Query 006973
Match_columns 623
No_of_seqs 275 out of 953
Neff 7.7
Searched_HMMs 46136
Date Thu Mar 28 17:08:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006973.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006973hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00617 rpa1 replication fac 100.0 5E-121 1E-125 1021.4 61.3 593 2-616 1-608 (608)
2 PRK12366 replication factor A; 100.0 4.3E-67 9.2E-72 590.4 47.0 436 28-603 192-637 (637)
3 PRK08402 replication factor A; 100.0 2.4E-46 5.3E-51 390.6 31.1 281 293-618 61-353 (355)
4 PRK07218 replication factor A; 100.0 5.5E-35 1.2E-39 311.1 38.1 361 171-613 55-420 (423)
5 cd04476 RPA1_DBD_C RPA1_DBD_C: 100.0 9.2E-36 2E-40 283.8 20.3 154 460-616 13-166 (166)
6 PF08646 Rep_fac-A_C: Replicat 100.0 3.3E-36 7.1E-41 280.7 13.9 144 464-610 1-146 (146)
7 PRK06386 replication factor A; 100.0 3.2E-31 7E-36 275.3 38.9 339 175-603 3-343 (358)
8 PRK12366 replication factor A; 100.0 9.7E-32 2.1E-36 303.7 31.8 283 171-544 60-345 (637)
9 PRK07211 replication factor A; 100.0 1.3E-31 2.9E-36 287.4 28.3 289 28-406 71-370 (485)
10 PRK07211 replication factor A; 100.0 2.6E-31 5.7E-36 285.1 30.4 274 173-539 52-328 (485)
11 PRK15491 replication factor A; 100.0 1.1E-29 2.3E-34 269.1 28.7 289 28-400 75-373 (374)
12 PRK15491 replication factor A; 100.0 1E-29 2.3E-34 269.2 28.0 277 172-540 55-336 (374)
13 PRK14699 replication factor A; 100.0 3.5E-29 7.6E-34 272.1 28.1 290 28-400 184-483 (484)
14 PRK14699 replication factor A; 100.0 6.4E-27 1.4E-31 254.5 35.1 362 27-541 74-447 (484)
15 cd04474 RPA1_DBD_A RPA1_DBD_A: 99.9 1.6E-27 3.5E-32 208.7 11.8 104 176-279 1-104 (104)
16 PF04057 Rep-A_N: Replication 99.9 1.3E-25 2.7E-30 194.5 8.8 92 5-103 1-100 (101)
17 cd04477 RPA1N RPA1N: A subfami 99.9 1.5E-24 3.3E-29 185.8 8.0 91 8-103 1-97 (97)
18 cd04475 RPA1_DBD_B RPA1_DBD_B: 99.9 7.7E-22 1.7E-26 172.2 13.1 101 309-415 1-101 (101)
19 cd04481 RPA1_DBD_B_like RPA1_D 99.8 7.1E-20 1.5E-24 161.2 12.9 101 311-413 1-104 (106)
20 cd04480 RPA1_DBD_A_like RPA1_D 99.8 1.5E-18 3.1E-23 146.9 9.4 86 188-277 1-86 (86)
21 PF02721 DUF223: Domain of unk 99.7 3.2E-16 6.9E-21 135.0 9.0 87 213-302 1-87 (95)
22 PRK08402 replication factor A; 99.6 9.7E-15 2.1E-19 153.4 19.7 178 173-361 61-270 (355)
23 PRK07217 replication factor A; 99.6 8.7E-14 1.9E-18 141.0 24.1 208 293-580 71-282 (311)
24 PRK06386 replication factor A; 99.4 1E-10 2.2E-15 122.6 27.1 248 26-361 15-288 (358)
25 PRK07218 replication factor A; 99.3 2.1E-10 4.5E-15 123.2 24.4 236 42-361 95-349 (423)
26 KOG0851 Single-stranded DNA-bi 99.2 9.2E-11 2E-15 118.8 13.6 214 173-418 3-218 (246)
27 cd04497 hPOT1_OB1_like hPOT1_O 99.1 4.9E-10 1.1E-14 103.3 12.2 89 292-392 1-92 (138)
28 COG1599 RFA1 Single-stranded D 99.1 5.1E-10 1.1E-14 121.7 13.1 207 172-423 160-369 (407)
29 cd04491 SoSSB_OBF SoSSB_OBF: A 98.9 6.8E-09 1.5E-13 86.8 10.4 81 188-279 1-81 (82)
30 PRK06461 single-stranded DNA-b 98.9 1.4E-08 3.1E-13 92.3 11.7 98 173-282 3-100 (129)
31 PRK06461 single-stranded DNA-b 98.9 1.3E-08 2.8E-13 92.6 11.3 95 294-402 4-99 (129)
32 cd04491 SoSSB_OBF SoSSB_OBF: A 98.8 4.9E-08 1.1E-12 81.6 11.3 80 311-400 1-81 (82)
33 PRK07217 replication factor A; 98.5 5.6E-06 1.2E-10 84.7 16.7 171 171-361 69-242 (311)
34 TIGR00617 rpa1 replication fac 98.4 4.2E-05 9.2E-10 87.1 22.1 258 41-361 217-535 (608)
35 COG1599 RFA1 Single-stranded D 98.2 3.1E-05 6.6E-10 84.5 15.1 186 172-388 47-234 (407)
36 PF01336 tRNA_anti-codon: OB-f 98.0 3.1E-05 6.8E-10 62.9 8.5 62 187-258 1-62 (75)
37 PF02765 POT1: Telomeric singl 98.0 0.00012 2.5E-09 68.3 12.9 85 294-388 1-93 (146)
38 cd04474 RPA1_DBD_A RPA1_DBD_A: 98.0 7.1E-05 1.5E-09 65.5 10.6 98 296-402 1-98 (104)
39 cd04475 RPA1_DBD_B RPA1_DBD_B: 97.6 0.00038 8.2E-09 60.5 9.7 84 188-281 3-88 (101)
40 KOG3416 Predicted nucleic acid 96.9 0.0019 4.2E-08 56.7 6.0 70 174-252 4-74 (134)
41 cd03524 RPA2_OBF_family RPA2_O 96.9 0.0064 1.4E-07 48.2 8.7 61 189-256 2-62 (75)
42 KOG3416 Predicted nucleic acid 96.4 0.015 3.2E-07 51.4 7.8 85 295-396 5-90 (134)
43 cd04497 hPOT1_OB1_like hPOT1_O 96.3 0.025 5.4E-07 52.1 9.5 84 174-261 3-90 (138)
44 cd04481 RPA1_DBD_B_like RPA1_D 96.2 0.065 1.4E-06 46.9 11.2 69 190-258 3-76 (106)
45 PF01336 tRNA_anti-codon: OB-f 95.8 0.062 1.3E-06 43.2 8.4 66 310-391 1-68 (75)
46 cd04483 hOBFC1_like hOBFC1_lik 95.7 0.047 1E-06 46.6 7.3 68 311-391 1-85 (92)
47 PF15489 CTC1: CST, telomere m 95.3 4.4 9.6E-05 48.7 24.0 319 180-552 700-1050(1144)
48 cd03524 RPA2_OBF_family RPA2_O 95.3 0.14 3.1E-06 40.2 8.8 64 311-387 1-64 (75)
49 cd04488 RecG_wedge_OBF RecG_we 95.2 0.16 3.4E-06 40.6 8.9 62 188-257 1-62 (75)
50 cd04485 DnaE_OBF DnaE_OBF: A s 94.9 0.14 3.1E-06 41.7 7.8 44 210-255 19-62 (84)
51 PF09103 BRCA-2_OB1: BRCA2, ol 94.1 0.059 1.3E-06 48.1 4.1 70 9-82 2-75 (118)
52 cd04490 PolII_SU_OBF PolII_SU_ 94.0 0.31 6.7E-06 40.3 7.7 55 310-379 2-58 (79)
53 PF06075 DUF936: Plant protein 93.6 0.14 3E-06 57.9 6.6 92 5-102 1-102 (579)
54 cd04490 PolII_SU_OBF PolII_SU_ 93.5 0.39 8.5E-06 39.7 7.6 54 188-250 3-58 (79)
55 cd04489 ExoVII_LU_OBF ExoVII_L 93.4 0.36 7.8E-06 39.3 7.2 54 188-250 3-56 (78)
56 PF15072 DUF4539: Domain of un 93.1 0.42 9E-06 40.2 7.1 61 211-278 20-80 (86)
57 cd04492 YhaM_OBF_like YhaM_OBF 92.5 0.47 1E-05 38.8 6.8 43 210-255 19-61 (83)
58 KOG0851 Single-stranded DNA-bi 90.8 0.42 9.2E-06 48.0 5.7 69 476-549 156-224 (246)
59 PTZ00401 aspartyl-tRNA synthet 90.7 2.1 4.5E-05 48.6 11.5 99 172-280 63-169 (550)
60 cd04485 DnaE_OBF DnaE_OBF: A s 90.1 2.3 4.9E-05 34.4 8.6 64 312-387 2-65 (84)
61 PF14951 DUF4503: Domain of un 90.1 0.83 1.8E-05 47.7 7.0 85 464-548 256-346 (389)
62 PRK02801 primosomal replicatio 89.7 1.7 3.8E-05 37.6 7.8 67 184-253 2-79 (101)
63 cd04495 BRCA2DBD_OB3 BRCA2DBD_ 89.7 2.8 6E-05 35.9 8.6 82 311-404 1-85 (100)
64 PRK06751 single-stranded DNA-b 89.4 1.4 3E-05 42.1 7.6 64 184-250 2-75 (173)
65 PRK13480 3'-5' exoribonuclease 89.2 1.2 2.6E-05 46.8 7.5 68 176-251 4-72 (314)
66 KOG4757 Predicted telomere bin 88.9 1.2 2.5E-05 47.6 7.1 86 292-388 7-94 (522)
67 cd04478 RPA2_DBD_D RPA2_DBD_D: 88.8 1.1 2.3E-05 38.2 5.8 57 188-255 3-62 (95)
68 COG1997 RPL43A Ribosomal prote 88.7 0.3 6.4E-06 40.5 2.1 30 482-511 35-65 (89)
69 PRK07275 single-stranded DNA-b 88.5 1.9 4.1E-05 40.8 7.7 64 184-250 2-75 (162)
70 PF02760 HIN: HIN-200/IF120x d 88.2 19 0.00041 33.7 13.5 144 189-360 5-154 (170)
71 PRK07373 DNA polymerase III su 88.1 1.5 3.2E-05 48.5 7.7 73 175-253 269-343 (449)
72 PF02765 POT1: Telomeric singl 87.7 3.2 7E-05 38.5 8.7 86 175-261 2-95 (146)
73 PF13240 zinc_ribbon_2: zinc-r 87.3 0.26 5.7E-06 30.5 0.8 21 485-508 2-22 (23)
74 PF09104 BRCA-2_OB3: BRCA2, ol 87.0 3.3 7.1E-05 38.1 7.9 108 295-415 4-120 (143)
75 PRK07459 single-stranded DNA-b 87.0 2.7 5.8E-05 37.8 7.4 64 184-250 3-72 (121)
76 PRK08763 single-stranded DNA-b 86.6 3.2 7E-05 39.3 8.0 65 183-250 4-80 (164)
77 PRK05813 single-stranded DNA-b 86.3 38 0.00082 33.8 17.5 166 184-386 8-183 (219)
78 cd04493 BRCA2DBD_OB1 BRCA2DBD_ 86.1 0.5 1.1E-05 40.7 2.0 52 29-80 6-61 (100)
79 PF07754 DUF1610: Domain of un 86.1 0.56 1.2E-05 29.4 1.7 23 485-507 1-24 (24)
80 cd04320 AspRS_cyto_N AspRS_cyt 86.0 13 0.00028 32.0 11.1 83 187-280 2-92 (102)
81 PF11325 DUF3127: Domain of un 85.9 5.9 0.00013 33.1 8.2 70 312-389 2-74 (84)
82 PRK07274 single-stranded DNA-b 85.8 3 6.5E-05 38.0 7.2 64 184-250 2-75 (131)
83 cd04489 ExoVII_LU_OBF ExoVII_L 85.3 3.5 7.6E-05 33.3 6.8 53 311-378 3-55 (78)
84 PRK13480 3'-5' exoribonuclease 85.0 5.4 0.00012 42.0 9.6 69 307-388 11-79 (314)
85 cd04322 LysRS_N LysRS_N: N-ter 84.6 15 0.00032 32.0 10.9 77 187-280 2-83 (108)
86 COG1571 Predicted DNA-binding 84.5 0.5 1.1E-05 50.9 1.7 30 482-511 350-379 (421)
87 PLN02850 aspartate-tRNA ligase 84.5 7.3 0.00016 44.1 11.0 98 172-280 67-172 (530)
88 PRK08486 single-stranded DNA-b 84.5 3.9 8.5E-05 39.5 7.7 63 185-250 3-77 (182)
89 PF02721 DUF223: Domain of unk 84.5 5.4 0.00012 34.0 7.8 61 338-402 1-61 (95)
90 cd04496 SSB_OBF SSB_OBF: A sub 84.5 4.2 9.2E-05 34.4 7.3 61 188-251 2-73 (100)
91 cd04484 polC_OBF polC_OBF: A s 84.3 5.6 0.00012 33.0 7.6 58 187-250 2-61 (82)
92 PF10341 TPP1: Shelterin compl 83.8 1.6 3.4E-05 38.1 4.3 59 26-84 25-91 (106)
93 cd04492 YhaM_OBF_like YhaM_OBF 83.5 5.7 0.00012 32.2 7.4 62 313-387 3-64 (83)
94 PRK07772 single-stranded DNA-b 83.5 6.6 0.00014 38.0 8.8 64 184-250 4-81 (186)
95 PRK08182 single-stranded DNA-b 83.4 4.9 0.00011 37.5 7.6 65 184-250 2-82 (148)
96 cd04100 Asp_Lys_Asn_RS_N Asp_L 83.3 11 0.00025 31.1 9.2 74 187-272 2-78 (85)
97 cd04478 RPA2_DBD_D RPA2_DBD_D: 83.2 8.2 0.00018 32.6 8.5 75 30-107 6-82 (95)
98 PRK06752 single-stranded DNA-b 83.2 5.1 0.00011 35.3 7.4 64 184-250 2-75 (112)
99 COG5235 RFA2 Single-stranded D 82.9 5.4 0.00012 38.7 7.6 71 309-394 68-139 (258)
100 KOG3056 Protein required for S 82.9 7.2 0.00016 43.4 9.6 102 173-280 167-275 (578)
101 cd04480 RPA1_DBD_A_like RPA1_D 82.6 6.8 0.00015 32.6 7.6 51 333-387 17-67 (86)
102 PRK05733 single-stranded DNA-b 82.5 5.9 0.00013 37.9 7.9 65 183-250 4-81 (172)
103 PRK13732 single-stranded DNA-b 82.3 5.9 0.00013 38.0 7.8 65 183-250 5-82 (175)
104 PRK06293 single-stranded DNA-b 81.9 5.4 0.00012 37.7 7.3 64 184-250 1-71 (161)
105 cd04483 hOBFC1_like hOBFC1_lik 81.8 3.5 7.5E-05 35.1 5.5 44 210-255 14-77 (92)
106 cd04323 AsnRS_cyto_like_N AsnR 81.8 11 0.00024 31.2 8.5 74 187-272 2-77 (84)
107 PRK09010 single-stranded DNA-b 81.1 5.9 0.00013 38.0 7.4 64 184-250 6-82 (177)
108 PRK06863 single-stranded DNA-b 80.9 6.5 0.00014 37.4 7.5 64 184-250 4-80 (168)
109 PF13742 tRNA_anti_2: OB-fold 80.9 12 0.00026 32.3 8.6 57 185-250 22-79 (99)
110 PF01780 Ribosomal_L37ae: Ribo 80.0 0.74 1.6E-05 38.8 0.7 28 483-510 36-64 (90)
111 cd04316 ND_PkAspRS_like_N ND_P 79.8 22 0.00049 30.9 10.2 81 185-280 13-97 (108)
112 PF00436 SSB: Single-strand bi 79.4 2.9 6.4E-05 35.8 4.4 63 185-250 2-76 (104)
113 TIGR00621 ssb single stranded 79.2 8.4 0.00018 36.5 7.7 64 184-250 4-79 (164)
114 PRK10917 ATP-dependent DNA hel 78.7 8.5 0.00019 45.1 9.3 74 173-255 49-122 (681)
115 PRK07373 DNA polymerase III su 78.1 8.2 0.00018 42.7 8.4 77 294-383 268-344 (449)
116 PRK05159 aspC aspartyl-tRNA sy 77.6 15 0.00032 40.7 10.2 93 174-281 4-101 (437)
117 PF13248 zf-ribbon_3: zinc-rib 76.9 1.1 2.4E-05 28.6 0.7 23 483-508 3-25 (26)
118 PF07191 zinc-ribbons_6: zinc- 76.9 1.3 2.7E-05 35.5 1.2 25 484-509 3-27 (70)
119 PRK10220 hypothetical protein; 75.6 1.9 4.1E-05 37.4 2.0 30 481-510 2-31 (111)
120 TIGR00643 recG ATP-dependent D 75.5 13 0.00029 43.1 9.5 74 174-257 23-97 (630)
121 PF10571 UPF0547: Uncharacteri 75.1 1.8 3.8E-05 27.8 1.3 23 484-509 2-24 (26)
122 PF11781 RRN7: RNA polymerase 74.9 2 4.4E-05 29.8 1.6 26 483-508 9-34 (36)
123 PRK05673 dnaE DNA polymerase I 73.7 8.5 0.00018 47.6 7.6 73 175-253 966-1040(1135)
124 cd04317 EcAspRS_like_N EcAspRS 73.5 30 0.00065 31.4 9.6 86 185-280 15-104 (135)
125 PRK05673 dnaE DNA polymerase I 73.3 10 0.00023 46.8 8.3 81 294-387 965-1045(1135)
126 PRK06958 single-stranded DNA-b 72.7 15 0.00033 35.4 7.5 64 184-250 4-80 (182)
127 PRK07135 dnaE DNA polymerase I 72.4 11 0.00024 45.6 8.0 75 175-258 889-963 (973)
128 PTZ00255 60S ribosomal protein 72.1 2 4.2E-05 36.3 1.2 33 482-514 36-69 (90)
129 PRK06642 single-stranded DNA-b 72.0 15 0.00032 34.4 7.2 64 184-250 5-82 (152)
130 COG0629 Ssb Single-stranded DN 72.0 14 0.0003 35.1 7.2 68 184-251 3-80 (167)
131 PF08271 TF_Zn_Ribbon: TFIIB z 71.8 2.8 6E-05 30.2 1.8 26 484-509 2-29 (43)
132 PRK07279 dnaE DNA polymerase I 71.8 9.5 0.00021 46.4 7.3 74 174-253 875-948 (1034)
133 COG2888 Predicted Zn-ribbon RN 71.6 2.5 5.4E-05 32.5 1.6 27 480-506 25-57 (61)
134 TIGR00280 L37a ribosomal prote 71.4 1.9 4.2E-05 36.3 1.0 30 482-511 35-65 (91)
135 PF09538 FYDLN_acid: Protein o 71.1 2.5 5.3E-05 37.2 1.7 29 482-510 9-37 (108)
136 PRK07374 dnaE DNA polymerase I 71.0 11 0.00023 46.7 7.7 73 175-253 989-1063(1170)
137 cd04498 hPOT1_OB2 hPOT1_OB2: A 70.8 18 0.00039 32.6 7.1 35 347-386 60-94 (123)
138 cd04318 EcAsnRS_like_N EcAsnRS 70.1 31 0.00068 28.2 8.1 73 187-273 2-76 (82)
139 TIGR02300 FYDLN_acid conserved 70.0 2.7 5.8E-05 37.6 1.7 29 482-510 9-37 (129)
140 cd04482 RPA2_OBF_like RPA2_OBF 69.9 7.1 0.00015 33.1 4.2 40 211-251 18-59 (91)
141 PRK03976 rpl37ae 50S ribosomal 69.8 2.1 4.6E-05 36.1 0.9 30 482-511 36-66 (90)
142 PRK14810 formamidopyrimidine-D 69.0 3.1 6.7E-05 42.9 2.2 25 483-507 245-272 (272)
143 COG1200 RecG RecG-like helicas 68.8 35 0.00077 39.3 10.5 75 174-257 51-125 (677)
144 TIGR00686 phnA alkylphosphonat 68.7 3.2 6.9E-05 36.0 1.8 30 482-511 2-31 (109)
145 PRK13945 formamidopyrimidine-D 68.7 3.4 7.4E-05 42.8 2.4 25 483-507 255-282 (282)
146 PRK00420 hypothetical protein; 68.4 3.4 7.3E-05 36.5 1.9 29 481-509 22-50 (112)
147 PRK00398 rpoP DNA-directed RNA 67.9 4 8.6E-05 29.8 2.0 27 483-509 4-31 (46)
148 PRK10445 endonuclease VIII; Pr 67.6 3.1 6.8E-05 42.6 1.9 25 483-507 236-263 (263)
149 KOG2593 Transcription initiati 67.5 2.6 5.7E-05 45.3 1.3 30 480-509 126-163 (436)
150 PRK06266 transcription initiat 67.1 2.6 5.7E-05 40.5 1.1 29 481-509 116-146 (178)
151 PHA00626 hypothetical protein 66.7 4.4 9.6E-05 30.8 2.0 26 484-509 2-33 (59)
152 PRK00432 30S ribosomal protein 66.7 3.7 8E-05 30.8 1.6 27 482-509 20-47 (50)
153 PRK01103 formamidopyrimidine/5 66.5 3.3 7.1E-05 42.7 1.8 25 483-507 246-273 (274)
154 cd04487 RecJ_OBF2_like RecJ_OB 66.3 9.4 0.0002 30.9 4.1 41 210-251 15-55 (73)
155 cd04319 PhAsnRS_like_N PhAsnRS 66.1 78 0.0017 27.1 10.2 79 187-280 2-83 (103)
156 PLN02502 lysyl-tRNA synthetase 65.2 47 0.001 37.9 10.7 78 186-280 110-194 (553)
157 cd04488 RecG_wedge_OBF RecG_we 65.0 63 0.0014 25.0 9.3 46 335-387 18-63 (75)
158 COG1096 Predicted RNA-binding 65.0 9.5 0.00021 36.6 4.4 43 466-509 124-175 (188)
159 PRK02801 primosomal replicatio 64.7 44 0.00096 28.8 8.2 63 309-380 4-77 (101)
160 PF09862 DUF2089: Protein of u 64.4 3.6 7.8E-05 36.4 1.3 22 485-509 1-22 (113)
161 COG1996 RPC10 DNA-directed RNA 64.4 3.9 8.4E-05 30.4 1.3 26 482-507 6-32 (49)
162 PRK14811 formamidopyrimidine-D 64.3 4.1 8.9E-05 41.9 2.0 27 483-509 236-265 (269)
163 COG2093 DNA-directed RNA polym 64.1 4.4 9.5E-05 31.5 1.6 32 481-515 3-34 (64)
164 PF08274 PhnA_Zn_Ribbon: PhnA 64.0 3.5 7.5E-05 27.4 0.9 26 482-507 2-27 (30)
165 PRK06920 dnaE DNA polymerase I 63.9 19 0.00042 44.3 7.8 73 175-253 933-1006(1107)
166 cd04100 Asp_Lys_Asn_RS_N Asp_L 63.0 19 0.0004 29.8 5.4 60 43-102 19-83 (85)
167 smart00531 TFIIE Transcription 62.5 4.8 0.0001 37.4 1.9 28 482-509 99-133 (147)
168 PRK05813 single-stranded DNA-b 62.4 38 0.00083 33.7 8.3 64 183-250 108-175 (219)
169 TIGR00458 aspS_arch aspartyl-t 62.3 67 0.0014 35.4 11.1 81 185-280 13-97 (428)
170 PRK11827 hypothetical protein; 62.2 5.5 0.00012 31.0 1.8 29 482-510 8-37 (60)
171 smart00661 RPOL9 RNA polymeras 61.8 10 0.00022 28.1 3.3 27 484-510 2-31 (52)
172 TIGR00373 conserved hypothetic 61.6 3.2 6.9E-05 39.1 0.5 27 482-508 109-137 (158)
173 smart00659 RPOLCX RNA polymera 61.6 6.3 0.00014 28.7 2.0 26 484-509 4-29 (44)
174 COG0017 AsnS Aspartyl/asparagi 60.9 58 0.0013 35.8 10.0 92 174-280 4-100 (435)
175 PRK07459 single-stranded DNA-b 60.5 1.1E+02 0.0024 27.3 10.3 69 309-386 5-80 (121)
176 PRK08182 single-stranded DNA-b 60.3 78 0.0017 29.4 9.5 35 348-386 55-90 (148)
177 COG3877 Uncharacterized protei 60.2 5.4 0.00012 34.3 1.6 32 482-519 6-37 (122)
178 PF03966 Trm112p: Trm112p-like 59.9 5.3 0.00012 31.8 1.5 28 482-509 7-63 (68)
179 PRK06393 rpoE DNA-directed RNA 59.8 8.3 0.00018 30.4 2.4 28 482-514 5-32 (64)
180 PF15489 CTC1: CST, telomere m 59.6 1.1E+02 0.0023 37.5 12.6 69 184-257 165-233 (1144)
181 TIGR02098 MJ0042_CXXC MJ0042 f 59.4 6.1 0.00013 27.4 1.6 28 482-509 2-35 (38)
182 TIGR00621 ssb single stranded 59.1 98 0.0021 29.2 10.2 35 348-386 52-87 (164)
183 PF03604 DNA_RNApol_7kD: DNA d 58.6 6.8 0.00015 26.4 1.6 24 484-507 2-25 (32)
184 PRK06341 single-stranded DNA-b 58.6 44 0.00095 31.8 7.6 64 184-250 5-82 (166)
185 TIGR00577 fpg formamidopyrimid 58.1 5.6 0.00012 41.0 1.7 24 483-506 246-272 (272)
186 PF07282 OrfB_Zn_ribbon: Putat 57.8 8 0.00017 30.7 2.2 30 480-509 26-56 (69)
187 PRK06751 single-stranded DNA-b 57.1 70 0.0015 30.6 8.8 35 348-386 48-83 (173)
188 cd04484 polC_OBF polC_OBF: A s 56.5 89 0.0019 25.8 8.3 55 515-591 20-74 (82)
189 PRK07374 dnaE DNA polymerase I 56.2 35 0.00076 42.4 8.2 77 294-383 988-1064(1170)
190 COG2824 PhnA Uncharacterized Z 56.2 11 0.00025 32.5 2.9 30 481-510 2-31 (112)
191 TIGR00499 lysS_bact lysyl-tRNA 55.0 88 0.0019 35.2 10.6 79 185-280 54-137 (496)
192 PF08792 A2L_zn_ribbon: A2L zi 54.4 9.1 0.0002 26.0 1.6 28 482-509 3-31 (33)
193 PF13717 zinc_ribbon_4: zinc-r 54.4 9.9 0.00022 26.3 1.9 27 483-509 3-35 (36)
194 cd04318 EcAsnRS_like_N EcAsnRS 54.2 38 0.00083 27.6 5.8 61 42-102 18-80 (82)
195 cd04323 AsnRS_cyto_like_N AsnR 53.7 36 0.00079 28.0 5.6 42 43-84 19-61 (84)
196 PRK06826 dnaE DNA polymerase I 53.5 44 0.00096 41.5 8.5 62 186-253 993-1054(1151)
197 PRK00484 lysS lysyl-tRNA synth 53.3 98 0.0021 34.8 10.6 78 185-280 55-137 (491)
198 COG1656 Uncharacterized conser 53.0 6.9 0.00015 36.8 1.2 28 482-509 97-140 (165)
199 TIGR01384 TFS_arch transcripti 52.9 14 0.00031 31.9 3.1 26 484-510 2-27 (104)
200 PF14446 Prok-RING_1: Prokaryo 52.9 9.6 0.00021 29.0 1.7 27 482-509 5-31 (54)
201 COG1379 PHP family phosphoeste 52.7 4 8.7E-05 42.3 -0.4 31 479-509 243-275 (403)
202 COG0266 Nei Formamidopyrimidin 52.6 8.5 0.00018 39.5 1.9 25 483-507 246-273 (273)
203 PF01927 Mut7-C: Mut7-C RNAse 52.4 7.9 0.00017 36.0 1.5 30 482-511 91-136 (147)
204 cd04496 SSB_OBF SSB_OBF: A sub 51.5 1.1E+02 0.0024 25.5 8.5 37 346-386 43-80 (100)
205 PF08646 Rep_fac-A_C: Replicat 51.1 19 0.00041 33.2 3.9 27 211-238 55-81 (146)
206 TIGR00459 aspS_bact aspartyl-t 50.7 1.2E+02 0.0027 34.7 11.0 86 185-280 16-104 (583)
207 PF12773 DZR: Double zinc ribb 50.7 8.5 0.00019 28.4 1.2 28 482-509 12-39 (50)
208 PF06827 zf-FPG_IleRS: Zinc fi 50.1 8.1 0.00018 25.4 0.9 25 483-507 2-29 (30)
209 PF13719 zinc_ribbon_5: zinc-r 50.0 14 0.0003 25.7 2.1 27 483-509 3-35 (37)
210 KOG0402 60S ribosomal protein 49.7 8.5 0.00018 31.7 1.1 31 483-513 37-68 (92)
211 PRK09010 single-stranded DNA-b 49.7 1.4E+02 0.003 28.8 9.5 36 348-387 55-91 (177)
212 PRK08351 DNA-directed RNA poly 49.5 15 0.00033 28.7 2.4 23 482-509 3-25 (61)
213 PRK06826 dnaE DNA polymerase I 49.1 56 0.0012 40.6 8.4 66 306-383 990-1055(1151)
214 PRK12445 lysyl-tRNA synthetase 48.3 1.1E+02 0.0024 34.5 10.0 78 186-280 67-149 (505)
215 PF12760 Zn_Tnp_IS1595: Transp 48.2 15 0.00033 26.8 2.2 25 483-507 19-45 (46)
216 cd04498 hPOT1_OB2 hPOT1_OB2: A 47.9 46 0.001 30.0 5.6 38 223-261 61-98 (123)
217 PRK07772 single-stranded DNA-b 47.8 1.2E+02 0.0027 29.3 8.9 35 348-386 54-89 (186)
218 PRK08763 single-stranded DNA-b 47.7 1.8E+02 0.0038 27.6 9.8 35 348-386 53-88 (164)
219 PF11325 DUF3127: Domain of un 47.6 1.2E+02 0.0025 25.5 7.5 59 189-249 2-62 (84)
220 KOG0556 Aspartyl-tRNA syntheta 47.4 1.7E+02 0.0037 31.8 10.4 99 171-279 67-174 (533)
221 cd04494 BRCA2DBD_OB2 BRCA2DBD_ 47.3 61 0.0013 32.9 6.9 57 223-282 181-237 (251)
222 PTZ00385 lysyl-tRNA synthetase 47.1 99 0.0021 36.0 9.5 77 186-279 109-191 (659)
223 PRK05853 hypothetical protein; 46.9 51 0.0011 31.1 6.0 33 218-250 39-71 (161)
224 COG1998 RPS31 Ribosomal protei 46.8 11 0.00023 28.0 1.1 27 482-508 19-46 (51)
225 PF14353 CpXC: CpXC protein 46.3 28 0.00061 31.3 4.1 33 499-536 38-70 (128)
226 PRK05672 dnaE2 error-prone DNA 45.9 50 0.0011 40.7 7.3 61 186-254 955-1015(1046)
227 cd04321 ScAspRS_mt_like_N ScAs 45.8 1.7E+02 0.0037 24.1 10.0 76 187-272 2-79 (86)
228 PRK05733 single-stranded DNA-b 45.6 1.2E+02 0.0027 28.9 8.5 35 348-386 54-89 (172)
229 PRK07275 single-stranded DNA-b 45.2 2E+02 0.0044 27.2 9.8 35 348-386 48-83 (162)
230 COG1594 RPB9 DNA-directed RNA 45.1 29 0.00062 30.8 3.8 48 484-531 4-57 (113)
231 PF10451 Stn1: Telomere regula 45.0 79 0.0017 32.3 7.5 64 309-381 68-132 (256)
232 PF08772 NOB1_Zn_bind: Nin one 44.7 18 0.00038 29.5 2.2 42 481-530 8-49 (73)
233 TIGR00375 conserved hypothetic 44.5 13 0.00028 40.1 1.9 40 468-509 226-268 (374)
234 TIGR00457 asnS asparaginyl-tRN 44.0 1.7E+02 0.0037 32.5 10.6 82 185-281 17-103 (453)
235 PRK07274 single-stranded DNA-b 43.6 2.1E+02 0.0045 25.9 9.4 34 348-385 48-82 (131)
236 COG2835 Uncharacterized conser 43.5 16 0.00035 28.4 1.7 29 482-510 8-37 (60)
237 PRK06863 single-stranded DNA-b 43.4 2.4E+02 0.0051 26.9 10.0 35 348-386 53-88 (168)
238 COG1570 XseA Exonuclease VII, 43.2 51 0.0011 36.1 6.1 56 208-272 40-96 (440)
239 PF06677 Auto_anti-p27: Sjogre 43.1 18 0.00039 25.9 1.8 25 482-506 17-41 (41)
240 PRK06958 single-stranded DNA-b 43.1 2.6E+02 0.0057 27.0 10.3 35 348-386 53-88 (182)
241 PF03107 C1_2: C1 domain; Int 42.6 15 0.00032 24.2 1.2 21 484-506 2-22 (30)
242 COG2888 Predicted Zn-ribbon RN 42.4 16 0.00034 28.3 1.5 27 482-508 9-36 (61)
243 PRK02983 lysS lysyl-tRNA synth 42.1 1.3E+02 0.0029 37.3 10.1 89 175-280 640-735 (1094)
244 PRK14890 putative Zn-ribbon RN 41.9 19 0.00041 27.9 1.8 10 482-491 25-34 (59)
245 PF13842 Tnp_zf-ribbon_2: DDE_ 41.9 15 0.00033 24.7 1.2 23 484-507 2-24 (32)
246 COG4530 Uncharacterized protei 41.7 14 0.0003 32.2 1.2 29 482-510 9-37 (129)
247 COG1645 Uncharacterized Zn-fin 41.3 16 0.00035 33.1 1.6 28 479-507 25-52 (131)
248 COG0587 DnaE DNA polymerase II 40.9 83 0.0018 39.0 8.0 71 175-250 967-1038(1139)
249 cd04322 LysRS_N LysRS_N: N-ter 40.8 41 0.0009 29.1 4.2 60 42-103 18-81 (108)
250 PRK00286 xseA exodeoxyribonucl 40.7 65 0.0014 35.6 6.7 56 186-250 25-80 (438)
251 PRK13732 single-stranded DNA-b 40.7 3.4E+02 0.0073 26.0 10.7 35 348-386 55-90 (175)
252 PRK06920 dnaE DNA polymerase I 40.7 87 0.0019 38.8 8.2 77 293-383 931-1007(1107)
253 PRK03932 asnC asparaginyl-tRNA 40.6 2.1E+02 0.0046 31.8 10.7 81 185-280 17-100 (450)
254 TIGR00237 xseA exodeoxyribonuc 40.2 67 0.0014 35.5 6.6 56 186-250 19-74 (432)
255 PF13742 tRNA_anti_2: OB-fold 40.2 1.2E+02 0.0026 26.0 6.9 71 29-100 27-98 (99)
256 PF03119 DNA_ligase_ZBD: NAD-d 39.8 18 0.00039 23.5 1.3 20 485-504 2-22 (28)
257 PRK02935 hypothetical protein; 39.7 16 0.00036 31.5 1.4 26 483-509 71-96 (110)
258 PRK12820 bifunctional aspartyl 39.5 2.3E+02 0.005 33.4 11.0 95 176-280 8-110 (706)
259 PRK06293 single-stranded DNA-b 39.3 2.7E+02 0.0058 26.3 9.6 35 348-386 44-79 (161)
260 PHA02942 putative transposase; 39.3 25 0.00053 38.2 3.0 37 471-509 316-352 (383)
261 PRK06752 single-stranded DNA-b 38.9 73 0.0016 27.9 5.5 35 348-386 48-83 (112)
262 PF05810 NinF: NinF protein; 38.7 6.1 0.00013 29.9 -1.2 21 485-507 20-40 (58)
263 PRK00448 polC DNA polymerase I 38.7 81 0.0018 40.2 7.6 73 173-250 225-299 (1437)
264 PTZ00417 lysine-tRNA ligase; P 38.3 1.6E+02 0.0034 34.0 9.3 77 186-279 134-218 (585)
265 PRK05672 dnaE2 error-prone DNA 38.1 77 0.0017 39.1 7.2 74 295-383 942-1015(1046)
266 PRK12496 hypothetical protein; 37.8 19 0.00041 34.2 1.6 36 472-509 118-153 (164)
267 PRK05853 hypothetical protein; 37.7 83 0.0018 29.7 5.9 36 348-386 44-79 (161)
268 KOG3056 Protein required for S 37.1 1.4E+02 0.0031 33.6 8.3 76 310-395 188-269 (578)
269 cd04476 RPA1_DBD_C RPA1_DBD_C: 36.9 44 0.00094 31.5 4.0 27 211-238 69-95 (166)
270 PRK14714 DNA polymerase II lar 36.6 21 0.00046 43.7 2.1 41 537-577 735-781 (1337)
271 PRK00476 aspS aspartyl-tRNA sy 35.9 2.8E+02 0.0061 32.0 11.0 87 185-281 18-107 (588)
272 PLN02903 aminoacyl-tRNA ligase 35.7 2.7E+02 0.0059 32.4 10.7 96 175-280 61-163 (652)
273 PRK03681 hypA hydrogenase nick 35.4 20 0.00044 31.7 1.4 27 482-508 70-96 (114)
274 TIGR00100 hypA hydrogenase nic 35.3 21 0.00044 31.8 1.4 26 482-508 70-95 (115)
275 PF14205 Cys_rich_KTR: Cystein 35.2 33 0.00071 26.1 2.2 27 483-509 5-38 (55)
276 cd04316 ND_PkAspRS_like_N ND_P 35.1 91 0.002 27.0 5.5 62 43-104 32-96 (108)
277 PRK00036 primosomal replicatio 34.0 2.8E+02 0.0062 24.3 8.1 70 185-258 2-82 (107)
278 PRK11088 rrmA 23S rRNA methylt 34.0 23 0.0005 36.3 1.7 32 483-516 3-34 (272)
279 PRK00564 hypA hydrogenase nick 33.7 48 0.001 29.5 3.5 27 482-508 71-97 (117)
280 PHA02998 RNA polymerase subuni 33.5 25 0.00055 33.4 1.7 36 482-517 143-189 (195)
281 PRK06556 vitamin B12-dependent 33.4 25 0.00054 42.5 2.1 28 481-509 923-950 (953)
282 cd04320 AspRS_cyto_N AspRS_cyt 33.2 85 0.0018 26.8 4.9 61 43-103 20-90 (102)
283 PRK07279 dnaE DNA polymerase I 33.1 1.8E+02 0.0038 35.9 9.0 74 295-383 876-949 (1034)
284 PRK12380 hydrogenase nickel in 32.8 24 0.00052 31.3 1.4 26 482-508 70-95 (113)
285 cd04319 PhAsnRS_like_N PhAsnRS 32.4 91 0.002 26.7 5.0 61 43-103 19-81 (103)
286 COG1675 TFA1 Transcription ini 31.9 15 0.00032 35.2 -0.1 28 482-509 113-142 (176)
287 PF13453 zf-TFIIB: Transcripti 31.9 24 0.00053 25.0 1.0 23 485-507 2-27 (41)
288 PF14803 Nudix_N_2: Nudix N-te 31.8 33 0.00071 23.5 1.6 24 484-507 2-30 (34)
289 PF10122 Mu-like_Com: Mu-like 31.7 18 0.0004 27.0 0.4 26 483-508 5-33 (51)
290 smart00734 ZnF_Rad18 Rad18-lik 31.6 20 0.00043 22.9 0.5 12 482-493 1-12 (26)
291 COG1107 Archaea-specific RecJ- 31.4 40 0.00087 38.0 3.0 67 174-250 202-269 (715)
292 cd00350 rubredoxin_like Rubred 31.1 31 0.00067 23.3 1.4 24 484-508 3-26 (33)
293 cd04317 EcAspRS_like_N EcAspRS 31.0 1E+02 0.0022 27.9 5.3 65 40-104 31-103 (135)
294 KOG4218 Nuclear hormone recept 30.9 19 0.00042 37.5 0.5 26 482-507 15-40 (475)
295 PF11023 DUF2614: Protein of u 30.8 21 0.00046 31.3 0.7 27 482-509 69-95 (114)
296 KOG3084 NADH pyrophosphatase I 30.7 43 0.00093 34.9 2.9 48 481-530 149-202 (345)
297 PF07975 C1_4: TFIIH C1-like d 30.4 24 0.00053 26.5 0.8 25 485-509 2-31 (51)
298 cd03574 NTR_complement_C345C N 30.3 3.3E+02 0.0071 25.1 8.6 45 237-283 76-120 (147)
299 PLN02221 asparaginyl-tRNA synt 30.2 3.7E+02 0.0081 30.8 10.6 83 185-280 51-137 (572)
300 COG1326 Uncharacterized archae 29.8 30 0.00065 33.4 1.5 30 481-510 5-41 (201)
301 cd04321 ScAspRS_mt_like_N ScAs 29.5 1.3E+02 0.0027 24.9 5.2 60 44-103 21-85 (86)
302 PF02150 RNA_POL_M_15KD: RNA p 29.3 18 0.0004 24.8 0.0 25 484-508 3-29 (35)
303 PRK03824 hypA hydrogenase nick 29.2 71 0.0015 29.2 3.9 27 482-508 70-116 (135)
304 COG5235 RFA2 Single-stranded D 29.2 1.9E+02 0.0041 28.4 6.8 74 519-616 86-159 (258)
305 PF06044 DRP: Dam-replacing fa 28.7 18 0.00039 36.2 -0.2 27 483-509 32-63 (254)
306 COG4640 Predicted membrane pro 28.3 29 0.00062 37.1 1.2 26 483-511 2-27 (465)
307 COG5189 SFP1 Putative transcri 28.2 26 0.00055 36.3 0.8 14 498-511 397-410 (423)
308 PF13695 zf-3CxxC: Zinc-bindin 28.0 72 0.0016 27.3 3.5 40 498-540 4-43 (98)
309 PF08696 Dna2: DNA replication 27.9 1.7E+02 0.0036 28.9 6.6 55 339-404 2-58 (209)
310 PF09297 zf-NADH-PPase: NADH p 27.9 39 0.00086 22.5 1.5 25 484-508 5-30 (32)
311 KOG1885 Lysyl-tRNA synthetase 26.8 2.3E+02 0.005 31.4 7.6 92 186-296 106-203 (560)
312 PF01599 Ribosomal_S27: Riboso 26.7 44 0.00094 24.7 1.6 26 482-507 18-46 (47)
313 COG0375 HybF Zn finger protein 26.4 32 0.0007 30.5 1.1 26 482-508 70-95 (115)
314 PF01155 HypA: Hydrogenase exp 26.3 24 0.00051 31.2 0.2 26 482-508 70-95 (113)
315 PF15072 DUF4539: Domain of un 26.3 1.3E+02 0.0029 25.2 4.7 56 40-97 19-74 (86)
316 PF04057 Rep-A_N: Replication 26.1 4E+02 0.0088 22.9 7.9 50 207-257 35-85 (101)
317 PRK08486 single-stranded DNA-b 25.8 6.1E+02 0.013 24.4 11.0 35 348-386 50-85 (182)
318 PF00096 zf-C2H2: Zinc finger, 25.7 27 0.00059 20.9 0.3 11 500-510 1-11 (23)
319 COG4085 Predicted RNA-binding 25.6 6.4E+02 0.014 24.6 11.4 72 186-273 53-129 (204)
320 smart00834 CxxC_CXXC_SSSS Puta 25.4 49 0.0011 22.9 1.7 28 481-508 4-35 (41)
321 PF14447 Prok-RING_4: Prokaryo 25.1 31 0.00066 26.4 0.6 15 480-494 37-51 (55)
322 PRK05978 hypothetical protein; 24.8 37 0.0008 31.6 1.2 29 482-510 33-63 (148)
323 COG4416 Com Mu-like prophage p 24.8 21 0.00045 26.9 -0.4 25 483-507 5-32 (60)
324 PF07649 C1_3: C1-like domain; 24.6 42 0.00092 21.9 1.1 22 484-507 2-23 (30)
325 CHL00174 accD acetyl-CoA carbo 24.5 27 0.00059 36.3 0.3 44 482-526 38-83 (296)
326 TIGR00515 accD acetyl-CoA carb 24.4 27 0.00059 36.2 0.3 42 482-524 26-69 (285)
327 PLN02603 asparaginyl-tRNA synt 24.0 7.3E+02 0.016 28.5 11.5 92 174-280 89-193 (565)
328 PF05876 Terminase_GpA: Phage 23.7 55 0.0012 37.4 2.5 34 478-511 196-241 (557)
329 PRK05654 acetyl-CoA carboxylas 23.7 28 0.0006 36.3 0.2 28 482-509 27-56 (292)
330 PF13824 zf-Mss51: Zinc-finger 23.6 44 0.00094 25.6 1.1 22 485-508 2-23 (55)
331 PF00130 C1_1: Phorbol esters/ 23.4 63 0.0014 23.9 2.1 26 483-508 12-37 (53)
332 PRK00241 nudC NADH pyrophospha 23.4 1.2E+02 0.0025 31.0 4.6 28 482-509 99-127 (256)
333 COG4332 Uncharacterized protei 22.7 46 0.001 31.7 1.4 10 500-509 50-59 (203)
334 PHA02768 hypothetical protein; 22.5 75 0.0016 24.3 2.2 27 484-510 7-42 (55)
335 TIGR03844 cysteate_syn cysteat 22.4 41 0.00088 36.7 1.1 24 481-506 1-24 (398)
336 COG5216 Uncharacterized conser 21.9 1E+02 0.0022 23.8 2.7 29 477-506 17-51 (67)
337 PF03833 PolC_DP2: DNA polymer 21.8 30 0.00066 40.7 0.0 20 213-232 350-372 (900)
338 TIGR00311 aIF-2beta translatio 21.7 68 0.0015 29.3 2.3 27 482-509 97-128 (133)
339 KOG3108 Single-stranded DNA-bi 21.7 2.8E+02 0.006 28.5 6.8 71 309-394 70-141 (265)
340 PRK12495 hypothetical protein; 21.6 57 0.0012 32.2 1.8 32 479-511 39-70 (226)
341 KOG4317 Predicted Zn-finger pr 21.5 48 0.001 34.3 1.4 23 482-509 7-29 (383)
342 PRK00762 hypA hydrogenase nick 21.3 1.2E+02 0.0025 27.3 3.7 27 500-526 93-122 (124)
343 COG0675 Transposase and inacti 21.3 67 0.0014 33.5 2.5 26 480-509 307-332 (364)
344 PF09889 DUF2116: Uncharacteri 21.3 13 0.00029 28.8 -2.1 24 483-509 4-28 (59)
345 PF02591 DUF164: Putative zinc 21.3 52 0.0011 25.0 1.2 24 484-507 24-54 (56)
346 cd04487 RecJ_OBF2_like RecJ_OB 21.3 3.2E+02 0.0069 22.0 5.9 58 40-102 15-73 (73)
347 PF15135 UPF0515: Uncharacteri 21.1 49 0.0011 33.2 1.3 26 485-510 135-166 (278)
348 COG4085 Predicted RNA-binding 21.1 1.1E+02 0.0023 29.7 3.5 26 517-542 71-96 (204)
349 PF03884 DUF329: Domain of unk 21.0 51 0.0011 25.5 1.1 24 483-506 3-29 (57)
350 PF03833 PolC_DP2: DNA polymer 20.9 32 0.0007 40.5 0.0 22 482-508 680-701 (900)
351 cd01759 PLAT_PL PLAT/LH2 domai 20.6 91 0.002 27.6 2.8 26 514-539 1-29 (113)
352 PRK00418 DNA gyrase inhibitor; 20.3 52 0.0011 25.8 1.0 26 482-507 6-34 (62)
No 1
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=5.1e-121 Score=1021.41 Aligned_cols=593 Identities=44% Similarity=0.715 Sum_probs=499.6
Q ss_pred CCCCCHHHHHHHhcCCCCCCCCCCCcceEEEeeeeecC-----ceEEEEEeCcccceeeccccccccccccCccceeeEE
Q 006973 2 DKTVSPDAISTILSNPSPDSSSDIPEIVVQVLDLKLTG-----NRYMFNASDGKKRLKAILPSNLSSEVISGNIQNKGLI 76 (623)
Q Consensus 2 ~~~lt~ga~~~i~~~~~~~~~~~~~~pvlQvl~~k~~~-----~ryr~~lSDG~~~~~~mlat~ln~~v~~~~l~~~sii 76 (623)
+..||+|||.+|+..... ......|||||+++|+++ +|||++||||.|++++|||||||++|++|+|++|+||
T Consensus 1 ~~~lt~ga~~~i~~~~~~--~~~~~~pv~Qv~~~k~~~~~~~~~ryr~~lsDg~~~~~~ml~t~~n~~~~~~~l~~~~iv 78 (608)
T TIGR00617 1 AVSLSNGAIALIMTNGEA--NGYPPDPVLQVLDLKPINGAQDPRRYRIVISDGIYYSKAMLATQLNPLVREGELQEGTII 78 (608)
T ss_pred CCccChhHHHHHhccccc--cCCCCCcEEEEEeeEEcCCCCCCceEEEEEECchHHHHHHHHHHHHHHHHhCCccCCCEE
Confidence 357999999999984321 112467999999999985 5999999999999999999999999999999999999
Q ss_pred EEcceeeecc-CCCceEEEEEEeeeeeccccchh-hccccCCCCCccc-CCCCCcccc--CCCCCC--cccCchhhhhhh
Q 006973 77 RLLDYALNEI-PTKSEKYLIVTKCEVVSPALEME-IKIEVKSDESGII-FKPKQEDEV--KKDGPG--IVLKPKQEMVAK 149 (623)
Q Consensus 77 rl~~y~~~~~-~~~~~~vlii~~lev~~~~~~~~-~~~~~~~~~~~~~-~~~~~~~~~--~~~~~~--~~~~~~~~~~~~ 149 (623)
||++|+++.+ +++ |++|||++|||+.+..+.. ++|+|..-..... ..+.....+ ...+.. ....|++.. .
T Consensus 79 ~l~~~~~~~~~~~~-~~~lii~~~ev~~~~~~~~~~ig~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~ 155 (608)
T TIGR00617 79 RLTKFEVNTIGKDG-RKVLIVYELEVVKPELKVRDKIGNPVTYEKYLDSWHEEQVLASKPATNPANPPNAKAPKNEV--A 155 (608)
T ss_pred EEeEEEEeEEccCC-cEEEEEEeeEEeecccccccccCCCccccccccccCccccccccccccCCCCCCccCCCccc--c
Confidence 9999999999 543 6999999999999765543 6777764322100 011100000 000000 001111100 0
Q ss_pred hhhhhhccccCCCCccccccCCcCeeeccccCCCCCCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEe
Q 006973 150 SAAQILRDQNGNMAPAARLAMTRRVHPLVSLNPYQGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMF 229 (623)
Q Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~L~p~~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~ 229 (623)
+..+...+++++++|+...++.++++||++|+||+++|+|+|||++||++|+|++++|+|++|+|+|+| +|++|+|++|
T Consensus 156 ~~~~~~~~~~~~~~~~~~~~~~~~~~pI~~L~py~~~wtIkaRV~~Ks~ir~~~~~~gegkvfsv~L~D-egg~Irat~f 234 (608)
T TIGR00617 156 SYNNAANPERGNAPPAPNSGSTRRVMPIASLSPYQNKWTIKARVTNKSEIRTWSNARGEGKLFNVELLD-ESGEIRATAF 234 (608)
T ss_pred cccCCCCcccCCCCCCccccCCcceEEHHHCCCCCCceEEEEEEEeccccceecCCCCCceeeEEEEec-CCCeEEEEEC
Confidence 001111112333333333334557999999999999999999999999999999999999999999999 6669999999
Q ss_pred chHHHHHHhhcccCcEEEEeeeEEEecCCCccccCCceEEEEccCcEEEEccCcCCCCCCCccccccccccccccCCcce
Q 006973 230 NEAARKFYDRFQLGKVYYISRGTLRVANKQFKTVQNDYEMNLNENSEVEEAVNETAFIPQTKFNFVPIDELGRYVNGTEL 309 (623)
Q Consensus 230 ~~~~~kf~~~l~eG~vy~is~~~V~~a~~~~~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~~~f~~i~di~~~~~~~~~ 309 (623)
++.+++|+++|++|+||+|++|+|++++++|++++|+|||+|+.+|.|++|.|. .++|.+.|+|++|+||.+ ...+.+
T Consensus 235 ~~~~dkf~~~l~eG~VY~Is~~~Vk~an~~y~~~~~~yei~f~~~T~I~~~~d~-~~iP~~~~~f~~i~dI~~-~~~~~~ 312 (608)
T TIGR00617 235 NEQADKFYDIIQEGKVYYISKGSLKPANKQFTNLGNDYEMTLDRDTVIEECEDE-TAIPKIQFNFVKIDDIGG-YEGNSL 312 (608)
T ss_pred chHHHHHhhhcccCCEEEECceEEEEccccccCCCCCEEEEECCCeEEEECCCc-ccCCcccccceEHHHhhh-hcCCCC
Confidence 999999999999999999999999999999999999999999999999999886 569999999999999987 455679
Q ss_pred eEEEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEEeeecccee
Q 006973 310 VDIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSPIVAIKSLKVGDFQGIS 389 (623)
Q Consensus 310 vDVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~kV~~f~G~~ 389 (623)
|||||+|++|+++.+|++|.+|++..||+|+|+|+||.+|+|||||++|..|. ...++||+|+++||++|+|++
T Consensus 313 VDVIGvV~~v~~~~~i~~k~~g~~~~kR~i~L~D~sg~sI~vTLWG~~A~~~~------~~~~~Vva~kg~~V~~f~g~s 386 (608)
T TIGR00617 313 VDVIGIVQSVSPTQTITSRKNNKEFPKRDITLVDDSGKSVRVTLWGDDATKFD------VSVQPVIAIKGVRVSDFGGKS 386 (608)
T ss_pred ccEEEEEeEecCceEEEEcCCCCeeeeEEEEEEeCCCCEEEEEEEhhhhhhcC------CCCCCEEEEEeEEEEecCCce
Confidence 99999999999999999888899999999999999999999999999999874 456899999999999999999
Q ss_pred eecccceEEEEcCChHHHHHHHHHHHhCCCccceeeecCCcCccccCCcccccccceehhccccCCCCC-CCCCeEEEEE
Q 006973 390 LSTLGRSTVLVSPDLPEAKKLKSWYESEGKGTSMASIGSGLGSLAKNGARSMYSDRVSLTHITSNPSLG-DEKPVFFSIK 468 (623)
Q Consensus 390 Ls~~~~S~i~iNPd~pe~~~l~~w~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~ti~~i~~~~~~~-~~~~~~~~v~ 468 (623)
||++++|+|++|||+||+++|+.||+++|....+.+++...++.. + . ...+++||+||++ .++| .++++||+|+
T Consensus 387 Ls~~~~S~i~iNPdipEa~~L~~w~~~~g~~~~~~s~~~~~~~~~-~-~--~~~~~ktI~ei~~-~~lg~~~k~~~f~v~ 461 (608)
T TIGR00617 387 LSTGGSSTIIVNPDIPEAEKLKGWYDNEGKGTMASSISDMMSGRV-G-G--SNAERKTIAEIQA-ENLGKSDKPDYFSVK 461 (608)
T ss_pred EeccCCceEEECCCcHHHHHHHHHHHhcCCCccceeehhcccccc-C-C--cccccccHHHHhh-hccCCCCCCcEEEEE
Confidence 999999999999999999999999999988665555543322111 1 1 2367899999998 5666 4899999999
Q ss_pred EEEEEEeCCCCeEeccccc--cccceecCCCCeeecCcCCCCccccceeEEEEEEEEeCCCcEEEEEehHhHHHHhCCCH
Q 006973 469 AYISLIKPDQAMWYRACKT--CNKKVTDALGSGYWCEGCQKNDEECSLRYIMVARVCDGSGEAWISIFNEEAERIIGCSA 546 (623)
Q Consensus 469 a~I~~i~~d~~~~Y~aC~~--C~KKv~~~~~~~~~C~kC~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~~~ae~llG~sA 546 (623)
|+|++|+.| +|||+|||. |+|||.++.+|.|+|++|++++++|.|||+|++.|+|+||++|+++||+.|++|||++|
T Consensus 462 atI~~Ik~d-~~~Y~ACp~~~CnKKV~~~~~g~~~CekC~~~~~~~~~RYil~~~i~D~Tg~~~~t~F~~~ae~llG~sA 540 (608)
T TIGR00617 462 ATISYLKPD-NALYRACPSEDCNKKVVDQGDGTYRCEKCNKNFAEFKYRYILQISISDETGQLWVTAFNDQAEQILGKSA 540 (608)
T ss_pred EEEEEEecC-CeEeccCChhhCCCccccCCCCCEECCCCCCCCCCccEEEEEEEEEEeCCCCEEEEEEhHHHHHHcCCCH
Confidence 999999998 899999986 99999987668999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhcCCchhHHHHHHHhcCceEEEEEEEEeeecCceeeeEEEEEEeeccCHHHHHHHHHHHHHh
Q 006973 547 DELNELKSQLGDDNSYQMKLKEVTWVPHLLRVSVAQQEYNNEKRQRVTVRAVAPVDFAAESKFLLEEISK 616 (623)
Q Consensus 547 ~el~~~~~~~~~~~~~~~~l~~~~~~~~~f~v~~k~~~y~~~~r~~~~v~~~~~vd~~~e~~~Ll~~i~~ 616 (623)
+||.++++++ +.+|+++|+++.|++|.|||++++++||||.|+||+|++++|+||++|+++||++|++
T Consensus 541 ~eL~~l~~~~--~~~~~~i~~~~~~~~~~f~~~~k~e~yn~e~r~~~~v~~~~~vd~~~e~~~L~~~i~~ 608 (608)
T TIGR00617 541 AELGELKEED--PDEFEAIFQEAQFVPYIFRLRVKQDTYNDESRQKYTVMSVDPVNYRAEAKYLLQEIEK 608 (608)
T ss_pred HHHHHHHhcC--HHHHHHHHHHhhCcEEEEEEEEEEcccCCEeeEEEEEEEeeeCCHHHHHHHHHHHhcC
Confidence 9999999754 5689999999999999999999999999999999999999999999999999999964
No 2
>PRK12366 replication factor A; Reviewed
Probab=100.00 E-value=4.3e-67 Score=590.42 Aligned_cols=436 Identities=19% Similarity=0.290 Sum_probs=362.0
Q ss_pred ceEEEeeeeec----C---ceEEEEEeCcccceeeccccccccccccCccceeeEEEEcceeeeccCCCceEEEEEEeee
Q 006973 28 IVVQVLDLKLT----G---NRYMFNASDGKKRLKAILPSNLSSEVISGNIQNKGLIRLLDYALNEIPTKSEKYLIVTKCE 100 (623)
Q Consensus 28 pvlQvl~~k~~----~---~ryr~~lSDG~~~~~~mlat~ln~~v~~~~l~~~siirl~~y~~~~~~~~~~~vlii~~le 100 (623)
-|+++.+++.+ | .+..++|.|.+..++..||-++.++ .|+.|++|+|+.|...--.+ ++|
T Consensus 192 ~V~~~~~~~~f~rkdg~~~~~r~~~l~D~TG~irvTlW~~~a~~----~~~~g~vv~i~g~~~~~~~~---------~~e 258 (637)
T PRK12366 192 EVTKAYPIKEFTRKDGSEGKLKSFILKDDTGSIRVTLWNDLTDI----EVNKGDIVRVKGYVKQGYRT---------GLE 258 (637)
T ss_pred EEEEccCcEEEEEcCCCeeEEEEEEEEcCCCcEEEEEEChhhcc----cCCCCCEEEEEeEEecCcCC---------ceE
Confidence 34555555554 2 4679999999999999999988865 68999999999876653211 233
Q ss_pred eeccccchhhccccCCCCCcccCCCCCccccCCCCCCcccCchhhhhhhhhhhhhccccCCCCccccccCCcCeeecccc
Q 006973 101 VVSPALEMEIKIEVKSDESGIIFKPKQEDEVKKDGPGIVLKPKQEMVAKSAAQILRDQNGNMAPAARLAMTRRVHPLVSL 180 (623)
Q Consensus 101 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~L 180 (623)
+-... .+++ ..... . .....++||++|
T Consensus 259 l~~~~--~~~i-----------~~~~~-----------~-----------------------------~~~~~~~pI~~L 285 (637)
T PRK12366 259 ISANN--IEIL-----------EKLEK-----------E-----------------------------EKELEIVNIEEL 285 (637)
T ss_pred EEeCC--ceee-----------ccccc-----------c-----------------------------ccccCceeHHHC
Confidence 22211 0010 00000 0 001136899999
Q ss_pred CCC-CC-CeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeEEEecCC
Q 006973 181 NPY-QG-NWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGTLRVANK 258 (623)
Q Consensus 181 ~p~-~~-~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~V~~a~~ 258 (623)
+|| .+ +|+|+|||+.|+++|+|++++|+|++|+++|.|++| +|++|+|++.+++|++ |++|+||+|++++|+..+.
