ATs~seI~F~~L~r~t~----------nrV~~~~V-d~~tGk~Ve~~d~VKGYE~~~ 70 (278)
T COG1273 3 MRAIWKGYIKFGL-VNCPVKLYPATSESEIRFHTLHRKTG----------NRVRYKYV-DSVTGKEVERDDIVKGYEYGK 70 (278)
T ss_pred ccccccceeEeee-EecceEeeecccccccchhhhhhhhC----------CceeeEEe-ccccCCccCccceeeeeEecC
Confidence 6889999999996 99999999999986688888888764 24457788 478999999999999999988
Q ss_pred -ceEeCChhhHHhhccCCCccEEEEeEeeCCCcccccccCceEEEEcCCCChhhHHHHHHHHHHHHhcCeEEEEEEEecC
Q 011878 295 -QVVPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQ 373 (475)
Q Consensus 295 -~~V~~~~~e~~~~k~~~~~~l~llGF~~~~~i~~~~~~~~~~~i~p~~~~~~s~~~f~aL~~am~~~~~vai~r~v~r~ 373 (475)
++|.++++|++.++..+.+.|+|..|+|.+.|++.||-++ ||+.|++ .+..||+.|.+||.+.+++||+|.|.++
T Consensus 71 ~~yViledeel~s~~~es~kti~I~~Fvp~~eId~iyfD~p-YYl~Pd~---~g~~af~lLReam~~~~~~aIar~vl~~ 146 (278)
T COG1273 71 GDYVILEDEELESVPLESTKTIEIEAFVPRDEIDPIYFDKP-YYLAPDK---VGEKAFALLREAMAETKKVAIARLVLRR 146 (278)
T ss_pred CcEEEecHHHHhhccccccceEeEEeecCHhhcCceeecCc-eeecCCC---CcchHHHHHHHHHHHcCcchhhhhhhhc
Confidence 9999999999999999999999999999999999999986 9999994 5677999999999999999999999999
Q ss_pred CCCceEEEEecccccCCCCCCCeEEEecCCCccccccCC--CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCCCCCcCC
Q 011878 374 GQQSVVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREFQ--FPSFSKFPVSWQPNEQQQEAADNLVKMLDLAPSGKGEIL 451 (475)
Q Consensus 374 ~~~~~~v~~L~P~~~~~~~~~~gl~~~~LPf~dDiR~~~--f~~l~~~~~~~~~~~~q~~~~~~lI~~l~l~~~~~~~~~ 451 (475)
+.+ +++|-|+ +.|+++.+|.|.|+||+.. ||.+.. ...+++++++|.+||+.|.-. |
T Consensus 147 Rer---~v~Lrp~-------~~glv~~TL~~~dEVRs~d~~f~~i~~----~~~d~eml~lA~~lI~~~~~~-------f 205 (278)
T COG1273 147 RER---LVLLRPR-------GKGLVLTTLRYPDEVRSPDEYFPGIPD----IKIDPEMLELAKQLIDKKTGT-------F 205 (278)
T ss_pred cce---eEEEEec-------CCcEEEEEecCchhccChhhhcCCCCc----ccCCHHHHHHHHHHHHHhcCC-------C
Confidence 864 3468887 6799999999999999988 777643 348999999999999999986 9
Q ss_pred CCCCCCChhhHHHHHHhhhc
Q 011878 452 QPELTPNPALEVLNICGYFG 471 (475)
Q Consensus 452 ~p~~~~NP~lq~~y~~l~~~ 471 (475)
+|+.|.+|+-+++-..+++.
T Consensus 206 dp~~y~D~y~~aL~elI~aK 225 (278)
T COG1273 206 DPDEYEDRYQEALMELIEAK 225 (278)
T ss_pred ChHHccCHHHHHHHHHHHHH
Confidence 99999999999998887753
No 12
>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=99.97 E-value=1.8e-29 Score=238.58 Aligned_cols=201 Identities=28% Similarity=0.406 Sum_probs=140.9
Q ss_pred EEEEEEecCCCcCCC-------chHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCC
Q 011878 7 ALLLLLDVSPSMHSV-------LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVD 79 (475)
Q Consensus 7 ~~vflID~s~sM~~~-------~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~ 79 (475)
|||||||||++|+++ |+.|++++..++++||+++++|+||||+|||++|+|+ .+.++|+||+++++++.|+
T Consensus 1 ~~vflID~s~sM~~~~~~~~~~l~~al~~i~~~~~~ki~~~~kD~vgvvl~gt~~t~n~--~~~~~~~~i~~l~~l~~~~ 78 (224)
T PF03731_consen 1 ATVFLIDVSPSMFEPSSESESPLEEALKAIEDLMQQKIISSPKDEVGVVLFGTDETNNP--DEDSGYENIFVLQPLDPPS 78 (224)
T ss_dssp EEEEEEE-SCGGGS-BTTCS-HHHHHHHHHHHHHHHHHHTT---EEEEEEES-SS-BST---TTT-STTEEEEEECC--B
T ss_pred CEEEEEECCHHHCCCCCCcchhHHHHHHHHHHHHHHHHcCCCCCeEEEEEEcCCCCCCc--ccccCCCceEEeecCCccC
Confidence 799999999999974 6789999999999999999999999999999999997 4456999999999999999
Q ss_pred HHHHHHhhcCCC----------CCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHH-
Q 011878 80 GHLVQSLKHLPQ----------GTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTI- 148 (475)
Q Consensus 80 ~~~i~~L~~l~~----------~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~- 148 (475)
++.|+.|.++.. +...+++.+|||+|+++|.+++.+++++.||||||||+++|+.. ....+.+...
T Consensus 79 ~~~l~~L~~~~~~~~~~~~~~~~~~~~~l~~al~v~~~~~~~~~~~~k~~~krI~l~Td~d~p~~~---~~~~~~~~~~l 155 (224)
T PF03731_consen 79 AERLKELEELLKPGDKFENFFSGSDEGDLSDALWVASDMFRERTCKKKKNKKRIFLFTDNDGPHED---DDELERIIQKL 155 (224)
T ss_dssp HHHHHHHHTTSHHHHHHHHHC-SSS---HHHHHHHHHHHHHCHCTTS-ECEEEEEEEES-SSTTT----CCCHHHHHHHH
T ss_pred HHHHHHHHHhhcccccccccCCCCCccCHHHHHHHHHHHHHHHhhcccCCCcEEEEEeCCCCCCCC---HHHHHHHHHhh
Confidence 999999999744 35578999999999999987656677899999999999999963 1234555555
Q ss_pred -HHHHhhcCcEEEEEEecc--CC-CCCCCccccccchHHHHHHhhcCCCeEeehhhHHHhhccCccccCCCce
Q 011878 149 -ARQMVAFGLRMKNIVVRA--SL-SGEPHMRVIIENDNLLNIFSKKSSAKTLFVDSTTSLRGARKTRDISPVT 217 (475)
Q Consensus 149 -~~~l~~~~I~l~~i~i~~--~~-~~~~~~~~~~~n~~~l~~~~~~~~g~~~~~~~~~~ll~~~~~r~~~~r~ 217 (475)
+.++++.||.+.++++.. .| .+.++..+...+....+.......|. ...+++++++.|..++|+
T Consensus 156 ~~~Dl~~~~i~~~~~~l~~~~~f~~~~fy~~~~~~~~~~~~~~~~~~~~~-----~~~~l~~~~~~~~~~kR~ 223 (224)
T PF03731_consen 156 KAKDLQDNGIEIELFFLPGSDKFDMDKFYKEILKLPEDEENEVMQSSSGE-----SVEDLLSRIRRKKFKKRA 223 (224)
T ss_dssp HHHHHHHHTEEEEEEECT-TT---CCCTCGHCCHHHHHHHHHHHHHHCSG-----CHHHHCCCCCCCHCG---
T ss_pred ccccchhcCcceeEeecCCCCCCChhhCcccccccchhhhcccccccccc-----cHHHHHHHHhhhcccccC
Confidence 888999999999999921 11 12233333333333344333333332 456778888888887774
No 13
>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=99.94 E-value=5.6e-26 Score=213.64 Aligned_cols=153 Identities=29% Similarity=0.458 Sum_probs=132.9
Q ss_pred ceEEEEEEecCCCcCC--------CchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecC
Q 011878 5 REALLLLLDVSPSMHS--------VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIK 76 (475)
Q Consensus 5 ke~~vflID~s~sM~~--------~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~ 76 (475)
||+++||||+|+||+. +|+.|++++..++++||+++++|+||||+|||+.++|+. +|+||++++|+.
T Consensus 1 ke~ivf~iDvS~SM~~~~~~~~~s~l~~a~~~i~~~~~~ki~~~~~D~vGlilf~t~~~~~~~-----~~~~i~v~~~l~ 75 (218)
T cd01458 1 KESVVFLVDVSPSMFESKDGEYESPFEEALKCIRQLMKSKIISSPKDLVGVVFYGTEESKNPV-----GYENIYVLLDLD 75 (218)
T ss_pred CcEEEEEEeCCHHHcCCCCCCCCChHHHHHHHHHHHHHhceeCCCCCeEEEEEEcccCCCCcC-----CCCceEEeecCC
Confidence 7999999999999973 367899999999999999999999999999999999863 899999999999
Q ss_pred CCCHHHHHHhhcCCC-C----------CCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhH
Q 011878 77 VVDGHLVQSLKHLPQ-G----------TCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQV 145 (475)
Q Consensus 77 ~~~~~~i~~L~~l~~-~----------~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~ 145 (475)
.++++.++.|.++.. + ...+++.+|||+|+++|.+ + ++++..|+||||||+++|++. +.....++
T Consensus 76 ~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~l~~aL~~a~~~~~~-~-~~~~~~k~IvL~TDg~~p~~~--~~~~~~~~ 151 (218)
T cd01458 76 TPGAERVEDLKELIEPGGLSFAGQVGDSGQVSLSDALWVCLDLFSK-G-KKKKSHKRIFLFTNNDDPHGG--DSIKDSQA 151 (218)
T ss_pred CCCHHHHHHHHHHhhcchhhhcccCCCCCCccHHHHHHHHHHHHHh-c-cccccccEEEEECCCCCCCCC--CHHHHHHH
Confidence 999999999998632 2 2356899999999999876 3 345778999999999999863 22345678
Q ss_pred HHHHHHHhhcCcEEEEEEecc
Q 011878 146 STIARQMVAFGLRMKNIVVRA 166 (475)
Q Consensus 146 ~~~~~~l~~~~I~l~~i~i~~ 166 (475)
..++++|++.||.+++|+++.
T Consensus 152 ~~~a~~l~~~gI~i~~i~i~~ 172 (218)
T cd01458 152 AVKAEDLKDKGIELELFPLSS 172 (218)
T ss_pred HHHHHHHHhCCcEEEEEecCC
Confidence 889999999999999999964
No 14
>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=99.49 E-value=1.4e-12 Score=119.06 Aligned_cols=164 Identities=16% Similarity=0.182 Sum_probs=116.4
Q ss_pred EEEEEEecCCCcCC------CchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCCH
Q 011878 7 ALLLLLDVSPSMHS------VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDG 80 (475)
Q Consensus 7 ~~vflID~s~sM~~------~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~~ 80 (475)
.++|+||+|+||.+ +++.|+.++..|++++.-.++.|+||||.|+... -+++.|++.-..
T Consensus 5 ~ivi~lD~S~SM~a~D~~ptRl~~ak~~~~~fi~~~~~~~~~~~vglv~f~~~~--------------a~~~~PlT~D~~ 70 (183)
T cd01453 5 HLIIVIDCSRSMEEQDLKPSRLAVVLKLLELFIEEFFDQNPISQLGIISIKNGR--------------AEKLTDLTGNPR 70 (183)
T ss_pred EEEEEEECcHHHhcCCCCchHHHHHHHHHHHHHHHHhhcCccccEEEEEEcCCc--------------cEEEECCCCCHH
Confidence 47999999999984 6889999999999887777899999999995432 123566654444
Q ss_pred HHHHHhhcCCCCCCCCChhHHHHHHHHHHHHHhccCcceee-EEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEE
Q 011878 81 HLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKK-HLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRM 159 (475)
Q Consensus 81 ~~i~~L~~l~~~~~~gd~~daL~va~~~l~~~~~~~~~~~k-rI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l 159 (475)
..+..|+.+....+..++.+||..|.++|.. .. ....+ .|+|+||+.+. . ...+..+++.+++.||.+
T Consensus 71 ~~~~~L~~~~~~~G~t~l~~aL~~A~~~l~~--~~-~~~~~~iiil~sd~~~~-~-------~~~~~~~~~~l~~~~I~v 139 (183)
T cd01453 71 KHIQALKTARECSGEPSLQNGLEMALESLKH--MP-SHGSREVLIIFSSLSTC-D-------PGNIYETIDKLKKENIRV 139 (183)
T ss_pred HHHHHhhcccCCCCchhHHHHHHHHHHHHhc--CC-ccCceEEEEEEcCCCcC-C-------hhhHHHHHHHHHHcCcEE
Confidence 5566666652222345899999999999864 11 12234 45566664432 1 123556788899999999
Q ss_pred EEEEeccCCCCCCCccccccchHHHHHHhhcCCCeEeehhhHHHhhccC
Q 011878 160 KNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDSTTSLRGAR 208 (475)
Q Consensus 160 ~~i~i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~~~~~~~~~ll~~~ 208 (475)
.+|+++. +...|+.++..++|+++...+..++-..+
T Consensus 140 ~~IgiG~-------------~~~~L~~ia~~tgG~~~~~~~~~~l~~~~ 175 (183)
T cd01453 140 SVIGLSA-------------EMHICKEICKATNGTYKVILDETHLKELL 175 (183)
T ss_pred EEEEech-------------HHHHHHHHHHHhCCeeEeeCCHHHHHHHH
Confidence 9999953 13579999999999999877765544433
No 15
>COG1240 ChlD Mg-chelatase subunit ChlD [Coenzyme metabolism]
Probab=99.39 E-value=2.1e-11 Score=112.92 Aligned_cols=168 Identities=18% Similarity=0.232 Sum_probs=130.5
Q ss_pred eEEEEEEecCCCcCCC--chHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCCHHHH
Q 011878 6 EALLLLLDVSPSMHSV--LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHLV 83 (475)
Q Consensus 6 e~~vflID~s~sM~~~--~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~~~~i 83 (475)
.-+||+||+|.||... +..|+.++..|++.- ++..|+||||.|+++++.- +.|++.--....
T Consensus 79 ~lvvfvVDASgSM~~~~Rm~aaKG~~~~lL~dA--Yq~RdkvavI~F~G~~A~l--------------ll~pT~sv~~~~ 142 (261)
T COG1240 79 NLIVFVVDASGSMAARRRMAAAKGAALSLLRDA--YQRRDKVAVIAFRGEKAEL--------------LLPPTSSVELAE 142 (261)
T ss_pred CcEEEEEeCcccchhHHHHHHHHHHHHHHHHHH--HHccceEEEEEecCCcceE--------------EeCCcccHHHHH
Confidence 4589999999999985 788899999999976 8999999999999986433 556665555667
Q ss_pred HHhhcCCCCCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEEE
Q 011878 84 QSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIV 163 (475)
Q Consensus 84 ~~L~~l~~~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l~~i~ 163 (475)
+.|+.++.|. .+++.+||..|.+++.+...+.-.....+++|||+..+...+ .....++...+..+...|+.+.+|.
T Consensus 143 ~~L~~l~~GG-~TPL~~aL~~a~ev~~r~~r~~p~~~~~~vviTDGr~n~~~~--~~~~~e~~~~a~~~~~~g~~~lvid 219 (261)
T COG1240 143 RALERLPTGG-KTPLADALRQAYEVLAREKRRGPDRRPVMVVITDGRANVPIP--LGPKAETLEAASKLRLRGIQLLVID 219 (261)
T ss_pred HHHHhCCCCC-CCchHHHHHHHHHHHHHhhccCCCcceEEEEEeCCccCCCCC--CchHHHHHHHHHHHhhcCCcEEEEe
Confidence 7899998865 569999999999998875322124577799999999766542 2235678888999999999999998
Q ss_pred eccCCCCCCCccccccchHHHHHHhhcCCCeEeehhhHH
Q 011878 164 VRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDSTT 202 (475)
Q Consensus 164 i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~~~~~~~~ 202 (475)
...++ ..-.+.+++|...+|.++.++++.
T Consensus 220 ~e~~~----------~~~g~~~~iA~~~Gg~~~~L~~l~ 248 (261)
T COG1240 220 TEGSE----------VRLGLAEEIARASGGEYYHLDDLS 248 (261)
T ss_pred cCCcc----------ccccHHHHHHHHhCCeEEeccccc
Confidence 73211 113567789999999999888763
No 16
>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=99.38 E-value=3e-11 Score=109.90 Aligned_cols=163 Identities=16% Similarity=0.212 Sum_probs=114.0
Q ss_pred EEEEEEecCCCcCC--CchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCCHHHHH
Q 011878 7 ALLLLLDVSPSMHS--VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHLVQ 84 (475)
Q Consensus 7 ~~vflID~s~sM~~--~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~~~~i~ 84 (475)
.++|+||+|+||.. ++..++.++..++... ..++|++|||.|++.... +..++........+
T Consensus 2 ~v~lvlD~SgSM~~~~rl~~ak~a~~~~~~~~--~~~~d~v~lv~F~~~~~~--------------~~~~~t~~~~~~~~ 65 (178)
T cd01451 2 LVIFVVDASGSMAARHRMAAAKGAVLSLLRDA--YQRRDKVALIAFRGTEAE--------------VLLPPTRSVELAKR 65 (178)
T ss_pred eEEEEEECCccCCCccHHHHHHHHHHHHHHHh--hcCCCEEEEEEECCCCce--------------EEeCCCCCHHHHHH
Confidence 47899999999985 5778888888887642 468999999999865211 13444433334456
Q ss_pred HhhcCCCCCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhH-HHHHHHHhhcCcEEEEEE
Q 011878 85 SLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQV-STIARQMVAFGLRMKNIV 163 (475)
Q Consensus 85 ~L~~l~~~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~-~~~~~~l~~~~I~l~~i~ 163 (475)
.|+.+..+. .+++.++|..|.+.+... .......+.||||||+....+. ...... ...++.+++.||.+.+|+
T Consensus 66 ~l~~l~~~G-~T~l~~aL~~a~~~l~~~-~~~~~~~~~ivliTDG~~~~g~----~~~~~~~~~~~~~l~~~gi~v~~I~ 139 (178)
T cd01451 66 RLARLPTGG-GTPLAAGLLAAYELAAEQ-ARDPGQRPLIVVITDGRANVGP----DPTADRALAAARKLRARGISALVID 139 (178)
T ss_pred HHHhCCCCC-CCcHHHHHHHHHHHHHHH-hcCCCCceEEEEECCCCCCCCC----CchhHHHHHHHHHHHhcCCcEEEEe
Confidence 677776543 358999999999988322 1112235899999999876542 111223 667889999999998888
Q ss_pred eccCCCCCCCccccccchHHHHHHhhcCCCeEeehhhH
Q 011878 164 VRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDST 201 (475)
Q Consensus 164 i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~~~~~~~ 201 (475)
++.. . .+...++.+++.++|.++.+.++
T Consensus 140 ~~~~-----~-----~~~~~l~~iA~~tgG~~~~~~d~ 167 (178)
T cd01451 140 TEGR-----P-----VRRGLAKDLARALGGQYVRLPDL 167 (178)
T ss_pred CCCC-----c-----cCccHHHHHHHHcCCeEEEcCcC
Confidence 7421 0 13578999999999999887665
No 17
>PRK13685 hypothetical protein; Provisional
Probab=99.33 E-value=6.4e-11 Score=118.06 Aligned_cols=178 Identities=16% Similarity=0.176 Sum_probs=120.4
Q ss_pred eEEEEEEecCCCcCC------CchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCC
Q 011878 6 EALLLLLDVSPSMHS------VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVD 79 (475)
Q Consensus 6 e~~vflID~s~sM~~------~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~ 79 (475)
-.++|+||+|+||.. +++.|+..+..++.+. +++|+||||.|+++. ++..|++.-.
T Consensus 89 ~~vvlvlD~S~SM~~~D~~p~RL~~ak~~~~~~l~~l---~~~d~vglv~Fa~~a---------------~~~~p~t~d~ 150 (326)
T PRK13685 89 AVVMLVIDVSQSMRATDVEPNRLAAAQEAAKQFADEL---TPGINLGLIAFAGTA---------------TVLVSPTTNR 150 (326)
T ss_pred ceEEEEEECCccccCCCCCCCHHHHHHHHHHHHHHhC---CCCCeEEEEEEcCce---------------eecCCCCCCH
Confidence 368999999999984 5788999999998842 579999999999872 1345665433
Q ss_pred HHHHHHhhcCCCCCCCCChhHHHHHHHHHHHHHh---cc-CcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhc
Q 011878 80 GHLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKY---GE-TYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAF 155 (475)
Q Consensus 80 ~~~i~~L~~l~~~~~~gd~~daL~va~~~l~~~~---~~-~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~ 155 (475)
......|+++..+. .+++.++|..|++.+.+.. +. .....++|+|+|||.+..+.. ..........++.+++.
T Consensus 151 ~~l~~~l~~l~~~~-~T~~g~al~~A~~~l~~~~~~~~~~~~~~~~~IILlTDG~~~~~~~--~~~~~~~~~aa~~a~~~ 227 (326)
T PRK13685 151 EATKNAIDKLQLAD-RTATGEAIFTALQAIATVGAVIGGGDTPPPARIVLMSDGKETVPTN--PDNPRGAYTAARTAKDQ 227 (326)
T ss_pred HHHHHHHHhCCCCC-CcchHHHHHHHHHHHHhhhcccccccCCCCCEEEEEcCCCCCCCCC--CCCcccHHHHHHHHHHc
Confidence 34555677776543 3567899999999876421 11 112357899999998865421 01112234567788899
Q ss_pred CcEEEEEEeccCC---CCCCCccccccchHHHHHHhhcCCCeEeehhhHHHh
Q 011878 156 GLRMKNIVVRASL---SGEPHMRVIIENDNLLNIFSKKSSAKTLFVDSTTSL 204 (475)
Q Consensus 156 ~I~l~~i~i~~~~---~~~~~~~~~~~n~~~l~~~~~~~~g~~~~~~~~~~l 204 (475)
||.+++|+++... ..++.......++..|++++..++|.++...+..++
T Consensus 228 gi~i~~Ig~G~~~g~~~~~g~~~~~~~d~~~L~~iA~~tgG~~~~~~~~~~L 279 (326)
T PRK13685 228 GVPISTISFGTPYGSVEINGQRQPVPVDDESLKKIAQLSGGEFYTAASLEEL 279 (326)
T ss_pred CCeEEEEEECCCCCCcCcCCceeeecCCHHHHHHHHHhcCCEEEEcCCHHHH
Confidence 9999999997521 001111112346789999999999999876665433
No 18
>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=99.32 E-value=9.6e-11 Score=106.09 Aligned_cols=152 Identities=15% Similarity=0.212 Sum_probs=112.2
Q ss_pred ceEEEEEEecCCCcCC------CchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCC
Q 011878 5 REALLLLLDVSPSMHS------VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV 78 (475)
Q Consensus 5 ke~~vflID~s~sM~~------~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~ 78 (475)
-|+++|+||+|.+|.+ +++.+++++..++..++-.+|.++||||.|++.. -+++.|++.-
T Consensus 3 ~ea~vi~lD~S~sM~a~D~~PnRL~aak~~i~~~~~~f~~~np~~~vGlv~fag~~--------------a~v~~plT~D 68 (187)
T cd01452 3 LEATMICIDNSEYMRNGDYPPTRFQAQADAVNLICQAKTRSNPENNVGLMTMAGNS--------------PEVLVTLTND 68 (187)
T ss_pred ceEEEEEEECCHHHHcCCCCCCHHHHHHHHHHHHHHHHHhcCCCccEEEEEecCCc--------------eEEEECCCCC
Confidence 6999999999999976 4788899999999888889999999999999963 2346677655
Q ss_pred CHHHHHHhhcCCCCCCCCChhHHHHHHHHHHHHHhccCcceeeE-EEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCc
Q 011878 79 DGHLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKH-LCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGL 157 (475)
Q Consensus 79 ~~~~i~~L~~l~~~~~~gd~~daL~va~~~l~~~~~~~~~~~kr-I~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I 157 (475)
-...+..|+++..+ +..++..||.+|...|.. . ..+...+| |+++++.-..+ ..++..+++.|++.||
T Consensus 69 ~~~~~~~L~~i~~~-g~~~l~~AL~~A~~~L~~-~-~~~~~~~rivi~v~S~~~~d--------~~~i~~~~~~lkk~~I 137 (187)
T cd01452 69 QGKILSKLHDVQPK-GKANFITGIQIAQLALKH-R-QNKNQKQRIVAFVGSPIEED--------EKDLVKLAKRLKKNNV 137 (187)
T ss_pred HHHHHHHHHhCCCC-CcchHHHHHHHHHHHHhc-C-CCcCCcceEEEEEecCCcCC--------HHHHHHHHHHHHHcCC
Confidence 55566777777543 345899999999999864 2 22223346 55555553332 2457788999999999
Q ss_pred EEEEEEeccCCCCCCCccccccchHHHHHHhhcC
Q 011878 158 RMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKS 191 (475)
Q Consensus 158 ~l~~i~i~~~~~~~~~~~~~~~n~~~l~~~~~~~ 191 (475)
.+.+|++|.. .+|...|+.|.+..
T Consensus 138 ~v~vI~~G~~----------~~~~~~l~~~~~~~ 161 (187)
T cd01452 138 SVDIINFGEI----------DDNTEKLTAFIDAV 161 (187)
T ss_pred eEEEEEeCCC----------CCCHHHHHHHHHHh
Confidence 9999999752 13456677666655
No 19
>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=99.28 E-value=2.3e-10 Score=104.87 Aligned_cols=152 Identities=16% Similarity=0.200 Sum_probs=107.4
Q ss_pred EEEEEecCCCcC-CCchHHHHHHHHHHHHHH------hcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCC--C
Q 011878 8 LLLLLDVSPSMH-SVLPDVEKLCSRLIQKKL------IYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKV--V 78 (475)
Q Consensus 8 ~vflID~s~sM~-~~~~~a~~~~~~l~~~ki------~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~--~ 78 (475)
++|+||.|.||. ..++.+++.+..++++.. +....++||||.|+++.. +..++.. .
T Consensus 5 vv~vlD~S~Sm~~~~~~~~k~~~~~~~~~l~~~~~~~i~~~~~rvglv~fs~~~~---------------~~~~l~~~~~ 69 (186)
T cd01480 5 ITFVLDSSESVGLQNFDITKNFVKRVAERFLKDYYRKDPAGSWRVGVVQYSDQQE---------------VEAGFLRDIR 69 (186)
T ss_pred EEEEEeCCCccchhhHHHHHHHHHHHHHHHhhhhccCCCCCceEEEEEEecCCce---------------eeEecccccC
Confidence 789999999999 467777777777777652 235679999999997721 2344442 2
Q ss_pred C-HHHHHHhhcCCCCCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCc
Q 011878 79 D-GHLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGL 157 (475)
Q Consensus 79 ~-~~~i~~L~~l~~~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I 157 (475)
+ ....+.|+++....+.+.+.+||..|.+.+.. ..+....|.|+|||||.+.... ...+...++.+++.||
T Consensus 70 ~~~~l~~~i~~l~~~gg~T~~~~AL~~a~~~l~~--~~~~~~~~~iillTDG~~~~~~------~~~~~~~~~~~~~~gi 141 (186)
T cd01480 70 NYTSLKEAVDNLEYIGGGTFTDCALKYATEQLLE--GSHQKENKFLLVITDGHSDGSP------DGGIEKAVNEADHLGI 141 (186)
T ss_pred CHHHHHHHHHhCccCCCCccHHHHHHHHHHHHhc--cCCCCCceEEEEEeCCCcCCCc------chhHHHHHHHHHHCCC
Confidence 3 34566677775323346889999999998765 2334567899999999873221 1356677888999999
Q ss_pred EEEEEEeccCCCCCCCccccccchHHHHHHhhcCCCe
Q 011878 158 RMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAK 194 (475)
Q Consensus 158 ~l~~i~i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~ 194 (475)
.+..++++. .++..|.+++....+.
T Consensus 142 ~i~~vgig~------------~~~~~L~~IA~~~~~~ 166 (186)
T cd01480 142 KIFFVAVGS------------QNEEPLSRIACDGKSA 166 (186)
T ss_pred EEEEEecCc------------cchHHHHHHHcCCcch
Confidence 999999953 1245688888766655
No 20
>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=99.27 E-value=5.7e-10 Score=100.35 Aligned_cols=161 Identities=17% Similarity=0.283 Sum_probs=111.9
Q ss_pred EEEEEecCCCcCCC-chHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCC-CH-HHHH
Q 011878 8 LLLLLDVSPSMHSV-LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV-DG-HLVQ 84 (475)
Q Consensus 8 ~vflID~s~sM~~~-~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~-~~-~~i~ 84 (475)
++|+||+|+||... ++.+++++..++.+ ..+.|+|||+.|+++... +.++... +. ...+
T Consensus 3 ~~~vlD~S~SM~~~~~~~~k~a~~~~~~~---l~~~~~v~li~f~~~~~~---------------~~~~~~~~~~~~l~~ 64 (170)
T cd01465 3 LVFVIDRSGSMDGPKLPLVKSALKLLVDQ---LRPDDRLAIVTYDGAAET---------------VLPATPVRDKAAILA 64 (170)
T ss_pred EEEEEECCCCCCChhHHHHHHHHHHHHHh---CCCCCEEEEEEecCCccE---------------EecCcccchHHHHHH
Confidence 78999999999763 66777777666652 357899999999987311 2233221 22 2334
Q ss_pred HhhcCCCCCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEEEe
Q 011878 85 SLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIVV 164 (475)
Q Consensus 85 ~L~~l~~~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l~~i~i 164 (475)
.|.++..+. .+++..+|..|...+.++.. ....++||||||+....+. ...+.+...++.+++.+|.+.+|++
T Consensus 65 ~l~~~~~~g-~T~~~~al~~a~~~~~~~~~--~~~~~~ivl~TDG~~~~~~----~~~~~~~~~~~~~~~~~v~i~~i~~ 137 (170)
T cd01465 65 AIDRLTAGG-STAGGAGIQLGYQEAQKHFV--PGGVNRILLATDGDFNVGE----TDPDELARLVAQKRESGITLSTLGF 137 (170)
T ss_pred HHHcCCCCC-CCCHHHHHHHHHHHHHhhcC--CCCeeEEEEEeCCCCCCCC----CCHHHHHHHHHHhhcCCeEEEEEEe
Confidence 466665432 45889999999988766432 1234889999999875432 1234566667778889999999999
Q ss_pred ccCCCCCCCccccccchHHHHHHhhcCCCeEeehhhHHHh
Q 011878 165 RASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDSTTSL 204 (475)
Q Consensus 165 ~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~~~~~~~~~l 204 (475)
+. ..+...|+.++...+|.++.+++..++
T Consensus 138 g~-----------~~~~~~l~~ia~~~~g~~~~~~~~~~~ 166 (170)
T cd01465 138 GD-----------NYNEDLMEAIADAGNGNTAYIDNLAEA 166 (170)
T ss_pred CC-----------CcCHHHHHHHHhcCCceEEEeCCHHHH
Confidence 63 123578999999999998877776554
No 21
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=99.26 E-value=2.4e-10 Score=121.14 Aligned_cols=165 Identities=16% Similarity=0.186 Sum_probs=122.0
Q ss_pred eEEEEEEecCCCcC-CCchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCCHHHHH
Q 011878 6 EALLLLLDVSPSMH-SVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHLVQ 84 (475)
Q Consensus 6 e~~vflID~s~sM~-~~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~~~~i~ 84 (475)
-.++|+||+|.||. .++..++.++..|+.+. +.++|+||||.|+++... ++.|++..-....+
T Consensus 402 ~~vvfvvD~SGSM~~~rl~~aK~a~~~ll~~a--y~~rD~v~lI~F~g~~a~--------------~~lppT~~~~~~~~ 465 (584)
T PRK13406 402 TTTIFVVDASGSAALHRLAEAKGAVELLLAEA--YVRRDQVALVAFRGRGAE--------------LLLPPTRSLVRAKR 465 (584)
T ss_pred ccEEEEEECCCCCcHhHHHHHHHHHHHHHHhh--cCCCCEEEEEEECCCcee--------------EEcCCCcCHHHHHH
Confidence 57899999999995 46888999999988764 689999999999887422 35566654344566
Q ss_pred HhhcCCCCCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCC---CCchhhHHHHHHHHhhcCcEEEE
Q 011878 85 SLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDV---GTKEDQVSTIARQMVAFGLRMKN 161 (475)
Q Consensus 85 ~L~~l~~~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~---~~~~~~~~~~~~~l~~~~I~l~~ 161 (475)
.|..+..+. .+++.+||..|++++.+... +...+.|||+|||..+.+.... .....+....+..++..||.+.+
T Consensus 466 ~L~~l~~gG-gTpL~~gL~~A~~~l~~~~~--~~~~~~iVLlTDG~~n~~~~~~~~~~~~~~~~~~~a~~~~~~gi~~~v 542 (584)
T PRK13406 466 SLAGLPGGG-GTPLAAGLDAAAALALQVRR--KGMTPTVVLLTDGRANIARDGTAGRAQAEEDALAAARALRAAGLPALV 542 (584)
T ss_pred HHhcCCCCC-CChHHHHHHHHHHHHHHhcc--CCCceEEEEEeCCCCCCCccccccccchhhHHHHHHHHHHhcCCeEEE
Confidence 777787654 46899999999999876422 2346899999999988753100 01124566778899999999998
Q ss_pred EEeccCCCCCCCccccccchHHHHHHhhcCCCeEeehhhH
Q 011878 162 IVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDST 201 (475)
Q Consensus 162 i~i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~~~~~~~ 201 (475)
|.++. . ....+.+++..++|.|+.+.++
T Consensus 543 Id~g~------~------~~~~~~~LA~~~gg~y~~l~~~ 570 (584)
T PRK13406 543 IDTSP------R------PQPQARALAEAMGARYLPLPRA 570 (584)
T ss_pred EecCC------C------CcHHHHHHHHhcCCeEEECCCC
Confidence 88742 1 1356788999999999987755
No 22
>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=99.23 E-value=5.3e-10 Score=102.31 Aligned_cols=152 Identities=13% Similarity=0.116 Sum_probs=101.8
Q ss_pred eEEEEEEecCCCcCCCchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCCHHHHHH
Q 011878 6 EALLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHLVQS 85 (475)
Q Consensus 6 e~~vflID~s~sM~~~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~~~~i~~ 85 (475)
--++|+||.|+||...+..+++.+..++++- .++.++||||.|+++. .+..++........+.
