Query 005544
Match_columns 691
No_of_seqs 253 out of 1498
Neff 8.0
Searched_HMMs 46136
Date Fri Mar 29 01:08:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005544.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005544hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00578 ku70 ATP-dependent D 100.0 2.3E-81 5E-86 708.9 46.5 473 4-521 9-516 (584)
2 KOG2326 DNA-binding subunit of 100.0 3.4E-76 7.3E-81 624.1 42.0 646 4-684 3-668 (669)
3 cd00873 KU80 Ku-core domain, K 100.0 6.9E-57 1.5E-61 473.6 31.0 296 217-517 2-300 (300)
4 cd00788 KU70 Ku-core domain, K 100.0 3.7E-50 8.1E-55 419.9 29.2 276 216-511 1-287 (287)
5 cd00594 KU Ku-core domain; inc 100.0 5.6E-50 1.2E-54 417.6 29.3 272 216-511 1-272 (272)
6 KOG2327 DNA-binding subunit of 100.0 3.9E-47 8.5E-52 407.0 32.6 476 4-518 17-529 (602)
7 cd00789 KU_like Ku-core domain 100.0 4.6E-47 1E-51 385.4 26.1 252 216-512 1-253 (256)
8 TIGR02772 Ku_bact Ku protein, 100.0 4.3E-46 9.3E-51 378.8 25.3 253 215-512 1-255 (258)
9 PF02735 Ku: Ku70/Ku80 beta-ba 100.0 7.9E-41 1.7E-45 332.4 18.0 199 223-433 1-200 (200)
10 PF08785 Ku_PK_bind: Ku C term 100.0 1.4E-38 3E-43 287.6 7.1 120 564-686 1-120 (120)
11 COG1273 Ku-homolog [Replicatio 100.0 6.8E-35 1.5E-39 284.3 18.8 260 215-521 3-266 (278)
12 smart00559 Ku78 Ku70 and Ku80 100.0 2.2E-34 4.7E-39 268.4 12.9 136 279-417 2-138 (140)
13 PF03731 Ku_N: Ku70/Ku80 N-ter 100.0 1.3E-27 2.9E-32 242.1 18.8 201 7-217 1-223 (224)
14 cd01458 vWA_ku Ku70/Ku80 N-ter 99.9 2.4E-24 5.1E-29 217.3 16.6 153 5-166 1-172 (218)
15 cd01453 vWA_transcription_fact 99.4 1.7E-11 3.7E-16 120.1 17.3 165 7-208 5-175 (183)
16 cd01451 vWA_Magnesium_chelatas 99.2 1.1E-09 2.3E-14 107.0 18.4 163 7-201 2-167 (178)
17 cd01452 VWA_26S_proteasome_sub 99.2 1.1E-09 2.3E-14 106.6 17.7 152 5-191 3-161 (187)
18 PRK13685 hypothetical protein; 99.2 1.7E-09 3.7E-14 115.8 19.4 178 6-204 89-279 (326)
19 cd01465 vWA_subgroup VWA subgr 99.1 3.7E-09 8.1E-14 101.9 19.6 161 8-204 3-166 (170)
20 cd01480 vWA_collagen_alpha_1-V 99.1 3.8E-09 8.2E-14 103.9 17.9 154 7-195 4-167 (186)
21 cd01467 vWA_BatA_type VWA BatA 99.1 7.2E-09 1.6E-13 101.1 18.1 163 7-201 4-177 (180)
22 cd01472 vWA_collagen von Wille 99.1 5.7E-09 1.2E-13 100.3 16.2 151 8-195 3-157 (164)
23 cd01474 vWA_ATR ATR (Anthrax T 99.0 1.2E-08 2.6E-13 100.2 18.0 155 5-195 4-161 (185)
24 cd01470 vWA_complement_factors 99.0 1.3E-08 2.8E-13 101.1 17.8 167 8-204 3-193 (198)
25 cd01456 vWA_ywmD_type VWA ywmD 99.0 8.6E-09 1.9E-13 103.1 16.3 162 5-201 20-203 (206)
26 PRK13406 bchD magnesium chelat 99.0 1.2E-08 2.6E-13 116.2 18.7 166 5-201 401-570 (584)
27 cd01482 vWA_collagen_alphaI-XI 99.0 1.9E-08 4.2E-13 96.7 16.5 147 8-191 3-153 (164)
28 TIGR03436 acidobact_VWFA VWFA- 99.0 1.5E-08 3.3E-13 107.2 16.8 168 6-198 54-238 (296)
29 COG1240 ChlD Mg-chelatase subu 99.0 3.6E-08 7.8E-13 98.3 17.5 166 7-201 80-247 (261)
30 cd01471 vWA_micronemal_protein 98.9 2.1E-08 4.6E-13 98.5 15.7 148 8-189 3-159 (186)
31 cd01476 VWA_integrin_invertebr 98.9 3.5E-08 7.5E-13 94.7 16.6 152 8-191 3-157 (163)
32 cd01469 vWA_integrins_alpha_su 98.9 4.1E-08 9E-13 95.7 17.2 164 8-201 3-171 (177)
33 PF13519 VWA_2: von Willebrand 98.9 6.2E-09 1.3E-13 99.9 11.1 147 8-198 2-158 (172)
34 cd01450 vWFA_subfamily_ECM Von 98.9 4.4E-08 9.5E-13 93.1 16.1 149 8-191 3-155 (161)
35 cd01463 vWA_VGCC_like VWA Volt 98.9 5.7E-08 1.2E-12 95.8 16.6 163 5-200 13-188 (190)
36 cd01473 vWA_CTRP CTRP for CS 98.9 2.3E-08 5E-13 98.8 13.4 138 8-166 3-149 (192)
37 PF03730 Ku_C: Ku70/Ku80 C-ter 98.9 8.1E-10 1.8E-14 96.2 2.6 65 450-516 4-68 (96)
38 TIGR02031 BchD-ChlD magnesium 98.9 6.5E-08 1.4E-12 111.2 18.6 165 7-201 409-583 (589)
39 cd01461 vWA_interalpha_trypsin 98.9 1.1E-07 2.4E-12 91.6 17.6 162 7-206 4-167 (171)
40 TIGR00868 hCaCC calcium-activa 98.8 1.2E-07 2.6E-12 110.9 18.9 152 7-200 306-462 (863)
41 cd01455 vWA_F11C1-5a_type Von 98.8 5.9E-08 1.3E-12 94.0 13.7 160 8-204 3-178 (191)
42 cd01466 vWA_C3HC4_type VWA C3H 98.8 7.7E-08 1.7E-12 91.7 14.3 147 8-198 3-154 (155)
43 cd01475 vWA_Matrilin VWA_Matri 98.8 1.6E-07 3.4E-12 95.3 17.3 157 7-200 4-168 (224)
44 cd01454 vWA_norD_type norD typ 98.8 2.4E-07 5.3E-12 90.0 17.3 143 7-166 2-152 (174)
45 TIGR02442 Cob-chelat-sub cobal 98.8 2.7E-07 5.8E-12 107.3 20.1 166 5-198 465-632 (633)
46 cd01477 vWA_F09G8-8_type VWA F 98.7 3.5E-07 7.6E-12 90.3 16.2 137 8-166 22-171 (193)
47 PTZ00441 sporozoite surface pr 98.7 5.9E-07 1.3E-11 99.9 18.5 138 5-166 42-188 (576)
48 cd00198 vWFA Von Willebrand fa 98.7 6.4E-07 1.4E-11 84.1 15.1 150 7-191 2-155 (161)
49 smart00327 VWA von Willebrand 98.7 1.1E-06 2.5E-11 84.5 17.1 156 7-196 3-163 (177)
50 PF13768 VWA_3: von Willebrand 98.7 7.4E-07 1.6E-11 84.7 15.3 148 7-195 2-153 (155)
51 cd01464 vWA_subfamily VWA subf 98.6 7.8E-07 1.7E-11 86.6 15.2 148 5-189 3-159 (176)
52 cd01481 vWA_collagen_alpha3-VI 98.6 2.6E-06 5.6E-11 82.1 16.3 133 8-165 3-142 (165)
53 cd01460 vWA_midasin VWA_Midasi 98.6 1.8E-06 3.9E-11 88.8 15.8 136 5-166 60-204 (266)
54 PF00092 VWA: von Willebrand f 98.5 1.9E-06 4E-11 83.4 13.8 159 8-200 2-167 (178)
55 cd01462 VWA_YIEM_type VWA YIEM 98.4 1.1E-05 2.3E-10 76.5 17.0 132 7-166 2-134 (152)
56 TIGR03788 marine_srt_targ mari 98.4 1E-05 2.2E-10 94.0 18.7 154 6-201 272-431 (596)
57 PF04056 Ssl1: Ssl1-like; Int 98.1 6.8E-05 1.5E-09 73.2 14.6 151 11-198 1-159 (193)
58 KOG2884 26S proteasome regulat 97.9 0.00055 1.2E-08 66.2 15.7 138 5-166 3-146 (259)
59 cd01457 vWA_ORF176_type VWA OR 97.6 0.0015 3.3E-08 64.8 14.9 136 7-166 4-151 (199)
60 COG5148 RPN10 26S proteasome r 97.5 0.0037 8.1E-08 59.1 14.6 135 5-166 3-146 (243)
61 PRK10997 yieM hypothetical pro 97.1 0.012 2.6E-07 65.5 15.6 131 4-165 322-456 (487)
62 COG4867 Uncharacterized protei 97.0 0.015 3.3E-07 61.7 14.5 152 4-196 462-631 (652)
63 PF11265 Med25_VWA: Mediator c 97.0 0.02 4.4E-07 57.1 14.5 148 6-164 14-185 (226)
64 KOG2807 RNA polymerase II tran 96.7 0.036 7.9E-07 57.0 13.6 156 7-200 62-224 (378)
65 COG4245 TerY Uncharacterized p 96.6 0.034 7.3E-07 53.3 12.1 103 6-131 4-119 (207)
66 COG2425 Uncharacterized protei 96.5 0.045 9.7E-07 60.0 14.2 129 7-166 274-406 (437)
67 PF05762 VWA_CoxE: VWA domain 96.4 0.029 6.3E-07 56.7 11.5 126 7-163 59-186 (222)
68 cd01479 Sec24-like Sec24-like: 96.0 0.38 8.2E-06 49.4 17.0 172 7-197 5-217 (244)
69 TIGR00627 tfb4 transcription f 95.6 0.2 4.2E-06 52.2 13.0 180 7-203 4-212 (279)
70 PF10138 vWA-TerF-like: vWA fo 95.5 0.74 1.6E-05 45.3 15.8 133 6-166 2-143 (200)
71 cd01468 trunk_domain trunk dom 95.1 1.5 3.2E-05 44.8 17.6 175 7-199 5-222 (239)
72 PF04811 Sec23_trunk: Sec23/Se 94.4 0.5 1.1E-05 48.4 12.3 176 6-198 4-223 (243)
73 TIGR01651 CobT cobaltochelatas 94.0 0.86 1.9E-05 51.7 13.6 150 6-166 393-567 (600)
74 COG5242 TFB4 RNA polymerase II 93.8 1 2.2E-05 44.3 11.8 173 7-202 22-216 (296)
75 PF03850 Tfb4: Transcription f 93.2 0.77 1.7E-05 47.9 11.0 181 7-205 3-212 (276)
76 PF12257 DUF3608: Protein of u 93.0 0.83 1.8E-05 47.4 10.6 154 7-166 72-270 (281)
77 COG4548 NorD Nitric oxide redu 92.5 0.46 9.9E-06 52.6 8.4 152 6-166 447-600 (637)
78 PF11775 CobT_C: Cobalamin bio 92.5 0.95 2.1E-05 45.0 9.9 152 6-167 13-188 (219)
79 KOG2487 RNA polymerase II tran 92.3 1.6 3.6E-05 44.2 11.3 174 7-201 25-228 (314)
80 KOG1984 Vesicle coat complex C 92.2 5.2 0.00011 47.0 16.5 211 6-238 418-679 (1007)
81 KOG2326 DNA-binding subunit of 92.2 0.0022 4.8E-08 70.7 -9.7 134 281-416 325-469 (669)
82 smart00187 INB Integrin beta s 91.9 2.6 5.6E-05 46.2 13.2 152 8-164 102-297 (423)
83 cd01478 Sec23-like Sec23-like: 91.8 6.7 0.00015 40.8 15.9 90 97-199 142-254 (267)
84 PLN00162 transport protein sec 91.6 4.6 9.9E-05 48.5 16.1 128 97-238 263-421 (761)
85 PTZ00395 Sec24-related protein 91.1 7.2 0.00016 48.3 16.7 217 6-237 953-1223(1560)
86 KOG3768 DEAD box RNA helicase 90.0 6.3 0.00014 44.3 13.8 110 7-130 3-133 (888)
87 KOG2353 L-type voltage-depende 89.8 3.4 7.4E-05 50.8 12.9 140 2-166 222-373 (1104)
88 PF09967 DUF2201: VWA-like dom 87.7 4 8.6E-05 37.3 9.1 41 8-53 1-42 (126)
89 COG5151 SSL1 RNA polymerase II 87.2 4.1 9E-05 42.0 9.5 154 7-197 89-252 (421)
90 cd01459 vWA_copine_like VWA Co 84.9 35 0.00075 35.2 15.2 137 6-166 32-195 (254)
91 KOG1986 Vesicle coat complex C 80.1 80 0.0017 36.8 16.8 169 8-196 124-359 (745)
92 COG2718 Uncharacterized conser 78.1 25 0.00054 37.9 11.3 105 4-135 244-351 (423)
93 TIGR02877 spore_yhbH sporulati 76.5 26 0.00056 37.9 11.1 100 5-134 202-306 (371)
94 PF04285 DUF444: Protein of un 76.2 17 0.00037 40.2 10.0 102 7-134 248-350 (421)
95 PRK05325 hypothetical protein; 73.3 27 0.00058 38.4 10.5 99 6-134 223-326 (401)
96 PF07002 Copine: Copine; Inte 68.3 1.1E+02 0.0023 28.8 12.7 127 21-165 12-146 (146)
97 PF06707 DUF1194: Protein of u 61.8 1.8E+02 0.0038 29.0 13.4 141 6-166 4-156 (205)
98 COG1721 Uncharacterized conser 57.9 16 0.00035 40.6 5.4 47 5-53 224-276 (416)
99 PF00362 Integrin_beta: Integr 55.7 38 0.00081 37.8 7.7 152 8-164 105-300 (426)
100 COG5028 Vesicle coat complex C 54.6 1.6E+02 0.0035 34.8 12.4 151 7-166 278-462 (861)
101 PF08064 UME: UME (NUC010) dom 46.8 30 0.00064 30.6 4.2 59 585-645 32-91 (107)
102 PF11443 DUF2828: Domain of un 45.1 3.3E+02 0.0071 31.4 13.0 130 6-159 341-477 (534)
103 KOG1985 Vesicle coat complex C 45.0 4.5E+02 0.0097 31.6 14.1 171 7-196 296-506 (887)
104 COG2304 Uncharacterized protei 43.9 3.5E+02 0.0075 29.3 13.2 138 5-166 37-177 (399)
105 COG3552 CoxE Protein containin 43.6 26 0.00057 37.6 3.9 46 5-56 218-263 (395)
106 COG5047 SEC23 Vesicle coat com 41.9 1.5E+02 0.0032 33.9 9.4 58 74-134 227-292 (755)
107 smart00544 MA3 Domain in DAP-5 36.7 54 0.0012 28.8 4.4 61 594-656 3-83 (113)
108 COG4547 CobT Cobalamin biosynt 35.9 1.4E+02 0.0031 33.0 7.9 151 7-166 415-588 (620)
109 cd03364 TOPRIM_DnaG_primases T 35.5 60 0.0013 26.6 4.2 35 120-162 43-77 (79)
110 smart00802 UME Domain in UVSB 34.9 53 0.0012 29.0 3.9 56 587-644 34-90 (107)
111 KOG0624 dsRNA-activated protei 33.1 1.6E+02 0.0035 31.6 7.6 69 568-644 125-199 (504)
112 PF13662 Toprim_4: Toprim doma 28.5 36 0.00078 28.1 1.7 35 120-162 46-80 (81)
113 KOG1327 Copine [Signal transdu 26.7 7E+02 0.015 28.6 11.7 144 5-166 285-452 (529)
114 COG4902 Uncharacterized protei 25.6 2.1E+02 0.0045 26.6 6.0 43 427-471 88-130 (189)
115 PF07744 SPOC: SPOC domain; I 22.9 1.2E+02 0.0027 26.7 4.3 41 344-385 79-119 (119)
116 PF13344 Hydrolase_6: Haloacid 22.1 1.3E+02 0.0028 26.1 4.1 29 120-159 30-58 (101)
117 PF01882 DUF58: Protein of unk 21.5 1.1E+02 0.0024 25.3 3.4 40 5-46 40-85 (86)
No 1
>TIGR00578 ku70 ATP-dependent DNA helicase ii, 70 kDa subunit (ku70). Proteins in this family are involved in non-homologous end joining, a process used for the repair of double stranded DNA breaks. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Cutoff does not detect the putative ku70 homologs in yeast.
Probab=100.00 E-value=2.3e-81 Score=708.94 Aligned_cols=473 Identities=19% Similarity=0.268 Sum_probs=399.6
Q ss_pred CCeEEEEEEecCCCccC---------ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEee
Q 005544 4 TREALLLLLDVSPSMHS---------VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQD 74 (691)
Q Consensus 4 ~Kea~vflIDvs~sM~~---------~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~ 74 (691)
.|||+|||||||++|++ ++..|++||.+++++|||++++|+||||||||+.|+|++ +|+||+|+++
T Consensus 9 ~keailflIDvs~sM~~~~~~~~~~s~~~~al~~i~~l~q~kIis~~~D~vGivlfgT~~t~n~~-----~~~~i~v~~~ 83 (584)
T TIGR00578 9 GRDSLIFLVDASKAMFEESQGEDELTPFDMSIQCIQSVYTSKIISSDKDLLAVVFYGTEKDKNSV-----NFKNIYVLQE 83 (584)
T ss_pred ceeEEEEEEECCHHHcCCCcCcCcCChHHHHHHHHHHHHHhcCCCCCCCeEEEEEEeccCCCCcc-----CCCceEEEee
Confidence 69999999999999996 267899999999999999999999999999999999987 6999999999
Q ss_pred cCCCCHHHHHHhhcCCCCCC------------CCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCch
Q 005544 75 IKVVDGHLVQSLKHLPQGTC------------AGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKE 142 (691)
Q Consensus 75 l~~~~~~~l~~L~~l~~~~~------------~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~ 142 (691)
|+.|+++.++.|++|..+.+ .+++.||||+|++||.+ + ++++.+||||||||+++|+.+ ++...
T Consensus 84 L~~p~a~~i~~L~~l~~~~~~~~~~~~~~~~~~~~l~daL~~~~~~f~~-~-~~k~~~kRI~lfTd~D~P~~~--~~~~~ 159 (584)
T TIGR00578 84 LDNPGAKRILELDQFKGDQGPKKFRDTYGHGSDYSLSEVLWVCANLFSD-V-QFRMSHKRIMLFTNEDNPHGN--DSAKA 159 (584)
T ss_pred CCCCCHHHHHHHHHHhhccCccchhhccCCCCCCcHHHHHHHHHHHHHh-c-chhhcCcEEEEECCCCCCCCC--chhHH
Confidence 99999999999998754311 23679999999999985 3 346789999999999999985 23344
Q ss_pred hhHHHHHHHHhhcCcEEEEEeeccCCCCCCCcchhhhhhHHHHHHhhcCCC----eEeehh-hhHHhhcccccccCCCcc
Q 005544 143 DQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSA----KTLFVD-STTSLRGARKTRDISPVT 217 (691)
Q Consensus 143 ~~l~~i~~~L~~~gI~l~vi~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g----~~~~~~-~a~~ll~~~~~k~~~~~~ 217 (691)
+++..+|++|++.||.|++|+++. +++|+.. .|+..+....++ ...... ...+++..++.|.+++|+
T Consensus 160 ~~a~~~a~dl~~~gi~ielf~l~~--~~~Fd~s------~Fy~dii~~~~~~~~~~~~~~~~~l~~l~~~l~~k~~~kR~ 231 (584)
T TIGR00578 160 SRARTKAGDLRDTGIFLDLMHLKK--PGGFDIS------LFYRDIITDAEDEDLGVHPEESSKLEDLLRKVRAKETRKRA 231 (584)
T ss_pred HHHHHHHHHHHhcCeEEEEEecCC--CCCCChh------hhhHhhhccccccccccCcchhHHHHHHHHHHhhcccceee
Confidence 566889999999999999999943 3444332 344444321111 111112 244667889999999999
Q ss_pred eeeeeEEecCCeEEEEEEEeecccccCCC-ceEeccCCCCCccccccceeEEEEEeecCCCCCCCCccccccccccCCce
Q 005544 218 IFRGDLELSEKMKIKVWVYKKTGEEKFPT-LKKYSDKAPSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYGPQV 296 (691)
Q Consensus 218 ~~~g~L~lg~~l~I~V~~Y~~~~~~k~p~-~~~~~~~~~~~~~~~~~~v~~~~~y~~~~d~~~~v~~ed~~kgy~yG~~~ 296 (691)
.|+|+|+||++++|+|++|.+++++++|. .+.+..+ ...|+.+|+|+ +.+++++|++++++|||+||+++
T Consensus 232 ~~~~~L~lg~~~~I~V~~Y~~~~~~~~~~~~~l~~~~--------~~~v~~~~~~~-~~dtg~~V~~~~i~Kgy~yGg~~ 302 (584)
T TIGR00578 232 LSRLKLKLNKDVVMSVGIYNLVQKAGKPAPVKLYRET--------NEPVKTKTRTF-NMDTGSLLLPSDTKRSQTYGGRQ 302 (584)
T ss_pred EEeccEEECCCCEEEEEEEEEEEeecCCceEEEecCC--------ceeeEEEEEEE-ecCCccccCHHHceeeeeECCEE
Confidence 99999999999999999999999987664 4666543 35788888887 57788899999999999999999
Q ss_pred EeCChhhHHhhccCCCccEEEEeEeeCCCCcceeccCCeEEEEcCCCC-hhhHHHHHHHHHHHHhcCceEEEEEEecCCC
Q 005544 297 VPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPGN-SRATVAVSALARAMKEMNKVAIVRCVWRQGQ 375 (691)
Q Consensus 297 Vp~s~~e~~~~k~~~~~~l~ilGF~~~~~i~~~~~~~~~~~i~p~~~~-~~s~~afsaL~~Am~e~~~vaI~r~v~r~~~ 375 (691)
|+|+++|++++|..++|+|+||||+|.+.|+++|+++++|||+|+++. .+|.+||+||+++|.++++|||||||+|+|+
T Consensus 303 V~~t~ee~~~lk~~~~~~l~ilGF~~~s~l~~~~~~~~s~fi~Pde~~~~gs~~afsaL~~~l~~~~kvAI~~~v~r~~~ 382 (584)
T TIGR00578 303 IYLEKEETEELKRFDPPGLQLMGFKPLSMLKKHHHLRPSLFVYPEESLVRGSTTLFSALLQKCLEKEVAALCRYISRRNQ 382 (584)
T ss_pred EecCHHHHHHHhccCCCceEEEeeccHHHCCchhhcCCceEEecCCcccccHHHHHHHHHHHHHhcCcEEEEEEEecCCC
Confidence 999999999999999999999999999999999999999999999864 4799999999999999999999999999998
Q ss_pred CceEEEEeeccccCCC-----CCCCeEEEecCCChhcccCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCcC
Q 005544 376 QSVVVGVLTPNVSEKI-----NIPDSFYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLVKMLDLAPSGKGEI 450 (691)
Q Consensus 376 ~p~~v~~L~P~~~~~~-----~~~~~l~~v~LPFaeDvR~~~fp~l~~~~~~~~p~~eq~~a~~~lI~~m~l~~~~~~e~ 450 (691)
.|. +++|+|+.++.. ..|+||++++|||+||||.++|++ ...++++|+++|++||++|++.
T Consensus 383 ~P~-lvaL~P~~~~~d~~~~q~~p~G~~l~~LPfadDIR~~~~~~------~~~~~~e~~~~a~~LI~~l~~~------- 448 (584)
T TIGR00578 383 PPY-FVALVPQEEELDDQKIQVTPPGFHLVFLPFADDKRKVPFTE------KVKATPEQVDKMKAIVEKLRFT------- 448 (584)
T ss_pred CCE-EEEEeCCcccccccCCccCCCeEEEEecCchhhccCCCCcc------cCCCCHHHHHHHHHHHHhcCCC-------
Confidence 755 556889865432 257899999999999999998742 2469999999999999999996
Q ss_pred CCCCCCCCchhHHHHHHHHHhhcCCCCCCCCCchhhhhhcCCCHHHH-HHHHHHHHHHHh-hcCCccCCcccc
Q 005544 451 LQPELTPNPALERFYHHLELKSEHQDAAPPPLDDSLKKITEPDPTLL-AESQSAIDAFCG-QFVIKENPKLKK 521 (691)
Q Consensus 451 ~~p~~~~NP~lqr~~~~l~~~al~~~~~~p~~~~~l~~~~~p~~~~~-~~~~~~le~~k~-~f~~~~~~~~~~ 521 (691)
|+|..|+||+|||||++|+++||+++.|.++.|.++ |+...+ +++++.+++|++ +|+.+.+++++.
T Consensus 449 y~P~~~~NP~LQ~hY~~LealAL~~~~~~~~~D~tl-----p~~~~i~~r~~~~i~~~~~~~~~~~~~~~~~~ 516 (584)
T TIGR00578 449 YRSDSFENPVLQQHFRNLEALALDMMEPEQAVDLTL-----PKVEAMKKRLGSLVDEFKELVYPPDYNPEGKV 516 (584)
T ss_pred CCcccCCChHHHHHHHHHHHHhCCCCCCCCCccccc-----CCHHHHHHHHHHHHHHHHHHhcccccCccccc
Confidence 999999999999999999999999999988888654 554445 478999999999 888888876443
No 2
>KOG2326 consensus DNA-binding subunit of a DNA-dependent protein kinase (Ku80 autoantigen) [Replication, recombination and repair]
Probab=100.00 E-value=3.4e-76 Score=624.08 Aligned_cols=646 Identities=18% Similarity=0.212 Sum_probs=526.8
Q ss_pred CCeEEEEEEecCCCccC-------ChhHHHHHHHHHHHHHHhcC-CccEEEEEEEcCCCCCccccccCCCcCcEEEEeec
Q 005544 4 TREALLLLLDVSPSMHS-------VLPDVEKLCSRLIQKKLIYG-KNHEVGVILFGTEETENELTKEVGGYEHVKVLQDI 75 (691)
Q Consensus 4 ~Kea~vflIDvs~sM~~-------~l~~a~~~~~~l~~~ki~~~-~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l 75 (691)
+++|++|++|||++|.. .++.|..++..++++|.+.. ++|.||||+|||+.|+|++. +...|+||+++.|+
T Consensus 3 ~se~ttfilDvG~~Ms~~~~~~~S~fE~a~~y~~~~lsrK~fa~rktD~is~vlyncD~ten~le-gg~~fqnisvl~p~ 81 (669)
T KOG2326|consen 3 SSESTTFILDVGPSMSKNNETGKSNFEKAMAYLEYTLSRKSFASRKTDWISCVLYNCDVTENSLE-GGNVFQNISVLAPV 81 (669)
T ss_pred CCcceEEEEecCccccccCCCccccHHHHHHHHHHHHHHHHhhccCCceEEEEEecCCCccCccc-cccccceeEEeecc
Confidence 78999999999999976 37889999999999999996 99999999999999999985 55699999999999
Q ss_pred CCCCHH-HHHHhhc-CCCCCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCC-CCCCCCCCCchhhHHHHHHHH
Q 005544 76 KVVDGH-LVQSLKH-LPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALC-PLKDPDVGTKEDQVSTIARQM 152 (691)
Q Consensus 76 ~~~~~~-~l~~L~~-l~~~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~-p~~~~~~~~~~~~l~~i~~~L 152 (691)
..|... +++.++. +++++..+|+.+||.|..+++.+++..+|...+|+||++++-. .+. .+.. |+++|
T Consensus 82 ~tpaf~~l~k~~~~~~qqns~q~Df~gal~vs~dL~~qhe~~~k~~~kr~Il~~~~l~~dfs-------d~~~--ive~l 152 (669)
T KOG2326|consen 82 TTPAFIGLIKRLKQYCQQNSHQSDFEGALSVSQDLLVQHEDIKKQFQKRKILKQIVLFTDFS-------DDLF--IVEDL 152 (669)
T ss_pred cchhhHHHHHHHHHhcCCCccccchhhhHHHHHHHHHHHHhccchhhceEEEEeecccccch-------hhHH--HHHHH
Confidence 888766 5555664 6888889999999999999888877655666777777766544 222 2333 99999
Q ss_pred hhcCcEEEEEeeccCC-----CCCCCcchhhhhhHHHHHHhhcCCCeEeehhhhHHhhcccccccCCCcceeeeeEEec-
Q 005544 153 VAFGLRMKNIVVRASL-----SGEPHMRVIIENDNLLNIFSKKSSAKTLFVDSTTSLRGARKTRDISPVTIFRGDLELS- 226 (691)
Q Consensus 153 ~~~gI~l~vi~i~~~~-----~~~~~~~~~~~ne~~l~~l~~~~~g~~~~~~~a~~ll~~~~~k~~~~~~~~~g~L~lg- 226 (691)
.+++|.|.++|++.+. +++.+.+.+..|+-+++....-+.++++++++....+..++++.++|..+|+|.|+||
T Consensus 153 ~~~didL~~~gldf~~e~id~s~dl~e~~kk~n~~~~q~~e~l~~~q~~~~~eiYn~i~spa~~~v~pv~if~g~l~ig~ 232 (669)
T KOG2326|consen 153 TDEDIDLLTEGLDFRIELIDCSKDLQEERKKSNYTWLQLVEALPNSQIYNMNEIYNEITSPATSVVKPVRIFSGELRIGA 232 (669)
T ss_pred hhcCcceeEeeccCCccccccCccccccccccchHHHHHHHhcchhhHHhHHHHHHhhcCcccccccceEEEeeeEeecc
Confidence 9999999999994311 1223344566677788887777899999999998889999999999988999999999
Q ss_pred CCeEEEEEEEeecccccCCCceEeccCC-CCCccccccceeEEEEEeecCCCCCCCCccccccccccCCceEeCChhhHH
Q 005544 227 EKMKIKVWVYKKTGEEKFPTLKKYSDKA-PSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYGPQVVPISSAEWE 305 (691)
Q Consensus 227 ~~l~I~V~~Y~~~~~~k~p~~~~~~~~~-~~~~~~~~~~v~~~~~y~~~~d~~~~v~~ed~~kgy~yG~~~Vp~s~~e~~ 305 (691)
+.++|.+..|..+...|++..+.....- ++.. ..+....+.|...++.+.+|-+++++.||.||..+||++..|.+
T Consensus 233 ~~Lsiq~a~y~g~~q~r~~~~~~~vea~~etk~---ke~~n~ktV~~~~d~d~~evlKed~~sGysyG~~iIp~s~nDen 309 (669)
T KOG2326|consen 233 DILSIQTANYSGSMQDRNECLCIKVEAFPETKA---KEGLNRKTVVEVEDSDKLEVLKEDYVSGYSYGEYIIPNSGNDEN 309 (669)
T ss_pred ceeEEeccCCCccccccccceeEEeecchhhcc---chhcccceeEEeecCCchhhHHHhhhhhcccceeEeccCCcchh
Confidence 7799999999999999998766554321 1111 12233334455444455688899999999999999999999999
Q ss_pred hhccCCCccEEEEeEeeCCCCcceeccCCeEEEEcCCCChhhHHHHHHHHHHHHhcCceEEEEEEecCCCCceEEEEeec
Q 005544 306 AVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQGQQSVVVGVLTP 385 (691)
Q Consensus 306 ~~k~~~~~~l~ilGF~~~~~i~~~~~~~~~~~i~p~~~~~~s~~afsaL~~Am~e~~~vaI~r~v~r~~~~p~~v~~L~P 385 (691)
.+++.+.+|+.||||+++++|+++|++|..+.|+|.-.+.++..|+++|++||...+++|||||++..++. |.+++|+|
T Consensus 310 v~e~dt~g~~~ilgFikkssv~~~Y~~g~~~~Vlpa~dd~~a~~a~ssli~al~~l~r~Al~Ry~~~~ks~-pql~vl~P 388 (669)
T KOG2326|consen 310 VSEDDTSGSSYILGFIKKSSVTKAYRYGADYVVLPAVDDDQAVYASSSLIDALGFLNREALPRYFLTSKSS-PQLAVLRP 388 (669)
T ss_pred hcccccCCceEEeeeeccccccceeeecCceEEecccCchHhHHhhhHHHHHHhhhhHHHhhhhhhccCCC-ceEeeecc
Confidence 99999999999999999999999999999899999966778999999999999999999999999999987 56789999
Q ss_pred cccCCCCCCCeEEEecCCChhcccCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHcCCCCC--CCCcCCCCCCCCCchhHH
Q 005544 386 NVSEKINIPDSFYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLVKMLDLAPS--GKGEILQPELTPNPALER 463 (691)
Q Consensus 386 ~~~~~~~~~~~l~~v~LPFaeDvR~~~fp~l~~~~~~~~p~~eq~~a~~~lI~~m~l~~~--~~~e~~~p~~~~NP~lqr 463 (691)
+...+-. ..||+.++|||+||+|.|.|+.+++. ....|+..|+-|+++|||.|+|..+ +..+.|.|.. +||..||
T Consensus 389 h~~~~~~-~~yLvdVqLPF~eD~R~y~Fskf~~~-~n~~pt~aql~AVsnlID~M~L~ksdtl~~~pf~p~~-~~mr~hr 465 (669)
T KOG2326|consen 389 HCQSDLA-FSYLVDVQLPFREDARAYYFSKFDSE-VNMCPTCAQLIAVSNLIDEMKLVKSDTLCRLPFAPPK-LDMRVHR 465 (669)
T ss_pred ccccccc-eeeEEEeeccchhhhHHhhcccccch-hccCchHHHHHHHHHHhhhhhhhhhccccCCCCCCCC-ccchhhh
Confidence 9887632 36899999999999999999999875 4578999999999999999999754 2344566655 8999999
Q ss_pred HHHHHHHhhcCCCCCCCCCchhhhhhcCCCHHHHHHHHHHHHHHHhhcCCccCCccccchhhhccCCCCCCCCCCCCCCC
Q 005544 464 FYHHLELKSEHQDAAPPPLDDSLKKITEPDPTLLAESQSAIDAFCGQFVIKENPKLKKSTRRFLREKPSGSDEPNGDGSV 543 (691)
Q Consensus 464 ~~~~l~~~al~~~~~~p~~~~~l~~~~~p~~~~~~~~~~~le~~k~~f~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~ 543 (691)
+.++|-|+|.+|+.++|+.+.+|.+++.||..|.+.+...+.+++..|++. +|+|.+- ... ..++ ..+.+.... -
T Consensus 466 L~qlllh~a~spe~~lp~tnq~l~~~lnPp~~V~~~~~~~l~kIk~~f~lq-ipkke~v-T~q-e~~~-dt~~pt~kK-q 540 (669)
T KOG2326|consen 466 LPQLLLHTATSPEPLLPETNQHLIDELNPPRFVDSMDTDELPKIKLGFYLQ-IPKKEVV-TDQ-ELPL-DTSLPTLKK-Q 540 (669)
T ss_pred HHHHhccccCCCCCCCCccchHHHHhhCcchhccccCchhhhhhcccceee-cccccee-ccc-cccc-ccCCcchhh-H
Confidence 999999999999999999999999999999999999999999999999998 5533221 111 0010 001111100 0
Q ss_pred ChhhhccccCCCCCcceeeccCCChhhHHHHHHhCCCCchhHHHHHHHHHHHHHHHhhccCCCCChHHHHHHHHHHHHHh
Q 005544 544 SDAQAVNSMESKPVVTVDKIGDLTPIQDFEAMMSRRDCPDWVDKAIEDMKNKIFGLLENSNEGINYPKAVELLVALRKGC 623 (691)
Q Consensus 544 ~~~~~~~~~~~~~~~~~~~ig~~~pv~dF~~~l~~~~~~~~~~~a~~qm~~~I~~lv~~s~~~~~y~ka~~cl~~~R~~~ 623 (691)
..+.....++++. ++...|+.++|-+.|...+.+....+.++.|+.||.+.|++++.. .+|+++++||+++|...
T Consensus 541 ~eeq~~sg~s~~e-g~kp~v~~v~~ke~v~~~i~qlk~~~~~e~ai~Emi~~iknfid~----~yf~k~~dsl~~~R~~~ 615 (669)
T KOG2326|consen 541 QEEQVKSGASQDE-GRKPTVFVVRQKEVVLEWIHQLKINDSREFAIPELIDSIKNFIDP----EYFHKKFDSLKLVRVLG 615 (669)
T ss_pred HHHhhhccccccc-ccccceeEechhhhHHHHHHHhccchhHhHHHHHHHHHHHhcCCc----HHHHHHHHHHHHHHHHH
Confidence 0011111122222 235778888888888888877766778999999999999999976 48999999999999999
Q ss_pred hhccCchHHHHHHHHHHHHHhcCCchhHHHHHHhCCccccccCccCCCCCCHHHHhccccc
Q 005544 624 ILEQEPKQFNDVLEKVCKICRKRNFSTFFDFLMSKKLSLISKSEAVDSDITDDEAGSFIVK 684 (691)
Q Consensus 624 i~~~e~~~~N~fl~~lk~~~~~~~~~~fw~~i~~~~l~lI~~~E~~~s~vt~~ea~~F~~~ 684 (691)
|+++|...||+||+.||+...-. +| .+.+.||++.|+..|+|+..+|.+|+..
T Consensus 616 Ik~se~~rFNe~Lk~Lke~e~i~---~l-----~k~~~lI~k~esSgs~v~~~na~~f~~~ 668 (669)
T KOG2326|consen 616 IKKSEKLRFNEELKTLKEREKIP---DL-----EKTLLLIGKQESSGSPVNSNNAAEFWEE 668 (669)
T ss_pred hhhhHHHHHHHHHHHHHHhhhcc---ch-----hhhcccccchhccCCccchhhHHhhccC
Confidence 99999999999999999986543 33 8899999999999999999999999964
No 3
>cd00873 KU80 Ku-core domain, Ku80 subfamily; Ku80 is a subunit of the Ku protein, which plays a key role in multiple nuclear processes such as DNA repair, chromosome maintenance, transcription regulation, and V(D)J recombination. The mechanism underlying the regulation of all the diverse functions of Ku is still unclear, although it seems that Ku is a multifunctional protein that works in nuclei. In mammalian cells, the Ku heterodimer recruits the catalytic subunit of DNA-dependent protein kinase (DNA-PK), which is dependent on its association with the Ku70/80 heterodimer bound to DNA for its protein kinase activity.
Probab=100.00 E-value=6.9e-57 Score=473.55 Aligned_cols=296 Identities=39% Similarity=0.620 Sum_probs=264.6
Q ss_pred ceeeeeEEecCCeEEEEEEEeecccccCCCceEeccCCCCCccccccceeEEEEEeecCCCCCCCCccccccccccCCce
Q 005544 217 TIFRGDLELSEKMKIKVWVYKKTGEEKFPTLKKYSDKAPSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYGPQV 296 (691)
Q Consensus 217 ~~~~g~L~lg~~l~I~V~~Y~~~~~~k~p~~~~~~~~~~~~~~~~~~~v~~~~~y~~~~d~~~~v~~ed~~kgy~yG~~~ 296 (691)
+.|+|.|+||.+++|+|++|++|+++++|+.+++....... ......|+..+.|..+++++.+|+++|++|||+||+++
T Consensus 2 ~~~~g~L~~g~~v~I~V~~y~at~~~~~~~~~~~~~~~~~~-e~~~~~v~~~~~~~~~~~~~~eV~~~~ivkgY~yg~~~ 80 (300)
T cd00873 2 AAFKGQLTLGSPLSIAVELYKKTKEERPPKLKKVSDAEKTG-EDAFEDVKSERSYDVNDDDKTEVEKEDLIKGYRYGRDI 80 (300)
T ss_pred CcccceeEecCceEEEEEEEEeeeeccCCceEEEEecccCC-ccccccceEEEEEEccCCCCcccCHHHhhhheecCCcE
Confidence 58999999998899999999999999988766665421000 00125699999998677888899999999999999999
Q ss_pred EeCChhhHHhhccCCCccEEEEeEeeCCCCcceeccCCeEEEEcCCCChhhHHHHHHHHHHHHhcCceEEEEEEecCCCC
Q 005544 297 VPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQGQQ 376 (691)
Q Consensus 297 Vp~s~~e~~~~k~~~~~~l~ilGF~~~~~i~~~~~~~~~~~i~p~~~~~~s~~afsaL~~Am~e~~~vaI~r~v~r~~~~ 376 (691)
|+|+++|++.+++.+++||+|+||+++++|+++|+|+++|||+|++++.++..||+||++||.+++++||||||+|+++.
T Consensus 81 V~~~~~e~~~~~~~~~~~l~ilgF~~~~~i~~~~~~~~s~~l~P~~~~~~~~~a~~aL~~am~~~~k~aI~r~v~r~~~~ 160 (300)
T cd00873 81 VPLSEEDEEATKLSTSKGLDILGFIKASNVPRYYLMGESSYVVPQQDDEAAALAFSALVRALAELDKYAIARYVYKDNSE 160 (300)
T ss_pred EecCHHHHHHHhcCCCCceEEEeeccHHHCChhheeCCcEEEEcCCCChhHHHHHHHHHHHHHhCCCEEEEEEEEcCCCC
Confidence 99999999999999999999999999999999999999999999998889999999999999999999999999999985
Q ss_pred ceEEEEeeccccCCCCCCCeEEEecCCChhcccCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHcCCCCCC---CCcCCCC
Q 005544 377 SVVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLVKMLDLAPSG---KGEILQP 453 (691)
Q Consensus 377 p~~v~~L~P~~~~~~~~~~~l~~v~LPFaeDvR~~~fp~l~~~~~~~~p~~eq~~a~~~lI~~m~l~~~~---~~e~~~p 453 (691)
|.+|+|+|++... ++||++++|||+||||.+.||+|....+...++++|+++|++||++|+|++.+ ..++|+|
T Consensus 161 -p~l~aL~P~~~~~---~~~l~l~~LPf~eDvR~~~f~~l~~~~~~~~~~~e~~~~a~~lId~m~l~~~~~~~~~~~f~p 236 (300)
T cd00873 161 -PQLGVLFPRIKED---YECLVLVRLPFAEDVRQYRFPSLDKLKTPNLPTEEQLEAMDDLVDSMDLDDDEEDDPEEALKP 236 (300)
T ss_pred -cEEEEEeccccCC---CCEEEEEecCchhhhhccCCCCCCcccCCCCCCHHHHHHHHHHHHhcCCCcccccccccccCc
Confidence 6688999998765 57999999999999999999998653222579999999999999999997532 3567999
Q ss_pred CCCCCchhHHHHHHHHHhhcCCCCCCCCCchhhhhhcCCCHHHHHHHHHHHHHHHhhcCCccCC
Q 005544 454 ELTPNPALERFYHHLELKSEHQDAAPPPLDDSLKKITEPDPTLLAESQSAIDAFCGQFVIKENP 517 (691)
Q Consensus 454 ~~~~NP~lqr~~~~l~~~al~~~~~~p~~~~~l~~~~~p~~~~~~~~~~~le~~k~~f~~~~~~ 517 (691)
+.++||++||+|++|+++|++|+.++|++++.|.+|++|+..+.++++..++++++.|++++++
T Consensus 237 ~~~~nP~~q~~~~~i~~~al~~~~~lp~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~f~l~~~~ 300 (300)
T cd00873 237 DETPNPVLQRIYQALRHRALHPDEPLPPLLQVLLRYLEPPEEVLEKSKEALKKIKEKFPLKEVP 300 (300)
T ss_pred ccCCChHHHHHHHHHHHHhcCCCCCCCCccHHHHHhcCCCHHHHHHHHHHHHHHHHhcCcccCC
Confidence 9999999999999999999999999999999999999999999999999999999999998753
No 4
>cd00788 KU70 Ku-core domain, Ku70 subfamily; Ku70 is a subunit of the Ku protein, which plays a key role in multiple nuclear processes such as DNA repair, chromosome maintenance, transcription regulation, and V(D)J recombination. The mechanism underlying the regulation of all the diverse functions of Ku is still unclear, although it seems that Ku is a multifunctional protein that works in the nuclei. In mammalian cells, the Ku heterodimer recruits the catalytic subunit of DNA-dependent protein kinase (DNA-PK), which is dependent on its association with the Ku70/80 heterodimer bound to DNA for its protein kinase activity.
Probab=100.00 E-value=3.7e-50 Score=419.93 Aligned_cols=276 Identities=25% Similarity=0.356 Sum_probs=237.8
Q ss_pred cceeeeeEEecCC--eEEEEEEEeecccccCCC-ceEeccCCCCCccccccceeEEEEEeecCCCCCCCCcccccccccc
Q 005544 216 VTIFRGDLELSEK--MKIKVWVYKKTGEEKFPT-LKKYSDKAPSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRY 292 (691)
Q Consensus 216 ~~~~~g~L~lg~~--l~I~V~~Y~~~~~~k~p~-~~~~~~~~~~~~~~~~~~v~~~~~y~~~~d~~~~v~~ed~~kgy~y 292 (691)
|+.|+|+|+||++ ++|+|++|.++++++.+. .+.+..++.. ...|+.+++|+ +.+++++|+++|++|||+|
T Consensus 1 R~~~~~~l~ig~~~~v~I~V~~Y~~~~~~~~~~~~~l~~~~~~~-----~~~v~~~~~~v-~~~~~~~v~~~di~kgy~~ 74 (287)
T cd00788 1 RALFRLPLELGPGNKLVISVKGYSLVSHAKKPRKYKLDREKNEE-----RREVKSKRKFF-DVESGKTLEKADIKKGYKI 74 (287)
T ss_pred CccEeeeEEECCCCCeEEEEEEEEEeecccCCceEEEecCCCcc-----ceeeEEEEEEE-ecCCCcccChhheEEeEEe
Confidence 4689999999998 999999999999988664 5565544321 11488888998 4667889999999999999
Q ss_pred CCceEeCChhhHHhhccCCCccEEEEeEeeCCCCcceeccCCeEEEEcCCC-ChhhHHHHHHHHHHHHhcCceEEEEEEe
Q 005544 293 GPQVVPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPG-NSRATVAVSALARAMKEMNKVAIVRCVW 371 (691)
Q Consensus 293 G~~~Vp~s~~e~~~~k~~~~~~l~ilGF~~~~~i~~~~~~~~~~~i~p~~~-~~~s~~afsaL~~Am~e~~~vaI~r~v~ 371 (691)
|+++|+|+++|++.++..+.+||+||||+++++|+++|+++++|||+|+++ ..+|..||+||++||.++++|||||||+
T Consensus 75 g~~~V~~~~~e~~~i~~~~~~~l~ilgF~~~~~i~~~~~~~~s~fl~P~~~~~~gs~~af~aL~~am~~~~kvaIa~~v~ 154 (287)
T cd00788 75 GGEKIIFTKEELKKIKSFGEPGLRLIGFKPRSTLKPYHNIKKSYFIYPDESDYKGSTRLFAALLRSCLKKNKVAICWYIL 154 (287)
T ss_pred CCEEEEeCHHHHHHHhccCCCceEEEeeccHHHCChhhccCCceeEecCcccccCcHHHHHHHHHHHHhcCcEEEEEEEe
Confidence 999999999999999999999999999999999999999999999999985 3578999999999999999999999999
Q ss_pred cCCCCceEEEEeeccccCCCC-----CCCeEEEecCCChhcccCCCCCCCCCCC-CCCCCCHHHHHHHHHHHHHcCCCCC
Q 005544 372 RQGQQSVVVGVLTPNVSEKIN-----IPDSFYFNVLPFAEDVREFQFPSFSKFP-VSWQPNEQQQEAADNLVKMLDLAPS 445 (691)
Q Consensus 372 r~~~~p~~v~~L~P~~~~~~~-----~~~~l~~v~LPFaeDvR~~~fp~l~~~~-~~~~p~~eq~~a~~~lI~~m~l~~~ 445 (691)
|.++.| .+|+|+|+.+...+ .+.||++++|||+||||.+ |++...+ ....++++|+++|++||++|++..
T Consensus 155 r~~~~p-~l~aL~P~~~~~~~~~~~~~~~gl~l~~LPfadDiR~~--p~~~~~~~~~~~~~~~~l~~a~~LI~~l~~~~- 230 (287)
T cd00788 155 RKNSPP-RLVALVPQEEELDEPDGQVLPPGFHLVPLPFADDIRKL--PSLLEENASAESASDELVDKAKQIIKKLRLLS- 230 (287)
T ss_pred cCCCCC-EEEEEeccccccCCCCCccCCCcEEEEecCchhhhccC--CcccccccCCCCCCHHHHHHHHHHHHHhcCCC-
Confidence 999865 57789999765422 3689999999999999996 3332211 245799999999999999999942
Q ss_pred CCCcCCCCCCCCCchhHHHHHHHHHhhcCCCCCCCCCchhhhhhcCCCHHHH-HHHHHHHHHHHhhc
Q 005544 446 GKGEILQPELTPNPALERFYHHLELKSEHQDAAPPPLDDSLKKITEPDPTLL-AESQSAIDAFCGQF 511 (691)
Q Consensus 446 ~~~e~~~p~~~~NP~lqr~~~~l~~~al~~~~~~p~~~~~l~~~~~p~~~~~-~~~~~~le~~k~~f 511 (691)
|+|+.++||++|+||++|+++|++++.+.|+.|. +.|+.+.+ +|+++.|+.|+..+
T Consensus 231 -----f~p~~~~NP~lq~~~~~l~a~al~~e~~~~~~d~-----~~pd~~~~~~r~~~~~~~~~~~~ 287 (287)
T cd00788 231 -----YDPDKFPNPSLQKHYKILEALALDEEDPEKPDDL-----TLPDTEGIDKRLGDLIEEFKKLL 287 (287)
T ss_pred -----CCcccCCChHHHHHHHHHHHHHhCCCCCCCcccc-----cCCchHHHHHHHHHHHHHHhhcC
Confidence 9999999999999999999999999998887664 67888887 89999999998753
No 5
>cd00594 KU Ku-core domain; includes the central DNA-binding beta-barrels, polypeptide rings, and the C-terminal arm of Ku proteins. The Ku protein consists of two tightly associated homologous subunits, Ku70 and Ku80, and was originally identified as an autoantigen recognized by the sera of patients with an autoimmunity disease. In eukaryotes, the Ku heterodimer contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by non-homologous end-joining. The bacterial Ku homologs does not contain the conserved N-terminal extension that is present in the eukaryotic Ku protein.
