Query 028376
Match_columns 210
No_of_seqs 225 out of 2198
Neff 8.7
Searched_HMMs 46136
Date Fri Mar 29 10:33:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028376.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028376hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1002 Nucleotide excision re 99.9 1.6E-26 3.4E-31 197.7 7.2 156 23-200 535-691 (791)
2 KOG1001 Helicase-like transcri 99.6 3.3E-16 7.1E-21 142.5 3.4 146 15-200 447-592 (674)
3 KOG0389 SNF2 family DNA-depend 99.4 2.6E-13 5.7E-18 122.2 7.6 78 119-210 758-835 (941)
4 KOG0298 DEAD box-containing he 99.2 6.8E-12 1.5E-16 117.8 5.0 124 14-194 1143-1266(1394)
5 PLN03208 E3 ubiquitin-protein 99.2 1.9E-11 4.2E-16 94.5 5.0 71 18-89 12-87 (193)
6 KOG0823 Predicted E3 ubiquitin 99.1 4.7E-11 1E-15 94.0 4.1 59 21-88 44-102 (230)
7 KOG0317 Predicted E3 ubiquitin 99.1 6.6E-11 1.4E-15 95.8 3.1 56 21-88 236-291 (293)
8 PHA02929 N1R/p28-like protein; 99.1 1.1E-10 2.5E-15 93.7 4.1 53 18-81 168-227 (238)
9 KOG0320 Predicted E3 ubiquitin 99.1 6.5E-11 1.4E-15 89.5 2.5 57 19-86 126-183 (187)
10 KOG0385 Chromatin remodeling c 99.0 5.6E-10 1.2E-14 100.9 6.9 72 119-199 468-539 (971)
11 PF13639 zf-RING_2: Ring finge 99.0 1E-10 2.2E-15 70.0 1.4 42 25-77 1-44 (44)
12 PF13923 zf-C3HC4_2: Zinc fing 99.0 1.3E-10 2.8E-15 67.6 1.8 39 27-76 1-39 (39)
13 PF15227 zf-C3HC4_4: zinc fing 99.0 1.5E-10 3.3E-15 68.3 2.1 42 27-76 1-42 (42)
14 PF13920 zf-C3HC4_3: Zinc fing 99.0 1.9E-10 4.2E-15 70.6 1.7 46 24-81 2-48 (50)
15 PLN03142 Probable chromatin-re 99.0 2.2E-09 4.7E-14 102.2 8.7 68 120-195 469-536 (1033)
16 PF00097 zf-C3HC4: Zinc finger 98.9 8.2E-10 1.8E-14 64.9 2.9 41 27-76 1-41 (41)
17 PHA02926 zinc finger-like prot 98.9 1.3E-09 2.8E-14 85.4 4.3 61 16-81 162-230 (242)
18 KOG2164 Predicted E3 ubiquitin 98.9 1.5E-09 3.2E-14 94.2 4.4 69 13-89 176-244 (513)
19 PF14634 zf-RING_5: zinc-RING 98.8 2.4E-09 5.2E-14 64.0 3.1 42 26-78 1-44 (44)
20 smart00504 Ubox Modified RING 98.8 3.4E-09 7.3E-14 68.1 3.7 51 25-87 2-52 (63)
21 KOG0387 Transcription-coupled 98.8 9.5E-09 2.1E-13 93.4 7.7 68 119-194 527-595 (923)
22 cd00162 RING RING-finger (Real 98.8 4.2E-09 9.2E-14 62.4 2.9 44 26-79 1-44 (45)
23 PF13445 zf-RING_UBOX: RING-ty 98.7 9.5E-09 2.1E-13 60.7 2.4 40 27-74 1-43 (43)
24 KOG0391 SNF2 family DNA-depend 98.7 4.3E-08 9.2E-13 92.3 7.7 68 119-194 1257-1324(1958)
25 KOG0384 Chromodomain-helicase 98.7 3.6E-08 7.9E-13 93.1 6.5 68 121-196 682-749 (1373)
26 PF12678 zf-rbx1: RING-H2 zinc 98.6 3.2E-08 7E-13 65.6 3.4 44 23-77 18-73 (73)
27 TIGR00599 rad18 DNA repair pro 98.6 2.6E-08 5.5E-13 85.8 3.3 51 23-85 25-75 (397)
28 KOG0978 E3 ubiquitin ligase in 98.5 3E-08 6.4E-13 90.0 1.4 54 23-87 642-695 (698)
29 TIGR00570 cdk7 CDK-activating 98.5 8.2E-08 1.8E-12 79.6 3.9 53 23-85 2-58 (309)
30 smart00184 RING Ring finger. E 98.5 8.3E-08 1.8E-12 54.7 2.8 39 27-76 1-39 (39)
31 COG5243 HRD1 HRD ubiquitin lig 98.5 8.4E-08 1.8E-12 80.4 3.7 51 21-82 284-346 (491)
32 KOG4439 RNA polymerase II tran 98.5 3E-07 6.5E-12 83.0 7.2 70 118-194 725-794 (901)
33 COG5574 PEX10 RING-finger-cont 98.5 5.3E-08 1.1E-12 78.2 2.2 53 22-85 213-266 (271)
34 KOG0287 Postreplication repair 98.5 3.7E-08 8E-13 81.5 1.2 50 24-85 23-72 (442)
35 COG5432 RAD18 RING-finger-cont 98.4 7.4E-08 1.6E-12 78.2 1.8 49 23-83 24-72 (391)
36 PF12861 zf-Apc11: Anaphase-pr 98.4 1.6E-07 3.5E-12 63.2 3.2 53 23-83 20-84 (85)
37 KOG0392 SNF2 family DNA-depend 98.4 5.9E-07 1.3E-11 85.2 7.9 74 119-199 1307-1395(1549)
38 PF14835 zf-RING_6: zf-RING of 98.4 5.5E-08 1.2E-12 61.6 0.3 49 25-86 8-56 (65)
39 PF04564 U-box: U-box domain; 98.4 2.6E-07 5.6E-12 61.3 3.2 53 23-86 3-55 (73)
40 COG5540 RING-finger-containing 98.4 2.1E-07 4.6E-12 76.1 2.4 49 24-82 323-373 (374)
41 COG0553 HepA Superfamily II DN 98.3 1.8E-06 3.8E-11 81.7 8.7 69 119-195 688-760 (866)
42 KOG4628 Predicted E3 ubiquitin 98.3 6.1E-07 1.3E-11 75.6 3.2 48 26-83 231-280 (348)
43 KOG4172 Predicted E3 ubiquitin 98.2 2.4E-07 5.2E-12 56.4 0.0 47 24-81 7-54 (62)
44 KOG0390 DNA repair protein, SN 98.2 5.3E-06 1.1E-10 76.7 7.7 71 117-194 573-643 (776)
45 KOG0383 Predicted helicase [Ge 98.2 8.6E-07 1.9E-11 81.0 2.3 66 120-194 613-678 (696)
46 KOG2879 Predicted E3 ubiquitin 98.1 1.5E-06 3.2E-11 70.3 2.9 51 22-81 237-287 (298)
47 KOG0802 E3 ubiquitin ligase [P 98.1 2.1E-06 4.6E-11 77.7 2.6 52 22-84 289-344 (543)
48 PRK04914 ATP-dependent helicas 98.0 2E-05 4.2E-10 75.3 8.5 67 119-195 476-543 (956)
49 KOG2177 Predicted E3 ubiquitin 98.0 3.1E-06 6.6E-11 70.1 1.9 45 22-78 11-55 (386)
50 KOG0824 Predicted E3 ubiquitin 98.0 3.6E-06 7.8E-11 68.9 1.8 50 23-83 6-55 (324)
51 KOG4265 Predicted E3 ubiquitin 97.9 5.5E-06 1.2E-10 69.5 2.2 49 22-82 288-337 (349)
52 KOG1000 Chromatin remodeling p 97.9 3.8E-05 8.3E-10 67.4 7.3 69 120-194 470-540 (689)
53 KOG4159 Predicted E3 ubiquitin 97.9 6.3E-06 1.4E-10 71.2 2.2 66 5-82 65-130 (398)
54 COG1111 MPH1 ERCC4-like helica 97.9 7.6E-05 1.7E-09 65.6 8.4 82 118-199 344-428 (542)
55 KOG1015 Transcription regulato 97.9 3.2E-05 6.9E-10 72.4 6.3 68 119-194 1123-1212(1567)
56 PRK13766 Hef nuclease; Provisi 97.8 9.2E-05 2E-09 69.8 9.6 79 119-197 344-424 (773)
57 KOG0388 SNF2 family DNA-depend 97.7 4.8E-05 1E-09 69.3 5.5 68 119-194 1025-1092(1185)
58 KOG0828 Predicted E3 ubiquitin 97.7 1.3E-05 2.7E-10 69.8 1.6 49 23-81 570-634 (636)
59 KOG0386 Chromatin remodeling c 97.7 5.3E-05 1.2E-09 71.1 5.7 70 120-197 708-777 (1157)
60 PF14447 Prok-RING_4: Prokaryo 97.7 1.8E-05 4E-10 48.6 1.4 49 23-85 6-54 (55)
61 KOG0311 Predicted E3 ubiquitin 97.6 5.7E-06 1.2E-10 69.2 -1.6 51 23-83 42-92 (381)
62 KOG1785 Tyrosine kinase negati 97.6 0.0001 2.3E-09 62.7 4.8 53 24-86 369-421 (563)
63 cd00079 HELICc Helicase superf 97.5 0.00071 1.5E-08 48.7 8.5 67 122-196 12-78 (131)
64 PF11789 zf-Nse: Zinc-finger o 97.5 3.8E-05 8.3E-10 48.2 1.3 45 22-75 9-53 (57)
65 COG5152 Uncharacterized conser 97.5 3.8E-05 8.1E-10 59.4 1.1 45 24-80 196-240 (259)
66 KOG2660 Locus-specific chromos 97.4 5.9E-05 1.3E-09 62.7 1.1 51 22-83 13-63 (331)
67 PF11793 FANCL_C: FANCL C-term 97.4 0.00012 2.6E-09 48.0 2.1 59 24-82 2-67 (70)
68 KOG1039 Predicted E3 ubiquitin 97.3 0.00013 2.9E-09 61.9 2.8 60 18-81 155-221 (344)
69 KOG3039 Uncharacterized conser 97.3 0.00023 5E-09 56.9 4.0 65 17-92 214-281 (303)
70 PF14570 zf-RING_4: RING/Ubox 97.3 0.00013 2.8E-09 43.8 2.0 44 27-80 1-47 (48)
71 KOG1813 Predicted E3 ubiquitin 97.3 8.4E-05 1.8E-09 60.9 0.9 45 25-81 242-286 (313)
72 PF04641 Rtf2: Rtf2 RING-finge 97.2 0.00042 9E-09 57.1 4.5 57 22-90 111-170 (260)
73 KOG4739 Uncharacterized protei 97.2 0.00017 3.7E-09 57.7 1.5 48 25-85 4-52 (233)
74 smart00744 RINGv The RING-vari 97.1 0.0006 1.3E-08 41.4 3.2 43 26-77 1-49 (49)
75 KOG0804 Cytoplasmic Zn-finger 97.1 0.00023 5E-09 61.4 1.9 49 20-81 171-222 (493)
76 KOG0331 ATP-dependent RNA heli 97.1 0.002 4.2E-08 57.6 7.7 69 120-195 322-390 (519)
77 KOG0333 U5 snRNP-like RNA heli 97.1 0.0024 5.1E-08 56.8 8.0 66 120-195 501-566 (673)
78 KOG1493 Anaphase-promoting com 97.1 0.0001 2.2E-09 48.2 -0.3 52 23-82 19-82 (84)
79 KOG1734 Predicted RING-contain 97.0 0.00018 3.8E-09 58.3 -0.2 55 22-85 222-285 (328)
80 KOG0297 TNF receptor-associate 96.9 0.0004 8.6E-09 60.5 1.9 51 23-85 20-71 (391)
81 COG5175 MOT2 Transcriptional r 96.9 0.00052 1.1E-08 57.4 2.2 58 23-90 13-73 (480)
82 KOG0825 PHD Zn-finger protein 96.9 0.00019 4.1E-09 65.8 -0.5 51 23-84 122-174 (1134)
83 KOG4692 Predicted E3 ubiquitin 96.9 0.00049 1.1E-08 57.8 1.8 50 20-81 418-467 (489)
84 PTZ00110 helicase; Provisional 96.8 0.0063 1.4E-07 55.4 8.6 68 121-196 360-427 (545)
85 KOG0827 Predicted E3 ubiquitin 96.8 0.00062 1.4E-08 57.9 1.9 47 24-78 4-53 (465)
86 KOG4275 Predicted E3 ubiquitin 96.8 0.00021 4.5E-09 58.5 -1.2 42 24-81 300-342 (350)
87 KOG3800 Predicted E3 ubiquitin 96.8 0.00092 2E-08 54.8 2.5 50 26-85 2-55 (300)
88 KOG1571 Predicted E3 ubiquitin 96.7 0.00062 1.3E-08 57.4 1.3 44 24-82 305-348 (355)
89 COG5219 Uncharacterized conser 96.7 0.00075 1.6E-08 63.2 1.9 68 5-81 1444-1523(1525)
90 COG5194 APC11 Component of SCF 96.7 0.001 2.2E-08 43.9 1.9 33 39-82 50-82 (88)
91 KOG1016 Predicted DNA helicase 96.6 0.0026 5.6E-08 59.0 4.6 70 121-199 702-789 (1387)
92 KOG1645 RING-finger-containing 96.6 0.0011 2.3E-08 56.8 1.7 54 24-86 4-61 (463)
93 TIGR00603 rad25 DNA repair hel 96.6 0.0094 2E-07 55.7 8.0 61 121-194 479-539 (732)
94 PRK04837 ATP-dependent RNA hel 96.6 0.012 2.6E-07 51.7 8.3 67 121-197 240-306 (423)
95 PRK11192 ATP-dependent RNA hel 96.5 0.017 3.6E-07 50.9 8.9 57 136-198 241-297 (434)
96 KOG4185 Predicted E3 ubiquitin 96.2 0.0037 8E-08 52.3 3.1 47 24-80 3-54 (296)
97 COG5236 Uncharacterized conser 96.2 0.0034 7.3E-08 52.8 2.7 51 20-80 57-107 (493)
98 PRK11776 ATP-dependent RNA hel 96.2 0.025 5.4E-07 50.2 8.3 66 121-196 227-292 (460)
99 COG5222 Uncharacterized conser 96.2 0.0028 6E-08 52.3 1.9 43 25-78 275-318 (427)
100 COG0513 SrmB Superfamily II DN 96.2 0.029 6.3E-07 50.7 8.6 65 122-196 259-323 (513)
101 PF10272 Tmpp129: Putative tra 96.2 0.0066 1.4E-07 52.0 4.2 66 22-87 269-357 (358)
102 PRK04537 ATP-dependent RNA hel 96.1 0.029 6.2E-07 51.4 8.3 67 121-197 242-308 (572)
103 COG5220 TFB3 Cdk activating ki 96.1 0.0012 2.5E-08 52.8 -0.6 54 21-84 7-67 (314)
104 PRK05298 excinuclease ABC subu 96.0 0.039 8.5E-07 51.3 9.0 69 120-196 428-496 (652)
105 KOG1941 Acetylcholine receptor 96.0 0.0026 5.7E-08 54.2 1.2 48 24-80 365-415 (518)
106 PRK01297 ATP-dependent RNA hel 96.0 0.036 7.8E-07 49.5 8.5 66 121-196 320-385 (475)
107 KOG2114 Vacuolar assembly/sort 96.0 0.0032 6.9E-08 58.5 1.5 41 25-79 841-881 (933)
108 KOG4445 Uncharacterized conser 96.0 0.0031 6.8E-08 52.0 1.2 73 11-83 100-188 (368)
109 KOG0334 RNA helicase [RNA proc 95.9 0.02 4.3E-07 54.6 6.3 66 120-194 596-661 (997)
110 KOG1814 Predicted E3 ubiquitin 95.9 0.0067 1.5E-07 52.1 2.9 52 23-77 183-236 (445)
111 TIGR00631 uvrb excinuclease AB 95.8 0.053 1.2E-06 50.4 8.6 70 119-196 423-492 (655)
112 KOG3970 Predicted E3 ubiquitin 95.8 0.012 2.6E-07 46.7 3.8 67 12-81 37-105 (299)
113 KOG2932 E3 ubiquitin ligase in 95.7 0.0048 1E-07 51.2 1.4 42 26-80 92-133 (389)
114 PRK11057 ATP-dependent DNA hel 95.7 0.058 1.2E-06 49.8 8.4 65 123-197 223-287 (607)
115 PHA02558 uvsW UvsW helicase; P 95.6 0.06 1.3E-06 48.5 8.2 67 123-197 329-395 (501)
116 PF05883 Baculo_RING: Baculovi 95.6 0.0083 1.8E-07 44.0 2.0 36 21-56 23-66 (134)
117 TIGR00614 recQ_fam ATP-depende 95.5 0.079 1.7E-06 47.3 8.7 67 122-197 211-277 (470)
118 PRK10590 ATP-dependent RNA hel 95.5 0.079 1.7E-06 47.1 8.5 55 136-196 241-295 (456)
119 TIGR01389 recQ ATP-dependent D 95.5 0.074 1.6E-06 48.9 8.5 68 121-198 209-276 (591)
120 PF05290 Baculo_IE-1: Baculovi 95.4 0.017 3.8E-07 42.1 3.3 63 14-84 70-135 (140)
121 KOG3002 Zn finger protein [Gen 95.2 0.015 3.2E-07 48.8 2.8 45 21-81 45-91 (299)
122 KOG0826 Predicted E3 ubiquitin 95.2 0.0092 2E-07 49.9 1.4 54 21-85 297-350 (357)
123 PRK11634 ATP-dependent RNA hel 95.2 0.12 2.6E-06 48.0 8.8 67 121-197 230-296 (629)
124 KOG2817 Predicted E3 ubiquitin 95.2 0.016 3.6E-07 49.6 2.9 49 24-80 334-384 (394)
125 KOG0330 ATP-dependent RNA heli 95.0 0.051 1.1E-06 46.9 5.4 66 122-197 286-351 (476)
126 PF10367 Vps39_2: Vacuolar sor 95.0 0.0093 2E-07 41.9 0.8 32 22-53 76-108 (109)
127 PTZ00424 helicase 45; Provisio 94.8 0.18 3.8E-06 43.7 8.6 55 136-196 263-317 (401)
128 PHA03096 p28-like protein; Pro 94.8 0.018 3.9E-07 48.0 2.0 34 25-58 179-219 (284)
129 KOG2034 Vacuolar sorting prote 94.7 0.016 3.6E-07 54.2 1.7 36 23-58 816-852 (911)
130 KOG2930 SCF ubiquitin ligase, 94.6 0.0095 2.1E-07 41.4 0.1 29 40-79 78-106 (114)
131 PLN00206 DEAD-box ATP-dependen 94.6 0.18 3.9E-06 45.7 8.2 69 121-197 350-419 (518)
132 KOG0332 ATP-dependent RNA heli 94.5 0.17 3.7E-06 43.6 7.2 67 121-197 315-381 (477)
133 KOG0335 ATP-dependent RNA heli 94.4 0.085 1.8E-06 46.8 5.3 69 120-194 312-385 (482)
134 PRK12900 secA preprotein trans 94.3 0.2 4.4E-06 48.3 7.9 64 121-194 581-644 (1025)
135 KOG0340 ATP-dependent RNA heli 94.2 0.21 4.6E-06 42.8 7.1 65 124-195 239-303 (442)
136 KOG0328 Predicted ATP-dependen 94.2 0.15 3.4E-06 42.3 6.1 63 123-195 253-315 (400)
137 TIGR03714 secA2 accessory Sec 94.1 0.21 4.6E-06 47.0 7.8 65 120-192 406-470 (762)
138 smart00490 HELICc helicase sup 94.0 0.13 2.9E-06 33.2 4.7 37 155-197 2-38 (82)
139 PRK12904 preprotein translocas 93.9 0.27 5.9E-06 46.8 8.1 66 121-196 413-478 (830)
140 PRK12898 secA preprotein trans 93.9 0.34 7.4E-06 45.0 8.5 64 121-194 456-519 (656)
141 KOG0339 ATP-dependent RNA heli 93.9 0.13 2.8E-06 46.0 5.4 68 119-195 450-517 (731)
142 TIGR00963 secA preprotein tran 93.8 0.34 7.3E-06 45.6 8.3 65 121-195 388-452 (745)
143 KOG1815 Predicted E3 ubiquitin 93.7 0.073 1.6E-06 47.3 3.7 63 21-86 67-131 (444)
144 COG1061 SSL2 DNA or RNA helica 93.6 0.3 6.5E-06 43.4 7.4 67 121-197 267-333 (442)
145 PRK13107 preprotein translocas 93.6 0.27 5.8E-06 47.0 7.3 67 121-195 432-498 (908)
146 KOG4367 Predicted Zn-finger pr 93.4 0.042 9.2E-07 47.8 1.7 35 23-58 3-37 (699)
147 KOG0348 ATP-dependent RNA heli 93.4 0.31 6.8E-06 43.9 7.1 68 121-194 406-495 (708)
148 KOG1428 Inhibitor of type V ad 93.4 0.068 1.5E-06 52.9 3.1 62 20-82 3482-3545(3738)
149 PF00271 Helicase_C: Helicase 93.4 0.13 2.9E-06 33.5 3.8 34 158-197 1-34 (78)
150 PLN03137 ATP-dependent DNA hel 93.3 0.4 8.6E-06 47.1 8.1 54 137-196 677-730 (1195)
151 PRK13104 secA preprotein trans 93.3 0.36 7.9E-06 46.2 7.7 67 121-195 427-493 (896)
152 KOG0354 DEAD-box like helicase 92.9 0.57 1.2E-05 43.9 8.3 78 120-197 393-475 (746)
153 KOG1812 Predicted E3 ubiquitin 92.9 0.06 1.3E-06 46.9 1.9 59 22-85 144-207 (384)
154 KOG1100 Predicted E3 ubiquitin 92.9 0.08 1.7E-06 42.1 2.4 40 27-82 161-201 (207)
155 PRK09200 preprotein translocas 92.6 0.56 1.2E-05 44.6 7.9 65 121-193 411-475 (790)
156 PHA02825 LAP/PHD finger-like p 92.5 0.15 3.2E-06 38.5 3.2 50 23-83 7-61 (162)
157 PF07191 zinc-ribbons_6: zinc- 92.5 0.016 3.5E-07 37.6 -1.6 40 25-81 2-41 (70)
158 PF11496 HDA2-3: Class II hist 92.4 0.24 5.1E-06 41.7 4.7 57 119-175 93-152 (297)
159 PF12906 RINGv: RING-variant d 92.1 0.15 3.3E-06 30.4 2.4 41 27-76 1-47 (47)
160 KOG1952 Transcription factor N 92.0 0.17 3.6E-06 47.6 3.7 56 21-80 188-246 (950)
161 TIGR02621 cas3_GSU0051 CRISPR- 91.9 0.92 2E-05 43.4 8.5 64 122-194 255-323 (844)
162 PHA02862 5L protein; Provision 91.8 0.17 3.6E-06 37.6 2.8 50 24-84 2-56 (156)
163 KOG0327 Translation initiation 91.8 0.66 1.4E-05 40.0 6.7 76 121-208 250-338 (397)
164 KOG2231 Predicted E3 ubiquitin 91.5 1.3 2.8E-05 41.1 8.7 163 26-205 2-182 (669)
165 PF07800 DUF1644: Protein of u 91.4 0.28 6.1E-06 37.0 3.6 62 23-85 1-95 (162)
166 PF14569 zf-UDP: Zinc-binding 90.9 0.24 5.1E-06 32.7 2.5 55 19-83 4-64 (80)
167 KOG3113 Uncharacterized conser 90.8 0.23 5E-06 40.3 2.9 52 25-89 112-166 (293)
168 KOG0345 ATP-dependent RNA heli 90.5 0.93 2E-05 40.3 6.5 66 119-194 238-305 (567)
169 PF02891 zf-MIZ: MIZ/SP-RING z 90.2 0.22 4.7E-06 30.2 1.8 48 25-79 3-50 (50)
170 KOG0342 ATP-dependent RNA heli 90.1 0.74 1.6E-05 41.0 5.6 65 121-194 314-378 (543)
171 PRK12906 secA preprotein trans 89.8 1.3 2.8E-05 42.2 7.3 64 121-194 423-486 (796)
172 TIGR03158 cas3_cyano CRISPR-as 89.7 1.7 3.7E-05 37.4 7.6 57 127-189 259-317 (357)
173 TIGR01587 cas3_core CRISPR-ass 89.4 2.1 4.6E-05 36.4 8.0 66 122-196 207-278 (358)
174 KOG3899 Uncharacterized conser 89.1 0.17 3.7E-06 41.8 1.0 47 43-89 325-373 (381)
175 PF03854 zf-P11: P-11 zinc fin 88.9 0.22 4.8E-06 29.7 1.1 32 39-81 14-46 (50)
176 KOG3039 Uncharacterized conser 88.4 0.3 6.6E-06 39.5 1.9 33 23-56 42-74 (303)
177 KOG0336 ATP-dependent RNA heli 88.1 0.63 1.4E-05 40.8 3.8 66 121-195 449-514 (629)
178 KOG4362 Transcriptional regula 88.1 0.12 2.6E-06 47.7 -0.6 52 24-84 21-72 (684)
179 KOG1940 Zn-finger protein [Gen 88.0 0.34 7.4E-06 40.1 2.0 45 23-78 157-204 (276)
180 PF08746 zf-RING-like: RING-li 87.6 0.39 8.4E-06 28.1 1.6 40 27-76 1-43 (43)
181 KOG0341 DEAD-box protein abstr 87.5 2 4.2E-05 37.6 6.3 67 122-199 408-474 (610)
182 COG5109 Uncharacterized conser 87.4 0.39 8.4E-06 40.2 2.0 50 25-82 337-388 (396)
183 KOG1123 RNA polymerase II tran 87.4 2.9 6.2E-05 37.8 7.4 62 120-194 525-586 (776)
184 PRK10689 transcription-repair 86.3 3.3 7.2E-05 41.3 8.1 54 140-199 809-864 (1147)
185 KOG3161 Predicted E3 ubiquitin 86.3 0.23 5.1E-06 45.3 0.2 33 24-56 11-46 (861)
186 TIGR00580 mfd transcription-re 85.8 4.1 8.9E-05 39.7 8.3 52 140-197 660-713 (926)
187 COG0514 RecQ Superfamily II DN 85.0 4.8 0.0001 37.1 7.9 54 137-196 227-280 (590)
188 TIGR03817 DECH_helic helicase/ 84.7 3.7 8E-05 39.0 7.3 52 140-197 271-330 (742)
189 KOG0351 ATP-dependent DNA heli 84.1 1.9 4.1E-05 41.9 5.1 66 125-196 470-535 (941)
190 KOG0338 ATP-dependent RNA heli 84.0 2.1 4.6E-05 38.6 5.0 51 140-196 426-476 (691)
191 KOG0343 RNA Helicase [RNA proc 83.7 5.6 0.00012 36.4 7.5 65 120-194 297-363 (758)
192 PF07975 C1_4: TFIIH C1-like d 83.4 0.92 2E-05 27.6 1.8 40 27-77 2-50 (51)
193 KOG3268 Predicted E3 ubiquitin 83.4 1.2 2.6E-05 34.3 2.8 59 23-82 164-229 (234)
194 PRK13767 ATP-dependent helicas 82.7 7.4 0.00016 37.7 8.6 64 125-196 271-340 (876)
195 PF10571 UPF0547: Uncharacteri 82.6 0.67 1.5E-05 24.0 0.9 22 26-47 2-24 (26)
196 KOG0347 RNA helicase [RNA proc 82.6 1.8 3.9E-05 39.4 4.0 49 140-194 463-511 (731)
197 COG5183 SSM4 Protein involved 82.2 0.92 2E-05 42.7 2.2 57 21-86 9-71 (1175)
198 cd03028 GRX_PICOT_like Glutare 82.0 5.7 0.00012 26.8 5.6 34 140-173 7-46 (90)
199 KOG4284 DEAD box protein [Tran 81.9 2.2 4.8E-05 39.6 4.4 62 127-194 259-320 (980)
200 KOG0326 ATP-dependent RNA heli 81.9 1.5 3.3E-05 37.2 3.2 66 120-195 306-371 (459)
201 PLN02189 cellulose synthase 81.0 1.5 3.3E-05 42.6 3.2 54 20-83 30-89 (1040)
202 PLN02436 cellulose synthase A 79.7 1.7 3.7E-05 42.3 3.1 55 19-83 31-91 (1094)
203 PLN02638 cellulose synthase A 79.3 1.7 3.8E-05 42.3 3.0 54 19-82 12-71 (1079)
204 PLN02400 cellulose synthase 79.1 1.4 3E-05 43.1 2.3 55 19-83 31-91 (1085)
205 TIGR01054 rgy reverse gyrase. 78.6 9.6 0.00021 38.2 8.0 62 123-199 314-378 (1171)
206 KOG3579 Predicted E3 ubiquitin 78.3 1.4 3E-05 36.5 1.8 48 21-75 265-316 (352)
207 TIGR01970 DEAH_box_HrpB ATP-de 78.2 12 0.00025 36.2 8.2 50 140-195 209-261 (819)
208 PRK10917 ATP-dependent DNA hel 77.3 17 0.00037 34.2 9.0 67 121-196 454-531 (681)
209 cd03418 GRX_GRXb_1_3_like Glut 77.1 12 0.00026 23.7 5.8 45 142-192 1-46 (75)
210 PF06906 DUF1272: Protein of u 76.8 1.8 3.8E-05 26.8 1.5 44 25-81 6-52 (57)
211 PLN02195 cellulose synthase A 76.6 2.7 5.8E-05 40.7 3.4 52 21-82 3-60 (977)
212 TIGR00365 monothiol glutaredox 76.2 14 0.0003 25.4 6.2 34 140-173 11-50 (97)
213 PF04216 FdhE: Protein involve 76.1 0.46 1E-05 39.7 -1.6 44 24-79 172-220 (290)
214 TIGR00643 recG ATP-dependent D 74.5 17 0.00038 33.8 8.1 68 123-198 433-510 (630)
215 PRK11664 ATP-dependent RNA hel 74.2 15 0.00032 35.5 7.7 50 139-194 211-263 (812)
216 TIGR00622 ssl1 transcription f 73.7 2.7 5.9E-05 30.0 2.1 43 24-77 55-110 (112)
217 KOG0346 RNA helicase [RNA proc 73.4 6.5 0.00014 35.0 4.7 50 140-195 268-317 (569)
218 TIGR01562 FdhE formate dehydro 73.2 0.99 2.1E-05 38.1 -0.3 51 24-88 184-239 (305)
219 PRK11448 hsdR type I restricti 72.7 17 0.00037 36.3 7.9 62 125-194 683-753 (1123)
220 PRK10824 glutaredoxin-4; Provi 71.3 9.3 0.0002 27.4 4.4 33 140-172 14-52 (115)
221 COG3813 Uncharacterized protei 71.0 2.3 5E-05 27.7 1.1 46 25-83 6-54 (84)
222 PF10235 Cript: Microtubule-as 69.0 3.2 7E-05 28.4 1.5 35 25-80 45-79 (90)
223 PRK09401 reverse gyrase; Revie 68.8 15 0.00033 36.9 6.7 62 122-199 315-379 (1176)
224 PRK03564 formate dehydrogenase 68.3 2.1 4.5E-05 36.2 0.6 52 23-88 186-241 (309)
225 KOG0337 ATP-dependent RNA heli 67.8 6.9 0.00015 34.6 3.6 68 119-195 243-310 (529)
226 PF04710 Pellino: Pellino; In 67.6 1.7 3.8E-05 37.6 0.0 43 39-83 361-403 (416)
227 PF15616 TerY-C: TerY-C metal 67.3 4.2 9E-05 29.9 1.9 42 24-83 77-118 (131)
228 PF10764 Gin: Inhibitor of sig 66.6 3.8 8.2E-05 24.3 1.3 30 26-57 1-30 (46)
229 PLN02915 cellulose synthase A 66.4 5.4 0.00012 39.0 2.9 50 23-82 14-69 (1044)
230 PF01363 FYVE: FYVE zinc finge 66.3 2.4 5.3E-05 27.1 0.5 35 21-55 6-43 (69)
231 KOG0350 DEAD-box ATP-dependent 66.2 12 0.00026 33.9 4.8 70 122-201 415-488 (620)
232 KOG3053 Uncharacterized conser 65.8 5.5 0.00012 32.6 2.5 56 22-80 18-81 (293)
233 KOG3842 Adaptor protein Pellin 65.5 5.6 0.00012 33.6 2.5 44 39-84 374-417 (429)
234 PF14446 Prok-RING_1: Prokaryo 65.5 7.2 0.00016 24.0 2.4 33 23-55 4-39 (54)
235 PRK10638 glutaredoxin 3; Provi 65.3 23 0.0005 23.2 5.2 32 142-173 3-35 (83)
236 cd03027 GRX_DEP Glutaredoxin ( 65.2 27 0.00059 22.1 5.4 34 142-175 2-36 (73)
237 smart00064 FYVE Protein presen 64.5 5.8 0.00013 25.2 2.0 35 21-55 7-44 (68)
238 KOG0309 Conserved WD40 repeat- 63.3 5.4 0.00012 37.6 2.3 36 23-58 1027-1063(1081)
239 PF13240 zinc_ribbon_2: zinc-r 63.2 1.5 3.3E-05 21.9 -0.7 9 71-79 14-22 (23)
240 TIGR00596 rad1 DNA repair prot 63.0 16 0.00036 35.1 5.5 46 120-165 268-320 (814)
241 PF05605 zf-Di19: Drought indu 62.5 2.3 5.1E-05 25.9 -0.1 40 23-79 1-40 (54)
242 cd01518 RHOD_YceA Member of th 62.3 23 0.00049 24.0 4.9 38 138-175 59-97 (101)
243 KOG4718 Non-SMC (structural ma 61.6 3.5 7.5E-05 32.7 0.6 45 23-78 180-224 (235)
244 KOG4185 Predicted E3 ubiquitin 61.3 1.6 3.5E-05 36.4 -1.3 45 25-79 208-265 (296)
245 KOG0006 E3 ubiquitin-protein l 61.2 7.8 0.00017 32.8 2.6 49 9-58 205-256 (446)
246 KOG2068 MOT2 transcription fac 60.5 7.8 0.00017 32.9 2.6 48 25-83 250-300 (327)
247 PTZ00062 glutaredoxin; Provisi 60.2 71 0.0015 25.3 7.9 58 127-194 102-165 (204)
248 PRK11131 ATP-dependent RNA hel 60.1 41 0.00088 34.2 7.7 62 123-191 270-334 (1294)
249 cd01520 RHOD_YbbB Member of th 59.5 32 0.0007 24.6 5.5 52 123-175 70-122 (128)
250 cd03029 GRX_hybridPRX5 Glutare 58.6 19 0.0004 22.8 3.7 33 141-173 1-34 (72)
251 cd03031 GRX_GRX_like Glutaredo 58.5 50 0.0011 24.7 6.4 44 142-191 1-51 (147)
252 KOG2807 RNA polymerase II tran 57.4 6.6 0.00014 33.3 1.6 43 24-77 330-374 (378)
253 PF04710 Pellino: Pellino; In 57.4 3.5 7.5E-05 35.8 0.0 52 23-82 276-340 (416)
254 KOG2979 Protein involved in DN 57.2 7.4 0.00016 31.8 1.8 49 18-75 170-218 (262)
255 KOG0825 PHD Zn-finger protein 57.2 6.9 0.00015 37.1 1.8 52 23-79 95-152 (1134)
256 PRK12326 preprotein translocas 56.9 49 0.0011 31.6 7.3 51 121-173 410-460 (764)
257 KOG3799 Rab3 effector RIM1 and 56.8 13 0.00028 27.4 2.9 32 22-58 63-94 (169)
258 TIGR00615 recR recombination p 56.8 71 0.0015 25.2 7.2 68 121-193 120-192 (195)
259 cd01524 RHOD_Pyr_redox Member 56.3 22 0.00048 23.5 3.9 38 138-175 49-86 (90)
260 COG5387 Chaperone required for 55.4 44 0.00095 27.2 5.9 59 125-196 111-182 (264)
261 PRK10329 glutaredoxin-like pro 54.8 52 0.0011 21.7 5.4 33 142-174 2-35 (81)
262 PF09413 DUF2007: Domain of un 54.8 26 0.00056 22.0 3.8 31 143-173 2-32 (67)
263 cd00291 SirA_YedF_YeeD SirA, Y 54.4 51 0.0011 20.5 5.6 45 127-171 13-57 (69)
264 TIGR03190 benz_CoA_bzdN benzoy 54.3 61 0.0013 28.1 7.2 64 122-193 300-368 (377)
265 PF04423 Rad50_zn_hook: Rad50 53.9 8.3 0.00018 23.4 1.3 26 10-36 7-32 (54)
266 smart00450 RHOD Rhodanese Homo 53.8 38 0.00082 22.0 4.8 42 134-175 50-92 (100)
267 PF13361 UvrD_C: UvrD-like hel 53.1 61 0.0013 26.7 6.9 52 123-175 59-111 (351)
268 cd00065 FYVE FYVE domain; Zinc 53.0 10 0.00022 23.0 1.6 32 24-55 2-36 (57)
269 TIGR01967 DEAH_box_HrpA ATP-de 52.9 50 0.0011 33.6 7.1 63 122-191 262-327 (1283)
270 PRK01415 hypothetical protein; 52.8 70 0.0015 26.2 6.9 37 137-173 168-205 (247)
271 KOG0349 Putative DEAD-box RNA 52.5 31 0.00067 30.9 5.0 53 138-196 503-558 (725)
272 PRK12903 secA preprotein trans 52.1 58 0.0013 31.7 7.0 52 120-173 408-459 (925)
273 TIGR02189 GlrX-like_plant Glut 51.9 26 0.00057 24.1 3.8 34 140-173 7-41 (99)
274 COG2247 LytB Putative cell wal 51.6 45 0.00097 28.4 5.6 68 121-198 61-128 (337)
275 PF14471 DUF4428: Domain of un 51.1 16 0.00034 22.2 2.2 29 26-55 1-30 (51)
276 PF10497 zf-4CXXC_R1: Zinc-fin 50.7 15 0.00033 25.8 2.4 34 44-79 37-70 (105)
277 COG0068 HypF Hydrogenase matur 50.4 9.4 0.0002 35.8 1.6 56 23-81 100-184 (750)
278 TIGR00595 priA primosomal prot 49.9 50 0.0011 29.9 6.2 67 125-199 185-315 (505)
279 cd01528 RHOD_2 Member of the R 49.8 54 0.0012 22.1 5.1 38 138-175 56-94 (101)
280 COG1202 Superfamily II helicas 49.8 67 0.0015 30.0 6.8 69 121-195 417-489 (830)
281 KOG2113 Predicted RNA binding 49.1 12 0.00027 31.6 1.9 41 24-78 343-384 (394)
282 TIGR03191 benz_CoA_bzdO benzoy 49.1 99 0.0021 27.5 7.8 50 122-175 348-402 (430)
283 PRK13280 N-glycosylase/DNA lya 48.8 19 0.00041 29.8 3.0 41 122-167 130-170 (269)
284 PF13248 zf-ribbon_3: zinc-rib 48.7 3.9 8.5E-05 21.0 -0.7 7 72-78 18-24 (26)
285 PF10879 DUF2674: Protein of u 48.2 37 0.00081 20.9 3.5 35 137-172 2-36 (67)
286 cd01521 RHOD_PspE2 Member of t 48.2 33 0.00071 23.7 3.8 38 138-175 62-101 (110)
287 PHA02653 RNA helicase NPH-II; 48.1 93 0.002 29.5 7.7 46 140-193 395-442 (675)
288 PRK09751 putative ATP-dependen 48.1 89 0.0019 32.4 8.0 51 140-196 244-327 (1490)
289 PRK09694 helicase Cas3; Provis 47.6 1.3E+02 0.0029 29.4 8.9 62 125-194 547-615 (878)
290 PF06844 DUF1244: Protein of u 47.0 13 0.00028 23.8 1.4 14 46-59 11-24 (68)
291 KOG1812 Predicted E3 ubiquitin 47.0 9.8 0.00021 33.2 1.1 35 22-56 304-342 (384)
292 PF00412 LIM: LIM domain; Int 46.6 16 0.00034 22.0 1.8 30 25-54 27-56 (58)
293 PF07503 zf-HYPF: HypF finger; 46.2 20 0.00043 19.9 1.9 32 47-81 1-32 (35)
294 TIGR02196 GlrX_YruB Glutaredox 45.9 68 0.0015 19.5 5.6 31 143-173 2-33 (74)
295 cd01523 RHOD_Lact_B Member of 45.6 31 0.00068 23.2 3.4 38 138-175 59-96 (100)
296 PRK02362 ski2-like helicase; P 45.4 98 0.0021 29.4 7.6 49 139-195 242-328 (737)
297 COG0556 UvrB Helicase subunit 45.3 1.6E+02 0.0035 27.2 8.4 70 121-198 429-498 (663)
298 PRK11595 DNA utilization prote 45.0 19 0.00042 28.8 2.5 40 25-81 6-45 (227)
299 COG4357 Zinc finger domain con 44.8 16 0.00034 25.3 1.6 50 26-83 37-93 (105)
300 COG1592 Rubrerythrin [Energy p 44.7 16 0.00035 28.0 1.9 23 9-31 119-141 (166)
301 cd01449 TST_Repeat_2 Thiosulfa 44.6 85 0.0018 21.6 5.6 37 138-174 76-113 (118)
302 PF12773 DZR: Double zinc ribb 44.6 17 0.00036 21.5 1.6 16 68-83 27-42 (50)
303 TIGR02263 benz_CoA_red_C benzo 44.5 96 0.0021 27.0 6.9 64 123-194 309-378 (380)
304 COG3310 Uncharacterized protei 44.5 77 0.0017 24.2 5.4 21 146-166 91-111 (196)
305 COG1205 Distinct helicase fami 44.3 84 0.0018 30.6 7.0 70 122-199 290-367 (851)
306 PRK00142 putative rhodanese-re 43.8 96 0.0021 26.3 6.6 39 137-175 168-207 (314)
307 PF10083 DUF2321: Uncharacteri 43.6 17 0.00036 27.5 1.7 26 44-83 27-52 (158)
308 TIGR02181 GRX_bact Glutaredoxi 43.4 72 0.0016 20.3 4.8 32 144-175 2-34 (79)
309 PRK00076 recR recombination pr 43.3 1.6E+02 0.0035 23.2 7.3 68 121-194 120-192 (196)
310 cd01542 PBP1_TreR_like Ligand- 43.3 81 0.0018 24.7 6.0 19 151-169 16-34 (259)
311 PF02318 FYVE_2: FYVE-type zin 43.0 13 0.00028 26.6 1.1 31 23-53 53-87 (118)
312 PRK13844 recombination protein 41.8 1.3E+02 0.0028 23.8 6.6 69 120-194 123-196 (200)
313 COG3172 NadR Predicted ATPase/ 41.8 56 0.0012 25.2 4.3 25 149-173 141-165 (187)
314 cd03419 GRX_GRXh_1_2_like Glut 41.6 45 0.00098 21.3 3.5 32 142-173 1-33 (82)
315 COG1201 Lhr Lhr-like helicases 41.0 1.4E+02 0.003 29.0 7.7 67 123-197 238-305 (814)
316 TIGR02190 GlrX-dom Glutaredoxi 41.0 53 0.0012 21.2 3.8 34 140-173 7-41 (79)
317 cd01534 4RHOD_Repeat_3 Member 40.8 41 0.00088 22.4 3.3 37 139-175 55-91 (95)
318 cd02066 GRX_family Glutaredoxi 40.8 81 0.0018 18.9 5.8 33 142-174 1-34 (72)
319 cd01529 4RHOD_Repeats Member o 40.5 1.1E+02 0.0023 20.3 5.7 38 138-175 54-92 (96)
320 PF07209 DUF1415: Protein of u 40.4 1.7E+02 0.0037 22.7 6.9 73 68-165 17-99 (174)
321 PF10146 zf-C4H2: Zinc finger- 40.3 20 0.00044 29.0 1.9 26 47-83 196-221 (230)
322 PF14353 CpXC: CpXC protein 40.2 24 0.00051 25.5 2.1 17 67-83 35-51 (128)
323 smart00132 LIM Zinc-binding do 40.2 20 0.00043 19.3 1.4 10 27-36 2-11 (39)
324 PRK01172 ski2-like helicase; P 40.1 1.4E+02 0.003 28.0 7.7 49 139-195 235-310 (674)
325 PRK12902 secA preprotein trans 39.7 1.3E+02 0.0027 29.6 7.2 51 121-173 422-472 (939)
326 cd01519 RHOD_HSP67B2 Member of 39.5 50 0.0011 22.3 3.7 38 138-175 64-102 (106)
327 PF09419 PGP_phosphatase: Mito 39.4 1.7E+02 0.0038 22.4 6.9 63 122-194 62-129 (168)
328 PRK14701 reverse gyrase; Provi 38.8 75 0.0016 33.3 6.0 59 125-199 320-381 (1638)
329 TIGR00376 DNA helicase, putati 38.8 1.6E+02 0.0034 27.7 7.7 56 116-173 178-234 (637)
330 TIGR03249 KdgD 5-dehydro-4-deo 37.9 88 0.0019 26.1 5.5 33 162-194 37-69 (296)
331 cd00408 DHDPS-like Dihydrodipi 37.9 82 0.0018 25.8 5.3 44 150-194 18-61 (281)
332 TIGR02260 benz_CoA_red_B benzo 37.8 1.8E+02 0.004 25.6 7.7 67 123-193 338-410 (413)
333 TIGR01407 dinG_rel DnaQ family 37.8 1.5E+02 0.0033 28.8 7.7 62 124-195 659-724 (850)
334 cd01447 Polysulfide_ST Polysul 37.7 34 0.00073 23.0 2.5 38 138-175 59-97 (103)
335 PRK13111 trpA tryptophan synth 37.6 2.3E+02 0.005 23.2 8.3 51 120-170 69-123 (258)
336 smart00734 ZnF_Rad18 Rad18-lik 36.5 12 0.00025 19.3 -0.0 12 71-82 2-13 (26)
337 PRK05580 primosome assembly pr 36.4 52 0.0011 31.1 4.2 50 146-199 432-483 (679)
338 PLN02417 dihydrodipicolinate s 36.2 81 0.0018 26.1 5.0 43 151-194 23-65 (280)
339 PF10281 Ish1: Putative stress 36.1 24 0.00053 19.7 1.3 35 146-193 1-35 (38)
340 KOG4218 Nuclear hormone recept 35.9 27 0.00059 30.0 2.0 56 22-79 13-76 (475)
341 COG4098 comFA Superfamily II D 35.7 16 0.00034 31.6 0.7 32 21-53 36-68 (441)
342 cd01533 4RHOD_Repeat_2 Member 35.5 1.2E+02 0.0027 20.6 5.2 38 138-175 64-103 (109)
343 PF00462 Glutaredoxin: Glutare 35.4 1E+02 0.0022 18.5 5.3 31 144-174 2-33 (60)
344 PF09889 DUF2116: Uncharacteri 35.1 20 0.00043 22.5 0.9 17 70-86 3-19 (59)
345 PRK12899 secA preprotein trans 34.9 1.6E+02 0.0035 29.1 7.2 51 121-173 551-601 (970)
346 cd00953 KDG_aldolase KDG (2-ke 34.8 1.1E+02 0.0023 25.3 5.5 35 160-194 29-63 (279)
347 smart00647 IBR In Between Ring 34.4 7.8 0.00017 23.9 -1.1 33 23-55 17-58 (64)
348 TIGR00143 hypF [NiFe] hydrogen 34.3 23 0.0005 33.6 1.6 57 23-82 67-152 (711)
349 KOG0344 ATP-dependent RNA heli 34.3 1.8E+02 0.0038 27.0 7.0 68 118-195 369-437 (593)
350 PF13086 AAA_11: AAA domain; P 34.2 2E+02 0.0044 21.9 6.9 57 117-173 23-94 (236)
351 cd00158 RHOD Rhodanese Homolog 34.2 77 0.0017 20.1 3.8 40 136-175 46-86 (89)
352 PF10740 DUF2529: Protein of u 33.9 46 0.00099 25.7 2.8 34 138-171 80-115 (172)
353 PF01206 TusA: Sulfurtransfera 33.8 1.1E+02 0.0024 19.1 4.4 44 127-170 14-57 (70)
354 PHA03050 glutaredoxin; Provisi 33.8 93 0.002 21.8 4.3 32 140-171 12-47 (108)
355 cd01448 TST_Repeat_1 Thiosulfa 33.7 1E+02 0.0022 21.4 4.6 39 137-175 76-116 (122)
356 PRK12901 secA preprotein trans 33.6 95 0.0021 31.0 5.5 51 121-173 611-661 (1112)
357 PLN02248 cellulose synthase-li 33.5 29 0.00064 34.4 2.1 34 41-85 148-181 (1135)
358 PRK03170 dihydrodipicolinate s 33.5 1.1E+02 0.0024 25.3 5.4 32 163-194 34-65 (292)
359 PRK04023 DNA polymerase II lar 33.3 37 0.00081 33.4 2.7 50 23-86 625-679 (1121)
360 cd08172 GlyDH-like1 Glycerol d 33.1 2.6E+02 0.0056 23.8 7.8 64 124-198 12-78 (347)
361 PF12646 DUF3783: Domain of un 33.0 66 0.0014 19.8 3.0 26 141-166 1-27 (58)
362 CHL00122 secA preprotein trans 32.7 1.9E+02 0.0042 28.2 7.3 51 121-173 407-457 (870)
363 KOG4451 Uncharacterized conser 32.6 31 0.00067 27.8 1.8 26 47-83 251-276 (286)
364 smart00290 ZnF_UBP Ubiquitin C 32.5 26 0.00057 20.5 1.1 24 27-51 2-25 (50)
365 cd06322 PBP1_ABC_sugar_binding 32.0 1.4E+02 0.0031 23.4 5.8 7 164-170 55-61 (267)
366 KOG2066 Vacuolar assembly/sort 31.9 16 0.00034 34.7 0.0 32 25-56 785-822 (846)
367 KOG1701 Focal adhesion adaptor 31.5 29 0.00063 30.6 1.6 39 21-59 299-337 (468)
368 PRK13103 secA preprotein trans 31.4 1.1E+02 0.0024 29.9 5.6 51 121-173 432-482 (913)
369 COG4047 Uncharacterized protei 31.2 61 0.0013 25.9 3.2 27 122-148 123-149 (243)
370 PRK09860 putative alcohol dehy 31.0 2.3E+02 0.005 24.6 7.1 45 152-199 47-91 (383)
371 TIGR01689 EcbF-BcbF capsule bi 30.7 1.6E+02 0.0035 21.3 5.2 44 125-170 27-83 (126)
372 COG4306 Uncharacterized protei 30.7 28 0.0006 25.4 1.1 26 45-84 28-53 (160)
373 cd01522 RHOD_1 Member of the R 30.5 1.3E+02 0.0028 21.0 4.7 38 138-175 62-100 (117)
374 cd01526 RHOD_ThiF Member of th 30.5 57 0.0012 23.0 2.8 38 138-175 70-109 (122)
375 cd00954 NAL N-Acetylneuraminic 30.4 1.3E+02 0.0029 24.8 5.4 44 151-194 22-65 (288)
376 TIGR00674 dapA dihydrodipicoli 30.4 1.3E+02 0.0029 24.7 5.4 43 151-194 20-62 (285)
377 TIGR01073 pcrA ATP-dependent D 30.3 1.5E+02 0.0033 28.1 6.3 51 123-175 325-378 (726)
378 PRK04147 N-acetylneuraminate l 30.2 1.2E+02 0.0025 25.2 5.0 41 154-194 28-68 (293)
379 KOG1609 Protein involved in mR 29.8 42 0.00091 27.9 2.3 51 24-83 78-136 (323)
380 COG0669 CoaD Phosphopantethein 29.4 1.6E+02 0.0035 22.4 5.1 50 151-200 17-66 (159)
381 KOG0824 Predicted E3 ubiquitin 29.4 21 0.00046 30.0 0.4 40 18-57 99-138 (324)
382 cd06280 PBP1_LacI_like_4 Ligan 29.4 1.9E+02 0.0041 22.8 6.0 14 160-173 51-64 (263)
383 PRK10653 D-ribose transporter 29.4 1.7E+02 0.0036 23.8 5.8 22 149-170 41-62 (295)
384 cd06354 PBP1_BmpA_PnrA_like Pe 28.6 1.7E+02 0.0036 23.4 5.6 17 150-166 18-34 (265)
385 COG3492 Uncharacterized protei 28.6 42 0.00092 23.0 1.7 15 46-60 42-56 (104)
386 cd06293 PBP1_LacI_like_11 Liga 28.4 2E+02 0.0043 22.7 6.0 33 140-173 29-64 (269)
387 cd06319 PBP1_ABC_sugar_binding 28.3 1.8E+02 0.004 22.9 5.8 30 140-170 29-61 (277)
388 PF02148 zf-UBP: Zn-finger in 28.2 26 0.00057 21.9 0.6 31 27-57 1-35 (63)
389 PF08273 Prim_Zn_Ribbon: Zinc- 28.2 31 0.00066 19.8 0.8 25 25-51 4-32 (40)
390 TIGR02634 xylF D-xylose ABC tr 28.1 1.8E+02 0.0039 23.8 5.8 20 149-168 13-32 (302)
391 cd01527 RHOD_YgaP Member of th 28.1 1E+02 0.0022 20.4 3.7 37 138-174 52-89 (99)
392 cd01831 Endoglucanase_E_like E 27.9 2.5E+02 0.0054 20.7 6.3 48 126-173 82-140 (169)
393 cd06301 PBP1_rhizopine_binding 27.7 1.9E+02 0.0042 22.8 5.8 33 140-173 30-65 (272)
394 cd06323 PBP1_ribose_binding Pe 27.7 1.8E+02 0.0039 22.7 5.6 7 152-158 44-50 (268)
395 PF13913 zf-C2HC_2: zinc-finge 27.7 16 0.00035 18.5 -0.4 13 71-83 3-15 (25)
396 KOG0827 Predicted E3 ubiquitin 27.6 24 0.00053 30.7 0.5 48 25-83 197-247 (465)
397 PRK14714 DNA polymerase II lar 27.6 27 0.00059 35.1 0.9 51 25-84 668-723 (1337)
398 PF11290 DUF3090: Protein of u 27.6 38 0.00083 26.1 1.5 17 67-83 151-167 (171)
399 cd06275 PBP1_PurR Ligand-bindi 27.1 2.1E+02 0.0045 22.5 5.9 13 160-172 51-63 (269)
400 cd00952 CHBPH_aldolase Trans-o 27.1 1.4E+02 0.003 25.1 4.9 32 163-194 41-72 (309)
401 PF08756 YfkB: YfkB-like domai 27.0 2.3E+02 0.005 21.2 5.4 35 168-202 34-75 (153)
402 cd01538 PBP1_ABC_xylose_bindin 26.8 2E+02 0.0043 23.2 5.8 23 149-171 14-36 (288)
403 PF06050 HGD-D: 2-hydroxygluta 26.8 1.5E+02 0.0033 24.8 5.2 49 122-174 273-327 (349)
404 TIGR02313 HpaI-NOT-DapA 2,4-di 26.5 1.6E+02 0.0035 24.5 5.2 33 162-194 32-64 (294)
405 PF04908 SH3BGR: SH3-binding, 26.3 1.8E+02 0.0039 20.2 4.6 34 153-192 20-53 (99)
406 PRK11493 sseA 3-mercaptopyruva 26.3 1.6E+02 0.0036 24.2 5.2 38 138-175 229-267 (281)
407 PRK11773 uvrD DNA-dependent he 26.2 2E+02 0.0043 27.4 6.3 50 124-175 330-381 (721)
408 cd06289 PBP1_MalI_like Ligand- 26.2 2.1E+02 0.0046 22.3 5.8 33 140-173 29-64 (268)
409 PRK11200 grxA glutaredoxin 1; 26.2 1.2E+02 0.0027 19.6 3.7 32 142-173 2-39 (85)
410 cd01532 4RHOD_Repeat_1 Member 26.1 1.3E+02 0.0029 19.8 3.9 37 139-175 49-88 (92)
411 TIGR02200 GlrX_actino Glutared 26.0 1.3E+02 0.0029 18.5 3.8 28 145-172 5-32 (77)
412 PRK11475 DNA-binding transcrip 26.0 1.4E+02 0.003 23.5 4.5 35 130-165 58-92 (207)
413 COG1199 DinG Rad3-related DNA 25.9 3.1E+02 0.0068 25.5 7.5 65 123-197 463-528 (654)
414 cd06305 PBP1_methylthioribose_ 25.8 2.2E+02 0.0047 22.4 5.8 7 140-146 29-35 (273)
415 COG0626 MetC Cystathionine bet 25.8 2E+02 0.0044 25.3 5.8 53 119-173 83-136 (396)
416 cd06270 PBP1_GalS_like Ligand 25.8 2.3E+02 0.0049 22.3 5.9 10 163-172 54-63 (268)
417 cd01575 PBP1_GntR Ligand-bindi 25.8 2E+02 0.0044 22.4 5.6 12 162-173 53-64 (268)
418 PRK11784 tRNA 2-selenouridine 25.6 3.1E+02 0.0067 23.6 6.9 49 139-194 87-136 (345)
419 PRK08074 bifunctional ATP-depe 25.6 3E+02 0.0065 27.1 7.5 63 124-195 737-803 (928)
420 cd06284 PBP1_LacI_like_6 Ligan 25.5 2.2E+02 0.0049 22.2 5.8 11 160-170 51-61 (267)
421 cd00950 DHDPS Dihydrodipicolin 25.5 1.6E+02 0.0035 24.1 5.0 33 162-194 32-64 (284)
422 PRK03620 5-dehydro-4-deoxygluc 25.4 1.4E+02 0.0031 24.9 4.8 35 160-194 37-71 (303)
423 PF06221 zf-C2HC5: Putative zi 25.3 44 0.00095 20.8 1.2 27 39-82 20-47 (57)
424 PRK00418 DNA gyrase inhibitor; 25.3 37 0.00079 21.5 0.9 13 69-81 5-17 (62)
425 KOG2857 Predicted MYND Zn-fing 25.2 32 0.0007 25.6 0.7 29 25-54 6-35 (157)
426 PF03884 DUF329: Domain of unk 25.2 24 0.00051 22.0 -0.0 12 71-82 3-14 (57)
427 COG2179 Predicted hydrolase of 25.0 2.2E+02 0.0048 22.0 5.2 61 121-194 48-108 (175)
428 PF07282 OrfB_Zn_ribbon: Putat 25.0 1.2E+02 0.0025 19.0 3.3 25 149-173 1-25 (69)
429 TIGR03847 conserved hypothetic 24.9 45 0.00098 25.7 1.5 17 67-83 153-169 (177)
430 TIGR01075 uvrD DNA helicase II 24.9 1.9E+02 0.004 27.5 5.9 50 124-175 325-376 (715)
431 cd06296 PBP1_CatR_like Ligand- 24.8 2.3E+02 0.0051 22.2 5.8 24 125-149 15-38 (270)
432 PRK00254 ski2-like helicase; P 24.7 3.4E+02 0.0074 25.7 7.6 24 167-196 298-321 (720)
433 PF00643 zf-B_box: B-box zinc 24.6 51 0.0011 18.4 1.4 31 23-54 2-32 (42)
434 PRK01343 zinc-binding protein; 24.6 39 0.00086 21.0 0.9 14 68-81 7-20 (57)
435 PRK10355 xylF D-xylose transpo 24.5 2.2E+02 0.0048 23.8 5.8 24 149-172 40-63 (330)
436 TIGR03117 cas_csf4 CRISPR-asso 24.4 4.3E+02 0.0094 24.9 8.0 63 123-195 454-517 (636)
437 cd08191 HHD 6-hydroxyhexanoate 24.3 4.7E+02 0.01 22.6 8.0 34 141-174 23-60 (386)
438 PRK12759 bifunctional gluaredo 23.9 1E+02 0.0022 27.1 3.7 32 142-173 3-35 (410)
439 PLN02160 thiosulfate sulfurtra 23.9 1.4E+02 0.003 21.7 3.9 38 138-175 79-117 (136)
440 COG3058 FdhE Uncharacterized p 23.9 40 0.00087 28.1 1.1 46 23-79 184-234 (308)
441 PF08915 tRNA-Thr_ED: Archaea- 23.8 3.1E+02 0.0067 20.4 6.5 47 123-169 55-113 (138)
442 COG0653 SecA Preprotein transl 23.8 2.3E+02 0.005 27.5 6.1 65 120-194 411-475 (822)
443 PF01485 IBR: IBR domain; Int 23.8 32 0.00069 21.0 0.4 32 24-55 18-58 (64)
444 cd08176 LPO Lactadehyde:propan 23.6 4.6E+02 0.01 22.5 7.7 55 141-198 29-87 (377)
445 cd06318 PBP1_ABC_sugar_binding 23.6 2.6E+02 0.0056 22.1 5.9 14 152-165 17-30 (282)
446 COG3364 Zn-ribbon containing p 23.5 42 0.00091 23.5 1.0 12 39-50 4-15 (112)
447 PF00628 PHD: PHD-finger; Int 23.5 47 0.001 19.4 1.1 47 26-77 1-49 (51)
448 PRK10703 DNA-binding transcrip 23.5 4.2E+02 0.0092 21.8 9.3 47 149-201 74-120 (341)
449 PF04343 DUF488: Protein of un 23.3 1.5E+02 0.0032 21.0 3.9 45 123-172 1-52 (122)
450 PF13297 Telomere_Sde2_2: Telo 23.3 1.8E+02 0.004 18.3 3.7 42 146-198 6-51 (60)
451 PF11497 NADH_Oxid_Nqo15: NADH 23.3 61 0.0013 23.2 1.7 25 145-169 9-33 (127)
452 COG5011 Uncharacterized protei 23.3 89 0.0019 24.8 2.8 37 146-183 15-51 (228)
453 COG3024 Uncharacterized protei 23.2 41 0.00089 21.4 0.8 15 68-82 5-19 (65)
454 PF09171 DUF1886: Domain of un 23.1 24 0.00052 28.9 -0.3 26 122-147 120-145 (246)
455 KOG2949 Ketopantoate hydroxyme 23.1 2E+02 0.0043 23.5 4.8 41 146-194 111-152 (306)
456 PF00290 Trp_syntA: Tryptophan 23.1 2.5E+02 0.0055 23.1 5.6 36 120-155 67-102 (259)
457 cd06285 PBP1_LacI_like_7 Ligan 23.0 2.9E+02 0.0062 21.7 6.0 33 140-173 29-64 (265)
458 PF09297 zf-NADH-PPase: NADH p 22.9 8.2 0.00018 20.7 -2.2 27 45-78 3-29 (32)
459 PF11019 DUF2608: Protein of u 22.9 2.9E+02 0.0062 22.6 5.9 49 120-170 160-208 (252)
460 PF09237 GAGA: GAGA factor; I 22.8 37 0.00079 20.7 0.5 15 68-82 22-36 (54)
461 PF03690 UPF0160: Uncharacteri 22.8 2.8E+02 0.006 23.7 5.9 38 136-173 207-248 (318)
462 KOG3849 GDP-fucose protein O-f 22.7 2E+02 0.0043 24.2 4.8 51 123-173 282-333 (386)
463 PF00701 DHDPS: Dihydrodipicol 22.7 2.2E+02 0.0048 23.4 5.4 32 162-193 33-64 (289)
464 cd06315 PBP1_ABC_sugar_binding 22.7 2.7E+02 0.0058 22.3 5.8 15 152-166 18-32 (280)
465 COG4647 AcxC Acetone carboxyla 22.6 41 0.00088 24.7 0.8 20 29-49 62-81 (165)
466 TIGR02981 phageshock_pspE phag 22.6 2.6E+02 0.0057 19.1 5.2 38 138-175 56-93 (101)
467 PRK05320 rhodanese superfamily 22.2 2.4E+02 0.0051 23.1 5.3 37 139-175 174-211 (257)
468 KOG1356 Putative transcription 22.1 32 0.00069 33.0 0.2 33 24-56 229-262 (889)
469 cd01445 TST_Repeats Thiosulfat 22.0 3.2E+02 0.0068 19.8 6.0 39 136-174 91-133 (138)
470 PF12683 DUF3798: Protein of u 22.0 74 0.0016 26.4 2.3 31 117-148 40-70 (275)
471 KOG2567 Uncharacterized conser 22.0 1.3E+02 0.0029 23.0 3.4 30 119-149 24-53 (179)
472 KOG2169 Zn-finger transcriptio 21.8 64 0.0014 30.3 2.1 54 26-86 308-361 (636)
473 TIGR03167 tRNA_sel_U_synt tRNA 21.7 2.7E+02 0.0059 23.5 5.7 50 123-174 59-109 (311)
474 cd01541 PBP1_AraR Ligand-bindi 21.5 3.1E+02 0.0067 21.6 5.9 32 140-172 29-63 (273)
475 KOG1829 Uncharacterized conser 21.5 33 0.00071 31.7 0.2 24 41-78 535-558 (580)
476 PF13986 DUF4224: Domain of un 21.4 82 0.0018 18.6 1.8 17 156-172 20-37 (47)
477 cd06288 PBP1_sucrose_transcrip 21.4 3.2E+02 0.0068 21.4 5.9 13 160-172 52-64 (269)
478 COG0329 DapA Dihydrodipicolina 21.3 1.9E+02 0.0041 24.2 4.7 33 161-193 35-67 (299)
479 cd01852 AIG1 AIG1 (avrRpt2-ind 21.1 2.7E+02 0.0059 21.2 5.3 54 121-174 97-163 (196)
480 COG1724 Predicted RNA binding 21.1 1.2E+02 0.0025 19.5 2.5 19 155-173 11-29 (66)
481 cd01444 GlpE_ST GlpE sulfurtra 21.1 1.5E+02 0.0033 19.3 3.5 37 138-174 54-91 (96)
482 PF01591 6PF2K: 6-phosphofruct 21.0 2.5E+02 0.0055 22.5 5.2 39 152-195 83-121 (222)
483 cd00951 KDGDH 5-dehydro-4-deox 20.9 2E+02 0.0044 23.8 4.8 33 162-194 32-64 (289)
484 COG2093 DNA-directed RNA polym 20.8 41 0.00089 21.3 0.4 12 68-79 16-27 (64)
485 PRK00420 hypothetical protein; 20.7 22 0.00047 25.4 -0.9 14 68-81 38-51 (112)
486 KOG1321 Protoheme ferro-lyase 20.6 1.1E+02 0.0023 26.3 2.9 36 138-173 152-199 (395)
487 COG1086 Predicted nucleoside-d 20.6 6.1E+02 0.013 23.7 7.9 72 116-199 255-328 (588)
488 PF10186 Atg14: UV radiation r 20.6 61 0.0013 26.6 1.6 22 26-56 1-22 (302)
489 PRK14559 putative protein seri 20.6 38 0.00082 31.8 0.4 32 121-152 130-162 (645)
490 PF13834 DUF4193: Domain of un 20.6 44 0.00095 23.3 0.6 33 19-51 65-98 (99)
491 PF03119 DNA_ligase_ZBD: NAD-d 20.5 43 0.00094 17.4 0.4 10 72-81 1-10 (28)
492 KOG1814 Predicted E3 ubiquitin 20.4 48 0.001 29.2 0.9 35 21-55 365-404 (445)
493 KOG4549 Magnesium-dependent ph 20.4 3.2E+02 0.007 20.2 5.0 43 142-194 42-84 (144)
494 KOG1842 FYVE finger-containing 20.4 27 0.00058 31.0 -0.6 49 7-55 163-214 (505)
495 KOG2272 Focal adhesion protein 20.4 33 0.00072 28.1 -0.0 12 70-81 195-206 (332)
496 PRK05580 primosome assembly pr 20.3 7.4E+02 0.016 23.4 9.1 71 120-198 172-243 (679)
497 cd06291 PBP1_Qymf_like Ligand 20.3 3.2E+02 0.007 21.3 5.8 20 149-168 14-33 (265)
498 cd01525 RHOD_Kc Member of the 20.3 1.7E+02 0.0037 19.5 3.6 36 140-175 65-101 (105)
499 TIGR03865 PQQ_CXXCW PQQ-depend 20.3 2.8E+02 0.0061 20.8 5.1 48 128-175 104-153 (162)
500 PF13607 Succ_CoA_lig: Succiny 20.0 2.3E+02 0.0049 20.8 4.4 56 142-202 3-58 (138)
No 1
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=99.93 E-value=1.6e-26 Score=197.71 Aligned_cols=156 Identities=23% Similarity=0.381 Sum_probs=122.5
Q ss_pred CccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEEccCccccCCCCCCCC
Q 028376 23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYADDRQDKSCNSDMPH 102 (210)
Q Consensus 23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~~~~~~~~~~~~~~~~ 102 (210)
+..+|.+|.++..+ ++.+.|.|.||.-|+.++++..+. +....||+|...++.+.-..... ...+.
T Consensus 535 ~~~~C~lc~d~aed-~i~s~ChH~FCrlCi~eyv~~f~~------~~nvtCP~C~i~LsiDlse~ale-------k~~l~ 600 (791)
T KOG1002|consen 535 GEVECGLCHDPAED-YIESSCHHKFCRLCIKEYVESFME------NNNVTCPVCHIGLSIDLSEPALE-------KTDLK 600 (791)
T ss_pred CceeecccCChhhh-hHhhhhhHHHHHHHHHHHHHhhhc------ccCCCCccccccccccccchhhh-------hcchh
Confidence 45689999999887 599999999999999999876542 44589999999887762111110 00111
Q ss_pred CCCCcccccCCcee-cCCCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchh
Q 028376 103 GVQDCEKGEESFTV-QGSYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSAN 181 (210)
Q Consensus 103 ~~~~~~~~~~~~~~-~~~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~ 181 (210)
+.+... ....+.+ .+..||||+||++.|..+++.+...|+|||||||+|||+|+..|.+.|+.++.++|+|.
T Consensus 601 ~Fk~sS-IlnRinm~~~qsSTKIEAL~EEl~~l~~rd~t~KsIVFSQFTSmLDLi~~rL~kaGfscVkL~GsMs------ 673 (791)
T KOG1002|consen 601 GFKASS-ILNRINMDDWQSSTKIEALVEELYFLRERDRTAKSIVFSQFTSMLDLIEWRLGKAGFSCVKLVGSMS------ 673 (791)
T ss_pred hhhhHH-HhhhcchhhhcchhHHHHHHHHHHHHHHcccchhhhhHHHHHHHHHHHHHHhhccCceEEEeccCCC------
Confidence 111100 0111221 56889999999999999999999999999999999999999999999999999999977
Q ss_pred hHhhhHHHHHHhhcCCCCC
Q 028376 182 LQHRNALQKELTRHMPSSQ 200 (210)
Q Consensus 182 ~~~R~~~l~~F~~~~p~~~ 200 (210)
+++|.++|+.|.+ ||++.
T Consensus 674 ~~ardatik~F~n-d~~c~ 691 (791)
T KOG1002|consen 674 PAARDATIKYFKN-DIDCR 691 (791)
T ss_pred hHHHHHHHHHhcc-CCCeE
Confidence 9999999999998 88875
No 2
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=99.60 E-value=3.3e-16 Score=142.46 Aligned_cols=146 Identities=21% Similarity=0.319 Sum_probs=113.3
Q ss_pred HHHhcCCCCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEEccCcccc
Q 028376 15 RIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYADDRQDK 94 (210)
Q Consensus 15 ~~~~l~~~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~~~~~~~~ 94 (210)
++..+... ..|++|.+ .. ..+++.|||.||.+|+...++. .....||.||..+...++......+..
T Consensus 447 ~i~~l~~~--~~c~ic~~-~~-~~~it~c~h~~c~~c~~~~i~~---------~~~~~~~~cr~~l~~~~l~s~~~~~~~ 513 (674)
T KOG1001|consen 447 LIVDLSVS--HWCHICCD-LD-SFFITRCGHDFCVECLKKSIQQ---------SENAPCPLCRNVLKEKKLLSANPLPSI 513 (674)
T ss_pred HHHHHhhc--cccccccc-cc-cceeecccchHHHHHHHhcccc---------ccCCCCcHHHHHHHHHHHhhcccccch
Confidence 45555544 89999999 44 4699999999999999998765 223389999998877766533222111
Q ss_pred CCCCCCCCCCCCcccccCCceecCCCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCC
Q 028376 95 SCNSDMPHGVQDCEKGEESFTVQGSYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGEN 174 (210)
Q Consensus 95 ~~~~~~~~~~~~~~~~~~~~~~~~~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m 174 (210)
..+ .. ..|+||.++++.|........ .|+||||||+.+|++++..|...|+.|.+|+|.|
T Consensus 514 ~~~------------------~~-~~s~ki~~~~~~l~~~~~s~~-~kiiifsq~~~~l~l~~~~l~~~~~~~~~~~g~~ 573 (674)
T KOG1001|consen 514 IND------------------LL-PESSKIYAFLKILQAKEMSEQ-PKIVIFSQLIWGLALVCLRLFFKGFVFLRYDGEM 573 (674)
T ss_pred hhh------------------cc-chhhhhHHHHHHHhhccCCCC-CceeeehhHHHHHHHhhhhhhhcccccchhhhhh
Confidence 100 00 168999999999985554444 6999999999999999999999999999999996
Q ss_pred CCCcchhhHhhhHHHHHHhhcCCCCC
Q 028376 175 HKLPSANLQHRNALQKELTRHMPSSQ 200 (210)
Q Consensus 175 ~~~~~~~~~~R~~~l~~F~~~~p~~~ 200 (210)
. .++|.+++..|.. +|++.
T Consensus 574 ~------~~~r~~s~~~~~~-~~~~~ 592 (674)
T KOG1001|consen 574 L------MKIRTKSFTDFPC-DPLVT 592 (674)
T ss_pred H------HHHHHhhhccccc-CccHH
Confidence 6 9999999999994 87754
No 3
>KOG0389 consensus SNF2 family DNA-dependent ATPase [Chromatin structure and dynamics]
Probab=99.43 E-value=2.6e-13 Score=122.21 Aligned_cols=78 Identities=21% Similarity=0.376 Sum_probs=71.9
Q ss_pred CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCC
Q 028376 119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPS 198 (210)
Q Consensus 119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~ 198 (210)
--|.|+..|-..|.+++.+ ++|+|||||||.||||++..|...|++|+|+||+.+ ...|+..|++|++
T Consensus 758 mdSgK~r~L~~LLp~~k~~--G~RVLiFSQFTqmLDILE~~L~~l~~~ylRLDGsTq------V~~RQ~lId~Fn~---- 825 (941)
T KOG0389|consen 758 MDSGKCRKLKELLPKIKKK--GDRVLIFSQFTQMLDILEVVLDTLGYKYLRLDGSTQ------VNDRQDLIDEFNT---- 825 (941)
T ss_pred hhhhhHhHHHHHHHHHhhc--CCEEEEeeHHHHHHHHHHHHHHhcCceEEeecCCcc------chHHHHHHHhhcc----
Confidence 4589999999999999865 699999999999999999999999999999999999 9999999999999
Q ss_pred CCCccccccccC
Q 028376 199 SQSQSLFKCYYS 210 (210)
Q Consensus 199 ~~~~~~~~~~~~ 210 (210)
..|+|.|+.|
T Consensus 826 --d~difVFLLS 835 (941)
T KOG0389|consen 826 --DKDIFVFLLS 835 (941)
T ss_pred --CCceEEEEEe
Confidence 7778877765
No 4
>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]
Probab=99.24 E-value=6.8e-12 Score=117.85 Aligned_cols=124 Identities=30% Similarity=0.514 Sum_probs=100.6
Q ss_pred HHHHhcCCCCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEEccCccc
Q 028376 14 HRIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYADDRQD 93 (210)
Q Consensus 14 ~~~~~l~~~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~~~~~~~ 93 (210)
.+...+...+...|.+|.+.+.....+..|||.+|..|...|... ...||.|.
