Query psy9195
Match_columns 139
No_of_seqs 140 out of 1371
Neff 8.0
Searched_HMMs 46136
Date Fri Aug 16 21:19:39 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9195.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9195hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2353|consensus 100.0 4.4E-29 9.6E-34 218.7 7.6 136 2-138 149-288 (1104)
2 cd01463 vWA_VGCC_like VWA Volt 99.6 5.3E-16 1.2E-20 113.7 8.2 75 62-137 1-75 (190)
3 PF08399 VWA_N: VWA N-terminal 99.4 3.9E-13 8.4E-18 92.7 5.5 50 2-51 74-123 (123)
4 PF13768 VWA_3: von Willebrand 99.1 1.8E-10 3.9E-15 81.4 6.7 51 76-127 2-52 (155)
5 cd01461 vWA_interalpha_trypsin 99.0 2.4E-09 5.2E-14 76.2 7.1 54 74-127 2-55 (171)
6 cd01466 vWA_C3HC4_type VWA C3H 98.9 2.5E-09 5.3E-14 76.1 6.5 53 76-128 2-54 (155)
7 TIGR03788 marine_srt_targ mari 98.9 5.4E-09 1.2E-13 88.8 7.2 55 73-127 270-324 (596)
8 cd01464 vWA_subfamily VWA subf 98.8 9.8E-09 2.1E-13 74.2 6.6 55 75-129 4-64 (176)
9 cd01465 vWA_subgroup VWA subgr 98.8 1.8E-08 3.9E-13 71.7 7.2 54 76-129 2-55 (170)
10 cd01470 vWA_complement_factors 98.8 1.9E-08 4.1E-13 74.0 6.8 53 76-128 2-57 (198)
11 PRK13685 hypothetical protein; 98.8 2.1E-08 4.6E-13 79.5 7.3 58 73-130 87-149 (326)
12 cd01456 vWA_ywmD_type VWA ywmD 98.8 1.9E-08 4.2E-13 74.5 6.5 51 71-121 17-73 (206)
13 cd01472 vWA_collagen von Wille 98.7 5.8E-08 1.3E-12 69.2 7.2 53 76-128 2-57 (164)
14 cd01451 vWA_Magnesium_chelatas 98.6 1.8E-07 3.9E-12 67.8 7.3 53 77-129 3-58 (178)
15 cd01480 vWA_collagen_alpha_1-V 98.6 2.2E-07 4.8E-12 67.9 6.6 56 74-129 2-66 (186)
16 cd01450 vWFA_subfamily_ECM Von 98.5 4.8E-07 1E-11 63.2 6.8 55 76-130 2-59 (161)
17 PRK13406 bchD magnesium chelat 98.5 4.4E-07 9.6E-12 77.1 7.4 58 73-130 400-459 (584)
18 cd01453 vWA_transcription_fact 98.5 3.2E-07 7E-12 67.2 5.8 56 75-130 4-68 (183)
19 cd01475 vWA_Matrilin VWA_Matri 98.5 6.5E-07 1.4E-11 67.2 7.3 56 74-129 2-60 (224)
20 cd01471 vWA_micronemal_protein 98.5 7.3E-07 1.6E-11 64.8 7.1 54 76-129 2-59 (186)
21 PF13519 VWA_2: von Willebrand 98.4 4.8E-07 1.1E-11 63.6 5.8 53 76-129 1-58 (172)
22 cd01482 vWA_collagen_alphaI-XI 98.4 8.9E-07 1.9E-11 63.2 7.1 53 76-128 2-57 (164)
23 TIGR00868 hCaCC calcium-activa 98.4 6.9E-07 1.5E-11 78.5 7.2 64 65-128 295-360 (863)
24 cd01454 vWA_norD_type norD typ 98.4 4.3E-07 9.3E-12 65.4 5.0 46 76-121 2-49 (174)
25 TIGR03436 acidobact_VWFA VWFA- 98.4 1E-06 2.3E-11 68.6 7.2 56 73-129 52-108 (296)
26 cd01462 VWA_YIEM_type VWA YIEM 98.4 8.1E-07 1.8E-11 62.4 5.7 47 75-121 1-48 (152)
27 COG4245 TerY Uncharacterized p 98.4 7.9E-07 1.7E-11 65.2 5.2 53 76-128 5-63 (207)
28 cd01477 vWA_F09G8-8_type VWA F 98.3 1.8E-06 3.8E-11 63.9 6.8 56 73-128 18-82 (193)
29 smart00327 VWA von Willebrand 98.3 2.5E-06 5.4E-11 60.2 7.0 54 74-127 1-57 (177)
30 PF00092 VWA: von Willebrand f 98.3 3.3E-06 7.2E-11 59.9 7.0 54 76-129 1-57 (178)
31 cd01474 vWA_ATR ATR (Anthrax T 98.3 3.5E-06 7.7E-11 61.3 7.1 57 73-130 3-60 (185)
32 cd01467 vWA_BatA_type VWA BatA 98.3 3.6E-06 7.8E-11 60.5 6.9 55 74-129 2-62 (180)
33 COG1240 ChlD Mg-chelatase subu 98.2 3.9E-06 8.4E-11 64.3 5.9 57 74-130 78-137 (261)
34 cd01469 vWA_integrins_alpha_su 98.2 8.9E-06 1.9E-10 59.0 7.3 53 76-128 2-57 (177)
35 TIGR02031 BchD-ChlD magnesium 98.2 6.4E-06 1.4E-10 70.3 7.3 56 75-130 408-465 (589)
36 cd01476 VWA_integrin_invertebr 98.1 1.4E-05 3E-10 56.6 6.8 51 76-127 2-57 (163)
37 cd00198 vWFA Von Willebrand fa 98.0 2.1E-05 4.6E-10 53.9 6.9 53 76-128 2-57 (161)
38 TIGR02442 Cob-chelat-sub cobal 97.9 3.5E-05 7.7E-10 66.3 7.5 57 74-130 465-524 (633)
39 cd01457 vWA_ORF176_type VWA OR 97.9 2.9E-05 6.4E-10 57.2 5.4 55 74-128 2-65 (199)
40 PRK10997 yieM hypothetical pro 97.8 6.7E-05 1.5E-09 62.6 6.3 52 73-124 322-374 (487)
41 cd01473 vWA_CTRP CTRP for CS 97.7 0.00015 3.3E-09 53.4 6.7 54 76-129 2-59 (192)
42 cd01481 vWA_collagen_alpha3-VI 97.6 0.00028 6E-09 50.8 7.0 53 75-127 1-56 (165)
43 PRK15426 putative diguanylate 97.5 0.00024 5.3E-09 59.5 6.7 69 4-72 144-213 (570)
44 cd01452 VWA_26S_proteasome_sub 97.5 0.00031 6.7E-09 51.8 6.2 55 76-130 5-68 (187)
45 COG2425 Uncharacterized protei 97.5 0.00023 5E-09 58.6 5.4 50 75-124 273-323 (437)
46 cd01460 vWA_midasin VWA_Midasi 97.5 0.00036 7.8E-09 54.2 6.1 67 63-131 47-120 (266)
47 PF09967 DUF2201: VWA-like dom 97.4 0.00045 9.7E-09 47.7 5.7 50 77-128 1-50 (126)
48 cd01458 vWA_ku Ku70/Ku80 N-ter 97.3 0.00066 1.4E-08 50.7 5.7 46 76-121 3-58 (218)
49 PF11775 CobT_C: Cobalamin bio 97.2 0.00076 1.7E-08 50.8 5.0 46 76-121 14-60 (219)
50 PTZ00441 sporozoite surface pr 97.0 0.0026 5.5E-08 54.1 7.2 58 73-130 41-102 (576)
51 PF10138 vWA-TerF-like: vWA fo 96.9 0.0029 6.2E-08 47.2 5.7 53 76-128 3-59 (200)
52 PF05762 VWA_CoxE: VWA domain 96.3 0.0054 1.2E-07 46.2 4.1 54 72-129 55-108 (222)
53 cd01468 trunk_domain trunk dom 96.2 0.018 3.8E-07 43.7 6.2 51 74-124 3-56 (239)
54 cd00181 TarH Taxis toward Aspa 96.2 0.00019 4.1E-09 48.6 -4.3 54 15-72 84-137 (140)
55 cd01478 Sec23-like Sec23-like: 95.9 0.028 6.2E-07 43.6 6.2 48 75-124 4-51 (267)
56 TIGR01651 CobT cobaltochelatas 95.8 0.018 3.9E-07 49.2 5.2 46 76-121 394-440 (600)
57 PF04811 Sec23_trunk: Sec23/Se 95.7 0.015 3.2E-07 44.2 4.1 50 75-124 4-56 (243)
58 cd01479 Sec24-like Sec24-like: 94.9 0.067 1.5E-06 40.8 5.5 51 74-124 3-57 (244)
59 COG4547 CobT Cobalamin biosynt 94.8 0.026 5.7E-07 46.9 3.1 45 77-121 416-461 (620)
60 PF03731 Ku_N: Ku70/Ku80 N-ter 94.8 0.085 1.8E-06 39.3 5.6 47 77-123 2-57 (224)
61 cd01455 vWA_F11C1-5a_type Von 94.8 0.056 1.2E-06 40.1 4.4 47 75-124 1-58 (191)
62 PLN00162 transport protein sec 94.6 0.093 2E-06 46.4 6.1 48 74-123 124-171 (761)
63 COG2304 Uncharacterized protei 94.3 0.14 3E-06 40.9 6.2 57 71-127 34-90 (399)
64 PRK05325 hypothetical protein; 93.9 0.063 1.4E-06 44.0 3.3 69 56-124 203-275 (401)
65 smart00319 TarH Homologues of 93.7 0.0063 1.4E-07 41.3 -2.3 57 15-75 76-132 (135)
66 COG1721 Uncharacterized conser 93.7 0.23 5E-06 40.7 6.4 54 74-127 224-283 (416)
67 TIGR02877 spore_yhbH sporulati 92.8 0.11 2.4E-06 42.1 3.2 68 57-124 184-255 (371)
68 PF04285 DUF444: Protein of un 92.7 0.52 1.1E-05 39.0 6.9 68 57-124 228-299 (421)
69 KOG3768|consensus 91.2 0.43 9.3E-06 41.2 4.9 45 77-121 4-59 (888)
70 PF11443 DUF2828: Domain of un 90.1 0.86 1.9E-05 38.9 5.8 47 75-122 341-388 (534)
71 TIGR00578 ku70 ATP-dependent D 89.8 0.75 1.6E-05 39.6 5.4 49 74-122 10-69 (584)
72 KOG4465|consensus 88.1 0.19 4.1E-06 40.9 0.6 79 56-136 409-492 (598)
73 COG2718 Uncharacterized conser 87.2 0.54 1.2E-05 38.4 2.7 66 59-124 230-299 (423)
74 COG4867 Uncharacterized protei 86.8 0.85 1.8E-05 38.0 3.6 51 74-124 463-517 (652)
75 COG3864 Uncharacterized protei 86.1 1.9 4.2E-05 34.5 5.1 47 76-124 263-309 (396)
76 PTZ00395 Sec24-related protein 85.5 1.6 3.5E-05 41.0 5.0 49 75-123 953-1003(1560)
77 smart00187 INB Integrin beta s 84.9 1.9 4E-05 35.8 4.8 53 68-120 93-147 (423)
78 KOG1985|consensus 83.6 2.5 5.4E-05 37.7 5.2 51 74-124 294-347 (887)
79 COG3552 CoxE Protein containin 80.3 1.6 3.5E-05 35.6 2.7 48 74-128 218-268 (395)
80 KOG1984|consensus 79.3 5.8 0.00013 35.8 5.9 62 62-124 405-471 (1007)
81 KOG1986|consensus 75.2 9.8 0.00021 33.6 6.1 49 74-124 121-169 (745)
82 PF01882 DUF58: Protein of unk 69.9 7.3 0.00016 24.2 3.3 40 74-113 40-85 (86)
83 PF00362 Integrin_beta: Integr 62.8 3.4 7.4E-05 34.3 0.9 54 69-122 97-152 (426)
84 PRK01322 6-carboxyhexanoate--C 61.6 3.2 7E-05 31.9 0.5 36 3-50 170-205 (242)
85 TIGR01204 bioW 6-carboxyhexano 61.5 3.2 7E-05 31.7 0.4 35 4-50 164-198 (232)
86 PF08496 Peptidase_S49_N: Pept 56.2 37 0.00081 24.3 5.1 40 75-114 97-136 (155)
87 KOG0070|consensus 51.5 43 0.00093 24.7 4.9 44 73-120 84-127 (181)
88 COG5028 Vesicle coat complex C 50.9 37 0.0008 30.6 5.1 51 73-124 275-330 (861)
89 PF03744 BioW: 6-carboxyhexano 48.0 7.5 0.00016 29.9 0.5 35 4-50 171-205 (239)
90 cd01459 vWA_copine_like VWA Co 46.5 73 0.0016 24.6 5.8 53 76-128 33-103 (254)
91 COG5047 SEC23 Vesicle coat com 46.1 63 0.0014 28.4 5.7 45 78-124 126-170 (755)
92 smart00467 GS GS motif. Aa app 44.7 20 0.00043 18.5 1.6 18 83-100 11-28 (30)
93 KOG0071|consensus 44.1 54 0.0012 23.6 4.3 39 73-114 84-122 (180)
94 PF00025 Arf: ADP-ribosylation 42.0 85 0.0018 22.1 5.2 29 74-105 82-110 (175)
95 PF14827 Cache_3: Sensory doma 40.4 16 0.00034 24.3 1.1 48 1-49 7-57 (116)
96 COG0102 RplM Ribosomal protein 39.2 71 0.0015 22.7 4.3 37 76-115 13-57 (148)
97 COG0275 Predicted S-adenosylme 38.3 61 0.0013 26.0 4.2 31 92-122 220-250 (314)
98 KOG2326|consensus 33.2 1.6E+02 0.0034 26.0 6.1 48 75-122 5-62 (669)
99 cd00392 Ribosomal_L13 Ribosoma 32.4 82 0.0018 21.3 3.6 34 79-115 2-43 (114)
100 KOG1226|consensus 32.0 40 0.00087 30.2 2.5 53 69-121 127-181 (783)
101 TIGR00006 S-adenosyl-methyltra 31.3 83 0.0018 25.0 4.0 29 92-120 216-244 (305)
102 PTZ00068 60S ribosomal protein 31.0 96 0.0021 23.3 4.1 32 78-116 5-36 (202)
103 COG1424 BioW Pimeloyl-CoA synt 30.1 19 0.00041 27.0 0.2 34 3-48 166-200 (239)
104 PF00352 TBP: Transcription fa 30.0 44 0.00095 21.0 1.9 49 57-106 31-82 (86)
105 PF08247 ENOD40: ENOD40 protei 29.6 7.6 0.00016 15.7 -1.1 8 10-17 2-9 (12)
106 KOG4115|consensus 28.8 1.8E+02 0.0038 19.2 5.3 48 78-125 21-80 (97)
107 PF07757 AdoMet_MTase: Predict 28.1 37 0.0008 23.0 1.3 60 5-67 34-95 (112)
108 cd03422 YedF YedF is a bacteri 26.9 1.5E+02 0.0032 17.7 4.2 8 107-114 24-31 (69)
109 PRK09216 rplM 50S ribosomal pr 25.0 1.6E+02 0.0036 20.7 4.2 35 78-115 15-57 (144)
110 CHL00159 rpl13 ribosomal prote 24.4 1.7E+02 0.0037 20.7 4.2 36 77-115 15-58 (143)
111 TIGR01066 rplM_bact ribosomal 23.6 1.8E+02 0.0038 20.4 4.2 36 77-115 12-55 (140)
112 PRK00050 16S rRNA m(4)C1402 me 23.6 1.4E+02 0.003 23.6 4.0 30 92-121 212-241 (296)
113 PF07849 DUF1641: Protein of u 23.1 92 0.002 17.0 2.2 18 3-20 21-38 (42)
114 PF00572 Ribosomal_L13: Riboso 22.3 1.2E+02 0.0025 20.9 3.0 35 78-115 1-43 (128)
115 KOG0090|consensus 22.1 1.3E+02 0.0029 23.0 3.5 23 61-83 93-118 (238)
116 PRK05659 sulfur carrier protei 21.6 94 0.002 18.1 2.2 13 105-117 50-62 (66)
117 PF06707 DUF1194: Protein of u 21.3 1.2E+02 0.0025 22.8 3.0 16 75-90 4-19 (205)
118 PRK05863 sulfur carrier protei 21.3 92 0.002 18.4 2.1 13 105-117 49-61 (65)
119 COG0776 HimA Bacterial nucleoi 21.2 1.2E+02 0.0027 19.8 2.8 21 99-119 30-50 (94)
120 PRK00299 sulfur transfer prote 20.2 2.3E+02 0.005 17.5 4.4 38 79-120 10-47 (81)
121 PF01206 TusA: Sulfurtransfera 20.1 2E+02 0.0043 16.8 4.0 35 81-119 3-37 (70)
No 1
>KOG2353|consensus
Probab=99.95 E-value=4.4e-29 Score=218.75 Aligned_cols=136 Identities=50% Similarity=0.848 Sum_probs=130.7
Q ss_pred CCCHHHHHhhhchHHHHHHHHHHhhcCcceeEeeeecccccEEECCCCCCCCc----cccccccccchhhhhhccccccE
Q psy9195 2 AEHDDVRAGLMWSEGLDEVFRENYMADPTLLWQYFGSAKGFLRTYPDKEDAPA----EDLIFDCRNRQWYIQATTCSKDV 77 (139)
Q Consensus 2 ~~~~~v~~~~~~~~~l~~~f~~~~~~~~~i~~~y~gs~~G~~~~~p~~~~~~~----~~~~yDpr~r~Wy~~a~~~~~~v 77 (139)
.++|+|+++++||+.|+..|+++.+.+|.+.|||||+..|..+.||+.+|..+ ..+.||+|.|+||.++..+|+++
T Consensus 149 ~~~~~vl~~~~WS~~ld~vf~~N~~~dP~l~wQ~Fgs~tG~~R~yPa~~W~~~~~~~~idl~D~R~r~Wyi~aAt~pKdi 228 (1104)
T KOG2353|consen 149 DRSPDVLNAIDWSEHLDFVFRDNRESDPTLSWQYFGSATGLLRYYPAAAWFDNNTDNSIDLYDCRNRSWYIQAATSPKDI 228 (1104)
T ss_pred ccCHHHHhhcccccchhHHHhhccccCchhhHHHhhhhhhhhhhCCCccCccCCCCCcceeeecccccccccccCCccce
Confidence 46899999999999999999999999999999999999999999999999742 46789999999999999999999
Q ss_pred EEEEcCCCCCCCchHHHHHHHHHHHHhhCCCCCEEEEEEeCCceeeeeecCCCCeeeeccc
Q psy9195 78 VILVDNSGSMAGMRNTTAKLVLHSLLQTFSNNDFINIFKFNLTVDTIVPCLGNYSLVQTLR 138 (139)
Q Consensus 78 vi~iD~sgSm~g~~l~~ak~~~~~~l~~l~~~d~~~v~~f~~~~~~~~~~~~~~~lv~a~~ 138 (139)
+|++|.||||.|.++.++|..+..+|++|+++|+|++++|+..+..+.||+++ +|||||+
T Consensus 229 viLlD~SgSm~g~~~~lak~tv~~iLdtLs~~Dfvni~tf~~~~~~v~pc~~~-~lvqAt~ 288 (1104)
T KOG2353|consen 229 VILLDVSGSMSGLRLDLAKQTVNEILDTLSDNDFVNILTFNSEVNPVSPCFNG-TLVQATM 288 (1104)
T ss_pred EEEEeccccccchhhHHHHHHHHHHHHhcccCCeEEEEeeccccCcccccccC-ceeecch
Confidence 99999999999999999999999999999999999999999999999999999 9999996
No 2
>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=99.65 E-value=5.3e-16 Score=113.75 Aligned_cols=75 Identities=53% Similarity=0.879 Sum_probs=69.9
Q ss_pred ccchhhhhhccccccEEEEEcCCCCCCCchHHHHHHHHHHHHhhCCCCCEEEEEEeCCceeeeeecCCCCeeeecc
Q psy9195 62 RNRQWYIQATTCSKDVVILVDNSGSMAGMRNTTAKLVLHSLLQTFSNNDFINIFKFNLTVDTIVPCLGNYSLVQTL 137 (139)
Q Consensus 62 r~r~Wy~~a~~~~~~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~~~d~~~v~~f~~~~~~~~~~~~~~~lv~a~ 137 (139)
|.|+||..+...|.++++++|+||||.+.+++.+|.++..+++.|.++|+++|+.|++.++.++||+++ .+++++
T Consensus 1 ~~~~~~~~~~~~p~~vv~llD~SgSM~~~~l~~ak~~~~~ll~~l~~~d~v~lv~F~~~~~~~~~~~~~-~~~~~~ 75 (190)
T cd01463 1 RNRSWYIQAATSPKDIVILLDVSGSMTGQRLHLAKQTVSSILDTLSDNDFFNIITFSNEVNPVVPCFND-TLVQAT 75 (190)
T ss_pred CCCcceeecccCCceEEEEEECCCCCCcHHHHHHHHHHHHHHHhCCCCCEEEEEEeCCCeeEEeeeccc-ceEecC
Confidence 689999988888999999999999999999999999999999999999999999999999999999987 676654
No 3
>PF08399 VWA_N: VWA N-terminal; InterPro: IPR013608 This domain is found at the N terminus of proteins containing von Willebrand factor type A (VWA, IPR002035 from INTERPRO) and Cache (IPR004010 from INTERPRO) domains. It has been found in vertebrates, Drosophila melanogaster (Fruit fly) and Caenorhabditis elegans but has not yet been identified in other eukaryotes. It is probably involved in the function of some voltage-dependent calcium channel subunits [].