Probab=100.00 E-value=5.6e-50 Score=417.65 Aligned_cols=272 Identities=33% Similarity=0.519 Sum_probs=237.4
Q ss_pred cceeeeeEEecCCeEEEEEEEeecccccCCCceEeccCCCCCccccccceeEEEEEeecCCCCCCCCccccccccccCCc
Q 005544 216 VTIFRGDLELSEKMKIKVWVYKKTGEEKFPTLKKYSDKAPSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYGPQ 295 (691)
Q Consensus 216 ~~~~~g~L~lg~~l~I~V~~Y~~~~~~k~p~~~~~~~~~~~~~~~~~~~v~~~~~y~~~~d~~~~v~~ed~~kgy~yG~~ 295 (691)
|+.|+|.|.||++++|+|++|+++++++++..+++.... ...++.++.+.. . .+.+|++++++|||+||++
T Consensus 1 r~~~~~~l~lg~~~~i~V~~y~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~-~-~~~~v~~~~i~kgy~~G~~ 71 (272)
T cd00594 1 RAIWKGALSLGLDVSIPVKLYSAATEEKPPSFKQLDRKT-------GERVKVKRVCKY-T-GGKEVEKEDIVKGYEYGGD 71 (272)
T ss_pred CcceeeeEEECCCCEEEEEEEeeeccccCCccEEeccCC-------CceeeEEEEEEe-e-cCcEeCHHHhhhheeeCCe
Confidence 468999999998899999999999999887555444311 123555555442 1 1479999999999999999
Q ss_pred eEeCChhhHHhhccCCCccEEEEeEeeCCCCcceeccCCeEEEEcCCCChhhHHHHHHHHHHHHhcCceEEEEEEecCCC
Q 005544 296 VVPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQGQ 375 (691)
Q Consensus 296 ~Vp~s~~e~~~~k~~~~~~l~ilGF~~~~~i~~~~~~~~~~~i~p~~~~~~s~~afsaL~~Am~e~~~vaI~r~v~r~~~ 375 (691)
+|+|+++|++.++..+++||+||||+++++|+++|++++++||+|++++.+|.+||+||++||.+++++||||||+|+|+
T Consensus 72 ~V~~~~~e~~~~~~~~~~~l~ilgF~~~~~i~~~~~~~~s~~l~P~~~~~~s~~af~aL~~am~~~~kvai~r~v~r~~~ 151 (272)
T cd00594 72 YVPLTEEELEQLKLETSKGLDILGFVPASEIPPYYFDKESYYLVPDDSDKGSEKAFSALRRALLEKDKVAIARYVLRRNS 151 (272)
T ss_pred EEecCHHHHHHhhcCCCCeEEEEeEechHhCCcceecCCcEEEEcCCCCcccHHHHHHHHHHHHHcCcEEEEEEEEcCCC
Confidence 99999999999999999999999999999999999999999999998878999999999999999999999999999997
Q ss_pred CceEEEEeeccccCCCCCCCeEEEecCCChhcccCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCcCCCCCC
Q 005544 376 QSVVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLVKMLDLAPSGKGEILQPEL 455 (691)
Q Consensus 376 ~p~~v~~L~P~~~~~~~~~~~l~~v~LPFaeDvR~~~fp~l~~~~~~~~p~~eq~~a~~~lI~~m~l~~~~~~e~~~p~~ 455 (691)
. |.+++|+|+.++. +.||++++|||+||||.++|+++... ....++++|+++|++||++|+++ .|+|+.
T Consensus 152 ~-p~l~aL~P~~~~~---~~gl~l~~LPfadDvR~~~~~~~~~~-~~~~~~~~~~~~a~~lI~~~~~~------~~~p~~ 220 (272)
T cd00594 152 R-PRLVALRPQEEED---PEGLVLVTLPFADDVRSYPFPLLLDI-KTEKPTDEELELAKQLIDSLDLD------DFDPEK 220 (272)
T ss_pred C-cEEEEEeccccCC---CCEEEEEccCCchhhhccCCcccccc-cccCCCHHHHHHHHHHHHhccCC------CCCccc
Confidence 6 5677899997663 68999999999999999999887543 22579999999999999999994 299999
Q ss_pred CCCchhHHHHHHHHHhhcCCCCCCCCCchhhhhhcCCCHHHHHHHHHHHHHHHhhc
Q 005544 456 TPNPALERFYHHLELKSEHQDAAPPPLDDSLKKITEPDPTLLAESQSAIDAFCGQF 511 (691)
Q Consensus 456 ~~NP~lqr~~~~l~~~al~~~~~~p~~~~~l~~~~~p~~~~~~~~~~~le~~k~~f 511 (691)
++||++|++|++|+++|++++.+.++.+. +..++..+.+++++.+++|+++|
T Consensus 221 ~~NP~lq~~~~~l~~~al~~~~~~~~~~~----~~~~~~~~~~~~~~~l~~~~~~~ 272 (272)
T cd00594 221 FPNPYLQRLYALLEAKALGEEIPEPPEDL----TLPPPEEIPKRVIDLLEALKKSL 272 (272)
T ss_pred CCCHHHHHHHHHHHHHhcCCCCCCCCCCc----cCCCcHHHHHHHHHHHHHHHhhC
Confidence 99999999999999999999998877664 56677888899999999999875
No 6
>KOG2327 consensus DNA-binding subunit of a DNA-dependent protein kinase (Ku70 autoantigen) [Replication, recombination and repair]
Probab=100.00 E-value=3.9e-47 Score=406.99 Aligned_cols=476 Identities=20% Similarity=0.239 Sum_probs=341.3
Q ss_pred CCeEEEEEEecCCCccC---------ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEee
Q 005544 4 TREALLLLLDVSPSMHS---------VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQD 74 (691)
Q Consensus 4 ~Kea~vflIDvs~sM~~---------~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~ 74 (691)
+|+++.||||++++|.. +|..++.|+..+..+++|+++.|.+|++++||..+.+. .|.+.+++
T Consensus 17 ~~~~ilfvi~~~~s~~~~~~~e~~lspl~~~L~~~~~l~~~~vitn~~~~~~v~~y~~~~~~~~--------~~~~~l~~ 88 (602)
T KOG2327|consen 17 GKEAILFVIDVNPSMKAEEPDEFKLSPLKMILDCIDRLCIQLVITNPIDSVGVLFYGTEETEGL--------ENNTLLFP 88 (602)
T ss_pred cccceEEEEecCHHhhccCcccchhhhHHHHHHHHHHHHhheeecCCCCccceEeecccccccC--------ccceEEee
Confidence 79999999999999875 25678999999999999999999999999999886653 34445555
Q ss_pred cCCCCHHHHHHhhcC-CC----C--------CCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCc
Q 005544 75 IKVVDGHLVQSLKHL-PQ----G--------TCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTK 141 (691)
Q Consensus 75 l~~~~~~~l~~L~~l-~~----~--------~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~ 141 (691)
+..+...-+.++.++ .. + ...+++...|+.|..|+.. +.++..++||++|||+++|+.. ++..
T Consensus 89 l~d~~~~~~~k~~~~~e~~~q~~~~~~~~~~~~~s~ls~vl~~c~~~~~~--~~~~~~~krv~l~Td~d~P~~~--~~~~ 164 (602)
T KOG2327|consen 89 LGDLGQEEVKKILELFEEENQLSAVNFYGGMHQKSDLSNVLNYCKRMVFA--SQKKLSNKRVFLFTDNDNPHER--DDFL 164 (602)
T ss_pred ccccChHHHHHHHHHhhhhhhhhhhhccCcccccccHHHHHHHHHHHHHH--HhhhcccceEEEEecCCCcccc--cchH
Confidence 544444433333332 11 1 2234688999999999876 3356889999999999999963 2222
Q ss_pred hhhHHHHHHHHhhcCcEEEEEeeccCCCCCCCcchhhhhhHHHHHHhhcCCCeEeehh--hhHHhhcccccccCCCccee
Q 005544 142 EDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVD--STTSLRGARKTRDISPVTIF 219 (691)
Q Consensus 142 ~~~l~~i~~~L~~~gI~l~vi~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~~~~~--~a~~ll~~~~~k~~~~~~~~ 219 (691)
.....+.+.++....|.+...+++..++..+....... ...-..+...++.+.+-. .+..++.+++.+....|..|
T Consensus 165 ~~a~l~r~k~~~~~~i~~~~~~l~~~~~~~~~~~~y~~--f~~i~~~~~~d~~~~~~~~~~~e~~~~ri~~k~~~kR~~f 242 (602)
T KOG2327|consen 165 ESAHLQRAKDLVTKDIGFHHKTLDEPSDIFLYEDFYKP--FDKISKAKELDSDLDTEVQSTLEDLLARILAKITAKRAHF 242 (602)
T ss_pred HHhhhhhhhhcccceeeeeecccCcccccccccccccc--cchheeeccccccccChhhhhHHHHHHHHHHHHHHHHhhh
Confidence 22233444444444444442223211111111000000 000000111233332222 33466677788888889999
Q ss_pred eeeEEecCCeEEEEEEEeecccccCC-CceEeccCCCCCccccccceeEEEE---EeecCCCCCCCCccccccccccCCc
Q 005544 220 RGDLELSEKMKIKVWVYKKTGEEKFP-TLKKYSDKAPSTDKFATHEVKVDYE---YKSVEDPSKVVPPEQRIKGYRYGPQ 295 (691)
Q Consensus 220 ~g~L~lg~~l~I~V~~Y~~~~~~k~p-~~~~~~~~~~~~~~~~~~~v~~~~~---y~~~~d~~~~v~~ed~~kgy~yG~~ 295 (691)
++.|.+|+++.|+|++|.++++++++ ..+.+...++ .|+..++ ++ +-+++.+.-+.++.+.|.||+.
T Consensus 243 ~l~l~lg~~v~i~V~~y~~~~~~~~~~~~~~y~~~~~--------~v~tk~~~~~~f-~~~tg~~~~~~~~~~s~~yG~~ 313 (602)
T KOG2327|consen 243 HLKLNLGPDVTIGVSVYNMVQRAKPADHSQLYRRDEE--------EVITKPSGYKFF-SCETGEELKRRDTKKSYEYGGE 313 (602)
T ss_pred eeeeccCCCeEEEEEEeeeeeccccCccceeEecccc--------eeeeecccceEe-ccccCCccccccceEEeccCCc
Confidence 99999999999999999999998755 6677766542 2333332 34 4567767888899999999999
Q ss_pred eEeCChhhHHhhccCCCccEEEEeEeeCCCCcceeccCCeEEEEcCCC-ChhhHHHHHHHHHHHHhcCceEEEEEEecCC
Q 005544 296 VVPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPG-NSRATVAVSALARAMKEMNKVAIVRCVWRQG 374 (691)
Q Consensus 296 ~Vp~s~~e~~~~k~~~~~~l~ilGF~~~~~i~~~~~~~~~~~i~p~~~-~~~s~~afsaL~~Am~e~~~vaI~r~v~r~~ 374 (691)
-|+|+.++.+.++...+|+|.|+||++.+++++|++++++.||+|++. ..||.+.|+||+..|.+++++|||||+.|.|
T Consensus 314 ~i~l~~dq~e~v~~~~~p~L~liGFk~~ssl~~~~~i~ps~fi~Pddq~~iGS~~~f~all~rcl~rdkiaic~~~~r~n 393 (602)
T KOG2327|consen 314 DIILSMDQLEYVREFNKPGLMLIGFKSMSSLKREHYIKPSKFIYPDDQTIIGSTRLFRALLKRCLARDKIAICWFQSRSN 393 (602)
T ss_pred ccccChhHHHHhhccCCcceEEEeeccccccCcccccCchhccCcchhhccchHHHHHHHHHHHHhhhhhhheeeccccc
Confidence 999999999999999999999999999999999999999999999986 7899999999999999999999999999999
Q ss_pred CCceEEEEeeccccC-----CCCCCCeEEEe-cCCChhcccCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHcCCCCCCCC
Q 005544 375 QQSVVVGVLTPNVSE-----KINIPDSFYFN-VLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLVKMLDLAPSGKG 448 (691)
Q Consensus 375 ~~p~~v~~L~P~~~~-----~~~~~~~l~~v-~LPFaeDvR~~~fp~l~~~~~~~~p~~eq~~a~~~lI~~m~l~~~~~~ 448 (691)
+.|+.|| |+++-.. ....++||+++ +||||||+|.++|+. ....+++|.+.|..++.+|.+.- .
T Consensus 394 ~~p~~vA-lv~~p~~~~d~~~~~l~~GF~LV~flp~aDdirk~p~~~------~v~~~p~~~eqmk~i~Qki~f~~---r 463 (602)
T KOG2327|consen 394 QKPRFVA-LVLQPQRGQDDSSESLPCGFQLVGFLPFADDIRKFPLQD------KVSTEPEQEEQMKAIVQKIRFKL---R 463 (602)
T ss_pred CCcceee-eecCccccccCcccccccceEEEEeecccchhccCCCcc------cccCCcchHHHHHHHHHHHHHHh---h
Confidence 9888775 6654321 12467899999 699999999998632 22334455566666666655531 1
Q ss_pred cCCCCCCCCCchhHHHHHHHHHhhcCCCCCCCCCchhhhhhcCCCHHHH-HHHHHHHHHHHhhcCCc-cCCc
Q 005544 449 EILQPELTPNPALERFYHHLELKSEHQDAAPPPLDDSLKKITEPDPTLL-AESQSAIDAFCGQFVIK-ENPK 518 (691)
Q Consensus 449 e~~~p~~~~NP~lqr~~~~l~~~al~~~~~~p~~~~~l~~~~~p~~~~~-~~~~~~le~~k~~f~~~-~~~~ 518 (691)
..+.| .|.||.||.||+.|++.||+.+.|....+.+ .|+.+.+ .|.+.+++++++.|... +.++
T Consensus 464 sd~~p-~feNP~Lq~h~knL~alaLd~e~p~~~vd~t-----lp~~~a~~KRvg~lvd~~~el~y~~d~ikE 529 (602)
T KOG2327|consen 464 SDYPP-FFENPSLQQHYKNLEALALDEETPEQAVDET-----LPKVEAMDKRVGELVDKYRELFYPPDYIKE 529 (602)
T ss_pred cCCcc-cccChHHHHHHHHHHHHhcccccchhhhccc-----CcchHHHHHHHHHHHHHHHHhcCCCcCCcc
Confidence 12666 8999999999999999999998876655554 3444444 45588999999977764 4443
No 7
>cd00789 KU_like Ku-core domain, Ku-like subfamily; composed of prokaryotic homologs of the eukaryotic DNA binding protein Ku. The alignment includes the core domain shared by the prokaryotic YkoV-like proteins and the eukaryotic Ku70 and Ku80. The prokaryotic Ku homologs are predicted to form homodimers. It is proposed that the Ku homologs are functionally associated with ATP-dependent DNA ligase and the eukaryotic-type primase, probably as components of a double-strand break repair system.
Probab=100.00 E-value=4.6e-47 Score=385.45 Aligned_cols=252 Identities=19% Similarity=0.309 Sum_probs=219.3
Q ss_pred cceeeeeEEecCCeEEEEEEEeecccccCCCceEeccCCCCCccccccceeEEEEEeecCCCCCCCCccccccccccC-C
Q 005544 216 VTIFRGDLELSEKMKIKVWVYKKTGEEKFPTLKKYSDKAPSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYG-P 294 (691)
Q Consensus 216 ~~~~~g~L~lg~~l~I~V~~Y~~~~~~k~p~~~~~~~~~~~~~~~~~~~v~~~~~y~~~~d~~~~v~~ed~~kgy~yG-~ 294 (691)
|++|+|.|+|| .++|||++|+++...++++++.+..++ ..|+ ++|. +++++++|+++|++|||+|| +
T Consensus 1 r~~wkG~l~fg-lV~ipV~ly~at~~~~i~f~~l~~~~~--------~~v~--~~~v-~~~~g~eV~~~divKgYeyg~~ 68 (256)
T cd00789 1 RAIWKGAISFG-LVNIPVKLYSATESEDISFHQLHKKDG--------ARIR--YQRV-CPETGKEVPRDDIVKGYEYEKG 68 (256)
T ss_pred CCceEEEEEEC-cEEEEEEEEEeeccCCcccEEEecCCC--------CEee--EEEE-CCCCCCCCCHHHceeeEEeCCC
Confidence 57999999999 999999999999889988888777643 3444 4565 68899999999999999999 8
Q ss_pred ceEeCChhhHHhhccCCCccEEEEeEeeCCCCcceeccCCeEEEEcCCCChhhHHHHHHHHHHHHhcCceEEEEEEecCC
Q 005544 295 QVVPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQG 374 (691)
Q Consensus 295 ~~Vp~s~~e~~~~k~~~~~~l~ilGF~~~~~i~~~~~~~~~~~i~p~~~~~~s~~afsaL~~Am~e~~~vaI~r~v~r~~ 374 (691)
++|+|+++|+++++..+.++|+|+||++.++|+++|+. .+|||+|++ ++..||++|++||.++++|||||||+|++
T Consensus 69 ~~V~~~~eel~~~~~~~~~~i~IlgFv~~~~I~~~y~~-~syyl~P~~---~~~kaf~~L~~Al~~~~kvaIar~V~r~~ 144 (256)
T cd00789 69 EYVILTDEELEALPPESTRTIEIVDFVPLDEIDPIYFD-KPYYLAPDK---GGEKAYALLREALRDTGKVAIAKVVLRTR 144 (256)
T ss_pred CEEEcCHHHHHhhccCCCCeEEEEeEeCHHHCCHhHcC-CCEEEecCC---CcchHHHHHHHHHHHcCCEEEEEEEEcCC
Confidence 99999999999999999999999999999999998885 579999998 46779999999999999999999999986
Q ss_pred CCceEEEEeeccccCCCCCCCeEEEecCCChhcccCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCcCCCCC
Q 005544 375 QQSVVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAADNLVKMLDLAPSGKGEILQPE 454 (691)
Q Consensus 375 ~~p~~v~~L~P~~~~~~~~~~~l~~v~LPFaeDvR~~~fp~l~~~~~~~~p~~eq~~a~~~lI~~m~l~~~~~~e~~~p~ 454 (691)
. .+|+|.|+. .||++++|||+||||+++|+++.. ....++++|+++|.+||++|+.. |+|+
T Consensus 145 ~---~l~aL~P~~-------~gL~l~~LpfaddvR~~~~~~~~~--~~~~~~~~el~~A~~LI~~m~~~-------fdp~ 205 (256)
T cd00789 145 E---RLAALRPRG-------KGLVLNTLRYPDEVRSPEELFLPI--KAVKVDPKELEMAKQLIEQLTGD-------FDPE 205 (256)
T ss_pred c---eEEEEEECC-------CEEEEEECCChhhccCccccCccc--ccCCCCHHHHHHHHHHHHHccCC-------CCcc
Confidence 3 478899983 699999999999999999987653 35679999999999999999986 9999
Q ss_pred CCCCchhHHHHHHHHHhhcCCCCCCCCCchhhhhhcCCCHHHHHHHHHHHHHHHhhcC
Q 005544 455 LTPNPALERFYHHLELKSEHQDAAPPPLDDSLKKITEPDPTLLAESQSAIDAFCGQFV 512 (691)
Q Consensus 455 ~~~NP~lqr~~~~l~~~al~~~~~~p~~~~~l~~~~~p~~~~~~~~~~~le~~k~~f~ 512 (691)
.|.||+.++++++|++|+.+.+...++..+ .+..+++ ++|++|++++.
T Consensus 206 ~~~d~y~~~l~~li~~K~~~~~~~~~~~~~------~~~~~v~----dlm~aL~~Sl~ 253 (256)
T cd00789 206 KYEDEYREALMELIEAKIEGKAIEAAEPAP------AASGNVV----DLMEALKKSLE 253 (256)
T ss_pred ccCCHHHHHHHHHHHHHHcCCCCCCCCCCC------CCCCCHH----HHHHHHHHHHh
Confidence 999999999999999999987765443221 1124555 99999999865
No 8
>TIGR02772 Ku_bact Ku protein, prokaryotic. Members of this protein family are Ku proteins of non-homologous end joining (NHEJ) DNA repair in bacteria and in at least one member of the archaea (Archaeoglobus fulgidus). Most members are encoded by a gene adjacent to the gene for the DNA ligase that completes the repair. The NHEJ system is broadly but rather sparsely distributed, being present in about one fifth of the first 250 completed prokarytotic genomes. A few species (e.g. Archaeoglobus fulgidus and Bradyrhizobium japonicum) have multiple copies that appear to represent recent paralogous family expansion.
Probab=100.00 E-value=4.3e-46 Score=378.80 Aligned_cols=253 Identities=19% Similarity=0.295 Sum_probs=216.6
Q ss_pred CcceeeeeEEecCCeEEEEEEEeecccccCCCceEeccCCCCCccccccceeEEEEEeecCCCCCCCCccccccccccCC
Q 005544 215 PVTIFRGDLELSEKMKIKVWVYKKTGEEKFPTLKKYSDKAPSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYGP 294 (691)
Q Consensus 215 ~~~~~~g~L~lg~~l~I~V~~Y~~~~~~k~p~~~~~~~~~~~~~~~~~~~v~~~~~y~~~~d~~~~v~~ed~~kgy~yG~ 294 (691)
+|++|+|.|+|| .++|||++|++|...++++++.+..++ ..|+ +.|. +++++++|+++|++|||+||+
T Consensus 1 ~r~~wkG~l~fg-lV~ipV~lY~at~~~~i~f~~l~~~~~--------~~v~--~~~v-~~~~g~eV~~~divKgYeyg~ 68 (258)
T TIGR02772 1 ARAIWKGAISFG-LVNCPVKLYPATESEDISFHQLHREDG--------NRVR--YQKV-CSETGKEVEREEIVKGYEYDK 68 (258)
T ss_pred CCCceEEEEEEc-cEEEEEEEEEeeecCCCccEEEEcCCC--------Ceee--EEEE-cCCCCCCCCHHHeeeeEEeCC
Confidence 478999999999 999999999999988888888777653 3455 4455 688999999999999999995
Q ss_pred -ceEeCChhhHHhhccCCCccEEEEeEeeCCCCcceeccCCeEEEEcCCCChhhHHHHHHHHHHHHhcCceEEEEEEecC
Q 005544 295 -QVVPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQ 373 (691)
Q Consensus 295 -~~Vp~s~~e~~~~k~~~~~~l~ilGF~~~~~i~~~~~~~~~~~i~p~~~~~~s~~afsaL~~Am~e~~~vaI~r~v~r~ 373 (691)
++|+|+++|+++++..++++|+|+||++.++|+++|+ +.+|||+|++ ++..||++|++||.+++++||||||+|.
T Consensus 69 g~~V~~~~eel~~~~~~~~~~i~I~gFv~~~~i~~~y~-~~syyl~P~~---~~~~a~~~L~~Al~~~~kvaIar~v~r~ 144 (258)
T TIGR02772 69 GKYVIIEDEDIESLPPESTKTIEIEAFVDADEIDPIYF-DTPYYLAPDK---GGEKAYALLREALEDTGKVGIAKVVLRG 144 (258)
T ss_pred CCEEEcCHHHHHhhcccCCCeEEEEEEeCHHHCChhee-CCCEEEccCC---CchHHHHHHHHHHHHcCCEEEEEEEEcC
Confidence 9999999999999999999999999999999999886 5579999983 5778999999999999999999999998
Q ss_pred CCCceEEEEeeccccCCCCCCCeEEEecCCChhcccCC-CCCCCCCCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCcCCC
Q 005544 374 GQQSVVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREF-QFPSFSKFPVSWQPNEQQQEAADNLVKMLDLAPSGKGEILQ 452 (691)
Q Consensus 374 ~~~p~~v~~L~P~~~~~~~~~~~l~~v~LPFaeDvR~~-~fp~l~~~~~~~~p~~eq~~a~~~lI~~m~l~~~~~~e~~~ 452 (691)
+. .+|+|.|+ .+||++++|||+||||.+ .|+++. ....++++|+++|.+||++|+.. |+
T Consensus 145 r~---~l~aL~P~-------~~gL~l~~LpfadEvR~~~~~~~~~---~~~~~~~~el~~A~~LI~~mt~~-------fd 204 (258)
T TIGR02772 145 RE---RLAALRPV-------GKGLVLTTLRYPDEVRSPDEFFGPI---KDVEVDPEELELAGQLIDKMTGK-------FD 204 (258)
T ss_pred Cc---EEEEEEEC-------CCeEEEEECCChhhccChhhccccc---ccCCCCHHHHHHHHHHHHHhccC-------CC
Confidence 63 37789998 359999999999999999 565542 34579999999999999999975 99
Q ss_pred CCCCCCchhHHHHHHHHHhhcCCCCCCCCCchhhhhhcCCCHHHHHHHHHHHHHHHhhcC
Q 005544 453 PELTPNPALERFYHHLELKSEHQDAAPPPLDDSLKKITEPDPTLLAESQSAIDAFCGQFV 512 (691)
Q Consensus 453 p~~~~NP~lqr~~~~l~~~al~~~~~~p~~~~~l~~~~~p~~~~~~~~~~~le~~k~~f~ 512 (691)
|+.|.||+.++++++|++|+.+++...|...+ ..++.+++ ++|++|+++..
T Consensus 205 p~~y~d~y~~~l~~~i~~K~~~~~~~~~~~~~-----~~~~~~vi----dlm~aL~~S~~ 255 (258)
T TIGR02772 205 PEDYHDEYREALLELVDAKLEGGKPPKAEEPA-----APAPGNVV----DLMDALKASLR 255 (258)
T ss_pred hhhCCCHHHHHHHHHHHHHHhCCCCCCCcccC-----CCCCCcHH----HHHHHHHHHHh
Confidence 99999999999999999999998764332110 01234566 99999999864
No 9
>PF02735 Ku: Ku70/Ku80 beta-barrel domain; InterPro: IPR006164 The Ku heterodimer is composed of Ku70 and Ku80 (or Ku86), 70 kDa and 80 kDa subunits of an ATP-dependent DNA helicase, which contributes to genomic integrity through its ability to bind DNA double-stranded breaks and facilitate repair by the non-homologous end-joining pathway. This is the central DNA-binding beta-barrel domain and is found in both the Ku70 and Ku80 proteins. Ku makes only a few contacts with the sugar-phosphate backbone, and none with the DNA bases, but it fits sterically to major and minor groove contours forming a ring that encircles duplex DNA, cradling two full turns of the DNA molecule. By forming a bridge between the broken DNA ends, Ku acts to structurally support and align the DNA ends, to protect them from degradation, and to prevent promiscuous binding to unbroken DNA. Ku effectively aligns the DNA, while still allowing access of polymerases, nucleases and ligases to the broken DNA ends to promote end joining [].; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0006303 double-strand break repair via nonhomologous end joining; PDB: 1JEY_B 1JEQ_B.
Probab=100.00 E-value=7.9e-41 Score=332.38 Aligned_cols=199 Identities=39% Similarity=0.602 Sum_probs=146.2
Q ss_pred EEecCCeEEEEEEEeecccccCCCceEeccCCCCCccccccceeEEEEEeecCCCCCCCCccccccccccCCceEeCChh
Q 005544 223 LELSEKMKIKVWVYKKTGEEKFPTLKKYSDKAPSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYGPQVVPISSA 302 (691)
Q Consensus 223 L~lg~~l~I~V~~Y~~~~~~k~p~~~~~~~~~~~~~~~~~~~v~~~~~y~~~~d~~~~v~~ed~~kgy~yG~~~Vp~s~~ 302 (691)
|+||++++|+|++|++++++++++++++.... ...++.++.|. +.+++.+|+++|++|||+||+++|+|+++
T Consensus 1 ~~ig~~v~I~V~~y~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~-~~~~~~~v~~~d~~kgy~~g~~~V~~~~~ 72 (200)
T PF02735_consen 1 LSIGPDVSIPVKLYKATKEAKPPFFKKLSRDT-------NEEVRSRTKYV-CPDTGEEVPPEDIIKGYRYGGEYVPFTDE 72 (200)
T ss_dssp EECTTTEEEEEEEEECE-----S--EEEETTT-------TTEEEEEEEEE-CTTT--EE-GGGEEEEEEECTEEEEE-HH
T ss_pred CEeCCCeEEEEEEEEeEeeccCCCcEEEEecC-------CcCceEEEEEE-cCCCCCccCHHHeEEEEEeCCEEEEeCHH
Confidence 68999999999999999999999888777641 24566666666 68888899999999999999999999999
Q ss_pred hHHhhccCCCccEEEEeEeeCCCCcceeccCCeEEEEcCCCCh-hhHHHHHHHHHHHHhcCceEEEEEEecCCCCceEEE
Q 005544 303 EWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPGNS-RATVAVSALARAMKEMNKVAIVRCVWRQGQQSVVVG 381 (691)
Q Consensus 303 e~~~~k~~~~~~l~ilGF~~~~~i~~~~~~~~~~~i~p~~~~~-~s~~afsaL~~Am~e~~~vaI~r~v~r~~~~p~~v~ 381 (691)
|++.++..++++|+||||+++++|+++|++++++||+|+++.. +|..+|+||++||.+++++||||||+|.++. |.+|
T Consensus 73 e~~~~~~~~~~~l~ilGF~~~~~i~~~~~~~~~~~i~p~~~~~~~s~~~f~aL~~am~~~~~vaI~r~v~r~~~~-p~l~ 151 (200)
T PF02735_consen 73 ELEAIKPETSPGLEILGFVPRSNIPPYYFMGESYFIVPDEKSGEGSAKAFSALVQAMLEKNKVAIARYVLRSNSR-PRLV 151 (200)
T ss_dssp HHHHCT--S-SEEEEEEEEEGGGS-CCG-ECEEEEEEEETTTECCHHHHHHHHHHHHHHCTEEEEEEEESSTTS---EEE
T ss_pred HHHhhhhcCCCeEEEEEEEcchhCCceEEeCCcEEEEECCCCcchhHHHHHHHHHHHHhcCcEEEEEEEEcCCCC-cEEE
Confidence 9999999999999999999999999999999999999998655 8999999999999999999999999999876 5577
Q ss_pred EeeccccCCCCCCCeEEEecCCChhcccCCCCCCCCCCCCCCCCCHHHHHHH
Q 005544 382 VLTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFSKFPVSWQPNEQQQEAA 433 (691)
Q Consensus 382 ~L~P~~~~~~~~~~~l~~v~LPFaeDvR~~~fp~l~~~~~~~~p~~eq~~a~ 433 (691)
+|+|+.+.. ..+.||++++|||+||||.++||++... ...|+++|+++|
T Consensus 152 aL~P~~~~~-~~~~gl~~~~Lpf~dDvR~~~~~~~~~~--~~~~~~eql~~a 200 (200)
T PF02735_consen 152 ALIPQIEES-DTPEGLVLIRLPFADDVRSFPFPSLSSA--KTKPTEEQLDAA 200 (200)
T ss_dssp EEEEEE-CE-EC-CEEEEEE---GGGB-------STT---TT---HHHHHH-
T ss_pred EEEEecccc-CCCCeEEEEEcCChhhccCccccCcCcC--CCCCCHHHhhcC
Confidence 899998653 1258999999999999999999998753 447999999987
No 10
>PF08785 Ku_PK_bind: Ku C terminal domain like; InterPro: IPR014893 The non-homologous end joining (NHEJ) pathway is one method by which double stranded breaks in chromosomal DNA are repaired. Ku is a component of a multi-protein complex that is involved in the NHEJ. Ku has affinity for DNA ends and recruits the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). This domain is found at the C-terminal of Ku which binds to DNA-PKcs []. ; GO: 0016817 hydrolase activity, acting on acid anhydrides; PDB: 1RW2_A 1Q2Z_A 3ISM_C.
Probab=100.00 E-value=1.4e-38 Score=287.62 Aligned_cols=120 Identities=43% Similarity=0.708 Sum_probs=109.1
Q ss_pred cCCChhhHHHHHHhCCCCchhHHHHHHHHHHHHHHHhhccCCCCChHHHHHHHHHHHHHhhhccCchHHHHHHHHHHHHH
Q 005544 564 GDLTPIQDFEAMMSRRDCPDWVDKAIEDMKNKIFGLLENSNEGINYPKAVELLVALRKGCILEQEPKQFNDVLEKVCKIC 643 (691)
Q Consensus 564 g~~~pv~dF~~~l~~~~~~~~~~~a~~qm~~~I~~lv~~s~~~~~y~ka~~cl~~~R~~~i~~~e~~~~N~fl~~lk~~~ 643 (691)
|++|||+||++||++++.+ |++|++||+++|++||.+| |+.+|+||++||++||++||.++||..||+||++||++|
T Consensus 1 Gsv~Pv~DFk~ll~~~d~~--~~~A~~qM~~vI~~Lv~~s-~~~~y~kalecl~~lR~~~i~~~ep~~yN~Fl~~LK~~~ 77 (120)
T PF08785_consen 1 GSVNPVQDFKALLAQRDSD--FQKAIQQMKNVIEQLVSDS-GDQNYDKALECLRALREECIEEEEPDEYNDFLRKLKKKL 77 (120)
T ss_dssp SSSSCCHHHHHHCCCCSSC--CCHHHHHHHHHHHHHHHCS-HCHHHHHHHHHHHHHHHHHHHHT-CHHHHHHHHHHHHHH
T ss_pred CCCChHHHHHHHHHcCCcc--HHHHHHHHHHHHHHHHhcc-CcchHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHH
Confidence 8999999999999998754 9999999999999999999 999999999999999999999999999999999999999
Q ss_pred hcCCchhHHHHHHhCCccccccCccCCCCCCHHHHhccccccC
Q 005544 644 RKRNFSTFFDFLMSKKLSLISKSEAVDSDITDDEAGSFIVKSQ 686 (691)
Q Consensus 644 ~~~~~~~fw~~i~~~~l~lI~~~E~~~s~vt~~ea~~F~~~~~ 686 (691)
+++++++||+.|++++|||||++|++.|+||++||++||.++|
T Consensus 78 ~~~~~~~FW~~i~~~~l~LI~~~E~~~S~vt~~eA~~Fl~~~~ 120 (120)
T PF08785_consen 78 LSKDRRDFWELIVSKKLGLISKDESESSDVTEEEAEEFLSQKE 120 (120)
T ss_dssp HCTTTCHHHHCCCCCT-SS-SSTTSSS-S--CHHHCCCT-SS-
T ss_pred HhccHHHHHHHHHHcCCCcccHhhcccCCCCHHHHHHHHhCCC
Confidence 9999999999999999999999999999999999999999876
No 11
>COG1273 Ku-homolog [Replication, recombination, and repair]
Probab=100.00 E-value=6.8e-35 Score=284.33 Aligned_cols=260 Identities=22% Similarity=0.348 Sum_probs=221.6
Q ss_pred CcceeeeeEEecCCeEEEEEEEeecccccCCCceEeccCCCCCccccccceeEEEEEeecCCCCCCCCccccccccccCC
Q 005544 215 PVTIFRGDLELSEKMKIKVWVYKKTGEEKFPTLKKYSDKAPSTDKFATHEVKVDYEYKSVEDPSKVVPPEQRIKGYRYGP 294 (691)
Q Consensus 215 ~~~~~~g~L~lg~~l~I~V~~Y~~~~~~k~p~~~~~~~~~~~~~~~~~~~v~~~~~y~~~~d~~~~v~~ed~~kgy~yG~ 294 (691)
+|+.|+|.|.|| .++|||++|.+|+..-+.+++++..++ ..|+ +.|. +..+|++|+++|++|||+||.
T Consensus 3 ~Ra~WKG~ikfg-LV~~PV~ly~ATs~seI~F~~L~r~t~--------nrV~--~~~V-d~~tGk~Ve~~d~VKGYE~~~ 70 (278)
T COG1273 3 MRAIWKGYIKFG-LVNCPVKLYPATSESEIRFHTLHRKTG--------NRVR--YKYV-DSVTGKEVERDDIVKGYEYGK 70 (278)
T ss_pred ccccccceeEee-eEecceEeeecccccccchhhhhhhhC--------Ccee--eEEe-ccccCCccCccceeeeeEecC
Confidence 688999999999 999999999999986688888887654 2343 4566 678999999999999999986
Q ss_pred -ceEeCChhhHHhhccCCCccEEEEeEeeCCCCcceeccCCeEEEEcCCCChhhHHHHHHHHHHHHhcCceEEEEEEecC
Q 005544 295 -QVVPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPGNSRATVAVSALARAMKEMNKVAIVRCVWRQ 373 (691)
Q Consensus 295 -~~Vp~s~~e~~~~k~~~~~~l~ilGF~~~~~i~~~~~~~~~~~i~p~~~~~~s~~afsaL~~Am~e~~~vaI~r~v~r~ 373 (691)
+||.++++|++.+...+.+.|+|..|+|.++|++.||-.+ ||+.|++ .++.||+.|..||.+++++||+|.|.++
T Consensus 71 ~~yViledeel~s~~~es~kti~I~~Fvp~~eId~iyfD~p-YYl~Pd~---~g~~af~lLReam~~~~~~aIar~vl~~ 146 (278)
T COG1273 71 GDYVILEDEELESVPLESTKTIEIEAFVPRDEIDPIYFDKP-YYLAPDK---VGEKAFALLREAMAETKKVAIARLVLRR 146 (278)
T ss_pred CcEEEecHHHHhhccccccceEeEEeecCHhhcCceeecCc-eeecCCC---CcchHHHHHHHHHHHcCcchhhhhhhhc
Confidence 9999999999999999999999999999999999999995 9999995 5678899999999999999999999999
Q ss_pred CCCceEEEEeeccccCCCCCCCeEEEecCCChhcccCCC--CCCCCCCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCcCC
Q 005544 374 GQQSVVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREFQ--FPSFSKFPVSWQPNEQQQEAADNLVKMLDLAPSGKGEIL 451 (691)
Q Consensus 374 ~~~p~~v~~L~P~~~~~~~~~~~l~~v~LPFaeDvR~~~--fp~l~~~~~~~~p~~eq~~a~~~lI~~m~l~~~~~~e~~ 451 (691)
+.. +++|.|+ ..|+++.+|.|.++||+.. ||.+.. ..+++++++++.+||+.|.-. |
T Consensus 147 Rer---~v~Lrp~-------~~glv~~TL~~~dEVRs~d~~f~~i~~----~~~d~eml~lA~~lI~~~~~~-------f 205 (278)
T COG1273 147 RER---LVLLRPR-------GKGLVLTTLRYPDEVRSPDEYFPGIPD----IKIDPEMLELAKQLIDKKTGT-------F 205 (278)
T ss_pred cce---eEEEEec-------CCcEEEEEecCchhccChhhhcCCCCc----ccCCHHHHHHHHHHHHHhcCC-------C
Confidence 864 4578997 5689999999999999998 776543 348999999999999999886 9
Q ss_pred CCCCCCCchhHHHHHHHHHhhcCCCCC-CCCCchhhhhhcCCCHHHHHHHHHHHHHHHhhcCCccCCcccc
Q 005544 452 QPELTPNPALERFYHHLELKSEHQDAA-PPPLDDSLKKITEPDPTLLAESQSAIDAFCGQFVIKENPKLKK 521 (691)
Q Consensus 452 ~p~~~~NP~lqr~~~~l~~~al~~~~~-~p~~~~~l~~~~~p~~~~~~~~~~~le~~k~~f~~~~~~~~~~ 521 (691)
+|+.|.+++-+++.++|+++.-+.... .|.-.+ .++.+++ ++|++|+++....+-+.+++
T Consensus 206 dp~~y~D~y~~aL~elI~aK~~g~~~~~~~~~~~------p~~~nVi----dL~daLk~S~~~~~~~~k~~ 266 (278)
T COG1273 206 DPDEYEDRYQEALMELIEAKLEGRKTVAAPKKEP------PEPSNVI----DLMDALKASLEARKKAGKKK 266 (278)
T ss_pred ChHHccCHHHHHHHHHHHHHHhCCCccccccCCC------CCcccHH----HHHHHHHHHHhccCCCCCCC
Confidence 999999999999999999999887632 111110 0134555 99999999998776554443
No 12
>smart00559 Ku78 Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen. This is a single stranded DNA- and ATP-depedent helicase that has a role in chromosome translocation. This is a domain of unknown function C-terminal to its von Willebrand factor A domain, that also occurs in bacterial hypothetical proteins.
Probab=100.00 E-value=2.2e-34 Score=268.37 Aligned_cols=136 Identities=35% Similarity=0.574 Sum_probs=126.6
Q ss_pred CCCCccccccccccCCceEeCChhhHHhhccCCCccEEEEeEeeCCCCcceeccCCeEEEEcCCC-ChhhHHHHHHHHHH
Q 005544 279 KVVPPEQRIKGYRYGPQVVPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAEPG-NSRATVAVSALARA 357 (691)
Q Consensus 279 ~~v~~ed~~kgy~yG~~~Vp~s~~e~~~~k~~~~~~l~ilGF~~~~~i~~~~~~~~~~~i~p~~~-~~~s~~afsaL~~A 357 (691)
.+|+++|++|||+||+++|+|+++|++.+|+.++++|+||||+++++|+++|+++++|||+|++. ..+|+.||+||++|
T Consensus 2 ~~v~~~~~~kgy~yG~~~V~~~~ee~~~~k~~~~~~l~ilgF~~~~~i~~~~~~~~s~~i~P~~~~~~~s~~a~~aL~~a 81 (140)
T smart00559 2 KEVKPEDIVKGYEYGGRYVPLSDEELEQLKYKSEPGLELLGFKPLSSLPPYYFLRPSYFLVPDDKSVIGSTKAFSALVEA 81 (140)
T ss_pred cccChHHceEeeEeCCEEeccCHHHHHHhhccCCCeEEEEeecChHHCCHhHccCCcEEEeeCCcccchhHHHHHHHHHH
Confidence 47899999999999999999999999999999999999999999999999999999999999985 67899999999999
Q ss_pred HHhcCceEEEEEEecCCCCceEEEEeeccccCCCCCCCeEEEecCCChhcccCCCCCCCC
Q 005544 358 MKEMNKVAIVRCVWRQGQQSVVVGVLTPNVSEKINIPDSFYFNVLPFAEDVREFQFPSFS 417 (691)
Q Consensus 358 m~e~~~vaI~r~v~r~~~~p~~v~~L~P~~~~~~~~~~~l~~v~LPFaeDvR~~~fp~l~ 417 (691)
|.+++++||||||+|+++. |.+++|+|+..+.. +.||++++|||+||||.++||+|.
T Consensus 82 m~~~~~~aiar~v~r~~~~-p~l~aL~P~~~~~~--~~~l~~~~LpfaedvR~~~~~~l~ 138 (140)
T smart00559 82 LLETDKIAIARYTLRTKSN-PRLVALRPYDEEDD--GEGLVLVQLPFADDVRKLDFPELN 138 (140)
T ss_pred HHhcCCEEEEEEEEcCCCC-CEEEEEEeeecccC--CCcEEEEecCCchhccCCCCcCcc
Confidence 9999999999999999975 56778999977542 469999999999999999999875
No 13
>PF03731 Ku_N: Ku70/Ku80 N-terminal alpha/beta domain; InterPro: IPR005161 The Ku heterodimer (composed of Ku70 P12956 from SWISSPROT and Ku80 P13010 from SWISSPROT) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the N-terminal alpha/beta domain. This domain only makes a small contribution to the dimer interface. The domain comprises a six stranded beta sheet of the Rossman fold [].; PDB: 1JEQ_A 1JEY_A.
Probab=99.95 E-value=1.3e-27 Score=242.14 Aligned_cols=201 Identities=28% Similarity=0.404 Sum_probs=139.5
Q ss_pred EEEEEEecCCCccCC-------hhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCC
Q 005544 7 ALLLLLDVSPSMHSV-------LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVD 79 (691)
Q Consensus 7 a~vflIDvs~sM~~~-------l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~ 79 (691)
|||||||||++|+++ |+.|++++..++++||+++++|+||||+|||++|+|+ .+.++|+||+++++|++|+
T Consensus 1 ~~vflID~s~sM~~~~~~~~~~l~~al~~i~~~~~~ki~~~~kD~vgvvl~gt~~t~n~--~~~~~~~~i~~l~~l~~~~ 78 (224)
T PF03731_consen 1 ATVFLIDVSPSMFEPSSESESPLEEALKAIEDLMQQKIISSPKDEVGVVLFGTDETNNP--DEDSGYENIFVLQPLDPPS 78 (224)
T ss_dssp EEEEEEE-SCGGGS-BTTCS-HHHHHHHHHHHHHHHHHHTT---EEEEEEES-SS-BST---TTT-STTEEEEEECC--B
T ss_pred CEEEEEECCHHHCCCCCCcchhHHHHHHHHHHHHHHHHcCCCCCeEEEEEEcCCCCCCc--ccccCCCceEEeecCCccC
Confidence 799999999999974 6789999999999999999999999999999999997 3456999999999999999
Q ss_pred HHHHHHhhcCC-C---------CCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHH-
Q 005544 80 GHLVQSLKHLP-Q---------GTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTI- 148 (691)
Q Consensus 80 ~~~l~~L~~l~-~---------~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i- 148 (691)
++.|+.|.++. . +...+++.+|||+|++||.+++++++++.||||||||+++|+.+ ....+.+...
T Consensus 79 ~~~l~~L~~~~~~~~~~~~~~~~~~~~~l~~al~v~~~~~~~~~~~~k~~~krI~l~Td~d~p~~~---~~~~~~~~~~l 155 (224)
T PF03731_consen 79 AERLKELEELLKPGDKFENFFSGSDEGDLSDALWVASDMFRERTCKKKKNKKRIFLFTDNDGPHED---DDELERIIQKL 155 (224)
T ss_dssp HHHHHHHHTTSHHHHHHHHHC-SSS---HHHHHHHHHHHHHCHCTTS-ECEEEEEEEES-SSTTT----CCCHHHHHHHH
T ss_pred HHHHHHHHHhhcccccccccCCCCCccCHHHHHHHHHHHHHHHhhcccCCCcEEEEEeCCCCCCCC---HHHHHHHHHhh
Confidence 99999999963 3 46678999999999999987656777899999999999999952 1223344444
Q ss_pred -HHHHhhcCcEEEEEeecc--CC-CCCCCcchhhhhhHHHHHHhhcCCCeEeehhhhHHhhcccccccCCCcc
Q 005544 149 -ARQMVAFGLRMKNIVVRA--SL-SGEPHMRVIIENDNLLNIFSKKSSAKTLFVDSTTSLRGARKTRDISPVT 217 (691)
Q Consensus 149 -~~~L~~~gI~l~vi~i~~--~~-~~~~~~~~~~~ne~~l~~l~~~~~g~~~~~~~a~~ll~~~~~k~~~~~~ 217 (691)
+.++++.||.+.++++.. .| .+.++......+............|. ...+++..++.|..+.|+
T Consensus 156 ~~~Dl~~~~i~~~~~~l~~~~~f~~~~fy~~~~~~~~~~~~~~~~~~~~~-----~~~~l~~~~~~~~~~kR~ 223 (224)
T PF03731_consen 156 KAKDLQDNGIEIELFFLPGSDKFDMDKFYKEILKLPEDEENEVMQSSSGE-----SVEDLLSRIRRKKFKKRA 223 (224)
T ss_dssp HHHHHHHHTEEEEEEECT-TT---CCCTCGHCCHHHHHHHHHHHHHHCSG-----CHHHHCCCCCCCHCG---
T ss_pred ccccchhcCcceeEeecCCCCCCChhhCcccccccchhhhcccccccccc-----cHHHHHHHHhhhcccccC
Confidence 778999999999999921 22 12333333323333333333333333 456777888888777664
No 14
>cd01458 vWA_ku Ku70/Ku80 N-terminal domain. The Ku78 heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks (DSB) in a preferred orientation. DSB's are repaired by either homologues recombination or non-homologues end joining and facilitate repair by the non-homologous end-joining pathway (NHEJ). The Ku heterodimer is required for accurate process that tends to preserve the sequence at the junction. Ku78 is found in all three kingdoms of life. However, only the eukaryotic proteins have a vWA domain fused to them at their N-termini. The vWA domain is not involved in DNA binding but may very likey mediate Ku78's interactions with other proteins. Members of this subgroup lack the conserved MIDAS motif.
Probab=99.92 E-value=2.4e-24 Score=217.31 Aligned_cols=153 Identities=30% Similarity=0.470 Sum_probs=132.5
Q ss_pred CeEEEEEEecCCCccC--------ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecC
Q 005544 5 REALLLLLDVSPSMHS--------VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIK 76 (691)
Q Consensus 5 Kea~vflIDvs~sM~~--------~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~ 76 (691)
||+++||||+|+||+. .|+.|++++..++++||+++++|+||||+|||+.++|+ ++|+||++++|+.
