Query 028156
Match_columns 213
No_of_seqs 127 out of 261
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 07:07:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028156.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028156hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03850 Tfb4: Transcription f 100.0 9E-59 1.9E-63 409.6 17.1 179 5-188 92-276 (276)
2 TIGR00627 tfb4 transcription f 100.0 7E-58 1.5E-62 403.9 16.9 181 5-191 95-279 (279)
3 KOG2487 RNA polymerase II tran 100.0 9.7E-57 2.1E-61 389.5 12.0 194 6-210 118-312 (314)
4 COG5242 TFB4 RNA polymerase II 100.0 1.9E-48 4.2E-53 331.2 13.0 177 6-193 109-286 (296)
5 KOG2807 RNA polymerase II tran 100.0 1.2E-35 2.6E-40 263.2 12.8 158 32-195 141-304 (378)
6 COG5151 SSL1 RNA polymerase II 99.9 1.2E-25 2.6E-30 199.1 9.9 157 33-195 169-336 (421)
7 PF04056 Ssl1: Ssl1-like; Int 99.8 9.2E-21 2E-25 159.9 12.1 102 32-139 78-179 (193)
8 cd01453 vWA_transcription_fact 99.2 2E-10 4.4E-15 95.6 10.5 99 33-137 85-183 (183)
9 TIGR00622 ssl1 transcription f 98.6 1.2E-08 2.6E-13 79.3 1.7 29 167-195 1-29 (112)
10 cd01452 VWA_26S_proteasome_sub 98.2 3.2E-05 7E-10 65.2 12.3 77 33-114 84-163 (187)
11 cd01467 vWA_BatA_type VWA BatA 98.1 6.6E-05 1.4E-09 60.8 11.2 86 33-124 82-179 (180)
12 cd01455 vWA_F11C1-5a_type Von 98.0 7.3E-05 1.6E-09 63.4 10.1 91 38-133 95-186 (191)
13 cd01461 vWA_interalpha_trypsin 97.9 0.00017 3.6E-09 57.5 11.5 91 33-130 79-170 (171)
14 cd01465 vWA_subgroup VWA subgr 97.9 0.00022 4.8E-09 56.8 11.6 93 33-128 74-169 (170)
15 PRK13685 hypothetical protein; 97.8 0.00036 7.8E-09 63.0 13.0 99 33-131 165-285 (326)
16 PF13519 VWA_2: von Willebrand 97.8 0.00031 6.7E-09 55.1 10.6 89 33-130 79-170 (172)
17 TIGR03436 acidobact_VWFA VWFA- 97.6 0.0017 3.7E-08 57.3 13.1 97 33-133 140-251 (296)
18 cd01466 vWA_C3HC4_type VWA C3H 97.6 0.00071 1.5E-08 54.2 9.6 78 33-119 76-154 (155)
19 cd01456 vWA_ywmD_type VWA ywmD 97.5 0.0011 2.5E-08 55.3 10.4 80 33-121 116-202 (206)
20 cd01451 vWA_Magnesium_chelatas 97.4 0.0031 6.8E-08 51.6 11.8 90 33-124 75-169 (178)
21 smart00327 VWA von Willebrand 97.0 0.01 2.2E-07 46.6 10.7 84 33-118 80-164 (177)
22 TIGR00868 hCaCC calcium-activa 97.0 0.0058 1.3E-07 62.1 11.3 84 33-124 382-465 (863)
23 PF13768 VWA_3: von Willebrand 97.0 0.012 2.6E-07 46.6 10.3 76 33-117 77-154 (155)
24 cd01463 vWA_VGCC_like VWA Volt 96.9 0.012 2.5E-07 48.6 10.5 87 33-122 94-189 (190)
25 cd01470 vWA_complement_factors 96.7 0.012 2.6E-07 48.8 9.2 95 34-128 85-196 (198)
26 cd01480 vWA_collagen_alpha_1-V 96.7 0.018 3.9E-07 47.4 9.7 84 33-119 87-170 (186)
27 cd01474 vWA_ATR ATR (Anthrax T 96.6 0.02 4.4E-07 46.9 9.6 93 33-126 79-171 (185)
28 cd01472 vWA_collagen von Wille 96.4 0.048 1E-06 43.5 10.5 82 34-120 79-161 (164)
29 cd00198 vWFA Von Willebrand fa 96.3 0.064 1.4E-06 40.6 10.3 80 33-116 79-160 (161)
30 cd01450 vWFA_subfamily_ECM Von 96.2 0.036 7.9E-07 43.0 8.3 81 33-116 79-159 (161)
31 TIGR03788 marine_srt_targ mari 95.9 0.11 2.4E-06 50.6 11.8 90 33-129 348-438 (596)
32 PF04811 Sec23_trunk: Sec23/Se 95.7 0.32 6.9E-06 41.8 12.7 87 31-123 113-227 (243)
33 cd01482 vWA_collagen_alphaI-XI 95.6 0.19 4.2E-06 40.2 10.3 81 33-117 78-158 (164)
34 cd01477 vWA_F09G8-8_type VWA F 95.0 0.52 1.1E-05 39.6 11.6 81 33-117 106-190 (193)
35 PTZ00441 sporozoite surface pr 94.8 0.53 1.1E-05 46.2 12.5 90 33-126 126-220 (576)
36 cd01473 vWA_CTRP CTRP for CS 94.7 0.51 1.1E-05 39.4 10.7 77 33-111 84-161 (192)
37 PRK13406 bchD magnesium chelat 94.7 0.55 1.2E-05 46.1 12.4 88 32-122 474-570 (584)
38 PF09538 FYDLN_acid: Protein o 94.2 0.035 7.6E-07 43.0 2.3 30 166-195 8-40 (108)
39 KOG2884 26S proteasome regulat 94.0 0.62 1.4E-05 40.7 9.9 78 34-115 85-164 (259)
40 PRK12496 hypothetical protein; 94.0 0.037 8E-07 45.7 2.2 34 162-195 122-157 (164)
41 cd01475 vWA_Matrilin VWA_Matri 93.7 1.1 2.5E-05 37.8 11.1 64 60-126 109-173 (224)
42 cd00729 rubredoxin_SM Rubredox 93.5 0.054 1.2E-06 33.4 1.9 24 167-190 2-27 (34)
43 cd01468 trunk_domain trunk dom 93.4 2.1 4.7E-05 36.7 12.4 86 31-122 113-224 (239)
44 TIGR02442 Cob-chelat-sub cobal 92.9 1.6 3.5E-05 43.1 12.1 86 33-119 540-632 (633)
45 cd01469 vWA_integrins_alpha_su 92.9 1.6 3.4E-05 35.6 10.3 87 34-122 79-171 (177)
46 cd01479 Sec24-like Sec24-like: 92.6 3.8 8.3E-05 35.5 12.8 81 32-120 113-219 (244)
47 COG5148 RPN10 26S proteasome r 92.6 1.2 2.7E-05 38.1 9.3 76 35-114 86-162 (243)
48 cd00350 rubredoxin_like Rubred 91.9 0.13 2.8E-06 31.3 2.0 23 168-190 2-26 (33)
49 cd01471 vWA_micronemal_protein 91.6 2.4 5.1E-05 34.4 9.9 76 33-111 84-160 (186)
50 COG1592 Rubrerythrin [Energy p 91.1 0.14 3E-06 42.7 1.9 24 167-190 134-158 (166)
51 TIGR02031 BchD-ChlD magnesium 90.8 3.6 7.8E-05 40.4 11.8 88 33-123 481-584 (589)
52 cd01458 vWA_ku Ku70/Ku80 N-ter 89.8 3.1 6.8E-05 35.0 9.3 66 32-100 104-173 (218)
53 TIGR00373 conserved hypothetic 89.1 0.23 4.9E-06 40.8 1.7 29 166-194 108-141 (158)
54 PF05191 ADK_lid: Adenylate ki 88.8 0.33 7.1E-06 30.4 1.9 26 168-193 2-33 (36)
55 cd01464 vWA_subfamily VWA subf 88.7 3.4 7.3E-05 33.4 8.4 77 33-110 78-159 (176)
56 TIGR02300 FYDLN_acid conserved 88.6 0.3 6.6E-06 39.0 2.0 30 166-195 8-40 (129)
57 PRK06266 transcription initiat 88.0 0.32 6.9E-06 40.7 1.9 29 166-194 116-149 (178)
58 PF10571 UPF0547: Uncharacteri 87.3 0.34 7.3E-06 28.2 1.2 24 169-192 2-25 (26)
59 PRK00398 rpoP DNA-directed RNA 87.1 0.52 1.1E-05 30.5 2.2 29 167-195 3-35 (46)
60 cd01478 Sec23-like Sec23-like: 85.6 16 0.00035 32.2 11.5 87 31-121 138-255 (267)
61 cd01462 VWA_YIEM_type VWA YIEM 85.6 12 0.00025 29.2 9.6 71 33-109 74-145 (152)
62 COG4867 Uncharacterized protei 85.3 11 0.00023 36.4 10.5 98 31-134 530-647 (652)
63 cd01476 VWA_integrin_invertebr 84.9 17 0.00036 28.5 10.6 76 33-113 79-155 (163)
64 cd01454 vWA_norD_type norD typ 84.5 8.8 0.00019 30.7 8.7 62 33-99 83-152 (174)
65 PF00092 VWA: von Willebrand f 83.5 12 0.00025 29.2 8.9 93 33-127 78-173 (178)
66 PF13248 zf-ribbon_3: zinc-rib 83.3 0.58 1.3E-05 26.9 0.9 24 168-191 3-26 (26)
67 PLN00162 transport protein sec 82.6 38 0.00083 34.5 14.0 99 32-134 260-391 (761)
68 cd00730 rubredoxin Rubredoxin; 82.5 0.79 1.7E-05 30.7 1.4 23 168-190 2-43 (50)
69 PF13240 zinc_ribbon_2: zinc-r 81.3 0.86 1.9E-05 25.6 1.1 22 170-191 2-23 (23)
70 COG1439 Predicted nucleic acid 79.8 1.1 2.3E-05 37.8 1.6 34 162-195 134-167 (177)
71 PF00301 Rubredoxin: Rubredoxi 79.7 1.4 3E-05 29.2 1.8 12 168-179 2-13 (47)
72 smart00531 TFIIE Transcription 78.9 1 2.2E-05 36.2 1.3 30 166-195 98-137 (147)
73 cd01457 vWA_ORF176_type VWA OR 77.8 38 0.00082 27.9 11.0 76 33-111 81-165 (199)
74 COG1996 RPC10 DNA-directed RNA 77.5 1.3 2.9E-05 29.6 1.3 32 164-195 3-38 (49)
75 COG1675 TFA1 Transcription ini 76.4 1.4 3.1E-05 36.9 1.5 31 165-195 111-146 (176)
76 smart00834 CxxC_CXXC_SSSS Puta 74.9 2.4 5.2E-05 26.1 1.9 25 167-191 5-36 (41)
77 cd05017 SIS_PGI_PMI_1 The memb 74.9 25 0.00054 26.6 8.0 55 61-123 46-100 (119)
78 PTZ00395 Sec24-related protein 74.5 20 0.00044 38.9 9.4 97 32-134 1074-1199(1560)
79 PF08271 TF_Zn_Ribbon: TFIIB z 73.0 1.4 3.1E-05 28.0 0.5 28 168-195 1-33 (43)
80 PF06221 zf-C2HC5: Putative zi 72.4 2.5 5.5E-05 29.1 1.6 42 154-195 2-49 (57)
81 cd01481 vWA_collagen_alpha3-VI 71.9 35 0.00075 27.5 8.6 33 77-109 121-153 (165)
82 TIGR02098 MJ0042_CXXC MJ0042 f 71.3 2.3 5.1E-05 26.1 1.2 25 168-192 3-36 (38)
83 COG1240 ChlD Mg-chelatase subu 70.9 78 0.0017 28.3 11.5 91 33-124 153-249 (261)
84 TIGR01206 lysW lysine biosynth 69.7 2.2 4.7E-05 29.1 0.8 28 167-195 2-36 (54)
85 PF07975 C1_4: TFIIH C1-like d 69.0 3 6.5E-05 28.1 1.4 24 165-188 19-50 (51)
86 cd01460 vWA_midasin VWA_Midasi 66.5 31 0.00066 30.7 7.7 66 32-100 137-205 (266)
87 PF12760 Zn_Tnp_IS1595: Transp 66.3 2.5 5.3E-05 27.4 0.5 22 167-188 18-44 (46)
88 KOG2593 Transcription initiati 65.4 1.9 4.2E-05 40.8 -0.2 30 166-195 127-167 (436)
89 PF05290 Baculo_IE-1: Baculovi 65.2 3.1 6.8E-05 33.6 1.0 22 174-195 114-135 (140)
90 PRK14892 putative transcriptio 63.5 3.9 8.4E-05 31.2 1.2 31 165-195 19-56 (99)
91 PRK11788 tetratricopeptide rep 63.3 4.1 8.9E-05 36.2 1.5 31 165-195 352-382 (389)
92 PF13717 zinc_ribbon_4: zinc-r 63.0 3.7 8.1E-05 25.4 0.9 24 168-191 3-35 (36)
93 PF10138 vWA-TerF-like: vWA fo 62.0 99 0.0022 26.5 9.6 95 34-133 83-187 (200)
94 TIGR02605 CxxC_CxxC_SSSS putat 61.6 4 8.7E-05 26.7 0.9 23 167-189 5-34 (52)
95 PF09723 Zn-ribbon_8: Zinc rib 59.4 7.3 0.00016 24.8 1.8 23 167-189 5-34 (42)
96 cd02010 TPP_ALS Thiamine pyrop 58.6 73 0.0016 25.9 8.1 71 59-133 66-157 (177)
97 PF14446 Prok-RING_1: Prokaryo 58.1 4.6 0.0001 27.6 0.7 14 165-178 19-32 (54)
98 PF04438 zf-HIT: HIT zinc fing 57.9 5.4 0.00012 23.8 0.9 16 165-180 11-26 (30)
99 PF03604 DNA_RNApol_7kD: DNA d 57.8 7.4 0.00016 23.7 1.5 25 168-192 1-28 (32)
100 cd02003 TPP_IolD Thiamine pyro 57.3 90 0.002 26.0 8.6 67 36-109 46-112 (205)
101 PRK00420 hypothetical protein; 57.2 5.4 0.00012 31.1 1.1 29 167-195 23-54 (112)
102 PF03731 Ku_N: Ku70/Ku80 N-ter 56.9 75 0.0016 26.4 8.1 65 32-97 103-172 (224)
103 PRK11595 DNA utilization prote 56.9 4.4 9.5E-05 34.7 0.6 40 153-192 4-45 (227)
104 PRK08617 acetolactate synthase 56.4 35 0.00075 32.8 6.7 71 59-133 432-523 (552)
105 cd02006 TPP_Gcl Thiamine pyrop 55.0 60 0.0013 26.9 7.1 45 59-107 75-119 (202)
106 PRK13130 H/ACA RNA-protein com 54.6 11 0.00023 25.9 2.1 26 168-195 6-31 (56)
107 PRK08611 pyruvate oxidase; Pro 54.5 54 0.0012 31.8 7.7 71 59-133 426-517 (576)
108 COG1545 Predicted nucleic-acid 53.5 9 0.0002 30.7 1.8 27 165-191 27-53 (140)
109 COG4245 TerY Uncharacterized p 53.4 1.5E+02 0.0032 25.6 9.2 97 32-131 77-179 (207)
110 smart00659 RPOLCX RNA polymera 52.8 9.6 0.00021 24.7 1.5 29 167-195 2-33 (44)
111 COG1645 Uncharacterized Zn-fin 52.7 4.9 0.00011 32.2 0.2 28 166-193 27-56 (131)
112 PRK00415 rps27e 30S ribosomal 50.7 8.5 0.00019 26.8 1.1 27 169-195 13-44 (59)
113 TIGR00622 ssl1 transcription f 49.5 12 0.00027 29.2 1.9 24 166-189 80-111 (112)
114 smart00154 ZnF_AN1 AN1-like Zi 49.1 11 0.00024 23.7 1.4 22 159-180 4-25 (39)
115 PRK05978 hypothetical protein; 48.9 11 0.00024 30.8 1.7 27 169-195 35-66 (148)
116 COG2176 PolC DNA polymerase II 48.6 7.8 0.00017 41.4 0.9 27 166-194 913-952 (1444)
117 PF12172 DUF35_N: Rubredoxin-l 48.0 10 0.00023 23.1 1.1 25 165-189 9-33 (37)
118 PF13719 zinc_ribbon_5: zinc-r 46.3 11 0.00024 23.3 1.0 10 169-178 4-13 (37)
119 COG2093 DNA-directed RNA polym 46.3 10 0.00022 26.7 0.9 24 169-192 6-30 (64)
120 KOG1985 Vesicle coat complex C 45.5 86 0.0019 32.4 7.5 94 6-117 387-506 (887)
121 PLN02470 acetolactate synthase 44.7 90 0.002 30.3 7.5 71 59-133 444-544 (585)
122 PRK06457 pyruvate dehydrogenas 43.7 76 0.0016 30.5 6.8 71 59-133 415-506 (549)
123 PF13894 zf-C2H2_4: C2H2-type 43.5 13 0.00029 19.3 1.0 9 168-176 1-9 (24)
124 PF12773 DZR: Double zinc ribb 43.3 14 0.0003 23.8 1.2 25 166-190 11-38 (50)
125 PRK08978 acetolactate synthase 42.6 1.1E+02 0.0024 29.4 7.7 71 59-133 419-512 (548)
126 PF06707 DUF1194: Protein of u 42.0 1.9E+02 0.0041 24.9 8.3 63 33-99 94-156 (205)
127 PRK07586 hypothetical protein; 41.9 1.1E+02 0.0024 29.0 7.5 45 59-107 403-447 (514)
128 PF00096 zf-C2H2: Zinc finger, 41.8 13 0.00029 19.7 0.8 10 184-193 3-12 (23)
129 PF01380 SIS: SIS domain SIS d 41.8 32 0.00069 25.6 3.2 44 60-109 55-98 (131)
130 COG1997 RPL43A Ribosomal prote 41.8 11 0.00025 28.2 0.6 32 167-198 35-70 (89)
131 KOG4317 Predicted Zn-finger pr 41.6 12 0.00026 34.5 0.8 36 158-193 9-48 (383)
132 cd02008 TPP_IOR_alpha Thiamine 41.4 1E+02 0.0023 24.9 6.4 64 59-126 69-154 (178)
133 PRK00448 polC DNA polymerase I 41.2 12 0.00027 40.7 1.1 29 164-194 905-946 (1437)
134 cd02015 TPP_AHAS Thiamine pyro 40.4 1.3E+02 0.0029 24.3 7.0 45 59-107 68-112 (186)
135 PRK07710 acetolactate synthase 40.4 1.1E+02 0.0025 29.5 7.5 71 59-133 442-535 (571)
136 PF03854 zf-P11: P-11 zinc fin 40.4 5.8 0.00012 26.6 -1.0 27 167-193 21-47 (50)
137 PRK03824 hypA hydrogenase nick 40.3 19 0.0004 28.7 1.7 14 166-179 69-82 (135)
138 PF14205 Cys_rich_KTR: Cystein 39.8 21 0.00045 24.5 1.6 28 168-195 5-42 (55)
139 PF03358 FMN_red: NADPH-depend 39.7 88 0.0019 24.1 5.5 38 61-98 2-40 (152)
140 PF09862 DUF2089: Protein of u 39.4 11 0.00023 29.6 0.2 21 159-179 4-24 (113)
141 TIGR01405 polC_Gram_pos DNA po 39.1 14 0.0003 39.6 1.1 29 164-194 680-721 (1213)
142 PF01428 zf-AN1: AN1-like Zinc 39.0 15 0.00032 23.4 0.8 21 159-180 6-26 (43)
143 PF06906 DUF1272: Protein of u 38.6 15 0.00033 25.3 0.8 28 168-195 27-55 (57)
144 PF07191 zinc-ribbons_6: zinc- 38.1 11 0.00023 27.1 0.0 33 159-192 7-41 (70)
145 cd01407 SIR2-fam SIR2 family o 38.0 70 0.0015 27.0 5.0 36 155-192 99-144 (218)
146 PRK07418 acetolactate synthase 37.9 1.3E+02 0.0029 29.4 7.6 71 59-133 452-546 (616)
147 cd02013 TPP_Xsc_like Thiamine 37.8 1.4E+02 0.0029 24.7 6.7 36 59-98 71-106 (196)
148 TIGR00578 ku70 ATP-dependent D 37.8 2.4E+02 0.0051 27.9 9.3 89 7-98 90-182 (584)
149 PRK08322 acetolactate synthase 37.7 1.3E+02 0.0028 28.8 7.3 71 59-133 424-515 (547)
150 cd02014 TPP_POX Thiamine pyrop 37.5 1.4E+02 0.0029 24.2 6.5 36 59-98 69-104 (178)
151 smart00547 ZnF_RBZ Zinc finger 37.5 17 0.00038 20.2 0.8 23 168-190 3-25 (26)
152 PRK06882 acetolactate synthase 36.6 1.4E+02 0.0031 28.7 7.5 71 59-133 439-532 (574)
153 cd05008 SIS_GlmS_GlmD_1 SIS (S 36.4 51 0.0011 24.5 3.6 45 61-111 49-93 (126)
154 KOG1986 Vesicle coat complex C 36.3 4.4E+02 0.0096 27.0 10.7 123 7-134 222-378 (745)
155 PF00641 zf-RanBP: Zn-finger i 36.0 29 0.00063 20.1 1.7 24 167-190 4-27 (30)
156 KOG0978 E3 ubiquitin ligase in 36.0 15 0.00033 37.0 0.7 25 171-195 659-692 (698)
157 PF13824 zf-Mss51: Zinc-finger 35.7 25 0.00054 24.1 1.5 25 170-194 2-27 (55)
158 PF05129 Elf1: Transcription e 35.1 10 0.00022 27.8 -0.5 32 164-195 19-60 (81)
159 PRK05858 hypothetical protein; 35.0 1.7E+02 0.0037 28.1 7.7 71 59-133 425-517 (542)
160 cd02004 TPP_BZL_OCoD_HPCL Thia 34.6 1.5E+02 0.0032 23.6 6.3 36 59-98 66-101 (172)
161 cd05014 SIS_Kpsf KpsF-like pro 34.5 47 0.001 24.9 3.1 44 61-110 50-93 (128)
162 PRK04023 DNA polymerase II lar 34.3 24 0.00051 37.2 1.7 52 125-195 1014-1067(1121)
163 PRK07064 hypothetical protein; 34.0 1.5E+02 0.0032 28.3 7.1 71 59-133 423-515 (544)
164 PRK04860 hypothetical protein; 33.3 59 0.0013 26.7 3.7 47 36-97 9-55 (160)
165 PRK09124 pyruvate dehydrogenas 33.1 1.6E+02 0.0034 28.5 7.2 71 59-133 426-517 (574)
166 COG4530 Uncharacterized protei 32.9 20 0.00043 28.2 0.7 29 167-195 9-40 (129)
167 PRK09107 acetolactate synthase 32.8 2.6E+02 0.0057 27.3 8.7 45 59-107 448-492 (595)
168 cd04192 GT_2_like_e Subfamily 32.8 2.5E+02 0.0054 22.3 9.0 70 60-134 29-108 (229)
169 PHA00626 hypothetical protein 32.8 25 0.00054 24.3 1.1 27 169-195 2-37 (59)
170 PF07754 DUF1610: Domain of un 32.7 28 0.00061 19.9 1.2 10 165-174 14-23 (24)
171 COG2051 RPS27A Ribosomal prote 32.3 18 0.00038 25.8 0.4 27 169-195 21-52 (67)
172 PF14206 Cys_rich_CPCC: Cystei 32.1 25 0.00053 25.7 1.1 25 168-192 2-31 (78)
173 PRK07789 acetolactate synthase 31.8 1.7E+02 0.0037 28.6 7.2 71 59-133 465-562 (612)
174 PF01936 NYN: NYN domain; Int 31.7 54 0.0012 24.9 3.1 45 60-111 97-141 (146)
175 PHA02768 hypothetical protein; 31.3 17 0.00038 24.8 0.2 29 165-193 3-43 (55)
176 PF09237 GAGA: GAGA factor; I 31.3 16 0.00034 24.9 -0.1 17 179-195 22-38 (54)
177 KOG2858 Uncharacterized conser 31.0 17 0.00037 33.9 0.2 18 164-181 26-43 (390)
178 PF03119 DNA_ligase_ZBD: NAD-d 30.9 21 0.00045 20.9 0.4 13 183-195 1-13 (28)
179 PRK06546 pyruvate dehydrogenas 30.3 1.8E+02 0.004 28.2 7.2 43 59-105 426-468 (578)
180 TIGR03394 indol_phenyl_DC indo 29.9 1.4E+02 0.003 28.8 6.2 88 38-133 403-507 (535)
181 PF05605 zf-Di19: Drought indu 29.7 30 0.00065 22.8 1.1 11 182-192 32-42 (54)
182 TIGR01504 glyox_carbo_lig glyo 29.6 1.9E+02 0.004 28.3 7.1 71 59-133 436-538 (588)
183 PRK10997 yieM hypothetical pro 29.5 4.4E+02 0.0096 25.6 9.4 72 33-110 396-468 (487)
184 TIGR02418 acolac_catab acetola 29.4 2.2E+02 0.0049 27.2 7.5 37 59-99 426-462 (539)
185 PRK05452 anaerobic nitric oxid 29.4 33 0.00072 32.8 1.8 27 164-190 422-467 (479)
186 PRK07525 sulfoacetaldehyde ace 29.1 2.2E+02 0.0048 27.7 7.4 36 59-98 453-488 (588)
187 cd02002 TPP_BFDC Thiamine pyro 29.0 2.9E+02 0.0064 21.9 7.5 49 59-111 67-115 (178)
188 PF02780 Transketolase_C: Tran 28.4 1.6E+02 0.0034 22.2 5.2 72 59-134 9-89 (124)
189 PRK06456 acetolactate synthase 28.4 2.4E+02 0.0052 27.2 7.5 46 59-108 439-484 (572)
190 PF10146 zf-C4H2: Zinc finger- 28.3 31 0.00068 30.1 1.3 14 182-195 209-222 (230)
191 PRK07765 para-aminobenzoate sy 28.1 1.8E+02 0.0039 24.6 5.9 53 61-119 48-100 (214)
192 TIGR00441 gmhA phosphoheptose 27.9 62 0.0013 25.7 2.9 45 60-110 81-125 (154)
193 PRK06965 acetolactate synthase 27.8 2.5E+02 0.0055 27.3 7.6 44 59-106 455-498 (587)
194 PF02701 zf-Dof: Dof domain, z 27.8 25 0.00054 24.7 0.5 37 167-203 5-52 (63)
195 PRK06393 rpoE DNA-directed RNA 27.5 31 0.00067 24.4 0.9 23 169-193 7-29 (64)
196 COG0512 PabA Anthranilate/para 27.3 1.8E+02 0.0039 24.8 5.7 60 58-124 44-103 (191)
197 PRK14890 putative Zn-ribbon RN 26.6 46 0.001 23.2 1.6 24 166-189 24-56 (59)
198 PHA00733 hypothetical protein 26.5 40 0.00087 26.5 1.5 30 166-195 72-113 (128)
199 COG0794 GutQ Predicted sugar p 26.4 1.3E+02 0.0027 25.9 4.6 71 32-107 49-130 (202)
200 PRK08351 DNA-directed RNA poly 26.4 34 0.00074 23.9 1.0 21 169-191 5-25 (61)
201 KOG2164 Predicted E3 ubiquitin 26.3 28 0.0006 33.9 0.7 30 166-195 185-239 (513)
202 PRK00432 30S ribosomal protein 26.3 35 0.00075 22.7 1.0 25 167-191 20-47 (50)
203 PRK08527 acetolactate synthase 26.1 2.5E+02 0.0053 27.1 7.2 70 59-132 432-524 (563)
204 CHL00099 ilvB acetohydroxyacid 26.1 2.9E+02 0.0062 26.9 7.7 45 59-107 448-492 (585)
205 PRK12474 hypothetical protein; 25.6 3E+02 0.0065 26.2 7.6 45 59-107 407-451 (518)
206 PRK14714 DNA polymerase II lar 25.6 65 0.0014 34.9 3.2 13 183-195 711-723 (1337)
207 PF10013 DUF2256: Uncharacteri 25.3 37 0.00081 22.0 0.9 13 180-192 6-19 (42)
208 PRK11269 glyoxylate carboligas 25.3 2.6E+02 0.0056 27.2 7.2 71 59-133 437-539 (591)
209 PHA02566 alt ADP-ribosyltransf 25.2 73 0.0016 32.2 3.3 50 71-120 84-147 (684)
210 PRK06466 acetolactate synthase 24.8 3.4E+02 0.0074 26.2 7.9 45 59-107 441-485 (574)
211 PF07295 DUF1451: Protein of u 24.7 46 0.001 27.0 1.6 34 157-190 101-139 (146)
212 PF00535 Glycos_transf_2: Glyc 23.8 2.9E+02 0.0064 20.1 6.6 70 57-133 25-103 (169)
213 COG4888 Uncharacterized Zn rib 23.8 39 0.00086 26.0 1.0 31 164-194 19-59 (104)
214 PF04423 Rad50_zn_hook: Rad50 23.5 29 0.00063 22.9 0.2 12 183-194 22-33 (54)
215 PRK08155 acetolactate synthase 23.5 2.8E+02 0.006 26.8 7.0 70 59-132 437-529 (564)
216 cd02009 TPP_SHCHC_synthase Thi 23.4 1.5E+02 0.0033 23.9 4.5 36 59-98 68-103 (175)
217 PRK04338 N(2),N(2)-dimethylgua 23.4 57 0.0012 30.4 2.1 30 165-194 240-274 (382)
218 COG1867 TRM1 N2,N2-dimethylgua 23.4 49 0.0011 31.1 1.7 29 166-194 237-270 (380)
219 cd06167 LabA_like LabA_like pr 23.4 2E+02 0.0044 22.0 5.1 44 60-110 101-144 (149)
220 cd05006 SIS_GmhA Phosphoheptos 23.3 1.1E+02 0.0025 24.5 3.7 45 61-111 104-148 (177)
221 TIGR00686 phnA alkylphosphonat 23.2 32 0.0007 26.8 0.4 26 169-194 4-32 (109)
222 PRK00414 gmhA phosphoheptose i 23.2 1E+02 0.0022 25.6 3.5 45 61-111 114-158 (192)
223 PRK03681 hypA hydrogenase nick 23.0 60 0.0013 25.0 1.9 23 168-190 71-96 (114)
224 PF10263 SprT-like: SprT-like 23.0 46 0.001 26.2 1.3 28 166-193 122-155 (157)
225 COG1379 PHP family phosphoeste 22.9 28 0.0006 32.4 -0.0 26 169-194 248-278 (403)
226 KOG0311 Predicted E3 ubiquitin 22.9 19 0.00042 33.5 -1.0 34 162-195 38-93 (381)
227 PLN00209 ribosomal protein S27 22.8 35 0.00076 25.5 0.5 27 169-195 38-69 (86)
228 cd03812 GT1_CapH_like This fam 22.7 3.9E+02 0.0084 22.8 7.2 38 61-98 1-38 (358)
229 KOG4602 Nanos and related prot 22.6 42 0.00091 30.1 1.0 20 166-185 267-294 (318)
230 PRK12380 hydrogenase nickel in 22.5 64 0.0014 24.8 1.9 22 168-189 71-94 (113)
231 PF02525 Flavodoxin_2: Flavodo 22.5 1.7E+02 0.0037 23.8 4.7 38 61-98 2-42 (199)
232 PF01927 Mut7-C: Mut7-C RNAse 22.3 2.3E+02 0.005 22.4 5.3 49 80-134 33-82 (147)
233 TIGR02720 pyruv_oxi_spxB pyruv 22.1 3.1E+02 0.0066 26.6 7.0 71 59-133 426-517 (575)
234 PRK10569 NAD(P)H-dependent FMN 21.9 2.3E+02 0.0049 23.6 5.3 38 61-98 2-40 (191)
235 smart00661 RPOL9 RNA polymeras 21.8 49 0.0011 21.2 1.0 26 170-195 3-34 (52)
236 COG1773 Rubredoxin [Energy pro 21.7 62 0.0013 22.2 1.5 13 167-179 3-15 (55)
237 KOG2462 C2H2-type Zn-finger pr 21.6 51 0.0011 29.7 1.4 28 168-195 131-175 (279)
238 PF04577 DUF563: Protein of un 21.5 2.3E+02 0.0051 22.6 5.3 67 59-129 102-168 (206)
239 PF08792 A2L_zn_ribbon: A2L zi 21.5 61 0.0013 19.7 1.3 21 157-177 6-31 (33)
240 PTZ00083 40S ribosomal protein 21.5 39 0.00084 25.2 0.5 27 169-195 37-68 (85)
241 PF13580 SIS_2: SIS domain; PD 21.5 1.8E+02 0.0038 22.6 4.3 33 58-94 103-135 (138)
242 TIGR00288 conserved hypothetic 21.5 2.4E+02 0.0051 23.3 5.2 35 73-110 116-150 (160)
243 PF09186 DUF1949: Domain of un 21.2 1.6E+02 0.0034 18.7 3.4 14 102-115 43-56 (56)
244 PRK08979 acetolactate synthase 21.0 3.9E+02 0.0085 25.8 7.5 44 59-106 439-482 (572)
245 PRK08199 thiamine pyrophosphat 20.9 3.2E+02 0.007 26.2 6.9 71 59-133 433-525 (557)
246 PF07627 PSCyt3: Protein of un 20.9 1.2E+02 0.0025 23.2 3.0 35 103-137 4-42 (101)
247 PF13913 zf-C2HC_2: zinc-finge 20.8 43 0.00093 18.9 0.5 14 182-195 3-16 (25)
248 COG1432 Uncharacterized conser 20.8 2.6E+02 0.0056 23.1 5.4 46 58-110 110-155 (181)
249 TIGR03846 sulfopy_beta sulfopy 20.8 3.1E+02 0.0067 22.5 5.9 68 59-130 59-141 (181)
250 PRK06276 acetolactate synthase 20.7 3.6E+02 0.0078 26.2 7.2 71 59-133 437-530 (586)
251 PF14835 zf-RING_6: zf-RING of 20.6 57 0.0012 23.1 1.2 22 168-191 29-50 (65)
252 PF10058 DUF2296: Predicted in 20.6 58 0.0012 22.0 1.2 13 164-176 41-53 (54)
253 KOG4451 Uncharacterized conser 20.5 30 0.00066 30.5 -0.3 15 181-195 263-277 (286)
254 PF04216 FdhE: Protein involve 20.5 51 0.0011 29.2 1.1 26 168-193 198-223 (290)
255 cd02005 TPP_PDC_IPDC Thiamine 20.1 2.8E+02 0.0062 22.5 5.5 70 60-133 69-160 (183)
No 1
>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=100.00 E-value=9e-59 Score=409.64 Aligned_cols=179 Identities=51% Similarity=0.925 Sum_probs=164.8
Q ss_pred HHHHHHHHHHHHhhhhccCCCCCCCcccccchHhHHHHHHHHHhhhhhcCC---CCCCcEEEE-EecCCCCCcchhhHHH
Q 028156 5 CATLLQNLEEFMNKDEQLGKQEPEGRIACSLLSGSLSMALCYIQRVFRSGL---LHPQPRILC-LQGSPDGPEQYVAIMN 80 (213)
Q Consensus 5 ~~~i~~~l~~l~~~~~~~~~~~~~~~~~~s~L~~aLs~ALc~inr~~~~~~---~~~~~rILi-is~S~d~~~qyi~imn 80 (213)
-+.|.++++++++++.+.+.. +.++.|+|||++|||||||+.++.. ..+++|||| +++|+|.+.||+++||
T Consensus 92 ~~~v~~~l~~l~~~~~~~~~~-----~~~s~LagALS~ALCyINR~~~~~~~~~~~~~~RILv~~s~s~d~~~QYi~~MN 166 (276)
T PF03850_consen 92 DETVLEELKKLMSETSESSDS-----TTSSLLAGALSMALCYINRISRESPSGGTSLKSRILVIVSGSPDSSSQYIPLMN 166 (276)
T ss_pred HHHHHHHHHHHHhhccccccc-----ccchhhHHHHHHHHHHHhhhhhcccCCCCCcCccEEEEEecCCCccHHHHHHHH
Confidence 355889999999886655432 2238999999999999999987654 489999999 8999999999999999
Q ss_pred HHHHHHhCCeeeeEEEcCCcChHHHHHHHHhhCCeeeccCCcchHHHHHHHHcCCCchhhcccCCCCCCCCCCceeeeec
Q 028156 81 AIFSAQRSMVPIDSCYLGAQNSAFLQQASYITGGVHHKPQQLDGLFQYLLTIFGTDLHSRNFLQLPKPVGVDFRASCFCH 160 (213)
Q Consensus 81 ~if~aqk~~I~Idv~~L~~~e~~iLqq~~~~TgG~Y~~~~~~~~l~~~Ll~~~~p~~~~r~~l~~P~~~~vd~~a~C~CH 160 (213)
+||+|||++|+||||.|+..++.|||||||+|||+|+.+.++++|+||||++|+|++.+|+.+.+|.+..|||||+||||
T Consensus 167 ~iFaAqk~~v~IDv~~L~~~~s~fLqQa~d~T~G~y~~~~~~~~l~q~L~~~fl~~~~~R~~l~~p~~~~vd~ra~Cfch 246 (276)
T PF03850_consen 167 CIFAAQKQKVPIDVCKLGGKDSTFLQQASDITGGIYLKVSKPEGLLQYLLTAFLPDPSSRSFLILPTQSSVDFRASCFCH 246 (276)
T ss_pred HHHHHhcCCceeEEEEecCCchHHHHHHHHHhCceeeccCccccHHHHHHHhhcCCHHHHhhccCCCCCCCCcceeeeec
Confidence 99999999999999999755999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCcccceeEcCCCCccccCCC--Ccccccc
Q 028156 161 KNTIDMGYICSVCLSIYCKHL--KKCSTCG 188 (213)
Q Consensus 161 ~~~v~~GyvCp~Clsi~C~~p--~~C~~C~ 188 (213)
++++|+|||||+||||||++| .+|+|||
T Consensus 247 ~k~vd~g~vCsvCLsIfc~~p~~~~C~tC~ 276 (276)
T PF03850_consen 247 RKVVDIGYVCSVCLSIFCEFPDGGICPTCG 276 (276)
T ss_pred CCcccceeEchhhhhhhhCCCCCCCCCCCC
Confidence 999999999999999999997 3999997
No 2
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=7e-58 Score=403.94 Aligned_cols=181 Identities=40% Similarity=0.682 Sum_probs=166.4
Q ss_pred HHHHHHHHHHHHhhhhccCCCCCCCcccccchHhHHHHHHHHHhhhhhcC--CCCCCcEEEEEecCCCCCcchhhHHHHH
Q 028156 5 CATLLQNLEEFMNKDEQLGKQEPEGRIACSLLSGSLSMALCYIQRVFRSG--LLHPQPRILCLQGSPDGPEQYVAIMNAI 82 (213)
Q Consensus 5 ~~~i~~~l~~l~~~~~~~~~~~~~~~~~~s~L~~aLs~ALc~inr~~~~~--~~~~~~rILiis~S~d~~~qyi~imn~i 82 (213)
-+.|+++|+++++++...... ..++.|+|||++|||||||+.++. ..++++|||||++|+|.+.||+++||+|
T Consensus 95 ~~~v~~~l~~l~~~~~~~~~~-----~~~s~lagals~ALcyinr~~~~~~~~~~~~~RIlii~~s~~~~~qYi~~mn~I 169 (279)
T TIGR00627 95 DETIVEEIKPLMAHADKHMKK-----DSRTVLAGALSDALGYINRSEQSETASEKLKSRILVISITPDMALQYIPLMNCI 169 (279)
T ss_pred HHHHHHHHHHHHhhchhcccc-----cccccchhHHHhhhhhhcccccccccCcCCcceEEEEECCCCchHHHHHHHHHH
Confidence 355899999999886554321 257899999999999999987643 2578999999999999999999999999
Q ss_pred HHHHhCCeeeeEEEcCCcC--hHHHHHHHHhhCCeeeccCCcchHHHHHHHHcCCCchhhcccCCCCCCCCCCceeeeec
Q 028156 83 FSAQRSMVPIDSCYLGAQN--SAFLQQASYITGGVHHKPQQLDGLFQYLLTIFGTDLHSRNFLQLPKPVGVDFRASCFCH 160 (213)
Q Consensus 83 f~aqk~~I~Idv~~L~~~e--~~iLqq~~~~TgG~Y~~~~~~~~l~~~Ll~~~~p~~~~r~~l~~P~~~~vd~~a~C~CH 160 (213)
|+|||+||+||||+|+ +| +.||||+||+|||+|+++.+++||+||||++|+|||..|+.|..|.+..+||||+||||
T Consensus 170 faaqk~~I~Idv~~L~-~e~~~~~lqQa~~~TgG~Y~~~~~~~~L~q~L~~~~~pp~~~r~~Li~P~~~~vd~ra~CfCh 248 (279)
T TIGR00627 170 FSAQKQNIPIDVVSIG-GDFTSGFLQQAADITGGSYLHVKKPQGLLQYLMTNMLPDPTLRAVLSKPNHNSVDYRASCFCH 248 (279)
T ss_pred HHHHHcCceEEEEEeC-CccccHHHHHHHHHhCCEEeccCCHhHHHHHHHHhcCCChhhhHhhcCCCCCCCCCcceeeec
Confidence 9999999999999995 55 99999999999999999999999999999999999999999999999999999999999
Q ss_pred cCcccceeEcCCCCccccCCCCccccccccc
Q 028156 161 KNTIDMGYICSVCLSIYCKHLKKCSTCGSVF 191 (213)
Q Consensus 161 ~~~v~~GyvCp~Clsi~C~~p~~C~~C~~~f 191 (213)
++++++|||||+|++|||++|++|++||++|
T Consensus 249 ~k~v~~GyvCs~Clsi~C~~p~~C~~Cgt~f 279 (279)
T TIGR00627 249 HQLVSIGFVCSVCLSVLCQYTPICKTCKTAF 279 (279)
T ss_pred CccccceEECCCccCCcCCCCCCCCCCCCCC
Confidence 9999999999999999999999999999987
No 3
>KOG2487 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 [Transcription; Replication, recombination and repair]
Probab=100.00 E-value=9.7e-57 Score=389.51 Aligned_cols=194 Identities=40% Similarity=0.693 Sum_probs=176.2
Q ss_pred HHHHHHHHHHHhhhhccCCCCCCCcccccchHhHHHHHHHHHhhhhhcC-CCCCCcEEEEEecCCCCCcchhhHHHHHHH
Q 028156 6 ATLLQNLEEFMNKDEQLGKQEPEGRIACSLLSGSLSMALCYIQRVFRSG-LLHPQPRILCLQGSPDGPEQYVAIMNAIFS 84 (213)
Q Consensus 6 ~~i~~~l~~l~~~~~~~~~~~~~~~~~~s~L~~aLs~ALc~inr~~~~~-~~~~~~rILiis~S~d~~~qyi~imn~if~ 84 (213)
+.|+.+|+++|......... ..+.|+|||+.||+|+||+.+++ ++..++|||||+.+.|...||+++||+||+
T Consensus 118 ~tiv~ei~~lm~~~~~~~~~------~rt~lagals~~L~yi~~~~ke~~~~~lkSRilV~t~t~d~~~qyi~~MNciFa 191 (314)
T KOG2487|consen 118 DTIVEEIYRLMEHPDKYDVG------DRTVLAGALSDALGYINRLHKEEASEKLKSRILVFTLTRDRALQYIPYMNCIFA 191 (314)
T ss_pred hHHHHHHHHHHhCccccccc------cceeeccchhhccchHhhhhhhhhhhhhhceEEEEEechHHHhhhhhHHHHHHH
Confidence 56899999999886655432 27899999999999999998764 457899999999999999999999999999
Q ss_pred HHhCCeeeeEEEcCCcChHHHHHHHHhhCCeeeccCCcchHHHHHHHHcCCCchhhcccCCCCCCCCCCceeeeeccCcc
Q 028156 85 AQRSMVPIDSCYLGAQNSAFLQQASYITGGVHHKPQQLDGLFQYLLTIFGTDLHSRNFLQLPKPVGVDFRASCFCHKNTI 164 (213)
Q Consensus 85 aqk~~I~Idv~~L~~~e~~iLqq~~~~TgG~Y~~~~~~~~l~~~Ll~~~~p~~~~r~~l~~P~~~~vd~~a~C~CH~~~v 164 (213)
|||+||+||||+|+ +++.||||+||+|||.|+.+.++++|+||||+.++|+|..|+.+..|.+..|||||.||||++++
T Consensus 192 AqKq~I~Idv~~l~-~~s~~LqQa~D~TGG~YL~v~~~~gLLqyLlt~~~~D~~~R~~l~kpnh~~VDfRAtC~CH~~lv 270 (314)
T KOG2487|consen 192 AQKQNIPIDVVSLG-GDSGFLQQACDITGGDYLHVEKPDGLLQYLLTLLLTDPELRAVLSKPNHNSVDFRATCYCHNRLV 270 (314)
T ss_pred HHhcCceeEEEEec-CCchHHHHHHhhcCCeeEecCCcchHHHHHHHHhcCCcchhhhccCCCCCCcCcceeeeeeccee
Confidence 99999999999995 78999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cceeEcCCCCccccCCCCccccccccccccccCCCCCccccccccC
Q 028156 165 DMGYICSVCLSIYCKHLKKCSTCGSVFGQAQTQSDEPSATNRKRKT 210 (213)
Q Consensus 165 ~~GyvCp~Clsi~C~~p~~C~~C~~~f~~~~~~~~~~~~~~~~~~~ 210 (213)
++|||||+|||+||+++|+|++|++.|..+. +|.++.+|||.