T Consensus 1143 ~~~y~~~~~~~~~c~ic~dil~~~~~I~~cgh~~c~~c~~~~l~~-----------~s~~~~~k---------------- 1195 (1394)
T KOG0298|consen 1143 DVRYLMNLSGHFVCEICLDILRNQGGIAGCGHEPCCRCDELWLYA-----------SSRCPICK---------------- 1195 (1394)
T ss_pred hHHHHHHhhcccchHHHHHHHHhcCCeeeechhHhhhHHHHHHHH-----------hccCcchh----------------
Confidence 344445556667999999999865789999999999999999644 44799886
Q ss_pred cCCCCCCCCCCCCcccccCCceecCCCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCC
Q 028376 94 KSCNSDMPHGVQDCEKGEESFTVQGSYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGE 173 (210)
Q Consensus 94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~ 173 (210)
...+.+++||.++...+++++.+++.+|+||||||+..||.++.++..|||.+.+..|+
T Consensus 1196 ---------------------si~~dfg~kI~~v~~~il~iK~k~~qekvIvfsqws~~ldV~e~~~~~N~I~~~~~~~t 1254 (1394)
T KOG0298|consen 1196 ---------------------SIKGDFGTKIDSVVIAILYIKFKNEQEKVIVFSQWSVVLDVKELRYLMNLIKKQLDGET 1254 (1394)
T ss_pred ---------------------hhhhhhccCchhHHHHHHHHhccCcCceEEEEEehHHHHHHHHHHHHhhhhHhhhccCC
Confidence 02356789999999999999999999999999999999999999999999999776654
Q ss_pred CCCCcchhhHhhhHHHHHHhh
Q 028376 174 NHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 174 m~~~~~~~~~~R~~~l~~F~~ 194 (210)
- .-...+..|.+
T Consensus 1255 ~---------d~~dc~~~fk~ 1266 (1394)
T KOG0298|consen 1255 E---------DFDDCIICFKS 1266 (1394)
T ss_pred c---------chhhhhhhccc
Confidence 2 34455555554
No 5
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=99.20 E-value=1.9e-11 Score=94.46 Aligned_cols=71 Identities=21% Similarity=0.453 Sum_probs=52.5
Q ss_pred hcCCCCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccc-----cCCCccccccCCcccccCCCeEEcc
Q 028376 18 SLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDN-----KVKNEWVMCPTCRQRTDIGNIAYAD 89 (210)
Q Consensus 18 ~l~~~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~-----~~~~~~~~CP~Cr~~~~~~~l~~~~ 89 (210)
.+...+..+|+||++.+.+ +++++|||.||..|+..|+........ ........||+||..+...+++.+.
T Consensus 12 ~~~~~~~~~CpICld~~~d-PVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~LvPiy 87 (193)
T PLN03208 12 LVDSGGDFDCNICLDQVRD-PVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLVPIY 87 (193)
T ss_pred eccCCCccCCccCCCcCCC-cEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEEEee
Confidence 3455677899999999887 589999999999999999754221100 0023457899999999988887443
No 6
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.12 E-value=4.7e-11 Score=93.98 Aligned_cols=59 Identities=22% Similarity=0.586 Sum_probs=50.8
Q ss_pred CCCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEEc
Q 028376 21 KADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYA 88 (210)
Q Consensus 21 ~~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~~ 88 (210)
+...++|.||++...+ ++++.|||+||-.|+.+|++- ......||+|+..+..+.|+-+
T Consensus 44 ~~~~FdCNICLd~akd-PVvTlCGHLFCWpClyqWl~~--------~~~~~~cPVCK~~Vs~~~vvPl 102 (230)
T KOG0823|consen 44 DGGFFDCNICLDLAKD-PVVTLCGHLFCWPCLYQWLQT--------RPNSKECPVCKAEVSIDTVVPL 102 (230)
T ss_pred CCCceeeeeeccccCC-CEEeecccceehHHHHHHHhh--------cCCCeeCCccccccccceEEee
Confidence 5667899999999987 599999999999999999865 3556689999999999988743
No 7
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=99.07 E-value=6.6e-11 Score=95.80 Aligned_cols=56 Identities=25% Similarity=0.644 Sum_probs=47.3
Q ss_pred CCCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEEc
Q 028376 21 KADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYA 88 (210)
Q Consensus 21 ~~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~~ 88 (210)
...+..|.+|++...+ +..++|||+||-.|+..|. +....||.||..+.+++++..
T Consensus 236 ~~a~~kC~LCLe~~~~-pSaTpCGHiFCWsCI~~w~-----------~ek~eCPlCR~~~~pskvi~L 291 (293)
T KOG0317|consen 236 PEATRKCSLCLENRSN-PSATPCGHIFCWSCILEWC-----------SEKAECPLCREKFQPSKVICL 291 (293)
T ss_pred CCCCCceEEEecCCCC-CCcCcCcchHHHHHHHHHH-----------ccccCCCcccccCCCcceeee
Confidence 3455789999999887 4899999999999999996 445569999999999987643
No 8
>PHA02929 N1R/p28-like protein; Provisional
Probab=99.07 E-value=1.1e-10 Score=93.74 Aligned_cols=53 Identities=26% Similarity=0.649 Sum_probs=41.2
Q ss_pred hcCCCCccccccccccccCC-------CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376 18 SLSKADEETCPICQEKLGNQ-------KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD 81 (210)
Q Consensus 18 ~l~~~~~~~C~iC~~~~~~~-------~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~ 81 (210)
......+.+|+||++.+..+ +++++|||.||..|+.+|++ ....||+||.++.
T Consensus 168 ~~~~~~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~-----------~~~tCPlCR~~~~ 227 (238)
T PHA02929 168 LYNRSKDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKK-----------EKNTCPVCRTPFI 227 (238)
T ss_pred hhcCCCCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHh-----------cCCCCCCCCCEee
Confidence 33445678999999986542 25679999999999999963 3458999999764
No 9
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.06 E-value=6.5e-11 Score=89.46 Aligned_cols=57 Identities=28% Similarity=0.694 Sum_probs=45.4
Q ss_pred cCCCCccccccccccccCCC-eecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376 19 LSKADEETCPICQEKLGNQK-MVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA 86 (210)
Q Consensus 19 l~~~~~~~C~iC~~~~~~~~-~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~ 86 (210)
.+.+....||||++.+.... +-+.|||+||..|++..+ ....+||+|++.+...+++
T Consensus 126 ~~~~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~al-----------k~~~~CP~C~kkIt~k~~~ 183 (187)
T KOG0320|consen 126 LRKEGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDAL-----------KNTNKCPTCRKKITHKQFH 183 (187)
T ss_pred cccccccCCCceecchhhccccccccchhHHHHHHHHHH-----------HhCCCCCCcccccchhhhe
Confidence 34455678999999887653 459999999999999986 3456899999988777654
No 10
>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]
Probab=99.02 E-value=5.6e-10 Score=100.94 Aligned_cols=72 Identities=18% Similarity=0.333 Sum_probs=64.2
Q ss_pred CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCC
Q 028376 119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPS 198 (210)
Q Consensus 119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~ 198 (210)
..|.|+.-|=+.|..+.++ +.|++||||||.||||++..+.-.|+.|.|+||+++ ...|.++|+.|+. +|+
T Consensus 468 ~nSGKm~vLDkLL~~Lk~~--GhRVLIFSQmt~mLDILeDyc~~R~y~ycRiDGSt~------~eeR~~aI~~fn~-~~s 538 (971)
T KOG0385|consen 468 TNSGKMLVLDKLLPKLKEQ--GHRVLIFSQMTRMLDILEDYCMLRGYEYCRLDGSTS------HEEREDAIEAFNA-PPS 538 (971)
T ss_pred hcCcceehHHHHHHHHHhC--CCeEEEeHHHHHHHHHHHHHHHhcCceeEeecCCCC------cHHHHHHHHhcCC-CCc
Confidence 3478988888888887754 899999999999999999999999999999999988 9999999999998 554
Q ss_pred C
Q 028376 199 S 199 (210)
Q Consensus 199 ~ 199 (210)
.
T Consensus 539 ~ 539 (971)
T KOG0385|consen 539 E 539 (971)
T ss_pred c
Confidence 3
No 11
>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=99.01 E-value=1e-10 Score=69.95 Aligned_cols=42 Identities=31% Similarity=0.796 Sum_probs=33.3
Q ss_pred ccccccccccc--CCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCc
Q 028376 25 ETCPICQEKLG--NQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCR 77 (210)
Q Consensus 25 ~~C~iC~~~~~--~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr 77 (210)
.+|+||++.+. ...+.++|||.||.+|+.+|++. ...||+||
T Consensus 1 d~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~-----------~~~CP~CR 44 (44)
T PF13639_consen 1 DECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKR-----------NNSCPVCR 44 (44)
T ss_dssp -CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHH-----------SSB-TTTH
T ss_pred CCCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHh-----------CCcCCccC
Confidence 37999999884 34577899999999999999854 24999997
No 12
>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=99.01 E-value=1.3e-10 Score=67.62 Aligned_cols=39 Identities=38% Similarity=0.917 Sum_probs=31.7
Q ss_pred cccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCC
Q 028376 27 CPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTC 76 (210)
Q Consensus 27 C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~C 76 (210)
|+||.+.+.++.++++|||.||.+|+.+|++. ...||.|
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~~~~~-----------~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKECIEKYLEK-----------NPKCPVC 39 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHHHHHHHHHC-----------TSB-TTT
T ss_pred CCCCCCcccCcCEECCCCCchhHHHHHHHHHC-----------cCCCcCC
Confidence 89999999885478999999999999999743 3689987
No 13
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=99.01 E-value=1.5e-10 Score=68.31 Aligned_cols=42 Identities=29% Similarity=0.819 Sum_probs=29.4
Q ss_pred cccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCC
Q 028376 27 CPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTC 76 (210)
Q Consensus 27 C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~C 76 (210)
|+||++.+.+ ++.++|||.||..|+..+.+.. ......||.|
T Consensus 1 CpiC~~~~~~-Pv~l~CGH~FC~~Cl~~~~~~~-------~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKD-PVSLPCGHSFCRSCLERLWKEP-------SGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SS-EEE-SSSSEEEHHHHHHHHCCS-------SSST---SSS
T ss_pred CCccchhhCC-ccccCCcCHHHHHHHHHHHHcc-------CCcCCCCcCC
Confidence 8999999998 5999999999999999995321 1222689987
No 14
>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=98.98 E-value=1.9e-10 Score=70.64 Aligned_cols=46 Identities=35% Similarity=0.858 Sum_probs=37.7
Q ss_pred ccccccccccccCCCeecCCCCc-chHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376 24 EETCPICQEKLGNQKMVFQCGHF-TCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD 81 (210)
Q Consensus 24 ~~~C~iC~~~~~~~~~~~~CgH~-fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~ 81 (210)
+..|.||.+...+ .++++|||. ||..|+.+|.. ....||.||+++.
T Consensus 2 ~~~C~iC~~~~~~-~~~~pCgH~~~C~~C~~~~~~-----------~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 2 DEECPICFENPRD-VVLLPCGHLCFCEECAERLLK-----------RKKKCPICRQPIE 48 (50)
T ss_dssp HSB-TTTSSSBSS-EEEETTCEEEEEHHHHHHHHH-----------TTSBBTTTTBB-S
T ss_pred cCCCccCCccCCc-eEEeCCCChHHHHHHhHHhcc-----------cCCCCCcCChhhc
Confidence 5689999998876 588999999 99999999963 3468999999874
No 15
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=98.96 E-value=2.2e-09 Score=102.16 Aligned_cols=68 Identities=18% Similarity=0.336 Sum_probs=62.5
Q ss_pred CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376 120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRH 195 (210)
Q Consensus 120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~ 195 (210)
.|.|+..|.+.|..+.. .+.|+||||||+.+|++|+..|...|++|++++|+++ ..+|.++|+.|+.+
T Consensus 469 ~SgKl~lLdkLL~~Lk~--~g~KVLIFSQft~~LdiLed~L~~~g~~y~rIdGsts------~~eRq~~Id~Fn~~ 536 (1033)
T PLN03142 469 NSGKMVLLDKLLPKLKE--RDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTG------GEDRDASIDAFNKP 536 (1033)
T ss_pred hhhHHHHHHHHHHHHHh--cCCeEEeehhHHHHHHHHHHHHHHcCCcEEEECCCCC------HHHHHHHHHHhccc
Confidence 47899998888888764 5899999999999999999999999999999999987 99999999999873
No 16
>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=98.92 E-value=8.2e-10 Score=64.90 Aligned_cols=41 Identities=37% Similarity=0.914 Sum_probs=34.7
Q ss_pred cccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCC
Q 028376 27 CPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTC 76 (210)
Q Consensus 27 C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~C 76 (210)
|+||.+.+..+..+++|||.||..|+.+|++. .....||.|
T Consensus 1 C~iC~~~~~~~~~~~~C~H~fC~~C~~~~~~~---------~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFEDPVILLPCGHSFCRDCLRKWLEN---------SGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSSEEEETTTSEEEEHHHHHHHHHH---------TSSSBTTTT
T ss_pred CCcCCccccCCCEEecCCCcchHHHHHHHHHh---------cCCccCCcC
Confidence 89999998875448999999999999999864 345679987
No 17
>PHA02926 zinc finger-like protein; Provisional
Probab=98.91 E-value=1.3e-09 Score=85.45 Aligned_cols=61 Identities=25% Similarity=0.511 Sum_probs=44.9
Q ss_pred HHhcCCCCccccccccccccC--------CCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376 16 IESLSKADEETCPICQEKLGN--------QKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD 81 (210)
Q Consensus 16 ~~~l~~~~~~~C~iC~~~~~~--------~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~ 81 (210)
-.+.+.+.+.+|+||++..-. .+++.+|+|.||..|+..|.+... . .+....||.||..+.
T Consensus 162 e~~~~~SkE~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~--~---~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 162 EDVYRVSKEKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTRR--E---TGASDNCPICRTRFR 230 (242)
T ss_pred HHHHhccCCCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhcc--c---cCcCCcCCCCcceee
Confidence 345556777999999987522 157889999999999999965321 1 245668999999764
No 18
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.89 E-value=1.5e-09 Score=94.19 Aligned_cols=69 Identities=20% Similarity=0.464 Sum_probs=53.7
Q ss_pred HHHHHhcCCCCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEEcc
Q 028376 13 KHRIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYAD 89 (210)
Q Consensus 13 ~~~~~~l~~~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~~~ 89 (210)
+++...+... +..||||++++.. +..+.|||+||..|+-+++.... ......||+|+..+...+|..+.
T Consensus 176 e~i~qv~~~t-~~~CPICL~~~~~-p~~t~CGHiFC~~CiLqy~~~s~------~~~~~~CPiC~s~I~~kdl~pv~ 244 (513)
T KOG2164|consen 176 EDIFQVYGST-DMQCPICLEPPSV-PVRTNCGHIFCGPCILQYWNYSA------IKGPCSCPICRSTITLKDLLPVF 244 (513)
T ss_pred HHhhhhhcCc-CCcCCcccCCCCc-ccccccCceeeHHHHHHHHhhhc------ccCCccCCchhhhccccceeeee
Confidence 3444444444 7899999999887 48888999999999999976531 46778999999999998886443
No 19
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=98.85 E-value=2.4e-09 Score=63.95 Aligned_cols=42 Identities=38% Similarity=0.891 Sum_probs=34.3
Q ss_pred ccccccccc--cCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcc
Q 028376 26 TCPICQEKL--GNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQ 78 (210)
Q Consensus 26 ~C~iC~~~~--~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~ 78 (210)
.|++|.+.+ ..++.+++|||+||..|+..+. .....||+||+
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~-----------~~~~~CP~C~k 44 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLK-----------GKSVKCPICRK 44 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhc-----------CCCCCCcCCCC
Confidence 489998887 3346899999999999999883 34578999985
No 20
>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=98.83 E-value=3.4e-09 Score=68.11 Aligned_cols=51 Identities=14% Similarity=0.123 Sum_probs=43.0
Q ss_pred cccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEE
Q 028376 25 ETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAY 87 (210)
Q Consensus 25 ~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~ 87 (210)
..|+||.+.+.+ +++++|||+||..|+.+|+.. ...||.|+.++...++..
T Consensus 2 ~~Cpi~~~~~~~-Pv~~~~G~v~~~~~i~~~~~~-----------~~~cP~~~~~~~~~~l~~ 52 (63)
T smart00504 2 FLCPISLEVMKD-PVILPSGQTYERRAIEKWLLS-----------HGTDPVTGQPLTHEDLIP 52 (63)
T ss_pred cCCcCCCCcCCC-CEECCCCCEEeHHHHHHHHHH-----------CCCCCCCcCCCChhhcee
Confidence 479999999988 589999999999999999743 348999999987776553
No 21
>KOG0387 consensus Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription; Replication, recombination and repair]
Probab=98.83 E-value=9.5e-09 Score=93.37 Aligned_cols=68 Identities=21% Similarity=0.336 Sum_probs=64.2
Q ss_pred CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHH-hCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFI-ANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~-~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
..|-|++.|.++|..|.++ ++|+++|||-..||++|+..|. .+|+.|+|+||+.+ .+.|...|++|+.
T Consensus 527 k~sGKm~vl~~ll~~W~kq--g~rvllFsqs~~mLdilE~fL~~~~~ysylRmDGtT~------~~~R~~lVd~Fne 595 (923)
T KOG0387|consen 527 KRSGKMKVLAKLLKDWKKQ--GDRVLLFSQSRQMLDILESFLRRAKGYSYLRMDGTTP------AALRQKLVDRFNE 595 (923)
T ss_pred hhcchHHHHHHHHHHHhhC--CCEEEEehhHHHHHHHHHHHHHhcCCceEEEecCCCc------cchhhHHHHhhcC
Confidence 4589999999999999966 6799999999999999999999 79999999999998 9999999999998
No 22
>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=98.79 E-value=4.2e-09 Score=62.40 Aligned_cols=44 Identities=32% Similarity=0.810 Sum_probs=35.1
Q ss_pred ccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccc
Q 028376 26 TCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQR 79 (210)
Q Consensus 26 ~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~ 79 (210)
.|+||.+.+.....+.+|||.||..|+..|++. ....||.|+..
T Consensus 1 ~C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~----------~~~~Cp~C~~~ 44 (45)
T cd00162 1 ECPICLEEFREPVVLLPCGHVFCRSCIDKWLKS----------GKNTCPLCRTP 44 (45)
T ss_pred CCCcCchhhhCceEecCCCChhcHHHHHHHHHh----------CcCCCCCCCCc
Confidence 599999988654455669999999999999643 34579999875
No 23
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=98.70 E-value=9.5e-09 Score=60.73 Aligned_cols=40 Identities=35% Similarity=0.980 Sum_probs=22.2
Q ss_pred cccccccccC---CCeecCCCCcchHhhHHHHHHHhhhccccCCCcccccc
Q 028376 27 CPICQEKLGN---QKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCP 74 (210)
Q Consensus 27 C~iC~~~~~~---~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP 74 (210)
|+||.+ +.+ ++++++|||+||.+|+.++.... .....+||
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l~~~~-------~~~~~kCP 43 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKLSKKS-------DRNRFKCP 43 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHHHHH--------S-S-B--T
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHHHhcC-------CCCeeeCc
Confidence 899988 543 35889999999999999997642 13566776
No 24
>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]
Probab=98.70 E-value=4.3e-08 Score=92.29 Aligned_cols=68 Identities=21% Similarity=0.378 Sum_probs=62.2
Q ss_pred CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
.-.-|+++|.=+|+.+... +.+++||+|-+.|||+++.+|.-+|..|+|+||+.. ..+|+..+++||.
T Consensus 1257 yDcGKLQtLAiLLqQLk~e--ghRvLIfTQMtkmLDVLeqFLnyHgylY~RLDg~t~------vEqRQaLmerFNa 1324 (1958)
T KOG0391|consen 1257 YDCGKLQTLAILLQQLKSE--GHRVLIFTQMTKMLDVLEQFLNYHGYLYVRLDGNTS------VEQRQALMERFNA 1324 (1958)
T ss_pred cccchHHHHHHHHHHHHhc--CceEEehhHHHHHHHHHHHHHhhcceEEEEecCCcc------HHHHHHHHHHhcC
Confidence 3478999988888877754 899999999999999999999999999999999977 9999999999998
No 25
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=98.67 E-value=3.6e-08 Score=93.08 Aligned_cols=68 Identities=15% Similarity=0.231 Sum_probs=56.5
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM 196 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~ 196 (210)
|-|+=-|=++|-+++ ..+.|||||||-+.|||||+..|...|++|-|+||+++ ...|.++|++|+.++
T Consensus 682 SGKlVLLDKLL~rLk--~~GHrVLIFSQMVRmLDIL~eYL~~r~ypfQRLDGsvr------gelRq~AIDhFnap~ 749 (1373)
T KOG0384|consen 682 SGKLVLLDKLLPRLK--EGGHRVLIFSQMVRMLDILAEYLSLRGYPFQRLDGSVR------GELRQQAIDHFNAPD 749 (1373)
T ss_pred cCcEEeHHHHHHHHh--cCCceEEEhHHHHHHHHHHHHHHHHcCCcceeccCCcc------hHHHHHHHHhccCCC
Confidence 455433333444444 45899999999999999999999999999999999988 999999999999744
No 26
>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=98.62 E-value=3.2e-08 Score=65.58 Aligned_cols=44 Identities=30% Similarity=0.706 Sum_probs=33.2
Q ss_pred CccccccccccccCC------------CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCc
Q 028376 23 DEETCPICQEKLGNQ------------KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCR 77 (210)
Q Consensus 23 ~~~~C~iC~~~~~~~------------~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr 77 (210)
.+..|+||++++.++ ....+|||.|+..|+.+|++ ....||+||
T Consensus 18 ~~d~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~-----------~~~~CP~CR 73 (73)
T PF12678_consen 18 ADDNCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLK-----------QNNTCPLCR 73 (73)
T ss_dssp CCSBETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHT-----------TSSB-TTSS
T ss_pred cCCcccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHh-----------cCCcCCCCC
Confidence 345699999988332 25568999999999999973 334999997
No 27
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.61 E-value=2.6e-08 Score=85.76 Aligned_cols=51 Identities=22% Similarity=0.563 Sum_probs=41.9
Q ss_pred CccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCe
Q 028376 23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNI 85 (210)
Q Consensus 23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l 85 (210)
....|+||.+.+..+ ++++|||.||..|+..++.. ...||.|+..+....+
T Consensus 25 ~~l~C~IC~d~~~~P-vitpCgH~FCs~CI~~~l~~-----------~~~CP~Cr~~~~~~~L 75 (397)
T TIGR00599 25 TSLRCHICKDFFDVP-VLTSCSHTFCSLCIRRCLSN-----------QPKCPLCRAEDQESKL 75 (397)
T ss_pred cccCCCcCchhhhCc-cCCCCCCchhHHHHHHHHhC-----------CCCCCCCCCccccccC
Confidence 457999999999874 78999999999999999632 3479999998765544
No 28
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=98.52 E-value=3e-08 Score=89.96 Aligned_cols=54 Identities=20% Similarity=0.599 Sum_probs=45.8
Q ss_pred CccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEE
Q 028376 23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAY 87 (210)
Q Consensus 23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~ 87 (210)
+...|+.|...+.+ .+++.|||+||..|+...++. ...+||.|..+|..+|+..
T Consensus 642 ~~LkCs~Cn~R~Kd-~vI~kC~H~FC~~Cvq~r~et----------RqRKCP~Cn~aFganDv~~ 695 (698)
T KOG0978|consen 642 ELLKCSVCNTRWKD-AVITKCGHVFCEECVQTRYET----------RQRKCPKCNAAFGANDVHR 695 (698)
T ss_pred hceeCCCccCchhh-HHHHhcchHHHHHHHHHHHHH----------hcCCCCCCCCCCCcccccc
Confidence 34579999988877 599999999999999998754 4568999999999998753
No 29
>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=98.52 E-value=8.2e-08 Score=79.60 Aligned_cols=53 Identities=28% Similarity=0.582 Sum_probs=39.5
Q ss_pred Ccccccccccc--ccCC--CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCe
Q 028376 23 DEETCPICQEK--LGNQ--KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNI 85 (210)
Q Consensus 23 ~~~~C~iC~~~--~~~~--~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l 85 (210)
++..||+|... +... ..+.+|||.||..|+..++ ..+...||.|+.++...++
T Consensus 2 d~~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~----------~~~~~~CP~C~~~lrk~~f 58 (309)
T TIGR00570 2 DDQGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLF----------VRGSGSCPECDTPLRKNNF 58 (309)
T ss_pred CCCCCCcCCCCCccCcccccccCCCCCcccHHHHHHHh----------cCCCCCCCCCCCccchhhc
Confidence 45789999773 3322 1334899999999999985 2345689999999988764
No 30
>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=98.51 E-value=8.3e-08 Score=54.75 Aligned_cols=39 Identities=38% Similarity=0.931 Sum_probs=31.6
Q ss_pred cccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCC
Q 028376 27 CPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTC 76 (210)
Q Consensus 27 C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~C 76 (210)
|+||.+.... .++++|||.||..|+..|++. ....||.|
T Consensus 1 C~iC~~~~~~-~~~~~C~H~~c~~C~~~~~~~----------~~~~CP~C 39 (39)
T smart00184 1 CPICLEELKD-PVVLPCGHTFCRSCIRKWLKS----------GNNTCPIC 39 (39)
T ss_pred CCcCccCCCC-cEEecCCChHHHHHHHHHHHh----------CcCCCCCC
Confidence 7899988654 588999999999999999741 33579987
No 31
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=98.51 E-value=8.4e-08 Score=80.35 Aligned_cols=51 Identities=25% Similarity=0.644 Sum_probs=41.5
Q ss_pred CCCccccccccccccCC------------CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376 21 KADEETCPICQEKLGNQ------------KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI 82 (210)
Q Consensus 21 ~~~~~~C~iC~~~~~~~------------~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~ 82 (210)
..++..|.||++.+..+ +..++|||+++..|++.|+|++ .+||.||.++-.
T Consensus 284 ~n~D~~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~ERq-----------QTCPICr~p~if 346 (491)
T COG5243 284 TNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQ-----------QTCPICRRPVIF 346 (491)
T ss_pred cCCCCeEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHHhc-----------cCCCcccCcccc
Confidence 56788999999985432 3678999999999999998763 489999998543
No 32
>KOG4439 consensus RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=98.50 E-value=3e-07 Score=82.97 Aligned_cols=70 Identities=20% Similarity=0.349 Sum_probs=65.4
Q ss_pred CCCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 118 GSYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 118 ~~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
..+|+|+..+++.+..+ .....+|+||-|||+++|+++...|+..|+.|..++|... .++|+.+++.|+.
T Consensus 725 ~r~S~Ki~~~l~~le~i-~~~skeK~viVSQwtsvLniv~~hi~~~g~~y~si~Gqv~------vK~Rq~iv~~FN~ 794 (901)
T KOG4439|consen 725 DRPSCKIAMVLEILETI-LTSSKEKVVIVSQWTSVLNIVRKHIQKGGHIYTSITGQVL------VKDRQEIVDEFNQ 794 (901)
T ss_pred ccchhHHHHHHHHHHHH-hhcccceeeehhHHHHHHHHHHHHHhhCCeeeeeecCccc------hhHHHHHHHHHHh
Confidence 36899999999999998 5677899999999999999999999999999999999966 9999999999996
No 33
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.50 E-value=5.3e-08 Score=78.20 Aligned_cols=53 Identities=25% Similarity=0.662 Sum_probs=42.9
Q ss_pred CCccccccccccccCCCeecCCCCcchHhhHHH-HHHHhhhccccCCCccccccCCcccccCCCe
Q 028376 22 ADEETCPICQEKLGNQKMVFQCGHFTCCKCFFA-MTEQRLIHDNKVKNEWVMCPTCRQRTDIGNI 85 (210)
Q Consensus 22 ~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~-~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l 85 (210)
..+..|++|.+.+.. +..++|||+||..|+.. |.. .....||.||+...+.++
T Consensus 213 ~~d~kC~lC~e~~~~-ps~t~CgHlFC~~Cl~~~~t~----------~k~~~CplCRak~~pk~v 266 (271)
T COG5574 213 LADYKCFLCLEEPEV-PSCTPCGHLFCLSCLLISWTK----------KKYEFCPLCRAKVYPKKV 266 (271)
T ss_pred ccccceeeeecccCC-cccccccchhhHHHHHHHHHh----------hccccCchhhhhccchhh
Confidence 446789999999987 58999999999999998 632 233459999998877765
No 34
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=98.49 E-value=3.7e-08 Score=81.51 Aligned_cols=50 Identities=26% Similarity=0.524 Sum_probs=43.4
Q ss_pred ccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCe
Q 028376 24 EETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNI 85 (210)
Q Consensus 24 ~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l 85 (210)
...|.||.+.+.. +++++|+|.||.-||..++ ...+.||.|+.++...++
T Consensus 23 lLRC~IC~eyf~i-p~itpCsHtfCSlCIR~~L-----------~~~p~CP~C~~~~~Es~L 72 (442)
T KOG0287|consen 23 LLRCGICFEYFNI-PMITPCSHTFCSLCIRKFL-----------SYKPQCPTCCVTVTESDL 72 (442)
T ss_pred HHHHhHHHHHhcC-ceeccccchHHHHHHHHHh-----------ccCCCCCceecccchhhh
Confidence 3589999999987 5999999999999999995 567899999998876654
No 35
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=98.45 E-value=7.4e-08 Score=78.23 Aligned_cols=49 Identities=24% Similarity=0.552 Sum_probs=41.8
Q ss_pred CccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376 23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG 83 (210)
Q Consensus 23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~ 83 (210)
....|.||.+.+.. +.+++|||.||.-||..++ +..+.||+||......
T Consensus 24 s~lrC~IC~~~i~i-p~~TtCgHtFCslCIR~hL-----------~~qp~CP~Cr~~~~es 72 (391)
T COG5432 24 SMLRCRICDCRISI-PCETTCGHTFCSLCIRRHL-----------GTQPFCPVCREDPCES 72 (391)
T ss_pred hHHHhhhhhheeec-ceecccccchhHHHHHHHh-----------cCCCCCccccccHHhh
Confidence 34679999999987 4999999999999999995 6678999999976544
No 36
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=98.45 E-value=1.6e-07 Score=63.16 Aligned_cols=53 Identities=21% Similarity=0.495 Sum_probs=39.0
Q ss_pred CccccccccccccC------------CCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376 23 DEETCPICQEKLGN------------QKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG 83 (210)
Q Consensus 23 ~~~~C~iC~~~~~~------------~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~ 83 (210)
++..|+||...+.. +.+.-.|+|.|+..||.+|++.. .....||+||++....
T Consensus 20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~--------~~~~~CPmCR~~w~~k 84 (85)
T PF12861_consen 20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQ--------SSKGQCPMCRQPWKFK 84 (85)
T ss_pred CCCceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccc--------cCCCCCCCcCCeeeeC
Confidence 36778888766542 12556899999999999998652 3356999999986543
No 37
>KOG0392 consensus SNF2 family DNA-dependent ATPase domain-containing protein [Transcription]
Probab=98.44 E-value=5.9e-07 Score=85.17 Aligned_cols=74 Identities=16% Similarity=0.321 Sum_probs=61.3
Q ss_pred CCCchHHHHHHHHHHHHhc------------CCCCcEEEEcchHHHHHHHHHHHHhC---CceEEEeeCCCCCCcchhhH
Q 028376 119 SYGTKIEAVTRRILWIKST------------DPKAKILVFSSWNDVLDVLEHAFIAN---NITCIKMKGENHKLPSANLQ 183 (210)
Q Consensus 119 ~~SsKi~al~~~L~~~~~~------------~~~~K~iVFSQf~~~L~li~~~L~~~---gi~~~~~~G~m~~~~~~~~~ 183 (210)
..+.|+.||.+.|.+=--. -.+.+++||.||.+|||+++..|-+. .+.|.|+||+.+ +.
T Consensus 1307 ~hspKl~AL~qLL~eCGig~~~~~~~g~~s~vsqHRiLIFcQlK~mlDlVekDL~k~~mpsVtymRLDGSVp------p~ 1380 (1549)
T KOG0392|consen 1307 QHSPKLSALKQLLSECGIGNNSDSEVGTPSDVSQHRILIFCQLKSMLDLVEKDLFKKYMPSVTYMRLDGSVP------PG 1380 (1549)
T ss_pred hhchhHHHHHHHHHHhCCCCCCcccccCcchhccceeEEeeeHHHHHHHHHHHHhhhhcCceeEEEecCCCC------cH
Confidence 3578999998888643221 13579999999999999999999864 567889999999 99
Q ss_pred hhhHHHHHHhhcCCCC
Q 028376 184 HRNALQKELTRHMPSS 199 (210)
Q Consensus 184 ~R~~~l~~F~~~~p~~ 199 (210)
+|.+++++||+ ||+.
T Consensus 1381 ~R~kiV~~FN~-DptI 1395 (1549)
T KOG0392|consen 1381 DRQKIVERFNE-DPTI 1395 (1549)
T ss_pred HHHHHHHHhcC-CCce
Confidence 99999999999 8864
No 38
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=98.42 E-value=5.5e-08 Score=61.61 Aligned_cols=49 Identities=27% Similarity=0.584 Sum_probs=24.8
Q ss_pred cccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376 25 ETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA 86 (210)
Q Consensus 25 ~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~ 86 (210)
..|++|.+.+..+..+..|.|+||..|+...+ + ..||+|+.|....|+.
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~-----------~--~~CPvC~~Paw~qD~~ 56 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCI-----------G--SECPVCHTPAWIQDIQ 56 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGGGGT-----------T--TB-SSS--B-S-SS--
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhHHhc-----------C--CCCCCcCChHHHHHHH
Confidence 57999999998876689999999999997653 1 2599999988777654
No 39
>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=98.39 E-value=2.6e-07 Score=61.26 Aligned_cols=53 Identities=23% Similarity=0.259 Sum_probs=40.3
Q ss_pred CccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376 23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA 86 (210)
Q Consensus 23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~ 86 (210)
+.+.|+|+.+.+.+ ++++++||.|++.|+..|++ .....||.|+.++...+++
T Consensus 3 ~~f~CpIt~~lM~d-PVi~~~G~tyer~~I~~~l~----------~~~~~~P~t~~~l~~~~l~ 55 (73)
T PF04564_consen 3 DEFLCPITGELMRD-PVILPSGHTYERSAIERWLE----------QNGGTDPFTRQPLSESDLI 55 (73)
T ss_dssp GGGB-TTTSSB-SS-EEEETTSEEEEHHHHHHHHC----------TTSSB-TTT-SB-SGGGSE
T ss_pred cccCCcCcCcHhhC-ceeCCcCCEEcHHHHHHHHH----------cCCCCCCCCCCcCCcccce
Confidence 45789999999998 49999999999999999973 3467899999998877664
No 40
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.35 E-value=2.1e-07 Score=76.07 Aligned_cols=49 Identities=22% Similarity=0.400 Sum_probs=40.0
Q ss_pred ccccccccccccC--CCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376 24 EETCPICQEKLGN--QKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI 82 (210)
Q Consensus 24 ~~~C~iC~~~~~~--~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~ 82 (210)
..+|.||+..+.. ..+++||.|.|+..|+++|+- +....||+||.++.+
T Consensus 323 GveCaICms~fiK~d~~~vlPC~H~FH~~Cv~kW~~----------~y~~~CPvCrt~iPP 373 (374)
T COG5540 323 GVECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLL----------GYSNKCPVCRTAIPP 373 (374)
T ss_pred CceEEEEhhhhcccceEEEeccCceechhHHHHHHh----------hhcccCCccCCCCCC
Confidence 4789999988753 357899999999999999972 456789999998753
No 41
>COG0553 HepA Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]
Probab=98.34 E-value=1.8e-06 Score=81.72 Aligned_cols=69 Identities=23% Similarity=0.387 Sum_probs=61.1
Q ss_pred CCC-chHHHHHHHH-HHHHhcCCCC--cEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 119 SYG-TKIEAVTRRI-LWIKSTDPKA--KILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 119 ~~S-sKi~al~~~L-~~~~~~~~~~--K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
..| .|+..+.+.| ..+..+ +. |+||||||+.+|++++..|...++.|++++|+++ .++|...|++|+.
T Consensus 688 ~~s~~k~~~l~~ll~~~~~~~--~~~~kvlifsq~t~~l~il~~~l~~~~~~~~~ldG~~~------~~~r~~~i~~f~~ 759 (866)
T COG0553 688 QLSKGKLQALDELLLDKLLEE--GHYHKVLIFSQFTPVLDLLEDYLKALGIKYVRLDGSTP------AKRRQELIDRFNA 759 (866)
T ss_pred hccchHHHHHHHHHHHHHHhh--cccccEEEEeCcHHHHHHHHHHHHhcCCcEEEEeCCCC------hhhHHHHHHHhhc
Confidence 345 8999999888 555544 45 9999999999999999999999999999999987 9999999999998
Q ss_pred c
Q 028376 195 H 195 (210)
Q Consensus 195 ~ 195 (210)
+
T Consensus 760 ~ 760 (866)
T COG0553 760 D 760 (866)
T ss_pred C
Confidence 4
No 42
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.26 E-value=6.1e-07 Score=75.62 Aligned_cols=48 Identities=25% Similarity=0.597 Sum_probs=39.0
Q ss_pred ccccccccccCC--CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376 26 TCPICQEKLGNQ--KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG 83 (210)
Q Consensus 26 ~C~iC~~~~~~~--~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~ 83 (210)
.|.||++.+... ..++||.|.|+..|++.|+.+ .+..||+|+..+...
T Consensus 231 ~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~----------~r~~CPvCK~di~~~ 280 (348)
T KOG4628|consen 231 TCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQ----------TRTFCPVCKRDIRTD 280 (348)
T ss_pred eEEEeecccccCCeeeEecCCCchhhccchhhHhh----------cCccCCCCCCcCCCC
Confidence 899999988653 467999999999999999854 345699999966543
No 43
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.22 E-value=2.4e-07 Score=56.36 Aligned_cols=47 Identities=30% Similarity=0.781 Sum_probs=37.7
Q ss_pred ccccccccccccCCCeecCCCC-cchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376 24 EETCPICQEKLGNQKMVFQCGH-FTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD 81 (210)
Q Consensus 24 ~~~C~iC~~~~~~~~~~~~CgH-~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~ 81 (210)
+.+|.||.+.+.+ .++..||| ..|.+|-.+.. ......||.||+++.
T Consensus 7 ~dECTICye~pvd-sVlYtCGHMCmCy~Cg~rl~----------~~~~g~CPiCRapi~ 54 (62)
T KOG4172|consen 7 SDECTICYEHPVD-SVLYTCGHMCMCYACGLRLK----------KALHGCCPICRAPIK 54 (62)
T ss_pred ccceeeeccCcch-HHHHHcchHHhHHHHHHHHH----------HccCCcCcchhhHHH
Confidence 4899999998887 48899999 57889987763 235568999999864
No 44
>KOG0390 consensus DNA repair protein, SNF2 family [Replication, recombination and repair]
Probab=98.18 E-value=5.3e-06 Score=76.69 Aligned_cols=71 Identities=17% Similarity=0.298 Sum_probs=63.2
Q ss_pred cCCCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 117 QGSYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 117 ~~~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
.+..|.|+..|+..+..++ +...+|+++-|.++.+|++++..++..|..++|+||+|+ .++|++++++|+.
T Consensus 573 ~~~ks~kl~~L~~ll~~~~-ek~~~~~v~Isny~~tldl~e~~~~~~g~~~~rLdG~~~------~~qRq~~vd~FN~ 643 (776)
T KOG0390|consen 573 DGSKSGKLLVLVFLLEVIR-EKLLVKSVLISNYTQTLDLFEQLCRWRGYEVLRLDGKTS------IKQRQKLVDTFND 643 (776)
T ss_pred cchhhhHHHHHHHHHHHHh-hhcceEEEEeccHHHHHHHHHHHHhhcCceEEEEcCCCc------hHHHHHHHHhccC
Confidence 4556889999998875554 457899999999999999999999999999999999987 9999999999997
No 45
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=98.17 E-value=8.6e-07 Score=81.02 Aligned_cols=66 Identities=20% Similarity=0.271 Sum_probs=59.6
Q ss_pred CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
.+.|..-|...+++++. .+++++||||++.+|||++..+...| .|.|+||+.. -..|+++|++|+-
T Consensus 613 ~~~k~~~l~~~~~~l~~--~ghrvl~~~q~~~~ldlled~~~~~~-~~~r~dG~~~------~~~rq~ai~~~n~ 678 (696)
T KOG0383|consen 613 ASGKLTLLLKMLKKLKS--SGHRVLIFSQMIHMLDLLEDYLTYEG-KYERIDGPIT------GPERQAAIDRFNA 678 (696)
T ss_pred HHHHHHHHHHHHHHHHh--cchhhHHHHHHHHHHHHhHHHHhccC-cceeccCCcc------chhhhhhccccCC
Confidence 36778888888888874 48999999999999999999999999 9999999966 8999999999996
No 46
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.14 E-value=1.5e-06 Score=70.31 Aligned_cols=51 Identities=24% Similarity=0.665 Sum_probs=41.4
Q ss_pred CCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376 22 ADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD 81 (210)
Q Consensus 22 ~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~ 81 (210)
..+.+|++|.+.+..|-++.+|||+||..|+...+.. .....||.|+.+..
T Consensus 237 t~~~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~---------~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 237 TSDTECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLW---------DASFTCPLCGENVE 287 (298)
T ss_pred cCCceeeccCCCCCCCeeeccccceeehhhhhhhhcc---------hhhcccCccCCCCc
Confidence 4668999999999887666779999999999987532 44579999988654
No 47
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.06 E-value=2.1e-06 Score=77.68 Aligned_cols=52 Identities=31% Similarity=0.546 Sum_probs=42.4
Q ss_pred CCccccccccccccCC----CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCC
Q 028376 22 ADEETCPICQEKLGNQ----KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGN 84 (210)
Q Consensus 22 ~~~~~C~iC~~~~~~~----~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~ 84 (210)
..+..|+||.+.+... +..++|||+||..|+..|+++. ..||.||..+....
T Consensus 289 ~~~~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~er~-----------qtCP~CR~~~~~~~ 344 (543)
T KOG0802|consen 289 LSDELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFERQ-----------QTCPTCRTVLYDYV 344 (543)
T ss_pred hcCCeeeeechhhccccccccceeecccchHHHHHHHHHHHh-----------CcCCcchhhhhccc
Confidence 3467899999998774 5889999999999999998763 48999999554443
No 48
>PRK04914 ATP-dependent helicase HepA; Validated
Probab=98.03 E-value=2e-05 Score=75.30 Aligned_cols=67 Identities=13% Similarity=0.132 Sum_probs=59.4
Q ss_pred CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHH-HhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376 119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAF-IANNITCIKMKGENHKLPSANLQHRNALQKELTRH 195 (210)
Q Consensus 119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L-~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~ 195 (210)
....|++.|++.|... .+.|+|||+++..+.+.|...| ...||+...|+|+|+ ..+|.++++.|+.+
T Consensus 476 ~~d~Ki~~L~~~L~~~----~~~KvLVF~~~~~t~~~L~~~L~~~~Gi~~~~ihG~~s------~~eR~~~~~~F~~~ 543 (956)
T PRK04914 476 NFDPRVEWLIDFLKSH----RSEKVLVICAKAATALQLEQALREREGIRAAVFHEGMS------IIERDRAAAYFADE 543 (956)
T ss_pred ccCHHHHHHHHHHHhc----CCCeEEEEeCcHHHHHHHHHHHhhccCeeEEEEECCCC------HHHHHHHHHHHhcC
Confidence 4568999999888653 4789999999999999999999 578999999999977 99999999999973
No 49
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.98 E-value=3.1e-06 Score=70.06 Aligned_cols=45 Identities=38% Similarity=0.844 Sum_probs=38.5
Q ss_pred CCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcc
Q 028376 22 ADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQ 78 (210)
Q Consensus 22 ~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~ 78 (210)
.+...|+||++.+..+ .+++|||.||..|+..+.. ....||.||.
T Consensus 11 ~~~~~C~iC~~~~~~p-~~l~C~H~~c~~C~~~~~~-----------~~~~Cp~cr~ 55 (386)
T KOG2177|consen 11 QEELTCPICLEYFREP-VLLPCGHNFCRACLTRSWE-----------GPLSCPVCRP 55 (386)
T ss_pred cccccChhhHHHhhcC-ccccccchHhHHHHHHhcC-----------CCcCCcccCC
Confidence 4667999999999986 8999999999999999842 3468999993
No 50
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.95 E-value=3.6e-06 Score=68.95 Aligned_cols=50 Identities=26% Similarity=0.482 Sum_probs=41.8
Q ss_pred CccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376 23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG 83 (210)
Q Consensus 23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~ 83 (210)
-..+|+||+....-+ +.+.|+|.||..|++-.. ......|++||.++..+
T Consensus 6 ~~~eC~IC~nt~n~P-v~l~C~HkFCyiCiKGsy----------~ndk~~CavCR~pids~ 55 (324)
T KOG0824|consen 6 KKKECLICYNTGNCP-VNLYCFHKFCYICIKGSY----------KNDKKTCAVCRFPIDST 55 (324)
T ss_pred cCCcceeeeccCCcC-ccccccchhhhhhhcchh----------hcCCCCCceecCCCCcc
Confidence 356899999988764 899999999999999764 35566899999999765
No 51
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.91 E-value=5.5e-06 Score=69.49 Aligned_cols=49 Identities=27% Similarity=0.644 Sum_probs=40.1
Q ss_pred CCccccccccccccCCCeecCCCC-cchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376 22 ADEETCPICQEKLGNQKMVFQCGH-FTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI 82 (210)
Q Consensus 22 ~~~~~C~iC~~~~~~~~~~~~CgH-~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~ 82 (210)
+...+|.||+....+ .+++||.| ..|.+|.+.+. -....||+||.++..
T Consensus 288 ~~gkeCVIClse~rd-t~vLPCRHLCLCs~Ca~~Lr-----------~q~n~CPICRqpi~~ 337 (349)
T KOG4265|consen 288 ESGKECVICLSESRD-TVVLPCRHLCLCSGCAKSLR-----------YQTNNCPICRQPIEE 337 (349)
T ss_pred cCCCeeEEEecCCcc-eEEecchhhehhHhHHHHHH-----------HhhcCCCccccchHh
Confidence 345789999999987 59999999 67999999872 344589999998754
No 52
>KOG1000 consensus Chromatin remodeling protein HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure and dynamics]
Probab=97.90 E-value=3.8e-05 Score=67.38 Aligned_cols=69 Identities=25% Similarity=0.303 Sum_probs=62.4
Q ss_pred CCchHHHHHHHHHH--HHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 120 YGTKIEAVTRRILW--IKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 120 ~SsKi~al~~~L~~--~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
-..|+.++.+.|.. +.-..++.|.|||-....+||-|+..+.+.|++++|+||+.+ ...|...++.|+.
T Consensus 470 giaK~~av~eyi~~~~~l~d~~~~KflVFaHH~~vLd~Iq~~~~~r~vg~IRIDGst~------s~~R~ll~qsFQ~ 540 (689)
T KOG1000|consen 470 GIAKAAAVCEYILENYFLPDAPPRKFLVFAHHQIVLDTIQVEVNKRKVGSIRIDGSTP------SHRRTLLCQSFQT 540 (689)
T ss_pred cccccHHHHHHHHhCcccccCCCceEEEEehhHHHHHHHHHHHHHcCCCeEEecCCCC------chhHHHHHHHhcc
Confidence 46899999999986 122467899999999999999999999999999999999988 9999999999998
No 53
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.88 E-value=6.3e-06 Score=71.16 Aligned_cols=66 Identities=23% Similarity=0.385 Sum_probs=47.7
Q ss_pred hhhccCchHHHHHhcCCCCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376 5 VVTISNSTKHRIESLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI 82 (210)
Q Consensus 5 ~~~~~~~~~~~~~~l~~~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~ 82 (210)
++..+..............+++|.+|...+.. ++.++|||.||..|+.+.+ .....||.||..+..
T Consensus 65 ~~~~~~~~~~~s~~~~~~sef~c~vc~~~l~~-pv~tpcghs~c~~Cl~r~l-----------d~~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 65 TMADSTPKALLSGPEEIRSEFECCVCSRALYP-PVVTPCGHSFCLECLDRSL-----------DQETECPLCRDELVE 130 (398)
T ss_pred hhhhhhhhhhhccCccccchhhhhhhHhhcCC-CccccccccccHHHHHHHh-----------ccCCCCccccccccc
Confidence 33333333333333334677899999998887 5889999999999988853 466789999998763
No 54
>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair]
Probab=97.85 E-value=7.6e-05 Score=65.59 Aligned_cols=82 Identities=10% Similarity=0.179 Sum_probs=70.0
Q ss_pred CCCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEE-EeeCC--CCCCcchhhHhhhHHHHHHhh
Q 028376 118 GSYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCI-KMKGE--NHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 118 ~~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~-~~~G~--m~~~~~~~~~~R~~~l~~F~~ 194 (210)
+....|++.|.+.|.+..+..++.++|||++|.+..+.|-..|...|+.-. +|-|. ......|+.++...+|+.|++
T Consensus 344 ~v~HPKl~~l~eilke~~~k~~~~RvIVFT~yRdTae~i~~~L~~~~~~~~~rFiGQa~r~~~~GMsQkeQ~eiI~~Fr~ 423 (542)
T COG1111 344 GVEHPKLEKLREILKEQLEKNGDSRVIVFTEYRDTAEEIVNFLKKIGIKARVRFIGQASREGDKGMSQKEQKEIIDQFRK 423 (542)
T ss_pred cCCCccHHHHHHHHHHHHhcCCCceEEEEehhHhHHHHHHHHHHhcCCcceeEEeeccccccccccCHHHHHHHHHHHhc
Confidence 445689999999999999888899999999999999999999999999876 88773 223366889999999999998
Q ss_pred cCCCC
Q 028376 195 HMPSS 199 (210)
Q Consensus 195 ~~p~~ 199 (210)
++=++
T Consensus 424 Ge~nV 428 (542)
T COG1111 424 GEYNV 428 (542)
T ss_pred CCceE
Confidence 65443
No 55
>KOG1015 consensus Transcription regulator XNP/ATRX, DEAD-box superfamily [Transcription]
Probab=97.85 E-value=3.2e-05 Score=72.35 Aligned_cols=68 Identities=19% Similarity=0.212 Sum_probs=59.0
Q ss_pred CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHh----------------------CCceEEEeeCCCCC
Q 028376 119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIA----------------------NNITCIKMKGENHK 176 (210)
Q Consensus 119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~----------------------~gi~~~~~~G~m~~ 176 (210)
..|.|+--|++.|..-- +=++|.|||||-...|++|+.+|.. .|..|.|+||+..
T Consensus 1123 ~~SgKmiLLleIL~mce--eIGDKlLVFSQSL~SLdLIe~fLe~v~r~gk~~~d~~~~~~~eGkW~~GkDyyriDGst~- 1199 (1567)
T KOG1015|consen 1123 EHSGKMILLLEILRMCE--EIGDKLLVFSQSLISLDLIEDFLELVSREGKEDKDKPLIYKGEGKWLRGKDYYRLDGSTT- 1199 (1567)
T ss_pred hcCcceehHHHHHHHHH--HhcceeEEeecccchhHHHHHHHHhhcccCccccccccccccccceecCCceEEecCccc-
Confidence 35889988888887543 4589999999999999999999974 3778999999987
Q ss_pred CcchhhHhhhHHHHHHhh
Q 028376 177 LPSANLQHRNALQKELTR 194 (210)
Q Consensus 177 ~~~~~~~~R~~~l~~F~~ 194 (210)
..+|.+..++|+.
T Consensus 1200 -----s~~R~k~~~~FNd 1212 (1567)
T KOG1015|consen 1200 -----SQSRKKWAEEFND 1212 (1567)
T ss_pred -----HHHHHHHHHHhcC
Confidence 9999999999986
No 56
>PRK13766 Hef nuclease; Provisional
Probab=97.85 E-value=9.2e-05 Score=69.81 Aligned_cols=79 Identities=13% Similarity=0.220 Sum_probs=66.4
Q ss_pred CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCC--cchhhHhhhHHHHHHhhcC
Q 028376 119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKL--PSANLQHRNALQKELTRHM 196 (210)
Q Consensus 119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~--~~~~~~~R~~~l~~F~~~~ 196 (210)
....|++.|.+.|.++....++.|+|||+++..+.+.|...|...|+++.++.|..+.. ..|+..+|.+++++|+++.
T Consensus 344 ~~~pK~~~L~~il~~~~~~~~~~kvlIF~~~~~t~~~L~~~L~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~g~ 423 (773)
T PRK13766 344 IEHPKLEKLREIVKEQLGKNPDSRIIVFTQYRDTAEKIVDLLEKEGIKAVRFVGQASKDGDKGMSQKEQIEILDKFRAGE 423 (773)
T ss_pred cCChHHHHHHHHHHHHHhcCCCCeEEEEeCcHHHHHHHHHHHHhCCCceEEEEccccccccCCCCHHHHHHHHHHHHcCC
Confidence 44689999999999888777899999999999999999999999999999999972110 1244899999999999854
Q ss_pred C
Q 028376 197 P 197 (210)
Q Consensus 197 p 197 (210)
.
T Consensus 424 ~ 424 (773)
T PRK13766 424 F 424 (773)
T ss_pred C
Confidence 3
No 57
>KOG0388 consensus SNF2 family DNA-dependent ATPase [Replication, recombination and repair]
Probab=97.74 E-value=4.8e-05 Score=69.34 Aligned_cols=68 Identities=12% Similarity=0.316 Sum_probs=61.8
Q ss_pred CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
.-|.|+..|=+.|.+++.. +.++++|-|-|.|+++++..|.-.|..|+|+||+-. ...|..++..|+.
T Consensus 1025 tdSgKL~~LDeLL~kLkae--gHRvL~yfQMTkM~dl~EdYl~yr~Y~ylRLDGSsk------~~dRrd~vrDwQ~ 1092 (1185)
T KOG0388|consen 1025 TDSGKLVVLDELLPKLKAE--GHRVLMYFQMTKMIDLIEDYLVYRGYTYLRLDGSSK------ASDRRDVVRDWQA 1092 (1185)
T ss_pred ccccceeeHHHHHHHhhcC--CceEEehhHHHHHHHHHHHHHHhhccceEEecCcch------hhHHHHHHhhccC
Confidence 4578888888888888754 899999999999999999999999999999999966 9999999999997
No 58
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.73 E-value=1.3e-05 Score=69.77 Aligned_cols=49 Identities=22% Similarity=0.575 Sum_probs=38.1
Q ss_pred CccccccccccccCC----------------CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376 23 DEETCPICQEKLGNQ----------------KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD 81 (210)
Q Consensus 23 ~~~~C~iC~~~~~~~----------------~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~ 81 (210)
....|+||+.++.-. .+++||.|+|+..|+.+|.+. ..-.||+||.++.
T Consensus 570 ~t~dC~ICMt~I~l~~~~s~~~~~~~~~~~nYm~tPC~HifH~~CL~~WMd~----------ykl~CPvCR~pLP 634 (636)
T KOG0828|consen 570 RTNDCVICMTPIDLRSTGSDCMVASMMVRRNYMLTPCHHIFHRQCLLQWMDT----------YKLICPVCRCPLP 634 (636)
T ss_pred ccccceEeccccceeeccCcchhhhhhhhccccccchHHHHHHHHHHHHHhh----------hcccCCccCCCCC
Confidence 346899998876421 367899999999999999642 3347999999875
No 59
>KOG0386 consensus Chromatin remodeling complex SWI/SNF, component SWI2 and related ATPases (DNA/RNA helicase superfamily) [Chromatin structure and dynamics; Transcription]
Probab=97.73 E-value=5.3e-05 Score=71.10 Aligned_cols=70 Identities=20% Similarity=0.370 Sum_probs=63.0
Q ss_pred CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376 120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP 197 (210)
Q Consensus 120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p 197 (210)
-+-|.+-|-+.|-++++. +.+++.|+|-|.++++++..|.-.++.|+|+||+.. ..+|...|+.|+.+|.
T Consensus 708 ~sGKfELLDRiLPKLkat--gHRVLlF~qMTrlmdimEdyL~~~~~kYlRLDG~TK------~~eRg~ll~~FN~Pds 777 (1157)
T KOG0386|consen 708 VSGKFELLDRILPKLKAT--GHRVLLFSQMTRLMDILEDYLQIREYKYLRLDGQTK------VEERGDLLEIFNAPDS 777 (1157)
T ss_pred hccHHHHHHhhhHHHHhc--CcchhhHHHHHHHHHHHHHHHhhhhhheeeecCCcc------hhhHHHHHHHhcCCCC
Confidence 367888888888888765 899999999999999999999999999999999988 9999999999997553
No 60
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=97.68 E-value=1.8e-05 Score=48.58 Aligned_cols=49 Identities=27% Similarity=0.636 Sum_probs=37.5
Q ss_pred CccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCe
Q 028376 23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNI 85 (210)
Q Consensus 23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l 85 (210)
....|..|...-.. .++++|||++|..|+.-. .-..||.|.+++...++
T Consensus 6 ~~~~~~~~~~~~~~-~~~~pCgH~I~~~~f~~~-------------rYngCPfC~~~~~~~~~ 54 (55)
T PF14447_consen 6 PEQPCVFCGFVGTK-GTVLPCGHLICDNCFPGE-------------RYNGCPFCGTPFEFDDP 54 (55)
T ss_pred cceeEEEccccccc-cccccccceeeccccChh-------------hccCCCCCCCcccCCCC
Confidence 44578888776555 589999999999998743 33479999999887653
No 61
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.65 E-value=5.7e-06 Score=69.15 Aligned_cols=51 Identities=27% Similarity=0.568 Sum_probs=40.2
Q ss_pred CccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376 23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG 83 (210)
Q Consensus 23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~ 83 (210)
....|+||++.+......-.|+|.||.+||...+. .+...||.||+.+...
T Consensus 42 ~~v~c~icl~llk~tmttkeClhrfc~~ci~~a~r----------~gn~ecptcRk~l~Sk 92 (381)
T KOG0311|consen 42 IQVICPICLSLLKKTMTTKECLHRFCFDCIWKALR----------SGNNECPTCRKKLVSK 92 (381)
T ss_pred hhhccHHHHHHHHhhcccHHHHHHHHHHHHHHHHH----------hcCCCCchHHhhcccc
Confidence 45689999998876545569999999999988753 4556899999976543
No 62
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=97.57 E-value=0.0001 Score=62.69 Aligned_cols=53 Identities=30% Similarity=0.610 Sum_probs=41.5
Q ss_pred ccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376 24 EETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA 86 (210)
Q Consensus 24 ~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~ 86 (210)
...|-||.+.-.+ ..+-+|||+.|..|+..|-+. .....||.||..+.-.+-+
T Consensus 369 FeLCKICaendKd-vkIEPCGHLlCt~CLa~WQ~s---------d~gq~CPFCRcEIKGte~v 421 (563)
T KOG1785|consen 369 FELCKICAENDKD-VKIEPCGHLLCTSCLAAWQDS---------DEGQTCPFCRCEIKGTEPV 421 (563)
T ss_pred HHHHHHhhccCCC-cccccccchHHHHHHHhhccc---------CCCCCCCceeeEeccccce
Confidence 3579999886555 577899999999999999422 3366899999998776543
No 63
>cd00079 HELICc Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process
Probab=97.54 E-value=0.00071 Score=48.69 Aligned_cols=67 Identities=19% Similarity=0.288 Sum_probs=59.9
Q ss_pred chHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376 122 TKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM 196 (210)
Q Consensus 122 sKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~ 196 (210)
.|++.+.+.+..... ++.|+|||......++.+...|...++++..+.|+++ ...|..+++.|++++
T Consensus 12 ~k~~~i~~~i~~~~~--~~~~~lvf~~~~~~~~~~~~~l~~~~~~~~~~~~~~~------~~~~~~~~~~f~~~~ 78 (131)
T cd00079 12 EKLEALLELLKEHLK--KGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDGS------QEEREEVLKDFREGE 78 (131)
T ss_pred HHHHHHHHHHHhccc--CCCcEEEEeCcHHHHHHHHHHHHhcCCcEEEEECCCC------HHHHHHHHHHHHcCC
Confidence 688888888877543 5789999999999999999999999999999999977 999999999999855
No 64
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=97.53 E-value=3.8e-05 Score=48.20 Aligned_cols=45 Identities=20% Similarity=0.380 Sum_probs=30.4
Q ss_pred CCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccC
Q 028376 22 ADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPT 75 (210)
Q Consensus 22 ~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~ 75 (210)
.-...|||...++.+|..-..|||+|..+.+.+++. ......||+
T Consensus 9 ~~~~~CPiT~~~~~~PV~s~~C~H~fek~aI~~~i~---------~~~~~~CPv 53 (57)
T PF11789_consen 9 TISLKCPITLQPFEDPVKSKKCGHTFEKEAILQYIQ---------RNGSKRCPV 53 (57)
T ss_dssp B--SB-TTTSSB-SSEEEESSS--EEEHHHHHHHCT---------TTS-EE-SC
T ss_pred EeccCCCCcCChhhCCcCcCCCCCeecHHHHHHHHH---------hcCCCCCCC
Confidence 345789999999998655579999999999999972 256778998
No 65
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=97.49 E-value=3.8e-05 Score=59.43 Aligned_cols=45 Identities=27% Similarity=0.583 Sum_probs=37.1
Q ss_pred ccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccc
Q 028376 24 EETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRT 80 (210)
Q Consensus 24 ~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~ 80 (210)
.+.|.||...... ++++.|||.||..|...-. .....|.+|.+..
T Consensus 196 PF~C~iCKkdy~s-pvvt~CGH~FC~~Cai~~y-----------~kg~~C~~Cgk~t 240 (259)
T COG5152 196 PFLCGICKKDYES-PVVTECGHSFCSLCAIRKY-----------QKGDECGVCGKAT 240 (259)
T ss_pred ceeehhchhhccc-hhhhhcchhHHHHHHHHHh-----------ccCCcceecchhh
Confidence 4689999999887 5999999999999987653 4456899998754
No 66
>KOG2660 consensus Locus-specific chromosome binding proteins [Function unknown]
Probab=97.39 E-value=5.9e-05 Score=62.73 Aligned_cols=51 Identities=25% Similarity=0.508 Sum_probs=43.3
Q ss_pred CCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376 22 ADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG 83 (210)
Q Consensus 22 ~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~ 83 (210)
.....|.+|...+.++..++-|-|.||..|+..+++. ...||.|...+...
T Consensus 13 n~~itC~LC~GYliDATTI~eCLHTFCkSCivk~l~~-----------~~~CP~C~i~ih~t 63 (331)
T KOG2660|consen 13 NPHITCRLCGGYLIDATTITECLHTFCKSCIVKYLEE-----------SKYCPTCDIVIHKT 63 (331)
T ss_pred ccceehhhccceeecchhHHHHHHHHHHHHHHHHHHH-----------hccCCccceeccCc
Confidence 4557899999999987788999999999999999854 45899999877654
No 67
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=97.35 E-value=0.00012 Score=47.98 Aligned_cols=59 Identities=19% Similarity=0.244 Sum_probs=26.5
Q ss_pred cccccccccccc-CC--C-ee---cCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376 24 EETCPICQEKLG-NQ--K-MV---FQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI 82 (210)
Q Consensus 24 ~~~C~iC~~~~~-~~--~-~~---~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~ 82 (210)
..+|+||..... .. + .+ ..|++.|+..|+.+|+.........-.-....||.|+.++..
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~ 67 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISW 67 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEG
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeE
Confidence 468999987643 21 1 11 389999999999999976432211001223469999998754
No 68
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.35 E-value=0.00013 Score=61.87 Aligned_cols=60 Identities=25% Similarity=0.587 Sum_probs=42.7
Q ss_pred hcCCCCccccccccccccCC-------CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376 18 SLSKADEETCPICQEKLGNQ-------KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD 81 (210)
Q Consensus 18 ~l~~~~~~~C~iC~~~~~~~-------~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~ 81 (210)
.++...+..|.||++.+... +++.+|.|.||..|+..|-.. .+.. ......||.||....
T Consensus 155 a~~~s~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~--~q~~--~~~sksCP~CRv~s~ 221 (344)
T KOG1039|consen 155 ALQKSSEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQA--TQFE--SKTSKSCPFCRVPSS 221 (344)
T ss_pred CcCccccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhh--hccc--cccccCCCcccCccc
Confidence 45557788999999877543 244789999999999999422 1110 233678999999754
No 69
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=97.35 E-value=0.00023 Score=56.92 Aligned_cols=65 Identities=14% Similarity=0.262 Sum_probs=51.2
Q ss_pred HhcCCCCccccccccccccCC---CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEEccCcc
Q 028376 17 ESLSKADEETCPICQEKLGNQ---KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYADDRQ 92 (210)
Q Consensus 17 ~~l~~~~~~~C~iC~~~~~~~---~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~~~~~~ 92 (210)
..+..+....||+|.+.+.+. .++.+|||++|.+|++.++. .-..||+|..++...+|+......
T Consensus 214 ~l~a~s~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir-----------~D~v~pv~d~plkdrdiI~LqrGG 281 (303)
T KOG3039|consen 214 KLIAASKRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIR-----------KDMVDPVTDKPLKDRDIIGLQRGG 281 (303)
T ss_pred hhhhhccceecccchhhhcCccceEEeccCCcEeeHHHHHHhcc-----------ccccccCCCCcCcccceEeeeccc
Confidence 334455678899999988763 36779999999999999963 334799999999999998776543
No 70
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=97.35 E-value=0.00013 Score=43.83 Aligned_cols=44 Identities=36% Similarity=0.878 Sum_probs=21.6
Q ss_pred cccccccccCCC-ee--cCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccc
Q 028376 27 CPICQEKLGNQK-MV--FQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRT 80 (210)
Q Consensus 27 C~iC~~~~~~~~-~~--~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~ 80 (210)
||+|.+.+.... -+ =+||+-+|..|+....+ .....||.||.+.
T Consensus 1 cp~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~----------~~~g~CPgCr~~Y 47 (48)
T PF14570_consen 1 CPLCDEELDETDKDFYPCECGFQICRFCYHDILE----------NEGGRCPGCREPY 47 (48)
T ss_dssp -TTTS-B--CCCTT--SSTTS----HHHHHHHTT----------SS-SB-TTT--B-
T ss_pred CCCcccccccCCCccccCcCCCcHHHHHHHHHHh----------ccCCCCCCCCCCC
Confidence 789988874321 22 37899999999998842 3466899999875
No 71
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.28 E-value=8.4e-05 Score=60.90 Aligned_cols=45 Identities=29% Similarity=0.620 Sum_probs=37.3
Q ss_pred cccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376 25 ETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD 81 (210)
Q Consensus 25 ~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~ 81 (210)
+.|.||..++.. ++++.|||.||..|....+ ....+|++|.+.+.
T Consensus 242 f~c~icr~~f~~-pVvt~c~h~fc~~ca~~~~-----------qk~~~c~vC~~~t~ 286 (313)
T KOG1813|consen 242 FKCFICRKYFYR-PVVTKCGHYFCEVCALKPY-----------QKGEKCYVCSQQTH 286 (313)
T ss_pred cccccccccccc-chhhcCCceeehhhhcccc-----------ccCCcceecccccc
Confidence 469999999988 5999999999999987763 34468999988654
No 72
>PF04641 Rtf2: Rtf2 RING-finger
Probab=97.23 E-value=0.00042 Score=57.10 Aligned_cols=57 Identities=18% Similarity=0.364 Sum_probs=44.3
Q ss_pred CCccccccccccccCC---CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEEccC
Q 028376 22 ADEETCPICQEKLGNQ---KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYADD 90 (210)
Q Consensus 22 ~~~~~C~iC~~~~~~~---~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~~~~ 90 (210)
...+.|||....+... ..+.+|||+|+..++.++ . ....||+|..++...+|+.+.+
T Consensus 111 ~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~~alke~-----------k-~~~~Cp~c~~~f~~~DiI~Lnp 170 (260)
T PF04641_consen 111 EGRFICPVTGKEFNGKHKFVYLRPCGCVFSEKALKEL-----------K-KSKKCPVCGKPFTEEDIIPLNP 170 (260)
T ss_pred CceeECCCCCcccCCceeEEEEcCCCCEeeHHHHHhh-----------c-ccccccccCCccccCCEEEecC
Confidence 3457899998887532 355699999999999987 1 2336999999999999886654
No 73
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=97.17 E-value=0.00017 Score=57.71 Aligned_cols=48 Identities=23% Similarity=0.497 Sum_probs=34.7
Q ss_pred cccccccccc-cCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCe
Q 028376 25 ETCPICQEKL-GNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNI 85 (210)
Q Consensus 25 ~~C~iC~~~~-~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l 85 (210)
.-|..|..-. .++..+|.|+|+||..|.... ....||.|++++...++
T Consensus 4 VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~-------------~~~~C~lCkk~ir~i~l 52 (233)
T KOG4739|consen 4 VHCNKCFRFPSQDPFFLTACRHVFCEPCLKAS-------------SPDVCPLCKKSIRIIQL 52 (233)
T ss_pred EEeccccccCCCCceeeeechhhhhhhhcccC-------------Cccccccccceeeeeec
Confidence 4577785443 344578999999999998743 22389999999766544
No 74
>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=97.12 E-value=0.0006 Score=41.40 Aligned_cols=43 Identities=19% Similarity=0.557 Sum_probs=31.4
Q ss_pred ccccccccc-cCCCeecCCC-----CcchHhhHHHHHHHhhhccccCCCccccccCCc
Q 028376 26 TCPICQEKL-GNQKMVFQCG-----HFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCR 77 (210)
Q Consensus 26 ~C~iC~~~~-~~~~~~~~Cg-----H~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr 77 (210)
.|.||++.. ...+.+.||. |.++..|+.+|+.. .....||+|+
T Consensus 1 ~CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~---------~~~~~C~iC~ 49 (49)
T smart00744 1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLERWINE---------SGNKTCEICK 49 (49)
T ss_pred CccCCCCCCCCCCeeEeccccCCchhHHHHHHHHHHHHH---------cCCCcCCCCC
Confidence 488998721 1224778995 89999999999865 3345899985
No 75
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=97.12 E-value=0.00023 Score=61.44 Aligned_cols=49 Identities=27% Similarity=0.702 Sum_probs=37.7
Q ss_pred CCCCccccccccccccCCC---eecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376 20 SKADEETCPICQEKLGNQK---MVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD 81 (210)
Q Consensus 20 ~~~~~~~C~iC~~~~~~~~---~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~ 81 (210)
.-.+...||+|++.+.... +.+.|.|.|...|+..|- ...||+||-...
T Consensus 171 ~~tELPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~-------------~~scpvcR~~q~ 222 (493)
T KOG0804|consen 171 GLTELPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWW-------------DSSCPVCRYCQS 222 (493)
T ss_pred CcccCCCcchhHhhcCccccceeeeecccccchHHHhhcc-------------cCcChhhhhhcC
Confidence 3456678999998876532 446999999999999992 247999988655
No 76
>KOG0331 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=97.11 E-value=0.002 Score=57.61 Aligned_cols=69 Identities=14% Similarity=0.261 Sum_probs=62.0
Q ss_pred CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376 120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRH 195 (210)
Q Consensus 120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~ 195 (210)
...|...|.+.|..+. .++..|+|||..-...-+-++..|...||+..-|+|.++ ..+|..+|+.|.++
T Consensus 322 ~~~K~~~l~~lL~~~~-~~~~~KvIIFc~tkr~~~~l~~~l~~~~~~a~~iHGd~s------Q~eR~~~L~~FreG 390 (519)
T KOG0331|consen 322 ETAKLRKLGKLLEDIS-SDSEGKVIIFCETKRTCDELARNLRRKGWPAVAIHGDKS------QSERDWVLKGFREG 390 (519)
T ss_pred HHHHHHHHHHHHHHHh-ccCCCcEEEEecchhhHHHHHHHHHhcCcceeeeccccc------HHHHHHHHHhcccC
Confidence 5677778888887776 677899999999999999999999999999999999976 99999999999873
No 77
>KOG0333 consensus U5 snRNP-like RNA helicase subunit [RNA processing and modification]
Probab=97.11 E-value=0.0024 Score=56.78 Aligned_cols=66 Identities=11% Similarity=0.112 Sum_probs=59.3
Q ss_pred CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376 120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRH 195 (210)
Q Consensus 120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~ 195 (210)
-++|..+|++.|... -+.-+|||.....-.+.|...|++.||..++|+|+.. ..||+.+|+.|+++
T Consensus 501 ed~k~kkL~eil~~~----~~ppiIIFvN~kk~~d~lAk~LeK~g~~~~tlHg~k~------qeQRe~aL~~fr~~ 566 (673)
T KOG0333|consen 501 EDEKRKKLIEILESN----FDPPIIIFVNTKKGADALAKILEKAGYKVTTLHGGKS------QEQRENALADFREG 566 (673)
T ss_pred chHHHHHHHHHHHhC----CCCCEEEEEechhhHHHHHHHHhhccceEEEeeCCcc------HHHHHHHHHHHHhc
Confidence 467888888888753 4678999999999999999999999999999999987 99999999999984
No 78
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=97.10 E-value=0.0001 Score=48.19 Aligned_cols=52 Identities=25% Similarity=0.478 Sum_probs=36.8
Q ss_pred CccccccccccccC------------CCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376 23 DEETCPICQEKLGN------------QKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI 82 (210)
Q Consensus 23 ~~~~C~iC~~~~~~------------~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~ 82 (210)
.++.|.||.-++.. +.+.-.|.|.|..-|+.+|+.. ......||+||.....