Probab=99.41 E-value=3.9e-13 Score=92.74 Aligned_cols=50 Identities=56% Similarity=1.050 Sum_probs=48.1
Q ss_pred CCCHHHHHhhhchHHHHHHHHHHhhcCcceeEeeeecccccEEECCCCCC
Q psy9195 2 AEHDDVRAGLMWSEGLDEVFRENYMADPTLLWQYFGSAKGFLRTYPDKED 51 (139)
Q Consensus 2 ~~~~~v~~~~~~~~~l~~~f~~~~~~~~~i~~~y~gs~~G~~~~~p~~~~ 51 (139)
+.||+|+++|+|++.|++.|+++.+.+|++.|||||++.|.++.||+.+|
T Consensus 74 ~~~~~vl~~i~ws~~Ld~~f~~N~~~dp~l~WQYFgS~~G~~r~yPa~~W 123 (123)
T PF08399_consen 74 DRDPDVLNAINWSEALDDVFRENYESDPTLKWQYFGSSTGFFRQYPASKW 123 (123)
T ss_pred cccHHHHhhccccHHHHHHHHHHhhcCCCceEEEEEcccCceeeccCCCC
Confidence 57899999999999999999999999999999999999999999999876
No 4
>PF13768 VWA_3: von Willebrand factor type A domain
Probab=99.12 E-value=1.8e-10 Score=81.44 Aligned_cols=51 Identities=41% Similarity=0.632 Sum_probs=48.1
Q ss_pred cEEEEEcCCCCCCCchHHHHHHHHHHHHhhCCCCCEEEEEEeCCceeeeeec
Q psy9195 76 DVVILVDNSGSMAGMRNTTAKLVLHSLLQTFSNNDFINIFKFNLTVDTIVPC 127 (139)
Q Consensus 76 ~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~~~d~~~v~~f~~~~~~~~~~ 127 (139)
+++|+||+|+||.|.+ +.+|.+++.++++|.++|+|+|+.|++++..+.|+
T Consensus 2 ~vvilvD~S~Sm~g~~-~~~k~al~~~l~~L~~~d~fnii~f~~~~~~~~~~ 52 (155)
T PF13768_consen 2 DVVILVDTSGSMSGEK-ELVKDALRAILRSLPPGDRFNIIAFGSSVRPLFPG 52 (155)
T ss_pred eEEEEEeCCCCCCCcH-HHHHHHHHHHHHhCCCCCEEEEEEeCCEeeEcchh
Confidence 6899999999999998 99999999999999999999999999998887765
No 5
>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=98.96 E-value=2.4e-09 Score=76.22 Aligned_cols=54 Identities=35% Similarity=0.592 Sum_probs=50.1
Q ss_pred cccEEEEEcCCCCCCCchHHHHHHHHHHHHhhCCCCCEEEEEEeCCceeeeeec
Q psy9195 74 SKDVVILVDNSGSMAGMRNTTAKLVLHSLLQTFSNNDFINIFKFNLTVDTIVPC 127 (139)
Q Consensus 74 ~~~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~~~d~~~v~~f~~~~~~~~~~ 127 (139)
|+++++++|+||||.|.+++.++.++..++..+.++|+++|+.|+++...+.|+
T Consensus 2 ~~~v~~vlD~S~SM~~~~~~~~~~al~~~l~~l~~~~~~~l~~Fs~~~~~~~~~ 55 (171)
T cd01461 2 PKEVVFVIDTSGSMSGTKIEQTKEALLTALKDLPPGDYFNIIGFSDTVEEFSPS 55 (171)
T ss_pred CceEEEEEECCCCCCChhHHHHHHHHHHHHHhCCCCCEEEEEEeCCCceeecCc
Confidence 578999999999999999999999999999999999999999999998877654
No 6
>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=98.94 E-value=2.5e-09 Score=76.07 Aligned_cols=53 Identities=28% Similarity=0.456 Sum_probs=49.3
Q ss_pred cEEEEEcCCCCCCCchHHHHHHHHHHHHhhCCCCCEEEEEEeCCceeeeeecC
Q psy9195 76 DVVILVDNSGSMAGMRNTTAKLVLHSLLQTFSNNDFINIFKFNLTVDTIVPCL 128 (139)
Q Consensus 76 ~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~~~d~~~v~~f~~~~~~~~~~~ 128 (139)
++++++|.||||.+.+++.+|.++..+++.|.++|+++|+.|++.++.+.|..
T Consensus 2 ~v~~vlD~S~SM~~~rl~~ak~a~~~l~~~l~~~~~~~li~F~~~~~~~~~~~ 54 (155)
T cd01466 2 DLVAVLDVSGSMAGDKLQLVKHALRFVISSLGDADRLSIVTFSTSAKRLSPLR 54 (155)
T ss_pred cEEEEEECCCCCCcHHHHHHHHHHHHHHHhCCCcceEEEEEecCCccccCCCc
Confidence 68899999999999999999999999999999999999999999998887754
No 7
>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=98.87 E-value=5.4e-09 Score=88.82 Aligned_cols=55 Identities=33% Similarity=0.491 Sum_probs=51.2
Q ss_pred ccccEEEEEcCCCCCCCchHHHHHHHHHHHHhhCCCCCEEEEEEeCCceeeeeec
Q psy9195 73 CSKDVVILVDNSGSMAGMRNTTAKLVLHSLLQTFSNNDFINIFKFNLTVDTIVPC 127 (139)
Q Consensus 73 ~~~~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~~~d~~~v~~f~~~~~~~~~~ 127 (139)
.|++++|++|+||||.|.+++.+|.++..++..|.++|+|+|+.|++++..+.|.
T Consensus 270 ~p~~vvfvlD~SgSM~g~~i~~ak~al~~~l~~L~~~d~~~ii~F~~~~~~~~~~ 324 (596)
T TIGR03788 270 LPRELVFVIDTSGSMAGESIEQAKSALLLALDQLRPGDRFNIIQFDSDVTLLFPV 324 (596)
T ss_pred CCceEEEEEECCCCCCCccHHHHHHHHHHHHHhCCCCCEEEEEEECCcceEeccc
Confidence 4678999999999999999999999999999999999999999999999988654
No 8
>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=98.84 E-value=9.8e-09 Score=74.23 Aligned_cols=55 Identities=27% Similarity=0.346 Sum_probs=49.2
Q ss_pred ccEEEEEcCCCCCCCchHHHHHHHHHHHHhhCCC------CCEEEEEEeCCceeeeeecCC
Q psy9195 75 KDVVILVDNSGSMAGMRNTTAKLVLHSLLQTFSN------NDFINIFKFNLTVDTIVPCLG 129 (139)
Q Consensus 75 ~~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~~------~d~~~v~~f~~~~~~~~~~~~ 129 (139)
-++++++|+||||.|.++..++.+++.+++.|.+ +++++|+.|+++++.+.|+..
T Consensus 4 ~~v~~llD~SgSM~~~~~~~~k~a~~~~~~~l~~~~~~~~~~~v~ii~F~~~a~~~~~l~~ 64 (176)
T cd01464 4 LPIYLLLDTSGSMAGEPIEALNQGLQMLQSELRQDPYALESVEISVITFDSAARVIVPLTP 64 (176)
T ss_pred CCEEEEEECCCCCCChHHHHHHHHHHHHHHHHhcChhhccccEEEEEEecCCceEecCCcc
Confidence 4688999999999999999999999999988864 569999999999999988764
No 9
>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=98.81 E-value=1.8e-08 Score=71.71 Aligned_cols=54 Identities=26% Similarity=0.474 Sum_probs=50.0
Q ss_pred cEEEEEcCCCCCCCchHHHHHHHHHHHHhhCCCCCEEEEEEeCCceeeeeecCC
Q psy9195 76 DVVILVDNSGSMAGMRNTTAKLVLHSLLQTFSNNDFINIFKFNLTVDTIVPCLG 129 (139)
Q Consensus 76 ~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~~~d~~~v~~f~~~~~~~~~~~~ 129 (139)
++++++|+||||.+.+++.+|.++..++..|.++|+++|+.|++....+.|+..
T Consensus 2 ~~~~vlD~S~SM~~~~~~~~k~a~~~~~~~l~~~~~v~li~f~~~~~~~~~~~~ 55 (170)
T cd01465 2 NLVFVIDRSGSMDGPKLPLVKSALKLLVDQLRPDDRLAIVTYDGAAETVLPATP 55 (170)
T ss_pred cEEEEEECCCCCCChhHHHHHHHHHHHHHhCCCCCEEEEEEecCCccEEecCcc
Confidence 578999999999998899999999999999999999999999999998887654
No 10
>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=98.79 E-value=1.9e-08 Score=74.04 Aligned_cols=53 Identities=21% Similarity=0.271 Sum_probs=48.7
Q ss_pred cEEEEEcCCCCCCCchHHHHHHHHHHHHhhCCC---CCEEEEEEeCCceeeeeecC
Q psy9195 76 DVVILVDNSGSMAGMRNTTAKLVLHSLLQTFSN---NDFINIFKFNLTVDTIVPCL 128 (139)
Q Consensus 76 ~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~~---~d~~~v~~f~~~~~~~~~~~ 128 (139)
+++|++|+||||.+.+++.+|.++..+++.|.. +|+++|+.|+++++.++|..
T Consensus 2 di~~vlD~SgSM~~~~~~~~k~~~~~l~~~l~~~~~~~~v~li~Fs~~~~~~~~~~ 57 (198)
T cd01470 2 NIYIALDASDSIGEEDFDEAKNAIKTLIEKISSYEVSPRYEIISYASDPKEIVSIR 57 (198)
T ss_pred cEEEEEECCCCccHHHHHHHHHHHHHHHHHccccCCCceEEEEEecCCceEEEecc
Confidence 588999999999999999999999999999863 89999999999999988764
No 11
>PRK13685 hypothetical protein; Provisional
Probab=98.78 E-value=2.1e-08 Score=79.49 Aligned_cols=58 Identities=19% Similarity=0.192 Sum_probs=52.9
Q ss_pred ccccEEEEEcCCCCCCC-----chHHHHHHHHHHHHhhCCCCCEEEEEEeCCceeeeeecCCC
Q psy9195 73 CSKDVVILVDNSGSMAG-----MRNTTAKLVLHSLLQTFSNNDFINIFKFNLTVDTIVPCLGN 130 (139)
Q Consensus 73 ~~~~vvi~iD~sgSm~g-----~~l~~ak~~~~~~l~~l~~~d~~~v~~f~~~~~~~~~~~~~ 130 (139)
.+.++++++|.|+||.+ ++++.+|.++..+++.+.++|+++++.|++++..+.|.+.+
T Consensus 87 ~~~~vvlvlD~S~SM~~~D~~p~RL~~ak~~~~~~l~~l~~~d~vglv~Fa~~a~~~~p~t~d 149 (326)
T PRK13685 87 NRAVVMLVIDVSQSMRATDVEPNRLAAAQEAAKQFADELTPGINLGLIAFAGTATVLVSPTTN 149 (326)
T ss_pred CCceEEEEEECCccccCCCCCCCHHHHHHHHHHHHHHhCCCCCeEEEEEEcCceeecCCCCCC
Confidence 44579999999999986 58999999999999999999999999999999999888766
No 12
>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=98.77 E-value=1.9e-08 Score=74.47 Aligned_cols=51 Identities=25% Similarity=0.363 Sum_probs=46.3
Q ss_pred ccccccEEEEEcCCCCCC------CchHHHHHHHHHHHHhhCCCCCEEEEEEeCCce
Q psy9195 71 TTCSKDVVILVDNSGSMA------GMRNTTAKLVLHSLLQTFSNNDFINIFKFNLTV 121 (139)
Q Consensus 71 ~~~~~~vvi~iD~sgSm~------g~~l~~ak~~~~~~l~~l~~~d~~~v~~f~~~~ 121 (139)
...+.+++++||+||||. +.+++.+|.++..+++.+.++|+++|+.|+++.
T Consensus 17 ~~~~~~vv~vlD~SgSM~~~~~~~~~rl~~ak~a~~~~l~~l~~~~~v~lv~F~~~~ 73 (206)
T cd01456 17 PQLPPNVAIVLDNSGSMREVDGGGETRLDNAKAALDETANALPDGTRLGLWTFSGDG 73 (206)
T ss_pred cCCCCcEEEEEeCCCCCcCCCCCcchHHHHHHHHHHHHHHhCCCCceEEEEEecCCC
Confidence 346788999999999998 579999999999999999999999999999964
No 13
>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=98.71 E-value=5.8e-08 Score=69.22 Aligned_cols=53 Identities=17% Similarity=0.178 Sum_probs=48.5
Q ss_pred cEEEEEcCCCCCCCchHHHHHHHHHHHHhhCC---CCCEEEEEEeCCceeeeeecC
Q psy9195 76 DVVILVDNSGSMAGMRNTTAKLVLHSLLQTFS---NNDFINIFKFNLTVDTIVPCL 128 (139)
Q Consensus 76 ~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~---~~d~~~v~~f~~~~~~~~~~~ 128 (139)
++++++|.||||.+.+++.+|++++.++..|. .+++++|+.|+++++...|+.
T Consensus 2 Dvv~vlD~SgSm~~~~~~~~k~~~~~~~~~l~~~~~~~~~giv~Fs~~~~~~~~~~ 57 (164)
T cd01472 2 DIVFLVDGSESIGLSNFNLVKDFVKRVVERLDIGPDGVRVGVVQYSDDPRTEFYLN 57 (164)
T ss_pred CEEEEEeCCCCCCHHHHHHHHHHHHHHHhhcccCCCCeEEEEEEEcCceeEEEecC
Confidence 68999999999999899999999999999886 567999999999999988876
No 14
>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=98.60 E-value=1.8e-07 Score=67.83 Aligned_cols=53 Identities=34% Similarity=0.500 Sum_probs=45.0
Q ss_pred EEEEEcCCCCCCCc-hHHHHHHHHHHHHh-hCCCCCEEEEEEeCCc-eeeeeecCC
Q psy9195 77 VVILVDNSGSMAGM-RNTTAKLVLHSLLQ-TFSNNDFINIFKFNLT-VDTIVPCLG 129 (139)
Q Consensus 77 vvi~iD~sgSm~g~-~l~~ak~~~~~~l~-~l~~~d~~~v~~f~~~-~~~~~~~~~ 129 (139)
+++++|+||||.+. +++.+|.++..++. .+.++|+++|+.|+++ .....|..+
T Consensus 3 v~lvlD~SgSM~~~~rl~~ak~a~~~~~~~~~~~~d~v~lv~F~~~~~~~~~~~t~ 58 (178)
T cd01451 3 VIFVVDASGSMAARHRMAAAKGAVLSLLRDAYQRRDKVALIAFRGTEAEVLLPPTR 58 (178)
T ss_pred EEEEEECCccCCCccHHHHHHHHHHHHHHHhhcCCCEEEEEEECCCCceEEeCCCC
Confidence 67899999999976 99999999999886 4678999999999975 666667654
No 15
>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=98.55 E-value=2.2e-07 Score=67.88 Aligned_cols=56 Identities=13% Similarity=0.176 Sum_probs=49.1
Q ss_pred cccEEEEEcCCCCCCCchHHHHHHHHHHHHhhC---------CCCCEEEEEEeCCceeeeeecCC
Q psy9195 74 SKDVVILVDNSGSMAGMRNTTAKLVLHSLLQTF---------SNNDFINIFKFNLTVDTIVPCLG 129 (139)
Q Consensus 74 ~~~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l---------~~~d~~~v~~f~~~~~~~~~~~~ 129 (139)
|.++++++|.|+||.+..++.+|..++.+++.| ..+++++|+.|+++....+|..+
T Consensus 2 ~~dvv~vlD~S~Sm~~~~~~~~k~~~~~~~~~l~~~~~~~i~~~~~rvglv~fs~~~~~~~~l~~ 66 (186)
T cd01480 2 PVDITFVLDSSESVGLQNFDITKNFVKRVAERFLKDYYRKDPAGSWRVGVVQYSDQQEVEAGFLR 66 (186)
T ss_pred CeeEEEEEeCCCccchhhHHHHHHHHHHHHHHHhhhhccCCCCCceEEEEEEecCCceeeEeccc
Confidence 568999999999999888999999888888888 34799999999999998888763
No 16
>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=98.49 E-value=4.8e-07 Score=63.19 Aligned_cols=55 Identities=16% Similarity=0.214 Sum_probs=49.1
Q ss_pred cEEEEEcCCCCCCCchHHHHHHHHHHHHhhCCC---CCEEEEEEeCCceeeeeecCCC
Q psy9195 76 DVVILVDNSGSMAGMRNTTAKLVLHSLLQTFSN---NDFINIFKFNLTVDTIVPCLGN 130 (139)
Q Consensus 76 ~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~~---~d~~~v~~f~~~~~~~~~~~~~ 130 (139)
++++++|+||||.+.+++.++.++..++..+.. +++++|+.|++......+++..
T Consensus 2 di~~llD~S~Sm~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~f~~~~~~~~~~~~~ 59 (161)
T cd01450 2 DIVFLLDGSESVGPENFEKVKDFIEKLVEKLDIGPDKTRVGLVQYSDDVRVEFSLNDY 59 (161)
T ss_pred cEEEEEeCCCCcCHHHHHHHHHHHHHHHHheeeCCCceEEEEEEEcCCceEEEECCCC
Confidence 688999999999988899999999999988774 9999999999999888887754
No 17
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=98.48 E-value=4.4e-07 Score=77.13 Aligned_cols=58 Identities=24% Similarity=0.326 Sum_probs=50.2
Q ss_pred ccccEEEEEcCCCCCCCchHHHHHHHHHHHHhh-CCCCCEEEEEEeCCc-eeeeeecCCC
Q psy9195 73 CSKDVVILVDNSGSMAGMRNTTAKLVLHSLLQT-FSNNDFINIFKFNLT-VDTIVPCLGN 130 (139)
Q Consensus 73 ~~~~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~-l~~~d~~~v~~f~~~-~~~~~~~~~~ 130 (139)
.+..++|+||+||||.+.+|..+|.++..+|.. +.+.|+++||.|+++ +..+.|++..
T Consensus 400 ~~~~vvfvvD~SGSM~~~rl~~aK~a~~~ll~~ay~~rD~v~lI~F~g~~a~~~lppT~~ 459 (584)
T PRK13406 400 SETTTIFVVDASGSAALHRLAEAKGAVELLLAEAYVRRDQVALVAFRGRGAELLLPPTRS 459 (584)
T ss_pred CCccEEEEEECCCCCcHhHHHHHHHHHHHHHHhhcCCCCEEEEEEECCCceeEEcCCCcC
Confidence 346788999999999999999999999998855 689999999999765 8888888753
No 18
>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=98.48 E-value=3.2e-07 Score=67.16 Aligned_cols=56 Identities=21% Similarity=0.342 Sum_probs=50.3
Q ss_pred ccEEEEEcCCCCCCC-----chHHHHHHHHHHHHhhC---CCCCEEEEEEe-CCceeeeeecCCC
Q psy9195 75 KDVVILVDNSGSMAG-----MRNTTAKLVLHSLLQTF---SNNDFINIFKF-NLTVDTIVPCLGN 130 (139)
Q Consensus 75 ~~vvi~iD~sgSm~g-----~~l~~ak~~~~~~l~~l---~~~d~~~v~~f-~~~~~~~~~~~~~ 130 (139)
.++++++|.|+||.. +|++.+|.++..+++.+ .++|+++|+.| ++.+..+.||+.+
T Consensus 4 r~ivi~lD~S~SM~a~D~~ptRl~~ak~~~~~fi~~~~~~~~~~~vglv~f~~~~a~~~~PlT~D 68 (183)
T cd01453 4 RHLIIVIDCSRSMEEQDLKPSRLAVVLKLLELFIEEFFDQNPISQLGIISIKNGRAEKLTDLTGN 68 (183)
T ss_pred eEEEEEEECcHHHhcCCCCchHHHHHHHHHHHHHHHHhhcCccccEEEEEEcCCccEEEECCCCC
Confidence 468899999999975 58999999999999864 68899999999 8999999999977
No 19
>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=98.46 E-value=6.5e-07 Score=67.24 Aligned_cols=56 Identities=20% Similarity=0.319 Sum_probs=50.3
Q ss_pred cccEEEEEcCCCCCCCchHHHHHHHHHHHHhhCC---CCCEEEEEEeCCceeeeeecCC
Q psy9195 74 SKDVVILVDNSGSMAGMRNTTAKLVLHSLLQTFS---NNDFINIFKFNLTVDTIVPCLG 129 (139)
Q Consensus 74 ~~~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~---~~d~~~v~~f~~~~~~~~~~~~ 129 (139)
|.+++|++|.|+||.+..++.+|..+..+++.|. .+++|+|+.|+++++..+|+..
