Query psy17260
Match_columns 679
No_of_seqs 283 out of 855
Neff 6.8
Searched_HMMs 46136
Date Fri Aug 16 17:26:40 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17260.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17260hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00162 transport protein sec 100.0 3.7E-99 8E-104 882.1 50.5 489 186-678 5-592 (761)
2 KOG1986|consensus 100.0 1.2E-98 3E-103 822.5 39.9 479 184-677 3-574 (745)
3 KOG1984|consensus 100.0 5E-92 1.1E-96 781.2 35.1 468 145-677 247-829 (1007)
4 COG5047 SEC23 Vesicle coat com 100.0 3E-90 6.6E-95 738.3 32.2 485 187-678 6-586 (755)
5 KOG1985|consensus 100.0 1.6E-83 3.4E-88 713.1 32.5 436 185-678 165-706 (887)
6 COG5028 Vesicle coat complex C 100.0 5.8E-77 1.3E-81 655.8 35.0 448 172-677 131-680 (861)
7 PTZ00395 Sec24-related protein 100.0 1.6E-73 3.5E-78 658.0 37.5 496 134-678 598-1377(1560)
8 cd01478 Sec23-like Sec23-like: 100.0 1.2E-34 2.6E-39 301.6 21.6 201 302-503 1-234 (267)
9 cd01479 Sec24-like Sec24-like: 100.0 7.8E-28 1.7E-32 248.0 15.8 171 302-503 1-199 (244)
10 cd01468 trunk_domain trunk dom 99.9 3.7E-26 8E-31 235.1 16.6 174 302-504 1-203 (239)
11 PF04811 Sec23_trunk: Sec23/Se 99.9 5.3E-26 1.2E-30 234.5 12.0 172 302-504 1-205 (243)
12 KOG1986|consensus 99.9 2.9E-27 6.4E-32 261.0 -1.0 135 25-178 135-269 (745)
13 COG5047 SEC23 Vesicle coat com 99.9 1.2E-23 2.5E-28 227.3 0.1 136 33-177 141-276 (755)
14 PF08033 Sec23_BS: Sec23/Sec24 99.8 1.5E-18 3.3E-23 153.6 8.6 87 507-601 10-96 (96)
15 cd01478 Sec23-like Sec23-like: 99.7 1.1E-18 2.4E-23 182.0 7.1 55 122-176 105-159 (267)
16 PLN00162 transport protein sec 99.7 9.4E-19 2E-23 206.0 0.0 156 13-176 119-280 (761)
17 PF04810 zf-Sec23_Sec24: Sec23 99.5 2.1E-15 4.5E-20 111.4 1.7 40 233-274 1-40 (40)
18 PF04815 Sec23_helical: Sec23/ 99.1 5.8E-11 1.3E-15 106.5 6.1 63 616-678 1-76 (103)
19 cd01468 trunk_domain trunk dom 97.6 2.4E-06 5.3E-11 88.2 -5.5 106 32-174 24-132 (239)
20 cd01479 Sec24-like Sec24-like: 97.0 0.00012 2.6E-09 75.9 -0.9 47 123-172 83-129 (244)
21 cd01463 vWA_VGCC_like VWA Volt 96.6 0.02 4.3E-07 56.7 11.7 50 303-352 12-63 (190)
22 cd01466 vWA_C3HC4_type VWA C3H 95.7 0.085 1.9E-06 50.5 10.3 45 307-351 3-49 (155)
23 PF04811 Sec23_trunk: Sec23/Se 95.4 0.0031 6.8E-08 65.1 -0.9 50 123-173 82-131 (243)
24 PRK13685 hypothetical protein; 94.7 0.19 4.1E-06 54.4 10.4 47 304-350 88-141 (326)
25 cd01456 vWA_ywmD_type VWA ywmD 94.4 0.082 1.8E-06 53.0 6.2 49 301-349 17-73 (206)
26 PF13768 VWA_3: von Willebrand 94.3 0.11 2.4E-06 49.4 6.6 47 307-353 3-50 (155)
27 cd01461 vWA_interalpha_trypsin 93.8 0.16 3.4E-06 48.7 6.6 49 304-352 2-52 (171)
28 cd01470 vWA_complement_factors 93.3 0.17 3.6E-06 50.4 6.1 45 307-351 3-52 (198)
29 cd01472 vWA_collagen von Wille 92.7 0.29 6.2E-06 47.0 6.6 45 307-351 3-52 (164)
30 PF00092 VWA: von Willebrand f 92.7 0.31 6.6E-06 46.7 6.8 45 307-351 2-51 (178)
31 cd01477 vWA_F09G8-8_type VWA F 92.5 0.3 6.4E-06 48.9 6.6 48 304-351 19-77 (193)
32 cd01464 vWA_subfamily VWA subf 92.4 0.2 4.3E-06 48.9 5.1 45 307-351 6-58 (176)
33 cd01469 vWA_integrins_alpha_su 92.4 0.33 7.1E-06 47.6 6.7 45 307-351 3-52 (177)
34 cd01465 vWA_subgroup VWA subgr 92.3 0.28 6.1E-06 46.9 6.0 45 307-351 3-49 (170)
35 cd01475 vWA_Matrilin VWA_Matri 92.2 0.36 7.8E-06 49.2 6.9 47 305-351 3-54 (224)
36 cd01471 vWA_micronemal_protein 92.1 0.3 6.4E-06 48.0 6.0 45 307-351 3-53 (186)
37 COG4245 TerY Uncharacterized p 92.1 0.24 5.3E-06 48.7 5.1 49 304-353 4-60 (207)
38 cd01482 vWA_collagen_alphaI-XI 92.0 0.39 8.5E-06 46.2 6.6 45 307-351 3-52 (164)
39 cd01452 VWA_26S_proteasome_sub 91.9 1.1 2.4E-05 44.7 9.7 125 306-501 5-147 (187)
40 TIGR03788 marine_srt_targ mari 91.5 0.38 8.3E-06 56.4 7.0 51 302-352 269-321 (596)
41 cd01481 vWA_collagen_alpha3-VI 91.2 0.53 1.1E-05 45.7 6.6 45 307-351 3-52 (165)
42 cd01480 vWA_collagen_alpha_1-V 90.9 0.43 9.4E-06 47.1 5.7 46 306-351 4-60 (186)
43 TIGR03436 acidobact_VWFA VWFA- 90.3 0.73 1.6E-05 48.9 7.2 49 303-351 52-102 (296)
44 cd01476 VWA_integrin_invertebr 90.3 0.83 1.8E-05 43.6 6.9 41 307-347 3-47 (163)
45 smart00327 VWA von Willebrand 88.7 1.2 2.5E-05 42.4 6.7 46 306-351 3-53 (177)
46 cd00198 vWFA Von Willebrand fa 88.4 1 2.2E-05 41.5 5.8 44 306-349 2-50 (161)
47 PF13519 VWA_2: von Willebrand 86.4 1.1 2.4E-05 42.3 5.0 42 307-349 2-50 (172)
48 cd01474 vWA_ATR ATR (Anthrax T 85.8 2 4.3E-05 42.2 6.5 47 305-351 5-53 (185)
49 cd01450 vWFA_subfamily_ECM Von 85.4 1.9 4.1E-05 40.3 6.0 44 307-350 3-51 (161)
50 PRK13406 bchD magnesium chelat 85.1 4.1 8.8E-05 47.7 9.6 46 303-348 400-448 (584)
51 cd01451 vWA_Magnesium_chelatas 84.4 2.3 5.1E-05 41.5 6.3 42 307-348 3-48 (178)
52 cd01467 vWA_BatA_type VWA BatA 82.5 3.1 6.8E-05 40.2 6.3 45 306-351 4-56 (180)
53 cd01473 vWA_CTRP CTRP for CS 82.2 2.9 6.4E-05 41.6 6.1 45 307-351 3-53 (192)
54 TIGR00868 hCaCC calcium-activa 81.8 3.2 6.8E-05 50.5 7.1 49 304-352 304-356 (863)
55 COG1240 ChlD Mg-chelatase subu 81.1 8.3 0.00018 40.2 8.9 90 304-457 78-171 (261)
56 cd01453 vWA_transcription_fact 80.5 2.9 6.3E-05 41.3 5.3 46 306-351 5-61 (183)
57 cd01462 VWA_YIEM_type VWA YIEM 79.0 3.1 6.8E-05 39.1 4.8 46 307-352 3-51 (152)
58 cd01454 vWA_norD_type norD typ 78.8 2.6 5.6E-05 40.9 4.3 43 306-348 2-48 (174)
59 TIGR02442 Cob-chelat-sub cobal 75.7 12 0.00026 44.4 9.4 45 304-348 465-513 (633)
60 PF09967 DUF2201: VWA-like dom 64.2 16 0.00035 33.9 5.7 44 308-353 2-47 (126)
61 TIGR02031 BchD-ChlD magnesium 64.0 12 0.00026 44.0 6.0 46 303-348 406-454 (589)
62 cd01458 vWA_ku Ku70/Ku80 N-ter 63.1 14 0.0003 37.3 5.6 43 306-348 3-57 (218)
63 PTZ00441 sporozoite surface pr 62.1 14 0.00031 42.9 5.9 53 304-356 42-101 (576)
64 TIGR01053 LSD1 zinc finger dom 58.6 8.8 0.00019 26.8 2.2 30 235-270 2-31 (31)
65 PF10058 DUF2296: Predicted in 57.0 6.6 0.00014 31.1 1.5 33 234-268 22-54 (54)
66 PRK00398 rpoP DNA-directed RNA 54.4 10 0.00023 28.6 2.2 29 235-269 4-32 (46)
67 cd01460 vWA_midasin VWA_Midasi 48.3 31 0.00067 36.4 5.3 46 303-350 59-111 (266)
68 cd01457 vWA_ORF176_type VWA OR 42.5 29 0.00064 34.4 4.0 45 305-349 3-58 (199)
69 smart00661 RPOL9 RNA polymeras 39.5 18 0.00038 27.8 1.4 33 237-273 3-35 (52)
70 PRK03954 ribonuclease P protei 37.9 21 0.00044 33.2 1.8 34 236-271 66-106 (121)
71 PF08879 WRC: WRC; InterPro: 37.1 16 0.00036 27.9 0.9 16 233-262 3-18 (46)
72 PF03731 Ku_N: Ku70/Ku80 N-ter 36.2 76 0.0016 31.9 5.9 41 306-347 1-53 (224)
73 PF08478 POTRA_1: POTRA domain 35.2 44 0.00095 26.9 3.2 46 79-149 4-49 (69)
74 PF02318 FYVE_2: FYVE-type zin 34.2 23 0.0005 32.5 1.6 32 235-268 72-104 (118)
75 COG0275 Predicted S-adenosylme 34.0 48 0.0011 35.6 4.1 28 319-346 219-246 (314)
76 COG1198 PriA Primosomal protei 31.0 1.7E+02 0.0037 35.4 8.4 109 235-356 436-572 (730)
77 PF13719 zinc_ribbon_5: zinc-r 30.7 28 0.00061 25.2 1.2 32 235-268 3-35 (37)
78 cd00350 rubredoxin_like Rubred 29.4 34 0.00073 24.0 1.4 11 257-267 16-26 (33)
79 PF09723 Zn-ribbon_8: Zinc rib 28.4 30 0.00065 25.7 1.0 30 235-267 6-35 (42)
80 PRK10997 yieM hypothetical pro 27.7 90 0.0019 35.9 5.1 50 306-356 325-378 (487)
81 cd00730 rubredoxin Rubredoxin; 27.4 27 0.00059 27.2 0.7 30 236-267 3-43 (50)
82 PF00641 zf-RanBP: Zn-finger i 27.2 22 0.00047 24.3 0.1 14 257-270 3-16 (30)
83 PF02748 PyrI_C: Aspartate car 27.0 64 0.0014 25.3 2.7 35 233-267 5-44 (52)
84 PF05762 VWA_CoxE: VWA domain 26.7 1.2E+02 0.0025 30.9 5.4 45 302-349 54-100 (222)
85 TIGR02605 CxxC_CxxC_SSSS putat 26.0 36 0.00077 26.2 1.1 31 235-268 6-36 (52)
86 PF13894 zf-C2H2_4: C2H2-type 25.7 30 0.00066 21.2 0.6 12 259-270 1-12 (24)
87 TIGR00006 S-adenosyl-methyltra 25.1 76 0.0017 34.2 3.8 28 319-346 215-242 (305)
88 PF09779 Ima1_N: Ima1 N-termin 24.9 48 0.0011 31.1 2.0 36 235-274 1-36 (131)
89 PF02891 zf-MIZ: MIZ/SP-RING z 24.7 8.8 0.00019 29.8 -2.5 30 236-266 20-49 (50)
90 KOG2353|consensus 23.9 1.1E+02 0.0023 38.8 5.1 51 302-352 223-275 (1104)
91 PF08271 TF_Zn_Ribbon: TFIIB z 23.8 84 0.0018 23.3 2.7 27 236-267 2-28 (43)
92 PF00301 Rubredoxin: Rubredoxi 23.0 30 0.00065 26.6 0.2 30 236-267 3-43 (47)
93 PRK00050 16S rRNA m(4)C1402 me 22.3 93 0.002 33.4 3.8 28 319-346 211-238 (296)
94 PF09082 DUF1922: Domain of un 22.2 45 0.00097 27.7 1.0 30 234-271 3-32 (68)
95 smart00187 INB Integrin beta s 21.8 2.2E+02 0.0047 32.1 6.6 50 303-352 98-152 (423)
96 COG1592 Rubrerythrin [Energy p 21.3 49 0.0011 32.4 1.3 15 255-269 131-145 (166)
97 PRK12380 hydrogenase nickel in 20.9 54 0.0012 29.9 1.4 26 235-268 71-96 (113)
98 COG1996 RPC10 DNA-directed RNA 20.6 53 0.0011 25.6 1.1 27 236-268 8-34 (49)
99 cd00729 rubredoxin_SM Rubredox 20.5 51 0.0011 23.4 0.9 13 257-269 1-13 (34)
100 TIGR00100 hypA hydrogenase nic 20.4 58 0.0013 29.8 1.5 26 235-268 71-96 (115)
101 TIGR00578 ku70 ATP-dependent D 20.1 1.6E+02 0.0035 34.7 5.5 44 305-348 11-67 (584)
No 1
>PLN00162 transport protein sec23; Provisional
Probab=100.00 E-value=3.7e-99 Score=882.12 Aligned_cols=489 Identities=44% Similarity=0.777 Sum_probs=440.0
Q ss_pred ccCCCCeeeeeccccCCCHHHHhhCCCCeEEEEccCCCCCCCCCccCCccccCCCCcccEEcCceeEecCCCeEEeccCC
Q psy17260 186 QNEERDGIRCTWNVWPSSKLEASRLVMPVGCLYQPLKEKPDLPPLQYEPLLCMRNQCRAILNPLCQVDYKSKLWVCNFCF 265 (679)
Q Consensus 186 ~n~~p~~iR~T~~~~P~t~~~~~~~~lPlg~vv~Pf~~~~~ip~v~~~p~RC~~~~C~AYiNpf~~~~~~g~~W~C~~C~ 265 (679)
+.++.++||+|||+||+++.++++++|||||+|+||++.+++|+++++|+||++ |+|||||||+|+++|++|+||||+
T Consensus 5 ~~e~~~gvR~s~n~~P~t~~~~~~~~iPlg~v~tPl~~~~~vp~v~~~pvRC~~--CraylNPf~~~d~~~~~W~C~~C~ 82 (761)
T PLN00162 5 ELEAIDGVRMSWNVWPSSKIEASKCVIPLAALYTPLKPLPELPVLPYDPLRCRT--CRAVLNPYCRVDFQAKIWICPFCF 82 (761)
T ss_pred hhcccCceEeeeecCCCCHHHHhcCCCCeEEEEecCCcCCCCCcCCCCCCccCC--CcCEECCceEEecCCCEEEccCCC
Confidence 567889999999999999999999999999999999988889999999999999 999999999999999999999999
Q ss_pred CCCCCCcccccccCCCCCCcccCCCcceEEecC---CCCCCCcEEEEEEECCcChhhHHHHHHHHHHHhhcCCCCcEEEE
Q psy17260 266 QRNAFPPQYAAITEQHQPAELHPQFTTIEYTIP---KMQCAPLVFLFVVDTCMDEEELGALRDSLQMSLSLLPKNALVGL 342 (679)
Q Consensus 266 ~~N~vp~~Y~~~~~~~~rpEL~~~~~tvEy~~~---~~~~~pp~~vFvIDvs~~a~~l~~l~~si~~~L~~Lp~~~~VG~ 342 (679)
..|++|++|..+++.++||||.++++||||.+| .+++.||+|+||||+|.++++++.++++|+++|+.||++++|||
T Consensus 83 ~~N~~P~~Y~~~~~~~~p~EL~p~~~TvEY~~p~~~~~~~~pp~fvFvID~s~~~~~l~~lk~sl~~~L~~LP~~a~VGl 162 (761)
T PLN00162 83 QRNHFPPHYSSISETNLPAELFPQYTTVEYTLPPGSGGAPSPPVFVFVVDTCMIEEELGALKSALLQAIALLPENALVGL 162 (761)
T ss_pred CCCCCchHhcccCccCCChhhcCCceeEEEECCCCCCCCCCCcEEEEEEecchhHHHHHHHHHHHHHHHHhCCCCCEEEE
Confidence 999999999988888999999777999999999 78899999999999999999999999999999999999999999
Q ss_pred EEECCeEEEEEcCCCCccceeeecCCCCCchhHHHHhhhcCCCCC-CCCCCCCC-CCCCCCCCCCCceeehHHhHHHHHH
Q psy17260 343 ITFGQMVQVHELGCEGISRSYVFRGTKDVPAQRLQEMLRIGKYSM-SAPAPAPR-PGQPPRPARTQFLQPVEACEMYATD 420 (679)
Q Consensus 343 ITfd~~V~~y~l~~~~~~~~~Vf~g~~~l~~~ql~~~l~l~d~~~-p~~~g~~~-~~~~~~~~~~~flvpl~e~~~~i~~ 420 (679)
||||++||||+|+.+++++++||+|+|+++.+|+.+++++++... ++..+... ......+..++||+|++||+..|++
T Consensus 163 ITF~s~V~~~~L~~~~~~~~~Vf~g~k~~t~~~l~~~l~l~~~~~~~~~~~~~~~~~~~~~p~~~~fLvpl~e~~~~i~~ 242 (761)
T PLN00162 163 ITFGTHVHVHELGFSECSKSYVFRGNKEVSKDQILEQLGLGGKKRRPAGGGIAGARDGLSSSGVNRFLLPASECEFTLNS 242 (761)
T ss_pred EEECCEEEEEEcCCCCCcceEEecCCccCCHHHHHHHhccccccccccccccccccccccCCCccceeEEHHHHHHHHHH
Confidence 999999999999988899999999999999999999998866322 22110000 0001123467999999999999999
Q ss_pred HHHHhcCCCCcccCCCCCCCchHHHHHHHHHHhhhc----c--------------------------CCCCCccCcCCCC
Q psy17260 421 LLAALQKGPVAVHQGREHCGPTGVAHVIAVGLLEGT----L--------------------------IRSHNDIHKGNNK 470 (679)
Q Consensus 421 lLe~L~~~~~~~~~~~~~~~c~G~AL~~A~~lL~~~----~--------------------------lrs~~di~~~~~~ 470 (679)
+||+|+++.|+++.++++.||+|+||++|..+|+.+ | +|+|+|+++++.+
T Consensus 243 lLe~L~~~~~~~~~~~rp~r~tG~AL~vA~~lL~~~~~~~gGrI~~F~sgppT~GpG~v~~r~~~~~~rsh~di~k~~~~ 322 (761)
T PLN00162 243 ALEELQKDPWPVPPGHRPARCTGAALSVAAGLLGACVPGTGARIMAFVGGPCTEGPGAIVSKDLSEPIRSHKDLDKDAAP 322 (761)
T ss_pred HHHhhhccccccCCCCCCCccHHHHHHHHHHHHhhccCCCceEEEEEeCCCCCCCCceeecccccccccCccccccchhh
Confidence 999999999999999999999999999999999843 2 6788888888889
Q ss_pred CCccchhHHHHHHHHHhh-hcceeEEEEcC-----------------------Cccccc-------------------c-
Q psy17260 471 LPGRMATKITKGLALRAA-YCRAIEYLLVP-----------------------PWINGL-------------------L- 506 (679)
Q Consensus 471 ~~~~~a~~fY~~La~~~~-~~~svD~~~~~-----------------------~sF~~~-------------------~- 506 (679)
++ +++.+||++||.+|+ .+++||+|..+ ++|+++ +
T Consensus 323 ~~-~~a~~fY~~la~~~~~~gisvDlF~~s~dqvglaem~~l~~~TGG~v~~~~sF~~~~f~~~l~r~~~r~~~~~~~~g 401 (761)
T PLN00162 323 YY-KKAVKFYEGLAKQLVAQGHVLDVFACSLDQVGVAEMKVAVERTGGLVVLAESFGHSVFKDSLRRVFERDGEGSLGLS 401 (761)
T ss_pred hc-chHHHHHHHHHHHHHHcCceEEEEEccccccCHHHHhhhHhhcCcEEEEeCCcChHHHHHHHHHHhccccccccccc
Confidence 99 999999999999999 99999977433 344321 1
Q ss_pred --------cCCCeEEeeeeccccccCCCCccccccccCCCCcCeEEEcCCCCCceEEEEEEEecCC-CCCCCCCCceEEE
Q psy17260 507 --------LEYELCLMGAIGPCVSLNLKNQCVSDQDLGMGGTASWKMCTLSPNTTLALFFEIVNQH-GAPIPQGGPGCIQ 577 (679)
Q Consensus 507 --------~S~gl~v~~~iG~~~~~~~~~~~isd~~ig~g~t~~~~l~~ld~dtsia~~fei~~~~-~~~l~~~~~~~iQ 577 (679)
||+|++|+++||||.....++.++||+++|+|+|+.|+++++++++|++|+|++++.. ..+++++..+|||
T Consensus 402 f~a~~~VrtS~glkv~g~~G~~~s~~~~~~~vsd~~iG~g~T~~w~l~~l~~~~t~av~f~~~~~~~~~~~~~~~~~~iQ 481 (761)
T PLN00162 402 FNGTFEVNCSKDVKVQGAIGPCASLEKKGPSVSDTEIGEGGTTAWKLCGLDKKTSLAVFFEVANSGQSNPQPPGQQFFLQ 481 (761)
T ss_pred ceeEEEEEecCCeEEeeeEcCcccccccCCccccccccCCCCceeeecCcCcCCEEEEEEEEccccccCCCCCCceEEEE
Confidence 9999999999999998888888999999999999999999999999999999999875 2345566789999
Q ss_pred EEEEeEcCCCCEEEEEEccccccccCCCCHHHHHhccCHHHHHHHHHHHHHHHhhcCChhHHHHHHHHHHHHhhccc---
Q psy17260 578 FITHYQAPSGEKKVRVTTIARNWADATTQLDHISSGFDQEAAAVIMGRMVVNRAEQDDGPDVMRWADRTLIRLEGGA--- 654 (679)
Q Consensus 578 ~allYt~~~GerriRV~T~~l~~~~~ss~~~~v~~s~D~ea~~~llaK~a~~~~~~~~~~d~~~~ld~~li~il~~y--- 654 (679)
||++||+.+|+|||||||++++|+. ++++.+++++|||||++++|||+|++++++++..|+++|||+.|++++++|
T Consensus 482 ~a~lYt~~~G~rRiRV~T~~~~~~~-~~~~~~v~~~fDqeA~a~llaR~av~k~~~~~~~d~~r~ld~~li~~~~~f~~Y 560 (761)
T PLN00162 482 FLTRYQHSNGQTRLRVTTVTRRWVE-GSSSEELVAGFDQEAAAVVMARLASHKMETEEEFDATRWLDRALIRLCSKFGDY 560 (761)
T ss_pred EEEEEEcCCCCEEEEEEccccCccC-CCCHHHHHHhcCHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHhhh
Confidence 9999999999999999999999863 347789999999999999999999999999999999999999999999776
Q ss_pred -------cccCCcccH-HHHHHHHhccccCCC
Q psy17260 655 -------PVLTEDVSL-QVFMEHLKKLAVSST 678 (679)
Q Consensus 655 -------liLPe~lkl-P~~~~~L~rS~~l~~ 678 (679)
|+||++||+ |+||||||||++|+.