T Consensus 19 ~~e~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~--------~tsq~~CPmcRq~~~~ 82 (84)
T KOG1493|consen 19 PDETCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNT--------PTSQGQCPMCRQTWQF 82 (84)
T ss_pred CCCccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcC--------ccccccCCcchheeEe
Confidence 34477777766542 1244589999999999999754 2445689999987643
No 79
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.96 E-value=0.00018 Score=58.32 Aligned_cols=55 Identities=16% Similarity=0.517 Sum_probs=42.0
Q ss_pred CCccccccccccccCC---------CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCe
Q 028376 22 ADEETCPICQEKLGNQ---------KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNI 85 (210)
Q Consensus 22 ~~~~~C~iC~~~~~~~---------~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l 85 (210)
.++..|.+|...+... ...++|+|+|+..|+.-|.- -+....||.|...+..+..
T Consensus 222 l~d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWci---------vGKkqtCPYCKekVdl~rm 285 (328)
T KOG1734|consen 222 LSDSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCI---------VGKKQTCPYCKEKVDLKRM 285 (328)
T ss_pred CCcchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhhee---------ecCCCCCchHHHHhhHhhh
Confidence 4667899997765432 24589999999999999952 3677899999988766643
No 80
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=96.95 E-value=0.0004 Score=60.49 Aligned_cols=51 Identities=29% Similarity=0.712 Sum_probs=41.2
Q ss_pred CccccccccccccCCCee-cCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCe
Q 028376 23 DEETCPICQEKLGNQKMV-FQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNI 85 (210)
Q Consensus 23 ~~~~C~iC~~~~~~~~~~-~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l 85 (210)
.+..|++|...+.++ +. +.|||.||..|+..|. .....||.|+..+...+.
T Consensus 20 ~~l~C~~C~~vl~~p-~~~~~cgh~fC~~C~~~~~-----------~~~~~cp~~~~~~~~~~~ 71 (391)
T KOG0297|consen 20 ENLLCPICMSVLRDP-VQTTTCGHRFCAGCLLESL-----------SNHQKCPVCRQELTQAEE 71 (391)
T ss_pred ccccCccccccccCC-CCCCCCCCcccccccchhh-----------ccCcCCcccccccchhhc
Confidence 457899999999885 66 5999999999999995 336799999887765543
No 81
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=96.92 E-value=0.00052 Score=57.39 Aligned_cols=58 Identities=28% Similarity=0.658 Sum_probs=43.8
Q ss_pred CccccccccccccCCC---eecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEEccC
Q 028376 23 DEETCPICQEKLGNQK---MVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYADD 90 (210)
Q Consensus 23 ~~~~C~iC~~~~~~~~---~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~~~~ 90 (210)
++..||.|.+++.... .--+||-.+|.-|+..+-+. -..+||.||+.....++.|++.
T Consensus 13 eed~cplcie~mditdknf~pc~cgy~ic~fc~~~irq~----------lngrcpacrr~y~denv~~~~~ 73 (480)
T COG5175 13 EEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQN----------LNGRCPACRRKYDDENVRYVTL 73 (480)
T ss_pred ccccCcccccccccccCCcccCCcccHHHHHHHHHHHhh----------ccCCChHhhhhccccceeEEec
Confidence 3445999999876432 23489999999999987432 3458999999999999887653
No 82
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=96.90 E-value=0.00019 Score=65.79 Aligned_cols=51 Identities=22% Similarity=0.369 Sum_probs=37.7
Q ss_pred CccccccccccccCCC--eecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCC
Q 028376 23 DEETCPICQEKLGNQK--MVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGN 84 (210)
Q Consensus 23 ~~~~C~iC~~~~~~~~--~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~ 84 (210)
....|++|+..+.+.. .-.+|+|.||..|+..|. ....+||+||..|..-.
T Consensus 122 ~~~~CP~Ci~s~~DqL~~~~k~c~H~FC~~Ci~sWs-----------R~aqTCPiDR~EF~~v~ 174 (1134)
T KOG0825|consen 122 VENQCPNCLKSCNDQLEESEKHTAHYFCEECVGSWS-----------RCAQTCPVDRGEFGEVK 174 (1134)
T ss_pred hhhhhhHHHHHHHHHhhccccccccccHHHHhhhhh-----------hhcccCchhhhhhheee
Confidence 4456888876655432 335899999999999994 45568999999876543
No 83
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.89 E-value=0.00049 Score=57.84 Aligned_cols=50 Identities=22% Similarity=0.523 Sum_probs=39.7
Q ss_pred CCCCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376 20 SKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD 81 (210)
Q Consensus 20 ~~~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~ 81 (210)
-+.++..|+||...+.+ .+..||+|.-|..|+.+++- ....|-.|...+.
T Consensus 418 p~sEd~lCpICyA~pi~-Avf~PC~H~SC~~CI~qHlm-----------N~k~CFfCktTv~ 467 (489)
T KOG4692|consen 418 PDSEDNLCPICYAGPIN-AVFAPCSHRSCYGCITQHLM-----------NCKRCFFCKTTVI 467 (489)
T ss_pred CCcccccCcceecccch-hhccCCCCchHHHHHHHHHh-----------cCCeeeEecceee
Confidence 35677889999887776 58999999999999999852 3447888877543
No 84
>PTZ00110 helicase; Provisional
Probab=96.81 E-value=0.0063 Score=55.35 Aligned_cols=68 Identities=16% Similarity=0.191 Sum_probs=59.3
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM 196 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~ 196 (210)
..|...|.+.|..+.. +..|+|||..-....+.|...|...|++...++|.|+ ..+|..+++.|+++.
T Consensus 360 ~~k~~~L~~ll~~~~~--~~~k~LIF~~t~~~a~~l~~~L~~~g~~~~~ihg~~~------~~eR~~il~~F~~G~ 427 (545)
T PTZ00110 360 HEKRGKLKMLLQRIMR--DGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKK------QEERTWVLNEFKTGK 427 (545)
T ss_pred hhHHHHHHHHHHHhcc--cCCeEEEEecChHHHHHHHHHHHHcCCcEEEEECCCc------HHHHHHHHHHHhcCC
Confidence 4677888877776553 5789999999999999999999999999999999977 999999999999743
No 85
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.81 E-value=0.00062 Score=57.85 Aligned_cols=47 Identities=26% Similarity=0.470 Sum_probs=34.0
Q ss_pred ccccccccccccC---CCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcc
Q 028376 24 EETCPICQEKLGN---QKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQ 78 (210)
Q Consensus 24 ~~~C~iC~~~~~~---~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~ 78 (210)
...|.||.+.... -..+..|||+|+..|+..|++... ....||.|+.
T Consensus 4 ~A~C~Ic~d~~p~~~~l~~i~~cGhifh~~cl~qwfe~~P--------s~R~cpic~i 53 (465)
T KOG0827|consen 4 MAECHICIDGRPNDHELGPIGTCGHIFHTTCLTQWFEGDP--------SNRGCPICQI 53 (465)
T ss_pred cceeeEeccCCccccccccccchhhHHHHHHHHHHHccCC--------ccCCCCceee
Confidence 3589999654432 134567999999999999986522 2268999984
No 86
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.77 E-value=0.00021 Score=58.52 Aligned_cols=42 Identities=38% Similarity=0.834 Sum_probs=34.3
Q ss_pred ccccccccccccCCCeecCCCC-cchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376 24 EETCPICQEKLGNQKMVFQCGH-FTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD 81 (210)
Q Consensus 24 ~~~C~iC~~~~~~~~~~~~CgH-~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~ 81 (210)
...|.||++.+.+ -++++||| +-|..|-.++ ..||+||+.+.
T Consensus 300 ~~LC~ICmDaP~D-CvfLeCGHmVtCt~CGkrm---------------~eCPICRqyi~ 342 (350)
T KOG4275|consen 300 RRLCAICMDAPRD-CVFLECGHMVTCTKCGKRM---------------NECPICRQYIV 342 (350)
T ss_pred HHHHHHHhcCCcc-eEEeecCcEEeehhhcccc---------------ccCchHHHHHH
Confidence 4579999999987 59999999 5688886655 38999998653
No 87
>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=96.77 E-value=0.00092 Score=54.80 Aligned_cols=50 Identities=28% Similarity=0.574 Sum_probs=37.3
Q ss_pred cccccccc-ccCC---CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCe
Q 028376 26 TCPICQEK-LGNQ---KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNI 85 (210)
Q Consensus 26 ~C~iC~~~-~~~~---~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l 85 (210)
.||+|... ..++ ..+-+|||..|.+|+..++. .+...||.|...+....+
T Consensus 2 ~Cp~CKt~~Y~np~lk~~in~C~H~lCEsCvd~iF~----------~g~~~CpeC~~iLRk~nf 55 (300)
T KOG3800|consen 2 ACPKCKTDRYLNPDLKLMINECGHRLCESCVDRIFS----------LGPAQCPECMVILRKNNF 55 (300)
T ss_pred CCcccccceecCccceeeeccccchHHHHHHHHHHh----------cCCCCCCcccchhhhccc
Confidence 59999543 2222 23459999999999999973 456689999998887654
No 88
>KOG1571 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.73 E-value=0.00062 Score=57.44 Aligned_cols=44 Identities=30% Similarity=0.864 Sum_probs=33.5
Q ss_pred ccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376 24 EETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI 82 (210)
Q Consensus 24 ~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~ 82 (210)
...|.||.+.+.+ .+..+|||..| |..-. ...+.||+||..+..
T Consensus 305 p~lcVVcl~e~~~-~~fvpcGh~cc--ct~cs------------~~l~~CPvCR~rI~~ 348 (355)
T KOG1571|consen 305 PDLCVVCLDEPKS-AVFVPCGHVCC--CTLCS------------KHLPQCPVCRQRIRL 348 (355)
T ss_pred CCceEEecCCccc-eeeecCCcEEE--chHHH------------hhCCCCchhHHHHHH
Confidence 3579999999887 58899999876 65543 234569999998754
No 89
>COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.73 E-value=0.00075 Score=63.24 Aligned_cols=68 Identities=21% Similarity=0.429 Sum_probs=47.7
Q ss_pred hhhccCchHHHHHhcCC------CCcccccccccccc------CCCeecCCCCcchHhhHHHHHHHhhhccccCCCcccc
Q 028376 5 VVTISNSTKHRIESLSK------ADEETCPICQEKLG------NQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVM 72 (210)
Q Consensus 5 ~~~~~~~~~~~~~~l~~------~~~~~C~iC~~~~~------~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~ 72 (210)
+..+-.++-+.+.+.+. ++..+|+||...+. +.-....|.|-|+..|+-+|+.. ++...
T Consensus 1444 ~~~~ngs~~D~l~l~kkNi~~~fsG~eECaICYsvL~~vdr~lPskrC~TCknKFH~~CLyKWf~S---------s~~s~ 1514 (1525)
T COG5219 1444 MIKKNGSFMDLLGLWKKNIDEKFSGHEECAICYSVLDMVDRSLPSKRCATCKNKFHTRCLYKWFAS---------SARSN 1514 (1525)
T ss_pred HHhccchHHHHHHHHHhhhhhhcCCcchhhHHHHHHHHHhccCCccccchhhhhhhHHHHHHHHHh---------cCCCC
Confidence 33444556666665543 46689999965543 11255689999999999999864 56679
Q ss_pred ccCCccccc
Q 028376 73 CPTCRQRTD 81 (210)
Q Consensus 73 CP~Cr~~~~ 81 (210)
||.||..+.
T Consensus 1515 CPlCRseit 1523 (1525)
T COG5219 1515 CPLCRSEIT 1523 (1525)
T ss_pred CCccccccc
Confidence 999997654
No 90
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=96.70 E-value=0.001 Score=43.91 Aligned_cols=33 Identities=21% Similarity=0.326 Sum_probs=26.7
Q ss_pred eecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376 39 MVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI 82 (210)
Q Consensus 39 ~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~ 82 (210)
+.-.|.|.|..-|+.+|+. ....||++|+....
T Consensus 50 ~wG~CnHaFH~HCI~rWL~-----------Tk~~CPld~q~w~~ 82 (88)
T COG5194 50 VWGVCNHAFHDHCIYRWLD-----------TKGVCPLDRQTWVL 82 (88)
T ss_pred EEEecchHHHHHHHHHHHh-----------hCCCCCCCCceeEE
Confidence 4568999999999999973 35589999987643
No 91
>KOG1016 consensus Predicted DNA helicase, DEAD-box superfamily [General function prediction only]
Probab=96.63 E-value=0.0026 Score=58.97 Aligned_cols=70 Identities=24% Similarity=0.314 Sum_probs=53.1
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhC------------------CceEEEeeCCCCCCcchhh
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIAN------------------NITCIKMKGENHKLPSANL 182 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~------------------gi~~~~~~G~m~~~~~~~~ 182 (210)
+-|+-.+++.+.+- ..-++|+|||||-...|++|+..|... ++.|+|+||+.. .
T Consensus 702 ~pk~V~~~~~~des--~~~g~kil~fSq~l~~Ld~ieeil~krq~pc~~gdnG~~aqkW~~n~sy~rldG~t~------a 773 (1387)
T KOG1016|consen 702 GPKIVISLEILDES--TQIGEKILIFSQNLTALDMIEEILKKRQIPCKDGDNGCPAQKWEKNRSYLRLDGTTS------A 773 (1387)
T ss_pred CCceEEEEeeeccc--cccCceEEEeecchhHHHHHHHHHhcccccCCCCCCCCchhhhhhccceecccCCcc------c
Confidence 34444444444332 234799999999999999999999864 357899999977 9
Q ss_pred HhhhHHHHHHhhcCCCC
Q 028376 183 QHRNALQKELTRHMPSS 199 (210)
Q Consensus 183 ~~R~~~l~~F~~~~p~~ 199 (210)
+.|.+.|++|+. .|+.
T Consensus 774 ~~rekLinqfN~-e~~l 789 (1387)
T KOG1016|consen 774 ADREKLINQFNS-EPGL 789 (1387)
T ss_pred chHHHHHHhccC-CCCc
Confidence 999999999997 5543
No 92
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.57 E-value=0.0011 Score=56.80 Aligned_cols=54 Identities=26% Similarity=0.618 Sum_probs=41.5
Q ss_pred ccccccccccccCC----CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376 24 EETCPICQEKLGNQ----KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA 86 (210)
Q Consensus 24 ~~~C~iC~~~~~~~----~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~ 86 (210)
...||||++....+ .+.+.|||.|-.+|++.|+.+ .....||.|...-...+|.
T Consensus 4 g~tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~k---------~~~~~cp~c~~katkr~i~ 61 (463)
T KOG1645|consen 4 GTTCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLGK---------KTKMQCPLCSGKATKRQIR 61 (463)
T ss_pred cccCceeeeeeeecCceEEeeecccccccHHHHHHHHhh---------hhhhhCcccCChhHHHHHH
Confidence 46899999887643 266899999999999999853 3456899998766555543
No 93
>TIGR00603 rad25 DNA repair helicase rad25. All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription as part of the TFIIH complex.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.57 E-value=0.0094 Score=55.69 Aligned_cols=61 Identities=20% Similarity=0.181 Sum_probs=49.0
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
..|+.++...|.+.. .++.|+|||++....++.+...| |.++ ++|.++ ..+|.++++.|+.
T Consensus 479 p~K~~~~~~Li~~he--~~g~kiLVF~~~~~~l~~~a~~L---~~~~--I~G~ts------~~ER~~il~~Fr~ 539 (732)
T TIGR00603 479 PNKFRACQFLIRFHE--QRGDKIIVFSDNVFALKEYAIKL---GKPF--IYGPTS------QQERMQILQNFQH 539 (732)
T ss_pred hHHHHHHHHHHHHHh--hcCCeEEEEeCCHHHHHHHHHHc---CCce--EECCCC------HHHHHHHHHHHHh
Confidence 467777776665432 46899999999999988888877 4554 789977 9999999999985
No 94
>PRK04837 ATP-dependent RNA helicase RhlB; Provisional
Probab=96.55 E-value=0.012 Score=51.66 Aligned_cols=67 Identities=13% Similarity=0.131 Sum_probs=56.3
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP 197 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p 197 (210)
..|+..|.+.+. .....|+|||..-....+.+...|...|+....+.|.|+ .++|..+++.|+++..
T Consensus 240 ~~k~~~l~~ll~----~~~~~~~lVF~~t~~~~~~l~~~L~~~g~~v~~lhg~~~------~~~R~~~l~~F~~g~~ 306 (423)
T PRK04837 240 EEKMRLLQTLIE----EEWPDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVA------QKKRLRILEEFTRGDL 306 (423)
T ss_pred HHHHHHHHHHHH----hcCCCeEEEEECCHHHHHHHHHHHHhCCCcEEEecCCCC------hhHHHHHHHHHHcCCC
Confidence 356666655543 345689999999999999999999999999999999977 9999999999998554
No 95
>PRK11192 ATP-dependent RNA helicase SrmB; Provisional
Probab=96.50 E-value=0.017 Score=50.89 Aligned_cols=57 Identities=21% Similarity=0.233 Sum_probs=51.0
Q ss_pred hcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCC
Q 028376 136 STDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPS 198 (210)
Q Consensus 136 ~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~ 198 (210)
......++|||..-....+.+...|...|+....++|.|+ ..+|..+++.|+.+..+
T Consensus 241 ~~~~~~~~lVF~~s~~~~~~l~~~L~~~~~~~~~l~g~~~------~~~R~~~l~~f~~G~~~ 297 (434)
T PRK11192 241 KQPEVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMV------QAKRNEAIKRLTDGRVN 297 (434)
T ss_pred hcCCCCeEEEEeCChHHHHHHHHHHHhCCCCEEEecCCCC------HHHHHHHHHHHhCCCCc
Confidence 3445789999999999999999999999999999999977 99999999999985544
No 96
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.24 E-value=0.0037 Score=52.33 Aligned_cols=47 Identities=34% Similarity=0.832 Sum_probs=38.0
Q ss_pred ccccccccccccCC-----CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccc
Q 028376 24 EETCPICQEKLGNQ-----KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRT 80 (210)
Q Consensus 24 ~~~C~iC~~~~~~~-----~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~ 80 (210)
...|-||.+.+... +.++.|||.+|..|+..++ ......||.||.+.
T Consensus 3 ~~~c~~c~~~~s~~~~~~~p~~l~c~h~~c~~c~~~l~----------~~~~i~cpfcR~~~ 54 (296)
T KOG4185|consen 3 FPECEICNEDYSSEDGDHIPRVLKCGHTICQNCASKLL----------GNSRILCPFCRETT 54 (296)
T ss_pred CCceeecCccccccCcccCCcccccCceehHhHHHHHh----------cCceeeccCCCCcc
Confidence 46799998776532 5778899999999999986 35667889999985
No 97
>COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.24 E-value=0.0034 Score=52.82 Aligned_cols=51 Identities=25% Similarity=0.615 Sum_probs=39.9
Q ss_pred CCCCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccc
Q 028376 20 SKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRT 80 (210)
Q Consensus 20 ~~~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~ 80 (210)
.+++...|.||.+.+.- ..++||+|..|.-|..+.-. ......||.||...
T Consensus 57 tDEen~~C~ICA~~~TY-s~~~PC~H~~CH~Ca~RlRA---------LY~~K~C~~CrTE~ 107 (493)
T COG5236 57 TDEENMNCQICAGSTTY-SARYPCGHQICHACAVRLRA---------LYMQKGCPLCRTET 107 (493)
T ss_pred cccccceeEEecCCceE-EEeccCCchHHHHHHHHHHH---------HHhccCCCcccccc
Confidence 35667889999998876 48899999999999887621 24556899999853
No 98
>PRK11776 ATP-dependent RNA helicase DbpA; Provisional
Probab=96.20 E-value=0.025 Score=50.23 Aligned_cols=66 Identities=14% Similarity=0.273 Sum_probs=56.7
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM 196 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~ 196 (210)
..|+++|.+.|.. .+..++|||..-....+.+...|...|+....|+|.|+ ..+|..+++.|.++.
T Consensus 227 ~~k~~~l~~ll~~----~~~~~~lVF~~t~~~~~~l~~~L~~~~~~v~~~hg~~~------~~eR~~~l~~F~~g~ 292 (460)
T PRK11776 227 DERLPALQRLLLH----HQPESCVVFCNTKKECQEVADALNAQGFSALALHGDLE------QRDRDQVLVRFANRS 292 (460)
T ss_pred HHHHHHHHHHHHh----cCCCceEEEECCHHHHHHHHHHHHhCCCcEEEEeCCCC------HHHHHHHHHHHHcCC
Confidence 3477777766643 34678999999999999999999999999999999977 999999999999743
No 99
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=96.17 E-value=0.0028 Score=52.28 Aligned_cols=43 Identities=33% Similarity=0.719 Sum_probs=35.4
Q ss_pred cccccccccccCCCeec-CCCCcchHhhHHHHHHHhhhccccCCCccccccCCcc
Q 028376 25 ETCPICQEKLGNQKMVF-QCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQ 78 (210)
Q Consensus 25 ~~C~iC~~~~~~~~~~~-~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~ 78 (210)
..|+.|...+.++ +.+ .|+|.||.+|+...+ ......||.|..
T Consensus 275 LkCplc~~Llrnp-~kT~cC~~~fc~eci~~al----------~dsDf~CpnC~r 318 (427)
T COG5222 275 LKCPLCHCLLRNP-MKTPCCGHTFCDECIGTAL----------LDSDFKCPNCSR 318 (427)
T ss_pred ccCcchhhhhhCc-ccCccccchHHHHHHhhhh----------hhccccCCCccc
Confidence 6799999988885 666 789999999999765 345678999976
No 100
>COG0513 SrmB Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]
Probab=96.16 E-value=0.029 Score=50.71 Aligned_cols=65 Identities=11% Similarity=0.240 Sum_probs=55.9
Q ss_pred chHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376 122 TKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM 196 (210)
Q Consensus 122 sKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~ 196 (210)
.|++.|...|.. ....++|||..=....+.+...|...|+....+.|.|+ ..+|.++++.|+++.
T Consensus 259 ~k~~~L~~ll~~----~~~~~~IVF~~tk~~~~~l~~~l~~~g~~~~~lhG~l~------q~~R~~~l~~F~~g~ 323 (513)
T COG0513 259 EKLELLLKLLKD----EDEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLP------QEERDRALEKFKDGE 323 (513)
T ss_pred HHHHHHHHHHhc----CCCCeEEEEeCcHHHHHHHHHHHHHCCCeEEEecCCCC------HHHHHHHHHHHHcCC
Confidence 477777766653 33448999999999999999999999999999999977 999999999999643
No 101
>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=96.16 E-value=0.0066 Score=51.96 Aligned_cols=66 Identities=26% Similarity=0.453 Sum_probs=43.1
Q ss_pred CCccccccccccccCCCeec----------------CCCCcc-----hHhhHHHHHHHhhhccc--cCCCccccccCCcc
Q 028376 22 ADEETCPICQEKLGNQKMVF----------------QCGHFT-----CCKCFFAMTEQRLIHDN--KVKNEWVMCPTCRQ 78 (210)
Q Consensus 22 ~~~~~C~iC~~~~~~~~~~~----------------~CgH~f-----C~~C~~~~~~~~~~~~~--~~~~~~~~CP~Cr~ 78 (210)
.+.+.|..|+....+--+.- +|+..+ |.+|+.+|+.....+.. .+..++..||+||+
T Consensus 269 ~e~e~CigC~~~~~~vkl~k~C~~~~~~g~~~~~~~~C~~C~CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa 348 (358)
T PF10272_consen 269 QELEPCIGCMQAQPNVKLVKRCADEEQEGSPLPNEPPCQQCYCRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRA 348 (358)
T ss_pred cccCCccccccCCCCcEEEeccCCcccCCcccccCCCCccccccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcc
Confidence 56678999987544311222 333333 78999999864332211 23577889999999
Q ss_pred cccCCCeEE
Q 028376 79 RTDIGNIAY 87 (210)
Q Consensus 79 ~~~~~~l~~ 87 (210)
.+...||.+
T Consensus 349 ~FCilDV~~ 357 (358)
T PF10272_consen 349 KFCILDVCY 357 (358)
T ss_pred cceeeeeec
Confidence 999888754
No 102
>PRK04537 ATP-dependent RNA helicase RhlB; Provisional
Probab=96.10 E-value=0.029 Score=51.41 Aligned_cols=67 Identities=10% Similarity=0.146 Sum_probs=56.1
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP 197 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p 197 (210)
..|+..|+..|. .....|+|||..-....+.|...|...|+....|+|.|+ ..+|..+++.|.++..
T Consensus 242 ~~k~~~L~~ll~----~~~~~k~LVF~nt~~~ae~l~~~L~~~g~~v~~lhg~l~------~~eR~~il~~Fr~G~~ 308 (572)
T PRK04537 242 EEKQTLLLGLLS----RSEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVP------QKKRESLLNRFQKGQL 308 (572)
T ss_pred HHHHHHHHHHHh----cccCCcEEEEeCCHHHHHHHHHHHHHcCCCEEEEeCCCC------HHHHHHHHHHHHcCCC
Confidence 345665555443 345789999999999999999999999999999999977 9999999999997543
No 103
>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=96.09 E-value=0.0012 Score=52.81 Aligned_cols=54 Identities=20% Similarity=0.502 Sum_probs=37.4
Q ss_pred CCCccccccccccc-cCCC---eecC-CCCcchHhhHHHHHHHhhhccccCCCcccccc--CCcccccCCC
Q 028376 21 KADEETCPICQEKL-GNQK---MVFQ-CGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCP--TCRQRTDIGN 84 (210)
Q Consensus 21 ~~~~~~C~iC~~~~-~~~~---~~~~-CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP--~Cr~~~~~~~ 84 (210)
+..+..||+|.... -+|. .+-| |.|..|.+|+.+++. .+...|| .|.+-++...
T Consensus 7 ~~~d~~CPvCksDrYLnPdik~linPECyHrmCESCvdRIFs----------~GpAqCP~~gC~kILRK~k 67 (314)
T COG5220 7 EMEDRRCPVCKSDRYLNPDIKILINPECYHRMCESCVDRIFS----------RGPAQCPYKGCGKILRKIK 67 (314)
T ss_pred hhhcccCCccccccccCCCeEEEECHHHHHHHHHHHHHHHhc----------CCCCCCCCccHHHHHHHhc
Confidence 34557899996432 2222 2235 999999999999973 4567898 7988766543
No 104
>PRK05298 excinuclease ABC subunit B; Provisional
Probab=96.03 E-value=0.039 Score=51.34 Aligned_cols=69 Identities=10% Similarity=0.062 Sum_probs=61.8
Q ss_pred CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376 120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM 196 (210)
Q Consensus 120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~ 196 (210)
+..+++.|++.|..+.. .+.++|||+.-....+.+...|..+|++...++|.|+ ..+|..+++.|..+.
T Consensus 428 ~~~q~~~L~~~L~~~~~--~g~~viIf~~t~~~ae~L~~~L~~~gi~~~~~h~~~~------~~~R~~~l~~f~~g~ 496 (652)
T PRK05298 428 TKGQVDDLLSEIRKRVA--KGERVLVTTLTKRMAEDLTDYLKELGIKVRYLHSDID------TLERVEIIRDLRLGE 496 (652)
T ss_pred ccccHHHHHHHHHHHHh--CCCEEEEEeCCHHHHHHHHHHHhhcceeEEEEECCCC------HHHHHHHHHHHHcCC
Confidence 45678999999998874 4789999999999999999999999999999999977 999999999998744
No 105
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=96.03 E-value=0.0026 Score=54.24 Aligned_cols=48 Identities=29% Similarity=0.670 Sum_probs=37.3
Q ss_pred ccccccccccccCC---CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccc
Q 028376 24 EETCPICQEKLGNQ---KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRT 80 (210)
Q Consensus 24 ~~~C~iC~~~~~~~---~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~ 80 (210)
...|..|.+.+.-. .--+||.|+|+..|+.+++++ +....||.||+-.
T Consensus 365 ~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~---------n~~rsCP~Crklr 415 (518)
T KOG1941|consen 365 ELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILEN---------NGTRSCPNCRKLR 415 (518)
T ss_pred hhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHh---------CCCCCCccHHHHH
Confidence 35699998766432 245899999999999999865 5677999999643
No 106
>PRK01297 ATP-dependent RNA helicase RhlB; Provisional
Probab=96.03 E-value=0.036 Score=49.49 Aligned_cols=66 Identities=14% Similarity=0.296 Sum_probs=55.1
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM 196 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~ 196 (210)
+.|...|.+.+. ..+..|+|||..-....+.+...|...|+....+.|.|+ ..+|..+++.|+++.
T Consensus 320 ~~k~~~l~~ll~----~~~~~~~IVF~~s~~~~~~l~~~L~~~~~~~~~~~g~~~------~~~R~~~~~~Fr~G~ 385 (475)
T PRK01297 320 SDKYKLLYNLVT----QNPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVP------QHKRIKTLEGFREGK 385 (475)
T ss_pred hhHHHHHHHHHH----hcCCCeEEEEeCCHHHHHHHHHHHHHcCCCEEEEECCCC------HHHHHHHHHHHhCCC
Confidence 456655554443 345679999999999999999999999999999999977 999999999998744
No 107
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=95.98 E-value=0.0032 Score=58.53 Aligned_cols=41 Identities=27% Similarity=0.597 Sum_probs=35.0
Q ss_pred cccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccc
Q 028376 25 ETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQR 79 (210)
Q Consensus 25 ~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~ 79 (210)
..|..|...+.-|.+...|||.|+..|+.. ....||.|+..
T Consensus 841 skCs~C~~~LdlP~VhF~CgHsyHqhC~e~--------------~~~~CP~C~~e 881 (933)
T KOG2114|consen 841 SKCSACEGTLDLPFVHFLCGHSYHQHCLED--------------KEDKCPKCLPE 881 (933)
T ss_pred eeecccCCccccceeeeecccHHHHHhhcc--------------CcccCCccchh
Confidence 579999999988888899999999999972 34589999873
No 108
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=95.95 E-value=0.0031 Score=51.98 Aligned_cols=73 Identities=23% Similarity=0.453 Sum_probs=47.8
Q ss_pred chHHHHHhcCCCC--ccccccccccccCC--CeecCCCCcchHhhHHHHHHHhhhccc---c---------CCCcccccc
Q 028376 11 STKHRIESLSKAD--EETCPICQEKLGNQ--KMVFQCGHFTCCKCFFAMTEQRLIHDN---K---------VKNEWVMCP 74 (210)
Q Consensus 11 ~~~~~~~~l~~~~--~~~C~iC~~~~~~~--~~~~~CgH~fC~~C~~~~~~~~~~~~~---~---------~~~~~~~CP 74 (210)
+.+..-+.|.+.+ ...|.||+.-+... .++|.|.|.|+..|+.+++........ . .......||
T Consensus 100 lie~~~e~LT~nn~p~gqCvICLygfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcp 179 (368)
T KOG4445|consen 100 LIEHCSEFLTENNHPNGQCVICLYGFASSPAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCP 179 (368)
T ss_pred HHHHHHHHcccCCCCCCceEEEEEeecCCCceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhh
Confidence 3344444455543 46899998877654 367899999999999999865432110 0 023344599
Q ss_pred CCcccccCC
Q 028376 75 TCRQRTDIG 83 (210)
Q Consensus 75 ~Cr~~~~~~ 83 (210)
+||.++...
T Consensus 180 Vcre~i~~e 188 (368)
T KOG4445|consen 180 VCRERIKIE 188 (368)
T ss_pred Hhhhhcccc
Confidence 999987654
No 109
>KOG0334 consensus RNA helicase [RNA processing and modification]
Probab=95.87 E-value=0.02 Score=54.57 Aligned_cols=66 Identities=12% Similarity=0.159 Sum_probs=61.7
Q ss_pred CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
-..|+..|+++|..+.. +.|+|||++=..-++.+-..|.+.|+.+..+.|..+ ...|...|+.|++
T Consensus 596 e~eKf~kL~eLl~e~~e---~~~tiiFv~~qe~~d~l~~~L~~ag~~~~slHGgv~------q~dR~sti~dfK~ 661 (997)
T KOG0334|consen 596 ENEKFLKLLELLGERYE---DGKTIIFVDKQEKADALLRDLQKAGYNCDSLHGGVD------QHDRSSTIEDFKN 661 (997)
T ss_pred chHHHHHHHHHHHHHhh---cCCEEEEEcCchHHHHHHHHHHhcCcchhhhcCCCc------hHHHHhHHHHHhc
Confidence 57999999999987764 789999999999999999999999999999999977 9999999999998
No 110
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.85 E-value=0.0067 Score=52.13 Aligned_cols=52 Identities=19% Similarity=0.406 Sum_probs=36.0
Q ss_pred CccccccccccccC--CCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCc
Q 028376 23 DEETCPICQEKLGN--QKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCR 77 (210)
Q Consensus 23 ~~~~C~iC~~~~~~--~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr 77 (210)
....|.||.+.... ....+||+|+||..|+..+++-... .| ......||.+.
T Consensus 183 slf~C~ICf~e~~G~~c~~~lpC~Hv~Ck~C~kdY~~~~i~-eg--~v~~l~Cp~~~ 236 (445)
T KOG1814|consen 183 SLFDCCICFEEQMGQHCFKFLPCSHVFCKSCLKDYFTIQIQ-EG--QVSCLKCPDPK 236 (445)
T ss_pred hcccceeeehhhcCcceeeecccchHHHHHHHHHHHHHhhh-cc--eeeeecCCCCC
Confidence 34679999876542 2366899999999999999865432 22 34556787543
No 111
>TIGR00631 uvrb excinuclease ABC, B subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University)
Probab=95.77 E-value=0.053 Score=50.44 Aligned_cols=70 Identities=11% Similarity=0.088 Sum_probs=62.2
Q ss_pred CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376 119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM 196 (210)
Q Consensus 119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~ 196 (210)
.+..+++.|++.|..+.. .+.++|||+.-....+.+...|...||+...++|.|+ ..+|.++++.|..+.
T Consensus 423 ~~~~qi~~Ll~eI~~~~~--~g~~vLIf~~tk~~ae~L~~~L~~~gi~~~~lh~~~~------~~eR~~~l~~fr~G~ 492 (655)
T TIGR00631 423 PTDGQVDDLLSEIRQRVA--RNERVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEID------TLERVEIIRDLRLGE 492 (655)
T ss_pred eccchHHHHHHHHHHHHc--CCCEEEEEECCHHHHHHHHHHHhhhccceeeeeCCCC------HHHHHHHHHHHhcCC
Confidence 346789999999998774 4789999999999999999999999999999999977 999999999998744
No 112
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.77 E-value=0.012 Score=46.67 Aligned_cols=67 Identities=19% Similarity=0.381 Sum_probs=48.5
Q ss_pred hHHHHHhcCCCCc-cccccccccccCC-CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376 12 TKHRIESLSKADE-ETCPICQEKLGNQ-KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD 81 (210)
Q Consensus 12 ~~~~~~~l~~~~~-~~C~iC~~~~~~~-~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~ 81 (210)
++++++=+++.+- ..|..|..++... .+.+.|.|+|+-.|+.++..+-.++. .-....||.|...+-
T Consensus 37 VQSYLqWL~DsDY~pNC~LC~t~La~gdt~RLvCyhlfHW~ClneraA~lPanT---APaGyqCP~Cs~eiF 105 (299)
T KOG3970|consen 37 VQSYLQWLQDSDYNPNCRLCNTPLASGDTTRLVCYHLFHWKCLNERAANLPANT---APAGYQCPCCSQEIF 105 (299)
T ss_pred HHHHHHHHhhcCCCCCCceeCCccccCcceeehhhhhHHHHHhhHHHhhCCCcC---CCCcccCCCCCCccC
Confidence 4566777888764 6899999888653 36689999999999999854432221 233457999998653
No 113
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=95.73 E-value=0.0048 Score=51.15 Aligned_cols=42 Identities=24% Similarity=0.617 Sum_probs=31.9
Q ss_pred ccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccc
Q 028376 26 TCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRT 80 (210)
Q Consensus 26 ~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~ 80 (210)
-|..|.-++..=..+.+|.|+||.+|... .....||.|..++
T Consensus 92 fCd~Cd~PI~IYGRmIPCkHvFCl~CAr~-------------~~dK~Cp~C~d~V 133 (389)
T KOG2932|consen 92 FCDRCDFPIAIYGRMIPCKHVFCLECARS-------------DSDKICPLCDDRV 133 (389)
T ss_pred eecccCCcceeeecccccchhhhhhhhhc-------------CccccCcCcccHH
Confidence 48889877665457899999999999763 2345799997754
No 114
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=95.67 E-value=0.058 Score=49.80 Aligned_cols=65 Identities=8% Similarity=0.114 Sum_probs=54.5
Q ss_pred hHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376 123 KIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP 197 (210)
Q Consensus 123 Ki~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p 197 (210)
+++.++..+. ..++.++|||..-....+.+...|...|++...|+|+|+ .++|..+++.|..+..
T Consensus 223 ~~~~l~~~l~----~~~~~~~IIFc~tr~~~e~la~~L~~~g~~v~~~Ha~l~------~~~R~~i~~~F~~g~~ 287 (607)
T PRK11057 223 PLDQLMRYVQ----EQRGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLD------NDVRADVQEAFQRDDL 287 (607)
T ss_pred hHHHHHHHHH----hcCCCCEEEEECcHHHHHHHHHHHHhCCCCEEEecCCCC------HHHHHHHHHHHHCCCC
Confidence 4555554443 346789999999999999999999999999999999977 9999999999997543
No 115
>PHA02558 uvsW UvsW helicase; Provisional
Probab=95.60 E-value=0.06 Score=48.48 Aligned_cols=67 Identities=12% Similarity=0.050 Sum_probs=53.9
Q ss_pred hHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376 123 KIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP 197 (210)
Q Consensus 123 Ki~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p 197 (210)
+...+.+.+..+. ..+.+++||...+.+.+.+...|...|++...++|.|+ ..+|.++++.|+++..
T Consensus 329 Rn~~I~~~~~~~~--~~~~~~lV~~~~~~h~~~L~~~L~~~g~~v~~i~G~~~------~~eR~~i~~~~~~~~~ 395 (501)
T PHA02558 329 RNKWIANLALKLA--KKGENTFVMFKYVEHGKPLYEMLKKVYDKVYYVSGEVD------TEDRNEMKKIAEGGKG 395 (501)
T ss_pred HHHHHHHHHHHHH--hcCCCEEEEEEEHHHHHHHHHHHHHcCCCEEEEeCCCC------HHHHHHHHHHHhCCCC
Confidence 3344454555544 34678999999999999999999999999999999977 9999999999987443
No 116
>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=95.56 E-value=0.0083 Score=43.98 Aligned_cols=36 Identities=19% Similarity=0.422 Sum_probs=28.8
Q ss_pred CCCccccccccccccC--CCeecCCC------CcchHhhHHHHH
Q 028376 21 KADEETCPICQEKLGN--QKMVFQCG------HFTCCKCFFAMT 56 (210)
Q Consensus 21 ~~~~~~C~iC~~~~~~--~~~~~~Cg------H~fC~~C~~~~~ 56 (210)
..-..+|.||.+.+.. +.+..+|| |.||.+|+.+|-
T Consensus 23 ~~~~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw~ 66 (134)
T PF05883_consen 23 PRCTVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRWR 66 (134)
T ss_pred cccCeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHHH
Confidence 3447899999998876 44556777 899999999993
No 117
>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=95.54 E-value=0.079 Score=47.28 Aligned_cols=67 Identities=9% Similarity=0.066 Sum_probs=54.6
Q ss_pred chHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376 122 TKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP 197 (210)
Q Consensus 122 sKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p 197 (210)
.+++.+++.|.. ..++.++|||..-....+.+...|...|++...|.|+|+ ..+|..+++.|..+..
T Consensus 211 ~~~~~l~~~l~~---~~~~~~~IIF~~s~~~~e~la~~L~~~g~~~~~~H~~l~------~~eR~~i~~~F~~g~~ 277 (470)
T TIGR00614 211 KILEDLLRFIRK---EFKGKSGIIYCPSRKKSEQVTASLQNLGIAAGAYHAGLE------ISARDDVHHKFQRDEI 277 (470)
T ss_pred cHHHHHHHHHHH---hcCCCceEEEECcHHHHHHHHHHHHhcCCCeeEeeCCCC------HHHHHHHHHHHHcCCC
Confidence 345555555442 345667799999999999999999999999999999977 9999999999997543
No 118
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=95.52 E-value=0.079 Score=47.10 Aligned_cols=55 Identities=13% Similarity=0.168 Sum_probs=49.2
Q ss_pred hcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376 136 STDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM 196 (210)
Q Consensus 136 ~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~ 196 (210)
......++|||..-....+.+...|...|+....|+|.|+ ..+|.++++.|.++.
T Consensus 241 ~~~~~~~~lVF~~t~~~~~~l~~~L~~~g~~~~~lhg~~~------~~~R~~~l~~F~~g~ 295 (456)
T PRK10590 241 GKGNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKS------QGARTRALADFKSGD 295 (456)
T ss_pred HcCCCCcEEEEcCcHHHHHHHHHHHHHCCCCEEEEECCCC------HHHHHHHHHHHHcCC
Confidence 3455679999999999999999999999999999999977 999999999999743
No 119
>TIGR01389 recQ ATP-dependent DNA helicase RecQ. The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ.
Probab=95.50 E-value=0.074 Score=48.88 Aligned_cols=68 Identities=9% Similarity=0.066 Sum_probs=56.8
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCC
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPS 198 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~ 198 (210)
..|...+++.|.. ..+.+.|||..-....+.+...|...|++...|+|+|+ ..+|..+++.|..+..+
T Consensus 209 ~~~~~~l~~~l~~----~~~~~~IIf~~sr~~~e~la~~L~~~g~~~~~~H~~l~------~~~R~~i~~~F~~g~~~ 276 (591)
T TIGR01389 209 NNKQKFLLDYLKK----HRGQSGIIYASSRKKVEELAERLESQGISALAYHAGLS------NKVRAENQEDFLYDDVK 276 (591)
T ss_pred CCHHHHHHHHHHh----cCCCCEEEEECcHHHHHHHHHHHHhCCCCEEEEECCCC------HHHHHHHHHHHHcCCCc
Confidence 3456666666553 33679999999999999999999999999999999977 99999999999986544
No 120
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=95.45 E-value=0.017 Score=42.09 Aligned_cols=63 Identities=19% Similarity=0.509 Sum_probs=45.5
Q ss_pred HHHHhcCCCCccccccccccccCCCee---cCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCC
Q 028376 14 HRIESLSKADEETCPICQEKLGNQKMV---FQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGN 84 (210)
Q Consensus 14 ~~~~~l~~~~~~~C~iC~~~~~~~~~~---~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~ 84 (210)
.++.+..+....+|-||.+...+...+ --||-.+|.-|...+-+. ..-.+.||+|+..+....
T Consensus 70 qvmnvF~d~~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~--------~~~ypvCPvCkTSFKss~ 135 (140)
T PF05290_consen 70 QVMNVFLDPKLYECNICKETSAEERFLKPNECCGYSICNACYANLWKF--------CNLYPVCPVCKTSFKSSS 135 (140)
T ss_pred HHheeecCCCceeccCcccccchhhcCCcccccchHHHHHHHHHHHHH--------cccCCCCCcccccccccc
Confidence 344444466667999999887665343 369999999999887433 356789999999886653
No 121
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=95.24 E-value=0.015 Score=48.81 Aligned_cols=45 Identities=38% Similarity=0.885 Sum_probs=36.1
Q ss_pred CCCccccccccccccCCCeecCC--CCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376 21 KADEETCPICQEKLGNQKMVFQC--GHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD 81 (210)
Q Consensus 21 ~~~~~~C~iC~~~~~~~~~~~~C--gH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~ 81 (210)
..+..+||+|.+.+..+ +.+| ||+.|..|-.+. ...||.||.++.
T Consensus 45 ~~~lleCPvC~~~l~~P--i~QC~nGHlaCssC~~~~--------------~~~CP~Cr~~~g 91 (299)
T KOG3002|consen 45 DLDLLDCPVCFNPLSPP--IFQCDNGHLACSSCRTKV--------------SNKCPTCRLPIG 91 (299)
T ss_pred chhhccCchhhccCccc--ceecCCCcEehhhhhhhh--------------cccCCccccccc
Confidence 44567999999999864 5666 899999998654 348999999886
No 122
>KOG0826 consensus Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones]
Probab=95.21 E-value=0.0092 Score=49.86 Aligned_cols=54 Identities=24% Similarity=0.608 Sum_probs=42.8
Q ss_pred CCCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCe
Q 028376 21 KADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNI 85 (210)
Q Consensus 21 ~~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l 85 (210)
..+...||+|.....++.++..-|-+||..|+-.++. ....||+=..+....++
T Consensus 297 ~~~~~~CpvClk~r~Nptvl~vSGyVfCY~Ci~~Yv~-----------~~~~CPVT~~p~~v~~l 350 (357)
T KOG0826|consen 297 PPDREVCPVCLKKRQNPTVLEVSGYVFCYPCIFSYVV-----------NYGHCPVTGYPASVDHL 350 (357)
T ss_pred CCccccChhHHhccCCCceEEecceEEeHHHHHHHHH-----------hcCCCCccCCcchHHHH
Confidence 3466789999988888778888899999999999973 34589987777655443
No 123
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=95.18 E-value=0.12 Score=47.97 Aligned_cols=67 Identities=15% Similarity=0.105 Sum_probs=57.3
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP 197 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p 197 (210)
..|.++|.+.|.. ....++|||..-....+.+...|...|+....++|.|+ ..+|.++++.|..+..
T Consensus 230 ~~k~~~L~~~L~~----~~~~~~IVF~~tk~~a~~l~~~L~~~g~~~~~lhgd~~------q~~R~~il~~Fr~G~~ 296 (629)
T PRK11634 230 MRKNEALVRFLEA----EDFDAAIIFVRTKNATLEVAEALERNGYNSAALNGDMN------QALREQTLERLKDGRL 296 (629)
T ss_pred hhHHHHHHHHHHh----cCCCCEEEEeccHHHHHHHHHHHHhCCCCEEEeeCCCC------HHHHHHHHHHHhCCCC
Confidence 4678888777653 34579999999999999999999999999999999977 9999999999998544
No 124
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.16 E-value=0.016 Score=49.61 Aligned_cols=49 Identities=22% Similarity=0.530 Sum_probs=35.7
Q ss_pred ccccccccccc--cCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccc
Q 028376 24 EETCPICQEKL--GNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRT 80 (210)
Q Consensus 24 ~~~C~iC~~~~--~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~ 80 (210)
.+.|||=.+.- ++||+.+.|||++|.+-+.++... +....+||.|-...
T Consensus 334 vF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~n--------g~~sfKCPYCP~e~ 384 (394)
T KOG2817|consen 334 VFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKN--------GSQSFKCPYCPVEQ 384 (394)
T ss_pred eeecccchhhccCCCCCeeeeccceecHHHHHHHhhC--------CCeeeeCCCCCccc
Confidence 45688754332 456899999999999999998532 34468999995543
No 125
>KOG0330 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=95.01 E-value=0.051 Score=46.88 Aligned_cols=66 Identities=11% Similarity=0.048 Sum_probs=55.2
Q ss_pred chHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376 122 TKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP 197 (210)
Q Consensus 122 sKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p 197 (210)
-|-..|+..|.+ ..+.-+|||+.-...-+.+...|...|+....+.|.|+ ..+|.-+++.|+.+..
T Consensus 286 ~K~~yLV~ll~e----~~g~s~iVF~~t~~tt~~la~~L~~lg~~a~~LhGqms------q~~Rlg~l~~Fk~~~r 351 (476)
T KOG0330|consen 286 DKDTYLVYLLNE----LAGNSVIVFCNTCNTTRFLALLLRNLGFQAIPLHGQMS------QSKRLGALNKFKAGAR 351 (476)
T ss_pred ccchhHHHHHHh----hcCCcEEEEEeccchHHHHHHHHHhcCcceecccchhh------HHHHHHHHHHHhccCC
Confidence 345556655553 45678999999999999999999999999999999966 9999999999998543
No 126
>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=94.98 E-value=0.0093 Score=41.93 Aligned_cols=32 Identities=34% Similarity=0.895 Sum_probs=25.7
Q ss_pred CCccccccccccccCCC-eecCCCCcchHhhHH
Q 028376 22 ADEETCPICQEKLGNQK-MVFQCGHFTCCKCFF 53 (210)
Q Consensus 22 ~~~~~C~iC~~~~~~~~-~~~~CgH~fC~~C~~ 53 (210)
.+...|++|...+.... ++.||||+++..|+.
T Consensus 76 ~~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 76 TESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 35577999999887643 558999999999975
No 127
>PTZ00424 helicase 45; Provisional
Probab=94.84 E-value=0.18 Score=43.73 Aligned_cols=55 Identities=15% Similarity=0.247 Sum_probs=49.0
Q ss_pred hcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376 136 STDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM 196 (210)
Q Consensus 136 ~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~ 196 (210)
...+..++|||..-....+.+...|...|+....++|.|+ ..+|..+++.|+++.
T Consensus 263 ~~~~~~~~ivF~~t~~~~~~l~~~l~~~~~~~~~~h~~~~------~~~R~~i~~~f~~g~ 317 (401)
T PTZ00424 263 ETLTITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMD------QKDRDLIMREFRSGS 317 (401)
T ss_pred HhcCCCeEEEEecCcHHHHHHHHHHHHCCCcEEEEeCCCC------HHHHHHHHHHHHcCC
Confidence 3445679999999999999999999999999999999977 999999999999744
No 128
>PHA03096 p28-like protein; Provisional
Probab=94.76 E-value=0.018 Score=47.95 Aligned_cols=34 Identities=18% Similarity=0.332 Sum_probs=27.5
Q ss_pred cccccccccccCC-------CeecCCCCcchHhhHHHHHHH
Q 028376 25 ETCPICQEKLGNQ-------KMVFQCGHFTCCKCFFAMTEQ 58 (210)
Q Consensus 25 ~~C~iC~~~~~~~-------~~~~~CgH~fC~~C~~~~~~~ 58 (210)
-.|.||++..... +++..|-|.||..|+..|...
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~ 219 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTE 219 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHh
Confidence 7899998865422 477899999999999999644
No 129
>KOG2034 consensus Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport]
Probab=94.67 E-value=0.016 Score=54.25 Aligned_cols=36 Identities=25% Similarity=0.515 Sum_probs=29.1
Q ss_pred CccccccccccccC-CCeecCCCCcchHhhHHHHHHH
Q 028376 23 DEETCPICQEKLGN-QKMVFQCGHFTCCKCFFAMTEQ 58 (210)
Q Consensus 23 ~~~~C~iC~~~~~~-~~~~~~CgH~fC~~C~~~~~~~ 58 (210)
....|.+|..++.. +.++.+|||.|+.+|+.+.+..
T Consensus 816 p~d~C~~C~~~ll~~pF~vf~CgH~FH~~Cl~~~v~~ 852 (911)
T KOG2034|consen 816 PQDSCDHCGRPLLIKPFYVFPCGHCFHRDCLIRHVLS 852 (911)
T ss_pred CccchHHhcchhhcCcceeeeccchHHHHHHHHHHHc
Confidence 45679999887654 4577899999999999988654
No 130
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=94.64 E-value=0.0095 Score=41.39 Aligned_cols=29 Identities=17% Similarity=0.290 Sum_probs=24.0
Q ss_pred ecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccc
Q 028376 40 VFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQR 79 (210)
Q Consensus 40 ~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~ 79 (210)
--.|.|.|+.-|+.+|+. .+..||+|.+.
T Consensus 78 WG~CNHaFH~hCisrWlk-----------tr~vCPLdn~e 106 (114)
T KOG2930|consen 78 WGVCNHAFHFHCISRWLK-----------TRNVCPLDNKE 106 (114)
T ss_pred eeecchHHHHHHHHHHHh-----------hcCcCCCcCcc
Confidence 358999999999999974 34589999774
No 131
>PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional
Probab=94.60 E-value=0.18 Score=45.67 Aligned_cols=69 Identities=17% Similarity=0.189 Sum_probs=55.7
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHh-CCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIA-NNITCIKMKGENHKLPSANLQHRNALQKELTRHMP 197 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~-~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p 197 (210)
..|...|.+.|.... ....++|||..-....+.+...|.. .|+....|.|.|+ ..+|..+++.|..+.-
T Consensus 350 ~~k~~~l~~~l~~~~--~~~~~~iVFv~s~~~a~~l~~~L~~~~g~~~~~~Hg~~~------~~eR~~il~~Fr~G~~ 419 (518)
T PLN00206 350 KQKKQKLFDILKSKQ--HFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKS------MKERREVMKSFLVGEV 419 (518)
T ss_pred hhHHHHHHHHHHhhc--ccCCCEEEEcCCchhHHHHHHHHhhccCcceEEeeCCCC------HHHHHHHHHHHHCCCC
Confidence 346667776665433 2245899999999999999999975 7999999999977 9999999999998543
No 132
>KOG0332 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=94.49 E-value=0.17 Score=43.57 Aligned_cols=67 Identities=12% Similarity=0.126 Sum_probs=57.0
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP 197 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p 197 (210)
-.|.++|.+...-+ .-..+|||.+=.....++...|.+.|.....+.|.|. ..+|.+++++|+.+.-
T Consensus 315 ~~K~~~l~~lyg~~----tigqsiIFc~tk~ta~~l~~~m~~~Gh~V~~l~G~l~------~~~R~~ii~~Fr~g~~ 381 (477)
T KOG0332|consen 315 DDKYQALVNLYGLL----TIGQSIIFCHTKATAMWLYEEMRAEGHQVSLLHGDLT------VEQRAAIIDRFREGKE 381 (477)
T ss_pred hhHHHHHHHHHhhh----hhhheEEEEeehhhHHHHHHHHHhcCceeEEeeccch------hHHHHHHHHHHhcCcc
Confidence 57888888744322 2468999999999999999999999999999999976 9999999999998543
No 133
>KOG0335 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=94.35 E-value=0.085 Score=46.79 Aligned_cols=69 Identities=14% Similarity=0.076 Sum_probs=59.3
Q ss_pred CCchHHHHHHHHHHHHhcCC-----CCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 120 YGTKIEAVTRRILWIKSTDP-----KAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 120 ~SsKi~al~~~L~~~~~~~~-----~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
-..|...|+++|........ .+|++||.-=..+.+-++..|..+|+++..+.|... ..+|.++|+.|..
T Consensus 312 ~~~kr~~Lldll~~~~~~~~~~~~~~e~tlvFvEt~~~~d~l~~~l~~~~~~~~sIhg~~t------q~er~~al~~Fr~ 385 (482)
T KOG0335|consen 312 EMEKRSKLLDLLNKDDGPPSDGEPKWEKTLVFVETKRGADELAAFLSSNGYPAKSIHGDRT------QIEREQALNDFRN 385 (482)
T ss_pred chhhHHHHHHHhhcccCCcccCCcccceEEEEeeccchhhHHHHHHhcCCCCceeecchhh------hhHHHHHHHHhhc
Confidence 36888999988876542212 349999999999999999999999999999999955 9999999999997
No 134
>PRK12900 secA preprotein translocase subunit SecA; Reviewed
Probab=94.25 E-value=0.2 Score=48.27 Aligned_cols=64 Identities=16% Similarity=0.132 Sum_probs=58.0
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
..|..+|++.|.+... .+..+|||+......+.|...|...||++..+.+. ..+|++.|..|..
T Consensus 581 ~eK~~Ali~~I~~~~~--~grpVLIft~Sve~sE~Ls~~L~~~gI~h~vLnak--------q~~REa~Iia~AG 644 (1025)
T PRK12900 581 REKYNAIVLKVEELQK--KGQPVLVGTASVEVSETLSRMLRAKRIAHNVLNAK--------QHDREAEIVAEAG 644 (1025)
T ss_pred HHHHHHHHHHHHHHhh--CCCCEEEEeCcHHHHHHHHHHHHHcCCCceeecCC--------HHHhHHHHHHhcC
Confidence 4689999999987764 37899999999999999999999999999999986 8899999999997
No 135
>KOG0340 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=94.19 E-value=0.21 Score=42.75 Aligned_cols=65 Identities=8% Similarity=0.108 Sum_probs=55.9
Q ss_pred HHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376 124 IEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRH 195 (210)
Q Consensus 124 i~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~ 195 (210)
=..|+..|.....+ +..-++||.|=+..-.++...|+..+++...+.+-|+ .++|.++|.+|+.+
T Consensus 239 daYLv~~Lr~~~~~-~~~simIFvnttr~cQ~l~~~l~~le~r~~~lHs~m~------Q~eR~~aLsrFrs~ 303 (442)
T KOG0340|consen 239 DAYLVHLLRDFENK-ENGSIMIFVNTTRECQLLSMTLKNLEVRVVSLHSQMP------QKERLAALSRFRSN 303 (442)
T ss_pred HHHHHHHHhhhhhc-cCceEEEEeehhHHHHHHHHHHhhhceeeeehhhcch------HHHHHHHHHHHhhc
Confidence 34566666665543 6788899999999999999999999999999999988 99999999999973
No 136
>KOG0328 consensus Predicted ATP-dependent RNA helicase FAL1, involved in rRNA maturation, DEAD-box superfamily [Translation, ribosomal structure and biogenesis]
Probab=94.17 E-value=0.15 Score=42.34 Aligned_cols=63 Identities=14% Similarity=0.242 Sum_probs=55.5
Q ss_pred hHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376 123 KIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRH 195 (210)
Q Consensus 123 Ki~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~ 195 (210)
|.++|.+....+. -.+.|||..-..-.|++..-++..++....+.|.|+ .++|.+++..|+.+
T Consensus 253 KfdtLcdLYd~Lt----ItQavIFcnTk~kVdwLtekm~~~nftVssmHGDm~------qkERd~im~dFRsg 315 (400)
T KOG0328|consen 253 KFDTLCDLYDTLT----ITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDME------QKERDKIMNDFRSG 315 (400)
T ss_pred hHhHHHHHhhhhe----hheEEEEecccchhhHHHHHHHhhCceeeeccCCcc------hhHHHHHHHHhhcC
Confidence 6777776665443 468999999999999999999999999999999998 99999999999973
No 137
>TIGR03714 secA2 accessory Sec system translocase SecA2. Members of this protein family are homologous to SecA and part of the accessory Sec system. This system, including both five core proteins for export and a variable number of proteins for glycosylation, operates in certain Gram-positive pathogens for the maturation and delivery of serine-rich glycoproteins such as the cell surface glycoprotein GspB in Streptococcus gordonii.
Probab=94.15 E-value=0.21 Score=47.03 Aligned_cols=65 Identities=8% Similarity=0.124 Sum_probs=52.6
Q ss_pred CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHH
Q 028376 120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKEL 192 (210)
Q Consensus 120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F 192 (210)
...|..++++.+..... .+..+|||.......+.+...|..+||++..+.|.|. ..+|..+.+.|
T Consensus 406 ~~~K~~ai~~~i~~~~~--~~~pvLIft~s~~~se~ls~~L~~~gi~~~~L~a~~~------~~E~~ii~~ag 470 (762)
T TIGR03714 406 LPEKLMATLEDVKEYHE--TGQPVLLITGSVEMSEIYSELLLREGIPHNLLNAQNA------AKEAQIIAEAG 470 (762)
T ss_pred HHHHHHHHHHHHHHHhh--CCCCEEEEECcHHHHHHHHHHHHHCCCCEEEecCCCh------HHHHHHHHHcC
Confidence 35689999999987653 3678999999999999999999999999999999965 55554444433
No 138
>smart00490 HELICc helicase superfamily c-terminal domain.
Probab=93.98 E-value=0.13 Score=33.21 Aligned_cols=37 Identities=11% Similarity=0.161 Sum_probs=32.2
Q ss_pred HHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376 155 VLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP 197 (210)
Q Consensus 155 li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p 197 (210)
.+...|...++++..++|.|+ ..+|..+++.|+.++.
T Consensus 2 ~l~~~l~~~~~~~~~~~~~~~------~~~r~~~~~~f~~~~~ 38 (82)
T smart00490 2 ELAELLKELGIKVARLHGGLS------QEEREEILEKFNNGKI 38 (82)
T ss_pred HHHHHHHHCCCeEEEEECCCC------HHHHHHHHHHHHcCCC
Confidence 467788889999999999977 9999999999998543
No 139
>PRK12904 preprotein translocase subunit SecA; Reviewed
Probab=93.95 E-value=0.27 Score=46.77 Aligned_cols=66 Identities=15% Similarity=0.057 Sum_probs=58.2
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM 196 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~ 196 (210)
..|..++++.+.+... .+..+|||+......+.+...|...||++..+.|. ..+|.+.|..|....
T Consensus 413 ~~K~~aI~~~I~~~~~--~grpVLIft~Si~~se~Ls~~L~~~gi~~~vLnak--------q~eREa~Iia~Ag~~ 478 (830)
T PRK12904 413 KEKFDAVVEDIKERHK--KGQPVLVGTVSIEKSELLSKLLKKAGIPHNVLNAK--------NHEREAEIIAQAGRP 478 (830)
T ss_pred HHHHHHHHHHHHHHHh--cCCCEEEEeCcHHHHHHHHHHHHHCCCceEeccCc--------hHHHHHHHHHhcCCC
Confidence 4689999999987653 36789999999999999999999999999999997 779999999999733
No 140
>PRK12898 secA preprotein translocase subunit SecA; Reviewed
Probab=93.89 E-value=0.34 Score=45.03 Aligned_cols=64 Identities=13% Similarity=0.061 Sum_probs=54.3
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
..|..+|++.+..+... +..+|||..-....+.+...|..+||++..+.|. ..+|++.+..|..
T Consensus 456 ~~K~~aL~~~i~~~~~~--~~pvLIft~t~~~se~L~~~L~~~gi~~~~Lhg~--------~~~rE~~ii~~ag 519 (656)
T PRK12898 456 AAKWAAVAARVRELHAQ--GRPVLVGTRSVAASERLSALLREAGLPHQVLNAK--------QDAEEAAIVARAG 519 (656)
T ss_pred HHHHHHHHHHHHHHHhc--CCCEEEEeCcHHHHHHHHHHHHHCCCCEEEeeCC--------cHHHHHHHHHHcC
Confidence 46899999988876532 3569999999999999999999999999999998 4478888888875
No 141
>KOG0339 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=93.87 E-value=0.13 Score=46.04 Aligned_cols=68 Identities=15% Similarity=0.271 Sum_probs=60.2
Q ss_pred CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376 119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRH 195 (210)
Q Consensus 119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~ 195 (210)
+.-.|+..|+++|..... ..|+|||..=..-.+-|...|+.+||....+.|.|. .+.|+.+|..|++.
T Consensus 450 s~~~Kl~wl~~~L~~f~S---~gkvlifVTKk~~~e~i~a~Lklk~~~v~llhgdkd------qa~rn~~ls~fKkk 517 (731)
T KOG0339|consen 450 SEEKKLNWLLRHLVEFSS---EGKVLIFVTKKADAEEIAANLKLKGFNVSLLHGDKD------QAERNEVLSKFKKK 517 (731)
T ss_pred CcHHHHHHHHHHhhhhcc---CCcEEEEEeccCCHHHHHHHhccccceeeeecCchh------hHHHHHHHHHHhhc
Confidence 456899999999987653 469999999888899999999999999999999966 99999999999984
No 142
>TIGR00963 secA preprotein translocase, SecA subunit. The proteins SecA-F and SecY, not all of which are necessary, comprise the standard prokaryotic protein translocation apparatus. Other, specialized translocation systems also exist but are not as broadly distributed. This model describes SecA, an essential member of the apparatus.
Probab=93.80 E-value=0.34 Score=45.59 Aligned_cols=65 Identities=15% Similarity=0.079 Sum_probs=57.9
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRH 195 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~ 195 (210)
-.|..++++.+.+... .+..+|||.....-.+.+...|.++||++..+.|. ...|++.|..|...
T Consensus 388 ~~k~~ai~~~i~~~~~--~grpvLV~t~si~~se~ls~~L~~~gi~~~~Lna~--------q~~rEa~ii~~ag~ 452 (745)
T TIGR00963 388 EEKWKAVVDEIKERHA--KGQPVLVGTTSVEKSELLSNLLKERGIPHNVLNAK--------NHEREAEIIAQAGR 452 (745)
T ss_pred HHHHHHHHHHHHHHHh--cCCCEEEEeCcHHHHHHHHHHHHHcCCCeEEeeCC--------hHHHHHHHHHhcCC
Confidence 3588899999887764 47889999999999999999999999999999998 77999999999873
No 143
>KOG1815 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.68 E-value=0.073 Score=47.26 Aligned_cols=63 Identities=21% Similarity=0.528 Sum_probs=44.3
Q ss_pred CCCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCcccccc--CCcccccCCCeE
Q 028376 21 KADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCP--TCRQRTDIGNIA 86 (210)
Q Consensus 21 ~~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP--~Cr~~~~~~~l~ 86 (210)
......|.||.+......+...|||.||..|+..++........ ....+|| .|+..+....+.
T Consensus 67 ~~~~~~c~ic~~~~~~~~~~~~c~H~~c~~cw~~yl~~kI~~~~---~~~i~cp~~~C~a~v~~~~i~ 131 (444)
T KOG1815|consen 67 KKGDVQCGICVESYDGEIIGLGCGHPFCPPCWTGYLGTKIHEGE---EAKIKCPAHGCPALVGEDTVE 131 (444)
T ss_pred CCccccCCcccCCCcchhhhcCCCcHHHHHHHHHHhhheeeccc---cccccCCCCCccccCCCceee
Confidence 34568899998877543466799999999999999877553221 2225676 587777666554
No 144
>COG1061 SSL2 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]
Probab=93.58 E-value=0.3 Score=43.36 Aligned_cols=67 Identities=24% Similarity=0.232 Sum_probs=55.7
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP 197 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p 197 (210)
..|+.++...+.... .+.+++||.+.......+...|...|+ ...++|..+ ...|.+++++|..++.
T Consensus 267 ~~~~~~~~~~~~~~~---~~~~~lif~~~~~~a~~i~~~~~~~~~-~~~it~~t~------~~eR~~il~~fr~g~~ 333 (442)
T COG1061 267 ERKIAAVRGLLLKHA---RGDKTLIFASDVEHAYEIAKLFLAPGI-VEAITGETP------KEEREAILERFRTGGI 333 (442)
T ss_pred HHHHHHHHHHHHHhc---CCCcEEEEeccHHHHHHHHHHhcCCCc-eEEEECCCC------HHHHHHHHHHHHcCCC
Confidence 455556665555432 478999999999999999999999999 788899987 9999999999998553
No 145
>PRK13107 preprotein translocase subunit SecA; Reviewed
Probab=93.56 E-value=0.27 Score=47.02 Aligned_cols=67 Identities=12% Similarity=0.115 Sum_probs=60.4
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRH 195 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~ 195 (210)
-.|..|+++.+.++.+. +-.+|||+.....-+++...|..+||++..+.|.+. ..+|..+.+.|+.+
T Consensus 432 ~~K~~Aii~ei~~~~~~--GrpVLV~t~sv~~se~ls~~L~~~gi~~~vLnak~~------~~Ea~ii~~Ag~~G 498 (908)
T PRK13107 432 DEKYQAIIKDIKDCRER--GQPVLVGTVSIEQSELLARLMVKEKIPHEVLNAKFH------EREAEIVAQAGRTG 498 (908)
T ss_pred HHHHHHHHHHHHHHHHc--CCCEEEEeCcHHHHHHHHHHHHHCCCCeEeccCccc------HHHHHHHHhCCCCC
Confidence 57889999999988754 788999999999999999999999999999999966 89999999998863
No 146
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=93.42 E-value=0.042 Score=47.75 Aligned_cols=35 Identities=26% Similarity=0.665 Sum_probs=29.6
Q ss_pred CccccccccccccCCCeecCCCCcchHhhHHHHHHH
Q 028376 23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQ 58 (210)
Q Consensus 23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~ 58 (210)
+...|++|..-+.+ +++++|+|.+|..|....+.+
T Consensus 3 eelkc~vc~~f~~e-piil~c~h~lc~~ca~~~~~~ 37 (699)
T KOG4367|consen 3 EELKCPVCGSFYRE-PIILPCSHNLCQACARNILVQ 37 (699)
T ss_pred ccccCceehhhccC-ceEeecccHHHHHHHHhhccc
Confidence 45689999988887 599999999999999876543
No 147
>KOG0348 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=93.42 E-value=0.31 Score=43.91 Aligned_cols=68 Identities=18% Similarity=0.291 Sum_probs=52.2
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHh----------------------CCceEEEeeCCCCCCc
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIA----------------------NNITCIKMKGENHKLP 178 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~----------------------~gi~~~~~~G~m~~~~ 178 (210)
...+=+|...|+..-+..+..|.|||-+-+++.+.--.+|.. .+.+|+|+.|+|.
T Consensus 406 KLRLV~Laa~L~~~~k~~~~qk~iVF~S~~d~VeFHy~lf~~~l~~~~e~~s~~~~s~g~~~l~~~~k~~rLHGsm~--- 482 (708)
T KOG0348|consen 406 KLRLVALAALLLNKVKFEEKQKMIVFFSCSDSVEFHYSLFSEALLSHLEGSSGAPDSEGLPPLFMDLKFYRLHGSME--- 482 (708)
T ss_pred chhHHHHHHHHHHHhhhhhhceeEEEEechhHHHHHHHHHHhhhhcccccccCCcccCCChhhhhcceEEEecCchh---
Confidence 345567888888877777788999998877776554444432 2457999999976
Q ss_pred chhhHhhhHHHHHHhh
Q 028376 179 SANLQHRNALQKELTR 194 (210)
Q Consensus 179 ~~~~~~R~~~l~~F~~ 194 (210)
...|..++..|..
T Consensus 483 ---QeeRts~f~~Fs~ 495 (708)
T KOG0348|consen 483 ---QEERTSVFQEFSH 495 (708)
T ss_pred ---HHHHHHHHHhhcc
Confidence 9999999999997
No 148
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=93.39 E-value=0.068 Score=52.94 Aligned_cols=62 Identities=19% Similarity=0.583 Sum_probs=43.8
Q ss_pred CCCCcccccccccc-cc-CCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376 20 SKADEETCPICQEK-LG-NQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI 82 (210)
Q Consensus 20 ~~~~~~~C~iC~~~-~~-~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~ 82 (210)
++..+..|.||... +. .+.+.+.|+|+|+..|....+++.+.... -.-+-..||.|..++..
T Consensus 3482 kQD~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vLE~RW~GPR-ItF~FisCPiC~n~InH 3545 (3738)
T KOG1428|consen 3482 KQDADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPR-ITFGFISCPICKNKINH 3545 (3738)
T ss_pred hcccCceEEEEehhhhCCCcceecCCccchhHHHHHHHHHhcccCCe-eEEeeeecccccchhhh
Confidence 45567789999654 33 23577999999999999999998763210 01233469999988753
No 149
>PF00271 Helicase_C: Helicase conserved C-terminal domain; InterPro: IPR001650 The domain, which defines this group of proteins is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase. The eukaryotic translation initiation factor 4A (eIF4A) is a member of the DEA(D/H)-box RNA helicase family This is a diverse group of proteins that couples an ATPase activity to RNA binding and unwinding. The structure of the carboxyl-terminal domain of eIF4A has been determined to 1.75 A resolution; it has a parallel alpha-beta topology that superimposes, with minor variations, on the structures and conserved motifs of the equivalent domain in other, distantly related helicases [].; GO: 0003676 nucleic acid binding, 0004386 helicase activity, 0005524 ATP binding; PDB: 2Z83_A 2JGN_C 2I4I_A 2BMF_A 2BHR_B 1WP9_E 2WAX_C 2WAY_C 3JUX_A 3DIN_B ....
Probab=93.38 E-value=0.13 Score=33.52 Aligned_cols=34 Identities=12% Similarity=0.171 Sum_probs=30.2
Q ss_pred HHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376 158 HAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP 197 (210)
Q Consensus 158 ~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p 197 (210)
..|+..|+.+..++|.|+ ..+|..+++.|+.+..
T Consensus 1 ~~L~~~~~~~~~i~~~~~------~~~r~~~~~~f~~~~~ 34 (78)
T PF00271_consen 1 KFLEKKGIKVAIIHGDMS------QKERQEILKKFNSGEI 34 (78)
T ss_dssp HHHHHTTSSEEEESTTSH------HHHHHHHHHHHHTTSS
T ss_pred CChHHCCCcEEEEECCCC------HHHHHHHHHHhhccCc
Confidence 368899999999999966 9999999999998555
No 150
>PLN03137 ATP-dependent DNA helicase; Q4-like; Provisional
Probab=93.31 E-value=0.4 Score=47.14 Aligned_cols=54 Identities=7% Similarity=0.007 Sum_probs=48.8
Q ss_pred cCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376 137 TDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM 196 (210)
Q Consensus 137 ~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~ 196 (210)
...+...|||.....-.+.+...|...|+....|.|+|+ ..+|..+++.|..+.
T Consensus 677 ~~~~esgIIYC~SRke~E~LAe~L~~~Gika~~YHAGLs------~eeR~~vqe~F~~Ge 730 (1195)
T PLN03137 677 NHFDECGIIYCLSRMDCEKVAERLQEFGHKAAFYHGSMD------PAQRAFVQKQWSKDE 730 (1195)
T ss_pred cccCCCceeEeCchhHHHHHHHHHHHCCCCeeeeeCCCC------HHHHHHHHHHHhcCC
Confidence 344678999999999999999999999999999999977 999999999999854
No 151
>PRK13104 secA preprotein translocase subunit SecA; Reviewed
Probab=93.26 E-value=0.36 Score=46.20 Aligned_cols=67 Identities=13% Similarity=0.105 Sum_probs=60.2
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRH 195 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~ 195 (210)
-.|..|+++.+.+... .+-=+|||+....--+.+...|.+.||++..+.|.+. ..+|..+.+.|+.+
T Consensus 427 ~~k~~av~~~i~~~~~--~g~PVLVgt~Sie~sE~ls~~L~~~gi~h~vLnak~~------q~Ea~iia~Ag~~G 493 (896)
T PRK13104 427 ADKFQAIIEDVRECGV--RKQPVLVGTVSIEASEFLSQLLKKENIKHQVLNAKFH------EKEAQIIAEAGRPG 493 (896)
T ss_pred HHHHHHHHHHHHHHHh--CCCCEEEEeCcHHHHHHHHHHHHHcCCCeEeecCCCC------hHHHHHHHhCCCCC
Confidence 4688899999988764 4778999999999999999999999999999999976 99999999999874
No 152
>KOG0354 consensus DEAD-box like helicase [General function prediction only]
Probab=92.93 E-value=0.57 Score=43.87 Aligned_cols=78 Identities=9% Similarity=0.143 Sum_probs=63.1
Q ss_pred CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHH---hCCceEEEeeC--CCCCCcchhhHhhhHHHHHHhh
Q 028376 120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFI---ANNITCIKMKG--ENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~---~~gi~~~~~~G--~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
-..|++.|.+.|.+....+++.++|||+-+......|-.+|. ..||+-.-|-| ......+|+.++...+|+.|+.