T Consensus 2 ~~DlvfllD~S~Sm~~~~~~~~k~f~~~l~~~l~~~~~~~rvglv~fs~~~~~~~~l~~ 60 (224)
T cd01475 2 PTDLVFLIDSSRSVRPENFELVKQFLNQIIDSLDVGPDATRVGLVQYSSTVKQEFPLGR 60 (224)
T ss_pred CccEEEEEeCCCCCCHHHHHHHHHHHHHHHHhcccCCCccEEEEEEecCceeEEecccc
Confidence 5789999999999999999999999999999886 3579999999999999888753
No 20
>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=98.45 E-value=7.3e-07 Score=64.75 Aligned_cols=54 Identities=22% Similarity=0.354 Sum_probs=47.8
Q ss_pred cEEEEEcCCCCCCCch-HHHHHHHHHHHHhhCC---CCCEEEEEEeCCceeeeeecCC
Q psy9195 76 DVVILVDNSGSMAGMR-NTTAKLVLHSLLQTFS---NNDFINIFKFNLTVDTIVPCLG 129 (139)
Q Consensus 76 ~vvi~iD~sgSm~g~~-l~~ak~~~~~~l~~l~---~~d~~~v~~f~~~~~~~~~~~~ 129 (139)
++++++|.||||.+.. +..+|..+..+++.+. ++.+++|+.|++.++.++|+..
T Consensus 2 Dv~~vlD~SgSm~~~~~~~~~k~~~~~~~~~~~~~~~~~~vglv~Fs~~~~~~~~l~~ 59 (186)
T cd01471 2 DLYLLVDGSGSIGYSNWVTHVVPFLHTFVQNLNISPDEINLYLVTFSTNAKELIRLSS 59 (186)
T ss_pred cEEEEEeCCCCccchhhHHHHHHHHHHHHHhcccCCCceEEEEEEecCCceEEEECCC
Confidence 6899999999999887 9999999999999875 5679999999999998887653
No 21
>PF13519 VWA_2: von Willebrand factor type A domain; PDB: 3IBS_B 3RAG_B 2X5N_A.
Probab=98.44 E-value=4.8e-07 Score=63.63 Aligned_cols=53 Identities=38% Similarity=0.552 Sum_probs=45.3
Q ss_pred cEEEEEcCCCCCCCc-----hHHHHHHHHHHHHhhCCCCCEEEEEEeCCceeeeeecCC
Q psy9195 76 DVVILVDNSGSMAGM-----RNTTAKLVLHSLLQTFSNNDFINIFKFNLTVDTIVPCLG 129 (139)
Q Consensus 76 ~vvi~iD~sgSm~g~-----~l~~ak~~~~~~l~~l~~~d~~~v~~f~~~~~~~~~~~~ 129 (139)
++++++|.||||.+. +++.++.++..+++.+. +++++|+.|++......|...
T Consensus 1 dvv~v~D~SgSM~~~~~~~~~~~~~~~~~~~~~~~~~-~~~v~l~~f~~~~~~~~~~t~ 58 (172)
T PF13519_consen 1 DVVFVLDNSGSMNGYDGNRTRIDQAKDALNELLANLP-GDRVGLVSFSDSSRTLSPLTS 58 (172)
T ss_dssp EEEEEEE-SGGGGTTTSSS-HHHHHHHHHHHHHHHHT-TSEEEEEEESTSCEEEEEEES
T ss_pred CEEEEEECCcccCCCCCCCcHHHHHHHHHHHHHHHCC-CCEEEEEEecccccccccccc
Confidence 588999999999876 79999999999999975 889999999998877776543
No 22
>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=98.43 E-value=8.9e-07 Score=63.24 Aligned_cols=53 Identities=21% Similarity=0.263 Sum_probs=47.4
Q ss_pred cEEEEEcCCCCCCCchHHHHHHHHHHHHhhCC---CCCEEEEEEeCCceeeeeecC
Q psy9195 76 DVVILVDNSGSMAGMRNTTAKLVLHSLLQTFS---NNDFINIFKFNLTVDTIVPCL 128 (139)
Q Consensus 76 ~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~---~~d~~~v~~f~~~~~~~~~~~ 128 (139)
++++++|.|+||.+..+..+|..+..+++.|. ++++++|+.|+++++..+|..
T Consensus 2 Dv~~vlD~S~Sm~~~~~~~~k~~~~~l~~~~~~~~~~~rvgli~fs~~~~~~~~l~ 57 (164)
T cd01482 2 DIVFLVDGSWSIGRSNFNLVRSFLSSVVEAFEIGPDGVQVGLVQYSDDPRTEFDLN 57 (164)
T ss_pred CEEEEEeCCCCcChhhHHHHHHHHHHHHhheeeCCCceEEEEEEECCCeeEEEecC
Confidence 68999999999988889999999999988774 679999999999998888764
No 23
>TIGR00868 hCaCC calcium-activated chloride channel protein 1. distributions. found a row in 1A13.INFO that was not parsed out
Probab=98.42 E-value=6.9e-07 Score=78.53 Aligned_cols=64 Identities=17% Similarity=0.208 Sum_probs=49.8
Q ss_pred hhhhhhccccccEEEEEcCCCCCCC-chHHHHHHHHHHH-HhhCCCCCEEEEEEeCCceeeeeecC
Q psy9195 65 QWYIQATTCSKDVVILVDNSGSMAG-MRNTTAKLVLHSL-LQTFSNNDFINIFKFNLTVDTIVPCL 128 (139)
Q Consensus 65 ~Wy~~a~~~~~~vvi~iD~sgSm~g-~~l~~ak~~~~~~-l~~l~~~d~~~v~~f~~~~~~~~~~~ 128 (139)
|+|..-...+..++++||.||||.+ .++..++.+++.+ .+.+.++|+++|+.|++++..+.|+.
T Consensus 295 P~Fs~lq~~~r~VVLVLDvSGSM~g~dRL~~lkqAA~~fL~~~l~~~DrVGLVtFsssA~vl~pLt 360 (863)
T TIGR00868 295 PTFSLLKIRQRIVCLVLDKSGSMTVEDRLKRMNQAAKLFLLQTVEKGSWVGMVTFDSAAYIKNELI 360 (863)
T ss_pred CceeecccCCceEEEEEECCccccccCHHHHHHHHHHHHHHHhCCCCCEEEEEEECCceeEeeccc
Confidence 4443322234568899999999986 5899999998765 46788999999999999998876654
No 24
>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=98.41 E-value=4.3e-07 Score=65.43 Aligned_cols=46 Identities=28% Similarity=0.265 Sum_probs=41.5
Q ss_pred cEEEEEcCCCCCCC-chHHHHHHHHHHHHhhCCC-CCEEEEEEeCCce
Q psy9195 76 DVVILVDNSGSMAG-MRNTTAKLVLHSLLQTFSN-NDFINIFKFNLTV 121 (139)
Q Consensus 76 ~vvi~iD~sgSm~g-~~l~~ak~~~~~~l~~l~~-~d~~~v~~f~~~~ 121 (139)
.+++++|+||||.+ .+++.||+++..++..+.. +|+++|+.|++..
T Consensus 2 ~v~~llD~SgSM~~~~kl~~ak~a~~~l~~~l~~~~d~~~l~~F~~~~ 49 (174)
T cd01454 2 AVTLLLDLSGSMRSDRRIDVAKKAAVLLAEALEACGVPHAILGFTTDA 49 (174)
T ss_pred EEEEEEECCCCCCCCcHHHHHHHHHHHHHHHHHHcCCcEEEEEecCCC
Confidence 37799999999998 5999999999999988885 9999999999873
No 25
>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=98.40 E-value=1e-06 Score=68.59 Aligned_cols=56 Identities=23% Similarity=0.297 Sum_probs=49.5
Q ss_pred ccccEEEEEcCCCCCCCchHHHHHHHHHHHHhh-CCCCCEEEEEEeCCceeeeeecCC
Q psy9195 73 CSKDVVILVDNSGSMAGMRNTTAKLVLHSLLQT-FSNNDFINIFKFNLTVDTIVPCLG 129 (139)
Q Consensus 73 ~~~~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~-l~~~d~~~v~~f~~~~~~~~~~~~ 129 (139)
.|.++++++|.||||.+ ++..++.++..+++. +.++|+++|+.|++++..+.|.+.
T Consensus 52 ~p~~vvlvlD~SgSM~~-~~~~a~~a~~~~l~~~l~~~d~v~lv~f~~~~~~~~~~t~ 108 (296)
T TIGR03436 52 LPLTVGLVIDTSGSMRN-DLDRARAAAIRFLKTVLRPNDRVFVVTFNTRLRLLQDFTS 108 (296)
T ss_pred CCceEEEEEECCCCchH-HHHHHHHHHHHHHHhhCCCCCEEEEEEeCCceeEeecCCC
Confidence 47889999999999976 688899999999987 889999999999999998887754
No 26
>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=98.38 E-value=8.1e-07 Score=62.43 Aligned_cols=47 Identities=34% Similarity=0.400 Sum_probs=42.0
Q ss_pred ccEEEEEcCCCCCCCchHHHHHHHHHHHHhhCC-CCCEEEEEEeCCce
Q psy9195 75 KDVVILVDNSGSMAGMRNTTAKLVLHSLLQTFS-NNDFINIFKFNLTV 121 (139)
Q Consensus 75 ~~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~-~~d~~~v~~f~~~~ 121 (139)
+++++++|+||||.+.++..++.++..++..+. .+|+++|+.|+++.
T Consensus 1 ~~v~illD~SgSM~~~k~~~a~~~~~~l~~~~~~~~~~v~li~F~~~~ 48 (152)
T cd01462 1 GPVILLVDQSGSMYGAPEEVAKAVALALLRIALAENRDTYLILFDSEF 48 (152)
T ss_pred CCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHcCCcEEEEEeCCCc
Confidence 468999999999999889999999998888776 49999999999983
No 27
>COG4245 TerY Uncharacterized protein encoded in toxicity protection region of plasmid R478, contains von Willebrand factor (vWF) domain [General function prediction only]
Probab=98.36 E-value=7.9e-07 Score=65.17 Aligned_cols=53 Identities=25% Similarity=0.347 Sum_probs=47.4
Q ss_pred cEEEEEcCCCCCCCchHHHHHHHHHHHHhhCCCCC------EEEEEEeCCceeeeeecC
Q psy9195 76 DVVILVDNSGSMAGMRNTTAKLVLHSLLQTFSNND------FINIFKFNLTVDTIVPCL 128 (139)
Q Consensus 76 ~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~~~d------~~~v~~f~~~~~~~~~~~ 128 (139)
-+++++|+||||.|++++..+..++.++++|..+- +++|++|++.++.+.|+.
T Consensus 5 P~~lllDtSgSM~Ge~IealN~Glq~m~~~Lkqdp~Ale~v~lsIVTF~~~a~~~~pf~ 63 (207)
T COG4245 5 PCYLLLDTSGSMIGEPIEALNAGLQMMIDTLKQDPYALERVELSIVTFGGPARVIQPFT 63 (207)
T ss_pred CEEEEEecCcccccccHHHHHHHHHHHHHHHHhChhhhheeEEEEEEecCcceEEechh
Confidence 36789999999999999999999999999987543 599999999999998875
No 28
>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=98.34 E-value=1.8e-06 Score=63.90 Aligned_cols=56 Identities=20% Similarity=0.216 Sum_probs=49.0
Q ss_pred ccccEEEEEcCCCCCCCchHHHHHHHHHHHHhhCCC---------CCEEEEEEeCCceeeeeecC
Q psy9195 73 CSKDVVILVDNSGSMAGMRNTTAKLVLHSLLQTFSN---------NDFINIFKFNLTVDTIVPCL 128 (139)
Q Consensus 73 ~~~~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~~---------~d~~~v~~f~~~~~~~~~~~ 128 (139)
.+.+++|+||.|+||...+++.+|..+..++..+.. +.+++|+.|+++++..+|+.
T Consensus 18 ~~~DivfvlD~S~Sm~~~~f~~~k~fi~~~~~~~~~~~~~~~~~~~~rVGlV~fs~~a~~~~~L~ 82 (193)
T cd01477 18 LWLDIVFVVDNSKGMTQGGLWQVRATISSLFGSSSQIGTDYDDPRSTRVGLVTYNSNATVVADLN 82 (193)
T ss_pred ceeeEEEEEeCCCCcchhhHHHHHHHHHHHHhhccccccccCCCCCcEEEEEEccCceEEEEecc
Confidence 468999999999999878899999999888776654 48999999999999999885
No 29
>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=98.31 E-value=2.5e-06 Score=60.24 Aligned_cols=54 Identities=30% Similarity=0.413 Sum_probs=48.8
Q ss_pred cccEEEEEcCCCCCCCchHHHHHHHHHHHHhhCCC---CCEEEEEEeCCceeeeeec
Q psy9195 74 SKDVVILVDNSGSMAGMRNTTAKLVLHSLLQTFSN---NDFINIFKFNLTVDTIVPC 127 (139)
Q Consensus 74 ~~~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~~---~d~~~v~~f~~~~~~~~~~ 127 (139)
|.++++++|.|+||.+.+++.++..+..++..+.. +++++|+.|++......|.
T Consensus 1 ~~~v~l~vD~S~SM~~~~~~~~~~~~~~~~~~~~~~~~~~~i~ii~f~~~~~~~~~~ 57 (177)
T smart00327 1 PLDVVFLLDGSGSMGPNRFEKAKEFVLKLVEQLDIGPDGDRVGLVTFSDDATVLFPL 57 (177)
T ss_pred CccEEEEEeCCCccchHHHHHHHHHHHHHHHhcCCCCCCcEEEEEEeCCCceEEEcc
Confidence 45789999999999988999999999999999887 9999999999988877765
No 30
>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=98.28 E-value=3.3e-06 Score=59.93 Aligned_cols=54 Identities=30% Similarity=0.426 Sum_probs=47.2
Q ss_pred cEEEEEcCCCCCCCchHHHHHHHHHHHHhh---CCCCCEEEEEEeCCceeeeeecCC
Q psy9195 76 DVVILVDNSGSMAGMRNTTAKLVLHSLLQT---FSNNDFINIFKFNLTVDTIVPCLG 129 (139)
Q Consensus 76 ~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~---l~~~d~~~v~~f~~~~~~~~~~~~ 129 (139)
+|+|++|.|+||.+..++.++.++..+++. ...+.+++|+.|++..+.+++...
T Consensus 1 DivflvD~S~sm~~~~~~~~~~~v~~~i~~~~~~~~~~rv~iv~f~~~~~~~~~~~~ 57 (178)
T PF00092_consen 1 DIVFLVDTSGSMSGDNFEKAKQFVKSIISRLSISNNGTRVGIVTFSDSARVLFSLTD 57 (178)
T ss_dssp EEEEEEE-STTSCHHHHHHHHHHHHHHHHHSTBSTTSEEEEEEEESSSEEEEEETTS
T ss_pred CEEEEEeCCCCCchHHHHHHHHHHHHHHHhhhccccccccceeeeeccccccccccc
Confidence 589999999999998999999999999984 568999999999999998876643
No 31
>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=98.27 E-value=3.5e-06 Score=61.31 Aligned_cols=57 Identities=21% Similarity=0.270 Sum_probs=42.5
Q ss_pred ccccEEEEEcCCCCCCCchHHHHHHHHHHHHhhC-CCCCEEEEEEeCCceeeeeecCCC
Q psy9195 73 CSKDVVILVDNSGSMAGMRNTTAKLVLHSLLQTF-SNNDFINIFKFNLTVDTIVPCLGN 130 (139)
Q Consensus 73 ~~~~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l-~~~d~~~v~~f~~~~~~~~~~~~~ 130 (139)
.+-++++++|.||||.+... ..+..++.++..+ .++++++|+.|+++++.++|+...
T Consensus 3 ~~~Dvv~llD~SgSm~~~~~-~~~~~~~~l~~~~~~~~~rvglv~Fs~~~~~~~~l~~~ 60 (185)
T cd01474 3 GHFDLYFVLDKSGSVAANWI-EIYDFVEQLVDRFNSPGLRFSFITFSTRATKILPLTDD 60 (185)
T ss_pred CceeEEEEEeCcCchhhhHH-HHHHHHHHHHHHcCCCCcEEEEEEecCCceEEEecccc
Confidence 45689999999999987532 2234455554443 478999999999999999888643
No 32
>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=98.26 E-value=3.6e-06 Score=60.49 Aligned_cols=55 Identities=33% Similarity=0.360 Sum_probs=45.9
Q ss_pred cccEEEEEcCCCCCCC------chHHHHHHHHHHHHhhCCCCCEEEEEEeCCceeeeeecCC
Q psy9195 74 SKDVVILVDNSGSMAG------MRNTTAKLVLHSLLQTFSNNDFINIFKFNLTVDTIVPCLG 129 (139)
Q Consensus 74 ~~~vvi~iD~sgSm~g------~~l~~ak~~~~~~l~~l~~~d~~~v~~f~~~~~~~~~~~~ 129 (139)
+.++++++|.|+||.+ .+++.++.++..++... ++|+++|+.|++....+.|...
T Consensus 2 ~~~vv~vlD~S~SM~~~~~~~~~r~~~a~~~~~~~~~~~-~~~~v~lv~f~~~~~~~~~~~~ 62 (180)
T cd01467 2 GRDIMIALDVSGSMLAQDFVKPSRLEAAKEVLSDFIDRR-ENDRIGLVVFAGAAFTQAPLTL 62 (180)
T ss_pred CceEEEEEECCcccccccCCCCCHHHHHHHHHHHHHHhC-CCCeEEEEEEcCCeeeccCCCc
Confidence 3578999999999974 36889999998888764 7999999999999887777654
No 33
>COG1240 ChlD Mg-chelatase subunit ChlD [Coenzyme metabolism]
Probab=98.19 E-value=3.9e-06 Score=64.31 Aligned_cols=57 Identities=30% Similarity=0.430 Sum_probs=48.9
Q ss_pred cccEEEEEcCCCCCCCc-hHHHHHHHHHHHHhh-CCCCCEEEEEEeC-CceeeeeecCCC
Q psy9195 74 SKDVVILVDNSGSMAGM-RNTTAKLVLHSLLQT-FSNNDFINIFKFN-LTVDTIVPCLGN 130 (139)
Q Consensus 74 ~~~vvi~iD~sgSm~g~-~l~~ak~~~~~~l~~-l~~~d~~~v~~f~-~~~~~~~~~~~~ 130 (139)
..-|+|++|+||||.+. ++..||.++..+|.. -...|+++||+|. .+++.+.|.+..
T Consensus 78 g~lvvfvVDASgSM~~~~Rm~aaKG~~~~lL~dAYq~RdkvavI~F~G~~A~lll~pT~s 137 (261)
T COG1240 78 GNLIVFVVDASGSMAARRRMAAAKGAALSLLRDAYQRRDKVAVIAFRGEKAELLLPPTSS 137 (261)
T ss_pred CCcEEEEEeCcccchhHHHHHHHHHHHHHHHHHHHHccceEEEEEecCCcceEEeCCccc
Confidence 35578999999999987 899999999888755 5589999999999 788888888764
No 34
>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=98.17 E-value=8.9e-06 Score=58.96 Aligned_cols=53 Identities=17% Similarity=0.253 Sum_probs=47.7
Q ss_pred cEEEEEcCCCCCCCchHHHHHHHHHHHHhhCCC---CCEEEEEEeCCceeeeeecC
Q psy9195 76 DVVILVDNSGSMAGMRNTTAKLVLHSLLQTFSN---NDFINIFKFNLTVDTIVPCL 128 (139)
Q Consensus 76 ~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~~---~d~~~v~~f~~~~~~~~~~~ 128 (139)
+++|++|.|+||.+..++.+|..++.+++.|.. +.+|+|+.|+++.+..+|+.
T Consensus 2 Di~fvlD~S~S~~~~~f~~~k~fi~~~i~~l~~~~~~~rvgvv~fs~~~~~~~~l~ 57 (177)
T cd01469 2 DIVFVLDGSGSIYPDDFQKVKNFLSTVMKKLDIGPTKTQFGLVQYSESFRTEFTLN 57 (177)
T ss_pred cEEEEEeCCCCCCHHHHHHHHHHHHHHHHHcCcCCCCcEEEEEEECCceeEEEecC
Confidence 689999999999888899999999999998875 68999999999998887764
No 35
>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=98.16 E-value=6.4e-06 Score=70.26 Aligned_cols=56 Identities=27% Similarity=0.390 Sum_probs=46.8
Q ss_pred ccEEEEEcCCCCCCCchHHHHHHHHHHHHhh-CCCCCEEEEEEeCCce-eeeeecCCC
Q psy9195 75 KDVVILVDNSGSMAGMRNTTAKLVLHSLLQT-FSNNDFINIFKFNLTV-DTIVPCLGN 130 (139)
Q Consensus 75 ~~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~-l~~~d~~~v~~f~~~~-~~~~~~~~~ 130 (139)
..++|++|+||||.+.++..+|.++..++.. +..+|+|+|+.|++.. ..+.|.+.+
T Consensus 408 ~~v~fvvD~SGSM~~~rl~~aK~av~~Ll~~~~~~~D~v~Li~F~~~~a~~~lp~t~~ 465 (589)
T TIGR02031 408 RLLIFVVDASGSAAVARMSEAKGAVELLLGEAYVHRDQVSLIAFRGTAAEVLLPPSRS 465 (589)
T ss_pred ceEEEEEECCCCCChHHHHHHHHHHHHHHHhhccCCCEEEEEEECCCCceEECCCCCC
Confidence 3477999999999989999999999999876 4589999999998764 677776643
No 36
>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=98.09 E-value=1.4e-05 Score=56.58 Aligned_cols=51 Identities=14% Similarity=0.264 Sum_probs=42.1
Q ss_pred cEEEEEcCCCCCCCchHHHHHHHHHHHHhhCCC---CCEEEEEEeCC--ceeeeeec
Q psy9195 76 DVVILVDNSGSMAGMRNTTAKLVLHSLLQTFSN---NDFINIFKFNL--TVDTIVPC 127 (139)
Q Consensus 76 ~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~~---~d~~~v~~f~~--~~~~~~~~ 127 (139)
++++++|.|+||.+ .++..+..+..++..|.. +++++|+.|++ .....+|.