T Consensus 561 rk~~~~s~~Lp~~~~~lP~f~~~LrRS~~l~~ 592 (761)
T PLN00162 561 RKDDPSSFRLSPNFSLYPQFMFNLRRSQFVQV 592 (761)
T ss_pred cccCCccccCCHHHHHHHHHHHHHhhhhhccC
Confidence 999999999 999999999999874
No 2
>KOG1986|consensus
Probab=100.00 E-value=1.2e-98 Score=822.48 Aligned_cols=479 Identities=53% Similarity=0.896 Sum_probs=445.7
Q ss_pred hhccCCCCeeeeeccccCCCHHHHhhCCCCeEEEEccCCCCCCCCCccCCccccCCCCcccEEcCceeEecCCCeEEecc
Q psy17260 184 FYQNEERDGIRCTWNVWPSSKLEASRLVMPVGCLYQPLKEKPDLPPLQYEPLLCMRNQCRAILNPLCQVDYKSKLWVCNF 263 (679)
Q Consensus 184 ~~~n~~p~~iR~T~~~~P~t~~~~~~~~lPlg~vv~Pf~~~~~ip~v~~~p~RC~~~~C~AYiNpf~~~~~~g~~W~C~~ 263 (679)
+..+++.++||+|||+||+++....++.+|++++|+||++.+++|++.|+|+||.+ |+||+||||++|.+.+.|.|+|
T Consensus 3 ~~~~e~~dGvR~twnvwPs~~~~~~~~vvPla~lytPl~e~~~~~~~~y~P~~C~~--C~AvlNPyc~vd~~a~~W~Cpf 80 (745)
T KOG1986|consen 3 IEDIEEIDGVRFTWNVWPSTRAEASRTVVPLACLYTPLKERPDLPPIQYDPLRCSK--CGAVLNPYCSVDFRAKSWICPF 80 (745)
T ss_pred ccccccCCCcccccccCCCcccccccccccHHHhccccccCCCCCccCCCCchhcc--chhhcCcceeecccCceEeccc
Confidence 34688899999999999999999999999999999999988888999999999999 9999999999999999999999
Q ss_pred CCCCCCCCcccccccCCCCCCcccCCCcceEEecCCCCCCCcEEEEEEECCcChhhHHHHHHHHHHHhhcCCCCcEEEEE
Q psy17260 264 CFQRNAFPPQYAAITEQHQPAELHPQFTTIEYTIPKMQCAPLVFLFVVDTCMDEEELGALRDSLQMSLSLLPKNALVGLI 343 (679)
Q Consensus 264 C~~~N~vp~~Y~~~~~~~~rpEL~~~~~tvEy~~~~~~~~pp~~vFvIDvs~~a~~l~~l~~si~~~L~~Lp~~~~VG~I 343 (679)
|+++|.+|++|..+++.|.|+||.++++||||..++....||+|+||||+++++++|+.+|++|+.+|+.||++++||||
T Consensus 81 C~qrN~~p~~Y~~is~~n~P~el~Pq~stvEy~l~~~~~~ppvf~fVvDtc~~eeeL~~LkssL~~~l~lLP~~alvGlI 160 (745)
T KOG1986|consen 81 CNQRNPFPPHYSGISENNLPPELLPQYSTVEYTLSPGRVSPPVFVFVVDTCMDEEELQALKSSLKQSLSLLPENALVGLI 160 (745)
T ss_pred cccCCCCChhhcccCccCCChhhcCCcceeEEecCCCCCCCceEEEEEeeccChHHHHHHHHHHHHHHhhCCCcceEEEE
Confidence 99999999999999999999999999999999999767779999999999999999999999999999999999999999
Q ss_pred EECCeEEEEEcCCCCccceeeecCCCCCchhHHHHhhhcCCCCCCCCCCCCCCCCCCCCCCCCceeehHHhHHHHHHHHH
Q psy17260 344 TFGQMVQVHELGCEGISRSYVFRGTKDVPAQRLQEMLRIGKYSMSAPAPAPRPGQPPRPARTQFLQPVEACEMYATDLLA 423 (679)
Q Consensus 344 Tfd~~V~~y~l~~~~~~~~~Vf~g~~~l~~~ql~~~l~l~d~~~p~~~g~~~~~~~~~~~~~~flvpl~e~~~~i~~lLe 423 (679)
||++.||+|+++..++++++||+|+|+++.+|++.++..+-.... |. + ......+||.|+++|+..+.++|+
T Consensus 161 tfg~~v~v~el~~~~~sk~~VF~G~ke~s~~q~~~~L~~~~~~~~---~~--~---~~~~~~rFL~P~~~c~~~L~~lle 232 (745)
T KOG1986|consen 161 TFGTMVQVHELGFEECSKSYVFSGNKEYSAKQLLDLLGLSGGAGK---GS--E---NQSASNRFLLPAQECEFKLTNLLE 232 (745)
T ss_pred EecceEEEEEcCCCcccceeEEeccccccHHHHHHHhcCCccccc---CC--c---ccccchhhhccHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999977541111 10 0 012356899999999999999999
Q ss_pred HhcCCCCcccCCCCCCCchHHHHHHHHHHhhhcc------------------------------CCCCCccCcCCCCCCc
Q psy17260 424 ALQKGPVAVHQGREHCGPTGVAHVIAVGLLEGTL------------------------------IRSHNDIHKGNNKLPG 473 (679)
Q Consensus 424 ~L~~~~~~~~~~~~~~~c~G~AL~~A~~lL~~~~------------------------------lrs~~di~~~~~~~~~ 473 (679)
+|.+|+|+++.++|+.||||+||++|+.||+.++ +|+|+||++++++|+
T Consensus 233 ~L~~d~wpV~~g~Rp~RcTG~Al~iA~~Ll~~c~p~~g~rIv~f~gGPcT~GpG~vv~~el~~piRshhdi~~d~a~y~- 311 (745)
T KOG1986|consen 233 ELQPDPWPVPPGHRPLRCTGVALSIASGLLEGCFPNTGARIVLFAGGPCTRGPGTVVSRELKEPIRSHHDIEKDNAPYY- 311 (745)
T ss_pred HhcCCCCCCCCCCCcccchhHHHHHHHHHhcccCCCCcceEEEeccCCCCcCCceecchhhcCCCcCcccccCcchHHH-
Confidence 9999999999999999999999999999999884 899999999999999
Q ss_pred cchhHHHHHHHHHhh--------hcceeE----------------EEEcCCcccccc-----------------------
Q psy17260 474 RMATKITKGLALRAA--------YCRAIE----------------YLLVPPWINGLL----------------------- 506 (679)
Q Consensus 474 ~~a~~fY~~La~~~~--------~~~svD----------------~~~~~~sF~~~~----------------------- 506 (679)
+++.|||++||++++ +++++| +++++|+|++++
T Consensus 312 kKa~KfY~~La~r~~~~ghvlDifa~~lDQvGi~EMk~l~~~TGG~lvl~dsF~~s~Fk~sfqR~f~~d~~~~l~~~fn~ 391 (745)
T KOG1986|consen 312 KKAIKFYEKLAERLANQGHVLDIFAAALDQVGILEMKPLVESTGGVLVLGDSFNTSIFKQSFQRIFTRDGEGDLKMGFNG 391 (745)
T ss_pred HHHHHHHHHHHHHHHhCCceEeeeeeeccccchHHHHHHhhcCCcEEEEecccchHHHHHHHHHHhccccccchhhhcCc
Confidence 999999999999999 555555 568899998655
Q ss_pred -----cCCCeEEeeeeccccccCCCCccccccccCCCCcCeEEEcCCCCCceEEEEEEEecCCCCCCCCCCceEEEEEEE
Q psy17260 507 -----LEYELCLMGAIGPCVSLNLKNQCVSDQDLGMGGTASWKMCTLSPNTTLALFFEIVNQHGAPIPQGGPGCIQFITH 581 (679)
Q Consensus 507 -----~S~gl~v~~~iG~~~~~~~~~~~isd~~ig~g~t~~~~l~~ld~dtsia~~fei~~~~~~~l~~~~~~~iQ~all 581 (679)
||++++|+++|||+.+.+.|+++|||++||.|+|..|+++.+++.+++++.||+...++ .+.+..+||||++.
T Consensus 392 ~leV~tSkdlkI~g~IGp~~Sl~~k~~~vsdt~ig~g~t~~wkm~~ls~~t~~s~~fei~~~~~--~~~~~~~~iQFiT~ 469 (745)
T KOG1986|consen 392 TLEVKTSKDLKIQGVIGPCVSLNKKGPNVSDTEIGEGNTSAWKMCGLSPSTTLSLFFEISNQHN--IPQSGQGYIQFITQ 469 (745)
T ss_pred eEEEEecCCcEEEecccccccccCCCCccccceeccccccceeeeccCCCceEEEEEEeccccC--CCCCCeeEEEEEEE
Confidence 99999999999999999999999999999999999999999999999999999999876 45567899999999
Q ss_pred eEcCCCCEEEEEEccccccccCCCCHHHHHhccCHHHHHHHHHHHHHHHhhcCChhHHHHHHHHHHHHhhccc-------
Q psy17260 582 YQAPSGEKKVRVTTIARNWADATTQLDHISSGFDQEAAAVIMGRMVVNRAEQDDGPDVMRWADRTLIRLEGGA------- 654 (679)
Q Consensus 582 Yt~~~GerriRV~T~~l~~~~~ss~~~~v~~s~D~ea~~~llaK~a~~~~~~~~~~d~~~~ld~~li~il~~y------- 654 (679)
|++++|++|+||+|++++|++..+ .++..+|||||++++|||.++.++.+++..|+++|+|+++||++++|
T Consensus 470 Yq~s~g~~riRVtT~~r~~~d~~~--~~i~~~FDqEaaAV~mAR~~~~kae~e~~~d~~rwlDr~Lirlc~kFg~y~k~d 547 (745)
T KOG1986|consen 470 YQHSSGQKRIRVTTLARPWADSGS--PEISQSFDQEAAAVLMARLALLKAETEDGPDVLRWLDRNLIRLCQKFGDYRKDD 547 (745)
T ss_pred EEcCCCcEEEEEEEeehhhccccc--hHhhhccchHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHHHHHhccCCCC
Confidence 999999999999999999985432 78999999999999999999999999999999999999999999999
Q ss_pred ---cccCCcccH-HHHHHHHhccccCC
Q psy17260 655 ---PVLTEDVSL-QVFMEHLKKLAVSS 677 (679)
Q Consensus 655 ---liLPe~lkl-P~~~~~L~rS~~l~ 677 (679)
|.|+++|++ |+||||||||++|.
T Consensus 548 Pssf~l~~~fsl~PQfmfhLRRS~fLq 574 (745)
T KOG1986|consen 548 PSSFRLSPNFSLYPQFMFHLRRSPFLQ 574 (745)
T ss_pred chhhcCChhhhhhHHHHHhhccchhhh
Confidence 999999999 99999999999986
No 3
>KOG1984|consensus
Probab=100.00 E-value=5e-92 Score=781.24 Aligned_cols=468 Identities=19% Similarity=0.272 Sum_probs=416.3
Q ss_pred CCCCCC-CCCCCCCCCcchhhhhhhhcccccCCccc--hhhhhhccCCCCeeeeeccccCCCHHHHhhCCCCeEEEEccC
Q psy17260 145 KDPWPV-HQGKRALRSTGVALSIAVGLLELKISMTT--YEEFFYQNEERDGIRCTWNVWPSSKLEASRLVMPVGCLYQPL 221 (679)
Q Consensus 145 ~d~~~v-~~~~R~~r~tg~al~va~~ll~~~~p~~~--~~~~~~~n~~p~~iR~T~~~~P~t~~~~~~~~lPlg~vv~Pf 221 (679)
+|+-.| .++++..|.|. .....|||+| |...|+|||+|+|||||+|++|+|.++++.++||||++|+||
T Consensus 247 Ps~~qv~~~d~~~~r~~~--------~~~~~PPl~TTd~~~~DqGN~sPr~mr~T~Y~iP~T~Dl~~as~iPLalvIqPf 318 (1007)
T KOG1984|consen 247 PSPPQVSIEDDSSFRSTD--------TRAQPPPLVTTDFFIQDQGNCSPRFMRCTMYTIPCTNDLLKASQIPLALVIQPF 318 (1007)
T ss_pred CCchhcccchhhhhhcCC--------ccCCCCCCcccceEEeccCCCCcchheeecccCCccHhHHHhcCCcceeEeccc
Confidence 344444 45677777743 2356777754 567788999999999999999999999999999999999999
Q ss_pred CCCC----CCCCccC---CccccCCCCcccEEcCceeEecCCCeEEeccCCCCCCCCcccccc-------cCCCCCCccc
Q psy17260 222 KEKP----DLPPLQY---EPLLCMRNQCRAILNPLCQVDYKSKLWVCNFCFQRNAFPPQYAAI-------TEQHQPAELH 287 (679)
Q Consensus 222 ~~~~----~ip~v~~---~p~RC~~~~C~AYiNpf~~~~~~g~~W~C~~C~~~N~vp~~Y~~~-------~~~~~rpEL~ 287 (679)
+... ++++|+. +|+||+| |+||||||++|+++|++|+||||+.+|++|++|+++ .|.++||||+
T Consensus 319 a~l~p~E~~~~vVd~g~sgPvRC~R--CkaYinPFmqF~~~gr~f~Cn~C~~~n~vp~~yf~~L~~~grr~D~~erpEL~ 396 (1007)
T KOG1984|consen 319 ATLTPNEAPVPVVDLGESGPVRCNR--CKAYINPFMQFIDGGRKFICNFCGSKNQVPDDYFNHLGPTGRRVDVEERPELC 396 (1007)
T ss_pred ccCCcccCCCceecCCCCCCcchhh--hhhhcCcceEEecCCceEEecCCCccccCChhhcccCCCcccccccccCchhc
Confidence 9652 4777876 5999999 999999999999999999999999999999999875 3678899998
Q ss_pred CCCcceEEecCC------CCCCCcEEEEEEECCcChhh---HHHHHHHHHHHhhcCCC---CcEEEEEEECCeEEEEEcC
Q psy17260 288 PQFTTIEYTIPK------MQCAPLVFLFVVDTCMDEEE---LGALRDSLQMSLSLLPK---NALVGLITFGQMVQVHELG 355 (679)
Q Consensus 288 ~~~~tvEy~~~~------~~~~pp~~vFvIDvs~~a~~---l~~l~~si~~~L~~Lp~---~~~VG~ITfd~~V~~y~l~ 355 (679)
.|||||++++ +++.||+|||+||||+++++ +.++|++|++.|+.+|. +.+|||||||++|||||++
T Consensus 397 --~Gt~dfvatk~Y~~~~k~p~ppafvFmIDVSy~Ai~~G~~~a~ce~ik~~l~~lp~~~p~~~Vgivtfd~tvhFfnl~ 474 (1007)
T KOG1984|consen 397 --LGTVDFVATKDYCRKTKPPKPPAFVFMIDVSYNAISNGAVKAACEAIKSVLEDLPREEPNIRVGIVTFDKTVHFFNLS 474 (1007)
T ss_pred --ccccceeeehhhhhcCCCCCCceEEEEEEeehhhhhcchHHHHHHHHHHHHhhcCccCCceEEEEEEecceeEeeccC
Confidence 7999999986 37999999999999999998 78999999999999984 6899999999999999998
Q ss_pred CCCccceeeecCCCCCchhHHHHhhhcCCCCCCCCCCCCCCCCCCCCCCCCceeehHHhHHHHHHHHHHhcCCCCcccCC
Q psy17260 356 CEGISRSYVFRGTKDVPAQRLQEMLRIGKYSMSAPAPAPRPGQPPRPARTQFLQPVEACEMYATDLLAALQKGPVAVHQG 435 (679)
Q Consensus 356 ~~~~~~~~Vf~g~~~l~~~ql~~~l~l~d~~~p~~~g~~~~~~~~~~~~~~flvpl~e~~~~i~~lLe~L~~~~~~~~~~ 435 (679)
+ .|.+++|++|.|++|.|.|| .+.++++..||+..|+.||++|+. +|.++
T Consensus 475 s-------------~L~qp~mliVsdv~dvfvPf--------------~~g~~V~~~es~~~i~~lLd~Ip~---mf~~s 524 (1007)
T KOG1984|consen 475 S-------------NLAQPQMLIVSDVDDVFVPF--------------LDGLFVNPNESRKVIELLLDSIPT---MFQDS 524 (1007)
T ss_pred c-------------cccCceEEEeeccccccccc--------------ccCeeccchHHHHHHHHHHHHhhh---hhccC
Confidence 6 58899999999998888886 467888999999999999999999 89999
Q ss_pred CCCCCchHHHHHHHHHHhhhc-c------------------CCCCCc---cC-cCCCCCCccchhHHHHHHHHHhh-hcc
Q psy17260 436 REHCGPTGVAHVIAVGLLEGT-L------------------IRSHND---IH-KGNNKLPGRMATKITKGLALRAA-YCR 491 (679)
Q Consensus 436 ~~~~~c~G~AL~~A~~lL~~~-~------------------lrs~~d---i~-~~~~~~~~~~a~~fY~~La~~~~-~~~ 491 (679)
+.++.|+|+||++|..+|+.+ | ++.+.| +. .++++++ .+++++|++||++|+ .+|
T Consensus 525 k~pes~~g~alqaa~lalk~~~gGKl~vF~s~Lpt~g~g~kl~~r~D~~l~~t~kek~l~-~pq~~~y~~LA~e~v~~g~ 603 (1007)
T KOG1984|consen 525 KIPESVFGSALQAAKLALKAADGGKLFVFHSVLPTAGAGGKLSNRDDRRLIGTDKEKNLL-QPQDKTYTTLAKEFVESGC 603 (1007)
T ss_pred CCCchhHHHHHHHHHHHHhccCCceEEEEecccccccCcccccccchhhhhcccchhhcc-CcchhHHHHHHHHHHHhCc
Confidence 999999999999999999988 3 233333 22 2445788 999999999999999 999
Q ss_pred eeEEEEcCCcccccc-------------------------------------------------cCCCeEEeeeeccccc
Q psy17260 492 AIEYLLVPPWINGLL-------------------------------------------------LEYELCLMGAIGPCVS 522 (679)
Q Consensus 492 svD~~~~~~sF~~~~-------------------------------------------------~S~gl~v~~~iG~~~~ 522 (679)
|||+|++...|.+.. ||+||++.+++|++..
T Consensus 604 svDlF~t~~ayvDvAtlg~v~~~TgG~vy~Y~~F~a~~D~~rl~nDL~~~vtk~~gf~a~mrvRtStGirv~~f~Gnf~~ 683 (1007)
T KOG1984|consen 604 SVDLFLTPNAYVDVATLGVVPALTGGQVYKYYPFQALTDGPRLLNDLVRNVTKKQGFDAVMRVRTSTGIRVQDFYGNFLM 683 (1007)
T ss_pred eEEEEEcccceeeeeeecccccccCceeEEecchhhcccHHHHHHHHHHhcccceeeeeEEEEeecCceeeeeeechhhh
Confidence 999998876553211 9999999999999997
Q ss_pred cCCCCccccccccCCCCcCeEEEcCCCCCceEEEEEEEecCCCCCCCCCCceEEEEEEEeEcCCCCEEEEEEcccccccc
Q psy17260 523 LNLKNQCVSDQDLGMGGTASWKMCTLSPNTTLALFFEIVNQHGAPIPQGGPGCIQFITHYQAPSGEKKVRVTTIARNWAD 602 (679)
Q Consensus 523 ~~~~~~~isd~~ig~g~t~~~~l~~ld~dtsia~~fei~~~~~~~l~~~~~~~iQ~allYt~~~GerriRV~T~~l~~~~ 602 (679)
++ +++++++.||+||+++++| +||++|+++..++||+|++||+.+|+||+||+|++++
T Consensus 684 ~~---------------~tDiela~lD~dkt~~v~f----khDdkLq~~s~~~fQ~AlLYTti~G~RR~Rv~Nlsl~--- 741 (1007)
T KOG1984|consen 684 RN---------------PTDIELAALDCDKTLTVEF----KHDDKLQDGSDVHFQTALLYTTIDGQRRLRVLNLSLA--- 741 (1007)
T ss_pred cC---------------CCCccccccccCceeEEEE----eccccccCCcceeEEEEEEEeccCCceeEEEEecchh---
Confidence 75 7899999999999999999 7777788889999999999999999999999999997
Q ss_pred CCCCHHHHHhccCHHHHHHHHHHHHHHHhhcCChhHHHHHHHHHHHHhhccc------------cccCCcccH-HHHHHH
Q psy17260 603 ATTQLDHISSGFDQEAAAVIMGRMVVNRAEQDDGPDVMRWADRTLIRLEGGA------------PVLTEDVSL-QVFMEH 669 (679)
Q Consensus 603 ~ss~~~~v~~s~D~ea~~~llaK~a~~~~~~~~~~d~~~~ld~~li~il~~y------------liLPe~lkl-P~~~~~ 669 (679)
++++++++|+++|+|+++++|+|.|+..+.....+++|+.|+++|+++|++| |||||+||+ |+||++
T Consensus 742 ~ts~l~~lyr~~~~d~l~a~maK~a~~~i~~~~lk~vre~l~~~~~~iL~~YRk~cas~~ssgQLILPeslKLlPly~la 821 (1007)
T KOG1984|consen 742 VTSQLSELYRSADTDPLIAIMAKQAAKAILDKPLKEVREQLVSQCAQILASYRKNCASPASSGQLILPESLKLLPLYMLA 821 (1007)
T ss_pred hhhhHHHHHHhcCccHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHhhcCCCCcccEechhhhHHHHHHHHH
Confidence 5689999999999999999999999999999999999999999999999999 999999999 999999
Q ss_pred HhccccCC
Q psy17260 670 LKKLAVSS 677 (679)
Q Consensus 670 L~rS~~l~ 677 (679)
|+||.+|+
T Consensus 822 ~lKs~~l~ 829 (1007)
T KOG1984|consen 822 LLKSSALR 829 (1007)
T ss_pred HHHhhccc
Confidence 99999998
No 4
>COG5047 SEC23 Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking and secretion]
Probab=100.00 E-value=3e-90 Score=738.31 Aligned_cols=485 Identities=44% Similarity=0.714 Sum_probs=442.8
Q ss_pred cCCCCeeeeeccccCCCHHHHhhCCCCeEEEEccCCCCCCCCCccCCccccCCCCcccEEcCceeEecCCCeEEeccCCC
Q psy17260 187 NEERDGIRCTWNVWPSSKLEASRLVMPVGCLYQPLKEKPDLPPLQYEPLLCMRNQCRAILNPLCQVDYKSKLWVCNFCFQ 266 (679)
Q Consensus 187 n~~p~~iR~T~~~~P~t~~~~~~~~lPlg~vv~Pf~~~~~ip~v~~~p~RC~~~~C~AYiNpf~~~~~~g~~W~C~~C~~ 266 (679)
+++.++||+|||+||+|+.++.++.+|++|+|+||++.+++++..|+|+.|..| |+||+||||.+|.+.+.|+|+||+.
T Consensus 6 iee~dgir~twnvfpat~~da~~~~iPia~lY~Pl~e~~~~~v~~yepv~C~~p-C~avlnpyC~id~r~~~W~CpfCnq 84 (755)
T COG5047 6 IEENDGIRLTWNVFPATRGDATRTVIPIACLYTPLHEDDALTVNYYEPVKCTAP-CKAVLNPYCHIDERNQSWICPFCNQ 84 (755)
T ss_pred hccccceEEEEecccCCccccccccccHHHhccccccccccCcccCCCceeccc-chhhcCcceeeccCCceEecceecC
Confidence 789999999999999999999999999999999999987888899999999997 9999999999999999999999999
Q ss_pred CCCCCcccccccCCCCCCcccCCCcceEEecCCCCCCCcEEEEEEECCcChhhHHHHHHHHHHHhhcCCCCcEEEEEEEC
Q psy17260 267 RNAFPPQYAAITEQHQPAELHPQFTTIEYTIPKMQCAPLVFLFVVDTCMDEEELGALRDSLQMSLSLLPKNALVGLITFG 346 (679)
Q Consensus 267 ~N~vp~~Y~~~~~~~~rpEL~~~~~tvEy~~~~~~~~pp~~vFvIDvs~~a~~l~~l~~si~~~L~~Lp~~~~VG~ITfd 346 (679)
.|.+|++|..++..+.++||-+++.|+||+.++.+..||+|+||||++++.++|.+++++|...|+.+|+++.||||||+
T Consensus 85 rn~lp~qy~~iS~~~LplellpqssTiey~lskp~~~ppvf~fvvD~~~D~e~l~~LkdslivslsllppeaLvglItyg 164 (755)
T COG5047 85 RNTLPPQYRDISNANLPLELLPQSSTIEYTLSKPVILPPVFFFVVDACCDEEELTALKDSLIVSLSLLPPEALVGLITYG 164 (755)
T ss_pred CCCCChhhcCCCcccCCccccCCCceEEEEccCCccCCceEEEEEEeecCHHHHHHHHHHHHHHHhcCCccceeeEEEec
Confidence 99999999999999999999889999999999888889999999999999999999999999999999999999999999
Q ss_pred CeEEEEEcCCCCccceeeecCCCCCchhHHHHhhhcCCCCCCCCCCC-C-CCCCCCCCCCCCceeehHHhHHHHHHHHHH
Q psy17260 347 QMVQVHELGCEGISRSYVFRGTKDVPAQRLQEMLRIGKYSMSAPAPA-P-RPGQPPRPARTQFLQPVEACEMYATDLLAA 424 (679)
Q Consensus 347 ~~V~~y~l~~~~~~~~~Vf~g~~~l~~~ql~~~l~l~d~~~p~~~g~-~-~~~~~~~~~~~~flvpl~e~~~~i~~lLe~ 424 (679)
+.|++|+++...+.|++||+|+++|+.+++.+|+.....-.| .|. + +++. ......+|+.|+++|+..+.++||+
T Consensus 165 t~i~v~el~ae~~~r~~VF~g~~eyt~~~L~~ll~~~~~~~~--~~~es~is~~-~~~~~~rFl~p~q~ce~~L~n~le~ 241 (755)
T COG5047 165 TSIQVHELNAENHRRSYVFSGNKEYTKENLQELLALSKPTKS--GGFESKISGI-GQFASSRFLLPTQQCEFKLLNILEQ 241 (755)
T ss_pred ceeEEEeccccccCcceeecchHHHHHHHHHHHhcccCCCCc--chhhhhcccc-cccchhhhhccHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999977522222 011 0 0100 0113457999999999999999999
Q ss_pred hcCCCCcccCCCCCCCchHHHHHHHHHHhhhcc------------------------------CCCCCccCcCCCCCCcc
Q psy17260 425 LQKGPVAVHQGREHCGPTGVAHVIAVGLLEGTL------------------------------IRSHNDIHKGNNKLPGR 474 (679)
Q Consensus 425 L~~~~~~~~~~~~~~~c~G~AL~~A~~lL~~~~------------------------------lrs~~di~~~~~~~~~~ 474 (679)
|.+|+|+++.++|+.||+|+||.+|+.+|+.++ +|+||+++.+.++|. +
T Consensus 242 L~pd~~~v~~~~Rp~RCTGsAl~ias~Ll~~~~p~~~~~i~lF~~GPcTvGpG~Vvs~elkEpmRshH~ie~d~aqh~-k 320 (755)
T COG5047 242 LQPDPWPVPAGKRPLRCTGSALNIASSLLEQCFPNAGCHIVLFAGGPCTVGPGTVVSTELKEPMRSHHDIESDSAQHS-K 320 (755)
T ss_pred hCCCCccCCCCCCCccccchhHHHHHHHHHhhccCcceeEEEEcCCCccccCceeeehhhcccccccccccccchhhc-c
Confidence 999999999999999999999999999999874 899999998889999 9
Q ss_pred chhHHHHHHHHHhh--------hcceeE----------------EEEcCCcccccc------------------------
Q psy17260 475 MATKITKGLALRAA--------YCRAIE----------------YLLVPPWINGLL------------------------ 506 (679)
Q Consensus 475 ~a~~fY~~La~~~~--------~~~svD----------------~~~~~~sF~~~~------------------------ 506 (679)
+++|||++||++++ +++|+| .++++|+|++++
T Consensus 321 ka~KFY~~laeR~a~~gh~~DifagcldqIGI~eM~~L~~sTgg~lvlsdsF~t~ifkqSfqrif~~d~~g~l~~gfNa~ 400 (755)
T COG5047 321 KATKFYKGLAERVANQGHALDIFAGCLDQIGIMEMEPLTTSTGGALVLSDSFTTSIFKQSFQRIFNRDSEGYLKMGFNAN 400 (755)
T ss_pred chHHHHHHHHHHHhccchhHHHHHHHHHhhhhhcchhhccCCcceEEEeccccHHHHHHHHHHHhCcCcccchhhhhccc
Confidence 99999999999998 666666 457888887655
Q ss_pred ----cCCCeEEeeeeccccccCCCCccccccccCCCCcCeEEEcCCCCCceEEEEEEEecCCCCCC-CCCCceEEEEEEE
Q psy17260 507 ----LEYELCLMGAIGPCVSLNLKNQCVSDQDLGMGGTASWKMCTLSPNTTLALFFEIVNQHGAPI-PQGGPGCIQFITH 581 (679)
Q Consensus 507 ----~S~gl~v~~~iG~~~~~~~~~~~isd~~ig~g~t~~~~l~~ld~dtsia~~fei~~~~~~~l-~~~~~~~iQ~all 581 (679)
||++++++|+||+....++++++|||.+||+|.|+.|+++++.|.+++++.||+...+.... +....+||||.+.
T Consensus 401 m~V~TsKnl~~~g~ig~a~~~~k~~~ni~~~eigi~~t~swkm~slsPk~nyal~fei~~~~~~~~~~~~~~a~iQfiT~ 480 (755)
T COG5047 401 MEVKTSKNLKIKGLIGHAVSVKKKANNISDSEIGIGATNSWKMASLSPKSNYALYFEIALGAASGSAQRPAEAYIQFITT 480 (755)
T ss_pred eeEeeccCceeeeeecceeeecccccccccccccccccccccccccCCCcceEEEEEeccccCCCccCCcccchhhhhhh
Confidence 99999999999999999999999999999999999999999999999999999998765432 2336799999999
Q ss_pred eEcCCCCEEEEEEccccccccCCCCHHHHHhccCHHHHHHHHHHHHHHHhhcCChhHHHHHHHHHHHHhhccc-------
Q psy17260 582 YQAPSGEKKVRVTTIARNWADATTQLDHISSGFDQEAAAVIMGRMVVNRAEQDDGPDVMRWADRTLIRLEGGA------- 654 (679)
Q Consensus 582 Yt~~~GerriRV~T~~l~~~~~ss~~~~v~~s~D~ea~~~llaK~a~~~~~~~~~~d~~~~ld~~li~il~~y------- 654 (679)
|++++|.-||||+|+++.+++ +....++++|||||+++++||+|++|+..++..|+.+|+|+.++|++++|
T Consensus 481 yQhss~t~riRVtTvar~f~~--~~~p~i~~SFdqEaaaV~~aR~a~~K~~~ed~~Dv~rw~dr~lirlcq~fa~y~k~d 558 (755)
T COG5047 481 YQHSSGTYRIRVTTVARMFTD--GGLPKINRSFDQEAAAVFMARIAAFKAETEDIIDVFRWIDRNLIRLCQKFADYRKDD 558 (755)
T ss_pred hhccCCcEEEEEeehhhhhcc--CCChhhhhcchhhHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHHHHhcCCCC
Confidence 999999999999999998874 44578999999999999999999999999999999999999999999999
Q ss_pred ---cccCCcccH-HHHHHHHhccccCCC
Q psy17260 655 ---PVLTEDVSL-QVFMEHLKKLAVSST 678 (679)
Q Consensus 655 ---liLPe~lkl-P~~~~~L~rS~~l~~ 678 (679)
|.|+++|.+ |+||||||||++|+.