T Consensus 271 ~iG~VCSVCLSVfC~~~PiC~~C~s~F~~t~----~Pv~p~~kkkl 312 (314)
T KOG2487|consen 271 LIGFVCSVCLSVFCRFVPICKTCKSKFSFTK----YPVKPNRKKKL 312 (314)
T ss_pred eeeeehHHHHHHhhCCCCccchhhhhccccc----Cccchhhhhhc
Confidence 9999999999999999999999999998443 56666665554
No 4
>COG5242 TFB4 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 [Transcription / DNA replication, recombination, and repair]
Probab=100.00 E-value=1.9e-48 Score=331.16 Aligned_cols=177 Identities=33% Similarity=0.572 Sum_probs=164.3
Q ss_pred HHHHHHHHHHHhhhhccCCCCCCCcccccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCC-CCCcchhhHHHHHHH
Q 028156 6 ATLLQNLEEFMNKDEQLGKQEPEGRIACSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSP-DGPEQYVAIMNAIFS 84 (213)
Q Consensus 6 ~~i~~~l~~l~~~~~~~~~~~~~~~~~~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~-d~~~qyi~imn~if~ 84 (213)
+.++.++++|++.+...+ ..+.++|||+.||.|+|++..+ ..+++||||++.|+ |...|||++|||||+
T Consensus 109 e~~i~eiyrl~e~~~k~s--------qr~~v~gams~glay~n~~~~e--~slkSriliftlsG~d~~~qYip~mnCiF~ 178 (296)
T COG5242 109 ETDITEIYRLIEHPHKNS--------QRYDVGGAMSLGLAYCNHRDEE--TSLKSRILIFTLSGRDRKDQYIPYMNCIFA 178 (296)
T ss_pred hHHHHHHHHHHhCccccc--------ceeehhhhhhhhHHHHhhhccc--ccccceEEEEEecCchhhhhhchhhhheee
Confidence 458889999998865543 3577999999999999998644 57999999999876 888999999999999
Q ss_pred HHhCCeeeeEEEcCCcChHHHHHHHHhhCCeeeccCCcchHHHHHHHHcCCCchhhcccCCCCCCCCCCceeeeeccCcc
Q 028156 85 AQRSMVPIDSCYLGAQNSAFLQQASYITGGVHHKPQQLDGLFQYLLTIFGTDLHSRNFLQLPKPVGVDFRASCFCHKNTI 164 (213)
Q Consensus 85 aqk~~I~Idv~~L~~~e~~iLqq~~~~TgG~Y~~~~~~~~l~~~Ll~~~~p~~~~r~~l~~P~~~~vd~~a~C~CH~~~v 164 (213)
|||.||+|||+++ .+.+.||+|.||.|||+|+.+.+++||+||||+.++|+++.|+.+.-|.+..|||||.|+||++++
T Consensus 179 Aqk~~ipI~v~~i-~g~s~fl~Q~~daTgG~Yl~ve~~eGllqyL~~~lf~d~~lrp~~~~pn~~svdFratCych~rvv 257 (296)
T COG5242 179 AQKFGIPISVFSI-FGNSKFLLQCCDATGGDYLTVEDTEGLLQYLLSLLFTDGELRPLGVKPNHGSVDFRATCYCHNRVV 257 (296)
T ss_pred hhhcCCceEEEEe-cCccHHHHHHhhccCCeeEeecCchhHHHHHHHHhcCCCCccccccCCCcccccccceeEEeccEE
Confidence 9999999999999 477999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cceeEcCCCCccccCCCCccccccccccc
Q 028156 165 DMGYICSVCLSIYCKHLKKCSTCGSVFGQ 193 (213)
Q Consensus 165 ~~GyvCp~Clsi~C~~p~~C~~C~~~f~~ 193 (213)
++|||||+|||+||++.+.|++|.++|..
T Consensus 258 ~~GfvCsVCLsvfc~p~~~C~~C~skF~~ 286 (296)
T COG5242 258 LLGFVCSVCLSVFCRPVPVCKKCKSKFSF 286 (296)
T ss_pred EEeeehhhhheeecCCcCcCccccccccc
Confidence 99999999999999999999999999974
No 5
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=100.00 E-value=1.2e-35 Score=263.24 Aligned_cols=158 Identities=17% Similarity=0.210 Sum_probs=149.6
Q ss_pred cccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHHHHHh
Q 028156 32 ACSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQASYI 111 (213)
Q Consensus 32 ~~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~~~~ 111 (213)
.+.+|+|||++|...++.++ .+.++|||||.+|. .+.|+++|+.+|.+.++.||||+|++| ++|+.+++.+|..
T Consensus 141 g~fSLqNaLe~a~~~Lk~~p----~H~sREVLii~ssl-sT~DPgdi~~tI~~lk~~kIRvsvIgL-saEv~icK~l~ka 214 (378)
T KOG2807|consen 141 GDFSLQNALELAREVLKHMP----GHVSREVLIIFSSL-STCDPGDIYETIDKLKAYKIRVSVIGL-SAEVFICKELCKA 214 (378)
T ss_pred CChHHHHHHHHHHHHhcCCC----cccceEEEEEEeee-cccCcccHHHHHHHHHhhCeEEEEEee-chhHHHHHHHHHh
Confidence 46789999999999999984 79999999999887 789999999999999999999999999 6999999999999
Q ss_pred hCCeeeccCCcchHHHHHHHHcCCCchhhc------ccCCCCCCCCCCceeeeeccCcccceeEcCCCCccccCCCCccc
Q 028156 112 TGGVHHKPQQLDGLFQYLLTIFGTDLHSRN------FLQLPKPVGVDFRASCFCHKNTIDMGYICSVCLSIYCKHLKKCS 185 (213)
Q Consensus 112 TgG~Y~~~~~~~~l~~~Ll~~~~p~~~~r~------~l~~P~~~~vd~~a~C~CH~~~v~~GyvCp~Clsi~C~~p~~C~ 185 (213)
|||.|.|+.|+.||.++|+.+..|||.... .||||++...|.+++|+||..++..||.||+|.+++|++|.+||
T Consensus 215 T~G~Y~V~lDe~HlkeLl~e~~~Pp~~~~~~~~sLvkmGFP~~~~e~~ps~C~CH~~~~~~Gy~CP~CkakvCsLP~eCp 294 (378)
T KOG2807|consen 215 TGGRYSVALDEGHLKELLLEHTHPPPANKSKECSLVKMGFPSRSPEDTPSFCACHSELSGGGYFCPQCKAKVCSLPIECP 294 (378)
T ss_pred hCCeEEEEeCHHHHHHHHHhcCCCCCcccccCCceEEecCCCcccccCcchheeccccccCceeCCcccCeeecCCccCC
Confidence 999999999999999999999999987643 58999999999999999999999999999999999999999999
Q ss_pred cccccccccc
Q 028156 186 TCGSVFGQAQ 195 (213)
Q Consensus 186 ~C~~~f~~~~ 195 (213)
+|+++|+++|
T Consensus 295 iC~ltLVss~ 304 (378)
T KOG2807|consen 295 ICSLTLVSSP 304 (378)
T ss_pred ccceeEecch
Confidence 9999999998
No 6
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=99.93 E-value=1.2e-25 Score=199.05 Aligned_cols=157 Identities=18% Similarity=0.250 Sum_probs=141.4
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHHHHHhh
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQASYIT 112 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~~~~T 112 (213)
..+|+|||+||.-.+-+. +.++.++||||.||. .+.|+++|..+|.++...+|||.+++| .+|..|++.+|..|
T Consensus 169 nfSLqNaLEmar~~l~~~----~~H~trEvLiifgS~-st~DPgdi~~tid~Lv~~~IrV~~igL-~aevaicKeickaT 242 (421)
T COG5151 169 NFSLQNALEMARIELMKN----TMHGTREVLIIFGST-STRDPGDIAETIDKLVAYNIRVHFIGL-CAEVAICKEICKAT 242 (421)
T ss_pred ChhHHhHHHHhhhhhccc----ccccceEEEEEEeec-ccCCCccHHHHHHHHHhhceEEEEEee-hhHHHHHHHHHhhc
Confidence 467999999997666654 368999999999997 677999999999999999999999999 59999999999999
Q ss_pred ----CCeeeccCCcchHHHHHHHHcCCCchhhc-------ccCCCCCCCCCCceeeeeccCcccceeEcCCCCccccCCC
Q 028156 113 ----GGVHHKPQQLDGLFQYLLTIFGTDLHSRN-------FLQLPKPVGVDFRASCFCHKNTIDMGYICSVCLSIYCKHL 181 (213)
Q Consensus 113 ----gG~Y~~~~~~~~l~~~Ll~~~~p~~~~r~-------~l~~P~~~~vd~~a~C~CH~~~v~~GyvCp~Clsi~C~~p 181 (213)
.|.|.++.|+.||.+++.....|++.-.. .|+||++.--+.+++|+||.++...||.||+|.+.+|.+|
T Consensus 243 n~~~e~~y~v~vde~Hl~el~~E~~~P~~~n~~k~~~sLVkmGFPs~~~E~~Ps~CaCHs~~~~gGy~CP~CktkVCsLP 322 (421)
T COG5151 243 NSSTEGRYYVPVDEGHLSELMRELSHPTDFNGTKTDLSLVKMGFPSPMMEQLPSVCACHSEVKGGGYECPVCKTKVCSLP 322 (421)
T ss_pred CcCcCceeEeeecHHHHHHHHHhcCCCCCCCccccCceEEEecCCchhhhcCccceeeeeeeccCceeCCcccceeecCC
Confidence 69999999999999999988887775321 5799998766889999999999999999999999999999
Q ss_pred Cccccccccccccc
Q 028156 182 KKCSTCGSVFGQAQ 195 (213)
Q Consensus 182 ~~C~~C~~~f~~~~ 195 (213)
..||.|.+.|+++.
T Consensus 323 i~CP~Csl~Lilst 336 (421)
T COG5151 323 ISCPICSLQLILST 336 (421)
T ss_pred ccCcchhHHHHHHH
Confidence 99999999999876
No 7
>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=99.85 E-value=9.2e-21 Score=159.90 Aligned_cols=102 Identities=20% Similarity=0.125 Sum_probs=95.3
Q ss_pred cccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHHHHHh
Q 028156 32 ACSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQASYI 111 (213)
Q Consensus 32 ~~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~~~~ 111 (213)
-+.+|+|||++|...+..++ .|.++|||+|.+|. .++|+.++..+|..+++++||||||+| ++|+++||++|+.
T Consensus 78 G~~SLqN~Le~A~~~L~~~p----~~~srEIlvi~gSl-~t~Dp~di~~ti~~l~~~~IrvsvI~l-aaEv~I~k~i~~~ 151 (193)
T PF04056_consen 78 GEPSLQNGLEMARSSLKHMP----SHGSREILVIFGSL-TTCDPGDIHETIESLKKENIRVSVISL-AAEVYICKKICKE 151 (193)
T ss_pred CChhHHHHHHHHHHHHhhCc----cccceEEEEEEeec-ccCCchhHHHHHHHHHHcCCEEEEEEE-hHHHHHHHHHHHh
Confidence 36889999999999998874 68999999999887 789999999999999999999999999 6999999999999
Q ss_pred hCCeeeccCCcchHHHHHHHHcCCCchh
Q 028156 112 TGGVHHKPQQLDGLFQYLLTIFGTDLHS 139 (213)
Q Consensus 112 TgG~Y~~~~~~~~l~~~Ll~~~~p~~~~ 139 (213)
|||.|.|+.|++||.++|+.+..|||+.
T Consensus 152 T~G~y~V~lde~H~~~lL~~~~~PP~~~ 179 (193)
T PF04056_consen 152 TGGTYGVILDEDHFKELLMEHVPPPPTS 179 (193)
T ss_pred hCCEEEEecCHHHHHHHHHhhCCCCccc
Confidence 9999999999999999999999888874
No 8
>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=99.17 E-value=2e-10 Score=95.60 Aligned_cols=99 Identities=16% Similarity=0.087 Sum_probs=76.8
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHHHHHhh
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQASYIT 112 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~~~~T 112 (213)
.+.|..||.+|+..+.+. +....++|+||..+. ...+...+.+.+..+++++|+|++|++| .+..+|+++|+.|
T Consensus 85 ~t~l~~aL~~A~~~l~~~----~~~~~~~iiil~sd~-~~~~~~~~~~~~~~l~~~~I~v~~IgiG-~~~~~L~~ia~~t 158 (183)
T cd01453 85 EPSLQNGLEMALESLKHM----PSHGSREVLIIFSSL-STCDPGNIYETIDKLKKENIRVSVIGLS-AEMHICKEICKAT 158 (183)
T ss_pred chhHHHHHHHHHHHHhcC----CccCceEEEEEEcCC-CcCChhhHHHHHHHHHHcCcEEEEEEec-hHHHHHHHHHHHh
Confidence 367888999998888753 123456777776432 2223334556788899999999999996 7899999999999
Q ss_pred CCeeeccCCcchHHHHHHHHcCCCc
Q 028156 113 GGVHHKPQQLDGLFQYLLTIFGTDL 137 (213)
Q Consensus 113 gG~Y~~~~~~~~l~~~Ll~~~~p~~ 137 (213)
||.|+.+.|+++|.+.+..+..|||
T Consensus 159 gG~~~~~~~~~~l~~~~~~~~~p~~ 183 (183)
T cd01453 159 NGTYKVILDETHLKELLLEHVTPPP 183 (183)
T ss_pred CCeeEeeCCHHHHHHHHHhcCCCCC
Confidence 9999999999999998888666654
No 9
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.62 E-value=1.2e-08 Score=79.28 Aligned_cols=29 Identities=28% Similarity=0.750 Sum_probs=28.5
Q ss_pred eeEcCCCCccccCCCCccccccccccccc
Q 028156 167 GYICSVCLSIYCKHLKKCSTCGSVFGQAQ 195 (213)
Q Consensus 167 GyvCp~Clsi~C~~p~~C~~C~~~f~~~~ 195 (213)
||+||+|.|++|++|.+|++||++|++++
T Consensus 1 GY~CPrC~skvC~LP~~CpiCgLtLVss~ 29 (112)
T TIGR00622 1 GYFCPQCRAKVCELPVECPICGLTLILST 29 (112)
T ss_pred CccCCCCCCCccCCCCcCCcCCCEEeccc
Confidence 89999999999999999999999999998
No 10
>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=98.19 E-value=3.2e-05 Score=65.23 Aligned_cols=77 Identities=18% Similarity=0.176 Sum_probs=61.6
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCC-cEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCc--ChHHHHHHH
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQ-PRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQ--NSAFLQQAS 109 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~-~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~--e~~iLqq~~ 109 (213)
.+.|++||.+|+-.+.... .+.+ .||++|.+|+ ..++..++.+++..++|+||+||++++|+. ....|+...
T Consensus 84 ~~~l~~AL~~A~~~L~~~~----~~~~~~rivi~v~S~-~~~d~~~i~~~~~~lkk~~I~v~vI~~G~~~~~~~~l~~~~ 158 (187)
T cd01452 84 KANFITGIQIAQLALKHRQ----NKNQKQRIVAFVGSP-IEEDEKDLVKLAKRLKKNNVSVDIINFGEIDDNTEKLTAFI 158 (187)
T ss_pred cchHHHHHHHHHHHHhcCC----CcCCcceEEEEEecC-CcCCHHHHHHHHHHHHHcCCeEEEEEeCCCCCCHHHHHHHH
Confidence 5679999999998887642 3445 4999998886 456777889999999999999999999853 466888888
Q ss_pred HhhCC
Q 028156 110 YITGG 114 (213)
Q Consensus 110 ~~TgG 114 (213)
+..++
T Consensus 159 ~~~~~ 163 (187)
T cd01452 159 DAVNG 163 (187)
T ss_pred HHhcC
Confidence 88753
No 11
>cd01467 vWA_BatA_type VWA BatA type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses. In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if
Probab=98.06 E-value=6.6e-05 Score=60.77 Aligned_cols=86 Identities=14% Similarity=0.078 Sum_probs=59.1
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCC------------c
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGA------------Q 100 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~------------~ 100 (213)
.+.+..+|..|+..+.+.. .....|++++-..+. ..+.........+++.+|+|+++.++. .
T Consensus 82 ~T~l~~al~~a~~~l~~~~-----~~~~~iiliTDG~~~-~g~~~~~~~~~~~~~~gi~i~~i~ig~~~~~~~~~~~~~~ 155 (180)
T cd01467 82 GTAIGDAIGLAIKRLKNSE-----AKERVIVLLTDGENN-AGEIDPATAAELAKNKGVRIYTIGVGKSGSGPKPDGSTIL 155 (180)
T ss_pred CCcHHHHHHHHHHHHHhcC-----CCCCEEEEEeCCCCC-CCCCCHHHHHHHHHHCCCEEEEEEecCCCCCcCCCCcccC
Confidence 3557777877777765431 223456666632222 223333445666788999999999985 4
Q ss_pred ChHHHHHHHHhhCCeeeccCCcch
Q 028156 101 NSAFLQQASYITGGVHHKPQQLDG 124 (213)
Q Consensus 101 e~~iLqq~~~~TgG~Y~~~~~~~~ 124 (213)
+...|+++++.|||.|+.+.+++.
T Consensus 156 ~~~~l~~la~~tgG~~~~~~~~~~ 179 (180)
T cd01467 156 DEDSLVEIADKTGGRIFRALDGFE 179 (180)
T ss_pred CHHHHHHHHHhcCCEEEEecCccc
Confidence 678999999999999999887753
No 12
>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=97.97 E-value=7.3e-05 Score=63.36 Aligned_cols=91 Identities=12% Similarity=-0.018 Sum_probs=63.9
Q ss_pred hHHHHHHHHHhhhhhcCCCCCCcEEEEEe-cCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHHHHHhhCCee
Q 028156 38 GSLSMALCYIQRVFRSGLLHPQPRILCLQ-GSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQASYITGGVH 116 (213)
Q Consensus 38 ~aLs~ALc~inr~~~~~~~~~~~rILiis-~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~~~~TgG~Y 116 (213)
.||.+|+-.+.+- ...++|++|+- -..++...--|..-....|++.+|+|.+|.+|..+-..|+.++++|||.|
T Consensus 95 dAi~~av~rl~~~-----~~a~~kvvILLTDG~n~~~~i~P~~aAa~lA~~~gV~iytIgiG~~d~~~l~~iA~~tgG~~ 169 (191)
T cd01455 95 EATEFAIKELAAK-----EDFDEAIVIVLSDANLERYGIQPKKLADALAREPNVNAFVIFIGSLSDEADQLQRELPAGKA 169 (191)
T ss_pred HHHHHHHHHHHhc-----CcCCCcEEEEEeCCCcCCCCCChHHHHHHHHHhCCCEEEEEEecCCCHHHHHHHHhCCCCcE
Confidence 7888887776411 12345555554 22223333233332456688999999999998667788999999999999
Q ss_pred eccCCcchHHHHHHHHc
Q 028156 117 HKPQQLDGLFQYLLTIF 133 (213)
Q Consensus 117 ~~~~~~~~l~~~Ll~~~ 133 (213)
+++.|.+.|-+.+-.+|
T Consensus 170 F~A~d~~~L~~iy~~I~ 186 (191)
T cd01455 170 FVCMDTSELPHIMQQIF 186 (191)
T ss_pred EEeCCHHHHHHHHHHHH
Confidence 99999988877766555
No 13
>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=97.95 E-value=0.00017 Score=57.47 Aligned_cols=91 Identities=16% Similarity=0.203 Sum_probs=65.6
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCC-cChHHHHHHHHh
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGA-QNSAFLQQASYI 111 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~-~e~~iLqq~~~~ 111 (213)
.+.+..+|..|+..+.+- ......|++|+-... .+.-.+.+.+..+.+.+|+|.+++++. .+..+|+++++.
T Consensus 79 ~T~l~~al~~a~~~l~~~-----~~~~~~iillTDG~~--~~~~~~~~~~~~~~~~~i~i~~i~~g~~~~~~~l~~ia~~ 151 (171)
T cd01461 79 GTNMNDALEAALELLNSS-----PGSVPQIILLTDGEV--TNESQILKNVREALSGRIRLFTFGIGSDVNTYLLERLARE 151 (171)
T ss_pred CcCHHHHHHHHHHhhccC-----CCCccEEEEEeCCCC--CCHHHHHHHHHHhcCCCceEEEEEeCCccCHHHHHHHHHc
Confidence 356777777777666541 234566777773322 122235566666677799999999974 478999999999
Q ss_pred hCCeeeccCCcchHHHHHH
Q 028156 112 TGGVHHKPQQLDGLFQYLL 130 (213)
Q Consensus 112 TgG~Y~~~~~~~~l~~~Ll 130 (213)
|||.|..+.+.+.+.+.+.
T Consensus 152 ~gG~~~~~~~~~~~~~~~~ 170 (171)
T cd01461 152 GRGIARRIYETDDIESQLL 170 (171)
T ss_pred CCCeEEEecChHHHHHHhc
Confidence 9999999999988887764
No 14
>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=97.91 E-value=0.00022 Score=56.83 Aligned_cols=93 Identities=11% Similarity=0.061 Sum_probs=67.5
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCC-C-cchhhHHHHHHHHHhCCeeeeEEEcCCc-ChHHHHHHH
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDG-P-EQYVAIMNAIFSAQRSMVPIDSCYLGAQ-NSAFLQQAS 109 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~-~-~qyi~imn~if~aqk~~I~Idv~~L~~~-e~~iLqq~~ 109 (213)
.+.+..+|..|+..+.+... ....++|++++-..+. + ..+-.+.+.+..+++.+|.|+++.++.. +...|+++|
T Consensus 74 ~T~~~~al~~a~~~~~~~~~---~~~~~~ivl~TDG~~~~~~~~~~~~~~~~~~~~~~~v~i~~i~~g~~~~~~~l~~ia 150 (170)
T cd01465 74 STAGGAGIQLGYQEAQKHFV---PGGVNRILLATDGDFNVGETDPDELARLVAQKRESGITLSTLGFGDNYNEDLMEAIA 150 (170)
T ss_pred CCCHHHHHHHHHHHHHhhcC---CCCeeEEEEEeCCCCCCCCCCHHHHHHHHHHhhcCCeEEEEEEeCCCcCHHHHHHHH
Confidence 46788999999988876421 1223667777743322 2 2234556667777889999999999743 678999999
Q ss_pred HhhCCeeeccCCcchHHHH
Q 028156 110 YITGGVHHKPQQLDGLFQY 128 (213)
Q Consensus 110 ~~TgG~Y~~~~~~~~l~~~ 128 (213)
..++|.|..+.+.+.+-++
T Consensus 151 ~~~~g~~~~~~~~~~~~~~ 169 (170)
T cd01465 151 DAGNGNTAYIDNLAEARKV 169 (170)
T ss_pred hcCCceEEEeCCHHHHHhh
Confidence 9999999999888776543
No 15
>PRK13685 hypothetical protein; Provisional
Probab=97.84 E-value=0.00036 Score=62.97 Aligned_cols=99 Identities=20% Similarity=0.218 Sum_probs=67.7
Q ss_pred ccchHhHHHHHHHHHhhhh---hcCCCCCCcEEEEEecCCCCC-c---chhhHHHHHHHHHhCCeeeeEEEcCCc-----
Q 028156 33 CSLLSGSLSMALCYIQRVF---RSGLLHPQPRILCLQGSPDGP-E---QYVAIMNAIFSAQRSMVPIDSCYLGAQ----- 100 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~---~~~~~~~~~rILiis~S~d~~-~---qyi~imn~if~aqk~~I~Idv~~L~~~----- 100 (213)
.+.+..+|..|+..+.+.. .+......++|++++-..+.. . +....+.....|++.+|+|+++++|..
T Consensus 165 ~T~~g~al~~A~~~l~~~~~~~~~~~~~~~~~IILlTDG~~~~~~~~~~~~~~~~aa~~a~~~gi~i~~Ig~G~~~g~~~ 244 (326)
T PRK13685 165 RTATGEAIFTALQAIATVGAVIGGGDTPPPARIVLMSDGKETVPTNPDNPRGAYTAARTAKDQGVPISTISFGTPYGSVE 244 (326)
T ss_pred CcchHHHHHHHHHHHHhhhcccccccCCCCCEEEEEcCCCCCCCCCCCCcccHHHHHHHHHHcCCeEEEEEECCCCCCcC
Confidence 3456778888887775431 111122346788887333322 1 223346778888999999999999852
Q ss_pred ----------ChHHHHHHHHhhCCeeeccCCcchHHHHHHH
Q 028156 101 ----------NSAFLQQASYITGGVHHKPQQLDGLFQYLLT 131 (213)
Q Consensus 101 ----------e~~iLqq~~~~TgG~Y~~~~~~~~l~~~Ll~ 131 (213)
+...||++|+.|||.|+.+.+++.|.+.+-.
T Consensus 245 ~~g~~~~~~~d~~~L~~iA~~tgG~~~~~~~~~~L~~if~~ 285 (326)
T PRK13685 245 INGQRQPVPVDDESLKKIAQLSGGEFYTAASLEELRAVYAT 285 (326)
T ss_pred cCCceeeecCCHHHHHHHHHhcCCEEEEcCCHHHHHHHHHH
Confidence 5579999999999999999988776655543
No 16
>PF13519 VWA_2: von Willebrand factor type A domain; PDB: 3IBS_B 3RAG_B 2X5N_A.
Probab=97.80 E-value=0.00031 Score=55.13 Aligned_cols=89 Identities=16% Similarity=0.153 Sum_probs=61.0
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcCh--HHHHHHHH
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNS--AFLQQASY 110 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~--~iLqq~~~ 110 (213)
.+.+..||..|..++.... ..++.|++|+-.. ...++. +.+..+++.+|+|.++.++..+. ..|++++.
T Consensus 79 ~t~~~~al~~a~~~~~~~~-----~~~~~iv~iTDG~-~~~~~~---~~~~~~~~~~i~i~~v~~~~~~~~~~~l~~la~ 149 (172)
T PF13519_consen 79 GTNLYDALQEAAKMLASSD-----NRRRAIVLITDGE-DNSSDI---EAAKALKQQGITIYTVGIGSDSDANEFLQRLAE 149 (172)
T ss_dssp S--HHHHHHHHHHHHHC-S-----SEEEEEEEEES-T-THCHHH---HHHHHHHCTTEEEEEEEES-TT-EHHHHHHHHH
T ss_pred CCcHHHHHHHHHHHHHhCC-----CCceEEEEecCCC-CCcchh---HHHHHHHHcCCeEEEEEECCCccHHHHHHHHHH
Confidence 4678888888888876641 2344455555322 222233 57778899999999999975433 59999999
Q ss_pred hhCCeeecc-CCcchHHHHHH
Q 028156 111 ITGGVHHKP-QQLDGLFQYLL 130 (213)
Q Consensus 111 ~TgG~Y~~~-~~~~~l~~~Ll 130 (213)
.|||.|+.+ .+.+.|.+.|-
T Consensus 150 ~tgG~~~~~~~~~~~l~~~~~ 170 (172)
T PF13519_consen 150 ATGGRYFHVDNDPEDLDDAFQ 170 (172)
T ss_dssp HTEEEEEEE-SSSHHHHHHHH
T ss_pred hcCCEEEEecCCHHHHHHHHh
Confidence 999999999 67877777664
No 17
>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=97.59 E-value=0.0017 Score=57.25 Aligned_cols=97 Identities=18% Similarity=0.143 Sum_probs=63.7
Q ss_pred ccchHhHHHHHHH-HHhhhhhcCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCC------------
Q 028156 33 CSLLSGSLSMALC-YIQRVFRSGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGA------------ 99 (213)
Q Consensus 33 ~s~L~~aLs~ALc-~inr~~~~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~------------ 99 (213)
.+.|..||.+|.- .+.+.... ...++.|++|+-..|..+ ..++-.++..+++.+|+|.+|.++.
T Consensus 140 ~T~l~~al~~aa~~~~~~~~~~--~p~rk~iIllTDG~~~~~-~~~~~~~~~~~~~~~v~vy~I~~~~~~~~~~~~~~~~ 216 (296)
T TIGR03436 140 GTALYDAITLAALEQLANALAG--IPGRKALIVISDGGDNRS-RDTLERAIDAAQRADVAIYSIDARGLRAPDLGAGAKA 216 (296)
T ss_pred cchhHHHHHHHHHHHHHHhhcC--CCCCeEEEEEecCCCcch-HHHHHHHHHHHHHcCCEEEEeccCccccCCccccccc
Confidence 4567888776643 33332111 123455666664443332 2355677888899999999999952
Q ss_pred --cChHHHHHHHHhhCCeeeccCCcchHHHHHHHHc
Q 028156 100 --QNSAFLQQASYITGGVHHKPQQLDGLFQYLLTIF 133 (213)
Q Consensus 100 --~e~~iLqq~~~~TgG~Y~~~~~~~~l~~~Ll~~~ 133 (213)
.....|+++|+.|||.|+.+ +.+.|.+.+....
T Consensus 217 ~~~~~~~L~~iA~~TGG~~~~~-~~~~l~~~f~~i~ 251 (296)
T TIGR03436 217 GLGGPEALERLAEETGGRAFYV-NSNDLDGAFAQIA 251 (296)
T ss_pred CCCcHHHHHHHHHHhCCeEecc-cCccHHHHHHHHH
Confidence 13579999999999999888 7777666555443
No 18
>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=97.57 E-value=0.00071 Score=54.25 Aligned_cols=78 Identities=24% Similarity=0.323 Sum_probs=55.8
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcC-CcChHHHHHHHHh
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLG-AQNSAFLQQASYI 111 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~-~~e~~iLqq~~~~ 111 (213)
.+.+..||..|...+.+.. ......+|++|+-..+.. . .....+++.+|.|.+++++ ..+...|+++|+.
T Consensus 76 ~T~~~~al~~a~~~~~~~~---~~~~~~~iillTDG~~~~-~-----~~~~~~~~~~v~v~~igig~~~~~~~l~~iA~~ 146 (155)
T cd01466 76 GTNVVGGLKKALKVLGDRR---QKNPVASIMLLSDGQDNH-G-----AVVLRADNAPIPIHTFGLGASHDPALLAFIAEI 146 (155)
T ss_pred CccHHHHHHHHHHHHhhcc---cCCCceEEEEEcCCCCCc-c-----hhhhcccCCCceEEEEecCCCCCHHHHHHHHhc
Confidence 5678999999988876531 123446777787332211 1 2334567789999999997 3578899999999
Q ss_pred hCCeeecc
Q 028156 112 TGGVHHKP 119 (213)
Q Consensus 112 TgG~Y~~~ 119 (213)
|||.|..+
T Consensus 147 t~G~~~~~ 154 (155)
T cd01466 147 TGGTFSYV 154 (155)
T ss_pred cCceEEEe
Confidence 99999875
No 19
>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=97.51 E-value=0.0011 Score=55.32 Aligned_cols=80 Identities=16% Similarity=0.214 Sum_probs=53.6
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCC-cchhhHHHHHHHHHh----CCeeeeEEEcCCc-ChHHHH
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGP-EQYVAIMNAIFSAQR----SMVPIDSCYLGAQ-NSAFLQ 106 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~-~qyi~imn~if~aqk----~~I~Idv~~L~~~-e~~iLq 106 (213)
.+.|..+|..|+.++. . .-.++|++|+-..+.. .+......- .++. .+|+|+++++|.. +..+|+
T Consensus 116 ~T~l~~aL~~a~~~l~--~-----~~~~~iillTDG~~~~~~~~~~~~~~--~~~~~~~~~~i~i~~igiG~~~~~~~l~ 186 (206)
T cd01456 116 WTPLAAALAEAAAYVD--P-----GRVNVVVLITDGEDTCGPDPCEVARE--LAKRRTPAPPIKVNVIDFGGDADRAELE 186 (206)
T ss_pred cChHHHHHHHHHHHhC--C-----CCcceEEEEcCCCccCCCCHHHHHHH--HHHhcCCCCCceEEEEEecCcccHHHHH
Confidence 5779999999988874 1 1126788888443322 222322222 2233 5999999999743 578999
Q ss_pred HHHHhhCCee-eccCC
Q 028156 107 QASYITGGVH-HKPQQ 121 (213)
Q Consensus 107 q~~~~TgG~Y-~~~~~ 121 (213)
++|+.|||.| ....+
T Consensus 187 ~iA~~tgG~~~~~~~~ 202 (206)
T cd01456 187 AIAEATGGTYAYNQSD 202 (206)
T ss_pred HHHHhcCCeEeccccc
Confidence 9999999999 65544
No 20
>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=97.43 E-value=0.0031 Score=51.56 Aligned_cols=90 Identities=11% Similarity=0.034 Sum_probs=60.8
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCC-Ccchh-hH-HHHHHHHHhCCeeeeEEEcCCc--ChHHHHH
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDG-PEQYV-AI-MNAIFSAQRSMVPIDSCYLGAQ--NSAFLQQ 107 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~-~~qyi-~i-mn~if~aqk~~I~Idv~~L~~~--e~~iLqq 107 (213)
.+.|..+|..|+..+++..+ .......|++|+-..+. +.++. .. ......+++.+|.|.++..+.. +..+|++
T Consensus 75 ~T~l~~aL~~a~~~l~~~~~--~~~~~~~ivliTDG~~~~g~~~~~~~~~~~~~~l~~~gi~v~~I~~~~~~~~~~~l~~ 152 (178)
T cd01451 75 GTPLAAGLLAAYELAAEQAR--DPGQRPLIVVITDGRANVGPDPTADRALAAARKLRARGISALVIDTEGRPVRRGLAKD 152 (178)
T ss_pred CCcHHHHHHHHHHHHHHHhc--CCCCceEEEEECCCCCCCCCCchhHHHHHHHHHHHhcCCcEEEEeCCCCccCccHHHH
Confidence 46789999999988832111 11224566667633222 22221 22 5667888999999999998532 3579999
Q ss_pred HHHhhCCeeeccCCcch
Q 028156 108 ASYITGGVHHKPQQLDG 124 (213)
Q Consensus 108 ~~~~TgG~Y~~~~~~~~ 124 (213)
+|+.|||.|+.+.+.++
T Consensus 153 iA~~tgG~~~~~~d~~~ 169 (178)
T cd01451 153 LARALGGQYVRLPDLSA 169 (178)
T ss_pred HHHHcCCeEEEcCcCCH
Confidence 99999999999887653
No 21
>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=97.04 E-value=0.01 Score=46.59 Aligned_cols=84 Identities=15% Similarity=0.095 Sum_probs=58.5
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCc-ChHHHHHHHHh
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQ-NSAFLQQASYI 111 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~-e~~iLqq~~~~ 111 (213)
.+.+..+|..|+..+.+.........++.|++|+... +.++..+...+..+++.+|.|..++++.. ....+++++..
T Consensus 80 ~~~~~~al~~~~~~~~~~~~~~~~~~~~~iviitDg~--~~~~~~~~~~~~~~~~~~i~i~~i~~~~~~~~~~l~~~~~~ 157 (177)
T smart00327 80 GTNLGAALQYALENLFSKSAGSRRGAPKVLILITDGE--SNDGGDLLKAAKELKRSGVKVFVVGVGNDVDEEELKKLASA 157 (177)
T ss_pred CchHHHHHHHHHHHhcCcCCCCCCCCCeEEEEEcCCC--CCCCccHHHHHHHHHHCCCEEEEEEccCccCHHHHHHHhCC
Confidence 4668888888887775322111112244555555322 22224567888899999999999999755 89999999999
Q ss_pred hCCeeec
Q 028156 112 TGGVHHK 118 (213)
Q Consensus 112 TgG~Y~~ 118 (213)
++|.|..
T Consensus 158 ~~~~~~~ 164 (177)
T smart00327 158 PGGVYVF 164 (177)
T ss_pred CcceEEe
Confidence 9999976
No 22
>TIGR00868 hCaCC calcium-activated chloride channel protein 1. distributions. found a row in 1A13.INFO that was not parsed out
Probab=97.04 E-value=0.0058 Score=62.13 Aligned_cols=84 Identities=19% Similarity=0.255 Sum_probs=63.1
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHHHHHhh
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQASYIT 112 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~~~~T 112 (213)
.+.|..||.+|+..+++... ....+.|++++-..+.. .-.++..+++.+|+|.++++|......|+++|+.|
T Consensus 382 GT~I~~GL~~Alq~L~~~~~---~~~~~~IILLTDGedn~-----~~~~l~~lk~~gVtI~TIg~G~dad~~L~~IA~~T 453 (863)
T TIGR00868 382 GTSICSGLKAAFQVIKKSYQ---STDGSEIVLLTDGEDNT-----ISSCFEEVKQSGAIIHTIALGPSAAKELEELSDMT 453 (863)
T ss_pred CCcHHHHHHHHHHHHHhccc---ccCCCEEEEEeCCCCCC-----HHHHHHHHHHcCCEEEEEEeCCChHHHHHHHHHhc
Confidence 57799999999998887521 12345777777333322 23567778899999999999876667799999999
Q ss_pred CCeeeccCCcch
Q 028156 113 GGVHHKPQQLDG 124 (213)
Q Consensus 113 gG~Y~~~~~~~~ 124 (213)
||.|+.+.+.+.
T Consensus 454 GG~~f~asd~~d 465 (863)
T TIGR00868 454 GGLRFYASDQAD 465 (863)
T ss_pred CCEEEEeCCHHH
Confidence 999998887553
No 23
>PF13768 VWA_3: von Willebrand factor type A domain
Probab=96.95 E-value=0.012 Score=46.56 Aligned_cols=76 Identities=28% Similarity=0.374 Sum_probs=52.4
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEe-cCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCC-cChHHHHHHHH
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQ-GSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGA-QNSAFLQQASY 110 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis-~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~-~e~~iLqq~~~ 110 (213)
.+.+.++|..|+....+ ....+.|++++ |.++... ..+.+.+..+. .+++|.++++|. .+..+|+++|.
T Consensus 77 ~t~l~~aL~~a~~~~~~------~~~~~~IilltDG~~~~~~--~~i~~~v~~~~-~~~~i~~~~~g~~~~~~~L~~LA~ 147 (155)
T PF13768_consen 77 GTDLLAALRAALALLQR------PGCVRAIILLTDGQPVSGE--EEILDLVRRAR-GHIRIFTFGIGSDADADFLRELAR 147 (155)
T ss_pred CccHHHHHHHHHHhccc------CCCccEEEEEEeccCCCCH--HHHHHHHHhcC-CCceEEEEEECChhHHHHHHHHHH
Confidence 46688888888765411 24566777777 3322222 34455554433 679999999985 46789999999
Q ss_pred hhCCeee
Q 028156 111 ITGGVHH 117 (213)
Q Consensus 111 ~TgG~Y~ 117 (213)
.|||.|.
T Consensus 148 ~~~G~~~ 154 (155)
T PF13768_consen 148 ATGGSFH 154 (155)
T ss_pred cCCCEEE
Confidence 9999995
No 24
>cd01463 vWA_VGCC_like VWA Voltage gated Calcium channel like: Voltage-gated calcium channels are a complex of five proteins: alpha 1, beta 1, gamma, alpha 2 and delta. The alpha 2 and delta subunits result from proteolytic processing of a single gene product and carries at its N-terminus the VWA and cache domains, The alpha 2 delta gene family has orthologues in D. melanogaster and C. elegans but none have been detected in aither A. thaliana or yeast. The exact biochemical function of the VWA domain is not known but the alpha 2 delta complex has been shown to regulate various functional properties of the channel complex.
Probab=96.93 E-value=0.012 Score=48.60 Aligned_cols=87 Identities=15% Similarity=0.194 Sum_probs=54.2
Q ss_pred ccchHhHHHHHHHHHhhhhh----cCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHh---CCeeeeEEEcCCc--ChH
Q 028156 33 CSLLSGSLSMALCYIQRVFR----SGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQR---SMVPIDSCYLGAQ--NSA 103 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~----~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk---~~I~Idv~~L~~~--e~~ 103 (213)
.+.+..+|..|+..+.+... +........|++|+-.. +.+...+...+. ..+ .+|+|.++++|.. +..
T Consensus 94 ~T~~~~al~~a~~~l~~~~~~~~~~~~~~~~~~iillTDG~--~~~~~~~~~~~~-~~~~~~~~v~i~tigiG~~~~d~~ 170 (190)
T cd01463 94 IANYTKALEFAFSLLLKNLQSNHSGSRSQCNQAIMLITDGV--PENYKEIFDKYN-WDKNSEIPVRVFTYLIGREVTDRR 170 (190)
T ss_pred cchHHHHHHHHHHHHHHhhhcccccccCCceeEEEEEeCCC--CCcHhHHHHHhc-ccccCCCcEEEEEEecCCccccch
Confidence 35688999999888776211 11123345677777322 112222222211 111 2599999999853 578
Q ss_pred HHHHHHHhhCCeeeccCCc
Q 028156 104 FLQQASYITGGVHHKPQQL 122 (213)
Q Consensus 104 iLqq~~~~TgG~Y~~~~~~ 122 (213)
+|+++|..+||.|..+.+.
T Consensus 171 ~L~~lA~~~~G~~~~i~~~ 189 (190)
T cd01463 171 EIQWMACENKGYYSHIQSL 189 (190)
T ss_pred HHHHHHhhcCCeEEEcccC
Confidence 9999999999999998775
No 25
>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=96.74 E-value=0.012 Score=48.78 Aligned_cols=95 Identities=8% Similarity=0.031 Sum_probs=57.0
Q ss_pred cchHhHHHHHHHHHhhhhhc---CCCCCCcEEEEEecC-CCCCcchhhHHHHHHHH----------HhCCeeeeEEEcCC
Q 028156 34 SLLSGSLSMALCYIQRVFRS---GLLHPQPRILCLQGS-PDGPEQYVAIMNAIFSA----------QRSMVPIDSCYLGA 99 (213)
Q Consensus 34 s~L~~aLs~ALc~inr~~~~---~~~~~~~rILiis~S-~d~~~qyi~imn~if~a----------qk~~I~Idv~~L~~ 99 (213)
+.+..||.+|+..+.+.... .....+..|++|+-. ++...++......+..+ ++.+|.|.+|++|.
T Consensus 85 T~~~~Al~~~~~~l~~~~~~~~~~~~~~~~~iillTDG~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~v~i~~iGvG~ 164 (198)
T cd01470 85 TNTAAALKKVYERMALEKVRNKEAFNETRHVIILFTDGKSNMGGSPLPTVDKIKNLVYKNNKSDNPREDYLDVYVFGVGD 164 (198)
T ss_pred hhHHHHHHHHHHHHHHHHhcCccchhhcceEEEEEcCCCcCCCCChhHHHHHHHHHHhcccccccchhcceeEEEEecCc
Confidence 45666777666655322110 012345567777733 22222343333434333 55689999999974
Q ss_pred -cChHHHHHHHHhhCC--eeeccCCcchHHHH
Q 028156 100 -QNSAFLQQASYITGG--VHHKPQQLDGLFQY 128 (213)
Q Consensus 100 -~e~~iLqq~~~~TgG--~Y~~~~~~~~l~~~ 128 (213)
.+...|+++|..||| .|+.+.+.+.|.+.
T Consensus 165 ~~~~~~L~~iA~~~~g~~~~f~~~~~~~l~~v 196 (198)
T cd01470 165 DVNKEELNDLASKKDNERHFFKLKDYEDLQEV 196 (198)
T ss_pred ccCHHHHHHHhcCCCCCceEEEeCCHHHHHHh
Confidence 478999999999999 35666776665543
No 26
>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=96.68 E-value=0.018 Score=47.44 Aligned_cols=84 Identities=13% Similarity=0.026 Sum_probs=59.0
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHHHHHhh
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQASYIT 112 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~~~~T 112 (213)
.+.+..||..|...+.+- ......+.|++++-..........+.+.+..+++.+|.|-++++|..+...|++++...