T Consensus 2 dv~~llD~S~Sm~~-~~~~~~~~~~~~~~~l~~~~~~~~v~lv~f~~~~~~~~~~~l 57 (163)
T cd01476 2 DLLFVLDSSGSVRG-KFEKYKKYIERIVEGLEIGPTATRVALITYSGRGRQRVRFNL 57 (163)
T ss_pred CEEEEEeCCcchhh-hHHHHHHHHHHHHHhcCCCCCCcEEEEEEEcCCCceEEEecC
Confidence 58899999999976 577788888888888875 89999999999 55555554
No 37
>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=98.04 E-value=2.1e-05 Score=53.90 Aligned_cols=53 Identities=32% Similarity=0.532 Sum_probs=46.8
Q ss_pred cEEEEEcCCCCCCCchHHHHHHHHHHHHhhCCC---CCEEEEEEeCCceeeeeecC
Q psy9195 76 DVVILVDNSGSMAGMRNTTAKLVLHSLLQTFSN---NDFINIFKFNLTVDTIVPCL 128 (139)
Q Consensus 76 ~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~~---~d~~~v~~f~~~~~~~~~~~ 128 (139)
++++++|.|+||....+..++.++..++..+.. +++++|+.|+.....+.+..
T Consensus 2 ~v~~viD~S~Sm~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~~f~~~~~~~~~~~ 57 (161)
T cd00198 2 DIVFLLDVSGSMGGEKLDKAKEALKALVSSLSASPPGDRVGLVTFGSNARVVLPLT 57 (161)
T ss_pred cEEEEEeCCCCcCcchHHHHHHHHHHHHHhcccCCCCcEEEEEEecCccceeeccc
Confidence 578999999999777899999999999999887 99999999999877776654
No 38
>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=97.92 E-value=3.5e-05 Score=66.26 Aligned_cols=57 Identities=30% Similarity=0.452 Sum_probs=47.0
Q ss_pred cccEEEEEcCCCCCCCc-hHHHHHHHHHHHHh-hCCCCCEEEEEEeCC-ceeeeeecCCC
Q psy9195 74 SKDVVILVDNSGSMAGM-RNTTAKLVLHSLLQ-TFSNNDFINIFKFNL-TVDTIVPCLGN 130 (139)
Q Consensus 74 ~~~vvi~iD~sgSm~g~-~l~~ak~~~~~~l~-~l~~~d~~~v~~f~~-~~~~~~~~~~~ 130 (139)
+..++|++|.||||.+. ++..+|.++..++. .+..+|+|+|+.|++ .+..+.|.+..
T Consensus 465 ~~~vv~vvD~SgSM~~~~rl~~ak~a~~~ll~~a~~~~D~v~lI~F~g~~a~~~~p~t~~ 524 (633)
T TIGR02442 465 GNLVIFVVDASGSMAARGRMAAAKGAVLSLLRDAYQKRDKVALITFRGEEAEVLLPPTSS 524 (633)
T ss_pred CceEEEEEECCccCCCccHHHHHHHHHHHHHHHhhcCCCEEEEEEECCCCceEEcCCCCC
Confidence 35688999999999874 89999999988875 467899999999986 57777777643
No 39
>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=97.87 E-value=2.9e-05 Score=57.18 Aligned_cols=55 Identities=25% Similarity=0.321 Sum_probs=45.4
Q ss_pred cccEEEEEcCCCCCCCc-------hHHHHHHHHHHHHhhCC--CCCEEEEEEeCCceeeeeecC
Q psy9195 74 SKDVVILVDNSGSMAGM-------RNTTAKLVLHSLLQTFS--NNDFINIFKFNLTVDTIVPCL 128 (139)
Q Consensus 74 ~~~vvi~iD~sgSm~g~-------~l~~ak~~~~~~l~~l~--~~d~~~v~~f~~~~~~~~~~~ 128 (139)
+.+++++||.||||... ++..+++++..++..+. +.|.++++.|++......|+.
T Consensus 2 ~~dvv~~ID~SgSM~~~~~~~~~~k~~~ak~~~~~l~~~~~~~D~d~i~l~~f~~~~~~~~~~~ 65 (199)
T cd01457 2 NRDYTLLIDKSGSMAEADEAKERSRWEEAQESTRALARKCEEYDSDGITVYLFSGDFRRYDNVN 65 (199)
T ss_pred CcCEEEEEECCCcCCCCCCCCCchHHHHHHHHHHHHHHHHHhcCCCCeEEEEecCCccccCCcC
Confidence 56899999999999742 78999999999887754 578899999999877666654
No 40
>PRK10997 yieM hypothetical protein; Provisional
Probab=97.76 E-value=6.7e-05 Score=62.58 Aligned_cols=52 Identities=29% Similarity=0.374 Sum_probs=43.1
Q ss_pred ccccEEEEEcCCCCCCCchHHHHHHHHHHHHh-hCCCCCEEEEEEeCCceeee
Q psy9195 73 CSKDVVILVDNSGSMAGMRNTTAKLVLHSLLQ-TFSNNDFINIFKFNLTVDTI 124 (139)
Q Consensus 73 ~~~~vvi~iD~sgSm~g~~l~~ak~~~~~~l~-~l~~~d~~~v~~f~~~~~~~ 124 (139)
.++.+++++|+||||.|.+...|+..+..+.. .+..+|.++++.|++.+...
T Consensus 322 ~kGpiII~VDtSGSM~G~ke~~AkalAaAL~~iAl~q~dr~~li~Fs~~i~~~ 374 (487)
T PRK10997 322 PRGPFIVCVDTSGSMGGFNEQCAKAFCLALMRIALAENRRCYIMLFSTEVVTY 374 (487)
T ss_pred CCCcEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHhcCCCEEEEEecCCceee
Confidence 45789999999999999888888886666544 57899999999999987653
No 41
>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=97.69 E-value=0.00015 Score=53.43 Aligned_cols=54 Identities=15% Similarity=0.270 Sum_probs=44.8
Q ss_pred cEEEEEcCCCCCCCchHH-HHHHHHHHHHhhCC---CCCEEEEEEeCCceeeeeecCC
Q psy9195 76 DVVILVDNSGSMAGMRNT-TAKLVLHSLLQTFS---NNDFINIFKFNLTVDTIVPCLG 129 (139)
Q Consensus 76 ~vvi~iD~sgSm~g~~l~-~ak~~~~~~l~~l~---~~d~~~v~~f~~~~~~~~~~~~ 129 (139)
+++|++|.|+||....+. .++..++.+++.|. .+.+++|+.|++..+..+|+..
T Consensus 2 Di~fllD~S~Si~~~~f~~~~~~f~~~lv~~l~i~~~~~rvgvv~fs~~~~~~~~~~~ 59 (192)
T cd01473 2 DLTLILDESASIGYSNWRKDVIPFTEKIINNLNISKDKVHVGILLFAEKNRDVVPFSD 59 (192)
T ss_pred cEEEEEeCCCcccHHHHHHHHHHHHHHHHHhCccCCCccEEEEEEecCCceeEEecCc
Confidence 689999999999766565 46778888887776 4589999999999998888764
No 42
>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=97.61 E-value=0.00028 Score=50.76 Aligned_cols=53 Identities=17% Similarity=0.258 Sum_probs=46.1
Q ss_pred ccEEEEEcCCCCCCCchHHHHHHHHHHHHhhCC---CCCEEEEEEeCCceeeeeec
Q psy9195 75 KDVVILVDNSGSMAGMRNTTAKLVLHSLLQTFS---NNDFINIFKFNLTVDTIVPC 127 (139)
Q Consensus 75 ~~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~---~~d~~~v~~f~~~~~~~~~~ 127 (139)
.+++|++|.|+|+....++.+|.-+..+++.|. .+-+++|+.|+++.+..+++
T Consensus 1 ~DivfllD~S~Si~~~~f~~~k~fi~~lv~~f~i~~~~~rVgvv~ys~~~~~~~~l 56 (165)
T cd01481 1 KDIVFLIDGSDNVGSGNFPAIRDFIERIVQSLDVGPDKIRVAVVQFSDTPRPEFYL 56 (165)
T ss_pred CCEEEEEeCCCCcCHHHHHHHHHHHHHHHhhccCCCCCcEEEEEEecCCeeEEEec
Confidence 378999999999987889999999999998887 45699999999999877655
No 43
>PRK15426 putative diguanylate cyclase YedQ; Provisional
Probab=97.54 E-value=0.00024 Score=59.53 Aligned_cols=69 Identities=16% Similarity=0.273 Sum_probs=50.6
Q ss_pred CHHHHHhhhchHHHHHHHHHHhhcCcceeEeeeecccccEEE-CCCCCCCCccccccccccchhhhhhcc
Q psy9195 4 HDDVRAGLMWSEGLDEVFRENYMADPTLLWQYFGSAKGFLRT-YPDKEDAPAEDLIFDCRNRQWYIQATT 72 (139)
Q Consensus 4 ~~~v~~~~~~~~~l~~~f~~~~~~~~~i~~~y~gs~~G~~~~-~p~~~~~~~~~~~yDpr~r~Wy~~a~~ 72 (139)
+|+...+......+.+.|....+.++.+..+|+.+.+|.++. +|...........|||+.|+||+.++.
T Consensus 144 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~d~~~r~WY~~a~~ 213 (570)
T PRK15426 144 DEDLANELTAALELGYLLRLAHNSSSLVERAMYVSRAGFYVSTYPTLFPSDVPTRYYQYVTQPWFIGQSQ 213 (570)
T ss_pred cHHHHHHHHHHHHHHHHhccccccCCceeEEEEEeCCceEEEeCCCCCccccccccCCcccChHHHhhhh
Confidence 455555665566788889999999999999988889998876 664322111135799999999998753
No 44
>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=97.51 E-value=0.00031 Score=51.85 Aligned_cols=55 Identities=13% Similarity=0.176 Sum_probs=46.5
Q ss_pred cEEEEEcCCCCCCC-----chHHHHHHHHHHHH---hhCCCCCEEEEEEeCC-ceeeeeecCCC
Q psy9195 76 DVVILVDNSGSMAG-----MRNTTAKLVLHSLL---QTFSNNDFINIFKFNL-TVDTIVPCLGN 130 (139)
Q Consensus 76 ~vvi~iD~sgSm~g-----~~l~~ak~~~~~~l---~~l~~~d~~~v~~f~~-~~~~~~~~~~~ 130 (139)
.+++++|.|.||.. +|++.+|.++..++ -...+++++||+.|.+ .+..+.|++.+
T Consensus 5 a~vi~lD~S~sM~a~D~~PnRL~aak~~i~~~~~~f~~~np~~~vGlv~fag~~a~v~~plT~D 68 (187)
T cd01452 5 ATMICIDNSEYMRNGDYPPTRFQAQADAVNLICQAKTRSNPENNVGLMTMAGNSPEVLVTLTND 68 (187)
T ss_pred EEEEEEECCHHHHcCCCCCCHHHHHHHHHHHHHHHHHhcCCCccEEEEEecCCceEEEECCCCC
Confidence 46799999999974 48999999998775 2355788999999999 89999999877
No 45
>COG2425 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=97.47 E-value=0.00023 Score=58.63 Aligned_cols=50 Identities=30% Similarity=0.436 Sum_probs=42.2
Q ss_pred ccEEEEEcCCCCCCCchHHHHHHHHHHHHhh-CCCCCEEEEEEeCCceeee
Q psy9195 75 KDVVILVDNSGSMAGMRNTTAKLVLHSLLQT-FSNNDFINIFKFNLTVDTI 124 (139)
Q Consensus 75 ~~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~-l~~~d~~~v~~f~~~~~~~ 124 (139)
+.+++++|.||||.|.+.+.||..+.++.+. |.+|-.+.++.|++.+..+
T Consensus 273 GpvilllD~SGSM~G~~e~~AKAvalAl~~~alaenR~~~~~lF~s~~~~~ 323 (437)
T COG2425 273 GPVILLLDKSGSMSGFKEQWAKAVALALMRIALAENRDCYVILFDSEVIEY 323 (437)
T ss_pred CCEEEEEeCCCCcCCcHHHHHHHHHHHHHHHHHHhccceEEEEecccceee
Confidence 6789999999999999999999888877654 6688889999999954443
No 46
>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=97.45 E-value=0.00036 Score=54.16 Aligned_cols=67 Identities=15% Similarity=0.286 Sum_probs=50.4
Q ss_pred cchhhhhhc--cccccEEEEEcCCCCCCCc-----hHHHHHHHHHHHHhhCCCCCEEEEEEeCCceeeeeecCCCC
Q psy9195 63 NRQWYIQAT--TCSKDVVILVDNSGSMAGM-----RNTTAKLVLHSLLQTFSNNDFINIFKFNLTVDTIVPCLGNY 131 (139)
Q Consensus 63 ~r~Wy~~a~--~~~~~vvi~iD~sgSm~g~-----~l~~ak~~~~~~l~~l~~~d~~~v~~f~~~~~~~~~~~~~~ 131 (139)
.+-|..... +.+-++++.||.|.||..+ +++ ++..+..+++.| ++|+++|+.|++++..+.|++.++
T Consensus 47 dkIwlRRtkpskr~~qIvlaID~S~SM~~~~~~~~ale-ak~lIs~al~~L-e~g~vgVv~Fg~~~~~v~Plt~d~ 120 (266)
T cd01460 47 DKIWLRRTKPAKRDYQILIAIDDSKSMSENNSKKLALE-SLCLVSKALTLL-EVGQLGVCSFGEDVQILHPFDEQF 120 (266)
T ss_pred CceEEEeccCCccCceEEEEEecchhcccccccccHHH-HHHHHHHHHHhC-cCCcEEEEEeCCCceEeCCCCCCc
Confidence 345665432 2345789999999999743 354 777777777666 579999999999999999998873
No 47
>PF09967 DUF2201: VWA-like domain (DUF2201); InterPro: IPR018698 This family of various hypothetical bacterial proteins has no known function.
Probab=97.42 E-value=0.00045 Score=47.74 Aligned_cols=50 Identities=18% Similarity=0.323 Sum_probs=40.1
Q ss_pred EEEEEcCCCCCCCchHHHHHHHHHHHHhhCCCCCEEEEEEeCCceeeeeecC
Q psy9195 77 VVILVDNSGSMAGMRNTTAKLVLHSLLQTFSNNDFINIFKFNLTVDTIVPCL 128 (139)
Q Consensus 77 vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~~~d~~~v~~f~~~~~~~~~~~ 128 (139)
+++.+|+||||...-+......+..+++.. +.++.|+.||..+.......
T Consensus 1 i~vaiDtSGSis~~~l~~fl~ev~~i~~~~--~~~v~vi~~D~~v~~~~~~~ 50 (126)
T PF09967_consen 1 IVVAIDTSGSISDEELRRFLSEVAGILRRF--PAEVHVIQFDAEVQDVQVFR 50 (126)
T ss_pred CEEEEECCCCCCHHHHHHHHHHHHHHHHhC--CCCEEEEEECCEeeeeeEEe
Confidence 468999999999887777777777777777 66799999999988765443
No 48
>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=97.29 E-value=0.00066 Score=50.68 Aligned_cols=46 Identities=28% Similarity=0.343 Sum_probs=40.5
Q ss_pred cEEEEEcCCCCCC----C---chHHHHHHHHHHHHhh---CCCCCEEEEEEeCCce
Q psy9195 76 DVVILVDNSGSMA----G---MRNTTAKLVLHSLLQT---FSNNDFINIFKFNLTV 121 (139)
Q Consensus 76 ~vvi~iD~sgSm~----g---~~l~~ak~~~~~~l~~---l~~~d~~~v~~f~~~~ 121 (139)
.++++||+|.||. | .+++.|+.++..+++. -.++|++||+.|+++.
T Consensus 3 ~ivf~iDvS~SM~~~~~~~~~s~l~~a~~~i~~~~~~ki~~~~~D~vGlilf~t~~ 58 (218)
T cd01458 3 SVVFLVDVSPSMFESKDGEYESPFEEALKCIRQLMKSKIISSPKDLVGVVFYGTEE 58 (218)
T ss_pred EEEEEEeCCHHHcCCCCCCCCChHHHHHHHHHHHHHhceeCCCCCeEEEEEEcccC
Confidence 4789999999994 2 4799999999999987 5899999999999975
No 49
>PF11775 CobT_C: Cobalamin biosynthesis protein CobT VWA domain
Probab=97.18 E-value=0.00076 Score=50.77 Aligned_cols=46 Identities=26% Similarity=0.332 Sum_probs=35.4
Q ss_pred cEEEEEcCCCCCCCchHHHHHHHHHHHHhhCC-CCCEEEEEEeCCce
Q psy9195 76 DVVILVDNSGSMAGMRNTTAKLVLHSLLQTFS-NNDFINIFKFNLTV 121 (139)
Q Consensus 76 ~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~-~~d~~~v~~f~~~~ 121 (139)
-|.++||+||||.|.++.+|...+..+.++|. -|=.+-|+.|++..
T Consensus 14 ~VtlLID~SGSMrgr~~~vA~~~adila~aL~~~gvp~EVlGFtT~a 60 (219)
T PF11775_consen 14 VVTLLIDCSGSMRGRPIEVAALCADILARALERCGVPVEVLGFTTRA 60 (219)
T ss_pred EEEEEEeCCcCCCCChHHHHHHHHHHHHHHHHhCCCCeEEEeeecCC
Confidence 35589999999999988888766555555554 47778899999873
No 50
>PTZ00441 sporozoite surface protein 2 (SSP2); Provisional
Probab=97.02 E-value=0.0026 Score=54.11 Aligned_cols=58 Identities=26% Similarity=0.295 Sum_probs=46.3
Q ss_pred ccccEEEEEcCCCCCCC-chHHHHHHHHHHHHhhCC-CCCEEEE--EEeCCceeeeeecCCC
Q psy9195 73 CSKDVVILVDNSGSMAG-MRNTTAKLVLHSLLQTFS-NNDFINI--FKFNLTVDTIVPCLGN 130 (139)
Q Consensus 73 ~~~~vvi~iD~sgSm~g-~~l~~ak~~~~~~l~~l~-~~d~~~v--~~f~~~~~~~~~~~~~ 130 (139)
...+++|+||.|+||.- ..++.+|..+..++..|. ..|.+.| +.|++....++|+...
T Consensus 41 ~~lDIvFLLD~SgSMg~~Nfle~AK~Fa~~LV~~l~Is~D~V~VgiV~FSd~~r~vfpL~s~ 102 (576)
T PTZ00441 41 EEVDLYLLVDGSGSIGYHNWITHVIPMLMGLIQQLNLSDDAINLYMSLFSNNTTELIRLGSG 102 (576)
T ss_pred CCceEEEEEeCCCccCCccHHHHHHHHHHHHHHHhccCCCceEEEEEEeCCCceEEEecCCC
Confidence 45789999999999963 345789999999998885 4555554 8999999999988643
No 51
>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=96.89 E-value=0.0029 Score=47.16 Aligned_cols=53 Identities=21% Similarity=0.313 Sum_probs=40.5
Q ss_pred cEEEEEcCCCCCCCc----hHHHHHHHHHHHHhhCCCCCEEEEEEeCCceeeeeecC
Q psy9195 76 DVVILVDNSGSMAGM----RNTTAKLVLHSLLQTFSNNDFINIFKFNLTVDTIVPCL 128 (139)
Q Consensus 76 ~vvi~iD~sgSm~g~----~l~~ak~~~~~~l~~l~~~d~~~v~~f~~~~~~~~~~~ 128 (139)
.|.++||.||||.+. ..+.+.+-+..+-..|+++-.+-|+.|+.+.+.+-+.+
T Consensus 3 rV~LVLD~SGSM~~~yk~G~vQ~~~Er~lalA~~~DdDG~i~v~~Fs~~~~~~~~vt 59 (200)
T PF10138_consen 3 RVYLVLDISGSMRPLYKDGTVQRVVERILALAAQFDDDGEIDVWFFSTEFDRLPDVT 59 (200)
T ss_pred EEEEEEeCCCCCchhhhCccHHHHHHHHHHHHhhcCCCCceEEEEeCCCCCcCCCcC
Confidence 588999999999863 34444555555556799999999999999988775544
No 52
>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=96.33 E-value=0.0054 Score=46.17 Aligned_cols=54 Identities=30% Similarity=0.468 Sum_probs=35.9
Q ss_pred cccccEEEEEcCCCCCCCchHHHHHHHHHHHHhhCCCCCEEEEEEeCCceeeeeecCC
Q psy9195 72 TCSKDVVILVDNSGSMAGMRNTTAKLVLHSLLQTFSNNDFINIFKFNLTVDTIVPCLG 129 (139)
Q Consensus 72 ~~~~~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~~~d~~~v~~f~~~~~~~~~~~~ 129 (139)
..+..+++++|+||||.+..-- +-..+..+...+ ..+.++.|++.+..+.+.+.