T Consensus 559 pssfrl~~~f~lypqf~y~lrRSpfL~v 586 (755)
T COG5047 559 PSSFRLDPNFTLYPQFMYHLRRSPFLSV 586 (755)
T ss_pred chhhcCCcchhhhhHHHhhhhccceeec
Confidence 999999999 999999999999874
No 5
>KOG1985|consensus
Probab=100.00 E-value=1.6e-83 Score=713.13 Aligned_cols=436 Identities=20% Similarity=0.308 Sum_probs=389.7
Q ss_pred hccCCCCeeeeeccccCCCHHHHhhCCCCeEEEEccCCCCC---CCCCcc-CCccccCCCCcccEEcCceeEecCCCeEE
Q psy17260 185 YQNEERDGIRCTWNVWPSSKLEASRLVMPVGCLYQPLKEKP---DLPPLQ-YEPLLCMRNQCRAILNPLCQVDYKSKLWV 260 (679)
Q Consensus 185 ~~n~~p~~iR~T~~~~P~t~~~~~~~~lPlg~vv~Pf~~~~---~ip~v~-~~p~RC~~~~C~AYiNpf~~~~~~g~~W~ 260 (679)
.-||+|+|+|+|++++|.+.+++++++||||++|+||++.+ .+|++. ..++||++ ||+||||||.|++.|++|+
T Consensus 165 ~~nc~p~y~RsTl~~iP~t~sLl~kskLPlglvv~Pf~~~~d~~~~p~~~~~~IvRCr~--CRtYiNPFV~fid~gr~Wr 242 (887)
T KOG1985|consen 165 SSNCSPSYVRSTLSAIPQTQSLLKKSKLPLGLVVHPFAHLDDIDPLPVITSTLIVRCRR--CRTYINPFVEFIDQGRRWR 242 (887)
T ss_pred ccCCCHHHHHHHHHhCCccHHHHHhcCCCceEEEeecccccccCCCCcccCCceeeehh--hhhhcCCeEEecCCCceee
Confidence 45999999999999999999999999999999999999543 445444 36899999 9999999999999999999
Q ss_pred eccCCCCCCCCcccccc------cCCCCCCcccCCCcceEEecCC----CCCCCcEEEEEEECCcChhh---HHHHHHHH
Q psy17260 261 CNFCFQRNAFPPQYAAI------TEQHQPAELHPQFTTIEYTIPK----MQCAPLVFLFVVDTCMDEEE---LGALRDSL 327 (679)
Q Consensus 261 C~~C~~~N~vp~~Y~~~------~~~~~rpEL~~~~~tvEy~~~~----~~~~pp~~vFvIDvs~~a~~---l~~l~~si 327 (679)
||+|+..|++|.+|... .+.++|||+. +++|||++|. ++|+|++|||+||||.++++ |+.++++|
T Consensus 243 CNlC~~~NdvP~~f~~~~~t~~~~~~~~RpEl~--~s~vE~iAP~eYmlR~P~Pavy~FliDVS~~a~ksG~L~~~~~sl 320 (887)
T KOG1985|consen 243 CNLCGRVNDVPDDFDWDPLTGAYGDPYSRPELT--SSVVEFIAPSEYMLRPPQPAVYVFLIDVSISAIKSGYLETVARSL 320 (887)
T ss_pred echhhhhcCCcHHhhcCccccccCCcccCcccc--ceeEEEecCcccccCCCCCceEEEEEEeehHhhhhhHHHHHHHHH
Confidence 99999999999998653 3678899996 8999999997 58999999999999999988 89999999
Q ss_pred HHHhhcCC--CCcEEEEEEECCeEEEEEcCCCCccceeeecCCCCCchhHHHHhhhcCCCCCCCCCCCCCCCCCCCCCCC
Q psy17260 328 QMSLSLLP--KNALVGLITFGQMVQVHELGCEGISRSYVFRGTKDVPAQRLQEMLRIGKYSMSAPAPAPRPGQPPRPART 405 (679)
Q Consensus 328 ~~~L~~Lp--~~~~VG~ITfd~~V~~y~l~~~~~~~~~Vf~g~~~l~~~ql~~~l~l~d~~~p~~~g~~~~~~~~~~~~~ 405 (679)
+..|+.|| ++++|||||||++||||+++++ ++++||+++.|++|.|.|+ .+
T Consensus 321 L~~LD~lpgd~Rt~igfi~fDs~ihfy~~~~~-------------~~qp~mm~vsdl~d~flp~--------------pd 373 (887)
T KOG1985|consen 321 LENLDALPGDPRTRIGFITFDSTIHFYSVQGD-------------LNQPQMMIVSDLDDPFLPM--------------PD 373 (887)
T ss_pred HHhhhcCCCCCcceEEEEEeeceeeEEecCCC-------------cCCCceeeeccccccccCC--------------ch
Confidence 99999999 6799999999999999999863 3588876666666665552 37
Q ss_pred CceeehHHhHHHHHHHHHHhcCCCCcccCCCCCCCchHHHHHHHHHHhhhcc------CCCCCccC--------------
Q psy17260 406 QFLQPVEACEMYATDLLAALQKGPVAVHQGREHCGPTGVAHVIAVGLLEGTL------IRSHNDIH-------------- 465 (679)
Q Consensus 406 ~flvpl~e~~~~i~~lLe~L~~~~~~~~~~~~~~~c~G~AL~~A~~lL~~~~------lrs~~di~-------------- 465 (679)
.||+|+++||+.|..+|++|+. +|.+++..++|+|+||++|..+|+..| ..++++++
T Consensus 374 ~lLv~L~~ck~~i~~lL~~lp~---~F~~~~~t~~alGpALkaaf~li~~~GGri~vf~s~lPnlG~G~L~~rEdp~~~~ 450 (887)
T KOG1985|consen 374 SLLVPLKECKDLIETLLKTLPE---MFQDTRSTGSALGPALKAAFNLIGSTGGRISVFQSTLPNLGAGKLKPREDPNVRS 450 (887)
T ss_pred hheeeHHHHHHHHHHHHHHHHH---HHhhccCcccccCHHHHHHHHHHhhcCCeEEEEeccCCCCCcccccccccccccc
Confidence 8999999999999999999999 899999999999999999999999987 33444321
Q ss_pred -cCCCCCCccchhHHHHHHHHHhh-hcceeEEEEcCCcccccc-------------------------------------
Q psy17260 466 -KGNNKLPGRMATKITKGLALRAA-YCRAIEYLLVPPWINGLL------------------------------------- 506 (679)
Q Consensus 466 -~~~~~~~~~~a~~fY~~La~~~~-~~~svD~~~~~~sF~~~~------------------------------------- 506 (679)
+++..++ .+++.|||+||.+|+ +++|||+|++++.|.+-.
T Consensus 451 s~~~~qlL-~~~t~FYK~~a~~cs~~qI~VDlFl~s~qY~DlAsLs~LskySgG~~y~YP~f~~s~p~~~~Kf~~el~r~ 529 (887)
T KOG1985|consen 451 SDEDSQLL-SPATDFYKDLALECSKSQICVDLFLFSEQYTDLASLSCLSKYSGGQVYYYPSFDGSNPHDVLKFARELARY 529 (887)
T ss_pred chhhhhcc-CCCchHHHHHHHHhccCceEEEEEeecccccchhhhhccccccCceeEEccCCCCCCHHHHHHHHHHHHHH
Confidence 2334577 999999999999999 999999998887653210
Q ss_pred --------------cCCCeEEeeeeccccccCCCCccccccccCCCCcCeEEEcCCCCCceEEEEEEEecCCCCCCCCCC
Q psy17260 507 --------------LEYELCLMGAIGPCVSLNLKNQCVSDQDLGMGGTASWKMCTLSPNTTLALFFEIVNQHGAPIPQGG 572 (679)
Q Consensus 507 --------------~S~gl~v~~~iG~~~~~~~~~~~isd~~ig~g~t~~~~l~~ld~dtsia~~fei~~~~~~~l~~~~ 572 (679)
||+|+++++++|||+.++ ++...++++++|++++|++++++... ..
T Consensus 530 Ltr~~~feaVmRiR~S~gl~~~~f~GnFF~RS---------------tDLla~~~v~~D~sy~~qisiEesl~-----~~ 589 (887)
T KOG1985|consen 530 LTRKIGFEAVMRIRCSTGLRMSSFFGNFFVRS---------------TDLLALPNVNPDQSYAFQISIEESLT-----TG 589 (887)
T ss_pred hhhhhhhheeEEeeccccccccceecccccCc---------------HHHhcccCCCCCccceEEEEeehhcC-----Cc
Confidence 999999999999999887 78999999999999999999998743 45
Q ss_pred ceEEEEEEEeEcCCCCEEEEEEccccccccCCCCHHHHHhccCHHHHHHHHHHHHHHHhhcCChhHHHHHHHHHHHHhhc
Q psy17260 573 PGCIQFITHYQAPSGEKKVRVTTIARNWADATTQLDHISSGFDQEAAAVIMGRMVVNRAEQDDGPDVMRWADRTLIRLEG 652 (679)
Q Consensus 573 ~~~iQ~allYt~~~GerriRV~T~~l~~~~~ss~~~~v~~s~D~ea~~~llaK~a~~~~~~~~~~d~~~~ld~~li~il~ 652 (679)
+.+||.|++||...|||||||||++++++ +++++||+++|++|++.+|+++|+.+.++..+.|+|+.|.+.+++++.
T Consensus 590 ~~~fQvAlLyT~~~GERRIRV~T~~lpt~---~sl~evY~saD~~AI~~lla~~Av~ksl~ssL~dardal~~~~~D~l~ 666 (887)
T KOG1985|consen 590 FCVFQVALLYTLSKGERRIRVHTLCLPTV---SSLNEVYASADQEAIASLLAKKAVEKSLSSSLSDARDALTNAVVDILN 666 (887)
T ss_pred eeEEEeeeeecccCCceeEEEEEeecccc---ccHHHHHhhcCHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHH
Confidence 68899999999999999999999999965 789999999999999999999999999999999999999999999999
Q ss_pred cc-------------cccCCcccH-HHHHHHHhccccCCC
Q psy17260 653 GA-------------PVLTEDVSL-QVFMEHLKKLAVSST 678 (679)
Q Consensus 653 ~y-------------liLPe~lkl-P~~~~~L~rS~~l~~ 678 (679)
.| |.+|.+|++ |+|+++|.|++.|++
T Consensus 667 aYk~~~~~~~~~~~~l~~p~~LrllPllvlALlK~~~fr~ 706 (887)
T KOG1985|consen 667 AYKKLVSNQNGQGITLSLPASLRLLPLLVLALLKHPAFRP 706 (887)
T ss_pred HHHHHhcccccCCcceecCcchhhhHHHHHHHhcCCcccC
Confidence 99 899999999 999999999999875
No 6
>COG5028 Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]
Probab=100.00 E-value=5.8e-77 Score=655.77 Aligned_cols=448 Identities=17% Similarity=0.288 Sum_probs=387.8
Q ss_pred cccCCcc-chhhhhhccCCCCeeeeeccccCCCHHHHhhCCCCeEEEEccCCCCC-C---CCCccC-CccccCCCCcccE
Q psy17260 172 ELKISMT-TYEEFFYQNEERDGIRCTWNVWPSSKLEASRLVMPVGCLYQPLKEKP-D---LPPLQY-EPLLCMRNQCRAI 245 (679)
Q Consensus 172 ~~~~p~~-~~~~~~~~n~~p~~iR~T~~~~P~t~~~~~~~~lPlg~vv~Pf~~~~-~---ip~v~~-~p~RC~~~~C~AY 245 (679)
...+|++ .+....++||+|+|+|+|+|++|.+.+++++++||||++|+||.++. + +|++.. .|+||++ ||+|
T Consensus 131 ~~~ppltt~~~~~e~~n~~p~yvrsT~yaiP~t~dl~~~skiPfgLVI~Pf~~l~~e~~~vpl~~d~~ivRCrr--CrsY 208 (861)
T COG5028 131 PIVPPLTTNFVGSEQSNCSPKYVRSTMYAIPETNDLLKKSKIPFGLVIRPFLELYPEEDPVPLVEDGSIVRCRR--CRSY 208 (861)
T ss_pred CCCCCcccceeeeccCCCCHHHHHHHHhhCCCchhHHHhcCCCceEEeehhhhcCccCCCCccCCCCcchhhhh--hHhh
Confidence 3455663 35678889999999999999999999999999999999999999763 2 333322 3899999 9999
Q ss_pred EcCceeEecCCCeEEeccCCCCCCCCcccccc-------cCCCCCCcccCCCcceEEecCC----CCCCCcEEEEEEECC
Q psy17260 246 LNPLCQVDYKSKLWVCNFCFQRNAFPPQYAAI-------TEQHQPAELHPQFTTIEYTIPK----MQCAPLVFLFVVDTC 314 (679)
Q Consensus 246 iNpf~~~~~~g~~W~C~~C~~~N~vp~~Y~~~-------~~~~~rpEL~~~~~tvEy~~~~----~~~~pp~~vFvIDvs 314 (679)
+|||..|+++|++|+||+|+.+|++|.+++.. .|.+.|+||. +++|||.+|+ +.+.||+|||+||||
T Consensus 209 iNPfv~fi~~g~kw~CNiC~~kN~vp~~~~~~~~~~~~r~d~~~r~El~--~~vvdf~ap~~Y~~~~p~P~~yvFlIDVS 286 (861)
T COG5028 209 INPFVQFIEQGRKWRCNICRSKNDVPEGFDNPSGPNDPRSDRYSRPELK--SGVVDFLAPKEYSLRQPPPPVYVFLIDVS 286 (861)
T ss_pred cCceEEEecCCcEEEEeeccccccCcccccCcCCCCCccccccccchhh--ceeeEEecccceeeccCCCCEEEEEEEee
Confidence 99999999999999999999999999998732 3477899997 7999999997 366799999999999
Q ss_pred cChhh---HHHHHHHHHHHhhcCC---CCcEEEEEEECCeEEEEEcCCCCccceeeecCCCCCchhHHHHhhhcCCCCCC
Q psy17260 315 MDEEE---LGALRDSLQMSLSLLP---KNALVGLITFGQMVQVHELGCEGISRSYVFRGTKDVPAQRLQEMLRIGKYSMS 388 (679)
Q Consensus 315 ~~a~~---l~~l~~si~~~L~~Lp---~~~~VG~ITfd~~V~~y~l~~~~~~~~~Vf~g~~~l~~~ql~~~l~l~d~~~p 388 (679)
..+.+ +.++.++|++.|+.+| +++||+||.||++||||+++.+ + .+|+.++.++++.|.|
T Consensus 287 ~~a~~~g~~~a~~r~Il~~l~~~~~~dpr~kIaii~fD~sl~ffk~s~d-------------~-~~~~~~vsdld~pFlP 352 (861)
T COG5028 287 FEAIKNGLVKAAIRAILENLDQIPNFDPRTKIAIICFDSSLHFFKLSPD-------------L-DEQMLIVSDLDEPFLP 352 (861)
T ss_pred hHhhhcchHHHHHHHHHhhccCCCCCCCcceEEEEEEcceeeEEecCCC-------------C-ccceeeeccccccccc
Confidence 99988 6777788888888876 4799999999999999999863 2 2354444444444444
Q ss_pred CCCCCCCCCCCCCCCCCCceeehHHhHHHHHHHHHHhcCCCCcccCCCCCCCchHHHHHHHHHHhhhcc------CCCCC
Q psy17260 389 APAPAPRPGQPPRPARTQFLQPVEACEMYATDLLAALQKGPVAVHQGREHCGPTGVAHVIAVGLLEGTL------IRSHN 462 (679)
Q Consensus 389 ~~~g~~~~~~~~~~~~~~flvpl~e~~~~i~~lLe~L~~~~~~~~~~~~~~~c~G~AL~~A~~lL~~~~------lrs~~ 462 (679)
| ..+.|++|+++|+..++.||+.++. .|.+++.++.|+|+||++|..+++.+| +.++|
T Consensus 353 f-------------~s~~fv~pl~~~k~~~etLl~~~~~---If~d~~~pk~~~G~aLk~a~~l~g~~GGkii~~~stlP 416 (861)
T COG5028 353 F-------------PSGLFVLPLKSCKQIIETLLDRVPR---IFQDNKSPKNALGPALKAAKSLIGGTGGKIIVFLSTLP 416 (861)
T ss_pred C-------------CcchhcccHHHHHHHHHHHHHHhhh---hhcccCCCccccCHHHHHHHHHhhccCceEEEEeecCC
Confidence 3 3468999999999988899999998 788899999999999999999999997 56777
Q ss_pred ccCc--------CCCCCCccchhHHHHHHHHHhh-hcceeEEEEcCCcccc-----------------------------
Q psy17260 463 DIHK--------GNNKLPGRMATKITKGLALRAA-YCRAIEYLLVPPWING----------------------------- 504 (679)
Q Consensus 463 di~~--------~~~~~~~~~a~~fY~~La~~~~-~~~svD~~~~~~sF~~----------------------------- 504 (679)
.++- ++..++ +...+||+++|.+|+ .+||||+|+.++.|.+
T Consensus 417 n~G~Gkl~~r~d~e~~ll-~c~d~fYk~~a~e~~k~gIsvd~Flt~~~yidvaTls~l~~~T~G~~~~Yp~f~~~~~~d~ 495 (861)
T COG5028 417 NMGIGKLQLREDKESSLL-SCKDSFYKEFAIECSKVGISVDLFLTSEDYIDVATLSHLCRYTGGQTYFYPNFSATRPNDA 495 (861)
T ss_pred Ccccccccccccchhhhc-cccchHHHHHHHHHHHhcceEEEEeccccccchhhhcchhhccCcceEEcCCcccCCchhH
Confidence 6531 234577 999999999999999 9999999988765421
Q ss_pred -----cc-----------------cCCCeEEeeeeccccccCCCCccccccccCCCCcCeEEEcCCCCCceEEEEEEEec
Q psy17260 505 -----LL-----------------LEYELCLMGAIGPCVSLNLKNQCVSDQDLGMGGTASWKMCTLSPNTTLALFFEIVN 562 (679)
Q Consensus 505 -----~~-----------------~S~gl~v~~~iG~~~~~~~~~~~isd~~ig~g~t~~~~l~~ld~dtsia~~fei~~ 562 (679)
++ ||+|+++.++|||++.+. .++..++.+++|+|+.|+|++++
T Consensus 496 ~kl~~dL~~~ls~~~gy~~~~rvR~S~glr~s~fyGnf~~rs---------------~dl~~F~tm~rd~Sl~~~~sid~ 560 (861)
T COG5028 496 TKLANDLVSHLSMEIGYEAVMRVRCSTGLRVSSFYGNFFNRS---------------SDLCAFSTMPRDTSLLVEFSIDE 560 (861)
T ss_pred HHHHHHHHHhhhhhhhhheeeEeeccCceehhhhhccccccC---------------cccccccccCCCceEEEEEEecc
Confidence 00 999999999999999886 46899999999999999999888
Q ss_pred CCCCCCCCCCceEEEEEEEeEcCCCCEEEEEEccccccccCCCCHHHHHhccCHHHHHHHHHHHHHHHhhcCChhHHHHH
Q psy17260 563 QHGAPIPQGGPGCIQFITHYQAPSGEKKVRVTTIARNWADATTQLDHISSGFDQEAAAVIMGRMVVNRAEQDDGPDVMRW 642 (679)
Q Consensus 563 ~~~~~l~~~~~~~iQ~allYt~~~GerriRV~T~~l~~~~~ss~~~~v~~s~D~ea~~~llaK~a~~~~~~~~~~d~~~~ 642 (679)
+ +. ...+|||+|++||..+|+|||||.|+++++ ++++.++|+++||+|++.+|+|+|+.++......++++.
T Consensus 561 ~----l~-~~~v~fQvAlL~T~~~GeRRiRVvn~s~~~---ss~~~evyasadq~aIa~~lak~a~~~~~~~s~~~~r~~ 632 (861)
T COG5028 561 K----LM-TSDVYFQVALLYTLNDGERRIRVVNLSLPT---SSSIREVYASADQLAIACILAKKASTKALNSSLKEARVL 632 (861)
T ss_pred c----cc-CCceEEEEEEEeeccCCceEEEEEEecccc---chhHHHHHHhccHHHHHHHHHHHHHHHhhhhhHHHHHHH
Confidence 7 33 378999999999999999999999999985 478899999999999999999999999999999999999
Q ss_pred HHHHHHHhhccc------------cccCCcccH-HHHHHHHhccccCC
Q psy17260 643 ADRTLIRLEGGA------------PVLTEDVSL-QVFMEHLKKLAVSS 677 (679)
Q Consensus 643 ld~~li~il~~y------------liLPe~lkl-P~~~~~L~rS~~l~ 677 (679)
|++.+++||+.| ++||+|+++ |++|++|.||-+|+
T Consensus 633 i~~s~~~IL~~Ykk~~~~snt~tql~Lp~nL~lLPll~lal~Ks~~~r 680 (861)
T COG5028 633 INKSMVDILKAYKKELVKSNTSTQLPLPANLKLLPLLMLALLKSSAFR 680 (861)
T ss_pred HHHHHHHHHHHHHHHHhhccCCccccchhhhHHHHHHHHHHhhhcccc
Confidence 999999999999 999999999 99999999999987
No 7
>PTZ00395 Sec24-related protein; Provisional
Probab=100.00 E-value=1.6e-73 Score=657.98 Aligned_cols=496 Identities=14% Similarity=0.114 Sum_probs=388.9
Q ss_pred cccchhhccccCCCCCCCCCCCCCCCcchhhhhhhhcccccCCc--cchhhhhhccCCCCeeeeeccccCCCHHHHhhCC
Q psy17260 134 MSLTDLLGGLQKDPWPVHQGKRALRSTGVALSIAVGLLELKISM--TTYEEFFYQNEERDGIRCTWNVWPSSKLEASRLV 211 (679)
Q Consensus 134 ~~l~~~le~L~~d~~~v~~~~R~~r~tg~al~va~~ll~~~~p~--~~~~~~~~~n~~p~~iR~T~~~~P~t~~~~~~~~ 211 (679)
++.+.|=-+=.+.|..+.+|+|..|+.-+. +|+ ....||+ +.|-..|+|||+|+|||+|+|.+|.+.++++.+.
T Consensus 598 ~~~~ri~~~~ip~p~~~~~~~~~~~~~~~~---~t~-k~~~pp~~~~~~~~~dtgn~dP~~~r~tmY~iP~~~~~~~~~~ 673 (1560)
T PTZ00395 598 KTINRIDMNKIPRPIINTQEKKKKKNLKVF---ETC-KYISPPSYYQPYISIDTGKADPRFLKSTLYQIPLFSETLKLSQ 673 (1560)
T ss_pred ccccccCcccCCCcccccccccccccchhh---hhc-cCCCCCCCCCceEEeecCCCChhhhhhhhhcCcchHHHHHhcC
Confidence 444555444456666777899998886544 555 3344454 3467889999999999999999999999999999
Q ss_pred CCeEEEEccCCCCC---CCCCcc-----------CCccccCCCCcccEEcCceeEecCCCeEEeccCCCCCCCCcc----
Q psy17260 212 MPVGCLYQPLKEKP---DLPPLQ-----------YEPLLCMRNQCRAILNPLCQVDYKSKLWVCNFCFQRNAFPPQ---- 273 (679)
Q Consensus 212 lPlg~vv~Pf~~~~---~ip~v~-----------~~p~RC~~~~C~AYiNpf~~~~~~g~~W~C~~C~~~N~vp~~---- 273 (679)
||||++++||+.+. ++|.++ ++++||.+ |++|+|+++.++- +++++|+||++.+.+.+.
T Consensus 674 iP~gi~v~Pfa~~~~~e~~~~~~~~~~~~d~~~~~~~~rc~~--c~~y~~~~~~~~~-~~~~~c~~c~~~~~i~e~~~~~ 750 (1560)
T PTZ00395 674 IPFGIIVNPFACLNEGEGIDKIDMKDIINDKEENIEILRCPK--CLGYLHATILEDI-SSSVQCVFCDTDFLINENVLFD 750 (1560)
T ss_pred CCceeecchhhhcCCCCCCcccchhhcccchhhccceeecch--hHhhhcchheecc-cceEEEEecCCcchhhHHHHHH
Confidence 99999999999853 355443 36899999 9999999999986 499999999999886432
Q ss_pred ---ccc-c----cCCC-----CCCcccCCCcceEEecCC-----------------------------------------
Q psy17260 274 ---YAA-I----TEQH-----QPAELHPQFTTIEYTIPK----------------------------------------- 299 (679)
Q Consensus 274 ---Y~~-~----~~~~-----~rpEL~~~~~tvEy~~~~----------------------------------------- 299 (679)
|.. + .+.+ ..|-| .|+||+++|.
T Consensus 751 ~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 827 (1560)
T PTZ00395 751 IFQYNEKIGHKESDHNEHGNSLSPLL---KGSVDIIIPPIYYHNVNKFKLTYTYLNKNINQTAFMITNKIMSFTKHISNS 827 (1560)
T ss_pred HHHHhhhhccccccccccccccchhh---cCceeEEccchhhccCCccceeeehhhcchhhhhhhhhhhhhhhhhhhcch
Confidence 100 0 0000 00111 1222211110
Q ss_pred --------------------------------------------------------------------------------
Q psy17260 300 -------------------------------------------------------------------------------- 299 (679)
Q Consensus 300 -------------------------------------------------------------------------------- 299 (679)
T Consensus 828 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 907 (1560)
T PTZ00395 828 LVANDSKGGNKATSASAFGDSGDANFLAGGGYTNYGGAGGYNTYDNQSGYNNHDVVNNRGGSGAGNHLYGKDHDVQNFDN 907 (1560)
T ss_pred heecccccccccchhhhcccccccccccccccccccccccccccccccccccccccccccccCcCcccccCcccccchhh
Confidence
Q ss_pred ----------------------------------------CCCCCcEEEEEEECCcChhh---HHHHHHHHHHHhhcCC-
Q psy17260 300 ----------------------------------------MQCAPLVFLFVVDTCMDEEE---LGALRDSLQMSLSLLP- 335 (679)
Q Consensus 300 ----------------------------------------~~~~pp~~vFvIDvs~~a~~---l~~l~~si~~~L~~Lp- 335 (679)
+.++||+|+||||||+.+++ +.+++++|+++|+.|+
T Consensus 908 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~PP~YvFLIDVS~~AVkSGLl~tacesIK~sLDsL~d 987 (1560)
T PTZ00395 908 VMDNANFTIHDMKNLICEKNGEPDSAKIRRNSFLAKYPQVKNMLPPYFVFVVECSYNAIYNNITYTILEGIRYAVQNVKC 987 (1560)
T ss_pred hccCCceeeecchhhhhcccCCchhhhhhccchhhccccccCCCCCEEEEEEECCHHHHhhChHHHHHHHHHHHHhcCCC
Confidence 03679999999999999998 7899999999999997
Q ss_pred CCcEEEEEEECCeEEEEEcCCCCccceeeecCCCCCchhHHHHhhhcCCCCCCCCCCCCCCCCCCCCCCCCceeehHHhH
Q psy17260 336 KNALVGLITFGQMVQVHELGCEGISRSYVFRGTKDVPAQRLQEMLRIGKYSMSAPAPAPRPGQPPRPARTQFLQPVEACE 415 (679)
Q Consensus 336 ~~~~VG~ITfd~~V~~y~l~~~~~~~~~Vf~g~~~l~~~ql~~~l~l~d~~~p~~~g~~~~~~~~~~~~~~flvpl~e~~ 415 (679)
++++|||||||++||||+|+...-....-=.+...++++||++|.||+|.|+|+ +.+.+|+++.|++
T Consensus 988 pRTRVGIITFDSsLHFYNLks~l~~~~~~~~~~~~l~qPQMLVVSDLDDPFLPl-------------P~ddLLVnL~ESR 1054 (1560)
T PTZ00395 988 PQTKIAIITFNSSIYFYHCKGGKGVSGEEGDGGGGSGNHQVIVMSDVDDPFLPL-------------PLEDLFFGCVEEI 1054 (1560)
T ss_pred CCcEEEEEEecCcEEEEecCcccccccccccccccCCCceEEeecCCccCcCCC-------------CccCeeechHHHH
Confidence 569999999999999999975300000000122346789987777777777663 3368999999999
Q ss_pred HHHHHHHHHhcCCCCcccCCCCCCCchHHHHHHHHHHhhhcc--------CCCCCccCc----------CCCCCCccchh
Q psy17260 416 MYATDLLAALQKGPVAVHQGREHCGPTGVAHVIAVGLLEGTL--------IRSHNDIHK----------GNNKLPGRMAT 477 (679)
Q Consensus 416 ~~i~~lLe~L~~~~~~~~~~~~~~~c~G~AL~~A~~lL~~~~--------lrs~~di~~----------~~~~~~~~~a~ 477 (679)
+.|+.||+.|+. ++......++|+|+||++|..+|+..| ..+.|.++- .+..++ .++.
