Query 001136
Match_columns 1143
No_of_seqs 578 out of 2101
Neff 5.9
Searched_HMMs 46136
Date Thu Mar 28 16:48:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001136.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001136hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1940 Zn-finger protein [Gen 100.0 6.1E-60 1.3E-64 513.0 6.7 270 853-1135 1-272 (276)
2 PF14599 zinc_ribbon_6: Zinc-r 99.9 5.6E-24 1.2E-28 182.8 0.5 61 1068-1128 1-61 (61)
3 PF05495 zf-CHY: CHY zinc fing 99.8 2.6E-21 5.6E-26 173.2 2.0 70 894-971 1-71 (71)
4 COG3945 Uncharacterized conser 99.4 8.4E-12 1.8E-16 127.6 15.2 169 41-220 9-182 (189)
5 PF01814 Hemerythrin: Hemeryth 99.4 2.7E-12 5.9E-17 125.4 10.0 129 41-172 2-133 (133)
6 PF01814 Hemerythrin: Hemeryth 99.2 1.9E-10 4.1E-15 112.4 12.2 125 302-435 1-133 (133)
7 PRK10992 iron-sulfur cluster r 99.2 2E-10 4.3E-15 124.8 13.5 132 43-174 78-218 (220)
8 PF13639 zf-RING_2: Ring finge 99.1 3.5E-11 7.6E-16 98.0 1.6 44 1021-1065 1-44 (44)
9 TIGR03652 FeS_repair_RIC iron- 99.1 8.2E-10 1.8E-14 119.9 11.7 130 43-172 74-216 (216)
10 COG4357 Zinc finger domain con 99.0 1.2E-10 2.6E-15 107.1 1.0 66 891-959 12-90 (105)
11 PF12861 zf-Apc11: Anaphase-pr 98.9 7.9E-10 1.7E-14 101.4 3.8 46 1021-1068 33-81 (85)
12 PRK13276 cell wall biosynthesi 98.9 9.7E-09 2.1E-13 111.2 12.0 130 43-172 81-223 (224)
13 COG2846 Regulator of cell morp 98.9 2.4E-08 5.1E-13 104.0 12.7 131 43-173 79-218 (221)
14 PRK10992 iron-sulfur cluster r 98.8 2.7E-08 5.8E-13 108.3 12.4 131 304-437 76-218 (220)
15 COG5194 APC11 Component of SCF 98.8 2.4E-09 5.3E-14 95.6 3.3 60 980-1069 21-81 (88)
16 COG5243 HRD1 HRD ubiquitin lig 98.8 1.9E-09 4.2E-14 120.0 2.8 57 1017-1073 284-350 (491)
17 PF12678 zf-rbx1: RING-H2 zinc 98.8 4.6E-09 9.9E-14 95.0 3.7 46 1020-1065 19-73 (73)
18 TIGR03652 FeS_repair_RIC iron- 98.7 4.9E-08 1.1E-12 106.1 11.7 129 304-435 72-216 (216)
19 KOG4628 Predicted E3 ubiquitin 98.7 4.3E-09 9.3E-14 119.5 2.8 49 1021-1070 230-279 (348)
20 KOG0804 Cytoplasmic Zn-finger 98.6 1.5E-08 3.3E-13 115.9 2.1 81 1021-1128 176-258 (493)
21 KOG2930 SCF ubiquitin ligase, 98.5 2.3E-08 5E-13 93.6 0.1 62 977-1068 44-107 (114)
22 COG3945 Uncharacterized conser 98.5 1.6E-06 3.5E-11 89.5 12.9 142 302-451 8-159 (189)
23 PHA02929 N1R/p28-like protein; 98.4 1.2E-07 2.6E-12 103.6 4.3 52 1018-1069 172-227 (238)
24 KOG1493 Anaphase-promoting com 98.4 4.1E-08 9E-13 87.2 -0.2 56 981-1068 22-80 (84)
25 COG5540 RING-finger-containing 98.4 1.3E-07 2.9E-12 103.4 3.2 54 1016-1070 319-373 (374)
26 cd00162 RING RING-finger (Real 98.4 2.9E-07 6.3E-12 73.5 3.5 44 1022-1068 1-45 (45)
27 PF13923 zf-C3HC4_2: Zinc fing 98.3 3.2E-07 6.9E-12 72.9 2.7 39 1023-1064 1-39 (39)
28 PRK13276 cell wall biosynthesi 98.3 3.4E-06 7.3E-11 91.7 11.4 129 304-435 79-223 (224)
29 PF13920 zf-C3HC4_3: Zinc fing 98.2 1.3E-06 2.8E-11 73.2 3.0 46 1020-1069 2-48 (50)
30 COG2846 Regulator of cell morp 98.1 1.4E-05 3.1E-10 83.7 11.0 130 303-435 76-217 (221)
31 PF14634 zf-RING_5: zinc-RING 98.0 3.5E-06 7.6E-11 68.8 3.5 44 1022-1066 1-44 (44)
32 KOG0320 Predicted E3 ubiquitin 98.0 3.4E-06 7.4E-11 87.0 2.7 48 1020-1069 131-178 (187)
33 smart00184 RING Ring finger. E 98.0 5.4E-06 1.2E-10 63.8 3.0 38 1023-1064 1-39 (39)
34 PF00097 zf-C3HC4: Zinc finger 97.9 6.5E-06 1.4E-10 65.8 3.0 39 1023-1064 1-41 (41)
35 PLN03208 E3 ubiquitin-protein 97.9 9.5E-06 2.1E-10 85.8 4.3 53 1014-1070 12-80 (193)
36 PF15227 zf-C3HC4_4: zinc fing 97.9 9.3E-06 2E-10 65.8 3.2 38 1023-1064 1-42 (42)
37 KOG0802 E3 ubiquitin ligase [P 97.9 3.9E-06 8.4E-11 103.0 1.4 53 1016-1068 287-340 (543)
38 PHA02926 zinc finger-like prot 97.8 1E-05 2.2E-10 86.3 3.3 54 1016-1069 166-230 (242)
39 PF13445 zf-RING_UBOX: RING-ty 97.7 3E-05 6.5E-10 63.2 2.6 39 1023-1062 1-43 (43)
40 smart00504 Ubox Modified RING 97.6 4.4E-05 9.6E-10 66.4 3.8 45 1021-1069 2-46 (63)
41 KOG0825 PHD Zn-finger protein 97.6 1.1E-05 2.3E-10 97.4 -0.8 52 1018-1070 121-172 (1134)
42 KOG0317 Predicted E3 ubiquitin 97.6 2.6E-05 5.6E-10 86.1 2.1 47 1021-1071 240-286 (293)
43 KOG1428 Inhibitor of type V ad 97.6 1.5E-05 3.2E-10 99.8 0.2 114 931-1068 3415-3543(3738)
44 KOG0823 Predicted E3 ubiquitin 97.4 7.6E-05 1.6E-09 80.4 2.9 49 1018-1070 45-96 (230)
45 KOG0828 Predicted E3 ubiquitin 97.4 5.8E-05 1.2E-09 87.7 1.6 50 1021-1070 572-635 (636)
46 TIGR00570 cdk7 CDK-activating 97.3 0.00017 3.7E-09 81.5 4.0 50 1020-1069 3-54 (309)
47 KOG0287 Postreplication repair 97.2 0.00015 3.3E-09 81.0 2.6 47 1022-1072 25-71 (442)
48 TIGR00599 rad18 DNA repair pro 97.2 0.00018 4E-09 84.3 3.3 47 1020-1070 26-72 (397)
49 KOG2164 Predicted E3 ubiquitin 97.2 0.00018 3.8E-09 85.0 2.5 53 1014-1070 180-237 (513)
50 KOG0827 Predicted E3 ubiquitin 97.0 0.00027 5.8E-09 80.5 1.6 48 1020-1068 4-55 (465)
51 PF11793 FANCL_C: FANCL C-term 97.0 0.0002 4.3E-09 64.5 0.4 50 1020-1069 2-66 (70)
52 KOG2177 Predicted E3 ubiquitin 97.0 0.0008 1.7E-08 74.3 5.0 43 1020-1066 13-55 (386)
53 smart00744 RINGv The RING-vari 97.0 0.00057 1.2E-08 57.4 2.8 42 1022-1065 1-49 (49)
54 KOG1734 Predicted RING-contain 96.9 0.00023 5.1E-09 77.6 0.4 49 1020-1068 224-280 (328)
55 COG2461 Uncharacterized conser 96.8 0.0076 1.7E-07 69.7 11.1 138 38-187 84-222 (409)
56 COG5574 PEX10 RING-finger-cont 96.7 0.00079 1.7E-08 73.9 2.0 47 1020-1070 215-263 (271)
57 PF04564 U-box: U-box domain; 96.5 0.0031 6.7E-08 57.2 4.2 48 1021-1072 5-53 (73)
58 COG5432 RAD18 RING-finger-cont 96.2 0.0025 5.5E-08 70.2 2.3 44 1021-1068 26-69 (391)
59 KOG1039 Predicted E3 ubiquitin 96.0 0.0026 5.6E-08 73.6 1.2 81 1018-1100 159-252 (344)
60 COG5219 Uncharacterized conser 95.9 0.003 6.5E-08 78.3 1.4 53 1017-1069 1466-1523(1525)
61 PF14835 zf-RING_6: zf-RING of 95.8 0.0046 1E-07 54.4 1.8 56 1022-1082 9-65 (65)
62 KOG4265 Predicted E3 ubiquitin 95.6 0.0071 1.5E-07 69.2 2.6 48 1018-1069 288-336 (349)
63 KOG4172 Predicted E3 ubiquitin 95.6 0.0032 7E-08 53.2 -0.1 48 1020-1071 7-56 (62)
64 KOG1941 Acetylcholine receptor 95.6 0.0033 7.1E-08 71.8 -0.1 61 1011-1072 357-419 (518)
65 KOG1645 RING-finger-containing 95.4 0.0089 1.9E-07 69.0 2.7 47 1021-1067 5-54 (463)
66 KOG0311 Predicted E3 ubiquitin 95.4 0.0028 6.1E-08 72.0 -1.2 47 1020-1069 43-90 (381)
67 KOG2879 Predicted E3 ubiquitin 95.1 0.016 3.6E-07 64.0 3.5 51 1019-1072 238-290 (298)
68 KOG1785 Tyrosine kinase negati 94.9 0.0083 1.8E-07 68.7 0.5 52 1013-1068 362-415 (563)
69 KOG0978 E3 ubiquitin ligase in 94.9 0.0089 1.9E-07 74.2 0.7 48 1021-1072 644-692 (698)
70 KOG0297 TNF receptor-associate 94.7 0.018 3.8E-07 68.5 2.6 108 1020-1139 21-139 (391)
71 PF14570 zf-RING_4: RING/Ubox 94.2 0.039 8.4E-07 46.2 2.7 46 1023-1068 1-47 (48)
72 COG2461 Uncharacterized conser 94.1 0.31 6.8E-06 56.9 10.6 133 301-451 85-223 (409)
73 KOG1940 Zn-finger protein [Gen 94.0 0.0069 1.5E-07 67.9 -2.6 133 597-759 17-149 (276)
74 KOG4445 Uncharacterized conser 93.7 0.022 4.7E-07 63.6 0.4 53 1017-1070 112-187 (368)
75 KOG0824 Predicted E3 ubiquitin 93.6 0.035 7.5E-07 62.3 1.9 47 1019-1069 6-53 (324)
76 KOG3039 Uncharacterized conser 92.3 0.11 2.4E-06 56.7 3.3 58 1015-1073 216-274 (303)
77 PF10367 Vps39_2: Vacuolar sor 92.1 0.064 1.4E-06 51.5 1.2 38 1013-1052 71-108 (109)
78 PF11789 zf-Nse: Zinc-finger o 91.7 0.12 2.6E-06 45.0 2.3 41 1020-1063 11-53 (57)
79 COG5152 Uncharacterized conser 91.4 0.1 2.3E-06 55.1 1.8 57 1022-1082 198-254 (259)
80 KOG0309 Conserved WD40 repeat- 90.8 0.14 3E-06 63.2 2.4 47 14-60 234-283 (1081)
81 KOG4275 Predicted E3 ubiquitin 90.5 0.048 1E-06 60.8 -1.6 57 1011-1075 288-348 (350)
82 KOG3970 Predicted E3 ubiquitin 90.3 0.25 5.4E-06 53.3 3.5 49 1019-1069 49-105 (299)
83 KOG3268 Predicted E3 ubiquitin 89.6 0.23 4.9E-06 51.8 2.5 30 1040-1069 188-228 (234)
84 KOG2272 Focal adhesion protein 89.4 0.12 2.6E-06 56.4 0.4 145 893-1074 63-237 (332)
85 KOG2660 Locus-specific chromos 89.3 0.1 2.2E-06 59.5 -0.4 47 1020-1069 15-61 (331)
86 KOG3800 Predicted E3 ubiquitin 89.1 0.27 5.8E-06 55.3 2.8 47 1022-1068 2-50 (300)
87 COG5592 Uncharacterized conser 88.4 1.7 3.8E-05 45.1 7.8 89 339-442 29-131 (171)
88 PF05883 Baculo_RING: Baculovi 88.3 0.22 4.8E-06 50.3 1.3 42 1020-1062 26-73 (134)
89 KOG4159 Predicted E3 ubiquitin 88.2 0.4 8.6E-06 57.0 3.6 51 1018-1072 82-132 (398)
90 KOG1701 Focal adhesion adaptor 88.1 0.061 1.3E-06 62.8 -3.1 70 974-1068 295-370 (468)
91 KOG2034 Vacuolar sorting prote 88.1 0.27 5.8E-06 62.3 2.2 36 1018-1055 815-850 (911)
92 PF14447 Prok-RING_4: Prokaryo 88.0 0.23 5E-06 42.7 1.1 31 1037-1069 20-50 (55)
93 COG5175 MOT2 Transcriptional r 87.9 0.22 4.7E-06 56.5 1.1 57 1020-1076 14-71 (480)
94 KOG4739 Uncharacterized protei 87.9 0.26 5.5E-06 54.3 1.6 36 1031-1068 12-47 (233)
95 PF12906 RINGv: RING-variant d 87.7 0.37 8.1E-06 40.2 2.1 40 1023-1064 1-47 (47)
96 PF03854 zf-P11: P-11 zinc fin 87.6 0.24 5.2E-06 41.2 0.9 44 1021-1070 3-47 (50)
97 KOG1814 Predicted E3 ubiquitin 87.2 0.57 1.2E-05 54.9 3.9 52 1011-1064 176-235 (445)
98 PF04641 Rtf2: Rtf2 RING-finge 87.1 0.46 1E-05 53.5 3.2 51 1017-1069 110-161 (260)
99 KOG1571 Predicted E3 ubiquitin 87.0 0.33 7.1E-06 56.1 1.9 46 1016-1068 301-346 (355)
100 KOG1813 Predicted E3 ubiquitin 86.1 0.42 9.1E-06 53.8 2.1 61 1022-1086 243-303 (313)
101 KOG1002 Nucleotide excision re 86.0 0.3 6.5E-06 58.2 0.9 50 1015-1068 531-585 (791)
102 PRK14890 putative Zn-ribbon RN 85.6 0.65 1.4E-05 40.5 2.5 47 931-984 5-56 (59)
103 KOG0269 WD40 repeat-containing 84.9 0.72 1.6E-05 57.6 3.5 70 974-1063 751-820 (839)
104 TIGR00100 hypA hydrogenase nic 83.6 0.72 1.6E-05 45.8 2.2 37 1093-1131 66-102 (115)
105 KOG2807 RNA polymerase II tran 83.5 0.48 1E-05 53.9 1.1 19 765-783 87-105 (378)
106 KOG4692 Predicted E3 ubiquitin 83.0 0.71 1.5E-05 52.8 2.1 50 1017-1070 419-468 (489)
107 PRK00564 hypA hydrogenase nick 82.7 0.82 1.8E-05 45.5 2.3 36 1093-1130 67-103 (117)
108 PHA02862 5L protein; Provision 82.4 0.91 2E-05 46.3 2.4 45 1020-1069 2-53 (156)
109 PRK04023 DNA polymerase II lar 82.2 1.1 2.3E-05 57.9 3.5 48 933-986 626-673 (1121)
110 COG5592 Uncharacterized conser 82.1 7 0.00015 40.8 8.6 121 45-184 8-137 (171)
111 PHA02825 LAP/PHD finger-like p 81.4 1.3 2.8E-05 46.1 3.1 44 1020-1068 8-58 (162)
112 KOG2114 Vacuolar assembly/sort 81.3 0.91 2E-05 57.4 2.4 47 550-596 332-378 (933)
113 KOG4185 Predicted E3 ubiquitin 81.2 1.3 2.8E-05 50.6 3.5 47 1021-1068 4-54 (296)
114 TIGR02481 hemeryth_dom hemeryt 80.6 6.4 0.00014 39.0 7.8 54 111-169 10-63 (126)
115 PRK12380 hydrogenase nickel in 80.4 1 2.3E-05 44.5 2.0 36 1094-1131 67-102 (113)
116 PRK03681 hypA hydrogenase nick 78.7 1.3 2.8E-05 43.9 2.1 37 1094-1131 67-103 (114)
117 KOG3002 Zn finger protein [Gen 78.6 2.1 4.6E-05 49.3 4.0 63 1021-1093 49-113 (299)
118 COG2888 Predicted Zn-ribbon RN 78.4 1.6 3.4E-05 38.2 2.2 45 933-984 9-58 (61)
119 PF08746 zf-RING-like: RING-li 77.0 1.6 3.5E-05 35.8 1.8 41 1023-1064 1-43 (43)
120 PRK03824 hypA hydrogenase nick 76.9 1.5 3.3E-05 44.7 2.1 36 1095-1130 68-122 (135)
121 KOG3161 Predicted E3 ubiquitin 76.6 0.92 2E-05 55.5 0.5 43 1021-1066 12-54 (861)
122 PF04216 FdhE: Protein involve 76.1 0.62 1.3E-05 53.3 -1.1 46 1018-1068 170-221 (290)
123 KOG1044 Actin-binding LIM Zn-f 75.5 2.4 5.2E-05 51.7 3.5 140 974-1127 14-172 (670)
124 PF07191 zinc-ribbons_6: zinc- 74.8 0.58 1.3E-05 42.3 -1.4 64 1021-1112 2-68 (70)
125 COG5236 Uncharacterized conser 73.8 2.9 6.2E-05 48.0 3.4 47 1018-1068 59-107 (493)
126 PF01155 HypA: Hydrogenase exp 72.9 1.3 2.8E-05 43.8 0.3 36 1094-1131 67-102 (113)
127 PF05502 Dynactin_p62: Dynacti 72.7 2.5 5.3E-05 51.9 2.8 29 934-969 6-34 (483)
128 KOG0827 Predicted E3 ubiquitin 72.3 0.27 5.8E-06 56.9 -5.1 52 1018-1069 194-245 (465)
129 PF01529 zf-DHHC: DHHC palmito 71.2 2.8 6.1E-05 43.7 2.5 47 956-1008 43-89 (174)
130 PRK03564 formate dehydrogenase 70.5 2.1 4.6E-05 49.4 1.4 42 1020-1066 187-234 (309)
131 PRK00762 hypA hydrogenase nick 70.2 2.8 6E-05 42.2 2.1 36 1094-1130 67-107 (124)
132 PF14446 Prok-RING_1: Prokaryo 69.9 5 0.00011 34.7 3.2 35 1019-1053 4-38 (54)
133 PHA03096 p28-like protein; Pro 69.3 2.5 5.4E-05 48.4 1.6 45 1021-1065 179-230 (284)
134 KOG2817 Predicted E3 ubiquitin 69.2 3.4 7.5E-05 48.6 2.8 44 1022-1066 336-382 (394)
135 PF05290 Baculo_IE-1: Baculovi 68.5 3.4 7.3E-05 41.8 2.2 47 1020-1070 80-133 (140)
136 PF09538 FYDLN_acid: Protein o 68.0 3.2 7E-05 40.8 1.9 26 947-985 10-35 (108)
137 TIGR01562 FdhE formate dehydro 66.4 3.8 8.3E-05 47.3 2.4 32 1097-1128 224-265 (305)
138 PF06524 NOA36: NOA36 protein; 66.4 2.7 6E-05 46.6 1.2 67 909-986 140-219 (314)
139 PRK14714 DNA polymerase II lar 65.5 5.4 0.00012 53.1 3.7 52 933-988 667-721 (1337)
140 PF12773 DZR: Double zinc ribb 65.4 4.8 0.0001 33.6 2.2 36 936-984 1-37 (50)
141 PF07191 zinc-ribbons_6: zinc- 65.3 2.9 6.3E-05 37.9 0.9 33 933-968 17-57 (70)
142 TIGR00595 priA primosomal prot 65.0 4.9 0.00011 49.7 3.1 45 903-951 214-258 (505)
143 COG0375 HybF Zn finger protein 64.4 4.1 9E-05 40.5 1.9 38 1093-1132 66-103 (115)
144 COG5222 Uncharacterized conser 64.2 4.7 0.0001 45.5 2.5 45 1021-1068 275-321 (427)
145 COG1198 PriA Primosomal protei 63.6 5.9 0.00013 50.8 3.6 54 903-963 436-489 (730)
146 smart00132 LIM Zinc-binding do 62.4 5.3 0.00011 30.7 1.8 37 1023-1069 2-38 (39)
147 KOG1044 Actin-binding LIM Zn-f 61.0 7.5 0.00016 47.7 3.6 164 931-1126 40-229 (670)
148 TIGR02481 hemeryth_dom hemeryt 60.6 1.5E+02 0.0033 29.1 12.4 113 42-170 10-124 (126)
149 PF14357 DUF4404: Domain of un 60.2 39 0.00085 31.9 7.5 82 52-135 2-83 (85)
150 COG5220 TFB3 Cdk activating ki 59.4 3.7 7.9E-05 45.1 0.6 48 1021-1068 11-63 (314)
151 cd00522 Hemerythrin Hemerythri 58.9 27 0.00059 34.2 6.6 45 112-168 13-57 (113)
152 PF10272 Tmpp129: Putative tra 58.7 8.7 0.00019 45.3 3.5 16 1054-1069 336-351 (358)
153 PRK12286 rpmF 50S ribosomal pr 58.7 7.2 0.00016 34.1 2.1 30 1095-1129 25-54 (57)
154 KOG0801 Predicted E3 ubiquitin 58.1 4.8 0.0001 41.8 1.1 30 1018-1048 175-204 (205)
155 COG1198 PriA Primosomal protei 57.2 9.6 0.00021 49.0 3.8 46 931-985 433-484 (730)
156 KOG2068 MOT2 transcription fac 56.9 7.3 0.00016 45.1 2.4 52 1018-1069 247-298 (327)
157 KOG4443 Putative transcription 56.7 5.4 0.00012 49.6 1.4 69 1021-1094 146-225 (694)
158 PRK14559 putative protein seri 56.2 7.2 0.00016 49.5 2.5 45 935-983 3-48 (645)
159 PF04216 FdhE: Protein involve 56.2 4.5 9.9E-05 46.3 0.7 29 1097-1129 197-225 (290)
160 PF07800 DUF1644: Protein of u 56.2 11 0.00023 39.5 3.3 33 1020-1055 2-46 (162)
161 PRK00808 hypothetical protein; 55.9 37 0.00081 35.1 7.3 52 111-168 14-65 (150)
162 TIGR02300 FYDLN_acid conserved 55.9 7.2 0.00016 39.3 1.9 19 968-986 18-36 (129)
163 COG3058 FdhE Uncharacterized p 55.4 4.4 9.4E-05 45.7 0.4 44 1019-1067 184-234 (308)
164 PRK05580 primosome assembly pr 55.2 8.6 0.00019 49.3 3.0 45 903-951 382-426 (679)
165 PRK14873 primosome assembly pr 54.5 8.3 0.00018 49.3 2.7 44 903-951 384-427 (665)
166 KOG0298 DEAD box-containing he 54.3 4.1 8.9E-05 54.0 -0.1 51 1020-1073 1153-1203(1394)
167 PF07227 DUF1423: Protein of u 54.0 8.9 0.00019 46.1 2.6 46 1022-1068 130-193 (446)
168 PRK04023 DNA polymerase II lar 53.9 8.2 0.00018 50.3 2.4 46 902-969 626-671 (1121)
169 PRK03564 formate dehydrogenase 53.5 10 0.00023 43.9 3.0 27 1097-1129 212-238 (309)
170 KOG1001 Helicase-like transcri 52.8 6.7 0.00015 50.0 1.4 43 1021-1068 455-499 (674)
171 cd00350 rubredoxin_like Rubred 52.6 9.5 0.00021 29.5 1.7 24 961-984 1-25 (33)
172 TIGR01031 rpmF_bact ribosomal 52.2 8.4 0.00018 33.4 1.5 29 1096-1129 25-53 (55)
173 PF09538 FYDLN_acid: Protein o 51.8 8.1 0.00018 38.1 1.5 32 901-946 8-39 (108)
174 KOG2066 Vacuolar assembly/sort 51.7 5.6 0.00012 50.4 0.5 92 413-508 391-487 (846)
175 PLN03086 PRLI-interacting fact 51.4 18 0.00039 45.2 4.7 13 1057-1069 503-515 (567)
176 TIGR02605 CxxC_CxxC_SSSS putat 51.3 9.8 0.00021 32.0 1.8 34 1097-1130 5-42 (52)
177 KOG3850 Predicted membrane pro 51.1 2.2E+02 0.0048 33.9 12.9 145 301-461 252-401 (455)
178 COG0143 MetG Methionyl-tRNA sy 51.1 10 0.00022 47.4 2.5 45 958-1008 123-168 (558)
179 KOG1829 Uncharacterized conser 50.0 5.7 0.00012 49.4 0.2 29 893-922 345-377 (580)
180 KOG1311 DHHC-type Zn-finger pr 49.8 12 0.00027 42.8 2.9 48 955-1008 107-154 (299)
181 KOG1952 Transcription factor N 49.7 9.2 0.0002 48.9 1.9 47 1019-1066 190-244 (950)
182 PF01783 Ribosomal_L32p: Ribos 48.7 12 0.00026 32.5 1.9 29 1096-1129 25-53 (56)
183 PF13901 DUF4206: Domain of un 48.7 8.5 0.00018 41.9 1.3 30 1031-1065 167-196 (202)
184 PRK00808 hypothetical protein; 48.6 3.3E+02 0.0071 28.1 13.3 116 39-175 11-130 (150)
185 PF14353 CpXC: CpXC protein 48.5 4.4 9.6E-05 40.6 -0.9 25 1092-1116 33-57 (128)
186 KOG4399 C2HC-type Zn-finger pr 48.5 4.1 9E-05 45.2 -1.1 65 933-1006 238-302 (325)
187 KOG2462 C2H2-type Zn-finger pr 47.4 14 0.00031 41.8 2.7 38 1059-1107 216-253 (279)
188 TIGR00373 conserved hypothetic 47.3 6.8 0.00015 41.1 0.3 14 970-983 121-135 (158)
189 COG2703 Hemerythrin [Inorganic 46.8 1.3E+02 0.0029 31.3 9.3 123 41-182 12-139 (144)
190 COG3058 FdhE Uncharacterized p 46.6 5.5 0.00012 44.9 -0.6 14 177-190 132-145 (308)
191 PRK00398 rpoP DNA-directed RNA 46.1 16 0.00035 30.2 2.2 23 961-983 3-28 (46)
192 PRK00398 rpoP DNA-directed RNA 46.1 14 0.0003 30.6 1.8 30 1097-1126 3-32 (46)
193 PLN03086 PRLI-interacting fact 46.1 11 0.00024 47.0 1.8 53 974-1029 451-513 (567)
194 PRK06266 transcription initiat 46.0 7.6 0.00016 41.5 0.4 22 962-983 118-143 (178)
195 KOG0826 Predicted E3 ubiquitin 46.0 15 0.00032 42.5 2.6 47 1020-1069 300-346 (357)
196 PF03833 PolC_DP2: DNA polymer 44.1 7.5 0.00016 49.9 0.0 48 931-984 653-700 (900)
197 PRK07219 DNA topoisomerase I; 44.0 29 0.00063 45.6 5.3 63 964-1031 672-744 (822)
198 PHA00626 hypothetical protein 43.5 21 0.00045 31.1 2.5 19 963-984 13-31 (59)
199 KOG2272 Focal adhesion protein 42.9 16 0.00034 40.7 2.2 80 897-990 115-206 (332)
200 PRK14714 DNA polymerase II lar 42.8 20 0.00044 48.1 3.5 49 947-1002 668-716 (1337)
201 PRK01917 cation-binding hemery 42.7 58 0.0013 33.3 6.2 48 111-168 14-61 (139)
202 KOG2593 Transcription initiati 42.7 10 0.00022 45.3 0.8 20 816-835 50-69 (436)
203 PF05502 Dynactin_p62: Dynacti 40.9 13 0.00028 45.9 1.3 34 910-944 4-37 (483)
204 COG5109 Uncharacterized conser 40.5 18 0.0004 41.4 2.3 43 1022-1065 338-383 (396)
205 PF08271 TF_Zn_Ribbon: TFIIB z 40.0 15 0.00032 30.0 1.1 14 970-983 13-26 (43)
206 cd00522 Hemerythrin Hemerythri 39.5 3.2E+02 0.0069 26.8 10.6 99 43-170 13-111 (113)
207 KOG3362 Predicted BBOX Zn-fing 39.2 9.6 0.00021 39.1 -0.1 25 960-988 117-143 (156)
208 PLN02189 cellulose synthase 39.2 21 0.00046 47.2 2.9 53 1015-1068 29-86 (1040)
209 TIGR00622 ssl1 transcription f 39.0 53 0.0012 32.7 4.9 44 1021-1065 56-110 (112)
210 PF02891 zf-MIZ: MIZ/SP-RING z 39.0 34 0.00073 29.0 3.1 40 1022-1067 4-50 (50)
211 KOG4718 Non-SMC (structural ma 38.9 15 0.00032 40.1 1.2 28 1038-1065 196-223 (235)
212 PF14445 Prok-RING_2: Prokaryo 38.4 2.8 6E-05 35.4 -3.3 48 957-1006 3-52 (57)
213 smart00659 RPOLCX RNA polymera 38.0 22 0.00047 29.5 1.8 26 1097-1123 2-27 (44)
214 KOG1280 Uncharacterized conser 36.8 28 0.00061 40.6 3.0 26 956-984 60-87 (381)
215 TIGR00058 Hemerythrin hemeryth 36.8 79 0.0017 31.2 5.9 45 111-168 15-59 (115)
216 cd00729 rubredoxin_SM Rubredox 36.7 26 0.00057 27.4 2.0 24 961-984 2-26 (34)
217 PF06220 zf-U1: U1 zinc finger 36.6 13 0.00028 29.8 0.3 13 959-971 1-13 (38)
218 PLN02436 cellulose synthase A 36.3 25 0.00055 46.6 2.9 53 1015-1068 31-88 (1094)
219 COG5151 SSL1 RNA polymerase II 35.9 14 0.00031 42.1 0.6 19 765-783 114-132 (421)
220 PRK01917 cation-binding hemery 35.6 4.9E+02 0.011 26.5 11.6 114 41-174 13-127 (139)
221 COG4888 Uncharacterized Zn rib 35.4 17 0.00036 35.3 0.8 30 974-1003 20-54 (104)
222 PF00412 LIM: LIM domain; Int 35.4 21 0.00045 30.2 1.4 40 1023-1072 1-40 (58)
223 PF00301 Rubredoxin: Rubredoxi 35.3 26 0.00057 29.5 1.9 10 975-984 33-42 (47)
224 PF12126 DUF3583: Protein of u 34.8 1.7E+02 0.0037 33.7 8.6 122 44-183 14-142 (324)
225 COG1996 RPC10 DNA-directed RNA 34.8 22 0.00047 30.3 1.3 27 1097-1123 6-32 (49)
226 KOG1100 Predicted E3 ubiquitin 34.5 20 0.00044 39.3 1.4 38 1023-1068 161-199 (207)
227 PF01907 Ribosomal_L37e: Ribos 33.9 23 0.0005 30.8 1.4 27 1093-1122 11-37 (55)
228 KOG1609 Protein involved in mR 33.5 20 0.00043 41.0 1.2 50 1020-1069 78-134 (323)
229 KOG2932 E3 ubiquitin ligase in 33.3 24 0.00051 40.5 1.7 29 1038-1068 105-133 (389)
230 COG1656 Uncharacterized conser 32.8 33 0.00072 36.2 2.6 49 1058-1113 97-146 (165)
231 PF07227 DUF1423: Protein of u 31.9 34 0.00074 41.3 2.8 31 824-856 21-51 (446)
232 PF13597 NRDD: Anaerobic ribon 31.9 21 0.00046 44.6 1.2 57 1070-1132 465-521 (546)
233 PF06937 EURL: EURL protein; 31.7 29 0.00062 39.2 2.0 42 1021-1063 31-75 (285)
234 smart00734 ZnF_Rad18 Rad18-lik 30.8 32 0.00068 25.4 1.5 19 1060-1079 3-21 (26)
235 COG5273 Uncharacterized protei 30.8 29 0.00063 40.3 2.0 47 956-1008 104-150 (309)
236 KOG1312 DHHC-type Zn-finger pr 30.2 16 0.00036 41.4 -0.1 39 980-1025 149-187 (341)
237 PF00628 PHD: PHD-finger; Int 30.2 15 0.00032 30.5 -0.4 42 1023-1065 2-49 (51)
238 cd01675 RNR_III Class III ribo 30.2 38 0.00082 42.6 3.0 55 1070-1130 493-547 (555)
239 PRK00366 ispG 4-hydroxy-3-meth 30.0 38 0.00081 40.0 2.7 51 1059-1113 269-321 (360)
240 PRK14873 primosome assembly pr 29.8 42 0.0009 43.1 3.3 46 930-985 380-431 (665)
241 PRK14892 putative transcriptio 29.8 39 0.00084 32.9 2.3 38 1096-1133 20-60 (99)
242 PRK01110 rpmF 50S ribosomal pr 29.8 33 0.00071 30.4 1.7 29 1096-1130 26-54 (60)
243 PF14952 zf-tcix: Putative tre 29.7 24 0.00052 29.2 0.8 13 1117-1129 13-25 (44)
244 KOG1703 Adaptor protein Enigma 29.1 26 0.00056 43.2 1.3 97 1011-1128 354-463 (479)
245 PF12773 DZR: Double zinc ribb 29.0 26 0.00057 29.1 0.9 22 1097-1122 29-50 (50)
246 smart00249 PHD PHD zinc finger 28.7 25 0.00054 27.8 0.7 30 1023-1053 2-31 (47)
247 TIGR02300 FYDLN_acid conserved 28.6 32 0.0007 34.8 1.6 32 901-946 8-39 (129)
248 PRK00432 30S ribosomal protein 28.5 31 0.00068 29.4 1.3 9 994-1002 36-44 (50)
249 PRK14559 putative protein seri 28.2 35 0.00076 43.6 2.2 35 933-971 15-51 (645)
250 PLN02638 cellulose synthase A 28.0 41 0.00088 44.9 2.8 52 1016-1068 13-69 (1079)
251 PF14569 zf-UDP: Zinc-binding 27.7 60 0.0013 30.3 3.0 50 1019-1068 8-61 (80)
252 COG1996 RPC10 DNA-directed RNA 27.6 38 0.00082 28.9 1.6 29 958-986 3-34 (49)
253 COG5183 SSM4 Protein involved 27.5 35 0.00076 43.6 2.0 47 1020-1068 12-65 (1175)
254 KOG1311 DHHC-type Zn-finger pr 27.4 32 0.0007 39.4 1.6 34 975-1015 112-145 (299)
255 PF09723 Zn-ribbon_8: Zinc rib 27.3 40 0.00086 27.5 1.6 31 1097-1127 5-38 (42)
256 PF03107 C1_2: C1 domain; Int 27.3 40 0.00087 25.4 1.6 21 981-1002 2-22 (30)
257 KOG1812 Predicted E3 ubiquitin 26.8 28 0.00062 41.7 1.0 36 1021-1056 147-182 (384)
258 TIGR00373 conserved hypothetic 26.8 72 0.0016 33.5 3.9 26 1057-1082 127-154 (158)
259 smart00531 TFIIE Transcription 26.3 26 0.00055 36.3 0.5 7 977-983 124-130 (147)
260 KOG4443 Putative transcription 26.1 42 0.00092 42.2 2.3 47 1021-1069 19-73 (694)
261 PF03604 DNA_RNApol_7kD: DNA d 25.9 41 0.00088 26.2 1.4 23 962-984 1-25 (32)
262 cd02341 ZZ_ZZZ3 Zinc finger, Z 25.6 42 0.0009 28.4 1.5 22 977-1002 1-22 (48)
263 KOG1313 DHHC-type Zn-finger pr 25.5 33 0.00071 39.0 1.1 45 958-1008 99-143 (309)
264 smart00451 ZnF_U1 U1-like zinc 25.5 32 0.00069 26.1 0.8 11 960-970 2-12 (35)
265 PRK03824 hypA hydrogenase nick 25.1 42 0.00091 34.4 1.7 10 975-984 106-115 (135)
266 PF01780 Ribosomal_L37ae: Ribo 25.1 28 0.0006 33.3 0.4 29 960-988 34-65 (90)
267 TIGR01562 FdhE formate dehydro 24.9 34 0.00074 39.7 1.2 43 1020-1067 184-233 (305)
268 COG5243 HRD1 HRD ubiquitin lig 24.6 26 0.00056 41.1 0.2 33 1000-1037 317-352 (491)
269 PHA00626 hypothetical protein 24.5 43 0.00093 29.3 1.4 33 934-971 1-33 (59)
270 KOG4399 C2HC-type Zn-finger pr 24.2 23 0.0005 39.6 -0.3 51 956-1009 199-249 (325)
271 PRK06266 transcription initiat 23.8 28 0.00061 37.3 0.2 10 974-983 115-124 (178)
272 KOG2462 C2H2-type Zn-finger pr 23.8 65 0.0014 36.7 3.0 27 1098-1124 216-252 (279)
273 PTZ00255 60S ribosomal protein 23.7 34 0.00075 32.7 0.8 31 959-989 34-67 (90)
274 PRK08271 anaerobic ribonucleos 23.4 60 0.0013 41.4 3.0 54 1070-1129 541-594 (623)
275 TIGR00280 L37a ribosomal prote 23.3 34 0.00073 32.8 0.6 31 959-989 33-66 (91)
276 KOG0006 E3 ubiquitin-protein l 23.3 69 0.0015 36.9 3.1 75 970-1054 169-253 (446)
277 PHA01486 nonstructural protein 23.1 77 0.0017 23.7 2.3 24 562-585 6-29 (32)
278 KOG2231 Predicted E3 ubiquitin 23.1 63 0.0014 41.2 3.1 43 1022-1068 2-51 (669)
279 TIGR01206 lysW lysine biosynth 22.8 56 0.0012 28.4 1.8 30 1059-1107 3-32 (54)
280 smart00659 RPOLCX RNA polymera 22.7 64 0.0014 26.8 2.0 24 961-984 2-27 (44)
281 KOG4684 Uncharacterized conser 22.4 39 0.00085 36.9 1.0 81 1033-1126 117-200 (275)
282 TIGR02159 PA_CoA_Oxy4 phenylac 22.2 42 0.00091 34.9 1.1 18 1115-1132 105-122 (146)
283 KOG3908 Queuine-tRNA ribosyltr 22.1 2.1E+02 0.0046 33.1 6.5 113 113-229 136-248 (396)
284 COG0333 RpmF Ribosomal protein 22.1 57 0.0012 28.7 1.7 28 1097-1129 27-54 (57)
285 PF09788 Tmemb_55A: Transmembr 21.9 83 0.0018 35.5 3.4 110 994-1123 64-185 (256)
286 PF04710 Pellino: Pellino; In 21.8 31 0.00067 41.0 0.1 49 1017-1068 274-338 (416)
287 PF09986 DUF2225: Uncharacteri 21.5 30 0.00064 38.1 -0.1 49 1056-1104 3-55 (214)
288 PF06524 NOA36: NOA36 protein; 21.4 85 0.0018 35.5 3.3 50 934-983 98-149 (314)
289 PF13894 zf-C2H2_4: C2H2-type 21.1 37 0.0008 23.0 0.3 17 1059-1075 1-17 (24)
290 PRK03976 rpl37ae 50S ribosomal 21.0 36 0.00077 32.6 0.3 31 959-989 34-67 (90)
291 KOG0954 PHD finger protein [Ge 21.0 18 0.0004 45.6 -2.1 30 738-780 121-150 (893)
292 PRK11020 hypothetical protein; 20.8 5.1E+02 0.011 26.0 8.0 76 374-449 5-84 (118)
293 PLN02400 cellulose synthase 20.7 56 0.0012 43.7 2.0 53 1015-1068 31-88 (1085)
294 COG3219 Uncharacterized protei 20.6 4E+02 0.0087 29.6 8.0 78 127-206 10-93 (237)
295 PF02701 zf-Dof: Dof domain, z 20.6 49 0.0011 29.5 1.0 15 1115-1129 5-19 (63)
296 KOG2807 RNA polymerase II tran 20.6 88 0.0019 36.4 3.3 47 1019-1066 329-375 (378)
297 PF03833 PolC_DP2: DNA polymer 20.6 33 0.00072 44.4 0.0 29 827-855 581-609 (900)
298 PRK00564 hypA hydrogenase nick 20.5 58 0.0013 32.5 1.7 9 977-985 89-97 (117)
299 PRK05978 hypothetical protein; 20.5 51 0.0011 34.4 1.3 33 1017-1068 30-62 (148)
300 TIGR00100 hypA hydrogenase nic 20.5 58 0.0013 32.4 1.7 9 976-984 86-94 (115)
301 KOG4323 Polycomb-like PHD Zn-f 20.5 37 0.0008 41.4 0.3 13 956-968 210-222 (464)
302 PF01529 zf-DHHC: DHHC palmito 20.4 50 0.0011 34.3 1.3 35 974-1015 46-80 (174)
303 TIGR00595 priA primosomal prot 20.4 70 0.0015 39.8 2.7 48 929-985 209-262 (505)
304 PF05129 Elf1: Transcription e 20.3 39 0.00084 31.7 0.4 9 975-983 21-29 (81)
305 KOG3896 Dynactin, subunit p62 20.3 39 0.00085 39.2 0.5 86 984-1121 26-111 (449)
306 PF13248 zf-ribbon_3: zinc-rib 20.1 53 0.0011 24.0 0.9 23 933-958 2-25 (26)
307 TIGR02487 NrdD anaerobic ribon 20.1 85 0.0018 39.8 3.4 54 1070-1129 499-552 (579)
No 1
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=100.00 E-value=6.1e-60 Score=512.96 Aligned_cols=270 Identities=49% Similarity=1.020 Sum_probs=247.9
Q ss_pred HHHHHHHhhhCCCCcCCCCCCCCCCCCCCCCCCCcccCCCCCccccccccccccccCCcccChhhhcccCCCCCCccccc
Q 001136 853 TSRWIATQQKLPQATAGESSKGEEGLDCYASYRDPEKQVFGCEHYKRNCKIRAACCGKLFTCRFCHDKASDHSMDRKATS 932 (1143)
Q Consensus 853 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gC~HY~r~c~l~~~cC~k~y~Cr~CHde~~~H~~~r~~~~ 932 (1143)
|+||++.|+....... ...+..+++.|++..++||+||+|+|++++|||+++|+|++||++..+|.++|+.+.
T Consensus 1 ~~~~~~~~~~~~~~~~-------~~~~~~~~~~d~~~~~~~c~hy~r~~~~~a~ccd~~~~C~hCH~~s~~h~~~r~~v~ 73 (276)
T KOG1940|consen 1 MSRLAADQSFLEEFAQ-------ALSSIHSDAEDEIAFPYGCPHYRRNCKSRAPCCDREITCRHCHNESEDHDLDRKTVY 73 (276)
T ss_pred CccchhhhhhhHHHHh-------hhhhcccccccccccccCCchhhhccccccccccceeeeEEecChhhhcccchhhhh
Confidence 3566666544322222 122346788899999999999999999999999999999999999999999999999
Q ss_pred eeeccccccccccCCCCCCCCCCCCcceeEeccccccccCC-CCcccCCCCCccccCCCCCccccccCCccccccccc-c
Q 001136 933 EMMCMHCLKIQAIGPNCTTPSCNGLSMAKYYCNICKFFDDE-RTVYHCPFCNLCRVGGGLGVDFFHCMTCNCCLGLKL-L 1010 (1143)
Q Consensus 933 ~~~C~~C~~~q~~~~~C~~~~cc~~~f~~y~C~~C~~~d~~-~~~yhC~~CgiCr~g~~l~~~~~hC~~C~~C~~~~~-~ 1010 (1143)
+++||.|.++||+++.|.+ |+..+|+|||.+||+|||+ ..||||+.|||||+|.++ +||||++|+.|++..+ +
T Consensus 74 ~~~C~~C~~~q~~~~~c~~---c~~~~g~~~c~~C~l~dd~~~~~~hC~~C~icr~g~~~--~~fhc~~c~~c~~~~~~~ 148 (276)
T KOG1940|consen 74 ELLCMKCRKIQPVGQICSN---CHVELGEYYCLICKLFDDDPSKQYHCDLCGICREGLGL--DFFHCKKCKACLSAYLSN 148 (276)
T ss_pred hhhhhhHHhhhhhhhcccc---chhhhhhhcCcccccccccccceecccccccccccccc--chhHHhhhHhHHhhhccc
Confidence 9999999999999999999 5788999999999999988 599999999999999885 9999999999999999 6
Q ss_pred cccccccccCCCCcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCCccccchhhhhhhhHHHHhhcCCChh
Q 001136 1011 NHKCLEKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLGDMAIYFGMIDALLAAEELPEE 1090 (1143)
Q Consensus 1011 ~H~C~e~~~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~~~m~~~~~~ld~~i~~~p~P~~ 1090 (1143)
.|+|+|++++.+||||.+++|++...+..++|||.+|..|+..+...+|+||+|.+ +.||..+|+++|.+++.+|||++
T Consensus 149 ~H~c~e~~~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~~~~y~CP~C~~-~~d~~~~~~~~d~~l~~~~~p~~ 227 (276)
T KOG1940|consen 149 WHKCVERSSEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMICEGYTCPICSK-PGDMSHYFRKLDKELAGSPMPEE 227 (276)
T ss_pred ccchhhhcccCCCchhHHHhccccccCCccCcccchHHHHHHHHhccCCCCCcccc-hHHHHHHHHHHHHHHhcCCCCch
Confidence 69999999999999999999999999999999999999999999888899999999 99999999999999999999999
Q ss_pred hhcCcceEEcCCCCCCCcccchhhcccCCCCCCccccccccCCCC
Q 001136 1091 YRNQVQDILCNDCEQKGAARFHWLYHKCGFCGSYNTRLIKNDTTV 1135 (1143)
Q Consensus 1091 y~~~~~~i~CndC~~~s~~~~h~l~~kC~~C~syNt~~~~~~~~~ 1135 (1143)
|.+++++|+||||+..++++|||||+||+.|+|||||+++.+...
T Consensus 228 y~~~~~~i~cndC~~~~~~k~~~l~~kc~~c~~~~~r~~~~~~~~ 272 (276)
T KOG1940|consen 228 YKNKTQDILCNDCGSGTNVKYHILYHKCGKCGSYNTRMISDPSKY 272 (276)
T ss_pred hhchhheeeccCCCCCCccceehhhhhCCCcccceeeeccCCCcc
Confidence 999999999999999999999999999999999999999844333
No 2
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=99.88 E-value=5.6e-24 Score=182.80 Aligned_cols=61 Identities=56% Similarity=0.992 Sum_probs=22.4
Q ss_pred ccchhhhhhhhHHHHhhcCCChhhhcCcceEEcCCCCCCCcccchhhcccCCCCCCccccc
Q 001136 1068 LGDMAIYFGMIDALLAAEELPEEYRNQVQDILCNDCEQKGAARFHWLYHKCGFCGSYNTRL 1128 (1143)
Q Consensus 1068 ~~~m~~~~~~ld~~i~~~p~P~~y~~~~~~i~CndC~~~s~~~~h~l~~kC~~C~syNt~~ 1128 (1143)
+.||+.+|++||++|+++|||++|+++++.|+||||+++|.++||||||||++|||||||+
T Consensus 1 v~dM~~~w~~LD~~i~~~pmP~~Y~~~~v~IlCNDC~~~s~v~fH~lg~KC~~C~SYNT~q 61 (61)
T PF14599_consen 1 VVDMSAYWRMLDAEIAATPMPEEYRNKKVWILCNDCNAKSEVPFHFLGHKCSHCGSYNTRQ 61 (61)
T ss_dssp ---------------------------EEEEEESSS--EEEEE--TT----TTTS---EEE
T ss_pred CCCHHHHHHHHHHHHHhCCCCHHHhCCEEEEECCCCCCccceeeeHhhhcCCCCCCcccCC
Confidence 4799999999999999999999999999999999999999999999999999999999986
No 3
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 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. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=99.82 E-value=2.6e-21 Score=173.16 Aligned_cols=70 Identities=46% Similarity=1.147 Sum_probs=53.6
Q ss_pred Ccccccc-ccccccccCCcccChhhhcccCCCCCCccccceeeccccccccccCCCCCCCCCCCCcceeEecccccccc
Q 001136 894 CEHYKRN-CKIRAACCGKLFTCRFCHDKASDHSMDRKATSEMMCMHCLKIQAIGPNCTTPSCNGLSMAKYYCNICKFFD 971 (1143)
Q Consensus 894 C~HY~r~-c~l~~~cC~k~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~~~cc~~~f~~y~C~~C~~~d 971 (1143)
|+||+|+ |+|+||||++|||||+|||+.++|+++|..+++|+||.|+++|++++. + | + |+|+|++|++||
T Consensus 1 C~HY~~~~~~~~~~cC~~~y~C~~CHde~~~H~~~~~~~~~v~Cg~C~~~~~~~~~--~--c-~---~~~~C~~C~~~~ 71 (71)
T PF05495_consen 1 CKHYHRSLCAIRFPCCGKYYPCRFCHDELEDHPFDRWPVKRVICGKCRTEQPIDEY--S--C-G---ADYFCPICGLYF 71 (71)
T ss_dssp -SS---S-EEEEETTTTEEESSHHHHHHCSSS---TTT--EEEETTT--EEES-SB--T--T------SEEETTTTEEE
T ss_pred CCCCCCCcEEEECCcccCeecHHHHHHHhccCccccccccCeECCCCCCccChhhh--h--c-C---CCccCcCcCCCC
Confidence 8999999 999999999999999999999999999999999999999999999977 4 4 5 999999999986
No 4
>COG3945 Uncharacterized conserved protein [Function unknown]
Probab=99.37 E-value=8.4e-12 Score=127.58 Aligned_cols=169 Identities=17% Similarity=0.226 Sum_probs=141.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccHHHHHHHHHHHHHH-hcccCccccccchHHHhhhcc----hHHHHHH
Q 001136 41 PILIFCFFHKAVRNELDALHQLAMNFATGHRVDILSLSERYRFLHSV-YKHHSNAEDEVIFPALDIRVK----NVARKYS 115 (1143)
Q Consensus 41 Pi~~m~~~H~aLRreL~~L~~la~~~~~gd~~~~~~L~~~~~~l~~~-L~~HH~~EDevLFPaL~~R~p----~vl~~le 115 (1143)
-+..|+..|..|.+.|..|+..+..+..| +.+..++...++|+..+ ..+||++||.++|+.+..+.. ..+..|.
T Consensus 9 ~i~~lvEeH~yIlraL~iLr~~~~~~~~g-~i~y~~v~~iidFi~nfaDkcHH~KEE~~LF~~m~~~g~~~~~~~i~~m~ 87 (189)
T COG3945 9 SIKLLVEEHTYILRALSILRKALDLIKNG-PIDYSDVKEIIDFIRNFADKCHHGKEEKLLFNYMEHEGGPFEEGPIYVMT 87 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcccCC-CCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCcccCceeeeh
Confidence 45789999999999999999999999877 66677777777777775 599999999999999998753 5788999
Q ss_pred HHHHHHHHHHHHHHHHHhhhccCCCCchHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhccCCHHHHHHHHHHHHhcCChh
Q 001136 116 LEHEGESNLFDHLFQLLNSYTQNDESFPKELASCSRALQTSINQHMSKEEQQVFPLLTQHFSLEEQASLVWQFFCSIPVN 195 (1143)
Q Consensus 116 ~EH~~i~~ll~~L~~~l~~~~~~~~~~~~eLa~~l~~l~~~L~~HL~~EE~~lfPLa~~~LS~eEw~~L~~~f~~sip~~ 195 (1143)
-||.....++..|.++++++..++..+-..++.-+..+...+.+|+++|+.++||+|.+.||.+ |..+..+........