T Consensus 5 ~Dvv~llD~SgSm~~~~~~~~~~~~~l~~~~--~~~~~rvglv~Fs~~~---------------~~~~~l~~~~~~~~~~ 67 (185)
T cd01474 5 FDLYFVLDKSGSVAANWIEIYDFVEQLVDRF--NSPGLRFSFITFSTRA---------------TKILPLTDDSSAIIKG 67 (185)
T ss_pred eeEEEEEeCcCchhhhHHHHHHHHHHHHHHc--CCCCcEEEEEEecCCc---------------eEEEeccccHHHHHHH
Confidence 3489999999999987666667777777653 3578999999999872 1245565544333344
Q ss_pred ---hhcCCCCCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEE
Q 011878 86 ---LKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNI 162 (475)
Q Consensus 86 ---L~~l~~~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l~~i 162 (475)
|..+..+ +.+++.+||..|.+.+...........+.|+|||||.+.-.. .......++.+++.||.+..+
T Consensus 68 l~~l~~~~~~-g~T~~~~aL~~a~~~l~~~~~~~r~~~~~villTDG~~~~~~------~~~~~~~a~~l~~~gv~i~~v 140 (185)
T cd01474 68 LEVLKKVTPS-GQTYIHEGLENANEQIFNRNGGGRETVSVIIALTDGQLLLNG------HKYPEHEAKLSRKLGAIVYCV 140 (185)
T ss_pred HHHHhccCCC-CCCcHHHHHHHHHHHHHhhccCCCCCCeEEEEEcCCCcCCCC------CcchHHHHHHHHHcCCEEEEE
Confidence 4444333 346889999999987754222111234889999999873111 122445567889999999999
Q ss_pred EeccCCCCCCCccccccchHHHHHHhhcCCC
Q 011878 163 VVRASLSGEPHMRVIIENDNLLNIFSKKSSA 193 (475)
Q Consensus 163 ~i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g 193 (475)
+++. .+...|+.++...++
T Consensus 141 gv~~------------~~~~~L~~iA~~~~~ 159 (185)
T cd01474 141 GVTD------------FLKSQLINIADSKEY 159 (185)
T ss_pred eech------------hhHHHHHHHhCCCCe
Confidence 9831 235668888876654
No 23
>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=99.22 E-value=8.8e-10 Score=100.23 Aligned_cols=165 Identities=20% Similarity=0.212 Sum_probs=102.4
Q ss_pred EEEEEEecCCCcCCC-------chHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCC
Q 011878 7 ALLLLLDVSPSMHSV-------LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVD 79 (475)
Q Consensus 7 ~~vflID~s~sM~~~-------~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~ 79 (475)
-++|+||+|+||... +..|+.++..++. ..++|+||||.|+++.. +..++..-.
T Consensus 4 ~vv~vlD~S~SM~~~~~~~~~r~~~a~~~~~~~~~----~~~~~~v~lv~f~~~~~---------------~~~~~~~~~ 64 (180)
T cd01467 4 DIMIALDVSGSMLAQDFVKPSRLEAAKEVLSDFID----RRENDRIGLVVFAGAAF---------------TQAPLTLDR 64 (180)
T ss_pred eEEEEEECCcccccccCCCCCHHHHHHHHHHHHHH----hCCCCeEEEEEEcCCee---------------eccCCCccH
Confidence 478999999999743 3455556655554 46899999999987621 123333211
Q ss_pred HHHHHHhhcCCC--CCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCc
Q 011878 80 GHLVQSLKHLPQ--GTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGL 157 (475)
Q Consensus 80 ~~~i~~L~~l~~--~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I 157 (475)
....+.|+.+.. ..+..++.+||..|++++.... ...+.|+||||+....+. ......++.+++.||
T Consensus 65 ~~~~~~l~~l~~~~~~g~T~l~~al~~a~~~l~~~~----~~~~~iiliTDG~~~~g~-------~~~~~~~~~~~~~gi 133 (180)
T cd01467 65 ESLKELLEDIKIGLAGQGTAIGDAIGLAIKRLKNSE----AKERVIVLLTDGENNAGE-------IDPATAAELAKNKGV 133 (180)
T ss_pred HHHHHHHHHhhhcccCCCCcHHHHHHHHHHHHHhcC----CCCCEEEEEeCCCCCCCC-------CCHHHHHHHHHHCCC
Confidence 122233444431 1223578899999999876521 234789999999765331 123344556678899
Q ss_pred EEEEEEeccCCCCCCCccccccchHHHHHHhhcCCCeEeehhhH
Q 011878 158 RMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDST 201 (475)
Q Consensus 158 ~l~~i~i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~~~~~~~ 201 (475)
.+.+|+++..-+..........+...++.++..++|.++...+.
T Consensus 134 ~i~~i~ig~~~~~~~~~~~~~~~~~~l~~la~~tgG~~~~~~~~ 177 (180)
T cd01467 134 RIYTIGVGKSGSGPKPDGSTILDEDSLVEIADKTGGRIFRALDG 177 (180)
T ss_pred EEEEEEecCCCCCcCCCCcccCCHHHHHHHHHhcCCEEEEecCc
Confidence 99999997511000000001234578999999999998876554
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=99.21 E-value=8.2e-10 Score=102.23 Aligned_cols=167 Identities=13% Similarity=0.142 Sum_probs=108.5
Q ss_pred EEEEEecCCCcC-CCchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCC----CHHH
Q 011878 8 LLLLLDVSPSMH-SVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV----DGHL 82 (475)
Q Consensus 8 ~vflID~s~sM~-~~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~----~~~~ 82 (475)
++|+||+|.||. .+++.++.++..++.+.-...++|++|||.|+++.. +..|+..+ ....
T Consensus 3 i~~vlD~SgSM~~~~~~~~k~~~~~l~~~l~~~~~~~~v~li~Fs~~~~---------------~~~~~~~~~~~~~~~~ 67 (198)
T cd01470 3 IYIALDASDSIGEEDFDEAKNAIKTLIEKISSYEVSPRYEIISYASDPK---------------EIVSIRDFNSNDADDV 67 (198)
T ss_pred EEEEEECCCCccHHHHHHHHHHHHHHHHHccccCCCceEEEEEecCCce---------------EEEecccCCCCCHHHH
Confidence 789999999997 468888999999988654445689999999999831 12343322 2346
Q ss_pred HHHhhcCCCC----CCCCChhHHHHHHHHHHHHHhccC----cceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHH--
Q 011878 83 VQSLKHLPQG----TCAGDFLDAIVVGVDMLIKKYGET----YKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQM-- 152 (475)
Q Consensus 83 i~~L~~l~~~----~~~gd~~daL~va~~~l~~~~~~~----~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l-- 152 (475)
+..|+.+... .+...+.+||..+.+.+....... ....+.|||||||....+. .. .+....++.+
T Consensus 68 ~~~l~~~~~~~~~~~ggT~~~~Al~~~~~~l~~~~~~~~~~~~~~~~~iillTDG~~~~g~----~~-~~~~~~~~~~~~ 142 (198)
T cd01470 68 IKRLEDFNYDDHGDKTGTNTAAALKKVYERMALEKVRNKEAFNETRHVIILFTDGKSNMGG----SP-LPTVDKIKNLVY 142 (198)
T ss_pred HHHHHhCCcccccCccchhHHHHHHHHHHHHHHHHhcCccchhhcceEEEEEcCCCcCCCC----Ch-hHHHHHHHHHHh
Confidence 6777776421 123478888888887663211110 1235679999999875431 11 1222222222
Q ss_pred --------hhcCcEEEEEEeccCCCCCCCccccccchHHHHHHhhcCCC--eEeehhhHHHhh
Q 011878 153 --------VAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSA--KTLFVDSTTSLR 205 (475)
Q Consensus 153 --------~~~~I~l~~i~i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g--~~~~~~~~~~ll 205 (475)
++.+|.+.+|+++.. .+...|+.+++.++| .++...+..++-
T Consensus 143 ~~~~~~~~~~~~v~i~~iGvG~~-----------~~~~~L~~iA~~~~g~~~~f~~~~~~~l~ 194 (198)
T cd01470 143 KNNKSDNPREDYLDVYVFGVGDD-----------VNKEELNDLASKKDNERHFFKLKDYEDLQ 194 (198)
T ss_pred cccccccchhcceeEEEEecCcc-----------cCHHHHHHHhcCCCCCceEEEeCCHHHHH
Confidence 556899999999641 236889999999888 467766655443
No 25
>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=99.20 E-value=6.8e-10 Score=99.48 Aligned_cols=151 Identities=17% Similarity=0.175 Sum_probs=104.9
Q ss_pred EEEEEecCCCcCC-CchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCC--CCHHHHH
Q 011878 8 LLLLLDVSPSMHS-VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKV--VDGHLVQ 84 (475)
Q Consensus 8 ~vflID~s~sM~~-~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~--~~~~~i~ 84 (475)
++|+||+|+||.. .+..+++++..++.+-...+.++++|||.|+++.. +..++.. ......+
T Consensus 3 vv~vlD~SgSm~~~~~~~~k~~~~~~~~~l~~~~~~~~~giv~Fs~~~~---------------~~~~~~~~~~~~~~~~ 67 (164)
T cd01472 3 IVFLVDGSESIGLSNFNLVKDFVKRVVERLDIGPDGVRVGVVQYSDDPR---------------TEFYLNTYRSKDDVLE 67 (164)
T ss_pred EEEEEeCCCCCCHHHHHHHHHHHHHHHhhcccCCCCeEEEEEEEcCcee---------------EEEecCCCCCHHHHHH
Confidence 6899999999987 57778888888887654456789999999997621 1344442 2234556
Q ss_pred HhhcCCCCCCCCChhHHHHHHHHHHHHHh-ccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEEE
Q 011878 85 SLKHLPQGTCAGDFLDAIVVGVDMLIKKY-GETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIV 163 (475)
Q Consensus 85 ~L~~l~~~~~~gd~~daL~va~~~l~~~~-~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l~~i~ 163 (475)
.|+.+....+..++.+||..|.+++.... ..+....+.|+||||+.++. .....+..+++.||.+.+|+
T Consensus 68 ~l~~l~~~~g~T~~~~al~~a~~~l~~~~~~~~~~~~~~iiliTDG~~~~----------~~~~~~~~l~~~gv~i~~ig 137 (164)
T cd01472 68 AVKNLRYIGGGTNTGKALKYVRENLFTEASGSREGVPKVLVVITDGKSQD----------DVEEPAVELKQAGIEVFAVG 137 (164)
T ss_pred HHHhCcCCCCCchHHHHHHHHHHHhCCcccCCCCCCCEEEEEEcCCCCCc----------hHHHHHHHHHHCCCEEEEEE
Confidence 67777643334589999999999876421 11223467799999995432 22334567888999999999
Q ss_pred eccCCCCCCCccccccchHHHHHHhhcCCCeE
Q 011878 164 VRASLSGEPHMRVIIENDNLLNIFSKKSSAKT 195 (475)
Q Consensus 164 i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~ 195 (475)
++. .+...|+.++...++.+
T Consensus 138 ~g~------------~~~~~L~~ia~~~~~~~ 157 (164)
T cd01472 138 VKN------------ADEEELKQIASDPKELY 157 (164)
T ss_pred CCc------------CCHHHHHHHHCCCchhe
Confidence 853 13678888888776643
No 26
>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=99.16 E-value=1.2e-09 Score=107.71 Aligned_cols=168 Identities=19% Similarity=0.223 Sum_probs=113.8
Q ss_pred eEEEEEEecCCCcCCCchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCCHHHHHH
Q 011878 6 EALLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHLVQS 85 (475)
Q Consensus 6 e~~vflID~s~sM~~~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~~~~i~~ 85 (475)
=.++|+||+|.||...+..+++++..+++.. ..++|+||||.|+++. .++++++.-.....+.
T Consensus 54 ~~vvlvlD~SgSM~~~~~~a~~a~~~~l~~~--l~~~d~v~lv~f~~~~---------------~~~~~~t~~~~~l~~~ 116 (296)
T TIGR03436 54 LTVGLVIDTSGSMRNDLDRARAAAIRFLKTV--LRPNDRVFVVTFNTRL---------------RLLQDFTSDPRLLEAA 116 (296)
T ss_pred ceEEEEEECCCCchHHHHHHHHHHHHHHHhh--CCCCCEEEEEEeCCce---------------eEeecCCCCHHHHHHH
Confidence 3689999999999998888999999999764 2689999999999752 1234555444455666
Q ss_pred hhcCCCC--------------CCCCChhHHHHHHH-HHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHH
Q 011878 86 LKHLPQG--------------TCAGDFLDAIVVGV-DMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIAR 150 (475)
Q Consensus 86 L~~l~~~--------------~~~gd~~daL~va~-~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~ 150 (475)
|..+... .+..++.+||..|. +++.+..+. ....|.|+||||+.+... ...+...++
T Consensus 117 l~~l~~~~~~~~~~~~~~~~~~g~T~l~~al~~aa~~~~~~~~~~-~p~rk~iIllTDG~~~~~-------~~~~~~~~~ 188 (296)
T TIGR03436 117 LNRLKPPLRTDYNSSGAFVRDGGGTALYDAITLAALEQLANALAG-IPGRKALIVISDGGDNRS-------RDTLERAID 188 (296)
T ss_pred HHhccCCCccccccccccccCCCcchhHHHHHHHHHHHHHHhhcC-CCCCeEEEEEecCCCcch-------HHHHHHHHH
Confidence 7776541 22347888987664 454443211 123578999999976432 346777888
Q ss_pred HHhhcCcEEEEEEeccCCCCCCCccc--cccchHHHHHHhhcCCCeEeeh
Q 011878 151 QMVAFGLRMKNIVVRASLSGEPHMRV--IIENDNLLNIFSKKSSAKTLFV 198 (475)
Q Consensus 151 ~l~~~~I~l~~i~i~~~~~~~~~~~~--~~~n~~~l~~~~~~~~g~~~~~ 198 (475)
.+++.+|.+..|+++........... ...++..|+++|..++|.++..
T Consensus 189 ~~~~~~v~vy~I~~~~~~~~~~~~~~~~~~~~~~~L~~iA~~TGG~~~~~ 238 (296)
T TIGR03436 189 AAQRADVAIYSIDARGLRAPDLGAGAKAGLGGPEALERLAEETGGRAFYV 238 (296)
T ss_pred HHHHcCCEEEEeccCccccCCcccccccCCCcHHHHHHHHHHhCCeEecc
Confidence 88999999999998631100000000 0024678999999999987664
No 27
>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=99.16 E-value=1.3e-09 Score=101.63 Aligned_cols=162 Identities=12% Similarity=0.107 Sum_probs=104.8
Q ss_pred ceEEEEEEecCCCcC-------CCchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEE----EEe
Q 011878 5 REALLLLLDVSPSMH-------SVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVK----VLQ 73 (475)
Q Consensus 5 ke~~vflID~s~sM~-------~~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~----~~~ 73 (475)
..-++|+||+|+||. .++..+++++..++.. ..++|+|||+.|++..+... .|.-+. ...
T Consensus 20 ~~~vv~vlD~SgSM~~~~~~~~~rl~~ak~a~~~~l~~---l~~~~~v~lv~F~~~~~~~~------~~~~~~p~~~~~~ 90 (206)
T cd01456 20 PPNVAIVLDNSGSMREVDGGGETRLDNAKAALDETANA---LPDGTRLGLWTFSGDGDNPL------DVRVLVPKGCLTA 90 (206)
T ss_pred CCcEEEEEeCCCCCcCCCCCcchHHHHHHHHHHHHHHh---CCCCceEEEEEecCCCCCCc------ccccccccccccc
Confidence 356899999999998 2577888888888874 35799999999999643211 111110 011
Q ss_pred ecCC---CCHH-HHHHhhcCC-CCCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHH
Q 011878 74 DIKV---VDGH-LVQSLKHLP-QGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTI 148 (475)
Q Consensus 74 ~l~~---~~~~-~i~~L~~l~-~~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~ 148 (475)
++.. .+.+ ..+.|+.+. .+ +..++.+||..|.+++. . ...+.||||||+....+. .....
T Consensus 91 ~~~~~~~~~~~~l~~~i~~i~~~~-G~T~l~~aL~~a~~~l~---~---~~~~~iillTDG~~~~~~--------~~~~~ 155 (206)
T cd01456 91 PVNGFPSAQRSALDAALNSLQTPT-GWTPLAAALAEAAAYVD---P---GRVNVVVLITDGEDTCGP--------DPCEV 155 (206)
T ss_pred ccCCCCcccHHHHHHHHHhhcCCC-CcChHHHHHHHHHHHhC---C---CCcceEEEEcCCCccCCC--------CHHHH
Confidence 1111 1222 344566665 32 34588999999988864 1 123899999999876431 11122
Q ss_pred HHHHh-h----cCcEEEEEEeccCCCCCCCccccccchHHHHHHhhcCCCeE-eehhhH
Q 011878 149 ARQMV-A----FGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKT-LFVDST 201 (475)
Q Consensus 149 ~~~l~-~----~~I~l~~i~i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~-~~~~~~ 201 (475)
+..+. . .+|.+.+|+++.. .+...|+.++..++|.+ +...+.
T Consensus 156 ~~~~~~~~~~~~~i~i~~igiG~~-----------~~~~~l~~iA~~tgG~~~~~~~~~ 203 (206)
T cd01456 156 ARELAKRRTPAPPIKVNVIDFGGD-----------ADRAELEAIAEATGGTYAYNQSDL 203 (206)
T ss_pred HHHHHHhcCCCCCceEEEEEecCc-----------ccHHHHHHHHHhcCCeEecccccc
Confidence 33333 3 4999999999641 23588999999999988 665544
No 28
>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=99.15 E-value=1.6e-09 Score=97.05 Aligned_cols=147 Identities=19% Similarity=0.224 Sum_probs=103.1
Q ss_pred EEEEEecCCCcCC-CchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCC-CC-HHHHH
Q 011878 8 LLLLLDVSPSMHS-VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKV-VD-GHLVQ 84 (475)
Q Consensus 8 ~vflID~s~sM~~-~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~-~~-~~~i~ 84 (475)
++|+||.|+||.. .+..+++.+..++.+.-+..++++||||.|+++.. +..++.. .+ ...++
T Consensus 3 v~~vlD~S~Sm~~~~~~~~k~~~~~l~~~~~~~~~~~rvgli~fs~~~~---------------~~~~l~~~~~~~~l~~ 67 (164)
T cd01482 3 IVFLVDGSWSIGRSNFNLVRSFLSSVVEAFEIGPDGVQVGLVQYSDDPR---------------TEFDLNAYTSKEDVLA 67 (164)
T ss_pred EEEEEeCCCCcChhhHHHHHHHHHHHHhheeeCCCceEEEEEEECCCee---------------EEEecCCCCCHHHHHH
Confidence 7899999999985 68888999998888754556899999999999831 1223332 12 24556
Q ss_pred HhhcCCCCCCCCChhHHHHHHHHHHHHH-hccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEEE
Q 011878 85 SLKHLPQGTCAGDFLDAIVVGVDMLIKK-YGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIV 163 (475)
Q Consensus 85 ~L~~l~~~~~~gd~~daL~va~~~l~~~-~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l~~i~ 163 (475)
.|.++....+...+..||..+.+.+.+. .+.+....|.|+|||||... +++..+++.+++.||.+.+|+
T Consensus 68 ~l~~~~~~~g~T~~~~aL~~a~~~~~~~~~~~r~~~~k~iillTDG~~~----------~~~~~~a~~lk~~gi~i~~ig 137 (164)
T cd01482 68 AIKNLPYKGGNTRTGKALTHVREKNFTPDAGARPGVPKVVILITDGKSQ----------DDVELPARVLRNLGVNVFAVG 137 (164)
T ss_pred HHHhCcCCCCCChHHHHHHHHHHHhcccccCCCCCCCEEEEEEcCCCCC----------chHHHHHHHHHHCCCEEEEEe
Confidence 6777653233457899999888765432 12233356779999999742 235667899999999999999
Q ss_pred eccCCCCCCCccccccchHHHHHHhhcC
Q 011878 164 VRASLSGEPHMRVIIENDNLLNIFSKKS 191 (475)
Q Consensus 164 i~~~~~~~~~~~~~~~n~~~l~~~~~~~ 191 (475)
++. .+...|.++++..
T Consensus 138 ~g~------------~~~~~L~~ia~~~ 153 (164)
T cd01482 138 VKD------------ADESELKMIASKP 153 (164)
T ss_pred cCc------------CCHHHHHHHhCCC
Confidence 852 1246677887754
No 29
>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=99.13 E-value=2e-09 Score=115.10 Aligned_cols=166 Identities=16% Similarity=0.229 Sum_probs=117.8
Q ss_pred EEEEEEecCCCcCC-CchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCCHHHHHH
Q 011878 7 ALLLLLDVSPSMHS-VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHLVQS 85 (475)
Q Consensus 7 ~~vflID~s~sM~~-~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~~~~i~~ 85 (475)
.++|+||+|+||.. ++..|+.++..++..- +.+.|+||||.|++.... ++.++..--....+.
T Consensus 409 ~v~fvvD~SGSM~~~rl~~aK~av~~Ll~~~--~~~~D~v~Li~F~~~~a~--------------~~lp~t~~~~~~~~~ 472 (589)
T TIGR02031 409 LLIFVVDASGSAAVARMSEAKGAVELLLGEA--YVHRDQVSLIAFRGTAAE--------------VLLPPSRSVEQAKRR 472 (589)
T ss_pred eEEEEEECCCCCChHHHHHHHHHHHHHHHhh--ccCCCEEEEEEECCCCce--------------EECCCCCCHHHHHHH
Confidence 37899999999964 6888889888888743 568999999999877421 123443222233456
Q ss_pred hhcCCCCCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCC----C----CchhhHHHHHHHHhhcCc
Q 011878 86 LKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDV----G----TKEDQVSTIARQMVAFGL 157 (475)
Q Consensus 86 L~~l~~~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~----~----~~~~~~~~~~~~l~~~~I 157 (475)
|..+..++ .+++.+||..|.+.+.+... +...+.|||||||..+++.... . ...+++..+++.+++.||
T Consensus 473 L~~l~~gG-gTpL~~gL~~A~~~~~~~~~--~~~~~~ivllTDG~~nv~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~gi 549 (589)
T TIGR02031 473 LDVLPGGG-GTPLAAGLAAAFQTALQARS--SGGTPTIVLITDGRGNIPLDGDPESIKADREQAAEEALALARKIREAGM 549 (589)
T ss_pred HhcCCCCC-CCcHHHHHHHHHHHHHHhcc--cCCceEEEEECCCCCCCCCCcccccccccchhHHHHHHHHHHHHHhcCC
Confidence 77776544 46899999999999876322 2456799999999988753100 0 113456677899999999
Q ss_pred EEEEEEeccCCCCCCCccccccchHHHHHHhhcCCCeEeehhhH
Q 011878 158 RMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDST 201 (475)
Q Consensus 158 ~l~~i~i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~~~~~~~ 201 (475)
.+.+|+++..+ ....++.++|+..+|.|+.++++
T Consensus 550 ~~~vid~~~~~----------~~~~~~~~lA~~~~g~y~~l~~~ 583 (589)
T TIGR02031 550 PALVIDTAMRF----------VSTGFAQKLARKMGAHYIYLPNA 583 (589)
T ss_pred eEEEEeCCCCC----------ccchHHHHHHHhcCCcEEeCCCC
Confidence 99999885321 11357889999999999987765
No 30
>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=99.12 E-value=1.9e-09 Score=98.75 Aligned_cols=136 Identities=18% Similarity=0.178 Sum_probs=95.1
Q ss_pred EEEEEecCCCcCCC--chHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCC---CHH-
Q 011878 8 LLLLLDVSPSMHSV--LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV---DGH- 81 (475)
Q Consensus 8 ~vflID~s~sM~~~--~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~---~~~- 81 (475)
++|+||.|.||... +..++..+..++++.-+...+.+||||.|+++.. +..++... +.+
T Consensus 3 v~~vlD~SgSm~~~~~~~~~k~~~~~~~~~~~~~~~~~~vglv~Fs~~~~---------------~~~~l~~~~~~~~~~ 67 (186)
T cd01471 3 LYLLVDGSGSIGYSNWVTHVVPFLHTFVQNLNISPDEINLYLVTFSTNAK---------------ELIRLSSPNSTNKDL 67 (186)
T ss_pred EEEEEeCCCCccchhhHHHHHHHHHHHHHhcccCCCceEEEEEEecCCce---------------EEEECCCccccchHH
Confidence 68999999999964 6788888888888765556788999999997631 13344332 112
Q ss_pred ---HHHHhhcCCCCCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcE
Q 011878 82 ---LVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLR 158 (475)
Q Consensus 82 ---~i~~L~~l~~~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~ 158 (475)
.++.|.......+..++.+||..|.+.+....+.+....+.|+|||||..... ......++.+++.||.
T Consensus 68 ~~~~i~~l~~~~~~~G~T~l~~aL~~a~~~l~~~~~~r~~~~~~villTDG~~~~~--------~~~~~~a~~l~~~gv~ 139 (186)
T cd01471 68 ALNAIRALLSLYYPNGSTNTTSALLVVEKHLFDTRGNRENAPQLVIIMTDGIPDSK--------FRTLKEARKLRERGVI 139 (186)
T ss_pred HHHHHHHHHhCcCCCCCccHHHHHHHHHHHhhccCCCcccCceEEEEEccCCCCCC--------cchhHHHHHHHHCCCE
Confidence 34555554333345689999999998876521223345688999999975321 2233567889999999
Q ss_pred EEEEEecc
Q 011878 159 MKNIVVRA 166 (475)
Q Consensus 159 l~~i~i~~ 166 (475)
+.+|+++.
T Consensus 140 v~~igiG~ 147 (186)
T cd01471 140 IAVLGVGQ 147 (186)
T ss_pred EEEEEeeh
Confidence 99999964
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=99.12 E-value=3.3e-09 Score=96.32 Aligned_cols=164 Identities=18% Similarity=0.149 Sum_probs=112.4
Q ss_pred EEEEEecCCCcCC-CchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCC--CHHHHH
Q 011878 8 LLLLLDVSPSMHS-VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV--DGHLVQ 84 (475)
Q Consensus 8 ~vflID~s~sM~~-~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~--~~~~i~ 84 (475)
++|+||.|.||.. .|+.++..+..++.+.-+...+++||||.|++... +..++... ..+.++
T Consensus 3 i~fvlD~S~S~~~~~f~~~k~fi~~~i~~l~~~~~~~rvgvv~fs~~~~---------------~~~~l~~~~~~~~~~~ 67 (177)
T cd01469 3 IVFVLDGSGSIYPDDFQKVKNFLSTVMKKLDIGPTKTQFGLVQYSESFR---------------TEFTLNEYRTKEEPLS 67 (177)
T ss_pred EEEEEeCCCCCCHHHHHHHHHHHHHHHHHcCcCCCCcEEEEEEECCcee---------------EEEecCccCCHHHHHH
Confidence 6899999999986 68889999999999877777899999999998731 12333321 124455
Q ss_pred HhhcCCCCCCCCChhHHHHHHHHHHHHH-hccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEEE
Q 011878 85 SLKHLPQGTCAGDFLDAIVVGVDMLIKK-YGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIV 163 (475)
Q Consensus 85 ~L~~l~~~~~~gd~~daL~va~~~l~~~-~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l~~i~ 163 (475)
.++.+....+.....+||..|.+++... .+.+....|-++|||||.+.-+. .....++.+++.||.+..++
T Consensus 68 ~i~~~~~~~g~T~~~~AL~~a~~~l~~~~~g~R~~~~kv~illTDG~~~~~~--------~~~~~~~~~k~~gv~v~~Vg 139 (177)
T cd01469 68 LVKHISQLLGLTNTATAIQYVVTELFSESNGARKDATKVLVVITDGESHDDP--------LLKDVIPQAEREGIIRYAIG 139 (177)
T ss_pred HHHhCccCCCCccHHHHHHHHHHHhcCcccCCCCCCCeEEEEEeCCCCCCcc--------ccHHHHHHHHHCCcEEEEEE
Confidence 5666643223368899999999886432 12333457789999999885321 12456778899999999999
Q ss_pred eccCCCCCCCccccccchHHHHHHhhcCCC-eEeehhhH
Q 011878 164 VRASLSGEPHMRVIIENDNLLNIFSKKSSA-KTLFVDST 201 (475)
Q Consensus 164 i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g-~~~~~~~~ 201 (475)
++..... ..+.+.|+.+++...+ .++..++.
T Consensus 140 vg~~~~~-------~~~~~~L~~ias~p~~~h~f~~~~~ 171 (177)
T cd01469 140 VGGHFQR-------ENSREELKTIASKPPEEHFFNVTDF 171 (177)
T ss_pred ecccccc-------cccHHHHHHHhcCCcHHhEEEecCH
Confidence 9742110 1235778888876543 35655554
No 32
>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=99.11 E-value=1e-09 Score=100.87 Aligned_cols=138 Identities=20% Similarity=0.225 Sum_probs=99.7
Q ss_pred EEEEEecCCCcCCC-ch-HHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCC---C-HH
Q 011878 8 LLLLLDVSPSMHSV-LP-DVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV---D-GH 81 (475)
Q Consensus 8 ~vflID~s~sM~~~-~~-~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~---~-~~ 81 (475)
++|+||.|.||... +. ..+..+..++++-.+...+++||||.|+++.. +..++... + .+
T Consensus 3 i~fllD~S~Si~~~~f~~~~~~f~~~lv~~l~i~~~~~rvgvv~fs~~~~---------------~~~~~~~~~~~~~~~ 67 (192)
T cd01473 3 LTLILDESASIGYSNWRKDVIPFTEKIINNLNISKDKVHVGILLFAEKNR---------------DVVPFSDEERYDKNE 67 (192)
T ss_pred EEEEEeCCCcccHHHHHHHHHHHHHHHHHhCccCCCccEEEEEEecCCce---------------eEEecCcccccCHHH
Confidence 68999999999875 66 47889999999888888999999999998831 23444432 1 24
Q ss_pred HHHHhhcCCC---CCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcE
Q 011878 82 LVQSLKHLPQ---GTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLR 158 (475)
Q Consensus 82 ~i~~L~~l~~---~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~ 158 (475)
.++.++++.. ..+.+...+||-.|.+.+....+.+....|-++|||||.+.... ...+...++.|++.||.
T Consensus 68 l~~~i~~l~~~~~~~g~T~~~~AL~~a~~~~~~~~~~r~~~~kv~IllTDG~s~~~~------~~~~~~~a~~lk~~gV~ 141 (192)
T cd01473 68 LLKKINDLKNSYRSGGETYIVEALKYGLKNYTKHGNRRKDAPKVTMLFTDGNDTSAS------KKELQDISLLYKEENVK 141 (192)
T ss_pred HHHHHHHHHhccCCCCcCcHHHHHHHHHHHhccCCCCcccCCeEEEEEecCCCCCcc------hhhHHHHHHHHHHCCCE
Confidence 4555665532 12345789999999887754222222346789999999885321 24577888999999999
Q ss_pred EEEEEecc
Q 011878 159 MKNIVVRA 166 (475)
Q Consensus 159 l~~i~i~~ 166 (475)
+.++|++.
T Consensus 142 i~~vGiG~ 149 (192)
T cd01473 142 LLVVGVGA 149 (192)
T ss_pred EEEEEecc
Confidence 99999963
No 33
>PF13519 VWA_2: von Willebrand factor type A domain; PDB: 3IBS_B 3RAG_B 2X5N_A.
Probab=99.10 E-value=8.6e-10 Score=98.83 Aligned_cols=148 Identities=17% Similarity=0.291 Sum_probs=103.6
Q ss_pred EEEEEecCCCcCCC------chHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCCHH
Q 011878 8 LLLLLDVSPSMHSV------LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGH 81 (475)
Q Consensus 8 ~vflID~s~sM~~~------~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~~~ 81 (475)
++|+||.|+||... +..++..+..++.+ .+.|+|||+.|+... .+..+++.--..
T Consensus 2 vv~v~D~SgSM~~~~~~~~~~~~~~~~~~~~~~~----~~~~~v~l~~f~~~~---------------~~~~~~t~~~~~ 62 (172)
T PF13519_consen 2 VVFVLDNSGSMNGYDGNRTRIDQAKDALNELLAN----LPGDRVGLVSFSDSS---------------RTLSPLTSDKDE 62 (172)
T ss_dssp EEEEEE-SGGGGTTTSSS-HHHHHHHHHHHHHHH----HTTSEEEEEEESTSC---------------EEEEEEESSHHH
T ss_pred EEEEEECCcccCCCCCCCcHHHHHHHHHHHHHHH----CCCCEEEEEEecccc---------------cccccccccHHH
Confidence 79999999999976 67788888888885 478999999999862 124555543334
Q ss_pred HHHHhhcCCC---CCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcE
Q 011878 82 LVQSLKHLPQ---GTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLR 158 (475)
Q Consensus 82 ~i~~L~~l~~---~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~ 158 (475)
..+.++++.. ..+..++.+||..|.+++... +...+.||||||+... ......++.++..||.
T Consensus 63 ~~~~l~~~~~~~~~~~~t~~~~al~~a~~~~~~~----~~~~~~iv~iTDG~~~----------~~~~~~~~~~~~~~i~ 128 (172)
T PF13519_consen 63 LKNALNKLSPQGMPGGGTNLYDALQEAAKMLASS----DNRRRAIVLITDGEDN----------SSDIEAAKALKQQGIT 128 (172)
T ss_dssp HHHHHHTHHHHG--SSS--HHHHHHHHHHHHHC-----SSEEEEEEEEES-TTH----------CHHHHHHHHHHCTTEE
T ss_pred HHHHhhcccccccCccCCcHHHHHHHHHHHHHhC----CCCceEEEEecCCCCC----------cchhHHHHHHHHcCCe
Confidence 4455655532 133568999999999987542 2467889999998543 1233478889999999
Q ss_pred EEEEEeccCCCCCCCccccccchHHHHHHhhcCCCeEeeh
Q 011878 159 MKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFV 198 (475)
Q Consensus 159 l~~i~i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~~~~ 198 (475)
+.+++++.. .. ....++.+++.++|.++..
T Consensus 129 i~~v~~~~~----~~------~~~~l~~la~~tgG~~~~~ 158 (172)
T PF13519_consen 129 IYTVGIGSD----SD------ANEFLQRLAEATGGRYFHV 158 (172)
T ss_dssp EEEEEES-T----T-------EHHHHHHHHHHTEEEEEEE
T ss_pred EEEEEECCC----cc------HHHHHHHHHHhcCCEEEEe
Confidence 999999641 11 1368889999999998876
No 34
>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=99.09 E-value=2.6e-09 Score=98.14 Aligned_cols=167 Identities=16% Similarity=0.212 Sum_probs=103.0
Q ss_pred ceEEEEEEecCCCcCC-CchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCc-cccccCCCcccEEEEeecCCCC-HH
Q 011878 5 REALLLLLDVSPSMHS-VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETEN-ELTKEVGGYEHVKVLQDIKVVD-GH 81 (475)
Q Consensus 5 ke~~vflID~s~sM~~-~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n-~~~~~~~~y~~i~~~~~l~~~~-~~ 81 (475)
.--++||||+|.||.. +++.+++++..++.+ ..++|++|||.|+++.... +.. ... +.....-+ ..
T Consensus 13 p~~vv~llD~SgSM~~~~l~~ak~~~~~ll~~---l~~~d~v~lv~F~~~~~~~~~~~-------~~~-~~~~~~~~~~~ 81 (190)
T cd01463 13 PKDIVILLDVSGSMTGQRLHLAKQTVSSILDT---LSDNDFFNIITFSNEVNPVVPCF-------NDT-LVQATTSNKKV 81 (190)
T ss_pred CceEEEEEECCCCCCcHHHHHHHHHHHHHHHh---CCCCCEEEEEEeCCCeeEEeeec-------ccc-eEecCHHHHHH
Confidence 3568999999999974 577888888888764 3678999999999984221 000 000 00111111 12
Q ss_pred HHHHhhcCCCCCCCCChhHHHHHHHHHHHHHh-----ccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHH-HHhhc
Q 011878 82 LVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKY-----GETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIAR-QMVAF 155 (475)
Q Consensus 82 ~i~~L~~l~~~~~~gd~~daL~va~~~l~~~~-----~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~-~l~~~ 155 (475)
..+.|..+..++ .+++..||..|++.+.... .......+.|+|||||..... .+-+..... .-.+.