T Consensus 1055 evIe~LLDkLPe---mFt~t~~~esCLGSALqAA~~aLk~~GGGGKIiVF~SSLPniGpGaLK~Re~~~KEk~Ll-~pqd 1130 (1560)
T PTZ00395 1055 DKINTLIDTIKS---VSTTMQSYGSCGNSALKIAMDMLKERNGLGSICMFYTTTPNCGIGAIKELKKDLQENFLE-VKQK 1130 (1560)
T ss_pred HHHHHHHHHHHH---HhhccCCCcccHHHHHHHHHHHHHhcCCCceEEEEEcCCCCCCCCccccccccccccccc-ccch
Confidence 999999999998 788777889999999999999999763 234443321 223455 7889
Q ss_pred HHHHHHHHHhh-hcceeEEEEcCCcccc-cc-------------------------------------------------
Q psy17260 478 KITKGLALRAA-YCRAIEYLLVPPWING-LL------------------------------------------------- 506 (679)
Q Consensus 478 ~fY~~La~~~~-~~~svD~~~~~~sF~~-~~------------------------------------------------- 506 (679)
+||++||.+|+ .+||||+|+++..|.+ ++
T Consensus 1131 ~FYK~LA~ECsk~qISVDLFLfSsqYvDVDVATLg~Lsr~TGGqlyyYPnFna~rD~~KL~~DL~r~LTre~iGyEAVMR 1210 (1560)
T PTZ00395 1131 IFYDSLLLDLYAFNISVDIFIISSNNVRVCVPSLQYVAQNTGGKILFVENFLWQKDYKEIYMNIMDTLTSEDIAYCCELK 1210 (1560)
T ss_pred HHHHHHHHHHHhcCCceEEEEccCcccccccccccchhcccceeEEEeCCCcccccHHHHHHHHHHHhhccceeeEEEEE
Confidence 99999999999 9999999988765432 00
Q ss_pred --cCCCeEEeeeecc--ccccCCCCccccccccCCCCcCeEEEcCCCCCceEEEEEEEecCCCCCCCCCCceEEEEEEEe
Q psy17260 507 --LEYELCLMGAIGP--CVSLNLKNQCVSDQDLGMGGTASWKMCTLSPNTTLALFFEIVNQHGAPIPQGGPGCIQFITHY 582 (679)
Q Consensus 507 --~S~gl~v~~~iG~--~~~~~~~~~~isd~~ig~g~t~~~~l~~ld~dtsia~~fei~~~~~~~l~~~~~~~iQ~allY 582 (679)
||+||+|+.++|+ ++... .+++++.++.+++|++|+|+|++++. +.+...+|||+||||
T Consensus 1211 VRCS~GLrVs~fyG~GnnF~s~-------------rStDLLaLP~Id~DqSfaVeLk~DEk----L~~~~~AYFQaALLY 1273 (1560)
T PTZ00395 1211 LRYSHHMSVKKLFCCNNNFNSI-------------ISVDTIKIPKIRHDQTFAFLLNYSDI----SESKKQIYFQCACIY 1273 (1560)
T ss_pred EECCCCeEEEEEeccCCccccc-------------cccccccccccCCCceEEEEEEeccc----cCCCCcEEEEEEEee
Confidence 9999999999954 33211 12578999999999999999977766 555678999999999
Q ss_pred EcCCCCEEEEEEccccccccCCCCHHHHHhccCHHHHHHHHHHHHHHHhhcCChhHHHHHHHHHHHHhhccc--------
Q psy17260 583 QAPSGEKKVRVTTIARNWADATTQLDHISSGFDQEAAAVIMGRMVVNRAEQDDGPDVMRWADRTLIRLEGGA-------- 654 (679)
Q Consensus 583 t~~~GerriRV~T~~l~~~~~ss~~~~v~~s~D~ea~~~llaK~a~~~~~~~~~~d~~~~ld~~li~il~~y-------- 654 (679)
|+.+|+|||||||+++|| ++++.+||+++|++|++.+|+|+|+.++++. .++|+.|.+.++++|..|
T Consensus 1274 TSssGERRIRVHTLALPV---TSsLseVFrsADqdAIvslLAK~AV~~aLss--sdARe~L~dklVdILtaYRK~CAsss 1348 (1560)
T PTZ00395 1274 TNLWGDRFVRLHTTHMNL---TSSLSTVFRYTDAEALMNILIKQLCTNILHN--DNYSKIIIDNLAAILFSYRINCASSA 1348 (1560)
T ss_pred ccCCCcEEEEEEeeeecc---cCCHHHHHHhhcHHHHHHHHHHHHHHHhccc--HHHHHHHHHHHHHHHHHHHHHhhccC
Confidence 999999999999999985 4799999999999999999999999999987 489999999999999999
Q ss_pred ----cccCCcccH-HHHHHHHhccccCCC
Q psy17260 655 ----PVLTEDVSL-QVFMEHLKKLAVSST 678 (679)
Q Consensus 655 ----liLPe~lkl-P~~~~~L~rS~~l~~ 678 (679)
|+|||+||+ |+|+++|+||++|++
T Consensus 1349 ssgQLILPESLKLLPLYILSLLKS~AfRt 1377 (1560)
T PTZ00395 1349 HSGQLILPDTLKLLPLFTSSLLKHNVTKK 1377 (1560)
T ss_pred CCccccchhHHHHHHHHHHHHhccccccC
Confidence 999999999 999999999999864
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=100.00 E-value=1.2e-34 Score=301.56 Aligned_cols=201 Identities=53% Similarity=0.716 Sum_probs=171.0
Q ss_pred CCCcEEEEEEECCcChhhHHHHHHHHHHHhhcCCCCcEEEEEEECCeEEEEEcCCCCccceeeecCCCCCchhHHHHhhh
Q psy17260 302 CAPLVFLFVVDTCMDEEELGALRDSLQMSLSLLPKNALVGLITFGQMVQVHELGCEGISRSYVFRGTKDVPAQRLQEMLR 381 (679)
Q Consensus 302 ~~pp~~vFvIDvs~~a~~l~~l~~si~~~L~~Lp~~~~VG~ITfd~~V~~y~l~~~~~~~~~Vf~g~~~l~~~ql~~~l~ 381 (679)
|.||+|+||||+|.++++++.++++|+++|+.||++++|||||||++||||+|+..++++++||+|+|+++.+|+..|++
T Consensus 1 p~pp~~vFviDvs~~~~el~~l~~sl~~~L~~lP~~a~VGlITfd~~V~~~~L~~~~~~~~~vf~g~~~~~~~~~~~~l~ 80 (267)
T cd01478 1 TSPPVFLFVVDTCMDEEELDALKESLIMSLSLLPPNALVGLITFGTMVQVHELGFEECSKSYVFRGNKDYTAKQIQDMLG 80 (267)
T ss_pred CCCCEEEEEEECccCHHHHHHHHHHHHHHHHhCCCCCEEEEEEECCEEEEEEcCCCcCceeeeccCCccCCHHHHHHHhc
Confidence 57899999999999999999999999999999999999999999999999999998999999999999999999988987
Q ss_pred cCCCCCCCCCCC-CC-CCCCCCCCCCCceeehHHhHHHHHHHHHHhcCCCCcccCCCCCCCchHHHHHHHHHHhhhc---
Q psy17260 382 IGKYSMSAPAPA-PR-PGQPPRPARTQFLQPVEACEMYATDLLAALQKGPVAVHQGREHCGPTGVAHVIAVGLLEGT--- 456 (679)
Q Consensus 382 l~d~~~p~~~g~-~~-~~~~~~~~~~~flvpl~e~~~~i~~lLe~L~~~~~~~~~~~~~~~c~G~AL~~A~~lL~~~--- 456 (679)
+++....-..+. +. ...+.+.+.++||+|++||++.|+++||+|+++.|.+++++++.||+|+||++|..+|+.+
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~p~~~~~flvpl~e~~~~i~~lLe~L~~~~~~~~~~~r~~r~~G~Al~~A~~ll~~~~~~ 160 (267)
T cd01478 81 LGGPAMRPSASQHPGAGNPLPSAAASRFLLPVSQCEFTLTDLLEQLQPDPWPVPAGHRPLRCTGVALSIAVGLLEACFPN 160 (267)
T ss_pred cccccccccccCcCCccccccccccccEEEEHHHHHHHHHHHHHhCcccccccCCCCCCCCchHHHHHHHHHHHHhhcCC
Confidence 754211000000 00 0001123457899999999999999999999999999999999999999999999999842
Q ss_pred -c--------------------------CCCCCccCcCCCCCCccchhHHHHHHHHHhh-hcceeEEEEcCCccc
Q psy17260 457 -L--------------------------IRSHNDIHKGNNKLPGRMATKITKGLALRAA-YCRAIEYLLVPPWIN 503 (679)
Q Consensus 457 -~--------------------------lrs~~di~~~~~~~~~~~a~~fY~~La~~~~-~~~svD~~~~~~sF~ 503 (679)
| +|+|.|+++++.+++ +++.+||++||.+|+ .+++||+|+.+.++.
T Consensus 161 ~gGki~~F~sg~pT~GpG~l~~r~~~~~~r~~~d~~~~~~~~~-~~a~~fY~~la~~~~~~~vsvDlF~~s~d~v 234 (267)
T cd01478 161 TGARIMLFAGGPCTVGPGAVVSTELKDPIRSHHDIDKDNAKYY-KKAVKFYDSLAKRLAANGHAVDIFAGCLDQV 234 (267)
T ss_pred CCcEEEEEECCCCCCCCceeeccccccccccccccccchhhhh-hhHHHHHHHHHHHHHhCCeEEEEEecccccc
Confidence 2 457778877777899 999999999999999 999999999887764
No 9
>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=99.95 E-value=7.8e-28 Score=248.02 Aligned_cols=171 Identities=20% Similarity=0.258 Sum_probs=141.5
Q ss_pred CCCcEEEEEEECCcChhh---HHHHHHHHHHHhhcCCCC---cEEEEEEECCeEEEEEcCCCCccceeeecCCCCCchhH
Q psy17260 302 CAPLVFLFVVDTCMDEEE---LGALRDSLQMSLSLLPKN---ALVGLITFGQMVQVHELGCEGISRSYVFRGTKDVPAQR 375 (679)
Q Consensus 302 ~~pp~~vFvIDvs~~a~~---l~~l~~si~~~L~~Lp~~---~~VG~ITfd~~V~~y~l~~~~~~~~~Vf~g~~~l~~~q 375 (679)
|+||+|+||||+|.++++ +++++++|+++|+.||++ ++|||||||+.||||+++.. ..++|
T Consensus 1 p~pp~~~FvIDvs~~a~~~g~~~~~~~si~~~L~~lp~~~~~~~VgiITfd~~v~~y~l~~~-------------~~~~q 67 (244)
T cd01479 1 PQPAVYVFLIDVSYNAIKSGLLATACEALLSNLDNLPGDDPRTRVGFITFDSTLHFFNLKSS-------------LEQPQ 67 (244)
T ss_pred CCCCEEEEEEEccHHHHhhChHHHHHHHHHHHHHhcCCCCCCeEEEEEEECCeEEEEECCCC-------------CCCCe
Confidence 579999999999999986 999999999999999977 99999999999999999753 34566
Q ss_pred HHHhhhcCCCCCCCCCCCCCCCCCCCCCCCCceeehHHhHHHHHHHHHHhcCCCCcccCCCCCCCchHHHHHHHHHHhhh
Q psy17260 376 LQEMLRIGKYSMSAPAPAPRPGQPPRPARTQFLQPVEACEMYATDLLAALQKGPVAVHQGREHCGPTGVAHVIAVGLLEG 455 (679)
Q Consensus 376 l~~~l~l~d~~~p~~~g~~~~~~~~~~~~~~flvpl~e~~~~i~~lLe~L~~~~~~~~~~~~~~~c~G~AL~~A~~lL~~ 455 (679)
+..+.|++|.+.| ..++||+|++||++.|+++|++|+. ++.+++++.+|+|+||++|..+|+.
T Consensus 68 ~~vv~dl~d~f~P--------------~~~~~lv~l~e~~~~i~~lL~~L~~---~~~~~~~~~~c~G~Al~~A~~lL~~ 130 (244)
T cd01479 68 MMVVSDLDDPFLP--------------LPDGLLVNLKESRQVIEDLLDQIPE---MFQDTKETESALGPALQAAFLLLKE 130 (244)
T ss_pred EEEeeCcccccCC--------------CCcceeecHHHHHHHHHHHHHHHHH---HHhcCCCCcccHHHHHHHHHHHHHh
Confidence 5555555554444 2467999999999999999999976 6788889999999999999999997
Q ss_pred cc------CCCCCcc--------------C-cCCCCCCccchhHHHHHHHHHhh-hcceeEEEEcCCccc
Q psy17260 456 TL------IRSHNDI--------------H-KGNNKLPGRMATKITKGLALRAA-YCRAIEYLLVPPWIN 503 (679)
Q Consensus 456 ~~------lrs~~di--------------~-~~~~~~~~~~a~~fY~~La~~~~-~~~svD~~~~~~sF~ 503 (679)
.| ..+.+.+ . +++.+++ +++.+||++||.+|+ .++|||+|+.+.+|.
T Consensus 131 ~GGkIi~f~s~~pt~GpG~l~~~~~~~~~~~~~e~~~~-~p~~~fY~~la~~~~~~~isvDlF~~~~~~~ 199 (244)
T cd01479 131 TGGKIIVFQSSLPTLGAGKLKSREDPKLLSTDKEKQLL-QPQTDFYKKLALECVKSQISVDLFLFSNQYV 199 (244)
T ss_pred cCCEEEEEeCCCCCcCCcccccCccccccCchhhhhhc-CcchHHHHHHHHHHHHcCeEEEEEEccCccc
Confidence 75 1222211 1 1234677 899999999999999 999999999988774
No 10
>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=99.94 E-value=3.7e-26 Score=235.09 Aligned_cols=174 Identities=28% Similarity=0.308 Sum_probs=139.8
Q ss_pred CCCcEEEEEEECCcCh---hhHHHHHHHHHHHhhcCC--CCcEEEEEEECCeEEEEEcCCCCccceeeecCCCCCchhHH
Q psy17260 302 CAPLVFLFVVDTCMDE---EELGALRDSLQMSLSLLP--KNALVGLITFGQMVQVHELGCEGISRSYVFRGTKDVPAQRL 376 (679)
Q Consensus 302 ~~pp~~vFvIDvs~~a---~~l~~l~~si~~~L~~Lp--~~~~VG~ITfd~~V~~y~l~~~~~~~~~Vf~g~~~l~~~ql 376 (679)
|+||+|+||||+|+++ .+++.++++|+++|+.|| ++++|||||||++||||++++.. .++++
T Consensus 1 p~pp~~vFvID~s~~ai~~~~l~~~~~sl~~~l~~lp~~~~~~igiITf~~~V~~~~~~~~~-------------~~~~~ 67 (239)
T cd01468 1 PQPPVFVFVIDVSYEAIKEGLLQALKESLLASLDLLPGDPRARVGLITYDSTVHFYNLSSDL-------------AQPKM 67 (239)
T ss_pred CCCCEEEEEEEcchHhccccHHHHHHHHHHHHHHhCCCCCCcEEEEEEeCCeEEEEECCCCC-------------CCCeE
Confidence 5799999999999994 459999999999999999 99999999999999999998632 23444
Q ss_pred HHhhhcCCCCCCCCCCCCCCCCCCCCCCCCceeehHHhHHHHHHHHHHhcCCCCcccCCCCCCCchHHHHHHHHHHhhhc
Q psy17260 377 QEMLRIGKYSMSAPAPAPRPGQPPRPARTQFLQPVEACEMYATDLLAALQKGPVAVHQGREHCGPTGVAHVIAVGLLEGT 456 (679)
Q Consensus 377 ~~~l~l~d~~~p~~~g~~~~~~~~~~~~~~flvpl~e~~~~i~~lLe~L~~~~~~~~~~~~~~~c~G~AL~~A~~lL~~~ 456 (679)
.++.|++|.+.| ..++|++|+.|+++.|.++|++|++..+.. ++.++.||+|+||++|..+|+..
T Consensus 68 ~v~~dl~d~f~p--------------~~~~~l~~~~e~~~~i~~~l~~l~~~~~~~-~~~~~~~~~G~Al~~A~~ll~~~ 132 (239)
T cd01468 68 YVVSDLKDVFLP--------------LPDRFLVPLSECKKVIHDLLEQLPPMFWPV-PTHRPERCLGPALQAAFLLLKGT 132 (239)
T ss_pred EEeCCCccCcCC--------------CcCceeeeHHHHHHHHHHHHHhhhhhcccc-CCCCCcccHHHHHHHHHHHHhhc
Confidence 444455554444 245799999999999999999999854322 27788999999999999999987
Q ss_pred --c------CCCCCc--------------cC-cCCCCCCccchhHHHHHHHHHhh-hcceeEEEEcCCcccc
Q psy17260 457 --L------IRSHND--------------IH-KGNNKLPGRMATKITKGLALRAA-YCRAIEYLLVPPWING 504 (679)
Q Consensus 457 --~------lrs~~d--------------i~-~~~~~~~~~~a~~fY~~La~~~~-~~~svD~~~~~~sF~~ 504 (679)
| +.+.+. +. +++++++ +++.+||++||.+|+ .++|||+|+.+.++.+
T Consensus 133 ~~gGkI~~f~sg~pt~GpG~l~~~~~~~~~~~~~e~~~~-~~a~~fY~~la~~~~~~~isvdlF~~~~~~~d 203 (239)
T cd01468 133 FAGGRIIVFQGGLPTVGPGKLKSREDKEPIRSHDEAQLL-KPATKFYKSLAKECVKSGICVDLFAFSLDYVD 203 (239)
T ss_pred CCCceEEEEECCCCCCCCCccccCcccccCCCccchhcc-cccHHHHHHHHHHHHHcCeEEEEEeccccccC
Confidence 4 122221 11 2345778 999999999999999 9999999999887653
No 11
>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=5.3e-26 Score=234.46 Aligned_cols=172 Identities=22% Similarity=0.279 Sum_probs=127.6
Q ss_pred CCCcEEEEEEECCcChhh---HHHHHHHHHHHhhcCC--CCcEEEEEEECCeEEEEEcCCCCccceeeecCCCCCchhHH
Q psy17260 302 CAPLVFLFVVDTCMDEEE---LGALRDSLQMSLSLLP--KNALVGLITFGQMVQVHELGCEGISRSYVFRGTKDVPAQRL 376 (679)
Q Consensus 302 ~~pp~~vFvIDvs~~a~~---l~~l~~si~~~L~~Lp--~~~~VG~ITfd~~V~~y~l~~~~~~~~~Vf~g~~~l~~~ql 376 (679)
|+||+|+||||+|.++++ ++.++++|+++|+.|| ++++|||||||+.||||+++.. ...+++
T Consensus 1 P~pp~y~FvID~s~~av~~g~~~~~~~sl~~~l~~l~~~~~~~vgiitfd~~V~~y~l~~~-------------~~~~~~ 67 (243)
T PF04811_consen 1 PQPPVYVFVIDVSYEAVQSGLLQSLIESLKSALDSLPGDERTRVGIITFDSSVHFYNLSSS-------------LSQPQM 67 (243)
T ss_dssp -S--EEEEEEE-SHHHHHHTHHHHHHHHHHHHGCTSSTSTT-EEEEEEESSSEEEEETTTT-------------SSSTEE
T ss_pred CCCCEEEEEEECchhhhhccHHHHHHHHHHHHHHhccCCCCcEEEEEEeCCEEEEEECCCC-------------cCCCcc
Confidence 679999999999999655 8999999999999999 8999999999999999999864 234554
Q ss_pred HHhhhcCCCCCCCCCCCCCCCCCCCCCCCCceeehHHhHHHHHHHHHHhcCCCCcccCC--CCCCCchHHHHHHHHHHhh
Q psy17260 377 QEMLRIGKYSMSAPAPAPRPGQPPRPARTQFLQPVEACEMYATDLLAALQKGPVAVHQG--REHCGPTGVAHVIAVGLLE 454 (679)
Q Consensus 377 ~~~l~l~d~~~p~~~g~~~~~~~~~~~~~~flvpl~e~~~~i~~lLe~L~~~~~~~~~~--~~~~~c~G~AL~~A~~lL~ 454 (679)
.++.|++|.+.| ..+.|+++++|+++.|.++|++|++ .++.. .++.+|+|+||++|..+|+
T Consensus 68 ~v~~dl~~~~~p--------------~~~~llv~~~e~~~~i~~ll~~L~~---~~~~~~~~~~~~c~G~Al~~A~~ll~ 130 (243)
T PF04811_consen 68 IVVSDLDDPFIP--------------LPDGLLVPLSECRDAIEELLESLPS---IFPETAGKRPERCLGSALSAALSLLS 130 (243)
T ss_dssp EEEHHTTSHHSS--------------TSSSSSEETTTCHHHHHHHHHHHHH---HSTT-TTB-----HHHHHHHHHHHHH
T ss_pred cchHHHhhcccC--------------CcccEEEEhHHhHHHHHHHHHHhhh---hcccccccCccccHHHHHHHHHHHHh
Confidence 456667665544 2378999999999999999999987 44444 7889999999999999999
Q ss_pred --hcc------CCCCCc-----------------cCcCCCCCCccchhHHHHHHHHHhh-hcceeEEEEcCCcccc
Q psy17260 455 --GTL------IRSHND-----------------IHKGNNKLPGRMATKITKGLALRAA-YCRAIEYLLVPPWING 504 (679)
Q Consensus 455 --~~~------lrs~~d-----------------i~~~~~~~~~~~a~~fY~~La~~~~-~~~svD~~~~~~sF~~ 504 (679)
..| +.+.+. ..++...++ +++.+||++||.+|+ .++|||+|+.+.++.+
T Consensus 131 ~~~~gGkI~~F~s~~pt~G~Gg~l~~~~~~~~~~~~~~~~~~~-~~~~~fY~~la~~~~~~~isvDlf~~~~~~~~ 205 (243)
T PF04811_consen 131 SRNTGGKILVFTSGPPTYGPGGSLKKREDSSHYDTEKEKALLL-PPANEFYKKLAEECSKQGISVDLFVFSSDYVD 205 (243)
T ss_dssp HHTS-EEEEEEESS---SSSTTSS-SBTTSCCCCHCTTHHCHS-HSSSHHHHHHHHHHHHCTEEEEEEEECSS--S
T ss_pred ccccCCEEEEEeccCCCCCCCceecccccccccccccchhhhc-cccchHHHHHHHHHHhcCCEEEEEeecCCCCC
Confidence 443 222221 122334566 788899999999999 9999999999887654
No 12
>KOG1986|consensus
Probab=99.92 E-value=2.9e-27 Score=261.04 Aligned_cols=135 Identities=39% Similarity=0.594 Sum_probs=118.6
Q ss_pred eecCCCCccceeEeecCCCCChHHHHHHHhcccccCCCCCCCCCCCCCCCCCCcceeeecCCccccHHHHHHHHhcccCC
Q psy17260 25 HELGCEGISRSYVFRGTKDVPAQRLQEMLRIGKYSMSAPAPAPRPGQPGCEGISRSYVFRGTKDVPAQRLQEMLRIGKYS 104 (679)
Q Consensus 25 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~vf~G~k~~~~~q~~~~l~~~~~~ 104 (679)
|||++ .|+-+......+|++.++++++||++++ +||||+++|+|+|||+|+||||++|++++||++.+.
T Consensus 135 eeL~~---LkssL~~~l~lLP~~alvGlItfg~~v~--------v~el~~~~~sk~~VF~G~ke~s~~q~~~~L~~~~~~ 203 (745)
T KOG1986|consen 135 EELQA---LKSSLKQSLSLLPENALVGLITFGTMVQ--------VHELGFEECSKSYVFSGNKEYSAKQLLDLLGLSGGA 203 (745)
T ss_pred HHHHH---HHHHHHHHHhhCCCcceEEEEEecceEE--------EEEcCCCcccceeEEeccccccHHHHHHHhcCCccc
Confidence 56665 5888899999999999999999999986 799999999999999999999999999999995321
Q ss_pred CCCCCCCCCCCCCCCCCCccceeeccccccccchhhccccCCCCCCCCCCCCCCCcchhhhhhhhcccccCCcc
Q psy17260 105 MSAPAPAPRPGQPPTPPVHKFLQPVEACEMSLTDLLGGLQKDPWPVHQGKRALRSTGVALSIAVGLLELKISMT 178 (679)
Q Consensus 105 ~~~~~~~~~~~~~~~~~~~rFl~P~~~~e~~l~~~le~L~~d~~~v~~~~R~~r~tg~al~va~~ll~~~~p~~ 178 (679)
. .+.....+.+|||+|+++|||+|+++||+||+|+|||++++||+||||+||+||++|+++|+|-+
T Consensus 204 ~--------~~~~~~~~~~rFL~P~~~c~~~L~~lle~L~~d~wpV~~g~Rp~RcTG~Al~iA~~Ll~~c~p~~ 269 (745)
T KOG1986|consen 204 G--------KGSENQSASNRFLLPAQECEFKLTNLLEELQPDPWPVPPGHRPLRCTGVALSIASGLLEGCFPNT 269 (745)
T ss_pred c--------cCCcccccchhhhccHHHHHHHHHHHHHHhcCCCCCCCCCCCcccchhHHHHHHHHHhcccCCCC
Confidence 1 11111134589999999999999999999999999999999999999999999999999999953
No 13
>COG5047 SEC23 Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking and secretion]
Probab=99.87 E-value=1.2e-23 Score=227.28 Aligned_cols=136 Identities=34% Similarity=0.510 Sum_probs=113.9
Q ss_pred cceeEeecCCCCChHHHHHHHhcccccCCCCCCCCCCCCCCCCCCcceeeecCCccccHHHHHHHHhcccCCCCCCCCCC
Q psy17260 33 SRSYVFRGTKDVPAQRLQEMLRIGKYSMSAPAPAPRPGQPGCEGISRSYVFRGTKDVPAQRLQEMLRIGKYSMSAPAPAP 112 (679)
Q Consensus 33 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~vf~G~k~~~~~q~~~~l~~~~~~~~~~~~~~ 112 (679)
.|.-+.-.-..+|.+.|+|++++|+.+| +|||+.+.++|+|||+|+||||+++|++|||++..-++.+....