T Consensus 1 ke~ivf~iDvS~SM~~~~~~~~~s~l~~a~~~i~~~~~~ki~~~~~D~vGlilf~t~~~~~~-----~~~~~i~v~~~l~ 75 (218)
T cd01458 1 KESVVFLVDVSPSMFESKDGEYESPFEEALKCIRQLMKSKIISSPKDLVGVVFYGTEESKNP-----VGYENIYVLLDLD 75 (218)
T ss_pred CcEEEEEEeCCHHHcCCCCCCCCChHHHHHHHHHHHHHhceeCCCCCeEEEEEEcccCCCCc-----CCCCceEEeecCC
Confidence 7999999999999973 36789999999999999999999999999999999887 4899999999999
Q ss_pred CCCHHHHHHhhcC-CCC----------CCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhH
Q 005544 77 VVDGHLVQSLKHL-PQG----------TCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQV 145 (691)
Q Consensus 77 ~~~~~~l~~L~~l-~~~----------~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l 145 (691)
.|+++.++.|.++ .++ ...+++.+|||+|+++|.. ++++++.|+||||||+++|++. +....+++
T Consensus 76 ~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~l~~aL~~a~~~~~~--~~~~~~~k~IvL~TDg~~p~~~--~~~~~~~~ 151 (218)
T cd01458 76 TPGAERVEDLKELIEPGGLSFAGQVGDSGQVSLSDALWVCLDLFSK--GKKKKSHKRIFLFTNNDDPHGG--DSIKDSQA 151 (218)
T ss_pred CCCHHHHHHHHHHhhcchhhhcccCCCCCCccHHHHHHHHHHHHHh--ccccccccEEEEECCCCCCCCC--CHHHHHHH
Confidence 9999999999985 232 2356899999999999876 3455789999999999999863 22334678
Q ss_pred HHHHHHHhhcCcEEEEEeecc
Q 005544 146 STIARQMVAFGLRMKNIVVRA 166 (691)
Q Consensus 146 ~~i~~~L~~~gI~l~vi~i~~ 166 (691)
..++++|++.||.+++|+++.
T Consensus 152 ~~~a~~l~~~gI~i~~i~i~~ 172 (218)
T cd01458 152 AVKAEDLKDKGIELELFPLSS 172 (218)
T ss_pred HHHHHHHHhCCcEEEEEecCC
Confidence 889999999999999999954
No 15
>cd01453 vWA_transcription_factor_IIH_type Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme. Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins contain a VWA domain. The p44 subunit of TFIIH functions as a DNA helicase in RNA polymerase II transcription initiation and DNA repair, and its transcriptional activity is dependent on its C-terminal Zn-binding domains. The function of the vWA domain is unclear, but may be involved in complex assembly. The MIDAS motif is not conserved in this sub-group.
Probab=99.38 E-value=1.7e-11 Score=120.07 Aligned_cols=165 Identities=15% Similarity=0.171 Sum_probs=115.9
Q ss_pred EEEEEEecCCCccC------ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCCH
Q 005544 7 ALLLLLDVSPSMHS------VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDG 80 (691)
Q Consensus 7 a~vflIDvs~sM~~------~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~~ 80 (691)
.+||+||+|+||.+ +++.|+.++..|++++.-.++.|+||||.|+... . +++.|+..-..
T Consensus 5 ~ivi~lD~S~SM~a~D~~ptRl~~ak~~~~~fi~~~~~~~~~~~vglv~f~~~~----------a----~~~~PlT~D~~ 70 (183)
T cd01453 5 HLIIVIDCSRSMEEQDLKPSRLAVVLKLLELFIEEFFDQNPISQLGIISIKNGR----------A----EKLTDLTGNPR 70 (183)
T ss_pred EEEEEEECcHHHhcCCCCchHHHHHHHHHHHHHHHHhhcCccccEEEEEEcCCc----------c----EEEECCCCCHH
Confidence 58999999999984 5889999999999877667899999999995432 1 24566643333
Q ss_pred HHHHHhhcCCCCCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEE
Q 005544 81 HLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMK 160 (691)
Q Consensus 81 ~~l~~L~~l~~~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~l~ 160 (691)
..+..|+.+....+..++.+||.+|.++|.. .......+.|+|+||+.+. + ...+..+++.+++.||.+.
T Consensus 71 ~~~~~L~~~~~~~G~t~l~~aL~~A~~~l~~--~~~~~~~~iiil~sd~~~~-~-------~~~~~~~~~~l~~~~I~v~ 140 (183)
T cd01453 71 KHIQALKTARECSGEPSLQNGLEMALESLKH--MPSHGSREVLIIFSSLSTC-D-------PGNIYETIDKLKKENIRVS 140 (183)
T ss_pred HHHHHhhcccCCCCchhHHHHHHHHHHHHhc--CCccCceEEEEEEcCCCcC-C-------hhhHHHHHHHHHHcCcEEE
Confidence 4566666551112234789999999999863 1111123456666765432 1 1245677889999999999
Q ss_pred EEeeccCCCCCCCcchhhhhhHHHHHHhhcCCCeEeehhhhHHhhccc
Q 005544 161 NIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDSTTSLRGAR 208 (691)
Q Consensus 161 vi~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~~~~~~a~~ll~~~ 208 (691)
+|+++. +...|+.++..++|+++...+..++-..+
T Consensus 141 ~IgiG~-------------~~~~L~~ia~~tgG~~~~~~~~~~l~~~~ 175 (183)
T cd01453 141 VIGLSA-------------EMHICKEICKATNGTYKVILDETHLKELL 175 (183)
T ss_pred EEEech-------------HHHHHHHHHHHhCCeeEeeCCHHHHHHHH
Confidence 999953 13579999999999999888775544443
No 16
>cd01451 vWA_Magnesium_chelatase Magnesium chelatase: Mg-chelatase catalyses the insertion of Mg into protoporphyrin IX (Proto). In chlorophyll biosynthesis, insertion of Mg2+ into protoporphyrin IX is catalysed by magnesium chelatase in an ATP-dependent reaction. Magnesium chelatase is a three sub-unit (BchI, BchD and BchH) enzyme with a novel arrangement of domains: the C-terminal helical domain is located behind the nucleotide binding site. The BchD domain contains a AAA domain at its N-terminus and a VWA domain at its C-terminus. The VWA domain has been speculated to be involved in mediating protein-protein interactions.
Probab=99.19 E-value=1.1e-09 Score=107.04 Aligned_cols=163 Identities=15% Similarity=0.205 Sum_probs=112.3
Q ss_pred EEEEEEecCCCccC--ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCCHHHHH
Q 005544 7 ALLLLLDVSPSMHS--VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHLVQ 84 (691)
Q Consensus 7 a~vflIDvs~sM~~--~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~~~~l~ 84 (691)
-++|+||+|+||.. .++.++.++..++... ....|++|||.|++... .+..|+........+
T Consensus 2 ~v~lvlD~SgSM~~~~rl~~ak~a~~~~~~~~--~~~~d~v~lv~F~~~~~--------------~~~~~~t~~~~~~~~ 65 (178)
T cd01451 2 LVIFVVDASGSMAARHRMAAAKGAVLSLLRDA--YQRRDKVALIAFRGTEA--------------EVLLPPTRSVELAKR 65 (178)
T ss_pred eEEEEEECCccCCCccHHHHHHHHHHHHHHHh--hcCCCEEEEEEECCCCc--------------eEEeCCCCCHHHHHH
Confidence 37899999999985 5778888888877532 35789999999986421 122343322233456
Q ss_pred HhhcCCCCCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhH-HHHHHHHhhcCcEEEEEe
Q 005544 85 SLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQV-STIARQMVAFGLRMKNIV 163 (691)
Q Consensus 85 ~L~~l~~~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l-~~i~~~L~~~gI~l~vi~ 163 (691)
.|+.++.+. ..++.+||..|.+.+... .......+.|||||||....+. ...... ...++.+++.||.+.+|+
T Consensus 66 ~l~~l~~~G-~T~l~~aL~~a~~~l~~~-~~~~~~~~~ivliTDG~~~~g~----~~~~~~~~~~~~~l~~~gi~v~~I~ 139 (178)
T cd01451 66 RLARLPTGG-GTPLAAGLLAAYELAAEQ-ARDPGQRPLIVVITDGRANVGP----DPTADRALAAARKLRARGISALVID 139 (178)
T ss_pred HHHhCCCCC-CCcHHHHHHHHHHHHHHH-hcCCCCceEEEEECCCCCCCCC----CchhHHHHHHHHHHHhcCCcEEEEe
Confidence 677776543 247889999999988321 1111235889999999876542 111223 677889999999998888
Q ss_pred eccCCCCCCCcchhhhhhHHHHHHhhcCCCeEeehhhh
Q 005544 164 VRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDST 201 (691)
Q Consensus 164 i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~~~~~~a 201 (691)
++... .+..+|+.+++.++|+++.+.++
T Consensus 140 ~~~~~----------~~~~~l~~iA~~tgG~~~~~~d~ 167 (178)
T cd01451 140 TEGRP----------VRRGLAKDLARALGGQYVRLPDL 167 (178)
T ss_pred CCCCc----------cCccHHHHHHHHcCCeEEEcCcC
Confidence 74310 13578999999999999988765
No 17
>cd01452 VWA_26S_proteasome_subunit 26S proteasome plays a major role in eukaryotic protein breakdown, especially for ubiquitin-tagged proteins. It is an ATP-dependent protease responsible for the bulk of non-lysosomal proteolysis in eukaryotes, often using covalent modification of proteins by ubiquitylation. It consists of a 20S proteolytic core particle (CP) and a 19S regulatory particle (RP). The CP is an ATP independent peptidase consisting of hydrolyzing activities. One or both ends of CP carry the RP that confers both ubiquitin and ATP dependence to the 26S proteosome. The RP's proposed functions include recognition of substrates and translocation of these to CP for proteolysis. The RP can dissociate into a stable lid and base subcomplexes. The base is composed of three non-ATPase subunits (Rpn 1, 2 and 10). A single residue in the vWA domain of Rpn10 has been implicated to be responsible for stabilizing the lid-base association.
Probab=99.18 E-value=1.1e-09 Score=106.63 Aligned_cols=152 Identities=15% Similarity=0.214 Sum_probs=110.4
Q ss_pred CeEEEEEEecCCCccC------ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCC
Q 005544 5 REALLLLLDVSPSMHS------VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV 78 (691)
Q Consensus 5 Kea~vflIDvs~sM~~------~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~ 78 (691)
-||++||||+|.||.+ +++.+++++..++..++-.++.++||||.|+... -+++.|+..-
T Consensus 3 ~ea~vi~lD~S~sM~a~D~~PnRL~aak~~i~~~~~~f~~~np~~~vGlv~fag~~--------------a~v~~plT~D 68 (187)
T cd01452 3 LEATMICIDNSEYMRNGDYPPTRFQAQADAVNLICQAKTRSNPENNVGLMTMAGNS--------------PEVLVTLTND 68 (187)
T ss_pred ceEEEEEEECCHHHHcCCCCCCHHHHHHHHHHHHHHHHHhcCCCccEEEEEecCCc--------------eEEEECCCCC
Confidence 6999999999999976 3778899999998888889999999999999853 1245666544
Q ss_pred CHHHHHHhhcCCCCCCCCchhhHHHHHHHHHHHHhccCCcccce-EEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCc
Q 005544 79 DGHLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKH-LCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGL 157 (691)
Q Consensus 79 ~~~~l~~L~~l~~~~~~gd~~daL~va~d~l~~~~~~~k~~~kr-IvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI 157 (691)
-...+..|+.+..+ +..++..||-+|...|.. ...+...+| |+++++..... ...+..+++.|++.||
T Consensus 69 ~~~~~~~L~~i~~~-g~~~l~~AL~~A~~~L~~--~~~~~~~~rivi~v~S~~~~d--------~~~i~~~~~~lkk~~I 137 (187)
T cd01452 69 QGKILSKLHDVQPK-GKANFITGIQIAQLALKH--RQNKNQKQRIVAFVGSPIEED--------EKDLVKLAKRLKKNNV 137 (187)
T ss_pred HHHHHHHHHhCCCC-CcchHHHHHHHHHHHHhc--CCCcCCcceEEEEEecCCcCC--------HHHHHHHHHHHHHcCC
Confidence 44456667776543 345799999999999864 222223346 55555543332 2468789999999999
Q ss_pred EEEEEeeccCCCCCCCcchhhhhhHHHHHHhhcC
Q 005544 158 RMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKS 191 (691)
Q Consensus 158 ~l~vi~i~~~~~~~~~~~~~~~ne~~l~~l~~~~ 191 (691)
.+.+|++|.. .+|...|..|.+..
T Consensus 138 ~v~vI~~G~~----------~~~~~~l~~~~~~~ 161 (187)
T cd01452 138 SVDIINFGEI----------DDNTEKLTAFIDAV 161 (187)
T ss_pred eEEEEEeCCC----------CCCHHHHHHHHHHh
Confidence 9999999752 23556777777655
No 18
>PRK13685 hypothetical protein; Provisional
Probab=99.16 E-value=1.7e-09 Score=115.76 Aligned_cols=178 Identities=16% Similarity=0.186 Sum_probs=119.1
Q ss_pred eEEEEEEecCCCccC------ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCC
Q 005544 6 EALLLLLDVSPSMHS------VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVD 79 (691)
Q Consensus 6 ea~vflIDvs~sM~~------~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~ 79 (691)
-.+||+||+|.||.. +++.|+.++..++.+ .+++|+||||.|+++. ++..|+..-.
T Consensus 89 ~~vvlvlD~S~SM~~~D~~p~RL~~ak~~~~~~l~~---l~~~d~vglv~Fa~~a---------------~~~~p~t~d~ 150 (326)
T PRK13685 89 AVVMLVIDVSQSMRATDVEPNRLAAAQEAAKQFADE---LTPGINLGLIAFAGTA---------------TVLVSPTTNR 150 (326)
T ss_pred ceEEEEEECCccccCCCCCCCHHHHHHHHHHHHHHh---CCCCCeEEEEEEcCce---------------eecCCCCCCH
Confidence 469999999999984 478899999999884 2579999999999863 1344554322
Q ss_pred HHHHHHhhcCCCCCCCCchhhHHHHHHHHHHHH---hcc-CCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhc
Q 005544 80 GHLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKK---YGE-TYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAF 155 (691)
Q Consensus 80 ~~~l~~L~~l~~~~~~gd~~daL~va~d~l~~~---~~~-~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~ 155 (691)
......|+.+..+. ..+..++|..|++.+... .+. .....++|||||||.++.+.. ..........++.+++.
T Consensus 151 ~~l~~~l~~l~~~~-~T~~g~al~~A~~~l~~~~~~~~~~~~~~~~~IILlTDG~~~~~~~--~~~~~~~~~aa~~a~~~ 227 (326)
T PRK13685 151 EATKNAIDKLQLAD-RTATGEAIFTALQAIATVGAVIGGGDTPPPARIVLMSDGKETVPTN--PDNPRGAYTAARTAKDQ 227 (326)
T ss_pred HHHHHHHHhCCCCC-CcchHHHHHHHHHHHHhhhcccccccCCCCCEEEEEcCCCCCCCCC--CCCcccHHHHHHHHHHc
Confidence 23455566675543 235678999999987641 010 112357899999998865420 00011234567888999
Q ss_pred CcEEEEEeeccCC---CCCCCcchhhhhhHHHHHHhhcCCCeEeehhhhHHh
Q 005544 156 GLRMKNIVVRASL---SGEPHMRVIIENDNLLNIFSKKSSAKTLFVDSTTSL 204 (691)
Q Consensus 156 gI~l~vi~i~~~~---~~~~~~~~~~~ne~~l~~l~~~~~g~~~~~~~a~~l 204 (691)
||.+.+|++|.+- ..++.......++..|+.++..++|+++...++.++
T Consensus 228 gi~i~~Ig~G~~~g~~~~~g~~~~~~~d~~~L~~iA~~tgG~~~~~~~~~~L 279 (326)
T PRK13685 228 GVPISTISFGTPYGSVEINGQRQPVPVDDESLKKIAQLSGGEFYTAASLEEL 279 (326)
T ss_pred CCeEEEEEECCCCCCcCcCCceeeecCCHHHHHHHHHhcCCEEEEcCCHHHH
Confidence 9999999997521 001111112346789999999999999987765443
No 19
>cd01465 vWA_subgroup VWA subgroup: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if n
Probab=99.15 E-value=3.7e-09 Score=101.92 Aligned_cols=161 Identities=17% Similarity=0.279 Sum_probs=111.7
Q ss_pred EEEEEecCCCccCC-hhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCC-CCHH-HHH
Q 005544 8 LLLLLDVSPSMHSV-LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKV-VDGH-LVQ 84 (691)
Q Consensus 8 ~vflIDvs~sM~~~-l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~-~~~~-~l~ 84 (691)
++|+||+|.||... ++.++.++..++.+ ..+.|.||||.|+++.. ++.+... .+.+ +..
T Consensus 3 ~~~vlD~S~SM~~~~~~~~k~a~~~~~~~---l~~~~~v~li~f~~~~~---------------~~~~~~~~~~~~~l~~ 64 (170)
T cd01465 3 LVFVIDRSGSMDGPKLPLVKSALKLLVDQ---LRPDDRLAIVTYDGAAE---------------TVLPATPVRDKAAILA 64 (170)
T ss_pred EEEEEECCCCCCChhHHHHHHHHHHHHHh---CCCCCEEEEEEecCCcc---------------EEecCcccchHHHHHH
Confidence 78999999999764 67777777766662 36889999999998531 1222221 1222 344
Q ss_pred HhhcCCCCCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEEee
Q 005544 85 SLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIVV 164 (691)
Q Consensus 85 ~L~~l~~~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~l~vi~i 164 (691)
.|.++..+. ..++..||..|.+.+.+... ....++|||||||....+. ...+.+...++.++..+|.+.+|++
T Consensus 65 ~l~~~~~~g-~T~~~~al~~a~~~~~~~~~--~~~~~~ivl~TDG~~~~~~----~~~~~~~~~~~~~~~~~v~i~~i~~ 137 (170)
T cd01465 65 AIDRLTAGG-STAGGAGIQLGYQEAQKHFV--PGGVNRILLATDGDFNVGE----TDPDELARLVAQKRESGITLSTLGF 137 (170)
T ss_pred HHHcCCCCC-CCCHHHHHHHHHHHHHhhcC--CCCeeEEEEEeCCCCCCCC----CCHHHHHHHHHHhhcCCeEEEEEEe
Confidence 566665432 34788999999998765322 2234889999999875432 1234566677788889999999999
Q ss_pred ccCCCCCCCcchhhhhhHHHHHHhhcCCCeEeehhhhHHh
Q 005544 165 RASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDSTTSL 204 (691)
Q Consensus 165 ~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~~~~~~a~~l 204 (691)
+.+ .+..+|+.++...+|.++.++++.++
T Consensus 138 g~~-----------~~~~~l~~ia~~~~g~~~~~~~~~~~ 166 (170)
T cd01465 138 GDN-----------YNEDLMEAIADAGNGNTAYIDNLAEA 166 (170)
T ss_pred CCC-----------cCHHHHHHHHhcCCceEEEeCCHHHH
Confidence 531 24678999999999998888777554
No 20
>cd01480 vWA_collagen_alpha_1-VI-type VWA_collagen alpha(VI) type: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.
Probab=99.11 E-value=3.8e-09 Score=103.89 Aligned_cols=154 Identities=16% Similarity=0.181 Sum_probs=107.2
Q ss_pred EEEEEEecCCCcc-CChhHHHHHHHHHHHHH------HhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCC--
Q 005544 7 ALLLLLDVSPSMH-SVLPDVEKLCSRLIQKK------LIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKV-- 77 (691)
Q Consensus 7 a~vflIDvs~sM~-~~l~~a~~~~~~l~~~k------i~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~-- 77 (691)
-++|+||.|.||. ..++.++..+..++.+. -+....++||||.|++..+ +..++..
T Consensus 4 dvv~vlD~S~Sm~~~~~~~~k~~~~~~~~~l~~~~~~~i~~~~~rvglv~fs~~~~---------------~~~~l~~~~ 68 (186)
T cd01480 4 DITFVLDSSESVGLQNFDITKNFVKRVAERFLKDYYRKDPAGSWRVGVVQYSDQQE---------------VEAGFLRDI 68 (186)
T ss_pred eEEEEEeCCCccchhhHHHHHHHHHHHHHHHhhhhccCCCCCceEEEEEEecCCce---------------eeEeccccc
Confidence 3799999999998 45777776666666654 2335679999999997531 2344431
Q ss_pred CC-HHHHHHhhcCCCCCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcC
Q 005544 78 VD-GHLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFG 156 (691)
Q Consensus 78 ~~-~~~l~~L~~l~~~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~g 156 (691)
.+ ....+.|+++....+.....+||..|.+++.. +.+....|.|+|||||.+.... ...+...++.+++.|
T Consensus 69 ~~~~~l~~~i~~l~~~gg~T~~~~AL~~a~~~l~~--~~~~~~~~~iillTDG~~~~~~------~~~~~~~~~~~~~~g 140 (186)
T cd01480 69 RNYTSLKEAVDNLEYIGGGTFTDCALKYATEQLLE--GSHQKENKFLLVITDGHSDGSP------DGGIEKAVNEADHLG 140 (186)
T ss_pred CCHHHHHHHHHhCccCCCCccHHHHHHHHHHHHhc--cCCCCCceEEEEEeCCCcCCCc------chhHHHHHHHHHHCC
Confidence 33 34566677775322234678999999998765 2334568999999999874221 135677788999999
Q ss_pred cEEEEEeeccCCCCCCCcchhhhhhHHHHHHhhcCCCeE
Q 005544 157 LRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKT 195 (691)
Q Consensus 157 I~l~vi~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~ 195 (691)
|.+.+|+++. .|+..|..++....+.+
T Consensus 141 i~i~~vgig~------------~~~~~L~~IA~~~~~~~ 167 (186)
T cd01480 141 IKIFFVAVGS------------QNEEPLSRIACDGKSAL 167 (186)
T ss_pred CEEEEEecCc------------cchHHHHHHHcCCcchh
Confidence 9999999943 13466888888776653
No 21
>cd01467 vWA_BatA_type VWA BatA type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses. In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if
Probab=99.07 E-value=7.2e-09 Score=101.10 Aligned_cols=163 Identities=21% Similarity=0.237 Sum_probs=103.4
Q ss_pred EEEEEEecCCCccCC-------hhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCC
Q 005544 7 ALLLLLDVSPSMHSV-------LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVD 79 (691)
Q Consensus 7 a~vflIDvs~sM~~~-------l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~ 79 (691)
-++||||+|.||... +..|+.++..++. ..+.|+||||.|++.. .+..++.. +
T Consensus 4 ~vv~vlD~S~SM~~~~~~~~~r~~~a~~~~~~~~~----~~~~~~v~lv~f~~~~---------------~~~~~~~~-~ 63 (180)
T cd01467 4 DIMIALDVSGSMLAQDFVKPSRLEAAKEVLSDFID----RRENDRIGLVVFAGAA---------------FTQAPLTL-D 63 (180)
T ss_pred eEEEEEECCcccccccCCCCCHHHHHHHHHHHHHH----hCCCCeEEEEEEcCCe---------------eeccCCCc-c
Confidence 479999999999642 4556666665555 5689999999998642 12233322 2
Q ss_pred HH-HHHHhhcCCC--CCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcC
Q 005544 80 GH-LVQSLKHLPQ--GTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFG 156 (691)
Q Consensus 80 ~~-~l~~L~~l~~--~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~g 156 (691)
.. ..+.|..+.. .....++.+||..|++++... ....+.|||||||....+. ......++.+++.|
T Consensus 64 ~~~~~~~l~~l~~~~~~g~T~l~~al~~a~~~l~~~----~~~~~~iiliTDG~~~~g~-------~~~~~~~~~~~~~g 132 (180)
T cd01467 64 RESLKELLEDIKIGLAGQGTAIGDAIGLAIKRLKNS----EAKERVIVLLTDGENNAGE-------IDPATAAELAKNKG 132 (180)
T ss_pred HHHHHHHHHHhhhcccCCCCcHHHHHHHHHHHHHhc----CCCCCEEEEEeCCCCCCCC-------CCHHHHHHHHHHCC
Confidence 22 2233444431 122346788999999997642 1235789999999765331 12334556677899
Q ss_pred cEEEEEeeccCCCCCCCc-chhhhhhHHHHHHhhcCCCeEeehhhh
Q 005544 157 LRMKNIVVRASLSGEPHM-RVIIENDNLLNIFSKKSSAKTLFVDST 201 (691)
Q Consensus 157 I~l~vi~i~~~~~~~~~~-~~~~~ne~~l~~l~~~~~g~~~~~~~a 201 (691)
|.+.+|+++.+-. .... .....+...|+.++..++|+++.+.+.
T Consensus 133 i~i~~i~ig~~~~-~~~~~~~~~~~~~~l~~la~~tgG~~~~~~~~ 177 (180)
T cd01467 133 VRIYTIGVGKSGS-GPKPDGSTILDEDSLVEIADKTGGRIFRALDG 177 (180)
T ss_pred CEEEEEEecCCCC-CcCCCCcccCCHHHHHHHHHhcCCEEEEecCc
Confidence 9999999975210 0000 001234578999999999999887655
No 22
>cd01472 vWA_collagen von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form heterodimers while in vWF it forms homodimers and multimers. There are different interaction surfaces of this domain as seen by its complexes with collagen with either integrin or human vWFA. In integrins collagen binding occurs via the metal ion-dependent adhesion site (MIDAS) and involves three surface loops located on the upper surface of the molecule. In human vWFA, collagen binding is thought to occur on the bottom of the molecule and does not involve the vestigial MIDAS motif.
Probab=99.05 E-value=5.7e-09 Score=100.34 Aligned_cols=151 Identities=17% Similarity=0.174 Sum_probs=104.5
Q ss_pred EEEEEecCCCccC-ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCC-CC-HHHHH
Q 005544 8 LLLLLDVSPSMHS-VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKV-VD-GHLVQ 84 (691)
Q Consensus 8 ~vflIDvs~sM~~-~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~-~~-~~~l~ 84 (691)
+||+||+|.||.. .++.+++++..++.+....+..+++|||.|++.. + +..++.. .+ ....+
T Consensus 3 vv~vlD~SgSm~~~~~~~~k~~~~~~~~~l~~~~~~~~~giv~Fs~~~-------------~--~~~~~~~~~~~~~~~~ 67 (164)
T cd01472 3 IVFLVDGSESIGLSNFNLVKDFVKRVVERLDIGPDGVRVGVVQYSDDP-------------R--TEFYLNTYRSKDDVLE 67 (164)
T ss_pred EEEEEeCCCCCCHHHHHHHHHHHHHHHhhcccCCCCeEEEEEEEcCce-------------e--EEEecCCCCCHHHHHH
Confidence 7899999999987 5677888888888765555678999999999753 1 2344442 22 34566
Q ss_pred HhhcCCCCCCCCchhhHHHHHHHHHHHHh-ccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEEe
Q 005544 85 SLKHLPQGTCAGDFLDAIVVGVDMLIKKY-GETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIV 163 (691)
Q Consensus 85 ~L~~l~~~~~~gd~~daL~va~d~l~~~~-~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~l~vi~ 163 (691)
.|+.++...+..++.+||..|.+++.... .......+.|+|||||.++- .....+..+++.||.+.+|+
T Consensus 68 ~l~~l~~~~g~T~~~~al~~a~~~l~~~~~~~~~~~~~~iiliTDG~~~~----------~~~~~~~~l~~~gv~i~~ig 137 (164)
T cd01472 68 AVKNLRYIGGGTNTGKALKYVRENLFTEASGSREGVPKVLVVITDGKSQD----------DVEEPAVELKQAGIEVFAVG 137 (164)
T ss_pred HHHhCcCCCCCchHHHHHHHHHHHhCCcccCCCCCCCEEEEEEcCCCCCc----------hHHHHHHHHHHCCCEEEEEE
Confidence 67777642223478899999999875421 11223467799999996542 23345567888999999999
Q ss_pred eccCCCCCCCcchhhhhhHHHHHHhhcCCCeE
Q 005544 164 VRASLSGEPHMRVIIENDNLLNIFSKKSSAKT 195 (691)
Q Consensus 164 i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~ 195 (691)
++. .+...|+.++...+|.+
T Consensus 138 ~g~------------~~~~~L~~ia~~~~~~~ 157 (164)
T cd01472 138 VKN------------ADEEELKQIASDPKELY 157 (164)
T ss_pred CCc------------CCHHHHHHHHCCCchhe
Confidence 843 14678889988776643
No 23
>cd01474 vWA_ATR ATR (Anthrax Toxin Receptor): Anthrax toxin is a key virulence factor for Bacillus anthracis, the causative agent of anthrax. ATR is the cellular receptor for the anthrax protective antigen and facilitates entry of the toxin into cells. The VWA domain in ATR contains the toxin binding site and mediates interaction with protective antigen. The binding is mediated by divalent cations that binds to the MIDAS motif. These proteins are a family of vertebrate ECM receptors expressed by endothelial cells.
Probab=99.04 E-value=1.2e-08 Score=100.22 Aligned_cols=155 Identities=12% Similarity=0.106 Sum_probs=101.5
Q ss_pred CeEEEEEEecCCCccCChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCCHHHHH
Q 005544 5 REALLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHLVQ 84 (691)
Q Consensus 5 Kea~vflIDvs~sM~~~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~~~~l~ 84 (691)
+--++|+||.|.||......+.+.+..++.+. ..+.++||||.|+++. .++.|+........+
T Consensus 4 ~~Dvv~llD~SgSm~~~~~~~~~~~~~l~~~~--~~~~~rvglv~Fs~~~---------------~~~~~l~~~~~~~~~ 66 (185)
T cd01474 4 HFDLYFVLDKSGSVAANWIEIYDFVEQLVDRF--NSPGLRFSFITFSTRA---------------TKILPLTDDSSAIIK 66 (185)
T ss_pred ceeEEEEEeCcCchhhhHHHHHHHHHHHHHHc--CCCCcEEEEEEecCCc---------------eEEEeccccHHHHHH
Confidence 34589999999999976655666677777643 3577999999999753 134555444333333
Q ss_pred H---hhcCCCCCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEE
Q 005544 85 S---LKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKN 161 (691)
Q Consensus 85 ~---L~~l~~~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~l~v 161 (691)
. |..+..+ +...+.+||..|.+.+...........+.|||||||.+.-.. .......++.+++.||.+.+
T Consensus 67 ~l~~l~~~~~~-g~T~~~~aL~~a~~~l~~~~~~~r~~~~~villTDG~~~~~~------~~~~~~~a~~l~~~gv~i~~ 139 (185)
T cd01474 67 GLEVLKKVTPS-GQTYIHEGLENANEQIFNRNGGGRETVSVIIALTDGQLLLNG------HKYPEHEAKLSRKLGAIVYC 139 (185)
T ss_pred HHHHHhccCCC-CCCcHHHHHHHHHHHHHhhccCCCCCCeEEEEEcCCCcCCCC------CcchHHHHHHHHHcCCEEEE
Confidence 3 4444333 234678999999987754221112234889999999873111 01244557789999999999
Q ss_pred EeeccCCCCCCCcchhhhhhHHHHHHhhcCCCeE
Q 005544 162 IVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKT 195 (691)
Q Consensus 162 i~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~ 195 (691)
||++. .+...|+.++...++.+
T Consensus 140 vgv~~------------~~~~~L~~iA~~~~~~f 161 (185)
T cd01474 140 VGVTD------------FLKSQLINIADSKEYVF 161 (185)
T ss_pred Eeech------------hhHHHHHHHhCCCCeeE
Confidence 99821 24567888887665433
No 24
>cd01470 vWA_complement_factors Complement factors B and C2 are two critical proteases for complement activation. They both contain three CCP or Sushi domains, a trypsin-type serine protease domain and a single VWA domain with a conserved metal ion dependent adhesion site referred commonly as the MIDAS motif. Orthologues of these molecules are found from echinoderms to chordates. During complement activation, the CCP domains are cleaved off, resulting in the formation of an active protease that cleaves and activates complement C3. Complement C2 is in the classical pathway and complement B is in the alternative pathway. The interaction of C2 with C4 and of factor B with C3b are both dependent on Mg2+ binding sites within the VWA domains and the VWA domain of factor B has been shown to mediate the binding of C3. This is consistent with the common inferred function of VWA domains as magnesium-dependent protein interaction domains.
Probab=99.02 E-value=1.3e-08 Score=101.14 Aligned_cols=167 Identities=15% Similarity=0.152 Sum_probs=106.9
Q ss_pred EEEEEecCCCcc-CChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCC---C-HHH
Q 005544 8 LLLLLDVSPSMH-SVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV---D-GHL 82 (691)
Q Consensus 8 ~vflIDvs~sM~-~~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~---~-~~~ 82 (691)
++||||+|.||. ..++.++.++..++.+.-.....|++|||.|+++.. ++.|+..+ + ...
T Consensus 3 i~~vlD~SgSM~~~~~~~~k~~~~~l~~~l~~~~~~~~v~li~Fs~~~~---------------~~~~~~~~~~~~~~~~ 67 (198)
T cd01470 3 IYIALDASDSIGEEDFDEAKNAIKTLIEKISSYEVSPRYEIISYASDPK---------------EIVSIRDFNSNDADDV 67 (198)
T ss_pred EEEEEECCCCccHHHHHHHHHHHHHHHHHccccCCCceEEEEEecCCce---------------EEEecccCCCCCHHHH
Confidence 799999999997 467888888888887653445689999999999731 22344322 2 346
Q ss_pred HHHhhcCCCC---C-CCCchhhHHHHHHHHHHHHhcc-C---CcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHH---
Q 005544 83 VQSLKHLPQG---T-CAGDFLDAIVVGVDMLIKKYGE-T---YKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQ--- 151 (691)
Q Consensus 83 l~~L~~l~~~---~-~~gd~~daL~va~d~l~~~~~~-~---k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~--- 151 (691)
+..|..+... . +..++.+||-.+.+.+...... . ....+.|||||||.+..+. .....+..+.+.
T Consensus 68 ~~~l~~~~~~~~~~~ggT~~~~Al~~~~~~l~~~~~~~~~~~~~~~~~iillTDG~~~~g~----~~~~~~~~~~~~~~~ 143 (198)
T cd01470 68 IKRLEDFNYDDHGDKTGTNTAAALKKVYERMALEKVRNKEAFNETRHVIILFTDGKSNMGG----SPLPTVDKIKNLVYK 143 (198)
T ss_pred HHHHHhCCcccccCccchhHHHHHHHHHHHHHHHHhcCccchhhcceEEEEEcCCCcCCCC----ChhHHHHHHHHHHhc
Confidence 6777776421 1 1236778888887765321111 0 1235679999999876431 111112222221
Q ss_pred ------HhhcCcEEEEEeeccCCCCCCCcchhhhhhHHHHHHhhcCCC--eEeehhhhHHh
Q 005544 152 ------MVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSA--KTLFVDSTTSL 204 (691)
Q Consensus 152 ------L~~~gI~l~vi~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g--~~~~~~~a~~l 204 (691)
+++.+|.+.+||++.+ .+...|+.++..++| .++.+.+..++
T Consensus 144 ~~~~~~~~~~~v~i~~iGvG~~-----------~~~~~L~~iA~~~~g~~~~f~~~~~~~l 193 (198)
T cd01470 144 NNKSDNPREDYLDVYVFGVGDD-----------VNKEELNDLASKKDNERHFFKLKDYEDL 193 (198)
T ss_pred ccccccchhcceeEEEEecCcc-----------cCHHHHHHHhcCCCCCceEEEeCCHHHH
Confidence 2556899999999642 246889999999888 46777665443
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=99.01 E-value=8.6e-09 Score=103.07 Aligned_cols=162 Identities=12% Similarity=0.108 Sum_probs=105.2
Q ss_pred CeEEEEEEecCCCcc-------CChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEE----EEe
Q 005544 5 REALLLLLDVSPSMH-------SVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVK----VLQ 73 (691)
Q Consensus 5 Kea~vflIDvs~sM~-------~~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~----v~~ 73 (691)
.-.++||||+|.||. .+++.++.++..++.. ..+.|+||||.|++..+... .|.-+. ...
T Consensus 20 ~~~vv~vlD~SgSM~~~~~~~~~rl~~ak~a~~~~l~~---l~~~~~v~lv~F~~~~~~~~------~~~~~~p~~~~~~ 90 (206)
T cd01456 20 PPNVAIVLDNSGSMREVDGGGETRLDNAKAALDETANA---LPDGTRLGLWTFSGDGDNPL------DVRVLVPKGCLTA 90 (206)
T ss_pred CCcEEEEEeCCCCCcCCCCCcchHHHHHHHHHHHHHHh---CCCCceEEEEEecCCCCCCc------ccccccccccccc
Confidence 346899999999998 2477888888888874 36799999999999642110 121110 011
Q ss_pred ecCC---CCHH-HHHHhhcCC-CCCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHH
Q 005544 74 DIKV---VDGH-LVQSLKHLP-QGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTI 148 (691)
Q Consensus 74 ~l~~---~~~~-~l~~L~~l~-~~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i 148 (691)
++.. .+.. +.+.|..+. .+ +..++.+||..|.+++. . ...+.|||||||...... .....
T Consensus 91 ~~~~~~~~~~~~l~~~i~~i~~~~-G~T~l~~aL~~a~~~l~---~---~~~~~iillTDG~~~~~~--------~~~~~ 155 (206)
T cd01456 91 PVNGFPSAQRSALDAALNSLQTPT-GWTPLAAALAEAAAYVD---P---GRVNVVVLITDGEDTCGP--------DPCEV 155 (206)
T ss_pred ccCCCCcccHHHHHHHHHhhcCCC-CcChHHHHHHHHHHHhC---C---CCcceEEEEcCCCccCCC--------CHHHH
Confidence 1111 1233 344566665 32 23477889999988863 1 124899999999876431 11223
Q ss_pred HHHHhh-----cCcEEEEEeeccCCCCCCCcchhhhhhHHHHHHhhcCCCeE-eehhhh
Q 005544 149 ARQMVA-----FGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKT-LFVDST 201 (691)
Q Consensus 149 ~~~L~~-----~gI~l~vi~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~-~~~~~a 201 (691)
+..+.. .+|.+.+|+++.+ .+...|+.++..++|.+ +...++
T Consensus 156 ~~~~~~~~~~~~~i~i~~igiG~~-----------~~~~~l~~iA~~tgG~~~~~~~~~ 203 (206)
T cd01456 156 ARELAKRRTPAPPIKVNVIDFGGD-----------ADRAELEAIAEATGGTYAYNQSDL 203 (206)
T ss_pred HHHHHHhcCCCCCceEEEEEecCc-----------ccHHHHHHHHHhcCCeEecccccc
Confidence 333333 4999999999642 24588999999999998 766554
No 26
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=99.00 E-value=1.2e-08 Score=116.18 Aligned_cols=166 Identities=16% Similarity=0.181 Sum_probs=118.5
Q ss_pred CeEEEEEEecCCCcc-CChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCCHHHH
Q 005544 5 REALLLLLDVSPSMH-SVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHLV 83 (691)
Q Consensus 5 Kea~vflIDvs~sM~-~~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~~~~l 83 (691)
.-.++||||+|.||. ..|..++.++..|+.+. +++.|+||||.|+++.. .++.|....-....
T Consensus 401 ~~~vvfvvD~SGSM~~~rl~~aK~a~~~ll~~a--y~~rD~v~lI~F~g~~a--------------~~~lppT~~~~~~~ 464 (584)
T PRK13406 401 ETTTIFVVDASGSAALHRLAEAKGAVELLLAEA--YVRRDQVALVAFRGRGA--------------ELLLPPTRSLVRAK 464 (584)
T ss_pred CccEEEEEECCCCCcHhHHHHHHHHHHHHHHhh--cCCCCEEEEEEECCCce--------------eEEcCCCcCHHHHH
Confidence 357899999999995 46788899998888652 57899999999987632 13445444223355
Q ss_pred HHhhcCCCCCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCC---CCchhhHHHHHHHHhhcCcEEE
Q 005544 84 QSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDV---GTKEDQVSTIARQMVAFGLRMK 160 (691)
Q Consensus 84 ~~L~~l~~~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~---~~~~~~l~~i~~~L~~~gI~l~ 160 (691)
+.|..++.+. ...+.+||..|.+++.... .+...++|||||||..+.+.... .....+...++..+...||.+.
T Consensus 465 ~~L~~l~~gG-gTpL~~gL~~A~~~l~~~~--~~~~~~~iVLlTDG~~n~~~~~~~~~~~~~~~~~~~a~~~~~~gi~~~ 541 (584)
T PRK13406 465 RSLAGLPGGG-GTPLAAGLDAAAALALQVR--RKGMTPTVVLLTDGRANIARDGTAGRAQAEEDALAAARALRAAGLPAL 541 (584)
T ss_pred HHHhcCCCCC-CChHHHHHHHHHHHHHHhc--cCCCceEEEEEeCCCCCCCccccccccchhhHHHHHHHHHHhcCCeEE
Confidence 6677777653 3478999999999987632 12346899999999998752100 0111345667889999999998
Q ss_pred EEeeccCCCCCCCcchhhhhhHHHHHHhhcCCCeEeehhhh
Q 005544 161 NIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDST 201 (691)
Q Consensus 161 vi~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~~~~~~a 201 (691)
+|.++.. ....+..|++.++|+|+.+..+
T Consensus 542 vId~g~~------------~~~~~~~LA~~~gg~y~~l~~~ 570 (584)
T PRK13406 542 VIDTSPR------------PQPQARALAEAMGARYLPLPRA 570 (584)
T ss_pred EEecCCC------------CcHHHHHHHHhcCCeEEECCCC
Confidence 8877321 1256788999999999988765
No 27
>cd01482 vWA_collagen_alphaI-XII-like Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.
Probab=98.98 E-value=1.9e-08 Score=96.74 Aligned_cols=147 Identities=19% Similarity=0.223 Sum_probs=102.0
Q ss_pred EEEEEecCCCccC-ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCC-CCH-HHHH
Q 005544 8 LLLLLDVSPSMHS-VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKV-VDG-HLVQ 84 (691)
Q Consensus 8 ~vflIDvs~sM~~-~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~-~~~-~~l~ 84 (691)
++|+||.|.||.. .+..++..+..++.+.-++.++++||||.|+++.. +..++.. .+. .+++
T Consensus 3 v~~vlD~S~Sm~~~~~~~~k~~~~~l~~~~~~~~~~~rvgli~fs~~~~---------------~~~~l~~~~~~~~l~~ 67 (164)
T cd01482 3 IVFLVDGSWSIGRSNFNLVRSFLSSVVEAFEIGPDGVQVGLVQYSDDPR---------------TEFDLNAYTSKEDVLA 67 (164)
T ss_pred EEEEEeCCCCcChhhHHHHHHHHHHHHhheeeCCCceEEEEEEECCCee---------------EEEecCCCCCHHHHHH
Confidence 7999999999985 68888888888888755566899999999999731 1223321 222 4566
Q ss_pred HhhcCCCCCCCCchhhHHHHHHHHHHHH-hccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEEe
Q 005544 85 SLKHLPQGTCAGDFLDAIVVGVDMLIKK-YGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIV 163 (691)
Q Consensus 85 ~L~~l~~~~~~gd~~daL~va~d~l~~~-~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~l~vi~ 163 (691)
.|.++....+..++..||..+.+.+.+. .+.+....|.|+|||||.+. +.+..++..|++.||.+.+|+
T Consensus 68 ~l~~~~~~~g~T~~~~aL~~a~~~~~~~~~~~r~~~~k~iillTDG~~~----------~~~~~~a~~lk~~gi~i~~ig 137 (164)
T cd01482 68 AIKNLPYKGGNTRTGKALTHVREKNFTPDAGARPGVPKVVILITDGKSQ----------DDVELPARVLRNLGVNVFAVG 137 (164)
T ss_pred HHHhCcCCCCCChHHHHHHHHHHHhcccccCCCCCCCEEEEEEcCCCCC----------chHHHHHHHHHHCCCEEEEEe
Confidence 6777653222346788998887654331 12222356779999999753 245678899999999999999
Q ss_pred eccCCCCCCCcchhhhhhHHHHHHhhcC
Q 005544 164 VRASLSGEPHMRVIIENDNLLNIFSKKS 191 (691)
Q Consensus 164 i~~~~~~~~~~~~~~~ne~~l~~l~~~~ 191 (691)
++. .+...|..++...
T Consensus 138 ~g~------------~~~~~L~~ia~~~ 153 (164)
T cd01482 138 VKD------------ADESELKMIASKP 153 (164)
T ss_pred cCc------------CCHHHHHHHhCCC
Confidence 843 1346677887754
No 28
>TIGR03436 acidobact_VWFA VWFA-related Acidobacterial domain. Members of this family are bacterial domains that include a region related to the von Willebrand factor type A (VWFA) domain (pfam00092). These domains are restricted to, and have undergone a large paralogous family expansion in, the Acidobacteria, including Solibacter usitatus and Acidobacterium capsulatum ATCC 51196.
Probab=98.97 E-value=1.5e-08 Score=107.18 Aligned_cols=168 Identities=20% Similarity=0.232 Sum_probs=112.8
Q ss_pred eEEEEEEecCCCccCChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCCHHHHHH
Q 005544 6 EALLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHLVQS 85 (691)
Q Consensus 6 ea~vflIDvs~sM~~~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~~~~l~~ 85 (691)
=.++||||+|.||...+..+++++..++...+ ++.|+||||.|++.. .++.++..-...+.+.
T Consensus 54 ~~vvlvlD~SgSM~~~~~~a~~a~~~~l~~~l--~~~d~v~lv~f~~~~---------------~~~~~~t~~~~~l~~~ 116 (296)
T TIGR03436 54 LTVGLVIDTSGSMRNDLDRARAAAIRFLKTVL--RPNDRVFVVTFNTRL---------------RLLQDFTSDPRLLEAA 116 (296)
T ss_pred ceEEEEEECCCCchHHHHHHHHHHHHHHHhhC--CCCCEEEEEEeCCce---------------eEeecCCCCHHHHHHH
Confidence 36899999999999988889999998887532 689999999999742 1234444333345666
Q ss_pred hhcCCCC--------------CCCCchhhHHHHHH-HHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHH
Q 005544 86 LKHLPQG--------------TCAGDFLDAIVVGV-DMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIAR 150 (691)
Q Consensus 86 L~~l~~~--------------~~~gd~~daL~va~-d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~ 150 (691)
|.++... .+..++.+||..|. +++.+..+ .....|.|||||||.+... ...+..+++
T Consensus 117 l~~l~~~~~~~~~~~~~~~~~~g~T~l~~al~~aa~~~~~~~~~-~~p~rk~iIllTDG~~~~~-------~~~~~~~~~ 188 (296)
T TIGR03436 117 LNRLKPPLRTDYNSSGAFVRDGGGTALYDAITLAALEQLANALA-GIPGRKALIVISDGGDNRS-------RDTLERAID 188 (296)
T ss_pred HHhccCCCccccccccccccCCCcchhHHHHHHHHHHHHHHhhc-CCCCCeEEEEEecCCCcch-------HHHHHHHHH
Confidence 7776431 12236788886664 55544221 1124678999999976532 346778888
Q ss_pred HHhhcCcEEEEEeeccCCC-CCC-CcchhhhhhHHHHHHhhcCCCeEeeh
Q 005544 151 QMVAFGLRMKNIVVRASLS-GEP-HMRVIIENDNLLNIFSKKSSAKTLFV 198 (691)
Q Consensus 151 ~L~~~gI~l~vi~i~~~~~-~~~-~~~~~~~ne~~l~~l~~~~~g~~~~~ 198 (691)
.++..+|.+.+|+++.... +.. .......++..|+.++..++|+++..
T Consensus 189 ~~~~~~v~vy~I~~~~~~~~~~~~~~~~~~~~~~~L~~iA~~TGG~~~~~ 238 (296)
T TIGR03436 189 AAQRADVAIYSIDARGLRAPDLGAGAKAGLGGPEALERLAEETGGRAFYV 238 (296)
T ss_pred HHHHcCCEEEEeccCccccCCcccccccCCCcHHHHHHHHHHhCCeEecc
Confidence 9999999999999853100 000 00000124678999999999998765
No 29
>COG1240 ChlD Mg-chelatase subunit ChlD [Coenzyme metabolism]
Probab=98.95 E-value=3.6e-08 Score=98.26 Aligned_cols=166 Identities=19% Similarity=0.235 Sum_probs=122.0
Q ss_pred EEEEEEecCCCccCC--hhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCCHHHHH
Q 005544 7 ALLLLLDVSPSMHSV--LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHLVQ 84 (691)
Q Consensus 7 a~vflIDvs~sM~~~--l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~~~~l~ 84 (691)
-+||+||.|.||... +..|+-++..|+..= ++..|+||||.|+.++.. ++.|....-...-+
T Consensus 80 lvvfvVDASgSM~~~~Rm~aaKG~~~~lL~dA--Yq~RdkvavI~F~G~~A~--------------lll~pT~sv~~~~~ 143 (261)
T COG1240 80 LIVFVVDASGSMAARRRMAAAKGAALSLLRDA--YQRRDKVAVIAFRGEKAE--------------LLLPPTSSVELAER 143 (261)
T ss_pred cEEEEEeCcccchhHHHHHHHHHHHHHHHHHH--HHccceEEEEEecCCcce--------------EEeCCcccHHHHHH
Confidence 489999999999976 788899999888864 689999999999986532 33444333334567
Q ss_pred HhhcCCCCCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEEee
Q 005544 85 SLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIVV 164 (691)
Q Consensus 85 ~L~~l~~~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~l~vi~i 164 (691)
.|+.++.|.. .++.+||..|.+++.+.....--..-.+|+||||..+...+ ......+...+..+...|+.+.||..
T Consensus 144 ~L~~l~~GG~-TPL~~aL~~a~ev~~r~~r~~p~~~~~~vviTDGr~n~~~~--~~~~~e~~~~a~~~~~~g~~~lvid~ 220 (261)
T COG1240 144 ALERLPTGGK-TPLADALRQAYEVLAREKRRGPDRRPVMVVITDGRANVPIP--LGPKAETLEAASKLRLRGIQLLVIDT 220 (261)
T ss_pred HHHhCCCCCC-CchHHHHHHHHHHHHHhhccCCCcceEEEEEeCCccCCCCC--CchHHHHHHHHHHHhhcCCcEEEEec
Confidence 7888988653 47899999999998874211113567799999999765532 11245677888999999999998876
Q ss_pred ccCCCCCCCcchhhhhhHHHHHHhhcCCCeEeehhhh
Q 005544 165 RASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDST 201 (691)
Q Consensus 165 ~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~~~~~~a 201 (691)
...+ ..-.+...|+...+|.++.+++.