T Consensus 82 ~~~~l~~l~~~G-~T~~~~al~~a~~~l~~~~~~~~~~~~~~~~~~iillTDG~~~~~-------~~~~~~~~~~~~~~~ 153 (190)
T cd01463 82 LKEALDMLEAKG-IANYTKALEFAFSLLLKNLQSNHSGSRSQCNQAIMLITDGVPENY-------KEIFDKYNWDKNSEI 153 (190)
T ss_pred HHHHHhhCCCCC-cchHHHHHHHHHHHHHHhhhcccccccCCceeEEEEEeCCCCCcH-------hHHHHHhcccccCCC
Confidence 344566665533 4578899999999876521 011134678999999986532 111211111 11123
Q ss_pred CcEEEEEEeccCCCCCCCccccccchHHHHHHhhcCCCeEeehhh
Q 011878 156 GLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDS 200 (475)
Q Consensus 156 ~I~l~~i~i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~~~~~~ 200 (475)
+|.+.+|+++.. . .+...|+.++...+|.++.+++
T Consensus 154 ~v~i~tigiG~~----~------~d~~~L~~lA~~~~G~~~~i~~ 188 (190)
T cd01463 154 PVRVFTYLIGRE----V------TDRREIQWMACENKGYYSHIQS 188 (190)
T ss_pred cEEEEEEecCCc----c------ccchHHHHHHhhcCCeEEEccc
Confidence 688889988641 0 1357899999999998877654
No 35
>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=99.08 E-value=3.3e-09 Score=94.86 Aligned_cols=152 Identities=18% Similarity=0.154 Sum_probs=102.6
Q ss_pred EEEEEecCCCcCCCchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCC-CH-HHHHH
Q 011878 8 LLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV-DG-HLVQS 85 (475)
Q Consensus 8 ~vflID~s~sM~~~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~-~~-~~i~~ 85 (475)
++|+||+|.||...++..++.+..++.+-....++++||||.|+++. +..+..++... +. ...+.
T Consensus 3 v~~llD~S~Sm~~~~~~~~~~~~~~~~~l~~~~~~~~v~lv~f~~~~-------------~~~~~~~l~~~~~~~~l~~~ 69 (163)
T cd01476 3 LLFVLDSSGSVRGKFEKYKKYIERIVEGLEIGPTATRVALITYSGRG-------------RQRVRFNLPKHNDGEELLEK 69 (163)
T ss_pred EEEEEeCCcchhhhHHHHHHHHHHHHHhcCCCCCCcEEEEEEEcCCC-------------ceEEEecCCCCCCHHHHHHH
Confidence 68999999999988888888888888766556679999999998862 12223444432 22 45667
Q ss_pred hhcCCCCCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhh-cCcEEEEEEe
Q 011878 86 LKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVA-FGLRMKNIVV 164 (475)
Q Consensus 86 L~~l~~~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~-~~I~l~~i~i 164 (475)
|+.+....+...+.+||..|.+++.+....+....+.|+|+|||.+.. .....++.|+. .||.+..|++
T Consensus 70 i~~l~~~gg~T~l~~aL~~a~~~l~~~~~~r~~~~~~villTDG~~~~----------~~~~~~~~l~~~~~v~v~~vg~ 139 (163)
T cd01476 70 VDNLRFIGGTTATGAAIEVALQQLDPSEGRREGIPKVVVVLTDGRSHD----------DPEKQARILRAVPNIETFAVGT 139 (163)
T ss_pred HHhCccCCCCccHHHHHHHHHHHhccccCCCCCCCeEEEEECCCCCCC----------chHHHHHHHhhcCCCEEEEEEC
Confidence 777753223458899999999987632222223458899999997641 13344666777 8899888988
Q ss_pred ccCCCCCCCccccccchHHHHHHhhcC
Q 011878 165 RASLSGEPHMRVIIENDNLLNIFSKKS 191 (475)
Q Consensus 165 ~~~~~~~~~~~~~~~n~~~l~~~~~~~ 191 (475)
+.. . ..+...|..++...
T Consensus 140 g~~-----~----~~~~~~L~~ia~~~ 157 (163)
T cd01476 140 GDP-----G----TVDTEELHSITGNE 157 (163)
T ss_pred CCc-----c----ccCHHHHHHHhCCC
Confidence 531 0 12356676665533
No 36
>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=99.08 E-value=6e-09 Score=112.65 Aligned_cols=165 Identities=20% Similarity=0.271 Sum_probs=116.1
Q ss_pred eEEEEEEecCCCcCC--CchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCCHHHH
Q 011878 6 EALLLLLDVSPSMHS--VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHLV 83 (475)
Q Consensus 6 e~~vflID~s~sM~~--~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~~~~i 83 (475)
-.++|+||+|.||.. ++..|+.++..++..- +...|+||||.|++... .++.|++..-....
T Consensus 466 ~~vv~vvD~SgSM~~~~rl~~ak~a~~~ll~~a--~~~~D~v~lI~F~g~~a--------------~~~~p~t~~~~~~~ 529 (633)
T TIGR02442 466 NLVIFVVDASGSMAARGRMAAAKGAVLSLLRDA--YQKRDKVALITFRGEEA--------------EVLLPPTSSVELAA 529 (633)
T ss_pred ceEEEEEECCccCCCccHHHHHHHHHHHHHHHh--hcCCCEEEEEEECCCCc--------------eEEcCCCCCHHHHH
Confidence 478999999999975 5777888888877643 57899999999986621 12445543323334
Q ss_pred HHhhcCCCCCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEEE
Q 011878 84 QSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIV 163 (475)
Q Consensus 84 ~~L~~l~~~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l~~i~ 163 (475)
+.|..+..+. .+++.+||..|.+++.+...+.....+.||||||+..+.+. ......+++..+++.+++.||.+.+|+
T Consensus 530 ~~L~~l~~gG-~Tpl~~aL~~A~~~l~~~~~~~~~~~~~vvliTDG~~n~~~-~~~~~~~~~~~~a~~l~~~~i~~~vId 607 (633)
T TIGR02442 530 RRLEELPTGG-RTPLAAGLLKAAEVLSNELLRDDDGRPLLVVITDGRANVAD-GGEPPTDDARTIAAKLAARGILFVVID 607 (633)
T ss_pred HHHHhCCCCC-CCCHHHHHHHHHHHHHHhhccCCCCceEEEEECCCCCCCCC-CCCChHHHHHHHHHHHHhcCCeEEEEe
Confidence 5677776643 46899999999999875322222456789999999887641 011233567778899999999988887
Q ss_pred eccCCCCCCCccccccchHHHHHHhhcCCCeEeeh
Q 011878 164 VRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFV 198 (475)
Q Consensus 164 i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~~~~ 198 (475)
....+ ....++..+|..++|+|+.+
T Consensus 608 t~~~~----------~~~~~~~~lA~~~gg~y~~l 632 (633)
T TIGR02442 608 TESGF----------VRLGLAEDLARALGGEYVRL 632 (633)
T ss_pred CCCCC----------cchhHHHHHHHhhCCeEEec
Confidence 63210 12467889999999998764
No 37
>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=99.02 E-value=1.6e-08 Score=90.82 Aligned_cols=163 Identities=13% Similarity=0.177 Sum_probs=107.7
Q ss_pred EEEEEEecCCCcCCC-chHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCC-HHHHH
Q 011878 7 ALLLLLDVSPSMHSV-LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVD-GHLVQ 84 (475)
Q Consensus 7 ~~vflID~s~sM~~~-~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~-~~~i~ 84 (475)
-++|+||+|+||... +..+++++..++.. ..+.|.++|+.|+++..... +. ..+...-+ ...++
T Consensus 4 ~v~~vlD~S~SM~~~~~~~~~~al~~~l~~---l~~~~~~~l~~Fs~~~~~~~--------~~---~~~~~~~~~~~~~~ 69 (171)
T cd01461 4 EVVFVIDTSGSMSGTKIEQTKEALLTALKD---LPPGDYFNIIGFSDTVEEFS--------PS---SVSATAENVAAAIE 69 (171)
T ss_pred eEEEEEECCCCCCChhHHHHHHHHHHHHHh---CCCCCEEEEEEeCCCceeec--------Cc---ceeCCHHHHHHHHH
Confidence 478999999999753 67777777776653 34678999999988732110 00 00111111 23345
Q ss_pred HhhcCCCCCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEEEe
Q 011878 85 SLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIVV 164 (475)
Q Consensus 85 ~L~~l~~~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l~~i~i 164 (475)
.|..+..+. .+++..||..|.+.+.. .....+.|++|||+.... ...+...++.+.+.+|.+.+|++
T Consensus 70 ~l~~~~~~g-~T~l~~al~~a~~~l~~----~~~~~~~iillTDG~~~~--------~~~~~~~~~~~~~~~i~i~~i~~ 136 (171)
T cd01461 70 YVNRLQALG-GTNMNDALEAALELLNS----SPGSVPQIILLTDGEVTN--------ESQILKNVREALSGRIRLFTFGI 136 (171)
T ss_pred HHHhcCCCC-CcCHHHHHHHHHHhhcc----CCCCccEEEEEeCCCCCC--------HHHHHHHHHHhcCCCceEEEEEe
Confidence 566665432 46889999999888643 123468899999997421 13455556666666999999999
Q ss_pred ccCCCCCCCccccccchHHHHHHhhcCCCeEeehhhHHHhhcc
Q 011878 165 RASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDSTTSLRGA 207 (475)
Q Consensus 165 ~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~~~~~~~~~ll~~ 207 (475)
+.. .+..+|+.++..++|.+..+.+..++...
T Consensus 137 g~~-----------~~~~~l~~ia~~~gG~~~~~~~~~~~~~~ 168 (171)
T cd01461 137 GSD-----------VNTYLLERLAREGRGIARRIYETDDIESQ 168 (171)
T ss_pred CCc-----------cCHHHHHHHHHcCCCeEEEecChHHHHHH
Confidence 631 12478999999999998887777665543
No 38
>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=99.02 E-value=1.8e-08 Score=91.15 Aligned_cols=144 Identities=21% Similarity=0.187 Sum_probs=95.4
Q ss_pred EEEEEEecCCCcCC--CchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEe--ecCCC-CHH
Q 011878 7 ALLLLLDVSPSMHS--VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQ--DIKVV-DGH 81 (475)
Q Consensus 7 ~~vflID~s~sM~~--~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~--~l~~~-~~~ 81 (475)
+++|+||+|.||.. +++.|++++..+.... ..++|++||+.|+++... ..++..+. +.... ...
T Consensus 2 ~v~~llD~SgSM~~~~kl~~ak~a~~~l~~~l--~~~~d~~~l~~F~~~~~~---------~~~~~~~~~~~~~~~~~~~ 70 (174)
T cd01454 2 AVTLLLDLSGSMRSDRRIDVAKKAAVLLAEAL--EACGVPHAILGFTTDAGG---------RERVRWIKIKDFDESLHER 70 (174)
T ss_pred EEEEEEECCCCCCCCcHHHHHHHHHHHHHHHH--HHcCCcEEEEEecCCCCC---------ccceEEEEecCcccccchh
Confidence 57899999999988 7888898888776643 347999999999998410 01111122 23222 123
Q ss_pred HHHHhhcCCCCCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCC--chhhHHHHHHHHhhcCcEE
Q 011878 82 LVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGT--KEDQVSTIARQMVAFGLRM 159 (475)
Q Consensus 82 ~i~~L~~l~~~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~--~~~~~~~~~~~l~~~~I~l 159 (475)
..+.|..+..+. .+++.+||+.|.+.+.+. ....+.||||||+.........+. ..++....++.+.+.||.+
T Consensus 71 ~~~~l~~~~~~g-~T~~~~al~~a~~~l~~~----~~~~~~iiliTDG~~~~~~~~~~~~~~~~~~~~~~~~~~~~gi~v 145 (174)
T cd01454 71 ARKRLAALSPGG-NTRDGAAIRHAAERLLAR----PEKRKILLVISDGEPNDLDYYEGNVFATEDALRAVIEARKLGIEV 145 (174)
T ss_pred HHHHHHccCCCC-CCcHHHHHHHHHHHHhcC----CCcCcEEEEEeCCCcCcccccCcchhHHHHHHHHHHHHHhCCcEE
Confidence 455677765543 458999999999987642 234678999999977543211111 1122333377888999999
Q ss_pred EEEEecc
Q 011878 160 KNIVVRA 166 (475)
Q Consensus 160 ~~i~i~~ 166 (475)
.+++++.
T Consensus 146 ~~igig~ 152 (174)
T cd01454 146 FGITIDR 152 (174)
T ss_pred EEEEecC
Confidence 9999975
No 39
>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=99.01 E-value=1.5e-08 Score=95.56 Aligned_cols=155 Identities=17% Similarity=0.191 Sum_probs=104.3
Q ss_pred EEEEEEecCCCcCC-CchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCC-C-HHHH
Q 011878 7 ALLLLLDVSPSMHS-VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV-D-GHLV 83 (475)
Q Consensus 7 ~~vflID~s~sM~~-~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~-~-~~~i 83 (475)
=++|+||.|.||.. .|+.++..+..++++.-+....++||||.|+++.. +..++... + .+..
T Consensus 4 DlvfllD~S~Sm~~~~~~~~k~f~~~l~~~l~~~~~~~rvglv~fs~~~~---------------~~~~l~~~~~~~~l~ 68 (224)
T cd01475 4 DLVFLIDSSRSVRPENFELVKQFLNQIIDSLDVGPDATRVGLVQYSSTVK---------------QEFPLGRFKSKADLK 68 (224)
T ss_pred cEEEEEeCCCCCCHHHHHHHHHHHHHHHHhcccCCCccEEEEEEecCcee---------------EEecccccCCHHHHH
Confidence 37999999999985 58888999999988755556789999999999831 23455432 2 2345
Q ss_pred HHhhcCCCCCCCCChhHHHHHHHHHHHHHh-ccCcc---eeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEE
Q 011878 84 QSLKHLPQGTCAGDFLDAIVVGVDMLIKKY-GETYK---GKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRM 159 (475)
Q Consensus 84 ~~L~~l~~~~~~gd~~daL~va~~~l~~~~-~~~~~---~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l 159 (475)
+.|..+....+.+....||..+.+.+.... +.+.. ..|-|+|||||.+. +++...++.+++.||.+
T Consensus 69 ~~i~~i~~~~~~t~tg~AL~~a~~~~~~~~~g~r~~~~~~~kvvillTDG~s~----------~~~~~~a~~lk~~gv~i 138 (224)
T cd01475 69 RAVRRMEYLETGTMTGLAIQYAMNNAFSEAEGARPGSERVPRVGIVVTDGRPQ----------DDVSEVAAKARALGIEM 138 (224)
T ss_pred HHHHhCcCCCCCChHHHHHHHHHHHhCChhcCCCCCCCCCCeEEEEEcCCCCc----------ccHHHHHHHHHHCCcEE
Confidence 556666432223356678888877644321 21211 25678999999753 23566788999999999
Q ss_pred EEEEeccCCCCCCCccccccchHHHHHHhhcCCC-eEeeh
Q 011878 160 KNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSA-KTLFV 198 (475)
Q Consensus 160 ~~i~i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g-~~~~~ 198 (475)
..++++. .+...|..+++..++ .++..
T Consensus 139 ~~VgvG~------------~~~~~L~~ias~~~~~~~f~~ 166 (224)
T cd01475 139 FAVGVGR------------ADEEELREIASEPLADHVFYV 166 (224)
T ss_pred EEEeCCc------------CCHHHHHHHhCCCcHhcEEEe
Confidence 9999853 124678888876543 34443
No 40
>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=99.01 E-value=9.4e-09 Score=91.13 Aligned_cols=149 Identities=16% Similarity=0.190 Sum_probs=106.0
Q ss_pred EEEEEecCCCcCC-CchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCC--CHHHHH
Q 011878 8 LLLLLDVSPSMHS-VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV--DGHLVQ 84 (475)
Q Consensus 8 ~vflID~s~sM~~-~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~--~~~~i~ 84 (475)
++|+||+|.||.. .+..++..+..++.......+++++||+.|+++.. ...++... ..+..+
T Consensus 3 i~~llD~S~Sm~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~f~~~~~---------------~~~~~~~~~~~~~~~~ 67 (161)
T cd01450 3 IVFLLDGSESVGPENFEKVKDFIEKLVEKLDIGPDKTRVGLVQYSDDVR---------------VEFSLNDYKSKDDLLK 67 (161)
T ss_pred EEEEEeCCCCcCHHHHHHHHHHHHHHHHheeeCCCceEEEEEEEcCCce---------------EEEECCCCCCHHHHHH
Confidence 6799999999998 67788888888888766566899999999999621 12333322 334566
Q ss_pred HhhcCCCCC-CCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEEE
Q 011878 85 SLKHLPQGT-CAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIV 163 (475)
Q Consensus 85 ~L~~l~~~~-~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l~~i~ 163 (475)
.|+.+.... ...++.+||..|.+++.+....+....+.|+||||+..... .+....++.+++.||.+.+|+
T Consensus 68 ~i~~~~~~~~~~t~~~~al~~a~~~~~~~~~~~~~~~~~iiliTDG~~~~~--------~~~~~~~~~~~~~~v~v~~i~ 139 (161)
T cd01450 68 AVKNLKYLGGGGTNTGKALQYALEQLFSESNARENVPKVIIVLTDGRSDDG--------GDPKEAAAKLKDEGIKVFVVG 139 (161)
T ss_pred HHHhcccCCCCCccHHHHHHHHHHHhcccccccCCCCeEEEEECCCCCCCC--------cchHHHHHHHHHCCCEEEEEe
Confidence 677664322 25689999999999876532112245788999999976432 147777888999999999999
Q ss_pred eccCCCCCCCccccccchHHHHHHhhcC
Q 011878 164 VRASLSGEPHMRVIIENDNLLNIFSKKS 191 (475)
Q Consensus 164 i~~~~~~~~~~~~~~~n~~~l~~~~~~~ 191 (475)
++. .+...|..++...
T Consensus 140 ~g~------------~~~~~l~~la~~~ 155 (161)
T cd01450 140 VGP------------ADEEELREIASCP 155 (161)
T ss_pred ccc------------cCHHHHHHHhCCC
Confidence 853 1246677777655
No 41
>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=99.00 E-value=8.8e-09 Score=91.42 Aligned_cols=146 Identities=16% Similarity=0.217 Sum_probs=97.9
Q ss_pred EEEEEecCCCcCC-CchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCCH---H-H
Q 011878 8 LLLLLDVSPSMHS-VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDG---H-L 82 (475)
Q Consensus 8 ~vflID~s~sM~~-~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~~---~-~ 82 (475)
++|+||.|+||.. ++..++.++..+++. -.+.|++|||.|+++.. +..++...+. + .
T Consensus 3 v~~vlD~S~SM~~~rl~~ak~a~~~l~~~---l~~~~~~~li~F~~~~~---------------~~~~~~~~~~~~~~~~ 64 (155)
T cd01466 3 LVAVLDVSGSMAGDKLQLVKHALRFVISS---LGDADRLSIVTFSTSAK---------------RLSPLRRMTAKGKRSA 64 (155)
T ss_pred EEEEEECCCCCCcHHHHHHHHHHHHHHHh---CCCcceEEEEEecCCcc---------------ccCCCcccCHHHHHHH
Confidence 6899999999986 577788877766652 24789999999999731 1234433222 2 2
Q ss_pred HHHhhcCCCCCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEE
Q 011878 83 VQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNI 162 (475)
Q Consensus 83 i~~L~~l~~~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l~~i 162 (475)
...+..+..+. .+++.+||..|.+.+... ......+.|+|+||+....+ .. .....+.+|.+.+|
T Consensus 65 ~~~i~~~~~~g-~T~~~~al~~a~~~~~~~--~~~~~~~~iillTDG~~~~~--------~~----~~~~~~~~v~v~~i 129 (155)
T cd01466 65 KRVVDGLQAGG-GTNVVGGLKKALKVLGDR--RQKNPVASIMLLSDGQDNHG--------AV----VLRADNAPIPIHTF 129 (155)
T ss_pred HHHHHhccCCC-CccHHHHHHHHHHHHhhc--ccCCCceEEEEEcCCCCCcc--------hh----hhcccCCCceEEEE
Confidence 33355554432 468999999999987542 11234578999999975421 01 11234578999999
Q ss_pred EeccCCCCCCCccccccchHHHHHHhhcCCCeEee
Q 011878 163 VVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLF 197 (475)
Q Consensus 163 ~i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~~~ 197 (475)
+++.. .+...++.+++.++|+++.
T Consensus 130 gig~~-----------~~~~~l~~iA~~t~G~~~~ 153 (155)
T cd01466 130 GLGAS-----------HDPALLAFIAEITGGTFSY 153 (155)
T ss_pred ecCCC-----------CCHHHHHHHHhccCceEEE
Confidence 99631 1247799999999998764
No 42
>TIGR00868 hCaCC calcium-activated chloride channel protein 1. distributions. found a row in 1A13.INFO that was not parsed out
Probab=98.99 E-value=1.8e-08 Score=109.79 Aligned_cols=151 Identities=16% Similarity=0.232 Sum_probs=104.8
Q ss_pred EEEEEEecCCCcCC--CchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCC-HHHH
Q 011878 7 ALLLLLDVSPSMHS--VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVD-GHLV 83 (475)
Q Consensus 7 ~~vflID~s~sM~~--~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~-~~~i 83 (475)
-++|+||+|+||.. ++..+++++..++.+. ..+.|+||||.|++..+ ++.+|.+.+ ....
T Consensus 306 ~VVLVLDvSGSM~g~dRL~~lkqAA~~fL~~~--l~~~DrVGLVtFsssA~---------------vl~pLt~Its~~dr 368 (863)
T TIGR00868 306 IVCLVLDKSGSMTVEDRLKRMNQAAKLFLLQT--VEKGSWVGMVTFDSAAY---------------IKNELIQITSSAER 368 (863)
T ss_pred eEEEEEECCccccccCHHHHHHHHHHHHHHHh--CCCCCEEEEEEECCcee---------------EeeccccCCcHHHH
Confidence 38899999999974 5677777777777654 46899999999999831 234554322 2333
Q ss_pred HHhhcC-CC-CCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEE
Q 011878 84 QSLKHL-PQ-GTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKN 161 (475)
Q Consensus 84 ~~L~~l-~~-~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l~~ 161 (475)
+.|.+. .. ..+..++.+||..|+++|.+.. .+...+.|+|+|||.... ....+..+++.||.+..
T Consensus 369 ~aL~~~L~~~A~GGT~I~~GL~~Alq~L~~~~--~~~~~~~IILLTDGedn~-----------~~~~l~~lk~~gVtI~T 435 (863)
T TIGR00868 369 DALTANLPTAASGGTSICSGLKAAFQVIKKSY--QSTDGSEIVLLTDGEDNT-----------ISSCFEEVKQSGAIIHT 435 (863)
T ss_pred HHHHHhhccccCCCCcHHHHHHHHHHHHHhcc--cccCCCEEEEEeCCCCCC-----------HHHHHHHHHHcCCEEEE
Confidence 444432 11 1234689999999999987632 123457999999997642 12345677889999999
Q ss_pred EEeccCCCCCCCccccccchHHHHHHhhcCCCeEeehh
Q 011878 162 IVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVD 199 (475)
Q Consensus 162 i~i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~~~~~ 199 (475)
|+++.. ....|+.+|..++|.++.+.
T Consensus 436 Ig~G~d------------ad~~L~~IA~~TGG~~f~as 461 (863)
T TIGR00868 436 IALGPS------------AAKELEELSDMTGGLRFYAS 461 (863)
T ss_pred EEeCCC------------hHHHHHHHHHhcCCEEEEeC
Confidence 999641 12458899999999877554
No 43
>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=98.97 E-value=1.6e-08 Score=91.29 Aligned_cols=163 Identities=15% Similarity=0.026 Sum_probs=97.7
Q ss_pred EEEEEEecCCCcCC----------CchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecC
Q 011878 7 ALLLLLDVSPSMHS----------VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIK 76 (475)
Q Consensus 7 ~~vflID~s~sM~~----------~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~ 76 (475)
-++++||+|.||.. +++.++.++..++. -+-.++.|+|| |+++..--++ ++.-.|++
T Consensus 2 ~l~lavDlSgSM~~~~~~dg~~~~RL~a~k~v~~~f~~-f~~~r~~DriG---~~g~~~~~~~---------lt~d~p~t 68 (191)
T cd01455 2 RLKLVVDVSGSMYRFNGYDGRLDRSLEAVVMVMEAFDG-FEDKIQYDIIG---HSGDGPCVPF---------VKTNHPPK 68 (191)
T ss_pred ceEEEEECcHhHHHHhccCCccccHHHHHHHHHHHHHH-HHHhCccceee---ecCcccccCc---------cccccCcc
Confidence 37899999999943 13334444444431 12378999999 3444211110 11112222
Q ss_pred CCC--HHHHHH-hhcCCCC-CCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHH-HHHH
Q 011878 77 VVD--GHLVQS-LKHLPQG-TCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVST-IARQ 151 (475)
Q Consensus 77 ~~~--~~~i~~-L~~l~~~-~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~-~~~~ 151 (475)
.-. ++.++. |+.++.+ .+.+-. |||-.|++.|.+. + ....|-|+|+||+.+.... -.... .+..
T Consensus 69 ~d~~~~~~l~~~l~~~q~g~ag~~Ta-dAi~~av~rl~~~-~--~a~~kvvILLTDG~n~~~~-------i~P~~aAa~l 137 (191)
T cd01455 69 NNKERLETLKMMHAHSQFCWSGDHTV-EATEFAIKELAAK-E--DFDEAIVIVLSDANLERYG-------IQPKKLADAL 137 (191)
T ss_pred cchhHHHHHHHHHHhcccCccCccHH-HHHHHHHHHHHhc-C--cCCCcEEEEEeCCCcCCCC-------CChHHHHHHH
Confidence 211 133333 3334443 122223 9999999998621 1 2347899999999986542 12444 3455
Q ss_pred HhhcCcEEEEEEeccCCCCCCCccccccchHHHHHHhhcCCCeEeehhhHHHhh
Q 011878 152 MVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDSTTSLR 205 (475)
Q Consensus 152 l~~~~I~l~~i~i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~~~~~~~~~ll 205 (475)
.++.||++++|+++. +++..++.+++.++|++|...+..+|-
T Consensus 138 A~~~gV~iytIgiG~------------~d~~~l~~iA~~tgG~~F~A~d~~~L~ 179 (191)
T cd01455 138 AREPNVNAFVIFIGS------------LSDEADQLQRELPAGKAFVCMDTSELP 179 (191)
T ss_pred HHhCCCEEEEEEecC------------CCHHHHHHHHhCCCCcEEEeCCHHHHH
Confidence 678999999999964 125678888999999999877665443
No 44
>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=98.96 E-value=2.2e-08 Score=91.96 Aligned_cols=137 Identities=15% Similarity=0.188 Sum_probs=92.8
Q ss_pred EEEEEecCCCcCC-CchHHHHHHHHHHHHHHhc------CCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCC-C
Q 011878 8 LLLLLDVSPSMHS-VLPDVEKLCSRLIQKKLIY------GKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV-D 79 (475)
Q Consensus 8 ~vflID~s~sM~~-~~~~a~~~~~~l~~~ki~~------~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~-~ 79 (475)
++|+||.|.||.. .|+.++..+..++...-+. ...++||||.|+++. ++..+|+.. +
T Consensus 22 ivfvlD~S~Sm~~~~f~~~k~fi~~~~~~~~~~~~~~~~~~~~rVGlV~fs~~a---------------~~~~~L~d~~~ 86 (193)
T cd01477 22 IVFVVDNSKGMTQGGLWQVRATISSLFGSSSQIGTDYDDPRSTRVGLVTYNSNA---------------TVVADLNDLQS 86 (193)
T ss_pred EEEEEeCCCCcchhhHHHHHHHHHHHHhhccccccccCCCCCcEEEEEEccCce---------------EEEEecccccC
Confidence 6999999999975 4778888887776654432 345899999999983 124455532 2
Q ss_pred H-HHHHHhhcC-CC--CCCCCChhHHHHHHHHHHHHH-hccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhh
Q 011878 80 G-HLVQSLKHL-PQ--GTCAGDFLDAIVVGVDMLIKK-YGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVA 154 (475)
Q Consensus 80 ~-~~i~~L~~l-~~--~~~~gd~~daL~va~~~l~~~-~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~ 154 (475)
. +.+..|+.. .. ..+...+..||..|.++|... .+.+....|.||||||+...-.. .+....++.|++
T Consensus 87 ~~~~~~ai~~~~~~~~~~ggT~ig~aL~~A~~~l~~~~~~~R~~v~kvvIllTDg~~~~~~-------~~~~~~a~~l~~ 159 (193)
T cd01477 87 FDDLYSQIQGSLTDVSSTNASYLDTGLQAAEQMLAAGKRTSRENYKKVVIVFASDYNDEGS-------NDPRPIAARLKS 159 (193)
T ss_pred HHHHHHHHHHHhhccccCCcchHHHHHHHHHHHHHhhhccccCCCCeEEEEEecCccCCCC-------CCHHHHHHHHHH
Confidence 2 334456641 11 122357889999999998752 12233346779999998553221 245677889999
Q ss_pred cCcEEEEEEecc
Q 011878 155 FGLRMKNIVVRA 166 (475)
Q Consensus 155 ~~I~l~~i~i~~ 166 (475)
.||.+..||++.
T Consensus 160 ~GI~i~tVGiG~ 171 (193)
T cd01477 160 TGIAIITVAFTQ 171 (193)
T ss_pred CCCEEEEEEeCC
Confidence 999999999964
No 45
>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=98.87 E-value=6.6e-08 Score=87.66 Aligned_cols=147 Identities=15% Similarity=0.114 Sum_probs=92.1
Q ss_pred eEEEEEEecCCCcCCC-chHHHHHHHHHHHHHHh---cCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCCHH
Q 011878 6 EALLLLLDVSPSMHSV-LPDVEKLCSRLIQKKLI---YGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGH 81 (475)
Q Consensus 6 e~~vflID~s~sM~~~-~~~a~~~~~~l~~~ki~---~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~~~ 81 (475)
=-++|+||+|+||... +..+++.+..++....- ..++++||||.|+++.. +..|+.....
T Consensus 4 ~~v~~llD~SgSM~~~~~~~~k~a~~~~~~~l~~~~~~~~~~~v~ii~F~~~a~---------------~~~~l~~~~~- 67 (176)
T cd01464 4 LPIYLLLDTSGSMAGEPIEALNQGLQMLQSELRQDPYALESVEISVITFDSAAR---------------VIVPLTPLES- 67 (176)
T ss_pred CCEEEEEECCCCCCChHHHHHHHHHHHHHHHHhcChhhccccEEEEEEecCCce---------------EecCCccHHh-
Confidence 3479999999999763 56666666666654321 13688999999999631 1233322110
Q ss_pred HHHHhhcCCCCCCCCChhHHHHHHHHHHHHHhcc-----CcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcC
Q 011878 82 LVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGE-----TYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFG 156 (475)
Q Consensus 82 ~i~~L~~l~~~~~~gd~~daL~va~~~l~~~~~~-----~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~ 156 (475)
..+..+..+ +..++.+||..|.+++...... +....+.|+|||||....+ .....+.++.+.+.+
T Consensus 68 --~~~~~l~~~-GgT~l~~aL~~a~~~l~~~~~~~~~~~~~~~~~~iillTDG~~~~~-------~~~~~~~~~~~~~~~ 137 (176)
T cd01464 68 --FQPPRLTAS-GGTSMGAALELALDCIDRRVQRYRADQKGDWRPWVFLLTDGEPTDD-------LTAAIERIKEARDSK 137 (176)
T ss_pred --cCCCcccCC-CCCcHHHHHHHHHHHHHHHHHHhcccCcCCcCcEEEEEcCCCCCch-------HHHHHHHHHhhcccC
Confidence 012233332 2458999999999998653211 1123467999999975311 123335566666678
Q ss_pred cEEEEEEeccCCCCCCCccccccchHHHHHHhh
Q 011878 157 LRMKNIVVRASLSGEPHMRVIIENDNLLNIFSK 189 (475)
Q Consensus 157 I~l~~i~i~~~~~~~~~~~~~~~n~~~l~~~~~ 189 (475)
+.+.+|+++.. .|...|+.++.
T Consensus 138 ~~i~~igiG~~-----------~~~~~L~~ia~ 159 (176)
T cd01464 138 GRIVACAVGPK-----------ADLDTLKQITE 159 (176)
T ss_pred CcEEEEEeccc-----------cCHHHHHHHHC
Confidence 99999999641 23577888775
No 46
>PTZ00441 sporozoite surface protein 2 (SSP2); Provisional
Probab=98.87 E-value=7.7e-08 Score=99.73 Aligned_cols=137 Identities=18% Similarity=0.141 Sum_probs=93.9
Q ss_pred eEEEEEEecCCCcCCC--chHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCC----
Q 011878 6 EALLLLLDVSPSMHSV--LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVD---- 79 (475)
Q Consensus 6 e~~vflID~s~sM~~~--~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~---- 79 (475)
-=++||||+|.||... +..|+..+..|+....++...-+||+++|.+... .+.++....
T Consensus 43 lDIvFLLD~SgSMg~~Nfle~AK~Fa~~LV~~l~Is~D~V~VgiV~FSd~~r---------------~vfpL~s~~s~Dk 107 (576)
T PTZ00441 43 VDLYLLVDGSGSIGYHNWITHVIPMLMGLIQQLNLSDDAINLYMSLFSNNTT---------------ELIRLGSGASKDK 107 (576)
T ss_pred ceEEEEEeCCCccCCccHHHHHHHHHHHHHHHhccCCCceEEEEEEeCCCce---------------EEEecCCCccccH
Confidence 3489999999999854 4678889999998776666666677799988721 123443221
Q ss_pred HHHHHHhhcCCC---CCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcC
Q 011878 80 GHLVQSLKHLPQ---GTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFG 156 (475)
Q Consensus 80 ~~~i~~L~~l~~---~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~ 156 (475)
...+..|.++.. ..+.+.+..||..+.+++.+. +.+....+.||||||+..... .++...++.|++.|
T Consensus 108 ~~aL~~I~sL~~~~~pgGgTnig~AL~~Aae~L~sr-~~R~nvpKVVILLTDG~sns~--------~dvleaAq~LR~~G 178 (576)
T PTZ00441 108 EQALIIVKSLRKTYLPYGKTNMTDALLEVRKHLNDR-VNRENAIQLVILMTDGIPNSK--------YRALEESRKLKDRN 178 (576)
T ss_pred HHHHHHHHHHHhhccCCCCccHHHHHHHHHHHHhhc-ccccCCceEEEEEecCCCCCc--------ccHHHHHHHHHHCC
Confidence 134445554422 123467899999988887653 223345688999999986321 23555678899999
Q ss_pred cEEEEEEecc
Q 011878 157 LRMKNIVVRA 166 (475)
Q Consensus 157 I~l~~i~i~~ 166 (475)
|+|.+|+++.
T Consensus 179 VeI~vIGVG~ 188 (576)
T PTZ00441 179 VKLAVIGIGQ 188 (576)
T ss_pred CEEEEEEeCC
Confidence 9999999964
No 47
>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=98.85 E-value=9.1e-08 Score=83.96 Aligned_cols=150 Identities=19% Similarity=0.277 Sum_probs=104.6
Q ss_pred EEEEEEecCCCc-CCCchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCC--CCHHHH
Q 011878 7 ALLLLLDVSPSM-HSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKV--VDGHLV 83 (475)
Q Consensus 7 ~~vflID~s~sM-~~~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~--~~~~~i 83 (475)
.++|+||.|.|| ...+..+++.+..++.+..-..+.+++||+.|++... +..++.. -.....