T Consensus 141 LkdslivslsllppeaLvglItygt~i~--------v~el~ae~~~r~~VF~g~~eyt~~~L~~ll~~~~~~~~~~~es~ 212 (755)
T COG5047 141 LKDSLIVSLSLLPPEALVGLITYGTSIQ--------VHELNAENHRRSYVFSGNKEYTKENLQELLALSKPTKSGGFESK 212 (755)
T ss_pred HHHHHHHHHhcCCccceeeEEEecceeE--------EEeccccccCcceeecchHHHHHHHHHHHhcccCCCCcchhhhh
Confidence 4566666677899999999999999887 79999999999999999999999999999998521122111122
Q ss_pred CCCCCCCCCCccceeeccccccccchhhccccCCCCCCCCCCCCCCCcchhhhhhhhcccccCCc
Q psy17260 113 RPGQPPTPPVHKFLQPVEACEMSLTDLLGGLQKDPWPVHQGKRALRSTGVALSIAVGLLELKISM 177 (679)
Q Consensus 113 ~~~~~~~~~~~rFl~P~~~~e~~l~~~le~L~~d~~~v~~~~R~~r~tg~al~va~~ll~~~~p~ 177 (679)
..+... ...+|||+|+++|||+|+++||+||+|+|||+.++||+||||+||+||+.|++.++|-
T Consensus 213 is~~~~-~~~~rFl~p~q~ce~~L~n~le~L~pd~~~v~~~~Rp~RCTGsAl~ias~Ll~~~~p~ 276 (755)
T COG5047 213 ISGIGQ-FASSRFLLPTQQCEFKLLNILEQLQPDPWPVPAGKRPLRCTGSALNIASSLLEQCFPN 276 (755)
T ss_pred cccccc-cchhhhhccHHHHHHHHHHHHHHhCCCCccCCCCCCCccccchhHHHHHHHHHhhccC
Confidence 333222 1247999999999999999999999999999999999999999999999999999993
No 14
>PF08033 Sec23_BS: Sec23/Sec24 beta-sandwich domain; InterPro: IPR012990 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 (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes part of the Sec23/24 beta-barrel domain, which is formed from approximately 180 residues from three segments of the polypeptide. The strands of the barrel are oriented roughly parallel to the membrane such that one end of the barrel forms part of the inner surface of the coat and the other end part of the membrane-distal surface. The barrel is constructed from two opposed sheets: a six-stranded beta sheet facing partly towards the zinc finger domain and partly towards the solvent, and a five-stranded beta sheet facing the helical domain.; PDB: 3EFO_B 3EG9_B 1PD0_A 1PD1_A 1M2V_B 1PCX_A 3EH2_C 3EGD_A 2NUP_A 3EGX_A ....
Probab=99.76 E-value=1.5e-18 Score=153.62 Aligned_cols=87 Identities=38% Similarity=0.706 Sum_probs=77.3
Q ss_pred cCCCeEEeeeeccccccCCCCccccccccCCCCcCeEEEcCCCCCceEEEEEEEecCCCCCCCCCCceEEEEEEEeEcCC
Q psy17260 507 LEYELCLMGAIGPCVSLNLKNQCVSDQDLGMGGTASWKMCTLSPNTTLALFFEIVNQHGAPIPQGGPGCIQFITHYQAPS 586 (679)
Q Consensus 507 ~S~gl~v~~~iG~~~~~~~~~~~isd~~ig~g~t~~~~l~~ld~dtsia~~fei~~~~~~~l~~~~~~~iQ~allYt~~~ 586 (679)
||+|++|.+++||+...+ ++|++++|.++++.|++++++++++++|+|+++++ +...+.+|||++++||+.+
T Consensus 10 ~S~gl~v~~~~G~~~~~~----~~s~~~~g~~~~~~~~~~~l~~~~s~~~~~~~~~~----~~~~~~~~iQ~~~~Yt~~~ 81 (96)
T PF08033_consen 10 CSKGLKVSGVIGPCFNRS----SVSDNEIGEGDTTRWKLPSLDPDTSFAFEFEIDED----LPNGSQAYIQFALLYTDSN 81 (96)
T ss_dssp E-TTEEEEEEESSSEESS----TBESSECSBSSCSEEEEEEEETT--EEEEEEESSB----TBTTSEEEEEEEEEEEETT
T ss_pred ECCCeEEEEEEcCccccc----cccceeeccCCccEEEecccCCCCEEEEEEEECCC----CCCCCeEEEEEEEEEECCC
Confidence 999999999999999884 68899999999999999999999999999999765 4557899999999999999
Q ss_pred CCEEEEEEccccccc
Q psy17260 587 GEKKVRVTTIARNWA 601 (679)
Q Consensus 587 GerriRV~T~~l~~~ 601 (679)
|+|||||||+++||+
T Consensus 82 G~r~iRV~T~~l~vt 96 (96)
T PF08033_consen 82 GERRIRVTTLSLPVT 96 (96)
T ss_dssp SEEEEEEEEEEEEEE
T ss_pred CCEEEEEEeeccccC
Confidence 999999999999864
No 15
>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=99.75 E-value=1.1e-18 Score=181.96 Aligned_cols=55 Identities=64% Similarity=1.020 Sum_probs=52.2
Q ss_pred CccceeeccccccccchhhccccCCCCCCCCCCCCCCCcchhhhhhhhcccccCC
Q psy17260 122 VHKFLQPVEACEMSLTDLLGGLQKDPWPVHQGKRALRSTGVALSIAVGLLELKIS 176 (679)
Q Consensus 122 ~~rFl~P~~~~e~~l~~~le~L~~d~~~v~~~~R~~r~tg~al~va~~ll~~~~p 176 (679)
.+|||+|++|||++|+++||+|++|+|++.+++|+.||||+||++|..+++.+.|
T Consensus 105 ~~~flvpl~e~~~~i~~lLe~L~~~~~~~~~~~r~~r~~G~Al~~A~~ll~~~~~ 159 (267)
T cd01478 105 ASRFLLPVSQCEFTLTDLLEQLQPDPWPVPAGHRPLRCTGVALSIAVGLLEACFP 159 (267)
T ss_pred cccEEEEHHHHHHHHHHHHHhCcccccccCCCCCCCCchHHHHHHHHHHHHhhcC
Confidence 3799999999999999999999999999999999999999999999999997755
No 16
>PLN00162 transport protein sec23; Provisional
Probab=99.71 E-value=9.4e-19 Score=206.03 Aligned_cols=156 Identities=32% Similarity=0.472 Sum_probs=121.1
Q ss_pred CCCCCCCCCCEEeecCCCCc----cceeEeecCCCCChHHHHHHHhcccccCCCCCCCCCCCCCCCCCCcceeeecCCcc
Q psy17260 13 APAPRPGQPPRVHELGCEGI----SRSYVFRGTKDVPAQRLQEMLRIGKYSMSAPAPAPRPGQPGCEGISRSYVFRGTKD 88 (679)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~vf~G~k~ 88 (679)
..+|.|-.-+-|=|+-+++. .|+-+-+....+|++.++++|+||+.++ .|+|++++|+|+|||+|+||
T Consensus 119 ~~~~~pp~fvFvID~s~~~~~l~~lk~sl~~~L~~LP~~a~VGlITF~s~V~--------~~~L~~~~~~~~~Vf~g~k~ 190 (761)
T PLN00162 119 GGAPSPPVFVFVVDTCMIEEELGALKSALLQAIALLPENALVGLITFGTHVH--------VHELGFSECSKSYVFRGNKE 190 (761)
T ss_pred CCCCCCcEEEEEEecchhHHHHHHHHHHHHHHHHhCCCCCEEEEEEECCEEE--------EEEcCCCCCcceEEecCCcc
Confidence 34444445566666666553 5666677777899999999999999886 79999999999999999999
Q ss_pred ccHHHHHHHHhcccCCCCC--CCCCCCCCCCCCCCCccceeeccccccccchhhccccCCCCCCCCCCCCCCCcchhhhh
Q psy17260 89 VPAQRLQEMLRIGKYSMSA--PAPAPRPGQPPTPPVHKFLQPVEACEMSLTDLLGGLQKDPWPVHQGKRALRSTGVALSI 166 (679)
Q Consensus 89 ~~~~q~~~~l~~~~~~~~~--~~~~~~~~~~~~~~~~rFl~P~~~~e~~l~~~le~L~~d~~~v~~~~R~~r~tg~al~v 166 (679)
||.+||+++||+....... +.+.+..+....+..+|||+|++|||++|+++||+|++|+||+++++|+.||||+||++
T Consensus 191 ~t~~~l~~~l~l~~~~~~~~~~~~~~~~~~~~~p~~~~fLvpl~e~~~~i~~lLe~L~~~~~~~~~~~rp~r~tG~AL~v 270 (761)
T PLN00162 191 VSKDQILEQLGLGGKKRRPAGGGIAGARDGLSSSGVNRFLLPASECEFTLNSALEELQKDPWPVPPGHRPARCTGAALSV 270 (761)
T ss_pred CCHHHHHHHhccccccccccccccccccccccCCCccceeEEHHHHHHHHHHHHHhhhccccccCCCCCCCccHHHHHHH
Confidence 9999999999994321100 00000000001223589999999999999999999999999999999999999999999
Q ss_pred hhhcccccCC
Q psy17260 167 AVGLLELKIS 176 (679)
Q Consensus 167 a~~ll~~~~p 176 (679)
|+++++.+.|
T Consensus 271 A~~lL~~~~~ 280 (761)
T PLN00162 271 AAGLLGACVP 280 (761)
T ss_pred HHHHHhhccC
Confidence 9999997655
No 17
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. 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, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=99.53 E-value=2.1e-15 Score=111.38 Aligned_cols=40 Identities=55% Similarity=1.269 Sum_probs=29.2
Q ss_pred CccccCCCCcccEEcCceeEecCCCeEEeccCCCCCCCCccc
Q psy17260 233 EPLLCMRNQCRAILNPLCQVDYKSKLWVCNFCFQRNAFPPQY 274 (679)
Q Consensus 233 ~p~RC~~~~C~AYiNpf~~~~~~g~~W~C~~C~~~N~vp~~Y 274 (679)
+|+||++ |+||||||++|++++++|+|+||++.|++|++|
T Consensus 1 ~p~rC~~--C~aylNp~~~~~~~~~~w~C~~C~~~N~lp~~Y 40 (40)
T PF04810_consen 1 GPVRCRR--CRAYLNPFCQFDDGGKTWICNFCGTKNPLPPHY 40 (40)
T ss_dssp -S-B-TT--T--BS-TTSEEETTTTEEEETTT--EEE--GGG
T ss_pred CccccCC--CCCEECCcceEcCCCCEEECcCCCCcCCCCCCC
Confidence 5899999 999999999999999999999999999999987
No 18
>PF04815 Sec23_helical: Sec23/Sec24 helical domain; InterPro: IPR006900 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 (IPR006896 from INTERPRO), an all-helical region, and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes the all-helical domain, which forms an approximately 105-residue segment with the C-terminal 30 residues. The linker between alpha-M and alpha-N contacts Sar1.; GO: 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EGD_B 2NUP_B 2NUT_B 3EGX_B 3EH2_C 3EH1_A 3EFO_B 3EG9_B 2QTV_A 1M2O_C ....
Probab=99.14 E-value=5.8e-11 Score=106.54 Aligned_cols=63 Identities=17% Similarity=0.263 Sum_probs=60.4
Q ss_pred HHHHHHHHHHHHHHHhhcCChhHHHHHHHHHHHHhhccc------------cccCCcccH-HHHHHHHhccccCCC
Q psy17260 616 QEAAAVIMGRMVVNRAEQDDGPDVMRWADRTLIRLEGGA------------PVLTEDVSL-QVFMEHLKKLAVSST 678 (679)
Q Consensus 616 ~ea~~~llaK~a~~~~~~~~~~d~~~~ld~~li~il~~y------------liLPe~lkl-P~~~~~L~rS~~l~~ 678 (679)
|||++++++|+++.++.+++..++|++++++|++++++| |+|||++|+ |+|+++|+||++|+.
T Consensus 1 Qda~~~llak~ai~~~~~~~l~~~r~~l~~~~v~il~~Yr~~~~~~~~~~qLilPe~lklLPly~l~llKs~alr~ 76 (103)
T PF04815_consen 1 QDAITSLLAKQAIDKALSSSLKDARESLDNRLVDILAAYRKNCASSSSSGQLILPESLKLLPLYILALLKSPALRP 76 (103)
T ss_dssp HHHHHHHHHHHHHHHHCCS-HHHHHHHHHHHHHHHHHHHHHHCTTECCCTEEEEEGGGTTHHHHHHHHHTSTTTSC
T ss_pred CHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHhhccCCCCchhhhCCHHHHHHHHHHHHHHcchhhcC
Confidence 799999999999999999999999999999999999999 899999999 999999999999975
No 19
>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=97.61 E-value=2.4e-06 Score=88.15 Aligned_cols=106 Identities=25% Similarity=0.315 Sum_probs=79.7
Q ss_pred ccceeEeecCCCCC--hHHHHHHHhcccccCCCCCCCCCCCCCCCCCC-cceeeecCCccccHHHHHHHHhcccCCCCCC
Q psy17260 32 ISRSYVFRGTKDVP--AQRLQEMLRIGKYSMSAPAPAPRPGQPGCEGI-SRSYVFRGTKDVPAQRLQEMLRIGKYSMSAP 108 (679)
Q Consensus 32 ~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~-~~~~vf~G~k~~~~~q~~~~l~~~~~~~~~~ 108 (679)
..|+.+....+.+| ++...++++|++.++ .|+++.... ++.+|+.+.+|+..
T Consensus 24 ~~~~sl~~~l~~lp~~~~~~igiITf~~~V~--------~~~~~~~~~~~~~~v~~dl~d~f~----------------- 78 (239)
T cd01468 24 ALKESLLASLDLLPGDPRARVGLITYDSTVH--------FYNLSSDLAQPKMYVVSDLKDVFL----------------- 78 (239)
T ss_pred HHHHHHHHHHHhCCCCCCcEEEEEEeCCeEE--------EEECCCCCCCCeEEEeCCCccCcC-----------------
Confidence 34444444455555 666677777765543 466666655 77888888777651
Q ss_pred CCCCCCCCCCCCCCccceeeccccccccchhhccccCCCCCCCCCCCCCCCcchhhhhhhhccccc
Q psy17260 109 APAPRPGQPPTPPVHKFLQPVEACEMSLTDLLGGLQKDPWPVHQGKRALRSTGVALSIAVGLLELK 174 (679)
Q Consensus 109 ~~~~~~~~~~~~~~~rFl~P~~~~e~~l~~~le~L~~d~~~v~~~~R~~r~tg~al~va~~ll~~~ 174 (679)
| ...+||+|++||+..|.++||+|.++.|++ +.+|+.||+|+||.+|+.+++..
T Consensus 79 -p----------~~~~~l~~~~e~~~~i~~~l~~l~~~~~~~-~~~~~~~~~G~Al~~A~~ll~~~ 132 (239)
T cd01468 79 -P----------LPDRFLVPLSECKKVIHDLLEQLPPMFWPV-PTHRPERCLGPALQAAFLLLKGT 132 (239)
T ss_pred -C----------CcCceeeeHHHHHHHHHHHHHhhhhhcccc-CCCCCcccHHHHHHHHHHHHhhc
Confidence 0 015799999999999999999999999987 68888999999999999999865
No 20
>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=97.01 E-value=0.00012 Score=75.87 Aligned_cols=47 Identities=23% Similarity=0.246 Sum_probs=42.8
Q ss_pred ccceeeccccccccchhhccccCCCCCCCCCCCCCCCcchhhhhhhhccc
Q psy17260 123 HKFLQPVEACEMSLTDLLGGLQKDPWPVHQGKRALRSTGVALSIAVGLLE 172 (679)
Q Consensus 123 ~rFl~P~~~~e~~l~~~le~L~~d~~~v~~~~R~~r~tg~al~va~~ll~ 172 (679)
++||+|++||++.|+++||+| + |.+.+++|+.||+|+||.+|..+++
T Consensus 83 ~~~lv~l~e~~~~i~~lL~~L-~--~~~~~~~~~~~c~G~Al~~A~~lL~ 129 (244)
T cd01479 83 DGLLVNLKESRQVIEDLLDQI-P--EMFQDTKETESALGPALQAAFLLLK 129 (244)
T ss_pred cceeecHHHHHHHHHHHHHHH-H--HHHhcCCCCcccHHHHHHHHHHHHH
Confidence 789999999999999999999 3 4455889999999999999999987
No 21
>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=96.65 E-value=0.02 Score=56.72 Aligned_cols=50 Identities=20% Similarity=0.302 Sum_probs=43.2
Q ss_pred CCcEEEEEEECCcChh--hHHHHHHHHHHHhhcCCCCcEEEEEEECCeEEEE
Q psy17260 303 APLVFLFVVDTCMDEE--ELGALRDSLQMSLSLLPKNALVGLITFGQMVQVH 352 (679)
Q Consensus 303 ~pp~~vFvIDvs~~a~--~l~~l~~si~~~L~~Lp~~~~VG~ITfd~~V~~y 352 (679)
.|-..+||||+|.+.. .++.+++++...++.++++.+||+|+|++.++..
T Consensus 12 ~p~~vv~llD~SgSM~~~~l~~ak~~~~~ll~~l~~~d~v~lv~F~~~~~~~ 63 (190)
T cd01463 12 SPKDIVILLDVSGSMTGQRLHLAKQTVSSILDTLSDNDFFNIITFSNEVNPV 63 (190)
T ss_pred CCceEEEEEECCCCCCcHHHHHHHHHHHHHHHhCCCCCEEEEEEeCCCeeEE
Confidence 4667899999998753 4889999999999999999999999999987753
No 22
>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=95.70 E-value=0.085 Score=50.49 Aligned_cols=45 Identities=18% Similarity=0.304 Sum_probs=38.4
Q ss_pred EEEEEECCcChh--hHHHHHHHHHHHhhcCCCCcEEEEEEECCeEEE
Q psy17260 307 FLFVVDTCMDEE--ELGALRDSLQMSLSLLPKNALVGLITFGQMVQV 351 (679)
Q Consensus 307 ~vFvIDvs~~a~--~l~~l~~si~~~L~~Lp~~~~VG~ITfd~~V~~ 351 (679)
.+|+||+|.+.. .++.+++++...++.|+++.++|+|+|++..+.
T Consensus 3 v~~vlD~S~SM~~~rl~~ak~a~~~l~~~l~~~~~~~li~F~~~~~~ 49 (155)
T cd01466 3 LVAVLDVSGSMAGDKLQLVKHALRFVISSLGDADRLSIVTFSTSAKR 49 (155)
T ss_pred EEEEEECCCCCCcHHHHHHHHHHHHHHHhCCCcceEEEEEecCCccc
Confidence 479999998765 488899999999999999899999999986543
No 23
>PF04811 Sec23_trunk: Sec23/Sec24 trunk domain; InterPro: IPR006896 COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger (IPR006895 from INTERPRO), an alpha/beta trunk domain, an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes the Sec23/24 alpha/beta trunk domain, which is formed from a single, approximately 250-residue segment plugged into the beta-barrel between strands beta-1 and beta-19. The trunk has an alpha/beta fold with a vWA topology, and it forms the dimer interface, primarily involving strand beta-14 on Sec23 and Sec24; in addition, the trunk domain of Sec23 contacts Sar1.; GO: 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EGD_A 2NUP_A 3EG9_A 3EFO_A 3EGX_A 2NUT_A 1PD0_A 1PD1_A 1M2V_B 1PCX_A ....
Probab=95.39 E-value=0.0031 Score=65.15 Aligned_cols=50 Identities=36% Similarity=0.575 Sum_probs=41.1
Q ss_pred ccceeeccccccccchhhccccCCCCCCCCCCCCCCCcchhhhhhhhcccc
Q psy17260 123 HKFLQPVEACEMSLTDLLGGLQKDPWPVHQGKRALRSTGVALSIAVGLLEL 173 (679)
Q Consensus 123 ~rFl~P~~~~e~~l~~~le~L~~d~~~v~~~~R~~r~tg~al~va~~ll~~ 173 (679)
.+||+|++||+..|.++||.|.+ .|+....+|+.||+|+||.+|..+++.
T Consensus 82 ~~llv~~~e~~~~i~~ll~~L~~-~~~~~~~~~~~~c~G~Al~~A~~ll~~ 131 (243)
T PF04811_consen 82 DGLLVPLSECRDAIEELLESLPS-IFPETAGKRPERCLGSALSAALSLLSS 131 (243)
T ss_dssp SSSSEETTTCHHHHHHHHHHHHH-HSTT-TTB-----HHHHHHHHHHHHHH
T ss_pred ccEEEEhHHhHHHHHHHHHHhhh-hcccccccCccccHHHHHHHHHHHHhc
Confidence 68999999999999999999998 888877899999999999999999983
No 24
>PRK13685 hypothetical protein; Provisional
Probab=94.73 E-value=0.19 Score=54.44 Aligned_cols=47 Identities=21% Similarity=0.306 Sum_probs=40.0
Q ss_pred CcEEEEEEECCcChh-------hHHHHHHHHHHHhhcCCCCcEEEEEEECCeEE
Q psy17260 304 PLVFLFVVDTCMDEE-------ELGALRDSLQMSLSLLPKNALVGLITFGQMVQ 350 (679)
Q Consensus 304 pp~~vFvIDvs~~a~-------~l~~l~~si~~~L~~Lp~~~~VG~ITfd~~V~ 350 (679)
+-..+|+||+|.+.. .++.++++++..++.++++.+||+|+|++..+
T Consensus 88 ~~~vvlvlD~S~SM~~~D~~p~RL~~ak~~~~~~l~~l~~~d~vglv~Fa~~a~ 141 (326)
T PRK13685 88 RAVVMLVIDVSQSMRATDVEPNRLAAAQEAAKQFADELTPGINLGLIAFAGTAT 141 (326)
T ss_pred CceEEEEEECCccccCCCCCCCHHHHHHHHHHHHHHhCCCCCeEEEEEEcCcee
Confidence 346799999998753 48999999999999998889999999987654
No 25
>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=94.36 E-value=0.082 Score=53.01 Aligned_cols=49 Identities=22% Similarity=0.264 Sum_probs=42.4
Q ss_pred CCCCcEEEEEEECCcChh--------hHHHHHHHHHHHhhcCCCCcEEEEEEECCeE
Q psy17260 301 QCAPLVFLFVVDTCMDEE--------ELGALRDSLQMSLSLLPKNALVGLITFGQMV 349 (679)
Q Consensus 301 ~~~pp~~vFvIDvs~~a~--------~l~~l~~si~~~L~~Lp~~~~VG~ITfd~~V 349 (679)
...+..++||||+|.+.. .++.+++++...++.++++.+||+++|++.+
T Consensus 17 ~~~~~~vv~vlD~SgSM~~~~~~~~~rl~~ak~a~~~~l~~l~~~~~v~lv~F~~~~ 73 (206)
T cd01456 17 PQLPPNVAIVLDNSGSMREVDGGGETRLDNAKAALDETANALPDGTRLGLWTFSGDG 73 (206)
T ss_pred cCCCCcEEEEEeCCCCCcCCCCCcchHHHHHHHHHHHHHHhCCCCceEEEEEecCCC
Confidence 345778999999999864 3889999999999999999999999999854
No 26
>PF13768 VWA_3: von Willebrand factor type A domain
Probab=94.28 E-value=0.11 Score=49.37 Aligned_cols=47 Identities=26% Similarity=0.336 Sum_probs=40.6
Q ss_pred EEEEEECCcChhh-HHHHHHHHHHHhhcCCCCcEEEEEEECCeEEEEE
Q psy17260 307 FLFVVDTCMDEEE-LGALRDSLQMSLSLLPKNALVGLITFGQMVQVHE 353 (679)
Q Consensus 307 ~vFvIDvs~~a~~-l~~l~~si~~~L~~Lp~~~~VG~ITfd~~V~~y~ 353 (679)
.|||||+|..... .+.++++++.+++.|+++.++.||+|++.+..|.
T Consensus 3 vvilvD~S~Sm~g~~~~~k~al~~~l~~L~~~d~fnii~f~~~~~~~~ 50 (155)
T PF13768_consen 3 VVILVDTSGSMSGEKELVKDALRAILRSLPPGDRFNIIAFGSSVRPLF 50 (155)
T ss_pred EEEEEeCCCCCCCcHHHHHHHHHHHHHhCCCCCEEEEEEeCCEeeEcc
Confidence 5899999997543 4889999999999999999999999999877653
No 27
>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=93.78 E-value=0.16 Score=48.72 Aligned_cols=49 Identities=24% Similarity=0.415 Sum_probs=41.2
Q ss_pred CcEEEEEEECCcChh--hHHHHHHHHHHHhhcCCCCcEEEEEEECCeEEEE
Q psy17260 304 PLVFLFVVDTCMDEE--ELGALRDSLQMSLSLLPKNALVGLITFGQMVQVH 352 (679)
Q Consensus 304 pp~~vFvIDvs~~a~--~l~~l~~si~~~L~~Lp~~~~VG~ITfd~~V~~y 352 (679)
|.-++|++|+|.+.. .++.+++++...+..++++.+|++++|++.++.+
T Consensus 2 ~~~v~~vlD~S~SM~~~~~~~~~~al~~~l~~l~~~~~~~l~~Fs~~~~~~ 52 (171)
T cd01461 2 PKEVVFVIDTSGSMSGTKIEQTKEALLTALKDLPPGDYFNIIGFSDTVEEF 52 (171)
T ss_pred CceEEEEEECCCCCCChhHHHHHHHHHHHHHhCCCCCEEEEEEeCCCceee
Confidence 567899999999764 3788899999999999988899999999876543
No 28
>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=93.29 E-value=0.17 Score=50.43 Aligned_cols=45 Identities=4% Similarity=0.185 Sum_probs=37.7
Q ss_pred EEEEEECCcChh--hHHHHHHHHHHHhhcCCC---CcEEEEEEECCeEEE
Q psy17260 307 FLFVVDTCMDEE--ELGALRDSLQMSLSLLPK---NALVGLITFGQMVQV 351 (679)
Q Consensus 307 ~vFvIDvs~~a~--~l~~l~~si~~~L~~Lp~---~~~VG~ITfd~~V~~ 351 (679)
++|+||+|.+.. .++.+++++...++.|+. +.+||+|+|++.++.
T Consensus 3 i~~vlD~SgSM~~~~~~~~k~~~~~l~~~l~~~~~~~~v~li~Fs~~~~~ 52 (198)
T cd01470 3 IYIALDASDSIGEEDFDEAKNAIKTLIEKISSYEVSPRYEIISYASDPKE 52 (198)
T ss_pred EEEEEECCCCccHHHHHHHHHHHHHHHHHccccCCCceEEEEEecCCceE
Confidence 689999998754 488999999999988863 679999999887654
No 29
>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=92.73 E-value=0.29 Score=47.03 Aligned_cols=45 Identities=16% Similarity=0.318 Sum_probs=36.0
Q ss_pred EEEEEECCcChh--hHHHHHHHHHHHhhcCC---CCcEEEEEEECCeEEE
Q psy17260 307 FLFVVDTCMDEE--ELGALRDSLQMSLSLLP---KNALVGLITFGQMVQV 351 (679)
Q Consensus 307 ~vFvIDvs~~a~--~l~~l~~si~~~L~~Lp---~~~~VG~ITfd~~V~~ 351 (679)
.+|+||+|.+.. .++.++++++..+..|. ++.++|+|+|++..+.
T Consensus 3 vv~vlD~SgSm~~~~~~~~k~~~~~~~~~l~~~~~~~~~giv~Fs~~~~~ 52 (164)
T cd01472 3 IVFLVDGSESIGLSNFNLVKDFVKRVVERLDIGPDGVRVGVVQYSDDPRT 52 (164)
T ss_pred EEEEEeCCCCCCHHHHHHHHHHHHHHHhhcccCCCCeEEEEEEEcCceeE
Confidence 489999998644 47888888888887774 5689999999987665
No 30
>PF00092 VWA: von Willebrand factor type A domain; InterPro: IPR002035 The von Willebrand factor is a large multimeric glycoprotein found in blood plasma. Mutant forms are involved in the aetiology of bleeding disorders []. In von Willebrand factor, the type A domain (vWF) is the prototype for a protein superfamily. The vWF domain is found in various plasma proteins: complement factors B, C2, CR3 and CR4; the integrins (I-domains); collagen types VI, VII, XII and XIV; and other extracellular proteins [, , ]. Although the majority of VWA-containing proteins are extracellular, the most ancient ones present in all eukaryotes are all intracellular proteins involved in functions such as transcription, DNA repair, ribosomal and membrane transport and the proteasome. A common feature appears to be involvement in multiprotein complexes. Proteins that incorporate vWF domains participate in numerous biological events (e.g. cell adhesion, migration, homing, pattern formation, and signal transduction), involving interaction with a large array of ligands []. A number of human diseases arise from mutations in VWA domains. Secondary structure prediction from 75 aligned vWF sequences has revealed a largely alternating sequence of alpha-helices and beta-strands []. Fold recognition algorithms were used to score sequence compatibility with a library of known structures: the vWF domain fold was predicted to be a doubly-wound, open, twisted beta-sheet flanked by alpha-helices []. 3D structures have been determined for the I-domains of integrins CD11b (with bound magnesium) [] and CD11a (with bound manganese) []. The domain adopts a classic alpha/beta Rossmann fold and contains an unusual metal ion coordination site at its surface. It has been suggested that this site represents a general metal ion-dependent adhesion site (MIDAS) for binding protein ligands []. The residues constituting the MIDAS motif in the CD11b and CD11a I-domains are completely conserved, but the manner in which the metal ion is coordinated differs slightly [].; GO: 0005515 protein binding; PDB: 2XGG_B 3ZQK_B 3GXB_A 3PPV_A 3PPX_A 3PPW_A 3PPY_A 1CQP_B 3TCX_B 2ICA_A ....
