Query psy16628
Match_columns 107
No_of_seqs 114 out of 382
Neff 5.1
Searched_HMMs 46136
Date Fri Aug 16 17:44:52 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16628.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16628hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00395 Sec24-related protein 99.9 2.1E-27 4.5E-32 215.4 10.5 82 25-107 948-1042(1560)
2 cd01479 Sec24-like Sec24-like: 99.9 7E-27 1.5E-31 180.0 10.6 80 28-107 2-82 (244)
3 KOG1984|consensus 99.9 1.2E-26 2.6E-31 204.1 9.1 96 10-106 399-495 (1007)
4 PF04811 Sec23_trunk: Sec23/Se 99.9 9.3E-26 2E-30 171.6 8.6 81 27-107 1-81 (243)
5 cd01468 trunk_domain trunk dom 99.9 4.8E-25 1E-29 168.1 10.6 80 28-107 2-81 (239)
6 KOG1985|consensus 99.9 4.4E-25 9.4E-30 193.3 9.6 83 25-107 290-372 (887)
7 COG5028 Vesicle coat complex C 99.8 8.2E-21 1.8E-25 166.0 9.8 94 10-107 260-354 (861)
8 cd01478 Sec23-like Sec23-like: 99.7 7.2E-18 1.6E-22 132.2 6.3 55 28-87 2-56 (267)
9 PLN00162 transport protein sec 99.5 1.8E-13 3.8E-18 120.3 10.0 68 24-97 119-186 (761)
10 KOG1986|consensus 97.9 5.3E-05 1.2E-09 67.1 7.9 64 18-86 110-173 (745)
11 COG5047 SEC23 Vesicle coat com 97.2 0.0013 2.8E-08 58.0 7.1 66 16-86 109-174 (755)
12 cd01471 vWA_micronemal_protein 96.7 0.0067 1.5E-07 43.7 6.7 55 32-86 3-59 (186)
13 PF13768 VWA_3: von Willebrand 96.7 0.0049 1.1E-07 43.1 5.5 48 32-83 3-50 (155)
14 PF00092 VWA: von Willebrand f 96.6 0.0064 1.4E-07 42.2 5.5 54 32-86 2-57 (178)
15 cd01464 vWA_subfamily VWA subf 96.5 0.0052 1.1E-07 44.2 4.8 50 31-81 5-58 (176)
16 cd01472 vWA_collagen von Wille 96.3 0.011 2.4E-07 41.7 5.5 49 32-81 3-52 (164)
17 cd01477 vWA_F09G8-8_type VWA F 96.2 0.014 3.1E-07 43.7 5.9 59 26-85 16-82 (193)
18 cd01463 vWA_VGCC_like VWA Volt 96.2 0.027 5.8E-07 41.0 7.2 60 18-82 4-63 (190)
19 cd00198 vWFA Von Willebrand fa 96.1 0.025 5.4E-07 37.4 5.9 50 31-81 2-52 (161)
20 cd01470 vWA_complement_factors 95.8 0.021 4.5E-07 41.7 5.0 50 31-81 2-52 (198)
21 cd01475 vWA_Matrilin VWA_Matri 95.7 0.033 7.1E-07 41.8 5.8 56 29-85 2-59 (224)
22 cd01482 vWA_collagen_alphaI-XI 95.6 0.033 7.1E-07 39.5 5.1 48 32-80 3-51 (164)
23 cd01461 vWA_interalpha_trypsin 95.5 0.049 1.1E-06 37.9 5.8 51 29-82 2-52 (171)
24 cd01456 vWA_ywmD_type VWA ywmD 95.5 0.04 8.7E-07 40.6 5.6 53 25-79 16-73 (206)
25 cd01465 vWA_subgroup VWA subgr 95.4 0.05 1.1E-06 37.9 5.5 49 31-82 2-50 (170)
26 cd01469 vWA_integrins_alpha_su 95.4 0.05 1.1E-06 39.4 5.7 53 32-85 3-57 (177)
27 smart00327 VWA von Willebrand 95.3 0.054 1.2E-06 37.1 5.5 52 30-82 2-54 (177)
28 cd01466 vWA_C3HC4_type VWA C3H 95.3 0.04 8.8E-07 39.0 4.9 48 32-82 3-50 (155)
29 TIGR03436 acidobact_VWFA VWFA- 95.2 0.098 2.1E-06 40.6 7.1 63 15-81 37-102 (296)
30 TIGR03788 marine_srt_targ mari 95.0 0.072 1.6E-06 45.8 6.4 52 28-82 270-321 (596)
31 cd01450 vWFA_subfamily_ECM Von 95.0 0.08 1.7E-06 35.9 5.5 49 32-81 3-52 (161)
32 cd01481 vWA_collagen_alpha3-VI 94.7 0.087 1.9E-06 38.1 5.2 54 32-86 3-58 (165)
33 cd01476 VWA_integrin_invertebr 94.6 0.16 3.4E-06 35.5 6.3 44 32-77 3-47 (163)
34 PF13519 VWA_2: von Willebrand 94.1 0.18 3.8E-06 34.4 5.5 45 32-79 2-50 (172)
35 COG4245 TerY Uncharacterized p 94.1 0.13 2.9E-06 39.9 5.2 50 33-83 7-60 (207)
36 cd01473 vWA_CTRP CTRP for CS 93.7 0.15 3.3E-06 37.8 5.0 49 32-80 3-52 (192)
37 cd01480 vWA_collagen_alpha_1-V 93.7 0.18 4E-06 36.6 5.2 56 29-85 2-65 (186)
38 cd01474 vWA_ATR ATR (Anthrax T 93.1 0.37 8E-06 34.8 6.0 54 29-85 4-58 (185)
39 cd01467 vWA_BatA_type VWA BatA 92.9 0.38 8.3E-06 33.9 5.8 49 30-81 3-56 (180)
40 cd01453 vWA_transcription_fact 92.6 0.48 1E-05 34.8 6.2 55 27-81 1-61 (183)
41 PRK13685 hypothetical protein; 92.1 0.57 1.2E-05 37.4 6.4 52 28-81 87-142 (326)
42 PTZ00441 sporozoite surface pr 89.7 1 2.2E-05 39.7 6.2 59 28-86 41-101 (576)
43 cd01454 vWA_norD_type norD typ 88.6 0.81 1.8E-05 32.5 4.1 47 31-78 2-48 (174)
44 cd01451 vWA_Magnesium_chelatas 88.5 1.4 2.9E-05 31.7 5.3 46 32-78 3-48 (178)
45 TIGR02031 BchD-ChlD magnesium 88.0 1.6 3.5E-05 38.0 6.3 60 18-79 396-455 (589)
46 cd01458 vWA_ku Ku70/Ku80 N-ter 87.9 1.8 3.8E-05 32.3 5.7 48 31-78 3-57 (218)
47 TIGR00578 ku70 ATP-dependent D 87.6 3 6.6E-05 36.4 7.7 69 30-102 11-87 (584)
48 cd01462 VWA_YIEM_type VWA YIEM 86.7 2 4.3E-05 29.6 5.1 50 32-83 3-52 (152)
49 cd01452 VWA_26S_proteasome_sub 85.8 1.1 2.3E-05 34.0 3.5 47 31-77 5-56 (187)
50 TIGR00868 hCaCC calcium-activa 85.8 3 6.5E-05 38.4 6.9 61 18-82 295-356 (863)
51 PF09967 DUF2201: VWA-like dom 80.4 5.2 0.00011 28.0 5.0 44 33-81 2-45 (126)
52 PF03731 Ku_N: Ku70/Ku80 N-ter 78.4 4.5 9.8E-05 29.9 4.5 48 31-78 1-54 (224)
53 PRK13406 bchD magnesium chelat 77.2 6 0.00013 34.7 5.5 48 29-78 401-448 (584)
54 TIGR02442 Cob-chelat-sub cobal 75.4 7.7 0.00017 34.0 5.7 48 29-77 465-512 (633)
55 cd01457 vWA_ORF176_type VWA OR 74.4 5.5 0.00012 29.1 4.0 49 31-79 4-58 (199)
56 PRK10997 yieM hypothetical pro 71.1 7.1 0.00015 33.8 4.4 56 29-86 323-378 (487)
57 PF09631 Sen15: Sen15 protein; 63.6 4.7 0.0001 27.2 1.5 41 52-92 58-99 (101)
58 smart00539 NIDO Extracellular 63.5 27 0.00059 25.4 5.6 80 18-103 1-81 (152)
59 cd01460 vWA_midasin VWA_Midasi 62.1 11 0.00024 30.0 3.6 50 28-80 59-111 (266)
60 PF02905 EBV-NA1: Epstein Barr 59.1 17 0.00037 26.8 3.8 31 49-79 113-144 (146)
61 PF05762 VWA_CoxE: VWA domain 57.4 22 0.00047 26.9 4.4 49 25-80 53-101 (222)
62 COG1240 ChlD Mg-chelatase subu 53.3 24 0.00051 28.5 4.1 45 30-76 79-124 (261)
63 PRK00528 rpmE 50S ribosomal pr 39.2 28 0.0006 22.5 2.1 16 6-21 33-48 (71)
64 PF05117 DUF695: Family of unk 38.8 1.1E+02 0.0024 21.0 5.3 50 31-82 35-93 (136)
65 PF10168 Nup88: Nuclear pore c 38.0 73 0.0016 28.9 5.2 37 66-102 160-196 (717)
66 KOG2807|consensus 36.8 54 0.0012 27.7 3.9 57 20-76 51-112 (378)
67 KOG0863|consensus 32.7 1.1E+02 0.0024 24.7 4.9 70 14-84 140-226 (264)
68 PF04459 DUF512: Protein of un 32.5 63 0.0014 24.8 3.5 29 46-75 77-105 (204)
69 PRK00019 rpmE 50S ribosomal pr 32.4 24 0.00051 23.0 1.0 16 7-22 32-47 (72)
70 TIGR00105 L31 ribosomal protei 30.4 28 0.00062 22.2 1.1 16 7-22 32-47 (68)
71 PF14581 SseB_C: SseB protein 28.3 57 0.0012 21.6 2.3 54 18-77 37-90 (108)
72 KOG1679|consensus 27.5 1.2E+02 0.0027 24.5 4.4 42 33-74 41-82 (291)
73 KOG1599|consensus 27.3 47 0.001 27.1 2.0 25 79-106 254-278 (297)
74 PF06884 DUF1264: Protein of u 26.4 46 0.001 25.3 1.7 21 74-94 109-133 (171)
75 cd04931 ACT_PAH ACT domain of 26.3 1.3E+02 0.0029 19.9 3.8 31 28-60 53-83 (90)
76 PHA02567 rnh RnaseH; Provision 26.2 1.5E+02 0.0032 24.4 4.7 49 32-82 15-78 (304)
77 TIGR02060 aprB adenosine phosp 24.0 86 0.0019 22.3 2.7 25 18-42 86-110 (132)
78 COG5256 TEF1 Translation elong 23.6 1.1E+02 0.0024 26.4 3.7 37 11-47 78-127 (428)
79 cd07265 2_3_CTD_N N-terminal d 23.4 14 0.00031 24.0 -1.4 21 1-21 3-23 (122)
80 CHL00136 rpl31 ribosomal prote 23.4 41 0.00088 21.7 0.8 16 7-22 32-47 (68)
81 cd06822 PLPDE_III_YBL036c_euk 22.8 2.3E+02 0.005 21.8 5.1 50 27-78 115-165 (227)
82 PF11979 DUF3480: Domain of un 22.2 56 0.0012 27.5 1.6 82 24-106 261-355 (356)
83 PF10238 Eapp_C: E2F-associate 21.5 94 0.002 22.6 2.5 20 66-85 115-134 (136)
84 KOG2353|consensus 21.5 1.6E+02 0.0035 28.3 4.6 55 26-83 222-276 (1104)
85 PF13218 DUF4026: Protein of u 21.4 39 0.00084 28.1 0.5 21 1-21 182-202 (323)
86 PF02513 Spin-Ssty: Spin/Ssty 20.8 54 0.0012 20.1 1.0 23 59-83 24-46 (50)
87 smart00368 LRR_RI Leucine rich 20.6 66 0.0014 16.6 1.2 22 35-56 6-27 (28)
88 cd04904 ACT_AAAH ACT domain of 20.4 1.6E+02 0.0034 18.2 3.1 13 28-40 39-51 (74)
89 COG5091 SGT1 Suppressor of G2 20.2 44 0.00094 27.9 0.6 22 65-86 73-94 (368)
90 PF14784 ECIST_Cterm: C-termin 20.1 1E+02 0.0022 22.1 2.4 30 73-102 26-55 (126)
No 1
>PTZ00395 Sec24-related protein; Provisional
Probab=99.94 E-value=2.1e-27 Score=215.43 Aligned_cols=82 Identities=24% Similarity=0.357 Sum_probs=76.8
Q ss_pred ccCCceeeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCCCCceEEEEEEecCeEEEEecCCC-------------CCCc
Q psy16628 25 ELGIFKCPLYFMVVKGYACYCKYQALQREVLLNQLKSMPGDRRTSIAIITYDSAVHFYSLAEG-------------QTQP 91 (107)
Q Consensus 25 ~~~~~~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs~vhFynl~~~-------------l~~p 91 (107)
+...|++|+|+||||++||++|++.++|++||++|++++ ++||||||||||++||||||+++ ++||
T Consensus 948 ~~p~PP~YvFLIDVS~~AVkSGLl~tacesIK~sLDsL~-dpRTRVGIITFDSsLHFYNLks~l~~~~~~~~~~~~l~qP 1026 (1560)
T PTZ00395 948 KNMLPPYFVFVVECSYNAIYNNITYTILEGIRYAVQNVK-CPQTKIAIITFNSSIYFYHCKGGKGVSGEEGDGGGGSGNH 1026 (1560)
T ss_pred cCCCCCEEEEEEECCHHHHhhChHHHHHHHHHHHHhcCC-CCCcEEEEEEecCcEEEEecCcccccccccccccccCCCc
Confidence 445689999999999999999999999999999999998 47999999999999999999875 5899
Q ss_pred cEEEeCCCCCCCCCCC
Q psy16628 92 SQMILTDIDDIFLPSP 107 (107)
Q Consensus 92 qmlVVsDldd~FvP~P 107 (107)
||+||+||||||+|+|
T Consensus 1027 QMLVVSDLDDPFLPlP 1042 (1560)
T PTZ00395 1027 QVIVMSDVDDPFLPLP 1042 (1560)
T ss_pred eEEeecCCccCcCCCC
Confidence 9999999999999987
No 2
>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=99.94 E-value=7e-27 Score=180.01 Aligned_cols=80 Identities=36% Similarity=0.604 Sum_probs=77.6
Q ss_pred CceeeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCCC-CceEEEEEEecCeEEEEecCCCCCCccEEEeCCCCCCCCCC
Q psy16628 28 IFKCPLYFMVVKGYACYCKYQALQREVLLNQLKSMPGD-RRTSIAIITYDSAVHFYSLAEGQTQPSQMILTDIDDIFLPS 106 (107)
Q Consensus 28 ~~~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~~-~~t~IgiITfDs~vhFynl~~~l~~pqmlVVsDldd~FvP~ 106 (107)
.|++|+|+||||+.|+++|+++++|++|+++|+++|++ +|++|||||||++|||||+++++++|||++++|++|+|+|+
T Consensus 2 ~pp~~~FvIDvs~~a~~~g~~~~~~~si~~~L~~lp~~~~~~~VgiITfd~~v~~y~l~~~~~~~q~~vv~dl~d~f~P~ 81 (244)
T cd01479 2 QPAVYVFLIDVSYNAIKSGLLATACEALLSNLDNLPGDDPRTRVGFITFDSTLHFFNLKSSLEQPQMMVVSDLDDPFLPL 81 (244)
T ss_pred CCCEEEEEEEccHHHHhhChHHHHHHHHHHHHHhcCCCCCCeEEEEEEECCeEEEEECCCCCCCCeEEEeeCcccccCCC
Confidence 58999999999999999999999999999999999986 89999999999999999999999999999999999999998
Q ss_pred C
Q psy16628 107 P 107 (107)
Q Consensus 107 P 107 (107)
|
T Consensus 82 ~ 82 (244)
T cd01479 82 P 82 (244)
T ss_pred C
Confidence 6
No 3
>KOG1984|consensus
Probab=99.94 E-value=1.2e-26 Score=204.14 Aligned_cols=96 Identities=23% Similarity=0.415 Sum_probs=89.8
Q ss_pred cccccCCCceeeeecccCCceeeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCC-CCceEEEEEEecCeEEEEecCCCC
Q psy16628 10 TLHLSNSHAYYTIVWELGIFKCPLYFMVVKGYACYCKYQALQREVLLNQLKSMPG-DRRTSIAIITYDSAVHFYSLAEGQ 88 (107)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~-~~~t~IgiITfDs~vhFynl~~~l 88 (107)
+.||-+++.|..+. +...+++|+|+||||++|+++|++.++|++||+.|+.+|. +++++|||+|||++|||||++++|
T Consensus 399 t~dfvatk~Y~~~~-k~p~ppafvFmIDVSy~Ai~~G~~~a~ce~ik~~l~~lp~~~p~~~Vgivtfd~tvhFfnl~s~L 477 (1007)
T KOG1984|consen 399 TVDFVATKDYCRKT-KPPKPPAFVFMIDVSYNAISNGAVKAACEAIKSVLEDLPREEPNIRVGIVTFDKTVHFFNLSSNL 477 (1007)
T ss_pred ccceeeehhhhhcC-CCCCCceEEEEEEeehhhhhcchHHHHHHHHHHHHhhcCccCCceEEEEEEecceeEeeccCccc
Confidence 34556778888887 7889999999999999999999999999999999999995 789999999999999999999999
Q ss_pred CCccEEEeCCCCCCCCCC
Q psy16628 89 TQPSQMILTDIDDIFLPS 106 (107)
Q Consensus 89 ~~pqmlVVsDldd~FvP~ 106 (107)
+||||+||+|++|+|+|+
T Consensus 478 ~qp~mliVsdv~dvfvPf 495 (1007)
T KOG1984|consen 478 AQPQMLIVSDVDDVFVPF 495 (1007)
T ss_pred cCceEEEeeccccccccc
Confidence 999999999999999996
No 4
>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=99.93 E-value=9.3e-26 Score=171.63 Aligned_cols=81 Identities=36% Similarity=0.571 Sum_probs=73.8
Q ss_pred CCceeeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCCCCceEEEEEEecCeEEEEecCCCCCCccEEEeCCCCCCCCCC
Q psy16628 27 GIFKCPLYFMVVKGYACYCKYQALQREVLLNQLKSMPGDRRTSIAIITYDSAVHFYSLAEGQTQPSQMILTDIDDIFLPS 106 (107)
Q Consensus 27 ~~~~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs~vhFynl~~~l~~pqmlVVsDldd~FvP~ 106 (107)
+.||+|+|+||+|++|+++|++++++++|+++|+++|+++++||||||||++||||+++++++++||++++|+||+|+|.