T Consensus 88 ~EH~~~R~i~r~lee~~~~~kngd~~~~~~~i~~A~~y~~likrHIdkEdnvlfp~a~~~~s~e-~~~v~~e~~~~~ee~ 166 (189)
T COG3945 88 VEHGEGRYIIRDLEEAYERLKNGDEDSKDDVIDYAVAYLNLIKRHIDKEDNVLFPFAESTLSEE-LNEVNSECFRFDEET 166 (189)
T ss_pred hhhhhHHHHHHHHHHHHHHHHccccchHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHH-HHHHHHHHHHhhhhh
Confidence 9999999999999999999999988888889999999999999999999999999999999999 888877765542221
Q ss_pred hhHhhhhhhccCCCHHHHHHHHHHh
Q 001136 196 MMAEFLPWLSSSISTNEYQDMRKCL 220 (1143)
Q Consensus 196 ~m~~~Lpwl~~~l~~eEr~~ll~~l 220 (1143)
+..--.+++..++..+
T Consensus 167 ---------~ke~i~e~y~~lle~l 182 (189)
T COG3945 167 ---------FKETIHERYAKLLEEL 182 (189)
T ss_pred ---------hhhhHHHHHHHHHHHH
Confidence 2333455565555544
No 5
>PF01814 Hemerythrin: Hemerythrin HHE cation binding domain; InterPro: IPR012312 The haemerythrin family is composed of haemerythrin proteins found in invertebrates, and a broader collection of bacterial and archaeal homologues. Haemerythrin is an oxygen-binding protein found in the vascular system and coelemic fluid, or in muscles (myohaemerythrin) in invertebrates []. Many of the homologous proteins found in prokaryotes are multi-domain proteins with signal-transducing domains such as the GGDEF diguanylate cyclase domain (IPR000160 from INTERPRO) and methyl-accepting chemotaxis protein (MCP) signalling domain (IPR004089 from INTERPRO). Most haemerythrins are oxygen-carriers with a bound non-haem iron, but at least one example is a cadmium-binding protein, apparently with a role in sequestering toxic metals rather than in binding oxygen. The prokaryote with the most instances of this domain is Magnetococcus sp. MC-1, a magnetotactic bacterium. Haemerythrins and myohaemerythrins [, ] are small proteins of about 110 to 129 amino acid residues that bind two iron atoms. They are left-twisted 4-alpha-helical bundles, which provide a hydrophobic pocket where dioxygen binds as a peroxo species, interacting with adjacent aliphatic side chains via van der Waals forces []. In both haemerythrins and myohaemerythrins, the active centre is a binuclear iron complex, bound directly to the protein via 7 amino acid side chains [], 5 His, 1 Glu and 1 Asp []. Ovohaemerythrin [], a yolk protein from the leech Theromyzon tessulatum seems to belong to this family of proteins, it may play a role in the detoxification of free iron after a blood meal []. This entry represents a haemerythrin/HHE cation-binding motif that occurs as a duplicated domain in haemerythrin and related proteins. This domain binds iron in haemerythrin, but can bind other metals in related proteins, such as cadmium in a Nereis diversicolor protein (P80255 from SWISSPROT). A bacterial protein, Q7WX96 from SWISSPROT, is a regulator of response to NO, which suggests a different set-up for its metal ligands. A protein from Cryptococcus neoformans (Filobasidiella neoformans) that contains haemerythrin/HHE cation-binding motifs is also involved in NO response []. A Staphylococcus aureus protein (P72360 from SWISSPROT) has been noted to be important when the organism switches to living in environments with low oxygen concentrations; perhaps this protein acts as an oxygen store or scavenger.; PDB: 3CAX_A 3V5Z_B 3U9M_G 3V5Y_A 3U9J_B 3V5X_A 2MHR_A 1A7E_A 1A7D_A 2IGF_P ....
Probab=99.35 E-value=2.7e-12 Score=125.36 Aligned_cols=129 Identities=33% Similarity=0.452 Sum_probs=116.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccHHHHHHHHHHHHHHhcccCccccccchHHHhhhcc---hHHHHHHHH
Q 001136 41 PILIFCFFHKAVRNELDALHQLAMNFATGHRVDILSLSERYRFLHSVYKHHSNAEDEVIFPALDIRVK---NVARKYSLE 117 (1143)
Q Consensus 41 Pi~~m~~~H~aLRreL~~L~~la~~~~~gd~~~~~~L~~~~~~l~~~L~~HH~~EDevLFPaL~~R~p---~vl~~le~E 117 (1143)
+++.+...|+.|++.++.+...+... ++..+...+...+.+|...+..||..||+++||.|..+.+ +.+..+..|
T Consensus 2 ~i~~l~~~H~~~~~~~~~l~~~~~~~--~~~~~~~~l~~~~~~l~~~l~~H~~~EE~~l~p~l~~~~~~~~~~~~~~~~e 79 (133)
T PF01814_consen 2 PIDELRRDHRALRRLLAELEEALDEL--PDDEDLRALRELLDELRRELRHHHAREEEYLFPALERRDPRGDALIAELRRE 79 (133)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHH-CCCHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhC--cCchhHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhccccchhhHHHH
Confidence 68899999999999999999999998 5666899999999999999999999999999999995543 788999999
Q ss_pred HHHHHHHHHHHHHHHhhhccCCCCchHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Q 001136 118 HEGESNLFDHLFQLLNSYTQNDESFPKELASCSRALQTSINQHMSKEEQQVFPLL 172 (1143)
Q Consensus 118 H~~i~~ll~~L~~~l~~~~~~~~~~~~eLa~~l~~l~~~L~~HL~~EE~~lfPLa 172 (1143)
|..+...++++...+.... +.......+...+..|...+.+|+.+||+.+||++
T Consensus 80 H~~~~~~l~~l~~~~~~~~-~~~~~~~~~~~~~~~l~~~l~~H~~~Ee~~l~P~~ 133 (133)
T PF01814_consen 80 HEEIRALLDELEEALARYS-GDEEDAEELREALRALAEWLRRHIAKEEEVLFPLL 133 (133)
T ss_dssp HHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHTHGGGHHHH
T ss_pred HHHHHHHHHHHHHHHhhCc-cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 9999999999999999886 33345678899999999999999999999999986
No 6
>PF01814 Hemerythrin: Hemerythrin HHE cation binding domain; InterPro: IPR012312 The haemerythrin family is composed of haemerythrin proteins found in invertebrates, and a broader collection of bacterial and archaeal homologues. Haemerythrin is an oxygen-binding protein found in the vascular system and coelemic fluid, or in muscles (myohaemerythrin) in invertebrates []. Many of the homologous proteins found in prokaryotes are multi-domain proteins with signal-transducing domains such as the GGDEF diguanylate cyclase domain (IPR000160 from INTERPRO) and methyl-accepting chemotaxis protein (MCP) signalling domain (IPR004089 from INTERPRO). Most haemerythrins are oxygen-carriers with a bound non-haem iron, but at least one example is a cadmium-binding protein, apparently with a role in sequestering toxic metals rather than in binding oxygen. The prokaryote with the most instances of this domain is Magnetococcus sp. MC-1, a magnetotactic bacterium. Haemerythrins and myohaemerythrins [, ] are small proteins of about 110 to 129 amino acid residues that bind two iron atoms. They are left-twisted 4-alpha-helical bundles, which provide a hydrophobic pocket where dioxygen binds as a peroxo species, interacting with adjacent aliphatic side chains via van der Waals forces []. In both haemerythrins and myohaemerythrins, the active centre is a binuclear iron complex, bound directly to the protein via 7 amino acid side chains [], 5 His, 1 Glu and 1 Asp []. Ovohaemerythrin [], a yolk protein from the leech Theromyzon tessulatum seems to belong to this family of proteins, it may play a role in the detoxification of free iron after a blood meal []. This entry represents a haemerythrin/HHE cation-binding motif that occurs as a duplicated domain in haemerythrin and related proteins. This domain binds iron in haemerythrin, but can bind other metals in related proteins, such as cadmium in a Nereis diversicolor protein (P80255 from SWISSPROT). A bacterial protein, Q7WX96 from SWISSPROT, is a regulator of response to NO, which suggests a different set-up for its metal ligands. A protein from Cryptococcus neoformans (Filobasidiella neoformans) that contains haemerythrin/HHE cation-binding motifs is also involved in NO response []. A Staphylococcus aureus protein (P72360 from SWISSPROT) has been noted to be important when the organism switches to living in environments with low oxygen concentrations; perhaps this protein acts as an oxygen store or scavenger.; PDB: 3CAX_A 3V5Z_B 3U9M_G 3V5Y_A 3U9J_B 3V5X_A 2MHR_A 1A7E_A 1A7D_A 2IGF_P ....
Probab=99.18 E-value=1.9e-10 Score=112.35 Aligned_cols=125 Identities=26% Similarity=0.351 Sum_probs=111.5
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHhhccCCcccHHHHHHHHHHHHHHhhhhhhcccccccccccc--------cccch
Q 001136 302 YPIDEILLWHNAIRQELNEIAEESRKIQLSGDFTNLLAFNERLQFIAEVLIFHCIAEVNVIFPAVDG--------ASSFS 373 (1143)
Q Consensus 302 ~Pi~~l~~~H~AiR~EL~~l~~~a~~~~~~~~~~~L~~L~~r~~f~~~vl~~Hs~aED~vlFPaL~~--------~~~~~ 373 (1143)
+||+.|...|+.|++.++.|...+... +...++..++..+.+|...+..|+..||.++||.|.. ...+.
T Consensus 1 ~~i~~l~~~H~~~~~~~~~l~~~~~~~---~~~~~~~~l~~~~~~l~~~l~~H~~~EE~~l~p~l~~~~~~~~~~~~~~~ 77 (133)
T PF01814_consen 1 MPIDELRRDHRALRRLLAELEEALDEL---PDDEDLRALRELLDELRRELRHHHAREEEYLFPALERRDPRGDALIAELR 77 (133)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHHHHHH---CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHHHH-CCCHHHHHHHH
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHhC---cCchhHHHHHHHHHHHHHHHHHHHHHHHHhhccccccchhccccchhhHH
Confidence 479999999999999999999999987 4555689999999999999999999999999999983 22899
Q ss_pred hhhHHHHhHHHHHHHHHHHHhhcCCccchHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhh
Q 001136 374 QKHAEEESQFNDFRLLIESIQNEGAISTSAEFYAKLCSHADQIMETIERHFHKVEVQVLPLA 435 (1143)
Q Consensus 374 ~EH~~i~~~~~~f~~ll~~~~~~~~~~~~~~~~~~L~~~l~~l~~~L~~Hf~kEE~qvfPL~ 435 (1143)
.||..+...++.+...+.... .. ......+...+..+...|..|+.+||+.|||++
T Consensus 78 ~eH~~~~~~l~~l~~~~~~~~-~~-----~~~~~~~~~~~~~l~~~l~~H~~~Ee~~l~P~~ 133 (133)
T PF01814_consen 78 REHEEIRALLDELEEALARYS-GD-----EEDAEELREALRALAEWLRRHIAKEEEVLFPLL 133 (133)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH-HH-----HHHHHHHHHHHHHHHHHHHHHHHHTHGGGHHHH
T ss_pred HHHHHHHHHHHHHHHHHhhCc-cc-----cchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 999999999999999988876 11 345789999999999999999999999999986
No 7
>PRK10992 iron-sulfur cluster repair di-iron protein; Provisional
Probab=99.17 E-value=2e-10 Score=124.78 Aligned_cols=132 Identities=20% Similarity=0.260 Sum_probs=114.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhc---CCCcccHHHHHHHHHHHHHHhcccCccccccchHHHhhhc----chHHHHHH
Q 001136 43 LIFCFFHKAVRNELDALHQLAMNFA---TGHRVDILSLSERYRFLHSVYKHHSNAEDEVIFPALDIRV----KNVARKYS 115 (1143)
Q Consensus 43 ~~m~~~H~aLRreL~~L~~la~~~~---~gd~~~~~~L~~~~~~l~~~L~~HH~~EDevLFPaL~~R~----p~vl~~le 115 (1143)
.++...|..+|+.+..|..++..+. +.+.+....+...+.+|...+..||.+||.+|||+|.+.. ...+..|.
T Consensus 78 yI~~~~H~~~r~~lp~L~~l~~kv~~vhg~~~~~~~~~~~l~~~~~~el~~H~~kEE~~LFP~l~~~~~~~~~~pi~vm~ 157 (220)
T PRK10992 78 HIIVRYHDRHREQLPELILLATKVERVHGDKPDCPRGLAKYLTALHEELSSHMMKEEQILFPMIKQGMGSQAMGPISVME 157 (220)
T ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhcccccccchHHHHH
Confidence 4558899999999999999998876 5555677889999999999999999999999999999633 25789999
Q ss_pred HHHHHHHHHHHHHHHHHhhhccCCC--CchHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhc
Q 001136 116 LEHEGESNLFDHLFQLLNSYTQNDE--SFPKELASCSRALQTSINQHMSKEEQQVFPLLTQ 174 (1143)
Q Consensus 116 ~EH~~i~~ll~~L~~~l~~~~~~~~--~~~~eLa~~l~~l~~~L~~HL~~EE~~lfPLa~~ 174 (1143)
.||.++...+.+|+++.+.+..+.+ ..+..+...+..|...|.+|+.+||.++||.+..
T Consensus 158 ~EHd~~~~~l~~L~~lt~~~~~p~~ac~~~~~l~~~l~~~~~dL~~HI~~EnniLFP~a~~ 218 (220)
T PRK10992 158 SEHDEAGELLEVIKHLTNNVTPPPEACTTWRALYNGINELIDDLMEHIHLENNVLFPRALA 218 (220)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCChhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 9999999999999999988754332 3467788899999999999999999999998864
No 8
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=99.08 E-value=3.5e-11 Score=97.96 Aligned_cols=44 Identities=39% Similarity=1.022 Sum_probs=38.7
Q ss_pred CCCcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCC
Q 001136 1021 TNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICS 1065 (1143)
Q Consensus 1021 ~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr 1065 (1143)
++|+||+++ |.....+..++|||.||.+|+.+|++.+++||+||
T Consensus 1 d~C~IC~~~-~~~~~~~~~l~C~H~fh~~Ci~~~~~~~~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEE-FEDGEKVVKLPCGHVFHRSCIKEWLKRNNSCPVCR 44 (44)
T ss_dssp -CETTTTCB-HHTTSCEEEETTSEEEEHHHHHHHHHHSSB-TTTH
T ss_pred CCCcCCChh-hcCCCeEEEccCCCeeCHHHHHHHHHhCCcCCccC
Confidence 479999999 66677888999999999999999999999999996
No 9
>TIGR03652 FeS_repair_RIC iron-sulfur cluster repair di-iron protein. Members of this protein family, designated variously as YftE, NorA, DrnN, and NipC, are di-iron proteins involved in the repair of iron-sulfur clusters. Previously assigned names reflect pleiotropic effects of damage from NO or other oxidative stress when this protein is mutated. The suggested name now is RIC, for Repair of Iron Centers.
Probab=99.06 E-value=8.2e-10 Score=119.89 Aligned_cols=130 Identities=27% Similarity=0.404 Sum_probs=110.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhc---CCCcccHHHHHHHHHHHHHHhcccCccccccchHHHhh--h-cc-----hHH
Q 001136 43 LIFCFFHKAVRNELDALHQLAMNFA---TGHRVDILSLSERYRFLHSVYKHHSNAEDEVIFPALDI--R-VK-----NVA 111 (1143)
Q Consensus 43 ~~m~~~H~aLRreL~~L~~la~~~~---~gd~~~~~~L~~~~~~l~~~L~~HH~~EDevLFPaL~~--R-~p-----~vl 111 (1143)
.+....|..||+.+..|..++..+. +.+.+.+..+...++.|...+..|+.+||++|||+|++ + .+ .++
T Consensus 74 ~i~~~hH~~i~~~l~~L~~l~~kv~~~hg~~~~~l~~l~~~~~~~~~eL~~H~~kEE~~LFP~l~~~~~g~~~~~~~~pi 153 (216)
T TIGR03652 74 HIVDRHHEYLREELPELIPLATKVARVHGDHHPELIGLAELFRELKAELEQHLMKEEQILFPAIIEYKRGNPAQAIGTPI 153 (216)
T ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHHHhCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHccCccccccchH
Confidence 6788899999999999999888875 34456778889999999999999999999999999985 2 11 288
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhccCCC--CchHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Q 001136 112 RKYSLEHEGESNLFDHLFQLLNSYTQNDE--SFPKELASCSRALQTSINQHMSKEEQQVFPLL 172 (1143)
Q Consensus 112 ~~le~EH~~i~~ll~~L~~~l~~~~~~~~--~~~~eLa~~l~~l~~~L~~HL~~EE~~lfPLa 172 (1143)
..|..||.++...+.+|+.+++.+..+.+ ..+..+...+..+...+.+|+.+||.++||.+
T Consensus 154 ~~m~~EH~~~~~~l~~L~~l~~~~~~p~~ac~~~~~~~~~l~~~~~~L~~HI~~En~iLFP~~ 216 (216)
T TIGR03652 154 SVMESEHDEAGDLLKELRELTNDYTPPEDACNTWRALYSGLEELEDDLHEHIHLENNILFPRA 216 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCC
Confidence 99999999999999999999988764333 34567778899999999999999999999963
No 10
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=98.98 E-value=1.2e-10 Score=107.12 Aligned_cols=66 Identities=24% Similarity=0.640 Sum_probs=53.5
Q ss_pred CCCCcccccc---ccccccccCCcccChhhhcccCCCCCCcc-----ccceeeccccccccc-----cCCCCCCCCCCCC
Q 001136 891 VFGCEHYKRN---CKIRAACCGKLFTCRFCHDKASDHSMDRK-----ATSEMMCMHCLKIQA-----IGPNCTTPSCNGL 957 (1143)
Q Consensus 891 ~~gC~HY~r~---c~l~~~cC~k~y~Cr~CHde~~~H~~~r~-----~~~~~~C~~C~~~q~-----~~~~C~~~~cc~~ 957 (1143)
..-|-||+.. ++|+|.||+|||+|..||||.++||+.+. ..+.|+||.|.++-. -...|++ |..
T Consensus 12 etRC~Hyht~~Diialkc~~C~kyYaCy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~---C~s 88 (105)
T COG4357 12 ETRCLHYHTPLDIIALKCKCCQKYYACYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRAEYGMCGSCPY---CQS 88 (105)
T ss_pred cceeeEecCccceEeeeechhhhhhhHHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHHHHhhcCCCCC---cCC
Confidence 3469999999 89999999999999999999999988763 455699999987632 2346887 466
Q ss_pred cc
Q 001136 958 SM 959 (1143)
Q Consensus 958 ~f 959 (1143)
+|
T Consensus 89 pF 90 (105)
T COG4357 89 PF 90 (105)
T ss_pred CC
Confidence 55
No 11
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.91 E-value=7.9e-10 Score=101.43 Aligned_cols=46 Identities=22% Similarity=0.527 Sum_probs=36.4
Q ss_pred CCCcccccccccCCcceEecCCCCccchhhHHHHhcc---CCCCcCCCccc
Q 001136 1021 TNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCS---HYTCPICSKSL 1068 (1143)
Q Consensus 1021 ~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~---~~~CPiCr~s~ 1068 (1143)
+.||.|..+ .+..++....|||.||.+||.+|+.+ +.+||+||+..
T Consensus 33 g~Cp~Ck~P--gd~Cplv~g~C~H~FH~hCI~kWl~~~~~~~~CPmCR~~w 81 (85)
T PF12861_consen 33 GCCPDCKFP--GDDCPLVWGKCSHNFHMHCILKWLSTQSSKGQCPMCRQPW 81 (85)
T ss_pred cCCCCccCC--CCCCceeeccCccHHHHHHHHHHHccccCCCCCCCcCCee
Confidence 567888754 34456677789999999999999864 57899999865
No 12
>PRK13276 cell wall biosynthesis protein ScdA; Provisional
Probab=98.89 E-value=9.7e-09 Score=111.16 Aligned_cols=130 Identities=21% Similarity=0.282 Sum_probs=115.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhc---CCCcccHHHHHHHHHHHHHHhcccCccccccchHHHhhhc--------chHH
Q 001136 43 LIFCFFHKAVRNELDALHQLAMNFA---TGHRVDILSLSERYRFLHSVYKHHSNAEDEVIFPALDIRV--------KNVA 111 (1143)
Q Consensus 43 ~~m~~~H~aLRreL~~L~~la~~~~---~gd~~~~~~L~~~~~~l~~~L~~HH~~EDevLFPaL~~R~--------p~vl 111 (1143)
.+....|..+|+++..|..++.++. +++.+....+.+.+..+...|..|..+||.+|||++.+.. .+.+
T Consensus 81 ~I~~~hH~~~r~~lp~l~~l~~kV~~VHg~~~p~l~~l~~lf~~l~~eL~~H~~KEE~ilFP~i~~~~~~~~~~~~~~pI 160 (224)
T PRK13276 81 YIQSAYHEPLREEFKNLTPYVTKLSKVHGPNHPYLVELKETYDTFKNGMLEHMQKEDDVDFPKLIKYEQGEVVDDINTVI 160 (224)
T ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhhccccchhhhhHH
Confidence 6688899999999999999998875 4566788899999999999999999999999999998632 2478
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhccCCC--CchHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Q 001136 112 RKYSLEHEGESNLFDHLFQLLNSYTQNDE--SFPKELASCSRALQTSINQHMSKEEQQVFPLL 172 (1143)
Q Consensus 112 ~~le~EH~~i~~ll~~L~~~l~~~~~~~~--~~~~eLa~~l~~l~~~L~~HL~~EE~~lfPLa 172 (1143)
..|..||+...+.+.+|+++.+.++...+ ..++.+...+.+|...|.+|++.|..++||.+
T Consensus 161 ~~m~~EH~~~g~~l~~i~~lTn~yt~P~~AC~t~r~ly~~L~~fe~dL~~HIhLENnILFPr~ 223 (224)
T PRK13276 161 DDLVSDHIATGQLLVKMSELTSSYEPPIEACGTWRLVYQRLKALEVLTHEHVHLENHVLFKKV 223 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCC
Confidence 99999999999999999999999976555 67788999999999999999999999999953
No 13
>COG2846 Regulator of cell morphogenesis and NO signaling [Cell division and chromosome partitioning]
Probab=98.85 E-value=2.4e-08 Score=103.99 Aligned_cols=131 Identities=22% Similarity=0.306 Sum_probs=115.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhc---CCCcccHHHHHHHHHHHHHHhcccCccccccchHHHhhhcc----hHHHHHH
Q 001136 43 LIFCFFHKAVRNELDALHQLAMNFA---TGHRVDILSLSERYRFLHSVYKHHSNAEDEVIFPALDIRVK----NVARKYS 115 (1143)
Q Consensus 43 ~~m~~~H~aLRreL~~L~~la~~~~---~gd~~~~~~L~~~~~~l~~~L~~HH~~EDevLFPaL~~R~p----~vl~~le 115 (1143)
.++...|...|.+|..|-.++.++. +..+.-...+...+..+...+.-|..+||+++||.+.+-.. .++..|+
T Consensus 79 hIi~ryH~~hReqlpeLi~latKverVHgd~p~~p~gl~~~L~~l~~eL~~HMmKEEqIlFPmi~~G~g~~a~~pI~vm~ 158 (221)
T COG2846 79 HIIVRYHERHREQLPELIPLATKVERVHGDKPSCPAGLAELLEALKEELESHMMKEEQILFPMIKQGMGSQAAGPISVME 158 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHhhHHHHhccCcccCcchHHHH
Confidence 6789999999999999988888875 34455778889999999999999999999999999986332 6899999
Q ss_pred HHHHHHHHHHHHHHHHHhhhccCCC--CchHHHHHHHHHHHHHHHHHHHHHHHhHHHHHh
Q 001136 116 LEHEGESNLFDHLFQLLNSYTQNDE--SFPKELASCSRALQTSINQHMSKEEQQVFPLLT 173 (1143)
Q Consensus 116 ~EH~~i~~ll~~L~~~l~~~~~~~~--~~~~eLa~~l~~l~~~L~~HL~~EE~~lfPLa~ 173 (1143)
.||.+...+++.+.++.+.+....+ ..++.+..-+.+|.+.+..|++.|..++||.+.
T Consensus 159 ~EHde~g~~l~~lk~lT~n~tpP~~AC~tWkalY~gl~~~~dDl~~HIHLENnvLFpr~~ 218 (221)
T COG2846 159 SEHDEAGELLEVLKHLTNNYTPPEEACGTWKALYNGLNEFIDDLMEHIHLENNVLFPRVL 218 (221)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCChHHHhHHHHHHHHHHHHHHHHHHHHHhhhccccchhc
Confidence 9999999999999999998875544 567889999999999999999999999999875
No 14
>PRK10992 iron-sulfur cluster repair di-iron protein; Provisional
Probab=98.82 E-value=2.7e-08 Score=108.30 Aligned_cols=131 Identities=19% Similarity=0.330 Sum_probs=108.9
Q ss_pred hHHH-HHHHHHHHHHHHHHHHHHHHhhc-cC-CcccHHHHHHHHHHHHHHhhhhhhccccccccccccc---------cc
Q 001136 304 IDEI-LLWHNAIRQELNEIAEESRKIQL-SG-DFTNLLAFNERLQFIAEVLIFHCIAEVNVIFPAVDGA---------SS 371 (1143)
Q Consensus 304 i~~l-~~~H~AiR~EL~~l~~~a~~~~~-~~-~~~~L~~L~~r~~f~~~vl~~Hs~aED~vlFPaL~~~---------~~ 371 (1143)
|+.| ...|..+|++|..|.+++.++.. -| +.+-+..++.-+.-|...+..|+..|+.++||+|.+. ..
T Consensus 76 idyI~~~~H~~~r~~lp~L~~l~~kv~~vhg~~~~~~~~~~~l~~~~~~el~~H~~kEE~~LFP~l~~~~~~~~~~pi~v 155 (220)
T PRK10992 76 IDHIIVRYHDRHREQLPELILLATKVERVHGDKPDCPRGLAKYLTALHEELSSHMMKEEQILFPMIKQGMGSQAMGPISV 155 (220)
T ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhcccccccchHHH
Confidence 5655 78899999999999999988852 23 2234789999999999999999999999999999971 28
Q ss_pred chhhhHHHHhHHHHHHHHHHHHhhcCCccchHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhh
Q 001136 372 FSQKHAEEESQFNDFRLLIESIQNEGAISTSAEFYAKLCSHADQIMETIERHFHKVEVQVLPLARN 437 (1143)
Q Consensus 372 ~~~EH~~i~~~~~~f~~ll~~~~~~~~~~~~~~~~~~L~~~l~~l~~~L~~Hf~kEE~qvfPL~~k 437 (1143)
|..||..+...+.++..++...... ..+...++.+-..+..+...|.+|..+||+.|||++..
T Consensus 156 m~~EHd~~~~~l~~L~~lt~~~~~p---~~ac~~~~~l~~~l~~~~~dL~~HI~~EnniLFP~a~~ 218 (220)
T PRK10992 156 MESEHDEAGELLEVIKHLTNNVTPP---PEACTTWRALYNGINELIDDLMEHIHLENNVLFPRALA 218 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCC---hhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 9999999999999999888765322 11234578888899999999999999999999998763
No 15
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=98.81 E-value=2.4e-09 Score=95.58 Aligned_cols=60 Identities=22% Similarity=0.368 Sum_probs=49.1
Q ss_pred CCCCccccCCCCCccccccCCcccccccccccccccccccCCCCcccccccc-cCCcceEecCCCCccchhhHHHHhccC
Q 001136 980 PFCNLCRVGGGLGVDFFHCMTCNCCLGLKLLNHKCLEKCLETNCPICCDFLF-TSSETVRALPCGHYMHLACFQAYTCSH 1058 (1143)
Q Consensus 980 ~~CgiCr~g~~l~~~~~hC~~C~~C~~~~~~~H~C~e~~~~~~CpIC~e~lf-~s~~~v~~lpCgH~fH~~Ci~~wl~~~ 1058 (1143)
|.|||||+... +.||-|...+- .+..++.+.-|.|.||.+||.+|+.++
T Consensus 21 d~CaICRnhim------------------------------~~C~eCq~~~~~~~eC~v~wG~CnHaFH~HCI~rWL~Tk 70 (88)
T COG5194 21 DVCAICRNHIM------------------------------GTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTK 70 (88)
T ss_pred chhhhhhcccc------------------------------CcCcccccCCCCCCcceEEEEecchHHHHHHHHHHHhhC
Confidence 88999999864 67888876432 233477778899999999999999999
Q ss_pred CCCcCCCcccc
Q 001136 1059 YTCPICSKSLG 1069 (1143)
Q Consensus 1059 ~~CPiCr~s~~ 1069 (1143)
..||+|+++..
T Consensus 71 ~~CPld~q~w~ 81 (88)
T COG5194 71 GVCPLDRQTWV 81 (88)
T ss_pred CCCCCCCceeE
Confidence 99999998763
No 16
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=98.80 E-value=1.9e-09 Score=119.98 Aligned_cols=57 Identities=35% Similarity=0.811 Sum_probs=48.5
Q ss_pred cccCCCCcccccccccCC---------cceEecCCCCccchhhHHHHhccCCCCcCCCcc-ccchhh
Q 001136 1017 KCLETNCPICCDFLFTSS---------ETVRALPCGHYMHLACFQAYTCSHYTCPICSKS-LGDMAI 1073 (1143)
Q Consensus 1017 ~~~~~~CpIC~e~lf~s~---------~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s-~~~m~~ 1073 (1143)
...+..|.||||+||.++ ...+.|||||.+|.+|++.|+.++++|||||.+ ++|+..
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~ifd~~~ 350 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPVIFDQSS 350 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhccCCCcccCccccccCC
Confidence 456788999999988765 234679999999999999999999999999999 567654
No 17
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 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 domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=98.77 E-value=4.6e-09 Score=95.04 Aligned_cols=46 Identities=33% Similarity=0.792 Sum_probs=36.9
Q ss_pred CCCCcccccccccC---------CcceEecCCCCccchhhHHHHhccCCCCcCCC
Q 001136 1020 ETNCPICCDFLFTS---------SETVRALPCGHYMHLACFQAYTCSHYTCPICS 1065 (1143)
Q Consensus 1020 ~~~CpIC~e~lf~s---------~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr 1065 (1143)
+++|+||++.|.+. ...+..++|||.||.+||.+|++.+.+||+||
T Consensus 19 ~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~~~CP~CR 73 (73)
T PF12678_consen 19 DDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQNNTCPLCR 73 (73)
T ss_dssp CSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTSSB-TTSS
T ss_pred CCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcCCcCCCCC
Confidence 56799999886322 34667779999999999999999999999997
No 18
>TIGR03652 FeS_repair_RIC iron-sulfur cluster repair di-iron protein. Members of this protein family, designated variously as YftE, NorA, DrnN, and NipC, are di-iron proteins involved in the repair of iron-sulfur clusters. Previously assigned names reflect pleiotropic effects of damage from NO or other oxidative stress when this protein is mutated. The suggested name now is RIC, for Repair of Iron Centers.
Probab=98.75 E-value=4.9e-08 Score=106.14 Aligned_cols=129 Identities=22% Similarity=0.342 Sum_probs=105.3
Q ss_pred hHHH-HHHHHHHHHHHHHHHHHHHHhhc--cCCcccHHHHHHHHHHHHHHhhhhhhcccccccccccc------------
Q 001136 304 IDEI-LLWHNAIRQELNEIAEESRKIQL--SGDFTNLLAFNERLQFIAEVLIFHCIAEVNVIFPAVDG------------ 368 (1143)
Q Consensus 304 i~~l-~~~H~AiR~EL~~l~~~a~~~~~--~~~~~~L~~L~~r~~f~~~vl~~Hs~aED~vlFPaL~~------------ 368 (1143)
|+.| ...|+.||++|..|...+.++.. ..+...+..+..-+..|.+.+..|+..|++++||+|.+
T Consensus 72 id~i~~~hH~~i~~~l~~L~~l~~kv~~~hg~~~~~l~~l~~~~~~~~~eL~~H~~kEE~~LFP~l~~~~~g~~~~~~~~ 151 (216)
T TIGR03652 72 IDHIVDRHHEYLREELPELIPLATKVARVHGDHHPELIGLAELFRELKAELEQHLMKEEQILFPAIIEYKRGNPAQAIGT 151 (216)
T ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHhCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHccCccccccc
Confidence 4444 56899999999999999988853 22333478999999999999999999999999999973
Q ss_pred -cccchhhhHHHHhHHHHHHHHHHHHhhcCCccchHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhh
Q 001136 369 -ASSFSQKHAEEESQFNDFRLLIESIQNEGAISTSAEFYAKLCSHADQIMETIERHFHKVEVQVLPLA 435 (1143)
Q Consensus 369 -~~~~~~EH~~i~~~~~~f~~ll~~~~~~~~~~~~~~~~~~L~~~l~~l~~~L~~Hf~kEE~qvfPL~ 435 (1143)
...|..||+.+.+.+.++..++..... +..+...+..+...+..+...|.+|..+||+.|||++
T Consensus 152 pi~~m~~EH~~~~~~l~~L~~l~~~~~~---p~~ac~~~~~~~~~l~~~~~~L~~HI~~En~iLFP~~ 216 (216)
T TIGR03652 152 PISVMESEHDEAGDLLKELRELTNDYTP---PEDACNTWRALYSGLEELEDDLHEHIHLENNILFPRA 216 (216)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHcCCCC---CcchhHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCC
Confidence 126999999999999999988876542 2222345678888899999999999999999999975
No 19
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.73 E-value=4.3e-09 Score=119.52 Aligned_cols=49 Identities=27% Similarity=0.854 Sum_probs=44.4
Q ss_pred CCCcccccccccCCcceEecCCCCccchhhHHHHhccC-CCCcCCCccccc
Q 001136 1021 TNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSH-YTCPICSKSLGD 1070 (1143)
Q Consensus 1021 ~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~-~~CPiCr~s~~~ 1070 (1143)
..|.||+|+ |..+++++.|||+|.||..|+++|+... ..||+|+..+..
T Consensus 230 ~~CaIClEd-Y~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~di~~ 279 (348)
T KOG4628|consen 230 DTCAICLED-YEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKRDIRT 279 (348)
T ss_pred ceEEEeecc-cccCCeeeEecCCCchhhccchhhHhhcCccCCCCCCcCCC
Confidence 589999999 9999999999999999999999998666 559999998854
No 20
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=98.59 E-value=1.5e-08 Score=115.92 Aligned_cols=81 Identities=27% Similarity=0.750 Sum_probs=66.6
Q ss_pred CCCcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCCccccchhhhhhhhHHHHhhcCCChhhhcCcceEEc
Q 001136 1021 TNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLGDMAIYFGMIDALLAAEELPEEYRNQVQDILC 1100 (1143)
Q Consensus 1021 ~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~~~m~~~~~~ld~~i~~~p~P~~y~~~~~~i~C 1100 (1143)
.+||||+|.|..+...+..+.|.|+||..|+..|. ..+||+||.... |+ ....-.|
T Consensus 176 PTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~--~~scpvcR~~q~------------------p~----~ve~~~c 231 (493)
T KOG0804|consen 176 PTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW--DSSCPVCRYCQS------------------PS----VVESSLC 231 (493)
T ss_pred CCcchhHhhcCccccceeeeecccccchHHHhhcc--cCcChhhhhhcC------------------cc----hhhhhhh
Confidence 47999999999999999999999999999999994 679999995443 11 1113469
Q ss_pred CCCCCCCcccchhhcccCCC--CCCccccc
Q 001136 1101 NDCEQKGAARFHWLYHKCGF--CGSYNTRL 1128 (1143)
Q Consensus 1101 ndC~~~s~~~~h~l~~kC~~--C~syNt~~ 1128 (1143)
..|+...+. |+++.|++ ||.|+-.-
T Consensus 232 ~~c~~~~~L---wicliCg~vgcgrY~egh 258 (493)
T KOG0804|consen 232 LACGCTEDL---WICLICGNVGCGRYKEGH 258 (493)
T ss_pred hhhcccccE---EEEEEccceecccccchh
Confidence 999988777 99999987 99998753
No 21
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=98.49 E-value=2.3e-08 Score=93.55 Aligned_cols=62 Identities=23% Similarity=0.384 Sum_probs=47.9
Q ss_pred ccCCCCCccccCCCCCccccccCCcccccccccccccccccccCCCCccccccc--ccCCcceEecCCCCccchhhHHHH
Q 001136 977 YHCPFCNLCRVGGGLGVDFFHCMTCNCCLGLKLLNHKCLEKCLETNCPICCDFL--FTSSETVRALPCGHYMHLACFQAY 1054 (1143)
Q Consensus 977 yhC~~CgiCr~g~~l~~~~~hC~~C~~C~~~~~~~H~C~e~~~~~~CpIC~e~l--f~s~~~v~~lpCgH~fH~~Ci~~w 1054 (1143)
.-||.|.|||+... +.|.-|+... -.....|.+.-|.|+||.+||.+|
T Consensus 44 i~vDnCAICRnHIM------------------------------d~CieCQa~~~~~~~EC~VaWG~CNHaFH~hCisrW 93 (114)
T KOG2930|consen 44 IVVDNCAICRNHIM------------------------------DLCIECQANQSATSEECTVAWGVCNHAFHFHCISRW 93 (114)
T ss_pred eeechhHHHHHHHH------------------------------HHHHhhccCCCCCCCceEEEeeecchHHHHHHHHHH
Confidence 45899999999864 3455555543 222345677789999999999999
Q ss_pred hccCCCCcCCCccc
Q 001136 1055 TCSHYTCPICSKSL 1068 (1143)
Q Consensus 1055 l~~~~~CPiCr~s~ 1068 (1143)
+++++.||+|.+.-
T Consensus 94 lktr~vCPLdn~eW 107 (114)
T KOG2930|consen 94 LKTRNVCPLDNKEW 107 (114)
T ss_pred HhhcCcCCCcCcce
Confidence 99999999998753
No 22
>COG3945 Uncharacterized conserved protein [Function unknown]
Probab=98.48 E-value=1.6e-06 Score=89.45 Aligned_cols=142 Identities=18% Similarity=0.230 Sum_probs=113.1
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHhhccCCcccHHHHHHHHHHHHHHh-hhhhhccccccccccccc---------cc
Q 001136 302 YPIDEILLWHNAIRQELNEIAEESRKIQLSGDFTNLLAFNERLQFIAEVL-IFHCIAEVNVIFPAVDGA---------SS 371 (1143)
Q Consensus 302 ~Pi~~l~~~H~AiR~EL~~l~~~a~~~~~~~~~~~L~~L~~r~~f~~~vl-~~Hs~aED~vlFPaL~~~---------~~ 371 (1143)
.-|..|+-=|+.|.+-|.-|+.....+. +| .-+-+.+..-++|++..- +.||..||.++||-|... ..
T Consensus 8 ~~i~~lvEeH~yIlraL~iLr~~~~~~~-~g-~i~y~~v~~iidFi~nfaDkcHH~KEE~~LF~~m~~~g~~~~~~~i~~ 85 (189)
T COG3945 8 DSIKLLVEEHTYILRALSILRKALDLIK-NG-PIDYSDVKEIIDFIRNFADKCHHGKEEKLLFNYMEHEGGPFEEGPIYV 85 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccc-CC-CCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHhCCCcccCceee
Confidence 4577889999999999999988888775 33 323345555555555433 479999999999998763 39
Q ss_pred chhhhHHHHhHHHHHHHHHHHHhhcCCccchHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhcCCHHHHHHHHHHH
Q 001136 372 FSQKHAEEESQFNDFRLLIESIQNEGAISTSAEFYAKLCSHADQIMETIERHFHKVEVQVLPLARNHFSFKRQREILYQS 451 (1143)
Q Consensus 372 ~~~EH~~i~~~~~~f~~ll~~~~~~~~~~~~~~~~~~L~~~l~~l~~~L~~Hf~kEE~qvfPL~~k~~S~eEQ~~L~~~~ 451 (1143)
|..||.....++-.|...+..+.+.+. +....++..+..-..-|.+|+++|++++||+|++.||.+ |.++.++.
T Consensus 86 m~~EH~~~R~i~r~lee~~~~~kngd~-----~~~~~~i~~A~~y~~likrHIdkEdnvlfp~a~~~~s~e-~~~v~~e~ 159 (189)
T COG3945 86 MTVEHGEGRYIIRDLEEAYERLKNGDE-----DSKDDVIDYAVAYLNLIKRHIDKEDNVLFPFAESTLSEE-LNEVNSEC 159 (189)
T ss_pred ehhhhhhHHHHHHHHHHHHHHHHcccc-----chHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHH-HHHHHHHH
Confidence 999999999999999999999986642 224678888888888999999999999999999999999 77776654
No 23
>PHA02929 N1R/p28-like protein; Provisional
Probab=98.45 E-value=1.2e-07 Score=103.60 Aligned_cols=52 Identities=19% Similarity=0.560 Sum_probs=41.5
Q ss_pred ccCCCCcccccccccCCc----ceEecCCCCccchhhHHHHhccCCCCcCCCcccc
Q 001136 1018 CLETNCPICCDFLFTSSE----TVRALPCGHYMHLACFQAYTCSHYTCPICSKSLG 1069 (1143)
Q Consensus 1018 ~~~~~CpIC~e~lf~s~~----~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~~ 1069 (1143)
+.+..||||++.+..... -....+|||.||..||.+|+..+.+||+||..+.
T Consensus 172 ~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~ 227 (238)
T PHA02929 172 SKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI 227 (238)
T ss_pred CCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence 446789999998554321 1234579999999999999999999999998875
No 24
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=98.42 E-value=4.1e-08 Score=87.16 Aligned_cols=56 Identities=25% Similarity=0.508 Sum_probs=42.4
Q ss_pred CCCccccCCCCCccccccCCcccccccccccccccccccCCCCcccccccccCCcceEecCCCCccchhhHHHHhc---c
Q 001136 981 FCNLCRVGGGLGVDFFHCMTCNCCLGLKLLNHKCLEKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTC---S 1057 (1143)
Q Consensus 981 ~CgiCr~g~~l~~~~~hC~~C~~C~~~~~~~H~C~e~~~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~---~ 1057 (1143)
.|||||+.+. +.||-|.-+ .+..++.+.-|.|.||.+||.+|+. +
T Consensus 22 ~CGiCRm~Fd------------------------------g~Cp~Ck~P--gDdCPLv~G~C~h~fh~hCI~~wl~~~ts 69 (84)
T KOG1493|consen 22 TCGICRMPFD------------------------------GCCPDCKLP--GDDCPLVWGYCLHAFHAHCILKWLNTPTS 69 (84)
T ss_pred ccceEecccC------------------------------CcCCCCcCC--CCCCccHHHHHHHHHHHHHHHHHhcCccc
Confidence 8999999874 456666533 3444555556999999999999974 3
Q ss_pred CCCCcCCCccc
Q 001136 1058 HYTCPICSKSL 1068 (1143)
Q Consensus 1058 ~~~CPiCr~s~ 1068 (1143)
...||+||++.
T Consensus 70 q~~CPmcRq~~ 80 (84)
T KOG1493|consen 70 QGQCPMCRQTW 80 (84)
T ss_pred cccCCcchhee
Confidence 47799999865
No 25
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.40 E-value=1.3e-07 Score=103.44 Aligned_cols=54 Identities=28% Similarity=0.746 Sum_probs=46.7
Q ss_pred ccccCCCCcccccccccCCcceEecCCCCccchhhHHHHhc-cCCCCcCCCccccc
Q 001136 1016 EKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTC-SHYTCPICSKSLGD 1070 (1143)
Q Consensus 1016 e~~~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~-~~~~CPiCr~s~~~ 1070 (1143)
|....-+|.|||++ |...+.++++||.|.||..|+++|+. .+..||+||..++.
T Consensus 319 ea~~GveCaICms~-fiK~d~~~vlPC~H~FH~~Cv~kW~~~y~~~CPvCrt~iPP 373 (374)
T COG5540 319 EADKGVECAICMSN-FIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCRTAIPP 373 (374)
T ss_pred hcCCCceEEEEhhh-hcccceEEEeccCceechhHHHHHHhhhcccCCccCCCCCC
Confidence 34445689999999 78888899999999999999999986 67899999987753
No 26
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=98.36 E-value=2.9e-07 Score=73.52 Aligned_cols=44 Identities=39% Similarity=0.951 Sum_probs=36.7
Q ss_pred CCcccccccccCCcceEecCCCCccchhhHHHHhcc-CCCCcCCCccc
Q 001136 1022 NCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCS-HYTCPICSKSL 1068 (1143)
Q Consensus 1022 ~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~-~~~CPiCr~s~ 1068 (1143)
.|+||++.+ ...+...+|||.||..|+..|+.. +.+||+|++.+
T Consensus 1 ~C~iC~~~~---~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~~~ 45 (45)
T cd00162 1 ECPICLEEF---REPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45 (45)
T ss_pred CCCcCchhh---hCceEecCCCChhcHHHHHHHHHhCcCCCCCCCCcC
Confidence 499999984 445566779999999999999876 78899999754
No 27
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=98.32 E-value=3.2e-07 Score=72.91 Aligned_cols=39 Identities=41% Similarity=0.982 Sum_probs=33.0
Q ss_pred CcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCC
Q 001136 1023 CPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPIC 1064 (1143)
Q Consensus 1023 CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiC 1064 (1143)
||||++.+. .++..++|||.|+..|+.+|++.+.+||+|
T Consensus 1 C~iC~~~~~---~~~~~~~CGH~fC~~C~~~~~~~~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELR---DPVVVTPCGHSFCKECIEKYLEKNPKCPVC 39 (39)
T ss_dssp ETTTTSB-S---SEEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred CCCCCCccc---CcCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence 899999732 366789999999999999999889999998
No 28
>PRK13276 cell wall biosynthesis protein ScdA; Provisional
Probab=98.32 E-value=3.4e-06 Score=91.71 Aligned_cols=129 Identities=13% Similarity=0.171 Sum_probs=110.8
Q ss_pred hHH-HHHHHHHHHHHHHHHHHHHHHhhc--cCCcccHHHHHHHHHHHHHHhhhhhhcccccccccccc------------
Q 001136 304 IDE-ILLWHNAIRQELNEIAEESRKIQL--SGDFTNLLAFNERLQFIAEVLIFHCIAEVNVIFPAVDG------------ 368 (1143)
Q Consensus 304 i~~-l~~~H~AiR~EL~~l~~~a~~~~~--~~~~~~L~~L~~r~~f~~~vl~~Hs~aED~vlFPaL~~------------ 368 (1143)
|+. +...|..+|++|-.|...+.++.. .++.+-+..+...+.-+..-|..|-..|+.++||++.+
T Consensus 79 id~I~~~hH~~~r~~lp~l~~l~~kV~~VHg~~~p~l~~l~~lf~~l~~eL~~H~~KEE~ilFP~i~~~~~~~~~~~~~~ 158 (224)
T PRK13276 79 IQYIQSAYHEPLREEFKNLTPYVTKLSKVHGPNHPYLVELKETYDTFKNGMLEHMQKEDDVDFPKLIKYEQGEVVDDINT 158 (224)
T ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhhccccchhhhh
Confidence 444 367899999999999999999853 33445689999999999999999999999999999965
Q ss_pred -cccchhhhHHHHhHHHHHHHHHHHHhhcCCccchHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhh
Q 001136 369 -ASSFSQKHAEEESQFNDFRLLIESIQNEGAISTSAEFYAKLCSHADQIMETIERHFHKVEVQVLPLA 435 (1143)
Q Consensus 369 -~~~~~~EH~~i~~~~~~f~~ll~~~~~~~~~~~~~~~~~~L~~~l~~l~~~L~~Hf~kEE~qvfPL~ 435 (1143)
+..|+.||+...+.+.+++.++..... |..+...++.|=..+.++...|-+|...|-+.|||-+
T Consensus 159 pI~~m~~EH~~~g~~l~~i~~lTn~yt~---P~~AC~t~r~ly~~L~~fe~dL~~HIhLENnILFPr~ 223 (224)
T PRK13276 159 VIDDLVSDHIATGQLLVKMSELTSSYEP---PIEACGTWRLVYQRLKALEVLTHEHVHLENHVLFKKV 223 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCCCC---CcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCC
Confidence 138999999999999999999988753 3344667899999999999999999999999999944
No 29
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=98.15 E-value=1.3e-06 Score=73.15 Aligned_cols=46 Identities=33% Similarity=0.826 Sum_probs=38.3
Q ss_pred CCCCcccccccccCCcceEecCCCCc-cchhhHHHHhccCCCCcCCCcccc
Q 001136 1020 ETNCPICCDFLFTSSETVRALPCGHY-MHLACFQAYTCSHYTCPICSKSLG 1069 (1143)
Q Consensus 1020 ~~~CpIC~e~lf~s~~~v~~lpCgH~-fH~~Ci~~wl~~~~~CPiCr~s~~ 1069 (1143)
+..|+||++. ...+..+||||. |+..|+..|.....+||+||+++.
T Consensus 2 ~~~C~iC~~~----~~~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFEN----PRDVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp HSB-TTTSSS----BSSEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred cCCCccCCcc----CCceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 3579999986 234678899999 999999999999999999999875
No 30
>COG2846 Regulator of cell morphogenesis and NO signaling [Cell division and chromosome partitioning]
Probab=98.14 E-value=1.4e-05 Score=83.70 Aligned_cols=130 Identities=19% Similarity=0.321 Sum_probs=111.0
Q ss_pred ch-HHHHHHHHHHHHHHHHHHHHHHHhhc-cCCccc-HHHHHHHHHHHHHHhhhhhhcccccccccccc---------cc
Q 001136 303 PI-DEILLWHNAIRQELNEIAEESRKIQL-SGDFTN-LLAFNERLQFIAEVLIFHCIAEVNVIFPAVDG---------AS 370 (1143)
Q Consensus 303 Pi-~~l~~~H~AiR~EL~~l~~~a~~~~~-~~~~~~-L~~L~~r~~f~~~vl~~Hs~aED~vlFPaL~~---------~~ 370 (1143)
-| ..+..+|+..|.||.+|-.+|.++.. -|+... +..|.+-+..|...|.-|=-.||+++||++.+ +.
T Consensus 76 lIdhIi~ryH~~hReqlpeLi~latKverVHgd~p~~p~gl~~~L~~l~~eL~~HMmKEEqIlFPmi~~G~g~~a~~pI~ 155 (221)
T COG2846 76 LIDHIIVRYHERHREQLPELIPLATKVERVHGDKPSCPAGLAELLEALKEELESHMMKEEQILFPMIKQGMGSQAAGPIS 155 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHhhHHHHhccCcccCcchH
Confidence 34 44688999999999999999999843 344443 68999999999999999999999999999988 22
Q ss_pred cchhhhHHHHhHHHHHHHHHHHHhhcCCccchHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhh
Q 001136 371 SFSQKHAEEESQFNDFRLLIESIQNEGAISTSAEFYAKLCSHADQIMETIERHFHKVEVQVLPLA 435 (1143)
Q Consensus 371 ~~~~EH~~i~~~~~~f~~ll~~~~~~~~~~~~~~~~~~L~~~l~~l~~~L~~Hf~kEE~qvfPL~ 435 (1143)
.|+.||++..++++.+..++.+.. .|..+...++.|=.-+..+.+.|-+|+.=|=++|||=+
T Consensus 156 vm~~EHde~g~~l~~lk~lT~n~t---pP~~AC~tWkalY~gl~~~~dDl~~HIHLENnvLFpr~ 217 (221)
T COG2846 156 VMESEHDEAGELLEVLKHLTNNYT---PPEEACGTWKALYNGLNEFIDDLMEHIHLENNVLFPRV 217 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCC---CChHHHhHHHHHHHHHHHHHHHHHHHHHhhhccccchh
Confidence 899999999999999999998875 33344566788889999999999999999999999954
No 31
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.05 E-value=3.5e-06 Score=68.80 Aligned_cols=44 Identities=30% Similarity=0.785 Sum_probs=38.3
Q ss_pred CCcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCCc
Q 001136 1022 NCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSK 1066 (1143)
Q Consensus 1022 ~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~ 1066 (1143)
.|+||.+. |++......++|||+|+..|+..+......||+|++
T Consensus 1 ~C~~C~~~-~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEK-YSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CCcCcCcc-ccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCCC
Confidence 49999998 566667788999999999999999866789999985
No 32
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.98 E-value=3.4e-06 Score=86.97 Aligned_cols=48 Identities=27% Similarity=0.650 Sum_probs=39.2
Q ss_pred CCCCcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCCcccc
Q 001136 1020 ETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLG 1069 (1143)
Q Consensus 1020 ~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~~ 1069 (1143)
...|||||+. ++...+ ....|||.|+..||..-++...+||+|+|.|.