T Consensus 286 ~~~~~g~~~~I~grV~~~~~~R~f~~~~g~gkv~s~~l~D~tG-~IR~t~w~~~~d~~~~-l~~G~vy~is~~~vk~y~~ 363 (637)
T PRK12366 286 TEFEDGEEVDVKGRIIAISDKREVERDDRTAEVQDIELADGTG-RVRVSFWGEKAKILEN-LKEGDAVKIENCKVRTYYD 363 (637)
T ss_pred CcccCCCEEEEEEEEEecCCceEEEcCCCcEEEEEEEEEcCCC-eEEEEEeCchhhhhcc-cCCCCEEEEecCEEeeccc
Confidence 999 55 899999999999999999999999999999999999 8999999999999998 5999999999999985443
Q ss_pred CccccCCceEEEEccCcEEEEccCcCCCCCCCccccccccccccccCCcceeEEEEEEEEeCCceEEEEccCCceeeEEE
Q 006973 259 QFKTVQNDYEMNLNENSEVEEAVNETAFIPQTKFNFVPIDELGRYVNGTELVDIIGVVQNVSPTMSIRRKSNNEMVPKRD 338 (623)
Q Consensus 259 ~~~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~~~f~~i~di~~~~~~~~~vDVIGvV~~v~~~~~i~~k~~g~~~~kr~ 338 (623)
. ...+.|||+++..|.|.+ +++ ..+|.+.|+|++|.+|.+....+..|||+|+|++++|+.+|+++ +|++..+|+
T Consensus 364 ~--~~~~~~El~~~~~s~I~~-d~~-~~~p~~~~~~~~i~dI~~~~~~~~~VdVig~V~~v~~~~~i~~k-~G~~~~~r~ 438 (637)
T PRK12366 364 N--EGEKRVDLNAGYSSEIIK-DES-ISFEEIEEKIYKIKDILNLEEDDNDITVIARVVEDYPVNEFERS-DGSKGKVRN 438 (637)
T ss_pred c--CCCcCEEEEcCCceEEEe-ccC-CcccceeeccccHHHhhcccCCCcEEEEEEEEEEccCceEEEec-CCCEeEEEE
Confidence 1 346789999999999998 333 46899999999999998733467899999999999999999876 588899999
Q ss_pred EEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEEeeeccc-eeeecccceEEEEcCChHHHHHHHHHHHhC
Q 006973 339 ITVADETKRTVTVSLWNELATNVGQELLDNADKSPIVAIKSLKVGDFQG-ISLSTLGRSTVLVSPDLPEAKKLKSWYESE 417 (623)
Q Consensus 339 i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~kV~~f~G-~~Ls~~~~S~i~iNPd~pe~~~l~~w~~~~ 417 (623)
++|.|+|| +|++||||+.|... ...+++|+|++++|++|+| .+||++++|+|.+||+.|+ |+
T Consensus 439 i~l~D~TG-~I~vtlWg~~a~~~-------~~~G~vi~i~~~~V~~~~g~~~Ls~~~~s~i~~~p~~~e---l~------ 501 (637)
T PRK12366 439 IELADGTG-SIRLTLWDDDAEIE-------IKEGDAIKILHPYVKENGDYLDLSIGRYGRIEINPEGEI---IK------ 501 (637)
T ss_pred EEEEeCCC-EEEEEEeccccccC-------CCCCCEEEEEeeEEEeCCCeeEEEecCcceEEECCCCcc---cc------
Confidence 99999999 99999999999731 4568999999999999999 5999999999999999876 21
Q ss_pred CCccceeeecCCcCccccCCcccccccceehhccccCCCCCCCCCeEEEEEEEEEEEeCCCCeEeccccccccceecCCC
Q 006973 418 GKGTSMASIGSGLGSLAKNGARSMYSDRVSLTHITSNPSLGDEKPVFFSIKAYISLIKPDQAMWYRACKTCNKKVTDALG 497 (623)
Q Consensus 418 g~~~~~~~~~~~~~~~~~~~~~~~~~~~~ti~~i~~~~~~~~~~~~~~~v~a~I~~i~~d~~~~Y~aC~~C~KKv~~~~~ 497 (623)
..+++|++|.+. ++|+++|+|++|+.+ ++||+|||.|+|||... +
T Consensus 502 -------------------------~~~~~I~~i~~~--------~~~~v~g~i~~i~~~-~~~y~aCp~CnkKv~~~-~ 546 (637)
T PRK12366 502 -------------------------SNRKFIADLEED--------DTVEIRGTVVDIRKQ-KIILYLCPNCRKRVEEV-D 546 (637)
T ss_pred -------------------------ccccCHHHcccC--------CeEEEEEEEEEEeCC-CEEEecccccCeEeEcC-C
Confidence 025678888762 359999999999987 68999999999999874 8
Q ss_pred CeeecCcCCCCccccceeEEEEEEEEeCCCcEEEEEehHhHHHHhCCCHHHHHHHHhhcCCchhHHHHHHHhcCceEEEE
Q 006973 498 SGYWCEGCQKNDEECSLRYIMVARVCDGSGEAWISIFNEEAERIIGCSADELNELKSQLGDDNSYQMKLKEVTWVPHLLR 577 (623)
Q Consensus 498 ~~~~C~kC~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~~~ae~llG~sA~el~~~~~~~~~~~~~~~~l~~~~~~~~~f~ 577 (623)
|.|+|++|++. +|.|||++++.|+|+||++|+++|++.|++||||+|+||.+|.+ +.|++++|++|.|+
T Consensus 547 g~~~C~~c~~~--~p~~~~~l~~~i~D~TG~~~~t~f~e~ae~l~G~sa~el~~l~~---------~~l~~~~g~~~~~~ 615 (637)
T PRK12366 547 GEYICEFCGEV--EPNELLMLNFTLDDGTGTINCRFYGKNVEKLLGMSKEELKELNL---------EALEDLLGEEVVFY 615 (637)
T ss_pred CcEECCCCCCC--CCcEEEEEEEEEEcCCCCEEEEEEhHHhHHHhCCCHHHHHHHHH---------HHHHHhcCcEEEEE
Confidence 99999999997 79999999999999999999999999999999999999998874 45667899999999
Q ss_pred EEEEeeecCceeeeEEEEEEeeccCH
Q 006973 578 VSVAQQEYNNEKRQRVTVRAVAPVDF 603 (623)
Q Consensus 578 v~~k~~~y~~~~r~~~~v~~~~~vd~ 603 (623)
++++++ |++ +||+|.++.|+|+
T Consensus 616 ~~~k~~--~~~--~r~~v~~v~~~d~ 637 (637)
T PRK12366 616 GNVSFR--NEE--LRFNVRRVNNVDV 637 (637)
T ss_pred EEEeec--Cce--eEEEEEEeecccC
Confidence 999987 665 5599999999985
No 3
>PRK08402 replication factor A; Reviewed
Probab=100.00 E-value=2.4e-46 Score=390.62 Aligned_cols=281 Identities=18% Similarity=0.297 Sum_probs=239.0
Q ss_pred ccccccccccccCCcceeEEEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCC
Q 006973 293 NFVPIDELGRYVNGTELVDIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKS 372 (623)
Q Consensus 293 ~f~~i~di~~~~~~~~~vDVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~ 372 (623)
..++|.||.. ....|.+.|.|+++++.+.|.++ +|.....++++|.|+|| .+++||||+.|..+. +.+..|
T Consensus 61 ~~~kI~dl~~---g~~~V~v~~rVl~~~~~r~f~rr-dG~~~~V~~i~l~DeTG-~ir~TlW~~~a~~~~----~~l~~G 131 (355)
T PRK08402 61 PLMHISDLVP---GMRGVNIVGRVLRKYPPREYTKK-DGSTGRVASLIIYDDTG-RARVVLWDAKVAKYY----NKINVG 131 (355)
T ss_pred CccCHHHccC---CCceeeEEEEEEEccCCceeecc-CCCcceEEEEEEEcCCC-eEEEEEechhhhhhc----ccCCCC
Confidence 4678888864 34579999999999999999887 48778899999999999 779999999998642 235779
Q ss_pred cEEEEEeEEeeec-cce-eeecccceEEEEcCChHHHHHHHHHHHhCCCccceeeecCCcCccccCCcccccccceehhc
Q 006973 373 PIVAIKSLKVGDF-QGI-SLSTLGRSTVLVSPDLPEAKKLKSWYESEGKGTSMASIGSGLGSLAKNGARSMYSDRVSLTH 450 (623)
Q Consensus 373 ~Vv~i~~~kV~~f-~G~-~Ls~~~~S~i~iNPd~pe~~~l~~w~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~ti~~ 450 (623)
+||.|++++|++| +|+ +||.+++|+|.+||++|+++.+. +++...+ ....+++|++
T Consensus 132 dvi~I~~a~V~e~~~G~~eLsvg~~s~i~~~pd~~ea~~i~-------------~~~~~~~---------~~~~~k~I~e 189 (355)
T PRK08402 132 DVIKVIDAQVRESLSGLPELHINFRARIILNPDDPRVEEIP-------------PLEEVRS---------YNYTRKKIGE 189 (355)
T ss_pred CEEEEECCEEeecCCCcEEEEECCCceEEeCCCcccccccc-------------ccccccc---------ccccccCHHH
Confidence 9999999999995 898 99999999999999999887721 2211100 1246788999
Q ss_pred cccCCCCCCCCCeEEEEEEEEEEEeCCCCeEecccccccccee-cCCCCeeecCcCCCCccccceeEEEEEEEEeCCCcE
Q 006973 451 ITSNPSLGDEKPVFFSIKAYISLIKPDQAMWYRACKTCNKKVT-DALGSGYWCEGCQKNDEECSLRYIMVARVCDGSGEA 529 (623)
Q Consensus 451 i~~~~~~~~~~~~~~~v~a~I~~i~~d~~~~Y~aC~~C~KKv~-~~~~~~~~C~kC~~~~~~~~~ry~l~~~i~D~Tg~~ 529 (623)
|.+ | .+||+++|+|++|+. +.+|+|||.|+|||. +++++.|+|+.|++. +|.|||+|++.|+|+||++
T Consensus 190 i~~----g---d~~v~v~g~Iv~i~~--~~~y~aCp~CnKkv~~~~~~~~~~Ce~~~~v--~p~~ryil~~~l~D~TG~~ 258 (355)
T PRK08402 190 LEG----G---ERFVEVRGTIAKVYR--VLVYDACPECRRKVDYDPATDTWICPEHGEV--EPIKITILDFGLDDGTGYI 258 (355)
T ss_pred ccc----C---CcEEEEEEEEEEEec--CeeEecCCCCCeEEEEecCCCCEeCCCCCCc--CcceeEEEEEEEEcCCCcE
Confidence 855 1 278999999999997 568999999999998 556789999999974 6899999999999999999
Q ss_pred EEEEehHhHHHHhCCCHHHHHHH-H---hhcCCc-----hhHHHHHHHhcCceEEEEEEEEeeecCceeeeEEEEEEeec
Q 006973 530 WISIFNEEAERIIGCSADELNEL-K---SQLGDD-----NSYQMKLKEVTWVPHLLRVSVAQQEYNNEKRQRVTVRAVAP 600 (623)
Q Consensus 530 ~~~~F~~~ae~llG~sA~el~~~-~---~~~~~~-----~~~~~~l~~~~~~~~~f~v~~k~~~y~~~~r~~~~v~~~~~ 600 (623)
|+++|++.|++|||++|+||.++ + +...++ ..|...++.++|++|.||++++++.|||+. |+|.++.|
T Consensus 259 ~vt~f~e~ae~llG~sa~el~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~rg~~~~d~y~~~~---~~v~~~~~ 335 (355)
T PRK08402 259 RVTLFGDDAAELLGVEPEEIAEKLKELIEMGLTPKEAARKLAEEEFYNIIGREIVVRGNVIEDRFLGLI---LKASSWDE 335 (355)
T ss_pred EEEEecHHHHHHhCCCHHHHHHHHHHhhhcccchhhhhhhHHHHHHHHhcCeEEEEEEEEEecccCCeE---EEEEEccc
Confidence 99999999999999999999998 4 322122 568888999999999999999999999965 99999999
Q ss_pred cCHHHHHHHHHHHHHhhh
Q 006973 601 VDFAAESKFLLEEISKKV 618 (623)
Q Consensus 601 vd~~~e~~~Ll~~i~~~~ 618 (623)
+||++|+++|+++|.++.
T Consensus 336 vd~~~e~~~l~~~i~~~~ 353 (355)
T PRK08402 336 VDYKREIERVRAELEELG 353 (355)
T ss_pred CCHHHHHHHHHHHHHHhh
Confidence 999999999999998874
No 4
>PRK07218 replication factor A; Provisional
Probab=100.00 E-value=5.5e-35 Score=311.05 Aligned_cols=361 Identities=19% Similarity=0.242 Sum_probs=285.9
Q ss_pred CcCeeeccccCCCCCCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEee
Q 006973 171 TRRVHPLVSLNPYQGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISR 250 (623)
Q Consensus 171 ~~~~~~I~~L~p~~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~ 250 (623)
.+....|++|.|...+.+|+|||+.+|+ |+|....++|.+.+++|.|++| .|+.|+|++. -|++|++|.|.|
T Consensus 55 ~~~~~kI~Di~~~~~~V~v~~kVl~i~~-rt~r~dg~~g~v~~~~igDeTG-~Ir~tlW~~~------~l~~Gdvv~I~n 126 (423)
T PRK07218 55 TPSSKDIKELSTDDKNVTVTGRVLTIGE-RSIRYQGDDHVIYEGILADETG-TISYTAWKDF------GLSPGDTVTIGN 126 (423)
T ss_pred CCCCccHhhCCCCCceeEEEEEEEEecc-eeEecCCCceEEEEEEEECCCC-eEEEEEECCC------CCCCCCEEEEec
Confidence 3457899999999989999999999999 9997666688999999999999 9999999965 299999999999
Q ss_pred eEEEecCCCccccCCceEEEEccCcEEEEccCcCCCCCCCccccccccccccccCCcceeEEEEEEEEeCCceEEEEccC
Q 006973 251 GTLRVANKQFKTVQNDYEMNLNENSEVEEAVNETAFIPQTKFNFVPIDELGRYVNGTELVDIIGVVQNVSPTMSIRRKSN 330 (623)
Q Consensus 251 ~~V~~a~~~~~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~~~f~~i~di~~~~~~~~~vDVIGvV~~v~~~~~i~~k~~ 330 (623)
+.++..+. .+++.++..|.|.+.++. ...|...+...+|.||.. ...-|+|.|.|.++.+ .+|.++ +
T Consensus 127 a~vre~~g-------~~el~ig~~t~I~~~de~-~~~~~~~~~~~kI~DL~~---g~~~V~v~g~Vl~~~~-r~f~~~-d 193 (423)
T PRK07218 127 AGVREWDG-------RPELNIGESTTVSLLDDS-SLPPYSIGGDKKLIDLGP---GDRGVNVEARVLELEH-REIDGR-D 193 (423)
T ss_pred cEeeccCC-------ceEEeccCcceEEEcCcc-cccCccccCccchhhccC---CCCceEEEEEEEEecc-eeEEcC-C
Confidence 99877543 389999999999987664 223322344556666653 3456999999999965 788876 4
Q ss_pred CceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEEeeeccce-eeecccceEEEEcCChHHHHH
Q 006973 331 NEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSPIVAIKSLKVGDFQGI-SLSTLGRSTVLVSPDLPEAKK 409 (623)
Q Consensus 331 g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~kV~~f~G~-~Ls~~~~S~i~iNPd~pe~~~ 409 (623)
|. ...++..|.|+|| +|++|||++.+. +..|.+|-|.++.+++|+|+ +|+....|+|..+|+..+
T Consensus 194 g~-~~v~~giigDeTG-~Ir~tlW~~~~~---------l~~Gd~v~I~na~v~e~~G~~elnv~~~t~I~~~d~~i~--- 259 (423)
T PRK07218 194 GE-TTILSGVLADETG-RLPFTDWDPLPE---------IEIGASIRIEDAYVREFRGVPSVNVSEFTTVEALDREVS--- 259 (423)
T ss_pred CC-eEEEEEEEECCCc-eEEEEEeccccc---------CCCCCEEEEeeeEEeccCCeEEEEECCceEEEECCCCcc---
Confidence 64 5689999999999 999999998752 35699999999999999986 899999999998885311
Q ss_pred HHHHHHhCCCccceeeecCCcCccccCCcccccccceehhccccCCCCCCCCCeE-EEEEEEEEEEeCCCCeEecccccc
Q 006973 410 LKSWYESEGKGTSMASIGSGLGSLAKNGARSMYSDRVSLTHITSNPSLGDEKPVF-FSIKAYISLIKPDQAMWYRACKTC 488 (623)
Q Consensus 410 l~~w~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~ti~~i~~~~~~~~~~~~~-~~v~a~I~~i~~d~~~~Y~aC~~C 488 (623)
+.. ...+++|.++.+. ...| ..+.|+|+.|... +..|..||.|
T Consensus 260 ----------------v~~-------------~~~~~~I~e~~~~------~g~~~Vev~G~Iv~i~~g-sgli~rCP~C 303 (423)
T PRK07218 260 ----------------VSK-------------DPPRLKIREAVER------GGIFDVELVGNIISVRDG-SGLIERCPEC 303 (423)
T ss_pred ----------------ccC-------------Cccccchhhhhcc------CCcceEEEEEEEEEeccC-CcceecCcCc
Confidence 100 1245678887661 1223 6899999999987 4569999999
Q ss_pred ccceecCCCCeeecCcCCCCccccceeEEEEEEEEeCCCcEEEEEehHhHHHHhCCCHHHHHHHHhhcCCchhHHHHH-H
Q 006973 489 NKKVTDALGSGYWCEGCQKNDEECSLRYIMVARVCDGSGEAWISIFNEEAERIIGCSADELNELKSQLGDDNSYQMKL-K 567 (623)
Q Consensus 489 ~KKv~~~~~~~~~C~kC~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~~~ae~llG~sA~el~~~~~~~~~~~~~~~~l-~ 567 (623)
+|+|.. |.|+-|++. ++.+-.++.+.+.|+||++.+++|++.+++|+|++.++..+|..+.-+.......+ .
T Consensus 304 ~r~v~~-----~~C~~hG~v--e~~~dlrik~vLDDGtg~~~~~~~~e~~e~l~G~~~e~a~~~~~~~~d~~~v~~~i~~ 376 (423)
T PRK07218 304 GRVIQK-----GQCRSHGAV--EGEDDLRIKAILDDGTGSVTVILDRELTEIVYGGTLEDAEELAREAMDKDVVAEDIRE 376 (423)
T ss_pred cccccC-----CcCCCCCCc--CCeeeeEEEEEEECCCCeEEEEEChhhhHhHhCCCHHHHHHHHHhhhcchhhHHHHHH
Confidence 999953 789999986 57788888999999999999999999999999999999988775433333333444 6
Q ss_pred HhcCceEEEEEEEEeeecCceeeeEEEEEEeeccC--HHHHHHHHHHH
Q 006973 568 EVTWVPHLLRVSVAQQEYNNEKRQRVTVRAVAPVD--FAAESKFLLEE 613 (623)
Q Consensus 568 ~~~~~~~~f~v~~k~~~y~~~~r~~~~v~~~~~vd--~~~e~~~Ll~~ 613 (623)
.++|+.|.|+..+..+.|. ..+.+.+...+| .++-++.||.+
T Consensus 377 ~llG~~~~v~G~~~~~~~g----~~~~a~~~~~~~~~~~~r~~~~l~~ 420 (423)
T PRK07218 377 RLVGREYRVRGNLSVDEYG----ANLVAESFWVPDDDPAKRAVALLAE 420 (423)
T ss_pred hhcCcEEEEEeccccccCC----cEEEEeEccccCCCHHHHHHHHHHh
Confidence 7999999999998888884 567888888886 34444455543
No 5
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=100.00 E-value=9.2e-36 Score=283.82 Aligned_cols=154 Identities=45% Similarity=0.766 Sum_probs=145.4
Q ss_pred CCCeEEEEEEEEEEEeCCCCeEeccccccccceecCCCCeeecCcCCCCccccceeEEEEEEEEeCCCcEEEEEehHhHH
Q 006973 460 EKPVFFSIKAYISLIKPDQAMWYRACKTCNKKVTDALGSGYWCEGCQKNDEECSLRYIMVARVCDGSGEAWISIFNEEAE 539 (623)
Q Consensus 460 ~~~~~~~v~a~I~~i~~d~~~~Y~aC~~C~KKv~~~~~~~~~C~kC~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~~~ae 539 (623)
+++++|.|+|+|..|+.+ +|||+|||.|+|||.+..++.|+|++|++...+|.+||+|++.|+|+||++|+++||+.|+
T Consensus 13 ~~~~~~~v~a~I~~I~~~-~~~Y~aC~~C~kkv~~~~~~~~~C~~C~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~~~ae 91 (166)
T cd04476 13 EKPDYFTVKATIVFIKPD-NWWYPACPGCNKKVVEEGNGTYRCEKCNKSVPNPEYRYILSLNVADHTGEAWLTLFDEVAE 91 (166)
T ss_pred CCCCEEEEEEEEEEEcCC-CeEEccccccCcccEeCCCCcEECCCCCCcCCCccEEEEEEEEEEeCCCCEEEEEehHHHH
Confidence 468899999999999998 8999999999999998744899999999999899999999999999999999999999999
Q ss_pred HHhCCCHHHHHHHHhhcCCchhHHHHHHHhcCceEEEEEEEEeeecCceeeeEEEEEEeeccCHHHHHHHHHHHHHh
Q 006973 540 RIIGCSADELNELKSQLGDDNSYQMKLKEVTWVPHLLRVSVAQQEYNNEKRQRVTVRAVAPVDFAAESKFLLEEISK 616 (623)
Q Consensus 540 ~llG~sA~el~~~~~~~~~~~~~~~~l~~~~~~~~~f~v~~k~~~y~~~~r~~~~v~~~~~vd~~~e~~~Ll~~i~~ 616 (623)
+|||++|+||.++.+++ +..++..|.++.|++|.|+++++.++||+|.|++|+|.++.|+++++|+++|++.|++
T Consensus 92 ~l~G~sa~el~~~~~~~--~~~~~~~i~~~~gk~~~f~v~~~~~~y~~e~~~~~~v~~i~~~~~~~~~~~l~~~i~~ 166 (166)
T cd04476 92 QIFGKSAEELLELKEED--PDAFPDAIQDLVGKTFLFRVSVKEETYNDEGRIRYTVVKVAPVDYKKESKRLIQSIEK 166 (166)
T ss_pred HHhCCCHHHHHHHhhcC--HHHHHHHHHHhhCceEEEEEEEEehhcCCcceEEEEEEEcccCCHHHHHHHHHHHhhC
Confidence 99999999999988654 4689999999999999999999999999999999999999999999999999999863
No 6
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=100.00 E-value=3.3e-36 Score=280.71 Aligned_cols=144 Identities=42% Similarity=0.751 Sum_probs=122.1
Q ss_pred EEEEEEEEEEEeCCCCeEecccc--ccccceecCCCCeeecCcCCCCccccceeEEEEEEEEeCCCcEEEEEehHhHHHH
Q 006973 464 FFSIKAYISLIKPDQAMWYRACK--TCNKKVTDALGSGYWCEGCQKNDEECSLRYIMVARVCDGSGEAWISIFNEEAERI 541 (623)
Q Consensus 464 ~~~v~a~I~~i~~d~~~~Y~aC~--~C~KKv~~~~~~~~~C~kC~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~~~ae~l 541 (623)
||+|+|+|..|..+ +|||+||| .|+|||...++|.|+|++|++..++|.+||+|++.|+|+||++|+++||+.|++|
T Consensus 1 ~~~v~a~I~~I~~~-~~~Y~aC~~~~C~kKv~~~~~~~y~C~~C~~~~~~~~~ry~l~~~i~D~tg~~~~~~F~~~a~~l 79 (146)
T PF08646_consen 1 YFTVRATIVEIKSD-NWYYPACPNEKCNKKVTENGDGSYRCEKCNKTVENPKYRYRLSLKISDGTGSIWVTLFDEEAEQL 79 (146)
T ss_dssp EEEEEEEEEEEETT-TTEEEE-TSTTTS-B-EEETTTEEEETTTTEEESS-EEEEEEEEEEEETTEEEEEEEEHHHHHHH
T ss_pred CEEEEEEEEEEECC-CcEECCCCCccCCCEeecCCCcEEECCCCCCcCCCeeEEEEEEEEEEeCCCeEEEEEEhHHHHHH
Confidence 79999999999987 89999999 9999999876789999999999889999999999999999999999999999999
Q ss_pred hCCCHHHHHHHHhhcCCchhHHHHHHHhcCceEEEEEEEEeeecCceeeeEEEEEEeeccCHHHHHHHH
Q 006973 542 IGCSADELNELKSQLGDDNSYQMKLKEVTWVPHLLRVSVAQQEYNNEKRQRVTVRAVAPVDFAAESKFL 610 (623)
Q Consensus 542 lG~sA~el~~~~~~~~~~~~~~~~l~~~~~~~~~f~v~~k~~~y~~~~r~~~~v~~~~~vd~~~e~~~L 610 (623)
||++|+||.++.+ .++..++.++++++|++|.|+++++.++|+++.|++++|++++|+||++|+++|
T Consensus 80 ~G~~a~el~~~~~--~~~~~~~~~~~~~~~~~~~f~v~~~~~~y~~e~r~~~~v~~i~~vd~~~e~~~l 146 (146)
T PF08646_consen 80 LGMSADELKELKE--EDPEEFPKIIKKLLGKEFVFRVRVKKESYNDESRVKYTVVRIEPVDYAEESKRL 146 (146)
T ss_dssp HCCHHCCCHHHCC--C-HHHHHHHHHCTTT-EEEEEEEEEE--------EEEEEEEEEE--HHHHHHHH
T ss_pred hCCCHHHHHHHHh--hchhHHHHHHHHhhCcEEEEEEEEEEhhhCCceEEEEEEEEeEeCCHHHHhhcC
Confidence 9999999999876 346689999999999999999999999999999999999999999999999987
No 7
>PRK06386 replication factor A; Reviewed
Probab=100.00 E-value=3.2e-31 Score=275.31 Aligned_cols=339 Identities=19% Similarity=0.232 Sum_probs=272.0
Q ss_pred eeccccCCCCCCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeEEE
Q 006973 175 HPLVSLNPYQGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGTLR 254 (623)
Q Consensus 175 ~~I~~L~p~~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~V~ 254 (623)
+.|++|.|...+-+|+|||+..| .|++..++|+..+.+-+|.|++| .|+.|+|+. .+.|++|++|.|.|+.++
T Consensus 3 ~kI~DI~~~~~~V~v~akVl~~~-~r~i~~~~g~~~~~~gllgDeTG-~I~fT~W~~-----~~~l~~Gd~v~i~na~v~ 75 (358)
T PRK06386 3 SKISDINAARQNVDLKVKVLSLN-KRTIKNDRGETIYYYGIIGDETG-TVPFTAWEF-----PDAVKSGDVIEIKYCYSK 75 (358)
T ss_pred cchhhcCCCCCcEEEEEEEEEcc-ceEEecCCCCeEEEEEEEECCcc-eEEEEecCC-----cccCCCCCEEEEEeEEEe
Confidence 57999999999999999999999 68998878776677889999999 999999995 246899999999999987
Q ss_pred ecCCCccccCCceEEEEccCcEEEEccCcCCCCCCCccccccccccccccCCcceeEEEEEEEEeCCceEEEEccCCcee
Q 006973 255 VANKQFKTVQNDYEMNLNENSEVEEAVNETAFIPQTKFNFVPIDELGRYVNGTELVDIIGVVQNVSPTMSIRRKSNNEMV 334 (623)
Q Consensus 255 ~a~~~~~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~~~f~~i~di~~~~~~~~~vDVIGvV~~v~~~~~i~~k~~g~~~ 334 (623)
..+. .++|.++..|+|.+..|.... +...+..++|.||.. ....|+|.|.|.++.+ .++.+ +|...
T Consensus 76 ~~~G-------~~~Lnv~~~t~v~~~~d~~ie-v~~~~~~~KI~DL~~---g~~~v~V~akVle~~e-~e~~~--~g~~~ 141 (358)
T PRK06386 76 EYNG-------KIRIYFDSRSEVMLKPDENIE-VKRTYKLVKIRDLSL---VTPYVSVIGKITGITK-KEYDS--DGTSK 141 (358)
T ss_pred eECC-------EEEEEEcCceEEEecCccccc-cccccCccEeEeccC---CCCceEEEEEEEEccC-ceEec--CCCcc
Confidence 7544 578999999999766543211 222356789999964 3567999999999976 57763 35567
Q ss_pred eEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEEeeeccce-eeecccceEEEEcCChHHHHHHHHH
Q 006973 335 PKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSPIVAIKSLKVGDFQGI-SLSTLGRSTVLVSPDLPEAKKLKSW 413 (623)
Q Consensus 335 ~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~kV~~f~G~-~Ls~~~~S~i~iNPd~pe~~~l~~w 413 (623)
..+++.|.|+|| +|++|||++. +..+.++-|.++.+.+|+|+ +|+.+..|+|...|+.-|
T Consensus 142 ~v~sg~lgDeTG-rIr~TlW~~~-----------l~eGd~v~i~na~v~e~~G~~el~v~~~t~I~~~~~~ie------- 202 (358)
T PRK06386 142 IVYQGYIEDDTA-RVRISSFGKP-----------LEDNRFVRIENARVSQYNGYIEISVGNKSVIKEVESDIN------- 202 (358)
T ss_pred EEEEEEEEcCCC-eEEEEEcccc-----------ccCCCEEEEeeeEEEccCCeEEEEeCCeEEEEECCCCcc-------
Confidence 889999999999 9999999872 34589999999999999996 899999999887664211
Q ss_pred HHhCCCccceeeecCCcCccccCCcccccccceehhccccCCCCCCCCCeEEEEEEEEEEEeCCCCeEecccccccccee
Q 006973 414 YESEGKGTSMASIGSGLGSLAKNGARSMYSDRVSLTHITSNPSLGDEKPVFFSIKAYISLIKPDQAMWYRACKTCNKKVT 493 (623)
Q Consensus 414 ~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~ti~~i~~~~~~~~~~~~~~~v~a~I~~i~~d~~~~Y~aC~~C~KKv~ 493 (623)
+ ...+++|.+|.+.. + -..+.|+|+.|... ...|..||.|+|+|.
T Consensus 203 ------------v---------------~~~~~~I~di~~~~--g-----~v~i~G~iv~i~~g-sgli~rCP~C~R~l~ 247 (358)
T PRK06386 203 ------------L---------------ESRNIFIFEIKSPV--G-----GITIMGFIVSVGQG-SRIFTKCSVCNKIIE 247 (358)
T ss_pred ------------c---------------CccccchhhhhccC--C-----eEEEEEEEEEEcCC-cEeEecCcCCCeEcc
Confidence 1 02357788887721 1 16788999999976 456999999999997
Q ss_pred cCCCCeeecCcCCCCccccceeEEEEEEEEeCCCcEEEEEehHhHHHHhCCCHHHHHHHHhhcCCchhHHHHH-HHhcCc
Q 006973 494 DALGSGYWCEGCQKNDEECSLRYIMVARVCDGSGEAWISIFNEEAERIIGCSADELNELKSQLGDDNSYQMKL-KEVTWV 572 (623)
Q Consensus 494 ~~~~~~~~C~kC~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~~~ae~llG~sA~el~~~~~~~~~~~~~~~~l-~~~~~~ 572 (623)
. +.|+.|++. .+.+-.++.+.+.|+||++.+++|++.+++|+|++-+|+.++.-. -+ .. ..+ ..++|+
T Consensus 248 ~-----g~C~~HG~v--~~~~dlr~k~vLDDGtg~~~~~l~~e~~e~l~G~~lee~~~~a~~-~~--~~-~~i~~~llGr 316 (358)
T PRK06386 248 D-----GVCKDHPDA--PVYLDIFGYFTISDGTGFVTCYANKDSFLPYININENEFARKASS-MN--PN-MLIKKNLLGK 316 (358)
T ss_pred C-----CcCCCCCCC--CCeeEEEEEEEEECCCCeEEEEEChHHhHHHhCCCHHHHHHHhhc-cC--HH-HHhhhhhccc
Confidence 4 489999973 466777778899999999999999999999999999999765421 11 22 222 578999
Q ss_pred eEEEEEEEEeeecCceeeeEEEEEEeeccCH
Q 006973 573 PHLLRVSVAQQEYNNEKRQRVTVRAVAPVDF 603 (623)
Q Consensus 573 ~~~f~v~~k~~~y~~~~r~~~~v~~~~~vd~ 603 (623)
.|.|+..+..+.|. +.+.|.++..+|.
T Consensus 317 ~~~v~G~~~~~~~~----~~~~~~~~~~~~~ 343 (358)
T PRK06386 317 CFSVTGDLRKKDDE----IDMNVISAKSITA 343 (358)
T ss_pred EEEEEcceEeccCC----eEEEEEEeeeccc
Confidence 99999999988777 6899999999986
No 8
>PRK12366 replication factor A; Reviewed
Probab=100.00 E-value=9.7e-32 Score=303.71 Aligned_cols=283 Identities=21% Similarity=0.301 Sum_probs=226.4
Q ss_pred CcCeeeccccCCCCCCeEEEEEEEeeccccccccCCC-cccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEe
Q 006973 171 TRRVHPLVSLNPYQGNWTIKVRVTSKGNMRTYKNARG-EGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYIS 249 (623)
Q Consensus 171 ~~~~~~I~~L~p~~~~w~I~~RV~~K~~~r~~~~~~g-~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is 249 (623)
..+++||++|+||+.+|+|+|||+.||++|+|.+.+| +|++|+++|.|++| +|++|+|++.++. ++.|++|+||.|+
T Consensus 60 ~~~~~~I~dl~p~~~~v~i~arV~~~~~~r~~~~~~G~eGkv~~~~v~DetG-~Ir~t~W~~~~~~-~~~le~G~v~~i~ 137 (637)
T PRK12366 60 EEEDFKISDIEEGQINVEITGRIIEISNIKTFTRKDGSTGKLANITIADNTG-TIRLTLWNDNAKL-LKGLKEGDVIKIE 137 (637)
T ss_pred ccceeEHHHCcCCCcceEEEEEEEEccCCeEEECCCCCccEEEEEEEEcCCC-EEEEEEEchhhhh-hccCCCCCEEEEe
Confidence 3468999999999999999999999999999998877 89999999999999 8999999999885 6899999999999
Q ss_pred eeEEEecCCCccccCCceEEEEccCcEEEEccC-cCCCCCCCccccccccccccccCCcceeEEEEEEEEeCCceEEEEc
Q 006973 250 RGTLRVANKQFKTVQNDYEMNLNENSEVEEAVN-ETAFIPQTKFNFVPIDELGRYVNGTELVDIIGVVQNVSPTMSIRRK 328 (623)
Q Consensus 250 ~~~V~~a~~~~~~~~~~yei~f~~~T~I~~~~d-~~~~iP~~~~~f~~i~di~~~~~~~~~vDVIGvV~~v~~~~~i~~k 328 (623)
++.++. .+++|+|+++..|+|.++++ ++..+|...++| +|.||.. +..|||+|+|++++|+..|++|
T Consensus 138 ~~~v~~-------~~~~~el~~~~~t~I~~~~~~d~~~i~~~~~~~-~I~el~~----g~~v~v~G~V~~~~~~~~f~rk 205 (637)
T PRK12366 138 NARSRK-------WNNDVELNSGSETRIDKLEKYDESRYPIIKENY-DIPELEP----NLSATIEGEVTKAYPIKEFTRK 205 (637)
T ss_pred ccEecc-------cCCceEEEcCCcceEEEccccccccCCcccccc-cccccCC----CCeEEEEEEEEEccCcEEEEEc
Confidence 998865 35779999999999999973 235788877666 7777753 5599999999999999999988
Q ss_pred cCCceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEEeeec-cceeeecccceEEEEcCChHHH
Q 006973 329 SNNEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSPIVAIKSLKVGDF-QGISLSTLGRSTVLVSPDLPEA 407 (623)
Q Consensus 329 ~~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~kV~~f-~G~~Ls~~~~S~i~iNPd~pe~ 407 (623)
+|++..+|++.|.|+|| +|++||||+.|... ...++++.|++..+..| +|..|+.+..+.|-...+.
T Consensus 206 -dg~~~~~r~~~l~D~TG-~irvTlW~~~a~~~-------~~~g~vv~i~g~~~~~~~~~~el~~~~~~~i~~~~~~--- 273 (637)
T PRK12366 206 -DGSEGKLKSFILKDDTG-SIRVTLWNDLTDIE-------VNKGDIVRVKGYVKQGYRTGLEISANNIEILEKLEKE--- 273 (637)
T ss_pred -CCCeeEEEEEEEEcCCC-cEEEEEEChhhccc-------CCCCCEEEEEeEEecCcCCceEEEeCCceeecccccc---
Confidence 79999999999999999 89999999999531 46799999999888889 5678888665544311100
Q ss_pred HHHHHHHHhCCCccceeeecCCcCccccCCcccccccceehhccccCCCCCCCCCeEEEEEEEEEEEeCCCCeEeccccc
Q 006973 408 KKLKSWYESEGKGTSMASIGSGLGSLAKNGARSMYSDRVSLTHITSNPSLGDEKPVFFSIKAYISLIKPDQAMWYRACKT 487 (623)
Q Consensus 408 ~~l~~w~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~ti~~i~~~~~~~~~~~~~~~v~a~I~~i~~d~~~~Y~aC~~ 487 (623)
. ...+...|++|..- +....++++|.|..+..-..|-
T Consensus 274 --------------~------------------~~~~~~pI~~L~~~-----~~g~~~~I~grV~~~~~~R~f~------ 310 (637)
T PRK12366 274 --------------E------------------KELEIVNIEELTEF-----EDGEEVDVKGRIIAISDKREVE------ 310 (637)
T ss_pred --------------c------------------cccCceeHHHCCcc-----cCCCEEEEEEEEEecCCceEEE------
Confidence 0 01133557777541 1123589999999986543331
Q ss_pred cccceecCCCCeeecCcCCCCccccceeEEEEEEEEeCCCcEEEEEehHhHHHHhCC
Q 006973 488 CNKKVTDALGSGYWCEGCQKNDEECSLRYIMVARVCDGSGEAWISIFNEEAERIIGC 544 (623)
Q Consensus 488 C~KKv~~~~~~~~~C~kC~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~~~ae~llG~ 544 (623)
.. +| .-...++.+.|.||++.+++|++.|.++.++
T Consensus 311 ------~~-~g---------------~gkv~s~~l~D~tG~IR~t~w~~~~d~~~~l 345 (637)
T PRK12366 311 ------RD-DR---------------TAEVQDIELADGTGRVRVSFWGEKAKILENL 345 (637)
T ss_pred ------cC-CC---------------cEEEEEEEEEcCCCeEEEEEeCchhhhhccc
Confidence 00 11 1366788999999999999999999877553
No 9
>PRK07211 replication factor A; Reviewed
Probab=100.00 E-value=1.3e-31 Score=287.36 Aligned_cols=289 Identities=21% Similarity=0.326 Sum_probs=226.4
Q ss_pred ceEEEeeeeecC-------ce-EEEEEeCcccceeeccccccccccccCccceeeEEEEcceeeeccCCCceEEEEEEee
Q 006973 28 IVVQVLDLKLTG-------NR-YMFNASDGKKRLKAILPSNLSSEVISGNIQNKGLIRLLDYALNEIPTKSEKYLIVTKC 99 (623)
Q Consensus 28 pvlQvl~~k~~~-------~r-yr~~lSDG~~~~~~mlat~ln~~v~~~~l~~~siirl~~y~~~~~~~~~~~vlii~~l 99 (623)
-|+++-++|.+. +| +.+.|.|-...+++.||.+..+.. -+.|+.|.+++|+..... ....+ +|
T Consensus 71 RV~~~~~~Rt~~~~~~~~eGkv~~v~l~DeTG~Ir~TlW~d~ad~~-~~~Le~GdV~~I~~~~~~----~ys~~----El 141 (485)
T PRK07211 71 KVLSIGDLRTFERDGEDEDGRVINVEVADETGSVRVAFWDEQAVAA-EEELEVGQVLRIKGRPKD----GYNGL----EV 141 (485)
T ss_pred EEeEccCceEEEeCCCCCCcEEEEEEEEcCCCeEEEEEechHhHhh-hcccCCCCEEEEeceEec----cccce----EE
Confidence 456666777652 23 589999999999999998876663 447999999999654321 11111 22
Q ss_pred eeeccccchhhccccCCCCCcccCCCCCccccCCCCCCcccCchhhhhhhhhhhhhccccCCCCccccccCCcCeeeccc
Q 006973 100 EVVSPALEMEIKIEVKSDESGIIFKPKQEDEVKKDGPGIVLKPKQEMVAKSAAQILRDQNGNMAPAARLAMTRRVHPLVS 179 (623)
Q Consensus 100 ev~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~ 179 (623)
.+- . + .+ .+.. ...+ ....++||++
T Consensus 142 ~i~--~--v----e~---------~~d~-----------~i~~---------------------------~~~~~~~I~d 166 (485)
T PRK07211 142 SVD--K--V----EP---------DPDA-----------EIDV---------------------------QIGDTYTVED 166 (485)
T ss_pred EEe--e--E----EE---------cccc-----------cccc---------------------------cccCCccHHH
Confidence 111 0 0 00 0000 0000 0124789999
Q ss_pred cCCCCCCeEEEEEEEeeccccccccCCC-cccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeEEEecCC
Q 006973 180 LNPYQGNWTIKVRVTSKGNMRTYKNARG-EGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGTLRVANK 258 (623)
Q Consensus 180 L~p~~~~w~I~~RV~~K~~~r~~~~~~g-~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~V~~a~~ 258 (623)
|+|++..|.|+|||+.++++|+|.+.+| +|++++++|.|++| +|++|+|++.+++| +.|++|+||.|++++|+..
T Consensus 167 L~~~~~~v~I~grV~~v~~iRtf~r~dGseGkv~sv~L~DeTG-~IR~TlW~d~Ad~~-~~le~G~Vv~I~~a~Vre~-- 242 (485)
T PRK07211 167 LSLGLSDVTLVGVVLDTDSVRTFDRDDGSEGRVSNLTVGDETG-RVRVTLWDDRADLA-EELDAGESVEIVDGYVRER-- 242 (485)
T ss_pred cCCCCCceEEEEEEEEcCCCeEEECCCCCeeEEEEEEEEcCCC-eEEEEEechhhhhh-ccCCCCCEEEEEeeEEEec--
Confidence 9999999999999999999999998887 89999999999999 79999999999999 7799999999999999875
Q ss_pred CccccCCceEEEEccCcEEEEccCcCCCCCCCccccccccccccccCCcceeEEEEEEEEeCCceEEEEccCCceeeEEE
Q 006973 259 QFKTVQNDYEMNLNENSEVEEAVNETAFIPQTKFNFVPIDELGRYVNGTELVDIIGVVQNVSPTMSIRRKSNNEMVPKRD 338 (623)
Q Consensus 259 ~~~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~~~f~~i~di~~~~~~~~~vDVIGvV~~v~~~~~i~~k~~g~~~~kr~ 338 (623)
.+.|+|+++..|.|++++++...+|. +.+|.+|. .+..|||+|+|++++++.+|+++ +|++..+|+
T Consensus 243 -----~g~~ELsl~~~s~I~~~~dev~~vp~----~~~I~dl~----~g~~vdV~GvV~~v~~~rtf~r~-dG~~~~vr~ 308 (485)
T PRK07211 243 -----DGSLELHVGDRGAVEEVDEDVEYVPD----TTPIESLE----IDETVDIAGVVRSADPKRTFDRD-DGSEGQVRN 308 (485)
T ss_pred -----CCcEEEEECCCceEEECCcccccccc----cccHhhcC----CCCceeEEEEEEEccCcEEEEcC-CCCEeEEEE
Confidence 37899999999999999764234564 35666654 45689999999999999999865 599999999
Q ss_pred EEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEEeeec--cceeeecccceEEEEcCChHH
Q 006973 339 ITVADETKRTVTVSLWNELATNVGQELLDNADKSPIVAIKSLKVGDF--QGISLSTLGRSTVLVSPDLPE 406 (623)
Q Consensus 339 i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~kV~~f--~G~~Ls~~~~S~i~iNPd~pe 406 (623)
++|.|+|| +|++||||+.|. + .+..+++|+|++++|++| +|++||+.++|.|.+-.+-|+
T Consensus 309 l~l~D~TG-~IrvTLWg~~A~-~------~i~~GdvV~Ikg~~V~dg~~ggleLS~g~~s~i~~~~~~~~ 370 (485)
T PRK07211 309 VRIQDDTG-DIRVALWGEKAD-L------DIGPGDEVVAADVEIQDGWQDDLEASAGWQSTVVVLDDGAD 370 (485)
T ss_pred EEEEcCCC-cEEEEEeCcccc-C------CCCCCCEEEEEccEEEecCCCCEEEEecCCceEEEcccccc
Confidence 99999999 899999999994 2 156799999999999998 689999998888876554333
No 10
>PRK07211 replication factor A; Reviewed
Probab=100.00 E-value=2.6e-31 Score=285.05 Aligned_cols=274 Identities=21% Similarity=0.343 Sum_probs=217.8
Q ss_pred CeeeccccCCCCCCeEEEEEEEeeccccccccC--CCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEee
Q 006973 173 RVHPLVSLNPYQGNWTIKVRVTSKGNMRTYKNA--RGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISR 250 (623)
Q Consensus 173 ~~~~I~~L~p~~~~w~I~~RV~~K~~~r~~~~~--~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~ 250 (623)
.+.+|++|+|++++|+|+|||+.|+++|+|+++ +++|++|+++|.|++| +|++|+|++.+++|++.|++|+||+|.+
T Consensus 52 e~~~I~dL~pg~~~vtI~aRV~~~~~~Rt~~~~~~~~eGkv~~v~l~DeTG-~Ir~TlW~d~ad~~~~~Le~GdV~~I~~ 130 (485)
T PRK07211 52 EVNGIADIEPGMDEVKFLAKVLSIGDLRTFERDGEDEDGRVINVEVADETG-SVRVAFWDEQAVAAEEELEVGQVLRIKG 130 (485)
T ss_pred ccccHhhCCCCCCceEEEEEEeEccCceEEEeCCCCCCcEEEEEEEEcCCC-eEEEEEechHhHhhhcccCCCCEEEEec
Confidence 467999999999999999999999999999986 4589999999999999 9999999999999999999999999964
Q ss_pred eEEEecCCCccccCCceEEEEccCcEEEEccCcCCCCCCCccccccccccccccCCcceeEEEEEEEEeCCceEEEEccC
Q 006973 251 GTLRVANKQFKTVQNDYEMNLNENSEVEEAVNETAFIPQTKFNFVPIDELGRYVNGTELVDIIGVVQNVSPTMSIRRKSN 330 (623)
Q Consensus 251 ~~V~~a~~~~~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~~~f~~i~di~~~~~~~~~vDVIGvV~~v~~~~~i~~k~~ 330 (623)
.++ +.|+.. ||+|+ .|+++.+. .+|....+|.+|.+|.. ....+||+|+|+.+++++++.++ +
T Consensus 131 -~~~---~~ys~~----El~i~---~ve~~~d~--~i~~~~~~~~~I~dL~~---~~~~v~I~grV~~v~~iRtf~r~-d 193 (485)
T PRK07211 131 -RPK---DGYNGL----EVSVD---KVEPDPDA--EIDVQIGDTYTVEDLSL---GLSDVTLVGVVLDTDSVRTFDRD-D 193 (485)
T ss_pred -eEe---ccccce----EEEEe---eEEEcccc--cccccccCCccHHHcCC---CCCceEEEEEEEEcCCCeEEECC-C
Confidence 443 667653 99998 48887764 34444569999999975 35689999999999999999765 5
Q ss_pred CceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEEeeeccc-eeeecccceEEEEcCChHHHHH
Q 006973 331 NEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSPIVAIKSLKVGDFQG-ISLSTLGRSTVLVSPDLPEAKK 409 (623)
Q Consensus 331 g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~kV~~f~G-~~Ls~~~~S~i~iNPd~pe~~~ 409 (623)
|++...+++.|.|+|| +|++|||++.|..|. .+..++|+.|++++|++|+| .+|+....|.|..-++. +
T Consensus 194 GseGkv~sv~L~DeTG-~IR~TlW~d~Ad~~~-----~le~G~Vv~I~~a~Vre~~g~~ELsl~~~s~I~~~~de--v-- 263 (485)
T PRK07211 194 GSEGRVSNLTVGDETG-RVRVTLWDDRADLAE-----ELDAGESVEIVDGYVRERDGSLELHVGDRGAVEEVDED--V-- 263 (485)
T ss_pred CCeeEEEEEEEEcCCC-eEEEEEechhhhhhc-----cCCCCCEEEEEeeEEEecCCcEEEEECCCceEEECCcc--c--
Confidence 8889999999999999 799999999999873 25679999999999999965 78998888888765541 0
Q ss_pred HHHHHHhCCCccceeeecCCcCccccCCcccccccceehhccccCCCCCCCCCeEEEEEEEEEEEeCCCCeEeccccccc
Q 006973 410 LKSWYESEGKGTSMASIGSGLGSLAKNGARSMYSDRVSLTHITSNPSLGDEKPVFFSIKAYISLIKPDQAMWYRACKTCN 489 (623)
Q Consensus 410 l~~w~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~ti~~i~~~~~~~~~~~~~~~v~a~I~~i~~d~~~~Y~aC~~C~ 489 (623)
.+ + .....|.++.. .....|.|.|..+..-..+
T Consensus 264 ------------~~--v----------------p~~~~I~dl~~--------g~~vdV~GvV~~v~~~rtf--------- 296 (485)
T PRK07211 264 ------------EY--V----------------PDTTPIESLEI--------DETVDIAGVVRSADPKRTF--------- 296 (485)
T ss_pred ------------cc--c----------------cccccHhhcCC--------CCceeEEEEEEEccCcEEE---------
Confidence 00 0 00122443322 1247788888888653222
Q ss_pred cceecCCCCeeecCcCCCCccccceeEEEEEEEEeCCCcEEEEEehHhHH
Q 006973 490 KKVTDALGSGYWCEGCQKNDEECSLRYIMVARVCDGSGEAWISIFNEEAE 539 (623)
Q Consensus 490 KKv~~~~~~~~~C~kC~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~~~ae 539 (623)
. .+++ ....+.++.|.|.||++++++|++.|+
T Consensus 297 ---~---------r~dG------~~~~vr~l~l~D~TG~IrvTLWg~~A~ 328 (485)
T PRK07211 297 ---D---------RDDG------SEGQVRNVRIQDDTGDIRVALWGEKAD 328 (485)
T ss_pred ---E---------cCCC------CEeEEEEEEEEcCCCcEEEEEeCcccc
Confidence 0 0112 235677899999999999999999984
No 11
>PRK15491 replication factor A; Provisional
Probab=99.97 E-value=1.1e-29 Score=269.14 Aligned_cols=289 Identities=20% Similarity=0.293 Sum_probs=224.9
Q ss_pred ceEEEeeeeec----C--ce-EEEEEeCcccceeeccccccccccccCccceeeEEEEcceeeeccCCCceEEEEEEeee
Q 006973 28 IVVQVLDLKLT----G--NR-YMFNASDGKKRLKAILPSNLSSEVISGNIQNKGLIRLLDYALNEIPTKSEKYLIVTKCE 100 (623)
Q Consensus 28 pvlQvl~~k~~----~--~r-yr~~lSDG~~~~~~mlat~ln~~v~~~~l~~~siirl~~y~~~~~~~~~~~vlii~~le 100 (623)
-|+++-++|.+ | +| +.+.|.|-+..+++.||....+++..+.|+.|.+++|..|....- +. +|
T Consensus 75 rVl~~~~~R~f~r~dGs~g~v~~~~v~DeTG~ir~tlW~~~a~~~~~~~le~G~v~~I~~~~~~~y----~g------~E 144 (374)
T PRK15491 75 KVVSIFEPKEFNRNDGTTGRVGNIIVADETGSIRLTLWDDLADLIKTGDIEVGKSLNISGYAKEGY----SG------IE 144 (374)
T ss_pred EEeeccCCeeeecCCCCceEEEEEEEEcCCCeEEEEEECchhhhhccCCcCCCCEEEEeeeeccCc----cc------EE
Confidence 45666677776 2 34 478999999999999999999888888999999999988732211 11 13
Q ss_pred eeccccchhhccccCCCCCcccCCCCCccccCCCCCCcccCchhhhhhhhhhhhhccccCCCCccccccCCcCeeecccc
Q 006973 101 VVSPALEMEIKIEVKSDESGIIFKPKQEDEVKKDGPGIVLKPKQEMVAKSAAQILRDQNGNMAPAARLAMTRRVHPLVSL 180 (623)
Q Consensus 101 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~L 180 (623)
+.-.... . ...... . . . ....+.+|++|
T Consensus 145 i~i~~~~--~-----------i~~~~~-----------~-~--------------~-------------~~~~~~~I~dl 172 (374)
T PRK15491 145 VNIGRYG--G-----------ISESDE-----------N-V--------------K-------------ASINSQKISDI 172 (374)
T ss_pred EEeCCCc--e-----------eeeccc-----------c-c--------------c-------------cccCcccHHHc
Confidence 2211100 0 000000 0 0 0 01135799999
Q ss_pred CCCCCCeEEEEEEEeeccccccccCCCc-ccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeEEEecCCC
Q 006973 181 NPYQGNWTIKVRVTSKGNMRTYKNARGE-GCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGTLRVANKQ 259 (623)
Q Consensus 181 ~p~~~~w~I~~RV~~K~~~r~~~~~~g~-g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~V~~a~~~ 259 (623)
.++...+.|+|||+.++++|+|.+.+|+ |+++++.|.|++| +|++|+|++.|++| +.|++|++|+|.++.++.
T Consensus 173 ~~~~~~V~I~g~V~~~~~~r~~~~~~G~~~~v~~~~l~DetG-~Ir~t~W~~~a~~~-~~l~~Gd~V~i~~~~~r~---- 246 (374)
T PRK15491 173 KDGDSDINIVGKVLDISDVRTFQKKDGSQGRVRNITIGDETG-KIRVTLWDGKTDLA-DKLENGDSVEIINGYART---- 246 (374)
T ss_pred CCCCccEEEEEEEEEccCceEEEecCCCeEEEEEEEEECCCC-eEEEEEecchhccc-ccCCCCCEEEEEeceEEE----
Confidence 9998899999999999999999987774 8999999999999 79999999999998 669999999999988864
Q ss_pred ccccCCceEEEEccCcEEEEccCcCCCCCCCccccccccccccccCCcceeEEEEEEEEeCCceEEEEccCCceeeEEEE
Q 006973 260 FKTVQNDYEMNLNENSEVEEAVNETAFIPQTKFNFVPIDELGRYVNGTELVDIIGVVQNVSPTMSIRRKSNNEMVPKRDI 339 (623)
Q Consensus 260 ~~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~~~f~~i~di~~~~~~~~~vDVIGvV~~v~~~~~i~~k~~g~~~~kr~i 339 (623)
+..+++|||+|...|.|.++++. +.+.++|++|+||.. +..+||+|+|++++++.+|+++ +|++..+|++
T Consensus 247 -~~~~g~~El~~~~~s~I~~~~~~----~e~~~~f~~I~dl~~----~~~~dv~G~V~~v~~~~~~~~~-~G~~~~~r~i 316 (374)
T PRK15491 247 -NNYSQEVEIQIGNHGSLRKTDRN----VEYEEDFTPIADIIP----GQPYSIKGAVSGLGDLKEFTKS-DGSENKVSNI 316 (374)
T ss_pred -eccCCCEEEEeCCCceEEECCcc----cccCCCccCHHHcCC----CCceeEEEEEEEcCCcEEEEcc-CCCEeEEEeE
Confidence 34578999999999999998653 355689999999975 3568999999999999999986 5999999999
Q ss_pred EEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEEeee-c-cceeeecccceEEEE
Q 006973 340 TVADETKRTVTVSLWNELATNVGQELLDNADKSPIVAIKSLKVGD-F-QGISLSTLGRSTVLV 400 (623)
Q Consensus 340 ~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~kV~~-f-~G~~Ls~~~~S~i~i 400 (623)
+|.|+|| +|++||||+.|+.... ...+..|.+-++.+++ | ++..||.+..|++.+
T Consensus 317 ~l~D~Tg-~Ir~tlWg~~a~~~~~-----~~~g~~i~i~~~~~k~g~~~~~e~s~g~~s~~~~ 373 (374)
T PRK15491 317 YVSDDTG-RIRIALWGEKAELVDK-----LDIDTPIKIIDAFSKSGYNEDVELSAGNRSRVVV 373 (374)
T ss_pred EEEeCCC-cEEEEEcccccccccc-----cCCCCeEEEEEEEEeecCCCcEEEEeCCcceEEe
Confidence 9999999 5999999999986321 2334555566777764 5 457999999998875
No 12
>PRK15491 replication factor A; Provisional
Probab=99.97 E-value=1e-29 Score=269.22 Aligned_cols=277 Identities=21% Similarity=0.310 Sum_probs=217.9
Q ss_pred cCeeeccccCCCCCCeEEEEEEEeeccccccccCCC-cccEEEEEEEeCCCCeEEEEEechHHHHHH-hhcccCcEEEEe
Q 006973 172 RRVHPLVSLNPYQGNWTIKVRVTSKGNMRTYKNARG-EGCVFNVELTDEDGTQIQATMFNEAARKFY-DRFQLGKVYYIS 249 (623)
Q Consensus 172 ~~~~~I~~L~p~~~~w~I~~RV~~K~~~r~~~~~~g-~g~~f~~~L~D~~G~~I~at~~~~~~~kf~-~~l~eG~vy~is 249 (623)
+++++|++|+|++++|+|+|||+.++++|+|.+.+| +|++++++|.|++| +|++|+|++.+++|+ +.|++|+||.|+
T Consensus 55 ~~~~kI~dL~~~~~~v~i~arVl~~~~~R~f~r~dGs~g~v~~~~v~DeTG-~ir~tlW~~~a~~~~~~~le~G~v~~I~ 133 (374)
T PRK15491 55 VDTTKIADINESSSNVNFTAKVVSIFEPKEFNRNDGTTGRVGNIIVADETG-SIRLTLWDDLADLIKTGDIEVGKSLNIS 133 (374)
T ss_pred cccccHHHCCCCCCceEEEEEEeeccCCeeeecCCCCceEEEEEEEEcCCC-eEEEEEECchhhhhccCCcCCCCEEEEe
Confidence 457899999999999999999999999999999888 89999999999999 899999999999998 689999999998
Q ss_pred eeEEEecCCCccccCCceEEEEccCcEEEEccCcCCCCCCCccccccccccccccCCcceeEEEEEEEEeCCceEEEEcc
Q 006973 250 RGTLRVANKQFKTVQNDYEMNLNENSEVEEAVNETAFIPQTKFNFVPIDELGRYVNGTELVDIIGVVQNVSPTMSIRRKS 329 (623)
Q Consensus 250 ~~~V~~a~~~~~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~~~f~~i~di~~~~~~~~~vDVIGvV~~v~~~~~i~~k~ 329 (623)
++ +++.|+. .||++++.|.|.++++. + ...|+|++|+||.. .+..|||.|.|+.++++++++++
T Consensus 134 ~~----~~~~y~g----~Ei~i~~~~~i~~~~~~---~-~~~~~~~~I~dl~~---~~~~V~I~g~V~~~~~~r~~~~~- 197 (374)
T PRK15491 134 GY----AKEGYSG----IEVNIGRYGGISESDEN---V-KASINSQKISDIKD---GDSDINIVGKVLDISDVRTFQKK- 197 (374)
T ss_pred ee----eccCccc----EEEEeCCCceeeecccc---c-ccccCcccHHHcCC---CCccEEEEEEEEEccCceEEEec-
Confidence 65 5556643 69999999999998654 2 34678999999975 34469999999999999999887
Q ss_pred CCceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEEEEEeE--Eeeeccc-eeeecccceEEEEcCChHH
Q 006973 330 NNEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSPIVAIKSL--KVGDFQG-ISLSTLGRSTVLVSPDLPE 406 (623)
Q Consensus 330 ~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~--kV~~f~G-~~Ls~~~~S~i~iNPd~pe 406 (623)
+|++...+++.|.|+|| .|++||||+.|..+. .+..|.+|-+.++ |...|+| ..|+....|.|..-.+.++
T Consensus 198 ~G~~~~v~~~~l~DetG-~Ir~t~W~~~a~~~~-----~l~~Gd~V~i~~~~~r~~~~~g~~El~~~~~s~I~~~~~~~e 271 (374)
T PRK15491 198 DGSQGRVRNITIGDETG-KIRVTLWDGKTDLAD-----KLENGDSVEIINGYARTNNYSQEVEIQIGNHGSLRKTDRNVE 271 (374)
T ss_pred CCCeEEEEEEEEECCCC-eEEEEEecchhcccc-----cCCCCCEEEEEeceEEEeccCCCEEEEeCCCceEEECCcccc
Confidence 48888999999999999 699999999998752 2456888888765 4456766 4788877777664332110
Q ss_pred HHHHHHHHHhCCCccceeeecCCcCccccCCcccccccceehhccccCCCCCCCCCeEEEEEEEEEEEeCCCCeEecccc
Q 006973 407 AKKLKSWYESEGKGTSMASIGSGLGSLAKNGARSMYSDRVSLTHITSNPSLGDEKPVFFSIKAYISLIKPDQAMWYRACK 486 (623)
Q Consensus 407 ~~~l~~w~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~ti~~i~~~~~~~~~~~~~~~v~a~I~~i~~d~~~~Y~aC~ 486 (623)
+ ..+...|.+|... ..+.+.|.|..+..-..+
T Consensus 272 -------------------~---------------~~~f~~I~dl~~~--------~~~dv~G~V~~v~~~~~~------ 303 (374)
T PRK15491 272 -------------------Y---------------EEDFTPIADIIPG--------QPYSIKGAVSGLGDLKEF------ 303 (374)
T ss_pred -------------------c---------------CCCccCHHHcCCC--------CceeEEEEEEEcCCcEEE------
Confidence 0 0123346666541 236888888888543222
Q ss_pred ccccceecCCCCeeecCcCCCCccccceeEEEEEEEEeCCCcEEEEEehHhHHH
Q 006973 487 TCNKKVTDALGSGYWCEGCQKNDEECSLRYIMVARVCDGSGEAWISIFNEEAER 540 (623)
Q Consensus 487 ~C~KKv~~~~~~~~~C~kC~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~~~ae~ 540 (623)
... + -....+-++.|.|.||.+.+++||+.|+.
T Consensus 304 ------~~~-~--------------G~~~~~r~i~l~D~Tg~Ir~tlWg~~a~~ 336 (374)
T PRK15491 304 ------TKS-D--------------GSENKVSNIYVSDDTGRIRIALWGEKAEL 336 (374)
T ss_pred ------Ecc-C--------------CCEeEEEeEEEEeCCCcEEEEEccccccc
Confidence 000 1 12345567899999999999999999964
No 13
>PRK14699 replication factor A; Provisional
Probab=99.97 E-value=3.5e-29 Score=272.11 Aligned_cols=290 Identities=20% Similarity=0.274 Sum_probs=219.9
Q ss_pred ceEEEeeeeecC------c-eEEEEEeCcccceeeccccccccccccCccceeeEEEEcceeeeccCCCceEEEEEEeee
Q 006973 28 IVVQVLDLKLTG------N-RYMFNASDGKKRLKAILPSNLSSEVISGNIQNKGLIRLLDYALNEIPTKSEKYLIVTKCE 100 (623)
Q Consensus 28 pvlQvl~~k~~~------~-ryr~~lSDG~~~~~~mlat~ln~~v~~~~l~~~siirl~~y~~~~~~~~~~~vlii~~le 100 (623)
-|+++-+.|.+. . -+.++|.|.+..++..||....++.. .|+.|++|+|.+--+.. +.- + -.+|
T Consensus 184 kVl~~~~~R~f~~~dG~~g~v~~~~igDeTG~ir~tlW~~~a~~~~--~l~~Gd~v~I~~a~vr~-~~~-~-----~~~e 254 (484)
T PRK14699 184 KVLEISEIRTFQRKDGTSGKVGNLLLGDETGTLRVTLWDDKTDFLN--QIEYGDTVELINAYARE-NAF-T-----QKVE 254 (484)
T ss_pred EEEeccCceEEecCCCCceEEEEEEEEcCCceEEEEEECccccccc--ccCCCCEEEEecceEee-ccc-C-----CceE
Confidence 355655666553 2 35789999999999999988655433 58999999985443321 000 0 0122
Q ss_pred eeccccchhhccccCCCCCcccCCCCCccccCCCCCCcccCchhhhhhhhhhhhhccccCCCCccccccCCcCeeecccc
Q 006973 101 VVSPALEMEIKIEVKSDESGIIFKPKQEDEVKKDGPGIVLKPKQEMVAKSAAQILRDQNGNMAPAARLAMTRRVHPLVSL 180 (623)
Q Consensus 101 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~L 180 (623)
+...... . ...... .+ . ....++||++|
T Consensus 255 l~~~~~s--~-----------i~~~~~-------------~~---------------e-----------~~~~~~~I~~L 282 (484)
T PRK14699 255 LQVGNRS--I-----------IRKSEK-------------KV---------------E-----------YEEEFTPIEDI 282 (484)
T ss_pred EEecCce--E-----------eecccc-------------cc---------------c-----------ccccccCHHHc
Confidence 2211100 0 000000 00 0 01136799999
Q ss_pred CCCCCCeEEEEEEEeeccccccccCCC-cccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeEEEecCCC
Q 006973 181 NPYQGNWTIKVRVTSKGNMRTYKNARG-EGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGTLRVANKQ 259 (623)
Q Consensus 181 ~p~~~~w~I~~RV~~K~~~r~~~~~~g-~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~V~~a~~~ 259 (623)
+|++++|+|+|||+.++++|+|.+.+| +|+++++.|.|++| +|++|+|++.+ +|++.|++|+++.+.++.++
T Consensus 283 ~~~~~~v~I~grV~~~~~~r~~~~~~Gseg~v~~~~l~DeTG-~Ir~T~W~~~a-~~~~~i~~Gd~v~i~~~y~~----- 355 (484)
T PRK14699 283 KADMNNINISGRVLDISEVRTFEKKDGSPGRVGNLLLGDSTG-KIRLTLWDEKT-NFLDEIDFDETVEVLNAYSR----- 355 (484)
T ss_pred CCCCceeEEEEEEEEcCCCeEEEcCCCCeeEEEEEEEECCCC-eEEEEEeCccc-ccccccCCCceEEEEeEEEE-----
Confidence 999999999999999999999998887 89999999999999 89999999999 77788999999888887754
Q ss_pred ccccCCceEEEEccCcEEEEccCcCCCCCCCccccccccccccccCCcceeEEEEEEEEeCCceEEEEccCCceeeEEEE
Q 006973 260 FKTVQNDYEMNLNENSEVEEAVNETAFIPQTKFNFVPIDELGRYVNGTELVDIIGVVQNVSPTMSIRRKSNNEMVPKRDI 339 (623)
Q Consensus 260 ~~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~~~f~~i~di~~~~~~~~~vDVIGvV~~v~~~~~i~~k~~g~~~~kr~i 339 (623)
++..+++|+|+|+..|.|.++++. +.+.++|++|.+|. .+..|||+|+|++++++.+|+++ +|++..+|++
T Consensus 356 ~~~~~~~~eL~~~~~t~I~~~~~~----~e~~~~~~~I~die----~~~~vdV~G~V~~v~~~~~~~~~-~g~~~~vr~i 426 (484)
T PRK14699 356 ENTFSQQVELNLGARGIIQKSEKK----VEYREKFTDIADII----PGESYSVQGKVSEIGELREFERE-DGTENVVANL 426 (484)
T ss_pred eccCCccEEEEecCceeEeecCCc----ceeeeccccHHHcc----CCCeeEEEEEEEEcCCcceEEec-CCCEEEEEEE
Confidence 556688999999999999998764 25678999999995 36689999999999999999987 4999999999
Q ss_pred EEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEEeee-ccc-eeeecccceEEEE
Q 006973 340 TVADETKRTVTVSLWNELATNVGQELLDNADKSPIVAIKSLKVGD-FQG-ISLSTLGRSTVLV 400 (623)
Q Consensus 340 ~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~kV~~-f~G-~~Ls~~~~S~i~i 400 (623)
+|.|.|| +|+|||||+.|..|.. +..+.-|.+.++.+.. |+| ..||.+.+|++.+
T Consensus 427 ~l~D~TG-~Ir~tlWg~~A~~~~~-----~~~~~~v~~~~~~~~~g~~~~~e~s~g~~s~~~~ 483 (484)
T PRK14699 427 QLKDETG-SIRLTLWGEQAYVIED-----LDIDSEIQIIDAYARYGLNEEIELSVGNRSRVII 483 (484)
T ss_pred EEEcCCC-eEEEEEcchhhhhccc-----cCCCCeEEEechhhhhcccccEEEEecCceEEEe
Confidence 9999999 9999999999997632 3445556666666664 454 6899999998864
No 14
>PRK14699 replication factor A; Provisional
Probab=99.96 E-value=6.4e-27 Score=254.47 Aligned_cols=362 Identities=18% Similarity=0.286 Sum_probs=268.4
Q ss_pred cceEEEeeeeecC------ceE-EEEEeCcccceeeccccccccccccCccceeeEEEEcceeeeccCCCceEEEEEEee
Q 006973 27 EIVVQVLDLKLTG------NRY-MFNASDGKKRLKAILPSNLSSEVISGNIQNKGLIRLLDYALNEIPTKSEKYLIVTKC 99 (623)
Q Consensus 27 ~pvlQvl~~k~~~------~ry-r~~lSDG~~~~~~mlat~ln~~v~~~~l~~~siirl~~y~~~~~~~~~~~vlii~~l 99 (623)
.-|+.+.+.|.+. .|+ .+.|.|-+..++..||..+.+++..|.|++|++|+|+.|...- .+ . +
T Consensus 74 ~rVl~i~~~r~f~r~dG~~g~v~~~~iaDeTG~ir~tlW~~~a~~~~~g~l~~GDvv~I~~~~r~~-~~---g------~ 143 (484)
T PRK14699 74 ARVVSVFDTKEFTRNDGTIGRVGNLIVGDETGKIKLTLWDNMADLIKAGKIKAGQTLQISGYAKQG-YS---G------V 143 (484)
T ss_pred EEEEEecCceEEecCCCCceEEEEEEEecCCCeEEEEEecCccchhhhcCCCCCCEEEEcceeccC-CC---C------c
Confidence 3577888888772 344 6899999999999999999999999999999999999974331 11 1 1
Q ss_pred eeec-cccchhhccccCCCCCcccCCCCCccccCCCCCCcccCchhhhhhhhhhhhhccccCCCCccccccCCcCeeecc
Q 006973 100 EVVS-PALEMEIKIEVKSDESGIIFKPKQEDEVKKDGPGIVLKPKQEMVAKSAAQILRDQNGNMAPAARLAMTRRVHPLV 178 (623)
Q Consensus 100 ev~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~ 178 (623)
|+.. +... ...+... . . .......|+
T Consensus 144 el~~~~~~~--------------i~~~~~~----------i-~----------------------------v~~~~~~I~ 170 (484)
T PRK14699 144 EVNIGNNGV--------------LTESEEE----------I-D----------------------------VAANSQKIK 170 (484)
T ss_pred eEEeCCCce--------------eeccCcc----------c-c----------------------------cCCCCcchh
Confidence 2111 0000 0000000 0 0 000135899
Q ss_pred ccCCCCCCeEEEEEEEeeccccccccCCC-cccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeEEEecC
Q 006973 179 SLNPYQGNWTIKVRVTSKGNMRTYKNARG-EGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGTLRVAN 257 (623)
Q Consensus 179 ~L~p~~~~w~I~~RV~~K~~~r~~~~~~g-~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~V~~a~ 257 (623)
+|.|.....+|+|||+.++++|+|...+| +|++++++|.|++| +|++|+|++.++ +++.|++|++|.|.++.++..