T Consensus 2 ~v~~viD~S~Sm~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~~f~~~~~---------------~~~~~~~~~~~~~~~ 66 (161)
T cd00198 2 DIVFLLDVSGSMGGEKLDKAKEALKALVSSLSASPPGDRVGLVTFGSNAR---------------VVLPLTTDTDKADLL 66 (161)
T ss_pred cEEEEEeCCCCcCcchHHHHHHHHHHHHHhcccCCCCcEEEEEEecCccc---------------eeecccccCCHHHHH
Confidence 479999999999 5567888888888888776666899999999998421 1222222 223445
Q ss_pred HHhhcCCC-CCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEE
Q 011878 84 QSLKHLPQ-GTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNI 162 (475)
Q Consensus 84 ~~L~~l~~-~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l~~i 162 (475)
+.+..+.. ..+..++..|+..+.+.+.... .....+.|++|||+...... .......+.+++.+|++.++
T Consensus 67 ~~~~~~~~~~~~~t~~~~al~~~~~~~~~~~--~~~~~~~lvvitDg~~~~~~-------~~~~~~~~~~~~~~v~v~~v 137 (161)
T cd00198 67 EAIDALKKGLGGGTNIGAALRLALELLKSAK--RPNARRVIILLTDGEPNDGP-------ELLAEAARELRKLGITVYTI 137 (161)
T ss_pred HHHHhcccCCCCCccHHHHHHHHHHHhcccC--CCCCceEEEEEeCCCCCCCc-------chhHHHHHHHHHcCCEEEEE
Confidence 55666653 3345689999999998876532 23457889999999764321 35667788888999999999
Q ss_pred EeccCCCCCCCccccccchHHHHHHhhcC
Q 011878 163 VVRASLSGEPHMRVIIENDNLLNIFSKKS 191 (475)
Q Consensus 163 ~i~~~~~~~~~~~~~~~n~~~l~~~~~~~ 191 (475)
+++. ..+...++.++...
T Consensus 138 ~~g~-----------~~~~~~l~~l~~~~ 155 (161)
T cd00198 138 GIGD-----------DANEDELKEIADKT 155 (161)
T ss_pred EcCC-----------CCCHHHHHHHhccc
Confidence 9953 01245666666544
No 48
>PF13768 VWA_3: von Willebrand factor type A domain
Probab=98.80 E-value=1.7e-07 Score=83.06 Aligned_cols=147 Identities=16% Similarity=0.276 Sum_probs=99.5
Q ss_pred EEEEEecCCCcCCCchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCCH----HHH
Q 011878 8 LLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDG----HLV 83 (475)
Q Consensus 8 ~vflID~s~sM~~~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~~----~~i 83 (475)
++|+||+|.||......+++++..++++ -.++|++.||.||+... .+ +++ +.+.+. ..+
T Consensus 3 vvilvD~S~Sm~g~~~~~k~al~~~l~~---L~~~d~fnii~f~~~~~--~~------~~~------~~~~~~~~~~~a~ 65 (155)
T PF13768_consen 3 VVILVDTSGSMSGEKELVKDALRAILRS---LPPGDRFNIIAFGSSVR--PL------FPG------LVPATEENRQEAL 65 (155)
T ss_pred EEEEEeCCCCCCCcHHHHHHHHHHHHHh---CCCCCEEEEEEeCCEee--Ec------chh------HHHHhHHHHHHHH
Confidence 7999999999998776667777777775 46899999999999621 11 111 122222 235
Q ss_pred HHhhcCCCCCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEEE
Q 011878 84 QSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIV 163 (475)
Q Consensus 84 ~~L~~l~~~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l~~i~ 163 (475)
+.|+.+....+.+++..||..|+..+ ......+.|+||||+.. ... .+.+...++.- ...+.+.+++
T Consensus 66 ~~I~~~~~~~G~t~l~~aL~~a~~~~-----~~~~~~~~IilltDG~~-~~~------~~~i~~~v~~~-~~~~~i~~~~ 132 (155)
T PF13768_consen 66 QWIKSLEANSGGTDLLAALRAALALL-----QRPGCVRAIILLTDGQP-VSG------EEEILDLVRRA-RGHIRIFTFG 132 (155)
T ss_pred HHHHHhcccCCCccHHHHHHHHHHhc-----ccCCCccEEEEEEeccC-CCC------HHHHHHHHHhc-CCCceEEEEE
Confidence 55666655344578999999888764 12355899999999975 221 13344444432 2568999999
Q ss_pred eccCCCCCCCccccccchHHHHHHhhcCCCeE
Q 011878 164 VRASLSGEPHMRVIIENDNLLNIFSKKSSAKT 195 (475)
Q Consensus 164 i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~ 195 (475)
++.. .+..+|+.++..++|.+
T Consensus 133 ~g~~-----------~~~~~L~~LA~~~~G~~ 153 (155)
T PF13768_consen 133 IGSD-----------ADADFLRELARATGGSF 153 (155)
T ss_pred ECCh-----------hHHHHHHHHHHcCCCEE
Confidence 9641 23588999999998864
No 49
>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=98.79 E-value=3.4e-07 Score=82.26 Aligned_cols=156 Identities=19% Similarity=0.217 Sum_probs=107.3
Q ss_pred EEEEEEecCCCc-CCCchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeec-CCCCH-HHH
Q 011878 7 ALLLLLDVSPSM-HSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDI-KVVDG-HLV 83 (475)
Q Consensus 7 ~~vflID~s~sM-~~~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l-~~~~~-~~i 83 (475)
-++|+||+|.|| ...+..++.++..+++......+++++|++.|+++... ..++ ...+. ...
T Consensus 3 ~v~l~vD~S~SM~~~~~~~~~~~~~~~~~~~~~~~~~~~i~ii~f~~~~~~---------------~~~~~~~~~~~~~~ 67 (177)
T smart00327 3 DVVFLLDGSGSMGPNRFEKAKEFVLKLVEQLDIGPDGDRVGLVTFSDDATV---------------LFPLNDSRSKDALL 67 (177)
T ss_pred cEEEEEeCCCccchHHHHHHHHHHHHHHHhcCCCCCCcEEEEEEeCCCceE---------------EEcccccCCHHHHH
Confidence 378999999999 55677788888888886655556999999999985211 1222 12333 344
Q ss_pred HHhhcCCC-CCCCCChhHHHHHHHHHHHHHhcc-CcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEE
Q 011878 84 QSLKHLPQ-GTCAGDFLDAIVVGVDMLIKKYGE-TYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKN 161 (475)
Q Consensus 84 ~~L~~l~~-~~~~gd~~daL~va~~~l~~~~~~-~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l~~ 161 (475)
..+..+.. ..+.+++.+||..+.+.+...... +....+.|++|||+..... ..+...++.+++.+|.+..
T Consensus 68 ~~i~~~~~~~~~~~~~~~al~~~~~~~~~~~~~~~~~~~~~iviitDg~~~~~--------~~~~~~~~~~~~~~i~i~~ 139 (177)
T smart00327 68 EALASLSYKLGGGTNLGAALQYALENLFSKSAGSRRGAPKVLILITDGESNDG--------GDLLKAAKELKRSGVKVFV 139 (177)
T ss_pred HHHHhcCCCCCCCchHHHHHHHHHHHhcCcCCCCCCCCCeEEEEEcCCCCCCC--------ccHHHHHHHHHHCCCEEEE
Confidence 55666664 344568999999999887532111 1122678999999877531 3577778888999999999
Q ss_pred EEeccCCCCCCCccccccchHHHHHHhhcCCCeEe
Q 011878 162 IVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTL 196 (475)
Q Consensus 162 i~i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~~ 196 (475)
++++.. .+...++.++...+|.+.
T Consensus 140 i~~~~~-----------~~~~~l~~~~~~~~~~~~ 163 (177)
T smart00327 140 VGVGND-----------VDEEELKKLASAPGGVYV 163 (177)
T ss_pred EEccCc-----------cCHHHHHHHhCCCcceEE
Confidence 998531 035778888887777653
No 50
>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=98.78 E-value=1.9e-07 Score=89.24 Aligned_cols=136 Identities=15% Similarity=0.124 Sum_probs=91.1
Q ss_pred ceEEEEEEecCCCcCCCc--h---HHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCC
Q 011878 5 REALLLLLDVSPSMHSVL--P---DVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVD 79 (475)
Q Consensus 5 ke~~vflID~s~sM~~~~--~---~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~ 79 (475)
.--++|+||.|.||.+.. . +|+..+.+++. ..+.|++||+.||++. .++.|++.+-
T Consensus 60 ~~qIvlaID~S~SM~~~~~~~~aleak~lIs~al~----~Le~g~vgVv~Fg~~~---------------~~v~Plt~d~ 120 (266)
T cd01460 60 DYQILIAIDDSKSMSENNSKKLALESLCLVSKALT----LLEVGQLGVCSFGEDV---------------QILHPFDEQF 120 (266)
T ss_pred CceEEEEEecchhcccccccccHHHHHHHHHHHHH----hCcCCcEEEEEeCCCc---------------eEeCCCCCCc
Confidence 456899999999998742 1 24555555555 6789999999999972 2456776543
Q ss_pred HH--HHHHhhcCCCCCCCCChhHHHHHHHHHHHHHhccCcc--eeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhc
Q 011878 80 GH--LVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYK--GKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAF 155 (475)
Q Consensus 80 ~~--~i~~L~~l~~~~~~gd~~daL~va~~~l~~~~~~~~~--~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~ 155 (475)
.. .++.+....-+.+.+++..+|-.|.++|.....+... ..+-|+|+|||..-.. ....+.+++.+.+.
T Consensus 121 ~~~a~~~~l~~~~f~~~~Tni~~aL~~a~~~f~~~~~~~~s~~~~qlilLISDG~~~~~-------e~~~~~~~r~a~e~ 193 (266)
T cd01460 121 SSQSGPRILNQFTFQQDKTDIANLLKFTAQIFEDARTQSSSGSLWQLLLIISDGRGEFS-------EGAQKVRLREAREQ 193 (266)
T ss_pred hhhHHHHHhCcccCCCCCCcHHHHHHHHHHHHHhhhccccccccccEEEEEECCCcccC-------ccHHHHHHHHHHHc
Confidence 22 2333433222233468999999999998664221112 1388999999985221 12234557888999
Q ss_pred CcEEEEEEecc
Q 011878 156 GLRMKNIVVRA 166 (475)
Q Consensus 156 ~I~l~~i~i~~ 166 (475)
||.+.++++++
T Consensus 194 ~i~l~~I~ld~ 204 (266)
T cd01460 194 NVFVVFIIIDN 204 (266)
T ss_pred CCeEEEEEEcC
Confidence 99999999986
No 51
>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=98.76 E-value=2.2e-07 Score=83.33 Aligned_cols=147 Identities=18% Similarity=0.165 Sum_probs=102.0
Q ss_pred EEEEEecCCCcC-CCchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCC--CCHHHHH
Q 011878 8 LLLLLDVSPSMH-SVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKV--VDGHLVQ 84 (475)
Q Consensus 8 ~vflID~s~sM~-~~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~--~~~~~i~ 84 (475)
++|+||.|.||. ..|+.+++.+..++.+--+....-+||||.|+++... ..++.. -..+.++
T Consensus 3 ivfllD~S~Si~~~~f~~~k~fi~~lv~~f~i~~~~~rVgvv~ys~~~~~---------------~~~l~~~~~~~~l~~ 67 (165)
T cd01481 3 IVFLIDGSDNVGSGNFPAIRDFIERIVQSLDVGPDKIRVAVVQFSDTPRP---------------EFYLNTHSTKADVLG 67 (165)
T ss_pred EEEEEeCCCCcCHHHHHHHHHHHHHHHhhccCCCCCcEEEEEEecCCeeE---------------EEeccccCCHHHHHH
Confidence 789999999999 5689999999999998777778899999999987311 122221 1245667
Q ss_pred HhhcCCCCCC-CCChhHHHHHHHHHHHHHh-ccC--cceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEE
Q 011878 85 SLKHLPQGTC-AGDFLDAIVVGVDMLIKKY-GET--YKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMK 160 (475)
Q Consensus 85 ~L~~l~~~~~-~gd~~daL~va~~~l~~~~-~~~--~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l~ 160 (475)
.++++....+ ......||-.+.+.++... +.+ ....|.++|||||.+. +++...++.|++.||.+.
T Consensus 68 ~i~~i~~~~g~~t~t~~AL~~~~~~~f~~~~g~R~~~~~~kv~vviTdG~s~----------d~~~~~a~~lr~~gv~i~ 137 (165)
T cd01481 68 AVRRLRLRGGSQLNTGSALDYVVKNLFTKSAGSRIEEGVPQFLVLITGGKSQ----------DDVERPAVALKRAGIVPF 137 (165)
T ss_pred HHHhcccCCCCcccHHHHHHHHHHhhcCccccCCccCCCCeEEEEEeCCCCc----------chHHHHHHHHHHCCcEEE
Confidence 7777754322 2467889988877654321 111 1234678999999753 346777899999999988
Q ss_pred EEEeccCCCCCCCccccccchHHHHHHhhcC
Q 011878 161 NIVVRASLSGEPHMRVIIENDNLLNIFSKKS 191 (475)
Q Consensus 161 ~i~i~~~~~~~~~~~~~~~n~~~l~~~~~~~ 191 (475)
.+|++. .+..-|..++...
T Consensus 138 ~vG~~~------------~~~~eL~~ias~p 156 (165)
T cd01481 138 AIGARN------------ADLAELQQIAFDP 156 (165)
T ss_pred EEeCCc------------CCHHHHHHHhCCC
Confidence 888741 1234576777544
No 52
>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=98.71 E-value=2.5e-07 Score=83.41 Aligned_cols=150 Identities=18% Similarity=0.273 Sum_probs=99.6
Q ss_pred EEEEEecCCCcCC-CchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCC-CH-HHHH
Q 011878 8 LLLLLDVSPSMHS-VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV-DG-HLVQ 84 (475)
Q Consensus 8 ~vflID~s~sM~~-~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~-~~-~~i~ 84 (475)
++|+||.|.||.. .+..+++.+..++++--...++++||||.|++... +..++... +. +...
T Consensus 2 ivflvD~S~sm~~~~~~~~~~~v~~~i~~~~~~~~~~rv~iv~f~~~~~---------------~~~~~~~~~~~~~~~~ 66 (178)
T PF00092_consen 2 IVFLVDTSGSMSGDNFEKAKQFVKSIISRLSISNNGTRVGIVTFSDSAR---------------VLFSLTDYQSKNDLLN 66 (178)
T ss_dssp EEEEEE-STTSCHHHHHHHHHHHHHHHHHSTBSTTSEEEEEEEESSSEE---------------EEEETTSHSSHHHHHH
T ss_pred EEEEEeCCCCCchHHHHHHHHHHHHHHHhhhccccccccceeeeecccc---------------cccccccccccccccc
Confidence 7999999999996 68889999999999555678999999999999842 23455432 32 3444
Q ss_pred Hh-hcCCCCCCCCChhHHHHHHHHHHHHH-hccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEE
Q 011878 85 SL-KHLPQGTCAGDFLDAIVVGVDMLIKK-YGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNI 162 (475)
Q Consensus 85 ~L-~~l~~~~~~gd~~daL~va~~~l~~~-~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l~~i 162 (475)
.+ ..+....+..++..||..|.+++... .+.+....+-|++|||+...-.. ..........+..||.+..+
T Consensus 67 ~i~~~~~~~~g~t~~~~aL~~a~~~l~~~~~~~r~~~~~~iiliTDG~~~~~~-------~~~~~~~~~~~~~~i~~~~i 139 (178)
T PF00092_consen 67 AINDSIPSSGGGTNLGAALKFAREQLFSSNNGGRPNSPKVIILITDGNSNDSD-------SPSEEAANLKKSNGIKVIAI 139 (178)
T ss_dssp HHHTTGGCCBSSB-HHHHHHHHHHHTTSGGGTTGTTSEEEEEEEESSSSSSHS-------GHHHHHHHHHHHCTEEEEEE
T ss_pred cccccccccchhhhHHHHHhhhhhcccccccccccccccceEEEEeecccCCc-------chHHHHHHHHHhcCcEEEEE
Confidence 45 44544445568999999999987653 11233457779999999774321 22333333333468887777
Q ss_pred EeccCCCCCCCccccccchHHHHHHhhcC
Q 011878 163 VVRASLSGEPHMRVIIENDNLLNIFSKKS 191 (475)
Q Consensus 163 ~i~~~~~~~~~~~~~~~n~~~l~~~~~~~ 191 (475)
+++. .+...|+.++...
T Consensus 140 g~~~------------~~~~~l~~la~~~ 156 (178)
T PF00092_consen 140 GIDN------------ADNEELRELASCP 156 (178)
T ss_dssp EESC------------CHHHHHHHHSHSS
T ss_pred ecCc------------CCHHHHHHHhCCC
Confidence 7621 2356777877543
No 53
>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=98.68 E-value=1.2e-06 Score=77.36 Aligned_cols=132 Identities=19% Similarity=0.188 Sum_probs=83.8
Q ss_pred EEEEEEecCCCcCCC-chHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCCHHHHHH
Q 011878 7 ALLLLLDVSPSMHSV-LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHLVQS 85 (475)
Q Consensus 7 ~~vflID~s~sM~~~-~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~~~~i~~ 85 (475)
.++|+||+|+||... +..++.++..++..- ...+|+++||.|+++.... ..+...--.+.++.
T Consensus 2 ~v~illD~SgSM~~~k~~~a~~~~~~l~~~~--~~~~~~v~li~F~~~~~~~--------------~~~~~~~~~~~~~~ 65 (152)
T cd01462 2 PVILLVDQSGSMYGAPEEVAKAVALALLRIA--LAENRDTYLILFDSEFQTK--------------IVDKTDDLEEPVEF 65 (152)
T ss_pred CEEEEEECCCCCCCCHHHHHHHHHHHHHHHH--HHcCCcEEEEEeCCCceEE--------------ecCCcccHHHHHHH
Confidence 478999999999853 556666666666532 2368999999999882111 11111111234555
Q ss_pred hhcCCCCCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEEEec
Q 011878 86 LKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIVVR 165 (475)
Q Consensus 86 L~~l~~~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l~~i~i~ 165 (475)
|..+..+. ..++.+||..+.+++.+. ......|++|||+..+-. . ..+...+...+..++.+.+++++
T Consensus 66 l~~~~~~g-gT~l~~al~~a~~~l~~~----~~~~~~ivliTDG~~~~~------~-~~~~~~~~~~~~~~~~v~~~~~g 133 (152)
T cd01462 66 LSGVQLGG-GTDINKALRYALELIERR----DPRKADIVLITDGYEGGV------S-DELLREVELKRSRVARFVALALG 133 (152)
T ss_pred HhcCCCCC-CcCHHHHHHHHHHHHHhc----CCCCceEEEECCCCCCCC------C-HHHHHHHHHHHhcCcEEEEEEec
Confidence 55554432 458999999999887652 123568999999954321 1 23333345556668999999997
Q ss_pred c
Q 011878 166 A 166 (475)
Q Consensus 166 ~ 166 (475)
.
T Consensus 134 ~ 134 (152)
T cd01462 134 D 134 (152)
T ss_pred C
Confidence 5
No 54
>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=98.56 E-value=3.2e-06 Score=91.30 Aligned_cols=154 Identities=16% Similarity=0.175 Sum_probs=100.4
Q ss_pred eEEEEEEecCCCcCC-CchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeec-CCCCHHH-
Q 011878 6 EALLLLLDVSPSMHS-VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDI-KVVDGHL- 82 (475)
Q Consensus 6 e~~vflID~s~sM~~-~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l-~~~~~~~- 82 (475)
.-++|+||+|+||.. .+..|+.++..++.+ -.++|+++||.|+++-.. +.+. ...+...
T Consensus 272 ~~vvfvlD~SgSM~g~~i~~ak~al~~~l~~---L~~~d~~~ii~F~~~~~~---------------~~~~~~~~~~~~~ 333 (596)
T TIGR03788 272 RELVFVIDTSGSMAGESIEQAKSALLLALDQ---LRPGDRFNIIQFDSDVTL---------------LFPVPVPATAHNL 333 (596)
T ss_pred ceEEEEEECCCCCCCccHHHHHHHHHHHHHh---CCCCCEEEEEEECCcceE---------------eccccccCCHHHH
Confidence 458999999999975 577788877776663 368999999999988321 1221 1233322
Q ss_pred ---HHHhhcCCCCCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEE
Q 011878 83 ---VQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRM 159 (475)
Q Consensus 83 ---i~~L~~l~~~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l 159 (475)
.+.|..+..+ +.+++..||..|+++... ......++|+|||||.... ...+...++. ...++.+
T Consensus 334 ~~a~~~i~~l~a~-GgT~l~~aL~~a~~~~~~---~~~~~~~~iillTDG~~~~--------~~~~~~~~~~-~~~~~ri 400 (596)
T TIGR03788 334 ARARQFVAGLQAD-GGTEMAGALSAALRDDGP---ESSGALRQVVFLTDGAVGN--------EDALFQLIRT-KLGDSRL 400 (596)
T ss_pred HHHHHHHhhCCCC-CCccHHHHHHHHHHhhcc---cCCCceeEEEEEeCCCCCC--------HHHHHHHHHH-hcCCceE
Confidence 3446666554 345899999998876321 1124568899999996421 1233333322 2346789
Q ss_pred EEEEeccCCCCCCCccccccchHHHHHHhhcCCCeEeehhhH
Q 011878 160 KNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDST 201 (475)
Q Consensus 160 ~~i~i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~~~~~~~ 201 (475)
.+||++.. .|..+|+.+|...+|.+..+.+.
T Consensus 401 ~tvGiG~~-----------~n~~lL~~lA~~g~G~~~~i~~~ 431 (596)
T TIGR03788 401 FTVGIGSA-----------PNSYFMRKAAQFGRGSFTFIGST 431 (596)
T ss_pred EEEEeCCC-----------cCHHHHHHHHHcCCCEEEECCCH
Confidence 99999641 24688999999988876654443
No 55
>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=98.29 E-value=1.6e-05 Score=72.24 Aligned_cols=149 Identities=14% Similarity=0.195 Sum_probs=111.2
Q ss_pred EEecCCCcCCC------chHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCCHHHHH
Q 011878 11 LLDVSPSMHSV------LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHLVQ 84 (475)
Q Consensus 11 lID~s~sM~~~------~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~~~~i~ 84 (475)
+||+|.+|.+. +.-.++++..|++...-.+|--.+|||........ .+.++.-.-.+.++
T Consensus 1 viD~S~~m~~~D~~PtRl~~~~~~l~~Fv~eff~qNPiSqlgii~~~~~~a~--------------~ls~lsgn~~~h~~ 66 (193)
T PF04056_consen 1 VIDMSEAMREKDLKPTRLQCVLKALEEFVREFFDQNPISQLGIIVMRDGRAE--------------RLSELSGNPQEHIE 66 (193)
T ss_pred CeechHhHHhCcCCccHHHHHHHHHHHHHHHHHhcCChhheeeeeeecceeE--------------EeeecCCCHHHHHH
Confidence 58999999863 56678888999998888999999999998866322 24566655555677
Q ss_pred HhhcCCCC--CCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEE
Q 011878 85 SLKHLPQG--TCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNI 162 (475)
Q Consensus 85 ~L~~l~~~--~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l~~i 162 (475)
.|+++... .++..+..||-.|...|.. . +....|.|++|.-.-.-++ ..++...++.|++.+|++.+|
T Consensus 67 ~L~~~~~~~~~G~~SLqN~Le~A~~~L~~-~--p~~~srEIlvi~gSl~t~D-------p~di~~ti~~l~~~~IrvsvI 136 (193)
T PF04056_consen 67 ALKKLRKLEPSGEPSLQNGLEMARSSLKH-M--PSHGSREILVIFGSLTTCD-------PGDIHETIESLKKENIRVSVI 136 (193)
T ss_pred HHHHhccCCCCCChhHHHHHHHHHHHHhh-C--ccccceEEEEEEeecccCC-------chhHHHHHHHHHHcCCEEEEE
Confidence 77776532 3345788999999998864 2 2356788888775444332 245778889999999999999
Q ss_pred EeccCCCCCCCccccccchHHHHHHhhcCCCeEe
Q 011878 163 VVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTL 196 (475)
Q Consensus 163 ~i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~~ 196 (475)
++.. .-..++.+++.++|.|.
T Consensus 137 ~laa-------------Ev~I~k~i~~~T~G~y~ 157 (193)
T PF04056_consen 137 SLAA-------------EVYICKKICKETGGTYG 157 (193)
T ss_pred EEhH-------------HHHHHHHHHHhhCCEEE
Confidence 9953 13688999999999875
No 56
>KOG2884 consensus 26S proteasome regulatory complex, subunit RPN10/PSMD4 [Posttranslational modification, protein turnover, chaperones]
Probab=98.21 E-value=7e-05 Score=67.45 Aligned_cols=138 Identities=17% Similarity=0.304 Sum_probs=102.8
Q ss_pred ceEEEEEEecCCCcCC------CchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCC
Q 011878 5 REALLLLLDVSPSMHS------VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV 78 (475)
Q Consensus 5 ke~~vflID~s~sM~~------~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~ 78 (475)
-|+|++|||=|.-|.. +|..=++.+..+.+.|+-++|-..|||+..... ++.|+..++.-
T Consensus 3 lEatmi~iDNse~mrNgDy~PtRf~aQ~daVn~v~~~K~~snpEntvGiitla~a--------------~~~vLsT~T~d 68 (259)
T KOG2884|consen 3 LEATMICIDNSEYMRNGDYLPTRFQAQKDAVNLVCQAKLRSNPENTVGIITLANA--------------SVQVLSTLTSD 68 (259)
T ss_pred cceEEEEEeChHHhhcCCCChHHHHHHHHHHHHHHHhhhcCCcccceeeEeccCC--------------Cceeeeecccc
Confidence 4899999999999875 355568899999999999999999999987765 23334445444
Q ss_pred CHHHHHHhhcCCCCCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcE
Q 011878 79 DGHLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLR 158 (475)
Q Consensus 79 ~~~~i~~L~~l~~~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~ 158 (475)
--..+-.++.++... ..++..+|..|...|+.+ ..|....||++|-. +|... .+..+-.+++.|+..+|.
T Consensus 69 ~gkils~lh~i~~~g-~~~~~~~i~iA~lalkhR--qnk~~~~riVvFvG--Spi~e-----~ekeLv~~akrlkk~~Va 138 (259)
T KOG2884|consen 69 RGKILSKLHGIQPHG-KANFMTGIQIAQLALKHR--QNKNQKQRIVVFVG--SPIEE-----SEKELVKLAKRLKKNKVA 138 (259)
T ss_pred chHHHHHhcCCCcCC-cccHHHHHHHHHHHHHhh--cCCCcceEEEEEec--Ccchh-----hHHHHHHHHHHHHhcCee
Confidence 444566666665532 458999999998777653 33456788999943 45442 345888999999999999
Q ss_pred EEEEEecc
Q 011878 159 MKNIVVRA 166 (475)
Q Consensus 159 l~~i~i~~ 166 (475)
+.+|.++.
T Consensus 139 idii~FGE 146 (259)
T KOG2884|consen 139 IDIINFGE 146 (259)
T ss_pred EEEEEecc
Confidence 99999864
No 57
>COG5148 RPN10 26S proteasome regulatory complex, subunit RPN10/PSMD4 [Posttranslational modification, protein turnover, chaperones]
Probab=98.10 E-value=0.00014 Score=63.86 Aligned_cols=135 Identities=13% Similarity=0.246 Sum_probs=99.4
Q ss_pred ceEEEEEEecCCCcCC------CchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCC
Q 011878 5 REALLLLLDVSPSMHS------VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV 78 (475)
Q Consensus 5 ke~~vflID~s~sM~~------~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~ 78 (475)
-|++|++||-|.-|.. +|+.-++.+..++++|+=.+|-..||||-.+....+. |..+
T Consensus 3 lEatvvliDNse~s~NgDy~ptRFeAQkd~ve~if~~K~ndnpEntiGli~~~~a~p~v-----------------lsT~ 65 (243)
T COG5148 3 LEATVVLIDNSEASQNGDYLPTRFEAQKDAVESIFSKKFNDNPENTIGLIPLVQAQPNV-----------------LSTP 65 (243)
T ss_pred cceEEEEEeChhhhhcCCCCcHHHHHHHHHHHHHHHHHhcCCccceeeeeecccCCcch-----------------hccc
Confidence 4899999999988765 3666689999999999988999999999887663221 3334
Q ss_pred CHHH---HHHhhcCCCCCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhc
Q 011878 79 DGHL---VQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAF 155 (475)
Q Consensus 79 ~~~~---i~~L~~l~~~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~ 155 (475)
+.+. +..|+.++.. +..++.++|..|...|+.+ ..+....||+.|-. +|... +++.+-.+++.|+.+
T Consensus 66 T~~~gkilt~lhd~~~~-g~a~~~~~lqiaql~lkhR--~nk~q~qriVaFvg--Spi~e-----sedeLirlak~lkkn 135 (243)
T COG5148 66 TKQRGKILTFLHDIRLH-GGADIMRCLQIAQLILKHR--DNKGQRQRIVAFVG--SPIQE-----SEDELIRLAKQLKKN 135 (243)
T ss_pred hhhhhHHHHHhcccccc-CcchHHHHHHHHHHHHhcc--cCCccceEEEEEec--Ccccc-----cHHHHHHHHHHHHhc
Confidence 4443 4445554431 2358999999998887653 34456788998853 44432 347888899999999
Q ss_pred CcEEEEEEecc
Q 011878 156 GLRMKNIVVRA 166 (475)
Q Consensus 156 ~I~l~~i~i~~ 166 (475)
||.+..|.++.
T Consensus 136 nVAidii~fGE 146 (243)
T COG5148 136 NVAIDIIFFGE 146 (243)
T ss_pred CeeEEEEehhh
Confidence 99999999863
No 58
>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=98.05 E-value=0.00014 Score=67.33 Aligned_cols=136 Identities=14% Similarity=0.152 Sum_probs=81.4
Q ss_pred EEEEEEecCCCcCCC--------chHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCC
Q 011878 7 ALLLLLDVSPSMHSV--------LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV 78 (475)
Q Consensus 7 ~~vflID~s~sM~~~--------~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~ 78 (475)
-++|+||+|.||... +..|++++..+.. .+.....|.+++++|.+.... +.++.
T Consensus 4 dvv~~ID~SgSM~~~~~~~~~~k~~~ak~~~~~l~~-~~~~~D~d~i~l~~f~~~~~~---------------~~~~~-- 65 (199)
T cd01457 4 DYTLLIDKSGSMAEADEAKERSRWEEAQESTRALAR-KCEEYDSDGITVYLFSGDFRR---------------YDNVN-- 65 (199)
T ss_pred CEEEEEECCCcCCCCCCCCCchHHHHHHHHHHHHHH-HHHhcCCCCeEEEEecCCccc---------------cCCcC--
Confidence 467999999999853 5778888887775 223457899999999766311 11222
Q ss_pred CHHHHH-HhhcCCCCCCCCChhHHHHHHHHHHHHHhcc--CcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhh-
Q 011878 79 DGHLVQ-SLKHLPQGTCAGDFLDAIVVGVDMLIKKYGE--TYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVA- 154 (475)
Q Consensus 79 ~~~~i~-~L~~l~~~~~~gd~~daL~va~~~l~~~~~~--~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~- 154 (475)
...+. .+.++..+ +.+++..+|..+++.+...... .+...+.|++|||+... +. ....+.+...++.|.+
T Consensus 66 -~~~v~~~~~~~~p~-G~T~l~~~l~~a~~~~~~~~~~~~~~p~~~~vIiiTDG~~~-d~---~~~~~~i~~a~~~l~~~ 139 (199)
T cd01457 66 -SSKVDQLFAENSPD-GGTNLAAVLQDALNNYFQRKENGATCPEGETFLVITDGAPD-DK---DAVERVIIKASDELDAD 139 (199)
T ss_pred -HHHHHHHHhcCCCC-CcCcHHHHHHHHHHHHHHHHhhccCCCCceEEEEEcCCCCC-cH---HHHHHHHHHHHHhhccc
Confidence 33333 34455433 2368899999888654432211 11125789999999863 21 0011222333444433
Q ss_pred cCcEEEEEEecc
Q 011878 155 FGLRMKNIVVRA 166 (475)
Q Consensus 155 ~~I~l~~i~i~~ 166 (475)
.+|.+.+++++.
T Consensus 140 ~~i~i~~v~vG~ 151 (199)
T cd01457 140 NELAISFLQIGR 151 (199)
T ss_pred cCceEEEEEeCC
Confidence 379999999964
No 59
>PRK10997 yieM hypothetical protein; Provisional
Probab=97.52 E-value=0.0022 Score=66.53 Aligned_cols=132 Identities=14% Similarity=0.191 Sum_probs=86.3
Q ss_pred CCceEEEEEEecCCCcC-CCchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCC-C-
Q 011878 3 RTREALLLLLDVSPSMH-SVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV-D- 79 (475)
Q Consensus 3 ~~ke~~vflID~s~sM~-~~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~-~- 79 (475)
..|.-+++|||.|+||. .+...|+.++..++. +..+.+|.+++++|+++...- ++... +
T Consensus 321 ~~kGpiII~VDtSGSM~G~ke~~AkalAaAL~~--iAl~q~dr~~li~Fs~~i~~~----------------~l~~~~gl 382 (487)
T PRK10997 321 QPRGPFIVCVDTSGSMGGFNEQCAKAFCLALMR--IALAENRRCYIMLFSTEVVTY----------------ELTGPDGL 382 (487)
T ss_pred CCCCcEEEEEECCCCCCCCHHHHHHHHHHHHHH--HHHhcCCCEEEEEecCCceee----------------ccCCccCH
Confidence 35778999999999998 333445555555544 235789999999999863211 22211 1
Q ss_pred HHHHHHhhcCCCCCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhh-cCcE
Q 011878 80 GHLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVA-FGLR 158 (475)
Q Consensus 80 ~~~i~~L~~l~~~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~-~~I~ 158 (475)
.+.++.|.... .+.+|+..+|-.+++.+.+ +....--||+|||...+.. .+.+...++.|++ .+.+
T Consensus 383 ~~ll~fL~~~f--~GGTDl~~aL~~al~~l~~----~~~r~adIVVISDF~~~~~-------~eel~~~L~~Lk~~~~~r 449 (487)
T PRK10997 383 EQAIRFLSQSF--RGGTDLAPCLRAIIEKMQG----REWFDADAVVISDFIAQRL-------PDELVAKVKELQRQHQHR 449 (487)
T ss_pred HHHHHHHHHhc--CCCCcHHHHHHHHHHHHcc----cccCCceEEEECCCCCCCC-------hHHHHHHHHHHHHhcCcE
Confidence 23455554432 2346899999888887643 1122344999999976532 1456667778877 7889
Q ss_pred EEEEEec
Q 011878 159 MKNIVVR 165 (475)
Q Consensus 159 l~~i~i~ 165 (475)
+..+.++
T Consensus 450 f~~l~i~ 456 (487)
T PRK10997 450 FHAVAMS 456 (487)
T ss_pred EEEEEeC
Confidence 9988885
No 60
>COG4867 Uncharacterized protein with a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=97.46 E-value=0.0036 Score=62.04 Aligned_cols=151 Identities=16% Similarity=0.166 Sum_probs=100.1
Q ss_pred CceEEEEEEecCCCcCC--CchHHHH---HHHHHHHHHHhcC-CccEEEEEEEccCCcCccccccCCCcccEEEEeecCC
Q 011878 4 TREALLLLLDVSPSMHS--VLPDVEK---LCSRLIQKKLIYG-KNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKV 77 (475)
Q Consensus 4 ~ke~~vflID~s~sM~~--~~~~a~~---~~~~l~~~ki~~~-~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~ 77 (475)
.--+++++||+|-||.. ++.-++. ++..++. ++ +.|.+.+|+||-...+.+
T Consensus 462 t~aAvallvDtS~SM~~eGRw~PmKQtALALhHLv~----TrfrGD~l~~i~Fgr~A~~v~------------------- 518 (652)
T COG4867 462 TQAAVALLVDTSFSMVMEGRWLPMKQTALALHHLVC----TRFRGDALQIIAFGRYARTVT------------------- 518 (652)
T ss_pred cccceeeeeeccHHHHHhccCCchHHHHHHHHHHHH----hcCCCcceEEEeccchhcccC-------------------
Confidence 35689999999999953 3444443 3345555 54 899999999998743332
Q ss_pred CCHHHHHHhhcCC-CCCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCC-CCCCCc-h----hhHHHH--
Q 011878 78 VDGHLVQSLKHLP-QGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKD-PDVGTK-E----DQVSTI-- 148 (475)
Q Consensus 78 ~~~~~i~~L~~l~-~~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~-~~~~~~-~----~~~~~~-- 148 (475)
+.+|-.++ .+.+..++..||.+|-.+|.+|. +..+.|+++||+....-. +.++.. . -+..++
T Consensus 519 -----v~eLt~l~~v~eqgTNlhhaL~LA~r~l~Rh~----~~~~~il~vTDGePtAhle~~DG~~~~f~yp~DP~t~~~ 589 (652)
T COG4867 519 -----AAELTGLAGVYEQGTNLHHALALAGRHLRRHA----GAQPVVLVVTDGEPTAHLEDGDGTSVFFDYPPDPRTIAH 589 (652)
T ss_pred -----HHHHhcCCCccccccchHHHHHHHHHHHHhCc----ccCceEEEEeCCCccccccCCCCceEecCCCCChhHHHH
Confidence 46676665 34555688999999998888753 446899999998542211 111100 0 122222
Q ss_pred ----HHHHhhcCcEEEEEEeccCCCCCCCccccccchHHHHHHhhcCCCeEe
Q 011878 149 ----ARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTL 196 (475)
Q Consensus 149 ----~~~l~~~~I~l~~i~i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~~ 196 (475)
..++...|+.+++|-++.. + .=+.|+++++..+.|+++
T Consensus 590 Tvr~~d~~~r~G~q~t~FrLg~D------p----gL~~Fv~qva~rv~G~vv 631 (652)
T COG4867 590 TVRGFDDMARLGAQVTIFRLGSD------P----GLARFIDQVARRVQGRVV 631 (652)
T ss_pred HHHHHHHHHhccceeeEEeecCC------H----hHHHHHHHHHHHhCCeEE
Confidence 3456789999999998641 1 115889999999988765
No 61
>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=97.33 E-value=0.0074 Score=56.03 Aligned_cols=148 Identities=11% Similarity=0.141 Sum_probs=91.2
Q ss_pred eEEEEEEecCCCcCCCchHHH-HHHHHHHHHHH--------h--cCCccEEEEEEEccCCcCccccccCCCcccEEE-Ee
Q 011878 6 EALLLLLDVSPSMHSVLPDVE-KLCSRLIQKKL--------I--YGKNHEVGVILFGTEETENELTKEVGGYEHVKV-LQ 73 (475)
Q Consensus 6 e~~vflID~s~sM~~~~~~a~-~~~~~l~~~ki--------~--~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~-~~ 73 (475)
.=+||+||.+..|+.-++..+ +.+.-+++.-- + ...+-+.|||+|++...-. ...+ -.