T Consensus 131 ~~~CPiCl~~-~sek~~-vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 131 TYKCPICLDS-VSEKVP-VSTKCGHVFCSQCIKDALKNTNKCPTCRKKIT 178 (187)
T ss_pred ccCCCceecc-hhhccc-cccccchhHHHHHHHHHHHhCCCCCCcccccc
Confidence 3779999998 443322 33689999999999999999999999998653
No 33
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=97.97 E-value=5.4e-06 Score=63.84 Aligned_cols=38 Identities=39% Similarity=0.975 Sum_probs=32.6
Q ss_pred CcccccccccCCcceEecCCCCccchhhHHHHhc-cCCCCcCC
Q 001136 1023 CPICCDFLFTSSETVRALPCGHYMHLACFQAYTC-SHYTCPIC 1064 (1143)
Q Consensus 1023 CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~-~~~~CPiC 1064 (1143)
|+||++. ......++|||.||..|+..|+. .+.+||+|
T Consensus 1 C~iC~~~----~~~~~~~~C~H~~c~~C~~~~~~~~~~~CP~C 39 (39)
T smart00184 1 CPICLEE----LKDPVVLPCGHTFCRSCIRKWLKSGNNTCPIC 39 (39)
T ss_pred CCcCccC----CCCcEEecCCChHHHHHHHHHHHhCcCCCCCC
Confidence 8899986 34567789999999999999987 66789998
No 34
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 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 C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=97.93 E-value=6.5e-06 Score=65.84 Aligned_cols=39 Identities=38% Similarity=1.025 Sum_probs=32.6
Q ss_pred CcccccccccCCcceEecCCCCccchhhHHHHhc--cCCCCcCC
Q 001136 1023 CPICCDFLFTSSETVRALPCGHYMHLACFQAYTC--SHYTCPIC 1064 (1143)
Q Consensus 1023 CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~--~~~~CPiC 1064 (1143)
|+||++. +. .++..++|||.|+..|+.+|+. ...+||+|
T Consensus 1 C~iC~~~-~~--~~~~~~~C~H~fC~~C~~~~~~~~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEP-FE--DPVILLPCGHSFCRDCLRKWLENSGSVKCPLC 41 (41)
T ss_dssp ETTTSSB-CS--SEEEETTTSEEEEHHHHHHHHHHTSSSBTTTT
T ss_pred CCcCCcc-cc--CCCEEecCCCcchHHHHHHHHHhcCCccCCcC
Confidence 8999997 32 3336899999999999999987 56889998
No 35
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=97.90 E-value=9.5e-06 Score=85.77 Aligned_cols=53 Identities=23% Similarity=0.648 Sum_probs=40.3
Q ss_pred ccccccCCCCcccccccccCCcceEecCCCCccchhhHHHHhcc----------------CCCCcCCCccccc
Q 001136 1014 CLEKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCS----------------HYTCPICSKSLGD 1070 (1143)
Q Consensus 1014 C~e~~~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~----------------~~~CPiCr~s~~~ 1070 (1143)
=++......||||++. +. .+ ..++|||.|+..||.+|+.. ..+||+||..+..
T Consensus 12 ~~~~~~~~~CpICld~-~~--dP-VvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 12 LVDSGGDFDCNICLDQ-VR--DP-VVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred eccCCCccCCccCCCc-CC--Cc-EEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 3444456789999997 32 23 55789999999999999732 3579999999854
No 36
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=97.89 E-value=9.3e-06 Score=65.83 Aligned_cols=38 Identities=39% Similarity=1.048 Sum_probs=26.9
Q ss_pred CcccccccccCCcceEecCCCCccchhhHHHHhccC----CCCcCC
Q 001136 1023 CPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSH----YTCPIC 1064 (1143)
Q Consensus 1023 CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~----~~CPiC 1064 (1143)
||||++. |++ .+.|+|||.|...||..|.+.. ..||+|
T Consensus 1 CpiC~~~-~~~---Pv~l~CGH~FC~~Cl~~~~~~~~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDL-FKD---PVSLPCGHSFCRSCLERLWKEPSGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB--SS---EEE-SSSSEEEHHHHHHHHCCSSSST---SSS
T ss_pred CCccchh-hCC---ccccCCcCHHHHHHHHHHHHccCCcCCCCcCC
Confidence 8999998 433 3569999999999999986432 679998
No 37
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.88 E-value=3.9e-06 Score=103.04 Aligned_cols=53 Identities=32% Similarity=0.712 Sum_probs=44.1
Q ss_pred ccccCCCCcccccccccCCc-ceEecCCCCccchhhHHHHhccCCCCcCCCccc
Q 001136 1016 EKCLETNCPICCDFLFTSSE-TVRALPCGHYMHLACFQAYTCSHYTCPICSKSL 1068 (1143)
Q Consensus 1016 e~~~~~~CpIC~e~lf~s~~-~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~ 1068 (1143)
.....+.|+||.|.|+.+.. ....+||||.||..|+..|++..++||+||..+
T Consensus 287 ~~~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~qtCP~CR~~~ 340 (543)
T KOG0802|consen 287 LALSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQQTCPTCRTVL 340 (543)
T ss_pred hhhcCCeeeeechhhccccccccceeecccchHHHHHHHHHHHhCcCCcchhhh
Confidence 34457889999999876533 346799999999999999999999999999844
No 38
>PHA02926 zinc finger-like protein; Provisional
Probab=97.83 E-value=1e-05 Score=86.31 Aligned_cols=54 Identities=20% Similarity=0.594 Sum_probs=40.0
Q ss_pred ccccCCCCcccccccccCCc----ceEe-cCCCCccchhhHHHHhcc------CCCCcCCCcccc
Q 001136 1016 EKCLETNCPICCDFLFTSSE----TVRA-LPCGHYMHLACFQAYTCS------HYTCPICSKSLG 1069 (1143)
Q Consensus 1016 e~~~~~~CpIC~e~lf~s~~----~v~~-lpCgH~fH~~Ci~~wl~~------~~~CPiCr~s~~ 1069 (1143)
..+.+..|+||+|.++.... .... .+|+|.|+..||..|.+. ..+||+||..+.
T Consensus 166 ~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~~~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 166 RVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRRETGASDNCPICRTRFR 230 (242)
T ss_pred hccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhccccCcCCcCCCCcceee
Confidence 34557889999998765421 1233 479999999999999754 256999998763
No 39
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=97.65 E-value=3e-05 Score=63.21 Aligned_cols=39 Identities=36% Similarity=0.907 Sum_probs=23.2
Q ss_pred CcccccccccCCcceEecCCCCccchhhHHHHhcc----CCCCc
Q 001136 1023 CPICCDFLFTSSETVRALPCGHYMHLACFQAYTCS----HYTCP 1062 (1143)
Q Consensus 1023 CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~----~~~CP 1062 (1143)
||||.+ +-+...+.+.|+|||+|...|++++.++ ..+||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKSDRNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH-S-S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcCCCCeeeCc
Confidence 899999 3444556688999999999999999763 35677
No 40
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=97.64 E-value=4.4e-05 Score=66.44 Aligned_cols=45 Identities=24% Similarity=0.422 Sum_probs=38.0
Q ss_pred CCCcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCCcccc
Q 001136 1021 TNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLG 1069 (1143)
Q Consensus 1021 ~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~~ 1069 (1143)
-.||||++. +++ + ..++|||.|...||.+|+..+.+||+|++.+.
T Consensus 2 ~~Cpi~~~~-~~~--P-v~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~ 46 (63)
T smart00504 2 FLCPISLEV-MKD--P-VILPSGQTYERRAIEKWLLSHGTDPVTGQPLT 46 (63)
T ss_pred cCCcCCCCc-CCC--C-EECCCCCEEeHHHHHHHHHHCCCCCCCcCCCC
Confidence 359999987 433 3 45799999999999999988899999998874
No 41
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.60 E-value=1.1e-05 Score=97.40 Aligned_cols=52 Identities=21% Similarity=0.496 Sum_probs=42.6
Q ss_pred ccCCCCcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCCccccc
Q 001136 1018 CLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLGD 1070 (1143)
Q Consensus 1018 ~~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~~~ 1070 (1143)
.....||+|+-. |.+.......+|+|.||.+||..|.+...+||+||+.+..
T Consensus 121 ~~~~~CP~Ci~s-~~DqL~~~~k~c~H~FC~~Ci~sWsR~aqTCPiDR~EF~~ 172 (1134)
T KOG0825|consen 121 HVENQCPNCLKS-CNDQLEESEKHTAHYFCEECVGSWSRCAQTCPVDRGEFGE 172 (1134)
T ss_pred hhhhhhhHHHHH-HHHHhhccccccccccHHHHhhhhhhhcccCchhhhhhhe
Confidence 445679999876 5555544557899999999999999999999999998843
No 42
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=97.60 E-value=2.6e-05 Score=86.10 Aligned_cols=47 Identities=23% Similarity=0.714 Sum_probs=38.6
Q ss_pred CCCcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCCccccch
Q 001136 1021 TNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLGDM 1071 (1143)
Q Consensus 1021 ~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~~~m 1071 (1143)
.-|.+|+|.. .....+||||.|+.+||..|......||+||..+..-
T Consensus 240 ~kC~LCLe~~----~~pSaTpCGHiFCWsCI~~w~~ek~eCPlCR~~~~ps 286 (293)
T KOG0317|consen 240 RKCSLCLENR----SNPSATPCGHIFCWSCILEWCSEKAECPLCREKFQPS 286 (293)
T ss_pred CceEEEecCC----CCCCcCcCcchHHHHHHHHHHccccCCCcccccCCCc
Confidence 3599999862 2335589999999999999999889999999877543
No 43
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=97.60 E-value=1.5e-05 Score=99.83 Aligned_cols=114 Identities=26% Similarity=0.565 Sum_probs=75.8
Q ss_pred cceeeccccccc-----cccCCCCCCCCCCCCcceeEeccccccccCCCCcccCCCCCccccCCCCCccccccCCccccc
Q 001136 931 TSEMMCMHCLKI-----QAIGPNCTTPSCNGLSMAKYYCNICKFFDDERTVYHCPFCNLCRVGGGLGVDFFHCMTCNCCL 1005 (1143)
Q Consensus 931 ~~~~~C~~C~~~-----q~~~~~C~~~~cc~~~f~~y~C~~C~~~d~~~~~yhC~~CgiCr~g~~l~~~~~hC~~C~~C~ 1005 (1143)
+..-.|.+|+.. |.++.+|....| ...|+--|++-+-..- .|| |. .+--||..|--|-
T Consensus 3415 sS~~aCRFCGs~~~tE~sav~~vCs~aDC--~eYAK~ACs~~H~C~H--------~CG----Gv---kNEE~CLPCl~Cd 3477 (3738)
T KOG1428|consen 3415 SSSEACRFCGSRSGTELSAVGSVCSDADC--QEYAKIACSKTHPCGH--------PCG----GV---KNEEHCLPCLHCD 3477 (3738)
T ss_pred cchhHhhhccCCCCcchhcccCccccHHH--HHHHHHHHhccCcCCC--------ccc----Cc---cchhhcccccccC
Confidence 334479999854 678888998877 5677777776332211 122 22 3445666666663
Q ss_pred ccccccccccccccCCCCcccccccccCCcceEecCCCCccchhhHHH-----Hhcc-----CCCCcCCCccc
Q 001136 1006 GLKLLNHKCLEKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQA-----YTCS-----HYTCPICSKSL 1068 (1143)
Q Consensus 1006 ~~~~~~H~C~e~~~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~-----wl~~-----~~~CPiCr~s~ 1068 (1143)
.-. .....++.|.||..+ --+..+...|.|||.||.+|... |+.- --.||+|...+
T Consensus 3478 ks~------tkQD~DDmCmICFTE-~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPRItF~FisCPiC~n~I 3543 (3738)
T KOG1428|consen 3478 KSA------TKQDADDMCMICFTE-ALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKI 3543 (3738)
T ss_pred hhh------hhcccCceEEEEehh-hhCCCcceecCCccchhHHHHHHHHHhcccCCeeEEeeeecccccchh
Confidence 211 133456789999887 55667888999999999999766 4422 25699999887
No 44
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.43 E-value=7.6e-05 Score=80.40 Aligned_cols=49 Identities=24% Similarity=0.626 Sum_probs=37.4
Q ss_pred ccCCCCcccccccccCCcceEecCCCCccchhhHHHHhcc---CCCCcCCCccccc
Q 001136 1018 CLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCS---HYTCPICSKSLGD 1070 (1143)
Q Consensus 1018 ~~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~---~~~CPiCr~s~~~ 1070 (1143)
...-+|.||+|- ..++| +..|||+|+..||-+|+.. +..||+|+-.|..
T Consensus 45 ~~~FdCNICLd~---akdPV-vTlCGHLFCWpClyqWl~~~~~~~~cPVCK~~Vs~ 96 (230)
T KOG0823|consen 45 GGFFDCNICLDL---AKDPV-VTLCGHLFCWPCLYQWLQTRPNSKECPVCKAEVSI 96 (230)
T ss_pred CCceeeeeeccc---cCCCE-EeecccceehHHHHHHHhhcCCCeeCCcccccccc
Confidence 345679999985 44554 4559999999999999854 4668999977743
No 45
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.40 E-value=5.8e-05 Score=87.71 Aligned_cols=50 Identities=24% Similarity=0.576 Sum_probs=37.8
Q ss_pred CCCcccccccc-------------cCCcceEecCCCCccchhhHHHHhc-cCCCCcCCCccccc
Q 001136 1021 TNCPICCDFLF-------------TSSETVRALPCGHYMHLACFQAYTC-SHYTCPICSKSLGD 1070 (1143)
Q Consensus 1021 ~~CpIC~e~lf-------------~s~~~v~~lpCgH~fH~~Ci~~wl~-~~~~CPiCr~s~~~ 1070 (1143)
.+|+|||.++- .-....+..||.|.||..|+.+|+. .+..||+||.+++.
T Consensus 572 ~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~ykl~CPvCR~pLPp 635 (636)
T KOG0828|consen 572 NDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDTYKLICPVCRCPLPP 635 (636)
T ss_pred ccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhhhcccCCccCCCCCC
Confidence 56888887752 1112345679999999999999997 45689999988764
No 46
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.31 E-value=0.00017 Score=81.50 Aligned_cols=50 Identities=22% Similarity=0.613 Sum_probs=38.8
Q ss_pred CCCCcccccccccCCc-ceEecCCCCccchhhHHH-HhccCCCCcCCCcccc
Q 001136 1020 ETNCPICCDFLFTSSE-TVRALPCGHYMHLACFQA-YTCSHYTCPICSKSLG 1069 (1143)
Q Consensus 1020 ~~~CpIC~e~lf~s~~-~v~~lpCgH~fH~~Ci~~-wl~~~~~CPiCr~s~~ 1069 (1143)
+..||+|..+.+.+.. .+.+.+|||.|+.+|++. |......||.|++++-
T Consensus 3 ~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lr 54 (309)
T TIGR00570 3 DQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLR 54 (309)
T ss_pred CCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccc
Confidence 3579999997555554 334448999999999999 5566678999999884
No 47
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=97.24 E-value=0.00015 Score=80.98 Aligned_cols=47 Identities=23% Similarity=0.707 Sum_probs=40.0
Q ss_pred CCcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCCccccchh
Q 001136 1022 NCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLGDMA 1072 (1143)
Q Consensus 1022 ~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~~~m~ 1072 (1143)
-|-||.|+ | ...++.||||+|+.-||..++..+..||.|+.++.+-.
T Consensus 25 RC~IC~ey-f---~ip~itpCsHtfCSlCIR~~L~~~p~CP~C~~~~~Es~ 71 (442)
T KOG0287|consen 25 RCGICFEY-F---NIPMITPCSHTFCSLCIRKFLSYKPQCPTCCVTVTESD 71 (442)
T ss_pred HHhHHHHH-h---cCceeccccchHHHHHHHHHhccCCCCCceecccchhh
Confidence 49999998 4 23467899999999999999999999999999885433
No 48
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.23 E-value=0.00018 Score=84.31 Aligned_cols=47 Identities=26% Similarity=0.642 Sum_probs=38.9
Q ss_pred CCCCcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCCccccc
Q 001136 1020 ETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLGD 1070 (1143)
Q Consensus 1020 ~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~~~ 1070 (1143)
...|+||++. |.. + ..++|||.||..|+..|+.....||+|+..+..
T Consensus 26 ~l~C~IC~d~-~~~--P-vitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~ 72 (397)
T TIGR00599 26 SLRCHICKDF-FDV--P-VLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQE 72 (397)
T ss_pred ccCCCcCchh-hhC--c-cCCCCCCchhHHHHHHHHhCCCCCCCCCCcccc
Confidence 4579999987 433 2 358999999999999999888899999998853
No 49
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.19 E-value=0.00018 Score=85.04 Aligned_cols=53 Identities=30% Similarity=0.631 Sum_probs=39.2
Q ss_pred ccccccCCCCcccccccccCCcceEecCCCCccchhhHHHHhcc-----CCCCcCCCccccc
Q 001136 1014 CLEKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCS-----HYTCPICSKSLGD 1070 (1143)
Q Consensus 1014 C~e~~~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~-----~~~CPiCr~s~~~ 1070 (1143)
++..++...||||+++ ...+++.. |||.|+..||-+|+.. -..||||+..|..
T Consensus 180 qv~~~t~~~CPICL~~---~~~p~~t~-CGHiFC~~CiLqy~~~s~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 180 QVYGSTDMQCPICLEP---PSVPVRTN-CGHIFCGPCILQYWNYSAIKGPCSCPICRSTITL 237 (513)
T ss_pred hhhcCcCCcCCcccCC---CCcccccc-cCceeeHHHHHHHHhhhcccCCccCCchhhhccc
Confidence 3333447889999987 34444444 9999999999997532 3679999988865
No 50
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.00 E-value=0.00027 Score=80.49 Aligned_cols=48 Identities=27% Similarity=0.636 Sum_probs=38.5
Q ss_pred CCCCcccccccccCCcceEecC-CCCccchhhHHHHhcc---CCCCcCCCccc
Q 001136 1020 ETNCPICCDFLFTSSETVRALP-CGHYMHLACFQAYTCS---HYTCPICSKSL 1068 (1143)
Q Consensus 1020 ~~~CpIC~e~lf~s~~~v~~lp-CgH~fH~~Ci~~wl~~---~~~CPiCr~s~ 1068 (1143)
...|.|| .++|.....+..+. |||+||..|+.+|... +.+||+|+-.+
T Consensus 4 ~A~C~Ic-~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~Ps~R~cpic~ik~ 55 (465)
T KOG0827|consen 4 MAECHIC-IDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDPSNRGCPICQIKL 55 (465)
T ss_pred cceeeEe-ccCCccccccccccchhhHHHHHHHHHHHccCCccCCCCceeecc
Confidence 3579999 66688877777665 9999999999999854 36899999433
No 51
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=96.99 E-value=0.0002 Score=64.53 Aligned_cols=50 Identities=28% Similarity=0.671 Sum_probs=22.8
Q ss_pred CCCCcccccccccC-CcceEec---CCCCccchhhHHHHhcc-----------CCCCcCCCcccc
Q 001136 1020 ETNCPICCDFLFTS-SETVRAL---PCGHYMHLACFQAYTCS-----------HYTCPICSKSLG 1069 (1143)
Q Consensus 1020 ~~~CpIC~e~lf~s-~~~v~~l---pCgH~fH~~Ci~~wl~~-----------~~~CPiCr~s~~ 1069 (1143)
+..|+||+.++.+. ..+..+- .|+..||..|+.+|+.. ..+||.|++.|.
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~ 66 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPIS 66 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEE
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeee
Confidence 35799999986623 3333333 59999999999999631 135999998773
No 52
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.96 E-value=0.0008 Score=74.25 Aligned_cols=43 Identities=37% Similarity=0.936 Sum_probs=36.7
Q ss_pred CCCCcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCCc
Q 001136 1020 ETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSK 1066 (1143)
Q Consensus 1020 ~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~ 1066 (1143)
.-.||||+++ |... ..+||||.|+..|+..+......||.||.
T Consensus 13 ~~~C~iC~~~-~~~p---~~l~C~H~~c~~C~~~~~~~~~~Cp~cr~ 55 (386)
T KOG2177|consen 13 ELTCPICLEY-FREP---VLLPCGHNFCRACLTRSWEGPLSCPVCRP 55 (386)
T ss_pred cccChhhHHH-hhcC---ccccccchHhHHHHHHhcCCCcCCcccCC
Confidence 4679999998 5554 77999999999999997666688999994
No 53
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=96.96 E-value=0.00057 Score=57.38 Aligned_cols=42 Identities=31% Similarity=0.738 Sum_probs=32.1
Q ss_pred CCcccccccccCCcceEecCCC-----CccchhhHHHHhc--cCCCCcCCC
Q 001136 1022 NCPICCDFLFTSSETVRALPCG-----HYMHLACFQAYTC--SHYTCPICS 1065 (1143)
Q Consensus 1022 ~CpIC~e~lf~s~~~v~~lpCg-----H~fH~~Ci~~wl~--~~~~CPiCr 1065 (1143)
.|-||++ +.+.......||. |++|..|+.+|+. .+.+||+|+
T Consensus 1 ~CrIC~~--~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHD--EGDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK 49 (49)
T ss_pred CccCCCC--CCCCCCeeEeccccCCchhHHHHHHHHHHHHHcCCCcCCCCC
Confidence 3889998 2334445678985 9999999999984 346899995
No 54
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.93 E-value=0.00023 Score=77.56 Aligned_cols=49 Identities=27% Similarity=0.684 Sum_probs=39.1
Q ss_pred CCCCcccccccccCC------cceEecCCCCccchhhHHHHh--ccCCCCcCCCccc
Q 001136 1020 ETNCPICCDFLFTSS------ETVRALPCGHYMHLACFQAYT--CSHYTCPICSKSL 1068 (1143)
Q Consensus 1020 ~~~CpIC~e~lf~s~------~~v~~lpCgH~fH~~Ci~~wl--~~~~~CPiCr~s~ 1068 (1143)
++.|.||...++.+. ++...|.|+|.||.-||..|- ...++||-|++.+
T Consensus 224 d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekV 280 (328)
T KOG1734|consen 224 DSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKV 280 (328)
T ss_pred cchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHh
Confidence 466999988866554 244578999999999999994 5679999998766
No 55
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=96.81 E-value=0.0076 Score=69.70 Aligned_cols=138 Identities=20% Similarity=0.206 Sum_probs=107.4
Q ss_pred CchhHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccHHHHHHHHHHHHHHhcccCccccccchHHHhhhcc-hHHHHHHH
Q 001136 38 DDSPILIFCFFHKAVRNELDALHQLAMNFATGHRVDILSLSERYRFLHSVYKHHSNAEDEVIFPALDIRVK-NVARKYSL 116 (1143)
Q Consensus 38 ~~~Pi~~m~~~H~aLRreL~~L~~la~~~~~gd~~~~~~L~~~~~~l~~~L~~HH~~EDevLFPaL~~R~p-~vl~~le~ 116 (1143)
..+|+..|...-++++ ..|.+++..... ..-...+...+..+..+-. |-..++..|||.+.++.- .+...|--
T Consensus 84 ~gHPv~tl~~EN~~i~---~ll~~~l~~~~~--~~ik~~l~~lv~~L~~vg~-Hy~RKe~lIfp~~Er~GitapptVmW~ 157 (409)
T COG2461 84 PGHPVRTLKRENKAIR---SLLANLLQFPPK--KEIKEKLVELVSELDKIGK-HYTRKEMLIFPYIERRGITAPPTVMWV 157 (409)
T ss_pred CCCcHHHHhcccHHHH---HHHHHHhhcccc--HHHHHHHHHHHHHHHHhcc-ccccccccchhHHHHcCCCCCCeeeec
Confidence 6789999999999999 444454444432 2233334445555555555 999999999999998743 45556778
Q ss_pred HHHHHHHHHHHHHHHHhhhccCCCCchHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhccCCHHHHHHHHHH
Q 001136 117 EHEGESNLFDHLFQLLNSYTQNDESFPKELASCSRALQTSINQHMSKEEQQVFPLLTQHFSLEEQASLVWQ 187 (1143)
Q Consensus 117 EH~~i~~ll~~L~~~l~~~~~~~~~~~~eLa~~l~~l~~~L~~HL~~EE~~lfPLa~~~LS~eEw~~L~~~ 187 (1143)
.|.++...+.++..++.. ....++......+.+.+..=+-+||..+.|.....||..||.+|..+
T Consensus 158 ~dDeiRe~lk~~~~~l~~------~s~~~~ve~~~~~~t~i~dmIFkEe~Ilypt~~d~~te~ew~~i~~~ 222 (409)
T COG2461 158 KDDEIREALKELLKLLKE------VSIEEFVEKAESVLTEIEDMIFKEENILYPTLLDLLTEGEWEAIKEQ 222 (409)
T ss_pred cCcHHHHHHHHHHHHhhc------cChHHHHHHHHHHHHHHHHHHHhhhhhHHhHHHHhcCHHHHHHHHhc
Confidence 899999999999998872 23477888888888999999999999999999999999999998775
No 56
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.67 E-value=0.00079 Score=73.85 Aligned_cols=47 Identities=30% Similarity=0.779 Sum_probs=37.7
Q ss_pred CCCCcccccccccCCcceEecCCCCccchhhHHH-HhccCCC-CcCCCccccc
Q 001136 1020 ETNCPICCDFLFTSSETVRALPCGHYMHLACFQA-YTCSHYT-CPICSKSLGD 1070 (1143)
Q Consensus 1020 ~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~-wl~~~~~-CPiCr~s~~~ 1070 (1143)
+..|+||++.. ......||||.|+.+|+.. |++..+- ||+||..+..
T Consensus 215 d~kC~lC~e~~----~~ps~t~CgHlFC~~Cl~~~~t~~k~~~CplCRak~~p 263 (271)
T COG5574 215 DYKCFLCLEEP----EVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYP 263 (271)
T ss_pred ccceeeeeccc----CCcccccccchhhHHHHHHHHHhhccccCchhhhhccc
Confidence 45699999873 3335689999999999999 9988777 9999876643
No 57
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=96.48 E-value=0.0031 Score=57.21 Aligned_cols=48 Identities=21% Similarity=0.361 Sum_probs=34.9
Q ss_pred CCCcccccccccCCcceEecCCCCccchhhHHHHhcc-CCCCcCCCccccchh
Q 001136 1021 TNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCS-HYTCPICSKSLGDMA 1072 (1143)
Q Consensus 1021 ~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~-~~~CPiCr~s~~~m~ 1072 (1143)
-.|||+.+-| .+ .+.+|+||+|-..||.+|+.. +.+||+|+..+...+
T Consensus 5 f~CpIt~~lM-~d---PVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~~~ 53 (73)
T PF04564_consen 5 FLCPITGELM-RD---PVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSESD 53 (73)
T ss_dssp GB-TTTSSB--SS---EEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SGGG
T ss_pred cCCcCcCcHh-hC---ceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCccc
Confidence 3599999864 22 256899999999999999987 899999999886543
No 58
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=96.20 E-value=0.0025 Score=70.22 Aligned_cols=44 Identities=23% Similarity=0.541 Sum_probs=36.9
Q ss_pred CCCcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCCccc
Q 001136 1021 TNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSL 1068 (1143)
Q Consensus 1021 ~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~ 1068 (1143)
.-|-||.+++ . .....+|||.|+.-||..++..+..||+||...
T Consensus 26 lrC~IC~~~i-~---ip~~TtCgHtFCslCIR~hL~~qp~CP~Cr~~~ 69 (391)
T COG5432 26 LRCRICDCRI-S---IPCETTCGHTFCSLCIRRHLGTQPFCPVCREDP 69 (391)
T ss_pred HHhhhhhhee-e---cceecccccchhHHHHHHHhcCCCCCccccccH
Confidence 4599999883 2 224568999999999999999999999999876
No 59
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.98 E-value=0.0026 Score=73.55 Aligned_cols=81 Identities=22% Similarity=0.534 Sum_probs=54.2
Q ss_pred ccCCCCcccccccccCC---cceEecC-CCCccchhhHHHHh--cc-----CCCCcCCCccc--cchhhhhhhhHHHHhh
Q 001136 1018 CLETNCPICCDFLFTSS---ETVRALP-CGHYMHLACFQAYT--CS-----HYTCPICSKSL--GDMAIYFGMIDALLAA 1084 (1143)
Q Consensus 1018 ~~~~~CpIC~e~lf~s~---~~v~~lp-CgH~fH~~Ci~~wl--~~-----~~~CPiCr~s~--~~m~~~~~~ld~~i~~ 1084 (1143)
+.+..|-|||+.+.... ....++| |.|.|+..||..|- .. ...||+||... ..-+.+|-...+ +.
T Consensus 159 s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~~v~pS~~Wv~t~~--~k 236 (344)
T KOG1039|consen 159 SSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSSFVNPSSFWVETKE--EK 236 (344)
T ss_pred cccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccccccccceeeeecc--cc
Confidence 55778999999865444 1123445 99999999999996 22 57899999876 333344533222 66
Q ss_pred cCCChhhhcCcceEEc
Q 001136 1085 EELPEEYRNQVQDILC 1100 (1143)
Q Consensus 1085 ~p~P~~y~~~~~~i~C 1100 (1143)
++++++|........|
T Consensus 237 ~~li~e~~~~~s~~~c 252 (344)
T KOG1039|consen 237 QKLIEEYEAEMSAKDC 252 (344)
T ss_pred cccHHHHHHHhhccch
Confidence 7788888655543334
No 60
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=95.91 E-value=0.003 Score=78.34 Aligned_cols=53 Identities=21% Similarity=0.538 Sum_probs=38.0
Q ss_pred cccCCCCcccccccc--cCCcceE-ecCCCCccchhhHHHHhc--cCCCCcCCCcccc
Q 001136 1017 KCLETNCPICCDFLF--TSSETVR-ALPCGHYMHLACFQAYTC--SHYTCPICSKSLG 1069 (1143)
Q Consensus 1017 ~~~~~~CpIC~e~lf--~s~~~v~-~lpCgH~fH~~Ci~~wl~--~~~~CPiCr~s~~ 1069 (1143)
=++...|+||..-|. +..-|.+ ...|.|-||..|+-+|.. .+.+||+||..+.
T Consensus 1466 fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~Ss~~s~CPlCRseit 1523 (1525)
T COG5219 1466 FSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLCRSEIT 1523 (1525)
T ss_pred cCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHhcCCCCCCccccccc
Confidence 466788999986543 1222222 234899999999999974 4689999996653
No 61
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=95.82 E-value=0.0046 Score=54.40 Aligned_cols=56 Identities=27% Similarity=0.560 Sum_probs=26.6
Q ss_pred CCcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCCccccchhhh-hhhhHHHH
Q 001136 1022 NCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLGDMAIY-FGMIDALL 1082 (1143)
Q Consensus 1022 ~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~~~m~~~-~~~ld~~i 1082 (1143)
-|++|.+.| ..+|....|+|.|...|+..-+ .+.||+|+.+.-..+.. .+.||..|
T Consensus 9 rCs~C~~~l---~~pv~l~~CeH~fCs~Ci~~~~--~~~CPvC~~Paw~qD~~~NrqLd~~i 65 (65)
T PF14835_consen 9 RCSICFDIL---KEPVCLGGCEHIFCSSCIRDCI--GSECPVCHTPAWIQDIQINRQLDSMI 65 (65)
T ss_dssp S-SSS-S-----SS-B---SSS--B-TTTGGGGT--TTB-SSS--B-S-SS----HHHHHHH
T ss_pred CCcHHHHHh---cCCceeccCccHHHHHHhHHhc--CCCCCCcCChHHHHHHHhhhhhhccC
Confidence 499999874 3456667899999999998854 35699999888544433 35566543
No 62
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.58 E-value=0.0071 Score=69.24 Aligned_cols=48 Identities=27% Similarity=0.643 Sum_probs=39.6
Q ss_pred ccCCCCcccccccccCCcceEecCCCCc-cchhhHHHHhccCCCCcCCCcccc
Q 001136 1018 CLETNCPICCDFLFTSSETVRALPCGHY-MHLACFQAYTCSHYTCPICSKSLG 1069 (1143)
Q Consensus 1018 ~~~~~CpIC~e~lf~s~~~v~~lpCgH~-fH~~Ci~~wl~~~~~CPiCr~s~~ 1069 (1143)
.....|.||+.+ ...+.+|||-|. ++..|-+...-..+.|||||..+.
T Consensus 288 ~~gkeCVIClse----~rdt~vLPCRHLCLCs~Ca~~Lr~q~n~CPICRqpi~ 336 (349)
T KOG4265|consen 288 ESGKECVICLSE----SRDTVVLPCRHLCLCSGCAKSLRYQTNNCPICRQPIE 336 (349)
T ss_pred cCCCeeEEEecC----CcceEEecchhhehhHhHHHHHHHhhcCCCccccchH
Confidence 335679999986 355678999998 999999987666788999998874
No 63
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.57 E-value=0.0032 Score=53.20 Aligned_cols=48 Identities=33% Similarity=0.763 Sum_probs=35.3
Q ss_pred CCCCcccccccccCCcceEecCCCCc-cchhhHHH-HhccCCCCcCCCccccch
Q 001136 1020 ETNCPICCDFLFTSSETVRALPCGHY-MHLACFQA-YTCSHYTCPICSKSLGDM 1071 (1143)
Q Consensus 1020 ~~~CpIC~e~lf~s~~~v~~lpCgH~-fH~~Ci~~-wl~~~~~CPiCr~s~~~m 1071 (1143)
.+.|.||+|. ....| .-.|||. ++..|-.+ |...+..||+||.++-+.
T Consensus 7 ~dECTICye~---pvdsV-lYtCGHMCmCy~Cg~rl~~~~~g~CPiCRapi~dv 56 (62)
T KOG4172|consen 7 SDECTICYEH---PVDSV-LYTCGHMCMCYACGLRLKKALHGCCPICRAPIKDV 56 (62)
T ss_pred ccceeeeccC---cchHH-HHHcchHHhHHHHHHHHHHccCCcCcchhhHHHHH
Confidence 3789999986 22222 2359997 88899666 656789999999888654
No 64
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=95.56 E-value=0.0033 Score=71.80 Aligned_cols=61 Identities=34% Similarity=0.750 Sum_probs=46.8
Q ss_pred cccccccccCCCCcccccccccCCcceEecCCCCccchhhHHHHhccC--CCCcCCCccccchh
Q 001136 1011 NHKCLEKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSH--YTCPICSKSLGDMA 1072 (1143)
Q Consensus 1011 ~H~C~e~~~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~--~~CPiCr~s~~~m~ 1072 (1143)
.|.|++. ++-+|..|.+.+=...+....|||.|.||..|+.+++.++ .+||-||+-...|.
T Consensus 357 a~~~~~e-~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~~rsCP~CrklrSs~~ 419 (518)
T KOG1941|consen 357 AHECVEE-TELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNGTRSCPNCRKLRSSMK 419 (518)
T ss_pred HHHHHHH-HhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCCCCCCccHHHHHhhcc
Confidence 4555543 5678999998865666778899999999999999998554 78999996554443
No 65
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.43 E-value=0.0089 Score=69.04 Aligned_cols=47 Identities=34% Similarity=0.798 Sum_probs=37.3
Q ss_pred CCCcccccccccCCcceE-ecCCCCccchhhHHHHhcc--CCCCcCCCcc
Q 001136 1021 TNCPICCDFLFTSSETVR-ALPCGHYMHLACFQAYTCS--HYTCPICSKS 1067 (1143)
Q Consensus 1021 ~~CpIC~e~lf~s~~~v~-~lpCgH~fH~~Ci~~wl~~--~~~CPiCr~s 1067 (1143)
.+||||++..-.+++... .+.|||.|-..|+.+|+.. ..+||.|.-.
T Consensus 5 ~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k~~~~~cp~c~~k 54 (463)
T KOG1645|consen 5 TTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGKKTKMQCPLCSGK 54 (463)
T ss_pred ccCceeeeeeeecCceEEeeecccccccHHHHHHHHhhhhhhhCcccCCh
Confidence 579999998766666554 4679999999999999843 4679999643
No 66
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.42 E-value=0.0028 Score=71.99 Aligned_cols=47 Identities=28% Similarity=0.634 Sum_probs=35.3
Q ss_pred CCCCcccccccccCCcceEecCCCCccchhhHHHHh-ccCCCCcCCCcccc
Q 001136 1020 ETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYT-CSHYTCPICSKSLG 1069 (1143)
Q Consensus 1020 ~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl-~~~~~CPiCr~s~~ 1069 (1143)
+-.||||++-|-.. .....|+|-|+..||..-+ .++..||.||+.+.
T Consensus 43 ~v~c~icl~llk~t---mttkeClhrfc~~ci~~a~r~gn~ecptcRk~l~ 90 (381)
T KOG0311|consen 43 QVICPICLSLLKKT---MTTKECLHRFCFDCIWKALRSGNNECPTCRKKLV 90 (381)
T ss_pred hhccHHHHHHHHhh---cccHHHHHHHHHHHHHHHHHhcCCCCchHHhhcc
Confidence 34699999864222 1234599999999998765 56789999999983
No 67
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.12 E-value=0.016 Score=64.00 Aligned_cols=51 Identities=24% Similarity=0.656 Sum_probs=41.9
Q ss_pred cCCCCcccccccccCCcceEecCCCCccchhhHHHHhc--cCCCCcCCCccccchh
Q 001136 1019 LETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTC--SHYTCPICSKSLGDMA 1072 (1143)
Q Consensus 1019 ~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~--~~~~CPiCr~s~~~m~ 1072 (1143)
...+||+|.++ +.-+-...+|||.|+--|+..=.. .+.+||.|+.++..|.
T Consensus 238 ~~~~C~~Cg~~---PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~~lq 290 (298)
T KOG2879|consen 238 SDTECPVCGEP---PTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVEPLQ 290 (298)
T ss_pred CCceeeccCCC---CCCCeeeccccceeehhhhhhhhcchhhcccCccCCCCcchh
Confidence 35679999997 777878889999999999998543 3589999998887654
No 68
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=94.89 E-value=0.0083 Score=68.71 Aligned_cols=52 Identities=29% Similarity=0.687 Sum_probs=43.2
Q ss_pred cccccccCCCCcccccccccCCcceEecCCCCccchhhHHHHhc-c-CCCCcCCCccc
Q 001136 1013 KCLEKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTC-S-HYTCPICSKSL 1068 (1143)
Q Consensus 1013 ~C~e~~~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~-~-~~~CPiCr~s~ 1068 (1143)
.|.-.++-.-|-||-|. .+.|++=||||.++..|+..|.. . .++||.||-.|
T Consensus 362 YceMgsTFeLCKICaen----dKdvkIEPCGHLlCt~CLa~WQ~sd~gq~CPFCRcEI 415 (563)
T KOG1785|consen 362 YCEMGSTFELCKICAEN----DKDVKIEPCGHLLCTSCLAAWQDSDEGQTCPFCRCEI 415 (563)
T ss_pred HHHccchHHHHHHhhcc----CCCcccccccchHHHHHHHhhcccCCCCCCCceeeEe
Confidence 35566677789999974 56788889999999999999973 3 68999999877
No 69
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=94.87 E-value=0.0089 Score=74.18 Aligned_cols=48 Identities=23% Similarity=0.544 Sum_probs=37.5
Q ss_pred CCCcccccccccCCcceEecCCCCccchhhHHHHhc-cCCCCcCCCccccchh
Q 001136 1021 TNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTC-SHYTCPICSKSLGDMA 1072 (1143)
Q Consensus 1021 ~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~-~~~~CPiCr~s~~~m~ 1072 (1143)
-.||+|-+. ...+.+..|||.|+..|+..-.. +..+||.|+..++.-+
T Consensus 644 LkCs~Cn~R----~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganD 692 (698)
T KOG0978|consen 644 LKCSVCNTR----WKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGAND 692 (698)
T ss_pred eeCCCccCc----hhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCccc
Confidence 358888743 44556678999999999999654 5688999999997544
No 70
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=94.71 E-value=0.018 Score=68.46 Aligned_cols=108 Identities=26% Similarity=0.484 Sum_probs=65.1
Q ss_pred CCCCcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCCccccchhhhhhhhHHHHhhcCCChhhhcCcceEE
Q 001136 1020 ETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLGDMAIYFGMIDALLAAEELPEEYRNQVQDIL 1099 (1143)
Q Consensus 1020 ~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~~~m~~~~~~ld~~i~~~p~P~~y~~~~~~i~ 1099 (1143)
+..||+|+.-+ ..++....|||.|+..|+..|+..+..||.|+..+..-..+. ....+...+.+. .|.
T Consensus 21 ~l~C~~C~~vl---~~p~~~~~cgh~fC~~C~~~~~~~~~~cp~~~~~~~~~~~~~-------~~~~~~~~~~~l--~i~ 88 (391)
T KOG0297|consen 21 NLLCPICMSVL---RDPVQTTTCGHRFCAGCLLESLSNHQKCPVCRQELTQAEELP-------VPRALRRELLKL--PIR 88 (391)
T ss_pred cccCccccccc---cCCCCCCCCCCcccccccchhhccCcCCcccccccchhhccC-------chHHHHHHHHhc--ccc
Confidence 45699999763 334444689999999999999988999999988775443332 011111222222 234
Q ss_pred c----CCCCCCC---cccchhh---cccCCC-CCCccccccccCCCCCCCC
Q 001136 1100 C----NDCEQKG---AARFHWL---YHKCGF-CGSYNTRLIKNDTTVSNSS 1139 (1143)
Q Consensus 1100 C----ndC~~~s---~~~~h~l---~~kC~~-C~syNt~~~~~~~~~~~~~ 1139 (1143)
| .+|.... ...-|.. ..+|++ |+--+-+....+....+|.
T Consensus 89 c~~~~~GC~~~~~l~~~~~Hl~~c~~~~C~~~C~~~~~~~d~~~hl~~~C~ 139 (391)
T KOG0297|consen 89 CIFASRGCRADLELEALQGHLSTCDPLKCPHRCGVQVPRDDLEDHLEAECP 139 (391)
T ss_pred cccCCCCccccccHHHHHhHhccCCcccCccccccccchHHHHHHHhcccc
Confidence 4 3455443 3445542 367877 8876665554444444443
No 71
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=94.16 E-value=0.039 Score=46.17 Aligned_cols=46 Identities=22% Similarity=0.550 Sum_probs=24.7
Q ss_pred CcccccccccCCcceEecCCCCccchhhHHHHhc-cCCCCcCCCccc
Q 001136 1023 CPICCDFLFTSSETVRALPCGHYMHLACFQAYTC-SHYTCPICSKSL 1068 (1143)
Q Consensus 1023 CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~-~~~~CPiCr~s~ 1068 (1143)
||+|.++|..+.....--+||+-+...|+..-+. .+..||-||+++
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILENEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B-
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCCC
Confidence 8999999744444444456999999999999886 579999999864
No 72
>COG2461 Uncharacterized conserved protein [Function unknown]
Probab=94.06 E-value=0.31 Score=56.86 Aligned_cols=133 Identities=17% Similarity=0.172 Sum_probs=105.5
Q ss_pred CCchHHHHHHHHHHHHHHHHHHHHHHHhhccCCcccHHHHHHHHHHHHHHhhhhhhcccccccccccccc------cchh
Q 001136 301 TYPIDEILLWHNAIRQELNEIAEESRKIQLSGDFTNLLAFNERLQFIAEVLIFHCIAEVNVIFPAVDGAS------SFSQ 374 (1143)
Q Consensus 301 ~~Pi~~l~~~H~AiR~EL~~l~~~a~~~~~~~~~~~L~~L~~r~~f~~~vl~~Hs~aED~vlFPaL~~~~------~~~~ 374 (1143)
-|||..|..=-++|+..|+.+.+- ..+.+-...+-....++..+=+ |=+++...|||-+.++- .|--
T Consensus 85 gHPv~tl~~EN~~i~~ll~~~l~~------~~~~~ik~~l~~lv~~L~~vg~-Hy~RKe~lIfp~~Er~GitapptVmW~ 157 (409)
T COG2461 85 GHPVRTLKRENKAIRSLLANLLQF------PPKKEIKEKLVELVSELDKIGK-HYTRKEMLIFPYIERRGITAPPTVMWV 157 (409)
T ss_pred CCcHHHHhcccHHHHHHHHHHhhc------cccHHHHHHHHHHHHHHHHhcc-ccccccccchhHHHHcCCCCCCeeeec
Confidence 589999999899999444333222 1222224677778888888888 99999999999999843 8888
Q ss_pred hhHHHHhHHHHHHHHHHHHhhcCCccchHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhcCCHHHHHHHHHHH
Q 001136 375 KHAEEESQFNDFRLLIESIQNEGAISTSAEFYAKLCSHADQIMETIERHFHKVEVQVLPLARNHFSFKRQREILYQS 451 (1143)
Q Consensus 375 EH~~i~~~~~~f~~ll~~~~~~~~~~~~~~~~~~L~~~l~~l~~~L~~Hf~kEE~qvfPL~~k~~S~eEQ~~L~~~~ 451 (1143)
.|+.+-..+..+..++. +++ ..++...+..+.+.+..=+++||+.+.|++--.||..||..+-.|+
T Consensus 158 ~dDeiRe~lk~~~~~l~----~~s-------~~~~ve~~~~~~t~i~dmIFkEe~Ilypt~~d~~te~ew~~i~~~~ 223 (409)
T COG2461 158 KDDEIREALKELLKLLK----EVS-------IEEFVEKAESVLTEIEDMIFKEENILYPTLLDLLTEGEWEAIKEQS 223 (409)
T ss_pred cCcHHHHHHHHHHHHhh----ccC-------hHHHHHHHHHHHHHHHHHHHhhhhhHHhHHHHhcCHHHHHHHHhcC
Confidence 99999888888887776 121 3678888889999999999999999999999999999999876654
No 73
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=94.04 E-value=0.0069 Score=67.90 Aligned_cols=133 Identities=20% Similarity=0.164 Sum_probs=91.8
Q ss_pred HHHHHHHhcccccccccccccccccccccccchhhhhHHHHHHHHHHHHHHHhhhhhcCCCCCcccccccccccCCchhh
Q 001136 597 GLYRAHSNAEDEIVFPALESKEALHNVSHSYTLDHKQEEKLFEDISCVLSEVSQLHESLPNADSEKEDKFSADYGSDNRR 676 (1143)
Q Consensus 597 ~v~~~Hs~aED~ivfPALe~~~~~~~vs~s~~~dH~~ee~lf~~I~~lL~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 676 (1143)
.++..|+.++|++-||+..+.....+...+...||.-.=.|..+.+. +.+.++..
T Consensus 17 ~~~~~~~~~~d~~~~~~~c~hy~r~~~~~a~ccd~~~~C~hCH~~s~-------------------------~h~~~r~~ 71 (276)
T KOG1940|consen 17 ALSSIHSDAEDEIAFPYGCPHYRRNCKSRAPCCDREITCRHCHNESE-------------------------DHDLDRKT 71 (276)
T ss_pred hhhhcccccccccccccCCchhhhccccccccccceeeeEEecChhh-------------------------hcccchhh
Confidence 78899999999999999999877667777776676554444433322 00113333
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHhhHHhhcCCHHHHHHHHHHHHhcCCHHHHHhhHhHhhcCCCHHHHHHHH
Q 001136 677 KYNELATKLQGMCKSIKVTLDQHILGEELELWPLFGRHFSVEEQDKIVGRIIGSTGAEVLQSMLPWVTSALTQDEQSKLI 756 (1143)
Q Consensus 677 ~~~~l~~kL~~~~~~~~~~l~~H~~~EE~e~~PL~~~hfS~~Eq~~l~~~~l~~~p~~~l~~~lpWl~~~Ls~~E~~~~L 756 (1143)
++.-+..+.....++..+-...|.. +.++|=++.+.|.++++ ++..-+.+.|--+-.+. +||.-....++..+.|
T Consensus 72 v~~~~C~~C~~~q~~~~~c~~c~~~--~g~~~c~~C~l~dd~~~-~~~hC~~C~icr~g~~~--~~fhc~~c~~c~~~~~ 146 (276)
T KOG1940|consen 72 VYELLCMKCRKIQPVGQICSNCHVE--LGEYYCLICKLFDDDPS-KQYHCDLCGICREGLGL--DFFHCKKCKACLSAYL 146 (276)
T ss_pred hhhhhhhhHHhhhhhhhccccchhh--hhhhcCccccccccccc-ceecccccccccccccc--chhHHhhhHhHHhhhc
Confidence 3333444444444555578888887 89999999999999999 88888866554433333 9999777777776665
Q ss_pred HHh
Q 001136 757 DTW 759 (1143)
Q Consensus 757 ~~~ 759 (1143)
.+|
T Consensus 147 ~~~ 149 (276)
T KOG1940|consen 147 SNW 149 (276)
T ss_pred ccc
Confidence 554
No 74
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=93.66 E-value=0.022 Score=63.56 Aligned_cols=53 Identities=32% Similarity=0.710 Sum_probs=42.6
Q ss_pred cccCCCCcccccccccCCcceEecCCCCccchhhHHHHhc-----------------------cCCCCcCCCccccc
Q 001136 1017 KCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTC-----------------------SHYTCPICSKSLGD 1070 (1143)
Q Consensus 1017 ~~~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~-----------------------~~~~CPiCr~s~~~ 1070 (1143)
+--.+.|.||+-- |.++......+|-|+||..|+.+|+. ..-.||+||..|.+
T Consensus 112 n~p~gqCvICLyg-fa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpVcre~i~~ 187 (368)
T KOG4445|consen 112 NHPNGQCVICLYG-FASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPVCRERIKI 187 (368)
T ss_pred CCCCCceEEEEEe-ecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhHhhhhccc
Confidence 4446789999976 88888888899999999999998852 12459999988853
No 75
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.61 E-value=0.035 Score=62.28 Aligned_cols=47 Identities=21% Similarity=0.494 Sum_probs=37.2
Q ss_pred cCCCCcccccccccCCcceEecCCCCccchhhHHHH-hccCCCCcCCCcccc
Q 001136 1019 LETNCPICCDFLFTSSETVRALPCGHYMHLACFQAY-TCSHYTCPICSKSLG 1069 (1143)
Q Consensus 1019 ~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~w-l~~~~~CPiCr~s~~ 1069 (1143)
+...|+||+.. ...+ ..|+|+|.|+.-||..- .....+||+||.++.