T Consensus 1 P~pp~y~FvID~s~~av~~g~~~~~~~sl~~~l~~l~~~~~~~vgiitfd~~V~~y~l~~~~~~~~~~v~~dl~~~~~p~ 80 (243)
T PF04811_consen 1 PQPPVYVFVIDVSYEAVQSGLLQSLIESLKSALDSLPGDERTRVGIITFDSSVHFYNLSSSLSQPQMIVVSDLDDPFIPL 80 (243)
T ss_dssp -S--EEEEEEE-SHHHHHHTHHHHHHHHHHHHGCTSSTSTT-EEEEEEESSSEEEEETTTTSSSTEEEEEHHTTSHHSST
T ss_pred CCCCEEEEEEECchhhhhccHHHHHHHHHHHHHHhccCCCCcEEEEEEeCCEEEEEECCCCcCCCcccchHHHhhcccCC
Confidence 35899999999999999999999999999999999997789999999999999999999999999999999999999998
Q ss_pred C
Q psy16628 107 P 107 (107)
Q Consensus 107 P 107 (107)
|
T Consensus 81 ~ 81 (243)
T PF04811_consen 81 P 81 (243)
T ss_dssp S
T ss_pred c
Confidence 6
No 5
>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=99.92 E-value=4.8e-25 Score=168.08 Aligned_cols=80 Identities=35% Similarity=0.578 Sum_probs=76.9
Q ss_pred CceeeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCCCCceEEEEEEecCeEEEEecCCCCCCccEEEeCCCCCCCCCCC
Q psy16628 28 IFKCPLYFMVVKGYACYCKYQALQREVLLNQLKSMPGDRRTSIAIITYDSAVHFYSLAEGQTQPSQMILTDIDDIFLPSP 107 (107)
Q Consensus 28 ~~~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs~vhFynl~~~l~~pqmlVVsDldd~FvP~P 107 (107)
.||+|+|+||+|++|+++|++++++++|+++|+++|++++++|||||||++|||||+++...+|||+|++|++|+|+|.|
T Consensus 2 ~pp~~vFvID~s~~ai~~~~l~~~~~sl~~~l~~lp~~~~~~igiITf~~~V~~~~~~~~~~~~~~~v~~dl~d~f~p~~ 81 (239)
T cd01468 2 QPPVFVFVIDVSYEAIKEGLLQALKESLLASLDLLPGDPRARVGLITYDSTVHFYNLSSDLAQPKMYVVSDLKDVFLPLP 81 (239)
T ss_pred CCCEEEEEEEcchHhccccHHHHHHHHHHHHHHhCCCCCCcEEEEEEeCCeEEEEECCCCCCCCeEEEeCCCccCcCCCc
Confidence 58999999999999999999999999999999999977899999999999999999999888899999999999999975
No 6
>KOG1985|consensus
Probab=99.92 E-value=4.4e-25 Score=193.35 Aligned_cols=83 Identities=37% Similarity=0.591 Sum_probs=81.0
Q ss_pred ccCCceeeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCCCCceEEEEEEecCeEEEEecCCCCCCccEEEeCCCCCCCC
Q psy16628 25 ELGIFKCPLYFMVVKGYACYCKYQALQREVLLNQLKSMPGDRRTSIAIITYDSAVHFYSLAEGQTQPSQMILTDIDDIFL 104 (107)
Q Consensus 25 ~~~~~~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs~vhFynl~~~l~~pqmlVVsDldd~Fv 104 (107)
++.-|+.|+|+||||..|+++|+++++|++|++.||.+|+++||||||||||++||||+++++++|||||+|+|+||+|+
T Consensus 290 R~P~Pavy~FliDVS~~a~ksG~L~~~~~slL~~LD~lpgd~Rt~igfi~fDs~ihfy~~~~~~~qp~mm~vsdl~d~fl 369 (887)
T KOG1985|consen 290 RPPQPAVYVFLIDVSISAIKSGYLETVARSLLENLDALPGDPRTRIGFITFDSTIHFYSVQGDLNQPQMMIVSDLDDPFL 369 (887)
T ss_pred CCCCCceEEEEEEeehHhhhhhHHHHHHHHHHHhhhcCCCCCcceEEEEEeeceeeEEecCCCcCCCceeeecccccccc
Confidence 56779999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCC
Q psy16628 105 PSP 107 (107)
Q Consensus 105 P~P 107 (107)
|+|
T Consensus 370 p~p 372 (887)
T KOG1985|consen 370 PMP 372 (887)
T ss_pred CCc
Confidence 987
No 7
>COG5028 Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]
Probab=99.84 E-value=8.2e-21 Score=165.98 Aligned_cols=94 Identities=27% Similarity=0.412 Sum_probs=86.7
Q ss_pred cccccCCCceeeeecccCCceeeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCC-CCceEEEEEEecCeEEEEecCCCC
Q psy16628 10 TLHLSNSHAYYTIVWELGIFKCPLYFMVVKGYACYCKYQALQREVLLNQLKSMPG-DRRTSIAIITYDSAVHFYSLAEGQ 88 (107)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~-~~~t~IgiITfDs~vhFynl~~~l 88 (107)
|-||-.|++|-+.+.. |++|||+||||+.|+++|++.+++++|++.|+.+|+ ++|+|||||.||++||||++++++
T Consensus 260 vvdf~ap~~Y~~~~p~---P~~yvFlIDVS~~a~~~g~~~a~~r~Il~~l~~~~~~dpr~kIaii~fD~sl~ffk~s~d~ 336 (861)
T COG5028 260 VVDFLAPKEYSLRQPP---PPVYVFLIDVSFEAIKNGLVKAAIRAILENLDQIPNFDPRTKIAIICFDSSLHFFKLSPDL 336 (861)
T ss_pred eeEEecccceeeccCC---CCEEEEEEEeehHhhhcchHHHHHHHHHhhccCCCCCCCcceEEEEEEcceeeEEecCCCC
Confidence 4566788888887766 999999999999999999999999999999999987 899999999999999999999988
Q ss_pred CCccEEEeCCCCCCCCCCC
Q psy16628 89 TQPSQMILTDIDDIFLPSP 107 (107)
Q Consensus 89 ~~pqmlVVsDldd~FvP~P 107 (107)
..||++|+|+||||+|.|
T Consensus 337 -~~~~~~vsdld~pFlPf~ 354 (861)
T COG5028 337 -DEQMLIVSDLDEPFLPFP 354 (861)
T ss_pred -ccceeeecccccccccCC
Confidence 349999999999999986
No 8
>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=99.72 E-value=7.2e-18 Score=132.24 Aligned_cols=55 Identities=16% Similarity=0.120 Sum_probs=51.2
Q ss_pred CceeeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCCCCceEEEEEEecCeEEEEecCCC
Q psy16628 28 IFKCPLYFMVVKGYACYCKYQALQREVLLNQLKSMPGDRRTSIAIITYDSAVHFYSLAEG 87 (107)
Q Consensus 28 ~~~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs~vhFynl~~~ 87 (107)
.|++|+|+||+|..+++ +++++++|+.+|+.+|. +++|||||||++||||||++.
T Consensus 2 ~pp~~vFviDvs~~~~e---l~~l~~sl~~~L~~lP~--~a~VGlITfd~~V~~~~L~~~ 56 (267)
T cd01478 2 SPPVFLFVVDTCMDEEE---LDALKESLIMSLSLLPP--NALVGLITFGTMVQVHELGFE 56 (267)
T ss_pred CCCEEEEEEECccCHHH---HHHHHHHHHHHHHhCCC--CCEEEEEEECCEEEEEEcCCC
Confidence 57999999999999998 77899999999999998 899999999999999999854
No 9
>PLN00162 transport protein sec23; Provisional
Probab=99.48 E-value=1.8e-13 Score=120.32 Aligned_cols=68 Identities=12% Similarity=0.111 Sum_probs=60.1
Q ss_pred cccCCceeeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCCCCceEEEEEEecCeEEEEecCCCCCCccEEEeC
Q psy16628 24 WELGIFKCPLYFMVVKGYACYCKYQALQREVLLNQLKSMPGDRRTSIAIITYDSAVHFYSLAEGQTQPSQMILT 97 (107)
Q Consensus 24 ~~~~~~~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs~vhFynl~~~l~~pqmlVVs 97 (107)
.+.+.||+|+|+||+|..+.+.| .++++|+.+|+.+|. +++|||||||++||||+|+.+. .|+++|++
T Consensus 119 ~~~~~pp~fvFvID~s~~~~~l~---~lk~sl~~~L~~LP~--~a~VGlITF~s~V~~~~L~~~~-~~~~~Vf~ 186 (761)
T PLN00162 119 GGAPSPPVFVFVVDTCMIEEELG---ALKSALLQAIALLPE--NALVGLITFGTHVHVHELGFSE-CSKSYVFR 186 (761)
T ss_pred CCCCCCcEEEEEEecchhHHHHH---HHHHHHHHHHHhCCC--CCEEEEEEECCEEEEEEcCCCC-CcceEEec
Confidence 56778999999999999999755 567899999999997 8999999999999999998643 68888887
No 10
>KOG1986|consensus
Probab=97.88 E-value=5.3e-05 Score=67.09 Aligned_cols=64 Identities=14% Similarity=0.064 Sum_probs=54.6
Q ss_pred ceeeeecccCCceeeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCCCCceEEEEEEecCeEEEEecCC
Q psy16628 18 AYYTIVWELGIFKCPLYFMVVKGYACYCKYQALQREVLLNQLKSMPGDRRTSIAIITYDSAVHFYSLAE 86 (107)
Q Consensus 18 ~~~~~~~~~~~~~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs~vhFynl~~ 86 (107)
-+|++.-....|+.|+|+||.-...- -+..+.++|+.+|+.+|. .+.||||||++.||.|.|+.
T Consensus 110 vEy~l~~~~~~ppvf~fVvDtc~~ee---eL~~LkssL~~~l~lLP~--~alvGlItfg~~v~v~el~~ 173 (745)
T KOG1986|consen 110 VEYTLSPGRVSPPVFVFVVDTCMDEE---ELQALKSSLKQSLSLLPE--NALVGLITFGTMVQVHELGF 173 (745)
T ss_pred eEEecCCCCCCCceEEEEEeeccChH---HHHHHHHHHHHHHhhCCC--cceEEEEEecceEEEEEcCC
Confidence 35677644555999999999988774 566778999999999998 89999999999999999976
No 11
>COG5047 SEC23 Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking and secretion]
Probab=97.18 E-value=0.0013 Score=58.01 Aligned_cols=66 Identities=15% Similarity=0.182 Sum_probs=57.4
Q ss_pred CCceeeeecccCCceeeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCCCCceEEEEEEecCeEEEEecCC
Q psy16628 16 SHAYYTIVWELGIFKCPLYFMVVKGYACYCKYQALQREVLLNQLKSMPGDRRTSIAIITYDSAVHFYSLAE 86 (107)
Q Consensus 16 ~~~~~~~~~~~~~~~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs~vhFynl~~ 86 (107)
+.-+|++.-....++.|+|++|+...-- -+.++.++|+.+|..+|. .+.||+|||.+.+|.+.++.
T Consensus 109 sTiey~lskp~~~ppvf~fvvD~~~D~e---~l~~Lkdslivslsllpp--eaLvglItygt~i~v~el~a 174 (755)
T COG5047 109 STIEYTLSKPVILPPVFFFVVDACCDEE---ELTALKDSLIVSLSLLPP--EALVGLITYGTSIQVHELNA 174 (755)
T ss_pred ceEEEEccCCccCCceEEEEEEeecCHH---HHHHHHHHHHHHHhcCCc--cceeeEEEecceeEEEeccc
Confidence 3457888888899999999999988433 577888999999999987 89999999999999999976
No 12
>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=96.74 E-value=0.0067 Score=43.66 Aligned_cols=55 Identities=9% Similarity=0.168 Sum_probs=43.1
Q ss_pred eEEEEEcchhhhhcChHHHHHHHHHHHhhcCCC-CCceEEEEEEecCeEE-EEecCC
Q psy16628 32 PLYFMVVKGYACYCKYQALQREVLLNQLKSMPG-DRRTSIAIITYDSAVH-FYSLAE 86 (107)
Q Consensus 32 yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~-~~~t~IgiITfDs~vh-Fynl~~ 86 (107)
.+|++|+|..--....+..+.+.+++.++.++- +++++||+|+|++..+ .+++..