Probab=92.68 E-value=0.31 Score=46.72 Aligned_cols=45 Identities=24% Similarity=0.406 Sum_probs=36.1
Q ss_pred EEEEEECCcChh--hHHHHHHHHHHHhhcC---CCCcEEEEEEECCeEEE
Q psy17260 307 FLFVVDTCMDEE--ELGALRDSLQMSLSLL---PKNALVGLITFGQMVQV 351 (679)
Q Consensus 307 ~vFvIDvs~~a~--~l~~l~~si~~~L~~L---p~~~~VG~ITfd~~V~~ 351 (679)
.+|+||.|.... +++.+++.+...++.+ +.+.+||+|+|++..+.
T Consensus 2 ivflvD~S~sm~~~~~~~~~~~v~~~i~~~~~~~~~~rv~iv~f~~~~~~ 51 (178)
T PF00092_consen 2 IVFLVDTSGSMSGDNFEKAKQFVKSIISRLSISNNGTRVGIVTFSDSARV 51 (178)
T ss_dssp EEEEEE-STTSCHHHHHHHHHHHHHHHHHSTBSTTSEEEEEEEESSSEEE
T ss_pred EEEEEeCCCCCchHHHHHHHHHHHHHHHhhhccccccccceeeeeccccc
Confidence 489999999755 4888888888888854 56799999999988874
No 31
>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=92.51 E-value=0.3 Score=48.91 Aligned_cols=48 Identities=27% Similarity=0.405 Sum_probs=37.4
Q ss_pred CcEEEEEEECCcC--hhhHHHHHHHHHHHhhcC---------CCCcEEEEEEECCeEEE
Q psy17260 304 PLVFLFVVDTCMD--EEELGALRDSLQMSLSLL---------PKNALVGLITFGQMVQV 351 (679)
Q Consensus 304 pp~~vFvIDvs~~--a~~l~~l~~si~~~L~~L---------p~~~~VG~ITfd~~V~~ 351 (679)
+--.||+||.|.. ..+++.+++.++..+..+ |+.+|||+|+|++..++
T Consensus 19 ~~DivfvlD~S~Sm~~~~f~~~k~fi~~~~~~~~~~~~~~~~~~~~rVGlV~fs~~a~~ 77 (193)
T cd01477 19 WLDIVFVVDNSKGMTQGGLWQVRATISSLFGSSSQIGTDYDDPRSTRVGLVTYNSNATV 77 (193)
T ss_pred eeeEEEEEeCCCCcchhhHHHHHHHHHHHHhhccccccccCCCCCcEEEEEEccCceEE
Confidence 3456999999997 445888888888876643 34689999999987766
No 32
>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=92.42 E-value=0.2 Score=48.89 Aligned_cols=45 Identities=29% Similarity=0.381 Sum_probs=36.1
Q ss_pred EEEEEECCcChh--hHHHHHHHHHHHhhcCCC------CcEEEEEEECCeEEE
Q psy17260 307 FLFVVDTCMDEE--ELGALRDSLQMSLSLLPK------NALVGLITFGQMVQV 351 (679)
Q Consensus 307 ~vFvIDvs~~a~--~l~~l~~si~~~L~~Lp~------~~~VG~ITfd~~V~~ 351 (679)
.+|+||+|.+.. .++.++++++..++.+.+ +.+||+|+|++..+.
T Consensus 6 v~~llD~SgSM~~~~~~~~k~a~~~~~~~l~~~~~~~~~~~v~ii~F~~~a~~ 58 (176)
T cd01464 6 IYLLLDTSGSMAGEPIEALNQGLQMLQSELRQDPYALESVEISVITFDSAARV 58 (176)
T ss_pred EEEEEECCCCCCChHHHHHHHHHHHHHHHHhcChhhccccEEEEEEecCCceE
Confidence 489999998753 478888888888887753 469999999987665
No 33
>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=92.40 E-value=0.33 Score=47.56 Aligned_cols=45 Identities=16% Similarity=0.337 Sum_probs=36.9
Q ss_pred EEEEEECCcChh--hHHHHHHHHHHHhhcCC---CCcEEEEEEECCeEEE
Q psy17260 307 FLFVVDTCMDEE--ELGALRDSLQMSLSLLP---KNALVGLITFGQMVQV 351 (679)
Q Consensus 307 ~vFvIDvs~~a~--~l~~l~~si~~~L~~Lp---~~~~VG~ITfd~~V~~ 351 (679)
.+|+||.|.... +++.+++.++..++.+. +++|||+|+|++..++
T Consensus 3 i~fvlD~S~S~~~~~f~~~k~fi~~~i~~l~~~~~~~rvgvv~fs~~~~~ 52 (177)
T cd01469 3 IVFVLDGSGSIYPDDFQKVKNFLSTVMKKLDIGPTKTQFGLVQYSESFRT 52 (177)
T ss_pred EEEEEeCCCCCCHHHHHHHHHHHHHHHHHcCcCCCCcEEEEEEECCceeE
Confidence 589999998753 58888988888888774 4689999999987654
No 34
>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=92.32 E-value=0.28 Score=46.94 Aligned_cols=45 Identities=16% Similarity=0.395 Sum_probs=38.0
Q ss_pred EEEEEECCcChh--hHHHHHHHHHHHhhcCCCCcEEEEEEECCeEEE
Q psy17260 307 FLFVVDTCMDEE--ELGALRDSLQMSLSLLPKNALVGLITFGQMVQV 351 (679)
Q Consensus 307 ~vFvIDvs~~a~--~l~~l~~si~~~L~~Lp~~~~VG~ITfd~~V~~ 351 (679)
++|++|+|.... .++.+++++...+..++++.+||+|+|++..+.
T Consensus 3 ~~~vlD~S~SM~~~~~~~~k~a~~~~~~~l~~~~~v~li~f~~~~~~ 49 (170)
T cd01465 3 LVFVIDRSGSMDGPKLPLVKSALKLLVDQLRPDDRLAIVTYDGAAET 49 (170)
T ss_pred EEEEEECCCCCCChhHHHHHHHHHHHHHhCCCCCEEEEEEecCCccE
Confidence 689999998754 378889999999999998899999999876544
No 35
>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=92.18 E-value=0.36 Score=49.18 Aligned_cols=47 Identities=19% Similarity=0.409 Sum_probs=38.4
Q ss_pred cEEEEEEECCcChh--hHHHHHHHHHHHhhcC---CCCcEEEEEEECCeEEE
Q psy17260 305 LVFLFVVDTCMDEE--ELGALRDSLQMSLSLL---PKNALVGLITFGQMVQV 351 (679)
Q Consensus 305 p~~vFvIDvs~~a~--~l~~l~~si~~~L~~L---p~~~~VG~ITfd~~V~~ 351 (679)
--.+|+||.|.... +++.+++.++..++.| |+..+||+|+|++.+++
T Consensus 3 ~DlvfllD~S~Sm~~~~~~~~k~f~~~l~~~l~~~~~~~rvglv~fs~~~~~ 54 (224)
T cd01475 3 TDLVFLIDSSRSVRPENFELVKQFLNQIIDSLDVGPDATRVGLVQYSSTVKQ 54 (224)
T ss_pred ccEEEEEeCCCCCCHHHHHHHHHHHHHHHHhcccCCCccEEEEEEecCceeE
Confidence 34699999998743 5889999999888877 45689999999988765
No 36
>cd01471 vWA_micronemal_protein Micronemal proteins: The Toxoplasma lytic cycle begins when the parasite actively invades a target cell. In association with invasion, T. gondii sequentially discharges three sets of secretory organelles beginning with the micronemes, which contain adhesive proteins involved in parasite attachment to a host cell. Deployed as protein complexes, several micronemal proteins possess vertebrate-derived adhesive sequences that function in binding receptors. The VWA domain likely mediates the protein-protein interactions of these with their interacting partners.
Probab=92.11 E-value=0.3 Score=47.96 Aligned_cols=45 Identities=16% Similarity=0.130 Sum_probs=36.7
Q ss_pred EEEEEECCcChh--h-HHHHHHHHHHHhhcCC---CCcEEEEEEECCeEEE
Q psy17260 307 FLFVVDTCMDEE--E-LGALRDSLQMSLSLLP---KNALVGLITFGQMVQV 351 (679)
Q Consensus 307 ~vFvIDvs~~a~--~-l~~l~~si~~~L~~Lp---~~~~VG~ITfd~~V~~ 351 (679)
++|+||.|.... . ++.+++.+...++.++ ++.+||+|+|++..+.
T Consensus 3 v~~vlD~SgSm~~~~~~~~~k~~~~~~~~~~~~~~~~~~vglv~Fs~~~~~ 53 (186)
T cd01471 3 LYLLVDGSGSIGYSNWVTHVVPFLHTFVQNLNISPDEINLYLVTFSTNAKE 53 (186)
T ss_pred EEEEEeCCCCccchhhHHHHHHHHHHHHHhcccCCCceEEEEEEecCCceE
Confidence 589999998743 4 7888888888888774 6789999999987663
No 37
>COG4245 TerY Uncharacterized protein encoded in toxicity protection region of plasmid R478, contains von Willebrand factor (vWF) domain [General function prediction only]
Probab=92.10 E-value=0.24 Score=48.73 Aligned_cols=49 Identities=24% Similarity=0.330 Sum_probs=39.8
Q ss_pred CcEEEEEEECCcChh--hHHHHHHHHHHHhhcCCC------CcEEEEEEECCeEEEEE
Q psy17260 304 PLVFLFVVDTCMDEE--ELGALRDSLQMSLSLLPK------NALVGLITFGQMVQVHE 353 (679)
Q Consensus 304 pp~~vFvIDvs~~a~--~l~~l~~si~~~L~~Lp~------~~~VG~ITfd~~V~~y~ 353 (679)
-|+ +|++|+|.... .++.+...|+..++.|.. .+.++|||||+.+++|.
T Consensus 4 lP~-~lllDtSgSM~Ge~IealN~Glq~m~~~Lkqdp~Ale~v~lsIVTF~~~a~~~~ 60 (207)
T COG4245 4 LPC-YLLLDTSGSMIGEPIEALNAGLQMMIDTLKQDPYALERVELSIVTFGGPARVIQ 60 (207)
T ss_pred CCE-EEEEecCcccccccHHHHHHHHHHHHHHHHhChhhhheeEEEEEEecCcceEEe
Confidence 355 68899998764 388999999999988854 47999999999888864
No 38
>cd01482 vWA_collagen_alphaI-XII-like Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.
Probab=91.96 E-value=0.39 Score=46.20 Aligned_cols=45 Identities=20% Similarity=0.392 Sum_probs=35.9
Q ss_pred EEEEEECCcChh--hHHHHHHHHHHHhhcC---CCCcEEEEEEECCeEEE
Q psy17260 307 FLFVVDTCMDEE--ELGALRDSLQMSLSLL---PKNALVGLITFGQMVQV 351 (679)
Q Consensus 307 ~vFvIDvs~~a~--~l~~l~~si~~~L~~L---p~~~~VG~ITfd~~V~~ 351 (679)
.+|++|.|.... .++.+++.++..+..+ +++.+||+|+|++..+.
T Consensus 3 v~~vlD~S~Sm~~~~~~~~k~~~~~l~~~~~~~~~~~rvgli~fs~~~~~ 52 (164)
T cd01482 3 IVFLVDGSWSIGRSNFNLVRSFLSSVVEAFEIGPDGVQVGLVQYSDDPRT 52 (164)
T ss_pred EEEEEeCCCCcChhhHHHHHHHHHHHHhheeeCCCceEEEEEEECCCeeE
Confidence 589999998754 4888888888877765 46799999999987544
No 39
>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=91.91 E-value=1.1 Score=44.73 Aligned_cols=125 Identities=15% Similarity=0.042 Sum_probs=76.0
Q ss_pred EEEEEEECCcChh-------hHHHHHHHHHHHh----hcCCCCcEEEEEEECC-eEEEEEcCCCCccceeeecCCCCCch
Q psy17260 306 VFLFVVDTCMDEE-------ELGALRDSLQMSL----SLLPKNALVGLITFGQ-MVQVHELGCEGISRSYVFRGTKDVPA 373 (679)
Q Consensus 306 ~~vFvIDvs~~a~-------~l~~l~~si~~~L----~~Lp~~~~VG~ITfd~-~V~~y~l~~~~~~~~~Vf~g~~~l~~ 373 (679)
+-+++||+|.... +++..++.+...+ +..|. .+||+|+|.+ .-++.
T Consensus 5 a~vi~lD~S~sM~a~D~~PnRL~aak~~i~~~~~~f~~~np~-~~vGlv~fag~~a~v~--------------------- 62 (187)
T cd01452 5 ATMICIDNSEYMRNGDYPPTRFQAQADAVNLICQAKTRSNPE-NNVGLMTMAGNSPEVL--------------------- 62 (187)
T ss_pred EEEEEEECCHHHHcCCCCCCHHHHHHHHHHHHHHHHHhcCCC-ccEEEEEecCCceEEE---------------------
Confidence 5699999998754 2788888877664 55666 5999999975 33221
Q ss_pred hHHHHhhhcCCCCCCCCCCCCCCCCCCCCCCCCceeehHHhHHHHHHHHHHhcCCCCcccCCCCCCCchHHHHHHHHHHh
Q psy17260 374 QRLQEMLRIGKYSMSAPAPAPRPGQPPRPARTQFLQPVEACEMYATDLLAALQKGPVAVHQGREHCGPTGVAHVIAVGLL 453 (679)
Q Consensus 374 ~ql~~~l~l~d~~~p~~~g~~~~~~~~~~~~~~flvpl~e~~~~i~~lLe~L~~~~~~~~~~~~~~~c~G~AL~~A~~lL 453 (679)
+|+......+...|+.+.. .....+|.||+.|...|
T Consensus 63 -----------------------------------~plT~D~~~~~~~L~~i~~---------~g~~~l~~AL~~A~~~L 98 (187)
T cd01452 63 -----------------------------------VTLTNDQGKILSKLHDVQP---------KGKANFITGIQIAQLAL 98 (187)
T ss_pred -----------------------------------ECCCCCHHHHHHHHHhCCC---------CCcchHHHHHHHHHHHH
Confidence 0111113456666676643 14456999999999999
Q ss_pred hhccCC-CCCcc----CcCCCCCCccchhHHHHHHHHHhh-hcceeEEEEcCCc
Q psy17260 454 EGTLIR-SHNDI----HKGNNKLPGRMATKITKGLALRAA-YCRAIEYLLVPPW 501 (679)
Q Consensus 454 ~~~~lr-s~~di----~~~~~~~~~~~a~~fY~~La~~~~-~~~svD~~~~~~s 501 (679)
++..-+ ++..+ ..+ . ....+-..++++++. .++.+|++-+.+.
T Consensus 99 ~~~~~~~~~~rivi~v~S~----~-~~d~~~i~~~~~~lkk~~I~v~vI~~G~~ 147 (187)
T cd01452 99 KHRQNKNQKQRIVAFVGSP----I-EEDEKDLVKLAKRLKKNNVSVDIINFGEI 147 (187)
T ss_pred hcCCCcCCcceEEEEEecC----C-cCCHHHHHHHHHHHHHcCCeEEEEEeCCC
Confidence 753211 11111 111 0 111122336777877 8999998877653
No 40
>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=91.51 E-value=0.38 Score=56.40 Aligned_cols=51 Identities=22% Similarity=0.338 Sum_probs=44.3
Q ss_pred CCCcEEEEEEECCcChh--hHHHHHHHHHHHhhcCCCCcEEEEEEECCeEEEE
Q psy17260 302 CAPLVFLFVVDTCMDEE--ELGALRDSLQMSLSLLPKNALVGLITFGQMVQVH 352 (679)
Q Consensus 302 ~~pp~~vFvIDvs~~a~--~l~~l~~si~~~L~~Lp~~~~VG~ITfd~~V~~y 352 (679)
+.|..++||||+|.+.. .++.+++++..+|..|+++.+++||+|++.++.+
T Consensus 269 ~~p~~vvfvlD~SgSM~g~~i~~ak~al~~~l~~L~~~d~~~ii~F~~~~~~~ 321 (596)
T TIGR03788 269 VLPRELVFVIDTSGSMAGESIEQAKSALLLALDQLRPGDRFNIIQFDSDVTLL 321 (596)
T ss_pred CCCceEEEEEECCCCCCCccHHHHHHHHHHHHHhCCCCCEEEEEEECCcceEe
Confidence 45667999999999764 4888999999999999999999999999988765
No 41
>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=91.23 E-value=0.53 Score=45.75 Aligned_cols=45 Identities=18% Similarity=0.334 Sum_probs=36.8
Q ss_pred EEEEEECCcCh--hhHHHHHHHHHHHhhcCC---CCcEEEEEEECCeEEE
Q psy17260 307 FLFVVDTCMDE--EELGALRDSLQMSLSLLP---KNALVGLITFGQMVQV 351 (679)
Q Consensus 307 ~vFvIDvs~~a--~~l~~l~~si~~~L~~Lp---~~~~VG~ITfd~~V~~ 351 (679)
.+|+||.|..- .+++.+++.++..++.++ +.++||+|+|++..+.
T Consensus 3 ivfllD~S~Si~~~~f~~~k~fi~~lv~~f~i~~~~~rVgvv~ys~~~~~ 52 (165)
T cd01481 3 IVFLIDGSDNVGSGNFPAIRDFIERIVQSLDVGPDKIRVAVVQFSDTPRP 52 (165)
T ss_pred EEEEEeCCCCcCHHHHHHHHHHHHHHHhhccCCCCCcEEEEEEecCCeeE
Confidence 48999999874 458999999999888774 5699999999876544
No 42
>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=90.91 E-value=0.43 Score=47.06 Aligned_cols=46 Identities=13% Similarity=0.231 Sum_probs=35.3
Q ss_pred EEEEEEECCcChh--hHHHHHHHHHHHhhcC---------CCCcEEEEEEECCeEEE
Q psy17260 306 VFLFVVDTCMDEE--ELGALRDSLQMSLSLL---------PKNALVGLITFGQMVQV 351 (679)
Q Consensus 306 ~~vFvIDvs~~a~--~l~~l~~si~~~L~~L---------p~~~~VG~ITfd~~V~~ 351 (679)
-.+|+||.|.... .++.+++.++..++.| +++.+||+|+|++..++
T Consensus 4 dvv~vlD~S~Sm~~~~~~~~k~~~~~~~~~l~~~~~~~i~~~~~rvglv~fs~~~~~ 60 (186)
T cd01480 4 DITFVLDSSESVGLQNFDITKNFVKRVAERFLKDYYRKDPAGSWRVGVVQYSDQQEV 60 (186)
T ss_pred eEEEEEeCCCccchhhHHHHHHHHHHHHHHHhhhhccCCCCCceEEEEEEecCCcee
Confidence 4589999998754 4777777777777766 45689999999977544
No 43
>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=90.28 E-value=0.73 Score=48.91 Aligned_cols=49 Identities=27% Similarity=0.283 Sum_probs=41.5
Q ss_pred CCcEEEEEEECCcChhh-HHHHHHHHHHHhhc-CCCCcEEEEEEECCeEEE
Q psy17260 303 APLVFLFVVDTCMDEEE-LGALRDSLQMSLSL-LPKNALVGLITFGQMVQV 351 (679)
Q Consensus 303 ~pp~~vFvIDvs~~a~~-l~~l~~si~~~L~~-Lp~~~~VG~ITfd~~V~~ 351 (679)
.|...+|+||+|.+... +..+++++...++. ++++.+||+|+|++.++.
T Consensus 52 ~p~~vvlvlD~SgSM~~~~~~a~~a~~~~l~~~l~~~d~v~lv~f~~~~~~ 102 (296)
T TIGR03436 52 LPLTVGLVIDTSGSMRNDLDRARAAAIRFLKTVLRPNDRVFVVTFNTRLRL 102 (296)
T ss_pred CCceEEEEEECCCCchHHHHHHHHHHHHHHHhhCCCCCEEEEEEeCCceeE
Confidence 57889999999987544 77888888888876 788899999999988765
No 44
>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=90.26 E-value=0.83 Score=43.56 Aligned_cols=41 Identities=22% Similarity=0.331 Sum_probs=32.5
Q ss_pred EEEEEECCcChhh-HHHHHHHHHHHhhcCC---CCcEEEEEEECC
Q psy17260 307 FLFVVDTCMDEEE-LGALRDSLQMSLSLLP---KNALVGLITFGQ 347 (679)
Q Consensus 307 ~vFvIDvs~~a~~-l~~l~~si~~~L~~Lp---~~~~VG~ITfd~ 347 (679)
++|++|+|.+... ++..++.++..+..+. +..+||+|+|++
T Consensus 3 v~~llD~S~Sm~~~~~~~~~~~~~~~~~l~~~~~~~~v~lv~f~~ 47 (163)
T cd01476 3 LLFVLDSSGSVRGKFEKYKKYIERIVEGLEIGPTATRVALITYSG 47 (163)
T ss_pred EEEEEeCCcchhhhHHHHHHHHHHHHHhcCCCCCCcEEEEEEEcC
Confidence 5899999987544 6667777777777764 478999999987
No 45
>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=88.74 E-value=1.2 Score=42.40 Aligned_cols=46 Identities=20% Similarity=0.255 Sum_probs=36.6
Q ss_pred EEEEEEECCcCh-h-hHHHHHHHHHHHhhcCCC---CcEEEEEEECCeEEE
Q psy17260 306 VFLFVVDTCMDE-E-ELGALRDSLQMSLSLLPK---NALVGLITFGQMVQV 351 (679)
Q Consensus 306 ~~vFvIDvs~~a-~-~l~~l~~si~~~L~~Lp~---~~~VG~ITfd~~V~~ 351 (679)
-++|+||+|... . .++.+++.+...+..+.. +.+||+++|++..+.
T Consensus 3 ~v~l~vD~S~SM~~~~~~~~~~~~~~~~~~~~~~~~~~~i~ii~f~~~~~~ 53 (177)
T smart00327 3 DVVFLLDGSGSMGPNRFEKAKEFVLKLVEQLDIGPDGDRVGLVTFSDDATV 53 (177)
T ss_pred cEEEEEeCCCccchHHHHHHHHHHHHHHHhcCCCCCCcEEEEEEeCCCceE
Confidence 478999999876 3 378888888888887765 789999999984433
No 46
>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=88.36 E-value=1 Score=41.50 Aligned_cols=44 Identities=30% Similarity=0.470 Sum_probs=36.5
Q ss_pred EEEEEEECCcCh--hhHHHHHHHHHHHhhcCCC---CcEEEEEEECCeE
Q psy17260 306 VFLFVVDTCMDE--EELGALRDSLQMSLSLLPK---NALVGLITFGQMV 349 (679)
Q Consensus 306 ~~vFvIDvs~~a--~~l~~l~~si~~~L~~Lp~---~~~VG~ITfd~~V 349 (679)
.++|+||+|... ..++.+++.+...+..++. ..++|++.|+...
T Consensus 2 ~v~~viD~S~Sm~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~~f~~~~ 50 (161)
T cd00198 2 DIVFLLDVSGSMGGEKLDKAKEALKALVSSLSASPPGDRVGLVTFGSNA 50 (161)
T ss_pred cEEEEEeCCCCcCcchHHHHHHHHHHHHHhcccCCCCcEEEEEEecCcc
Confidence 368999999975 3488888899999888876 7899999999743
No 47
>PF13519 VWA_2: von Willebrand factor type A domain; PDB: 3IBS_B 3RAG_B 2X5N_A.
Probab=86.36 E-value=1.1 Score=42.28 Aligned_cols=42 Identities=29% Similarity=0.484 Sum_probs=33.9
Q ss_pred EEEEEECCcChh-------hHHHHHHHHHHHhhcCCCCcEEEEEEECCeE
Q psy17260 307 FLFVVDTCMDEE-------ELGALRDSLQMSLSLLPKNALVGLITFGQMV 349 (679)
Q Consensus 307 ~vFvIDvs~~a~-------~l~~l~~si~~~L~~Lp~~~~VG~ITfd~~V 349 (679)
++||||+|.+.. .++.+++++...++.+|. .+||+++|++..
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 589999998754 278889999999998885 499999998753
No 48
>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=85.79 E-value=2 Score=42.25 Aligned_cols=47 Identities=15% Similarity=0.168 Sum_probs=30.7
Q ss_pred cEEEEEEECCcChhh-HHHHHHHHHHHhhcC-CCCcEEEEEEECCeEEE
Q psy17260 305 LVFLFVVDTCMDEEE-LGALRDSLQMSLSLL-PKNALVGLITFGQMVQV 351 (679)
Q Consensus 305 p~~vFvIDvs~~a~~-l~~l~~si~~~L~~L-p~~~~VG~ITfd~~V~~ 351 (679)
--.+|+||+|.+... .....+.++..++.+ .++.+||+|+|++..+.
T Consensus 5 ~Dvv~llD~SgSm~~~~~~~~~~~~~l~~~~~~~~~rvglv~Fs~~~~~ 53 (185)
T cd01474 5 FDLYFVLDKSGSVAANWIEIYDFVEQLVDRFNSPGLRFSFITFSTRATK 53 (185)
T ss_pred eeEEEEEeCcCchhhhHHHHHHHHHHHHHHcCCCCcEEEEEEecCCceE
Confidence 456999999997543 222334445444433 34699999999876544
No 49
>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=85.39 E-value=1.9 Score=40.33 Aligned_cols=44 Identities=18% Similarity=0.382 Sum_probs=34.7
Q ss_pred EEEEEECCcChh--hHHHHHHHHHHHhhcCC---CCcEEEEEEECCeEE
Q psy17260 307 FLFVVDTCMDEE--ELGALRDSLQMSLSLLP---KNALVGLITFGQMVQ 350 (679)
Q Consensus 307 ~vFvIDvs~~a~--~l~~l~~si~~~L~~Lp---~~~~VG~ITfd~~V~ 350 (679)
.+|++|+|.... .++.+++.+...+..+. ++.++|+++|++..+
T Consensus 3 i~~llD~S~Sm~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~f~~~~~ 51 (161)
T cd01450 3 IVFLLDGSESVGPENFEKVKDFIEKLVEKLDIGPDKTRVGLVQYSDDVR 51 (161)
T ss_pred EEEEEeCCCCcCHHHHHHHHHHHHHHHHheeeCCCceEEEEEEEcCCce
Confidence 479999998754 47788888888887765 478999999987543
No 50
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=85.09 E-value=4.1 Score=47.73 Aligned_cols=46 Identities=20% Similarity=0.323 Sum_probs=36.6
Q ss_pred CCcEEEEEEECCcChh--hHHHHHHHHHHHhhc-CCCCcEEEEEEECCe
Q psy17260 303 APLVFLFVVDTCMDEE--ELGALRDSLQMSLSL-LPKNALVGLITFGQM 348 (679)
Q Consensus 303 ~pp~~vFvIDvs~~a~--~l~~l~~si~~~L~~-Lp~~~~VG~ITfd~~ 348 (679)
.+-.++||||+|.+.. .+..+|.++...|.. +.++-+||+|+|++.