T Consensus 87 ~T~~~~AL~~a~~~l~~~---~~~~~~~~iillTDG~~~~~~~~~~~~~~~~~~~~gi~i~~vgig~~~~~~L~~IA~~~ 163 (186)
T cd01480 87 GTFTDCALKYATEQLLEG---SHQKENKFLLVITDGHSDGSPDGGIEKAVNEADHLGIKIFFVAVGSQNEEPLSRIACDG 163 (186)
T ss_pred CccHHHHHHHHHHHHhcc---CCCCCceEEEEEeCCCcCCCcchhHHHHHHHHHHCCCEEEEEecCccchHHHHHHHcCC
Confidence 466888888888777651 11244556666663321122223456778889999999999999877888999999999
Q ss_pred CCeeecc
Q 028156 113 GGVHHKP 119 (213)
Q Consensus 113 gG~Y~~~ 119 (213)
+|.|...
T Consensus 164 ~~~~~~~ 170 (186)
T cd01480 164 KSALYRE 170 (186)
T ss_pred cchhhhc
Confidence 9987754
No 27
>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=96.62 E-value=0.02 Score=46.94 Aligned_cols=93 Identities=10% Similarity=-0.119 Sum_probs=59.9
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHHHHHhh
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQASYIT 112 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~~~~T 112 (213)
.+.+..||.+|+..+.+...... ...+.|++|+-..+..............+++.+|.|.+++++..+...|+++|..+
T Consensus 79 ~T~~~~aL~~a~~~l~~~~~~~r-~~~~~villTDG~~~~~~~~~~~~~a~~l~~~gv~i~~vgv~~~~~~~L~~iA~~~ 157 (185)
T cd01474 79 QTYIHEGLENANEQIFNRNGGGR-ETVSVIIALTDGQLLLNGHKYPEHEAKLSRKLGAIVYCVGVTDFLKSQLINIADSK 157 (185)
T ss_pred CCcHHHHHHHHHHHHHhhccCCC-CCCeEEEEEcCCCcCCCCCcchHHHHHHHHHcCCEEEEEeechhhHHHHHHHhCCC
Confidence 46688888888877753221111 12244555552221112222345666788999999999999666788999999999
Q ss_pred CCeeeccCCcchHH
Q 028156 113 GGVHHKPQQLDGLF 126 (213)
Q Consensus 113 gG~Y~~~~~~~~l~ 126 (213)
+++|.+..+.+.|.
T Consensus 158 ~~~f~~~~~~~~l~ 171 (185)
T cd01474 158 EYVFPVTSGFQALS 171 (185)
T ss_pred CeeEecCccHHHHH
Confidence 98887766655443
No 28
>cd01472 vWA_collagen von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form heterodimers while in vWF it forms homodimers and multimers. There are different interaction surfaces of this domain as seen by its complexes with collagen with either integrin or human vWFA. In integrins collagen binding occurs via the metal ion-dependent adhesion site (MIDAS) and involves three surface loops located on the upper surface of the molecule. In human vWFA, collagen binding is thought to occur on the bottom of the molecule and does not involve the vestigial MIDAS motif.
Probab=96.43 E-value=0.048 Score=43.54 Aligned_cols=82 Identities=6% Similarity=0.014 Sum_probs=54.5
Q ss_pred cchHhHHHHHHHHHhhhhhcCCCCCCcEE-EEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHHHHHhh
Q 028156 34 SLLSGSLSMALCYIQRVFRSGLLHPQPRI-LCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQASYIT 112 (213)
Q Consensus 34 s~L~~aLs~ALc~inr~~~~~~~~~~~rI-Liis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~~~~T 112 (213)
+.+..||..|...+..... ......+++ ++++-. .... ........+++.+|+|.+++++..+...|++++..+
T Consensus 79 T~~~~al~~a~~~l~~~~~-~~~~~~~~~iiliTDG-~~~~---~~~~~~~~l~~~gv~i~~ig~g~~~~~~L~~ia~~~ 153 (164)
T cd01472 79 TNTGKALKYVRENLFTEAS-GSREGVPKVLVVITDG-KSQD---DVEEPAVELKQAGIEVFAVGVKNADEEELKQIASDP 153 (164)
T ss_pred chHHHHHHHHHHHhCCccc-CCCCCCCEEEEEEcCC-CCCc---hHHHHHHHHHHCCCEEEEEECCcCCHHHHHHHHCCC
Confidence 5688888888877764310 111233444 444422 1222 233455667889999999999867999999999999
Q ss_pred CCeeeccC
Q 028156 113 GGVHHKPQ 120 (213)
Q Consensus 113 gG~Y~~~~ 120 (213)
+|.|.-..
T Consensus 154 ~~~~~~~~ 161 (164)
T cd01472 154 KELYVFNV 161 (164)
T ss_pred chheEEec
Confidence 99887543
No 29
>cd00198 vWFA Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains.
Probab=96.33 E-value=0.064 Score=40.61 Aligned_cols=80 Identities=15% Similarity=0.144 Sum_probs=54.2
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCC-cChHHHHHHHHh
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGA-QNSAFLQQASYI 111 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~-~e~~iLqq~~~~ 111 (213)
.+.+..+|..|+..+.+.. .....+.|++|+-.. .......+...+..+++.+|.|.++.++. .....|+.++..
T Consensus 79 ~t~~~~al~~~~~~~~~~~---~~~~~~~lvvitDg~-~~~~~~~~~~~~~~~~~~~v~v~~v~~g~~~~~~~l~~l~~~ 154 (161)
T cd00198 79 GTNIGAALRLALELLKSAK---RPNARRVIILLTDGE-PNDGPELLAEAARELRKLGITVYTIGIGDDANEDELKEIADK 154 (161)
T ss_pred CccHHHHHHHHHHHhcccC---CCCCceEEEEEeCCC-CCCCcchhHHHHHHHHHcCCEEEEEEcCCCCCHHHHHHHhcc
Confidence 4567788888777776642 123344555555322 22221355677888899999999999986 678899999999
Q ss_pred h-CCee
Q 028156 112 T-GGVH 116 (213)
Q Consensus 112 T-gG~Y 116 (213)
| +|.|
T Consensus 155 ~~~~~~ 160 (161)
T cd00198 155 TTGGAV 160 (161)
T ss_pred cccccc
Confidence 8 5544
No 30
>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=96.19 E-value=0.036 Score=42.96 Aligned_cols=81 Identities=11% Similarity=0.009 Sum_probs=54.4
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHHHHHhh
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQASYIT 112 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~~~~T 112 (213)
.+.+..||..|...+.+... ........|++++-+.+.... ..-+.+..+++++|+|.++++++.+...|+++++.|
T Consensus 79 ~t~~~~al~~a~~~~~~~~~-~~~~~~~~iiliTDG~~~~~~--~~~~~~~~~~~~~v~v~~i~~g~~~~~~l~~la~~~ 155 (161)
T cd01450 79 GTNTGKALQYALEQLFSESN-ARENVPKVIIVLTDGRSDDGG--DPKEAAAKLKDEGIKVFVVGVGPADEEELREIASCP 155 (161)
T ss_pred CccHHHHHHHHHHHhccccc-ccCCCCeEEEEECCCCCCCCc--chHHHHHHHHHCCCEEEEEeccccCHHHHHHHhCCC
Confidence 56678888888887766421 011233344445432222211 456778888999999999999766899999999999
Q ss_pred CCee
Q 028156 113 GGVH 116 (213)
Q Consensus 113 gG~Y 116 (213)
|+.|
T Consensus 156 ~~~~ 159 (161)
T cd01450 156 SERH 159 (161)
T ss_pred CCCc
Confidence 5554
No 31
>TIGR03788 marine_srt_targ marine proteobacterial sortase target protein. Members of this protein family are restricted to the Proteobacteria. Each contains a C-terminal sortase-recognition motif, transmembrane domain, and basic residues cluster at the the C-terminus, and is encoded adjacent to a sortase gene. This protein is frequently the only sortase target in its genome, which is as unusual its occurrence in Gram-negative rather than Gram-positive genomes. Many bacteria with this system are marine. In addition to the LPXTG signal, members carry a vault protein inter-alpha-trypsin inhibitor domain (pfam08487) and a von Willebrand factor type A domain (pfam00092).
Probab=95.86 E-value=0.11 Score=50.61 Aligned_cols=90 Identities=17% Similarity=0.121 Sum_probs=59.0
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCc-ChHHHHHHHHh
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQ-NSAFLQQASYI 111 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~-e~~iLqq~~~~ 111 (213)
.+.|..+|..|+..... ......+.|++|+-... .+-..++..+.. ...+++|.++++|.. +..+|+++|+.
T Consensus 348 gT~l~~aL~~a~~~~~~----~~~~~~~~iillTDG~~--~~~~~~~~~~~~-~~~~~ri~tvGiG~~~n~~lL~~lA~~ 420 (596)
T TIGR03788 348 GTEMAGALSAALRDDGP----ESSGALRQVVFLTDGAV--GNEDALFQLIRT-KLGDSRLFTVGIGSAPNSYFMRKAAQF 420 (596)
T ss_pred CccHHHHHHHHHHhhcc----cCCCceeEEEEEeCCCC--CCHHHHHHHHHH-hcCCceEEEEEeCCCcCHHHHHHHHHc
Confidence 35577788877764211 11233456777773322 122344555533 345799999999864 78999999999
Q ss_pred hCCeeeccCCcchHHHHH
Q 028156 112 TGGVHHKPQQLDGLFQYL 129 (213)
Q Consensus 112 TgG~Y~~~~~~~~l~~~L 129 (213)
+||.|..+.+++.+-+.+
T Consensus 421 g~G~~~~i~~~~~~~~~~ 438 (596)
T TIGR03788 421 GRGSFTFIGSTDEVQRKM 438 (596)
T ss_pred CCCEEEECCCHHHHHHHH
Confidence 999999998876654433
No 32
>PF04811 Sec23_trunk: Sec23/Sec24 trunk domain; InterPro: IPR006896 COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger (IPR006895 from INTERPRO), an alpha/beta trunk domain, an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes the Sec23/24 alpha/beta trunk domain, which is formed from a single, approximately 250-residue segment plugged into the beta-barrel between strands beta-1 and beta-19. The trunk has an alpha/beta fold with a vWA topology, and it forms the dimer interface, primarily involving strand beta-14 on Sec23 and Sec24; in addition, the trunk domain of Sec23 contacts Sar1.; GO: 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EGD_A 2NUP_A 3EG9_A 3EFO_A 3EGX_A 2NUT_A 1PD0_A 1PD1_A 1M2V_B 1PCX_A ....
Probab=95.67 E-value=0.32 Score=41.81 Aligned_cols=87 Identities=16% Similarity=0.149 Sum_probs=58.1
Q ss_pred ccccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCC---C------C---c---------ch-----hhHHHHHHH
Q 028156 31 IACSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPD---G------P---E---------QY-----VAIMNAIFS 84 (213)
Q Consensus 31 ~~~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d---~------~---~---------qy-----i~imn~if~ 84 (213)
.....+..||..|...+... ....||+++.+++- . . . .| .-+-+....
T Consensus 113 ~~~~c~G~Al~~A~~ll~~~------~~gGkI~~F~s~~pt~G~Gg~l~~~~~~~~~~~~~~~~~~~~~~~~fY~~la~~ 186 (243)
T PF04811_consen 113 RPERCLGSALSAALSLLSSR------NTGGKILVFTSGPPTYGPGGSLKKREDSSHYDTEKEKALLLPPANEFYKKLAEE 186 (243)
T ss_dssp -----HHHHHHHHHHHHHHH------TS-EEEEEEESS---SSSTTSS-SBTTSCCCCHCTTHHCHSHSSSHHHHHHHHH
T ss_pred CccccHHHHHHHHHHHHhcc------ccCCEEEEEeccCCCCCCCceecccccccccccccchhhhccccchHHHHHHHH
Confidence 34667889999999998865 24578888876531 0 0 0 01 123467788
Q ss_pred HHhCCeeeeEEEcCCc--ChHHHHHHHHhhCCeeeccCCcc
Q 028156 85 AQRSMVPIDSCYLGAQ--NSAFLQQASYITGGVHHKPQQLD 123 (213)
Q Consensus 85 aqk~~I~Idv~~L~~~--e~~iLqq~~~~TgG~Y~~~~~~~ 123 (213)
+.+.+|.||++..+.. +..-+..++..|||.-....+-.
T Consensus 187 ~~~~~isvDlf~~~~~~~~l~tl~~l~~~TGG~l~~y~~f~ 227 (243)
T PF04811_consen 187 CSKQGISVDLFVFSSDYVDLATLGPLARYTGGSLYYYPNFN 227 (243)
T ss_dssp HHHCTEEEEEEEECSS--SHHHHTHHHHCTT-EEEEETTTT
T ss_pred HHhcCCEEEEEeecCCCCCcHhHHHHHHhCceeEEEeCCCC
Confidence 8999999999998632 57889999999999988776544
No 33
>cd01482 vWA_collagen_alphaI-XII-like Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions.
Probab=95.56 E-value=0.19 Score=40.24 Aligned_cols=81 Identities=5% Similarity=-0.130 Sum_probs=51.3
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHHHHHhh
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQASYIT 112 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~~~~T 112 (213)
.+.+..||..|...+-+...+.....++-|++++-. .+. .++......+++.+|.|.+++++.++...|++++..+
T Consensus 78 ~T~~~~aL~~a~~~~~~~~~~~r~~~~k~iillTDG-~~~---~~~~~~a~~lk~~gi~i~~ig~g~~~~~~L~~ia~~~ 153 (164)
T cd01482 78 NTRTGKALTHVREKNFTPDAGARPGVPKVVILITDG-KSQ---DDVELPARVLRNLGVNVFAVGVKDADESELKMIASKP 153 (164)
T ss_pred CChHHHHHHHHHHHhcccccCCCCCCCEEEEEEcCC-CCC---chHHHHHHHHHHCCCEEEEEecCcCCHHHHHHHhCCC
Confidence 345777777777654332111112233344444421 121 2456778899999999999999877788999999887
Q ss_pred CCeee
Q 028156 113 GGVHH 117 (213)
Q Consensus 113 gG~Y~ 117 (213)
++.++
T Consensus 154 ~~~~~ 158 (164)
T cd01482 154 SETHV 158 (164)
T ss_pred chheE
Confidence 76544
No 34
>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=95.01 E-value=0.52 Score=39.61 Aligned_cols=81 Identities=14% Similarity=0.070 Sum_probs=52.7
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecC--CCCC-cchhhHHHHHHHHHhCCeeeeEEEcCCc-ChHHHHHH
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGS--PDGP-EQYVAIMNAIFSAQRSMVPIDSCYLGAQ-NSAFLQQA 108 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S--~d~~-~qyi~imn~if~aqk~~I~Idv~~L~~~-e~~iLqq~ 108 (213)
.+.+..||.+|+..+..-.+.. ....+|++||-.. .+.. .+.. .....+++++|.|.+|++|.. +...++|+
T Consensus 106 gT~ig~aL~~A~~~l~~~~~~~-R~~v~kvvIllTDg~~~~~~~~~~---~~a~~l~~~GI~i~tVGiG~~~d~~~~~~L 181 (193)
T cd01477 106 ASYLDTGLQAAEQMLAAGKRTS-RENYKKVVIVFASDYNDEGSNDPR---PIAARLKSTGIAIITVAFTQDESSNLLDKL 181 (193)
T ss_pred cchHHHHHHHHHHHHHhhhccc-cCCCCeEEEEEecCccCCCCCCHH---HHHHHHHHCCCEEEEEEeCCCCCHHHHHHH
Confidence 4668999999988776421111 1234565555422 1122 2333 456678999999999999743 55789999
Q ss_pred HHhhCCeee
Q 028156 109 SYITGGVHH 117 (213)
Q Consensus 109 ~~~TgG~Y~ 117 (213)
+++..+-|.
T Consensus 182 ~~ias~~~~ 190 (193)
T cd01477 182 GKIASPGMN 190 (193)
T ss_pred HHhcCCCCC
Confidence 999887665
No 35
>PTZ00441 sporozoite surface protein 2 (SSP2); Provisional
Probab=94.82 E-value=0.53 Score=46.17 Aligned_cols=90 Identities=6% Similarity=-0.049 Sum_probs=57.0
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCC-cChHHHHHHH--
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGA-QNSAFLQQAS-- 109 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~-~e~~iLqq~~-- 109 (213)
.+.+..||.+|..++.+.. ......+-|++|+-..+. .+ ...+..+..+++.+|.|-++++|. .+..+|++++
T Consensus 126 gTnig~AL~~Aae~L~sr~--~R~nvpKVVILLTDG~sn-s~-~dvleaAq~LR~~GVeI~vIGVG~g~n~e~LrlIAgC 201 (576)
T PTZ00441 126 KTNMTDALLEVRKHLNDRV--NRENAIQLVILMTDGIPN-SK-YRALEESRKLKDRNVKLAVIGIGQGINHQFNRLLAGC 201 (576)
T ss_pred CccHHHHHHHHHHHHhhcc--cccCCceEEEEEecCCCC-Cc-ccHHHHHHHHHHCCCEEEEEEeCCCcCHHHHHHHhcc
Confidence 4668889988888776531 112233344444422221 12 245566778899999999999974 3567889888
Q ss_pred --HhhCCeeeccCCcchHH
Q 028156 110 --YITGGVHHKPQQLDGLF 126 (213)
Q Consensus 110 --~~TgG~Y~~~~~~~~l~ 126 (213)
...+|.|+...+.+.|.
T Consensus 202 ~p~~g~c~~Y~vadf~eL~ 220 (576)
T PTZ00441 202 RPREGKCKFYSDADWEEAK 220 (576)
T ss_pred CCCCCCCceEEeCCHHHHH
Confidence 34667788776654433
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=94.68 E-value=0.51 Score=39.40 Aligned_cols=77 Identities=12% Similarity=0.082 Sum_probs=47.6
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEE-ecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHHHHHh
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQPRILCL-QGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQASYI 111 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~~rILii-s~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~~~~ 111 (213)
.+.+..||.+|+..+-+. .......++|+|| +-+.+...+--.+......+++++|.|-++++|..+..-|+.++.-
T Consensus 84 ~T~~~~AL~~a~~~~~~~--~~~r~~~~kv~IllTDG~s~~~~~~~~~~~a~~lk~~gV~i~~vGiG~~~~~el~~ia~~ 161 (192)
T cd01473 84 ETYIVEALKYGLKNYTKH--GNRRKDAPKVTMLFTDGNDTSASKKELQDISLLYKEENVKLLVVGVGAASENKLKLLAGC 161 (192)
T ss_pred cCcHHHHHHHHHHHhccC--CCCcccCCeEEEEEecCCCCCcchhhHHHHHHHHHHCCCEEEEEEeccccHHHHHHhcCC
Confidence 355788888887665332 1111222555555 4322222122245566778899999999999987777778888753
No 37
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=94.67 E-value=0.55 Score=46.15 Aligned_cols=88 Identities=11% Similarity=0.025 Sum_probs=62.2
Q ss_pred cccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCC---------cchhhHHHHHHHHHhCCeeeeEEEcCCcCh
Q 028156 32 ACSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGP---------EQYVAIMNAIFSAQRSMVPIDSCYLGAQNS 102 (213)
Q Consensus 32 ~~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~---------~qyi~imn~if~aqk~~I~Idv~~L~~~e~ 102 (213)
-.+.|+.+|.+|+..+.+... ....+.|++|+-...+. ............+.+.+|++-||..+....
T Consensus 474 GgTpL~~gL~~A~~~l~~~~~---~~~~~~iVLlTDG~~n~~~~~~~~~~~~~~~~~~~a~~~~~~gi~~~vId~g~~~~ 550 (584)
T PRK13406 474 GGTPLAAGLDAAAALALQVRR---KGMTPTVVLLTDGRANIARDGTAGRAQAEEDALAAARALRAAGLPALVIDTSPRPQ 550 (584)
T ss_pred CCChHHHHHHHHHHHHHHhcc---CCCceEEEEEeCCCCCCCccccccccchhhHHHHHHHHHHhcCCeEEEEecCCCCc
Confidence 357899999999998877532 12456777777221111 112334556777888999999999865555
Q ss_pred HHHHHHHHhhCCeeeccCCc
Q 028156 103 AFLQQASYITGGVHHKPQQL 122 (213)
Q Consensus 103 ~iLqq~~~~TgG~Y~~~~~~ 122 (213)
..++++|+.|||.|+.+.+.
T Consensus 551 ~~~~~LA~~~gg~y~~l~~~ 570 (584)
T PRK13406 551 PQARALAEAMGARYLPLPRA 570 (584)
T ss_pred HHHHHHHHhcCCeEEECCCC
Confidence 68999999999999988754
No 38
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=94.18 E-value=0.035 Score=43.04 Aligned_cols=30 Identities=20% Similarity=0.497 Sum_probs=26.0
Q ss_pred ceeEcCCCCccccCC---CCccccccccccccc
Q 028156 166 MGYICSVCLSIYCKH---LKKCSTCGSVFGQAQ 195 (213)
Q Consensus 166 ~GyvCp~Clsi~C~~---p~~C~~C~~~f~~~~ 195 (213)
+-.+||.|.++|=.| |.+||.||+.|...+
T Consensus 8 tKR~Cp~CG~kFYDLnk~PivCP~CG~~~~~~~ 40 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLNKDPIVCPKCGTEFPPEP 40 (108)
T ss_pred CcccCCCCcchhccCCCCCccCCCCCCccCccc
Confidence 347999999999987 578999999999883
No 39
>KOG2884 consensus 26S proteasome regulatory complex, subunit RPN10/PSMD4 [Posttranslational modification, protein turnover, chaperones]
Probab=94.02 E-value=0.62 Score=40.65 Aligned_cols=78 Identities=15% Similarity=0.161 Sum_probs=57.1
Q ss_pred cchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcCh--HHHHHHHHh
Q 028156 34 SLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNS--AFLQQASYI 111 (213)
Q Consensus 34 s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~--~iLqq~~~~ 111 (213)
..+..+|..|.--++... ...-+-||+++-+|+-..+. ..+...+...+|++|.||+|.+|+.+. ..|...-+.
T Consensus 85 ~~~~~~i~iA~lalkhRq---nk~~~~riVvFvGSpi~e~e-keLv~~akrlkk~~Vaidii~FGE~~~~~e~l~~fida 160 (259)
T KOG2884|consen 85 ANFMTGIQIAQLALKHRQ---NKNQKQRIVVFVGSPIEESE-KELVKLAKRLKKNKVAIDIINFGEAENNTEKLFEFIDA 160 (259)
T ss_pred ccHHHHHHHHHHHHHhhc---CCCcceEEEEEecCcchhhH-HHHHHHHHHHHhcCeeEEEEEeccccccHHHHHHHHHH
Confidence 456677777777776652 23456799999999743322 378888999999999999999986532 577777788
Q ss_pred hCCe
Q 028156 112 TGGV 115 (213)
Q Consensus 112 TgG~ 115 (213)
+||.
T Consensus 161 ~N~~ 164 (259)
T KOG2884|consen 161 LNGK 164 (259)
T ss_pred hcCC
Confidence 8874
No 40
>PRK12496 hypothetical protein; Provisional
Probab=93.96 E-value=0.037 Score=45.74 Aligned_cols=34 Identities=24% Similarity=0.528 Sum_probs=27.4
Q ss_pred CcccceeEcCCCCccccCCC--Cccccccccccccc
Q 028156 162 NTIDMGYICSVCLSIYCKHL--KKCSTCGSVFGQAQ 195 (213)
Q Consensus 162 ~~v~~GyvCp~Clsi~C~~p--~~C~~C~~~f~~~~ 195 (213)
+...+.|+|+-|...|=+-+ ..||+||..+...+
T Consensus 122 ~~~~w~~~C~gC~~~~~~~~~~~~C~~CG~~~~r~~ 157 (164)
T PRK12496 122 KVIKWRKVCKGCKKKYPEDYPDDVCEICGSPVKRKM 157 (164)
T ss_pred hheeeeEECCCCCccccCCCCCCcCCCCCChhhhcc
Confidence 55678999999999997643 56999998886554
No 41
>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=93.74 E-value=1.1 Score=37.80 Aligned_cols=64 Identities=8% Similarity=0.021 Sum_probs=44.3
Q ss_pred cEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHHHHHhhCC-eeeccCCcchHH
Q 028156 60 PRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQASYITGG-VHHKPQQLDGLF 126 (213)
Q Consensus 60 ~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~~~~TgG-~Y~~~~~~~~l~ 126 (213)
++++||..-..+.. ++...+..+++.+|.|-+|++|..+...|++++..+++ .|+.+.+.+.|-
T Consensus 109 ~kvvillTDG~s~~---~~~~~a~~lk~~gv~i~~VgvG~~~~~~L~~ias~~~~~~~f~~~~~~~l~ 173 (224)
T cd01475 109 PRVGIVVTDGRPQD---DVSEVAAKARALGIEMFAVGVGRADEEELREIASEPLADHVFYVEDFSTIE 173 (224)
T ss_pred CeEEEEEcCCCCcc---cHHHHHHHHHHCCcEEEEEeCCcCCHHHHHHHhCCCcHhcEEEeCCHHHHH
Confidence 46655542222222 35566788899999999999988788899999988765 455666655433
No 42
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=93.53 E-value=0.054 Score=33.41 Aligned_cols=24 Identities=33% Similarity=0.724 Sum_probs=20.0
Q ss_pred eeEcCCCCccccC--CCCcccccccc
Q 028156 167 GYICSVCLSIYCK--HLKKCSTCGSV 190 (213)
Q Consensus 167 GyvCp~Clsi~C~--~p~~C~~C~~~ 190 (213)
-|+|++|.-++=. .|..||+||..
T Consensus 2 ~~~C~~CG~i~~g~~~p~~CP~Cg~~ 27 (34)
T cd00729 2 VWVCPVCGYIHEGEEAPEKCPICGAP 27 (34)
T ss_pred eEECCCCCCEeECCcCCCcCcCCCCc
Confidence 4999999999764 47899999973
No 43
>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=93.44 E-value=2.1 Score=36.70 Aligned_cols=86 Identities=19% Similarity=0.134 Sum_probs=60.2
Q ss_pred ccccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCC-----------CCcc-------------hhhHHHHHHHHH
Q 028156 31 IACSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPD-----------GPEQ-------------YVAIMNAIFSAQ 86 (213)
Q Consensus 31 ~~~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d-----------~~~q-------------yi~imn~if~aq 86 (213)
.....+..||..|...+... ....||+++.+++- .... ..-+-+....+.
T Consensus 113 ~~~~~~G~Al~~A~~ll~~~------~~gGkI~~f~sg~pt~GpG~l~~~~~~~~~~~~~e~~~~~~a~~fY~~la~~~~ 186 (239)
T cd01468 113 RPERCLGPALQAAFLLLKGT------FAGGRIIVFQGGLPTVGPGKLKSREDKEPIRSHDEAQLLKPATKFYKSLAKECV 186 (239)
T ss_pred CCcccHHHHHHHHHHHHhhc------CCCceEEEEECCCCCCCCCccccCcccccCCCccchhcccccHHHHHHHHHHHH
Confidence 34677888999998888875 13567888775431 0001 111234677789
Q ss_pred hCCeeeeEEEcCCc--ChHHHHHHHHhhCCeeeccCCc
Q 028156 87 RSMVPIDSCYLGAQ--NSAFLQQASYITGGVHHKPQQL 122 (213)
Q Consensus 87 k~~I~Idv~~L~~~--e~~iLqq~~~~TgG~Y~~~~~~ 122 (213)
+.+|.||++..+.. +...++.++..|||......+-
T Consensus 187 ~~~isvdlF~~~~~~~dl~~l~~l~~~TGG~v~~y~~f 224 (239)
T cd01468 187 KSGICVDLFAFSLDYVDVATLKQLAKSTGGQVYLYDSF 224 (239)
T ss_pred HcCeEEEEEeccccccCHHHhhhhhhcCCceEEEeCCC
Confidence 99999999987533 6678999999999998876653
No 44
>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=92.92 E-value=1.6 Score=43.14 Aligned_cols=86 Identities=8% Similarity=-0.029 Sum_probs=55.1
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCC----cch-hhHHHHHHHHHhCCeeeeEEEcCCc--ChHHH
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGP----EQY-VAIMNAIFSAQRSMVPIDSCYLGAQ--NSAFL 105 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~----~qy-i~imn~if~aqk~~I~Idv~~L~~~--e~~iL 105 (213)
.+.|+.+|..|...+.+..+.. ...++.|++||-..+.. .+. -........+++.+|.+.||..... ...++
T Consensus 540 ~Tpl~~aL~~A~~~l~~~~~~~-~~~~~~vvliTDG~~n~~~~~~~~~~~~~~~a~~l~~~~i~~~vIdt~~~~~~~~~~ 618 (633)
T TIGR02442 540 RTPLAAGLLKAAEVLSNELLRD-DDGRPLLVVITDGRANVADGGEPPTDDARTIAAKLAARGILFVVIDTESGFVRLGLA 618 (633)
T ss_pred CCCHHHHHHHHHHHHHHhhccC-CCCceEEEEECCCCCCCCCCCCChHHHHHHHHHHHHhcCCeEEEEeCCCCCcchhHH
Confidence 4779999999998887532211 23455666666222111 121 1233344555678899888877422 35799
Q ss_pred HHHHHhhCCeeecc
Q 028156 106 QQASYITGGVHHKP 119 (213)
Q Consensus 106 qq~~~~TgG~Y~~~ 119 (213)
+++|+.+||.|+.+
T Consensus 619 ~~lA~~~gg~y~~l 632 (633)
T TIGR02442 619 EDLARALGGEYVRL 632 (633)
T ss_pred HHHHHhhCCeEEec
Confidence 99999999999864
No 45
>cd01469 vWA_integrins_alpha_subunit Integrins are a class of adhesion receptors that link the extracellular matrix to the cytoskeleton and cooperate with growth factor receptors to promote celll survival, cell cycle progression and cell migration. Integrins consist of an alpha and a beta sub-unit. Each sub-unit has a large extracellular portion, a single transmembrane segment and a short cytoplasmic domain. The N-terminal domains of the alpha and beta subunits associate to form the integrin headpiece, which contains the ligand binding site, whereas the C-terminal segments traverse the plasma membrane and mediate interaction with the cytoskeleton and with signalling proteins.The VWA domains present in the alpha subunits of integrins seem to be a chordate specific radiation of the gene family being found only in vertebrates. They mediate protein-protein interactions.
Probab=92.91 E-value=1.6 Score=35.60 Aligned_cols=87 Identities=8% Similarity=0.044 Sum_probs=49.2
Q ss_pred cchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCc-----ChHHHHHH
Q 028156 34 SLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQ-----NSAFLQQA 108 (213)
Q Consensus 34 s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~-----e~~iLqq~ 108 (213)
+.+..||..|+..+-....+. ....++++||-.-.....+... ...+..|++.+|.|-++++|.. ....|+.+
T Consensus 79 T~~~~AL~~a~~~l~~~~~g~-R~~~~kv~illTDG~~~~~~~~-~~~~~~~k~~gv~v~~Vgvg~~~~~~~~~~~L~~i 156 (177)
T cd01469 79 TNTATAIQYVVTELFSESNGA-RKDATKVLVVITDGESHDDPLL-KDVIPQAEREGIIRYAIGVGGHFQRENSREELKTI 156 (177)
T ss_pred ccHHHHHHHHHHHhcCcccCC-CCCCCeEEEEEeCCCCCCcccc-HHHHHHHHHCCcEEEEEEecccccccccHHHHHHH
Confidence 556777777766552211111 1234455555422111111211 4467788999999999999742 15788888
Q ss_pred HHhhCCeeec-cCCc
Q 028156 109 SYITGGVHHK-PQQL 122 (213)
Q Consensus 109 ~~~TgG~Y~~-~~~~ 122 (213)
|..+++.|.. +.+.
T Consensus 157 as~p~~~h~f~~~~~ 171 (177)
T cd01469 157 ASKPPEEHFFNVTDF 171 (177)
T ss_pred hcCCcHHhEEEecCH
Confidence 8888764443 3443
No 46
>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=92.62 E-value=3.8 Score=35.52 Aligned_cols=81 Identities=22% Similarity=0.196 Sum_probs=56.9
Q ss_pred cccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCC--------CCc----------------chhhHHHHHHHHHh
Q 028156 32 ACSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPD--------GPE----------------QYVAIMNAIFSAQR 87 (213)
Q Consensus 32 ~~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d--------~~~----------------qyi~imn~if~aqk 87 (213)
....+..||..|...+... ..||+++.+++- ... +..-+-+....+.+
T Consensus 113 ~~~c~G~Al~~A~~lL~~~--------GGkIi~f~s~~pt~GpG~l~~~~~~~~~~~~~e~~~~~p~~~fY~~la~~~~~ 184 (244)
T cd01479 113 TESALGPALQAAFLLLKET--------GGKIIVFQSSLPTLGAGKLKSREDPKLLSTDKEKQLLQPQTDFYKKLALECVK 184 (244)
T ss_pred CcccHHHHHHHHHHHHHhc--------CCEEEEEeCCCCCcCCcccccCccccccCchhhhhhcCcchHHHHHHHHHHHH
Confidence 4567888888888777732 357777765520 000 11122357788899
Q ss_pred CCeeeeEEEcCCc--ChHHHHHHHHhhCCeeeccC
Q 028156 88 SMVPIDSCYLGAQ--NSAFLQQASYITGGVHHKPQ 120 (213)
Q Consensus 88 ~~I~Idv~~L~~~--e~~iLqq~~~~TgG~Y~~~~ 120 (213)
.+|.||++..+.. +..-+..++..|||.-....
T Consensus 185 ~~isvDlF~~~~~~~dla~l~~l~~~TGG~v~~y~ 219 (244)
T cd01479 185 SQISVDLFLFSNQYVDVATLGCLSRLTGGQVYYYP 219 (244)
T ss_pred cCeEEEEEEccCcccChhhhhhhhhhcCceEEEEC
Confidence 9999999987533 67789999999999887766
No 47
>COG5148 RPN10 26S proteasome regulatory complex, subunit RPN10/PSMD4 [Posttranslational modification, protein turnover, chaperones]
Probab=92.56 E-value=1.2 Score=38.10 Aligned_cols=76 Identities=20% Similarity=0.152 Sum_probs=54.1
Q ss_pred chHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCc-ChHHHHHHHHhhC
Q 028156 35 LLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQ-NSAFLQQASYITG 113 (213)
Q Consensus 35 ~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~-e~~iLqq~~~~Tg 113 (213)
-+..+|..|+-.++... ...-+-||+.+-+|+-..+. -.+.-.+...+|+||.||.+.+|+. ++.-|..--|.||
T Consensus 86 ~~~~~lqiaql~lkhR~---nk~q~qriVaFvgSpi~ese-deLirlak~lkknnVAidii~fGE~~n~~~l~efIda~N 161 (243)
T COG5148 86 DIMRCLQIAQLILKHRD---NKGQRQRIVAFVGSPIQESE-DELIRLAKQLKKNNVAIDIIFFGEAANMAGLFEFIDATN 161 (243)
T ss_pred hHHHHHHHHHHHHhccc---CCccceEEEEEecCcccccH-HHHHHHHHHHHhcCeeEEEEehhhhhhhhHHHHHHHhhc
Confidence 35566666666666642 22345688888898743333 6778888999999999999999854 5667777777777
Q ss_pred C
Q 028156 114 G 114 (213)
Q Consensus 114 G 114 (213)
-
T Consensus 162 ~ 162 (243)
T COG5148 162 F 162 (243)
T ss_pred c
Confidence 5
No 48
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=91.90 E-value=0.13 Score=31.33 Aligned_cols=23 Identities=39% Similarity=0.885 Sum_probs=19.6
Q ss_pred eEcCCCCccccCC--CCcccccccc
Q 028156 168 YICSVCLSIYCKH--LKKCSTCGSV 190 (213)
Q Consensus 168 yvCp~Clsi~C~~--p~~C~~C~~~ 190 (213)
|+|++|.-++=.. +-.||+||..
T Consensus 2 ~~C~~CGy~y~~~~~~~~CP~Cg~~ 26 (33)
T cd00350 2 YVCPVCGYIYDGEEAPWVCPVCGAP 26 (33)
T ss_pred EECCCCCCEECCCcCCCcCcCCCCc
Confidence 8999999998765 6799999973
No 49
>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=91.63 E-value=2.4 Score=34.37 Aligned_cols=76 Identities=9% Similarity=0.006 Sum_probs=50.2
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCC-cChHHHHHHHHh
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGA-QNSAFLQQASYI 111 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~-~e~~iLqq~~~~ 111 (213)
.+.+..||..|...+.+. +.......+.|++++-.. +.+.....+....+++.+|.|.++++|. .+..+|+.++..
T Consensus 84 ~T~l~~aL~~a~~~l~~~-~~~r~~~~~~villTDG~--~~~~~~~~~~a~~l~~~gv~v~~igiG~~~d~~~l~~ia~~ 160 (186)
T cd01471 84 STNTTSALLVVEKHLFDT-RGNRENAPQLVIIMTDGI--PDSKFRTLKEARKLRERGVIIAVLGVGQGVNHEENRSLVGC 160 (186)
T ss_pred CccHHHHHHHHHHHhhcc-CCCcccCceEEEEEccCC--CCCCcchhHHHHHHHHCCCEEEEEEeehhhCHHHHHHhcCC
Confidence 467999999998888653 112223445666666322 1222233466778889999999999974 477788887764
No 50
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=91.08 E-value=0.14 Score=42.69 Aligned_cols=24 Identities=25% Similarity=0.592 Sum_probs=19.5
Q ss_pred eeEcCCCCccccC-CCCcccccccc
Q 028156 167 GYICSVCLSIYCK-HLKKCSTCGSV 190 (213)
Q Consensus 167 GyvCp~Clsi~C~-~p~~C~~C~~~ 190 (213)
-|||++|+-++=. -|..||+||..
T Consensus 134 ~~vC~vCGy~~~ge~P~~CPiCga~ 158 (166)
T COG1592 134 VWVCPVCGYTHEGEAPEVCPICGAP 158 (166)
T ss_pred EEEcCCCCCcccCCCCCcCCCCCCh
Confidence 5999999877664 56799999963
No 51
>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=90.76 E-value=3.6 Score=40.42 Aligned_cols=88 Identities=11% Similarity=0.064 Sum_probs=59.0
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecC-CCCC-c------c--h----hhHHHHHHHHHhCCeeeeEEEcC
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGS-PDGP-E------Q--Y----VAIMNAIFSAQRSMVPIDSCYLG 98 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S-~d~~-~------q--y----i~imn~if~aqk~~I~Idv~~L~ 98 (213)
.+.|..+|.+|+..+.+... .....+|++|+-. ...+ . . + -.+.......++.+|.+.||..+
T Consensus 481 gTpL~~gL~~A~~~~~~~~~---~~~~~~ivllTDG~~nv~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~gi~~~vid~~ 557 (589)
T TIGR02031 481 GTPLAAGLAAAFQTALQARS---SGGTPTIVLITDGRGNIPLDGDPESIKADREQAAEEALALARKIREAGMPALVIDTA 557 (589)
T ss_pred CCcHHHHHHHHHHHHHHhcc---cCCceEEEEECCCCCCCCCCcccccccccchhHHHHHHHHHHHHHhcCCeEEEEeCC
Confidence 47799999999988876432 1345677777722 1111 0 0 0 12234456678899999999885
Q ss_pred Cc--ChHHHHHHHHhhCCeeeccCCcc
Q 028156 99 AQ--NSAFLQQASYITGGVHHKPQQLD 123 (213)
Q Consensus 99 ~~--e~~iLqq~~~~TgG~Y~~~~~~~ 123 (213)
.. +..+++++|+..||.|+.+.+.+
T Consensus 558 ~~~~~~~~~~~lA~~~~g~y~~l~~~~ 584 (589)
T TIGR02031 558 MRFVSTGFAQKLARKMGAHYIYLPNAT 584 (589)
T ss_pred CCCccchHHHHHHHhcCCcEEeCCCCC
Confidence 32 35689999999999999877643
No 52
>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=89.85 E-value=3.1 Score=34.98 Aligned_cols=66 Identities=12% Similarity=0.039 Sum_probs=46.2
Q ss_pred cccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCC----cchhhHHHHHHHHHhCCeeeeEEEcCCc
Q 028156 32 ACSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGP----EQYVAIMNAIFSAQRSMVPIDSCYLGAQ 100 (213)
Q Consensus 32 ~~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~----~qyi~imn~if~aqk~~I~Idv~~L~~~ 100 (213)
..+.+..||-.|+-.+.+. .....++||++|+-..+.. .....+...+..+++.+|.|.++.++..
T Consensus 104 ~~~~l~~aL~~a~~~~~~~---~~~~~~k~IvL~TDg~~p~~~~~~~~~~~~~~a~~l~~~gI~i~~i~i~~~ 173 (218)
T cd01458 104 GQVSLSDALWVCLDLFSKG---KKKKSHKRIFLFTNNDDPHGGDSIKDSQAAVKAEDLKDKGIELELFPLSSP 173 (218)
T ss_pred CCccHHHHHHHHHHHHHhc---cccccccEEEEECCCCCCCCCCHHHHHHHHHHHHHHHhCCcEEEEEecCCC
Confidence 4678999999999988762 1235678888888543321 2234445667777888999999999743
No 53
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=89.15 E-value=0.23 Score=40.75 Aligned_cols=29 Identities=21% Similarity=0.426 Sum_probs=23.6
Q ss_pred ceeEcCCCCccccC-----CCCcccccccccccc
Q 028156 166 MGYICSVCLSIYCK-----HLKKCSTCGSVFGQA 194 (213)
Q Consensus 166 ~GyvCp~Clsi~C~-----~p~~C~~C~~~f~~~ 194 (213)
.+|+||.|...|-. ..-.||.||..|..-
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~L~~~ 141 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAMELNFTCPRCGAMLDYL 141 (158)
T ss_pred CeEECCCCCcEeeHHHHHHcCCcCCCCCCEeeec
Confidence 47999999998874 357899999998753
No 54
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=88.85 E-value=0.33 Score=30.36 Aligned_cols=26 Identities=35% Similarity=0.680 Sum_probs=21.8
Q ss_pred eEcCCCCccccCC------CCccccccccccc
Q 028156 168 YICSVCLSIYCKH------LKKCSTCGSVFGQ 193 (213)
Q Consensus 168 yvCp~Clsi~C~~------p~~C~~C~~~f~~ 193 (213)
++|+.|..+|-.. ..+|..||..|+.
T Consensus 2 r~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L~q 33 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPPKVEGVCDNCGGELVQ 33 (36)
T ss_dssp EEETTTTEEEETTTB--SSTTBCTTTTEBEBE
T ss_pred cCcCCCCCccccccCCCCCCCccCCCCCeeEe
Confidence 6899999999863 3799999998864
No 55
>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=88.67 E-value=3.4 Score=33.35 Aligned_cols=77 Identities=21% Similarity=0.241 Sum_probs=49.7
Q ss_pred ccchHhHHHHHHHHHhhhhhc----CCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCC-cChHHHHH
Q 028156 33 CSLLSGSLSMALCYIQRVFRS----GLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGA-QNSAFLQQ 107 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~----~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~-~e~~iLqq 107 (213)
.+.+..||..|+..+.+.... ......+.|++++-.. ...++......+..+++.+++|.++++|. .+..+|++
T Consensus 78 gT~l~~aL~~a~~~l~~~~~~~~~~~~~~~~~~iillTDG~-~~~~~~~~~~~~~~~~~~~~~i~~igiG~~~~~~~L~~ 156 (176)
T cd01464 78 GTSMGAALELALDCIDRRVQRYRADQKGDWRPWVFLLTDGE-PTDDLTAAIERIKEARDSKGRIVACAVGPKADLDTLKQ 156 (176)
T ss_pred CCcHHHHHHHHHHHHHHHHHHhcccCcCCcCcEEEEEcCCC-CCchHHHHHHHHHhhcccCCcEEEEEeccccCHHHHHH
Confidence 467888888888887654211 0112345677777332 22334333456777777889999999984 57778888
Q ss_pred HHH
Q 028156 108 ASY 110 (213)
Q Consensus 108 ~~~ 110 (213)
+++
T Consensus 157 ia~ 159 (176)
T cd01464 157 ITE 159 (176)
T ss_pred HHC
Confidence 874
No 56
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=88.55 E-value=0.3 Score=38.96 Aligned_cols=30 Identities=17% Similarity=0.163 Sum_probs=26.0
Q ss_pred ceeEcCCCCccccCC---CCccccccccccccc
Q 028156 166 MGYICSVCLSIYCKH---LKKCSTCGSVFGQAQ 195 (213)
Q Consensus 166 ~GyvCp~Clsi~C~~---p~~C~~C~~~f~~~~ 195 (213)
+-.+||.|.++|=.+ |..||.||+.+...+
T Consensus 8 tKr~Cp~cg~kFYDLnk~p~vcP~cg~~~~~~~ 40 (129)
T TIGR02300 8 TKRICPNTGSKFYDLNRRPAVSPYTGEQFPPEE 40 (129)
T ss_pred ccccCCCcCccccccCCCCccCCCcCCccCcch
Confidence 357999999999876 689999999998774
No 57
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=88.01 E-value=0.32 Score=40.74 Aligned_cols=29 Identities=21% Similarity=0.540 Sum_probs=23.9
Q ss_pred ceeEcCCCCccccC-----CCCcccccccccccc
Q 028156 166 MGYICSVCLSIYCK-----HLKKCSTCGSVFGQA 194 (213)
Q Consensus 166 ~GyvCp~Clsi~C~-----~p~~C~~C~~~f~~~ 194 (213)
.+|+||.|...|-. ..-.||.||..|..-
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~~ 149 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAMEYGFRCPQCGEMLEEY 149 (178)
T ss_pred CEEECCCCCcEEeHHHHhhcCCcCCCCCCCCeec
Confidence 47999999998874 356899999999853
No 58
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=87.31 E-value=0.34 Score=28.19 Aligned_cols=24 Identities=29% Similarity=0.577 Sum_probs=21.0
Q ss_pred EcCCCCccccCCCCcccccccccc
Q 028156 169 ICSVCLSIYCKHLKKCSTCGSVFG 192 (213)
Q Consensus 169 vCp~Clsi~C~~p~~C~~C~~~f~ 192 (213)
.||.|...+-.--..|+.||-.|.