T Consensus 55 ~~~~~lvvl~DvSGSM~~~s~~-~l~~~~~l~~~~---~~~~~f~F~~~l~~vT~~l~ 108 (222)
T PF05762_consen 55 RKPRRLVVLCDVSGSMAGYSEF-MLAFLYALQRQF---RRVRVFVFSTRLTEVTPLLR 108 (222)
T ss_pred CCCccEEEEEeCCCChHHHHHH-HHHHHHHHHHhC---CCEEEEEEeeehhhhhhhhc
Confidence 3455899999999999884211 112223333333 38999999999888766554
No 53
>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=96.17 E-value=0.018 Score=43.72 Aligned_cols=51 Identities=16% Similarity=0.117 Sum_probs=42.2
Q ss_pred cccEEEEEcCCCC-CCCchHHHHHHHHHHHHhhCC--CCCEEEEEEeCCceeee
Q psy9195 74 SKDVVILVDNSGS-MAGMRNTTAKLVLHSLLQTFS--NNDFINIFKFNLTVDTI 124 (139)
Q Consensus 74 ~~~vvi~iD~sgS-m~g~~l~~ak~~~~~~l~~l~--~~d~~~v~~f~~~~~~~ 124 (139)
|-.++++||+|.. ....-++.++++++..|++|. ++-+|++++|++.++..
T Consensus 3 pp~~vFvID~s~~ai~~~~l~~~~~sl~~~l~~lp~~~~~~igiITf~~~V~~~ 56 (239)
T cd01468 3 PPVFVFVIDVSYEAIKEGLLQALKESLLASLDLLPGDPRARVGLITYDSTVHFY 56 (239)
T ss_pred CCEEEEEEEcchHhccccHHHHHHHHHHHHHHhCCCCCCcEEEEEEeCCeEEEE
Confidence 3457899999885 333458999999999999999 99999999999887654
No 54
>cd00181 TarH Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These transmembrane signalers monitor the chemical environment by means of specific ligand-binding sites arrayed on the periplasmic side of the membrane, and in turn control cytoplasmic signals that modulate the flagellar rotational machinery. Aspartate is detected through direct binding to Tar molecules, whereas maltose is detected indirectly when complexed with the periplasmic maltose-binding protein.
Probab=96.15 E-value=0.00019 Score=48.57 Aligned_cols=54 Identities=20% Similarity=0.262 Sum_probs=43.4
Q ss_pred HHHHHHHHHHhhcCcceeEeeeecccccEEECCCCCCCCccccccccccchhhhhhcc
Q psy9195 15 EGLDEVFRENYMADPTLLWQYFGSAKGFLRTYPDKEDAPAEDLIFDCRNRQWYIQATT 72 (139)
Q Consensus 15 ~~l~~~f~~~~~~~~~i~~~y~gs~~G~~~~~p~~~~~~~~~~~yDpr~r~Wy~~a~~ 72 (139)
+.|...|..+.+.++.+..+|.|..+|.++..|.... +..||++.|+||+.++.
T Consensus 84 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~d~~~~~wyk~a~~ 137 (140)
T cd00181 84 AELKEKFKQYFQALAELIQILASGNMNAFFDQPTQGM----QNDFEAVYRDWLQQAEA 137 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHhCchHHH----HHHHHHHHHHHHHHHHH
Confidence 3477778888777788888999999999988884333 38999999999997754
No 55
>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=95.87 E-value=0.028 Score=43.60 Aligned_cols=48 Identities=17% Similarity=0.165 Sum_probs=41.4
Q ss_pred ccEEEEEcCCCCCCCchHHHHHHHHHHHHhhCCCCCEEEEEEeCCceeee
Q psy9195 75 KDVVILVDNSGSMAGMRNTTAKLVLHSLLQTFSNNDFINIFKFNLTVDTI 124 (139)
Q Consensus 75 ~~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~~~d~~~v~~f~~~~~~~ 124 (139)
--++++||++-. ...++.+|.++...|+.|.++.+|++|+|+..++..
T Consensus 4 p~~vFviDvs~~--~~el~~l~~sl~~~L~~lP~~a~VGlITfd~~V~~~ 51 (267)
T cd01478 4 PVFLFVVDTCMD--EEELDALKESLIMSLSLLPPNALVGLITFGTMVQVH 51 (267)
T ss_pred CEEEEEEECccC--HHHHHHHHHHHHHHHHhCCCCCEEEEEEECCEEEEE
Confidence 347799999774 456889999999999999999999999999998653
No 56
>TIGR01651 CobT cobaltochelatase, CobT subunit. This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit, with a MW ~70 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobS (TIGR01650) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobT gene product, the P. denitrificans gene symbol is not used in the name of this model.
Probab=95.83 E-value=0.018 Score=49.20 Aligned_cols=46 Identities=33% Similarity=0.377 Sum_probs=35.0
Q ss_pred cEEEEEcCCCCCCCchHHHHHHHHHHHHhhCC-CCCEEEEEEeCCce
Q psy9195 76 DVVILVDNSGSMAGMRNTTAKLVLHSLLQTFS-NNDFINIFKFNLTV 121 (139)
Q Consensus 76 ~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~-~~d~~~v~~f~~~~ 121 (139)
-|.++||+||||.|.+..+|...+..+.++|. -|=.+-|+.|.+.+
T Consensus 394 ~V~LLID~SGSM~~r~~~vA~~~a~iLa~aL~~~gIp~eVlGFtt~a 440 (600)
T TIGR01651 394 VVTLLIDNSGSMRGRPITVAATCADILARTLERCGVKVEILGFTTRA 440 (600)
T ss_pred EEEEEEECCccCCCCHHHHHHHHHHHHHHHHHHCCCCeEEEeecccc
Confidence 35589999999999888877765555555554 47778999999763
No 57
>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=95.74 E-value=0.015 Score=44.16 Aligned_cols=50 Identities=18% Similarity=0.159 Sum_probs=39.7
Q ss_pred ccEEEEEcCCCC-CCCchHHHHHHHHHHHHhhCC--CCCEEEEEEeCCceeee
Q psy9195 75 KDVVILVDNSGS-MAGMRNTTAKLVLHSLLQTFS--NNDFINIFKFNLTVDTI 124 (139)
Q Consensus 75 ~~vvi~iD~sgS-m~g~~l~~ak~~~~~~l~~l~--~~d~~~v~~f~~~~~~~ 124 (139)
-.++|+||+|.. .....++.++++++..|+.+. ++.+|++++||..++..
T Consensus 4 p~y~FvID~s~~av~~g~~~~~~~sl~~~l~~l~~~~~~~vgiitfd~~V~~y 56 (243)
T PF04811_consen 4 PVYVFVIDVSYEAVQSGLLQSLIESLKSALDSLPGDERTRVGIITFDSSVHFY 56 (243)
T ss_dssp -EEEEEEE-SHHHHHHTHHHHHHHHHHHHGCTSSTSTT-EEEEEEESSSEEEE
T ss_pred CEEEEEEECchhhhhccHHHHHHHHHHHHHHhccCCCCcEEEEEEeCCEEEEE
Confidence 347899999864 334568999999999999999 99999999999988654
No 58
>cd01479 Sec24-like Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes of vesicular carriers within the endocytic and the biosynthetic pathways are COP- and clathrin-coated vesicles. Formation of COPII vesicles requires the ordered assembly of the coat built from several cytosolic components GTPase Sar1, complexes of Sec23-Sec24 and Sec13-Sec31. The process is initiated by the conversion of GDP to GTP by the GTPase Sar1 which then recruits the heterodimeric complex of Sec23 and Sec24. This heterodimeric complex generates the pre-budding complex. The final step leading to membrane deformation and budding of COPII-coated vesicles is carried by the heterodimeric complex Sec13-Sec31. The members of this CD belong to the Sec23-like family. Sec 24 is very similar to Sec23. The Sec23 and Sec24
Probab=94.95 E-value=0.067 Score=40.83 Aligned_cols=51 Identities=22% Similarity=0.159 Sum_probs=41.2
Q ss_pred cccEEEEEcCCCCCC-CchHHHHHHHHHHHHhhCCCC---CEEEEEEeCCceeee
Q psy9195 74 SKDVVILVDNSGSMA-GMRNTTAKLVLHSLLQTFSNN---DFINIFKFNLTVDTI 124 (139)
Q Consensus 74 ~~~vvi~iD~sgSm~-g~~l~~ak~~~~~~l~~l~~~---d~~~v~~f~~~~~~~ 124 (139)
|-.++|+||+|-.-. ..-++.++++++..|+.+.++ -+|++++||..++..
T Consensus 3 pp~~~FvIDvs~~a~~~g~~~~~~~si~~~L~~lp~~~~~~~VgiITfd~~v~~y 57 (244)
T cd01479 3 PAVYVFLIDVSYNAIKSGLLATACEALLSNLDNLPGDDPRTRVGFITFDSTLHFF 57 (244)
T ss_pred CCEEEEEEEccHHHHhhChHHHHHHHHHHHHHhcCCCCCCeEEEEEEECCeEEEE
Confidence 345789999977642 225789999999999999977 999999999988643
No 59
>COG4547 CobT Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]
Probab=94.85 E-value=0.026 Score=46.94 Aligned_cols=45 Identities=31% Similarity=0.392 Sum_probs=37.7
Q ss_pred EEEEEcCCCCCCCchHHHHHHHHHHHHhhCC-CCCEEEEEEeCCce
Q psy9195 77 VVILVDNSGSMAGMRNTTAKLVLHSLLQTFS-NNDFINIFKFNLTV 121 (139)
Q Consensus 77 vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~-~~d~~~v~~f~~~~ 121 (139)
|.++||.||||.|.++++|...+..+-++|. -|=.+-|+.|.+++
T Consensus 416 VtlviDnSGSMrGRpItvAatcAdilArtLeRcgVk~eIlGFTT~a 461 (620)
T COG4547 416 VTLVIDNSGSMRGRPITVAATCADILARTLERCGVKVEILGFTTKA 461 (620)
T ss_pred heeeeccCCCcCCcceehhHHHHHHHHHHHHHcCCceEEeeeeecc
Confidence 4589999999999999999999988888876 56677788888754
No 60
>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=94.78 E-value=0.085 Score=39.25 Aligned_cols=47 Identities=26% Similarity=0.239 Sum_probs=31.1
Q ss_pred EEEEEcCCCCCCC------chHHHHHHHHHHHHhh---CCCCCEEEEEEeCCceee
Q psy9195 77 VVILVDNSGSMAG------MRNTTAKLVLHSLLQT---FSNNDFINIFKFNLTVDT 123 (139)
Q Consensus 77 vvi~iD~sgSm~g------~~l~~ak~~~~~~l~~---l~~~d~~~v~~f~~~~~~ 123 (139)
++++||+|.||.. ..++.|..++..++.. -++.|.+||+.|+++-+.
T Consensus 2 ~vflID~s~sM~~~~~~~~~~l~~al~~i~~~~~~ki~~~~kD~vgvvl~gt~~t~ 57 (224)
T PF03731_consen 2 TVFLIDVSPSMFEPSSESESPLEEALKAIEDLMQQKIISSPKDEVGVVLFGTDETN 57 (224)
T ss_dssp EEEEEE-SCGGGS-BTTCS-HHHHHHHHHHHHHHHHHHTT---EEEEEEES-SS-B
T ss_pred EEEEEECCHHHCCCCCCcchhHHHHHHHHHHHHHHHHcCCCCCeEEEEEEcCCCCC
Confidence 6799999999973 2477777777766554 456799999999987654
No 61
>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=94.78 E-value=0.056 Score=40.05 Aligned_cols=47 Identities=23% Similarity=0.243 Sum_probs=33.1
Q ss_pred ccEEEEEcCCCCCC------C---chHHHHHHHHHHHHh--hCCCCCEEEEEEeCCceeee
Q psy9195 75 KDVVILVDNSGSMA------G---MRNTTAKLVLHSLLQ--TFSNNDFINIFKFNLTVDTI 124 (139)
Q Consensus 75 ~~vvi~iD~sgSm~------g---~~l~~ak~~~~~~l~--~l~~~d~~~v~~f~~~~~~~ 124 (139)
+.+++++|.||||. | .+|+.+|..+..+.+ .-..+|+++ |.+..-.+
T Consensus 1 ~~l~lavDlSgSM~~~~~~dg~~~~RL~a~k~v~~~f~~f~~~r~~DriG---~~g~~~~~ 58 (191)
T cd01455 1 KRLKLVVDVSGSMYRFNGYDGRLDRSLEAVVMVMEAFDGFEDKIQYDIIG---HSGDGPCV 58 (191)
T ss_pred CceEEEEECcHhHHHHhccCCccccHHHHHHHHHHHHHHHHHhCccceee---ecCccccc
Confidence 35789999999992 2 368888888877762 445789998 44444333
No 62
>PLN00162 transport protein sec23; Provisional
Probab=94.59 E-value=0.093 Score=46.45 Aligned_cols=48 Identities=17% Similarity=0.203 Sum_probs=41.1
Q ss_pred cccEEEEEcCCCCCCCchHHHHHHHHHHHHhhCCCCCEEEEEEeCCceee
Q psy9195 74 SKDVVILVDNSGSMAGMRNTTAKLVLHSLLQTFSNNDFINIFKFNLTVDT 123 (139)
Q Consensus 74 ~~~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~~~d~~~v~~f~~~~~~ 123 (139)
|--++++||+|-. ...+..+|.++...|+.|.++.+||+|+|+..++.
T Consensus 124 pp~fvFvID~s~~--~~~l~~lk~sl~~~L~~LP~~a~VGlITF~s~V~~ 171 (761)
T PLN00162 124 PPVFVFVVDTCMI--EEELGALKSALLQAIALLPENALVGLITFGTHVHV 171 (761)
T ss_pred CcEEEEEEecchh--HHHHHHHHHHHHHHHHhCCCCCEEEEEEECCEEEE
Confidence 4567789999853 45688899999999999999999999999998864
No 63
>COG2304 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=94.34 E-value=0.14 Score=40.94 Aligned_cols=57 Identities=25% Similarity=0.401 Sum_probs=49.8
Q ss_pred ccccccEEEEEcCCCCCCCchHHHHHHHHHHHHhhCCCCCEEEEEEeCCceeeeeec
Q psy9195 71 TTCSKDVVILVDNSGSMAGMRNTTAKLVLHSLLQTFSNNDFINIFKFNLTVDTIVPC 127 (139)
Q Consensus 71 ~~~~~~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~~~d~~~v~~f~~~~~~~~~~ 127 (139)
...+.+.++.+|.++||.+..+..++.++..++..+.+.+.+.++.|......+.|.
T Consensus 34 ~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~ 90 (399)
T COG2304 34 LLVPANLTLAIDTSGSMTGALLELAKSAAIELVNGLNPGDLLSIVTFAGSADVLIPP 90 (399)
T ss_pred cccCcceEEEeccCCCccchhHHHHHHHHHHHhcccCCCCceEEEEecCCcceecCc
Confidence 345677889999999999988999999999999999999999999999977666543
No 64
>PRK05325 hypothetical protein; Provisional
Probab=93.87 E-value=0.063 Score=44.04 Aligned_cols=69 Identities=25% Similarity=0.277 Sum_probs=43.0
Q ss_pred ccccccccchhhhhhccccccEEE-EEcCCCCCCCchHHHHHHHHH---HHHhhCCCCCEEEEEEeCCceeee
Q psy9195 56 DLIFDCRNRQWYIQATTCSKDVVI-LVDNSGSMAGMRNTTAKLVLH---SLLQTFSNNDFINIFKFNLTVDTI 124 (139)
Q Consensus 56 ~~~yDpr~r~Wy~~a~~~~~~vvi-~iD~sgSm~g~~l~~ak~~~~---~~l~~l~~~d~~~v~~f~~~~~~~ 124 (139)
.+.+|-|.|.|-.........|+| +.|+||||.+.+-.+||.--- .+|..=-.+=.+-.|.=++.++.+
T Consensus 203 ~d~~DlRYr~~~~~~~p~s~AVmfclMDvSGSM~~~~K~lakrff~lly~fL~r~Y~~vEvvFI~H~t~AkEV 275 (401)
T PRK05325 203 IDPFDLRYRNWEKVPKPESQAVMFCLMDVSGSMDEAEKDLAKRFFFLLYLFLRRKYENVEVVFIRHHTEAKEV 275 (401)
T ss_pred CCcccccccccccccCccCcEEEEEEEeCCCCCchHHHHHHHHHHHHHHHHHHhccCceEEEEEeecCceeEc
Confidence 366789999998755444455654 999999998877667665432 223333333344444555555554
No 65
>smart00319 TarH Homologues of the ligand binding domain of Tar. Homologues of the ligand binding domain of the wild-type bacterial aspartate receptor, Tar.
Probab=93.74 E-value=0.0063 Score=41.29 Aligned_cols=57 Identities=23% Similarity=0.197 Sum_probs=44.1
Q ss_pred HHHHHHHHHHhhcCcceeEeeeecccccEEECCCCCCCCccccccccccchhhhhhccccc
Q psy9195 15 EGLDEVFRENYMADPTLLWQYFGSAKGFLRTYPDKEDAPAEDLIFDCRNRQWYIQATTCSK 75 (139)
Q Consensus 15 ~~l~~~f~~~~~~~~~i~~~y~gs~~G~~~~~p~~~~~~~~~~~yDpr~r~Wy~~a~~~~~ 75 (139)
..|...|..+.+.++.+...|.+...|.+...|.... ...|+++.+.||+.+...++
T Consensus 76 ~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~----~~~~~~~~~~w~~~a~~~~~ 132 (135)
T smart00319 76 AELKEKFQQYITALQELIQILGNGNLGAFFDQPTQGM----QDGFDPAYRDWLQQAVALKG 132 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCcchHHhCchhhc----hhhhcHHHHHHHHHHHHhhc
Confidence 3467777777777777778899999999888886544 38999999999997765443
No 66
>COG1721 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]
Probab=93.71 E-value=0.23 Score=40.74 Aligned_cols=54 Identities=24% Similarity=0.255 Sum_probs=40.9
Q ss_pred cccEEEEEcCCCCCCC-----chHHHHHHHHHHH-HhhCCCCCEEEEEEeCCceeeeeec
Q psy9195 74 SKDVVILVDNSGSMAG-----MRNTTAKLVLHSL-LQTFSNNDFINIFKFNLTVDTIVPC 127 (139)
Q Consensus 74 ~~~vvi~iD~sgSm~g-----~~l~~ak~~~~~~-l~~l~~~d~~~v~~f~~~~~~~~~~ 127 (139)
..++++++|+|.||.. .+++.+..++..+ ..-+..||+++++.|+.......|.