T Consensus 3 v~~vlD~SgSm~~~~~~~~~k~~~~~~~~~~~~~~~~~~vglv~Fs~~~~~~~~l~~ 59 (186)
T cd01471 3 LYLLVDGSGSIGYSNWVTHVVPFLHTFVQNLNISPDEINLYLVTFSTNAKELIRLSS 59 (186)
T ss_pred EEEEEeCCCCccchhhHHHHHHHHHHHHHhcccCCCceEEEEEEecCCceEEEECCC
Confidence 689999988765554477888888888887753 4589999999999887 566665
No 13
>PF13768 VWA_3: von Willebrand factor type A domain
Probab=96.70 E-value=0.0049 Score=43.05 Aligned_cols=48 Identities=23% Similarity=0.277 Sum_probs=40.8
Q ss_pred eEEEEEcchhhhhcChHHHHHHHHHHHhhcCCCCCceEEEEEEecCeEEEEe
Q psy16628 32 PLYFMVVKGYACYCKYQALQREVLLNQLKSMPGDRRTSIAIITYDSAVHFYS 83 (107)
Q Consensus 32 yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs~vhFyn 83 (107)
-+|+||+|...-... ..+.++++..|++++. +.++.+|+|++..+.|.
T Consensus 3 vvilvD~S~Sm~g~~--~~~k~al~~~l~~L~~--~d~fnii~f~~~~~~~~ 50 (155)
T PF13768_consen 3 VVILVDTSGSMSGEK--ELVKDALRAILRSLPP--GDRFNIIAFGSSVRPLF 50 (155)
T ss_pred EEEEEeCCCCCCCcH--HHHHHHHHHHHHhCCC--CCEEEEEEeCCEeeEcc
Confidence 489999998776443 8899999999999976 78999999999988665
No 14
>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=96.59 E-value=0.0064 Score=42.21 Aligned_cols=54 Identities=11% Similarity=0.285 Sum_probs=39.6
Q ss_pred eEEEEEcchhhhhcChHHHHHHHHHHHhhcC-CCCCceEEEEEEecCeEE-EEecCC
Q psy16628 32 PLYFMVVKGYACYCKYQALQREVLLNQLKSM-PGDRRTSIAIITYDSAVH-FYSLAE 86 (107)
Q Consensus 32 yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~l-p~~~~t~IgiITfDs~vh-Fynl~~ 86 (107)
-+|+||.|...-..+ ++.+.+.++..+..+ ..+.++|||+++|++..+ .+++..
T Consensus 2 ivflvD~S~sm~~~~-~~~~~~~v~~~i~~~~~~~~~~rv~iv~f~~~~~~~~~~~~ 57 (178)
T PF00092_consen 2 IVFLVDTSGSMSGDN-FEKAKQFVKSIISRLSISNNGTRVGIVTFSDSARVLFSLTD 57 (178)
T ss_dssp EEEEEE-STTSCHHH-HHHHHHHHHHHHHHSTBSTTSEEEEEEEESSSEEEEEETTS
T ss_pred EEEEEeCCCCCchHH-HHHHHHHHHHHHHhhhccccccccceeeeeccccccccccc
Confidence 379999998766543 555888888888876 346799999999998885 344543
No 15
>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=96.51 E-value=0.0052 Score=44.15 Aligned_cols=50 Identities=18% Similarity=0.145 Sum_probs=36.6
Q ss_pred eeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCCC----CceEEEEEEecCeEEE
Q psy16628 31 CPLYFMVVKGYACYCKYQALQREVLLNQLKSMPGD----RRTSIAIITYDSAVHF 81 (107)
Q Consensus 31 ~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~~----~~t~IgiITfDs~vhF 81 (107)
-.+|+||+|..- ...-+..+.++++..++.+..+ ++.+||+|+|++..|.
T Consensus 5 ~v~~llD~SgSM-~~~~~~~~k~a~~~~~~~l~~~~~~~~~~~v~ii~F~~~a~~ 58 (176)
T cd01464 5 PIYLLLDTSGSM-AGEPIEALNQGLQMLQSELRQDPYALESVEISVITFDSAARV 58 (176)
T ss_pred CEEEEEECCCCC-CChHHHHHHHHHHHHHHHHhcChhhccccEEEEEEecCCceE
Confidence 357999998744 3334566777777777776542 5789999999998765
No 16
>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=96.34 E-value=0.011 Score=41.72 Aligned_cols=49 Identities=4% Similarity=0.072 Sum_probs=36.2
Q ss_pred eEEEEEcchhhhhcChHHHHHHHHHHHhhcCCC-CCceEEEEEEecCeEEE
Q psy16628 32 PLYFMVVKGYACYCKYQALQREVLLNQLKSMPG-DRRTSIAIITYDSAVHF 81 (107)
Q Consensus 32 yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~-~~~t~IgiITfDs~vhF 81 (107)
-+|++|+|..-- .+-+..+.+.++..+..+.. +.+.++|+|+|++..+-
T Consensus 3 vv~vlD~SgSm~-~~~~~~~k~~~~~~~~~l~~~~~~~~~giv~Fs~~~~~ 52 (164)
T cd01472 3 IVFLVDGSESIG-LSNFNLVKDFVKRVVERLDIGPDGVRVGVVQYSDDPRT 52 (164)
T ss_pred EEEEEeCCCCCC-HHHHHHHHHHHHHHHhhcccCCCCeEEEEEEEcCceeE
Confidence 379999987443 33456677777877777643 35789999999998765
No 17
>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=96.24 E-value=0.014 Score=43.69 Aligned_cols=59 Identities=14% Similarity=0.108 Sum_probs=41.7
Q ss_pred cCCceeeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCC-------CCceEEEEEEecCeEEE-EecC
Q psy16628 26 LGIFKCPLYFMVVKGYACYCKYQALQREVLLNQLKSMPG-------DRRTSIAIITYDSAVHF-YSLA 85 (107)
Q Consensus 26 ~~~~~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~-------~~~t~IgiITfDs~vhF-ynl~ 85 (107)
....+--+|+||.|..--+.+ ++.+.+.++..+..+.. +..+|||+|+|++..|. |+|.
T Consensus 16 ~~~~~DivfvlD~S~Sm~~~~-f~~~k~fi~~~~~~~~~~~~~~~~~~~~rVGlV~fs~~a~~~~~L~ 82 (193)
T cd01477 16 KNLWLDIVFVVDNSKGMTQGG-LWQVRATISSLFGSSSQIGTDYDDPRSTRVGLVTYNSNATVVADLN 82 (193)
T ss_pred ccceeeEEEEEeCCCCcchhh-HHHHHHHHHHHHhhccccccccCCCCCcEEEEEEccCceEEEEecc
Confidence 556788899999998755443 56676777776665443 45799999999988632 3554
No 18
>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=96.23 E-value=0.027 Score=40.98 Aligned_cols=60 Identities=17% Similarity=0.159 Sum_probs=45.4
Q ss_pred ceeeeecccCCceeeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCCCCceEEEEEEecCeEEEE
Q psy16628 18 AYYTIVWELGIFKCPLYFMVVKGYACYCKYQALQREVLLNQLKSMPGDRRTSIAIITYDSAVHFY 82 (107)
Q Consensus 18 ~~~~~~~~~~~~~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs~vhFy 82 (107)
+.|.-.. -.|...+|+||+|..--.+ -+..+.++++..++.++. +.++|+++|++.++..
T Consensus 4 ~~~~~~~--~~p~~vv~llD~SgSM~~~-~l~~ak~~~~~ll~~l~~--~d~v~lv~F~~~~~~~ 63 (190)
T cd01463 4 SWYIQAA--TSPKDIVILLDVSGSMTGQ-RLHLAKQTVSSILDTLSD--NDFFNIITFSNEVNPV 63 (190)
T ss_pred cceeecc--cCCceEEEEEECCCCCCcH-HHHHHHHHHHHHHHhCCC--CCEEEEEEeCCCeeEE
Confidence 4554443 3588899999999754333 456778888888888876 6799999999998864
No 19
>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=96.07 E-value=0.025 Score=37.45 Aligned_cols=50 Identities=14% Similarity=0.207 Sum_probs=40.1
Q ss_pred eeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCC-CCceEEEEEEecCeEEE
Q psy16628 31 CPLYFMVVKGYACYCKYQALQREVLLNQLKSMPG-DRRTSIAIITYDSAVHF 81 (107)
Q Consensus 31 ~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~-~~~t~IgiITfDs~vhF 81 (107)
..+|+||.|... ....+..+.+.+...+..++. .++.++|+++|+...+.
T Consensus 2 ~v~~viD~S~Sm-~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~~f~~~~~~ 52 (161)
T cd00198 2 DIVFLLDVSGSM-GGEKLDKAKEALKALVSSLSASPPGDRVGLVTFGSNARV 52 (161)
T ss_pred cEEEEEeCCCCc-CcchHHHHHHHHHHHHHhcccCCCCcEEEEEEecCccce
Confidence 468999999876 456888888888888888876 45799999999975543
No 20
>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=95.82 E-value=0.021 Score=41.75 Aligned_cols=50 Identities=8% Similarity=0.001 Sum_probs=37.8
Q ss_pred eeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCC-CCceEEEEEEecCeEEE
Q psy16628 31 CPLYFMVVKGYACYCKYQALQREVLLNQLKSMPG-DRRTSIAIITYDSAVHF 81 (107)
Q Consensus 31 ~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~-~~~t~IgiITfDs~vhF 81 (107)
..+|+||+|..- ...=+..+.+.++..++.++. ..+.++|+|+|++..+-
T Consensus 2 di~~vlD~SgSM-~~~~~~~~k~~~~~l~~~l~~~~~~~~v~li~Fs~~~~~ 52 (198)
T cd01470 2 NIYIALDASDSI-GEEDFDEAKNAIKTLIEKISSYEVSPRYEIISYASDPKE 52 (198)
T ss_pred cEEEEEECCCCc-cHHHHHHHHHHHHHHHHHccccCCCceEEEEEecCCceE
Confidence 468999998754 333467778888888888864 34789999999987653
No 21
>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=95.71 E-value=0.033 Score=41.79 Aligned_cols=56 Identities=14% Similarity=0.188 Sum_probs=40.1
Q ss_pred ceeeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCC-CCceEEEEEEecCeEEE-EecC
Q psy16628 29 FKCPLYFMVVKGYACYCKYQALQREVLLNQLKSMPG-DRRTSIAIITYDSAVHF-YSLA 85 (107)
Q Consensus 29 ~~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~-~~~t~IgiITfDs~vhF-ynl~ 85 (107)
+.--+|+||.|..-- .--++.+.+.+++.++.+.- +..+|||+|+|++..+. +.|.
T Consensus 2 ~~DlvfllD~S~Sm~-~~~~~~~k~f~~~l~~~l~~~~~~~rvglv~fs~~~~~~~~l~ 59 (224)
T cd01475 2 PTDLVFLIDSSRSVR-PENFELVKQFLNQIIDSLDVGPDATRVGLVQYSSTVKQEFPLG 59 (224)
T ss_pred CccEEEEEeCCCCCC-HHHHHHHHHHHHHHHHhcccCCCccEEEEEEecCceeEEeccc
Confidence 456799999987533 22466777888887777643 45899999999998764 3443
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=95.58 E-value=0.033 Score=39.54 Aligned_cols=48 Identities=8% Similarity=0.098 Sum_probs=36.4
Q ss_pred eEEEEEcchhhhhcChHHHHHHHHHHHhhcCCC-CCceEEEEEEecCeEE
Q psy16628 32 PLYFMVVKGYACYCKYQALQREVLLNQLKSMPG-DRRTSIAIITYDSAVH 80 (107)
Q Consensus 32 yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~-~~~t~IgiITfDs~vh 80 (107)
.+|++|.|..--+.+ +..+.+.++..+..+.- +++++||+|+|++..+
T Consensus 3 v~~vlD~S~Sm~~~~-~~~~k~~~~~l~~~~~~~~~~~rvgli~fs~~~~ 51 (164)
T cd01482 3 IVFLVDGSWSIGRSN-FNLVRSFLSSVVEAFEIGPDGVQVGLVQYSDDPR 51 (164)
T ss_pred EEEEEeCCCCcChhh-HHHHHHHHHHHHhheeeCCCceEEEEEEECCCee
Confidence 589999987655444 56778888888877643 3589999999998864
No 23
>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=95.52 E-value=0.049 Score=37.85 Aligned_cols=51 Identities=22% Similarity=0.286 Sum_probs=39.8
Q ss_pred ceeeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCCCCceEEEEEEecCeEEEE
Q psy16628 29 FKCPLYFMVVKGYACYCKYQALQREVLLNQLKSMPGDRRTSIAIITYDSAVHFY 82 (107)
Q Consensus 29 ~~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs~vhFy 82 (107)
|...+|++|+|..--. .-+..+.+++...+..++. ..++++++|++..+.+
T Consensus 2 ~~~v~~vlD~S~SM~~-~~~~~~~~al~~~l~~l~~--~~~~~l~~Fs~~~~~~ 52 (171)
T cd01461 2 PKEVVFVIDTSGSMSG-TKIEQTKEALLTALKDLPP--GDYFNIIGFSDTVEEF 52 (171)
T ss_pred CceEEEEEECCCCCCC-hhHHHHHHHHHHHHHhCCC--CCEEEEEEeCCCceee
Confidence 5678999999976542 2367778888888888876 5689999999988764
No 24
>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=95.51 E-value=0.04 Score=40.56 Aligned_cols=53 Identities=11% Similarity=0.039 Sum_probs=41.3
Q ss_pred ccCCceeeEEEEEcchhhhh-----cChHHHHHHHHHHHhhcCCCCCceEEEEEEecCeE
Q psy16628 25 ELGIFKCPLYFMVVKGYACY-----CKYQALQREVLLNQLKSMPGDRRTSIAIITYDSAV 79 (107)
Q Consensus 25 ~~~~~~~yvFvIDVS~~Ai~-----sG~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs~v 79 (107)
+...+...+|+||+|..--. ..-+..+.++++..++.++. +.+||+++|++..
T Consensus 16 ~~~~~~~vv~vlD~SgSM~~~~~~~~~rl~~ak~a~~~~l~~l~~--~~~v~lv~F~~~~ 73 (206)
T cd01456 16 EPQLPPNVAIVLDNSGSMREVDGGGETRLDNAKAALDETANALPD--GTRLGLWTFSGDG 73 (206)
T ss_pred ccCCCCcEEEEEeCCCCCcCCCCCcchHHHHHHHHHHHHHHhCCC--CceEEEEEecCCC
Confidence 45668899999999875431 22567788888888888865 6899999999854
No 25
>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=95.40 E-value=0.05 Score=37.87 Aligned_cols=49 Identities=20% Similarity=0.196 Sum_probs=38.0
Q ss_pred eeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCCCCceEEEEEEecCeEEEE
Q psy16628 31 CPLYFMVVKGYACYCKYQALQREVLLNQLKSMPGDRRTSIAIITYDSAVHFY 82 (107)
Q Consensus 31 ~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs~vhFy 82 (107)
.++|++|+|..--... +..+.++++..+..++. +.+||+++|++..+..
T Consensus 2 ~~~~vlD~S~SM~~~~-~~~~k~a~~~~~~~l~~--~~~v~li~f~~~~~~~ 50 (170)
T cd01465 2 NLVFVIDRSGSMDGPK-LPLVKSALKLLVDQLRP--DDRLAIVTYDGAAETV 50 (170)
T ss_pred cEEEEEECCCCCCChh-HHHHHHHHHHHHHhCCC--CCEEEEEEecCCccEE
Confidence 4789999998554333 67777888888888866 6799999999877653
No 26
>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=95.39 E-value=0.05 Score=39.38 Aligned_cols=53 Identities=11% Similarity=0.175 Sum_probs=39.4
Q ss_pred eEEEEEcchhhhhcChHHHHHHHHHHHhhcCCC-CCceEEEEEEecCeEEE-EecC
Q psy16628 32 PLYFMVVKGYACYCKYQALQREVLLNQLKSMPG-DRRTSIAIITYDSAVHF-YSLA 85 (107)
Q Consensus 32 yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~-~~~t~IgiITfDs~vhF-ynl~ 85 (107)
.+|+||.|..--.. -++.+.+.+++.++++.. ++.+|||+|+|.+..+. ++|.