T Consensus 171 dL~~~~~~V~i~gkVl~~~~~R~f~~~dG~~g~v~~~~igDeTG-~ir~tlW~~~a~-~~~~l~~Gd~v~I~~a~vr~~- 247 (484)
T PRK14699 171 DIKDGMGDLNLTGKVLEISEIRTFQRKDGTSGKVGNLLLGDETG-TLRVTLWDDKTD-FLNQIEYGDTVELINAYAREN- 247 (484)
T ss_pred hcCCCCCceEEEEEEEeccCceEEecCCCCceEEEEEEEEcCCc-eEEEEEECcccc-cccccCCCCEEEEecceEeec-
Confidence 99999888899999999999999998777 78999999999999 999999999885 777899999999999988763
Q ss_pred CCccccCCceEEEEccCcEEEEccCcCCCCCCCccccccccccccccCCcceeEEEEEEEEeCCceEEEEccCCceeeEE
Q 006973 258 KQFKTVQNDYEMNLNENSEVEEAVNETAFIPQTKFNFVPIDELGRYVNGTELVDIIGVVQNVSPTMSIRRKSNNEMVPKR 337 (623)
Q Consensus 258 ~~~~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~~~f~~i~di~~~~~~~~~vDVIGvV~~v~~~~~i~~k~~g~~~~kr 337 (623)
.| .+.++|+++..|.|...++. ..+ ..++++|.+|.. ....++|.|.|+++++++++.++ +|++...+
T Consensus 248 -~~---~~~~el~~~~~s~i~~~~~~-~e~---~~~~~~I~~L~~---~~~~v~I~grV~~~~~~r~~~~~-~Gseg~v~ 315 (484)
T PRK14699 248 -AF---TQKVELQVGNRSIIRKSEKK-VEY---EEEFTPIEDIKA---DMNNINISGRVLDISEVRTFEKK-DGSPGRVG 315 (484)
T ss_pred -cc---CCceEEEecCceEeeccccc-ccc---cccccCHHHcCC---CCceeEEEEEEEEcCCCeEEEcC-CCCeeEEE
Confidence 23 36899999999988887544 222 236889999974 35689999999999999999865 58788999
Q ss_pred EEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEEeee--ccc-eeeecccceEEEEcCChHHHHHHHHHH
Q 006973 338 DITVADETKRTVTVSLWNELATNVGQELLDNADKSPIVAIKSLKVGD--FQG-ISLSTLGRSTVLVSPDLPEAKKLKSWY 414 (623)
Q Consensus 338 ~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~kV~~--f~G-~~Ls~~~~S~i~iNPd~pe~~~l~~w~ 414 (623)
++.|.|+|| .|++||||+.|..+ . .+..+.++-+.++.+++ |++ ..|+....|.|...++..+.
T Consensus 316 ~~~l~DeTG-~Ir~T~W~~~a~~~-~----~i~~Gd~v~i~~~y~~~~~~~~~~eL~~~~~t~I~~~~~~~e~------- 382 (484)
T PRK14699 316 NLLLGDSTG-KIRLTLWDEKTNFL-D----EIDFDETVEVLNAYSRENTFSQQVELNLGARGIIQKSEKKVEY------- 382 (484)
T ss_pred EEEEECCCC-eEEEEEeCcccccc-c----ccCCCceEEEEeEEEEeccCCccEEEEecCceeEeecCCccee-------
Confidence 999999999 79999999999432 2 24557788888888874 445 47888877766555432210
Q ss_pred HhCCCccceeeecCCcCccccCCcccccccceehhccccCCCCCCCCCeEEEEEEEEEEEeCCCCeEeccccccccceec
Q 006973 415 ESEGKGTSMASIGSGLGSLAKNGARSMYSDRVSLTHITSNPSLGDEKPVFFSIKAYISLIKPDQAMWYRACKTCNKKVTD 494 (623)
Q Consensus 415 ~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~ti~~i~~~~~~~~~~~~~~~v~a~I~~i~~d~~~~Y~aC~~C~KKv~~ 494 (623)
..++..|.+|... ..+.|.|+|..+.....+ ..
T Consensus 383 ---------------------------~~~~~~I~die~~--------~~vdV~G~V~~v~~~~~~------------~~ 415 (484)
T PRK14699 383 ---------------------------REKFTDIADIIPG--------ESYSVQGKVSEIGELREF------------ER 415 (484)
T ss_pred ---------------------------eeccccHHHccCC--------CeeEEEEEEEEcCCcceE------------Ee
Confidence 0134557777331 247899999999764322 11
Q ss_pred CCCCeeecCcCCCCccccceeEEEEEEEEeCCCcEEEEEehHhHHHH
Q 006973 495 ALGSGYWCEGCQKNDEECSLRYIMVARVCDGSGEAWISIFNEEAERI 541 (623)
Q Consensus 495 ~~~~~~~C~kC~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~~~ae~l 541 (623)
. +| ....+-++.+.|.||++.+++||+.|+++
T Consensus 416 ~-~g--------------~~~~vr~i~l~D~TG~Ir~tlWg~~A~~~ 447 (484)
T PRK14699 416 E-DG--------------TENVVANLQLKDETGSIRLTLWGEQAYVI 447 (484)
T ss_pred c-CC--------------CEEEEEEEEEEcCCCeEEEEEcchhhhhc
Confidence 1 11 24566789999999999999999999864
No 15
>cd04474 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds corresponding to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ funct
Probab=99.95 E-value=1.6e-27 Score=208.71 Aligned_cols=104 Identities=57% Similarity=1.035 Sum_probs=100.7
Q ss_pred eccccCCCCCCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeEEEe
Q 006973 176 PLVSLNPYQGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGTLRV 255 (623)
Q Consensus 176 ~I~~L~p~~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~V~~ 255 (623)
||++|+|+.++|+|+|||++||++|.|.+.+++|++|+|+|+|++|++|+|++|++.+++|+++|+||+||+|++|+|++
T Consensus 1 pI~~L~p~~~~~~I~~rV~~k~~~~~f~~~~~~g~~~~~~l~De~~~~I~~t~~~~~~~~f~~~l~eG~vy~i~~~~V~~ 80 (104)
T cd04474 1 PISSLNPYQNKWTIKARVTNKSDIRTWSNARGEGKLFSFDLLDEDGGEIRATFFNDAVDKFYDLLEVGKVYYISKGSVKV 80 (104)
T ss_pred ChhHccCCCCcEEEEEEEeeccccccccCCCCCcEEEEEEEEECCCCEEEEEEehHHHHHhhcccccccEEEEeccEEee
Confidence 79999999999999999999999999999888999999999999999999999999999999999999999999999999
Q ss_pred cCCCccccCCceEEEEccCcEEEE
Q 006973 256 ANKQFKTVQNDYEMNLNENSEVEE 279 (623)
Q Consensus 256 a~~~~~~~~~~yei~f~~~T~I~~ 279 (623)
++++|++++|+|||.|+.+|.|++
T Consensus 81 a~~~y~~~~~~yeI~f~~~t~~~~ 104 (104)
T cd04474 81 ANKKFNTLKNDYEITFNRDTSIIE 104 (104)
T ss_pred ccccCCCCCCcEEEEECCCcEEeC
Confidence 999999999999999999988863
No 16
>PF04057 Rep-A_N: Replication factor-A protein 1, N-terminal domain; InterPro: IPR007199 Replication factor-a protein 1 (RPA1) forms a multiprotein complex with RPA2 and RPA3 that binds single-stranded DNA and functions in the recognition of DNA damage for nucleotide excision repair. The complex binds to single-stranded DNA sequences participating in DNA replication in addition to those mediating transcriptional repression and activation, and stimulates the activity of cognate strand exchange protein Sep1. It cooperates with T-AG and DNA topoisomerase I to unwind template DNA containing the Simian Virus 40 origin of replication [].; GO: 0003677 DNA binding, 0006260 DNA replication, 0005634 nucleus; PDB: 1EWI_A 2B3G_A 2B29_A.
Probab=99.92 E-value=1.3e-25 Score=194.48 Aligned_cols=92 Identities=35% Similarity=0.539 Sum_probs=80.4
Q ss_pred CCHHHHHHHhc-CCCCCCCCCCCcceEEEeeeeecC-------ceEEEEEeCcccceeeccccccccccccCccceeeEE
Q 006973 5 VSPDAISTILS-NPSPDSSSDIPEIVVQVLDLKLTG-------NRYMFNASDGKKRLKAILPSNLSSEVISGNIQNKGLI 76 (623)
Q Consensus 5 lt~ga~~~i~~-~~~~~~~~~~~~pvlQvl~~k~~~-------~ryr~~lSDG~~~~~~mlat~ln~~v~~~~l~~~sii 76 (623)
||+|||++|++ ++. ..+|||||+++|+++ +|||++||||+|+++||||||||++|++|.|++||||
T Consensus 1 LT~Gai~~I~~~~~~------~~~pvlQVl~~k~i~~~~~~~~~RyR~~lSDG~~~~~amLatqln~lv~~g~l~~~sii 74 (101)
T PF04057_consen 1 LTPGAIEAIFSSGDV------NDNPVLQVLNIKKINSKQGGGSDRYRLVLSDGVHSIQAMLATQLNHLVESGELQKGSII 74 (101)
T ss_dssp S-TTHHHHHHHHTSS------S--TEEEEEEEEEE----TTS--EEEEEEESSSEEEEEEESGGGHHHHHTTSSSTT-EE
T ss_pred CChHHHHHHHhCCCC------CCCcEEEEEeeEEccCCCCCCCceEEEEEEChHHHHHHHhHHHhHHHHhcCCcccCCEE
Confidence 89999999999 442 357999999999973 8999999999999999999999999999999999999
Q ss_pred EEcceeeeccCCCceEEEEEEeeeeec
Q 006973 77 RLLDYALNEIPTKSEKYLIVTKCEVVS 103 (623)
Q Consensus 77 rl~~y~~~~~~~~~~~vlii~~lev~~ 103 (623)
||++|.++.+++ +|+++||+++||+.
T Consensus 75 rl~~y~~n~v~~-~k~iiiil~leVv~ 100 (101)
T PF04057_consen 75 RLKQYTCNTVKN-GKKIIIILDLEVVQ 100 (101)
T ss_dssp EEEEEEEEESTT-SSEEEEEEEEEEEE
T ss_pred EEeEEEEeeccC-CCEEEEEEeeEEEe
Confidence 999999999984 27999999999985
No 17
>cd04477 RPA1N RPA1N: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA1N is known to specifically interact with the p53 tumor suppressor, DNA polymerase alpha, and transcription factors. In addition to RPA1N, RPA1 contains three other OB folds: ssDNA-binding domain (DBD)-A, DBD-B, and DBD-C.
Probab=99.91 E-value=1.5e-24 Score=185.77 Aligned_cols=91 Identities=33% Similarity=0.475 Sum_probs=83.2
Q ss_pred HHHHHHhcCCCCCCCCCCCcceEEEeeeeecC------ceEEEEEeCcccceeeccccccccccccCccceeeEEEEcce
Q 006973 8 DAISTILSNPSPDSSSDIPEIVVQVLDLKLTG------NRYMFNASDGKKRLKAILPSNLSSEVISGNIQNKGLIRLLDY 81 (623)
Q Consensus 8 ga~~~i~~~~~~~~~~~~~~pvlQvl~~k~~~------~ryr~~lSDG~~~~~~mlat~ln~~v~~~~l~~~siirl~~y 81 (623)
||+++|++++.+ ...+.|||||+++|+++ +|||++||||+|+++|||+||||+++++|+|++||||||++|
T Consensus 1 Gai~~i~~~~~~---~~~~~PvlQv~~ik~i~~~~~~~~RyRi~lSDG~~~~~amLatqln~~v~~g~l~~~sIirl~~y 77 (97)
T cd04477 1 GALAAIFNGEDR---SNVIKPVLQVLNIKKIDSSNGSSERYRILLSDGVYYVQAMLATQLNPLVESGQLQRGSIIRLKRF 77 (97)
T ss_pred ChHHHhhcCCCc---CCCCCCEEEEEEEEEccCCCCCcceEEEEEEChhHHHHHHHhhhhhhHHhcCCccCCcEEEECeE
Confidence 899999998753 13567999999999984 699999999999999999999999999999999999999999
Q ss_pred eeeccCCCceEEEEEEeeeeec
Q 006973 82 ALNEIPTKSEKYLIVTKCEVVS 103 (623)
Q Consensus 82 ~~~~~~~~~~~vlii~~lev~~ 103 (623)
+|+.+++ |+++||+++||+.
T Consensus 78 ~~~~i~~--k~viiIldlevl~ 97 (97)
T cd04477 78 ICNVIKG--KRILIILDLEVVQ 97 (97)
T ss_pred EEEEecC--cEEEEEEeeEEeC
Confidence 9999986 5899999999973
No 18
>cd04475 RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds corresponding to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ functiona
Probab=99.87 E-value=7.7e-22 Score=172.21 Aligned_cols=101 Identities=45% Similarity=0.813 Sum_probs=94.5
Q ss_pred eeEEEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEEeeeccce
Q 006973 309 LVDIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSPIVAIKSLKVGDFQGI 388 (623)
Q Consensus 309 ~vDVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~kV~~f~G~ 388 (623)
+|||+|+|++++++.++++|.+|++..+|+|+|.|+|+.++.|||||++|..+... .++|++|+++|+++|+|+
T Consensus 1 ~vDvig~V~~v~~~~~i~~k~~g~~~~~r~v~i~D~t~~~i~vtLWg~~a~~~~~~------~~~vv~~~~~~i~~~~~~ 74 (101)
T cd04475 1 IVDVIGVVKSVGPVTTITTKSTGRELDKREITLVDESGHSVELTLWGEQAELFDGS------ENPVIAIKGVKVSEFNGK 74 (101)
T ss_pred CEeEEEEEeEccCcEEEEEecCCCceeEEEEEEEeCCCCEEEEEEEHHHhhhcccC------CCCEEEEEeeEEEecCCe
Confidence 58999999999999999999778999999999999999999999999999997532 289999999999999999
Q ss_pred eeecccceEEEEcCChHHHHHHHHHHH
Q 006973 389 SLSTLGRSTVLVSPDLPEAKKLKSWYE 415 (623)
Q Consensus 389 ~Ls~~~~S~i~iNPd~pe~~~l~~w~~ 415 (623)
+|+++.+|+|++||++||+.+|+.||.
T Consensus 75 ~l~~~~~s~i~~np~~~e~~~l~~w~~ 101 (101)
T cd04475 75 SLSTGSSSTIIINPDIPEAHKLRGWYD 101 (101)
T ss_pred EEeecCceeEEECCCcHHHHHHHHhhC
Confidence 999999999999999999999999984
No 19
>cd04481 RPA1_DBD_B_like RPA1_DBD_B_like: A subgroup of uncharacterized, plant OB folds with similarity to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change.
Probab=99.83 E-value=7.1e-20 Score=161.15 Aligned_cols=101 Identities=30% Similarity=0.540 Sum_probs=91.9
Q ss_pred EEEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEEEEE-eEEeeeccc-e
Q 006973 311 DIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSPIVAIK-SLKVGDFQG-I 388 (623)
Q Consensus 311 DVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~-~~kV~~f~G-~ 388 (623)
||||+|++|+++..+..+ |++..+|+|+|+|.++.++.|||||++|.+|...+......+||||+. ++||++|+| +
T Consensus 1 DviG~i~~v~~~~~~~~~--~~~~~kr~~~i~D~~~~~l~~tlwG~~A~~f~~~~~~~~~~~~VVav~~~~rV~~~~g~~ 78 (106)
T cd04481 1 DVIGVIVDVGPLEELPPV--NKPSRKLDFEIRDLSDERLKCTLWGEYAEEFDAKFQSAGNGEPVVAVLRFWKIKEYKGPK 78 (106)
T ss_pred CeeEEEEEecceEecccC--CccceEEEEEEEeCCCCEEEEEEEHHHHHHHHHHHHHhCCCCcEEEEEEeEEEEEEcCCc
Confidence 899999999999999887 778999999999999999999999999999998875446779999885 599999997 7
Q ss_pred eeecc-cceEEEEcCChHHHHHHHHH
Q 006973 389 SLSTL-GRSTVLVSPDLPEAKKLKSW 413 (623)
Q Consensus 389 ~Ls~~-~~S~i~iNPd~pe~~~l~~w 413 (623)
+|++. +.|++++||++||+.+++..
T Consensus 79 ~ls~~~~~s~v~inp~ipe~~~~~~~ 104 (106)
T cd04481 79 SLSNSFGASKVYINPDIPEVPEIKMS 104 (106)
T ss_pred EEEcCCCceEEEECCCcHHHHHHHhh
Confidence 99998 99999999999999999864
No 20
>cd04480 RPA1_DBD_A_like RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.
Probab=99.77 E-value=1.5e-18 Score=146.86 Aligned_cols=86 Identities=26% Similarity=0.347 Sum_probs=80.3
Q ss_pred EEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeEEEecCCCccccCCce
Q 006973 188 TIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGTLRVANKQFKTVQNDY 267 (623)
Q Consensus 188 ~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~V~~a~~~~~~~~~~y 267 (623)
+|+|||+++|+.+... +|..++|+|+|++|++|+|+++++++++|+++|+||+||.|++|.|.++++.|++++|+|
T Consensus 1 ~I~Vrv~r~W~~~~~~----~~~~~~miL~De~G~~I~a~i~~~~~~~f~~~L~eg~vy~is~f~v~~~~~~y~~~~~~y 76 (86)
T cd04480 1 KICVRVLRLWDVYNNA----SGESLEMVLVDEKGNRIHATIPKRLAAKFRPLLKEGKWYTISNFEVAPNTGSYRPTDHPY 76 (86)
T ss_pred CEEEEEEEEEcCcCCC----CCcEEEEEEEcCCCCEEEEEECHHHHHhhhhhceeCCEEEEeeEEEEcCCCcccccCCcE
Confidence 4899999999876532 678999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEccCcEE
Q 006973 268 EMNLNENSEV 277 (623)
Q Consensus 268 ei~f~~~T~I 277 (623)
+|.|..+|+|
T Consensus 77 ~I~f~~~T~V 86 (86)
T cd04480 77 KIKFMSDTVV 86 (86)
T ss_pred EEEeecCcCC
Confidence 9999998865
No 21
>PF02721 DUF223: Domain of unknown function DUF223; InterPro: IPR003871 The function of this domain has not been characterised, but may be involved in nucleic acid or nucleotide binding.
Probab=99.66 E-value=3.2e-16 Score=135.04 Aligned_cols=87 Identities=33% Similarity=0.486 Sum_probs=81.2
Q ss_pred EEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeEEEecCCCccccCCceEEEEccCcEEEEccCcCCCCCCCcc
Q 006973 213 NVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGTLRVANKQFKTVQNDYEMNLNENSEVEEAVNETAFIPQTKF 292 (623)
Q Consensus 213 ~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~V~~a~~~~~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~~ 292 (623)
+|+|+|++|+.|+|+++++++++|.+.|+||+||.|++|.|.++.+.|++++|+|+|.|..+|+|.++++. ...| .|
T Consensus 1 emvL~De~G~~I~A~I~~~~~~~f~~~l~Eg~~y~i~~F~V~~~~~~yr~t~h~y~I~f~~~T~V~~~~~~-~~~~--~~ 77 (95)
T PF02721_consen 1 EMVLVDEKGDKIQATIPKELVDKFKDSLKEGSWYTISNFTVSPNSGSYRPTDHKYKINFMPNTKVTEIDPP-SDPP--FF 77 (95)
T ss_pred CEEEEecCCCEEEEEECHHHHHHHHhhcccCCEEEeEeEEEEeCCCceeccCCCEEEEECCcCeEEECCCC-CCCc--eE
Confidence 47899999999999999999999999999999999999999999999999999999999999999999765 3334 79
Q ss_pred cccccccccc
Q 006973 293 NFVPIDELGR 302 (623)
Q Consensus 293 ~f~~i~di~~ 302 (623)
+|++|++|.+
T Consensus 78 ~f~~F~~I~~ 87 (95)
T PF02721_consen 78 NFTPFDEILE 87 (95)
T ss_pred eecCHHHHhc
Confidence 9999999986
No 22
>PRK08402 replication factor A; Reviewed
Probab=99.64 E-value=9.7e-15 Score=153.40 Aligned_cols=178 Identities=20% Similarity=0.317 Sum_probs=141.7
Q ss_pred CeeeccccCCCCCCeEEEEEEEeeccccccccCCC-cccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeee
Q 006973 173 RVHPLVSLNPYQGNWTIKVRVTSKGNMRTYKNARG-EGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRG 251 (623)
Q Consensus 173 ~~~~I~~L~p~~~~w~I~~RV~~K~~~r~~~~~~g-~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~ 251 (623)
+..+|++|.|+...|++.|||+.+++.|+|...+| .|++.+++|.|++| .|+.|+|++.++++++.|++|+|+.|.++
T Consensus 61 ~~~kI~dl~~g~~~V~v~~rVl~~~~~r~f~rrdG~~~~V~~i~l~DeTG-~ir~TlW~~~a~~~~~~l~~Gdvi~I~~a 139 (355)
T PRK08402 61 PLMHISDLVPGMRGVNIVGRVLRKYPPREYTKKDGSTGRVASLIIYDDTG-RARVVLWDAKVAKYYNKINVGDVIKVIDA 139 (355)
T ss_pred CccCHHHccCCCceeeEEEEEEEccCCceeeccCCCcceEEEEEEEcCCC-eEEEEEechhhhhhcccCCCCCEEEEECC
Confidence 57899999999999999999999999999987555 58899999999999 89999999999998889999999999999
Q ss_pred EEEecCCCccccCCceEEEEccCcEEEEccCcC--CCCCCC------ccccccccccccccCCcceeEEEEEEEEeCCce
Q 006973 252 TLRVANKQFKTVQNDYEMNLNENSEVEEAVNET--AFIPQT------KFNFVPIDELGRYVNGTELVDIIGVVQNVSPTM 323 (623)
Q Consensus 252 ~V~~a~~~~~~~~~~yei~f~~~T~I~~~~d~~--~~iP~~------~~~f~~i~di~~~~~~~~~vDVIGvV~~v~~~~ 323 (623)
.|+... ...++|.+...|+|...+|.+ ..+|.+ .+.+.+|.+|.. .+.++.|.|.|.++.+-.
T Consensus 140 ~V~e~~------~G~~eLsvg~~s~i~~~pd~~ea~~i~~~~~~~~~~~~~k~I~ei~~---gd~~v~v~g~Iv~i~~~~ 210 (355)
T PRK08402 140 QVRESL------SGLPELHINFRARIILNPDDPRVEEIPPLEEVRSYNYTRKKIGELEG---GERFVEVRGTIAKVYRVL 210 (355)
T ss_pred EEeecC------CCcEEEEECCCceEEeCCCcccccccccccccccccccccCHHHccc---CCcEEEEEEEEEEEecCe
Confidence 997642 234699999999999887753 245554 367788899865 346799999999998711
Q ss_pred ----------EEEEcc---------CCc-eee---EEEEEEEeCCccEEEEEEechhhhhh
Q 006973 324 ----------SIRRKS---------NNE-MVP---KRDITVADETKRTVTVSLWNELATNV 361 (623)
Q Consensus 324 ----------~i~~k~---------~g~-~~~---kr~i~l~D~sg~~I~vtLWg~~A~~~ 361 (623)
.+.... .|+ .-. ...+.|.|.|| .+.|+||++.|+.+
T Consensus 211 ~y~aCp~CnKkv~~~~~~~~~~Ce~~~~v~p~~ryil~~~l~D~TG-~~~vt~f~e~ae~l 270 (355)
T PRK08402 211 VYDACPECRRKVDYDPATDTWICPEHGEVEPIKITILDFGLDDGTG-YIRVTLFGDDAAEL 270 (355)
T ss_pred eEecCCCCCeEEEEecCCCCEeCCCCCCcCcceeEEEEEEEEcCCC-cEEEEEecHHHHHH
Confidence 111000 121 112 23678999999 89999999998765
No 23
>PRK07217 replication factor A; Reviewed
Probab=99.63 E-value=8.7e-14 Score=141.01 Aligned_cols=208 Identities=13% Similarity=0.189 Sum_probs=156.6
Q ss_pred ccccccccccccCCcceeEEEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCC
Q 006973 293 NFVPIDELGRYVNGTELVDIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKS 372 (623)
Q Consensus 293 ~f~~i~di~~~~~~~~~vDVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~ 372 (623)
..++|.||.. .+.-|+|.|.|..+++.. .+. ..+.=.|.|+|| +|++|+|++.... .+..|
T Consensus 71 ~~~kI~Di~~---~~~~VsV~aKVl~l~e~~------~~s--i~qvGllgDETG-~IkfT~W~~s~~~-------~leeG 131 (311)
T PRK07217 71 ELVNIADIDE---PEQWVDVTAKVVQLWEPS------SDS--IAQVGLLGDETG-TIKFTKWAKSDLP-------ELEEG 131 (311)
T ss_pred CceeeeecCC---CCCcEEEEEEEEEecCCC------CCc--eEEEEEEEcCCc-eEEEEEccCCCCC-------cccCC
Confidence 3567888864 456899999999998753 122 233346999999 8999999974211 14669
Q ss_pred cEEEEEeEEeeeccce-eeecccceEEEEcCChHHHHHHHHHHHhCCCccceeeecCCcCccccCCcccccccceehhcc
Q 006973 373 PIVAIKSLKVGDFQGI-SLSTLGRSTVLVSPDLPEAKKLKSWYESEGKGTSMASIGSGLGSLAKNGARSMYSDRVSLTHI 451 (623)
Q Consensus 373 ~Vv~i~~~kV~~f~G~-~Ls~~~~S~i~iNPd~pe~~~l~~w~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~ti~~i 451 (623)
.++-|.++.+.+|+|+ +|+.+..|+|...++. + ++
T Consensus 132 d~~rI~na~v~ey~G~~~lnlg~~t~I~~~de~---------------------I-----------------------eV 167 (311)
T PRK07217 132 KSYLLKNVVTDEYQGRFSVKLNRTTSIEELDED---------------------I-----------------------EV 167 (311)
T ss_pred CEEEEEeEEEeeECCEEEEEeCCceEEEeCCCC---------------------c-----------------------cc
Confidence 9999999999999996 8988888888765531 0 00
Q ss_pred ccCCCCCCCCCeEEEEEEEEEEEeCCCCeEeccccc--cccceecCCCCeeecCcCCCCccccceeEEEEEEEEeCCCcE
Q 006973 452 TSNPSLGDEKPVFFSIKAYISLIKPDQAMWYRACKT--CNKKVTDALGSGYWCEGCQKNDEECSLRYIMVARVCDGSGEA 529 (623)
Q Consensus 452 ~~~~~~~~~~~~~~~v~a~I~~i~~d~~~~Y~aC~~--C~KKv~~~~~~~~~C~kC~~~~~~~~~ry~l~~~i~D~Tg~~ 529 (623)
.+ . -..+.|.++.|..... ....||. |+|.+.. +.|+.|++.- +.+-.++.+.+.|+||++
T Consensus 168 ~~-~--------~vei~G~lVdi~~Gsg-lI~rCP~~~C~Rvl~~-----g~C~~HG~ve--~~~DLrik~vlDDGt~~~ 230 (311)
T PRK07217 168 GD-D--------EVEVEGALVDIQSGSG-LIKRCPEEDCTRVLQN-----GRCSEHGKVE--GEFDLRIKGVLDDGEEVQ 230 (311)
T ss_pred cC-c--------cccceeEEEEEeCCCC-CeecCCccccCccccC-----CCCCCCCCcC--CceeeEEEEEEECCCCeE
Confidence 01 0 0346789999988755 4889999 9999943 4899999764 678888899999999999
Q ss_pred EEEEehHhHHHHhCCCHHHHHHHHhhcCCchhHHHHH-HHhcCceEEEEEEE
Q 006973 530 WISIFNEEAERIIGCSADELNELKSQLGDDNSYQMKL-KEVTWVPHLLRVSV 580 (623)
Q Consensus 530 ~~~~F~~~ae~llG~sA~el~~~~~~~~~~~~~~~~l-~~~~~~~~~f~v~~ 580 (623)
.+.+-.+..++|.|++-+|+++|..+.-|.......| +.++|+.|.|+...
T Consensus 231 ~~~~~~e~te~l~G~~l~eak~~a~dald~~vv~~~i~~~llGr~~~v~G~~ 282 (311)
T PRK07217 231 EVIFNREATEELTGITLEEAKQMAMDALDTGVVLDELKEKLLGRYYRVTGPT 282 (311)
T ss_pred EEEEChHHhHHHhCCCHHHHHHHHHHhhchhhHHHHHHHhhcCceEEEEecc
Confidence 9999999999999999999998874322222233334 56899999888854
No 24
>PRK06386 replication factor A; Reviewed
Probab=99.42 E-value=1e-10 Score=122.58 Aligned_cols=248 Identities=15% Similarity=0.139 Sum_probs=170.5
Q ss_pred CcceEEEeeee--ecC------ceEEEEEeCcccceeeccccccccccccCccceeeEEEEcceeeeccCCCceEEEEEE
Q 006973 26 PEIVVQVLDLK--LTG------NRYMFNASDGKKRLKAILPSNLSSEVISGNIQNKGLIRLLDYALNEIPTKSEKYLIVT 97 (623)
Q Consensus 26 ~~pvlQvl~~k--~~~------~ryr~~lSDG~~~~~~mlat~ln~~v~~~~l~~~siirl~~y~~~~~~~~~~~vlii~ 97 (623)
-+-...||++- .+. ..+..+|.|++..+...+|.+. ..|+.|+.|+|.+..+..-++. .-|-+.
T Consensus 15 V~v~akVl~~~~r~i~~~~g~~~~~~gllgDeTG~I~fT~W~~~------~~l~~Gd~v~i~na~v~~~~G~--~~Lnv~ 86 (358)
T PRK06386 15 VDLKVKVLSLNKRTIKNDRGETIYYYGIIGDETGTVPFTAWEFP------DAVKSGDVIEIKYCYSKEYNGK--IRIYFD 86 (358)
T ss_pred EEEEEEEEEccceEEecCCCCeEEEEEEEECCcceEEEEecCCc------ccCCCCCEEEEEeEEEeeECCE--EEEEEc
Confidence 34556666544 332 3567789999999999998852 3579999999999988765542 221111
Q ss_pred eeeeeccccchhhccccCCCCCcccCCCCCccccCCCCCCcccCchhhhhhhhhhhhhccccCCCCccccccCCcCeeec
Q 006973 98 KCEVVSPALEMEIKIEVKSDESGIIFKPKQEDEVKKDGPGIVLKPKQEMVAKSAAQILRDQNGNMAPAARLAMTRRVHPL 177 (623)
Q Consensus 98 ~lev~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I 177 (623)
.. .. + ...+.. .... .+ ..+..+|
T Consensus 87 -----~~-t~--v-----------~~~~d~-----------~iev--------------------~~------~~~~~KI 110 (358)
T PRK06386 87 -----SR-SE--V-----------MLKPDE-----------NIEV--------------------KR------TYKLVKI 110 (358)
T ss_pred -----Cc-eE--E-----------EecCcc-----------cccc--------------------cc------ccCccEe
Confidence 00 00 0 000000 0000 00 0135799
Q ss_pred cccCCCCCCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeEEEecC
Q 006973 178 VSLNPYQGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGTLRVAN 257 (623)
Q Consensus 178 ~~L~p~~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~V~~a~ 257 (623)
++|.|....-+|.|||+..|+ |+|....+.|.+.++.|.|++| +|+.|.|++ .|++|++|.|.|+.+...+
T Consensus 111 ~DL~~g~~~v~V~akVle~~e-~e~~~~g~~~~v~sg~lgDeTG-rIr~TlW~~-------~l~eGd~v~i~na~v~e~~ 181 (358)
T PRK06386 111 RDLSLVTPYVSVIGKITGITK-KEYDSDGTSKIVYQGYIEDDTA-RVRISSFGK-------PLEDNRFVRIENARVSQYN 181 (358)
T ss_pred EeccCCCCceEEEEEEEEccC-ceEecCCCccEEEEEEEEcCCC-eEEEEEccc-------cccCCCEEEEeeeEEEccC
Confidence 999999866689999999987 7887545568899999999999 999999986 3899999999999876653
Q ss_pred CCccccCCceEEEEccCcEEEEccCcCCCCCCCccccccccccccccCCcceeEEEEEEEEeCC-ceEEEEcc-------
Q 006973 258 KQFKTVQNDYEMNLNENSEVEEAVNETAFIPQTKFNFVPIDELGRYVNGTELVDIIGVVQNVSP-TMSIRRKS------- 329 (623)
Q Consensus 258 ~~~~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~~~f~~i~di~~~~~~~~~vDVIGvV~~v~~-~~~i~~k~------- 329 (623)
..++|+++..|.|++.+++ +. ..-.+.+|.||.+ ....+-+.|.|++|.+ ..-|.+-.
T Consensus 182 -------G~~el~v~~~t~I~~~~~~---ie-v~~~~~~I~di~~---~~g~v~i~G~iv~i~~gsgli~rCP~C~R~l~ 247 (358)
T PRK06386 182 -------GYIEISVGNKSVIKEVESD---IN-LESRNIFIFEIKS---PVGGITIMGFIVSVGQGSRIFTKCSVCNKIIE 247 (358)
T ss_pred -------CeEEEEeCCeEEEEECCCC---cc-cCccccchhhhhc---cCCeEEEEEEEEEEcCCcEeEecCcCCCeEcc
Confidence 4589999999999998654 22 2335788899876 2334888899999885 32222110
Q ss_pred ----------CCceeeEEEEEEEeCCccEEEEEEechhhhhh
Q 006973 330 ----------NNEMVPKRDITVADETKRTVTVSLWNELATNV 361 (623)
Q Consensus 330 ----------~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~ 361 (623)
.+....+-.+.|-|.+| .++|+|.++.++.+
T Consensus 248 ~g~C~~HG~v~~~~dlr~k~vLDDGtg-~~~~~l~~e~~e~l 288 (358)
T PRK06386 248 DGVCKDHPDAPVYLDIFGYFTISDGTG-FVTCYANKDSFLPY 288 (358)
T ss_pred CCcCCCCCCCCCeeEEEEEEEEECCCC-eEEEEEChHHhHHH
Confidence 12222333488888888 89999999998875
No 25
>PRK07218 replication factor A; Provisional
Probab=99.34 E-value=2.1e-10 Score=123.25 Aligned_cols=236 Identities=18% Similarity=0.193 Sum_probs=167.7
Q ss_pred EEEEEeCcccceeeccccccccccccCccceeeEEEEcceeeeccCCCceEEEEEEeeeeeccccchhhccccCCCCCcc
Q 006973 42 YMFNASDGKKRLKAILPSNLSSEVISGNIQNKGLIRLLDYALNEIPTKSEKYLIVTKCEVVSPALEMEIKIEVKSDESGI 121 (623)
Q Consensus 42 yr~~lSDG~~~~~~mlat~ln~~v~~~~l~~~siirl~~y~~~~~~~~~~~vlii~~lev~~~~~~~~~~~~~~~~~~~~ 121 (623)
..++|.|.+..++..||..+ .|+.|++|+|.+-.+..-++ +. +|.+ .....+.
T Consensus 95 ~~~~igDeTG~Ir~tlW~~~-------~l~~Gdvv~I~na~vre~~g--~~-----el~i-g~~t~I~------------ 147 (423)
T PRK07218 95 YEGILADETGTISYTAWKDF-------GLSPGDTVTIGNAGVREWDG--RP-----ELNI-GESTTVS------------ 147 (423)
T ss_pred EEEEEECCCCeEEEEEECCC-------CCCCCCEEEEeccEeeccCC--ce-----EEec-cCcceEE------------
Confidence 37899999999999999955 28999999999766554333 11 1110 0110100
Q ss_pred cCCCCCccccCCCCCCcccCchhhhhhhhhhhhhccccCCCCccccccCCcCeeeccccCCCCCCeEEEEEEEeeccccc
Q 006973 122 IFKPKQEDEVKKDGPGIVLKPKQEMVAKSAAQILRDQNGNMAPAARLAMTRRVHPLVSLNPYQGNWTIKVRVTSKGNMRT 201 (623)
Q Consensus 122 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~L~p~~~~w~I~~RV~~K~~~r~ 201 (623)
..+.. . .| |. ......+|.+|.|.....+|.|||+..++ |+
T Consensus 148 -~~de~-----------~-~~---------------------~~----~~~~~~kI~DL~~g~~~V~v~g~Vl~~~~-r~ 188 (423)
T PRK07218 148 -LLDDS-----------S-LP---------------------PY----SIGGDKKLIDLGPGDRGVNVEARVLELEH-RE 188 (423)
T ss_pred -EcCcc-----------c-cc---------------------Cc----cccCccchhhccCCCCceEEEEEEEEecc-ee
Confidence 00000 0 00 00 01124689999999988899999999976 89
Q ss_pred cccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeEEEecCCCccccCCceEEEEccCcEEEEcc
Q 006973 202 YKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGTLRVANKQFKTVQNDYEMNLNENSEVEEAV 281 (623)
Q Consensus 202 ~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~V~~a~~~~~~~~~~yei~f~~~T~I~~~~ 281 (623)
|...+|++.+.+.+|.|++| .|+.|.|++.+ .|++|++|.|.|+.++..+ ..++|++++.|+|+..+
T Consensus 189 f~~~dg~~~v~~giigDeTG-~Ir~tlW~~~~-----~l~~Gd~v~I~na~v~e~~-------G~~elnv~~~t~I~~~d 255 (423)
T PRK07218 189 IDGRDGETTILSGVLADETG-RLPFTDWDPLP-----EIEIGASIRIEDAYVREFR-------GVPSVNVSEFTTVEALD 255 (423)
T ss_pred EEcCCCCeEEEEEEEECCCc-eEEEEEecccc-----cCCCCCEEEEeeeEEeccC-------CeEEEEECCceEEEECC
Confidence 98878888899999999999 99999999853 4899999999999997653 45899999999999986
Q ss_pred CcCCCCCCCccccccccccccccCCcc-eeEEEEEEEEeCCceEEEEc------------------cCCceeeEEEEEEE
Q 006973 282 NETAFIPQTKFNFVPIDELGRYVNGTE-LVDIIGVVQNVSPTMSIRRK------------------SNNEMVPKRDITVA 342 (623)
Q Consensus 282 d~~~~iP~~~~~f~~i~di~~~~~~~~-~vDVIGvV~~v~~~~~i~~k------------------~~g~~~~kr~i~l~ 342 (623)
++ ..++. .+.-++|.++.+. .+. .|.|.|.|++|.+-.-+..+ -.+....+..+.|-
T Consensus 256 ~~-i~v~~-~~~~~~I~e~~~~--~g~~~Vev~G~Iv~i~~gsgli~rCP~C~r~v~~~~C~~hG~ve~~~dlrik~vLD 331 (423)
T PRK07218 256 RE-VSVSK-DPPRLKIREAVER--GGIFDVELVGNIISVRDGSGLIERCPECGRVIQKGQCRSHGAVEGEDDLRIKAILD 331 (423)
T ss_pred CC-ccccC-Cccccchhhhhcc--CCcceEEEEEEEEEeccCCcceecCcCccccccCCcCCCCCCcCCeeeeEEEEEEE
Confidence 54 23332 2445778888752 333 48999999999877432211 02333456788899
Q ss_pred eCCccEEEEEEechhhhhh
Q 006973 343 DETKRTVTVSLWNELATNV 361 (623)
Q Consensus 343 D~sg~~I~vtLWg~~A~~~ 361 (623)
|.+| +++|+|.++.++.+
T Consensus 332 DGtg-~~~~~~~~e~~e~l 349 (423)
T PRK07218 332 DGTG-SVTVILDRELTEIV 349 (423)
T ss_pred CCCC-eEEEEEChhhhHhH
Confidence 9999 89999999988754
No 26
>KOG0851 consensus Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [Replication, recombination and repair]
Probab=99.23 E-value=9.2e-11 Score=118.83 Aligned_cols=214 Identities=22% Similarity=0.283 Sum_probs=156.6
Q ss_pred CeeeccccCCCCCCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeE
Q 006973 173 RVHPLVSLNPYQGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGT 252 (623)
Q Consensus 173 ~~~~I~~L~p~~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~ 252 (623)
.++++.+|+|..+.|+|.++|++.|+.. .+. .|..+.|+|.|+.|..|+|++......+|...|.+|+|+.|.+|.
T Consensus 3 ~~~~l~~l~~~~t~w~i~~~vl~v~~~~--~~~--~~~~~~~il~D~~~~~i~a~i~~~~~~~~~~~l~~~~w~~i~~f~ 78 (246)
T KOG0851|consen 3 GFHRLRDLSPSITGWRIQVKVLRVWKKY--SNP--NGEELRLVLADEHGVKIEATVGRRLSSKYEDNLIENEWKIITTFG 78 (246)
T ss_pred cccchhhcCcCceeeEEEEEEEEEEEec--CCC--CccEEEEEEEecCCcEEEEEcchHHHhhhhhheecceeEEeeeee
Confidence 3789999999999999999999987643 332 357899999999999999999999999999999999999999999
Q ss_pred EEecCCCccccCCceEEEEccCcEEEEccCcCCCCCCCccccccccccccc-cCCcceeEEEE-EEEEeCCceEEEEccC
Q 006973 253 LRVANKQFKTVQNDYEMNLNENSEVEEAVNETAFIPQTKFNFVPIDELGRY-VNGTELVDIIG-VVQNVSPTMSIRRKSN 330 (623)
Q Consensus 253 V~~a~~~~~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~~~f~~i~di~~~-~~~~~~vDVIG-vV~~v~~~~~i~~k~~ 330 (623)
|.++...++.+.|+|++.|...+.+.........+| ..+|.++..+.+. .....++|++| .+..|+.+..- ...
T Consensus 79 v~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~v~~~~~~~~~v~~~~~~~~~v~~~~~~--~~~ 154 (246)
T KOG0851|consen 79 VNPNSGQVRATTHSFKINFMDFTVVTSSDTRLPCTP--WGKFTPFDSIVEDKSDKRVLVDLIGVAVYDVSQLTVT--PAI 154 (246)
T ss_pred ecccccceeeeeeEEEEEeccceeeccCCCCcccee--ccccchhhhhhccccCCcEEEEeeceeEEEeeeeEec--ccc
Confidence 999999999999999999987777766543212223 3567777555442 45667899999 67777655421 123
Q ss_pred CceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEEeeeccceeeecccceEEEEcCChHHHHHH
Q 006973 331 NEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSPIVAIKSLKVGDFQGISLSTLGRSTVLVSPDLPEAKKL 410 (623)
Q Consensus 331 g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~kV~~f~G~~Ls~~~~S~i~iNPd~pe~~~l 410 (623)
++....+.+...+.++ | .. .+.-.++..++..+.+| +++ ...+.+.+..+|+ +..+
T Consensus 155 ~~~~~~~~~~~~~~~~-------~-----~~-------~~~~~~c~~~~~~~~~~-~~~-~~l~~~~~~~~~~---l~~~ 210 (246)
T KOG0851|consen 155 DTDVDGFYLTFKICNK-------S-----KF-------SKPVLWCEACGEQATDF-GRK-RSLGGGVIVIAPE---LLFW 210 (246)
T ss_pred cCCcceEEEEEeeccc-------c-----cc-------cCceEEehhhcchHHhh-hhh-eEecCCcEEccch---heee
Confidence 5567888888888776 1 00 11113344456666677 545 5667777888887 5555
Q ss_pred HHHHHhCC
Q 006973 411 KSWYESEG 418 (623)
Q Consensus 411 ~~w~~~~g 418 (623)
+.|....|
T Consensus 211 ~~~~~~~G 218 (246)
T KOG0851|consen 211 KIWRYFDG 218 (246)
T ss_pred cccccccC
Confidence 55665555
No 27
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=99.14 E-value=4.9e-10 Score=103.31 Aligned_cols=89 Identities=18% Similarity=0.353 Sum_probs=75.1
Q ss_pred cccccccccccccCCcceeEEEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCc---cEEEEEEechhhhhhhhHhhhc
Q 006973 292 FNFVPIDELGRYVNGTELVDIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETK---RTVTVSLWNELATNVGQELLDN 368 (623)
Q Consensus 292 ~~f~~i~di~~~~~~~~~vDVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg---~~I~vtLWg~~A~~~~~~~~~~ 368 (623)
|+|++|++|.+ ..+..|||||+|++++++.. ..|++ -++.|+|+|.|+ ..+.|++|++.++.+..
T Consensus 1 ~~f~~i~~~~~--~~~~~v~vigVV~~~~~p~~----s~g~d-~~~tl~i~D~S~~~~~~l~v~~F~~~~~~LP~----- 68 (138)
T cd04497 1 YKYTPLSSALK--ESGGSVNVIGVVVDAGPPVR----SKGTD-YCCTLTITDPSLANSDGLTVKLFRPNEESLPI----- 68 (138)
T ss_pred CceEeHHHHHh--ccCCeEEEEEEEeecCCCcc----cCCCc-EEEEEEEECCCCCCCCcEEEEEECCChhhCCC-----
Confidence 57999999986 35789999999999998753 33655 799999999998 78999999999998753
Q ss_pred CCCCcEEEEEeEEeeeccceeeec
Q 006973 369 ADKSPIVAIKSLKVGDFQGISLST 392 (623)
Q Consensus 369 ~~~~~Vv~i~~~kV~~f~G~~Ls~ 392 (623)
...|+||++++++|..|+|+.+..
T Consensus 69 v~~GDVIll~~~kv~~~~g~~~~~ 92 (138)
T cd04497 69 VKVGDIILLRRVKIQSYNGKPQGI 92 (138)
T ss_pred CCCCCEEEEEEEEEEEECCceEEE
Confidence 467999999999999999975433
No 28
>COG1599 RFA1 Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [DNA replication, recombination, and repair]
Probab=99.11 E-value=5.1e-10 Score=121.66 Aligned_cols=207 Identities=32% Similarity=0.446 Sum_probs=156.0
Q ss_pred cCeeeccccCCCCCCeEEEEEEEeeccccccccCCCcccEEEEEEEeCC-CCeEEEEEechHHHHHHhhcccCcEEEEee
Q 006973 172 RRVHPLVSLNPYQGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDED-GTQIQATMFNEAARKFYDRFQLGKVYYISR 250 (623)
Q Consensus 172 ~~~~~I~~L~p~~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~-G~~I~at~~~~~~~kf~~~l~eG~vy~is~ 250 (623)
..+.++..+.|+. ++||+.+.++|+|.+++|++++|+..|.|++ | .+..+.|.+. ++|++|.+.+
T Consensus 160 ~~i~~~~~~~~~~-----~~~v~~g~~ik~~~~~~ge~~~~~~~~~d~~~~-~~~~~~~~~~--------~~g~~~~ie~ 225 (407)
T COG1599 160 REIGEESLLSPYQ-----KARVVVGSEIKTFDNQGGESKVFSNELEDEERG-VIVFTDWDPS--------QDGDVYRIEG 225 (407)
T ss_pred cccccccccCccc-----eEEEEecccceeEecCCCccceEeeeeccccee-EEEeccCccc--------ccceeeeecC
Confidence 4567888888887 9999999999999999999999999999998 4 5555555542 9999999999
Q ss_pred eEEEecCCCccccCCceEEEEccC--cEEEEccCcCCCCCCCccccccccccccccCCcceeEEEEEEEEeCCceEEEEc
Q 006973 251 GTLRVANKQFKTVQNDYEMNLNEN--SEVEEAVNETAFIPQTKFNFVPIDELGRYVNGTELVDIIGVVQNVSPTMSIRRK 328 (623)
Q Consensus 251 ~~V~~a~~~~~~~~~~yei~f~~~--T~I~~~~d~~~~iP~~~~~f~~i~di~~~~~~~~~vDVIGvV~~v~~~~~i~~k 328 (623)
.+|+..++++... +.+++.+... +.+.++.+. ..+|...+. ....++. +..+| |+.+.+...+..+
T Consensus 226 ~~v~~~~~~~~~~-~~~e~~~~~~~~~~i~~~~~~-~~~~~~~~~-~~~~~~~-----~~~v~----v~~~~~c~~~~~~ 293 (407)
T COG1599 226 ARVKTKNKQPEEN-LAEELVLRVEVRVAIEKAERE-EFVDEVKES-VSLVEAD-----GAVVD----VTRVPECERVVRK 293 (407)
T ss_pred cEEEEeccccccc-ccceEEEeecceeeccCCCCc-cccceeecc-cccceec-----cceEE----EEECCCceEEEeC
Confidence 9999999988877 9999999887 444444332 233332222 2222221 23344 7777777776554
Q ss_pred cCCceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEEeeeccceeeecccceEEEEcCChHHHH
Q 006973 329 SNNEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSPIVAIKSLKVGDFQGISLSTLGRSTVLVSPDLPEAK 408 (623)
Q Consensus 329 ~~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~kV~~f~G~~Ls~~~~S~i~iNPd~pe~~ 408 (623)
++.....+++.+.|.+| .++|+|||+.++.. .+.+.+.++++.++.++.|+.+++ .++++.
T Consensus 294 -~~~~~~~~~~~l~D~~g-~~rv~~~~~~~e~~-------~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~~ 354 (407)
T COG1599 294 -GGCKGHGKDIGLDDLTG-KIRVTLWGDATEVL-------INEESVEALKGINVEDASGIALSA----------LDTEAV 354 (407)
T ss_pred -CCcccccccceEecCce-EEEEecCCCceEEE-------ecccchhheeeeeeeeccchhhhh----------hhhhhh
Confidence 46667889999999988 89999999844332 466888999999999999987654 667888
Q ss_pred HHHHHHHhCCCccce
Q 006973 409 KLKSWYESEGKGTSM 423 (623)
Q Consensus 409 ~l~~w~~~~g~~~~~ 423 (623)
.+..||...|+...+
T Consensus 355 a~~~~~~~~Gk~~~v 369 (407)
T COG1599 355 ALEIWYDILGKYLRV 369 (407)
T ss_pred hhhcchhcccceEEe
Confidence 899999998876443
No 29
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=98.94 E-value=6.8e-09 Score=86.84 Aligned_cols=81 Identities=30% Similarity=0.424 Sum_probs=70.7
Q ss_pred EEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeEEEecCCCccccCCce
Q 006973 188 TIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGTLRVANKQFKTVQNDY 267 (623)
Q Consensus 188 ~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~V~~a~~~~~~~~~~y 267 (623)
+|.|||+.+++.|+|.+..++++++++.|.|++| .|++++|++.+ .+.|++|++|.|.++.++..+ ..+
T Consensus 1 ~v~~~V~~~~~~~~~~~~g~~~~~~~~~l~D~TG-~i~~~~W~~~~---~~~~~~G~vv~i~~~~v~~~~-------g~~ 69 (82)
T cd04491 1 SVEGKVLSISEPREFTRDGSEGKVQSGLVGDETG-TIRFTLWDEKA---ADDLEPGDVVRIENAYVREFN-------GRL 69 (82)
T ss_pred CEEEEEEEccCCeEeccCCCeeEEEEEEEECCCC-EEEEEEECchh---cccCCCCCEEEEEeEEEEecC-------CcE
Confidence 4789999999999998444578899999999999 99999999876 777999999999999987754 568
Q ss_pred EEEEccCcEEEE
Q 006973 268 EMNLNENSEVEE 279 (623)
Q Consensus 268 ei~f~~~T~I~~ 279 (623)
+|.++..|.|++
T Consensus 70 ql~i~~~~~i~~ 81 (82)
T cd04491 70 ELSVGKNSEIEK 81 (82)
T ss_pred EEEeCCceEEEE
Confidence 999999998875
No 30
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=98.90 E-value=1.4e-08 Score=92.33 Aligned_cols=98 Identities=18% Similarity=0.311 Sum_probs=84.4
Q ss_pred CeeeccccCCCCCCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeE
Q 006973 173 RVHPLVSLNPYQGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGT 252 (623)
Q Consensus 173 ~~~~I~~L~p~~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~ 252 (623)
.+.+|++|.|...+..+.++|+.+++.+.+....+.+++.++.|.|++| .|++++|++.++ .|++|+|+.|.|+.
T Consensus 3 ~~~kI~dL~~g~~~v~~~~~V~~i~~~~~~~~k~~~~~v~~~~l~D~TG-~I~~tlW~~~a~----~l~~GdvV~I~na~ 77 (129)
T PRK06461 3 MITKIKDLKPGMERVNVTVRVLEVGEPKVIQTKGGPRTISEAVVGDETG-RVKLTLWGEQAG----SLKEGEVVEIENAW 77 (129)
T ss_pred CceEHHHcCCCCCceEEEEEEEEcCCceEEEeCCCceEEEEEEEECCCC-EEEEEEeCCccc----cCCCCCEEEEECcE
Confidence 3689999999988999999999999988887666667799999999999 799999998654 58999999999998
Q ss_pred EEecCCCccccCCceEEEEccCcEEEEccC
Q 006973 253 LRVANKQFKTVQNDYEMNLNENSEVEEAVN 282 (623)
Q Consensus 253 V~~a~~~~~~~~~~yei~f~~~T~I~~~~d 282 (623)
+...+ ...+|.+..+|.|.++++
T Consensus 78 v~~f~-------G~lqL~i~~~~~i~~~~~ 100 (129)
T PRK06461 78 TTLYR-------GKVQLNVGKYGSISESDD 100 (129)
T ss_pred EeeeC-------CEEEEEECCCEEEEECCc
Confidence 87543 347899999999998765
No 31
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=98.90 E-value=1.3e-08 Score=92.63 Aligned_cols=95 Identities=24% Similarity=0.313 Sum_probs=78.9
Q ss_pred cccccccccccCCcceeEEEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCc
Q 006973 294 FVPIDELGRYVNGTELVDIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSP 373 (623)
Q Consensus 294 f~~i~di~~~~~~~~~vDVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~ 373 (623)
+++|+||.. ....|+++|+|.++++...+.+| ++ ....++++|.|+|| +|+++||++.|..+ ..+.
T Consensus 4 ~~kI~dL~~---g~~~v~~~~~V~~i~~~~~~~~k-~~-~~~v~~~~l~D~TG-~I~~tlW~~~a~~l--------~~Gd 69 (129)
T PRK06461 4 ITKIKDLKP---GMERVNVTVRVLEVGEPKVIQTK-GG-PRTISEAVVGDETG-RVKLTLWGEQAGSL--------KEGE 69 (129)
T ss_pred ceEHHHcCC---CCCceEEEEEEEEcCCceEEEeC-CC-ceEEEEEEEECCCC-EEEEEEeCCccccC--------CCCC
Confidence 577888864 23579999999999999888887 24 45688999999999 79999999987653 5689
Q ss_pred EEEEEeEEeeeccce-eeecccceEEEEcC
Q 006973 374 IVAIKSLKVGDFQGI-SLSTLGRSTVLVSP 402 (623)
Q Consensus 374 Vv~i~~~kV~~f~G~-~Ls~~~~S~i~iNP 402 (623)
||.|+++++++|+|+ +|+....|.|..-+
T Consensus 70 vV~I~na~v~~f~G~lqL~i~~~~~i~~~~ 99 (129)
T PRK06461 70 VVEIENAWTTLYRGKVQLNVGKYGSISESD 99 (129)
T ss_pred EEEEECcEEeeeCCEEEEEECCCEEEEECC
Confidence 999999999999996 89988888887533
No 32
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=98.82 E-value=4.9e-08 Score=81.61 Aligned_cols=80 Identities=25% Similarity=0.377 Sum_probs=68.7
Q ss_pred EEEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEEeeeccc-ee
Q 006973 311 DIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSPIVAIKSLKVGDFQG-IS 389 (623)
Q Consensus 311 DVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~kV~~f~G-~~ 389 (623)
+|+|.|+.+++...+. + +|+....+++.|.|+|| +|++++|++.+.. .+..+.++.++++++++|+| ..
T Consensus 1 ~v~~~V~~~~~~~~~~-~-~g~~~~~~~~~l~D~TG-~i~~~~W~~~~~~-------~~~~G~vv~i~~~~v~~~~g~~q 70 (82)
T cd04491 1 SVEGKVLSISEPREFT-R-DGSEGKVQSGLVGDETG-TIRFTLWDEKAAD-------DLEPGDVVRIENAYVREFNGRLE 70 (82)
T ss_pred CEEEEEEEccCCeEec-c-CCCeeEEEEEEEECCCC-EEEEEEECchhcc-------cCCCCCEEEEEeEEEEecCCcEE
Confidence 4789999999999998 5 68889999999999999 9999999998711 25678999999999999987 58
Q ss_pred eecccceEEEE
Q 006973 390 LSTLGRSTVLV 400 (623)
Q Consensus 390 Ls~~~~S~i~i 400 (623)
|+....|.|..
T Consensus 71 l~i~~~~~i~~ 81 (82)
T cd04491 71 LSVGKNSEIEK 81 (82)
T ss_pred EEeCCceEEEE
Confidence 88887777754
No 33
>PRK07217 replication factor A; Reviewed
Probab=98.48 E-value=5.6e-06 Score=84.69 Aligned_cols=171 Identities=12% Similarity=0.089 Sum_probs=107.4
Q ss_pred CcCeeeccccCCCCCCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEee
Q 006973 171 TRRVHPLVSLNPYQGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISR 250 (623)
Q Consensus 171 ~~~~~~I~~L~p~~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~ 250 (623)
....++|++|+|...+.+|+|||+..|+.+. +.....-+|.|++| +|+.|.|.+. -.+.|++|++|.|.|
T Consensus 69 ~~~~~kI~Di~~~~~~VsV~aKVl~l~e~~~------~si~qvGllgDETG-~IkfT~W~~s---~~~~leeGd~~rI~n 138 (311)
T PRK07217 69 GSELVNIADIDEPEQWVDVTAKVVQLWEPSS------DSIAQVGLLGDETG-TIKFTKWAKS---DLPELEEGKSYLLKN 138 (311)
T ss_pred CCCceeeeecCCCCCcEEEEEEEEEecCCCC------CceEEEEEEEcCCc-eEEEEEccCC---CCCcccCCCEEEEEe
Confidence 3457899999999999999999999987552 21233357999999 9999999963 145599999999999
Q ss_pred eEEEecCCCccccCCceEEEEccCcEEEEccCcCCCCCCCcccc-ccccccccccC--CcceeEEEEEEEEeCCceEEEE
Q 006973 251 GTLRVANKQFKTVQNDYEMNLNENSEVEEAVNETAFIPQTKFNF-VPIDELGRYVN--GTELVDIIGVVQNVSPTMSIRR 327 (623)
Q Consensus 251 ~~V~~a~~~~~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~~~f-~~i~di~~~~~--~~~~vDVIGvV~~v~~~~~i~~ 327 (623)
+.+...+. .++|.++..|+|++.+++ ..++...-.. -.+-+|...-. ..+..+=++.|..-+.... .-
T Consensus 139 a~v~ey~G-------~~~lnlg~~t~I~~~de~-IeV~~~~vei~G~lVdi~~GsglI~rCP~~~C~Rvl~~g~C~~-HG 209 (311)
T PRK07217 139 VVTDEYQG-------RFSVKLNRTTSIEELDED-IEVGDDEVEVEGALVDIQSGSGLIKRCPEEDCTRVLQNGRCSE-HG 209 (311)
T ss_pred EEEeeECC-------EEEEEeCCceEEEeCCCC-ccccCccccceeEEEEEeCCCCCeecCCccccCccccCCCCCC-CC
Confidence 99877654 488999999999998654 2222110000 01112211000 0000000222322221110 01
Q ss_pred ccCCceeeEEEEEEEeCCccEEEEEEechhhhhh
Q 006973 328 KSNNEMVPKRDITVADETKRTVTVSLWNELATNV 361 (623)
Q Consensus 328 k~~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~ 361 (623)
+-.+..-.+....|-|.+| ++.|.|-.+..+.+
T Consensus 210 ~ve~~~DLrik~vlDDGt~-~~~~~~~~e~te~l 242 (311)
T PRK07217 210 KVEGEFDLRIKGVLDDGEE-VQEVIFNREATEEL 242 (311)
T ss_pred CcCCceeeEEEEEEECCCC-eEEEEEChHHhHHH
Confidence 1134444566788888888 89999988776653
No 34
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.36 E-value=4.2e-05 Score=87.11 Aligned_cols=258 Identities=14% Similarity=0.168 Sum_probs=158.2
Q ss_pred eEEEEEeCcccceeeccccccccccccCccceeeEEEEcceeeeccCCCceEEEEEEeeeeeccccchhhccccCCCCCc
Q 006973 41 RYMFNASDGKKRLKAILPSNLSSEVISGNIQNKGLIRLLDYALNEIPTKSEKYLIVTKCEVVSPALEMEIKIEVKSDESG 120 (623)
Q Consensus 41 ryr~~lSDG~~~~~~mlat~ln~~v~~~~l~~~siirl~~y~~~~~~~~~~~vlii~~lev~~~~~~~~~~~~~~~~~~~ 120 (623)
-|.+.|.|....+++.+..+..+...+ .|+.|.+..|.++.+...+. ++- .+....+ +.-+..+ .
T Consensus 217 vfsv~L~Degg~Irat~f~~~~dkf~~-~l~eG~VY~Is~~~Vk~an~---~y~------~~~~~ye--i~f~~~T---~ 281 (608)
T TIGR00617 217 LFNVELLDESGEIRATAFNEQADKFYD-IIQEGKVYYISKGSLKPANK---QFT------NLGNDYE--MTLDRDT---V 281 (608)
T ss_pred eeEEEEecCCCeEEEEECchHHHHHhh-hcccCCEEEECceEEEEccc---ccc------CCCCCEE--EEECCCe---E
Confidence 478889997777888887776665554 68999999999988875432 110 0111111 1000000 0
Q ss_pred ccCCCCCccccCCCCCCcccCchhhhhhhhhhhhhccccCCCCccccccCCcCeeeccccCCCCC--CeEEEEEEEeecc
Q 006973 121 IIFKPKQEDEVKKDGPGIVLKPKQEMVAKSAAQILRDQNGNMAPAARLAMTRRVHPLVSLNPYQG--NWTIKVRVTSKGN 198 (623)
Q Consensus 121 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~L~p~~~--~w~I~~RV~~K~~ 198 (623)
+..-+.. ..-|. ..-.++||++|..... .--|.|.|+..++
T Consensus 282 I~~~~d~-----------~~iP~--------------------------~~~~f~~i~dI~~~~~~~~VDVIGvV~~v~~ 324 (608)
T TIGR00617 282 IEECEDE-----------TAIPK--------------------------IQFNFVKIDDIGGYEGNSLVDVIGIVQSVSP 324 (608)
T ss_pred EEECCCc-----------ccCCc--------------------------ccccceEHHHhhhhcCCCCccEEEEEeEecC
Confidence 0000000 00000 0124789999976543 5679999999999
Q ss_pred cccccc-CC-CcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeEEEecCCCccccCCceEEEEccCcE
Q 006973 199 MRTYKN-AR-GEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGTLRVANKQFKTVQNDYEMNLNENSE 276 (623)
Q Consensus 199 ~r~~~~-~~-g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~V~~a~~~~~~~~~~yei~f~~~T~ 276 (623)
++++.. .. .++..-+|.|.|++|..|++|+|++.+..|. ..+|.|+.|.+++|+..+. ..|.....|.
T Consensus 325 ~~~i~~k~~g~~~~kR~i~L~D~sg~sI~vTLWG~~A~~~~--~~~~~Vva~kg~~V~~f~g--------~sLs~~~~S~ 394 (608)
T TIGR00617 325 TQTITSRKNNKEFPKRDITLVDDSGKSVRVTLWGDDATKFD--VSVQPVIAIKGVRVSDFGG--------KSLSTGGSST 394 (608)
T ss_pred ceEEEEcCCCCeeeeEEEEEEeCCCCEEEEEEEhhhhhhcC--CCCCCEEEEEeEEEEecCC--------ceEeccCCce
Confidence 998862 22 2445679999999998999999999999987 6899999999999976533 3444444555
Q ss_pred EEEccCcC-------------CC-----C---C-----CCccccccccccccc-c---CCcceeEEEEEEEEeCCceEE-
Q 006973 277 VEEAVNET-------------AF-----I---P-----QTKFNFVPIDELGRY-V---NGTELVDIIGVVQNVSPTMSI- 325 (623)
Q Consensus 277 I~~~~d~~-------------~~-----i---P-----~~~~~f~~i~di~~~-~---~~~~~vDVIGvV~~v~~~~~i- 325 (623)
|..-+|.+ .. + . ...+...+|.+|.+. + ++...+.|.|.|..+..-...