T Consensus 14 ~~vVfvvEgTAalgpy~~~Lkt~Yl~P~le~f~~g~~~e~~~~~~~~~t~y~LVvf~t~d~~~----------~~~v~~~ 83 (226)
T PF11265_consen 14 AQVVFVVEGTAALGPYWNTLKTNYLDPILEYFNGGPIAERDFGGDYSNTEYGLVVFNTADCYP----------EPIVQRS 83 (226)
T ss_pred ceEEEEEecchhhhhhHHHHHHHHHHHHHHHhcCCCcccccccccCCCceEEEEEEeccCCCc----------ccceecc
Confidence 349999999999998766543 23333333221 0 1356899999999996432 2111 11
Q ss_pred ecCCCCHHHHHHhhcCCC-C---CCCCChhHHHHHHHHHHHHHhc-----cCcceeeEEEEEeCCCCCCCCCCCC---Cc
Q 011878 74 DIKVVDGHLVQSLKHLPQ-G---TCAGDFLDAIVVGVDMLIKKYG-----ETYKGKKHLCLITDALCPLKDPDVG---TK 141 (475)
Q Consensus 74 ~l~~~~~~~i~~L~~l~~-~---~~~gd~~daL~va~~~l~~~~~-----~~~~~~krI~l~Td~~~p~~~~~~~---~~ 141 (475)
..+.--...++.|+++.- | .....+.+||-.|+.+|..... .+....|+.+|++|- .|...+..+ ..
T Consensus 84 g~T~~~~~fl~~L~~I~f~GGG~e~~a~iaEGLa~AL~~fd~~~~~r~~~~~~~~~khcILI~nS-pP~~~p~~~~~~~~ 162 (226)
T PF11265_consen 84 GPTSSPQKFLQWLDAIQFSGGGFESCAAIAEGLAEALQCFDDFKQMRQQQQQTDVQKHCILICNS-PPYRLPVNECPQYS 162 (226)
T ss_pred CCcCCHHHHHHHHHccCcCCCCcccchhHHHHHHHHHHHhcchhhhccccCcccccceEEEEeCC-CCccccccCCCccc
Confidence 122222346777888742 2 1233589999999988763211 111257899999986 444432111 12
Q ss_pred hhhHHHHHHHHhhcCcEEEEEEe
Q 011878 142 EDQVSTIARQMVAFGLRMKNIVV 164 (475)
Q Consensus 142 ~~~~~~~~~~l~~~~I~l~~i~i 164 (475)
...+++.+..+.+.+|.|.+|..
T Consensus 163 ~~~~d~la~~~~~~~I~LSiisP 185 (226)
T PF11265_consen 163 GKTCDQLAVLISERNISLSIISP 185 (226)
T ss_pred CCCHHHHHHHHHhcCceEEEEcC
Confidence 24678888999999999999975
No 62
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=97.20 E-value=0.0087 Score=57.37 Aligned_cols=154 Identities=15% Similarity=0.210 Sum_probs=100.6
Q ss_pred EEEEEEecCCCcCCC------chHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCCH
Q 011878 7 ALLLLLDVSPSMHSV------LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDG 80 (475)
Q Consensus 7 ~~vflID~s~sM~~~------~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~~ 80 (475)
.++++||+|..|.+. +....+.+..|+..-.=.+|-..+|+|......+.. +.++.-.--
T Consensus 62 hl~iviD~S~am~e~Df~P~r~a~~~K~le~Fv~eFFdQNPiSQigii~~k~g~A~~--------------lt~ltgnp~ 127 (378)
T KOG2807|consen 62 HLYIVIDCSRAMEEKDFRPSRFANVIKYLEGFVPEFFDQNPISQIGIISIKDGKADR--------------LTDLTGNPR 127 (378)
T ss_pred eEEEEEEhhhhhhhccCCchHHHHHHHHHHHHHHHHhccCchhheeEEEEecchhhH--------------HHHhcCCHH
Confidence 578999999999763 344566666666655447899999999988654332 122221122
Q ss_pred HHHHHhhcCCCCCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEE
Q 011878 81 HLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMK 160 (475)
Q Consensus 81 ~~i~~L~~l~~~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l~ 160 (475)
..|+.|..+....+...+.+||-.|...|+. . +.-..|-|+++-..-+..+ ..++-..++.|+..+|++.
T Consensus 128 ~hI~aL~~~~~~~g~fSLqNaLe~a~~~Lk~-~--p~H~sREVLii~sslsT~D-------Pgdi~~tI~~lk~~kIRvs 197 (378)
T KOG2807|consen 128 IHIHALKGLTECSGDFSLQNALELAREVLKH-M--PGHVSREVLIIFSSLSTCD-------PGDIYETIDKLKAYKIRVS 197 (378)
T ss_pred HHHHHHhcccccCCChHHHHHHHHHHHHhcC-C--CcccceEEEEEEeeecccC-------cccHHHHHHHHHhhCeEEE
Confidence 3577777776444455678888888887654 1 1233455555433222221 1346666788999999999
Q ss_pred EEEeccCCCCCCCccccccchHHHHHHhhcCCCeEee
Q 011878 161 NIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLF 197 (475)
Q Consensus 161 ~i~i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~~~ 197 (475)
+||+.. + -.+.+.++++++|.|.-
T Consensus 198 vIgLsa----E---------v~icK~l~kaT~G~Y~V 221 (378)
T KOG2807|consen 198 VIGLSA----E---------VFICKELCKATGGRYSV 221 (378)
T ss_pred EEeech----h---------HHHHHHHHHhhCCeEEE
Confidence 999943 1 36778899999997653
No 63
>COG4245 TerY Uncharacterized protein encoded in toxicity protection region of plasmid R478, contains von Willebrand factor (vWF) domain [General function prediction only]
Probab=97.04 E-value=0.012 Score=52.32 Aligned_cols=106 Identities=21% Similarity=0.211 Sum_probs=63.3
Q ss_pred ceEEEEEEecCCCcCCC-chHHHHHHHHHHHHH---HhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCCH
Q 011878 5 REALLLLLDVSPSMHSV-LPDVEKLCSRLIQKK---LIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDG 80 (475)
Q Consensus 5 ke~~vflID~s~sM~~~-~~~a~~~~~~l~~~k---i~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~~ 80 (475)
|=-++|+||+|.||-.. ++..-.++..++... -..-..-+++||.|++.. .+.+|+..
T Consensus 3 RlP~~lllDtSgSM~Ge~IealN~Glq~m~~~Lkqdp~Ale~v~lsIVTF~~~a---------------~~~~pf~~--- 64 (207)
T COG4245 3 RLPCYLLLDTSGSMIGEPIEALNAGLQMMIDTLKQDPYALERVELSIVTFGGPA---------------RVIQPFTD--- 64 (207)
T ss_pred CCCEEEEEecCcccccccHHHHHHHHHHHHHHHHhChhhhheeEEEEEEecCcc---------------eEEechhh---
Confidence 33578999999999764 333323333333222 122357899999999842 12344431
Q ss_pred HHHHHhh--cCCCCCCCCChhHHHHHHHHHHHHHhc-----cCcceeeEEEEEeCCCC
Q 011878 81 HLVQSLK--HLPQGTCAGDFLDAIVVGVDMLIKKYG-----ETYKGKKHLCLITDALC 131 (475)
Q Consensus 81 ~~i~~L~--~l~~~~~~gd~~daL~va~~~l~~~~~-----~~~~~~krI~l~Td~~~ 131 (475)
+..+. .|..+ +...+..||-.|.+++.++.. .++.+..-+||+||+.-
T Consensus 65 --~~nF~~p~L~a~-GgT~lGaAl~~a~d~Ie~~~~~~~a~~kgdyrP~vfLiTDG~P 119 (207)
T COG4245 65 --AANFNPPILTAQ-GGTPLGAALTLALDMIEERKRKYDANGKGDYRPWVFLITDGEP 119 (207)
T ss_pred --HhhcCCCceecC-CCCchHHHHHHHHHHHHHHHhhcccCCccccceEEEEecCCCc
Confidence 11111 12222 245789999999999877521 13456777999999955
No 64
>COG2425 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=96.84 E-value=0.018 Score=58.83 Aligned_cols=130 Identities=20% Similarity=0.241 Sum_probs=86.3
Q ss_pred eEEEEEEecCCCcCCCchH-HHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCC---HH
Q 011878 6 EALLLLLDVSPSMHSVLPD-VEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVD---GH 81 (475)
Q Consensus 6 e~~vflID~s~sM~~~~~~-a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~---~~ 81 (475)
.-+++|||-|+||+..-.. |+.++..+++.- -..+=.+.+++|.+.- +-+.+..+. -+
T Consensus 273 GpvilllD~SGSM~G~~e~~AKAvalAl~~~a--laenR~~~~~lF~s~~----------------~~~el~~k~~~~~e 334 (437)
T COG2425 273 GPVILLLDKSGSMSGFKEQWAKAVALALMRIA--LAENRDCYVILFDSEV----------------IEYELYEKKIDIEE 334 (437)
T ss_pred CCEEEEEeCCCCcCCcHHHHHHHHHHHHHHHH--HHhccceEEEEecccc----------------eeeeecCCccCHHH
Confidence 4589999999999975433 455555555522 3445568999999831 012233333 34
Q ss_pred HHHHhhcCCCCCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEE
Q 011878 82 LVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKN 161 (475)
Q Consensus 82 ~i~~L~~l~~~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l~~ 161 (475)
.|+.|.....|+ +|+..+|..|++-++++ +...-.|++|||+.+++. .+-+....+..+..+.++.-
T Consensus 335 ~i~fL~~~f~GG--TD~~~~l~~al~~~k~~----~~~~adiv~ITDg~~~~~-------~~~~~~v~e~~k~~~~rl~a 401 (437)
T COG2425 335 LIEFLSYVFGGG--TDITKALRSALEDLKSR----ELFKADIVVITDGEDERL-------DDFLRKVKELKKRRNARLHA 401 (437)
T ss_pred HHHHHhhhcCCC--CChHHHHHHHHHHhhcc----cccCCCEEEEeccHhhhh-------hHHHHHHHHHHHHhhceEEE
Confidence 556665555554 79999999999987652 234478999999998763 13344455555578899999
Q ss_pred EEecc
Q 011878 162 IVVRA 166 (475)
Q Consensus 162 i~i~~ 166 (475)
+.|+.
T Consensus 402 V~I~~ 406 (437)
T COG2425 402 VLIGG 406 (437)
T ss_pred EEecC
Confidence 98864
No 65
>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=96.71 E-value=0.018 Score=54.21 Aligned_cols=128 Identities=20% Similarity=0.136 Sum_probs=76.4
Q ss_pred ce-EEEEEEecCCCcCCCchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCC-HHH
Q 011878 5 RE-ALLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVD-GHL 82 (475)
Q Consensus 5 ke-~~vflID~s~sM~~~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~-~~~ 82 (475)
+. -+|+|+|+|+||...-...+..+..+.+ . ...+.+++|+++-.... ..+...+ .+.
T Consensus 56 ~~~~lvvl~DvSGSM~~~s~~~l~~~~~l~~----~--~~~~~~f~F~~~l~~vT--------------~~l~~~~~~~~ 115 (222)
T PF05762_consen 56 KPRRLVVLCDVSGSMAGYSEFMLAFLYALQR----Q--FRRVRVFVFSTRLTEVT--------------PLLRRRDPEEA 115 (222)
T ss_pred CCccEEEEEeCCCChHHHHHHHHHHHHHHHH----h--CCCEEEEEEeeehhhhh--------------hhhccCCHHHH
Confidence 44 7999999999998633333444444433 2 22899999998743211 1122111 234
Q ss_pred HHHhhcCCC-CCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEE
Q 011878 83 VQSLKHLPQ-GTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKN 161 (475)
Q Consensus 83 i~~L~~l~~-~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l~~ 161 (475)
+..+..... ..+.+|+..||-.+.+.+.. .......++++||+...- ....+....+.|+..+.++..
T Consensus 116 l~~~~~~~~~~~GgTdi~~aL~~~~~~~~~----~~~~~t~vvIiSDg~~~~-------~~~~~~~~l~~l~~r~~rviw 184 (222)
T PF05762_consen 116 LARLSALVQSFGGGTDIGQALREFLRQYAR----PDLRRTTVVIISDGWDTN-------DPEPLAEELRRLRRRGRRVIW 184 (222)
T ss_pred HHHHHhhccCCCCccHHHHHHHHHHHHhhc----ccccCcEEEEEecccccC-------ChHHHHHHHHHHHHhCCEEEE
Confidence 555543222 23346888888777766432 223456688999983321 225677777889999887666
Q ss_pred EE
Q 011878 162 IV 163 (475)
Q Consensus 162 i~ 163 (475)
+.
T Consensus 185 Ln 186 (222)
T PF05762_consen 185 LN 186 (222)
T ss_pred EC
Confidence 54
No 66
>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=96.64 E-value=0.093 Score=47.94 Aligned_cols=136 Identities=18% Similarity=0.230 Sum_probs=77.6
Q ss_pred eEEEEEEecCCCcCCCchH--HHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCCH-HH
Q 011878 6 EALLLLLDVSPSMHSVLPD--VEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDG-HL 82 (475)
Q Consensus 6 e~~vflID~s~sM~~~~~~--a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~~-~~ 82 (475)
--+.++||.|+||...+.. +-.++.+++-=-.--.+.-.|=+++|+++...-+. ++.-+. ..
T Consensus 2 ArV~LVLD~SGSM~~~yk~G~vQ~~~Er~lalA~~~DdDG~i~v~~Fs~~~~~~~~---------------vt~~~~~~~ 66 (200)
T PF10138_consen 2 ARVYLVLDISGSMRPLYKDGTVQRVVERILALAAQFDDDGEIDVWFFSTEFDRLPD---------------VTLDNYEGY 66 (200)
T ss_pred cEEEEEEeCCCCCchhhhCccHHHHHHHHHHHHhhcCCCCceEEEEeCCCCCcCCC---------------cCHHHHHHH
Confidence 3588999999999876543 11222222211111345556999999998543321 111111 12
Q ss_pred HHHhhc-CC--CCCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEE
Q 011878 83 VQSLKH-LP--QGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRM 159 (475)
Q Consensus 83 i~~L~~-l~--~~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l 159 (475)
++.+.. +. ...+..+...+|--.++....+-. ...---|+++|||... ++..+.+++....+..|..
T Consensus 67 v~~~~~~~~~~~~~G~t~y~~vm~~v~~~y~~~~~--~~~P~~VlFiTDG~~~--------~~~~~~~~i~~as~~pifw 136 (200)
T PF10138_consen 67 VDELHAGLPDWGRMGGTNYAPVMEDVLDHYFKREP--SDAPALVLFITDGGPD--------DRRAIEKLIREASDEPIFW 136 (200)
T ss_pred HHHHhccccccCCCCCcchHHHHHHHHHHHhhcCC--CCCCeEEEEEecCCcc--------chHHHHHHHHhccCCCeeE
Confidence 333322 10 111235777788777776553211 1112357777999753 2366888888889999999
Q ss_pred EEEEecc
Q 011878 160 KNIVVRA 166 (475)
Q Consensus 160 ~~i~i~~ 166 (475)
.+++++.
T Consensus 137 qFVgiG~ 143 (200)
T PF10138_consen 137 QFVGIGD 143 (200)
T ss_pred EEEEecC
Confidence 9999974
No 67
>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=96.34 E-value=0.1 Score=49.79 Aligned_cols=172 Identities=15% Similarity=0.164 Sum_probs=97.1
Q ss_pred eEEEEEEecCCCcCC--CchHHHHHHHHHHHHHHhcC-CccEEEEEEEccCCcCccccccCCCcccEEEEeecCCC----
Q 011878 6 EALLLLLDVSPSMHS--VLPDVEKLCSRLIQKKLIYG-KNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV---- 78 (475)
Q Consensus 6 e~~vflID~s~sM~~--~~~~a~~~~~~l~~~ki~~~-~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~---- 78 (475)
-..+|+||+|..=-+ .++.+++.+...+.. +-.. ++-+||+|.|++.=.--++.... .-.+..+.-+++.+
T Consensus 4 p~~~FvIDvs~~a~~~g~~~~~~~si~~~L~~-lp~~~~~~~VgiITfd~~v~~y~l~~~~-~~~q~~vv~dl~d~f~P~ 81 (244)
T cd01479 4 AVYVFLIDVSYNAIKSGLLATACEALLSNLDN-LPGDDPRTRVGFITFDSTLHFFNLKSSL-EQPQMMVVSDLDDPFLPL 81 (244)
T ss_pred CEEEEEEEccHHHHhhChHHHHHHHHHHHHHh-cCCCCCCeEEEEEEECCeEEEEECCCCC-CCCeEEEeeCcccccCCC
Confidence 367999999864332 255667777777763 1122 56899999999864322221110 11122233233221
Q ss_pred -----------CHHHHHHhhcCCC----C-CCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCC-----C
Q 011878 79 -----------DGHLVQSLKHLPQ----G-TCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDP-----D 137 (475)
Q Consensus 79 -----------~~~~i~~L~~l~~----~-~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~-----~ 137 (475)
......-|++|+. + .....+..||.+|..+|.. .+ =||++|+.+-...+.. .
T Consensus 82 ~~~~lv~l~e~~~~i~~lL~~L~~~~~~~~~~~~c~G~Al~~A~~lL~~-~G------GkIi~f~s~~pt~GpG~l~~~~ 154 (244)
T cd01479 82 PDGLLVNLKESRQVIEDLLDQIPEMFQDTKETESALGPALQAAFLLLKE-TG------GKIIVFQSSLPTLGAGKLKSRE 154 (244)
T ss_pred CcceeecHHHHHHHHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHh-cC------CEEEEEeCCCCCcCCcccccCc
Confidence 1111222333321 1 1224678999999998873 33 3788888764333310 0
Q ss_pred C----C---------CchhhHHHHHHHHhhcCcEEEEEEeccCCCCCCCccccccchHHHHHHhhcCCCeEe
Q 011878 138 V----G---------TKEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTL 196 (475)
Q Consensus 138 ~----~---------~~~~~~~~~~~~l~~~~I~l~~i~i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~~ 196 (475)
+ + ...+-+..++..+.+.||.+++|..... . -+-..+..++..++|.++
T Consensus 155 ~~~~~~~~~e~~~~~p~~~fY~~la~~~~~~~isvDlF~~~~~-----~-----~dla~l~~l~~~TGG~v~ 216 (244)
T cd01479 155 DPKLLSTDKEKQLLQPQTDFYKKLALECVKSQISVDLFLFSNQ-----Y-----VDVATLGCLSRLTGGQVY 216 (244)
T ss_pred cccccCchhhhhhcCcchHHHHHHHHHHHHcCeEEEEEEccCc-----c-----cChhhhhhhhhhcCceEE
Confidence 0 0 0124566789999999999999987421 1 113456677888999754
No 68
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.34 E-value=0.059 Score=52.12 Aligned_cols=179 Identities=11% Similarity=0.159 Sum_probs=114.7
Q ss_pred eEEEEEEecCCCcC---C------CchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcC----ccccc---cC-CCccc
Q 011878 6 EALLLLLDVSPSMH---S------VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETE----NELTK---EV-GGYEH 68 (475)
Q Consensus 6 e~~vflID~s~sM~---~------~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~----n~~~~---~~-~~y~~ 68 (475)
..++++||.+|.-- . .+..+++.+.-|+---+..+...+|+||..++.+.. ++..+ .. ....+
T Consensus 3 slL~vvlD~np~~W~~~~~~~~~~~l~~~l~sllvF~NahL~l~~~N~vaVIAs~~~~~~~LYps~~~~~~~~~~~~~~~ 82 (279)
T TIGR00627 3 SLLVVIIEANPCSWGMLALAHGKRTISKVLRAIVVFLNAHLAFNANNKLAVIASHSQDNKYLYPSTRCEDRNASELDPKR 82 (279)
T ss_pred cEEEEEEeCCHHHHHHHhhccCCCcHHHHHHHHHHHHHHHHhcCccCCEEEEEecCCcceEEecCCcccccccccccccc
Confidence 35789999998632 1 356778888888888888899999999999876543 11100 00 01111
Q ss_pred E--EEEeecCCCCHHHHHHhhcCCCC-------CCCCChhHHHHHHHHHHHHHhcc---CcceeeEEEEEeCCCCCCCCC
Q 011878 69 V--KVLQDIKVVDGHLVQSLKHLPQG-------TCAGDFLDAIVVGVDMLIKKYGE---TYKGKKHLCLITDALCPLKDP 136 (475)
Q Consensus 69 i--~~~~~l~~~~~~~i~~L~~l~~~-------~~~gd~~daL~va~~~l~~~~~~---~~~~~krI~l~Td~~~p~~~~ 136 (475)
+ ..+.++...+...++.|.++... ..++.+..||-.|+=.+++..+. ......||++|+-.++..
T Consensus 83 ~~~~~y~~f~~v~~~v~~~l~~l~~~~~~~~~~~~~s~lagals~ALcyinr~~~~~~~~~~~~~RIlii~~s~~~~--- 159 (279)
T TIGR00627 83 LRELLYRDFRTVDETIVEEIKPLMAHADKHMKKDSRTVLAGALSDALGYINRSEQSETASEKLKSRILVISITPDMA--- 159 (279)
T ss_pred ccchhccchhHHHHHHHHHHHHHHhhchhcccccccccchhHHHhhhhhhcccccccccCcCCcceEEEEECCCCch---
Confidence 1 12334555666677777664221 12445788888888776653221 124578999998743311
Q ss_pred CCCCchhhHHHHHHHHhhcCcEEEEEEeccCCCCCCCccccccchHHHHHHhhcCCCeEeehhhH
Q 011878 137 DVGTKEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDST 201 (475)
Q Consensus 137 ~~~~~~~~~~~~~~~l~~~~I~l~~i~i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~~~~~~~ 201 (475)
...-.+...+..+++.+|.+.+++++. + + ...++++++..++|.|..+.+.
T Consensus 160 ---~qYi~~mn~Ifaaqk~~I~Idv~~L~~----e-~------~~~~lqQa~~~TgG~Y~~~~~~ 210 (279)
T TIGR00627 160 ---LQYIPLMNCIFSAQKQNIPIDVVSIGG----D-F------TSGFLQQAADITGGSYLHVKKP 210 (279)
T ss_pred ---HHHHHHHHHHHHHHHcCceEEEEEeCC----c-c------ccHHHHHHHHHhCCEEeccCCH
Confidence 112344566788899999999999953 1 1 1478999999999988765443
No 69
>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=96.05 E-value=0.49 Score=44.96 Aligned_cols=175 Identities=13% Similarity=0.165 Sum_probs=98.0
Q ss_pred eEEEEEEecCCCc-CC-CchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCC-----
Q 011878 6 EALLLLLDVSPSM-HS-VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV----- 78 (475)
Q Consensus 6 e~~vflID~s~sM-~~-~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~----- 78 (475)
-+.+|+||+|..- .+ .++.+++.+...++.. =..++-+||+|.|++.=+--.+.... .-...+++.+++.+
T Consensus 4 p~~vFvID~s~~ai~~~~l~~~~~sl~~~l~~l-p~~~~~~igiITf~~~V~~~~~~~~~-~~~~~~v~~dl~d~f~p~~ 81 (239)
T cd01468 4 PVFVFVIDVSYEAIKEGLLQALKESLLASLDLL-PGDPRARVGLITYDSTVHFYNLSSDL-AQPKMYVVSDLKDVFLPLP 81 (239)
T ss_pred CEEEEEEEcchHhccccHHHHHHHHHHHHHHhC-CCCCCcEEEEEEeCCeEEEEECCCCC-CCCeEEEeCCCccCcCCCc
Confidence 4679999999752 22 3555667777777632 01278999999998643221111100 01233344343322
Q ss_pred ------CHH----HHHHhhcCCCC-------CCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCC---
Q 011878 79 ------DGH----LVQSLKHLPQG-------TCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDV--- 138 (475)
Q Consensus 79 ------~~~----~i~~L~~l~~~-------~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~--- 138 (475)
-++ ....|++|... .....+..||.+|..++.... ..=+|++|+.+-...+. +-
T Consensus 82 ~~~l~~~~e~~~~i~~~l~~l~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~~-----~gGkI~~f~sg~pt~Gp-G~l~~ 155 (239)
T cd01468 82 DRFLVPLSECKKVIHDLLEQLPPMFWPVPTHRPERCLGPALQAAFLLLKGTF-----AGGRIIVFQGGLPTVGP-GKLKS 155 (239)
T ss_pred CceeeeHHHHHHHHHHHHHhhhhhccccCCCCCcccHHHHHHHHHHHHhhcC-----CCceEEEEECCCCCCCC-Ccccc
Confidence 011 12223333221 112357889999999876521 24578888876443221 00
Q ss_pred ----------------CCchhhHHHHHHHHhhcCcEEEEEEeccCCCCCCCccccccchHHHHHHhhcCCCeEeeh
Q 011878 139 ----------------GTKEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFV 198 (475)
Q Consensus 139 ----------------~~~~~~~~~~~~~l~~~~I~l~~i~i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~~~~ 198 (475)
....+-+..++..+.+.||.+++|.... + . -+-..+..++..++|.++-.
T Consensus 156 ~~~~~~~~~~~e~~~~~~a~~fY~~la~~~~~~~isvdlF~~~~----~-~-----~dl~~l~~l~~~TGG~v~~y 221 (239)
T cd01468 156 REDKEPIRSHDEAQLLKPATKFYKSLAKECVKSGICVDLFAFSL----D-Y-----VDVATLKQLAKSTGGQVYLY 221 (239)
T ss_pred CcccccCCCccchhcccccHHHHHHHHHHHHHcCeEEEEEeccc----c-c-----cCHHHhhhhhhcCCceEEEe
Confidence 0112456788999999999999998742 1 1 11345666788889976543
No 70
>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=95.64 E-value=0.13 Score=49.12 Aligned_cols=176 Identities=13% Similarity=0.164 Sum_probs=93.0
Q ss_pred ceEEEEEEecCCC-cC-CCchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEee--------
Q 011878 5 REALLLLLDVSPS-MH-SVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQD-------- 74 (475)
Q Consensus 5 ke~~vflID~s~s-M~-~~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~-------- 74 (475)
.-+.+|+||+|.. .. ..++.+++.+...+... -..++.+||+|.|++.=.--.+.... ......+..+
T Consensus 3 pp~y~FvID~s~~av~~g~~~~~~~sl~~~l~~l-~~~~~~~vgiitfd~~V~~y~l~~~~-~~~~~~v~~dl~~~~~p~ 80 (243)
T PF04811_consen 3 PPVYVFVIDVSYEAVQSGLLQSLIESLKSALDSL-PGDERTRVGIITFDSSVHFYNLSSSL-SQPQMIVVSDLDDPFIPL 80 (243)
T ss_dssp --EEEEEEE-SHHHHHHTHHHHHHHHHHHHGCTS-STSTT-EEEEEEESSSEEEEETTTTS-SSTEEEEEHHTTSHHSST
T ss_pred CCEEEEEEECchhhhhccHHHHHHHHHHHHHHhc-cCCCCcEEEEEEeCCEEEEEECCCCc-CCCcccchHHHhhcccCC
Confidence 3478999999954 21 23566677777777532 24589999999998753222221110 1122223333
Q ss_pred -------cCCCCHH---HHHHhhcCCCCC----CCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCC-----
Q 011878 75 -------IKVVDGH---LVQSLKHLPQGT----CAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKD----- 135 (475)
Q Consensus 75 -------l~~~~~~---~i~~L~~l~~~~----~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~----- 135 (475)
+...... .++.|.++.... ....+..||.+|..+|.... ..=||++|+.+-...+.
T Consensus 81 ~~~llv~~~e~~~~i~~ll~~L~~~~~~~~~~~~~~c~G~Al~~A~~ll~~~~-----~gGkI~~F~s~~pt~G~Gg~l~ 155 (243)
T PF04811_consen 81 PDGLLVPLSECRDAIEELLESLPSIFPETAGKRPERCLGSALSAALSLLSSRN-----TGGKILVFTSGPPTYGPGGSLK 155 (243)
T ss_dssp SSSSSEETTTCHHHHHHHHHHHHHHSTT-TTB-----HHHHHHHHHHHHHHHT-----S-EEEEEEESS---SSSTTSS-
T ss_pred cccEEEEhHHhHHHHHHHHHHhhhhcccccccCccccHHHHHHHHHHHHhccc-----cCCEEEEEeccCCCCCCCceec
Confidence 2221111 233333322111 12367899999999987521 23578888766332221
Q ss_pred -CCC----C----------CchhhHHHHHHHHhhcCcEEEEEEeccCCCCCCCccccccchHHHHHHhhcCCCeEee
Q 011878 136 -PDV----G----------TKEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLF 197 (475)
Q Consensus 136 -~~~----~----------~~~~~~~~~~~~l~~~~I~l~~i~i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~~~ 197 (475)
..+ + ...+-+..++..+.+.||.+++|..... . -+-..+..++..++|.++.
T Consensus 156 ~~~~~~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~-----~-----~~l~tl~~l~~~TGG~l~~ 222 (243)
T PF04811_consen 156 KREDSSHYDTEKEKALLLPPANEFYKKLAEECSKQGISVDLFVFSSD-----Y-----VDLATLGPLARYTGGSLYY 222 (243)
T ss_dssp SBTTSCCCCHCTTHHCHSHSSSHHHHHHHHHHHHCTEEEEEEEECSS------------SHHHHTHHHHCTT-EEEE
T ss_pred ccccccccccccchhhhccccchHHHHHHHHHHhcCCEEEEEeecCC-----C-----CCcHhHHHHHHhCceeEEE
Confidence 000 0 0112578899999999999999987431 1 1235567788889998653
No 71
>KOG3768 consensus DEAD box RNA helicase [General function prediction only]
Probab=95.64 E-value=0.24 Score=51.49 Aligned_cols=109 Identities=24% Similarity=0.302 Sum_probs=66.6
Q ss_pred EEEEEEecCCCcCCC-------chHHHHHHHHHHHHHHhcC--CccEEEEEEEccCCcCccccccCCCcccEEEEeecCC
Q 011878 7 ALLLLLDVSPSMHSV-------LPDVEKLCSRLIQKKLIYG--KNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKV 77 (475)
Q Consensus 7 ~~vflID~s~sM~~~-------~~~a~~~~~~l~~~ki~~~--~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~ 77 (475)
+++|+||-|.||..+ |..|+.++..|++++-... -.|+.=++.|---.. +|.+ -...