T Consensus 3 i~fvlD~S~S~~~~-~f~~~k~fi~~~i~~l~~~~~~~rvgvv~fs~~~~~~~~l~ 57 (177)
T cd01469 3 IVFVLDGSGSIYPD-DFQKVKNFLSTVMKKLDIGPTKTQFGLVQYSESFRTEFTLN 57 (177)
T ss_pred EEEEEeCCCCCCHH-HHHHHHHHHHHHHHHcCcCCCCcEEEEEEECCceeEEEecC
Confidence 58999998764433 466777888888887765 45899999999988653 3554
No 27
>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=95.35 E-value=0.054 Score=37.15 Aligned_cols=52 Identities=8% Similarity=0.125 Sum_probs=39.2
Q ss_pred eeeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCC-CCceEEEEEEecCeEEEE
Q psy16628 30 KCPLYFMVVKGYACYCKYQALQREVLLNQLKSMPG-DRRTSIAIITYDSAVHFY 82 (107)
Q Consensus 30 ~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~-~~~t~IgiITfDs~vhFy 82 (107)
...+|++|+|..-- ..-+..+.+.+...+..++. ++..+||+++|++..+-+
T Consensus 2 ~~v~l~vD~S~SM~-~~~~~~~~~~~~~~~~~~~~~~~~~~i~ii~f~~~~~~~ 54 (177)
T smart00327 2 LDVVFLLDGSGSMG-PNRFEKAKEFVLKLVEQLDIGPDGDRVGLVTFSDDATVL 54 (177)
T ss_pred ccEEEEEeCCCccc-hHHHHHHHHHHHHHHHhcCCCCCCcEEEEEEeCCCceEE
Confidence 45789999987664 34667777778888877765 458999999999876443
No 28
>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=95.32 E-value=0.04 Score=38.96 Aligned_cols=48 Identities=15% Similarity=0.175 Sum_probs=35.5
Q ss_pred eEEEEEcchhhhhcChHHHHHHHHHHHhhcCCCCCceEEEEEEecCeEEEE
Q psy16628 32 PLYFMVVKGYACYCKYQALQREVLLNQLKSMPGDRRTSIAIITYDSAVHFY 82 (107)
Q Consensus 32 yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs~vhFy 82 (107)
.+|+||.|..- ...=+..+.++++..++.++. +.++|+|+|++..|-.
T Consensus 3 v~~vlD~S~SM-~~~rl~~ak~a~~~l~~~l~~--~~~~~li~F~~~~~~~ 50 (155)
T cd01466 3 LVAVLDVSGSM-AGDKLQLVKHALRFVISSLGD--ADRLSIVTFSTSAKRL 50 (155)
T ss_pred EEEEEECCCCC-CcHHHHHHHHHHHHHHHhCCC--cceEEEEEecCCcccc
Confidence 47899998744 222356677788888888876 6789999999876543
No 29
>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=95.22 E-value=0.098 Score=40.56 Aligned_cols=63 Identities=8% Similarity=0.113 Sum_probs=45.9
Q ss_pred CCCceeeeeccc--CCceeeEEEEEcchhhhhcChHHHHHHHHHHHhhc-CCCCCceEEEEEEecCeEEE
Q psy16628 15 NSHAYYTIVWEL--GIFKCPLYFMVVKGYACYCKYQALQREVLLNQLKS-MPGDRRTSIAIITYDSAVHF 81 (107)
Q Consensus 15 ~~~~~~~~~~~~--~~~~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~-lp~~~~t~IgiITfDs~vhF 81 (107)
+.++.++-..+. ..|+..+|++|+|..-- +-+..+.++++..|+. ++ ++.++|+++|++.++.
T Consensus 37 ~g~~q~i~~f~~~~~~p~~vvlvlD~SgSM~--~~~~~a~~a~~~~l~~~l~--~~d~v~lv~f~~~~~~ 102 (296)
T TIGR03436 37 DGKPQTIASFRRETDLPLTVGLVIDTSGSMR--NDLDRARAAAIRFLKTVLR--PNDRVFVVTFNTRLRL 102 (296)
T ss_pred CCeEEEEEEEecCCCCCceEEEEEECCCCch--HHHHHHHHHHHHHHHhhCC--CCCEEEEEEeCCceeE
Confidence 345555555443 35899999999997543 2466777888888876 54 3799999999999876
No 30
>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=95.00 E-value=0.072 Score=45.83 Aligned_cols=52 Identities=17% Similarity=0.247 Sum_probs=42.1
Q ss_pred CceeeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCCCCceEEEEEEecCeEEEE
Q psy16628 28 IFKCPLYFMVVKGYACYCKYQALQREVLLNQLKSMPGDRRTSIAIITYDSAVHFY 82 (107)
Q Consensus 28 ~~~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs~vhFy 82 (107)
.+..++|+||+|..-- .+-+..+.+++...|.+++. +.++++|+||+.++.+
T Consensus 270 ~p~~vvfvlD~SgSM~-g~~i~~ak~al~~~l~~L~~--~d~~~ii~F~~~~~~~ 321 (596)
T TIGR03788 270 LPRELVFVIDTSGSMA-GESIEQAKSALLLALDQLRP--GDRFNIIQFDSDVTLL 321 (596)
T ss_pred CCceEEEEEECCCCCC-CccHHHHHHHHHHHHHhCCC--CCEEEEEEECCcceEe
Confidence 4667999999998543 33467788889988999876 6799999999999865
No 31
>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=95.00 E-value=0.08 Score=35.92 Aligned_cols=49 Identities=6% Similarity=0.127 Sum_probs=36.7
Q ss_pred eEEEEEcchhhhhcChHHHHHHHHHHHhhcCCC-CCceEEEEEEecCeEEE
Q psy16628 32 PLYFMVVKGYACYCKYQALQREVLLNQLKSMPG-DRRTSIAIITYDSAVHF 81 (107)
Q Consensus 32 yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~-~~~t~IgiITfDs~vhF 81 (107)
.+|++|+|..- ...-+..+.+.+.+.+..+.. +++.++|+++|++..+.
T Consensus 3 i~~llD~S~Sm-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~f~~~~~~ 52 (161)
T cd01450 3 IVFLLDGSESV-GPENFEKVKDFIEKLVEKLDIGPDKTRVGLVQYSDDVRV 52 (161)
T ss_pred EEEEEeCCCCc-CHHHHHHHHHHHHHHHHheeeCCCceEEEEEEEcCCceE
Confidence 46899998754 333667777888888877754 46899999999976654
No 32
>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=94.69 E-value=0.087 Score=38.14 Aligned_cols=54 Identities=7% Similarity=0.137 Sum_probs=39.7
Q ss_pred eEEEEEcchhhhhcChHHHHHHHHHHHhhcCCC-CCceEEEEEEecCeEE-EEecCC
Q psy16628 32 PLYFMVVKGYACYCKYQALQREVLLNQLKSMPG-DRRTSIAIITYDSAVH-FYSLAE 86 (107)
Q Consensus 32 yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~-~~~t~IgiITfDs~vh-Fynl~~ 86 (107)
-+|++|.|. ++...-++.+.+-+++.++.++- +..+|||+|+|.+..+ -|+|..
T Consensus 3 ivfllD~S~-Si~~~~f~~~k~fi~~lv~~f~i~~~~~rVgvv~ys~~~~~~~~l~~ 58 (165)
T cd01481 3 IVFLIDGSD-NVGSGNFPAIRDFIERIVQSLDVGPDKIRVAVVQFSDTPRPEFYLNT 58 (165)
T ss_pred EEEEEeCCC-CcCHHHHHHHHHHHHHHHhhccCCCCCcEEEEEEecCCeeEEEeccc
Confidence 479999976 44445677888888888888764 5689999999987653 345543
No 33
>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=94.64 E-value=0.16 Score=35.48 Aligned_cols=44 Identities=18% Similarity=0.232 Sum_probs=33.6
Q ss_pred eEEEEEcchhhhhcChHHHHHHHHHHHhhcCCC-CCceEEEEEEecC
Q psy16628 32 PLYFMVVKGYACYCKYQALQREVLLNQLKSMPG-DRRTSIAIITYDS 77 (107)
Q Consensus 32 yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~-~~~t~IgiITfDs 77 (107)
.+|++|+|..- ..+ +....+.+++.+..+.. ..+.+||+|+|++
T Consensus 3 v~~llD~S~Sm-~~~-~~~~~~~~~~~~~~l~~~~~~~~v~lv~f~~ 47 (163)
T cd01476 3 LLFVLDSSGSV-RGK-FEKYKKYIERIVEGLEIGPTATRVALITYSG 47 (163)
T ss_pred EEEEEeCCcch-hhh-HHHHHHHHHHHHHhcCCCCCCcEEEEEEEcC
Confidence 58999998744 333 56677778888877753 4579999999999
No 34
>PF13519 VWA_2: von Willebrand factor type A domain; PDB: 3IBS_B 3RAG_B 2X5N_A.
Probab=94.10 E-value=0.18 Score=34.38 Aligned_cols=45 Identities=11% Similarity=0.296 Sum_probs=34.9
Q ss_pred eEEEEEcchhhhhcC----hHHHHHHHHHHHhhcCCCCCceEEEEEEecCeE
Q psy16628 32 PLYFMVVKGYACYCK----YQALQREVLLNQLKSMPGDRRTSIAIITYDSAV 79 (107)
Q Consensus 32 yvFvIDVS~~Ai~sG----~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs~v 79 (107)
.+|++|+|..--..+ ....+.+++...+.++|+ .+||+++|++..
T Consensus 2 vv~v~D~SgSM~~~~~~~~~~~~~~~~~~~~~~~~~~---~~v~l~~f~~~~ 50 (172)
T PF13519_consen 2 VVFVLDNSGSMNGYDGNRTRIDQAKDALNELLANLPG---DRVGLVSFSDSS 50 (172)
T ss_dssp EEEEEE-SGGGGTTTSSS-HHHHHHHHHHHHHHHHTT---SEEEEEEESTSC
T ss_pred EEEEEECCcccCCCCCCCcHHHHHHHHHHHHHHHCCC---CEEEEEEecccc
Confidence 489999998665442 578888888888888775 399999999754
No 35
>COG4245 TerY Uncharacterized protein encoded in toxicity protection region of plasmid R478, contains von Willebrand factor (vWF) domain [General function prediction only]
Probab=94.07 E-value=0.13 Score=39.90 Aligned_cols=50 Identities=10% Similarity=0.119 Sum_probs=33.4
Q ss_pred EEEEEcchhhhhcChHHHHHHHHHHHhhcCCC----CCceEEEEEEecCeEEEEe
Q psy16628 33 LYFMVVKGYACYCKYQALQREVLLNQLKSMPG----DRRTSIAIITYDSAVHFYS 83 (107)
Q Consensus 33 vFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~----~~~t~IgiITfDs~vhFyn 83 (107)
++++|+|-.-+. --++++-..|...++.|.. .++..++|||||+..+-+.
T Consensus 7 ~lllDtSgSM~G-e~IealN~Glq~m~~~Lkqdp~Ale~v~lsIVTF~~~a~~~~ 60 (207)
T COG4245 7 YLLLDTSGSMIG-EPIEALNAGLQMMIDTLKQDPYALERVELSIVTFGGPARVIQ 60 (207)
T ss_pred EEEEecCccccc-ccHHHHHHHHHHHHHHHHhChhhhheeEEEEEEecCcceEEe
Confidence 478999975442 2444555555555554443 3789999999998887763
No 36
>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=93.72 E-value=0.15 Score=37.76 Aligned_cols=49 Identities=4% Similarity=0.059 Sum_probs=36.3
Q ss_pred eEEEEEcchhhhhcChHHHHHHHHHHHhhcCCC-CCceEEEEEEecCeEE
Q psy16628 32 PLYFMVVKGYACYCKYQALQREVLLNQLKSMPG-DRRTSIAIITYDSAVH 80 (107)
Q Consensus 32 yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~-~~~t~IgiITfDs~vh 80 (107)
-+|++|.|..--+..+-..+.+-++..++.+.- ..++|||+|+|.+..+
T Consensus 3 i~fllD~S~Si~~~~f~~~~~~f~~~lv~~l~i~~~~~rvgvv~fs~~~~ 52 (192)
T cd01473 3 LTLILDESASIGYSNWRKDVIPFTEKIINNLNISKDKVHVGILLFAEKNR 52 (192)
T ss_pred EEEEEeCCCcccHHHHHHHHHHHHHHHHHhCccCCCccEEEEEEecCCce
Confidence 479999988766555544566667777766653 4589999999998775
No 37
>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=93.68 E-value=0.18 Score=36.61 Aligned_cols=56 Identities=2% Similarity=-0.024 Sum_probs=36.9
Q ss_pred ceeeEEEEEcchhhhhcChHHHHHHHHHHHhhcC------CC-CCceEEEEEEecCeEE-EEecC
Q psy16628 29 FKCPLYFMVVKGYACYCKYQALQREVLLNQLKSM------PG-DRRTSIAIITYDSAVH-FYSLA 85 (107)
Q Consensus 29 ~~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~l------p~-~~~t~IgiITfDs~vh-Fynl~ 85 (107)
+.--+|++|.|..--.+. ++...+.++..++.+ +. +.+.|||+|+|++..+ .+.+.
T Consensus 2 ~~dvv~vlD~S~Sm~~~~-~~~~k~~~~~~~~~l~~~~~~~i~~~~~rvglv~fs~~~~~~~~l~ 65 (186)
T cd01480 2 PVDITFVLDSSESVGLQN-FDITKNFVKRVAERFLKDYYRKDPAGSWRVGVVQYSDQQEVEAGFL 65 (186)
T ss_pred CeeEEEEEeCCCccchhh-HHHHHHHHHHHHHHHhhhhccCCCCCceEEEEEEecCCceeeEecc
Confidence 345689999987554343 445566666666665 22 3479999999998753 34443
No 38
>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=93.09 E-value=0.37 Score=34.82 Aligned_cols=54 Identities=7% Similarity=0.122 Sum_probs=34.6
Q ss_pred ceeeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCCCCceEEEEEEecCeEE-EEecC
Q psy16628 29 FKCPLYFMVVKGYACYCKYQALQREVLLNQLKSMPGDRRTSIAIITYDSAVH-FYSLA 85 (107)
Q Consensus 29 ~~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs~vh-Fynl~ 85 (107)
++-.+|+||.|..-- .... ...+.+++.++.+-. +++|||+|+|++..+ .+.+.
T Consensus 4 ~~Dvv~llD~SgSm~-~~~~-~~~~~~~~l~~~~~~-~~~rvglv~Fs~~~~~~~~l~ 58 (185)
T cd01474 4 HFDLYFVLDKSGSVA-ANWI-EIYDFVEQLVDRFNS-PGLRFSFITFSTRATKILPLT 58 (185)
T ss_pred ceeEEEEEeCcCchh-hhHH-HHHHHHHHHHHHcCC-CCcEEEEEEecCCceEEEecc
Confidence 456789999987643 2232 334556666665533 459999999998654 33443
No 39
>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=92.92 E-value=0.38 Score=33.93 Aligned_cols=49 Identities=14% Similarity=0.150 Sum_probs=32.8
Q ss_pred eeeEEEEEcchhhhhcC-----hHHHHHHHHHHHhhcCCCCCceEEEEEEecCeEEE
Q psy16628 30 KCPLYFMVVKGYACYCK-----YQALQREVLLNQLKSMPGDRRTSIAIITYDSAVHF 81 (107)
Q Consensus 30 ~~yvFvIDVS~~Ai~sG-----~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs~vhF 81 (107)
...+|++|+|..--... -+..+.+.+...+...| +.+||+++|++..+.