T Consensus 400 ~~~~vvfvvD~SGSM~~~rl~~aK~a~~~ll~~ay~~rD~v~lI~F~g~ 448 (584)
T PRK13406 400 SETTTIFVVDASGSAALHRLAEAKGAVELLLAEAYVRRDQVALVAFRGR 448 (584)
T ss_pred CCccEEEEEECCCCCcHhHHHHHHHHHHHHHHhhcCCCCEEEEEEECCC
Confidence 3468899999999864 488899988888855 566679999999654
No 51
>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=84.40 E-value=2.3 Score=41.47 Aligned_cols=42 Identities=24% Similarity=0.317 Sum_probs=33.7
Q ss_pred EEEEEECCcChh---hHHHHHHHHHHHhhc-CCCCcEEEEEEECCe
Q psy17260 307 FLFVVDTCMDEE---ELGALRDSLQMSLSL-LPKNALVGLITFGQM 348 (679)
Q Consensus 307 ~vFvIDvs~~a~---~l~~l~~si~~~L~~-Lp~~~~VG~ITfd~~ 348 (679)
++|+||+|.+.. .++.+++++...+.. ++++.+||+|+|++.
T Consensus 3 v~lvlD~SgSM~~~~rl~~ak~a~~~~~~~~~~~~d~v~lv~F~~~ 48 (178)
T cd01451 3 VIFVVDASGSMAARHRMAAAKGAVLSLLRDAYQRRDKVALIAFRGT 48 (178)
T ss_pred EEEEEECCccCCCccHHHHHHHHHHHHHHHhhcCCCEEEEEEECCC
Confidence 589999999754 578888888887754 567789999999864
No 52
>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=82.55 E-value=3.1 Score=40.21 Aligned_cols=45 Identities=18% Similarity=0.211 Sum_probs=33.6
Q ss_pred EEEEEEECCcChh--------hHHHHHHHHHHHhhcCCCCcEEEEEEECCeEEE
Q psy17260 306 VFLFVVDTCMDEE--------ELGALRDSLQMSLSLLPKNALVGLITFGQMVQV 351 (679)
Q Consensus 306 ~~vFvIDvs~~a~--------~l~~l~~si~~~L~~Lp~~~~VG~ITfd~~V~~ 351 (679)
-++|+||+|.+.. .++.+++.+...+...| +.+||+|+|++.++.
T Consensus 4 ~vv~vlD~S~SM~~~~~~~~~r~~~a~~~~~~~~~~~~-~~~v~lv~f~~~~~~ 56 (180)
T cd01467 4 DIMIALDVSGSMLAQDFVKPSRLEAAKEVLSDFIDRRE-NDRIGLVVFAGAAFT 56 (180)
T ss_pred eEEEEEECCcccccccCCCCCHHHHHHHHHHHHHHhCC-CCeEEEEEEcCCeee
Confidence 4689999988642 25677777777766654 579999999876643
No 53
>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=82.16 E-value=2.9 Score=41.60 Aligned_cols=45 Identities=11% Similarity=0.144 Sum_probs=34.8
Q ss_pred EEEEEECCcChhh--HH-HHHHHHHHHhhcC---CCCcEEEEEEECCeEEE
Q psy17260 307 FLFVVDTCMDEEE--LG-ALRDSLQMSLSLL---PKNALVGLITFGQMVQV 351 (679)
Q Consensus 307 ~vFvIDvs~~a~~--l~-~l~~si~~~L~~L---p~~~~VG~ITfd~~V~~ 351 (679)
.+|+||.|.+..+ ++ .+++.++..++.+ ++++|||+|+|++..++
T Consensus 3 i~fllD~S~Si~~~~f~~~~~~f~~~lv~~l~i~~~~~rvgvv~fs~~~~~ 53 (192)
T cd01473 3 LTLILDESASIGYSNWRKDVIPFTEKIINNLNISKDKVHVGILLFAEKNRD 53 (192)
T ss_pred EEEEEeCCCcccHHHHHHHHHHHHHHHHHhCccCCCccEEEEEEecCCcee
Confidence 4899999987543 55 4777888887776 45799999999987764
No 54
>TIGR00868 hCaCC calcium-activated chloride channel protein 1. distributions. found a row in 1A13.INFO that was not parsed out
Probab=81.79 E-value=3.2 Score=50.49 Aligned_cols=49 Identities=18% Similarity=0.339 Sum_probs=39.3
Q ss_pred CcEEEEEEECCcChh---hHHHHHHHHHHHh-hcCCCCcEEEEEEECCeEEEE
Q psy17260 304 PLVFLFVVDTCMDEE---ELGALRDSLQMSL-SLLPKNALVGLITFGQMVQVH 352 (679)
Q Consensus 304 pp~~vFvIDvs~~a~---~l~~l~~si~~~L-~~Lp~~~~VG~ITfd~~V~~y 352 (679)
+...+||||+|.+.. .++.++++++..+ ..++++.+||+|+|++..++.
T Consensus 304 ~r~VVLVLDvSGSM~g~dRL~~lkqAA~~fL~~~l~~~DrVGLVtFsssA~vl 356 (863)
T TIGR00868 304 QRIVCLVLDKSGSMTVEDRLKRMNQAAKLFLLQTVEKGSWVGMVTFDSAAYIK 356 (863)
T ss_pred CceEEEEEECCccccccCHHHHHHHHHHHHHHHhCCCCCEEEEEEECCceeEe
Confidence 356899999999864 3888888888765 457888999999999987763
No 55
>COG1240 ChlD Mg-chelatase subunit ChlD [Coenzyme metabolism]
Probab=81.07 E-value=8.3 Score=40.18 Aligned_cols=90 Identities=20% Similarity=0.165 Sum_probs=59.9
Q ss_pred CcEEEEEEECCcChhh---HHHHHHHHHHHhhc-CCCCcEEEEEEECCeEEEEEcCCCCccceeeecCCCCCchhHHHHh
Q psy17260 304 PLVFLFVVDTCMDEEE---LGALRDSLQMSLSL-LPKNALVGLITFGQMVQVHELGCEGISRSYVFRGTKDVPAQRLQEM 379 (679)
Q Consensus 304 pp~~vFvIDvs~~a~~---l~~l~~si~~~L~~-Lp~~~~VG~ITfd~~V~~y~l~~~~~~~~~Vf~g~~~l~~~ql~~~ 379 (679)
.--+|||||.|.+..- .+++|-++...|.. ....-+|++|+|... +.
T Consensus 78 g~lvvfvVDASgSM~~~~Rm~aaKG~~~~lL~dAYq~RdkvavI~F~G~------------------------~A----- 128 (261)
T COG1240 78 GNLIVFVVDASGSMAARRRMAAAKGAALSLLRDAYQRRDKVAVIAFRGE------------------------KA----- 128 (261)
T ss_pred CCcEEEEEeCcccchhHHHHHHHHHHHHHHHHHHHHccceEEEEEecCC------------------------cc-----
Confidence 3467999999997543 66777666666643 345679999998521 01
Q ss_pred hhcCCCCCCCCCCCCCCCCCCCCCCCCceeehHHhHHHHHHHHHHhcCCCCcccCCCCCCCchHHHHHHHHHHhhhcc
Q psy17260 380 LRIGKYSMSAPAPAPRPGQPPRPARTQFLQPVEACEMYATDLLAALQKGPVAVHQGREHCGPTGVAHVIAVGLLEGTL 457 (679)
Q Consensus 380 l~l~d~~~p~~~g~~~~~~~~~~~~~~flvpl~e~~~~i~~lLe~L~~~~~~~~~~~~~~~c~G~AL~~A~~lL~~~~ 457 (679)
.+++|...+-+.+.+.|+.|+. ..++-+..||..|..++....
T Consensus 129 --------------------------~lll~pT~sv~~~~~~L~~l~~---------GG~TPL~~aL~~a~ev~~r~~ 171 (261)
T COG1240 129 --------------------------ELLLPPTSSVELAERALERLPT---------GGKTPLADALRQAYEVLAREK 171 (261)
T ss_pred --------------------------eEEeCCcccHHHHHHHHHhCCC---------CCCCchHHHHHHHHHHHHHhh
Confidence 1222222234567788888876 234569999999999998654
No 56
>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=80.50 E-value=2.9 Score=41.32 Aligned_cols=46 Identities=15% Similarity=0.267 Sum_probs=34.8
Q ss_pred EEEEEEECCcChh-------hHHHHHHHHHHHhhcC---CCCcEEEEEEE-CCeEEE
Q psy17260 306 VFLFVVDTCMDEE-------ELGALRDSLQMSLSLL---PKNALVGLITF-GQMVQV 351 (679)
Q Consensus 306 ~~vFvIDvs~~a~-------~l~~l~~si~~~L~~L---p~~~~VG~ITf-d~~V~~ 351 (679)
..+|+||+|.+.. .++.++..+...++.+ .++.+||+|+| ++.-++
T Consensus 5 ~ivi~lD~S~SM~a~D~~ptRl~~ak~~~~~fi~~~~~~~~~~~vglv~f~~~~a~~ 61 (183)
T cd01453 5 HLIIVIDCSRSMEEQDLKPSRLAVVLKLLELFIEEFFDQNPISQLGIISIKNGRAEK 61 (183)
T ss_pred EEEEEEECcHHHhcCCCCchHHHHHHHHHHHHHHHHhhcCccccEEEEEEcCCccEE
Confidence 4589999998754 4889999998888754 34479999999 554443
No 57
>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=79.01 E-value=3.1 Score=39.15 Aligned_cols=46 Identities=17% Similarity=0.092 Sum_probs=33.3
Q ss_pred EEEEEECCcChhh--HHHHHHHHHHHhhcCC-CCcEEEEEEECCeEEEE
Q psy17260 307 FLFVVDTCMDEEE--LGALRDSLQMSLSLLP-KNALVGLITFGQMVQVH 352 (679)
Q Consensus 307 ~vFvIDvs~~a~~--l~~l~~si~~~L~~Lp-~~~~VG~ITfd~~V~~y 352 (679)
++|+||+|.+... +...+..+...+..+. ++.+|++|+|++....+
T Consensus 3 v~illD~SgSM~~~k~~~a~~~~~~l~~~~~~~~~~v~li~F~~~~~~~ 51 (152)
T cd01462 3 VILLVDQSGSMYGAPEEVAKAVALALLRIALAENRDTYLILFDSEFQTK 51 (152)
T ss_pred EEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHcCCcEEEEEeCCCceEE
Confidence 5899999997653 5566666666666554 46799999999884443
No 58
>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=78.82 E-value=2.6 Score=40.85 Aligned_cols=43 Identities=7% Similarity=0.102 Sum_probs=34.8
Q ss_pred EEEEEEECCcChh---hHHHHHHHHHHHhhcCCC-CcEEEEEEECCe
Q psy17260 306 VFLFVVDTCMDEE---ELGALRDSLQMSLSLLPK-NALVGLITFGQM 348 (679)
Q Consensus 306 ~~vFvIDvs~~a~---~l~~l~~si~~~L~~Lp~-~~~VG~ITfd~~ 348 (679)
+++|+||+|.+.. .++.+++++...++.+.+ +.++|+++|++.
T Consensus 2 ~v~~llD~SgSM~~~~kl~~ak~a~~~l~~~l~~~~d~~~l~~F~~~ 48 (174)
T cd01454 2 AVTLLLDLSGSMRSDRRIDVAKKAAVLLAEALEACGVPHAILGFTTD 48 (174)
T ss_pred EEEEEEECCCCCCCCcHHHHHHHHHHHHHHHHHHcCCcEEEEEecCC
Confidence 4789999999753 478888888877777764 789999999875
No 59
>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=75.71 E-value=12 Score=44.37 Aligned_cols=45 Identities=27% Similarity=0.282 Sum_probs=34.1
Q ss_pred CcEEEEEEECCcChh---hHHHHHHHHHHHhhc-CCCCcEEEEEEECCe
Q psy17260 304 PLVFLFVVDTCMDEE---ELGALRDSLQMSLSL-LPKNALVGLITFGQM 348 (679)
Q Consensus 304 pp~~vFvIDvs~~a~---~l~~l~~si~~~L~~-Lp~~~~VG~ITfd~~ 348 (679)
.-.++|+||+|.+.. .+..++.++...+.. +..+.+||+|+|++.
T Consensus 465 ~~~vv~vvD~SgSM~~~~rl~~ak~a~~~ll~~a~~~~D~v~lI~F~g~ 513 (633)
T TIGR02442 465 GNLVIFVVDASGSMAARGRMAAAKGAVLSLLRDAYQKRDKVALITFRGE 513 (633)
T ss_pred CceEEEEEECCccCCCccHHHHHHHHHHHHHHHhhcCCCEEEEEEECCC
Confidence 457789999999763 477788777777653 456789999999743
No 60
>PF09967 DUF2201: VWA-like domain (DUF2201); InterPro: IPR018698 This family of various hypothetical bacterial proteins has no known function.
Probab=64.24 E-value=16 Score=33.92 Aligned_cols=44 Identities=27% Similarity=0.237 Sum_probs=34.2
Q ss_pred EEEEECCcCh--hhHHHHHHHHHHHhhcCCCCcEEEEEEECCeEEEEE
Q psy17260 308 LFVVDTCMDE--EELGALRDSLQMSLSLLPKNALVGLITFGQMVQVHE 353 (679)
Q Consensus 308 vFvIDvs~~a--~~l~~l~~si~~~L~~Lp~~~~VG~ITfd~~V~~y~ 353 (679)
+++||+|.+- .+|+.+...+..++... +.+|-+|.||..|+-..
T Consensus 2 ~vaiDtSGSis~~~l~~fl~ev~~i~~~~--~~~v~vi~~D~~v~~~~ 47 (126)
T PF09967_consen 2 VVAIDTSGSISDEELRRFLSEVAGILRRF--PAEVHVIQFDAEVQDVQ 47 (126)
T ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHHhC--CCCEEEEEECCEeeeee
Confidence 6899999974 44777777788877777 45689999998887544
No 61
>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=64.04 E-value=12 Score=44.03 Aligned_cols=46 Identities=20% Similarity=0.336 Sum_probs=36.1
Q ss_pred CCcEEEEEEECCcChh--hHHHHHHHHHHHhhc-CCCCcEEEEEEECCe
Q psy17260 303 APLVFLFVVDTCMDEE--ELGALRDSLQMSLSL-LPKNALVGLITFGQM 348 (679)
Q Consensus 303 ~pp~~vFvIDvs~~a~--~l~~l~~si~~~L~~-Lp~~~~VG~ITfd~~ 348 (679)
..-.++|+||+|.+.. .++.+|.++...+.. +.++-+||+|+|++.
T Consensus 406 ~~~~v~fvvD~SGSM~~~rl~~aK~av~~Ll~~~~~~~D~v~Li~F~~~ 454 (589)
T TIGR02031 406 SGRLLIFVVDASGSAAVARMSEAKGAVELLLGEAYVHRDQVSLIAFRGT 454 (589)
T ss_pred cCceEEEEEECCCCCChHHHHHHHHHHHHHHHhhccCCCEEEEEEECCC
Confidence 3456889999999764 388899998888875 445569999999754
No 62
>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=63.06 E-value=14 Score=37.30 Aligned_cols=43 Identities=16% Similarity=0.301 Sum_probs=32.4
Q ss_pred EEEEEEECCcCh---------hhHHHHHHHHHHHhhcC---CCCcEEEEEEECCe
Q psy17260 306 VFLFVVDTCMDE---------EELGALRDSLQMSLSLL---PKNALVGLITFGQM 348 (679)
Q Consensus 306 ~~vFvIDvs~~a---------~~l~~l~~si~~~L~~L---p~~~~VG~ITfd~~ 348 (679)
..+|+||+|.+. ..|+.+++.+...+... -++.+||+|.|++.
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 469999999854 23778888888888752 34569999999754
No 63
>PTZ00441 sporozoite surface protein 2 (SSP2); Provisional
Probab=62.13 E-value=14 Score=42.85 Aligned_cols=53 Identities=13% Similarity=0.083 Sum_probs=38.5
Q ss_pred CcEEEEEEECCcChhh---HHHHHHHHHHHhhcC---CCCcEEEEEEECCeEE-EEEcCC
Q psy17260 304 PLVFLFVVDTCMDEEE---LGALRDSLQMSLSLL---PKNALVGLITFGQMVQ-VHELGC 356 (679)
Q Consensus 304 pp~~vFvIDvs~~a~~---l~~l~~si~~~L~~L---p~~~~VG~ITfd~~V~-~y~l~~ 356 (679)
.--.+||||+|.+... ++.++..+..++..+ ++.++||+|+|++..+ ++.+..
T Consensus 42 ~lDIvFLLD~SgSMg~~Nfle~AK~Fa~~LV~~l~Is~D~V~VgiV~FSd~~r~vfpL~s 101 (576)
T PTZ00441 42 EVDLYLLVDGSGSIGYHNWITHVIPMLMGLIQQLNLSDDAINLYMSLFSNNTTELIRLGS 101 (576)
T ss_pred CceEEEEEeCCCccCCccHHHHHHHHHHHHHHHhccCCCceEEEEEEeCCCceEEEecCC
Confidence 4567999999987643 467777788877776 3568999999987654 445543
No 64
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=58.61 E-value=8.8 Score=26.85 Aligned_cols=30 Identities=23% Similarity=0.496 Sum_probs=23.1
Q ss_pred cccCCCCcccEEcCceeEecCCCeEEeccCCCCCCC
Q psy17260 235 LLCMRNQCRAILNPLCQVDYKSKLWVCNFCFQRNAF 270 (679)
Q Consensus 235 ~RC~~~~C~AYiNpf~~~~~~g~~W~C~~C~~~N~v 270 (679)
+.|.. |+..|- .-.+..+++|.+|...|.+
T Consensus 2 ~~C~~--C~t~L~----yP~gA~~vrCs~C~~vt~v 31 (31)
T TIGR01053 2 VVCGG--CRTLLM----YPRGASSVRCALCQTVNLV 31 (31)
T ss_pred cCcCC--CCcEee----cCCCCCeEECCCCCeEecC
Confidence 56888 998764 2267889999999988753
No 65
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=57.00 E-value=6.6 Score=31.08 Aligned_cols=33 Identities=18% Similarity=0.491 Sum_probs=23.2
Q ss_pred ccccCCCCcccEEcCceeEecCCCeEEeccCCCCC
Q psy17260 234 PLLCMRNQCRAILNPLCQVDYKSKLWVCNFCFQRN 268 (679)
Q Consensus 234 p~RC~~~~C~AYiNpf~~~~~~g~~W~C~~C~~~N 268 (679)
++-|++ |+.-=--+-+-+...-+|+|+.|+..|
T Consensus 22 aLIC~~--C~~hNGla~~~~~~~i~y~C~~Cg~~N 54 (54)
T PF10058_consen 22 ALICSK--CFSHNGLAPKEEFEEIQYRCPYCGALN 54 (54)
T ss_pred eEECcc--cchhhcccccccCCceEEEcCCCCCcC
Confidence 466998 987533332444455689999999987
No 66
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=54.45 E-value=10 Score=28.61 Aligned_cols=29 Identities=24% Similarity=0.441 Sum_probs=20.9
Q ss_pred cccCCCCcccEEcCceeEecCCCeEEeccCCCCCC
Q psy17260 235 LLCMRNQCRAILNPLCQVDYKSKLWVCNFCFQRNA 269 (679)
Q Consensus 235 ~RC~~~~C~AYiNpf~~~~~~g~~W~C~~C~~~N~ 269 (679)
.+|.+ |++-+ .+++....+.|+.||..-.
T Consensus 4 y~C~~--CG~~~----~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 4 YKCAR--CGREV----ELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EECCC--CCCEE----EECCCCCceECCCCCCeEE
Confidence 58999 99964 3344444799999997654
No 67
>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=48.28 E-value=31 Score=36.39 Aligned_cols=46 Identities=26% Similarity=0.339 Sum_probs=35.2
Q ss_pred CCcEEEEEEECCcChhh-------HHHHHHHHHHHhhcCCCCcEEEEEEECCeEE
Q psy17260 303 APLVFLFVVDTCMDEEE-------LGALRDSLQMSLSLLPKNALVGLITFGQMVQ 350 (679)
Q Consensus 303 ~pp~~vFvIDvs~~a~~-------l~~l~~si~~~L~~Lp~~~~VG~ITfd~~V~ 350 (679)
...-.+++||.|.+..+ ++ .+..|..+++.++. -+||++.|+..+.
T Consensus 59 r~~qIvlaID~S~SM~~~~~~~~ale-ak~lIs~al~~Le~-g~vgVv~Fg~~~~ 111 (266)
T cd01460 59 RDYQILIAIDDSKSMSENNSKKLALE-SLCLVSKALTLLEV-GQLGVCSFGEDVQ 111 (266)
T ss_pred cCceEEEEEecchhcccccccccHHH-HHHHHHHHHHhCcC-CcEEEEEeCCCce
Confidence 45788999999987643 44 45577777787877 6999999987654
No 68
>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=42.50 E-value=29 Score=34.38 Aligned_cols=45 Identities=7% Similarity=0.028 Sum_probs=32.5
Q ss_pred cEEEEEEECCcChh---------hHHHHHHHHHHHhhcCC--CCcEEEEEEECCeE
Q psy17260 305 LVFLFVVDTCMDEE---------ELGALRDSLQMSLSLLP--KNALVGLITFGQMV 349 (679)
Q Consensus 305 p~~vFvIDvs~~a~---------~l~~l~~si~~~L~~Lp--~~~~VG~ITfd~~V 349 (679)
.-++|+||.|.+.. .++.+++++...+..+. +...+++++|++..
T Consensus 3 ~dvv~~ID~SgSM~~~~~~~~~~k~~~ak~~~~~l~~~~~~~D~d~i~l~~f~~~~ 58 (199)
T cd01457 3 RDYTLLIDKSGSMAEADEAKERSRWEEAQESTRALARKCEEYDSDGITVYLFSGDF 58 (199)
T ss_pred cCEEEEEECCCcCCCCCCCCCchHHHHHHHHHHHHHHHHHhcCCCCeEEEEecCCc
Confidence 35799999999764 36788888887776553 23568888887654
No 69
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=39.50 E-value=18 Score=27.76 Aligned_cols=33 Identities=21% Similarity=0.532 Sum_probs=21.9
Q ss_pred cCCCCcccEEcCceeEecCCCeEEeccCCCCCCCCcc
Q psy17260 237 CMRNQCRAILNPLCQVDYKSKLWVCNFCFQRNAFPPQ 273 (679)
Q Consensus 237 C~~~~C~AYiNpf~~~~~~g~~W~C~~C~~~N~vp~~ 273 (679)
|.. |+..+-+- -..++..|.|+-|+....+.+.
T Consensus 3 Cp~--Cg~~l~~~--~~~~~~~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 3 CPK--CGNMLIPK--EGKEKRRFVCRKCGYEEPIEQK 35 (52)
T ss_pred CCC--CCCccccc--cCCCCCEEECCcCCCeEECCCc
Confidence 777 99976332 2222358999999987766443
No 70
>PRK03954 ribonuclease P protein component 4; Validated
Probab=37.91 E-value=21 Score=33.16 Aligned_cols=34 Identities=26% Similarity=0.551 Sum_probs=24.3
Q ss_pred ccCCCCcccEEcCc----eeEecCC---CeEEeccCCCCCCCC
Q psy17260 236 LCMRNQCRAILNPL----CQVDYKS---KLWVCNFCFQRNAFP 271 (679)
Q Consensus 236 RC~~~~C~AYiNpf----~~~~~~g---~~W~C~~C~~~N~vp 271 (679)
-|.+ |.+||=|- +++..++ -.++|..||+..-+|
T Consensus 66 ~CK~--C~t~LiPG~n~~vRi~~~~~~~vvitCl~CG~~kR~P 106 (121)
T PRK03954 66 YCKR--CHSFLVPGVNARVRLRQKRMPHVVITCLECGHIMRYP 106 (121)
T ss_pred Hhhc--CCCeeecCCceEEEEecCCcceEEEECccCCCEEeec
Confidence 4999 99998663 3344332 224999999998887
No 71
>PF08879 WRC: WRC; InterPro: IPR014977 WRC is named after the conserved Trp-Arg-Cys motif, it contains two distinctive features: a putative nuclear localisation signal and a zinc-finger motif (C3H). It is suggested that WRC functions in DNA binding []. ; GO: 0005515 protein binding
Probab=37.08 E-value=16 Score=27.92 Aligned_cols=16 Identities=44% Similarity=0.951 Sum_probs=13.0
Q ss_pred CccccCCCCcccEEcCceeEecCCCeEEec
Q psy17260 233 EPLLCMRNQCRAILNPLCQVDYKSKLWVCN 262 (679)
Q Consensus 233 ~p~RC~~~~C~AYiNpf~~~~~~g~~W~C~ 262 (679)
++.||.+ .+|+.|.|.
T Consensus 3 e~~RC~R--------------~DGK~WrC~ 18 (46)
T PF08879_consen 3 EPWRCRR--------------NDGKGWRCS 18 (46)
T ss_pred ccceeeC--------------CCCCccccC
Confidence 4578888 679999996
No 72
>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=36.20 E-value=76 Score=31.93 Aligned_cols=41 Identities=24% Similarity=0.381 Sum_probs=23.6
Q ss_pred EEEEEEECCcChhh--------HHHHHHHHHHHhh----cCCCCcEEEEEEECC
Q psy17260 306 VFLFVVDTCMDEEE--------LGALRDSLQMSLS----LLPKNALVGLITFGQ 347 (679)
Q Consensus 306 ~~vFvIDvs~~a~~--------l~~l~~si~~~L~----~Lp~~~~VG~ITfd~ 347 (679)
+.+|+||++....+ |+.+.+++...+. .-|. ..||+|.|++
T Consensus 1 ~~vflID~s~sM~~~~~~~~~~l~~al~~i~~~~~~ki~~~~k-D~vgvvl~gt 53 (224)
T PF03731_consen 1 ATVFLIDVSPSMFEPSSESESPLEEALKAIEDLMQQKIISSPK-DEVGVVLFGT 53 (224)
T ss_dssp EEEEEEE-SCGGGS-BTTCS-HHHHHHHHHHHHHHHHHHTT----EEEEEEES-
T ss_pred CEEEEEECCHHHCCCCCCcchhHHHHHHHHHHHHHHHHcCCCC-CeEEEEEEcC
Confidence 35899999987542 4444444444443 2344 7899999974
No 73
>PF08478 POTRA_1: POTRA domain, FtsQ-type; InterPro: IPR013685 FtsQ/DivIB bacterial division proteins (IPR005548 from INTERPRO) contain an N-terminal POTRA domain (for polypeptide-transport-associated domain). This is found in different types of proteins, usually associated with a transmembrane beta-barrel. FtsQ/DivIB may have chaperone-like roles, which has also been postulated for the POTRA domain in other contexts []. ; PDB: 2ALJ_A 2VH1_B 3J00_Z 2VH2_B.
Probab=35.19 E-value=44 Score=26.89 Aligned_cols=46 Identities=22% Similarity=0.395 Sum_probs=31.0
Q ss_pred ceeeecCCccccHHHHHHHHhcccCCCCCCCCCCCCCCCCCCCCccceeeccccccccchhhccccCCCCC
Q psy17260 79 RSYVFRGTKDVPAQRLQEMLRIGKYSMSAPAPAPRPGQPPTPPVHKFLQPVEACEMSLTDLLGGLQKDPWP 149 (679)
Q Consensus 79 ~~~vf~G~k~~~~~q~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~rFl~P~~~~e~~l~~~le~L~~d~~~ 149 (679)
+...+.|++.++.++|.+.+|+..| . +=| .+.+..+-+.|..+||-
T Consensus 4 ~~I~V~G~~~~~~~~i~~~~~~~~~------------~------~~~-------~~~~~~~~~~l~~~p~V 49 (69)
T PF08478_consen 4 KKIEVSGNSYLSKEEILQALGIQKG------------K------NLF-------SLDLKKIEQRLEKLPWV 49 (69)
T ss_dssp -EEEEES-SSS-HHHHHHHHCTTST------------T------TCC-------CSHHHHHHHCCCCTTTE
T ss_pred cEEEEECCCcCCHHHHHHHhCcCCC------------C------eEE-------EECHHHHHHHHHcCCCE
Confidence 3456889999999999999988321 0 112 25677777888888884
No 74
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=34.25 E-value=23 Score=32.47 Aligned_cols=32 Identities=25% Similarity=0.792 Sum_probs=25.5
Q ss_pred cccCCCCcccEEcCceeEec-CCCeEEeccCCCCC
Q psy17260 235 LLCMRNQCRAILNPLCQVDY-KSKLWVCNFCFQRN 268 (679)
Q Consensus 235 ~RC~~~~C~AYiNpf~~~~~-~g~~W~C~~C~~~N 268 (679)
..|.. |+-.+..-|.+.. +...|.|++|....