T Consensus 395 i~iNPdipEa~~L~~w~~~~g~~~~~~s~~~~~~~~~~~~~~~~ktI~ei~~~~lg~~~k~~~f~v~atI~~Ik~d~~~Y 474 (608)
T TIGR00617 395 IIVNPDIPEAEKLKGWYDNEGKGTMASSISDMMSGRVGGSNAERKTIAEIQAENLGKSDKPDYFSVKATISYLKPDNALY 474 (608)
T ss_pred EEECCCcHHHHHHHHHHHhcCCCccceeehhccccccCCcccccccHHHHhhhccCCCCCCcEEEEEEEEEEEecCCeEe
Confidence 54322210 00 0 0 002455677777542 1 234578899999988642110
Q ss_pred --------EEc----cCC--------ce---e---eEEEEEEEeCCccEEEEEEechhhhhh
Q 006973 326 --------RRK----SNN--------EM---V---PKRDITVADETKRTVTVSLWNELATNV 361 (623)
Q Consensus 326 --------~~k----~~g--------~~---~---~kr~i~l~D~sg~~I~vtLWg~~A~~~ 361 (623)
..| .+| +. . -...+.|.|.|| .+.++++|+.|+.+
T Consensus 475 ~ACp~~~CnKKV~~~~~g~~~CekC~~~~~~~~~RYil~~~i~D~Tg-~~~~t~F~~~ae~l 535 (608)
T TIGR00617 475 RACPSEDCNKKVVDQGDGTYRCEKCNKNFAEFKYRYILQISISDETG-QLWVTAFNDQAEQI 535 (608)
T ss_pred ccCChhhCCCccccCCCCCEECCCCCCCCCCccEEEEEEEEEEeCCC-CEEEEEEhHHHHHH
Confidence 001 001 11 1 124788999999 79999999999764
No 35
>COG1599 RFA1 Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [DNA replication, recombination, and repair]
Probab=98.17 E-value=3.1e-05 Score=84.46 Aligned_cols=186 Identities=16% Similarity=0.200 Sum_probs=132.9
Q ss_pred cCeeeccccCCCCCCeEEEEEEEeeccccccccCCCc-ccEEEEEEEeCCCCeEEE-EEechHHHHHHhhcccCcEEEEe
Q 006973 172 RRVHPLVSLNPYQGNWTIKVRVTSKGNMRTYKNARGE-GCVFNVELTDEDGTQIQA-TMFNEAARKFYDRFQLGKVYYIS 249 (623)
Q Consensus 172 ~~~~~I~~L~p~~~~w~I~~RV~~K~~~r~~~~~~g~-g~~f~~~L~D~~G~~I~a-t~~~~~~~kf~~~l~eG~vy~is 249 (623)
..+..|+++.+...+-.+.+||...+..+.|....|. +++.+..+.|+.| .++. +.|+..+.. .++.|+++.|.
T Consensus 47 ~~~~~i~~~~~~~~~~~v~~~V~~~~e~~~~~~k~g~~~~l~~~~v~Detg-~v~~~~~~~~~a~~---~~e~Gdv~~i~ 122 (407)
T COG1599 47 ESIGKISDISEASSRVNVTGRVLSIGEKKTFDRKRGAEGKLAEVLVGDETG-SVKTVTLWNIAALE---KLEPGDVIRIR 122 (407)
T ss_pred hhcccccccchhhccccEEEEECccccceeeecccccccceEEEEEecCCC-CEEEEeeccccccc---cCCccceEEec
Confidence 3578999999999999999999999998888777765 8899999999999 7888 788876542 47999999998
Q ss_pred eeEEEecCCCccccCCceEEEEccCcEEEEccCcCCCCCCCccccccccccccccCCcceeEEEEEEEEeCCceEEEEcc
Q 006973 250 RGTLRVANKQFKTVQNDYEMNLNENSEVEEAVNETAFIPQTKFNFVPIDELGRYVNGTELVDIIGVVQNVSPTMSIRRKS 329 (623)
Q Consensus 250 ~~~V~~a~~~~~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~~~f~~i~di~~~~~~~~~vDVIGvV~~v~~~~~i~~k~ 329 (623)
++.+... ....++.+...+.+...++. ...+...+.-..+.++... ...+ .+.|..-.++..+..
T Consensus 123 ~~~~~~~-------~~~~~~~~~~~~~v~~~~~~-~~~~~~~~~~~~i~~~~~~----~~~~-~~~v~~g~~ik~~~~-- 187 (407)
T COG1599 123 NAYTSLY-------RGGKRLSVGRVGSVADVDDE-EDEARESEDAREIGEESLL----SPYQ-KARVVVGSEIKTFDN-- 187 (407)
T ss_pred Ccccccc-------cCceeeecccccccccCchh-hcccccccccccccccccc----Cccc-eEEEEecccceeEec--
Confidence 8765332 34577888888888877654 1222222222333333321 1122 566667777776655
Q ss_pred CCceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEEeeeccce
Q 006973 330 NNEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSPIVAIKSLKVGDFQGI 388 (623)
Q Consensus 330 ~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~kV~~f~G~ 388 (623)
++.....+...+.|++-..+.+++|... ..+.+.-+.+++|.-|++.
T Consensus 188 ~~ge~~~~~~~~~d~~~~~~~~~~~~~~------------~~g~~~~ie~~~v~~~~~~ 234 (407)
T COG1599 188 QGGESKVFSNELEDEERGVIVFTDWDPS------------QDGDVYRIEGARVKTKNKQ 234 (407)
T ss_pred CCCccceEeeeecccceeEEEeccCccc------------ccceeeeecCcEEEEeccc
Confidence 3455678888899998338999999765 2256777788888887764
No 36
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=98.01 E-value=3.1e-05 Score=62.89 Aligned_cols=62 Identities=31% Similarity=0.476 Sum_probs=52.9
Q ss_pred eEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeEEEecCC
Q 006973 187 WTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGTLRVANK 258 (623)
Q Consensus 187 w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~V~~a~~ 258 (623)
++|.|+|+++. ++.++++.++|.|++| .|++.+|++...++.+.|++|+++.+. |.++..+.
T Consensus 1 V~v~G~V~~~~--------~~~~~~~~~~l~D~tg-~i~~~~~~~~~~~~~~~l~~g~~v~v~-G~v~~~~~ 62 (75)
T PF01336_consen 1 VTVEGRVTSIR--------RSGGKIVFFTLEDGTG-SIQVVFFNEEYERFREKLKEGDIVRVR-GKVKRYNG 62 (75)
T ss_dssp EEEEEEEEEEE--------EEETTEEEEEEEETTE-EEEEEEETHHHHHHHHTS-TTSEEEEE-EEEEEETT
T ss_pred CEEEEEEEEEE--------cCCCCEEEEEEEECCc-cEEEEEccHHhhHHhhcCCCCeEEEEE-EEEEEECC
Confidence 47999999875 2245799999999998 999999999999999999999999999 88877744
No 37
>PF02765 POT1: Telomeric single stranded DNA binding POT1/CDC13; InterPro: IPR011564 This entry represents a domain that binds single stranded telomeric DNA and adopts an OB fold []. It includes the proteins POT1 and CDC13 which have been shown to regulate telomere length, replication and capping [, , ]. ; GO: 0003677 DNA binding, 0000723 telomere maintenance, 0000784 nuclear chromosome, telomeric region; PDB: 1S40_A 1KXL_A 1PH7_A 1PH9_A 1PH2_A 1OTC_A 1PHJ_A 1JB7_A 1PA6_A 1PH1_A ....
Probab=97.98 E-value=0.00012 Score=68.28 Aligned_cols=85 Identities=19% Similarity=0.379 Sum_probs=66.0
Q ss_pred cccccccccccCCcceeEEEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCc-------cEEEEEEechhhhhhhhHhh
Q 006973 294 FVPIDELGRYVNGTELVDIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETK-------RTVTVSLWNELATNVGQELL 366 (623)
Q Consensus 294 f~~i~di~~~~~~~~~vDVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg-------~~I~vtLWg~~A~~~~~~~~ 366 (623)
|+++.+... ..+..|||+|+|++..+.....+| |+ --...++|.|.|. ..|.|.++-+..+.+..
T Consensus 1 ~~~l~~~~~--~~~~~vnvigVV~~~~~p~~~~t~--g~-D~~~tl~i~D~S~~~~~~~~~~l~v~iF~~~~~~LP~--- 72 (146)
T PF02765_consen 1 YTPLSTAKE--KFGKFVNVIGVVVDFSPPNPKKTR--GT-DYMCTLTITDPSLNDSNQKLSGLTVNIFRPHKESLPN--- 72 (146)
T ss_dssp BCCGGGSCT--TSSEEEEEEEEEEEEEEECTEEES--SS-CEEEEEEEEBTTCSCSSCCCCEEEEEEEESSHHHSCT---
T ss_pred Cccchhhhh--cCCCEEEEEEEEEEccCCcceEcC--CC-cEEEEEEEECCCCCccccccCCEEEEEECCCHHHCCC---
Confidence 456664443 357899999999999887444454 43 3578999999996 68999999888877653
Q ss_pred hcCCC-CcEEEEEeEEeeeccce
Q 006973 367 DNADK-SPIVAIKSLKVGDFQGI 388 (623)
Q Consensus 367 ~~~~~-~~Vv~i~~~kV~~f~G~ 388 (623)
... |.||.++.++|..|+|+
T Consensus 73 --v~~~GDii~l~r~kv~~~~~~ 93 (146)
T PF02765_consen 73 --VKSVGDIIRLRRVKVQSYNGK 93 (146)
T ss_dssp --TCSTTHEEEEEEEEEEEETTE
T ss_pred --CCCCCCEEEEEEEEEEEECCE
Confidence 334 89999999999999986
No 38
>cd04474 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds corresponding to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ funct
Probab=97.97 E-value=7.1e-05 Score=65.53 Aligned_cols=98 Identities=13% Similarity=0.060 Sum_probs=72.4
Q ss_pred cccccccccCCcceeEEEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEE
Q 006973 296 PIDELGRYVNGTELVDIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSPIV 375 (623)
Q Consensus 296 ~i~di~~~~~~~~~vDVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv 375 (623)
||++|... ....-+.|.|+..+++..+..+. .+....++.|.|+.|..|++|+|++.|+.|.+. +..|.|+
T Consensus 1 pI~~L~p~---~~~~~I~~rV~~k~~~~~f~~~~--~~g~~~~~~l~De~~~~I~~t~~~~~~~~f~~~----l~eG~vy 71 (104)
T cd04474 1 PISSLNPY---QNKWTIKARVTNKSDIRTWSNAR--GEGKLFSFDLLDEDGGEIRATFFNDAVDKFYDL----LEVGKVY 71 (104)
T ss_pred ChhHccCC---CCcEEEEEEEeeccccccccCCC--CCcEEEEEEEEECCCCEEEEEEehHHHHHhhcc----cccccEE
Confidence 46677542 23588999999999999887653 234566999999977799999999999988654 5679999
Q ss_pred EEEeEEeeeccceeeecccceEEEEcC
Q 006973 376 AIKSLKVGDFQGISLSTLGRSTVLVSP 402 (623)
Q Consensus 376 ~i~~~kV~~f~G~~Ls~~~~S~i~iNP 402 (623)
.|.+++|+.-++..-.+...-.|.++.
T Consensus 72 ~i~~~~V~~a~~~y~~~~~~yeI~f~~ 98 (104)
T cd04474 72 YISKGSVKVANKKFNTLKNDYEITFNR 98 (104)
T ss_pred EEeccEEeeccccCCCCCCcEEEEECC
Confidence 999999987665433333344455544
No 39
>cd04475 RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds corresponding to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ functiona
Probab=97.64 E-value=0.00038 Score=60.49 Aligned_cols=84 Identities=21% Similarity=0.192 Sum_probs=67.2
Q ss_pred EEEEEEEeeccccccccCC-C-cccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeEEEecCCCccccCC
Q 006973 188 TIKVRVTSKGNMRTYKNAR-G-EGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGTLRVANKQFKTVQN 265 (623)
Q Consensus 188 ~I~~RV~~K~~~r~~~~~~-g-~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~V~~a~~~~~~~~~ 265 (623)
-|.|.|+..++++++.... | ++...++.|.|++|..|.+|+|++.++.|.... |.++.|.++++...+
T Consensus 3 Dvig~V~~v~~~~~i~~k~~g~~~~~r~v~i~D~t~~~i~vtLWg~~a~~~~~~~--~~vv~~~~~~i~~~~-------- 72 (101)
T cd04475 3 DVIGVVKSVGPVTTITTKSTGRELDKREITLVDESGHSVELTLWGEQAELFDGSE--NPVIAIKGVKVSEFN-------- 72 (101)
T ss_pred eEEEEEeEccCcEEEEEecCCCceeEEEEEEEeCCCCEEEEEEEHHHhhhcccCC--CCEEEEEeeEEEecC--------
Confidence 4789999999999986543 3 566889999999999999999999999988754 999999999886543
Q ss_pred ceEEEEccCcEEEEcc
Q 006973 266 DYEMNLNENSEVEEAV 281 (623)
Q Consensus 266 ~yei~f~~~T~I~~~~ 281 (623)
...+.....|.|..-+
T Consensus 73 ~~~l~~~~~s~i~~np 88 (101)
T cd04475 73 GKSLSTGSSSTIIINP 88 (101)
T ss_pred CeEEeecCceeEEECC
Confidence 1455556677777644
No 40
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=96.94 E-value=0.0019 Score=56.75 Aligned_cols=70 Identities=21% Similarity=0.283 Sum_probs=55.8
Q ss_pred eeeccccCCCCCCeEEEEEEEeeccccccccCCCcc-cEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeE
Q 006973 174 VHPLVSLNPYQGNWTIKVRVTSKGNMRTYKNARGEG-CVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGT 252 (623)
Q Consensus 174 ~~~I~~L~p~~~~w~I~~RV~~K~~~r~~~~~~g~g-~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~ 252 (623)
.++|++|.|+.++..+..-|+.-...+.-+ +| .+-++.+.|++| .|++.+|++ +-..|+.||++.++++-
T Consensus 4 ~i~ikdi~P~~kN~~v~fIvl~~g~~tkTk----dg~~v~~~kVaD~Tg-sI~isvW~e----~~~~~~PGDIirLt~Gy 74 (134)
T KOG3416|consen 4 MIFIKDIKPGLKNINVTFIVLEYGRATKTK----DGHEVRSCKVADETG-SINISVWDE----EGCLIQPGDIIRLTGGY 74 (134)
T ss_pred chhHhhcChhhhcceEEEEEEeeceeeecc----CCCEEEEEEEecccc-eEEEEEecC----cCcccCCccEEEecccc
Confidence 479999999999988877777654443322 34 588899999999 899999996 45579999999999863
No 41
>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco
Probab=96.91 E-value=0.0064 Score=48.24 Aligned_cols=61 Identities=33% Similarity=0.465 Sum_probs=49.5
Q ss_pred EEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeEEEec
Q 006973 189 IKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGTLRVA 256 (623)
Q Consensus 189 I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~V~~a 256 (623)
+.|+|+.....++ | +..+.+.|.|.+|+.|.+++|.+..+.+...+++|+++.+. +++...
T Consensus 2 v~g~v~~~~~~~~-----~-~~~~~~~l~D~~~~~i~~~~~~~~~~~~~~~~~~g~~v~v~-g~v~~~ 62 (75)
T cd03524 2 IVGIVVAVEEIRT-----E-GKVLIFTLTDGTGGTIRVTLFGELAEELENLLKEGQVVYIK-GKVKKF 62 (75)
T ss_pred eEEEEEeeccccc-----C-CeEEEEEEEcCCCCEEEEEEEchHHHHHHhhccCCCEEEEE-EEEEec
Confidence 6778887655443 1 24788999999955999999999999999999999999998 888654
No 42
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=96.42 E-value=0.015 Score=51.37 Aligned_cols=85 Identities=20% Similarity=0.298 Sum_probs=61.2
Q ss_pred ccccccccccCCcceeEEEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcE
Q 006973 295 VPIDELGRYVNGTELVDIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSPI 374 (623)
Q Consensus 295 ~~i~di~~~~~~~~~vDVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~V 374 (623)
.+|.||...+. .+.|+=+|.+.+..+. +| +|+ ..|...+.|+|| +|.+.+|++.... +..+.|
T Consensus 5 i~ikdi~P~~k---N~~v~fIvl~~g~~tk--Tk-dg~--~v~~~kVaD~Tg-sI~isvW~e~~~~--------~~PGDI 67 (134)
T KOG3416|consen 5 IFIKDIKPGLK---NINVTFIVLEYGRATK--TK-DGH--EVRSCKVADETG-SINISVWDEEGCL--------IQPGDI 67 (134)
T ss_pred hhHhhcChhhh---cceEEEEEEeeceeee--cc-CCC--EEEEEEEecccc-eEEEEEecCcCcc--------cCCccE
Confidence 35677765332 3556667777775542 33 465 578999999999 9999999977655 367999
Q ss_pred EEEEeEEeeeccc-eeeecccce
Q 006973 375 VAIKSLKVGDFQG-ISLSTLGRS 396 (623)
Q Consensus 375 v~i~~~kV~~f~G-~~Ls~~~~S 396 (623)
|-+++.-.+-|+| ..|.++.+.
T Consensus 68 irLt~Gy~Si~qg~LtL~~GK~G 90 (134)
T KOG3416|consen 68 IRLTGGYASIFQGCLTLYVGKGG 90 (134)
T ss_pred EEecccchhhhcCceEEEecCCc
Confidence 9999998888876 577765443
No 43
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=96.34 E-value=0.025 Score=52.13 Aligned_cols=84 Identities=15% Similarity=0.205 Sum_probs=67.1
Q ss_pred eeeccccC-CCCCCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCC---CeEEEEEechHHHHHHhhcccCcEEEEe
Q 006973 174 VHPLVSLN-PYQGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDG---TQIQATMFNEAARKFYDRFQLGKVYYIS 249 (623)
Q Consensus 174 ~~~I~~L~-p~~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G---~~I~at~~~~~~~kf~~~l~eG~vy~is 249 (623)
++||++|. .....-.+.|-|+...+.+. .+|.--..+|.|.|+++ ..+++.+|++..+.|-.. ++|+|+.+.
T Consensus 3 f~~i~~~~~~~~~~v~vigVV~~~~~p~~---s~g~d~~~tl~i~D~S~~~~~~l~v~~F~~~~~~LP~v-~~GDVIll~ 78 (138)
T cd04497 3 YTPLSSALKESGGSVNVIGVVVDAGPPVR---SKGTDYCCTLTITDPSLANSDGLTVKLFRPNEESLPIV-KVGDIILLR 78 (138)
T ss_pred eEeHHHHHhccCCeEEEEEEEeecCCCcc---cCCCcEEEEEEEECCCCCCCCcEEEEEECCChhhCCCC-CCCCEEEEE
Confidence 68888887 34457889999998777653 22333577899999988 789999999998887765 999999999
Q ss_pred eeEEEecCCCcc
Q 006973 250 RGTLRVANKQFK 261 (623)
Q Consensus 250 ~~~V~~a~~~~~ 261 (623)
+++|+.-+.+..
T Consensus 79 ~~kv~~~~g~~~ 90 (138)
T cd04497 79 RVKIQSYNGKPQ 90 (138)
T ss_pred EEEEEEECCceE
Confidence 999998876543
No 44
>cd04481 RPA1_DBD_B_like RPA1_DBD_B_like: A subgroup of uncharacterized, plant OB folds with similarity to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change.
Probab=96.24 E-value=0.065 Score=46.89 Aligned_cols=69 Identities=14% Similarity=0.207 Sum_probs=52.8
Q ss_pred EEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhc----ccCcEEEEee-eEEEecCC
Q 006973 190 KVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRF----QLGKVYYISR-GTLRVANK 258 (623)
Q Consensus 190 ~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l----~eG~vy~is~-~~V~~a~~ 258 (623)
.|-|+.-+++.+......+....++.|.|.+|..++++.|++.|..|...+ +.+-|+.+-. .+|+..++
T Consensus 3 iG~i~~v~~~~~~~~~~~~~~kr~~~i~D~~~~~l~~tlwG~~A~~f~~~~~~~~~~~~VVav~~~~rV~~~~g 76 (106)
T cd04481 3 IGVIVDVGPLEELPPVNKPSRKLDFEIRDLSDERLKCTLWGEYAEEFDAKFQSAGNGEPVVAVLRFWKIKEYKG 76 (106)
T ss_pred eEEEEEecceEecccCCccceEEEEEEEeCCCCEEEEEEEHHHHHHHHHHHHHhCCCCcEEEEEEeEEEEEEcC
Confidence 455666666665544334556789999999999999999999999999887 4677777766 78877753
No 45
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=95.80 E-value=0.062 Score=43.22 Aligned_cols=66 Identities=24% Similarity=0.340 Sum_probs=47.1
Q ss_pred eEEEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEEeeeccc--
Q 006973 310 VDIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSPIVAIKSLKVGDFQG-- 387 (623)
Q Consensus 310 vDVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~kV~~f~G-- 387 (623)
|.|.|.|+.+. +. + .....++|.|.|| .|.|++|++.+..+.+ ....+.+|.+. +++..|++
T Consensus 1 V~v~G~V~~~~-------~~-~--~~~~~~~l~D~tg-~i~~~~~~~~~~~~~~----~l~~g~~v~v~-G~v~~~~~~~ 64 (75)
T PF01336_consen 1 VTVEGRVTSIR-------RS-G--GKIVFFTLEDGTG-SIQVVFFNEEYERFRE----KLKEGDIVRVR-GKVKRYNGGE 64 (75)
T ss_dssp EEEEEEEEEEE-------EE-E--TTEEEEEEEETTE-EEEEEEETHHHHHHHH----TS-TTSEEEEE-EEEEEETTSS
T ss_pred CEEEEEEEEEE-------cC-C--CCEEEEEEEECCc-cEEEEEccHHhhHHhh----cCCCCeEEEEE-EEEEEECCcc
Confidence 56889998876 11 1 2466899999998 9999999965555433 35678999888 78887754
Q ss_pred eeee
Q 006973 388 ISLS 391 (623)
Q Consensus 388 ~~Ls 391 (623)
.+|.
T Consensus 65 ~~l~ 68 (75)
T PF01336_consen 65 LELI 68 (75)
T ss_dssp EEEE
T ss_pred EEEE
Confidence 4443
No 46
>cd04483 hOBFC1_like hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1). Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The OB fold domain of RPA2 has dual roles in ssDNA binding and trimerization.
Probab=95.65 E-value=0.047 Score=46.60 Aligned_cols=68 Identities=16% Similarity=0.270 Sum_probs=45.5
Q ss_pred EEEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCccEEEEEEechhhhhh--h--------------hHhhhcCCCCcE
Q 006973 311 DIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKRTVTVSLWNELATNV--G--------------QELLDNADKSPI 374 (623)
Q Consensus 311 DVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~--~--------------~~~~~~~~~~~V 374 (623)
|++|+|.++.+- ..+..++|.|.|| .|+|.+|......- . ....+.+..+.+
T Consensus 1 ~ivG~V~sv~~~-----------~~~~~~tLdDgTG-~Ie~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~G~v 68 (92)
T cd04483 1 DILGTVVSRRER-----------ETFYSFGVDDGTG-VVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVLEIGDL 68 (92)
T ss_pred CeEEEEEEEEec-----------CCeEEEEEecCCc-eEEEEEEcCcCcccccccccccccccccccccccccccCCCCE
Confidence 689999887421 2468899999999 79999998753110 0 001122456778
Q ss_pred EEEEeEEeeeccce-eee
Q 006973 375 VAIKSLKVGDFQGI-SLS 391 (623)
Q Consensus 375 v~i~~~kV~~f~G~-~Ls 391 (623)
+-++ .+++.|+|+ .|.
T Consensus 69 vrV~-G~i~~frg~~ql~ 85 (92)
T cd04483 69 LRVR-GSIRTYRGEREIN 85 (92)
T ss_pred EEEE-EEEeccCCeeEEE
Confidence 7776 678899984 554
No 47
>PF15489 CTC1: CST, telomere maintenance, complex subunit CTC1
Probab=95.30 E-value=4.4 Score=48.75 Aligned_cols=319 Identities=16% Similarity=0.170 Sum_probs=167.5
Q ss_pred cCCCCCCeEEEEEEEeeccccccccCCCcccEEEEEEEeCC-CCeEEEEEechHHHHHHhhcccCcEEEEeee-----EE
Q 006973 180 LNPYQGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDED-GTQIQATMFNEAARKFYDRFQLGKVYYISRG-----TL 253 (623)
Q Consensus 180 L~p~~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~-G~~I~at~~~~~~~kf~~~l~eG~vy~is~~-----~V 253 (623)
..+....+.+.|..++.+.... +...+.|+. + ...|+. ..++-..|.+. .-+|++.|+.|.||.+--- .|
T Consensus 700 ~~~~~~tlsF~~~g~wlGg~q~-~eg~~~~~~-e-~~~~~~~~~kVlLlF~G~-svrWF~fLhpg~vYRLva~~~~~p~l 775 (1144)
T PF15489_consen 700 SEVPKPTLSFQVSGSWLGGTQR-KEGTGWGPP-E-PLEDENKDQKVLLLFLGS-SVRWFPFLHPGQVYRLVAPNSPDPML 775 (1144)
T ss_pred cccCCCceEEEEEEEEecceEe-ccCcccCCC-C-cCcccCCCceEEEEEecC-ceeeEeEecCCcEEEEecCCCCCcee
Confidence 3334457888888888776644 222222221 0 112233 33555555554 5689999999999987421 11
Q ss_pred EecCC--Cc--cccCCceEEEEccCcEEEEccCcCCCCCCC-----ccccccccccccccCCcceeEEEEEEEEeCCceE
Q 006973 254 RVANK--QF--KTVQNDYEMNLNENSEVEEAVNETAFIPQT-----KFNFVPIDELGRYVNGTELVDIIGVVQNVSPTMS 324 (623)
Q Consensus 254 ~~a~~--~~--~~~~~~yei~f~~~T~I~~~~d~~~~iP~~-----~~~f~~i~di~~~~~~~~~vDVIGvV~~v~~~~~ 324 (623)
-.+.. .. -...-.-.+++..+=+++.... .++|.. .+--.++.|+.+.-..+.+|.+-|+|.+..-...
T Consensus 776 ~~~s~~s~r~l~~~~~~scl~vq~~W~le~~~~--~d~~~~l~~~~~~~~ssl~~lls~s~s~sLVSFs~~I~srt~ce~ 853 (1144)
T PF15489_consen 776 FGSSCVSQRPLELAGCPSCLTVQDDWTLELESS--QDIPPVLRISKLLPESSLSELLSSSSSDSLVSFSAEILSRTLCEP 853 (1144)
T ss_pred ecCCCcccccccccCCCccEEeCCCceeccccc--ccchhhhhhcccCccccHHHHhccCCCCceEEEEEEEEEeeeccC
Confidence 10000 00 0011112233332222222211 234421 1123466676653345789999999988632221
Q ss_pred ----EEEccCCce----ee--EEEEEEEeCCccEEEEEEechhhh-hhhhHhhhcCCCCcEEEEEe--EEeeeccceeee
Q 006973 325 ----IRRKSNNEM----VP--KRDITVADETKRTVTVSLWNELAT-NVGQELLDNADKSPIVAIKS--LKVGDFQGISLS 391 (623)
Q Consensus 325 ----i~~k~~g~~----~~--kr~i~l~D~sg~~I~vtLWg~~A~-~~~~~~~~~~~~~~Vv~i~~--~kV~~f~G~~Ls 391 (623)
..+|..+.. .. ..-+++.|..+. -.+.+.-+... -+.- -.-.|.+|-|.+ .||+.++++++.
T Consensus 854 ~~~~~~~~~~~~~~~~~~vkltv~L~v~D~~~p-~~ldVYi~~~h~p~pl----GLLPGA~V~f~~lerkVSRs~nVYC~ 928 (1144)
T PF15489_consen 854 LNARRWSKPGNAIASRGCVKLTVALTVADCESP-PHLDVYIEDPHLPYPL----GLLPGARVLFSQLERKVSRSHNVYCC 928 (1144)
T ss_pred CccccccCCCCCcccccccceEEEEEEecCCCC-CeEEEEecCCCCCCcc----cccCCceeeeehhhhhhhccCcEEEE
Confidence 112211111 11 234566666662 22444333221 1110 022466777764 466666667766
Q ss_pred cccceEEEEcCChHHHHHHHHHHHhCCCccceeeecCCcCccccCCcccccccceehhccccCCCCCCCCCeEEEEEEEE
Q 006973 392 TLGRSTVLVSPDLPEAKKLKSWYESEGKGTSMASIGSGLGSLAKNGARSMYSDRVSLTHITSNPSLGDEKPVFFSIKAYI 471 (623)
Q Consensus 392 ~~~~S~i~iNPd~pe~~~l~~w~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~ti~~i~~~~~~~~~~~~~~~v~a~I 471 (623)
....|.+.+.-..++ . . . +.......+.+.... ...+....+.+.|
T Consensus 929 ~~psS~VtVlS~p~~------------t--~---~-------------~~~~P~~~L~~~~~~----~~~~~~a~~~chV 974 (1144)
T PF15489_consen 929 FLPSSSVTVLSFPPE------------T--N---V-------------SPPLPHIYLAELLQG----SQSPFQARVSCHV 974 (1144)
T ss_pred EcCCceEEEEecCcc------------c--C---C-------------CCCCCeEEehhhhCC----CCCCceEEEEEEE
Confidence 666666554332100 0 0 0 011244556555441 1223356778899
Q ss_pred EEEeCCCCeEeccccccccceecCCCCeeecCc----CCCCccccceeEEEEEEEEeCCCcEEEEEehHhHHHHhCCCHH
Q 006973 472 SLIKPDQAMWYRACKTCNKKVTDALGSGYWCEG----CQKNDEECSLRYIMVARVCDGSGEAWISIFNEEAERIIGCSAD 547 (623)
Q Consensus 472 ~~i~~d~~~~Y~aC~~C~KKv~~~~~~~~~C~k----C~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~~~ae~llG~sA~ 547 (623)
+.|..- . --..|..|+.-..+ | +|.. |... ....+-..++.+.|+||++.+++-|+..-.+||.+..
T Consensus 975 V~V~~l-~-L~WvCa~C~si~~q---g--~Csr~~p~C~s~--~sV~qA~ar~~vEDGTaeA~v~~~~~~V~~lLgL~~~ 1045 (1144)
T PF15489_consen 975 VSVLSL-Q-LQWVCAHCGSICPQ---G--RCSRQSPPCPSQ--TSVFQASARLLVEDGTAEAVVWCRGHHVAALLGLSPS 1045 (1144)
T ss_pred EEEEEE-E-eeehhhhccCcccC---C--cCCCCCCCCCCC--cceeeEEEEEEEecCCeeEEEEECCcHHHHHhCCCHH
Confidence 888653 2 36689999865443 2 4633 5432 3456778889999999999999999999999999998
Q ss_pred HHHHH
Q 006973 548 ELNEL 552 (623)
Q Consensus 548 el~~~ 552 (623)
|...+
T Consensus 1046 eW~~L 1050 (1144)
T PF15489_consen 1046 EWESL 1050 (1144)
T ss_pred HHHHH
Confidence 76544
No 48
>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco
Probab=95.29 E-value=0.14 Score=40.23 Aligned_cols=64 Identities=31% Similarity=0.415 Sum_probs=46.9
Q ss_pred EEEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEEeeeccc
Q 006973 311 DIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSPIVAIKSLKVGDFQG 387 (623)
Q Consensus 311 DVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~kV~~f~G 387 (623)
++.|+|.++.+... |+ ....++|.|.+|..++|++|.+....+.. ....+.++.+. +++..|+|
T Consensus 1 ~v~g~v~~~~~~~~------~~--~~~~~~l~D~~~~~i~~~~~~~~~~~~~~----~~~~g~~v~v~-g~v~~~~~ 64 (75)
T cd03524 1 TIVGIVVAVEEIRT------EG--KVLIFTLTDGTGGTIRVTLFGELAEELEN----LLKEGQVVYIK-GKVKKFRG 64 (75)
T ss_pred CeEEEEEeeccccc------CC--eEEEEEEEcCCCCEEEEEEEchHHHHHHh----hccCCCEEEEE-EEEEecCC
Confidence 47899988865432 32 36789999999559999999987776532 24567788887 88887765
No 49
>cd04488 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched cha
Probab=95.22 E-value=0.16 Score=40.56 Aligned_cols=62 Identities=21% Similarity=0.257 Sum_probs=43.0
Q ss_pred EEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeEEEecC
Q 006973 188 TIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGTLRVAN 257 (623)
Q Consensus 188 ~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~V~~a~ 257 (623)
+|.|+|.+.... .. + .++.+.+.+.|++| .|.+++|+.. ......|++|+.|.+. +++...+
T Consensus 1 ~i~~~V~~~~~~-~~---~-~~~~~~~~~~D~~g-~i~~~~F~~~-~~~~~~~~~G~~~~v~-Gkv~~~~ 62 (75)
T cd04488 1 TVEGTVVSVEVV-PR---R-GRRRLKVTLSDGTG-TLTLVFFNFQ-PYLKKQLPPGTRVRVS-GKVKRFR 62 (75)
T ss_pred CEEEEEEEEEec-cC---C-CccEEEEEEEcCCC-EEEEEEECCC-HHHHhcCCCCCEEEEE-EEEeecC
Confidence 367888775321 11 1 23589999999988 8999999831 2345679999999887 5555443
No 50
>cd04485 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains two copies of this replicative polymerase, each of which copies a different DNA strand. This group also contains Bacillus subtilis DnaE. Replication in B. subtilis and Staphylococcus aureus requires two different type C polymerases, polC and DnaE, both of which are thought to be included in the DNA polymerase holoenzyme. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Probab=94.86 E-value=0.14 Score=41.71 Aligned_cols=44 Identities=23% Similarity=0.359 Sum_probs=37.6
Q ss_pred cEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeEEEe
Q 006973 210 CVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGTLRV 255 (623)
Q Consensus 210 ~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~V~~ 255 (623)
+.+.+.|.|.+| .+.+++|++..+++.+.|++|.+|.+. +++..
T Consensus 19 ~~~~~~l~D~tg-~~~~~~f~~~~~~~~~~l~~g~~v~v~-G~v~~ 62 (84)
T cd04485 19 RMAFVTLEDLTG-SIEVVVFPETYEKYRDLLKEDALLLVE-GKVER 62 (84)
T ss_pred EEEEEEEEeCCC-eEEEEECHHHHHHHHHHhcCCCEEEEE-EEEEe
Confidence 478899999999 899999998877889999999999887 45543
No 51
>PF09103 BRCA-2_OB1: BRCA2, oligonucleotide/oligosaccharide-binding, domain 1; InterPro: IPR015187 This domain assumes an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB1 has a shallow groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for weak single strand DNA binding. The domain also binds the 70-amino acid DSS1 (deleted in split-hand/split foot syndrome) protein, which was originally identified as one of three genes that map to a 1.5-Mb locus deleted in an inherited developmental malformation syndrome []. ; GO: 0000724 double-strand break repair via homologous recombination; PDB: 1IYJ_D 1MIU_A.
Probab=94.14 E-value=0.059 Score=48.11 Aligned_cols=70 Identities=21% Similarity=0.265 Sum_probs=42.9
Q ss_pred HHHHHhcCCCCCCCCCCCcceEEEeeeeec----CceEEEEEeCcccceeeccccccccccccCccceeeEEEEccee
Q 006973 9 AISTILSNPSPDSSSDIPEIVVQVLDLKLT----GNRYMFNASDGKKRLKAILPSNLSSEVISGNIQNKGLIRLLDYA 82 (623)
Q Consensus 9 a~~~i~~~~~~~~~~~~~~pvlQvl~~k~~----~~ryr~~lSDG~~~~~~mlat~ln~~v~~~~l~~~siirl~~y~ 82 (623)
||.+|++++.+.+ ..-||=|.++..- ++...+.||||=|.+++.+...|..++..|.|..|.-++|..-.
T Consensus 2 aLrrI~E~D~~~~----~~mVL~Vs~i~~~~~~~~~~~~lelTDGWY~Ika~lD~~L~~~l~~gki~vG~KL~v~GA~ 75 (118)
T PF09103_consen 2 ALRRILEGDDSAS----KPMVLCVSSISSSDNDSPESAILELTDGWYSIKAQLDPPLTRLLRKGKIRVGQKLRVCGAE 75 (118)
T ss_dssp HHHHHHTTSSTTB-----SEEEEEEE-------------EEEE-SS-EEEE---HHHHHHHHTT-S-TT-EEEESSBE
T ss_pred HhHHHhhCCCCcC----CcEEEEEEEEccCCCCCCccCEEEEecCCEEEEEEeCHHHHHHHHhCCccCCccEEEECce
Confidence 7899999986542 2247777777222 16789999999999999999999999999999999988874433
No 52
>cd04490 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds corresponding to the OB fold found in Pyrococcus abyssi DNA polymerase II (PolII) small subunit. PolII is a family D DNA polymerase, having a 3-prime to 5-prime exonuclease activity. P. abyssi PolII is heterodimeric. The large subunit appears to be the polymerase, and the small subunit may be the exonuclease. The small subunit contains a calcineurin-like phosphatase superfamily domain C-terminal to this OB-fold domain.
Probab=93.95 E-value=0.31 Score=40.28 Aligned_cols=55 Identities=22% Similarity=0.345 Sum_probs=40.3
Q ss_pred eEEEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCccEEEEEEechhhh--hhhhHhhhcCCCCcEEEEEe
Q 006973 310 VDIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKRTVTVSLWNELAT--NVGQELLDNADKSPIVAIKS 379 (623)
Q Consensus 310 vDVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~--~~~~~~~~~~~~~~Vv~i~~ 379 (623)
+-++|+|.++. .+|+ |+. -++|.|.+| ++++++|.+..+ .+... ...+.+|.+++
T Consensus 2 v~i~GiI~~v~-----~TK~-g~~----~~~leD~~G-~~Ev~~F~~~~~~~~~~~~----l~~d~~v~v~g 58 (79)
T cd04490 2 VSIIGMVNDVR-----STKN-GHR----IVELEDTTG-RITVLLTKDKEELFEEAED----ILPDEVIGVSG 58 (79)
T ss_pred EEEEEEEeEEE-----EcCC-CCE----EEEEECCCC-EEEEEEeCchhhhhhhhhh----ccCCCEEEEEE
Confidence 34789999987 3453 543 899999999 899999998887 65433 45566776665
No 53
>PF06075 DUF936: Plant protein of unknown function (DUF936); InterPro: IPR010341 This family consists of several hypothetical proteins from plants. The function of this family is unknown.
Probab=93.59 E-value=0.14 Score=57.93 Aligned_cols=92 Identities=15% Similarity=0.243 Sum_probs=72.5
Q ss_pred CCHHHHHHHhcCCCCCC--CCCCCcceEEEeeeeec--C------ceEEEEEeCcccceeeccccccccccccCccceee
Q 006973 5 VSPDAISTILSNPSPDS--SSDIPEIVVQVLDLKLT--G------NRYMFNASDGKKRLKAILPSNLSSEVISGNIQNKG 74 (623)
Q Consensus 5 lt~ga~~~i~~~~~~~~--~~~~~~pvlQvl~~k~~--~------~ryr~~lSDG~~~~~~mlat~ln~~v~~~~l~~~s 74 (623)
||||-|.+++++...+. .++--.++|||++|=+. + .-|.|-|||+-|.+..-|..+=++||.++.|+-|-
T Consensus 1 L~pGvL~klL~~mn~~~k~~gehRs~lLQV~~IvPaL~~~~l~p~~gF~lkvSDsshs~Yvsl~~~~~dlils~klqlGq 80 (579)
T PF06075_consen 1 LTPGVLLKLLQHMNSDVKVTGEHRSSLLQVTSIVPALAGSDLWPNQGFYLKVSDSSHSTYVSLPDEDDDLILSNKLQLGQ 80 (579)
T ss_pred CCchHHHHHHHhcCCCCccCCcccccceeeeeeeecccccccCcCCceEEEecccccceeeecChhcccceecCCccccc
Confidence 89999999999653321 22334689999999985 1 45999999999999999999999999999999999
Q ss_pred EEEEcceeeeccCCCceEEEEEEeeeee
Q 006973 75 LIRLLDYALNEIPTKSEKYLIVTKCEVV 102 (623)
Q Consensus 75 iirl~~y~~~~~~~~~~~vlii~~lev~ 102 (623)
+|.|.+...- ..|=++.++..|
T Consensus 81 fi~vdrle~~------~PvP~l~g~rp~ 102 (579)
T PF06075_consen 81 FIYVDRLEAA------SPVPVLRGVRPV 102 (579)
T ss_pred eEEEcccccC------CCCceeecCccC
Confidence 9999887543 245555566555
No 54
>cd04490 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds corresponding to the OB fold found in Pyrococcus abyssi DNA polymerase II (PolII) small subunit. PolII is a family D DNA polymerase, having a 3-prime to 5-prime exonuclease activity. P. abyssi PolII is heterodimeric. The large subunit appears to be the polymerase, and the small subunit may be the exonuclease. The small subunit contains a calcineurin-like phosphatase superfamily domain C-terminal to this OB-fold domain.
Probab=93.52 E-value=0.39 Score=39.66 Aligned_cols=54 Identities=22% Similarity=0.213 Sum_probs=42.7
Q ss_pred EEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHH--HHHhhcccCcEEEEee
Q 006973 188 TIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAAR--KFYDRFQLGKVYYISR 250 (623)
Q Consensus 188 ~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~--kf~~~l~eG~vy~is~ 250 (623)
.+.|.|+.. | . +.+| +. -+.|-|.+| .+.+++|++..+ ++.++|++|.++.+..
T Consensus 3 ~i~GiI~~v---~-~-TK~g--~~-~~~leD~~G-~~Ev~~F~~~~~~~~~~~~l~~d~~v~v~g 58 (79)
T cd04490 3 SIIGMVNDV---R-S-TKNG--HR-IVELEDTTG-RITVLLTKDKEELFEEAEDILPDEVIGVSG 58 (79)
T ss_pred EEEEEEeEE---E-E-cCCC--CE-EEEEECCCC-EEEEEEeCchhhhhhhhhhccCCCEEEEEE
Confidence 456667664 3 2 2233 34 788999999 899999999999 9999999999999975
No 55
>cd04489 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis.
Probab=93.37 E-value=0.36 Score=39.28 Aligned_cols=54 Identities=19% Similarity=0.334 Sum_probs=43.0
Q ss_pred EEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEee
Q 006973 188 TIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISR 250 (623)
Q Consensus 188 ~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~ 250 (623)
.|.|-|+. +|. . . .| ..-++|.|.+| .|.+++|.+...++.+.|++|+.+.+..
T Consensus 3 ~v~g~v~~---i~~-t-k--~g-~~~~~L~D~~~-~i~~~~f~~~~~~~~~~l~~g~~v~v~g 56 (78)
T cd04489 3 WVEGEISN---LKR-P-S--SG-HLYFTLKDEDA-SIRCVMWRSNARRLGFPLEEGMEVLVRG 56 (78)
T ss_pred EEEEEEec---CEE-C-C--Cc-EEEEEEEeCCe-EEEEEEEcchhhhCCCCCCCCCEEEEEE
Confidence 46667764 443 2 1 34 77789999998 9999999999999999999999998864
No 56
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=93.10 E-value=0.42 Score=40.16 Aligned_cols=61 Identities=21% Similarity=0.250 Sum_probs=47.5
Q ss_pred EEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeEEEecCCCccccCCceEEEEccCcEEE
Q 006973 211 VFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGTLRVANKQFKTVQNDYEMNLNENSEVE 278 (623)
Q Consensus 211 ~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~V~~a~~~~~~~~~~yei~f~~~T~I~ 278 (623)
-..++|.|.+| +|+|++..+..+.|.+.|..|.|..+.+..|-. +....+-|..+....+.
T Consensus 20 D~~v~l~DpTG-~i~~tiH~~v~~~y~~~l~~GavLlLk~V~Vf~------ps~~~~yLnIt~~Nlv~ 80 (86)
T PF15072_consen 20 DAFVVLKDPTG-EIRGTIHRKVLEEYGDELSPGAVLLLKDVTVFS------PSPRSHYLNITLNNLVR 80 (86)
T ss_pred CeEEEEECCCC-cEEEEEeHHHHhhcCCccccCEEEEEeeeeEEe------cCCCccEEEEehhHeee
Confidence 35688999999 999999999999999999999999999987743 33444555555444433
No 57
>cd04492 YhaM_OBF_like YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1). Both these proteins are 3'-to-5'exoribonucleases. YhaM requires Mn2+ or Co2+ for activity and is inactive in the presence of Mg2+. YhaM also has a Mn2+ dependent 3'-to-5'single-stranded DNA exonuclease activity. SaCBF is also a double-stranded DNA binding protein, binding specifically to cmp, the replication enhancer found in S. aureus plasmid pT181. Proteins in this group combine an N-terminal OB fold with a C-terminal HD domain. The HD domain is found in metal-dependent phosphohydrolases.
Probab=92.50 E-value=0.47 Score=38.81 Aligned_cols=43 Identities=19% Similarity=0.448 Sum_probs=35.9
Q ss_pred cEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeEEEe
Q 006973 210 CVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGTLRV 255 (623)
Q Consensus 210 ~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~V~~ 255 (623)
+.+.+.|.|.+| .|.+++|++.. .+...|++|.++.+. ++|..
T Consensus 19 ~~~~~~l~D~tg-~i~~~~f~~~~-~~~~~l~~g~~v~v~-G~v~~ 61 (83)
T cd04492 19 PYLALTLQDKTG-EIEAKLWDASE-EDEEKFKPGDIVHVK-GRVEE 61 (83)
T ss_pred cEEEEEEEcCCC-eEEEEEcCCCh-hhHhhCCCCCEEEEE-EEEEE
Confidence 478999999999 89999999654 457889999999998 66644
No 58
>KOG0851 consensus Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [Replication, recombination and repair]
Probab=90.83 E-value=0.42 Score=48.02 Aligned_cols=69 Identities=20% Similarity=0.290 Sum_probs=51.3
Q ss_pred CCCCeEeccccccccceecCCCCeeecCcCCCCccccceeEEEEEEEEeCCCcEEEEEehHhHHHHhCCCHHHH
Q 006973 476 PDQAMWYRACKTCNKKVTDALGSGYWCEGCQKNDEECSLRYIMVARVCDGSGEAWISIFNEEAERIIGCSADEL 549 (623)
Q Consensus 476 ~d~~~~Y~aC~~C~KKv~~~~~~~~~C~kC~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~~~ae~llG~sA~el 549 (623)
.+-.|+|..|+.|+| .......+.|+.|+....+...+|.+.....+.++. ..|...+..+.|.++..+
T Consensus 156 ~~~~~~~~~~~~~~~--~~~~~~~~~c~~~~~~~~~~~~~~~l~~~~~~~~~~---l~~~~~~~~~~G~~~~~~ 224 (246)
T KOG0851|consen 156 TDVDGFYLTFKICNK--SKFSKPVLWCEACGEQATDFGRKRSLGGGVIVIAPE---LLFWKIWRYFDGKNVRIV 224 (246)
T ss_pred CCcceEEEEEeeccc--ccccCceEEehhhcchHHhhhhheEecCCcEEccch---heeecccccccCCchhee
Confidence 344789999999998 111134589999998877776667887777777777 778888888888666544
No 59
>PTZ00401 aspartyl-tRNA synthetase; Provisional
Probab=90.68 E-value=2.1 Score=48.56 Aligned_cols=99 Identities=19% Similarity=0.252 Sum_probs=69.6
Q ss_pred cCeeeccccCCCC---CCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEec-----hHHHHHHhhcccC
Q 006973 172 RRVHPLVSLNPYQ---GNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFN-----EAARKFYDRFQLG 243 (623)
Q Consensus 172 ~~~~~I~~L~p~~---~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~-----~~~~kf~~~l~eG 243 (623)
+.++.|++|++.. ..-+|+|||.++ |. .|++.=++|.|.+| .|++++-. +..-+|...|..|
T Consensus 63 ~~~~~i~~l~~~~~~g~~V~v~Grv~~~---R~------~Gk~~Fl~LRd~~~-~iQ~v~~~~~~~~~~~~~~~~~l~~e 132 (550)
T PTZ00401 63 RTFIPVAVLSKPELVDKTVLIRARVSTT---RK------KGKMAFMVLRDGSD-SVQAMAAVEGDVPKEMIDFIGQIPTE 132 (550)
T ss_pred CceEEHHHCCccccCCCEEEEEEEEEEE---ec------CCCeEEEEEEeCCc-CEEEEEECCCccCHHHHHHHhcCCCC
Confidence 5689999998754 467899999763 32 34555578999999 89999841 3344566779999
Q ss_pred cEEEEeeeEEEecCCCccccCCceEEEEccCcEEEEc
Q 006973 244 KVYYISRGTLRVANKQFKTVQNDYEMNLNENSEVEEA 280 (623)
Q Consensus 244 ~vy~is~~~V~~a~~~~~~~~~~yei~f~~~T~I~~~ 280 (623)
+++.+.+.-+++..+.-+....++||....-..+.++
T Consensus 133 siV~V~G~v~~~~~~~~~~~~~~~El~v~~i~vls~a 169 (550)
T PTZ00401 133 SIVDVEATVCKVEQPITSTSHSDIELKVKKIHTVTES 169 (550)
T ss_pred CEEEEEEEEEecCccCCCCCCccEEEEeeEEEEEeCC
Confidence 9999998655543322234566799988776555554
No 60
>cd04485 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains two copies of this replicative polymerase, each of which copies a different DNA strand. This group also contains Bacillus subtilis DnaE. Replication in B. subtilis and Staphylococcus aureus requires two different type C polymerases, polC and DnaE, both of which are thought to be included in the DNA polymerase holoenzyme. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Probab=90.12 E-value=2.3 Score=34.40 Aligned_cols=64 Identities=20% Similarity=0.263 Sum_probs=41.6
Q ss_pred EEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEEeeeccc
Q 006973 312 IIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSPIVAIKSLKVGDFQG 387 (623)
Q Consensus 312 VIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~kV~~f~G 387 (623)
++|+|.++.. ..+|+ |+ ....++|.|.+| .+++++|.+....+... ...+.++.+. .++..|+|
T Consensus 2 i~g~v~~~~~---~~~k~-g~--~~~~~~l~D~tg-~~~~~~f~~~~~~~~~~----l~~g~~v~v~-G~v~~~~~ 65 (84)
T cd04485 2 VAGLVTSVRR---RRTKK-GK--RMAFVTLEDLTG-SIEVVVFPETYEKYRDL----LKEDALLLVE-GKVERRDG 65 (84)
T ss_pred EEEEEEEeEE---EEcCC-CC--EEEEEEEEeCCC-eEEEEECHHHHHHHHHH----hcCCCEEEEE-EEEEecCC
Confidence 5678876542 22342 44 357889999999 79999998664444332 3456677665 46777765
No 61
>PF14951 DUF4503: Domain of unknown function (DUF4503)
Probab=90.12 E-value=0.83 Score=47.73 Aligned_cols=85 Identities=13% Similarity=0.266 Sum_probs=67.7
Q ss_pred EEEEEEEEEEEeCCCCeEecccccccc-ceec--CCCCeeecCcCCCCccccceeEEEEEEEEeCC---CcEEEEEehHh
Q 006973 464 FFSIKAYISLIKPDQAMWYRACKTCNK-KVTD--ALGSGYWCEGCQKNDEECSLRYIMVARVCDGS---GEAWISIFNEE 537 (623)
Q Consensus 464 ~~~v~a~I~~i~~d~~~~Y~aC~~C~K-Kv~~--~~~~~~~C~kC~~~~~~~~~ry~l~~~i~D~T---g~~~~~~F~~~ 537 (623)
...|.|+|+.++.+-.+.++.|..|+. |+.. ++.|.|+|..|.+.+..|..|--|.+-+.=.+ .++.+-+..+.
T Consensus 256 iCsvqG~VvgVdE~TAfSWPvCd~CGn~rLe~~pe~rg~~~C~~Cs~~V~sP~~r~~LeVfl~Cps~p~ctvKVKL~q~s 335 (389)
T PF14951_consen 256 ICSVQGTVVGVDESTAFSWPVCDRCGNGRLEQSPEDRGAFSCGDCSRVVTSPVLRMHLEVFLDCPSRPQCTVKVKLLQRS 335 (389)
T ss_pred eEEEeeEEEEecCcccccCccccccCCccceeCccCCCceeccchhhhccCcceeeeEEEEEeCCCCCCceEEEEEhHHH
Confidence 477999999999988888999999974 5542 34688999999999999888888887766333 46788888888
Q ss_pred HHHHhCCCHHH
Q 006973 538 AERIIGCSADE 548 (623)
Q Consensus 538 ae~llG~sA~e 548 (623)
-..||.-.|.|
T Consensus 336 IsslL~~aa~e 346 (389)
T PF14951_consen 336 ISSLLMSAASE 346 (389)
T ss_pred HHHHHhhhhcc
Confidence 88888776644
No 62
>PRK02801 primosomal replication protein N; Provisional
Probab=89.73 E-value=1.7 Score=37.62 Aligned_cols=67 Identities=7% Similarity=0.037 Sum_probs=51.4
Q ss_pred CCCeEEEEEEEeeccccccccCCCcccEEEEEEEeC-----CCC------eEEEEEechHHHHHHhhcccCcEEEEeeeE
Q 006973 184 QGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDE-----DGT------QIQATMFNEAARKFYDRFQLGKVYYISRGT 252 (623)
Q Consensus 184 ~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~-----~G~------~I~at~~~~~~~kf~~~l~eG~vy~is~~~ 252 (623)
+++..+.||+++.-++|...+ | ..+.+|.|.=+ .|. .|.|++|++.++.+...+..|+.+.++++-
T Consensus 2 mN~v~L~Grl~~dpelr~Tp~--G-~~v~~f~La~~~~~~ea~~~r~~~~~i~~va~G~~Ae~~~~~l~kGs~v~V~G~L 78 (101)
T PRK02801 2 TNRLVLSGTVCRTPKRKVSPS--G-IPHCQFVLEHRSVQEEAGLHRQAWCRMPVIVSGNQFQAITQSITVGSKITVQGFI 78 (101)
T ss_pred ccEEEEEEEECcCcceEECCC--C-CeEEEEEEEEeCeEecCCCceeEEEEEEEEEEcHHHHHHHhhcCCCCEEEEEEEE
Confidence 467889999999999987643 3 24666655322 232 299999999999999999999999999764
Q ss_pred E
Q 006973 253 L 253 (623)
Q Consensus 253 V 253 (623)
-
T Consensus 79 ~ 79 (101)
T PRK02801 79 S 79 (101)
T ss_pred E
Confidence 4
No 63
>cd04495 BRCA2DBD_OB3 BRCA2DBD_OB3: A subfamily of OB folds corresponding to the third OB fold (OB3) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA).
Probab=89.71 E-value=2.8 Score=35.88 Aligned_cols=82 Identities=23% Similarity=0.293 Sum_probs=59.1
Q ss_pred EEEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEEeeecc--ce
Q 006973 311 DIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSPIVAIKSLKVGDFQ--GI 388 (623)
Q Consensus 311 DVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~kV~~f~--G~ 388 (623)
|++|+|++|+... +...-.+.|.|++-.-+-+.+|........+ |....+..|++.++..+-+. |.
T Consensus 1 D~VGvVvsV~~~~---------~g~~~~vYLaDe~~nll~vkfw~~l~~~~~E---Dvvk~~~lia~SNLQwR~~s~~~i 68 (100)
T cd04495 1 DTVGVVISVGKPI---------EGKFPAVYLADECLNLLCVKFWSSLEQYAYE---DVVKRRVLLAASNLQWRTESTSGV 68 (100)
T ss_pred CceEEEEEEcccc---------cCccceEEEecCCcCEEEEEEecchHHhhhh---hhcccceEEEEecceEeccccCCC
Confidence 7899999998653 1234578999999999999999976654433 34566788898877666443 44
Q ss_pred -eeecccceEEEEcCCh
Q 006973 389 -SLSTLGRSTVLVSPDL 404 (623)
Q Consensus 389 -~Ls~~~~S~i~iNPd~ 404 (623)
+|-.+..|.+-.||.-
T Consensus 69 Ptl~Age~t~FS~nPKe 85 (100)
T cd04495 69 PTLFAGEYSTFSANPKE 85 (100)
T ss_pred ceeeeecceeecCCccH
Confidence 4555677888888853
No 64
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=89.44 E-value=1.4 Score=42.13 Aligned_cols=64 Identities=17% Similarity=0.267 Sum_probs=49.4
Q ss_pred CCCeEEEEEEEeeccccccccCCCcccEEEEEEE------eCCC----CeEEEEEechHHHHHHhhcccCcEEEEee
Q 006973 184 QGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELT------DEDG----TQIQATMFNEAARKFYDRFQLGKVYYISR 250 (623)
Q Consensus 184 ~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~------D~~G----~~I~at~~~~~~~kf~~~l~eG~vy~is~ 250 (623)
++...|.|||++--++|...+ | ..+.+|.|+ ++.| +-|.|++|+..|+.+...|+.|+-+.|.+
T Consensus 2 mN~V~LiGrL~~DpelR~t~s--G-~~v~~fslAvnr~~~~~~ge~~tdwi~~v~wgk~Ae~~~~~l~KG~~V~VeG 75 (173)
T PRK06751 2 MNRVILVGRLTKDPDLRYTPN--G-VAVATFTLAVNRAFANQQGEREADFINCVIWRKQAENVANYLKKGSLAGVDG 75 (173)
T ss_pred ceEEEEEEEECCCCcEEECCC--C-CEEEEEEEEEccceecCCCCEEEEEEEEEEeCcHHHHHHHHcCCCCEEEEEE
Confidence 467889999999888886543 2 246666554 3334 36899999999999999999999999874
No 65
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=89.19 E-value=1.2 Score=46.83 Aligned_cols=68 Identities=12% Similarity=0.135 Sum_probs=48.7
Q ss_pred eccccCCCCCCeEEEEEEEeeccccccccCCCcc-cEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeee
Q 006973 176 PLVSLNPYQGNWTIKVRVTSKGNMRTYKNARGEG-CVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRG 251 (623)
Q Consensus 176 ~I~~L~p~~~~w~I~~RV~~K~~~r~~~~~~g~g-~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~ 251 (623)
.|++|.++. .......|..+. +|+-+ .| ..+.++|.|.+| +|.|.+|+.. +.....+++|+++.+.+-
T Consensus 4 ~i~~l~~g~-~v~~~~lv~~~~-~~~~k----nG~~yl~l~l~D~tG-~I~ak~W~~~-~~~~~~~~~g~vv~v~G~ 72 (314)
T PRK13480 4 GIEELEVGE-QVDHFLLIKSAT-KGVAS----NGKPFLTLILQDKSG-DIEAKLWDVS-PEDEATYVPETIVHVKGD 72 (314)
T ss_pred hHhhcCCCC-EeeEEEEEEEce-eeecC----CCCeEEEEEEEcCCc-EEEEEeCCCC-hhhHhhcCCCCEEEEEEE
Confidence 578888875 344444555442 34322 23 488999999999 8999999964 556778999999988753
No 66
>KOG4757 consensus Predicted telomere binding protein [General function prediction only]
Probab=88.86 E-value=1.2 Score=47.61 Aligned_cols=86 Identities=14% Similarity=0.299 Sum_probs=62.6
Q ss_pred cccccccccccccCCcceeEEEEEEEEeCCceEEEEccCCceeeEEEEEEEe--CCccEEEEEEechhhhhhhhHhhhcC
Q 006973 292 FNFVPIDELGRYVNGTELVDIIGVVQNVSPTMSIRRKSNNEMVPKRDITVAD--ETKRTVTVSLWNELATNVGQELLDNA 369 (623)
Q Consensus 292 ~~f~~i~di~~~~~~~~~vDVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D--~sg~~I~vtLWg~~A~~~~~~~~~~~ 369 (623)
++|+.+.+=.. -.+..|+++|+|++.+|... ++ |++ -...+.|+| .|+..+.|-|+....++++.- .
T Consensus 7 ~k~Iri~da~k--k~~tiVNl~GiVkef~pp~q--s~--g~D-~~~tv~IvDp~~ss~gLtv~lfSkt~edLP~I----k 75 (522)
T KOG4757|consen 7 LKLIRISDALK--KKNTIVNLIGIVKEFTPPRQ--SL--GKD-WVCTVYIVDPDYSSIGLTVHLFSKTGEDLPVI----K 75 (522)
T ss_pred hheeechHHHH--hcCcEEEEEEEEEeccChhh--cc--CCc-eEEEEEEeCCCCCCCCcEEEEecCchhhCccc----c
Confidence 34455554332 24689999999999998764 22 443 356889999 677789999999888877531 3
Q ss_pred CCCcEEEEEeEEeeeccce
Q 006973 370 DKSPIVAIKSLKVGDFQGI 388 (623)
Q Consensus 370 ~~~~Vv~i~~~kV~~f~G~ 388 (623)
..|.+|.+...|+.-|+.+
T Consensus 76 ~~GDiillhRiKiq~y~~r 94 (522)
T KOG4757|consen 76 QVGDIILLHRIKIQSYRDR 94 (522)
T ss_pred ccCcEEEEEEEEEEEhhhh
Confidence 4689999999999888754
No 67
>cd04478 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA dam
Probab=88.80 E-value=1.1 Score=38.15 Aligned_cols=57 Identities=14% Similarity=0.201 Sum_probs=40.9
Q ss_pred EEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHH---HHHhhcccCcEEEEeeeEEEe
Q 006973 188 TIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAAR---KFYDRFQLGKVYYISRGTLRV 255 (623)
Q Consensus 188 ~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~---kf~~~l~eG~vy~is~~~V~~ 255 (623)
++.|+|.++.. .+..+.+.|.|.+| .|.|.+|...-. ...+.+++|+++.+. |+++.
T Consensus 3 ~~vG~V~~~~~---------~~~~~~~tL~D~TG-~I~~~~W~~~~~~~~~~~~~~~~g~~v~v~-G~v~~ 62 (95)
T cd04478 3 TLVGVVRNVEE---------QSTNITYTIDDGTG-TIEVRQWLDDDNDDSSEVEPIEEGTYVRVF-GNLKS 62 (95)
T ss_pred EEEEEEEeeeE---------cccEEEEEEECCCC-cEEEEEeCCCCCcccccccccccCCEEEEE-EEEcc
Confidence 46677766432 23578999999999 899999986533 356779999988775 44433
No 68
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=88.69 E-value=0.3 Score=40.51 Aligned_cols=30 Identities=13% Similarity=0.352 Sum_probs=22.9
Q ss_pred eccccccccce-ecCCCCeeecCcCCCCccc
Q 006973 482 YRACKTCNKKV-TDALGSGYWCEGCQKNDEE 511 (623)
Q Consensus 482 Y~aC~~C~KKv-~~~~~~~~~C~kC~~~~~~ 511 (623)
-..||.|+++- .....|.|.|.+|+..+..
T Consensus 35 ~~~Cp~C~~~~VkR~a~GIW~C~kCg~~fAG 65 (89)
T COG1997 35 KHVCPFCGRTTVKRIATGIWKCRKCGAKFAG 65 (89)
T ss_pred CCcCCCCCCcceeeeccCeEEcCCCCCeecc
Confidence 45799999874 3345789999999987643
No 69
>PRK07275 single-stranded DNA-binding protein; Provisional
Probab=88.50 E-value=1.9 Score=40.83 Aligned_cols=64 Identities=16% Similarity=0.245 Sum_probs=50.2
Q ss_pred CCCeEEEEEEEeeccccccccCCCcccEEEEEEE------eCCC----CeEEEEEechHHHHHHhhcccCcEEEEee
Q 006973 184 QGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELT------DEDG----TQIQATMFNEAARKFYDRFQLGKVYYISR 250 (623)
Q Consensus 184 ~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~------D~~G----~~I~at~~~~~~~kf~~~l~eG~vy~is~ 250 (623)
++...|.||+++--++|...+ |. .+.+|.|+ +..| +-|+|++|+..|+.+...|+.|+-+.|.+
T Consensus 2 ~N~v~LiGrL~~DPElr~t~s--G~-~v~~ftlAv~r~~~~~~ge~~tdfi~vv~wgk~Ae~~~~~l~KG~~V~VeG 75 (162)
T PRK07275 2 INNVVLVGRMTRDAELRYTPS--NV-AVATFTLAVNRTFKSQNGEREADFINCVIWRQQAENLANWAKKGALIGVTG 75 (162)
T ss_pred eeEEEEEEEECCCCeEEECCC--CC-EEEEEEEEEcCceecCCCCEeeeEEEEEEEcHHHHHHHHHcCCCCEEEEEE
Confidence 357789999999888887653 21 46666664 4334 46999999999999999999999999874
No 70
>PF02760 HIN: HIN-200/IF120x domain; InterPro: IPR004021 This domain has no known function. It is found in one or two copies per protein, and is found associated with the PAAD/DAPIN domain IPR004020 from INTERPRO.; PDB: 3RN2_A 3RN5_C 2OQ0_A 3B6Y_A 3RLN_A 3RNU_A 3RLO_A.
Probab=88.23 E-value=19 Score=33.68 Aligned_cols=144 Identities=17% Similarity=0.196 Sum_probs=86.9
Q ss_pred EEEEEEeeccccccccCC-CcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeEEEecCCCccccCCce
Q 006973 189 IKVRVTSKGNMRTYKNAR-GEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGTLRVANKQFKTVQNDY 267 (623)
Q Consensus 189 I~~RV~~K~~~r~~~~~~-g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~V~~a~~~~~~~~~~y 267 (623)
..|.|+.-.+.-+|..+. |..+.|+-+++-++. -.++-+|+- .+.+.+..++++.||+..- +.-
T Consensus 5 ~~VmVLkaTepF~Ye~~e~gkk~MFHATVATet~-fF~VKVfn~---~LKeKF~~kkiI~IS~Y~~-----------~~g 69 (170)
T PF02760_consen 5 KTVMVLKATEPFEYESPEEGKKKMFHATVATETE-FFRVKVFNI---NLKEKFIPKKIIAISDYFG-----------RNG 69 (170)
T ss_dssp EEEEEEEE---EEEECTTTCEEEEEEEEEE-SS--EEEEEES-G---GGCCTCSTTSEEEEESEEE-----------ETT
T ss_pred eEEEEEeccCCeEEeCcccCcceEEEEEEecccc-EEEEEEecc---hhHhhcCCCcEEEEehhhc-----------ccc
Confidence 456777777777887665 556799999999988 899999996 5677889999999998632 223
Q ss_pred EEEEccCcEEEEccC-cCCCCCCCc----cccccccccccccCCcceeEEEEEEEEeCCceEEEEccCCceeeEEEEEEE
Q 006973 268 EMNLNENSEVEEAVN-ETAFIPQTK----FNFVPIDELGRYVNGTELVDIIGVVQNVSPTMSIRRKSNNEMVPKRDITVA 342 (623)
Q Consensus 268 ei~f~~~T~I~~~~d-~~~~iP~~~----~~f~~i~di~~~~~~~~~vDVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~ 342 (623)
-|..++.|.|.++.. ..-.+|... -.--+|++|.. ...+.+|+=+=.|... +.+ .......|.