T Consensus 3 i~lFllDTS~SM~qrah~~~tylD~AKgaVEtFiK~R~r~~~~~gdryml~TfeepP~------------~vk~--~~~~ 68 (888)
T KOG3768|consen 3 IFLFLLDTSGSMSQRAHPQFTYLDLAKGAVETFIKQRTRVGRETGDRYMLTTFEEPPK------------NVKV--ACEK 68 (888)
T ss_pred eEEEEEecccchhhhccCCchhhHHHHHHHHHHHHHHhccccccCceEEEEecccCch------------hhhh--HHhh
Confidence 789999999999875 5678999999999875432 356666666543211 1111 1223
Q ss_pred CCHHHHHHhhcCCCCCCCCChhHHHHHHHHHHHHH--------hcc-C---cceeeEEEEEeCC
Q 011878 78 VDGHLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKK--------YGE-T---YKGKKHLCLITDA 129 (475)
Q Consensus 78 ~~~~~i~~L~~l~~~~~~gd~~daL~va~~~l~~~--------~~~-~---~~~~krI~l~Td~ 129 (475)
..+-.+++|++|......+-...++.-|.++|.-. ++. + +..--.|++||||
T Consensus 69 ~~a~~~~eik~l~a~~~s~~~~~~~t~AFdlLnlnR~qtGID~yGqGR~pf~lEP~~iI~iTDG 132 (888)
T KOG3768|consen 69 LGAVVIEEIKKLHAPYGSCQLHHAITEAFDLLNLNRVQTGIDGYGQGRLPFNLEPVTIILITDG 132 (888)
T ss_pred cccHHHHHHHhhcCccchhhhhHHHHHHhhhhhhhhhhhcccccccccCccccCceEEEEEecC
Confidence 44567889999875433333344555577765321 111 0 1234569999999
No 72
>COG4548 NorD Nitric oxide reductase activation protein [Inorganic ion transport and metabolism]
Probab=95.19 E-value=0.082 Score=54.41 Aligned_cols=151 Identities=18% Similarity=0.184 Sum_probs=80.5
Q ss_pred EEEEEEecCCCcCCCchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCCHHHH-HH
Q 011878 7 ALLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHLV-QS 85 (475)
Q Consensus 7 ~~vflID~s~sM~~~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~~~~i-~~ 85 (475)
++.++||||.||+..+.+.++++..+.+....-. +|+=.+|-...-+..++..-.+.-|.++.+++...-+.+ -+
T Consensus 448 a~TLLvD~S~St~a~mdetrRvidl~~eaL~~la----~~~qa~gd~~~~~~fts~rr~~vri~tvk~FDes~~~~~~~R 523 (637)
T COG4548 448 AFTLLVDVSASTDAKMDETRRVIDLFHEALLVLA----HGHQALGDSEDILDFTSRRRPWVRINTVKDFDESMGETVGPR 523 (637)
T ss_pred eeEEEeecccchHHHhhhhhhhHHHHHHHHHHhh----chhhhhCCHHHhcCchhhcCcceeeeeeeccccccccccchh
Confidence 5778999999999988777666665554332221 111122222211211111112233334444433322221 12
Q ss_pred hhcCCCCCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCC-CchhhHHHHHHHHhhcCcEEEEEEe
Q 011878 86 LKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVG-TKEDQVSTIARQMVAFGLRMKNIVV 164 (475)
Q Consensus 86 L~~l~~~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~-~~~~~~~~~~~~l~~~~I~l~~i~i 164 (475)
|..|..+. ..-..-||-.|..-|.. +....|-++|||||.-+--+-.++ ...++.+..+...+..||.+..+.+
T Consensus 524 ImALePg~-ytR~G~AIR~As~kL~~----rpq~qklLivlSDGkPnd~d~YEgr~gIeDTr~AV~eaRk~Gi~VF~Vtl 598 (637)
T COG4548 524 IMALEPGY-YTRDGAAIRHASAKLME----RPQRQKLLIVLSDGKPNDFDHYEGRFGIEDTREAVIEARKSGIEVFNVTL 598 (637)
T ss_pred heecCccc-cccccHHHHHHHHHHhc----CcccceEEEEecCCCcccccccccccchhhHHHHHHHHHhcCceEEEEEe
Confidence 33343332 11345678777776543 224467799999996543220111 2235677778889999999888888
Q ss_pred cc
Q 011878 165 RA 166 (475)
Q Consensus 165 ~~ 166 (475)
+.
T Consensus 599 d~ 600 (637)
T COG4548 599 DR 600 (637)
T ss_pred cc
Confidence 64
No 73
>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=94.75 E-value=1.5 Score=42.46 Aligned_cols=175 Identities=15% Similarity=0.164 Sum_probs=96.2
Q ss_pred eEEEEEEecCCCcCCCchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccE----------------
Q 011878 6 EALLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHV---------------- 69 (475)
Q Consensus 6 e~~vflID~s~sM~~~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i---------------- 69 (475)
-..+|+||++..=- .++.+++.+...+.. --++.+||+|.||+.=.-.++..+ ++...
T Consensus 4 p~~vFviDvs~~~~-el~~l~~sl~~~L~~---lP~~a~VGlITfd~~V~~~~L~~~--~~~~~~vf~g~~~~~~~~~~~ 77 (267)
T cd01478 4 PVFLFVVDTCMDEE-ELDALKESLIMSLSL---LPPNALVGLITFGTMVQVHELGFE--ECSKSYVFRGNKDYTAKQIQD 77 (267)
T ss_pred CEEEEEEECccCHH-HHHHHHHHHHHHHHh---CCCCCEEEEEEECCEEEEEEcCCC--cCceeeeccCCccCCHHHHHH
Confidence 36799999997522 245555555555542 235789999999987432222110 00000
Q ss_pred -----------------------------EEEeecCCCCHHHHHHhhcCCCC--------CCCCChhHHHHHHHHHHHHH
Q 011878 70 -----------------------------KVLQDIKVVDGHLVQSLKHLPQG--------TCAGDFLDAIVVGVDMLIKK 112 (475)
Q Consensus 70 -----------------------------~~~~~l~~~~~~~i~~L~~l~~~--------~~~gd~~daL~va~~~l~~~ 112 (475)
..+.|+.........-|++|+.. ........||.+|..++..-
T Consensus 78 ~l~~~~~~~~~~~~~~~~~~~~~~p~~~~~flvpl~e~~~~i~~lLe~L~~~~~~~~~~~r~~r~~G~Al~~A~~ll~~~ 157 (267)
T cd01478 78 MLGLGGPAMRPSASQHPGAGNPLPSAAASRFLLPVSQCEFTLTDLLEQLQPDPWPVPAGHRPLRCTGVALSIAVGLLEAC 157 (267)
T ss_pred HhccccccccccccCcCCccccccccccccEEEEHHHHHHHHHHHHHhCcccccccCCCCCCCCchHHHHHHHHHHHHhh
Confidence 12233333222333335555332 11235789999999988752
Q ss_pred hccCcceeeEEEEEeCCCCCCCCC-----C-----------CC-------CchhhHHHHHHHHhhcCcEEEEEEeccCCC
Q 011878 113 YGETYKGKKHLCLITDALCPLKDP-----D-----------VG-------TKEDQVSTIARQMVAFGLRMKNIVVRASLS 169 (475)
Q Consensus 113 ~~~~~~~~krI~l~Td~~~p~~~~-----~-----------~~-------~~~~~~~~~~~~l~~~~I~l~~i~i~~~~~ 169 (475)
+ + ...=||++|+.+-...+.- + +. ...+-...++..+.+.||.+++|....
T Consensus 158 ~--~-~~gGki~~F~sg~pT~GpG~l~~r~~~~~~r~~~d~~~~~~~~~~~a~~fY~~la~~~~~~~vsvDlF~~s~--- 231 (267)
T cd01478 158 F--P-NTGARIMLFAGGPCTVGPGAVVSTELKDPIRSHHDIDKDNAKYYKKAVKFYDSLAKRLAANGHAVDIFAGCL--- 231 (267)
T ss_pred c--C-CCCcEEEEEECCCCCCCCceeeccccccccccccccccchhhhhhhHHHHHHHHHHHHHhCCeEEEEEeccc---
Confidence 2 1 2346888888874433210 0 00 001234456777888999999998732
Q ss_pred CCCCccccccchHHHHHHhhcCCCeEeehh
Q 011878 170 GEPHMRVIIENDNLLNIFSKKSSAKTLFVD 199 (475)
Q Consensus 170 ~~~~~~~~~~n~~~l~~~~~~~~g~~~~~~ 199 (475)
+ . -+-..+..++..++|.++-.+
T Consensus 232 -d-~-----vglaem~~l~~~TGG~v~~~~ 254 (267)
T cd01478 232 -D-Q-----VGLLEMKVLVNSTGGHVVLSD 254 (267)
T ss_pred -c-c-----cCHHHHHHHHHhcCcEEEEeC
Confidence 1 1 113456667888999865433
No 74
>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=94.68 E-value=0.35 Score=46.89 Aligned_cols=180 Identities=13% Similarity=0.129 Sum_probs=108.7
Q ss_pred EEEEEEecCCCcC------CCchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCc--cccc--cCCCcccE-------
Q 011878 7 ALLLLLDVSPSMH------SVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETEN--ELTK--EVGGYEHV------- 69 (475)
Q Consensus 7 ~~vflID~s~sM~------~~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n--~~~~--~~~~y~~i------- 69 (475)
.++++||++|.-- ..+..+++.+.-|+..-+..+...+|+||..+...+.- |... +...-.++
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 5789999998532 24677888888999988889999999999999887542 1100 00000000
Q ss_pred EEEeecCCCCHHHHHHhhcCCCC-----C--CCCChhHHHHHHHHHHHHHhccC----cceeeEEEE-EeCCCCCCCCCC
Q 011878 70 KVLQDIKVVDGHLVQSLKHLPQG-----T--CAGDFLDAIVVGVDMLIKKYGET----YKGKKHLCL-ITDALCPLKDPD 137 (475)
Q Consensus 70 ~~~~~l~~~~~~~i~~L~~l~~~-----~--~~gd~~daL~va~~~l~~~~~~~----~~~~krI~l-~Td~~~p~~~~~ 137 (475)
..+.++...+....+.++++... . ..+.+.-||-.|+=.+++..... .....||++ ++..++...
T Consensus 83 ~~y~~f~~v~~~v~~~l~~l~~~~~~~~~~~~~s~LagALS~ALCyINR~~~~~~~~~~~~~~RILv~~s~s~d~~~--- 159 (276)
T PF03850_consen 83 NKYRQFRNVDETVLEELKKLMSETSESSDSTTSSLLAGALSMALCYINRISRESPSGGTSLKSRILVIVSGSPDSSS--- 159 (276)
T ss_pred chhHHHHHHHHHHHHHHHHHHhhcccccccccchhhHHHHHHHHHHHhhhhhcccCCCCCcCccEEEEEecCCCccH---
Confidence 00112222233334555554221 1 12467788888887766642211 245678888 555433211
Q ss_pred CCCchhhHHHHHHHHhhcCcEEEEEEeccCCCCCCCccccccchHHHHHHhhcCCCeEeehhhHHHh
Q 011878 138 VGTKEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDSTTSL 204 (475)
Q Consensus 138 ~~~~~~~~~~~~~~l~~~~I~l~~i~i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~~~~~~~~~l 204 (475)
..-.+...+=..++.+|.+.+..++. ....+|++.+..++|.|+.+.+...|
T Consensus 160 ---QYi~~MN~iFaAqk~~v~IDv~~L~~------------~~s~fLqQa~d~T~G~y~~~~~~~~l 211 (276)
T PF03850_consen 160 ---QYIPLMNCIFAAQKQKVPIDVCKLGG------------KDSTFLQQASDITGGIYLKVSKPEGL 211 (276)
T ss_pred ---HHHHHHHHHHHHhcCCceeEEEEecC------------CchHHHHHHHHHhCceeeccCccccH
Confidence 11223334445789999999999853 12488999999999998877664333
No 75
>KOG2487 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 [Transcription; Replication, recombination and repair]
Probab=94.41 E-value=0.78 Score=43.34 Aligned_cols=174 Identities=15% Similarity=0.163 Sum_probs=100.8
Q ss_pred EEEEEEecCC---CcCCC------chHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCcccccc-CCCcccEEEE----
Q 011878 7 ALLLLLDVSP---SMHSV------LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKE-VGGYEHVKVL---- 72 (475)
Q Consensus 7 ~~vflID~s~---sM~~~------~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~-~~~y~~i~~~---- 72 (475)
.++++||++| .|+.. ....++.+--|.-.-...+.+.+|+||..+....+--..+. .+.-+|...+
T Consensus 25 lL~vlId~~p~~Wg~~as~~~~~ti~kvl~aivVFlNAHL~~~~~NrvaViA~~~q~~~~lyp~st~~e~~n~~~~~~t~ 104 (314)
T KOG2487|consen 25 LLVVLIDANPCSWGMLASAENWETISKVLNAIVVFLNAHLAFSRNNRVAVIASHSQVDNYLYPSSTRCEDRNASELDPTR 104 (314)
T ss_pred eEEEEEecCcchhhhhhhhcCceeHHHHHHHHHHHHHHHHhhccCCcEEEEEecccccceeccccccCCccCccccCchh
Confidence 5788999999 56542 33456677777777888899999999999776543210000 0011122221
Q ss_pred ------eecCCCCHHHHHHhhcCCCC-------C---CCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCC
Q 011878 73 ------QDIKVVDGHLVQSLKHLPQG-------T---CAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDP 136 (475)
Q Consensus 73 ------~~l~~~~~~~i~~L~~l~~~-------~---~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~ 136 (475)
..+...+.-.++.+..+... + -.|.+.+||-..-.+=+++ ..-+..-||++||-...-..
T Consensus 105 ~~~~~y~~~~~~d~tiv~ei~~lm~~~~~~~~~~rt~lagals~~L~yi~~~~ke~--~~~~lkSRilV~t~t~d~~~-- 180 (314)
T KOG2487|consen 105 LVLFDYSEFRTVDDTIVEEIYRLMEHPDKYDVGDRTVLAGALSDALGYINRLHKEE--ASEKLKSRILVFTLTRDRAL-- 180 (314)
T ss_pred hhcchhhhhcccchHHHHHHHHHHhCccccccccceeeccchhhccchHhhhhhhh--hhhhhhceEEEEEechHHHh--
Confidence 12344444445666554221 1 1245666665554332222 12245788999988433211
Q ss_pred CCCCchhhHHHHHHHHhhcCcEEEEEEeccCCCCCCCccccccchHHHHHHhhcCCCeEeehhhH
Q 011878 137 DVGTKEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDST 201 (475)
Q Consensus 137 ~~~~~~~~~~~~~~~l~~~~I~l~~i~i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~~~~~~~ 201 (475)
..-.+...+=..++.+|.+.++.+++ +..+|.+-+..+||.|...+..
T Consensus 181 ----qyi~~MNciFaAqKq~I~Idv~~l~~-------------~s~~LqQa~D~TGG~YL~v~~~ 228 (314)
T KOG2487|consen 181 ----QYIPYMNCIFAAQKQNIPIDVVSLGG-------------DSGFLQQACDITGGDYLHVEKP 228 (314)
T ss_pred ----hhhhHHHHHHHHHhcCceeEEEEecC-------------CchHHHHHHhhcCCeeEecCCc
Confidence 01112222334578999999999953 1378888888899988876644
No 76
>COG5242 TFB4 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 [Transcription / DNA replication, recombination, and repair]
Probab=94.39 E-value=2.8 Score=38.55 Aligned_cols=173 Identities=16% Similarity=0.204 Sum_probs=97.8
Q ss_pred EEEEEEecCCCcCCCch------HHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCc--cc------cccCCCcccEEEE
Q 011878 7 ALLLLLDVSPSMHSVLP------DVEKLCSRLIQKKLIYGKNHEVGVILFGTEETEN--EL------TKEVGGYEHVKVL 72 (475)
Q Consensus 7 ~~vflID~s~sM~~~~~------~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n--~~------~~~~~~y~~i~~~ 72 (475)
.++.+||+.|.--..+. ..++-+.-++---...+.+.+|+||.-.++...- |. +.|.+.-+|-..+
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 45677899887655432 2344455556666667889999998876654321 00 0111111111122
Q ss_pred eecCCCCHHHHHHhhc---CCCC-CCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeC-CCCCCCCCCCCCchhhHHH
Q 011878 73 QDIKVVDGHLVQSLKH---LPQG-TCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITD-ALCPLKDPDVGTKEDQVST 147 (475)
Q Consensus 73 ~~l~~~~~~~i~~L~~---l~~~-~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td-~~~p~~~~~~~~~~~~~~~ 147 (475)
..++..+--.+..+.+ ...+ +++.++.-|+-.++....+. .....-.-||++||- |.+ ...|.--
T Consensus 102 rrfr~vde~~i~eiyrl~e~~~k~sqr~~v~gams~glay~n~~-~~e~slkSriliftlsG~d---------~~~qYip 171 (296)
T COG5242 102 RRFRNVDETDITEIYRLIEHPHKNSQRYDVGGAMSLGLAYCNHR-DEETSLKSRILIFTLSGRD---------RKDQYIP 171 (296)
T ss_pred hhhcccchHHHHHHHHHHhCcccccceeehhhhhhhhHHHHhhh-cccccccceEEEEEecCch---------hhhhhch
Confidence 2233333333343333 3322 44567777887777765542 223345678999987 211 1122222
Q ss_pred HHH---HHhhcCcEEEEEEeccCCCCCCCccccccchHHHHHHhhcCCCeEeehhhHH
Q 011878 148 IAR---QMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDSTT 202 (475)
Q Consensus 148 ~~~---~l~~~~I~l~~i~i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~~~~~~~~ 202 (475)
+.+ ..+..||.+.++.+.+ |..+|.+-+..++|.|.+.++..
T Consensus 172 ~mnCiF~Aqk~~ipI~v~~i~g-------------~s~fl~Q~~daTgG~Yl~ve~~e 216 (296)
T COG5242 172 YMNCIFAAQKFGIPISVFSIFG-------------NSKFLLQCCDATGGDYLTVEDTE 216 (296)
T ss_pred hhhheeehhhcCCceEEEEecC-------------ccHHHHHHhhccCCeeEeecCch
Confidence 211 3467899999998842 24788888888999998888754
No 77
>KOG1984 consensus Vesicle coat complex COPII, subunit SFB3 [Intracellular trafficking, secretion, and vesicular transport]
Probab=94.28 E-value=1.8 Score=47.44 Aligned_cols=210 Identities=15% Similarity=0.162 Sum_probs=109.5
Q ss_pred eEEEEEEecCCCcCC--CchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcC----ccccccCCCcccEEEEeecCCC-
Q 011878 6 EALLLLLDVSPSMHS--VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETE----NELTKEVGGYEHVKVLQDIKVV- 78 (475)
Q Consensus 6 e~~vflID~s~sM~~--~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~----n~~~~~~~~y~~i~~~~~l~~~- 78 (475)
-+.||+||||=+--. ....+.+.+++++..--...++-+||+|+|...-.- .+++ =.++.++.+++.+
T Consensus 418 pafvFmIDVSy~Ai~~G~~~a~ce~ik~~l~~lp~~~p~~~Vgivtfd~tvhFfnl~s~L~-----qp~mliVsdv~dvf 492 (1007)
T KOG1984|consen 418 PAFVFMIDVSYNAISNGAVKAACEAIKSVLEDLPREEPNIRVGIVTFDKTVHFFNLSSNLA-----QPQMLIVSDVDDVF 492 (1007)
T ss_pred ceEEEEEEeehhhhhcchHHHHHHHHHHHHhhcCccCCceEEEEEEecceeEeeccCcccc-----CceEEEeecccccc
Confidence 478999999854222 234445566666665555678899999999865221 1111 1233333332221
Q ss_pred -------------CHHHHHHh-hcCC---CC--CCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCC--
Q 011878 79 -------------DGHLVQSL-KHLP---QG--TCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPD-- 137 (475)
Q Consensus 79 -------------~~~~i~~L-~~l~---~~--~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~-- 137 (475)
+.+.|+.| ++++ .+ .-+.-+.+||.+|...|+. + . .-++|+|++--.-.+...
T Consensus 493 vPf~~g~~V~~~es~~~i~~lLd~Ip~mf~~sk~pes~~g~alqaa~lalk~-~----~-gGKl~vF~s~Lpt~g~g~kl 566 (1007)
T KOG1984|consen 493 VPFLDGLFVNPNESRKVIELLLDSIPTMFQDSKIPESVFGSALQAAKLALKA-A----D-GGKLFVFHSVLPTAGAGGKL 566 (1007)
T ss_pred cccccCeeccchHHHHHHHHHHHHhhhhhccCCCCchhHHHHHHHHHHHHhc-c----C-CceEEEEecccccccCcccc
Confidence 11223322 2222 11 2244678888888877653 1 1 345777877543333210
Q ss_pred ----C----CCch---------hhHHHHHHHHhhcCcEEEEEEeccCCCCCCCccccccchHHHHHHhhcCCCeEeehh-
Q 011878 138 ----V----GTKE---------DQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVD- 199 (475)
Q Consensus 138 ----~----~~~~---------~~~~~~~~~l~~~~I~l~~i~i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~~~~~- 199 (475)
| +.++ +.+.++|+++-+.||.+.+|.....+ .+ -..+-.++..++|++|...
T Consensus 567 ~~r~D~~l~~t~kek~l~~pq~~~y~~LA~e~v~~g~svDlF~t~~ay-----vD-----vAtlg~v~~~TgG~vy~Y~~ 636 (1007)
T KOG1984|consen 567 SNRDDRRLIGTDKEKNLLQPQDKTYTTLAKEFVESGCSVDLFLTPNAY-----VD-----VATLGVVPALTGGQVYKYYP 636 (1007)
T ss_pred cccchhhhhcccchhhccCcchhHHHHHHHHHHHhCceEEEEEcccce-----ee-----eeeecccccccCceeEEecc
Confidence 0 0111 23668999999999999999874321 11 1223234555677654322
Q ss_pred -----hHHHhhccCccccCCCceeeeeeEeecCCeEEEEEEEe
Q 011878 200 -----STTSLRGARKTRDISPVTIFRGDLELSEKMKIKVWVYK 237 (475)
Q Consensus 200 -----~~~~ll~~~~~r~~~~r~~~~~~l~ig~~~~I~V~~y~ 237 (475)
+...++..++.--.++ .-|.+-++....--|.|..|.
T Consensus 637 F~a~~D~~rl~nDL~~~vtk~-~gf~a~mrvRtStGirv~~f~ 678 (1007)
T KOG1984|consen 637 FQALTDGPRLLNDLVRNVTKK-QGFDAVMRVRTSTGIRVQDFY 678 (1007)
T ss_pred hhhcccHHHHHHHHHHhcccc-eeeeeEEEEeecCceeeeeee
Confidence 2335555443322232 246666666554445555443
No 78
>PLN00162 transport protein sec23; Provisional
Probab=94.07 E-value=1.5 Score=48.90 Aligned_cols=126 Identities=15% Similarity=0.105 Sum_probs=69.7
Q ss_pred ChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCC------------------------CCchhhHHHHHHHH
Q 011878 97 DFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDV------------------------GTKEDQVSTIARQM 152 (475)
Q Consensus 97 d~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~------------------------~~~~~~~~~~~~~l 152 (475)
....||.+|..+|.... . ...=||++|+.+-...+ ++- ....+-...++..+
T Consensus 263 ~tG~AL~vA~~lL~~~~-~--~~gGrI~~F~sgppT~G-pG~v~~r~~~~~~rsh~di~k~~~~~~~~a~~fY~~la~~~ 338 (761)
T PLN00162 263 CTGAALSVAAGLLGACV-P--GTGARIMAFVGGPCTEG-PGAIVSKDLSEPIRSHKDLDKDAAPYYKKAVKFYEGLAKQL 338 (761)
T ss_pred cHHHHHHHHHHHHhhcc-C--CCceEEEEEeCCCCCCC-CceeecccccccccCccccccchhhhcchHHHHHHHHHHHH
Confidence 57889999998886522 1 33568888887643222 100 00112345678888
Q ss_pred hhcCcEEEEEEeccCCCCCCCccccccchHHHHHHhhcCCCeEeehhhH-----HHhhccCccccC--CCceeeeeeEee
Q 011878 153 VAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDST-----TSLRGARKTRDI--SPVTIFRGDLEL 225 (475)
Q Consensus 153 ~~~~I~l~~i~i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~~~~~~~-----~~ll~~~~~r~~--~~r~~~~~~l~i 225 (475)
.+.||.+.+|.... + . -+-..+..++..++|.++-.+.. .+.+.++-.|.. .....|.+.+++
T Consensus 339 ~~~gisvDlF~~s~----d-q-----vglaem~~l~~~TGG~v~~~~sF~~~~f~~~l~r~~~r~~~~~~~~gf~a~~~V 408 (761)
T PLN00162 339 VAQGHVLDVFACSL----D-Q-----VGVAEMKVAVERTGGLVVLAESFGHSVFKDSLRRVFERDGEGSLGLSFNGTFEV 408 (761)
T ss_pred HHcCceEEEEEccc----c-c-----cCHHHHhhhHhhcCcEEEEeCCcChHHHHHHHHHHhcccccccccccceeEEEE
Confidence 89999999997632 1 1 11345666788889976432221 222222222211 011367788887
Q ss_pred cCCeEEEEEEE
Q 011878 226 SEKMKIKVWVY 236 (475)
Q Consensus 226 g~~~~I~V~~y 236 (475)
...-.|.|.+|
T Consensus 409 rtS~glkv~g~ 419 (761)
T PLN00162 409 NCSKDVKVQGA 419 (761)
T ss_pred EecCCeEEeee
Confidence 75544555544
No 79
>PF11775 CobT_C: Cobalamin biosynthesis protein CobT VWA domain
Probab=93.66 E-value=1.1 Score=41.54 Aligned_cols=154 Identities=17% Similarity=0.140 Sum_probs=72.0
Q ss_pred eEEEEEEecCCCcCCC-chHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCcc----ccccCC--CcccEE------EE
Q 011878 6 EALLLLLDVSPSMHSV-LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENE----LTKEVG--GYEHVK------VL 72 (475)
Q Consensus 6 e~~vflID~s~sM~~~-~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~----~~~~~~--~y~~i~------~~ 72 (475)
-++-|+||+|+||..+ ...|..++.-+.+-. .+-+=-+=|+-|.|..-+-. .+.+.| .+++-. ++
T Consensus 13 ~~VtlLID~SGSMrgr~~~vA~~~adila~aL--~~~gvp~EVlGFtT~aw~gg~~~~~w~~~G~p~~pgrln~l~h~vy 90 (219)
T PF11775_consen 13 TVVTLLIDCSGSMRGRPIEVAALCADILARAL--ERCGVPVEVLGFTTRAWKGGRSREAWLAAGRPRYPGRLNDLRHIVY 90 (219)
T ss_pred eEEEEEEeCCcCCCCChHHHHHHHHHHHHHHH--HhCCCCeEEEeeecCCcCCcchHHHHHhcCCCCCChHHHHHHHHHH
Confidence 4677999999999974 566665555555533 23333444566666632110 011111 111110 01
Q ss_pred eecCCCCHHHHHHhhcCC-CC-CCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCC---CCC--CchhhH
Q 011878 73 QDIKVVDGHLVQSLKHLP-QG-TCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDP---DVG--TKEDQV 145 (475)
Q Consensus 73 ~~l~~~~~~~i~~L~~l~-~~-~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~---~~~--~~~~~~ 145 (475)
.+.+.|.-..-+.|.-+. .+ ..++-=.+||.-|...|..+ .-..|-+++|+|+ .|.+.. .+. --...+
T Consensus 91 k~a~~~wrraR~~l~~m~~~~~~~eniDGeAl~~a~~rL~~r----~e~rkiLiViSDG-~P~d~st~~~n~~~~L~~HL 165 (219)
T PF11775_consen 91 KDADTPWRRARRNLGLMMREGLLKENIDGEALRWAAERLLAR----PEQRKILIVISDG-APADDSTLSANDGDYLDAHL 165 (219)
T ss_pred HhcCChhhhHHHhHHHHhhccccccCCcHHHHHHHHHHHHcC----CccceEEEEEeCC-CcCcccccccCChHHHHHHH
Confidence 111111111111111111 01 01112256766666665442 2334567777887 555321 011 112456
Q ss_pred HHHHHHHhh-cCcEEEEEEecc
Q 011878 146 STIARQMVA-FGLRMKNIVVRA 166 (475)
Q Consensus 146 ~~~~~~l~~-~~I~l~~i~i~~ 166 (475)
+..++.+.. .+|++.-||++.
T Consensus 166 r~vi~~ie~~~~Vel~aiGIg~ 187 (219)
T PF11775_consen 166 RQVIAEIETRSDVELIAIGIGH 187 (219)
T ss_pred HHHHHHHhccCCcEEEEEEcCC
Confidence 777777775 478888888853
No 80
>KOG2353 consensus L-type voltage-dependent Ca2+ channel, alpha2/delta subunit [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=93.62 E-value=0.88 Score=52.04 Aligned_cols=141 Identities=16% Similarity=0.182 Sum_probs=91.0
Q ss_pred CCCceEEEEEEecCCCcCC-CchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCCH
Q 011878 2 ARTREALLLLLDVSPSMHS-VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDG 80 (475)
Q Consensus 2 ~~~ke~~vflID~s~sM~~-~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~~ 80 (475)
|+...-++|++|+|+||.. ++..|+..+..++.- -+.+|.|-++.|+.+...-.. - ....+=+.+.
T Consensus 222 At~pKdiviLlD~SgSm~g~~~~lak~tv~~iLdt---Ls~~Dfvni~tf~~~~~~v~p-----c-----~~~~lvqAt~ 288 (1104)
T KOG2353|consen 222 ATSPKDIVILLDVSGSMSGLRLDLAKQTVNEILDT---LSDNDFVNILTFNSEVNPVSP-----C-----FNGTLVQATM 288 (1104)
T ss_pred cCCccceEEEEeccccccchhhHHHHHHHHHHHHh---cccCCeEEEEeeccccCcccc-----c-----ccCceeecch
Confidence 4567789999999999986 577788888888883 379999999999988533220 0 1223444555
Q ss_pred HHHHHhhcCCC---CCCCCChhHHHHHHHHHHHHHhccC-----cceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHH
Q 011878 81 HLVQSLKHLPQ---GTCAGDFLDAIVVGVDMLIKKYGET-----YKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQM 152 (475)
Q Consensus 81 ~~i~~L~~l~~---~~~~gd~~daL~va~~~l~~~~~~~-----~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l 152 (475)
.-++.+.+... ..+.+.+..|+-.|.+.|.....+. ..-.+-|+||||+-.. ....+.+..
T Consensus 289 ~nk~~~~~~i~~l~~k~~a~~~~~~e~aF~lL~~~n~s~~~~~~~~C~~~iml~tdG~~~-----------~~~~If~~y 357 (1104)
T KOG2353|consen 289 RNKKVFKEAIETLDAKGIANYTAALEYAFSLLRDYNDSRANTQRSPCNQAIMLITDGVDE-----------NAKEIFEKY 357 (1104)
T ss_pred HHHHHHHHHHhhhccccccchhhhHHHHHHHHHHhccccccccccccceeeEEeecCCcc-----------cHHHHHHhh
Confidence 55555555322 2334577889999999887532111 1146779999966432 233343333
Q ss_pred h--hcCcEEEEEEecc
Q 011878 153 V--AFGLRMKNIVVRA 166 (475)
Q Consensus 153 ~--~~~I~l~~i~i~~ 166 (475)
. ...|++..+.+|.
T Consensus 358 n~~~~~Vrvftflig~ 373 (1104)
T KOG2353|consen 358 NWPDKKVRVFTFLIGD 373 (1104)
T ss_pred ccCCCceEEEEEEecc
Confidence 3 4567777777763
No 81
>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=93.29 E-value=1.7 Score=46.04 Aligned_cols=63 Identities=16% Similarity=0.262 Sum_probs=40.8
Q ss_pred hHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCC---C--CCchhhHHHHHHHHhhc-CcEEEEEEecc
Q 011878 99 LDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPD---V--GTKEDQVSTIARQMVAF-GLRMKNIVVRA 166 (475)
Q Consensus 99 ~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~---~--~~~~~~~~~~~~~l~~~-~I~l~~i~i~~ 166 (475)
.+||..|.+.|..+ .-..|-+++|||| .|..... + ......++.++..+... ||.|.-|||+.
T Consensus 499 GeAl~wa~~rL~~R----~e~rKiL~ViSDG-~P~D~~TlsvN~~~~l~~hLr~vi~~~e~~~~vel~aigIg~ 567 (600)
T TIGR01651 499 GEALMWAHQRLIAR----PEQRRILMMISDG-APVDDSTLSVNPGNYLERHLRAVIEEIETRSPVELLAIGIGH 567 (600)
T ss_pred hHHHHHHHHHHhcC----cccceEEEEEeCC-CcCCccccccCchhHHHHHHHHHHHHHhccCCceEEEeeccc
Confidence 56887777776542 2335677888888 4454210 0 01234577888888885 99999999963
No 82
>PTZ00395 Sec24-related protein; Provisional
Probab=93.22 E-value=3.6 Score=47.54 Aligned_cols=216 Identities=13% Similarity=0.113 Sum_probs=109.0
Q ss_pred eEEEEEEecCCC-cCCC-chHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCcccc----------ccCCCc--ccEEE
Q 011878 6 EALLLLLDVSPS-MHSV-LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELT----------KEVGGY--EHVKV 71 (475)
Q Consensus 6 e~~vflID~s~s-M~~~-~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~----------~~~~~y--~~i~~ 71 (475)
-..+||||||.. +..- +..+.+.|+..+.+. ..++-+||+|.|.+.=---.+. +.+++. .++.|
T Consensus 953 P~YvFLIDVS~~AVkSGLl~tacesIK~sLDsL--~dpRTRVGIITFDSsLHFYNLks~l~~~~~~~~~~~~l~qPQMLV 1030 (1560)
T PTZ00395 953 PYFVFVVECSYNAIYNNITYTILEGIRYAVQNV--KCPQTKIAIITFNSSIYFYHCKGGKGVSGEEGDGGGGSGNHQVIV 1030 (1560)
T ss_pred CEEEEEEECCHHHHhhChHHHHHHHHHHHHhcC--CCCCcEEEEEEecCcEEEEecCcccccccccccccccCCCceEEe
Confidence 478999999974 3332 455677777777653 4678899999998753111110 001111 23333
Q ss_pred EeecCCCC---------------HHHHH----HhhcCCCC--CCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCC
Q 011878 72 LQDIKVVD---------------GHLVQ----SLKHLPQG--TCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDAL 130 (475)
Q Consensus 72 ~~~l~~~~---------------~~~i~----~L~~l~~~--~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~ 130 (475)
+-+|+.|= .+.|+ .|.++... .....+..||.+|..+|... +. .=+|++|...-
T Consensus 1031 VSDLDDPFLPlP~ddLLVnL~ESRevIe~LLDkLPemFt~t~~~esCLGSALqAA~~aLk~~-GG----GGKIiVF~SSL 1105 (1560)
T PTZ00395 1031 MSDVDDPFLPLPLEDLFFGCVEEIDKINTLIDTIKSVSTTMQSYGSCGNSALKIAMDMLKER-NG----LGSICMFYTTT 1105 (1560)
T ss_pred ecCCccCcCCCCccCeeechHHHHHHHHHHHHHHHHHhhccCCCcccHHHHHHHHHHHHHhc-CC----CceEEEEEcCC
Confidence 33332111 11222 22222111 22346789999999987652 21 13455554422
Q ss_pred CCCCCC-------------CCCCchhhHHHHHHHHhhcCcEEEEEEeccCCCCCCCccccccchHHHHHHhhcCCCeEee
Q 011878 131 CPLKDP-------------DVGTKEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLF 197 (475)
Q Consensus 131 ~p~~~~-------------~~~~~~~~~~~~~~~l~~~~I~l~~i~i~~~~~~~~~~~~~~~n~~~l~~~~~~~~g~~~~ 197 (475)
-..+.. .......-+..++.++.+.+|.|.+|.+...+ .+ ..-..|-.+++.++|.++.
T Consensus 1106 PniGpGaLK~Re~~~KEk~Ll~pqd~FYK~LA~ECsk~qISVDLFLfSsqY-----vD---VDVATLg~Lsr~TGGqlyy 1177 (1560)
T PTZ00395 1106 PNCGIGAIKELKKDLQENFLEVKQKIFYDSLLLDLYAFNISVDIFIISSNN-----VR---VCVPSLQYVAQNTGGKILF 1177 (1560)
T ss_pred CCCCCCcccccccccccccccccchHHHHHHHHHHHhcCCceEEEEccCcc-----cc---cccccccchhcccceeEEE
Confidence 212110 00012246678899999999999999874311 10 0013344566778887542
Q ss_pred hh------hHHHhhccCccccCCCceeeeeeEeecCCeEEEEEEE
Q 011878 198 VD------STTSLRGARKTRDISPVTIFRGDLELSEKMKIKVWVY 236 (475)
Q Consensus 198 ~~------~~~~ll~~~~~r~~~~r~~~~~~l~ig~~~~I~V~~y 236 (475)
.. +...+...+...-.+.-..|.+.|++...=-|.|.-|
T Consensus 1178 YPnFna~rD~~KL~~DL~r~LTre~iGyEAVMRVRCS~GLrVs~f 1222 (1560)
T PTZ00395 1178 VENFLWQKDYKEIYMNIMDTLTSEDIAYCCELKLRYSHHMSVKKL 1222 (1560)
T ss_pred eCCCcccccHHHHHHHHHHHhhccceeeEEEEEEECCCCeEEEEE
Confidence 22 1223333332222221136787777764333344333
No 83
>PF12257 DUF3608: Protein of unknown function (DUF3608); InterPro: IPR022046 This domain family is found in eukaryotes, and is approximately 280 amino acids in length. The family is found in association with PF00610 from PFAM.