T Consensus 72 ~~C~~--C~~~VC~~C~~~~~~~~~WlC~vC~k~r 104 (118)
T PF02318_consen 72 RVCVD--CKHRVCKKCGVYSKKEPIWLCKVCQKQR 104 (118)
T ss_dssp EEETT--TTEEEETTSEEETSSSCCEEEHHHHHHH
T ss_pred CcCCc--CCccccCccCCcCCCCCCEEChhhHHHH
Confidence 67888 8888888888774 57899999997543
No 75
>COG0275 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]
Probab=33.96 E-value=48 Score=35.55 Aligned_cols=28 Identities=32% Similarity=0.552 Sum_probs=25.9
Q ss_pred hHHHHHHHHHHHhhcCCCCcEEEEEEEC
Q psy17260 319 ELGALRDSLQMSLSLLPKNALVGLITFG 346 (679)
Q Consensus 319 ~l~~l~~si~~~L~~Lp~~~~VG~ITfd 346 (679)
||+.++++|..+++.|.++.|+++|||.
T Consensus 219 EL~~L~~~L~~a~~~L~~gGRl~VIsFH 246 (314)
T COG0275 219 ELEELEEALEAALDLLKPGGRLAVISFH 246 (314)
T ss_pred HHHHHHHHHHHHHHhhCCCcEEEEEEec
Confidence 6899999999999999999999999874
No 76
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=30.95 E-value=1.7e+02 Score=35.44 Aligned_cols=109 Identities=19% Similarity=0.301 Sum_probs=69.4
Q ss_pred cccCCCCcccEE-cCcee----EecCCCeEEeccCCCCCCCCcccccccCCCCCCcccCCCcceEEecCC----------
Q psy17260 235 LLCMRNQCRAIL-NPLCQ----VDYKSKLWVCNFCFQRNAFPPQYAAITEQHQPAELHPQFTTIEYTIPK---------- 299 (679)
Q Consensus 235 ~RC~~~~C~AYi-Npf~~----~~~~g~~W~C~~C~~~N~vp~~Y~~~~~~~~rpEL~~~~~tvEy~~~~---------- 299 (679)
+.|.. |+-.. +|.|. +-...+.-.|..||+.-.+|.. .||.- +..+-|..+.
T Consensus 436 l~C~~--Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~---------Cp~Cg--s~~L~~~G~GterieeeL~~ 502 (730)
T COG1198 436 LLCRD--CGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQS---------CPECG--SEHLRAVGPGTERIEEELKR 502 (730)
T ss_pred eeccc--CCCcccCCCCCcceEEecCCCeeEeCCCCCCCCCCCC---------CCCCC--CCeeEEecccHHHHHHHHHH
Confidence 45555 55443 34443 3456788999999999877742 45553 2334444332
Q ss_pred CCCCCcEEEEEEECCcChhhHHHHHHHHHHHh-------------hcCCCCcEEEEEEECCeEEEEEcCC
Q psy17260 300 MQCAPLVFLFVVDTCMDEEELGALRDSLQMSL-------------SLLPKNALVGLITFGQMVQVHELGC 356 (679)
Q Consensus 300 ~~~~pp~~vFvIDvs~~a~~l~~l~~si~~~L-------------~~Lp~~~~VG~ITfd~~V~~y~l~~ 356 (679)
--|..+++.|--|++.....++.+...+..-= ..+|+=+.||++--|..++.-|+..
T Consensus 503 ~FP~~rv~r~d~Dtt~~k~~~~~~l~~~~~ge~dILiGTQmiaKG~~fp~vtLVgvl~aD~~L~~~DfRA 572 (730)
T COG1198 503 LFPGARIIRIDSDTTRRKGALEDLLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDFRA 572 (730)
T ss_pred HCCCCcEEEEccccccchhhHHHHHHHHhCCCCCeeecchhhhcCCCcccceEEEEEechhhhcCCCcch
Confidence 13667888888888887776666554444311 1245558999999999888877765
No 77
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=30.74 E-value=28 Score=25.16 Aligned_cols=32 Identities=16% Similarity=0.316 Sum_probs=23.3
Q ss_pred cccCCCCcccEEc-CceeEecCCCeEEeccCCCCC
Q psy17260 235 LLCMRNQCRAILN-PLCQVDYKSKLWVCNFCFQRN 268 (679)
Q Consensus 235 ~RC~~~~C~AYiN-pf~~~~~~g~~W~C~~C~~~N 268 (679)
++|.+ |++-.+ |--++..+|++-+|+-|++.-
T Consensus 3 i~CP~--C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPN--CQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCC--CCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 57887 888766 333455678889999998764
No 78
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=29.39 E-value=34 Score=24.02 Aligned_cols=11 Identities=36% Similarity=0.933 Sum_probs=8.3
Q ss_pred CeEEeccCCCC
Q psy17260 257 KLWVCNFCFQR 267 (679)
Q Consensus 257 ~~W~C~~C~~~ 267 (679)
..|.|+.|+..
T Consensus 16 ~~~~CP~Cg~~ 26 (33)
T cd00350 16 APWVCPVCGAP 26 (33)
T ss_pred CCCcCcCCCCc
Confidence 56888888863
No 79
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=28.45 E-value=30 Score=25.72 Aligned_cols=30 Identities=17% Similarity=0.288 Sum_probs=25.0
Q ss_pred cccCCCCcccEEcCceeEecCCCeEEeccCCCC
Q psy17260 235 LLCMRNQCRAILNPLCQVDYKSKLWVCNFCFQR 267 (679)
Q Consensus 235 ~RC~~~~C~AYiNpf~~~~~~g~~W~C~~C~~~ 267 (679)
-||.. |+....-...+.+ .....|+-||..
T Consensus 6 y~C~~--Cg~~fe~~~~~~~-~~~~~CP~Cg~~ 35 (42)
T PF09723_consen 6 YRCEE--CGHEFEVLQSISE-DDPVPCPECGST 35 (42)
T ss_pred EEeCC--CCCEEEEEEEcCC-CCCCcCCCCCCC
Confidence 47998 9988888887777 678899999984
No 80
>PRK10997 yieM hypothetical protein; Provisional
Probab=27.70 E-value=90 Score=35.88 Aligned_cols=50 Identities=22% Similarity=0.198 Sum_probs=33.4
Q ss_pred EEEEEEECCcChh-h-HHHHHHHHHHHhh--cCCCCcEEEEEEECCeEEEEEcCC
Q psy17260 306 VFLFVVDTCMDEE-E-LGALRDSLQMSLS--LLPKNALVGLITFGQMVQVHELGC 356 (679)
Q Consensus 306 ~~vFvIDvs~~a~-~-l~~l~~si~~~L~--~Lp~~~~VG~ITfd~~V~~y~l~~ 356 (679)
-++++||+|.+.. . -...+ ++..+|- .+.++-++++|.|++.+.-|.+..
T Consensus 325 piII~VDtSGSM~G~ke~~Ak-alAaAL~~iAl~q~dr~~li~Fs~~i~~~~l~~ 378 (487)
T PRK10997 325 PFIVCVDTSGSMGGFNEQCAK-AFCLALMRIALAENRRCYIMLFSTEVVTYELTG 378 (487)
T ss_pred cEEEEEECCCCCCCCHHHHHH-HHHHHHHHHHHhcCCCEEEEEecCCceeeccCC
Confidence 4699999999764 1 22223 3333332 356678999999999888876653
No 81
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=27.41 E-value=27 Score=27.17 Aligned_cols=30 Identities=27% Similarity=0.589 Sum_probs=19.6
Q ss_pred ccCCCCcccEEcCc-----------eeEecCCCeEEeccCCCC
Q psy17260 236 LCMRNQCRAILNPL-----------CQVDYKSKLWVCNFCFQR 267 (679)
Q Consensus 236 RC~~~~C~AYiNpf-----------~~~~~~g~~W~C~~C~~~ 267 (679)
+|.- |+=..+|- ..|++-...|+|+.|+..
T Consensus 3 ~C~~--CgyiYd~~~Gd~~~~i~pGt~f~~Lp~~w~CP~C~a~ 43 (50)
T cd00730 3 ECRI--CGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGAG 43 (50)
T ss_pred CCCC--CCeEECCCCCCcccCcCCCCCHhHCCCCCCCCCCCCc
Confidence 5777 87666653 334444567899999853
No 82
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=27.16 E-value=22 Score=24.25 Aligned_cols=14 Identities=29% Similarity=0.525 Sum_probs=12.1
Q ss_pred CeEEeccCCCCCCC
Q psy17260 257 KLWVCNFCFQRNAF 270 (679)
Q Consensus 257 ~~W~C~~C~~~N~v 270 (679)
+.|.|+.|...|..
T Consensus 3 g~W~C~~C~~~N~~ 16 (30)
T PF00641_consen 3 GDWKCPSCTFMNPA 16 (30)
T ss_dssp SSEEETTTTEEEES
T ss_pred cCccCCCCcCCchH
Confidence 47999999999964
No 83
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=26.99 E-value=64 Score=25.35 Aligned_cols=35 Identities=17% Similarity=0.365 Sum_probs=21.8
Q ss_pred CccccCCCCcccEE-----cCceeEecCCCeEEeccCCCC
Q psy17260 233 EPLLCMRNQCRAIL-----NPLCQVDYKSKLWVCNFCFQR 267 (679)
Q Consensus 233 ~p~RC~~~~C~AYi-----Npf~~~~~~g~~W~C~~C~~~ 267 (679)
+.++|.+|+|=+=- .-|--.+.+...++|-.|++.
T Consensus 5 gvl~C~Np~CITn~~E~v~~~F~v~~~~~~~~rC~YCe~~ 44 (52)
T PF02748_consen 5 GVLKCPNPNCITNSNEPVESRFYVIDKEPIKLRCHYCERI 44 (52)
T ss_dssp SSSE-SSTTBTTT-TSSS--EEEEEETTTCEEEETTT--E
T ss_pred eEEEcCCCCcccCCCCCCCceEEEEeCCCCEEEeeCCCCE
Confidence 46889888886652 233334567899999999875
No 84
>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=26.67 E-value=1.2e+02 Score=30.92 Aligned_cols=45 Identities=9% Similarity=-0.002 Sum_probs=27.2
Q ss_pred CCCc-EEEEEEECCcChhhHH-HHHHHHHHHhhcCCCCcEEEEEEECCeE
Q psy17260 302 CAPL-VFLFVVDTCMDEEELG-ALRDSLQMSLSLLPKNALVGLITFGQMV 349 (679)
Q Consensus 302 ~~pp-~~vFvIDvs~~a~~l~-~l~~si~~~L~~Lp~~~~VG~ITfd~~V 349 (679)
+..| -+|+++|+|.+..... .+...+..+....+ ++.++.|++.+
T Consensus 54 ~~~~~~lvvl~DvSGSM~~~s~~~l~~~~~l~~~~~---~~~~f~F~~~l 100 (222)
T PF05762_consen 54 PRKPRRLVVLCDVSGSMAGYSEFMLAFLYALQRQFR---RVRVFVFSTRL 100 (222)
T ss_pred cCCCccEEEEEeCCCChHHHHHHHHHHHHHHHHhCC---CEEEEEEeeeh
Confidence 3444 8899999999877633 23333333333333 67777777654
No 85
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=26.03 E-value=36 Score=26.16 Aligned_cols=31 Identities=19% Similarity=0.350 Sum_probs=22.2
Q ss_pred cccCCCCcccEEcCceeEecCCCeEEeccCCCCC
Q psy17260 235 LLCMRNQCRAILNPLCQVDYKSKLWVCNFCFQRN 268 (679)
Q Consensus 235 ~RC~~~~C~AYiNpf~~~~~~g~~W~C~~C~~~N 268 (679)
-||.+ |+....-+..+.+ .....|+-||..+
T Consensus 6 y~C~~--Cg~~fe~~~~~~~-~~~~~CP~Cg~~~ 36 (52)
T TIGR02605 6 YRCTA--CGHRFEVLQKMSD-DPLATCPECGGEK 36 (52)
T ss_pred EEeCC--CCCEeEEEEecCC-CCCCCCCCCCCCc
Confidence 37998 9986666555544 4567899999854
No 86
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=25.74 E-value=30 Score=21.20 Aligned_cols=12 Identities=17% Similarity=0.412 Sum_probs=7.4
Q ss_pred EEeccCCCCCCC
Q psy17260 259 WVCNFCFQRNAF 270 (679)
Q Consensus 259 W~C~~C~~~N~v 270 (679)
|.|++|+....-
T Consensus 1 ~~C~~C~~~~~~ 12 (24)
T PF13894_consen 1 FQCPICGKSFRS 12 (24)
T ss_dssp EE-SSTS-EESS
T ss_pred CCCcCCCCcCCc
Confidence 789999876543
No 87
>TIGR00006 S-adenosyl-methyltransferase MraW. Genetics paper in 1972 links mra cluster to peptidoglycan biosynthesis in E. coli. Seems to be common in proteobacteria.wn.
Probab=25.06 E-value=76 Score=34.18 Aligned_cols=28 Identities=32% Similarity=0.542 Sum_probs=25.4
Q ss_pred hHHHHHHHHHHHhhcCCCCcEEEEEEEC
Q psy17260 319 ELGALRDSLQMSLSLLPKNALVGLITFG 346 (679)
Q Consensus 319 ~l~~l~~si~~~L~~Lp~~~~VG~ITfd 346 (679)
||+.+...|..+.+.|.++.++++|||.
T Consensus 215 EL~~L~~~L~~~~~~L~~gGrl~VISfH 242 (305)
T TIGR00006 215 ELEELEEALQFAPNLLAPGGRLSIISFH 242 (305)
T ss_pred hHHHHHHHHHHHHHHhcCCCEEEEEecC
Confidence 5889999999999999999999999984
No 88
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=24.87 E-value=48 Score=31.05 Aligned_cols=36 Identities=25% Similarity=0.485 Sum_probs=24.4
Q ss_pred cccCCCCcccEEcCceeEecCCCeEEeccCCCCCCCCccc
Q psy17260 235 LLCMRNQCRAILNPLCQVDYKSKLWVCNFCFQRNAFPPQY 274 (679)
Q Consensus 235 ~RC~~~~C~AYiNpf~~~~~~g~~W~C~~C~~~N~vp~~Y 274 (679)
++|.- |+..- ....+...+.|.|+-|+..|.+..+-
T Consensus 1 v~C~f--C~~~s--~~~~~~~~~~w~C~~C~q~N~f~e~G 36 (131)
T PF09779_consen 1 VNCWF--CGQNS--KVPYDNRNSNWTCPHCEQYNGFDEDG 36 (131)
T ss_pred Ceecc--CCCCC--CCCCCCCCCeeECCCCCCccCccccC
Confidence 46777 77642 23334444569999999999987643
No 89
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=24.71 E-value=8.8 Score=29.76 Aligned_cols=30 Identities=23% Similarity=0.644 Sum_probs=10.0
Q ss_pred ccCCCCcccEEcCceeEecCCCeEEeccCCC
Q psy17260 236 LCMRNQCRAILNPLCQVDYKSKLWVCNFCFQ 266 (679)
Q Consensus 236 RC~~~~C~AYiNpf~~~~~~g~~W~C~~C~~ 266 (679)
.|.+.+|-= +..|.......+.|.|++|++
T Consensus 20 ~C~H~~CFD-l~~fl~~~~~~~~W~CPiC~~ 49 (50)
T PF02891_consen 20 NCKHLQCFD-LESFLESNQRTPKWKCPICNK 49 (50)
T ss_dssp T--SS--EE-HHHHHHHHHHS---B-TTT--
T ss_pred cCcccceEC-HHHHHHHhhccCCeECcCCcC
Confidence 366533321 223333334467799999986
No 90
>KOG2353|consensus
Probab=23.90 E-value=1.1e+02 Score=38.80 Aligned_cols=51 Identities=20% Similarity=0.315 Sum_probs=44.1
Q ss_pred CCCcEEEEEEECCcChh--hHHHHHHHHHHHhhcCCCCcEEEEEEECCeEEEE
Q psy17260 302 CAPLVFLFVVDTCMDEE--ELGALRDSLQMSLSLLPKNALVGLITFGQMVQVH 352 (679)
Q Consensus 302 ~~pp~~vFvIDvs~~a~--~l~~l~~si~~~L~~Lp~~~~VG~ITfd~~V~~y 352 (679)
..|--.+|++|+|.... .+...+..+.++|+.|.++..|-++||++.++.-
T Consensus 223 t~pKdiviLlD~SgSm~g~~~~lak~tv~~iLdtLs~~Dfvni~tf~~~~~~v 275 (1104)
T KOG2353|consen 223 TSPKDIVILLDVSGSMSGLRLDLAKQTVNEILDTLSDNDFVNILTFNSEVNPV 275 (1104)
T ss_pred CCccceEEEEeccccccchhhHHHHHHHHHHHHhcccCCeEEEEeeccccCcc
Confidence 45678899999998743 4889999999999999999999999999887763
No 91
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=23.84 E-value=84 Score=23.29 Aligned_cols=27 Identities=22% Similarity=0.287 Sum_probs=20.1
Q ss_pred ccCCCCcccEEcCceeEecCCCeEEeccCCCC
Q psy17260 236 LCMRNQCRAILNPLCQVDYKSKLWVCNFCFQR 267 (679)
Q Consensus 236 RC~~~~C~AYiNpf~~~~~~g~~W~C~~C~~~ 267 (679)
+|.. |++-- .-+|.....++|.-||..
T Consensus 2 ~Cp~--Cg~~~---~~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 2 KCPN--CGSKE---IVFDPERGELVCPNCGLV 28 (43)
T ss_dssp SBTT--TSSSE---EEEETTTTEEEETTT-BB
T ss_pred CCcC--CcCCc---eEEcCCCCeEECCCCCCE
Confidence 5777 98832 567777888999999965
No 92
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=23.02 E-value=30 Score=26.61 Aligned_cols=30 Identities=23% Similarity=0.547 Sum_probs=15.0
Q ss_pred ccCCCCcccEEcCce-----------eEecCCCeEEeccCCCC
Q psy17260 236 LCMRNQCRAILNPLC-----------QVDYKSKLWVCNFCFQR 267 (679)
Q Consensus 236 RC~~~~C~AYiNpf~-----------~~~~~g~~W~C~~C~~~ 267 (679)
+|.. |+-..+|-- .|++-...|+|+.|+..
T Consensus 3 ~C~~--CgyvYd~~~Gd~~~~i~pGt~F~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 3 QCPV--CGYVYDPEKGDPENGIPPGTPFEDLPDDWVCPVCGAP 43 (47)
T ss_dssp EETT--TSBEEETTTBBGGGTB-TT--GGGS-TT-B-TTTSSB
T ss_pred CCCC--CCEEEcCCcCCcccCcCCCCCHHHCCCCCcCcCCCCc
Confidence 4666 765554433 23444456888888753
No 93
>PRK00050 16S rRNA m(4)C1402 methyltranserfase; Provisional
Probab=22.31 E-value=93 Score=33.38 Aligned_cols=28 Identities=32% Similarity=0.516 Sum_probs=25.4
Q ss_pred hHHHHHHHHHHHhhcCCCCcEEEEEEEC
Q psy17260 319 ELGALRDSLQMSLSLLPKNALVGLITFG 346 (679)
Q Consensus 319 ~l~~l~~si~~~L~~Lp~~~~VG~ITfd 346 (679)
||+.+...|..+.+.|.++.++++|||.
T Consensus 211 El~~L~~~L~~~~~~L~~gGrl~visfH 238 (296)
T PRK00050 211 ELEELERALEAALDLLKPGGRLAVISFH 238 (296)
T ss_pred hHHHHHHHHHHHHHHhcCCCEEEEEecC
Confidence 5889999999999999999999999984
No 94
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=22.16 E-value=45 Score=27.71 Aligned_cols=30 Identities=20% Similarity=0.332 Sum_probs=20.1
Q ss_pred ccccCCCCcccEEcCceeEecCCCeEEeccCCCCCCCC
Q psy17260 234 PLLCMRNQCRAILNPLCQVDYKSKLWVCNFCFQRNAFP 271 (679)
Q Consensus 234 p~RC~~~~C~AYiNpf~~~~~~g~~W~C~~C~~~N~vp 271 (679)
+.|| + |+.|+ --+++.++-+| .||....+.
T Consensus 3 ifrC-~--Cgr~l----ya~e~~kTkkC-~CG~~l~vk 32 (68)
T PF09082_consen 3 IFRC-D--CGRYL----YAKEGAKTKKC-VCGKTLKVK 32 (68)
T ss_dssp EEEE-T--TS--E----EEETT-SEEEE-TTTEEEE--
T ss_pred EEEe-c--CCCEE----EecCCcceeEe-cCCCeeeee
Confidence 5799 6 99974 34677889999 999988774
No 95
>smart00187 INB Integrin beta subunits (N-terminal portion of extracellular region). Portion of beta integrins that lies N-terminal to their EGF-like repeats. Integrins are cell adhesion molecules that mediate cell-extracellular matrix and cell-cell interactions. They contain both alpha and beta subunits. Beta integrins are proposed to have a von Willebrand factor type-A "insert" or "I" -like domain (although this remains to be confirmed).
Probab=21.84 E-value=2.2e+02 Score=32.14 Aligned_cols=50 Identities=22% Similarity=0.362 Sum_probs=37.5
Q ss_pred CCcEEEEEEECCcChhh----HHHHHHHHHHHhhcCCCCcEEEEEEE-CCeEEEE
Q psy17260 303 APLVFLFVVDTCMDEEE----LGALRDSLQMSLSLLPKNALVGLITF-GQMVQVH 352 (679)
Q Consensus 303 ~pp~~vFvIDvs~~a~~----l~~l~~si~~~L~~Lp~~~~VG~ITf-d~~V~~y 352 (679)
.|-=..|+.|+|.+..+ +..+-..|...|..+-.+.|+||=+| |+.|.=|
T Consensus 98 yPvDLYyLMDlS~SM~ddl~~lk~lg~~L~~~m~~it~n~rlGfGsFVDK~v~P~ 152 (423)
T smart00187 98 YPVDLYYLMDLSYSMKDDLDNLKSLGDDLAREMKGLTSNFRLGFGSFVDKTVSPF 152 (423)
T ss_pred CccceEEEEeCCccHHHHHHHHHHHHHHHHHHHHhcccCceeeEEEeecCccCCc
Confidence 45556799999998765 45555667777778888999999999 6666444
No 96
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=21.35 E-value=49 Score=32.40 Aligned_cols=15 Identities=33% Similarity=0.899 Sum_probs=11.3
Q ss_pred CCCeEEeccCCCCCC
Q psy17260 255 KSKLWVCNFCFQRNA 269 (679)
Q Consensus 255 ~g~~W~C~~C~~~N~ 269 (679)
.|+.|+|+.||+.-.
T Consensus 131 ~~~~~vC~vCGy~~~ 145 (166)
T COG1592 131 EGKVWVCPVCGYTHE 145 (166)
T ss_pred cCCEEEcCCCCCccc
Confidence 356899999987654
No 97
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=20.91 E-value=54 Score=29.92 Aligned_cols=26 Identities=15% Similarity=0.469 Sum_probs=18.9
Q ss_pred cccCCCCcccEEcCceeEecCCCeEEeccCCCCC
Q psy17260 235 LLCMRNQCRAILNPLCQVDYKSKLWVCNFCFQRN 268 (679)
Q Consensus 235 ~RC~~~~C~AYiNpf~~~~~~g~~W~C~~C~~~N 268 (679)
.||.. |+....+ ....|.|+-||..+
T Consensus 71 ~~C~~--Cg~~~~~------~~~~~~CP~Cgs~~ 96 (113)
T PRK12380 71 AWCWD--CSQVVEI------HQHDAQCPHCHGER 96 (113)
T ss_pred EEccc--CCCEEec------CCcCccCcCCCCCC
Confidence 68999 9955332 23567899999775
No 98
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=20.63 E-value=53 Score=25.56 Aligned_cols=27 Identities=26% Similarity=0.620 Sum_probs=17.4
Q ss_pred ccCCCCcccEEcCceeEecCCCeEEeccCCCCC
Q psy17260 236 LCMRNQCRAILNPLCQVDYKSKLWVCNFCFQRN 268 (679)
Q Consensus 236 RC~~~~C~AYiNpf~~~~~~g~~W~C~~C~~~N 268 (679)
+|.+ |++-+ ..+....--.|+-||+.=
T Consensus 8 ~C~~--Cg~~~----~~~~~~~~irCp~Cg~rI 34 (49)
T COG1996 8 KCAR--CGREV----ELDQETRGIRCPYCGSRI 34 (49)
T ss_pred Ehhh--cCCee----ehhhccCceeCCCCCcEE
Confidence 5777 77765 434445667788887653
No 99
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=20.51 E-value=51 Score=23.40 Aligned_cols=13 Identities=38% Similarity=0.940 Sum_probs=10.2
Q ss_pred CeEEeccCCCCCC
Q psy17260 257 KLWVCNFCFQRNA 269 (679)
Q Consensus 257 ~~W~C~~C~~~N~ 269 (679)
..|+|..||..-+
T Consensus 1 ~~~~C~~CG~i~~ 13 (34)
T cd00729 1 KVWVCPVCGYIHE 13 (34)
T ss_pred CeEECCCCCCEeE
Confidence 3699999998743
No 100
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=20.40 E-value=58 Score=29.79 Aligned_cols=26 Identities=23% Similarity=0.551 Sum_probs=19.5
Q ss_pred cccCCCCcccEEcCceeEecCCCeEEeccCCCCC
Q psy17260 235 LLCMRNQCRAILNPLCQVDYKSKLWVCNFCFQRN 268 (679)
Q Consensus 235 ~RC~~~~C~AYiNpf~~~~~~g~~W~C~~C~~~N 268 (679)
.||.+ |+.+..+ ....|.|+-||..+
T Consensus 71 ~~C~~--Cg~~~~~------~~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 71 CECED--CSEEVSP------EIDLYRCPKCHGIM 96 (115)
T ss_pred EEccc--CCCEEec------CCcCccCcCCcCCC
Confidence 68999 9965443 23468999999876
No 101
>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=20.14 E-value=1.6e+02 Score=34.73 Aligned_cols=44 Identities=16% Similarity=0.243 Sum_probs=28.9
Q ss_pred cEEEEEEECCcChhh----------HHHHHHHHHHHhhcC---CCCcEEEEEEECCe
Q psy17260 305 LVFLFVVDTCMDEEE----------LGALRDSLQMSLSLL---PKNALVGLITFGQM 348 (679)
Q Consensus 305 p~~vFvIDvs~~a~~----------l~~l~~si~~~L~~L---p~~~~VG~ITfd~~ 348 (679)
-+.||+||+|....+ +..+.+++...+... .++..||++.|++.
T Consensus 11 eailflIDvs~sM~~~~~~~~~~s~~~~al~~i~~l~q~kIis~~~D~vGivlfgT~ 67 (584)
T TIGR00578 11 DSLIFLVDASKAMFEESQGEDELTPFDMSIQCIQSVYTSKIISSDKDLLAVVFYGTE 67 (584)
T ss_pred eEEEEEEECCHHHcCCCcCcCcCChHHHHHHHHHHHHHhcCCCCCCCeEEEEEEecc
Confidence 467999999986431 444445555555432 34689999999753
Done!