T Consensus 70 fLEi~~aSsVse~~~dq~~eVp~~ii~~A~~TpKI~~L~~-q~~Gt~V~G~F~v~KK------~v~-----~~~~~YeI~ 137 (170)
T PF02760_consen 70 FLEINEASSVSEVNPDQKMEVPNSIIRRANETPKINDLQK-QASGTFVNGLFTVHKK------TVN-----KKNTIYEIQ 137 (170)
T ss_dssp EEEE-TTSEEEE--TTC-----HHHHHHHCS---HHHHTT-SSTTEEEEEEEEEEEE------EEE-----SSEEEEEEE
T ss_pred eEEEeeccEEEecCCCceEEccHHHHHhhccCCchhHHhc-CCCCcEEeEEEEEEEE------EEc-----CCeEEEEEe
Confidence 466678888888753 223455321 12246777765 3456676643333221 111 124467899
Q ss_pred eCCccEEEEEEechhhhh
Q 006973 343 DETKRTVTVSLWNELATN 360 (623)
Q Consensus 343 D~sg~~I~vtLWg~~A~~ 360 (623)
|++| .++|...|....-
T Consensus 138 DnTG-~MeVvv~G~~~ni 154 (170)
T PF02760_consen 138 DNTG-KMEVVVYGKWHNI 154 (170)
T ss_dssp ETTE-EEEEEEEGGGCGC
T ss_pred cCCC-cEEEEEeccCccc
Confidence 9999 8999999987653
No 71
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=88.08 E-value=1.5 Score=48.55 Aligned_cols=73 Identities=16% Similarity=0.190 Sum_probs=53.1
Q ss_pred eeccccC--CCCCCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeE
Q 006973 175 HPLVSLN--PYQGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGT 252 (623)
Q Consensus 175 ~~I~~L~--p~~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~ 252 (623)
.++++|. +.....+|-|.|+.... ...++|+ .+.-+.|-|.+| .|.+++|.+..+++.+.|++|.++.|.+ +
T Consensus 269 ~~~~~l~~~~~~~~v~vaG~I~~ik~---~~TKkG~-~maf~~leD~tG-~ie~vvFp~~y~~~~~~l~~~~~v~v~G-~ 342 (449)
T PRK07373 269 INLSELEEQKEKTKVSAVVMLNEVKK---IVTKKGD-PMAFLQLEDLSG-QSEAVVFPKSYERISELLQVDARLIIWG-K 342 (449)
T ss_pred cCHHHHhcccCCCEEEEEEEEEEeEe---cccCCCC-EEEEEEEEECCC-CEEEEECHHHHHHHHHHhccCCEEEEEE-E
Confidence 4566664 23345678888887443 3333333 345568899999 8999999999999999999999999964 4
Q ss_pred E
Q 006973 253 L 253 (623)
Q Consensus 253 V 253 (623)
|
T Consensus 343 v 343 (449)
T PRK07373 343 V 343 (449)
T ss_pred E
Confidence 4
No 72
>PF02765 POT1: Telomeric single stranded DNA binding POT1/CDC13; InterPro: IPR011564 This entry represents a domain that binds single stranded telomeric DNA and adopts an OB fold []. It includes the proteins POT1 and CDC13 which have been shown to regulate telomere length, replication and capping [, , ]. ; GO: 0003677 DNA binding, 0000723 telomere maintenance, 0000784 nuclear chromosome, telomeric region; PDB: 1S40_A 1KXL_A 1PH7_A 1PH9_A 1PH2_A 1OTC_A 1PHJ_A 1JB7_A 1PA6_A 1PH1_A ....
Probab=87.68 E-value=3.2 Score=38.46 Aligned_cols=86 Identities=14% Similarity=0.187 Sum_probs=61.3
Q ss_pred eeccccCC-CCCCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCC-------CeEEEEEechHHHHHHhhcccCcEE
Q 006973 175 HPLVSLNP-YQGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDG-------TQIQATMFNEAARKFYDRFQLGKVY 246 (623)
Q Consensus 175 ~~I~~L~p-~~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G-------~~I~at~~~~~~~kf~~~l~eG~vy 246 (623)
+||+++.. ....-.|.|-|+.....+... .+|..-.++|.|.|.+. ..|.+.+|....+.+-..-..|||+
T Consensus 2 ~~l~~~~~~~~~~vnvigVV~~~~~p~~~~-t~g~D~~~tl~i~D~S~~~~~~~~~~l~v~iF~~~~~~LP~v~~~GDii 80 (146)
T PF02765_consen 2 TPLSTAKEKFGKFVNVIGVVVDFSPPNPKK-TRGTDYMCTLTITDPSLNDSNQKLSGLTVNIFRPHKESLPNVKSVGDII 80 (146)
T ss_dssp CCGGGSCTTSSEEEEEEEEEEEEEEECTEE-ESSSCEEEEEEEEBTTCSCSSCCCCEEEEEEEESSHHHSCTTCSTTHEE
T ss_pred ccchhhhhcCCCEEEEEEEEEEccCCcceE-cCCCcEEEEEEEECCCCCccccccCCEEEEEECCCHHHCCCCCCCCCEE
Confidence 56664333 334677888888876662222 13333477899999985 5799999988888886655559999
Q ss_pred EEeeeEEEecCCCcc
Q 006973 247 YISRGTLRVANKQFK 261 (623)
Q Consensus 247 ~is~~~V~~a~~~~~ 261 (623)
.+.+++|+..+.+..
T Consensus 81 ~l~r~kv~~~~~~~~ 95 (146)
T PF02765_consen 81 RLRRVKVQSYNGKPQ 95 (146)
T ss_dssp EEEEEEEEEETTEEE
T ss_pred EEEEEEEEEECCEEE
Confidence 999999998876533
No 73
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=87.29 E-value=0.26 Score=30.54 Aligned_cols=21 Identities=24% Similarity=0.879 Sum_probs=17.1
Q ss_pred ccccccceecCCCCeeecCcCCCC
Q 006973 485 CKTCNKKVTDALGSGYWCEGCQKN 508 (623)
Q Consensus 485 C~~C~KKv~~~~~~~~~C~kC~~~ 508 (623)
||.|++++.+ +.-+|++|+..
T Consensus 2 Cp~CG~~~~~---~~~fC~~CG~~ 22 (23)
T PF13240_consen 2 CPNCGAEIED---DAKFCPNCGTP 22 (23)
T ss_pred CcccCCCCCC---cCcchhhhCCc
Confidence 9999999975 34579999964
No 74
>PF09104 BRCA-2_OB3: BRCA2, oligonucleotide/oligosaccharide-binding, domain 3; InterPro: IPR015188 This domain assumes an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB3 has a pronounced groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for strong ssDNA binding []. ; PDB: 1IYJ_D 1MIU_A.
Probab=87.00 E-value=3.3 Score=38.08 Aligned_cols=108 Identities=22% Similarity=0.266 Sum_probs=57.0
Q ss_pred ccccccccc--cCCcceeEEEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCC
Q 006973 295 VPIDELGRY--VNGTELVDIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKS 372 (623)
Q Consensus 295 ~~i~di~~~--~~~~~~vDVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~ 372 (623)
+.|++|.+- ...-.-||++|+|+.|. .+ .| ..--+.|.|....-+-+..|++...-- +.|.+..+
T Consensus 4 ~~f~~l~~p~f~pp~~EvD~VG~VvsV~------~~-~~---f~~~vYLsD~~~Nll~Ikfw~~l~~~~---~eDilk~~ 70 (143)
T PF09104_consen 4 THFSDLQDPDFQPPYGEVDTVGFVVSVS------KK-QG---FQPLVYLSDECHNLLAIKFWTGLNQYG---YEDILKPG 70 (143)
T ss_dssp --CGGGGSTT--TCCCEEEEEEEEEEEE---------TT---S--EEEEE-TTS-EEEEEESS----------SS---TT
T ss_pred echhhhcCcccCCCccccceEEEEEEEE------ec-CC---CceeEEeecCCccEEEEEeccCccccc---hhhhcCcc
Confidence 355666541 12334699999999991 11 12 223478899999899999999876322 23446789
Q ss_pred cEEEEEeEEee-ec-cce-eeecccceEEEEcCCh----HHHHHHHHHHH
Q 006973 373 PIVAIKSLKVG-DF-QGI-SLSTLGRSTVLVSPDL----PEAKKLKSWYE 415 (623)
Q Consensus 373 ~Vv~i~~~kV~-~f-~G~-~Ls~~~~S~i~iNPd~----pe~~~l~~w~~ 415 (623)
.+||+.++.-+ +. .|. .+-.+..|.+.-||.. .....|+.-+.
T Consensus 71 ~liA~SNLqwR~~s~s~iP~~~A~d~S~FS~nPK~~hLqe~~~~Lk~~i~ 120 (143)
T PF09104_consen 71 SLIAASNLQWRPESTSGIPTLFATDLSVFSANPKESHLQEAFNKLKNTIE 120 (143)
T ss_dssp -EEEEEEEEE-S-TTSSS-EEEEECCEEEESS-SSCCCHHHHHHHCHHHH
T ss_pred eEEEEeeeEeecccccCCCeeEeccceeeecCccHHHHHHHHHHHHHHhh
Confidence 99999876554 22 344 4556677888889853 34445554443
No 75
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=87.00 E-value=2.7 Score=37.77 Aligned_cols=64 Identities=17% Similarity=0.247 Sum_probs=50.0
Q ss_pred CCCeEEEEEEEeeccccccccCCCcccEEEEEEEe------CCCCeEEEEEechHHHHHHhhcccCcEEEEee
Q 006973 184 QGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTD------EDGTQIQATMFNEAARKFYDRFQLGKVYYISR 250 (623)
Q Consensus 184 ~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D------~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~ 250 (623)
.+...|.||+.+--++|...+ |. .+.+|.|+- +..+-+.+++|+..|+.+.+.|+.|+-+.+.+
T Consensus 3 ~N~v~LiGrL~~DPelr~t~~--G~-~v~~fslAv~~~~~~~~t~w~~v~~wg~~Ae~~~~~l~KG~~V~V~G 72 (121)
T PRK07459 3 LNSVTLVGRAGRDPEVRYFES--GS-VVCNLTLAVNRRSRDDEPDWFNLEIWGKTAQVAADYVKKGSLIGITG 72 (121)
T ss_pred ccEEEEEEEccCCCEEEEcCC--CC-EEEEEEEEecccccCCCceEEEEEEehHHHHHHHHHcCCCCEEEEEE
Confidence 356789999999877886543 21 466776653 23457999999999999999999999999974
No 76
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=86.61 E-value=3.2 Score=39.32 Aligned_cols=65 Identities=12% Similarity=0.205 Sum_probs=49.6
Q ss_pred CCCCeEEEEEEEeeccccccccCCCcccEEEEEEE------eCCCC------eEEEEEechHHHHHHhhcccCcEEEEee
Q 006973 183 YQGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELT------DEDGT------QIQATMFNEAARKFYDRFQLGKVYYISR 250 (623)
Q Consensus 183 ~~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~------D~~G~------~I~at~~~~~~~kf~~~l~eG~vy~is~ 250 (623)
..++..|.||+.+--++|...+ | ..+.+|.|+ |+.|. -+++++|+.+++.....|+.|+-++|.+
T Consensus 4 ~~Nkv~LiGrLg~DPelr~t~~--G-~~va~fsVA~~~~~k~~~G~~~e~t~w~~Vv~fgk~Ae~v~~~L~KGs~V~VeG 80 (164)
T PRK08763 4 GINKVILVGNLGNDPDIKYTQS--G-MTITRISLATTSVRKDREGNTQERTEWHRVKFFGKLGEIAGEYLRKGSQCYIEG 80 (164)
T ss_pred cceEEEEEEEecCCCeEEEcCC--C-CeEEEEEEEeccceecCCCCeeccceEEEEEEehHHHHHHHHhcCCCCEEEEEE
Confidence 3678999999999777776543 2 246566554 44452 3899999999999999999999999974
No 77
>PRK05813 single-stranded DNA-binding protein; Provisional
Probab=86.29 E-value=38 Score=33.75 Aligned_cols=166 Identities=13% Similarity=0.179 Sum_probs=95.0
Q ss_pred CCCeEEEEEEEeeccccccccCCCcccEEEEEE-----EeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeEEEecCC
Q 006973 184 QGNWTIKVRVTSKGNMRTYKNARGEGCVFNVEL-----TDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGTLRVANK 258 (623)
Q Consensus 184 ~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L-----~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~V~~a~~ 258 (623)
.++-.+.||+++--++|+-. .|++ +..|.| .|+ -+.|.+++|..+++... |..|+-+.+.+ +++..++
T Consensus 8 ~NkV~L~Grl~~d~e~~~~~--~G~~-~~~f~laV~R~s~~-~D~i~v~v~~rlae~~~--l~kG~~v~VeG-qlrsy~~ 80 (219)
T PRK05813 8 NNKVYLEGKVVSELEFSHEM--YGEG-FYNFKLEVPRLSDS-KDILPVTVSERLLAGMD--LKVGTLVIVEG-QLRSYNK 80 (219)
T ss_pred cCEEEEEEEEcCCceEEEEe--CCeE-EEEEEEEeeccCCC-ccEEEEEEEhhhhhhhc--ccCCCEEEEEE-EEEEecc
Confidence 45788999999988887632 3443 334433 233 35999999999998877 99999999874 4442221
Q ss_pred CccccCCceEEEEccCcEEEEccCcCCCCCCCccccccccccccccCCcceeEEEEEEEEeCCceEEEEccCCceeeEEE
Q 006973 259 QFKTVQNDYEMNLNENSEVEEAVNETAFIPQTKFNFVPIDELGRYVNGTELVDIIGVVQNVSPTMSIRRKSNNEMVPKRD 338 (623)
Q Consensus 259 ~~~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~~~f~~i~di~~~~~~~~~vDVIGvV~~v~~~~~i~~k~~g~~~~kr~ 338 (623)
. ....+.|.+.+-.. .|..+... .+ ...-..|-++|.+..--.+.. +. +|+. .-.
T Consensus 81 ~-~~G~~R~vl~V~a~-~i~~l~~~--------------~~----~~~~N~V~LiGrL~~DPelR~--t~-~G~~--va~ 135 (219)
T PRK05813 81 F-IDGKNRLILTVFAR-NIEYCDER--------------SD----IKNPNEIFLDGYICKEPVYRT--TP-FGRE--IAD 135 (219)
T ss_pred C-CCCcEEEEEEEEEE-EEEEccCC--------------Cc----cCCccEEEEEEEccCCCeEEE--CC-CCCE--EEE
Confidence 1 12344455443321 12222211 01 112236788898876433321 22 3553 344
Q ss_pred EEEEeCC----ccEEEEEEechhhhhhhhHhhhcCCCCcEEEEEe-EEeeecc
Q 006973 339 ITVADET----KRTVTVSLWNELATNVGQELLDNADKSPIVAIKS-LKVGDFQ 386 (623)
Q Consensus 339 i~l~D~s----g~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~-~kV~~f~ 386 (623)
|.|.=.. -.-|.|++||..|+.. .. ...|.-|++.| .+...|.
T Consensus 136 f~lAvnr~~~~td~i~~v~wg~~Ae~~-~~----l~KG~~V~V~GrL~sr~y~ 183 (219)
T PRK05813 136 LLLAVNRPYNKSDYIPCIAWGRNARFC-KT----LEVGDNIRVWGRVQSREYQ 183 (219)
T ss_pred EEEEEcCCCCCceEEEEEEEhHHhHHH-hh----CCCCCEEEEEEEEEecceE
Confidence 4444321 2379999999999754 22 45577776654 3444453
No 78
>cd04493 BRCA2DBD_OB1 BRCA2DBD_OB1: A subfamily of OB folds corresponding to the first OB fold (OB1) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA). BRCA2DBD OB1 binds DNA weakly.
Probab=86.06 E-value=0.5 Score=40.68 Aligned_cols=52 Identities=19% Similarity=0.252 Sum_probs=41.5
Q ss_pred eEEEeeeeecC----ceEEEEEeCcccceeeccccccccccccCccceeeEEEEcc
Q 006973 29 VVQVLDLKLTG----NRYMFNASDGKKRLKAILPSNLSSEVISGNIQNKGLIRLLD 80 (623)
Q Consensus 29 vlQvl~~k~~~----~ryr~~lSDG~~~~~~mlat~ln~~v~~~~l~~~siirl~~ 80 (623)
||=|..+...+ .-=.+.|+||=|.+++.|...|+.++++|.|..|.-++|..
T Consensus 6 VL~Vs~I~~~~~~~~~~~~lEltDGWYsi~a~lD~~L~~~l~~gkl~vGqKL~i~G 61 (100)
T cd04493 6 VLCVSGINSEERLSPHMPIIELTDGWYSIRAQLDPPLTNLVRKGKLRVGQKLRICG 61 (100)
T ss_pred EEEEEEEeeccCCCCcccEEEEecCeEEEEEEeCHHHHHHHHcCCeecccEEEEEC
Confidence 44555555443 23389999999999999999999999999999998888743
No 79
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=86.05 E-value=0.56 Score=29.38 Aligned_cols=23 Identities=17% Similarity=0.628 Sum_probs=17.8
Q ss_pred ccccccceecCC-CCeeecCcCCC
Q 006973 485 CKTCNKKVTDAL-GSGYWCEGCQK 507 (623)
Q Consensus 485 C~~C~KKv~~~~-~~~~~C~kC~~ 507 (623)
|..|++.+.... .-.|.|++|+.
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCcccCceEeCCCCCC
Confidence 778988887643 56799999984
No 80
>cd04320 AspRS_cyto_N AspRS_cyto_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae and human cytoplasmic aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis.
Probab=86.00 E-value=13 Score=31.97 Aligned_cols=83 Identities=20% Similarity=0.270 Sum_probs=52.5
Q ss_pred eEEEEEEEeeccccccccCCCcc-cEEEEEEEeCCCCeEEEEEechH------HHHHHhhcccCcEEEEeeeEEEecCCC
Q 006973 187 WTIKVRVTSKGNMRTYKNARGEG-CVFNVELTDEDGTQIQATMFNEA------ARKFYDRFQLGKVYYISRGTLRVANKQ 259 (623)
Q Consensus 187 w~I~~RV~~K~~~r~~~~~~g~g-~~f~~~L~D~~G~~I~at~~~~~------~~kf~~~l~eG~vy~is~~~V~~a~~~ 259 (623)
.+|+|||.++ |. .| ++.=++|.|.+| .|++.+-.+. .-++...|..|+++.+.+- +....+.
T Consensus 2 V~i~Gwv~~~---R~------~g~k~~Fi~LrD~sg-~iQ~v~~~~~~~~~~~~~~~~~~l~~es~V~V~G~-v~~~~~~ 70 (102)
T cd04320 2 VLIRARVHTS---RA------QGAKLAFLVLRQQGY-TIQGVLAASAEGVSKQMVKWAGSLSKESIVDVEGT-VKKPEEP 70 (102)
T ss_pred EEEEEEEEEe---ec------CCCceEEEEEecCCc-eEEEEEeCCcccCCHHHHHHHhcCCCccEEEEEEE-EECCCCc
Confidence 5788999763 33 23 444467899998 8999997432 2233456899999999985 3332221
Q ss_pred ccc-cCCceEEEEccCcEEEEc
Q 006973 260 FKT-VQNDYEMNLNENSEVEEA 280 (623)
Q Consensus 260 ~~~-~~~~yei~f~~~T~I~~~ 280 (623)
.+. ....|||....-..+.++
T Consensus 71 ~~~~~~~~~El~~~~i~il~~~ 92 (102)
T cd04320 71 IKSCTQQDVELHIEKIYVVSEA 92 (102)
T ss_pred ccCCCcCcEEEEEEEEEEEecC
Confidence 111 236799988765555544
No 81
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=85.86 E-value=5.9 Score=33.07 Aligned_cols=70 Identities=19% Similarity=0.302 Sum_probs=48.2
Q ss_pred EEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCc--cEEEEEEechhhhhhhhHhhhcCCCCcEEEE-EeEEeeeccce
Q 006973 312 IIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETK--RTVTVSLWNELATNVGQELLDNADKSPIVAI-KSLKVGDFQGI 388 (623)
Q Consensus 312 VIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg--~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i-~~~kV~~f~G~ 388 (623)
+-|.|..+-|..+-.++ +| ..||++.|..+.- ..|.+.+||+.+..+. ....|..|.+ -+++-.+|+|+
T Consensus 2 i~Gkii~~l~~~~g~s~-~G--w~Kre~Vlet~~qYP~~i~f~~~~dk~~~l~-----~~~~Gd~V~Vsf~i~~RE~~gr 73 (84)
T PF11325_consen 2 ITGKIIKVLPEQQGVSK-NG--WKKREFVLETEEQYPQKICFEFWGDKIDLLD-----NFQVGDEVKVSFNIEGREWNGR 73 (84)
T ss_pred cccEEEEEecCcccCcC-CC--cEEEEEEEeCCCcCCceEEEEEEcchhhhhc-----cCCCCCEEEEEEEeeccEecce
Confidence 34676555555544454 36 8999999985543 4899999999988742 2455666655 57777889887
Q ss_pred e
Q 006973 389 S 389 (623)
Q Consensus 389 ~ 389 (623)
.
T Consensus 74 ~ 74 (84)
T PF11325_consen 74 W 74 (84)
T ss_pred E
Confidence 4
No 82
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=85.78 E-value=3 Score=38.00 Aligned_cols=64 Identities=17% Similarity=0.234 Sum_probs=47.9
Q ss_pred CCCeEEEEEEEeeccccccccCCCcccEEEEEEE------eCCC----CeEEEEEechHHHHHHhhcccCcEEEEee
Q 006973 184 QGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELT------DEDG----TQIQATMFNEAARKFYDRFQLGKVYYISR 250 (623)
Q Consensus 184 ~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~------D~~G----~~I~at~~~~~~~kf~~~l~eG~vy~is~ 250 (623)
++...|.||+..--.+|...+ |. .+.+|.|+ |+.| +-+++++|+..++.+...|+.|+-+.+.+
T Consensus 2 mN~v~LiGrL~~dPelr~t~~--g~-~~~~fslAv~~~~k~~~g~~~t~w~~v~~fg~~Ae~v~~~l~KG~~V~V~G 75 (131)
T PRK07274 2 YNKVILIGRLTATPELVKTAN--DK-SVARVTLAVNRRFKNQNGEREADFINVVLWGKLAETLASYASKGSLISIDG 75 (131)
T ss_pred eeEEEEEEEccCCCeEEECCC--CC-EEEEEEEEEcCceecCCCCEEEEEEEEEEehHHHHHHHHHcCCCCEEEEEE
Confidence 467889999998877775533 21 45555554 3444 35889999999999999999999999874
No 83
>cd04489 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis.
Probab=85.31 E-value=3.5 Score=33.32 Aligned_cols=53 Identities=19% Similarity=0.313 Sum_probs=36.5
Q ss_pred EEEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEEEEE
Q 006973 311 DIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSPIVAIK 378 (623)
Q Consensus 311 DVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~ 378 (623)
=|.|.|.++.. +|+ | .--++|.|.++ .+++++|.+....+.. ....+.+|.+.
T Consensus 3 ~v~g~v~~i~~-----tk~-g----~~~~~L~D~~~-~i~~~~f~~~~~~~~~----~l~~g~~v~v~ 55 (78)
T cd04489 3 WVEGEISNLKR-----PSS-G----HLYFTLKDEDA-SIRCVMWRSNARRLGF----PLEEGMEVLVR 55 (78)
T ss_pred EEEEEEecCEE-----CCC-c----EEEEEEEeCCe-EEEEEEEcchhhhCCC----CCCCCCEEEEE
Confidence 36788877642 332 3 67899999998 8999999987666533 24556666554
No 84
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=85.00 E-value=5.4 Score=41.95 Aligned_cols=69 Identities=17% Similarity=0.320 Sum_probs=48.4
Q ss_pred cceeEEEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEEeeecc
Q 006973 307 TELVDIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSPIVAIKSLKVGDFQ 386 (623)
Q Consensus 307 ~~~vDVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~kV~~f~ 386 (623)
+..++.+..|++..-- .+| +|+ ....++|.|.|| +|+..+|+..-+.. .....+.||-++| +|.+|+
T Consensus 11 g~~v~~~~lv~~~~~~---~~k-nG~--~yl~l~l~D~tG-~I~ak~W~~~~~~~-----~~~~~g~vv~v~G-~v~~y~ 77 (314)
T PRK13480 11 GEQVDHFLLIKSATKG---VAS-NGK--PFLTLILQDKSG-DIEAKLWDVSPEDE-----ATYVPETIVHVKG-DIINYR 77 (314)
T ss_pred CCEeeEEEEEEEceee---ecC-CCC--eEEEEEEEcCCc-EEEEEeCCCChhhH-----hhcCCCCEEEEEE-EEEEEC
Confidence 5678888888876421 123 454 478999999999 89999998653322 1246677887664 567899
Q ss_pred ce
Q 006973 387 GI 388 (623)
Q Consensus 387 G~ 388 (623)
|.
T Consensus 78 g~ 79 (314)
T PRK13480 78 GR 79 (314)
T ss_pred Cc
Confidence 84
No 85
>cd04322 LysRS_N LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Included in this group are E. coli LysS and LysU. These two isoforms of LysRS are encoded by distinct genes which are differently regulated. Eukaryotes contain 2 sets of aaRSs, both of which encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein
Probab=84.60 E-value=15 Score=31.97 Aligned_cols=77 Identities=18% Similarity=0.262 Sum_probs=50.4
Q ss_pred eEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEech-----HHHHHHhhcccCcEEEEeeeEEEecCCCcc
Q 006973 187 WTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNE-----AARKFYDRFQLGKVYYISRGTLRVANKQFK 261 (623)
Q Consensus 187 w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~-----~~~kf~~~l~eG~vy~is~~~V~~a~~~~~ 261 (623)
-+|+|||.+ +|. .|++.=++|.|.+| .+++++... ...++...|..|+++.+.+. +.....
T Consensus 2 v~v~GwV~~---~R~------~g~~~Fi~lrd~~~-~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~G~-v~~~~~--- 67 (108)
T cd04322 2 VSVAGRIMS---KRG------SGKLSFADLQDESG-KIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTGT-PFKTKT--- 67 (108)
T ss_pred EEEEEEEEE---Eec------CCCeEEEEEEECCe-EEEEEEECCCCCHHHHHHHHhcCCCCCEEEEEEE-EEecCC---
Confidence 368888876 333 34555578999987 899988643 23445555999999999764 333321
Q ss_pred ccCCceEEEEccCcEEEEc
Q 006973 262 TVQNDYEMNLNENSEVEEA 280 (623)
Q Consensus 262 ~~~~~yei~f~~~T~I~~~ 280 (623)
..+||....-..+.++
T Consensus 68 ---g~~El~~~~~~ils~~ 83 (108)
T cd04322 68 ---GELSIFVKEFTLLSKS 83 (108)
T ss_pred ---CCEEEEeCEeEEeecc
Confidence 4588876655555544
No 86
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=84.54 E-value=0.5 Score=50.93 Aligned_cols=30 Identities=23% Similarity=0.649 Sum_probs=25.1
Q ss_pred eccccccccceecCCCCeeecCcCCCCccc
Q 006973 482 YRACKTCNKKVTDALGSGYWCEGCQKNDEE 511 (623)
Q Consensus 482 Y~aC~~C~KKv~~~~~~~~~C~kC~~~~~~ 511 (623)
-|-||.|++.+...+.+.|+|.||+...+.
T Consensus 350 ~p~Cp~Cg~~m~S~G~~g~rC~kCg~~~~~ 379 (421)
T COG1571 350 NPVCPRCGGRMKSAGRNGFRCKKCGTRARE 379 (421)
T ss_pred CCCCCccCCchhhcCCCCcccccccccCCc
Confidence 578999999998876668999999987644
No 87
>PLN02850 aspartate-tRNA ligase
Probab=84.53 E-value=7.3 Score=44.07 Aligned_cols=98 Identities=17% Similarity=0.165 Sum_probs=67.5
Q ss_pred cCeeeccccCCCC--CCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEech------HHHHHHhhcccC
Q 006973 172 RRVHPLVSLNPYQ--GNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNE------AARKFYDRFQLG 243 (623)
Q Consensus 172 ~~~~~I~~L~p~~--~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~------~~~kf~~~l~eG 243 (623)
+..+.|.+|++.. ...+|+|||.+ +| ..|++.=++|.|..| .|++++... ..-+|...|..|
T Consensus 67 ~~~~~i~~l~~~~~g~~V~v~Grv~~---~R------~~gk~~Fl~Lrd~~~-~iQ~v~~~~~~~~~~~~~~~~~~l~~e 136 (530)
T PLN02850 67 REWTDVSDLGEELAGSEVLIRGRVHT---IR------GKGKSAFLVLRQSGF-TVQCVVFVSEVTVSKGMVKYAKQLSRE 136 (530)
T ss_pred ceEeEhhhcchhhCCCEEEEEEEEEE---Ec------cCCCeEEEEEEeCCc-CEEEEEECCccccCHHHHHHHhCCCCC
Confidence 4679999998743 47889999976 33 244554467889877 899998643 344667789999
Q ss_pred cEEEEeeeEEEecCCCccccCCceEEEEccCcEEEEc
Q 006973 244 KVYYISRGTLRVANKQFKTVQNDYEMNLNENSEVEEA 280 (623)
Q Consensus 244 ~vy~is~~~V~~a~~~~~~~~~~yei~f~~~T~I~~~ 280 (623)
+++.+.+--+++.. .-+....++||....-..+.++
T Consensus 137 s~V~V~G~v~~~~~-~~~~~t~~~El~~~~i~vls~a 172 (530)
T PLN02850 137 SVVDVEGVVSVPKK-PVKGTTQQVEIQVRKIYCVSKA 172 (530)
T ss_pred CEEEEEEEEEccCc-CCCCCCccEEEEEeEEEEEeCC
Confidence 99999875444322 2222334899988776666554
No 88
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=84.52 E-value=3.9 Score=39.46 Aligned_cols=63 Identities=17% Similarity=0.258 Sum_probs=47.8
Q ss_pred CCeEEEEEEEeeccccccccCCCcccEEEEEEE------eCCC------CeEEEEEechHHHHHHhhcccCcEEEEee
Q 006973 185 GNWTIKVRVTSKGNMRTYKNARGEGCVFNVELT------DEDG------TQIQATMFNEAARKFYDRFQLGKVYYISR 250 (623)
Q Consensus 185 ~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~------D~~G------~~I~at~~~~~~~kf~~~l~eG~vy~is~ 250 (623)
+...|.||+++--++|...+ |. .+.+|.|+ +..| +-|.+++|+..|+.+...|+.|+-+.|.+
T Consensus 3 N~V~LvGrL~~DPElr~t~s--G~-~va~fslAv~r~~~~~~Ge~~e~t~fi~v~~fg~~AE~~~~~l~KG~~V~VeG 77 (182)
T PRK08486 3 NKVILVGNLTRDVELRYLPS--GS-AIATIGLATSRRFKKQDGEKGEEVCFIDIRLFGRTAEIANQYLSKGSKVLIEG 77 (182)
T ss_pred eEEEEEEEecCCCEEEECCC--CC-EEEEEEEEEecceecCCCCCcccceEEEEEEEhHHHHHHHHHcCCCCEEEEEE
Confidence 56789999999888887653 21 35555542 3333 36899999999999999999999999974
No 89
>PF02721 DUF223: Domain of unknown function DUF223; InterPro: IPR003871 The function of this domain has not been characterised, but may be involved in nucleic acid or nucleotide binding.
Probab=84.49 E-value=5.4 Score=33.96 Aligned_cols=61 Identities=15% Similarity=0.209 Sum_probs=44.9
Q ss_pred EEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEEeeeccceeeecccceEEEEcC
Q 006973 338 DITVADETKRTVTVSLWNELATNVGQELLDNADKSPIVAIKSLKVGDFQGISLSTLGRSTVLVSP 402 (623)
Q Consensus 338 ~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~kV~~f~G~~Ls~~~~S~i~iNP 402 (623)
++.|+|+.|..|..+++.+.+..|... ..+|.+..+....|..-.|..-.+...=+|.+.+
T Consensus 1 emvL~De~G~~I~A~I~~~~~~~f~~~----l~Eg~~y~i~~F~V~~~~~~yr~t~h~y~I~f~~ 61 (95)
T PF02721_consen 1 EMVLVDEKGDKIQATIPKELVDKFKDS----LKEGSWYTISNFTVSPNSGSYRPTDHKYKINFMP 61 (95)
T ss_pred CEEEEecCCCEEEEEECHHHHHHHHhh----cccCCEEEeEeEEEEeCCCceeccCCCEEEEECC
Confidence 478999999999999999999888654 4678999999999987655432232333444444
No 90
>cd04496 SSB_OBF SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date oligomerize to bring together four OB folds in their active state. The majority (e.g. Escherichia coli SSB) have a single OB fold per monomer, which oligomerize to form a homotetramer. However, Deinococcus and Thermus SSB proteins have two OB folds per monomer, which oligomerize to form a homodimer. Mycobacterium tuberculosis SSB varies in quaternary structure from E. coli SSB. It forms a dimer of dimers having a unique dimer interface, which lends the protein greater stability. Included in this group are OB folds similar to Escherichia coli PriB. E.coli PriB is homodimeric with each monomer having a single OB fold. It does not appear to form higher order oligomers. PriB is an essential protein for the replication restart
Probab=84.46 E-value=4.2 Score=34.43 Aligned_cols=61 Identities=18% Similarity=0.266 Sum_probs=42.2
Q ss_pred EEEEEEEeeccccccccCCCcccEEEEEE--E---------eCCCCeEEEEEechHHHHHHhhcccCcEEEEeee
Q 006973 188 TIKVRVTSKGNMRTYKNARGEGCVFNVEL--T---------DEDGTQIQATMFNEAARKFYDRFQLGKVYYISRG 251 (623)
Q Consensus 188 ~I~~RV~~K~~~r~~~~~~g~g~~f~~~L--~---------D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~ 251 (623)
+|.|||...-.+|...+ | ..+.+|.| - +..-.-+++++|++.++.+...++.|+.+.+.+.
T Consensus 2 ~l~G~l~~~p~~~~~~~--g-~~~~~~~v~~~~~~~~~~~~~~~~~~~~v~~~g~~a~~~~~~~~kG~~V~v~G~ 73 (100)
T cd04496 2 ILIGRLGKDPELRYTPS--G-TPVARFSLAVNRRRKDRDEEEEETDWIRVVAFGKLAENAAKYLKKGDLVYVEGR 73 (100)
T ss_pred EEEEEecCCCEEEECCC--C-CEEEEEEEEEcCceecccccccccEEEEEEEEhHHHHHHHHHhCCCCEEEEEEE
Confidence 46677777666655443 1 13333332 1 2344579999999999999999999999999864
No 91
>cd04484 polC_OBF polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding domain of Bacillus subtilis type C replicative DNA polymerase III alpha subunit (polC). Replication in B. subtilis and Staphylococcus aureus requires two different polymerases, polC and DnaE. The holoenzyme is thought to include the two different polymerases. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Probab=84.33 E-value=5.6 Score=33.00 Aligned_cols=58 Identities=16% Similarity=0.247 Sum_probs=42.9
Q ss_pred eEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEec-hHHHHHHhhcc-cCcEEEEee
Q 006973 187 WTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFN-EAARKFYDRFQ-LGKVYYISR 250 (623)
Q Consensus 187 w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~-~~~~kf~~~l~-eG~vy~is~ 250 (623)
-.|+|.|... +.|+.++ | ..++++.|.|.++ .|.|..|. +..+.+ ..|+ +|+|+.+.+
T Consensus 2 v~i~G~Vf~~-e~re~k~--g-~~i~~~~itD~t~-Si~~K~F~~~~~~~~-~~ik~~G~~v~v~G 61 (82)
T cd04484 2 VVVEGEVFDL-EIRELKS--G-RKILTFKVTDYTS-SITVKKFLRKDEKDK-EELKSKGDWVRVRG 61 (82)
T ss_pred EEEEEEEEEE-EEEEecC--C-CEEEEEEEEcCCC-CEEEEEeccCChhHH-hhcccCCCEEEEEE
Confidence 4688888765 4565553 2 3588999999998 89999998 344444 5589 999999874
No 92
>PF10341 TPP1: Shelterin complex subunit, TPP1/ACD; InterPro: IPR019437 EST3 is a component of the telomerase holoenzyme, involved in telomere replication. It has been demonstrated that Est3 dimerises and binds to DNA and RNA. Furthermore, Est3 stimulates the dissociation of RNA/DNA hetero-duplexes [, ]. ; GO: 0042162 telomeric DNA binding, 0007004 telomere maintenance via telomerase, 0032508 DNA duplex unwinding, 0000781 chromosome, telomeric region, 0005697 telomerase holoenzyme complex; PDB: 2I46_B.
Probab=83.79 E-value=1.6 Score=38.14 Aligned_cols=59 Identities=20% Similarity=0.251 Sum_probs=30.5
Q ss_pred CcceEEEeee-eec-CceEEEEEeCcccceeeccccccccccccCc------cceeeEEEEcceeee
Q 006973 26 PEIVVQVLDL-KLT-GNRYMFNASDGKKRLKAILPSNLSSEVISGN------IQNKGLIRLLDYALN 84 (623)
Q Consensus 26 ~~pvlQvl~~-k~~-~~ryr~~lSDG~~~~~~mlat~ln~~v~~~~------l~~~siirl~~y~~~ 84 (623)
...++||+.. +.. +....++||||+|++.|.|+.+.=...+... =-+|++|.|++|.+.
T Consensus 25 ~~q~~ri~~~~~~~~~~~i~a~lsDs~~~I~a~ft~eai~~fe~~~~~~~t~~t~g~li~I~~~~l~ 91 (106)
T PF10341_consen 25 PPQLLRILKFAKSTSDGAITALLSDSTHQILAIFTREAIENFEREEKKRITSSTKGCLILIKDFNLV 91 (106)
T ss_dssp EEEEEEEEE-S---TTS-EEEEEE-SS-EEEEEE-HHHHHTS--TTS-SSSTT-TTEEEEEEEEEEE
T ss_pred CCeEEEEEEEecCCCCCcEEEEEEcCCeEEEEEECHHHHHHHHHhccCcccccCCceEEEEEEEEEE
Confidence 3466777776 222 2788999999999999999633222211111 124666666666554
No 93
>cd04492 YhaM_OBF_like YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1). Both these proteins are 3'-to-5'exoribonucleases. YhaM requires Mn2+ or Co2+ for activity and is inactive in the presence of Mg2+. YhaM also has a Mn2+ dependent 3'-to-5'single-stranded DNA exonuclease activity. SaCBF is also a double-stranded DNA binding protein, binding specifically to cmp, the replication enhancer found in S. aureus plasmid pT181. Proteins in this group combine an N-terminal OB fold with a C-terminal HD domain. The HD domain is found in metal-dependent phosphohydrolases.
Probab=83.55 E-value=5.7 Score=32.21 Aligned_cols=62 Identities=19% Similarity=0.379 Sum_probs=38.9
Q ss_pred EEEEEEeCCceEEEEccCCceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEEeeeccc
Q 006973 313 IGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSPIVAIKSLKVGDFQG 387 (623)
Q Consensus 313 IGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~kV~~f~G 387 (623)
+.+|.++.. ..+|+ |+ ....++|.|.+| .+++++|++.... ......+.++.+. ++|..|+|
T Consensus 3 ~~~v~~~~~---~~tk~-g~--~~~~~~l~D~tg-~i~~~~f~~~~~~-----~~~l~~g~~v~v~-G~v~~~~~ 64 (83)
T cd04492 3 FFLIKSKEL---RTAKN-GK--PYLALTLQDKTG-EIEAKLWDASEED-----EEKFKPGDIVHVK-GRVEEYRG 64 (83)
T ss_pred EEEEEEeee---ecccC-CC--cEEEEEEEcCCC-eEEEEEcCCChhh-----HhhCCCCCEEEEE-EEEEEeCC
Confidence 445555532 22332 43 367899999999 7999999865422 1224556666666 66776765
No 94
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=83.51 E-value=6.6 Score=37.99 Aligned_cols=64 Identities=14% Similarity=0.251 Sum_probs=47.1
Q ss_pred CCCeEEEEEEEeeccccccccCCCcccEEEEEEEe--------------CCCCeEEEEEechHHHHHHhhcccCcEEEEe
Q 006973 184 QGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTD--------------EDGTQIQATMFNEAARKFYDRFQLGKVYYIS 249 (623)
Q Consensus 184 ~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D--------------~~G~~I~at~~~~~~~kf~~~l~eG~vy~is 249 (623)
.+..+|.+|+++--++|...+ | ..+.+|.|+- .+-.-|.|++|+.+++.+...|+.|+-+.+.
T Consensus 4 ~~~VtLiGrL~~DPElR~t~s--G-~~va~FrVAv~~r~~~~~~g~~~d~~t~fi~V~~Wg~~Ae~va~~L~KGd~V~V~ 80 (186)
T PRK07772 4 DTTITVVGNLTADPELRFTPS--G-AAVANFTVASTPRTFDRQTNEWKDGEALFLRCSIWRQAAENVAESLTKGMRVIVT 80 (186)
T ss_pred cCEEEEEEEeCCCCeEEEcCC--C-CEEEEEEEEecCcceecCCCcEeccCceEEEEEEecHHHHHHHHhcCCCCEEEEE
Confidence 456788899988888876543 2 1355555541 1223679999999999999999999999987
Q ss_pred e
Q 006973 250 R 250 (623)
Q Consensus 250 ~ 250 (623)
.
T Consensus 81 G 81 (186)
T PRK07772 81 G 81 (186)
T ss_pred E
Confidence 4
No 95
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=83.43 E-value=4.9 Score=37.45 Aligned_cols=65 Identities=14% Similarity=0.264 Sum_probs=50.4
Q ss_pred CCCeEEEEEEEeeccccccccCCCc---ccEEEEEEE------eCCC-------CeEEEEEechHHHHHHhhcccCcEEE
Q 006973 184 QGNWTIKVRVTSKGNMRTYKNARGE---GCVFNVELT------DEDG-------TQIQATMFNEAARKFYDRFQLGKVYY 247 (623)
Q Consensus 184 ~~~w~I~~RV~~K~~~r~~~~~~g~---g~~f~~~L~------D~~G-------~~I~at~~~~~~~kf~~~l~eG~vy~ 247 (623)
++.+.|.||+.+--++|.+.+ |. -.+.+|.|+ +..| +-+.+++|+..++.+...|+.|+-+.
T Consensus 2 ~N~V~LiGrLg~DPElr~t~~--G~~~~~~va~fslA~~r~~~~~~Ge~~~~~t~w~~V~~wg~~Ae~v~~~l~KG~~V~ 79 (148)
T PRK08182 2 STHFVGEGNIGSAPEYREFPN--GNDEPRRLLRLNVYFDNPVPTKDGEYEDRGGFWAPVELWHRDAEHWARLYQKGMRVL 79 (148)
T ss_pred ccEEEEEEECCCCCeEEECCC--CCeeeeeEEEEEEEecCceECCCCCEEecCcEEEEEEEEhHHHHHHHHhcCCCCEEE
Confidence 467889999999888887654 32 127788775 3334 24899999999999999999999999
Q ss_pred Eee
Q 006973 248 ISR 250 (623)
Q Consensus 248 is~ 250 (623)
+.+
T Consensus 80 V~G 82 (148)
T PRK08182 80 VEG 82 (148)
T ss_pred EEE
Confidence 985
No 96
>cd04100 Asp_Lys_Asn_RS_N Asp_Lys_Asn_RS_N: N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases (AspRS, AsnRS, and LysRS). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Included in this group are archeal and archeal-like A
Probab=83.33 E-value=11 Score=31.08 Aligned_cols=74 Identities=16% Similarity=0.226 Sum_probs=46.8
Q ss_pred eEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHH---HHHhhcccCcEEEEeeeEEEecCCCcccc
Q 006973 187 WTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAAR---KFYDRFQLGKVYYISRGTLRVANKQFKTV 263 (623)
Q Consensus 187 w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~---kf~~~l~eG~vy~is~~~V~~a~~~~~~~ 263 (623)
-+|+|||.+ +|. .|++.=++|.|.+| .+++.+-.+..+ ++...|..|+++.+.+.-.....+. ..
T Consensus 2 V~i~Gwv~~---~R~------~g~~~Fi~Lrd~~~-~iQ~v~~~~~~~~~~~~~~~l~~~s~V~v~G~~~~~~~~~--~~ 69 (85)
T cd04100 2 VTLAGWVHS---RRD------HGGLIFIDLRDGSG-IVQVVVNKEELGEFFEEAEKLRTESVVGVTGTVVKRPEGN--LA 69 (85)
T ss_pred EEEEEEEeh---hcc------CCCEEEEEEEeCCe-eEEEEEECCcChHHHHHHhCCCCCCEEEEEeEEEECCCCC--CC
Confidence 367888865 332 34554467899988 899988754322 3445699999999987543322111 23
Q ss_pred CCceEEEEc
Q 006973 264 QNDYEMNLN 272 (623)
Q Consensus 264 ~~~yei~f~ 272 (623)
..++||..+
T Consensus 70 ~~~~El~~~ 78 (85)
T cd04100 70 TGEIELQAE 78 (85)
T ss_pred CCCEEEEEe
Confidence 466888654
No 97
>cd04478 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA dam
Probab=83.22 E-value=8.2 Score=32.58 Aligned_cols=75 Identities=11% Similarity=0.073 Sum_probs=53.2
Q ss_pred EEEeeeeecCceEEEEEeCcccceeeccccccccc--cccCccceeeEEEEcceeeeccCCCceEEEEEEeeeeeccccc
Q 006973 30 VQVLDLKLTGNRYMFNASDGKKRLKAILPSNLSSE--VISGNIQNKGLIRLLDYALNEIPTKSEKYLIVTKCEVVSPALE 107 (623)
Q Consensus 30 lQvl~~k~~~~ryr~~lSDG~~~~~~mlat~ln~~--v~~~~l~~~siirl~~y~~~~~~~~~~~vlii~~lev~~~~~~ 107 (623)
=.|.+++..+.+++++|.||+..+.+.+|..-+.. -....++.|++|++..-.-.. ++ ++-|.+..+..+....+
T Consensus 6 G~V~~~~~~~~~~~~tL~D~TG~I~~~~W~~~~~~~~~~~~~~~~g~~v~v~G~v~~~-~g--~~ql~i~~i~~v~d~ne 82 (95)
T cd04478 6 GVVRNVEEQSTNITYTIDDGTGTIEVRQWLDDDNDDSSEVEPIEEGTYVRVFGNLKSF-QG--KKSIMAFSIRPVTDFNE 82 (95)
T ss_pred EEEEeeeEcccEEEEEEECCCCcEEEEEeCCCCCcccccccccccCCEEEEEEEEccc-CC--eeEEEEEEEEEeCCccH
Confidence 34556665567889999999999999998655431 124468999999998776543 33 57777777877765543
No 98
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=83.20 E-value=5.1 Score=35.31 Aligned_cols=64 Identities=16% Similarity=0.145 Sum_probs=48.2
Q ss_pred CCCeEEEEEEEeeccccccccCCCcccEEEEEEEeC------CC----CeEEEEEechHHHHHHhhcccCcEEEEee
Q 006973 184 QGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDE------DG----TQIQATMFNEAARKFYDRFQLGKVYYISR 250 (623)
Q Consensus 184 ~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~------~G----~~I~at~~~~~~~kf~~~l~eG~vy~is~ 250 (623)
++...|.||+.+--++|...+ | ..+.+|.|+-. .| +-+.+++|+..|+.+...++.|+-+.+.+
T Consensus 2 mN~v~liGrl~~dPelr~t~~--G-~~~~~f~lAv~~~~~~~~g~~~t~~~~v~~wg~~Ae~~~~~l~KG~~V~V~G 75 (112)
T PRK06752 2 MNRVVLIGRLTKEPELYYTKQ--G-VAYARVCVAVNRGFRNSLGEQQVDFINCVVWRKSAENVTEYCTKGSLVGITG 75 (112)
T ss_pred ceEEEEEEECcCCCEEEECCC--C-CEEEEEEEEECCCeEcCCCCEEEEEEEEEEehHHHHHHHHhcCCCCEEEEEE
Confidence 356788999998877776543 2 24666666532 23 45889999999999999999999999874
No 99
>COG5235 RFA2 Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair]
Probab=82.92 E-value=5.4 Score=38.69 Aligned_cols=71 Identities=23% Similarity=0.360 Sum_probs=42.9
Q ss_pred eeEEEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEEeeeccce
Q 006973 309 LVDIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSPIVAIKSLKVGDFQGI 388 (623)
Q Consensus 309 ~vDVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~kV~~f~G~ 388 (623)
.|-++|+|.++. ...+ -.-+.|.|.+| +|+|+.|-..+.+..+. .+ ..++..|-+ +.-++.|+|+
T Consensus 68 ~V~fVGvvrni~------~~tt-----n~~~~iEDGTG-~Ievr~W~~~~~~~e~~-~d-~~~~~yvkV-~G~lk~F~GK 132 (258)
T COG5235 68 NVQFVGVVRNIK------TSTT-----NSMFVIEDGTG-SIEVRFWPGNSYEEEQC-KD-LEEQNYVKV-NGSLKTFNGK 132 (258)
T ss_pred eEEEEEEEEeee------eccc-----ceEEEEecCCc-eEEEEecCCCchHHHhc-cc-cccccEEEE-ecceeeeCCe
Confidence 355666666553 2222 34578999999 99999998876654321 11 123444443 3456789995
Q ss_pred -eeeccc
Q 006973 389 -SLSTLG 394 (623)
Q Consensus 389 -~Ls~~~ 394 (623)
+++...
T Consensus 133 ~~I~~~~ 139 (258)
T COG5235 133 RSISASH 139 (258)
T ss_pred eEEehhh
Confidence 665433
No 100
>KOG3056 consensus Protein required for S-phase initiation or completion [Cell cycle control, cell division, chromosome partitioning]
Probab=82.92 E-value=7.2 Score=43.39 Aligned_cols=102 Identities=12% Similarity=0.279 Sum_probs=69.8
Q ss_pred Ceeecc----ccCCC---CCCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcE
Q 006973 173 RVHPLV----SLNPY---QGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKV 245 (623)
Q Consensus 173 ~~~~I~----~L~p~---~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~v 245 (623)
..++|+ .|-+. ..+|.+.|-|+.|+.++.-.+.+ .-.++.+.-+++. ..|.+-+|+++..+++. ++.|.|
T Consensus 167 k~i~ls~~~~~l~r~~kf~~~Wvt~GvI~~K~~~K~t~~G~-~y~iwkL~dLk~~-q~vslfLFG~a~k~~wk-~k~GtV 243 (578)
T KOG3056|consen 167 KLIRLSGKLFNLIRGPKFEENWVTMGVIVEKSDPKFTSNGN-PYSIWKLTDLKDH-QTVSLFLFGKAHKRYWK-IKLGTV 243 (578)
T ss_pred cceeehhhhhhcccCcccccCeEEEEEEeecCCcccccCCC-ceEEEEeeecCcc-ceeEEEEecHHHHHHhh-hccCcE
Confidence 446666 44433 34999999999999998765422 2234455433434 58999999998888776 899999
Q ss_pred EEEeeeEEEecCCCccccCCceEEEEccCcEEEEc
Q 006973 246 YYISRGTLRVANKQFKTVQNDYEMNLNENSEVEEA 280 (623)
Q Consensus 246 y~is~~~V~~a~~~~~~~~~~yei~f~~~T~I~~~ 280 (623)
+-|-|+.|.+-+.. ..-.|.|.++..-.|.++
T Consensus 244 ialLNp~v~k~~~g---s~~~f~LsIds~~~ilei 275 (578)
T KOG3056|consen 244 IALLNPEVLKDRPG---SRKSFSLSIDSSKKILEI 275 (578)
T ss_pred EEEeCccccCCCCC---CcceEEEEecCccceEEe
Confidence 99999988665431 114577777766445444
No 101
>cd04480 RPA1_DBD_A_like RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.
Probab=82.60 E-value=6.8 Score=32.59 Aligned_cols=51 Identities=14% Similarity=0.181 Sum_probs=42.3
Q ss_pred eeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEEeeeccc
Q 006973 333 MVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSPIVAIKSLKVGDFQG 387 (623)
Q Consensus 333 ~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~kV~~f~G 387 (623)
.....++.|.|+.|..|.++.+.+.+..|... ..+|.+..+.+.+|..-.+
T Consensus 17 ~~~~~~miL~De~G~~I~a~i~~~~~~~f~~~----L~eg~vy~is~f~v~~~~~ 67 (86)
T cd04480 17 SGESLEMVLVDEKGNRIHATIPKRLAAKFRPL----LKEGKWYTISNFEVAPNTG 67 (86)
T ss_pred CCcEEEEEEEcCCCCEEEEEECHHHHHhhhhh----ceeCCEEEEeeEEEEcCCC
Confidence 45667999999999999999999999988654 4568899898888876554
No 102
>PRK05733 single-stranded DNA-binding protein; Provisional
Probab=82.54 E-value=5.9 Score=37.86 Aligned_cols=65 Identities=18% Similarity=0.227 Sum_probs=48.8
Q ss_pred CCCCeEEEEEEEeeccccccccCCCcccEEEEEEE------eC-CC------CeEEEEEechHHHHHHhhcccCcEEEEe
Q 006973 183 YQGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELT------DE-DG------TQIQATMFNEAARKFYDRFQLGKVYYIS 249 (623)
Q Consensus 183 ~~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~------D~-~G------~~I~at~~~~~~~kf~~~l~eG~vy~is 249 (623)
.++..+|.|||.+--++|.+.+.. .+.+|.|+ |. .| +-+.+++|+..++.+.+.|+.|+.++|.
T Consensus 4 ~mNkV~LiGrlg~DPElr~t~nG~---~va~fsVAv~~~~k~~~~Ge~~e~T~w~~Vv~fgk~Ae~v~~~l~KGs~V~Ve 80 (172)
T PRK05733 4 GVNKVILVGTCGQDPEVRYLPNGN---AVTNLSLATSEQWTDKQSGQKVERTEWHRVSLFGKVAEIAGEYLRKGSQVYIE 80 (172)
T ss_pred cceEEEEEEEecCCCEEEECCCCC---EEEEEEEEEcCccccCCCCcccccceEEEEEEehHHHHHHHHHhCCCCEEEEE
Confidence 367788999999977788765422 45555543 22 23 2399999999999999999999999997
Q ss_pred e
Q 006973 250 R 250 (623)
Q Consensus 250 ~ 250 (623)
+
T Consensus 81 G 81 (172)
T PRK05733 81 G 81 (172)
T ss_pred E
Confidence 4
No 103
>PRK13732 single-stranded DNA-binding protein; Provisional
Probab=82.34 E-value=5.9 Score=37.96 Aligned_cols=65 Identities=20% Similarity=0.268 Sum_probs=50.4
Q ss_pred CCCCeEEEEEEEeeccccccccCCCcccEEEEEEEeC-------CC------CeEEEEEechHHHHHHhhcccCcEEEEe
Q 006973 183 YQGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDE-------DG------TQIQATMFNEAARKFYDRFQLGKVYYIS 249 (623)
Q Consensus 183 ~~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~-------~G------~~I~at~~~~~~~kf~~~l~eG~vy~is 249 (623)
..+..+|.||+.+--++|...+ | ..+.+|.|+-. .| +-+++++|+..++.+...|+.|+.+++.
T Consensus 5 ~mN~V~LiGrLg~DPElR~t~n--G-~~va~fslAvn~~~kd~~~Ge~~e~t~w~~Vv~wgk~Ae~v~~~L~KG~~V~Ve 81 (175)
T PRK13732 5 GINKVILVGRLGKDPEVRYIPN--G-GAVANLQVATSESWRDKQTGEMREQTEWHRVVLFGKLAEVAGEYLRKGAQVYIE 81 (175)
T ss_pred CceEEEEEEEecCCCEEEEcCC--C-CEEEEEEEEEcCccccCCCCceecceeEEEEEEecHHHHHHHHhcCCCCEEEEE
Confidence 3578999999999888887654 2 25666666422 23 2478999999999999999999999997
Q ss_pred e
Q 006973 250 R 250 (623)
Q Consensus 250 ~ 250 (623)
+
T Consensus 82 G 82 (175)
T PRK13732 82 G 82 (175)
T ss_pred E
Confidence 5
No 104
>PRK06293 single-stranded DNA-binding protein; Provisional
Probab=81.90 E-value=5.4 Score=37.67 Aligned_cols=64 Identities=13% Similarity=0.075 Sum_probs=48.9
Q ss_pred CCCeEEEEEEEeeccccccccCCCcccEEEEEEEeC-------CCCeEEEEEechHHHHHHhhcccCcEEEEee
Q 006973 184 QGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDE-------DGTQIQATMFNEAARKFYDRFQLGKVYYISR 250 (623)
Q Consensus 184 ~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~-------~G~~I~at~~~~~~~kf~~~l~eG~vy~is~ 250 (623)
++..+|.||+.+--++|...+ | ..+.+|.|+=. +-+-|+|++|+..++.....|+.|+-+.+.+
T Consensus 1 MN~V~LiGrLg~DPElR~t~s--G-~~v~~FsLAvn~~~~~~~~T~wi~v~awg~~Ae~v~~yL~KG~~V~VeG 71 (161)
T PRK06293 1 MMFGYIVGRLGADPEERMTSK--G-KRVVVLRLGVKSRVGSKDETVWCRCNIWGNRYDKMLPYLKKGSGVIVAG 71 (161)
T ss_pred CeEEEEEEEecCCCeEEEcCC--C-CEEEEEEEEEeCCCCCccceEEEEEEEEhHHHHHHHHhCCCCCEEEEEE
Confidence 356789999999877876543 2 24667766522 2236999999999999999999999999975
No 105
>cd04483 hOBFC1_like hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1). Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The OB fold domain of RPA2 has dual roles in ssDNA binding and trimerization.
Probab=81.78 E-value=3.5 Score=35.11 Aligned_cols=44 Identities=14% Similarity=0.408 Sum_probs=33.8
Q ss_pred cEEEEEEEeCCCCeEEEEEechHH--H------------------HHHhhcccCcEEEEeeeEEEe
Q 006973 210 CVFNVELTDEDGTQIQATMFNEAA--R------------------KFYDRFQLGKVYYISRGTLRV 255 (623)
Q Consensus 210 ~~f~~~L~D~~G~~I~at~~~~~~--~------------------kf~~~l~eG~vy~is~~~V~~ 255 (623)
..+.+.|-|.+| .|.|.+|.... + +..+.|++|+++.+. +.++.
T Consensus 14 ~~~~~tLdDgTG-~Ie~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~G~vvrV~-G~i~~ 77 (92)
T cd04483 14 TFYSFGVDDGTG-VVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVLEIGDLLRVR-GSIRT 77 (92)
T ss_pred CeEEEEEecCCc-eEEEEEEcCcCcccccccccccccccccccccccccccCCCCEEEEE-EEEec
Confidence 468899999999 89999998542 1 466679999998887 44443
No 106
>cd04323 AsnRS_cyto_like_N AsnRS_cyto_like_N: N-terminal, anticodon recognition domain of the type found in human and Saccharomyces cerevisiae cytoplasmic asparaginyl-tRNA synthetase (AsnRS), in Brugia malayai AsnRs and, in various putative bacterial AsnRSs. This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, whereas the other exclusively with
Probab=81.78 E-value=11 Score=31.17 Aligned_cols=74 Identities=11% Similarity=0.118 Sum_probs=47.0
Q ss_pred eEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHH--HHHhhcccCcEEEEeeeEEEecCCCccccC
Q 006973 187 WTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAAR--KFYDRFQLGKVYYISRGTLRVANKQFKTVQ 264 (623)
Q Consensus 187 w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~--kf~~~l~eG~vy~is~~~V~~a~~~~~~~~ 264 (623)
-+|+|||.++ |. .|++.=++|.|.+| .+++.+-.+... ++...|..|+++.+.+ .+....... ...
T Consensus 2 V~v~Gwv~~~---R~------~g~~~Fi~LrD~~~-~iQ~v~~~~~~~~~~~~~~l~~es~V~V~G-~v~~~~~~~-~~~ 69 (84)
T cd04323 2 VKVFGWVHRL---RS------QKKLMFLVLRDGTG-FLQCVLSKKLVTEFYDAKSLTQESSVEVTG-EVKEDPRAK-QAP 69 (84)
T ss_pred EEEEEEEEEE---ec------CCCcEEEEEEcCCe-EEEEEEcCCcchhHHHHhcCCCcCEEEEEE-EEEECCccc-CCC
Confidence 3678888653 32 23454467899988 799988654322 2334588999999976 454443222 335
Q ss_pred CceEEEEc
Q 006973 265 NDYEMNLN 272 (623)
Q Consensus 265 ~~yei~f~ 272 (623)
.++||...
T Consensus 70 ~~~Ei~~~ 77 (84)
T cd04323 70 GGYELQVD 77 (84)
T ss_pred CCEEEEEE
Confidence 67888764
No 107
>PRK09010 single-stranded DNA-binding protein; Provisional
Probab=81.14 E-value=5.9 Score=38.04 Aligned_cols=64 Identities=22% Similarity=0.316 Sum_probs=49.5
Q ss_pred CCCeEEEEEEEeeccccccccCCCcccEEEEEEE------eC-CC------CeEEEEEechHHHHHHhhcccCcEEEEee
Q 006973 184 QGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELT------DE-DG------TQIQATMFNEAARKFYDRFQLGKVYYISR 250 (623)
Q Consensus 184 ~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~------D~-~G------~~I~at~~~~~~~kf~~~l~eG~vy~is~ 250 (623)
.+..+|.+|+.+--++|.+.+ | ..+.+|.|+ |. .| +-+++++|+..++.+...|+.|+-+++..
T Consensus 6 ~N~V~LiGrLg~DPelR~t~n--G-~~v~~fsVAvn~~~kd~~~Ge~~e~t~w~~V~~fgk~Ae~~~~~L~KGs~V~VeG 82 (177)
T PRK09010 6 VNKVILVGNLGQDPEVRYMPN--G-GAVANITLATSESWRDKQTGEMKEQTEWHRVVLFGKLAEVAGEYLRKGSQVYIEG 82 (177)
T ss_pred ceEEEEEEEeCCCceEEEcCC--C-CEEEEEEEEEcCccccCcccccccceEEEEEEEehhHHHHHHHhcCCCCEEEEEE
Confidence 568899999999888888764 2 256666554 22 23 24799999999999999999999999975
No 108
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=80.91 E-value=6.5 Score=37.41 Aligned_cols=64 Identities=17% Similarity=0.254 Sum_probs=49.2
Q ss_pred CCCeEEEEEEEeeccccccccCCCcccEEEEEEE------eC-CC------CeEEEEEechHHHHHHhhcccCcEEEEee
Q 006973 184 QGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELT------DE-DG------TQIQATMFNEAARKFYDRFQLGKVYYISR 250 (623)
Q Consensus 184 ~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~------D~-~G------~~I~at~~~~~~~kf~~~l~eG~vy~is~ 250 (623)
.+...|.||+.+.-++|.+.+.. .+.+|.|+ |. .| +-+++++|+..++.+...|+.|+-+.+.+
T Consensus 4 ~N~V~LiGrLg~DPElR~t~nG~---~va~fsVAvn~~~~d~~~Ge~~e~t~w~~Vv~fgk~AE~v~~~LkKGs~V~VeG 80 (168)
T PRK06863 4 INKVIIVGHLGNDPEIRTMPNGE---AVANISVATSESWTDKNTGERREVTEWHRIVFYRRQAEVAGEYLRKGSQVYVEG 80 (168)
T ss_pred ccEEEEEEEcCCCCEEEEcCCCC---EEEEEEEEecCcccccCCCcccccceEEEEEEEhHHHHHHHHHCCCCCEEEEEE
Confidence 56788999999988888875422 46666554 21 12 35899999999999999999999999975
No 109
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=80.86 E-value=12 Score=32.26 Aligned_cols=57 Identities=16% Similarity=0.243 Sum_probs=43.3
Q ss_pred CCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHH-hhcccCcEEEEee
Q 006973 185 GNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFY-DRFQLGKVYYISR 250 (623)
Q Consensus 185 ~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~-~~l~eG~vy~is~ 250 (623)
.+..|+|=|+. ++.. .+....|+|.|++. .|+|++|.....+.. ..+++|+-+.+..
T Consensus 22 ~~vwV~GEIs~---~~~~-----~~gh~YftLkD~~a-~i~~~~~~~~~~~i~~~~l~~G~~V~v~g 79 (99)
T PF13742_consen 22 PNVWVEGEISN---LKRH-----SSGHVYFTLKDEEA-SISCVIFRSRARRIRGFDLKDGDKVLVRG 79 (99)
T ss_pred CCEEEEEEEee---cEEC-----CCceEEEEEEcCCc-EEEEEEEHHHHhhCCCCCCCCCCEEEEEE
Confidence 45557787765 3221 12478899999885 999999999888888 7899999887763
No 110
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=80.00 E-value=0.74 Score=38.77 Aligned_cols=28 Identities=21% Similarity=0.446 Sum_probs=21.3
Q ss_pred ccccccccce-ecCCCCeeecCcCCCCcc
Q 006973 483 RACKTCNKKV-TDALGSGYWCEGCQKNDE 510 (623)
Q Consensus 483 ~aC~~C~KKv-~~~~~~~~~C~kC~~~~~ 510 (623)
.-||.|+|.. .....|.|.|.+|+..+.
T Consensus 36 y~Cp~Cgk~~vkR~a~GIW~C~~C~~~~A 64 (90)
T PF01780_consen 36 YTCPFCGKTSVKRVATGIWKCKKCGKKFA 64 (90)
T ss_dssp BEESSSSSSEEEEEETTEEEETTTTEEEE
T ss_pred CcCCCCCCceeEEeeeEEeecCCCCCEEe
Confidence 4599999874 334568999999998763
No 111
>cd04316 ND_PkAspRS_like_N ND_PkAspRS_like_N: N-terminal, anticodon recognition domain of the type found in the homodimeric non-discriminating (ND) Pyrococcus kodakaraensis aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. P. kodakaraensis AspRS is a class 2b aaRS. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. P. kodakaraensis ND-AspRS can charge both tRNAAsp and tRNAAsn. Some of the enzymes in this group may be discriminating, based on the presence of homologs of asparaginyl-tRNA synthetase (AsnRS) in their completed genomes.
Probab=79.79 E-value=22 Score=30.88 Aligned_cols=81 Identities=22% Similarity=0.201 Sum_probs=52.4
Q ss_pred CCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechH----HHHHHhhcccCcEEEEeeeEEEecCCCc
Q 006973 185 GNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEA----ARKFYDRFQLGKVYYISRGTLRVANKQF 260 (623)
Q Consensus 185 ~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~----~~kf~~~l~eG~vy~is~~~V~~a~~~~ 260 (623)
...+|+|||.+ +|. .|++.=++|.|.+| .|++.+-.+. .-++-..|..|+++.+.+- +.....