T Consensus 393 ~npkle~l~~~l~e~f~~~~dsR~IIFve~R~sa~~l~~~l~~~~~~~ir~~~fiGq~~s~~~~gmtqk~Q~evl~~Fr~ 472 (746)
T KOG0354|consen 393 ENPKLEKLVEILVEQFEQNPDSRTIIFVETRESALALKKWLLQLHELGIKAEIFIGQGKSTQSTGMTQKEQKEVLDKFRD 472 (746)
T ss_pred cChhHHHHHHHHHHHhhcCCCccEEEEEehHHHHHHHHHHHHhhhhcccccceeeeccccccccccCHHHHHHHHHHHhC
Confidence 368999999999999999999999999999888777777777 45666555544 4445578999999999999998
Q ss_pred cCC
Q 028376 195 HMP 197 (210)
Q Consensus 195 ~~p 197 (210)
++=
T Consensus 473 G~~ 475 (746)
T KOG0354|consen 473 GEI 475 (746)
T ss_pred CCc
Confidence 543
No 153
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.87 E-value=0.06 Score=46.87 Aligned_cols=59 Identities=29% Similarity=0.624 Sum_probs=39.7
Q ss_pred CCcccccccc-ccccCC--CeecCCCCcchHhhHHHHHHHhhhccccCCCcccccc--CCcccccCCCe
Q 028376 22 ADEETCPICQ-EKLGNQ--KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCP--TCRQRTDIGNI 85 (210)
Q Consensus 22 ~~~~~C~iC~-~~~~~~--~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP--~Cr~~~~~~~l 85 (210)
....+|.||. +.+... ..+..|+|.||.+|+.++++-... .+..+.|| .|...+...+.
T Consensus 144 ~~~~~C~iC~~e~~~~~~~f~~~~C~H~fC~~C~k~~iev~~~-----~~~~~~C~~~~C~~~l~~~~c 207 (384)
T KOG1812|consen 144 LPKEECGICFVEDPEAEDMFSVLKCGHRFCKDCVKQHIEVKLL-----SGTVIRCPHDGCESRLTLESC 207 (384)
T ss_pred cccccCccCccccccHhhhHHHhcccchhhhHHhHHHhhhhhc-----cCCCccCCCCCCCccCCHHHH
Confidence 3467899998 433321 235689999999999999875411 35677887 46666655443
No 154
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.86 E-value=0.08 Score=42.10 Aligned_cols=40 Identities=28% Similarity=0.719 Sum_probs=29.9
Q ss_pred cccccccccCCCeecCCCC-cchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376 27 CPICQEKLGNQKMVFQCGH-FTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI 82 (210)
Q Consensus 27 C~iC~~~~~~~~~~~~CgH-~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~ 82 (210)
|-.|.+.-.. ..++||.| .+|..|-.. ...||+|+.+...
T Consensus 161 Cr~C~~~~~~-VlllPCrHl~lC~~C~~~---------------~~~CPiC~~~~~s 201 (207)
T KOG1100|consen 161 CRKCGEREAT-VLLLPCRHLCLCGICDES---------------LRICPICRSPKTS 201 (207)
T ss_pred ceecCcCCce-EEeecccceEeccccccc---------------CccCCCCcChhhc
Confidence 9999886654 57789998 678888432 4579999886543
No 155
>PRK09200 preprotein translocase subunit SecA; Reviewed
Probab=92.56 E-value=0.56 Score=44.55 Aligned_cols=65 Identities=9% Similarity=0.057 Sum_probs=53.0
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHh
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELT 193 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~ 193 (210)
..|..+|++.+..... .+.++|||.......+.+...|...||++..+.|.|. ..+|..+...|.
T Consensus 411 ~~K~~al~~~i~~~~~--~~~pvLIf~~t~~~se~l~~~L~~~gi~~~~L~~~~~------~~e~~~i~~ag~ 475 (790)
T PRK09200 411 DEKYKAVIEEVKERHE--TGRPVLIGTGSIEQSETFSKLLDEAGIPHNLLNAKNA------AKEAQIIAEAGQ 475 (790)
T ss_pred HHHHHHHHHHHHHHHh--cCCCEEEEeCcHHHHHHHHHHHHHCCCCEEEecCCcc------HHHHHHHHHcCC
Confidence 5789999999987543 4789999999999999999999999999999999965 555554444443
No 156
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=92.48 E-value=0.15 Score=38.52 Aligned_cols=50 Identities=16% Similarity=0.394 Sum_probs=37.5
Q ss_pred CccccccccccccCCCeecCCCC-----cchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376 23 DEETCPICQEKLGNQKMVFQCGH-----FTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG 83 (210)
Q Consensus 23 ~~~~C~iC~~~~~~~~~~~~CgH-----~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~ 83 (210)
....|-||.+.... ...||.- ..+.+|+.+|+.. ++...|+.|+.++...
T Consensus 7 ~~~~CRIC~~~~~~--~~~PC~CkGs~k~VH~sCL~rWi~~---------s~~~~CeiC~~~Y~i~ 61 (162)
T PHA02825 7 MDKCCWICKDEYDV--VTNYCNCKNENKIVHKECLEEWINT---------SKNKSCKICNGPYNIK 61 (162)
T ss_pred CCCeeEecCCCCCC--ccCCcccCCCchHHHHHHHHHHHhc---------CCCCcccccCCeEEEE
Confidence 45689999887543 3467765 4489999999854 4667899999987655
No 157
>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=92.47 E-value=0.016 Score=37.59 Aligned_cols=40 Identities=38% Similarity=0.846 Sum_probs=24.5
Q ss_pred cccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376 25 ETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD 81 (210)
Q Consensus 25 ~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~ 81 (210)
..||.|..++.... ||..|..|-..+ .....||.|..++.
T Consensus 2 ~~CP~C~~~L~~~~-----~~~~C~~C~~~~------------~~~a~CPdC~~~Le 41 (70)
T PF07191_consen 2 NTCPKCQQELEWQG-----GHYHCEACQKDY------------KKEAFCPDCGQPLE 41 (70)
T ss_dssp -B-SSS-SBEEEET-----TEEEETTT--EE------------EEEEE-TTT-SB-E
T ss_pred CcCCCCCCccEEeC-----CEEECccccccc------------eecccCCCcccHHH
Confidence 47999998875432 899999998876 45668999998764
No 158
>PF11496 HDA2-3: Class II histone deacetylase complex subunits 2 and 3; InterPro: IPR021006 This entry contains the class II histone deacetylase complex subunits HDA2 and HDA3 is found in fungi. The member from Schizosaccharomyces pombe (Fission yeast) is referred to as Ccq1 in Q10432 from SWISSPROT. These proteins associate with HDA1 to generate the activity of the HDA1 histone deacetylase complex. HDA1 interacts with itself and with the HDA2-HDA3 subcomplex to form a probable tetramer and these interactions are necessary for catalytic activity. The HDA1 histone deacetylase complex is responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. HDA2 and HDA3 have a conserved coiled-coil domain towards their C terminus []. ; PDB: 3HGQ_C 3HGT_B.
Probab=92.39 E-value=0.24 Score=41.69 Aligned_cols=57 Identities=19% Similarity=0.229 Sum_probs=44.6
Q ss_pred CCCchHHHHHHHHHHHHh---cCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCC
Q 028376 119 SYGTKIEAVTRRILWIKS---TDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENH 175 (210)
Q Consensus 119 ~~SsKi~al~~~L~~~~~---~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~ 175 (210)
..|+|...|-+.|..+.. .+.+.++||.++-...+|+||..|...++.|.|++|.+-
T Consensus 93 ~tS~KF~~L~~Li~~li~~~~~~~~~~ilIv~~~~k~ldllE~~llGk~~~~kr~sg~~l 152 (297)
T PF11496_consen 93 YTSGKFQFLNDLIDSLIDRDRREYPLHILIVSRSGKELDLLEGLLLGKKLNYKRYSGESL 152 (297)
T ss_dssp HT-HHHHHHHHHHHHH-----TTSSEEEEEEE-STHHHHHHHHHHTTSSSEEEESSS--S
T ss_pred HcCchHHHHHHHHHHHHhhhcccCCceEEEEecCccHHHHHHHHHccCCeeEEecCCCCC
Confidence 458999887777766622 455789999999999999999999999999999999864
No 159
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=92.06 E-value=0.15 Score=30.45 Aligned_cols=41 Identities=20% Similarity=0.512 Sum_probs=25.3
Q ss_pred cccccccccCC-CeecCCCC-----cchHhhHHHHHHHhhhccccCCCccccccCC
Q 028376 27 CPICQEKLGNQ-KMVFQCGH-----FTCCKCFFAMTEQRLIHDNKVKNEWVMCPTC 76 (210)
Q Consensus 27 C~iC~~~~~~~-~~~~~CgH-----~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~C 76 (210)
|-||.+.-... +.+.||+- ..+..|+.+|+.. .+...|++|
T Consensus 1 CrIC~~~~~~~~~li~pC~C~Gs~~~vH~~CL~~W~~~---------~~~~~C~~C 47 (47)
T PF12906_consen 1 CRICLEGEEEDEPLISPCRCKGSMKYVHRSCLERWIRE---------SGNRKCEIC 47 (47)
T ss_dssp ETTTTEE-SSSS-EE-SSS-SSCCGSEECCHHHHHHHH---------HT-SB-TTT
T ss_pred CeEeCCcCCCCCceecccccCCCcchhHHHHHHHHHHh---------cCCCcCCCC
Confidence 67887765543 47788852 5688999999875 234468877
No 160
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=92.04 E-value=0.17 Score=47.56 Aligned_cols=56 Identities=18% Similarity=0.373 Sum_probs=40.1
Q ss_pred CCCccccccccccccCC---CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccc
Q 028376 21 KADEETCPICQEKLGNQ---KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRT 80 (210)
Q Consensus 21 ~~~~~~C~iC~~~~~~~---~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~ 80 (210)
..+..+|.||.+.+... +.-..|.|+|...||..|...... . ....-.||.|+...
T Consensus 188 ~~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek-~---~~~~WrCP~Cqsv~ 246 (950)
T KOG1952|consen 188 SNRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEK-T---GQDGWRCPACQSVS 246 (950)
T ss_pred hcCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhh-c---cCccccCCcccchh
Confidence 45678999999987643 233578999999999999766221 1 23555799998543
No 161
>TIGR02621 cas3_GSU0051 CRISPR-associated helicase Cas3, Anaes-subtype. This model describes a CRISPR-associated putative DEAH-box helicase, or Cas3, of a subtype found in Actinomyces naeslundii MG1, Geobacter sulfurreducens PCA, Gemmata obscuriglobus UQM 2246, and Desulfotalea psychrophila. This protein includes both DEAH and HD motifs.
Probab=91.90 E-value=0.92 Score=43.39 Aligned_cols=64 Identities=11% Similarity=0.133 Sum_probs=52.2
Q ss_pred chHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhh-----HHHHHHhh
Q 028376 122 TKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRN-----ALQKELTR 194 (210)
Q Consensus 122 sKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~-----~~l~~F~~ 194 (210)
.|+..++..|..+.. ..+.++|||..-....+.+...|...|+ ..+.|.|. ..+|. +++++|..
T Consensus 255 ~Kl~~lv~~L~~ll~-e~g~~vLVF~NTv~~Aq~L~~~L~~~g~--~lLHG~m~------q~dR~~~~~~~il~~Fk~ 323 (844)
T TIGR02621 255 KFLSTMVKELNLLMK-DSGGAILVFCRTVKHVRKVFAKLPKEKF--ELLTGTLR------GAERDDLVKKEIFNRFLP 323 (844)
T ss_pred HHHHHHHHHHHHHHh-hCCCcEEEEECCHHHHHHHHHHHHhcCC--eEeeCCCC------HHHHhhHHHHHHHHHHhc
Confidence 356666666655443 3467899999999999999999999998 78999977 99999 88999986
No 162
>PHA02862 5L protein; Provisional
Probab=91.77 E-value=0.17 Score=37.59 Aligned_cols=50 Identities=20% Similarity=0.451 Sum_probs=37.3
Q ss_pred ccccccccccccCCCeecCCC-----CcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCC
Q 028376 24 EETCPICQEKLGNQKMVFQCG-----HFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGN 84 (210)
Q Consensus 24 ~~~C~iC~~~~~~~~~~~~Cg-----H~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~ 84 (210)
...|-||.+.-.+ ...||. ...+.+|+.+|+.. .+...|+.|+.++....
T Consensus 2 ~diCWIC~~~~~e--~~~PC~C~GS~K~VHq~CL~~WIn~---------S~k~~CeLCkteY~Ik~ 56 (156)
T PHA02862 2 SDICWICNDVCDE--RNNFCGCNEEYKVVHIKCMQLWINY---------SKKKECNLCKTKYNIKK 56 (156)
T ss_pred CCEEEEecCcCCC--CcccccccCcchhHHHHHHHHHHhc---------CCCcCccCCCCeEEEEE
Confidence 3579999887543 256775 36789999999843 56779999999876543
No 163
>KOG0327 consensus Translation initiation factor 4F, helicase subunit (eIF-4A) and related helicases [Translation, ribosomal structure and biogenesis]
Probab=91.75 E-value=0.66 Score=39.99 Aligned_cols=76 Identities=18% Similarity=0.271 Sum_probs=62.3
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC---
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP--- 197 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p--- 197 (210)
..|+..|..... .-..++||-.-..-++.+...|..+|+...-+.|-|. ..+|..++++|+.+.-
T Consensus 250 ~~k~~~l~dl~~------~~~q~~if~nt~r~v~~l~~~L~~~~~~~s~~~~d~~------q~~R~~~~~ef~~gssrvl 317 (397)
T KOG0327|consen 250 EEKLDTLCDLYR------RVTQAVIFCNTRRKVDNLTDKLRAHGFTVSAIHGDME------QNERDTLMREFRSGSSRVL 317 (397)
T ss_pred cccccHHHHHHH------hhhcceEEecchhhHHHHHHHHhhCCceEEEeecccc------hhhhhHHHHHhhcCCceEE
Confidence 347777776665 2458899999999999999999999999999999987 9999999999998443
Q ss_pred ----------CCCCccccccc
Q 028376 198 ----------SSQSQSLFKCY 208 (210)
Q Consensus 198 ----------~~~~~~~~~~~ 208 (210)
+++..|+..||
T Consensus 318 Ittdl~argidv~~~slviny 338 (397)
T KOG0327|consen 318 ITTDLLARGIDVQQVSLVVNY 338 (397)
T ss_pred eeccccccccchhhcceeeee
Confidence 34556666665
No 164
>KOG2231 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.48 E-value=1.3 Score=41.06 Aligned_cols=163 Identities=18% Similarity=0.204 Sum_probs=88.8
Q ss_pred ccccccccccCCCeecCCCC-cchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE-EccCccccCCCCCCCCC
Q 028376 26 TCPICQEKLGNQKMVFQCGH-FTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA-YADDRQDKSCNSDMPHG 103 (210)
Q Consensus 26 ~C~iC~~~~~~~~~~~~CgH-~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~-~~~~~~~~~~~~~~~~~ 103 (210)
.|+||...+.- ...-.||| ..|..|+.++..... +......||+||..+....+. +........ +. ....
T Consensus 2 ~c~ic~~s~~~-~~~~s~~h~~v~~~~~~R~~~~~~-----~~~~~~~~~vcr~~~~~~s~~~~~~~~~t~~-~~-~~~~ 73 (669)
T KOG2231|consen 2 SCAICAFSPDF-VGRGSCGHNEVCATCVVRLRFELN-----NRKCSNECPVCRREVETKSNGDSSDAVGTFP-EG-RKCD 73 (669)
T ss_pred CcceeecCccc-cccccccccccchhhhhhhhhhcc-----cccccccCcccccceeeeccccccccccccc-cc-cccc
Confidence 59999887764 47789999 999999998843311 123455679998865433221 111000000 00 0000
Q ss_pred CCCcccccCCce-ecCCCCchHHHHHHHHHH-----HHhcCCCCcEEEEcchHHHHHHHHHHHHhC----------CceE
Q 028376 104 VQDCEKGEESFT-VQGSYGTKIEAVTRRILW-----IKSTDPKAKILVFSSWNDVLDVLEHAFIAN----------NITC 167 (210)
Q Consensus 104 ~~~~~~~~~~~~-~~~~~SsKi~al~~~L~~-----~~~~~~~~K~iVFSQf~~~L~li~~~L~~~----------gi~~ 167 (210)
....+.. ..+. .....-+|++++...-=. .....++.-...+.-|..+..|=.++-..+ +-.+
T Consensus 74 ~~~~e~~-~~if~~d~~~y~~~~~~~~~~C~~C~~~~~~~~~~~~~~~c~~~~s~~~Lk~H~~~~H~~~~c~lC~~~~ki 152 (669)
T KOG2231|consen 74 FDEHEDT-CVIFFADKLTYTKLEACLHHSCHICDRRFRALYNKKECLHCTEFKSVENLKNHMRDQHKLHLCSLCLQNLKI 152 (669)
T ss_pred cccccce-eeeeeccccHHHHHHHHHhhhcCccccchhhhcccCCCccccchhHHHHHHHHHHHhhhhhcccccccccee
Confidence 0001100 1111 223445777777764311 111122223345566777777766664444 4444
Q ss_pred EEeeCCCCCCcchhhHhhhHHHHHHhhcCCCCCCcccc
Q 028376 168 IKMKGENHKLPSANLQHRNALQKELTRHMPSSQSQSLF 205 (210)
Q Consensus 168 ~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~~~~~~~~ 205 (210)
..+.++ ...|..+...-+.+||+.++-+-+
T Consensus 153 f~~e~k--------~Yt~~el~~h~~~gd~d~~s~rGh 182 (669)
T KOG2231|consen 153 FINERK--------LYTRAELNLHLMFGDPDDESCRGH 182 (669)
T ss_pred eeeeee--------hehHHHHHHHHhcCCCccccccCC
Confidence 555566 778888888888889987776654
No 165
>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=91.37 E-value=0.28 Score=36.99 Aligned_cols=62 Identities=21% Similarity=0.499 Sum_probs=36.0
Q ss_pred CccccccccccccCCCeecCCC-------Ccc------hHhhHHHHHHHhhhccc--------------------cCCCc
Q 028376 23 DEETCPICQEKLGNQKMVFQCG-------HFT------CCKCFFAMTEQRLIHDN--------------------KVKNE 69 (210)
Q Consensus 23 ~~~~C~iC~~~~~~~~~~~~Cg-------H~f------C~~C~~~~~~~~~~~~~--------------------~~~~~ 69 (210)
++..||||++.+=+. +++.|. -.+ ...|++++......... .....
T Consensus 1 ed~~CpICme~PHNA-VLLlCSS~~kgcRpymc~Ts~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (162)
T PF07800_consen 1 EDVTCPICMEHPHNA-VLLLCSSHEKGCRPYMCDTSYRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQP 79 (162)
T ss_pred CCccCceeccCCCce-EEEEeccccCCccccccCCccchhHHHHHHHHHhcCCCCccccccccCcCCCcccccccccccc
Confidence 457899999988774 666542 222 35788887543221110 00123
Q ss_pred cccccCCcccccCCCe
Q 028376 70 WVMCPTCRQRTDIGNI 85 (210)
Q Consensus 70 ~~~CP~Cr~~~~~~~l 85 (210)
...||+||..+.--.+
T Consensus 80 ~L~CPLCRG~V~GWtv 95 (162)
T PF07800_consen 80 ELACPLCRGEVKGWTV 95 (162)
T ss_pred cccCccccCceeceEE
Confidence 5579999987655433
No 166
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=90.90 E-value=0.24 Score=32.74 Aligned_cols=55 Identities=24% Similarity=0.616 Sum_probs=21.8
Q ss_pred cCCCCccccccccccccCC----Ce--ecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376 19 LSKADEETCPICQEKLGNQ----KM--VFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG 83 (210)
Q Consensus 19 l~~~~~~~C~iC~~~~~~~----~~--~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~ 83 (210)
++..+...|.||.+.+... ++ .--|+-..|+.|++-- . ..+...||.|+.++...
T Consensus 4 ~k~~~~qiCqiCGD~VGl~~~Ge~FVAC~eC~fPvCr~CyEYE--r--------keg~q~CpqCkt~ykr~ 64 (80)
T PF14569_consen 4 LKNLNGQICQICGDDVGLTENGEVFVACHECAFPVCRPCYEYE--R--------KEGNQVCPQCKTRYKRH 64 (80)
T ss_dssp -S--SS-B-SSS--B--B-SSSSB--S-SSS-----HHHHHHH--H--------HTS-SB-TTT--B----
T ss_pred hhhcCCcccccccCccccCCCCCEEEEEcccCCccchhHHHHH--h--------hcCcccccccCCCcccc
Confidence 4556778999998876421 12 2478889999999843 2 35677899999876543
No 167
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=90.80 E-value=0.23 Score=40.26 Aligned_cols=52 Identities=12% Similarity=0.307 Sum_probs=40.0
Q ss_pred cccccccccccCC---CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEEcc
Q 028376 25 ETCPICQEKLGNQ---KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYAD 89 (210)
Q Consensus 25 ~~C~iC~~~~~~~---~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~~~ 89 (210)
+.|||-.-++... ..+.+|||+|-..-+.++ ....|++|...+...+++.+.
T Consensus 112 fiCPvtgleMng~~~F~~l~~CGcV~SerAlKei-------------kas~C~~C~a~y~~~dvIvlN 166 (293)
T KOG3113|consen 112 FICPVTGLEMNGKYRFCALRCCGCVFSERALKEI-------------KASVCHVCGAAYQEDDVIVLN 166 (293)
T ss_pred eecccccceecceEEEEEEeccceeccHHHHHHh-------------hhccccccCCcccccCeEeeC
Confidence 5699887666542 255799999999888876 245899999999999987544
No 168
>KOG0345 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=90.52 E-value=0.93 Score=40.30 Aligned_cols=66 Identities=11% Similarity=0.169 Sum_probs=48.9
Q ss_pred CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHH--hCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFI--ANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~--~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
.+--|+..|++.|.. ....|+|||=.--...+.....|. ..++..+.++|+|. ..+|+++++.|..
T Consensus 238 ~a~eK~~~lv~~L~~----~~~kK~iVFF~TCasVeYf~~~~~~~l~~~~i~~iHGK~~------q~~R~k~~~~F~~ 305 (567)
T KOG0345|consen 238 EADEKLSQLVHLLNN----NKDKKCIVFFPTCASVEYFGKLFSRLLKKREIFSIHGKMS------QKARAKVLEAFRK 305 (567)
T ss_pred cHHHHHHHHHHHHhc----cccccEEEEecCcchHHHHHHHHHHHhCCCcEEEecchhc------chhHHHHHHHHHh
Confidence 345678888877775 446899998554444444444444 46888999999976 9999999999997
No 169
>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=90.23 E-value=0.22 Score=30.21 Aligned_cols=48 Identities=19% Similarity=0.438 Sum_probs=23.7
Q ss_pred cccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccc
Q 028376 25 ETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQR 79 (210)
Q Consensus 25 ~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~ 79 (210)
..||+....+..+..-..|.|.-|-+ ++.+++.... ...-.||.|+++
T Consensus 3 L~CPls~~~i~~P~Rg~~C~H~~CFD-l~~fl~~~~~------~~~W~CPiC~~~ 50 (50)
T PF02891_consen 3 LRCPLSFQRIRIPVRGKNCKHLQCFD-LESFLESNQR------TPKWKCPICNKP 50 (50)
T ss_dssp SB-TTTSSB-SSEEEETT--SS--EE-HHHHHHHHHH------S---B-TTT---
T ss_pred eeCCCCCCEEEeCccCCcCcccceEC-HHHHHHHhhc------cCCeECcCCcCc
Confidence 46999988888876678999998754 3445544331 334689999864
No 170
>KOG0342 consensus ATP-dependent RNA helicase pitchoune [RNA processing and modification]
Probab=90.12 E-value=0.74 Score=41.02 Aligned_cols=65 Identities=12% Similarity=0.135 Sum_probs=56.5
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
..++..|...|++... .-|+|||-.--.+.+.+...|..-.++.+.+.|+++ ..+|..+..+|.+
T Consensus 314 ~~~f~ll~~~LKk~~~---~~KiiVF~sT~~~vk~~~~lL~~~dlpv~eiHgk~~------Q~kRT~~~~~F~k 378 (543)
T KOG0342|consen 314 DSRFSLLYTFLKKNIK---RYKIIVFFSTCMSVKFHAELLNYIDLPVLEIHGKQK------QNKRTSTFFEFCK 378 (543)
T ss_pred cchHHHHHHHHHHhcC---CceEEEEechhhHHHHHHHHHhhcCCchhhhhcCCc------ccccchHHHHHhh
Confidence 4556777777775443 389999999999999999999999999999999988 9999999999998
No 171
>PRK12906 secA preprotein translocase subunit SecA; Reviewed
Probab=89.85 E-value=1.3 Score=42.19 Aligned_cols=64 Identities=19% Similarity=0.127 Sum_probs=53.2
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
..|..+|++.+.... ..+..+|||.....-.+.+...|.++||++..+.|.+. +|++.+-.+..
T Consensus 423 ~~K~~al~~~i~~~~--~~g~pvLI~t~si~~se~ls~~L~~~gi~~~~Lna~~~--------~~Ea~ii~~ag 486 (796)
T PRK12906 423 DSKFNAVVKEIKERH--AKGQPVLVGTVAIESSERLSHLLDEAGIPHAVLNAKNH--------AKEAEIIMNAG 486 (796)
T ss_pred HHHHHHHHHHHHHHH--hCCCCEEEEeCcHHHHHHHHHHHHHCCCCeeEecCCcH--------HHHHHHHHhcC
Confidence 458889999998765 34789999999999999999999999999999999943 66666655554
No 172
>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type. subtype of CRISPR/Cas locus, found in several species of Cyanobacteria and several archaeal species. It contains helicase motifs and appears to represent the Cas3 protein of the Cyano subtype of CRISPR/Cas system.
Probab=89.67 E-value=1.7 Score=37.38 Aligned_cols=57 Identities=9% Similarity=0.024 Sum_probs=43.3
Q ss_pred HHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCC--ceEEEeeCCCCCCcchhhHhhhHHH
Q 028376 127 VTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANN--ITCIKMKGENHKLPSANLQHRNALQ 189 (210)
Q Consensus 127 l~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~g--i~~~~~~G~m~~~~~~~~~~R~~~l 189 (210)
+++.+.+..+..++.|+|||..-....+.+...|+.+| +.+..+.|.|+ ..+|.+++
T Consensus 259 l~~~i~~~~~~~~~~k~LIf~nt~~~~~~l~~~L~~~~~~~~~~~l~g~~~------~~~R~~~~ 317 (357)
T TIGR03158 259 LAEEVIERFRQLPGERGAIILDSLDEVNRLSDLLQQQGLGDDIGRITGFAP------KKDRERAM 317 (357)
T ss_pred HHHHHHHHHhccCCCeEEEEECCHHHHHHHHHHHhhhCCCceEEeeecCCC------HHHHHHhc
Confidence 34444433334567899999999999999999999875 57788999977 88887654
No 173
>TIGR01587 cas3_core CRISPR-associated helicase Cas3. This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.
Probab=89.39 E-value=2.1 Score=36.43 Aligned_cols=66 Identities=15% Similarity=0.191 Sum_probs=49.9
Q ss_pred chHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCc--eEEEeeCCCCCCcchhhHhhhH----HHHHHhhc
Q 028376 122 TKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNI--TCIKMKGENHKLPSANLQHRNA----LQKELTRH 195 (210)
Q Consensus 122 sKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi--~~~~~~G~m~~~~~~~~~~R~~----~l~~F~~~ 195 (210)
.|.+.+.+.+..+ ..+.|+|||..-....+.+...|.+++. ....+.|.|+ ..+|.+ +++.|.++
T Consensus 207 ~~~~~l~~l~~~~---~~~~~~lVf~~t~~~~~~~~~~L~~~~~~~~~~~~h~~~~------~~~r~~~~~~~~~~f~~~ 277 (358)
T TIGR01587 207 GEISSLERLLEFI---KKGGKIAIIVNTVDRAQEFYQQLKENAPEEEIMLLHSRFT------EKDRAKKEAELLEEMKKN 277 (358)
T ss_pred cCHHHHHHHHHHh---hCCCeEEEEECCHHHHHHHHHHHHhhcCCCeEEEEECCCC------HHHHHHHHHHHHHHhcCC
Confidence 4555555444332 2367999999999999999999998877 4888999976 888866 48889874
Q ss_pred C
Q 028376 196 M 196 (210)
Q Consensus 196 ~ 196 (210)
.
T Consensus 278 ~ 278 (358)
T TIGR01587 278 E 278 (358)
T ss_pred C
Confidence 4
No 174
>KOG3899 consensus Uncharacterized conserved protein [Function unknown]
Probab=89.12 E-value=0.17 Score=41.84 Aligned_cols=47 Identities=23% Similarity=0.448 Sum_probs=32.0
Q ss_pred CCCcchHhhHHHHHHHhhhccc--cCCCccccccCCcccccCCCeEEcc
Q 028376 43 CGHFTCCKCFFAMTEQRLIHDN--KVKNEWVMCPTCRQRTDIGNIAYAD 89 (210)
Q Consensus 43 CgH~fC~~C~~~~~~~~~~~~~--~~~~~~~~CP~Cr~~~~~~~l~~~~ 89 (210)
|...-|.+|+.+|+.....+-. ....+...||+||+.+...++.++.
T Consensus 325 crp~wc~~cla~~f~~rq~~v~r~~~~~~~~~cp~cr~~fci~dv~~v~ 373 (381)
T KOG3899|consen 325 CRPLWCRSCLAQIFIGRQDNVYRYEYHRGSAQCPTCRKNFCIRDVHCVD 373 (381)
T ss_pred cccHHHHHHHHHHHhhcccchhHHHHHhcCCCCcchhhceEEeeeeEEE
Confidence 3455678999999743211100 1246788999999999999887664
No 175
>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=88.89 E-value=0.22 Score=29.67 Aligned_cols=32 Identities=25% Similarity=0.699 Sum_probs=21.9
Q ss_pred eecCC-CCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376 39 MVFQC-GHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD 81 (210)
Q Consensus 39 ~~~~C-gH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~ 81 (210)
-+..| .|..|..|+..++ .....||+|..++.
T Consensus 14 ~Li~C~dHYLCl~CLt~ml-----------~~s~~C~iC~~~LP 46 (50)
T PF03854_consen 14 GLIKCSDHYLCLNCLTLML-----------SRSDRCPICGKPLP 46 (50)
T ss_dssp SEEE-SS-EEEHHHHHHT------------SSSSEETTTTEE--
T ss_pred CeeeecchhHHHHHHHHHh-----------ccccCCCcccCcCc
Confidence 34556 5999999999884 56678999998764
No 176
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=88.43 E-value=0.3 Score=39.47 Aligned_cols=33 Identities=6% Similarity=0.125 Sum_probs=28.7
Q ss_pred CccccccccccccCCCeecCCCCcchHhhHHHHH
Q 028376 23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMT 56 (210)
Q Consensus 23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~ 56 (210)
+..-|..|+.+..+ +++++=||+||.+||.+++
T Consensus 42 ~FdcCsLtLqPc~d-Pvit~~GylfdrEaILe~i 74 (303)
T KOG3039|consen 42 PFDCCSLTLQPCRD-PVITPDGYLFDREAILEYI 74 (303)
T ss_pred CcceeeeecccccC-CccCCCCeeeeHHHHHHHH
Confidence 34568999999988 5999999999999998875
No 177
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=88.12 E-value=0.63 Score=40.77 Aligned_cols=66 Identities=18% Similarity=0.282 Sum_probs=54.3
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRH 195 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~ 195 (210)
+.|.+.+-..+.. ..+++|+|||..-.-+.|.+..-|...||..-.+.|... ...|+.+|+.|+.+
T Consensus 449 ~~k~~~~~~f~~~---ms~ndKvIiFv~~K~~AD~LSSd~~l~gi~~q~lHG~r~------Q~DrE~al~~~ksG 514 (629)
T KOG0336|consen 449 SEKLEIVQFFVAN---MSSNDKVIIFVSRKVMADHLSSDFCLKGISSQSLHGNRE------QSDREMALEDFKSG 514 (629)
T ss_pred HHHHHHHHHHHHh---cCCCceEEEEEechhhhhhccchhhhcccchhhccCChh------hhhHHHHHHhhhcC
Confidence 4455433333333 356899999999999999999999999999999999976 88999999999973
No 178
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=88.11 E-value=0.12 Score=47.70 Aligned_cols=52 Identities=23% Similarity=0.514 Sum_probs=41.1
Q ss_pred ccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCC
Q 028376 24 EETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGN 84 (210)
Q Consensus 24 ~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~ 84 (210)
..+|+||......+ +.+.|.|.||..|+...+.. ......||+|+..+....
T Consensus 21 ~lEc~ic~~~~~~p-~~~kc~~~~l~~~~n~~f~~--------~~~~~~~~lc~~~~eK~s 72 (684)
T KOG4362|consen 21 ILECPICLEHVKEP-SLLKCDHIFLKFCLNKLFES--------KKGPKQCALCKSDIEKRS 72 (684)
T ss_pred hccCCceeEEeecc-chhhhhHHHHhhhhhceeec--------cCccccchhhhhhhhhhh
Confidence 46899999988774 89999999999999987654 234668999997665443
No 179
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=88.00 E-value=0.34 Score=40.10 Aligned_cols=45 Identities=38% Similarity=0.868 Sum_probs=34.8
Q ss_pred Ccccccccccccc---CCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcc
Q 028376 23 DEETCPICQEKLG---NQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQ 78 (210)
Q Consensus 23 ~~~~C~iC~~~~~---~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~ 78 (210)
....||+|.+.+. ..+..++|||.....|+..+. ..+ -+||.|.+
T Consensus 157 ~~~ncPic~e~l~~s~~~~~~~~CgH~~h~~cf~e~~----------~~~-y~CP~C~~ 204 (276)
T KOG1940|consen 157 SEFNCPICKEYLFLSFEDAGVLKCGHYMHSRCFEEMI----------CEG-YTCPICSK 204 (276)
T ss_pred ccCCCchhHHHhccccccCCccCcccchHHHHHHHHh----------ccC-CCCCcccc
Confidence 3456999977653 235778999999999999885 234 89999988
No 180
>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=87.58 E-value=0.39 Score=28.13 Aligned_cols=40 Identities=23% Similarity=0.504 Sum_probs=21.2
Q ss_pred cccccccccCCCee-c--CCCCcchHhhHHHHHHHhhhccccCCCccccccCC
Q 028376 27 CPICQEKLGNQKMV-F--QCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTC 76 (210)
Q Consensus 27 C~iC~~~~~~~~~~-~--~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~C 76 (210)
|.+|.+.+... +. . .|+=.++..|+..++.. .....||.|
T Consensus 1 C~~C~~iv~~G-~~C~~~~C~~r~H~~C~~~y~r~---------~~~~~CP~C 43 (43)
T PF08746_consen 1 CEACKEIVTQG-QRCSNRDCNVRLHDDCFKKYFRH---------RSNPKCPNC 43 (43)
T ss_dssp -TTT-SB-SSS-EE-SS--S--EE-HHHHHHHTTT----------SS-B-TTT
T ss_pred CcccchhHeee-ccCCCCccCchHHHHHHHHHHhc---------CCCCCCcCC
Confidence 67788777654 43 3 48888999999999643 223379987
No 181
>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]
Probab=87.50 E-value=2 Score=37.56 Aligned_cols=67 Identities=10% Similarity=0.212 Sum_probs=54.7
Q ss_pred chHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCCC
Q 028376 122 TKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPSS 199 (210)
Q Consensus 122 sKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~~ 199 (210)
+|+-.|++-|. .-.-+++||.-=..-.|-|...|-..|+.-+.+.|+.. ...|..+|+.|+.+.-|+
T Consensus 408 aKiVylLeCLQ-----KT~PpVLIFaEkK~DVD~IhEYLLlKGVEavaIHGGKD------QedR~~ai~afr~gkKDV 474 (610)
T KOG0341|consen 408 AKIVYLLECLQ-----KTSPPVLIFAEKKADVDDIHEYLLLKGVEAVAIHGGKD------QEDRHYAIEAFRAGKKDV 474 (610)
T ss_pred hhhhhHHHHhc-----cCCCceEEEeccccChHHHHHHHHHccceeEEeecCcc------hhHHHHHHHHHhcCCCce
Confidence 45555555544 23568999999888899999999999999999999977 999999999999865554
No 182
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=87.43 E-value=0.39 Score=40.25 Aligned_cols=50 Identities=20% Similarity=0.493 Sum_probs=35.6
Q ss_pred cccccccccc--cCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376 25 ETCPICQEKL--GNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI 82 (210)
Q Consensus 25 ~~C~iC~~~~--~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~ 82 (210)
+.||+=.+.- +++++.+.|||++-.+-+..+-++ +....+||.|-.....
T Consensus 337 FiCPVlKe~~t~ENpP~ml~CgHVIskeal~~LS~n--------G~~~FKCPYCP~~~~~ 388 (396)
T COG5109 337 FICPVLKELCTDENPPVMLECGHVISKEALSVLSQN--------GVLSFKCPYCPEMSKY 388 (396)
T ss_pred eeccccHhhhcccCCCeeeeccceeeHHHHHHHhhc--------CcEEeeCCCCCcchhh
Confidence 5688643322 456799999999999998887433 4668899999654333
No 183
>KOG1123 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 3'-5' helicase subunit SSL2 [Transcription; Replication, recombination and repair]
Probab=87.41 E-value=2.9 Score=37.81 Aligned_cols=62 Identities=21% Similarity=0.161 Sum_probs=42.5
Q ss_pred CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
..+|..+.-=+|+... ..++|+||||--.-.|. +.+++ .|=+| +.|..+ ..+|.++|+.|+.
T Consensus 525 NP~KFraCqfLI~~HE--~RgDKiIVFsDnvfALk--~YAik-l~Kpf--IYG~Ts------q~ERm~ILqnFq~ 586 (776)
T KOG1123|consen 525 NPNKFRACQFLIKFHE--RRGDKIIVFSDNVFALK--EYAIK-LGKPF--IYGPTS------QNERMKILQNFQT 586 (776)
T ss_pred CcchhHHHHHHHHHHH--hcCCeEEEEeccHHHHH--HHHHH-cCCce--EECCCc------hhHHHHHHHhccc
Confidence 3567776655555443 36999999998654433 33443 34454 568766 9999999999998
No 184
>PRK10689 transcription-repair coupling factor; Provisional
Probab=86.33 E-value=3.3 Score=41.26 Aligned_cols=54 Identities=2% Similarity=-0.029 Sum_probs=46.3
Q ss_pred CCcEEEEcchHHHHHHHHHHHHhC--CceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCCC
Q 028376 140 KAKILVFSSWNDVLDVLEHAFIAN--NITCIKMKGENHKLPSANLQHRNALQKELTRHMPSS 199 (210)
Q Consensus 140 ~~K~iVFSQf~~~L~li~~~L~~~--gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~~ 199 (210)
+.+++||..-...++.+...|.+. +++...++|.|+ ..+|.+++..|.++..++
T Consensus 809 ~gqv~vf~n~i~~ie~la~~L~~~~p~~~v~~lHG~m~------q~eRe~im~~Fr~Gk~~V 864 (1147)
T PRK10689 809 GGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMR------ERELERVMNDFHHQRFNV 864 (1147)
T ss_pred CCeEEEEECCHHHHHHHHHHHHHhCCCCcEEEEeCCCC------HHHHHHHHHHHHhcCCCE
Confidence 568999988888888888899886 888889999977 999999999999865443
No 185
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.28 E-value=0.23 Score=45.32 Aligned_cols=33 Identities=27% Similarity=0.602 Sum_probs=25.3
Q ss_pred ccccccccccccC---CCeecCCCCcchHhhHHHHH
Q 028376 24 EETCPICQEKLGN---QKMVFQCGHFTCCKCFFAMT 56 (210)
Q Consensus 24 ~~~C~iC~~~~~~---~~~~~~CgH~fC~~C~~~~~ 56 (210)
...|+||...+.. .++.+.|||..|..|+....
T Consensus 11 ~l~c~ic~n~f~~~~~~Pvsl~cghtic~~c~~~ly 46 (861)
T KOG3161|consen 11 LLLCDICLNLFVVQRLEPVSLQCGHTICGHCVQLLY 46 (861)
T ss_pred HhhchHHHHHHHHHhcCcccccccchHHHHHHHhHh
Confidence 3579999655432 24778999999999999874
No 186
>TIGR00580 mfd transcription-repair coupling factor (mfd). All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transacribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families.
Probab=85.82 E-value=4.1 Score=39.71 Aligned_cols=52 Identities=6% Similarity=0.024 Sum_probs=46.2
Q ss_pred CCcEEEEcchHHHHHHHHHHHHhC--CceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376 140 KAKILVFSSWNDVLDVLEHAFIAN--NITCIKMKGENHKLPSANLQHRNALQKELTRHMP 197 (210)
Q Consensus 140 ~~K~iVFSQf~~~L~li~~~L~~~--gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p 197 (210)
+.+++||..-....+.+...|+.. +++...++|.|+ ..+|.++++.|.++.-
T Consensus 660 g~qv~if~n~i~~~e~l~~~L~~~~p~~~v~~lHG~m~------~~eRe~im~~F~~Gk~ 713 (926)
T TIGR00580 660 GGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMT------ENELEEVMLEFYKGEF 713 (926)
T ss_pred CCeEEEEECCcHHHHHHHHHHHHhCCCCeEEEecCCCC------HHHHHHHHHHHHcCCC
Confidence 579999999999999999999884 899999999977 9999999999998543
No 187
>COG0514 RecQ Superfamily II DNA helicase [DNA replication, recombination, and repair]
Probab=85.03 E-value=4.8 Score=37.10 Aligned_cols=54 Identities=9% Similarity=0.082 Sum_probs=47.7
Q ss_pred cCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376 137 TDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM 196 (210)
Q Consensus 137 ~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~ 196 (210)
..++.-.|||..-...-+-+...|..+|+.-..|+|+|. ...|..+-++|.+++
T Consensus 227 ~~~~~~GIIYc~sRk~~E~ia~~L~~~g~~a~~YHaGl~------~~eR~~~q~~f~~~~ 280 (590)
T COG0514 227 PQLSKSGIIYCLTRKKVEELAEWLRKNGISAGAYHAGLS------NEERERVQQAFLNDE 280 (590)
T ss_pred cccCCCeEEEEeeHHhHHHHHHHHHHCCCceEEecCCCC------HHHHHHHHHHHhcCC
Confidence 344555799999999999999999999999999999976 999999999999844
No 188
>TIGR03817 DECH_helic helicase/secretion neighborhood putative DEAH-box helicase. A conserved gene neighborhood widely spread in the Actinobacteria contains this uncharacterized DEAH-box family helicase encoded convergently towards an operon of genes for protein homologous to type II secretion and pilus formation proteins. The context suggests that this helicase may play a role in conjugal transfer of DNA.
Probab=84.73 E-value=3.7 Score=39.03 Aligned_cols=52 Identities=12% Similarity=0.049 Sum_probs=43.7
Q ss_pred CCcEEEEcchHHHHHHHHHHHHhC--------CceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376 140 KAKILVFSSWNDVLDVLEHAFIAN--------NITCIKMKGENHKLPSANLQHRNALQKELTRHMP 197 (210)
Q Consensus 140 ~~K~iVFSQf~~~L~li~~~L~~~--------gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p 197 (210)
+.|+|||..-....+.+...|... +.+...|.|+|. ..+|.++++.|.++.-
T Consensus 271 ~~~~IVF~~sr~~ae~l~~~l~~~l~~~~~~l~~~v~~~hgg~~------~~eR~~ie~~f~~G~i 330 (742)
T TIGR03817 271 GARTLTFVRSRRGAELVAAIARRLLGEVDPDLAERVAAYRAGYL------PEDRRELERALRDGEL 330 (742)
T ss_pred CCCEEEEcCCHHHHHHHHHHHHHHHHhhccccccchhheecCCC------HHHHHHHHHHHHcCCc
Confidence 679999999999999998887653 566677899966 9999999999998543
No 189
>KOG0351 consensus ATP-dependent DNA helicase [Replication, recombination and repair]
Probab=84.10 E-value=1.9 Score=41.89 Aligned_cols=66 Identities=9% Similarity=0.043 Sum_probs=58.9
Q ss_pred HHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376 125 EAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM 196 (210)
Q Consensus 125 ~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~ 196 (210)
+++...+..+....++.-+|||.......+.|+..|...|+...-|..+|+ ..+|..+.+.|..+.
T Consensus 470 ~~~~~~~~~~~~~~~~~s~IIYC~sr~~ce~vs~~L~~~~~~a~~YHAGl~------~~~R~~Vq~~w~~~~ 535 (941)
T KOG0351|consen 470 DALLDILEESKLRHPDQSGIIYCLSRKECEQVSAVLRSLGKSAAFYHAGLP------PKERETVQKAWMSDK 535 (941)
T ss_pred cchHHHHHHhhhcCCCCCeEEEeCCcchHHHHHHHHHHhchhhHhhhcCCC------HHHHHHHHHHHhcCC
Confidence 556666777777788999999999999999999999999999999999977 999999999999844
No 190
>KOG0338 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=84.05 E-value=2.1 Score=38.59 Aligned_cols=51 Identities=10% Similarity=0.120 Sum_probs=47.3
Q ss_pred CCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376 140 KAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHM 196 (210)
Q Consensus 140 ~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~ 196 (210)
..++|||.+-......+...|...|+..-.+.|+ |+..||-.+|+.|.+..
T Consensus 426 ~~~~ivFv~tKk~AHRl~IllGLlgl~agElHGs------LtQ~QRlesL~kFk~~e 476 (691)
T KOG0338|consen 426 QDRTIVFVRTKKQAHRLRILLGLLGLKAGELHGS------LTQEQRLESLEKFKKEE 476 (691)
T ss_pred ccceEEEEehHHHHHHHHHHHHHhhchhhhhccc------ccHHHHHHHHHHHHhcc
Confidence 5799999999999999999999999999999999 56999999999999844
No 191
>KOG0343 consensus RNA Helicase [RNA processing and modification]
Probab=83.73 E-value=5.6 Score=36.38 Aligned_cols=65 Identities=25% Similarity=0.252 Sum_probs=53.0
Q ss_pred CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHh--CCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIA--NNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~--~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
..-||+.|-.-|.. .+..|+|||-+--.=...+-.+|.+ -||+..-+.|+|+ ..+|..+.+.|..
T Consensus 297 l~~Ki~~L~sFI~s----hlk~K~iVF~SscKqvkf~~e~F~rlrpg~~l~~L~G~~~------Q~~R~ev~~~F~~ 363 (758)
T KOG0343|consen 297 LEDKIDMLWSFIKS----HLKKKSIVFLSSCKQVKFLYEAFCRLRPGIPLLALHGTMS------QKKRIEVYKKFVR 363 (758)
T ss_pred hhhHHHHHHHHHHh----ccccceEEEEehhhHHHHHHHHHHhcCCCCceeeeccchh------HHHHHHHHHHHHH
Confidence 35788877777764 5678999987777766777777764 6999999999977 9999999999987
No 192
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=83.37 E-value=0.92 Score=27.62 Aligned_cols=40 Identities=23% Similarity=0.562 Sum_probs=22.4
Q ss_pred cccccccccCC---------CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCc
Q 028376 27 CPICQEKLGNQ---------KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCR 77 (210)
Q Consensus 27 C~iC~~~~~~~---------~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr 77 (210)
|..|..++... ..-..|++.||.+|=.=+ ...-..||.|.
T Consensus 2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fi-----------HE~LH~CPGC~ 50 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFI-----------HETLHNCPGCE 50 (51)
T ss_dssp ETTTTEE-TTS-------EEE--TTTT--B-HHHHHTT-----------TTTS-SSSTT-
T ss_pred CccCCCCCCCcccccccCCeEECCCCCCccccCcChhh-----------hccccCCcCCC
Confidence 66777776653 122589999999996533 35566899884
No 193
>KOG3268 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.35 E-value=1.2 Score=34.34 Aligned_cols=59 Identities=19% Similarity=0.304 Sum_probs=35.4
Q ss_pred CccccccccccccCC------CeecCCCCcchHhhHHHHHHHhhhccccC-CCccccccCCcccccC
Q 028376 23 DEETCPICQEKLGNQ------KMVFQCGHFTCCKCFFAMTEQRLIHDNKV-KNEWVMCPTCRQRTDI 82 (210)
Q Consensus 23 ~~~~C~iC~~~~~~~------~~~~~CgH~fC~~C~~~~~~~~~~~~~~~-~~~~~~CP~Cr~~~~~ 82 (210)
+...|.||...--+. .-..+||..|+.-|+..|++.-. +.... .---..||.|..++..
T Consensus 164 ~~~~cgicyayqldGTipDqtCdN~qCgkpFHqiCL~dWLRgil-TsRQSFdiiFGeCPYCS~Pial 229 (234)
T KOG3268|consen 164 ELGACGICYAYQLDGTIPDQTCDNIQCGKPFHQICLTDWLRGIL-TSRQSFDIIFGECPYCSDPIAL 229 (234)
T ss_pred hhhcccceeeeecCCccccccccccccCCcHHHHHHHHHHHHHh-hccceeeeeeccCCCCCCccee
Confidence 345677775432111 13469999999999999986422 21100 1112369999888754
No 194
>PRK13767 ATP-dependent helicase; Provisional
Probab=82.74 E-value=7.4 Score=37.75 Aligned_cols=64 Identities=11% Similarity=0.052 Sum_probs=49.1
Q ss_pred HHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHh------CCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376 125 EAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIA------NNITCIKMKGENHKLPSANLQHRNALQKELTRHM 196 (210)
Q Consensus 125 ~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~------~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~ 196 (210)
..+.+.|.++... ..++|||..-....+.+...|.. .+.....+.|+|+ ..+|..+++.|+++.
T Consensus 271 ~~l~~~L~~~i~~--~~~~LVF~nTr~~ae~la~~L~~~~~~~~~~~~i~~hHg~ls------~~~R~~ve~~fk~G~ 340 (876)
T PRK13767 271 EALYETLHELIKE--HRTTLIFTNTRSGAERVLYNLRKRFPEEYDEDNIGAHHSSLS------REVRLEVEEKLKRGE 340 (876)
T ss_pred HHHHHHHHHHHhc--CCCEEEEeCCHHHHHHHHHHHHHhchhhccccceeeeeCCCC------HHHHHHHHHHHHcCC
Confidence 4455555554432 56899999999888888888876 3466777899966 999999999999854
No 195
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=82.64 E-value=0.67 Score=24.03 Aligned_cols=22 Identities=27% Similarity=0.558 Sum_probs=10.5
Q ss_pred ccccccccccCCCee-cCCCCcc
Q 028376 26 TCPICQEKLGNQKMV-FQCGHFT 47 (210)
Q Consensus 26 ~C~iC~~~~~~~~~~-~~CgH~f 47 (210)
.||.|...+...... ..|||.|
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCCC
Confidence 466666554432222 2366654
No 196
>KOG0347 consensus RNA helicase [RNA processing and modification]
Probab=82.57 E-value=1.8 Score=39.36 Aligned_cols=49 Identities=14% Similarity=0.150 Sum_probs=46.1
Q ss_pred CCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 140 KAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 140 ~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
+.+.|||..-.+....|...|..-+|+-+-+...|. .++|.+.|++|..
T Consensus 463 PGrTlVF~NsId~vKRLt~~L~~L~i~p~~LHA~M~------QKqRLknLEkF~~ 511 (731)
T KOG0347|consen 463 PGRTLVFCNSIDCVKRLTVLLNNLDIPPLPLHASMI------QKQRLKNLEKFKQ 511 (731)
T ss_pred CCceEEEechHHHHHHHHHHHhhcCCCCchhhHHHH------HHHHHHhHHHHhc
Confidence 358999999999999999999999999999999965 9999999999998
No 197
>COG5183 SSM4 Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=82.20 E-value=0.92 Score=42.72 Aligned_cols=57 Identities=18% Similarity=0.511 Sum_probs=42.0
Q ss_pred CCCcccccccccc-ccCCCeecCCCC-----cchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376 21 KADEETCPICQEK-LGNQKMVFQCGH-----FTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA 86 (210)
Q Consensus 21 ~~~~~~C~iC~~~-~~~~~~~~~CgH-----~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~ 86 (210)
..++..|.||... ..+.+..-||.. ..+.+|+.+|++. ++..+|-.|..++...++.
T Consensus 9 N~d~~~CRICr~e~~~d~pLfhPCKC~GSIkYiH~eCL~eW~~~---------s~~~kCdiChy~~~Fk~IY 71 (1175)
T COG5183 9 NEDKRSCRICRTEDIRDDPLFHPCKCSGSIKYIHRECLMEWMEC---------SGTKKCDICHYEYKFKDIY 71 (1175)
T ss_pred CccchhceeecCCCCCCCcCcccccccchhHHHHHHHHHHHHhc---------CCCcceeeecceeeeeeec
Confidence 3466899999654 334345567753 4688999999863 6678999999999888774
No 198
>cd03028 GRX_PICOT_like Glutaredoxin (GRX) family, PKC-interacting cousin of TRX (PICOT)-like subfamily; composed of PICOT and GRX-PICOT-like proteins. The non-PICOT members of this family contain only the GRX-like domain, whereas PICOT contains an N-terminal TRX-like domain followed by one to three GRX-like domains. It is interesting to note that PICOT from plants contain three repeats of the GRX-like domain, metazoan proteins (except for insect) have two repeats, while fungal sequences contain only one copy of the domain. PICOT is a protein that interacts with protein kinase C (PKC) theta, a calcium independent PKC isoform selectively expressed in skeletal muscle and T lymphocytes. PICOT inhibits the activation of c-Jun N-terminal kinase and the transcription factors, AP-1 and NF-kB, induced by PKC theta or T-cell activating stimuli. Both GRX and TRX domains of PICOT are required for its activity. Characterized non-PICOT members of this family include CXIP1, a CAX-interacting protein
Probab=81.98 E-value=5.7 Score=26.80 Aligned_cols=34 Identities=3% Similarity=-0.048 Sum_probs=30.1
Q ss_pred CCcEEEEcc------hHHHHHHHHHHHHhCCceEEEeeCC
Q 028376 140 KAKILVFSS------WNDVLDVLEHAFIANNITCIKMKGE 173 (210)
Q Consensus 140 ~~K~iVFSQ------f~~~L~li~~~L~~~gi~~~~~~G~ 173 (210)
..+++|||. |-.+-..+...|+..||.|..++=.
T Consensus 7 ~~~vvvf~k~~~~~~~Cp~C~~ak~~L~~~~i~y~~idv~ 46 (90)
T cd03028 7 ENPVVLFMKGTPEEPRCGFSRKVVQILNQLGVDFGTFDIL 46 (90)
T ss_pred cCCEEEEEcCCCCCCCCcHHHHHHHHHHHcCCCeEEEEcC
Confidence 569999987 8888899999999999999998754
No 199
>KOG4284 consensus DEAD box protein [Transcription]
Probab=81.91 E-value=2.2 Score=39.63 Aligned_cols=62 Identities=11% Similarity=0.146 Sum_probs=52.8
Q ss_pred HHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 127 VTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 127 l~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
-++.|..+...-|-..+|||+.-.+=.+-+...|...||...-+.|.|+ ..+|..+++..+.
T Consensus 259 klq~L~~vf~~ipy~QAlVF~~~~sra~~~a~~L~ssG~d~~~ISgaM~------Q~~Rl~a~~~lr~ 320 (980)
T KOG4284|consen 259 KLQKLTHVFKSIPYVQALVFCDQISRAEPIATHLKSSGLDVTFISGAMS------QKDRLLAVDQLRA 320 (980)
T ss_pred HHHHHHHHHhhCchHHHHhhhhhhhhhhHHHHHhhccCCCeEEeccccc------hhHHHHHHHHhhh
Confidence 3445555555667889999999999999999999999999999999977 9999999888765
No 200
>KOG0326 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=81.90 E-value=1.5 Score=37.23 Aligned_cols=66 Identities=11% Similarity=0.247 Sum_probs=57.5
Q ss_pred CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376 120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRH 195 (210)
Q Consensus 120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~ 195 (210)
.+-|+..|--.+.+++ -..+|||...+.-.+++..-..+.|..+..+..+|- ...|+++...|.++
T Consensus 306 e~qKvhCLntLfskLq----INQsIIFCNS~~rVELLAkKITelGyscyyiHakM~------Q~hRNrVFHdFr~G 371 (459)
T KOG0326|consen 306 ERQKVHCLNTLFSKLQ----INQSIIFCNSTNRVELLAKKITELGYSCYYIHAKMA------QEHRNRVFHDFRNG 371 (459)
T ss_pred hhhhhhhHHHHHHHhc----ccceEEEeccchHhHHHHHHHHhccchhhHHHHHHH------Hhhhhhhhhhhhcc
Confidence 4678877777777666 458999999999999999999999999999999966 99999999999873
No 201
>PLN02189 cellulose synthase
Probab=80.98 E-value=1.5 Score=42.59 Aligned_cols=54 Identities=26% Similarity=0.633 Sum_probs=37.7
Q ss_pred CCCCccccccccccccCC----C--eecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376 20 SKADEETCPICQEKLGNQ----K--MVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG 83 (210)
Q Consensus 20 ~~~~~~~C~iC~~~~~~~----~--~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~ 83 (210)
+......|.||.+.+... + ..-.|+--.|..|.+ + ++ .++...||.|+.++...
T Consensus 30 ~~~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cye-y-er--------~eg~q~CpqCkt~Y~r~ 89 (1040)
T PLN02189 30 RNLDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYE-Y-ER--------REGTQNCPQCKTRYKRL 89 (1040)
T ss_pred ccccCccccccccccCcCCCCCEEEeeccCCCccccchhh-h-hh--------hcCCccCcccCCchhhc
Confidence 344556899999886521 1 223578889999995 3 22 46778999999988743
No 202
>PLN02436 cellulose synthase A
Probab=79.70 E-value=1.7 Score=42.34 Aligned_cols=55 Identities=22% Similarity=0.564 Sum_probs=37.8
Q ss_pred cCCCCccccccccccccCC----C--eecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376 19 LSKADEETCPICQEKLGNQ----K--MVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG 83 (210)
Q Consensus 19 l~~~~~~~C~iC~~~~~~~----~--~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~ 83 (210)
++......|.||.+.+... + ..--|+--.|..|.+ + ++ ..+...||.|+.++...
T Consensus 31 ~~~~~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cye-y-er--------~eg~~~Cpqckt~Y~r~ 91 (1094)
T PLN02436 31 VQELSGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYE-Y-ER--------REGNQACPQCKTRYKRI 91 (1094)
T ss_pred ccccCCccccccccccCcCCCCCEEEeeccCCCccccchhh-h-hh--------hcCCccCcccCCchhhc
Confidence 3444556899999886421 1 223577779999995 3 22 36778999999988743
No 203
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=79.26 E-value=1.7 Score=42.34 Aligned_cols=54 Identities=22% Similarity=0.623 Sum_probs=38.3
Q ss_pred cCCCCccccccccccccCC----C--eecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376 19 LSKADEETCPICQEKLGNQ----K--MVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI 82 (210)
Q Consensus 19 l~~~~~~~C~iC~~~~~~~----~--~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~ 82 (210)
++..+...|.||.+.+... + ..--||--.|+.|.+ + |+ .++...||.|+.++..
T Consensus 12 ~~~~~~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYE-Y-Er--------~eG~q~CPqCktrYkr 71 (1079)
T PLN02638 12 MKHGGGQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYE-Y-ER--------KDGNQSCPQCKTKYKR 71 (1079)
T ss_pred ccccCCceeeecccccCcCCCCCEEEEeccCCCccccchhh-h-hh--------hcCCccCCccCCchhh
Confidence 4455667999999876431 1 224677779999995 4 33 4677899999998763
No 204
>PLN02400 cellulose synthase
Probab=79.08 E-value=1.4 Score=43.06 Aligned_cols=55 Identities=25% Similarity=0.623 Sum_probs=38.4
Q ss_pred cCCCCccccccccccccCC----C--eecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376 19 LSKADEETCPICQEKLGNQ----K--MVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG 83 (210)
Q Consensus 19 l~~~~~~~C~iC~~~~~~~----~--~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~ 83 (210)
++......|.||.+.+... + ..-.|+--.|+.|.+ + |+ +.+...||.|+.++...
T Consensus 31 ~~~~~gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYE-Y-ER--------keGnq~CPQCkTrYkR~ 91 (1085)
T PLN02400 31 LKNLNGQICQICGDDVGVTETGDVFVACNECAFPVCRPCYE-Y-ER--------KDGTQCCPQCKTRYRRH 91 (1085)
T ss_pred ccccCCceeeecccccCcCCCCCEEEEEccCCCccccchhh-e-ec--------ccCCccCcccCCccccc
Confidence 3444556899999886432 1 234677779999995 3 22 46778999999988643
No 205
>TIGR01054 rgy reverse gyrase. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.
Probab=78.58 E-value=9.6 Score=38.22 Aligned_cols=62 Identities=5% Similarity=0.049 Sum_probs=48.1
Q ss_pred hHHHHHHHHHHHHhcCCCCcEEEEcchH---HHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCCC
Q 028376 123 KIEAVTRRILWIKSTDPKAKILVFSSWN---DVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPSS 199 (210)
Q Consensus 123 Ki~al~~~L~~~~~~~~~~K~iVFSQf~---~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~~ 199 (210)
+.+.|++.|..+ +.++|||.+-. ...+.+...|..+|++...+.|.|+ .++++.|.++.-++
T Consensus 314 ~~~~L~~ll~~l-----~~~~IVFv~t~~~~~~a~~l~~~L~~~g~~a~~lhg~~~----------~~~l~~Fr~G~~~v 378 (1171)
T TIGR01054 314 LKETLLEIVKKL-----GTGGIVYVSIDYGKEKAEEIAEFLENHGVKAVAYHATKP----------KEDYEKFAEGEIDV 378 (1171)
T ss_pred HHHHHHHHHHHc-----CCCEEEEEeccccHHHHHHHHHHHHhCCceEEEEeCCCC----------HHHHHHHHcCCCCE
Confidence 355666555432 35899999887 8899999999999999999999954 27999999855443
No 206
>KOG3579 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=78.26 E-value=1.4 Score=36.52 Aligned_cols=48 Identities=27% Similarity=0.577 Sum_probs=35.9
Q ss_pred CCCccccccccccccCCCeecCC----CCcchHhhHHHHHHHhhhccccCCCccccccC
Q 028376 21 KADEETCPICQEKLGNQKMVFQC----GHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPT 75 (210)
Q Consensus 21 ~~~~~~C~iC~~~~~~~~~~~~C----gH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~ 75 (210)
......|.+|.+.+++. ...+| .|-||..|-.+.+.++- ..+..-||.
T Consensus 265 ~~apLcCTLC~ERLEDT-HFVQCPSVp~HKFCFPCSResIK~Qg------~sgevYCPS 316 (352)
T KOG3579|consen 265 PSAPLCCTLCHERLEDT-HFVQCPSVPSHKFCFPCSRESIKQQG------ASGEVYCPS 316 (352)
T ss_pred CCCceeehhhhhhhccC-ceeecCCCcccceecccCHHHHHhhc------CCCceeCCC
Confidence 34456799999999874 66677 69999999999987643 344566764
No 207
>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB. This model represents HrpB, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria, but also in a few species of other lineages. The member from Rhizobium meliloti has been designated HelO. HrpB is typically about 800 residues in length, while its paralog HrpA (TIGR01967), also uncharacterized, is about 1300 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.
Probab=78.24 E-value=12 Score=36.16 Aligned_cols=50 Identities=16% Similarity=0.195 Sum_probs=43.8
Q ss_pred CCcEEEEcchHHHHHHHHHHHHh---CCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376 140 KAKILVFSSWNDVLDVLEHAFIA---NNITCIKMKGENHKLPSANLQHRNALQKELTRH 195 (210)
Q Consensus 140 ~~K~iVFSQf~~~L~li~~~L~~---~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~ 195 (210)
..++|||-.-..-++.+...|.. .++..+-+.|.|+ ..+|.++++.|..+
T Consensus 209 ~g~iLVFlpg~~eI~~l~~~L~~~~~~~~~v~pLHg~L~------~~eq~~~~~~~~~G 261 (819)
T TIGR01970 209 TGSILVFLPGQAEIRRVQEQLAERLDSDVLICPLYGELS------LAAQDRAIKPDPQG 261 (819)
T ss_pred CCcEEEEECCHHHHHHHHHHHHhhcCCCcEEEEecCCCC------HHHHHHHHhhcccC
Confidence 56899999988888888888887 5899999999977 99999999999864
No 208
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=77.28 E-value=17 Score=34.18 Aligned_cols=67 Identities=9% Similarity=0.067 Sum_probs=45.5
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcch---------HHHHHHHHHHHHhC--CceEEEeeCCCCCCcchhhHhhhHHH
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSW---------NDVLDVLEHAFIAN--NITCIKMKGENHKLPSANLQHRNALQ 189 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf---------~~~L~li~~~L~~~--gi~~~~~~G~m~~~~~~~~~~R~~~l 189 (210)
..+.+.+++.+.+.. ..+.+++||..- ... .-+...|... +++...++|+|+ ..+|.+++
T Consensus 454 ~~~~~~~~~~i~~~~--~~g~q~~v~~~~ie~s~~l~~~~~-~~~~~~L~~~~~~~~v~~lHG~m~------~~eR~~i~ 524 (681)
T PRK10917 454 DSRRDEVYERIREEI--AKGRQAYVVCPLIEESEKLDLQSA-EETYEELQEAFPELRVGLLHGRMK------PAEKDAVM 524 (681)
T ss_pred cccHHHHHHHHHHHH--HcCCcEEEEEcccccccchhHHHH-HHHHHHHHHHCCCCcEEEEeCCCC------HHHHHHHH
Confidence 445556666665544 346799998642 222 2334445443 578889999977 99999999
Q ss_pred HHHhhcC
Q 028376 190 KELTRHM 196 (210)
Q Consensus 190 ~~F~~~~ 196 (210)
+.|.++.
T Consensus 525 ~~F~~g~ 531 (681)
T PRK10917 525 AAFKAGE 531 (681)
T ss_pred HHHHcCC
Confidence 9999854
No 209
>cd03418 GRX_GRXb_1_3_like Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH - GSH reductase - GSH - GRX - protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes are known i
Probab=77.11 E-value=12 Score=23.70 Aligned_cols=45 Identities=4% Similarity=0.021 Sum_probs=32.5
Q ss_pred cEEEEc-chHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHH
Q 028376 142 KILVFS-SWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKEL 192 (210)
Q Consensus 142 K~iVFS-Qf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F 192 (210)
|++||+ .|-..-..+...|++.||.|..++-... ...+...++..
T Consensus 1 ~i~ly~~~~Cp~C~~ak~~L~~~~i~~~~i~i~~~------~~~~~~~~~~~ 46 (75)
T cd03418 1 KVEIYTKPNCPYCVRAKALLDKKGVDYEEIDVDGD------PALREEMINRS 46 (75)
T ss_pred CEEEEeCCCChHHHHHHHHHHHCCCcEEEEECCCC------HHHHHHHHHHh
Confidence 566777 5777788889999999999998888743 45555444443
No 210
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=76.80 E-value=1.8 Score=26.78 Aligned_cols=44 Identities=23% Similarity=0.606 Sum_probs=28.6
Q ss_pred cccccccccccCCC-eecCCC--CcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376 25 ETCPICQEKLGNQK-MVFQCG--HFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD 81 (210)
Q Consensus 25 ~~C~iC~~~~~~~~-~~~~Cg--H~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~ 81 (210)
..|-.|...+.... -..-|. ..||.+|.+..+. ..||.|+..+.
T Consensus 6 pnCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~-------------~~CPNCgGelv 52 (57)
T PF06906_consen 6 PNCECCDKDLPPDSPEAYICSFECTFCADCAETMLN-------------GVCPNCGGELV 52 (57)
T ss_pred CCccccCCCCCCCCCcceEEeEeCcccHHHHHHHhc-------------CcCcCCCCccc
Confidence 46777866654321 122343 4899999998752 37999987654
No 211
>PLN02195 cellulose synthase A
Probab=76.62 E-value=2.7 Score=40.71 Aligned_cols=52 Identities=23% Similarity=0.517 Sum_probs=37.9
Q ss_pred CCCccccccccccccCC----C--eecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376 21 KADEETCPICQEKLGNQ----K--MVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI 82 (210)
Q Consensus 21 ~~~~~~C~iC~~~~~~~----~--~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~ 82 (210)
+.....|.||.+.+... + ..-.|+--.|+.|.+ + ++ ..+...||.|+.+...
T Consensus 3 ~~~~~~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCye-y-er--------~eg~q~CpqCkt~Yk~ 60 (977)
T PLN02195 3 ESGAPICATCGEEVGVDSNGEAFVACHECSYPLCKACLE-Y-EI--------KEGRKVCLRCGGPYDA 60 (977)
T ss_pred cCCCccceecccccCcCCCCCeEEEeccCCCccccchhh-h-hh--------hcCCccCCccCCcccc
Confidence 45567899998866421 1 334788889999995 4 33 4677899999999883
No 212
>TIGR00365 monothiol glutaredoxin, Grx4 family. The gene for the member of this glutaredoxin family in E. coli, originally designated ydhD, is now designated grxD. Its protein, Grx4, is a monothiol glutaredoxin similar to Grx5 of yeast, which is involved in iron-sulfur cluster formation.
Probab=76.24 E-value=14 Score=25.37 Aligned_cols=34 Identities=3% Similarity=-0.036 Sum_probs=29.7
Q ss_pred CCcEEEEcc------hHHHHHHHHHHHHhCCceEEEeeCC
Q 028376 140 KAKILVFSS------WNDVLDVLEHAFIANNITCIKMKGE 173 (210)
Q Consensus 140 ~~K~iVFSQ------f~~~L~li~~~L~~~gi~~~~~~G~ 173 (210)
..|++||+. |-.+-..+...|+..||.|..++=.
T Consensus 11 ~~~Vvvf~kg~~~~~~Cp~C~~ak~lL~~~~i~~~~~di~ 50 (97)
T TIGR00365 11 ENPVVLYMKGTPQFPQCGFSARAVQILKACGVPFAYVNVL 50 (97)
T ss_pred cCCEEEEEccCCCCCCCchHHHHHHHHHHcCCCEEEEECC
Confidence 579999984 7788889999999999999988765
No 213
>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=76.09 E-value=0.46 Score=39.70 Aligned_cols=44 Identities=18% Similarity=0.418 Sum_probs=22.2
Q ss_pred ccccccccccccCCCeecC-----CCCcchHhhHHHHHHHhhhccccCCCccccccCCccc
Q 028376 24 EETCPICQEKLGNQKMVFQ-----CGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQR 79 (210)
Q Consensus 24 ~~~C~iC~~~~~~~~~~~~-----CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~ 79 (210)
...||+|...+.-. .+.. =.|.+|.-|-..| ...+..||.|...
T Consensus 172 ~g~CPvCGs~P~~s-~l~~~~~~G~R~L~Cs~C~t~W-----------~~~R~~Cp~Cg~~ 220 (290)
T PF04216_consen 172 RGYCPVCGSPPVLS-VLRGGEREGKRYLHCSLCGTEW-----------RFVRIKCPYCGNT 220 (290)
T ss_dssp -SS-TTT---EEEE-EEE------EEEEEETTT--EE-----------E--TTS-TTT---
T ss_pred CCcCCCCCCcCceE-EEecCCCCccEEEEcCCCCCee-----------eecCCCCcCCCCC
Confidence 46899998876543 3322 2578999999999 4567799999874
No 214
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=74.47 E-value=17 Score=33.80 Aligned_cols=68 Identities=10% Similarity=0.016 Sum_probs=44.6
Q ss_pred hHHHHHHHHHHHHhcCCCCcEEEEcchH--------HHHHHHHHHHHh--CCceEEEeeCCCCCCcchhhHhhhHHHHHH
Q 028376 123 KIEAVTRRILWIKSTDPKAKILVFSSWN--------DVLDVLEHAFIA--NNITCIKMKGENHKLPSANLQHRNALQKEL 192 (210)
Q Consensus 123 Ki~al~~~L~~~~~~~~~~K~iVFSQf~--------~~L~li~~~L~~--~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F 192 (210)
+.+.+++.+.+... .+.+++||.... .....+...|.. .+++...++|.|+ ..+|.++++.|
T Consensus 433 ~~~~~~~~i~~~l~--~g~q~~v~~~~i~~s~~~~~~~a~~~~~~L~~~~~~~~v~~lHG~m~------~~eR~~i~~~F 504 (630)
T TIGR00643 433 EKDIVYEFIEEEIA--KGRQAYVVYPLIEESEKLDLKAAEALYERLKKAFPKYNVGLLHGRMK------SDEKEAVMEEF 504 (630)
T ss_pred hHHHHHHHHHHHHH--hCCcEEEEEccccccccchHHHHHHHHHHHHhhCCCCcEEEEeCCCC------HHHHHHHHHHH
Confidence 33556666654332 367888886532 122233344443 4788889999977 99999999999
Q ss_pred hhcCCC
Q 028376 193 TRHMPS 198 (210)
Q Consensus 193 ~~~~p~ 198 (210)
.++..+
T Consensus 505 ~~g~~~ 510 (630)
T TIGR00643 505 REGEVD 510 (630)
T ss_pred HcCCCC
Confidence 985443
No 215
>PRK11664 ATP-dependent RNA helicase HrpB; Provisional
Probab=74.18 E-value=15 Score=35.47 Aligned_cols=50 Identities=8% Similarity=0.123 Sum_probs=44.0
Q ss_pred CCCcEEEEcchHHHHHHHHHHHHh---CCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 139 PKAKILVFSSWNDVLDVLEHAFIA---NNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 139 ~~~K~iVFSQf~~~L~li~~~L~~---~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
...++|||-.-..-++.+...|.. .++....+.|.|+ ..+|.++++.|.+
T Consensus 211 ~~g~iLVFlpg~~ei~~l~~~L~~~~~~~~~v~~Lhg~l~------~~eq~~~~~~~~~ 263 (812)
T PRK11664 211 ESGSLLLFLPGVGEIQRVQEQLASRVASDVLLCPLYGALS------LAEQQKAILPAPA 263 (812)
T ss_pred CCCCEEEEcCCHHHHHHHHHHHHHhccCCceEEEeeCCCC------HHHHHHHhccccC
Confidence 357899999999999999999987 7899999999977 9999999998875
No 216
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=73.66 E-value=2.7 Score=29.96 Aligned_cols=43 Identities=21% Similarity=0.503 Sum_probs=30.2
Q ss_pred ccccccccccccCCC-------------eecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCc
Q 028376 24 EETCPICQEKLGNQK-------------MVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCR 77 (210)
Q Consensus 24 ~~~C~iC~~~~~~~~-------------~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr 77 (210)
...|..|...+...+ .-..|.+.||.+|=.-+- +.-..||.|.