T Consensus 6 ~~~eC~IC~nt---~n~P-v~l~C~HkFCyiCiKGsy~ndk~~CavCR~pid 53 (324)
T KOG0824|consen 6 KKKECLICYNT---GNCP-VNLYCFHKFCYICIKGSYKNDKKTCAVCRFPID 53 (324)
T ss_pred cCCcceeeecc---CCcC-ccccccchhhhhhhcchhhcCCCCCceecCCCC
Confidence 45789999976 3344 56899999999999884 345677999999983
No 76
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=92.30 E-value=0.11 Score=56.71 Aligned_cols=58 Identities=24% Similarity=0.449 Sum_probs=48.6
Q ss_pred cccccCCCCcccccccccCCcceEec-CCCCccchhhHHHHhccCCCCcCCCccccchhh
Q 001136 1015 LEKCLETNCPICCDFLFTSSETVRAL-PCGHYMHLACFQAYTCSHYTCPICSKSLGDMAI 1073 (1143)
Q Consensus 1015 ~e~~~~~~CpIC~e~lf~s~~~v~~l-pCgH~fH~~Ci~~wl~~~~~CPiCr~s~~~m~~ 1073 (1143)
+..+....||||.+. .++..+..+| ||||.+...|..+.+.....||+|.+++.+.+.
T Consensus 216 ~a~s~ryiCpvtrd~-LtNt~~ca~Lr~sg~Vv~~ecvEklir~D~v~pv~d~plkdrdi 274 (303)
T KOG3039|consen 216 IAASKRYICPVTRDT-LTNTTPCAVLRPSGHVVTKECVEKLIRKDMVDPVTDKPLKDRDI 274 (303)
T ss_pred hhhccceecccchhh-hcCccceEEeccCCcEeeHHHHHHhccccccccCCCCcCcccce
Confidence 334456789999998 6777777776 799999999999999999999999999976553
No 77
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=92.09 E-value=0.064 Score=51.46 Aligned_cols=38 Identities=26% Similarity=0.658 Sum_probs=29.4
Q ss_pred cccccccCCCCcccccccccCCcceEecCCCCccchhhHH
Q 001136 1013 KCLEKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQ 1052 (1143)
Q Consensus 1013 ~C~e~~~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~ 1052 (1143)
.++.-.....|++|...|+. ....+.||||.||..|++
T Consensus 71 ~~v~i~~~~~C~vC~k~l~~--~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 71 RSVVITESTKCSVCGKPLGN--SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred ceEEECCCCCccCcCCcCCC--ceEEEeCCCeEEeccccc
Confidence 34444556789999999655 456778999999999985
No 78
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=91.71 E-value=0.12 Score=44.97 Aligned_cols=41 Identities=27% Similarity=0.643 Sum_probs=28.6
Q ss_pred CCCCcccccccccCCcceEecCCCCccchhhHHHHhc--cCCCCcC
Q 001136 1020 ETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTC--SHYTCPI 1063 (1143)
Q Consensus 1020 ~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~--~~~~CPi 1063 (1143)
...|||.+.. | ..+|....|||+|-+..|.+|++ ....||+
T Consensus 11 ~~~CPiT~~~-~--~~PV~s~~C~H~fek~aI~~~i~~~~~~~CPv 53 (57)
T PF11789_consen 11 SLKCPITLQP-F--EDPVKSKKCGHTFEKEAILQYIQRNGSKRCPV 53 (57)
T ss_dssp -SB-TTTSSB----SSEEEESSS--EEEHHHHHHHCTTTS-EE-SC
T ss_pred ccCCCCcCCh-h--hCCcCcCCCCCeecHHHHHHHHHhcCCCCCCC
Confidence 4579999987 3 35777789999999999999993 3577998
No 79
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=91.36 E-value=0.1 Score=55.12 Aligned_cols=57 Identities=21% Similarity=0.349 Sum_probs=41.0
Q ss_pred CCcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCCccccchhhhhhhhHHHH
Q 001136 1022 NCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLGDMAIYFGMIDALL 1082 (1143)
Q Consensus 1022 ~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~~~m~~~~~~ld~~i 1082 (1143)
.|-||..+ |.+. ++..|||.|+..|+-.=.+...+|-+|.+...-.-..-..++..+
T Consensus 198 ~C~iCKkd-y~sp---vvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G~f~V~~d~~kmL 254 (259)
T COG5152 198 LCGICKKD-YESP---VVTECGHSFCSLCAIRKYQKGDECGVCGKATYGRFWVVSDLQKML 254 (259)
T ss_pred eehhchhh-ccch---hhhhcchhHHHHHHHHHhccCCcceecchhhccceeHHhhHHHHH
Confidence 48999988 5553 456799999999988866778999999987743333334444443
No 80
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=90.81 E-value=0.14 Score=63.19 Aligned_cols=47 Identities=19% Similarity=-0.092 Sum_probs=33.4
Q ss_pred ccccC---CCCCCCCCCCCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHH
Q 001136 14 VVTES---VETTSPSSSKSSDLDEEEDDDSPILIFCFFHKAVRNELDALH 60 (1143)
Q Consensus 14 ~~~~~---~~~~~~~~s~~~~~~~~~~~~~Pi~~m~~~H~aLRreL~~L~ 60 (1143)
-+.|| ++|-.|.+-+-.++.++.-...|+.+-..+|...++..+...
T Consensus 234 St~e~~~~vtt~~piw~~r~~Pfg~g~~~mp~~G~n~v~~~~c~n~d~e~ 283 (1081)
T KOG0309|consen 234 STTESKRTVTTNFPIWRGRYLPFGEGYCIMPMVGGNMVPQLRCENSDLEW 283 (1081)
T ss_pred cccccceeccccCcceeccccccCceeEeccccCCeeeeeccccchhhhh
Confidence 45666 566678888888888887777777666677777776666553
No 81
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.49 E-value=0.048 Score=60.76 Aligned_cols=57 Identities=26% Similarity=0.493 Sum_probs=39.0
Q ss_pred ccccccccc---CCCCcccccccccCCcceEecCCCCc-cchhhHHHHhccCCCCcCCCccccchhhhh
Q 001136 1011 NHKCLEKCL---ETNCPICCDFLFTSSETVRALPCGHY-MHLACFQAYTCSHYTCPICSKSLGDMAIYF 1075 (1143)
Q Consensus 1011 ~H~C~e~~~---~~~CpIC~e~lf~s~~~v~~lpCgH~-fH~~Ci~~wl~~~~~CPiCr~s~~~m~~~~ 1075 (1143)
+|.+..+.. +.-|.||++- ......|+|||. -+..|... -..|||||+-+...-.+|
T Consensus 288 ~~g~~~~~s~~~~~LC~ICmDa----P~DCvfLeCGHmVtCt~CGkr----m~eCPICRqyi~rvvrif 348 (350)
T KOG4275|consen 288 NDGEQHSRSLATRRLCAICMDA----PRDCVFLECGHMVTCTKCGKR----MNECPICRQYIVRVVRIF 348 (350)
T ss_pred ccccccccchhHHHHHHHHhcC----CcceEEeecCcEEeehhhccc----cccCchHHHHHHHHHhhh
Confidence 444444444 7789999974 566788999997 35566544 348999998776544444
No 82
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.30 E-value=0.25 Score=53.30 Aligned_cols=49 Identities=33% Similarity=0.748 Sum_probs=38.7
Q ss_pred cCCCCcccccccccCCcceEecCCCCccchhhHHHHhc--------cCCCCcCCCcccc
Q 001136 1019 LETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTC--------SHYTCPICSKSLG 1069 (1143)
Q Consensus 1019 ~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~--------~~~~CPiCr~s~~ 1069 (1143)
...||..|...| .+++. .-|-|=|.||-.|+++|.. ..|+||-|...|.
T Consensus 49 Y~pNC~LC~t~L-a~gdt-~RLvCyhlfHW~ClneraA~lPanTAPaGyqCP~Cs~eiF 105 (299)
T KOG3970|consen 49 YNPNCRLCNTPL-ASGDT-TRLVCYHLFHWKCLNERAANLPANTAPAGYQCPCCSQEIF 105 (299)
T ss_pred CCCCCceeCCcc-ccCcc-eeehhhhhHHHHHhhHHHhhCCCcCCCCcccCCCCCCccC
Confidence 356899999884 44444 4477999999999999952 3699999999884
No 83
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.57 E-value=0.23 Score=51.82 Aligned_cols=30 Identities=27% Similarity=0.774 Sum_probs=24.9
Q ss_pred cCCCCccchhhHHHHhcc-----------CCCCcCCCcccc
Q 001136 1040 LPCGHYMHLACFQAYTCS-----------HYTCPICSKSLG 1069 (1143)
Q Consensus 1040 lpCgH~fH~~Ci~~wl~~-----------~~~CPiCr~s~~ 1069 (1143)
+.||-.||.-|+..|++. -..||.|++++.
T Consensus 188 ~qCgkpFHqiCL~dWLRgilTsRQSFdiiFGeCPYCS~Pia 228 (234)
T KOG3268|consen 188 IQCGKPFHQICLTDWLRGILTSRQSFDIIFGECPYCSDPIA 228 (234)
T ss_pred cccCCcHHHHHHHHHHHHHhhccceeeeeeccCCCCCCcce
Confidence 579999999999999742 156999999884
No 84
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=89.43 E-value=0.12 Score=56.43 Aligned_cols=145 Identities=26% Similarity=0.528 Sum_probs=80.7
Q ss_pred CCccccccccccccccCC--------------------cccChhhhcccCCCCCCccccceeeccccccccccCCCCCCC
Q 001136 893 GCEHYKRNCKIRAACCGK--------------------LFTCRFCHDKASDHSMDRKATSEMMCMHCLKIQAIGPNCTTP 952 (1143)
Q Consensus 893 gC~HY~r~c~l~~~cC~k--------------------~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~~ 952 (1143)
=|+|=- =-|.+|||+| -|.|..|.....|--+-|..- ..+|-.|+....+
T Consensus 63 YCEhDF--~~LfaPcC~kC~EFiiGrVikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqg-r~LC~~Cn~k~Ka------- 132 (332)
T KOG2272|consen 63 YCEHDF--HVLFAPCCGKCGEFIIGRVIKAMNNSWHPACFRCDLCNKHLADQGFYRNQG-RALCRECNQKEKA------- 132 (332)
T ss_pred cccccc--hhhhchhhcccccchhhHHHHhhccccCcccchhHHHHHHHhhhhhHhhcc-hHHhhhhhhhhcc-------
Confidence 366632 2377888877 367878877776666666543 6788888765422
Q ss_pred CCCCCcceeEecccccc-ccCC-----CCcccCCCCCccccCCCCCccccccCCcccccccccccccccccccCCCCccc
Q 001136 953 SCNGLSMAKYYCNICKF-FDDE-----RTVYHCPFCNLCRVGGGLGVDFFHCMTCNCCLGLKLLNHKCLEKCLETNCPIC 1026 (1143)
Q Consensus 953 ~cc~~~f~~y~C~~C~~-~d~~-----~~~yhC~~CgiCr~g~~l~~~~~hC~~C~~C~~~~~~~H~C~e~~~~~~CpIC 1026 (1143)
..-|+|-|.+|+- .|++ .++|| ..-|.|.+||.=+.... .|-.++--|+-|
T Consensus 133 ----~~~g~YvC~KCh~~iD~~~l~fr~d~yH--------------~yHFkCt~C~keL~sda-----Revk~eLyClrC 189 (332)
T KOG2272|consen 133 ----KGRGRYVCQKCHAHIDEQPLTFRGDPYH--------------PYHFKCTTCGKELTSDA-----REVKGELYCLRC 189 (332)
T ss_pred ----cccceeehhhhhhhcccccccccCCCCC--------------ccceecccccccccchh-----hhhccceecccc
Confidence 2468999999995 4555 56777 45688888886553321 122223345555
Q ss_pred ccccccCCcceEecCCCCccchhhH----HHHhccCCCCcCCCccccchhhh
Q 001136 1027 CDFLFTSSETVRALPCGHYMHLACF----QAYTCSHYTCPICSKSLGDMAIY 1074 (1143)
Q Consensus 1027 ~e~lf~s~~~v~~lpCgH~fH~~Ci----~~wl~~~~~CPiCr~s~~~m~~~ 1074 (1143)
.+.|--. +...|.-.+-..=+ ..|--.+.+|-.|-|++..-..|
T Consensus 190 hD~mgip----iCgaC~rpIeervi~amgKhWHveHFvCa~CekPFlGHrHY 237 (332)
T KOG2272|consen 190 HDKMGIP----ICGACRRPIEERVIFAMGKHWHVEHFVCAKCEKPFLGHRHY 237 (332)
T ss_pred ccccCCc----ccccccCchHHHHHHHhccccchhheeehhcCCcccchhhh
Confidence 4431000 00011111111111 12444578888888887644433
No 85
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=89.26 E-value=0.1 Score=59.51 Aligned_cols=47 Identities=21% Similarity=0.587 Sum_probs=38.6
Q ss_pred CCCCcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCCcccc
Q 001136 1020 ETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLG 1069 (1143)
Q Consensus 1020 ~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~~ 1069 (1143)
...|.+|..+|-+.++ +.-|=|+|+.+||.+++..+.+||+|+..+.
T Consensus 15 ~itC~LC~GYliDATT---I~eCLHTFCkSCivk~l~~~~~CP~C~i~ih 61 (331)
T KOG2660|consen 15 HITCRLCGGYLIDATT---ITECLHTFCKSCIVKYLEESKYCPTCDIVIH 61 (331)
T ss_pred ceehhhccceeecchh---HHHHHHHHHHHHHHHHHHHhccCCccceecc
Confidence 3579999999654443 3459999999999999988999999988773
No 86
>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]
Probab=89.11 E-value=0.27 Score=55.26 Aligned_cols=47 Identities=23% Similarity=0.506 Sum_probs=38.1
Q ss_pred CCcccccccccCCcce-EecCCCCccchhhHHHHh-ccCCCCcCCCccc
Q 001136 1022 NCPICCDFLFTSSETV-RALPCGHYMHLACFQAYT-CSHYTCPICSKSL 1068 (1143)
Q Consensus 1022 ~CpIC~e~lf~s~~~v-~~lpCgH~fH~~Ci~~wl-~~~~~CPiCr~s~ 1068 (1143)
.||+|..+.+.+..-+ ++-+|||.++.+|++... .+.+.||-|.+.+
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~~g~~~CpeC~~iL 50 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFSLGPAQCPECMVIL 50 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHhcCCCCCCcccchh
Confidence 4999998877776633 344899999999999975 5669999999877
No 87
>COG5592 Uncharacterized conserved protein [Function unknown]
Probab=88.45 E-value=1.7 Score=45.11 Aligned_cols=89 Identities=16% Similarity=0.147 Sum_probs=68.3
Q ss_pred HHHHHHHHHHHHhhhhhhcccccccccccccc--------------cchhhhHHHHhHHHHHHHHHHHHhhcCCccchHH
Q 001136 339 AFNERLQFIAEVLIFHCIAEVNVIFPAVDGAS--------------SFSQKHAEEESQFNDFRLLIESIQNEGAISTSAE 404 (1143)
Q Consensus 339 ~L~~r~~f~~~vl~~Hs~aED~vlFPaL~~~~--------------~~~~EH~~i~~~~~~f~~ll~~~~~~~~~~~~~~ 404 (1143)
.+-+-..|...+.+.|-.-|.+.+||+.-... ++..+|..|+-+.+.+... +.
T Consensus 29 e~le~~gf~~k~~k~h~e~Ee~ilF~v~Vd~~~ed~~~fkdt~~~~~i~~DHkliE~l~tnlik~------kR------- 95 (171)
T COG5592 29 EILEFEGFNEKLGKDHVELEEKILFPVIVDADMEDLYVFKDTPEVDRIKNDHKLIETLATNLIKW------KR------- 95 (171)
T ss_pred HHHhhcchHHHHhhhHHHHHHHhhhhhccchHHHHHHhhhccchhhHhHhhHHHHHHHHHHHHhh------cc-------
Confidence 33344447899999999999999999875511 7888999998888775432 11
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhcCCHH
Q 001136 405 FYAKLCSHADQIMETIERHFHKVEVQVLPLARNHFSFK 442 (1143)
Q Consensus 405 ~~~~L~~~l~~l~~~L~~Hf~kEE~qvfPL~~k~~S~e 442 (1143)
+++....+.+.+.+|++|=..||.++||-... ++.|
T Consensus 96 -~~k~~e~~p~fyK~LtdHn~aEE~~IfPrvks-~~~E 131 (171)
T COG5592 96 -PDKIKERVPLFYKTLTDHNLAEEEYIFPRVKS-LKGE 131 (171)
T ss_pred -chHHHHHHHHHHHHHHHccccccchhhHHHHh-hcch
Confidence 24677788999999999999999999998764 4433
No 88
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=88.27 E-value=0.22 Score=50.32 Aligned_cols=42 Identities=19% Similarity=0.370 Sum_probs=33.4
Q ss_pred CCCCcccccccccCCcceEecCCC------CccchhhHHHHhccCCCCc
Q 001136 1020 ETNCPICCDFLFTSSETVRALPCG------HYMHLACFQAYTCSHYTCP 1062 (1143)
Q Consensus 1020 ~~~CpIC~e~lf~s~~~v~~lpCg------H~fH~~Ci~~wl~~~~~CP 1062 (1143)
...|.||++.+-. ..+|+.++|| |.||.+|+.+|.....+=|
T Consensus 26 ~~EC~IC~~~I~~-~~GvV~vt~~g~lnLEkmfc~~C~~rw~~~~~rDP 73 (134)
T PF05883_consen 26 TVECQICFDRIDN-NDGVVYVTDGGTLNLEKMFCADCDKRWRRERNRDP 73 (134)
T ss_pred Ceeehhhhhhhhc-CCCEEEEecCCeehHHHHHHHHHHHHHHhhccCCC
Confidence 4579999999765 6788999998 9999999999954443334
No 89
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.21 E-value=0.4 Score=57.00 Aligned_cols=51 Identities=27% Similarity=0.689 Sum_probs=40.3
Q ss_pred ccCCCCcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCCccccchh
Q 001136 1018 CLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLGDMA 1072 (1143)
Q Consensus 1018 ~~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~~~m~ 1072 (1143)
..+-.|.||+.-++.. ..+||||+|+..|+.+-+....-||+||..+....
T Consensus 82 ~sef~c~vc~~~l~~p----v~tpcghs~c~~Cl~r~ld~~~~cp~Cr~~l~e~~ 132 (398)
T KOG4159|consen 82 RSEFECCVCSRALYPP----VVTPCGHSFCLECLDRSLDQETECPLCRDELVELP 132 (398)
T ss_pred cchhhhhhhHhhcCCC----ccccccccccHHHHHHHhccCCCCcccccccccch
Confidence 4466799998765433 34699999999999998777888999999986433
No 90
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=88.13 E-value=0.061 Score=62.82 Aligned_cols=70 Identities=30% Similarity=0.751 Sum_probs=39.6
Q ss_pred CCccc--CCCCCccccCCCCCccccccCC---cccccccccccccccccccCCCCcccccccccCCcceEec-CCCCccc
Q 001136 974 RTVYH--CPFCNLCRVGGGLGVDFFHCMT---CNCCLGLKLLNHKCLEKCLETNCPICCDFLFTSSETVRAL-PCGHYMH 1047 (1143)
Q Consensus 974 ~~~yh--C~~CgiCr~g~~l~~~~~hC~~---C~~C~~~~~~~H~C~e~~~~~~CpIC~e~lf~s~~~v~~l-pCgH~fH 1047 (1143)
+.+|| |=.|+.|+.... |..||--+. |--|+-.+ -+-|..|.+.+.+ ++| .||-+||
T Consensus 295 ~~~fHv~CFtC~~C~r~L~-Gq~FY~v~~k~~CE~cyq~t-----------lekC~~Cg~~I~d-----~iLrA~GkayH 357 (468)
T KOG1701|consen 295 DQLFHVQCFTCRTCRRQLA-GQSFYQVDGKPYCEGCYQDT-----------LEKCNKCGEPIMD-----RILRALGKAYH 357 (468)
T ss_pred hhhhcccceehHhhhhhhc-cccccccCCcccchHHHHHH-----------HHHHhhhhhHHHH-----HHHHhcccccC
Confidence 45666 777888887765 666765432 33333222 1236677654211 223 3777777
Q ss_pred hhhHHHHhccCCCCcCCCccc
Q 001136 1048 LACFQAYTCSHYTCPICSKSL 1068 (1143)
Q Consensus 1048 ~~Ci~~wl~~~~~CPiCr~s~ 1068 (1143)
..|| +|=+|.+.+
T Consensus 358 p~CF--------~Cv~C~r~l 370 (468)
T KOG1701|consen 358 PGCF--------TCVVCARCL 370 (468)
T ss_pred CCce--------EEEEecccc
Confidence 7776 555666555
No 91
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=88.11 E-value=0.27 Score=62.30 Aligned_cols=36 Identities=25% Similarity=0.588 Sum_probs=28.0
Q ss_pred ccCCCCcccccccccCCcceEecCCCCccchhhHHHHh
Q 001136 1018 CLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYT 1055 (1143)
Q Consensus 1018 ~~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl 1055 (1143)
.....|-+|.-.|+. .+-..-||||.||..|+.+-.
T Consensus 815 ep~d~C~~C~~~ll~--~pF~vf~CgH~FH~~Cl~~~v 850 (911)
T KOG2034|consen 815 EPQDSCDHCGRPLLI--KPFYVFPCGHCFHRDCLIRHV 850 (911)
T ss_pred cCccchHHhcchhhc--CcceeeeccchHHHHHHHHHH
Confidence 345679999987543 366778999999999998854
No 92
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=88.00 E-value=0.23 Score=42.65 Aligned_cols=31 Identities=32% Similarity=0.797 Sum_probs=25.1
Q ss_pred eEecCCCCccchhhHHHHhccCCCCcCCCcccc
Q 001136 1037 VRALPCGHYMHLACFQAYTCSHYTCPICSKSLG 1069 (1143)
Q Consensus 1037 v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~~ 1069 (1143)
-..+||||.+...|+.-+ +-+-||+|.+.+.
T Consensus 20 ~~~~pCgH~I~~~~f~~~--rYngCPfC~~~~~ 50 (55)
T PF14447_consen 20 GTVLPCGHLICDNCFPGE--RYNGCPFCGTPFE 50 (55)
T ss_pred cccccccceeeccccChh--hccCCCCCCCccc
Confidence 356899999999998774 4466999998874
No 93
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=87.95 E-value=0.22 Score=56.52 Aligned_cols=57 Identities=21% Similarity=0.563 Sum_probs=43.8
Q ss_pred CCCCcccccccccCCcceEecCCCCccchhhHHHHhc-cCCCCcCCCccccchhhhhh
Q 001136 1020 ETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTC-SHYTCPICSKSLGDMAIYFG 1076 (1143)
Q Consensus 1020 ~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~-~~~~CPiCr~s~~~m~~~~~ 1076 (1143)
++.||.|+|+|.-+.+...-.|||--++.-|+..--. -+.+||-||+.+.+-.+.|.
T Consensus 14 ed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~denv~~~ 71 (480)
T COG5175 14 EDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENVRYV 71 (480)
T ss_pred cccCcccccccccccCCcccCCcccHHHHHHHHHHHhhccCCChHhhhhccccceeEE
Confidence 3459999999877766666778999999999877543 37899999998866555443
No 94
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=87.88 E-value=0.26 Score=54.27 Aligned_cols=36 Identities=33% Similarity=0.701 Sum_probs=28.7
Q ss_pred ccCCcceEecCCCCccchhhHHHHhccCCCCcCCCccc
Q 001136 1031 FTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSL 1068 (1143)
Q Consensus 1031 f~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~ 1068 (1143)
|.+..+...+.|+|.|+..|...- ....||+|++++
T Consensus 12 ~~~~~~f~LTaC~HvfC~~C~k~~--~~~~C~lCkk~i 47 (233)
T KOG4739|consen 12 FPSQDPFFLTACRHVFCEPCLKAS--SPDVCPLCKKSI 47 (233)
T ss_pred cCCCCceeeeechhhhhhhhcccC--Ccccccccccee
Confidence 556666677889999999999763 234999999997
No 95
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=87.69 E-value=0.37 Score=40.21 Aligned_cols=40 Identities=28% Similarity=0.703 Sum_probs=25.4
Q ss_pred CcccccccccCCcceEecCCC-----CccchhhHHHHhc--cCCCCcCC
Q 001136 1023 CPICCDFLFTSSETVRALPCG-----HYMHLACFQAYTC--SHYTCPIC 1064 (1143)
Q Consensus 1023 CpIC~e~lf~s~~~v~~lpCg-----H~fH~~Ci~~wl~--~~~~CPiC 1064 (1143)
|=||++.-.++. ..+.||+ -..|.+|+.+|+. .+.+|++|
T Consensus 1 CrIC~~~~~~~~--~li~pC~C~Gs~~~vH~~CL~~W~~~~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEEEDE--PLISPCRCKGSMKYVHRSCLERWIRESGNRKCEIC 47 (47)
T ss_dssp ETTTTEE-SSSS---EE-SSS-SSCCGSEECCHHHHHHHHHT-SB-TTT
T ss_pred CeEeCCcCCCCC--ceecccccCCCcchhHHHHHHHHHHhcCCCcCCCC
Confidence 568887722222 3456765 4789999999975 56889998
No 96
>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=87.61 E-value=0.24 Score=41.19 Aligned_cols=44 Identities=34% Similarity=0.831 Sum_probs=25.8
Q ss_pred CCCcccccccccCCcceEecCCC-CccchhhHHHHhccCCCCcCCCccccc
Q 001136 1021 TNCPICCDFLFTSSETVRALPCG-HYMHLACFQAYTCSHYTCPICSKSLGD 1070 (1143)
Q Consensus 1021 ~~CpIC~e~lf~s~~~v~~lpCg-H~fH~~Ci~~wl~~~~~CPiCr~s~~~ 1070 (1143)
.+|--|. |.... .+.|. |+.+..|++..+..+..||||+++++.
T Consensus 3 ~nCKsCW---f~~k~---Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPt 47 (50)
T PF03854_consen 3 YNCKSCW---FANKG---LIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPT 47 (50)
T ss_dssp ----SS----S--SS---EEE-SS-EEEHHHHHHT-SSSSEETTTTEE---
T ss_pred ccChhhh---hcCCC---eeeecchhHHHHHHHHHhccccCCCcccCcCcc
Confidence 4566676 33322 35686 999999999999999999999998863
No 97
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.18 E-value=0.57 Score=54.92 Aligned_cols=52 Identities=25% Similarity=0.529 Sum_probs=37.8
Q ss_pred cccccccccCCCCcccccccccCCcceEecCCCCccchhhHHHHhc--------cCCCCcCC
Q 001136 1011 NHKCLEKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTC--------SHYTCPIC 1064 (1143)
Q Consensus 1011 ~H~C~e~~~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~--------~~~~CPiC 1064 (1143)
+|.+.-++. -.|.||++. +....-...+||+|+|+..|...|.. +.-.||-+
T Consensus 176 ~~~~F~~sl-f~C~ICf~e-~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~eg~v~~l~Cp~~ 235 (445)
T KOG1814|consen 176 TLEKFVNSL-FDCCICFEE-QMGQHCFKFLPCSHVFCKSCLKDYFTIQIQEGQVSCLKCPDP 235 (445)
T ss_pred HHHHHHhhc-ccceeeehh-hcCcceeeecccchHHHHHHHHHHHHHhhhcceeeeecCCCC
Confidence 444444443 569999987 55556667899999999999999842 23668765
No 98
>PF04641 Rtf2: Rtf2 RING-finger
Probab=87.10 E-value=0.46 Score=53.52 Aligned_cols=51 Identities=22% Similarity=0.490 Sum_probs=40.5
Q ss_pred cccCCCCcccccccccCCcceEec-CCCCccchhhHHHHhccCCCCcCCCcccc
Q 001136 1017 KCLETNCPICCDFLFTSSETVRAL-PCGHYMHLACFQAYTCSHYTCPICSKSLG 1069 (1143)
Q Consensus 1017 ~~~~~~CpIC~e~lf~s~~~v~~l-pCgH~fH~~Ci~~wl~~~~~CPiCr~s~~ 1069 (1143)
......|||.... |++.....+| ||||+|-..++.+.- ....||+|.+++.
T Consensus 110 ~~~~~~CPvt~~~-~~~~~~fv~l~~cG~V~s~~alke~k-~~~~Cp~c~~~f~ 161 (260)
T PF04641_consen 110 SEGRFICPVTGKE-FNGKHKFVYLRPCGCVFSEKALKELK-KSKKCPVCGKPFT 161 (260)
T ss_pred CCceeECCCCCcc-cCCceeEEEEcCCCCEeeHHHHHhhc-ccccccccCCccc
Confidence 3445679999988 5666665555 899999999999984 4678999999984
No 99
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.96 E-value=0.33 Score=56.11 Aligned_cols=46 Identities=26% Similarity=0.563 Sum_probs=33.1
Q ss_pred ccccCCCCcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCCccc
Q 001136 1016 EKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSL 1068 (1143)
Q Consensus 1016 e~~~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~ 1068 (1143)
+.....+|.||.+. + .....+||||.-+ |..-. +...+||+||..+
T Consensus 301 ~~~~p~lcVVcl~e-~---~~~~fvpcGh~cc--ct~cs-~~l~~CPvCR~rI 346 (355)
T KOG1571|consen 301 ELPQPDLCVVCLDE-P---KSAVFVPCGHVCC--CTLCS-KHLPQCPVCRQRI 346 (355)
T ss_pred ccCCCCceEEecCC-c---cceeeecCCcEEE--chHHH-hhCCCCchhHHHH
Confidence 44557899999987 3 3368899999955 55443 2346699999876
No 100
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.13 E-value=0.42 Score=53.82 Aligned_cols=61 Identities=21% Similarity=0.368 Sum_probs=41.6
Q ss_pred CCcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCCccccchhhhhhhhHHHHhhcC
Q 001136 1022 NCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLGDMAIYFGMIDALLAAEE 1086 (1143)
Q Consensus 1022 ~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~~~m~~~~~~ld~~i~~~p 1086 (1143)
.|-||..+ |-+. ++..|||+|+..|...=++.+..|++|.+.+-.....-..|...+...+
T Consensus 243 ~c~icr~~-f~~p---Vvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g~~~~akeL~~~L~~kk 303 (313)
T KOG1813|consen 243 KCFICRKY-FYRP---VVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHGSFNVAKELLVSLKLKK 303 (313)
T ss_pred cccccccc-cccc---hhhcCCceeehhhhccccccCCcceecccccccccchHHHHHHHHHhhh
Confidence 49999988 4332 4577999999999888777789999998877432222233444444333
No 101
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=85.97 E-value=0.3 Score=58.24 Aligned_cols=50 Identities=30% Similarity=0.608 Sum_probs=39.9
Q ss_pred cccccCCCCcccccccccCCcceEecCCCCccchhhHHHHh-----ccCCCCcCCCccc
Q 001136 1015 LEKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYT-----CSHYTCPICSKSL 1068 (1143)
Q Consensus 1015 ~e~~~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl-----~~~~~CPiCr~s~ 1068 (1143)
.++..+..|-+|-++ .+......|-|.|++-|+.+|. ..+-+||.|...+
T Consensus 531 ~enk~~~~C~lc~d~----aed~i~s~ChH~FCrlCi~eyv~~f~~~~nvtCP~C~i~L 585 (791)
T KOG1002|consen 531 DENKGEVECGLCHDP----AEDYIESSCHHKFCRLCIKEYVESFMENNNVTCPVCHIGL 585 (791)
T ss_pred ccccCceeecccCCh----hhhhHhhhhhHHHHHHHHHHHHHhhhcccCCCCccccccc
Confidence 466777889999876 2344567899999999999995 2468899998877
No 102
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=85.56 E-value=0.65 Score=40.54 Aligned_cols=47 Identities=26% Similarity=0.494 Sum_probs=30.9
Q ss_pred cceeeccccccccccC-----CCCCCCCCCCCcceeEeccccccccCCCCcccCCCCCc
Q 001136 931 TSEMMCMHCLKIQAIG-----PNCTTPSCNGLSMAKYYCNICKFFDDERTVYHCPFCNL 984 (1143)
Q Consensus 931 ~~~~~C~~C~~~q~~~-----~~C~~~~cc~~~f~~y~C~~C~~~d~~~~~yhC~~Cgi 984 (1143)
.....|..|+..-... -.|+| ||.. -=|-|..|+-.. ..|.|++||+
T Consensus 5 ~~~~~CtSCg~~i~~~~~~~~F~CPn---CG~~-~I~RC~~CRk~~---~~Y~CP~CGF 56 (59)
T PRK14890 5 MEPPKCTSCGIEIAPREKAVKFLCPN---CGEV-IIYRCEKCRKQS---NPYTCPKCGF 56 (59)
T ss_pred ccCccccCCCCcccCCCccCEeeCCC---CCCe-eEeechhHHhcC---CceECCCCCC
Confidence 3455788888654322 35888 4653 235588888775 4589999986
No 103
>KOG0269 consensus WD40 repeat-containing protein [Function unknown]
Probab=84.92 E-value=0.72 Score=57.57 Aligned_cols=70 Identities=23% Similarity=0.469 Sum_probs=48.7
Q ss_pred CCcccCCCCCccccCCCCCccccccCCcccccccccccccccccccCCCCcccccccccCCcceEecCCCCccchhhHHH
Q 001136 974 RTVYHCPFCNLCRVGGGLGVDFFHCMTCNCCLGLKLLNHKCLEKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQA 1053 (1143)
Q Consensus 974 ~~~yhC~~CgiCr~g~~l~~~~~hC~~C~~C~~~~~~~H~C~e~~~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~ 1053 (1143)
-=+|-|+.|+---+++++ --|++|-.|.+. .|.+|-..+- +..+..--|||-.|.+|+..
T Consensus 751 ~i~~~~~nc~a~~~~~~~----~~c~rc~s~a~~--------------~CtVC~~vi~--G~~~~c~~C~H~gH~sh~~s 810 (839)
T KOG0269|consen 751 TIHYACPNCDAPMVLTKL----WQCDRCESRASA--------------KCTVCDLVIR--GVDVWCQVCGHGGHDSHLKS 810 (839)
T ss_pred eeeccccccCCccccccc----eeechHHHHhhc--------------Cceeecceee--eeEeecccccccccHHHHHH
Confidence 456888888877777653 457777777553 4999976531 11122234999999999999
Q ss_pred HhccCCCCcC
Q 001136 1054 YTCSHYTCPI 1063 (1143)
Q Consensus 1054 wl~~~~~CPi 1063 (1143)
|...+.-||.
T Consensus 811 w~~~~s~ca~ 820 (839)
T KOG0269|consen 811 WFFKASPCAK 820 (839)
T ss_pred HHhcCCCCcc
Confidence 9987777765
No 104
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=83.58 E-value=0.72 Score=45.76 Aligned_cols=37 Identities=14% Similarity=0.370 Sum_probs=27.1
Q ss_pred cCcceEEcCCCCCCCcccchhhcccCCCCCCcccccccc
Q 001136 1093 NQVQDILCNDCEQKGAARFHWLYHKCGFCGSYNTRLIKN 1131 (1143)
Q Consensus 1093 ~~~~~i~CndC~~~s~~~~h~l~~kC~~C~syNt~~~~~ 1131 (1143)
.......|++|+....... .+..||.|||++++++.-
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~--~~~~CP~Cgs~~~~i~~G 102 (115)
T TIGR00100 66 DEPVECECEDCSEEVSPEI--DLYRCPKCHGIMLQVRAG 102 (115)
T ss_pred eeCcEEEcccCCCEEecCC--cCccCcCCcCCCcEEecC
Confidence 3455789999997765532 235799999999888643
No 105
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=83.48 E-value=0.48 Score=53.87 Aligned_cols=19 Identities=11% Similarity=0.134 Sum_probs=14.9
Q ss_pred hhhHHHHHHHhhcCCCCCC
Q 001136 765 NTMFNEWLDECWKGPHESS 783 (1143)
Q Consensus 765 ~t~F~~WL~~w~~~~~~~~ 783 (1143)
..+....+.|.|+..|.|.
T Consensus 87 ~K~le~Fv~eFFdQNPiSQ 105 (378)
T KOG2807|consen 87 IKYLEGFVPEFFDQNPISQ 105 (378)
T ss_pred HHHHHHHHHHHhccCchhh
Confidence 4667888889999888765
No 106
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.00 E-value=0.71 Score=52.85 Aligned_cols=50 Identities=22% Similarity=0.468 Sum_probs=41.8
Q ss_pred cccCCCCcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCCccccc
Q 001136 1017 KCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLGD 1070 (1143)
Q Consensus 1017 ~~~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~~~ 1070 (1143)
.+.++.||||... .-..+.-||||-=+..||.+-+.++..|=.|+.++.+
T Consensus 419 ~sEd~lCpICyA~----pi~Avf~PC~H~SC~~CI~qHlmN~k~CFfCktTv~~ 468 (489)
T KOG4692|consen 419 DSEDNLCPICYAG----PINAVFAPCSHRSCYGCITQHLMNCKRCFFCKTTVID 468 (489)
T ss_pred CcccccCcceecc----cchhhccCCCCchHHHHHHHHHhcCCeeeEecceeee
Confidence 3557889999864 3344667999999999999999999999999998875
No 107
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=82.71 E-value=0.82 Score=45.49 Aligned_cols=36 Identities=22% Similarity=0.523 Sum_probs=26.8
Q ss_pred cCcceEEcCCCCCCCccc-chhhcccCCCCCCccccccc
Q 001136 1093 NQVQDILCNDCEQKGAAR-FHWLYHKCGFCGSYNTRLIK 1130 (1143)
Q Consensus 1093 ~~~~~i~CndC~~~s~~~-~h~l~~kC~~C~syNt~~~~ 1130 (1143)
.......|++||...... ++ +.+||.|||++..+++
T Consensus 67 ~vp~~~~C~~Cg~~~~~~~~~--~~~CP~Cgs~~~~i~~ 103 (117)
T PRK00564 67 DEKVELECKDCSHVFKPNALD--YGVCEKCHSKNVIITQ 103 (117)
T ss_pred ecCCEEEhhhCCCccccCCcc--CCcCcCCCCCceEEec
Confidence 345678999999776653 32 3469999999988764
No 108
>PHA02862 5L protein; Provisional
Probab=82.38 E-value=0.91 Score=46.33 Aligned_cols=45 Identities=27% Similarity=0.632 Sum_probs=32.7
Q ss_pred CCCCcccccccccCCcceEecCCC-----CccchhhHHHHhcc--CCCCcCCCcccc
Q 001136 1020 ETNCPICCDFLFTSSETVRALPCG-----HYMHLACFQAYTCS--HYTCPICSKSLG 1069 (1143)
Q Consensus 1020 ~~~CpIC~e~lf~s~~~v~~lpCg-----H~fH~~Ci~~wl~~--~~~CPiCr~s~~ 1069 (1143)
.+.|=||.+. .... .-||. -..|..|+.+|+.. +..||+|+..+.
T Consensus 2 ~diCWIC~~~---~~e~--~~PC~C~GS~K~VHq~CL~~WIn~S~k~~CeLCkteY~ 53 (156)
T PHA02862 2 SDICWICNDV---CDER--NNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYN 53 (156)
T ss_pred CCEEEEecCc---CCCC--cccccccCcchhHHHHHHHHHHhcCCCcCccCCCCeEE
Confidence 4568899876 2222 24654 57899999999854 577999998874
No 109
>PRK04023 DNA polymerase II large subunit; Validated
Probab=82.17 E-value=1.1 Score=57.92 Aligned_cols=48 Identities=23% Similarity=0.438 Sum_probs=26.4
Q ss_pred eeeccccccccccCCCCCCCCCCCCcceeEeccccccccCCCCcccCCCCCccc
Q 001136 933 EMMCMHCLKIQAIGPNCTTPSCNGLSMAKYYCNICKFFDDERTVYHCPFCNLCR 986 (1143)
Q Consensus 933 ~~~C~~C~~~q~~~~~C~~~~cc~~~f~~y~C~~C~~~d~~~~~yhC~~CgiCr 986 (1143)
.-.|..|+++. +...|++ |....-.-|||+.|.- .-..|.|++||.=.
T Consensus 626 ~RfCpsCG~~t-~~frCP~--CG~~Te~i~fCP~CG~---~~~~y~CPKCG~El 673 (1121)
T PRK04023 626 RRKCPSCGKET-FYRRCPF--CGTHTEPVYRCPRCGI---EVEEDECEKCGREP 673 (1121)
T ss_pred CccCCCCCCcC-CcccCCC--CCCCCCcceeCccccC---cCCCCcCCCCCCCC
Confidence 34566666654 3346766 4333455667777722 23346677777633
No 110
>COG5592 Uncharacterized conserved protein [Function unknown]
Probab=82.11 E-value=7 Score=40.83 Aligned_cols=121 Identities=20% Similarity=0.277 Sum_probs=81.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCCcccHHHHHHHHHHHHHHhcccCccccccchHHHhhh-------cc--hHHHHHH
Q 001136 45 FCFFHKAVRNELDALHQLAMNFATGHRVDILSLSERYRFLHSVYKHHSNAEDEVIFPALDIR-------VK--NVARKYS 115 (1143)
Q Consensus 45 m~~~H~aLRreL~~L~~la~~~~~gd~~~~~~L~~~~~~l~~~L~~HH~~EDevLFPaL~~R-------~p--~vl~~le 115 (1143)
+...|..+|+.=+.+... ++..+.....+......-|-..|+..+||..... .. +..+.+.
T Consensus 8 ~~v~~l~~r~len~~~~~----------~~~e~le~~gf~~k~~k~h~e~Ee~ilF~v~Vd~~~ed~~~fkdt~~~~~i~ 77 (171)
T COG5592 8 LMVLHLSIRNLENLAYGK----------DLLEILEFEGFNEKLGKDHVELEEKILFPVIVDADMEDLYVFKDTPEVDRIK 77 (171)
T ss_pred HhhhhhhhhhchhHHhHH----------HHHHHHhhcchHHHHhhhHHHHHHHhhhhhccchHHHHHHhhhccchhhHhH
Confidence 344566665543333322 2333444444566678889999999999985421 11 3578889
Q ss_pred HHHHHHHHHHHHHHHHHhhhccCCCCchHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhccCCHHHHHHH
Q 001136 116 LEHEGESNLFDHLFQLLNSYTQNDESFPKELASCSRALQTSINQHMSKEEQQVFPLLTQHFSLEEQASL 184 (1143)
Q Consensus 116 ~EH~~i~~ll~~L~~~l~~~~~~~~~~~~eLa~~l~~l~~~L~~HL~~EE~~lfPLa~~~LS~eEw~~L 184 (1143)
.+|+-+.-+...+...-+ + .....-+..|...|..|=..||..+||.+...-...++.++
T Consensus 78 ~DHkliE~l~tnlik~kR------~---~k~~e~~p~fyK~LtdHn~aEE~~IfPrvks~~~E~~~~~~ 137 (171)
T COG5592 78 NDHKLIETLATNLIKWKR------P---DKIKERVPLFYKTLTDHNLAEEEYIFPRVKSLKGEDEQSAL 137 (171)
T ss_pred hhHHHHHHHHHHHHhhcc------c---hHHHHHHHHHHHHHHHccccccchhhHHHHhhcchhhHHHH
Confidence 999988888776655422 1 35667788899999999999999999999876555444443
No 111
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=81.39 E-value=1.3 Score=46.08 Aligned_cols=44 Identities=23% Similarity=0.548 Sum_probs=31.6
Q ss_pred CCCCcccccccccCCcceEecCCC--C---ccchhhHHHHhc--cCCCCcCCCccc
Q 001136 1020 ETNCPICCDFLFTSSETVRALPCG--H---YMHLACFQAYTC--SHYTCPICSKSL 1068 (1143)
Q Consensus 1020 ~~~CpIC~e~lf~s~~~v~~lpCg--H---~fH~~Ci~~wl~--~~~~CPiCr~s~ 1068 (1143)
+..|=||.+. .+. ..-||. . ..|.+|+.+|+. +..+||+|+..+
T Consensus 8 ~~~CRIC~~~---~~~--~~~PC~CkGs~k~VH~sCL~rWi~~s~~~~CeiC~~~Y 58 (162)
T PHA02825 8 DKCCWICKDE---YDV--VTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPY 58 (162)
T ss_pred CCeeEecCCC---CCC--ccCCcccCCCchHHHHHHHHHHHhcCCCCcccccCCeE
Confidence 4579999876 112 224654 3 569999999974 457799999877
No 112
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=81.32 E-value=0.91 Score=57.38 Aligned_cols=47 Identities=19% Similarity=0.110 Sum_probs=35.0
Q ss_pred CChhhHHHHHHHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHH
Q 001136 550 ERPIDTIFKFHKAISKDLEYLDMESAKLSDCDETFLRQFIGRFRLLW 596 (1143)
Q Consensus 550 ~~PiD~i~~~HkAiRkdL~~l~~~~~~l~~~D~~~l~~~~~R~~~l~ 596 (1143)
-.|.|.=..+-.-++|.|-.++.-+++=...|+.+++++...+.-.+
T Consensus 332 L~ek~le~kL~iL~kK~ly~~Ai~LAk~~~~d~d~~~~i~~kYgd~L 378 (933)
T KOG2114|consen 332 LIEKDLETKLDILFKKNLYKVAINLAKSQHLDEDTLAEIHRKYGDYL 378 (933)
T ss_pred eeeccHHHHHHHHHHhhhHHHHHHHHHhcCCCHHHHHHHHHHHHHHH
Confidence 44666667777778888888888888877678888888776665443
No 113
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=81.18 E-value=1.3 Score=50.56 Aligned_cols=47 Identities=28% Similarity=0.699 Sum_probs=37.6
Q ss_pred CCCcccccccccCCcce---EecCCCCccchhhHHHHhccC-CCCcCCCccc
Q 001136 1021 TNCPICCDFLFTSSETV---RALPCGHYMHLACFQAYTCSH-YTCPICSKSL 1068 (1143)
Q Consensus 1021 ~~CpIC~e~lf~s~~~v---~~lpCgH~fH~~Ci~~wl~~~-~~CPiCr~s~ 1068 (1143)
..|-||-++ |++.... +.|.|||++...|+.+.+... ..||.||.+.
T Consensus 4 ~~c~~c~~~-~s~~~~~~~p~~l~c~h~~c~~c~~~l~~~~~i~cpfcR~~~ 54 (296)
T KOG4185|consen 4 PECEICNED-YSSEDGDHIPRVLKCGHTICQNCASKLLGNSRILCPFCRETT 54 (296)
T ss_pred CceeecCcc-ccccCcccCCcccccCceehHhHHHHHhcCceeeccCCCCcc
Confidence 459999998 7776433 567899999999999987554 6699999994
No 114
>TIGR02481 hemeryth_dom hemerythrin-like metal-binding domain. This model describes both members of the hemerythrin (TIGR00058) family of marine invertebrates and a broader collection of bacterial and archaeal homologs. Many of the latter group are multidomain proteins with signal-transducing domains such as the GGDEF diguanylate cyclase domain (TIGR00254, pfam00990) and methyl-accepting chemotaxis protein signaling domain (pfam00015). Most hemerythrins are oxygen-carriers with a bound non-heme iron, but at least one example is a cadmium-binding protein, apparently with a role in sequestering toxic metals rather than in binding oxygen. Patterns of conserved residues suggest that all prokaryotic instances of this domain bind iron or another heavy metal, but the exact function is unknown. Not surprisingly, the prokaryote with the most instances of this domain is Magnetococcus sp. MC-1, a magnetotactic bacterium.
Probab=80.59 E-value=6.4 Score=38.98 Aligned_cols=54 Identities=19% Similarity=0.225 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhccCCCCchHHHHHHHHHHHHHHHHHHHHHHHhHH
Q 001136 111 ARKYSLEHEGESNLFDHLFQLLNSYTQNDESFPKELASCSRALQTSINQHMSKEEQQVF 169 (1143)
Q Consensus 111 l~~le~EH~~i~~ll~~L~~~l~~~~~~~~~~~~eLa~~l~~l~~~L~~HL~~EE~~lf 169 (1143)
+..+..+|+.+-.++++|..++..- ....++...+..|......|+..||..+-
T Consensus 10 ~~~ID~qH~~l~~~in~l~~a~~~~-----~~~~~~~~~l~~L~~y~~~HF~~EE~~M~ 63 (126)
T TIGR02481 10 IEEIDAQHKELFELINELYDALSAG-----NGKDELKEILDELIDYTENHFADEEELME 63 (126)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHcC-----CCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3468899999999999998877532 22467888999999999999999999763
No 115
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=80.36 E-value=1 Score=44.50 Aligned_cols=36 Identities=19% Similarity=0.315 Sum_probs=26.1
Q ss_pred CcceEEcCCCCCCCcccchhhcccCCCCCCcccccccc
Q 001136 1094 QVQDILCNDCEQKGAARFHWLYHKCGFCGSYNTRLIKN 1131 (1143)
Q Consensus 1094 ~~~~i~CndC~~~s~~~~h~l~~kC~~C~syNt~~~~~ 1131 (1143)
......|++|+....... ....||.|||++..+++-
T Consensus 67 vp~~~~C~~Cg~~~~~~~--~~~~CP~Cgs~~~~i~~G 102 (113)
T PRK12380 67 KPAQAWCWDCSQVVEIHQ--HDAQCPHCHGERLRVDTG 102 (113)
T ss_pred eCcEEEcccCCCEEecCC--cCccCcCCCCCCcEEccC
Confidence 445789999997765532 223599999999887653
No 116
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=78.66 E-value=1.3 Score=43.88 Aligned_cols=37 Identities=19% Similarity=0.402 Sum_probs=26.1
Q ss_pred CcceEEcCCCCCCCcccchhhcccCCCCCCcccccccc
Q 001136 1094 QVQDILCNDCEQKGAARFHWLYHKCGFCGSYNTRLIKN 1131 (1143)
Q Consensus 1094 ~~~~i~CndC~~~s~~~~h~l~~kC~~C~syNt~~~~~ 1131 (1143)
......|++|+......-+ .+..||.|||+++.++.-
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~-~~~~CP~Cgs~~~~i~~G 103 (114)
T PRK03681 67 QEAECWCETCQQYVTLLTQ-RVRRCPQCHGDMLRIVAD 103 (114)
T ss_pred eCcEEEcccCCCeeecCCc-cCCcCcCcCCCCcEEccC
Confidence 3456799999976554322 124699999999888653
No 117
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=78.56 E-value=2.1 Score=49.28 Aligned_cols=63 Identities=22% Similarity=0.581 Sum_probs=46.7
Q ss_pred CCCcccccccccCCcceEecCC--CCccchhhHHHHhccCCCCcCCCccccchhhhhhhhHHHHhhcCCChhhhc
Q 001136 1021 TNCPICCDFLFTSSETVRALPC--GHYMHLACFQAYTCSHYTCPICSKSLGDMAIYFGMIDALLAAEELPEEYRN 1093 (1143)
Q Consensus 1021 ~~CpIC~e~lf~s~~~v~~lpC--gH~fH~~Ci~~wl~~~~~CPiCr~s~~~m~~~~~~ld~~i~~~p~P~~y~~ 1093 (1143)
-+||||.++|.. + +..| ||..+..|-.+ ..+.||.|+.++++.. -+.++..++....|=.|..