T Consensus 13 ~~V~v~Gwv~~---~R~------~g~~~Fi~LrD~~g-~iQ~v~~~~~~~~~~~~~~~~l~~es~V~V~G~-v~~~~~-- 79 (108)
T cd04316 13 EEVTVAGWVHE---IRD------LGGIKFVILRDREG-IVQVTAPKKKVDKELFKTVRKLSRESVISVTGT-VKAEPK-- 79 (108)
T ss_pred CEEEEEEEEEe---eec------cCCeEEEEEecCCe-eEEEEEeCCCCCHHHHHHHhCCCCcCEEEEEEE-EEeCCC--
Confidence 36889999976 333 23444467899988 7999887542 1223345899999999875 333321
Q ss_pred cccCCceEEEEccCcEEEEc
Q 006973 261 KTVQNDYEMNLNENSEVEEA 280 (623)
Q Consensus 261 ~~~~~~yei~f~~~T~I~~~ 280 (623)
...+|||..+.-..+.++
T Consensus 80 --~~~~~Ei~~~~i~il~~~ 97 (108)
T cd04316 80 --APNGVEIIPEEIEVLSEA 97 (108)
T ss_pred --CCCCEEEEEeEEEEEeCC
Confidence 235799988665555443
No 112
>PF00436 SSB: Single-strand binding protein family; InterPro: IPR000424 The Escherichia coli single-strand binding protein [] (gene ssb), also known as the helix-destabilising protein, is a protein of 177 amino acids. It binds tightly, as a homotetramer, to single-stranded DNA (ss-DNA) and plays an important role in DNA replication, recombination and repair. Closely related variants of SSB are encoded in the genome of a variety of large self-transmissible plasmids. SSB has also been characterised in bacteria such as Proteus mirabilis or Serratia marcescens. Eukaryotic mitochondrial proteins that bind ss-DNA and are probably involved in mitochondrial DNA replication are structurally and evolutionary related to prokaryotic SSB.; GO: 0003697 single-stranded DNA binding; PDB: 3UDG_B 1SE8_A 2CWA_A 3ULL_B 1S3O_A 2DUD_A 3AFP_A 3AFQ_A 3VDY_A 3EIV_C ....
Probab=79.37 E-value=2.9 Score=35.79 Aligned_cols=63 Identities=21% Similarity=0.270 Sum_probs=42.3
Q ss_pred CCeEEEEEEEeeccccccccCCCcccEEEEEEEeCC------C------CeEEEEEechHHHHHHhhcccCcEEEEee
Q 006973 185 GNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDED------G------TQIQATMFNEAARKFYDRFQLGKVYYISR 250 (623)
Q Consensus 185 ~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~------G------~~I~at~~~~~~~kf~~~l~eG~vy~is~ 250 (623)
+...|.|||.+--.+|+..+ | ..+.+|.|+-.. + +-+++++|++.|+.+.+.++.|+.+.|.+
T Consensus 2 N~v~l~G~l~~~p~~~~~~~--g-~~~~~f~la~~~~~~~~~~~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G 76 (104)
T PF00436_consen 2 NKVTLIGRLGKDPELRYTKN--G-TPVARFSLAVNRRFKDDGGEGDEKTDWINVVAWGKLAENVAEYLKKGDRVYVEG 76 (104)
T ss_dssp EEEEEEEEESSSEEEEEETT--S-EEEEEEEEEEEEEEEETTSCEEEEEEEEEEEEEHHHHHHHHHH--TT-EEEEEE
T ss_pred cEEEEEEEECCCcEEEECCC--C-CEEEEEEEEEecEEeeeeccCccceEEEEEEeeeecccccceEEcCCCEEEEEE
Confidence 45678899988777776552 2 134444332211 2 36899999999999999999999999986
No 113
>TIGR00621 ssb single stranded DNA-binding protein (ssb). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=79.18 E-value=8.4 Score=36.51 Aligned_cols=64 Identities=22% Similarity=0.319 Sum_probs=46.6
Q ss_pred CCCeEEEEEEEeeccccccccCCCcccEEEEEEE------eCCC------CeEEEEEechHHHHHHhhcccCcEEEEee
Q 006973 184 QGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELT------DEDG------TQIQATMFNEAARKFYDRFQLGKVYYISR 250 (623)
Q Consensus 184 ~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~------D~~G------~~I~at~~~~~~~kf~~~l~eG~vy~is~ 250 (623)
.+..+|.+||.+--.+|...+ |. .+.+|.|+ |+.| +-|++++|+..++.+...|+.|+.+.+.+
T Consensus 4 ~N~V~L~G~l~~dPe~r~t~~--G~-~v~~fsvA~~~~~~~~~G~~~~~t~~~~v~~wg~~Ae~~~~~l~KG~~V~V~G 79 (164)
T TIGR00621 4 VNKVILVGRLTRDPELRYTPS--GN-AVANFTLATNRRWKDQDGEWKEETEWHDIVIFGRLAEVAAQYLKKGSLVYVEG 79 (164)
T ss_pred ccEEEEEEEeCCCCEEEECCC--CC-EEEEEEEEEcCceecCCCCEeccceEEEEEEehHHHHHHHHhCCCCCEEEEEE
Confidence 356788899988777776543 21 34444332 2222 47999999999999999999999999986
No 114
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=78.72 E-value=8.5 Score=45.09 Aligned_cols=74 Identities=19% Similarity=0.294 Sum_probs=53.2
Q ss_pred CeeeccccCCCCCCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeE
Q 006973 173 RVHPLVSLNPYQGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGT 252 (623)
Q Consensus 173 ~~~~I~~L~p~~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~ 252 (623)
.+.+|+++.++. .-+|.|+|......+. ..+.+.+.+.|++| .|.+++|+-.-.-....|++|+.|.+++ +
T Consensus 49 ~~~~i~~l~~g~-~vtv~g~V~~~~~~~~------~~~~~~v~l~D~tg-~i~l~~F~~n~~~~~~~l~~G~~~~v~G-k 119 (681)
T PRK10917 49 RLKPIAELRPGE-KVTVEGEVLSAEVVFG------KRRRLTVTVSDGTG-NLTLRFFNFNQPYLKKQLKVGKRVAVYG-K 119 (681)
T ss_pred CcCCHHHCCCCC-EEEEEEEEEEEEEccC------CceEEEEEEEECCe-EEEEEEEccCcHHHHhhCCCCCEEEEEE-E
Confidence 357888987764 7999999988632221 12589999999999 8999999410112257799999999874 4
Q ss_pred EEe
Q 006973 253 LRV 255 (623)
Q Consensus 253 V~~ 255 (623)
|..
T Consensus 120 v~~ 122 (681)
T PRK10917 120 VKR 122 (681)
T ss_pred EEe
Confidence 444
No 115
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=78.15 E-value=8.2 Score=42.72 Aligned_cols=77 Identities=13% Similarity=0.152 Sum_probs=53.1
Q ss_pred cccccccccccCCcceeEEEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCc
Q 006973 294 FVPIDELGRYVNGTELVDIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSP 373 (623)
Q Consensus 294 f~~i~di~~~~~~~~~vDVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~ 373 (623)
.+++++|.. ...+..|-|.|+|+.+... .+|+ |+ ..--++|.|.+| .+++++|-+..+.+... ...+.
T Consensus 268 ~~~~~~l~~-~~~~~~v~vaG~I~~ik~~---~TKk-G~--~maf~~leD~tG-~ie~vvFp~~y~~~~~~----l~~~~ 335 (449)
T PRK07373 268 PINLSELEE-QKEKTKVSAVVMLNEVKKI---VTKK-GD--PMAFLQLEDLSG-QSEAVVFPKSYERISEL----LQVDA 335 (449)
T ss_pred CcCHHHHhc-ccCCCEEEEEEEEEEeEec---ccCC-CC--EEEEEEEEECCC-CEEEEECHHHHHHHHHH----hccCC
Confidence 356666642 2345678899999998644 3553 54 345789999999 89999999887776544 34567
Q ss_pred EEEEEeEEee
Q 006973 374 IVAIKSLKVG 383 (623)
Q Consensus 374 Vv~i~~~kV~ 383 (623)
++.+++ +|.
T Consensus 336 ~v~v~G-~v~ 344 (449)
T PRK07373 336 RLIIWG-KVD 344 (449)
T ss_pred EEEEEE-EEE
Confidence 777765 443
No 116
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional
Probab=77.64 E-value=15 Score=40.67 Aligned_cols=93 Identities=18% Similarity=0.125 Sum_probs=64.1
Q ss_pred eeeccccCCCC--CCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechH---HHHHHhhcccCcEEEE
Q 006973 174 VHPLVSLNPYQ--GNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEA---ARKFYDRFQLGKVYYI 248 (623)
Q Consensus 174 ~~~I~~L~p~~--~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~---~~kf~~~l~eG~vy~i 248 (623)
-+.|.+|++.. ..-+|+|||.++ |. .|++.=++|.|.+| .|++++-.+. ..++-..|..|+++.+
T Consensus 4 ~~~~~~l~~~~~g~~V~i~GrV~~~---R~------~gk~~Fl~LrD~~g-~iQ~v~~~~~~~~~~~~~~~L~~gs~V~v 73 (437)
T PRK05159 4 RHLTSELTPELDGEEVTLAGWVHEI---RD------LGGIAFLILRDRSG-IIQVVVKKKVDEELFETIKKLKRESVVSV 73 (437)
T ss_pred eeEhhhCChhhCCCEEEEEEEeEee---ec------CCCeEEEEEEcCCc-EEEEEEeCCccHHHHHHHhCCCCCcEEEE
Confidence 36788888765 578899999774 32 34555578999999 7999986542 2233456899999999
Q ss_pred eeeEEEecCCCccccCCceEEEEccCcEEEEcc
Q 006973 249 SRGTLRVANKQFKTVQNDYEMNLNENSEVEEAV 281 (623)
Q Consensus 249 s~~~V~~a~~~~~~~~~~yei~f~~~T~I~~~~ 281 (623)
.+.-++ ..+ ....+||....-+.+.++.
T Consensus 74 ~G~v~~-~~~----~~~~~el~~~~i~vls~a~ 101 (437)
T PRK05159 74 TGTVKA-NPK----APGGVEVIPEEIEVLNKAE 101 (437)
T ss_pred EEEEEc-CCC----CCCCEEEEEeEEEEEeCCC
Confidence 975443 321 2356889887666666553
No 117
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=76.92 E-value=1.1 Score=28.56 Aligned_cols=23 Identities=17% Similarity=0.686 Sum_probs=17.5
Q ss_pred ccccccccceecCCCCeeecCcCCCC
Q 006973 483 RACKTCNKKVTDALGSGYWCEGCQKN 508 (623)
Q Consensus 483 ~aC~~C~KKv~~~~~~~~~C~kC~~~ 508 (623)
..||.|++.+.. +.-+|++|+..
T Consensus 3 ~~Cp~Cg~~~~~---~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDP---DAKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCc---ccccChhhCCC
Confidence 469999996643 45689999864
No 118
>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=76.88 E-value=1.3 Score=35.52 Aligned_cols=25 Identities=36% Similarity=0.904 Sum_probs=17.6
Q ss_pred cccccccceecCCCCeeecCcCCCCc
Q 006973 484 ACKTCNKKVTDALGSGYWCEGCQKND 509 (623)
Q Consensus 484 aC~~C~KKv~~~~~~~~~C~kC~~~~ 509 (623)
.||.|+.-+... ++.|+|+.|++.+
T Consensus 3 ~CP~C~~~L~~~-~~~~~C~~C~~~~ 27 (70)
T PF07191_consen 3 TCPKCQQELEWQ-GGHYHCEACQKDY 27 (70)
T ss_dssp B-SSS-SBEEEE-TTEEEETTT--EE
T ss_pred cCCCCCCccEEe-CCEEECccccccc
Confidence 599999999887 6899999998753
No 119
>PRK10220 hypothetical protein; Provisional
Probab=75.64 E-value=1.9 Score=37.39 Aligned_cols=30 Identities=23% Similarity=0.437 Sum_probs=25.6
Q ss_pred EeccccccccceecCCCCeeecCcCCCCcc
Q 006973 481 WYRACKTCNKKVTDALGSGYWCEGCQKNDE 510 (623)
Q Consensus 481 ~Y~aC~~C~KKv~~~~~~~~~C~kC~~~~~ 510 (623)
.+|+||.|+...+-+.+..|-|+-|...+.
T Consensus 2 ~lP~CP~C~seytY~d~~~~vCpeC~hEW~ 31 (111)
T PRK10220 2 SLPHCPKCNSEYTYEDNGMYICPECAHEWN 31 (111)
T ss_pred CCCcCCCCCCcceEcCCCeEECCcccCcCC
Confidence 369999999998877678999999998764
No 120
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=75.47 E-value=13 Score=43.11 Aligned_cols=74 Identities=19% Similarity=0.259 Sum_probs=53.7
Q ss_pred eeeccccCCCCCCeEEEEEEEeeccccccccCCCcccEEEEEEEe-CCCCeEEEEEechHHHHHHhhcccCcEEEEeeeE
Q 006973 174 VHPLVSLNPYQGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTD-EDGTQIQATMFNEAARKFYDRFQLGKVYYISRGT 252 (623)
Q Consensus 174 ~~~I~~L~p~~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D-~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~ 252 (623)
+.+|+++.++. .-+|.|+|+... ... ++..+.+.+.+.| ++| .+.+++|+.. -....|..|+.|.+++ +
T Consensus 23 ~~~i~~~~~g~-~~~~~~~v~~~~---~~~--~~~~~~~~~~~~d~~~~-~~~~~~F~~~--~~~~~~~~g~~~~~~G-k 92 (630)
T TIGR00643 23 LQTIGELLPGE-RATIVGEVLSHC---IFG--FKRRKVLKLRLKDGGYK-KLELRFFNRA--FLKKKFKVGSKVVVYG-K 92 (630)
T ss_pred ccCHHHcCCCC-EEEEEEEEEEeE---ecc--CCCCceEEEEEEECCCC-EEEEEEECCH--HHHhhCCCCCEEEEEE-E
Confidence 56899998875 688999998732 111 1223589999999 888 8999999832 3457899999999874 4
Q ss_pred EEecC
Q 006973 253 LRVAN 257 (623)
Q Consensus 253 V~~a~ 257 (623)
|...+
T Consensus 93 ~~~~~ 97 (630)
T TIGR00643 93 VKSSK 97 (630)
T ss_pred EEeeC
Confidence 54433
No 121
>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=75.05 E-value=1.8 Score=27.76 Aligned_cols=23 Identities=22% Similarity=0.712 Sum_probs=18.5
Q ss_pred cccccccceecCCCCeeecCcCCCCc
Q 006973 484 ACKTCNKKVTDALGSGYWCEGCQKND 509 (623)
Q Consensus 484 aC~~C~KKv~~~~~~~~~C~kC~~~~ 509 (623)
-||.|++.|... .-.|+.|+-.+
T Consensus 2 ~CP~C~~~V~~~---~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPES---AKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchhh---cCcCCCCCCCC
Confidence 599999999753 56899999654
No 122
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=74.86 E-value=2 Score=29.78 Aligned_cols=26 Identities=19% Similarity=0.616 Sum_probs=21.2
Q ss_pred ccccccccceecCCCCeeecCcCCCC
Q 006973 483 RACKTCNKKVTDALGSGYWCEGCQKN 508 (623)
Q Consensus 483 ~aC~~C~KKv~~~~~~~~~C~kC~~~ 508 (623)
..|+.|+.......+|.|.|..|+..
T Consensus 9 ~~C~~C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 9 EPCPVCGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CcCCCCCCeEeEccCCEEEhhhCceE
Confidence 46999998876666899999999853
No 123
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=73.68 E-value=8.5 Score=47.57 Aligned_cols=73 Identities=25% Similarity=0.314 Sum_probs=52.4
Q ss_pred eeccccCC--CCCCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeE
Q 006973 175 HPLVSLNP--YQGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGT 252 (623)
Q Consensus 175 ~~I~~L~p--~~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~ 252 (623)
+++.+|.. ....-.+.+.|+.+... ..++|+ ...-++|-|.+| .|.+++|.+..+++.+.|++|.++.|.+ +
T Consensus 966 ~~~~~l~~~~~g~~V~v~G~I~~vk~~---~TKkG~-~mafltLeD~TG-~iEvviFp~~ye~~~~~L~~g~iV~V~G-k 1039 (1135)
T PRK05673 966 TRLADLEPTEGGSVVTVAGLVVSVRRR---VTKRGN-KMAIVTLEDLSG-RIEVMLFSEALEKYRDLLEEDRIVVVKG-Q 1039 (1135)
T ss_pred cCHHHHhccccCceEEEEEEEEEEEec---ccCCCC-eEEEEEEEeCCC-cEEEEECHHHHHHHHHHhccCCEEEEEE-E
Confidence 46666642 23356677777764433 223332 355678999999 8999999999999999999999999964 4
Q ss_pred E
Q 006973 253 L 253 (623)
Q Consensus 253 V 253 (623)
|
T Consensus 1040 V 1040 (1135)
T PRK05673 1040 V 1040 (1135)
T ss_pred E
Confidence 4
No 124
>cd04317 EcAspRS_like_N EcAspRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli aspartyl-tRNA synthetase (AspRS), the human mitochondrial (mt) AspRS-2, the discriminating (D) Thermus thermophilus AspRS-1, and the nondiscriminating (ND) Helicobacter pylori AspRS. These homodimeric enzymes are class2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, wh
Probab=73.46 E-value=30 Score=31.39 Aligned_cols=86 Identities=17% Similarity=0.162 Sum_probs=53.8
Q ss_pred CCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHH--HHHhhcccCcEEEEeeeEEEecC--CCc
Q 006973 185 GNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAAR--KFYDRFQLGKVYYISRGTLRVAN--KQF 260 (623)
Q Consensus 185 ~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~--kf~~~l~eG~vy~is~~~V~~a~--~~~ 260 (623)
..-+|+|||.+ +|. .|++.=++|.|.+| .+++.+-....+ ++...|..|+++.+.+.-..... +.-
T Consensus 15 ~~V~i~Gwv~~---~R~------~gk~~Fi~LrD~~g-~~Q~v~~~~~~~~~~~~~~l~~gs~V~V~G~~~~~~~~~~~~ 84 (135)
T cd04317 15 QEVTLCGWVQR---RRD------HGGLIFIDLRDRYG-IVQVVFDPEEAPEFELAEKLRNESVIQVTGKVRARPEGTVNP 84 (135)
T ss_pred CEEEEEEeEeh---hcc------cCCEEEEEEecCCe-eEEEEEeCCchhHHHHHhCCCCccEEEEEEEEECCCccccCC
Confidence 36889999966 333 33554467899988 799988654333 23346999999999985333211 111
Q ss_pred cccCCceEEEEccCcEEEEc
Q 006973 261 KTVQNDYEMNLNENSEVEEA 280 (623)
Q Consensus 261 ~~~~~~yei~f~~~T~I~~~ 280 (623)
.....++||....-..+.++
T Consensus 85 ~~~~~~~El~~~~i~vl~~~ 104 (135)
T cd04317 85 KLPTGEIEVVASELEVLNKA 104 (135)
T ss_pred CCCCCcEEEEEeEEEEEECC
Confidence 12345688887665445444
No 125
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=73.31 E-value=10 Score=46.80 Aligned_cols=81 Identities=21% Similarity=0.275 Sum_probs=55.2
Q ss_pred cccccccccccCCcceeEEEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCc
Q 006973 294 FVPIDELGRYVNGTELVDIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSP 373 (623)
Q Consensus 294 f~~i~di~~~~~~~~~vDVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~ 373 (623)
..++.+|.. ...+..|.+.|+|+++... .+|+ |+ ..--++|.|.+| ++++++|.+..+.+... ...+.
T Consensus 965 ~~~~~~l~~-~~~g~~V~v~G~I~~vk~~---~TKk-G~--~mafltLeD~TG-~iEvviFp~~ye~~~~~----L~~g~ 1032 (1135)
T PRK05673 965 DTRLADLEP-TEGGSVVTVAGLVVSVRRR---VTKR-GN--KMAIVTLEDLSG-RIEVMLFSEALEKYRDL----LEEDR 1032 (1135)
T ss_pred CcCHHHHhc-cccCceEEEEEEEEEEEec---ccCC-CC--eEEEEEEEeCCC-cEEEEECHHHHHHHHHH----hccCC
Confidence 346666643 2345679999999988643 3553 54 345789999999 89999999876665443 45577
Q ss_pred EEEEEeEEeeeccc
Q 006973 374 IVAIKSLKVGDFQG 387 (623)
Q Consensus 374 Vv~i~~~kV~~f~G 387 (623)
+|.+++ +|..+.|
T Consensus 1033 iV~V~G-kVe~~~~ 1045 (1135)
T PRK05673 1033 IVVVKG-QVSFDDG 1045 (1135)
T ss_pred EEEEEE-EEEecCC
Confidence 887765 5554433
No 126
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=72.65 E-value=15 Score=35.41 Aligned_cols=64 Identities=19% Similarity=0.297 Sum_probs=47.7
Q ss_pred CCCeEEEEEEEeeccccccccCCCcccEEEEEEE------eC-CC------CeEEEEEechHHHHHHhhcccCcEEEEee
Q 006973 184 QGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELT------DE-DG------TQIQATMFNEAARKFYDRFQLGKVYYISR 250 (623)
Q Consensus 184 ~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~------D~-~G------~~I~at~~~~~~~kf~~~l~eG~vy~is~ 250 (623)
.+..+|.+|+.+--.+|...+ |. .+.+|.|+ |. +| +-+++++|+.+++.+...|+.|+-+.|..
T Consensus 4 ~N~V~LiGrLg~DPElr~t~n--G~-~va~fsVAv~~~~kdk~sGe~~e~T~w~~V~~fGk~AE~v~~~LkKGs~V~VeG 80 (182)
T PRK06958 4 VNKVILVGNLGADPEVRYLPS--GD-AVANIRLATTDRYKDKASGEFKEATEWHRVAFFGRLAEIVGEYLKKGSSVYIEG 80 (182)
T ss_pred ccEEEEEEEecCCCeEEEcCC--CC-EEEEEEEEeccccccccCCcccccceEEEEEEehHHHHHHHHHhCCCCEEEEEE
Confidence 467889999998877776543 21 35555553 22 12 36899999999999999999999999985
No 127
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=72.36 E-value=11 Score=45.59 Aligned_cols=75 Identities=17% Similarity=0.201 Sum_probs=51.9
Q ss_pred eeccccCCCCCCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeEEE
Q 006973 175 HPLVSLNPYQGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGTLR 254 (623)
Q Consensus 175 ~~I~~L~p~~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~V~ 254 (623)
.+|.+|. .....+|-|.|+..-..+ ++|+ ...-++|-|.+| .|.+++|.+...++.. +.+|++|.++ ++..
T Consensus 889 ~~~~~l~-~~~~~~v~g~i~~~~~~~----K~g~-~maf~~~eD~~~-~~e~~~F~~~~~~~~~-l~~~~~~~~~-~~~~ 959 (973)
T PRK07135 889 IRLKDLR-INTEYRLAIEVKNVKRLR----KANK-EYKKVILSDDSV-EITIFVNDNDYLLFET-LKKGDIYEFL-ISKS 959 (973)
T ss_pred hhHHHhc-CCCeEEEEEEEEEEEEEe----eCCC-eEEEEEEEECCC-cEEEEEcHHHHHHHHH-hhcCCEEEEE-EEEc
Confidence 4667774 233457888887754433 2333 345568999999 8999999999999887 8888898884 4444
Q ss_pred ecCC
Q 006973 255 VANK 258 (623)
Q Consensus 255 ~a~~ 258 (623)
.+|+
T Consensus 960 ~~~~ 963 (973)
T PRK07135 960 KNNK 963 (973)
T ss_pred CCCc
Confidence 4433
No 128
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=72.05 E-value=2 Score=36.27 Aligned_cols=33 Identities=24% Similarity=0.464 Sum_probs=23.7
Q ss_pred eccccccccc-eecCCCCeeecCcCCCCccccce
Q 006973 482 YRACKTCNKK-VTDALGSGYWCEGCQKNDEECSL 514 (623)
Q Consensus 482 Y~aC~~C~KK-v~~~~~~~~~C~kC~~~~~~~~~ 514 (623)
-..||-|+|. |.....|.|.|.+|+..+.--.|
T Consensus 36 ~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGGAy 69 (90)
T PTZ00255 36 KYFCPFCGKHAVKRQAVGIWRCKGCKKTVAGGAW 69 (90)
T ss_pred CccCCCCCCCceeeeeeEEEEcCCCCCEEeCCcc
Confidence 4469999764 55555689999999988754333
No 129
>PRK06642 single-stranded DNA-binding protein; Provisional
Probab=72.02 E-value=15 Score=34.42 Aligned_cols=64 Identities=19% Similarity=0.227 Sum_probs=48.9
Q ss_pred CCCeEEEEEEEeeccccccccCCCcccEEEEEEE------eC-CC------CeEEEEEech-HHHHHHhhcccCcEEEEe
Q 006973 184 QGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELT------DE-DG------TQIQATMFNE-AARKFYDRFQLGKVYYIS 249 (623)
Q Consensus 184 ~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~------D~-~G------~~I~at~~~~-~~~kf~~~l~eG~vy~is 249 (623)
.+..+|.||+.+--++|...+ | ..+.+|.|+ |. .| +-+++++|++ .++.+...|+.|+-+++.
T Consensus 5 ~N~V~LiGrLg~DPElr~t~~--G-~~v~~fslAv~~~~k~~~~G~~~~~T~w~~v~~~g~~~Ae~~~~~l~KG~~V~V~ 81 (152)
T PRK06642 5 LNKVILIGNVGRDPEIRTTGE--G-KKIINLSLATTETWKDRITSERKERTEWHRVVIFSEGLVSVVERYVTKGSKLYIE 81 (152)
T ss_pred ceEEEEEEEccCCceEEECCC--C-CEEEEEEEEeccccccccCCccccceeEEEEEEeChHHHHHHHHhCCCCCEEEEE
Confidence 567899999999888887643 2 146677665 22 23 2588999996 899999999999999997
Q ss_pred e
Q 006973 250 R 250 (623)
Q Consensus 250 ~ 250 (623)
+
T Consensus 82 G 82 (152)
T PRK06642 82 G 82 (152)
T ss_pred E
Confidence 5
No 130
>COG0629 Ssb Single-stranded DNA-binding protein [DNA replication, recombination, and repair]
Probab=71.96 E-value=14 Score=35.13 Aligned_cols=68 Identities=15% Similarity=0.223 Sum_probs=48.4
Q ss_pred CCCeEEEEEEEeeccccccccCCCcccEEEEE---EEeCCC-------CeEEEEEechHHHHHHhhcccCcEEEEeee
Q 006973 184 QGNWTIKVRVTSKGNMRTYKNARGEGCVFNVE---LTDEDG-------TQIQATMFNEAARKFYDRFQLGKVYYISRG 251 (623)
Q Consensus 184 ~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~---L~D~~G-------~~I~at~~~~~~~kf~~~l~eG~vy~is~~ 251 (623)
.++..+.+|+++.-++|...+......+|... ..|..+ +-|++++|+.+++.....|+.|.-++|.+.
T Consensus 3 ~Nkv~LvG~l~~DPE~r~t~~g~~~v~~~~~a~~r~~~~~~~~~~~~t~~~~vv~wgk~Ae~~~~yl~KG~~V~VeG~ 80 (167)
T COG0629 3 MNKVILVGRLTRDPELRYTPNGGAVVALFSAAVNRRFDNQSGERDEETDWIRVVIWGKLAENAAEYLKKGSLVYVEGR 80 (167)
T ss_pred cceEEEEeecccCcceeecCCCCeeeEEEEEEeccccccCCcccccccceEEEEEehHHHHHHHHHhcCCCEEEEEEE
Confidence 56788899999998888776322111122221 233222 579999999999999999999999999863
No 131
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=71.78 E-value=2.8 Score=30.18 Aligned_cols=26 Identities=23% Similarity=0.436 Sum_probs=19.0
Q ss_pred cccccccce--ecCCCCeeecCcCCCCc
Q 006973 484 ACKTCNKKV--TDALGSGYWCEGCQKND 509 (623)
Q Consensus 484 aC~~C~KKv--~~~~~~~~~C~kC~~~~ 509 (623)
.||.|+.+. .+...|.+.|..|+...
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCGLVL 29 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-BBE
T ss_pred CCcCCcCCceEEcCCCCeEECCCCCCEe
Confidence 599999874 34456889999998654
No 132
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=71.77 E-value=9.5 Score=46.43 Aligned_cols=74 Identities=27% Similarity=0.477 Sum_probs=53.4
Q ss_pred eeeccccCCCCCCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeEE
Q 006973 174 VHPLVSLNPYQGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGTL 253 (623)
Q Consensus 174 ~~~I~~L~p~~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~V 253 (623)
..++++|.. .....+.|.|+.....++- ++|+ .+.-++|-|.+| .|.+++|.+..+++.+.|++|.++.+.+ +|
T Consensus 875 ~~~~~~l~~-~~~~~~~~~i~~~~~~~tk--~~g~-~maf~~leD~~g-~ie~~vFp~~y~~~~~~l~~~~~~~v~G-~v 948 (1034)
T PRK07279 875 FTPISQLVK-NSEATILVQIQSIRVIRTK--TKGQ-QMAFLSVTDTKK-KLDVTLFPETYRQYKDELKEGKFYYLKG-KI 948 (1034)
T ss_pred CccHHHHhc-CCcceEEEEEEEEEEEEEc--CCCC-eEEEEEEeeCCC-cEEEEECHHHHHHHHHHhccCCEEEEEE-EE
Confidence 356777753 3345677888764433331 1333 355678999999 8999999999999999999999999964 44
No 133
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=71.64 E-value=2.5 Score=32.52 Aligned_cols=27 Identities=26% Similarity=0.560 Sum_probs=16.3
Q ss_pred eEeccccccccceec------CCCCeeecCcCC
Q 006973 480 MWYRACKTCNKKVTD------ALGSGYWCEGCQ 506 (623)
Q Consensus 480 ~~Y~aC~~C~KKv~~------~~~~~~~C~kC~ 506 (623)
..-..||+|++-++. ..+..|+|++|+
T Consensus 25 ~v~F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CG 57 (61)
T COG2888 25 AVKFPCPNCGEVEIYRCAKCRKLGNPYRCPKCG 57 (61)
T ss_pred eeEeeCCCCCceeeehhhhHHHcCCceECCCcC
Confidence 345568877744432 125568888887
No 134
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=71.39 E-value=1.9 Score=36.33 Aligned_cols=30 Identities=23% Similarity=0.408 Sum_probs=22.5
Q ss_pred eccccccccc-eecCCCCeeecCcCCCCccc
Q 006973 482 YRACKTCNKK-VTDALGSGYWCEGCQKNDEE 511 (623)
Q Consensus 482 Y~aC~~C~KK-v~~~~~~~~~C~kC~~~~~~ 511 (623)
-..||-|+|. |....-|.|.|.+|++.+.-
T Consensus 35 ~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AG 65 (91)
T TIGR00280 35 KYVCPFCGKKTVKRGSTGIWTCRKCGAKFAG 65 (91)
T ss_pred CccCCCCCCCceEEEeeEEEEcCCCCCEEeC
Confidence 4469999765 55455689999999988644
No 135
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=71.11 E-value=2.5 Score=37.16 Aligned_cols=29 Identities=24% Similarity=0.460 Sum_probs=22.7
Q ss_pred eccccccccceecCCCCeeecCcCCCCcc
Q 006973 482 YRACKTCNKKVTDALGSGYWCEGCQKNDE 510 (623)
Q Consensus 482 Y~aC~~C~KKv~~~~~~~~~C~kC~~~~~ 510 (623)
-..||.|++|-..-.-..-.|++|+..++
T Consensus 9 KR~Cp~CG~kFYDLnk~PivCP~CG~~~~ 37 (108)
T PF09538_consen 9 KRTCPSCGAKFYDLNKDPIVCPKCGTEFP 37 (108)
T ss_pred cccCCCCcchhccCCCCCccCCCCCCccC
Confidence 56799999998765334567999999874
No 136
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=71.03 E-value=11 Score=46.74 Aligned_cols=73 Identities=15% Similarity=0.249 Sum_probs=52.9
Q ss_pred eeccccC--CCCCCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeE
Q 006973 175 HPLVSLN--PYQGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGT 252 (623)
Q Consensus 175 ~~I~~L~--p~~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~ 252 (623)
.++++|. +.....+|-|-|+..-.. ..++|+ .+.-++|-|.+| .+.+++|.+..+++...|++|.++.+.+ +
T Consensus 989 ~~~~~l~~~~~~~~v~v~g~i~~~k~~---~Tk~G~-~maf~~leD~tg-~~e~vvFp~~y~~~~~~l~~~~~~~v~g-~ 1062 (1170)
T PRK07374 989 ISLSSLEEQPDKAKVSAIAMIPEMKQV---TTRKGD-RMAILQLEDLTG-SCEAVVFPKSYERLSDHLMTDTRLLVWA-K 1062 (1170)
T ss_pred cCHHHHhcccCCCEEEEEEEEEEeEec---ccCCCC-EEEEEEEEECCC-CEEEEECHHHHHHHHHHhccCCEEEEEE-E
Confidence 4566664 223456788888774433 333332 344568999999 8999999999999999999999999964 4
Q ss_pred E
Q 006973 253 L 253 (623)
Q Consensus 253 V 253 (623)
|
T Consensus 1063 v 1063 (1170)
T PRK07374 1063 V 1063 (1170)
T ss_pred E
Confidence 4
No 137
>cd04498 hPOT1_OB2 hPOT1_OB2: A subfamily of OB folds similar to the second OB fold (OB2) of human protection of telomeres 1 protein (hPOT1). POT1 proteins bind to the single-stranded (ss) 3-prime ends of the telomere. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB2) which cooperate to bind telomeric ssDNA. OB1 makes more extensive contact with the ssDNA than OB2. OB2 protects the 3' end of the ssDNA. hPOT1 is implicated in telomere length regulation.
Probab=70.84 E-value=18 Score=32.57 Aligned_cols=35 Identities=9% Similarity=0.185 Sum_probs=28.2
Q ss_pred cEEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEEeeecc
Q 006973 347 RTVTVSLWNELATNVGQELLDNADKSPIVAIKSLKVGDFQ 386 (623)
Q Consensus 347 ~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~kV~~f~ 386 (623)
.+|.||||++.|.-. .+ .+.+..|.|++++++...
T Consensus 60 ~ti~It~yD~H~~~a----r~-lK~GdfV~L~NVhiK~~~ 94 (123)
T cd04498 60 LTIDILVYDNHVELA----KS-LKPGDFVRIYNVHAKSYS 94 (123)
T ss_pred EEEEEEEEcchHHHH----hh-CCCCCEEEEEEEEEEecc
Confidence 689999999998643 22 578999999999987643
No 138
>cd04318 EcAsnRS_like_N EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial
Probab=70.09 E-value=31 Score=28.19 Aligned_cols=73 Identities=16% Similarity=0.153 Sum_probs=45.7
Q ss_pred eEEEEEEEeeccccccccCCCcccEEEEEEEeCCCC-eEEEEEechHH-HHHHhhcccCcEEEEeeeEEEecCCCccccC
Q 006973 187 WTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGT-QIQATMFNEAA-RKFYDRFQLGKVYYISRGTLRVANKQFKTVQ 264 (623)
Q Consensus 187 w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~-~I~at~~~~~~-~kf~~~l~eG~vy~is~~~V~~a~~~~~~~~ 264 (623)
-+|+|||.+ +|. .|++.=++|.|.+|. .+++++..+.. -++...|..|+++.+.+--. ...+. .
T Consensus 2 v~v~Gwv~~---~R~------~g~~~Fi~LrD~s~~~~lQvv~~~~~~~~~~~~~l~~gs~V~v~G~v~-~~~~~----~ 67 (82)
T cd04318 2 VTVNGWVRS---VRD------SKKISFIELNDGSCLKNLQVVVDKELTNFKEILKLSTGSSIRVEGVLV-KSPGA----K 67 (82)
T ss_pred EEEEEeEEE---EEc------CCcEEEEEEECCCCccCEEEEEeCcccCHHHHhcCCCceEEEEEEEEE-eCCCC----C
Confidence 367888865 332 234544678898884 59998865432 13334689999999997533 33221 3
Q ss_pred CceEEEEcc
Q 006973 265 NDYEMNLNE 273 (623)
Q Consensus 265 ~~yei~f~~ 273 (623)
.++||....
T Consensus 68 ~~~El~~~~ 76 (82)
T cd04318 68 QPFELQAEK 76 (82)
T ss_pred CCEEEEEEE
Confidence 568877643
No 139
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=70.01 E-value=2.7 Score=37.63 Aligned_cols=29 Identities=14% Similarity=-0.015 Sum_probs=23.3
Q ss_pred eccccccccceecCCCCeeecCcCCCCcc
Q 006973 482 YRACKTCNKKVTDALGSGYWCEGCQKNDE 510 (623)
Q Consensus 482 Y~aC~~C~KKv~~~~~~~~~C~kC~~~~~ 510 (623)
-..||.|++|...-....-.|++|+..++
T Consensus 9 Kr~Cp~cg~kFYDLnk~p~vcP~cg~~~~ 37 (129)
T TIGR02300 9 KRICPNTGSKFYDLNRRPAVSPYTGEQFP 37 (129)
T ss_pred cccCCCcCccccccCCCCccCCCcCCccC
Confidence 56799999998775445678999998863
No 140
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende
Probab=69.86 E-value=7.1 Score=33.10 Aligned_cols=40 Identities=13% Similarity=0.204 Sum_probs=33.7
Q ss_pred EEEEEEEeCCCCeEEEEEechH--HHHHHhhcccCcEEEEeee
Q 006973 211 VFNVELTDEDGTQIQATMFNEA--ARKFYDRFQLGKVYYISRG 251 (623)
Q Consensus 211 ~f~~~L~D~~G~~I~at~~~~~--~~kf~~~l~eG~vy~is~~ 251 (623)
...|.|.|+.+ .|+|.+|... +.+....|++|+-+.+.+.
T Consensus 18 H~yFtlkD~~~-~i~cv~f~~~g~~~~~~~~l~~Gd~V~v~G~ 59 (91)
T cd04482 18 HVFFKISDGTG-EIDCAAYEPTKEFRDVVRLLIPGDEVTVYGS 59 (91)
T ss_pred CEEEEEECCCc-EEEEEEECcccccccccCCCCCCCEEEEEEE
Confidence 56788899887 9999999987 7788888999998888753
No 141
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=69.84 E-value=2.1 Score=36.06 Aligned_cols=30 Identities=17% Similarity=0.372 Sum_probs=22.2
Q ss_pred eccccccccc-eecCCCCeeecCcCCCCccc
Q 006973 482 YRACKTCNKK-VTDALGSGYWCEGCQKNDEE 511 (623)
Q Consensus 482 Y~aC~~C~KK-v~~~~~~~~~C~kC~~~~~~ 511 (623)
-..||-|+|. |....-|.|.|.+|+..+.-
T Consensus 36 ~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AG 66 (90)
T PRK03976 36 KHVCPVCGRPKVKRVGTGIWECRKCGAKFAG 66 (90)
T ss_pred CccCCCCCCCceEEEEEEEEEcCCCCCEEeC
Confidence 4469999764 54445689999999987643
No 142
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=69.00 E-value=3.1 Score=42.91 Aligned_cols=25 Identities=32% Similarity=0.713 Sum_probs=19.5
Q ss_pred ccccccccceec---CCCCeeecCcCCC
Q 006973 483 RACKTCNKKVTD---ALGSGYWCEGCQK 507 (623)
Q Consensus 483 ~aC~~C~KKv~~---~~~~~~~C~kC~~ 507 (623)
..||.|+.++.. .+-++|+|++|++
T Consensus 245 ~pCprCG~~I~~~~~~gR~t~~CP~CQ~ 272 (272)
T PRK14810 245 EPCLNCKTPIRRVVVAGRSSHYCPHCQK 272 (272)
T ss_pred CcCCCCCCeeEEEEECCCccEECcCCcC
Confidence 689999987753 2357899999984
No 143
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=68.76 E-value=35 Score=39.29 Aligned_cols=75 Identities=20% Similarity=0.296 Sum_probs=55.2
Q ss_pred eeeccccCCCCCCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeEE
Q 006973 174 VHPLVSLNPYQGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGTL 253 (623)
Q Consensus 174 ~~~I~~L~p~~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~V 253 (623)
..+|.++.++. ..+|.++|..-.... .+..+.+.+.+.|.+| .|.++||+..+ .....|++|+.+.++ +++
T Consensus 51 ~~~i~~~~~g~-~vti~g~V~~~~~~~-----~~~~~~l~v~~~d~~~-~l~l~fFn~~~-~l~~~~~~G~~v~v~-Gk~ 121 (677)
T COG1200 51 LPGIAEARPGE-IVTIEGTVLSHEKFP-----FGKRKLLKVTLSDGTG-VLTLVFFNFPA-YLKKKLKVGERVIVY-GKV 121 (677)
T ss_pred cCChhhcCCCc-eEEEEEEEEeeeccC-----CCCCceEEEEEecCcE-EEEEEEECccH-HHHhhCCCCCEEEEE-EEE
Confidence 45667776543 678999998754332 2234689999999777 99999999765 666789999999987 455
Q ss_pred EecC
Q 006973 254 RVAN 257 (623)
Q Consensus 254 ~~a~ 257 (623)
+..+
T Consensus 122 ~~~~ 125 (677)
T COG1200 122 KRFK 125 (677)
T ss_pred eecc
Confidence 5543
No 144
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=68.69 E-value=3.2 Score=36.03 Aligned_cols=30 Identities=27% Similarity=0.506 Sum_probs=25.1
Q ss_pred eccccccccceecCCCCeeecCcCCCCccc
Q 006973 482 YRACKTCNKKVTDALGSGYWCEGCQKNDEE 511 (623)
Q Consensus 482 Y~aC~~C~KKv~~~~~~~~~C~kC~~~~~~ 511 (623)
.|+||.|+.-.+-+.+..|-|+-|+..+..
T Consensus 2 lp~CP~C~seytY~dg~~~iCpeC~~EW~~ 31 (109)
T TIGR00686 2 LPPCPKCNSEYTYHDGTQLICPSCLYEWNE 31 (109)
T ss_pred CCcCCcCCCcceEecCCeeECccccccccc
Confidence 589999999887776778999999987643
No 145
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=68.66 E-value=3.4 Score=42.82 Aligned_cols=25 Identities=36% Similarity=0.937 Sum_probs=19.4
Q ss_pred ccccccccceec---CCCCeeecCcCCC
Q 006973 483 RACKTCNKKVTD---ALGSGYWCEGCQK 507 (623)
Q Consensus 483 ~aC~~C~KKv~~---~~~~~~~C~kC~~ 507 (623)
..|+.|+.++.. .+-++|+|++|++
T Consensus 255 ~pC~~Cg~~I~~~~~~gR~t~~CP~CQ~ 282 (282)
T PRK13945 255 KPCRKCGTPIERIKLAGRSTHWCPNCQK 282 (282)
T ss_pred CCCCcCCCeeEEEEECCCccEECCCCcC
Confidence 579999987753 2457899999984
No 146
>PRK00420 hypothetical protein; Validated
Probab=68.42 E-value=3.4 Score=36.49 Aligned_cols=29 Identities=14% Similarity=0.209 Sum_probs=23.3
Q ss_pred EeccccccccceecCCCCeeecCcCCCCc
Q 006973 481 WYRACKTCNKKVTDALGSGYWCEGCQKND 509 (623)
Q Consensus 481 ~Y~aC~~C~KKv~~~~~~~~~C~kC~~~~ 509 (623)
-...||.|+-.+....+|..+|+.|+...
T Consensus 22 l~~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 22 LSKHCPVCGLPLFELKDGEVVCPVHGKVY 50 (112)
T ss_pred ccCCCCCCCCcceecCCCceECCCCCCee
Confidence 35789999998876347899999999743
No 147
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=67.92 E-value=4 Score=29.81 Aligned_cols=27 Identities=22% Similarity=0.421 Sum_probs=20.0
Q ss_pred ccccccccceecCCC-CeeecCcCCCCc
Q 006973 483 RACKTCNKKVTDALG-SGYWCEGCQKND 509 (623)
Q Consensus 483 ~aC~~C~KKv~~~~~-~~~~C~kC~~~~ 509 (623)
..|+.|+..+.-+.. +..+|+.|+...
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeE
Confidence 369999998865433 378999999643
No 148
>PRK10445 endonuclease VIII; Provisional
Probab=67.64 E-value=3.1 Score=42.65 Aligned_cols=25 Identities=40% Similarity=1.035 Sum_probs=19.4
Q ss_pred ccccccccceec---CCCCeeecCcCCC
Q 006973 483 RACKTCNKKVTD---ALGSGYWCEGCQK 507 (623)
Q Consensus 483 ~aC~~C~KKv~~---~~~~~~~C~kC~~ 507 (623)
..||.|+-++.. .+-++|+|++|++
T Consensus 236 ~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ~ 263 (263)
T PRK10445 236 EACERCGGIIEKTTLSSRPFYWCPGCQK 263 (263)
T ss_pred CCCCCCCCEeEEEEECCCCcEECCCCcC
Confidence 579999977643 2457899999984
No 149
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=67.54 E-value=2.6 Score=45.30 Aligned_cols=30 Identities=27% Similarity=0.509 Sum_probs=22.8
Q ss_pred eEeccccccccceec--------CCCCeeecCcCCCCc
Q 006973 480 MWYRACKTCNKKVTD--------ALGSGYWCEGCQKND 509 (623)
Q Consensus 480 ~~Y~aC~~C~KKv~~--------~~~~~~~C~kC~~~~ 509 (623)
.--..||.|+||.+. ...|.|+|+.|+...
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEALQLLDNETGEFHCENCGGEL 163 (436)
T ss_pred cccccCCccccchhhhHHHHhhcccCceEEEecCCCch
Confidence 346689999999542 236899999999765
No 150
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=67.14 E-value=2.6 Score=40.51 Aligned_cols=29 Identities=21% Similarity=0.539 Sum_probs=22.5
Q ss_pred EeccccccccceecC--CCCeeecCcCCCCc
Q 006973 481 WYRACKTCNKKVTDA--LGSGYWCEGCQKND 509 (623)
Q Consensus 481 ~Y~aC~~C~KKv~~~--~~~~~~C~kC~~~~ 509 (623)
-|.-||.|+++.+.. .+..|.|+.||...
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L 146 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAMEYGFRCPQCGEML 146 (178)
T ss_pred CEEECCCCCcEEeHHHHhhcCCcCCCCCCCC
Confidence 366799999998753 23569999999865
No 151
>PHA00626 hypothetical protein
Probab=66.69 E-value=4.4 Score=30.77 Aligned_cols=26 Identities=27% Similarity=0.753 Sum_probs=17.5
Q ss_pred cccccccc-eec-----CCCCeeecCcCCCCc
Q 006973 484 ACKTCNKK-VTD-----ALGSGYWCEGCQKND 509 (623)
Q Consensus 484 aC~~C~KK-v~~-----~~~~~~~C~kC~~~~ 509 (623)
.||.|+.. +.. .....|.|.+|+-.+
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~f 33 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYND 33 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCee
Confidence 59999873 332 124679999998543
No 152
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=66.66 E-value=3.7 Score=30.77 Aligned_cols=27 Identities=15% Similarity=0.521 Sum_probs=20.4
Q ss_pred ecccccccc-ceecCCCCeeecCcCCCCc
Q 006973 482 YRACKTCNK-KVTDALGSGYWCEGCQKND 509 (623)
Q Consensus 482 Y~aC~~C~K-Kv~~~~~~~~~C~kC~~~~ 509 (623)
-.-||.|+. -+... .+.|.|.+|+-+.
T Consensus 20 ~~fCP~Cg~~~m~~~-~~r~~C~~Cgyt~ 47 (50)
T PRK00432 20 NKFCPRCGSGFMAEH-LDRWHCGKCGYTE 47 (50)
T ss_pred cCcCcCCCcchhecc-CCcEECCCcCCEE
Confidence 447999998 55544 6899999998653
No 153
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=66.49 E-value=3.3 Score=42.74 Aligned_cols=25 Identities=28% Similarity=0.825 Sum_probs=19.2
Q ss_pred ccccccccceec---CCCCeeecCcCCC
Q 006973 483 RACKTCNKKVTD---ALGSGYWCEGCQK 507 (623)
Q Consensus 483 ~aC~~C~KKv~~---~~~~~~~C~kC~~ 507 (623)
..||.|+.++.. .+-++|+|+.|++
T Consensus 246 ~pC~~Cg~~I~~~~~~gR~t~~CP~CQ~ 273 (274)
T PRK01103 246 EPCRRCGTPIEKIKQGGRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCCeeEEEEECCCCcEECcCCCC
Confidence 469999977643 2357899999986
No 154
>cd04487 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB folds corresponding to the second OB fold (OBF2) of archaeal-specific proteins with similarity to eubacterial RecJ. RecJ is an ssDNA-specific exonuclease. Although the overall sequence similarity of these proteins to eubacterial RecJ proteins is marginal, they appear to carry motifs, which have been shown to be essential for nuclease function in Escherichia coli RecJ. In addition to this OB fold, most proteins in this subfamily contain: i) an N-terminal OB fold belonging to a different domain family (the ribosomal S1-like RNA-binding family); and ii) a domain, C-terminal to OBF2, characteristic of DHH family proteins. DHH family proteins include E. coli RecJ, and are predicted to have a phosphoesterase function.
Probab=66.30 E-value=9.4 Score=30.94 Aligned_cols=41 Identities=24% Similarity=0.380 Sum_probs=32.9
Q ss_pred cEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeee
Q 006973 210 CVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRG 251 (623)
Q Consensus 210 ~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~ 251 (623)
-...|.|.|+.+ .|+|.+|.....+....+++|+-+.+.+-
T Consensus 15 GHvyfsLkD~~a-~i~cv~f~~~~~~~~~~l~~Gd~V~v~G~ 55 (73)
T cd04487 15 GPTIFTLRDETG-TVWAAAFEEAGVRAYPEVEVGDIVRVTGE 55 (73)
T ss_pred CCEEEEEEcCCE-EEEEEEEchhccCCcCCCCCCCEEEEEEE
Confidence 357788899776 89999999877667778999998777653
No 155
>cd04319 PhAsnRS_like_N PhAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Pyrococcus horikoshii AsnRS asparaginyl-tRNA synthetase (AsnRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The archeal enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose.
Probab=66.10 E-value=78 Score=27.14 Aligned_cols=79 Identities=14% Similarity=0.176 Sum_probs=48.6
Q ss_pred eEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHH-HHHH--hhcccCcEEEEeeeEEEecCCCcccc
Q 006973 187 WTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAA-RKFY--DRFQLGKVYYISRGTLRVANKQFKTV 263 (623)
Q Consensus 187 w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~-~kf~--~~l~eG~vy~is~~~V~~a~~~~~~~ 263 (623)
-+|.|||.++ |. .|++.=++|.|.+| .+++.+..+.. +.|. ..|..|+++.+.+. ++.... .
T Consensus 2 V~v~Gwv~~~---R~------~gk~~Fi~lrD~~g-~iQ~v~~~~~~~~~~~~~~~l~~~s~v~V~G~-v~~~~~----~ 66 (103)
T cd04319 2 VTLAGWVYRK---RE------VGKKAFIVLRDSTG-IVQAVFSKDLNEEAYREAKKVGIESSVIVEGA-VKADPR----A 66 (103)
T ss_pred EEEEEEEEeE---Ec------CCCeEEEEEecCCe-eEEEEEeCCCCHHHHHHHhCCCCCCEEEEEEE-EEECCC----C
Confidence 3678888663 32 23444457899998 79998865411 1122 34789999999874 443321 2
Q ss_pred CCceEEEEccCcEEEEc
Q 006973 264 QNDYEMNLNENSEVEEA 280 (623)
Q Consensus 264 ~~~yei~f~~~T~I~~~ 280 (623)
...+||....-..+.++
T Consensus 67 ~~~~Ei~~~~i~vl~~a 83 (103)
T cd04319 67 PGGAEVHGEKLEIIQNV 83 (103)
T ss_pred CCCEEEEEEEEEEEecC
Confidence 34699988654444443
No 156
>PLN02502 lysyl-tRNA synthetase
Probab=65.22 E-value=47 Score=37.86 Aligned_cols=78 Identities=14% Similarity=0.165 Sum_probs=53.8
Q ss_pred CeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechH-------HHHHHhhcccCcEEEEeeeEEEecCC
Q 006973 186 NWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEA-------ARKFYDRFQLGKVYYISRGTLRVANK 258 (623)
Q Consensus 186 ~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~-------~~kf~~~l~eG~vy~is~~~V~~a~~ 258 (623)
..+|.|||.++ |. .|++.=++|.|.+| .|++.+-.+. .+.+...|..|+++.+.+.-.+..
T Consensus 110 ~V~v~GrV~~~---R~------~Gk~~F~~LrD~~g-~iQv~~~~~~~~~~~~~~~~~~~~l~~gdiV~V~G~~~~t~-- 177 (553)
T PLN02502 110 SVSVAGRIMAK---RA------FGKLAFYDLRDDGG-KIQLYADKKRLDLDEEEFEKLHSLVDRGDIVGVTGTPGKTK-- 177 (553)
T ss_pred EEEEEEEEEEE---ec------CCCeEEEEEecCCc-cEEEEEECccccchhHHHHHHHhCCCCCcEEEEEEEEEecC--
Confidence 58899999874 32 34666678999998 8999886432 233445589999999987644332
Q ss_pred CccccCCceEEEEccCcEEEEc
Q 006973 259 QFKTVQNDYEMNLNENSEVEEA 280 (623)
Q Consensus 259 ~~~~~~~~yei~f~~~T~I~~~ 280 (623)
...++|..+.-+.+.++
T Consensus 178 -----~gelel~~~~i~vLs~~ 194 (553)
T PLN02502 178 -----KGELSIFPTSFEVLTKC 194 (553)
T ss_pred -----CCCEEEEEeEEEEEecc
Confidence 23677777666555555
No 157
>cd04488 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched cha
Probab=65.05 E-value=63 Score=25.03 Aligned_cols=46 Identities=24% Similarity=0.268 Sum_probs=30.0
Q ss_pred eEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEEeeeccc
Q 006973 335 PKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSPIVAIKSLKVGDFQG 387 (623)
Q Consensus 335 ~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~kV~~f~G 387 (623)
....+.+.|++| .+.++.|+... +. ......|..+.+. .+++.|+|
T Consensus 18 ~~~~~~~~D~~g-~i~~~~F~~~~--~~---~~~~~~G~~~~v~-Gkv~~~~~ 63 (75)
T cd04488 18 RRLKVTLSDGTG-TLTLVFFNFQP--YL---KKQLPPGTRVRVS-GKVKRFRG 63 (75)
T ss_pred cEEEEEEEcCCC-EEEEEEECCCH--HH---HhcCCCCCEEEEE-EEEeecCC
Confidence 367889999988 89999997321 11 1124556666554 56677765
No 158
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=65.00 E-value=9.5 Score=36.61 Aligned_cols=43 Identities=19% Similarity=0.479 Sum_probs=32.3
Q ss_pred EEEEEEEEEe---------CCCCeEeccccccccceecCCCCeeecCcCCCCc
Q 006973 466 SIKAYISLIK---------PDQAMWYRACKTCNKKVTDALGSGYWCEGCQKND 509 (623)
Q Consensus 466 ~v~a~I~~i~---------~d~~~~Y~aC~~C~KKv~~~~~~~~~C~kC~~~~ 509 (623)
.++|.|.... ++-...|--|+.|+--+... +...+|++|+.+.
T Consensus 124 ivrA~Vis~~~~~~Lst~~~dlGVI~A~CsrC~~~L~~~-~~~l~Cp~Cg~tE 175 (188)
T COG1096 124 IVRARVISTGDPIQLSTKGNDLGVIYARCSRCRAPLVKK-GNMLKCPNCGNTE 175 (188)
T ss_pred EEEEEEEecCCCeEEEecCCcceEEEEEccCCCcceEEc-CcEEECCCCCCEE
Confidence 3667766542 33466799999999988874 6789999999764
No 159
>PRK02801 primosomal replication protein N; Provisional
Probab=64.75 E-value=44 Score=28.85 Aligned_cols=63 Identities=8% Similarity=0.053 Sum_probs=38.9
Q ss_pred eeEEEEEEEEeCCceEEEEccCCceeeEEEEEEEe-----CCcc------EEEEEEechhhhhhhhHhhhcCCCCcEEEE
Q 006973 309 LVDIIGVVQNVSPTMSIRRKSNNEMVPKRDITVAD-----ETKR------TVTVSLWNELATNVGQELLDNADKSPIVAI 377 (623)
Q Consensus 309 ~vDVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D-----~sg~------~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i 377 (623)
.|-++|.++.--++.. +. .|..+ ..++|.= +.+. .|.|++||+.|+.+.+. ...|..|.+
T Consensus 4 ~v~L~Grl~~dpelr~--Tp-~G~~v--~~f~La~~~~~~ea~~~r~~~~~i~~va~G~~Ae~~~~~----l~kGs~v~V 74 (101)
T PRK02801 4 RLVLSGTVCRTPKRKV--SP-SGIPH--CQFVLEHRSVQEEAGLHRQAWCRMPVIVSGNQFQAITQS----ITVGSKITV 74 (101)
T ss_pred EEEEEEEECcCcceEE--CC-CCCeE--EEEEEEEeCeEecCCCceeEEEEEEEEEEcHHHHHHHhh----cCCCCEEEE
Confidence 4667888877666543 22 35433 3333322 2222 39999999999987543 466888888
Q ss_pred EeE
Q 006973 378 KSL 380 (623)
Q Consensus 378 ~~~ 380 (623)
.|-
T Consensus 75 ~G~ 77 (101)
T PRK02801 75 QGF 77 (101)
T ss_pred EEE
Confidence 754
No 160
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=64.44 E-value=3.6 Score=36.35 Aligned_cols=22 Identities=18% Similarity=0.561 Sum_probs=18.8
Q ss_pred ccccccceecCCCCeeecCcCCCCc
Q 006973 485 CKTCNKKVTDALGSGYWCEGCQKND 509 (623)
Q Consensus 485 C~~C~KKv~~~~~~~~~C~kC~~~~ 509 (623)
||.|+.++.-. .++|+.|+..+
T Consensus 1 CPvCg~~l~vt---~l~C~~C~t~i 22 (113)
T PF09862_consen 1 CPVCGGELVVT---RLKCPSCGTEI 22 (113)
T ss_pred CCCCCCceEEE---EEEcCCCCCEE
Confidence 99999998754 69999999865
No 161
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=64.36 E-value=3.9 Score=30.42 Aligned_cols=26 Identities=23% Similarity=0.497 Sum_probs=19.8
Q ss_pred eccccccccceec-CCCCeeecCcCCC
Q 006973 482 YRACKTCNKKVTD-ALGSGYWCEGCQK 507 (623)
Q Consensus 482 Y~aC~~C~KKv~~-~~~~~~~C~kC~~ 507 (623)
-.-|..|++++.. ......+|+.|+-
T Consensus 6 ~Y~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 6 EYKCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred EEEhhhcCCeeehhhccCceeCCCCCc
Confidence 3469999999973 3456789999984
No 162
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=64.32 E-value=4.1 Score=41.93 Aligned_cols=27 Identities=19% Similarity=0.538 Sum_probs=20.7
Q ss_pred ccccccccceec---CCCCeeecCcCCCCc
Q 006973 483 RACKTCNKKVTD---ALGSGYWCEGCQKND 509 (623)
Q Consensus 483 ~aC~~C~KKv~~---~~~~~~~C~kC~~~~ 509 (623)
..||.|+.++.. .+-++|+|+.|++-.
T Consensus 236 ~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ~~~ 265 (269)
T PRK14811 236 QPCPRCGTPIEKIVVGGRGTHFCPQCQPLR 265 (269)
T ss_pred CCCCcCCCeeEEEEECCCCcEECCCCcCCC
Confidence 579999987653 235789999999753
No 163
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=64.06 E-value=4.4 Score=31.53 Aligned_cols=32 Identities=22% Similarity=0.395 Sum_probs=23.2
Q ss_pred EeccccccccceecCCCCeeecCcCCCCcccccee
Q 006973 481 WYRACKTCNKKVTDALGSGYWCEGCQKNDEECSLR 515 (623)
Q Consensus 481 ~Y~aC~~C~KKv~~~~~~~~~C~kC~~~~~~~~~r 515 (623)
.|.||..|++-+.++ .-.|+.|+.+....+|+
T Consensus 3 ~~kAC~~Ck~l~~~d---~e~CP~Cgs~~~te~W~ 34 (64)
T COG2093 3 TEKACKNCKRLTPED---TEICPVCGSTDLTEEWF 34 (64)
T ss_pred hhHHHhhccccCCCC---CccCCCCCCcccchhhc
Confidence 488999999988754 34699999764333444
No 164
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=64.01 E-value=3.5 Score=27.41 Aligned_cols=26 Identities=23% Similarity=0.478 Sum_probs=13.8
Q ss_pred eccccccccceecCCCCeeecCcCCC
Q 006973 482 YRACKTCNKKVTDALGSGYWCEGCQK 507 (623)
Q Consensus 482 Y~aC~~C~KKv~~~~~~~~~C~kC~~ 507 (623)
.++||.|+.--+-.++..|-|+.|+.
T Consensus 2 ~p~Cp~C~se~~y~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 2 LPKCPLCGSEYTYEDGELLVCPECGH 27 (30)
T ss_dssp S---TTT-----EE-SSSEEETTTTE
T ss_pred CCCCCCCCCcceeccCCEEeCCcccc
Confidence 57899999876655567899999974
No 165
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=63.93 E-value=19 Score=44.29 Aligned_cols=73 Identities=21% Similarity=0.322 Sum_probs=52.4
Q ss_pred eeccccCCC-CCCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeEE
Q 006973 175 HPLVSLNPY-QGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGTL 253 (623)
Q Consensus 175 ~~I~~L~p~-~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~V 253 (623)
.++.+|... ....+|-|-|+... ....++|+ .+.-++|-|.+| .+.+++|.+..+++.+.|++|.++.+. ++|
T Consensus 933 ~~~~~l~~~~~~~v~v~g~i~~~~---~~~tk~g~-~maf~~leD~tg-~~e~~vFp~~y~~~~~~l~~~~~~~v~-G~v 1006 (1107)
T PRK06920 933 PSLAQAMRHKKKVQRAIVYITSVK---VIRTKKGQ-KMAFITFCDQND-EMEAVVFPETYIHFSDKLQEGAIVLVD-GTI 1006 (1107)
T ss_pred cCHHHHhhcCCCEEEEEEEEEEeE---eecCCCCC-eEEEEEEeeCCC-cEEEEECHHHHHHHHHHhccCCEEEEE-EEE
Confidence 466666432 23466777777643 33333343 244568899999 899999999999999999999999996 444
No 166
>cd04100 Asp_Lys_Asn_RS_N Asp_Lys_Asn_RS_N: N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases (AspRS, AsnRS, and LysRS). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Included in this group are archeal and archeal-like A
Probab=63.00 E-value=19 Score=29.79 Aligned_cols=60 Identities=10% Similarity=0.154 Sum_probs=38.4
Q ss_pred EEEEeCcccceeecccccccc--ccccCccceeeEEEEcceeeeccC---CCceEEEEEEeeeee
Q 006973 43 MFNASDGKKRLKAILPSNLSS--EVISGNIQNKGLIRLLDYALNEIP---TKSEKYLIVTKCEVV 102 (623)
Q Consensus 43 r~~lSDG~~~~~~mlat~ln~--~v~~~~l~~~siirl~~y~~~~~~---~~~~~vlii~~lev~ 102 (623)
=+.|.||...+++++...... .-.-..|..||+|.+.......-. .++..=|.+.+++++
T Consensus 19 Fi~Lrd~~~~iQ~v~~~~~~~~~~~~~~~l~~~s~V~v~G~~~~~~~~~~~~~~~El~~~~i~il 83 (85)
T cd04100 19 FIDLRDGSGIVQVVVNKEELGEFFEEAEKLRTESVVGVTGTVVKRPEGNLATGEIELQAEELEVL 83 (85)
T ss_pred EEEEEeCCeeEEEEEECCcChHHHHHHhCCCCCCEEEEEeEEEECCCCCCCCCCEEEEEeEEEEE
Confidence 467899999999998655432 112236899999999998876421 111234445555544
No 167
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=62.55 E-value=4.8 Score=37.39 Aligned_cols=28 Identities=25% Similarity=0.603 Sum_probs=20.7
Q ss_pred eccccccccceecC-------CCCeeecCcCCCCc
Q 006973 482 YRACKTCNKKVTDA-------LGSGYWCEGCQKND 509 (623)
Q Consensus 482 Y~aC~~C~KKv~~~-------~~~~~~C~kC~~~~ 509 (623)
+.-||.|+++.... .++.+.|+.|+...
T Consensus 99 ~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 99 YYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEEL 133 (147)
T ss_pred EEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEE
Confidence 55699999988642 23459999999764
No 168
>PRK05813 single-stranded DNA-binding protein; Provisional
Probab=62.42 E-value=38 Score=33.68 Aligned_cols=64 Identities=13% Similarity=0.090 Sum_probs=49.0
Q ss_pred CCCCeEEEEEEEeeccccccccCCCcccEEEEEEEeCC----CCeEEEEEechHHHHHHhhcccCcEEEEee
Q 006973 183 YQGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDED----GTQIQATMFNEAARKFYDRFQLGKVYYISR 250 (623)
Q Consensus 183 ~~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~----G~~I~at~~~~~~~kf~~~l~eG~vy~is~ 250 (623)
..+...+.||+++.-.+|...+ |. .+.+|.|+=.. -+-|.+++|+..|+... .|+.|+-+.+.+
T Consensus 108 ~~N~V~LiGrL~~DPelR~t~~--G~-~va~f~lAvnr~~~~td~i~~v~wg~~Ae~~~-~l~KG~~V~V~G 175 (219)
T PRK05813 108 NPNEIFLDGYICKEPVYRTTPF--GR-EIADLLLAVNRPYNKSDYIPCIAWGRNARFCK-TLEVGDNIRVWG 175 (219)
T ss_pred CccEEEEEEEccCCCeEEECCC--CC-EEEEEEEEEcCCCCCceEEEEEEEhHHhHHHh-hCCCCCEEEEEE
Confidence 3568899999999988887543 22 57777776332 35799999999988765 599999999874
No 169
>TIGR00458 aspS_arch aspartyl-tRNA synthetase, archaeal type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_arch, represents aspartyl-tRNA synthetases from the eukaryotic cytosol and from the Archaea. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn).