T Consensus 55 ~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fiH-----------e~Lh~CPGC~ 110 (112)
T TIGR00622 55 SRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFVH-----------ESLHCCPGCI 110 (112)
T ss_pred CCcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhhh-----------hhccCCcCCC
Confidence 356999988775421 246899999999966542 3445799985
No 217
>KOG0346 consensus RNA helicase [RNA processing and modification]
Probab=73.43 E-value=6.5 Score=34.96 Aligned_cols=50 Identities=16% Similarity=0.133 Sum_probs=46.5
Q ss_pred CCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376 140 KAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRH 195 (210)
Q Consensus 140 ~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~ 195 (210)
..|+|||..-.+.--.+.-.|+.-||+-+.+.|-++ ..-|-.+|+.|+.+
T Consensus 268 ~gKsliFVNtIdr~YrLkLfLeqFGiksciLNseLP------~NSR~Hii~QFNkG 317 (569)
T KOG0346|consen 268 RGKSLIFVNTIDRCYRLKLFLEQFGIKSCILNSELP------ANSRCHIIEQFNKG 317 (569)
T ss_pred cCceEEEEechhhhHHHHHHHHHhCcHhhhhccccc------ccchhhHHHHhhCc
Confidence 469999999999988999999999999999999988 99999999999974
No 218
>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=73.20 E-value=0.99 Score=38.07 Aligned_cols=51 Identities=22% Similarity=0.501 Sum_probs=34.8
Q ss_pred ccccccccccccCCCeec---CCC--CcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEEc
Q 028376 24 EETCPICQEKLGNQKMVF---QCG--HFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYA 88 (210)
Q Consensus 24 ~~~C~iC~~~~~~~~~~~---~Cg--H~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~~ 88 (210)
...||+|...+....+.. .=| |..|.-|-.+| ...+..||.|... .++.|.
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW-----------~~~R~~C~~Cg~~---~~l~y~ 239 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEW-----------HYVRVKCSHCEES---KHLAYL 239 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcc-----------cccCccCCCCCCC---CceeeE
Confidence 348999988764321211 233 67899999999 4678899999874 445444
No 219
>PRK11448 hsdR type I restriction enzyme EcoKI subunit R; Provisional
Probab=72.70 E-value=17 Score=36.34 Aligned_cols=62 Identities=15% Similarity=0.259 Sum_probs=43.0
Q ss_pred HHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhC------Cc---eEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 125 EAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIAN------NI---TCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 125 ~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~------gi---~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
+.+++.|.+......+.|+|||..-..+.+.+...|.+. ++ ....++|++ .+|.++|++|.+
T Consensus 683 ~~i~~~l~~~l~~~~~~KtiIF~~s~~HA~~i~~~L~~~f~~~~~~~~~~~v~~itg~~--------~~~~~li~~Fk~ 753 (1123)
T PRK11448 683 RVVCEELAKYLDPTGEGKTLIFAATDAHADMVVRLLKEAFKKKYGQVEDDAVIKITGSI--------DKPDQLIRRFKN 753 (1123)
T ss_pred HHHHHHHHHHHhccCCCcEEEEEcCHHHHHHHHHHHHHHHHhhcCCcCccceEEEeCCc--------cchHHHHHHHhC
Confidence 344555544433333579999999999988777776642 23 345689984 478899999987
No 220
>PRK10824 glutaredoxin-4; Provisional
Probab=71.27 E-value=9.3 Score=27.41 Aligned_cols=33 Identities=12% Similarity=-0.020 Sum_probs=28.3
Q ss_pred CCcEEEEcc------hHHHHHHHHHHHHhCCceEEEeeC
Q 028376 140 KAKILVFSS------WNDVLDVLEHAFIANNITCIKMKG 172 (210)
Q Consensus 140 ~~K~iVFSQ------f~~~L~li~~~L~~~gi~~~~~~G 172 (210)
..+++||+. |-.+-..+...|...|+.|..++=
T Consensus 14 ~~~Vvvf~Kg~~~~p~Cpyc~~ak~lL~~~~i~~~~idi 52 (115)
T PRK10824 14 ENPILLYMKGSPKLPSCGFSAQAVQALSACGERFAYVDI 52 (115)
T ss_pred cCCEEEEECCCCCCCCCchHHHHHHHHHHcCCCceEEEe
Confidence 579999998 777888899999999999877754
No 221
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=70.97 E-value=2.3 Score=27.70 Aligned_cols=46 Identities=17% Similarity=0.410 Sum_probs=28.8
Q ss_pred cccccccccccCC---CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376 25 ETCPICQEKLGNQ---KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG 83 (210)
Q Consensus 25 ~~C~iC~~~~~~~---~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~ 83 (210)
..|--|...+... ..+-.=-|.||.+|.+..++ ..||.|...+...
T Consensus 6 PnCECCDrDLpp~s~dA~ICtfEcTFCadCae~~l~-------------g~CPnCGGelv~R 54 (84)
T COG3813 6 PNCECCDRDLPPDSTDARICTFECTFCADCAENRLH-------------GLCPNCGGELVAR 54 (84)
T ss_pred CCCcccCCCCCCCCCceeEEEEeeehhHhHHHHhhc-------------CcCCCCCchhhcC
Confidence 3566675544321 23333358999999997642 3799998865443
No 222
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=68.95 E-value=3.2 Score=28.38 Aligned_cols=35 Identities=26% Similarity=0.732 Sum_probs=25.8
Q ss_pred cccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccc
Q 028376 25 ETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRT 80 (210)
Q Consensus 25 ~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~ 80 (210)
..|-+|...+... ||.||..|.-. ...|.+|.+.+
T Consensus 45 ~~C~~CK~~v~q~------g~~YCq~CAYk---------------kGiCamCGKki 79 (90)
T PF10235_consen 45 SKCKICKTKVHQP------GAKYCQTCAYK---------------KGICAMCGKKI 79 (90)
T ss_pred ccccccccccccC------CCccChhhhcc---------------cCcccccCCee
Confidence 4688887655442 78899999542 34899999976
No 223
>PRK09401 reverse gyrase; Reviewed
Probab=68.83 E-value=15 Score=36.87 Aligned_cols=62 Identities=8% Similarity=-0.004 Sum_probs=47.1
Q ss_pred chHHHHHHHHHHHHhcCCCCcEEEEcchHHH---HHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCC
Q 028376 122 TKIEAVTRRILWIKSTDPKAKILVFSSWNDV---LDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPS 198 (210)
Q Consensus 122 sKi~al~~~L~~~~~~~~~~K~iVFSQf~~~---L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~ 198 (210)
.|.+.|.+.+..+ +.++|||.+-..- .+.+...|..+||+...+.|. | .+.++.|.++.-+
T Consensus 315 ~k~~~L~~ll~~l-----~~~~LIFv~t~~~~~~ae~l~~~L~~~gi~v~~~hg~------l-----~~~l~~F~~G~~~ 378 (1176)
T PRK09401 315 DSVEKLVELVKRL-----GDGGLIFVPSDKGKEYAEELAEYLEDLGINAELAISG------F-----ERKFEKFEEGEVD 378 (1176)
T ss_pred cHHHHHHHHHHhc-----CCCEEEEEecccChHHHHHHHHHHHHCCCcEEEEeCc------H-----HHHHHHHHCCCCC
Confidence 5777777666533 3489999886544 999999999999999999999 2 3356999986544
Q ss_pred C
Q 028376 199 S 199 (210)
Q Consensus 199 ~ 199 (210)
+
T Consensus 379 V 379 (1176)
T PRK09401 379 V 379 (1176)
T ss_pred E
Confidence 3
No 224
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=68.25 E-value=2.1 Score=36.20 Aligned_cols=52 Identities=21% Similarity=0.452 Sum_probs=35.3
Q ss_pred CccccccccccccCCCeec--CC--CCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeEEc
Q 028376 23 DEETCPICQEKLGNQKMVF--QC--GHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIAYA 88 (210)
Q Consensus 23 ~~~~C~iC~~~~~~~~~~~--~C--gH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~~~ 88 (210)
....||+|...+....+.. .= .|..|.-|-..| ...+..||.|.. ..++.|.
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW-----------~~~R~~C~~Cg~---~~~l~y~ 241 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEW-----------HVVRVKCSNCEQ---SGKLHYW 241 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcc-----------cccCccCCCCCC---CCceeee
Confidence 3578999988765321211 22 367899999999 467889999986 3455543
No 225
>KOG0337 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=67.80 E-value=6.9 Score=34.57 Aligned_cols=68 Identities=7% Similarity=-0.018 Sum_probs=58.9
Q ss_pred CCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376 119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRH 195 (210)
Q Consensus 119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~ 195 (210)
.+-.|..+|+..+..... +...|||.-=..+.+.+...|..+|+....+.|+|. ...|...+..|+..
T Consensus 243 ~~a~K~aaLl~il~~~~~---~~~t~vf~~tk~hve~~~~ll~~~g~~~s~iysslD------~~aRk~~~~~F~~~ 310 (529)
T KOG0337|consen 243 RKAEKEAALLSILGGRIK---DKQTIVFVATKHHVEYVRGLLRDFGGEGSDIYSSLD------QEARKINGRDFRGR 310 (529)
T ss_pred ccHHHHHHHHHHHhcccc---ccceeEEecccchHHHHHHHHHhcCCCccccccccC------hHhhhhccccccCC
Confidence 456888888888876553 567999999999999999999999999999999955 99999999999873
No 226
>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=67.56 E-value=1.7 Score=37.60 Aligned_cols=43 Identities=23% Similarity=0.305 Sum_probs=0.0
Q ss_pred eecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376 39 MVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG 83 (210)
Q Consensus 39 ~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~ 83 (210)
...||||+.-.....-|.+-.+++.. ......||.|-.++...
T Consensus 361 aF~PCGHv~SekTa~yWs~i~lPhGt--~~f~a~CPFCa~~L~g~ 403 (416)
T PF04710_consen 361 AFNPCGHVCSEKTAKYWSQIPLPHGT--HAFHAACPFCATPLDGE 403 (416)
T ss_dssp ---------------------------------------------
T ss_pred eecccccccchhhhhhhhcCCCCCCc--ccccccCCcccCcccCC
Confidence 55699998777777767443333221 35567899999888643
No 227
>PF15616 TerY-C: TerY-C metal binding domain
Probab=67.28 E-value=4.2 Score=29.91 Aligned_cols=42 Identities=29% Similarity=0.694 Sum_probs=30.9
Q ss_pred ccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376 24 EETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG 83 (210)
Q Consensus 24 ~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~ 83 (210)
...||-|..... .++-.||+++|.. ......||.|.......
T Consensus 77 ~PgCP~CGn~~~--fa~C~CGkl~Ci~----------------g~~~~~CPwCg~~g~~~ 118 (131)
T PF15616_consen 77 APGCPHCGNQYA--FAVCGCGKLFCID----------------GEGEVTCPWCGNEGSFG 118 (131)
T ss_pred CCCCCCCcChhc--EEEecCCCEEEeC----------------CCCCEECCCCCCeeeec
Confidence 377999987653 3556899999852 35678999998866544
No 228
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=66.57 E-value=3.8 Score=24.34 Aligned_cols=30 Identities=23% Similarity=0.633 Sum_probs=23.9
Q ss_pred ccccccccccCCCeecCCCCcchHhhHHHHHH
Q 028376 26 TCPICQEKLGNQKMVFQCGHFTCCKCFFAMTE 57 (210)
Q Consensus 26 ~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~ 57 (210)
.|.+|....... +.-.|+.+|.+|-.+++.
T Consensus 1 ~CiiC~~~~~~G--I~I~~~fIC~~CE~~iv~ 30 (46)
T PF10764_consen 1 KCIICGKEKEEG--IHIYGKFICSDCEKEIVN 30 (46)
T ss_pred CeEeCCCcCCCC--EEEECeEehHHHHHHhcc
Confidence 489999887763 445799999999998863
No 229
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=66.40 E-value=5.4 Score=39.01 Aligned_cols=50 Identities=28% Similarity=0.715 Sum_probs=35.8
Q ss_pred CccccccccccccCC----C--eecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376 23 DEETCPICQEKLGNQ----K--MVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI 82 (210)
Q Consensus 23 ~~~~C~iC~~~~~~~----~--~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~ 82 (210)
+...|.||.+.+... + ..-.|+--.|+.|.+ + ++ ..+...||.|+.++..
T Consensus 14 ~~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cye-y-e~--------~~g~~~cp~c~t~y~~ 69 (1044)
T PLN02915 14 DAKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCYE-Y-ER--------SEGNQCCPQCNTRYKR 69 (1044)
T ss_pred CcchhhccccccCcCCCCCEEEEeccCCCccccchhh-h-hh--------hcCCccCCccCCchhh
Confidence 557899998876432 1 224677779999994 3 22 4677899999998763
No 230
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 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 FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=66.29 E-value=2.4 Score=27.06 Aligned_cols=35 Identities=23% Similarity=0.582 Sum_probs=18.1
Q ss_pred CCCccccccccccccCC---CeecCCCCcchHhhHHHH
Q 028376 21 KADEETCPICQEKLGNQ---KMVFQCGHFTCCKCFFAM 55 (210)
Q Consensus 21 ~~~~~~C~iC~~~~~~~---~~~~~CgH~fC~~C~~~~ 55 (210)
+.+...|.+|...+.-- -.--.||++||..|....
T Consensus 6 d~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~ 43 (69)
T PF01363_consen 6 DSEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQR 43 (69)
T ss_dssp GGG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EE
T ss_pred CCCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCE
Confidence 34567899998887431 122589999999998654
No 231
>KOG0350 consensus DEAD-box ATP-dependent RNA helicase [RNA processing and modification]
Probab=66.15 E-value=12 Score=33.85 Aligned_cols=70 Identities=20% Similarity=0.154 Sum_probs=50.6
Q ss_pred chHHHHHHHHHHHHhcCCCCcEEEEcchHHHH----HHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376 122 TKIEAVTRRILWIKSTDPKAKILVFSSWNDVL----DVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMP 197 (210)
Q Consensus 122 sKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L----~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p 197 (210)
-|.-++...|..+. ..++|+|+.-.+.- .++...+..-++.+-.|.|. ++.+.|.+.++.|+.++-
T Consensus 415 ~kpl~~~~lI~~~k----~~r~lcf~~S~~sa~Rl~~~L~v~~~~~~~~~s~~t~~------l~~k~r~k~l~~f~~g~i 484 (620)
T KOG0350|consen 415 FKPLAVYALITSNK----LNRTLCFVNSVSSANRLAHVLKVEFCSDNFKVSEFTGQ------LNGKRRYKMLEKFAKGDI 484 (620)
T ss_pred cchHhHHHHHHHhh----cceEEEEecchHHHHHHHHHHHHHhccccchhhhhhhh------hhHHHHHHHHHHHhcCCc
Confidence 45556666665443 67999998766554 44444555678888889999 559999999999999776
Q ss_pred CCCC
Q 028376 198 SSQS 201 (210)
Q Consensus 198 ~~~~ 201 (210)
++.+
T Consensus 485 ~vLI 488 (620)
T KOG0350|consen 485 NVLI 488 (620)
T ss_pred eEEE
Confidence 5543
No 232
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=65.77 E-value=5.5 Score=32.61 Aligned_cols=56 Identities=20% Similarity=0.433 Sum_probs=38.6
Q ss_pred CCccccccccccccCCC---eecCCC-----CcchHhhHHHHHHHhhhccccCCCccccccCCcccc
Q 028376 22 ADEETCPICQEKLGNQK---MVFQCG-----HFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRT 80 (210)
Q Consensus 22 ~~~~~C~iC~~~~~~~~---~~~~Cg-----H~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~ 80 (210)
+.+..|-||...-++.. -+-||. |..+..|+..|+..+.... ......||-|+...
T Consensus 18 e~eR~CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n---~~q~V~C~QCqTEY 81 (293)
T KOG3053|consen 18 ELERCCWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGN---PLQTVSCPQCQTEY 81 (293)
T ss_pred ccceeEEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCC---CCceeechhhcchh
Confidence 34567999976544321 334663 7889999999998754422 46778999998864
No 233
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=65.53 E-value=5.6 Score=33.59 Aligned_cols=44 Identities=20% Similarity=0.289 Sum_probs=24.9
Q ss_pred eecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCC
Q 028376 39 MVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGN 84 (210)
Q Consensus 39 ~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~ 84 (210)
...||||+--..=+.-|.+--.++ .+......||.|...+.-..
T Consensus 374 aF~PCGHv~sekt~~YWs~iplPh--GT~~f~a~CPFC~~~L~ge~ 417 (429)
T KOG3842|consen 374 AFNPCGHVCSEKTVKYWSQIPLPH--GTHAFHAACPFCATQLAGEQ 417 (429)
T ss_pred ccCCcccccchhhhhHhhcCcCCC--ccccccccCcchhhhhccCC
Confidence 557999964433333332111111 12466778999988776543
No 234
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=65.48 E-value=7.2 Score=24.00 Aligned_cols=33 Identities=21% Similarity=0.568 Sum_probs=24.4
Q ss_pred Ccccccccccccc--CCC-eecCCCCcchHhhHHHH
Q 028376 23 DEETCPICQEKLG--NQK-MVFQCGHFTCCKCFFAM 55 (210)
Q Consensus 23 ~~~~C~iC~~~~~--~~~-~~~~CgH~fC~~C~~~~ 55 (210)
....|++|.+.+. ++. +-..||-.++++|++..
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKA 39 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHhhC
Confidence 3467999999984 332 22689999999998764
No 235
>PRK10638 glutaredoxin 3; Provisional
Probab=65.34 E-value=23 Score=23.19 Aligned_cols=32 Identities=0% Similarity=0.061 Sum_probs=27.3
Q ss_pred cEEEEc-chHHHHHHHHHHHHhCCceEEEeeCC
Q 028376 142 KILVFS-SWNDVLDVLEHAFIANNITCIKMKGE 173 (210)
Q Consensus 142 K~iVFS-Qf~~~L~li~~~L~~~gi~~~~~~G~ 173 (210)
++++|+ .|-.+-..+...|+++||.|..++=.
T Consensus 3 ~v~ly~~~~Cp~C~~a~~~L~~~gi~y~~~dv~ 35 (83)
T PRK10638 3 NVEIYTKATCPFCHRAKALLNSKGVSFQEIPID 35 (83)
T ss_pred cEEEEECCCChhHHHHHHHHHHcCCCcEEEECC
Confidence 677887 57888899999999999999888665
No 236
>cd03027 GRX_DEP Glutaredoxin (GRX) family, Dishevelled, Egl-10, and Pleckstrin (DEP) subfamily; composed of uncharacterized proteins containing a GRX domain and additional domains DEP and DUF547, both of which have unknown functions. GRX is a glutathione (GSH) dependent reductase containing a redox active CXXC motif in a TRX fold. It has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. By altering the redox state of target proteins, GRX is involved in many cellular functions.
Probab=65.18 E-value=27 Score=22.10 Aligned_cols=34 Identities=3% Similarity=0.114 Sum_probs=26.6
Q ss_pred cEEEEcc-hHHHHHHHHHHHHhCCceEEEeeCCCC
Q 028376 142 KILVFSS-WNDVLDVLEHAFIANNITCIKMKGENH 175 (210)
Q Consensus 142 K~iVFSQ-f~~~L~li~~~L~~~gi~~~~~~G~m~ 175 (210)
+++||+. +-..-..+...|+++||+|..++=...
T Consensus 2 ~v~ly~~~~C~~C~ka~~~L~~~gi~~~~~di~~~ 36 (73)
T cd03027 2 RVTIYSRLGCEDCTAVRLFLREKGLPYVEINIDIF 36 (73)
T ss_pred EEEEEecCCChhHHHHHHHHHHCCCceEEEECCCC
Confidence 5666665 567778889999999999998876643
No 237
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=63.26 E-value=5.4 Score=37.57 Aligned_cols=36 Identities=19% Similarity=0.452 Sum_probs=25.7
Q ss_pred CccccccccccccC-CCeecCCCCcchHhhHHHHHHH
Q 028376 23 DEETCPICQEKLGN-QKMVFQCGHFTCCKCFFAMTEQ 58 (210)
Q Consensus 23 ~~~~C~iC~~~~~~-~~~~~~CgH~fC~~C~~~~~~~ 58 (210)
-...|.+|.-.+.. ..+...|||+.+.+|.++|++.
T Consensus 1027 ~~~~C~~C~l~V~gss~~Cg~C~Hv~H~sc~~eWf~~ 1063 (1081)
T KOG0309|consen 1027 FTFQCAICHLAVRGSSNFCGTCGHVGHTSCMMEWFRT 1063 (1081)
T ss_pred ceeeeeeEeeEeeccchhhccccccccHHHHHHHHhc
Confidence 34567887544432 1355799999999999999854
No 239
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=63.22 E-value=1.5 Score=21.92 Aligned_cols=9 Identities=33% Similarity=1.077 Sum_probs=4.3
Q ss_pred ccccCCccc
Q 028376 71 VMCPTCRQR 79 (210)
Q Consensus 71 ~~CP~Cr~~ 79 (210)
..||.|+.+
T Consensus 14 ~fC~~CG~~ 22 (23)
T PF13240_consen 14 KFCPNCGTP 22 (23)
T ss_pred cchhhhCCc
Confidence 345555443
No 240
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=62.98 E-value=16 Score=35.11 Aligned_cols=46 Identities=22% Similarity=0.148 Sum_probs=38.2
Q ss_pred CCchHHHHHHHHHHHHhc-------CCCCcEEEEcchHHHHHHHHHHHHhCCc
Q 028376 120 YGTKIEAVTRRILWIKST-------DPKAKILVFSSWNDVLDVLEHAFIANNI 165 (210)
Q Consensus 120 ~SsKi~al~~~L~~~~~~-------~~~~K~iVFSQf~~~L~li~~~L~~~gi 165 (210)
...|.+.|.+.|.++... +++.++|||.++.++..-|...|...|+
T Consensus 268 e~PKw~~L~eiL~eI~~~~~~~~~~~~~~~iLI~~~d~~T~~qL~~~L~~~~~ 320 (814)
T TIGR00596 268 ENPKWEVLTDVLKEISHEMRMTNRLQGPGKVLIMCSDNRTCLQLRDYLTTSNK 320 (814)
T ss_pred cCCCHHHHHHHHHHHHhHHhhhcccCCCCcEEEEEcchHHHHHHHHHHHhccc
Confidence 578899998888887765 5778999999999999999999966344
No 241
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=62.51 E-value=2.3 Score=25.90 Aligned_cols=40 Identities=28% Similarity=0.595 Sum_probs=22.0
Q ss_pred CccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccc
Q 028376 23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQR 79 (210)
Q Consensus 23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~ 79 (210)
+.+.||.|...+... . ++.-|..... . ......||+|...
T Consensus 1 ~~f~CP~C~~~~~~~---~-----L~~H~~~~H~-------~--~~~~v~CPiC~~~ 40 (54)
T PF05605_consen 1 DSFTCPYCGKGFSES---S-----LVEHCEDEHR-------S--ESKNVVCPICSSR 40 (54)
T ss_pred CCcCCCCCCCccCHH---H-----HHHHHHhHCc-------C--CCCCccCCCchhh
Confidence 357899998854321 1 2223333321 0 2346789999864
No 242
>cd01518 RHOD_YceA Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins.
Probab=62.34 E-value=23 Score=24.01 Aligned_cols=38 Identities=11% Similarity=0.074 Sum_probs=26.4
Q ss_pred CCCCcEEEEcchHHHHHHHHHHHHhCCce-EEEeeCCCC
Q 028376 138 DPKAKILVFSSWNDVLDVLEHAFIANNIT-CIKMKGENH 175 (210)
Q Consensus 138 ~~~~K~iVFSQf~~~L~li~~~L~~~gi~-~~~~~G~m~ 175 (210)
+++.++||+.+--.--......|...|+. ...++|++.
T Consensus 59 ~~~~~ivvyC~~G~rs~~a~~~L~~~G~~~v~~l~GG~~ 97 (101)
T cd01518 59 LKGKKVLMYCTGGIRCEKASAYLKERGFKNVYQLKGGIL 97 (101)
T ss_pred cCCCEEEEECCCchhHHHHHHHHHHhCCcceeeechhHH
Confidence 55677888887533334456678899996 667899853
No 243
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=61.58 E-value=3.5 Score=32.74 Aligned_cols=45 Identities=16% Similarity=0.373 Sum_probs=33.9
Q ss_pred CccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcc
Q 028376 23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQ 78 (210)
Q Consensus 23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~ 78 (210)
....|.+|...+......-.||-.+...|+..+++ ....||.|+-
T Consensus 180 nlk~Cn~Ch~LvIqg~rCg~c~i~~h~~c~qty~q-----------~~~~cphc~d 224 (235)
T KOG4718|consen 180 NLKNCNLCHCLVIQGIRCGSCNIQYHRGCIQTYLQ-----------RRDICPHCGD 224 (235)
T ss_pred HHHHHhHhHHHhheeeccCcccchhhhHHHHHHhc-----------ccCcCCchhc
Confidence 44579999887765444567887888999999963 3668999965
No 244
>KOG4185 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=61.29 E-value=1.6 Score=36.39 Aligned_cols=45 Identities=29% Similarity=0.665 Sum_probs=32.5
Q ss_pred ccccccccccc-C----CCeecC--------CCCcchHhhHHHHHHHhhhccccCCCccccccCCccc
Q 028376 25 ETCPICQEKLG-N----QKMVFQ--------CGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQR 79 (210)
Q Consensus 25 ~~C~iC~~~~~-~----~~~~~~--------CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~ 79 (210)
..|.+|..... + .+.+.. |||..|..|....+.+ .. ..||.|+..
T Consensus 208 ~~c~ic~~~~~~n~~~~~p~vl~~~~~~~~~c~htlc~~c~~~~l~~---------~~-~~cp~~~~~ 265 (296)
T KOG4185|consen 208 KLCEICERIYSENDEKLAPLVLSLSRLKEKIEGHTLCKECIDTILLQ---------AG-IKCPFCTWS 265 (296)
T ss_pred HHHHHHHHHhhccccccchhHHHHHHHHHHHHHHHHHhcchHHHHHH---------hh-hcCCcccce
Confidence 56999965544 1 134444 9999999999998644 22 789999875
No 245
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=61.22 E-value=7.8 Score=32.78 Aligned_cols=49 Identities=27% Similarity=0.574 Sum_probs=36.8
Q ss_pred cCchHHHHHhcCC-CCccccccccccccCCCeecCCC--CcchHhhHHHHHHH
Q 028376 9 SNSTKHRIESLSK-ADEETCPICQEKLGNQKMVFQCG--HFTCCKCFFAMTEQ 58 (210)
Q Consensus 9 ~~~~~~~~~~l~~-~~~~~C~iC~~~~~~~~~~~~Cg--H~fC~~C~~~~~~~ 58 (210)
.+.+...+.+++. .....|..|.+.-. +..+++|. |+.|.+|+..+...
T Consensus 205 ~k~~aa~lhli~~N~~ni~C~~Ctdv~~-~vlvf~Cns~HvtC~dCFr~yc~~ 256 (446)
T KOG0006|consen 205 DKETAAALHLIATNSRNITCITCTDVRS-PVLVFQCNSRHVTCLDCFRLYCVT 256 (446)
T ss_pred cccchhHHHHhhcccccceeEEecCCcc-ceEEEecCCceeehHHhhhhHhhh
Confidence 3446667777776 45678999998654 46789998 99999999977543
No 246
>KOG2068 consensus MOT2 transcription factor [Transcription]
Probab=60.52 E-value=7.8 Score=32.87 Aligned_cols=48 Identities=29% Similarity=0.654 Sum_probs=34.9
Q ss_pred cccccccccccC---CCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376 25 ETCPICQEKLGN---QKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG 83 (210)
Q Consensus 25 ~~C~iC~~~~~~---~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~ 83 (210)
..|++|.++... ..+-.+||+..|..|+.... .....||.||++....
T Consensus 250 ~s~p~~~~~~~~~d~~~lP~~~~~~~~l~~~~t~~-----------~~~~~~~~~rk~~~~~ 300 (327)
T KOG2068|consen 250 PSCPICYEDLDLTDSNFLPCPCGFRLCLFCHKTIS-----------DGDGRCPGCRKPYERN 300 (327)
T ss_pred CCCCCCCCcccccccccccccccccchhhhhhccc-----------ccCCCCCccCCccccC
Confidence 679999886621 12335889999999998873 5667999999765443
No 247
>PTZ00062 glutaredoxin; Provisional
Probab=60.17 E-value=71 Score=25.30 Aligned_cols=58 Identities=12% Similarity=0.135 Sum_probs=41.1
Q ss_pred HHHHHHHHHhcCCCCcEEEEcc------hHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 127 VTRRILWIKSTDPKAKILVFSS------WNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 127 l~~~L~~~~~~~~~~K~iVFSQ------f~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
+.+.|.++.. ..+++||+. |-.+-..+...|+..||.|..+|=... ...|+. +.++.+
T Consensus 102 ~~~~v~~li~---~~~Vvvf~Kg~~~~p~C~~C~~~k~~L~~~~i~y~~~DI~~d------~~~~~~-l~~~sg 165 (204)
T PTZ00062 102 TVEKIERLIR---NHKILLFMKGSKTFPFCRFSNAVVNMLNSSGVKYETYNIFED------PDLREE-LKVYSN 165 (204)
T ss_pred HHHHHHHHHh---cCCEEEEEccCCCCCCChhHHHHHHHHHHcCCCEEEEEcCCC------HHHHHH-HHHHhC
Confidence 4444444442 579999988 778888899999999999998876533 444444 555553
No 248
>PRK11131 ATP-dependent RNA helicase HrpA; Provisional
Probab=60.06 E-value=41 Score=34.22 Aligned_cols=62 Identities=13% Similarity=0.141 Sum_probs=48.2
Q ss_pred hHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCce---EEEeeCCCCCCcchhhHhhhHHHHH
Q 028376 123 KIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNIT---CIKMKGENHKLPSANLQHRNALQKE 191 (210)
Q Consensus 123 Ki~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~---~~~~~G~m~~~~~~~~~~R~~~l~~ 191 (210)
++.++++.+..+.. .+..++|||-.-..-++.+...|...|++ .+-+.|.|+ ..+|.++++.
T Consensus 270 ~l~~ll~~V~~l~~-~~~GdILVFLpg~~EIe~lae~L~~~~~~~~~VlpLhg~Ls------~~eQ~~Vf~~ 334 (1294)
T PRK11131 270 QLQAIFDAVDELGR-EGPGDILIFMSGEREIRDTADALNKLNLRHTEILPLYARLS------NSEQNRVFQS 334 (1294)
T ss_pred HHHHHHHHHHHHhc-CCCCCEEEEcCCHHHHHHHHHHHHhcCCCcceEeecccCCC------HHHHHHHhcc
Confidence 45666666655543 45678999999999999999999998876 456789966 9999988764
No 249
>cd01520 RHOD_YbbB Member of the Rhodanese Homology Domain superfamily. This CD includes several putative ATP /GTP binding proteins including E. coli YbbB.
Probab=59.54 E-value=32 Score=24.60 Aligned_cols=52 Identities=12% Similarity=0.148 Sum_probs=32.2
Q ss_pred hHHHHHHHHHHHHhcCCCCcEEEEcch-HHHHHHHHHHHHhCCceEEEeeCCCC
Q 028376 123 KIEAVTRRILWIKSTDPKAKILVFSSW-NDVLDVLEHAFIANNITCIKMKGENH 175 (210)
Q Consensus 123 Ki~al~~~L~~~~~~~~~~K~iVFSQf-~~~L~li~~~L~~~gi~~~~~~G~m~ 175 (210)
+++.+.+.+... .-+++.++|||.+- -..-......|+..|+....++|+++
T Consensus 70 ~~~~~~~~~~~~-~i~~~~~vvvyC~~~G~rs~~a~~~L~~~G~~v~~L~GG~~ 122 (128)
T cd01520 70 KLKRILNEAWEA-RLERDPKLLIYCARGGMRSQSLAWLLESLGIDVPLLEGGYK 122 (128)
T ss_pred hHHHHHHHHHHh-ccCCCCeEEEEeCCCCccHHHHHHHHHHcCCceeEeCCcHH
Confidence 344444444321 23567788999862 12223445888889999888899954
No 250
>cd03029 GRX_hybridPRX5 Glutaredoxin (GRX) family, PRX5 hybrid subfamily; composed of hybrid proteins containing peroxiredoxin (PRX) and GRX domains, which is found in some pathogenic bacteria and cyanobacteria. PRXs are thiol-specific antioxidant (TSA) proteins that confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins. PRX-GRX hybrid proteins from Haemophilus influenza and Neisseria meningitis exhibit GSH-dependent peroxidase activity. The flow of reducing equivalents in the catalytic cycle of the hybrid protein goes from NADPH - GSH reductase - GSH - GRX domain of hybrid - PRX domain of hybrid - peroxide substrate.
Probab=58.63 E-value=19 Score=22.80 Aligned_cols=33 Identities=12% Similarity=0.077 Sum_probs=26.5
Q ss_pred CcEEEEcc-hHHHHHHHHHHHHhCCceEEEeeCC
Q 028376 141 AKILVFSS-WNDVLDVLEHAFIANNITCIKMKGE 173 (210)
Q Consensus 141 ~K~iVFSQ-f~~~L~li~~~L~~~gi~~~~~~G~ 173 (210)
+|++|||. |-.+-......|++.||+|..++=.
T Consensus 1 ~~v~lys~~~Cp~C~~ak~~L~~~~i~~~~~~v~ 34 (72)
T cd03029 1 ESVSLFTKPGCPFCARAKAALQENGISYEEIPLG 34 (72)
T ss_pred CeEEEEECCCCHHHHHHHHHHHHcCCCcEEEECC
Confidence 36777775 7777888899999999999888755
No 251
>cd03031 GRX_GRX_like Glutaredoxin (GRX) family, GRX-like domain containing protein subfamily; composed of uncharacterized eukaryotic proteins containing a GRX-like domain having only one conserved cysteine, aligning to the C-terminal cysteine of the CXXC motif of GRXs. This subfamily is predominantly composed of plant proteins. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins via a redox active CXXC motif using a similar dithiol mechanism employed by TRXs. GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. Proteins containing only the C-terminal cysteine are generally redox inactive.
Probab=58.50 E-value=50 Score=24.70 Aligned_cols=44 Identities=5% Similarity=0.060 Sum_probs=32.9
Q ss_pred cEEEEcch-------HHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHH
Q 028376 142 KILVFSSW-------NDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKE 191 (210)
Q Consensus 142 K~iVFSQf-------~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~ 191 (210)
|++||+.- -..=..+...|+..||.|..+|=+|. ...|+..-+.
T Consensus 1 ~VvlYttsl~giR~t~~~C~~ak~iL~~~~V~~~e~DVs~~------~~~~~EL~~~ 51 (147)
T cd03031 1 RVVLYTTSLRGVRKTFEDCNNVRAILESFRVKFDERDVSMD------SGFREELREL 51 (147)
T ss_pred CEEEEEcCCcCCCCcChhHHHHHHHHHHCCCcEEEEECCCC------HHHHHHHHHH
Confidence 56777763 46668889999999999999998865 6666654443
No 252
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=57.40 E-value=6.6 Score=33.28 Aligned_cols=43 Identities=23% Similarity=0.527 Sum_probs=28.9
Q ss_pred ccccccccccccCCC--eecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCc
Q 028376 24 EETCPICQEKLGNQK--MVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCR 77 (210)
Q Consensus 24 ~~~C~iC~~~~~~~~--~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr 77 (210)
...|..|.+...... .--.|.|.||.+|-.-+ . +.-..||.|.
T Consensus 330 ~~~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv~i-H----------esLh~CpgCe 374 (378)
T KOG2807|consen 330 SRFCFACQGELLSSGRYRCESCKNVFCLDCDVFI-H----------ESLHNCPGCE 374 (378)
T ss_pred CcceeeeccccCCCCcEEchhccceeeccchHHH-H----------hhhhcCCCcC
Confidence 345999965544322 33589999999996644 2 3345799996
No 253
>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=57.37 E-value=3.5 Score=35.84 Aligned_cols=52 Identities=21% Similarity=0.404 Sum_probs=0.0
Q ss_pred Ccccccccccccc-------------CCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccC
Q 028376 23 DEETCPICQEKLG-------------NQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDI 82 (210)
Q Consensus 23 ~~~~C~iC~~~~~-------------~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~ 82 (210)
...+||+=+..+. .+.+.+.|||++-.. .|-.... .......||+|+.+-..
T Consensus 276 ~rpQCPVglnTL~fp~~~~~~~~~~~qP~VYl~CGHVhG~h---~Wg~~~~-----~~~~~r~CPlCr~~g~~ 340 (416)
T PF04710_consen 276 GRPQCPVGLNTLVFPSKSRKDVPDERQPWVYLNCGHVHGYH---NWGQDSD-----RDPRSRTCPLCRQVGPY 340 (416)
T ss_dssp -------------------------------------------------------------------------
T ss_pred cCCCCCcCCCccccccccccccccccCceeeccccceeeec---ccccccc-----cccccccCCCccccCCc
Confidence 3468988754432 124778999987543 3321110 01347799999986444
No 254
>KOG2979 consensus Protein involved in DNA repair [General function prediction only]
Probab=57.24 E-value=7.4 Score=31.84 Aligned_cols=49 Identities=16% Similarity=0.255 Sum_probs=36.3
Q ss_pred hcCCCCccccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccC
Q 028376 18 SLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPT 75 (210)
Q Consensus 18 ~l~~~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~ 75 (210)
..+..-...||+=..++.+|.+-..|||+|=++-+..++. ......||+
T Consensus 170 i~~e~fs~rdPis~~~I~nPviSkkC~HvydrDsI~~~l~---------~~~~i~CPv 218 (262)
T KOG2979|consen 170 IGQEVFSNRDPISKKPIVNPVISKKCGHVYDRDSIMQILC---------DEITIRCPV 218 (262)
T ss_pred hhhhhhcccCchhhhhhhchhhhcCcCcchhhhhHHHHhc---------cCceeeccc
Confidence 3344445679987777777666689999999999998853 245678996
No 255
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=57.17 E-value=6.9 Score=37.11 Aligned_cols=52 Identities=15% Similarity=0.283 Sum_probs=31.3
Q ss_pred CccccccccccccC---C---CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccc
Q 028376 23 DEETCPICQEKLGN---Q---KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQR 79 (210)
Q Consensus 23 ~~~~C~iC~~~~~~---~---~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~ 79 (210)
+...|.+|...+.+ . ..+..|+|.+|..||..|.++... ......|+.|..-
T Consensus 95 ~s~Ss~~C~~E~S~~~ds~~i~P~~~~~~~~CP~Ci~s~~DqL~~-----~~k~c~H~FC~~C 152 (1134)
T KOG0825|consen 95 ESDTSPVCEKEHSPDVDSSNICPVQTHVENQCPNCLKSCNDQLEE-----SEKHTAHYFCEEC 152 (1134)
T ss_pred cccccchhheecCCcccccCcCchhhhhhhhhhHHHHHHHHHhhc-----cccccccccHHHH
Confidence 33456666443332 1 244569999999999999766432 2344456666553
No 256
>PRK12326 preprotein translocase subunit SecA; Reviewed
Probab=56.85 E-value=49 Score=31.58 Aligned_cols=51 Identities=16% Similarity=0.165 Sum_probs=45.1
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCC
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGE 173 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~ 173 (210)
-.|..|+++.+.+..+. +-=+||.++...--+.+...|.+.||++..+..+
T Consensus 410 ~~k~~Aii~ei~~~~~~--GrPVLVgt~sI~~SE~ls~~L~~~gI~h~vLNAk 460 (764)
T PRK12326 410 AEKNDAIVEHIAEVHET--GQPVLVGTHDVAESEELAERLRAAGVPAVVLNAK 460 (764)
T ss_pred HHHHHHHHHHHHHHHHc--CCCEEEEeCCHHHHHHHHHHHHhCCCcceeeccC
Confidence 46888999999887654 6779999999999999999999999999988776
No 257
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=56.76 E-value=13 Score=27.38 Aligned_cols=32 Identities=31% Similarity=0.783 Sum_probs=21.7
Q ss_pred CCccccccccccccCCCeecCCCCcchHhhHHHHHHH
Q 028376 22 ADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQ 58 (210)
Q Consensus 22 ~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~ 58 (210)
.++..|.||...- +.-.||| .|..|-.+...+
T Consensus 63 ~ddatC~IC~KTK----FADG~GH-~C~YCq~r~CAR 94 (169)
T KOG3799|consen 63 GDDATCGICHKTK----FADGCGH-NCSYCQTRFCAR 94 (169)
T ss_pred CcCcchhhhhhcc----cccccCc-ccchhhhhHHHh
Confidence 5778999997532 3346899 577777666443
No 258
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=56.75 E-value=71 Score=25.21 Aligned_cols=68 Identities=9% Similarity=0.075 Sum_probs=46.5
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcc-----hHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHh
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSS-----WNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELT 193 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQ-----f~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~ 193 (210)
.-+++.|++.|.+ .+.|=||+.- -..+...|...|+..||+..|+--+.|....+.-......-..|.
T Consensus 120 ~l~i~~L~~Ri~~-----~~v~EVIlAt~~tvEGe~Ta~yi~~~lk~~~ikvtRlA~GiP~G~~ley~D~~TL~~Al~ 192 (195)
T TIGR00615 120 DLTIAALLKRLQE-----ESVKEVILATNPTVEGEATALYIARLLQPFGVKVTRIASGLPVGGDLEYADEVTLARALE 192 (195)
T ss_pred hcCHHHHHHHHhc-----CCCcEEEEeCCCCchHHHHHHHHHHHhhhcCCcEEeeeecCCCCcceeecCHHHHHHHHH
Confidence 4678888888762 3466666554 234567788889989999999988887665555555555554444
No 259
>cd01524 RHOD_Pyr_redox Member of the Rhodanese Homology Domain superfamily. Included in this CD are the Lactococcus lactis NADH oxidase, Bacillus cereus NADH dehydrogenase, and Bacteroides thetaiotaomicron pyridine nucleotide-disulphide oxidoreductase, and similar rhodanese-like domains found C-terminal of the pyridine nucleotide-disulphide oxidoreductase (Pyr-redox) domain and the Pyr-redox dimerization domain.
Probab=56.33 E-value=22 Score=23.52 Aligned_cols=38 Identities=11% Similarity=0.145 Sum_probs=28.3
Q ss_pred CCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCC
Q 028376 138 DPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENH 175 (210)
Q Consensus 138 ~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~ 175 (210)
+++.++|+|..-..-.......|+..|+....++|++.
T Consensus 49 ~~~~~vvl~c~~g~~a~~~a~~L~~~G~~v~~l~GG~~ 86 (90)
T cd01524 49 PKDKEIIVYCAVGLRGYIAARILTQNGFKVKNLDGGYK 86 (90)
T ss_pred CCCCcEEEEcCCChhHHHHHHHHHHCCCCEEEecCCHH
Confidence 45667888876544556667789999998788999964
No 260
>COG5387 Chaperone required for the assembly of the mitochondrial F1-ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=55.42 E-value=44 Score=27.23 Aligned_cols=59 Identities=20% Similarity=0.336 Sum_probs=43.9
Q ss_pred HHHHHHHHHHHhcCCCCcEEEEcc-------------hHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHH
Q 028376 125 EAVTRRILWIKSTDPKAKILVFSS-------------WNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKE 191 (210)
Q Consensus 125 ~al~~~L~~~~~~~~~~K~iVFSQ-------------f~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~ 191 (210)
+++.++|.+.... + .++|+- |...++..+.. .|++|..++|.|. ..|-..+++.
T Consensus 111 ~~v~~~ilrf~~t---D-lLcYra~sp~eLv~rQ~e~w~Piidw~e~~---lg~rf~~vdgvih------~~Qp~E~va~ 177 (264)
T COG5387 111 QAVFEQILRFLDT---D-LLCYRAESPFELVERQNENWDPIIDWAENF---LGARFILVDGVIH------GEQPREAVAA 177 (264)
T ss_pred HHHHHHHHHHccC---C-eeEecCCCHHHHHHHHHhhhHHHHHHHHHh---hCceEEeehhhhc------CCCcHHHHHH
Confidence 4566666665533 3 889986 66666665544 8999999999866 9999999999
Q ss_pred HhhcC
Q 028376 192 LTRHM 196 (210)
Q Consensus 192 F~~~~ 196 (210)
|...-
T Consensus 178 ~a~~l 182 (264)
T COG5387 178 FAVKL 182 (264)
T ss_pred HHHHH
Confidence 98743
No 261
>PRK10329 glutaredoxin-like protein; Provisional
Probab=54.79 E-value=52 Score=21.65 Aligned_cols=33 Identities=6% Similarity=0.066 Sum_probs=27.5
Q ss_pred cEEEEc-chHHHHHHHHHHHHhCCceEEEeeCCC
Q 028376 142 KILVFS-SWNDVLDVLEHAFIANNITCIKMKGEN 174 (210)
Q Consensus 142 K~iVFS-Qf~~~L~li~~~L~~~gi~~~~~~G~m 174 (210)
|++||+ .|-.+-+.+...|++.||.|..++-..
T Consensus 2 ~v~lYt~~~Cp~C~~ak~~L~~~gI~~~~idi~~ 35 (81)
T PRK10329 2 RITIYTRNDCVQCHATKRAMESRGFDFEMINVDR 35 (81)
T ss_pred EEEEEeCCCCHhHHHHHHHHHHCCCceEEEECCC
Confidence 678888 477788889999999999998887763
No 262
>PF09413 DUF2007: Domain of unknown function (DUF2007); InterPro: IPR018551 This is a family of proteins with unknown function. ; PDB: 2HFV_A.
Probab=54.77 E-value=26 Score=21.97 Aligned_cols=31 Identities=10% Similarity=-0.004 Sum_probs=18.4
Q ss_pred EEEEcchHHHHHHHHHHHHhCCceEEEeeCC
Q 028376 143 ILVFSSWNDVLDVLEHAFIANNITCIKMKGE 173 (210)
Q Consensus 143 ~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~ 173 (210)
-|..+...--..+|...|+.+||++...+-.
T Consensus 2 ~l~~~~~~~ea~~i~~~L~~~gI~~~v~~~~ 32 (67)
T PF09413_consen 2 KLYTAGDPIEAELIKGLLEENGIPAFVKNEH 32 (67)
T ss_dssp EEEEE--HHHHHHHHHHHHHTT--EE--S--
T ss_pred EEEEcCCHHHHHHHHHHHHhCCCcEEEECCc
Confidence 4555666677899999999999998765444
No 263
>cd00291 SirA_YedF_YeeD SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=54.35 E-value=51 Score=20.52 Aligned_cols=45 Identities=4% Similarity=-0.026 Sum_probs=35.5
Q ss_pred HHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEee
Q 028376 127 VTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMK 171 (210)
Q Consensus 127 l~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~ 171 (210)
+++..+.+..-.+++.+.|-+.......-|...++.+|+.+....
T Consensus 13 l~~~~~~l~~l~~g~~l~v~~d~~~~~~~i~~~~~~~g~~~~~~~ 57 (69)
T cd00291 13 VLKTKKALEKLKSGEVLEVLLDDPGAVEDIPAWAKETGHEVLEVE 57 (69)
T ss_pred HHHHHHHHhcCCCCCEEEEEecCCcHHHHHHHHHHHcCCEEEEEE
Confidence 444555555566788988988898889999999999999987654
No 264
>TIGR03190 benz_CoA_bzdN benzoyl-CoA reductase, bzd-type, N subunit. Members of this family are the N subunit of one of two related types of four-subunit ATP-dependent benzoyl-CoA reductase. This enzyme system catalyzes the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for a number of different aromatic compounds, such as phenol and toluene.
Probab=54.28 E-value=61 Score=28.12 Aligned_cols=64 Identities=9% Similarity=-0.001 Sum_probs=39.9
Q ss_pred chHHHHHHHHHHHHhcCCCCcEEEEcc-----hHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHh
Q 028376 122 TKIEAVTRRILWIKSTDPKAKILVFSS-----WNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELT 193 (210)
Q Consensus 122 sKi~al~~~L~~~~~~~~~~K~iVFSQ-----f~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~ 193 (210)
.+++.+.+.+++.+ -+=+|.|.. |.--.-.|...|++.||+++.++|... .+..|=..-|+.|-
T Consensus 300 ~R~~~i~~lv~~~~----~DGVI~~~~kfC~~~~~e~~~lk~~l~e~GIP~L~iE~D~~----~~~gQi~TRlEAFl 368 (377)
T TIGR03190 300 TRYDHVLGLAKEYN----VQGAIFLQQKFCDPHEGDYPDLKRHLEANGIPTLFLEFDIT----NPIGPFRIRIEAFL 368 (377)
T ss_pred HHHHHHHHHHHHhC----CCEEEEecccCCCcchhhhHHHHHHHHHCCCCEEEEecCCC----CchHHHHHHHHHHH
Confidence 35566665555432 344555544 344455688899999999999999865 33444444556664
No 265
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=53.85 E-value=8.3 Score=23.43 Aligned_cols=26 Identities=35% Similarity=0.689 Sum_probs=15.2
Q ss_pred CchHHHHHhcCCCCccccccccccccC
Q 028376 10 NSTKHRIESLSKADEETCPICQEKLGN 36 (210)
Q Consensus 10 ~~~~~~~~~l~~~~~~~C~iC~~~~~~ 36 (210)
..++..+..+...+. .||+|..++..
T Consensus 7 ~~~~k~i~~l~~~~~-~CPlC~r~l~~ 32 (54)
T PF04423_consen 7 EELKKYIEELKEAKG-CCPLCGRPLDE 32 (54)
T ss_dssp HHHHHHHHHHTT-SE-E-TTT--EE-H
T ss_pred HHHHHHHHHHhcCCC-cCCCCCCCCCH
Confidence 345666777777666 99999988764
No 266
>smart00450 RHOD Rhodanese Homology Domain. An alpha beta fold found duplicated in the Rhodanese protein. The the Cysteine containing enzymatically active version of the domain is also found in the CDC25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and stress proteins such as Senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions with a loss of the cysteine are also seen in Dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases. These are likely to play a role in protein interactions.
Probab=53.82 E-value=38 Score=22.03 Aligned_cols=42 Identities=7% Similarity=0.043 Sum_probs=31.1
Q ss_pred HHhcCCCCcEEEEcchHHHHHHHHHHHHhCCce-EEEeeCCCC
Q 028376 134 IKSTDPKAKILVFSSWNDVLDVLEHAFIANNIT-CIKMKGENH 175 (210)
Q Consensus 134 ~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~-~~~~~G~m~ 175 (210)
.....++.++|||..-..-...+...|...|+. ...++|++.
T Consensus 50 ~~~~~~~~~iv~~c~~g~~a~~~~~~l~~~G~~~v~~l~GG~~ 92 (100)
T smart00450 50 RLGLDKDKPVVVYCRSGNRSAKAAWLLRELGFKNVYLLDGGYK 92 (100)
T ss_pred HcCCCCCCeEEEEeCCCcHHHHHHHHHHHcCCCceEEecCCHH
Confidence 334566788899886555567788889999998 666799854
No 267
>PF13361 UvrD_C: UvrD-like helicase C-terminal domain; PDB: 1UAA_B 3U4Q_A 3U44_A 1W36_B 3K70_B 2IS6_B 3LFU_A 2IS2_B 2IS1_B 2IS4_A ....
Probab=53.10 E-value=61 Score=26.69 Aligned_cols=52 Identities=19% Similarity=0.277 Sum_probs=34.2
Q ss_pred hHHHHHHHHHHHHhc-CCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCC
Q 028376 123 KIEAVTRRILWIKST-DPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENH 175 (210)
Q Consensus 123 Ki~al~~~L~~~~~~-~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~ 175 (210)
-.+.+.+.|.++... .+..++.|-.-....+..|+.+|..+||+| ++.|+..
T Consensus 59 e~~~i~~~I~~l~~~~~~~~diAVL~R~~~~~~~i~~~L~~~gIp~-~~~~~~~ 111 (351)
T PF13361_consen 59 EAEYIAEEIKELIRNGIPPSDIAVLVRTNSQIKEIEDALKEAGIPY-RISGSKS 111 (351)
T ss_dssp HHHHHHHHHHHHHHTTS-GGGEEEEESSGGHHHHHHHHHHHTTS-E-EESSSSB
T ss_pred HHHHHHHHHHHHhhcCCCcccEEEEEECchhHHHHHHHHhhhccee-Eeccccc
Confidence 345677777776542 333445444444777889999999999997 6777755
No 268
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=53.05 E-value=10 Score=23.00 Aligned_cols=32 Identities=22% Similarity=0.519 Sum_probs=23.0
Q ss_pred ccccccccccccC---CCeecCCCCcchHhhHHHH
Q 028376 24 EETCPICQEKLGN---QKMVFQCGHFTCCKCFFAM 55 (210)
Q Consensus 24 ~~~C~iC~~~~~~---~~~~~~CgH~fC~~C~~~~ 55 (210)
...|.+|...+.. ...-..||++||..|....
T Consensus 2 ~~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~ 36 (57)
T cd00065 2 ASSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNR 36 (57)
T ss_pred cCcCcccCccccCCccccccCcCcCCcChHHcCCe
Confidence 3578899776643 1233689999999998765
No 269
>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA. This model represents HrpA, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterized, is about 800 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.
Probab=52.89 E-value=50 Score=33.59 Aligned_cols=63 Identities=10% Similarity=0.111 Sum_probs=49.0
Q ss_pred chHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCc---eEEEeeCCCCCCcchhhHhhhHHHHH
Q 028376 122 TKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNI---TCIKMKGENHKLPSANLQHRNALQKE 191 (210)
Q Consensus 122 sKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi---~~~~~~G~m~~~~~~~~~~R~~~l~~ 191 (210)
.+++++++.|..+... ...++|||-.-..-++.+...|...++ ..+-+.|.|+ ..+|.++++.
T Consensus 262 ~~~~~i~~~I~~l~~~-~~GdILVFLpg~~EI~~l~~~L~~~~~~~~~VlpLhg~Ls------~~eQ~~vf~~ 327 (1283)
T TIGR01967 262 DQLEAILDAVDELFAE-GPGDILIFLPGEREIRDAAEILRKRNLRHTEILPLYARLS------NKEQQRVFQP 327 (1283)
T ss_pred hHHHHHHHHHHHHHhh-CCCCEEEeCCCHHHHHHHHHHHHhcCCCCcEEEeccCCCC------HHHHHHHhCC
Confidence 3667777777766544 457899999999999999999998754 4677899966 9999888543
No 270
>PRK01415 hypothetical protein; Validated
Probab=52.84 E-value=70 Score=26.20 Aligned_cols=37 Identities=11% Similarity=-0.015 Sum_probs=28.9
Q ss_pred cCCCCcEEEEcchHHHHHHHHHHHHhCCce-EEEeeCC
Q 028376 137 TDPKAKILVFSSWNDVLDVLEHAFIANNIT-CIKMKGE 173 (210)
Q Consensus 137 ~~~~~K~iVFSQf~~~L~li~~~L~~~gi~-~~~~~G~ 173 (210)
.+++.++++|..--.--......|.+.|+. ...+.|+
T Consensus 168 ~~k~k~Iv~yCtgGiRs~kAa~~L~~~Gf~~Vy~L~GG 205 (247)
T PRK01415 168 LLKGKKIAMVCTGGIRCEKSTSLLKSIGYDEVYHLKGG 205 (247)
T ss_pred hcCCCeEEEECCCChHHHHHHHHHHHcCCCcEEEechH
Confidence 345677889987666667778889999997 5678998
No 271
>KOG0349 consensus Putative DEAD-box RNA helicase DDX1 [RNA processing and modification]
Probab=52.45 E-value=31 Score=30.86 Aligned_cols=53 Identities=17% Similarity=0.312 Sum_probs=42.8
Q ss_pred CCCCcEEEEcchHHHHHHHHHHHHhCC---ceEEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376 138 DPKAKILVFSSWNDVLDVLEHAFIANN---ITCIKMKGENHKLPSANLQHRNALQKELTRHM 196 (210)
Q Consensus 138 ~~~~K~iVFSQf~~~L~li~~~L~~~g---i~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~ 196 (210)
...+|+|||.--..--|-+++++.+.| +.++-+.|... +.+|.+.|+.|.+.|
T Consensus 503 h~mdkaiifcrtk~dcDnLer~~~qkgg~~~scvclhgDrk------P~Erk~nle~Fkk~d 558 (725)
T KOG0349|consen 503 HAMDKAIIFCRTKQDCDNLERMMNQKGGKHYSCVCLHGDRK------PDERKANLESFKKFD 558 (725)
T ss_pred hccCceEEEEeccccchHHHHHHHHcCCccceeEEEecCCC------hhHHHHHHHhhhhcC
Confidence 457899999877777788888888654 46677889877 999999999999843
No 272
>PRK12903 secA preprotein translocase subunit SecA; Reviewed
Probab=52.10 E-value=58 Score=31.74 Aligned_cols=52 Identities=15% Similarity=0.201 Sum_probs=45.7
Q ss_pred CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCC
Q 028376 120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGE 173 (210)
Q Consensus 120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~ 173 (210)
...|..|+++.+.+..+ .+-=+||.+....--+.|...|.++||++..+..+
T Consensus 408 ~~~K~~Aii~ei~~~~~--~gqPVLVgT~SIe~SE~ls~~L~~~gi~h~vLNAk 459 (925)
T PRK12903 408 KHAKWKAVVKEVKRVHK--KGQPILIGTAQVEDSETLHELLLEANIPHTVLNAK 459 (925)
T ss_pred HHHHHHHHHHHHHHHHh--cCCCEEEEeCcHHHHHHHHHHHHHCCCCceeeccc
Confidence 35788999999988764 36779999999999999999999999999988876
No 273
>TIGR02189 GlrX-like_plant Glutaredoxin-like family. This family of glutaredoxin-like proteins is aparrently limited to plants. Multiple isoforms are found in A. thaliana and O.sativa.
Probab=51.88 E-value=26 Score=24.06 Aligned_cols=34 Identities=9% Similarity=0.142 Sum_probs=28.0
Q ss_pred CCcEEEEcc-hHHHHHHHHHHHHhCCceEEEeeCC
Q 028376 140 KAKILVFSS-WNDVLDVLEHAFIANNITCIKMKGE 173 (210)
Q Consensus 140 ~~K~iVFSQ-f~~~L~li~~~L~~~gi~~~~~~G~ 173 (210)
..+++|||. |-.+-......|...||+|..++=.
T Consensus 7 ~~~Vvvysk~~Cp~C~~ak~~L~~~~i~~~~vdid 41 (99)
T TIGR02189 7 EKAVVIFSRSSCCMCHVVKRLLLTLGVNPAVHEID 41 (99)
T ss_pred cCCEEEEECCCCHHHHHHHHHHHHcCCCCEEEEcC
Confidence 468999998 7778888899999999988766554
No 274
>COG2247 LytB Putative cell wall-binding domain [Cell envelope biogenesis, outer membrane]
Probab=51.62 E-value=45 Score=28.42 Aligned_cols=68 Identities=21% Similarity=0.246 Sum_probs=49.8
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCC
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPS 198 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~ 198 (210)
+.=-++++..+.++ .++++||---=...-.-.+.+|+.-||++.|+-|... ...-.++.+.|++.-|.
T Consensus 61 g~ynes~~~eI~~l----npd~VLIIGGp~AVs~~yE~~Lks~GitV~RigG~nR------~ETa~~v~~~~~~~yp~ 128 (337)
T COG2247 61 GIYNESVLDEIIEL----NPDLVLIIGGPIAVSPNYENALKSLGITVKRIGGANR------YETAEKVAKFFREDYPN 128 (337)
T ss_pred ccccHHHHHHHHhh----CCceEEEECCCCcCChhHHHHHHhCCcEEEEecCcch------HHHHHHHHHHHHhhchh
Confidence 34445666666654 3678888766555556678899999999999999865 67777888888765554
No 275
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=51.11 E-value=16 Score=22.15 Aligned_cols=29 Identities=28% Similarity=0.797 Sum_probs=21.0
Q ss_pred ccccccccccCC-CeecCCCCcchHhhHHHH
Q 028376 26 TCPICQEKLGNQ-KMVFQCGHFTCCKCFFAM 55 (210)
Q Consensus 26 ~C~iC~~~~~~~-~~~~~CgH~fC~~C~~~~ 55 (210)
.|+||...+.-- .+.+.=| ..|.+|+..+
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHh
Confidence 499998876431 1456777 7999999876
No 276
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=50.72 E-value=15 Score=25.82 Aligned_cols=34 Identities=18% Similarity=0.286 Sum_probs=22.3
Q ss_pred CCcchHhhHHHHHHHhhhccccCCCccccccCCccc
Q 028376 44 GHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQR 79 (210)
Q Consensus 44 gH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~ 79 (210)
.=.||..|+............ ....-.||.||..
T Consensus 37 ~~~fC~~CL~~ryge~~~ev~--~~~~W~CP~Crgi 70 (105)
T PF10497_consen 37 RGKFCGGCLRNRYGENVEEVL--EDPNWKCPKCRGI 70 (105)
T ss_pred cceehHhHHHHHHhhhHHHHh--cCCceECCCCCCe
Confidence 567999999988654332211 2445679999873
No 277
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=50.37 E-value=9.4 Score=35.80 Aligned_cols=56 Identities=21% Similarity=0.434 Sum_probs=37.1
Q ss_pred CccccccccccccCC---------CeecCCCCcc--------------------hHhhHHHHHHHhhhccccCCCccccc
Q 028376 23 DEETCPICQEKLGNQ---------KMVFQCGHFT--------------------CCKCFFAMTEQRLIHDNKVKNEWVMC 73 (210)
Q Consensus 23 ~~~~C~iC~~~~~~~---------~~~~~CgH~f--------------------C~~C~~~~~~~~~~~~~~~~~~~~~C 73 (210)
|...|.-|++++.++ ...|.||-.| |..|..++-.. ...|-..+...|
T Consensus 100 D~a~C~~Cl~Ei~dp~~rrY~YPF~~CT~CGPRfTIi~alPYDR~nTsM~~F~lC~~C~~EY~dP---~nRRfHAQp~aC 176 (750)
T COG0068 100 DAATCEDCLEEIFDPNSRRYLYPFINCTNCGPRFTIIEALPYDRENTSMADFPLCPFCDKEYKDP---LNRRFHAQPIAC 176 (750)
T ss_pred chhhhHHHHHHhcCCCCcceeccccccCCCCcceeeeccCCCCcccCccccCcCCHHHHHHhcCc---cccccccccccC
Confidence 456799998877654 1336777766 99999988321 112224566789
Q ss_pred cCCccccc
Q 028376 74 PTCRQRTD 81 (210)
Q Consensus 74 P~Cr~~~~ 81 (210)
|.|.-.+.
T Consensus 177 p~CGP~~~ 184 (750)
T COG0068 177 PKCGPHLF 184 (750)
T ss_pred cccCCCeE
Confidence 99987543
No 278
>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=49.88 E-value=50 Score=29.95 Aligned_cols=67 Identities=7% Similarity=0.104 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHhcCCCCcEEEEcchHHH----------------------------------------------------
Q 028376 125 EAVTRRILWIKSTDPKAKILVFSSWNDV---------------------------------------------------- 152 (210)
Q Consensus 125 ~al~~~L~~~~~~~~~~K~iVFSQf~~~---------------------------------------------------- 152 (210)
+.|++.|++..+. +.++|||..=..+
T Consensus 185 ~~l~~~i~~~l~~--g~qvLvflnrrGya~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 185 PELITAIEQTLAA--GEQSILFLNRRGYSKNLLCRSCGYILCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred HHHHHHHHHHHHc--CCcEEEEEeCCcCCCeeEhhhCcCccCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCC
Q ss_pred --------HHHHHHHHHhC--CceEEEeeCCCCCCcchhhHhh--hHHHHHHhhcCCCC
Q 028376 153 --------LDVLEHAFIAN--NITCIKMKGENHKLPSANLQHR--NALQKELTRHMPSS 199 (210)
Q Consensus 153 --------L~li~~~L~~~--gi~~~~~~G~m~~~~~~~~~~R--~~~l~~F~~~~p~~ 199 (210)
.+.++..|++. +.+..++|+.+. ..++ .++++.|.+++++.
T Consensus 263 ~l~~~g~Gte~~~e~l~~~fp~~~v~~~d~d~~------~~~~~~~~~l~~f~~g~~~I 315 (505)
T TIGR00595 263 DLVYKGYGTEQVEEELAKLFPGARIARIDSDTT------SRKGAHEALLNQFANGKADI 315 (505)
T ss_pred eeEeecccHHHHHHHHHhhCCCCcEEEEecccc------cCccHHHHHHHHHhcCCCCE
No 279
>cd01528 RHOD_2 Member of the Rhodanese Homology Domain superfamily, subgroup 2. Subgroup 2 includes uncharacterized putative rhodanese-related domains.
Probab=49.82 E-value=54 Score=22.08 Aligned_cols=38 Identities=11% Similarity=0.230 Sum_probs=27.9
Q ss_pred CCCCcEEEEcchHHHHHHHHHHHHhCCce-EEEeeCCCC
Q 028376 138 DPKAKILVFSSWNDVLDVLEHAFIANNIT-CIKMKGENH 175 (210)
Q Consensus 138 ~~~~K~iVFSQf~~~L~li~~~L~~~gi~-~~~~~G~m~ 175 (210)
+++.++|||.+--..-......|.+.|+. ...++|++.
T Consensus 56 ~~~~~vv~~c~~g~rs~~~~~~l~~~G~~~v~~l~GG~~ 94 (101)
T cd01528 56 NPDKDIVVLCHHGGRSMQVAQWLLRQGFENVYNLQGGID 94 (101)
T ss_pred CCCCeEEEEeCCCchHHHHHHHHHHcCCccEEEecCCHH
Confidence 34677888887655556667788889996 567899854
No 280
>COG1202 Superfamily II helicase, archaea-specific [General function prediction only]
Probab=49.80 E-value=67 Score=29.96 Aligned_cols=69 Identities=12% Similarity=0.180 Sum_probs=54.0
Q ss_pred CchHHHHHHHHHHHHh----cCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376 121 GTKIEAVTRRILWIKS----TDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRH 195 (210)
Q Consensus 121 SsKi~al~~~L~~~~~----~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~ 195 (210)
+.|.+-+.+..+.-.. ..-..+.|||+-...=-+.|..+|...|++-.-|+++++ -.+|..+=..|...
T Consensus 417 ~eK~~ii~~L~k~E~~~~sskg~rGQtIVFT~SRrr~h~lA~~L~~kG~~a~pYHaGL~------y~eRk~vE~~F~~q 489 (830)
T COG1202 417 SEKWDIIARLVKREFSTESSKGYRGQTIVFTYSRRRCHELADALTGKGLKAAPYHAGLP------YKERKSVERAFAAQ 489 (830)
T ss_pred hHHHHHHHHHHHHHHhhhhccCcCCceEEEecchhhHHHHHHHhhcCCcccccccCCCc------HHHHHHHHHHHhcC
Confidence 5566555555532222 122368899999999999999999999999999999976 99999999999873
No 281
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=49.11 E-value=12 Score=31.57 Aligned_cols=41 Identities=10% Similarity=-0.103 Sum_probs=31.2
Q ss_pred ccccccccccccCCCeecCCCC-cchHhhHHHHHHHhhhccccCCCccccccCCcc
Q 028376 24 EETCPICQEKLGNQKMVFQCGH-FTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQ 78 (210)
Q Consensus 24 ~~~C~iC~~~~~~~~~~~~CgH-~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~ 78 (210)
..+|..|...+.. .+..+|+| .||.+|... ...+.||+|..
T Consensus 343 ~~~~~~~~~~~~s-t~~~~~~~n~~~~~~a~~-------------s~~~~~~~c~~ 384 (394)
T KOG2113|consen 343 SLKGTSAGFGLLS-TIWSGGNMNLSPGSLASA-------------SASPTSSTCDH 384 (394)
T ss_pred hcccccccCceee-eEeecCCcccChhhhhhc-------------ccCCccccccc
Confidence 3569999877665 47889999 789988762 34578999965
No 282
>TIGR03191 benz_CoA_bzdO benzoyl-CoA reductase, bzd-type, O subunit. Members of this family are the O subunit of one of two related types of four-subunit ATP-dependent benzoyl-CoA reductase. This enzyme system catalyzes the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for a number of different aromatic compounds, such as phenol and toluene.
Probab=49.11 E-value=99 Score=27.46 Aligned_cols=50 Identities=10% Similarity=-0.045 Sum_probs=35.8
Q ss_pred chHHHHHHHHHHHHhcCCCCcEEEEcc-----hHHHHHHHHHHHHhCCceEEEeeCCCC
Q 028376 122 TKIEAVTRRILWIKSTDPKAKILVFSS-----WNDVLDVLEHAFIANNITCIKMKGENH 175 (210)
Q Consensus 122 sKi~al~~~L~~~~~~~~~~K~iVFSQ-----f~~~L~li~~~L~~~gi~~~~~~G~m~ 175 (210)
.+++.+.+.+++.+ -+=+|.|+. |.--.-.+...|++.||+|+.|+|.+.
T Consensus 348 ~R~~~l~~li~e~~----vDGVI~~~~~~C~~~s~e~~~ik~~l~~~GIP~L~ietD~~ 402 (430)
T TIGR03191 348 IKSEMMLNIARDWN----VDGCMLHLNRGCEGLSIGIMENRLAIAKAGIPIMTFEGNMG 402 (430)
T ss_pred HHHHHHHHHHHHHC----CCEEEEcCCCCCccchHhHHHHHHHHHHcCCCEEEEECCCC
Confidence 57777777666543 556777765 322223578899999999999999865
No 283
>PRK13280 N-glycosylase/DNA lyase; Provisional
Probab=48.80 E-value=19 Score=29.84 Aligned_cols=41 Identities=17% Similarity=0.197 Sum_probs=31.3
Q ss_pred chHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceE
Q 028376 122 TKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITC 167 (210)
Q Consensus 122 sKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~ 167 (210)
..++.|.+.|..+...++..|+|||+ ..+...++...+-.+
T Consensus 130 ~~l~~l~~~La~~L~s~~~~KTiVFA-----vKM~~Ya~r~~~~~~ 170 (269)
T PRK13280 130 EDLEELLEQLAKILGAKKESKTVVFA-----VKMFGYACRAAFGEF 170 (269)
T ss_pred hhHHHHHHHHHHHhCCCCCcceeeeH-----HHHHHHHHHHhcccc
Confidence 67899999999999999999999997 345555555444333
No 284
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=48.65 E-value=3.9 Score=20.95 Aligned_cols=7 Identities=43% Similarity=1.497 Sum_probs=3.2
Q ss_pred cccCCcc
Q 028376 72 MCPTCRQ 78 (210)
Q Consensus 72 ~CP~Cr~ 78 (210)
.||.|..
T Consensus 18 fC~~CG~ 24 (26)
T PF13248_consen 18 FCPNCGA 24 (26)
T ss_pred cChhhCC
Confidence 4444443
No 285
>PF10879 DUF2674: Protein of unknown function (DUF2674); InterPro: IPR024246 This family of proteins with unknown function appears to be restricted to Rickettsia spp.
Probab=48.20 E-value=37 Score=20.88 Aligned_cols=35 Identities=14% Similarity=0.347 Sum_probs=28.2
Q ss_pred cCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeC
Q 028376 137 TDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKG 172 (210)
Q Consensus 137 ~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G 172 (210)
++|..|+|-||-...-++.|....+ .||..+++--
T Consensus 2 qnp~qk~isfsehkadierikk~ie-egwaivklvp 36 (67)
T PF10879_consen 2 QNPTQKVISFSEHKADIERIKKSIE-EGWAIVKLVP 36 (67)
T ss_pred CCchhceeehhhhhhhHHHHHHHHh-cCeEEEEEcc
Confidence 3688999999999998888887764 6888887744
No 286
>cd01521 RHOD_PspE2 Member of the Rhodanese Homology Domain superfamily. This CD includes the putative rhodanese-like protein, Psp2, of Yersinia pestis biovar Medievalis and other similar uncharacterized proteins.
Probab=48.18 E-value=33 Score=23.73 Aligned_cols=38 Identities=11% Similarity=0.059 Sum_probs=28.3
Q ss_pred CCCCcEEEEcchH--HHHHHHHHHHHhCCceEEEeeCCCC
Q 028376 138 DPKAKILVFSSWN--DVLDVLEHAFIANNITCIKMKGENH 175 (210)
Q Consensus 138 ~~~~K~iVFSQf~--~~L~li~~~L~~~gi~~~~~~G~m~ 175 (210)
+++.++|||.+-. .....+...|...|+....++|++.
T Consensus 62 ~~~~~vvvyc~~g~~~~s~~~a~~l~~~G~~v~~l~GG~~ 101 (110)
T cd01521 62 DKEKLFVVYCDGPGCNGATKAALKLAELGFPVKEMIGGLD 101 (110)
T ss_pred CCCCeEEEEECCCCCchHHHHHHHHHHcCCeEEEecCCHH
Confidence 4577888887633 3556677888999998777899853
No 287
>PHA02653 RNA helicase NPH-II; Provisional
Probab=48.12 E-value=93 Score=29.46 Aligned_cols=46 Identities=7% Similarity=0.042 Sum_probs=39.2
Q ss_pred CCcEEEEcchHHHHHHHHHHHHhC--CceEEEeeCCCCCCcchhhHhhhHHHHHHh
Q 028376 140 KAKILVFSSWNDVLDVLEHAFIAN--NITCIKMKGENHKLPSANLQHRNALQKELT 193 (210)
Q Consensus 140 ~~K~iVFSQf~~~L~li~~~L~~~--gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~ 193 (210)
+.++|||-.-..-.+.+...|... |+...-+.|.|+ ++.++++.|.
T Consensus 395 ~g~iLVFlpg~~ei~~l~~~L~~~~~~~~v~~LHG~Ls--------q~eq~l~~ff 442 (675)
T PHA02653 395 GSSGIVFVASVSQCEEYKKYLEKRLPIYDFYIIHGKVP--------NIDEILEKVY 442 (675)
T ss_pred CCcEEEEECcHHHHHHHHHHHHhhcCCceEEeccCCcC--------HHHHHHHHHh
Confidence 458999999999999999999987 799999999966 4577888884
No 288
>PRK09751 putative ATP-dependent helicase Lhr; Provisional
Probab=48.09 E-value=89 Score=32.45 Aligned_cols=51 Identities=12% Similarity=0.134 Sum_probs=39.9
Q ss_pred CCcEEEEcchHHHHHHHHHHHHhCC---------------------------------ceEEEeeCCCCCCcchhhHhhh
Q 028376 140 KAKILVFSSWNDVLDVLEHAFIANN---------------------------------ITCIKMKGENHKLPSANLQHRN 186 (210)
Q Consensus 140 ~~K~iVFSQf~~~L~li~~~L~~~g---------------------------------i~~~~~~G~m~~~~~~~~~~R~ 186 (210)
..++|||..-....+.+...|.+.+ +...-+.|+|+ ..+|.
T Consensus 244 ~~stLVFvNSR~~AE~La~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ia~~HHGsLS------keeR~ 317 (1490)
T PRK09751 244 HRSTIVFTNSRGLAEKLTARLNELYAARLQRSPSIAVDAAHFESTSGATSNRVQSSDVFIARSHHGSVS------KEQRA 317 (1490)
T ss_pred CCCEEEECCCHHHHHHHHHHHHHhhhhhccccccccchhhhhhhccccchhccccccceeeeeccccCC------HHHHH
Confidence 5689999999999888888886531 11345679965 99999
Q ss_pred HHHHHHhhcC
Q 028376 187 ALQKELTRHM 196 (210)
Q Consensus 187 ~~l~~F~~~~ 196 (210)
.+.+.|+++.