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCCc
Confidence 499999999877899999998875
No 59
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=87.14 E-value=0.52 Score=30.54 Aligned_cols=29 Identities=21% Similarity=0.346 Sum_probs=23.5
Q ss_pred eeEcCCCCccccCC----CCccccccccccccc
Q 028156 167 GYICSVCLSIYCKH----LKKCSTCGSVFGQAQ 195 (213)
Q Consensus 167 GyvCp~Clsi~C~~----p~~C~~C~~~f~~~~ 195 (213)
-|.|+.|...+=.- ...||.||..+....
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~ 35 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYRILFKE 35 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCeEEEcc
Confidence 59999999987532 478999999998755
No 60
>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=85.64 E-value=16 Score=32.24 Aligned_cols=87 Identities=14% Similarity=0.052 Sum_probs=58.1
Q ss_pred ccccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCC-----------CCc---chh--------------hHHH-H
Q 028156 31 IACSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPD-----------GPE---QYV--------------AIMN-A 81 (213)
Q Consensus 31 ~~~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d-----------~~~---qyi--------------~imn-~ 81 (213)
.....+..||..|...+.... .+...||+++.+++- ... ++. ...+ .
T Consensus 138 r~~r~~G~Al~~A~~ll~~~~----~~~gGki~~F~sg~pT~GpG~l~~r~~~~~~r~~~d~~~~~~~~~~~a~~fY~~l 213 (267)
T cd01478 138 RPLRCTGVALSIAVGLLEACF----PNTGARIMLFAGGPCTVGPGAVVSTELKDPIRSHHDIDKDNAKYYKKAVKFYDSL 213 (267)
T ss_pred CCCCchHHHHHHHHHHHHhhc----CCCCcEEEEEECCCCCCCCceeeccccccccccccccccchhhhhhhHHHHHHHH
Confidence 456778899999998887542 234578888876531 000 111 1122 3
Q ss_pred HHHHHhCCeeeeEEEcCC--cChHHHHHHHHhhCCeeeccCC
Q 028156 82 IFSAQRSMVPIDSCYLGA--QNSAFLQQASYITGGVHHKPQQ 121 (213)
Q Consensus 82 if~aqk~~I~Idv~~L~~--~e~~iLqq~~~~TgG~Y~~~~~ 121 (213)
...+-+.+|.||++..+. .+..-++.+++.|||.-+...+
T Consensus 214 a~~~~~~~vsvDlF~~s~d~vglaem~~l~~~TGG~v~~~~~ 255 (267)
T cd01478 214 AKRLAANGHAVDIFAGCLDQVGLLEMKVLVNSTGGHVVLSDS 255 (267)
T ss_pred HHHHHhCCeEEEEEeccccccCHHHHHHHHHhcCcEEEEeCC
Confidence 344577999999998743 3678999999999998776554
No 61
>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=85.60 E-value=12 Score=29.17 Aligned_cols=71 Identities=14% Similarity=0.167 Sum_probs=42.7
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCc-ChHHHHHHH
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQ-NSAFLQQAS 109 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~-e~~iLqq~~ 109 (213)
.+.+..+|..++..+.+. ......|++|+-..+.. ....++...+.+++.+++|.+++++.. +..+.+-++
T Consensus 74 gT~l~~al~~a~~~l~~~-----~~~~~~ivliTDG~~~~-~~~~~~~~~~~~~~~~~~v~~~~~g~~~~~~~~~~~~ 145 (152)
T cd01462 74 GTDINKALRYALELIERR-----DPRKADIVLITDGYEGG-VSDELLREVELKRSRVARFVALALGDHGNPGYDRISA 145 (152)
T ss_pred CcCHHHHHHHHHHHHHhc-----CCCCceEEEECCCCCCC-CCHHHHHHHHHHHhcCcEEEEEEecCCCCchHHHHhh
Confidence 456888888888777653 12245677777322221 122334556667788999999999854 333433333
No 62
>COG4867 Uncharacterized protein with a von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=85.30 E-value=11 Score=36.36 Aligned_cols=98 Identities=21% Similarity=0.212 Sum_probs=70.8
Q ss_pred ccccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecC-C-------C-------CCcchhhHHH---HHHHHHhCCeee
Q 028156 31 IACSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGS-P-------D-------GPEQYVAIMN---AIFSAQRSMVPI 92 (213)
Q Consensus 31 ~~~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S-~-------d-------~~~qyi~imn---~if~aqk~~I~I 92 (213)
...+.+.++|.+|=-++.|. ...++-||||+-. + | .+-++--+.. -+....|.++.|
T Consensus 530 eqgTNlhhaL~LA~r~l~Rh-----~~~~~~il~vTDGePtAhle~~DG~~~~f~yp~DP~t~~~Tvr~~d~~~r~G~q~ 604 (652)
T COG4867 530 EQGTNLHHALALAGRHLRRH-----AGAQPVVLVVTDGEPTAHLEDGDGTSVFFDYPPDPRTIAHTVRGFDDMARLGAQV 604 (652)
T ss_pred ccccchHHHHHHHHHHHHhC-----cccCceEEEEeCCCccccccCCCCceEecCCCCChhHHHHHHHHHHHHHhcccee
Confidence 34678999999999999886 3567788888732 1 1 1222222322 245567899999
Q ss_pred eEEEcCCc--ChHHHHHHHHhhCCeeeccCCcchHHHHHHHHcC
Q 028156 93 DSCYLGAQ--NSAFLQQASYITGGVHHKPQQLDGLFQYLLTIFG 134 (213)
Q Consensus 93 dv~~L~~~--e~~iLqq~~~~TgG~Y~~~~~~~~l~~~Ll~~~~ 134 (213)
..+-|+.. =..|++|+++.|+|.-.+ .+++++-+|...-|+
T Consensus 605 t~FrLg~DpgL~~Fv~qva~rv~G~vv~-pdldglGaaVvgdyl 647 (652)
T COG4867 605 TIFRLGSDPGLARFIDQVARRVQGRVVV-PDLDGLGAAVVGDYL 647 (652)
T ss_pred eEEeecCCHhHHHHHHHHHHHhCCeEEe-cCcchhhHHHHHHHH
Confidence 99999632 256999999999998765 678888888877664
No 63
>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=84.90 E-value=17 Score=28.46 Aligned_cols=76 Identities=9% Similarity=-0.000 Sum_probs=41.3
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHh-CCeeeeEEEcCCcChHHHHHHHHh
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQR-SMVPIDSCYLGAQNSAFLQQASYI 111 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk-~~I~Idv~~L~~~e~~iLqq~~~~ 111 (213)
.+.+..||..|...+.+.. .......+.|++++- .....++ ......+++ .+|.|.+|+++...-.=.+++.++
T Consensus 79 ~T~l~~aL~~a~~~l~~~~-~~r~~~~~~villTD-G~~~~~~---~~~~~~l~~~~~v~v~~vg~g~~~~~~~~~L~~i 153 (163)
T cd01476 79 TTATGAAIEVALQQLDPSE-GRREGIPKVVVVLTD-GRSHDDP---EKQARILRAVPNIETFAVGTGDPGTVDTEELHSI 153 (163)
T ss_pred CccHHHHHHHHHHHhcccc-CCCCCCCeEEEEECC-CCCCCch---HHHHHHHhhcCCCEEEEEECCCccccCHHHHHHH
Confidence 4678899998888886321 111223344555542 2122222 344556677 899999999964300224444444
Q ss_pred hC
Q 028156 112 TG 113 (213)
Q Consensus 112 Tg 113 (213)
+|
T Consensus 154 a~ 155 (163)
T cd01476 154 TG 155 (163)
T ss_pred hC
Confidence 44
No 64
>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=84.49 E-value=8.8 Score=30.73 Aligned_cols=62 Identities=13% Similarity=0.161 Sum_probs=38.2
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEe-cCCCCCcchh----hHHHH---HHHHHhCCeeeeEEEcCC
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQ-GSPDGPEQYV----AIMNA---IFSAQRSMVPIDSCYLGA 99 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis-~S~d~~~qyi----~imn~---if~aqk~~I~Idv~~L~~ 99 (213)
.+.+..||..|+..+.+. ....+.|++|+ |.++.+..|. .+..+ +..|++.+|.+.+++++.
T Consensus 83 ~T~~~~al~~a~~~l~~~-----~~~~~~iiliTDG~~~~~~~~~~~~~~~~~~~~~~~~~~~~gi~v~~igig~ 152 (174)
T cd01454 83 NTRDGAAIRHAAERLLAR-----PEKRKILLVISDGEPNDLDYYEGNVFATEDALRAVIEARKLGIEVFGITIDR 152 (174)
T ss_pred CCcHHHHHHHHHHHHhcC-----CCcCcEEEEEeCCCcCcccccCcchhHHHHHHHHHHHHHhCCcEEEEEEecC
Confidence 356788888887777653 12344455556 3222222221 23344 788899999999999973
No 65
>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=83.49 E-value=12 Score=29.20 Aligned_cols=93 Identities=11% Similarity=0.078 Sum_probs=53.5
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHh-CCeeeeEEEcCCcChHHHHHHHHh
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQR-SMVPIDSCYLGAQNSAFLQQASYI 111 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk-~~I~Idv~~L~~~e~~iLqq~~~~ 111 (213)
.+.+..||..|+..+....... ....++++|+.... .+.+....-......++ .+|.+=+++.+..+...|+.++..
T Consensus 78 ~t~~~~aL~~a~~~l~~~~~~~-r~~~~~~iiliTDG-~~~~~~~~~~~~~~~~~~~~i~~~~ig~~~~~~~~l~~la~~ 155 (178)
T PF00092_consen 78 GTNLGAALKFAREQLFSSNNGG-RPNSPKVIILITDG-NSNDSDSPSEEAANLKKSNGIKVIAIGIDNADNEELRELASC 155 (178)
T ss_dssp SB-HHHHHHHHHHHTTSGGGTT-GTTSEEEEEEEESS-SSSSHSGHHHHHHHHHHHCTEEEEEEEESCCHHHHHHHHSHS
T ss_pred hhhHHHHHhhhhhccccccccc-ccccccceEEEEee-cccCCcchHHHHHHHHHhcCcEEEEEecCcCCHHHHHHHhCC
Confidence 5668999999999887641111 23455555554222 22222222233333333 588888888744789999999977
Q ss_pred h-C-CeeeccCCcchHHH
Q 028156 112 T-G-GVHHKPQQLDGLFQ 127 (213)
Q Consensus 112 T-g-G~Y~~~~~~~~l~~ 127 (213)
+ + |.++.+.+...+.+
T Consensus 156 ~~~~~~~~~~~~~~~l~~ 173 (178)
T PF00092_consen 156 PTSEGHVFYLADFSDLSQ 173 (178)
T ss_dssp STCHHHEEEESSHHHHHH
T ss_pred CCCCCcEEEcCCHHHHHH
Confidence 5 2 55555666555544
No 66
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=83.27 E-value=0.58 Score=26.89 Aligned_cols=24 Identities=25% Similarity=0.591 Sum_probs=18.5
Q ss_pred eEcCCCCccccCCCCccccccccc
Q 028156 168 YICSVCLSIYCKHLKKCSTCGSVF 191 (213)
Q Consensus 168 yvCp~Clsi~C~~p~~C~~C~~~f 191 (213)
..||.|....=.--..|+.||..|
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGAKL 26 (26)
T ss_pred CCCcccCCcCCcccccChhhCCCC
Confidence 468999986555568899999865
No 67
>PLN00162 transport protein sec23; Provisional
Probab=82.56 E-value=38 Score=34.47 Aligned_cols=99 Identities=19% Similarity=0.171 Sum_probs=66.1
Q ss_pred cccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCC-----------CCCc------c-------h----hhHH-HHH
Q 028156 32 ACSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSP-----------DGPE------Q-------Y----VAIM-NAI 82 (213)
Q Consensus 32 ~~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~-----------d~~~------q-------y----i~im-n~i 82 (213)
....+..||+.|...+.... .....||+++.+++ +... + | .... +..
T Consensus 260 p~r~tG~AL~vA~~lL~~~~----~~~gGrI~~F~sgppT~GpG~v~~r~~~~~~rsh~di~k~~~~~~~~a~~fY~~la 335 (761)
T PLN00162 260 PARCTGAALSVAAGLLGACV----PGTGARIMAFVGGPCTEGPGAIVSKDLSEPIRSHKDLDKDAAPYYKKAVKFYEGLA 335 (761)
T ss_pred CCccHHHHHHHHHHHHhhcc----CCCceEEEEEeCCCCCCCCceeecccccccccCccccccchhhhcchHHHHHHHHH
Confidence 45668889999988887542 24567888887653 1000 0 0 0122 345
Q ss_pred HHHHhCCeeeeEEEcCC--cChHHHHHHHHhhCCeeeccCCcc--hHHHHHHHHcC
Q 028156 83 FSAQRSMVPIDSCYLGA--QNSAFLQQASYITGGVHHKPQQLD--GLFQYLLTIFG 134 (213)
Q Consensus 83 f~aqk~~I~Idv~~L~~--~e~~iLqq~~~~TgG~Y~~~~~~~--~l~~~Ll~~~~ 134 (213)
..+.+++|.||++.-+. .+..-++.+++.|||.-+...+-+ .+.+-|...|.
T Consensus 336 ~~~~~~gisvDlF~~s~dqvglaem~~l~~~TGG~v~~~~sF~~~~f~~~l~r~~~ 391 (761)
T PLN00162 336 KQLVAQGHVLDVFACSLDQVGVAEMKVAVERTGGLVVLAESFGHSVFKDSLRRVFE 391 (761)
T ss_pred HHHHHcCceEEEEEccccccCHHHHhhhHhhcCcEEEEeCCcChHHHHHHHHHHhc
Confidence 66788999999997642 378899999999999988766543 35566655554
No 68
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=82.51 E-value=0.79 Score=30.73 Aligned_cols=23 Identities=35% Similarity=0.798 Sum_probs=18.6
Q ss_pred eEcCCCCccccC-----------------CCC--cccccccc
Q 028156 168 YICSVCLSIYCK-----------------HLK--KCSTCGSV 190 (213)
Q Consensus 168 yvCp~Clsi~C~-----------------~p~--~C~~C~~~ 190 (213)
|+|.+|.-+|=+ +|. .||+|+..
T Consensus 2 y~C~~CgyiYd~~~Gd~~~~i~pGt~f~~Lp~~w~CP~C~a~ 43 (50)
T cd00730 2 YECRICGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGAG 43 (50)
T ss_pred cCCCCCCeEECCCCCCcccCcCCCCCHhHCCCCCCCCCCCCc
Confidence 899999999984 453 89999863
No 69
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=81.28 E-value=0.86 Score=25.63 Aligned_cols=22 Identities=27% Similarity=0.656 Sum_probs=16.3
Q ss_pred cCCCCccccCCCCccccccccc
Q 028156 170 CSVCLSIYCKHLKKCSTCGSVF 191 (213)
Q Consensus 170 Cp~Clsi~C~~p~~C~~C~~~f 191 (213)
||.|....-+--..|+.||+.|
T Consensus 2 Cp~CG~~~~~~~~fC~~CG~~l 23 (23)
T PF13240_consen 2 CPNCGAEIEDDAKFCPNCGTPL 23 (23)
T ss_pred CcccCCCCCCcCcchhhhCCcC
Confidence 7777777766667788888764
No 70
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=79.83 E-value=1.1 Score=37.79 Aligned_cols=34 Identities=21% Similarity=0.454 Sum_probs=28.7
Q ss_pred CcccceeEcCCCCccccCCCCccccccccccccc
Q 028156 162 NTIDMGYICSVCLSIYCKHLKKCSTCGSVFGQAQ 195 (213)
Q Consensus 162 ~~v~~GyvCp~Clsi~C~~p~~C~~C~~~f~~~~ 195 (213)
+...+.|+|--|..+|=+..-.|+.||..+....
T Consensus 134 ~v~~w~~rC~GC~~~f~~~~~~Cp~CG~~~~~~~ 167 (177)
T COG1439 134 KVRKWRLRCHGCKRIFPEPKDFCPICGSPLKRKR 167 (177)
T ss_pred eEeeeeEEEecCceecCCCCCcCCCCCCceEEee
Confidence 4567899999999999977789999999966555
No 71
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=79.71 E-value=1.4 Score=29.18 Aligned_cols=12 Identities=42% Similarity=0.930 Sum_probs=10.2
Q ss_pred eEcCCCCccccC
Q 028156 168 YICSVCLSIYCK 179 (213)
Q Consensus 168 yvCp~Clsi~C~ 179 (213)
|+|++|..+|=+
T Consensus 2 y~C~~CgyvYd~ 13 (47)
T PF00301_consen 2 YQCPVCGYVYDP 13 (47)
T ss_dssp EEETTTSBEEET
T ss_pred cCCCCCCEEEcC
Confidence 889999988874
No 72
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=78.94 E-value=1 Score=36.24 Aligned_cols=30 Identities=30% Similarity=0.614 Sum_probs=23.9
Q ss_pred ceeEcCCCCccccC-----CC-----Cccccccccccccc
Q 028156 166 MGYICSVCLSIYCK-----HL-----KKCSTCGSVFGQAQ 195 (213)
Q Consensus 166 ~GyvCp~Clsi~C~-----~p-----~~C~~C~~~f~~~~ 195 (213)
.+|+||.|...|-. +. -.||.||..+....
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~~d 137 (147)
T smart00531 98 AYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEEDD 137 (147)
T ss_pred cEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEEcC
Confidence 47999999998874 23 57999999997644
No 73
>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=77.81 E-value=38 Score=27.86 Aligned_cols=76 Identities=21% Similarity=0.268 Sum_probs=41.1
Q ss_pred ccchHhHHHHHHH-HHhhhhhcCCCCCCcEEEEE-ecCCCCCcchhhHHHHH-HHHHh----CCeeeeEEEcCCc--ChH
Q 028156 33 CSLLSGSLSMALC-YIQRVFRSGLLHPQPRILCL-QGSPDGPEQYVAIMNAI-FSAQR----SMVPIDSCYLGAQ--NSA 103 (213)
Q Consensus 33 ~s~L~~aLs~ALc-~inr~~~~~~~~~~~rILii-s~S~d~~~qyi~imn~i-f~aqk----~~I~Idv~~L~~~--e~~ 103 (213)
.+.+..+|..|+. +..+...+. .....+++|| +-.. ..+-..+-+.| .++++ .+|.|.++.+|.. ...
T Consensus 81 ~T~l~~~l~~a~~~~~~~~~~~~-~~p~~~~vIiiTDG~--~~d~~~~~~~i~~a~~~l~~~~~i~i~~v~vG~~~~~~~ 157 (199)
T cd01457 81 GTNLAAVLQDALNNYFQRKENGA-TCPEGETFLVITDGA--PDDKDAVERVIIKASDELDADNELAISFLQIGRDPAATA 157 (199)
T ss_pred cCcHHHHHHHHHHHHHHHHhhcc-CCCCceEEEEEcCCC--CCcHHHHHHHHHHHHHhhccccCceEEEEEeCCcHHHHH
Confidence 3678888888874 443321111 0111344444 4221 11222333433 33333 4799999999753 456
Q ss_pred HHHHHHHh
Q 028156 104 FLQQASYI 111 (213)
Q Consensus 104 iLqq~~~~ 111 (213)
+|+++.+.
T Consensus 158 ~L~~ld~~ 165 (199)
T cd01457 158 FLKALDDQ 165 (199)
T ss_pred HHHHHhHH
Confidence 89999887
No 74
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=77.52 E-value=1.3 Score=29.62 Aligned_cols=32 Identities=25% Similarity=0.369 Sum_probs=26.3
Q ss_pred ccceeEcCCCCccccCC----CCccccccccccccc
Q 028156 164 IDMGYICSVCLSIYCKH----LKKCSTCGSVFGQAQ 195 (213)
Q Consensus 164 v~~GyvCp~Clsi~C~~----p~~C~~C~~~f~~~~ 195 (213)
....|+|..|...+-.+ ...|+-||.+....+
T Consensus 3 ~~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~rIl~K~ 38 (49)
T COG1996 3 AMMEYKCARCGREVELDQETRGIRCPYCGSRILVKE 38 (49)
T ss_pred ceEEEEhhhcCCeeehhhccCceeCCCCCcEEEEec
Confidence 34689999999999423 379999999998877
No 75
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=76.45 E-value=1.4 Score=36.94 Aligned_cols=31 Identities=23% Similarity=0.556 Sum_probs=24.5
Q ss_pred cceeEcCCCCcccc-----CCCCccccccccccccc
Q 028156 165 DMGYICSVCLSIYC-----KHLKKCSTCGSVFGQAQ 195 (213)
Q Consensus 165 ~~GyvCp~Clsi~C-----~~p~~C~~C~~~f~~~~ 195 (213)
..+|+||.|...|- +.--.||.||..+...-
T Consensus 111 ~~~y~C~~~~~r~sfdeA~~~~F~Cp~Cg~~L~~~d 146 (176)
T COG1675 111 NNYYVCPNCHVKYSFDEAMELGFTCPKCGEDLEEYD 146 (176)
T ss_pred CCceeCCCCCCcccHHHHHHhCCCCCCCCchhhhcc
Confidence 35799999999887 35578999999887543
No 76
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=74.94 E-value=2.4 Score=26.12 Aligned_cols=25 Identities=28% Similarity=0.670 Sum_probs=19.5
Q ss_pred eeEcCCCCccccC-------CCCccccccccc
Q 028156 167 GYICSVCLSIYCK-------HLKKCSTCGSVF 191 (213)
Q Consensus 167 GyvCp~Clsi~C~-------~p~~C~~C~~~f 191 (213)
.|.|+.|...|=. ....||.||...
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~ 36 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISDDPLATCPECGGDV 36 (41)
T ss_pred EEEcCCCCCEEEEEEecCCCCCCCCCCCCCcc
Confidence 6899999997752 346899999843
No 77
>cd05017 SIS_PGI_PMI_1 The members of this protein family contain the SIS (Sugar ISomerase) domain and have both the phosphoglucose isomerase (PGI) and the phosphomannose isomerase (PMI) functions. These functions catalyze the reversible reactions of glucose 6-phosphate to fructose 6-phosphate, and mannose 6-phosphate to fructose 6-phosphate, respectively at an equal rate. This protein contains two SIS domains. This alignment is based on the first SIS domain.
Probab=74.92 E-value=25 Score=26.57 Aligned_cols=55 Identities=11% Similarity=-0.011 Sum_probs=36.6
Q ss_pred EEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHHHHHhhCCeeeccCCcc
Q 028156 61 RILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQASYITGGVHHKPQQLD 123 (213)
Q Consensus 61 rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~~~~TgG~Y~~~~~~~ 123 (213)
-++++|.|..+. .+.+.+..|++.++++ +.+. .+.. +.++++..||.-+.+++..
T Consensus 46 l~I~iS~SG~t~----e~i~~~~~a~~~g~~i--I~IT-~~~~-l~~~~~~~~~~~~~~p~~~ 100 (119)
T cd05017 46 LVIAVSYSGNTE----ETLSAVEQAKERGAKI--VAIT-SGGK-LLEMAREHGVPVIIIPKGL 100 (119)
T ss_pred EEEEEECCCCCH----HHHHHHHHHHHCCCEE--EEEe-CCch-HHHHHHHcCCcEEECCCCC
Confidence 455566555333 5667888889998765 5553 3333 8889998888777765543
No 78
>PTZ00395 Sec24-related protein; Provisional
Probab=74.47 E-value=20 Score=38.86 Aligned_cols=97 Identities=12% Similarity=0.125 Sum_probs=62.6
Q ss_pred cccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCC----CC---------------cchhhHHHHHHHHHhCCeee
Q 028156 32 ACSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPD----GP---------------EQYVAIMNAIFSAQRSMVPI 92 (213)
Q Consensus 32 ~~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d----~~---------------~qyi~imn~if~aqk~~I~I 92 (213)
..+.+..||..|+..|... .+..+|+++.+|.- .. .+-.-+-+....+-+.+|.|
T Consensus 1074 ~esCLGSALqAA~~aLk~~------GGGGKIiVF~SSLPniGpGaLK~Re~~~KEk~Ll~pqd~FYK~LA~ECsk~qISV 1147 (1560)
T PTZ00395 1074 YGSCGNSALKIAMDMLKER------NGLGSICMFYTTTPNCGIGAIKELKKDLQENFLEVKQKIFYDSLLLDLYAFNISV 1147 (1560)
T ss_pred CcccHHHHHHHHHHHHHhc------CCCceEEEEEcCCCCCCCCcccccccccccccccccchHHHHHHHHHHHhcCCce
Confidence 4677899999998888875 23567888876531 00 11122234677788999999
Q ss_pred eEEEcCCc--C--hHHHHHHHHhhCCeeeccC------CcchHHHHHHHHcC
Q 028156 93 DSCYLGAQ--N--SAFLQQASYITGGVHHKPQ------QLDGLFQYLLTIFG 134 (213)
Q Consensus 93 dv~~L~~~--e--~~iLqq~~~~TgG~Y~~~~------~~~~l~~~Ll~~~~ 134 (213)
|++..+.. + +.-|..++..|||.-+.-. |...|..-|...+.
T Consensus 1148 DLFLfSsqYvDVDVATLg~Lsr~TGGqlyyYPnFna~rD~~KL~~DL~r~LT 1199 (1560)
T PTZ00395 1148 DIFIISSNNVRVCVPSLQYVAQNTGGKILFVENFLWQKDYKEIYMNIMDTLT 1199 (1560)
T ss_pred EEEEccCcccccccccccchhcccceeEEEeCCCcccccHHHHHHHHHHHhh
Confidence 99988432 2 3458999999999544433 23344455555554
No 79
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=73.00 E-value=1.4 Score=28.04 Aligned_cols=28 Identities=25% Similarity=0.434 Sum_probs=18.5
Q ss_pred eEcCCCCccc--cCC---CCccccccccccccc
Q 028156 168 YICSVCLSIY--CKH---LKKCSTCGSVFGQAQ 195 (213)
Q Consensus 168 yvCp~Clsi~--C~~---p~~C~~C~~~f~~~~ 195 (213)
|+||.|.+.. -+. -..|+.||+.+....
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl~e~~ 33 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGLVLEENI 33 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-BBEE-TT
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCCEeeccc
Confidence 7899999954 111 248999999887655
No 80
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=72.44 E-value=2.5 Score=29.14 Aligned_cols=42 Identities=24% Similarity=0.597 Sum_probs=31.8
Q ss_pred ceeeeeccCcccc---eeEcCCCCccccCC--C-Cccccccccccccc
Q 028156 154 RASCFCHKNTIDM---GYICSVCLSIYCKH--L-KKCSTCGSVFGQAQ 195 (213)
Q Consensus 154 ~a~C~CH~~~v~~---GyvCp~Clsi~C~~--p-~~C~~C~~~f~~~~ 195 (213)
|-.|+|....=.. .=-|-.|.-|+|+. | ..|+.||+.+.+..
T Consensus 2 r~~C~C~a~~H~L~~~~~NCl~CGkIiC~~Eg~~~pC~fCg~~l~~~~ 49 (57)
T PF06221_consen 2 RRKCNCQARRHPLFPYAPNCLNCGKIICEQEGPLGPCPFCGTPLLSSE 49 (57)
T ss_pred CcccccccccCCCccccccccccChhhcccccCcCcCCCCCCcccCHH
Confidence 4578888754333 66799999999975 3 68999998777644
No 81
>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=71.87 E-value=35 Score=27.52 Aligned_cols=33 Identities=15% Similarity=0.005 Sum_probs=25.3
Q ss_pred hHHHHHHHHHhCCeeeeEEEcCCcChHHHHHHH
Q 028156 77 AIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQAS 109 (213)
Q Consensus 77 ~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~~ 109 (213)
++......+++.+|.|-+++++..+..-|+++|
T Consensus 121 ~~~~~a~~lr~~gv~i~~vG~~~~~~~eL~~ia 153 (165)
T cd01481 121 DVERPAVALKRAGIVPFAIGARNADLAELQQIA 153 (165)
T ss_pred hHHHHHHHHHHCCcEEEEEeCCcCCHHHHHHHh
Confidence 456778889999999999999645666666665
No 82
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=71.27 E-value=2.3 Score=26.07 Aligned_cols=25 Identities=24% Similarity=0.630 Sum_probs=18.2
Q ss_pred eEcCCCCccccCC---------CCcccccccccc
Q 028156 168 YICSVCLSIYCKH---------LKKCSTCGSVFG 192 (213)
Q Consensus 168 yvCp~Clsi~C~~---------p~~C~~C~~~f~ 192 (213)
+.||.|.+.|--- ...|+.||..|.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 6789999876622 147999988775
No 83
>COG1240 ChlD Mg-chelatase subunit ChlD [Coenzyme metabolism]
Probab=70.92 E-value=78 Score=28.30 Aligned_cols=91 Identities=12% Similarity=0.118 Sum_probs=57.2
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecC-CCCCcchhhHHHHHH---HHHhCCeeeeEEEcCCcC--hHHHH
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGS-PDGPEQYVAIMNAIF---SAQRSMVPIDSCYLGAQN--SAFLQ 106 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S-~d~~~qyi~imn~if---~aqk~~I~Idv~~L~~~e--~~iLq 106 (213)
.++|+.+|-+|...+-|..+..+ .....+++|+-. ...+..-.+.-.+.. .+...++.+-|+..-..+ ..+.+
T Consensus 153 ~TPL~~aL~~a~ev~~r~~r~~p-~~~~~~vviTDGr~n~~~~~~~~~e~~~~a~~~~~~g~~~lvid~e~~~~~~g~~~ 231 (261)
T COG1240 153 KTPLADALRQAYEVLAREKRRGP-DRRPVMVVITDGRANVPIPLGPKAETLEAASKLRLRGIQLLVIDTEGSEVRLGLAE 231 (261)
T ss_pred CCchHHHHHHHHHHHHHhhccCC-CcceEEEEEeCCccCCCCCCchHHHHHHHHHHHhhcCCcEEEEecCCccccccHHH
Confidence 56799999999999988754322 345566666622 111111112233333 344567777777663223 46899
Q ss_pred HHHHhhCCeeeccCCcch
Q 028156 107 QASYITGGVHHKPQQLDG 124 (213)
Q Consensus 107 q~~~~TgG~Y~~~~~~~~ 124 (213)
++|..-||.|+.+.+..+
T Consensus 232 ~iA~~~Gg~~~~L~~l~~ 249 (261)
T COG1240 232 EIARASGGEYYHLDDLSD 249 (261)
T ss_pred HHHHHhCCeEEecccccc
Confidence 999999999999877644
No 84
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=69.72 E-value=2.2 Score=29.13 Aligned_cols=28 Identities=18% Similarity=0.393 Sum_probs=20.9
Q ss_pred eeEcCCCCccccCCC-------Cccccccccccccc
Q 028156 167 GYICSVCLSIYCKHL-------KKCSTCGSVFGQAQ 195 (213)
Q Consensus 167 GyvCp~Clsi~C~~p-------~~C~~C~~~f~~~~ 195 (213)
.|.||.|..-+= ++ ..|+.||+.|-.-.
T Consensus 2 ~~~CP~CG~~ie-v~~~~~GeiV~Cp~CGaeleVv~ 36 (54)
T TIGR01206 2 QFECPDCGAEIE-LENPELGELVICDECGAELEVVS 36 (54)
T ss_pred ccCCCCCCCEEe-cCCCccCCEEeCCCCCCEEEEEe
Confidence 478999998663 33 48999999987644
No 85
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=69.04 E-value=3 Score=28.15 Aligned_cols=24 Identities=29% Similarity=0.873 Sum_probs=12.0
Q ss_pred cceeEcCCCCccccC--------CCCcccccc
Q 028156 165 DMGYICSVCLSIYCK--------HLKKCSTCG 188 (213)
Q Consensus 165 ~~GyvCp~Clsi~C~--------~p~~C~~C~ 188 (213)
...|.||+|...||- .--.||.|.
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~LH~CPGC~ 50 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETLHNCPGCE 50 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS-SSSTT-
T ss_pred CCeEECCCCCCccccCcChhhhccccCCcCCC
Confidence 357999999999993 235688775
No 86
>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=66.55 E-value=31 Score=30.74 Aligned_cols=66 Identities=8% Similarity=-0.095 Sum_probs=41.4
Q ss_pred cccchHhHHHHHHHHHhhhhhcCC-CCCCcEEEEEecCC--CCCcchhhHHHHHHHHHhCCeeeeEEEcCCc
Q 028156 32 ACSLLSGSLSMALCYIQRVFRSGL-LHPQPRILCLQGSP--DGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQ 100 (213)
Q Consensus 32 ~~s~L~~aLs~ALc~inr~~~~~~-~~~~~rILiis~S~--d~~~qyi~imn~if~aqk~~I~Idv~~L~~~ 100 (213)
..+.+..+|..|+.++.....+.. ....+-||+||-+. ++. ...-..+..|++.+|.+-++.|..+
T Consensus 137 ~~Tni~~aL~~a~~~f~~~~~~~~s~~~~qlilLISDG~~~~~e---~~~~~~~r~a~e~~i~l~~I~ld~~ 205 (266)
T cd01460 137 DKTDIANLLKFTAQIFEDARTQSSSGSLWQLLLIISDGRGEFSE---GAQKVRLREAREQNVFVVFIIIDNP 205 (266)
T ss_pred CCCcHHHHHHHHHHHHHhhhccccccccccEEEEEECCCcccCc---cHHHHHHHHHHHcCCeEEEEEEcCC
Confidence 356799999999999976532111 01235566666322 221 1122337888999999999999644
No 87
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=66.34 E-value=2.5 Score=27.38 Aligned_cols=22 Identities=27% Similarity=0.798 Sum_probs=14.1
Q ss_pred eeEcCCCCcc-ccCCC----Ccccccc
Q 028156 167 GYICSVCLSI-YCKHL----KKCSTCG 188 (213)
Q Consensus 167 GyvCp~Clsi-~C~~p----~~C~~C~ 188 (213)
|++||.|.+. +..+. =.|..|+
T Consensus 18 g~~CP~Cg~~~~~~~~~~~~~~C~~C~ 44 (46)
T PF12760_consen 18 GFVCPHCGSTKHYRLKTRGRYRCKACR 44 (46)
T ss_pred CCCCCCCCCeeeEEeCCCCeEECCCCC
Confidence 7889999984 33332 2566665
No 88
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=65.40 E-value=1.9 Score=40.81 Aligned_cols=30 Identities=27% Similarity=0.722 Sum_probs=24.6
Q ss_pred ceeEcCCCCccccCC-----------CCccccccccccccc
Q 028156 166 MGYICSVCLSIYCKH-----------LKKCSTCGSVFGQAQ 195 (213)
Q Consensus 166 ~GyvCp~Clsi~C~~-----------p~~C~~C~~~f~~~~ 195 (213)
-||+||.|.+.|-.+ .=.|..|+..++.--
T Consensus 127 ~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelveDe 167 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLEALQLLDNETGEFHCENCGGELVEDE 167 (436)
T ss_pred ccccCCccccchhhhHHHHhhcccCceEEEecCCCchhccc
Confidence 499999999998864 237999999998644
No 89
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=65.20 E-value=3.1 Score=33.56 Aligned_cols=22 Identities=23% Similarity=0.637 Sum_probs=19.2
Q ss_pred CccccCCCCccccccccccccc
Q 028156 174 LSIYCKHLKKCSTCGSVFGQAQ 195 (213)
Q Consensus 174 lsi~C~~p~~C~~C~~~f~~~~ 195 (213)
|=.+|.+.|.||+|++.|.++.
T Consensus 114 LWK~~~~ypvCPvCkTSFKss~ 135 (140)
T PF05290_consen 114 LWKFCNLYPVCPVCKTSFKSSS 135 (140)
T ss_pred HHHHcccCCCCCcccccccccc
Confidence 3378899999999999999876
No 90
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=63.47 E-value=3.9 Score=31.25 Aligned_cols=31 Identities=16% Similarity=0.359 Sum_probs=22.7
Q ss_pred cceeEcCCCCccccC-------CCCccccccccccccc
Q 028156 165 DMGYICSVCLSIYCK-------HLKKCSTCGSVFGQAQ 195 (213)
Q Consensus 165 ~~GyvCp~Clsi~C~-------~p~~C~~C~~~f~~~~ 195 (213)
..-|.||.|.+..-. ....|++||..+....
T Consensus 19 pt~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~~~~V 56 (99)
T PRK14892 19 PKIFECPRCGKVSISVKIKKNIAIITCGNCGLYTEFEV 56 (99)
T ss_pred CcEeECCCCCCeEeeeecCCCcceEECCCCCCccCEEC
Confidence 345999999964332 2579999999988654
No 91
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=63.28 E-value=4.1 Score=36.23 Aligned_cols=31 Identities=16% Similarity=0.228 Sum_probs=25.4
Q ss_pred cceeEcCCCCccccCCCCccccccccccccc
Q 028156 165 DMGYICSVCLSIYCKHLKKCSTCGSVFGQAQ 195 (213)
Q Consensus 165 ~~GyvCp~Clsi~C~~p~~C~~C~~~f~~~~ 195 (213)
+-.|+|+.|..+.=+....||.||+-=...|
T Consensus 352 ~p~~~c~~cg~~~~~~~~~c~~c~~~~~~~~ 382 (389)
T PRK11788 352 KPRYRCRNCGFTARTLYWHCPSCKAWETIKP 382 (389)
T ss_pred CCCEECCCCCCCCccceeECcCCCCccCcCC
Confidence 3479999999999999999999997554444
No 92
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=63.04 E-value=3.7 Score=25.40 Aligned_cols=24 Identities=38% Similarity=0.813 Sum_probs=15.6
Q ss_pred eEcCCCCccccC----CC-----Cccccccccc
Q 028156 168 YICSVCLSIYCK----HL-----KKCSTCGSVF 191 (213)
Q Consensus 168 yvCp~Clsi~C~----~p-----~~C~~C~~~f 191 (213)
.+||.|.+.|=- +| ..|+.||..|
T Consensus 3 i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 467777777762 23 4677777665
No 93
>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=62.00 E-value=99 Score=26.49 Aligned_cols=95 Identities=20% Similarity=0.176 Sum_probs=63.6
Q ss_pred cchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHHHHHhhC
Q 028156 34 SLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQASYITG 113 (213)
Q Consensus 34 s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~~~~Tg 113 (213)
+..+.+|..++-+.-... +... + .+||..+.-...+--.+++.|-.|.+..|-...|++|..+-.||+++-++.|
T Consensus 83 t~y~~vm~~v~~~y~~~~---~~~~-P-~~VlFiTDG~~~~~~~~~~~i~~as~~pifwqFVgiG~~~f~fL~kLD~l~g 157 (200)
T PF10138_consen 83 TNYAPVMEDVLDHYFKRE---PSDA-P-ALVLFITDGGPDDRRAIEKLIREASDEPIFWQFVGIGDSNFGFLEKLDDLAG 157 (200)
T ss_pred cchHHHHHHHHHHHhhcC---CCCC-C-eEEEEEecCCccchHHHHHHHHhccCCCeeEEEEEecCCcchHHHHhhccCC
Confidence 557778887777766431 1111 2 2333333223345567899999999999999999999888889999999644
Q ss_pred C-----eeeccCC-----cchHHHHHHHHc
Q 028156 114 G-----VHHKPQQ-----LDGLFQYLLTIF 133 (213)
Q Consensus 114 G-----~Y~~~~~-----~~~l~~~Ll~~~ 133 (213)
- -|+.+.+ .+.|.+.||..|
T Consensus 158 R~vDNa~Ff~~~d~~~lsD~eLy~~LL~Ef 187 (200)
T PF10138_consen 158 RVVDNAGFFAIDDIDELSDEELYDRLLAEF 187 (200)
T ss_pred cccCCcCeEecCCcccCCHHHHHHHHHHHH
Confidence 2 1333332 446888888777
No 94
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=61.59 E-value=4 Score=26.68 Aligned_cols=23 Identities=30% Similarity=0.792 Sum_probs=18.6
Q ss_pred eeEcCCCCccccCC-------CCccccccc
Q 028156 167 GYICSVCLSIYCKH-------LKKCSTCGS 189 (213)
Q Consensus 167 GyvCp~Clsi~C~~-------p~~C~~C~~ 189 (213)
.|.|+.|...|=.+ ...||.||.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 58999999977654 347999998
No 95
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=59.45 E-value=7.3 Score=24.77 Aligned_cols=23 Identities=30% Similarity=0.680 Sum_probs=19.0
Q ss_pred eeEcCCCCccccC-------CCCccccccc
Q 028156 167 GYICSVCLSIYCK-------HLKKCSTCGS 189 (213)
Q Consensus 167 GyvCp~Clsi~C~-------~p~~C~~C~~ 189 (213)
.|.|+.|...|-. .+..||.||.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEEeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 5999999977764 3579999998
No 96
>cd02010 TPP_ALS Thiamine pyrophosphate (TPP) family, Acetolactate synthase (ALS) subfamily, TPP-binding module; composed of proteins similar to Klebsiella pneumoniae ALS, a catabolic enzyme required for butanediol fermentation. ALS catalyzes the conversion of 2 molecules of pyruvate to acetolactate and carbon dioxide. ALS does not contain FAD, and requires TPP and a divalent metal cation for activity.
Probab=58.58 E-value=73 Score=25.91 Aligned_cols=71 Identities=14% Similarity=0.198 Sum_probs=44.7
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHH---------------------HHHHhhCCeee
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQ---------------------QASYITGGVHH 117 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLq---------------------q~~~~TgG~Y~ 117 (213)
.++++.|.| |.+.++. ++.+.+|.+.++++=++.+....-...+ ++++.-|+.+.
T Consensus 66 ~~~vv~i~G--DG~f~m~--~~eL~ta~~~~l~vi~vV~NN~~~g~~~~~~~~~~~~~~~~~~~~~d~~~~a~a~G~~~~ 141 (177)
T cd02010 66 DRKVVAVSG--DGGFMMN--SQELETAVRLKIPLVVLIWNDNGYGLIKWKQEKEYGRDSGVDFGNPDFVKYAESFGAKGY 141 (177)
T ss_pred CCcEEEEEc--chHHHhH--HHHHHHHHHHCCCeEEEEEECCcchHHHHHHHHhcCCcccCcCCCCCHHHHHHHCCCEEE
Confidence 457777775 5555543 3568889999999999988533333333 24555556666
Q ss_pred ccCCcchHHHHHHHHc
Q 028156 118 KPQQLDGLFQYLLTIF 133 (213)
Q Consensus 118 ~~~~~~~l~~~Ll~~~ 133 (213)
.+.+.+.|.+.|-..+
T Consensus 142 ~v~~~~el~~al~~a~ 157 (177)
T cd02010 142 RIESADDLLPVLERAL 157 (177)
T ss_pred EECCHHHHHHHHHHHH
Confidence 6666666666665444
No 97
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=58.09 E-value=4.6 Score=27.59 Aligned_cols=14 Identities=29% Similarity=0.508 Sum_probs=7.4
Q ss_pred cceeEcCCCCcccc
Q 028156 165 DMGYICSVCLSIYC 178 (213)
Q Consensus 165 ~~GyvCp~Clsi~C 178 (213)
+-.-|||.|.+.|-
T Consensus 19 dDiVvCp~CgapyH 32 (54)
T PF14446_consen 19 DDIVVCPECGAPYH 32 (54)
T ss_pred CCEEECCCCCCccc
Confidence 34555555555553
No 98
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=57.94 E-value=5.4 Score=23.83 Aligned_cols=16 Identities=31% Similarity=0.752 Sum_probs=11.0
Q ss_pred cceeEcCCCCccccCC
Q 028156 165 DMGYICSVCLSIYCKH 180 (213)
Q Consensus 165 ~~GyvCp~Clsi~C~~ 180 (213)
..-|.||.|...+|.+
T Consensus 11 ~~kY~Cp~C~~~~CSl 26 (30)
T PF04438_consen 11 PAKYRCPRCGARYCSL 26 (30)
T ss_dssp EESEE-TTT--EESSH
T ss_pred CCEEECCCcCCceeCc
Confidence 6679999999999975
No 99
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=57.77 E-value=7.4 Score=23.67 Aligned_cols=25 Identities=28% Similarity=0.591 Sum_probs=18.0
Q ss_pred eEcCCCCccccCC---CCcccccccccc
Q 028156 168 YICSVCLSIYCKH---LKKCSTCGSVFG 192 (213)
Q Consensus 168 yvCp~Clsi~C~~---p~~C~~C~~~f~ 192 (213)
|+|..|.+.+--- +..|+-||-+..