T Consensus 221 e~~~----------~~~g~~~~iA~~~Gg~~~~L~~l 247 (261)
T COG1240 221 EGSE----------VRLGLAEEIARASGGEYYHLDDL 247 (261)
T ss_pred CCcc----------ccccHHHHHHHHhCCeEEecccc
Confidence 2210 11256677888899999988876
No 30
>cd01471 vWA_micronemal_protein Micronemal proteins: The Toxoplasma lytic cycle begins when the parasite actively invades a target cell. In association with invasion, T. gondii sequentially discharges three sets of secretory organelles beginning with the micronemes, which contain adhesive proteins involved in parasite attachment to a host cell. Deployed as protein complexes, several micronemal proteins possess vertebrate-derived adhesive sequences that function in binding receptors. The VWA domain likely mediates the protein-protein interactions of these with their interacting partners.
Probab=98.94 E-value=2.1e-08 Score=98.49 Aligned_cols=148 Identities=18% Similarity=0.155 Sum_probs=100.5
Q ss_pred EEEEEecCCCccCC--hhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCC---CHH-
Q 005544 8 LLLLLDVSPSMHSV--LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV---DGH- 81 (691)
Q Consensus 8 ~vflIDvs~sM~~~--l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~---~~~- 81 (691)
++|+||.|.||... +..++..+..++++.-+...+.+||||.|++... +..++... +..
T Consensus 3 v~~vlD~SgSm~~~~~~~~~k~~~~~~~~~~~~~~~~~~vglv~Fs~~~~---------------~~~~l~~~~~~~~~~ 67 (186)
T cd01471 3 LYLLVDGSGSIGYSNWVTHVVPFLHTFVQNLNISPDEINLYLVTFSTNAK---------------ELIRLSSPNSTNKDL 67 (186)
T ss_pred EEEEEeCCCCccchhhHHHHHHHHHHHHHhcccCCCceEEEEEEecCCce---------------EEEECCCccccchHH
Confidence 78999999999965 6788888888888654556778999999997531 23343322 222
Q ss_pred ---HHHHhhcCCCCCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcE
Q 005544 82 ---LVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLR 158 (691)
Q Consensus 82 ---~l~~L~~l~~~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~ 158 (691)
.++.|.......+..++.+||..|.+.+....+.+....+.|||||||..... ......++.+++.||.
T Consensus 68 ~~~~i~~l~~~~~~~G~T~l~~aL~~a~~~l~~~~~~r~~~~~~villTDG~~~~~--------~~~~~~a~~l~~~gv~ 139 (186)
T cd01471 68 ALNAIRALLSLYYPNGSTNTTSALLVVEKHLFDTRGNRENAPQLVIIMTDGIPDSK--------FRTLKEARKLRERGVI 139 (186)
T ss_pred HHHHHHHHHhCcCCCCCccHHHHHHHHHHHhhccCCCcccCceEEEEEccCCCCCC--------cchhHHHHHHHHCCCE
Confidence 34555544332334578999999998876521122345688999999975322 1233567889999999
Q ss_pred EEEEeeccCCCCCCCcchhhhhhHHHHHHhh
Q 005544 159 MKNIVVRASLSGEPHMRVIIENDNLLNIFSK 189 (691)
Q Consensus 159 l~vi~i~~~~~~~~~~~~~~~ne~~l~~l~~ 189 (691)
+.+|++|.+ .|...|+.++.
T Consensus 140 v~~igiG~~-----------~d~~~l~~ia~ 159 (186)
T cd01471 140 IAVLGVGQG-----------VNHEENRSLVG 159 (186)
T ss_pred EEEEEeehh-----------hCHHHHHHhcC
Confidence 999999642 23466777665
No 31
>cd01476 VWA_integrin_invertebrates VWA_integrin (invertebrates): Integrins are a family of cell surface receptors that have diverse functions in cell-cell and cell-extracellular matrix interactions. Because of their involvement in many biologically important adhesion processes, integrins are conserved across a wide range of multicellular animals. Integrins from invertebrates have been identified from six phyla. There are no data to date to suggest any immunological functions for the invertebrate integrins. The members of this sub-group have the conserved MIDAS motif that is charateristic of this domain suggesting the involvement of the integrins in the recognition and binding of multi-ligands.
Probab=98.94 E-value=3.5e-08 Score=94.66 Aligned_cols=152 Identities=18% Similarity=0.147 Sum_probs=101.7
Q ss_pred EEEEEecCCCccCChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCC-CH-HHHHH
Q 005544 8 LLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV-DG-HLVQS 85 (691)
Q Consensus 8 ~vflIDvs~sM~~~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~-~~-~~l~~ 85 (691)
++|+||+|.||...++.+++.+..++.+.....+.++||||.|+++. +..+..++... +. ..++.
T Consensus 3 v~~llD~S~Sm~~~~~~~~~~~~~~~~~l~~~~~~~~v~lv~f~~~~-------------~~~~~~~l~~~~~~~~l~~~ 69 (163)
T cd01476 3 LLFVLDSSGSVRGKFEKYKKYIERIVEGLEIGPTATRVALITYSGRG-------------RQRVRFNLPKHNDGEELLEK 69 (163)
T ss_pred EEEEEeCCcchhhhHHHHHHHHHHHHHhcCCCCCCcEEEEEEEcCCC-------------ceEEEecCCCCCCHHHHHHH
Confidence 68999999999987777888888888766566779999999998852 12233444332 22 46667
Q ss_pred hhcCCCCCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhh-cCcEEEEEee
Q 005544 86 LKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVA-FGLRMKNIVV 164 (691)
Q Consensus 86 L~~l~~~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~-~gI~l~vi~i 164 (691)
|.++........+.+||..|.+++.+..+.+....+.|+|+|||.+.. .....++.|+. .||.+..|++
T Consensus 70 i~~l~~~gg~T~l~~aL~~a~~~l~~~~~~r~~~~~~villTDG~~~~----------~~~~~~~~l~~~~~v~v~~vg~ 139 (163)
T cd01476 70 VDNLRFIGGTTATGAAIEVALQQLDPSEGRREGIPKVVVVLTDGRSHD----------DPEKQARILRAVPNIETFAVGT 139 (163)
T ss_pred HHhCccCCCCccHHHHHHHHHHHhccccCCCCCCCeEEEEECCCCCCC----------chHHHHHHHhhcCCCEEEEEEC
Confidence 777753222347789999999987532222223457899999997642 13345667777 8999988888
Q ss_pred ccCCCCCCCcchhhhhhHHHHHHhhcC
Q 005544 165 RASLSGEPHMRVIIENDNLLNIFSKKS 191 (691)
Q Consensus 165 ~~~~~~~~~~~~~~~ne~~l~~l~~~~ 191 (691)
+.. ...|...|..++...
T Consensus 140 g~~---------~~~~~~~L~~ia~~~ 157 (163)
T cd01476 140 GDP---------GTVDTEELHSITGNE 157 (163)
T ss_pred CCc---------cccCHHHHHHHhCCC
Confidence 541 012456677765543
No 32
>cd01469 vWA_integrins_alpha_subunit Integrins are a class of adhesion receptors that link the extracellular matrix to the cytoskeleton and cooperate with growth factor receptors to promote celll survival, cell cycle progression and cell migration. Integrins consist of an alpha and a beta sub-unit. Each sub-unit has a large extracellular portion, a single transmembrane segment and a short cytoplasmic domain. The N-terminal domains of the alpha and beta subunits associate to form the integrin headpiece, which contains the ligand binding site, whereas the C-terminal segments traverse the plasma membrane and mediate interaction with the cytoskeleton and with signalling proteins.The VWA domains present in the alpha subunits of integrins seem to be a chordate specific radiation of the gene family being found only in vertebrates. They mediate protein-protein interactions.
Probab=98.93 E-value=4.1e-08 Score=95.71 Aligned_cols=164 Identities=18% Similarity=0.149 Sum_probs=111.8
Q ss_pred EEEEEecCCCccC-ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCC--CHHHHH
Q 005544 8 LLLLLDVSPSMHS-VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV--DGHLVQ 84 (691)
Q Consensus 8 ~vflIDvs~sM~~-~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~--~~~~l~ 84 (691)
++|+||.|.||.. .++.++..+..++.+.-++..+++||||.|++..+ +..++... ..+.++
T Consensus 3 i~fvlD~S~S~~~~~f~~~k~fi~~~i~~l~~~~~~~rvgvv~fs~~~~---------------~~~~l~~~~~~~~~~~ 67 (177)
T cd01469 3 IVFVLDGSGSIYPDDFQKVKNFLSTVMKKLDIGPTKTQFGLVQYSESFR---------------TEFTLNEYRTKEEPLS 67 (177)
T ss_pred EEEEEeCCCCCCHHHHHHHHHHHHHHHHHcCcCCCCcEEEEEEECCcee---------------EEEecCccCCHHHHHH
Confidence 6899999999986 58888999999998877777899999999998631 12233211 124556
Q ss_pred HhhcCCCCCCCCchhhHHHHHHHHHHHH-hccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEEe
Q 005544 85 SLKHLPQGTCAGDFLDAIVVGVDMLIKK-YGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIV 163 (691)
Q Consensus 85 ~L~~l~~~~~~gd~~daL~va~d~l~~~-~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~l~vi~ 163 (691)
.++.+....+.....+||..|.+++... .+.+....|.+||||||.+.-+. .....++.+++.||.+.+||
T Consensus 68 ~i~~~~~~~g~T~~~~AL~~a~~~l~~~~~g~R~~~~kv~illTDG~~~~~~--------~~~~~~~~~k~~gv~v~~Vg 139 (177)
T cd01469 68 LVKHISQLLGLTNTATAIQYVVTELFSESNGARKDATKVLVVITDGESHDDP--------LLKDVIPQAEREGIIRYAIG 139 (177)
T ss_pred HHHhCccCCCCccHHHHHHHHHHHhcCcccCCCCCCCeEEEEEeCCCCCCcc--------ccHHHHHHHHHCCcEEEEEE
Confidence 6666643222357789999999886431 12233457789999999886331 12556778999999999999
Q ss_pred eccCCCCCCCcchhhhhhHHHHHHhhcCCC-eEeehhhh
Q 005544 164 VRASLSGEPHMRVIIENDNLLNIFSKKSSA-KTLFVDST 201 (691)
Q Consensus 164 i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g-~~~~~~~a 201 (691)
++..+.. ..+...|+.++....+ .++.+.+.
T Consensus 140 vg~~~~~-------~~~~~~L~~ias~p~~~h~f~~~~~ 171 (177)
T cd01469 140 VGGHFQR-------ENSREELKTIASKPPEEHFFNVTDF 171 (177)
T ss_pred ecccccc-------cccHHHHHHHhcCCcHHhEEEecCH
Confidence 9653211 1234677888876543 45655554
No 33
>PF13519 VWA_2: von Willebrand factor type A domain; PDB: 3IBS_B 3RAG_B 2X5N_A.
Probab=98.93 E-value=6.2e-09 Score=99.94 Aligned_cols=147 Identities=18% Similarity=0.300 Sum_probs=103.2
Q ss_pred EEEEEecCCCccCC------hhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCCHH
Q 005544 8 LLLLLDVSPSMHSV------LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGH 81 (691)
Q Consensus 8 ~vflIDvs~sM~~~------l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~~~ 81 (691)
+|||||.|.||... +..++..+..++.. .+.|+|||+.|+... .+..++. .+..
T Consensus 2 vv~v~D~SgSM~~~~~~~~~~~~~~~~~~~~~~~----~~~~~v~l~~f~~~~---------------~~~~~~t-~~~~ 61 (172)
T PF13519_consen 2 VVFVLDNSGSMNGYDGNRTRIDQAKDALNELLAN----LPGDRVGLVSFSDSS---------------RTLSPLT-SDKD 61 (172)
T ss_dssp EEEEEE-SGGGGTTTSSS-HHHHHHHHHHHHHHH----HTTSEEEEEEESTSC---------------EEEEEEE-SSHH
T ss_pred EEEEEECCcccCCCCCCCcHHHHHHHHHHHHHHH----CCCCEEEEEEecccc---------------ccccccc-ccHH
Confidence 79999999999976 67788888888884 478999999999842 1344554 3444
Q ss_pred -HHHHhhcCCC---CCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCc
Q 005544 82 -LVQSLKHLPQ---GTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGL 157 (691)
Q Consensus 82 -~l~~L~~l~~---~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI 157 (691)
....|.++.. .....++.+||..|.+++... ....+.|||||||... . .....++.++..||
T Consensus 62 ~~~~~l~~~~~~~~~~~~t~~~~al~~a~~~~~~~----~~~~~~iv~iTDG~~~-~---------~~~~~~~~~~~~~i 127 (172)
T PF13519_consen 62 ELKNALNKLSPQGMPGGGTNLYDALQEAAKMLASS----DNRRRAIVLITDGEDN-S---------SDIEAAKALKQQGI 127 (172)
T ss_dssp HHHHHHHTHHHHG--SSS--HHHHHHHHHHHHHC-----SSEEEEEEEEES-TTH-C---------HHHHHHHHHHCTTE
T ss_pred HHHHHhhcccccccCccCCcHHHHHHHHHHHHHhC----CCCceEEEEecCCCCC-c---------chhHHHHHHHHcCC
Confidence 4445555532 133457889999999997541 2457899999998553 1 23358889999999
Q ss_pred EEEEEeeccCCCCCCCcchhhhhhHHHHHHhhcCCCeEeeh
Q 005544 158 RMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFV 198 (691)
Q Consensus 158 ~l~vi~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~~~~ 198 (691)
.+.+|+++.+. . ....|+.++..++|.++.+
T Consensus 128 ~i~~v~~~~~~----~------~~~~l~~la~~tgG~~~~~ 158 (172)
T PF13519_consen 128 TIYTVGIGSDS----D------ANEFLQRLAEATGGRYFHV 158 (172)
T ss_dssp EEEEEEES-TT-----------EHHHHHHHHHHTEEEEEEE
T ss_pred eEEEEEECCCc----c------HHHHHHHHHHhcCCEEEEe
Confidence 99999995421 1 1368899999999999887
No 34
>cd01450 vWFA_subfamily_ECM Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A
Probab=98.91 E-value=4.4e-08 Score=93.09 Aligned_cols=149 Identities=16% Similarity=0.190 Sum_probs=105.1
Q ss_pred EEEEEecCCCccC-ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCC-C-HHHHH
Q 005544 8 LLLLLDVSPSMHS-VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV-D-GHLVQ 84 (691)
Q Consensus 8 ~vflIDvs~sM~~-~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~-~-~~~l~ 84 (691)
++|+||+|.||.. .+..+...+..++.......+.+++||+.|++... ...++... + ....+
T Consensus 3 i~~llD~S~Sm~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~f~~~~~---------------~~~~~~~~~~~~~~~~ 67 (161)
T cd01450 3 IVFLLDGSESVGPENFEKVKDFIEKLVEKLDIGPDKTRVGLVQYSDDVR---------------VEFSLNDYKSKDDLLK 67 (161)
T ss_pred EEEEEeCCCCcCHHHHHHHHHHHHHHHHheeeCCCceEEEEEEEcCCce---------------EEEECCCCCCHHHHHH
Confidence 6899999999997 57778888888887665566899999999998521 12233222 2 34566
Q ss_pred HhhcCCCCC-CCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEEe
Q 005544 85 SLKHLPQGT-CAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIV 163 (691)
Q Consensus 85 ~L~~l~~~~-~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~l~vi~ 163 (691)
.|..+.... ...++.+||..|.+++.+.........+.|||||||..... ......++.+++.||.+.+|+
T Consensus 68 ~i~~~~~~~~~~t~~~~al~~a~~~~~~~~~~~~~~~~~iiliTDG~~~~~--------~~~~~~~~~~~~~~v~v~~i~ 139 (161)
T cd01450 68 AVKNLKYLGGGGTNTGKALQYALEQLFSESNARENVPKVIIVLTDGRSDDG--------GDPKEAAAKLKDEGIKVFVVG 139 (161)
T ss_pred HHHhcccCCCCCccHHHHHHHHHHHhcccccccCCCCeEEEEECCCCCCCC--------cchHHHHHHHHHCCCEEEEEe
Confidence 676664322 24578999999999886532112245678999999976532 157788999999999999999
Q ss_pred eccCCCCCCCcchhhhhhHHHHHHhhcC
Q 005544 164 VRASLSGEPHMRVIIENDNLLNIFSKKS 191 (691)
Q Consensus 164 i~~~~~~~~~~~~~~~ne~~l~~l~~~~ 191 (691)
++. .+...|..++..+
T Consensus 140 ~g~------------~~~~~l~~la~~~ 155 (161)
T cd01450 140 VGP------------ADEEELREIASCP 155 (161)
T ss_pred ccc------------cCHHHHHHHhCCC
Confidence 843 1346777777655
No 35
>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=98.89 E-value=5.7e-08 Score=95.85 Aligned_cols=163 Identities=17% Similarity=0.245 Sum_probs=102.2
Q ss_pred CeEEEEEEecCCCccC-ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCc-cccccCCCcCcEEEEeecCCCCH-H
Q 005544 5 REALLLLLDVSPSMHS-VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETEN-ELTKEVGGYEHVKVLQDIKVVDG-H 81 (691)
Q Consensus 5 Kea~vflIDvs~sM~~-~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n-~l~~e~~~y~nI~v~~~l~~~~~-~ 81 (691)
.--++||||+|.||.. .++.++.++..++.+ ..+.|+||||.|+++.+.- +. . ... +.....-+. .
T Consensus 13 p~~vv~llD~SgSM~~~~l~~ak~~~~~ll~~---l~~~d~v~lv~F~~~~~~~~~~------~-~~~-~~~~~~~~~~~ 81 (190)
T cd01463 13 PKDIVILLDVSGSMTGQRLHLAKQTVSSILDT---LSDNDFFNIITFSNEVNPVVPC------F-NDT-LVQATTSNKKV 81 (190)
T ss_pred CceEEEEEECCCCCCcHHHHHHHHHHHHHHHh---CCCCCEEEEEEeCCCeeEEeee------c-ccc-eEecCHHHHHH
Confidence 3468999999999974 577888888888763 3678999999999974210 00 0 000 000111122 2
Q ss_pred HHHHhhcCCCCCCCCchhhHHHHHHHHHHHHh-----ccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHh---
Q 005544 82 LVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKY-----GETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMV--- 153 (691)
Q Consensus 82 ~l~~L~~l~~~~~~gd~~daL~va~d~l~~~~-----~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~--- 153 (691)
.+..|..+..+. ..++..||..|++++.... .......+.|||||||..... . .+...++
T Consensus 82 ~~~~l~~l~~~G-~T~~~~al~~a~~~l~~~~~~~~~~~~~~~~~~iillTDG~~~~~--------~---~~~~~~~~~~ 149 (190)
T cd01463 82 LKEALDMLEAKG-IANYTKALEFAFSLLLKNLQSNHSGSRSQCNQAIMLITDGVPENY--------K---EIFDKYNWDK 149 (190)
T ss_pred HHHHHhhCCCCC-cchHHHHHHHHHHHHHHhhhcccccccCCceeEEEEEeCCCCCcH--------h---HHHHHhcccc
Confidence 444566665432 3477889999999876511 011133578999999987532 1 1222222
Q ss_pred --hcCcEEEEEeeccCCCCCCCcchhhhhhHHHHHHhhcCCCeEeehhh
Q 005544 154 --AFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDS 200 (691)
Q Consensus 154 --~~gI~l~vi~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~~~~~~ 200 (691)
+.+|.+.+|++|.+. .|...|+.++..++|.++.+.+
T Consensus 150 ~~~~~v~i~tigiG~~~----------~d~~~L~~lA~~~~G~~~~i~~ 188 (190)
T cd01463 150 NSEIPVRVFTYLIGREV----------TDRREIQWMACENKGYYSHIQS 188 (190)
T ss_pred cCCCcEEEEEEecCCcc----------ccchHHHHHHhhcCCeEEEccc
Confidence 236888889885410 1357899999999999887654
No 36
>cd01473 vWA_CTRP CTRP for CS protein-TRAP-related protein: Adhesion of Plasmodium to host cells is an important phenomenon in parasite invasion and in malaria associated pathology.CTRP encodes a protein containing a putative signal sequence followed by a long extracellular region of 1990 amino acids, a transmembrane domain, and a short cytoplasmic segment. The extracellular region of CTRP contains two separated adhesive domains. The first domain contains six 210-amino acid-long homologous VWA domain repeats. The second domain contains seven repeats of 87-60 amino acids in length, which share similarities with the thrombospondin type 1 domain found in a variety of adhesive molecules. Finally, CTRP also contains consensus motifs found in the superfamily of haematopoietin receptors. The VWA domains in these proteins likely mediate protein-protein interactions.
Probab=98.88 E-value=2.3e-08 Score=98.76 Aligned_cols=138 Identities=20% Similarity=0.225 Sum_probs=98.1
Q ss_pred EEEEEecCCCccCC-hh-HHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCC---C-HH
Q 005544 8 LLLLLDVSPSMHSV-LP-DVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV---D-GH 81 (691)
Q Consensus 8 ~vflIDvs~sM~~~-l~-~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~---~-~~ 81 (691)
++|+||.|.||... +. .++..+..++.+-.++..+.+||||.|++... +..|+... + .+
T Consensus 3 i~fllD~S~Si~~~~f~~~~~~f~~~lv~~l~i~~~~~rvgvv~fs~~~~---------------~~~~~~~~~~~~~~~ 67 (192)
T cd01473 3 LTLILDESASIGYSNWRKDVIPFTEKIINNLNISKDKVHVGILLFAEKNR---------------DVVPFSDEERYDKNE 67 (192)
T ss_pred EEEEEeCCCcccHHHHHHHHHHHHHHHHHhCccCCCccEEEEEEecCCce---------------eEEecCcccccCHHH
Confidence 78999999999875 65 47888999999888889999999999998641 23344332 2 23
Q ss_pred HHHHhhcCCCC---CCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcE
Q 005544 82 LVQSLKHLPQG---TCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLR 158 (691)
Q Consensus 82 ~l~~L~~l~~~---~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~ 158 (691)
.++.+.++... .+.....+||-.|.+.+...-+.+....|-+||||||.+.-.. ...+...++.|++.||.
T Consensus 68 l~~~i~~l~~~~~~~g~T~~~~AL~~a~~~~~~~~~~r~~~~kv~IllTDG~s~~~~------~~~~~~~a~~lk~~gV~ 141 (192)
T cd01473 68 LLKKINDLKNSYRSGGETYIVEALKYGLKNYTKHGNRRKDAPKVTMLFTDGNDTSAS------KKELQDISLLYKEENVK 141 (192)
T ss_pred HHHHHHHHHhccCCCCcCcHHHHHHHHHHHhccCCCCcccCCeEEEEEecCCCCCcc------hhhHHHHHHHHHHCCCE
Confidence 55556555321 1233568899988887654211122236789999999886421 23577889999999999
Q ss_pred EEEEeecc
Q 005544 159 MKNIVVRA 166 (691)
Q Consensus 159 l~vi~i~~ 166 (691)
+.+||+|.
T Consensus 142 i~~vGiG~ 149 (192)
T cd01473 142 LLVVGVGA 149 (192)
T ss_pred EEEEEecc
Confidence 99999964
No 37
>PF03730 Ku_C: Ku70/Ku80 C-terminal arm; InterPro: IPR005160 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 C-terminal arm. This alpha helical region embraces the beta-barrel domain IPR006164 from INTERPRO of the opposite subunit [].; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0006303 double-strand break repair via nonhomologous end joining; PDB: 1JEY_B 1JEQ_B 1RW2_A 3RZ9_B 3RZX_B.
Probab=98.88 E-value=8.1e-10 Score=96.23 Aligned_cols=65 Identities=29% Similarity=0.511 Sum_probs=46.0
Q ss_pred CCCCCCCCCchhHHHHHHHHHhhcCCCCCCCCCchhhhhhcCCCHHHHHHHHHHHHHHHhhcCCccC
Q 005544 450 ILQPELTPNPALERFYHHLELKSEHQDAAPPPLDDSLKKITEPDPTLLAESQSAIDAFCGQFVIKEN 516 (691)
Q Consensus 450 ~~~p~~~~NP~lqr~~~~l~~~al~~~~~~p~~~~~l~~~~~p~~~~~~~~~~~le~~k~~f~~~~~ 516 (691)
.|+|+.|+||+|||||++|+++||+++.|+|+.|.++.++..++..+ +++..|++|+++|.+...
T Consensus 4 ~y~P~~~~NP~LQ~hY~~L~a~AL~~d~p~~~~D~t~p~~~~~~~~~--~~~~~i~~~k~~~~~~~~ 68 (96)
T PF03730_consen 4 SYDPDKFPNPSLQRHYKCLQALALDEDEPEPPEDQTLPDYEEIDKEL--RVGEKIEEFKELFYLEDY 68 (96)
T ss_dssp S--CCCS--HHHHHHHHHHHHHHCTTTS------CCCHHHHCHHHHH--HHCCHHHHHHHHCS-CC-
T ss_pred CCCcCCcCCchHHHHHHHHHHHHcCCCCCCCcccccchhhhccCHHH--HHHHHHHHHHHHhchhhh
Confidence 39999999999999999999999999999999998888887776533 466779999999998776
No 38
>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. Unlike subunit I (TIGR02030), this subunit is not found in archaea.
Probab=98.87 E-value=6.5e-08 Score=111.18 Aligned_cols=165 Identities=16% Similarity=0.239 Sum_probs=115.7
Q ss_pred EEEEEEecCCCccC-ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCCHH-HHH
Q 005544 7 ALLLLLDVSPSMHS-VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGH-LVQ 84 (691)
Q Consensus 7 a~vflIDvs~sM~~-~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~~~-~l~ 84 (691)
.++|+||+|.||.. .+..|+.++..++.. .+.+.|+||||.|++.... ++.+.. .+.. ..+
T Consensus 409 ~v~fvvD~SGSM~~~rl~~aK~av~~Ll~~--~~~~~D~v~Li~F~~~~a~--------------~~lp~t-~~~~~~~~ 471 (589)
T TIGR02031 409 LLIFVVDASGSAAVARMSEAKGAVELLLGE--AYVHRDQVSLIAFRGTAAE--------------VLLPPS-RSVEQAKR 471 (589)
T ss_pred eEEEEEECCCCCChHHHHHHHHHHHHHHHh--hccCCCEEEEEEECCCCce--------------EECCCC-CCHHHHHH
Confidence 37899999999964 578888888888763 2468899999999875311 223332 2333 345
Q ss_pred HhhcCCCCCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCC--C------CchhhHHHHHHHHhhcC
Q 005544 85 SLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDV--G------TKEDQVSTIARQMVAFG 156 (691)
Q Consensus 85 ~L~~l~~~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~--~------~~~~~l~~i~~~L~~~g 156 (691)
.|..++.+. ..++.+||..|.+++.+. . .+...++|||||||..++..... + ...+.+..++..+++.|
T Consensus 472 ~L~~l~~gG-gTpL~~gL~~A~~~~~~~-~-~~~~~~~ivllTDG~~nv~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~g 548 (589)
T TIGR02031 472 RLDVLPGGG-GTPLAAGLAAAFQTALQA-R-SSGGTPTIVLITDGRGNIPLDGDPESIKADREQAAEEALALARKIREAG 548 (589)
T ss_pred HHhcCCCCC-CCcHHHHHHHHHHHHHHh-c-ccCCceEEEEECCCCCCCCCCcccccccccchhHHHHHHHHHHHHHhcC
Confidence 677776543 347889999999998753 2 22446789999999988752100 0 11245567789999999
Q ss_pred cEEEEEeeccCCCCCCCcchhhhhhHHHHHHhhcCCCeEeehhhh
Q 005544 157 LRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDST 201 (691)
Q Consensus 157 I~l~vi~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~~~~~~a 201 (691)
|.+.+|+++..| ....++..+++..+|.|+.+.++
T Consensus 549 i~~~vid~~~~~----------~~~~~~~~lA~~~~g~y~~l~~~ 583 (589)
T TIGR02031 549 MPALVIDTAMRF----------VSTGFAQKLARKMGAHYIYLPNA 583 (589)
T ss_pred CeEEEEeCCCCC----------ccchHHHHHHHhcCCcEEeCCCC
Confidence 999999884321 11357889999999999988765
No 39
>cd01461 vWA_interalpha_trypsin_inhibitor vWA_interalpha trypsin inhibitor (ITI): ITI is a glycoprotein composed of three polypeptides- two heavy chains and one light chain (bikunin). Bikunin confers the protease-inhibitor function while the heavy chains are involved in rendering stability to the extracellular matrix by binding to hyaluronic acid. The heavy chains carry the VWA domain with a conserved MIDAS motif. Although the exact role of the VWA domains remains unknown, it has been speculated to be involved in mediating protein-protein interactions with the components of the extracellular matrix.
Probab=98.87 E-value=1.1e-07 Score=91.59 Aligned_cols=162 Identities=14% Similarity=0.175 Sum_probs=106.6
Q ss_pred EEEEEEecCCCccCC-hhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCC-HHHHH
Q 005544 7 ALLLLLDVSPSMHSV-LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVD-GHLVQ 84 (691)
Q Consensus 7 a~vflIDvs~sM~~~-l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~-~~~l~ 84 (691)
-++|+||+|+||... ++.+..++..++.. ..+.|.++|+.|+++.... +.. ..+....+ ...+.
T Consensus 4 ~v~~vlD~S~SM~~~~~~~~~~al~~~l~~---l~~~~~~~l~~Fs~~~~~~--------~~~---~~~~~~~~~~~~~~ 69 (171)
T cd01461 4 EVVFVIDTSGSMSGTKIEQTKEALLTALKD---LPPGDYFNIIGFSDTVEEF--------SPS---SVSATAENVAAAIE 69 (171)
T ss_pred eEEEEEECCCCCCChhHHHHHHHHHHHHHh---CCCCCEEEEEEeCCCceee--------cCc---ceeCCHHHHHHHHH
Confidence 478999999999754 67777777777663 3467899999999863110 000 00111111 12345
Q ss_pred HhhcCCCCCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEEee
Q 005544 85 SLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIVV 164 (691)
Q Consensus 85 ~L~~l~~~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~l~vi~i 164 (691)
.|..+..+. ..++..||-.|.+.+.. .....+.||+||||.... ...+...++.+.+.+|.+.+|++
T Consensus 70 ~l~~~~~~g-~T~l~~al~~a~~~l~~----~~~~~~~iillTDG~~~~--------~~~~~~~~~~~~~~~i~i~~i~~ 136 (171)
T cd01461 70 YVNRLQALG-GTNMNDALEAALELLNS----SPGSVPQIILLTDGEVTN--------ESQILKNVREALSGRIRLFTFGI 136 (171)
T ss_pred HHHhcCCCC-CcCHHHHHHHHHHhhcc----CCCCccEEEEEeCCCCCC--------HHHHHHHHHHhcCCCceEEEEEe
Confidence 555665432 34788899888888643 123468999999998421 13455556666667999999999
Q ss_pred ccCCCCCCCcchhhhhhHHHHHHhhcCCCeEeehhhhHHhhc
Q 005544 165 RASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDSTTSLRG 206 (691)
Q Consensus 165 ~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~~~~~~a~~ll~ 206 (691)
+.. .+..+|+.++..++|.+..+.+..++..
T Consensus 137 g~~-----------~~~~~l~~ia~~~gG~~~~~~~~~~~~~ 167 (171)
T cd01461 137 GSD-----------VNTYLLERLAREGRGIARRIYETDDIES 167 (171)
T ss_pred CCc-----------cCHHHHHHHHHcCCCeEEEecChHHHHH
Confidence 541 1347899999999999988877765543
No 40
>TIGR00868 hCaCC calcium-activated chloride channel protein 1. distributions. found a row in 1A13.INFO that was not parsed out
Probab=98.83 E-value=1.2e-07 Score=110.85 Aligned_cols=152 Identities=16% Similarity=0.221 Sum_probs=105.0
Q ss_pred EEEEEEecCCCccC--ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCC-HHHH
Q 005544 7 ALLLLLDVSPSMHS--VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVD-GHLV 83 (691)
Q Consensus 7 a~vflIDvs~sM~~--~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~-~~~l 83 (691)
-++||||+|.||.. ++..+..++..++.+. ..+.|+||||.|++..+ ++.+|.+.+ ....
T Consensus 306 ~VVLVLDvSGSM~g~dRL~~lkqAA~~fL~~~--l~~~DrVGLVtFsssA~---------------vl~pLt~Its~~dr 368 (863)
T TIGR00868 306 IVCLVLDKSGSMTVEDRLKRMNQAAKLFLLQT--VEKGSWVGMVTFDSAAY---------------IKNELIQITSSAER 368 (863)
T ss_pred eEEEEEECCccccccCHHHHHHHHHHHHHHHh--CCCCCEEEEEEECCcee---------------EeeccccCCcHHHH
Confidence 38899999999974 4666677777766543 35899999999998631 345554322 2334
Q ss_pred HHhhc-CCC-CCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEE
Q 005544 84 QSLKH-LPQ-GTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKN 161 (691)
Q Consensus 84 ~~L~~-l~~-~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~l~v 161 (691)
+.|.. ++. ..+..++.+||..|+++|.+. . .+...+.|||||||..+. ....+..+++.||.+..
T Consensus 369 ~aL~~~L~~~A~GGT~I~~GL~~Alq~L~~~-~-~~~~~~~IILLTDGedn~-----------~~~~l~~lk~~gVtI~T 435 (863)
T TIGR00868 369 DALTANLPTAASGGTSICSGLKAAFQVIKKS-Y-QSTDGSEIVLLTDGEDNT-----------ISSCFEEVKQSGAIIHT 435 (863)
T ss_pred HHHHHhhccccCCCCcHHHHHHHHHHHHHhc-c-cccCCCEEEEEeCCCCCC-----------HHHHHHHHHHcCCEEEE
Confidence 44444 221 122347899999999998763 2 223468999999998642 23456678889999999
Q ss_pred EeeccCCCCCCCcchhhhhhHHHHHHhhcCCCeEeehhh
Q 005544 162 IVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDS 200 (691)
Q Consensus 162 i~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~~~~~~ 200 (691)
|++|.+ ....|+.++..++|+++.+.+
T Consensus 436 Ig~G~d------------ad~~L~~IA~~TGG~~f~asd 462 (863)
T TIGR00868 436 IALGPS------------AAKELEELSDMTGGLRFYASD 462 (863)
T ss_pred EEeCCC------------hHHHHHHHHHhcCCEEEEeCC
Confidence 999541 124589999999999876653
No 41
>cd01455 vWA_F11C1-5a_type Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A
Probab=98.83 E-value=5.9e-08 Score=94.04 Aligned_cols=160 Identities=18% Similarity=0.080 Sum_probs=96.5
Q ss_pred EEEEEecCCCccC----------ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCC
Q 005544 8 LLLLLDVSPSMHS----------VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKV 77 (691)
Q Consensus 8 ~vflIDvs~sM~~----------~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~ 77 (691)
++++||+|.||.. .|+.++.++..+. +-+-.++.|+||. +|..-.-.+ ++.-.|+.
T Consensus 3 l~lavDlSgSM~~~~~~dg~~~~RL~a~k~v~~~f~-~f~~~r~~DriG~--~g~~~~~~~----------lt~d~p~t- 68 (191)
T cd01455 3 LKLVVDVSGSMYRFNGYDGRLDRSLEAVVMVMEAFD-GFEDKIQYDIIGH--SGDGPCVPF----------VKTNHPPK- 68 (191)
T ss_pred eEEEEECcHhHHHHhccCCccccHHHHHHHHHHHHH-HHHHhCccceeee--cCcccccCc----------cccccCcc-
Confidence 7899999999943 1334455544443 1123689999993 332211111 11111111
Q ss_pred CCHHHHHHhh----cCCCC-CCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHH-HHHH
Q 005544 78 VDGHLVQSLK----HLPQG-TCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVST-IARQ 151 (691)
Q Consensus 78 ~~~~~l~~L~----~l~~~-~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~-i~~~ 151 (691)
.+.+.++.|. ..+.+ .+.+.. |||-.|++.|.+. .. ...|-|||||||++.... . .... .+.-
T Consensus 69 ~d~~~~~~l~~~l~~~q~g~ag~~Ta-dAi~~av~rl~~~-~~--a~~kvvILLTDG~n~~~~----i---~P~~aAa~l 137 (191)
T cd01455 69 NNKERLETLKMMHAHSQFCWSGDHTV-EATEFAIKELAAK-ED--FDEAIVIVLSDANLERYG----I---QPKKLADAL 137 (191)
T ss_pred cchhHHHHHHHHHHhcccCccCccHH-HHHHHHHHHHHhc-Cc--CCCcEEEEEeCCCcCCCC----C---ChHHHHHHH
Confidence 1122233333 33433 223345 9999999998621 22 337899999999986542 1 2334 3455
Q ss_pred HhhcCcEEEEEeeccCCCCCCCcchhhhhhHHHHHHhhcCCCeEeehhhhHHh
Q 005544 152 MVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDSTTSL 204 (691)
Q Consensus 152 L~~~gI~l~vi~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~~~~~~a~~l 204 (691)
.++.||++++|+||.. ++..|+.++..++|++|...+..+|
T Consensus 138 A~~~gV~iytIgiG~~------------d~~~l~~iA~~tgG~~F~A~d~~~L 178 (191)
T cd01455 138 AREPNVNAFVIFIGSL------------SDEADQLQRELPAGKAFVCMDTSEL 178 (191)
T ss_pred HHhCCCEEEEEEecCC------------CHHHHHHHHhCCCCcEEEeCCHHHH
Confidence 6789999999999651 3567888999999999977766443
No 42
>cd01466 vWA_C3HC4_type VWA C3HC4-type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most,
Probab=98.82 E-value=7.7e-08 Score=91.67 Aligned_cols=147 Identities=16% Similarity=0.232 Sum_probs=98.3
Q ss_pred EEEEEecCCCccC-ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCC---HH-H
Q 005544 8 LLLLLDVSPSMHS-VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVD---GH-L 82 (691)
Q Consensus 8 ~vflIDvs~sM~~-~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~---~~-~ 82 (691)
++|+||.|+||.. +++.++.++..++.. ..+.|++|||.|++... ++.|+...+ .+ .
T Consensus 3 v~~vlD~S~SM~~~rl~~ak~a~~~l~~~---l~~~~~~~li~F~~~~~---------------~~~~~~~~~~~~~~~~ 64 (155)
T cd01466 3 LVAVLDVSGSMAGDKLQLVKHALRFVISS---LGDADRLSIVTFSTSAK---------------RLSPLRRMTAKGKRSA 64 (155)
T ss_pred EEEEEECCCCCCcHHHHHHHHHHHHHHHh---CCCcceEEEEEecCCcc---------------ccCCCcccCHHHHHHH
Confidence 6899999999986 477788877777662 25779999999998531 123343322 22 2
Q ss_pred HHHhhcCCCCCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEE
Q 005544 83 VQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNI 162 (691)
Q Consensus 83 l~~L~~l~~~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~l~vi 162 (691)
...|..+..+. ..++.+||..|.+++... ......++|+|||||..... .......+.+|.+.+|
T Consensus 65 ~~~i~~~~~~g-~T~~~~al~~a~~~~~~~--~~~~~~~~iillTDG~~~~~------------~~~~~~~~~~v~v~~i 129 (155)
T cd01466 65 KRVVDGLQAGG-GTNVVGGLKKALKVLGDR--RQKNPVASIMLLSDGQDNHG------------AVVLRADNAPIPIHTF 129 (155)
T ss_pred HHHHHhccCCC-CccHHHHHHHHHHHHhhc--ccCCCceEEEEEcCCCCCcc------------hhhhcccCCCceEEEE
Confidence 33355554432 347889999999987542 12234578999999976421 1112345679999999
Q ss_pred eeccCCCCCCCcchhhhhhHHHHHHhhcCCCeEeeh
Q 005544 163 VVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFV 198 (691)
Q Consensus 163 ~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~~~~ 198 (691)
+++.+ .+...|+.+++.++|+++.+
T Consensus 130 gig~~-----------~~~~~l~~iA~~t~G~~~~~ 154 (155)
T cd01466 130 GLGAS-----------HDPALLAFIAEITGGTFSYV 154 (155)
T ss_pred ecCCC-----------CCHHHHHHHHhccCceEEEe
Confidence 99541 13477999999999987653
No 43
>cd01475 vWA_Matrilin VWA_Matrilin: In cartilaginous plate, extracellular matrix molecules mediate cell-matrix and matrix-matrix interactions thereby providing tissue integrity. Some members of the matrilin family are expressed specifically in developing cartilage rudiments. The matrilin family consists of at least four members. All the members of the matrilin family contain VWA domains, EGF-like domains and a heptad repeat coiled-coiled domain at the carboxy terminus which is responsible for the oligomerization of the matrilins. The VWA domains have been shown to be essential for matrilin network formation by interacting with matrix ligands.
Probab=98.82 E-value=1.6e-07 Score=95.25 Aligned_cols=157 Identities=17% Similarity=0.198 Sum_probs=104.6
Q ss_pred EEEEEEecCCCccC-ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCC-CH-HHH
Q 005544 7 ALLLLLDVSPSMHS-VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV-DG-HLV 83 (691)
Q Consensus 7 a~vflIDvs~sM~~-~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~-~~-~~l 83 (691)
-++|+||.|.||.. .++.++..+..++.+.-++...++||||.|+++. .+..++... +. +..
T Consensus 4 DlvfllD~S~Sm~~~~~~~~k~f~~~l~~~l~~~~~~~rvglv~fs~~~---------------~~~~~l~~~~~~~~l~ 68 (224)
T cd01475 4 DLVFLIDSSRSVRPENFELVKQFLNQIIDSLDVGPDATRVGLVQYSSTV---------------KQEFPLGRFKSKADLK 68 (224)
T ss_pred cEEEEEeCCCCCCHHHHHHHHHHHHHHHHhcccCCCccEEEEEEecCce---------------eEEecccccCCHHHHH
Confidence 48999999999985 5888899999888876566678999999999863 123455432 22 345
Q ss_pred HHhhcCCCCCCCCchhhHHHHHHHHHHHHh-ccCCc---ccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEE
Q 005544 84 QSLKHLPQGTCAGDFLDAIVVGVDMLIKKY-GETYK---GKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRM 159 (691)
Q Consensus 84 ~~L~~l~~~~~~gd~~daL~va~d~l~~~~-~~~k~---~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~l 159 (691)
+.|..+..-........||-.|++.+.... +.+.. +.|.|||||||.+. +.+...++.++..||.+
T Consensus 69 ~~i~~i~~~~~~t~tg~AL~~a~~~~~~~~~g~r~~~~~~~kvvillTDG~s~----------~~~~~~a~~lk~~gv~i 138 (224)
T cd01475 69 RAVRRMEYLETGTMTGLAIQYAMNNAFSEAEGARPGSERVPRVGIVVTDGRPQ----------DDVSEVAAKARALGIEM 138 (224)
T ss_pred HHHHhCcCCCCCChHHHHHHHHHHHhCChhcCCCCCCCCCCeEEEEEcCCCCc----------ccHHHHHHHHHHCCcEE
Confidence 556666432212234567877777643211 11211 25678999999753 23667789999999999
Q ss_pred EEEeeccCCCCCCCcchhhhhhHHHHHHhhcCCC-eEeehhh
Q 005544 160 KNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSA-KTLFVDS 200 (691)
Q Consensus 160 ~vi~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g-~~~~~~~ 200 (691)
.+||++. .+...|+.++....+ .++..++
T Consensus 139 ~~VgvG~------------~~~~~L~~ias~~~~~~~f~~~~ 168 (224)
T cd01475 139 FAVGVGR------------ADEEELREIASEPLADHVFYVED 168 (224)
T ss_pred EEEeCCc------------CCHHHHHHHhCCCcHhcEEEeCC
Confidence 9999953 134678888876543 4444433
No 44
>cd01454 vWA_norD_type norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases. Denitrification plays a major role in completing the nitrogen cycle by converting nitrate or nitrite to nitrogen gas. The pathway for microbial denitrification has been established as NO3- ------ NO2- ------ NO ------- N2O --------- N2. This reaction generally occurs under oxygen limiting conditions. Genetic and biochemical studies have shown that the first srep of the biochemical pathway is catalyzed by periplasmic nitrate reductases. This family is widely present in proteobacteria and firmicutes. This version of the domain is also present in some archaeal members. The function of the vWA domain in this sub-group is not known. Members of this subgroup have a conserved MIDAS motif.
Probab=98.80 E-value=2.4e-07 Score=89.96 Aligned_cols=143 Identities=22% Similarity=0.190 Sum_probs=93.8
Q ss_pred EEEEEEecCCCccC--ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEe--ecCCCC-HH
Q 005544 7 ALLLLLDVSPSMHS--VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQ--DIKVVD-GH 81 (691)
Q Consensus 7 a~vflIDvs~sM~~--~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~--~l~~~~-~~ 81 (691)
+++|+||+|.||.. .++.|++++..++.. +....|.+||+.|++... ...+...+. +..... ..
T Consensus 2 ~v~~llD~SgSM~~~~kl~~ak~a~~~l~~~--l~~~~d~~~l~~F~~~~~---------~~~~~~~~~~~~~~~~~~~~ 70 (174)
T cd01454 2 AVTLLLDLSGSMRSDRRIDVAKKAAVLLAEA--LEACGVPHAILGFTTDAG---------GRERVRWIKIKDFDESLHER 70 (174)
T ss_pred EEEEEEECCCCCCCCcHHHHHHHHHHHHHHH--HHHcCCcEEEEEecCCCC---------CccceEEEEecCcccccchh
Confidence 68999999999988 688888888877663 234789999999998730 011111222 222221 23
Q ss_pred HHHHhhcCCCCCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHH---HHHHhhcCcE
Q 005544 82 LVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTI---ARQMVAFGLR 158 (691)
Q Consensus 82 ~l~~L~~l~~~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i---~~~L~~~gI~ 158 (691)
..+.|..+..+. ..++.+||..|.+.+... ....+.|||||||.........+. ...++.. +..+.+.||.
T Consensus 71 ~~~~l~~~~~~g-~T~~~~al~~a~~~l~~~----~~~~~~iiliTDG~~~~~~~~~~~-~~~~~~~~~~~~~~~~~gi~ 144 (174)
T cd01454 71 ARKRLAALSPGG-NTRDGAAIRHAAERLLAR----PEKRKILLVISDGEPNDLDYYEGN-VFATEDALRAVIEARKLGIE 144 (174)
T ss_pred HHHHHHccCCCC-CCcHHHHHHHHHHHHhcC----CCcCcEEEEEeCCCcCcccccCcc-hhHHHHHHHHHHHHHhCCcE
Confidence 455666665433 247789999999997641 234678999999987643211111 0023333 7788899999
Q ss_pred EEEEeecc
Q 005544 159 MKNIVVRA 166 (691)
Q Consensus 159 l~vi~i~~ 166 (691)
+.+|+++.
T Consensus 145 v~~igig~ 152 (174)
T cd01454 145 VFGITIDR 152 (174)
T ss_pred EEEEEecC
Confidence 99999965
No 45
>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=98.79 E-value=2.7e-07 Score=107.32 Aligned_cols=166 Identities=20% Similarity=0.267 Sum_probs=113.3
Q ss_pred CeEEEEEEecCCCccC--ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCCHHH
Q 005544 5 REALLLLLDVSPSMHS--VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHL 82 (691)
Q Consensus 5 Kea~vflIDvs~sM~~--~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~~~~ 82 (691)
.-.++|+||+|.||.. .+..|+.++..++.. .+...|.||||.|+.... .++.|+...-...
T Consensus 465 ~~~vv~vvD~SgSM~~~~rl~~ak~a~~~ll~~--a~~~~D~v~lI~F~g~~a--------------~~~~p~t~~~~~~ 528 (633)
T TIGR02442 465 GNLVIFVVDASGSMAARGRMAAAKGAVLSLLRD--AYQKRDKVALITFRGEEA--------------EVLLPPTSSVELA 528 (633)
T ss_pred CceEEEEEECCccCCCccHHHHHHHHHHHHHHH--hhcCCCEEEEEEECCCCc--------------eEEcCCCCCHHHH
Confidence 3478999999999975 577788888777653 246789999999986421 1344543222233
Q ss_pred HHHhhcCCCCCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEE
Q 005544 83 VQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNI 162 (691)
Q Consensus 83 l~~L~~l~~~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~l~vi 162 (691)
.+.|..++.+. ..++.+||..|.+++.....+.......|||||||..+..+ ......+++..++..+.+.||.+.+|
T Consensus 529 ~~~L~~l~~gG-~Tpl~~aL~~A~~~l~~~~~~~~~~~~~vvliTDG~~n~~~-~~~~~~~~~~~~a~~l~~~~i~~~vI 606 (633)
T TIGR02442 529 ARRLEELPTGG-RTPLAAGLLKAAEVLSNELLRDDDGRPLLVVITDGRANVAD-GGEPPTDDARTIAAKLAARGILFVVI 606 (633)
T ss_pred HHHHHhCCCCC-CCCHHHHHHHHHHHHHHhhccCCCCceEEEEECCCCCCCCC-CCCChHHHHHHHHHHHHhcCCeEEEE
Confidence 45677776643 34788999999999874322222346789999999987631 00112345677889999999999888
Q ss_pred eeccCCCCCCCcchhhhhhHHHHHHhhcCCCeEeeh
Q 005544 163 VVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFV 198 (691)
Q Consensus 163 ~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~~~~ 198 (691)
.....+ ....++..|++.++|+|+.+
T Consensus 607 dt~~~~----------~~~~~~~~lA~~~gg~y~~l 632 (633)
T TIGR02442 607 DTESGF----------VRLGLAEDLARALGGEYVRL 632 (633)
T ss_pred eCCCCC----------cchhHHHHHHHhhCCeEEec
Confidence 763210 12367889999999998865
No 46
>cd01477 vWA_F09G8-8_type VWA F09G8.8 type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of mo
Probab=98.73 E-value=3.5e-07 Score=90.25 Aligned_cols=137 Identities=16% Similarity=0.202 Sum_probs=92.0
Q ss_pred EEEEEecCCCccC-ChhHHHHHHHHHHHHHHhc------CCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCC-C
Q 005544 8 LLLLLDVSPSMHS-VLPDVEKLCSRLIQKKLIY------GKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV-D 79 (691)
Q Consensus 8 ~vflIDvs~sM~~-~l~~a~~~~~~l~~~ki~~------~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~-~ 79 (691)
+||+||.|.||.. .++.++..+..++...-+. ...++||||.|++.. .+..+|... +
T Consensus 22 ivfvlD~S~Sm~~~~f~~~k~fi~~~~~~~~~~~~~~~~~~~~rVGlV~fs~~a---------------~~~~~L~d~~~ 86 (193)
T cd01477 22 IVFVVDNSKGMTQGGLWQVRATISSLFGSSSQIGTDYDDPRSTRVGLVTYNSNA---------------TVVADLNDLQS 86 (193)
T ss_pred EEEEEeCCCCcchhhHHHHHHHHHHHHhhccccccccCCCCCcEEEEEEccCce---------------EEEEecccccC
Confidence 7999999999975 4777888887766654432 345899999999863 134455432 2
Q ss_pred H-HHHHHhhc-CCC--CCCCCchhhHHHHHHHHHHHH-hccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhh
Q 005544 80 G-HLVQSLKH-LPQ--GTCAGDFLDAIVVGVDMLIKK-YGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVA 154 (691)
Q Consensus 80 ~-~~l~~L~~-l~~--~~~~gd~~daL~va~d~l~~~-~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~ 154 (691)
. +.+..|+. +.. ..+......||..|.++|... .+.+.-..|.||||||+.+.-.. .+....++.|++
T Consensus 87 ~~~~~~ai~~~~~~~~~~ggT~ig~aL~~A~~~l~~~~~~~R~~v~kvvIllTDg~~~~~~-------~~~~~~a~~l~~ 159 (193)
T cd01477 87 FDDLYSQIQGSLTDVSSTNASYLDTGLQAAEQMLAAGKRTSRENYKKVVIVFASDYNDEGS-------NDPRPIAARLKS 159 (193)
T ss_pred HHHHHHHHHHHhhccccCCcchHHHHHHHHHHHHHhhhccccCCCCeEEEEEecCccCCCC-------CCHHHHHHHHHH
Confidence 2 34445664 111 112236788999999998642 12222346779999998554221 246678999999
Q ss_pred cCcEEEEEeecc
Q 005544 155 FGLRMKNIVVRA 166 (691)
Q Consensus 155 ~gI~l~vi~i~~ 166 (691)
.||.+..||++.