T Consensus 3 ~~vv~vlD~S~SM~~~~~~~~~r~~~a~~~~~~~~~~~~---~~~v~lv~f~~~~~~ 56 (180)
T cd01467 3 RDIMIALDVSGSMLAQDFVKPSRLEAAKEVLSDFIDRRE---NDRIGLVVFAGAAFT 56 (180)
T ss_pred ceEEEEEECCcccccccCCCCCHHHHHHHHHHHHHHhCC---CCeEEEEEEcCCeee
Confidence 35789999987532211 24555666666665544 579999999998764
No 40
>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=92.63 E-value=0.48 Score=34.85 Aligned_cols=55 Identities=11% Similarity=0.073 Sum_probs=38.2
Q ss_pred CCceeeEEEEEcchhhhhcC----hHHHHHHHHHHHhhcCCC-CCceEEEEEEe-cCeEEE
Q psy16628 27 GIFKCPLYFMVVKGYACYCK----YQALQREVLLNQLKSMPG-DRRTSIAIITY-DSAVHF 81 (107)
Q Consensus 27 ~~~~~yvFvIDVS~~Ai~sG----~l~~~~~sIk~~L~~lp~-~~~t~IgiITf-Ds~vhF 81 (107)
|+...-+++||+|..-.++- =+..+.+.+...++++.. ++..+||+|+| ++.-|.
T Consensus 1 ~~~r~ivi~lD~S~SM~a~D~~ptRl~~ak~~~~~fi~~~~~~~~~~~vglv~f~~~~a~~ 61 (183)
T cd01453 1 GIMRHLIIVIDCSRSMEEQDLKPSRLAVVLKLLELFIEEFFDQNPISQLGIISIKNGRAEK 61 (183)
T ss_pred CceeEEEEEEECcHHHhcCCCCchHHHHHHHHHHHHHHHHhhcCccccEEEEEEcCCccEE
Confidence 56678899999998865443 455666666666665433 35689999999 665544
No 41
>PRK13685 hypothetical protein; Provisional
Probab=92.08 E-value=0.57 Score=37.39 Aligned_cols=52 Identities=8% Similarity=0.029 Sum_probs=40.8
Q ss_pred CceeeEEEEEcchhhhhc----ChHHHHHHHHHHHhhcCCCCCceEEEEEEecCeEEE
Q psy16628 28 IFKCPLYFMVVKGYACYC----KYQALQREVLLNQLKSMPGDRRTSIAIITYDSAVHF 81 (107)
Q Consensus 28 ~~~~yvFvIDVS~~Ai~s----G~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs~vhF 81 (107)
.....+|++|+|..=... .=+..+.+.+++.+++++. +.+||+|+|++..+.
T Consensus 87 ~~~~vvlvlD~S~SM~~~D~~p~RL~~ak~~~~~~l~~l~~--~d~vglv~Fa~~a~~ 142 (326)
T PRK13685 87 NRAVVMLVIDVSQSMRATDVEPNRLAAAQEAAKQFADELTP--GINLGLIAFAGTATV 142 (326)
T ss_pred CCceEEEEEECCccccCCCCCCCHHHHHHHHHHHHHHhCCC--CCeEEEEEEcCceee
Confidence 345789999998764432 3577888889999998865 578999999999875
No 42
>PTZ00441 sporozoite surface protein 2 (SSP2); Provisional
Probab=89.73 E-value=1 Score=39.75 Aligned_cols=59 Identities=8% Similarity=0.084 Sum_probs=44.7
Q ss_pred CceeeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCC-CCceEEEEEEecCeEE-EEecCC
Q psy16628 28 IFKCPLYFMVVKGYACYCKYQALQREVLLNQLKSMPG-DRRTSIAIITYDSAVH-FYSLAE 86 (107)
Q Consensus 28 ~~~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~-~~~t~IgiITfDs~vh-Fynl~~ 86 (107)
..+-.+|+||+|..--...++..+..-++..++.+.. ..+++||+++|++..+ ++.+.+
T Consensus 41 ~~lDIvFLLD~SgSMg~~Nfle~AK~Fa~~LV~~l~Is~D~V~VgiV~FSd~~r~vfpL~s 101 (576)
T PTZ00441 41 EEVDLYLLVDGSGSIGYHNWITHVIPMLMGLIQQLNLSDDAINLYMSLFSNNTTELIRLGS 101 (576)
T ss_pred CCceEEEEEeCCCccCCccHHHHHHHHHHHHHHHhccCCCceEEEEEEeCCCceEEEecCC
Confidence 4678899999987665566667777777777777754 4589999999998874 566654
No 43
>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=88.62 E-value=0.81 Score=32.55 Aligned_cols=47 Identities=6% Similarity=0.084 Sum_probs=31.5
Q ss_pred eeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCCCCceEEEEEEecCe
Q psy16628 31 CPLYFMVVKGYACYCKYQALQREVLLNQLKSMPGDRRTSIAIITYDSA 78 (107)
Q Consensus 31 ~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs~ 78 (107)
+.+|++|+|..=-...=++.+.+++...++.+.. .+-++|+++|++.
T Consensus 2 ~v~~llD~SgSM~~~~kl~~ak~a~~~l~~~l~~-~~d~~~l~~F~~~ 48 (174)
T cd01454 2 AVTLLLDLSGSMRSDRRIDVAKKAAVLLAEALEA-CGVPHAILGFTTD 48 (174)
T ss_pred EEEEEEECCCCCCCCcHHHHHHHHHHHHHHHHHH-cCCcEEEEEecCC
Confidence 5789999997543223455566665555555543 3679999999876
No 44
>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=88.53 E-value=1.4 Score=31.72 Aligned_cols=46 Identities=17% Similarity=0.304 Sum_probs=30.0
Q ss_pred eEEEEEcchhhhhcChHHHHHHHHHHHhhcCCCCCceEEEEEEecCe
Q psy16628 32 PLYFMVVKGYACYCKYQALQREVLLNQLKSMPGDRRTSIAIITYDSA 78 (107)
Q Consensus 32 yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs~ 78 (107)
.+|+||+|..=-...=+..+.+.+...+..... ++.++|+++|++.
T Consensus 3 v~lvlD~SgSM~~~~rl~~ak~a~~~~~~~~~~-~~d~v~lv~F~~~ 48 (178)
T cd01451 3 VIFVVDASGSMAARHRMAAAKGAVLSLLRDAYQ-RRDKVALIAFRGT 48 (178)
T ss_pred EEEEEECCccCCCccHHHHHHHHHHHHHHHhhc-CCCEEEEEEECCC
Confidence 578999997433221355666666666654322 3789999999864
No 45
>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=88.00 E-value=1.6 Score=37.98 Aligned_cols=60 Identities=7% Similarity=0.051 Sum_probs=41.0
Q ss_pred ceeeeecccCCceeeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCCCCceEEEEEEecCeE
Q psy16628 18 AYYTIVWELGIFKCPLYFMVVKGYACYCKYQALQREVLLNQLKSMPGDRRTSIAIITYDSAV 79 (107)
Q Consensus 18 ~~~~~~~~~~~~~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs~v 79 (107)
.+|.-.-+.......+|++|.|. |...+=+..+.+++...+...-. ++-+||+|+|++.-
T Consensus 396 dl~~k~~~~~~~~~v~fvvD~SG-SM~~~rl~~aK~av~~Ll~~~~~-~~D~v~Li~F~~~~ 455 (589)
T TIGR02031 396 DIRIKRYRRKSGRLLIFVVDASG-SAAVARMSEAKGAVELLLGEAYV-HRDQVSLIAFRGTA 455 (589)
T ss_pred cceEEeeccccCceEEEEEECCC-CCChHHHHHHHHHHHHHHHhhcc-CCCEEEEEEECCCC
Confidence 34555555566777889999998 44444567777787777764311 25689999998543
No 46
>cd01458 vWA_ku Ku70/Ku80 N-terminal domain. The Ku78 heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks (DSB) in a preferred orientation. DSB's are repaired by either homologues recombination or non-homologues end joining and facilitate repair by the non-homologous end-joining pathway (NHEJ). The Ku heterodimer is required for accurate process that tends to preserve the sequence at the junction. Ku78 is found in all three kingdoms of life. However, only the eukaryotic proteins have a vWA domain fused to them at their N-termini. The vWA domain is not involved in DNA binding but may very likey mediate Ku78's interactions with other proteins. Members of this subgroup lack the conserved MIDAS motif.
Probab=87.87 E-value=1.8 Score=32.26 Aligned_cols=48 Identities=8% Similarity=0.076 Sum_probs=33.6
Q ss_pred eeEEEEEcchhhhh------cChHHHHHHHHHHHhhcC-CCCCceEEEEEEecCe
Q psy16628 31 CPLYFMVVKGYACY------CKYQALQREVLLNQLKSM-PGDRRTSIAIITYDSA 78 (107)
Q Consensus 31 ~yvFvIDVS~~Ai~------sG~l~~~~~sIk~~L~~l-p~~~~t~IgiITfDs~ 78 (107)
+-+|+||||..=.+ ..-++.+.+.+...+.+. -..+.-+||+|.|.+.
T Consensus 3 ~ivf~iDvS~SM~~~~~~~~~s~l~~a~~~i~~~~~~ki~~~~~D~vGlilf~t~ 57 (218)
T cd01458 3 SVVFLVDVSPSMFESKDGEYESPFEEALKCIRQLMKSKIISSPKDLVGVVFYGTE 57 (218)
T ss_pred EEEEEEeCCHHHcCCCCCCCCChHHHHHHHHHHHHHhceeCCCCCeEEEEEEccc
Confidence 46899999985431 235677777777777642 1234589999999876
No 47
>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=87.60 E-value=3 Score=36.37 Aligned_cols=69 Identities=7% Similarity=0.138 Sum_probs=42.9
Q ss_pred eeeEEEEEcchhhhh-------cChHHHHHHHHHHHhhc-CCCCCceEEEEEEecCeEEEEecCCCCCCccEEEeCCCCC
Q psy16628 30 KCPLYFMVVKGYACY-------CKYQALQREVLLNQLKS-MPGDRRTSIAIITYDSAVHFYSLAEGQTQPSQMILTDIDD 101 (107)
Q Consensus 30 ~~yvFvIDVS~~Ai~-------sG~l~~~~~sIk~~L~~-lp~~~~t~IgiITfDs~vhFynl~~~l~~pqmlVVsDldd 101 (107)
=+-+|+||||..-.+ ..-+..+.+++...+.+ +=..++..||++.|.+.=. ++.++-+..+|+.||+.
T Consensus 11 eailflIDvs~sM~~~~~~~~~~s~~~~al~~i~~l~q~kIis~~~D~vGivlfgT~~t----~n~~~~~~i~v~~~L~~ 86 (584)
T TIGR00578 11 DSLIFLVDASKAMFEESQGEDELTPFDMSIQCIQSVYTSKIISSDKDLLAVVFYGTEKD----KNSVNFKNIYVLQELDN 86 (584)
T ss_pred eEEEEEEECCHHHcCCCcCcCcCChHHHHHHHHHHHHHhcCCCCCCCeEEEEEEeccCC----CCccCCCceEEEeeCCC
Confidence 367999999988553 12345566666665542 2224679999998865322 22334456777777775
Q ss_pred C
Q psy16628 102 I 102 (107)
Q Consensus 102 ~ 102 (107)
|
T Consensus 87 p 87 (584)
T TIGR00578 87 P 87 (584)
T ss_pred C
Confidence 5
No 48
>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=86.72 E-value=2 Score=29.61 Aligned_cols=50 Identities=14% Similarity=0.135 Sum_probs=30.6
Q ss_pred eEEEEEcchhhhhcChHHHHHHHHHHHhhcCCCCCceEEEEEEecCeEEEEe
Q psy16628 32 PLYFMVVKGYACYCKYQALQREVLLNQLKSMPGDRRTSIAIITYDSAVHFYS 83 (107)
Q Consensus 32 yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs~vhFyn 83 (107)
.+|+||+|..--. +-...+.+.+...+..+.. .+.++++++|++..+.+.
T Consensus 3 v~illD~SgSM~~-~k~~~a~~~~~~l~~~~~~-~~~~v~li~F~~~~~~~~ 52 (152)
T cd01462 3 VILLVDQSGSMYG-APEEVAKAVALALLRIALA-ENRDTYLILFDSEFQTKI 52 (152)
T ss_pred EEEEEECCCCCCC-CHHHHHHHHHHHHHHHHHH-cCCcEEEEEeCCCceEEe
Confidence 6899999975432 2233444444444444432 256899999999855443
No 49
>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=85.81 E-value=1.1 Score=33.95 Aligned_cols=47 Identities=9% Similarity=0.106 Sum_probs=30.2
Q ss_pred eeEEEEEcchhhhhcCh----HHHHHHHHHHHh-hcCCCCCceEEEEEEecC
Q psy16628 31 CPLYFMVVKGYACYCKY----QALQREVLLNQL-KSMPGDRRTSIAIITYDS 77 (107)
Q Consensus 31 ~yvFvIDVS~~Ai~sG~----l~~~~~sIk~~L-~~lp~~~~t~IgiITfDs 77 (107)
+-+++||+|....+.-+ +.++.+.+...+ +.+...+..+||+|+|-.
T Consensus 5 a~vi~lD~S~sM~a~D~~PnRL~aak~~i~~~~~~f~~~np~~~vGlv~fag 56 (187)
T cd01452 5 ATMICIDNSEYMRNGDYPPTRFQAQADAVNLICQAKTRSNPENNVGLMTMAG 56 (187)
T ss_pred EEEEEEECCHHHHcCCCCCCHHHHHHHHHHHHHHHHHhcCCCccEEEEEecC
Confidence 56899999998775444 344444444443 111234457999999987
No 50
>TIGR00868 hCaCC calcium-activated chloride channel protein 1. distributions. found a row in 1A13.INFO that was not parsed out
Probab=85.78 E-value=3 Score=38.43 Aligned_cols=61 Identities=10% Similarity=0.031 Sum_probs=39.3
Q ss_pred ceeeeecccCCceeeEEEEEcchhhhhcChHHHHHHHHHHHhhc-CCCCCceEEEEEEecCeEEEE
Q psy16628 18 AYYTIVWELGIFKCPLYFMVVKGYACYCKYQALQREVLLNQLKS-MPGDRRTSIAIITYDSAVHFY 82 (107)
Q Consensus 18 ~~~~~~~~~~~~~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~-lp~~~~t~IgiITfDs~vhFy 82 (107)
|-|.+.-+.+ ...+++||+|..=-...-+..+-++++..|.+ ++. +.+||+|+||+..+..
T Consensus 295 P~Fs~lq~~~--r~VVLVLDvSGSM~g~dRL~~lkqAA~~fL~~~l~~--~DrVGLVtFsssA~vl 356 (863)
T TIGR00868 295 PTFSLLKIRQ--RIVCLVLDKSGSMTVEDRLKRMNQAAKLFLLQTVEK--GSWVGMVTFDSAAYIK 356 (863)
T ss_pred CceeecccCC--ceEEEEEECCccccccCHHHHHHHHHHHHHHHhCCC--CCEEEEEEECCceeEe
Confidence 4444443333 34899999998643323455566666665543 443 7899999999987653
No 51
>PF09967 DUF2201: VWA-like domain (DUF2201); InterPro: IPR018698 This family of various hypothetical bacterial proteins has no known function.