T Consensus 318 ~IE~~fK~G~ 327 (1490)
T PRK09751 318 ITEQALKSGE 327 (1490)
T ss_pred HHHHHHHhCC
Confidence 9999999843
No 289
>PRK09694 helicase Cas3; Provisional
Probab=47.63 E-value=1.3e+02 Score=29.38 Aligned_cols=62 Identities=11% Similarity=0.138 Sum_probs=46.8
Q ss_pred HHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCC---ceEEEeeCCCCCCcchhhHhh----hHHHHHHhh
Q 028376 125 EAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANN---ITCIKMKGENHKLPSANLQHR----NALQKELTR 194 (210)
Q Consensus 125 ~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~g---i~~~~~~G~m~~~~~~~~~~R----~~~l~~F~~ 194 (210)
+++++.|.+... .+.+++||..-..-..-+-..|++.+ +....+.|.+. ..+| .++++.|.+
T Consensus 547 ~~~l~~i~~~~~--~g~~vLVf~NTV~~Aq~ly~~L~~~~~~~~~v~llHsrf~------~~dR~~~E~~vl~~fgk 615 (878)
T PRK09694 547 LTLLQRMIAAAN--AGAQVCLICNLVDDAQKLYQRLKELNNTQVDIDLFHARFT------LNDRREKEQRVIENFGK 615 (878)
T ss_pred HHHHHHHHHHHh--cCCEEEEEECCHHHHHHHHHHHHhhCCCCceEEEEeCCCC------HHHHHHHHHHHHHHHHh
Confidence 455566654432 36789999999999888988998765 67888999977 7777 567889944
No 290
>PF06844 DUF1244: Protein of unknown function (DUF1244); InterPro: IPR009654 This family consists of several short bacterial proteins of around 100 residues in length. The function of this family is unknown.; PDB: 2O35_A 3FYB_B.
Probab=47.00 E-value=13 Score=23.85 Aligned_cols=14 Identities=14% Similarity=0.278 Sum_probs=9.8
Q ss_pred cchHhhHHHHHHHh
Q 028376 46 FTCCKCFFAMTEQR 59 (210)
Q Consensus 46 ~fC~~C~~~~~~~~ 59 (210)
.||+.|+.+|....
T Consensus 11 gFCRNCLskWy~~a 24 (68)
T PF06844_consen 11 GFCRNCLSKWYREA 24 (68)
T ss_dssp S--HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHH
Confidence 39999999998653
No 291
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=46.98 E-value=9.8 Score=33.24 Aligned_cols=35 Identities=26% Similarity=0.512 Sum_probs=23.7
Q ss_pred CCccccccccccccCC----CeecCCCCcchHhhHHHHH
Q 028376 22 ADEETCPICQEKLGNQ----KMVFQCGHFTCCKCFFAMT 56 (210)
Q Consensus 22 ~~~~~C~iC~~~~~~~----~~~~~CgH~fC~~C~~~~~ 56 (210)
..-..|+.|...+.-. .+.=.|||-||..|...|.
T Consensus 304 ~~wr~CpkC~~~ie~~~GCnhm~CrC~~~fcy~C~~~~~ 342 (384)
T KOG1812|consen 304 KRWRQCPKCKFMIELSEGCNHMTCRCGHQFCYMCGGDWK 342 (384)
T ss_pred HhcCcCcccceeeeecCCcceEEeeccccchhhcCcchh
Confidence 3456799997654321 1333599999999998873
No 292
>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=46.56 E-value=16 Score=22.00 Aligned_cols=30 Identities=20% Similarity=0.472 Sum_probs=22.0
Q ss_pred cccccccccccCCCeecCCCCcchHhhHHH
Q 028376 25 ETCPICQEKLGNQKMVFQCGHFTCCKCFFA 54 (210)
Q Consensus 25 ~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~ 54 (210)
..|..|...+........=|.++|..|..+
T Consensus 27 f~C~~C~~~l~~~~~~~~~~~~~C~~c~~~ 56 (58)
T PF00412_consen 27 FKCSKCGKPLNDGDFYEKDGKPYCKDCYQK 56 (58)
T ss_dssp SBETTTTCBTTTSSEEEETTEEEEHHHHHH
T ss_pred cccCCCCCccCCCeeEeECCEEECHHHHhh
Confidence 467788877776556666778888888765
No 293
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 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. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=46.16 E-value=20 Score=19.92 Aligned_cols=32 Identities=16% Similarity=0.571 Sum_probs=15.8
Q ss_pred chHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376 47 TCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD 81 (210)
Q Consensus 47 fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~ 81 (210)
+|.+|..++... ...+-......|+.|+-.+.
T Consensus 1 lC~~C~~Ey~~p---~~RR~~~~~isC~~CGPr~~ 32 (35)
T PF07503_consen 1 LCDDCLKEYFDP---SNRRFHYQFISCTNCGPRYS 32 (35)
T ss_dssp --HHHHHHHCST---TSTTTT-TT--BTTCC-SCC
T ss_pred CCHHHHHHHcCC---CCCcccCcCccCCCCCCCEE
Confidence 488898887422 11222355667999987654
No 294
>TIGR02196 GlrX_YruB Glutaredoxin-like protein, YruB-family. This glutaredoxin-like protein family contains the conserved CxxC motif and includes the Clostridium pasteurianum protein YruB which has been cloned from a rubredoxin operon. Somewhat related to NrdH, it is unknown whether this protein actually interacts with glutathione/glutathione reducatase, or, like NrdH, some other reductant system.
Probab=45.86 E-value=68 Score=19.49 Aligned_cols=31 Identities=13% Similarity=0.282 Sum_probs=20.7
Q ss_pred EEEEc-chHHHHHHHHHHHHhCCceEEEeeCC
Q 028376 143 ILVFS-SWNDVLDVLEHAFIANNITCIKMKGE 173 (210)
Q Consensus 143 ~iVFS-Qf~~~L~li~~~L~~~gi~~~~~~G~ 173 (210)
+.+|+ .|-..-..+...|.+.|+.|...+=.
T Consensus 2 i~lf~~~~C~~C~~~~~~l~~~~i~~~~vdi~ 33 (74)
T TIGR02196 2 VKVYTTPWCPPCKKAKEYLTSKGIAFEEIDVE 33 (74)
T ss_pred EEEEcCCCChhHHHHHHHHHHCCCeEEEEecc
Confidence 34444 46666666777788888888777654
No 295
>cd01523 RHOD_Lact_B Member of the Rhodanese Homology Domain superfamily. This CD includes predicted proteins with rhodanese-like domains found N-terminal of the metallo-beta-lactamase domain.
Probab=45.58 E-value=31 Score=23.21 Aligned_cols=38 Identities=5% Similarity=0.053 Sum_probs=27.7
Q ss_pred CCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCC
Q 028376 138 DPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENH 175 (210)
Q Consensus 138 ~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~ 175 (210)
+++.++||+..--..-......|...|+....+.|++.
T Consensus 59 ~~~~~ivv~C~~G~rs~~aa~~L~~~G~~~~~l~GG~~ 96 (100)
T cd01523 59 PDDQEVTVICAKEGSSQFVAELLAERGYDVDYLAGGMK 96 (100)
T ss_pred CCCCeEEEEcCCCCcHHHHHHHHHHcCceeEEeCCcHH
Confidence 34556777766544556778899999999777899854
No 296
>PRK02362 ski2-like helicase; Provisional
Probab=45.42 E-value=98 Score=29.44 Aligned_cols=49 Identities=12% Similarity=0.109 Sum_probs=35.4
Q ss_pred CCCcEEEEcchHHHHHHHHHHHHh--------------------------------------CCceEEEeeCCCCCCcch
Q 028376 139 PKAKILVFSSWNDVLDVLEHAFIA--------------------------------------NNITCIKMKGENHKLPSA 180 (210)
Q Consensus 139 ~~~K~iVFSQf~~~L~li~~~L~~--------------------------------------~gi~~~~~~G~m~~~~~~ 180 (210)
++.++|||..-......+...|.. .|+ ..+.|+|+
T Consensus 242 ~~~~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~L~~~l~~gv--a~hHagl~----- 314 (737)
T PRK02362 242 EGGQCLVFVSSRRNAEGFAKRAASALKKTLTAAERAELAELAEEIREVSDTETSKDLADCVAKGA--AFHHAGLS----- 314 (737)
T ss_pred cCCCeEEEEeCHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHhccCccccHHHHHHHHhCE--EeecCCCC-----
Confidence 467999998876665555444432 244 44689966
Q ss_pred hhHhhhHHHHHHhhc
Q 028376 181 NLQHRNALQKELTRH 195 (210)
Q Consensus 181 ~~~~R~~~l~~F~~~ 195 (210)
..+|..+.+.|+++
T Consensus 315 -~~eR~~ve~~Fr~G 328 (737)
T PRK02362 315 -REHRELVEDAFRDR 328 (737)
T ss_pred -HHHHHHHHHHHHcC
Confidence 99999999999974
No 297
>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]
Probab=45.28 E-value=1.6e+02 Score=27.23 Aligned_cols=70 Identities=10% Similarity=0.068 Sum_probs=59.0
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCC
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPS 198 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~ 198 (210)
..-++-|+..|+.-.+ .+++++|=+-=..|-.-+...|.+.||+...++.... .-+|..+|...+.+.=|
T Consensus 429 ~~QvdDL~~EI~~r~~--~~eRvLVTtLTKkmAEdLT~Yl~e~gikv~YlHSdid------TlER~eIirdLR~G~~D 498 (663)
T COG0556 429 KGQVDDLLSEIRKRVA--KNERVLVTTLTKKMAEDLTEYLKELGIKVRYLHSDID------TLERVEIIRDLRLGEFD 498 (663)
T ss_pred CCcHHHHHHHHHHHHh--cCCeEEEEeehHHHHHHHHHHHHhcCceEEeeeccch------HHHHHHHHHHHhcCCcc
Confidence 3568888888887654 3699999999999999999999999999888888854 89999999998875443
No 298
>PRK11595 DNA utilization protein GntX; Provisional
Probab=45.02 E-value=19 Score=28.82 Aligned_cols=40 Identities=23% Similarity=0.440 Sum_probs=26.0
Q ss_pred cccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCccccc
Q 028376 25 ETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTD 81 (210)
Q Consensus 25 ~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~ 81 (210)
..|.+|...+... .+.+|..|...+- .-...||.|..+..
T Consensus 6 ~~C~~C~~~~~~~------~~~lC~~C~~~l~-----------~~~~~C~~Cg~~~~ 45 (227)
T PRK11595 6 GLCWLCRMPLALS------HWGICSVCSRALR-----------TLKTCCPQCGLPAT 45 (227)
T ss_pred CcCccCCCccCCC------CCcccHHHHhhCC-----------cccCcCccCCCcCC
Confidence 4699998765321 2348999988761 11247999987653
No 299
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=44.82 E-value=16 Score=25.31 Aligned_cols=50 Identities=22% Similarity=0.496 Sum_probs=26.7
Q ss_pred ccccccccccCCCeecCCC-------CcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376 26 TCPICQEKLGNQKMVFQCG-------HFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG 83 (210)
Q Consensus 26 ~C~iC~~~~~~~~~~~~Cg-------H~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~ 83 (210)
.|.-|.+.+..-+ +.+-+ -++|.-|...+....- .....||.|+.++.+.
T Consensus 37 aCy~CHdel~~Hp-f~p~~~~~~~~~~iiCGvC~~~LT~~EY-------~~~~~Cp~C~spFNp~ 93 (105)
T COG4357 37 ACYHCHDELEDHP-FEPWGLQEFNPKAIICGVCRKLLTRAEY-------GMCGSCPYCQSPFNPG 93 (105)
T ss_pred hHHHHHhHHhcCC-CccCChhhcCCccEEhhhhhhhhhHHHH-------hhcCCCCCcCCCCCcc
Confidence 4666766665421 11111 1456667666532211 2344699999888654
No 300
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=44.74 E-value=16 Score=28.00 Aligned_cols=23 Identities=22% Similarity=0.531 Sum_probs=14.5
Q ss_pred cCchHHHHHhcCCCCcccccccc
Q 028376 9 SNSTKHRIESLSKADEETCPICQ 31 (210)
Q Consensus 9 ~~~~~~~~~~l~~~~~~~C~iC~ 31 (210)
...++..++.+.......|++|.
T Consensus 119 ~~~~~~~Le~~~~~~~~vC~vCG 141 (166)
T COG1592 119 AEMFRGLLERLEEGKVWVCPVCG 141 (166)
T ss_pred HHHHHHHHHhhhcCCEEEcCCCC
Confidence 34455666777666667777773
No 301
>cd01449 TST_Repeat_2 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue.
Probab=44.64 E-value=85 Score=21.61 Aligned_cols=37 Identities=16% Similarity=0.099 Sum_probs=27.3
Q ss_pred CCCCcEEEEcchHHHHHHHHHHHHhCCce-EEEeeCCC
Q 028376 138 DPKAKILVFSSWNDVLDVLEHAFIANNIT-CIKMKGEN 174 (210)
Q Consensus 138 ~~~~K~iVFSQf~~~L~li~~~L~~~gi~-~~~~~G~m 174 (210)
+++.++|||..--.-...+...|...|++ ...|+|++
T Consensus 76 ~~~~~iv~yc~~g~~s~~~~~~l~~~G~~~v~~l~GG~ 113 (118)
T cd01449 76 TPDKPVIVYCGSGVTACVLLLALELLGYKNVRLYDGSW 113 (118)
T ss_pred CCCCCEEEECCcHHHHHHHHHHHHHcCCCCeeeeCChH
Confidence 45778888877544556677889999995 66789985
No 302
>PF12773 DZR: Double zinc ribbon
Probab=44.56 E-value=17 Score=21.47 Aligned_cols=16 Identities=19% Similarity=0.545 Sum_probs=10.1
Q ss_pred CccccccCCcccccCC
Q 028376 68 NEWVMCPTCRQRTDIG 83 (210)
Q Consensus 68 ~~~~~CP~Cr~~~~~~ 83 (210)
.....||.|...+...
T Consensus 27 ~~~~~C~~Cg~~~~~~ 42 (50)
T PF12773_consen 27 QSKKICPNCGAENPPN 42 (50)
T ss_pred CCCCCCcCCcCCCcCC
Confidence 3456788887765443
No 303
>TIGR02263 benz_CoA_red_C benzoyl-CoA reductase, subunit C. This model describes C subunit of benzoyl-CoA reductase, a 4-subunit enzyme. Many aromatic compounds are metabolized by way of benzoyl-CoA. This enzyme acts under anaerobic conditions.
Probab=44.53 E-value=96 Score=26.97 Aligned_cols=64 Identities=9% Similarity=-0.018 Sum_probs=41.3
Q ss_pred hHHHHHHHHHHHHhcCCCCcEEEEcc-----hHHHHHHHHHHHHhCCceEEEeeCCCCCCcchh-hHhhhHHHHHHhh
Q 028376 123 KIEAVTRRILWIKSTDPKAKILVFSS-----WNDVLDVLEHAFIANNITCIKMKGENHKLPSAN-LQHRNALQKELTR 194 (210)
Q Consensus 123 Ki~al~~~L~~~~~~~~~~K~iVFSQ-----f~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~-~~~R~~~l~~F~~ 194 (210)
+++.|++.+++.+ -+=+|.|.. |.--.-.|...|++.||+|+.++-+.. +. ..|=...|++|..
T Consensus 309 R~~~i~~lvke~~----aDGVI~~~~~~C~~~~~e~~~lk~~l~e~GIP~L~id~~~~----~~~~~q~~t~~~~f~e 378 (380)
T TIGR02263 309 KGKYLLDQVRKNA----AEGVIFAAPSFCDPALLERPMLAARCKEHGIPQIAFKYAEN----SGQMQPIREQAGTFAD 378 (380)
T ss_pred HHHHHHHHHHHhC----CCEEEEhHhhcCChhhhhHHHHHHHHHHCCCCEEEEEecCc----cchHHHHHHHHHHHHh
Confidence 6766776666533 344555544 344456778999999999999865532 22 2555667788865
No 304
>COG3310 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.46 E-value=77 Score=24.23 Aligned_cols=21 Identities=33% Similarity=0.756 Sum_probs=18.8
Q ss_pred EcchHHHHHHHHHHHHhCCce
Q 028376 146 FSSWNDVLDVLEHAFIANNIT 166 (210)
Q Consensus 146 FSQf~~~L~li~~~L~~~gi~ 166 (210)
|--|.+|+|+++..+.++|+.
T Consensus 91 F~d~n~~ld~~dA~i~~~~~e 111 (196)
T COG3310 91 FDDFNDMLDIADAAIVENGLE 111 (196)
T ss_pred hhHHHHHHHHHHHHHHhcCcc
Confidence 777999999999999999884
No 305
>COG1205 Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only]
Probab=44.35 E-value=84 Score=30.61 Aligned_cols=70 Identities=10% Similarity=0.137 Sum_probs=51.8
Q ss_pred chHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHH----HHHHhCC----ceEEEeeCCCCCCcchhhHhhhHHHHHHh
Q 028376 122 TKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLE----HAFIANN----ITCIKMKGENHKLPSANLQHRNALQKELT 193 (210)
Q Consensus 122 sKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~----~~L~~~g----i~~~~~~G~m~~~~~~~~~~R~~~l~~F~ 193 (210)
++...+-..+.... ..+.|.++|.-+.....++. ..+...| .....|.|+|. ..+|.++...|.
T Consensus 290 s~~~~~~~~~~~~~--~~~~~tL~F~~sr~~~e~~~~~~~~~~~~~~~~l~~~v~~~~~~~~------~~er~~ie~~~~ 361 (851)
T COG1205 290 SALAELATLAALLV--RNGIQTLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLH------REERRRIEAEFK 361 (851)
T ss_pred chHHHHHHHHHHHH--HcCceEEEEEehhhhhhhhhhchhHHHhhcchhhhhheeeccccCC------HHHHHHHHHHHh
Confidence 44444333333333 24899999999999999996 6666666 66778899977 999999999999
Q ss_pred hcCCCC
Q 028376 194 RHMPSS 199 (210)
Q Consensus 194 ~~~p~~ 199 (210)
.++..+
T Consensus 362 ~g~~~~ 367 (851)
T COG1205 362 EGELLG 367 (851)
T ss_pred cCCccE
Confidence 866544
No 306
>PRK00142 putative rhodanese-related sulfurtransferase; Provisional
Probab=43.82 E-value=96 Score=26.26 Aligned_cols=39 Identities=5% Similarity=0.031 Sum_probs=28.2
Q ss_pred cCCCCcEEEEcchHHHHHHHHHHHHhCCce-EEEeeCCCC
Q 028376 137 TDPKAKILVFSSWNDVLDVLEHAFIANNIT-CIKMKGENH 175 (210)
Q Consensus 137 ~~~~~K~iVFSQf~~~L~li~~~L~~~gi~-~~~~~G~m~ 175 (210)
..++.++|||.+--.--......|.+.|+. ...++|++.
T Consensus 168 ~~kdk~IvvyC~~G~Rs~~aa~~L~~~Gf~~V~~L~GGi~ 207 (314)
T PRK00142 168 PLKDKKVVMYCTGGIRCEKASAWMKHEGFKEVYQLEGGII 207 (314)
T ss_pred CCCcCeEEEECCCCcHHHHHHHHHHHcCCCcEEEecchHH
Confidence 346778999987444445667788899996 667899943
No 307
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=43.56 E-value=17 Score=27.54 Aligned_cols=26 Identities=23% Similarity=0.441 Sum_probs=21.2
Q ss_pred CCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376 44 GHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG 83 (210)
Q Consensus 44 gH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~ 83 (210)
.+-||..|-.+.+. .||.|..+++-.
T Consensus 27 ~~~fC~kCG~~tI~--------------~Cp~C~~~IrG~ 52 (158)
T PF10083_consen 27 REKFCSKCGAKTIT--------------SCPNCSTPIRGD 52 (158)
T ss_pred HHHHHHHhhHHHHH--------------HCcCCCCCCCCc
Confidence 46799999988763 699999998765
No 308
>TIGR02181 GRX_bact Glutaredoxin, GrxC family. This family of glutaredoxins includes the E. coli protein GrxC (Grx3) which appears to have a secondary role in reducing ribonucleotide reductase (in the absence of GrxA) possibly indicating a role in the reduction of other protein disulfides.
Probab=43.36 E-value=72 Score=20.31 Aligned_cols=32 Identities=3% Similarity=0.180 Sum_probs=22.2
Q ss_pred EEEc-chHHHHHHHHHHHHhCCceEEEeeCCCC
Q 028376 144 LVFS-SWNDVLDVLEHAFIANNITCIKMKGENH 175 (210)
Q Consensus 144 iVFS-Qf~~~L~li~~~L~~~gi~~~~~~G~m~ 175 (210)
+||+ .|-..-.-+...|++.||.|..++-.+.
T Consensus 2 ~ly~~~~Cp~C~~a~~~L~~~~i~~~~~di~~~ 34 (79)
T TIGR02181 2 TIYTKPYCPYCTRAKALLSSKGVTFTEIRVDGD 34 (79)
T ss_pred EEEecCCChhHHHHHHHHHHcCCCcEEEEecCC
Confidence 3444 4666677777888888888877776643
No 309
>PRK00076 recR recombination protein RecR; Reviewed
Probab=43.33 E-value=1.6e+02 Score=23.22 Aligned_cols=68 Identities=7% Similarity=0.119 Sum_probs=46.7
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcc-----hHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSS-----WNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQ-----f~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
.-+++.|++.+ + .+.|-||+-- -..+...|...|+..++++.|+--+.|....+.-......-+.|.+
T Consensus 120 ~l~i~~L~~ri----~--~~v~EVIlA~~pt~EGe~Ta~yi~~~lk~~~ikvtRiA~GiP~G~~ley~D~~TL~~Al~~ 192 (196)
T PRK00076 120 DLNIDELLERL----D--GEVKEVILATNPTVEGEATAHYIARLLKPLGVKVTRLAHGVPVGGELEYVDEGTLSRALEG 192 (196)
T ss_pred ccCHHHHHHHH----h--CCCCEEEEeCCCCchHHHHHHHHHHHHHHcCCCeeeeeeCCCCCcceeeCCHHHHHHHHHh
Confidence 45778888877 1 2456666544 3345677889999999999999888886666655555555555553
No 310
>cd01542 PBP1_TreR_like Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of TreR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding wh
Probab=43.28 E-value=81 Score=24.73 Aligned_cols=19 Identities=11% Similarity=0.088 Sum_probs=7.5
Q ss_pred HHHHHHHHHHHhCCceEEE
Q 028376 151 DVLDVLEHAFIANNITCIK 169 (210)
Q Consensus 151 ~~L~li~~~L~~~gi~~~~ 169 (210)
.+++-++.++.+.|+....
T Consensus 16 ~~~~gi~~~~~~~g~~~~~ 34 (259)
T cd01542 16 RTVKGILAALYENGYQMLL 34 (259)
T ss_pred HHHHHHHHHHHHCCCEEEE
Confidence 3333344444444443333
No 311
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=42.96 E-value=13 Score=26.63 Aligned_cols=31 Identities=29% Similarity=0.742 Sum_probs=20.5
Q ss_pred Ccccccccccccc----CCCeecCCCCcchHhhHH
Q 028376 23 DEETCPICQEKLG----NQKMVFQCGHFTCCKCFF 53 (210)
Q Consensus 23 ~~~~C~iC~~~~~----~~~~~~~CgH~fC~~C~~ 53 (210)
+...|.+|..++. ....-..|+|.+|..|-.
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~ 87 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGV 87 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEE
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCC
Confidence 5678999987653 123457888999988854
No 312
>PRK13844 recombination protein RecR; Provisional
Probab=41.80 E-value=1.3e+02 Score=23.81 Aligned_cols=69 Identities=7% Similarity=0.016 Sum_probs=47.3
Q ss_pred CCchHHHHHHHHHHHHhcCCCCcEEEEcc-----hHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 120 YGTKIEAVTRRILWIKSTDPKAKILVFSS-----WNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQ-----f~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
..-+++.|++.+.+ ...+=||+.- -..+...|...|+. |++..|+--+.|....+.-......-..|.+
T Consensus 123 ~~l~i~~L~~Ri~~-----~~v~EVIlAt~~t~EGe~Ta~yi~~~lk~-~vkvtRlA~GiP~G~~ley~D~~TL~~Al~~ 196 (200)
T PRK13844 123 SELKLDILQQIIAD-----RKIDEVILAISPTVEGETTAHFISQMIAK-DIKISRIGFGVPFGGELEYLDQQTLLHAFNA 196 (200)
T ss_pred hhcCHHHHHHHHhc-----CCCcEEEEeCCCCccHHHHHHHHHHHhcC-CCcEEeeeecCcCCcceeecCHHHHHHHHHh
Confidence 34678888877762 2455555543 23456678888988 9999999888886666666666666666654
No 313
>COG3172 NadR Predicted ATPase/kinase involved in NAD metabolism [Coenzyme metabolism]
Probab=41.77 E-value=56 Score=25.24 Aligned_cols=25 Identities=28% Similarity=0.506 Sum_probs=21.6
Q ss_pred hHHHHHHHHHHHHhCCceEEEeeCC
Q 028376 149 WNDVLDVLEHAFIANNITCIKMKGE 173 (210)
Q Consensus 149 f~~~L~li~~~L~~~gi~~~~~~G~ 173 (210)
=..|-.+++.+|.+++++|+.++|.
T Consensus 141 R~~F~~~l~~~L~~~~~~~v~i~~~ 165 (187)
T COG3172 141 RQEFQNLLEQMLEENNIPFVVIEGE 165 (187)
T ss_pred HHHHHHHHHHHHHHhCCcEEEEcCC
Confidence 3467788999999999999999994
No 314
>cd03419 GRX_GRXh_1_2_like Glutaredoxin (GRX) family, GRX human class 1 and 2 (h_1_2)-like subfamily; composed of proteins similar to human GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH - GSH reductase - GSH - GRX - protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes
Probab=41.65 E-value=45 Score=21.27 Aligned_cols=32 Identities=9% Similarity=0.097 Sum_probs=24.0
Q ss_pred cEEEEcc-hHHHHHHHHHHHHhCCceEEEeeCC
Q 028376 142 KILVFSS-WNDVLDVLEHAFIANNITCIKMKGE 173 (210)
Q Consensus 142 K~iVFSQ-f~~~L~li~~~L~~~gi~~~~~~G~ 173 (210)
|+++|+. |-..-..+...|.+.++.|..++=.
T Consensus 1 ~v~~y~~~~Cp~C~~~~~~l~~~~~~~~~~~v~ 33 (82)
T cd03419 1 PVVVFSKSYCPYCKRAKSLLKELGVKPAVVELD 33 (82)
T ss_pred CEEEEEcCCCHHHHHHHHHHHHcCCCcEEEEEe
Confidence 4667766 8888888888898888877666543
No 315
>COG1201 Lhr Lhr-like helicases [General function prediction only]
Probab=40.97 E-value=1.4e+02 Score=29.02 Aligned_cols=67 Identities=13% Similarity=0.063 Sum_probs=54.1
Q ss_pred hHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCC-ceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376 123 KIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANN-ITCIKMKGENHKLPSANLQHRNALQKELTRHMP 197 (210)
Q Consensus 123 Ki~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~g-i~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p 197 (210)
=..++++.|.++.++ ...++||..-.++-..+...|...+ ....-=+|+ ||..+|..+=++|.++..
T Consensus 238 ~~~~~~~~i~~~v~~--~~ttLIF~NTR~~aE~l~~~L~~~~~~~i~~HHgS------lSre~R~~vE~~lk~G~l 305 (814)
T COG1201 238 LWAALYERIAELVKK--HRTTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGS------LSRELRLEVEERLKEGEL 305 (814)
T ss_pred hhHHHHHHHHHHHhh--cCcEEEEEeChHHHHHHHHHHHHhcCCceeeeccc------ccHHHHHHHHHHHhcCCc
Confidence 345566677666655 3489999999999999999999987 777777899 559999999999998553
No 316
>TIGR02190 GlrX-dom Glutaredoxin-family domain. This C-terminal domain with homology to glutaredoxin is fused to an N-terminal peroxiredoxin-like domain.
Probab=40.96 E-value=53 Score=21.20 Aligned_cols=34 Identities=6% Similarity=0.013 Sum_probs=27.6
Q ss_pred CCcEEEEcc-hHHHHHHHHHHHHhCCceEEEeeCC
Q 028376 140 KAKILVFSS-WNDVLDVLEHAFIANNITCIKMKGE 173 (210)
Q Consensus 140 ~~K~iVFSQ-f~~~L~li~~~L~~~gi~~~~~~G~ 173 (210)
..+++||+. |-.+-..+...|+..||.|..++=.
T Consensus 7 ~~~V~ly~~~~Cp~C~~ak~~L~~~gi~y~~idi~ 41 (79)
T TIGR02190 7 PESVVVFTKPGCPFCAKAKATLKEKGYDFEEIPLG 41 (79)
T ss_pred CCCEEEEECCCCHhHHHHHHHHHHcCCCcEEEECC
Confidence 567777775 8888888999999999999887644
No 317
>cd01534 4RHOD_Repeat_3 Member of the Rhodanese Homology Domain superfamily, repeat 3. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 3rd repeat which does not contain the putative catalytic Cys residue.
Probab=40.84 E-value=41 Score=22.45 Aligned_cols=37 Identities=11% Similarity=0.008 Sum_probs=25.7
Q ss_pred CCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCC
Q 028376 139 PKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENH 175 (210)
Q Consensus 139 ~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~ 175 (210)
++.++|+|.+--.--......|...|+....++|++.
T Consensus 55 ~~~~iv~~c~~G~rs~~aa~~L~~~G~~v~~l~GG~~ 91 (95)
T cd01534 55 RGARIVLADDDGVRADMTASWLAQMGWEVYVLEGGLA 91 (95)
T ss_pred CCCeEEEECCCCChHHHHHHHHHHcCCEEEEecCcHH
Confidence 3567888887433334556778899999555799853
No 318
>cd02066 GRX_family Glutaredoxin (GRX) family; composed of GRX, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH - GSH reductase - GSH - GRX - protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes are known including human GRX1 and GRX2, as well as E. coli GRX1 and GRX3, which
Probab=40.82 E-value=81 Score=18.94 Aligned_cols=33 Identities=18% Similarity=0.085 Sum_probs=25.6
Q ss_pred cEEEEc-chHHHHHHHHHHHHhCCceEEEeeCCC
Q 028376 142 KILVFS-SWNDVLDVLEHAFIANNITCIKMKGEN 174 (210)
Q Consensus 142 K~iVFS-Qf~~~L~li~~~L~~~gi~~~~~~G~m 174 (210)
++++|+ .|-..-..+...|.++|+.|..++=..
T Consensus 1 ~v~ly~~~~Cp~C~~~~~~L~~~~i~~~~~di~~ 34 (72)
T cd02066 1 KVVVFSKSTCPYCKRAKRLLESLGIEFEEIDILE 34 (72)
T ss_pred CEEEEECCCCHHHHHHHHHHHHcCCcEEEEECCC
Confidence 355555 688888889999999999998886653
No 319
>cd01529 4RHOD_Repeats Member of the Rhodanese Homology Domain superfamily. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. Only the second and most of the fourth repeats contain the putative catalytic Cys residue. This CD aligns the 1st , 2nd, 3rd, and 4th repeats.
Probab=40.54 E-value=1.1e+02 Score=20.30 Aligned_cols=38 Identities=5% Similarity=0.032 Sum_probs=27.3
Q ss_pred CCCCcEEEEcchHHHHHHHHHHHHhCCce-EEEeeCCCC
Q 028376 138 DPKAKILVFSSWNDVLDVLEHAFIANNIT-CIKMKGENH 175 (210)
Q Consensus 138 ~~~~K~iVFSQf~~~L~li~~~L~~~gi~-~~~~~G~m~ 175 (210)
.++.++||+..-..........|...|+. ...++|+|.
T Consensus 54 ~~~~~ivv~c~~g~~s~~~~~~l~~~G~~~v~~l~GG~~ 92 (96)
T cd01529 54 GRATRYVLTCDGSLLARFAAQELLALGGKPVALLDGGTS 92 (96)
T ss_pred CCCCCEEEEeCChHHHHHHHHHHHHcCCCCEEEeCCCHH
Confidence 45678888887655556667778889985 555799853
No 320
>PF07209 DUF1415: Protein of unknown function (DUF1415); InterPro: IPR009858 This family consists of several hypothetical bacterial proteins of around 180 residues in length. The function of this family is unknown.
Probab=40.41 E-value=1.7e+02 Score=22.66 Aligned_cols=73 Identities=18% Similarity=0.362 Sum_probs=45.6
Q ss_pred CccccccCCcccccCCCeEEccCccccCCCCCCCCCCCCcccccCCceecCCCCchHHHHHHHHHHHHhcCC---CCcEE
Q 028376 68 NEWVMCPTCRQRTDIGNIAYADDRQDKSCNSDMPHGVQDCEKGEESFTVQGSYGTKIEAVTRRILWIKSTDP---KAKIL 144 (210)
Q Consensus 68 ~~~~~CP~Cr~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~SsKi~al~~~L~~~~~~~~---~~K~i 144 (210)
-+-.-||.-+++.....|.+...... ....=++.|.+.+..+....+ ..-.|
T Consensus 17 IglNLCPFAk~~~~~~~Ir~~V~~a~-------------------------~~~~ll~~l~~El~~L~~~~~~~ieTTLl 71 (174)
T PF07209_consen 17 IGLNLCPFAKRPRVKGQIRYVVSEAT-------------------------DPEDLLEDLLEELQRLAADDEPEIETTLL 71 (174)
T ss_pred hccCCCCCCCccccCCCEEEEEeCCC-------------------------CHHHHHHHHHHHHHHHhcCCccccceEEE
Confidence 34558999999998888877663210 001235566666666633221 23335
Q ss_pred EEc-------chHHHHHHHHHHHHhCCc
Q 028376 145 VFS-------SWNDVLDVLEHAFIANNI 165 (210)
Q Consensus 145 VFS-------Qf~~~L~li~~~L~~~gi 165 (210)
||- .|.++|++++..|...|+
T Consensus 72 i~P~~l~dF~dy~dfl~~a~~ll~~~~~ 99 (174)
T PF07209_consen 72 IFPNGLDDFDDYNDFLDMADALLEELGL 99 (174)
T ss_pred ECCCcccCHHHHHHHHHHHHHHHHHcCC
Confidence 543 477778888888988776
No 321
>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.
Probab=40.28 E-value=20 Score=28.96 Aligned_cols=26 Identities=23% Similarity=0.700 Sum_probs=20.0
Q ss_pred chHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376 47 TCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG 83 (210)
Q Consensus 47 fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~ 83 (210)
-|..|-..+ ....+.||+|...-+..
T Consensus 196 ~C~sC~qqI-----------HRNAPiCPlCK~KsRSr 221 (230)
T PF10146_consen 196 TCQSCHQQI-----------HRNAPICPLCKAKSRSR 221 (230)
T ss_pred hhHhHHHHH-----------hcCCCCCcccccccccC
Confidence 489999887 46778999998765443
No 322
>PF14353 CpXC: CpXC protein
Probab=40.21 E-value=24 Score=25.47 Aligned_cols=17 Identities=18% Similarity=0.469 Sum_probs=13.0
Q ss_pred CCccccccCCcccccCC
Q 028376 67 KNEWVMCPTCRQRTDIG 83 (210)
Q Consensus 67 ~~~~~~CP~Cr~~~~~~ 83 (210)
.-....||.|+..+...
T Consensus 35 ~l~~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 35 SLFSFTCPSCGHKFRLE 51 (128)
T ss_pred CcCEEECCCCCCceecC
Confidence 35577899999987654
No 323
>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=40.21 E-value=20 Score=19.27 Aligned_cols=10 Identities=20% Similarity=0.687 Sum_probs=6.9
Q ss_pred cccccccccC
Q 028376 27 CPICQEKLGN 36 (210)
Q Consensus 27 C~iC~~~~~~ 36 (210)
|..|...+..
T Consensus 2 C~~C~~~i~~ 11 (39)
T smart00132 2 CAGCGKPIRG 11 (39)
T ss_pred ccccCCcccC
Confidence 7778776654
No 324
>PRK01172 ski2-like helicase; Provisional
Probab=40.15 E-value=1.4e+02 Score=28.00 Aligned_cols=49 Identities=12% Similarity=0.173 Sum_probs=35.3
Q ss_pred CCCcEEEEcchHHHHHHHHHHHHh---------------------------CCceEEEeeCCCCCCcchhhHhhhHHHHH
Q 028376 139 PKAKILVFSSWNDVLDVLEHAFIA---------------------------NNITCIKMKGENHKLPSANLQHRNALQKE 191 (210)
Q Consensus 139 ~~~K~iVFSQf~~~L~li~~~L~~---------------------------~gi~~~~~~G~m~~~~~~~~~~R~~~l~~ 191 (210)
.+.++|||..-..-...+...|.. .||. .+.|+|+ ..+|..+.+.
T Consensus 235 ~~~~vLVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~--~~hagl~------~~eR~~ve~~ 306 (674)
T PRK01172 235 DGGQVLVFVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVA--FHHAGLS------NEQRRFIEEM 306 (674)
T ss_pred CCCcEEEEeccHHHHHHHHHHHHHhhhhcccccccccccccccHHHHHHHhcCEE--EecCCCC------HHHHHHHHHH
Confidence 367899998876655555554433 2444 3689866 9999999999
Q ss_pred Hhhc
Q 028376 192 LTRH 195 (210)
Q Consensus 192 F~~~ 195 (210)
|.++
T Consensus 307 f~~g 310 (674)
T PRK01172 307 FRNR 310 (674)
T ss_pred HHcC
Confidence 9974
No 325
>PRK12902 secA preprotein translocase subunit SecA; Reviewed
Probab=39.72 E-value=1.3e+02 Score=29.63 Aligned_cols=51 Identities=14% Similarity=0.085 Sum_probs=45.2
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCC
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGE 173 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~ 173 (210)
-.|..|+++.+.+.... +-=++|-+.....-++|...|.++||++..+..+
T Consensus 422 ~~K~~Ai~~ei~~~~~~--GrPVLIgT~SVe~SE~ls~~L~~~gi~h~vLNAk 472 (939)
T PRK12902 422 IAKWRAVANETAEMHKQ--GRPVLVGTTSVEKSELLSALLQEQGIPHNLLNAK 472 (939)
T ss_pred HHHHHHHHHHHHHHHhC--CCCEEEeeCCHHHHHHHHHHHHHcCCchheeeCC
Confidence 47899999999987654 6779999999999999999999999999888776
No 326
>cd01519 RHOD_HSP67B2 Member of the Rhodanese Homology Domain superfamily. This CD includes the heat shock protein 67B2 of Drosophila melanogaster and other similar proteins, many of which are uncharacterized.
Probab=39.52 E-value=50 Score=22.28 Aligned_cols=38 Identities=3% Similarity=-0.081 Sum_probs=27.3
Q ss_pred CCCCcEEEEcchHHHHHHHHHHHHhCCce-EEEeeCCCC
Q 028376 138 DPKAKILVFSSWNDVLDVLEHAFIANNIT-CIKMKGENH 175 (210)
Q Consensus 138 ~~~~K~iVFSQf~~~L~li~~~L~~~gi~-~~~~~G~m~ 175 (210)
+++..+|||..--..-..+...|...|+. ...|+|+|.
T Consensus 64 ~~~~~ivv~c~~g~~s~~~~~~l~~~G~~~v~~~~Gg~~ 102 (106)
T cd01519 64 SKDKELIFYCKAGVRSKAAAELARSLGYENVGNYPGSWL 102 (106)
T ss_pred CCCCeEEEECCCcHHHHHHHHHHHHcCCccceecCCcHH
Confidence 34667888877655556778889999996 455788853
No 327
>PF09419 PGP_phosphatase: Mitochondrial PGP phosphatase; InterPro: IPR010021 This group of hypothetical proteins is a part of the IIIA subfamily of the haloacid dehalogenase (HAD) superfamily of hydrolases. All characterised members of this subfamily and most characterised members of the HAD superfamily are phosphatases. HAD superfamily phosphatases contain active site residues in several conserved catalytic motifs [], all of which are found conserved here. This family consists of sequences from fungi, plants, cyanobacteria, Gram-positive bacteria and Deinococcus. There is presently no characterisation of any sequence in this family.
Probab=39.39 E-value=1.7e+02 Score=22.36 Aligned_cols=63 Identities=13% Similarity=0.045 Sum_probs=38.2
Q ss_pred chHHHHHHHHHHHHhcCCCCcEEEEcchHH-----HHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 122 TKIEAVTRRILWIKSTDPKAKILVFSSWND-----VLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 122 sKi~al~~~L~~~~~~~~~~K~iVFSQf~~-----~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
..+...++. +++..+.++++|+|.-.. --.-++..-+.-||+++++.-+. +.-+..+++.|..
T Consensus 62 ~~~~~~~~~---l~~~~~~~~v~IvSNsaGs~~d~~~~~a~~~~~~lgIpvl~h~~kK-------P~~~~~i~~~~~~ 129 (168)
T PF09419_consen 62 PEYAEWLNE---LKKQFGKDRVLIVSNSAGSSDDPDGERAEALEKALGIPVLRHRAKK-------PGCFREILKYFKC 129 (168)
T ss_pred HHHHHHHHH---HHHHCCCCeEEEEECCCCcccCccHHHHHHHHHhhCCcEEEeCCCC-------CccHHHHHHHHhh
Confidence 444444444 445666779999999631 11233334445679988875433 4556678888875
No 328
>PRK14701 reverse gyrase; Provisional
Probab=38.80 E-value=75 Score=33.32 Aligned_cols=59 Identities=8% Similarity=0.048 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHhcCCCCcEEEEcchHH---HHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCCC
Q 028376 125 EAVTRRILWIKSTDPKAKILVFSSWND---VLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPSS 199 (210)
Q Consensus 125 ~al~~~L~~~~~~~~~~K~iVFSQf~~---~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~~ 199 (210)
..|++.|..+ +..+|||.+-.. ..+.+...|..+||+...+.| .|.++++.|.+++-++
T Consensus 320 ~~L~~ll~~~-----g~~gIVF~~t~~~~e~ae~la~~L~~~Gi~a~~~h~-----------~R~~~l~~F~~G~~~V 381 (1638)
T PRK14701 320 EHVRELLKKL-----GKGGLIFVPIDEGAEKAEEIEKYLLEDGFKIELVSA-----------KNKKGFDLFEEGEIDY 381 (1638)
T ss_pred HHHHHHHHhC-----CCCeEEEEeccccchHHHHHHHHHHHCCCeEEEecc-----------hHHHHHHHHHcCCCCE
Confidence 4555554432 458999987543 468899999999999988877 3889999999865543
No 329
>TIGR00376 DNA helicase, putative. The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases.
Probab=38.76 E-value=1.6e+02 Score=27.68 Aligned_cols=56 Identities=16% Similarity=0.197 Sum_probs=44.2
Q ss_pred ecCCCC-chHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCC
Q 028376 116 VQGSYG-TKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGE 173 (210)
Q Consensus 116 ~~~~~S-sKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~ 173 (210)
+.|.|+ -|...+++.+..+... +.+++|.+.-....+-|-..|...|+.++|+-+.
T Consensus 178 I~GpPGTGKT~t~~~ii~~~~~~--g~~VLv~a~sn~Avd~l~e~l~~~~~~vvRlg~~ 234 (637)
T TIGR00376 178 IHGPPGTGKTRTLVELIRQLVKR--GLRVLVTAPSNIAVDNLLERLALCDQKIVRLGHP 234 (637)
T ss_pred EEcCCCCCHHHHHHHHHHHHHHc--CCCEEEEcCcHHHHHHHHHHHHhCCCcEEEeCCc
Confidence 456555 5877777777766644 4599999999999999999999989999999655
No 330
>TIGR03249 KdgD 5-dehydro-4-deoxyglucarate dehydratase. 5-dehydro-4-deoxyglucarate dehydratase not only catalyzes the dehydration of the substrate (diol to ketone + water), but causes the decarboxylation of the intermediate product to yield 2-oxoglutarate semialdehyde (2,5-dioxopentanoate). The gene for the enzyme is usually observed in the vicinity of transporters and dehydratases handling D-galactarate and D-gluconate as well as aldehyde dehydrogenases which convert the product to alpha-ketoglutarate.
Probab=37.88 E-value=88 Score=26.05 Aligned_cols=33 Identities=6% Similarity=0.014 Sum_probs=26.5
Q ss_pred hCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 162 ANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 162 ~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
.+|+.-+.+-|+..+...|+.++|.++++....
T Consensus 37 ~~Gv~gi~v~GstGE~~~Lt~eEr~~v~~~~~~ 69 (296)
T TIGR03249 37 GYGLEALFAAGGTGEFFSLTPAEYEQVVEIAVS 69 (296)
T ss_pred hcCCCEEEECCCCcCcccCCHHHHHHHHHHHHH
Confidence 477777778888888888888888888887765
No 331
>cd00408 DHDPS-like Dihydrodipicolinate synthase family. A member of the class I aldolases, which use an active-site lysine which stablilzes a reaction intermediate via Schiff base formation, and have TIM beta/alpha barrel fold. The dihydrodipicolinate synthase family comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways and includes such proteins as N-acetylneuraminate lyase, MosA protein, 5-keto-4-deoxy-glucarate dehydratase, trans-o-hydroxybenzylidenepyruvate hydratase-aldolase, trans-2'-carboxybenzalpyruvate hydratase-aldolase, and 2-keto-3-deoxy- gluconate aldolase. The family is also referred to as the N-acetylneuraminate lyase (NAL) family.
Probab=37.87 E-value=82 Score=25.78 Aligned_cols=44 Identities=9% Similarity=0.215 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 150 NDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 150 ~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
..+-.+++..++ +|+.-+.+-|+..+...|+.++|.++++....
T Consensus 18 ~~~~~~i~~l~~-~Gv~gi~~~GstGE~~~ls~~Er~~l~~~~~~ 61 (281)
T cd00408 18 DALRRLVEFLIE-AGVDGLVVLGTTGEAPTLTDEERKEVIEAVVE 61 (281)
T ss_pred HHHHHHHHHHHH-cCCCEEEECCCCcccccCCHHHHHHHHHHHHH
Confidence 333333433333 47766677777777777888888887777665
No 332
>TIGR02260 benz_CoA_red_B benzoyl-CoA reductase, bcr type, subunit B. This model describes B, or beta, subunit of the bcr type of benzoyl-CoA reductase, a 4-subunit enzyme. Many aromatic compounds are metabolized by way of benzoyl-CoA.
Probab=37.79 E-value=1.8e+02 Score=25.62 Aligned_cols=67 Identities=4% Similarity=-0.036 Sum_probs=38.7
Q ss_pred hHHHHHHHHHHHHhcCCCCcEEEEcc-----hHHHHHHHHHHHHh-CCceEEEeeCCCCCCcchhhHhhhHHHHHHh
Q 028376 123 KIEAVTRRILWIKSTDPKAKILVFSS-----WNDVLDVLEHAFIA-NNITCIKMKGENHKLPSANLQHRNALQKELT 193 (210)
Q Consensus 123 Ki~al~~~L~~~~~~~~~~K~iVFSQ-----f~~~L~li~~~L~~-~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~ 193 (210)
+++.|++.+++.. -+=+|.|+. |.--...+...+.+ .||+|+.++|.+...+--+..|=..-|+.|-
T Consensus 338 R~~~l~~l~ke~~----aDGVI~~~~~~C~~~~~e~~~~~~~l~e~~GIP~L~iE~D~~d~r~~d~gQ~~TRiEAFl 410 (413)
T TIGR02260 338 RVDLLEKYINEYE----ADGLLINSIKSCNSFSAGQLLMMREIEKRTGKPAAFIETDLVDPRYFSAANVKNRLESYF 410 (413)
T ss_pred HHHHHHHHHHHhC----CCEEEEeccCCCCcchhhhHHHHHHHHHHcCCCEEEEEcCCCCcccCCHHHHHHHHHHHH
Confidence 5666666665433 455666655 34434555566654 8999999999865222223344444555553
No 333
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.
Probab=37.77 E-value=1.5e+02 Score=28.77 Aligned_cols=62 Identities=16% Similarity=0.253 Sum_probs=40.6
Q ss_pred HHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHh----CCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376 124 IEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIA----NNITCIKMKGENHKLPSANLQHRNALQKELTRH 195 (210)
Q Consensus 124 i~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~----~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~ 195 (210)
.+++.+.|.++....+ .+++||-.--.+++.+...|.. .++..+. .|. ...|.+++++|..+
T Consensus 659 ~~~ia~~i~~l~~~~~-g~~LVlftS~~~l~~v~~~L~~~~~~~~~~~l~-q~~--------~~~r~~ll~~F~~~ 724 (850)
T TIGR01407 659 AQEIASYIIEITAITS-PKILVLFTSYEMLHMVYDMLNELPEFEGYEVLA-QGI--------NGSRAKIKKRFNNG 724 (850)
T ss_pred HHHHHHHHHHHHHhcC-CCEEEEeCCHHHHHHHHHHHhhhccccCceEEe-cCC--------CccHHHHHHHHHhC
Confidence 3466666666655444 4788777777777888888865 4555322 232 24789999999973
No 334
>cd01447 Polysulfide_ST Polysulfide-sulfurtransferase - Rhodanese Homology Domain. This domain is believed to serve as a polysulfide binding and transferase domain in anaerobic gram-negative bacteria, functioning in oxidative phosphorylation with polysulfide-sulfur as a terminal electron acceptor. The active site contains the same conserved cysteine that is the catalytic residue in other Rhodanese Homology Domain proteins.
Probab=37.71 E-value=34 Score=22.95 Aligned_cols=38 Identities=3% Similarity=0.041 Sum_probs=27.2
Q ss_pred CCCCcEEEEcchHHHHHHHHHHHHhCCce-EEEeeCCCC
Q 028376 138 DPKAKILVFSSWNDVLDVLEHAFIANNIT-CIKMKGENH 175 (210)
Q Consensus 138 ~~~~K~iVFSQf~~~L~li~~~L~~~gi~-~~~~~G~m~ 175 (210)
+++.++|||.+--.........|...|+. ...|+|++.
T Consensus 59 ~~~~~ivv~c~~g~~s~~~~~~l~~~G~~~v~~l~Gg~~ 97 (103)
T cd01447 59 AEDKPFVFYCASGWRSALAGKTLQDMGLKPVYNIEGGFK 97 (103)
T ss_pred CCCCeEEEEcCCCCcHHHHHHHHHHcChHHhEeecCcHH
Confidence 45678888886533445667888899987 567899853
No 335
>PRK13111 trpA tryptophan synthase subunit alpha; Provisional
Probab=37.58 E-value=2.3e+02 Score=23.25 Aligned_cols=51 Identities=14% Similarity=0.284 Sum_probs=35.4
Q ss_pred CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHH----HHHHHHHhCCceEEEe
Q 028376 120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLD----VLEHAFIANNITCIKM 170 (210)
Q Consensus 120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~----li~~~L~~~gi~~~~~ 170 (210)
.+.+++.+++.+.++++..++..+|+++=|..++. -.-..+.+.|+.=+-+
T Consensus 69 ~G~~~~~~~~~~~~~r~~~~~~p~vlm~Y~N~i~~~G~e~f~~~~~~aGvdGvii 123 (258)
T PRK13111 69 AGVTLADVFELVREIREKDPTIPIVLMTYYNPIFQYGVERFAADAAEAGVDGLII 123 (258)
T ss_pred cCCCHHHHHHHHHHHHhcCCCCCEEEEecccHHhhcCHHHHHHHHHHcCCcEEEE
Confidence 35778889999999986677888899998877655 2334444556544444
No 336
>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=36.45 E-value=12 Score=19.27 Aligned_cols=12 Identities=33% Similarity=0.786 Sum_probs=8.8
Q ss_pred ccccCCcccccC
Q 028376 71 VMCPTCRQRTDI 82 (210)
Q Consensus 71 ~~CP~Cr~~~~~ 82 (210)
..||+|.+.+..
T Consensus 2 v~CPiC~~~v~~ 13 (26)
T smart00734 2 VQCPVCFREVPE 13 (26)
T ss_pred CcCCCCcCcccH
Confidence 369999887633
No 337
>PRK05580 primosome assembly protein PriA; Validated
Probab=36.39 E-value=52 Score=31.07 Aligned_cols=50 Identities=8% Similarity=0.075 Sum_probs=38.6
Q ss_pred EcchHHHHHHHHHHHHhC--CceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCCC
Q 028376 146 FSSWNDVLDVLEHAFIAN--NITCIKMKGENHKLPSANLQHRNALQKELTRHMPSS 199 (210)
Q Consensus 146 FSQf~~~L~li~~~L~~~--gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~~ 199 (210)
|.....-.+.++..|++. |++..++||.+. .+..+|+++++.|.+++++.
T Consensus 432 l~~~g~G~e~~~e~l~~~fp~~~v~~~~~d~~----~~~~~~~~~l~~f~~g~~~I 483 (679)
T PRK05580 432 LVPVGPGTERLEEELAELFPEARILRIDRDTT----RRKGALEQLLAQFARGEADI 483 (679)
T ss_pred eEEeeccHHHHHHHHHHhCCCCcEEEEecccc----ccchhHHHHHHHHhcCCCCE
Confidence 444455678889999886 899999999875 33567999999999866553
No 338
>PLN02417 dihydrodipicolinate synthase
Probab=36.22 E-value=81 Score=26.07 Aligned_cols=43 Identities=7% Similarity=-0.018 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 151 DVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 151 ~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
.+-++++..+. +|+.-+-+-|+..+...|+.++|.++++....
T Consensus 23 ~~~~~i~~l~~-~Gv~Gi~~~GstGE~~~ls~~Er~~~~~~~~~ 65 (280)
T PLN02417 23 AYDSLVNMQIE-NGAEGLIVGGTTGEGQLMSWDEHIMLIGHTVN 65 (280)
T ss_pred HHHHHHHHHHH-cCCCEEEECccCcchhhCCHHHHHHHHHHHHH
Confidence 33334443333 56666667777777777777777777766554
No 339
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=36.14 E-value=24 Score=19.67 Aligned_cols=35 Identities=23% Similarity=0.378 Sum_probs=23.2
Q ss_pred EcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHh
Q 028376 146 FSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELT 193 (210)
Q Consensus 146 FSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~ 193 (210)
|+.|+. +-|...|..+||.+- .+ ...|...|+.-+
T Consensus 1 fdtWs~--~~L~~wL~~~gi~~~---~~--------~~~rd~Ll~~~k 35 (38)
T PF10281_consen 1 FDTWSD--SDLKSWLKSHGIPVP---KS--------AKTRDELLKLAK 35 (38)
T ss_pred CCCCCH--HHHHHHHHHcCCCCC---CC--------CCCHHHHHHHHH
Confidence 566666 678889999999852 11 236777776544
No 340
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=35.91 E-value=27 Score=29.99 Aligned_cols=56 Identities=23% Similarity=0.508 Sum_probs=29.1
Q ss_pred CCccccccccccccCC-CeecCCCCcchHhhHHHHHHHhhhcc-------ccCCCccccccCCccc
Q 028376 22 ADEETCPICQEKLGNQ-KMVFQCGHFTCCKCFFAMTEQRLIHD-------NKVKNEWVMCPTCRQR 79 (210)
Q Consensus 22 ~~~~~C~iC~~~~~~~-~~~~~CgH~fC~~C~~~~~~~~~~~~-------~~~~~~~~~CP~Cr~~ 79 (210)
...+.||+|.+....= .-++.|- -|..-+++.+++..... .-++..+.+||.||..
T Consensus 13 dl~ElCPVCGDkVSGYHYGLLTCE--SCKGFFKRTVQNnK~YtC~e~qnC~iDkTqRKRCP~CRFQ 76 (475)
T KOG4218|consen 13 DLGELCPVCGDKVSGYHYGLLTCE--SCKGFFKRTVQNNKQYTCSEEQNCHIDKTQRKRCPSCRFQ 76 (475)
T ss_pred ccccccccccCccccceeeeeehh--hhhhHHHHHhhcCcceecccccccccchHhhccCCchhHH
Confidence 4457899999877531 1233332 13333444443321110 0124566789999874
No 341
>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]
Probab=35.74 E-value=16 Score=31.63 Aligned_cols=32 Identities=19% Similarity=0.586 Sum_probs=24.2
Q ss_pred CCCcccccccccc-ccCCCeecCCCCcchHhhHH
Q 028376 21 KADEETCPICQEK-LGNQKMVFQCGHFTCCKCFF 53 (210)
Q Consensus 21 ~~~~~~C~iC~~~-~~~~~~~~~CgH~fC~~C~~ 53 (210)
......|..|... +.. ...++||-.||..|+.
T Consensus 36 ~~gk~~C~RC~~~~~~~-~~~lp~~~~YCr~Cl~ 68 (441)
T COG4098 36 ENGKYRCNRCGNTHIEL-FAKLPCGCLYCRNCLM 68 (441)
T ss_pred ccCcEEehhcCCcchhh-hcccccceEeehhhhh
Confidence 3455689999743 333 4678999999999997
No 342
>cd01533 4RHOD_Repeat_2 Member of the Rhodanese Homology Domain superfamily, repeat 2. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 2nd repeat which does contain the putative catalytic Cys residue.
Probab=35.54 E-value=1.2e+02 Score=20.62 Aligned_cols=38 Identities=13% Similarity=0.230 Sum_probs=25.9
Q ss_pred CCCCcEEEEcchHHHHHHHHHHHHhCCce--EEEeeCCCC
Q 028376 138 DPKAKILVFSSWNDVLDVLEHAFIANNIT--CIKMKGENH 175 (210)
Q Consensus 138 ~~~~K~iVFSQf~~~L~li~~~L~~~gi~--~~~~~G~m~ 175 (210)
+++..+|||.+--.--......|...|+. ...++|+|.
T Consensus 64 ~~~~~ivv~C~~G~rs~~a~~~L~~~G~~~~v~~l~gG~~ 103 (109)
T cd01533 64 DPRTPIVVNCAGRTRSIIGAQSLINAGLPNPVAALRNGTQ 103 (109)
T ss_pred CCCCeEEEECCCCchHHHHHHHHHHCCCCcceeEecCCHH
Confidence 34567888876433334466788999995 667899954
No 343
>PF00462 Glutaredoxin: Glutaredoxin; InterPro: IPR002109 Glutaredoxins [, , ], also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system []. Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond []. It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond. Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed [] that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro. This entry represents Glutaredoxin.; GO: 0009055 electron carrier activity, 0015035 protein disulfide oxidoreductase activity, 0045454 cell redox homeostasis; PDB: 1QFN_A 1GRX_A 1EGO_A 1EGR_A 3RHC_A 3RHB_A 3IPZ_A 1NHO_A 3GX8_A 3D5J_A ....
Probab=35.43 E-value=1e+02 Score=18.46 Aligned_cols=31 Identities=6% Similarity=0.041 Sum_probs=22.8
Q ss_pred EEEcc-hHHHHHHHHHHHHhCCceEEEeeCCC
Q 028376 144 LVFSS-WNDVLDVLEHAFIANNITCIKMKGEN 174 (210)
Q Consensus 144 iVFSQ-f~~~L~li~~~L~~~gi~~~~~~G~m 174 (210)
++|+. +-..-..+...|+..|++|..++=..
T Consensus 2 ~vy~~~~C~~C~~~~~~L~~~~i~y~~~dv~~ 33 (60)
T PF00462_consen 2 VVYTKPGCPYCKKAKEFLDEKGIPYEEVDVDE 33 (60)
T ss_dssp EEEESTTSHHHHHHHHHHHHTTBEEEEEEGGG
T ss_pred EEEEcCCCcCHHHHHHHHHHcCCeeeEccccc
Confidence 44544 55566778889999999998887663
No 344
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=35.09 E-value=20 Score=22.49 Aligned_cols=17 Identities=18% Similarity=0.382 Sum_probs=12.8
Q ss_pred cccccCCcccccCCCeE
Q 028376 70 WVMCPTCRQRTDIGNIA 86 (210)
Q Consensus 70 ~~~CP~Cr~~~~~~~l~ 86 (210)
+..||.|+.++..++.+
T Consensus 3 HkHC~~CG~~Ip~~~~f 19 (59)
T PF09889_consen 3 HKHCPVCGKPIPPDESF 19 (59)
T ss_pred CCcCCcCCCcCCcchhh
Confidence 45799999998776543
No 345
>PRK12899 secA preprotein translocase subunit SecA; Reviewed
Probab=34.85 E-value=1.6e+02 Score=29.09 Aligned_cols=51 Identities=20% Similarity=0.193 Sum_probs=44.7
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCC
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGE 173 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~ 173 (210)
..|..|+++.+...... +-=++|-+.....-+.+...|.++||++..+..+
T Consensus 551 ~~k~~ai~~ei~~~~~~--grPvLigt~si~~se~ls~~L~~~gi~h~vLNak 601 (970)
T PRK12899 551 REKYHAIVAEIASIHRK--GNPILIGTESVEVSEKLSRILRQNRIEHTVLNAK 601 (970)
T ss_pred HHHHHHHHHHHHHHHhC--CCCEEEEeCcHHHHHHHHHHHHHcCCcceecccc
Confidence 47889999999888754 5569999999999999999999999999888776
No 346
>cd00953 KDG_aldolase KDG (2-keto-3-deoxygluconate) aldolases found in archaea. This subfamily of enzymes is adapted for high thermostability and shows specificity for non-phosphorylated substrates. The enzyme catalyses the reversible aldol cleavage of 2-keto-3-dexoygluconate to pyruvate and glyceraldehyde, the third step of a modified non-phosphorylated Entner-Doudoroff pathway of glucose oxidation. KDG aldolase shows no significant sequence similarity to microbial 2-keto-3-deoxyphosphogluconate (KDPG) aldolases, and the enzyme shows no activity with glyceraldehyde 3-phosphate as substrate. The enzyme is a tetramer and a member of the DHDPS family of Schiff-base-dependent class I aldolases.
Probab=34.77 E-value=1.1e+02 Score=25.34 Aligned_cols=35 Identities=23% Similarity=0.316 Sum_probs=28.5
Q ss_pred HHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 160 FIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 160 L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
|..+|+.-+-+-|++.+...|+.++|.++++....
T Consensus 29 l~~~Gv~Gl~~~GstGE~~~Lt~eEr~~l~~~~~~ 63 (279)
T cd00953 29 LISKGIDYVFVAGTTGLGPSLSFQEKLELLKAYSD 63 (279)
T ss_pred HHHcCCcEEEEcccCCCcccCCHHHHHHHHHHHHH
Confidence 34578888888888888888999999998888765
No 347
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=34.38 E-value=7.8 Score=23.91 Aligned_cols=33 Identities=24% Similarity=0.627 Sum_probs=21.2
Q ss_pred Cccccc--cccccccC------CCeec-CCCCcchHhhHHHH
Q 028376 23 DEETCP--ICQEKLGN------QKMVF-QCGHFTCCKCFFAM 55 (210)
Q Consensus 23 ~~~~C~--iC~~~~~~------~~~~~-~CgH~fC~~C~~~~ 55 (210)
+...|| -|...+.. ..+.- .|||.||..|...|
T Consensus 17 ~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~ 58 (64)
T smart00647 17 DLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPW 58 (64)
T ss_pred CccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcC
Confidence 445688 78443321 12333 78999999998776
No 348
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=34.30 E-value=23 Score=33.59 Aligned_cols=57 Identities=23% Similarity=0.550 Sum_probs=36.9
Q ss_pred CccccccccccccCC-------C--eecCCCCcc--------------------hHhhHHHHHHHhhhccccCCCccccc
Q 028376 23 DEETCPICQEKLGNQ-------K--MVFQCGHFT--------------------CCKCFFAMTEQRLIHDNKVKNEWVMC 73 (210)
Q Consensus 23 ~~~~C~iC~~~~~~~-------~--~~~~CgH~f--------------------C~~C~~~~~~~~~~~~~~~~~~~~~C 73 (210)
|...|.-|..++.++ + -.|.||-.| |.+|..++... ...+-......|
T Consensus 67 D~a~C~~Cl~E~~dp~~Rry~YpF~nCt~CGPr~~i~~~lpydr~~t~m~~f~~C~~C~~ey~~p---~~rr~h~~~~~C 143 (711)
T TIGR00143 67 DVATCSDCLEEMLDKNDRRYLYPFISCTHCGPRFTIIEALPYDRENTSMADFPLCPDCAKEYKDP---LDRRFHAQPIAC 143 (711)
T ss_pred chhhHHHHHHHhcCCCcccccCCcccccCCCCCeEEeecCCCCCCCcCCCCCcCCHHHHHHhcCC---ccccCCCCCccC
Confidence 556799998877654 1 225666555 99999998321 222224566789
Q ss_pred cCCcccccC
Q 028376 74 PTCRQRTDI 82 (210)
Q Consensus 74 P~Cr~~~~~ 82 (210)
|.|.-.+..
T Consensus 144 ~~Cgp~l~l 152 (711)
T TIGR00143 144 PRCGPQLNF 152 (711)
T ss_pred CCCCcEEEE
Confidence 999887643
No 349
>KOG0344 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=34.26 E-value=1.8e+02 Score=27.00 Aligned_cols=68 Identities=21% Similarity=0.217 Sum_probs=52.2
Q ss_pred CCCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHH-HhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376 118 GSYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAF-IANNITCIKMKGENHKLPSANLQHRNALQKELTRH 195 (210)
Q Consensus 118 ~~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L-~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~ 195 (210)
|.-..|+-|+.+.+..- -.--++||-|--.--.-+-..| .-.+|..-.+.|..+ ..+|..++++|+.+
T Consensus 369 gse~~K~lA~rq~v~~g----~~PP~lIfVQs~eRak~L~~~L~~~~~i~v~vIh~e~~------~~qrde~~~~FR~g 437 (593)
T KOG0344|consen 369 GSEKGKLLALRQLVASG----FKPPVLIFVQSKERAKQLFEELEIYDNINVDVIHGERS------QKQRDETMERFRIG 437 (593)
T ss_pred ecchhHHHHHHHHHhcc----CCCCeEEEEecHHHHHHHHHHhhhccCcceeeEecccc------hhHHHHHHHHHhcc
Confidence 34456777777777654 3446899999877666666777 667888888999965 99999999999973
No 350
>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A.
Probab=34.23 E-value=2e+02 Score=21.94 Aligned_cols=57 Identities=26% Similarity=0.279 Sum_probs=36.8
Q ss_pred cCCC-CchHHHHHHHHHHH------HhcCCCCcEEEEcchHHHHHHHHHHHHh--------CCceEEEeeCC
Q 028376 117 QGSY-GTKIEAVTRRILWI------KSTDPKAKILVFSSWNDVLDVLEHAFIA--------NNITCIKMKGE 173 (210)
Q Consensus 117 ~~~~-SsKi~al~~~L~~~------~~~~~~~K~iVFSQf~~~L~li~~~L~~--------~gi~~~~~~G~ 173 (210)
.|.| +-|...+...+..+ ....++.+++|-++-...+|-+-..|.+ ..+.++|+...
T Consensus 23 ~GpPGTGKT~~l~~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~~~~~~~~~~~~~~ir~~~~ 94 (236)
T PF13086_consen 23 QGPPGTGKTTTLASIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKKLLDEDGKVYKPKIIRLGSE 94 (236)
T ss_dssp E-STTSSHHHHHHHHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC--------TT--EEE---G
T ss_pred ECCCCCChHHHHHHHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHhhccccccccccchhhhccc
Confidence 4444 45777777777776 2357889999999988888888888777 55667776443
No 351
>cd00158 RHOD Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins.
Probab=34.19 E-value=77 Score=20.14 Aligned_cols=40 Identities=13% Similarity=0.093 Sum_probs=30.2
Q ss_pred hcCCCCcEEEEcchHHHHHHHHHHHHhCCce-EEEeeCCCC
Q 028376 136 STDPKAKILVFSSWNDVLDVLEHAFIANNIT-CIKMKGENH 175 (210)
Q Consensus 136 ~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~-~~~~~G~m~ 175 (210)
...++.++||+..-......+...|...|.. ...+.|++.
T Consensus 46 ~~~~~~~vv~~c~~~~~a~~~~~~l~~~G~~~v~~l~gG~~ 86 (89)
T cd00158 46 ELDKDKPIVVYCRSGNRSARAAKLLRKAGGTNVYNLEGGML 86 (89)
T ss_pred ccCCCCeEEEEeCCCchHHHHHHHHHHhCcccEEEecCChh
Confidence 3456788888888767778889999999865 445788854
No 352
>PF10740 DUF2529: Protein of unknown function (DUF2529); InterPro: IPR019676 This entry represents a protein family conserved in the Bacillales. Their function is not known. ; PDB: 3JX9_A.
Probab=33.92 E-value=46 Score=25.67 Aligned_cols=34 Identities=18% Similarity=0.399 Sum_probs=21.8
Q ss_pred CCCCcEEEEcchHHHHH--HHHHHHHhCCceEEEee
Q 028376 138 DPKAKILVFSSWNDVLD--VLEHAFIANNITCIKMK 171 (210)
Q Consensus 138 ~~~~K~iVFSQf~~~L~--li~~~L~~~gi~~~~~~ 171 (210)
.+.+++++||-|..--+ -+...|...||+|+-+.
T Consensus 80 t~~DRVllfs~~~~~~e~~~~a~~L~~~gi~~v~Vs 115 (172)
T PF10740_consen 80 TETDRVLLFSPFSTDEEAVALAKQLIEQGIPFVGVS 115 (172)
T ss_dssp -TT-EEEEEES-S--HHHHHHHHHHHHHT--EEEEE
T ss_pred cccceEEEEeCCCCCHHHHHHHHHHHHCCCCEEEEE
Confidence 56899999999988733 34567889999999887
No 353
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=33.83 E-value=1.1e+02 Score=19.10 Aligned_cols=44 Identities=9% Similarity=0.071 Sum_probs=33.7
Q ss_pred HHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEe
Q 028376 127 VTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKM 170 (210)
Q Consensus 127 l~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~ 170 (210)
++...+.+..-.+++...|.+.......-|...++.+|..++..
T Consensus 14 ll~~~~~l~~l~~G~~l~v~~d~~~~~~di~~~~~~~g~~~~~~ 57 (70)
T PF01206_consen 14 LLKAKKALKELPPGEVLEVLVDDPAAVEDIPRWCEENGYEVVEV 57 (70)
T ss_dssp HHHHHHHHHTSGTT-EEEEEESSTTHHHHHHHHHHHHTEEEEEE
T ss_pred HHHHHHHHHhcCCCCEEEEEECCccHHHHHHHHHHHCCCEEEEE
Confidence 34444444455678888899999999999999999999998776
No 354
>PHA03050 glutaredoxin; Provisional
Probab=33.82 E-value=93 Score=21.78 Aligned_cols=32 Identities=6% Similarity=-0.045 Sum_probs=25.9
Q ss_pred CCcEEEEcc-hHHHHHHHHHHHHhCCc---eEEEee
Q 028376 140 KAKILVFSS-WNDVLDVLEHAFIANNI---TCIKMK 171 (210)
Q Consensus 140 ~~K~iVFSQ-f~~~L~li~~~L~~~gi---~~~~~~ 171 (210)
..+++|||. |-.+-..+...|+..|| .|..++
T Consensus 12 ~~~V~vys~~~CPyC~~ak~~L~~~~i~~~~~~~i~ 47 (108)
T PHA03050 12 NNKVTIFVKFTCPFCRNALDILNKFSFKRGAYEIVD 47 (108)
T ss_pred cCCEEEEECCCChHHHHHHHHHHHcCCCcCCcEEEE
Confidence 468999987 88888889999999999 565544
No 355
>cd01448 TST_Repeat_1 Thiosulfate sulfurtransferase (TST), N-terminal, inactive domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the 1st repeat, which does not contain the catalytically active Cys residue. The role of the 1st repeat is uncertain, but it is believed to be involved in protein interaction.
Probab=33.68 E-value=1e+02 Score=21.42 Aligned_cols=39 Identities=5% Similarity=-0.065 Sum_probs=27.2
Q ss_pred cCCCCcEEEEcch-HHHHHHHHHHHHhCCce-EEEeeCCCC
Q 028376 137 TDPKAKILVFSSW-NDVLDVLEHAFIANNIT-CIKMKGENH 175 (210)
Q Consensus 137 ~~~~~K~iVFSQf-~~~L~li~~~L~~~gi~-~~~~~G~m~ 175 (210)
.+++..+|||..- ..........|...|++ ...|+|++.
T Consensus 76 ~~~~~~vv~~c~~g~~~a~~~~~~l~~~G~~~v~~l~GG~~ 116 (122)
T cd01448 76 ISNDDTVVVYDDGGGFFAARAWWTLRYFGHENVRVLDGGLQ 116 (122)
T ss_pred CCCCCEEEEECCCCCccHHHHHHHHHHcCCCCEEEecCCHH
Confidence 3456667777765 24556677889999987 667799854
No 356
>PRK12901 secA preprotein translocase subunit SecA; Reviewed
Probab=33.56 E-value=95 Score=30.97 Aligned_cols=51 Identities=16% Similarity=0.179 Sum_probs=45.0
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCC
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGE 173 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~ 173 (210)
-.|..|+++.+.++... +-=+||=+.....-.+|...|..+||+|-.+..+
T Consensus 611 ~eK~~Aii~ei~~~~~~--GrPVLVGT~SVe~SE~lS~~L~~~gI~H~VLNAK 661 (1112)
T PRK12901 611 REKYNAVIEEITELSEA--GRPVLVGTTSVEISELLSRMLKMRKIPHNVLNAK 661 (1112)
T ss_pred HHHHHHHHHHHHHHHHC--CCCEEEEeCcHHHHHHHHHHHHHcCCcHHHhhcc
Confidence 47889999999988754 6779999999999999999999999999877665
No 357
>PLN02248 cellulose synthase-like protein
Probab=33.49 E-value=29 Score=34.41 Aligned_cols=34 Identities=21% Similarity=0.747 Sum_probs=26.1
Q ss_pred cCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCe
Q 028376 41 FQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNI 85 (210)
Q Consensus 41 ~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l 85 (210)
-.|++.+|.+|....+ .....||.|..+....+.
T Consensus 148 ~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~ 181 (1135)
T PLN02248 148 CECGFKICRDCYIDAV-----------KSGGICPGCKEPYKVTDL 181 (1135)
T ss_pred ccccchhHHhHhhhhh-----------hcCCCCCCCccccccccc
Confidence 3678999999998774 234589999998866554
No 358
>PRK03170 dihydrodipicolinate synthase; Provisional
Probab=33.48 E-value=1.1e+02 Score=25.27 Aligned_cols=32 Identities=13% Similarity=0.256 Sum_probs=23.9
Q ss_pred CCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 163 NNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 163 ~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
.|+.-+-+-|++.+...|+.++|.++++....