T Consensus 49 leCPvC~~~l~~---P--i~QC~nGHlaCssC~~~---~~~~CP~Cr~~~g~~R--~~amEkV~e~~~vpC~~~~ 113 (299)
T KOG3002|consen 49 LDCPVCFNPLSP---P--IFQCDNGHLACSSCRTK---VSNKCPTCRLPIGNIR--CRAMEKVAEAVLVPCKNAK 113 (299)
T ss_pred ccCchhhccCcc---c--ceecCCCcEehhhhhhh---hcccCCccccccccHH--HHHHHHHHHhceecccccc
Confidence 479999998532 2 2445 89999999864 5789999999999653 3457777888877766544
No 118
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=78.42 E-value=1.6 Score=38.20 Aligned_cols=45 Identities=29% Similarity=0.702 Sum_probs=32.1
Q ss_pred eeeccccccccccC-----CCCCCCCCCCCcceeEeccccccccCCCCcccCCCCCc
Q 001136 933 EMMCMHCLKIQAIG-----PNCTTPSCNGLSMAKYYCNICKFFDDERTVYHCPFCNL 984 (1143)
Q Consensus 933 ~~~C~~C~~~q~~~-----~~C~~~~cc~~~f~~y~C~~C~~~d~~~~~yhC~~Cgi 984 (1143)
...|..|+.+-.++ -.|+| ||. .-=|-|..|+-.. ..|.|++||+
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPn---CGe-~~I~Rc~~CRk~g---~~Y~Cp~CGF 58 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPN---CGE-VEIYRCAKCRKLG---NPYRCPKCGF 58 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCC---CCc-eeeehhhhHHHcC---CceECCCcCc
Confidence 56899998876443 34888 462 3357788888775 4699999986
No 119
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=77.01 E-value=1.6 Score=35.84 Aligned_cols=41 Identities=27% Similarity=0.698 Sum_probs=20.2
Q ss_pred CcccccccccCCcceEecCCCCccchhhHHHHhccCC--CCcCC
Q 001136 1023 CPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHY--TCPIC 1064 (1143)
Q Consensus 1023 CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~--~CPiC 1064 (1143)
|.+|.+- .+.+.....-.|+=.+|..|+..|.+... +||.|
T Consensus 1 C~~C~~i-v~~G~~C~~~~C~~r~H~~C~~~y~r~~~~~~CP~C 43 (43)
T PF08746_consen 1 CEACKEI-VTQGQRCSNRDCNVRLHDDCFKKYFRHRSNPKCPNC 43 (43)
T ss_dssp -TTT-SB--SSSEE-SS--S--EE-HHHHHHHTTT-SS-B-TTT
T ss_pred Ccccchh-HeeeccCCCCccCchHHHHHHHHHHhcCCCCCCcCC
Confidence 5566654 33322222224888899999999986654 79988
No 120
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=76.93 E-value=1.5 Score=44.72 Aligned_cols=36 Identities=25% Similarity=0.620 Sum_probs=25.3
Q ss_pred cceEEcCCCCCCCccc-------------ch------hhcccCCCCCCccccccc
Q 001136 1095 VQDILCNDCEQKGAAR-------------FH------WLYHKCGFCGSYNTRLIK 1130 (1143)
Q Consensus 1095 ~~~i~CndC~~~s~~~-------------~h------~l~~kC~~C~syNt~~~~ 1130 (1143)
.....|++||...... +| ..+.+||.|||++..++.
T Consensus 68 p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~ 122 (135)
T PRK03824 68 EAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIVK 122 (135)
T ss_pred ceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEec
Confidence 3567899999665432 22 234679999999988764
No 121
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=76.56 E-value=0.92 Score=55.53 Aligned_cols=43 Identities=26% Similarity=0.592 Sum_probs=33.7
Q ss_pred CCCcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCCc
Q 001136 1021 TNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSK 1066 (1143)
Q Consensus 1021 ~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~ 1066 (1143)
-+|+||+..+|.+.-..+.+.|||+++.+|.... .+.+|| |.+
T Consensus 12 l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~l--yn~scp-~~~ 54 (861)
T KOG3161|consen 12 LLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLL--YNASCP-TKR 54 (861)
T ss_pred hhchHHHHHHHHHhcCcccccccchHHHHHHHhH--hhccCC-CCc
Confidence 3699998876766666677889999999999875 367888 643
No 122
>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=76.06 E-value=0.62 Score=53.27 Aligned_cols=46 Identities=20% Similarity=0.424 Sum_probs=18.2
Q ss_pred ccCCCCccccccc----ccCCc--ceEecCCCCccchhhHHHHhccCCCCcCCCccc
Q 001136 1018 CLETNCPICCDFL----FTSSE--TVRALPCGHYMHLACFQAYTCSHYTCPICSKSL 1068 (1143)
Q Consensus 1018 ~~~~~CpIC~e~l----f~s~~--~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~ 1068 (1143)
+..+.||||...= ..+.. ..+ |.++.-|-..|--....||.|..+=
T Consensus 170 w~~g~CPvCGs~P~~s~l~~~~~~G~R-----~L~Cs~C~t~W~~~R~~Cp~Cg~~~ 221 (290)
T PF04216_consen 170 WQRGYCPVCGSPPVLSVLRGGEREGKR-----YLHCSLCGTEWRFVRIKCPYCGNTD 221 (290)
T ss_dssp TT-SS-TTT---EEEEEEE------EE-----EEEETTT--EEE--TTS-TTT---S
T ss_pred ccCCcCCCCCCcCceEEEecCCCCccE-----EEEcCCCCCeeeecCCCCcCCCCCC
Confidence 3346799997541 11111 123 4455567788877788999997554
No 123
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=75.51 E-value=2.4 Score=51.71 Aligned_cols=140 Identities=19% Similarity=0.334 Sum_probs=70.7
Q ss_pred CCcccCCCCCccccCCCCC--ccccc-----cCCcccccccccccccccccccCCCCcccccccccCCcceEecCCCCcc
Q 001136 974 RTVYHCPFCNLCRVGGGLG--VDFFH-----CMTCNCCLGLKLLNHKCLEKCLETNCPICCDFLFTSSETVRALPCGHYM 1046 (1143)
Q Consensus 974 ~~~yhC~~CgiCr~g~~l~--~~~~h-----C~~C~~C~~~~~~~H~C~e~~~~~~CpIC~e~lf~s~~~v~~lpCgH~f 1046 (1143)
+.+.||++|+-=--|.-|. .++|| |.+|+.=+.-...=+|+.+.-. ++ .-|.+. ..+. .+..=|-+|
T Consensus 14 ~~~i~c~~c~~kc~gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~~~y-gt-~~c~~~--~~ge--vvsa~gkty 87 (670)
T KOG1044|consen 14 KQGIKCDKCRKKCSGEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPENRLY-GT-DDCRAF--VEGE--VVSTLGKTY 87 (670)
T ss_pred ccceehhhhCCccccceeEeeccccceeeeeccccCCCcccccceecccceee-cc-cchhhh--ccce--eEeccccee
Confidence 5667777776422222222 23333 4444433332223455555211 11 233332 2222 334458999
Q ss_pred chhhHHHHhccCCCCcCCCccccchhhh-hhhh--HHHHhhcCCChhhhcCcceEEcCCCCCCC---------cccchhh
Q 001136 1047 HLACFQAYTCSHYTCPICSKSLGDMAIY-FGMI--DALLAAEELPEEYRNQVQDILCNDCEQKG---------AARFHWL 1114 (1143)
Q Consensus 1047 H~~Ci~~wl~~~~~CPiCr~s~~~m~~~-~~~l--d~~i~~~p~P~~y~~~~~~i~CndC~~~s---------~~~~h~l 1114 (1143)
|..|+ +|-+|+.++...+.. |.-- --..-.++||-.-.....--.|-.|+..- ..++|+.
T Consensus 88 h~~cf--------~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~llald~qwhv~ 159 (670)
T KOG1044|consen 88 HPKCF--------SCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLALDKQWHVS 159 (670)
T ss_pred ccccc--------eecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccceeeeeccceeee
Confidence 99887 677788777433322 2111 11122345554322223344688888542 3579999
Q ss_pred cccCCCCCCcccc
Q 001136 1115 YHKCGFCGSYNTR 1127 (1143)
Q Consensus 1115 ~~kC~~C~syNt~ 1127 (1143)
+-||..|+-.=+.
T Consensus 160 cfkc~~c~~vL~g 172 (670)
T KOG1044|consen 160 CFKCKSCSAVLNG 172 (670)
T ss_pred eeehhhhcccccc
Confidence 9999998754433
No 124
>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=74.84 E-value=0.58 Score=42.29 Aligned_cols=64 Identities=33% Similarity=0.662 Sum_probs=33.8
Q ss_pred CCCcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCCccccchhhhhhhhHHHHhhcCCChhhhcCcceEEc
Q 001136 1021 TNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLGDMAIYFGMIDALLAAEELPEEYRNQVQDILC 1100 (1143)
Q Consensus 1021 ~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~~~m~~~~~~ld~~i~~~p~P~~y~~~~~~i~C 1100 (1143)
..||.|..+|-..+ ||+....|-..+. ....||-|...+....+ =..+++.|
T Consensus 2 ~~CP~C~~~L~~~~--------~~~~C~~C~~~~~-~~a~CPdC~~~Le~LkA-------------------CGAvdYFC 53 (70)
T PF07191_consen 2 NTCPKCQQELEWQG--------GHYHCEACQKDYK-KEAFCPDCGQPLEVLKA-------------------CGAVDYFC 53 (70)
T ss_dssp -B-SSS-SBEEEET--------TEEEETTT--EEE-EEEE-TTT-SB-EEEEE-------------------TTEEEEE-
T ss_pred CcCCCCCCccEEeC--------CEEECccccccce-ecccCCCcccHHHHHHH-------------------hcccceee
Confidence 47999998852222 7778888877653 35679999987743321 12257889
Q ss_pred CCCC---CCCcccch
Q 001136 1101 NDCE---QKGAARFH 1112 (1143)
Q Consensus 1101 ndC~---~~s~~~~h 1112 (1143)
|.|+ .|+.+.|.
T Consensus 54 ~~c~gLiSKkrV~f~ 68 (70)
T PF07191_consen 54 NHCHGLISKKRVRFE 68 (70)
T ss_dssp TTTT-EE-TTTSEEE
T ss_pred ccCCceeecceEEEE
Confidence 9998 34455553
No 125
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=73.81 E-value=2.9 Score=48.00 Aligned_cols=47 Identities=28% Similarity=0.610 Sum_probs=36.6
Q ss_pred ccCCCCcccccccccCCcceEecCCCCccchhhHHHH--hccCCCCcCCCccc
Q 001136 1018 CLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAY--TCSHYTCPICSKSL 1068 (1143)
Q Consensus 1018 ~~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~w--l~~~~~CPiCr~s~ 1068 (1143)
..+..|-||-+. .+.+..+||||-++--|.-+. +-....||+||..-
T Consensus 59 Een~~C~ICA~~----~TYs~~~PC~H~~CH~Ca~RlRALY~~K~C~~CrTE~ 107 (493)
T COG5236 59 EENMNCQICAGS----TTYSARYPCGHQICHACAVRLRALYMQKGCPLCRTET 107 (493)
T ss_pred cccceeEEecCC----ceEEEeccCCchHHHHHHHHHHHHHhccCCCcccccc
Confidence 345689999975 355677999999999997764 55677899998654
No 126
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=72.88 E-value=1.3 Score=43.84 Aligned_cols=36 Identities=22% Similarity=0.392 Sum_probs=22.8
Q ss_pred CcceEEcCCCCCCCcccchhhcccCCCCCCcccccccc
Q 001136 1094 QVQDILCNDCEQKGAARFHWLYHKCGFCGSYNTRLIKN 1131 (1143)
Q Consensus 1094 ~~~~i~CndC~~~s~~~~h~l~~kC~~C~syNt~~~~~ 1131 (1143)
......|++||.......+. ..||.|||++..+++-
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~--~~CP~Cgs~~~~i~~G 102 (113)
T PF01155_consen 67 VPARARCRDCGHEFEPDEFD--FSCPRCGSPDVEIISG 102 (113)
T ss_dssp E--EEEETTTS-EEECHHCC--HH-SSSSSS-EEEEES
T ss_pred cCCcEECCCCCCEEecCCCC--CCCcCCcCCCcEEccC
Confidence 44578999999987654322 4599999999877643
No 127
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=72.71 E-value=2.5 Score=51.91 Aligned_cols=29 Identities=41% Similarity=1.100 Sum_probs=15.9
Q ss_pred eeccccccccccCCCCCCCCCCCCcceeEecccccc
Q 001136 934 MMCMHCLKIQAIGPNCTTPSCNGLSMAKYYCNICKF 969 (1143)
Q Consensus 934 ~~C~~C~~~q~~~~~C~~~~cc~~~f~~y~C~~C~~ 969 (1143)
..|-.|..+. |+. |....+-.|||+.|-+
T Consensus 6 ~fC~~C~~ir-----c~~--c~~~Ei~~~yCp~CL~ 34 (483)
T PF05502_consen 6 YFCEHCHKIR-----CPR--CVSEEIDSYYCPNCLF 34 (483)
T ss_pred eecccccccC-----Chh--hcccccceeECccccc
Confidence 3455565543 433 4455666666666654
No 128
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=72.34 E-value=0.27 Score=56.93 Aligned_cols=52 Identities=23% Similarity=0.486 Sum_probs=44.4
Q ss_pred ccCCCCcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCCcccc
Q 001136 1018 CLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLG 1069 (1143)
Q Consensus 1018 ~~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~~ 1069 (1143)
+.-..|.||.+.+...-..+..+-|||.+|..|+.+|+.+...||.|++.+.
T Consensus 194 slv~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~~~kl~~~~rel~ 245 (465)
T KOG0827|consen 194 SLVGSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLATKRKLPSCRRELP 245 (465)
T ss_pred HHHhhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHhHHHHhhhh
Confidence 4456799999986655567778889999999999999988999999999884
No 129
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 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 DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=71.21 E-value=2.8 Score=43.67 Aligned_cols=47 Identities=28% Similarity=0.590 Sum_probs=39.5
Q ss_pred CCcceeEeccccccccCCCCcccCCCCCccccCCCCCccccccCCcccccccc
Q 001136 956 GLSMAKYYCNICKFFDDERTVYHCPFCNLCRVGGGLGVDFFHCMTCNCCLGLK 1008 (1143)
Q Consensus 956 ~~~f~~y~C~~C~~~d~~~~~yhC~~CgiCr~g~~l~~~~~hC~~C~~C~~~~ 1008 (1143)
+......||..|+.+... ..+||..||.|-.+. -.||.=-|.|++..
T Consensus 43 ~~~~~~~~C~~C~~~kp~-Rs~HC~~C~~CV~~~-----DHHC~w~~~cIG~~ 89 (174)
T PF01529_consen 43 DENGELKYCSTCKIIKPP-RSHHCRVCNRCVLRF-----DHHCPWLGNCIGRR 89 (174)
T ss_pred ccCCCCEECcccCCcCCC-cceeccccccccccc-----cccchhhccccccc
Confidence 557788899999999666 589999999999986 36999989998765
No 130
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=70.49 E-value=2.1 Score=49.42 Aligned_cols=42 Identities=21% Similarity=0.630 Sum_probs=26.4
Q ss_pred CCCCccccccc------ccCCcceEecCCCCccchhhHHHHhccCCCCcCCCc
Q 001136 1020 ETNCPICCDFL------FTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSK 1066 (1143)
Q Consensus 1020 ~~~CpIC~e~l------f~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~ 1066 (1143)
.+.||||...= .......+++-| .-|-..|--.+..||-|..
T Consensus 187 ~~~CPvCGs~P~~s~v~~~~~~G~RyL~C-----slC~teW~~~R~~C~~Cg~ 234 (309)
T PRK03564 187 RQFCPVCGSMPVSSVVQIGTTQGLRYLHC-----NLCESEWHVVRVKCSNCEQ 234 (309)
T ss_pred CCCCCCCCCcchhheeeccCCCCceEEEc-----CCCCCcccccCccCCCCCC
Confidence 46688887641 111223344444 4677788777899999985
No 131
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=70.24 E-value=2.8 Score=42.20 Aligned_cols=36 Identities=22% Similarity=0.600 Sum_probs=24.5
Q ss_pred CcceEEcCCCCCCCccc-c---hh-hcccCCCCCCccccccc
Q 001136 1094 QVQDILCNDCEQKGAAR-F---HW-LYHKCGFCGSYNTRLIK 1130 (1143)
Q Consensus 1094 ~~~~i~CndC~~~s~~~-~---h~-l~~kC~~C~syNt~~~~ 1130 (1143)
......| +|+...... + |+ .+..||.|||++..++.
T Consensus 67 vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~ 107 (124)
T PRK00762 67 IPVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHILG 107 (124)
T ss_pred cCeeEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEec
Confidence 4456899 999774321 1 11 23569999999998764
No 132
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=69.86 E-value=5 Score=34.67 Aligned_cols=35 Identities=23% Similarity=0.575 Sum_probs=25.8
Q ss_pred cCCCCcccccccccCCcceEecCCCCccchhhHHH
Q 001136 1019 LETNCPICCDFLFTSSETVRALPCGHYMHLACFQA 1053 (1143)
Q Consensus 1019 ~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~ 1053 (1143)
....|++|.+.+......|+--.||-.+|+.|..+
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 34679999999443444444455999999999876
No 133
>PHA03096 p28-like protein; Provisional
Probab=69.26 E-value=2.5 Score=48.36 Aligned_cols=45 Identities=18% Similarity=0.305 Sum_probs=30.2
Q ss_pred CCCcccccccccCC---cceEecC-CCCccchhhHHHHhcc---CCCCcCCC
Q 001136 1021 TNCPICCDFLFTSS---ETVRALP-CGHYMHLACFQAYTCS---HYTCPICS 1065 (1143)
Q Consensus 1021 ~~CpIC~e~lf~s~---~~v~~lp-CgH~fH~~Ci~~wl~~---~~~CPiCr 1065 (1143)
-.|.||++...... .....|+ |.|.|+..|+..|... ..+||.|+
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~~~e~~~~c~ 230 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENR 230 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhhhcccCcccc
Confidence 56999998865432 2223454 9999999999999532 24455554
No 134
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=69.17 E-value=3.4 Score=48.58 Aligned_cols=44 Identities=20% Similarity=0.538 Sum_probs=35.5
Q ss_pred CCcccccccccCCcceEecCCCCccchhhHHHHhccC---CCCcCCCc
Q 001136 1022 NCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSH---YTCPICSK 1066 (1143)
Q Consensus 1022 ~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~---~~CPiCr~ 1066 (1143)
.|||=.+. -+...+.+.|.|||.+-..-+++..+++ .+||.|-.
T Consensus 336 ~CPVlKeq-tsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~ 382 (394)
T KOG2817|consen 336 ICPVLKEQ-TSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPV 382 (394)
T ss_pred ecccchhh-ccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCc
Confidence 58888775 4555688899999999999999987543 68999953
No 135
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=68.47 E-value=3.4 Score=41.84 Aligned_cols=47 Identities=34% Similarity=0.737 Sum_probs=34.5
Q ss_pred CCCCcccccccccCCcceEec-C---CCCccchhhHHH-Hh--ccCCCCcCCCccccc
Q 001136 1020 ETNCPICCDFLFTSSETVRAL-P---CGHYMHLACFQA-YT--CSHYTCPICSKSLGD 1070 (1143)
Q Consensus 1020 ~~~CpIC~e~lf~s~~~v~~l-p---CgH~fH~~Ci~~-wl--~~~~~CPiCr~s~~~ 1070 (1143)
-..|.||.|. |.+. +.| | ||-.++..|... |- ....+||+|+.|+-.
T Consensus 80 lYeCnIC~et---S~ee-~FLKPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKs 133 (140)
T PF05290_consen 80 LYECNICKET---SAEE-RFLKPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKS 133 (140)
T ss_pred ceeccCcccc---cchh-hcCCcccccchHHHHHHHHHHHHHcccCCCCCcccccccc
Confidence 4579999985 4333 334 3 999999999887 74 346889999998843
No 136
>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=68.05 E-value=3.2 Score=40.85 Aligned_cols=26 Identities=31% Similarity=0.703 Sum_probs=21.1
Q ss_pred CCCCCCCCCCCcceeEeccccccccCCCCcccCCCCCcc
Q 001136 947 PNCTTPSCNGLSMAKYYCNICKFFDDERTVYHCPFCNLC 985 (1143)
Q Consensus 947 ~~C~~~~cc~~~f~~y~C~~C~~~d~~~~~yhC~~CgiC 985 (1143)
.+|++ ||. ||||=.|.+..||+||-=
T Consensus 10 R~Cp~---CG~----------kFYDLnk~PivCP~CG~~ 35 (108)
T PF09538_consen 10 RTCPS---CGA----------KFYDLNKDPIVCPKCGTE 35 (108)
T ss_pred ccCCC---Ccc----------hhccCCCCCccCCCCCCc
Confidence 57887 465 778989999999999953
No 137
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=66.42 E-value=3.8 Score=47.29 Aligned_cols=32 Identities=25% Similarity=0.569 Sum_probs=19.3
Q ss_pred eEEcCCCCCCCcccchhhc----------ccCCCCCCccccc
Q 001136 1097 DILCNDCEQKGAARFHWLY----------HKCGFCGSYNTRL 1128 (1143)
Q Consensus 1097 ~i~CndC~~~s~~~~h~l~----------~kC~~C~syNt~~ 1128 (1143)
-+.|..||......|+-+- .-|..|+||=-.+
T Consensus 224 R~~C~~Cg~~~~l~y~~~e~~~~~~~~r~e~C~~C~~YlK~~ 265 (305)
T TIGR01562 224 RVKCSHCEESKHLAYLSLEHDAEKAVLKAETCDSCQGYLKIL 265 (305)
T ss_pred CccCCCCCCCCceeeEeecCCCCCcceEEeeccccccchhhh
Confidence 3578888876554443331 1588888885443
No 138
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=66.36 E-value=2.7 Score=46.63 Aligned_cols=67 Identities=28% Similarity=0.779 Sum_probs=43.8
Q ss_pred CCcccChhhhccc-CCCCCCccccceeeccccccccccCCCCCCCCCCCCcceeEecccccc-ccCC-----------CC
Q 001136 909 GKLFTCRFCHDKA-SDHSMDRKATSEMMCMHCLKIQAIGPNCTTPSCNGLSMAKYYCNICKF-FDDE-----------RT 975 (1143)
Q Consensus 909 ~k~y~Cr~CHde~-~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~~~cc~~~f~~y~C~~C~~-~d~~-----------~~ 975 (1143)
|+.|.|-||++-. +|-.++..+ .|+....-.-.|.. | + .+|.|.|-.||. |-|+ ..
T Consensus 140 Grif~CsfC~~flCEDDQFEHQA-------sCQvLe~E~~KC~S--C-N-rlGq~sCLRCK~cfCddHvrrKg~ky~k~k 208 (314)
T PF06524_consen 140 GRIFKCSFCDNFLCEDDQFEHQA-------SCQVLESETFKCQS--C-N-RLGQYSCLRCKICFCDDHVRRKGFKYEKGK 208 (314)
T ss_pred CeEEEeecCCCeeeccchhhhhh-------hhhhhhcccccccc--c-c-cccchhhhheeeeehhhhhhhcccccccCC
Confidence 6689999998774 444444322 35555555667876 5 3 699999999996 3332 35
Q ss_pred cccCCCCCccc
Q 001136 976 VYHCPFCNLCR 986 (1143)
Q Consensus 976 ~yhC~~CgiCr 986 (1143)
++-||+||.=.
T Consensus 209 ~~PCPKCg~et 219 (314)
T PF06524_consen 209 PIPCPKCGYET 219 (314)
T ss_pred CCCCCCCCCcc
Confidence 67777777643
No 139
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=65.46 E-value=5.4 Score=53.12 Aligned_cols=52 Identities=25% Similarity=0.494 Sum_probs=28.9
Q ss_pred eeeccccccccccCCCCCCCCCCCCcc-eeEeccccccc--cCCCCcccCCCCCccccC
Q 001136 933 EMMCMHCLKIQAIGPNCTTPSCNGLSM-AKYYCNICKFF--DDERTVYHCPFCNLCRVG 988 (1143)
Q Consensus 933 ~~~C~~C~~~q~~~~~C~~~~cc~~~f-~~y~C~~C~~~--d~~~~~yhC~~CgiCr~g 988 (1143)
...|..|+++-+. ..|+. | |... ..|+|..|..- .|+.....|++||.=-+.
T Consensus 667 ~rkCPkCG~~t~~-~fCP~--C-Gs~te~vy~CPsCGaev~~des~a~~CP~CGtplv~ 721 (1337)
T PRK14714 667 RRRCPSCGTETYE-NRCPD--C-GTHTEPVYVCPDCGAEVPPDESGRVECPRCDVELTP 721 (1337)
T ss_pred EEECCCCCCcccc-ccCcc--c-CCcCCCceeCccCCCccCCCccccccCCCCCCcccc
Confidence 4556666655432 36666 3 4432 45667777662 122336689999964433
No 140
>PF12773 DZR: Double zinc ribbon
Probab=65.35 E-value=4.8 Score=33.60 Aligned_cols=36 Identities=22% Similarity=0.529 Sum_probs=20.7
Q ss_pred ccccccccc-cCCCCCCCCCCCCcceeEeccccccccCCCCcccCCCCCc
Q 001136 936 CMHCLKIQA-IGPNCTTPSCNGLSMAKYYCNICKFFDDERTVYHCPFCNL 984 (1143)
Q Consensus 936 C~~C~~~q~-~~~~C~~~~cc~~~f~~y~C~~C~~~d~~~~~yhC~~Cgi 984 (1143)
|..|+++.+ ....|++ ||..+. ..+...+.|+.||-
T Consensus 1 Cp~Cg~~~~~~~~fC~~---CG~~l~----------~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 1 CPHCGTPNPDDAKFCPH---CGTPLP----------PPDQSKKICPNCGA 37 (50)
T ss_pred CCCcCCcCCccccCChh---hcCChh----------hccCCCCCCcCCcC
Confidence 566776643 3466777 476665 22244556666654
No 141
>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=65.27 E-value=2.9 Score=37.93 Aligned_cols=33 Identities=30% Similarity=0.764 Sum_probs=15.2
Q ss_pred eeeccccccccccCCCCCCCCCCCCc--------ceeEeccccc
Q 001136 933 EMMCMHCLKIQAIGPNCTTPSCNGLS--------MAKYYCNICK 968 (1143)
Q Consensus 933 ~~~C~~C~~~q~~~~~C~~~~cc~~~--------f~~y~C~~C~ 968 (1143)
...|..|+........||. | +.+ -+.|||..|+
T Consensus 17 ~~~C~~C~~~~~~~a~CPd--C-~~~Le~LkACGAvdYFC~~c~ 57 (70)
T PF07191_consen 17 HYHCEACQKDYKKEAFCPD--C-GQPLEVLKACGAVDYFCNHCH 57 (70)
T ss_dssp EEEETTT--EEEEEEE-TT--T--SB-EEEEETTEEEEE-TTTT
T ss_pred EEECccccccceecccCCC--c-ccHHHHHHHhcccceeeccCC
Confidence 4555555554333334544 2 222 3688888887
No 142
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=64.99 E-value=4.9 Score=49.69 Aligned_cols=45 Identities=20% Similarity=0.514 Sum_probs=39.4
Q ss_pred ccccccCCcccChhhhcccCCCCCCccccceeeccccccccccCCCCCC
Q 001136 903 IRAACCGKLFTCRFCHDKASDHSMDRKATSEMMCMHCLKIQAIGPNCTT 951 (1143)
Q Consensus 903 l~~~cC~k~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~ 951 (1143)
+.|.-||....|..|.-...-|.. ...+.|-.|+..+++...|++
T Consensus 214 ~~C~~Cg~~~~C~~C~~~l~~h~~----~~~l~Ch~Cg~~~~~~~~Cp~ 258 (505)
T TIGR00595 214 LLCRSCGYILCCPNCDVSLTYHKK----EGKLRCHYCGYQEPIPKTCPQ 258 (505)
T ss_pred eEhhhCcCccCCCCCCCceEEecC----CCeEEcCCCcCcCCCCCCCCC
Confidence 789999999999999877776743 448999999999998899998
No 143
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=64.38 E-value=4.1 Score=40.47 Aligned_cols=38 Identities=32% Similarity=0.497 Sum_probs=28.8
Q ss_pred cCcceEEcCCCCCCCcccchhhcccCCCCCCccccccccC
Q 001136 1093 NQVQDILCNDCEQKGAARFHWLYHKCGFCGSYNTRLIKND 1132 (1143)
Q Consensus 1093 ~~~~~i~CndC~~~s~~~~h~l~~kC~~C~syNt~~~~~~ 1132 (1143)
.....+.|-+|+......-|.++ ||.|||-|.+++.-+
T Consensus 66 ~~p~~~~C~~C~~~~~~e~~~~~--CP~C~s~~~~i~~G~ 103 (115)
T COG0375 66 EEPAECWCLDCGQEVELEELDYR--CPKCGSINLRIIGGD 103 (115)
T ss_pred EeccEEEeccCCCeecchhheeE--CCCCCCCceEEecCC
Confidence 34567899999887665555444 999999999987543
No 144
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=64.19 E-value=4.7 Score=45.49 Aligned_cols=45 Identities=31% Similarity=0.755 Sum_probs=32.3
Q ss_pred CCCcccccccccCCcceEecCCCCccchhhHHHH-hccCCCCcCCC-ccc
Q 001136 1021 TNCPICCDFLFTSSETVRALPCGHYMHLACFQAY-TCSHYTCPICS-KSL 1068 (1143)
Q Consensus 1021 ~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~w-l~~~~~CPiCr-~s~ 1068 (1143)
-.||.|..-| +.+++.--|||.|+..||..- +.....||.|. +.+
T Consensus 275 LkCplc~~Ll---rnp~kT~cC~~~fc~eci~~al~dsDf~CpnC~rkdv 321 (427)
T COG5222 275 LKCPLCHCLL---RNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSRKDV 321 (427)
T ss_pred ccCcchhhhh---hCcccCccccchHHHHHHhhhhhhccccCCCcccccc
Confidence 4599987643 233444348999999999975 46779999994 444
No 145
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=63.61 E-value=5.9 Score=50.80 Aligned_cols=54 Identities=20% Similarity=0.420 Sum_probs=42.9
Q ss_pred ccccccCCcccChhhhcccCCCCCCccccceeeccccccccccCCCCCCCCCCCCcceeEe
Q 001136 903 IRAACCGKLFTCRFCHDKASDHSMDRKATSEMMCMHCLKIQAIGPNCTTPSCNGLSMAKYY 963 (1143)
Q Consensus 903 l~~~cC~k~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~~~cc~~~f~~y~ 963 (1143)
+.|..||-.+.|++|=.-..=|.- +..+.|-.|+..+++-..|++ ||...=+|+
T Consensus 436 l~C~~Cg~v~~Cp~Cd~~lt~H~~----~~~L~CH~Cg~~~~~p~~Cp~---Cgs~~L~~~ 489 (730)
T COG1198 436 LLCRDCGYIAECPNCDSPLTLHKA----TGQLRCHYCGYQEPIPQSCPE---CGSEHLRAV 489 (730)
T ss_pred eecccCCCcccCCCCCcceEEecC----CCeeEeCCCCCCCCCCCCCCC---CCCCeeEEe
Confidence 889999999999999655554433 469999999999999999998 476544443
No 146
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=62.41 E-value=5.3 Score=30.66 Aligned_cols=37 Identities=35% Similarity=0.725 Sum_probs=24.9
Q ss_pred CcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCCcccc
Q 001136 1023 CPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLG 1069 (1143)
Q Consensus 1023 CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~~ 1069 (1143)
|+.|...+......+.. =|..||.+|+ +|..|++++.
T Consensus 2 C~~C~~~i~~~~~~~~~--~~~~~H~~Cf--------~C~~C~~~L~ 38 (39)
T smart00132 2 CAGCGKPIRGGELVLRA--LGKVWHPECF--------KCSKCGKPLG 38 (39)
T ss_pred ccccCCcccCCcEEEEe--CCccccccCC--------CCcccCCcCc
Confidence 77888875444222222 3789999887 7888887764
No 147
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=61.03 E-value=7.5 Score=47.69 Aligned_cols=164 Identities=26% Similarity=0.546 Sum_probs=85.7
Q ss_pred cceeeccccccccccCCCCCCCCCCCCcceeEecc-ccccccCC------CCccc--CCCCCccccCCCCCcccc-----
Q 001136 931 TSEMMCMHCLKIQAIGPNCTTPSCNGLSMAKYYCN-ICKFFDDE------RTVYH--CPFCNLCRVGGGLGVDFF----- 996 (1143)
Q Consensus 931 ~~~~~C~~C~~~q~~~~~C~~~~cc~~~f~~y~C~-~C~~~d~~------~~~yh--C~~CgiCr~g~~l~~~~~----- 996 (1143)
+.-..|..|+.--..+..|.. ++. +|||. .|.-|--. -..|| |-.|.+|+.....|....
T Consensus 40 i~cf~c~~cg~~la~~gff~k---~~~---~~ygt~~c~~~~~gevvsa~gktyh~~cf~cs~ck~pf~~g~~vt~~gk~ 113 (670)
T KOG1044|consen 40 INCFQCKKCGRNLAEGGFFTK---PEN---RLYGTDDCRAFVEGEVVSTLGKTYHPKCFSCSTCKSPFKSGDKVTFSGKE 113 (670)
T ss_pred eeeeeccccCCCcccccceec---ccc---eeecccchhhhccceeEecccceeccccceecccCCCCCCCCeeeecchh
Confidence 445566666654444446665 233 66664 34433221 46676 788888888776554322
Q ss_pred -ccCCcccccccccccccccccccCCCCcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCCccccchhhhh
Q 001136 997 -HCMTCNCCLGLKLLNHKCLEKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLGDMAIYF 1075 (1143)
Q Consensus 997 -hC~~C~~C~~~~~~~H~C~e~~~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~~~m~~~~ 1075 (1143)
-|.+|..=+++. =.+...-.+|..|.+.|. ++..+..| +-.+|..|| .|--|.+.+.. + |
T Consensus 114 ~~c~~c~~~~~~~-----p~~~~~ps~cagc~~~lk-~gq~llal--d~qwhv~cf--------kc~~c~~vL~g-e-y- 174 (670)
T KOG1044|consen 114 CLCQTCSQPMPVS-----PAESYGPSTCAGCGEELK-NGQALLAL--DKQWHVSCF--------KCKSCSAVLNG-E-Y- 174 (670)
T ss_pred hhhhhhcCcccCC-----cccccCCccccchhhhhh-ccceeeee--ccceeeeee--------ehhhhcccccc-e-e-
Confidence 223332222221 112345678999999854 44433333 555666665 56666655421 0 0
Q ss_pred hhhHHHHhhcCCC---hhhhcCcceEEcCCCCCC--------CcccchhhcccCCCCCCccc
Q 001136 1076 GMIDALLAAEELP---EEYRNQVQDILCNDCEQK--------GAARFHWLYHKCGFCGSYNT 1126 (1143)
Q Consensus 1076 ~~ld~~i~~~p~P---~~y~~~~~~i~CndC~~~--------s~~~~h~l~~kC~~C~syNt 1126 (1143)
+..--.| ..|.... -|.|..|.+- +.--||--+-+|.-||.-=|
T Consensus 175 ------~skdg~pyce~dy~~~f-gvkc~~c~~fisgkvLqag~kh~HPtCARCsRCgqmF~ 229 (670)
T KOG1044|consen 175 ------MSKDGVPYCEKDYQAKF-GVKCEECEKFISGKVLQAGDKHFHPTCARCSRCGQMFG 229 (670)
T ss_pred ------eccCCCcchhhhhhhhc-CeehHHhhhhhhhhhhhccCcccCcchhhhhhhccccc
Confidence 1111222 2243333 4678888743 22357777777777776543
No 148
>TIGR02481 hemeryth_dom hemerythrin-like metal-binding domain. This model describes both members of the hemerythrin (TIGR00058) family of marine invertebrates and a broader collection of bacterial and archaeal homologs. Many of the latter group are multidomain proteins with signal-transducing domains such as the GGDEF diguanylate cyclase domain (TIGR00254, pfam00990) and methyl-accepting chemotaxis protein signaling domain (pfam00015). Most hemerythrins are oxygen-carriers with a bound non-heme iron, but at least one example is a cadmium-binding protein, apparently with a role in sequestering toxic metals rather than in binding oxygen. Patterns of conserved residues suggest that all prokaryotic instances of this domain bind iron or another heavy metal, but the exact function is unknown. Not surprisingly, the prokaryote with the most instances of this domain is Magnetococcus sp. MC-1, a magnetotactic bacterium.
Probab=60.59 E-value=1.5e+02 Score=29.12 Aligned_cols=113 Identities=19% Similarity=0.160 Sum_probs=71.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccHHHHHHHHHHHHHHhcccCccccccchHHHhhh-cchHHHHHHHHHHH
Q 001136 42 ILIFCFFHKAVRNELDALHQLAMNFATGHRVDILSLSERYRFLHSVYKHHSNAEDEVIFPALDIR-VKNVARKYSLEHEG 120 (1143)
Q Consensus 42 i~~m~~~H~aLRreL~~L~~la~~~~~gd~~~~~~L~~~~~~l~~~L~~HH~~EDevLFPaL~~R-~p~vl~~le~EH~~ 120 (1143)
+..+-.-|+.|-..++.|...+.. +. ....+...+..|......|=..||.++ ++. .| -+..-..+|+.
T Consensus 10 ~~~ID~qH~~l~~~in~l~~a~~~---~~--~~~~~~~~l~~L~~y~~~HF~~EE~~M----~~~~yp-~~~~H~~~H~~ 79 (126)
T TIGR02481 10 IEEIDAQHKELFELINELYDALSA---GN--GKDELKEILDELIDYTENHFADEEELM----EEYGYP-DLEEHKKEHEK 79 (126)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHc---CC--CHHHHHHHHHHHHHHHHHHHHHHHHHH----HHcCCC-CHHHHHHHHHH
Confidence 345667888888888888776543 22 235677778888888888988888543 211 22 22333556666
Q ss_pred HHHHHHHHHHHHhhhccC-CCCchHHHHHHHHHHHHHHHHHHHHHHHhHHH
Q 001136 121 ESNLFDHLFQLLNSYTQN-DESFPKELASCSRALQTSINQHMSKEEQQVFP 170 (1143)
Q Consensus 121 i~~ll~~L~~~l~~~~~~-~~~~~~eLa~~l~~l~~~L~~HL~~EE~~lfP 170 (1143)
+-..+.++...+ ..+ .. ......+.-+.+-+..|+..+...+.+
T Consensus 80 ~l~~l~~l~~~~---~~~~~~---~~~~~~~~~l~~Wl~~HI~~~D~~~~~ 124 (126)
T TIGR02481 80 FVKKIEELQEAV---AEGADE---SLAEELLDFLKDWLVNHILKEDKKYAP 124 (126)
T ss_pred HHHHHHHHHHHH---HcCCch---hHHHHHHHHHHHHHHHHhHHHhHHHHh
Confidence 666665555444 333 22 223345666778899999999887755
No 149
>PF14357 DUF4404: Domain of unknown function (DUF4404)
Probab=60.18 E-value=39 Score=31.91 Aligned_cols=82 Identities=15% Similarity=0.138 Sum_probs=65.0
Q ss_pred HHHHHHHHHHHHHhhcCCCcccHHHHHHHHHHHHHHhcccCccccccchHHHhhhcchHHHHHHHHHHHHHHHHHHHHHH
Q 001136 52 VRNELDALHQLAMNFATGHRVDILSLSERYRFLHSVYKHHSNAEDEVIFPALDIRVKNVARKYSLEHEGESNLFDHLFQL 131 (1143)
Q Consensus 52 LRreL~~L~~la~~~~~gd~~~~~~L~~~~~~l~~~L~~HH~~EDevLFPaL~~R~p~vl~~le~EH~~i~~ll~~L~~~ 131 (1143)
|+..|+.|+..+....+-|....+.+....+.+...+.. ..+...-=+.|..++...+.+++.+|=.+...++.|...
T Consensus 2 L~~~L~~L~~eL~~~~~ld~~~~~~L~~l~~dIe~~L~~--~~~~~~~~~~l~d~l~~av~~FE~~HP~l~~~lr~i~~s 79 (85)
T PF14357_consen 2 LQELLEKLHQELEQNPPLDEETRAELSSLDDDIEAQLAE--EDEAEAEDESLVDRLNEAVERFEASHPKLAGILRNIMDS 79 (85)
T ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhc--CCcccccchhHHHHHHHHHHHHHHhCCcHHHHHHHHHHH
Confidence 678899999999988776777777777777777776654 445555667788888889999999999999999988887
Q ss_pred Hhhh
Q 001136 132 LNSY 135 (1143)
Q Consensus 132 l~~~ 135 (1143)
+...
T Consensus 80 La~M 83 (85)
T PF14357_consen 80 LANM 83 (85)
T ss_pred HHHC
Confidence 7543
No 150
>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=59.44 E-value=3.7 Score=45.11 Aligned_cols=48 Identities=27% Similarity=0.566 Sum_probs=38.0
Q ss_pred CCCcccccccccCCcceEe-cC-CCCccchhhHHHHhccC-CCCc--CCCccc
Q 001136 1021 TNCPICCDFLFTSSETVRA-LP-CGHYMHLACFQAYTCSH-YTCP--ICSKSL 1068 (1143)
Q Consensus 1021 ~~CpIC~e~lf~s~~~v~~-lp-CgH~fH~~Ci~~wl~~~-~~CP--iCr~s~ 1068 (1143)
..||||..+.+-+..-... -| |=|-|+.+|.++-.... -.|| -|.+.+
T Consensus 11 ~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs~GpAqCP~~gC~kIL 63 (314)
T COG5220 11 RRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFSRGPAQCPYKGCGKIL 63 (314)
T ss_pred ccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhcCCCCCCCCccHHHHH
Confidence 4799999998877764443 35 99999999999976554 6799 888766
No 151
>cd00522 Hemerythrin Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the muscle tissue of sipunculids as well as in polycheate and oligocheate annelids. In addition to oxygen transport, Mhr proteins are involved in cadmium fixation and host anti-bacterial defense. Hr and Mhr proteins have the same "four alpha helix bundle" motif and active site structure. Hr forms oligomers, the octameric form being most prevalent, while Mhr is monomeric.
Probab=58.90 E-value=27 Score=34.25 Aligned_cols=45 Identities=22% Similarity=0.151 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhccCCCCchHHHHHHHHHHHHHHHHHHHHHHHhH
Q 001136 112 RKYSLEHEGESNLFDHLFQLLNSYTQNDESFPKELASCSRALQTSINQHMSKEEQQV 168 (1143)
Q Consensus 112 ~~le~EH~~i~~ll~~L~~~l~~~~~~~~~~~~eLa~~l~~l~~~L~~HL~~EE~~l 168 (1143)
..+..||+.+-.++++|.+++.. ...+..|......|+..||...
T Consensus 13 ~~ID~qH~~L~~l~n~l~~a~~~------------~~~l~~L~~y~~~HF~~EE~~M 57 (113)
T cd00522 13 EVIDDEHKTLFNGINDLSEANNR------------ADNLKELVDYTVKHFKDEEALM 57 (113)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhH------------HHHHHHHHHHHHHHHHHHHHHH
Confidence 46788999999999998888754 4568888899999999999976
No 152
>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans. They are purported to be transmembrane protein-precursors but their function is unknown.
Probab=58.73 E-value=8.7 Score=45.31 Aligned_cols=16 Identities=19% Similarity=0.688 Sum_probs=12.2
Q ss_pred HhccCCCCcCCCcccc
Q 001136 1054 YTCSHYTCPICSKSLG 1069 (1143)
Q Consensus 1054 wl~~~~~CPiCr~s~~ 1069 (1143)
|+.++-+||+||+.+-
T Consensus 336 Wl~~~~~CPtCRa~FC 351 (358)
T PF10272_consen 336 WLSGKCPCPTCRAKFC 351 (358)
T ss_pred hhcCCCCCCCCcccce
Confidence 4556678999998764
No 153
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=58.69 E-value=7.2 Score=34.12 Aligned_cols=30 Identities=27% Similarity=0.586 Sum_probs=22.5
Q ss_pred cceEEcCCCCCCCcccchhhcccCCCCCCcccccc
Q 001136 1095 VQDILCNDCEQKGAARFHWLYHKCGFCGSYNTRLI 1129 (1143)
Q Consensus 1095 ~~~i~CndC~~~s~~~~h~l~~kC~~C~syNt~~~ 1129 (1143)
...+.|..||..-- .| +.|++||.||-+++
T Consensus 25 ~~l~~C~~CG~~~~--~H---~vC~~CG~Y~gr~v 54 (57)
T PRK12286 25 PGLVECPNCGEPKL--PH---RVCPSCGYYKGREV 54 (57)
T ss_pred CcceECCCCCCccC--Ce---EECCCCCcCCCEEe
Confidence 34678999997532 23 35999999999886
No 154
>KOG0801 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=58.12 E-value=4.8 Score=41.81 Aligned_cols=30 Identities=27% Similarity=0.518 Sum_probs=24.9
Q ss_pred ccCCCCcccccccccCCcceEecCCCCccch
Q 001136 1018 CLETNCPICCDFLFTSSETVRALPCGHYMHL 1048 (1143)
Q Consensus 1018 ~~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~ 1048 (1143)
...+.|.||+|+ ...+..+..|||=..||+
T Consensus 175 ddkGECvICLEd-L~~GdtIARLPCLCIYHK 204 (205)
T KOG0801|consen 175 DDKGECVICLED-LEAGDTIARLPCLCIYHK 204 (205)
T ss_pred ccCCcEEEEhhh-ccCCCceeccceEEEeec
Confidence 346789999999 567777888999989886
No 155
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=57.19 E-value=9.6 Score=48.97 Aligned_cols=46 Identities=22% Similarity=0.585 Sum_probs=30.7
Q ss_pred cceeeccccccccccCCCCCCCCCCCCcc------eeEeccccccccCCCCcccCCCCCcc
Q 001136 931 TSEMMCMHCLKIQAIGPNCTTPSCNGLSM------AKYYCNICKFFDDERTVYHCPFCNLC 985 (1143)
Q Consensus 931 ~~~~~C~~C~~~q~~~~~C~~~~cc~~~f------~~y~C~~C~~~d~~~~~yhC~~CgiC 985 (1143)
.+.++|..|+.+- .|+| |...+ +...|..|..= .+.+.+|+.||-=
T Consensus 433 s~~l~C~~Cg~v~----~Cp~---Cd~~lt~H~~~~~L~CH~Cg~~--~~~p~~Cp~Cgs~ 484 (730)
T COG1198 433 APLLLCRDCGYIA----ECPN---CDSPLTLHKATGQLRCHYCGYQ--EPIPQSCPECGSE 484 (730)
T ss_pred cceeecccCCCcc----cCCC---CCcceEEecCCCeeEeCCCCCC--CCCCCCCCCCCCC
Confidence 4589999999876 7998 45544 34455555443 3567777777743
No 156
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=56.86 E-value=7.3 Score=45.06 Aligned_cols=52 Identities=27% Similarity=0.614 Sum_probs=40.0
Q ss_pred ccCCCCcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCCcccc
Q 001136 1018 CLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLG 1069 (1143)
Q Consensus 1018 ~~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~~ 1069 (1143)
+....||||.+++........-.|||+-++..|...-...+.+||.||++..
T Consensus 247 ~v~~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~~~~~~~~~~rk~~~ 298 (327)
T KOG2068|consen 247 SVPPSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTISDGDGRCPGCRKPYE 298 (327)
T ss_pred ccCCCCCCCCCcccccccccccccccccchhhhhhcccccCCCCCccCCccc
Confidence 3346799999986444444444568999999999888888999999998774
No 157
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=56.68 E-value=5.4 Score=49.57 Aligned_cols=69 Identities=19% Similarity=0.404 Sum_probs=40.0
Q ss_pred CCCcccccccccCCcceEecC---CCCccchhhHHHH----h----ccCCCCcCCCccccchhhhhhhhHHHHhhcCCCh
Q 001136 1021 TNCPICCDFLFTSSETVRALP---CGHYMHLACFQAY----T----CSHYTCPICSKSLGDMAIYFGMIDALLAAEELPE 1089 (1143)
Q Consensus 1021 ~~CpIC~e~lf~s~~~v~~lp---CgH~fH~~Ci~~w----l----~~~~~CPiCr~s~~~m~~~~~~ld~~i~~~p~P~ 1089 (1143)
..||+|+-. |...+....+. |.=-.|..|..-. . ...|.|-+|| .-..+-..+...+...-+|.
T Consensus 146 ~~cPvc~~~-Y~~~e~~~~~~c~~c~rwsh~~c~~~sdd~~~q~~vD~~~~CS~CR----~es~qvKdi~~~vqe~~~~k 220 (694)
T KOG4443|consen 146 SYCPVCLIV-YQDSESLPMVCCSICQRWSHGGCDGISDDKYMQAQVDLQYKCSTCR----GESYQVKDISDALQETWKAK 220 (694)
T ss_pred ccCchHHHh-hhhccchhhHHHHHhcccccCCCCccchHHHHHHhhhhhcccceee----hhhhhhhhHHHHHHhhcchh
Confidence 469999854 55544442233 4455777785433 2 2369999999 22223445555566666666
Q ss_pred hhhcC
Q 001136 1090 EYRNQ 1094 (1143)
Q Consensus 1090 ~y~~~ 1094 (1143)
.|.+.
T Consensus 221 ~~~~~ 225 (694)
T KOG4443|consen 221 DKPDK 225 (694)
T ss_pred hcccc
Confidence 65443
No 158
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=56.21 E-value=7.2 Score=49.54 Aligned_cols=45 Identities=24% Similarity=0.481 Sum_probs=21.0
Q ss_pred ecccccccccc-CCCCCCCCCCCCcceeEeccccccccCCCCcccCCCCC
Q 001136 935 MCMHCLKIQAI-GPNCTTPSCNGLSMAKYYCNICKFFDDERTVYHCPFCN 983 (1143)
Q Consensus 935 ~C~~C~~~q~~-~~~C~~~~cc~~~f~~y~C~~C~~~d~~~~~yhC~~Cg 983 (1143)
+|..|+.+-|. +..|++ ||..+..-.|..|.-- ...+.-.|+.||
T Consensus 3 ~Cp~Cg~~n~~~akFC~~---CG~~l~~~~Cp~CG~~-~~~~~~fC~~CG 48 (645)
T PRK14559 3 ICPQCQFENPNNNRFCQK---CGTSLTHKPCPQCGTE-VPVDEAHCPNCG 48 (645)
T ss_pred cCCCCCCcCCCCCccccc---cCCCCCCCcCCCCCCC-CCcccccccccC
Confidence 56666665433 344665 3555543344444432 112333455555
No 159
>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=56.17 E-value=4.5 Score=46.30 Aligned_cols=29 Identities=21% Similarity=0.714 Sum_probs=12.1
Q ss_pred eEEcCCCCCCCcccchhhcccCCCCCCcccccc
Q 001136 1097 DILCNDCEQKGAARFHWLYHKCGFCGSYNTRLI 1129 (1143)
Q Consensus 1097 ~i~CndC~~~s~~~~h~l~~kC~~C~syNt~~~ 1129 (1143)
.-.|.-|+ ..+|+.-.+|++||+-+-..+
T Consensus 197 ~L~Cs~C~----t~W~~~R~~Cp~Cg~~~~~~l 225 (290)
T PF04216_consen 197 YLHCSLCG----TEWRFVRIKCPYCGNTDHEKL 225 (290)
T ss_dssp EEEETTT------EEE--TTS-TTT---SS-EE
T ss_pred EEEcCCCC----CeeeecCCCCcCCCCCCCcce
Confidence 45666666 456666666666666555443
No 160
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=56.15 E-value=11 Score=39.46 Aligned_cols=33 Identities=27% Similarity=0.815 Sum_probs=20.5
Q ss_pred CCCCcccccccccCCcceE-----------ecCCCC-ccchhhHHHHh
Q 001136 1020 ETNCPICCDFLFTSSETVR-----------ALPCGH-YMHLACFQAYT 1055 (1143)
Q Consensus 1020 ~~~CpIC~e~lf~s~~~v~-----------~lpCgH-~fH~~Ci~~wl 1055 (1143)
+..||||||. .-..|- -.=|+- .-|..|++++-
T Consensus 2 d~~CpICme~---PHNAVLLlCSS~~kgcRpymc~Ts~rhSNCLdqfk 46 (162)
T PF07800_consen 2 DVTCPICMEH---PHNAVLLLCSSHEKGCRPYMCDTSYRHSNCLDQFK 46 (162)
T ss_pred CccCceeccC---CCceEEEEeccccCCccccccCCccchhHHHHHHH
Confidence 3579999996 222221 112664 45899999983
No 161
>PRK00808 hypothetical protein; Provisional
Probab=55.90 E-value=37 Score=35.06 Aligned_cols=52 Identities=19% Similarity=0.195 Sum_probs=42.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhccCCCCchHHHHHHHHHHHHHHHHHHHHHHHhH
Q 001136 111 ARKYSLEHEGESNLFDHLFQLLNSYTQNDESFPKELASCSRALQTSINQHMSKEEQQV 168 (1143)
Q Consensus 111 l~~le~EH~~i~~ll~~L~~~l~~~~~~~~~~~~eLa~~l~~l~~~L~~HL~~EE~~l 168 (1143)
+..+..||+++-.++++|..++.. +. ...+...+..|......|+..||...