T Consensus 224 ~~~v~l~lD~~~~m~~~~~~~~~~e~av~~a~~la~~~l~~gd~vg~~~~~~~~~~~~~p 283 (416)
T COG1721 224 GRTVVLVLDASRSMLFGSGVASKFEEAVRAAASLAYAALKNGDRVGLLIFGGGGPKWIPP 283 (416)
T ss_pred CceEEEEEeCCccccCCCCCccHHHHHHHHHHHHHHHHHhCCCeeEEEEECCCcceeeCC
Confidence 5678999999999983 5777777666555 3457799999999999766544443
No 67
>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=92.82 E-value=0.11 Score=42.13 Aligned_cols=68 Identities=25% Similarity=0.321 Sum_probs=42.7
Q ss_pred cccccccchhhhhhccccccEEE-EEcCCCCCCCchHHHHHHHHH---HHHhhCCCCCEEEEEEeCCceeee
Q psy9195 57 LIFDCRNRQWYIQATTCSKDVVI-LVDNSGSMAGMRNTTAKLVLH---SLLQTFSNNDFINIFKFNLTVDTI 124 (139)
Q Consensus 57 ~~yDpr~r~Wy~~a~~~~~~vvi-~iD~sgSm~g~~l~~ak~~~~---~~l~~l~~~d~~~v~~f~~~~~~~ 124 (139)
+..|.|.|.|-.........|+| +.|+||||...+..+||.--- .+|.+=-.+=.+-.|.=++.++.+
T Consensus 184 ~~~DlRYr~~~~~~~P~s~AV~fc~MDvSGSM~~~~K~lak~ff~~ly~FL~~~Y~~VeivFI~H~t~AkEV 255 (371)
T TIGR02877 184 TKEDLRYKTWKENEKPESNAVVIAMMDTSGSMGQFKKYIARSFFFWMVKFLRTKYENVEICFISHHTEAKEV 255 (371)
T ss_pred CcccccccccccccCccCcEEEEEEEeCCCCCCHHHHHHHHHHHHHHHHHHHhccCceEEEEEeecCeeEEc
Confidence 46788999998755444455654 999999998877667666432 223333344444445555555554
No 68
>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=92.66 E-value=0.52 Score=39.02 Aligned_cols=68 Identities=26% Similarity=0.273 Sum_probs=45.9
Q ss_pred cccccccchhhhhhccccccEEE-EEcCCCCCCCchHHHHHHHH---HHHHhhCCCCCEEEEEEeCCceeee
Q psy9195 57 LIFDCRNRQWYIQATTCSKDVVI-LVDNSGSMAGMRNTTAKLVL---HSLLQTFSNNDFINIFKFNLTVDTI 124 (139)
Q Consensus 57 ~~yDpr~r~Wy~~a~~~~~~vvi-~iD~sgSm~g~~l~~ak~~~---~~~l~~l~~~d~~~v~~f~~~~~~~ 124 (139)
...|.|.|.|-.........|+| +.|+||||...+-.+||.-. ..+|..=-++=.+-.|..++.++.+
T Consensus 228 ~~~DlRyr~~~~~~~p~s~AVv~~lmDvSGSM~~~~K~lak~ff~~l~~fL~~~Y~~Ve~vfI~H~t~A~EV 299 (421)
T PF04285_consen 228 DPEDLRYRRWEEVPKPESNAVVFCLMDVSGSMGEFKKDLAKRFFFWLYLFLRRKYENVEIVFIRHHTEAKEV 299 (421)
T ss_pred CccccccccCccccCCcCcEEEEEEEeCCCCCchHHHHHHHHHHHHHHHHHHhccCceEEEEEeecCceEEe
Confidence 45688888887654433455554 99999999887777777654 3334444455556667777777766
No 69
>KOG3768|consensus
Probab=91.20 E-value=0.43 Score=41.19 Aligned_cols=45 Identities=22% Similarity=0.249 Sum_probs=36.2
Q ss_pred EEEEEcCCCCCCCc------hHHHHHHHHHHHHhh-----CCCCCEEEEEEeCCce
Q psy9195 77 VVILVDNSGSMAGM------RNTTAKLVLHSLLQT-----FSNNDFINIFKFNLTV 121 (139)
Q Consensus 77 vvi~iD~sgSm~g~------~l~~ak~~~~~~l~~-----l~~~d~~~v~~f~~~~ 121 (139)
+.|++|+||||... =+++||.++.+++.. -..|||+.+++|..--
T Consensus 4 ~lFllDTS~SM~qrah~~~tylD~AKgaVEtFiK~R~r~~~~~gdryml~TfeepP 59 (888)
T KOG3768|consen 4 FLFLLDTSGSMSQRAHPQFTYLDLAKGAVETFIKQRTRVGRETGDRYMLTTFEEPP 59 (888)
T ss_pred EEEEEecccchhhhccCCchhhHHHHHHHHHHHHHHhccccccCceEEEEecccCc
Confidence 45899999999742 389999999999854 3368999999998654
No 70
>PF11443 DUF2828: Domain of unknown function (DUF2828); InterPro: IPR024553 This uncharacterised domain is found in eukaryotic, bacterial and viral proteins.
Probab=90.06 E-value=0.86 Score=38.86 Aligned_cols=47 Identities=21% Similarity=0.297 Sum_probs=33.9
Q ss_pred ccEEEEEcCCCCCCCchHHHHHHHHHHHHhhCCCCCE-EEEEEeCCcee
Q psy9195 75 KDVVILVDNSGSMAGMRNTTAKLVLHSLLQTFSNNDF-INIFKFNLTVD 122 (139)
Q Consensus 75 ~~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~~~d~-~~v~~f~~~~~ 122 (139)
.+.+.+.|.||||.|.++..|..... ++..+..+-+ =.+|+|+.+-+
T Consensus 341 ~n~iav~DvSGSM~~~pm~vaiaLgl-l~ae~~~~pf~~~~ITFs~~P~ 388 (534)
T PF11443_consen 341 ENCIAVCDVSGSMSGPPMDVAIALGL-LIAELNKGPFKGRFITFSENPQ 388 (534)
T ss_pred cceEEEEecCCccCccHHHHHHHHHH-HHHHhcccccCCeEEeecCCce
Confidence 57888999999999998888765554 4445554443 34789998743
No 71
>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=89.85 E-value=0.75 Score=39.62 Aligned_cols=49 Identities=18% Similarity=0.289 Sum_probs=38.8
Q ss_pred cccEEEEEcCCCCCCC--------chHHHHHHHHHHHHhh---CCCCCEEEEEEeCCcee
Q psy9195 74 SKDVVILVDNSGSMAG--------MRNTTAKLVLHSLLQT---FSNNDFINIFKFNLTVD 122 (139)
Q Consensus 74 ~~~vvi~iD~sgSm~g--------~~l~~ak~~~~~~l~~---l~~~d~~~v~~f~~~~~ 122 (139)
...++++||+|.||-. .++..|..++..+++. -+++|.+||+.|+++-+
T Consensus 10 keailflIDvs~sM~~~~~~~~~~s~~~~al~~i~~l~q~kIis~~~D~vGivlfgT~~t 69 (584)
T TIGR00578 10 RDSLIFLVDASKAMFEESQGEDELTPFDMSIQCIQSVYTSKIISSDKDLLAVVFYGTEKD 69 (584)
T ss_pred eeEEEEEEECCHHHcCCCcCcCcCChHHHHHHHHHHHHHhcCCCCCCCeEEEEEEeccCC
Confidence 3558899999999973 3577888888777765 34899999999998654
No 72
>KOG4465|consensus
Probab=88.06 E-value=0.19 Score=40.95 Aligned_cols=79 Identities=16% Similarity=0.080 Sum_probs=48.0
Q ss_pred ccccccccchhhhhhccccccEEEEEcCCCCCCC----chHHHHHHHH-HHHHhhCCCCCEEEEEEeCCceeeeeecCCC
Q psy9195 56 DLIFDCRNRQWYIQATTCSKDVVILVDNSGSMAG----MRNTTAKLVL-HSLLQTFSNNDFINIFKFNLTVDTIVPCLGN 130 (139)
Q Consensus 56 ~~~yDpr~r~Wy~~a~~~~~~vvi~iD~sgSm~g----~~l~~ak~~~-~~~l~~l~~~d~~~v~~f~~~~~~~~~~~~~ 130 (139)
++..|..+-.=|+++...++.+.+-+|.|+||.. ..|. +++++ ..-+-.+...-..-++.|.++... +|.+++
T Consensus 409 ~dalda~fykaf~na~ptgkr~~laldvs~sm~~rv~~s~ln-~reaaa~m~linlhnead~~~vaf~d~lte-~pftkd 486 (598)
T KOG4465|consen 409 CDALDAAFYKAFKNAEPTGKRFCLALDVSASMNQRVLGSILN-AREAAAAMCLINLHNEADSRCVAFCDELTE-CPFTKD 486 (598)
T ss_pred HHHHHHHHHHHhccCCCCCceEEEEEecchhhhhhhhccccc-hHHHHhhhheeeeccccceeEEEecccccc-CCCccc
Confidence 5555555544455665566889999999999974 3332 22222 122223444455778899988754 577777
Q ss_pred Ceeeec
Q psy9195 131 YSLVQT 136 (139)
Q Consensus 131 ~~lv~a 136 (139)
..+-|+
T Consensus 487 ~kigqv 492 (598)
T KOG4465|consen 487 MKIGQV 492 (598)
T ss_pred ccHHHH
Confidence 555554
No 73
>COG2718 Uncharacterized conserved protein [Function unknown]
Probab=87.23 E-value=0.54 Score=38.41 Aligned_cols=66 Identities=23% Similarity=0.216 Sum_probs=41.3
Q ss_pred cccccchhhhhhccccccEEE-EEcCCCCCCCchHHHHHHHH---HHHHhhCCCCCEEEEEEeCCceeee
Q psy9195 59 FDCRNRQWYIQATTCSKDVVI-LVDNSGSMAGMRNTTAKLVL---HSLLQTFSNNDFINIFKFNLTVDTI 124 (139)
Q Consensus 59 yDpr~r~Wy~~a~~~~~~vvi-~iD~sgSm~g~~l~~ak~~~---~~~l~~l~~~d~~~v~~f~~~~~~~ 124 (139)
+|.|.+.|-.......+.|++ +.|+||||....-.+||..- .-+|..--++-.|..|.=++.+..+
T Consensus 230 ~DlRf~~~~~~p~pes~AVmfclMDvSGSM~~~~KdlAkrFF~lL~~FL~~kYenveivfIrHht~A~EV 299 (423)
T COG2718 230 EDLRYKRYEKVPKPESNAVMFCLMDVSGSMDQSEKDLAKRFFFLLYLFLRRKYENVEIVFIRHHTEAKEV 299 (423)
T ss_pred cchhccCCccccCCccceEEEEEEecCCCcchHHHHHHHHHHHHHHHHHhcccceeEEEEEeecCcceec
Confidence 888988887755544455665 89999999876666666543 2223333344445555555565554
No 74
>COG4867 Uncharacterized protein with a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=86.76 E-value=0.85 Score=38.04 Aligned_cols=51 Identities=33% Similarity=0.339 Sum_probs=38.0
Q ss_pred cccEEEEEcCCCCCCCc-hH---HHHHHHHHHHHhhCCCCCEEEEEEeCCceeee
Q psy9195 74 SKDVVILVDNSGSMAGM-RN---TTAKLVLHSLLQTFSNNDFINIFKFNLTVDTI 124 (139)
Q Consensus 74 ~~~vvi~iD~sgSm~g~-~l---~~ak~~~~~~l~~l~~~d~~~v~~f~~~~~~~ 124 (139)
...+++++|||-||.-+ ++ .+..-++.-++.|--+||.+.+|.|...+..+
T Consensus 463 ~aAvallvDtS~SM~~eGRw~PmKQtALALhHLv~TrfrGD~l~~i~Fgr~A~~v 517 (652)
T COG4867 463 QAAVALLVDTSFSMVMEGRWLPMKQTALALHHLVCTRFRGDALQIIAFGRYARTV 517 (652)
T ss_pred ccceeeeeeccHHHHHhccCCchHHHHHHHHHHHHhcCCCcceEEEeccchhccc
Confidence 45688999999998532 44 44444445567888899999999999887754
No 75
>COG3864 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=86.12 E-value=1.9 Score=34.53 Aligned_cols=47 Identities=23% Similarity=0.326 Sum_probs=37.3
Q ss_pred cEEEEEcCCCCCCCchHHHHHHHHHHHHhhCCCCCEEEEEEeCCceeee
Q psy9195 76 DVVILVDNSGSMAGMRNTTAKLVLHSLLQTFSNNDFINIFKFNLTVDTI 124 (139)
Q Consensus 76 ~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~~~d~~~v~~f~~~~~~~ 124 (139)
.+++.+|+||||...-++.+..-+..++ -.++-++.++.-|..+...
T Consensus 263 ~i~vaVDtSGS~~d~ei~a~~~Ei~~Il--~~~~~eltli~~D~~v~~~ 309 (396)
T COG3864 263 KIVVAVDTSGSMTDAEIDAAMTEIFDIL--KNKNYELTLIECDNIVRRM 309 (396)
T ss_pred heEEEEecCCCccHHHHHHHHHHHHHHH--hCCCcEEEEEEecchhhhh
Confidence 3778999999999887777777777776 3478889999888877643
No 76
>PTZ00395 Sec24-related protein; Provisional
Probab=85.53 E-value=1.6 Score=41.05 Aligned_cols=49 Identities=18% Similarity=0.083 Sum_probs=37.6
Q ss_pred ccEEEEEcCCCCCC-CchHHHHHHHHHHHHhhCC-CCCEEEEEEeCCceee
Q psy9195 75 KDVVILVDNSGSMA-GMRNTTAKLVLHSLLQTFS-NNDFINIFKFNLTVDT 123 (139)
Q Consensus 75 ~~vvi~iD~sgSm~-g~~l~~ak~~~~~~l~~l~-~~d~~~v~~f~~~~~~ 123 (139)
-.++|+||+|-... ..-+..+..+++..|+.+. ++.+|++|+||.+++-
T Consensus 953 P~YvFLIDVS~~AVkSGLl~tacesIK~sLDsL~dpRTRVGIITFDSsLHF 1003 (1560)
T PTZ00395 953 PYFVFVVECSYNAIYNNITYTILEGIRYAVQNVKCPQTKIAIITFNSSIYF 1003 (1560)
T ss_pred CEEEEEEECCHHHHhhChHHHHHHHHHHHHhcCCCCCcEEEEEEecCcEEE
Confidence 45779999987643 3346777788888888875 6789999999999853
No 77
>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=84.94 E-value=1.9 Score=35.80 Aligned_cols=53 Identities=21% Similarity=0.051 Sum_probs=37.6
Q ss_pred hhhccccccEEEEEcCCCCCCCc--hHHHHHHHHHHHHhhCCCCCEEEEEEeCCc
Q psy9195 68 IQATTCSKDVVILVDNSGSMAGM--RNTTAKLVLHSLLQTFSNNDFINIFKFNLT 120 (139)
Q Consensus 68 ~~a~~~~~~vvi~iD~sgSm~g~--~l~~ak~~~~~~l~~l~~~d~~~v~~f~~~ 120 (139)
+++...|-++.++.|.|+||... .+..+-..+..-++.+..+=++|+-.|-++
T Consensus 93 ~~a~~yPvDLYyLMDlS~SM~ddl~~lk~lg~~L~~~m~~it~n~rlGfGsFVDK 147 (423)
T smart00187 93 RQAEDYPVDLYYLMDLSYSMKDDLDNLKSLGDDLAREMKGLTSNFRLGFGSFVDK 147 (423)
T ss_pred EecccCccceEEEEeCCccHHHHHHHHHHHHHHHHHHHHhcccCceeeEEEeecC
Confidence 34566789999999999999764 233222333333566788999999888876
No 78
>KOG1985|consensus
Probab=83.55 E-value=2.5 Score=37.73 Aligned_cols=51 Identities=22% Similarity=0.133 Sum_probs=41.1
Q ss_pred cccEEEEEcCCCCCCCc-hHHHHHHHHHHHHhhCC--CCCEEEEEEeCCceeee
Q psy9195 74 SKDVVILVDNSGSMAGM-RNTTAKLVLHSLLQTFS--NNDFINIFKFNLTVDTI 124 (139)
Q Consensus 74 ~~~vvi~iD~sgSm~g~-~l~~ak~~~~~~l~~l~--~~d~~~v~~f~~~~~~~ 124 (139)
|.-+++++|+|-|.... -++.++.++..-|+.|. ++-+|++++||+.++-.
T Consensus 294 Pavy~FliDVS~~a~ksG~L~~~~~slL~~LD~lpgd~Rt~igfi~fDs~ihfy 347 (887)
T KOG1985|consen 294 PAVYVFLIDVSISAIKSGYLETVARSLLENLDALPGDPRTRIGFITFDSTIHFY 347 (887)
T ss_pred CceEEEEEEeehHhhhhhHHHHHHHHHHHhhhcCCCCCcceEEEEEeeceeeEE
Confidence 34567899998875444 57888888888888888 78889999999998754
No 79
>COG3552 CoxE Protein containing von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=80.32 E-value=1.6 Score=35.59 Aligned_cols=48 Identities=23% Similarity=0.375 Sum_probs=30.9
Q ss_pred cccEEEEEcCCCCCCCch---HHHHHHHHHHHHhhCCCCCEEEEEEeCCceeeeeecC
Q psy9195 74 SKDVVILVDNSGSMAGMR---NTTAKLVLHSLLQTFSNNDFINIFKFNLTVDTIVPCL 128 (139)
Q Consensus 74 ~~~vvi~iD~sgSm~g~~---l~~ak~~~~~~l~~l~~~d~~~v~~f~~~~~~~~~~~ 128 (139)
+..++++.|+||||++.. |.++..+.+ ...++-+..|++.+..+.+.+
T Consensus 218 ~~~lvvL~DVSGSm~~ys~~~L~l~hAl~q-------~~~R~~~F~F~TRLt~vT~~l 268 (395)
T COG3552 218 KPPLVVLCDVSGSMSGYSRIFLHLLHALRQ-------QRSRVHVFLFGTRLTRVTHML 268 (395)
T ss_pred CCCeEEEEecccchhhhHHHHHHHHHHHHh-------cccceeEEEeechHHHHHHHh
Confidence 456889999999999863 233222222 234455889998877765443
No 80
>KOG1984|consensus
Probab=79.34 E-value=5.8 Score=35.85 Aligned_cols=62 Identities=19% Similarity=0.151 Sum_probs=40.3
Q ss_pred ccchhhhhhccccccEEEEEcCCCCC--CCchHHHHHHHHHHHHhh---CCCCCEEEEEEeCCceeee
Q psy9195 62 RNRQWYIQATTCSKDVVILVDNSGSM--AGMRNTTAKLVLHSLLQT---FSNNDFINIFKFNLTVDTI 124 (139)
Q Consensus 62 r~r~Wy~~a~~~~~~vvi~iD~sgSm--~g~~l~~ak~~~~~~l~~---l~~~d~~~v~~f~~~~~~~ 124 (139)
.+.-|-++..-.+-.++|+||+|-.. .|. ...+-++++.+|.. +.++-+|++++||.+++-+
T Consensus 405 tk~Y~~~~k~p~ppafvFmIDVSy~Ai~~G~-~~a~ce~ik~~l~~lp~~~p~~~Vgivtfd~tvhFf 471 (1007)
T KOG1984|consen 405 TKDYCRKTKPPKPPAFVFMIDVSYNAISNGA-VKAACEAIKSVLEDLPREEPNIRVGIVTFDKTVHFF 471 (1007)
T ss_pred ehhhhhcCCCCCCceEEEEEEeehhhhhcch-HHHHHHHHHHHHhhcCccCCceEEEEEEecceeEee
Confidence 33334433223456788999997663 342 34555566666655 4578999999999998754
No 81
>KOG1986|consensus
Probab=75.19 E-value=9.8 Score=33.55 Aligned_cols=49 Identities=18% Similarity=0.222 Sum_probs=41.2
Q ss_pred cccEEEEEcCCCCCCCchHHHHHHHHHHHHhhCCCCCEEEEEEeCCceeee
Q psy9195 74 SKDVVILVDNSGSMAGMRNTTAKLVLHSLLQTFSNNDFINIFKFNLTVDTI 124 (139)
Q Consensus 74 ~~~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~~~d~~~v~~f~~~~~~~ 124 (139)
|--+++++|+.-. .+.++.+|.++...|+.|.++-.+|+|+|+..++..
T Consensus 121 ppvf~fVvDtc~~--eeeL~~LkssL~~~l~lLP~~alvGlItfg~~v~v~ 169 (745)
T KOG1986|consen 121 PPVFVFVVDTCMD--EEELQALKSSLKQSLSLLPENALVGLITFGTMVQVH 169 (745)
T ss_pred CceEEEEEeeccC--hHHHHHHHHHHHHHHhhCCCcceEEEEEecceEEEE
Confidence 3345678888643 467899999999999999999999999999988766
No 82
>PF01882 DUF58: Protein of unknown function DUF58; InterPro: IPR002881 This domain is found in a family of prokaryotic proteins that have no known function. Proteins belonging to this family include hypothetical proteins from eubacteria and archaebacteria. Some of these proteins also contain the Von Willebrand factor, type A domain (see IPR002035 from INTERPRO).
Probab=69.91 E-value=7.3 Score=24.24 Aligned_cols=40 Identities=28% Similarity=0.169 Sum_probs=26.5
Q ss_pred cccEEEEEcCCCCCCC-----chHHHHHHHHHHHHhh-CCCCCEEE
Q psy9195 74 SKDVVILVDNSGSMAG-----MRNTTAKLVLHSLLQT-FSNNDFIN 113 (139)
Q Consensus 74 ~~~vvi~iD~sgSm~g-----~~l~~ak~~~~~~l~~-l~~~d~~~ 113 (139)
...+.+++|.+++|.. ..++.+...+..++.. +..|+.++
T Consensus 40 ~~~~~i~ld~~~~~~~~~~~~~~~e~~l~~a~~l~~~~~~~g~~v~ 85 (86)
T PF01882_consen 40 SQPVWIVLDLSPSMYFGSNGRSKFERALSAAASLANQALRQGDPVG 85 (86)
T ss_pred CCcEEEEEECCCccccCcCCCCHHHHHHHHHHHHHHHHHhcCCccc
Confidence 3668899999999864 4566666666555443 34555554
No 83
>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=62.79 E-value=3.4 Score=34.30 Aligned_cols=54 Identities=19% Similarity=0.024 Sum_probs=33.9
Q ss_pred hhccccccEEEEEcCCCCCCCch--HHHHHHHHHHHHhhCCCCCEEEEEEeCCcee
Q psy9195 69 QATTCSKDVVILVDNSGSMAGMR--NTTAKLVLHSLLQTFSNNDFINIFKFNLTVD 122 (139)
Q Consensus 69 ~a~~~~~~vvi~iD~sgSm~g~~--l~~ak~~~~~~l~~l~~~d~~~v~~f~~~~~ 122 (139)
.+...|-++.++.|-|+||.... |...-..+..-++.+..+=++|.-.|=++.-
T Consensus 97 ~a~~yPvDLYyLmDlS~Sm~ddl~~l~~lg~~l~~~~~~it~~~~~GfGsfvdK~~ 152 (426)
T PF00362_consen 97 PAEDYPVDLYYLMDLSYSMKDDLENLKSLGQDLAEEMRNITSNFRLGFGSFVDKPV 152 (426)
T ss_dssp BSSS--EEEEEEEE-SGGGHHHHHHHCCCCHHHHHHHHTT-SSEEEEEEEESSSSS
T ss_pred eccccceeEEEEeechhhhhhhHHHHHHHHHHHHHHHHhcCccceEechhhccccc
Confidence 45567889999999999998642 2211222333456788899999999987743
No 84
>PRK01322 6-carboxyhexanoate--CoA ligase; Provisional
Probab=61.60 E-value=3.2 Score=31.88 Aligned_cols=36 Identities=28% Similarity=0.380 Sum_probs=28.3
Q ss_pred CCHHHHHhhhchHHHHHHHHHHhhcCcceeEeeeecccccEEECCCCC
Q psy9195 3 EHDDVRAGLMWSEGLDEVFRENYMADPTLLWQYFGSAKGFLRTYPDKE 50 (139)
Q Consensus 3 ~~~~v~~~~~~~~~l~~~f~~~~~~~~~i~~~y~gs~~G~~~~~p~~~ 50 (139)
..|+|..+||||. ||++.-=|+++.+.+|...|..+
T Consensus 170 ~~pgivAElC~SD------------DP~YtTGYVA~~~~gY~RI~~mK 205 (242)
T PRK01322 170 AHPGVIAELCWSD------------DPDYTTGYVATKKLGYHRITNLK 205 (242)
T ss_pred cCCCeEEEEEecC------------CCCCeeEEEEeCCCCeEeCcccc
Confidence 3688999999986 69999999999985566555444
No 85
>TIGR01204 bioW 6-carboxyhexanoate--CoA ligase. Alternate name: pimeloyl-CoA synthase.