T Consensus 160 ~GI~i~tVGiG~ 171 (193)
T cd01477 160 TGIAIITVAFTQ 171 (193)
T ss_pred CCCEEEEEEeCC
Confidence 999999999965
No 47
>PTZ00441 sporozoite surface protein 2 (SSP2); Provisional
Probab=98.71 E-value=5.9e-07 Score=99.90 Aligned_cols=138 Identities=19% Similarity=0.154 Sum_probs=93.3
Q ss_pred CeEEEEEEecCCCccCC--hhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCC---C
Q 005544 5 REALLLLLDVSPSMHSV--LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV---D 79 (691)
Q Consensus 5 Kea~vflIDvs~sM~~~--l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~---~ 79 (691)
+--++||||+|.||... ++.|+..+..|+....++...-.||+|+|.+... .+.++... +
T Consensus 42 ~lDIvFLLD~SgSMg~~Nfle~AK~Fa~~LV~~l~Is~D~V~VgiV~FSd~~r---------------~vfpL~s~~s~D 106 (576)
T PTZ00441 42 EVDLYLLVDGSGSIGYHNWITHVIPMLMGLIQQLNLSDDAINLYMSLFSNNTT---------------ELIRLGSGASKD 106 (576)
T ss_pred CceEEEEEeCCCccCCccHHHHHHHHHHHHHHHhccCCCceEEEEEEeCCCce---------------EEEecCCCcccc
Confidence 34589999999999865 4678888998888766666666777799987531 22344222 1
Q ss_pred H-HHHHHhhcCCCC---CCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhc
Q 005544 80 G-HLVQSLKHLPQG---TCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAF 155 (691)
Q Consensus 80 ~-~~l~~L~~l~~~---~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~ 155 (691)
. ..+..|.++... .+..++..||-.+.+++.+. ..+....+.|||||||.+... .++...++.|++.
T Consensus 107 k~~aL~~I~sL~~~~~pgGgTnig~AL~~Aae~L~sr-~~R~nvpKVVILLTDG~sns~--------~dvleaAq~LR~~ 177 (576)
T PTZ00441 107 KEQALIIVKSLRKTYLPYGKTNMTDALLEVRKHLNDR-VNRENAIQLVILMTDGIPNSK--------YRALEESRKLKDR 177 (576)
T ss_pred HHHHHHHHHHHHhhccCCCCccHHHHHHHHHHHHhhc-ccccCCceEEEEEecCCCCCc--------ccHHHHHHHHHHC
Confidence 1 244455544221 22346788998888887642 223345688999999986321 2344567899999
Q ss_pred CcEEEEEeecc
Q 005544 156 GLRMKNIVVRA 166 (691)
Q Consensus 156 gI~l~vi~i~~ 166 (691)
||+|.+|+||.
T Consensus 178 GVeI~vIGVG~ 188 (576)
T PTZ00441 178 NVKLAVIGIGQ 188 (576)
T ss_pred CCEEEEEEeCC
Confidence 99999999964
No 48
>cd00198 vWFA Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains.
Probab=98.66 E-value=6.4e-07 Score=84.15 Aligned_cols=150 Identities=19% Similarity=0.303 Sum_probs=104.0
Q ss_pred EEEEEEecCCCc-cCChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCC-CC-HHHH
Q 005544 7 ALLLLLDVSPSM-HSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKV-VD-GHLV 83 (691)
Q Consensus 7 a~vflIDvs~sM-~~~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~-~~-~~~l 83 (691)
.++|+||.|.|| ...+..+...+..++.......+.+.+||+.|++... +..++.. .+ ....
T Consensus 2 ~v~~viD~S~Sm~~~~~~~~~~~~~~~~~~~~~~~~~~~i~v~~f~~~~~---------------~~~~~~~~~~~~~~~ 66 (161)
T cd00198 2 DIVFLLDVSGSMGGEKLDKAKEALKALVSSLSASPPGDRVGLVTFGSNAR---------------VVLPLTTDTDKADLL 66 (161)
T ss_pred cEEEEEeCCCCcCcchHHHHHHHHHHHHHhcccCCCCcEEEEEEecCccc---------------eeecccccCCHHHHH
Confidence 479999999999 5567788888888888665566899999999997321 1222221 22 3345
Q ss_pred HHhhcCCC-CCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEE
Q 005544 84 QSLKHLPQ-GTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNI 162 (691)
Q Consensus 84 ~~L~~l~~-~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~l~vi 162 (691)
+.+..+.. .....++..||..+.+.+.... .....+.|++|||+...... ......++.++..+|.+.+|
T Consensus 67 ~~~~~~~~~~~~~t~~~~al~~~~~~~~~~~--~~~~~~~lvvitDg~~~~~~-------~~~~~~~~~~~~~~v~v~~v 137 (161)
T cd00198 67 EAIDALKKGLGGGTNIGAALRLALELLKSAK--RPNARRVIILLTDGEPNDGP-------ELLAEAARELRKLGITVYTI 137 (161)
T ss_pred HHHHhcccCCCCCccHHHHHHHHHHHhcccC--CCCCceEEEEEeCCCCCCCc-------chhHHHHHHHHHcCCEEEEE
Confidence 55666653 3344578899999999876521 23457889999999765321 35677888899999999999
Q ss_pred eeccCCCCCCCcchhhhhhHHHHHHhhcC
Q 005544 163 VVRASLSGEPHMRVIIENDNLLNIFSKKS 191 (691)
Q Consensus 163 ~i~~~~~~~~~~~~~~~ne~~l~~l~~~~ 191 (691)
+++.+ .+...++.++...
T Consensus 138 ~~g~~-----------~~~~~l~~l~~~~ 155 (161)
T cd00198 138 GIGDD-----------ANEDELKEIADKT 155 (161)
T ss_pred EcCCC-----------CCHHHHHHHhccc
Confidence 98531 2345666666544
No 49
>smart00327 VWA von Willebrand factor (vWF) type A domain. VWA domains in extracellular eukaryotic proteins mediate adhesion via metal ion-dependent adhesion sites (MIDAS). Intracellular VWA domains and homologues in prokaryotes have recently been identified. The proposed VWA domains in integrin beta subunits have recently been substantiated using sequence-based methods.
Probab=98.66 E-value=1.1e-06 Score=84.54 Aligned_cols=156 Identities=19% Similarity=0.231 Sum_probs=107.0
Q ss_pred EEEEEEecCCCc-cCChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeec-CCCCHH-HH
Q 005544 7 ALLLLLDVSPSM-HSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDI-KVVDGH-LV 83 (691)
Q Consensus 7 a~vflIDvs~sM-~~~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l-~~~~~~-~l 83 (691)
.++||||+|.|| ...+..+..++..+++......++++||++.|++... ...++ ...+.+ ..
T Consensus 3 ~v~l~vD~S~SM~~~~~~~~~~~~~~~~~~~~~~~~~~~i~ii~f~~~~~---------------~~~~~~~~~~~~~~~ 67 (177)
T smart00327 3 DVVFLLDGSGSMGPNRFEKAKEFVLKLVEQLDIGPDGDRVGLVTFSDDAT---------------VLFPLNDSRSKDALL 67 (177)
T ss_pred cEEEEEeCCCccchHHHHHHHHHHHHHHHhcCCCCCCcEEEEEEeCCCce---------------EEEcccccCCHHHHH
Confidence 479999999999 5567778888888887654455699999999998421 11222 233444 44
Q ss_pred HHhhcCCC-CCCCCchhhHHHHHHHHHHHHhcc-CCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEE
Q 005544 84 QSLKHLPQ-GTCAGDFLDAIVVGVDMLIKKYGE-TYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKN 161 (691)
Q Consensus 84 ~~L~~l~~-~~~~gd~~daL~va~d~l~~~~~~-~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~l~v 161 (691)
..+..+.. ..+..++.+||..+.+.+...... +....+.|++|||+..... +.+...++.+++.+|.+..
T Consensus 68 ~~i~~~~~~~~~~~~~~~al~~~~~~~~~~~~~~~~~~~~~iviitDg~~~~~--------~~~~~~~~~~~~~~i~i~~ 139 (177)
T smart00327 68 EALASLSYKLGGGTNLGAALQYALENLFSKSAGSRRGAPKVLILITDGESNDG--------GDLLKAAKELKRSGVKVFV 139 (177)
T ss_pred HHHHhcCCCCCCCchHHHHHHHHHHHhcCcCCCCCCCCCeEEEEEcCCCCCCC--------ccHHHHHHHHHHCCCEEEE
Confidence 55666654 344468899999999887531111 1112578999999977532 3577888899999999999
Q ss_pred EeeccCCCCCCCcchhhhhhHHHHHHhhcCCCeEe
Q 005544 162 IVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTL 196 (691)
Q Consensus 162 i~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~~ 196 (691)
|+++.. .+...++.++...+|.+.
T Consensus 140 i~~~~~-----------~~~~~l~~~~~~~~~~~~ 163 (177)
T smart00327 140 VGVGND-----------VDEEELKKLASAPGGVYV 163 (177)
T ss_pred EEccCc-----------cCHHHHHHHhCCCcceEE
Confidence 998431 034778888887777553
No 50
>PF13768 VWA_3: von Willebrand factor type A domain
Probab=98.65 E-value=7.4e-07 Score=84.74 Aligned_cols=148 Identities=16% Similarity=0.270 Sum_probs=100.2
Q ss_pred EEEEEEecCCCccCChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCCHH----H
Q 005544 7 ALLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGH----L 82 (691)
Q Consensus 7 a~vflIDvs~sM~~~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~~~----~ 82 (691)
-+||+||+|.||....+.+++++..++++ -.++|.+.||.||+... .+ +++ +.+.+.+ .
T Consensus 2 ~vvilvD~S~Sm~g~~~~~k~al~~~l~~---L~~~d~fnii~f~~~~~--~~------~~~------~~~~~~~~~~~a 64 (155)
T PF13768_consen 2 DVVILVDTSGSMSGEKELVKDALRAILRS---LPPGDRFNIIAFGSSVR--PL------FPG------LVPATEENRQEA 64 (155)
T ss_pred eEEEEEeCCCCCCCcHHHHHHHHHHHHHh---CCCCCEEEEEEeCCEee--Ec------chh------HHHHhHHHHHHH
Confidence 37999999999998776667777777774 47999999999998421 11 111 2223322 4
Q ss_pred HHHhhcCCCCCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEE
Q 005544 83 VQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNI 162 (691)
Q Consensus 83 l~~L~~l~~~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~l~vi 162 (691)
++.++++....+..++..||-.|+..+ ......+.|+|||||.. ... .+.+...++.-. ..+.+.++
T Consensus 65 ~~~I~~~~~~~G~t~l~~aL~~a~~~~-----~~~~~~~~IilltDG~~-~~~------~~~i~~~v~~~~-~~~~i~~~ 131 (155)
T PF13768_consen 65 LQWIKSLEANSGGTDLLAALRAALALL-----QRPGCVRAIILLTDGQP-VSG------EEEILDLVRRAR-GHIRIFTF 131 (155)
T ss_pred HHHHHHhcccCCCccHHHHHHHHHHhc-----ccCCCccEEEEEEeccC-CCC------HHHHHHHHHhcC-CCceEEEE
Confidence 555666655344568899999888775 12245899999999975 221 123334443322 56999999
Q ss_pred eeccCCCCCCCcchhhhhhHHHHHHhhcCCCeE
Q 005544 163 VVRASLSGEPHMRVIIENDNLLNIFSKKSSAKT 195 (691)
Q Consensus 163 ~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~ 195 (691)
++|.. .+..+|+.|+..++|.+
T Consensus 132 ~~g~~-----------~~~~~L~~LA~~~~G~~ 153 (155)
T PF13768_consen 132 GIGSD-----------ADADFLRELARATGGSF 153 (155)
T ss_pred EECCh-----------hHHHHHHHHHHcCCCEE
Confidence 98541 24589999999998864
No 51
>cd01464 vWA_subfamily VWA subfamily: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if
Probab=98.64 E-value=7.8e-07 Score=86.60 Aligned_cols=148 Identities=16% Similarity=0.126 Sum_probs=91.3
Q ss_pred CeEEEEEEecCCCccCC-hhHHHHHHHHHHHHHH---hcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCCH
Q 005544 5 REALLLLLDVSPSMHSV-LPDVEKLCSRLIQKKL---IYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDG 80 (691)
Q Consensus 5 Kea~vflIDvs~sM~~~-l~~a~~~~~~l~~~ki---~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~~ 80 (691)
+=-++||||+|.||... +..+...+..++.... ..++.++||||.|++... +..|+.....
T Consensus 3 ~~~v~~llD~SgSM~~~~~~~~k~a~~~~~~~l~~~~~~~~~~~v~ii~F~~~a~---------------~~~~l~~~~~ 67 (176)
T cd01464 3 RLPIYLLLDTSGSMAGEPIEALNQGLQMLQSELRQDPYALESVEISVITFDSAAR---------------VIVPLTPLES 67 (176)
T ss_pred CCCEEEEEECCCCCCChHHHHHHHHHHHHHHHHhcChhhccccEEEEEEecCCce---------------EecCCccHHh
Confidence 33589999999999753 5666666666665422 123678999999998531 1223322110
Q ss_pred HHHHHhhcCCCCCCCCchhhHHHHHHHHHHHHhcc-----CCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhc
Q 005544 81 HLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGE-----TYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAF 155 (691)
Q Consensus 81 ~~l~~L~~l~~~~~~gd~~daL~va~d~l~~~~~~-----~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~ 155 (691)
..+..+..+ +..++.+||..|++++...... +....+.|||||||...-+ .......++.+...
T Consensus 68 ---~~~~~l~~~-GgT~l~~aL~~a~~~l~~~~~~~~~~~~~~~~~~iillTDG~~~~~-------~~~~~~~~~~~~~~ 136 (176)
T cd01464 68 ---FQPPRLTAS-GGTSMGAALELALDCIDRRVQRYRADQKGDWRPWVFLLTDGEPTDD-------LTAAIERIKEARDS 136 (176)
T ss_pred ---cCCCcccCC-CCCcHHHHHHHHHHHHHHHHHHhcccCcCCcCcEEEEEcCCCCCch-------HHHHHHHHHhhccc
Confidence 012223332 2347899999999998653211 1123468999999975321 12233455666667
Q ss_pred CcEEEEEeeccCCCCCCCcchhhhhhHHHHHHhh
Q 005544 156 GLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSK 189 (691)
Q Consensus 156 gI~l~vi~i~~~~~~~~~~~~~~~ne~~l~~l~~ 189 (691)
++.+.+||+|.+ .|...|+.++.
T Consensus 137 ~~~i~~igiG~~-----------~~~~~L~~ia~ 159 (176)
T cd01464 137 KGRIVACAVGPK-----------ADLDTLKQITE 159 (176)
T ss_pred CCcEEEEEeccc-----------cCHHHHHHHHC
Confidence 899999999652 24677888875
No 52
>cd01481 vWA_collagen_alpha3-VI-like VWA_collagen alpha 3(VI) like: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.
Probab=98.56 E-value=2.6e-06 Score=82.08 Aligned_cols=133 Identities=19% Similarity=0.186 Sum_probs=94.0
Q ss_pred EEEEEecCCCcc-CChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCC--CCHHHHH
Q 005544 8 LLLLLDVSPSMH-SVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKV--VDGHLVQ 84 (691)
Q Consensus 8 ~vflIDvs~sM~-~~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~--~~~~~l~ 84 (691)
++|+||.|.||. ..++.+++.+..++.+--++...-+||||.|++... +..+|.. -..+.+.
T Consensus 3 ivfllD~S~Si~~~~f~~~k~fi~~lv~~f~i~~~~~rVgvv~ys~~~~---------------~~~~l~~~~~~~~l~~ 67 (165)
T cd01481 3 IVFLIDGSDNVGSGNFPAIRDFIERIVQSLDVGPDKIRVAVVQFSDTPR---------------PEFYLNTHSTKADVLG 67 (165)
T ss_pred EEEEEeCCCCcCHHHHHHHHHHHHHHHhhccCCCCCcEEEEEEecCCee---------------EEEeccccCCHHHHHH
Confidence 799999999999 468899999999998877788899999999998631 1122221 1234677
Q ss_pred HhhcCCCCCC-CCchhhHHHHHHHHHHHHh-ccC--CcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEE
Q 005544 85 SLKHLPQGTC-AGDFLDAIVVGVDMLIKKY-GET--YKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMK 160 (691)
Q Consensus 85 ~L~~l~~~~~-~gd~~daL~va~d~l~~~~-~~~--k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~l~ 160 (691)
.+.+++...+ ..+...||-.+.+.+.... +.+ .-..|.+||||||.+. +++...+..|++.||.+.
T Consensus 68 ~i~~i~~~~g~~t~t~~AL~~~~~~~f~~~~g~R~~~~~~kv~vviTdG~s~----------d~~~~~a~~lr~~gv~i~ 137 (165)
T cd01481 68 AVRRLRLRGGSQLNTGSALDYVVKNLFTKSAGSRIEEGVPQFLVLITGGKSQ----------DDVERPAVALKRAGIVPF 137 (165)
T ss_pred HHHhcccCCCCcccHHHHHHHHHHhhcCccccCCccCCCCeEEEEEeCCCCc----------chHHHHHHHHHHCCcEEE
Confidence 7777753222 2356788888776554321 111 1234678999999764 347778899999999998
Q ss_pred EEeec
Q 005544 161 NIVVR 165 (691)
Q Consensus 161 vi~i~ 165 (691)
.+|++
T Consensus 138 ~vG~~ 142 (165)
T cd01481 138 AIGAR 142 (165)
T ss_pred EEeCC
Confidence 88874
No 53
>cd01460 vWA_midasin VWA_Midasin: Midasin is a member of the AAA ATPase family. The proteins of this family are unified by their common archetectural organization that is based upon a conserved ATPase domain. The AAA domain of midasin contains six tandem AAA protomers. The AAA domains in midasin is followed by a D/E rich domain that is following by a VWA domain. The members of this subgroup have a conserved MIDAS motif. The function of this domain is not exactly known although it has been speculated to play a crucial role in midasin function.
Probab=98.55 E-value=1.8e-06 Score=88.75 Aligned_cols=136 Identities=14% Similarity=0.122 Sum_probs=91.1
Q ss_pred CeEEEEEEecCCCccCCh--h---HHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCC
Q 005544 5 REALLLLLDVSPSMHSVL--P---DVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVD 79 (691)
Q Consensus 5 Kea~vflIDvs~sM~~~l--~---~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~ 79 (691)
.--++|+||.|.||.+.. . +++..+..++. ....|++|||.||+.. .++.|+..+-
T Consensus 60 ~~qIvlaID~S~SM~~~~~~~~aleak~lIs~al~----~Le~g~vgVv~Fg~~~---------------~~v~Plt~d~ 120 (266)
T cd01460 60 DYQILIAIDDSKSMSENNSKKLALESLCLVSKALT----LLEVGQLGVCSFGEDV---------------QILHPFDEQF 120 (266)
T ss_pred CceEEEEEecchhcccccccccHHHHHHHHHHHHH----hCcCCcEEEEEeCCCc---------------eEeCCCCCCc
Confidence 456899999999998742 1 25555555555 6889999999999852 3566775533
Q ss_pred H--HHHHHhhcCCCCCCCCchhhHHHHHHHHHHHHhccCCc--ccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhc
Q 005544 80 G--HLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYK--GKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAF 155 (691)
Q Consensus 80 ~--~~l~~L~~l~~~~~~gd~~daL~va~d~l~~~~~~~k~--~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~ 155 (691)
. ..++.+..+.-+....++..+|-.|++++......... ..+-|+|||||.+-... .....+++.+.+.
T Consensus 121 ~~~a~~~~l~~~~f~~~~Tni~~aL~~a~~~f~~~~~~~~s~~~~qlilLISDG~~~~~e-------~~~~~~~r~a~e~ 193 (266)
T cd01460 121 SSQSGPRILNQFTFQQDKTDIANLLKFTAQIFEDARTQSSSGSLWQLLLIISDGRGEFSE-------GAQKVRLREAREQ 193 (266)
T ss_pred hhhHHHHHhCcccCCCCCCcHHHHHHHHHHHHHhhhccccccccccEEEEEECCCcccCc-------cHHHHHHHHHHHc
Confidence 2 23344443322233457899999999998653211111 13889999999853221 2344568899999
Q ss_pred CcEEEEEeecc
Q 005544 156 GLRMKNIVVRA 166 (691)
Q Consensus 156 gI~l~vi~i~~ 166 (691)
||.+.+|+++.
T Consensus 194 ~i~l~~I~ld~ 204 (266)
T cd01460 194 NVFVVFIIIDN 204 (266)
T ss_pred CCeEEEEEEcC
Confidence 99999999965
No 54
>PF00092 VWA: von Willebrand factor type A domain; InterPro: IPR002035 The von Willebrand factor is a large multimeric glycoprotein found in blood plasma. Mutant forms are involved in the aetiology of bleeding disorders []. In von Willebrand factor, the type A domain (vWF) is the prototype for a protein superfamily. The vWF domain is found in various plasma proteins: complement factors B, C2, CR3 and CR4; the integrins (I-domains); collagen types VI, VII, XII and XIV; and other extracellular proteins [, , ]. Although the majority of VWA-containing proteins are extracellular, the most ancient ones present in all eukaryotes are all intracellular proteins involved in functions such as transcription, DNA repair, ribosomal and membrane transport and the proteasome. A common feature appears to be involvement in multiprotein complexes. Proteins that incorporate vWF domains participate in numerous biological events (e.g. cell adhesion, migration, homing, pattern formation, and signal transduction), involving interaction with a large array of ligands []. A number of human diseases arise from mutations in VWA domains. Secondary structure prediction from 75 aligned vWF sequences has revealed a largely alternating sequence of alpha-helices and beta-strands []. Fold recognition algorithms were used to score sequence compatibility with a library of known structures: the vWF domain fold was predicted to be a doubly-wound, open, twisted beta-sheet flanked by alpha-helices []. 3D structures have been determined for the I-domains of integrins CD11b (with bound magnesium) [] and CD11a (with bound manganese) []. The domain adopts a classic alpha/beta Rossmann fold and contains an unusual metal ion coordination site at its surface. It has been suggested that this site represents a general metal ion-dependent adhesion site (MIDAS) for binding protein ligands []. The residues constituting the MIDAS motif in the CD11b and CD11a I-domains are completely conserved, but the manner in which the metal ion is coordinated differs slightly [].; GO: 0005515 protein binding; PDB: 2XGG_B 3ZQK_B 3GXB_A 3PPV_A 3PPX_A 3PPW_A 3PPY_A 1CQP_B 3TCX_B 2ICA_A ....
Probab=98.50 E-value=1.9e-06 Score=83.36 Aligned_cols=159 Identities=17% Similarity=0.280 Sum_probs=103.0
Q ss_pred EEEEEecCCCccC-ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCC-CH-HHHH
Q 005544 8 LLLLLDVSPSMHS-VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV-DG-HLVQ 84 (691)
Q Consensus 8 ~vflIDvs~sM~~-~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~-~~-~~l~ 84 (691)
++|+||.|.||.. .+..++..+..++.+--+...+++||||.|++... ++.++... +. +.+.
T Consensus 2 ivflvD~S~sm~~~~~~~~~~~v~~~i~~~~~~~~~~rv~iv~f~~~~~---------------~~~~~~~~~~~~~~~~ 66 (178)
T PF00092_consen 2 IVFLVDTSGSMSGDNFEKAKQFVKSIISRLSISNNGTRVGIVTFSDSAR---------------VLFSLTDYQSKNDLLN 66 (178)
T ss_dssp EEEEEE-STTSCHHHHHHHHHHHHHHHHHSTBSTTSEEEEEEEESSSEE---------------EEEETTSHSSHHHHHH
T ss_pred EEEEEeCCCCCchHHHHHHHHHHHHHHHhhhccccccccceeeeecccc---------------cccccccccccccccc
Confidence 7999999999996 67888999999998555788999999999998641 33444332 32 3455
Q ss_pred Hh-hcCCCCCCCCchhhHHHHHHHHHHHH-hccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEE
Q 005544 85 SL-KHLPQGTCAGDFLDAIVVGVDMLIKK-YGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNI 162 (691)
Q Consensus 85 ~L-~~l~~~~~~gd~~daL~va~d~l~~~-~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~l~vi 162 (691)
.+ ..+....+..++..||..|.+++... .+.+....+-|||||||...-.. ..........+..||.+..|
T Consensus 67 ~i~~~~~~~~g~t~~~~aL~~a~~~l~~~~~~~r~~~~~~iiliTDG~~~~~~-------~~~~~~~~~~~~~~i~~~~i 139 (178)
T PF00092_consen 67 AINDSIPSSGGGTNLGAALKFAREQLFSSNNGGRPNSPKVIILITDGNSNDSD-------SPSEEAANLKKSNGIKVIAI 139 (178)
T ss_dssp HHHTTGGCCBSSB-HHHHHHHHHHHTTSGGGTTGTTSEEEEEEEESSSSSSHS-------GHHHHHHHHHHHCTEEEEEE
T ss_pred cccccccccchhhhHHHHHhhhhhcccccccccccccccceEEEEeecccCCc-------chHHHHHHHHHhcCcEEEEE
Confidence 55 45554445567899999999997652 11223456779999999775321 22333333333358888888
Q ss_pred eeccCCCCCCCcchhhhhhHHHHHHhhcC--CCeEeehhh
Q 005544 163 VVRASLSGEPHMRVIIENDNLLNIFSKKS--SAKTLFVDS 200 (691)
Q Consensus 163 ~i~~~~~~~~~~~~~~~ne~~l~~l~~~~--~g~~~~~~~ 200 (691)
|++. .+...|+.++... .+.++...+
T Consensus 140 g~~~------------~~~~~l~~la~~~~~~~~~~~~~~ 167 (178)
T PF00092_consen 140 GIDN------------ADNEELRELASCPTSEGHVFYLAD 167 (178)
T ss_dssp EESC------------CHHHHHHHHSHSSTCHHHEEEESS
T ss_pred ecCc------------CCHHHHHHHhCCCCCCCcEEEcCC
Confidence 7711 2457788887543 234444443
No 55
>cd01462 VWA_YIEM_type VWA YIEM type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if
Probab=98.44 E-value=1.1e-05 Score=76.46 Aligned_cols=132 Identities=19% Similarity=0.182 Sum_probs=82.6
Q ss_pred EEEEEEecCCCccCC-hhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCCHHHHHH
Q 005544 7 ALLLLLDVSPSMHSV-LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHLVQS 85 (691)
Q Consensus 7 a~vflIDvs~sM~~~-l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~~~~l~~ 85 (691)
.++||||+|+||... +..+..++..++..- ...+|.++||.|+++.. . ...+...--...++.
T Consensus 2 ~v~illD~SgSM~~~k~~~a~~~~~~l~~~~--~~~~~~v~li~F~~~~~-------------~-~~~~~~~~~~~~~~~ 65 (152)
T cd01462 2 PVILLVDQSGSMYGAPEEVAKAVALALLRIA--LAENRDTYLILFDSEFQ-------------T-KIVDKTDDLEEPVEF 65 (152)
T ss_pred CEEEEEECCCCCCCCHHHHHHHHHHHHHHHH--HHcCCcEEEEEeCCCce-------------E-EecCCcccHHHHHHH
Confidence 479999999999853 556666666555422 23689999999998621 0 111111111234555
Q ss_pred hhcCCCCCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEEeec
Q 005544 86 LKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIVVR 165 (691)
Q Consensus 86 L~~l~~~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~l~vi~i~ 165 (691)
|..+..+. ..++.+||..+..++.+. ......|++||||..+-.. ..+...+...+..++.+.+|+++
T Consensus 66 l~~~~~~g-gT~l~~al~~a~~~l~~~----~~~~~~ivliTDG~~~~~~-------~~~~~~~~~~~~~~~~v~~~~~g 133 (152)
T cd01462 66 LSGVQLGG-GTDINKALRYALELIERR----DPRKADIVLITDGYEGGVS-------DELLREVELKRSRVARFVALALG 133 (152)
T ss_pred HhcCCCCC-CcCHHHHHHHHHHHHHhc----CCCCceEEEECCCCCCCCC-------HHHHHHHHHHHhcCcEEEEEEec
Confidence 65554432 347899999999987642 1235789999999543211 22323355556778999999996
Q ss_pred c
Q 005544 166 A 166 (691)
Q Consensus 166 ~ 166 (691)
.
T Consensus 134 ~ 134 (152)
T cd01462 134 D 134 (152)
T ss_pred C
Confidence 5
No 56
>TIGR03788 marine_srt_targ marine proteobacterial sortase target protein. Members of this protein family are restricted to the Proteobacteria. Each contains a C-terminal sortase-recognition motif, transmembrane domain, and basic residues cluster at the the C-terminus, and is encoded adjacent to a sortase gene. This protein is frequently the only sortase target in its genome, which is as unusual its occurrence in Gram-negative rather than Gram-positive genomes. Many bacteria with this system are marine. In addition to the LPXTG signal, members carry a vault protein inter-alpha-trypsin inhibitor domain (pfam08487) and a von Willebrand factor type A domain (pfam00092).
Probab=98.40 E-value=1e-05 Score=93.97 Aligned_cols=154 Identities=16% Similarity=0.197 Sum_probs=100.9
Q ss_pred eEEEEEEecCCCccC-ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeec-CCCCHH--
Q 005544 6 EALLLLLDVSPSMHS-VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDI-KVVDGH-- 81 (691)
Q Consensus 6 ea~vflIDvs~sM~~-~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l-~~~~~~-- 81 (691)
..++||||+|.||.. .++.|+.++..++.+ -+++|+++||.|++... .+.+. ...+..
T Consensus 272 ~~vvfvlD~SgSM~g~~i~~ak~al~~~l~~---L~~~d~~~ii~F~~~~~---------------~~~~~~~~~~~~~~ 333 (596)
T TIGR03788 272 RELVFVIDTSGSMAGESIEQAKSALLLALDQ---LRPGDRFNIIQFDSDVT---------------LLFPVPVPATAHNL 333 (596)
T ss_pred ceEEEEEECCCCCCCccHHHHHHHHHHHHHh---CCCCCEEEEEEECCcce---------------EeccccccCCHHHH
Confidence 458999999999975 577788877776663 37899999999998631 12221 223333
Q ss_pred --HHHHhhcCCCCCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEE
Q 005544 82 --LVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRM 159 (691)
Q Consensus 82 --~l~~L~~l~~~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~l 159 (691)
....|.++..+ +..++..||..|+++... ......++|||||||... + .+.+...++. ...++.+
T Consensus 334 ~~a~~~i~~l~a~-GgT~l~~aL~~a~~~~~~---~~~~~~~~iillTDG~~~-~-------~~~~~~~~~~-~~~~~ri 400 (596)
T TIGR03788 334 ARARQFVAGLQAD-GGTEMAGALSAALRDDGP---ESSGALRQVVFLTDGAVG-N-------EDALFQLIRT-KLGDSRL 400 (596)
T ss_pred HHHHHHHhhCCCC-CCccHHHHHHHHHHhhcc---cCCCceeEEEEEeCCCCC-C-------HHHHHHHHHH-hcCCceE
Confidence 23446666554 234788999988877321 122446899999999732 1 1233333322 2346889
Q ss_pred EEEeeccCCCCCCCcchhhhhhHHHHHHhhcCCCeEeehhhh
Q 005544 160 KNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDST 201 (691)
Q Consensus 160 ~vi~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~~~~~~a 201 (691)
.+||+|.+ .|..+|+.++..++|.+..+.+.
T Consensus 401 ~tvGiG~~-----------~n~~lL~~lA~~g~G~~~~i~~~ 431 (596)
T TIGR03788 401 FTVGIGSA-----------PNSYFMRKAAQFGRGSFTFIGST 431 (596)
T ss_pred EEEEeCCC-----------cCHHHHHHHHHcCCCEEEECCCH
Confidence 99999652 24688999999999987665544
No 57
>PF04056 Ssl1: Ssl1-like; InterPro: IPR007198 Ssl1-like proteins are 40 kDa subunits of the transcription factor II H complex. This domain is often found associated with the C2H2 type Zn-finger (IPR007087 from INTERPRO).; GO: 0008270 zinc ion binding, 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent
Probab=98.12 E-value=6.8e-05 Score=73.21 Aligned_cols=151 Identities=13% Similarity=0.192 Sum_probs=110.6
Q ss_pred EEecCCCccCC------hhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCCHHHHH
Q 005544 11 LLDVSPSMHSV------LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHLVQ 84 (691)
Q Consensus 11 lIDvs~sM~~~------l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~~~~l~ 84 (691)
+||+|.+|.+. +..+.+++..+++...-.+|--++|||..+... ...+.++.---.+.++
T Consensus 1 viD~S~~m~~~D~~PtRl~~~~~~l~~Fv~eff~qNPiSqlgii~~~~~~--------------a~~ls~lsgn~~~h~~ 66 (193)
T PF04056_consen 1 VIDMSEAMREKDLKPTRLQCVLKALEEFVREFFDQNPISQLGIIVMRDGR--------------AERLSELSGNPQEHIE 66 (193)
T ss_pred CeechHhHHhCcCCccHHHHHHHHHHHHHHHHHhcCChhheeeeeeecce--------------eEEeeecCCCHHHHHH
Confidence 58999999863 556678888888887778999999999998643 1134556544345677
Q ss_pred HhhcCCCC--CCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEE
Q 005544 85 SLKHLPQG--TCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNI 162 (691)
Q Consensus 85 ~L~~l~~~--~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~l~vi 162 (691)
.|+++... .++..+..||-+|...|.. . .....|.|++|.-.-.-.+ ...+...++.|++.+|++.+|
T Consensus 67 ~L~~~~~~~~~G~~SLqN~Le~A~~~L~~-~--p~~~srEIlvi~gSl~t~D-------p~di~~ti~~l~~~~IrvsvI 136 (193)
T PF04056_consen 67 ALKKLRKLEPSGEPSLQNGLEMARSSLKH-M--PSHGSREILVIFGSLTTCD-------PGDIHETIESLKKENIRVSVI 136 (193)
T ss_pred HHHHhccCCCCCChhHHHHHHHHHHHHhh-C--ccccceEEEEEEeecccCC-------chhHHHHHHHHHHcCCEEEEE
Confidence 77776422 3344678999999999864 2 2356788888876555443 246888999999999999999
Q ss_pred eeccCCCCCCCcchhhhhhHHHHHHhhcCCCeEeeh
Q 005544 163 VVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFV 198 (691)
Q Consensus 163 ~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~~~~ 198 (691)
++... -..++.+++.++|.|.-+
T Consensus 137 ~laaE-------------v~I~k~i~~~T~G~y~V~ 159 (193)
T PF04056_consen 137 SLAAE-------------VYICKKICKETGGTYGVI 159 (193)
T ss_pred EEhHH-------------HHHHHHHHHhhCCEEEEe
Confidence 99441 268899999999987643
No 58
>KOG2884 consensus 26S proteasome regulatory complex, subunit RPN10/PSMD4 [Posttranslational modification, protein turnover, chaperones]
Probab=97.89 E-value=0.00055 Score=66.23 Aligned_cols=138 Identities=17% Similarity=0.305 Sum_probs=102.0
Q ss_pred CeEEEEEEecCCCccC------ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCC
Q 005544 5 REALLLLLDVSPSMHS------VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV 78 (691)
Q Consensus 5 Kea~vflIDvs~sM~~------~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~ 78 (691)
-|+|++|||=|.-|.. +|..=.+.+..+.+.|+-++|-..||++...... +.|+..+..-
T Consensus 3 lEatmi~iDNse~mrNgDy~PtRf~aQ~daVn~v~~~K~~snpEntvGiitla~a~--------------~~vLsT~T~d 68 (259)
T KOG2884|consen 3 LEATMICIDNSEYMRNGDYLPTRFQAQKDAVNLVCQAKLRSNPENTVGIITLANAS--------------VQVLSTLTSD 68 (259)
T ss_pred cceEEEEEeChHHhhcCCCChHHHHHHHHHHHHHHHhhhcCCcccceeeEeccCCC--------------ceeeeecccc
Confidence 5899999999988865 2444578889999999999999999999887642 2244444433
Q ss_pred CHHHHHHhhcCCCCCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcE
Q 005544 79 DGHLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLR 158 (691)
Q Consensus 79 ~~~~l~~L~~l~~~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~ 158 (691)
-...+-.+..++... ..++..+|-.|...|..+ ..|..+.|||+|-. +|+.. .+..+-.+++.|++.+|.
T Consensus 69 ~gkils~lh~i~~~g-~~~~~~~i~iA~lalkhR--qnk~~~~riVvFvG--Spi~e-----~ekeLv~~akrlkk~~Va 138 (259)
T KOG2884|consen 69 RGKILSKLHGIQPHG-KANFMTGIQIAQLALKHR--QNKNQKQRIVVFVG--SPIEE-----SEKELVKLAKRLKKNKVA 138 (259)
T ss_pred chHHHHHhcCCCcCC-cccHHHHHHHHHHHHHhh--cCCCcceEEEEEec--Ccchh-----hHHHHHHHHHHHHhcCee
Confidence 334555666665532 358999999999887653 23455788999954 66653 234788999999999999
Q ss_pred EEEEeecc
Q 005544 159 MKNIVVRA 166 (691)
Q Consensus 159 l~vi~i~~ 166 (691)
+.+|.+|.
T Consensus 139 idii~FGE 146 (259)
T KOG2884|consen 139 IDIINFGE 146 (259)
T ss_pred EEEEEecc
Confidence 99999965
No 59
>cd01457 vWA_ORF176_type VWA ORF176 type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses. In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most
Probab=97.61 E-value=0.0015 Score=64.82 Aligned_cols=136 Identities=15% Similarity=0.175 Sum_probs=79.4
Q ss_pred EEEEEEecCCCccCC--------hhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCC
Q 005544 7 ALLLLLDVSPSMHSV--------LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV 78 (691)
Q Consensus 7 a~vflIDvs~sM~~~--------l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~ 78 (691)
-++|+||+|.||... +..|..++..++. .+.....|.+++++|.+... .+ .++
T Consensus 4 dvv~~ID~SgSM~~~~~~~~~~k~~~ak~~~~~l~~-~~~~~D~d~i~l~~f~~~~~---------~~------~~~--- 64 (199)
T cd01457 4 DYTLLIDKSGSMAEADEAKERSRWEEAQESTRALAR-KCEEYDSDGITVYLFSGDFR---------RY------DNV--- 64 (199)
T ss_pred CEEEEEECCCcCCCCCCCCCchHHHHHHHHHHHHHH-HHHhcCCCCeEEEEecCCcc---------cc------CCc---
Confidence 478999999999853 5777777777665 22246789999999966431 11 122
Q ss_pred CHHHH-HHhhcCCCCCCCCchhhHHHHHHHHHHHHhcc--CCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhh-
Q 005544 79 DGHLV-QSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGE--TYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVA- 154 (691)
Q Consensus 79 ~~~~l-~~L~~l~~~~~~gd~~daL~va~d~l~~~~~~--~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~- 154 (691)
+...+ +.+.++.++ +..++..+|..+++.+...... .+...+.|++||||... +. ....+.+...++.|.+
T Consensus 65 ~~~~v~~~~~~~~p~-G~T~l~~~l~~a~~~~~~~~~~~~~~p~~~~vIiiTDG~~~-d~---~~~~~~i~~a~~~l~~~ 139 (199)
T cd01457 65 NSSKVDQLFAENSPD-GGTNLAAVLQDALNNYFQRKENGATCPEGETFLVITDGAPD-DK---DAVERVIIKASDELDAD 139 (199)
T ss_pred CHHHHHHHHhcCCCC-CcCcHHHHHHHHHHHHHHHHhhccCCCCceEEEEEcCCCCC-cH---HHHHHHHHHHHHhhccc
Confidence 23333 334455333 2247788888887544332111 11125779999999863 21 0001112233333433
Q ss_pred cCcEEEEEeecc
Q 005544 155 FGLRMKNIVVRA 166 (691)
Q Consensus 155 ~gI~l~vi~i~~ 166 (691)
.+|.+.+++||.
T Consensus 140 ~~i~i~~v~vG~ 151 (199)
T cd01457 140 NELAISFLQIGR 151 (199)
T ss_pred cCceEEEEEeCC
Confidence 379999999964
No 60
>COG5148 RPN10 26S proteasome regulatory complex, subunit RPN10/PSMD4 [Posttranslational modification, protein turnover, chaperones]
Probab=97.50 E-value=0.0037 Score=59.13 Aligned_cols=135 Identities=14% Similarity=0.264 Sum_probs=98.1
Q ss_pred CeEEEEEEecCCCccC------ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCC
Q 005544 5 REALLLLLDVSPSMHS------VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV 78 (691)
Q Consensus 5 Kea~vflIDvs~sM~~------~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~ 78 (691)
-|+||++||=|.-|.. +++.-++.+..++++|+=.++...||+|-.+.... | .|..|
T Consensus 3 lEatvvliDNse~s~NgDy~ptRFeAQkd~ve~if~~K~ndnpEntiGli~~~~a~p-~----------------vlsT~ 65 (243)
T COG5148 3 LEATVVLIDNSEASQNGDYLPTRFEAQKDAVESIFSKKFNDNPENTIGLIPLVQAQP-N----------------VLSTP 65 (243)
T ss_pred cceEEEEEeChhhhhcCCCCcHHHHHHHHHHHHHHHHHhcCCccceeeeeecccCCc-c----------------hhccc
Confidence 5899999999977754 24555889999999999889999999998876531 1 12334
Q ss_pred CHH---HHHHhhcCCCCCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhc
Q 005544 79 DGH---LVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAF 155 (691)
Q Consensus 79 ~~~---~l~~L~~l~~~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~ 155 (691)
+.+ .+..|..++-. +..++.++|-.|...|..+ ..|-.+.|||.|-. +|+.. +.+.+-.++..|+..
T Consensus 66 T~~~gkilt~lhd~~~~-g~a~~~~~lqiaql~lkhR--~nk~q~qriVaFvg--Spi~e-----sedeLirlak~lkkn 135 (243)
T COG5148 66 TKQRGKILTFLHDIRLH-GGADIMRCLQIAQLILKHR--DNKGQRQRIVAFVG--SPIQE-----SEDELIRLAKQLKKN 135 (243)
T ss_pred hhhhhHHHHHhcccccc-CcchHHHHHHHHHHHHhcc--cCCccceEEEEEec--Ccccc-----cHHHHHHHHHHHHhc
Confidence 443 34444444431 2348899999999887653 33455788998854 56653 346788899999999
Q ss_pred CcEEEEEeecc
Q 005544 156 GLRMKNIVVRA 166 (691)
Q Consensus 156 gI~l~vi~i~~ 166 (691)
|+-+.+|.+|.
T Consensus 136 nVAidii~fGE 146 (243)
T COG5148 136 NVAIDIIFFGE 146 (243)
T ss_pred CeeEEEEehhh
Confidence 99999999864
No 61
>PRK10997 yieM hypothetical protein; Provisional
Probab=97.09 E-value=0.012 Score=65.52 Aligned_cols=131 Identities=15% Similarity=0.220 Sum_probs=84.5
Q ss_pred CCeEEEEEEecCCCccC-ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCC-C-H
Q 005544 4 TREALLLLLDVSPSMHS-VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV-D-G 80 (691)
Q Consensus 4 ~Kea~vflIDvs~sM~~-~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~-~-~ 80 (691)
.|.-+|+|||.|+||.. .-..|+.++..++. +..+.+|.+++++|++.... | ++... . .
T Consensus 322 ~kGpiII~VDtSGSM~G~ke~~AkalAaAL~~--iAl~q~dr~~li~Fs~~i~~---------~-------~l~~~~gl~ 383 (487)
T PRK10997 322 PRGPFIVCVDTSGSMGGFNEQCAKAFCLALMR--IALAENRRCYIMLFSTEVVT---------Y-------ELTGPDGLE 383 (487)
T ss_pred CCCcEEEEEECCCCCCCCHHHHHHHHHHHHHH--HHHhcCCCEEEEEecCCcee---------e-------ccCCccCHH
Confidence 46779999999999983 33445554444443 23578999999999985311 1 22211 1 2
Q ss_pred HHHHHhhcCCCCCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhh-cCcEE
Q 005544 81 HLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVA-FGLRM 159 (691)
Q Consensus 81 ~~l~~L~~l~~~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~-~gI~l 159 (691)
+.++.|.... .+..|+..+|-.+++.+.+ +...+--||+|||+..+.. .+.+...++.|++ .|..+
T Consensus 384 ~ll~fL~~~f--~GGTDl~~aL~~al~~l~~----~~~r~adIVVISDF~~~~~-------~eel~~~L~~Lk~~~~~rf 450 (487)
T PRK10997 384 QAIRFLSQSF--RGGTDLAPCLRAIIEKMQG----REWFDADAVVISDFIAQRL-------PDELVAKVKELQRQHQHRF 450 (487)
T ss_pred HHHHHHHHhc--CCCCcHHHHHHHHHHHHcc----cccCCceEEEECCCCCCCC-------hHHHHHHHHHHHHhcCcEE
Confidence 3455554432 2235788888888888643 2222344999999976532 1456777778877 89999
Q ss_pred EEEeec
Q 005544 160 KNIVVR 165 (691)
Q Consensus 160 ~vi~i~ 165 (691)
+.+.|+
T Consensus 451 ~~l~i~ 456 (487)
T PRK10997 451 HAVAMS 456 (487)
T ss_pred EEEEeC
Confidence 988884
No 62
>COG4867 Uncharacterized protein with a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=97.01 E-value=0.015 Score=61.66 Aligned_cols=152 Identities=15% Similarity=0.179 Sum_probs=98.9
Q ss_pred CCeEEEEEEecCCCccC-----ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCC
Q 005544 4 TREALLLLLDVSPSMHS-----VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV 78 (691)
Q Consensus 4 ~Kea~vflIDvs~sM~~-----~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~ 78 (691)
.--|+++++|+|-||.- ++....-+..+++.. .-+.|.+.+|+||-..- +|
T Consensus 462 t~aAvallvDtS~SM~~eGRw~PmKQtALALhHLv~T---rfrGD~l~~i~Fgr~A~------------~v--------- 517 (652)
T COG4867 462 TQAAVALLVDTSFSMVMEGRWLPMKQTALALHHLVCT---RFRGDALQIIAFGRYAR------------TV--------- 517 (652)
T ss_pred cccceeeeeeccHHHHHhccCCchHHHHHHHHHHHHh---cCCCcceEEEeccchhc------------cc---------
Confidence 45689999999999954 233333344455552 24999999999996531 21
Q ss_pred CHHHHHHhhcCCC-CCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCC-CCCCCC--------chhhHH--
Q 005544 79 DGHLVQSLKHLPQ-GTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLK-DPDVGT--------KEDQVS-- 146 (691)
Q Consensus 79 ~~~~l~~L~~l~~-~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~-~~~~~~--------~~~~l~-- 146 (691)
.+.+|..++. +....+..-||.+|-.+|.++- +..+.|++||||....- .+.++. +..-+-
T Consensus 518 ---~v~eLt~l~~v~eqgTNlhhaL~LA~r~l~Rh~----~~~~~il~vTDGePtAhle~~DG~~~~f~yp~DP~t~~~T 590 (652)
T COG4867 518 ---TAAELTGLAGVYEQGTNLHHALALAGRHLRRHA----GAQPVVLVVTDGEPTAHLEDGDGTSVFFDYPPDPRTIAHT 590 (652)
T ss_pred ---CHHHHhcCCCccccccchHHHHHHHHHHHHhCc----ccCceEEEEeCCCccccccCCCCceEecCCCCChhHHHHH
Confidence 1455666652 3344578899999999987742 44689999999965321 111221 111121
Q ss_pred -HHHHHHhhcCcEEEEEeeccCCCCCCCcchhhhhhHHHHHHhhcCCCeEe
Q 005544 147 -TIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTL 196 (691)
Q Consensus 147 -~i~~~L~~~gI~l~vi~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~~ 196 (691)
.-..++...||.+++|-++.++ +=+.|+..++..+.|+++
T Consensus 591 vr~~d~~~r~G~q~t~FrLg~Dp----------gL~~Fv~qva~rv~G~vv 631 (652)
T COG4867 591 VRGFDDMARLGAQVTIFRLGSDP----------GLARFIDQVARRVQGRVV 631 (652)
T ss_pred HHHHHHHHhccceeeEEeecCCH----------hHHHHHHHHHHHhCCeEE
Confidence 1235678899999999986531 125789999999999865
No 63
>PF11265 Med25_VWA: Mediator complex subunit 25 von Willebrand factor type A; InterPro: IPR021419 The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA domain which is this one, an SD2 domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This VWA or von Willebrand factor type A domain when bound to RAR and the histone acetyltransferase CBP is responsible for recruiting Med1 to the rest of the Mediator complex [].