T Consensus 34 ~Gv~gi~~~Gs~GE~~~ls~~Er~~~~~~~~~ 65 (292)
T PRK03170 34 NGTDGLVVVGTTGESPTLTHEEHEELIRAVVE 65 (292)
T ss_pred cCCCEEEECCcCCccccCCHHHHHHHHHHHHH
Confidence 67766667777777777888888888777665
No 359
>PRK04023 DNA polymerase II large subunit; Validated
Probab=33.26 E-value=37 Score=33.38 Aligned_cols=50 Identities=20% Similarity=0.444 Sum_probs=33.6
Q ss_pred CccccccccccccCCCeecCCCC-----cchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376 23 DEETCPICQEKLGNQKMVFQCGH-----FTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA 86 (210)
Q Consensus 23 ~~~~C~iC~~~~~~~~~~~~CgH-----~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~ 86 (210)
....|+-|...... .....||. .||..|-.. .....||.|........-.
T Consensus 625 g~RfCpsCG~~t~~-frCP~CG~~Te~i~fCP~CG~~-------------~~~y~CPKCG~El~~~s~~ 679 (1121)
T PRK04023 625 GRRKCPSCGKETFY-RRCPFCGTHTEPVYRCPRCGIE-------------VEEDECEKCGREPTPYSKR 679 (1121)
T ss_pred cCccCCCCCCcCCc-ccCCCCCCCCCcceeCccccCc-------------CCCCcCCCCCCCCCccceE
Confidence 45679999876432 24456884 599999332 3345799999987765443
No 360
>cd08172 GlyDH-like1 Glycerol dehydrogenases-like. Glycerol dehydrogenases-like. The proteins in this family have not been characterized, but they show sequence homology with glycerol dehydrogenase. Glycerol dehydrogenases (GlyDH) is a key enzyme in the glycerol dissimilation pathway. In anaerobic conditions, many microorganisms utilize glycerol as a source of carbon through coupled oxidative and reductive pathways. One of the pathways involves the oxidation of glycerol to dihydroxyacetone with the reduction of NAD+ to NADH catalyzed by glycerol dehydrogenases. Dihydroxyacetone is then phosphorylated by dihydroxyacetone kinase and enters the glycolytic pathway for further degradation. The activity of GlyDH is zinc-dependent. The zinc ion plays a role in stabilizing an alkoxide intermediate at the active site.
Probab=33.13 E-value=2.6e+02 Score=23.77 Aligned_cols=64 Identities=11% Similarity=0.230 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHHhcCCCCcEEEEcc---hHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCC
Q 028376 124 IEAVTRRILWIKSTDPKAKILVFSS---WNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPS 198 (210)
Q Consensus 124 i~al~~~L~~~~~~~~~~K~iVFSQ---f~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~ 198 (210)
++.+-+.+.++ ..|++|.+. |..+.+.+...|+..++.+..|+|-.+ ...=.++++.+...++|
T Consensus 12 l~~l~~~~~~~-----~~~~liv~d~~~~~~~~~~l~~~L~~~~~~~~~~~~~p~------~~~v~~~~~~~~~~~~D 78 (347)
T cd08172 12 LDELGELLKRF-----GKRPLIVTGPRSWAAAKPYLPESLAAGEAFVLRYDGECS------EENIERLAAQAKENGAD 78 (347)
T ss_pred HHHHHHHHHHh-----CCeEEEEECHHHHHHHHHHHHHHHhcCeEEEEEeCCCCC------HHHHHHHHHHHHhcCCC
Confidence 44444444433 357766654 666777777778778888888888733 55556667777665554
No 361
>PF12646 DUF3783: Domain of unknown function (DUF3783); InterPro: IPR016621 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=32.97 E-value=66 Score=19.80 Aligned_cols=26 Identities=27% Similarity=0.420 Sum_probs=19.0
Q ss_pred CcEEEEcchHH-HHHHHHHHHHhCCce
Q 028376 141 AKILVFSSWND-VLDVLEHAFIANNIT 166 (210)
Q Consensus 141 ~K~iVFSQf~~-~L~li~~~L~~~gi~ 166 (210)
++.++|+.|++ -|+.+=..+++.|++
T Consensus 1 e~~ll~~g~~~~el~~~l~~~r~~~~~ 27 (58)
T PF12646_consen 1 EEFLLFSGFSGEELDKFLDALRKAGIP 27 (58)
T ss_pred CCEEEECCCCHHHHHHHHHHHHHcCCC
Confidence 36778888876 577777777777774
No 362
>CHL00122 secA preprotein translocase subunit SecA; Validated
Probab=32.66 E-value=1.9e+02 Score=28.23 Aligned_cols=51 Identities=14% Similarity=0.137 Sum_probs=44.5
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCC
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGE 173 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~ 173 (210)
-.|..|+++.+.+.... +-=++|-+.....-+.|...|..+||++..+..+
T Consensus 407 ~~K~~AI~~ei~~~~~~--grPVLIgT~SIe~SE~ls~~L~~~gi~h~vLNAk 457 (870)
T CHL00122 407 LSKWRAIADECLQMHQT--GRPILIGTTTIEKSELLSQLLKEYRLPHQLLNAK 457 (870)
T ss_pred HHHHHHHHHHHHHHHhc--CCCEEEeeCCHHHHHHHHHHHHHcCCccceeeCC
Confidence 46888999999877643 6779999999999999999999999999888876
No 363
>KOG4451 consensus Uncharacterized conserved protein (tumor-associated antigen HCA127 in humans) [Function unknown]
Probab=32.64 E-value=31 Score=27.85 Aligned_cols=26 Identities=19% Similarity=0.680 Sum_probs=19.4
Q ss_pred chHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376 47 TCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG 83 (210)
Q Consensus 47 fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~ 83 (210)
.|..|-.++ ....+.||+|....+..
T Consensus 251 ~ClsChqqI-----------HRNAPiCPlCKaKsRSr 276 (286)
T KOG4451|consen 251 VCLSCHQQI-----------HRNAPICPLCKAKSRSR 276 (286)
T ss_pred HHHHHHHHH-----------hcCCCCCcchhhccccC
Confidence 588888877 46778999998765443
No 364
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=32.53 E-value=26 Score=20.49 Aligned_cols=24 Identities=21% Similarity=0.703 Sum_probs=16.1
Q ss_pred cccccccccCCCeecCCCCcchHhh
Q 028376 27 CPICQEKLGNQKMVFQCGHFTCCKC 51 (210)
Q Consensus 27 C~iC~~~~~~~~~~~~CgH~fC~~C 51 (210)
|..|..... -.+-+.|+|++|..-
T Consensus 2 C~~C~~~~~-l~~CL~C~~~~c~~~ 25 (50)
T smart00290 2 CSVCGTIEN-LWLCLTCGQVGCGRY 25 (50)
T ss_pred cccCCCcCC-eEEecCCCCcccCCC
Confidence 677765443 356788999998543
No 365
>cd06322 PBP1_ABC_sugar_binding_like_12 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=32.00 E-value=1.4e+02 Score=23.44 Aligned_cols=7 Identities=14% Similarity=0.453 Sum_probs=3.0
Q ss_pred CceEEEe
Q 028376 164 NITCIKM 170 (210)
Q Consensus 164 gi~~~~~ 170 (210)
++.-+-+
T Consensus 55 ~vdgiii 61 (267)
T cd06322 55 KVDAIVL 61 (267)
T ss_pred CCCEEEE
Confidence 4444444
No 366
>KOG2066 consensus Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport]
Probab=31.89 E-value=16 Score=34.75 Aligned_cols=32 Identities=31% Similarity=0.695 Sum_probs=25.2
Q ss_pred ccccccccccc------CCCeecCCCCcchHhhHHHHH
Q 028376 25 ETCPICQEKLG------NQKMVFQCGHFTCCKCFFAMT 56 (210)
Q Consensus 25 ~~C~iC~~~~~------~~~~~~~CgH~fC~~C~~~~~ 56 (210)
..|..|.++.. ....++.|||.|+..|+.-..
T Consensus 785 ~rc~~c~~~~l~~~~~~~~~~v~~c~h~yhk~c~~~~~ 822 (846)
T KOG2066|consen 785 ERCSSCFEPNLPSGAAFDSVVVFHCGHMYHKECLMMES 822 (846)
T ss_pred hhhhhhcccccccCcccceeeEEEccchhhhcccccHH
Confidence 47999988765 234778999999999998653
No 367
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=31.53 E-value=29 Score=30.64 Aligned_cols=39 Identities=23% Similarity=0.399 Sum_probs=26.0
Q ss_pred CCCccccccccccccCCCeecCCCCcchHhhHHHHHHHh
Q 028376 21 KADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQR 59 (210)
Q Consensus 21 ~~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~ 59 (210)
-.+=+.|..|...+.-..+...=+-.||..|....+++.
T Consensus 299 Hv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tlekC 337 (468)
T KOG1701|consen 299 HVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTLEKC 337 (468)
T ss_pred cccceehHhhhhhhccccccccCCcccchHHHHHHHHHH
Confidence 344566777766665544555667788888888777654
No 368
>PRK13103 secA preprotein translocase subunit SecA; Reviewed
Probab=31.35 E-value=1.1e+02 Score=29.93 Aligned_cols=51 Identities=12% Similarity=0.064 Sum_probs=44.4
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCC
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGE 173 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~ 173 (210)
..|..|+++.+.++... +-=+||-+.....-+.|...|.+.||++-.+.-+
T Consensus 432 ~eK~~Ai~~ei~~~~~~--GrPVLVGT~SVe~SE~ls~~L~~~gi~h~VLNAk 482 (913)
T PRK13103 432 EEKYAAIITDIKECMAL--GRPVLVGTATIETSEHMSNLLKKEGIEHKVLNAK 482 (913)
T ss_pred HHHHHHHHHHHHHHHhC--CCCEEEEeCCHHHHHHHHHHHHHcCCcHHHhccc
Confidence 57889999999988754 6779999999999999999999999999766655
No 369
>COG4047 Uncharacterized protein conserved in archaea [Function unknown]
Probab=31.20 E-value=61 Score=25.88 Aligned_cols=27 Identities=19% Similarity=0.278 Sum_probs=21.1
Q ss_pred chHHHHHHHHHHHHhcCCCCcEEEEcc
Q 028376 122 TKIEAVTRRILWIKSTDPKAKILVFSS 148 (210)
Q Consensus 122 sKi~al~~~L~~~~~~~~~~K~iVFSQ 148 (210)
-.+..+.+.|......++..|.+|||=
T Consensus 123 edm~~l~~~la~~lg~d~esKT~VFsV 149 (243)
T COG4047 123 EDMSLLLEALARALGADRESKTVVFSV 149 (243)
T ss_pred hhHHHHHHHHHHHhCCCcccceEEEEe
Confidence 345567777777777899999999993
No 370
>PRK09860 putative alcohol dehydrogenase; Provisional
Probab=31.05 E-value=2.3e+02 Score=24.60 Aligned_cols=45 Identities=18% Similarity=0.132 Sum_probs=25.2
Q ss_pred HHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCCC
Q 028376 152 VLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPSS 199 (210)
Q Consensus 152 ~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~~ 199 (210)
+++.+...|+++||.+..|+|-.++ =+...=.++++.++...+|.
T Consensus 47 ~~~~v~~~L~~~~i~~~~f~~v~~n---p~~~~v~~~~~~~~~~~~D~ 91 (383)
T PRK09860 47 MAGDVQKALEERNIFSVIYDGTQPN---PTTENVAAGLKLLKENNCDS 91 (383)
T ss_pred cHHHHHHHHHHcCCeEEEeCCCCCC---cCHHHHHHHHHHHHHcCCCE
Confidence 5667777777777777777764320 11333444555555544443
No 371
>TIGR01689 EcbF-BcbF capsule biosynthesis phosphatase. Due to the likelihood that the substrates of these enzymes are different depending on the nature of the particular polysaccharides associated with each species, this model has been classified as a subfamily despite the close homology.
Probab=30.70 E-value=1.6e+02 Score=21.29 Aligned_cols=44 Identities=18% Similarity=0.170 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHhcCCCCcEEEEcc--hH-----------HHHHHHHHHHHhCCceEEEe
Q 028376 125 EAVTRRILWIKSTDPKAKILVFSS--WN-----------DVLDVLEHAFIANNITCIKM 170 (210)
Q Consensus 125 ~al~~~L~~~~~~~~~~K~iVFSQ--f~-----------~~L~li~~~L~~~gi~~~~~ 170 (210)
...++.|..+++ .+.++++.|- .. ..+.++...|.++|++|-.+
T Consensus 27 ~~~ie~L~~l~~--~G~~IiiaTGR~~~~~~~n~~~i~~~~~~~t~~wL~k~~ipYd~l 83 (126)
T TIGR01689 27 LAVIEKLRHYKA--LGFEIVISSSRNMRTYEGNVGKINIHTLPIIILWLNQHNVPYDEI 83 (126)
T ss_pred HHHHHHHHHHHH--CCCEEEEECCCCchhhhccccccchhhHHHHHHHHHHcCCCCceE
Confidence 345556666653 3677877774 22 24479999999999998554
No 372
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.69 E-value=28 Score=25.38 Aligned_cols=26 Identities=27% Similarity=0.462 Sum_probs=19.6
Q ss_pred CcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCC
Q 028376 45 HFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGN 84 (210)
Q Consensus 45 H~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~ 84 (210)
..||..|-+..+ ..||.|..+++-+.
T Consensus 28 eafcskcgeati--------------~qcp~csasirgd~ 53 (160)
T COG4306 28 EAFCSKCGEATI--------------TQCPICSASIRGDY 53 (160)
T ss_pred HHHHhhhchHHH--------------hcCCccCCcccccc
Confidence 358888877654 36999999987764
No 373
>cd01522 RHOD_1 Member of the Rhodanese Homology Domain superfamily, subgroup 1. This CD includes the putative rhodanese-related sulfurtransferases of several uncharacterized proteins.
Probab=30.54 E-value=1.3e+02 Score=21.01 Aligned_cols=38 Identities=8% Similarity=0.005 Sum_probs=28.4
Q ss_pred CCCCcEEEEcchHHHHHHHHHHHHhCCceEE-EeeCCCC
Q 028376 138 DPKAKILVFSSWNDVLDVLEHAFIANNITCI-KMKGENH 175 (210)
Q Consensus 138 ~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~-~~~G~m~ 175 (210)
+++.++|||.+--..-......|...|+.-+ .+.|++.
T Consensus 62 ~~~~~ivv~C~~G~rs~~aa~~L~~~G~~~v~~l~gG~~ 100 (117)
T cd01522 62 GKDRPVLLLCRSGNRSIAAAEAAAQAGFTNVYNVLEGFE 100 (117)
T ss_pred CCCCeEEEEcCCCccHHHHHHHHHHCCCCeEEECcCcee
Confidence 4567788888765556677888999999744 4788865
No 374
>cd01526 RHOD_ThiF Member of the Rhodanese Homology Domain superfamily. This CD includes several putative molybdopterin synthase sulfurylases including the molybdenum cofactor biosynthetic protein (CnxF) of Aspergillus nidulans and the molybdenum cofactor synthesis protein 3 (MOCS3) of Homo sapiens. These rhodanese-like domains are found C-terminal of the ThiF and MoeZ_MoeB domains.
Probab=30.47 E-value=57 Score=22.96 Aligned_cols=38 Identities=11% Similarity=0.058 Sum_probs=27.4
Q ss_pred CCCCcEEEEcchHHHHHHHHHHHHhCCc--eEEEeeCCCC
Q 028376 138 DPKAKILVFSSWNDVLDVLEHAFIANNI--TCIKMKGENH 175 (210)
Q Consensus 138 ~~~~K~iVFSQf~~~L~li~~~L~~~gi--~~~~~~G~m~ 175 (210)
+++..+|||.+--..-......|...|+ ....++|++.
T Consensus 70 ~~~~~ivv~C~~G~rs~~aa~~L~~~G~~~~v~~l~GG~~ 109 (122)
T cd01526 70 DKDSPIYVVCRRGNDSQTAVRKLKELGLERFVRDIIGGLK 109 (122)
T ss_pred CCCCcEEEECCCCCcHHHHHHHHHHcCCccceeeecchHH
Confidence 4567778887654445566778999999 4778899853
No 375
>cd00954 NAL N-Acetylneuraminic acid aldolase, also called N-acetylneuraminate lyase (NAL), which catalyses the reversible aldol reaction of N-acetyl-D-mannosamine and pyruvate to give N-acetyl-D-neuraminic acid (D-sialic acid). It has a widespread application as biocatalyst for the synthesis of sialic acid and its derivatives. This enzyme has been shown to be quite specific for pyruvate as the donor, but flexible to a variety of D- and, to some extent, L-hexoses and pentoses as acceptor substrates. NAL is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases.
Probab=30.41 E-value=1.3e+02 Score=24.79 Aligned_cols=44 Identities=5% Similarity=0.104 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 151 DVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 151 ~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
.+-.+++..+...|+.-+-+-|++.+...|+.++|.+.++....
T Consensus 22 ~~~~~i~~l~~~~Gv~gi~~~GstGE~~~Lt~~Er~~~~~~~~~ 65 (288)
T cd00954 22 VLRAIVDYLIEKQGVDGLYVNGSTGEGFLLSVEERKQIAEIVAE 65 (288)
T ss_pred HHHHHHHHHHhcCCCCEEEECcCCcCcccCCHHHHHHHHHHHHH
Confidence 34444444444327777778888888888888888888887665
No 376
>TIGR00674 dapA dihydrodipicolinate synthase. Dihydrodipicolinate synthase is a homotetrameric enzyme of lysine biosynthesis. E. coli has several paralogs closely related to dihydrodipicoline synthase (DapA), as well as the more distant N-acetylneuraminate lyase. In Pyrococcus horikoshii, the bidirectional best hit with E. coli is to an uncharacterized paralog of DapA, not DapA itself, and it is omitted from the seed. The putative members from the Chlamydias (pathogens with a parasitic metabolism) are easily the most divergent members of the multiple alignment.
Probab=30.37 E-value=1.3e+02 Score=24.75 Aligned_cols=43 Identities=9% Similarity=0.210 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 151 DVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 151 ~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
.+-++++..+ ..|+.-+-.-|++.+...|+..+|.++++....
T Consensus 20 ~~~~~i~~l~-~~Gv~Gi~~~GstGE~~~Ls~~Er~~~~~~~~~ 62 (285)
T TIGR00674 20 ALEKLIDFQI-ENGTDAIVVVGTTGESPTLSHEEHKKVIEFVVD 62 (285)
T ss_pred HHHHHHHHHH-HcCCCEEEECccCcccccCCHHHHHHHHHHHHH
Confidence 3334444333 477777777788888888888888888887765
No 377
>TIGR01073 pcrA ATP-dependent DNA helicase PcrA. Designed to identify pcrA members of the uvrD/rep subfamily.
Probab=30.27 E-value=1.5e+02 Score=28.09 Aligned_cols=51 Identities=16% Similarity=0.171 Sum_probs=34.7
Q ss_pred hHHHHHHHHHHHHhcC---CCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCC
Q 028376 123 KIEAVTRRILWIKSTD---PKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENH 175 (210)
Q Consensus 123 Ki~al~~~L~~~~~~~---~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~ 175 (210)
-.+.+.+.|..+.... +.+=+|++-. ......++.+|.++||+|... |+.+
T Consensus 325 Ea~~ia~~I~~l~~~~~~~~~diAVL~R~-~~~~~~l~~~L~~~gIP~~~~-g~~~ 378 (726)
T TIGR01073 325 EAQFVAGEIDKLVKNGERKYGDFAILYRT-NAQSRVFEETLLKANIPYKIV-GGLK 378 (726)
T ss_pred HHHHHHHHHHHHHHcCCCCcCCEEEEEeC-chhHHHHHHHHHHcCCCEEEe-CCcc
Confidence 3455677777665542 3344566666 555799999999999999765 4444
No 378
>PRK04147 N-acetylneuraminate lyase; Provisional
Probab=30.20 E-value=1.2e+02 Score=25.24 Aligned_cols=41 Identities=5% Similarity=0.090 Sum_probs=25.7
Q ss_pred HHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 154 DVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 154 ~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
.+++..+...|+.-+-+-|++.+...|+.++|.++++..-.
T Consensus 28 ~li~~l~~~~Gv~gi~v~GstGE~~~Ls~eEr~~~~~~~~~ 68 (293)
T PRK04147 28 RLVRFNIEKQGIDGLYVGGSTGEAFLLSTEEKKQVLEIVAE 68 (293)
T ss_pred HHHHHHHhcCCCCEEEECCCccccccCCHHHHHHHHHHHHH
Confidence 33443333366666667777777777777777777765554
No 379
>KOG1609 consensus Protein involved in mRNA turnover and stability [RNA processing and modification]
Probab=29.79 E-value=42 Score=27.88 Aligned_cols=51 Identities=16% Similarity=0.345 Sum_probs=36.0
Q ss_pred ccccccccccccCC---CeecCCC-----CcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376 24 EETCPICQEKLGNQ---KMVFQCG-----HFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG 83 (210)
Q Consensus 24 ~~~C~iC~~~~~~~---~~~~~Cg-----H~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~ 83 (210)
...|.||....... ..+.+|. +..+..|+..|+. ..+...|..|.......
T Consensus 78 ~~~cRIc~~~~~~~~~~~l~~pC~C~g~l~~vH~~cl~~W~~---------~~~~~~CeiC~~~~~~~ 136 (323)
T KOG1609|consen 78 GPICRICHEEDEESNGLLLISPCSCKGSLAYVHRSCLEKWFS---------IKGNITCEICKSFFINV 136 (323)
T ss_pred CCcEEEEecccccccccccccCccccCcHHHHHHHHHHhhhc---------cccCeeeecccccceec
Confidence 36799998765432 3667774 4568899999963 25667899998866554
No 380
>COG0669 CoaD Phosphopantetheine adenylyltransferase [Coenzyme metabolism]
Probab=29.41 E-value=1.6e+02 Score=22.36 Aligned_cols=50 Identities=24% Similarity=0.340 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCCCC
Q 028376 151 DVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPSSQ 200 (210)
Q Consensus 151 ~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~~~ 200 (210)
.+||+|++++..-.--++-+--.-..++-.+..+|...+++=..+-|+++
T Consensus 17 GHlDii~RA~~~Fd~viVaV~~np~K~plFsleER~~l~~~~~~~l~nV~ 66 (159)
T COG0669 17 GHLDIIKRASALFDEVIVAVAINPSKKPLFSLEERVELIREATKHLPNVE 66 (159)
T ss_pred chHHHHHHHHHhccEEEEEEEeCCCcCCCcCHHHHHHHHHHHhcCCCceE
Confidence 47899999998876666666544445677888999999998888777774
No 381
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=29.41 E-value=21 Score=30.00 Aligned_cols=40 Identities=25% Similarity=0.372 Sum_probs=30.1
Q ss_pred hcCCCCccccccccccccCCCeecCCCCcchHhhHHHHHH
Q 028376 18 SLSKADEETCPICQEKLGNQKMVFQCGHFTCCKCFFAMTE 57 (210)
Q Consensus 18 ~l~~~~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~ 57 (210)
+-...+...|.+|...+..+...-.|+|-||.-|...+.+
T Consensus 99 A~~~~~~~~~~~~~g~l~vpt~~qg~w~qf~~~~p~~~~~ 138 (324)
T KOG0824|consen 99 AGFQQDHDICYICYGKLTVPTRIQGCWHQFCYVCPKSNFA 138 (324)
T ss_pred ccccCCccceeeeeeeEEecccccCceeeeeecCCchhhh
Confidence 3344566789999887766555567999999999988853
No 382
>cd06280 PBP1_LacI_like_4 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=29.38 E-value=1.9e+02 Score=22.80 Aligned_cols=14 Identities=7% Similarity=0.102 Sum_probs=7.1
Q ss_pred HHhCCceEEEeeCC
Q 028376 160 FIANNITCIKMKGE 173 (210)
Q Consensus 160 L~~~gi~~~~~~G~ 173 (210)
|...++.-+-+.+.
T Consensus 51 l~~~~~dgiii~~~ 64 (263)
T cd06280 51 MEEERVTGVIFAPT 64 (263)
T ss_pred HHhCCCCEEEEeCC
Confidence 44555555555443
No 383
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=29.37 E-value=1.7e+02 Score=23.79 Aligned_cols=22 Identities=5% Similarity=-0.035 Sum_probs=10.9
Q ss_pred hHHHHHHHHHHHHhCCceEEEe
Q 028376 149 WNDVLDVLEHAFIANNITCIKM 170 (210)
Q Consensus 149 f~~~L~li~~~L~~~gi~~~~~ 170 (210)
|..++.-++.+++++|+....+
T Consensus 41 ~~~~~~~i~~~~~~~G~~~~~~ 62 (295)
T PRK10653 41 FVSLKDGAQKEADKLGYNLVVL 62 (295)
T ss_pred HHHHHHHHHHHHHHcCCeEEEe
Confidence 4444555555555555554443
No 384
>cd06354 PBP1_BmpA_PnrA_like Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea. Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea. The PnrA lipoprotein, also known as Tp0319 or TmpC, represents a novel family of bacterial purine nucleoside receptor encoded within an ATP-binding cassette (ABC) transport system (pnrABCDE). It shows a striking structural similarity to another basic membrane lipoprotein Med which regulates the competence transcription factor gene, comK, in Bacillus subtilis. The members of PnrA-like subgroup are likely to have similar nucleoside-binding functions and a similar type I periplasmic sugar-binding protein-like fold.
Probab=28.65 E-value=1.7e+02 Score=23.43 Aligned_cols=17 Identities=24% Similarity=0.149 Sum_probs=6.9
Q ss_pred HHHHHHHHHHHHhCCce
Q 028376 150 NDVLDVLEHAFIANNIT 166 (210)
Q Consensus 150 ~~~L~li~~~L~~~gi~ 166 (210)
..++.-++.+++++|+.
T Consensus 18 ~~~~~gi~~~~~~~gy~ 34 (265)
T cd06354 18 QSAWEGLERAAKELGIE 34 (265)
T ss_pred HHHHHHHHHHHHHcCCe
Confidence 33334444444444443
No 385
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.64 E-value=42 Score=22.95 Aligned_cols=15 Identities=13% Similarity=0.235 Sum_probs=12.2
Q ss_pred cchHhhHHHHHHHhh
Q 028376 46 FTCCKCFFAMTEQRL 60 (210)
Q Consensus 46 ~fC~~C~~~~~~~~~ 60 (210)
.||+.|+..|.....
T Consensus 42 gFCRNCLs~Wy~eaa 56 (104)
T COG3492 42 GFCRNCLSNWYREAA 56 (104)
T ss_pred HHHHHHHHHHHHHHH
Confidence 499999999986643
No 386
>cd06293 PBP1_LacI_like_11 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=28.41 E-value=2e+02 Score=22.72 Aligned_cols=33 Identities=9% Similarity=0.118 Sum_probs=15.7
Q ss_pred CCcEEEEcc---hHHHHHHHHHHHHhCCceEEEeeCC
Q 028376 140 KAKILVFSS---WNDVLDVLEHAFIANNITCIKMKGE 173 (210)
Q Consensus 140 ~~K~iVFSQ---f~~~L~li~~~L~~~gi~~~~~~G~ 173 (210)
+-+++++.. ...-.+.++. +...++.-+-+.+.
T Consensus 29 gy~v~~~~~~~~~~~~~~~i~~-~~~~~~dgiii~~~ 64 (269)
T cd06293 29 GLSLVLCATRNRPERELTYLRW-LDTNHVDGLIFVTN 64 (269)
T ss_pred CCEEEEEeCCCCHHHHHHHHHH-HHHCCCCEEEEeCC
Confidence 456666542 2222333333 44555665555554
No 387
>cd06319 PBP1_ABC_sugar_binding_like_10 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=28.26 E-value=1.8e+02 Score=22.95 Aligned_cols=30 Identities=17% Similarity=0.155 Sum_probs=12.3
Q ss_pred CCcEEEEcc---hHHHHHHHHHHHHhCCceEEEe
Q 028376 140 KAKILVFSS---WNDVLDVLEHAFIANNITCIKM 170 (210)
Q Consensus 140 ~~K~iVFSQ---f~~~L~li~~~L~~~gi~~~~~ 170 (210)
+-++++|.. -....+.++..+. .++.-+-+
T Consensus 29 g~~~~~~~~~~~~~~~~~~i~~~~~-~~~dgiii 61 (277)
T cd06319 29 GYDAVELSAENSAKKELENLRTAID-KGVSGIII 61 (277)
T ss_pred CCeEEEecCCCCHHHHHHHHHHHHh-cCCCEEEE
Confidence 345555432 2223444444332 34443333
No 388
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=28.23 E-value=26 Score=21.90 Aligned_cols=31 Identities=19% Similarity=0.536 Sum_probs=18.7
Q ss_pred cccccccccCCCeecCCCCcchHh----hHHHHHH
Q 028376 27 CPICQEKLGNQKMVFQCGHFTCCK----CFFAMTE 57 (210)
Q Consensus 27 C~iC~~~~~~~~~~~~CgH~fC~~----C~~~~~~ 57 (210)
|..|........+-+.||+++|.. ......+
T Consensus 1 C~~C~~~~~~lw~CL~Cg~~~C~~~~~~Ha~~H~~ 35 (63)
T PF02148_consen 1 CSVCGSTNSNLWLCLTCGYVGCGRYSNGHALKHYK 35 (63)
T ss_dssp -SSSHTCSSSEEEETTTS-EEETTTSTSHHHHHHH
T ss_pred CCCCCCcCCceEEeCCCCcccccCCcCcHHHHhhc
Confidence 566765422234668999999986 6666554
No 389
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=28.19 E-value=31 Score=19.80 Aligned_cols=25 Identities=36% Similarity=0.978 Sum_probs=12.1
Q ss_pred cccccccccccCCCeecCC----CCcchHhh
Q 028376 25 ETCPICQEKLGNQKMVFQC----GHFTCCKC 51 (210)
Q Consensus 25 ~~C~iC~~~~~~~~~~~~C----gH~fC~~C 51 (210)
..||+|... +...+.+= ||.+|..|
T Consensus 4 ~pCP~CGG~--DrFri~~d~~~~G~~~C~~C 32 (40)
T PF08273_consen 4 GPCPICGGK--DRFRIFDDKDGRGTWICRQC 32 (40)
T ss_dssp E--TTTT-T--TTEEEETT----S-EEETTT
T ss_pred CCCCCCcCc--cccccCcCcccCCCEECCCC
Confidence 469999542 22222333 88888888
No 390
>TIGR02634 xylF D-xylose ABC transporter, substrate-binding protein. Members of this family are periplasmic (when in Gram-negative bacteria) binding proteins for D-xylose import by a high-affinity ATP-binding cassette (ABC) transporter.
Probab=28.09 E-value=1.8e+02 Score=23.84 Aligned_cols=20 Identities=15% Similarity=0.228 Sum_probs=8.9
Q ss_pred hHHHHHHHHHHHHhCCceEE
Q 028376 149 WNDVLDVLEHAFIANNITCI 168 (210)
Q Consensus 149 f~~~L~li~~~L~~~gi~~~ 168 (210)
|..+.+-++.++++.|+...
T Consensus 13 ~~~~~~~i~~~a~~~g~~v~ 32 (302)
T TIGR02634 13 WQKDRDIFVAAAESLGAKVF 32 (302)
T ss_pred HHHHHHHHHHHHHhcCCEEE
Confidence 44444444444444444433
No 391
>cd01527 RHOD_YgaP Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YgaP, and similar uncharacterized putative rhodanese-related sulfurtransferases.
Probab=28.09 E-value=1e+02 Score=20.45 Aligned_cols=37 Identities=8% Similarity=-0.062 Sum_probs=25.6
Q ss_pred CCCCcEEEEcchHHHHHHHHHHHHhCCce-EEEeeCCC
Q 028376 138 DPKAKILVFSSWNDVLDVLEHAFIANNIT-CIKMKGEN 174 (210)
Q Consensus 138 ~~~~K~iVFSQf~~~L~li~~~L~~~gi~-~~~~~G~m 174 (210)
+++.++|++...-.--......|.+.|+. ...++|++
T Consensus 52 ~~~~~iv~~c~~g~~s~~~~~~L~~~g~~~v~~l~gG~ 89 (99)
T cd01527 52 VGANAIIFHCRSGMRTQQNAERLAAISAGEAYVLEGGL 89 (99)
T ss_pred CCCCcEEEEeCCCchHHHHHHHHHHcCCccEEEeeCCH
Confidence 34566777766544456778888888884 55689984
No 392
>cd01831 Endoglucanase_E_like Endoglucanase E-like members of the SGNH hydrolase family; Endoglucanase E catalyzes the endohydrolysis of 1,4-beta-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans.
Probab=27.87 E-value=2.5e+02 Score=20.67 Aligned_cols=48 Identities=17% Similarity=0.214 Sum_probs=30.8
Q ss_pred HHHHHHHHHHhcCCCCcEEEEcch--------HHHHHHHHHHHHhCC---ceEEEeeCC
Q 028376 126 AVTRRILWIKSTDPKAKILVFSSW--------NDVLDVLEHAFIANN---ITCIKMKGE 173 (210)
Q Consensus 126 al~~~L~~~~~~~~~~K~iVFSQf--------~~~L~li~~~L~~~g---i~~~~~~G~ 173 (210)
.+.+.|..+++..|..++++-+-+ ..+...+...+++.+ +.|+.+.+.
T Consensus 82 ~~~~li~~i~~~~p~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~id~~~~ 140 (169)
T cd01831 82 AYVEFIEELRKRYPDAPIVLMLGPMLFGPYGTEEEIKRVAEAFKDQKSKKVHYFDTPGI 140 (169)
T ss_pred HHHHHHHHHHHHCCCCeEEEEecCccccccccHHHHHHHHHHHHhcCCceEEEEecccc
Confidence 333444455556788888776543 356777888888775 777766543
No 393
>cd06301 PBP1_rhizopine_binding_like Periplasmic binding proteins specific to rhizopines. Periplasmic binding proteins specific to rhizopines, which are simple sugar-like compounds produced in the nodules induced by the symbiotic root nodule bacteria, such as Rhizobium and Sinorhizobium. Rhizopine-binding-like proteins from other bacteria are also included. Two inositol based rhizopine compounds are known to date: L-3-O-methly-scyllo-inosamine (3-O-MSI) and scyllo-inosamine. Bacterial strains that can metabolize rhizopine have a greater competitive advantage in nodulation and rhizopine synthesis is regulated by NifA/NtrA regulatory transcription activators which are maximally expressed at the onset of nitrogen fixation in bacteroids. The members of this group belong to the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily.
Probab=27.71 E-value=1.9e+02 Score=22.79 Aligned_cols=33 Identities=9% Similarity=0.056 Sum_probs=15.4
Q ss_pred CCcEEEEcc---hHHHHHHHHHHHHhCCceEEEeeCC
Q 028376 140 KAKILVFSS---WNDVLDVLEHAFIANNITCIKMKGE 173 (210)
Q Consensus 140 ~~K~iVFSQ---f~~~L~li~~~L~~~gi~~~~~~G~ 173 (210)
+..++++.. .....+.++..+. .++.-+-+.+.
T Consensus 30 ~~~~~~~~~~~~~~~~~~~i~~l~~-~~vdgiii~~~ 65 (272)
T cd06301 30 GVELQFEDAKNDVATQLSQVENFIA-QGVDAIIVVPV 65 (272)
T ss_pred CcEEEEeCCCCCHHHHHHHHHHHHH-cCCCEEEEecC
Confidence 455555432 3344555555333 35554444443
No 394
>cd06323 PBP1_ribose_binding Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Members of this group are belonging to the type I periplasmic binding protein superfamily, whose members are involved in chemotaxis, ATP-binding cassette transport, and intercellular communication in central nervous system. The thermophilic and mesophilic ribose-binding proteins are structurally very similar, but differ substantially in thermal stability.
Probab=27.70 E-value=1.8e+02 Score=22.74 Aligned_cols=7 Identities=29% Similarity=0.411 Sum_probs=3.0
Q ss_pred HHHHHHH
Q 028376 152 VLDVLEH 158 (210)
Q Consensus 152 ~L~li~~ 158 (210)
..+.++.
T Consensus 44 ~~~~~~~ 50 (268)
T cd06323 44 QLNDIED 50 (268)
T ss_pred HHHHHHH
Confidence 3344444
No 395
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=27.68 E-value=16 Score=18.47 Aligned_cols=13 Identities=31% Similarity=0.812 Sum_probs=9.9
Q ss_pred ccccCCcccccCC
Q 028376 71 VMCPTCRQRTDIG 83 (210)
Q Consensus 71 ~~CP~Cr~~~~~~ 83 (210)
..||.|+..+..+
T Consensus 3 ~~C~~CgR~F~~~ 15 (25)
T PF13913_consen 3 VPCPICGRKFNPD 15 (25)
T ss_pred CcCCCCCCEECHH
Confidence 4799999887554
No 396
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=27.59 E-value=24 Score=30.72 Aligned_cols=48 Identities=21% Similarity=0.313 Sum_probs=34.9
Q ss_pred cccccccccccCC---CeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCC
Q 028376 25 ETCPICQEKLGNQ---KMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIG 83 (210)
Q Consensus 25 ~~C~iC~~~~~~~---~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~ 83 (210)
..|.||...+... .--..|||.+..+|+..|+.. ..+||.|+..+...
T Consensus 197 ~sl~I~~~slK~~y~k~~~~~~g~~~~~~kL~k~L~~-----------~~kl~~~~rel~~~ 247 (465)
T KOG0827|consen 197 GSLSICFESLKQNYDKISAIVCGHIYHHGKLSKWLAT-----------KRKLPSCRRELPKN 247 (465)
T ss_pred hhhHhhHHHHHHHHHHHHHHhhcccchhhHHHHHHHH-----------HHHhHHHHhhhhhh
Confidence 3588986655321 234689999999999999854 34799998876543
No 397
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=27.59 E-value=27 Score=35.08 Aligned_cols=51 Identities=24% Similarity=0.526 Sum_probs=33.5
Q ss_pred cccccccccccCCCeecCCCCc-----chHhhHHHHHHHhhhccccCCCccccccCCcccccCCC
Q 028376 25 ETCPICQEKLGNQKMVFQCGHF-----TCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGN 84 (210)
Q Consensus 25 ~~C~iC~~~~~~~~~~~~CgH~-----fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~ 84 (210)
..||-|...... .....||+. .|..|-..... . ......||.|..++....
T Consensus 668 rkCPkCG~~t~~-~fCP~CGs~te~vy~CPsCGaev~~-----d---es~a~~CP~CGtplv~~~ 723 (1337)
T PRK14714 668 RRCPSCGTETYE-NRCPDCGTHTEPVYVCPDCGAEVPP-----D---ESGRVECPRCDVELTPYQ 723 (1337)
T ss_pred EECCCCCCcccc-ccCcccCCcCCCceeCccCCCccCC-----C---ccccccCCCCCCcccccc
Confidence 679999876543 355678865 48888765410 0 122568999998776543
No 398
>PF11290 DUF3090: Protein of unknown function (DUF3090); InterPro: IPR021441 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=27.59 E-value=38 Score=26.06 Aligned_cols=17 Identities=24% Similarity=0.429 Sum_probs=14.0
Q ss_pred CCccccccCCcccccCC
Q 028376 67 KNEWVMCPTCRQRTDIG 83 (210)
Q Consensus 67 ~~~~~~CP~Cr~~~~~~ 83 (210)
..+++.||.|..++...
T Consensus 151 aAGRP~CPlCg~PlDP~ 167 (171)
T PF11290_consen 151 AAGRPPCPLCGEPLDPE 167 (171)
T ss_pred hCCCCCCCCCCCCCCCC
Confidence 47789999999998654
No 399
>cd06275 PBP1_PurR Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. This dimeric PurR belongs to the LacI-GalR family of transcription regulators and is activated to bind to DNA operator sites by initially binding either of high affinity corepressors, hypoxanthine or guanine. PurR is composed of two functional domains: aan N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the purine transcription repressor undergoes a
Probab=27.12 E-value=2.1e+02 Score=22.47 Aligned_cols=13 Identities=0% Similarity=0.056 Sum_probs=5.9
Q ss_pred HHhCCceEEEeeC
Q 028376 160 FIANNITCIKMKG 172 (210)
Q Consensus 160 L~~~gi~~~~~~G 172 (210)
|...++.-+-+.+
T Consensus 51 l~~~~vdgiii~~ 63 (269)
T cd06275 51 LAQKRVDGLLVMC 63 (269)
T ss_pred HHHcCCCEEEEec
Confidence 3344555444444
No 400
>cd00952 CHBPH_aldolase Trans-o-hydroxybenzylidenepyruvate hydratase-aldolase (HBPHA) and trans-2'-carboxybenzalpyruvate hydratase-aldolase (CBPHA). HBPHA catalyzes HBP to salicyaldehyde and pyruvate. This reaction is part of the degradative pathways for naphthalene and naphthalenesulfonates by bacteria. CBPHA is homologous to HBPHA and catalyzes the cleavage of CBP to 2-carboxylbenzaldehyde and pyruvate during the degradation of phenanthrene. They are member of the DHDPS family of Schiff-base-dependent class I aldolases.
Probab=27.10 E-value=1.4e+02 Score=25.14 Aligned_cols=32 Identities=9% Similarity=0.141 Sum_probs=22.6
Q ss_pred CCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 163 NNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 163 ~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
+|+.-+-+-|++.+...|+..+|.++++....
T Consensus 41 ~Gv~Gi~v~GstGE~~~Lt~eEr~~v~~~~~~ 72 (309)
T cd00952 41 AGVDGILTMGTFGECATLTWEEKQAFVATVVE 72 (309)
T ss_pred cCCCEEEECcccccchhCCHHHHHHHHHHHHH
Confidence 56666666777777777777777777776654
No 401
>PF08756 YfkB: YfkB-like domain; InterPro: IPR014866 YfkB is adjacent to YfkA in Bacillus subtilis. In other bacterial species, it is fused to this protein. As YfkA contains a Radical SAM domain it suggests this domain is interacts with them.
Probab=27.03 E-value=2.3e+02 Score=21.18 Aligned_cols=35 Identities=23% Similarity=0.241 Sum_probs=25.3
Q ss_pred EEeeCCCCCCcchhhHhhhHHHHHHhh-------cCCCCCCc
Q 028376 168 IKMKGENHKLPSANLQHRNALQKELTR-------HMPSSQSQ 202 (210)
Q Consensus 168 ~~~~G~m~~~~~~~~~~R~~~l~~F~~-------~~p~~~~~ 202 (210)
-.+-|+.++.+.-+..+-.+.|++.+. +|||+.++
T Consensus 34 WMLFGTLPfy~Cs~~eeD~~Ll~RL~~~~NVTvRNDPDGRsR 75 (153)
T PF08756_consen 34 WMLFGTLPFYPCSDDEEDLALLKRLRSEPNVTVRNDPDGRSR 75 (153)
T ss_pred eEEecccccccCCCCHHHHHHHHHHHhCCCCeeecCCCccce
Confidence 456688887777777777788888775 56776653
No 402
>cd01538 PBP1_ABC_xylose_binding Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.
Probab=26.83 E-value=2e+02 Score=23.20 Aligned_cols=23 Identities=17% Similarity=0.130 Sum_probs=11.1
Q ss_pred hHHHHHHHHHHHHhCCceEEEee
Q 028376 149 WNDVLDVLEHAFIANNITCIKMK 171 (210)
Q Consensus 149 f~~~L~li~~~L~~~gi~~~~~~ 171 (210)
|..++.-++.+++++|+....++
T Consensus 14 ~~~~~~gi~~~a~~~g~~~~~~~ 36 (288)
T cd01538 14 WIRDRPNFEAALKELGAEVIVQN 36 (288)
T ss_pred HHHHHHHHHHHHHHcCCEEEEEC
Confidence 44444555555555555444443
No 403
>PF06050 HGD-D: 2-hydroxyglutaryl-CoA dehydratase, D-component ; InterPro: IPR010327 Degradation of glutamate via the hydroxyglutarate pathway involves the syn-elimination of water from 2-hydroxyglutaryl-CoA. This anaerobic process is catalysed by 2-hydroxyglutaryl-CoA dehydratase, an enzyme with two components (A and D) that reversibly associate during reaction cycles. This component contains one non-reducible [4Fe-4S]2+ cluster and a reduced riboflavin 5'-monophosphate [].; PDB: 3O3O_B 3O3N_D 3O3M_D.
Probab=26.76 E-value=1.5e+02 Score=24.85 Aligned_cols=49 Identities=14% Similarity=0.123 Sum_probs=30.2
Q ss_pred chHHHHHHHHHHHHhcCCCCcEEEEcch-----HHHHHHHHHHHHhC-CceEEEeeCCC
Q 028376 122 TKIEAVTRRILWIKSTDPKAKILVFSSW-----NDVLDVLEHAFIAN-NITCIKMKGEN 174 (210)
Q Consensus 122 sKi~al~~~L~~~~~~~~~~K~iVFSQf-----~~~L~li~~~L~~~-gi~~~~~~G~m 174 (210)
..++.+.+.+.+ ..-+-+|.+..+ .....++...|++. ||+.+.++|.+
T Consensus 273 ~r~~~~~~~~~~----~~~dgvi~~~~~~C~~~~~~~~~l~~~~~~~~gIP~l~le~d~ 327 (349)
T PF06050_consen 273 RRIEYIDDLIEK----YGADGVIFHGHKGCDPYSYDQPLLKEALREFLGIPVLFLEGDY 327 (349)
T ss_dssp CHHHHHHHHHHH----TT-SEEEEEEETT-HHHHCCHHHHHHHHHCCHT--EEEEEE-T
T ss_pred hHHHHHHHHHHH----hCCCEEEEhHhcCCCcHHHHHHHHHHHHHHhcCCCeEeecccc
Confidence 444555544443 323455555554 35688999999999 99999999875
No 404
>TIGR02313 HpaI-NOT-DapA 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase. This model represents a subset of the DapA (dihydrodipicolinate synthase) family which has apparently evolved a separate function. The product of DapA, dihydrodipicolinate, results from the non-enzymatic cyclization and dehydration of 6-amino-2,4-dihydroxyhept-2-ene-1,7-dioic acid, which is different from the substrate of this reaction only in the presence of the amino group. In the absence of this amino group, and running the reaction in the opposite direction, the reaction corresponds to the HpaI aldolase component of the 4-hydroxyphenylacetic acid catabolism pathway (see TIGR02311). At present, this variant of DapA is found only in Oceanobacillus iheyensis HTE831 and Thermus thermophilus HB27. In both of these cases, one or more other DapA genes can be found and the one identified by this model is part of an operon for 4-hydroxyphenylacetic acid catabolism.
Probab=26.47 E-value=1.6e+02 Score=24.50 Aligned_cols=33 Identities=15% Similarity=0.173 Sum_probs=24.1
Q ss_pred hCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 162 ANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 162 ~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
.+|+.-+-+-|+..+...|+..+|.+.++....
T Consensus 32 ~~Gv~gi~v~GstGE~~~Ls~~Er~~l~~~~~~ 64 (294)
T TIGR02313 32 EGGSHAISVGGTSGEPGSLTLEERKQAIENAID 64 (294)
T ss_pred HcCCCEEEECccCcccccCCHHHHHHHHHHHHH
Confidence 367766667777777778888888888776654
No 405
>PF04908 SH3BGR: SH3-binding, glutamic acid-rich protein; InterPro: IPR006993 This family of proteins, which contains SH3BGRL3, is functionally uncharacterised. SH3BGRL3 is a highly conserved small protein, which is widely expressed and shows a significant similarity to glutaredoxin 1 (GRX1) of Escherichia coli which is predicted to belong to the thioredoxin superfamily. However, SH3BGRL3 lacks both conserved cysteine residues, which characterise the enzymatic active site of GRX. This structural feature raises the possibility that SH3BGRL3 and its homologues could function as endogenous modulators of GRX activity []. ; PDB: 1SJ6_A 1U6T_A 1WRY_A 1T1V_B 1J0F_A 2CT6_A.
Probab=26.35 E-value=1.8e+02 Score=20.17 Aligned_cols=34 Identities=9% Similarity=0.005 Sum_probs=23.5
Q ss_pred HHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHH
Q 028376 153 LDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKEL 192 (210)
Q Consensus 153 L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F 192 (210)
-..|...|+.++|+|-.+|-++. ...|...-+.=
T Consensus 20 q~~v~~iL~a~kI~fe~vDIa~~------e~~r~~mr~~~ 53 (99)
T PF04908_consen 20 QQRVLMILEAKKIPFEEVDIAMD------EEARQWMRENA 53 (99)
T ss_dssp HHHHHHHHHHTT--EEEEETTT-------HHHHHHHHHHT
T ss_pred HHHHHHHHHHcCCCcEEEeCcCC------HHHHHHHHHhc
Confidence 34577889999999999999966 77776655543
No 406
>PRK11493 sseA 3-mercaptopyruvate sulfurtransferase; Provisional
Probab=26.31 E-value=1.6e+02 Score=24.15 Aligned_cols=38 Identities=11% Similarity=0.004 Sum_probs=29.4
Q ss_pred CCCCcEEEEcchHHHHHHHHHHHHhCCce-EEEeeCCCC
Q 028376 138 DPKAKILVFSSWNDVLDVLEHAFIANNIT-CIKMKGENH 175 (210)
Q Consensus 138 ~~~~K~iVFSQf~~~L~li~~~L~~~gi~-~~~~~G~m~ 175 (210)
+++.++|+|.+--.--.++..+|...|+. ...|+|++.
T Consensus 229 ~~~~~ii~yC~~G~~A~~~~~~l~~~G~~~v~~y~Gs~~ 267 (281)
T PRK11493 229 SFDRPIIASCGSGVTAAVVVLALATLDVPNVKLYDGAWS 267 (281)
T ss_pred CCCCCEEEECCcHHHHHHHHHHHHHcCCCCceeeCCCHH
Confidence 45677888888666667788889999996 567899954
No 407
>PRK11773 uvrD DNA-dependent helicase II; Provisional
Probab=26.20 E-value=2e+02 Score=27.35 Aligned_cols=50 Identities=22% Similarity=0.211 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHhc--CCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCC
Q 028376 124 IEAVTRRILWIKST--DPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENH 175 (210)
Q Consensus 124 i~al~~~L~~~~~~--~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~ 175 (210)
.+.+.+.|..+... .+.+=+|++-. ......++.+|.++||+|... |+..
T Consensus 330 a~~ia~~I~~l~~~g~~~~diAVL~R~-~~~~~~le~~L~~~gIPy~~~-g~~~ 381 (721)
T PRK11773 330 ARFVVERIKTWQDNGGALSDCAILYRS-NAQSRVLEEALLQAGIPYRIY-GGMR 381 (721)
T ss_pred HHHHHHHHHHHHHcCCCcccEEEEEec-chhHHHHHHHHHHCCCCEEEE-CCCC
Confidence 45566777666543 23344566666 667899999999999999766 4444
No 408
>cd06289 PBP1_MalI_like Ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. This group includes the ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. They are members of the LacI-GalR family of repressor proteins which are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=26.19 E-value=2.1e+02 Score=22.33 Aligned_cols=33 Identities=9% Similarity=0.100 Sum_probs=16.5
Q ss_pred CCcEEEEcc---hHHHHHHHHHHHHhCCceEEEeeCC
Q 028376 140 KAKILVFSS---WNDVLDVLEHAFIANNITCIKMKGE 173 (210)
Q Consensus 140 ~~K~iVFSQ---f~~~L~li~~~L~~~gi~~~~~~G~ 173 (210)
+.+++++.. ...-.++++..+ ..++.-+-+.+.
T Consensus 29 g~~~~~~~~~~~~~~~~~~i~~~~-~~~vdgiii~~~ 64 (268)
T cd06289 29 GYTVFLANSGEDVERQEQLLSTML-EHGVAGIILCPA 64 (268)
T ss_pred CCeEEEecCCCChHHHHHHHHHHH-HcCCCEEEEeCC
Confidence 456666643 233445555533 455655555443
No 409
>PRK11200 grxA glutaredoxin 1; Provisional
Probab=26.16 E-value=1.2e+02 Score=19.64 Aligned_cols=32 Identities=3% Similarity=-0.100 Sum_probs=21.2
Q ss_pred cEEEEcc-hHHHHHHHHHHHHh-----CCceEEEeeCC
Q 028376 142 KILVFSS-WNDVLDVLEHAFIA-----NNITCIKMKGE 173 (210)
Q Consensus 142 K~iVFSQ-f~~~L~li~~~L~~-----~gi~~~~~~G~ 173 (210)
|++||+. |-.+-+.+...|++ .||.|..++=.
T Consensus 2 ~v~iy~~~~C~~C~~a~~~L~~l~~~~~~i~~~~idi~ 39 (85)
T PRK11200 2 FVVIFGRPGCPYCVRAKELAEKLSEERDDFDYRYVDIH 39 (85)
T ss_pred EEEEEeCCCChhHHHHHHHHHhhcccccCCcEEEEECC
Confidence 4556654 66666667777777 78888777554
No 410
>cd01532 4RHOD_Repeat_1 Member of the Rhodanese Homology Domain superfamily, repeat 1. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 1st repeat which does not contain the putative catalytic Cys residue.
Probab=26.06 E-value=1.3e+02 Score=19.76 Aligned_cols=37 Identities=14% Similarity=0.158 Sum_probs=26.2
Q ss_pred CCCcEEEEcch--HHHHHHHHHHHHhCCce-EEEeeCCCC
Q 028376 139 PKAKILVFSSW--NDVLDVLEHAFIANNIT-CIKMKGENH 175 (210)
Q Consensus 139 ~~~K~iVFSQf--~~~L~li~~~L~~~gi~-~~~~~G~m~ 175 (210)
++.++|||.+- ..........|...|+. ...++|+|.
T Consensus 49 ~~~~ivl~c~~G~~~~s~~aa~~L~~~G~~~v~~l~GG~~ 88 (92)
T cd01532 49 RDTPIVVYGEGGGEDLAPRAARRLSELGYTDVALLEGGLQ 88 (92)
T ss_pred CCCeEEEEeCCCCchHHHHHHHHHHHcCccCEEEccCCHH
Confidence 46678888775 34345677888999985 456788853
No 411
>TIGR02200 GlrX_actino Glutaredoxin-like protein. This family of glutaredoxin-like proteins is limited to the Actinobacteria and contains the conserved CxxC motif.
Probab=26.04 E-value=1.3e+02 Score=18.53 Aligned_cols=28 Identities=7% Similarity=-0.070 Sum_probs=19.2
Q ss_pred EEcchHHHHHHHHHHHHhCCceEEEeeC
Q 028376 145 VFSSWNDVLDVLEHAFIANNITCIKMKG 172 (210)
Q Consensus 145 VFSQf~~~L~li~~~L~~~gi~~~~~~G 172 (210)
.++.|-..-..+...|.++|+.|..++-
T Consensus 5 y~~~~C~~C~~~~~~L~~~~~~~~~idi 32 (77)
T TIGR02200 5 YGTTWCGYCAQLMRTLDKLGAAYEWVDI 32 (77)
T ss_pred EECCCChhHHHHHHHHHHcCCceEEEeC
Confidence 3446777777777777777777766653
No 412
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=25.99 E-value=1.4e+02 Score=23.48 Aligned_cols=35 Identities=9% Similarity=0.083 Sum_probs=22.4
Q ss_pred HHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCc
Q 028376 130 RILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNI 165 (210)
Q Consensus 130 ~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi 165 (210)
.+.+++...|..|+||+|.+..-..++ .++.+.|.
T Consensus 58 ~~~~l~~~~p~~~iIvlt~~~~~~~~~-~~~~~~Ga 92 (207)
T PRK11475 58 CLTELAIKFPRMRRLVIADDDIEARLI-GSLSPSPL 92 (207)
T ss_pred HHHHHHHHCCCCCEEEEeCCCCHHHHH-HHHHHcCC
Confidence 444444568899999999876553333 44445565
No 413
>COG1199 DinG Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]
Probab=25.94 E-value=3.1e+02 Score=25.49 Aligned_cols=65 Identities=14% Similarity=0.152 Sum_probs=42.1
Q ss_pred hHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCce-EEEeeCCCCCCcchhhHhhhHHHHHHhhcCC
Q 028376 123 KIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNIT-CIKMKGENHKLPSANLQHRNALQKELTRHMP 197 (210)
Q Consensus 123 Ki~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~-~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p 197 (210)
=...+.+.|..+....|+ ++|||-.--.+|+.+...|....+. .+...| ...+...++.|...+.
T Consensus 463 ~~~~~~~~i~~~~~~~~~-~~lvlF~Sy~~l~~~~~~~~~~~~~~~v~~q~---------~~~~~~~l~~f~~~~~ 528 (654)
T COG1199 463 LLAKLAAYLREILKASPG-GVLVLFPSYEYLKRVAERLKDERSTLPVLTQG---------EDEREELLEKFKASGE 528 (654)
T ss_pred HHHHHHHHHHHHHhhcCC-CEEEEeccHHHHHHHHHHHhhcCccceeeecC---------CCcHHHHHHHHHHhcC
Confidence 455666677777777777 6655544445557777777777663 344444 4466699999998443
No 414
>cd06305 PBP1_methylthioribose_binding_like Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. The sugar-binding domain of the periplasmic proteins in this group is also homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR), DNA-binding transcriptional repressors such as LacI and GalR.
Probab=25.83 E-value=2.2e+02 Score=22.42 Aligned_cols=7 Identities=14% Similarity=0.430 Sum_probs=2.8
Q ss_pred CCcEEEE
Q 028376 140 KAKILVF 146 (210)
Q Consensus 140 ~~K~iVF 146 (210)
+.+++++
T Consensus 29 g~~~~~~ 35 (273)
T cd06305 29 GGDLRVY 35 (273)
T ss_pred CCEEEEE
Confidence 3444443
No 415
>COG0626 MetC Cystathionine beta-lyases/cystathionine gamma-synthases [Amino acid transport and metabolism]
Probab=25.81 E-value=2e+02 Score=25.32 Aligned_cols=53 Identities=8% Similarity=0.209 Sum_probs=43.6
Q ss_pred CCCchHHHHHHHHHHHHhcCCCCcEEEEcc-hHHHHHHHHHHHHhCCceEEEeeCC
Q 028376 119 SYGTKIEAVTRRILWIKSTDPKAKILVFSS-WNDVLDVLEHAFIANNITCIKMKGE 173 (210)
Q Consensus 119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQ-f~~~L~li~~~L~~~gi~~~~~~G~ 173 (210)
.++|-+.|+-..+..+. .+++++|+... |-....+++..|++.||.+..+|.+
T Consensus 83 afsSGmaAI~~~~l~ll--~~GD~vl~~~~~YG~t~~~~~~~l~~~gi~~~~~d~~ 136 (396)
T COG0626 83 AFSSGMAAISTALLALL--KAGDHVLLPDDLYGGTYRLFEKILQKFGVEVTFVDPG 136 (396)
T ss_pred EecCcHHHHHHHHHHhc--CCCCEEEecCCccchHHHHHHHHHHhcCeEEEEECCC
Confidence 35788888887777666 45889988777 9999999999999999998878766
No 416
>cd06270 PBP1_GalS_like Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalS is a dimeric protein like GalR,and its major role is in regulating expression of the high-affinity galactose transporter encoded by the mgl operon, whereas GalR is the exclusive regulator of galactose permease, the low-affinity galactose transporter. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type I periplasmic binding protein-like fold. Hence, they are homologous to the periplasmic sugar bindi
Probab=25.81 E-value=2.3e+02 Score=22.32 Aligned_cols=10 Identities=0% Similarity=0.152 Sum_probs=4.7
Q ss_pred CCceEEEeeC
Q 028376 163 NNITCIKMKG 172 (210)
Q Consensus 163 ~gi~~~~~~G 172 (210)
.++.-+-+.+
T Consensus 54 ~~vdgii~~~ 63 (268)
T cd06270 54 RRCDALILHS 63 (268)
T ss_pred cCCCEEEEec
Confidence 4455444444
No 417
>cd01575 PBP1_GntR Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. This group represents the ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of GntR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding,
Probab=25.77 E-value=2e+02 Score=22.43 Aligned_cols=12 Identities=8% Similarity=0.144 Sum_probs=5.7
Q ss_pred hCCceEEEeeCC
Q 028376 162 ANNITCIKMKGE 173 (210)
Q Consensus 162 ~~gi~~~~~~G~ 173 (210)
..++.-+-+.+.
T Consensus 53 ~~~vdgiii~~~ 64 (268)
T cd01575 53 SRRPAGLILTGL 64 (268)
T ss_pred HcCCCEEEEeCC
Confidence 444554444444
No 418
>PRK11784 tRNA 2-selenouridine synthase; Provisional
Probab=25.63 E-value=3.1e+02 Score=23.61 Aligned_cols=49 Identities=10% Similarity=0.112 Sum_probs=33.9
Q ss_pred CCCcEEEEcch-HHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 139 PKAKILVFSSW-NDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 139 ~~~K~iVFSQf-~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
++.++|||..- -.--..+...|...|+....++|++. .=|...++.|..
T Consensus 87 ~~~~ivvyC~rgG~RS~~aa~~L~~~G~~v~~L~GG~~-------awr~~~~~~~~~ 136 (345)
T PRK11784 87 ANPRGLLYCWRGGLRSGSVQQWLKEAGIDVPRLEGGYK-------AYRRFVIDTLEE 136 (345)
T ss_pred CCCeEEEEECCCChHHHHHHHHHHHcCCCcEEEcCCHH-------HHHHhhHHHHhh
Confidence 46677777631 22345567889999999889999963 345666677764
No 419
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=25.62 E-value=3e+02 Score=27.15 Aligned_cols=63 Identities=19% Similarity=0.241 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhC----CceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376 124 IEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIAN----NITCIKMKGENHKLPSANLQHRNALQKELTRH 195 (210)
Q Consensus 124 i~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~----gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~ 195 (210)
.+++.+.|.++....++.-.|.|+++ .+|..+...|... ++.. ...| +. ...|.+.+++|...
T Consensus 737 ~~~la~~i~~l~~~~~g~~LVLFtSy-~~l~~v~~~l~~~~~~~~~~l-l~Qg-~~------~~~r~~l~~~F~~~ 803 (928)
T PRK08074 737 IEEVAAYIAKIAKATKGRMLVLFTSY-EMLKKTYYNLKNEEELEGYVL-LAQG-VS------SGSRARLTKQFQQF 803 (928)
T ss_pred HHHHHHHHHHHHHhCCCCEEEEECCH-HHHHHHHHHHhhcccccCceE-EecC-CC------CCCHHHHHHHHHhc
Confidence 46777777777655555444557766 5556666666543 3332 2233 21 35789999999973
No 420
>cd06284 PBP1_LacI_like_6 Ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group includes the ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group belongs to the the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding.
Probab=25.48 E-value=2.2e+02 Score=22.18 Aligned_cols=11 Identities=9% Similarity=0.075 Sum_probs=4.6
Q ss_pred HHhCCceEEEe
Q 028376 160 FIANNITCIKM 170 (210)
Q Consensus 160 L~~~gi~~~~~ 170 (210)
|...++.-+-+
T Consensus 51 ~~~~~vdgiii 61 (267)
T cd06284 51 LRRKQADGIIL 61 (267)
T ss_pred HHHcCCCEEEE
Confidence 44444443333
No 421
>cd00950 DHDPS Dihydrodipicolinate synthase (DHDPS) is a key enzyme in lysine biosynthesis. It catalyzes the aldol condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a Schiff base formation between pyruvate and a lysine residue. The functional enzyme is a homotetramer consisting of a dimer of dimers. DHDPS is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways.
Probab=25.48 E-value=1.6e+02 Score=24.13 Aligned_cols=33 Identities=12% Similarity=0.207 Sum_probs=21.8
Q ss_pred hCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 162 ANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 162 ~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
..|+.-+-+-|++.+...|+.++|.++++.-..
T Consensus 32 ~~Gv~gl~v~GstGE~~~lt~~Er~~l~~~~~~ 64 (284)
T cd00950 32 ENGTDGLVVCGTTGESPTLSDEEHEAVIEAVVE 64 (284)
T ss_pred HcCCCEEEECCCCcchhhCCHHHHHHHHHHHHH
Confidence 366666666677766666777777777766554
No 422
>PRK03620 5-dehydro-4-deoxyglucarate dehydratase; Provisional
Probab=25.43 E-value=1.4e+02 Score=24.90 Aligned_cols=35 Identities=6% Similarity=0.051 Sum_probs=25.9
Q ss_pred HHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 160 FIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 160 L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
|..+|+.-+-.-|+..+...|+.++|.+.++....
T Consensus 37 l~~~Gv~Gi~~~GstGE~~~Lt~eEr~~~~~~~~~ 71 (303)
T PRK03620 37 LAPYGAAALFAAGGTGEFFSLTPDEYSQVVRAAVE 71 (303)
T ss_pred HHHcCCCEEEECcCCcCcccCCHHHHHHHHHHHHH
Confidence 33467777777788888888888888888877654
No 423
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=25.30 E-value=44 Score=20.81 Aligned_cols=27 Identities=22% Similarity=0.528 Sum_probs=19.0
Q ss_pred eecCCCCcchHhhHHHHHHHhhhccccCCCc-cccccCCcccccC
Q 028376 39 MVFQCGHFTCCKCFFAMTEQRLIHDNKVKNE-WVMCPTCRQRTDI 82 (210)
Q Consensus 39 ~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~-~~~CP~Cr~~~~~ 82 (210)
--+.||-++|. ..+ ...||.|..++..
T Consensus 20 NCl~CGkIiC~-----------------~Eg~~~pC~fCg~~l~~ 47 (57)
T PF06221_consen 20 NCLNCGKIICE-----------------QEGPLGPCPFCGTPLLS 47 (57)
T ss_pred cccccChhhcc-----------------cccCcCcCCCCCCcccC
Confidence 44788888875 234 5789999876644
No 424
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=25.29 E-value=37 Score=21.55 Aligned_cols=13 Identities=38% Similarity=0.780 Sum_probs=10.0
Q ss_pred ccccccCCccccc
Q 028376 69 EWVMCPTCRQRTD 81 (210)
Q Consensus 69 ~~~~CP~Cr~~~~ 81 (210)
....||.|++++.
T Consensus 5 ~~v~CP~C~k~~~ 17 (62)
T PRK00418 5 ITVNCPTCGKPVE 17 (62)
T ss_pred ccccCCCCCCccc
Confidence 3568999999753
No 425
>KOG2857 consensus Predicted MYND Zn-finger protein/hormone receptor interactor [Transcription]
Probab=25.24 E-value=32 Score=25.56 Aligned_cols=29 Identities=31% Similarity=0.541 Sum_probs=12.9
Q ss_pred cccccccccccCCCeecCCCCcchH-hhHHH
Q 028376 25 ETCPICQEKLGNQKMVFQCGHFTCC-KCFFA 54 (210)
Q Consensus 25 ~~C~iC~~~~~~~~~~~~CgH~fC~-~C~~~ 54 (210)
..|.||.+.... ..-..|.--||. .|+..
T Consensus 6 ~tC~ic~e~~~K-YKCpkC~vPYCSl~CfKi 35 (157)
T KOG2857|consen 6 TTCVICLESEIK-YKCPKCSVPYCSLPCFKI 35 (157)
T ss_pred eeehhhhcchhh-ccCCCCCCccccchhhhh
Confidence 345555553322 233445545553 45443
No 426
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=25.21 E-value=24 Score=22.00 Aligned_cols=12 Identities=33% Similarity=0.902 Sum_probs=6.2
Q ss_pred ccccCCcccccC
Q 028376 71 VMCPTCRQRTDI 82 (210)
Q Consensus 71 ~~CP~Cr~~~~~ 82 (210)
..||.|++++..
T Consensus 3 v~CP~C~k~~~~ 14 (57)
T PF03884_consen 3 VKCPICGKPVEW 14 (57)
T ss_dssp EE-TTT--EEE-
T ss_pred ccCCCCCCeecc
Confidence 579999997654
No 427
>COG2179 Predicted hydrolase of the HAD superfamily [General function prediction only]
Probab=25.03 E-value=2.2e+02 Score=22.00 Aligned_cols=61 Identities=13% Similarity=0.059 Sum_probs=43.6
Q ss_pred CchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 121 GTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
+.-+.+.+..++ ..+.|++|+|. .-=..++.+++.-||+|+.--++-. ...=.++|++++-
T Consensus 48 tpe~~~W~~e~k-----~~gi~v~vvSN--n~e~RV~~~~~~l~v~fi~~A~KP~------~~~fr~Al~~m~l 108 (175)
T COG2179 48 TPELRAWLAELK-----EAGIKVVVVSN--NKESRVARAAEKLGVPFIYRAKKPF------GRAFRRALKEMNL 108 (175)
T ss_pred CHHHHHHHHHHH-----hcCCEEEEEeC--CCHHHHHhhhhhcCCceeecccCcc------HHHHHHHHHHcCC
Confidence 344555555555 45899999999 4456889999999999987666633 4455577888776
No 428
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=25.02 E-value=1.2e+02 Score=19.02 Aligned_cols=25 Identities=12% Similarity=0.139 Sum_probs=20.5
Q ss_pred hHHHHHHHHHHHHhCCceEEEeeCC
Q 028376 149 WNDVLDVLEHAFIANNITCIKMKGE 173 (210)
Q Consensus 149 f~~~L~li~~~L~~~gi~~~~~~G~ 173 (210)
|-.+...|+....+.|+.++..+-.
T Consensus 1 f~~~~~~L~yka~~~G~~v~~v~~~ 25 (69)
T PF07282_consen 1 FGQFRQRLEYKAEEYGIQVVEVDEA 25 (69)
T ss_pred CHHHHHHHHHHHHHhCCEEEEECCC
Confidence 5677888999999999999877544
No 429
>TIGR03847 conserved hypothetical protein. The conserved hypothetical protein described here occurs as part of the trio of uncharacterized proteins common in the Actinobacteria.
Probab=24.94 E-value=45 Score=25.72 Aligned_cols=17 Identities=24% Similarity=0.456 Sum_probs=14.0
Q ss_pred CCccccccCCcccccCC
Q 028376 67 KNEWVMCPTCRQRTDIG 83 (210)
Q Consensus 67 ~~~~~~CP~Cr~~~~~~ 83 (210)
..+++.||.|..++...
T Consensus 153 aAGRP~CPlCg~PldP~ 169 (177)
T TIGR03847 153 AAGRPPCPLCGRPIDPD 169 (177)
T ss_pred hCCCCCCCCCCCCCCCC
Confidence 46789999999998754
No 430
>TIGR01075 uvrD DNA helicase II. Designed to identify uvrD members of the uvrD/rep subfamily.
Probab=24.90 E-value=1.9e+02 Score=27.47 Aligned_cols=50 Identities=22% Similarity=0.204 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHHhc--CCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCC
Q 028376 124 IEAVTRRILWIKST--DPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENH 175 (210)
Q Consensus 124 i~al~~~L~~~~~~--~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~ 175 (210)
.+.+.+.|..+... .+.+=+|++-. ......++.+|..+||+|... |+..
T Consensus 325 a~~ia~~I~~l~~~g~~~~diAVL~R~-~~~~~~le~~L~~~gIPy~~~-g~~~ 376 (715)
T TIGR01075 325 ARFVVSRIKTWQRNGGALDECAVLYRS-NAQSRVLEEALLQASIPYRIY-GGMR 376 (715)
T ss_pred HHHHHHHHHHHHHcCCCccCEEEEEec-CchHHHHHHHHHHcCCCEEEe-CCcc
Confidence 45677777766543 23344555555 566899999999999999766 5444
No 431
>cd06296 PBP1_CatR_like Ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group includes the ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=24.84 E-value=2.3e+02 Score=22.21 Aligned_cols=24 Identities=13% Similarity=0.035 Sum_probs=11.5
Q ss_pred HHHHHHHHHHHhcCCCCcEEEEcch
Q 028376 125 EAVTRRILWIKSTDPKAKILVFSSW 149 (210)
Q Consensus 125 ~al~~~L~~~~~~~~~~K~iVFSQf 149 (210)
..+++.+....++ .+.+++++...
T Consensus 15 ~~~~~gi~~~~~~-~g~~~~~~~~~ 38 (270)
T cd06296 15 SEVLRGVEEAAAA-AGYDVVLSESG 38 (270)
T ss_pred HHHHHHHHHHHHH-cCCeEEEecCC
Confidence 3444444443332 35666665543
No 432
>PRK00254 ski2-like helicase; Provisional
Probab=24.71 E-value=3.4e+02 Score=25.73 Aligned_cols=24 Identities=4% Similarity=-0.017 Sum_probs=19.6
Q ss_pred EEEeeCCCCCCcchhhHhhhHHHHHHhhcC
Q 028376 167 CIKMKGENHKLPSANLQHRNALQKELTRHM 196 (210)
Q Consensus 167 ~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~ 196 (210)
..-+.|+|+ ..+|..+.+.|+++.
T Consensus 298 v~~hHagl~------~~eR~~ve~~F~~G~ 321 (720)
T PRK00254 298 VAFHHAGLG------RTERVLIEDAFREGL 321 (720)
T ss_pred EEEeCCCCC------HHHHHHHHHHHHCCC
Confidence 344789966 999999999999743
No 433
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=24.64 E-value=51 Score=18.38 Aligned_cols=31 Identities=23% Similarity=0.485 Sum_probs=21.4
Q ss_pred CccccccccccccCCCeecCCCCcchHhhHHH
Q 028376 23 DEETCPICQEKLGNQKMVFQCGHFTCCKCFFA 54 (210)
Q Consensus 23 ~~~~C~iC~~~~~~~~~~~~CgH~fC~~C~~~ 54 (210)
+...|..+.+.... ..-..|+-.+|..|...
T Consensus 2 ~~~~C~~H~~~~~~-~~C~~C~~~~C~~C~~~ 32 (42)
T PF00643_consen 2 QEPKCPEHPEEPLS-LFCEDCNEPLCSECTVS 32 (42)
T ss_dssp SSSB-SSTTTSBEE-EEETTTTEEEEHHHHHT
T ss_pred cCccCccCCccceE-EEecCCCCccCccCCCC
Confidence 34578888765332 35678999999999874
No 434
>PRK01343 zinc-binding protein; Provisional
Probab=24.62 E-value=39 Score=21.01 Aligned_cols=14 Identities=21% Similarity=0.560 Sum_probs=10.8
Q ss_pred CccccccCCccccc
Q 028376 68 NEWVMCPTCRQRTD 81 (210)
Q Consensus 68 ~~~~~CP~Cr~~~~ 81 (210)
.....||+|++++.