T Consensus 14 ~~~ID~qH~~L~~lin~l~~a~~~---~~---~~~i~~~l~~L~~y~~~HF~~EE~lM 65 (150)
T PRK00808 14 IDVIDQQHKRIVDYINHLHDAQDS---PD---RLAVAEVIDELIDYTLSHFAFEESLM 65 (150)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHc---Cc---HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 457889999999999998877632 11 45788889999999999999999975
No 162
>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=55.88 E-value=7.2 Score=39.30 Aligned_cols=19 Identities=26% Similarity=0.347 Sum_probs=16.4
Q ss_pred ccccCCCCcccCCCCCccc
Q 001136 968 KFFDDERTVYHCPFCNLCR 986 (1143)
Q Consensus 968 ~~~d~~~~~yhC~~CgiCr 986 (1143)
||||-.|.+..||+||.=-
T Consensus 18 kFYDLnk~p~vcP~cg~~~ 36 (129)
T TIGR02300 18 KFYDLNRRPAVSPYTGEQF 36 (129)
T ss_pred cccccCCCCccCCCcCCcc
Confidence 7789889999999999753
No 163
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=55.37 E-value=4.4 Score=45.68 Aligned_cols=44 Identities=23% Similarity=0.586 Sum_probs=26.4
Q ss_pred cCCCCccccccc-------ccCCcceEecCCCCccchhhHHHHhccCCCCcCCCcc
Q 001136 1019 LETNCPICCDFL-------FTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKS 1067 (1143)
Q Consensus 1019 ~~~~CpIC~e~l-------f~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s 1067 (1143)
....||+|...= +...+..+++.|. -|..+|...+.+|--|..+
T Consensus 184 ~~~~CPvCGS~PvaSmV~~g~~~~GlRYL~Cs-----lC~teW~~VR~KC~nC~~t 234 (308)
T COG3058 184 SRQYCPVCGSMPVASMVQIGETEQGLRYLHCS-----LCETEWHYVRVKCSNCEQS 234 (308)
T ss_pred ccccCCCcCCCCcceeeeecCccccchhhhhh-----hHHHHHHHHHHHhcccccc
Confidence 345688886431 1133444555554 5788887777778777643
No 164
>PRK05580 primosome assembly protein PriA; Validated
Probab=55.22 E-value=8.6 Score=49.31 Aligned_cols=45 Identities=22% Similarity=0.540 Sum_probs=39.2
Q ss_pred ccccccCCcccChhhhcccCCCCCCccccceeeccccccccccCCCCCC
Q 001136 903 IRAACCGKLFTCRFCHDKASDHSMDRKATSEMMCMHCLKIQAIGPNCTT 951 (1143)
Q Consensus 903 l~~~cC~k~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~ 951 (1143)
+.|.-||....|..|.-...-|.. ...+.|-.|+..++....|++
T Consensus 382 ~~C~~Cg~~~~C~~C~~~l~~h~~----~~~l~Ch~Cg~~~~~~~~Cp~ 426 (679)
T PRK05580 382 LLCRDCGWVAECPHCDASLTLHRF----QRRLRCHHCGYQEPIPKACPE 426 (679)
T ss_pred eEhhhCcCccCCCCCCCceeEECC----CCeEECCCCcCCCCCCCCCCC
Confidence 789999999999999887766643 458999999999988889998
No 165
>PRK14873 primosome assembly protein PriA; Provisional
Probab=54.53 E-value=8.3 Score=49.25 Aligned_cols=44 Identities=23% Similarity=0.390 Sum_probs=36.7
Q ss_pred ccccccCCcccChhhhcccCCCCCCccccceeeccccccccccCCCCCC
Q 001136 903 IRAACCGKLFTCRFCHDKASDHSMDRKATSEMMCMHCLKIQAIGPNCTT 951 (1143)
Q Consensus 903 l~~~cC~k~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~ 951 (1143)
+.|..||....|..|.--..=|. ....+.|-.|+..+ ....|++
T Consensus 384 l~C~~Cg~~~~C~~C~~~L~~h~----~~~~l~Ch~CG~~~-~p~~Cp~ 427 (665)
T PRK14873 384 LACARCRTPARCRHCTGPLGLPS----AGGTPRCRWCGRAA-PDWRCPR 427 (665)
T ss_pred eEhhhCcCeeECCCCCCceeEec----CCCeeECCCCcCCC-cCccCCC
Confidence 79999999999999988876664 24578999999977 4679998
No 166
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=54.25 E-value=4.1 Score=54.01 Aligned_cols=51 Identities=29% Similarity=0.577 Sum_probs=40.0
Q ss_pred CCCCcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCCccccchhh
Q 001136 1020 ETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLGDMAI 1073 (1143)
Q Consensus 1020 ~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~~~m~~ 1073 (1143)
.-.|+||++-+-.. -.+..|||.++..|+..|+..+..||+|....++...
T Consensus 1153 ~~~c~ic~dil~~~---~~I~~cgh~~c~~c~~~~l~~~s~~~~~ksi~~dfg~ 1203 (1394)
T KOG0298|consen 1153 HFVCEICLDILRNQ---GGIAGCGHEPCCRCDELWLYASSRCPICKSIKGDFGT 1203 (1394)
T ss_pred ccchHHHHHHHHhc---CCeeeechhHhhhHHHHHHHHhccCcchhhhhhhhcc
Confidence 34799999874322 2345699999999999999999999999977666543
No 167
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=53.96 E-value=8.9 Score=46.09 Aligned_cols=46 Identities=30% Similarity=0.669 Sum_probs=31.0
Q ss_pred CCcccccccccCCcceEecC---CCCccchhhHHH-Hh--------------ccCCCCcCCCccc
Q 001136 1022 NCPICCDFLFTSSETVRALP---CGHYMHLACFQA-YT--------------CSHYTCPICSKSL 1068 (1143)
Q Consensus 1022 ~CpIC~e~lf~s~~~v~~lp---CgH~fH~~Ci~~-wl--------------~~~~~CPiCr~s~ 1068 (1143)
.|+||.-+ ..+..+..|+. |||.-|..|--+ .+ ...|.|--|++.-
T Consensus 130 ~C~iC~kf-D~~~n~~~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~s 193 (446)
T PF07227_consen 130 MCCICSKF-DDNKNTCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKTS 193 (446)
T ss_pred CccccCCc-ccCCCCeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCChh
Confidence 48999764 33445666764 899999999655 21 1146788887765
No 168
>PRK04023 DNA polymerase II large subunit; Validated
Probab=53.90 E-value=8.2 Score=50.35 Aligned_cols=46 Identities=22% Similarity=0.402 Sum_probs=27.7
Q ss_pred cccccccCCcccChhhhcccCCCCCCccccceeeccccccccccCCCCCCCCCCCCcceeEecccccc
Q 001136 902 KIRAACCGKLFTCRFCHDKASDHSMDRKATSEMMCMHCLKIQAIGPNCTTPSCNGLSMAKYYCNICKF 969 (1143)
Q Consensus 902 ~l~~~cC~k~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~~~C~~~~cc~~~f~~y~C~~C~~ 969 (1143)
.-+||-||+. +....|..|++.-.....|+. ||...+.|.|+.|.+
T Consensus 626 ~RfCpsCG~~-------------------t~~frCP~CG~~Te~i~fCP~---CG~~~~~y~CPKCG~ 671 (1121)
T PRK04023 626 RRKCPSCGKE-------------------TFYRRCPFCGTHTEPVYRCPR---CGIEVEEDECEKCGR 671 (1121)
T ss_pred CccCCCCCCc-------------------CCcccCCCCCCCCCcceeCcc---ccCcCCCCcCCCCCC
Confidence 3578888874 134556666655444446666 366666666777764
No 169
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=53.49 E-value=10 Score=43.87 Aligned_cols=27 Identities=30% Similarity=0.680 Sum_probs=19.5
Q ss_pred eEEcCCCCCCCcccchhhcccCCCCCCcccccc
Q 001136 1097 DILCNDCEQKGAARFHWLYHKCGFCGSYNTRLI 1129 (1143)
Q Consensus 1097 ~i~CndC~~~s~~~~h~l~~kC~~C~syNt~~~ 1129 (1143)
...|+-|+ ..+|+.-.+|++||+ +..+
T Consensus 212 yL~CslC~----teW~~~R~~C~~Cg~--~~~l 238 (309)
T PRK03564 212 YLHCNLCE----SEWHVVRVKCSNCEQ--SGKL 238 (309)
T ss_pred EEEcCCCC----CcccccCccCCCCCC--CCce
Confidence 56788887 667788888888884 5443
No 170
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=52.78 E-value=6.7 Score=50.04 Aligned_cols=43 Identities=30% Similarity=0.835 Sum_probs=33.9
Q ss_pred CCCcccccccccCCcceEecCCCCccchhhHHHHhcc--CCCCcCCCccc
Q 001136 1021 TNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCS--HYTCPICSKSL 1068 (1143)
Q Consensus 1021 ~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~--~~~CPiCr~s~ 1068 (1143)
..|+||++. +.....+|||.|+..|+.+.... ...||+|+..+
T Consensus 455 ~~c~ic~~~-----~~~~it~c~h~~c~~c~~~~i~~~~~~~~~~cr~~l 499 (674)
T KOG1001|consen 455 HWCHICCDL-----DSFFITRCGHDFCVECLKKSIQQSENAPCPLCRNVL 499 (674)
T ss_pred ccccccccc-----ccceeecccchHHHHHHHhccccccCCCCcHHHHHH
Confidence 679999982 55677899999999999996532 34699998554
No 171
>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=52.64 E-value=9.5 Score=29.47 Aligned_cols=24 Identities=38% Similarity=1.106 Sum_probs=19.1
Q ss_pred eEeccccccc-cCCCCcccCCCCCc
Q 001136 961 KYYCNICKFF-DDERTVYHCPFCNL 984 (1143)
Q Consensus 961 ~y~C~~C~~~-d~~~~~yhC~~Cgi 984 (1143)
.|-|.+|.+. +.++..+.||.||.
T Consensus 1 ~~~C~~CGy~y~~~~~~~~CP~Cg~ 25 (33)
T cd00350 1 KYVCPVCGYIYDGEEAPWVCPVCGA 25 (33)
T ss_pred CEECCCCCCEECCCcCCCcCcCCCC
Confidence 4788899876 55578999999986
No 172
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=52.24 E-value=8.4 Score=33.43 Aligned_cols=29 Identities=24% Similarity=0.613 Sum_probs=21.7
Q ss_pred ceEEcCCCCCCCcccchhhcccCCCCCCcccccc
Q 001136 1096 QDILCNDCEQKGAARFHWLYHKCGFCGSYNTRLI 1129 (1143)
Q Consensus 1096 ~~i~CndC~~~s~~~~h~l~~kC~~C~syNt~~~ 1129 (1143)
..+.|..||+.- .+ -+.|++||.|+-+++
T Consensus 25 ~l~~C~~cG~~~-~~----H~vc~~cG~Y~gr~v 53 (55)
T TIGR01031 25 TLVVCPNCGEFK-LP----HRVCPSCGYYKGRQV 53 (55)
T ss_pred cceECCCCCCcc-cC----eeECCccCeECCEEc
Confidence 467899999732 22 345999999999876
No 173
>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=51.76 E-value=8.1 Score=38.09 Aligned_cols=32 Identities=22% Similarity=0.406 Sum_probs=23.3
Q ss_pred ccccccccCCcccChhhhcccCCCCCCccccceeeccccccccccC
Q 001136 901 CKIRAACCGKLFTCRFCHDKASDHSMDRKATSEMMCMHCLKIQAIG 946 (1143)
Q Consensus 901 c~l~~~cC~k~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~ 946 (1143)
.|-.||-||+-| .+-.. ..++|.+|+++|++.
T Consensus 8 tKR~Cp~CG~kF-------------YDLnk-~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 8 TKRTCPSCGAKF-------------YDLNK-DPIVCPKCGTEFPPE 39 (108)
T ss_pred CcccCCCCcchh-------------ccCCC-CCccCCCCCCccCcc
Confidence 466789998744 23323 578999999998776
No 174
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=51.72 E-value=5.6 Score=50.42 Aligned_cols=92 Identities=13% Similarity=0.037 Sum_probs=68.5
Q ss_pred HHHHHHHHHHHHHhhh-----hhhhhhhhhcCCHHHHHHHHHHHhhcCCHHHHHHHhhhhcCCCCHHHHHHHHHHhhhcC
Q 001136 413 ADQIMETIERHFHKVE-----VQVLPLARNHFSFKRQREILYQSLCEMPLKLIERVLPWLMGSLTENEARSVLKNMQSAA 487 (1143)
Q Consensus 413 l~~l~~~L~~Hf~kEE-----~qvfPL~~k~~S~eEQ~~L~~~~l~~~Pl~ll~~vlpW~~~~ls~~E~~~~l~~l~~~~ 487 (1143)
+..+-..+-.|+..|+ .-+.|.+=.+ +.+||+..|++|.-.=-+..+.-+||=.-..|+|.-+..+|.-.-.
T Consensus 391 i~kv~~~yI~HLl~~~~y~~Aas~~p~m~gn-~~~eWe~~V~~f~e~~~l~~Ia~~lPt~~~rL~p~vYemvLve~L~-- 467 (846)
T KOG2066|consen 391 IKKVGKTYIDHLLFEGKYDEAASLCPKMLGN-NAAEWELWVFKFAELDQLTDIAPYLPTGPPRLKPLVYEMVLVEFLA-- 467 (846)
T ss_pred hHHHHHHHHHHHHhcchHHHHHhhhHHHhcc-hHHHHHHHHHHhccccccchhhccCCCCCcccCchHHHHHHHHHHH--
Confidence 3444455566665444 3466665554 4579999999999888888899999999999999999999976554
Q ss_pred CCchhHHHHHHhhhccCCCCC
Q 001136 488 PATDAALIILFSGWGCKGRNQ 508 (1143)
Q Consensus 488 p~~~~~~~~l~~~w~~~~~~~ 508 (1143)
|..+ -|-.+++.|.+.-|+.
T Consensus 468 ~~~~-~F~e~i~~Wp~~Lys~ 487 (846)
T KOG2066|consen 468 SDVK-GFLELIKEWPGHLYSV 487 (846)
T ss_pred HHHH-HHHHHHHhCChhhhhh
Confidence 5555 6888999997655533
No 175
>PLN03086 PRLI-interacting factor K; Provisional
Probab=51.39 E-value=18 Score=45.22 Aligned_cols=13 Identities=23% Similarity=0.593 Sum_probs=10.1
Q ss_pred cCCCCcCCCcccc
Q 001136 1057 SHYTCPICSKSLG 1069 (1143)
Q Consensus 1057 ~~~~CPiCr~s~~ 1069 (1143)
....|+.|.+.+.
T Consensus 503 Kpi~C~fC~~~v~ 515 (567)
T PLN03086 503 RLITCRFCGDMVQ 515 (567)
T ss_pred CceeCCCCCCccc
Confidence 3578999998874
No 176
>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=51.30 E-value=9.8 Score=32.02 Aligned_cols=34 Identities=21% Similarity=0.449 Sum_probs=22.0
Q ss_pred eEEcCCCCCCCcccchh---hcccCCCCCCccc-cccc
Q 001136 1097 DILCNDCEQKGAARFHW---LYHKCGFCGSYNT-RLIK 1130 (1143)
Q Consensus 1097 ~i~CndC~~~s~~~~h~---l~~kC~~C~syNt-~~~~ 1130 (1143)
...|++||.....-..+ -...|+.||+-+. +++.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r~~s 42 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGGEKLRRLLS 42 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCCCceeEEec
Confidence 45799999865542211 1347999999876 4443
No 177
>KOG3850 consensus Predicted membrane protein [Function unknown]
Probab=51.08 E-value=2.2e+02 Score=33.94 Aligned_cols=145 Identities=19% Similarity=0.221 Sum_probs=74.2
Q ss_pred CCchHHHHHHHHHHHHHHHHHHHHHHHhhccCCcccH-HHHHHHHHHHHHHhhhhhhcccccccccccccccchhhhHHH
Q 001136 301 TYPIDEILLWHNAIRQELNEIAEESRKIQLSGDFTNL-LAFNERLQFIAEVLIFHCIAEVNVIFPAVDGASSFSQKHAEE 379 (1143)
Q Consensus 301 ~~Pi~~l~~~H~AiR~EL~~l~~~a~~~~~~~~~~~L-~~L~~r~~f~~~vl~~Hs~aED~vlFPaL~~~~~~~~EH~~i 379 (1143)
.+|.+.=..-=+||..||++|.+.-..+. .+..+| .++..-+.|+.+-|. |+.+-+--|++.. |+..
T Consensus 252 ~n~~~s~~~~l~aileeL~eIk~~q~~Le--esye~Lke~~krdy~fi~etLQ-----EERyR~erLEEqL-----Ndlt 319 (455)
T KOG3850|consen 252 ANPYHSQGAALDAILEELREIKETQALLE--ESYERLKEQIKRDYKFIAETLQ-----EERYRYERLEEQL-----NDLT 319 (455)
T ss_pred CCcccccchHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHH-----hHHH
Confidence 44554444445788889999988877775 334456 667777777777664 3322222222211 1111
Q ss_pred HhHHHHHHHHHHHHhhcCCccchHHHH-HHHHHHHHHHHHHHHHHHHhhhhhhh---hhhhhcCCHHHHHHHHHHHhhcC
Q 001136 380 ESQFNDFRLLIESIQNEGAISTSAEFY-AKLCSHADQIMETIERHFHKVEVQVL---PLARNHFSFKRQREILYQSLCEM 455 (1143)
Q Consensus 380 ~~~~~~f~~ll~~~~~~~~~~~~~~~~-~~L~~~l~~l~~~L~~Hf~kEE~qvf---PL~~k~~S~eEQ~~L~~~~l~~~ 455 (1143)
+-+.+++..|-..+..-. ++.++- =+=+..+.+++++...|+.|=|.+.- -..-+.+++.-++.|+..+|-.+
T Consensus 320 eLqQnEi~nLKqElasme---ervaYQsyERaRdIqEalEscqtrisKlEl~qq~qqv~Q~e~~~na~a~~llgk~iNii 396 (455)
T KOG3850|consen 320 ELQQNEIANLKQELASME---ERVAYQSYERARDIQEALESCQTRISKLELQQQQQQVVQLEGLENAVARRLLGKFINII 396 (455)
T ss_pred HHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHH
Confidence 111111111111110000 000000 13344566777777788888776543 23356777778888888887543
Q ss_pred CHHHHH
Q 001136 456 PLKLIE 461 (1143)
Q Consensus 456 Pl~ll~ 461 (1143)
|.+|.
T Consensus 397 -Lalm~ 401 (455)
T KOG3850|consen 397 -LALMT 401 (455)
T ss_pred -HHHHH
Confidence 34443
No 178
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=51.05 E-value=10 Score=47.45 Aligned_cols=45 Identities=24% Similarity=0.510 Sum_probs=36.4
Q ss_pred cceeEeccccccccCC-CCcccCCCCCccccCCCCCccccccCCcccccccc
Q 001136 958 SMAKYYCNICKFFDDE-RTVYHCPFCNLCRVGGGLGVDFFHCMTCNCCLGLK 1008 (1143)
Q Consensus 958 ~f~~y~C~~C~~~d~~-~~~yhC~~CgiCr~g~~l~~~~~hC~~C~~C~~~~ 1008 (1143)
....+||..|.-|=.| .-.=.|++||.+..++. +|+.||.++...
T Consensus 123 ~~~~~Yc~~~e~fl~dr~v~g~cp~cg~~~arGD------~Ce~Cg~~~~P~ 168 (558)
T COG0143 123 EYEGLYCVSCERFLPDRYVEGTCPKCGGEDARGD------QCENCGRTLDPT 168 (558)
T ss_pred ceeeeEcccccccccchheeccCCCcCccccCcc------hhhhccCcCCch
Confidence 5667889999887666 56668999999999875 899999987653
No 179
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=50.01 E-value=5.7 Score=49.40 Aligned_cols=29 Identities=31% Similarity=0.622 Sum_probs=23.4
Q ss_pred CCcccccc----ccccccccCCcccChhhhcccC
Q 001136 893 GCEHYKRN----CKIRAACCGKLFTCRFCHDKAS 922 (1143)
Q Consensus 893 gC~HY~r~----c~l~~~cC~k~y~Cr~CHde~~ 922 (1143)
||.|+--. ..-.|.-+|+|| |..||....
T Consensus 345 gC~~~i~~~~~~~~R~C~y~G~y~-C~~Ch~~~~ 377 (580)
T KOG1829|consen 345 GCGHTIGPDLEQRPRLCRYLGKYF-CDCCHQNDK 377 (580)
T ss_pred ccCCCcccccccchhHhhhhhhhh-CchhcccCc
Confidence 89888772 557788899988 999998754
No 180
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=49.76 E-value=12 Score=42.81 Aligned_cols=48 Identities=31% Similarity=0.792 Sum_probs=39.4
Q ss_pred CCCcceeEeccccccccCCCCcccCCCCCccccCCCCCccccccCCcccccccc
Q 001136 955 NGLSMAKYYCNICKFFDDERTVYHCPFCNLCRVGGGLGVDFFHCMTCNCCLGLK 1008 (1143)
Q Consensus 955 c~~~f~~y~C~~C~~~d~~~~~yhC~~CgiCr~g~~l~~~~~hC~~C~~C~~~~ 1008 (1143)
.|....-+||+.|+++-.. .-.||.-||.|-.+.. -||.==|.|+...
T Consensus 107 ~~~~~~~~~C~~C~~~rPp-Rs~HCsvC~~CV~rfD-----HHC~WvnnCVG~r 154 (299)
T KOG1311|consen 107 NGIQVEWKYCDTCQLYRPP-RSSHCSVCNNCVLRFD-----HHCPWLNNCIGER 154 (299)
T ss_pred CCcccceEEcCcCcccCCC-CcccchhhcccccccC-----CCCCCccceECCC
Confidence 4778888999999999554 6789999999988764 6888888887754
No 181
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=49.65 E-value=9.2 Score=48.88 Aligned_cols=47 Identities=26% Similarity=0.681 Sum_probs=33.4
Q ss_pred cCCCCcccccccccCCcceE-ecCCCCccchhhHHHHhc-------cCCCCcCCCc
Q 001136 1019 LETNCPICCDFLFTSSETVR-ALPCGHYMHLACFQAYTC-------SHYTCPICSK 1066 (1143)
Q Consensus 1019 ~~~~CpIC~e~lf~s~~~v~-~lpCgH~fH~~Ci~~wl~-------~~~~CPiCr~ 1066 (1143)
....|.||.+.|- ...++- --.|=|.||..||.+|.. ..-.||-|..
T Consensus 190 ~~yeCmIC~e~I~-~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqs 244 (950)
T KOG1952|consen 190 RKYECMICTERIK-RTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQS 244 (950)
T ss_pred CceEEEEeeeecc-ccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccc
Confidence 3567999999853 333322 234779999999999953 2467999983
No 182
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=48.72 E-value=12 Score=32.50 Aligned_cols=29 Identities=24% Similarity=0.574 Sum_probs=21.9
Q ss_pred ceEEcCCCCCCCcccchhhcccCCCCCCcccccc
Q 001136 1096 QDILCNDCEQKGAARFHWLYHKCGFCGSYNTRLI 1129 (1143)
Q Consensus 1096 ~~i~CndC~~~s~~~~h~l~~kC~~C~syNt~~~ 1129 (1143)
..+.|..||...- . .+.|++||-|+.+++
T Consensus 25 ~l~~c~~cg~~~~--~---H~vc~~cG~y~~r~v 53 (56)
T PF01783_consen 25 NLVKCPNCGEPKL--P---HRVCPSCGYYKGRQV 53 (56)
T ss_dssp SEEESSSSSSEES--T---TSBCTTTBBSSSSSS
T ss_pred ceeeeccCCCEec--c---cEeeCCCCeECCEEE
Confidence 4678999996322 2 346999999999886
No 183
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=48.69 E-value=8.5 Score=41.94 Aligned_cols=30 Identities=37% Similarity=0.867 Sum_probs=21.5
Q ss_pred ccCCcceEecCCCCccchhhHHHHhccCCCCcCCC
Q 001136 1031 FTSSETVRALPCGHYMHLACFQAYTCSHYTCPICS 1065 (1143)
Q Consensus 1031 f~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr 1065 (1143)
|.....++--.|+-.||..|+.+ ..||-|.
T Consensus 167 F~~~~~~~C~~C~~v~H~~C~~~-----~~CpkC~ 196 (202)
T PF13901_consen 167 FQIDTTVRCPKCKSVFHKSCFRK-----KSCPKCA 196 (202)
T ss_pred CCCCCeeeCCcCccccchhhcCC-----CCCCCcH
Confidence 34434445556999999999962 6699994
No 184
>PRK00808 hypothetical protein; Provisional
Probab=48.57 E-value=3.3e+02 Score=28.13 Aligned_cols=116 Identities=14% Similarity=0.147 Sum_probs=75.2
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccHHHHHHHHHHHHHHhcccCccccccc----hHHHhhhcchHHHHH
Q 001136 39 DSPILIFCFFHKAVRNELDALHQLAMNFATGHRVDILSLSERYRFLHSVYKHHSNAEDEVI----FPALDIRVKNVARKY 114 (1143)
Q Consensus 39 ~~Pi~~m~~~H~aLRreL~~L~~la~~~~~gd~~~~~~L~~~~~~l~~~L~~HH~~EDevL----FPaL~~R~p~vl~~l 114 (1143)
.--+..+-.-|+.|-..++.|...+.. ++ ...+...+..|......|=..||.+. ||.+ ..-
T Consensus 11 ~~G~~~ID~qH~~L~~lin~l~~a~~~---~~---~~~i~~~l~~L~~y~~~HF~~EE~lM~~~~Yp~~--------~~H 76 (150)
T PRK00808 11 NTGIDVIDQQHKRIVDYINHLHDAQDS---PD---RLAVAEVIDELIDYTLSHFAFEESLMEEAGYPFL--------VPH 76 (150)
T ss_pred ccCCHHHHHHHHHHHHHHHHHHHHHHc---Cc---HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCH--------HHH
Confidence 333455667898888888887766532 22 34677778888888888988888543 3333 233
Q ss_pred HHHHHHHHHHHHHHHHHHhhhccCCCCchHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhcc
Q 001136 115 SLEHEGESNLFDHLFQLLNSYTQNDESFPKELASCSRALQTSINQHMSKEEQQVFPLLTQH 175 (1143)
Q Consensus 115 e~EH~~i~~ll~~L~~~l~~~~~~~~~~~~eLa~~l~~l~~~L~~HL~~EE~~lfPLa~~~ 175 (1143)
..+|+.+-.-+.++ ...+..+. ......+.-+..-+..|+..+.....+.+.+.
T Consensus 77 ~~~H~~fl~~l~~l---~~~~~~g~----~~~~~l~~~L~~WL~~HI~~~D~~~~~~l~~~ 130 (150)
T PRK00808 77 KRVHELFIKRVEEY---RERFQAGE----DVADELHGMLSRWLFNHIRNDDAAYVDAVKAN 130 (150)
T ss_pred HHHHHHHHHHHHHH---HHHHHccc----hHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHh
Confidence 34555554444444 44443332 12234566778889999999999999888764
No 185
>PF14353 CpXC: CpXC protein
Probab=48.51 E-value=4.4 Score=40.61 Aligned_cols=25 Identities=24% Similarity=0.539 Sum_probs=18.1
Q ss_pred hcCcceEEcCCCCCCCcccchhhcc
Q 001136 1092 RNQVQDILCNDCEQKGAARFHWLYH 1116 (1143)
Q Consensus 1092 ~~~~~~i~CndC~~~s~~~~h~l~~ 1116 (1143)
.+.--.+.|..||.+..+.|-++||
T Consensus 33 ~g~l~~~~CP~Cg~~~~~~~p~lY~ 57 (128)
T PF14353_consen 33 DGSLFSFTCPSCGHKFRLEYPLLYH 57 (128)
T ss_pred cCCcCEEECCCCCCceecCCCEEEE
Confidence 3444578899999998777666664
No 186
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=48.49 E-value=4.1 Score=45.20 Aligned_cols=65 Identities=22% Similarity=0.292 Sum_probs=46.1
Q ss_pred eeeccccccccccCCCCCCCCCCCCcceeEeccccccccCCCCcccCCCCCccccCCCCCccccccCCcccccc
Q 001136 933 EMMCMHCLKIQAIGPNCTTPSCNGLSMAKYYCNICKFFDDERTVYHCPFCNLCRVGGGLGVDFFHCMTCNCCLG 1006 (1143)
Q Consensus 933 ~~~C~~C~~~q~~~~~C~~~~cc~~~f~~y~C~~C~~~d~~~~~yhC~~CgiCr~g~~l~~~~~hC~~C~~C~~ 1006 (1143)
-.+|..|....-+ .|+- |+..-++-+|.||--+|-++ -|||.|.-||.-.. -..-||..|..|..
T Consensus 238 ~~~~~~~~~~~~i--~C~~---~~~~A~~~~C~iC~~~~~~R--~~C~~~kA~~~~~Q--~K~N~~~~~~~~~q 302 (325)
T KOG4399|consen 238 CFLCKKCVKPSWI--HCSI---CNHCAVKHGCFICGELDHKR--STCPNIKAVRKQKQ--RKSNKMKMETTKGQ 302 (325)
T ss_pred hHHhhhhccccee--eeec---ccchhhhcceeecccccccc--ccCccHHHHHHHHh--cccchhhhhhhhhh
Confidence 3455666555432 4555 35556677899999998877 89999999997654 34678888877754
No 187
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=47.36 E-value=14 Score=41.78 Aligned_cols=38 Identities=18% Similarity=0.467 Sum_probs=23.8
Q ss_pred CCCcCCCccccchhhhhhhhHHHHhhcCCChhhhcCcceEEcCCCCCCC
Q 001136 1059 YTCPICSKSLGDMAIYFGMIDALLAAEELPEEYRNQVQDILCNDCEQKG 1107 (1143)
Q Consensus 1059 ~~CPiCr~s~~~m~~~~~~ld~~i~~~p~P~~y~~~~~~i~CndC~~~s 1107 (1143)
+.||.|+|.+.|.+.+-.-+ +- -.+.+ ...|.-|++..
T Consensus 216 F~C~hC~kAFADRSNLRAHm----QT------HS~~K-~~qC~~C~KsF 253 (279)
T KOG2462|consen 216 FSCPHCGKAFADRSNLRAHM----QT------HSDVK-KHQCPRCGKSF 253 (279)
T ss_pred ccCCcccchhcchHHHHHHH----Hh------hcCCc-cccCcchhhHH
Confidence 88999999998876542222 11 12222 45788888764
No 188
>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=47.34 E-value=6.8 Score=41.07 Aligned_cols=14 Identities=29% Similarity=0.985 Sum_probs=8.0
Q ss_pred ccCC-CCcccCCCCC
Q 001136 970 FDDE-RTVYHCPFCN 983 (1143)
Q Consensus 970 ~d~~-~~~yhC~~Cg 983 (1143)
|++. ...|+||.||
T Consensus 121 f~eA~~~~F~Cp~Cg 135 (158)
T TIGR00373 121 FNEAMELNFTCPRCG 135 (158)
T ss_pred HHHHHHcCCcCCCCC
Confidence 4444 4456666666
No 189
>COG2703 Hemerythrin [Inorganic ion transport and metabolism]
Probab=46.82 E-value=1.3e+02 Score=31.27 Aligned_cols=123 Identities=18% Similarity=0.191 Sum_probs=74.1
Q ss_pred hHHHHHHHHHHHHHHHH-HHHHHHHhhcCCCcccHHHHHHHHHHHHHHhcccCccccccc----hHHHhhhcchHHHHHH
Q 001136 41 PILIFCFFHKAVRNELD-ALHQLAMNFATGHRVDILSLSERYRFLHSVYKHHSNAEDEVI----FPALDIRVKNVARKYS 115 (1143)
Q Consensus 41 Pi~~m~~~H~aLRreL~-~L~~la~~~~~gd~~~~~~L~~~~~~l~~~L~~HH~~EDevL----FPaL~~R~p~vl~~le 115 (1143)
-+..+-..|+.|=+.++ .+...+. .......+...++.|......|=..|+.+. ||.|. .-.
T Consensus 12 gn~~iD~qHk~l~ei~N~~~~~~~~-----~~~~~~~i~~~l~el~~y~e~HF~~EE~~Me~igyp~l~--------~Hk 78 (144)
T COG2703 12 GNAAIDNQHKELFEILNKKLLLDAQ-----NHKSKAEIKQLLDELLNYTEDHFKEEEKLMEEIGYPPLE--------EHK 78 (144)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHH-----ccccHHHHHHHHHHHHHHHHHHHhhHHHHHHHcCCCcHH--------HHH
Confidence 34556678888888886 2222111 223455666677777777777888888554 44443 233
Q ss_pred HHHHHHHHHHHHHHHHHhhhccCCCCchHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhccCCHHHHH
Q 001136 116 LEHEGESNLFDHLFQLLNSYTQNDESFPKELASCSRALQTSINQHMSKEEQQVFPLLTQHFSLEEQA 182 (1143)
Q Consensus 116 ~EH~~i~~ll~~L~~~l~~~~~~~~~~~~eLa~~l~~l~~~L~~HL~~EE~~lfPLa~~~LS~eEw~ 182 (1143)
.+|+.+-..+.++ +.....++....+ ..+.-+..-+..|+..|....--.+.+.++..+-.
T Consensus 79 k~H~~~i~~v~e~---~~~~~~~~~~~~~---~L~~~l~~Wl~~Hia~~D~~~~~~~~~~~~~~~~e 139 (144)
T COG2703 79 KEHDTFIKRVKEV---LRKIAKGDEKLGR---ELLEFLVDWLAEHIAKEDRKYADWLKEKGSDAEEE 139 (144)
T ss_pred HHHHHHHHHHHHH---HHHHHhcHHHHHH---HHHHHHHHHHHHHHhHHhHHHHHHHHHhcchhhhh
Confidence 3555544444443 3333334333333 34556667899999999998877777777665543
No 190
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=46.56 E-value=5.5 Score=44.89 Aligned_cols=14 Identities=21% Similarity=0.221 Sum_probs=6.0
Q ss_pred CHHHHHHHHHHHHh
Q 001136 177 SLEEQASLVWQFFC 190 (1143)
Q Consensus 177 S~eEw~~L~~~f~~ 190 (1143)
+.+|...+...+++
T Consensus 132 ~~~el~~~a~~lla 145 (308)
T COG3058 132 SEQELESMASALLA 145 (308)
T ss_pred hHHHHHHHHHHHHh
Confidence 33444444444443
No 191
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=46.15 E-value=16 Score=30.20 Aligned_cols=23 Identities=35% Similarity=0.918 Sum_probs=11.2
Q ss_pred eEecccccc---ccCCCCcccCCCCC
Q 001136 961 KYYCNICKF---FDDERTVYHCPFCN 983 (1143)
Q Consensus 961 ~y~C~~C~~---~d~~~~~yhC~~Cg 983 (1143)
.|-|..|.- +++.....+|++||
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG 28 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCG 28 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCC
Confidence 344444442 22223356677766
No 192
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=46.09 E-value=14 Score=30.60 Aligned_cols=30 Identities=17% Similarity=0.335 Sum_probs=19.5
Q ss_pred eEEcCCCCCCCcccchhhcccCCCCCCccc
Q 001136 1097 DILCNDCEQKGAARFHWLYHKCGFCGSYNT 1126 (1143)
Q Consensus 1097 ~i~CndC~~~s~~~~h~l~~kC~~C~syNt 1126 (1143)
.+.|.+||+.-...-.....+|+.||+.-.
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCeEE
Confidence 467899997654322222568999997543
No 193
>PLN03086 PRLI-interacting factor K; Provisional
Probab=46.05 E-value=11 Score=47.01 Aligned_cols=53 Identities=23% Similarity=0.580 Sum_probs=26.9
Q ss_pred CCcccCCCCCccccCCCCC------ccccccCCccccccccc-cccc---ccccccCCCCcccccc
Q 001136 974 RTVYHCPFCNLCRVGGGLG------VDFFHCMTCNCCLGLKL-LNHK---CLEKCLETNCPICCDF 1029 (1143)
Q Consensus 974 ~~~yhC~~CgiCr~g~~l~------~~~~hC~~C~~C~~~~~-~~H~---C~e~~~~~~CpIC~e~ 1029 (1143)
+..+||+.||-=-....|. ..-+.|. |+..+.... ..|. |.++ .-.|+.|.-.
T Consensus 451 ~~H~~C~~Cgk~f~~s~LekH~~~~Hkpv~Cp-Cg~~~~R~~L~~H~~thCp~K--pi~C~fC~~~ 513 (567)
T PLN03086 451 KNHVHCEKCGQAFQQGEMEKHMKVFHEPLQCP-CGVVLEKEQMVQHQASTCPLR--LITCRFCGDM 513 (567)
T ss_pred ccCccCCCCCCccchHHHHHHHHhcCCCccCC-CCCCcchhHHHhhhhccCCCC--ceeCCCCCCc
Confidence 5667888886411111110 0123466 665443332 5663 5544 3568888765
No 194
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=46.00 E-value=7.6 Score=41.53 Aligned_cols=22 Identities=32% Similarity=1.132 Sum_probs=11.6
Q ss_pred Eecccccc---ccCC-CCcccCCCCC
Q 001136 962 YYCNICKF---FDDE-RTVYHCPFCN 983 (1143)
Q Consensus 962 y~C~~C~~---~d~~-~~~yhC~~Cg 983 (1143)
|+|+.|+. |++. ...|+||.||
T Consensus 118 Y~Cp~C~~rytf~eA~~~~F~Cp~Cg 143 (178)
T PRK06266 118 FFCPNCHIRFTFDEAMEYGFRCPQCG 143 (178)
T ss_pred EECCCCCcEEeHHHHhhcCCcCCCCC
Confidence 44555542 4444 4456666665
No 195
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=45.97 E-value=15 Score=42.46 Aligned_cols=47 Identities=17% Similarity=0.409 Sum_probs=34.9
Q ss_pred CCCCcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCCcccc
Q 001136 1020 ETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLG 1069 (1143)
Q Consensus 1020 ~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~~ 1069 (1143)
.+.||||+-. -..+...--=|-.|+-.|+..|+.+..+||+=..+..
T Consensus 300 ~~~CpvClk~---r~Nptvl~vSGyVfCY~Ci~~Yv~~~~~CPVT~~p~~ 346 (357)
T KOG0826|consen 300 REVCPVCLKK---RQNPTVLEVSGYVFCYPCIFSYVVNYGHCPVTGYPAS 346 (357)
T ss_pred cccChhHHhc---cCCCceEEecceEEeHHHHHHHHHhcCCCCccCCcch
Confidence 4679999865 2222222234999999999999999999999877653
No 196
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=44.11 E-value=7.5 Score=49.89 Aligned_cols=48 Identities=25% Similarity=0.537 Sum_probs=0.0
Q ss_pred cceeeccccccccccCCCCCCCCCCCCcceeEeccccccccCCCCcccCCCCCc
Q 001136 931 TSEMMCMHCLKIQAIGPNCTTPSCNGLSMAKYYCNICKFFDDERTVYHCPFCNL 984 (1143)
Q Consensus 931 ~~~~~C~~C~~~q~~~~~C~~~~cc~~~f~~y~C~~C~~~d~~~~~yhC~~Cgi 984 (1143)
+-.-.|..|+++.. ...|+. |.+...-.|+|+.|+.--++. +|+.||.
T Consensus 653 i~~r~Cp~Cg~~t~-~~~Cp~--CG~~T~~~~~Cp~C~~~~~~~---~C~~C~~ 700 (900)
T PF03833_consen 653 IGRRRCPKCGKETF-YNRCPE--CGSHTEPVYVCPDCGIEVEED---ECPKCGR 700 (900)
T ss_dssp ------------------------------------------------------
T ss_pred eecccCcccCCcch-hhcCcc--cCCccccceeccccccccCcc---ccccccc
Confidence 33456777776643 336766 544455667777776532221 6777765
No 197
>PRK07219 DNA topoisomerase I; Validated
Probab=44.03 E-value=29 Score=45.61 Aligned_cols=63 Identities=25% Similarity=0.514 Sum_probs=33.1
Q ss_pred ccccccccCC----CCcccCCCCCcc---ccCCCCCccccccCC---cccccccccccccccccccCCCCcccccccc
Q 001136 964 CNICKFFDDE----RTVYHCPFCNLC---RVGGGLGVDFFHCMT---CNCCLGLKLLNHKCLEKCLETNCPICCDFLF 1031 (1143)
Q Consensus 964 C~~C~~~d~~----~~~yhC~~CgiC---r~g~~l~~~~~hC~~---C~~C~~~~~~~H~C~e~~~~~~CpIC~e~lf 1031 (1143)
|+.|+..... .....|+.||-- |.|. -|. |+-|.+ |+.-.++.-..+. ......||-|...++
T Consensus 672 CP~C~~~~~~~~~~~~~~~CP~Cg~~l~~k~gr-~G~-F~~Cs~yp~C~~~~~l~~~~~~---~~~~~~CpkCg~~l~ 744 (822)
T PRK07219 672 CPDCEAEKEEEDPDEVIGPCPKCGGELAIKQLK-YGS-FLGCTNYPKCKYTLPLPRRGKI---TVTDEKCPECGLPLL 744 (822)
T ss_pred CCCCCCCccccccccccccCCCCCCeeEEEcCC-CCC-eeeCCCCCCCCceeeccccccc---ccccCCCCCCCCeEE
Confidence 7778765432 346899999721 2222 234 888864 6543332111100 123457888876543
No 198
>PHA00626 hypothetical protein
Probab=43.52 E-value=21 Score=31.13 Aligned_cols=19 Identities=16% Similarity=0.243 Sum_probs=10.4
Q ss_pred eccccccccCCCCcccCCCCCc
Q 001136 963 YCNICKFFDDERTVYHCPFCNL 984 (1143)
Q Consensus 963 ~C~~C~~~d~~~~~yhC~~Cgi 984 (1143)
-|.+|+-+ ++.|.|++||.
T Consensus 13 rcg~cr~~---snrYkCkdCGY 31 (59)
T PHA00626 13 KEKTMRGW---SDDYVCCDCGY 31 (59)
T ss_pred eeceeccc---CcceEcCCCCC
Confidence 45555544 33466666664
No 199
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=42.87 E-value=16 Score=40.67 Aligned_cols=80 Identities=20% Similarity=0.484 Sum_probs=52.4
Q ss_pred ccccccccccccCC--------cccChhhhcccCCCCC----CccccceeeccccccccccCCCCCCCCCCCCcceeEec
Q 001136 897 YKRNCKIRAACCGK--------LFTCRFCHDKASDHSM----DRKATSEMMCMHCLKIQAIGPNCTTPSCNGLSMAKYYC 964 (1143)
Q Consensus 897 Y~r~c~l~~~cC~k--------~y~Cr~CHde~~~H~~----~r~~~~~~~C~~C~~~q~~~~~C~~~~cc~~~f~~y~C 964 (1143)
|+..=...|.-|+. .|.|..||.-..+-++ |-+..-...|..|+++-.... ...-+.-||
T Consensus 115 ~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~~l~fr~d~yH~yHFkCt~C~keL~sda--------Revk~eLyC 186 (332)
T KOG2272|consen 115 YRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQPLTFRGDPYHPYHFKCTTCGKELTSDA--------REVKGELYC 186 (332)
T ss_pred HhhcchHHhhhhhhhhcccccceeehhhhhhhcccccccccCCCCCccceecccccccccchh--------hhhccceec
Confidence 44444455555643 6999999977654332 445566889999999865431 223456777
Q ss_pred cccccccCCCCcccCCCCCccccCCC
Q 001136 965 NICKFFDDERTVYHCPFCNLCRVGGG 990 (1143)
Q Consensus 965 ~~C~~~d~~~~~yhC~~CgiCr~g~~ 990 (1143)
.-|. +.+-|+-||-||....
T Consensus 187 lrCh------D~mgipiCgaC~rpIe 206 (332)
T KOG2272|consen 187 LRCH------DKMGIPICGACRRPIE 206 (332)
T ss_pred cccc------cccCCcccccccCchH
Confidence 7774 4567899999997643
No 200
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=42.80 E-value=20 Score=48.11 Aligned_cols=49 Identities=27% Similarity=0.612 Sum_probs=26.5
Q ss_pred CCCCCCCCCCCcceeEeccccccccCCCCcccCCCCCccccCCCCCccccccCCcc
Q 001136 947 PNCTTPSCNGLSMAKYYCNICKFFDDERTVYHCPFCNLCRVGGGLGVDFFHCMTCN 1002 (1143)
Q Consensus 947 ~~C~~~~cc~~~f~~y~C~~C~~~d~~~~~yhC~~CgiCr~g~~l~~~~~hC~~C~ 1002 (1143)
..|++ | |..--..||+.|.-.- +.+|+|+.||.=-....-+ ...|..||
T Consensus 668 rkCPk--C-G~~t~~~fCP~CGs~t--e~vy~CPsCGaev~~des~--a~~CP~CG 716 (1337)
T PRK14714 668 RRCPS--C-GTETYENRCPDCGTHT--EPVYVCPDCGAEVPPDESG--RVECPRCD 716 (1337)
T ss_pred EECCC--C-CCccccccCcccCCcC--CCceeCccCCCccCCCccc--cccCCCCC
Confidence 45776 4 5543344777776442 3567777777732221111 33577776
No 201
>PRK01917 cation-binding hemerythrin HHE family protein; Provisional
Probab=42.66 E-value=58 Score=33.27 Aligned_cols=48 Identities=13% Similarity=0.113 Sum_probs=37.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhccCCCCchHHHHHHHHHHHHHHHHHHHHHHHhH
Q 001136 111 ARKYSLEHEGESNLFDHLFQLLNSYTQNDESFPKELASCSRALQTSINQHMSKEEQQV 168 (1143)
Q Consensus 111 l~~le~EH~~i~~ll~~L~~~l~~~~~~~~~~~~eLa~~l~~l~~~L~~HL~~EE~~l 168 (1143)
++.+..||+++-.++++|.+.. ...+...+..|......|+..||...
T Consensus 14 i~~ID~qH~~Lf~lin~l~~~~----------~~~i~~~l~~L~~y~~~HF~~EE~lM 61 (139)
T PRK01917 14 DPFTDATHAEFVQLLNAVARAD----------DADFLQALDAWIDHTRHHFAQEERWM 61 (139)
T ss_pred ChhhhHHHHHHHHHHHHHHcCC----------HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3567889998888877776541 24477889999999999999999865
No 202
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=42.66 E-value=10 Score=45.30 Aligned_cols=20 Identities=20% Similarity=0.466 Sum_probs=15.5
Q ss_pred HHHHhcCHHHHHHHHhhhcC
Q 001136 816 KDIFRMNQNELEAEIRKVYR 835 (1143)
Q Consensus 816 ~~~~~~~~~~l~~~i~~~~~ 835 (1143)
...+++|+.+||..|++.-.
T Consensus 50 ~~llk~~~KqLR~li~~Lre 69 (436)
T KOG2593|consen 50 KELLKFNKKQLRKLIASLRE 69 (436)
T ss_pred HHHhcccHHHHHHHHHHhhh
Confidence 34667899999988887765
No 203
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=40.89 E-value=13 Score=45.87 Aligned_cols=34 Identities=21% Similarity=0.507 Sum_probs=16.4
Q ss_pred CcccChhhhcccCCCCCCccccceeeccccccccc
Q 001136 910 KLFTCRFCHDKASDHSMDRKATSEMMCMHCLKIQA 944 (1143)
Q Consensus 910 k~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~ 944 (1143)
+.|-|+.||.=....- .-..+.-..|..|..+.|
T Consensus 4 ~L~fC~~C~~irc~~c-~~~Ei~~~yCp~CL~~~p 37 (483)
T PF05502_consen 4 ELYFCEHCHKIRCPRC-VSEEIDSYYCPNCLFEVP 37 (483)
T ss_pred cceecccccccCChhh-cccccceeECccccccCC
Confidence 4577888885432210 011222455555555544
No 204
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=40.51 E-value=18 Score=41.41 Aligned_cols=43 Identities=23% Similarity=0.647 Sum_probs=33.0
Q ss_pred CCcccccccccCCcceEecCCCCccchhhHHHHhcc---CCCCcCCC
Q 001136 1022 NCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCS---HYTCPICS 1065 (1143)
Q Consensus 1022 ~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~---~~~CPiCr 1065 (1143)
.|||=.+. -+...+...|.|||.+-..-++...++ +..||.|-
T Consensus 338 iCPVlKe~-~t~ENpP~ml~CgHVIskeal~~LS~nG~~~FKCPYCP 383 (396)
T COG5109 338 ICPVLKEL-CTDENPPVMLECGHVISKEALSVLSQNGVLSFKCPYCP 383 (396)
T ss_pred eccccHhh-hcccCCCeeeeccceeeHHHHHHHhhcCcEEeeCCCCC
Confidence 36666654 555667788999999999999988654 47899994
No 205
>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=39.97 E-value=15 Score=30.00 Aligned_cols=14 Identities=50% Similarity=1.004 Sum_probs=7.4
Q ss_pred ccCCCCcccCCCCC
Q 001136 970 FDDERTVYHCPFCN 983 (1143)
Q Consensus 970 ~d~~~~~yhC~~Cg 983 (1143)
+|...+.+-|..||
T Consensus 13 ~D~~~g~~vC~~CG 26 (43)
T PF08271_consen 13 FDPERGELVCPNCG 26 (43)
T ss_dssp EETTTTEEEETTT-
T ss_pred EcCCCCeEECCCCC
Confidence 34446666666665
No 206
>cd00522 Hemerythrin Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the muscle tissue of sipunculids as well as in polycheate and oligocheate annelids. In addition to oxygen transport, Mhr proteins are involved in cadmium fixation and host anti-bacterial defense. Hr and Mhr proteins have the same "four alpha helix bundle" motif and active site structure. Hr forms oligomers, the octameric form being most prevalent, while Mhr is monomeric.