Probab=61.49 E-value=3.2 Score=31.68 Aligned_cols=35 Identities=23% Similarity=0.267 Sum_probs=27.7
Q ss_pred CHHHHHhhhchHHHHHHHHHHhhcCcceeEeeeecccccEEECCCCC
Q psy9195 4 HDDVRAGLMWSEGLDEVFRENYMADPTLLWQYFGSAKGFLRTYPDKE 50 (139)
Q Consensus 4 ~~~v~~~~~~~~~l~~~f~~~~~~~~~i~~~y~gs~~G~~~~~p~~~ 50 (139)
.|+|..++|||. ||++.-=|+++.+-+|...|..+
T Consensus 164 ~pgvvAElC~SD------------DP~YtTGYVA~~~~gY~RI~~lK 198 (232)
T TIGR01204 164 CPAVVAELCWSD------------DPDYVTGYVSGKEIGYVRITPLK 198 (232)
T ss_pred CCCeEEEEEecC------------CCCCeeEEEEeCCCCeEeCcccc
Confidence 588999999986 69999999999985566555444
No 86
>PF08496 Peptidase_S49_N: Peptidase family S49 N-terminal; InterPro: IPR013703 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found to the N terminus of bacterial signal peptidases that belong to the MEROPS peptidase family S49 (protease IV family, clan SK) (see also IPR002142 from INTERPRO) [, ]. ; GO: 0004252 serine-type endopeptidase activity, 0005886 plasma membrane
Probab=56.16 E-value=37 Score=24.25 Aligned_cols=40 Identities=13% Similarity=0.228 Sum_probs=34.3
Q ss_pred ccEEEEEcCCCCCCCchHHHHHHHHHHHHhhCCCCCEEEE
Q psy9195 75 KDVVILVDNSGSMAGMRNTTAKLVLHSLLQTFSNNDFINI 114 (139)
Q Consensus 75 ~~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~~~d~~~v 114 (139)
+.-++++|-.|+|.....+..++-+..+|..-.++|.+-|
T Consensus 97 ~~r~~VldF~Gdi~A~~v~~LReeisail~~a~~~DeV~~ 136 (155)
T PF08496_consen 97 KPRLFVLDFKGDIKASEVESLREEISAILSVATPEDEVLV 136 (155)
T ss_pred CCeEEEEecCCCccHHHHHHHHHHHHHHHHhCCCCCeEEE
Confidence 4567999999999988778888888888989999999865
No 87
>KOG0070|consensus
Probab=51.50 E-value=43 Score=24.67 Aligned_cols=44 Identities=23% Similarity=0.240 Sum_probs=30.8
Q ss_pred ccccEEEEEcCCCCCCCchHHHHHHHHHHHHhhCCCCCEEEEEEeCCc
Q psy9195 73 CSKDVVILVDNSGSMAGMRNTTAKLVLHSLLQTFSNNDFINIFKFNLT 120 (139)
Q Consensus 73 ~~~~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~~~d~~~v~~f~~~ 120 (139)
...-+++++|++. ..++..||+-+..+++.-. -+..-++.|..+
T Consensus 84 ~t~~lIfVvDS~D---r~Ri~eak~eL~~~l~~~~-l~~~~llv~aNK 127 (181)
T KOG0070|consen 84 NTQGLIFVVDSSD---RERIEEAKEELHRMLAEPE-LRNAPLLVFANK 127 (181)
T ss_pred CCcEEEEEEeCCc---HHHHHHHHHHHHHHHcCcc-cCCceEEEEech
Confidence 3355889999988 5788899999988875443 234556666644
No 88
>COG5028 Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]
Probab=50.87 E-value=37 Score=30.56 Aligned_cols=51 Identities=22% Similarity=0.200 Sum_probs=32.8
Q ss_pred ccccEEEEEcCCCC--CCCchHHHHHHHHHHHHhh---CCCCCEEEEEEeCCceeee
Q psy9195 73 CSKDVVILVDNSGS--MAGMRNTTAKLVLHSLLQT---FSNNDFINIFKFNLTVDTI 124 (139)
Q Consensus 73 ~~~~vvi~iD~sgS--m~g~~l~~ak~~~~~~l~~---l~~~d~~~v~~f~~~~~~~ 124 (139)
.|-.+||+||+|=. +.|. ...+..+++..|+. ++++.+++++.||++++-+
T Consensus 275 ~P~~yvFlIDVS~~a~~~g~-~~a~~r~Il~~l~~~~~~dpr~kIaii~fD~sl~ff 330 (861)
T COG5028 275 PPPVYVFLIDVSFEAIKNGL-VKAAIRAILENLDQIPNFDPRTKIAIICFDSSLHFF 330 (861)
T ss_pred CCCEEEEEEEeehHhhhcch-HHHHHHHHHhhccCCCCCCCcceEEEEEEcceeeEE
Confidence 35678899999654 3342 22223333333333 4578899999999998865
No 89
>PF03744 BioW: 6-carboxyhexanoate--CoA ligase; InterPro: IPR005499 This family contains the enzyme 6-carboxyhexanoate--CoA ligase 6.2.1.14 from EC. This enzyme is involved in the first step of biotin synthesis, where it converts pimelate into pimeloyl-CoA []. The enzyme requires magnesium as a cofactor and forms a homodimer [].; GO: 0009102 biotin biosynthetic process
Probab=47.96 E-value=7.5 Score=29.86 Aligned_cols=35 Identities=26% Similarity=0.329 Sum_probs=27.1
Q ss_pred CHHHHHhhhchHHHHHHHHHHhhcCcceeEeeeecccccEEECCCCC
Q psy9195 4 HDDVRAGLMWSEGLDEVFRENYMADPTLLWQYFGSAKGFLRTYPDKE 50 (139)
Q Consensus 4 ~~~v~~~~~~~~~l~~~f~~~~~~~~~i~~~y~gs~~G~~~~~p~~~ 50 (139)
.|+|..+||||. ||++.-=|+++..=+|..-|..+
T Consensus 171 ~PgiiaELC~SD------------DP~YtTGYVA~~~~GY~RI~~mK 205 (239)
T PF03744_consen 171 APGIIAELCWSD------------DPDYTTGYVASKKFGYHRITNMK 205 (239)
T ss_pred CCcceEEEEecC------------CCCCceEEEEeCCcceEECcccc
Confidence 588999999986 69999999999874455555444
No 90
>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=46.49 E-value=73 Score=24.60 Aligned_cols=53 Identities=17% Similarity=0.322 Sum_probs=41.1
Q ss_pred cEEEEEcCCCCCC---------------CchHHHHHHHHHHHHhhCCCCCEEEEEEeCCcee---eeeecC
Q psy9195 76 DVVILVDNSGSMA---------------GMRNTTAKLVLHSLLQTFSNNDFINIFKFNLTVD---TIVPCL 128 (139)
Q Consensus 76 ~vvi~iD~sgSm~---------------g~~l~~ak~~~~~~l~~l~~~d~~~v~~f~~~~~---~~~~~~ 128 (139)
++++-||.++|-. -+.-+.|..++..++..++++..+-++.|+.+.. .+.+|+
T Consensus 33 nl~vaIDfT~SNg~p~~~~SLHy~~~~~~N~Yq~aI~~vg~il~~yD~D~~ip~~GFGa~~~~~~~v~~~f 103 (254)
T cd01459 33 NLIVAIDFTKSNGWPGEKRSLHYISPGRLNPYQKAIRIVGEVLQPYDSDKLIPAFGFGAIVTKDQSVFSFF 103 (254)
T ss_pred eEEEEEEeCCCCCCCCCCCCcccCCCCCccHHHHHHHHHHHHHHhcCCCCceeeEeecccCCCCCcccccc
Confidence 6778888887742 1346788888999999999999999999998754 345665
No 91
>COG5047 SEC23 Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking and secretion]
Probab=46.13 E-value=63 Score=28.37 Aligned_cols=45 Identities=13% Similarity=0.178 Sum_probs=39.2
Q ss_pred EEEEcCCCCCCCchHHHHHHHHHHHHhhCCCCCEEEEEEeCCceeee
Q psy9195 78 VILVDNSGSMAGMRNTTAKLVLHSLLQTFSNNDFINIFKFNLTVDTI 124 (139)
Q Consensus 78 vi~iD~sgSm~g~~l~~ak~~~~~~l~~l~~~d~~~v~~f~~~~~~~ 124 (139)
.+++|... .++.++..|+++...|..|.+.--+|+++|...+...
T Consensus 126 ~fvvD~~~--D~e~l~~LkdslivslsllppeaLvglItygt~i~v~ 170 (755)
T COG5047 126 FFVVDACC--DEEELTALKDSLIVSLSLLPPEALVGLITYGTSIQVH 170 (755)
T ss_pred EEEEEeec--CHHHHHHHHHHHHHHHhcCCccceeeEEEecceeEEE
Confidence 35888766 4678999999999999999999999999999988766
No 92
>smart00467 GS GS motif. Aa approx. 30 amino acid motif that precedes the kinase domain in types I and II TGF beta receptors. Mutation of two or more of the serines or threonines in the TTSGSGSG of TGF-beta type I receptor impairs phosphorylation and signaling activity.
Probab=44.73 E-value=20 Score=18.50 Aligned_cols=18 Identities=28% Similarity=0.322 Sum_probs=12.1
Q ss_pred CCCCCCCchHHHHHHHHH
Q psy9195 83 NSGSMAGMRNTTAKLVLH 100 (139)
Q Consensus 83 ~sgSm~g~~l~~ak~~~~ 100 (139)
+|||+.|..+-.=+..++
T Consensus 11 tSGSGSG~p~LvqRTiar 28 (30)
T smart00467 11 TSGSGSGLPLLVQRTVAR 28 (30)
T ss_pred cCCCCCCchhHHHHHHhh
Confidence 799999976554444444
No 93
>KOG0071|consensus
Probab=44.07 E-value=54 Score=23.60 Aligned_cols=39 Identities=21% Similarity=0.303 Sum_probs=27.8
Q ss_pred ccccEEEEEcCCCCCCCchHHHHHHHHHHHHhhCCCCCEEEE
Q psy9195 73 CSKDVVILVDNSGSMAGMRNTTAKLVLHSLLQTFSNNDFINI 114 (139)
Q Consensus 73 ~~~~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~l~~~d~~~v 114 (139)
....++|++|++.| ++++.|+.-+..+++.-.-.+-+-+
T Consensus 84 gtqglIFV~Dsa~~---dr~eeAr~ELh~ii~~~em~~~~~L 122 (180)
T KOG0071|consen 84 GTQGLIFVVDSADR---DRIEEARNELHRIINDREMRDAIIL 122 (180)
T ss_pred CCceEEEEEeccch---hhHHHHHHHHHHHhCCHhhhcceEE
Confidence 34568899999887 7899999999888754333333333
No 94
>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=41.99 E-value=85 Score=22.11 Aligned_cols=29 Identities=31% Similarity=0.397 Sum_probs=23.0
Q ss_pred cccEEEEEcCCCCCCCchHHHHHHHHHHHHhh
Q psy9195 74 SKDVVILVDNSGSMAGMRNTTAKLVLHSLLQT 105 (139)
Q Consensus 74 ~~~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~ 105 (139)
...+++++|++. ..++..++.-+..++..
T Consensus 82 ~~~iIfVvDssd---~~~l~e~~~~L~~ll~~ 110 (175)
T PF00025_consen 82 ADGIIFVVDSSD---PERLQEAKEELKELLND 110 (175)
T ss_dssp ESEEEEEEETTG---GGGHHHHHHHHHHHHTS
T ss_pred cceeEEEEeccc---ceeecccccchhhhcch
Confidence 355889999997 35788899988888765
No 95
>PF14827 Cache_3: Sensory domain of two-component sensor kinase; PDB: 1OJG_A 3BY8_A 1P0Z_I 2V9A_A 2J80_B.
Probab=40.37 E-value=16 Score=24.26 Aligned_cols=48 Identities=13% Similarity=0.160 Sum_probs=33.9
Q ss_pred CCCCHHHHHhhhchHH---HHHHHHHHhhcCcceeEeeeecccccEEECCCC
Q psy9195 1 MAEHDDVRAGLMWSEG---LDEVFRENYMADPTLLWQYFGSAKGFLRTYPDK 49 (139)
Q Consensus 1 ~~~~~~v~~~~~~~~~---l~~~f~~~~~~~~~i~~~y~gs~~G~~~~~p~~ 49 (139)
++.+|.|+..+.-... ++..++.+.+. +.+.++++.+.+|..+.-|..
T Consensus 7 ~A~~p~v~~al~~~~~~~~lq~~~~~~~~~-~~~~~i~v~D~~g~~l~~s~~ 57 (116)
T PF14827_consen 7 LASDPAVIEALAQGDPEAELQALLEQLRKE-SDIDYIVVTDRDGIVLAHSDP 57 (116)
T ss_dssp HCTSCHHHHHCCTTGHHSCCCCHHHHHHHH-CT-SEEEEECTTSBECE-SSC
T ss_pred HHCCHHHHHHHhcCCccHHHHHHHHHHHhh-cCCeEEEEEcCCCCEEEcCCh
Confidence 3678888887776553 45566666654 789999999999998877743
No 96
>COG0102 RplM Ribosomal protein L13 [Translation, ribosomal structure and biogenesis]
Probab=39.18 E-value=71 Score=22.75 Aligned_cols=37 Identities=19% Similarity=0.306 Sum_probs=26.8
Q ss_pred cEEEEEcCCCCCCCchHHHHHHHHHHHHhh--------CCCCCEEEEE
Q psy9195 76 DVVILVDNSGSMAGMRNTTAKLVLHSLLQT--------FSNNDFINIF 115 (139)
Q Consensus 76 ~vvi~iD~sgSm~g~~l~~ak~~~~~~l~~--------l~~~d~~~v~ 115 (139)
.-+++||..|-.-|. +|-.++..++.. .+-||++-|+
T Consensus 13 r~w~vIDA~g~vLGR---LAs~VA~~Lrgkhkp~ytP~~d~Gd~ViVI 57 (148)
T COG0102 13 RKWYVIDAEGKVLGR---LASEVAKRLRGKHKPTYTPHVDTGDYVIVI 57 (148)
T ss_pred ceEEEEeCCCCChHH---HHHHHHHHHhcCCCCCcCcCcCCCCEEEEE
Confidence 345799999966664 788888877654 4445998887
No 97
>COG0275 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]
Probab=38.30 E-value=61 Score=25.97 Aligned_cols=31 Identities=13% Similarity=0.161 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHhhCCCCCEEEEEEeCCcee
Q psy9195 92 NTTAKLVLHSLLQTFSNNDFINIFKFNLTVD 122 (139)
Q Consensus 92 l~~ak~~~~~~l~~l~~~d~~~v~~f~~~~~ 122 (139)
|...+.++...++.|.+|-++.||+|-+=-+
T Consensus 220 L~~L~~~L~~a~~~L~~gGRl~VIsFHSLED 250 (314)
T COG0275 220 LEELEEALEAALDLLKPGGRLAVISFHSLED 250 (314)
T ss_pred HHHHHHHHHHHHHhhCCCcEEEEEEecchHH
Confidence 6788888889999999999999999987433
No 98
>KOG2326|consensus
Probab=33.24 E-value=1.6e+02 Score=25.98 Aligned_cols=48 Identities=23% Similarity=0.300 Sum_probs=33.7
Q ss_pred ccEEEEEcCCCCCCCc------hHHHHHHHHHHHHhh--C--CCCCEEEEEEeCCcee
Q psy9195 75 KDVVILVDNSGSMAGM------RNTTAKLVLHSLLQT--F--SNNDFINIFKFNLTVD 122 (139)
Q Consensus 75 ~~vvi~iD~sgSm~g~------~l~~ak~~~~~~l~~--l--~~~d~~~v~~f~~~~~ 122 (139)
...++++|.+.+|... .++.|+..+.-.+.. + ..-|.|+++.|+.+.+
T Consensus 5 e~ttfilDvG~~Ms~~~~~~~S~fE~a~~y~~~~lsrK~fa~rktD~is~vlyncD~t 62 (669)
T KOG2326|consen 5 ESTTFILDVGPSMSKNNETGKSNFEKAMAYLEYTLSRKSFASRKTDWISCVLYNCDVT 62 (669)
T ss_pred cceEEEEecCccccccCCCccccHHHHHHHHHHHHHHHHhhccCCceEEEEEecCCCc
Confidence 3455666999999732 478888777555432 2 2569999999998765
No 99
>cd00392 Ribosomal_L13 Ribosomal protein L13. Protein L13, a large ribosomal subunit protein, is one of five proteins required for an early folding intermediate of 23S rRNA in the assembly of the large subunit. L13 is situated on the bottom of the large subunit, near the polypeptide exit site. It interacts with proteins L3 and L6, and forms an extensive network of interactions with 23S rRNA. L13 has been identified as a homolog of the human breast basic conserved protein 1 (BBC1), a protein identified through its increased expression in breast cancer. L13 expression is also upregulated in a variety of human gastrointestinal cancers, suggesting it may play a role in the etiology of a variety of human malignancies.
Probab=32.37 E-value=82 Score=21.27 Aligned_cols=34 Identities=24% Similarity=0.397 Sum_probs=23.5
Q ss_pred EEEcCCCCCCCchHHHHHHHHHHHHh--------hCCCCCEEEEE
Q psy9195 79 ILVDNSGSMAGMRNTTAKLVLHSLLQ--------TFSNNDFINIF 115 (139)
Q Consensus 79 i~iD~sgSm~g~~l~~ak~~~~~~l~--------~l~~~d~~~v~ 115 (139)
++||+.+-.-| ++|..++..++. ..+-||+|-|+
T Consensus 2 ~viDA~~~~lG---RlAs~iA~~L~gKhKp~y~p~~d~Gd~VvVi 43 (114)
T cd00392 2 HVIDAKGQVLG---RLASKVAKLLLGKHKPTYTPHVDCGDYVVVV 43 (114)
T ss_pred EEEeCCCCchH---HHHHHHHHHHcCCCCCCcCCCccCCCEEEEE
Confidence 68898885555 477777776654 23449998887
No 100
>KOG1226|consensus
Probab=31.99 E-value=40 Score=30.19 Aligned_cols=53 Identities=21% Similarity=0.091 Sum_probs=38.7
Q ss_pred hhccccccEEEEEcCCCCCCCc--hHHHHHHHHHHHHhhCCCCCEEEEEEeCCce
Q psy9195 69 QATTCSKDVVILVDNSGSMAGM--RNTTAKLVLHSLLQTFSNNDFINIFKFNLTV 121 (139)
Q Consensus 69 ~a~~~~~~vvi~iD~sgSm~g~--~l~~ak~~~~~~l~~l~~~d~~~v~~f~~~~ 121 (139)
++...|-++.++.|-|.||... ++..+=+.+..-++.|..+=++|.-.|=++.
T Consensus 127 ~a~~yPVDLYyLMDlS~SM~DDl~~l~~LG~~L~~~m~~lT~nfrlGFGSFVDK~ 181 (783)
T KOG1226|consen 127 QAEDYPVDLYYLMDLSYSMKDDLENLKSLGTDLAREMRKLTSNFRLGFGSFVDKT 181 (783)
T ss_pred eccCCCeeEEEEeecchhhhhhHHHHHHHHHHHHHHHHHHhccCCccccchhccc
Confidence 5677899999999999999875 4554445555556677788888876665553
No 101
>TIGR00006 S-adenosyl-methyltransferase MraW. Genetics paper in 1972 links mra cluster to peptidoglycan biosynthesis in E. coli. Seems to be common in proteobacteria.wn.