Probab=96.99 E-value=0.02 Score=57.10 Aligned_cols=148 Identities=12% Similarity=0.161 Sum_probs=90.5
Q ss_pred eEEEEEEecCCCccCChhH-----HHHHHHHHHH-----HHH-hcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEee
Q 005544 6 EALLLLLDVSPSMHSVLPD-----VEKLCSRLIQ-----KKL-IYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQD 74 (691)
Q Consensus 6 ea~vflIDvs~sM~~~l~~-----a~~~~~~l~~-----~ki-~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~ 74 (691)
.=+||+||-+..|+..+.. ...++..+-. +.. -...+-+.|||+|++... |....+-.-
T Consensus 14 ~~vVfvvEgTAalgpy~~~Lkt~Yl~P~le~f~~g~~~e~~~~~~~~~t~y~LVvf~t~d~----------~~~~~v~~~ 83 (226)
T PF11265_consen 14 AQVVFVVEGTAALGPYWNTLKTNYLDPILEYFNGGPIAERDFGGDYSNTEYGLVVFNTADC----------YPEPIVQRS 83 (226)
T ss_pred ceEEEEEecchhhhhhHHHHHHHHHHHHHHHhcCCCcccccccccCCCceEEEEEEeccCC----------Ccccceecc
Confidence 3499999999999987643 3444444432 110 013678999999999752 332222111
Q ss_pred cCCCCHH-HHHHhhcCCC-C--CCC-CchhhHHHHHHHHHHHHh-----ccCCcccceEEEEeCCCCCCCCCCCC---Cc
Q 005544 75 IKVVDGH-LVQSLKHLPQ-G--TCA-GDFLDAIVVGVDMLIKKY-----GETYKGKKHLCLITDALCPLKDPDVG---TK 141 (691)
Q Consensus 75 l~~~~~~-~l~~L~~l~~-~--~~~-gd~~daL~va~d~l~~~~-----~~~k~~~krIvL~TD~~~p~~~~~~~---~~ 141 (691)
=-..+.+ .++.|++++- | ..+ +.+.+||..|+.++.... ....-..|+.|||+|. .|..-+... ..
T Consensus 84 g~T~~~~~fl~~L~~I~f~GGG~e~~a~iaEGLa~AL~~fd~~~~~r~~~~~~~~~khcILI~nS-pP~~~p~~~~~~~~ 162 (226)
T PF11265_consen 84 GPTSSPQKFLQWLDAIQFSGGGFESCAAIAEGLAEALQCFDDFKQMRQQQQQTDVQKHCILICNS-PPYRLPVNECPQYS 162 (226)
T ss_pred CCcCCHHHHHHHHHccCcCCCCcccchhHHHHHHHHHHHhcchhhhccccCcccccceEEEEeCC-CCccccccCCCccc
Confidence 1223333 6777888743 2 222 358899999999876321 0111247899999986 344322111 11
Q ss_pred hhhHHHHHHHHhhcCcEEEEEee
Q 005544 142 EDQVSTIARQMVAFGLRMKNIVV 164 (691)
Q Consensus 142 ~~~l~~i~~~L~~~gI~l~vi~i 164 (691)
...++..+..+.+.+|.|.+|..
T Consensus 163 ~~~~d~la~~~~~~~I~LSiisP 185 (226)
T PF11265_consen 163 GKTCDQLAVLISERNISLSIISP 185 (226)
T ss_pred CCCHHHHHHHHHhcCceEEEEcC
Confidence 23577888888899999999975
No 64
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=96.67 E-value=0.036 Score=57.02 Aligned_cols=156 Identities=14% Similarity=0.194 Sum_probs=100.2
Q ss_pred EEEEEEecCCCccCC------hhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeec-CCCC
Q 005544 7 ALLLLLDVSPSMHSV------LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDI-KVVD 79 (691)
Q Consensus 7 a~vflIDvs~sM~~~------l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l-~~~~ 79 (691)
.++++||+|.+|.+. +....+.+..++..--=.+|-..+|+|.......+- +..+ +.|
T Consensus 62 hl~iviD~S~am~e~Df~P~r~a~~~K~le~Fv~eFFdQNPiSQigii~~k~g~A~~--------------lt~ltgnp- 126 (378)
T KOG2807|consen 62 HLYIVIDCSRAMEEKDFRPSRFANVIKYLEGFVPEFFDQNPISQIGIISIKDGKADR--------------LTDLTGNP- 126 (378)
T ss_pred eEEEEEEhhhhhhhccCCchHHHHHHHHHHHHHHHHhccCchhheeEEEEecchhhH--------------HHHhcCCH-
Confidence 578999999999763 334456666555544336899999999988543211 1111 112
Q ss_pred HHHHHHhhcCCCCCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEE
Q 005544 80 GHLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRM 159 (691)
Q Consensus 80 ~~~l~~L~~l~~~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~l 159 (691)
-..+..|..+....+...+.+||-.|...|.. . ..-..|-|++|-..-+..+. .++-..++.|+...|++
T Consensus 127 ~~hI~aL~~~~~~~g~fSLqNaLe~a~~~Lk~-~--p~H~sREVLii~sslsT~DP-------gdi~~tI~~lk~~kIRv 196 (378)
T KOG2807|consen 127 RIHIHALKGLTECSGDFSLQNALELAREVLKH-M--PGHVSREVLIIFSSLSTCDP-------GDIYETIDKLKAYKIRV 196 (378)
T ss_pred HHHHHHHhcccccCCChHHHHHHHHHHHHhcC-C--CcccceEEEEEEeeecccCc-------ccHHHHHHHHHhhCeEE
Confidence 13567777765333333467888888888754 2 12345666666544443331 35777888999999999
Q ss_pred EEEeeccCCCCCCCcchhhhhhHHHHHHhhcCCCeEeehhh
Q 005544 160 KNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDS 200 (691)
Q Consensus 160 ~vi~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~~~~~~ 200 (691)
.+||+... -.+.+.+++.++|.|.-+-+
T Consensus 197 svIgLsaE-------------v~icK~l~kaT~G~Y~V~lD 224 (378)
T KOG2807|consen 197 SVIGLSAE-------------VFICKELCKATGGRYSVALD 224 (378)
T ss_pred EEEeechh-------------HHHHHHHHHhhCCeEEEEeC
Confidence 99999431 26778899999998764433
No 65
>COG4245 TerY Uncharacterized protein encoded in toxicity protection region of plasmid R478, contains von Willebrand factor (vWF) domain [General function prediction only]
Probab=96.62 E-value=0.034 Score=53.25 Aligned_cols=103 Identities=20% Similarity=0.213 Sum_probs=63.4
Q ss_pred eEEEEEEecCCCccC-ChhHHHHHHHHHHHHH---HhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCCHH
Q 005544 6 EALLLLLDVSPSMHS-VLPDVEKLCSRLIQKK---LIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGH 81 (691)
Q Consensus 6 ea~vflIDvs~sM~~-~l~~a~~~~~~l~~~k---i~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~~~ 81 (691)
=-++|+||+|.||-. +.+..-.++..++... -..-..-+++||.|++. +.+.+|+.
T Consensus 4 lP~~lllDtSgSM~Ge~IealN~Glq~m~~~Lkqdp~Ale~v~lsIVTF~~~---------------a~~~~pf~----- 63 (207)
T COG4245 4 LPCYLLLDTSGSMIGEPIEALNAGLQMMIDTLKQDPYALERVELSIVTFGGP---------------ARVIQPFT----- 63 (207)
T ss_pred CCEEEEEecCcccccccHHHHHHHHHHHHHHHHhChhhhheeEEEEEEecCc---------------ceEEechh-----
Confidence 347899999999965 4444433444443322 12346779999999973 22455552
Q ss_pred HHHHhhcC--CCC--CCCCchhhHHHHHHHHHHHHh-----ccCCcccceEEEEeCCCC
Q 005544 82 LVQSLKHL--PQG--TCAGDFLDAIVVGVDMLIKKY-----GETYKGKKHLCLITDALC 131 (691)
Q Consensus 82 ~l~~L~~l--~~~--~~~gd~~daL~va~d~l~~~~-----~~~k~~~krIvL~TD~~~ 131 (691)
.+.++ +.- .+...+..||-.|.+|+.++. ..++.|+--+||+|||..
T Consensus 64 ---~~~nF~~p~L~a~GgT~lGaAl~~a~d~Ie~~~~~~~a~~kgdyrP~vfLiTDG~P 119 (207)
T COG4245 64 ---DAANFNPPILTAQGGTPLGAALTLALDMIEERKRKYDANGKGDYRPWVFLITDGEP 119 (207)
T ss_pred ---hHhhcCCCceecCCCCchHHHHHHHHHHHHHHHhhcccCCccccceEEEEecCCCc
Confidence 22232 111 112246688999999987651 123467888999999965
No 66
>COG2425 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=96.52 E-value=0.045 Score=59.99 Aligned_cols=129 Identities=21% Similarity=0.261 Sum_probs=85.1
Q ss_pred EEEEEEecCCCccCChhH-HHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCC---HHH
Q 005544 7 ALLLLLDVSPSMHSVLPD-VEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVD---GHL 82 (691)
Q Consensus 7 a~vflIDvs~sM~~~l~~-a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~---~~~ 82 (691)
-+++|||-|+||+-.... |+-+|..+++ +..+-+=.+.+++|.+.- +-..+..+. -+.
T Consensus 274 pvilllD~SGSM~G~~e~~AKAvalAl~~--~alaenR~~~~~lF~s~~----------------~~~el~~k~~~~~e~ 335 (437)
T COG2425 274 PVILLLDKSGSMSGFKEQWAKAVALALMR--IALAENRDCYVILFDSEV----------------IEYELYEKKIDIEEL 335 (437)
T ss_pred CEEEEEeCCCCcCCcHHHHHHHHHHHHHH--HHHHhccceEEEEecccc----------------eeeeecCCccCHHHH
Confidence 479999999999876443 3333444444 123455568999999831 111222222 346
Q ss_pred HHHhhcCCCCCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEE
Q 005544 83 VQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNI 162 (691)
Q Consensus 83 l~~L~~l~~~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~l~vi 162 (691)
|+.|.....|. .|+.-+|..|++-+..+ +...-.|++||||.+.+.+ +-+..+-+..+.+..+|..+
T Consensus 336 i~fL~~~f~GG--TD~~~~l~~al~~~k~~----~~~~adiv~ITDg~~~~~~-------~~~~~v~e~~k~~~~rl~aV 402 (437)
T COG2425 336 IEFLSYVFGGG--TDITKALRSALEDLKSR----ELFKADIVVITDGEDERLD-------DFLRKVKELKKRRNARLHAV 402 (437)
T ss_pred HHHHhhhcCCC--CChHHHHHHHHHHhhcc----cccCCCEEEEeccHhhhhh-------HHHHHHHHHHHHhhceEEEE
Confidence 77777765554 59999999999987642 2334789999999998741 23444445555889999999
Q ss_pred eecc
Q 005544 163 VVRA 166 (691)
Q Consensus 163 ~i~~ 166 (691)
.|+.
T Consensus 403 ~I~~ 406 (437)
T COG2425 403 LIGG 406 (437)
T ss_pred EecC
Confidence 9854
No 67
>PF05762 VWA_CoxE: VWA domain containing CoxE-like protein; InterPro: IPR008912 This group of proteins contains a VWA type domain and the function of this family is unknown. It is found as part of a CO oxidising (Cox) system operon in several bacteria [].
Probab=96.44 E-value=0.029 Score=56.70 Aligned_cols=126 Identities=19% Similarity=0.123 Sum_probs=76.7
Q ss_pred EEEEEEecCCCccCChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCC-HHHHHH
Q 005544 7 ALLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVD-GHLVQS 85 (691)
Q Consensus 7 a~vflIDvs~sM~~~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~-~~~l~~ 85 (691)
-+|+|+|+|.||...-..+...+..+.. ..+ .+.+++|+|+-+.- -..+...+ .+.+..
T Consensus 59 ~lvvl~DvSGSM~~~s~~~l~~~~~l~~----~~~--~~~~f~F~~~l~~v--------------T~~l~~~~~~~~l~~ 118 (222)
T PF05762_consen 59 RLVVLCDVSGSMAGYSEFMLAFLYALQR----QFR--RVRVFVFSTRLTEV--------------TPLLRRRDPEEALAR 118 (222)
T ss_pred cEEEEEeCCCChHHHHHHHHHHHHHHHH----hCC--CEEEEEEeeehhhh--------------hhhhccCCHHHHHHH
Confidence 6999999999998643334444444443 222 89999999864221 11222122 234555
Q ss_pred hhcCC-CCCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEEe
Q 005544 86 LKHLP-QGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIV 163 (691)
Q Consensus 86 L~~l~-~~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~l~vi~ 163 (691)
+.... ...+..|+..||-.+.+.+.. .......+++|||+...-. .+.+......|+..+..+..+.
T Consensus 119 ~~~~~~~~~GgTdi~~aL~~~~~~~~~----~~~~~t~vvIiSDg~~~~~-------~~~~~~~l~~l~~r~~rviwLn 186 (222)
T PF05762_consen 119 LSALVQSFGGGTDIGQALREFLRQYAR----PDLRRTTVVIISDGWDTND-------PEPLAEELRRLRRRGRRVIWLN 186 (222)
T ss_pred HHhhccCCCCccHHHHHHHHHHHHhhc----ccccCcEEEEEecccccCC-------hHHHHHHHHHHHHhCCEEEEEC
Confidence 54332 223344788888777776432 2234566899999933221 2567778889999999887654
No 68
>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=95.96 E-value=0.38 Score=49.38 Aligned_cols=172 Identities=15% Similarity=0.173 Sum_probs=95.7
Q ss_pred EEEEEEecCCCccC--ChhHHHHHHHHHHHHHHhcC-CccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCC-----
Q 005544 7 ALLLLLDVSPSMHS--VLPDVEKLCSRLIQKKLIYG-KNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV----- 78 (691)
Q Consensus 7 a~vflIDvs~sM~~--~l~~a~~~~~~l~~~ki~~~-~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~----- 78 (691)
+.+|+||+|..--+ .++.+.+.+...+.. +-.. ++-+||+|.|++.-.=-++... .......++.++..+
T Consensus 5 ~~~FvIDvs~~a~~~g~~~~~~~si~~~L~~-lp~~~~~~~VgiITfd~~v~~y~l~~~-~~~~q~~vv~dl~d~f~P~~ 82 (244)
T cd01479 5 VYVFLIDVSYNAIKSGLLATACEALLSNLDN-LPGDDPRTRVGFITFDSTLHFFNLKSS-LEQPQMMVVSDLDDPFLPLP 82 (244)
T ss_pred EEEEEEEccHHHHhhChHHHHHHHHHHHHHh-cCCCCCCeEEEEEEECCeEEEEECCCC-CCCCeEEEeeCcccccCCCC
Confidence 67999999864322 255667777766663 2222 5689999999986432222110 011122233323211
Q ss_pred C----------HHHHHHhhcCCC----CC-CCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCC----CC
Q 005544 79 D----------GHLVQSLKHLPQ----GT-CAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPD----VG 139 (691)
Q Consensus 79 ~----------~~~l~~L~~l~~----~~-~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~----~~ 139 (691)
+ .....-|++|+. +. ...-+..||.+|..+|.. ++ =||++|+.+-...+... +.
T Consensus 83 ~~~lv~l~e~~~~i~~lL~~L~~~~~~~~~~~~c~G~Al~~A~~lL~~-~G------GkIi~f~s~~pt~GpG~l~~~~~ 155 (244)
T cd01479 83 DGLLVNLKESRQVIEDLLDQIPEMFQDTKETESALGPALQAAFLLLKE-TG------GKIIVFQSSLPTLGAGKLKSRED 155 (244)
T ss_pred cceeecHHHHHHHHHHHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHh-cC------CEEEEEeCCCCCcCCcccccCcc
Confidence 1 111222333321 11 122467899999999864 33 37888888754333100 00
Q ss_pred --------------CchhhHHHHHHHHhhcCcEEEEEeeccCCCCCCCcchhhhhhHHHHHHhhcCCCeEee
Q 005544 140 --------------TKEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLF 197 (691)
Q Consensus 140 --------------~~~~~l~~i~~~L~~~gI~l~vi~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~~~ 197 (691)
...+-...++..+...||.+++|....++ -+-..+..++..++|.++.
T Consensus 156 ~~~~~~~~e~~~~~p~~~fY~~la~~~~~~~isvDlF~~~~~~----------~dla~l~~l~~~TGG~v~~ 217 (244)
T cd01479 156 PKLLSTDKEKQLLQPQTDFYKKLALECVKSQISVDLFLFSNQY----------VDVATLGCLSRLTGGQVYY 217 (244)
T ss_pred ccccCchhhhhhcCcchHHHHHHHHHHHHcCeEEEEEEccCcc----------cChhhhhhhhhhcCceEEE
Confidence 01134568999999999999999873311 1124466778888997543
No 69
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=95.58 E-value=0.2 Score=52.18 Aligned_cols=180 Identities=11% Similarity=0.157 Sum_probs=115.2
Q ss_pred EEEEEEecCCCcc---C------ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCC----ccccc---cC-CCcCcE
Q 005544 7 ALLLLLDVSPSMH---S------VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETE----NELTK---EV-GGYEHV 69 (691)
Q Consensus 7 a~vflIDvs~sM~---~------~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~----n~l~~---e~-~~y~nI 69 (691)
-++++||++|--. . .+..+++.+..++.--+..+...+|+||..++.... ++... .. .....+
T Consensus 4 lL~vvlD~np~~W~~~~~~~~~~~l~~~l~sllvF~NahL~l~~~N~vaVIAs~~~~~~~LYps~~~~~~~~~~~~~~~~ 83 (279)
T TIGR00627 4 LLVVIIEANPCSWGMLALAHGKRTISKVLRAIVVFLNAHLAFNANNKLAVIASHSQDNKYLYPSTRCEDRNASELDPKRL 83 (279)
T ss_pred EEEEEEeCCHHHHHHHhhccCCCcHHHHHHHHHHHHHHHHhcCccCCEEEEEecCCcceEEecCCccccccccccccccc
Confidence 5789999998643 1 356778888888888888899999999998876432 11000 00 011111
Q ss_pred --EEEeecCCCCHHHHHHhhcCC-C----CC--CCCchhhHHHHHHHHHHHHhcc---CCcccceEEEEeCCCCCCCCCC
Q 005544 70 --KVLQDIKVVDGHLVQSLKHLP-Q----GT--CAGDFLDAIVVGVDMLIKKYGE---TYKGKKHLCLITDALCPLKDPD 137 (691)
Q Consensus 70 --~v~~~l~~~~~~~l~~L~~l~-~----~~--~~gd~~daL~va~d~l~~~~~~---~k~~~krIvL~TD~~~p~~~~~ 137 (691)
..+.++..++...++.|.++. . +. ....+..||-.|+=.+.+.... ...-+.||++|+-..+..
T Consensus 84 ~~~~y~~f~~v~~~v~~~l~~l~~~~~~~~~~~~~s~lagals~ALcyinr~~~~~~~~~~~~~RIlii~~s~~~~---- 159 (279)
T TIGR00627 84 RELLYRDFRTVDETIVEEIKPLMAHADKHMKKDSRTVLAGALSDALGYINRSEQSETASEKLKSRILVISITPDMA---- 159 (279)
T ss_pred cchhccchhHHHHHHHHHHHHHHhhchhcccccccccchhHHHhhhhhhcccccccccCcCCcceEEEEECCCCch----
Confidence 123445556666777776642 1 11 2334677888888776653211 124478999998753321
Q ss_pred CCCchhhHHHHHHHHhhcCcEEEEEeeccCCCCCCCcchhhhhhHHHHHHhhcCCCeEeehhhhHH
Q 005544 138 VGTKEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDSTTS 203 (691)
Q Consensus 138 ~~~~~~~l~~i~~~L~~~gI~l~vi~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~~~~~~a~~ 203 (691)
..+-.+-..+..+++.+|.+.+++++. + + .-.+|+++++.++|.|..+.+...
T Consensus 160 --~qYi~~mn~Ifaaqk~~I~Idv~~L~~----e-~------~~~~lqQa~~~TgG~Y~~~~~~~~ 212 (279)
T TIGR00627 160 --LQYIPLMNCIFSAQKQNIPIDVVSIGG----D-F------TSGFLQQAADITGGSYLHVKKPQG 212 (279)
T ss_pred --HHHHHHHHHHHHHHHcCceEEEEEeCC----c-c------ccHHHHHHHHHhCCEEeccCCHhH
Confidence 223445678889999999999999943 1 0 237899999999999887655433
No 70
>PF10138 vWA-TerF-like: vWA found in TerF C terminus ; InterPro: IPR019303 This entry represents the N-terminal domain of a family of proteins that confer resistance to the metalloid element tellurium and its salts.
Probab=95.47 E-value=0.74 Score=45.32 Aligned_cols=133 Identities=20% Similarity=0.257 Sum_probs=72.4
Q ss_pred eEEEEEEecCCCccCChh-----HHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCCH
Q 005544 6 EALLLLLDVSPSMHSVLP-----DVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDG 80 (691)
Q Consensus 6 ea~vflIDvs~sM~~~l~-----~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~~ 80 (691)
-.+.+|||.|.||..... .+.+-+.-+..+ ..+.-.|=|++|+++... +..| ..-+.
T Consensus 2 ArV~LVLD~SGSM~~~yk~G~vQ~~~Er~lalA~~---~DdDG~i~v~~Fs~~~~~---------~~~v------t~~~~ 63 (200)
T PF10138_consen 2 ARVYLVLDISGSMRPLYKDGTVQRVVERILALAAQ---FDDDGEIDVWFFSTEFDR---------LPDV------TLDNY 63 (200)
T ss_pred cEEEEEEeCCCCCchhhhCccHHHHHHHHHHHHhh---cCCCCceEEEEeCCCCCc---------CCCc------CHHHH
Confidence 368999999999986432 222222222221 345666999999997532 2111 11111
Q ss_pred H-HHHHhhc-CCC-C-CCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcC
Q 005544 81 H-LVQSLKH-LPQ-G-TCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFG 156 (691)
Q Consensus 81 ~-~l~~L~~-l~~-~-~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~g 156 (691)
. .++.+.. +.. + .+..+..-+|--.++..... .....---|++||||... + ...+..++.......
T Consensus 64 ~~~v~~~~~~~~~~~~~G~t~y~~vm~~v~~~y~~~--~~~~~P~~VlFiTDG~~~-~-------~~~~~~~i~~as~~p 133 (200)
T PF10138_consen 64 EGYVDELHAGLPDWGRMGGTNYAPVMEDVLDHYFKR--EPSDAPALVLFITDGGPD-D-------RRAIEKLIREASDEP 133 (200)
T ss_pred HHHHHHHhccccccCCCCCcchHHHHHHHHHHHhhc--CCCCCCeEEEEEecCCcc-c-------hHHHHHHHHhccCCC
Confidence 1 2233321 100 1 11234555555555543321 111112347777999753 2 356788888889999
Q ss_pred cEEEEEeecc
Q 005544 157 LRMKNIVVRA 166 (691)
Q Consensus 157 I~l~vi~i~~ 166 (691)
|..+.||+|.
T Consensus 134 ifwqFVgiG~ 143 (200)
T PF10138_consen 134 IFWQFVGIGD 143 (200)
T ss_pred eeEEEEEecC
Confidence 9999999965
No 71
>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=95.05 E-value=1.5 Score=44.78 Aligned_cols=175 Identities=15% Similarity=0.181 Sum_probs=96.6
Q ss_pred EEEEEEecCCC-ccC-ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCC-----C
Q 005544 7 ALLLLLDVSPS-MHS-VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVV-----D 79 (691)
Q Consensus 7 a~vflIDvs~s-M~~-~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~-----~ 79 (691)
+.+|+||+|.. ..+ .++.+...+...+... =..++-+||+|.|++.-+=-.+... ..-....++.++..+ .
T Consensus 5 ~~vFvID~s~~ai~~~~l~~~~~sl~~~l~~l-p~~~~~~igiITf~~~V~~~~~~~~-~~~~~~~v~~dl~d~f~p~~~ 82 (239)
T cd01468 5 VFVFVIDVSYEAIKEGLLQALKESLLASLDLL-PGDPRARVGLITYDSTVHFYNLSSD-LAQPKMYVVSDLKDVFLPLPD 82 (239)
T ss_pred EEEEEEEcchHhccccHHHHHHHHHHHHHHhC-CCCCCcEEEEEEeCCeEEEEECCCC-CCCCeEEEeCCCccCcCCCcC
Confidence 67999999964 222 2455666666666531 1127889999999865322112110 001223344443222 0
Q ss_pred ------HH----HHHHhhcCCCC-------CCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCC-----
Q 005544 80 ------GH----LVQSLKHLPQG-------TCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPD----- 137 (691)
Q Consensus 80 ------~~----~l~~L~~l~~~-------~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~----- 137 (691)
.+ ...-|++|+.. ....-+..||.+|..++... . ..=||++|+.+-...+ +.
T Consensus 83 ~~l~~~~e~~~~i~~~l~~l~~~~~~~~~~~~~~~~G~Al~~A~~ll~~~-~----~gGkI~~f~sg~pt~G-pG~l~~~ 156 (239)
T cd01468 83 RFLVPLSECKKVIHDLLEQLPPMFWPVPTHRPERCLGPALQAAFLLLKGT-F----AGGRIIVFQGGLPTVG-PGKLKSR 156 (239)
T ss_pred ceeeeHHHHHHHHHHHHHhhhhhccccCCCCCcccHHHHHHHHHHHHhhc-C----CCceEEEEECCCCCCC-CCccccC
Confidence 11 12223333221 11224678999999998652 1 2457888887644322 11
Q ss_pred C--------------CCchhhHHHHHHHHhhcCcEEEEEeeccCCCCCCCcchhhhhhHHHHHHhhcCCCeEeehh
Q 005544 138 V--------------GTKEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVD 199 (691)
Q Consensus 138 ~--------------~~~~~~l~~i~~~L~~~gI~l~vi~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~~~~~ 199 (691)
+ ....+-.+.++..+...||.+++|....++ -+-..+..++..++|.++...
T Consensus 157 ~~~~~~~~~~e~~~~~~a~~fY~~la~~~~~~~isvdlF~~~~~~----------~dl~~l~~l~~~TGG~v~~y~ 222 (239)
T cd01468 157 EDKEPIRSHDEAQLLKPATKFYKSLAKECVKSGICVDLFAFSLDY----------VDVATLKQLAKSTGGQVYLYD 222 (239)
T ss_pred cccccCCCccchhcccccHHHHHHHHHHHHHcCeEEEEEeccccc----------cCHHHhhhhhhcCCceEEEeC
Confidence 0 011234578999999999999999873311 112446677888888865433
No 72
>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=94.43 E-value=0.5 Score=48.39 Aligned_cols=176 Identities=13% Similarity=0.179 Sum_probs=92.5
Q ss_pred eEEEEEEecCCC-cc-CChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeec--------
Q 005544 6 EALLLLLDVSPS-MH-SVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDI-------- 75 (691)
Q Consensus 6 ea~vflIDvs~s-M~-~~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l-------- 75 (691)
=+.+|+||+|.. .. ..++.+.+.+...+.. +-..++.+||+|.|++.-+=-.+.... ......+..++
T Consensus 4 p~y~FvID~s~~av~~g~~~~~~~sl~~~l~~-l~~~~~~~vgiitfd~~V~~y~l~~~~-~~~~~~v~~dl~~~~~p~~ 81 (243)
T PF04811_consen 4 PVYVFVIDVSYEAVQSGLLQSLIESLKSALDS-LPGDERTRVGIITFDSSVHFYNLSSSL-SQPQMIVVSDLDDPFIPLP 81 (243)
T ss_dssp -EEEEEEE-SHHHHHHTHHHHHHHHHHHHGCT-SSTSTT-EEEEEEESSSEEEEETTTTS-SSTEEEEEHHTTSHHSSTS
T ss_pred CEEEEEEECchhhhhccHHHHHHHHHHHHHHh-ccCCCCcEEEEEEeCCEEEEEECCCCc-CCCcccchHHHhhcccCCc
Confidence 367999999954 11 2345667777776642 223589999999998764222221110 11222233332
Q ss_pred -------CCCCH---HHHHHhhcCCCCC----CCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCC----
Q 005544 76 -------KVVDG---HLVQSLKHLPQGT----CAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPD---- 137 (691)
Q Consensus 76 -------~~~~~---~~l~~L~~l~~~~----~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~---- 137 (691)
..... ..|+.|.++.... ...-+..||.+|..+|.... ..=||++|+.+-...+...
T Consensus 82 ~~llv~~~e~~~~i~~ll~~L~~~~~~~~~~~~~~c~G~Al~~A~~ll~~~~-----~gGkI~~F~s~~pt~G~Gg~l~~ 156 (243)
T PF04811_consen 82 DGLLVPLSECRDAIEELLESLPSIFPETAGKRPERCLGSALSAALSLLSSRN-----TGGKILVFTSGPPTYGPGGSLKK 156 (243)
T ss_dssp SSSSEETTTCHHHHHHHHHHHHHHSTT-TTB-----HHHHHHHHHHHHHHHT-----S-EEEEEEESS---SSSTTSS-S
T ss_pred ccEEEEhHHhHHHHHHHHHHhhhhcccccccCccccHHHHHHHHHHHHhccc-----cCCEEEEEeccCCCCCCCceecc
Confidence 22111 1334444422211 12247789999999987421 2347888876643222100
Q ss_pred ------CC----------CchhhHHHHHHHHhhcCcEEEEEeeccCCCCCCCcchhhhhhHHHHHHhhcCCCeEeeh
Q 005544 138 ------VG----------TKEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFV 198 (691)
Q Consensus 138 ------~~----------~~~~~l~~i~~~L~~~gI~l~vi~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~~~~ 198 (691)
.+ ...+-...++..+...||.+++|....++ -+-..+..++..++|.++..
T Consensus 157 ~~~~~~~~~~~~~~~~~~~~~~fY~~la~~~~~~~isvDlf~~~~~~----------~~l~tl~~l~~~TGG~l~~y 223 (243)
T PF04811_consen 157 REDSSHYDTEKEKALLLPPANEFYKKLAEECSKQGISVDLFVFSSDY----------VDLATLGPLARYTGGSLYYY 223 (243)
T ss_dssp BTTSCCCCHCTTHHCHSHSSSHHHHHHHHHHHHCTEEEEEEEECSS------------SHHHHTHHHHCTT-EEEEE
T ss_pred cccccccccccchhhhccccchHHHHHHHHHHhcCCEEEEEeecCCC----------CCcHhHHHHHHhCceeEEEe
Confidence 00 01124688999999999999999884311 12345677888899986543
No 73
>TIGR01651 CobT cobaltochelatase, CobT subunit. This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit, with a MW ~70 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobS (TIGR01650) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobT gene product, the P. denitrificans gene symbol is not used in the name of this model.
Probab=93.96 E-value=0.86 Score=51.66 Aligned_cols=150 Identities=16% Similarity=0.164 Sum_probs=76.7
Q ss_pred eEEEEEEecCCCccCChhH-HHHHHHHHHHHHHhcCCccEEEEEEEcCCCC---C-ccccc------cCCC---cCcEEE
Q 005544 6 EALLLLLDVSPSMHSVLPD-VEKLCSRLIQKKLIYGKNHEVGVILFGTEET---E-NELTK------EVGG---YEHVKV 71 (691)
Q Consensus 6 ea~vflIDvs~sM~~~l~~-a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t---~-n~l~~------e~~~---y~nI~v 71 (691)
-++-|+||+|.||...... |..++..|.+.. .+-.=-+-|+.|-|..- . ...+- ..|. ..|| |
T Consensus 393 ~~V~LLID~SGSM~~r~~~vA~~~a~iLa~aL--~~~gIp~eVlGFtt~aw~gg~~re~w~~~g~p~~PgRlN~l~hi-i 469 (600)
T TIGR01651 393 TVVTLLIDNSGSMRGRPITVAATCADILARTL--ERCGVKVEILGFTTRAWKGGQSREKWLKAGKPAAPGRLNDLRHI-I 469 (600)
T ss_pred cEEEEEEECCccCCCCHHHHHHHHHHHHHHHH--HHCCCCeEEEeecccccccccchHHHHhcCCCCCCcccchhhhh-h
Confidence 4678999999999976554 333444333322 23344456777777621 1 00000 0111 1233 2
Q ss_pred EeecCCCCHHHHHHhhcC-----CCCCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCC-----CCCc
Q 005544 72 LQDIKVVDGHLVQSLKHL-----PQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPD-----VGTK 141 (691)
Q Consensus 72 ~~~l~~~~~~~l~~L~~l-----~~~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~-----~~~~ 141 (691)
+..-..|--..-+.|..+ ....-+ ..||..|.+.|..+ .-..|-+++||||. |.+... ...-
T Consensus 470 yk~ad~~wr~~r~~l~~mm~~~~~~eN~D---GeAl~wa~~rL~~R----~e~rKiL~ViSDG~-P~D~~TlsvN~~~~l 541 (600)
T TIGR01651 470 YKSADAPWRRARRNLGLMMREGLLKENID---GEALMWAHQRLIAR----PEQRRILMMISDGA-PVDDSTLSVNPGNYL 541 (600)
T ss_pred hhccccchhhhccchhhhhhccccccCCc---hHHHHHHHHHHhcC----cccceEEEEEeCCC-cCCccccccCchhHH
Confidence 333333311111111111 111112 36777777766542 12356678888884 454211 0112
Q ss_pred hhhHHHHHHHHhhc-CcEEEEEeecc
Q 005544 142 EDQVSTIARQMVAF-GLRMKNIVVRA 166 (691)
Q Consensus 142 ~~~l~~i~~~L~~~-gI~l~vi~i~~ 166 (691)
...++.++..+... ||.|.-|||+.
T Consensus 542 ~~hLr~vi~~~e~~~~vel~aigIg~ 567 (600)
T TIGR01651 542 ERHLRAVIEEIETRSPVELLAIGIGH 567 (600)
T ss_pred HHHHHHHHHHHhccCCceEEEeeccc
Confidence 33577888888885 99999999965
No 74
>COG5242 TFB4 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 [Transcription / DNA replication, recombination, and repair]
Probab=93.76 E-value=1 Score=44.32 Aligned_cols=173 Identities=17% Similarity=0.198 Sum_probs=99.0
Q ss_pred EEEEEEecCCCccCCh------hHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCcc-------c-cccCCCcCcEEEE
Q 005544 7 ALLLLLDVSPSMHSVL------PDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENE-------L-TKEVGGYEHVKVL 72 (691)
Q Consensus 7 a~vflIDvs~sM~~~l------~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~-------l-~~e~~~y~nI~v~ 72 (691)
-++.+||+.|.-...+ ..++.-+.-++.-.+-.+.+.+|+||.-.++...-- + +.|.+.-.|--.+
T Consensus 22 lL~viid~~p~~W~~~~ek~~~~kvl~di~VFLNAhlaf~~~NrVaVva~~s~~~~yLypss~s~~k~se~e~tr~sd~y 101 (296)
T COG5242 22 LLFVIIDLEPENWELTTEKGSRDKVLNDIVVFLNAHLAFSRNNRVAVVAGYSQGKTYLYPSSESALKASESENTRNSDMY 101 (296)
T ss_pred eEEEEEecChhhcccccccccHHHHHHHHHHHHHHHHhhccCCeEEEEEeccCceEEeccCcchhhhhhcccCccchhhh
Confidence 4677899998776644 234555666677777778999999998766542110 0 0111111122222
Q ss_pred eecCCCCHHHHHH---hhcCCCC-CCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeC-CCCCCCCCCCCCchhhHHH
Q 005544 73 QDIKVVDGHLVQS---LKHLPQG-TCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITD-ALCPLKDPDVGTKEDQVST 147 (691)
Q Consensus 73 ~~l~~~~~~~l~~---L~~l~~~-~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD-~~~p~~~~~~~~~~~~l~~ 147 (691)
+.+..++--.+.. |-+.+.. +...++..|+-.++....+. .+...-+-||++||- |.+- .+|.--
T Consensus 102 rrfr~vde~~i~eiyrl~e~~~k~sqr~~v~gams~glay~n~~-~~e~slkSriliftlsG~d~---------~~qYip 171 (296)
T COG5242 102 RRFRNVDETDITEIYRLIEHPHKNSQRYDVGGAMSLGLAYCNHR-DEETSLKSRILIFTLSGRDR---------KDQYIP 171 (296)
T ss_pred hhhcccchHHHHHHHHHHhCcccccceeehhhhhhhhHHHHhhh-cccccccceEEEEEecCchh---------hhhhch
Confidence 2233333333333 3333332 33456666777777665442 333344678999987 2111 122211
Q ss_pred H---HHHHhhcCcEEEEEeeccCCCCCCCcchhhhhhHHHHHHhhcCCCeEeehhhhH
Q 005544 148 I---ARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDSTT 202 (691)
Q Consensus 148 i---~~~L~~~gI~l~vi~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~~~~~~a~ 202 (691)
+ +=..++.||.+.++.|.+ |..+|.+-++.++|.|.++++..
T Consensus 172 ~mnCiF~Aqk~~ipI~v~~i~g-------------~s~fl~Q~~daTgG~Yl~ve~~e 216 (296)
T COG5242 172 YMNCIFAAQKFGIPISVFSIFG-------------NSKFLLQCCDATGGDYLTVEDTE 216 (296)
T ss_pred hhhheeehhhcCCceEEEEecC-------------ccHHHHHHhhccCCeeEeecCch
Confidence 1 223567899999998843 34788888888999999888853
No 75
>PF03850 Tfb4: Transcription factor Tfb4; InterPro: IPR004600 Members of this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. The core-TFIIH basal transcription factor complex has six subunits, this is the p34 subunit.; GO: 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent, 0000439 core TFIIH complex
Probab=93.24 E-value=0.77 Score=47.87 Aligned_cols=181 Identities=14% Similarity=0.134 Sum_probs=109.5
Q ss_pred EEEEEEecCCCccC------ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCc----cccccCCCcCcE-------
Q 005544 7 ALLLLLDVSPSMHS------VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETEN----ELTKEVGGYEHV------- 69 (691)
Q Consensus 7 a~vflIDvs~sM~~------~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n----~l~~e~~~y~nI------- 69 (691)
-+|++||++|.-.. .+..+++.+..++..-+..+...+|+||..+...+.- +...+...-.++
T Consensus 3 LLvIILD~nP~~W~~~~~~~~l~~~l~~llvFlNahL~l~~~N~vaVIAs~~~~s~~LYP~~~~~~~~~~~~~~~~~~~~ 82 (276)
T PF03850_consen 3 LLVIILDTNPLAWGQLSDQLSLSQFLDSLLVFLNAHLALNHSNQVAVIASHSNSSKFLYPSPSSSESSNSGDVEMNSSDS 82 (276)
T ss_pred EEEEEEECCHHHHhhccccccHHHHHHHHHHHHHHHHhhCccCCEEEEEEcCCccEEEeCCCccccccCCCccccccccc
Confidence 57999999986432 3677888888899988889999999999999876421 100000000000
Q ss_pred EEEeecCCCCHHHHHHhhcCCCC-------CCCCchhhHHHHHHHHHHHHhcc----CCcccceEEE-EeCCCCCCCCCC
Q 005544 70 KVLQDIKVVDGHLVQSLKHLPQG-------TCAGDFLDAIVVGVDMLIKKYGE----TYKGKKHLCL-ITDALCPLKDPD 137 (691)
Q Consensus 70 ~v~~~l~~~~~~~l~~L~~l~~~-------~~~gd~~daL~va~d~l~~~~~~----~k~~~krIvL-~TD~~~p~~~~~ 137 (691)
.-+.++...+-...+.|+++... +....+..||-.|+=.+.+.... ....+.||++ ++...+..
T Consensus 83 ~~y~~f~~v~~~v~~~l~~l~~~~~~~~~~~~~s~LagALS~ALCyINR~~~~~~~~~~~~~~RILv~~s~s~d~~---- 158 (276)
T PF03850_consen 83 NKYRQFRNVDETVLEELKKLMSETSESSDSTTSSLLAGALSMALCYINRISRESPSGGTSLKSRILVIVSGSPDSS---- 158 (276)
T ss_pred chhHHHHHHHHHHHHHHHHHHhhcccccccccchhhHHHHHHHHHHHhhhhhcccCCCCCcCccEEEEEecCCCcc----
Confidence 01112222233344555554211 11245667888888776663211 1245778888 55543321
Q ss_pred CCCchhhHHHHHHHHhhcCcEEEEEeeccCCCCCCCcchhhhhhHHHHHHhhcCCCeEeehhhhHHhh
Q 005544 138 VGTKEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDSTTSLR 205 (691)
Q Consensus 138 ~~~~~~~l~~i~~~L~~~gI~l~vi~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~~~~~~a~~ll 205 (691)
..+-.+-..+=..++.+|.+++..++. .+..+|++.+.-++|.|..+.+...++
T Consensus 159 --~QYi~~MN~iFaAqk~~v~IDv~~L~~------------~~s~fLqQa~d~T~G~y~~~~~~~~l~ 212 (276)
T PF03850_consen 159 --SQYIPLMNCIFAAQKQKVPIDVCKLGG------------KDSTFLQQASDITGGIYLKVSKPEGLL 212 (276)
T ss_pred --HHHHHHHHHHHHHhcCCceeEEEEecC------------CchHHHHHHHHHhCceeeccCccccHH
Confidence 112234455667789999999999843 124789999999999998877654333
No 76
>PF12257 DUF3608: Protein of unknown function (DUF3608); InterPro: IPR022046 This domain family is found in eukaryotes, and is approximately 280 amino acids in length. The family is found in association with PF00610 from PFAM.
Probab=92.97 E-value=0.83 Score=47.40 Aligned_cols=154 Identities=18% Similarity=0.318 Sum_probs=100.9
Q ss_pred EEEEEEecCCCccCC-------hhHHHH-HHHHHHHHHHhcCCccEEEEEEEcCCCCC----ccccc-c----CCCcCcE
Q 005544 7 ALLLLLDVSPSMHSV-------LPDVEK-LCSRLIQKKLIYGKNHEVGVILFGTEETE----NELTK-E----VGGYEHV 69 (691)
Q Consensus 7 a~vflIDvs~sM~~~-------l~~a~~-~~~~l~~~ki~~~~~D~VGvVlfgt~~t~----n~l~~-e----~~~y~nI 69 (691)
-+++.|.+|..|... ++.+.+ ....++++---..-++.|.+|||..-.-+ .++.. + ..+|-.|
T Consensus 72 r~~~~IQmS~EMW~fd~~Ge~~fek~vn~Fl~~lf~kWk~~~~~H~vTIVlfsRv~~~~~~~~~l~~~~~~~~y~DfYrV 151 (281)
T PF12257_consen 72 RVYIFIQMSSEMWDFDEDGEIYFEKAVNGFLPELFKKWKEIGTHHLVTIVLFSRVDYDDISFRDLPPGERGKNYKDFYRV 151 (281)
T ss_pred eeeehHhhhHHHhCcCccHHHHHHHHHHHHHHHHHHHHhhcCCCceEEEEEEEEEccccchhhcCCccccCCCCCcceEE
Confidence 357788999999763 344443 44555554444568899999999843211 11211 1 1255566
Q ss_pred EEEeecCCCCHHH-HHHhhc--------C----C---C------C----CCCCchhhHHHHHHHHHHHHhccCC--cccc
Q 005544 70 KVLQDIKVVDGHL-VQSLKH--------L----P---Q------G----TCAGDFLDAIVVGVDMLIKKYGETY--KGKK 121 (691)
Q Consensus 70 ~v~~~l~~~~~~~-l~~L~~--------l----~---~------~----~~~gd~~daL~va~d~l~~~~~~~k--~~~k 121 (691)
|++.....+|.. +..|+. + + . | ..+|++++||-+|++.+.+++..+. ....
T Consensus 152 -Vv~~~~~~~W~~il~~Lk~eF~~f~rdi~~~~~~~~~~~~~i~g~~s~A~~gNiLEaINlaln~~~~~~idRdl~rTG~ 230 (281)
T PF12257_consen 152 -VVDEENSQDWTSILVTLKKEFNQFQRDILLYHQSDEDGTTRIKGRFSPAIKGNILEAINLALNQFDKHYIDRDLRRTGQ 230 (281)
T ss_pred -EEeccccccHHHHHHHHHHHHHHHHHHhhcccccccCCCccccceEeecccccHHHHHHHHhhhcccccccCcccccCc
Confidence 455665566653 333332 1 1 0 0 2357899999999999887765432 3567
Q ss_pred eEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEEeecc
Q 005544 122 HLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIVVRA 166 (691)
Q Consensus 122 rIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~l~vi~i~~ 166 (691)
.|++||-|.+=++. +++-+....+.|-+.||.+.+|-++.
T Consensus 231 ~iivITpG~Gvf~V-----d~~ll~~T~~rl~~~gi~~DlIcL~~ 270 (281)
T PF12257_consen 231 SIIVITPGTGVFEV-----DYDLLRLTTQRLLDNGIGIDLICLSK 270 (281)
T ss_pred eEEEEcCCCceEEE-----CHHHHHHHHHHHHhcCccEEEEEcCC
Confidence 79999999887763 45677778889999999999999865
No 77
>COG4548 NorD Nitric oxide reductase activation protein [Inorganic ion transport and metabolism]
Probab=92.54 E-value=0.46 Score=52.58 Aligned_cols=152 Identities=18% Similarity=0.184 Sum_probs=78.1
Q ss_pred eEEEEEEecCCCccCChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCCHHHH-H
Q 005544 6 EALLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHLV-Q 84 (691)
Q Consensus 6 ea~vflIDvs~sM~~~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~~~~l-~ 84 (691)
-++.++||||.||+..+++.++.+..+......-. +|+=.+|-...-+..++..-.+..|.++.+++..-.+.+ -
T Consensus 447 la~TLLvD~S~St~a~mdetrRvidl~~eaL~~la----~~~qa~gd~~~~~~fts~rr~~vri~tvk~FDes~~~~~~~ 522 (637)
T COG4548 447 LAFTLLVDVSASTDAKMDETRRVIDLFHEALLVLA----HGHQALGDSEDILDFTSRRRPWVRINTVKDFDESMGETVGP 522 (637)
T ss_pred ceeEEEeecccchHHHhhhhhhhHHHHHHHHHHhh----chhhhhCCHHHhcCchhhcCcceeeeeeeccccccccccch
Confidence 36789999999999988776555544443221111 111122222211221111112223334444433222211 1
Q ss_pred HhhcCCCCCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCC-CchhhHHHHHHHHhhcCcEEEEEe
Q 005544 85 SLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVG-TKEDQVSTIARQMVAFGLRMKNIV 163 (691)
Q Consensus 85 ~L~~l~~~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~-~~~~~l~~i~~~L~~~gI~l~vi~ 163 (691)
.+..|.++... -..-||-+|..-|.. +....|-++|||||..+--+-++| ..-++....+...+..||++..+.
T Consensus 523 RImALePg~yt-R~G~AIR~As~kL~~----rpq~qklLivlSDGkPnd~d~YEgr~gIeDTr~AV~eaRk~Gi~VF~Vt 597 (637)
T COG4548 523 RIMALEPGYYT-RDGAAIRHASAKLME----RPQRQKLLIVLSDGKPNDFDHYEGRFGIEDTREAVIEARKSGIEVFNVT 597 (637)
T ss_pred hheecCccccc-cccHHHHHHHHHHhc----CcccceEEEEecCCCcccccccccccchhhHHHHHHHHHhcCceEEEEE
Confidence 23334333211 124577777776543 223467799999997643221221 222345667788899999998888
Q ss_pred ecc
Q 005544 164 VRA 166 (691)
Q Consensus 164 i~~ 166 (691)
++.
T Consensus 598 ld~ 600 (637)
T COG4548 598 LDR 600 (637)
T ss_pred ecc
Confidence 843
No 78
>PF11775 CobT_C: Cobalamin biosynthesis protein CobT VWA domain
Probab=92.52 E-value=0.95 Score=45.01 Aligned_cols=152 Identities=16% Similarity=0.147 Sum_probs=73.4
Q ss_pred eEEEEEEecCCCccCC-hhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCc--c--ccccCC--CcCcE------EEE
Q 005544 6 EALLLLLDVSPSMHSV-LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETEN--E--LTKEVG--GYEHV------KVL 72 (691)
Q Consensus 6 ea~vflIDvs~sM~~~-l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n--~--l~~e~~--~y~nI------~v~ 72 (691)
-++-|+||+|.||..+ ...|..++..+.+-. .+-+=-+=|+.|.|..-+- . .+...| .|++- .++
T Consensus 13 ~~VtlLID~SGSMrgr~~~vA~~~adila~aL--~~~gvp~EVlGFtT~aw~gg~~~~~w~~~G~p~~pgrln~l~h~vy 90 (219)
T PF11775_consen 13 TVVTLLIDCSGSMRGRPIEVAALCADILARAL--ERCGVPVEVLGFTTRAWKGGRSREAWLAAGRPRYPGRLNDLRHIVY 90 (219)
T ss_pred eEEEEEEeCCcCCCCChHHHHHHHHHHHHHHH--HhCCCCeEEEeeecCCcCCcchHHHHHhcCCCCCChHHHHHHHHHH
Confidence 4678999999999874 555655555555432 2334445567787763211 0 011111 11110 011
Q ss_pred eecCCCCHHHHHHhhcC-----CCCCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCC---CC--Cch
Q 005544 73 QDIKVVDGHLVQSLKHL-----PQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPD---VG--TKE 142 (691)
Q Consensus 73 ~~l~~~~~~~l~~L~~l-----~~~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~---~~--~~~ 142 (691)
...+.|.-..-+.|.-+ ....-+ .+||..|...|.. ..-..|-+++|+|| .|.+++. +. .-.