Probab=80.37 E-value=5.2 Score=27.97 Aligned_cols=44 Identities=11% Similarity=0.091 Sum_probs=33.9
Q ss_pred EEEEEcchhhhhcChHHHHHHHHHHHhhcCCCCCceEEEEEEecCeEEE
Q psy16628 33 LYFMVVKGYACYCKYQALQREVLLNQLKSMPGDRRTSIAIITYDSAVHF 81 (107)
Q Consensus 33 vFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs~vhF 81 (107)
+++||+|.. +....++.++..+...+.+. +.+|-++.||..||=
T Consensus 2 ~vaiDtSGS-is~~~l~~fl~ev~~i~~~~----~~~v~vi~~D~~v~~ 45 (126)
T PF09967_consen 2 VVAIDTSGS-ISDEELRRFLSEVAGILRRF----PAEVHVIQFDAEVQD 45 (126)
T ss_pred EEEEECCCC-CCHHHHHHHHHHHHHHHHhC----CCCEEEEEECCEeee
Confidence 578999864 44457888888888888776 346999999999864
No 52
>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=78.43 E-value=4.5 Score=29.91 Aligned_cols=48 Identities=2% Similarity=0.114 Sum_probs=27.5
Q ss_pred eeEEEEEcchhhhhc-----ChHHHHHHHHHHHhhc-CCCCCceEEEEEEecCe
Q psy16628 31 CPLYFMVVKGYACYC-----KYQALQREVLLNQLKS-MPGDRRTSIAIITYDSA 78 (107)
Q Consensus 31 ~yvFvIDVS~~Ai~s-----G~l~~~~~sIk~~L~~-lp~~~~t~IgiITfDs~ 78 (107)
+=+|+||+|..=.+. +-+..+++++...+.+ +-..+...||++.|.+.
T Consensus 1 ~~vflID~s~sM~~~~~~~~~~l~~al~~i~~~~~~ki~~~~kD~vgvvl~gt~ 54 (224)
T PF03731_consen 1 ATVFLIDVSPSMFEPSSESESPLEEALKAIEDLMQQKIISSPKDEVGVVLFGTD 54 (224)
T ss_dssp EEEEEEE-SCGGGS-BTTCS-HHHHHHHHHHHHHHHHHHTT---EEEEEEES-S
T ss_pred CEEEEEECCHHHCCCCCCcchhHHHHHHHHHHHHHHHHcCCCCCeEEEEEEcCC
Confidence 348999999876621 2466666776666642 22234588999998753
No 53
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=77.16 E-value=6 Score=34.75 Aligned_cols=48 Identities=15% Similarity=0.155 Sum_probs=33.3
Q ss_pred ceeeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCCCCceEEEEEEecCe
Q psy16628 29 FKCPLYFMVVKGYACYCKYQALQREVLLNQLKSMPGDRRTSIAIITYDSA 78 (107)
Q Consensus 29 ~~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs~ 78 (107)
....+|++|+|..- ...=+..+..+++..|...-. ++-+||+|+|++.
T Consensus 401 ~~~vvfvvD~SGSM-~~~rl~~aK~a~~~ll~~ay~-~rD~v~lI~F~g~ 448 (584)
T PRK13406 401 ETTTIFVVDASGSA-ALHRLAEAKGAVELLLAEAYV-RRDQVALVAFRGR 448 (584)
T ss_pred CccEEEEEECCCCC-cHhHHHHHHHHHHHHHHhhcC-CCCEEEEEEECCC
Confidence 67889999999854 333456666666666644222 3679999999765
No 54
>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=75.39 E-value=7.7 Score=34.01 Aligned_cols=48 Identities=17% Similarity=0.234 Sum_probs=32.9
Q ss_pred ceeeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCCCCceEEEEEEecC
Q psy16628 29 FKCPLYFMVVKGYACYCKYQALQREVLLNQLKSMPGDRRTSIAIITYDS 77 (107)
Q Consensus 29 ~~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs 77 (107)
....+|++|+|..--..+=+..+..++...+..... .+-+||+|+|+.
T Consensus 465 ~~~vv~vvD~SgSM~~~~rl~~ak~a~~~ll~~a~~-~~D~v~lI~F~g 512 (633)
T TIGR02442 465 GNLVIFVVDASGSMAARGRMAAAKGAVLSLLRDAYQ-KRDKVALITFRG 512 (633)
T ss_pred CceEEEEEECCccCCCccHHHHHHHHHHHHHHHhhc-CCCEEEEEEECC
Confidence 457789999998654434556666666666643322 378999999985
No 55
>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=74.38 E-value=5.5 Score=29.09 Aligned_cols=49 Identities=6% Similarity=-0.031 Sum_probs=31.3
Q ss_pred eeEEEEEcchhhhhc----C--hHHHHHHHHHHHhhcCCCCCceEEEEEEecCeE
Q psy16628 31 CPLYFMVVKGYACYC----K--YQALQREVLLNQLKSMPGDRRTSIAIITYDSAV 79 (107)
Q Consensus 31 ~yvFvIDVS~~Ai~s----G--~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs~v 79 (107)
-++|+||+|..--.. | =+..+.+++...+..++..+..++++++|++..
T Consensus 4 dvv~~ID~SgSM~~~~~~~~~~k~~~ak~~~~~l~~~~~~~D~d~i~l~~f~~~~ 58 (199)
T cd01457 4 DYTLLIDKSGSMAEADEAKERSRWEEAQESTRALARKCEEYDSDGITVYLFSGDF 58 (199)
T ss_pred CEEEEEECCCcCCCCCCCCCchHHHHHHHHHHHHHHHHHhcCCCCeEEEEecCCc
Confidence 578999999766532 1 245556666665554443334568889988765
No 56
>PRK10997 yieM hypothetical protein; Provisional
Probab=71.08 E-value=7.1 Score=33.82 Aligned_cols=56 Identities=11% Similarity=0.062 Sum_probs=39.6
Q ss_pred ceeeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCCCCceEEEEEEecCeEEEEecCC
Q psy16628 29 FKCPLYFMVVKGYACYCKYQALQREVLLNQLKSMPGDRRTSIAIITYDSAVHFYSLAE 86 (107)
Q Consensus 29 ~~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs~vhFynl~~ 86 (107)
.--+++++|+|..= +|.-...+.++..+|-.+...++-++++|.|++.++.|.+++
T Consensus 323 kGpiII~VDtSGSM--~G~ke~~AkalAaAL~~iAl~q~dr~~li~Fs~~i~~~~l~~ 378 (487)
T PRK10997 323 RGPFIVCVDTSGSM--GGFNEQCAKAFCLALMRIALAENRRCYIMLFSTEVVTYELTG 378 (487)
T ss_pred CCcEEEEEECCCCC--CCCHHHHHHHHHHHHHHHHHhcCCCEEEEEecCCceeeccCC
Confidence 34578999998754 255556666666666554444477899999999998876653
No 57
>PF09631 Sen15: Sen15 protein; InterPro: IPR018593 The Sen15 subunit of the tRNA intron-splicing endonuclease is one of the two structural subunits of this heterotetrameric enzyme. Residues 36-157 of this subunit possess a novel homodimeric fold. Each monomer consists of three alpha-helices and a mixed antiparallel/parallel beta-sheet. Two monomers of Sen15 fold with two monomers of Sen34, one of the two catalytic subunits, to form an alpha2-beta2 tetramer as part of the functional endonuclease assembly []. ; PDB: 2GW6_B.
Probab=63.56 E-value=4.7 Score=27.24 Aligned_cols=41 Identities=24% Similarity=0.545 Sum_probs=21.6
Q ss_pred HHHHHHHhhcCCC-CCceEEEEEEecCeEEEEecCCCCCCcc
Q psy16628 52 REVLLNQLKSMPG-DRRTSIAIITYDSAVHFYSLAEGQTQPS 92 (107)
Q Consensus 52 ~~sIk~~L~~lp~-~~~t~IgiITfDs~vhFynl~~~l~~pq 92 (107)
++++-..|...++ .+|.-+||+.=|++|-+|.+.+|...|+
T Consensus 58 i~~~f~~l~~~~~~~~ri~LAiv~~DsTiVYY~i~~GivkP~ 99 (101)
T PF09631_consen 58 IDEVFDSLPNPSGDPKRILLAIVDDDSTIVYYKIHDGIVKPR 99 (101)
T ss_dssp HHHHHHHHHHHCT---EEEEEEE-TTS-EEEEEEE-------
T ss_pred HHHHHHHhcccCCCCcEEEEEEEcCCCCEEEEEEeCCccCCC
Confidence 3344444443332 4689999999999999999999888775
No 58
>smart00539 NIDO Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins.
Probab=63.50 E-value=27 Score=25.41 Aligned_cols=80 Identities=16% Similarity=0.152 Sum_probs=55.0
Q ss_pred ceeeeecccCCceeeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCCCCceEEEEEEecCeEEEEecCC-CCCCccEEEe
Q psy16628 18 AYYTIVWELGIFKCPLYFMVVKGYACYCKYQALQREVLLNQLKSMPGDRRTSIAIITYDSAVHFYSLAE-GQTQPSQMIL 96 (107)
Q Consensus 18 ~~~~~~~~~~~~~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs~vhFynl~~-~l~~pqmlVV 96 (107)
|||+..|..+....|...- + ...+|..+.+.|++.....++-..+.+-++|.++.-++-.-.. +.+..|++.+
T Consensus 1 pF~~d~d~~~~G~V~yre~--~----d~~~L~ra~~~v~~~f~~~~~F~a~~v~vvTW~~V~~~~~~~~~~~NTFQ~VL~ 74 (152)
T smart00539 1 PFWADADTEGTGKVYYRET--T----DHAILDRATESVREGFTDMGGFRAKSVVIVTWENVAAYGSQSSDGTNTFQAVLA 74 (152)
T ss_pred CCccccCCCCCCCEEEEEe--C----CHHHHHHHHHHHHHHCCCCcCcceeEEEEEECcCcccccccCCCCCceeEEEEE
Confidence 4666667655555555554 1 3457888889999988776665788999999998665533332 3567899988
Q ss_pred CCCCCCC
Q psy16628 97 TDIDDIF 103 (107)
Q Consensus 97 sDldd~F 103 (107)
+|=..-|
T Consensus 75 tdg~~sf 81 (152)
T smart00539 75 TDGSRTY 81 (152)
T ss_pred ECCCceE
Confidence 8855444
No 59
>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=62.13 E-value=11 Score=29.98 Aligned_cols=50 Identities=10% Similarity=-0.000 Sum_probs=34.8
Q ss_pred CceeeEEEEEcchhhhhcChHHHHHH---HHHHHhhcCCCCCceEEEEEEecCeEE
Q psy16628 28 IFKCPLYFMVVKGYACYCKYQALQRE---VLLNQLKSMPGDRRTSIAIITYDSAVH 80 (107)
Q Consensus 28 ~~~~yvFvIDVS~~Ai~sG~l~~~~~---sIk~~L~~lp~~~~t~IgiITfDs~vh 80 (107)
+....+++||+|..=.++..-...++ .|.+++..++. -++|++.|..++.
T Consensus 59 r~~qIvlaID~S~SM~~~~~~~~aleak~lIs~al~~Le~---g~vgVv~Fg~~~~ 111 (266)
T cd01460 59 RDYQILIAIDDSKSMSENNSKKLALESLCLVSKALTLLEV---GQLGVCSFGEDVQ 111 (266)
T ss_pred cCceEEEEEecchhcccccccccHHHHHHHHHHHHHhCcC---CcEEEEEeCCCce
Confidence 46778999999987655555444444 34455555544 7999999998864
No 60
>PF02905 EBV-NA1: Epstein Barr virus nuclear antigen-1, DNA-binding domain; InterPro: IPR004186 The Epstein-Barr virus (strain GD1) nuclear antigen 1 (EBNA1) binds to and activates DNA replication from the latent origin of replication. The crystal structure of the DNA-binding and dimerization domains were solved [], and it was found that EBNA1 appears to bind DNA via two independent regions, the core and the flanking DNA-binding domains. This DNA-binding domain has a ferredoxin-like fold.; GO: 0003677 DNA binding, 0003688 DNA replication origin binding, 0006260 DNA replication, 0006275 regulation of DNA replication, 0045893 positive regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1B3T_B 1VHI_B.
Probab=59.09 E-value=17 Score=26.76 Aligned_cols=31 Identities=13% Similarity=0.355 Sum_probs=22.5
Q ss_pred HHHHHHHHHHhhcCCCC-CceEEEEEEecCeE
Q psy16628 49 ALQREVLLNQLKSMPGD-RRTSIAIITYDSAV 79 (107)
Q Consensus 49 ~~~~~sIk~~L~~lp~~-~~t~IgiITfDs~v 79 (107)
+.+.++|+.-+.+-|.+ .+++|.+++||+.|
T Consensus 113 e~vkDAi~Dyi~T~P~PT~~~~Vt~~~Fd~~V 144 (146)
T PF02905_consen 113 ECVKDAIRDYIMTRPQPTCNTQVTVCSFDDGV 144 (146)
T ss_dssp HHHHHHHHHHHCTS-TTGGGEEEEEEEEEEEE
T ss_pred HHHHHHHHHHhcCCCCCCcceEEEEEeCCCCC
Confidence 45666677666666663 67999999999876
No 61
>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=57.36 E-value=22 Score=26.88 Aligned_cols=49 Identities=8% Similarity=0.143 Sum_probs=29.8
Q ss_pred ccCCceeeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCCCCceEEEEEEecCeEE
Q psy16628 25 ELGIFKCPLYFMVVKGYACYCKYQALQREVLLNQLKSMPGDRRTSIAIITYDSAVH 80 (107)
Q Consensus 25 ~~~~~~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs~vh 80 (107)
++..+.-.++++|||. |++ ++...++..+..+....+ ++..+.|++.+.
T Consensus 53 r~~~~~~lvvl~DvSG-SM~-~~s~~~l~~~~~l~~~~~-----~~~~f~F~~~l~ 101 (222)
T PF05762_consen 53 RPRKPRRLVVLCDVSG-SMA-GYSEFMLAFLYALQRQFR-----RVRVFVFSTRLT 101 (222)
T ss_pred ccCCCccEEEEEeCCC-ChH-HHHHHHHHHHHHHHHhCC-----CEEEEEEeeehh
Confidence 3455669999999997 443 244444433333333332 778888887764
No 62
>COG1240 ChlD Mg-chelatase subunit ChlD [Coenzyme metabolism]
Probab=53.32 E-value=24 Score=28.49 Aligned_cols=45 Identities=18% Similarity=0.317 Sum_probs=28.0
Q ss_pred eeeEEEEEcchhhhhcChHHHHHHHHHHHhh-cCCCCCceEEEEEEec
Q psy16628 30 KCPLYFMVVKGYACYCKYQALQREVLLNQLK-SMPGDRRTSIAIITYD 76 (107)
Q Consensus 30 ~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~-~lp~~~~t~IgiITfD 76 (107)
.-++|++|.|-.--..+=.+++.-++...|. .-. .|-|||+|+|.
T Consensus 79 ~lvvfvVDASgSM~~~~Rm~aaKG~~~~lL~dAYq--~RdkvavI~F~ 124 (261)
T COG1240 79 NLIVFVVDASGSMAARRRMAAAKGAALSLLRDAYQ--RRDKVAVIAFR 124 (261)
T ss_pred CcEEEEEeCcccchhHHHHHHHHHHHHHHHHHHHH--ccceEEEEEec
Confidence 3479999998644333234444444444442 222 38999999997
No 63
>PRK00528 rpmE 50S ribosomal protein L31; Reviewed
Probab=39.15 E-value=28 Score=22.49 Aligned_cols=16 Identities=31% Similarity=0.235 Sum_probs=13.6
Q ss_pred eEEecccccCCCceee
Q psy16628 6 VEFRTLHLSNSHAYYT 21 (107)
Q Consensus 6 ~~~~~~~~~~~~~~~~ 21 (107)
-+++++--|+.||+|+
T Consensus 33 ~~i~vdv~s~~HPfyT 48 (71)
T PRK00528 33 PELRLDIDSGNHPAWT 48 (71)
T ss_pred CeEEEEECCCCCccEe
Confidence 3577888899999999
No 64
>PF05117 DUF695: Family of unknown function (DUF695) ; InterPro: IPR016097 This entry is found at the N terminus of a number of proteobacterial proteins of unknown function.