T Consensus 7 ~p~~~CP~C~k~~~ 20 (57)
T PRK01343 7 RPTRPCPECGKPST 20 (57)
T ss_pred CCCCcCCCCCCcCc
Confidence 35678999999764
No 435
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=24.52 E-value=2.2e+02 Score=23.83 Aligned_cols=24 Identities=8% Similarity=0.142 Sum_probs=11.8
Q ss_pred hHHHHHHHHHHHHhCCceEEEeeC
Q 028376 149 WNDVLDVLEHAFIANNITCIKMKG 172 (210)
Q Consensus 149 f~~~L~li~~~L~~~gi~~~~~~G 172 (210)
|..++.-++.++.++|+......+
T Consensus 40 ~~~~~~gi~~~a~~~g~~l~i~~~ 63 (330)
T PRK10355 40 WQKDRDIFVKKAESLGAKVFVQSA 63 (330)
T ss_pred HHHHHHHHHHHHHHcCCEEEEECC
Confidence 445555555555555555444433
No 436
>TIGR03117 cas_csf4 CRISPR-associated DEAD/DEAH-box helicase Csf4. Members of this family show up near CRISPR repeats in Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens DSM 15236. In the latter two species, the CRISPR/cas locus is found on a plasmid. This family is one of several characteristic of a type of CRISPR-associated (cas) gene cluster we designate Aferr after A. ferrooxidans, where it is both chromosomal and the only type of cas gene cluster found. The gene is designated csf4 (CRISPR/cas Subtype as in A. ferrooxidans protein 1), as it lies farthest (fourth closest) from the repeats in the A. ferrooxidans genome.
Probab=24.36 E-value=4.3e+02 Score=24.91 Aligned_cols=63 Identities=10% Similarity=0.142 Sum_probs=42.8
Q ss_pred hHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceE-EEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376 123 KIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITC-IKMKGENHKLPSANLQHRNALQKELTRH 195 (210)
Q Consensus 123 Ki~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~-~~~~G~m~~~~~~~~~~R~~~l~~F~~~ 195 (210)
-.+++.+.|..+.....+.--|.||+|..|-.+ ...|.. ++++ +.+.|. ...|...+++|...
T Consensus 454 ~~~~~~~~~~~~~~~~~G~~lvLfTS~~~~~~~-~~~l~~-~l~~~~l~qg~--------~~~~~~l~~~f~~~ 517 (636)
T TIGR03117 454 WLENVSLSTAAILRKAQGGTLVLTTAFSHISAI-GQLVEL-GIPAEIVIQSE--------KNRLASAEQQFLAL 517 (636)
T ss_pred HHHHHHHHHHHHHHHcCCCEEEEechHHHHHHH-HHHHHh-hcCCCEEEeCC--------CccHHHHHHHHHHh
Confidence 456677777777776667667889999988654 444543 3333 345665 33678899999984
No 437
>cd08191 HHD 6-hydroxyhexanoate dehydrogenase (HHD) catalyzes the oxidation of 6-hydroxyhexanoate to 6-oxohexanoate. 6-hydroxyhexanoate dehydrogenase (HHD). The 6-hydroxyhexanoate dehydrogenase catalyzes the oxidation of 6-hydroxyhexanoate to 6-oxohexanoate. Some bacteria can grow on cyclic ketones, cyclohexylamine, and alcohols as sole carbon source. Cyclohexylamine is an insecticide and antiseptic in various industries and is considered a possible environmental pollutant. The degradation of these chemical compounds are through the cyclohexanol and cyclohexanone biological oxidation pathway. The intermediates of this pathway include cyclohexanol, cyclohexanone, e-caprolactone, 6-hydroxyhexanoate, 6-oxohexanoate and adipate. The 6-hydroxyhexanoate dehydrogenase catalyzes the oxidation of 6-hydroxyhexanoate to 6-oxohexanoate.
Probab=24.33 E-value=4.7e+02 Score=22.63 Aligned_cols=34 Identities=18% Similarity=0.231 Sum_probs=25.2
Q ss_pred CcEEEEcc---h-HHHHHHHHHHHHhCCceEEEeeCCC
Q 028376 141 AKILVFSS---W-NDVLDVLEHAFIANNITCIKMKGEN 174 (210)
Q Consensus 141 ~K~iVFSQ---f-~~~L~li~~~L~~~gi~~~~~~G~m 174 (210)
.|++|.+. + ...++.+...|+.+|+.+..|+|-.
T Consensus 23 ~~~livt~~~~~~~~~~~~v~~~L~~~~~~~~~f~~v~ 60 (386)
T cd08191 23 SRALIVTDERMAGTPVFAELVQALAAAGVEVEVFDGVL 60 (386)
T ss_pred CeEEEEECcchhhcchHHHHHHHHHHcCCeEEEECCCC
Confidence 56766553 2 2577888888999999988888875
No 438
>PRK12759 bifunctional gluaredoxin/ribonucleoside-diphosphate reductase subunit beta; Provisional
Probab=23.94 E-value=1e+02 Score=27.13 Aligned_cols=32 Identities=16% Similarity=0.242 Sum_probs=28.0
Q ss_pred cEEEEcc-hHHHHHHHHHHHHhCCceEEEeeCC
Q 028376 142 KILVFSS-WNDVLDVLEHAFIANNITCIKMKGE 173 (210)
Q Consensus 142 K~iVFSQ-f~~~L~li~~~L~~~gi~~~~~~G~ 173 (210)
+++|||+ |-..-..+...|+.+||+|..++=.
T Consensus 3 ~V~vys~~~Cp~C~~aK~~L~~~gi~~~~idi~ 35 (410)
T PRK12759 3 EVRIYTKTNCPFCDLAKSWFGANDIPFTQISLD 35 (410)
T ss_pred cEEEEeCCCCHHHHHHHHHHHHCCCCeEEEECC
Confidence 6889988 7788889999999999999888665
No 439
>PLN02160 thiosulfate sulfurtransferase
Probab=23.92 E-value=1.4e+02 Score=21.67 Aligned_cols=38 Identities=16% Similarity=0.063 Sum_probs=28.4
Q ss_pred CCCCcEEEEcchHHHHHHHHHHHHhCCce-EEEeeCCCC
Q 028376 138 DPKAKILVFSSWNDVLDVLEHAFIANNIT-CIKMKGENH 175 (210)
Q Consensus 138 ~~~~K~iVFSQf~~~L~li~~~L~~~gi~-~~~~~G~m~ 175 (210)
+++.++|+|..--.--......|...|+. ...|+|+|.
T Consensus 79 ~~~~~IivyC~sG~RS~~Aa~~L~~~G~~~v~~l~GG~~ 117 (136)
T PLN02160 79 NPADDILVGCQSGARSLKATTELVAAGYKKVRNKGGGYL 117 (136)
T ss_pred CCCCcEEEECCCcHHHHHHHHHHHHcCCCCeeecCCcHH
Confidence 45677888888666666678888999996 556899854
No 440
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=23.91 E-value=40 Score=28.10 Aligned_cols=46 Identities=22% Similarity=0.482 Sum_probs=30.6
Q ss_pred CccccccccccccCCCeecC---CC--CcchHhhHHHHHHHhhhccccCCCccccccCCccc
Q 028376 23 DEETCPICQEKLGNQKMVFQ---CG--HFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQR 79 (210)
Q Consensus 23 ~~~~C~iC~~~~~~~~~~~~---Cg--H~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~ 79 (210)
....||+|...+....+... =| -.-|.-|...|. ..+.+|-.|...
T Consensus 184 ~~~~CPvCGS~PvaSmV~~g~~~~GlRYL~CslC~teW~-----------~VR~KC~nC~~t 234 (308)
T COG3058 184 SRQYCPVCGSMPVASMVQIGETEQGLRYLHCSLCETEWH-----------YVRVKCSNCEQS 234 (308)
T ss_pred ccccCCCcCCCCcceeeeecCccccchhhhhhhHHHHHH-----------HHHHHhcccccc
Confidence 34579999887765322221 22 234899999993 456799999774
No 441
>PF08915 tRNA-Thr_ED: Archaea-specific editing domain of threonyl-tRNA synthetase; InterPro: IPR015011 Archaea-specific editing domain of threonyl-tRNA synthetase, with marked structural similarity to D-amino acids deacylases found in eubacteria and eukaryotes. This domain can bind D-amino acids, and ensures high fidelity during translation. It is especially responsible for removing incorrectly attached serine from tRNA-Thr. The domain forms a fold that can be defined as two layers of beta-sheets (a three-stranded sheet and a five-stranded sheet), with two alpha-helices located adjacent to the five-stranded sheet []. ; GO: 0004829 threonine-tRNA ligase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0005737 cytoplasm; PDB: 3PD4_B 3PD3_A 2HL0_A 2HL1_A 2HKZ_A 3PD5_B 2HL2_A 3PD2_B 1Y2Q_A.
Probab=23.83 E-value=3.1e+02 Score=20.37 Aligned_cols=47 Identities=15% Similarity=0.348 Sum_probs=35.5
Q ss_pred hHHHHHHHHHHHHhcCCCCcEEEEcc------------hHHHHHHHHHHHHhCCceEEE
Q 028376 123 KIEAVTRRILWIKSTDPKAKILVFSS------------WNDVLDVLEHAFIANNITCIK 169 (210)
Q Consensus 123 Ki~al~~~L~~~~~~~~~~K~iVFSQ------------f~~~L~li~~~L~~~gi~~~~ 169 (210)
=++..++.|.++..+-...++|||+- =..+|+-++..|+..|+...|
T Consensus 55 vv~~av~eI~~~a~kv~~~~ivlyPyAHLSs~La~P~~A~~iL~~le~~L~~~g~eV~r 113 (138)
T PF08915_consen 55 VVEKAVEEIKWVAKKVKAKRIVLYPYAHLSSSLASPDVAVEILKKLEERLKSRGFEVYR 113 (138)
T ss_dssp HHHHHHHHHHHHHHHTT-SEEEEEE-GGGSSSB--HHHHHHHHHHHHHHHHHTT-EEEE
T ss_pred HHHHHHHHHHHHHHhcCCCEEEEeCcccccCCcCChHHHHHHHHHHHHHHHhCCCeEEE
Confidence 47788888888888777888888764 456789999999999987654
No 442
>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]
Probab=23.81 E-value=2.3e+02 Score=27.53 Aligned_cols=65 Identities=14% Similarity=0.042 Sum_probs=52.9
Q ss_pred CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
.-.|..|+++.+.+.... +..+||-+-...--..++..|.++||++..+.-+ -..|.+-|-.+..
T Consensus 411 ~~~K~~Aiv~~I~~~~~~--gqPvLvgT~sie~SE~ls~~L~~~~i~h~VLNAk--------~h~~EA~Iia~AG 475 (822)
T COG0653 411 EEEKFKAIVEDIKERHEK--GQPVLVGTVSIEKSELLSKLLRKAGIPHNVLNAK--------NHAREAEIIAQAG 475 (822)
T ss_pred hHHHHHHHHHHHHHHHhc--CCCEEEcCcceecchhHHHHHHhcCCCceeeccc--------cHHHHHHHHhhcC
Confidence 357899999999887754 7899999998888899999999999999888877 4466666665553
No 443
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=23.79 E-value=32 Score=20.98 Aligned_cols=32 Identities=25% Similarity=0.501 Sum_probs=16.4
Q ss_pred cccccc--ccccccCC----C--ee-cCCCCcchHhhHHHH
Q 028376 24 EETCPI--CQEKLGNQ----K--MV-FQCGHFTCCKCFFAM 55 (210)
Q Consensus 24 ~~~C~i--C~~~~~~~----~--~~-~~CgH~fC~~C~~~~ 55 (210)
...||- |...+... . +. ..|++.||..|-..|
T Consensus 18 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~ 58 (64)
T PF01485_consen 18 IRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPW 58 (64)
T ss_dssp CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSES
T ss_pred ccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCccc
Confidence 357877 86654321 1 22 348999999887655
No 444
>cd08176 LPO Lactadehyde:propanediol oxidoreductase (LPO) catalyzes the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria. Lactadehyde:propanediol oxidoreductase (LPO) is a member of the group III iron-activated dehydrogenases which catalyze the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria. L-Fucose and L-rhamnose is used by Escherichia coli through an inducible pathway mediated by the fucose regulon comprising four linked oeprons fucO, fucA, fucPIK, and fucR. The fucA-encoded aldolase catalyzes the formation of dihydroxyacetone phosphate and L-lactaldehyde. Under anaerobic conditions, with NADH as a cofactor, lactaldehyde is converted by a fucO-encoded Lactadehyde:propanediol oxidoreductase (LPO) to L-1,2-propanediol, which is excreted as a fermentation product. In mutant strains, E. coli adapted to grow on L-1,2-propanediol, FucO catalyzes the oxidation of the polyol to
Probab=23.58 E-value=4.6e+02 Score=22.54 Aligned_cols=55 Identities=9% Similarity=0.125 Sum_probs=29.5
Q ss_pred CcEEEEcc---hH-HHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCC
Q 028376 141 AKILVFSS---WN-DVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPS 198 (210)
Q Consensus 141 ~K~iVFSQ---f~-~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~ 198 (210)
.|++|.+. +. ..++.+...|+.+|+.+..|+|-.++ -+...=.++++.++..++|
T Consensus 29 ~~~lvv~~~~~~~~~~~~~v~~~L~~~~~~~~~f~~v~~~---p~~~~v~~~~~~~~~~~~D 87 (377)
T cd08176 29 KKALIVTDKGLVKIGVVEKVTDVLDEAGIDYVIYDGVKPN---PTITNVKDGLAVFKKEGCD 87 (377)
T ss_pred CeEEEECCchHhhcCcHHHHHHHHHHcCCeEEEeCCCCCC---CCHHHHHHHHHHHHhcCCC
Confidence 35655432 22 35667777787778877777663210 1123334455555554444
No 445
>cd06318 PBP1_ABC_sugar_binding_like_9 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=23.56 E-value=2.6e+02 Score=22.14 Aligned_cols=14 Identities=7% Similarity=-0.083 Sum_probs=5.2
Q ss_pred HHHHHHHHHHhCCc
Q 028376 152 VLDVLEHAFIANNI 165 (210)
Q Consensus 152 ~L~li~~~L~~~gi 165 (210)
++.-++.++++.|+
T Consensus 17 ~~~~i~~~~~~~g~ 30 (282)
T cd06318 17 LTEAAKAHAKALGY 30 (282)
T ss_pred HHHHHHHHHHHcCC
Confidence 33333333333333
No 446
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=23.53 E-value=42 Score=23.52 Aligned_cols=12 Identities=17% Similarity=0.202 Sum_probs=9.1
Q ss_pred eecCCCCcchHh
Q 028376 39 MVFQCGHFTCCK 50 (210)
Q Consensus 39 ~~~~CgH~fC~~ 50 (210)
..+.|||+|=..
T Consensus 4 ~CtrCG~vf~~g 15 (112)
T COG3364 4 QCTRCGEVFDDG 15 (112)
T ss_pred eecccccccccc
Confidence 457899998665
No 447
>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=23.51 E-value=47 Score=19.39 Aligned_cols=47 Identities=23% Similarity=0.563 Sum_probs=27.1
Q ss_pred ccccccccccCCCee--cCCCCcchHhhHHHHHHHhhhccccCCCccccccCCc
Q 028376 26 TCPICQEKLGNQKMV--FQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCR 77 (210)
Q Consensus 26 ~C~iC~~~~~~~~~~--~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr 77 (210)
.|.+|........++ -.|+..|+..|+......... ....-.||.|+
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~-----~~~~w~C~~C~ 49 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEKAEEI-----PSGDWYCPNCR 49 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHSHHSH-----HSSSBSSHHHH
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCCCChhhccC-----CCCcEECcCCc
Confidence 378887744433344 378888888888765332111 12245677764
No 448
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=23.46 E-value=4.2e+02 Score=21.81 Aligned_cols=47 Identities=15% Similarity=0.219 Sum_probs=33.1
Q ss_pred hHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCCCCC
Q 028376 149 WNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPSSQS 201 (210)
Q Consensus 149 f~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~~~~ 201 (210)
|..+++-++.+++++|+....+..... ...-.+.++.+....+++.+
T Consensus 74 ~~~~~~gi~~~~~~~g~~~~~~~~~~~------~~~~~~~i~~l~~~~vdgii 120 (341)
T PRK10703 74 FAEIIEAVEKNCYQKGYTLILCNAWNN------LEKQRAYLSMLAQKRVDGLL 120 (341)
T ss_pred HHHHHHHHHHHHHHCCCEEEEEeCCCC------HHHHHHHHHHHHHcCCCEEE
Confidence 778888888889999988777665433 55556677777765666543
No 449
>PF04343 DUF488: Protein of unknown function, DUF488; InterPro: IPR007438 This family includes several proteins of uncharacterised function.
Probab=23.35 E-value=1.5e+02 Score=21.03 Aligned_cols=45 Identities=16% Similarity=0.161 Sum_probs=31.2
Q ss_pred hHHHHHHHHHHHHhcCCCCcEEEE-cchHH------HHHHHHHHHHhCCceEEEeeC
Q 028376 123 KIEAVTRRILWIKSTDPKAKILVF-SSWND------VLDVLEHAFIANNITCIKMKG 172 (210)
Q Consensus 123 Ki~al~~~L~~~~~~~~~~K~iVF-SQf~~------~L~li~~~L~~~gi~~~~~~G 172 (210)
|++.+++.|. ..+.++||= -.|+. -=+.++..|..+||.|+-+..
T Consensus 1 ~~e~f~~~l~-----~~~i~~lVDVR~~P~S~~~~~~k~~l~~~l~~~gi~Y~~~~~ 52 (122)
T PF04343_consen 1 SIERFYDLLK-----KNGIRVLVDVRLWPRSRKPGFNKEDLASFLEEAGIEYVWLPE 52 (122)
T ss_pred CHHHHHHHHH-----HCCCeEEEEECCCCCCCCCCCCHHHHHHHHHHCCceEeechh
Confidence 4566666444 347778876 44444 347788999999999987743
No 450
>PF13297 Telomere_Sde2_2: Telomere stability C-terminal
Probab=23.35 E-value=1.8e+02 Score=18.26 Aligned_cols=42 Identities=33% Similarity=0.421 Sum_probs=29.2
Q ss_pred EcchHHH----HHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCC
Q 028376 146 FSSWNDV----LDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPS 198 (210)
Q Consensus 146 FSQf~~~----L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~ 198 (210)
|+.+.++ ++.+..+|...|.++ -|+ ..+|++-+=.-+...++
T Consensus 6 f~sa~eLe~lGldrLK~~L~a~GLKc---GGT--------l~ERA~RLfs~kg~~~~ 51 (60)
T PF13297_consen 6 FSSAEELEALGLDRLKSALMALGLKC---GGT--------LQERAARLFSVKGLPLE 51 (60)
T ss_pred cCCHHHHHHhCHHHHHHHHHHcCCcc---CCC--------HHHHHHHHHHhcCCChh
Confidence 5566555 788999999999986 354 78888776555543333
No 451
>PF11497 NADH_Oxid_Nqo15: NADH-quinone oxidoreductase chain 15; InterPro: IPR021093 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This entry represents subunit 15 of NADH-quinone oxidoreductase, also known as Complex I. The nqo15 subunit has probably a role in complex stabilisation, and may be also involved in the storage of iron for iron-sulphur cluster regeneration in the complex [].; PDB: 3M9S_7 3I9V_7 3IAM_H 2FUG_H 3IAS_7 2YBB_7.
Probab=23.32 E-value=61 Score=23.20 Aligned_cols=25 Identities=16% Similarity=0.379 Sum_probs=18.9
Q ss_pred EEcchHHHHHHHHHHHHhCCceEEE
Q 028376 145 VFSSWNDVLDVLEHAFIANNITCIK 169 (210)
Q Consensus 145 VFSQf~~~L~li~~~L~~~gi~~~~ 169 (210)
+|-+|..+|.+++..-.+.|+.|-+
T Consensus 9 lY~aWvell~Wl~eyA~~~g~~fek 33 (127)
T PF11497_consen 9 LYRAWVELLGWLREYAAERGLRFEK 33 (127)
T ss_dssp HHHHHHHHHHHHHHHHHHTT-EEEE
T ss_pred HHHHHHHHHHHHHHHHHHcCCceee
Confidence 4678888888888888888887754
No 452
>COG5011 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.26 E-value=89 Score=24.81 Aligned_cols=37 Identities=16% Similarity=0.341 Sum_probs=26.5
Q ss_pred EcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhH
Q 028376 146 FSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQ 183 (210)
Q Consensus 146 FSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~ 183 (210)
|.+-.+.+.++++..+++|++. -|+|+-+-.+.|+.+
T Consensus 15 fvShLdlmRlidR~iRRAglpi-ayT~GFhP~prmsia 51 (228)
T COG5011 15 FVSHLDLMRLIDRTIRRAGLPI-AYTGGFHPHPRMSIA 51 (228)
T ss_pred HHHHHHHHHHHHHHHHhcCCce-eecCCCCCCCceeec
Confidence 4455566778899999999995 588887744545443
No 453
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.16 E-value=41 Score=21.43 Aligned_cols=15 Identities=33% Similarity=0.514 Sum_probs=11.5
Q ss_pred CccccccCCcccccC
Q 028376 68 NEWVMCPTCRQRTDI 82 (210)
Q Consensus 68 ~~~~~CP~Cr~~~~~ 82 (210)
.....||.|.+++.-
T Consensus 5 ~~~v~CP~Cgkpv~w 19 (65)
T COG3024 5 RITVPCPTCGKPVVW 19 (65)
T ss_pred cccccCCCCCCcccc
Confidence 456789999998654
No 454
>PF09171 DUF1886: Domain of unknown function (DUF1886); InterPro: IPR015254 This entry represents a set of known and suspected archaeal N-glycosylase/DNA lyases. These DNA repair enzymes are part of the base excision repair (BER) pathway; they protect from oxidative damage by removing the major product of DNA oxidation, 8-oxoguanine (GO), from single- and double-stranded DNA substrates [].Cleavage of the N-glycosidic bond between the aberrant base and the sugar-phosphate backbone generates an apurinic (AP) site. Subsequently, the phosphodiester bond 3' from the AP site is cleaved by an elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate. The protein contains two alpha-helical subdomains, with the 8-oxoguanine binding site located in a cleft at their interface. A helix-hairpin-helix (HhH) structural motif and a Gly/Pro-rich sequence followed by a conserved Asp (HhH-GPD motif) are present [].; GO: 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0016799 hydrolase activity, hydrolyzing N-glycosyl compounds; PDB: 1XQP_A 1XQO_A 1XG7_A.
Probab=23.10 E-value=24 Score=28.86 Aligned_cols=26 Identities=27% Similarity=0.512 Sum_probs=22.6
Q ss_pred chHHHHHHHHHHHHhcCCCCcEEEEc
Q 028376 122 TKIEAVTRRILWIKSTDPKAKILVFS 147 (210)
Q Consensus 122 sKi~al~~~L~~~~~~~~~~K~iVFS 147 (210)
..+..|.+.|......++..|.|||+
T Consensus 120 ~~l~~l~~~La~~L~~~~~~KTiVFA 145 (246)
T PF09171_consen 120 EDLEELWRELAKILNSKPESKTIVFA 145 (246)
T ss_dssp CTHHHHHHHHHHHHTS-TTSHHHHHH
T ss_pred hhHHHHHHHHHHHhCCCCccchhhHH
Confidence 66889999999988999999999997
No 455
>KOG2949 consensus Ketopantoate hydroxymethyltransferase [Coenzyme transport and metabolism]
Probab=23.07 E-value=2e+02 Score=23.49 Aligned_cols=41 Identities=22% Similarity=0.440 Sum_probs=34.2
Q ss_pred E-cchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 146 F-SSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 146 F-SQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
| |.|.+-++-.-..+++.|...+++.|+ .+-|..++++.-.
T Consensus 111 yeS~~sda~knAv~vmk~~g~~~vK~EgG--------s~~~~~~~~~l~e 152 (306)
T KOG2949|consen 111 YESSWSDAVKNAVRVMKEGGMDAVKLEGG--------SNSRITAAKRLVE 152 (306)
T ss_pred ccccHHHHHHHHHHHHHhcCCceEEEccC--------cHHHHHHHHHHHH
Confidence 5 889999999999999999999999998 5577777777654
No 456
>PF00290 Trp_syntA: Tryptophan synthase alpha chain; InterPro: IPR002028 Tryptophan synthase (4.2.1.20 from EC) catalyzes the last step in the biosynthesis of tryptophan [, ]: L-serine + 1-(indol-3-yl)glycerol 3-phosphate = L-tryptophan + glyceraldehyde 3-phosphate + H2O It has two functional domains, each found in bacteria and plants on a separate subunit. In Escherichia coli, the 2 subunits, A and B, are encoded by the trpA and trpB genes respectively. The alpha chain is for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate and the beta chain IPR006653 from INTERPRO is for the synthesis of tryptophan from indole and serine. In fungi the two domains are fused together in a single multifunctional protein, in the order: (NH2-A-B-COOH) [, ]. The two domains of the Neurospora crassa polypeptide are linked by a connector of 54-amino acid residues that has less than 25% identity to the 45-residue connector of the Saccharomyces cerevisiae (Baker's yeast) polypeptide. Two acidic residues are believed to serve as proton donors/acceptors in the enzyme's catalytic mechanism.; GO: 0004834 tryptophan synthase activity, 0006568 tryptophan metabolic process; PDB: 1TJR_B 1RD5_B 1K8X_A 1QOQ_A 1KFE_A 1KFB_A 2CLO_A 1TTP_A 2RH9_A 1K7F_A ....
Probab=23.06 E-value=2.5e+02 Score=23.12 Aligned_cols=36 Identities=17% Similarity=0.391 Sum_probs=28.2
Q ss_pred CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHH
Q 028376 120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDV 155 (210)
Q Consensus 120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~l 155 (210)
.+..++.+++.+.+++...++..+|+++=|..++..
T Consensus 67 ~G~~~~~~~~~~~~ir~~~~~~pivlm~Y~N~i~~~ 102 (259)
T PF00290_consen 67 NGFTLEKIFELVKEIRKKEPDIPIVLMTYYNPIFQY 102 (259)
T ss_dssp TT--HHHHHHHHHHHHHHCTSSEEEEEE-HHHHHHH
T ss_pred CCCCHHHHHHHHHHHhccCCCCCEEEEeeccHHhcc
Confidence 468899999999999977899999999998877654
No 457
>cd06285 PBP1_LacI_like_7 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=22.99 E-value=2.9e+02 Score=21.68 Aligned_cols=33 Identities=6% Similarity=0.098 Sum_probs=16.6
Q ss_pred CCcEEEEcch---HHHHHHHHHHHHhCCceEEEeeCC
Q 028376 140 KAKILVFSSW---NDVLDVLEHAFIANNITCIKMKGE 173 (210)
Q Consensus 140 ~~K~iVFSQf---~~~L~li~~~L~~~gi~~~~~~G~ 173 (210)
+-+++++... ....+.++. |...++.-+-+.+.
T Consensus 29 ~~~~~~~~~~~~~~~~~~~i~~-l~~~~~dgiii~~~ 64 (265)
T cd06285 29 GYSTFVANTGDNPDAQRRAIEM-LLDRRVDGLILGDA 64 (265)
T ss_pred CCEEEEEeCCCCHHHHHHHHHH-HHHcCCCEEEEecC
Confidence 4566665543 233344444 44555665555443
No 458
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=22.94 E-value=8.2 Score=20.71 Aligned_cols=27 Identities=22% Similarity=0.436 Sum_probs=10.8
Q ss_pred CcchHhhHHHHHHHhhhccccCCCccccccCCcc
Q 028376 45 HFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQ 78 (210)
Q Consensus 45 H~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~ 78 (210)
|.||..|=.+.... . .+....||.|+.
T Consensus 3 ~rfC~~CG~~t~~~----~---~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 3 HRFCGRCGAPTKPA----P---GGWARRCPSCGH 29 (32)
T ss_dssp TSB-TTT--BEEE-----S---SSS-EEESSSS-
T ss_pred CcccCcCCccccCC----C---CcCEeECCCCcC
Confidence 55666665543110 0 234556777764
No 459
>PF11019 DUF2608: Protein of unknown function (DUF2608); InterPro: IPR022565 This family is conserved in Bacteria. The function is not known.
Probab=22.94 E-value=2.9e+02 Score=22.56 Aligned_cols=49 Identities=20% Similarity=0.148 Sum_probs=38.2
Q ss_pred CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhCCceEEEe
Q 028376 120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIANNITCIKM 170 (210)
Q Consensus 120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~ 170 (210)
.-.|-.+|...|..+.. ...|+|....=...|.-++.+|...||.|.-|
T Consensus 160 ~~~KG~~L~~fL~~~~~--~pk~IIfIDD~~~nl~sv~~a~k~~~I~f~G~ 208 (252)
T PF11019_consen 160 GQDKGEVLKYFLDKINQ--SPKKIIFIDDNKENLKSVEKACKKSGIDFIGF 208 (252)
T ss_pred CCccHHHHHHHHHHcCC--CCCeEEEEeCCHHHHHHHHHHHhhCCCcEEEE
Confidence 35677777777766543 35578888889999999999999999998655
No 460
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=22.79 E-value=37 Score=20.71 Aligned_cols=15 Identities=20% Similarity=0.470 Sum_probs=7.5
Q ss_pred CccccccCCcccccC
Q 028376 68 NEWVMCPTCRQRTDI 82 (210)
Q Consensus 68 ~~~~~CP~Cr~~~~~ 82 (210)
....+||.|...+..
T Consensus 22 ~~PatCP~C~a~~~~ 36 (54)
T PF09237_consen 22 EQPATCPICGAVIRQ 36 (54)
T ss_dssp S--EE-TTT--EESS
T ss_pred CCCCCCCcchhhccc
Confidence 556789999887654
No 461
>PF03690 UPF0160: Uncharacterised protein family (UPF0160); InterPro: IPR003226 The function of this domain is not known, but it is found in several uncharacterised proteins and a probable metal dependent protein hydrolase.
Probab=22.75 E-value=2.8e+02 Score=23.69 Aligned_cols=38 Identities=24% Similarity=0.425 Sum_probs=28.7
Q ss_pred hcCCCCcEEEEcc---hHHHHHHHHHHHHh-CCceEEEeeCC
Q 028376 136 STDPKAKILVFSS---WNDVLDVLEHAFIA-NNITCIKMKGE 173 (210)
Q Consensus 136 ~~~~~~K~iVFSQ---f~~~L~li~~~L~~-~gi~~~~~~G~ 173 (210)
+.+++.++|+|.+ |..+|.-++..+.. ..|.|+-|...
T Consensus 207 ~v~~sg~Il~l~~~~Pwk~~l~~le~e~~~~~~i~fvi~p~~ 248 (318)
T PF03690_consen 207 EVHPSGRILVLDRSCPWKEHLFELEEELKIEGEILFVIYPDG 248 (318)
T ss_pred ccCCCCCEEEecCCCcHHHHHHHHhhhhCCCCceEEEEEECC
Confidence 3578899999998 77888888877664 35778877544
No 462
>KOG3849 consensus GDP-fucose protein O-fucosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=22.73 E-value=2e+02 Score=24.17 Aligned_cols=51 Identities=20% Similarity=0.205 Sum_probs=39.5
Q ss_pred hHHHHHHHHHHHHhcCCCCcEE-EEcchHHHHHHHHHHHHhCCceEEEeeCC
Q 028376 123 KIEAVTRRILWIKSTDPKAKIL-VFSSWNDVLDVLEHAFIANNITCIKMKGE 173 (210)
Q Consensus 123 Ki~al~~~L~~~~~~~~~~K~i-VFSQf~~~L~li~~~L~~~gi~~~~~~G~ 173 (210)
-.+++++.|+.+...-.+.|+| |=|.-..|++-|..+|...+|...++.-.
T Consensus 282 sk~~I~rqik~~v~si~dakSVfVAsDs~hmi~Eln~aL~~~~i~vh~l~pd 333 (386)
T KOG3849|consen 282 SKQQILRQIKEKVGSIGDAKSVFVASDSDHMIDELNEALKPYEIEVHRLEPD 333 (386)
T ss_pred cHHHHHHHHHHHHhhhcccceEEEeccchhhhHHHHHhhcccceeEEecCcc
Confidence 3466777777666655567775 66788899999999999999998887543
No 463
>PF00701 DHDPS: Dihydrodipicolinate synthetase family; InterPro: IPR002220 Dihydropicolinate synthase (DHDPS) is the key enzyme in lysine biosynthesis via the diaminopimelate pathway of prokaryotes, some phycomycetes and higher plants. The enzyme catalyses the condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a ping-pong mechanism in which pyruvate binds to the enzyme by forming a Schiff-base with a lysine residue []. Three other proteins are structurally related to DHDPS and probably also act via a similar catalytic mechanism. These are Escherichia coli N-acetylneuraminate lyase (4.1.3.3 from EC) (gene nanA), which catalyzes the condensation of N-acetyl-D-mannosamine and pyruvate to form N-acetylneuraminate; Rhizobium meliloti (Sinorhizobium meliloti) protein mosA [], which is involved in the biosynthesis of the rhizopine 3-o-methyl-scyllo-inosamine; and E. coli hypothetical protein yjhH. The sequences of DHDPS from different sources are well-conserved. The structure takes the form of a homotetramer, in which 2 monomers are related by an approximate 2-fold symmetry []. Each monomer comprises 2 domains: an 8-fold alpha-/beta-barrel, and a C-terminal alpha-helical domain. The fold resembles that of N-acetylneuraminate lyase. The active site lysine is located in the barrel domain, and has access via 2 channels on the C-terminal side of the barrel.; GO: 0016829 lyase activity, 0008152 metabolic process; PDB: 3B4U_B 3S8H_A 3QZE_B 1XXX_F 3L21_F 3IRD_A 3A5F_B 3G0S_B 3DAQ_C 3UQN_A ....
Probab=22.73 E-value=2.2e+02 Score=23.40 Aligned_cols=32 Identities=13% Similarity=0.165 Sum_probs=18.3
Q ss_pred hCCceEEEeeCCCCCCcchhhHhhhHHHHHHh
Q 028376 162 ANNITCIKMKGENHKLPSANLQHRNALQKELT 193 (210)
Q Consensus 162 ~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~ 193 (210)
.+|+.-+.+-|++.+...|+.++|.+.++.-.
T Consensus 33 ~~Gv~gl~~~GstGE~~~Lt~~Er~~l~~~~~ 64 (289)
T PF00701_consen 33 EAGVDGLVVLGSTGEFYSLTDEERKELLEIVV 64 (289)
T ss_dssp HTTSSEEEESSTTTTGGGS-HHHHHHHHHHHH
T ss_pred HcCCCEEEECCCCcccccCCHHHHHHHHHHHH
Confidence 44565555666666666666666666655543
No 464
>cd06315 PBP1_ABC_sugar_binding_like_6 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=22.72 E-value=2.7e+02 Score=22.32 Aligned_cols=15 Identities=20% Similarity=-0.048 Sum_probs=6.0
Q ss_pred HHHHHHHHHHhCCce
Q 028376 152 VLDVLEHAFIANNIT 166 (210)
Q Consensus 152 ~L~li~~~L~~~gi~ 166 (210)
+++-++..++++|+.
T Consensus 18 ~~~gi~~~a~~~gy~ 32 (280)
T cd06315 18 VGEGVREAAKAIGWN 32 (280)
T ss_pred HHHHHHHHHHHcCcE
Confidence 333344444444433
No 465
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=22.65 E-value=41 Score=24.65 Aligned_cols=20 Identities=30% Similarity=0.507 Sum_probs=13.0
Q ss_pred cccccccCCCeecCCCCcchH
Q 028376 29 ICQEKLGNQKMVFQCGHFTCC 49 (210)
Q Consensus 29 iC~~~~~~~~~~~~CgH~fC~ 49 (210)
||...-. ..+.-.|||.||.
T Consensus 62 i~qs~~~-rv~rcecghsf~d 81 (165)
T COG4647 62 ICQSAQK-RVIRCECGHSFGD 81 (165)
T ss_pred EEecccc-cEEEEeccccccC
Confidence 5555333 2455689999995
No 466
>TIGR02981 phageshock_pspE phage shock operon rhodanese PspE. Members of this very narrowly defined protein family are proteins active as rhodanese (EC 2.8.1.1) and found in the extended variants of the phage shock protein (psp operon) in Escherichia coli and a few closely related species. Note that the designation phage shock protein PspE has been applied, incorrectly, in many instances where the genome lacks the phage shock regulon entirely.
Probab=22.60 E-value=2.6e+02 Score=19.10 Aligned_cols=38 Identities=8% Similarity=0.111 Sum_probs=25.3
Q ss_pred CCCCcEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCC
Q 028376 138 DPKAKILVFSSWNDVLDVLEHAFIANNITCIKMKGENH 175 (210)
Q Consensus 138 ~~~~K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~ 175 (210)
+.+.++||+..--.--......|.+.|+.-+...|++.
T Consensus 56 ~~~~~vvlyC~~G~rS~~aa~~L~~~G~~~v~~~GG~~ 93 (101)
T TIGR02981 56 DKNDTVKLYCNAGRQSGMAKDILLDMGYTHAENAGGIK 93 (101)
T ss_pred CCCCeEEEEeCCCHHHHHHHHHHHHcCCCeEEecCCHH
Confidence 34456666665444555667899999998666678743
No 467
>PRK05320 rhodanese superfamily protein; Provisional
Probab=22.22 E-value=2.4e+02 Score=23.15 Aligned_cols=37 Identities=8% Similarity=0.048 Sum_probs=28.7
Q ss_pred CCCcEEEEcchHHHHHHHHHHHHhCCce-EEEeeCCCC
Q 028376 139 PKAKILVFSSWNDVLDVLEHAFIANNIT-CIKMKGENH 175 (210)
Q Consensus 139 ~~~K~iVFSQf~~~L~li~~~L~~~gi~-~~~~~G~m~ 175 (210)
++.++++|.+--.--......|+..|+. ...+.|++.
T Consensus 174 kdk~IvvyC~~G~Rs~~Aa~~L~~~Gf~~V~~L~GGi~ 211 (257)
T PRK05320 174 AGKTVVSFCTGGIRCEKAAIHMQEVGIDNVYQLEGGIL 211 (257)
T ss_pred CCCeEEEECCCCHHHHHHHHHHHHcCCcceEEeccCHH
Confidence 4667889988766667778889999996 567899953
No 468
>KOG1356 consensus Putative transcription factor 5qNCA, contains JmjC domain [Transcription]
Probab=22.15 E-value=32 Score=33.01 Aligned_cols=33 Identities=27% Similarity=0.553 Sum_probs=25.8
Q ss_pred ccccccccccccC-CCeecCCCCcchHhhHHHHH
Q 028376 24 EETCPICQEKLGN-QKMVFQCGHFTCCKCFFAMT 56 (210)
Q Consensus 24 ~~~C~iC~~~~~~-~~~~~~CgH~fC~~C~~~~~ 56 (210)
...|..|...+.+ ..+...|||.+|..|+..|.
T Consensus 229 ~~mC~~C~~tlfn~hw~C~~C~~~~Cl~C~r~~~ 262 (889)
T KOG1356|consen 229 REMCDRCETTLFNIHWRCPRCGFGVCLDCYRKWY 262 (889)
T ss_pred chhhhhhcccccceeEEccccCCeeeecchhhcc
Confidence 4568889766553 45668999999999999983
No 469
>cd01445 TST_Repeats Thiosulfate sulfurtransferases (TST) contain 2 copies of the Rhodanese Homology Domain. Only the second repeat contains the catalytically active Cys residue. The role of the 1st repeat is uncertain, but believed to be involved in protein interaction. This CD aligns the 1st and 2nd repeats.
Probab=22.05 E-value=3.2e+02 Score=19.82 Aligned_cols=39 Identities=8% Similarity=-0.122 Sum_probs=26.5
Q ss_pred hcCCCCcEEEEcch---HHHHHHHHHHHHhCCceE-EEeeCCC
Q 028376 136 STDPKAKILVFSSW---NDVLDVLEHAFIANNITC-IKMKGEN 174 (210)
Q Consensus 136 ~~~~~~K~iVFSQf---~~~L~li~~~L~~~gi~~-~~~~G~m 174 (210)
.-+++.++|||..- ...--.+-.+|+..|..- .-|+|+.
T Consensus 91 GI~~~~~vVvY~~~~~~g~~A~r~~~~l~~~G~~~v~ildGG~ 133 (138)
T cd01445 91 GIDLDKHLIATDGDDLGGFTACHIALAARLCGHPDVAILDGGF 133 (138)
T ss_pred CCCCCCeEEEECCCCCcchHHHHHHHHHHHcCCCCeEEeCCCH
Confidence 35678899999853 333345556788888874 4579984
No 470
>PF12683 DUF3798: Protein of unknown function (DUF3798); InterPro: IPR024258 This entry represents functionally uncharacterised proteins that are found in bacteria. They are typically between 247 and 417 amino acids in length. Most of the proteins in this entry have an N-terminal lipoprotein attachment site. These proteins have distant similarity to periplasmic ligand binding families suggesting that this family has a similar role.; PDB: 3QI7_A.
Probab=22.02 E-value=74 Score=26.44 Aligned_cols=31 Identities=23% Similarity=0.403 Sum_probs=23.3
Q ss_pred cCCCCchHHHHHHHHHHHHhcCCCCcEEEEcc
Q 028376 117 QGSYGTKIEAVTRRILWIKSTDPKAKILVFSS 148 (210)
Q Consensus 117 ~~~~SsKi~al~~~L~~~~~~~~~~K~iVFSQ 148 (210)
...+++-.+..+..|..+. .||..|+|||+|
T Consensus 40 Pdnf~~e~EttIskI~~lA-dDp~mKaIVv~q 70 (275)
T PF12683_consen 40 PDNFMSEQETTISKIVSLA-DDPDMKAIVVSQ 70 (275)
T ss_dssp -TTGGGCHHHHHHHHHGGG-G-TTEEEEEEE-
T ss_pred CCcccchHHHHHHHHHHhc-cCCCccEEEEeC
Confidence 3456777888999998775 589999999999
No 471
>KOG2567 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.97 E-value=1.3e+02 Score=23.02 Aligned_cols=30 Identities=20% Similarity=0.200 Sum_probs=23.8
Q ss_pred CCCchHHHHHHHHHHHHhcCCCCcEEEEcch
Q 028376 119 SYGTKIEAVTRRILWIKSTDPKAKILVFSSW 149 (210)
Q Consensus 119 ~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf 149 (210)
..++||.-++..-..+.+ ++..+.||||--
T Consensus 24 ~~g~kirN~i~~A~~~L~-~~~~r~VVfsg~ 53 (179)
T KOG2567|consen 24 KSGSKIRNLIEFATELLQ-KGSHRCVVFSGS 53 (179)
T ss_pred ccCchHHHHHHHHHHHhh-CCCeeEEEEecC
Confidence 446999999988776664 678999999973
No 472
>KOG2169 consensus Zn-finger transcription factor [Transcription]
Probab=21.77 E-value=64 Score=30.27 Aligned_cols=54 Identities=19% Similarity=0.576 Sum_probs=29.2
Q ss_pred ccccccccccCCCeecCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcccccCCCeE
Q 028376 26 TCPICQEKLGNQKMVFQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQRTDIGNIA 86 (210)
Q Consensus 26 ~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~~~~~~~l~ 86 (210)
.|+++...+.-+..-..|.|+ .|+....--.+ +. ....-.||+|.+.....++.
T Consensus 308 ~CPl~~~Rm~~P~r~~~CkHl---QcFD~~~~lq~-n~---~~pTW~CPVC~~~~~~e~l~ 361 (636)
T KOG2169|consen 308 NCPLSKMRMSLPARGHTCKHL---QCFDALSYLQM-NE---QKPTWRCPVCQKAAPFEGLI 361 (636)
T ss_pred cCCcccceeecCCcccccccc---eecchhhhHHh-cc---CCCeeeCccCCccccccchh
Confidence 366665444333333455555 55554321111 11 35666899999987776653
No 473
>TIGR03167 tRNA_sel_U_synt tRNA 2-selenouridine synthase. The Escherichia coli YbbB protein was shown to encode a selenophosphate-dependent tRNA 2-selenouridine synthase, essential for modification of some tRNAs to replace a sulfur atom with selenium. This enzyme works with SelD, the selenium donor protein, which also acts in selenocysteine incorporation. Although the members of this protein family show a fairly deep split, sequences from both sides of the split are supported by co-occurence with, and often proximity to, the selD gene.
Probab=21.72 E-value=2.7e+02 Score=23.55 Aligned_cols=50 Identities=10% Similarity=0.046 Sum_probs=31.3
Q ss_pred hHHHHHHHHHHHHhcCCCCcEEEEcc-hHHHHHHHHHHHHhCCceEEEeeCCC
Q 028376 123 KIEAVTRRILWIKSTDPKAKILVFSS-WNDVLDVLEHAFIANNITCIKMKGEN 174 (210)
Q Consensus 123 Ki~al~~~L~~~~~~~~~~K~iVFSQ-f~~~L~li~~~L~~~gi~~~~~~G~m 174 (210)
|+...++.+.... +.+.++|||.. --.--......|...|+....++|++
T Consensus 59 ~l~~~i~~~~~~~--~~~~~vvvyC~~gG~RS~~aa~~L~~~G~~v~~L~GG~ 109 (311)
T TIGR03167 59 NLAAHVEQWRAFA--DGPPQPLLYCWRGGMRSGSLAWLLAQIGFRVPRLEGGY 109 (311)
T ss_pred HHHHHHHHHHhhc--CCCCcEEEEECCCChHHHHHHHHHHHcCCCEEEecChH
Confidence 4555444443332 22335777763 22335566788999999988999995
No 474
>cd01541 PBP1_AraR Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of AraR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which i
Probab=21.53 E-value=3.1e+02 Score=21.60 Aligned_cols=32 Identities=16% Similarity=0.168 Sum_probs=15.6
Q ss_pred CCcEEEEcc---hHHHHHHHHHHHHhCCceEEEeeC
Q 028376 140 KAKILVFSS---WNDVLDVLEHAFIANNITCIKMKG 172 (210)
Q Consensus 140 ~~K~iVFSQ---f~~~L~li~~~L~~~gi~~~~~~G 172 (210)
+-+++++.. ...-+..++..+ ..++.-+-+.+
T Consensus 29 g~~~~~~~~~~~~~~~~~~i~~l~-~~~vdgii~~~ 63 (273)
T cd01541 29 GYSLLLASTNNDPERERKCLENML-SQGIDGLIIEP 63 (273)
T ss_pred CCEEEEEeCCCCHHHHHHHHHHHH-HcCCCEEEEec
Confidence 456655432 333455555533 34555544444
No 475
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=21.52 E-value=33 Score=31.67 Aligned_cols=24 Identities=25% Similarity=0.488 Sum_probs=18.4
Q ss_pred cCCCCcchHhhHHHHHHHhhhccccCCCccccccCCcc
Q 028376 41 FQCGHFTCCKCFFAMTEQRLIHDNKVKNEWVMCPTCRQ 78 (210)
Q Consensus 41 ~~CgH~fC~~C~~~~~~~~~~~~~~~~~~~~~CP~Cr~ 78 (210)
..||++|+..|+..- ...||.|-.
T Consensus 535 ~~C~avfH~~C~~r~--------------s~~CPrC~R 558 (580)
T KOG1829|consen 535 STCLAVFHKKCLRRK--------------SPCCPRCER 558 (580)
T ss_pred HHHHHHHHHHHHhcc--------------CCCCCchHH
Confidence 589999999998753 233999955
No 476
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=21.43 E-value=82 Score=18.59 Aligned_cols=17 Identities=18% Similarity=0.120 Sum_probs=12.9
Q ss_pred HHHHHHhCCceEEEe-eC
Q 028376 156 LEHAFIANNITCIKM-KG 172 (210)
Q Consensus 156 i~~~L~~~gi~~~~~-~G 172 (210)
-..+|+.+||+|..= +|
T Consensus 20 Q~~~L~~~Gi~~~~~~~G 37 (47)
T PF13986_consen 20 QIRWLRRNGIPFVVRADG 37 (47)
T ss_pred HHHHHHHCCCeeEECCCC
Confidence 457899999998763 44
No 477
>cd06288 PBP1_sucrose_transcription_regulator Ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=21.37 E-value=3.2e+02 Score=21.37 Aligned_cols=13 Identities=8% Similarity=0.189 Sum_probs=6.1
Q ss_pred HHhCCceEEEeeC
Q 028376 160 FIANNITCIKMKG 172 (210)
Q Consensus 160 L~~~gi~~~~~~G 172 (210)
|...++.-+-+.+
T Consensus 52 l~~~~~dgiii~~ 64 (269)
T cd06288 52 LLDHRVDGIIYAT 64 (269)
T ss_pred HHHcCCCEEEEec
Confidence 3444555444444
No 478
>COG0329 DapA Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]
Probab=21.28 E-value=1.9e+02 Score=24.22 Aligned_cols=33 Identities=18% Similarity=0.366 Sum_probs=18.4
Q ss_pred HhCCceEEEeeCCCCCCcchhhHhhhHHHHHHh
Q 028376 161 IANNITCIKMKGENHKLPSANLQHRNALQKELT 193 (210)
Q Consensus 161 ~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~ 193 (210)
..+|+.-+.+-|+..+...|+.++|.++++...
T Consensus 35 i~~Gv~gi~~~GttGE~~~Ls~eEr~~v~~~~v 67 (299)
T COG0329 35 IAAGVDGLVVLGTTGESPTLTLEERKEVLEAVV 67 (299)
T ss_pred HHcCCCEEEECCCCccchhcCHHHHHHHHHHHH
Confidence 344444455556666666666666666655544
No 479
>cd01852 AIG1 AIG1 (avrRpt2-induced gene 1). This represents Arabidoposis protein AIG1 that appears to be involved in plant resistance to bacteria. The Arabidopsis disease resistance gene RPS2 is involved in recognition of bacterial pathogens carrying the avirulence gene avrRpt2. AIG1 exhibits RPS2- and avrRpt1-dependent induction early after infection with Pseudomonas syringae carrying avrRpt2. This subfamily also includes IAN-4 protein, which has GTP-binding activity and shares sequence homology with a novel family of putative GTP-binding proteins: the immuno-associated nucleotide (IAN) family. The evolutionary conservation of the IAN family provides a unique example of a plant pathogen response gene conserved in animals. The IAN/IMAP subfamily has been proposed to regulate apoptosis in vertebrates and angiosperm plants, particularly in relation to cancer, diabetes, and infections. The human IAN genes were renamed GIMAP (GTPase of the immunity associated proteins).
Probab=21.14 E-value=2.7e+02 Score=21.16 Aligned_cols=54 Identities=9% Similarity=0.110 Sum_probs=34.6
Q ss_pred CchHHHHHHHHHHHHhcCCC-CcEEEEcchHHHH------------HHHHHHHHhCCceEEEeeCCC
Q 028376 121 GTKIEAVTRRILWIKSTDPK-AKILVFSSWNDVL------------DVLEHAFIANNITCIKMKGEN 174 (210)
Q Consensus 121 SsKi~al~~~L~~~~~~~~~-~K~iVFSQf~~~L------------~li~~~L~~~gi~~~~~~G~m 174 (210)
+.--..+++.|.++.....- .-+|||++|..+- ..+...+++.|-+|..|+..-
T Consensus 97 t~~d~~~l~~l~~~fg~~~~~~~ivv~T~~d~l~~~~~~~~~~~~~~~l~~l~~~c~~r~~~f~~~~ 163 (196)
T cd01852 97 TEEEEQAVETLQELFGEKVLDHTIVLFTRGDDLEGGTLEDYLENSCEALKRLLEKCGGRYVAFNNKA 163 (196)
T ss_pred CHHHHHHHHHHHHHhChHhHhcEEEEEECccccCCCcHHHHHHhccHHHHHHHHHhCCeEEEEeCCC
Confidence 33344566666665433222 3358899887653 456777778899999998863
No 480
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=21.11 E-value=1.2e+02 Score=19.51 Aligned_cols=19 Identities=16% Similarity=0.282 Sum_probs=16.5
Q ss_pred HHHHHHHhCCceEEEeeCC
Q 028376 155 VLEHAFIANNITCIKMKGE 173 (210)
Q Consensus 155 li~~~L~~~gi~~~~~~G~ 173 (210)
-+...|+.+||..+|-.|+
T Consensus 11 e~ik~Le~~Gf~~vrqkGS 29 (66)
T COG1724 11 EVIKALEKDGFQLVRQKGS 29 (66)
T ss_pred HHHHHHHhCCcEEEEeecc
Confidence 4567899999999999998
No 481
>cd01444 GlpE_ST GlpE sulfurtransferase (ST) and homologs are members of the Rhodanese Homology Domain superfamily. Unlike other rhodanese sulfurtransferases, GlpE is a single domain protein but indications are that it functions as a dimer. The active site contains a catalytically active cysteine.
Probab=21.11 E-value=1.5e+02 Score=19.28 Aligned_cols=37 Identities=16% Similarity=0.229 Sum_probs=27.5
Q ss_pred CCCCcEEEEcchHHHHHHHHHHHHhCCce-EEEeeCCC
Q 028376 138 DPKAKILVFSSWNDVLDVLEHAFIANNIT-CIKMKGEN 174 (210)
Q Consensus 138 ~~~~K~iVFSQf~~~L~li~~~L~~~gi~-~~~~~G~m 174 (210)
.++.++||+.+--.....+...|...|+. ...++|++
T Consensus 54 ~~~~~ivv~c~~g~~s~~a~~~l~~~G~~~v~~l~gG~ 91 (96)
T cd01444 54 DRDRPVVVYCYHGNSSAQLAQALREAGFTDVRSLAGGF 91 (96)
T ss_pred CCCCCEEEEeCCCChHHHHHHHHHHcCCceEEEcCCCH
Confidence 35677888887555567788899999986 55678884
No 482
>PF01591 6PF2K: 6-phosphofructo-2-kinase; InterPro: IPR013079 6-Phosphofructo-2-kinase (2.7.1.105 from EC, 3.1.3.46 from EC) is a bifunctional enzyme that catalyses both the synthesis and the degradation of fructose-2, 6-bisphosphate. The fructose-2,6-bisphosphatase reaction involves a phosphohistidine intermediate. The catalytic pathway is: ATP + D-fructose 6-phosphate = ADP + D-fructose 2,6-bisphosphate D-fructose 2,6-bisphosphate + H2O = 6-fructose 6-phosphate + Pi The enzyme is important in the regulation of hepatic carbohydrate metabolism and is found in greatest quantities in the liver, kidney and heart. In mammals, several genes often encode different isoforms, each of which differs in its tissue distribution and enzymatic activity []. The family described here bears a resemblance to the ATP-driven phospho-fructokinases, however, they share little sequence similarity, although a few residues seem key to their interaction with fructose 6-phosphate []. This domain forms the N-terminal region of this enzyme, while IPR013078 from INTERPRO forms the C-terminal domain.; GO: 0003873 6-phosphofructo-2-kinase activity, 0005524 ATP binding, 0006000 fructose metabolic process; PDB: 2DWO_A 3QPW_A 3QPV_A 3QPU_A 2I1V_B 2DWP_A 2AXN_A 1K6M_B 3BIF_A 2BIF_A ....
Probab=21.05 E-value=2.5e+02 Score=22.49 Aligned_cols=39 Identities=15% Similarity=0.174 Sum_probs=24.5
Q ss_pred HHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhc
Q 028376 152 VLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRH 195 (210)
Q Consensus 152 ~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~ 195 (210)
.|+-+-..|...|....-||++.. +.++|..+++.|...
T Consensus 83 ~l~dl~~~l~~~~G~VAI~DATN~-----T~~RR~~l~~~~~~~ 121 (222)
T PF01591_consen 83 ALEDLIEWLQEEGGQVAIFDATNS-----TRERRKMLVERFKEH 121 (222)
T ss_dssp HHHHHHHHHHTS--SEEEEES--------SHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHhcCCCeEEEEeCCCC-----CHHHHHHHHHHHHHc
Confidence 344455567767777888999865 667888888888764
No 483
>cd00951 KDGDH 5-dehydro-4-deoxyglucarate dehydratase, also called 5-keto-4-deoxy-glucarate dehydratase (KDGDH), which is member of dihydrodipicolinate synthase (DHDPS) family that comprises several pyruvate-dependent class I aldolases. The enzyme is involved in glucarate metabolism, and its mechanism presumbly involves a Schiff-base intermediate similar to members of DHDPS family. While in the case of Pseudomonas sp. 5-dehydro-4-deoxy-D-glucarate is degraded by KDGDH to 2,5-dioxopentanoate, in certain species of Enterobacteriaceae it is degraded instead to pyruvate and glycerate.
Probab=20.91 E-value=2e+02 Score=23.76 Aligned_cols=33 Identities=6% Similarity=0.038 Sum_probs=23.7
Q ss_pred hCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 162 ANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 162 ~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
.+|+.-+-+-|+..+...|+.++|.+.++.--.
T Consensus 32 ~~Gv~gi~v~GstGE~~~Ls~eEr~~l~~~~~~ 64 (289)
T cd00951 32 SYGAAALFAAGGTGEFFSLTPDEYAQVVRAAVE 64 (289)
T ss_pred HcCCCEEEECcCCcCcccCCHHHHHHHHHHHHH
Confidence 467766667777777777888888777776554
No 484
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=20.82 E-value=41 Score=21.33 Aligned_cols=12 Identities=25% Similarity=0.841 Sum_probs=9.0
Q ss_pred CccccccCCccc
Q 028376 68 NEWVMCPTCRQR 79 (210)
Q Consensus 68 ~~~~~CP~Cr~~ 79 (210)
.....||+|...
T Consensus 16 ~d~e~CP~Cgs~ 27 (64)
T COG2093 16 EDTEICPVCGST 27 (64)
T ss_pred CCCccCCCCCCc
Confidence 445579999886
No 485
>PRK00420 hypothetical protein; Validated
Probab=20.74 E-value=22 Score=25.44 Aligned_cols=14 Identities=21% Similarity=0.304 Sum_probs=9.1
Q ss_pred CccccccCCccccc
Q 028376 68 NEWVMCPTCRQRTD 81 (210)
Q Consensus 68 ~~~~~CP~Cr~~~~ 81 (210)
.+...||.|...+.
T Consensus 38 ~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 38 DGEVVCPVHGKVYI 51 (112)
T ss_pred CCceECCCCCCeee
Confidence 44557888877543
No 486
>KOG1321 consensus Protoheme ferro-lyase (ferrochelatase) [Coenzyme transport and metabolism]
Probab=20.65 E-value=1.1e+02 Score=26.32 Aligned_cols=36 Identities=19% Similarity=0.266 Sum_probs=28.2
Q ss_pred CCCCcEEEEcchHHH--------HHHHHHHHHhC----CceEEEeeCC
Q 028376 138 DPKAKILVFSSWNDV--------LDVLEHAFIAN----NITCIKMKGE 173 (210)
Q Consensus 138 ~~~~K~iVFSQf~~~--------L~li~~~L~~~----gi~~~~~~G~ 173 (210)
|.-.|.|+||||..+ |+.|...+++. +|++..+|.-
T Consensus 152 d~v~r~VafsqYPQyS~sTsGSSln~l~r~~r~~~~~~~~~wsiIdrW 199 (395)
T KOG1321|consen 152 DGVTRAVAFSQYPQYSCSTSGSSLNELWRQFREDGYERDIKWSIIDRW 199 (395)
T ss_pred cCceeEEeeccCCceeeecCcccHHHHHHHHHhcCcccCCceEeeccc
Confidence 667899999998754 88999999875 5677777664
No 487
>COG1086 Predicted nucleoside-diphosphate sugar epimerases [Cell envelope biogenesis, outer membrane / Carbohydrate transport and metabolism]
Probab=20.64 E-value=6.1e+02 Score=23.66 Aligned_cols=72 Identities=18% Similarity=0.278 Sum_probs=56.9
Q ss_pred ecCCCCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHhC--CceEEEeeCCCCCCcchhhHhhhHHHHHHh
Q 028376 116 VQGSYGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIAN--NITCIKMKGENHKLPSANLQHRNALQKELT 193 (210)
Q Consensus 116 ~~~~~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~~--gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~ 193 (210)
..|..+|==.+|.+++.+. ...++++|+.-..-+..+...|... ..+...+-|+ ...|++.-+.|+
T Consensus 255 VTGagGSiGsel~~qil~~----~p~~i~l~~~~E~~~~~i~~el~~~~~~~~~~~~igd--------VrD~~~~~~~~~ 322 (588)
T COG1086 255 VTGGGGSIGSELCRQILKF----NPKEIILFSRDEYKLYLIDMELREKFPELKLRFYIGD--------VRDRDRVERAME 322 (588)
T ss_pred EeCCCCcHHHHHHHHHHhc----CCCEEEEecCchHHHHHHHHHHHhhCCCcceEEEecc--------cccHHHHHHHHh
Confidence 3455666667888888764 4679999999999999999999984 5777778898 668888888888
Q ss_pred hcCCCC
Q 028376 194 RHMPSS 199 (210)
Q Consensus 194 ~~~p~~ 199 (210)
...||.
T Consensus 323 ~~kvd~ 328 (588)
T COG1086 323 GHKVDI 328 (588)
T ss_pred cCCCce
Confidence 766653
No 488
>PF10186 Atg14: UV radiation resistance protein and autophagy-related subunit 14; InterPro: IPR018791 Class III phosphatidylinositol 3-kinase (PI3-kinase) regulates multiple membrane trafficking. In yeast, two distinct PI3-kinase complexes are known: complex I (Vps34, Vps15, Vps30/Atg6, and Atg14) is involved in autophagy, and complex II (Vps34, Vps15, Vps30/Atg6, and Vps38) functions in the vacuolar protein sorting pathway. In mammals, the counterparts of Vps34, Vps15, and Vps30/Atg6 are Vps34, p150, and Beclin 1, respectively. Mammalian UV irradiation resistance-associated gene (UVRAG) has been identified as identical to yeast Vps38 []. The Atg14 (autophagy-related protein 14) proteins are hydrophilic proteins and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole []. This entry represents Atg14 and UVRAG, which bind Beclin 1 to forms two distinct PI3-kinase complexes. This entry also includes Bakor (beclin-1-associated autophagy-related key regulator), also known as autophagy-related protein 14-like protein, which share sequence similarity to the yeast Atg14 protein []. Barkor positively regulates autophagy through its interaction with Beclin-1, with decreased levels of autophagosome formation observed when Barkor expression is eliminated []. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. ; GO: 0010508 positive regulation of autophagy
Probab=20.59 E-value=61 Score=26.56 Aligned_cols=22 Identities=32% Similarity=0.809 Sum_probs=15.2
Q ss_pred ccccccccccCCCeecCCCCcchHhhHHHHH
Q 028376 26 TCPICQEKLGNQKMVFQCGHFTCCKCFFAMT 56 (210)
Q Consensus 26 ~C~iC~~~~~~~~~~~~CgH~fC~~C~~~~~ 56 (210)
.|++|. .+-.+.+|..|+..-+
T Consensus 1 ~C~iC~---------~~~~~~~C~~C~~~~L 22 (302)
T PF10186_consen 1 QCPICH---------NSRRRFYCANCVNNRL 22 (302)
T ss_pred CCCCCC---------CCCCCeECHHHHHHHH
Confidence 488888 2334568888988654
No 489
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=20.58 E-value=38 Score=31.80 Aligned_cols=32 Identities=13% Similarity=0.234 Sum_probs=16.7
Q ss_pred CchHHHHHHHHHHHHh-cCCCCcEEEEcchHHH
Q 028376 121 GTKIEAVTRRILWIKS-TDPKAKILVFSSWNDV 152 (210)
Q Consensus 121 SsKi~al~~~L~~~~~-~~~~~K~iVFSQf~~~ 152 (210)
-|=++++++.+..+.. ......++.+.+|..+
T Consensus 130 ~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 162 (645)
T PRK14559 130 PSPLEALLEQLEDLLNPLADPTEVLPTLLWQQL 162 (645)
T ss_pred cCHHHHHHHHhhhhhhcccCcccccCccchhcc
Confidence 4667888877765421 0112344455555443
No 490
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=20.56 E-value=44 Score=23.27 Aligned_cols=33 Identities=30% Similarity=0.382 Sum_probs=17.6
Q ss_pred cCCCCcccccccccccc-CCCeecCCCCcchHhh
Q 028376 19 LSKADEETCPICQEKLG-NQKMVFQCGHFTCCKC 51 (210)
Q Consensus 19 l~~~~~~~C~iC~~~~~-~~~~~~~CgH~fC~~C 51 (210)
.++.+.+.|.-|.-.-- .......=|+.+|.+|
T Consensus 65 P~q~DEFTCssCFLV~HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 65 PKQADEFTCSSCFLVHHRSQLAREKDGQPICRDC 98 (99)
T ss_pred cCCCCceeeeeeeeEechhhhccccCCCEecccc
Confidence 45667778888853211 1111233467777776
No 491
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=20.54 E-value=43 Score=17.43 Aligned_cols=10 Identities=30% Similarity=0.923 Sum_probs=4.9
Q ss_pred cccCCccccc
Q 028376 72 MCPTCRQRTD 81 (210)
Q Consensus 72 ~CP~Cr~~~~ 81 (210)
.||.|...+.
T Consensus 1 ~CP~C~s~l~ 10 (28)
T PF03119_consen 1 TCPVCGSKLV 10 (28)
T ss_dssp B-TTT--BEE
T ss_pred CcCCCCCEeE
Confidence 4899987654
No 492
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.41 E-value=48 Score=29.16 Aligned_cols=35 Identities=20% Similarity=0.640 Sum_probs=26.4
Q ss_pred CCCccccccccccccCC-----CeecCCCCcchHhhHHHH
Q 028376 21 KADEETCPICQEKLGNQ-----KMVFQCGHFTCCKCFFAM 55 (210)
Q Consensus 21 ~~~~~~C~iC~~~~~~~-----~~~~~CgH~fC~~C~~~~ 55 (210)
..+...||-|...+... -.-+.|||.||.-|-..+
T Consensus 365 ~~N~krCP~C~v~IEr~eGCnKM~C~~c~~~fc~~c~~~l 404 (445)
T KOG1814|consen 365 ESNSKRCPKCKVVIERSEGCNKMHCTKCGTYFCWICAELL 404 (445)
T ss_pred HhcCCCCCcccceeecCCCccceeeccccccceeehhhhc
Confidence 34667899998776532 255899999999998766
No 493
>KOG4549 consensus Magnesium-dependent phosphatase [General function prediction only]
Probab=20.39 E-value=3.2e+02 Score=20.17 Aligned_cols=43 Identities=9% Similarity=0.081 Sum_probs=22.5
Q ss_pred cEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhh
Q 028376 142 KILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTR 194 (210)
Q Consensus 142 K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~ 194 (210)
-.++|++=+..| ..|+.+||.......+|. ++--++.|+.|+-
T Consensus 42 e~~fY~Di~rIL----~dLk~~GVtl~~ASRt~a------p~iA~q~L~~fkv 84 (144)
T KOG4549|consen 42 EMIFYDDIRRIL----VDLKKLGVTLIHASRTMA------PQIASQGLETFKV 84 (144)
T ss_pred eeeeccchhHHH----HHHHhcCcEEEEecCCCC------HHHHHHHHHHhcc
Confidence 344444443332 345556666555555544 5555556666654
No 494
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=20.38 E-value=27 Score=31.00 Aligned_cols=49 Identities=18% Similarity=0.417 Sum_probs=33.1
Q ss_pred hccCchHHHHHhcCCCCccccccccccccCC---CeecCCCCcchHhhHHHH
Q 028376 7 TISNSTKHRIESLSKADEETCPICQEKLGNQ---KMVFQCGHFTCCKCFFAM 55 (210)
Q Consensus 7 ~~~~~~~~~~~~l~~~~~~~C~iC~~~~~~~---~~~~~CgH~fC~~C~~~~ 55 (210)
......++++-=+-+.+...||.|...+... -..--||-+.|.+|...+
T Consensus 163 k~k~~EqsvVpW~DDs~V~~CP~Ca~~F~l~rRrHHCRLCG~VmC~~C~k~i 214 (505)
T KOG1842|consen 163 KRKRLEQSVVPWLDDSSVQFCPECANSFGLTRRRHHCRLCGRVMCRDCSKFI 214 (505)
T ss_pred HHHHHHhccccccCCCcccccccccchhhhHHHhhhhhhcchHHHHHHHHhc
Confidence 3333444455555567778899999887532 123469999999998865
No 495
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=20.37 E-value=33 Score=28.15 Aligned_cols=12 Identities=25% Similarity=0.786 Sum_probs=6.5
Q ss_pred cccccCCccccc
Q 028376 70 WVMCPTCRQRTD 81 (210)
Q Consensus 70 ~~~CP~Cr~~~~ 81 (210)
.+.|..||+++.
T Consensus 195 ipiCgaC~rpIe 206 (332)
T KOG2272|consen 195 IPICGACRRPIE 206 (332)
T ss_pred CcccccccCchH
Confidence 344555666655
No 496
>PRK05580 primosome assembly protein PriA; Validated
Probab=20.32 E-value=7.4e+02 Score=23.45 Aligned_cols=71 Identities=13% Similarity=-0.021 Sum_probs=51.9
Q ss_pred CCchHHHHHHHHHHHHhcCCCCcEEEEcchHHHHHHHHHHHHh-CCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCC
Q 028376 120 YGTKIEAVTRRILWIKSTDPKAKILVFSSWNDVLDVLEHAFIA-NNITCIKMKGENHKLPSANLQHRNALQKELTRHMPS 198 (210)
Q Consensus 120 ~SsKi~al~~~L~~~~~~~~~~K~iVFSQf~~~L~li~~~L~~-~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~ 198 (210)
.|-|....+..+...... +.++||-.--..+..-+...|++ -|+....++|+++ ..+|.+......+++++
T Consensus 172 GSGKT~v~l~~i~~~l~~--g~~vLvLvPt~~L~~Q~~~~l~~~fg~~v~~~~s~~s------~~~r~~~~~~~~~g~~~ 243 (679)
T PRK05580 172 GSGKTEVYLQAIAEVLAQ--GKQALVLVPEIALTPQMLARFRARFGAPVAVLHSGLS------DGERLDEWRKAKRGEAK 243 (679)
T ss_pred CChHHHHHHHHHHHHHHc--CCeEEEEeCcHHHHHHHHHHHHHHhCCCEEEEECCCC------HHHHHHHHHHHHcCCCC
Confidence 466888877766655433 56788888877777767777765 4888899999966 88888887777665544
No 497
>cd06291 PBP1_Qymf_like Ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs. This group includes the ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs. Qymf is a strict anaerobe that could be grown in the presence of borax and its cells are straight rods that produce endospores. This group is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription
Probab=20.32 E-value=3.2e+02 Score=21.34 Aligned_cols=20 Identities=10% Similarity=0.295 Sum_probs=9.0
Q ss_pred hHHHHHHHHHHHHhCCceEE
Q 028376 149 WNDVLDVLEHAFIANNITCI 168 (210)
Q Consensus 149 f~~~L~li~~~L~~~gi~~~ 168 (210)
|..++.-++.+++++|+...
T Consensus 14 ~~~~~~gi~~~~~~~g~~~~ 33 (265)
T cd06291 14 FSELARAVEKELYKKGYKLI 33 (265)
T ss_pred HHHHHHHHHHHHHHCCCeEE
Confidence 44444444444444444433
No 498
>cd01525 RHOD_Kc Member of the Rhodanese Homology Domain superfamily. Included in this CD are the rhodanese-like domains found C-terminal of the serine/threonine protein kinases catalytic (S_TKc) domain and the Tre-2, BUB2p, Cdc16p (TBC) domain. The putative active site Cys residue is not present in this CD.
Probab=20.30 E-value=1.7e+02 Score=19.52 Aligned_cols=36 Identities=8% Similarity=0.130 Sum_probs=24.5
Q ss_pred CCcEEEEcchHHHHHHHHHHHHhCCce-EEEeeCCCC
Q 028376 140 KAKILVFSSWNDVLDVLEHAFIANNIT-CIKMKGENH 175 (210)
Q Consensus 140 ~~K~iVFSQf~~~L~li~~~L~~~gi~-~~~~~G~m~ 175 (210)
+.++||+..-...-......|...|+. ...++|+++
T Consensus 65 ~~~vv~~c~~g~~s~~~a~~L~~~G~~~v~~l~GG~~ 101 (105)
T cd01525 65 GKIIVIVSHSHKHAALFAAFLVKCGVPRVCILDGGIN 101 (105)
T ss_pred CCeEEEEeCCCccHHHHHHHHHHcCCCCEEEEeCcHH
Confidence 556777775433344556688899996 556899864
No 499
>TIGR03865 PQQ_CXXCW PQQ-dependent catabolism-associated CXXCW motif protein. Members of this protein family have a CXXXCW motif, consistent with a possible role in redox cofactor binding. This protein family shows strong relationships by phylogenetic profiling and conserved gene neighborhoods with a transport system for alcohols metabolized by PQQ-dependent enzymes.
Probab=20.29 E-value=2.8e+02 Score=20.77 Aligned_cols=48 Identities=6% Similarity=-0.012 Sum_probs=29.2
Q ss_pred HHHHHHHHhcCCCCcEEEEcchHH-HHHHHHHHHHhCCceEE-EeeCCCC
Q 028376 128 TRRILWIKSTDPKAKILVFSSWND-VLDVLEHAFIANNITCI-KMKGENH 175 (210)
Q Consensus 128 ~~~L~~~~~~~~~~K~iVFSQf~~-~L~li~~~L~~~gi~~~-~~~G~m~ 175 (210)
.+.+..+...+++..+|+|..--. .-......|...|+.-+ .|+|++.
T Consensus 104 ~~~l~~~~~~~~d~~IVvYC~~G~~~S~~aa~~L~~~G~~~V~~l~GG~~ 153 (162)
T TIGR03865 104 RRGLERATGGDKDRPLVFYCLADCWMSWNAAKRALAYGYSNVYWYPDGTD 153 (162)
T ss_pred HHHHHHhcCCCCCCEEEEEECCCCHHHHHHHHHHHhcCCcceEEecCCHH
Confidence 334433332346677888877321 23346778899999854 5799854
No 500
>PF13607 Succ_CoA_lig: Succinyl-CoA ligase like flavodoxin domain; PDB: 2CSU_A.
Probab=20.05 E-value=2.3e+02 Score=20.83 Aligned_cols=56 Identities=9% Similarity=-0.029 Sum_probs=35.4
Q ss_pred cEEEEcchHHHHHHHHHHHHhCCceEEEeeCCCCCCcchhhHhhhHHHHHHhhcCCCCCCc
Q 028376 142 KILVFSSWNDVLDVLEHAFIANNITCIKMKGENHKLPSANLQHRNALQKELTRHMPSSQSQ 202 (210)
Q Consensus 142 K~iVFSQf~~~L~li~~~L~~~gi~~~~~~G~m~~~~~~~~~~R~~~l~~F~~~~p~~~~~ 202 (210)
.+=++||--.+...+-..+...|+++-.+-+..++ ..-.=...|+.|.. ||+.+..
T Consensus 3 ~valisQSG~~~~~~~~~~~~~g~g~s~~vs~Gn~----~dv~~~d~l~~~~~-D~~t~~I 58 (138)
T PF13607_consen 3 GVALISQSGALGTAILDWAQDRGIGFSYVVSVGNE----ADVDFADLLEYLAE-DPDTRVI 58 (138)
T ss_dssp SEEEEES-HHHHHHHHHHHHHTT-EESEEEE-TT-----SSS-HHHHHHHHCT--SS--EE
T ss_pred CEEEEECCHHHHHHHHHHHHHcCCCeeEEEEeCcc----ccCCHHHHHHHHhc-CCCCCEE
Confidence 45689999999999999999998888766544441 12345567888887 8876643
Done!