T Consensus 91 k~a~~~wrraR~~l~~m~~~~~~~eniD---GeAl~~a~~rL~~----r~e~rkiLiViSDG-~P~d~st~~~n~~~~L~ 162 (219)
T PF11775_consen 91 KDADTPWRRARRNLGLMMREGLLKENID---GEALRWAAERLLA----RPEQRKILIVISDG-APADDSTLSANDGDYLD 162 (219)
T ss_pred HhcCChhhhHHHhHHHHhhccccccCCc---HHHHHHHHHHHHc----CCccceEEEEEeCC-CcCcccccccCChHHHH
Confidence 11122211111111111 111112 3566555555543 22234567777887 4553210 11 112
Q ss_pred hhHHHHHHHHhhc-CcEEEEEeeccC
Q 005544 143 DQVSTIARQMVAF-GLRMKNIVVRAS 167 (691)
Q Consensus 143 ~~l~~i~~~L~~~-gI~l~vi~i~~~ 167 (691)
..+..+++.+... +|+|.-|||+.+
T Consensus 163 ~HLr~vi~~ie~~~~Vel~aiGIg~D 188 (219)
T PF11775_consen 163 AHLRQVIAEIETRSDVELIAIGIGHD 188 (219)
T ss_pred HHHHHHHHHHhccCCcEEEEEEcCCC
Confidence 3567788888764 799988888653
No 79
>KOG2487 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 [Transcription; Replication, recombination and repair]
Probab=92.33 E-value=1.6 Score=44.20 Aligned_cols=174 Identities=15% Similarity=0.158 Sum_probs=100.9
Q ss_pred EEEEEEecCC---CccCC------hhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCcccccc-CCCcCcEEEEe---
Q 005544 7 ALLLLLDVSP---SMHSV------LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKE-VGGYEHVKVLQ--- 73 (691)
Q Consensus 7 a~vflIDvs~---sM~~~------l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e-~~~y~nI~v~~--- 73 (691)
-++++||++| .|+.. ...+++.+.-+....+..+.+.+|+||..+.+..+--..+. .+.-+|...+-
T Consensus 25 lL~vlId~~p~~Wg~~as~~~~~ti~kvl~aivVFlNAHL~~~~~NrvaViA~~~q~~~~lyp~st~~e~~n~~~~~~t~ 104 (314)
T KOG2487|consen 25 LLVVLIDANPCSWGMLASAENWETISKVLNAIVVFLNAHLAFSRNNRVAVIASHSQVDNYLYPSSTRCEDRNASELDPTR 104 (314)
T ss_pred eEEEEEecCcchhhhhhhhcCceeHHHHHHHHHHHHHHHHhhccCCcEEEEEecccccceeccccccCCccCccccCchh
Confidence 4789999999 45442 23456677777788888899999999999877532111000 01112222222
Q ss_pred -------ecCCCCHHHHHHhhcCCC---CC-------CCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCC
Q 005544 74 -------DIKVVDGHLVQSLKHLPQ---GT-------CAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDP 136 (691)
Q Consensus 74 -------~l~~~~~~~l~~L~~l~~---~~-------~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~ 136 (691)
.+...+.-.++.+..+-. .. -.|.+.+||-....+-++. ..-+-+-||++||-...-..
T Consensus 105 ~~~~~y~~~~~~d~tiv~ei~~lm~~~~~~~~~~rt~lagals~~L~yi~~~~ke~--~~~~lkSRilV~t~t~d~~~-- 180 (314)
T KOG2487|consen 105 LVLFDYSEFRTVDDTIVEEIYRLMEHPDKYDVGDRTVLAGALSDALGYINRLHKEE--ASEKLKSRILVFTLTRDRAL-- 180 (314)
T ss_pred hhcchhhhhcccchHHHHHHHHHHhCccccccccceeeccchhhccchHhhhhhhh--hhhhhhceEEEEEechHHHh--
Confidence 223333334555554311 11 1234455555554443332 11245789999998543211
Q ss_pred CCCCchhhHHHHHHHHhhcCcEEEEEeeccCCCCCCCcchhhhhhHHHHHHhhcCCCeEeehhhh
Q 005544 137 DVGTKEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVDST 201 (691)
Q Consensus 137 ~~~~~~~~l~~i~~~L~~~gI~l~vi~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~~~~~~a 201 (691)
.+-.+-..+=..++.+|-+.++.++++ ..+|.+-++.++|.|..++..
T Consensus 181 ----qyi~~MNciFaAqKq~I~Idv~~l~~~-------------s~~LqQa~D~TGG~YL~v~~~ 228 (314)
T KOG2487|consen 181 ----QYIPYMNCIFAAQKQNIPIDVVSLGGD-------------SGFLQQACDITGGDYLHVEKP 228 (314)
T ss_pred ----hhhhHHHHHHHHHhcCceeEEEEecCC-------------chHHHHHHhhcCCeeEecCCc
Confidence 111233444466789999999999541 378888888889998887754
No 80
>KOG1984 consensus Vesicle coat complex COPII, subunit SFB3 [Intracellular trafficking, secretion, and vesicular transport]
Probab=92.20 E-value=5.2 Score=47.00 Aligned_cols=211 Identities=14% Similarity=0.184 Sum_probs=111.4
Q ss_pred eEEEEEEecCCCc--cCChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCC----CccccccCCCcCcEEEEeecCCC-
Q 005544 6 EALLLLLDVSPSM--HSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEET----ENELTKEVGGYEHVKVLQDIKVV- 78 (691)
Q Consensus 6 ea~vflIDvs~sM--~~~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t----~n~l~~e~~~y~nI~v~~~l~~~- 78 (691)
-+.||.||||=.- -.....+-+.++.++.......++-+||+|+|...-. +..|+ =.++.++.+++.+
T Consensus 418 pafvFmIDVSy~Ai~~G~~~a~ce~ik~~l~~lp~~~p~~~Vgivtfd~tvhFfnl~s~L~-----qp~mliVsdv~dvf 492 (1007)
T KOG1984|consen 418 PAFVFMIDVSYNAISNGAVKAACEAIKSVLEDLPREEPNIRVGIVTFDKTVHFFNLSSNLA-----QPQMLIVSDVDDVF 492 (1007)
T ss_pred ceEEEEEEeehhhhhcchHHHHHHHHHHHHhhcCccCCceEEEEEEecceeEeeccCcccc-----CceEEEeecccccc
Confidence 4789999998321 1122333455555555444467889999999986421 11111 1223333332211
Q ss_pred -------------CHHHHHH-hhcCC---CC--CCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCC--
Q 005544 79 -------------DGHLVQS-LKHLP---QG--TCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPD-- 137 (691)
Q Consensus 79 -------------~~~~l~~-L~~l~---~~--~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~-- 137 (691)
+...|+. |.+++ .+ ..+.-+.+||-+|+..|.. . . .-++++|++-..-.+.+.
T Consensus 493 vPf~~g~~V~~~es~~~i~~lLd~Ip~mf~~sk~pes~~g~alqaa~lalk~--~--~--gGKl~vF~s~Lpt~g~g~kl 566 (1007)
T KOG1984|consen 493 VPFLDGLFVNPNESRKVIELLLDSIPTMFQDSKIPESVFGSALQAAKLALKA--A--D--GGKLFVFHSVLPTAGAGGKL 566 (1007)
T ss_pred cccccCeeccchHHHHHHHHHHHHhhhhhccCCCCchhHHHHHHHHHHHHhc--c--C--CceEEEEecccccccCcccc
Confidence 1112222 12232 11 2234577888888888653 1 1 345777777544333210
Q ss_pred --------CCCchh---------hHHHHHHHHhhcCcEEEEEeeccCCCCCCCcchhhhhhHHHHHHhhcCCCeEeeh--
Q 005544 138 --------VGTKED---------QVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFV-- 198 (691)
Q Consensus 138 --------~~~~~~---------~l~~i~~~L~~~gI~l~vi~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~~~~-- 198 (691)
.+++++ -..++++++-+.||.+++|.....|. +-..+-.++.-++|++|..
T Consensus 567 ~~r~D~~l~~t~kek~l~~pq~~~y~~LA~e~v~~g~svDlF~t~~ayv----------DvAtlg~v~~~TgG~vy~Y~~ 636 (1007)
T KOG1984|consen 567 SNRDDRRLIGTDKEKNLLQPQDKTYTTLAKEFVESGCSVDLFLTPNAYV----------DVATLGVVPALTGGQVYKYYP 636 (1007)
T ss_pred cccchhhhhcccchhhccCcchhHHHHHHHHHHHhCceEEEEEccccee----------eeeeecccccccCceeEEecc
Confidence 011111 25689999999999999998733211 0122223455567875432
Q ss_pred -h---hhHHhhcccccccCCCcceeeeeEEecCCeEEEEEEEee
Q 005544 199 -D---STTSLRGARKTRDISPVTIFRGDLELSEKMKIKVWVYKK 238 (691)
Q Consensus 199 -~---~a~~ll~~~~~k~~~~~~~~~g~L~lg~~l~I~V~~Y~~ 238 (691)
. +...++..++.--.++. -|++.++....--|.|..|.-
T Consensus 637 F~a~~D~~rl~nDL~~~vtk~~-gf~a~mrvRtStGirv~~f~G 679 (1007)
T KOG1984|consen 637 FQALTDGPRLLNDLVRNVTKKQ-GFDAVMRVRTSTGIRVQDFYG 679 (1007)
T ss_pred hhhcccHHHHHHHHHHhcccce-eeeeEEEEeecCceeeeeeec
Confidence 2 22355555544334433 677777777666666766654
No 81
>KOG2326 consensus DNA-binding subunit of a DNA-dependent protein kinase (Ku80 autoantigen) [Replication, recombination and repair]
Probab=92.16 E-value=0.0022 Score=70.71 Aligned_cols=134 Identities=19% Similarity=0.279 Sum_probs=94.8
Q ss_pred CCccccccccccCCceEeCChhhHHhhccCCCccEEEEeEeeCCCCcceeccCCeEEEEcC--CCChhhHHHHHHHHHHH
Q 005544 281 VPPEQRIKGYRYGPQVVPISSAEWEAVKFKPEKSVKLLGFTDASNILRHYYMKDVNLFIAE--PGNSRATVAVSALARAM 358 (691)
Q Consensus 281 v~~ed~~kgy~yG~~~Vp~s~~e~~~~k~~~~~~l~ilGF~~~~~i~~~~~~~~~~~i~p~--~~~~~s~~afsaL~~Am 358 (691)
+.++.+.++|.||..++.+..-+-.+.++.+.+.++.+||-.+..|+||.+-+.+.+++.. +.. .+..||++|+.-+
T Consensus 325 ikkssv~~~Y~~g~~~~Vlpa~dd~~a~~a~ssli~al~~l~r~Al~Ry~~~~ks~pql~vl~Ph~-~~~~~~~yLvdVq 403 (669)
T KOG2326|consen 325 IKKSSVTKAYRYGADYVVLPAVDDDQAVYASSSLIDALGFLNREALPRYFLTSKSSPQLAVLRPHC-QSDLAFSYLVDVQ 403 (669)
T ss_pred eccccccceeeecCceEEecccCchHhHHhhhHHHHHHhhhhHHHhhhhhhccCCCceEeeecccc-ccccceeeEEEee
Confidence 5788999999999999999996666777888999999999999999999997776544432 333 3444889999888
Q ss_pred HhcCceEEEEEEecCCCCceEEEEeeccccCCCCCCCe------EEEecCCChh---cccCCCCCCC
Q 005544 359 KEMNKVAIVRCVWRQGQQSVVVGVLTPNVSEKINIPDS------FYFNVLPFAE---DVREFQFPSF 416 (691)
Q Consensus 359 ~e~~~vaI~r~v~r~~~~p~~v~~L~P~~~~~~~~~~~------l~~v~LPFae---DvR~~~fp~l 416 (691)
+.--.-+.++++.+-... ..++-+.|+...-.++-+| .-++.+||++ +.|.-.+|.+
T Consensus 404 LPF~eD~R~y~Fskf~~~-~n~~pt~aql~AVsnlID~M~L~ksdtl~~~pf~p~~~~mr~hrL~ql 469 (669)
T KOG2326|consen 404 LPFREDARAYYFSKFDSE-VNMCPTCAQLIAVSNLIDEMKLVKSDTLCRLPFAPPKLDMRVHRLPQL 469 (669)
T ss_pred ccchhhhHHhhcccccch-hccCchHHHHHHHHHHhhhhhhhhhccccCCCCCCCCccchhhhHHHH
Confidence 887777778888776543 4455555654432211111 2345678877 6665554443
No 82
>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=91.94 E-value=2.6 Score=46.18 Aligned_cols=152 Identities=18% Similarity=0.206 Sum_probs=82.2
Q ss_pred EEEEEecCCCccCChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCC-----------Ccccccc------CCCcCcEE
Q 005544 8 LLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEET-----------ENELTKE------VGGYEHVK 70 (691)
Q Consensus 8 ~vflIDvs~sM~~~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t-----------~n~l~~e------~~~y~nI~ 70 (691)
+.|++|+|.||...++..+.....|++..--..++=++|+=.|--... .|+-... .=+|+|+
T Consensus 102 LYyLMDlS~SM~ddl~~lk~lg~~L~~~m~~it~n~rlGfGsFVDK~v~P~~~t~p~~l~~PC~~~~~~c~p~f~f~~~- 180 (423)
T smart00187 102 LYYLMDLSYSMKDDLDNLKSLGDDLAREMKGLTSNFRLGFGSFVDKTVSPFVSTRPEKLENPCPNYNLTCEPPYGFKHV- 180 (423)
T ss_pred eEEEEeCCccHHHHHHHHHHHHHHHHHHHHhcccCceeeEEEeecCccCCcccCCHHHhcCCCcCCCCCcCCCcceeee-
Confidence 579999999999988877777666665443356888888866553311 1221110 0177886
Q ss_pred EEeecCCCCHHHHHHhhcCC-CCCCC--CchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCC----------
Q 005544 71 VLQDIKVVDGHLVQSLKHLP-QGTCA--GDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPD---------- 137 (691)
Q Consensus 71 v~~~l~~~~~~~l~~L~~l~-~~~~~--gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~---------- 137 (691)
.+|..-.-..-+.+.+.. +|..+ -.=+|||..|.=- .++.+=++...|-+|+.||+..-+.++.
T Consensus 181 --L~LT~~~~~F~~~V~~~~iSgN~D~PEgG~DAimQaaVC-~~~IGWR~~a~rllv~~TDa~fH~AGDGkLaGIv~PND 257 (423)
T smart00187 181 --LSLTDDTDEFNEEVKKQRISGNLDAPEGGFDAIMQAAVC-TEQIGWREDARRLLVFSTDAGFHFAGDGKLAGIVQPND 257 (423)
T ss_pred --ccCCCCHHHHHHHHhhceeecCCcCCcccHHHHHHHHhh-ccccccCCCceEEEEEEcCCCccccCCcceeeEecCCC
Confidence 566554444555566542 22111 0127777655411 1111212223344556677654322100
Q ss_pred --------------CCCchhhHHHHHHHHhhcCcEEEEEee
Q 005544 138 --------------VGTKEDQVSTIARQMVAFGLRMKNIVV 164 (691)
Q Consensus 138 --------------~~~~~~~l~~i~~~L~~~gI~l~vi~i 164 (691)
...++-.+..+++.|.+++|.+. |.+
T Consensus 258 g~CHL~~~g~Yt~s~~~DYPSi~ql~~kL~e~nI~~I-FAV 297 (423)
T smart00187 258 GQCHLDNNGEYTMSTTQDYPSIGQLNQKLAENNINPI-FAV 297 (423)
T ss_pred CcceeCCCCCcCccCcCCCCCHHHHHHHHHhcCceEE-EEE
Confidence 00122357889999999999553 444
No 83
>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=91.81 E-value=6.7 Score=40.78 Aligned_cols=90 Identities=10% Similarity=0.084 Sum_probs=54.6
Q ss_pred chhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCC----C---------CCc----------hhhHHHHHHHHh
Q 005544 97 DFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPD----V---------GTK----------EDQVSTIARQMV 153 (691)
Q Consensus 97 d~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~----~---------~~~----------~~~l~~i~~~L~ 153 (691)
-...||.+|..++.. +. + ...=||++|+.+-...+... + +.. .+-...++.++.
T Consensus 142 ~~G~Al~~A~~ll~~-~~-~-~~gGki~~F~sg~pT~GpG~l~~r~~~~~~r~~~d~~~~~~~~~~~a~~fY~~la~~~~ 218 (267)
T cd01478 142 CTGVALSIAVGLLEA-CF-P-NTGARIMLFAGGPCTVGPGAVVSTELKDPIRSHHDIDKDNAKYYKKAVKFYDSLAKRLA 218 (267)
T ss_pred chHHHHHHHHHHHHh-hc-C-CCCcEEEEEECCCCCCCCceeeccccccccccccccccchhhhhhhHHHHHHHHHHHHH
Confidence 467899999999875 22 1 23468888888754332100 0 000 122345778888
Q ss_pred hcCcEEEEEeeccCCCCCCCcchhhhhhHHHHHHhhcCCCeEeehh
Q 005544 154 AFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVD 199 (691)
Q Consensus 154 ~~gI~l~vi~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~~~~~ 199 (691)
+.||.+++|....+. -+-.-+..++..++|.++..+
T Consensus 219 ~~~vsvDlF~~s~d~----------vglaem~~l~~~TGG~v~~~~ 254 (267)
T cd01478 219 ANGHAVDIFAGCLDQ----------VGLLEMKVLVNSTGGHVVLSD 254 (267)
T ss_pred hCCeEEEEEeccccc----------cCHHHHHHHHHhcCcEEEEeC
Confidence 899999998873211 112446677888899866443
No 84
>PLN00162 transport protein sec23; Provisional
Probab=91.57 E-value=4.6 Score=48.45 Aligned_cols=128 Identities=15% Similarity=0.106 Sum_probs=73.1
Q ss_pred chhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCC-----C---------C----------CchhhHHHHHHHH
Q 005544 97 DFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPD-----V---------G----------TKEDQVSTIARQM 152 (691)
Q Consensus 97 d~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~-----~---------~----------~~~~~l~~i~~~L 152 (691)
-...||.+|..+|.. +. . ...=||++|+.|-...+ ++ + + ...+-.+.++..+
T Consensus 263 ~tG~AL~vA~~lL~~-~~-~-~~gGrI~~F~sgppT~G-pG~v~~r~~~~~~rsh~di~k~~~~~~~~a~~fY~~la~~~ 338 (761)
T PLN00162 263 CTGAALSVAAGLLGA-CV-P-GTGARIMAFVGGPCTEG-PGAIVSKDLSEPIRSHKDLDKDAAPYYKKAVKFYEGLAKQL 338 (761)
T ss_pred cHHHHHHHHHHHHhh-cc-C-CCceEEEEEeCCCCCCC-CceeecccccccccCccccccchhhhcchHHHHHHHHHHHH
Confidence 367899999999865 22 1 23568888887643221 11 0 0 0012245688889
Q ss_pred hhcCcEEEEEeeccCCCCCCCcchhhhhhHHHHHHhhcCCCeEeehh---hh--H-Hhhccccccc-CCCcceeeeeEEe
Q 005544 153 VAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLFVD---ST--T-SLRGARKTRD-ISPVTIFRGDLEL 225 (691)
Q Consensus 153 ~~~gI~l~vi~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~~~~~---~a--~-~ll~~~~~k~-~~~~~~~~g~L~l 225 (691)
.+.||.+++|....++ -+-.-++.++..++|.++-.+ .. . ++...+.+.. .-....|.+.|++
T Consensus 339 ~~~gisvDlF~~s~dq----------vglaem~~l~~~TGG~v~~~~sF~~~~f~~~l~r~~~r~~~~~~~~gf~a~~~V 408 (761)
T PLN00162 339 VAQGHVLDVFACSLDQ----------VGVAEMKVAVERTGGLVVLAESFGHSVFKDSLRRVFERDGEGSLGLSFNGTFEV 408 (761)
T ss_pred HHcCceEEEEEccccc----------cCHHHHhhhHhhcCcEEEEeCCcChHHHHHHHHHHhcccccccccccceeEEEE
Confidence 9999999999763211 112446677888899865332 21 1 2222222110 0012478888988
Q ss_pred cCCeEEEEEEEee
Q 005544 226 SEKMKIKVWVYKK 238 (691)
Q Consensus 226 g~~l~I~V~~Y~~ 238 (691)
...-.|.|.+|.-
T Consensus 409 rtS~glkv~g~~G 421 (761)
T PLN00162 409 NCSKDVKVQGAIG 421 (761)
T ss_pred EecCCeEEeeeEc
Confidence 8666677776653
No 85
>PTZ00395 Sec24-related protein; Provisional
Probab=91.06 E-value=7.2 Score=48.30 Aligned_cols=217 Identities=12% Similarity=0.114 Sum_probs=112.1
Q ss_pred eEEEEEEecCCC-ccCC-hhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCC----Cccc------cccCCCc--CcEEE
Q 005544 6 EALLLLLDVSPS-MHSV-LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEET----ENEL------TKEVGGY--EHVKV 71 (691)
Q Consensus 6 ea~vflIDvs~s-M~~~-l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t----~n~l------~~e~~~y--~nI~v 71 (691)
-+.+||||||.. +..- +..+.+.|...+.+. ..+.-+||+|.|.+.-. +..+ .+..++. ....|
T Consensus 953 P~YvFLIDVS~~AVkSGLl~tacesIK~sLDsL--~dpRTRVGIITFDSsLHFYNLks~l~~~~~~~~~~~~l~qPQMLV 1030 (1560)
T PTZ00395 953 PYFVFVVECSYNAIYNNITYTILEGIRYAVQNV--KCPQTKIAIITFNSSIYFYHCKGGKGVSGEEGDGGGGSGNHQVIV 1030 (1560)
T ss_pred CEEEEEEECCHHHHhhChHHHHHHHHHHHHhcC--CCCCcEEEEEEecCcEEEEecCcccccccccccccccCCCceEEe
Confidence 368999999964 2222 345566666666542 35778999999987531 0000 0001112 23334
Q ss_pred EeecCC-----C-C---------HH----HHHHhhcCCCC--CCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCC
Q 005544 72 LQDIKV-----V-D---------GH----LVQSLKHLPQG--TCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDAL 130 (691)
Q Consensus 72 ~~~l~~-----~-~---------~~----~l~~L~~l~~~--~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~ 130 (691)
+.+|.. | + .+ +|..|.++-.. ....-+..||.+|+.+|.. .+. .=+|++|...-
T Consensus 1031 VSDLDDPFLPlP~ddLLVnL~ESRevIe~LLDkLPemFt~t~~~esCLGSALqAA~~aLk~-~GG----GGKIiVF~SSL 1105 (1560)
T PTZ00395 1031 MSDVDDPFLPLPLEDLFFGCVEEIDKINTLIDTIKSVSTTMQSYGSCGNSALKIAMDMLKE-RNG----LGSICMFYTTT 1105 (1560)
T ss_pred ecCCccCcCCCCccCeeechHHHHHHHHHHHHHHHHHhhccCCCcccHHHHHHHHHHHHHh-cCC----CceEEEEEcCC
Confidence 444321 1 1 11 23333332111 2233567899999999865 221 13455554432
Q ss_pred CCCCCC-------------CCCCchhhHHHHHHHHhhcCcEEEEEeeccCCCCCCCcchhhhhhHHHHHHhhcCCCeEee
Q 005544 131 CPLKDP-------------DVGTKEDQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTLF 197 (691)
Q Consensus 131 ~p~~~~-------------~~~~~~~~l~~i~~~L~~~gI~l~vi~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~~~ 197 (691)
..++.. ......+-...++.++.+.+|.|++|.+...+.+ -.-..|-.++..++|+++.
T Consensus 1106 PniGpGaLK~Re~~~KEk~Ll~pqd~FYK~LA~ECsk~qISVDLFLfSsqYvD--------VDVATLg~Lsr~TGGqlyy 1177 (1560)
T PTZ00395 1106 PNCGIGAIKELKKDLQENFLEVKQKIFYDSLLLDLYAFNISVDIFIISSNNVR--------VCVPSLQYVAQNTGGKILF 1177 (1560)
T ss_pred CCCCCCcccccccccccccccccchHHHHHHHHHHHhcCCceEEEEccCcccc--------cccccccchhcccceeEEE
Confidence 222110 0001223567899999999999999987431110 0012344567778887543
Q ss_pred hh------hhHHhhcccccccCCCcceeeeeEEecCCeEEEEEEEe
Q 005544 198 VD------STTSLRGARKTRDISPVTIFRGDLELSEKMKIKVWVYK 237 (691)
Q Consensus 198 ~~------~a~~ll~~~~~k~~~~~~~~~g~L~lg~~l~I~V~~Y~ 237 (691)
.. +...+...+...-.+.-..|.+.|++...=-|.|..|.
T Consensus 1178 YPnFna~rD~~KL~~DL~r~LTre~iGyEAVMRVRCS~GLrVs~fy 1223 (1560)
T PTZ00395 1178 VENFLWQKDYKEIYMNIMDTLTSEDIAYCCELKLRYSHHMSVKKLF 1223 (1560)
T ss_pred eCCCcccccHHHHHHHHHHHhhccceeeEEEEEEECCCCeEEEEEe
Confidence 22 12233333332222222479999998865556666665
No 86
>KOG3768 consensus DEAD box RNA helicase [General function prediction only]
Probab=89.98 E-value=6.3 Score=44.30 Aligned_cols=110 Identities=23% Similarity=0.265 Sum_probs=63.8
Q ss_pred EEEEEEecCCCccCC-------hhHHHHHHHHHHHHHHhc--CCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCC
Q 005544 7 ALLLLLDVSPSMHSV-------LPDVEKLCSRLIQKKLIY--GKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKV 77 (691)
Q Consensus 7 a~vflIDvs~sM~~~-------l~~a~~~~~~l~~~ki~~--~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~ 77 (691)
+++|+||-|.||.+. |+.|+.++.++++++-.. .-.|+.=++.|--.. .||-+... .
T Consensus 3 i~lFllDTS~SM~qrah~~~tylD~AKgaVEtFiK~R~r~~~~~gdryml~TfeepP------------~~vk~~~~--~ 68 (888)
T KOG3768|consen 3 IFLFLLDTSGSMSQRAHPQFTYLDLAKGAVETFIKQRTRVGRETGDRYMLTTFEEPP------------KNVKVACE--K 68 (888)
T ss_pred eEEEEEecccchhhhccCCchhhHHHHHHHHHHHHHHhccccccCceEEEEecccCc------------hhhhhHHh--h
Confidence 789999999999874 678899999999866432 244555455443221 12222111 1
Q ss_pred CCHHHHHHhhcCCCCCCCCchhhHHHHHHHHHHHH--------hcc-C---CcccceEEEEeCCC
Q 005544 78 VDGHLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKK--------YGE-T---YKGKKHLCLITDAL 130 (691)
Q Consensus 78 ~~~~~l~~L~~l~~~~~~gd~~daL~va~d~l~~~--------~~~-~---k~~~krIvL~TD~~ 130 (691)
..+-.+++|++|......+-...++.-|.|+|.-. ++. + ..---.||+||||.
T Consensus 69 ~~a~~~~eik~l~a~~~s~~~~~~~t~AFdlLnlnR~qtGID~yGqGR~pf~lEP~~iI~iTDG~ 133 (888)
T KOG3768|consen 69 LGAVVIEEIKKLHAPYGSCQLHHAITEAFDLLNLNRVQTGIDGYGQGRLPFNLEPVTIILITDGG 133 (888)
T ss_pred cccHHHHHHHhhcCccchhhhhHHHHHHhhhhhhhhhhhcccccccccCccccCceEEEEEecCC
Confidence 22346788888765433333345555577776421 111 1 11234599999994
No 87
>KOG2353 consensus L-type voltage-dependent Ca2+ channel, alpha2/delta subunit [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=89.81 E-value=3.4 Score=50.78 Aligned_cols=140 Identities=17% Similarity=0.237 Sum_probs=90.1
Q ss_pred CCCCeEEEEEEecCCCccC-ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCCH
Q 005544 2 ARTREALLLLLDVSPSMHS-VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDG 80 (691)
Q Consensus 2 a~~Kea~vflIDvs~sM~~-~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~~ 80 (691)
|++..-+||++|+|+||.. .++-|+..+..++.. -+.+|.|-++.|+... |++.. . -...|-+.++
T Consensus 222 At~pKdiviLlD~SgSm~g~~~~lak~tv~~iLdt---Ls~~Dfvni~tf~~~~--~~v~p--c------~~~~lvqAt~ 288 (1104)
T KOG2353|consen 222 ATSPKDIVILLDVSGSMSGLRLDLAKQTVNEILDT---LSDNDFVNILTFNSEV--NPVSP--C------FNGTLVQATM 288 (1104)
T ss_pred cCCccceEEEEeccccccchhhHHHHHHHHHHHHh---cccCCeEEEEeecccc--Ccccc--c------ccCceeecch
Confidence 4567789999999999976 467778888888873 4899999999999864 22210 0 1233444555
Q ss_pred HHHHHhhcCCC---CCCCCchhhHHHHHHHHHHHHhccCC------cccceEEEEeCCCCCCCCCCCCCchhhHHHHHHH
Q 005544 81 HLVQSLKHLPQ---GTCAGDFLDAIVVGVDMLIKKYGETY------KGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQ 151 (691)
Q Consensus 81 ~~l~~L~~l~~---~~~~gd~~daL~va~d~l~~~~~~~k------~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~ 151 (691)
.-++.|.+... ..+.+++--|+-.|.++|.. +.... --.+-|+|||||-.. ....|.+.
T Consensus 289 ~nk~~~~~~i~~l~~k~~a~~~~~~e~aF~lL~~-~n~s~~~~~~~~C~~~iml~tdG~~~-----------~~~~If~~ 356 (1104)
T KOG2353|consen 289 RNKKVFKEAIETLDAKGIANYTAALEYAFSLLRD-YNDSRANTQRSPCNQAIMLITDGVDE-----------NAKEIFEK 356 (1104)
T ss_pred HHHHHHHHHHhhhccccccchhhhHHHHHHHHHH-hccccccccccccceeeEEeecCCcc-----------cHHHHHHh
Confidence 55555555321 22345677788889998875 32211 146779999976432 34455555
Q ss_pred Hhh--cCcEEEEEeecc
Q 005544 152 MVA--FGLRMKNIVVRA 166 (691)
Q Consensus 152 L~~--~gI~l~vi~i~~ 166 (691)
-+. ..|++..+.+|.
T Consensus 357 yn~~~~~Vrvftflig~ 373 (1104)
T KOG2353|consen 357 YNWPDKKVRVFTFLIGD 373 (1104)
T ss_pred hccCCCceEEEEEEecc
Confidence 443 567777777753
No 88
>PF09967 DUF2201: VWA-like domain (DUF2201); InterPro: IPR018698 This family of various hypothetical bacterial proteins has no known function.
Probab=87.70 E-value=4 Score=37.28 Aligned_cols=41 Identities=24% Similarity=0.323 Sum_probs=27.4
Q ss_pred EEEEEecCCCccCC-hhHHHHHHHHHHHHHHhcCCccEEEEEEEcCC
Q 005544 8 LLLLLDVSPSMHSV-LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTE 53 (691)
Q Consensus 8 ~vflIDvs~sM~~~-l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~ 53 (691)
++++||.|.||... +..++.-+..++++ . ..+|-||-|-+.
T Consensus 1 i~vaiDtSGSis~~~l~~fl~ev~~i~~~----~-~~~v~vi~~D~~ 42 (126)
T PF09967_consen 1 IVVAIDTSGSISDEELRRFLSEVAGILRR----F-PAEVHVIQFDAE 42 (126)
T ss_pred CEEEEECCCCCCHHHHHHHHHHHHHHHHh----C-CCCEEEEEECCE
Confidence 57999999999863 44445444555552 2 556888877765
No 89
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=87.16 E-value=4.1 Score=42.00 Aligned_cols=154 Identities=16% Similarity=0.204 Sum_probs=83.4
Q ss_pred EEEEEEecCCCccCC------hhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCCH
Q 005544 7 ALLLLLDVSPSMHSV------LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDG 80 (691)
Q Consensus 7 a~vflIDvs~sM~~~------l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~~ 80 (691)
.++++||||.+|-+. ...+.+.+..++-.-.-.+|-..+|+|.....-. .| + ..+.----
T Consensus 89 hl~l~lD~Seam~e~Df~p~r~a~vikya~~Fv~eFf~qNPiSqlsii~irdg~a---------~~--~---s~~~gnpq 154 (421)
T COG5151 89 HLHLILDVSEAMDESDFLPTRRANVIKYAEGFVPEFFSQNPISQLSIISIRDGCA---------KY--T---SSMDGNPQ 154 (421)
T ss_pred eeEEEEEhhhhhhhhhccchHHHHHHHHHHHHhHHHhccCCchheeeeehhhhHH---------HH--h---hhcCCCHH
Confidence 578999999999874 1223344443333222267888889888764210 00 0 01110001
Q ss_pred HHHHHhhcCCCCCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEE
Q 005544 81 HLVQSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMK 160 (691)
Q Consensus 81 ~~l~~L~~l~~~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~l~ 160 (691)
..|.+|+++..-.+...+..||-.|.-.+... ..-..|-|.+|-..-+..+ ..++-..++.|...+|++.
T Consensus 155 ~hi~~lkS~rd~~gnfSLqNaLEmar~~l~~~---~~H~trEvLiifgS~st~D-------Pgdi~~tid~Lv~~~IrV~ 224 (421)
T COG5151 155 AHIGQLKSKRDCSGNFSLQNALEMARIELMKN---TMHGTREVLIIFGSTSTRD-------PGDIAETIDKLVAYNIRVH 224 (421)
T ss_pred HHHHHhhcccccCCChhHHhHHHHhhhhhccc---ccccceEEEEEEeecccCC-------CccHHHHHHHHHhhceEEE
Confidence 35667776653222233456666553333221 1122455544433222211 1346677889999999999
Q ss_pred EEeeccCCCCCCCcchhhhhhHHHHHHhhcC----CCeEee
Q 005544 161 NIVVRASLSGEPHMRVIIENDNLLNIFSKKS----SAKTLF 197 (691)
Q Consensus 161 vi~i~~~~~~~~~~~~~~~ne~~l~~l~~~~----~g~~~~ 197 (691)
++|+.. .-.+.++++..+ .|.|+-
T Consensus 225 ~igL~a-------------evaicKeickaTn~~~e~~y~v 252 (421)
T COG5151 225 FIGLCA-------------EVAICKEICKATNSSTEGRYYV 252 (421)
T ss_pred EEeehh-------------HHHHHHHHHhhcCcCcCceeEe
Confidence 999833 136677787776 456553
No 90
>cd01459 vWA_copine_like VWA Copine: Copines are phospholipid-binding proteins originally identified in paramecium. They are found in human and orthologues have been found in C. elegans and Arabidopsis Thaliana. None have been found in D. Melanogaster or S. Cereviciae. Phylogenetic distribution suggests that copines have been lost in some eukaryotes. No functional properties have been assigned to the VWA domains present in copines. The members of this subgroup contain a functional MIDAS motif based on their preferential binding to magnesium and manganese. However, the MIDAS motif is not totally conserved, in most cases the MIDAS consists of the sequence DxTxS instead of the motif DxSxS that is found in most cases. The C2 domains present in copines mediate phospholipid binding.
Probab=84.88 E-value=35 Score=35.22 Aligned_cols=137 Identities=13% Similarity=0.186 Sum_probs=77.8
Q ss_pred eEEEEEEecCCCccCC----------------hhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcE
Q 005544 6 EALLLLLDVSPSMHSV----------------LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHV 69 (691)
Q Consensus 6 ea~vflIDvs~sM~~~----------------l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI 69 (691)
-.+++.||.+.|=+.+ .+.|+..+-.+++. +...-.+-+.+||+..+.+. ...|
T Consensus 32 ~nl~vaIDfT~SNg~p~~~~SLHy~~~~~~N~Yq~aI~~vg~il~~---yD~D~~ip~~GFGa~~~~~~------~v~~- 101 (254)
T cd01459 32 SNLIVAIDFTKSNGWPGEKRSLHYISPGRLNPYQKAIRIVGEVLQP---YDSDKLIPAFGFGAIVTKDQ------SVFS- 101 (254)
T ss_pred eeEEEEEEeCCCCCCCCCCCCcccCCCCCccHHHHHHHHHHHHHHh---cCCCCceeeEeecccCCCCC------cccc-
Confidence 3578999998874321 23455555555552 67889999999999654332 1111
Q ss_pred EEEee--cCCC---CHH-HHHHhhc----CCCCCCCCchhhHHHHHHHHHHHHhccCCcccce-EEEEeCCCCCCCCCCC
Q 005544 70 KVLQD--IKVV---DGH-LVQSLKH----LPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKH-LCLITDALCPLKDPDV 138 (691)
Q Consensus 70 ~v~~~--l~~~---~~~-~l~~L~~----l~~~~~~gd~~daL~va~d~l~~~~~~~k~~~kr-IvL~TD~~~p~~~~~~ 138 (691)
+.| ...| ..+ .++..++ +.- .+..++...|--|+++..+. .. ..+-. +++||||.-.
T Consensus 102 --~f~~~~~~p~~~Gi~gvl~aY~~~l~~v~l-sGpT~fapvI~~a~~~a~~~-~~--~~~Y~VLLIiTDG~i~------ 169 (254)
T cd01459 102 --FFPGYSESPECQGFEGVLRAYREALPNVSL-SGPTNFAPVIRAAANIAKAS-NS--QSKYHILLIITDGEIT------ 169 (254)
T ss_pred --ccCCCCCCCcccCHHHHHHHHHHHhceeee-cCcchHHHHHHHHHHHHHHh-cC--CCceEEEEEECCCCcc------
Confidence 111 0111 112 3333333 221 22346666676777764431 11 11234 6667999652
Q ss_pred CCchhhHHHHHHHHhhcCcEEEEEeecc
Q 005544 139 GTKEDQVSTIARQMVAFGLRMKNIVVRA 166 (691)
Q Consensus 139 ~~~~~~l~~i~~~L~~~gI~l~vi~i~~ 166 (691)
+.++....+.+..+.-+.+.++|+|.
T Consensus 170 --D~~~t~~aIv~AS~~PlSIiiVGVGd 195 (254)
T cd01459 170 --DMNETIKAIVEASKYPLSIVIVGVGD 195 (254)
T ss_pred --cHHHHHHHHHHHhcCCeEEEEEEeCC
Confidence 23556666667788899999999964
No 91
>KOG1986 consensus Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking, secretion, and vesicular transport]
Probab=80.14 E-value=80 Score=36.76 Aligned_cols=169 Identities=14% Similarity=0.149 Sum_probs=89.2
Q ss_pred EEEEEecCCCccC-ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEee------------
Q 005544 8 LLLLLDVSPSMHS-VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQD------------ 74 (691)
Q Consensus 8 ~vflIDvs~sM~~-~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~------------ 74 (691)
.+|+||.- |.+ .+...+.++...+. +...+-.||+|.||+--.-..++.+ +....+|+..
T Consensus 124 f~fVvDtc--~~eeeL~~LkssL~~~l~---lLP~~alvGlItfg~~v~v~el~~~--~~sk~~VF~G~ke~s~~q~~~~ 196 (745)
T KOG1986|consen 124 FVFVVDTC--MDEEELQALKSSLKQSLS---LLPENALVGLITFGTMVQVHELGFE--ECSKSYVFSGNKEYSAKQLLDL 196 (745)
T ss_pred EEEEEeec--cChHHHHHHHHHHHHHHh---hCCCcceEEEEEecceEEEEEcCCC--cccceeEEeccccccHHHHHHH
Confidence 47788765 544 34444444444443 3578999999999987533333111 2222233333
Q ss_pred -----------------------cCCCCHHHHHHhhcCCCCC-----CCC---chhhHHHHHHHHHHHHhccCCcccceE
Q 005544 75 -----------------------IKVVDGHLVQSLKHLPQGT-----CAG---DFLDAIVVGVDMLIKKYGETYKGKKHL 123 (691)
Q Consensus 75 -----------------------l~~~~~~~l~~L~~l~~~~-----~~g---d~~daL~va~d~l~~~~~~~k~~~krI 123 (691)
+......+..-|.+|++.. ++- --.-||-+|+.+|.. +. .....||
T Consensus 197 L~~~~~~~~~~~~~~~~~rFL~P~~~c~~~L~~lle~L~~d~wpV~~g~Rp~RcTG~Al~iA~~Ll~~-c~--p~~g~rI 273 (745)
T KOG1986|consen 197 LGLSGGAGKGSENQSASNRFLLPAQECEFKLTNLLEELQPDPWPVPPGHRPLRCTGVALSIASGLLEG-CF--PNTGARI 273 (745)
T ss_pred hcCCcccccCCcccccchhhhccHHHHHHHHHHHHHHhcCCCCCCCCCCCcccchhHHHHHHHHHhcc-cC--CCCcceE
Confidence 3333333333333343320 000 135688899999865 32 2557999
Q ss_pred EEEeCCCCCCCC----------C---CCCCch----------hhHHHHHHHHhhcCcEEEEEeeccCCCCCCCcchhhhh
Q 005544 124 CLITDALCPLKD----------P---DVGTKE----------DQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIEN 180 (691)
Q Consensus 124 vL~TD~~~p~~~----------~---~~~~~~----------~~l~~i~~~L~~~gI~l~vi~i~~~~~~~~~~~~~~~n 180 (691)
++|+.|-+..+. | .-+.+. .-.+.+++.+..+|--++++.-.-+ . -.
T Consensus 274 v~f~gGPcT~GpG~vv~~el~~piRshhdi~~d~a~y~kKa~KfY~~La~r~~~~ghvlDifa~~lD--Q--------vG 343 (745)
T KOG1986|consen 274 VLFAGGPCTRGPGTVVSRELKEPIRSHHDIEKDNAPYYKKAIKFYEKLAERLANQGHVLDIFAAALD--Q--------VG 343 (745)
T ss_pred EEeccCCCCcCCceecchhhcCCCcCcccccCcchHHHHHHHHHHHHHHHHHHhCCceEeeeeeecc--c--------cc
Confidence 999999332110 0 000000 1235678888899988887753111 0 11
Q ss_pred hHHHHHHhhcCCCeEe
Q 005544 181 DNLLNIFSKKSSAKTL 196 (691)
Q Consensus 181 e~~l~~l~~~~~g~~~ 196 (691)
---++.++..++|-+.
T Consensus 344 i~EMk~l~~~TGG~lv 359 (745)
T KOG1986|consen 344 ILEMKPLVESTGGVLV 359 (745)
T ss_pred hHHHHHHhhcCCcEEE
Confidence 2335566777777654
No 92
>COG2718 Uncharacterized conserved protein [Function unknown]
Probab=78.11 E-value=25 Score=37.90 Aligned_cols=105 Identities=15% Similarity=0.230 Sum_probs=60.2
Q ss_pred CCeEEEEE-EecCCCccCChhH-HHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCCHH
Q 005544 4 TREALLLL-LDVSPSMHSVLPD-VEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGH 81 (691)
Q Consensus 4 ~Kea~vfl-IDvs~sM~~~l~~-a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~~~ 81 (691)
+..|+||| +|||.||.+.-.+ |+... ++-.+-+.++-+.|-||+..-....-.. +|. .|
T Consensus 244 es~AVmfclMDvSGSM~~~~KdlAkrFF--~lL~~FL~~kYenveivfIrHht~A~EV-dE~-dF--------------- 304 (423)
T COG2718 244 ESNAVMFCLMDVSGSMDQSEKDLAKRFF--FLLYLFLRRKYENVEIVFIRHHTEAKEV-DET-DF--------------- 304 (423)
T ss_pred ccceEEEEEEecCCCcchHHHHHHHHHH--HHHHHHHhcccceeEEEEEeecCcceec-chh-hc---------------
Confidence 34456655 6999999975322 22211 1112223477777877777654311111 010 11
Q ss_pred HHHHhhcCCCCCCCCc-hhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCC
Q 005544 82 LVQSLKHLPQGTCAGD-FLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKD 135 (691)
Q Consensus 82 ~l~~L~~l~~~~~~gd-~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~ 135 (691)
+-.....|. .++||-.+.+++..+|. ..-|+.-.+-++||++-+++
T Consensus 305 -------F~~~esGGTivSSAl~~m~evi~ErYp-~aeWNIY~fqaSDGDN~~dD 351 (423)
T COG2718 305 -------FYSQESGGTIVSSALKLMLEVIKERYP-PAEWNIYAFQASDGDNWADD 351 (423)
T ss_pred -------eeecCCCCeEeHHHHHHHHHHHHhhCC-hhheeeeeeeecCCccccCC
Confidence 111111233 56899999999988775 34788888888999997764
No 93
>TIGR02877 spore_yhbH sporulation protein YhbH. This protein family, typified by YhbH in Bacillus subtilis, is found in nearly every endospore-forming bacterium and in no other genome (but note that the trusted cutoff score is set high to exclude a single high-scoring sequence from Nitrosococcus oceani ATCC 19707, which is classified in the Gammaproteobacteria). The gene in Bacillus subtilis was shown to be in the regulon of the sporulation sigma factor, sigma-E, and its mutation was shown to create a sporulation defect.
Probab=76.51 E-value=26 Score=37.92 Aligned_cols=100 Identities=13% Similarity=0.222 Sum_probs=58.4
Q ss_pred CeEEEEEEecCCCccCChhHHHHH----HHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCCH
Q 005544 5 REALLLLLDVSPSMHSVLPDVEKL----CSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDG 80 (691)
Q Consensus 5 Kea~vflIDvs~sM~~~l~~a~~~----~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~~ 80 (691)
+-.+++++|||+||.+...+..+. +..+++ ++-..|=+|+..-+...-..+++ .|
T Consensus 202 ~AV~fc~MDvSGSM~~~~K~lak~ff~~ly~FL~-----~~Y~~VeivFI~H~t~AkEVdEe--eF-------------- 260 (371)
T TIGR02877 202 NAVVIAMMDTSGSMGQFKKYIARSFFFWMVKFLR-----TKYENVEICFISHHTEAKEVTEE--EF-------------- 260 (371)
T ss_pred cEEEEEEEeCCCCCCHHHHHHHHHHHHHHHHHHH-----hccCceEEEEEeecCeeEEcCHH--Hh--------------
Confidence 334556679999999864443322 233444 44556666665543321111000 11
Q ss_pred HHHHHhhcCCCCCCCC-chhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCC
Q 005544 81 HLVQSLKHLPQGTCAG-DFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLK 134 (691)
Q Consensus 81 ~~l~~L~~l~~~~~~g-d~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~ 134 (691)
+......| -.++|+-.|.+++.+++.. .-|+-=.+-+||||+=.+
T Consensus 261 --------F~~~EsGGT~vSSA~~l~~eII~~rYpp-~~wNIY~f~aSDGDNw~~ 306 (371)
T TIGR02877 261 --------FHKGESGGTYCSSGYKKALEIIDERYNP-ARYNIYAFHFSDGDNLTS 306 (371)
T ss_pred --------cccCCCCCeEehHHHHHHHHHHHhhCCh-hhCeeEEEEcccCCCccC
Confidence 11111123 3578999999999988753 578888888899998544
No 94
>PF04285 DUF444: Protein of unknown function (DUF444); InterPro: IPR006698 This entry is represented by Thermus phage phiYS40, Orf56. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches [].
Probab=76.19 E-value=17 Score=40.18 Aligned_cols=102 Identities=16% Similarity=0.186 Sum_probs=57.5
Q ss_pred EEEEEEecCCCccCChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCCHHHHHHh
Q 005544 7 ALLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGHLVQSL 86 (691)
Q Consensus 7 a~vflIDvs~sM~~~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~~~~l~~L 86 (691)
.++++.|||.||.+...+..+....++.. .+.++-+.|=+|+..-+...-... | +.|
T Consensus 248 Vv~~lmDvSGSM~~~~K~lak~ff~~l~~-fL~~~Y~~Ve~vfI~H~t~A~EVd-E-e~F-------------------- 304 (421)
T PF04285_consen 248 VVFCLMDVSGSMGEFKKDLAKRFFFWLYL-FLRRKYENVEIVFIRHHTEAKEVD-E-EEF-------------------- 304 (421)
T ss_pred EEEEEEeCCCCCchHHHHHHHHHHHHHHH-HHHhccCceEEEEEeecCceEEec-H-HHh--------------------
Confidence 45556799999998754443332222221 122444556666655433211110 0 011
Q ss_pred hcCCCCCCCC-chhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCC
Q 005544 87 KHLPQGTCAG-DFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLK 134 (691)
Q Consensus 87 ~~l~~~~~~g-d~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~ 134 (691)
+..+.+.| -+++|+-.|.+++.++|.. .-|+-=.+-+|||++=.+
T Consensus 305 --F~~~esGGT~vSSA~~l~~~ii~erypp-~~wNiY~~~~SDGDN~~~ 350 (421)
T PF04285_consen 305 --FHSRESGGTRVSSAYELALEIIEERYPP-SDWNIYVFHASDGDNWSS 350 (421)
T ss_pred --cccCCCCCeEehHHHHHHHHHHHhhCCh-hhceeeeEEcccCccccC
Confidence 11111223 4678999999999987753 478777888899998543
No 95
>PRK05325 hypothetical protein; Provisional
Probab=73.28 E-value=27 Score=38.37 Aligned_cols=99 Identities=18% Similarity=0.215 Sum_probs=58.5
Q ss_pred eEEEEEEecCCCccCChhHHHH----HHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCCHH
Q 005544 6 EALLLLLDVSPSMHSVLPDVEK----LCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDGH 81 (691)
Q Consensus 6 ea~vflIDvs~sM~~~l~~a~~----~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~~~ 81 (691)
-.+++++|||+||.+...+..+ .+..+++ ++-..|-+|+..-+...-... | +.|
T Consensus 223 AVmfclMDvSGSM~~~~K~lakrff~lly~fL~-----r~Y~~vEvvFI~H~t~AkEVd-E-eeF--------------- 280 (401)
T PRK05325 223 AVMFCLMDVSGSMDEAEKDLAKRFFFLLYLFLR-----RKYENVEVVFIRHHTEAKEVD-E-EEF--------------- 280 (401)
T ss_pred EEEEEEEeCCCCCchHHHHHHHHHHHHHHHHHH-----hccCceEEEEEeecCceeEcC-H-HHc---------------
Confidence 3455567999999986544332 2334444 455666666665443211110 0 011
Q ss_pred HHHHhhcCCCCCCCC-chhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCC
Q 005544 82 LVQSLKHLPQGTCAG-DFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLK 134 (691)
Q Consensus 82 ~l~~L~~l~~~~~~g-d~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~ 134 (691)
+......| -.++|+-.|.+++.+++.. .-|+-=.+-+||||+=.+
T Consensus 281 -------F~~~esGGT~vSSA~~l~~eIi~~rYpp-~~wNIY~f~aSDGDNw~~ 326 (401)
T PRK05325 281 -------FYSRESGGTIVSSAYKLALEIIEERYPP-AEWNIYAFQASDGDNWSS 326 (401)
T ss_pred -------cccCCCCCeEehHHHHHHHHHHHhhCCH-hHCeeEEEEcccCCCcCC
Confidence 11111123 4578999999999987753 478888888899998543
No 96
>PF07002 Copine: Copine; InterPro: IPR010734 This represents a conserved region approximately 180 residues long within eukaryotic copines. Copines are Ca2+-dependent phospholipid-binding proteins that are thought to be involved in membrane-trafficking, and may also be involved in cell division and growth [].