Probab=39.55 E-value=3.2e+02 Score=26.75 Aligned_cols=99 Identities=13% Similarity=0.048 Sum_probs=60.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcCCCcccHHHHHHHHHHHHHHhcccCccccccchHHHhhhcchHHHHHHHHHHHHH
Q 001136 43 LIFCFFHKAVRNELDALHQLAMNFATGHRVDILSLSERYRFLHSVYKHHSNAEDEVIFPALDIRVKNVARKYSLEHEGES 122 (1143)
Q Consensus 43 ~~m~~~H~aLRreL~~L~~la~~~~~gd~~~~~~L~~~~~~l~~~L~~HH~~EDevLFPaL~~R~p~vl~~le~EH~~i~ 122 (1143)
..+-.-|+.|-..++.|...... ...+..|......|=..||.++ ++..=+-+..-..+|+..-
T Consensus 13 ~~ID~qH~~L~~l~n~l~~a~~~------------~~~l~~L~~y~~~HF~~EE~~M----~~~~yp~~~~H~~~H~~f~ 76 (113)
T cd00522 13 EVIDDEHKTLFNGINDLSEANNR------------ADNLKELVDYTVKHFKDEEALM----EAAGYPDYEEHKKIHEDFV 76 (113)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhH------------HHHHHHHHHHHHHHHHHHHHHH----HHcCCCCHHHHHHHHHHHH
Confidence 44557788888887777776543 3456667777777888888543 2111022233355666665
Q ss_pred HHHHHHHHHHhhhccCCCCchHHHHHHHHHHHHHHHHHHHHHHHhHHH
Q 001136 123 NLFDHLFQLLNSYTQNDESFPKELASCSRALQTSINQHMSKEEQQVFP 170 (1143)
Q Consensus 123 ~ll~~L~~~l~~~~~~~~~~~~eLa~~l~~l~~~L~~HL~~EE~~lfP 170 (1143)
..+.++...+ ....+.-+..-+..|+..+...+.+
T Consensus 77 ~~~~~~~~~~-------------~~~~~~~l~~Wl~~HI~~~D~~~~~ 111 (113)
T cd00522 77 EKVGGLKAPV-------------GQADLKYLKDWLVNHIKTEDFKYKG 111 (113)
T ss_pred HHHHHHHHHH-------------HHHHHHHHHHHHHHHhHhHHHHhhh
Confidence 5555554332 1223455678899999998876644
No 207
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=39.23 E-value=9.6 Score=39.05 Aligned_cols=25 Identities=28% Similarity=0.925 Sum_probs=17.2
Q ss_pred eeEeccccccccCCCCcccCCCCC--ccccC
Q 001136 960 AKYYCNICKFFDDERTVYHCPFCN--LCRVG 988 (1143)
Q Consensus 960 ~~y~C~~C~~~d~~~~~yhC~~Cg--iCr~g 988 (1143)
.+-||.+|-+| ++|-|-.|| +|-|+
T Consensus 117 ~r~fCaVCG~~----S~ysC~~CG~kyCsv~ 143 (156)
T KOG3362|consen 117 LRKFCAVCGYD----SKYSCVNCGTKYCSVR 143 (156)
T ss_pred cchhhhhcCCC----chhHHHhcCCceeech
Confidence 45577777755 677888887 56665
No 208
>PLN02189 cellulose synthase
Probab=39.21 E-value=21 Score=47.17 Aligned_cols=53 Identities=25% Similarity=0.516 Sum_probs=36.9
Q ss_pred cccccCCCCcccccccccC--CcceEecC-CCCccchhhHHHHh--ccCCCCcCCCccc
Q 001136 1015 LEKCLETNCPICCDFLFTS--SETVRALP-CGHYMHLACFQAYT--CSHYTCPICSKSL 1068 (1143)
Q Consensus 1015 ~e~~~~~~CpIC~e~lf~s--~~~v~~lp-CgH~fH~~Ci~~wl--~~~~~CPiCr~s~ 1068 (1143)
.++.....|.||.|++-.. ++...... ||--.++.|+ +|. ..++.||.|+..+
T Consensus 29 ~~~~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cy-eyer~eg~q~CpqCkt~Y 86 (1040)
T PLN02189 29 LRNLDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCY-EYERREGTQNCPQCKTRY 86 (1040)
T ss_pred cccccCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhhhcCCccCcccCCch
Confidence 3444556899999986433 33333333 8888999999 554 4578899999877
No 209
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=39.03 E-value=53 Score=32.71 Aligned_cols=44 Identities=20% Similarity=0.301 Sum_probs=25.2
Q ss_pred CCCcccccccccCCc-----------ceEecCCCCccchhhHHHHhccCCCCcCCC
Q 001136 1021 TNCPICCDFLFTSSE-----------TVRALPCGHYMHLACFQAYTCSHYTCPICS 1065 (1143)
Q Consensus 1021 ~~CpIC~e~lf~s~~-----------~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr 1065 (1143)
..|-.|+.. |.... ...--.|++.|..+|-.-+-..-..||-|.
T Consensus 56 ~~C~~C~~~-f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiHe~Lh~CPGC~ 110 (112)
T TIGR00622 56 RFCFGCQGP-FPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVHESLHCCPGCI 110 (112)
T ss_pred CcccCcCCC-CCCcccccccccccccceeCCCCCCccccccchhhhhhccCCcCCC
Confidence 469999887 44321 112234667777777555544445577664
No 210
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=38.98 E-value=34 Score=29.04 Aligned_cols=40 Identities=33% Similarity=0.889 Sum_probs=18.8
Q ss_pred CCcccccccccCCcceEecCCCCccchhhHHH--Hh-----ccCCCCcCCCcc
Q 001136 1022 NCPICCDFLFTSSETVRALPCGHYMHLACFQA--YT-----CSHYTCPICSKS 1067 (1143)
Q Consensus 1022 ~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~--wl-----~~~~~CPiCr~s 1067 (1143)
.|||....| ..+++...|.|. .||+- |+ .....||+|+++
T Consensus 4 ~CPls~~~i---~~P~Rg~~C~H~---~CFDl~~fl~~~~~~~~W~CPiC~~~ 50 (50)
T PF02891_consen 4 RCPLSFQRI---RIPVRGKNCKHL---QCFDLESFLESNQRTPKWKCPICNKP 50 (50)
T ss_dssp B-TTTSSB----SSEEEETT--SS-----EEHHHHHHHHHHS---B-TTT---
T ss_pred eCCCCCCEE---EeCccCCcCccc---ceECHHHHHHHhhccCCeECcCCcCc
Confidence 588888764 347788889876 46443 44 234679999874
No 211
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=38.92 E-value=15 Score=40.11 Aligned_cols=28 Identities=32% Similarity=0.702 Sum_probs=23.7
Q ss_pred EecCCCCccchhhHHHHhccCCCCcCCC
Q 001136 1038 RALPCGHYMHLACFQAYTCSHYTCPICS 1065 (1143)
Q Consensus 1038 ~~lpCgH~fH~~Ci~~wl~~~~~CPiCr 1065 (1143)
+...||=-||..|++.|+.....||-|+
T Consensus 196 rCg~c~i~~h~~c~qty~q~~~~cphc~ 223 (235)
T KOG4718|consen 196 RCGSCNIQYHRGCIQTYLQRRDICPHCG 223 (235)
T ss_pred ccCcccchhhhHHHHHHhcccCcCCchh
Confidence 3455777899999999999899999995
No 212
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=38.38 E-value=2.8 Score=35.43 Aligned_cols=48 Identities=21% Similarity=0.680 Sum_probs=29.6
Q ss_pred CcceeEeccccccccCCCCcccCCCCCc--cccCCCCCccccccCCcccccc
Q 001136 957 LSMAKYYCNICKFFDDERTVYHCPFCNL--CRVGGGLGVDFFHCMTCNCCLG 1006 (1143)
Q Consensus 957 ~~f~~y~C~~C~~~d~~~~~yhC~~Cgi--Cr~g~~l~~~~~hC~~C~~C~~ 1006 (1143)
.+|++|.|+.|+---.-++.-.|--||- |-.- -.+.|+.|..||.=+.
T Consensus 3 ~SFsry~CDLCn~~~p~~~LRQCvlCGRWaC~sC--W~deYY~CksC~Gii~ 52 (57)
T PF14445_consen 3 HSFSRYSCDLCNSSHPISELRQCVLCGRWACNSC--WQDEYYTCKSCNGIIN 52 (57)
T ss_pred hHHhhHhHHhhcccCcHHHHHHHhhhchhhhhhh--hhhhHhHHHhhhchhh
Confidence 4689999999985444355556666662 2111 1256888887775443
No 213
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=38.05 E-value=22 Score=29.51 Aligned_cols=26 Identities=19% Similarity=0.556 Sum_probs=17.3
Q ss_pred eEEcCCCCCCCcccchhhcccCCCCCC
Q 001136 1097 DILCNDCEQKGAARFHWLYHKCGFCGS 1123 (1143)
Q Consensus 1097 ~i~CndC~~~s~~~~h~l~~kC~~C~s 1123 (1143)
...|.+||..-... ---..+|+.||+
T Consensus 2 ~Y~C~~Cg~~~~~~-~~~~irC~~CG~ 27 (44)
T smart00659 2 IYICGECGRENEIK-SKDVVRCRECGY 27 (44)
T ss_pred EEECCCCCCEeecC-CCCceECCCCCc
Confidence 35788888765443 234578888886
No 214
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=36.79 E-value=28 Score=40.55 Aligned_cols=26 Identities=19% Similarity=0.743 Sum_probs=20.1
Q ss_pred CCcceeEe--ccccccccCCCCcccCCCCCc
Q 001136 956 GLSMAKYY--CNICKFFDDERTVYHCPFCNL 984 (1143)
Q Consensus 956 ~~~f~~y~--C~~C~~~d~~~~~yhC~~Cgi 984 (1143)
...|--|| |.||+.++. -|-|++||+
T Consensus 60 ~~dfeL~f~Ge~i~~y~~q---SftCPyC~~ 87 (381)
T KOG1280|consen 60 RVDFELYFGGEPISHYDPQ---SFTCPYCGI 87 (381)
T ss_pred ccceeeEecCccccccccc---cccCCcccc
Confidence 34566666 888887765 799999997
No 215
>TIGR00058 Hemerythrin hemerythrin family non-heme iron proteins. This family includes oxygen carrier proteins of various oligomeric states from the vascular fluid (hemerythrin) and muscle (myohemerythrin) of some marine invertebrates. Each unit binds 2 non-heme Fe using 5 H, one E and one D. One member of this family,from the sandworm Nereis diversicolor, is an unusual (non-metallothionein) cadmium-binding protein. Homologous proteins, excluded from this narrowly defined family, are found in archaea and bacteria (see pfam01814).
Probab=36.79 E-value=79 Score=31.24 Aligned_cols=45 Identities=20% Similarity=0.046 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhccCCCCchHHHHHHHHHHHHHHHHHHHHHHHhH
Q 001136 111 ARKYSLEHEGESNLFDHLFQLLNSYTQNDESFPKELASCSRALQTSINQHMSKEEQQV 168 (1143)
Q Consensus 111 l~~le~EH~~i~~ll~~L~~~l~~~~~~~~~~~~eLa~~l~~l~~~L~~HL~~EE~~l 168 (1143)
+..+..||+++-.++++|..... ...+..|......|+..||...
T Consensus 15 ~~~ID~qH~~L~~lin~l~~~~~-------------~~~l~~L~~y~~~HF~~EE~lM 59 (115)
T TIGR00058 15 YDNLDEEHKTLFNGIFALAADNS-------------ATALKELIDVTVLHFLDEEAMM 59 (115)
T ss_pred CHHHHHHHHHHHHHHHHHHhcch-------------HHHHHHHHHHHHHHHHHHHHHH
Confidence 35678899988888887754221 3568888999999999999865
No 216
>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=36.68 E-value=26 Score=27.38 Aligned_cols=24 Identities=25% Similarity=0.913 Sum_probs=17.2
Q ss_pred eEeccccccc-cCCCCcccCCCCCc
Q 001136 961 KYYCNICKFF-DDERTVYHCPFCNL 984 (1143)
Q Consensus 961 ~y~C~~C~~~-d~~~~~yhC~~Cgi 984 (1143)
.|-|.+|.+. +.++.+..||.||.
T Consensus 2 ~~~C~~CG~i~~g~~~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCPVCGYIHEGEEAPEKCPICGA 26 (34)
T ss_pred eEECCCCCCEeECCcCCCcCcCCCC
Confidence 4778888876 44467778888875
No 217
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=36.60 E-value=13 Score=29.85 Aligned_cols=13 Identities=46% Similarity=1.239 Sum_probs=5.5
Q ss_pred ceeEecccccccc
Q 001136 959 MAKYYCNICKFFD 971 (1143)
Q Consensus 959 f~~y~C~~C~~~d 971 (1143)
|.+|||+.|+.|=
T Consensus 1 m~ryyCdyC~~~~ 13 (38)
T PF06220_consen 1 MPRYYCDYCKKYL 13 (38)
T ss_dssp --S-B-TTT--B-
T ss_pred CcCeeccccccee
Confidence 5689999999874
No 218
>PLN02436 cellulose synthase A
Probab=36.34 E-value=25 Score=46.63 Aligned_cols=53 Identities=19% Similarity=0.504 Sum_probs=36.7
Q ss_pred cccccCCCCcccccccccCCcceEec---CCCCccchhhHHHHh--ccCCCCcCCCccc
Q 001136 1015 LEKCLETNCPICCDFLFTSSETVRAL---PCGHYMHLACFQAYT--CSHYTCPICSKSL 1068 (1143)
Q Consensus 1015 ~e~~~~~~CpIC~e~lf~s~~~v~~l---pCgH~fH~~Ci~~wl--~~~~~CPiCr~s~ 1068 (1143)
......+.|.||.|++=.+.+.-... -||--.++.|+ +|. ..++.||.|+..+
T Consensus 31 ~~~~~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cy-eyer~eg~~~Cpqckt~Y 88 (1094)
T PLN02436 31 VQELSGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCY-EYERREGNQACPQCKTRY 88 (1094)
T ss_pred ccccCCccccccccccCcCCCCCEEEeeccCCCccccchh-hhhhhcCCccCcccCCch
Confidence 44445668999999963333322223 37788999999 554 4568899998877
No 219
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=35.91 E-value=14 Score=42.08 Aligned_cols=19 Identities=11% Similarity=0.051 Sum_probs=13.8
Q ss_pred hhhHHHHHHHhhcCCCCCC
Q 001136 765 NTMFNEWLDECWKGPHESS 783 (1143)
Q Consensus 765 ~t~F~~WL~~w~~~~~~~~ 783 (1143)
-.+..+...|.|+..|.|.
T Consensus 114 ikya~~Fv~eFf~qNPiSq 132 (421)
T COG5151 114 IKYAEGFVPEFFSQNPISQ 132 (421)
T ss_pred HHHHHHHhHHHhccCCchh
Confidence 3667777888888777664
No 220
>PRK01917 cation-binding hemerythrin HHE family protein; Provisional
Probab=35.60 E-value=4.9e+02 Score=26.52 Aligned_cols=114 Identities=12% Similarity=0.013 Sum_probs=70.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccHHHHHHHHHHHHHHhcccCccccccchHHHhhhcc-hHHHHHHHHHH
Q 001136 41 PILIFCFFHKAVRNELDALHQLAMNFATGHRVDILSLSERYRFLHSVYKHHSNAEDEVIFPALDIRVK-NVARKYSLEHE 119 (1143)
Q Consensus 41 Pi~~m~~~H~aLRreL~~L~~la~~~~~gd~~~~~~L~~~~~~l~~~L~~HH~~EDevLFPaL~~R~p-~vl~~le~EH~ 119 (1143)
-+..+-.-|+.|=..++.|.... ...+...+..|......|=..||... ++.. +.+..-..+|+
T Consensus 13 Gi~~ID~qH~~Lf~lin~l~~~~----------~~~i~~~l~~L~~y~~~HF~~EE~lM-----~~~~YP~~~~H~~eH~ 77 (139)
T PRK01917 13 GDPFTDATHAEFVQLLNAVARAD----------DADFLQALDAWIDHTRHHFAQEERWM-----EATKFGPRHCHRAEHD 77 (139)
T ss_pred CChhhhHHHHHHHHHHHHHHcCC----------HHHHHHHHHHHHHHHHHHHHHHHHHH-----HHcCCCChHHHHHHHH
Confidence 34556677887777766666531 12366778888888888888888432 2221 22333445666
Q ss_pred HHHHHHHHHHHHHhhhccCCCCchHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhc
Q 001136 120 GESNLFDHLFQLLNSYTQNDESFPKELASCSRALQTSINQHMSKEEQQVFPLLTQ 174 (1143)
Q Consensus 120 ~i~~ll~~L~~~l~~~~~~~~~~~~eLa~~l~~l~~~L~~HL~~EE~~lfPLa~~ 174 (1143)
..-.-+.++...+..- +.. ......+.-+..-+..|+..+...+.+.+.+
T Consensus 78 ~fl~~v~~l~~~~~~~--g~~---~~~~~l~~~L~~Wl~~HI~~~D~~~~~~l~~ 127 (139)
T PRK01917 78 EVLAVAADVREKVARD--GDF---ELGRRLVAELPEWFDQHVRTMDAMMVSHLKM 127 (139)
T ss_pred HHHHHHHHHHHHHHhc--CCH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6655555555544221 221 2234456677788999999999988777664
No 221
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=35.44 E-value=17 Score=35.29 Aligned_cols=30 Identities=23% Similarity=0.655 Sum_probs=20.3
Q ss_pred CCcccCCCCC-----ccccCCCCCccccccCCccc
Q 001136 974 RTVYHCPFCN-----LCRVGGGLGVDFFHCMTCNC 1003 (1143)
Q Consensus 974 ~~~yhC~~Cg-----iCr~g~~l~~~~~hC~~C~~ 1003 (1143)
+..|-|+.|| +|-|.++.+..+-+|..||.
T Consensus 20 ~k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGl 54 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGL 54 (104)
T ss_pred CceEecCccCCeeeeEEEEEecCceeEEEcccCcc
Confidence 3556777777 57777766666777776664
No 222
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=35.43 E-value=21 Score=30.19 Aligned_cols=40 Identities=30% Similarity=0.744 Sum_probs=27.9
Q ss_pred CcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCCccccchh
Q 001136 1023 CPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLGDMA 1072 (1143)
Q Consensus 1023 CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~~~m~ 1072 (1143)
|+.|...+... . .....-|..||..|+ +|-.|++++.+..
T Consensus 1 C~~C~~~I~~~-~-~~~~~~~~~~H~~Cf--------~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 1 CARCGKPIYGT-E-IVIKAMGKFWHPECF--------KCSKCGKPLNDGD 40 (58)
T ss_dssp BTTTSSBESSS-S-EEEEETTEEEETTTS--------BETTTTCBTTTSS
T ss_pred CCCCCCCccCc-E-EEEEeCCcEEEcccc--------ccCCCCCccCCCe
Confidence 67788775422 2 222246899999887 8999999887654
No 223
>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=35.35 E-value=26 Score=29.51 Aligned_cols=10 Identities=30% Similarity=0.969 Sum_probs=4.7
Q ss_pred CcccCCCCCc
Q 001136 975 TVYHCPFCNL 984 (1143)
Q Consensus 975 ~~yhC~~Cgi 984 (1143)
+-|.|+.||.
T Consensus 33 ~~w~CP~C~a 42 (47)
T PF00301_consen 33 DDWVCPVCGA 42 (47)
T ss_dssp TT-B-TTTSS
T ss_pred CCCcCcCCCC
Confidence 4566666664
No 224
>PF12126 DUF3583: Protein of unknown function (DUF3583); InterPro: IPR021978 This domain is found in eukaryotes, and is typically between 302 and 338 amino acids in length. It is found in association with PF00097 from PFAM and PF00643 from PFAM. Most members are promyelocytic leukemia proteins, and this family lies towards the C terminus.
Probab=34.84 E-value=1.7e+02 Score=33.70 Aligned_cols=122 Identities=14% Similarity=0.164 Sum_probs=74.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcCCCcccHHHHHHHHHHHHHHhcccCccccccchHHHhhhcchHHHHHHHHHHHHHH
Q 001136 44 IFCFFHKAVRNELDALHQLAMNFATGHRVDILSLSERYRFLHSVYKHHSNAEDEVIFPALDIRVKNVARKYSLEHEGESN 123 (1143)
Q Consensus 44 ~m~~~H~aLRreL~~L~~la~~~~~gd~~~~~~L~~~~~~l~~~L~~HH~~EDevLFPaL~~R~p~vl~~le~EH~~i~~ 123 (1143)
.|...|..++.....|.+.-.. --..++.+++.+.. |-.+.+..|.- .+-.+|+.+|+++..
T Consensus 14 ~F~aahaqm~sav~qL~~~r~~-------teelIr~rVrq~V~----hVqaqEreLLe-------~v~~rYqR~y~ema~ 75 (324)
T PF12126_consen 14 AFGAAHAQMRSAVSQLGRARAD-------TEELIRARVRQVVA----HVQAQERELLE-------AVEARYQRDYEEMAG 75 (324)
T ss_pred hHHHHHHHHHHHHHHHHHHHhh-------HHHHHHHHHHHHHH----HHHHHHHHHHH-------HHHHHHHHHHHHHHH
Confidence 4667777777776666554222 23446667777666 55555544433 344578899999999
Q ss_pred HHHHHHHHHhhhccCCC-------CchHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhccCCHHHHHH
Q 001136 124 LFDHLFQLLNSYTQNDE-------SFPKELASCSRALQTSINQHMSKEEQQVFPLLTQHFSLEEQAS 183 (1143)
Q Consensus 124 ll~~L~~~l~~~~~~~~-------~~~~eLa~~l~~l~~~L~~HL~~EE~~lfPLa~~~LS~eEw~~ 183 (1143)
-+.+|.+.|.++..+.. ++-..=...+..|...-..+|..||-+-+-.+-++=..+|...
T Consensus 76 ~L~~LeavLqRir~G~~LVekM~~YASDQEVLdMh~FlreAL~rLrqeePq~lqa~V~td~F~E~k~ 142 (324)
T PF12126_consen 76 QLGRLEAVLQRIRTGGALVEKMKLYASDQEVLDMHGFLREALERLRQEEPQNLQAAVRTDGFDEFKA 142 (324)
T ss_pred HHhHHHHHHHHHHhHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhhhhcCcccccceecccHHHHHH
Confidence 99999999999976532 0001111122333334556788888877655555555555433
No 225
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=34.77 E-value=22 Score=30.30 Aligned_cols=27 Identities=22% Similarity=0.535 Sum_probs=19.4
Q ss_pred eEEcCCCCCCCcccchhhcccCCCCCC
Q 001136 1097 DILCNDCEQKGAARFHWLYHKCGFCGS 1123 (1143)
Q Consensus 1097 ~i~CndC~~~s~~~~h~l~~kC~~C~s 1123 (1143)
.+.|-.||+.-....---+.+|+.||+
T Consensus 6 ~Y~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 6 EYKCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred EEEhhhcCCeeehhhccCceeCCCCCc
Confidence 567888887765444456778888887
No 226
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=34.48 E-value=20 Score=39.29 Aligned_cols=38 Identities=34% Similarity=0.727 Sum_probs=27.3
Q ss_pred CcccccccccCCcceEecCCCCc-cchhhHHHHhccCCCCcCCCccc
Q 001136 1023 CPICCDFLFTSSETVRALPCGHY-MHLACFQAYTCSHYTCPICSKSL 1068 (1143)
Q Consensus 1023 CpIC~e~lf~s~~~v~~lpCgH~-fH~~Ci~~wl~~~~~CPiCr~s~ 1068 (1143)
|-.|.+. ...|..+||-|. ++..|-.. -.+||+|+...
T Consensus 161 Cr~C~~~----~~~VlllPCrHl~lC~~C~~~----~~~CPiC~~~~ 199 (207)
T KOG1100|consen 161 CRKCGER----EATVLLLPCRHLCLCGICDES----LRICPICRSPK 199 (207)
T ss_pred ceecCcC----CceEEeecccceEeccccccc----CccCCCCcChh
Confidence 8888775 345788999976 56667643 45699998654
No 227
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=33.94 E-value=23 Score=30.80 Aligned_cols=27 Identities=26% Similarity=0.747 Sum_probs=20.6
Q ss_pred cCcceEEcCCCCCCCcccchhhcccCCCCC
Q 001136 1093 NQVQDILCNDCEQKGAARFHWLYHKCGFCG 1122 (1143)
Q Consensus 1093 ~~~~~i~CndC~~~s~~~~h~l~~kC~~C~ 1122 (1143)
+.+..|+|.-||+ ..||+--..|..||
T Consensus 11 ~~ktH~~CrRCG~---~syH~qK~~CasCG 37 (55)
T PF01907_consen 11 HNKTHTLCRRCGR---RSYHIQKKTCASCG 37 (55)
T ss_dssp -S-SEEE-TTTSS---EEEETTTTEETTTB
T ss_pred CCccEeeecccCC---eeeecCCCcccccC
Confidence 4457899999997 45788888999999
No 228
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=33.46 E-value=20 Score=40.98 Aligned_cols=50 Identities=26% Similarity=0.563 Sum_probs=35.9
Q ss_pred CCCCcccccccccCCcceEecCCC-----CccchhhHHHHhc--cCCCCcCCCcccc
Q 001136 1020 ETNCPICCDFLFTSSETVRALPCG-----HYMHLACFQAYTC--SHYTCPICSKSLG 1069 (1143)
Q Consensus 1020 ~~~CpIC~e~lf~s~~~v~~lpCg-----H~fH~~Ci~~wl~--~~~~CPiCr~s~~ 1069 (1143)
...|=||.++.+.........||. ...|..|+..|.. ++.+|.+|.....
T Consensus 78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~~~~~~~CeiC~~~~~ 134 (323)
T KOG1609|consen 78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFSIKGNITCEICKSFFI 134 (323)
T ss_pred CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhccccCeeeecccccce
Confidence 356999988754333223456764 7789999999985 6788999987663
No 229
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=33.33 E-value=24 Score=40.51 Aligned_cols=29 Identities=34% Similarity=0.902 Sum_probs=21.5
Q ss_pred EecCCCCccchhhHHHHhccCCCCcCCCccc
Q 001136 1038 RALPCGHYMHLACFQAYTCSHYTCPICSKSL 1068 (1143)
Q Consensus 1038 ~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~ 1068 (1143)
+.+||.|+|+.+|-.. .....||.|...|
T Consensus 105 RmIPCkHvFCl~CAr~--~~dK~Cp~C~d~V 133 (389)
T KOG2932|consen 105 RMIPCKHVFCLECARS--DSDKICPLCDDRV 133 (389)
T ss_pred cccccchhhhhhhhhc--CccccCcCcccHH
Confidence 4579999999999754 2245799997655
No 230
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=32.81 E-value=33 Score=36.24 Aligned_cols=49 Identities=29% Similarity=0.553 Sum_probs=34.7
Q ss_pred CCCCcCCCccccchhhhhhhhHHHHhhcCCChh-hhcCcceEEcCCCCCCCcccchh
Q 001136 1058 HYTCPICSKSLGDMAIYFGMIDALLAAEELPEE-YRNQVQDILCNDCEQKGAARFHW 1113 (1143)
Q Consensus 1058 ~~~CPiCr~s~~~m~~~~~~ld~~i~~~p~P~~-y~~~~~~i~CndC~~~s~~~~h~ 1113 (1143)
...||.|+..+...+ .+.....+|+. |........|..||+.-...-||
T Consensus 97 ~~RCp~CN~~L~~vs-------~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~GsHw 146 (165)
T COG1656 97 FSRCPECNGELEKVS-------REEVKEKVPEKVYRNYEEFYRCPKCGKIYWKGSHW 146 (165)
T ss_pred cccCcccCCEeccCc-------HHHHhhccchhhhhcccceeECCCCcccccCchHH
Confidence 577999998886543 33344556654 56666667799999988777777
No 231
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=31.88 E-value=34 Score=41.35 Aligned_cols=31 Identities=23% Similarity=0.336 Sum_probs=18.8
Q ss_pred HHHHHHHhhhcCCCCCCHHHHHHHHHHHHHHHH
Q 001136 824 NELEAEIRKVYRDPTLDPRRKAYLAQNLMTSRW 856 (1143)
Q Consensus 824 ~~l~~~i~~~~~~~~~~~~~k~~~~q~l~~~~~ 856 (1143)
..|+..||.|--. .+.+..-...|+++-.|-
T Consensus 21 ~~lk~~lr~i~~~--~~~r~e~~~lQ~~l~~Rs 51 (446)
T PF07227_consen 21 EELKEYLREILEG--PEKREEFVALQKLLQRRS 51 (446)
T ss_pred HHHHHHHHHHHhC--cchHHHHHHHHHHHhccc
Confidence 3567777777754 444555566677765543
No 232
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=31.87 E-value=21 Score=44.63 Aligned_cols=57 Identities=21% Similarity=0.301 Sum_probs=25.0
Q ss_pred chhhhhhhhHHHHhhcCCChhhhcCcceEEcCCCCCCCcccchhhcccCCCCCCccccccccC
Q 001136 1070 DMAIYFGMIDALLAAEELPEEYRNQVQDILCNDCEQKGAARFHWLYHKCGFCGSYNTRLIKND 1132 (1143)
Q Consensus 1070 ~m~~~~~~ld~~i~~~p~P~~y~~~~~~i~CndC~~~s~~~~h~l~~kC~~C~syNt~~~~~~ 1132 (1143)
+.++....++.......+|----+. ..-.|++||....- +.+||.|||-|+.+++..
T Consensus 465 n~~al~~lv~~~~~~~~i~Y~~in~-~~~~C~~CG~~~~~-----~~~CP~CGs~~~~~~~Rv 521 (546)
T PF13597_consen 465 NPEALEKLVRYAMENTGIPYFTINP-PIDICPDCGYIGGE-----GDKCPKCGSENIEVYSRV 521 (546)
T ss_dssp -HHHHHHHHHHHHH--H-SEEEEE---EEEETTT---S-------EEE-CCC----EEEEB-S
T ss_pred CHHHHHHHHHHHHHhCCCCeEEEec-CcccccCCCcCCCC-----CCCCCCCCCcccceEEEe
Confidence 4555555566665545555332222 34579999987653 458999999998776443
No 233
>PF06937 EURL: EURL protein; InterPro: IPR009704 This family consists of several animal EURL proteins. EURL is preferentially expressed in chick retinal precursor cells as well as in the anterior epithelial cells of the lens at early stages of development. EURL transcripts are found primarily in the peripheral dorsal retina, i.e., the most undifferentiated part of the dorsal retina. EURL transcripts are also detected in the lens at stage 18 and remain abundant in the proliferating epithelial cells of the lens until at least day 11. The distribution pattern of EURL in the developing retina and lens suggest a role before the events leading to cell determination and differentiation [].
Probab=31.67 E-value=29 Score=39.19 Aligned_cols=42 Identities=24% Similarity=0.485 Sum_probs=24.2
Q ss_pred CCCcccccccccCCcceEecCC--CCccchhhHHHH-hccCCCCcC
Q 001136 1021 TNCPICCDFLFTSSETVRALPC--GHYMHLACFQAY-TCSHYTCPI 1063 (1143)
Q Consensus 1021 ~~CpIC~e~lf~s~~~v~~lpC--gH~fH~~Ci~~w-l~~~~~CPi 1063 (1143)
.-|+||.+- ...+.+-..|.= .=-=|+.||.+| +--+..||-
T Consensus 31 sfChiCfEl-~iegvpks~llHtkSlRGHrdCFEK~HlIanQ~~pr 75 (285)
T PF06937_consen 31 SFCHICFEL-SIEGVPKSNLLHTKSLRGHRDCFEKYHLIANQDCPR 75 (285)
T ss_pred eecceeecc-ccccCccccccccccccchHHHHHHHHHHHcCCCCc
Confidence 458999874 322222111110 001389999999 556888993
No 234
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=30.80 E-value=32 Score=25.36 Aligned_cols=19 Identities=21% Similarity=0.670 Sum_probs=12.9
Q ss_pred CCcCCCccccchhhhhhhhH
Q 001136 1060 TCPICSKSLGDMAIYFGMID 1079 (1143)
Q Consensus 1060 ~CPiCr~s~~~m~~~~~~ld 1079 (1143)
.||+|.+.+ .+....+-+|
T Consensus 3 ~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREV-PENLINSHLD 21 (26)
T ss_pred cCCCCcCcc-cHHHHHHHHH
Confidence 699999888 4444455555
No 235
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=30.79 E-value=29 Score=40.34 Aligned_cols=47 Identities=28% Similarity=0.737 Sum_probs=36.2
Q ss_pred CCcceeEeccccccccCCCCcccCCCCCccccCCCCCccccccCCcccccccc
Q 001136 956 GLSMAKYYCNICKFFDDERTVYHCPFCNLCRVGGGLGVDFFHCMTCNCCLGLK 1008 (1143)
Q Consensus 956 ~~~f~~y~C~~C~~~d~~~~~yhC~~CgiCr~g~~l~~~~~hC~~C~~C~~~~ 1008 (1143)
+.-..+=||..|+.|-.+ ...||..||.|-.... -||.==|-|++.+
T Consensus 104 ~~~~~~~~C~~C~~~KP~-RS~HC~~Cn~CV~k~D-----HHC~Wi~nCVG~~ 150 (309)
T COG5273 104 GKFGTENFCSTCNIYKPP-RSHHCSICNRCVLKFD-----HHCPWINNCVGFR 150 (309)
T ss_pred CccccceeccccccccCC-CCccchhhcchhhccC-----ccCcccccccCcc
Confidence 666667789999999777 4678888988887643 6787777777654
No 236
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=30.25 E-value=16 Score=41.43 Aligned_cols=39 Identities=28% Similarity=0.675 Sum_probs=27.6
Q ss_pred CCCCccccCCCCCccccccCCcccccccccccccccccccCCCCcc
Q 001136 980 PFCNLCRVGGGLGVDFFHCMTCNCCLGLKLLNHKCLEKCLETNCPI 1025 (1143)
Q Consensus 980 ~~CgiCr~g~~l~~~~~hC~~C~~C~~~~~~~H~C~e~~~~~~CpI 1025 (1143)
.+|..|+..+. ....||..||.|+.. .+|.|+=- +||..
T Consensus 149 ~kCSTCki~KP--ARSKHCsiCNrCV~r--fDHHCiWi---NNCIG 187 (341)
T KOG1312|consen 149 VKCSTCKIRKP--ARSKHCSICNRCVHR--FDHHCIWI---NNCIG 187 (341)
T ss_pred CccccccCCCc--cccccchHHHHHHHH--hccceEee---ecccc
Confidence 56777777763 567899999999654 58888754 55654
No 237
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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 PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=30.23 E-value=15 Score=30.55 Aligned_cols=42 Identities=21% Similarity=0.706 Sum_probs=29.0
Q ss_pred CcccccccccCCcceEecCCCCccchhhHHHHh------ccCCCCcCCC
Q 001136 1023 CPICCDFLFTSSETVRALPCGHYMHLACFQAYT------CSHYTCPICS 1065 (1143)
Q Consensus 1023 CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl------~~~~~CPiCr 1065 (1143)
|+||... .....-+.--.|+-.||..|+..-. ...+.||.|+
T Consensus 2 C~vC~~~-~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~ 49 (51)
T PF00628_consen 2 CPVCGQS-DDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCR 49 (51)
T ss_dssp BTTTTSS-CTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHH
T ss_pred CcCCCCc-CCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCc
Confidence 7888874 3344444445799999999987642 2368888875
No 238
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=30.21 E-value=38 Score=42.58 Aligned_cols=55 Identities=24% Similarity=0.310 Sum_probs=33.1
Q ss_pred chhhhhhhhHHHHhhcCCChhhhcCcceEEcCCCCCCCcccchhhcccCCCCCCccccccc
Q 001136 1070 DMAIYFGMIDALLAAEELPEEYRNQVQDILCNDCEQKGAARFHWLYHKCGFCGSYNTRLIK 1130 (1143)
Q Consensus 1070 ~m~~~~~~ld~~i~~~p~P~~y~~~~~~i~CndC~~~s~~~~h~l~~kC~~C~syNt~~~~ 1130 (1143)
+.++....++........+ -..+.... .|++||.... ..+.+|+.|||-|+.+++
T Consensus 493 n~~al~~lv~~a~~~~~~y-~~~~~p~~-~C~~CG~~~~----~~~~~CP~CGs~~~~~~~ 547 (555)
T cd01675 493 NPEALEALVKKAAKRGVIY-FGINTPID-ICNDCGYIGE----GEGFKCPKCGSEDVEVIS 547 (555)
T ss_pred CHHHHHHHHHHHHHcCCce-EEEecCCc-cCCCCCCCCc----CCCCCCcCCCCcCceEEE
Confidence 4455555555554432222 22334444 8999997553 345799999998866654
No 239
>PRK00366 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed
Probab=30.02 E-value=38 Score=39.98 Aligned_cols=51 Identities=20% Similarity=0.346 Sum_probs=41.5
Q ss_pred CCCcCCCccccchhhhhhhhHHHHhhcCCChhhhcCcceEEc--CCCCCCCcccchh
Q 001136 1059 YTCPICSKSLGDMAIYFGMIDALLAAEELPEEYRNQVQDILC--NDCEQKGAARFHW 1113 (1143)
Q Consensus 1059 ~~CPiCr~s~~~m~~~~~~ld~~i~~~p~P~~y~~~~~~i~C--ndC~~~s~~~~h~ 1113 (1143)
..||.|++...|.-..-..+++.+...++| -+....-| |.|+......+=+
T Consensus 269 isCPgCgR~~~D~~~la~~vee~~~~~~~P----lkIAVmGC~VNgpGEa~~aDIGI 321 (360)
T PRK00366 269 ISCPTCGRTEFDVIQELAEVEQRLEHIKMP----LKVAVMGCVVNGPGEAKEADIGI 321 (360)
T ss_pred EECCCCCCCcccHHHHHHHHHHHhcCCCCC----cEEEEeCCCCCCCCchhhCcEeE
Confidence 569999999999998888999999988888 34456779 9999877766544
No 240
>PRK14873 primosome assembly protein PriA; Provisional
Probab=29.83 E-value=42 Score=43.13 Aligned_cols=46 Identities=17% Similarity=0.436 Sum_probs=29.6
Q ss_pred ccceeeccccccccccCCCCCCCCCCCCcce------eEeccccccccCCCCcccCCCCCcc
Q 001136 930 ATSEMMCMHCLKIQAIGPNCTTPSCNGLSMA------KYYCNICKFFDDERTVYHCPFCNLC 985 (1143)
Q Consensus 930 ~~~~~~C~~C~~~q~~~~~C~~~~cc~~~f~------~y~C~~C~~~d~~~~~yhC~~CgiC 985 (1143)
....++|..|+..- .|++ |+..+. .-.|..|.+- ..+..|+.||--
T Consensus 380 yap~l~C~~Cg~~~----~C~~---C~~~L~~h~~~~~l~Ch~CG~~---~~p~~Cp~Cgs~ 431 (665)
T PRK14873 380 YVPSLACARCRTPA----RCRH---CTGPLGLPSAGGTPRCRWCGRA---APDWRCPRCGSD 431 (665)
T ss_pred CCCeeEhhhCcCee----ECCC---CCCceeEecCCCeeECCCCcCC---CcCccCCCCcCC
Confidence 34578999999876 7888 455554 2346666542 246677777754
No 241
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=29.78 E-value=39 Score=32.95 Aligned_cols=38 Identities=18% Similarity=0.425 Sum_probs=23.9
Q ss_pred ceEEcCCCCCCCcc-cc--hhhcccCCCCCCccccccccCC
Q 001136 1096 QDILCNDCEQKGAA-RF--HWLYHKCGFCGSYNTRLIKNDT 1133 (1143)
Q Consensus 1096 ~~i~CndC~~~s~~-~~--h~l~~kC~~C~syNt~~~~~~~ 1133 (1143)
....|..|+..+.. ++ ...-+.|+.||-|+.+++....
T Consensus 20 t~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~~~~V~~l~ 60 (99)
T PRK14892 20 KIFECPRCGKVSISVKIKKNIAIITCGNCGLYTEFEVPSVY 60 (99)
T ss_pred cEeECCCCCCeEeeeecCCCcceEECCCCCCccCEECCccc
Confidence 35678888854321 11 1123469999999999875443
No 242
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=29.77 E-value=33 Score=30.39 Aligned_cols=29 Identities=17% Similarity=0.119 Sum_probs=21.0
Q ss_pred ceEEcCCCCCCCcccchhhcccCCCCCCccccccc
Q 001136 1096 QDILCNDCEQKGAARFHWLYHKCGFCGSYNTRLIK 1130 (1143)
Q Consensus 1096 ~~i~CndC~~~s~~~~h~l~~kC~~C~syNt~~~~ 1130 (1143)
..+.|..||..- .+ | +.|. ||.||.+++-
T Consensus 26 ~~~~c~~cg~~~-~p-H---~vc~-cG~Y~gr~v~ 54 (60)
T PRK01110 26 TLSVDKTTGEYH-LP-H---HVSP-KGYYKGRKVL 54 (60)
T ss_pred ceeEcCCCCcee-cc-c---eecC-CcccCCeEee
Confidence 357899999642 22 3 2499 9999999874
No 243
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=29.74 E-value=24 Score=29.24 Aligned_cols=13 Identities=46% Similarity=0.846 Sum_probs=10.7
Q ss_pred cCCCCCCcccccc
Q 001136 1117 KCGFCGSYNTRLI 1129 (1143)
Q Consensus 1117 kC~~C~syNt~~~ 1129 (1143)
||+.||-||-..-
T Consensus 13 kCp~CGt~NG~R~ 25 (44)
T PF14952_consen 13 KCPKCGTYNGTRG 25 (44)
T ss_pred cCCcCcCccCccc
Confidence 7999999996543
No 244
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=29.06 E-value=26 Score=43.15 Aligned_cols=97 Identities=27% Similarity=0.562 Sum_probs=59.6
Q ss_pred cccccccccCCCCcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCCccccchhhhhhhhHHHHhhcCCC--
Q 001136 1011 NHKCLEKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSLGDMAIYFGMIDALLAAEELP-- 1088 (1143)
Q Consensus 1011 ~H~C~e~~~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~~~m~~~~~~ld~~i~~~p~P-- 1088 (1143)
-|.|.......+|.-|...+.... +..+ |+.||..|+ +|=.|.+.+.+...++.. -+|
T Consensus 354 c~~~~~~~~~p~C~~C~~~i~~~~--v~a~--~~~wH~~cf--------~C~~C~~~~~~~~~~~~~--------~~pyc 413 (479)
T KOG1703|consen 354 CHECFHAPFRPNCKRCLLPILEEG--VCAL--GRLWHPECF--------VCADCGKPLKNSSFFESD--------GEPYC 413 (479)
T ss_pred HHHHHHHhhCccccccCCchHHhH--hhhc--cCeechhce--------eeecccCCCCCCcccccC--------Cccch
Confidence 567777888889999988754333 2334 899999887 666787777554433211 111
Q ss_pred hh-hhcCcceEEcCCC----------CCCCcccchhhcccCCCCCCccccc
Q 001136 1089 EE-YRNQVQDILCNDC----------EQKGAARFHWLYHKCGFCGSYNTRL 1128 (1143)
Q Consensus 1089 ~~-y~~~~~~i~CndC----------~~~s~~~~h~l~~kC~~C~syNt~~ 1128 (1143)
+. |.... ...|.-| -+.....||--+-+|..|.--++..
T Consensus 414 e~~~~~~~-~~~~~~~~~p~~~~~~~ie~~~~~~h~~~F~c~~c~~~l~~~ 463 (479)
T KOG1703|consen 414 EDHYKKLF-TTKCDYCKKPVEFGSRQIEADGSPFHGDCFRCANCMKKLTKK 463 (479)
T ss_pred hhhHhhhc-cccchhccchhHhhhhHhhccCccccccceehhhhhccccCC
Confidence 11 11111 1234434 3445678999999999998877743
No 245
>PF12773 DZR: Double zinc ribbon
Probab=29.03 E-value=26 Score=29.14 Aligned_cols=22 Identities=23% Similarity=0.711 Sum_probs=12.1
Q ss_pred eEEcCCCCCCCcccchhhcccCCCCC
Q 001136 1097 DILCNDCEQKGAARFHWLYHKCGFCG 1122 (1143)
Q Consensus 1097 ~i~CndC~~~s~~~~h~l~~kC~~C~ 1122 (1143)
.+.|..|++.-..... .|+.||
T Consensus 29 ~~~C~~Cg~~~~~~~~----fC~~CG 50 (50)
T PF12773_consen 29 KKICPNCGAENPPNAK----FCPNCG 50 (50)
T ss_pred CCCCcCCcCCCcCCcC----ccCccc
Confidence 4568888876332221 277665
No 246
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the 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=28.57 E-value=32 Score=34.84 Aligned_cols=32 Identities=13% Similarity=0.010 Sum_probs=22.2
Q ss_pred ccccccccCCcccChhhhcccCCCCCCccccceeeccccccccccC
Q 001136 901 CKIRAACCGKLFTCRFCHDKASDHSMDRKATSEMMCMHCLKIQAIG 946 (1143)
Q Consensus 901 c~l~~~cC~k~y~Cr~CHde~~~H~~~r~~~~~~~C~~C~~~q~~~ 946 (1143)
-|-.||.||+-|= -+.| ..++|.+|++.+++.
T Consensus 8 tKr~Cp~cg~kFY-----------DLnk---~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 8 TKRICPNTGSKFY-----------DLNR---RPAVSPYTGEQFPPE 39 (129)
T ss_pred ccccCCCcCcccc-----------ccCC---CCccCCCcCCccCcc
Confidence 4567899987441 1222 588999999998765
No 248
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=28.46 E-value=31 Score=29.39 Aligned_cols=9 Identities=44% Similarity=1.150 Sum_probs=4.3
Q ss_pred cccccCCcc
Q 001136 994 DFFHCMTCN 1002 (1143)
Q Consensus 994 ~~~hC~~C~ 1002 (1143)
+.++|.+||
T Consensus 36 ~r~~C~~Cg 44 (50)
T PRK00432 36 DRWHCGKCG 44 (50)
T ss_pred CcEECCCcC
Confidence 345555544
No 249
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=28.23 E-value=35 Score=43.57 Aligned_cols=35 Identities=17% Similarity=0.365 Sum_probs=20.3
Q ss_pred eeeccccccccccCCCCCCCCCCCC--cceeEecccccccc
Q 001136 933 EMMCMHCLKIQAIGPNCTTPSCNGL--SMAKYYCNICKFFD 971 (1143)
Q Consensus 933 ~~~C~~C~~~q~~~~~C~~~~cc~~--~f~~y~C~~C~~~d 971 (1143)
.-.|..|++.... ..|++ ||. ..+.-||+.|-..-
T Consensus 15 akFC~~CG~~l~~-~~Cp~---CG~~~~~~~~fC~~CG~~~ 51 (645)
T PRK14559 15 NRFCQKCGTSLTH-KPCPQ---CGTEVPVDEAHCPNCGAET 51 (645)
T ss_pred CccccccCCCCCC-CcCCC---CCCCCCcccccccccCCcc
Confidence 3457777666532 35666 344 45666777776543
No 250
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=27.95 E-value=41 Score=44.86 Aligned_cols=52 Identities=19% Similarity=0.420 Sum_probs=35.6
Q ss_pred ccccCCCCcccccccccCCcceEe---cCCCCccchhhHHHHh--ccCCCCcCCCccc
Q 001136 1016 EKCLETNCPICCDFLFTSSETVRA---LPCGHYMHLACFQAYT--CSHYTCPICSKSL 1068 (1143)
Q Consensus 1016 e~~~~~~CpIC~e~lf~s~~~v~~---lpCgH~fH~~Ci~~wl--~~~~~CPiCr~s~ 1068 (1143)
++...+.|-||.|++=-+.+.-.. --||--.++.|+ +|. ..++.||.|+..+
T Consensus 13 ~~~~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCY-EYEr~eG~q~CPqCktrY 69 (1079)
T PLN02638 13 KHGGGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCY-EYERKDGNQSCPQCKTKY 69 (1079)
T ss_pred cccCCceeeecccccCcCCCCCEEEEeccCCCccccchh-hhhhhcCCccCCccCCch
Confidence 344556899999986333222222 247788999999 664 4578899998776
No 251
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=27.73 E-value=60 Score=30.28 Aligned_cols=50 Identities=18% Similarity=0.352 Sum_probs=21.2
Q ss_pred cCCCCcccccccccCCcceEe---cCCCCccchhhHHHHh-ccCCCCcCCCccc
Q 001136 1019 LETNCPICCDFLFTSSETVRA---LPCGHYMHLACFQAYT-CSHYTCPICSKSL 1068 (1143)
Q Consensus 1019 ~~~~CpIC~e~lf~s~~~v~~---lpCgH~fH~~Ci~~wl-~~~~~CPiCr~s~ 1068 (1143)
....|.||.+++=.....-.. .-|+-..++.|+.-=. ..+..||.|+..+
T Consensus 8 ~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYErkeg~q~CpqCkt~y 61 (80)
T PF14569_consen 8 NGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYERKEGNQVCPQCKTRY 61 (80)
T ss_dssp SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHHHHTS-SB-TTT--B-
T ss_pred CCcccccccCccccCCCCCEEEEEcccCCccchhHHHHHhhcCcccccccCCCc
Confidence 356799999986433332222 3488889999997644 4578899999554
No 252
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=27.56 E-value=38 Score=28.91 Aligned_cols=29 Identities=24% Similarity=0.629 Sum_probs=21.0
Q ss_pred cceeEecccccc-ccCC--CCcccCCCCCccc
Q 001136 958 SMAKYYCNICKF-FDDE--RTVYHCPFCNLCR 986 (1143)
Q Consensus 958 ~f~~y~C~~C~~-~d~~--~~~yhC~~CgiCr 986 (1143)
.+..|-|..|.- ++.+ ..-+.|++||.=.
T Consensus 3 ~~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~rI 34 (49)
T COG1996 3 AMMEYKCARCGREVELDQETRGIRCPYCGSRI 34 (49)
T ss_pred ceEEEEhhhcCCeeehhhccCceeCCCCCcEE
Confidence 467788888873 4433 7889999999644
No 253
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=27.52 E-value=35 Score=43.60 Aligned_cols=47 Identities=23% Similarity=0.576 Sum_probs=30.9
Q ss_pred CCCCcccccccccCCcceEecCCC-----CccchhhHHHHhcc--CCCCcCCCccc
Q 001136 1020 ETNCPICCDFLFTSSETVRALPCG-----HYMHLACFQAYTCS--HYTCPICSKSL 1068 (1143)
Q Consensus 1020 ~~~CpIC~e~lf~s~~~v~~lpCg-----H~fH~~Ci~~wl~~--~~~CPiCr~s~ 1068 (1143)
...|-||..+ -....+ -.=||. -.+|.+|+.+|+.. ...|-+|...+
T Consensus 12 ~~~CRICr~e-~~~d~p-LfhPCKC~GSIkYiH~eCL~eW~~~s~~~kCdiChy~~ 65 (1175)
T COG5183 12 KRSCRICRTE-DIRDDP-LFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEY 65 (1175)
T ss_pred chhceeecCC-CCCCCc-CcccccccchhHHHHHHHHHHHHhcCCCcceeeeccee
Confidence 3568888654 222222 223443 57999999999854 46799998777
No 254
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=27.38 E-value=32 Score=39.43 Aligned_cols=34 Identities=32% Similarity=0.677 Sum_probs=27.0
Q ss_pred CcccCCCCCccccCCCCCccccccCCccccccccccccccc
Q 001136 975 TVYHCPFCNLCRVGGGLGVDFFHCMTCNCCLGLKLLNHKCL 1015 (1143)
Q Consensus 975 ~~yhC~~CgiCr~g~~l~~~~~hC~~C~~C~~~~~~~H~C~ 1015 (1143)
+...|+.|.+-|-. ...||..||.|+.. .+|.|.
T Consensus 112 ~~~~C~~C~~~rPp-----Rs~HCsvC~~CV~r--fDHHC~ 145 (299)
T KOG1311|consen 112 EWKYCDTCQLYRPP-----RSSHCSVCNNCVLR--FDHHCP 145 (299)
T ss_pred ceEEcCcCcccCCC-----Ccccchhhcccccc--cCCCCC
Confidence 57899999988765 37999999999765 477774
No 255
>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=27.27 E-value=40 Score=27.51 Aligned_cols=31 Identities=23% Similarity=0.356 Sum_probs=19.1
Q ss_pred eEEcCCCCCCCcccch---hhcccCCCCCCcccc
Q 001136 1097 DILCNDCEQKGAARFH---WLYHKCGFCGSYNTR 1127 (1143)
Q Consensus 1097 ~i~CndC~~~s~~~~h---~l~~kC~~C~syNt~ 1127 (1143)
...|.+||....+-.. -....|+.||+-+.+
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~ 38 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISEDDPVPCPECGSTEVR 38 (42)
T ss_pred EEEeCCCCCEEEEEEEcCCCCCCcCCCCCCCceE
Confidence 4578888866532211 235679999985443
No 256
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=27.25 E-value=40 Score=25.43 Aligned_cols=21 Identities=33% Similarity=0.871 Sum_probs=11.9
Q ss_pred CCCccccCCCCCccccccCCcc
Q 001136 981 FCNLCRVGGGLGVDFFHCMTCN 1002 (1143)
Q Consensus 981 ~CgiCr~g~~l~~~~~hC~~C~ 1002 (1143)
.|++|+.-..-.. +|+|..|+
T Consensus 2 ~C~~C~~~~~~~~-~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFY-FYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCE-eEEeCCCC
Confidence 3666655443112 77887776
No 257
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=26.80 E-value=28 Score=41.66 Aligned_cols=36 Identities=22% Similarity=0.416 Sum_probs=25.5
Q ss_pred CCCcccccccccCCcceEecCCCCccchhhHHHHhc
Q 001136 1021 TNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTC 1056 (1143)
Q Consensus 1021 ~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~ 1056 (1143)
..|.||..+............|||.|+.+|..++..