T Consensus 1 Y~C~~Cg~~~~~~~~~~irC~~CG~RIl 28 (32)
T PF03604_consen 1 YICGECGAEVELKPGDPIRCPECGHRIL 28 (32)
T ss_dssp EBESSSSSSE-BSTSSTSSBSSSS-SEE
T ss_pred CCCCcCCCeeEcCCCCcEECCcCCCeEE
Confidence 8899999887732 468999997654
No 100
>cd02003 TPP_IolD Thiamine pyrophosphate (TPP) family, IolD subfamily, TPP-binding module; composed of proteins similar to Rhizobium leguminosarum bv. viciae IolD. IolD plays an important role in myo-inositol catabolism.
Probab=57.33 E-value=90 Score=25.98 Aligned_cols=67 Identities=12% Similarity=0.122 Sum_probs=42.2
Q ss_pred hHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHHHH
Q 028156 36 LSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQAS 109 (213)
Q Consensus 36 L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~~ 109 (213)
..++|..|+....-..-. ...++++.|.| |.+.++. ++.+.+|.+.++++-++.+....-.+.++.-
T Consensus 46 ~~gsmG~~lpaAiGa~la---~p~~~vv~i~G--DGsf~m~--~~eL~Ta~~~~lpv~ivV~NN~~~g~~~~~q 112 (205)
T cd02003 46 GYSCMGYEIAAGLGAKLA---KPDREVYVLVG--DGSYLML--HSEIVTAVQEGLKIIIVLFDNHGFGCINNLQ 112 (205)
T ss_pred CcchhhhHHHHHHHHHHh---CCCCeEEEEEc--cchhhcc--HHHHHHHHHcCCCCEEEEEECCccHHHHHHH
Confidence 346666666665554211 22567777765 6665653 3678889999999999999543334444433
No 101
>PRK00420 hypothetical protein; Validated
Probab=57.21 E-value=5.4 Score=31.14 Aligned_cols=29 Identities=21% Similarity=0.297 Sum_probs=21.5
Q ss_pred eeEcCCCCccccCC---CCccccccccccccc
Q 028156 167 GYICSVCLSIYCKH---LKKCSTCGSVFGQAQ 195 (213)
Q Consensus 167 GyvCp~Clsi~C~~---p~~C~~C~~~f~~~~ 195 (213)
+-.||+|.+.+=.+ ...||.||..+.-..
T Consensus 23 ~~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~v~~ 54 (112)
T PRK00420 23 SKHCPVCGLPLFELKDGEVVCPVHGKVYIVKS 54 (112)
T ss_pred cCCCCCCCCcceecCCCceECCCCCCeeeecc
Confidence 46799999866553 378999999776543
No 102
>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=56.89 E-value=75 Score=26.44 Aligned_cols=65 Identities=15% Similarity=0.127 Sum_probs=42.6
Q ss_pred cccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCC--C-CCcchhhHHHH--HHHHHhCCeeeeEEEc
Q 028156 32 ACSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSP--D-GPEQYVAIMNA--IFSAQRSMVPIDSCYL 97 (213)
Q Consensus 32 ~~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~--d-~~~qyi~imn~--if~aqk~~I~Idv~~L 97 (213)
.+..+..+|-.|+-.+.+.. ......++||++|+-.. . ...+.-.+..- +...+..+|.++++.|
T Consensus 103 ~~~~l~~al~v~~~~~~~~~-~~~k~~~krI~l~Td~d~p~~~~~~~~~~~~~l~~~Dl~~~~i~~~~~~l 172 (224)
T PF03731_consen 103 DEGDLSDALWVASDMFRERT-CKKKKNKKRIFLFTDNDGPHEDDDELERIIQKLKAKDLQDNGIEIELFFL 172 (224)
T ss_dssp S---HHHHHHHHHHHHHCHC-TTS-ECEEEEEEEES-SSTTT-CCCHHHHHHHHHHHHHHHHTEEEEEEEC
T ss_pred CccCHHHHHHHHHHHHHHHh-hcccCCCcEEEEEeCCCCCCCCHHHHHHHHHhhccccchhcCcceeEeec
Confidence 45678888888888776532 12346789999998432 2 33455555555 6668999999999999
No 103
>PRK11595 DNA utilization protein GntX; Provisional
Probab=56.88 E-value=4.4 Score=34.72 Aligned_cols=40 Identities=23% Similarity=0.428 Sum_probs=25.5
Q ss_pred CceeeeeccCcccc--eeEcCCCCccccCCCCcccccccccc
Q 028156 153 FRASCFCHKNTIDM--GYICSVCLSIYCKHLKKCSTCGSVFG 192 (213)
Q Consensus 153 ~~a~C~CH~~~v~~--GyvCp~Clsi~C~~p~~C~~C~~~f~ 192 (213)
|+..|...++.+.. .++|+.|...+=.+.+.|+.||..+.
T Consensus 4 ~P~~C~~C~~~~~~~~~~lC~~C~~~l~~~~~~C~~Cg~~~~ 45 (227)
T PRK11595 4 VPGLCWLCRMPLALSHWGICSVCSRALRTLKTCCPQCGLPAT 45 (227)
T ss_pred CCCcCccCCCccCCCCCcccHHHHhhCCcccCcCccCCCcCC
Confidence 44556655555432 25899888766444567888887653
No 104
>PRK08617 acetolactate synthase; Reviewed
Probab=56.39 E-value=35 Score=32.82 Aligned_cols=71 Identities=14% Similarity=0.106 Sum_probs=50.9
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHH---------------------HHHHHhhCCeee
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFL---------------------QQASYITGGVHH 117 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iL---------------------qq~~~~TgG~Y~ 117 (213)
.++++.|.| |.+.+|. ++.+.+|.+.|++|=++.+......++ ..+++..|+.|.
T Consensus 432 ~~~vv~i~G--DGsf~m~--~~eL~Ta~~~~lpv~~vV~NN~~~~~~~~~~~~~~~~~~~~~~~~~d~~~lA~a~G~~~~ 507 (552)
T PRK08617 432 GKKVVSVSG--DGGFLFS--AMELETAVRLKLNIVHIIWNDGHYNMVEFQEEMKYGRSSGVDFGPVDFVKYAESFGAKGL 507 (552)
T ss_pred CCcEEEEEe--chHHhhh--HHHHHHHHHhCCCeEEEEEECCccchHHHHHHhhcCCcccCCCCCCCHHHHHHHCCCeEE
Confidence 457777775 6666665 577899999999998888853322232 346667778888
Q ss_pred ccCCcchHHHHHHHHc
Q 028156 118 KPQQLDGLFQYLLTIF 133 (213)
Q Consensus 118 ~~~~~~~l~~~Ll~~~ 133 (213)
.+.+++.|.+.|-..+
T Consensus 508 ~v~~~~eL~~al~~a~ 523 (552)
T PRK08617 508 RVTSPDELEPVLREAL 523 (552)
T ss_pred EECCHHHHHHHHHHHH
Confidence 8888888888887665
No 105
>cd02006 TPP_Gcl Thiamine pyrophosphate (TPP) family, Gcl subfamily, TPP-binding module; composed of proteins similar to Escherichia coli glyoxylate carboligase (Gcl). E. coli glyoxylate carboligase, plays a key role in glyoxylate metabolism where it catalyzes the condensation of two molecules of glyoxylate to give tartronic semialdehyde and carbon dioxide. This enzyme requires TPP, magnesium ion and FAD as cofactors.
Probab=55.01 E-value=60 Score=26.91 Aligned_cols=45 Identities=13% Similarity=0.296 Sum_probs=32.0
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHH
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQ 107 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq 107 (213)
.++++.|.| |.+-+|. ++.+.+|.+.++++=++.+....-.+++|
T Consensus 75 ~~~vv~i~G--DG~f~m~--~~eL~Ta~~~~lpviivV~NN~~yg~~~~ 119 (202)
T cd02006 75 DRQVVALSG--DYDFQFM--IEELAVGAQHRIPYIHVLVNNAYLGLIRQ 119 (202)
T ss_pred CCeEEEEEe--ChHhhcc--HHHHHHHHHhCCCeEEEEEeCchHHHHHH
Confidence 567887875 5665555 46788999999999999995433344454
No 106
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=54.61 E-value=11 Score=25.94 Aligned_cols=26 Identities=19% Similarity=0.423 Sum_probs=21.2
Q ss_pred eEcCCCCccccCCCCccccccccccccc
Q 028156 168 YICSVCLSIYCKHLKKCSTCGSVFGQAQ 195 (213)
Q Consensus 168 yvCp~Clsi~C~~p~~C~~C~~~f~~~~ 195 (213)
-.|+.|....= ...||.||....++.
T Consensus 6 r~C~~CgvYTL--k~~CP~CG~~t~~~~ 31 (56)
T PRK13130 6 RKCPKCGVYTL--KEICPVCGGKTKNPH 31 (56)
T ss_pred eECCCCCCEEc--cccCcCCCCCCCCCC
Confidence 46898887764 789999999988765
No 107
>PRK08611 pyruvate oxidase; Provisional
Probab=54.54 E-value=54 Score=31.81 Aligned_cols=71 Identities=21% Similarity=0.283 Sum_probs=51.6
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHH---------------------HHHHHhhCCeee
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFL---------------------QQASYITGGVHH 117 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iL---------------------qq~~~~TgG~Y~ 117 (213)
.++++.|.| |.+.+|. ++.+.+|.++++++=++.+......++ ..+++..|+.|.
T Consensus 426 ~~~Vv~i~G--DGsf~m~--~~eL~Ta~r~~l~~iivV~NN~~~g~i~~~q~~~~~~~~~~~~~~~d~~~lA~a~G~~~~ 501 (576)
T PRK08611 426 DRQAIAICG--DGGFSMV--MQDFVTAVKYKLPIVVVVLNNQQLAFIKYEQQAAGELEYAIDLSDMDYAKFAEACGGKGY 501 (576)
T ss_pred CCcEEEEEc--ccHHhhh--HHHHHHHHHhCCCeEEEEEeCCcchHHHHHHHHhcCCcccccCCCCCHHHHHHHCCCeEE
Confidence 567777776 6676665 577889999999999998853333332 235666678888
Q ss_pred ccCCcchHHHHHHHHc
Q 028156 118 KPQQLDGLFQYLLTIF 133 (213)
Q Consensus 118 ~~~~~~~l~~~Ll~~~ 133 (213)
.+.+.+.|.+.|-..+
T Consensus 502 ~v~~~~eL~~al~~a~ 517 (576)
T PRK08611 502 RVEKAEELDPAFEEAL 517 (576)
T ss_pred EeCCHHHHHHHHHHHH
Confidence 8888888888886655
No 108
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=53.52 E-value=9 Score=30.72 Aligned_cols=27 Identities=30% Similarity=0.619 Sum_probs=23.8
Q ss_pred cceeEcCCCCccccCCCCccccccccc
Q 028156 165 DMGYICSVCLSIYCKHLKKCSTCGSVF 191 (213)
Q Consensus 165 ~~GyvCp~Clsi~C~~p~~C~~C~~~f 191 (213)
-+|=-|+.|.++|--....|+.|+..-
T Consensus 27 l~g~kC~~CG~v~~PPr~~Cp~C~~~~ 53 (140)
T COG1545 27 LLGTKCKKCGRVYFPPRAYCPKCGSET 53 (140)
T ss_pred EEEEEcCCCCeEEcCCcccCCCCCCCC
Confidence 357789999999998889999999873
No 109
>COG4245 TerY Uncharacterized protein encoded in toxicity protection region of plasmid R478, contains von Willebrand factor (vWF) domain [General function prediction only]
Probab=53.41 E-value=1.5e+02 Score=25.58 Aligned_cols=97 Identities=14% Similarity=0.167 Sum_probs=57.3
Q ss_pred cccchHhHHHHHHHHHhhhhhc----CCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcC-C-cChHHH
Q 028156 32 ACSLLSGSLSMALCYIQRVFRS----GLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLG-A-QNSAFL 105 (213)
Q Consensus 32 ~~s~L~~aLs~ALc~inr~~~~----~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~-~-~e~~iL 105 (213)
-.++|..||..|+-.|-+..+. ...+.++=+++++-+. +.++|-.=.+..+.-.+.+.+|=.|++| + ++...|
T Consensus 77 GgT~lGaAl~~a~d~Ie~~~~~~~a~~kgdyrP~vfLiTDG~-PtD~w~~~~~~~~~~~~~~k~v~a~~~G~~~ad~~~L 155 (207)
T COG4245 77 GGTPLGAALTLALDMIEERKRKYDANGKGDYRPWVFLITDGE-PTDDWQAGAALVFQGERRAKSVAAFSVGVQGADNKTL 155 (207)
T ss_pred CCCchHHHHHHHHHHHHHHHhhcccCCccccceEEEEecCCC-cchHHHhHHHHhhhcccccceEEEEEecccccccHHH
Confidence 3567899999999988775332 2356788888888332 2445543333333333444445455554 2 588999
Q ss_pred HHHHHhhCCeeeccCCcchHHHHHHH
Q 028156 106 QQASYITGGVHHKPQQLDGLFQYLLT 131 (213)
Q Consensus 106 qq~~~~TgG~Y~~~~~~~~l~~~Ll~ 131 (213)
+|+++.-+=.|- .+...+.+++-+
T Consensus 156 ~qit~~V~~~~t--~d~~~f~~fFkW 179 (207)
T COG4245 156 NQITEKVRQFLT--LDGLQFREFFKW 179 (207)
T ss_pred HHHHHhhccccc--cchHHHHHHHHH
Confidence 999866543332 344445555533
No 110
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=52.83 E-value=9.6 Score=24.73 Aligned_cols=29 Identities=24% Similarity=0.458 Sum_probs=23.5
Q ss_pred eeEcCCCCccccCC---CCccccccccccccc
Q 028156 167 GYICSVCLSIYCKH---LKKCSTCGSVFGQAQ 195 (213)
Q Consensus 167 GyvCp~Clsi~C~~---p~~C~~C~~~f~~~~ 195 (213)
-|+|..|...+-.- +..|+-||....-..
T Consensus 2 ~Y~C~~Cg~~~~~~~~~~irC~~CG~rIlyK~ 33 (44)
T smart00659 2 IYICGECGRENEIKSKDVVRCRECGYRILYKK 33 (44)
T ss_pred EEECCCCCCEeecCCCCceECCCCCceEEEEe
Confidence 49999999977643 579999999887655
No 111
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=52.70 E-value=4.9 Score=32.25 Aligned_cols=28 Identities=18% Similarity=0.312 Sum_probs=20.4
Q ss_pred ceeEcCCCCccccCCC--Cccccccccccc
Q 028156 166 MGYICSVCLSIYCKHL--KKCSTCGSVFGQ 193 (213)
Q Consensus 166 ~GyvCp~Clsi~C~~p--~~C~~C~~~f~~ 193 (213)
.++-||.|++-.=+.. ..||+||.+.+.
T Consensus 27 L~~hCp~Cg~PLF~KdG~v~CPvC~~~~~~ 56 (131)
T COG1645 27 LAKHCPKCGTPLFRKDGEVFCPVCGYREVV 56 (131)
T ss_pred HHhhCcccCCcceeeCCeEECCCCCceEEE
Confidence 4788999998554432 689999965553
No 112
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=50.67 E-value=8.5 Score=26.76 Aligned_cols=27 Identities=19% Similarity=0.559 Sum_probs=21.7
Q ss_pred EcCCCCcccc-----CCCCccccccccccccc
Q 028156 169 ICSVCLSIYC-----KHLKKCSTCGSVFGQAQ 195 (213)
Q Consensus 169 vCp~Clsi~C-----~~p~~C~~C~~~f~~~~ 195 (213)
-||.|..+.- .....|..||..|..+.
T Consensus 13 kCp~C~n~q~vFsha~t~V~C~~Cg~~L~~Pt 44 (59)
T PRK00415 13 KCPDCGNEQVVFSHASTVVRCLVCGKTLAEPT 44 (59)
T ss_pred ECCCCCCeEEEEecCCcEEECcccCCCcccCC
Confidence 4999988763 44689999999998765
No 113
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=49.50 E-value=12 Score=29.19 Aligned_cols=24 Identities=33% Similarity=1.000 Sum_probs=18.7
Q ss_pred ceeEcCCCCccccC--------CCCccccccc
Q 028156 166 MGYICSVCLSIYCK--------HLKKCSTCGS 189 (213)
Q Consensus 166 ~GyvCp~Clsi~C~--------~p~~C~~C~~ 189 (213)
.+|.|+.|...||. .--.||.|..
T Consensus 80 ~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~~ 111 (112)
T TIGR00622 80 HRYVCAVCKNVFCVDCDVFVHESLHCCPGCIH 111 (112)
T ss_pred cceeCCCCCCccccccchhhhhhccCCcCCCC
Confidence 47999999999993 2256888874
No 114
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=49.14 E-value=11 Score=23.70 Aligned_cols=22 Identities=27% Similarity=0.797 Sum_probs=16.2
Q ss_pred eccCcccceeEcCCCCccccCC
Q 028156 159 CHKNTIDMGYICSVCLSIYCKH 180 (213)
Q Consensus 159 CH~~~v~~GyvCp~Clsi~C~~ 180 (213)
|.++..-++|.|..|.-+||..
T Consensus 4 C~~~~~l~~f~C~~C~~~FC~~ 25 (39)
T smart00154 4 CRKKVGLTGFKCRHCGNLFCGE 25 (39)
T ss_pred cCCcccccCeECCccCCccccc
Confidence 4544433499999999999964
No 115
>PRK05978 hypothetical protein; Provisional
Probab=48.93 E-value=11 Score=30.78 Aligned_cols=27 Identities=26% Similarity=0.754 Sum_probs=21.1
Q ss_pred EcCCCCc-----cccCCCCccccccccccccc
Q 028156 169 ICSVCLS-----IYCKHLKKCSTCGSVFGQAQ 195 (213)
Q Consensus 169 vCp~Cls-----i~C~~p~~C~~C~~~f~~~~ 195 (213)
-||+|.. -|=+....|+.||..|...+
T Consensus 35 rCP~CG~G~LF~g~Lkv~~~C~~CG~~~~~~~ 66 (148)
T PRK05978 35 RCPACGEGKLFRAFLKPVDHCAACGEDFTHHR 66 (148)
T ss_pred cCCCCCCCcccccccccCCCccccCCccccCC
Confidence 4899975 34467899999999998765
No 116
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=48.57 E-value=7.8 Score=41.37 Aligned_cols=27 Identities=30% Similarity=0.823 Sum_probs=20.3
Q ss_pred ceeEcCCCCccccC------------CC-Ccccccccccccc
Q 028156 166 MGYICSVCLSIYCK------------HL-KKCSTCGSVFGQA 194 (213)
Q Consensus 166 ~GyvCp~Clsi~C~------------~p-~~C~~C~~~f~~~ 194 (213)
-.|+||.|. |+| +| ..||.||+.|.--
T Consensus 913 PHY~Cp~Ck--y~Ef~~d~svgsGfDLpdK~CPkCg~pl~kD 952 (1444)
T COG2176 913 PHYLCPECK--YSEFIDDGSVGSGFDLPDKDCPKCGTPLKKD 952 (1444)
T ss_pred ccccCCCCc--eeeeecCCCcCCCCCCCCCCCCcCCCccccC
Confidence 479999985 444 33 6899999998743
No 117
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=47.99 E-value=10 Score=23.11 Aligned_cols=25 Identities=28% Similarity=0.572 Sum_probs=15.9
Q ss_pred cceeEcCCCCccccCCCCccccccc
Q 028156 165 DMGYICSVCLSIYCKHLKKCSTCGS 189 (213)
Q Consensus 165 ~~GyvCp~Clsi~C~~p~~C~~C~~ 189 (213)
-++..|..|..++=.....|+.|+.
T Consensus 9 l~~~rC~~Cg~~~~pPr~~Cp~C~s 33 (37)
T PF12172_consen 9 LLGQRCRDCGRVQFPPRPVCPHCGS 33 (37)
T ss_dssp EEEEE-TTT--EEES--SEETTTT-
T ss_pred EEEEEcCCCCCEecCCCcCCCCcCc
Confidence 3578899999998777789999985
No 118
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=46.33 E-value=11 Score=23.29 Aligned_cols=10 Identities=20% Similarity=0.700 Sum_probs=5.1
Q ss_pred EcCCCCcccc
Q 028156 169 ICSVCLSIYC 178 (213)
Q Consensus 169 vCp~Clsi~C 178 (213)
.||.|.+.|=
T Consensus 4 ~CP~C~~~f~ 13 (37)
T PF13719_consen 4 TCPNCQTRFR 13 (37)
T ss_pred ECCCCCceEE
Confidence 3555555554
No 119
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=46.29 E-value=10 Score=26.72 Aligned_cols=24 Identities=25% Similarity=0.668 Sum_probs=18.2
Q ss_pred EcCCCCccccCCCCcccccccc-cc
Q 028156 169 ICSVCLSIYCKHLKKCSTCGSV-FG 192 (213)
Q Consensus 169 vCp~Clsi~C~~p~~C~~C~~~-f~ 192 (213)
.|-.|+.+.-+-...||+||+. |+
T Consensus 6 AC~~Ck~l~~~d~e~CP~Cgs~~~t 30 (64)
T COG2093 6 ACKNCKRLTPEDTEICPVCGSTDLT 30 (64)
T ss_pred HHhhccccCCCCCccCCCCCCcccc
Confidence 4667877777777789999987 44
No 120
>KOG1985 consensus Vesicle coat complex COPII, subunit SEC24/subunit SFB2 [Intracellular trafficking, secretion, and vesicular transport]
Probab=45.47 E-value=86 Score=32.45 Aligned_cols=94 Identities=22% Similarity=0.235 Sum_probs=61.6
Q ss_pred HHHHHHHHHHHhhhhccCCCCCCCcccccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCC--------CCCcchh-
Q 028156 6 ATLLQNLEEFMNKDEQLGKQEPEGRIACSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSP--------DGPEQYV- 76 (213)
Q Consensus 6 ~~i~~~l~~l~~~~~~~~~~~~~~~~~~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~--------d~~~qyi- 76 (213)
+..+++|.++++.+.. ..+.|..||..|.-+|+.. .+||.++.++. +..+||.
T Consensus 387 ~~lL~~lp~~F~~~~~----------t~~alGpALkaaf~li~~~--------GGri~vf~s~lPnlG~G~L~~rEdp~~ 448 (887)
T KOG1985|consen 387 ETLLKTLPEMFQDTRS----------TGSALGPALKAAFNLIGST--------GGRISVFQSTLPNLGAGKLKPREDPNV 448 (887)
T ss_pred HHHHHHHHHHHhhccC----------cccccCHHHHHHHHHHhhc--------CCeEEEEeccCCCCCcccccccccccc
Confidence 3455666666655422 2466888888888888774 34888888652 2222221
Q ss_pred --------------hHH-HHHHHHHhCCeeeeEEEcCC--cChHHHHHHHHhhCCeee
Q 028156 77 --------------AIM-NAIFSAQRSMVPIDSCYLGA--QNSAFLQQASYITGGVHH 117 (213)
Q Consensus 77 --------------~im-n~if~aqk~~I~Idv~~L~~--~e~~iLqq~~~~TgG~Y~ 117 (213)
++- +..-.+-+..|.||.+.+.+ .|+.-|.-++.-|||.-+
T Consensus 449 ~~s~~~~qlL~~~t~FYK~~a~~cs~~qI~VDlFl~s~qY~DlAsLs~LskySgG~~y 506 (887)
T KOG1985|consen 449 RSSDEDSQLLSPATDFYKDLALECSKSQICVDLFLFSEQYTDLASLSCLSKYSGGQVY 506 (887)
T ss_pred ccchhhhhccCCCchHHHHHHHHhccCceEEEEEeecccccchhhhhccccccCceeE
Confidence 111 23345678999999999953 278889999999999533
No 121
>PLN02470 acetolactate synthase
Probab=44.74 E-value=90 Score=30.32 Aligned_cols=71 Identities=10% Similarity=0.115 Sum_probs=47.0
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHH------------------------------HH
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQ------------------------------QA 108 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLq------------------------------q~ 108 (213)
.++++.|.| |.+.+|. ++.+.+|.+.++++-++.+......+++ ++
T Consensus 444 ~~~Vv~i~G--DG~f~m~--~~eL~Ta~~~~l~v~ivV~NN~~yg~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~i 519 (585)
T PLN02470 444 DAIVVDIDG--DGSFIMN--IQELATIHVENLPVKIMVLNNQHLGMVVQWEDRFYKANRAHTYLGDPDAEAEIFPDFLKF 519 (585)
T ss_pred CCcEEEEEc--cchhhcc--HHHHHHHHHhCCCeEEEEEeCCcchHHHHHHHHHhCCceeeeecCccccccCCCCCHHHH
Confidence 457777775 6776776 5889999999999999988533333333 34
Q ss_pred HHhhCCeeeccCCcchHHHHHHHHc
Q 028156 109 SYITGGVHHKPQQLDGLFQYLLTIF 133 (213)
Q Consensus 109 ~~~TgG~Y~~~~~~~~l~~~Ll~~~ 133 (213)
++..|+.+..+.+.+.|.+.|-..+
T Consensus 520 A~a~G~~~~~v~~~~el~~al~~a~ 544 (585)
T PLN02470 520 AEGCKIPAARVTRKSDLREAIQKML 544 (585)
T ss_pred HHHCCCeEEEECCHHHHHHHHHHHH
Confidence 4555566666666666666654443
No 122
>PRK06457 pyruvate dehydrogenase; Provisional
Probab=43.72 E-value=76 Score=30.55 Aligned_cols=71 Identities=10% Similarity=0.181 Sum_probs=49.7
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHH---------------------HHHHHhhCCeee
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFL---------------------QQASYITGGVHH 117 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iL---------------------qq~~~~TgG~Y~ 117 (213)
.++++.|.| |.+.+|. ++.+.+|.++++++-++.+......++ .++++..|+.|.
T Consensus 415 ~~~Vv~i~G--DGsf~~~--~~eL~Ta~~~~lpi~ivV~NN~~~g~i~~~q~~~~~~~~~~~~~~~d~~~lA~a~G~~~~ 490 (549)
T PRK06457 415 KRQVISFVG--DGGFTMT--MMELITAKKYDLPVKIIIYNNSKLGMIKFEQEVMGYPEWGVDLYNPDFTKIAESIGFKGF 490 (549)
T ss_pred CCeEEEEEc--ccHHhhh--HHHHHHHHHHCCCeEEEEEECCccchHHHHHHHhcCCcccccCCCCCHHHHHHHCCCeEE
Confidence 568888876 6676666 578899999999998888853333232 345666667777
Q ss_pred ccCCcchHHHHHHHHc
Q 028156 118 KPQQLDGLFQYLLTIF 133 (213)
Q Consensus 118 ~~~~~~~l~~~Ll~~~ 133 (213)
.+.+++.|...|-..+
T Consensus 491 ~v~~~~el~~al~~a~ 506 (549)
T PRK06457 491 RLEEPKEAEEIIEEFL 506 (549)
T ss_pred EeCCHHHHHHHHHHHH
Confidence 7777777777766554
No 123
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=43.53 E-value=13 Score=19.30 Aligned_cols=9 Identities=22% Similarity=0.874 Sum_probs=3.2
Q ss_pred eEcCCCCcc
Q 028156 168 YICSVCLSI 176 (213)
Q Consensus 168 yvCp~Clsi 176 (213)
|.|+.|...
T Consensus 1 ~~C~~C~~~ 9 (24)
T PF13894_consen 1 FQCPICGKS 9 (24)
T ss_dssp EE-SSTS-E
T ss_pred CCCcCCCCc
Confidence 445544443
No 124
>PF12773 DZR: Double zinc ribbon
Probab=43.26 E-value=14 Score=23.77 Aligned_cols=25 Identities=24% Similarity=0.510 Sum_probs=12.2
Q ss_pred ceeEcCCCCcccc--C-CCCcccccccc
Q 028156 166 MGYICSVCLSIYC--K-HLKKCSTCGSV 190 (213)
Q Consensus 166 ~GyvCp~Clsi~C--~-~p~~C~~C~~~ 190 (213)
..=.|+.|.+..= . ....|+.||..
T Consensus 11 ~~~fC~~CG~~l~~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 11 DAKFCPHCGTPLPPPDQSKKICPNCGAE 38 (50)
T ss_pred cccCChhhcCChhhccCCCCCCcCCcCC
Confidence 3444555555544 1 12356666654
No 125
>PRK08978 acetolactate synthase 2 catalytic subunit; Reviewed
Probab=42.59 E-value=1.1e+02 Score=29.37 Aligned_cols=71 Identities=17% Similarity=0.260 Sum_probs=47.0
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHH-----------------------HHHHhhCCe
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQ-----------------------QASYITGGV 115 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLq-----------------------q~~~~TgG~ 115 (213)
.++++.|.| |.+.+|. ++.+.+|.+.++++-++.+......+++ ++++.-|+.
T Consensus 419 ~~~vv~i~G--DG~f~~~--~~eL~ta~~~~l~v~ivV~NN~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~la~a~G~~ 494 (548)
T PRK08978 419 DDTVICVSG--DGSFMMN--VQELGTIKRKQLPVKIVLLDNQRLGMVRQWQQLFFDERYSETDLSDNPDFVMLASAFGIP 494 (548)
T ss_pred CCcEEEEEc--cchhhcc--HHHHHHHHHhCCCeEEEEEeCCccHHHHHHHHHHhCCcceecCCCCCCCHHHHHHHCCCe
Confidence 568888876 6676666 5889999999999999998543333333 344444555
Q ss_pred eeccCCcchHHHHHHHHc
Q 028156 116 HHKPQQLDGLFQYLLTIF 133 (213)
Q Consensus 116 Y~~~~~~~~l~~~Ll~~~ 133 (213)
|..+.+.+.|.+.|-..+
T Consensus 495 ~~~v~~~~el~~al~~a~ 512 (548)
T PRK08978 495 GQTITRKDQVEAALDTLL 512 (548)
T ss_pred EEEECCHHHHHHHHHHHH
Confidence 666666666666654443
No 126
>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=42.03 E-value=1.9e+02 Score=24.86 Aligned_cols=63 Identities=11% Similarity=0.087 Sum_probs=42.9
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCC
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGA 99 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~ 99 (213)
.+.+.+||..|.-++.+.. ....+|++=||+-...-..+-+.-..-.++...+|.||.+.+..
T Consensus 94 ~Taig~Al~~a~~ll~~~~----~~~~RrVIDvSGDG~~N~G~~p~~~ard~~~~~GitINgL~I~~ 156 (205)
T PF06707_consen 94 RTAIGSALDFAAALLAQNP----FECWRRVIDVSGDGPNNQGPRPVTSARDAAVAAGITINGLAILD 156 (205)
T ss_pred CchHHHHHHHHHHHHHhCC----CCCceEEEEECCCCCCCCCCCccHHHHHHHHHCCeEEeeeEecC
Confidence 3778888888888888752 33788888787532111122333355667788999999999953
No 127
>PRK07586 hypothetical protein; Validated
Probab=41.90 E-value=1.1e+02 Score=29.04 Aligned_cols=45 Identities=24% Similarity=0.536 Sum_probs=33.7
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHH
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQ 107 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq 107 (213)
.++++.|.| |.+.+|. ++.+.+|.+.++++-++.+....-.++++
T Consensus 403 ~r~Vv~i~G--DGsf~m~--~~EL~Ta~~~~lpv~ivV~NN~~y~~~~~ 447 (514)
T PRK07586 403 DRKVLALQG--DGSAMYT--IQALWTQARENLDVTTVIFANRAYAILRG 447 (514)
T ss_pred CCeEEEEEe--chHHHhH--HHHHHHHHHcCCCCEEEEEeCchhHHHHH
Confidence 567787776 6777776 68899999999999999995434445554
No 128
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=41.82 E-value=13 Score=19.70 Aligned_cols=10 Identities=40% Similarity=1.202 Sum_probs=5.4
Q ss_pred cccccccccc
Q 028156 184 CSTCGSVFGQ 193 (213)
Q Consensus 184 C~~C~~~f~~ 193 (213)
|+.|+..|..
T Consensus 3 C~~C~~~f~~ 12 (23)
T PF00096_consen 3 CPICGKSFSS 12 (23)
T ss_dssp ETTTTEEESS
T ss_pred CCCCCCccCC
Confidence 5555555544
No 129
>PF01380 SIS: SIS domain SIS domain web page.; InterPro: IPR001347 The SIS (Sugar ISomerase) domain is a phosphosugar-binding domain [] found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars possibly by binding to the end-product of the pathway.; GO: 0005529 sugar binding, 0005975 carbohydrate metabolic process; PDB: 3TBF_C 2V4M_A 2ZJ4_A 2ZJ3_A 3FKJ_A 3ODP_A 3EUA_H 1VIV_A 1M3S_B 1TZB_A ....
Probab=41.78 E-value=32 Score=25.59 Aligned_cols=44 Identities=9% Similarity=0.157 Sum_probs=24.8
Q ss_pred cEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHHHH
Q 028156 60 PRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQAS 109 (213)
Q Consensus 60 ~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~~ 109 (213)
.-+++++.|+ .+. .+.+++..|++.++++ +.+...+..-+.+.+
T Consensus 55 d~vi~is~sg-~~~---~~~~~~~~ak~~g~~v--i~iT~~~~~~l~~~a 98 (131)
T PF01380_consen 55 DLVIIISYSG-ETR---ELIELLRFAKERGAPV--ILITSNSESPLARLA 98 (131)
T ss_dssp EEEEEEESSS-TTH---HHHHHHHHHHHTTSEE--EEEESSTTSHHHHHS
T ss_pred ceeEeeeccc-cch---hhhhhhHHHHhcCCeE--EEEeCCCCCchhhhC
Confidence 3455555454 333 4457777889999888 445433333444444
No 130
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=41.75 E-value=11 Score=28.21 Aligned_cols=32 Identities=25% Similarity=0.591 Sum_probs=23.2
Q ss_pred eeEcCCCCccccCC----CCccccccccccccccCC
Q 028156 167 GYICSVCLSIYCKH----LKKCSTCGSVFGQAQTQS 198 (213)
Q Consensus 167 GyvCp~Clsi~C~~----p~~C~~C~~~f~~~~~~~ 198 (213)
-|+||.|.+.-=+- --.|..||..|.=..-+|
T Consensus 35 ~~~Cp~C~~~~VkR~a~GIW~C~kCg~~fAGgay~P 70 (89)
T COG1997 35 KHVCPFCGRTTVKRIATGIWKCRKCGAKFAGGAYTP 70 (89)
T ss_pred CCcCCCCCCcceeeeccCeEEcCCCCCeeccccccc
Confidence 59999999873322 148999999998765443
No 131
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=41.56 E-value=12 Score=34.48 Aligned_cols=36 Identities=22% Similarity=0.564 Sum_probs=22.9
Q ss_pred eecc-CcccceeEcCCCCccccCCC--Ccccc-ccccccc
Q 028156 158 FCHK-NTIDMGYICSVCLSIYCKHL--KKCST-CGSVFGQ 193 (213)
Q Consensus 158 ~CH~-~~v~~GyvCp~Clsi~C~~p--~~C~~-C~~~f~~ 193 (213)
+||- .+...-|.||+|-..||.++ ..=.+ |--.|-.
T Consensus 9 ~C~ic~vq~~~YtCPRCn~~YCsl~CYr~h~~~CsE~Fyr 48 (383)
T KOG4317|consen 9 ACGICGVQKREYTCPRCNLLYCSLKCYRNHKHSCSEKFYR 48 (383)
T ss_pred eccccccccccccCCCCCccceeeeeecCCCccchHHHHH
Confidence 4553 33344599999999999985 11122 7666653
No 132
>cd02008 TPP_IOR_alpha Thiamine pyrophosphate (TPP) family, IOR-alpha subfamily, TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as indolepyruvate or phenylpyruvate, which are generated by the transamination of aromatic amino acids, to the corresponding aryl acetyl-CoA.
Probab=41.42 E-value=1e+02 Score=24.88 Aligned_cols=64 Identities=11% Similarity=0.050 Sum_probs=42.7
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChH----------------------HHHHHHHhhCCee
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSA----------------------FLQQASYITGGVH 116 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~----------------------iLqq~~~~TgG~Y 116 (213)
.++++.|.+ |.+.++.. ++.+.+|.+.++++-++.+. .+.+ =+.++++.-|..|
T Consensus 69 ~~~Vv~i~G--DG~f~~~g-~~eL~ta~~~~l~i~vvV~n-N~~~g~~~~~~~~~~~~~~~~~~~~~d~~~~a~a~G~~~ 144 (178)
T cd02008 69 DKKVVAVIG--DSTFFHSG-ILGLINAVYNKANITVVILD-NRTTAMTGGQPHPGTGKTLTEPTTVIDIEALVRAIGVKR 144 (178)
T ss_pred CCCEEEEec--ChHHhhcc-HHHHHHHHHcCCCEEEEEEC-CcceeccCCCCCCCCcccccCCCCccCHHHHHHHCCCCE
Confidence 467887775 55544432 57788899999999999885 2211 1455666667777
Q ss_pred eccCCcchHH
Q 028156 117 HKPQQLDGLF 126 (213)
Q Consensus 117 ~~~~~~~~l~ 126 (213)
..+.+++.|.
T Consensus 145 ~~v~~~~~l~ 154 (178)
T cd02008 145 VVVVDPYDLK 154 (178)
T ss_pred EEecCccCHH
Confidence 7777766665
No 133
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=41.17 E-value=12 Score=40.66 Aligned_cols=29 Identities=28% Similarity=0.812 Sum_probs=21.9
Q ss_pred ccceeEcCCCCccccCC------------C-Ccccccccccccc
Q 028156 164 IDMGYICSVCLSIYCKH------------L-KKCSTCGSVFGQA 194 (213)
Q Consensus 164 v~~GyvCp~Clsi~C~~------------p-~~C~~C~~~f~~~ 194 (213)
+.-.|+||.|. |.++ | ..||.||+.+..-
T Consensus 905 L~phy~C~~C~--~~ef~~~~~~~sG~Dlpdk~Cp~Cg~~~~kd 946 (1437)
T PRK00448 905 LPPHYVCPNCK--YSEFFTDGSVGSGFDLPDKDCPKCGTKLKKD 946 (1437)
T ss_pred CCccccCcccc--cccccccccccccccCccccCcccccccccc
Confidence 44589999994 6655 3 5799999998753
No 134
>cd02015 TPP_AHAS Thiamine pyrophosphate (TPP) family, Acetohydroxyacid synthase (AHAS) subfamily, TPP-binding module; composed of proteins similar to the large catalytic subunit of AHAS. AHAS catalyzes the condensation of two molecules of pyruvate to give the acetohydroxyacid, 2-acetolactate. 2-Acetolactate is the precursor of the branched chain amino acids, valine and leucine. AHAS also catalyzes the condensation of pyruvate and 2-ketobutyrate to form 2-aceto-2-hydroxybutyrate in isoleucine biosynthesis. In addition to requiring TPP and a divalent metal ion as cofactors, AHAS requires FAD.
Probab=40.44 E-value=1.3e+02 Score=24.32 Aligned_cols=45 Identities=20% Similarity=0.454 Sum_probs=30.3
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHH
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQ 107 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq 107 (213)
.++++.|.| |.+-+|. ++.+.+|.+.++++-++.+....-.+.++
T Consensus 68 ~~~vv~i~G--DG~f~~~--~~eL~ta~~~~lpi~ivV~nN~~~~~~~~ 112 (186)
T cd02015 68 DKTVICIDG--DGSFQMN--IQELATAAQYNLPVKIVILNNGSLGMVRQ 112 (186)
T ss_pred CCeEEEEEc--ccHHhcc--HHHHHHHHHhCCCeEEEEEECCccHHHHH
Confidence 457777765 5565553 56788999999999999885333334443
No 135
>PRK07710 acetolactate synthase catalytic subunit; Reviewed
Probab=40.43 E-value=1.1e+02 Score=29.50 Aligned_cols=71 Identities=13% Similarity=0.135 Sum_probs=46.5
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHH-----------------------HHHhhCCe
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQ-----------------------ASYITGGV 115 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq-----------------------~~~~TgG~ 115 (213)
.++++.|.| |.+.+|. ++.+.+|.+.++++-++.+......++++ +++..|+.
T Consensus 442 ~~~vv~i~G--DGsf~m~--~~eL~ta~r~~lpi~ivV~NN~~~~~i~~~~~~~~~~~~~~~~~~~~~d~~~~A~a~G~~ 517 (571)
T PRK07710 442 DETVVAIVG--DGGFQMT--LQELSVIKELSLPVKVVILNNEALGMVRQWQEEFYNQRYSHSLLSCQPDFVKLAEAYGIK 517 (571)
T ss_pred CCcEEEEEc--chHHhhh--HHHHHHHHHhCCCeEEEEEECchHHHHHHHHHHHhCCcceeccCCCCCCHHHHHHHCCCe
Confidence 456777765 6676764 46789999999999999985443334433 44555566
Q ss_pred eeccCCcchHHHHHHHHc
Q 028156 116 HHKPQQLDGLFQYLLTIF 133 (213)
Q Consensus 116 Y~~~~~~~~l~~~Ll~~~ 133 (213)
|..+.+.+.|.+.|-..+
T Consensus 518 ~~~v~~~~el~~al~~a~ 535 (571)
T PRK07710 518 GVRIDDELEAKEQLQHAI 535 (571)
T ss_pred EEEECCHHHHHHHHHHHH
Confidence 666666666666554444
No 136
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=40.41 E-value=5.8 Score=26.57 Aligned_cols=27 Identities=26% Similarity=0.795 Sum_probs=21.1
Q ss_pred eeEcCCCCccccCCCCccccccccccc
Q 028156 167 GYICSVCLSIYCKHLKKCSTCGSVFGQ 193 (213)
Q Consensus 167 GyvCp~Clsi~C~~p~~C~~C~~~f~~ 193 (213)
.|.|=.|+++.=.....|++|+-.|..
T Consensus 21 HYLCl~CLt~ml~~s~~C~iC~~~LPt 47 (50)
T PF03854_consen 21 HYLCLNCLTLMLSRSDRCPICGKPLPT 47 (50)
T ss_dssp -EEEHHHHHHT-SSSSEETTTTEE---
T ss_pred hhHHHHHHHHHhccccCCCcccCcCcc
Confidence 599999999999999999999987753
No 137
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=40.33 E-value=19 Score=28.72 Aligned_cols=14 Identities=14% Similarity=0.249 Sum_probs=10.4
Q ss_pred ceeEcCCCCccccC
Q 028156 166 MGYICSVCLSIYCK 179 (213)
Q Consensus 166 ~GyvCp~Clsi~C~ 179 (213)
.-|.|+.|...+-.
T Consensus 69 ~~~~C~~CG~~~~~ 82 (135)
T PRK03824 69 AVLKCRNCGNEWSL 82 (135)
T ss_pred eEEECCCCCCEEec
Confidence 45889999877753
No 138
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=39.84 E-value=21 Score=24.51 Aligned_cols=28 Identities=14% Similarity=0.274 Sum_probs=20.4
Q ss_pred eEcCCCCccc----------cCCCCccccccccccccc
Q 028156 168 YICSVCLSIY----------CKHLKKCSTCGSVFGQAQ 195 (213)
Q Consensus 168 yvCp~Clsi~----------C~~p~~C~~C~~~f~~~~ 195 (213)
..||+|...- =.+|-.||.|+.......