Probab=68.32 E-value=1.1e+02 Score=28.80 Aligned_cols=127 Identities=12% Similarity=0.147 Sum_probs=69.9
Q ss_pred ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEee-cCCCC---HH-HHHHhhc-CCCC--
Q 005544 21 VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQD-IKVVD---GH-LVQSLKH-LPQG-- 92 (691)
Q Consensus 21 ~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~-l~~~~---~~-~l~~L~~-l~~~-- 92 (691)
..+.|+.++-.+++. +...-.+-+..||..-+... ...|++-+.. ...|. .+ .++..++ ++.-
T Consensus 12 ~Y~~ai~~vg~il~~---Yd~dk~~p~~GFGa~~~~~~------~vsh~F~ln~~~~~p~~~Gi~gvl~~Y~~~~~~v~l 82 (146)
T PF07002_consen 12 PYQQAIRAVGEILQD---YDSDKMIPAYGFGAKIPPDY------SVSHCFPLNGNPQNPECQGIDGVLEAYRKALPKVQL 82 (146)
T ss_pred HHHHHHHHHHHHHHh---hccCCccceeccCCcCCCCc------ccccceeeecCCCCCcccCHHHHHHHHHHHhhheEE
Confidence 456788888877773 57888999999998654211 1233333321 11111 22 3333333 2211
Q ss_pred CCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEEeec
Q 005544 93 TCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNIVVR 165 (691)
Q Consensus 93 ~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~l~vi~i~ 165 (691)
.+...|...|-.|+++-... .+....---+++||||.-. +.++..+.+.+..+.-+.+.++|+|
T Consensus 83 ~GPT~fapiI~~a~~~a~~~-~~~~~~Y~iLlIlTDG~i~--------D~~~T~~aIv~AS~~PlSIIiVGVG 146 (146)
T PF07002_consen 83 SGPTNFAPIINHAAKIAKQS-NQNGQQYFILLILTDGQIT--------DMEETIDAIVEASKLPLSIIIVGVG 146 (146)
T ss_pred CCCccHHHHHHHHHHHHhhh-ccCCceEEEEEEecccccc--------cHHHHHHHHHHHccCCeEEEEEEeC
Confidence 23446777777777775431 1122223346677999742 1234444455566778888888874
No 97
>PF06707 DUF1194: Protein of unknown function (DUF1194); InterPro: IPR010607 This family consists of several hypothetical Rhizobiales specific proteins of around 270 residues in length. The function of this family is unknown.
Probab=61.83 E-value=1.8e+02 Score=29.04 Aligned_cols=141 Identities=15% Similarity=0.133 Sum_probs=76.5
Q ss_pred eEEEEEEecCCCccCC---hh---HHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecC-CC
Q 005544 6 EALLLLLDVSPSMHSV---LP---DVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIK-VV 78 (691)
Q Consensus 6 ea~vflIDvs~sM~~~---l~---~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~-~~ 78 (691)
-++|++||+|.||-.. |+ +|.-+-.--+.+-|...+.-.|+|-+|-=.... .+. ++.|=. .-
T Consensus 4 laLvLavDvS~SVD~~E~~lQ~~G~A~Al~dp~V~~Ai~~g~~g~Iav~~~eWsg~~---------~q~--~~v~Wt~i~ 72 (205)
T PF06707_consen 4 LALVLAVDVSGSVDADEYRLQREGYAAALRDPEVIAAILSGPIGRIAVAVVEWSGPG---------RQR--VVVPWTRID 72 (205)
T ss_pred ceeeeeeeccCCCCHHHHHHHHHHHHHHHCCHHHHHHHhcCCCCeEEEEEEEecCCC---------Cce--EEeCCEEeC
Confidence 4789999999999763 11 121122223444455677778877776533211 122 222311 12
Q ss_pred CHH----HHHHhhcCCCCC-CCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHh
Q 005544 79 DGH----LVQSLKHLPQGT-CAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMV 153 (691)
Q Consensus 79 ~~~----~l~~L~~l~~~~-~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~ 153 (691)
+.. ....|...+... ....+..||..|..+|.+. ...-+.|.|=+-.||-++.+. .-.....+.+.
T Consensus 73 ~~~da~a~A~~l~~~~r~~~~~Taig~Al~~a~~ll~~~--~~~~~RrVIDvSGDG~~N~G~-------~p~~~ard~~~ 143 (205)
T PF06707_consen 73 SPADAEAFAARLRAAPRRFGGRTAIGSALDFAAALLAQN--PFECWRRVIDVSGDGPNNQGP-------RPVTSARDAAV 143 (205)
T ss_pred CHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHHHHhC--CCCCceEEEEECCCCCCCCCC-------CccHHHHHHHH
Confidence 223 334445544332 2246788999999998752 211334444455666665441 11224455667
Q ss_pred hcCcEEEEEeecc
Q 005544 154 AFGLRMKNIVVRA 166 (691)
Q Consensus 154 ~~gI~l~vi~i~~ 166 (691)
..||.+.-+.|..
T Consensus 144 ~~GitINgL~I~~ 156 (205)
T PF06707_consen 144 AAGITINGLAILD 156 (205)
T ss_pred HCCeEEeeeEecC
Confidence 7899999888743
No 98
>COG1721 Uncharacterized conserved protein (some members contain a von Willebrand factor type A (vWA) domain) [General function prediction only]
Probab=57.87 E-value=16 Score=40.58 Aligned_cols=47 Identities=26% Similarity=0.422 Sum_probs=37.4
Q ss_pred CeEEEEEEecCCCcc------CChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCC
Q 005544 5 REALLLLLDVSPSMH------SVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTE 53 (691)
Q Consensus 5 Kea~vflIDvs~sM~------~~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~ 53 (691)
...+++++|+|.+|. ..+++|...+..+.. +....+|.||+.+||..
T Consensus 224 ~~~v~l~lD~~~~m~~~~~~~~~~e~av~~a~~la~--~~l~~gd~vg~~~~~~~ 276 (416)
T COG1721 224 GRTVVLVLDASRSMLFGSGVASKFEEAVRAAASLAY--AALKNGDRVGLLIFGGG 276 (416)
T ss_pred CceEEEEEeCCccccCCCCCccHHHHHHHHHHHHHH--HHHhCCCeeEEEEECCC
Confidence 457899999999998 457888777766655 23578999999999964
No 99
>PF00362 Integrin_beta: Integrin, beta chain; InterPro: IPR002369 Integrins are the major metazoan receptors for cell adhesion to extracellular matrix proteins and, in vertebrates, also play important roles in certain cell-cell adhesions, make transmembrane connections to the cytoskeleton and activate many intracellular signalling pathways [, ]. The integrin receptors are composed of alpha and beta subunit heterodimers. Each subunit crosses the membrane once, with most of the polypeptide residing in the extracellular space, and has two short cytoplasmic domains. Some members of this family have EGF repeats at the C terminus and also have a vWA domain inserted within the integrin domain at the N terminus. Most integrins recognise relatively short peptide motifs, and in general require an acidic amino acid to be present. Ligand specificity depends upon both the alpha and beta subunits []. There are at least 18 types of alpha and 8 types of beta subunits recognised in humans []. Each alpha subunit tends to associate only with one type of beta subunit, but there are exceptions to this rule []. Each association of alpha and beta subunits has its own binding specificity and signalling properties. Many integrins require activation on the cell surface before they can bind ligands. Integrins frequently intercommunicate, and binding at one integrin receptor activate or inhibit another. The structure of unliganded alphaV beta3 showed the molecule to be folded, with the head bent over towards the C termini of the legs which would normally be inserted into the membrane []. The head comprises a beta propeller domain at the end terminus of the alphaV subunit and an I/A domain inserted into a loop on the top of the hybrid domain in the beta subunit. The I/A domain consists of a Rossman fold with a core of beta parallel sheets surrounded by amphipathic alpha helices. Integrins are important therapeutic targets in conditions such as atherosclerosis, thrombosis, cancer and asthma []. At the N terminus of the beta subunit is a cysteine-containing domain reminiscent of that found in presenillins and semaphorins, which has hence been termed the PSI domain. C-terminal to the PSI domain is an A-domain, which has been predicted to adopt a Rossmann fold similar to that of the alpha subunit, but with additional loops between the second and third beta strands []. The murine gene Pactolus shares significant similarity with the beta subunit [], but lacks either one or both of the inserted loops. The C-terminal portion of the beta subunit extracellular domain contains an internally disulphide-bonded cysteine-rich region, while the intracellular tail contains putative sites of interaction with a variety of intracellular signalling and cytoskeletal proteins, such as focal adhesion kinase and alpha-actinin respectively []. Integrin cytoplasmic domains are normally less than 50 amino acids in length, with the beta-subunit sequences exhibiting greater homology to each other than the alpha-subunit sequences. This is consistent with current evidence that the beta subunit is the principal site for binding of cytoskeletal and signalling molecules, whereas the alpha subunit has a regulatory role. The first 20 amino acids of the beta-subunit cytoplasmic domain are also alpha helical, but the final 25 residues are disordered and, apart from a turn that follows a conserved NPxY motif, appear to lack defined structure, suggesting that this is adopted on effector binding. The two membrane-proximal helices mediate the link between the subunits via a series of hydrophobic and electrostatic contacts. This entry represents the N-terminal portion of the extracellular region of integrin beta subunits.; GO: 0005488 binding, 0007155 cell adhesion, 0007160 cell-matrix adhesion; PDB: 3VI4_B 3VI3_B 2VDQ_B 3IJE_B 1M1X_B 2VDR_B 3NIF_B 3NID_D 1TYE_F 2Q6W_F ....
Probab=55.72 E-value=38 Score=37.77 Aligned_cols=152 Identities=18% Similarity=0.185 Sum_probs=70.9
Q ss_pred EEEEEecCCCccCChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCC-----------CccccccC------CCcCcEE
Q 005544 8 LLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEET-----------ENELTKEV------GGYEHVK 70 (691)
Q Consensus 8 ~vflIDvs~sM~~~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t-----------~n~l~~e~------~~y~nI~ 70 (691)
+.|++|+|.||...++..+.....|++..---.++=++|+=.|--... .|+..... =+|+|+
T Consensus 105 LYyLmDlS~Sm~ddl~~l~~lg~~l~~~~~~it~~~~~GfGsfvdK~~~P~~~~~p~~l~~pc~~~~~~c~~~~~f~~~- 183 (426)
T PF00362_consen 105 LYYLMDLSYSMKDDLENLKSLGQDLAEEMRNITSNFRLGFGSFVDKPVMPFVSTTPEKLKNPCPSKNPNCQPPFSFRHV- 183 (426)
T ss_dssp EEEEEE-SGGGHHHHHHHCCCCHHHHHHHHTT-SSEEEEEEEESSSSSTTTST-SSHCHHSTSCCTTS--B---SEEEE-
T ss_pred EEEEeechhhhhhhHHHHHHHHHHHHHHHHhcCccceEechhhcccccCCcccCChhhhcCcccccCCCCCCCeeeEEe-
Confidence 579999999999887766444333333211134666666655554321 11210000 167775
Q ss_pred EEeecCCCCHHHHHHhhcCC-CCC--CCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCC----------
Q 005544 71 VLQDIKVVDGHLVQSLKHLP-QGT--CAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPD---------- 137 (691)
Q Consensus 71 v~~~l~~~~~~~l~~L~~l~-~~~--~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~---------- 137 (691)
.+|..-.....+.+.+.. ++. ..-.-+|||..|+=- .++.+=+....|-|++.||+..-+.++.
T Consensus 184 --l~Lt~~~~~F~~~v~~~~is~n~D~PEgg~dal~Qa~vC-~~~igWr~~a~~llv~~TD~~fH~agDg~l~gi~~pnd 260 (426)
T PF00362_consen 184 --LSLTDDITEFNEEVNKQKISGNLDAPEGGLDALMQAAVC-QEEIGWRNEARRLLVFSTDAGFHFAGDGKLAGIVKPND 260 (426)
T ss_dssp --EEEES-HHHHHHHHHTS--B--SSSSBSHHHHHHHHHH--HHHHT--STSEEEEEEEESS-B--TTGGGGGT--S---
T ss_pred --ecccchHHHHHHhhhhccccCCCCCCccccchheeeeec-ccccCcccCceEEEEEEcCCccccccccccceeeecCC
Confidence 455443334566666642 221 111247888765422 1112212234555666688754332210
Q ss_pred -----CC---------CchhhHHHHHHHHhhcCcEEEEEee
Q 005544 138 -----VG---------TKEDQVSTIARQMVAFGLRMKNIVV 164 (691)
Q Consensus 138 -----~~---------~~~~~l~~i~~~L~~~gI~l~vi~i 164 (691)
+. .++-.+..+.+.|.+.+|... |.+
T Consensus 261 ~~Chl~~~~~y~~~~~~DYPSv~ql~~~l~e~~i~~I-FAV 300 (426)
T PF00362_consen 261 GKCHLDDNGMYTASTEQDYPSVGQLVRKLSENNINPI-FAV 300 (426)
T ss_dssp SS--BSTTSBBGGGGCS----HHHHHHHHHHTTEEEE-EEE
T ss_pred CceEECCCCcccccccccCCCHHHHHHHHHHcCCEEE-EEE
Confidence 00 122246678888888888553 444
No 100
>COG5028 Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]
Probab=54.62 E-value=1.6e+02 Score=34.83 Aligned_cols=151 Identities=13% Similarity=0.180 Sum_probs=76.0
Q ss_pred EEEEEEecCC-CccCC-hhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCc-CcEEEEeecCCC-----
Q 005544 7 ALLLLLDVSP-SMHSV-LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGY-EHVKVLQDIKVV----- 78 (691)
Q Consensus 7 a~vflIDvs~-sM~~~-l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y-~nI~v~~~l~~~----- 78 (691)
..||+||||- +|... +..+.+.|..-+.+.-=..++-+||+|+|...-.=-.+ .++. +|..+..++..|
T Consensus 278 ~yvFlIDVS~~a~~~g~~~a~~r~Il~~l~~~~~~dpr~kIaii~fD~sl~ffk~---s~d~~~~~~~vsdld~pFlPf~ 354 (861)
T COG5028 278 VYVFLIDVSFEAIKNGLVKAAIRAILENLDQIPNFDPRTKIAIICFDSSLHFFKL---SPDLDEQMLIVSDLDEPFLPFP 354 (861)
T ss_pred EEEEEEEeehHhhhcchHHHHHHHHHhhccCCCCCCCcceEEEEEEcceeeEEec---CCCCccceeeecccccccccCC
Confidence 6799999985 33332 23334444443332222348899999999764210000 0111 133333332211
Q ss_pred ------CHH--------HHHHhhcCCCC--CCCCchhhHHHHHHHHHHHHhccCCcccceEEEE-e---CCCCCCC--CC
Q 005544 79 ------DGH--------LVQSLKHLPQG--TCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLI-T---DALCPLK--DP 136 (691)
Q Consensus 79 ------~~~--------~l~~L~~l~~~--~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~-T---D~~~p~~--~~ 136 (691)
..+ +++.+..+..+ .....+.+||-+|..++.. + +.|.|+++ | =|-+... .+
T Consensus 355 s~~fv~pl~~~k~~~etLl~~~~~If~d~~~pk~~~G~aLk~a~~l~g~-~-----GGkii~~~stlPn~G~Gkl~~r~d 428 (861)
T COG5028 355 SGLFVLPLKSCKQIIETLLDRVPRIFQDNKSPKNALGPALKAAKSLIGG-T-----GGKIIVFLSTLPNMGIGKLQLRED 428 (861)
T ss_pred cchhcccHHHHHHHHHHHHHHhhhhhcccCCCccccCHHHHHHHHHhhc-c-----CceEEEEeecCCCccccccccccc
Confidence 111 12233333222 2223567999999887533 2 24667776 4 0111111 00
Q ss_pred C----CCCchhhHHHHHHHHhhcCcEEEEEeecc
Q 005544 137 D----VGTKEDQVSTIARQMVAFGLRMKNIVVRA 166 (691)
Q Consensus 137 ~----~~~~~~~l~~i~~~L~~~gI~l~vi~i~~ 166 (691)
. -.....-...++.++.+.||.+++|....
T Consensus 429 ~e~~ll~c~d~fYk~~a~e~~k~gIsvd~Flt~~ 462 (861)
T COG5028 429 KESSLLSCKDSFYKEFAIECSKVGISVDLFLTSE 462 (861)
T ss_pred chhhhccccchHHHHHHHHHHHhcceEEEEeccc
Confidence 0 00111224678899999999999998743
No 101
>PF08064 UME: UME (NUC010) domain; InterPro: IPR012993 This domain is characteristic of UVSB PI-3 kinase, MEI-41 and ESR1 [].; GO: 0004674 protein serine/threonine kinase activity
Probab=46.75 E-value=30 Score=30.56 Aligned_cols=59 Identities=14% Similarity=0.081 Sum_probs=40.1
Q ss_pred HHHHHHHHHHHHHHHhhccCCCCChHHHHHHHHH-HHHHhhhccCchHHHHHHHHHHHHHhc
Q 005544 585 VDKAIEDMKNKIFGLLENSNEGINYPKAVELLVA-LRKGCILEQEPKQFNDVLEKVCKICRK 645 (691)
Q Consensus 585 ~~~a~~qm~~~I~~lv~~s~~~~~y~ka~~cl~~-~R~~~i~~~e~~~~N~fl~~lk~~~~~ 645 (691)
=..|+.-|+.+|+ +...+. ...-.|.+.||++ ++..-....-...|+.|++.|...-++
T Consensus 32 k~~~l~si~~lI~-~~~~~i-~~~~pQI~a~L~sal~~~~l~~~al~~W~~fi~~L~~~~l~ 91 (107)
T PF08064_consen 32 KKRALRSIEELIK-LGGSHI-SSARPQIMACLQSALEIPELREEALSCWNCFIKTLDEEDLG 91 (107)
T ss_pred HHHHHHHHHHHHH-HhHHHH-HHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHCCHHHHH
Confidence 4457888888888 666554 3457899999992 233333333357899999999875444
No 102
>PF11443 DUF2828: Domain of unknown function (DUF2828); InterPro: IPR024553 This uncharacterised domain is found in eukaryotic, bacterial and viral proteins.
Probab=45.14 E-value=3.3e+02 Score=31.35 Aligned_cols=130 Identities=19% Similarity=0.203 Sum_probs=67.1
Q ss_pred eEEEEEEecCCCccCC-hhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCC-HHHH
Q 005544 6 EALLLLLDVSPSMHSV-LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVD-GHLV 83 (691)
Q Consensus 6 ea~vflIDvs~sM~~~-l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~-~~~l 83 (691)
+.++-+.|||+||... ++-|.-.. .++... +.+--.=.+|.|.... . +..|...+ .+.+
T Consensus 341 ~n~iav~DvSGSM~~~pm~vaiaLg-ll~ae~--~~~pf~~~~ITFs~~P----------~------~~~i~g~~l~ekv 401 (534)
T PF11443_consen 341 ENCIAVCDVSGSMSGPPMDVAIALG-LLIAEL--NKGPFKGRFITFSENP----------Q------LHKIKGDTLREKV 401 (534)
T ss_pred cceEEEEecCCccCccHHHHHHHHH-HHHHHh--cccccCCeEEeecCCc----------e------EEEecCCCHHHHH
Confidence 5678889999999875 33333222 222322 4555556788887653 1 22222222 2344
Q ss_pred HHhhcCCCCCCCCchhhHHHHHHHHHHHHhccCC----cccceEEEEeCCCCCCCCCCCC-CchhhHHHHHHHHhhcCcE
Q 005544 84 QSLKHLPQGTCAGDFLDAIVVGVDMLIKKYGETY----KGKKHLCLITDALCPLKDPDVG-TKEDQVSTIARQMVAFGLR 158 (691)
Q Consensus 84 ~~L~~l~~~~~~gd~~daL~va~d~l~~~~~~~k----~~~krIvL~TD~~~p~~~~~~~-~~~~~l~~i~~~L~~~gI~ 158 (691)
+.+.+..-+. ..|+-.++ ++|.....+.+ ---|+||+|||=+-........ .-....+.|.+..++.|-.
T Consensus 402 ~~~~~~~wg~-nTn~~aVF----dlIL~~Av~~~l~~e~M~k~lfV~SDMeFD~a~~~~~~~w~T~~e~i~~~f~~aGY~ 476 (534)
T PF11443_consen 402 RFIRRMDWGM-NTNFQAVF----DLILETAVKNKLKQEDMPKRLFVFSDMEFDQASNSSDRPWETNFEAIKRKFEEAGYE 476 (534)
T ss_pred HHHHhCCccc-CCcHHHHH----HHHHHHHHHcCCChHHCCceEEEEeccccccccccccCccccHHHHHHHHHHHhCCC
Confidence 4444444332 23544333 43332111111 2358999999743322210000 0124577889999999987
Q ss_pred E
Q 005544 159 M 159 (691)
Q Consensus 159 l 159 (691)
+
T Consensus 477 ~ 477 (534)
T PF11443_consen 477 L 477 (534)
T ss_pred C
Confidence 4
No 103
>KOG1985 consensus Vesicle coat complex COPII, subunit SEC24/subunit SFB2 [Intracellular trafficking, secretion, and vesicular transport]
Probab=45.00 E-value=4.5e+02 Score=31.62 Aligned_cols=171 Identities=16% Similarity=0.170 Sum_probs=84.4
Q ss_pred EEEEEEecCCCc-cCC-hhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCC-------
Q 005544 7 ALLLLLDVSPSM-HSV-LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKV------- 77 (691)
Q Consensus 7 a~vflIDvs~sM-~~~-l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~------- 77 (691)
-.+|+||||-+- ... ++.+...+..-+.. +=..+..+||+|.|...--=-.+. ++-.+.+-.++.++..
T Consensus 296 vy~FliDVS~~a~ksG~L~~~~~slL~~LD~-lpgd~Rt~igfi~fDs~ihfy~~~-~~~~qp~mm~vsdl~d~flp~pd 373 (887)
T KOG1985|consen 296 VYVFLIDVSISAIKSGYLETVARSLLENLDA-LPGDPRTRIGFITFDSTIHFYSVQ-GDLNQPQMMIVSDLDDPFLPMPD 373 (887)
T ss_pred eEEEEEEeehHhhhhhHHHHHHHHHHHhhhc-CCCCCcceEEEEEeeceeeEEecC-CCcCCCceeeeccccccccCCch
Confidence 568999999753 321 33333333333332 224578899999987542100000 0001222222222211
Q ss_pred ---CCH--------HHHHHhhcC-CCC-CCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCC-----CC-
Q 005544 78 ---VDG--------HLVQSLKHL-PQG-TCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDP-----DV- 138 (691)
Q Consensus 78 ---~~~--------~~l~~L~~l-~~~-~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~-----~~- 138 (691)
++. .+|+.|..+ ... .....+..||-+|.+++.. .++ ||++|-..--+.+.. .+
T Consensus 374 ~lLv~L~~ck~~i~~lL~~lp~~F~~~~~t~~alGpALkaaf~li~~-~GG------ri~vf~s~lPnlG~G~L~~rEdp 446 (887)
T KOG1985|consen 374 SLLVPLKECKDLIETLLKTLPEMFQDTRSTGSALGPALKAAFNLIGS-TGG------RISVFQSTLPNLGAGKLKPREDP 446 (887)
T ss_pred hheeeHHHHHHHHHHHHHHHHHHHhhccCcccccCHHHHHHHHHHhh-cCC------eEEEEeccCCCCCcccccccccc
Confidence 111 233444443 111 2233578999999999865 332 566665543333210 00
Q ss_pred ---CCch---------hhHHHHHHHHhhcCcEEEEEeeccCCCCCCCcchhhhhhHHHHHHhhcCCCeEe
Q 005544 139 ---GTKE---------DQVSTIARQMVAFGLRMKNIVVRASLSGEPHMRVIIENDNLLNIFSKKSSAKTL 196 (691)
Q Consensus 139 ---~~~~---------~~l~~i~~~L~~~gI~l~vi~i~~~~~~~~~~~~~~~ne~~l~~l~~~~~g~~~ 196 (691)
++++ +-....+-+....+|.+++|.+...+ + .-..|..++..++|.++
T Consensus 447 ~~~~s~~~~qlL~~~t~FYK~~a~~cs~~qI~VDlFl~s~qY-----~-----DlAsLs~LskySgG~~y 506 (887)
T KOG1985|consen 447 NVRSSDEDSQLLSPATDFYKDLALECSKSQICVDLFLFSEQY-----T-----DLASLSCLSKYSGGQVY 506 (887)
T ss_pred ccccchhhhhccCCCchHHHHHHHHhccCceEEEEEeecccc-----c-----chhhhhccccccCceeE
Confidence 0111 12346677788899999999884422 1 12345556666677643
No 104
>COG2304 Uncharacterized protein containing a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=43.92 E-value=3.5e+02 Score=29.28 Aligned_cols=138 Identities=15% Similarity=0.214 Sum_probs=80.6
Q ss_pred CeEEEEEEecCCCccCC-hhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCcEEEEeecCCCCH-HH
Q 005544 5 REALLLLLDVSPSMHSV-LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEHVKVLQDIKVVDG-HL 82 (691)
Q Consensus 5 Kea~vflIDvs~sM~~~-l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~nI~v~~~l~~~~~-~~ 82 (691)
.....+++|.+.||... +..+..+...++. .....|.+++++|.. .. +.. ..+....+. ..
T Consensus 37 ~~~~~~~~~~~~s~~~~~~~~~~~~~~~~v~---~~~~~~~~~~~~~~~-~~-~~~------------~~~~~~~~~~~~ 99 (399)
T COG2304 37 PANLTLAIDTSGSMTGALLELAKSAAIELVN---GLNPGDLLSIVTFAG-SA-DVL------------IPPTGATNKESI 99 (399)
T ss_pred CcceEEEeccCCCccchhHHHHHHHHHHHhc---ccCCCCceEEEEecC-Cc-cee------------cCcccccCHHHH
Confidence 45678999999999764 3344455554444 368999999999998 31 111 111112222 23
Q ss_pred HHHhhc-CCCCCCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEE
Q 005544 83 VQSLKH-LPQGTCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKN 161 (691)
Q Consensus 83 l~~L~~-l~~~~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~l~v 161 (691)
...+.. ++.... ....-++..+.+.+... . ......++.+.||+.+.+.. .+...+....+.....+|.+..
T Consensus 100 ~~~i~~~~~~~~~-~~~~~~~~~~~~~~~~~-~-~~~~~~~~~~~tdg~~~~~~----~d~~~~~~~~~~~~~~~i~~~~ 172 (399)
T COG2304 100 TAAIDQSLQAGGA-TAVEASLSLAVELAAKA-L-PRGTLNRILLLTDGENNLGL----VDPSRLSALAKLAAGKGIVLDT 172 (399)
T ss_pred HHHHhhhhccccc-cHHHHHHHHHHHHhhhc-C-CccceeeEeeeccCccccCC----CCHHHHHHHhcccccCceEEEE
Confidence 444554 333221 12233455555554432 1 23557889999998876542 2234555566666667999999
Q ss_pred Eeecc
Q 005544 162 IVVRA 166 (691)
Q Consensus 162 i~i~~ 166 (691)
++++.
T Consensus 173 ~g~~~ 177 (399)
T COG2304 173 LGLGD 177 (399)
T ss_pred Eeccc
Confidence 99854
No 105
>COG3552 CoxE Protein containing von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=43.63 E-value=26 Score=37.62 Aligned_cols=46 Identities=37% Similarity=0.353 Sum_probs=34.6
Q ss_pred CeEEEEEEecCCCccCChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCC
Q 005544 5 REALLLLLDVSPSMHSVLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETE 56 (691)
Q Consensus 5 Kea~vflIDvs~sM~~~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~ 56 (691)
|-=+|+++|||.||...-.-.+.++..+.+ .. +.+-+.+|||.-|+
T Consensus 218 ~~~lvvL~DVSGSm~~ys~~~L~l~hAl~q----~~--~R~~~F~F~TRLt~ 263 (395)
T COG3552 218 KPPLVVLCDVSGSMSGYSRIFLHLLHALRQ----QR--SRVHVFLFGTRLTR 263 (395)
T ss_pred CCCeEEEEecccchhhhHHHHHHHHHHHHh----cc--cceeEEEeechHHH
Confidence 445899999999999866666778877777 33 34449999998654
No 106
>COG5047 SEC23 Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking and secretion]
Probab=41.87 E-value=1.5e+02 Score=33.90 Aligned_cols=58 Identities=14% Similarity=0.142 Sum_probs=36.2
Q ss_pred ecCCCCHHHHHHhhcCCCCC-----CCC---chhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCC
Q 005544 74 DIKVVDGHLVQSLKHLPQGT-----CAG---DFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLK 134 (691)
Q Consensus 74 ~l~~~~~~~l~~L~~l~~~~-----~~g---d~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~ 134 (691)
|+++.-..+++.|.+|+++. +.- --..||.+|+.++.. +. ....-||+||++|-+.++
T Consensus 227 p~q~ce~~L~n~le~L~pd~~~v~~~~Rp~RCTGsAl~ias~Ll~~-~~--p~~~~~i~lF~~GPcTvG 292 (755)
T COG5047 227 PTQQCEFKLLNILEQLQPDPWPVPAGKRPLRCTGSALNIASSLLEQ-CF--PNAGCHIVLFAGGPCTVG 292 (755)
T ss_pred cHHHHHHHHHHHHHHhCCCCccCCCCCCCccccchhHHHHHHHHHh-hc--cCcceeEEEEcCCCcccc
Confidence 34444445556666664431 000 125799999999876 32 245789999999977665
No 107
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=36.74 E-value=54 Score=28.78 Aligned_cols=61 Identities=20% Similarity=0.316 Sum_probs=34.2
Q ss_pred HHHHHHhhccCCCCChHHHHHHHHHHHHH-------------hhhccCchHHHHHHHHHHHHHhcCCc-------hhHHH
Q 005544 594 NKIFGLLENSNEGINYPKAVELLVALRKG-------------CILEQEPKQFNDVLEKVCKICRKRNF-------STFFD 653 (691)
Q Consensus 594 ~~I~~lv~~s~~~~~y~ka~~cl~~~R~~-------------~i~~~e~~~~N~fl~~lk~~~~~~~~-------~~fw~ 653 (691)
..|+.++++.+....+..|++||..|.-- |+ ++-..||+++-.|=..+...+. ..||.
T Consensus 3 k~i~~~l~ey~~~~D~~ea~~~l~~L~~~~~~~~vv~~~i~~~l--e~~~~~~~~~~~Ll~~L~~~~~~~~~~~~~~f~~ 80 (113)
T smart00544 3 KKIFLIIEEYLSSGDTDEAVHCLLELKLPEQHHEVVKVLLTCAL--EEKRTYREMYSVLLSRLCQANVISTKQFEKGFWR 80 (113)
T ss_pred hHHHHHHHHHHHcCCHHHHHHHHHHhCCCcchHHHHHHHHHHHH--cCCccHHHHHHHHHHHHHHcCCcCHHHHHHHHHH
Confidence 34555666666566677777777765421 33 3334677776666544443222 46666
Q ss_pred HHH
Q 005544 654 FLM 656 (691)
Q Consensus 654 ~i~ 656 (691)
.+.
T Consensus 81 ~~~ 83 (113)
T smart00544 81 LLE 83 (113)
T ss_pred HHh
Confidence 554
No 108
>COG4547 CobT Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]
Probab=35.93 E-value=1.4e+02 Score=33.02 Aligned_cols=151 Identities=16% Similarity=0.178 Sum_probs=71.6
Q ss_pred EEEEEEecCCCccC-ChhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCc----cccccCC--CcCcEEEEeec----
Q 005544 7 ALLLLLDVSPSMHS-VLPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETEN----ELTKEVG--GYEHVKVLQDI---- 75 (691)
Q Consensus 7 a~vflIDvs~sM~~-~l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n----~l~~e~~--~y~nI~v~~~l---- 75 (691)
++-++||.|.||.- +..-|.-|+..|.... -+-+=.+-|..|-|..=.. ..+-..| .+++ -+.+|
T Consensus 415 vVtlviDnSGSMrGRpItvAatcAdilArtL--eRcgVk~eIlGFTT~awkGg~sre~wlk~Gkp~~pg--rlndlrhii 490 (620)
T COG4547 415 VVTLVIDNSGSMRGRPITVAATCADILARTL--ERCGVKVEILGFTTKAWKGGQSRETWLKRGKPAFPG--RLNDLRHII 490 (620)
T ss_pred hheeeeccCCCcCCcceehhHHHHHHHHHHH--HHcCCceEEeeeeeccccCCccHHHHHhcCCCCCch--hhhhHHHHH
Confidence 56789999999975 4566666666555533 2333344455666632111 0000001 1111 01111
Q ss_pred -CCCCHHHHHHhhcCCCCCCCCch-----hhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCC-----CCCchhh
Q 005544 76 -KVVDGHLVQSLKHLPQGTCAGDF-----LDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPD-----VGTKEDQ 144 (691)
Q Consensus 76 -~~~~~~~l~~L~~l~~~~~~gd~-----~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~-----~~~~~~~ 144 (691)
...+....+.=++|-.-..+|-+ .+||.-|.+.|.. + --.|+|.++-....|++.+. -..-...
T Consensus 491 yksAdaPwrRARrnlGlmmreglLkeNiDGEal~wah~rl~g----R-pEqrkIlmmiSDGAPvddstlsvnpGnylerH 565 (620)
T COG4547 491 YKSADAPWRRARRNLGLMMREGLLKENIDGEALMWAHQRLIG----R-PEQRKILMMISDGAPVDDSTLSVNPGNYLERH 565 (620)
T ss_pred HhccCCHHHHHHhhcchhhhcchhhccCChHHHHHHHHHHhc----C-hhhceEEEEecCCCcccccccccCCchHHHHH
Confidence 11222222222222000111111 3566666666543 1 23566665544446666321 0112345
Q ss_pred HHHHHHHHhh-cCcEEEEEeecc
Q 005544 145 VSTIARQMVA-FGLRMKNIVVRA 166 (691)
Q Consensus 145 l~~i~~~L~~-~gI~l~vi~i~~ 166 (691)
++.+++.+.. ..|+|.-|||+.
T Consensus 566 LRaVieeIEtrSpveLlAIGigh 588 (620)
T COG4547 566 LRAVIEEIETRSPVELLAIGIGH 588 (620)
T ss_pred HHHHHHHHhcCCchhheeeeccc
Confidence 7788888775 468888888865
No 109
>cd03364 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. E. coli DnaG is a single subunit enzyme.
Probab=35.53 E-value=60 Score=26.58 Aligned_cols=35 Identities=14% Similarity=0.170 Sum_probs=28.3
Q ss_pred cceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEE
Q 005544 120 KKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNI 162 (691)
Q Consensus 120 ~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~l~vi 162 (691)
.++|++++|+|.+- ......+++.|...|+.+.++
T Consensus 43 ~~~vii~~D~D~aG--------~~a~~~~~~~l~~~g~~~~~~ 77 (79)
T cd03364 43 AKEVILAFDGDEAG--------QKAALRALELLLKLGLNVRVL 77 (79)
T ss_pred CCeEEEEECCCHHH--------HHHHHHHHHHHHHCCCeEEEE
Confidence 58999999998752 345778889999999988765
No 110
>smart00802 UME Domain in UVSB PI-3 kinase, MEI-41 and ESR-1. Characteristic domain in UVSP PI-3 kinase, MEI-41 and ESR-1. Found in nucleolar proteins. Associated with FAT, FATC, PI3_PI4_kinase modules.
Probab=34.95 E-value=53 Score=29.05 Aligned_cols=56 Identities=13% Similarity=0.098 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHHhhccCCCCChHHHHHHHH-HHHHHhhhccCchHHHHHHHHHHHHHh
Q 005544 587 KAIEDMKNKIFGLLENSNEGINYPKAVELLV-ALRKGCILEQEPKQFNDVLEKVCKICR 644 (691)
Q Consensus 587 ~a~~qm~~~I~~lv~~s~~~~~y~ka~~cl~-~~R~~~i~~~e~~~~N~fl~~lk~~~~ 644 (691)
.++.-|+.+|+ +...+. ...-+|.+.||+ +|+..-.+..--..|+.|++.|...-+
T Consensus 34 ~~i~ai~~lI~-~~g~~i-~~a~pQI~acL~saL~~~eL~~~al~~W~~~i~~L~~~~l 90 (107)
T smart00802 34 RALRSIGFLIK-LMGKHI-SSALPQIMACLQSALEIPELRSLALRCWHVLIKTLKEEEL 90 (107)
T ss_pred HHHHHHHHHHH-HHHHHH-HHHHHHHHHHHHHHhCchhHHHHHHHHHHHHHHhCCHHHH
Confidence 46666666666 454443 345689999998 333333333345789999999987543
No 111
>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]
Probab=33.13 E-value=1.6e+02 Score=31.60 Aligned_cols=69 Identities=17% Similarity=0.201 Sum_probs=45.8
Q ss_pred hhhHHHHHHhCCCCchhHHHH------HHHHHHHHHHHhhccCCCCChHHHHHHHHHHHHHhhhccCchHHHHHHHHHHH
Q 005544 568 PIQDFEAMMSRRDCPDWVDKA------IEDMKNKIFGLLENSNEGINYPKAVELLVALRKGCILEQEPKQFNDVLEKVCK 641 (691)
Q Consensus 568 pv~dF~~~l~~~~~~~~~~~a------~~qm~~~I~~lv~~s~~~~~y~ka~~cl~~~R~~~i~~~e~~~~N~fl~~lk~ 641 (691)
+..||+++|...-+...+.+| +++|...+.+|+.-+ |+..|.-|++.|..+=|.|+ |..=|+.++.
T Consensus 125 A~~DF~~vl~~~~s~~~~~eaqskl~~~~e~~~l~~ql~s~~-~~GD~~~ai~~i~~llEi~~-------Wda~l~~~Ra 196 (504)
T KOG0624|consen 125 AEADFDQVLQHEPSNGLVLEAQSKLALIQEHWVLVQQLKSAS-GSGDCQNAIEMITHLLEIQP-------WDASLRQARA 196 (504)
T ss_pred HHHHHHHHHhcCCCcchhHHHHHHHHhHHHHHHHHHHHHHHh-cCCchhhHHHHHHHHHhcCc-------chhHHHHHHH
Confidence 567899999765433344444 567778888888654 55568999998877665554 5555666655
Q ss_pred HHh
Q 005544 642 ICR 644 (691)
Q Consensus 642 ~~~ 644 (691)
+|.
T Consensus 197 kc~ 199 (504)
T KOG0624|consen 197 KCY 199 (504)
T ss_pred HHH
Confidence 554
No 112
>PF13662 Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=28.53 E-value=36 Score=28.09 Aligned_cols=35 Identities=20% Similarity=0.353 Sum_probs=19.8
Q ss_pred cceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEEEEE
Q 005544 120 KKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRMKNI 162 (691)
Q Consensus 120 ~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~l~vi 162 (691)
.++|++++|+|.+= ......+.+.|...||++..+
T Consensus 46 ~~~Vii~~D~D~~G--------~~~a~~i~~~l~~~gi~v~~v 80 (81)
T PF13662_consen 46 VKEVIIAFDNDKAG--------EKAAQKIAKKLLPLGIRVTRV 80 (81)
T ss_dssp -SEEEEEEESSHHH--------HHHHHHHHHHHG---------
T ss_pred CceEEEEeCcCHHH--------HHHHHHHHHHHHhhccccccC
Confidence 69999999998862 345677788898889988654
No 113
>KOG1327 consensus Copine [Signal transduction mechanisms]
Probab=26.69 E-value=7e+02 Score=28.58 Aligned_cols=144 Identities=13% Similarity=0.066 Sum_probs=75.2
Q ss_pred CeEEEEEEecCCCccCC----------------hhHHHHHHHHHHHHHHhcCCccEEEEEEEcCCCCCccccccCCCcCc
Q 005544 5 REALLLLLDVSPSMHSV----------------LPDVEKLCSRLIQKKLIYGKNHEVGVILFGTEETENELTKEVGGYEH 68 (691)
Q Consensus 5 Kea~vflIDvs~sM~~~----------------l~~a~~~~~~l~~~ki~~~~~D~VGvVlfgt~~t~n~l~~e~~~y~n 68 (691)
+--.++.||.+.|=+.+ .+.|+.++-.+++ .+.+..++...+||..-...- .-.|
T Consensus 285 ~lnf~vgIDfTaSNg~p~~~sSLHyi~p~~~N~Y~~Ai~~vG~~lq---~ydsdk~fpa~GFGakip~~~------~vs~ 355 (529)
T KOG1327|consen 285 QLNFTVGIDFTASNGDPRNPSSLHYIDPHQPNPYEQAIRSVGETLQ---DYDSDKLFPAFGFGAKIPPDG------QVSH 355 (529)
T ss_pred eeeeEEEEEEeccCCCCCCCCcceecCCCCCCHHHHHHHHHhhhhc---ccCCCCccccccccccCCCCc------cccc
Confidence 34578899998874332 3456777766666 378999999999998832100 0111
Q ss_pred EEEEe--ecCCC--CH-HHHHHhhcCCCC---CCCCchhhHHHHHHHHHHHHhccCCcccceEEEEeCCCCCCCCCCCCC
Q 005544 69 VKVLQ--DIKVV--DG-HLVQSLKHLPQG---TCAGDFLDAIVVGVDMLIKKYGETYKGKKHLCLITDALCPLKDPDVGT 140 (691)
Q Consensus 69 I~v~~--~l~~~--~~-~~l~~L~~l~~~---~~~gd~~daL~va~d~l~~~~~~~k~~~krIvL~TD~~~p~~~~~~~~ 140 (691)
.+++. |-.+. .. ..+...+..... .+..+|.-.|-.++.+-.+... ....---+++||||.-.
T Consensus 356 ~f~ln~~~~~~~c~Gi~gVl~aY~~~lp~v~l~GPTnFaPII~~va~~a~~~~~-~~~qY~VLlIitDG~vT-------- 426 (529)
T KOG1327|consen 356 EFVLNFNPEDPECRGIEGVLEAYRKALPNVQLYGPTNFSPIINHVARIAQQSGN-TAGQYHVLLIITDGVVT-------- 426 (529)
T ss_pred ceeecCCCCCCccccHHHHHHHHHhhcccccccCCCccHHHHHHHHHHHHHhcc-CCcceEEEEEEeCCccc--------
Confidence 11110 00000 01 123444432211 2234566555556665443211 10112346777998542
Q ss_pred chhhHHHHHHHHhhcCcEEEEEeecc
Q 005544 141 KEDQVSTIARQMVAFGLRMKNIVVRA 166 (691)
Q Consensus 141 ~~~~l~~i~~~L~~~gI~l~vi~i~~ 166 (691)
+.....+.+-..-.+=+.+.++|+|.
T Consensus 427 dm~~T~~AIV~AS~lPlSIIiVGVGd 452 (529)
T KOG1327|consen 427 DMKETRDAIVSASDLPLSIIIVGVGD 452 (529)
T ss_pred cHHHHHHHHHhhccCCeEEEEEEeCC
Confidence 23444555556667777888888863
No 114
>COG4902 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.58 E-value=2.1e+02 Score=26.64 Aligned_cols=43 Identities=16% Similarity=0.351 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHcCCCCCCCCcCCCCCCCCCchhHHHHHHHHHh
Q 005544 427 EQQQEAADNLVKMLDLAPSGKGEILQPELTPNPALERFYHHLELK 471 (691)
Q Consensus 427 ~eq~~a~~~lI~~m~l~~~~~~e~~~p~~~~NP~lqr~~~~l~~~ 471 (691)
.+..+|+..|+.+..+.+.. ..-....+.||.+|.+|.-+..+
T Consensus 88 Q~HmDAVk~LlekYnv~dP~--~~~siGvF~NpelqeLYn~Lve~ 130 (189)
T COG4902 88 QEHMDAVKSLLEKYNVQDPA--STTSIGVFTNPELQELYNQLVEQ 130 (189)
T ss_pred HHHHHHHHHHHHHcCCCCCC--ccCcceeecCHHHHHHHHHHHHc
Confidence 45689999999999996422 11234567899999999776554
No 115
>PF07744 SPOC: SPOC domain; InterPro: IPR012921 Spen (split end) proteins regulate the expression of key transcriptional effectors in diverse signalling pathways. They are large proteins characterised by N-terminal RNA-binding motifs and a highly conserved C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. The function of the SPOC domain is unknown, but the SPOC domain of the SHARP Spen protein has been implicated in the interaction of SHARP with the SMRT/NcoR corepressor, where SHARP plays an essential role in the repressor complex []. The SPOC domain is folded into a single compact domain consisting of a beta-barrel with seven strands framed by six alpha helices. A number of deep grooves and clefts in the surface, plus two nonpolar loops, render the SPOC domain well suited to protein-protein interactions; most of the conserved residues occur on the protein surface rather than in the core. Other proteins containing a SPOC domain include drosophila Split ends, which promotes sclerite development in the head and restricts it in the thorax, and mouse MINT (homologue of SHARP), which is involved in skeletal and neuronal development via its repression of Msx2.; PDB: 1OW1_A.
Probab=22.94 E-value=1.2e+02 Score=26.67 Aligned_cols=41 Identities=17% Similarity=0.112 Sum_probs=26.6
Q ss_pred ChhhHHHHHHHHHHHHhcCceEEEEEEecCCCCceEEEEeec
Q 005544 344 NSRATVAVSALARAMKEMNKVAIVRCVWRQGQQSVVVGVLTP 385 (691)
Q Consensus 344 ~~~s~~afsaL~~Am~e~~~vaI~r~v~r~~~~p~~v~~L~P 385 (691)
.......|..|++-|.++++++|+..-...... .....|+|
T Consensus 79 ~~~~~~~~~~l~~Yl~~k~r~GVv~~~~~~~~~-~~dlYl~P 119 (119)
T PF07744_consen 79 SNSDRRPFQKLVDYLKSKQRAGVVSVGNSPSGQ-VKDLYLFP 119 (119)
T ss_dssp HHHHHHHHHHTHHHHHHHTEEEEEEE--TT--S--EEEEEE-
T ss_pred CHHHHHHHHHHHHHHhhCCEEEEEecCCCCCCc-eeEEEEcC
Confidence 445677899999999999999999766543322 33335665
No 116
>PF13344 Hydrolase_6: Haloacid dehalogenase-like hydrolase; PDB: 2HO4_B 1YV9_A 1WVI_B 3EPR_A 2P27_A 2OYC_A 2CFT_A 2P69_A 2CFS_A 2CFR_A ....
Probab=22.13 E-value=1.3e+02 Score=26.07 Aligned_cols=29 Identities=14% Similarity=0.302 Sum_probs=21.2
Q ss_pred cceEEEEeCCCCCCCCCCCCCchhhHHHHHHHHhhcCcEE
Q 005544 120 KKHLCLITDALCPLKDPDVGTKEDQVSTIARQMVAFGLRM 159 (691)
Q Consensus 120 ~krIvL~TD~~~p~~~~~~~~~~~~l~~i~~~L~~~gI~l 159 (691)
.++++++||+.+. .....++.|+.+||.+
T Consensus 30 g~~~~~lTNns~~-----------s~~~~~~~L~~~Gi~~ 58 (101)
T PF13344_consen 30 GKPVVFLTNNSSR-----------SREEYAKKLKKLGIPV 58 (101)
T ss_dssp TSEEEEEES-SSS------------HHHHHHHHHHTTTT-
T ss_pred CCCEEEEeCCCCC-----------CHHHHHHHHHhcCcCC
Confidence 4899999998664 2457788999999864
No 117
>PF01882 DUF58: Protein of unknown function DUF58; InterPro: IPR002881 This domain is found in a family of prokaryotic proteins that have no known function. Proteins belonging to this family include hypothetical proteins from eubacteria and archaebacteria. Some of these proteins also contain the Von Willebrand factor, type A domain (see IPR002035 from INTERPRO).
Probab=21.49 E-value=1.1e+02 Score=25.26 Aligned_cols=40 Identities=23% Similarity=0.353 Sum_probs=26.1
Q ss_pred CeEEEEEEecCCCccC------ChhHHHHHHHHHHHHHHhcCCccEEE
Q 005544 5 REALLLLLDVSPSMHS------VLPDVEKLCSRLIQKKLIYGKNHEVG 46 (691)
Q Consensus 5 Kea~vflIDvs~sM~~------~l~~a~~~~~~l~~~ki~~~~~D~VG 46 (691)
...+++++|.+++|.. .++.++.++..++..- .+.++.||
T Consensus 40 ~~~~~i~ld~~~~~~~~~~~~~~~e~~l~~a~~l~~~~--~~~g~~v~ 85 (86)
T PF01882_consen 40 SQPVWIVLDLSPSMYFGSNGRSKFERALSAAASLANQA--LRQGDPVG 85 (86)
T ss_pred CCcEEEEEECCCccccCcCCCCHHHHHHHHHHHHHHHH--HhcCCccc
Confidence 4568899999999974 3566666666655532 34555554
Done!