Probab=31.32 E-value=83 Score=25.04 Aligned_cols=29 Identities=10% Similarity=0.065 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHhhCCCCCEEEEEEeCCc
Q psy9195 92 NTTAKLVLHSLLQTFSNNDFINIFKFNLT 120 (139)
Q Consensus 92 l~~ak~~~~~~l~~l~~~d~~~v~~f~~~ 120 (139)
|...+.++..+.+-|.+|-++.||+|.+=
T Consensus 216 L~~L~~~L~~~~~~L~~gGrl~VISfHSL 244 (305)
T TIGR00006 216 LEELEEALQFAPNLLAPGGRLSIISFHSL 244 (305)
T ss_pred HHHHHHHHHHHHHHhcCCCEEEEEecCcH
Confidence 45667777777888999999999999873
No 102
>PTZ00068 60S ribosomal protein L13a; Provisional
Probab=30.95 E-value=96 Score=23.26 Aligned_cols=32 Identities=31% Similarity=0.469 Sum_probs=23.7
Q ss_pred EEEEcCCCCCCCchHHHHHHHHHHHHhhCCCCCEEEEEE
Q psy9195 78 VILVDNSGSMAGMRNTTAKLVLHSLLQTFSNNDFINIFK 116 (139)
Q Consensus 78 vi~iD~sgSm~g~~l~~ak~~~~~~l~~l~~~d~~~v~~ 116 (139)
+++||..|-.-|- +|-.++..++ .||+|-|+-
T Consensus 5 w~vIDA~g~vLGR---LAS~VAk~Ll----~Gd~VVVVN 36 (202)
T PTZ00068 5 VIVIDCKGHLLGR---LASVVAKELL----LGQKIVVVR 36 (202)
T ss_pred eEEEECCCCcHHH---HHHHHHHHHh----CCCEEEEEe
Confidence 4699999877664 6777776654 799988873
No 103
>COG1424 BioW Pimeloyl-CoA synthetase [Coenzyme metabolism]
Probab=30.10 E-value=19 Score=27.01 Aligned_cols=34 Identities=32% Similarity=0.498 Sum_probs=26.1
Q ss_pred CCHHHHHhhhchHHHHHHHHHHhhcCcceeEeeeecc-cccEEECCC
Q psy9195 3 EHDDVRAGLMWSEGLDEVFRENYMADPTLLWQYFGSA-KGFLRTYPD 48 (139)
Q Consensus 3 ~~~~v~~~~~~~~~l~~~f~~~~~~~~~i~~~y~gs~-~G~~~~~p~ 48 (139)
.+|.|..++|||. ||++.--|++.. -|-.+.+|-
T Consensus 166 ~hp~VvaELC~SD------------d~dY~TGYvagkkiGY~Rit~l 200 (239)
T COG1424 166 AHPGVVAELCWSD------------DPDYTTGYVAGKKIGYHRITDL 200 (239)
T ss_pred cCcceeEEEeecC------------CCcceeeeeecceeeeEEeecc
Confidence 5788999999986 578888888876 566666663
No 104
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=30.04 E-value=44 Score=21.03 Aligned_cols=49 Identities=16% Similarity=0.249 Sum_probs=33.4
Q ss_pred cccccccchhhhhhccccccEEEEEcCCCCC--CCc-hHHHHHHHHHHHHhhC
Q psy9195 57 LIFDCRNRQWYIQATTCSKDVVILVDNSGSM--AGM-RNTTAKLVLHSLLQTF 106 (139)
Q Consensus 57 ~~yDpr~r~Wy~~a~~~~~~vvi~iD~sgSm--~g~-~l~~ak~~~~~~l~~l 106 (139)
..|+|...++..=.+..| ...+.+=.||.+ .|. ..+.++.++..++..|
T Consensus 31 ~~YePe~fpgl~~r~~~p-~~t~~IF~sGki~itGaks~~~~~~a~~~i~~~L 82 (86)
T PF00352_consen 31 VEYEPERFPGLIYRLRNP-KATVLIFSSGKIVITGAKSEEEAKKAIEKILPIL 82 (86)
T ss_dssp EEEETTTESSEEEEETTT-TEEEEEETTSEEEEEEESSHHHHHHHHHHHHHHH
T ss_pred cEEeeccCCeEEEeecCC-cEEEEEEcCCEEEEEecCCHHHHHHHHHHHHHHH
Confidence 688998877754334444 466777789986 354 5778888887776544
No 105
>PF08247 ENOD40: ENOD40 protein; InterPro: IPR013186 The soybean early nodulin 40 (ENOD40) mRNA contains two short overlapping ORFs; in vitro translation yields two peptides of 12 and 24 amino acids []. The putative role of the ENOD40 genes has been in favour of organogenesis, such as induction of the cortical cell divisions that lead to initiation of nodule primordia, in developing lateral roots and embryonic tissues. This supports the hypothesis for a role of ENOD40 in lateral organ development [].
Probab=29.59 E-value=7.6 Score=15.66 Aligned_cols=8 Identities=25% Similarity=0.879 Sum_probs=5.0
Q ss_pred hhhchHHH
Q psy9195 10 GLMWSEGL 17 (139)
Q Consensus 10 ~~~~~~~l 17 (139)
++||+.++
T Consensus 2 ~l~wqksi 9 (12)
T PF08247_consen 2 ELCWQKSI 9 (12)
T ss_pred ceeEeeee
Confidence 46777654
No 106
>KOG4115|consensus
Probab=28.76 E-value=1.8e+02 Score=19.24 Aligned_cols=48 Identities=15% Similarity=0.216 Sum_probs=36.4
Q ss_pred EEEEcCCCCCCC------------chHHHHHHHHHHHHhhCCCCCEEEEEEeCCceeeee
Q psy9195 78 VILVDNSGSMAG------------MRNTTAKLVLHSLLQTFSNNDFINIFKFNLTVDTIV 125 (139)
Q Consensus 78 vi~iD~sgSm~g------------~~l~~ak~~~~~~l~~l~~~d~~~v~~f~~~~~~~~ 125 (139)
++++|..|..-. ..++.....++..++.|++++.+..+..-++-+++.
T Consensus 21 iiv~d~~GvpikTt~d~~~t~~ya~~l~~L~~kars~VrdlDpsn~LtflRlRTkk~Eim 80 (97)
T KOG4115|consen 21 IIVVDNAGVPIKTTLDNTTTQQYAALLHPLVEKARSVVRDLDPSNDLTFLRLRTKKHEIM 80 (97)
T ss_pred EEEECCCCcEeEeccCchHHHHHHHHHHHHHHHHHHHHHccCCcCceEEEEEeeccceEE
Confidence 367888776432 135666777888889999999999999988877664
No 107
>PF07757 AdoMet_MTase: Predicted AdoMet-dependent methyltransferase; InterPro: IPR011671 tRNA (uracil-O(2)-)-methyltransferase catalyses the formation of O(2)-methyl-uracil at position 44 (m2U44) in tRNA(Ser) [].; GO: 0008168 methyltransferase activity
Probab=28.09 E-value=37 Score=23.04 Aligned_cols=60 Identities=22% Similarity=0.267 Sum_probs=42.1
Q ss_pred HHHHHhhhchHHHHHHHHHHhhcCcceeEeeeecccccEEEC-CCCCCCCccccccccccc-hhh
Q psy9195 5 DDVRAGLMWSEGLDEVFRENYMADPTLLWQYFGSAKGFLRTY-PDKEDAPAEDLIFDCRNR-QWY 67 (139)
Q Consensus 5 ~~v~~~~~~~~~l~~~f~~~~~~~~~i~~~y~gs~~G~~~~~-p~~~~~~~~~~~yDpr~r-~Wy 67 (139)
..|-.++...+-|...++......+....+=+|.-||.+..- ...-.+ .-++|.|.| .|-
T Consensus 34 K~VfEDlaIAAyLi~LW~~~~~~~~~~~FVDlGCGNGLLV~IL~~EGy~---G~GiD~R~Rk~W~ 95 (112)
T PF07757_consen 34 KHVFEDLAIAAYLIELWRDMYGEQKFQGFVDLGCGNGLLVYILNSEGYP---GWGIDARRRKSWD 95 (112)
T ss_pred hhHHHHHHHHHHHHHHHhcccCCCCCCceEEccCCchHHHHHHHhCCCC---ccccccccccchh
Confidence 357788888888888888877666666778899999986642 111111 368899888 463
No 108
>cd03422 YedF YedF is a bacterial SirA-like protein of unknown function. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=26.93 E-value=1.5e+02 Score=17.71 Aligned_cols=8 Identities=0% Similarity=0.422 Sum_probs=3.4
Q ss_pred CCCCEEEE
Q psy9195 107 SNNDFINI 114 (139)
Q Consensus 107 ~~~d~~~v 114 (139)
.+|+.+-|
T Consensus 24 ~~G~~l~V 31 (69)
T cd03422 24 KPGEILEV 31 (69)
T ss_pred CCCCEEEE
Confidence 44444443
No 109
>PRK09216 rplM 50S ribosomal protein L13; Reviewed
Probab=25.04 E-value=1.6e+02 Score=20.73 Aligned_cols=35 Identities=23% Similarity=0.348 Sum_probs=25.2
Q ss_pred EEEEcCCCCCCCchHHHHHHHHHHHHh--------hCCCCCEEEEE
Q psy9195 78 VILVDNSGSMAGMRNTTAKLVLHSLLQ--------TFSNNDFINIF 115 (139)
Q Consensus 78 vi~iD~sgSm~g~~l~~ak~~~~~~l~--------~l~~~d~~~v~ 115 (139)
++++|+.+-.-| ++|..++..++. ..+.||+|-|+
T Consensus 15 W~viDA~~~~lG---RlAs~IAk~L~GKhKp~y~p~~d~Gd~VvVi 57 (144)
T PRK09216 15 WYVIDAEGKVLG---RLASEVASILRGKHKPTFTPHVDTGDFVIVI 57 (144)
T ss_pred EEEEeCCCCchH---HHHHHHHHHHhccCCCCcCCCCCCCCEEEEE
Confidence 578999886555 477777776642 34589999887
No 110
>CHL00159 rpl13 ribosomal protein L13; Validated
Probab=24.42 E-value=1.7e+02 Score=20.66 Aligned_cols=36 Identities=14% Similarity=0.238 Sum_probs=25.5
Q ss_pred EEEEEcCCCCCCCchHHHHHHHHHHHHh--------hCCCCCEEEEE
Q psy9195 77 VVILVDNSGSMAGMRNTTAKLVLHSLLQ--------TFSNNDFINIF 115 (139)
Q Consensus 77 vvi~iD~sgSm~g~~l~~ak~~~~~~l~--------~l~~~d~~~v~ 115 (139)
-++++|+.|-.-|. +|..++..+.. ..+.||+|-|+
T Consensus 15 ~W~viDA~~~~lGR---lAs~iA~~L~GKhKp~ytP~~d~Gd~VVVi 58 (143)
T CHL00159 15 KWYIIDAKDQTLGR---LATKIASLLRGKNKPSYHPSVDTGDYVIVI 58 (143)
T ss_pred CEEEEeCCCCchHH---HHHHHHHHHhccCCCCcCCCcCCCCEEEEE
Confidence 35799999866564 77777776542 24579998876
No 111
>TIGR01066 rplM_bact ribosomal protein L13, bacterial type. This model distinguishes ribosomal protein L13 of bacteria and organelles from its eukarytotic and archaeal counterparts.
Probab=23.62 E-value=1.8e+02 Score=20.45 Aligned_cols=36 Identities=22% Similarity=0.279 Sum_probs=25.5
Q ss_pred EEEEEcCCCCCCCchHHHHHHHHHHHHh--------hCCCCCEEEEE
Q psy9195 77 VVILVDNSGSMAGMRNTTAKLVLHSLLQ--------TFSNNDFINIF 115 (139)
Q Consensus 77 vvi~iD~sgSm~g~~l~~ak~~~~~~l~--------~l~~~d~~~v~ 115 (139)
-++++|+.+-.-| ++|..++..++. ..+.||+|-|+
T Consensus 12 ~W~viDA~~~~lG---RLAs~iAk~L~GKhKp~y~p~~d~Gd~VvVi 55 (140)
T TIGR01066 12 KWYVVDAAGKTLG---RLASEVARLLRGKHKPTYTPHVDCGDYVIVI 55 (140)
T ss_pred cEEEEeCCCCchH---HHHHHHHHHHhccCCCccCCCccCCCEEEEE
Confidence 3679999886555 377777776652 24579998886
No 112
>PRK00050 16S rRNA m(4)C1402 methyltranserfase; Provisional
Probab=23.56 E-value=1.4e+02 Score=23.62 Aligned_cols=30 Identities=10% Similarity=0.121 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHhhCCCCCEEEEEEeCCce
Q psy9195 92 NTTAKLVLHSLLQTFSNNDFINIFKFNLTV 121 (139)
Q Consensus 92 l~~ak~~~~~~l~~l~~~d~~~v~~f~~~~ 121 (139)
|...+..+..+.+-|.+|-++.|++|.+=-
T Consensus 212 l~~L~~~L~~~~~~L~~gGrl~visfHSlE 241 (296)
T PRK00050 212 LEELERALEAALDLLKPGGRLAVISFHSLE 241 (296)
T ss_pred HHHHHHHHHHHHHHhcCCCEEEEEecCcHH
Confidence 456666777777889999999999998743
No 113
>PF07849 DUF1641: Protein of unknown function (DUF1641); InterPro: IPR012440 Archaeal and bacterial hypothetical proteins are found in this family, with the region in question being approximately 40 residues long.
Probab=23.10 E-value=92 Score=17.01 Aligned_cols=18 Identities=22% Similarity=0.274 Sum_probs=12.7
Q ss_pred CCHHHHHhhhchHHHHHH
Q psy9195 3 EHDDVRAGLMWSEGLDEV 20 (139)
Q Consensus 3 ~~~~v~~~~~~~~~l~~~ 20 (139)
+||||+..+-.--++-+.
T Consensus 21 ~DpdvqrgL~~ll~~lk~ 38 (42)
T PF07849_consen 21 RDPDVQRGLGFLLAFLKA 38 (42)
T ss_pred cCHHHHHHHHHHHHHHHH
Confidence 799999988765554443
No 114
>PF00572 Ribosomal_L13: Ribosomal protein L13; InterPro: IPR005822 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L13 is one of the proteins from the large ribosomal subunit []. In Escherichia coli, L13 is known to be one of the early assembly proteins of the 50S ribosomal subunit.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 4A17_I 4A1E_I 4A1A_I 4A1C_I 3D5B_N 3MS1_J 1VSP_H 3PYT_J 3PYO_J 3PYV_J ....
Probab=22.30 E-value=1.2e+02 Score=20.93 Aligned_cols=35 Identities=20% Similarity=0.344 Sum_probs=23.9
Q ss_pred EEEEcCCCCCCCchHHHHHHHHHHHHhh--------CCCCCEEEEE
Q psy9195 78 VILVDNSGSMAGMRNTTAKLVLHSLLQT--------FSNNDFINIF 115 (139)
Q Consensus 78 vi~iD~sgSm~g~~l~~ak~~~~~~l~~--------l~~~d~~~v~ 115 (139)
+++||+.+-.-| ++|..++..++.. .+.||+|-|+
T Consensus 1 W~viDA~~~~lG---RLAs~iAk~L~GKhk~~y~p~~d~Gd~VvVi 43 (128)
T PF00572_consen 1 WYVIDAKGQILG---RLASKIAKLLLGKHKPTYTPNVDCGDHVVVI 43 (128)
T ss_dssp EEEEETTTBBHH---HHHHHHHHHHCTTSSTSSBTTSSTTEEEEEE
T ss_pred CEEEeCCCCchH---HHHHHHHHHHhCCCCCccCcCccCCCEEEEE
Confidence 368898885545 4788888776522 3489987766
No 115
>KOG0090|consensus
Probab=22.10 E-value=1.3e+02 Score=23.01 Aligned_cols=23 Identities=26% Similarity=0.407 Sum_probs=17.2
Q ss_pred cccchhhhhhcc---ccccEEEEEcC
Q psy9195 61 CRNRQWYIQATT---CSKDVVILVDN 83 (139)
Q Consensus 61 pr~r~Wy~~a~~---~~~~vvi~iD~ 83 (139)
+|.|.|..+-.. +-+.+||++|+
T Consensus 93 ~rlR~kl~e~~~~~~~akaiVFVVDS 118 (238)
T KOG0090|consen 93 SRLRRKLLEYLKHNYSAKAIVFVVDS 118 (238)
T ss_pred HHHHHHHHHHccccccceeEEEEEec
Confidence 478888876554 44778999998
No 116
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=21.55 E-value=94 Score=18.14 Aligned_cols=13 Identities=15% Similarity=0.383 Sum_probs=11.4
Q ss_pred hCCCCCEEEEEEe
Q psy9195 105 TFSNNDFINIFKF 117 (139)
Q Consensus 105 ~l~~~d~~~v~~f 117 (139)
.|.+||++.|+.|
T Consensus 50 ~l~~gD~vei~~~ 62 (66)
T PRK05659 50 ALREGDVVEIVHA 62 (66)
T ss_pred cCCCCCEEEEEEE
Confidence 4789999999987
No 117
>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=21.32 E-value=1.2e+02 Score=22.82 Aligned_cols=16 Identities=38% Similarity=0.420 Sum_probs=13.1
Q ss_pred ccEEEEEcCCCCCCCc
Q psy9195 75 KDVVILVDNSGSMAGM 90 (139)
Q Consensus 75 ~~vvi~iD~sgSm~g~ 90 (139)
-..++.+|.|+||...
T Consensus 4 laLvLavDvS~SVD~~ 19 (205)
T PF06707_consen 4 LALVLAVDVSGSVDAD 19 (205)
T ss_pred ceeeeeeeccCCCCHH
Confidence 3578999999999864
No 118
>PRK05863 sulfur carrier protein ThiS; Provisional
Probab=21.32 E-value=92 Score=18.41 Aligned_cols=13 Identities=0% Similarity=0.148 Sum_probs=11.3
Q ss_pred hCCCCCEEEEEEe
Q psy9195 105 TFSNNDFINIFKF 117 (139)
Q Consensus 105 ~l~~~d~~~v~~f 117 (139)
.|.+||++.|+.|
T Consensus 49 ~L~~gD~ieIv~~ 61 (65)
T PRK05863 49 KLRDGARLEVVTA 61 (65)
T ss_pred hcCCCCEEEEEee
Confidence 3789999999987
No 119
>COG0776 HimA Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]
Probab=21.20 E-value=1.2e+02 Score=19.77 Aligned_cols=21 Identities=10% Similarity=0.332 Sum_probs=16.6
Q ss_pred HHHHHhhCCCCCEEEEEEeCC
Q psy9195 99 LHSLLQTFSNNDFINIFKFNL 119 (139)
Q Consensus 99 ~~~~l~~l~~~d~~~v~~f~~ 119 (139)
+..+.+.|..|+.+.|..|..
T Consensus 30 ~~~i~~aL~~G~~V~l~gFG~ 50 (94)
T COG0776 30 LEEITEALAKGERVELRGFGT 50 (94)
T ss_pred HHHHHHHHHcCCeEEEeeeee
Confidence 344456788999999999986
No 120
>PRK00299 sulfur transfer protein SirA; Reviewed
Probab=20.19 E-value=2.3e+02 Score=17.52 Aligned_cols=38 Identities=8% Similarity=0.018 Sum_probs=24.2
Q ss_pred EEEcCCCCCCCchHHHHHHHHHHHHhhCCCCCEEEEEEeCCc
Q psy9195 79 ILVDNSGSMAGMRNTTAKLVLHSLLQTFSNNDFINIFKFNLT 120 (139)
Q Consensus 79 i~iD~sgSm~g~~l~~ak~~~~~~l~~l~~~d~~~v~~f~~~ 120 (139)
..+|++|-.--.++-.++.+++ .+.+|+.+-|+.=|..
T Consensus 10 ~~lD~~Gl~CP~Pll~~kk~l~----~l~~G~~l~V~~dd~~ 47 (81)
T PRK00299 10 HTLDALGLRCPEPVMMVRKTVR----NMQPGETLLIIADDPA 47 (81)
T ss_pred eEEecCCCCCCHHHHHHHHHHH----cCCCCCEEEEEeCCcc
Confidence 3577777655555656666655 5677888777655443
No 121
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=20.15 E-value=2e+02 Score=16.81 Aligned_cols=35 Identities=17% Similarity=0.190 Sum_probs=15.4
Q ss_pred EcCCCCCCCchHHHHHHHHHHHHhhCCCCCEEEEEEeCC
Q psy9195 81 VDNSGSMAGMRNTTAKLVLHSLLQTFSNNDFINIFKFNL 119 (139)
Q Consensus 81 iD~sgSm~g~~l~~ak~~~~~~l~~l~~~d~~~v~~f~~ 119 (139)
+|+.|-.--..+-.++.++. .+.+|+.+-|+.=+.
T Consensus 3 lD~rg~~CP~Pll~~~~~l~----~l~~G~~l~v~~d~~ 37 (70)
T PF01206_consen 3 LDLRGLSCPMPLLKAKKALK----ELPPGEVLEVLVDDP 37 (70)
T ss_dssp EECSS-STTHHHHHHHHHHH----TSGTT-EEEEEESST
T ss_pred EeCCCCCCCHHHHHHHHHHH----hcCCCCEEEEEECCc
Confidence 44544332233334444433 456666666555443
Done!