T Consensus 5 i~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~EtlI~v 42 (55)
T PF14205_consen 5 ILCPICGNKTRLKIREDTVLKNFPLYCPKCKQETLIDV 42 (55)
T ss_pred EECCCCCCccceeeecCceeccccccCCCCCceEEEEe
Confidence 5699999643 358899999987655443
No 139
>PF03358 FMN_red: NADPH-dependent FMN reductase; InterPro: IPR005025 NADPH-dependent FMN reductase (1.5.1.29 from EC) reduces FMN and also reduces riboflavin and FAD, although more slowly. Members of this entry catalyse the reaction NAD(P)H + FMN = NAD(P)(+) + FMNH(2).; PDB: 3SVL_B 3GFS_F 3GFQ_A 1NNI_1 2GSW_B 3GFR_D 1T0I_B 3D7N_A 2R97_A 3B6K_A ....
Probab=39.75 E-value=88 Score=24.12 Aligned_cols=38 Identities=16% Similarity=0.229 Sum_probs=27.4
Q ss_pred EEEEEecCCCCCcchhhHHH-HHHHHHhCCeeeeEEEcC
Q 028156 61 RILCLQGSPDGPEQYVAIMN-AIFSAQRSMVPIDSCYLG 98 (213)
Q Consensus 61 rILiis~S~d~~~qyi~imn-~if~aqk~~I~Idv~~L~ 98 (213)
+||+|.+|+...+.=-.+.+ ....+++.++.++++.|.
T Consensus 2 kilii~gS~r~~~~t~~l~~~~~~~l~~~g~e~~~i~l~ 40 (152)
T PF03358_consen 2 KILIINGSPRKNSNTRKLAEAVAEQLEEAGAEVEVIDLA 40 (152)
T ss_dssp EEEEEESSSSTTSHHHHHHHHHHHHHHHTTEEEEEEECT
T ss_pred EEEEEECcCCCCCHHHHHHHHHHHHHHHcCCEEEEEecc
Confidence 79999999854433344555 455666779999999994
No 140
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=39.39 E-value=11 Score=29.59 Aligned_cols=21 Identities=14% Similarity=0.273 Sum_probs=13.6
Q ss_pred eccCcccceeEcCCCCccccC
Q 028156 159 CHKNTIDMGYICSVCLSIYCK 179 (213)
Q Consensus 159 CH~~~v~~GyvCp~Clsi~C~ 179 (213)
|+++++-..+.|+.|.+.+--
T Consensus 4 Cg~~l~vt~l~C~~C~t~i~G 24 (113)
T PF09862_consen 4 CGGELVVTRLKCPSCGTEIEG 24 (113)
T ss_pred CCCceEEEEEEcCCCCCEEEe
Confidence 666666667777777665543
No 141
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=39.10 E-value=14 Score=39.60 Aligned_cols=29 Identities=28% Similarity=0.803 Sum_probs=21.5
Q ss_pred ccceeEcCCCCccccCC------------C-Ccccccccccccc
Q 028156 164 IDMGYICSVCLSIYCKH------------L-KKCSTCGSVFGQA 194 (213)
Q Consensus 164 v~~GyvCp~Clsi~C~~------------p-~~C~~C~~~f~~~ 194 (213)
+.-.|+||.|. |.++ | ..||.||+.+..-
T Consensus 680 L~phy~c~~c~--~~ef~~~~~~~sg~dlp~k~cp~c~~~~~~d 721 (1213)
T TIGR01405 680 LPPHYLCPNCK--YSEFITDGSVGSGFDLPDKDCPKCGAPLKKD 721 (1213)
T ss_pred CcccccCcccc--cccccccccccccccCccccCcccccccccc
Confidence 34589999994 6544 3 5799999988753
No 142
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=38.96 E-value=15 Score=23.39 Aligned_cols=21 Identities=24% Similarity=0.815 Sum_probs=11.5
Q ss_pred eccCcccceeEcCCCCccccCC
Q 028156 159 CHKNTIDMGYICSVCLSIYCKH 180 (213)
Q Consensus 159 CH~~~v~~GyvCp~Clsi~C~~ 180 (213)
|..+.. ++|.|+.|.-.||.-
T Consensus 6 C~~~~~-~~~~C~~C~~~FC~~ 26 (43)
T PF01428_consen 6 CKKKDF-LPFKCKHCGKSFCLK 26 (43)
T ss_dssp T--BCT-SHEE-TTTS-EE-TT
T ss_pred CcCccC-CCeECCCCCcccCcc
Confidence 343333 789999999999963
No 143
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=38.64 E-value=15 Score=25.31 Aligned_cols=28 Identities=18% Similarity=0.494 Sum_probs=21.0
Q ss_pred eEcCCCCccccCC-CCccccccccccccc
Q 028156 168 YICSVCLSIYCKH-LKKCSTCGSVFGQAQ 195 (213)
Q Consensus 168 yvCp~Clsi~C~~-p~~C~~C~~~f~~~~ 195 (213)
|.|..|..-.=.. ..+||.||=.|+..|
T Consensus 27 fECTFC~~C~e~~l~~~CPNCgGelv~RP 55 (57)
T PF06906_consen 27 FECTFCADCAETMLNGVCPNCGGELVRRP 55 (57)
T ss_pred EeCcccHHHHHHHhcCcCcCCCCccccCC
Confidence 6666666554444 799999999998766
No 144
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=38.05 E-value=11 Score=27.15 Aligned_cols=33 Identities=24% Similarity=0.592 Sum_probs=18.2
Q ss_pred eccCcc--cceeEcCCCCccccCCCCcccccccccc
Q 028156 159 CHKNTI--DMGYICSVCLSIYCKHLKKCSTCGSVFG 192 (213)
Q Consensus 159 CH~~~v--~~GyvCp~Clsi~C~~p~~C~~C~~~f~ 192 (213)
||..+. ...|.|..|..-|= .-+.||.|+..|-
T Consensus 7 C~~~L~~~~~~~~C~~C~~~~~-~~a~CPdC~~~Le 41 (70)
T PF07191_consen 7 CQQELEWQGGHYHCEACQKDYK-KEAFCPDCGQPLE 41 (70)
T ss_dssp S-SBEEEETTEEEETTT--EEE-EEEE-TTT-SB-E
T ss_pred CCCccEEeCCEEECccccccce-ecccCCCcccHHH
Confidence 555553 34799999998664 3467888887764
No 145
>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.
Probab=38.02 E-value=70 Score=27.02 Aligned_cols=36 Identities=19% Similarity=0.492 Sum_probs=24.4
Q ss_pred eeeeeccCcccceeEcCCCCcccc----------CCCCcccccccccc
Q 028156 155 ASCFCHKNTIDMGYICSVCLSIYC----------KHLKKCSTCGSVFG 192 (213)
Q Consensus 155 a~C~CH~~~v~~GyvCp~Clsi~C----------~~p~~C~~C~~~f~ 192 (213)
...-+|+.+-. ..|+.|...+- ...+.|+.||..+.
T Consensus 99 ~v~elHG~~~~--~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~lr 144 (218)
T cd01407 99 KVIELHGSLFR--VRCTKCGKEYPRDELQADIDREEVPRCPKCGGLLR 144 (218)
T ss_pred CEEECcCCcCc--ceeCCCcCCCcHHHHhHhhccCCCCcCCCCCCccC
Confidence 46677876655 55888876553 23578999996643
No 146
>PRK07418 acetolactate synthase 3 catalytic subunit; Reviewed
Probab=37.89 E-value=1.3e+02 Score=29.39 Aligned_cols=71 Identities=8% Similarity=0.135 Sum_probs=50.7
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHH------------------------HHHHhhCC
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQ------------------------QASYITGG 114 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLq------------------------q~~~~TgG 114 (213)
.++++.|.| |.+.+|. ++.+.+|.+.+++|=++.+......+++ ++++.-|+
T Consensus 452 ~r~Vv~i~G--DG~f~m~--~~eL~Ta~r~~lpvi~vV~NN~~~g~i~~~q~~~~~~~~~~~~~~~~~~d~~~~A~a~G~ 527 (616)
T PRK07418 452 DEEVICIAG--DASFLMN--IQELGTLAQYGINVKTVIINNGWQGMVRQWQESFYGERYSASNMEPGMPDFVKLAEAFGV 527 (616)
T ss_pred CCcEEEEEc--chHhhhh--HHHHHHHHHhCCCeEEEEEECCcchHHHHHHHHhcCCCceeecCCCCCCCHHHHHHHCCC
Confidence 457777775 6676665 5678999999999999998543333333 35666677
Q ss_pred eeeccCCcchHHHHHHHHc
Q 028156 115 VHHKPQQLDGLFQYLLTIF 133 (213)
Q Consensus 115 ~Y~~~~~~~~l~~~Ll~~~ 133 (213)
.+..+.+++.|.+.|-..+
T Consensus 528 ~g~~V~~~~el~~al~~a~ 546 (616)
T PRK07418 528 KGMVISERDQLKDAIAEAL 546 (616)
T ss_pred eEEEeCCHHHHHHHHHHHH
Confidence 7788888888888776654
No 147
>cd02013 TPP_Xsc_like Thiamine pyrophosphate (TPP) family, Xsc-like subfamily, TPP-binding module; composed of proteins similar to Alcaligenes defragrans sulfoacetaldehyde acetyltransferase (Xsc). Xsc plays a key role in the degradation of taurine, catalyzing the desulfonation of 2-sulfoacetaldehyde into sulfite and acetyl phosphate. This enzyme requires TPP and divalent metal ions for activity.
Probab=37.82 E-value=1.4e+02 Score=24.70 Aligned_cols=36 Identities=22% Similarity=0.423 Sum_probs=27.7
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcC
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLG 98 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~ 98 (213)
.+++++|.| |.+.+|. ++.+.+|.++++++=++.+.
T Consensus 71 ~r~vv~i~G--DG~f~m~--~~eL~Ta~~~~lpvi~vV~N 106 (196)
T cd02013 71 DRPVVAIAG--DGAWGMS--MMEIMTAVRHKLPVTAVVFR 106 (196)
T ss_pred CCcEEEEEc--chHHhcc--HHHHHHHHHhCCCeEEEEEE
Confidence 467777776 6666664 46778899999999999884
No 148
>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=37.81 E-value=2.4e+02 Score=27.88 Aligned_cols=89 Identities=12% Similarity=0.061 Sum_probs=46.7
Q ss_pred HHHHHHHHHHhhhhccCCCCCCCcccccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCCcc----hhhHHHHH
Q 028156 7 TLLQNLEEFMNKDEQLGKQEPEGRIACSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGPEQ----YVAIMNAI 82 (213)
Q Consensus 7 ~i~~~l~~l~~~~~~~~~~~~~~~~~~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~~q----yi~imn~i 82 (213)
+.+++|++|+..+....-...-.......|..+|=.|.-.+.+. .....++||++|+--.++-.+ .-....-+
T Consensus 90 ~~i~~L~~l~~~~~~~~~~~~~~~~~~~~l~daL~~~~~~f~~~---~~k~~~kRI~lfTd~D~P~~~~~~~~~~a~~~a 166 (584)
T TIGR00578 90 KRILELDQFKGDQGPKKFRDTYGHGSDYSLSEVLWVCANLFSDV---QFRMSHKRIMLFTNEDNPHGNDSAKASRARTKA 166 (584)
T ss_pred HHHHHHHHHhhccCccchhhccCCCCCCcHHHHHHHHHHHHHhc---chhhcCcEEEEECCCCCCCCCchhHHHHHHHHH
Confidence 45677777765422111100000011235566665555444432 224678999999943322111 11112346
Q ss_pred HHHHhCCeeeeEEEcC
Q 028156 83 FSAQRSMVPIDSCYLG 98 (213)
Q Consensus 83 f~aqk~~I~Idv~~L~ 98 (213)
..++..+|.|+++.|.
T Consensus 167 ~dl~~~gi~ielf~l~ 182 (584)
T TIGR00578 167 GDLRDTGIFLDLMHLK 182 (584)
T ss_pred HHHHhcCeEEEEEecC
Confidence 7778999999999885
No 149
>PRK08322 acetolactate synthase; Reviewed
Probab=37.73 E-value=1.3e+02 Score=28.78 Aligned_cols=71 Identities=17% Similarity=0.199 Sum_probs=46.4
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHH---------------------HHHHhhCCeee
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQ---------------------QASYITGGVHH 117 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLq---------------------q~~~~TgG~Y~ 117 (213)
.++++.|.| |.+.+|. ++.+.+|.+.++++=++.+......+++ ++++.-|+.|.
T Consensus 424 ~~~vv~i~G--DGsf~m~--~~eL~Ta~~~~lpv~iiV~NN~~~g~~~~~~~~~~~~~~~~~~~~~df~~lA~a~G~~~~ 499 (547)
T PRK08322 424 DRKVLAVCG--DGGFMMN--SQELETAVRLGLPLVVLILNDNAYGMIRWKQENMGFEDFGLDFGNPDFVKYAESYGAKGY 499 (547)
T ss_pred CCcEEEEEc--chhHhcc--HHHHHHHHHhCCCeEEEEEeCCCcchHHHHHHhhcCCcccccCCCCCHHHHHHHCCCeEE
Confidence 457777775 6666654 4678889999999999988533333443 34444555666
Q ss_pred ccCCcchHHHHHHHHc
Q 028156 118 KPQQLDGLFQYLLTIF 133 (213)
Q Consensus 118 ~~~~~~~l~~~Ll~~~ 133 (213)
.+.+.+.|.+.|-..+
T Consensus 500 ~v~~~~eL~~al~~a~ 515 (547)
T PRK08322 500 RVESADDLLPTLEEAL 515 (547)
T ss_pred EeCCHHHHHHHHHHHH
Confidence 6666666666665554
No 150
>cd02014 TPP_POX Thiamine pyrophosphate (TPP) family, Pyruvate oxidase (POX) subfamily, TPP-binding module; composed of proteins similar to Lactobacillus plantarum POX, which plays a key role in controlling acetate production under aerobic conditions. POX decarboxylates pyruvate, producing hydrogen peroxide and the energy-storage metabolite acetylphosphate. It requires FAD in addition to TPP and a divalent cation as cofactors.
Probab=37.52 E-value=1.4e+02 Score=24.16 Aligned_cols=36 Identities=19% Similarity=0.409 Sum_probs=27.4
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcC
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLG 98 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~ 98 (213)
.++++.|.| |.+.+|. ++.+.+|.+.++++-++.+.
T Consensus 69 ~~~vv~i~G--DG~f~~~--~~el~t~~~~~lp~~~iv~N 104 (178)
T cd02014 69 DRQVIALSG--DGGFAML--MGDLITAVKYNLPVIVVVFN 104 (178)
T ss_pred CCcEEEEEc--chHHHhh--HHHHHHHHHhCCCcEEEEEE
Confidence 467787775 6666666 56678899999999888884
No 151
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=37.47 E-value=17 Score=20.17 Aligned_cols=23 Identities=26% Similarity=0.704 Sum_probs=16.1
Q ss_pred eEcCCCCccccCCCCcccccccc
Q 028156 168 YICSVCLSIYCKHLKKCSTCGSV 190 (213)
Q Consensus 168 yvCp~Clsi~C~~p~~C~~C~~~ 190 (213)
+.|+.|.-.-=.-...|..|++.
T Consensus 3 W~C~~C~~~N~~~~~~C~~C~~p 25 (26)
T smart00547 3 WECPACTFLNFASRSKCFACGAP 25 (26)
T ss_pred ccCCCCCCcChhhhccccccCCc
Confidence 67888875555555788888864
No 152
>PRK06882 acetolactate synthase 3 catalytic subunit; Validated
Probab=36.65 E-value=1.4e+02 Score=28.72 Aligned_cols=71 Identities=20% Similarity=0.307 Sum_probs=44.9
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHH-----------------------HHHHhhCCe
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQ-----------------------QASYITGGV 115 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLq-----------------------q~~~~TgG~ 115 (213)
.+++++|.| |.+.+|. ++.+.+|.+.++++-++.+......+++ ++++.-|+.
T Consensus 439 ~~~vv~i~G--DG~f~~~--~~eL~ta~~~~lpv~~vV~NN~~~~~i~~~q~~~~~~~~~~~~~~~~~d~~~la~a~G~~ 514 (574)
T PRK06882 439 EATVVCVTG--DGSIQMN--IQELSTAKQYDIPVVIVSLNNRFLGMVKQWQDLIYSGRHSQVYMNSLPDFAKLAEAYGHV 514 (574)
T ss_pred CCcEEEEEc--chhhhcc--HHHHHHHHHhCCCeEEEEEECchhHHHHHHHHHhcCCcccccCCCCCCCHHHHHHHCCCe
Confidence 457777775 6666665 4788899999999999988533223333 344555555
Q ss_pred eeccCCcchHHHHHHHHc
Q 028156 116 HHKPQQLDGLFQYLLTIF 133 (213)
Q Consensus 116 Y~~~~~~~~l~~~Ll~~~ 133 (213)
+..+.+.+.|...|-..+
T Consensus 515 ~~~v~~~~eL~~al~~a~ 532 (574)
T PRK06882 515 GIQIDTPDELEEKLTQAF 532 (574)
T ss_pred EEEeCCHHHHHHHHHHHH
Confidence 556666666555554443
No 153
>cd05008 SIS_GlmS_GlmD_1 SIS (Sugar ISomerase) domain repeat 1 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal glutaminase domain and two C-terminal SIS domains and catalyzes the first step in hexosamine metabolism, converting fructose 6-phosphate into glucosamine 6-phosphate using glutamine as nitrogen source. The glutaminase domain hydrolyzes glutamine to glutamate and ammonia. Ammonia is transferred through a channel to the isomerase domain for glucosamine 6-phosphate synthesis. The end product of the pathway is N-acetylglucosamine, which plays multiple roles in eukaryotic cells including being a building block of bacterial and fungal cell walls. In the absence of glutamine, GlmS catalyzes the isomerization of fructose 6-phosphate into glucose 6- phosphate (PGI-like activity). Glucosamine-6-phosphate deaminase (GlmD) cont
Probab=36.35 E-value=51 Score=24.55 Aligned_cols=45 Identities=9% Similarity=0.059 Sum_probs=27.6
Q ss_pred EEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHHHHHh
Q 028156 61 RILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQASYI 111 (213)
Q Consensus 61 rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~~~~ 111 (213)
-+++||.|+.+. .+...+..|++.+++| +.+...+..-|.+.+|.
T Consensus 49 ~~I~iS~sG~t~----e~~~~~~~a~~~g~~v--i~iT~~~~s~la~~ad~ 93 (126)
T cd05008 49 LVIAISQSGETA----DTLAALRLAKEKGAKT--VAITNVVGSTLAREADY 93 (126)
T ss_pred EEEEEeCCcCCH----HHHHHHHHHHHcCCeE--EEEECCCCChHHHhCCE
Confidence 355556555333 5678888999999765 44443344455666664
No 154
>KOG1986 consensus Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking, secretion, and vesicular transport]
Probab=36.26 E-value=4.4e+02 Score=27.00 Aligned_cols=123 Identities=15% Similarity=0.077 Sum_probs=70.9
Q ss_pred HHHHHHHHHHhhhhccCCCCCCCc-ccccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCC----------------
Q 028156 7 TLLQNLEEFMNKDEQLGKQEPEGR-IACSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSP---------------- 69 (213)
Q Consensus 7 ~i~~~l~~l~~~~~~~~~~~~~~~-~~~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~---------------- 69 (213)
+....|.+++++-....-.- .++ ..---...||+.|+-.+--- .....+||+.+.+.+
T Consensus 222 ~c~~~L~~lle~L~~d~wpV-~~g~Rp~RcTG~Al~iA~~Ll~~c----~p~~g~rIv~f~gGPcT~GpG~vv~~el~~p 296 (745)
T KOG1986|consen 222 ECEFKLTNLLEELQPDPWPV-PPGHRPLRCTGVALSIASGLLEGC----FPNTGARIVLFAGGPCTRGPGTVVSRELKEP 296 (745)
T ss_pred HHHHHHHHHHHHhcCCCCCC-CCCCCcccchhHHHHHHHHHhccc----CCCCcceEEEeccCCCCcCCceecchhhcCC
Confidence 45556666666544322211 111 22234567788888777664 346677887776542
Q ss_pred -----CCCcc---h----hhHH-HHHHHHHhCCeeeeEEEcC--CcChHHHHHHHHhhCCeeeccCCc--chHHHHHHHH
Q 028156 70 -----DGPEQ---Y----VAIM-NAIFSAQRSMVPIDSCYLG--AQNSAFLQQASYITGGVHHKPQQL--DGLFQYLLTI 132 (213)
Q Consensus 70 -----d~~~q---y----i~im-n~if~aqk~~I~Idv~~L~--~~e~~iLqq~~~~TgG~Y~~~~~~--~~l~~~Ll~~ 132 (213)
|-..+ | +..+ +....+.+++-.+|+..=+ .--...+|.+++.|||.-..-.+- +-+.+-+-..
T Consensus 297 iRshhdi~~d~a~y~kKa~KfY~~La~r~~~~ghvlDifa~~lDQvGi~EMk~l~~~TGG~lvl~dsF~~s~Fk~sfqR~ 376 (745)
T KOG1986|consen 297 IRSHHDIEKDNAPYYKKAIKFYEKLAERLANQGHVLDIFAAALDQVGILEMKPLVESTGGVLVLGDSFNTSIFKQSFQRI 376 (745)
T ss_pred CcCcccccCcchHHHHHHHHHHHHHHHHHHhCCceEeeeeeeccccchHHHHHHhhcCCcEEEEecccchHHHHHHHHHH
Confidence 00111 1 1122 4567778889999887542 123568899999999987765543 3455666666
Q ss_pred cC
Q 028156 133 FG 134 (213)
Q Consensus 133 ~~ 134 (213)
|.
T Consensus 377 f~ 378 (745)
T KOG1986|consen 377 FT 378 (745)
T ss_pred hc
Confidence 64
No 155
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=36.04 E-value=29 Score=20.10 Aligned_cols=24 Identities=25% Similarity=0.659 Sum_probs=16.9
Q ss_pred eeEcCCCCccccCCCCcccccccc
Q 028156 167 GYICSVCLSIYCKHLKKCSTCGSV 190 (213)
Q Consensus 167 GyvCp~Clsi~C~~p~~C~~C~~~ 190 (213)
.+.|+.|.-.-=.-...|..|++.
T Consensus 4 ~W~C~~C~~~N~~~~~~C~~C~~~ 27 (30)
T PF00641_consen 4 DWKCPSCTFMNPASRSKCVACGAP 27 (30)
T ss_dssp SEEETTTTEEEESSSSB-TTT--B
T ss_pred CccCCCCcCCchHHhhhhhCcCCC
Confidence 578999987777777899999863
No 156
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=35.96 E-value=15 Score=36.99 Aligned_cols=25 Identities=28% Similarity=0.951 Sum_probs=18.4
Q ss_pred CCCCccccCC---------CCccccccccccccc
Q 028156 171 SVCLSIYCKH---------LKKCSTCGSVFGQAQ 195 (213)
Q Consensus 171 p~Clsi~C~~---------p~~C~~C~~~f~~~~ 195 (213)
+-|.=.||+- -..||+|++.|...-
T Consensus 659 ~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganD 692 (698)
T KOG0978|consen 659 TKCGHVFCEECVQTRYETRQRKCPKCNAAFGAND 692 (698)
T ss_pred HhcchHHHHHHHHHHHHHhcCCCCCCCCCCCccc
Confidence 4566678852 379999999998654
No 157
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=35.66 E-value=25 Score=24.10 Aligned_cols=25 Identities=28% Similarity=0.533 Sum_probs=16.8
Q ss_pred cCCCCccccCC-CCcccccccccccc
Q 028156 170 CSVCLSIYCKH-LKKCSTCGSVFGQA 194 (213)
Q Consensus 170 Cp~Clsi~C~~-p~~C~~C~~~f~~~ 194 (213)
||+|....|.. .-.||-||...--+
T Consensus 2 Cpv~~~~~~~~v~~~Cp~cGipthcS 27 (55)
T PF13824_consen 2 CPVCKKDLPAHVNFECPDCGIPTHCS 27 (55)
T ss_pred CCCCccccccccCCcCCCCCCcCccC
Confidence 77777777654 35788888765433
No 158
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=35.05 E-value=10 Score=27.78 Aligned_cols=32 Identities=25% Similarity=0.521 Sum_probs=16.5
Q ss_pred ccceeEcCCCC---ccccCCC-------Cccccccccccccc
Q 028156 164 IDMGYICSVCL---SIYCKHL-------KKCSTCGSVFGQAQ 195 (213)
Q Consensus 164 v~~GyvCp~Cl---si~C~~p-------~~C~~C~~~f~~~~ 195 (213)
.+.-|-||.|. |+-|++- ..|.+||..|....
T Consensus 19 l~~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~i 60 (81)
T PF05129_consen 19 LPKVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTKI 60 (81)
T ss_dssp -SS----TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE-
T ss_pred CCceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEcc
Confidence 45679999998 4566542 58999999997654
No 159
>PRK05858 hypothetical protein; Provisional
Probab=34.96 E-value=1.7e+02 Score=28.08 Aligned_cols=71 Identities=18% Similarity=0.148 Sum_probs=47.2
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHH----------------------HHHHhhCCee
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQ----------------------QASYITGGVH 116 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLq----------------------q~~~~TgG~Y 116 (213)
.++++.|.| |.+.+|. .+.+.+|.++++++-++.+....-.+.+ ++++.-|+.+
T Consensus 425 ~r~vv~i~G--DG~f~~~--~~eL~Ta~~~~lpi~ivV~NN~~y~~~~~~~~~~~~~~~~~~~~~~~d~~~lA~a~G~~~ 500 (542)
T PRK05858 425 SRQVVLLQG--DGAFGFS--LMDVDTLVRHNLPVVSVIGNNGIWGLEKHPMEALYGYDVAADLRPGTRYDEVVRALGGHG 500 (542)
T ss_pred CCcEEEEEc--CchhcCc--HHHHHHHHHcCCCEEEEEEeCCchhhHHHHHHHhcCCccccccCCCCCHHHHHHHCCCeE
Confidence 467777775 6665554 3568888899999999999532222223 3555666667
Q ss_pred eccCCcchHHHHHHHHc
Q 028156 117 HKPQQLDGLFQYLLTIF 133 (213)
Q Consensus 117 ~~~~~~~~l~~~Ll~~~ 133 (213)
..+.+++.|.+.|-..+
T Consensus 501 ~~v~~~~eL~~al~~a~ 517 (542)
T PRK05858 501 ELVTVPAELGPALERAF 517 (542)
T ss_pred EEeCCHHHHHHHHHHHH
Confidence 77777777777765554
No 160
>cd02004 TPP_BZL_OCoD_HPCL Thiamine pyrophosphate (TPP) family, BZL_OCoD_HPCL subfamily, TPP-binding module; composed of proteins similar to benzaldehyde lyase (BZL), oxalyl-CoA decarboxylase (OCoD) and 2-hydroxyphytanoyl-CoA lyase (2-HPCL). Pseudomonas fluorescens biovar I BZL cleaves the acyloin linkage of benzoin producing 2 molecules of benzaldehyde and enabling the Pseudomonas to grow on benzoin as the sole carbon and energy source. OCoD has a role in the detoxification of oxalate, catalyzing the decarboxylation of oxalyl-CoA to formate. 2-HPCL is a peroxisomal enzyme which plays a role in the alpha-oxidation of 3-methyl-branched fatty acids, catalyzing the cleavage of 2-hydroxy-3-methylacyl-CoA into formyl-CoA and a 2-methyl-branched fatty aldehyde. All these enzymes depend on Mg2+ and TPP for activity.
Probab=34.59 E-value=1.5e+02 Score=23.65 Aligned_cols=36 Identities=22% Similarity=0.278 Sum_probs=27.2
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcC
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLG 98 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~ 98 (213)
.++++.|.+ |.+.++. ++.+.+|.+.++++=++.+.
T Consensus 66 ~~~vv~i~G--DG~f~~~--~~el~ta~~~~lpv~ivv~N 101 (172)
T cd02004 66 DKRVVLVEG--DGAFGFS--GMELETAVRYNLPIVVVVGN 101 (172)
T ss_pred CCeEEEEEc--chhhcCC--HHHHHHHHHcCCCEEEEEEE
Confidence 467777775 5565553 57788999999999888884
No 161
>cd05014 SIS_Kpsf KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose 5-phosphate to arabinose 5-phosphate. This is the second step in the CMP-Kdo biosynthesis pathway.
Probab=34.55 E-value=47 Score=24.85 Aligned_cols=44 Identities=16% Similarity=0.239 Sum_probs=27.6
Q ss_pred EEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHHHHH
Q 028156 61 RILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQASY 110 (213)
Q Consensus 61 rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~~~ 110 (213)
-+++++.|..+. .+.+.+..|++.+++| +.|......-|.+.||
T Consensus 50 ~vi~iS~sG~t~----~~~~~~~~a~~~g~~v--i~iT~~~~s~la~~ad 93 (128)
T cd05014 50 VVIAISNSGETD----ELLNLLPHLKRRGAPI--IAITGNPNSTLAKLSD 93 (128)
T ss_pred EEEEEeCCCCCH----HHHHHHHHHHHCCCeE--EEEeCCCCCchhhhCC
Confidence 455666555333 6678889999999765 5554444445555555
No 162
>PRK04023 DNA polymerase II large subunit; Validated
Probab=34.34 E-value=24 Score=37.24 Aligned_cols=52 Identities=23% Similarity=0.385 Sum_probs=38.1
Q ss_pred HHHHHHHHcCCCchhhcccCCCCCCCCCCceeeeeccCcccceeEcCCCCccccCCC--Cccccccccccccc
Q 028156 125 LFQYLLTIFGTDLHSRNFLQLPKPVGVDFRASCFCHKNTIDMGYICSVCLSIYCKHL--KKCSTCGSVFGQAQ 195 (213)
Q Consensus 125 l~~~Ll~~~~p~~~~r~~l~~P~~~~vd~~a~C~CH~~~v~~GyvCp~Clsi~C~~p--~~C~~C~~~f~~~~ 195 (213)
--..|.+||+|+.-- +.||+ -.-+|-|..|.+.|=..| ..|+.||-.++.+.
T Consensus 1014 AerVi~sHFlPDl~G------------NLRaF-------srQ~fRC~kC~~kYRR~PL~G~C~kCGg~lilTV 1067 (1121)
T PRK04023 1014 AERVISSHFLPDLIG------------NLRAF-------SRQEFRCTKCGAKYRRPPLSGKCPKCGGNLILTV 1067 (1121)
T ss_pred HHHHHHhccchhhhh------------hhhhh-------cccceeecccCcccccCCCCCcCccCCCeEEEEE
Confidence 345678999988631 12222 123589999999999877 89999999998766
No 163
>PRK07064 hypothetical protein; Provisional
Probab=33.99 E-value=1.5e+02 Score=28.32 Aligned_cols=71 Identities=13% Similarity=0.113 Sum_probs=47.3
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHH----------------------HHHHhhCCee
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQ----------------------QASYITGGVH 116 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLq----------------------q~~~~TgG~Y 116 (213)
.++++.|.| |.+.+|. ++.+.+|.+.++++=++.+......+++ ++++.-|+.|
T Consensus 423 ~~~vv~i~G--DGsf~m~--~~eL~Ta~~~~lpv~ivV~NN~~yg~~~~~~~~~~~~~~~~~~~~~~d~~~lA~a~G~~~ 498 (544)
T PRK07064 423 GRKTVGLVG--DGGLMLN--LGELATAVQENANMVIVLMNDGGYGVIRNIQDAQYGGRRYYVELHTPDFALLAASLGLPH 498 (544)
T ss_pred CCcEEEEEc--chHhhhh--HHHHHHHHHhCCCeEEEEEeCChhHHHHHHHHHhcCCccccccCCCCCHHHHHHHCCCeE
Confidence 457777775 6676665 5788999999999999888543333443 2445555666
Q ss_pred eccCCcchHHHHHHHHc
Q 028156 117 HKPQQLDGLFQYLLTIF 133 (213)
Q Consensus 117 ~~~~~~~~l~~~Ll~~~ 133 (213)
..+.+.+.|.+.|-..+
T Consensus 499 ~~v~~~~eL~~al~~a~ 515 (544)
T PRK07064 499 WRVTSADDFEAVLREAL 515 (544)
T ss_pred EEeCCHHHHHHHHHHHH
Confidence 66666667766665554
No 164
>PRK04860 hypothetical protein; Provisional
Probab=33.27 E-value=59 Score=26.75 Aligned_cols=47 Identities=21% Similarity=0.359 Sum_probs=25.0
Q ss_pred hHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEc
Q 028156 36 LSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYL 97 (213)
Q Consensus 36 L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L 97 (213)
+...|.+|..|.|+-. ..+.|.+ .....++.. .-.+..+|+++-..+
T Consensus 9 ~~~~~~~a~~~f~~~f------~~p~~~f-~~R~rtaG~--------~~l~~~~I~~Np~ll 55 (160)
T PRK04860 9 LRECLAQANLYFKRTF------PEPKVSY-TQRGTSAGT--------AWLQSNEIRLNPVLL 55 (160)
T ss_pred HHHHHHHHHHHhCCCC------CCCEEEE-eecchhhcc--------hhHhcCCeeeCHHHH
Confidence 4456777888888843 2223322 211212212 334677888877766
No 165
>PRK09124 pyruvate dehydrogenase; Provisional
Probab=33.12 E-value=1.6e+02 Score=28.52 Aligned_cols=71 Identities=17% Similarity=0.224 Sum_probs=47.8
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHH---------------------HHHHHhhCCeee
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFL---------------------QQASYITGGVHH 117 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iL---------------------qq~~~~TgG~Y~ 117 (213)
.++++.|.| |.+.+|. ++.+.+|.+.++++-++.+....-.++ .++++.-|+.+.
T Consensus 426 ~r~vv~i~G--DGsf~m~--~~eL~Ta~~~~lpv~ivV~NN~~~g~i~~~~~~~~~~~~~~~~~~~d~~~lA~a~G~~~~ 501 (574)
T PRK09124 426 GRQVVALSG--DGGFSML--MGDFLSLVQLKLPVKIVVFNNSVLGFVAMEMKAGGYLTDGTDLHNPDFAAIAEACGITGI 501 (574)
T ss_pred CCeEEEEec--CcHHhcc--HHHHHHHHHhCCCeEEEEEeCCccccHHHHHHhcCCccccCcCCCCCHHHHHHHCCCeEE
Confidence 567888876 6676665 567889999999999998853222222 234555566666
Q ss_pred ccCCcchHHHHHHHHc
Q 028156 118 KPQQLDGLFQYLLTIF 133 (213)
Q Consensus 118 ~~~~~~~l~~~Ll~~~ 133 (213)
.+.+.+.|.+.|-..+
T Consensus 502 ~v~~~~eL~~al~~a~ 517 (574)
T PRK09124 502 RVEKASELDGALQRAF 517 (574)
T ss_pred EeCCHHHHHHHHHHHH
Confidence 6677777777776654
No 166
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.87 E-value=20 Score=28.20 Aligned_cols=29 Identities=7% Similarity=-0.057 Sum_probs=24.6
Q ss_pred eeEcCCCCccccCC---CCccccccccccccc
Q 028156 167 GYICSVCLSIYCKH---LKKCSTCGSVFGQAQ 195 (213)
Q Consensus 167 GyvCp~Clsi~C~~---p~~C~~C~~~f~~~~ 195 (213)
--+||-|.++|=.+ |.+||-||..|..+-
T Consensus 9 KridPetg~KFYDLNrdPiVsPytG~s~P~s~ 40 (129)
T COG4530 9 KRIDPETGKKFYDLNRDPIVSPYTGKSYPRSY 40 (129)
T ss_pred cccCccccchhhccCCCccccCcccccchHHH
Confidence 46899999999987 689999999986654
No 167
>PRK09107 acetolactate synthase 3 catalytic subunit; Validated
Probab=32.81 E-value=2.6e+02 Score=27.30 Aligned_cols=45 Identities=18% Similarity=0.304 Sum_probs=32.5
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHH
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQ 107 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq 107 (213)
.++++.|.| |.+.+|. ...+.+|.+.++++-++.+......++++
T Consensus 448 ~r~Vv~i~G--DG~f~m~--~~EL~Ta~r~~lpvi~vV~NN~~y~~i~~ 492 (595)
T PRK09107 448 DALVIDIAG--DASIQMC--IQEMSTAVQYNLPVKIFILNNQYMGMVRQ 492 (595)
T ss_pred CCeEEEEEc--Cchhhcc--HHHHHHHHHhCCCeEEEEEeCCccHHHHH
Confidence 567777775 6665655 35789999999999999996444445553
No 168
>cd04192 GT_2_like_e Subfamily of Glycosyltransferase Family GT2 of unknown function. GT-2 includes diverse families of glycosyltransferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. Glycosyltransferases have been classified into more than 90 distinct sequence based families.
Probab=32.79 E-value=2.5e+02 Score=22.25 Aligned_cols=70 Identities=16% Similarity=0.184 Sum_probs=41.3
Q ss_pred cEEEEEe-cCCCCCcchhhHHHHHHHHHhCCeeeeEEEcC----CcChHHHHHHHHhhCCeeeccCCcc-----hHHHHH
Q 028156 60 PRILCLQ-GSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLG----AQNSAFLQQASYITGGVHHKPQQLD-----GLFQYL 129 (213)
Q Consensus 60 ~rILiis-~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~----~~e~~iLqq~~~~TgG~Y~~~~~~~-----~l~~~L 129 (213)
-||+||. +|.|.+.+ ++. +.++..+.++-++... .+-..-+..+....+|.|+...|.+ +.++.+
T Consensus 29 ~eiivvdd~s~d~t~~---~~~--~~~~~~~~~v~~~~~~~~~~~g~~~a~n~g~~~~~~d~i~~~D~D~~~~~~~l~~l 103 (229)
T cd04192 29 FEVILVDDHSTDGTVQ---ILE--FAAAKPNFQLKILNNSRVSISGKKNALTTAIKAAKGDWIVTTDADCVVPSNWLLTF 103 (229)
T ss_pred eEEEEEcCCCCcChHH---HHH--HHHhCCCcceEEeeccCcccchhHHHHHHHHHHhcCCEEEEECCCcccCHHHHHHH
Confidence 5888887 44444333 223 3455556666666542 1123456677788889999988754 355556
Q ss_pred HHHcC
Q 028156 130 LTIFG 134 (213)
Q Consensus 130 l~~~~ 134 (213)
+..+.
T Consensus 104 ~~~~~ 108 (229)
T cd04192 104 VAFIQ 108 (229)
T ss_pred HHHhh
Confidence 65443
No 169
>PHA00626 hypothetical protein
Probab=32.79 E-value=25 Score=24.33 Aligned_cols=27 Identities=30% Similarity=0.408 Sum_probs=18.8
Q ss_pred EcCCCCc--cc-cC---C---CCccccccccccccc
Q 028156 169 ICSVCLS--IY-CK---H---LKKCSTCGSVFGQAQ 195 (213)
Q Consensus 169 vCp~Cls--i~-C~---~---p~~C~~C~~~f~~~~ 195 (213)
.||.|.| |+ |. - .=.|+.||-.|....
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSKDA 37 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeechhh
Confidence 5899988 22 22 2 247999999998765
No 170
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=32.73 E-value=28 Score=19.88 Aligned_cols=10 Identities=20% Similarity=0.634 Sum_probs=7.4
Q ss_pred cceeEcCCCC
Q 028156 165 DMGYICSVCL 174 (213)
Q Consensus 165 ~~GyvCp~Cl 174 (213)
.+.|.||.|.
T Consensus 14 ~v~f~CPnCG 23 (24)
T PF07754_consen 14 AVPFPCPNCG 23 (24)
T ss_pred CceEeCCCCC
Confidence 4568899885
No 171
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=32.34 E-value=18 Score=25.80 Aligned_cols=27 Identities=19% Similarity=0.517 Sum_probs=21.9
Q ss_pred EcCCCCccccCC-----CCccccccccccccc
Q 028156 169 ICSVCLSIYCKH-----LKKCSTCGSVFGQAQ 195 (213)
Q Consensus 169 vCp~Clsi~C~~-----p~~C~~C~~~f~~~~ 195 (213)
-||-|.-..+-+ ...|.+||..|..+.
T Consensus 21 kCpdC~N~q~vFshast~V~C~~CG~~l~~PT 52 (67)
T COG2051 21 KCPDCGNEQVVFSHASTVVTCLICGTTLAEPT 52 (67)
T ss_pred ECCCCCCEEEEeccCceEEEecccccEEEecC
Confidence 399999877754 368999999999776
No 172
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=32.07 E-value=25 Score=25.74 Aligned_cols=25 Identities=20% Similarity=0.309 Sum_probs=15.7
Q ss_pred eEcCCCCccccCC-CC----cccccccccc
Q 028156 168 YICSVCLSIYCKH-LK----KCSTCGSVFG 192 (213)
Q Consensus 168 yvCp~Clsi~C~~-p~----~C~~C~~~f~ 192 (213)
|-||.|....=+- +. +|++|+=.-.
T Consensus 2 ~~CPCCg~~Tl~~~~~~~ydIC~VC~WEdD 31 (78)
T PF14206_consen 2 YPCPCCGYYTLEERGEGTYDICPVCFWEDD 31 (78)
T ss_pred ccCCCCCcEEeccCCCcCceECCCCCcccC
Confidence 6688887765432 22 7888865444
No 173
>PRK07789 acetolactate synthase 1 catalytic subunit; Validated
Probab=31.76 E-value=1.7e+02 Score=28.61 Aligned_cols=71 Identities=13% Similarity=0.153 Sum_probs=47.5
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHH---------------------------HHHHHh
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFL---------------------------QQASYI 111 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iL---------------------------qq~~~~ 111 (213)
.++++.|.| |.+.+|. ++.+.+|.+.++++-++.+......++ .++++.
T Consensus 465 ~~~Vv~i~G--DG~f~m~--~~eL~Ta~~~~lpv~ivV~NN~~~g~i~~~q~~~~~~~~~~~~~~~~~~~~~d~~~lA~a 540 (612)
T PRK07789 465 DKEVWAIDG--DGCFQMT--NQELATCAIEGIPIKVALINNGNLGMVRQWQTLFYEERYSNTDLHTHSHRIPDFVKLAEA 540 (612)
T ss_pred CCcEEEEEc--chhhhcc--HHHHHHHHHcCCCeEEEEEECCchHHHHHHHHHhhCCCcceeecCcCCCCCCCHHHHHHH
Confidence 567777765 6676665 478999999999999998853333333 335555
Q ss_pred hCCeeeccCCcchHHHHHHHHc
Q 028156 112 TGGVHHKPQQLDGLFQYLLTIF 133 (213)
Q Consensus 112 TgG~Y~~~~~~~~l~~~Ll~~~ 133 (213)
.|+.|..+.+.+.|.+.|-..+
T Consensus 541 ~G~~~~~V~~~~eL~~al~~a~ 562 (612)
T PRK07789 541 YGCVGLRCEREEDVDAVIEKAR 562 (612)
T ss_pred CCCeEEEECCHHHHHHHHHHHH
Confidence 6666666666666666664443
No 174
>PF01936 NYN: NYN domain; InterPro: IPR021139 This highly conserved domain has no known function. However it contains many conserved aspartates, suggesting an enzymatic function such as an endonuclease or glycosyl hydrolase.; PDB: 2QIP_A.
Probab=31.70 E-value=54 Score=24.85 Aligned_cols=45 Identities=13% Similarity=0.110 Sum_probs=27.0
Q ss_pred cEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHHHHHh
Q 028156 60 PRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQASYI 111 (213)
Q Consensus 60 ~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~~~~ 111 (213)
..++++|+ | .+|.++. ..+++.+++|.+++....-+.-|+.+||.
T Consensus 97 d~ivLvSg--D--~Df~~~v---~~l~~~g~~V~v~~~~~~~s~~L~~~ad~ 141 (146)
T PF01936_consen 97 DTIVLVSG--D--SDFAPLV---RKLRERGKRVIVVGAEDSASEALRSAADE 141 (146)
T ss_dssp SEEEEE-------GGGHHHH---HHHHHH--EEEEEE-GGGS-HHHHHHSSE
T ss_pred CEEEEEEC--c--HHHHHHH---HHHHHcCCEEEEEEeCCCCCHHHHHhcCE
Confidence 67788875 2 4566555 55589999999998534567788888763
No 175
>PHA02768 hypothetical protein; Provisional
Probab=31.34 E-value=17 Score=24.83 Aligned_cols=29 Identities=34% Similarity=0.613 Sum_probs=22.5
Q ss_pred cceeEcCCCCccccC------------CCCccccccccccc
Q 028156 165 DMGYICSVCLSIYCK------------HLKKCSTCGSVFGQ 193 (213)
Q Consensus 165 ~~GyvCp~Clsi~C~------------~p~~C~~C~~~f~~ 193 (213)
-.||.|+.|.-.|-. -|-.|..|+-.|..