Probab=62.30 E-value=67 Score=35.45 Aligned_cols=81 Identities=22% Similarity=0.222 Sum_probs=54.6
Q ss_pred CCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechH----HHHHHhhcccCcEEEEeeeEEEecCCCc
Q 006973 185 GNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEA----ARKFYDRFQLGKVYYISRGTLRVANKQF 260 (623)
Q Consensus 185 ~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~----~~kf~~~l~eG~vy~is~~~V~~a~~~~ 260 (623)
..-+|+|||.++ |. .|++.=++|.|.+| .|++++.... .-++-..|..|+++.+.+.- ....+
T Consensus 13 ~~v~i~G~v~~~---R~------~g~~~Fi~lrd~~g-~iQ~v~~~~~~~~~~~~~~~~l~~~s~v~v~G~v-~~~~~-- 79 (428)
T TIGR00458 13 QEVTFMGWVHEI---RD------LGGLIFVLLRDREG-LIQITAPAKKVSKNLFKWAKKLNLESVVAVRGIV-KIKEK-- 79 (428)
T ss_pred CEEEEEEEEEEE---ec------CCCcEEEEEEeCCe-eEEEEEECCcCCHHHHHHHhCCCCCcEEEEEEEE-EecCC--
Confidence 467899999763 32 34555578999999 8999986432 22333569999999998744 33221
Q ss_pred cccCCceEEEEccCcEEEEc
Q 006973 261 KTVQNDYEMNLNENSEVEEA 280 (623)
Q Consensus 261 ~~~~~~yei~f~~~T~I~~~ 280 (623)
....+||....-+.+.++
T Consensus 80 --~~~~~el~~~~i~vl~~~ 97 (428)
T TIGR00458 80 --APGGFEIIPTKIEVINEA 97 (428)
T ss_pred --CCCcEEEEEeEEEEEecC
Confidence 245789988776666655
No 170
>PRK11827 hypothetical protein; Provisional
Probab=62.17 E-value=5.5 Score=31.02 Aligned_cols=29 Identities=21% Similarity=0.187 Sum_probs=21.9
Q ss_pred eccccccccceecCC-CCeeecCcCCCCcc
Q 006973 482 YRACKTCNKKVTDAL-GSGYWCEGCQKNDE 510 (623)
Q Consensus 482 Y~aC~~C~KKv~~~~-~~~~~C~kC~~~~~ 510 (623)
-.+||.|+..+.... .....|+.|+..++
T Consensus 8 ILaCP~ckg~L~~~~~~~~Lic~~~~laYP 37 (60)
T PRK11827 8 IIACPVCNGKLWYNQEKQELICKLDNLAFP 37 (60)
T ss_pred heECCCCCCcCeEcCCCCeEECCccCeecc
Confidence 368999999987542 34688999997763
No 171
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=61.77 E-value=10 Score=28.15 Aligned_cols=27 Identities=19% Similarity=0.587 Sum_probs=19.6
Q ss_pred cccccccceecCCC---CeeecCcCCCCcc
Q 006973 484 ACKTCNKKVTDALG---SGYWCEGCQKNDE 510 (623)
Q Consensus 484 aC~~C~KKv~~~~~---~~~~C~kC~~~~~ 510 (623)
-||.|+.-+....+ ..|.|+.|+-...
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~ 31 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEEP 31 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeEE
Confidence 49999988755422 2799999997653
No 172
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=61.61 E-value=3.2 Score=39.13 Aligned_cols=27 Identities=15% Similarity=0.352 Sum_probs=21.0
Q ss_pred eccccccccceecC--CCCeeecCcCCCC
Q 006973 482 YRACKTCNKKVTDA--LGSGYWCEGCQKN 508 (623)
Q Consensus 482 Y~aC~~C~KKv~~~--~~~~~~C~kC~~~ 508 (623)
|.-||.|+++.+.. .+..|.|+.||..
T Consensus 109 ~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 109 FFICPNMCVRFTFNEAMELNFTCPRCGAM 137 (158)
T ss_pred eEECCCCCcEeeHHHHHHcCCcCCCCCCE
Confidence 66799999998753 1346999999975
No 173
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=61.56 E-value=6.3 Score=28.65 Aligned_cols=26 Identities=15% Similarity=0.336 Sum_probs=21.2
Q ss_pred cccccccceecCCCCeeecCcCCCCc
Q 006973 484 ACKTCNKKVTDALGSGYWCEGCQKND 509 (623)
Q Consensus 484 aC~~C~KKv~~~~~~~~~C~kC~~~~ 509 (623)
-|..|+..+.....+.-+|+.|+...
T Consensus 4 ~C~~Cg~~~~~~~~~~irC~~CG~rI 29 (44)
T smart00659 4 ICGECGRENEIKSKDVVRCRECGYRI 29 (44)
T ss_pred ECCCCCCEeecCCCCceECCCCCceE
Confidence 58999999887666789999998643
No 174
>COG0017 AsnS Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]
Probab=60.92 E-value=58 Score=35.76 Aligned_cols=92 Identities=20% Similarity=0.270 Sum_probs=62.9
Q ss_pred eeeccccCCCC--CCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEech-H-HHHH-HhhcccCcEEEE
Q 006973 174 VHPLVSLNPYQ--GNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNE-A-ARKF-YDRFQLGKVYYI 248 (623)
Q Consensus 174 ~~~I~~L~p~~--~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~-~-~~kf-~~~l~eG~vy~i 248 (623)
.+.|+++.+.. ..-+|.|-|-++ |+.|++.=+.|.|.+| .|+|++... . -+.| -..|.-+.++.+
T Consensus 4 ~~~i~di~~~~~~~~V~v~GWV~~~---------R~~g~i~Fi~lrDgsg-~iQ~v~~~~~~~~~~~~~~~L~~es~v~V 73 (435)
T COG0017 4 RTYIKDIKPHVGGQEVTVRGWVHNK---------RDLGKIIFLVLRDGSG-FIQAVVPKNKVYEELFKAKKLTLESSVVV 73 (435)
T ss_pred eeeHHhhhccCCCcEEEEEEEeeee---------cccCCeEEEEEEcCCc-EEEEEEECCCCcHHHhhhhcCCCccEEEE
Confidence 36777777655 477788877553 3355655578999999 699999852 2 1222 346888899988
Q ss_pred eeeEEEecCCCccccCCceEEEEccCcEEEEc
Q 006973 249 SRGTLRVANKQFKTVQNDYEMNLNENSEVEEA 280 (623)
Q Consensus 249 s~~~V~~a~~~~~~~~~~yei~f~~~T~I~~~ 280 (623)
.+- |+.+.+ .+..|||....=..+..+
T Consensus 74 ~G~-v~~~~~----a~~g~El~v~~i~Vl~~a 100 (435)
T COG0017 74 TGI-VKASPK----APQGFELQVEKIEVLGEA 100 (435)
T ss_pred EEE-EEcCCC----CCCCEEEEEEEEEEeecc
Confidence 754 444432 678999999886666666
No 175
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=60.45 E-value=1.1e+02 Score=27.30 Aligned_cols=69 Identities=16% Similarity=0.263 Sum_probs=39.9
Q ss_pred eeEEEEEEEEeCCceEEEEccCCceeeEEEEEEEeC------CccEEEEEEechhhhhhhhHhhhcCCCCcEEEEE-eEE
Q 006973 309 LVDIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADE------TKRTVTVSLWNELATNVGQELLDNADKSPIVAIK-SLK 381 (623)
Q Consensus 309 ~vDVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~------sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~-~~k 381 (623)
.|-++|.+..--++. .+. +|.. .-.+.|.-. ...-+.|++||+.|+.+.+. ...|.-|.+. .++
T Consensus 5 ~v~LiGrL~~DPelr--~t~-~G~~--v~~fslAv~~~~~~~~t~w~~v~~wg~~Ae~~~~~----l~KG~~V~V~G~l~ 75 (121)
T PRK07459 5 SVTLVGRAGRDPEVR--YFE-SGSV--VCNLTLAVNRRSRDDEPDWFNLEIWGKTAQVAADY----VKKGSLIGITGSLK 75 (121)
T ss_pred EEEEEEEccCCCEEE--EcC-CCCE--EEEEEEEecccccCCCceEEEEEEehHHHHHHHHH----cCCCCEEEEEEEEE
Confidence 466888887632222 122 3543 333444322 22369999999999887554 4556666664 456
Q ss_pred eeecc
Q 006973 382 VGDFQ 386 (623)
Q Consensus 382 V~~f~ 386 (623)
...|.
T Consensus 76 ~~~~~ 80 (121)
T PRK07459 76 FDRWT 80 (121)
T ss_pred ecceE
Confidence 66663
No 176
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=60.29 E-value=78 Score=29.44 Aligned_cols=35 Identities=17% Similarity=0.272 Sum_probs=24.7
Q ss_pred EEEEEEechhhhhhhhHhhhcCCCCcEEEEE-eEEeeecc
Q 006973 348 TVTVSLWNELATNVGQELLDNADKSPIVAIK-SLKVGDFQ 386 (623)
Q Consensus 348 ~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~-~~kV~~f~ 386 (623)
-+.|++||..|+.+.+. +..|.-|++. .++...|.
T Consensus 55 w~~V~~wg~~Ae~v~~~----l~KG~~V~V~GrL~~~~w~ 90 (148)
T PRK08182 55 WAPVELWHRDAEHWARL----YQKGMRVLVEGRMERDEWT 90 (148)
T ss_pred EEEEEEEhHHHHHHHHh----cCCCCEEEEEEEEEecccC
Confidence 58999999999887554 3456655554 46666674
No 177
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.23 E-value=5.4 Score=34.34 Aligned_cols=32 Identities=19% Similarity=0.500 Sum_probs=23.6
Q ss_pred eccccccccceecCCCCeeecCcCCCCccccceeEEEE
Q 006973 482 YRACKTCNKKVTDALGSGYWCEGCQKNDEECSLRYIMV 519 (623)
Q Consensus 482 Y~aC~~C~KKv~~~~~~~~~C~kC~~~~~~~~~ry~l~ 519 (623)
-+.||.|++++.-. ..+|.+|..++. -+|+++
T Consensus 6 ~~~cPvcg~~~iVT---eL~c~~~etTVr---g~F~~s 37 (122)
T COG3877 6 INRCPVCGRKLIVT---ELKCSNCETTVR---GNFKMS 37 (122)
T ss_pred CCCCCcccccceeE---EEecCCCCceEe---cceecc
Confidence 46799999998753 589999998753 355543
No 178
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=59.85 E-value=5.3 Score=31.83 Aligned_cols=28 Identities=18% Similarity=0.536 Sum_probs=21.5
Q ss_pred eccccccccce-----------------------------ecCCCCeeecCcCCCCc
Q 006973 482 YRACKTCNKKV-----------------------------TDALGSGYWCEGCQKND 509 (623)
Q Consensus 482 Y~aC~~C~KKv-----------------------------~~~~~~~~~C~kC~~~~ 509 (623)
..+||.|+..+ .+..+|...|+.|++.+
T Consensus 7 iL~Cp~ck~pL~~~~l~~~~~~~~~~lp~~~~~~~~~l~~~~i~eg~L~Cp~c~r~Y 63 (68)
T PF03966_consen 7 ILACPVCKGPLDWEALVETAQLGLSELPKELPEDYHVLLEVEIVEGELICPECGREY 63 (68)
T ss_dssp TBB-TTTSSBEHHHHHHHHHHCCCCHCHHCHHCHCEHHCTEETTTTEEEETTTTEEE
T ss_pred hhcCCCCCCcchHHHHHHHHHhCcccCCCCCccchhhhhcccccCCEEEcCCCCCEE
Confidence 46899999888 34557999999999765
No 179
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=59.79 E-value=8.3 Score=30.39 Aligned_cols=28 Identities=25% Similarity=0.567 Sum_probs=20.9
Q ss_pred eccccccccceecCCCCeeecCcCCCCccccce
Q 006973 482 YRACKTCNKKVTDALGSGYWCEGCQKNDEECSL 514 (623)
Q Consensus 482 Y~aC~~C~KKv~~~~~~~~~C~kC~~~~~~~~~ 514 (623)
+.||..|+.-+..+ .|+.|+.+.....|
T Consensus 5 ~~AC~~C~~i~~~~-----~Cp~Cgs~~~S~~w 32 (64)
T PRK06393 5 YRACKKCKRLTPEK-----TCPVHGDEKTTTEW 32 (64)
T ss_pred hhhHhhCCcccCCC-----cCCCCCCCcCCcCc
Confidence 78999999988432 79999976534333
No 180
>PF15489 CTC1: CST, telomere maintenance, complex subunit CTC1
Probab=59.57 E-value=1.1e+02 Score=37.53 Aligned_cols=69 Identities=12% Similarity=0.206 Sum_probs=53.4
Q ss_pred CCCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeEEEecC
Q 006973 184 QGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGTLRVAN 257 (623)
Q Consensus 184 ~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~V~~a~ 257 (623)
...-.|-|+|++.+.+-..+. . ..|=+.|.| .+..+.+.+-...---|+..|..|+.|.|++-+|..-.
T Consensus 165 ~~~~~v~G~v~~ls~l~~~~~---k-~fF~l~L~~-~~~~v~viVq~pa~l~Wh~~L~~G~~yvlT~Lrvs~ir 233 (1144)
T PF15489_consen 165 GRQLNVAGKVVRLSALVKSHG---K-TFFILSLGD-AGSHVPVIVQEPAQLVWHRALRPGRAYVLTSLRVSKIR 233 (1144)
T ss_pred cCceeeeeEEEEeeceEEEcc---e-EEEEEEeCC-CCceeEEEEEecchhhhhhhcccCCeEEEeeeEEEEec
Confidence 346789999999998866543 1 366667775 45588877777777889999999999999999887543
No 181
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=59.45 E-value=6.1 Score=27.41 Aligned_cols=28 Identities=18% Similarity=0.360 Sum_probs=19.3
Q ss_pred eccccccccceecC------CCCeeecCcCCCCc
Q 006973 482 YRACKTCNKKVTDA------LGSGYWCEGCQKND 509 (623)
Q Consensus 482 Y~aC~~C~KKv~~~------~~~~~~C~kC~~~~ 509 (623)
...||.|+....-. .++..+|++|+..+
T Consensus 2 ~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 2 RIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EEECCCCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 35799999865322 13468999999764
No 182
>TIGR00621 ssb single stranded DNA-binding protein (ssb). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=59.05 E-value=98 Score=29.25 Aligned_cols=35 Identities=17% Similarity=0.301 Sum_probs=25.1
Q ss_pred EEEEEEechhhhhhhhHhhhcCCCCcEEEEE-eEEeeecc
Q 006973 348 TVTVSLWNELATNVGQELLDNADKSPIVAIK-SLKVGDFQ 386 (623)
Q Consensus 348 ~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~-~~kV~~f~ 386 (623)
-+.|++||+.|+.+... +..+.-|.|. .++...|.
T Consensus 52 ~~~v~~wg~~Ae~~~~~----l~KG~~V~V~G~L~~~~~~ 87 (164)
T TIGR00621 52 WHDIVIFGRLAEVAAQY----LKKGSLVYVEGRLRTRKWE 87 (164)
T ss_pred EEEEEEehHHHHHHHHh----CCCCCEEEEEEEEEeceEE
Confidence 79999999999887544 4556766665 45666674
No 183
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=58.56 E-value=6.8 Score=26.43 Aligned_cols=24 Identities=25% Similarity=0.602 Sum_probs=18.2
Q ss_pred cccccccceecCCCCeeecCcCCC
Q 006973 484 ACKTCNKKVTDALGSGYWCEGCQK 507 (623)
Q Consensus 484 aC~~C~KKv~~~~~~~~~C~kC~~ 507 (623)
-|..|+..+.....+.-+|..|+-
T Consensus 2 ~C~~Cg~~~~~~~~~~irC~~CG~ 25 (32)
T PF03604_consen 2 ICGECGAEVELKPGDPIRCPECGH 25 (32)
T ss_dssp BESSSSSSE-BSTSSTSSBSSSS-
T ss_pred CCCcCCCeeEcCCCCcEECCcCCC
Confidence 488999999876566789999984
No 184
>PRK06341 single-stranded DNA-binding protein; Provisional
Probab=58.56 E-value=44 Score=31.78 Aligned_cols=64 Identities=16% Similarity=0.253 Sum_probs=46.3
Q ss_pred CCCeEEEEEEEeeccccccccCCCcccEEEEEEEeC-------CCC------eEEEEEech-HHHHHHhhcccCcEEEEe
Q 006973 184 QGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDE-------DGT------QIQATMFNE-AARKFYDRFQLGKVYYIS 249 (623)
Q Consensus 184 ~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~-------~G~------~I~at~~~~-~~~kf~~~l~eG~vy~is 249 (623)
.+..+|.+|+.+--++|...+ | ..+.+|.|+=. .|. -+++++|++ .++.+...|+.|+.+.+.
T Consensus 5 mN~V~LiGrLg~DPElR~t~s--G-~~v~~fsVAvn~~~kd~~~Ge~~e~T~w~~Vv~fg~~~Ae~~~~~LkKG~~V~Ve 81 (166)
T PRK06341 5 VNKVILIGNLGADPEIRRTQD--G-RPIANLRIATSETWRDRNSGERKEKTEWHRVVIFNEGLCKVAEQYLKKGAKVYIE 81 (166)
T ss_pred ceEEEEEEEecCCCEEEEcCC--C-CEEEEEEEEEccceecCCCCcccccceEEEEEEeChHHHHHHHHhcCCCCEEEEE
Confidence 467889999999777776543 2 14555544322 232 368999996 899999999999999987
Q ss_pred e
Q 006973 250 R 250 (623)
Q Consensus 250 ~ 250 (623)
.
T Consensus 82 G 82 (166)
T PRK06341 82 G 82 (166)
T ss_pred E
Confidence 4
No 185
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=58.06 E-value=5.6 Score=40.99 Aligned_cols=24 Identities=21% Similarity=0.689 Sum_probs=18.5
Q ss_pred ccccccccceec---CCCCeeecCcCC
Q 006973 483 RACKTCNKKVTD---ALGSGYWCEGCQ 506 (623)
Q Consensus 483 ~aC~~C~KKv~~---~~~~~~~C~kC~ 506 (623)
..||.|+..+.. .+-++|+|+.|+
T Consensus 246 ~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (272)
T TIGR00577 246 EPCRRCGTPIEKIKVGGRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCCeeEEEEECCCCCEECCCCC
Confidence 479999977653 235789999996
No 186
>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=57.82 E-value=8 Score=30.70 Aligned_cols=30 Identities=17% Similarity=0.438 Sum_probs=23.3
Q ss_pred eEeccccccccceec-CCCCeeecCcCCCCc
Q 006973 480 MWYRACKTCNKKVTD-ALGSGYWCEGCQKND 509 (623)
Q Consensus 480 ~~Y~aC~~C~KKv~~-~~~~~~~C~kC~~~~ 509 (623)
..-..||.|+..... .....|.|+.|+...
T Consensus 26 ~TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 26 YTSQTCPRCGHRNKKRRSGRVFTCPNCGFEM 56 (69)
T ss_pred CCccCccCcccccccccccceEEcCCCCCEE
Confidence 467889999988876 235689999999753
No 187
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=57.09 E-value=70 Score=30.63 Aligned_cols=35 Identities=17% Similarity=0.467 Sum_probs=25.6
Q ss_pred EEEEEEechhhhhhhhHhhhcCCCCcEEEEE-eEEeeecc
Q 006973 348 TVTVSLWNELATNVGQELLDNADKSPIVAIK-SLKVGDFQ 386 (623)
Q Consensus 348 ~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~-~~kV~~f~ 386 (623)
-+.|++||+.|+.+.+. +..|.-|.|. .++...|.
T Consensus 48 wi~~v~wgk~Ae~~~~~----l~KG~~V~VeGrL~~r~ye 83 (173)
T PRK06751 48 FINCVIWRKQAENVANY----LKKGSLAGVDGRLQTRNYE 83 (173)
T ss_pred EEEEEEeCcHHHHHHHH----cCCCCEEEEEEEEEeCccC
Confidence 79999999999887654 4556666664 46666774
No 188
>cd04484 polC_OBF polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding domain of Bacillus subtilis type C replicative DNA polymerase III alpha subunit (polC). Replication in B. subtilis and Staphylococcus aureus requires two different polymerases, polC and DnaE. The holoenzyme is thought to include the two different polymerases. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Probab=56.49 E-value=89 Score=25.77 Aligned_cols=55 Identities=20% Similarity=0.126 Sum_probs=36.7
Q ss_pred eEEEEEEEEeCCCcEEEEEehHhHHHHhCCCHHHHHHHHhhcCCchhHHHHHHHhcCceEEEEEEEEeeecCceeee
Q 006973 515 RYIMVARVCDGSGEAWISIFNEEAERIIGCSADELNELKSQLGDDNSYQMKLKEVTWVPHLLRVSVAQQEYNNEKRQ 591 (623)
Q Consensus 515 ry~l~~~i~D~Tg~~~~~~F~~~ae~llG~sA~el~~~~~~~~~~~~~~~~l~~~~~~~~~f~v~~k~~~y~~~~r~ 591 (623)
++++.+.++|.|+++.+-.|.+ ...+.+.+ ++ ..|.-..++.++..++|..+.-+
T Consensus 20 ~~i~~~~itD~t~Si~~K~F~~-------~~~~~~~~--------------ik-~~G~~v~v~G~v~~D~f~~e~~~ 74 (82)
T cd04484 20 RKILTFKVTDYTSSITVKKFLR-------KDEKDKEE--------------LK-SKGDWVRVRGKVQYDTFSKELVL 74 (82)
T ss_pred CEEEEEEEEcCCCCEEEEEecc-------CChhHHhh--------------cc-cCCCEEEEEEEEEEccCCCceEE
Confidence 7889999999999999999964 11111111 11 03455778888888898876443
No 189
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=56.19 E-value=35 Score=42.39 Aligned_cols=77 Identities=9% Similarity=0.138 Sum_probs=52.6
Q ss_pred cccccccccccCCcceeEEEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCc
Q 006973 294 FVPIDELGRYVNGTELVDIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSP 373 (623)
Q Consensus 294 f~~i~di~~~~~~~~~vDVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~ 373 (623)
.+++++|.. ...+..|-|+|+|+.+... .+|+ |+ ..--++|.|.+| .+++++|-+....+... ...+.
T Consensus 988 ~~~~~~l~~-~~~~~~v~v~g~i~~~k~~---~Tk~-G~--~maf~~leD~tg-~~e~vvFp~~y~~~~~~----l~~~~ 1055 (1170)
T PRK07374 988 PISLSSLEE-QPDKAKVSAIAMIPEMKQV---TTRK-GD--RMAILQLEDLTG-SCEAVVFPKSYERLSDH----LMTDT 1055 (1170)
T ss_pred CcCHHHHhc-ccCCCEEEEEEEEEEeEec---ccCC-CC--EEEEEEEEECCC-CEEEEECHHHHHHHHHH----hccCC
Confidence 345666643 2345678999999988644 4553 54 245689999999 79999998877776543 34567
Q ss_pred EEEEEeEEee
Q 006973 374 IVAIKSLKVG 383 (623)
Q Consensus 374 Vv~i~~~kV~ 383 (623)
++.+++ +|.
T Consensus 1056 ~~~v~g-~v~ 1064 (1170)
T PRK07374 1056 RLLVWA-KVD 1064 (1170)
T ss_pred EEEEEE-EEE
Confidence 777765 444
No 190
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=56.15 E-value=11 Score=32.53 Aligned_cols=30 Identities=23% Similarity=0.459 Sum_probs=24.4
Q ss_pred EeccccccccceecCCCCeeecCcCCCCcc
Q 006973 481 WYRACKTCNKKVTDALGSGYWCEGCQKNDE 510 (623)
Q Consensus 481 ~Y~aC~~C~KKv~~~~~~~~~C~kC~~~~~ 510 (623)
+.+-||.|+.--+-+..+.|.|+.|...+.
T Consensus 2 ~lp~cp~c~sEytYed~~~~~cpec~~ew~ 31 (112)
T COG2824 2 SLPPCPKCNSEYTYEDGGQLICPECAHEWN 31 (112)
T ss_pred CCCCCCccCCceEEecCceEeCchhccccc
Confidence 367899999887766577899999987764
No 191
>TIGR00499 lysS_bact lysyl-tRNA synthetase, eukaryotic and non-spirochete bacterial. This model represents the lysyl-tRNA synthetases that are class II amino-acyl tRNA synthetases. It includes all eukaryotic and most bacterial examples of the enzyme, but not archaeal or spirochete forms.
Probab=55.03 E-value=88 Score=35.23 Aligned_cols=79 Identities=19% Similarity=0.215 Sum_probs=53.5
Q ss_pred CCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechH----H-HHHHhhcccCcEEEEeeeEEEecCCC
Q 006973 185 GNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEA----A-RKFYDRFQLGKVYYISRGTLRVANKQ 259 (623)
Q Consensus 185 ~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~----~-~kf~~~l~eG~vy~is~~~V~~a~~~ 259 (623)
...+|.|||.++ |. .|++.=++|.|.+| .|++.+-.+. . +.+...|..|+++.+.+.-.+..
T Consensus 54 ~~v~v~Grv~~~---R~------~gk~~F~~l~D~~g-~iQ~~~~~~~~~~~~~~~~~~~l~~gd~V~v~G~~~~t~--- 120 (496)
T TIGR00499 54 IEVSIAGRIMAR---RS------MGKATFITLQDESG-QIQLYVNKDDLPEDFYEFDEYLLDLGDIIGVTGYPFKTK--- 120 (496)
T ss_pred CEEEEEEEEEEE---ec------CCCeEEEEEEcCCc-cEEEEEECCcCcHHHHHHHHhcCCCCCEEEEEEEEEECC---
Confidence 358899999873 42 34565578999999 8999886432 1 22233589999999998543221
Q ss_pred ccccCCceEEEEccCcEEEEc
Q 006973 260 FKTVQNDYEMNLNENSEVEEA 280 (623)
Q Consensus 260 ~~~~~~~yei~f~~~T~I~~~ 280 (623)
...++|..+.-+.+.++
T Consensus 121 ----~gelel~~~~i~ilsk~ 137 (496)
T TIGR00499 121 ----TGELSVHVTELQILTKA 137 (496)
T ss_pred ----CCcEEEEeeEEEEEecC
Confidence 34588887776666555
No 192
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=54.38 E-value=9.1 Score=26.02 Aligned_cols=28 Identities=14% Similarity=0.210 Sum_probs=20.9
Q ss_pred eccccccccceec-CCCCeeecCcCCCCc
Q 006973 482 YRACKTCNKKVTD-ALGSGYWCEGCQKND 509 (623)
Q Consensus 482 Y~aC~~C~KKv~~-~~~~~~~C~kC~~~~ 509 (623)
...|+.|+.-+.- ..++.+.|..|+..+
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccCCcEe
Confidence 4578899876544 447789999999764
No 193
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=54.37 E-value=9.9 Score=26.30 Aligned_cols=27 Identities=22% Similarity=0.431 Sum_probs=19.1
Q ss_pred ccccccccceecC------CCCeeecCcCCCCc
Q 006973 483 RACKTCNKKVTDA------LGSGYWCEGCQKND 509 (623)
Q Consensus 483 ~aC~~C~KKv~~~------~~~~~~C~kC~~~~ 509 (623)
..||.|+++-.-. .+..-+|.+|+..+
T Consensus 3 i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 4699999875321 24568999999754
No 194
>cd04318 EcAsnRS_like_N EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial
Probab=54.23 E-value=38 Score=27.65 Aligned_cols=61 Identities=18% Similarity=0.147 Sum_probs=36.9
Q ss_pred EEEEEeCcccc--eeeccccccccccccCccceeeEEEEcceeeeccCCCceEEEEEEeeeee
Q 006973 42 YMFNASDGKKR--LKAILPSNLSSEVISGNIQNKGLIRLLDYALNEIPTKSEKYLIVTKCEVV 102 (623)
Q Consensus 42 yr~~lSDG~~~--~~~mlat~ln~~v~~~~l~~~siirl~~y~~~~~~~~~~~vlii~~lev~ 102 (623)
-=+.|.||.+. +|+++......+-.-..|..||+|+++......-...+..=|.+.+++++
T Consensus 18 ~Fi~LrD~s~~~~lQvv~~~~~~~~~~~~~l~~gs~V~v~G~v~~~~~~~~~~El~~~~i~il 80 (82)
T cd04318 18 SFIELNDGSCLKNLQVVVDKELTNFKEILKLSTGSSIRVEGVLVKSPGAKQPFELQAEKIEVL 80 (82)
T ss_pred EEEEEECCCCccCEEEEEeCcccCHHHHhcCCCceEEEEEEEEEeCCCCCCCEEEEEEEEEEe
Confidence 35789999885 88888543221111235899999999998776422112244455555544
No 195
>cd04323 AsnRS_cyto_like_N AsnRS_cyto_like_N: N-terminal, anticodon recognition domain of the type found in human and Saccharomyces cerevisiae cytoplasmic asparaginyl-tRNA synthetase (AsnRS), in Brugia malayai AsnRs and, in various putative bacterial AsnRSs. This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, whereas the other exclusively with
Probab=53.71 E-value=36 Score=28.00 Aligned_cols=42 Identities=12% Similarity=0.172 Sum_probs=30.0
Q ss_pred EEEEeCcccceeecccccccc-ccccCccceeeEEEEcceeee
Q 006973 43 MFNASDGKKRLKAILPSNLSS-EVISGNIQNKGLIRLLDYALN 84 (623)
Q Consensus 43 r~~lSDG~~~~~~mlat~ln~-~v~~~~l~~~siirl~~y~~~ 84 (623)
=+.|.||...+++++....+. .-.-..|..+|+|.++.....
T Consensus 19 Fi~LrD~~~~iQ~v~~~~~~~~~~~~~~l~~es~V~V~G~v~~ 61 (84)
T cd04323 19 FLVLRDGTGFLQCVLSKKLVTEFYDAKSLTQESSVEVTGEVKE 61 (84)
T ss_pred EEEEEcCCeEEEEEEcCCcchhHHHHhcCCCcCEEEEEEEEEE
Confidence 467899999999988644332 111135889999999987765
No 196
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=53.49 E-value=44 Score=41.52 Aligned_cols=62 Identities=15% Similarity=0.185 Sum_probs=45.9
Q ss_pred CeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeEE
Q 006973 186 NWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGTL 253 (623)
Q Consensus 186 ~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~V 253 (623)
.-+|.|-|+.. |....++|+ .+.-+.|-|.+| .+.+++|.+..+++...|++|.++.+.+ +|
T Consensus 993 ~v~v~g~i~~~---~~~~tk~G~-~maf~~leD~~g-~~e~~vfp~~~~~~~~~l~~~~~~~v~g-~v 1054 (1151)
T PRK06826 993 KVIIGGIITEV---KRKTTRNNE-MMAFLTLEDLYG-TVEVIVFPKVYEKYRSLLNEDNIVLIKG-RV 1054 (1151)
T ss_pred EEEEEEEEEEe---EeeccCCCC-eEEEEEEEECCC-cEEEEECHHHHHHHHHHhccCCEEEEEE-EE
Confidence 44566677653 333333332 344568899999 8999999999999999999999999864 44
No 197
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=53.34 E-value=98 Score=34.80 Aligned_cols=78 Identities=18% Similarity=0.238 Sum_probs=53.6
Q ss_pred CCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechH-----HHHHHhhcccCcEEEEeeeEEEecCCC
Q 006973 185 GNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEA-----ARKFYDRFQLGKVYYISRGTLRVANKQ 259 (623)
Q Consensus 185 ~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~-----~~kf~~~l~eG~vy~is~~~V~~a~~~ 259 (623)
...+|.|||.++ |. .|++.=++|.|.+| .|++.+-.+. .+.+.. |..|+++.+.+.-++..
T Consensus 55 ~~v~v~G~v~~~---R~------~g~~~Fi~lrD~~g-~iQ~v~~~~~~~~~~~~~~~~-l~~g~~v~v~G~v~~t~--- 120 (491)
T PRK00484 55 IEVSVAGRVMLK---RV------MGKASFATLQDGSG-RIQLYVSKDDVGEEALEAFKK-LDLGDIIGVEGTLFKTK--- 120 (491)
T ss_pred cEEEEEEEEEEE---ec------CCceEEEEEEcCCc-cEEEEEECCcCCHHHHHHHhc-CCCCCEEEEEEEEEEcC---
Confidence 458999999874 33 34566678999999 8999886432 223333 99999999987544322
Q ss_pred ccccCCceEEEEccCcEEEEc
Q 006973 260 FKTVQNDYEMNLNENSEVEEA 280 (623)
Q Consensus 260 ~~~~~~~yei~f~~~T~I~~~ 280 (623)
...++|..+.-..+.++
T Consensus 121 ----~ge~el~~~~~~vls~~ 137 (491)
T PRK00484 121 ----TGELSVKATELTLLTKS 137 (491)
T ss_pred ----CCcEEEEEeEEEEEecc
Confidence 24688887766555554
No 198
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=53.02 E-value=6.9 Score=36.81 Aligned_cols=28 Identities=25% Similarity=0.610 Sum_probs=20.7
Q ss_pred eccccccccceecC----------------CCCeeecCcCCCCc
Q 006973 482 YRACKTCNKKVTDA----------------LGSGYWCEGCQKND 509 (623)
Q Consensus 482 Y~aC~~C~KKv~~~----------------~~~~~~C~kC~~~~ 509 (623)
+..||.||-.+... .+.-|+|++|++.+
T Consensus 97 ~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiY 140 (165)
T COG1656 97 FSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIY 140 (165)
T ss_pred cccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccc
Confidence 77899999766431 23468899999876
No 199
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=52.95 E-value=14 Score=31.95 Aligned_cols=26 Identities=27% Similarity=0.630 Sum_probs=21.2
Q ss_pred cccccccceecCCCCeeecCcCCCCcc
Q 006973 484 ACKTCNKKVTDALGSGYWCEGCQKNDE 510 (623)
Q Consensus 484 aC~~C~KKv~~~~~~~~~C~kC~~~~~ 510 (623)
-||.|+.-+... .+.+.|+.|+....
T Consensus 2 fC~~Cg~~l~~~-~~~~~C~~C~~~~~ 27 (104)
T TIGR01384 2 FCPKCGSLMTPK-NGVYVCPSCGYEKE 27 (104)
T ss_pred CCcccCcccccC-CCeEECcCCCCccc
Confidence 499999999765 57899999996643
No 200
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=52.94 E-value=9.6 Score=28.97 Aligned_cols=27 Identities=26% Similarity=0.458 Sum_probs=22.3
Q ss_pred eccccccccceecCCCCeeecCcCCCCc
Q 006973 482 YRACKTCNKKVTDALGSGYWCEGCQKND 509 (623)
Q Consensus 482 Y~aC~~C~KKv~~~~~~~~~C~kC~~~~ 509 (623)
-..|+.|++++.+. ++.-.|+.|+..+
T Consensus 5 ~~~C~~Cg~~~~~~-dDiVvCp~Cgapy 31 (54)
T PF14446_consen 5 GCKCPVCGKKFKDG-DDIVVCPECGAPY 31 (54)
T ss_pred CccChhhCCcccCC-CCEEECCCCCCcc
Confidence 35689999999875 6788999999865
No 201
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=52.75 E-value=4 Score=42.29 Aligned_cols=31 Identities=16% Similarity=0.383 Sum_probs=22.7
Q ss_pred CeEeccccccccceecC--CCCeeecCcCCCCc
Q 006973 479 AMWYRACKTCNKKVTDA--LGSGYWCEGCQKND 509 (623)
Q Consensus 479 ~~~Y~aC~~C~KKv~~~--~~~~~~C~kC~~~~ 509 (623)
..+-.||..|..+...+ ....|+|++|+...
T Consensus 243 KY~~TAC~rC~t~y~le~A~~~~wrCpkCGg~i 275 (403)
T COG1379 243 KYHLTACSRCYTRYSLEEAKSLRWRCPKCGGKI 275 (403)
T ss_pred chhHHHHHHhhhccCcchhhhhcccCcccccch
Confidence 45678999999776543 24569999998643
No 202
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=52.64 E-value=8.5 Score=39.46 Aligned_cols=25 Identities=28% Similarity=0.801 Sum_probs=18.5
Q ss_pred ccccccccceec---CCCCeeecCcCCC
Q 006973 483 RACKTCNKKVTD---ALGSGYWCEGCQK 507 (623)
Q Consensus 483 ~aC~~C~KKv~~---~~~~~~~C~kC~~ 507 (623)
..|+.|+-.+.. .+-+.|+|++|++
T Consensus 246 epC~~CGt~I~k~~~~gR~t~~CP~CQ~ 273 (273)
T COG0266 246 EPCRRCGTPIEKIKLGGRSTFYCPVCQK 273 (273)
T ss_pred CCCCccCCEeEEEEEcCCcCEeCCCCCC
Confidence 569999865433 3468999999984
No 203
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=52.41 E-value=7.9 Score=35.96 Aligned_cols=30 Identities=27% Similarity=0.584 Sum_probs=21.1
Q ss_pred eccccccccceecC----------------CCCeeecCcCCCCccc
Q 006973 482 YRACKTCNKKVTDA----------------LGSGYWCEGCQKNDEE 511 (623)
Q Consensus 482 Y~aC~~C~KKv~~~----------------~~~~~~C~kC~~~~~~ 511 (623)
...|+.||..+... .+.-|+|++|++.+-.
T Consensus 91 ~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~ 136 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWE 136 (147)
T ss_pred CCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecc
Confidence 67888888766431 1336899999997643
No 204
>cd04496 SSB_OBF SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date oligomerize to bring together four OB folds in their active state. The majority (e.g. Escherichia coli SSB) have a single OB fold per monomer, which oligomerize to form a homotetramer. However, Deinococcus and Thermus SSB proteins have two OB folds per monomer, which oligomerize to form a homodimer. Mycobacterium tuberculosis SSB varies in quaternary structure from E. coli SSB. It forms a dimer of dimers having a unique dimer interface, which lends the protein greater stability. Included in this group are OB folds similar to Escherichia coli PriB. E.coli PriB is homodimeric with each monomer having a single OB fold. It does not appear to form higher order oligomers. PriB is an essential protein for the replication restart
Probab=51.53 E-value=1.1e+02 Score=25.50 Aligned_cols=37 Identities=19% Similarity=0.334 Sum_probs=25.2
Q ss_pred ccEEEEEEechhhhhhhhHhhhcCCCCcEEEEE-eEEeeecc
Q 006973 346 KRTVTVSLWNELATNVGQELLDNADKSPIVAIK-SLKVGDFQ 386 (623)
Q Consensus 346 g~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~-~~kV~~f~ 386 (623)
...+.|++||+.|+.+.+. ...|..|.+. ..+...|.
T Consensus 43 ~~~~~v~~~g~~a~~~~~~----~~kG~~V~v~G~l~~~~~~ 80 (100)
T cd04496 43 TDWIRVVAFGKLAENAAKY----LKKGDLVYVEGRLRTRSWE 80 (100)
T ss_pred cEEEEEEEEhHHHHHHHHH----hCCCCEEEEEEEEEeceeE
Confidence 3479999999999887554 3456666664 45555554
No 205
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=51.14 E-value=19 Score=33.20 Aligned_cols=27 Identities=26% Similarity=0.554 Sum_probs=24.3
Q ss_pred EEEEEEEeCCCCeEEEEEechHHHHHHh
Q 006973 211 VFNVELTDEDGTQIQATMFNEAARKFYD 238 (623)
Q Consensus 211 ~f~~~L~D~~G~~I~at~~~~~~~kf~~ 238 (623)
.+++.+.|.+| .+.+++|++.++++-.
T Consensus 55 ~l~~~i~D~tg-~~~~~~F~~~a~~l~G 81 (146)
T PF08646_consen 55 RLSLKISDGTG-SIWVTLFDEEAEQLLG 81 (146)
T ss_dssp EEEEEEEETTE-EEEEEEEHHHHHHHHC
T ss_pred EEEEEEEeCCC-eEEEEEEhHHHHHHhC
Confidence 57899999999 8999999999888775
No 206
>TIGR00459 aspS_bact aspartyl-tRNA synthetase, bacterial type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_bact, represents aspartyl-tRNA synthetases from the Bacteria and from mitochondria. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). This model generates very low scores for the archaeal type of aspS and for asnS; scores between the trusted and noise cutoffs represent fragmentary sequences.
Probab=50.72 E-value=1.2e+02 Score=34.75 Aligned_cols=86 Identities=14% Similarity=0.125 Sum_probs=56.1
Q ss_pred CCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEech-HHHHHHhhcccCcEEEEeeeEEEecCCCcc--
Q 006973 185 GNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNE-AARKFYDRFQLGKVYYISRGTLRVANKQFK-- 261 (623)
Q Consensus 185 ~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~-~~~kf~~~l~eG~vy~is~~~V~~a~~~~~-- 261 (623)
...+|+|||.+ +|. .|++.=++|.|.+| .|++++-.+ ..-+....|..|+++.+.+.-.+...+.-+
T Consensus 16 ~~V~l~GwV~~---~R~------~Gkl~Fi~LrD~sg-~iQvv~~~~~~~~~~~~~L~~esvV~V~G~v~~r~~~~~n~~ 85 (583)
T TIGR00459 16 QTVTLAGWVNR---RRD------LGGLIFIDLRDRSG-IVQVVCDPDADALKLAKGLRNEDVVQVKGKVSARPEGNINRN 85 (583)
T ss_pred CEEEEEEEEEE---EEc------CCCcEEEEEEeCCc-cEEEEEeCCHHHHHHHhcCCCCCEEEEEEEEEeCCccccCcc
Confidence 46889999976 333 34565678999999 899988654 222334568999999998754432211111
Q ss_pred ccCCceEEEEccCcEEEEc
Q 006973 262 TVQNDYEMNLNENSEVEEA 280 (623)
Q Consensus 262 ~~~~~yei~f~~~T~I~~~ 280 (623)
.....+||....-+.+..+
T Consensus 86 ~~tg~iEl~~~~i~iL~~a 104 (583)
T TIGR00459 86 LDTGEIEILAESITLLNKS 104 (583)
T ss_pred CCCCcEEEEEeEEEEeecC
Confidence 2346788887766555544
No 207
>PF12773 DZR: Double zinc ribbon
Probab=50.67 E-value=8.5 Score=28.40 Aligned_cols=28 Identities=18% Similarity=0.459 Sum_probs=19.1
Q ss_pred eccccccccceecCCCCeeecCcCCCCc
Q 006973 482 YRACKTCNKKVTDALGSGYWCEGCQKND 509 (623)
Q Consensus 482 Y~aC~~C~KKv~~~~~~~~~C~kC~~~~ 509 (623)
..-|+.|+.++.........|++|+...
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~~Cg~~~ 39 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICPNCGAEN 39 (50)
T ss_pred ccCChhhcCChhhccCCCCCCcCCcCCC
Confidence 4558888888873224567888888764
No 208
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=50.11 E-value=8.1 Score=25.36 Aligned_cols=25 Identities=36% Similarity=0.725 Sum_probs=14.8
Q ss_pred ccccccccceecC---CCCeeecCcCCC
Q 006973 483 RACKTCNKKVTDA---LGSGYWCEGCQK 507 (623)
Q Consensus 483 ~aC~~C~KKv~~~---~~~~~~C~kC~~ 507 (623)
..|+.|...+... +...|.|+.|.+
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCPRCQK 29 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-TTTCC
T ss_pred CcCccCCCcceEeEecCCCCeECcCCcC
Confidence 4799998876543 245799999975
No 209
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=49.97 E-value=14 Score=25.70 Aligned_cols=27 Identities=22% Similarity=0.452 Sum_probs=19.0
Q ss_pred ccccccccceec------CCCCeeecCcCCCCc
Q 006973 483 RACKTCNKKVTD------ALGSGYWCEGCQKND 509 (623)
Q Consensus 483 ~aC~~C~KKv~~------~~~~~~~C~kC~~~~ 509 (623)
..||.|+....- ..++.-+|++|+..+
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 579999875422 125678999998754
No 210
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=49.72 E-value=8.5 Score=31.67 Aligned_cols=31 Identities=23% Similarity=0.422 Sum_probs=22.2
Q ss_pred ccccccccceec-CCCCeeecCcCCCCccccc
Q 006973 483 RACKTCNKKVTD-ALGSGYWCEGCQKNDEECS 513 (623)
Q Consensus 483 ~aC~~C~KKv~~-~~~~~~~C~kC~~~~~~~~ 513 (623)
.-|+-|+|+-.. ..-|.|.|..|.+.+.-..
T Consensus 37 y~CsfCGK~~vKR~AvGiW~C~~C~kv~agga 68 (92)
T KOG0402|consen 37 YTCSFCGKKTVKRKAVGIWKCGSCKKVVAGGA 68 (92)
T ss_pred hhhhhcchhhhhhhceeEEecCCccceeccce
Confidence 358889987543 3358999999998765433
No 211
>PRK09010 single-stranded DNA-binding protein; Provisional
Probab=49.67 E-value=1.4e+02 Score=28.76 Aligned_cols=36 Identities=25% Similarity=0.305 Sum_probs=25.5
Q ss_pred EEEEEEechhhhhhhhHhhhcCCCCcEEEEE-eEEeeeccc
Q 006973 348 TVTVSLWNELATNVGQELLDNADKSPIVAIK-SLKVGDFQG 387 (623)
Q Consensus 348 ~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~-~~kV~~f~G 387 (623)
-++|++||..|+.+.+. +..+.-|.|. .++...|.+
T Consensus 55 w~~V~~fgk~Ae~~~~~----L~KGs~V~VeGrL~~~~yed 91 (177)
T PRK09010 55 WHRVVLFGKLAEVAGEY----LRKGSQVYIEGQLRTRKWTD 91 (177)
T ss_pred EEEEEEehhHHHHHHHh----cCCCCEEEEEEEEEeccccC
Confidence 68999999999887554 4556666665 466667753
No 212
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=49.47 E-value=15 Score=28.66 Aligned_cols=23 Identities=30% Similarity=0.745 Sum_probs=18.2
Q ss_pred eccccccccceecCCCCeeecCcCCCCc
Q 006973 482 YRACKTCNKKVTDALGSGYWCEGCQKND 509 (623)
Q Consensus 482 Y~aC~~C~KKv~~~~~~~~~C~kC~~~~ 509 (623)
+.||..|+.-+..+ .|+.|+...
T Consensus 3 ~kAC~~C~~i~~~~-----~CP~Cgs~~ 25 (61)
T PRK08351 3 EKACRHCHYITTED-----RCPVCGSRD 25 (61)
T ss_pred hhhhhhCCcccCCC-----cCCCCcCCc
Confidence 46999999988542 699999754
No 213
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=49.11 E-value=56 Score=40.64 Aligned_cols=66 Identities=24% Similarity=0.272 Sum_probs=46.5
Q ss_pred CcceeEEEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEEee
Q 006973 306 GTELVDIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSPIVAIKSLKVG 383 (623)
Q Consensus 306 ~~~~vDVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~kV~ 383 (623)
.+..|-|.|+|+.+... .+|+ |+ ..--++|.|.+| .+++++|.+..+.+... ...+.++.+++ +|.
T Consensus 990 ~~~~v~v~g~i~~~~~~---~tk~-G~--~maf~~leD~~g-~~e~~vfp~~~~~~~~~----l~~~~~~~v~g-~v~ 1055 (1151)
T PRK06826 990 DGDKVIIGGIITEVKRK---TTRN-NE--MMAFLTLEDLYG-TVEVIVFPKVYEKYRSL----LNEDNIVLIKG-RVS 1055 (1151)
T ss_pred CCcEEEEEEEEEEeEee---ccCC-CC--eEEEEEEEECCC-cEEEEECHHHHHHHHHH----hccCCEEEEEE-EEE
Confidence 35578899999988643 4553 54 245688999999 89999999877666443 34567777765 454
No 214
>PRK12445 lysyl-tRNA synthetase; Reviewed
Probab=48.29 E-value=1.1e+02 Score=34.54 Aligned_cols=78 Identities=17% Similarity=0.270 Sum_probs=53.0
Q ss_pred CeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHH-----HHHHhhcccCcEEEEeeeEEEecCCCc
Q 006973 186 NWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAA-----RKFYDRFQLGKVYYISRGTLRVANKQF 260 (623)
Q Consensus 186 ~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~-----~kf~~~l~eG~vy~is~~~V~~a~~~~ 260 (623)
..+|.|||.++ |. .|++.=++|.|.+| .|++.+-.+.. +.....|..|+++.+.+.-.+..
T Consensus 67 ~v~v~Grv~~~---R~------~Gk~~F~~lrD~~g-~iQ~~~~~~~~~~~~~~~~~~~l~~Gd~V~v~G~~~~t~---- 132 (505)
T PRK12445 67 EVSVAGRMMTR---RI------MGKASFVTLQDVGG-RIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQ---- 132 (505)
T ss_pred EEEEEEEEEEE---ec------CCCcEEEEEEeCCc-cEEEEEECCccchhhHHHHHhcCCCCCEEEEEEEEEecC----
Confidence 58899999873 33 34555578999998 89998874321 22234689999999987544332
Q ss_pred cccCCceEEEEccCcEEEEc
Q 006973 261 KTVQNDYEMNLNENSEVEEA 280 (623)
Q Consensus 261 ~~~~~~yei~f~~~T~I~~~ 280 (623)
...++|..+.-+.+.++
T Consensus 133 ---~gelel~~~~~~llsk~ 149 (505)
T PRK12445 133 ---TGELSIHCTELRLLTKA 149 (505)
T ss_pred ---CCcEEEEEeEEEEEecC
Confidence 24688877666656554
No 215
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=48.18 E-value=15 Score=26.75 Aligned_cols=25 Identities=24% Similarity=0.626 Sum_probs=16.9
Q ss_pred ccccccccc-eecC-CCCeeecCcCCC
Q 006973 483 RACKTCNKK-VTDA-LGSGYWCEGCQK 507 (623)
Q Consensus 483 ~aC~~C~KK-v~~~-~~~~~~C~kC~~ 507 (623)
..||.|+.. +... ..+.|+|..|.+
T Consensus 19 ~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 459999863 3222 247899999975
No 216
>cd04498 hPOT1_OB2 hPOT1_OB2: A subfamily of OB folds similar to the second OB fold (OB2) of human protection of telomeres 1 protein (hPOT1). POT1 proteins bind to the single-stranded (ss) 3-prime ends of the telomere. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB2) which cooperate to bind telomeric ssDNA. OB1 makes more extensive contact with the ssDNA than OB2. OB2 protects the 3' end of the ssDNA. hPOT1 is implicated in telomere length regulation.
Probab=47.88 E-value=46 Score=29.96 Aligned_cols=38 Identities=8% Similarity=0.086 Sum_probs=30.7
Q ss_pred eEEEEEechHHHHHHhhcccCcEEEEeeeEEEecCCCcc
Q 006973 223 QIQATMFNEAARKFYDRFQLGKVYYISRGTLRVANKQFK 261 (623)
Q Consensus 223 ~I~at~~~~~~~kf~~~l~eG~vy~is~~~V~~a~~~~~ 261 (623)
.|++++|.+.+.--.+ |++|+.+.|.|..++....++-
T Consensus 61 ti~It~yD~H~~~ar~-lK~GdfV~L~NVhiK~~~~~~~ 98 (123)
T cd04498 61 TIDILVYDNHVELAKS-LKPGDFVRIYNVHAKSYSSKNE 98 (123)
T ss_pred EEEEEEEcchHHHHhh-CCCCCEEEEEEEEEEeccCCcc
Confidence 6889999988764444 9999999999999988765433
No 217
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=47.78 E-value=1.2e+02 Score=29.35 Aligned_cols=35 Identities=26% Similarity=0.444 Sum_probs=24.7
Q ss_pred EEEEEEechhhhhhhhHhhhcCCCCcEEEEE-eEEeeecc
Q 006973 348 TVTVSLWNELATNVGQELLDNADKSPIVAIK-SLKVGDFQ 386 (623)
Q Consensus 348 ~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~-~~kV~~f~ 386 (623)
-++|++|++.|+.+.+. +..+.-|.|. .++...|.
T Consensus 54 fi~V~~Wg~~Ae~va~~----L~KGd~V~V~GrL~~r~we 89 (186)
T PRK07772 54 FLRCSIWRQAAENVAES----LTKGMRVIVTGRLKQRSYE 89 (186)
T ss_pred EEEEEEecHHHHHHHHh----cCCCCEEEEEEEEEcCceE
Confidence 68999999999987554 3455555554 56666775
No 218
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=47.65 E-value=1.8e+02 Score=27.65 Aligned_cols=35 Identities=20% Similarity=0.288 Sum_probs=24.7
Q ss_pred EEEEEEechhhhhhhhHhhhcCCCCcEEEEE-eEEeeecc
Q 006973 348 TVTVSLWNELATNVGQELLDNADKSPIVAIK-SLKVGDFQ 386 (623)
Q Consensus 348 ~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~-~~kV~~f~ 386 (623)
-++|++||+.|+...+. +..|.-|.|. .++...|.
T Consensus 53 w~~Vv~fgk~Ae~v~~~----L~KGs~V~VeGrL~~~~y~ 88 (164)
T PRK08763 53 WHRVKFFGKLGEIAGEY----LRKGSQCYIEGSIRYDKFT 88 (164)
T ss_pred EEEEEEehHHHHHHHHh----cCCCCEEEEEEEEEeceeE
Confidence 49999999999876544 4557766665 45666674
No 219
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=47.56 E-value=1.2e+02 Score=25.49 Aligned_cols=59 Identities=15% Similarity=0.095 Sum_probs=37.5
Q ss_pred EEEEEEeeccccccccCCCcccEEEEEEEeC--CCCeEEEEEechHHHHHHhhcccCcEEEEe
Q 006973 189 IKVRVTSKGNMRTYKNARGEGCVFNVELTDE--DGTQIQATMFNEAARKFYDRFQLGKVYYIS 249 (623)
Q Consensus 189 I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~--~G~~I~at~~~~~~~kf~~~l~eG~vy~is 249 (623)
|.|+|+.+-+..+=..++| =+--+++|--+ --..|...+|++-++.+++ +++|+.+.++
T Consensus 2 i~Gkii~~l~~~~g~s~~G-w~Kre~Vlet~~qYP~~i~f~~~~dk~~~l~~-~~~Gd~V~Vs 62 (84)
T PF11325_consen 2 ITGKIIKVLPEQQGVSKNG-WKKREFVLETEEQYPQKICFEFWGDKIDLLDN-FQVGDEVKVS 62 (84)
T ss_pred cccEEEEEecCcccCcCCC-cEEEEEEEeCCCcCCceEEEEEEcchhhhhcc-CCCCCEEEEE
Confidence 5677666655543222233 12224444311 1258999999999988666 8999999987
No 220
>KOG0556 consensus Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=47.35 E-value=1.7e+02 Score=31.80 Aligned_cols=99 Identities=14% Similarity=0.176 Sum_probs=69.6
Q ss_pred CcCeeeccccCCCC--CCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEec-------hHHHHHHhhcc
Q 006973 171 TRRVHPLVSLNPYQ--GNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFN-------EAARKFYDRFQ 241 (623)
Q Consensus 171 ~~~~~~I~~L~p~~--~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~-------~~~~kf~~~l~ 241 (623)
.+.++++++|+... ....|+|||-. .+-.|++.=++|.+ .|..|+|.+.- ...-+|...|.
T Consensus 67 ~~~~~~v~dl~~~~~~~~V~vRgrVht---------sr~~GK~~FlvLRq-~~~tVQ~~~~~~~~~~isk~Mvkf~~~is 136 (533)
T KOG0556|consen 67 GRELTDVSDLDESNDGSEVLVRGRVHT---------SRLKGKLCFLVLRQ-QGSTVQCLVAVNEDGTISKQMVKFAGSIS 136 (533)
T ss_pred ccceeehhhhhhhcCCceEEEEEEEee---------ccccceEEEEEEec-cCceEEEEEEcCCCchHHHHHHHHHhhcC
Confidence 45689999997754 35568999832 23456665555655 67799999953 35678999999
Q ss_pred cCcEEEEeeeEEEecCCCccccCCceEEEEccCcEEEE
Q 006973 242 LGKVYYISRGTLRVANKQFKTVQNDYEMNLNENSEVEE 279 (623)
Q Consensus 242 eG~vy~is~~~V~~a~~~~~~~~~~yei~f~~~T~I~~ 279 (623)
--.++.+.+.-+++..+--.-+..+.||....--.|..
T Consensus 137 ~ESiV~v~g~v~k~~~~i~scT~qdvEi~v~~iyviS~ 174 (533)
T KOG0556|consen 137 KESIVDVRGVVVKVKEPIKSCTVQDVEIHVRKIYVISI 174 (533)
T ss_pred cceEEEEEEEEecCCCcccccccceeEEEEEEEEEEec
Confidence 99999988776666665544577888988876555544
No 221
>cd04494 BRCA2DBD_OB2 BRCA2DBD_OB2: A subfamily of OB folds corresponding to the second OB fold (OB2) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA).
Probab=47.34 E-value=61 Score=32.91 Aligned_cols=57 Identities=7% Similarity=0.081 Sum_probs=41.7
Q ss_pred eEEEEEechHHHHHHhhcccCcEEEEeeeEEEecCCCccccCCceEEEEccCcEEEEccC
Q 006973 223 QIQATMFNEAARKFYDRFQLGKVYYISRGTLRVANKQFKTVQNDYEMNLNENSEVEEAVN 282 (623)
Q Consensus 223 ~I~at~~~~~~~kf~~~l~eG~vy~is~~~V~~a~~~~~~~~~~yei~f~~~T~I~~~~d 282 (623)
..-.|+|+.. +.+.++|+||+.|.|.+-..... +-........|+-...|.-.+++.
T Consensus 181 ~~~LTIWrPt-edl~s~L~EG~ry~i~~L~~s~~--k~~~~~~~vqLtatk~Tr~~~l~~ 237 (251)
T cd04494 181 SGLLSIWRPT-EDLRSLLTEGKRYRIYGLATSNS--KKRSGNEEVQLTATKKTRYQPLPV 237 (251)
T ss_pred eEEEEEeCCC-HHHHhhhcCCcEEEEEeccccCC--CCCCCcceEEEEecCcccceECCH
Confidence 5667899864 56777899999999998664333 222345678888888898888753
No 222
>PTZ00385 lysyl-tRNA synthetase; Provisional
Probab=47.14 E-value=99 Score=35.98 Aligned_cols=77 Identities=13% Similarity=0.105 Sum_probs=52.2
Q ss_pred CeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechH------HHHHHhhcccCcEEEEeeeEEEecCCC
Q 006973 186 NWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEA------ARKFYDRFQLGKVYYISRGTLRVANKQ 259 (623)
Q Consensus 186 ~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~------~~kf~~~l~eG~vy~is~~~V~~a~~~ 259 (623)
..+|.|||.++ |. -|++.=++|.|.+| .|++.+-.+. ...+...|..|+++.+.+.-. ..
T Consensus 109 ~V~vaGrV~~~---R~------~Gk~~F~~LrD~~G-~IQvv~~~~~~~~~~~~~~~~~~l~~gdiV~V~G~v~-~t--- 174 (659)
T PTZ00385 109 TVRVAGRVTSV---RD------IGKIIFVTIRSNGN-ELQVVGQVGEHFTREDLKKLKVSLRVGDIIGADGVPC-RM--- 174 (659)
T ss_pred EEEEEEEEEee---ec------cCCeEEEEEEECCc-eEEEEEECCccCCHHHHHHHHhCCCCCCEEEEEEEEE-ec---
Confidence 48899999874 32 34655578899999 9999996532 223334689999999987533 22
Q ss_pred ccccCCceEEEEccCcEEEE
Q 006973 260 FKTVQNDYEMNLNENSEVEE 279 (623)
Q Consensus 260 ~~~~~~~yei~f~~~T~I~~ 279 (623)
-...++|....-+.+.+
T Consensus 175 ---~~GeleI~~~~i~lLsk 191 (659)
T PTZ00385 175 ---QRGELSVAASRMLILSP 191 (659)
T ss_pred ---CCceEEEEeeEEEEech
Confidence 13456776666666655
No 223
>PRK05853 hypothetical protein; Validated
Probab=46.90 E-value=51 Score=31.14 Aligned_cols=33 Identities=6% Similarity=0.010 Sum_probs=28.3
Q ss_pred eCCCCeEEEEEechHHHHHHhhcccCcEEEEee
Q 006973 218 DEDGTQIQATMFNEAARKFYDRFQLGKVYYISR 250 (623)
Q Consensus 218 D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~ 250 (623)
|..-+-|.+++|+..++.+...|..|+-+.+.+
T Consensus 39 d~~T~wi~V~~wg~lAe~v~~~L~KG~~V~V~G 71 (161)
T PRK05853 39 PGNSLFITVNCWGRLVTGVGAALGKGAPVIVVG 71 (161)
T ss_pred ccCccEEEEEEEhHHHHHHHHHcCCCCEEEEEE
Confidence 334456999999999999999999999999875
No 224
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=46.80 E-value=11 Score=28.03 Aligned_cols=27 Identities=22% Similarity=0.437 Sum_probs=19.3
Q ss_pred eccccccccceec-CCCCeeecCcCCCC
Q 006973 482 YRACKTCNKKVTD-ALGSGYWCEGCQKN 508 (623)
Q Consensus 482 Y~aC~~C~KKv~~-~~~~~~~C~kC~~~ 508 (623)
-+-||.|+-.|.. +..+.|.|-+|+-+
T Consensus 19 ~~~CPrCG~gvfmA~H~dR~~CGkCgyT 46 (51)
T COG1998 19 NRFCPRCGPGVFMADHKDRWACGKCGYT 46 (51)
T ss_pred cccCCCCCCcchhhhcCceeEeccccce
Confidence 3469999965432 24668999999954
No 225
>PF14353 CpXC: CpXC protein
Probab=46.25 E-value=28 Score=31.26 Aligned_cols=33 Identities=18% Similarity=0.257 Sum_probs=22.9
Q ss_pred eeecCcCCCCccccceeEEEEEEEEeCCCcEEEEEehH
Q 006973 499 GYWCEGCQKNDEECSLRYIMVARVCDGSGEAWISIFNE 536 (623)
Q Consensus 499 ~~~C~kC~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~~ 536 (623)
.+.|++|+... +.-..+..-|......+.++-+
T Consensus 38 ~~~CP~Cg~~~-----~~~~p~lY~D~~~~~~i~~~P~ 70 (128)
T PF14353_consen 38 SFTCPSCGHKF-----RLEYPLLYHDPEKKFMIYYFPD 70 (128)
T ss_pred EEECCCCCCce-----ecCCCEEEEcCCCCEEEEEcCC
Confidence 68999999764 3344556778777777666655
No 226
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=45.91 E-value=50 Score=40.67 Aligned_cols=61 Identities=18% Similarity=0.216 Sum_probs=44.7
Q ss_pred CeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEeeeEEE
Q 006973 186 NWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISRGTLR 254 (623)
Q Consensus 186 ~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~V~ 254 (623)
...|-+.|+.+...++ + .| +.-+.|-|++| .+.+++|.+..+++...|++|.++.+. ++|.
T Consensus 955 ~v~v~g~i~~~~~~~T---k--kG-maf~~leD~~g-~~e~~ifp~~~~~~~~~l~~~~~~~v~-g~v~ 1015 (1046)
T PRK05672 955 RVRVAGVVTHRQRPGT---A--SG-VTFLTLEDETG-MVNVVVWPGLWERQRREALGARLLLVR-GRVQ 1015 (1046)
T ss_pred EEEEEEEEEEEEEecC---C--Cc-eEEEEEecCCC-CEEEEECHHHHHHHHHHhccCCEEEEE-EEEE
Confidence 3456666655433222 2 34 44567899999 899999999999999999999999996 4553
No 227
>cd04321 ScAspRS_mt_like_N ScAspRS_mt_like_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae mitochondrial (mt) aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this fungal group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Mutations in the gene for
Probab=45.77 E-value=1.7e+02 Score=24.11 Aligned_cols=76 Identities=12% Similarity=0.142 Sum_probs=43.7
Q ss_pred eEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHH--hhcccCcEEEEeeeEEEecCCCccccC
Q 006973 187 WTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFY--DRFQLGKVYYISRGTLRVANKQFKTVQ 264 (623)
Q Consensus 187 w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~--~~l~eG~vy~is~~~V~~a~~~~~~~~ 264 (623)
.+|.|+|.+ +|.. .|++.=++|.|.+|..|++++-.+. +.|. ..|..|+++.+.+ .+......-..-.
T Consensus 2 V~v~Gwv~~---~R~~-----~~~~~Fi~LrD~~g~~iQvv~~~~~-~~~~~~~~l~~~s~V~V~G-~v~~~~~~~~~~~ 71 (86)
T cd04321 2 VTLNGWIDR---KPRI-----VKKLSFADLRDPNGDIIQLVSTAKK-DAFSLLKSITAESPVQVRG-KLQLKEAKSSEKN 71 (86)
T ss_pred EEEEEeEee---EeCC-----CCceEEEEEECCCCCEEEEEECCCH-HHHHHHhcCCCCcEEEEEE-EEEeCCCcCCCCC
Confidence 467778765 2321 1344446789999956998775432 3333 2488999999976 4444322110112
Q ss_pred CceEEEEc
Q 006973 265 NDYEMNLN 272 (623)
Q Consensus 265 ~~yei~f~ 272 (623)
..+||..+
T Consensus 72 ~~~Ei~~~ 79 (86)
T cd04321 72 DEWELVVD 79 (86)
T ss_pred CCEEEEEE
Confidence 55777653
No 228
>PRK05733 single-stranded DNA-binding protein; Provisional
Probab=45.64 E-value=1.2e+02 Score=28.94 Aligned_cols=35 Identities=26% Similarity=0.344 Sum_probs=25.2
Q ss_pred EEEEEEechhhhhhhhHhhhcCCCCcEEEEEe-EEeeecc
Q 006973 348 TVTVSLWNELATNVGQELLDNADKSPIVAIKS-LKVGDFQ 386 (623)
Q Consensus 348 ~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~-~kV~~f~ 386 (623)
-+.|++||..|+.+.+. +..|.-|.|.| ++...|.
T Consensus 54 w~~Vv~fgk~Ae~v~~~----l~KGs~V~VeGrLr~~~y~ 89 (172)
T PRK05733 54 WHRVSLFGKVAEIAGEY----LRKGSQVYIEGKLQTREWE 89 (172)
T ss_pred EEEEEEehHHHHHHHHH----hCCCCEEEEEEEEEeCcEe
Confidence 49999999999887554 45677777754 5555563
No 229
>PRK07275 single-stranded DNA-binding protein; Provisional
Probab=45.21 E-value=2e+02 Score=27.17 Aligned_cols=35 Identities=14% Similarity=0.493 Sum_probs=25.6
Q ss_pred EEEEEEechhhhhhhhHhhhcCCCCcEEEEEe-EEeeecc
Q 006973 348 TVTVSLWNELATNVGQELLDNADKSPIVAIKS-LKVGDFQ 386 (623)
Q Consensus 348 ~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~-~kV~~f~ 386 (623)
-|.|++||+.|+.+.+. +..|.-|+|.| .+...|.