Probab=38.79 E-value=1.1e+02 Score=21.01 Aligned_cols=50 Identities=12% Similarity=-0.004 Sum_probs=32.7
Q ss_pred eeEEEEEcchhh-hhcCh--------HHHHHHHHHHHhhcCCCCCceEEEEEEecCeEEEE
Q psy16628 31 CPLYFMVVKGYA-CYCKY--------QALQREVLLNQLKSMPGDRRTSIAIITYDSAVHFY 82 (107)
Q Consensus 31 ~yvFvIDVS~~A-i~sG~--------l~~~~~sIk~~L~~lp~~~~t~IgiITfDs~vhFy 82 (107)
.++..|-+.+.+ -++|+ +..+.+.|...|...++ ...||-+|.|+...+|
T Consensus 35 ~~~v~i~i~y~~~~e~GlP~~ee~~~L~~iEd~i~~~l~~~~~--~i~vG~~t~~g~r~~~ 93 (136)
T PF05117_consen 35 PWRVQISIKYKGPDENGLPSEEEYEELNDIEDAIIEALEADGN--AIYVGRITGNGRREFY 93 (136)
T ss_pred CEEEEEEEEecCCCCCCCCCHHHHHHHHHHHHHHHHHhhcCCc--ceEEEEEEECCEEEEE
Confidence 345555555555 45554 55666666666665544 7999999999876444
No 65
>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs. It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].
Probab=37.97 E-value=73 Score=28.85 Aligned_cols=37 Identities=14% Similarity=0.296 Sum_probs=28.8
Q ss_pred CceEEEEEEecCeEEEEecCCCCCCccEEEeCCCCCC
Q psy16628 66 RRTSIAIITYDSAVHFYSLAEGQTQPSQMILTDIDDI 102 (107)
Q Consensus 66 ~~t~IgiITfDs~vhFynl~~~l~~pqmlVVsDldd~ 102 (107)
..+.+.+.|-|+++.+||+.+...-.|.+.+++.+..
T Consensus 160 ~~~~l~vLtsdn~lR~y~~~~~~~p~~v~~~~~~~~~ 196 (717)
T PF10168_consen 160 SDSHLVVLTSDNTLRLYDISDPQHPWQVLSLSPGEKS 196 (717)
T ss_pred CCCeEEEEecCCEEEEEecCCCCCCeEEEEcccCccc
Confidence 4789999999999999999865555577776655543
No 66
>KOG2807|consensus
Probab=36.77 E-value=54 Score=27.68 Aligned_cols=57 Identities=12% Similarity=0.100 Sum_probs=39.6
Q ss_pred eeeecccCCceeeEEEEEcchhhhhcChHHH----HHHHHHHHhhcC-CCCCceEEEEEEec
Q psy16628 20 YTIVWELGIFKCPLYFMVVKGYACYCKYQAL----QREVLLNQLKSM-PGDRRTSIAIITYD 76 (107)
Q Consensus 20 ~~~~~~~~~~~~yvFvIDVS~~Ai~sG~l~~----~~~sIk~~L~~l-p~~~~t~IgiITfD 76 (107)
|.-+-++|+..+-..+||+|...-+.-+.-+ +++.+..-+... ..++=++||||+--
T Consensus 51 ~~t~~r~GiiRhl~iviD~S~am~e~Df~P~r~a~~~K~le~Fv~eFFdQNPiSQigii~~k 112 (378)
T KOG2807|consen 51 YSTRIRKGIIRHLYIVIDCSRAMEEKDFRPSRFANVIKYLEGFVPEFFDQNPISQIGIISIK 112 (378)
T ss_pred ccchhhhhhheeEEEEEEhhhhhhhccCCchHHHHHHHHHHHHHHHHhccCchhheeEEEEe
Confidence 3456789999999999999998887666544 333333333332 23566999999874
No 67
>KOG0863|consensus
Probab=32.73 E-value=1.1e+02 Score=24.72 Aligned_cols=70 Identities=17% Similarity=0.240 Sum_probs=43.2
Q ss_pred cCCCceeeeecccCCceeeEEEEEcchhhh------------hcChHHHHHHHHHHHhhcCCC-----CCceEEEEEEec
Q psy16628 14 SNSHAYYTIVWELGIFKCPLYFMVVKGYAC------------YCKYQALQREVLLNQLKSMPG-----DRRTSIAIITYD 76 (107)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~yvFvIDVS~~Ai------------~sG~l~~~~~sIk~~L~~lp~-----~~~t~IgiITfD 76 (107)
|-+|-|+..|+- -++-+.-+.|-.-.+|- +++.=+.++.+|+..-+++|. .+++.|+|+.-|
T Consensus 140 ~G~hl~e~~Psg-~v~e~~g~sIGsRSQsARTyLEr~~e~f~~~~~eELI~~gi~Alr~tlp~de~lt~~nvsI~Ivgkd 218 (264)
T KOG0863|consen 140 SGPHLYEFCPSG-NVFECKGMSIGSRSQSARTYLERNLEEFEDSSPEELIKHGIMALRETLPEDEDLTGENVSIAIVGKD 218 (264)
T ss_pred CCceeEEEcCCc-cEEEEeeeecccchhhHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhcCcccccccceeEEEEEeCC
Confidence 356666665542 22334444444333332 344555566666666677774 378999999999
Q ss_pred CeEEEEec
Q psy16628 77 SAVHFYSL 84 (107)
Q Consensus 77 s~vhFynl 84 (107)
+..++|+=
T Consensus 219 ~pf~~~d~ 226 (264)
T KOG0863|consen 219 EPFTILDQ 226 (264)
T ss_pred CceEeecH
Confidence 99999863
No 68
>PF04459 DUF512: Protein of unknown function (DUF512); InterPro: IPR007549 This is a domain of uncharacterised prokaryotic proteins. It is often found C-terminal to the radical SAM domain (IPR007197 from INTERPRO).
Probab=32.53 E-value=63 Score=24.76 Aligned_cols=29 Identities=17% Similarity=0.257 Sum_probs=23.9
Q ss_pred ChHHHHHHHHHHHhhcCCCCCceEEEEEEe
Q psy16628 46 KYQALQREVLLNQLKSMPGDRRTSIAIITY 75 (107)
Q Consensus 46 G~l~~~~~sIk~~L~~lp~~~~t~IgiITf 75 (107)
|+++.+.+..++.+.++| ....++.++|=
T Consensus 77 Gm~r~f~~e~~~~l~~l~-~~~~~v~ivTG 105 (204)
T PF04459_consen 77 GMVRLFLDEWEEALRKLP-KKPRRVTIVTG 105 (204)
T ss_pred eEhHHHHHHHHHHHhhcC-CCCeeEEEEee
Confidence 678888899999998888 56788888883
No 69
>PRK00019 rpmE 50S ribosomal protein L31; Reviewed
Probab=32.38 E-value=24 Score=23.03 Aligned_cols=16 Identities=31% Similarity=0.370 Sum_probs=13.7
Q ss_pred EEecccccCCCceeee
Q psy16628 7 EFRTLHLSNSHAYYTI 22 (107)
Q Consensus 7 ~~~~~~~~~~~~~~~~ 22 (107)
|++++--|.+||+|+=
T Consensus 32 ~i~vdi~s~~HPFyTG 47 (72)
T PRK00019 32 EINVDVCSKCHPFYTG 47 (72)
T ss_pred cEEEEeCCCCCCcCcC
Confidence 5788888999999983
No 70
>TIGR00105 L31 ribosomal protein L31. This family consists exclusively of bacterial (and organellar) 50S ribosomal protein L31. In some species, such as Bacillus subtilis, this protein exists in two forms (RpmE and YtiA), one of which (RpmE) contains a pair of motifs, CXC and CXXC, for binding zinc.
Probab=30.39 E-value=28 Score=22.23 Aligned_cols=16 Identities=25% Similarity=0.283 Sum_probs=13.7
Q ss_pred EEecccccCCCceeee
Q psy16628 7 EFRTLHLSNSHAYYTI 22 (107)
Q Consensus 7 ~~~~~~~~~~~~~~~~ 22 (107)
|++++--|+.||+|+=
T Consensus 32 ~i~vdi~s~~HPfyTG 47 (68)
T TIGR00105 32 TLNLDICSKCHPFYTG 47 (68)
T ss_pred eEEEEECCCCcccCCC
Confidence 5888888999999983
No 71
>PF14581 SseB_C: SseB protein C-terminal domain
Probab=28.26 E-value=57 Score=21.62 Aligned_cols=54 Identities=11% Similarity=0.035 Sum_probs=32.0
Q ss_pred ceeeeecccCCceeeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCCCCceEEEEEEecC
Q psy16628 18 AYYTIVWELGIFKCPLYFMVVKGYACYCKYQALQREVLLNQLKSMPGDRRTSIAIITYDS 77 (107)
Q Consensus 18 ~~~~~~~~~~~~~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs 77 (107)
+|-......+..++|++++|+.. +-..-+++.+.+..+.. +++ ..-|-++++|+
T Consensus 37 Ayl~~~~~~~~~~~~li~vd~~~-~~~~~~~~~i~~~~~~~---~~~--~~~vd~~~~~~ 90 (108)
T PF14581_consen 37 AYLALMQDEDEQPSLLIGVDFDG-EDIEEIFQEIGRAARPY---LPD--GWPVDFVLLDD 90 (108)
T ss_pred hHHHHhhccCCCceEEEEEeccC-hhHHHHHHHHHHHhhhc---CCC--CceEEEEEccC
Confidence 44444444678999999999988 22222344444433332 333 56777787775
No 72
>KOG1679|consensus
Probab=27.45 E-value=1.2e+02 Score=24.47 Aligned_cols=42 Identities=12% Similarity=0.108 Sum_probs=36.3
Q ss_pred EEEEEcchhhhhcChHHHHHHHHHHHhhcCCCCCceEEEEEE
Q psy16628 33 LYFMVVKGYACYCKYQALQREVLLNQLKSMPGDRRTSIAIIT 74 (107)
Q Consensus 33 vFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~~~~t~IgiIT 74 (107)
+-+|-+...|-++.+-+.+.+.+++.|+.+..|+.+||-++-
T Consensus 41 Itvl~mNRpa~kNsl~r~~~~~l~~~l~~lk~D~~~Rvvilr 82 (291)
T KOG1679|consen 41 ITILNMNRPAKKNSLGRVFVKQLREVLDELKYDNKVRVVILR 82 (291)
T ss_pred eEEEecCChhhhccHHHHHHHHHHHHHHHHhhCCceeEEEEe
Confidence 457778888889999999999999999999998889887663
No 73
>KOG1599|consensus
Probab=27.26 E-value=47 Score=27.15 Aligned_cols=25 Identities=20% Similarity=0.521 Sum_probs=18.6
Q ss_pred EEEEecCCCCCCccEEEeCCCCCCCCCC
Q psy16628 79 VHFYSLAEGQTQPSQMILTDIDDIFLPS 106 (107)
Q Consensus 79 vhFynl~~~l~~pqmlVVsDldd~FvP~ 106 (107)
.||||++.. |....+.+.+|+++|.
T Consensus 254 kHyf~vnls---~~~~~l~~~~eV~lP~ 278 (297)
T KOG1599|consen 254 KHYFNVNLS---PFAINLGLNKEVYLPA 278 (297)
T ss_pred cceeeccch---hhhccccccceeeeec
Confidence 799998652 3333589999999985
No 74
>PF06884 DUF1264: Protein of unknown function (DUF1264); InterPro: IPR010686 This family contains a number of bacterial and eukaryotic proteins of unknown function that are approximately 200 residues long. Some family members are annotated as putative lipoproteins.
Probab=26.42 E-value=46 Score=25.29 Aligned_cols=21 Identities=29% Similarity=0.520 Sum_probs=16.9
Q ss_pred EecCeEEEEecCCC----CCCccEE
Q psy16628 74 TYDSAVHFYSLAEG----QTQPSQM 94 (107)
Q Consensus 74 TfDs~vhFynl~~~----l~~pqml 94 (107)
||.++.|+|+...+ +..||.|
T Consensus 109 tYGKt~HtWq~Drgd~LPlG~P~LM 133 (171)
T PF06884_consen 109 TYGKTWHTWQVDRGDKLPLGPPQLM 133 (171)
T ss_pred hhCCeEEeccCCCCCCCCCCCCeec
Confidence 78999999997663 6678866
No 75
>cd04931 ACT_PAH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe. In PAH, an autoregulatory sequence, N-terminal of the ACT domain, extends across the catalytic domain active site and regulates the enzyme by intrasteric regulation. It appears that the activation by L-Phe induces a conformational change that converts the enzyme to a high-affinity and high-activity state. Modulation of activity is achieved through inhibition by BH4 and activation by phosphorylation of serine residues of the autoregulatory region. The molecular basis for the cooperative activation process is not fully understood yet. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=26.35 E-value=1.3e+02 Score=19.89 Aligned_cols=31 Identities=10% Similarity=-0.076 Sum_probs=21.2
Q ss_pred CceeeEEEEEcchhhhhcChHHHHHHHHHHHhh
Q psy16628 28 IFKCPLYFMVVKGYACYCKYQALQREVLLNQLK 60 (107)
Q Consensus 28 ~~~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~ 60 (107)
....|.|.||+..+ +..-+..+++.|++-|.
T Consensus 53 ~~~~Y~FfVDieg~--~~~~~~~~l~~L~~~~~ 83 (90)
T cd04931 53 NKDEYEFFINLDKK--SAPALDPIIKSLRNDIG 83 (90)
T ss_pred CCceEEEEEEEEcC--CCHHHHHHHHHHHHHhC
Confidence 45679999999875 23445566677776553
No 76
>PHA02567 rnh RnaseH; Provisional
Probab=26.19 E-value=1.5e+02 Score=24.39 Aligned_cols=49 Identities=8% Similarity=0.165 Sum_probs=30.8
Q ss_pred eEEEEEcchhhhh-------------cChH-HHHHHHHHHHhhcCCCCCceEEEEEEecCeE-EEE
Q psy16628 32 PLYFMVVKGYACY-------------CKYQ-ALQREVLLNQLKSMPGDRRTSIAIITYDSAV-HFY 82 (107)
Q Consensus 32 yvFvIDVS~~Ai~-------------sG~l-~~~~~sIk~~L~~lp~~~~t~IgiITfDs~v-hFy 82 (107)
=+.+||.|+-+.+ .|++ +.++++|++.+...... .+.+ +++||..- ..|
T Consensus 15 ~~~LiDgs~i~~~~~~a~l~~~~~~~~~~ir~~v~nsL~~~v~~~k~~-~~~i-~vaFD~~~~~tf 78 (304)
T PHA02567 15 GVNLIDFSQIIIATIMANFKPKDKINEAMVRHLVLNSIRYNVKKFKEE-YPEI-VLAFDNSKSGYW 78 (304)
T ss_pred CEEEEehHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHHHHHhcCC-CCeE-EEEEeCCCCCCc
Confidence 3567888877652 2344 44777777777665443 4555 88999863 344
No 77
>TIGR02060 aprB adenosine phosphosulphate reductase, beta subunit. During dissimilatory sulfate reduction and sulfur oxidation, adenylylsulfate (APS) reductase catalyzes reversibly the two-electron reduction of APS to sulfite and AMP. Found in several bacterial lineages and in Archaeoglobales, APS reductase is a heterodimer composed of an alpha subunit containing a noncovalently bound FAD, and a beta subunit containing two [4Fe-4S] clusters. Described by this model is the beta subunit of APS reductase, sharing common evolutionary origin with other iron-sulfur cluster-binding proteins.