Probab=92.97 E-value=1.1 Score=43.36 Aligned_cols=154 Identities=18% Similarity=0.315 Sum_probs=99.8
Q ss_pred EEEEEEecCCCcCCC-------chHHHH-HHHHHHHHHHhcCCccEEEEEEEccCCcCc----ccccc-----CCCcccE
Q 011878 7 ALLLLLDVSPSMHSV-------LPDVEK-LCSRLIQKKLIYGKNHEVGVILFGTEETEN----ELTKE-----VGGYEHV 69 (475)
Q Consensus 7 ~~vflID~s~sM~~~-------~~~a~~-~~~~l~~~ki~~~~~D~vglvlfgt~~t~n----~~~~~-----~~~y~~i 69 (475)
-++++|..|..|..- ++.+++ .+..+.++---..-++.|.+|||..=.-+. ++..+ ..+|-.|
T Consensus 72 r~~~~IQmS~EMW~fd~~Ge~~fek~vn~Fl~~lf~kWk~~~~~H~vTIVlfsRv~~~~~~~~~l~~~~~~~~y~DfYrV 151 (281)
T PF12257_consen 72 RVYIFIQMSSEMWDFDEDGEIYFEKAVNGFLPELFKKWKEIGTHHLVTIVLFSRVDYDDISFRDLPPGERGKNYKDFYRV 151 (281)
T ss_pred eeeehHhhhHHHhCcCccHHHHHHHHHHHHHHHHHHHHhhcCCCceEEEEEEEEEccccchhhcCCccccCCCCCcceEE
Confidence 367888999999753 345553 555666554445679999999998433221 11111 1255555
Q ss_pred EEEeecCCCCHHHH-HHhh--------cC--C-----C------C----CCCCChhHHHHHHHHHHHHHhccCc--ceee
Q 011878 70 KVLQDIKVVDGHLV-QSLK--------HL--P-----Q------G----TCAGDFLDAIVVGVDMLIKKYGETY--KGKK 121 (475)
Q Consensus 70 ~~~~~l~~~~~~~i-~~L~--------~l--~-----~------~----~~~gd~~daL~va~~~l~~~~~~~~--~~~k 121 (475)
|.+.....+|..+ ..|+ ++ . . | ..+|++++||-+|++.+.+++-.+. ....
T Consensus 152 -Vv~~~~~~~W~~il~~Lk~eF~~f~rdi~~~~~~~~~~~~~i~g~~s~A~~gNiLEaINlaln~~~~~~idRdl~rTG~ 230 (281)
T PF12257_consen 152 -VVDEENSQDWTSILVTLKKEFNQFQRDILLYHQSDEDGTTRIKGRFSPAIKGNILEAINLALNQFDKHYIDRDLRRTGQ 230 (281)
T ss_pred -EEeccccccHHHHHHHHHHHHHHHHHHhhcccccccCCCccccceEeecccccHHHHHHHHhhhcccccccCcccccCc
Confidence 4455556676543 3332 11 0 0 0 1357899999999999888765442 3567
Q ss_pred EEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEEEecc
Q 011878 122 HLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIVVRA 166 (475)
Q Consensus 122 rI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l~~i~i~~ 166 (475)
.|+++|=|..=+. .+.+-++..-+.|-+.||.+.+|-++.
T Consensus 231 ~iivITpG~Gvf~-----Vd~~ll~~T~~rl~~~gi~~DlIcL~~ 270 (281)
T PF12257_consen 231 SIIVITPGTGVFE-----VDYDLLRLTTQRLLDNGIGIDLICLSK 270 (281)
T ss_pred eEEEEcCCCceEE-----ECHHHHHHHHHHHHhcCccEEEEEcCC
Confidence 7999999877654 345667777888999999999998865
No 84
>PF09967 DUF2201: VWA-like domain (DUF2201); InterPro: IPR018698 This family of various hypothetical bacterial proteins has no known function.
Probab=92.37 E-value=1.2 Score=37.90 Aligned_cols=41 Identities=24% Similarity=0.338 Sum_probs=27.5
Q ss_pred EEEEEecCCCcCC-CchHHHHHHHHHHHHHHhcCCccEEEEEEEccC
Q 011878 8 LLLLLDVSPSMHS-VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTE 53 (475)
Q Consensus 8 ~vflID~s~sM~~-~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~ 53 (475)
++++||.|+||.. .+..++.-+..+.++. ..+|-||.|-++
T Consensus 1 i~vaiDtSGSis~~~l~~fl~ev~~i~~~~-----~~~v~vi~~D~~ 42 (126)
T PF09967_consen 1 IVVAIDTSGSISDEELRRFLSEVAGILRRF-----PAEVHVIQFDAE 42 (126)
T ss_pred CEEEEECCCCCCHHHHHHHHHHHHHHHHhC-----CCCEEEEEECCE
Confidence 4789999999986 3555555555555532 445777776655
No 85
>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=91.52 E-value=5.9 Score=37.93 Aligned_cols=139 Identities=13% Similarity=0.168 Sum_probs=80.5
Q ss_pred EEEEEEecCCCcCC----------------CchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEE
Q 011878 7 ALLLLLDVSPSMHS----------------VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVK 70 (475)
Q Consensus 7 ~~vflID~s~sM~~----------------~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~ 70 (475)
.++++||.+.|=.. ..+.|++.+-.+++. +...-++-+..||+..+.+. ...|.+
T Consensus 33 nl~vaIDfT~SNg~p~~~~SLHy~~~~~~N~Yq~aI~~vg~il~~---yD~D~~ip~~GFGa~~~~~~------~v~~~f 103 (254)
T cd01459 33 NLIVAIDFTKSNGWPGEKRSLHYISPGRLNPYQKAIRIVGEVLQP---YDSDKLIPAFGFGAIVTKDQ------SVFSFF 103 (254)
T ss_pred eEEEEEEeCCCCCCCCCCCCcccCCCCCccHHHHHHHHHHHHHHh---cCCCCceeeEeecccCCCCC------cccccc
Confidence 57899999887332 134566666555553 67889999999999754432 111111
Q ss_pred EEeecCCCC----HHHHHHhhcCCCC---CCCCChhHHHHHHHHHHHHHhccCcceeeE-EEEEeCCCCCCCCCCCCCch
Q 011878 71 VLQDIKVVD----GHLVQSLKHLPQG---TCAGDFLDAIVVGVDMLIKKYGETYKGKKH-LCLITDALCPLKDPDVGTKE 142 (475)
Q Consensus 71 ~~~~l~~~~----~~~i~~L~~l~~~---~~~gd~~daL~va~~~l~~~~~~~~~~~kr-I~l~Td~~~p~~~~~~~~~~ 142 (475)
. -....|. -..++..++.... .+.+.+...|-.|.++..+. .. ...-. +++||||.-. +.
T Consensus 104 ~-~~~~~p~~~Gi~gvl~aY~~~l~~v~lsGpT~fapvI~~a~~~a~~~-~~--~~~Y~VLLIiTDG~i~--------D~ 171 (254)
T cd01459 104 P-GYSESPECQGFEGVLRAYREALPNVSLSGPTNFAPVIRAAANIAKAS-NS--QSKYHILLIITDGEIT--------DM 171 (254)
T ss_pred C-CCCCCCcccCHHHHHHHHHHHhceeeecCcchHHHHHHHHHHHHHHh-cC--CCceEEEEEECCCCcc--------cH
Confidence 0 0011111 1233333332111 23457888888888775542 11 11344 6677999652 23
Q ss_pred hhHHHHHHHHhhcCcEEEEEEecc
Q 011878 143 DQVSTIARQMVAFGLRMKNIVVRA 166 (475)
Q Consensus 143 ~~~~~~~~~l~~~~I~l~~i~i~~ 166 (475)
++....+....+.-+.+.++|+|.
T Consensus 172 ~~t~~aIv~AS~~PlSIiiVGVGd 195 (254)
T cd01459 172 NETIKAIVEASKYPLSIVIVGVGD 195 (254)
T ss_pred HHHHHHHHHHhcCCeEEEEEEeCC
Confidence 556666667778889999999964
No 86
>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=90.50 E-value=6.2 Score=40.34 Aligned_cols=152 Identities=18% Similarity=0.200 Sum_probs=83.4
Q ss_pred EEEEEecCCCcCCCchHHHHHHHHHHHHHHhcCCccEEEEEEEccCC-----------cCcccccc---C---CCcccEE
Q 011878 8 LLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEE-----------TENELTKE---V---GGYEHVK 70 (475)
Q Consensus 8 ~vflID~s~sM~~~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~-----------t~n~~~~~---~---~~y~~i~ 70 (475)
+.|+.|+|.||...++..+.....|.+..--..++=++|+=-|--.. -.||-... + =+|+|+
T Consensus 102 LYyLMDlS~SM~ddl~~lk~lg~~L~~~m~~it~n~rlGfGsFVDK~v~P~~~t~p~~l~~PC~~~~~~c~p~f~f~~~- 180 (423)
T smart00187 102 LYYLMDLSYSMKDDLDNLKSLGDDLAREMKGLTSNFRLGFGSFVDKTVSPFVSTRPEKLENPCPNYNLTCEPPYGFKHV- 180 (423)
T ss_pred eEEEEeCCccHHHHHHHHHHHHHHHHHHHHhcccCceeeEEEeecCccCCcccCCHHHhcCCCcCCCCCcCCCcceeee-
Confidence 56999999999998887777776666654334578888875554321 12222110 0 167776
Q ss_pred EEeecCCCCHHHHHHhhcCCCC-C--CCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCC----------
Q 011878 71 VLQDIKVVDGHLVQSLKHLPQG-T--CAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPD---------- 137 (475)
Q Consensus 71 ~~~~l~~~~~~~i~~L~~l~~~-~--~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~---------- 137 (475)
.+|+.-....-+.+.+...+ + ..-.=+|||..|.-- .++.+=++...|-+++.||+..=.+..+
T Consensus 181 --L~LT~~~~~F~~~V~~~~iSgN~D~PEgG~DAimQaaVC-~~~IGWR~~a~rllv~~TDa~fH~AGDGkLaGIv~PND 257 (423)
T smart00187 181 --LSLTDDTDEFNEEVKKQRISGNLDAPEGGFDAIMQAAVC-TEQIGWREDARRLLVFSTDAGFHFAGDGKLAGIVQPND 257 (423)
T ss_pred --ccCCCCHHHHHHHHhhceeecCCcCCcccHHHHHHHHhh-ccccccCCCceEEEEEEcCCCccccCCcceeeEecCCC
Confidence 67776655666667765332 1 111236777655411 1111212233444555577654222100
Q ss_pred ------------C--CCchhhHHHHHHHHhhcCcEEEEEEe
Q 011878 138 ------------V--GTKEDQVSTIARQMVAFGLRMKNIVV 164 (475)
Q Consensus 138 ------------~--~~~~~~~~~~~~~l~~~~I~l~~i~i 164 (475)
. ..+.=.+.++++.|.+.+|. .+|.+
T Consensus 258 g~CHL~~~g~Yt~s~~~DYPSi~ql~~kL~e~nI~-~IFAV 297 (423)
T smart00187 258 GQCHLDNNGEYTMSTTQDYPSIGQLNQKLAENNIN-PIFAV 297 (423)
T ss_pred CcceeCCCCCcCccCcCCCCCHHHHHHHHHhcCce-EEEEE
Confidence 0 01122577889999999885 34444
No 87
>KOG2326 consensus DNA-binding subunit of a DNA-dependent protein kinase (Ku80 autoantigen) [Replication, recombination and repair]
Probab=89.76 E-value=0.0036 Score=64.64 Aligned_cols=135 Identities=19% Similarity=0.254 Sum_probs=98.7
Q ss_pred CCcccccccceeCCceEeCChhhHHhhccCCCccEEEEeEeeCCCcccccccCceEEEEcCCC-ChhhHHHHHHHHHHHH
Q 011878 281 VPPEQRIKGYRYGPQVVPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPG-NSRATVAVSALARAMK 359 (475)
Q Consensus 281 v~~~~~~k~y~yG~~~V~~~~~e~~~~k~~~~~~l~llGF~~~~~i~~~~~~~~~~~i~p~~~-~~~s~~~f~aL~~am~ 359 (475)
+.++.+.++|.||..++.+..-+-.+.++.+.+.|+.+||-.+..|+|+.+...+.++...-- ...+..+|.+|+.-++
T Consensus 325 ikkssv~~~Y~~g~~~~Vlpa~dd~~a~~a~ssli~al~~l~r~Al~Ry~~~~ks~pql~vl~Ph~~~~~~~~yLvdVqL 404 (669)
T KOG2326|consen 325 IKKSSVTKAYRYGADYVVLPAVDDDQAVYASSSLIDALGFLNREALPRYFLTSKSSPQLAVLRPHCQSDLAFSYLVDVQL 404 (669)
T ss_pred eccccccceeeecCceEEecccCchHhHHhhhHHHHHHhhhhHHHhhhhhhccCCCceEeeeccccccccceeeEEEeec
Confidence 678899999999999999999766777888999999999999999999999777554433211 1234448899999888
Q ss_pred hcCeEEEEEEEecCCCCceEEEEecccccCCCC------CCCeEEEecCCCcc---ccccCCCCCC
Q 011878 360 EMNKVAIVRCVWRQGQQSVVVGVLTPNVSEKIN------IPDSFYFNVLPFAE---DVREFQFPSF 416 (475)
Q Consensus 360 ~~~~vai~r~v~r~~~~~~~v~~L~P~~~~~~~------~~~gl~~~~LPf~d---DiR~~~f~~l 416 (475)
.-..-+-++++.+-.. ....+.+.|+.....+ ...-.-+..+||++ +.|.-.++.+
T Consensus 405 PF~eD~R~y~Fskf~~-~~n~~pt~aql~AVsnlID~M~L~ksdtl~~~pf~p~~~~mr~hrL~ql 469 (669)
T KOG2326|consen 405 PFREDARAYYFSKFDS-EVNMCPTCAQLIAVSNLIDEMKLVKSDTLCRLPFAPPKLDMRVHRLPQL 469 (669)
T ss_pred cchhhhHHhhcccccc-hhccCchHHHHHHHHHHhhhhhhhhhccccCCCCCCCCccchhhhHHHH
Confidence 8888888888887765 3556666676543210 01112466899999 7777666554
No 88
>KOG1986 consensus Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking, secretion, and vesicular transport]
Probab=88.82 E-value=22 Score=38.37 Aligned_cols=147 Identities=16% Similarity=0.139 Sum_probs=83.2
Q ss_pred EEEEEecCCCcCC-CchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCCHHHHHHh
Q 011878 8 LLLLLDVSPSMHS-VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHLVQSL 86 (475)
Q Consensus 8 ~vflID~s~sM~~-~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~~~~i~~L 86 (475)
.+|+||.. |.+ .+...+.++...+. +-.++-.||+|.||+--.-..++.+ +....+|+.--..++++.++.+
T Consensus 124 f~fVvDtc--~~eeeL~~LkssL~~~l~---lLP~~alvGlItfg~~v~v~el~~~--~~sk~~VF~G~ke~s~~q~~~~ 196 (745)
T KOG1986|consen 124 FVFVVDTC--MDEEELQALKSSLKQSLS---LLPENALVGLITFGTMVQVHELGFE--ECSKSYVFSGNKEYSAKQLLDL 196 (745)
T ss_pred EEEEEeec--cChHHHHHHHHHHHHHHh---hCCCcceEEEEEecceEEEEEcCCC--cccceeEEeccccccHHHHHHH
Confidence 47888876 544 23444444443333 3568999999999987544444222 3344455555545555555544
Q ss_pred hcCCC-----------------------------------C-----CCC---CChhHHHHHHHHHHHHHhccCcceeeEE
Q 011878 87 KHLPQ-----------------------------------G-----TCA---GDFLDAIVVGVDMLIKKYGETYKGKKHL 123 (475)
Q Consensus 87 ~~l~~-----------------------------------~-----~~~---gd~~daL~va~~~l~~~~~~~~~~~krI 123 (475)
-.+.. . .++ -...-||-+|+.+|.. +. .....||
T Consensus 197 L~~~~~~~~~~~~~~~~~rFL~P~~~c~~~L~~lle~L~~d~wpV~~g~Rp~RcTG~Al~iA~~Ll~~-c~--p~~g~rI 273 (745)
T KOG1986|consen 197 LGLSGGAGKGSENQSASNRFLLPAQECEFKLTNLLEELQPDPWPVPPGHRPLRCTGVALSIASGLLEG-CF--PNTGARI 273 (745)
T ss_pred hcCCcccccCCcccccchhhhccHHHHHHHHHHHHHHhcCCCCCCCCCCCcccchhHHHHHHHHHhcc-cC--CCCcceE
Confidence 43322 1 000 0135678888888765 22 2567899
Q ss_pred EEEeCCCCCCC------------------CCCCCC-----chhhHHHHHHHHhhcCcEEEEEEe
Q 011878 124 CLITDALCPLK------------------DPDVGT-----KEDQVSTIARQMVAFGLRMKNIVV 164 (475)
Q Consensus 124 ~l~Td~~~p~~------------------~~~~~~-----~~~~~~~~~~~l~~~~I~l~~i~i 164 (475)
++|+.|-+-.+ ...+.+ ..+-.+.+++.+...|.-++++.-
T Consensus 274 v~f~gGPcT~GpG~vv~~el~~piRshhdi~~d~a~y~kKa~KfY~~La~r~~~~ghvlDifa~ 337 (745)
T KOG1986|consen 274 VLFAGGPCTRGPGTVVSRELKEPIRSHHDIEKDNAPYYKKAIKFYEKLAERLANQGHVLDIFAA 337 (745)
T ss_pred EEeccCCCCcCCceecchhhcCCCcCcccccCcchHHHHHHHHHHHHHHHHHHhCCceEeeeee
Confidence 99999943222 100000 012345678888899988888753
No 89
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=88.63 E-value=6.1 Score=38.11 Aligned_cols=145 Identities=17% Similarity=0.205 Sum_probs=80.3
Q ss_pred EEEEEEecCCCcCCC------chHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCCH
Q 011878 7 ALLLLLDVSPSMHSV------LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDG 80 (475)
Q Consensus 7 ~~vflID~s~sM~~~------~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~~ 80 (475)
.++++||+|.+|.+. .....+++..++-.-.-.+|-..+|+|.....-..- ...+.-.--
T Consensus 89 hl~l~lD~Seam~e~Df~p~r~a~vikya~~Fv~eFf~qNPiSqlsii~irdg~a~~--------------~s~~~gnpq 154 (421)
T COG5151 89 HLHLILDVSEAMDESDFLPTRRANVIKYAEGFVPEFFSQNPISQLSIISIRDGCAKY--------------TSSMDGNPQ 154 (421)
T ss_pred eeEEEEEhhhhhhhhhccchHHHHHHHHHHHHhHHHhccCCchheeeeehhhhHHHH--------------hhhcCCCHH
Confidence 578999999999874 223345555555543336788888888765331110 011111112
Q ss_pred HHHHHhhcCCCCCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEe---CCCCCCCCCCCCCchhhHHHHHHHHhhcCc
Q 011878 81 HLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLIT---DALCPLKDPDVGTKEDQVSTIARQMVAFGL 157 (475)
Q Consensus 81 ~~i~~L~~l~~~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~T---d~~~p~~~~~~~~~~~~~~~~~~~l~~~~I 157 (475)
..|.+|+++..-.+.-.+..||-.|.-.|.. ...-..|-|++|- -..+| .++.+.+..|...+|
T Consensus 155 ~hi~~lkS~rd~~gnfSLqNaLEmar~~l~~---~~~H~trEvLiifgS~st~DP----------gdi~~tid~Lv~~~I 221 (421)
T COG5151 155 AHIGQLKSKRDCSGNFSLQNALEMARIELMK---NTMHGTREVLIIFGSTSTRDP----------GDIAETIDKLVAYNI 221 (421)
T ss_pred HHHHHhhcccccCCChhHHhHHHHhhhhhcc---cccccceEEEEEEeecccCCC----------ccHHHHHHHHHhhce
Confidence 3467777765323334456666555333221 0111234444442 22233 346666788899999
Q ss_pred EEEEEEeccCCCCCCCccccccchHHHHHHhhcC
Q 011878 158 RMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKS 191 (475)
Q Consensus 158 ~l~~i~i~~~~~~~~~~~~~~~n~~~l~~~~~~~ 191 (475)
++.++|+-.. -.+.++++.++
T Consensus 222 rV~~igL~ae-------------vaicKeickaT 242 (421)
T COG5151 222 RVHFIGLCAE-------------VAICKEICKAT 242 (421)
T ss_pred EEEEEeehhH-------------HHHHHHHHhhc
Confidence 9999998431 35667777766
No 90
>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=86.14 E-value=22 Score=30.94 Aligned_cols=133 Identities=11% Similarity=0.125 Sum_probs=76.1
Q ss_pred CCCcCCCchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEee-cCCCCH----HHHHHhhcC
Q 011878 15 SPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQD-IKVVDG----HLVQSLKHL 89 (475)
Q Consensus 15 s~sM~~~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~-l~~~~~----~~i~~L~~l 89 (475)
++.-...++.|+..+-.+++. +...-++-+.-||+.-+... ...|++-+.. .+.|.. ..++..++.
T Consensus 6 ~~~~~N~Y~~ai~~vg~il~~---Yd~dk~~p~~GFGa~~~~~~------~vsh~F~ln~~~~~p~~~Gi~gvl~~Y~~~ 76 (146)
T PF07002_consen 6 SPNQPNPYQQAIRAVGEILQD---YDSDKMIPAYGFGAKIPPDY------SVSHCFPLNGNPQNPECQGIDGVLEAYRKA 76 (146)
T ss_pred CCCCCCHHHHHHHHHHHHHHh---hccCCccceeccCCcCCCCc------ccccceeeecCCCCCcccCHHHHHHHHHHH
Confidence 333344577888888888874 57788899999998644321 2234433331 111221 234444442
Q ss_pred CCC---CCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEEEec
Q 011878 90 PQG---TCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIVVR 165 (475)
Q Consensus 90 ~~~---~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l~~i~i~ 165 (475)
... .+...|...+-.|..+..+ ..+.....--+++|||+.-. +.++....+.+..+.-+.+.++|+|
T Consensus 77 ~~~v~l~GPT~fapiI~~a~~~a~~-~~~~~~~Y~iLlIlTDG~i~--------D~~~T~~aIv~AS~~PlSIIiVGVG 146 (146)
T PF07002_consen 77 LPKVQLSGPTNFAPIINHAAKIAKQ-SNQNGQQYFILLILTDGQIT--------DMEETIDAIVEASKLPLSIIIVGVG 146 (146)
T ss_pred hhheEECCCccHHHHHHHHHHHHhh-hccCCceEEEEEEecccccc--------cHHHHHHHHHHHccCCeEEEEEEeC
Confidence 211 3356788888888887654 12222344557777999753 1234444445556677777777764
No 91
>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=83.54 E-value=20 Score=36.14 Aligned_cols=36 Identities=6% Similarity=-0.022 Sum_probs=29.6
Q ss_pred ChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCC
Q 011878 97 DFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPL 133 (475)
Q Consensus 97 d~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~ 133 (475)
-.++|+-.|.+++.+++. ...|+-=.+-+||||+=.
T Consensus 270 ~vSSA~~l~~eII~~rYp-p~~wNIY~f~aSDGDNw~ 305 (371)
T TIGR02877 270 YCSSGYKKALEIIDERYN-PARYNIYAFHFSDGDNLT 305 (371)
T ss_pred EehHHHHHHHHHHHhhCC-hhhCeeEEEEcccCCCcc
Confidence 578999999999998875 346777788889999854
No 92
>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=83.09 E-value=18 Score=37.27 Aligned_cols=36 Identities=8% Similarity=0.010 Sum_probs=29.3
Q ss_pred ChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCC
Q 011878 97 DFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPL 133 (475)
Q Consensus 97 d~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~ 133 (475)
-+++|+-.|.+++..++. ...|+-=.|-+||||+=.
T Consensus 314 ~vSSA~~l~~~ii~eryp-p~~wNiY~~~~SDGDN~~ 349 (421)
T PF04285_consen 314 RVSSAYELALEIIEERYP-PSDWNIYVFHASDGDNWS 349 (421)
T ss_pred EehHHHHHHHHHHHhhCC-hhhceeeeEEcccCcccc
Confidence 578999999999998775 346777788889999853
No 93
>PRK05325 hypothetical protein; Provisional
Probab=79.53 E-value=32 Score=35.17 Aligned_cols=36 Identities=8% Similarity=-0.042 Sum_probs=29.6
Q ss_pred ChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCC
Q 011878 97 DFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPL 133 (475)
Q Consensus 97 d~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~ 133 (475)
-.++|+-+|.+++.+++. ...|+-=.|-+||||+=.
T Consensus 290 ~vSSA~~l~~eIi~~rYp-p~~wNIY~f~aSDGDNw~ 325 (401)
T PRK05325 290 IVSSAYKLALEIIEERYP-PAEWNIYAFQASDGDNWS 325 (401)
T ss_pred EehHHHHHHHHHHHhhCC-HhHCeeEEEEcccCCCcC
Confidence 578999999999998875 347777788889999854
No 94
>COG1721 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]
Probab=75.39 E-value=5.8 Score=41.01 Aligned_cols=47 Identities=26% Similarity=0.428 Sum_probs=38.1
Q ss_pred ceEEEEEEecCCCcC------CCchHHHHHHHHHHHHHHhcCCccEEEEEEEccC
Q 011878 5 REALLLLLDVSPSMH------SVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTE 53 (475)
Q Consensus 5 ke~~vflID~s~sM~------~~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~ 53 (475)
..-+++++|+|.+|. ..++.|...+..+... ....+|.||+.+||..
T Consensus 224 ~~~v~l~lD~~~~m~~~~~~~~~~e~av~~a~~la~~--~l~~gd~vg~~~~~~~ 276 (416)
T COG1721 224 GRTVVLVLDASRSMLFGSGVASKFEEAVRAAASLAYA--ALKNGDRVGLLIFGGG 276 (416)
T ss_pred CceEEEEEeCCccccCCCCCccHHHHHHHHHHHHHHH--HHhCCCeeEEEEECCC
Confidence 567899999999998 4678888877766663 3678999999999965
No 95
>COG2718 Uncharacterized conserved protein [Function unknown]
Probab=75.29 E-value=47 Score=33.49 Aligned_cols=38 Identities=11% Similarity=0.007 Sum_probs=30.3
Q ss_pred ChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCC
Q 011878 97 DFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKD 135 (475)
Q Consensus 97 d~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~ 135 (475)
=.+.||-.+.+.+..++. ...|+.=.+-++|||+-+++
T Consensus 314 ivSSAl~~m~evi~ErYp-~aeWNIY~fqaSDGDN~~dD 351 (423)
T COG2718 314 IVSSALKLMLEVIKERYP-PAEWNIYAFQASDGDNWADD 351 (423)
T ss_pred EeHHHHHHHHHHHHhhCC-hhheeeeeeeecCCccccCC
Confidence 468899999999988774 34678778888999997653
No 96
>COG5028 Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]
Probab=73.03 E-value=49 Score=36.31 Aligned_cols=151 Identities=13% Similarity=0.150 Sum_probs=78.5
Q ss_pred eEEEEEEecCCC-cCCC-chHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCc-ccEEEEeecCCCCH--
Q 011878 6 EALLLLLDVSPS-MHSV-LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGY-EHVKVLQDIKVVDG-- 80 (475)
Q Consensus 6 e~~vflID~s~s-M~~~-~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y-~~i~~~~~l~~~~~-- 80 (475)
-..||+||||-. |... +..+.+.|..-+...-=..++-+||+|+|-..=.--.+ .++. +|..+.-+++.|=.
T Consensus 277 ~~yvFlIDVS~~a~~~g~~~a~~r~Il~~l~~~~~~dpr~kIaii~fD~sl~ffk~---s~d~~~~~~~vsdld~pFlPf 353 (861)
T COG5028 277 PVYVFLIDVSFEAIKNGLVKAAIRAILENLDQIPNFDPRTKIAIICFDSSLHFFKL---SPDLDEQMLIVSDLDEPFLPF 353 (861)
T ss_pred CEEEEEEEeehHhhhcchHHHHHHHHHhhccCCCCCCCcceEEEEEEcceeeEEec---CCCCccceeeecccccccccC
Confidence 367999999863 3333 33344555544443322348999999999765321110 1111 13444443332211
Q ss_pred ---------H--------HHHHhhcCCCC--CCCCChhHHHHHHHHHHHHHhccCcceeeEEEEE-eC---CCCCCCCCC
Q 011878 81 ---------H--------LVQSLKHLPQG--TCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLI-TD---ALCPLKDPD 137 (475)
Q Consensus 81 ---------~--------~i~~L~~l~~~--~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~-Td---~~~p~~~~~ 137 (475)
+ +++.+..+..+ .....+.+||.+|..++.. .+.|.|+++ |= |-.....-.
T Consensus 354 ~s~~fv~pl~~~k~~~etLl~~~~~If~d~~~pk~~~G~aLk~a~~l~g~------~GGkii~~~stlPn~G~Gkl~~r~ 427 (861)
T COG5028 354 PSGLFVLPLKSCKQIIETLLDRVPRIFQDNKSPKNALGPALKAAKSLIGG------TGGKIIVFLSTLPNMGIGKLQLRE 427 (861)
T ss_pred CcchhcccHHHHHHHHHHHHHHhhhhhcccCCCccccCHHHHHHHHHhhc------cCceEEEEeecCCCcccccccccc
Confidence 1 12223333222 2234689999999876432 334666666 40 111111000
Q ss_pred C------CCchhhHHHHHHHHhhcCcEEEEEEec
Q 011878 138 V------GTKEDQVSTIARQMVAFGLRMKNIVVR 165 (475)
Q Consensus 138 ~------~~~~~~~~~~~~~l~~~~I~l~~i~i~ 165 (475)
+ .-...-...++.++.+.||.+.+|...
T Consensus 428 d~e~~ll~c~d~fYk~~a~e~~k~gIsvd~Flt~ 461 (861)
T COG5028 428 DKESSLLSCKDSFYKEFAIECSKVGISVDLFLTS 461 (861)
T ss_pred cchhhhccccchHHHHHHHHHHHhcceEEEEecc
Confidence 0 011134567889999999999999873
No 97
>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=66.69 E-value=23 Score=36.72 Aligned_cols=121 Identities=19% Similarity=0.188 Sum_probs=60.3
Q ss_pred EEEEEecCCCcCCCchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCc-----------CccccccCC------CcccEE
Q 011878 8 LLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEET-----------ENELTKEVG------GYEHVK 70 (475)
Q Consensus 8 ~vflID~s~sM~~~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t-----------~n~~~~~~~------~y~~i~ 70 (475)
+.||+|+|.||...++..+.....|.++----.++=++|+=-|--... .||.....+ +|+|+
T Consensus 105 LYyLmDlS~Sm~ddl~~l~~lg~~l~~~~~~it~~~~~GfGsfvdK~~~P~~~~~p~~l~~pc~~~~~~c~~~~~f~~~- 183 (426)
T PF00362_consen 105 LYYLMDLSYSMKDDLENLKSLGQDLAEEMRNITSNFRLGFGSFVDKPVMPFVSTTPEKLKNPCPSKNPNCQPPFSFRHV- 183 (426)
T ss_dssp EEEEEE-SGGGHHHHHHHCCCCHHHHHHHHTT-SSEEEEEEEESSSSSTTTST-SSHCHHSTSCCTTS--B---SEEEE-
T ss_pred EEEEeechhhhhhhHHHHHHHHHHHHHHHHhcCccceEechhhcccccCCcccCChhhhcCcccccCCCCCCCeeeEEe-
Confidence 568999999999877665444444333221124666777666643321 112101011 67776
Q ss_pred EEeecCCCCHHHHHHhhcCCCC---CCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCC
Q 011878 71 VLQDIKVVDGHLVQSLKHLPQG---TCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCP 132 (475)
Q Consensus 71 ~~~~l~~~~~~~i~~L~~l~~~---~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p 132 (475)
.+|+.-..+..+.+.+...+ +..-.-+|||..|.=- .++.+=+....|-|++.||+..-
T Consensus 184 --l~Lt~~~~~F~~~v~~~~is~n~D~PEgg~dal~Qa~vC-~~~igWr~~a~~llv~~TD~~fH 245 (426)
T PF00362_consen 184 --LSLTDDITEFNEEVNKQKISGNLDAPEGGLDALMQAAVC-QEEIGWRNEARRLLVFSTDAGFH 245 (426)
T ss_dssp --EEEES-HHHHHHHHHTS--B--SSSSBSHHHHHHHHHH--HHHHT--STSEEEEEEEESS-B-
T ss_pred --ecccchHHHHHHhhhhccccCCCCCCccccchheeeeec-ccccCcccCceEEEEEEcCCccc
Confidence 56776666677777775332 1122357887765321 12122223445556666887543
No 98
>COG4902 Uncharacterized protein conserved in archaea [Function unknown]
Probab=59.80 E-value=18 Score=31.02 Aligned_cols=42 Identities=14% Similarity=0.180 Sum_probs=32.5
Q ss_pred CHHHHHHHHHHHHhcCCCCCCCCcCCCCCCCCChhhHHHHHHhh
Q 011878 426 NEQQQEAADNLVKMLDLAPSGKGEILQPELTPNPALEVLNICGY 469 (475)
Q Consensus 426 ~~~q~~~~~~lI~~l~l~~~~~~~~~~p~~~~NP~lq~~y~~l~ 469 (475)
.++.++|++.|+.+..+.++.. .-.-..|.||.+|.+|.-|.
T Consensus 87 EQ~HmDAVk~LlekYnv~dP~~--~~siGvF~NpelqeLYn~Lv 128 (189)
T COG4902 87 EQEHMDAVKSLLEKYNVQDPAS--TTSIGVFTNPELQELYNQLV 128 (189)
T ss_pred HHHHHHHHHHHHHHcCCCCCCc--cCcceeecCHHHHHHHHHHH
Confidence 3567899999999999976532 22346789999999998664
No 99
>KOG1985 consensus Vesicle coat complex COPII, subunit SEC24/subunit SFB2 [Intracellular trafficking, secretion, and vesicular transport]
Probab=59.27 E-value=2.4e+02 Score=31.57 Aligned_cols=152 Identities=14% Similarity=0.159 Sum_probs=75.3
Q ss_pred eEEEEEEecCCC-cCCC-chHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCC-----
Q 011878 6 EALLLLLDVSPS-MHSV-LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV----- 78 (475)
Q Consensus 6 e~~vflID~s~s-M~~~-~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~----- 78 (475)
-..+|+||||-+ |... ++.+.+.+..=+..+ =..++.+||+|.|-+.=---.+..+ -...+--++.++..+
T Consensus 295 avy~FliDVS~~a~ksG~L~~~~~slL~~LD~l-pgd~Rt~igfi~fDs~ihfy~~~~~-~~qp~mm~vsdl~d~flp~p 372 (887)
T KOG1985|consen 295 AVYVFLIDVSISAIKSGYLETVARSLLENLDAL-PGDPRTRIGFITFDSTIHFYSVQGD-LNQPQMMIVSDLDDPFLPMP 372 (887)
T ss_pred ceEEEEEEeehHhhhhhHHHHHHHHHHHhhhcC-CCCCcceEEEEEeeceeeEEecCCC-cCCCceeeeccccccccCCc
Confidence 457999999975 3332 344444444434332 1457889999998654210000000 011121122221110
Q ss_pred -----CH--------HHHHHhhcCCC--CCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCC-----CCC
Q 011878 79 -----DG--------HLVQSLKHLPQ--GTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKD-----PDV 138 (475)
Q Consensus 79 -----~~--------~~i~~L~~l~~--~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~-----~~~ 138 (475)
+. ..+++|..+-. ......+..||.+|.+++... +. ||++|-..--+.+. .++
T Consensus 373 d~lLv~L~~ck~~i~~lL~~lp~~F~~~~~t~~alGpALkaaf~li~~~-GG------ri~vf~s~lPnlG~G~L~~rEd 445 (887)
T KOG1985|consen 373 DSLLVPLKECKDLIETLLKTLPEMFQDTRSTGSALGPALKAAFNLIGST-GG------RISVFQSTLPNLGAGKLKPRED 445 (887)
T ss_pred hhheeeHHHHHHHHHHHHHHHHHHHhhccCcccccCHHHHHHHHHHhhc-CC------eEEEEeccCCCCCccccccccc
Confidence 11 12333333211 123457899999999987663 22 56666554332321 001
Q ss_pred ----CCc---------hhhHHHHHHHHhhcCcEEEEEEecc
Q 011878 139 ----GTK---------EDQVSTIARQMVAFGLRMKNIVVRA 166 (475)
Q Consensus 139 ----~~~---------~~~~~~~~~~l~~~~I~l~~i~i~~ 166 (475)
+.+ .+-....+-+....+|.+.+|.+..