T Consensus 147 ~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~ie 182 (384)
T KOG1812|consen 147 EECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIE 182 (384)
T ss_pred ccCccCccccccHhhhHHHhcccchhhhHHhHHHhh
Confidence 579999944233323333567999999999999864
No 258
>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=26.76 E-value=72 Score=33.52 Aligned_cols=26 Identities=19% Similarity=0.485 Sum_probs=15.4
Q ss_pred cCCCCcCCCccccchhh--hhhhhHHHH
Q 001136 1057 SHYTCPICSKSLGDMAI--YFGMIDALL 1082 (1143)
Q Consensus 1057 ~~~~CPiCr~s~~~m~~--~~~~ld~~i 1082 (1143)
.+++||.|+..+..++. ....|...|
T Consensus 127 ~~F~Cp~Cg~~L~~~dn~~~i~~l~~~i 154 (158)
T TIGR00373 127 LNFTCPRCGAMLDYLDNSEAIEKLEEQI 154 (158)
T ss_pred cCCcCCCCCCEeeeccCHHHHHHHHHHH
Confidence 47788888887754443 234444443
No 259
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=26.26 E-value=26 Score=36.26 Aligned_cols=7 Identities=43% Similarity=1.549 Sum_probs=4.7
Q ss_pred ccCCCCC
Q 001136 977 YHCPFCN 983 (1143)
Q Consensus 977 yhC~~Cg 983 (1143)
|.||.||
T Consensus 124 f~Cp~Cg 130 (147)
T smart00531 124 FTCPRCG 130 (147)
T ss_pred EECCCCC
Confidence 6666665
No 260
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=26.13 E-value=42 Score=42.16 Aligned_cols=47 Identities=23% Similarity=0.600 Sum_probs=31.5
Q ss_pred CCCcccccccccCCcceEe---cCCCCccchhhHHHHhc-----cCCCCcCCCcccc
Q 001136 1021 TNCPICCDFLFTSSETVRA---LPCGHYMHLACFQAYTC-----SHYTCPICSKSLG 1069 (1143)
Q Consensus 1021 ~~CpIC~e~lf~s~~~v~~---lpCgH~fH~~Ci~~wl~-----~~~~CPiCr~s~~ 1069 (1143)
..|++|.. +.....-.. -.||-.||..|..-|+. +...||-|++...
T Consensus 19 ~mc~l~~s--~G~~~ag~m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe~ 73 (694)
T KOG4443|consen 19 LMCPLCGS--SGKGRAGRLLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCEA 73 (694)
T ss_pred hhhhhhcc--ccccccCcchhhhhhcccCCcchhhHHHhHHHhcCCcccCCceeeee
Confidence 35777764 233332222 24899999999999963 4577999987663
No 261
>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=25.89 E-value=41 Score=26.16 Aligned_cols=23 Identities=26% Similarity=0.619 Sum_probs=12.9
Q ss_pred Eeccccccc-cCC-CCcccCCCCCc
Q 001136 962 YYCNICKFF-DDE-RTVYHCPFCNL 984 (1143)
Q Consensus 962 y~C~~C~~~-d~~-~~~yhC~~Cgi 984 (1143)
|.|..|..- +.. ++...|++||-
T Consensus 1 Y~C~~Cg~~~~~~~~~~irC~~CG~ 25 (32)
T PF03604_consen 1 YICGECGAEVELKPGDPIRCPECGH 25 (32)
T ss_dssp EBESSSSSSE-BSTSSTSSBSSSS-
T ss_pred CCCCcCCCeeEcCCCCcEECCcCCC
Confidence 555566542 222 66778888874
No 262
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=25.59 E-value=42 Score=28.41 Aligned_cols=22 Identities=27% Similarity=0.972 Sum_probs=14.1
Q ss_pred ccCCCCCccccCCCCCccccccCCcc
Q 001136 977 YHCPFCNLCRVGGGLGVDFFHCMTCN 1002 (1143)
Q Consensus 977 yhC~~CgiCr~g~~l~~~~~hC~~C~ 1002 (1143)
|.|+.||...+-+ -.|||..|.
T Consensus 1 y~Cd~C~~~pI~G----~R~~C~~C~ 22 (48)
T cd02341 1 FKCDSCGIEPIPG----TRYHCSECD 22 (48)
T ss_pred CCCCCCCCCcccc----ceEECCCCC
Confidence 6788888744332 257777765
No 263
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=25.51 E-value=33 Score=38.95 Aligned_cols=45 Identities=29% Similarity=0.668 Sum_probs=36.1
Q ss_pred cceeEeccccccccCCCCcccCCCCCccccCCCCCccccccCCcccccccc
Q 001136 958 SMAKYYCNICKFFDDERTVYHCPFCNLCRVGGGLGVDFFHCMTCNCCLGLK 1008 (1143)
Q Consensus 958 ~f~~y~C~~C~~~d~~~~~yhC~~CgiCr~g~~l~~~~~hC~~C~~C~~~~ 1008 (1143)
.-+--||.+|+-|..+ ..-||.-||-|-.+- --||.-=|-|+...
T Consensus 99 ~~~~SfC~KC~~pK~p-rTHHCsiC~kCVL~M-----DHHCPwinnCVG~~ 143 (309)
T KOG1313|consen 99 LENDSFCNKCNYPKSP-RTHHCSICNKCVLKM-----DHHCPWINNCVGAH 143 (309)
T ss_pred CccccHHhhcCCCCCC-CcchhhHHhhHhhcc-----ccCCchhhcccccc
Confidence 4455689999999777 578999999999874 46899888898764
No 264
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=25.48 E-value=32 Score=26.14 Aligned_cols=11 Identities=27% Similarity=1.138 Sum_probs=8.5
Q ss_pred eeEeccccccc
Q 001136 960 AKYYCNICKFF 970 (1143)
Q Consensus 960 ~~y~C~~C~~~ 970 (1143)
+.|||++|+.+
T Consensus 2 ~~~~C~~C~~~ 12 (35)
T smart00451 2 GGFYCKLCNVT 12 (35)
T ss_pred cCeEccccCCc
Confidence 56888888865
No 265
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=25.11 E-value=42 Score=34.36 Aligned_cols=10 Identities=30% Similarity=0.896 Sum_probs=6.3
Q ss_pred CcccCCCCCc
Q 001136 975 TVYHCPFCNL 984 (1143)
Q Consensus 975 ~~yhC~~Cgi 984 (1143)
..|.||.||-
T Consensus 106 ~~~~CP~Cgs 115 (135)
T PRK03824 106 AFLKCPKCGS 115 (135)
T ss_pred cCcCCcCCCC
Confidence 3456777774
No 266
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=25.08 E-value=28 Score=33.33 Aligned_cols=29 Identities=28% Similarity=0.591 Sum_probs=12.8
Q ss_pred eeEeccccccccCC---CCcccCCCCCccccC
Q 001136 960 AKYYCNICKFFDDE---RTVYHCPFCNLCRVG 988 (1143)
Q Consensus 960 ~~y~C~~C~~~d~~---~~~yhC~~CgiCr~g 988 (1143)
++|+|+.|.--.=. -+|++|..||.=-.|
T Consensus 34 ~ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~AG 65 (90)
T PF01780_consen 34 AKYTCPFCGKTSVKRVATGIWKCKKCGKKFAG 65 (90)
T ss_dssp S-BEESSSSSSEEEEEETTEEEETTTTEEEE-
T ss_pred CCCcCCCCCCceeEEeeeEEeecCCCCCEEeC
Confidence 44555555432211 455666666544333
No 267
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=24.91 E-value=34 Score=39.71 Aligned_cols=43 Identities=26% Similarity=0.569 Sum_probs=27.6
Q ss_pred CCCCccccccc-----cc--CCcceEecCCCCccchhhHHHHhccCCCCcCCCcc
Q 001136 1020 ETNCPICCDFL-----FT--SSETVRALPCGHYMHLACFQAYTCSHYTCPICSKS 1067 (1143)
Q Consensus 1020 ~~~CpIC~e~l-----f~--s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s 1067 (1143)
.+.||||...= -. .....+++-|+ -|-.+|--....||.|..+
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~Cs-----lC~teW~~~R~~C~~Cg~~ 233 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCS-----LCATEWHYVRVKCSHCEES 233 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcC-----CCCCcccccCccCCCCCCC
Confidence 45788887641 01 02334455444 6778887788999999864
No 268
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=24.57 E-value=26 Score=41.06 Aligned_cols=33 Identities=36% Similarity=0.811 Sum_probs=22.6
Q ss_pred Cccccccccccccccccccc--CCCCcccccc-cccCCcce
Q 001136 1000 TCNCCLGLKLLNHKCLEKCL--ETNCPICCDF-LFTSSETV 1037 (1143)
Q Consensus 1000 ~C~~C~~~~~~~H~C~e~~~--~~~CpIC~e~-lf~s~~~v 1037 (1143)
.||-|+-.. |..+++ .++||||.-+ +|+...++
T Consensus 317 pCGHilHl~-----CLknW~ERqQTCPICr~p~ifd~~~~~ 352 (491)
T COG5243 317 PCGHILHLH-----CLKNWLERQQTCPICRRPVIFDQSSPT 352 (491)
T ss_pred cccceeeHH-----HHHHHHHhccCCCcccCccccccCCCC
Confidence 477775543 777776 4689999888 56655543
No 269
>PHA00626 hypothetical protein
Probab=24.51 E-value=43 Score=29.27 Aligned_cols=33 Identities=24% Similarity=0.342 Sum_probs=19.7
Q ss_pred eeccccccccccCCCCCCCCCCCCcceeEecccccccc
Q 001136 934 MMCMHCLKIQAIGPNCTTPSCNGLSMAKYYCNICKFFD 971 (1143)
Q Consensus 934 ~~C~~C~~~q~~~~~C~~~~cc~~~f~~y~C~~C~~~d 971 (1143)
|.|..|+..+-+ .|.. | ...-.+|-|..|.+.+
T Consensus 1 m~CP~CGS~~Iv--rcg~--c-r~~snrYkCkdCGY~f 33 (59)
T PHA00626 1 MSCPKCGSGNIA--KEKT--M-RGWSDDYVCCDCGYND 33 (59)
T ss_pred CCCCCCCCceee--eece--e-cccCcceEcCCCCCee
Confidence 457777665433 3444 2 3445678888888764
No 270
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=24.18 E-value=23 Score=39.62 Aligned_cols=51 Identities=24% Similarity=0.619 Sum_probs=37.4
Q ss_pred CCcceeEeccccccccCCCCcccCCCCCccccCCCCCccccccCCccccccccc
Q 001136 956 GLSMAKYYCNICKFFDDERTVYHCPFCNLCRVGGGLGVDFFHCMTCNCCLGLKL 1009 (1143)
Q Consensus 956 ~~~f~~y~C~~C~~~d~~~~~yhC~~CgiCr~g~~l~~~~~hC~~C~~C~~~~~ 1009 (1143)
+..-+-.||..|-.|=. +..-||..|+-|..-.| +.+-||..|-.|+-.++
T Consensus 199 ~~EE~~~~~~~~~~Yv~-~~~~H~~~~~S~~~~~~--~~~~H~~~~~~~~~~~~ 249 (325)
T KOG4399|consen 199 PTEEGYRFCSPCQRYVS-LENQHCEHCNSCTSKDG--RKWNHCFLCKKCVKPSW 249 (325)
T ss_pred ccccceEEEeehHHHHH-HHhhhchhhcccccchh--HHHhHhHHhhhhcccce
Confidence 44556667988887733 45679999999877654 57888888888876654
No 271
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=23.83 E-value=28 Score=37.29 Aligned_cols=10 Identities=30% Similarity=1.115 Sum_probs=7.1
Q ss_pred CCcccCCCCC
Q 001136 974 RTVYHCPFCN 983 (1143)
Q Consensus 974 ~~~yhC~~Cg 983 (1143)
..-|+|+.||
T Consensus 115 ~~~Y~Cp~C~ 124 (178)
T PRK06266 115 NMFFFCPNCH 124 (178)
T ss_pred CCEEECCCCC
Confidence 5677777776
No 272
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=23.77 E-value=65 Score=36.70 Aligned_cols=27 Identities=30% Similarity=0.677 Sum_probs=15.1
Q ss_pred EEcCCCCCC----Ccccchhh------cccCCCCCCc
Q 001136 1098 ILCNDCEQK----GAARFHWL------YHKCGFCGSY 1124 (1143)
Q Consensus 1098 i~CndC~~~----s~~~~h~l------~~kC~~C~sy 1124 (1143)
..|-.|++. |+..-|.- -++|+.|+-+
T Consensus 216 F~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~Ks 252 (279)
T KOG2462|consen 216 FSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKS 252 (279)
T ss_pred ccCCcccchhcchHHHHHHHHhhcCCccccCcchhhH
Confidence 357777754 34444443 3466667643
No 273
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=23.68 E-value=34 Score=32.71 Aligned_cols=31 Identities=29% Similarity=0.729 Sum_probs=16.2
Q ss_pred ceeEeccccccc---cCCCCcccCCCCCccccCC
Q 001136 959 MAKYYCNICKFF---DDERTVYHCPFCNLCRVGG 989 (1143)
Q Consensus 959 f~~y~C~~C~~~---d~~~~~yhC~~CgiCr~g~ 989 (1143)
-++|.|+.|.-- -...+|++|..||.=-.|+
T Consensus 34 ~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGG 67 (90)
T PTZ00255 34 HAKYFCPFCGKHAVKRQAVGIWRCKGCKKTVAGG 67 (90)
T ss_pred hCCccCCCCCCCceeeeeeEEEEcCCCCCEEeCC
Confidence 345666666421 1115667777776555443
No 274
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=23.42 E-value=60 Score=41.39 Aligned_cols=54 Identities=20% Similarity=0.274 Sum_probs=30.5
Q ss_pred chhhhhhhhHHHHhhcCCChhhhcCcceEEcCCCCCCCcccchhhcccCCCCCCcccccc
Q 001136 1070 DMAIYFGMIDALLAAEELPEEYRNQVQDILCNDCEQKGAARFHWLYHKCGFCGSYNTRLI 1129 (1143)
Q Consensus 1070 ~m~~~~~~ld~~i~~~p~P~~y~~~~~~i~CndC~~~s~~~~h~l~~kC~~C~syNt~~~ 1129 (1143)
+.++....++.... ..+|----+.. .-.|++||..... .+..||.|||-|+.++
T Consensus 541 n~eal~~lv~~~~~-~~i~Yf~in~~-~~iC~~CG~~~~g----~~~~CP~CGs~~~ev~ 594 (623)
T PRK08271 541 SEEGYRKLLNIAAK-TGCNYFAFNVK-ITICNDCHHIDKR----TGKRCPICGSENIDYY 594 (623)
T ss_pred CHHHHHHHHHHHHH-cCCceEEeCCC-CccCCCCCCcCCC----CCcCCcCCCCcchhHH
Confidence 34444444444433 44543322333 3469999975321 3568999999876554
No 275
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=23.30 E-value=34 Score=32.81 Aligned_cols=31 Identities=29% Similarity=0.619 Sum_probs=18.3
Q ss_pred ceeEecccccccc---CCCCcccCCCCCccccCC
Q 001136 959 MAKYYCNICKFFD---DERTVYHCPFCNLCRVGG 989 (1143)
Q Consensus 959 f~~y~C~~C~~~d---~~~~~yhC~~CgiCr~g~ 989 (1143)
-++|.|+.|.--. -..+|++|..||.=-.|+
T Consensus 33 ~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGG 66 (91)
T TIGR00280 33 KAKYVCPFCGKKTVKRGSTGIWTCRKCGAKFAGG 66 (91)
T ss_pred hcCccCCCCCCCceEEEeeEEEEcCCCCCEEeCC
Confidence 3567777774211 116777777777655554
No 276
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=23.28 E-value=69 Score=36.93 Aligned_cols=75 Identities=28% Similarity=0.531 Sum_probs=50.6
Q ss_pred ccCC----CCcccCCCCCccccCCCCCccccccCCccccccccc----ccccccccccCCCCcccccccccCCcceEecC
Q 001136 970 FDDE----RTVYHCPFCNLCRVGGGLGVDFFHCMTCNCCLGLKL----LNHKCLEKCLETNCPICCDFLFTSSETVRALP 1041 (1143)
Q Consensus 970 ~d~~----~~~yhC~~CgiCr~g~~l~~~~~hC~~C~~C~~~~~----~~H~C~e~~~~~~CpIC~e~lf~s~~~v~~lp 1041 (1143)
|||- +-+=||..|-. .| +-..|| -+|++|.+-.- ..|--..|+..-.|..|-+- ..+|..++
T Consensus 169 WdDVLks~Ripg~Ces~~~--pg--~fAEFf--FKC~ah~~~~k~~aa~lhli~~N~~ni~C~~Ctdv----~~~vlvf~ 238 (446)
T KOG0006|consen 169 WDDVLKSKRIPGVCESCCT--PG--LFAEFF--FKCGAHPTSDKETAAALHLIATNSRNITCITCTDV----RSPVLVFQ 238 (446)
T ss_pred hhhhhhcccCccccccccC--Cc--chHhhe--ehhccCCCccccchhHHHHhhcccccceeEEecCC----ccceEEEe
Confidence 6664 45667776632 22 233444 26666665422 36666677777889999874 46778899
Q ss_pred CC--CccchhhHHHH
Q 001136 1042 CG--HYMHLACFQAY 1054 (1143)
Q Consensus 1042 Cg--H~fH~~Ci~~w 1054 (1143)
|. |..+..||.-|
T Consensus 239 Cns~HvtC~dCFr~y 253 (446)
T KOG0006|consen 239 CNSRHVTCLDCFRLY 253 (446)
T ss_pred cCCceeehHHhhhhH
Confidence 99 99999999877
No 277
>PHA01486 nonstructural protein
Probab=23.11 E-value=77 Score=23.74 Aligned_cols=24 Identities=25% Similarity=0.450 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHhccCCCCCHHHH
Q 001136 562 AISKDLEYLDMESAKLSDCDETFL 585 (1143)
Q Consensus 562 AiRkdL~~l~~~~~~l~~~D~~~l 585 (1143)
-||+||..|+-.++++..+..+.|
T Consensus 6 dirrdlrsiairlrklpassdqml 29 (32)
T PHA01486 6 DIRRDLRSIAIRLRKLPASSDQML 29 (32)
T ss_pred hHHHHHHHHHHHHHhCCCcHHHHH
Confidence 489999999999999986554443
No 278
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.06 E-value=63 Score=41.17 Aligned_cols=43 Identities=26% Similarity=0.670 Sum_probs=31.9
Q ss_pred CCcccccccccCCcceEecCCCC-ccchhhHHHHh--cc----CCCCcCCCccc
Q 001136 1022 NCPICCDFLFTSSETVRALPCGH-YMHLACFQAYT--CS----HYTCPICSKSL 1068 (1143)
Q Consensus 1022 ~CpIC~e~lf~s~~~v~~lpCgH-~fH~~Ci~~wl--~~----~~~CPiCr~s~ 1068 (1143)
.|+||-.. ...+..-.||| .....|..... .. ...||+|+..+
T Consensus 2 ~c~ic~~s----~~~~~~~s~~h~~v~~~~~~R~~~~~~~~~~~~~~~vcr~~~ 51 (669)
T KOG2231|consen 2 SCAICAFS----PDFVGRGSCGHNEVCATCVVRLRFELNNRKCSNECPVCRREV 51 (669)
T ss_pred CcceeecC----ccccccccccccccchhhhhhhhhhcccccccccCcccccce
Confidence 69999864 34445567999 89999988863 33 46689999866
No 279
>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=22.84 E-value=56 Score=28.41 Aligned_cols=30 Identities=20% Similarity=0.634 Sum_probs=20.0
Q ss_pred CCCcCCCccccchhhhhhhhHHHHhhcCCChhhhcCcceEEcCCCCCCC
Q 001136 1059 YTCPICSKSLGDMAIYFGMIDALLAAEELPEEYRNQVQDILCNDCEQKG 1107 (1143)
Q Consensus 1059 ~~CPiCr~s~~~m~~~~~~ld~~i~~~p~P~~y~~~~~~i~CndC~~~s 1107 (1143)
.+||.|..++. +|.... ...+.|.+||..-
T Consensus 3 ~~CP~CG~~ie-----------------v~~~~~--GeiV~Cp~CGael 32 (54)
T TIGR01206 3 FECPDCGAEIE-----------------LENPEL--GELVICDECGAEL 32 (54)
T ss_pred cCCCCCCCEEe-----------------cCCCcc--CCEEeCCCCCCEE
Confidence 58999997662 333333 4467899999653
No 280
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=22.66 E-value=64 Score=26.81 Aligned_cols=24 Identities=25% Similarity=0.592 Sum_probs=14.9
Q ss_pred eEecccccc-ccCC-CCcccCCCCCc
Q 001136 961 KYYCNICKF-FDDE-RTVYHCPFCNL 984 (1143)
Q Consensus 961 ~y~C~~C~~-~d~~-~~~yhC~~Cgi 984 (1143)
.|-|..|.- ++-+ ++...|++||-
T Consensus 2 ~Y~C~~Cg~~~~~~~~~~irC~~CG~ 27 (44)
T smart00659 2 IYICGECGRENEIKSKDVVRCRECGY 27 (44)
T ss_pred EEECCCCCCEeecCCCCceECCCCCc
Confidence 366666654 2222 67788888884
No 281
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=22.43 E-value=39 Score=36.89 Aligned_cols=81 Identities=15% Similarity=0.394 Sum_probs=48.7
Q ss_pred CCcceEecCCCCccchhhHHHHhccCCCC--cCCCccccchhhhhhhhHHHHhhcCCChhhhcCcceEEcCCCCCCCc-c
Q 001136 1033 SSETVRALPCGHYMHLACFQAYTCSHYTC--PICSKSLGDMAIYFGMIDALLAAEELPEEYRNQVQDILCNDCEQKGA-A 1109 (1143)
Q Consensus 1033 s~~~v~~lpCgH~fH~~Ci~~wl~~~~~C--PiCr~s~~~m~~~~~~ld~~i~~~p~P~~y~~~~~~i~CndC~~~s~-~ 1109 (1143)
.++++..-||....= -+-.++.-.| |-|++.|. ||-.+...+.|.. +-..+-+.|+-|+...- .
T Consensus 117 pGKKYVRCPCNCLLI----CK~sSqRIACPRpnCkRiIn--------L~p~~~~p~~P~~-~P~gcRV~CgHC~~tFLfn 183 (275)
T KOG4684|consen 117 PGKKYVRCPCNCLLI----CKASSQRIACPRPNCKRIIN--------LDPLIEKPRDPGT-APTGCRVKCGHCNETFLFN 183 (275)
T ss_pred CCCceeecCCcEEEE----EecccceeccCCCCcceeee--------cCCCCCCCCCCCC-CCcceEEEecCccceeehh
Confidence 345555567763210 0112345668 56876552 3444444555554 44457899999998763 4
Q ss_pred cchhhcccCCCCCCccc
Q 001136 1110 RFHWLYHKCGFCGSYNT 1126 (1143)
Q Consensus 1110 ~~h~l~~kC~~C~syNt 1126 (1143)
.||----+|++|.-|-+
T Consensus 184 t~tnaLArCPHCrKvSs 200 (275)
T KOG4684|consen 184 TLTNALARCPHCRKVSS 200 (275)
T ss_pred hHHHHHhcCCcccchhh
Confidence 56777779999987654
No 282
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=22.19 E-value=42 Score=34.90 Aligned_cols=18 Identities=28% Similarity=0.407 Sum_probs=15.1
Q ss_pred cccCCCCCCccccccccC
Q 001136 1115 YHKCGFCGSYNTRLIKND 1132 (1143)
Q Consensus 1115 ~~kC~~C~syNt~~~~~~ 1132 (1143)
...|+.|||-||+++..=
T Consensus 105 ~~~cp~c~s~~t~~~s~f 122 (146)
T TIGR02159 105 SVQCPRCGSADTTITSIF 122 (146)
T ss_pred CCcCCCCCCCCcEeecCC
Confidence 368999999999998654
No 283
>KOG3908 consensus Queuine-tRNA ribosyltransferase [RNA processing and modification]
Probab=22.11 E-value=2.1e+02 Score=33.05 Aligned_cols=113 Identities=15% Similarity=0.198 Sum_probs=83.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhccCCCCchHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhccCCHHHHHHHHHHHHhcC
Q 001136 113 KYSLEHEGESNLFDHLFQLLNSYTQNDESFPKELASCSRALQTSINQHMSKEEQQVFPLLTQHFSLEEQASLVWQFFCSI 192 (1143)
Q Consensus 113 ~le~EH~~i~~ll~~L~~~l~~~~~~~~~~~~eLa~~l~~l~~~L~~HL~~EE~~lfPLa~~~LS~eEw~~L~~~f~~si 192 (1143)
.++-|-.-..+.+=+|.+.+.....++. .-+.....+.=+-.-+.+|-..+|+.+||++..-|...=-++-...++..-
T Consensus 136 Si~iQnalG~DImMQLDdVV~~~ttg~r-veeAM~RsIRWlDRCi~Ah~R~d~Q~lFpIiQGGLd~~LR~~c~~em~kR~ 214 (396)
T KOG3908|consen 136 SIEIQNALGADIMMQLDDVVHTLTTGPR-VEEAMYRSIRWLDRCIMAHNRDDEQNLFPIIQGGLDEGLRAECIAEMLKRS 214 (396)
T ss_pred hHHHHHHhchhhhhhhhccccccCCchH-HHHHHHHHHHHHHHHHHHhcCccchhhhhhhhcccchHHHHHHHHHHHhcC
Confidence 4556666677777888888877765542 113345566666677889999999999999999999877777777777665
Q ss_pred ChhhhHhhhhhhccCCCHHHHHHHHHHhhhcCChhhH
Q 001136 193 PVNMMAEFLPWLSSSISTNEYQDMRKCLSKIVPEEKL 229 (1143)
Q Consensus 193 p~~~m~~~Lpwl~~~l~~eEr~~ll~~l~~~aP~~~~ 229 (1143)
++ +.-.+=|.++-...++-++.+.-....|+.++
T Consensus 215 ~~---G~AiGGLSGGEeK~~Fwr~V~~ct~~LP~dkP 248 (396)
T KOG3908|consen 215 VP---GIAIGGLSGGEEKSEFWRMVAFCTSSLPPDKP 248 (396)
T ss_pred CC---ceEecccCCCchHHHHHHHHHHHHccCCCCCC
Confidence 44 44567778888888888888888888887554
No 284
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=22.09 E-value=57 Score=28.72 Aligned_cols=28 Identities=25% Similarity=0.561 Sum_probs=21.5
Q ss_pred eEEcCCCCCCCcccchhhcccCCCCCCcccccc
Q 001136 1097 DILCNDCEQKGAARFHWLYHKCGFCGSYNTRLI 1129 (1143)
Q Consensus 1097 ~i~CndC~~~s~~~~h~l~~kC~~C~syNt~~~ 1129 (1143)
.+.|..||.. +.-.+.|..||.|+-+++
T Consensus 27 ~~~c~~cG~~-----~l~Hrvc~~cg~Y~g~~v 54 (57)
T COG0333 27 LSVCPNCGEY-----KLPHRVCLKCGYYKGRQV 54 (57)
T ss_pred ceeccCCCCc-----ccCceEcCCCCCccCeEe
Confidence 5789999963 333556999999998875
No 285
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=21.86 E-value=83 Score=35.50 Aligned_cols=110 Identities=14% Similarity=0.403 Sum_probs=58.9
Q ss_pred cccccCCcccccccccccccccccccCCCCccccccc--c--cCCcceEecCCCCccchhhHHHH--hccCCCCcC--CC
Q 001136 994 DFFHCMTCNCCLGLKLLNHKCLEKCLETNCPICCDFL--F--TSSETVRALPCGHYMHLACFQAY--TCSHYTCPI--CS 1065 (1143)
Q Consensus 994 ~~~hC~~C~~C~~~~~~~H~C~e~~~~~~CpIC~e~l--f--~s~~~v~~lpCgH~fH~~Ci~~w--l~~~~~CPi--Cr 1065 (1143)
....|..|+.=+.+....|.-+= .|+.|-|-- . ..++++.--||+ |+--- ..++-.||. |+
T Consensus 64 p~v~CrVCq~~I~i~gk~~QhVV-----kC~~CnEATPIr~aPpGKKYVRCPCN------CLLICk~sS~rIaCPRp~Ck 132 (256)
T PF09788_consen 64 PVVTCRVCQSLIDIEGKMHQHVV-----KCSVCNEATPIRNAPPGKKYVRCPCN------CLLICKSSSQRIACPRPNCK 132 (256)
T ss_pred ceEEeecCCceecccCccceeeE-----ECCCCCccccccCCCCCCeeEecCCc------eEEEeecccccccCCCCCCc
Confidence 34566666666666553333332 277776631 1 134455566777 43222 234567987 99
Q ss_pred ccccchhhhhhhhHHHHhhcCCChhh--hcCcceEEcCCCCCCCcc-cch-hhcccCCCCCC
Q 001136 1066 KSLGDMAIYFGMIDALLAAEELPEEY--RNQVQDILCNDCEQKGAA-RFH-WLYHKCGFCGS 1123 (1143)
Q Consensus 1066 ~s~~~m~~~~~~ld~~i~~~p~P~~y--~~~~~~i~CndC~~~s~~-~~h-~l~~kC~~C~s 1123 (1143)
+.+.-... .+.|..++. +.....+.|.-|....-- .+. ---.+|++|..
T Consensus 133 RiI~L~~~---------~~~p~~~~~~~~p~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrK 185 (256)
T PF09788_consen 133 RIINLGPS---------HQGPVTPPVPTQPGSCRVICGHCSNTFLFNTLTSNTLARCPHCRK 185 (256)
T ss_pred ceEEeCCc---------cCCCCCCCCCCCCCceeEECCCCCCcEeccCCCCCccccCCCCce
Confidence 87742221 122332222 233456899999987532 222 12348999973
No 286
>PF04710 Pellino: Pellino; InterPro: IPR006800 Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase [, , ].; PDB: 3EGB_B 3EGA_A.
Probab=21.79 E-value=31 Score=41.03 Aligned_cols=49 Identities=24% Similarity=0.513 Sum_probs=0.5
Q ss_pred cccCCCCccccccc-c---------cCCcceEecCCCCccchhhHHHHhc------cCCCCcCCCccc
Q 001136 1017 KCLETNCPICCDFL-F---------TSSETVRALPCGHYMHLACFQAYTC------SHYTCPICSKSL 1068 (1143)
Q Consensus 1017 ~~~~~~CpIC~e~l-f---------~s~~~v~~lpCgH~fH~~Ci~~wl~------~~~~CPiCr~s~ 1068 (1143)
|.+.-.|||=+..| | +...+..++.|||.+-.+ .|-. ...+||+|+..=
T Consensus 274 Na~rpQCPVglnTL~fp~~~~~~~~~~~qP~VYl~CGHVhG~h---~Wg~~~~~~~~~r~CPlCr~~g 338 (416)
T PF04710_consen 274 NAGRPQCPVGLNTLVFPSKSRKDVPDERQPWVYLNCGHVHGYH---NWGQDSDRDPRSRTCPLCRQVG 338 (416)
T ss_dssp S-------------------------------------------------------------------
T ss_pred hhcCCCCCcCCCccccccccccccccccCceeeccccceeeec---ccccccccccccccCCCccccC
Confidence 56677899987665 2 233456788999875543 4632 357899998644
No 287
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=21.51 E-value=30 Score=38.11 Aligned_cols=49 Identities=20% Similarity=0.481 Sum_probs=0.0
Q ss_pred ccCCCCcCCCccccchhhhhhhhHHHHhhcCCChhhhcCcc----eEEcCCCC
Q 001136 1056 CSHYTCPICSKSLGDMAIYFGMIDALLAAEELPEEYRNQVQ----DILCNDCE 1104 (1143)
Q Consensus 1056 ~~~~~CPiCr~s~~~m~~~~~~ld~~i~~~p~P~~y~~~~~----~i~CndC~ 1104 (1143)
....+||+|++.+..-...-+.+.-.-.....-+.|.+... .+.|..||
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~Cg 55 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCG 55 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCC
No 288
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=21.44 E-value=85 Score=35.45 Aligned_cols=50 Identities=20% Similarity=0.632 Sum_probs=31.6
Q ss_pred eeccccccccccCCCCCCCCCCCCcceeEeccccc--cccCCCCcccCCCCC
Q 001136 934 MMCMHCLKIQAIGPNCTTPSCNGLSMAKYYCNICK--FFDDERTVYHCPFCN 983 (1143)
Q Consensus 934 ~~C~~C~~~q~~~~~C~~~~cc~~~f~~y~C~~C~--~~d~~~~~yhC~~Cg 983 (1143)
-+|-+|-.--=-+..|....-|.-++..-.|-.|. .||-.-.+|.|.+|+
T Consensus 98 aiCDfCEawvCHgrkCl~~HaC~Cpl~da~C~EC~R~vw~hGGrif~CsfC~ 149 (314)
T PF06524_consen 98 AICDFCEAWVCHGRKCLSTHACTCPLQDAVCIECERGVWDHGGRIFKCSFCD 149 (314)
T ss_pred hhhccchhheeccccccccccccCcCCCcEeeeeecccccCCCeEEEeecCC
Confidence 35666654333333444433345567777777786 577777888888887
No 289
>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=21.13 E-value=37 Score=22.95 Aligned_cols=17 Identities=35% Similarity=0.800 Sum_probs=10.8
Q ss_pred CCCcCCCccccchhhhh
Q 001136 1059 YTCPICSKSLGDMAIYF 1075 (1143)
Q Consensus 1059 ~~CPiCr~s~~~m~~~~ 1075 (1143)
+.||+|++.+.....+.
T Consensus 1 ~~C~~C~~~~~~~~~l~ 17 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELR 17 (24)
T ss_dssp EE-SSTS-EESSHHHHH
T ss_pred CCCcCCCCcCCcHHHHH
Confidence 46999998887766554
No 290
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=21.00 E-value=36 Score=32.62 Aligned_cols=31 Identities=26% Similarity=0.496 Sum_probs=17.9
Q ss_pred ceeEeccccccc--c-CCCCcccCCCCCccccCC
Q 001136 959 MAKYYCNICKFF--D-DERTVYHCPFCNLCRVGG 989 (1143)
Q Consensus 959 f~~y~C~~C~~~--d-~~~~~yhC~~CgiCr~g~ 989 (1143)
-++|.|+.|.-- . -.-+|++|..||.=-.|+
T Consensus 34 ~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGG 67 (90)
T PRK03976 34 RAKHVCPVCGRPKVKRVGTGIWECRKCGAKFAGG 67 (90)
T ss_pred hcCccCCCCCCCceEEEEEEEEEcCCCCCEEeCC
Confidence 456777777321 1 115777777777655554
No 291
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=20.97 E-value=18 Score=45.64 Aligned_cols=30 Identities=37% Similarity=0.483 Sum_probs=20.4
Q ss_pred hhHhHhhcCCCHHHHHHHHHHhhhhcchhhHHHHHHHhhcCCC
Q 001136 738 SMLPWVTSALTQDEQSKLIDTWKHATKNTMFNEWLDECWKGPH 780 (1143)
Q Consensus 738 ~~lpWl~~~Ls~~E~~~~L~~~~~a~~~t~F~~WL~~w~~~~~ 780 (1143)
.++||. .++.+.++..|-+.|++ ||-+|--
T Consensus 121 mkl~ds-e~~~p~~y~~~~D~wk~------------ewekgvQ 150 (893)
T KOG0954|consen 121 MKLPDS-EHLNPDEYLDFADPWKQ------------EWEKGVQ 150 (893)
T ss_pred ccCccc-cccCccceeecCCccch------------hhhcccc
Confidence 567775 56677888777666655 7777753
No 292
>PRK11020 hypothetical protein; Provisional
Probab=20.85 E-value=5.1e+02 Score=26.04 Aligned_cols=76 Identities=14% Similarity=0.178 Sum_probs=48.5
Q ss_pred hhhHHHHhHHHHHHHHHHHHhhcCCccchHHHH---HHHHHHHHHHHHHHHHHHHhhhhhhhhh-hhhcCCHHHHHHHHH
Q 001136 374 QKHAEEESQFNDFRLLIESIQNEGAISTSAEFY---AKLCSHADQIMETIERHFHKVEVQVLPL-ARNHFSFKRQREILY 449 (1143)
Q Consensus 374 ~EH~~i~~~~~~f~~ll~~~~~~~~~~~~~~~~---~~L~~~l~~l~~~L~~Hf~kEE~qvfPL-~~k~~S~eEQ~~L~~ 449 (1143)
.|=....+.++.+++.+++....++..-.+.|. ++|..++.++-..=+.-+.+|-..|.-| +.+-+|-+||+.++.
T Consensus 5 ~Eiq~L~drLD~~~~Klaaa~~rgd~~~i~qf~~E~~~l~k~I~~lk~~~~~~lske~~~l~~lpF~R~iTK~EQADMGk 84 (118)
T PRK11020 5 NEIKRLSDRLDAIRHKLAAASLRGDAEKYAQFEKEKATLEAEIARLKEVQSQKLSKEAQKLMKLPFSRAITKKEQADMGK 84 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcchhccHHHHHhHHH
Confidence 355667788888988888877666533222232 2445555555555566677777776554 466777888887764
No 293
>PLN02400 cellulose synthase
Probab=20.74 E-value=56 Score=43.68 Aligned_cols=53 Identities=21% Similarity=0.431 Sum_probs=36.6
Q ss_pred cccccCCCCcccccccccCCcce---EecCCCCccchhhHHHHh--ccCCCCcCCCccc
Q 001136 1015 LEKCLETNCPICCDFLFTSSETV---RALPCGHYMHLACFQAYT--CSHYTCPICSKSL 1068 (1143)
Q Consensus 1015 ~e~~~~~~CpIC~e~lf~s~~~v---~~lpCgH~fH~~Ci~~wl--~~~~~CPiCr~s~ 1068 (1143)
..+...+.|-||.|++=...+.- ..--||--.++.|+ +|. ..++.||.|+..+
T Consensus 31 ~~~~~gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCY-EYERkeGnq~CPQCkTrY 88 (1085)
T PLN02400 31 LKNLNGQICQICGDDVGVTETGDVFVACNECAFPVCRPCY-EYERKDGTQCCPQCKTRY 88 (1085)
T ss_pred ccccCCceeeecccccCcCCCCCEEEEEccCCCccccchh-heecccCCccCcccCCcc
Confidence 44445668999999863333322 22347888999999 664 4578899998776
No 294
>COG3219 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.64 E-value=4e+02 Score=29.56 Aligned_cols=78 Identities=18% Similarity=0.118 Sum_probs=49.9
Q ss_pred HHHHHHhhhccCCCCchHHHHHHHHHHHHHHHHHHHHHHHhHHHHHhccCCHHHHHHHHHHHHhcCC---h---hhhHhh
Q 001136 127 HLFQLLNSYTQNDESFPKELASCSRALQTSINQHMSKEEQQVFPLLTQHFSLEEQASLVWQFFCSIP---V---NMMAEF 200 (1143)
Q Consensus 127 ~L~~~l~~~~~~~~~~~~eLa~~l~~l~~~L~~HL~~EE~~lfPLa~~~LS~eEw~~L~~~f~~sip---~---~~m~~~ 200 (1143)
+|..++..-.+++....++ ..+..+...++.-+.-=-..-||.++.+|++++|..+...|++.-. | .-.+.|
T Consensus 10 ~lA~aiRdg~a~~~~gia~--~RLaVY~rL~rNni~GfIdrcF~e~r~~~~~~~W~~lke~Fvre~ra~tPyFq~IageF 87 (237)
T COG3219 10 RLAQAIRDGEADPPPGIAQ--ERLAVYIRLFRNNIFGFIDRCFPELRQLFDEERWHRLKEGFVREGRAHTPYFQDIAGEF 87 (237)
T ss_pred HHHHHHhcccCCCCCCchH--HHHHHHHHHHHhhhHHHHHhcchHHHhhcCHHHHHHHHHHHHHhcccCCchHHHhhHHH
Confidence 3444444333333333322 4566667777777776677789999999999999999999996421 1 122456
Q ss_pred hhhhcc
Q 001136 201 LPWLSS 206 (1143)
Q Consensus 201 Lpwl~~ 206 (1143)
|.|.-+
T Consensus 88 l~~cq~ 93 (237)
T COG3219 88 LQYCQS 93 (237)
T ss_pred HHHHHh
Confidence 666643
No 295
>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=20.62 E-value=49 Score=29.51 Aligned_cols=15 Identities=33% Similarity=0.510 Sum_probs=12.9
Q ss_pred cccCCCCCCcccccc
Q 001136 1115 YHKCGFCGSYNTRLI 1129 (1143)
Q Consensus 1115 ~~kC~~C~syNt~~~ 1129 (1143)
.++|+.|+|.||+.-
T Consensus 5 ~~~CPRC~S~nTKFc 19 (63)
T PF02701_consen 5 PLPCPRCDSTNTKFC 19 (63)
T ss_pred CCCCCCcCCCCCEEE
Confidence 368999999999874
No 296
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=20.62 E-value=88 Score=36.42 Aligned_cols=47 Identities=28% Similarity=0.368 Sum_probs=30.4
Q ss_pred cCCCCcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCCc
Q 001136 1019 LETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSK 1066 (1143)
Q Consensus 1019 ~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~ 1066 (1143)
....|-.|.+.+ .+...++.-.|.+.|+..|-.---.+--.||-|..
T Consensus 329 ~~~~Cf~C~~~~-~~~~~y~C~~Ck~~FCldCDv~iHesLh~CpgCeh 375 (378)
T KOG2807|consen 329 GSRFCFACQGEL-LSSGRYRCESCKNVFCLDCDVFIHESLHNCPGCEH 375 (378)
T ss_pred CCcceeeecccc-CCCCcEEchhccceeeccchHHHHhhhhcCCCcCC
Confidence 344588887773 34344555668899999995443334466888853
No 297
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=20.59 E-value=33 Score=44.39 Aligned_cols=29 Identities=14% Similarity=0.070 Sum_probs=0.0
Q ss_pred HHHHhhhcCCCCCCHHHHHHHHHHHHHHH
Q 001136 827 EAEIRKVYRDPTLDPRRKAYLAQNLMTSR 855 (1143)
Q Consensus 827 ~~~i~~~~~~~~~~~~~k~~~~q~l~~~~ 855 (1143)
...+.-|+..|.+.=+.||.--=---|+|
T Consensus 581 ~~~l~~vn~~sg~~ir~raptrIG~RmGR 609 (900)
T PF03833_consen 581 KNALEAVNELSGFKIRDRAPTRIGARMGR 609 (900)
T ss_dssp -----------------------------
T ss_pred ccHHHHHHHhCCCEecccCcceeecccCC
Confidence 34555666666666666665433333443
No 298
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=20.52 E-value=58 Score=32.49 Aligned_cols=9 Identities=22% Similarity=0.353 Sum_probs=5.2
Q ss_pred ccCCCCCcc
Q 001136 977 YHCPFCNLC 985 (1143)
Q Consensus 977 yhC~~CgiC 985 (1143)
++||.||--
T Consensus 89 ~~CP~Cgs~ 97 (117)
T PRK00564 89 GVCEKCHSK 97 (117)
T ss_pred CcCcCCCCC
Confidence 357777643
No 299
>PRK05978 hypothetical protein; Provisional
Probab=20.50 E-value=51 Score=34.43 Aligned_cols=33 Identities=21% Similarity=0.682 Sum_probs=26.3
Q ss_pred cccCCCCcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcCCCccc
Q 001136 1017 KCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPICSKSL 1068 (1143)
Q Consensus 1017 ~~~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPiCr~s~ 1068 (1143)
......||-|.+ |+.|+ .|++.+.+||.|+..+
T Consensus 30 rGl~grCP~CG~--------------G~LF~-----g~Lkv~~~C~~CG~~~ 62 (148)
T PRK05978 30 RGFRGRCPACGE--------------GKLFR-----AFLKPVDHCAACGEDF 62 (148)
T ss_pred HHHcCcCCCCCC--------------Ccccc-----cccccCCCccccCCcc
Confidence 345678999986 56665 6888999999999887
No 300
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=20.47 E-value=58 Score=32.39 Aligned_cols=9 Identities=44% Similarity=1.268 Sum_probs=5.4
Q ss_pred cccCCCCCc
Q 001136 976 VYHCPFCNL 984 (1143)
Q Consensus 976 ~yhC~~Cgi 984 (1143)
.|.||.||-
T Consensus 86 ~~~CP~Cgs 94 (115)
T TIGR00100 86 LYRCPKCHG 94 (115)
T ss_pred CccCcCCcC
Confidence 456666663
No 301
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=20.46 E-value=37 Score=41.39 Aligned_cols=13 Identities=23% Similarity=1.073 Sum_probs=9.6
Q ss_pred CCcceeEeccccc
Q 001136 956 GLSMAKYYCNICK 968 (1143)
Q Consensus 956 ~~~f~~y~C~~C~ 968 (1143)
|-+|..|||..|+
T Consensus 210 ~D~~~~w~C~~C~ 222 (464)
T KOG4323|consen 210 GDPFYEWFCDVCN 222 (464)
T ss_pred cCccceEeehhhc
Confidence 4577888888776
No 302
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 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 DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=20.44 E-value=50 Score=34.31 Aligned_cols=35 Identities=26% Similarity=0.632 Sum_probs=24.1
Q ss_pred CCcccCCCCCccccCCCCCccccccCCccccccccccccccc
Q 001136 974 RTVYHCPFCNLCRVGGGLGVDFFHCMTCNCCLGLKLLNHKCL 1015 (1143)
Q Consensus 974 ~~~yhC~~CgiCr~g~~l~~~~~hC~~C~~C~~~~~~~H~C~ 1015 (1143)
.....|..|.+=|. ..-.||..||.|+..- +|.|.
T Consensus 46 ~~~~~C~~C~~~kp-----~Rs~HC~~C~~CV~~~--DHHC~ 80 (174)
T PF01529_consen 46 GELKYCSTCKIIKP-----PRSHHCRVCNRCVLRF--DHHCP 80 (174)
T ss_pred CCCEECcccCCcCC-----Ccceeccccccccccc--cccch
Confidence 56667777776544 3479999999997643 55554
No 303
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.36 E-value=70 Score=39.77 Aligned_cols=48 Identities=25% Similarity=0.593 Sum_probs=30.1
Q ss_pred cccceeeccccccccccCCCCCCCCCCCCcce------eEeccccccccCCCCcccCCCCCcc
Q 001136 929 KATSEMMCMHCLKIQAIGPNCTTPSCNGLSMA------KYYCNICKFFDDERTVYHCPFCNLC 985 (1143)
Q Consensus 929 ~~~~~~~C~~C~~~q~~~~~C~~~~cc~~~f~------~y~C~~C~~~d~~~~~yhC~~CgiC 985 (1143)
-..+.++|..|+..- .|++ |+..+. .-.|..|.+- .+-+..|+.||--
T Consensus 209 Gya~~~~C~~Cg~~~----~C~~---C~~~l~~h~~~~~l~Ch~Cg~~--~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 209 GYSKNLLCRSCGYIL----CCPN---CDVSLTYHKKEGKLRCHYCGYQ--EPIPKTCPQCGSE 262 (505)
T ss_pred cCCCeeEhhhCcCcc----CCCC---CCCceEEecCCCeEEcCCCcCc--CCCCCCCCCCCCC
Confidence 345688999999876 7988 465553 2335555421 1345677777754
No 304
>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=20.35 E-value=39 Score=31.69 Aligned_cols=9 Identities=67% Similarity=1.863 Sum_probs=2.3
Q ss_pred CcccCCCCC
Q 001136 975 TVYHCPFCN 983 (1143)
Q Consensus 975 ~~yhC~~Cg 983 (1143)
..|.||+||
T Consensus 21 ~~F~CPfC~ 29 (81)
T PF05129_consen 21 KVFDCPFCN 29 (81)
T ss_dssp S----TTT-
T ss_pred ceEcCCcCC
Confidence 455666665
No 305
>KOG3896 consensus Dynactin, subunit p62 [Cell motility]
Probab=20.26 E-value=39 Score=39.16 Aligned_cols=86 Identities=23% Similarity=0.571 Sum_probs=0.0
Q ss_pred ccccCCCCCccccccCCcccccccccccccccccccCCCCcccccccccCCcceEecCCCCccchhhHHHHhccCCCCcC
Q 001136 984 LCRVGGGLGVDFFHCMTCNCCLGLKLLNHKCLEKCLETNCPICCDFLFTSSETVRALPCGHYMHLACFQAYTCSHYTCPI 1063 (1143)
Q Consensus 984 iCr~g~~l~~~~~hC~~C~~C~~~~~~~H~C~e~~~~~~CpIC~e~lf~s~~~v~~lpCgH~fH~~Ci~~wl~~~~~CPi 1063 (1143)
+||--.. -+|+.|++-.+++| -||-|+|.+-......+.-.|. +.+-||-
T Consensus 26 FCRyC~k--------lrc~~Cv~hEvdsh---------fCp~CLEn~ps~EArlKKn~CA-------------nCfDCP~ 75 (449)
T KOG3896|consen 26 FCRYCFK--------LRCDDCVLHEVDSH---------FCPRCLENSPSPEARLKKNKCA-------------NCFDCPK 75 (449)
T ss_pred eeecccc--------cccccccccccccc---------cchhhccCCCchHHHhhhcccc-------------ccccCcc
Q ss_pred CCccccchhhhhhhhHHHHhhcCCChhhhcCcceEEcCCCCCCCcccchhhcccCCCC
Q 001136 1064 CSKSLGDMAIYFGMIDALLAAEELPEEYRNQVQDILCNDCEQKGAARFHWLYHKCGFC 1121 (1143)
Q Consensus 1064 Cr~s~~~m~~~~~~ld~~i~~~p~P~~y~~~~~~i~CndC~~~s~~~~h~l~~kC~~C 1121 (1143)
|..++....... .+.+|.+ -++++.+- .+|+-|++|
T Consensus 76 C~htLSaRa~~~--------stq~p~d-------------paktt~kk-~yYL~C~~C 111 (449)
T KOG3896|consen 76 CAHTLSARAEND--------STQLPDD-------------PAKTTMKK-NYYLVCQYC 111 (449)
T ss_pred hhhhhhhhcccc--------cccCCCC-------------hhhhhhhh-eeEEeeeee
No 306
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=20.11 E-value=53 Score=24.03 Aligned_cols=23 Identities=26% Similarity=0.491 Sum_probs=15.0
Q ss_pred eeeccccccc-cccCCCCCCCCCCCCc
Q 001136 933 EMMCMHCLKI-QAIGPNCTTPSCNGLS 958 (1143)
Q Consensus 933 ~~~C~~C~~~-q~~~~~C~~~~cc~~~ 958 (1143)
.+.|..|+++ .+....|++ ||..
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~~---CG~~ 25 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCPN---CGAK 25 (26)
T ss_pred cCCCcccCCcCCcccccChh---hCCC
Confidence 4678888876 334466887 4654
No 307
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=20.07 E-value=85 Score=39.76 Aligned_cols=54 Identities=24% Similarity=0.356 Sum_probs=29.7
Q ss_pred chhhhhhhhHHHHhhcCCChhhhcCcceEEcCCCCCCCcccchhhcccCCCCCCcccccc
Q 001136 1070 DMAIYFGMIDALLAAEELPEEYRNQVQDILCNDCEQKGAARFHWLYHKCGFCGSYNTRLI 1129 (1143)
Q Consensus 1070 ~m~~~~~~ld~~i~~~p~P~~y~~~~~~i~CndC~~~s~~~~h~l~~kC~~C~syNt~~~ 1129 (1143)
+.++....++...... ++----+.. .-.|++||-.+.- +..+|+.|||-|..++
T Consensus 499 n~eal~~lv~~a~~~~-i~Y~~~n~~-~~~C~~CG~~g~~----~~~~CP~Cgs~~~~~~ 552 (579)
T TIGR02487 499 DPEALKDITKKAMKNG-IGYFGINPP-VDVCEDCGYTGEG----LNDKCPKCGSHDIEVI 552 (579)
T ss_pred CHHHHHHHHHHHHhcC-CceEEeccC-CccCCCCCCCCCC----CCCcCcCCCCccceeh
Confidence 3444444444444332 443322233 3469999964432 1258999999886554
Done!