Probab=23.96 E-value=86 Score=22.32 Aligned_cols=25 Identities=8% Similarity=0.109 Sum_probs=22.1
Q ss_pred ceeeeecccCCceeeEEEEEcchhh
Q psy16628 18 AYYTIVWELGIFKCPLYFMVVKGYA 42 (107)
Q Consensus 18 ~~~~~~~~~~~~~~yvFvIDVS~~A 42 (107)
++.++..++|.-..+-|+||||..-
T Consensus 86 ~~~~v~~~~g~~~~~~f~~~vtp~c 110 (132)
T TIGR02060 86 IMWTVKFRNGKVMRFKFPIRTTPWG 110 (132)
T ss_pred eeEEEEcCCCCEEEEEeEEecCCCc
Confidence 7888899999999999999999754
No 78
>COG5256 TEF1 Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and biogenesis]
Probab=23.59 E-value=1.1e+02 Score=26.41 Aligned_cols=37 Identities=8% Similarity=0.086 Sum_probs=29.7
Q ss_pred ccccCCCceeeeecccCC-------------ceeeEEEEEcchhhhhcCh
Q psy16628 11 LHLSNSHAYYTIVWELGI-------------FKCPLYFMVVKGYACYCKY 47 (107)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~-------------~~~yvFvIDVS~~Ai~sG~ 47 (107)
-.|..+|.+|+|.|-+|- +=+.+++||++....+.|+
T Consensus 78 ~~fet~k~~~tIiDaPGHrdFvknmItGasqAD~aVLVV~a~~~efE~g~ 127 (428)
T COG5256 78 SKFETDKYNFTIIDAPGHRDFVKNMITGASQADVAVLVVDARDGEFEAGF 127 (428)
T ss_pred EEeecCCceEEEeeCCchHHHHHHhhcchhhccEEEEEEECCCCcccccc
Confidence 345556669999999885 6789999999999877773
No 79
>cd07265 2_3_CTD_N N-terminal domain of catechol 2,3-dioxygenase. This subfamily contains the N-terminal, non-catalytic, domain of catechol 2,3-dioxygenase. Catechol 2,3-dioxygenase (2,3-CTD, catechol:oxygen 2,3-oxidoreductase) catalyzes an extradiol cleavage of catechol to form 2-hydroxymuconate semialdehyde with the insertion of two atoms of oxygen. The enzyme is a homotetramer and contains catalytically essential Fe(II) . The reaction proceeds by an ordered bi-unit mechanism. First, catechol binds to the enzyme, this is then followed by the binding of dioxygen to form a tertiary complex, and then the aromatic ring is cleaved to produce 2-hydroxymuconate semialdehyde. Catechol 2,3-dioxygenase belongs to the type I extradiol dioxygenase family. The subunit comprises the N- and C-terminal domains of similar structure fold, resulting from an ancient gene duplication. The active site is located in a funnel-shaped space of the C-terminal domain. This subfamily represents the N-terminal do
Probab=23.41 E-value=14 Score=23.97 Aligned_cols=21 Identities=29% Similarity=0.463 Sum_probs=17.9
Q ss_pred CCcceeEEecccccCCCceee
Q psy16628 1 MGLGYVEFRTLHLSNSHAYYT 21 (107)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~ 21 (107)
+|++.|++.|.++..+++||+
T Consensus 3 ~~l~hv~l~v~Dl~~s~~FY~ 23 (122)
T cd07265 3 LRPGHVQLRVLDLEEAIKHYR 23 (122)
T ss_pred ceEeEEEEEeCCHHHHHHHHH
Confidence 578889999999888888885
No 80
>CHL00136 rpl31 ribosomal protein L31; Validated
Probab=23.37 E-value=41 Score=21.68 Aligned_cols=16 Identities=31% Similarity=0.412 Sum_probs=12.9
Q ss_pred EEecccccCCCceeee
Q psy16628 7 EFRTLHLSNSHAYYTI 22 (107)
Q Consensus 7 ~~~~~~~~~~~~~~~~ 22 (107)
+++++--|..||+|+=
T Consensus 32 ~i~vdv~s~~HPfyTG 47 (68)
T CHL00136 32 ELNVDIWSGNHPFYTG 47 (68)
T ss_pred CEEEEeCCCCCccCcC
Confidence 4667778999999983
No 81
>cd06822 PLPDE_III_YBL036c_euk Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Eukaryotic YBL036c-like proteins. This subfamily contains mostly uncharacterized eukaryotic proteins with similarity to the yeast hypothetical protein YBL036c, which is homologous to a Pseudomonas aeruginosa gene that is co-transcribed with a known proline biosynthetic gene. YBL036c is a single domain monomeric protein with a typical TIM barrel fold. It binds the PLP cofactor and has been shown to exhibit amino acid racemase activity. The YBL036c structure is similar to the N-terminal domain of the fold type III PLP-dependent enzymes, bacterial alanine racemase and eukaryotic ornithine decarboxylase, which are two-domain dimeric proteins. The lack of a second domain in YBL036c may explain limited D- to L-alanine racemase or non-specific racemase activity. Some members of this subfamily are also referred to as PROSC (Proline synthetase co-transcribed bacterial homolog)
Probab=22.78 E-value=2.3e+02 Score=21.80 Aligned_cols=50 Identities=10% Similarity=-0.003 Sum_probs=38.1
Q ss_pred CCceeeEEEEEcchhhhhcChHHHHHHHHHHHhh-cCCCCCceEEEEEEecCe
Q psy16628 27 GIFKCPLYFMVVKGYACYCKYQALQREVLLNQLK-SMPGDRRTSIAIITYDSA 78 (107)
Q Consensus 27 ~~~~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~-~lp~~~~t~IgiITfDs~ 78 (107)
+.++..+.=||++...-++|+...-+..+...+. ++|+ =.-.|+||+...
T Consensus 115 ~~~~~VlIqVn~g~e~~K~Gv~~~e~~~l~~~i~~~~~~--L~l~GLMt~~~~ 165 (227)
T cd06822 115 REPLKVMVQVNTSGEESKSGLEPSEAVELVKHIIEECPN--LKFSGLMTIGSF 165 (227)
T ss_pred CCCCcEEEEEeCCCCCCCCCCCHHHHHHHHHHHHhhCCC--ceEEEEEeeCCC
Confidence 6677788889999988999996555566666665 6666 566799999864
No 82
>PF11979 DUF3480: Domain of unknown function (DUF3480); InterPro: IPR022557 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 350 to 362 amino acids in length. This domain is found C-terminal to PF01363 from PFAM.
Probab=22.17 E-value=56 Score=27.46 Aligned_cols=82 Identities=21% Similarity=0.239 Sum_probs=55.3
Q ss_pred cccCCceeeEEEEEcchhh-----------hhcChHHHHHHHHHHHhhcCCCCCceEEEE-EEecCeEEEEecCCC-CCC
Q psy16628 24 WELGIFKCPLYFMVVKGYA-----------CYCKYQALQREVLLNQLKSMPGDRRTSIAI-ITYDSAVHFYSLAEG-QTQ 90 (107)
Q Consensus 24 ~~~~~~~~yvFvIDVS~~A-----------i~sG~l~~~~~sIk~~L~~lp~~~~t~Igi-ITfDs~vhFynl~~~-l~~ 90 (107)
+.+.+-.+=||.+.....+ ...-+..++|.+|..-|+.|..+.-++||+ ||.|+.--=|.-.++ ..-
T Consensus 261 ~~~~IRwTeVF~l~~~~~~~~~~~~~~~~~laE~IA~a~c~AL~PhL~lL~~~G~~kigLRvtld~d~VeY~AGs~Gq~L 340 (356)
T PF11979_consen 261 NGKIIRWTEVFFLQKDDDSNGPSDPSDHSRLAEQIAKACCAALCPHLKLLKENGMNKIGLRVTLDSDEVEYQAGSGGQPL 340 (356)
T ss_pred CCeEEEEEEEEEEecCccccCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHCCCcEEEEEEEEchhHeEEeccCCCCcC
Confidence 3455566778888777661 122355667777777778887777899998 788877666666443 334
Q ss_pred ccEEEeCCCCCCCCCC
Q psy16628 91 PSQMILTDIDDIFLPS 106 (107)
Q Consensus 91 pqmlVVsDldd~FvP~ 106 (107)
|+. -+.|||...+|.
T Consensus 341 P~~-Y~n~LD~~LiPv 355 (356)
T PF11979_consen 341 PQQ-YMNDLDSALIPV 355 (356)
T ss_pred CHH-HHHHhhhhhccc
Confidence 565 348888888874
No 83
>PF10238 Eapp_C: E2F-associated phosphoprotein; InterPro: IPR019370 This entry represents E2F binding proteins. E2F transcription factors play an essential role in cell proliferation and apoptosis and their activity is frequently deregulated in human cancers. E2F activity is regulated by a variety of mechanisms, frequently mediated by proteins binding to individual members or a subgroup of the family. E2F-associated phosphoprotein (EAPP)interacts with a subset of E2F factors and influences E2F-dependent promoter activity. EAPP is present throughout the cell cycle but disappears during mitosis [].
Probab=21.54 E-value=94 Score=22.56 Aligned_cols=20 Identities=25% Similarity=0.494 Sum_probs=17.8
Q ss_pred CceEEEEEEecCeEEEEecC
Q psy16628 66 RRTSIAIITYDSAVHFYSLA 85 (107)
Q Consensus 66 ~~t~IgiITfDs~vhFynl~ 85 (107)
-+|.||.+=-|..-||||.=
T Consensus 115 C~TeVaV~D~DEVYHFFNVL 134 (136)
T PF10238_consen 115 CSTEVAVYDKDEVYHFFNVL 134 (136)
T ss_pred CCCEEEEEeccCceEEEeec
Confidence 57899999999999999963
No 84
>KOG2353|consensus
Probab=21.52 E-value=1.6e+02 Score=28.33 Aligned_cols=55 Identities=18% Similarity=0.162 Sum_probs=41.3
Q ss_pred cCCceeeEEEEEcchhhhhcChHHHHHHHHHHHhhcCCCCCceEEEEEEecCeEEEEe
Q psy16628 26 LGIFKCPLYFMVVKGYACYCKYQALQREVLLNQLKSMPGDRRTSIAIITYDSAVHFYS 83 (107)
Q Consensus 26 ~~~~~~yvFvIDVS~~Ai~sG~l~~~~~sIk~~L~~lp~~~~t~IgiITfDs~vhFyn 83 (107)
+-.+..-+|++|+|.. +..--+..+-..+.++|+.|.+ .--+-++||++.+++-.
T Consensus 222 At~pKdiviLlD~SgS-m~g~~~~lak~tv~~iLdtLs~--~Dfvni~tf~~~~~~v~ 276 (1104)
T KOG2353|consen 222 ATSPKDIVILLDVSGS-MSGLRLDLAKQTVNEILDTLSD--NDFVNILTFNSEVNPVS 276 (1104)
T ss_pred cCCccceEEEEecccc-ccchhhHHHHHHHHHHHHhccc--CCeEEEEeeccccCccc
Confidence 3447778999999974 4333556666677788888876 67899999999988754
No 85
>PF13218 DUF4026: Protein of unknown function (DUF4026)
Probab=21.42 E-value=39 Score=28.08 Aligned_cols=21 Identities=24% Similarity=0.305 Sum_probs=16.1
Q ss_pred CCcceeEEecccccCCCceee
Q psy16628 1 MGLGYVEFRTLHLSNSHAYYT 21 (107)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~ 21 (107)
.|||++|+..+.=+-...||.
T Consensus 182 ~RcG~~ElEIL~~~~~~syyg 202 (323)
T PF13218_consen 182 CRCGSSELEILIPNPLESYYG 202 (323)
T ss_pred cccCCeeEEEecccchhhhcc
Confidence 489999999986655566773
No 86
>PF02513 Spin-Ssty: Spin/Ssty Family; InterPro: IPR003671 Spindlin (Spin) and Ssty were first identified for their involvement in gametogenesis. Spindlin was identified as a maternal transcript present in the unfertilised egg and early embryo, and was subsequently shown to interact with the spindle apparatus during oogenesis, and may therefore be important for mitosis []. In addition, spindlin appears to be a target for cell cycle-dependent phosphorylation, and as such may play a role in cell cycle regulation during the transition from gamete to embryo []. Ssty is a multi-copy, Y-linked spermatogenesis-specific transcript that appears to be required for normal spermatogenesis []. Ssty may play an analogous role to spindlin in sperm cells, namely during the transition from sperm cells to early embryo, and in mitosis.; GO: 0007276 gamete generation; PDB: 2NS2_A.
Probab=20.83 E-value=54 Score=20.11 Aligned_cols=23 Identities=35% Similarity=0.681 Sum_probs=15.8
Q ss_pred hhcCCCCCceEEEEEEecCeEEEEe
Q psy16628 59 LKSMPGDRRTSIAIITYDSAVHFYS 83 (107)
Q Consensus 59 L~~lp~~~~t~IgiITfDs~vhFyn 83 (107)
|++.|- +..+-+|+||.-.|.|-
T Consensus 24 l~Qvp~--~ps~y~Ikyd~d~~iY~ 46 (50)
T PF02513_consen 24 LHQVPA--KPSLYYIKYDGDDHIYV 46 (50)
T ss_dssp EEE-TT--STTEEEEEETTESBEEE
T ss_pred EEEeec--CCcEEEEEECCCcEEEE
Confidence 345555 56788999998777764
No 87
>smart00368 LRR_RI Leucine rich repeat, ribonuclease inhibitor type.
Probab=20.60 E-value=66 Score=16.59 Aligned_cols=22 Identities=9% Similarity=-0.203 Sum_probs=15.5
Q ss_pred EEEcchhhhhcChHHHHHHHHH
Q psy16628 35 FMVVKGYACYCKYQALQREVLL 56 (107)
Q Consensus 35 vIDVS~~Ai~sG~l~~~~~sIk 56 (107)
.+|+|.+.+...=..++|++|+
T Consensus 6 ~LdL~~N~i~~~G~~~L~~~L~ 27 (28)
T smart00368 6 ELDLSNNKLGDEGARALAEALK 27 (28)
T ss_pred EEECCCCCCCHHHHHHHHHHhc
Confidence 4788888886555667777664
No 88
>cd04904 ACT_AAAH ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe; TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines; and TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxy
Probab=20.39 E-value=1.6e+02 Score=18.23 Aligned_cols=13 Identities=8% Similarity=-0.205 Sum_probs=11.0
Q ss_pred CceeeEEEEEcch
Q psy16628 28 IFKCPLYFMVVKG 40 (107)
Q Consensus 28 ~~~~yvFvIDVS~ 40 (107)
.+-.|.|.||+..
T Consensus 39 ~~~~y~Ffvd~~~ 51 (74)
T cd04904 39 NGSEYEFFVDCEV 51 (74)
T ss_pred CCceEEEEEEEEc
Confidence 4667999999997
No 89
>COG5091 SGT1 Suppressor of G2 allele of skp1 and related proteins [General function prediction only]
Probab=20.15 E-value=44 Score=27.87 Aligned_cols=22 Identities=23% Similarity=0.683 Sum_probs=19.8
Q ss_pred CCceEEEEEEecCeEEEEecCC
Q psy16628 65 DRRTSIAIITYDSAVHFYSLAE 86 (107)
Q Consensus 65 ~~~t~IgiITfDs~vhFynl~~ 86 (107)
.+|.+||++-|=--|||||++.
T Consensus 73 ~D~~~IG~~~~~~~v~~~~ik~ 94 (368)
T COG5091 73 GDRSKIGLVNFRYFVHFFNIKD 94 (368)
T ss_pred CCcceeeeehhhhHHHhhhHHH
Confidence 5799999999999999999864
No 90
>PF14784 ECIST_Cterm: C-terminal domain of the ECSIT protein
Probab=20.10 E-value=1e+02 Score=22.11 Aligned_cols=30 Identities=27% Similarity=0.461 Sum_probs=22.4
Q ss_pred EEecCeEEEEecCCCCCCccEEEeCCCCCC
Q psy16628 73 ITYDSAVHFYSLAEGQTQPSQMILTDIDDI 102 (107)
Q Consensus 73 ITfDs~vhFynl~~~l~~pqmlVVsDldd~ 102 (107)
=.=|++|+||-|++....+....--|+||.
T Consensus 26 wLrd~~V~YfvLradp~p~~~~~~~d~Dd~ 55 (126)
T PF14784_consen 26 WLRDKCVYYFVLRADPKPPEEFEKEDIDDV 55 (126)
T ss_pred EEcCceEEEEEEeCCCCCccccccccCCCc
Confidence 345899999999997766666666666664
Done!