T Consensus 3 ~~~y~C~~CGK~Fs~~~~L~~H~r~H~k~~kc~~C~k~f~~ 43 (55)
T PHA02768 3 LLGYECPICGEIYIKRKSMITHLRKHNTNLKLSNCKRISLR 43 (55)
T ss_pred ccccCcchhCCeeccHHHHHHHHHhcCCcccCCcccceecc
Confidence 369999999998874 25588999887764
No 176
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=31.26 E-value=16 Score=24.93 Aligned_cols=17 Identities=29% Similarity=0.765 Sum_probs=8.1
Q ss_pred CCCCccccccccccccc
Q 028156 179 KHLKKCSTCGSVFGQAQ 195 (213)
Q Consensus 179 ~~p~~C~~C~~~f~~~~ 195 (213)
+.|..||.|+..+.++-
T Consensus 22 ~~PatCP~C~a~~~~sr 38 (54)
T PF09237_consen 22 EQPATCPICGAVIRQSR 38 (54)
T ss_dssp S--EE-TTT--EESSHH
T ss_pred CCCCCCCcchhhccchh
Confidence 45677888888776543
No 177
>KOG2858 consensus Uncharacterized conserved protein [General function prediction only]
Probab=31.01 E-value=17 Score=33.87 Aligned_cols=18 Identities=28% Similarity=0.578 Sum_probs=15.5
Q ss_pred ccceeEcCCCCccccCCC
Q 028156 164 IDMGYICSVCLSIYCKHL 181 (213)
Q Consensus 164 v~~GyvCp~Clsi~C~~p 181 (213)
...+|-||+|++.+|.|-
T Consensus 26 nE~KYkCPRCl~rtCsLe 43 (390)
T KOG2858|consen 26 NEPKYKCPRCLARTCSLE 43 (390)
T ss_pred CcccccCcchhhhheecc
Confidence 466999999999999763
No 178
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=30.85 E-value=21 Score=20.88 Aligned_cols=13 Identities=31% Similarity=0.833 Sum_probs=6.9
Q ss_pred ccccccccccccc
Q 028156 183 KCSTCGSVFGQAQ 195 (213)
Q Consensus 183 ~C~~C~~~f~~~~ 195 (213)
.||+||+.++...
T Consensus 1 ~CP~C~s~l~~~~ 13 (28)
T PF03119_consen 1 TCPVCGSKLVREE 13 (28)
T ss_dssp B-TTT--BEEE-C
T ss_pred CcCCCCCEeEcCC
Confidence 4899999988554
No 179
>PRK06546 pyruvate dehydrogenase; Provisional
Probab=30.35 E-value=1.8e+02 Score=28.21 Aligned_cols=43 Identities=9% Similarity=0.338 Sum_probs=30.2
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHH
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFL 105 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iL 105 (213)
.++++.|.| |.+.+|. ++.+.+|.+.+++|=++.+.......+
T Consensus 426 ~~~vv~i~G--DGsf~~~--~~el~Ta~~~~lpv~~vV~NN~~~g~i 468 (578)
T PRK06546 426 GRQVISMSG--DGGLSML--LGELLTVKLYDLPVKVVVFNNSTLGMV 468 (578)
T ss_pred CCcEEEEEc--CchHhhh--HHHHHHHHHhCCCeEEEEEECCccccH
Confidence 457777776 6666663 456789999999999998853333333
No 180
>TIGR03394 indol_phenyl_DC indolepyruvate/phenylpyruvate decarboxylase, Azospirillum family. A family of closely related, thiamine pyrophosphate-dependent enzymes includes indolepyruvate decarboxylase (EC 4.1.1.74), phenylpyruvate decarboxylase (EC 4.1.1.43), pyruvate decarboxylase (EC 4.1.1.1), branched-chain alpha-ketoacid decarboxylase, etc.. Members of this group of homologs may overlap in specificity. This model represents a clade that includes a Azospirillum brasilense member active as both phenylpyruvate decarboxylase and indolepyruvate decarboxylase.
Probab=29.93 E-value=1.4e+02 Score=28.79 Aligned_cols=88 Identities=17% Similarity=0.073 Sum_probs=55.5
Q ss_pred hHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHH------------
Q 028156 38 GSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFL------------ 105 (213)
Q Consensus 38 ~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iL------------ 105 (213)
++|..+|-+.--..-. + .+|.++|.| |.+.+|. ++.+.+|.+.|+++-++.+......++
T Consensus 403 g~mG~glpaaiGa~lA---~-~~r~v~i~G--DG~f~m~--~~EL~Ta~r~~lpv~~vV~NN~~y~~~~~~~~~~~~~~~ 474 (535)
T TIGR03394 403 AGMGFGVPAGIGAQCT---S-GKRILTLVG--DGAFQMT--GWELGNCRRLGIDPIVILFNNASWEMLRVFQPESAFNDL 474 (535)
T ss_pred chhhhHHHHHHHHHhC---C-CCCeEEEEe--ChHHHhH--HHHHHHHHHcCCCcEEEEEECCccceeehhccCCCcccC
Confidence 5566665554443211 1 245655654 6776665 578899999999999999853222222
Q ss_pred -----HHHHHhhCCeeeccCCcchHHHHHHHHc
Q 028156 106 -----QQASYITGGVHHKPQQLDGLFQYLLTIF 133 (213)
Q Consensus 106 -----qq~~~~TgG~Y~~~~~~~~l~~~Ll~~~ 133 (213)
..+++..|+.+..+.+.+.|.+.|-..+
T Consensus 475 ~~~d~~~lA~a~G~~~~~v~~~~eL~~al~~a~ 507 (535)
T TIGR03394 475 DDWRFADMAAGMGGDGVRVRTRAELAAALDKAF 507 (535)
T ss_pred CCCCHHHHHHHcCCCceEeCCHHHHHHHHHHHH
Confidence 2356666677777777777777776655
No 181
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=29.74 E-value=30 Score=22.82 Aligned_cols=11 Identities=27% Similarity=0.576 Sum_probs=7.0
Q ss_pred Ccccccccccc
Q 028156 182 KKCSTCGSVFG 192 (213)
Q Consensus 182 ~~C~~C~~~f~ 192 (213)
..||+|...+.
T Consensus 32 v~CPiC~~~~~ 42 (54)
T PF05605_consen 32 VVCPICSSRVT 42 (54)
T ss_pred ccCCCchhhhh
Confidence 56777776543
No 182
>TIGR01504 glyox_carbo_lig glyoxylate carboligase. Glyoxylate carboligase, also called tartronate-semialdehyde synthase, releases CO2 while synthesizing a single molecule of tartronate semialdehyde from two molecules of glyoxylate. It is a thiamine pyrophosphate-dependent enzyme, closely related in sequence to the large subunit of acetolactate synthase. In the D-glycerate pathway, part of allantoin degradation in the Enterobacteriaceae, tartronate semialdehyde is converted to D-glycerate and then 3-phosphoglycerate, a product of glycolysis and entry point in the general metabolism.
Probab=29.61 E-value=1.9e+02 Score=28.27 Aligned_cols=71 Identities=10% Similarity=0.114 Sum_probs=46.7
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHH-------------------------------
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQ------------------------------- 107 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq------------------------------- 107 (213)
.++++.|.| |.+.++. ...+.+|.++|+++=++.+......++++
T Consensus 436 dr~Vv~i~G--DG~f~m~--~~EL~Ta~r~~lpvv~iV~NN~~yg~i~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~d~~ 511 (588)
T TIGR01504 436 KRNVVALSG--DYDFQFM--IEELAVGAQHNIPYIHVLVNNAYLGLIRQAQRAFDMDYCVQLAFENINSSEVNGYGVDHV 511 (588)
T ss_pred CCcEEEEEc--chHhhcc--HHHHHHHHHhCCCeEEEEEeCCchHHHHHHHHHhcccccceeeccccccccccCCCCCHH
Confidence 567777775 6666665 46789999999999999995333334333
Q ss_pred -HHHhhCCeeeccCCcchHHHHHHHHc
Q 028156 108 -ASYITGGVHHKPQQLDGLFQYLLTIF 133 (213)
Q Consensus 108 -~~~~TgG~Y~~~~~~~~l~~~Ll~~~ 133 (213)
+++..|+.+..+.+++.|.+.|-..+
T Consensus 512 ~lA~a~G~~~~~V~~~~eL~~al~~a~ 538 (588)
T TIGR01504 512 KVAEGLGCKAIRVFKPEEIAPAFEQAK 538 (588)
T ss_pred HHHHHCCCEEEEECCHHHHHHHHHHHH
Confidence 44444566666666666666665544
No 183
>PRK10997 yieM hypothetical protein; Provisional
Probab=29.48 E-value=4.4e+02 Score=25.63 Aligned_cols=72 Identities=8% Similarity=-0.034 Sum_probs=45.9
Q ss_pred ccchHhHHHHHHHHHhhhhhcCCCCCCcEEEEEecCCCCCcchhhHHHHHHHHHh-CCeeeeEEEcCCcChHHHHHHHH
Q 028156 33 CSLLSGSLSMALCYIQRVFRSGLLHPQPRILCLQGSPDGPEQYVAIMNAIFSAQR-SMVPIDSCYLGAQNSAFLQQASY 110 (213)
Q Consensus 33 ~s~L~~aLs~ALc~inr~~~~~~~~~~~rILiis~S~d~~~qyi~imn~if~aqk-~~I~Idv~~L~~~e~~iLqq~~~ 110 (213)
.+.+..+|..|+..+.+. .+-.+-|+|||--. ....+-.+.+.+..+++ .+.++..+.++.....-+..++|
T Consensus 396 GTDl~~aL~~al~~l~~~-----~~r~adIVVISDF~-~~~~~eel~~~L~~Lk~~~~~rf~~l~i~~~~~p~l~~ifD 468 (487)
T PRK10997 396 GTDLAPCLRAIIEKMQGR-----EWFDADAVVISDFI-AQRLPDELVAKVKELQRQHQHRFHAVAMSAHGKPGIMRIFD 468 (487)
T ss_pred CCcHHHHHHHHHHHHccc-----ccCCceEEEECCCC-CCCChHHHHHHHHHHHHhcCcEEEEEEeCCCCCchHHHhcC
Confidence 355888888888887763 23455667776221 22224567788888877 89999999996433333344443
No 184
>TIGR02418 acolac_catab acetolactate synthase, catabolic. Acetolactate synthase (EC 2.2.1.6) combines two molecules of pyruvate to yield 2-acetolactate with the release of CO2. This reaction may be involved in either valine biosynthesis (biosynthetic) or conversion of pyruvate to acetoin and possibly to 2,3-butanediol (catabolic). The biosynthetic type, described by TIGR00118, is also capable of forming acetohydroxybutyrate from pyruvate and 2-oxobutyrate for isoleucine biosynthesis. The family described here, part of the same larger family of thiamine pyrophosphate-dependent enzymes (pfam00205, pfam02776) is the catabolic form, generally found associated with in species with acetolactate decarboxylase and usually found in the same operon. The model may not encompass all catabolic acetolactate synthases, but rather one particular clade in the larger TPP-dependent enzyme family.
Probab=29.39 E-value=2.2e+02 Score=27.16 Aligned_cols=37 Identities=16% Similarity=0.215 Sum_probs=28.1
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCC
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGA 99 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~ 99 (213)
.++++.|.| |.+.+|. ++.+.+|.+.++++=++.+..
T Consensus 426 ~~~vv~i~G--DGsf~m~--~~eL~Ta~~~~lpi~ivV~NN 462 (539)
T TIGR02418 426 NTKVVSVSG--DGGFLFS--SMELETAVRLKLNIVHIIWND 462 (539)
T ss_pred CCcEEEEEc--chhhhch--HHHHHHHHHhCCCeEEEEEEC
Confidence 456777775 6676765 467889999999999998853
No 185
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=29.38 E-value=33 Score=32.82 Aligned_cols=27 Identities=30% Similarity=0.481 Sum_probs=21.2
Q ss_pred ccceeEcCCCCccccCC-----------------C--Ccccccccc
Q 028156 164 IDMGYICSVCLSIYCKH-----------------L--KKCSTCGSV 190 (213)
Q Consensus 164 v~~GyvCp~Clsi~C~~-----------------p--~~C~~C~~~ 190 (213)
....|+|.+|.-+|-+- | -.||+||..
T Consensus 422 ~~~~~~c~~c~~~yd~~~g~~~~~~~~gt~~~~lp~~~~cp~c~~~ 467 (479)
T PRK05452 422 LGPRMQCSVCQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSLG 467 (479)
T ss_pred CCCeEEECCCCeEECCCCCCcccCCCCCCChhhCCCCCcCcCCCCc
Confidence 34589999999999853 2 389999964
No 186
>PRK07525 sulfoacetaldehyde acetyltransferase; Validated
Probab=29.05 E-value=2.2e+02 Score=27.68 Aligned_cols=36 Identities=22% Similarity=0.387 Sum_probs=28.4
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcC
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLG 98 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~ 98 (213)
.+++++|.| |.+.+|. ++.+.+|.++++++=++.+.
T Consensus 453 ~r~vv~i~G--DG~f~~~--~~el~Ta~~~~lpv~ivV~N 488 (588)
T PRK07525 453 DRPVVGFAG--DGAWGIS--MNEVMTAVRHNWPVTAVVFR 488 (588)
T ss_pred CCcEEEEEc--CchHhcc--HHHHHHHHHhCCCeEEEEEe
Confidence 467777775 6676665 57788999999999999884
No 187
>cd02002 TPP_BFDC Thiamine pyrophosphate (TPP) family, BFDC subfamily, TPP-binding module; composed of proteins similar to Pseudomonas putida benzoylformate decarboxylase (BFDC). P. putida BFDC plays a role in the mandelate pathway, catalyzing the conversion of benzoylformate to benzaldehyde and carbon dioxide. This enzyme is dependent on TPP and a divalent metal cation as cofactors.
Probab=29.01 E-value=2.9e+02 Score=21.87 Aligned_cols=49 Identities=20% Similarity=0.376 Sum_probs=32.7
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHHHHHh
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQASYI 111 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~~~~ 111 (213)
.++++++.| |.+.++. ++.+.+|.+.++++=++.+....-.+.++.-+.
T Consensus 67 ~~~vv~i~G--DG~f~~~--~~el~ta~~~~~p~~~iV~nN~~~~~~~~~~~~ 115 (178)
T cd02002 67 DRKVVAIIG--DGSFMYT--IQALWTAARYGLPVTVVILNNRGYGALRSFLKR 115 (178)
T ss_pred CCeEEEEEc--Cchhhcc--HHHHHHHHHhCCCeEEEEEcCccHHHHHHHHHH
Confidence 457777775 5665655 478888899999999998853334455544443
No 188
>PF02780 Transketolase_C: Transketolase, C-terminal domain; InterPro: IPR005476 Transketolase 2.2.1.1 from EC (TK) catalyzes the reversible transfer of a two-carbon ketol unit from xylulose 5-phosphate to an aldose receptor, such as ribose 5-phosphate, to form sedoheptulose 7-phosphate and glyceraldehyde 3- phosphate. This enzyme, together with transaldolase, provides a link between the glycolytic and pentose-phosphate pathways. TK requires thiamine pyrophosphate as a cofactor. In most sources where TK has been purified, it is a homodimer of approximately 70 Kd subunits. TK sequences from a variety of eukaryotic and prokaryotic sources [, ] show that the enzyme has been evolutionarily conserved. In the peroxisomes of methylotrophic yeast Pichia angusta (Yeast) (Hansenula polymorpha), there is a highly related enzyme, dihydroxy-acetone synthase (DHAS) 2.2.1.3 from EC (also known as formaldehyde transketolase), which exhibits a very unusual specificity by including formaldehyde amongst its substrates. 1-deoxyxylulose-5-phosphate synthase (DXP synthase) [] is an enzyme so far found in bacteria (gene dxs) and plants (gene CLA1) which catalyzes the thiamine pyrophosphoate-dependent acyloin condensation reaction between carbon atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D- xylulose-5-phosphate (dxp), a precursor in the biosynthetic pathway to isoprenoids, thiamine (vitamin B1), and pyridoxol (vitamin B6). DXP synthase is evolutionary related to TK. The N-terminal section, contains a histidine residue which appears to function in proton transfer during catalysis []. In the central section there are conserved acidic residues that are part of the active cleft and may participate in substrate-binding []. This family includes transketolase enzymes 2.2.1.1 from EC and also partially matches to 2-oxoisovalerate dehydrogenase beta subunit P37941 from SWISSPROT 1.2.4.4 from EC. Both these enzymes utilise thiamine pyrophosphate as a cofactor, suggesting there may be common aspects in their mechanism of catalysis.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 1NGS_B 1TKA_A 1TRK_B 1TKB_A 1GPU_B 1AY0_B 1TKC_B 2E6K_A 3JU3_A 2R8P_B ....
Probab=28.43 E-value=1.6e+02 Score=22.20 Aligned_cols=72 Identities=13% Similarity=-0.020 Sum_probs=44.7
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcC---CcChHHHHHHHHhhCCeeeccCC------cchHHHHH
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLG---AQNSAFLQQASYITGGVHHKPQQ------LDGLFQYL 129 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~---~~e~~iLqq~~~~TgG~Y~~~~~------~~~l~~~L 129 (213)
...|+||+.. .-.-..++++..+.+.+|.+.++.+. .-+...+.++...++-+..+-.+ ...+..+|
T Consensus 9 g~di~iia~G----~~~~~al~A~~~L~~~Gi~~~vi~~~~i~P~d~~~l~~~~~~~~~vvvvee~~~~gg~g~~i~~~l 84 (124)
T PF02780_consen 9 GADITIIAYG----SMVEEALEAAEELEEEGIKAGVIDLRTIKPFDEEALLESLKKTGRVVVVEEHYKIGGLGSAIAEYL 84 (124)
T ss_dssp SSSEEEEEET----THHHHHHHHHHHHHHTTCEEEEEEEEEEESSBHHHHHHHSHHHHHHHHSETCESEEEEHSSHHHHH
T ss_pred CCCEEEEeeh----HHHHHHHHHHHHHHHcCCceeEEeeEEEecccccchHHHHHHhccccccccccccccHHHHHHHHH
Confidence 3467777732 23445678888889999998888773 12566667766666555544333 23456666
Q ss_pred HHHcC
Q 028156 130 LTIFG 134 (213)
Q Consensus 130 l~~~~ 134 (213)
...-.
T Consensus 85 ~~~~~ 89 (124)
T PF02780_consen 85 AENGF 89 (124)
T ss_dssp HHHTT
T ss_pred HHhCC
Confidence 55443
No 189
>PRK06456 acetolactate synthase catalytic subunit; Reviewed
Probab=28.38 E-value=2.4e+02 Score=27.21 Aligned_cols=46 Identities=17% Similarity=0.273 Sum_probs=33.2
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHHH
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQA 108 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~ 108 (213)
.++++.|.| |.+.+|. ++.+.+|.++++++-++.+......+.++.
T Consensus 439 ~~~vv~i~G--DG~f~m~--~~eL~Ta~~~~l~i~ivV~NN~~yg~i~~~ 484 (572)
T PRK06456 439 DKVVVDLDG--DGSFLMT--GTNLATAVDEHIPVISVIFDNRTLGLVRQV 484 (572)
T ss_pred CCeEEEEEc--cchHhcc--hHHHHHHHHhCCCeEEEEEECCchHHHHHH
Confidence 456777775 6676766 578899999999999999964444455544
No 190
>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.
Probab=28.31 E-value=31 Score=30.08 Aligned_cols=14 Identities=14% Similarity=0.339 Sum_probs=9.5
Q ss_pred Cccccccccccccc
Q 028156 182 KKCSTCGSVFGQAQ 195 (213)
Q Consensus 182 ~~C~~C~~~f~~~~ 195 (213)
|+||.|+++=-|..
T Consensus 209 PiCPlCK~KsRSrn 222 (230)
T PF10146_consen 209 PICPLCKAKSRSRN 222 (230)
T ss_pred CCCcccccccccCC
Confidence 66777777666655
No 191
>PRK07765 para-aminobenzoate synthase component II; Provisional
Probab=28.09 E-value=1.8e+02 Score=24.57 Aligned_cols=53 Identities=19% Similarity=0.233 Sum_probs=39.7
Q ss_pred EEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHHHHHhhCCeeecc
Q 028156 61 RILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQASYITGGVHHKP 119 (213)
Q Consensus 61 rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~~~~TgG~Y~~~ 119 (213)
.-|||++++....+....++.+..+.+.+++|=-|.+| .|.++..-||.-...
T Consensus 48 dgliisGGp~~~~~~~~~~~~i~~~~~~~~PiLGIC~G------~Qlla~a~GG~v~~~ 100 (214)
T PRK07765 48 DGVLLSPGPGTPERAGASIDMVRACAAAGTPLLGVCLG------HQAIGVAFGATVDRA 100 (214)
T ss_pred CEEEECCCCCChhhcchHHHHHHHHHhCCCCEEEEccC------HHHHHHHhCCEEeeC
Confidence 34888877644444455668888889999998777776 578899999987754
No 192
>TIGR00441 gmhA phosphoheptose isomerase. Involved in lipopolysaccharide biosynthesis it may have a role in virulence in Haemophilus ducreyi.
Probab=27.85 E-value=62 Score=25.71 Aligned_cols=45 Identities=11% Similarity=0.089 Sum_probs=27.2
Q ss_pred cEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHHHHH
Q 028156 60 PRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQASY 110 (213)
Q Consensus 60 ~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~~~ 110 (213)
.-+++||.|..+. .+++.+..|++.|+++=++. .....-|.+.||
T Consensus 81 D~~i~iS~sG~t~----~~~~~~~~a~~~g~~ii~iT--~~~~s~l~~~ad 125 (154)
T TIGR00441 81 DVLLGISTSGNSK----NVLKAIEAAKDKGMKTITLA--GKDGGKMAGLAD 125 (154)
T ss_pred CEEEEEcCCCCCH----HHHHHHHHHHHCCCEEEEEe--CCCCCchhhhCC
Confidence 3456666665433 66788899999997764443 333334444444
No 193
>PRK06965 acetolactate synthase 3 catalytic subunit; Validated
Probab=27.83 E-value=2.5e+02 Score=27.27 Aligned_cols=44 Identities=14% Similarity=0.375 Sum_probs=31.6
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHH
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQ 106 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLq 106 (213)
.++++.|.| |.+.+|. .+.+.+|.++++++=++.+......+++
T Consensus 455 ~r~Vv~i~G--DGsf~m~--~~eL~Ta~r~~lpviivV~NN~~~~~i~ 498 (587)
T PRK06965 455 DDDVVCITG--EGSIQMC--IQELSTCLQYDTPVKIISLNNRYLGMVR 498 (587)
T ss_pred CCcEEEEEc--chhhhcC--HHHHHHHHHcCCCeEEEEEECCcchHHH
Confidence 457777775 6676666 4778999999999999999544333443
No 194
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=27.79 E-value=25 Score=24.74 Aligned_cols=37 Identities=22% Similarity=0.459 Sum_probs=28.6
Q ss_pred eeEcCCCCc---cccCCC--------CccccccccccccccCCCCCcc
Q 028156 167 GYICSVCLS---IYCKHL--------KKCSTCGSVFGQAQTQSDEPSA 203 (213)
Q Consensus 167 GyvCp~Cls---i~C~~p--------~~C~~C~~~f~~~~~~~~~~~~ 203 (213)
...||+|.| +||.+. -.|..|.-.+.....++.-|..
T Consensus 5 ~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~GG~lRnVPvg 52 (63)
T PF02701_consen 5 PLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTHGGTLRNVPVG 52 (63)
T ss_pred CCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHhcceecCCccC
Confidence 567999987 788642 5899999999988866666644
No 195
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=27.46 E-value=31 Score=24.38 Aligned_cols=23 Identities=22% Similarity=0.436 Sum_probs=15.2
Q ss_pred EcCCCCccccCCCCccccccccccc
Q 028156 169 ICSVCLSIYCKHLKKCSTCGSVFGQ 193 (213)
Q Consensus 169 vCp~Clsi~C~~p~~C~~C~~~f~~ 193 (213)
.|-.|..+. -...||.||..-.+
T Consensus 7 AC~~C~~i~--~~~~Cp~Cgs~~~S 29 (64)
T PRK06393 7 ACKKCKRLT--PEKTCPVHGDEKTT 29 (64)
T ss_pred hHhhCCccc--CCCcCCCCCCCcCC
Confidence 466677666 34578888887433
No 196
>COG0512 PabA Anthranilate/para-aminobenzoate synthases component II [Amino acid transport and metabolism / Coenzyme metabolism]
Probab=27.31 E-value=1.8e+02 Score=24.79 Aligned_cols=60 Identities=18% Similarity=0.228 Sum_probs=48.6
Q ss_pred CCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHHHHHhhCCeeeccCCcch
Q 028156 58 PQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQASYITGGVHHKPQQLDG 124 (213)
Q Consensus 58 ~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~~~~TgG~Y~~~~~~~~ 124 (213)
.+...+|||-.+.++.++...+++|..+ ..+++|=-|-|| .|-+++.-||.-..+..+-|
T Consensus 44 ~~pd~iviSPGPG~P~d~G~~~~~i~~~-~~~~PiLGVCLG------HQai~~~fGg~V~~a~~~~H 103 (191)
T COG0512 44 LKPDAIVISPGPGTPKDAGISLELIRRF-AGRIPILGVCLG------HQAIAEAFGGKVVRAKEPMH 103 (191)
T ss_pred cCCCEEEEcCCCCChHHcchHHHHHHHh-cCCCCEEEECcc------HHHHHHHhCCEEEecCCCcC
Confidence 4567899997777888999999999888 788999888886 47789999998888765433
No 197
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=26.62 E-value=46 Score=23.15 Aligned_cols=24 Identities=25% Similarity=0.883 Sum_probs=15.3
Q ss_pred ceeEcCCCCcc---ccC------CCCccccccc
Q 028156 166 MGYICSVCLSI---YCK------HLKKCSTCGS 189 (213)
Q Consensus 166 ~GyvCp~Clsi---~C~------~p~~C~~C~~ 189 (213)
+.|.||.|... -|+ .+-.||.||.
T Consensus 24 ~~F~CPnCG~~~I~RC~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 24 VKFLCPNCGEVIIYRCEKCRKQSNPYTCPKCGF 56 (59)
T ss_pred CEeeCCCCCCeeEeechhHHhcCCceECCCCCC
Confidence 45889999765 122 2457887774
No 198
>PHA00733 hypothetical protein
Probab=26.50 E-value=40 Score=26.54 Aligned_cols=30 Identities=33% Similarity=0.891 Sum_probs=22.0
Q ss_pred ceeEcCCCCccccC------------CCCccccccccccccc
Q 028156 166 MGYICSVCLSIYCK------------HLKKCSTCGSVFGQAQ 195 (213)
Q Consensus 166 ~GyvCp~Clsi~C~------------~p~~C~~C~~~f~~~~ 195 (213)
..|+|+.|.-.|-. .+-.|..|+..|....
T Consensus 72 kPy~C~~Cgk~Fss~s~L~~H~r~h~~~~~C~~CgK~F~~~~ 113 (128)
T PHA00733 72 SPYVCPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKEFRNTD 113 (128)
T ss_pred CCccCCCCCCcCCCHHHHHHHHhcCCcCccCCCCCCccCCHH
Confidence 35888888876552 2458999999988754
No 199
>COG0794 GutQ Predicted sugar phosphate isomerase involved in capsule formation [Cell envelope biogenesis, outer membrane]
Probab=26.43 E-value=1.3e+02 Score=25.91 Aligned_cols=71 Identities=13% Similarity=0.132 Sum_probs=44.3
Q ss_pred cccchHhHHHHHHHHHhhhh---h------c-CC-CCCCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCc
Q 028156 32 ACSLLSGSLSMALCYIQRVF---R------S-GL-LHPQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQ 100 (213)
Q Consensus 32 ~~s~L~~aLs~ALc~inr~~---~------~-~~-~~~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~ 100 (213)
.+..++..+++-|-++=.-. . . .+ -.-..-++.||+|.++. .+.|.+..||+.+++|=.+.- .+
T Consensus 49 kSG~Igkk~Aa~L~s~G~~a~fv~p~ea~hgdlg~i~~~DvviaiS~SGeT~----el~~~~~~aK~~g~~liaiT~-~~ 123 (202)
T COG0794 49 KSGLIGKKFAARLASTGTPAFFVGPAEALHGDLGMITPGDVVIAISGSGETK----ELLNLAPKAKRLGAKLIAITS-NP 123 (202)
T ss_pred hhHHHHHHHHHHHHccCCceEEecCchhccCCccCCCCCCEEEEEeCCCcHH----HHHHHHHHHHHcCCcEEEEeC-CC
Confidence 35566777777766532210 0 0 11 12334566678887665 678999999999999877766 46
Q ss_pred ChHHHHH
Q 028156 101 NSAFLQQ 107 (213)
Q Consensus 101 e~~iLqq 107 (213)
++.+=+.
T Consensus 124 ~SsLak~ 130 (202)
T COG0794 124 DSSLAKA 130 (202)
T ss_pred CChHHHh
Confidence 6665544
No 200
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=26.39 E-value=34 Score=23.89 Aligned_cols=21 Identities=33% Similarity=0.700 Sum_probs=13.0
Q ss_pred EcCCCCccccCCCCccccccccc
Q 028156 169 ICSVCLSIYCKHLKKCSTCGSVF 191 (213)
Q Consensus 169 vCp~Clsi~C~~p~~C~~C~~~f 191 (213)
.|-.|..+. -...||.||..-
T Consensus 5 AC~~C~~i~--~~~~CP~Cgs~~ 25 (61)
T PRK08351 5 ACRHCHYIT--TEDRCPVCGSRD 25 (61)
T ss_pred hhhhCCccc--CCCcCCCCcCCc
Confidence 466666666 234688887754
No 201
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=26.28 E-value=28 Score=33.89 Aligned_cols=30 Identities=30% Similarity=0.759 Sum_probs=22.7
Q ss_pred ceeEcCCCCc------------ccc-------------CCCCccccccccccccc
Q 028156 166 MGYICSVCLS------------IYC-------------KHLKKCSTCGSVFGQAQ 195 (213)
Q Consensus 166 ~GyvCp~Cls------------i~C-------------~~p~~C~~C~~~f~~~~ 195 (213)
.++.||+||. +|| .-+..||.|..++...-
T Consensus 185 t~~~CPICL~~~~~p~~t~CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~kd 239 (513)
T KOG2164|consen 185 TDMQCPICLEPPSVPVRTNCGHIFCGPCILQYWNYSAIKGPCSCPICRSTITLKD 239 (513)
T ss_pred cCCcCCcccCCCCcccccccCceeeHHHHHHHHhhhcccCCccCCchhhhccccc
Confidence 3899999987 676 23578999999887633
No 202
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=26.25 E-value=35 Score=22.68 Aligned_cols=25 Identities=28% Similarity=0.616 Sum_probs=15.2
Q ss_pred eeEcCCCCc-cccCC--CCccccccccc
Q 028156 167 GYICSVCLS-IYCKH--LKKCSTCGSVF 191 (213)
Q Consensus 167 GyvCp~Cls-i~C~~--p~~C~~C~~~f 191 (213)
.=.||.|.+ +.=.. .-.|..||.+.
T Consensus 20 ~~fCP~Cg~~~m~~~~~r~~C~~Cgyt~ 47 (50)
T PRK00432 20 NKFCPRCGSGFMAEHLDRWHCGKCGYTE 47 (50)
T ss_pred cCcCcCCCcchheccCCcEECCCcCCEE
Confidence 336888887 33322 34788887654
No 203
>PRK08527 acetolactate synthase 3 catalytic subunit; Validated
Probab=26.11 E-value=2.5e+02 Score=27.13 Aligned_cols=70 Identities=13% Similarity=0.217 Sum_probs=43.2
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHH-----------------------HHHHhhCCe
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQ-----------------------QASYITGGV 115 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLq-----------------------q~~~~TgG~ 115 (213)
.+++++|.| |.+.+|. ++.+.+|.+.|+++=++.+......+.+ ++++.-|+.
T Consensus 432 ~~~vv~i~G--DG~f~m~--~~eL~Ta~~~~lpvi~vV~NN~~~~~i~~~~~~~~~~~~~~~~~~~~~d~~~~a~a~G~~ 507 (563)
T PRK08527 432 DKVVINFTG--DGSILMN--IQELMTAVEYKIPVINIILNNNFLGMVRQWQTFFYEERYSETDLSTQPDFVKLAESFGGI 507 (563)
T ss_pred CCcEEEEec--Cchhccc--HHHHHHHHHhCCCeEEEEEECCcchhHHHHHHhhcCCceeeccCCCCCCHHHHHHHCCCe
Confidence 457777775 6666663 3567888999999988888533323333 344455555
Q ss_pred eeccCCcchHHHHHHHH
Q 028156 116 HHKPQQLDGLFQYLLTI 132 (213)
Q Consensus 116 Y~~~~~~~~l~~~Ll~~ 132 (213)
|..+.+.+.|.+.|-..
T Consensus 508 ~~~v~~~~el~~al~~a 524 (563)
T PRK08527 508 GFRVTTKEEFDKALKEA 524 (563)
T ss_pred EEEECCHHHHHHHHHHH
Confidence 55555555555555443
No 204
>CHL00099 ilvB acetohydroxyacid synthase large subunit
Probab=26.09 E-value=2.9e+02 Score=26.87 Aligned_cols=45 Identities=16% Similarity=0.338 Sum_probs=31.6
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHH
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQ 107 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq 107 (213)
.++++.|.| |.+.+|. ++.+.+|.+.++++=++.+......++++
T Consensus 448 ~~~vv~i~G--DG~f~m~--~~eL~Ta~~~~l~~~~vV~NN~~y~~i~~ 492 (585)
T CHL00099 448 NELVICISG--DASFQMN--LQELGTIAQYNLPIKIIIINNKWQGMVRQ 492 (585)
T ss_pred CCeEEEEEc--chhhhhh--HHHHHHHHHhCCCeEEEEEECCcchHHHH
Confidence 467777775 6676665 46889999999999888885433344443
No 205
>PRK12474 hypothetical protein; Provisional
Probab=25.63 E-value=3e+02 Score=26.24 Aligned_cols=45 Identities=24% Similarity=0.540 Sum_probs=33.5
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHH
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQ 107 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq 107 (213)
.++++.|.| |.+.++. +..+.+|.+.++++-++.+....-.++++
T Consensus 407 ~r~vv~i~G--DG~f~m~--~qEL~Ta~r~~lpv~iiV~NN~~y~~i~~ 451 (518)
T PRK12474 407 DRKVVCPQG--DGGAAYT--MQALWTMARENLDVTVVIFANRSYAILNG 451 (518)
T ss_pred CCcEEEEEc--Cchhcch--HHHHHHHHHHCCCcEEEEEcCCcchHHHH
Confidence 567887776 6676766 57889999999999999995444445553
No 206
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=25.58 E-value=65 Score=34.86 Aligned_cols=13 Identities=23% Similarity=0.585 Sum_probs=7.4
Q ss_pred ccccccccccccc
Q 028156 183 KCSTCGSVFGQAQ 195 (213)
Q Consensus 183 ~C~~C~~~f~~~~ 195 (213)
.|+-||+.++...
T Consensus 711 ~CP~CGtplv~~~ 723 (1337)
T PRK14714 711 ECPRCDVELTPYQ 723 (1337)
T ss_pred cCCCCCCcccccc
Confidence 5666666655443
No 207
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=25.35 E-value=37 Score=22.03 Aligned_cols=13 Identities=38% Similarity=0.789 Sum_probs=10.2
Q ss_pred CC-Ccccccccccc
Q 028156 180 HL-KKCSTCGSVFG 192 (213)
Q Consensus 180 ~p-~~C~~C~~~f~ 192 (213)
+| ..|++||..|.
T Consensus 6 lp~K~C~~C~rpf~ 19 (42)
T PF10013_consen 6 LPSKICPVCGRPFT 19 (42)
T ss_pred CCCCcCcccCCcch
Confidence 44 58999998886
No 208
>PRK11269 glyoxylate carboligase; Provisional
Probab=25.34 E-value=2.6e+02 Score=27.19 Aligned_cols=71 Identities=10% Similarity=0.102 Sum_probs=47.3
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHH--------------------------------
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQ-------------------------------- 106 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLq-------------------------------- 106 (213)
.++++.|.| |.+.+|. .+.+.+|.+.++++-++.+......+++
T Consensus 437 ~r~Vv~i~G--DG~f~m~--~~eL~Ta~~~~lpv~~vV~NN~~~g~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~df~ 512 (591)
T PRK11269 437 DRNVVALSG--DYDFQFL--IEELAVGAQFNLPYIHVLVNNAYLGLIRQAQRAFDMDYCVQLAFENINSPELNGYGVDHV 512 (591)
T ss_pred CCcEEEEEc--cchhhcC--HHHHHHHHHhCCCeEEEEEeCCchhHHHHHHHHhccCccceeeccccccccccCCCCCHH
Confidence 467777775 6676665 4778999999999999988533222333
Q ss_pred HHHHhhCCeeeccCCcchHHHHHHHHc
Q 028156 107 QASYITGGVHHKPQQLDGLFQYLLTIF 133 (213)
Q Consensus 107 q~~~~TgG~Y~~~~~~~~l~~~Ll~~~ 133 (213)
++++..|+.+..+.+.+.|.+-|-..+
T Consensus 513 ~lA~a~G~~~~~v~~~~eL~~al~~a~ 539 (591)
T PRK11269 513 KVAEGLGCKAIRVFKPEDIAPALEQAK 539 (591)
T ss_pred HHHHHCCCeEEEECCHHHHHHHHHHHH
Confidence 455555666666666777766665544
No 209
>PHA02566 alt ADP-ribosyltransferase; Provisional
Probab=25.16 E-value=73 Score=32.16 Aligned_cols=50 Identities=16% Similarity=0.161 Sum_probs=35.1
Q ss_pred CCcchhhHHHHHHHHH---hCCeeeeEEEcC------CcChHHHHHHHH-----hhCCeeeccC
Q 028156 71 GPEQYVAIMNAIFSAQ---RSMVPIDSCYLG------AQNSAFLQQASY-----ITGGVHHKPQ 120 (213)
Q Consensus 71 ~~~qyi~imn~if~aq---k~~I~Idv~~L~------~~e~~iLqq~~~-----~TgG~Y~~~~ 120 (213)
-++++|+.||+||.-. =.+.++|+|-+- .+....+|.+++ .|||.|.+..
T Consensus 84 LG~~PI~amN~ifd~v~~~m~k~r~DA~lfRfptkk~kGq~~~vqrI~~RLv~~r~gGrf~vl~ 147 (684)
T PHA02566 84 LGSDPIGAMNSIFDVVMETMKKYRMDAVLFRFPTKKLKGQAKTVQRIAERLVRTRGGGRFKVLP 147 (684)
T ss_pred CCCChHHHHHHHHHHHHHHHHHhccceeEEecchhhhcCcchHHHHHHHHHHhcccCCcEEEeH
Confidence 4689999999988642 245788988773 134455555554 7899999864
No 210
>PRK06466 acetolactate synthase 3 catalytic subunit; Validated
Probab=24.81 E-value=3.4e+02 Score=26.23 Aligned_cols=45 Identities=16% Similarity=0.347 Sum_probs=32.6
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHH
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQ 107 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq 107 (213)
.++++.|.| |.+.+|. ++.+.+|.++|+++-++.+......++++
T Consensus 441 ~r~Vv~i~G--DG~f~m~--~~eL~Ta~r~~lpv~ivV~NN~~y~~i~~ 485 (574)
T PRK06466 441 DQDVACVTG--EGSIQMN--IQELSTCLQYGLPVKIINLNNGALGMVRQ 485 (574)
T ss_pred CCeEEEEEc--chhhhcc--HHHHHHHHHhCCCeEEEEEeCCccHHHHH
Confidence 467777775 6676666 47889999999999999985433344444
No 211
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=24.70 E-value=46 Score=27.02 Aligned_cols=34 Identities=18% Similarity=0.442 Sum_probs=23.7
Q ss_pred eeeccCccc-ceeEcCCCCccccCC----CCcccccccc
Q 028156 157 CFCHKNTID-MGYICSVCLSIYCKH----LKKCSTCGSV 190 (213)
Q Consensus 157 C~CH~~~v~-~GyvCp~Clsi~C~~----p~~C~~C~~~ 190 (213)
++..+.++. .-|+|-.|.-...-. -+.||.||-.
T Consensus 101 ~Y~sGE~~g~G~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 101 VYHSGEVVGPGTLVCENCGHEVELTHPERLPPCPKCGHT 139 (146)
T ss_pred CeecCcEecCceEecccCCCEEEecCCCcCCCCCCCCCC
Confidence 444555544 469999999988742 3679999853
No 212
>PF00535 Glycos_transf_2: Glycosyl transferase family 2; InterPro: IPR001173 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. This domain is found in a diverse family of glycosyl transferases that transfer the sugar from UDP-glucose, UDP-N-acetyl-galactosamine, GDP-mannose or CDP-abequose, to a range of substrates including cellulose, dolichol phosphate and teichoic acids.; PDB: 2Z87_A 2Z86_B 2D7R_A 2D7I_A 3CKN_A 3CKQ_A 3CKJ_A 3CKV_A 3CKO_A 2FFU_A ....
Probab=23.78 E-value=2.9e+02 Score=20.10 Aligned_cols=70 Identities=19% Similarity=0.085 Sum_probs=43.3
Q ss_pred CCCcEEEEEe-cCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcC---hHHHHHHHHhhCCeeeccCCcc-----hHHH
Q 028156 57 HPQPRILCLQ-GSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQN---SAFLQQASYITGGVHHKPQQLD-----GLFQ 127 (213)
Q Consensus 57 ~~~~rILiis-~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e---~~iLqq~~~~TgG~Y~~~~~~~-----~l~~ 127 (213)
...-+|+|+. +|.|.. .+.+....+.+..+.++... .. ..-+..+.+...|.|+...|.+ +.++
T Consensus 25 ~~~~eiivvdd~s~d~~------~~~~~~~~~~~~~i~~i~~~-~n~g~~~~~n~~~~~a~~~~i~~ld~D~~~~~~~l~ 97 (169)
T PF00535_consen 25 DPDFEIIVVDDGSTDET------EEILEEYAESDPNIRYIRNP-ENLGFSAARNRGIKHAKGEYILFLDDDDIISPDWLE 97 (169)
T ss_dssp GCEEEEEEEECS-SSSH------HHHHHHHHCCSTTEEEEEHC-CCSHHHHHHHHHHHH--SSEEEEEETTEEE-TTHHH
T ss_pred CCCEEEEEecccccccc------cccccccccccccccccccc-ccccccccccccccccceeEEEEeCCCceEcHHHHH
Confidence 3566888887 433322 34555556678888899884 44 3456678888889999987753 3555
Q ss_pred HHHHHc
Q 028156 128 YLLTIF 133 (213)
Q Consensus 128 ~Ll~~~ 133 (213)
.|+..+
T Consensus 98 ~l~~~~ 103 (169)
T PF00535_consen 98 ELVEAL 103 (169)
T ss_dssp HHHHHH
T ss_pred HHHHHH
Confidence 555444
No 213
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=23.75 E-value=39 Score=26.01 Aligned_cols=31 Identities=23% Similarity=0.578 Sum_probs=22.0
Q ss_pred ccceeEcCCCCcc---ccCC-------CCcccccccccccc
Q 028156 164 IDMGYICSVCLSI---YCKH-------LKKCSTCGSVFGQA 194 (213)
Q Consensus 164 v~~GyvCp~Clsi---~C~~-------p~~C~~C~~~f~~~ 194 (213)
.+.-|.||+|... .|.+ ...|..||+.|-.-
T Consensus 19 L~k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~e 59 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFECE 59 (104)
T ss_pred CCceEecCccCCeeeeEEEEEecCceeEEEcccCcceEEEe
Confidence 3556999999864 3322 36899999998654
No 214
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=23.53 E-value=29 Score=22.92 Aligned_cols=12 Identities=25% Similarity=0.769 Sum_probs=5.2
Q ss_pred cccccccccccc
Q 028156 183 KCSTCGSVFGQA 194 (213)
Q Consensus 183 ~C~~C~~~f~~~ 194 (213)
.||+|+..|...
T Consensus 22 ~CPlC~r~l~~e 33 (54)
T PF04423_consen 22 CCPLCGRPLDEE 33 (54)
T ss_dssp E-TTT--EE-HH
T ss_pred cCCCCCCCCCHH
Confidence 677777777643
No 215
>PRK08155 acetolactate synthase catalytic subunit; Validated
Probab=23.49 E-value=2.8e+02 Score=26.75 Aligned_cols=70 Identities=13% Similarity=0.178 Sum_probs=43.5
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHH-----------------------HHHHhhCCe
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQ-----------------------QASYITGGV 115 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLq-----------------------q~~~~TgG~ 115 (213)
.++++.|.| |.+.+|. ++.+.+|.+.++++=++.+......+++ ++++..|+.