T Consensus 446 p~~~~s~~~~qlL~~~t~FYK~~a~~cs~~qI~VDlFl~s~ 486 (887)
T KOG1985|consen 446 PNVRSSDEDSQLLSPATDFYKDLALECSKSQICVDLFLFSE 486 (887)
T ss_pred cccccchhhhhccCCCchHHHHHHHHhccCceEEEEEeecc
Confidence 000 1123456667778999999998853
No 100
>COG2304 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=56.01 E-value=2.3e+02 Score=28.56 Aligned_cols=139 Identities=15% Similarity=0.192 Sum_probs=81.2
Q ss_pred ceEEEEEEecCCCcCCCc-hHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCCHHHH
Q 011878 5 REALLLLLDVSPSMHSVL-PDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHLV 83 (475)
Q Consensus 5 ke~~vflID~s~sM~~~~-~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~~~~i 83 (475)
.....+++|.+.||.... ..+..+...++. ...+.|.+++++|.. ...-.. ............
T Consensus 37 ~~~~~~~~~~~~s~~~~~~~~~~~~~~~~v~---~~~~~~~~~~~~~~~-~~~~~~------------~~~~~~~~~~~~ 100 (399)
T COG2304 37 PANLTLAIDTSGSMTGALLELAKSAAIELVN---GLNPGDLLSIVTFAG-SADVLI------------PPTGATNKESIT 100 (399)
T ss_pred CcceEEEeccCCCccchhHHHHHHHHHHHhc---ccCCCCceEEEEecC-Ccceec------------CcccccCHHHHH
Confidence 456789999999998643 334444444433 368999999999998 322110 001112222334
Q ss_pred HHhhc-CCCCCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEE
Q 011878 84 QSLKH-LPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNI 162 (475)
Q Consensus 84 ~~L~~-l~~~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l~~i 162 (475)
..+.. +.... .....-+++.+.+.+.... ......++.+.||+.+.+.. .+...+....+.....+|.+..+
T Consensus 101 ~~i~~~~~~~~-~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~tdg~~~~~~----~d~~~~~~~~~~~~~~~i~~~~~ 173 (399)
T COG2304 101 AAIDQSLQAGG-ATAVEASLSLAVELAAKAL--PRGTLNRILLLTDGENNLGL----VDPSRLSALAKLAAGKGIVLDTL 173 (399)
T ss_pred HHHhhhhcccc-ccHHHHHHHHHHHHhhhcC--CccceeeEeeeccCccccCC----CCHHHHHHHhcccccCceEEEEE
Confidence 44554 33322 2234445555655554422 23567889999998776542 23345555555555679999999
Q ss_pred Eecc
Q 011878 163 VVRA 166 (475)
Q Consensus 163 ~i~~ 166 (475)
+++.
T Consensus 174 g~~~ 177 (399)
T COG2304 174 GLGD 177 (399)
T ss_pred eccc
Confidence 9854
No 101
>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=55.95 E-value=1.7e+02 Score=27.04 Aligned_cols=140 Identities=15% Similarity=0.158 Sum_probs=76.8
Q ss_pred eEEEEEEecCCCcCCC---ch---HHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCC-C
Q 011878 6 EALLLLLDVSPSMHSV---LP---DVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKV-V 78 (475)
Q Consensus 6 e~~vflID~s~sM~~~---~~---~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~-~ 78 (475)
-.+++++|+|.||-.. ++ .|--.-.--+.+-|...+.-.|+|-+|-=..... -.+..|-+. -
T Consensus 4 laLvLavDvS~SVD~~E~~lQ~~G~A~Al~dp~V~~Ai~~g~~g~Iav~~~eWsg~~~-----------q~~~v~Wt~i~ 72 (205)
T PF06707_consen 4 LALVLAVDVSGSVDADEYRLQREGYAAALRDPEVIAAILSGPIGRIAVAVVEWSGPGR-----------QRVVVPWTRID 72 (205)
T ss_pred ceeeeeeeccCCCCHHHHHHHHHHHHHHHCCHHHHHHHhcCCCCeEEEEEEEecCCCC-----------ceEEeCCEEeC
Confidence 3689999999999863 22 1212222344455557777777777765332111 112333221 1
Q ss_pred CHH----HHHHhhcCCCC-CCCCChhHHHHHHHHHHHHHhccCcceeeEEEEE-eCCCCCCCCCCCCCchhhHHHHHHHH
Q 011878 79 DGH----LVQSLKHLPQG-TCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLI-TDALCPLKDPDVGTKEDQVSTIARQM 152 (475)
Q Consensus 79 ~~~----~i~~L~~l~~~-~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~-Td~~~p~~~~~~~~~~~~~~~~~~~l 152 (475)
+.. ....|...+.. ...+.+..||..|..+|.+. .-...||++=+ .|+.++.+. .. .......+
T Consensus 73 ~~~da~a~A~~l~~~~r~~~~~Taig~Al~~a~~ll~~~---~~~~~RrVIDvSGDG~~N~G~----~p---~~~ard~~ 142 (205)
T PF06707_consen 73 SPADAEAFAARLRAAPRRFGGRTAIGSALDFAAALLAQN---PFECWRRVIDVSGDGPNNQGP----RP---VTSARDAA 142 (205)
T ss_pred CHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHHHHhC---CCCCceEEEEECCCCCCCCCC----Cc---cHHHHHHH
Confidence 222 23344444332 22368999999999998752 22244555544 666665542 11 12333455
Q ss_pred hhcCcEEEEEEecc
Q 011878 153 VAFGLRMKNIVVRA 166 (475)
Q Consensus 153 ~~~~I~l~~i~i~~ 166 (475)
...||.+.-+.|..
T Consensus 143 ~~~GitINgL~I~~ 156 (205)
T PF06707_consen 143 VAAGITINGLAILD 156 (205)
T ss_pred HHCCeEEeeeEecC
Confidence 67899888887743
No 102
>PF11443 DUF2828: Domain of unknown function (DUF2828); InterPro: IPR024553 This uncharacterised domain is found in eukaryotic, bacterial and viral proteins.
Probab=55.45 E-value=1.8e+02 Score=31.05 Aligned_cols=136 Identities=18% Similarity=0.178 Sum_probs=67.2
Q ss_pred eEEEEEEecCCCcCCCchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccEEEEeecCCCC-HHHHH
Q 011878 6 EALLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVD-GHLVQ 84 (475)
Q Consensus 6 e~~vflID~s~sM~~~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i~~~~~l~~~~-~~~i~ 84 (475)
+-+|-+.|+|+||... .....+...|+-.-. +.+-=.=.+|.|..+. . ++.+.-.+ .+.++
T Consensus 341 ~n~iav~DvSGSM~~~-pm~vaiaLgll~ae~-~~~pf~~~~ITFs~~P----------~------~~~i~g~~l~ekv~ 402 (534)
T PF11443_consen 341 ENCIAVCDVSGSMSGP-PMDVAIALGLLIAEL-NKGPFKGRFITFSENP----------Q------LHKIKGDTLREKVR 402 (534)
T ss_pred cceEEEEecCCccCcc-HHHHHHHHHHHHHHh-cccccCCeEEeecCCc----------e------EEEecCCCHHHHHH
Confidence 4677889999999976 222222222222111 3222223467777662 1 22332222 23444
Q ss_pred HhhcCCCCCCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCC-CchhhHHHHHHHHhhcCcEEE
Q 011878 85 SLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVG-TKEDQVSTIARQMVAFGLRMK 160 (475)
Q Consensus 85 ~L~~l~~~~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~-~~~~~~~~~~~~l~~~~I~l~ 160 (475)
.+.+..-+ ..+++-.++-+=+++..+.--++-.--|+||+|||=+-........ .-....+.+.+..++.|-.+-
T Consensus 403 ~~~~~~wg-~nTn~~aVFdlIL~~Av~~~l~~e~M~k~lfV~SDMeFD~a~~~~~~~w~T~~e~i~~~f~~aGY~~P 478 (534)
T PF11443_consen 403 FIRRMDWG-MNTNFQAVFDLILETAVKNKLKQEDMPKRLFVFSDMEFDQASNSSDRPWETNFEAIKRKFEEAGYELP 478 (534)
T ss_pred HHHhCCcc-cCCcHHHHHHHHHHHHHHcCCChHHCCceEEEEeccccccccccccCccccHHHHHHHHHHHhCCCCC
Confidence 45544443 2456665553333433221111112468999999843322210000 012467778888999888753
No 103
>PF09968 DUF2202: Uncharacterized protein domain (DUF2202); InterPro: IPR019243 This domain, found in various hypothetical archaeal proteins, has no known function.; PDB: 3Q4O_A 3Q4Q_A 3Q4R_A 3Q4N_A.
Probab=53.21 E-value=24 Score=31.21 Aligned_cols=43 Identities=19% Similarity=0.073 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHhcCCCCCCCCcCCCCCCCCChhhHHHHHHhhhc
Q 011878 427 EQQQEAADNLVKMLDLAPSGKGEILQPELTPNPALEVLNICGYFG 471 (475)
Q Consensus 427 ~~q~~~~~~lI~~l~l~~~~~~~~~~p~~~~NP~lq~~y~~l~~~ 471 (475)
...++++..|+++..+.++- .....+.|.||.||.+|.-|...
T Consensus 39 q~Hmdav~~Ll~kY~l~dP~--~~~~~G~f~~~~lq~LY~~Lv~~ 81 (162)
T PF09968_consen 39 QRHMDAVKALLEKYGLEDPV--EGDPVGVFTNPELQELYNQLVEQ 81 (162)
T ss_dssp HHHHHHHHHHHHHTT---S---SS-STT--SSHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCCCCC--ccCCCCCcCcHHHHHHHHHHHHH
Confidence 34678999999999997542 23556899999999999988653
No 104
>COG3552 CoxE Protein containing von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=50.95 E-value=18 Score=36.16 Aligned_cols=47 Identities=36% Similarity=0.362 Sum_probs=35.6
Q ss_pred ceEEEEEEecCCCcCCCchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCc
Q 011878 5 REALLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETEN 57 (475)
Q Consensus 5 ke~~vflID~s~sM~~~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n 57 (475)
|--+|+++|||+||.......+.++.-+.++ .+++-+.+|||.-|+.
T Consensus 218 ~~~lvvL~DVSGSm~~ys~~~L~l~hAl~q~------~~R~~~F~F~TRLt~v 264 (395)
T COG3552 218 KPPLVVLCDVSGSMSGYSRIFLHLLHALRQQ------RSRVHVFLFGTRLTRV 264 (395)
T ss_pred CCCeEEEEecccchhhhHHHHHHHHHHHHhc------ccceeEEEeechHHHH
Confidence 5568999999999997666667777777773 3445599999996553
No 105
>cd03364 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. E. coli DnaG is a single subunit enzyme.
Probab=49.66 E-value=29 Score=26.33 Aligned_cols=35 Identities=14% Similarity=0.201 Sum_probs=28.0
Q ss_pred eeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEE
Q 011878 120 KKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNI 162 (475)
Q Consensus 120 ~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l~~i 162 (475)
.++|++++|+|.+ .......+++.|...|+.+.++
T Consensus 43 ~~~vii~~D~D~a--------G~~a~~~~~~~l~~~g~~~~~~ 77 (79)
T cd03364 43 AKEVILAFDGDEA--------GQKAALRALELLLKLGLNVRVL 77 (79)
T ss_pred CCeEEEEECCCHH--------HHHHHHHHHHHHHHCCCeEEEE
Confidence 5899999999875 2356778888999999887765
No 106
>COG5047 SEC23 Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking and secretion]
Probab=49.56 E-value=1.1e+02 Score=32.78 Aligned_cols=33 Identities=15% Similarity=0.314 Sum_probs=25.4
Q ss_pred hHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCC
Q 011878 99 LDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLK 134 (475)
Q Consensus 99 ~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~ 134 (475)
..||.+|+.++..-+. ...-+|+||++|-..++
T Consensus 260 GsAl~ias~Ll~~~~p---~~~~~i~lF~~GPcTvG 292 (755)
T COG5047 260 GSALNIASSLLEQCFP---NAGCHIVLFAGGPCTVG 292 (755)
T ss_pred chhHHHHHHHHHhhcc---CcceeEEEEcCCCcccc
Confidence 6788999998876332 45789999999977655
No 107
>KOG0071 consensus GTP-binding ADP-ribosylation factor Arf6 (dArf3) [Intracellular trafficking, secretion, and vesicular transport]
Probab=47.78 E-value=87 Score=27.11 Aligned_cols=47 Identities=13% Similarity=0.293 Sum_probs=35.9
Q ss_pred CceEEEEEEecCCCcCCCchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCc
Q 011878 4 TREALLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEET 55 (475)
Q Consensus 4 ~ke~~vflID~s~sM~~~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t 55 (475)
+-.++||++|.+.+ .++++|..-+.++++.+ .-.|.+=||+.|-..-
T Consensus 84 gtqglIFV~Dsa~~--dr~eeAr~ELh~ii~~~---em~~~~~LvlANkQDl 130 (180)
T KOG0071|consen 84 GTQGLIFVVDSADR--DRIEEARNELHRIINDR---EMRDAIILILANKQDL 130 (180)
T ss_pred CCceEEEEEeccch--hhHHHHHHHHHHHhCCH---hhhcceEEEEecCccc
Confidence 56799999999887 77899988888777743 3467777888776643
No 108
>PF13662 Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=42.28 E-value=16 Score=27.96 Aligned_cols=35 Identities=20% Similarity=0.384 Sum_probs=20.2
Q ss_pred eeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEE
Q 011878 120 KKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNI 162 (475)
Q Consensus 120 ~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l~~i 162 (475)
.++|++++|+|.+ .+.....+.+.|...|+++..+
T Consensus 46 ~~~Vii~~D~D~~--------G~~~a~~i~~~l~~~gi~v~~v 80 (81)
T PF13662_consen 46 VKEVIIAFDNDKA--------GEKAAQKIAKKLLPLGIRVTRV 80 (81)
T ss_dssp -SEEEEEEESSHH--------HHHHHHHHHHHHG---------
T ss_pred CceEEEEeCcCHH--------HHHHHHHHHHHHHhhccccccC
Confidence 6899999999985 2456777778888889887654
No 109
>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=40.81 E-value=34 Score=26.29 Aligned_cols=41 Identities=22% Similarity=0.359 Sum_probs=27.3
Q ss_pred ceEEEEEEecCCCcCC------CchHHHHHHHHHHHHHHhcCCccEEEE
Q 011878 5 REALLLLLDVSPSMHS------VLPDVEKLCSRLIQKKLIYGKNHEVGV 47 (475)
Q Consensus 5 ke~~vflID~s~sM~~------~~~~a~~~~~~l~~~ki~~~~~D~vgl 47 (475)
..-+++++|.+++|.. .++.++.++..++..- .+.++.|||
T Consensus 40 ~~~~~i~ld~~~~~~~~~~~~~~~e~~l~~a~~l~~~~--~~~g~~v~L 86 (86)
T PF01882_consen 40 SQPVWIVLDLSPSMYFGSNGRSKFERALSAAASLANQA--LRQGDPVGL 86 (86)
T ss_pred CCcEEEEEECCCccccCcCCCCHHHHHHHHHHHHHHHH--HhcCCcccC
Confidence 4568899999999974 3566677766666543 345555543
No 110
>COG4547 CobT Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]
Probab=39.32 E-value=1.6e+02 Score=30.64 Aligned_cols=151 Identities=16% Similarity=0.186 Sum_probs=71.1
Q ss_pred eEEEEEEecCCCcCC-CchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCcc----ccccCC--CcccEEEEeec---
Q 011878 6 EALLLLLDVSPSMHS-VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENE----LTKEVG--GYEHVKVLQDI--- 75 (475)
Q Consensus 6 e~~vflID~s~sM~~-~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~----~~~~~~--~y~~i~~~~~l--- 75 (475)
-++-++||-|+||.. ++..|..|+..|-+.. -+-+-.|-|.-|-|..=+.. .+-..| .+++- +.+|
T Consensus 414 tvVtlviDnSGSMrGRpItvAatcAdilArtL--eRcgVk~eIlGFTT~awkGg~sre~wlk~Gkp~~pgr--lndlrhi 489 (620)
T COG4547 414 TVVTLVIDNSGSMRGRPITVAATCADILARTL--ERCGVKVEILGFTTKAWKGGQSRETWLKRGKPAFPGR--LNDLRHI 489 (620)
T ss_pred hhheeeeccCCCcCCcceehhHHHHHHHHHHH--HHcCCceEEeeeeeccccCCccHHHHHhcCCCCCchh--hhhHHHH
Confidence 367789999999976 5777777777666644 22233333444444321110 000000 11110 1111
Q ss_pred --CCCCHHHHHHhhcCCCCCCCCCh-----hHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCC---C-C-Cchh
Q 011878 76 --KVVDGHLVQSLKHLPQGTCAGDF-----LDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPD---V-G-TKED 143 (475)
Q Consensus 76 --~~~~~~~i~~L~~l~~~~~~gd~-----~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~---~-~-~~~~ 143 (475)
...++...+.=++|-.-..+|-+ .+||.-|-+.|.. + -..|+|+++..+..|+..+. + + --..
T Consensus 490 iyksAdaPwrRARrnlGlmmreglLkeNiDGEal~wah~rl~g----R-pEqrkIlmmiSDGAPvddstlsvnpGnyler 564 (620)
T COG4547 490 IYKSADAPWRRARRNLGLMMREGLLKENIDGEALMWAHQRLIG----R-PEQRKILMMISDGAPVDDSTLSVNPGNYLER 564 (620)
T ss_pred HHhccCCHHHHHHhhcchhhhcchhhccCChHHHHHHHHHHhc----C-hhhceEEEEecCCCcccccccccCCchHHHH
Confidence 12222223322222000011211 4465555555442 1 33566666555556776310 0 1 1235
Q ss_pred hHHHHHHHHhh-cCcEEEEEEec
Q 011878 144 QVSTIARQMVA-FGLRMKNIVVR 165 (475)
Q Consensus 144 ~~~~~~~~l~~-~~I~l~~i~i~ 165 (475)
.+++.++.+.. .-|+|--|||+
T Consensus 565 HLRaVieeIEtrSpveLlAIGig 587 (620)
T COG4547 565 HLRAVIEEIETRSPVELLAIGIG 587 (620)
T ss_pred HHHHHHHHHhcCCchhheeeecc
Confidence 67777877765 46777778875
No 111
>KOG1327 consensus Copine [Signal transduction mechanisms]
Probab=38.89 E-value=4.3e+02 Score=28.16 Aligned_cols=143 Identities=13% Similarity=0.064 Sum_probs=78.8
Q ss_pred eEEEEEEecCCCcCC----------------CchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCcCccccccCCCcccE
Q 011878 6 EALLLLLDVSPSMHS----------------VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHV 69 (475)
Q Consensus 6 e~~vflID~s~sM~~----------------~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t~n~~~~~~~~y~~i 69 (475)
-..++.||.+.|=.. +++.|+.++-..++ -+.+..++...-||..-...- .--|.
T Consensus 286 lnf~vgIDfTaSNg~p~~~sSLHyi~p~~~N~Y~~Ai~~vG~~lq---~ydsdk~fpa~GFGakip~~~------~vs~~ 356 (529)
T KOG1327|consen 286 LNFTVGIDFTASNGDPRNPSSLHYIDPHQPNPYEQAIRSVGETLQ---DYDSDKLFPAFGFGAKIPPDG------QVSHE 356 (529)
T ss_pred eeeEEEEEEeccCCCCCCCCcceecCCCCCCHHHHHHHHHhhhhc---ccCCCCccccccccccCCCCc------ccccc
Confidence 356889999887332 24567777777766 378899999999998832210 00111
Q ss_pred EEEe--ecCCCC---HHHHHHhhcCCCC---CCCCChhHHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCc
Q 011878 70 KVLQ--DIKVVD---GHLVQSLKHLPQG---TCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTK 141 (475)
Q Consensus 70 ~~~~--~l~~~~---~~~i~~L~~l~~~---~~~gd~~daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~ 141 (475)
+++. |-.+.. -..++..++.... .+.++++..|..+..+..+... .....--+++||||.-. +
T Consensus 357 f~ln~~~~~~~c~Gi~gVl~aY~~~lp~v~l~GPTnFaPII~~va~~a~~~~~-~~~qY~VLlIitDG~vT--------d 427 (529)
T KOG1327|consen 357 FVLNFNPEDPECRGIEGVLEAYRKALPNVQLYGPTNFSPIINHVARIAQQSGN-TAGQYHVLLIITDGVVT--------D 427 (529)
T ss_pred eeecCCCCCCccccHHHHHHHHHhhcccccccCCCccHHHHHHHHHHHHHhcc-CCcceEEEEEEeCCccc--------c
Confidence 1111 111111 1235555553222 2345777777777777655321 11223446777998542 2
Q ss_pred hhhHHHHHHHHhhcCcEEEEEEecc
Q 011878 142 EDQVSTIARQMVAFGLRMKNIVVRA 166 (475)
Q Consensus 142 ~~~~~~~~~~l~~~~I~l~~i~i~~ 166 (475)
..+....+-...++=..|.++|+|.
T Consensus 428 m~~T~~AIV~AS~lPlSIIiVGVGd 452 (529)
T KOG1327|consen 428 MKETRDAIVSASDLPLSIIIVGVGD 452 (529)
T ss_pred HHHHHHHHHhhccCCeEEEEEEeCC
Confidence 2344444555566666777778763
No 112
>PF07744 SPOC: SPOC domain; InterPro: IPR012921 Spen (split end) proteins regulate the expression of key transcriptional effectors in diverse signalling pathways. They are large proteins characterised by N-terminal RNA-binding motifs and a highly conserved C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. The function of the SPOC domain is unknown, but the SPOC domain of the SHARP Spen protein has been implicated in the interaction of SHARP with the SMRT/NcoR corepressor, where SHARP plays an essential role in the repressor complex []. The SPOC domain is folded into a single compact domain consisting of a beta-barrel with seven strands framed by six alpha helices. A number of deep grooves and clefts in the surface, plus two nonpolar loops, render the SPOC domain well suited to protein-protein interactions; most of the conserved residues occur on the protein surface rather than in the core. Other proteins containing a SPOC domain include drosophila Split ends, which promotes sclerite development in the head and restricts it in the thorax, and mouse MINT (homologue of SHARP), which is involved in skeletal and neuronal development via its repression of Msx2.; PDB: 1OW1_A.
Probab=37.64 E-value=61 Score=26.54 Aligned_cols=41 Identities=17% Similarity=0.112 Sum_probs=27.1
Q ss_pred ChhhHHHHHHHHHHHHhcCeEEEEEEEecCCCCceEEEEecc
Q 011878 344 NSRATVAVSALARAMKEMNKVAIVRCVWRQGQQSVVVGVLTP 385 (475)
Q Consensus 344 ~~~s~~~f~aL~~am~~~~~vai~r~v~r~~~~~~~v~~L~P 385 (475)
.......|..|++=|.++++++|+..-...... .....|+|
T Consensus 79 ~~~~~~~~~~l~~Yl~~k~r~GVv~~~~~~~~~-~~dlYl~P 119 (119)
T PF07744_consen 79 SNSDRRPFQKLVDYLKSKQRAGVVSVGNSPSGQ-VKDLYLFP 119 (119)
T ss_dssp HHHHHHHHHHTHHHHHHHTEEEEEEE--TT--S--EEEEEE-
T ss_pred CHHHHHHHHHHHHHHhhCCEEEEEecCCCCCCc-eeEEEEcC
Confidence 445678899999999999999999776544333 33335666
No 113
>PF13344 Hydrolase_6: Haloacid dehalogenase-like hydrolase; PDB: 2HO4_B 1YV9_A 1WVI_B 3EPR_A 2P27_A 2OYC_A 2CFT_A 2P69_A 2CFS_A 2CFR_A ....
Probab=26.01 E-value=1.1e+02 Score=24.52 Aligned_cols=29 Identities=14% Similarity=0.302 Sum_probs=20.4
Q ss_pred eeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEE
Q 011878 120 KKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRM 159 (475)
Q Consensus 120 ~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l 159 (475)
.++++++||+.+. .....++.|+..|+.+
T Consensus 30 g~~~~~lTNns~~-----------s~~~~~~~L~~~Gi~~ 58 (101)
T PF13344_consen 30 GKPVVFLTNNSSR-----------SREEYAKKLKKLGIPV 58 (101)
T ss_dssp TSEEEEEES-SSS------------HHHHHHHHHHTTTT-
T ss_pred CCCEEEEeCCCCC-----------CHHHHHHHHHhcCcCC
Confidence 4899999999653 2456678888999874
No 114
>PF01975 SurE: Survival protein SurE; InterPro: IPR002828 This entry represents a SurE-like structural domain with a 3-layer alpha/bete/alpha topology that bears some topological similarity to the N-terminal domain of the glutaminase/asparaginase family. This domain is found in the stationary phase survival protein SurE, a metal ion-dependent phosphatase found in eubacteria, archaea and eukaryotes. In Escherichia coli, SurE also has activity as a nucleotidase and exopolyphosphatase, and may be involved in the stress response []. E. coli cells with mutations in the surE gene survive poorly in stationary phase []. The structure of SurE homologues have been determined from Thermotoga maritima [] and the archaea Pyrobaculum aerophilum []. The T. maritima SurE homologue has phosphatase activity that is inhibited by vanadate or tungstate, both of which bind adjacent to the divalent metal ion. This domain is found in acid phosphatases (3.1.3.2 from EC), 5'-nucleotidases (3.1.3.5 from EC), 3'-nucleotidases (3.1.3.6 from EC) and exopolyphosphatases (3.6.1.11 from EC).; GO: 0016787 hydrolase activity; PDB: 1L5X_B 2V4O_D 2V4N_A 2WQK_B 2E6G_G 2E69_D 2E6C_C 2E6B_D 2E6E_A 2E6H_A ....
Probab=25.57 E-value=1.8e+02 Score=26.63 Aligned_cols=34 Identities=15% Similarity=0.159 Sum_probs=26.3
Q ss_pred EEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEEEec
Q 011878 124 CLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIVVR 165 (475)
Q Consensus 124 ~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l~~i~i~ 165 (475)
+|+||+|.... ..++.+++.|++.|-++.++...
T Consensus 3 ILlTNDDGi~a--------~Gi~aL~~~L~~~g~~V~VvAP~ 36 (196)
T PF01975_consen 3 ILLTNDDGIDA--------PGIRALAKALSALGHDVVVVAPD 36 (196)
T ss_dssp EEEE-SS-TTS--------HHHHHHHHHHTTTSSEEEEEEES
T ss_pred EEEEcCCCCCC--------HHHHHHHHHHHhcCCeEEEEeCC
Confidence 68999999643 47999999998888899888764
No 115
>PRK14465 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=23.99 E-value=5.6e+02 Score=25.72 Aligned_cols=56 Identities=4% Similarity=0.122 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHHhccCcceeeEEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEEEecc
Q 011878 100 DAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIVVRA 166 (475)
Q Consensus 100 daL~va~~~l~~~~~~~~~~~krI~l~Td~~~p~~~~~~~~~~~~~~~~~~~l~~~~I~l~~i~i~~ 166 (475)
+.+.-++..+.+..+ +...=+.+|+.+-.+ ..+++..+++-++..++++.+++.+.
T Consensus 239 e~ll~al~~~~~~~~--r~v~ieyvLI~GvND---------s~eda~~L~~ll~~l~~kVnLIPyN~ 294 (342)
T PRK14465 239 EELLQAAKDFTRELK--RRITFEYVMIPGVNM---------GRENANKLVKIARSLDCKINVIPLNT 294 (342)
T ss_pred HHHHHHHHHHHHHcC--CEEEEEEEEECCccC---------CHHHHHHHHHHHhhCCCcEEEEccCC
Confidence 555556555444332 234455677754322 23678888888888899999999864
No 116
>cd05006 SIS_GmhA Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of gram-negative bacteria inner core lipopolysaccharide precursor, L-glycero-D-mannoheptose (Gmh).
Probab=23.98 E-value=1.9e+02 Score=25.59 Aligned_cols=75 Identities=13% Similarity=0.159 Sum_probs=51.0
Q ss_pred CCcccccccceeCCceEeCChhhHHhhccCCCccEEEEeEeeCCCcccccccCceEEEEcCCCChhhHHHHHHHHHHHHh
Q 011878 281 VPPEQRIKGYRYGPQVVPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPGNSRATVAVSALARAMKE 360 (475)
Q Consensus 281 v~~~~~~k~y~yG~~~V~~~~~e~~~~k~~~~~~l~llGF~~~~~i~~~~~~~~~~~i~p~~~~~~s~~~f~aL~~am~~ 360 (475)
+.++|++=++.+.|. +++-++.++...++|.++++++....=+..- ..+..+.+|....+........+++++.+
T Consensus 99 ~~~~Dv~I~iS~SG~----t~~~i~~~~~ak~~Ga~vI~IT~~~~s~La~-~aD~~l~~~~~~~~~~~~~~~~~~~~~~~ 173 (177)
T cd05006 99 GQPGDVLIGISTSGN----SPNVLKALEAAKERGMKTIALTGRDGGKLLE-LADIEIHVPSDDTPRIQEVHLLIGHILCE 173 (177)
T ss_pred CCCCCEEEEEeCCCC----CHHHHHHHHHHHHCCCEEEEEeCCCCCchhh-hCCEEEEeCCCChHHHHHHHHHHHHHHHH
Confidence 566777777777553 4466677777888899999999875544322 24445666776666677777777777765
No 117
>PF00025 Arf: ADP-ribosylation factor family The prints entry specific to Sar1 proteins The Prosite entry specific to Sar1 proteins; InterPro: IPR006689 Small GTPases form an independent superfamily within the larger class of regulatory GTP hydrolases. This superfamily contains proteins that control a vast number of important processes and possess a common, structurally preserved GTP-binding domain [, ]. Sequence comparisons of small G proteins from various species have revealed that they are conserved in primary structures at the level of 30-55% similarity []. Crystallographic analysis of various small G proteins revealed the presence of a 20 kDa catalytic domain that is unique for the whole superfamily [, ]. The domain is built of five alpha helices (A1-A5), six beta-strands (B1-B6) and five polypeptide loops (G1-G5). A structural comparison of the GTP- and GDP-bound form, allows one to distinguish two functional loop regions: switch I and switch II that surround the gamma-phosphate group of the nucleotide. The G1 loop (also called the P-loop) that connects the B1 strand and the A1 helix is responsible for the binding of the phosphate groups. The G3 loop provides residues for Mg(2+) and phosphate binding and is located at the N terminus of the A2 helix. The G1 and G3 loops are sequentially similar to Walker A and Walker B boxes that are found in other nucleotide binding motifs. The G2 loop connects the A1 helix and the B2 strand and contains a conserved Thr residue responsible for Mg(2+) binding. The guanine base is recognised by the G4 and G5 loops. The consensus sequence NKXD of the G4 loop contains Lys and Asp residues directly interacting with the nucleotide. Part of the G5 loop located between B6 and A5 acts as a recognition site for the guanine base []. The small GTPase superfamily can be divided into at least 8 different families, including: Arf small GTPases. GTP-binding proteins involved in protein trafficking by modulating vesicle budding and uncoating within the Golgi apparatus. Ran small GTPases. GTP-binding proteins involved in nucleocytoplasmic transport. Required for the import of proteins into the nucleus and also for RNA export. Rab small GTPases. GTP-binding proteins involved in vesicular traffic. Rho small GTPases. GTP-binding proteins that control cytoskeleton reorganisation. Ras small GTPases. GTP-binding proteins involved in signalling pathways. Sar1 small GTPases. Small GTPase component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). Mitochondrial Rho (Miro). Small GTPase domain found in mitochondrial proteins involved in mitochondrial trafficking. Roc small GTPases domain. Small GTPase domain always found associated with the COR domain. This entry represents a branch of the small GTPase superfamily that includes the ADP ribosylation factor Arf, Arl (Arf-like), Arp (Arf-related proteins) and the remotely related Sar (Secretion-associated and Ras-related) proteins. Arf proteins are major regulators of vesicle biogenesis in intracellular traffic []. They cycle between inactive GDP-bound and active GTP-bound forms that bind selectively to effectors. The classical structural GDP/GTP switch is characterised by conformational changes at the so-called switch 1 and switch 2 regions, which bind tightly to the gamma-phosphate of GTP but poorly or not at all to the GDP nucleotide. Structural studies of Arf1 and Arf6 have revealed that although these proteins feature the switch 1 and 2 conformational changes, they depart from other small GTP-binding proteins in that they use an additional, unique switch to propagate structural information from one side of the protein to the other. The GDP/GTP structural cycles of human Arf1 and Arf6 feature a unique conformational change that affects the beta2-beta3 strands connecting switch 1 and switch 2 (interswitch) and also the amphipathic helical N terminus. In GDP-bound Arf1 and Arf6, the interswitch is retracted and forms a pocket to which the N-terminal helix binds, the latter serving as a molecular hasp to maintain the inactive conformation. In the GTP-bound form of these proteins, the interswitch undergoes a two-residue register shift that pulls switch 1 and switch 2 up, restoring an active conformation that can bind GTP. In this conformation, the interswitch projects out of the protein and extrudes the N-terminal hasp by occluding its binding pocket.; GO: 0005525 GTP binding; PDB: 2H57_B 2W83_B 3N5C_B 2J5X_A 3LVR_E 2BAO_A 3LVQ_E 2A5F_A 3PCR_B 1E0S_A ....
Probab=21.13 E-value=1.7e+02 Score=25.81 Aligned_cols=47 Identities=13% Similarity=0.243 Sum_probs=31.6
Q ss_pred CceEEEEEEecCCCcCCCchHHHHHHHHHHHHHHhcCCccEEEEEEEccCCc
Q 011878 4 TREALLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEET 55 (475)
Q Consensus 4 ~ke~~vflID~s~sM~~~~~~a~~~~~~l~~~ki~~~~~D~vglvlfgt~~t 55 (475)
+-+++||+||.+.. +++.++.+.+..++.+.-. ++.-=||++|-.+.
T Consensus 81 ~~~~iIfVvDssd~--~~l~e~~~~L~~ll~~~~~---~~~piLIl~NK~D~ 127 (175)
T PF00025_consen 81 NADGIIFVVDSSDP--ERLQEAKEELKELLNDPEL---KDIPILILANKQDL 127 (175)
T ss_dssp TESEEEEEEETTGG--GGHHHHHHHHHHHHTSGGG---TTSEEEEEEESTTS
T ss_pred ccceeEEEEecccc--eeecccccchhhhcchhhc---ccceEEEEeccccc
Confidence 34789999999953 3578888888887775422 24455666665543
Done!