T Consensus 437 ~~~vv~i~G--DGsf~~~--~~eL~ta~~~~lpvi~vV~NN~~~g~~~~~q~~~~~~~~~~~~~~~~~d~~~~a~a~G~~ 512 (564)
T PRK08155 437 ERKVLCFSG--DGSLMMN--IQEMATAAENQLDVKIILMNNEALGLVHQQQSLFYGQRVFAATYPGKINFMQIAAGFGLE 512 (564)
T ss_pred CCcEEEEEc--cchhhcc--HHHHHHHHHhCCCeEEEEEeCCcccccHHHHHHhcCCCeeeccCCCCCCHHHHHHHCCCe
Confidence 456776765 6777774 4667788999999988888533223332 345555555
Q ss_pred eeccCCcchHHHHHHHH
Q 028156 116 HHKPQQLDGLFQYLLTI 132 (213)
Q Consensus 116 Y~~~~~~~~l~~~Ll~~ 132 (213)
+..+.+.+.|.+.|-..
T Consensus 513 ~~~v~~~~el~~al~~a 529 (564)
T PRK08155 513 TCDLNNEADPQAALQEA 529 (564)
T ss_pred EEEeCCHHHHHHHHHHH
Confidence 55566666665555444
No 216
>cd02009 TPP_SHCHC_synthase Thiamine pyrophosphate (TPP) family, SHCHC synthase subfamily, TPP-binding module; composed of proteins similar to Escherichia coli 2-succinyl-6-hydroxyl-2,4-cyclohexadiene-1-carboxylic acid (SHCHC) synthase (also called MenD). SHCHC synthase plays a key role in the menaquinone biosynthetic pathway, converting isochorismate and 2-oxoglutarate to SHCHC, pyruvate and carbon dioxide. The enzyme requires TPP and a divalent metal cation for activity.
Probab=23.44 E-value=1.5e+02 Score=23.88 Aligned_cols=36 Identities=11% Similarity=0.140 Sum_probs=27.2
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcC
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLG 98 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~ 98 (213)
.++++.|.| |.+-+|. ++.+.+|.+.++++-++.+.
T Consensus 68 ~~~Vv~i~G--DGsf~m~--~~eL~ta~~~~l~v~ivVlN 103 (175)
T cd02009 68 DKPTVLLTG--DLSFLHD--LNGLLLGKQEPLNLTIVVIN 103 (175)
T ss_pred CCCEEEEEe--hHHHHHh--HHHHHhccccCCCeEEEEEE
Confidence 456777765 5665655 57788899999999999885
No 217
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=23.40 E-value=57 Score=30.38 Aligned_cols=30 Identities=37% Similarity=0.886 Sum_probs=22.9
Q ss_pred cceeE--cCCCCcccc---CCCCcccccccccccc
Q 028156 165 DMGYI--CSVCLSIYC---KHLKKCSTCGSVFGQA 194 (213)
Q Consensus 165 ~~Gyv--Cp~Clsi~C---~~p~~C~~C~~~f~~~ 194 (213)
.+||+ |+.|....= ..+..|+.||..++..
T Consensus 240 ~~g~~~~C~~c~~~~~~~~~~~~~C~~c~~~~~~~ 274 (382)
T PRK04338 240 NLGYVYYCPKCLYREEVEGLPPEECPVCGGKFGTA 274 (382)
T ss_pred hceeEEECCCCCcEEEecCCCCCCCCCCCCcceec
Confidence 46888 999998542 3467899999987654
No 218
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=23.37 E-value=49 Score=31.12 Aligned_cols=29 Identities=38% Similarity=0.715 Sum_probs=21.6
Q ss_pred ce--eEcCCCCccc---cCCCCcccccccccccc
Q 028156 166 MG--YICSVCLSIY---CKHLKKCSTCGSVFGQA 194 (213)
Q Consensus 166 ~G--yvCp~Clsi~---C~~p~~C~~C~~~f~~~ 194 (213)
.| |.|+.|+-++ -+....|+.||..+...
T Consensus 237 ~g~~~~c~~cg~~~~~~~~~~~~c~~Cg~~~~~~ 270 (380)
T COG1867 237 LGYIYHCSRCGEIVGSFREVDEKCPHCGGKVHLA 270 (380)
T ss_pred cCcEEEcccccceecccccccccCCcccccceec
Confidence 46 8899997333 34458999999988764
No 219
>cd06167 LabA_like LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression.
Probab=23.36 E-value=2e+02 Score=21.99 Aligned_cols=44 Identities=18% Similarity=0.190 Sum_probs=31.1
Q ss_pred cEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHHHHH
Q 028156 60 PRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQASY 110 (213)
Q Consensus 60 ~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~~~ 110 (213)
..|+++|+ |. +|.+++ ..+++.+.+|-+++....-+.-|+.+||
T Consensus 101 d~ivLvSg--D~--Df~~~i---~~lr~~G~~V~v~~~~~~~s~~L~~~~d 144 (149)
T cd06167 101 DTIVLVSG--DS--DFVPLV---ERLRELGKRVIVVGFEAKTSRELRKAAD 144 (149)
T ss_pred CEEEEEEC--Cc--cHHHHH---HHHHHcCCEEEEEccCccChHHHHHhCC
Confidence 46666765 32 566555 5559999999999884356778888777
No 220
>cd05006 SIS_GmhA Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of gram-negative bacteria inner core lipopolysaccharide precursor, L-glycero-D-mannoheptose (Gmh).
Probab=23.25 E-value=1.1e+02 Score=24.51 Aligned_cols=45 Identities=13% Similarity=0.187 Sum_probs=27.6
Q ss_pred EEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHHHHHh
Q 028156 61 RILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQASYI 111 (213)
Q Consensus 61 rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~~~~ 111 (213)
-+++||.|+.+. ++.+++..|++.++++=++. .....-|.+.||.
T Consensus 104 v~I~iS~SG~t~----~~i~~~~~ak~~Ga~vI~IT--~~~~s~La~~aD~ 148 (177)
T cd05006 104 VLIGISTSGNSP----NVLKALEAAKERGMKTIALT--GRDGGKLLELADI 148 (177)
T ss_pred EEEEEeCCCCCH----HHHHHHHHHHHCCCEEEEEe--CCCCCchhhhCCE
Confidence 455566665444 67788899999997764443 2233336666654
No 221
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=23.24 E-value=32 Score=26.75 Aligned_cols=26 Identities=27% Similarity=0.522 Sum_probs=19.1
Q ss_pred EcCCCCccccCCC---Ccccccccccccc
Q 028156 169 ICSVCLSIYCKHL---KKCSTCGSVFGQA 194 (213)
Q Consensus 169 vCp~Clsi~C~~p---~~C~~C~~~f~~~ 194 (213)
-||.|.|-|-..- -+||-|+-.....
T Consensus 4 ~CP~C~seytY~dg~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 4 PCPKCNSEYTYHDGTQLICPSCLYEWNEN 32 (109)
T ss_pred cCCcCCCcceEecCCeeECcccccccccc
Confidence 4899999888643 5899998776543
No 222
>PRK00414 gmhA phosphoheptose isomerase; Reviewed
Probab=23.17 E-value=1e+02 Score=25.60 Aligned_cols=45 Identities=16% Similarity=0.148 Sum_probs=27.4
Q ss_pred EEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHHHHHh
Q 028156 61 RILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQASYI 111 (213)
Q Consensus 61 rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~~~~ 111 (213)
-+++||.|..+. +++..+..|++.++++=++. .....-|.+.||.
T Consensus 114 v~I~iS~SG~t~----~~i~~~~~ak~~g~~iI~iT--~~~~s~l~~~ad~ 158 (192)
T PRK00414 114 VLLGISTSGNSG----NIIKAIEAARAKGMKVITLT--GKDGGKMAGLADI 158 (192)
T ss_pred EEEEEeCCCCCH----HHHHHHHHHHHCCCeEEEEe--CCCCChhHHhCCE
Confidence 455566665444 67788899999997764443 3333344444443
No 223
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=22.96 E-value=60 Score=25.02 Aligned_cols=23 Identities=17% Similarity=0.521 Sum_probs=11.0
Q ss_pred eEcCCCCccccCC--C-Ccccccccc
Q 028156 168 YICSVCLSIYCKH--L-KKCSTCGSV 190 (213)
Q Consensus 168 yvCp~Clsi~C~~--p-~~C~~C~~~ 190 (213)
+.|..|...|=.. . ..||.||..
T Consensus 71 ~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 71 CWCETCQQYVTLLTQRVRRCPQCHGD 96 (114)
T ss_pred EEcccCCCeeecCCccCCcCcCcCCC
Confidence 4455555544332 1 336666644
No 224
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=22.96 E-value=46 Score=26.17 Aligned_cols=28 Identities=32% Similarity=0.758 Sum_probs=18.7
Q ss_pred ceeEcCCCCccccCCCC------ccccccccccc
Q 028156 166 MGYICSVCLSIYCKHLK------KCSTCGSVFGQ 193 (213)
Q Consensus 166 ~GyvCp~Clsi~C~~p~------~C~~C~~~f~~ 193 (213)
.-|+|+.|...+-.... .|+.|+-.|+.
T Consensus 122 ~~~~C~~C~~~~~r~~~~~~~~~~C~~C~~~l~~ 155 (157)
T PF10263_consen 122 YVYRCPSCGREYKRHRRSKRKRYRCGRCGGPLVQ 155 (157)
T ss_pred eEEEcCCCCCEeeeecccchhhEECCCCCCEEEE
Confidence 46888888866543322 58888877763
No 225
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=22.89 E-value=28 Score=32.41 Aligned_cols=26 Identities=27% Similarity=0.681 Sum_probs=20.7
Q ss_pred EcCCCCccccC-----CCCcccccccccccc
Q 028156 169 ICSVCLSIYCK-----HLKKCSTCGSVFGQA 194 (213)
Q Consensus 169 vCp~Clsi~C~-----~p~~C~~C~~~f~~~ 194 (213)
.|++|.++|-- ....|+.||-+++..
T Consensus 248 AC~rC~t~y~le~A~~~~wrCpkCGg~ikKG 278 (403)
T COG1379 248 ACSRCYTRYSLEEAKSLRWRCPKCGGKIKKG 278 (403)
T ss_pred HHHHhhhccCcchhhhhcccCcccccchhhh
Confidence 49999999884 347999999988743
No 226
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.86 E-value=19 Score=33.50 Aligned_cols=34 Identities=29% Similarity=0.773 Sum_probs=25.6
Q ss_pred CcccceeEcCCCCcc-------------ccC---------CCCccccccccccccc
Q 028156 162 NTIDMGYICSVCLSI-------------YCK---------HLKKCSTCGSVFGQAQ 195 (213)
Q Consensus 162 ~~v~~GyvCp~Clsi-------------~C~---------~p~~C~~C~~~f~~~~ 195 (213)
..++.-+.||+||++ ||. -...||+|...++|.-
T Consensus 38 ~~~~~~v~c~icl~llk~tmttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~Skr 93 (381)
T KOG0311|consen 38 AMFDIQVICPICLSLLKKTMTTKECLHRFCFDCIWKALRSGNNECPTCRKKLVSKR 93 (381)
T ss_pred HHhhhhhccHHHHHHHHhhcccHHHHHHHHHHHHHHHHHhcCCCCchHHhhccccc
Confidence 345667889888874 553 2479999999999976
No 227
>PLN00209 ribosomal protein S27; Provisional
Probab=22.82 E-value=35 Score=25.47 Aligned_cols=27 Identities=26% Similarity=0.626 Sum_probs=21.2
Q ss_pred EcCCCCccccCC-----CCccccccccccccc
Q 028156 169 ICSVCLSIYCKH-----LKKCSTCGSVFGQAQ 195 (213)
Q Consensus 169 vCp~Clsi~C~~-----p~~C~~C~~~f~~~~ 195 (213)
-||.|..+.--+ ...|..||+.|..+.
T Consensus 38 kCp~C~n~q~VFShA~t~V~C~~Cg~~L~~PT 69 (86)
T PLN00209 38 KCQGCFNITTVFSHSQTVVVCGSCQTVLCQPT 69 (86)
T ss_pred ECCCCCCeeEEEecCceEEEccccCCEeeccC
Confidence 489998765543 479999999998766
No 228
>cd03812 GT1_CapH_like This family is most closely related to the GT1 family of glycosyltransferases. capH in Staphylococcus aureus has been shown to be required for the biosynthesis of the type 1 capsular polysaccharide (CP1).
Probab=22.71 E-value=3.9e+02 Score=22.76 Aligned_cols=38 Identities=24% Similarity=0.201 Sum_probs=22.9
Q ss_pred EEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcC
Q 028156 61 RILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLG 98 (213)
Q Consensus 61 rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~ 98 (213)
|||++..+.+.+..-.-+.+...++.+.+..|+++...
T Consensus 1 kIl~~~~~~~~GG~~~~~~~l~~~L~~~~~~v~~i~~~ 38 (358)
T cd03812 1 KILHIVGTMNRGGIETFIMNYYRNLDRSKIQFDFLVTS 38 (358)
T ss_pred CEEEEeCCCCCccHHHHHHHHHHhcCccceEEEEEEeC
Confidence 46666655444444444556666666677777777763
No 229
>KOG4602 consensus Nanos and related proteins [General function prediction only]
Probab=22.64 E-value=42 Score=30.15 Aligned_cols=20 Identities=25% Similarity=0.653 Sum_probs=12.3
Q ss_pred ceeEcCCCCc--------cccCCCCccc
Q 028156 166 MGYICSVCLS--------IYCKHLKKCS 185 (213)
Q Consensus 166 ~GyvCp~Cls--------i~C~~p~~C~ 185 (213)
.-||||+|.+ +||-+-..|.
T Consensus 267 R~YVCPiCGATgDnAHTiKyCPl~~~~~ 294 (318)
T KOG4602|consen 267 RSYVCPICGATGDNAHTIKYCPLAFGDD 294 (318)
T ss_pred hhhcCccccccCCcccceecccccCCCC
Confidence 4677888876 5665544443
No 230
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=22.47 E-value=64 Score=24.82 Aligned_cols=22 Identities=23% Similarity=0.501 Sum_probs=10.6
Q ss_pred eEcCCCCccccC--CCCccccccc
Q 028156 168 YICSVCLSIYCK--HLKKCSTCGS 189 (213)
Q Consensus 168 yvCp~Clsi~C~--~p~~C~~C~~ 189 (213)
+.|..|...|=. ..-.||.||.
T Consensus 71 ~~C~~Cg~~~~~~~~~~~CP~Cgs 94 (113)
T PRK12380 71 AWCWDCSQVVEIHQHDAQCPHCHG 94 (113)
T ss_pred EEcccCCCEEecCCcCccCcCCCC
Confidence 455555544432 1223666664
No 231
>PF02525 Flavodoxin_2: Flavodoxin-like fold; InterPro: IPR003680 This family consists of a domain with a flavodoxin-like fold. The family includes bacterial and eukaryotic NAD(P)H dehydrogenase (quinone) 1.6.99.2 from EC. These enzymes catalyse the NAD(P)H-dependent two-electron reductions of quinones and protect cells against damage by free radicals and reactive oxygen species []. This enzyme uses a FAD cofactor. The equation for this reaction is NAD(P)H + acceptor = NAD(P)(+) + reduced acceptor. This enzyme is also involved in the bioactivation of prodrugs used in chemotherapy []. The family also includes acyl carrier protein phosphodiesterase 3.1.4.14 from EC. This enzyme converts holo-ACP to apo-ACP by hydrolytic cleavage of the phosphopantetheine residue from ACP []. This family is related to FMN_red IPR005025 from INTERPRO and Flavodoxin_1 IPR008254 from INTERPRO.; GO: 0009055 electron carrier activity, 0016491 oxidoreductase activity, 0050662 coenzyme binding; PDB: 1T5B_B 1DXQ_B 2B3D_A 2Z9D_B 2Z9C_A 2Z98_A 2D5I_A 2Z9B_A 1TIK_A 1V4B_A ....
Probab=22.47 E-value=1.7e+02 Score=23.79 Aligned_cols=38 Identities=16% Similarity=0.197 Sum_probs=26.4
Q ss_pred EEEEEecCCCCCcchhh-HHH-HHHHHHhCC-eeeeEEEcC
Q 028156 61 RILCLQGSPDGPEQYVA-IMN-AIFSAQRSM-VPIDSCYLG 98 (213)
Q Consensus 61 rILiis~S~d~~~qyi~-imn-~if~aqk~~-I~Idv~~L~ 98 (213)
+||+|.+|++....+.. +-+ .+..+++.+ ..|.++-|.
T Consensus 2 kiLvI~asp~~~~S~s~~l~~~~~~~~~~~~~~~v~~~dL~ 42 (199)
T PF02525_consen 2 KILVINASPRPEGSFSRALADAFLEGLQEAGPHEVEIRDLY 42 (199)
T ss_dssp EEEEEE--SSTTTSHHHHHHHHHHHHHHHHTTSEEEEEETT
T ss_pred EEEEEEcCCCCccCHHHHHHHHHHHHHHHcCCCEEEEEECc
Confidence 79999999976444433 333 577788888 899999995
No 232
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=22.26 E-value=2.3e+02 Score=22.44 Aligned_cols=49 Identities=18% Similarity=0.332 Sum_probs=24.1
Q ss_pred HHHHHHHhCCeeeeEEEcCCcChHHHHHHHHhhCCe-eeccCCcchHHHHHHHHcC
Q 028156 80 NAIFSAQRSMVPIDSCYLGAQNSAFLQQASYITGGV-HHKPQQLDGLFQYLLTIFG 134 (213)
Q Consensus 80 n~if~aqk~~I~Idv~~L~~~e~~iLqq~~~~TgG~-Y~~~~~~~~l~~~Ll~~~~ 134 (213)
..+..|++++-.| | ..+..+.++ ....+|. +..-.+...-+.-++.+|-
T Consensus 33 ~il~~A~~e~Ril----l-Trd~~l~~~-~~~~~~~~li~~~~~~~QL~ev~~~~~ 82 (147)
T PF01927_consen 33 EILELAREEGRIL----L-TRDRDLLKR-RRVSGGVILIRSDDPEEQLREVLERFG 82 (147)
T ss_pred HHHHHhhhCCeEE----E-ECCHHHHHH-hhccCCEEEEcCCCHHHHHHHHHHHcC
Confidence 4556666665444 4 245555554 4455553 3333334444444455554
No 233
>TIGR02720 pyruv_oxi_spxB pyruvate oxidase. Members of this family are examples of pyruvate oxidase (EC 1.2.3.3), an enzyme with FAD and TPP as cofactors that catalyzes the reaction pyruvate + phosphate + O2 + H2O = acetyl phosphate + CO2 + H2O2. It should not be confused with pyruvate dehydrogenase [cytochrome] (EC 1.2.2.2) as in E. coli PoxB, although the E. coli enzyme is closely homologous and has pyruvate oxidase as an alternate name.
Probab=22.07 E-value=3.1e+02 Score=26.63 Aligned_cols=71 Identities=14% Similarity=0.249 Sum_probs=46.5
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHH---------------------HHHhhCCeee
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQ---------------------ASYITGGVHH 117 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq---------------------~~~~TgG~Y~ 117 (213)
.++++.|.| |.+.+|. ++.+.+|.++++++-++.+......++++ +++..|+.+.
T Consensus 426 ~r~Vv~i~G--DGsf~m~--~~eL~Tavr~~lpi~~VV~NN~~yg~i~~~~~~~~~~~~~~~~~~~df~~iA~a~G~~~~ 501 (575)
T TIGR02720 426 DRQVFNLAG--DGAFSMT--MQDLLTQVQYHLPVINIVFSNCTYGFIKDEQEDTNQPLIGVDFNDADFAKIAEGVGAVGF 501 (575)
T ss_pred CCcEEEEEc--ccHHHhh--HHHHHHHHHhCCCeEEEEEeCCccHHHHHHHHHhCCCcccccCCCCCHHHHHHHCCCEEE
Confidence 467777775 6776775 56789999999999999885444444443 3444455555
Q ss_pred ccCCcchHHHHHHHHc
Q 028156 118 KPQQLDGLFQYLLTIF 133 (213)
Q Consensus 118 ~~~~~~~l~~~Ll~~~ 133 (213)
.+.+.+.|.+.|-..+
T Consensus 502 ~v~~~~el~~al~~a~ 517 (575)
T TIGR02720 502 RVNKIEQLPAVFEQAK 517 (575)
T ss_pred EeCCHHHHHHHHHHHH
Confidence 5566666666665544
No 234
>PRK10569 NAD(P)H-dependent FMN reductase; Provisional
Probab=21.93 E-value=2.3e+02 Score=23.56 Aligned_cols=38 Identities=24% Similarity=0.219 Sum_probs=27.5
Q ss_pred EEEEEecCCCCCcchhhHHHH-HHHHHhCCeeeeEEEcC
Q 028156 61 RILCLQGSPDGPEQYVAIMNA-IFSAQRSMVPIDSCYLG 98 (213)
Q Consensus 61 rILiis~S~d~~~qyi~imn~-if~aqk~~I~Idv~~L~ 98 (213)
+||+|+||+...+.-..+.+. +..+...++.+..+.|.
T Consensus 2 kIl~I~GSpr~~S~t~~l~~~~~~~l~~~g~ev~~idL~ 40 (191)
T PRK10569 2 RVITLAGSPRFPSRSSALLEYAREWLNGLGVEVYHWNLQ 40 (191)
T ss_pred EEEEEEcCCCCCChHHHHHHHHHHHHHhCCCEEEEEEcc
Confidence 699999998655544555654 45667788999888884
No 235
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=21.81 E-value=49 Score=21.17 Aligned_cols=26 Identities=23% Similarity=0.404 Sum_probs=15.0
Q ss_pred cCCCCccccC--C----CCccccccccccccc
Q 028156 170 CSVCLSIYCK--H----LKKCSTCGSVFGQAQ 195 (213)
Q Consensus 170 Cp~Clsi~C~--~----p~~C~~C~~~f~~~~ 195 (213)
||.|.++.=. . .-.|+.||-.+...+
T Consensus 3 Cp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~~~~ 34 (52)
T smart00661 3 CPKCGNMLIPKEGKEKRRFVCRKCGYEEPIEQ 34 (52)
T ss_pred CCCCCCccccccCCCCCEEECCcCCCeEECCC
Confidence 6667665421 1 235777777666554
No 236
>COG1773 Rubredoxin [Energy production and conversion]
Probab=21.74 E-value=62 Score=22.17 Aligned_cols=13 Identities=38% Similarity=0.771 Sum_probs=9.5
Q ss_pred eeEcCCCCccccC
Q 028156 167 GYICSVCLSIYCK 179 (213)
Q Consensus 167 GyvCp~Clsi~C~ 179 (213)
-|.|++|.=+|=+
T Consensus 3 ~~~C~~CG~vYd~ 15 (55)
T COG1773 3 RWRCSVCGYVYDP 15 (55)
T ss_pred ceEecCCceEecc
Confidence 3788888877763
No 237
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=21.60 E-value=51 Score=29.70 Aligned_cols=28 Identities=29% Similarity=0.667 Sum_probs=0.0
Q ss_pred eEcCCCCccccCCC-----------------Cccccccccccccc
Q 028156 168 YICSVCLSIYCKHL-----------------KKCSTCGSVFGQAQ 195 (213)
Q Consensus 168 yvCp~Clsi~C~~p-----------------~~C~~C~~~f~~~~ 195 (213)
|.|+.|+-.|-... -.|++||..+++.|
T Consensus 131 ~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmp 175 (279)
T KOG2462|consen 131 YKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMP 175 (279)
T ss_pred eeccccccccccccccchhhcccccccccccccCCCCCceeeehH
No 238
>PF04577 DUF563: Protein of unknown function (DUF563); InterPro: IPR007657 This is a family of uncharacterised glycosyltransferases belonging to glycosyltransferase family 61. Sequences are further processed into a mature form.; GO: 0016757 transferase activity, transferring glycosyl groups
Probab=21.54 E-value=2.3e+02 Score=22.65 Aligned_cols=67 Identities=13% Similarity=0.135 Sum_probs=43.9
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHHHHHhhCCeeeccCCcchHHHHH
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQASYITGGVHHKPQQLDGLFQYL 129 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~~~~TgG~Y~~~~~~~~l~~~L 129 (213)
++||++++-.......-.|.-..+..+++.++ .++.. ++..+.+|+.-..+=..++-....++...+
T Consensus 102 ~p~i~~i~R~~~~~R~i~Ne~el~~~l~~~~~--~~v~~--~~~s~~eqv~~~~~a~viig~hGs~l~n~~ 168 (206)
T PF04577_consen 102 RPRILYISRRKSGSRRILNEDELLEILKKYGF--EVVDP--EDLSFEEQVKLFASAKVIIGPHGSALTNLL 168 (206)
T ss_pred CCeEEEEecCCCCCCcCcCHHHHHHHHhhCCe--EEEeC--CCCCHHHHHHHhcCCCEEEecCchHhheee
Confidence 45999999732222233333344555666664 45555 488899999999888888888777655443
No 239
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=21.54 E-value=61 Score=19.68 Aligned_cols=21 Identities=38% Similarity=0.713 Sum_probs=13.1
Q ss_pred ee-eccCcc----cceeEcCCCCccc
Q 028156 157 CF-CHKNTI----DMGYICSVCLSIY 177 (213)
Q Consensus 157 C~-CH~~~v----~~GyvCp~Clsi~ 177 (213)
|. |++..+ +..|+|+.|.++|
T Consensus 6 C~~C~~~~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 6 CSKCGGNGIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred cCCCCCCeEEEecCCeEEcccCCcEe
Confidence 44 655432 4578888887764
No 240
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=21.53 E-value=39 Score=25.20 Aligned_cols=27 Identities=26% Similarity=0.498 Sum_probs=21.3
Q ss_pred EcCCCCccccCC-----CCccccccccccccc
Q 028156 169 ICSVCLSIYCKH-----LKKCSTCGSVFGQAQ 195 (213)
Q Consensus 169 vCp~Clsi~C~~-----p~~C~~C~~~f~~~~ 195 (213)
-||.|..+.--+ ...|..||+.|..+.
T Consensus 37 kCp~C~n~q~VFShA~t~V~C~~Cg~~L~~PT 68 (85)
T PTZ00083 37 KCPGCSQITTVFSHAQTVVLCGGCSSQLCQPT 68 (85)
T ss_pred ECCCCCCeeEEEecCceEEEccccCCEeeccC
Confidence 489998766543 478999999998766
No 241
>PF13580 SIS_2: SIS domain; PDB: 1TK9_C 2I22_B 2I2W_A 1X92_A 3BJZ_D 2XBL_B 2X3Y_F 2YVA_B 3CVJ_D 3TRJ_D ....
Probab=21.49 E-value=1.8e+02 Score=22.61 Aligned_cols=33 Identities=15% Similarity=0.303 Sum_probs=21.5
Q ss_pred CCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeE
Q 028156 58 PQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDS 94 (213)
Q Consensus 58 ~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv 94 (213)
-..-+++||.|..++ ++.+.+..|++.++++=+
T Consensus 103 ~gDvli~iS~SG~s~----~vi~a~~~Ak~~G~~vIa 135 (138)
T PF13580_consen 103 PGDVLIVISNSGNSP----NVIEAAEEAKERGMKVIA 135 (138)
T ss_dssp TT-EEEEEESSS-SH----HHHHHHHHHHHTT-EEEE
T ss_pred CCCEEEEECCCCCCH----HHHHHHHHHHHCCCEEEE
Confidence 344566677776554 677888999999887643
No 242
>TIGR00288 conserved hypothetical protein TIGR00288. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.
Probab=21.47 E-value=2.4e+02 Score=23.31 Aligned_cols=35 Identities=11% Similarity=0.014 Sum_probs=25.3
Q ss_pred cchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHHHHH
Q 028156 73 EQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQASY 110 (213)
Q Consensus 73 ~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~~~ 110 (213)
+||.++. ..++..|.+|-+++....-+.-|+++||
T Consensus 116 ~DF~~Lv---~~lre~G~~V~v~g~~~~ts~~L~~acd 150 (160)
T TIGR00288 116 ADFLPVI---NKAKENGKETIVIGAEPGFSTALQNSAD 150 (160)
T ss_pred HhHHHHH---HHHHHCCCEEEEEeCCCCChHHHHHhcC
Confidence 3555554 5558999999999873336668898887
No 243
>PF09186 DUF1949: Domain of unknown function (DUF1949); InterPro: IPR015269 Members of this entry are a set of functionally uncharacterised hypothetical bacterial proteins. They adopt a ferredoxin-like fold, with a beta-alpha-beta-beta-alpha-beta arrangement []. This entry contains the protein Impact, which is a translational regulator that ensures constant high levels of translation under amino acid starvation. It acts by interacting with Gcn1/Gcn1L1, thereby preventing activation of Gcn2 protein kinases (EIF2AK1 to 4) and subsequent down-regulation of protein synthesis. It is evolutionary conserved from eukaryotes to archaea []. ; PDB: 2CVE_A 1VI7_A.
Probab=21.17 E-value=1.6e+02 Score=18.67 Aligned_cols=14 Identities=29% Similarity=0.368 Sum_probs=11.7
Q ss_pred hHHHHHHHHhhCCe
Q 028156 102 SAFLQQASYITGGV 115 (213)
Q Consensus 102 ~~iLqq~~~~TgG~ 115 (213)
-.|.++++++|+|.
T Consensus 43 ~~f~~~l~~~t~G~ 56 (56)
T PF09186_consen 43 EEFKAQLTDLTSGR 56 (56)
T ss_dssp HHHHHHHHHHTTT-
T ss_pred HHHHHHHHHHcCCC
Confidence 56999999999994
No 244
>PRK08979 acetolactate synthase 3 catalytic subunit; Validated
Probab=21.03 E-value=3.9e+02 Score=25.83 Aligned_cols=44 Identities=18% Similarity=0.397 Sum_probs=31.6
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHH
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQ 106 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLq 106 (213)
.++++.|.| |.+.+|. ++.+.+|.++++++=++.+.......++
T Consensus 439 ~~~vv~i~G--DG~f~m~--~~EL~Ta~r~~lpv~~vV~NN~~y~~i~ 482 (572)
T PRK08979 439 DETVVCVTG--DGSIQMN--IQELSTALQYDIPVKIINLNNRFLGMVK 482 (572)
T ss_pred CCeEEEEEc--chHhhcc--HHHHHHHHHcCCCeEEEEEeCCccHHHH
Confidence 467777775 6665555 4679999999999999999544334444
No 245
>PRK08199 thiamine pyrophosphate protein; Validated
Probab=20.88 E-value=3.2e+02 Score=26.22 Aligned_cols=71 Identities=11% Similarity=0.108 Sum_probs=44.2
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHH----------------------HHHHhhCCee
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQ----------------------QASYITGGVH 116 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLq----------------------q~~~~TgG~Y 116 (213)
.+++++|.| |.+.+|. ++.+.+|.+.+++|=+|.+....-.+++ ++++.-|+.+
T Consensus 433 ~~~vv~i~G--DGsf~~~--~~el~ta~~~~l~i~~vv~nN~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~a~a~G~~~ 508 (557)
T PRK08199 433 ERTVVAFAG--DGCFLMN--GQELATAVQYGLPIIVIVVNNGMYGTIRMHQEREYPGRVSGTDLTNPDFAALARAYGGHG 508 (557)
T ss_pred CCcEEEEEc--chHhhcc--HHHHHHHHHhCCCeEEEEEeCCcchHHHHHHHHhcCCccccccCCCCCHHHHHHHCCCeE
Confidence 457777775 5555553 3778889999999999988533233333 2344445555
Q ss_pred eccCCcchHHHHHHHHc
Q 028156 117 HKPQQLDGLFQYLLTIF 133 (213)
Q Consensus 117 ~~~~~~~~l~~~Ll~~~ 133 (213)
..+.+.+.|.+.|-..+
T Consensus 509 ~~v~~~~el~~al~~a~ 525 (557)
T PRK08199 509 ETVERTEDFAPAFERAL 525 (557)
T ss_pred EEeCCHHHHHHHHHHHH
Confidence 66666666666654443
No 246
>PF07627 PSCyt3: Protein of unknown function (DUF1588); InterPro: IPR013039 A region of similarity shared by several Rhodopirellula baltica cytochrome-like proteins that are predicted to be secreted. These proteins also contain IPR011478 from INTERPRO, IPR013036 from INTERPRO, IPR013042 from INTERPRO and IPR013043 from INTERPRO.
Probab=20.86 E-value=1.2e+02 Score=23.18 Aligned_cols=35 Identities=14% Similarity=0.060 Sum_probs=20.4
Q ss_pred HHHHHHHHhhCCeeeccCCcch----HHHHHHHHcCCCc
Q 028156 103 AFLQQASYITGGVHHKPQQLDG----LFQYLLTIFGTDL 137 (213)
Q Consensus 103 ~iLqq~~~~TgG~Y~~~~~~~~----l~~~Ll~~~~p~~ 137 (213)
.||-|++-+|...+..-.++-+ +.+.||-.-+|||
T Consensus 4 GlLt~~~~Lt~~s~~~~tsPv~RG~~v~~~lLc~~~ppP 42 (101)
T PF07627_consen 4 GLLTQGAFLTRTSDGDRTSPVHRGVWVRERLLCQPPPPP 42 (101)
T ss_pred hhhhhHHHHhccCCCCCCCchHHHHHHHHHHcCCCCCCC
Confidence 5778888888777666555544 3344444444433
No 247
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=20.84 E-value=43 Score=18.86 Aligned_cols=14 Identities=29% Similarity=0.800 Sum_probs=10.8
Q ss_pred Cccccccccccccc
Q 028156 182 KKCSTCGSVFGQAQ 195 (213)
Q Consensus 182 ~~C~~C~~~f~~~~ 195 (213)
..|++||-.|....
T Consensus 3 ~~C~~CgR~F~~~~ 16 (25)
T PF13913_consen 3 VPCPICGRKFNPDR 16 (25)
T ss_pred CcCCCCCCEECHHH
Confidence 46999999996544
No 248
>COG1432 Uncharacterized conserved protein [Function unknown]
Probab=20.81 E-value=2.6e+02 Score=23.09 Aligned_cols=46 Identities=15% Similarity=0.238 Sum_probs=32.3
Q ss_pred CCcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHHHHHHHH
Q 028156 58 PQPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAFLQQASY 110 (213)
Q Consensus 58 ~~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~iLqq~~~ 110 (213)
.-..|.++|+ | .+..++ +.+|+..+.++.++++...-+.=|+.+||
T Consensus 110 ~~D~ivl~Sg--D--~DF~p~---v~~~~~~G~rv~v~~~~~~~s~~L~~~aD 155 (181)
T COG1432 110 NVDTIVLFSG--D--GDFIPL---VEAARDKGKRVEVAGIEPMTSSDLRNAAD 155 (181)
T ss_pred CCCEEEEEcC--C--ccHHHH---HHHHHHcCCEEEEEecCCcCHHHHHHhhc
Confidence 3456777765 2 244444 88899999999999996545556666665
No 249
>TIGR03846 sulfopy_beta sulfopyruvate decarboxylase, beta subunit. Nearly every member of this protein family is the beta subunit, or else the C-terminal region, of sulfopyruvate decarboxylase, in an archaeal species capable of coenzyme M biosynthesis. However, the enzyme also occurs in Roseovarius nubinhibens ISM in a degradative pathway, where the resulting sulfoacetaldehyde is desulfonated to acetyl phosphate, then converted to acetyl-CoA (see PubMed:19581363).
Probab=20.79 E-value=3.1e+02 Score=22.47 Aligned_cols=68 Identities=12% Similarity=0.076 Sum_probs=43.5
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCC-eeeeEEEcCCcChH-------------HHHHHHHhhCCeeec-cCCcc
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSM-VPIDSCYLGAQNSA-------------FLQQASYITGGVHHK-PQQLD 123 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~-I~Idv~~L~~~e~~-------------iLqq~~~~TgG~Y~~-~~~~~ 123 (213)
.++++.|.| |.+.++. ++.+.+|.+.+ +++-++.+....-. =+..+++.-|..|.. +.+++
T Consensus 59 ~~~Vv~i~G--DG~f~m~--~~el~ta~~~~~~pv~~vV~NN~~yg~~~~q~~~~~~~~d~~~lA~a~G~~~~~~v~~~~ 134 (181)
T TIGR03846 59 DRTVIVIDG--DGSLLMN--LGVLPTIAAESPKNLILVILDNGAYGSTGNQPTPASRRTDLELVAKAAGIRNVEKVADEE 134 (181)
T ss_pred CCcEEEEEc--chHHHhh--hhHHHHHHHhCCCCeEEEEEeCCccccccCcCCCCCCCCCHHHHHHHCCCCeEEEeCCHH
Confidence 457777775 5554443 35677777777 48877777422101 134577777888877 77888
Q ss_pred hHHHHHH
Q 028156 124 GLFQYLL 130 (213)
Q Consensus 124 ~l~~~Ll 130 (213)
.|.+.|-
T Consensus 135 ~l~~al~ 141 (181)
T TIGR03846 135 ELRDALK 141 (181)
T ss_pred HHHHHHH
Confidence 7777774
No 250
>PRK06276 acetolactate synthase catalytic subunit; Reviewed
Probab=20.67 E-value=3.6e+02 Score=26.17 Aligned_cols=71 Identities=11% Similarity=0.199 Sum_probs=48.5
Q ss_pred CcEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcChHH-----------------------HHHHHHhhCCe
Q 028156 59 QPRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNSAF-----------------------LQQASYITGGV 115 (213)
Q Consensus 59 ~~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~~i-----------------------Lqq~~~~TgG~ 115 (213)
.++++.|.| |.+.+|. ++.+.+|.+.++++=++.+....-.. +.++++..|+.
T Consensus 437 ~~~Vv~i~G--DGsf~m~--~~eL~Ta~~~~lpv~~vV~NN~~~g~~~~~~~~~~~~~~~~~~~~~~~d~~~la~a~G~~ 512 (586)
T PRK06276 437 DANVIAITG--DGGFLMN--SQELATIAEYDIPVVICIFDNRTLGMVYQWQNLYYGKRQSEVHLGETPDFVKLAESYGVK 512 (586)
T ss_pred CCcEEEEEc--chHhhcc--HHHHHHHHHhCCCeEEEEEeCCchHHHHHHHHHHhCCCcccccCCCCCCHHHHHHHCCCe
Confidence 356777775 6666665 57899999999999999885332111 23456666777
Q ss_pred eeccCCcchHHHHHHHHc
Q 028156 116 HHKPQQLDGLFQYLLTIF 133 (213)
Q Consensus 116 Y~~~~~~~~l~~~Ll~~~ 133 (213)
+..+.+++.|...|-..+
T Consensus 513 ~~~v~~~~el~~al~~a~ 530 (586)
T PRK06276 513 ADRVEKPDEIKEALKEAI 530 (586)
T ss_pred EEEECCHHHHHHHHHHHH
Confidence 777777777777765554
No 251
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=20.63 E-value=57 Score=23.10 Aligned_cols=22 Identities=23% Similarity=0.525 Sum_probs=10.5
Q ss_pred eEcCCCCccccCCCCccccccccc
Q 028156 168 YICSVCLSIYCKHLKKCSTCGSVF 191 (213)
Q Consensus 168 yvCp~Clsi~C~~p~~C~~C~~~f 191 (213)
..|+.|-+. .+...||+|.+.-
T Consensus 29 ~fCs~Ci~~--~~~~~CPvC~~Pa 50 (65)
T PF14835_consen 29 IFCSSCIRD--CIGSECPVCHTPA 50 (65)
T ss_dssp -B-TTTGGG--GTTTB-SSS--B-
T ss_pred HHHHHHhHH--hcCCCCCCcCChH
Confidence 456666655 3557799998754
No 252
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=20.56 E-value=58 Score=21.99 Aligned_cols=13 Identities=23% Similarity=0.736 Sum_probs=9.7
Q ss_pred ccceeEcCCCCcc
Q 028156 164 IDMGYICSVCLSI 176 (213)
Q Consensus 164 v~~GyvCp~Clsi 176 (213)
..+-|+||.|...
T Consensus 41 ~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 41 EEIQYRCPYCGAL 53 (54)
T ss_pred CceEEEcCCCCCc
Confidence 3568999999753
No 253
>KOG4451 consensus Uncharacterized conserved protein (tumor-associated antigen HCA127 in humans) [Function unknown]
Probab=20.52 E-value=30 Score=30.54 Aligned_cols=15 Identities=13% Similarity=0.290 Sum_probs=10.5
Q ss_pred CCccccccccccccc
Q 028156 181 LKKCSTCGSVFGQAQ 195 (213)
Q Consensus 181 p~~C~~C~~~f~~~~ 195 (213)
-++||.|+.+-.|..
T Consensus 263 APiCPlCKaKsRSrN 277 (286)
T KOG4451|consen 263 APICPLCKAKSRSRN 277 (286)
T ss_pred CCCCcchhhccccCC
Confidence 467888887766654
No 254
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=20.50 E-value=51 Score=29.24 Aligned_cols=26 Identities=27% Similarity=0.507 Sum_probs=13.0
Q ss_pred eEcCCCCccccCCCCccccccccccc
Q 028156 168 YICSVCLSIYCKHLKKCSTCGSVFGQ 193 (213)
Q Consensus 168 yvCp~Clsi~C~~p~~C~~C~~~f~~ 193 (213)
..||.|.+-.=.....|+.||..=..
T Consensus 198 L~Cs~C~t~W~~~R~~Cp~Cg~~~~~ 223 (290)
T PF04216_consen 198 LHCSLCGTEWRFVRIKCPYCGNTDHE 223 (290)
T ss_dssp EEETTT--EEE--TTS-TTT---SS-
T ss_pred EEcCCCCCeeeecCCCCcCCCCCCCc
Confidence 56888888877777888888876443
No 255
>cd02005 TPP_PDC_IPDC Thiamine pyrophosphate (TPP) family, PDC_IPDC subfamily, TPP-binding module; composed of proteins similar to pyruvate decarboxylase (PDC) and indolepyruvate decarboxylase (IPDC). PDC, a key enzyme in alcoholic fermentation, catalyzes the conversion of pyruvate to acetaldehyde and CO2. It is able to utilize other 2-oxo acids as substrates. In plants and various plant-associated bacteria, IPDC plays a role in the indole-3-pyruvic acid (IPA) pathway, a tryptophan-dependent biosynthetic route to indole-3-acetaldehyde (IAA). IPDC catalyzes the decarboxylation of IPA to IAA. Both PDC and IPDC depend on TPP and Mg2+ as cofactors.
Probab=20.11 E-value=2.8e+02 Score=22.52 Aligned_cols=70 Identities=16% Similarity=0.146 Sum_probs=47.8
Q ss_pred cEEEEEecCCCCCcchhhHHHHHHHHHhCCeeeeEEEcCCcCh------------------HHHHHHHHhhC----Ceee
Q 028156 60 PRILCLQGSPDGPEQYVAIMNAIFSAQRSMVPIDSCYLGAQNS------------------AFLQQASYITG----GVHH 117 (213)
Q Consensus 60 ~rILiis~S~d~~~qyi~imn~if~aqk~~I~Idv~~L~~~e~------------------~iLqq~~~~Tg----G~Y~ 117 (213)
+++++|.| |.+.+|. ++.+.+|.+.++++-++.+....- .=+.++++..| +.|.
T Consensus 69 ~~vv~i~G--DG~f~~~--~~el~ta~~~~~p~~ivV~nN~~~~~~~~~~~~~~~~~~~~~~d~~~ia~a~G~~~~~~~~ 144 (183)
T cd02005 69 RRVILLVG--DGSFQMT--VQELSTMIRYGLNPIIFLINNDGYTIERAIHGPEASYNDIANWNYTKLPEVFGGGGGGLSF 144 (183)
T ss_pred CeEEEEEC--Cchhhcc--HHHHHHHHHhCCCCEEEEEECCCcEEEEEeccCCcCcccCCCCCHHHHHHHhCCCccccEE
Confidence 56777765 6666663 567889999999988888742110 11356777777 5778
Q ss_pred ccCCcchHHHHHHHHc
Q 028156 118 KPQQLDGLFQYLLTIF 133 (213)
Q Consensus 118 ~~~~~~~l~~~Ll~~~ 133 (213)
.+.+.+.|.+.|-..+
T Consensus 145 ~v~~~~el~~al~~a~ 160 (183)
T cd02005 145 RVKTEGELDEALKDAL 160 (183)
T ss_pred EecCHHHHHHHHHHHH
Confidence 8888888877776655
Done!