T Consensus 48 fi~vv~wgk~Ae~~~~~----l~KG~~V~VeGrl~~r~y~ 83 (162)
T PRK07275 48 FINCVIWRQQAENLANW----AKKGALIGVTGRIQTRNYE 83 (162)
T ss_pred EEEEEEEcHHHHHHHHH----cCCCCEEEEEEEEEeceEE
Confidence 68999999999987554 45677777754 5556673
No 230
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=45.14 E-value=29 Score=30.79 Aligned_cols=48 Identities=19% Similarity=0.383 Sum_probs=31.9
Q ss_pred cccccccceecC---CCCeeecCcCCCCccccc---eeEEEEEEEEeCCCcEEE
Q 006973 484 ACKTCNKKVTDA---LGSGYWCEGCQKNDEECS---LRYIMVARVCDGSGEAWI 531 (623)
Q Consensus 484 aC~~C~KKv~~~---~~~~~~C~kC~~~~~~~~---~ry~l~~~i~D~Tg~~~~ 531 (623)
-||.|+--+... .++.+.|.+|+-...... ++|.+...+.+.....-.
T Consensus 4 FCp~Cgsll~p~~~~~~~~l~C~kCgye~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 (113)
T COG1594 4 FCPKCGSLLYPKKDDEGGKLVCRKCGYEEEASNKKVYRYSVKEAVEKKKEVVLV 57 (113)
T ss_pred ccCCccCeeEEeEcCCCcEEECCCCCcchhccccceeEEEEeeccCCcceeeee
Confidence 499999877652 367899999997664332 666666665555544433
No 231
>PF10451 Stn1: Telomere regulation protein Stn1; InterPro: IPR018856 The budding yeast protein Stn1 is a DNA-binding protein which has specificity for telomeric DNA. Structural profiling has predicted an OB-fold []. This entry represents the N-terminal part of the molecule, which adopts the OB fold. Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution [].; PDB: 3KF6_A 3KF8_A.
Probab=44.98 E-value=79 Score=32.28 Aligned_cols=64 Identities=22% Similarity=0.249 Sum_probs=40.9
Q ss_pred eeEEEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCcc-EEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEE
Q 006973 309 LVDIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKR-TVTVSLWNELATNVGQELLDNADKSPIVAIKSLK 381 (623)
Q Consensus 309 ~vDVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg~-~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~k 381 (623)
.|.|+|+|+.+..- .+ + + ..+.-++|-|.||. .|.|.+|-+......-.+.+. .|.+|.++|.-
T Consensus 68 ~v~i~G~Vv~~~~~-~~--~--~--~~~~~l~iDD~Sg~~~i~~~~~~~~~~~~~l~~~~~--~G~~V~VkG~v 132 (256)
T PF10451_consen 68 WVRIVGVVVGIDYK-WI--E--N--EDRIILTIDDSSGANTIECKCSKSSYLSMGLPINDL--IGKVVEVKGTV 132 (256)
T ss_dssp EEEEEEEEEEEEEE-E---B--B--TCEEEEEEE-SSCS-EEEEEEEHHHHHCCCHHCTT---TT-EEEEEEEE
T ss_pred EEEEEEEEEEEEEE-ee--c--c--cceEEEEEeCCCCceeEEEEEEcccccccCCCccCC--CCcEEEEEEEE
Confidence 58999999998522 11 1 1 23567888888887 999999987655443333222 58888888653
No 232
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=44.73 E-value=18 Score=29.45 Aligned_cols=42 Identities=21% Similarity=0.431 Sum_probs=16.9
Q ss_pred EeccccccccceecCCCCeeecCcCCCCccccceeEEEEEEEEeCCCcEE
Q 006973 481 WYRACKTCNKKVTDALGSGYWCEGCQKNDEECSLRYIMVARVCDGSGEAW 530 (623)
Q Consensus 481 ~Y~aC~~C~KKv~~~~~~~~~C~kC~~~~~~~~~ry~l~~~i~D~Tg~~~ 530 (623)
|-..|-.|.+-..+ .+..+|++|+... -.++.+.+. ..|++.
T Consensus 8 ~vlrC~aCf~~t~~--~~k~FCp~CGn~T-----L~rvsvsv~-~~G~~~ 49 (73)
T PF08772_consen 8 WVLRCHACFKITKD--MTKQFCPKCGNAT-----LKRVSVSVD-EDGKIK 49 (73)
T ss_dssp EEEE-SSS--EES---SS--S-SSS--S-------EEEE-B---SS---B
T ss_pred eeEEccccccCcCC--CCceeCcccCCCc-----ceEEEEEEC-CCCCEE
Confidence 56778889987765 4678999999753 334444443 555543
No 233
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=44.50 E-value=13 Score=40.06 Aligned_cols=40 Identities=18% Similarity=0.224 Sum_probs=27.7
Q ss_pred EEEEEEEeCCCCeEeccccccccceecCCCC---eeecCcCCCCc
Q 006973 468 KAYISLIKPDQAMWYRACKTCNKKVTDALGS---GYWCEGCQKND 509 (623)
Q Consensus 468 ~a~I~~i~~d~~~~Y~aC~~C~KKv~~~~~~---~~~C~kC~~~~ 509 (623)
.+++-+.-......+.+|..|+..+... .. .|+|+ |++..
T Consensus 226 ~~~~g~~P~~GKYh~~~c~~C~~~~~~~-~~~~~~~~Cp-CG~~i 268 (374)
T TIGR00375 226 IANYGLDPLLGKYHQTACEACGEPAVSE-DAETACANCP-CGGRI 268 (374)
T ss_pred EeeeeECcCCCccchhhhcccCCcCCch-hhhhcCCCCC-CCCcc
Confidence 4554444455566788999999988764 22 38999 98753
No 234
>TIGR00457 asnS asparaginyl-tRNA synthetase. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, asnS, represents asparaginyl-tRNA synthetases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn.
Probab=43.98 E-value=1.7e+02 Score=32.52 Aligned_cols=82 Identities=20% Similarity=0.217 Sum_probs=54.7
Q ss_pred CCeEEEEEEEeeccccccccCCCcccEEEEEEEeCC--CCeEEEEEech---HHHHHHhhcccCcEEEEeeeEEEecCCC
Q 006973 185 GNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDED--GTQIQATMFNE---AARKFYDRFQLGKVYYISRGTLRVANKQ 259 (623)
Q Consensus 185 ~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~--G~~I~at~~~~---~~~kf~~~l~eG~vy~is~~~V~~a~~~ 259 (623)
..-+|+|||.+ +|. .|++.=++|.|.+ | .|++++-.. ...++...|..|+++.+.+.-.+ ...
T Consensus 17 ~~v~v~Gwv~~---~R~------~~~~~F~~lrD~~~~g-~iQ~v~~~~~~~~~~~~~~~l~~gs~V~v~G~v~~-~~~- 84 (453)
T TIGR00457 17 DEVTVSGWVRT---KRS------SKKIIFLELNDGSSLG-PIQAVINGEDNPYLFQLLKSLTTGSSVSVTGKVVE-SPG- 84 (453)
T ss_pred CEEEEEEEeEE---EEc------CCCeEEEEEECCCCCc-cEEEEEeCCcChHHHHHHHcCCCCcEEEEEEEEEc-CCC-
Confidence 46889999976 342 2355557789998 7 899998764 22234456999999999875433 211
Q ss_pred ccccCCceEEEEccCcEEEEcc
Q 006973 260 FKTVQNDYEMNLNENSEVEEAV 281 (623)
Q Consensus 260 ~~~~~~~yei~f~~~T~I~~~~ 281 (623)
....+||....-..+.++.
T Consensus 85 ---~~~~~El~~~~i~vl~~~~ 103 (453)
T TIGR00457 85 ---KGQPVELQVKKIEVVGEAE 103 (453)
T ss_pred ---CCCCEEEEEeEEEEEecCC
Confidence 2367888887665565553
No 235
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=43.55 E-value=2.1e+02 Score=25.88 Aligned_cols=34 Identities=26% Similarity=0.590 Sum_probs=24.6
Q ss_pred EEEEEEechhhhhhhhHhhhcCCCCcEEEEE-eEEeeec
Q 006973 348 TVTVSLWNELATNVGQELLDNADKSPIVAIK-SLKVGDF 385 (623)
Q Consensus 348 ~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~-~~kV~~f 385 (623)
-++|++||..|+.+.+. ...|.-|.+. ..+...|
T Consensus 48 w~~v~~fg~~Ae~v~~~----l~KG~~V~V~Grl~~~~y 82 (131)
T PRK07274 48 FINVVLWGKLAETLASY----ASKGSLISIDGELRTRKY 82 (131)
T ss_pred EEEEEEehHHHHHHHHH----cCCCCEEEEEEEEEeccC
Confidence 68999999999887544 4556766665 4566667
No 236
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=43.53 E-value=16 Score=28.35 Aligned_cols=29 Identities=17% Similarity=0.354 Sum_probs=21.9
Q ss_pred eccccccccceecC-CCCeeecCcCCCCcc
Q 006973 482 YRACKTCNKKVTDA-LGSGYWCEGCQKNDE 510 (623)
Q Consensus 482 Y~aC~~C~KKv~~~-~~~~~~C~kC~~~~~ 510 (623)
-.|||.|+-++.-. ..+...|+.|+..++
T Consensus 8 iLaCP~~kg~L~~~~~~~~L~c~~~~~aYp 37 (60)
T COG2835 8 ILACPVCKGPLVYDEEKQELICPRCKLAYP 37 (60)
T ss_pred eeeccCcCCcceEeccCCEEEecccCceee
Confidence 46899999886432 356889999998763
No 237
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=43.40 E-value=2.4e+02 Score=26.91 Aligned_cols=35 Identities=20% Similarity=0.252 Sum_probs=24.8
Q ss_pred EEEEEEechhhhhhhhHhhhcCCCCcEEEEE-eEEeeecc
Q 006973 348 TVTVSLWNELATNVGQELLDNADKSPIVAIK-SLKVGDFQ 386 (623)
Q Consensus 348 ~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~-~~kV~~f~ 386 (623)
-+.|++||..|+.+.+. +..|.-|.+. .++...|.
T Consensus 53 w~~Vv~fgk~AE~v~~~----LkKGs~V~VeGrL~~r~w~ 88 (168)
T PRK06863 53 WHRIVFYRRQAEVAGEY----LRKGSQVYVEGRLKTRKWQ 88 (168)
T ss_pred EEEEEEEhHHHHHHHHH----CCCCCEEEEEEEEEeCCcc
Confidence 68999999999887554 4556666564 45666674
No 238
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=43.16 E-value=51 Score=36.14 Aligned_cols=56 Identities=25% Similarity=0.348 Sum_probs=42.8
Q ss_pred cccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEee-eEEEecCCCccccCCceEEEEc
Q 006973 208 EGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISR-GTLRVANKQFKTVQNDYEMNLN 272 (623)
Q Consensus 208 ~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~-~~V~~a~~~~~~~~~~yei~f~ 272 (623)
.| +..|.|-|+.. .|+|++|.....++.-.+++|.=+.+.+ ..+-+. ..+|.|..+
T Consensus 40 sg-H~YFtLKD~~A-~i~c~mf~~~~~~l~f~p~eG~~V~v~G~is~Y~~-------rG~YQi~~~ 96 (440)
T COG1570 40 SG-HLYFTLKDERA-QIRCVMFKGNNRRLKFRPEEGMQVLVRGKISLYEP-------RGDYQIVAE 96 (440)
T ss_pred Cc-cEEEEEccCCc-eEEEEEEcCcccccCCCccCCCEEEEEEEEEEEcC-------CCceEEEEe
Confidence 45 88999999988 9999999988888887899998877763 333333 355777665
No 239
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=43.13 E-value=18 Score=25.89 Aligned_cols=25 Identities=16% Similarity=0.546 Sum_probs=18.1
Q ss_pred eccccccccceecCCCCeeecCcCC
Q 006973 482 YRACKTCNKKVTDALGSGYWCEGCQ 506 (623)
Q Consensus 482 Y~aC~~C~KKv~~~~~~~~~C~kC~ 506 (623)
-..||.|+--+-...+|...|..|+
T Consensus 17 ~~~Cp~C~~PL~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDCGTPLMRDKDGKIYCVSCG 41 (41)
T ss_pred cCccCCCCCeeEEecCCCEECCCCC
Confidence 4568888777666446778888885
No 240
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=43.08 E-value=2.6e+02 Score=26.98 Aligned_cols=35 Identities=26% Similarity=0.351 Sum_probs=24.9
Q ss_pred EEEEEEechhhhhhhhHhhhcCCCCcEEEEE-eEEeeecc
Q 006973 348 TVTVSLWNELATNVGQELLDNADKSPIVAIK-SLKVGDFQ 386 (623)
Q Consensus 348 ~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~-~~kV~~f~ 386 (623)
-+.|++|++.|+.+.+. +..+..|.|. .++...|.
T Consensus 53 w~~V~~fGk~AE~v~~~----LkKGs~V~VeGrL~~~~ye 88 (182)
T PRK06958 53 WHRVAFFGRLAEIVGEY----LKKGSSVYIEGRIRTRKWQ 88 (182)
T ss_pred EEEEEEehHHHHHHHHH----hCCCCEEEEEEEEEeCceE
Confidence 78999999999877544 4556666665 45666675
No 241
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=42.56 E-value=15 Score=24.23 Aligned_cols=21 Identities=29% Similarity=0.711 Sum_probs=16.9
Q ss_pred cccccccceecCCCCeeecCcCC
Q 006973 484 ACKTCNKKVTDALGSGYWCEGCQ 506 (623)
Q Consensus 484 aC~~C~KKv~~~~~~~~~C~kC~ 506 (623)
.|..|+|++... . .|+|+.|+
T Consensus 2 ~C~~C~~~~~~~-~-~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGF-Y-FYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCC-E-eEEeCCCC
Confidence 588899998754 2 89999997
No 242
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=42.40 E-value=16 Score=28.26 Aligned_cols=27 Identities=15% Similarity=0.573 Sum_probs=21.2
Q ss_pred eccccccccce-ecCCCCeeecCcCCCC
Q 006973 482 YRACKTCNKKV-TDALGSGYWCEGCQKN 508 (623)
Q Consensus 482 Y~aC~~C~KKv-~~~~~~~~~C~kC~~~ 508 (623)
++.|..|+.-+ ..+....|.|++|++.
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~ 36 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGEV 36 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCce
Confidence 68899999999 4444567899999954
No 243
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=42.11 E-value=1.3e+02 Score=37.30 Aligned_cols=89 Identities=15% Similarity=0.141 Sum_probs=59.7
Q ss_pred eeccccCC--CCCCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechH-----HHHHHhhcccCcEEE
Q 006973 175 HPLVSLNP--YQGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEA-----ARKFYDRFQLGKVYY 247 (623)
Q Consensus 175 ~~I~~L~p--~~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~-----~~kf~~~l~eG~vy~ 247 (623)
+.+.++.. .....+|.|||.++ |. .|++.=++|.|.+| .|++.+-.+. .+.|...|..|+++.
T Consensus 640 ~~~~~~~~~~~~~~V~v~Grv~~~---R~------~G~~~F~~lrD~~g-~iQ~v~~~~~~~~~~~~~~~~~l~~gd~V~ 709 (1094)
T PRK02983 640 HTVAEALDAPTGEEVSVSGRVLRI---RD------YGGVLFADLRDWSG-ELQVLLDASRLEQGSLADFRAAVDLGDLVE 709 (1094)
T ss_pred cCHHHHHHhcCCCEEEEEEEEEEE---ee------CCCeEEEEEEeCCe-eEEEEEECCccchhhHHHHHhcCCCCCEEE
Confidence 34555532 12358999999874 43 34565578999998 8999986542 345566799999999
Q ss_pred EeeeEEEecCCCccccCCceEEEEccCcEEEEc
Q 006973 248 ISRGTLRVANKQFKTVQNDYEMNLNENSEVEEA 280 (623)
Q Consensus 248 is~~~V~~a~~~~~~~~~~yei~f~~~T~I~~~ 280 (623)
+.+.-.+.. ...++|..+..+.+.++
T Consensus 710 v~G~v~~t~-------~ge~ei~~~~i~ll~k~ 735 (1094)
T PRK02983 710 VTGTMGTSR-------NGTLSLLVTSWRLAGKC 735 (1094)
T ss_pred EEEEEEEcC-------CCCEEEEEeEEEEEecc
Confidence 997544322 14688877776666655
No 244
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=41.87 E-value=19 Score=27.87 Aligned_cols=10 Identities=20% Similarity=0.544 Sum_probs=6.0
Q ss_pred eccccccccc
Q 006973 482 YRACKTCNKK 491 (623)
Q Consensus 482 Y~aC~~C~KK 491 (623)
-..||+|++-
T Consensus 25 ~F~CPnCG~~ 34 (59)
T PRK14890 25 KFLCPNCGEV 34 (59)
T ss_pred EeeCCCCCCe
Confidence 4456766664
No 245
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=41.86 E-value=15 Score=24.70 Aligned_cols=23 Identities=35% Similarity=0.855 Sum_probs=16.6
Q ss_pred cccccccceecCCCCeeecCcCCC
Q 006973 484 ACKTCNKKVTDALGSGYWCEGCQK 507 (623)
Q Consensus 484 aC~~C~KKv~~~~~~~~~C~kC~~ 507 (623)
.|..|.++-... +..|+|++|+.
T Consensus 2 rC~vC~~~k~rk-~T~~~C~~C~v 24 (32)
T PF13842_consen 2 RCKVCSKKKRRK-DTRYMCSKCDV 24 (32)
T ss_pred CCeECCcCCccc-eeEEEccCCCC
Confidence 577787765433 47899999974
No 246
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.73 E-value=14 Score=32.15 Aligned_cols=29 Identities=17% Similarity=-0.085 Sum_probs=22.5
Q ss_pred eccccccccceecCCCCeeecCcCCCCcc
Q 006973 482 YRACKTCNKKVTDALGSGYWCEGCQKNDE 510 (623)
Q Consensus 482 Y~aC~~C~KKv~~~~~~~~~C~kC~~~~~ 510 (623)
-.-||.|+||...-.-..--|+.|++.++
T Consensus 9 KridPetg~KFYDLNrdPiVsPytG~s~P 37 (129)
T COG4530 9 KRIDPETGKKFYDLNRDPIVSPYTGKSYP 37 (129)
T ss_pred cccCccccchhhccCCCccccCcccccch
Confidence 45799999998764345568999999884
No 247
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=41.29 E-value=16 Score=33.10 Aligned_cols=28 Identities=18% Similarity=0.507 Sum_probs=22.8
Q ss_pred CeEeccccccccceecCCCCeeecCcCCC
Q 006973 479 AMWYRACKTCNKKVTDALGSGYWCEGCQK 507 (623)
Q Consensus 479 ~~~Y~aC~~C~KKv~~~~~~~~~C~kC~~ 507 (623)
.+--..||.|+--+..- +|.-+|+.|+.
T Consensus 25 kML~~hCp~Cg~PLF~K-dG~v~CPvC~~ 52 (131)
T COG1645 25 KMLAKHCPKCGTPLFRK-DGEVFCPVCGY 52 (131)
T ss_pred HHHHhhCcccCCcceee-CCeEECCCCCc
Confidence 34567899999988874 88899999994
No 248
>COG0587 DnaE DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]
Probab=40.94 E-value=83 Score=38.98 Aligned_cols=71 Identities=13% Similarity=0.192 Sum_probs=51.5
Q ss_pred eeccccCCCCCCeEEEEEEEeeccccccccCCCccc-EEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEee
Q 006973 175 HPLVSLNPYQGNWTIKVRVTSKGNMRTYKNARGEGC-VFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISR 250 (623)
Q Consensus 175 ~~I~~L~p~~~~w~I~~RV~~K~~~r~~~~~~g~g~-~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~ 250 (623)
.++.++.+....|.+-|-|+..- .-... ..|. +--+.|.|++| .+.+++|.....+++..+.+++.|.+.+
T Consensus 967 ~~~~~~~~~~~~~~~~~~i~~vr---~~~tk-~~G~~~~f~tl~D~~g-~~e~v~f~~~~~~~~~~l~~~~~~~v~g 1038 (1139)
T COG0587 967 IRLLDLVEDGRRVVLAGGIVAVR---QRPTK-AKGNKMAFLTLEDETG-ILEVVVFPSEYERYRRLLLEGRLLIVKG 1038 (1139)
T ss_pred cchhhhccccceeEEEEEEEEEE---Eeecc-CCCCEEEEEEEecCCC-cEEEEEcHHHHHHHHHHhccCcEEEEEE
Confidence 45555555554588777777643 22222 1244 44568999999 9999999999999999999998888864
No 249
>cd04322 LysRS_N LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Included in this group are E. coli LysS and LysU. These two isoforms of LysRS are encoded by distinct genes which are differently regulated. Eukaryotes contain 2 sets of aaRSs, both of which encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein
Probab=40.79 E-value=41 Score=29.14 Aligned_cols=60 Identities=8% Similarity=0.063 Sum_probs=38.2
Q ss_pred EEEEEeCcccceeecccccc---ccccc-cCccceeeEEEEcceeeeccCCCceEEEEEEeeeeec
Q 006973 42 YMFNASDGKKRLKAILPSNL---SSEVI-SGNIQNKGLIRLLDYALNEIPTKSEKYLIVTKCEVVS 103 (623)
Q Consensus 42 yr~~lSDG~~~~~~mlat~l---n~~v~-~~~l~~~siirl~~y~~~~~~~~~~~vlii~~lev~~ 103 (623)
.=+.|.||.+.+|+++.... ..+.. ...|..||+|.++......-.+ .--|.+.++++++
T Consensus 18 ~Fi~lrd~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~G~v~~~~~g--~~El~~~~~~ils 81 (108)
T cd04322 18 SFADLQDESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTGTPFKTKTG--ELSIFVKEFTLLS 81 (108)
T ss_pred EEEEEEECCeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEEEEEEEecCCC--CEEEEeCEeEEee
Confidence 34789999999999884332 11111 1238999999999988765332 2344556666654
No 250
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=40.72 E-value=65 Score=35.55 Aligned_cols=56 Identities=18% Similarity=0.264 Sum_probs=41.6
Q ss_pred CeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEee
Q 006973 186 NWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISR 250 (623)
Q Consensus 186 ~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~ 250 (623)
+..|+|=|++ |+.. .. ..+.|.|.|+.. .|+|++|...+.+..-.+++|.-+.+.+
T Consensus 25 ~v~v~gEis~------~~~~-~s-GH~Yf~Lkd~~a-~i~~~~~~~~~~~~~~~~~~G~~v~v~g 80 (438)
T PRK00286 25 QVWVRGEISN------FTRH-SS-GHWYFTLKDEIA-QIRCVMFKGSARRLKFKPEEGMKVLVRG 80 (438)
T ss_pred cEEEEEEeCC------CeeC-CC-CeEEEEEEcCCc-EEEEEEEcChhhcCCCCCCCCCEEEEEE
Confidence 4456666654 3222 12 378899999977 9999999988888777799999888764
No 251
>PRK13732 single-stranded DNA-binding protein; Provisional
Probab=40.70 E-value=3.4e+02 Score=26.05 Aligned_cols=35 Identities=26% Similarity=0.328 Sum_probs=24.7
Q ss_pred EEEEEEechhhhhhhhHhhhcCCCCcEEEEE-eEEeeecc
Q 006973 348 TVTVSLWNELATNVGQELLDNADKSPIVAIK-SLKVGDFQ 386 (623)
Q Consensus 348 ~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~-~~kV~~f~ 386 (623)
-++|++||+.|+.+.+. +..|..|.|. .++...|.
T Consensus 55 w~~Vv~wgk~Ae~v~~~----L~KG~~V~VeGrL~~r~ye 90 (175)
T PRK13732 55 WHRVVLFGKLAEVAGEY----LRKGAQVYIEGQLRTRSWE 90 (175)
T ss_pred EEEEEEecHHHHHHHHh----cCCCCEEEEEEEEEeeeEc
Confidence 57999999999887554 4556766665 45555563
No 252
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=40.68 E-value=87 Score=38.82 Aligned_cols=77 Identities=14% Similarity=0.217 Sum_probs=52.2
Q ss_pred ccccccccccccCCcceeEEEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCC
Q 006973 293 NFVPIDELGRYVNGTELVDIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKS 372 (623)
Q Consensus 293 ~f~~i~di~~~~~~~~~vDVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~ 372 (623)
..+++.+|.. ..+..|-|.|+|+.+... ++|+ |+ ..--++|.|.+| .+++++|.+..+.+... ...+
T Consensus 931 ~~~~~~~l~~--~~~~~v~v~g~i~~~~~~---~tk~-g~--~maf~~leD~tg-~~e~~vFp~~y~~~~~~----l~~~ 997 (1107)
T PRK06920 931 EIPSLAQAMR--HKKKVQRAIVYITSVKVI---RTKK-GQ--KMAFITFCDQND-EMEAVVFPETYIHFSDK----LQEG 997 (1107)
T ss_pred CCcCHHHHhh--cCCCEEEEEEEEEEeEee---cCCC-CC--eEEEEEEeeCCC-cEEEEECHHHHHHHHHH----hccC
Confidence 3456666643 234578899999988643 4553 54 245689999999 89999999877776544 3456
Q ss_pred cEEEEEeEEee
Q 006973 373 PIVAIKSLKVG 383 (623)
Q Consensus 373 ~Vv~i~~~kV~ 383 (623)
.++.+++ +|.
T Consensus 998 ~~~~v~G-~v~ 1007 (1107)
T PRK06920 998 AIVLVDG-TIE 1007 (1107)
T ss_pred CEEEEEE-EEE
Confidence 7777765 443
No 253
>PRK03932 asnC asparaginyl-tRNA synthetase; Validated
Probab=40.56 E-value=2.1e+02 Score=31.75 Aligned_cols=81 Identities=14% Similarity=0.170 Sum_probs=52.6
Q ss_pred CCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEech---HHHHHHhhcccCcEEEEeeeEEEecCCCcc
Q 006973 185 GNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNE---AARKFYDRFQLGKVYYISRGTLRVANKQFK 261 (623)
Q Consensus 185 ~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~---~~~kf~~~l~eG~vy~is~~~V~~a~~~~~ 261 (623)
...+|+|||.+ +|. .|++.=++|.|.+| .|++.+-.+ ..-++...|..|+++.+.+. |.....
T Consensus 17 ~~V~i~G~v~~---~R~------~g~~~Fi~lrD~~g-~iq~~~~~~~~~~~~~~~~~l~~~s~v~v~G~-v~~~~~--- 82 (450)
T PRK03932 17 QEVTVRGWVRT---KRD------SGKIAFLQLRDGSC-FKQLQVVKDNGEEYFEEIKKLTTGSSVIVTGT-VVESPR--- 82 (450)
T ss_pred CEEEEEEEEEE---EEe------CCCeEEEEEECCCC-cEEEEEEcCCChHHHHHHhcCCCCcEEEEEEE-EEcCCC---
Confidence 46899999977 343 23565578999998 788877532 22223345899999999764 443321
Q ss_pred ccCCceEEEEccCcEEEEc
Q 006973 262 TVQNDYEMNLNENSEVEEA 280 (623)
Q Consensus 262 ~~~~~yei~f~~~T~I~~~ 280 (623)
....+||....-+.+.++
T Consensus 83 -~~~~~el~~~~i~vl~~~ 100 (450)
T PRK03932 83 -AGQGYELQATKIEVIGED 100 (450)
T ss_pred -CCCCEEEEEEEEEEccCC
Confidence 235688887665555543
No 254
>TIGR00237 xseA exodeoxyribonuclease VII, large subunit. This family consist of exodeoxyribonuclease VII, large subunit XseA which catalyses exonucleolytic cleavage in either the 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. Exonuclease VII consists of one large subunit and four small subunits.
Probab=40.19 E-value=67 Score=35.49 Aligned_cols=56 Identities=20% Similarity=0.312 Sum_probs=41.2
Q ss_pred CeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEee
Q 006973 186 NWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISR 250 (623)
Q Consensus 186 ~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~ 250 (623)
+..|+|=|++ |+.. ..| .+.|+|.|+.. .|+|++|...+.++.-.+++|.=+.+.+
T Consensus 19 ~v~V~GEisn------~~~~-~sG-H~YFtLkD~~a-~i~~vmf~~~~~~l~f~~~~G~~V~v~g 74 (432)
T TIGR00237 19 QVWIQGEISN------FTQP-VSG-HWYFTLKDENA-QVRCVMFRGNNNRLKFRPQNGQQVLVRG 74 (432)
T ss_pred cEEEEEEecC------CeeC-CCc-eEEEEEEcCCc-EEEEEEEcChhhCCCCCCCCCCEEEEEE
Confidence 4446676654 3221 123 78899999876 9999999988888777789999888764
No 255
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=40.16 E-value=1.2e+02 Score=25.97 Aligned_cols=71 Identities=11% Similarity=0.126 Sum_probs=46.3
Q ss_pred eEEEeeeeecC-ceEEEEEeCcccceeeccccccccccccCccceeeEEEEcceeeeccCCCceEEEEEEeee
Q 006973 29 VVQVLDLKLTG-NRYMFNASDGKKRLKAILPSNLSSEVISGNIQNKGLIRLLDYALNEIPTKSEKYLIVTKCE 100 (623)
Q Consensus 29 vlQvl~~k~~~-~ryr~~lSDG~~~~~~mlat~ln~~v~~~~l~~~siirl~~y~~~~~~~~~~~vlii~~le 100 (623)
.=||.+++... +=+.+.|.|+...++++++..-...+....++.|.-|.+..-.-.+...+ +--++|.+++
T Consensus 27 ~GEIs~~~~~~~gh~YftLkD~~a~i~~~~~~~~~~~i~~~~l~~G~~V~v~g~~~~y~~~G-~~sl~v~~i~ 98 (99)
T PF13742_consen 27 EGEISNLKRHSSGHVYFTLKDEEASISCVIFRSRARRIRGFDLKDGDKVLVRGRVSFYEPRG-SLSLIVEDID 98 (99)
T ss_pred EEEEeecEECCCceEEEEEEcCCcEEEEEEEHHHHhhCCCCCCCCCCEEEEEEEEEEECCCc-EEEEEEEEeE
Confidence 35788888754 56799999999999877765555544445678887777765544443332 4555555543
No 256
>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=39.76 E-value=18 Score=23.53 Aligned_cols=20 Identities=20% Similarity=0.537 Sum_probs=10.4
Q ss_pred ccccccceecCC-CCeeecCc
Q 006973 485 CKTCNKKVTDAL-GSGYWCEG 504 (623)
Q Consensus 485 C~~C~KKv~~~~-~~~~~C~k 504 (623)
||.|+.++.... +-.|+|.+
T Consensus 2 CP~C~s~l~~~~~ev~~~C~N 22 (28)
T PF03119_consen 2 CPVCGSKLVREEGEVDIRCPN 22 (28)
T ss_dssp -TTT--BEEE-CCTTCEEE--
T ss_pred cCCCCCEeEcCCCCEeEECCC
Confidence 999999997542 34788864
No 257
>PRK02935 hypothetical protein; Provisional
Probab=39.69 E-value=16 Score=31.52 Aligned_cols=26 Identities=23% Similarity=0.438 Sum_probs=18.5
Q ss_pred ccccccccceecCCCCeeecCcCCCCc
Q 006973 483 RACKTCNKKVTDALGSGYWCEGCQKND 509 (623)
Q Consensus 483 ~aC~~C~KKv~~~~~~~~~C~kC~~~~ 509 (623)
.-||+|+|--.-- +-...|..|++..
T Consensus 71 V~CP~C~K~TKmL-GrvD~CM~C~~PL 96 (110)
T PRK02935 71 VICPSCEKPTKML-GRVDACMHCNQPL 96 (110)
T ss_pred eECCCCCchhhhc-cceeecCcCCCcC
Confidence 3699999854332 4467899999865
No 258
>PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional
Probab=39.50 E-value=2.3e+02 Score=33.40 Aligned_cols=95 Identities=17% Similarity=0.125 Sum_probs=59.7
Q ss_pred eccccCCCC--CCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechH----HHHHHhhcccCcEEEEe
Q 006973 176 PLVSLNPYQ--GNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEA----ARKFYDRFQLGKVYYIS 249 (623)
Q Consensus 176 ~I~~L~p~~--~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~----~~kf~~~l~eG~vy~is 249 (623)
...+|++.. ..-+|+|||.+ +|. -|++.=++|.|.+| .|++++-.+. .-++...|..|+++.+.
T Consensus 8 ~cg~l~~~~~g~~V~l~GWV~~---~R~------~G~l~FidLRD~~G-~iQvV~~~~~~~~~~~~~~~~L~~EsvV~V~ 77 (706)
T PRK12820 8 FCGHLSLDDTGREVCLAGWVDA---FRD------HGELLFIHLRDRNG-FIQAVFSPEAAPADVYELAASLRAEFCVALQ 77 (706)
T ss_pred ccccCChhhCCCEEEEEEEEEE---EEc------CCCcEEEEEEeCCc-cEEEEEeCCcCCHHHHHHHhcCCCCCEEEEE
Confidence 445555532 35889999976 343 23555578999999 7999886432 22233568999999999
Q ss_pred eeEEEecCCCccc--cCCceEEEEccCcEEEEc
Q 006973 250 RGTLRVANKQFKT--VQNDYEMNLNENSEVEEA 280 (623)
Q Consensus 250 ~~~V~~a~~~~~~--~~~~yei~f~~~T~I~~~ 280 (623)
+.-.....+.-++ ....+||....-+.+.++
T Consensus 78 G~v~~r~~~~~n~~~~tg~iEl~~~~i~iL~~a 110 (706)
T PRK12820 78 GEVQKRLEETENPHIETGDIEVFVRELSILAAS 110 (706)
T ss_pred eEEeccCccccCCCCCCCcEEEEeeEEEEEecC
Confidence 8544322121111 235688888766666554
No 259
>PRK06293 single-stranded DNA-binding protein; Provisional
Probab=39.32 E-value=2.7e+02 Score=26.34 Aligned_cols=35 Identities=9% Similarity=0.144 Sum_probs=24.7
Q ss_pred EEEEEEechhhhhhhhHhhhcCCCCcEEEEE-eEEeeecc
Q 006973 348 TVTVSLWNELATNVGQELLDNADKSPIVAIK-SLKVGDFQ 386 (623)
Q Consensus 348 ~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~-~~kV~~f~ 386 (623)
-++|++||+.|+...+. +..|.-|++. .++...|.
T Consensus 44 wi~v~awg~~Ae~v~~y----L~KG~~V~VeGrL~~~~y~ 79 (161)
T PRK06293 44 WCRCNIWGNRYDKMLPY----LKKGSGVIVAGEMSPESYV 79 (161)
T ss_pred EEEEEEEhHHHHHHHHh----CCCCCEEEEEEEEEeCccC
Confidence 68999999999876543 4556666664 46666674
No 260
>PHA02942 putative transposase; Provisional
Probab=39.27 E-value=25 Score=38.21 Aligned_cols=37 Identities=16% Similarity=0.556 Sum_probs=24.8
Q ss_pred EEEEeCCCCeEeccccccccceecCCCCeeecCcCCCCc
Q 006973 471 ISLIKPDQAMWYRACKTCNKKVTDALGSGYWCEGCQKND 509 (623)
Q Consensus 471 I~~i~~d~~~~Y~aC~~C~KKv~~~~~~~~~C~kC~~~~ 509 (623)
|..+.+. ..-..||.|+.+........|.|+.||...
T Consensus 316 Vv~V~p~--yTSq~Cs~CG~~~~~l~~r~f~C~~CG~~~ 352 (383)
T PHA02942 316 VEFVNPS--YSSVSCPKCGHKMVEIAHRYFHCPSCGYEN 352 (383)
T ss_pred EEEECCC--CCCccCCCCCCccCcCCCCEEECCCCCCEe
Confidence 4445432 346779999987654334579999999754
No 261
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=38.94 E-value=73 Score=27.93 Aligned_cols=35 Identities=20% Similarity=0.474 Sum_probs=24.9
Q ss_pred EEEEEEechhhhhhhhHhhhcCCCCcEEEEE-eEEeeecc
Q 006973 348 TVTVSLWNELATNVGQELLDNADKSPIVAIK-SLKVGDFQ 386 (623)
Q Consensus 348 ~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~-~~kV~~f~ 386 (623)
-+.|++||+.|+.+.+. ...|.-|++. .++...|.
T Consensus 48 ~~~v~~wg~~Ae~~~~~----l~KG~~V~V~G~l~~~~~~ 83 (112)
T PRK06752 48 FINCVVWRKSAENVTEY----CTKGSLVGITGRIHTRNYE 83 (112)
T ss_pred EEEEEEehHHHHHHHHh----cCCCCEEEEEEEEEeCccC
Confidence 68999999999987554 4556666665 45555664
No 262
>PF05810 NinF: NinF protein; InterPro: IPR008712 This family consists of several bacteriophage NinF proteins as well as related sequences from Escherichia coli.
Probab=38.70 E-value=6.1 Score=29.94 Aligned_cols=21 Identities=29% Similarity=0.737 Sum_probs=17.5
Q ss_pred ccccccceecCCCCeeecCcCCC
Q 006973 485 CKTCNKKVTDALGSGYWCEGCQK 507 (623)
Q Consensus 485 C~~C~KKv~~~~~~~~~C~kC~~ 507 (623)
|.+|+|++.. +..|-|+.|=.
T Consensus 20 Ca~C~~~L~~--~E~h~Ce~C~~ 40 (58)
T PF05810_consen 20 CANCGQKLHP--DETHVCEECCA 40 (58)
T ss_pred HhccCccccc--chhhHHHHHHH
Confidence 9999999986 46899999843
No 263
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=38.65 E-value=81 Score=40.20 Aligned_cols=73 Identities=15% Similarity=0.251 Sum_probs=55.9
Q ss_pred CeeeccccCCCCCCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechH--HHHHHhhcccCcEEEEee
Q 006973 173 RVHPLVSLNPYQGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEA--ARKFYDRFQLGKVYYISR 250 (623)
Q Consensus 173 ~~~~I~~L~p~~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~--~~kf~~~l~eG~vy~is~ 250 (623)
.+++|.++.....+.+|.|.|... +.|..++ ...++++.+.|.++ .|.+..|... -.+..+.|+.|+|+.+.+
T Consensus 225 ~~~~~~~i~~~~~~v~i~G~if~~-e~~~~k~---~~~~~~~~~td~~~-s~~~k~f~~~~~~~~~~~~~~~g~~v~~~g 299 (1437)
T PRK00448 225 EITPMKEINEEERRVVVEGYVFKV-EIKELKS---GRHILTFKITDYTS-SIIVKKFSRDKEDLKKFDEIKKGDWVKVRG 299 (1437)
T ss_pred CcccHHHhhccCCeEEEEEEEEEE-EEEeccC---CCEEEEEEEEcCCC-CEEEEEEecCcchhHHHhcCCCCCEEEEEE
Confidence 568999999888899999999775 3555543 23578999999998 8999998722 223446799999999874
No 264
>PTZ00417 lysine-tRNA ligase; Provisional
Probab=38.29 E-value=1.6e+02 Score=33.97 Aligned_cols=77 Identities=13% Similarity=0.119 Sum_probs=47.9
Q ss_pred CeEEEEEEEeeccccccccCCCcc-cEEEEEEEeCCCCeEEEEEechH-------HHHHHhhcccCcEEEEeeeEEEecC
Q 006973 186 NWTIKVRVTSKGNMRTYKNARGEG-CVFNVELTDEDGTQIQATMFNEA-------ARKFYDRFQLGKVYYISRGTLRVAN 257 (623)
Q Consensus 186 ~w~I~~RV~~K~~~r~~~~~~g~g-~~f~~~L~D~~G~~I~at~~~~~-------~~kf~~~l~eG~vy~is~~~V~~a~ 257 (623)
..+|.|||.++ |. .| ++.=++|.|..| .|++.+-.+. .+.+...|..|+++.+.+.-.+
T Consensus 134 ~v~v~Grv~~~---R~------~G~k~~F~~L~d~~g-~iQv~~~~~~~~~~~~~~~~~~~~l~~Gd~V~V~G~~~~--- 200 (585)
T PTZ00417 134 ILNVTGRIMRV---SA------SGQKLRFFDLVGDGA-KIQVLANFAFHDHTKSNFAECYDKIRRGDIVGIVGFPGK--- 200 (585)
T ss_pred eEEEEEEEEee---ec------CCCCCEEEEEEeCCe-eEEEEEECCccCCCHHHHHHHHhcCCCCCEEEEEeEEcC---
Confidence 47899999873 43 33 344456779877 8999997431 2233456999999999987221
Q ss_pred CCccccCCceEEEEccCcEEEE
Q 006973 258 KQFKTVQNDYEMNLNENSEVEE 279 (623)
Q Consensus 258 ~~~~~~~~~yei~f~~~T~I~~ 279 (623)
+....++|....-+.+.+
T Consensus 201 ----t~~gel~i~~~~i~llsk 218 (585)
T PTZ00417 201 ----SKKGELSIFPKETIILSP 218 (585)
T ss_pred ----CCCceEEEEEEEEEEEec
Confidence 113345555554444443
No 265
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=38.15 E-value=77 Score=39.11 Aligned_cols=74 Identities=27% Similarity=0.323 Sum_probs=49.6
Q ss_pred ccccccccccCCcceeEEEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcE
Q 006973 295 VPIDELGRYVNGTELVDIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSPI 374 (623)
Q Consensus 295 ~~i~di~~~~~~~~~vDVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~V 374 (623)
+++++|.+ ...+..|=|.|+|+.+... .+|+ | .--++|.|.+| .+++++|.+..+.+... ...+.+
T Consensus 942 ~~~~~l~~-~~~~~~v~v~g~i~~~~~~---~Tkk-G----maf~~leD~~g-~~e~~ifp~~~~~~~~~----l~~~~~ 1007 (1046)
T PRK05672 942 VSAAELLD-VEDGRRVRVAGVVTHRQRP---GTAS-G----VTFLTLEDETG-MVNVVVWPGLWERQRRE----ALGARL 1007 (1046)
T ss_pred cCHHHHhh-ccCCCEEEEEEEEEEEEEe---cCCC-c----eEEEEEecCCC-CEEEEECHHHHHHHHHH----hccCCE
Confidence 45556543 2234568899999887543 2443 4 45689999999 79999999887776443 355777
Q ss_pred EEEEeEEee
Q 006973 375 VAIKSLKVG 383 (623)
Q Consensus 375 v~i~~~kV~ 383 (623)
+.+++ +|.
T Consensus 1008 ~~v~g-~v~ 1015 (1046)
T PRK05672 1008 LLVRG-RVQ 1015 (1046)
T ss_pred EEEEE-EEE
Confidence 77765 444
No 266
>PRK12496 hypothetical protein; Provisional
Probab=37.80 E-value=19 Score=34.19 Aligned_cols=36 Identities=31% Similarity=0.506 Sum_probs=23.6
Q ss_pred EEEeCCCCeEeccccccccceecCCCCeeecCcCCCCc
Q 006973 472 SLIKPDQAMWYRACKTCNKKVTDALGSGYWCEGCQKND 509 (623)
Q Consensus 472 ~~i~~d~~~~Y~aC~~C~KKv~~~~~~~~~C~kC~~~~ 509 (623)
..|+.. .-|-.-|+.|+|....+ ...-.|+.||...
T Consensus 118 ~~i~~~-~~w~~~C~gC~~~~~~~-~~~~~C~~CG~~~ 153 (164)
T PRK12496 118 KGIKKV-IKWRKVCKGCKKKYPED-YPDDVCEICGSPV 153 (164)
T ss_pred ccchhh-eeeeEECCCCCccccCC-CCCCcCCCCCChh
Confidence 445544 33566799999887543 2234799999754
No 267
>PRK05853 hypothetical protein; Validated
Probab=37.68 E-value=83 Score=29.73 Aligned_cols=36 Identities=25% Similarity=0.633 Sum_probs=24.6
Q ss_pred EEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEEeeecc
Q 006973 348 TVTVSLWNELATNVGQELLDNADKSPIVAIKSLKVGDFQ 386 (623)
Q Consensus 348 ~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~kV~~f~ 386 (623)
-+.|++||..|+.+.+.+ .+..+|++.-.++...|.
T Consensus 44 wi~V~~wg~lAe~v~~~L---~KG~~V~V~GrL~~~~we 79 (161)
T PRK05853 44 FITVNCWGRLVTGVGAAL---GKGAPVIVVGHVYTSEYE 79 (161)
T ss_pred EEEEEEEhHHHHHHHHHc---CCCCEEEEEEEEEccceE
Confidence 689999999999876543 233445544456777774
No 268
>KOG3056 consensus Protein required for S-phase initiation or completion [Cell cycle control, cell division, chromosome partitioning]
Probab=37.14 E-value=1.4e+02 Score=33.57 Aligned_cols=76 Identities=20% Similarity=0.149 Sum_probs=50.5
Q ss_pred eEEEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCc-cEEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEEeeecc-c
Q 006973 310 VDIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETK-RTVTVSLWNELATNVGQELLDNADKSPIVAIKSLKVGDFQ-G 387 (623)
Q Consensus 310 vDVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg-~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~kV~~f~-G 387 (623)
-=++|+|++-+++... . .|..+ .-..|-|..+ ..|.|-|+|+ |-. ..|. ...|.||+|-++-|-+.+ |
T Consensus 188 Wvt~GvI~~K~~~K~t--~-~G~~y--~iwkL~dLk~~q~vslfLFG~-a~k--~~wk--~k~GtVialLNp~v~k~~~g 257 (578)
T KOG3056|consen 188 WVTMGVIVEKSDPKFT--S-NGNPY--SIWKLTDLKDHQTVSLFLFGK-AHK--RYWK--IKLGTVIALLNPEVLKDRPG 257 (578)
T ss_pred eEEEEEEeecCCcccc--c-CCCce--EEEEeeecCccceeEEEEecH-HHH--HHhh--hccCcEEEEeCccccCCCCC
Confidence 3468999999988642 2 36544 3445555555 5999999999 333 2343 467999999998887654 3
Q ss_pred e----eeecccc
Q 006973 388 I----SLSTLGR 395 (623)
Q Consensus 388 ~----~Ls~~~~ 395 (623)
. +|+..+.
T Consensus 258 s~~~f~LsIds~ 269 (578)
T KOG3056|consen 258 SRKSFSLSIDSS 269 (578)
T ss_pred CcceEEEEecCc
Confidence 2 5665444
No 269
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=36.93 E-value=44 Score=31.47 Aligned_cols=27 Identities=22% Similarity=0.599 Sum_probs=23.1
Q ss_pred EEEEEEEeCCCCeEEEEEechHHHHHHh
Q 006973 211 VFNVELTDEDGTQIQATMFNEAARKFYD 238 (623)
Q Consensus 211 ~f~~~L~D~~G~~I~at~~~~~~~kf~~ 238 (623)
.+++.|.|.+| .+.+++|++.++++..
T Consensus 69 ~l~~~i~D~Tg-~~~~~~F~~~ae~l~G 95 (166)
T cd04476 69 ILSLNVADHTG-EAWLTLFDEVAEQIFG 95 (166)
T ss_pred EEEEEEEeCCC-CEEEEEehHHHHHHhC
Confidence 57889999999 8999999998877644
No 270
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=36.58 E-value=21 Score=43.75 Aligned_cols=41 Identities=15% Similarity=0.082 Sum_probs=20.2
Q ss_pred hHHHHhCCCH---HHHHH---HHhhcCCchhHHHHHHHhcCceEEEE
Q 006973 537 EAERIIGCSA---DELNE---LKSQLGDDNSYQMKLKEVTWVPHLLR 577 (623)
Q Consensus 537 ~ae~llG~sA---~el~~---~~~~~~~~~~~~~~l~~~~~~~~~f~ 577 (623)
.|.+=+|... +.|+- |...+.-+..++.-+-.+..--|.||
T Consensus 735 ~A~~~~g~~~~~~~~~KgVkgl~S~~k~~EplEKGiLRak~~v~vFK 781 (1337)
T PRK14714 735 SALENVGERENAFDLLKGVKGLTSREKIPEPLEKGILRAKHDVYVFK 781 (1337)
T ss_pred HHHHHhCcccccccccccceecccCCCCCcchHhhhhhhhcCeeEec
Confidence 3445556554 33322 32233334455555555655567776
No 271
>PRK00476 aspS aspartyl-tRNA synthetase; Validated
Probab=35.87 E-value=2.8e+02 Score=31.95 Aligned_cols=87 Identities=14% Similarity=0.139 Sum_probs=54.7
Q ss_pred CCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEech-HHHHHHhhcccCcEEEEeeeEEEecCCCccc-
Q 006973 185 GNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNE-AARKFYDRFQLGKVYYISRGTLRVANKQFKT- 262 (623)
Q Consensus 185 ~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~-~~~kf~~~l~eG~vy~is~~~V~~a~~~~~~- 262 (623)
..-+|+|||.+ +|. .|++.=++|.|.+| .|++++-.. ..-+....|..|+++.+.+--.+...+.-++
T Consensus 18 ~~V~l~GwV~~---~R~------~g~l~Fi~LrD~~g-~iQ~v~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~n~~ 87 (588)
T PRK00476 18 QTVTLCGWVHR---RRD------HGGLIFIDLRDREG-IVQVVFDPDAEAFEVAESLRSEYVIQVTGTVRARPEGTVNPN 87 (588)
T ss_pred CEEEEEEEEEE---EEe------CCCeEEEEEEeCCc-eEEEEEeCCHHHHHHHhCCCCCCEEEEEEEEEecCCcccCcc
Confidence 35889999976 343 23565678999999 799988642 1112234589999999987444322121221
Q ss_pred -cCCceEEEEccCcEEEEcc
Q 006973 263 -VQNDYEMNLNENSEVEEAV 281 (623)
Q Consensus 263 -~~~~yei~f~~~T~I~~~~ 281 (623)
....+||....-..+.++.
T Consensus 88 ~~~g~~El~~~~i~il~~a~ 107 (588)
T PRK00476 88 LPTGEIEVLASELEVLNKSK 107 (588)
T ss_pred CCCCcEEEEEeEEEEEecCC
Confidence 2356899887766665553
No 272
>PLN02903 aminoacyl-tRNA ligase
Probab=35.70 E-value=2.7e+02 Score=32.42 Aligned_cols=96 Identities=14% Similarity=0.093 Sum_probs=60.0
Q ss_pred eeccccCCCC--CCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechH---HHHHHhhcccCcEEEEe
Q 006973 175 HPLVSLNPYQ--GNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEA---ARKFYDRFQLGKVYYIS 249 (623)
Q Consensus 175 ~~I~~L~p~~--~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~---~~kf~~~l~eG~vy~is 249 (623)
+...+|+... ..-+|+|||.+ +|. .|++.=++|.|.+| .|++++-.+. +-+.-..|..|+++.+.
T Consensus 61 ~~cg~l~~~~~gk~V~l~GWV~~---~R~------~G~l~FidLRD~~G-~iQvV~~~~~~~~~~~~~~~L~~esvV~V~ 130 (652)
T PLN02903 61 HLCGALSVNDVGSRVTLCGWVDL---HRD------MGGLTFLDVRDHTG-IVQVVTLPDEFPEAHRTANRLRNEYVVAVE 130 (652)
T ss_pred CchhhcchhhCCCEEEEEEEEEE---Eec------CCCcEEEEEEcCCc-cEEEEEeCCccHHHHHHHhcCCCCCEEEEE
Confidence 3445555432 36889999976 343 23455578999999 7999886532 22233569999999998
Q ss_pred eeEEEecCCCcc--ccCCceEEEEccCcEEEEc
Q 006973 250 RGTLRVANKQFK--TVQNDYEMNLNENSEVEEA 280 (623)
Q Consensus 250 ~~~V~~a~~~~~--~~~~~yei~f~~~T~I~~~ 280 (623)
+--.....+.-+ .....+||....-..+.++
T Consensus 131 G~V~~r~~~~~n~~~~tGeiEl~~~~i~VL~~a 163 (652)
T PLN02903 131 GTVRSRPQESPNKKMKTGSVEVVAESVDILNVV 163 (652)
T ss_pred EEEEeCCCcCcCCCCCCCCEEEEEeEEEEEecC
Confidence 743332111111 2235699988876666655
No 273
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=35.44 E-value=20 Score=31.74 Aligned_cols=27 Identities=26% Similarity=0.416 Sum_probs=17.4
Q ss_pred eccccccccceecCCCCeeecCcCCCC
Q 006973 482 YRACKTCNKKVTDALGSGYWCEGCQKN 508 (623)
Q Consensus 482 Y~aC~~C~KKv~~~~~~~~~C~kC~~~ 508 (623)
---|+.|+.-........+.|++|+..
T Consensus 70 ~~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 70 ECWCETCQQYVTLLTQRVRRCPQCHGD 96 (114)
T ss_pred EEEcccCCCeeecCCccCCcCcCcCCC
Confidence 345888987765532223669999854
No 274
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=35.29 E-value=21 Score=31.76 Aligned_cols=26 Identities=23% Similarity=0.556 Sum_probs=18.7
Q ss_pred eccccccccceecCCCCeeecCcCCCC
Q 006973 482 YRACKTCNKKVTDALGSGYWCEGCQKN 508 (623)
Q Consensus 482 Y~aC~~C~KKv~~~~~~~~~C~kC~~~ 508 (623)
---|+.|++..... ...+.|++|+..
T Consensus 70 ~~~C~~Cg~~~~~~-~~~~~CP~Cgs~ 95 (115)
T TIGR00100 70 ECECEDCSEEVSPE-IDLYRCPKCHGI 95 (115)
T ss_pred EEEcccCCCEEecC-CcCccCcCCcCC
Confidence 45688999777654 345789999864
No 275
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=35.15 E-value=33 Score=26.08 Aligned_cols=27 Identities=19% Similarity=0.594 Sum_probs=17.2
Q ss_pred cccccccccee----cC---CCCeeecCcCCCCc
Q 006973 483 RACKTCNKKVT----DA---LGSGYWCEGCQKND 509 (623)
Q Consensus 483 ~aC~~C~KKv~----~~---~~~~~~C~kC~~~~ 509 (623)
.-||.|+.|-. ++ .+=..+|++|.+..
T Consensus 5 i~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~Et 38 (55)
T PF14205_consen 5 ILCPICGNKTRLKIREDTVLKNFPLYCPKCKQET 38 (55)
T ss_pred EECCCCCCccceeeecCceeccccccCCCCCceE
Confidence 46999985542 11 12247899998754
No 276
>cd04316 ND_PkAspRS_like_N ND_PkAspRS_like_N: N-terminal, anticodon recognition domain of the type found in the homodimeric non-discriminating (ND) Pyrococcus kodakaraensis aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. P. kodakaraensis AspRS is a class 2b aaRS. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. P. kodakaraensis ND-AspRS can charge both tRNAAsp and tRNAAsn. Some of the enzymes in this group may be discriminating, based on the presence of homologs of asparaginyl-tRNA synthetase (AsnRS) in their completed genomes.
Probab=35.13 E-value=91 Score=26.99 Aligned_cols=62 Identities=13% Similarity=0.110 Sum_probs=40.3
Q ss_pred EEEEeCcccceeeccccccc--ccc-ccCccceeeEEEEcceeeeccCCCceEEEEEEeeeeecc
Q 006973 43 MFNASDGKKRLKAILPSNLS--SEV-ISGNIQNKGLIRLLDYALNEIPTKSEKYLIVTKCEVVSP 104 (623)
Q Consensus 43 r~~lSDG~~~~~~mlat~ln--~~v-~~~~l~~~siirl~~y~~~~~~~~~~~vlii~~lev~~~ 104 (623)
=+.|.||...+++++....+ ++. .-..|..+|+|.++......-...+..-|.+.++++++.
T Consensus 32 Fi~LrD~~g~iQ~v~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~~~Ei~~~~i~il~~ 96 (108)
T cd04316 32 FVILRDREGIVQVTAPKKKVDKELFKTVRKLSRESVISVTGTVKAEPKAPNGVEIIPEEIEVLSE 96 (108)
T ss_pred EEEEecCCeeEEEEEeCCCCCHHHHHHHhCCCCcCEEEEEEEEEeCCCCCCCEEEEEeEEEEEeC
Confidence 46889999999998864321 111 123589999999999876642222234566677777653
No 277
>PRK00036 primosomal replication protein N; Reviewed
Probab=33.96 E-value=2.8e+02 Score=24.31 Aligned_cols=70 Identities=21% Similarity=0.236 Sum_probs=48.9
Q ss_pred CCeEEEEEEEeeccccccccCCCcccEEEEEEEe-----CCC------CeEEEEEechHHHHHHhhcccCcEEEEeeeEE
Q 006973 185 GNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTD-----EDG------TQIQATMFNEAARKFYDRFQLGKVYYISRGTL 253 (623)
Q Consensus 185 ~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D-----~~G------~~I~at~~~~~~~kf~~~l~eG~vy~is~~~V 253 (623)
|.+.+.|+|+..-.+|. + +-|- .+.+|.|-- |-| -+|.|.+.++.++++.. +..|..+.+++|--
T Consensus 2 N~l~Ltg~v~~~~~lry-T-PAGI-p~~~~~LeH~S~q~EAG~~Rqv~~~i~ava~G~~a~~~~~-l~~Gs~v~v~GFLa 77 (107)
T PRK00036 2 NTLELSARVLECGAMRH-T-PAGL-PALELLLVHESEVVEAGHPRRVELTISAVALGDLALLLAD-TPLGTEMQVQGFLA 77 (107)
T ss_pred CEEEEEEEEeccCcccc-C-CCCC-ceEEEEEEEeEEeEeCCCcceEEEEEEEEEEhhHHHHhcc-cCCCCEEEEEEEEE
Confidence 57888899988766653 3 2221 255555522 223 27999999999998887 99999999999976
Q ss_pred EecCC
Q 006973 254 RVANK 258 (623)
Q Consensus 254 ~~a~~ 258 (623)
..+++
T Consensus 78 ~~~~~ 82 (107)
T PRK00036 78 PARKD 82 (107)
T ss_pred ECCCC
Confidence 64443
No 278
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=33.95 E-value=23 Score=36.25 Aligned_cols=32 Identities=16% Similarity=0.366 Sum_probs=22.3
Q ss_pred ccccccccceecCCCCeeecCcCCCCccccceeE
Q 006973 483 RACKTCNKKVTDALGSGYWCEGCQKNDEECSLRY 516 (623)
Q Consensus 483 ~aC~~C~KKv~~~~~~~~~C~kC~~~~~~~~~ry 516 (623)
..||.|+..+... +.+|+|+++.. ++..+.=|
T Consensus 3 ~~CP~C~~~l~~~-~~~~~C~~~h~-fd~a~~Gy 34 (272)
T PRK11088 3 YQCPLCHQPLTLE-ENSWICPQNHQ-FDCAKEGY 34 (272)
T ss_pred ccCCCCCcchhcC-CCEEEcCCCCC-CccccCce
Confidence 4799999999765 67899999544 43333333
No 279
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=33.75 E-value=48 Score=29.53 Aligned_cols=27 Identities=22% Similarity=0.399 Sum_probs=17.2
Q ss_pred eccccccccceecCCCCeeecCcCCCC
Q 006973 482 YRACKTCNKKVTDALGSGYWCEGCQKN 508 (623)
Q Consensus 482 Y~aC~~C~KKv~~~~~~~~~C~kC~~~ 508 (623)
..-|..|++..........+|++|+..
T Consensus 71 ~~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 97 (117)
T PRK00564 71 ELECKDCSHVFKPNALDYGVCEKCHSK 97 (117)
T ss_pred EEEhhhCCCccccCCccCCcCcCCCCC
Confidence 456888997765431222349999864
No 280
>PHA02998 RNA polymerase subunit; Provisional
Probab=33.52 E-value=25 Score=33.39 Aligned_cols=36 Identities=25% Similarity=0.377 Sum_probs=24.4
Q ss_pred eccccccccce-e---------cC-CCCeeecCcCCCCccccceeEE
Q 006973 482 YRACKTCNKKV-T---------DA-LGSGYWCEGCQKNDEECSLRYI 517 (623)
Q Consensus 482 Y~aC~~C~KKv-~---------~~-~~~~~~C~kC~~~~~~~~~ry~ 517 (623)
-..||.|+.+- . ++ ...-|.|.+|+..+..|++|+.
T Consensus 143 ~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkppkf~~~ 189 (195)
T PHA02998 143 NTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKPPKFRDK 189 (195)
T ss_pred CCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCCcccccc
Confidence 46799997542 1 11 1235899999999877776664
No 281
>PRK06556 vitamin B12-dependent ribonucleotide reductase; Validated
Probab=33.45 E-value=25 Score=42.53 Aligned_cols=28 Identities=39% Similarity=0.779 Sum_probs=23.1
Q ss_pred EeccccccccceecCCCCeeecCcCCCCc
Q 006973 481 WYRACKTCNKKVTDALGSGYWCEGCQKND 509 (623)
Q Consensus 481 ~Y~aC~~C~KKv~~~~~~~~~C~kC~~~~ 509 (623)
.-|.|++|+-++... +.=|.|+.|+.+.
T Consensus 923 ~~~~c~~c~~~~~~~-g~c~~c~~cg~t~ 950 (953)
T PRK06556 923 DAPLCPTCGTKMVRN-GSCYVCEGCGSTS 950 (953)
T ss_pred cCCcCCCccCeeeEC-CceEeccCCCCCC
Confidence 356699999999886 6679999999763
No 282
>cd04320 AspRS_cyto_N AspRS_cyto_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae and human cytoplasmic aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis.
Probab=33.16 E-value=85 Score=26.81 Aligned_cols=61 Identities=13% Similarity=0.146 Sum_probs=39.2
Q ss_pred EEEEeCcccceeecccccc----cccccc-CccceeeEEEEcceeeeccCCC-----ceEEEEEEeeeeec
Q 006973 43 MFNASDGKKRLKAILPSNL----SSEVIS-GNIQNKGLIRLLDYALNEIPTK-----SEKYLIVTKCEVVS 103 (623)
Q Consensus 43 r~~lSDG~~~~~~mlat~l----n~~v~~-~~l~~~siirl~~y~~~~~~~~-----~~~vlii~~lev~~ 103 (623)
=+.|.||...+|+++.... .++... ..|..+|+|.++......-... +..-|.+.++++++
T Consensus 20 Fi~LrD~sg~iQ~v~~~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~~~~~~~~El~~~~i~il~ 90 (102)
T cd04320 20 FLVLRQQGYTIQGVLAASAEGVSKQMVKWAGSLSKESIVDVEGTVKKPEEPIKSCTQQDVELHIEKIYVVS 90 (102)
T ss_pred EEEEecCCceEEEEEeCCcccCCHHHHHHHhcCCCccEEEEEEEEECCCCcccCCCcCcEEEEEEEEEEEe
Confidence 4678999999999996543 122211 3588999999999876531110 23556666676664
No 283
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=33.08 E-value=1.8e+02 Score=35.91 Aligned_cols=74 Identities=23% Similarity=0.347 Sum_probs=48.4
Q ss_pred ccccccccccCCcceeEEEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcE
Q 006973 295 VPIDELGRYVNGTELVDIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSPI 374 (623)
Q Consensus 295 ~~i~di~~~~~~~~~vDVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~V 374 (623)
.++++|.. +..+-++|+|+.+.. +++|..|+ ..--++|.|.+| .+++++|.+....+... ...+.+
T Consensus 876 ~~~~~l~~----~~~~~~~~~i~~~~~---~~tk~~g~--~maf~~leD~~g-~ie~~vFp~~y~~~~~~----l~~~~~ 941 (1034)
T PRK07279 876 TPISQLVK----NSEATILVQIQSIRV---IRTKTKGQ--QMAFLSVTDTKK-KLDVTLFPETYRQYKDE----LKEGKF 941 (1034)
T ss_pred ccHHHHhc----CCcceEEEEEEEEEE---EEEcCCCC--eEEEEEEeeCCC-cEEEEECHHHHHHHHHH----hccCCE
Confidence 45555532 334678888887753 34452354 345689999999 89999999877666443 345677
Q ss_pred EEEEeEEee
Q 006973 375 VAIKSLKVG 383 (623)
Q Consensus 375 v~i~~~kV~ 383 (623)
+.+++ +|.
T Consensus 942 ~~v~G-~v~ 949 (1034)
T PRK07279 942 YYLKG-KIQ 949 (1034)
T ss_pred EEEEE-EEE
Confidence 77765 444
No 284
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=32.77 E-value=24 Score=31.25 Aligned_cols=26 Identities=19% Similarity=0.374 Sum_probs=17.3
Q ss_pred eccccccccceecCCCCeeecCcCCCC
Q 006973 482 YRACKTCNKKVTDALGSGYWCEGCQKN 508 (623)
Q Consensus 482 Y~aC~~C~KKv~~~~~~~~~C~kC~~~ 508 (623)
--.|+.|+...... ...+.|++|+..
T Consensus 70 ~~~C~~Cg~~~~~~-~~~~~CP~Cgs~ 95 (113)
T PRK12380 70 QAWCWDCSQVVEIH-QHDAQCPHCHGE 95 (113)
T ss_pred EEEcccCCCEEecC-CcCccCcCCCCC
Confidence 34588888766543 345679999853
No 285
>cd04319 PhAsnRS_like_N PhAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Pyrococcus horikoshii AsnRS asparaginyl-tRNA synthetase (AsnRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The archeal enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose.
Probab=32.43 E-value=91 Score=26.73 Aligned_cols=61 Identities=8% Similarity=0.080 Sum_probs=37.3
Q ss_pred EEEEeCcccceeeccccccc-cccc-cCccceeeEEEEcceeeeccCCCceEEEEEEeeeeec
Q 006973 43 MFNASDGKKRLKAILPSNLS-SEVI-SGNIQNKGLIRLLDYALNEIPTKSEKYLIVTKCEVVS 103 (623)
Q Consensus 43 r~~lSDG~~~~~~mlat~ln-~~v~-~~~l~~~siirl~~y~~~~~~~~~~~vlii~~lev~~ 103 (623)
=+.|.||...+++++...+. ++.. -..|..||+|.++......-......=|.+.++++++
T Consensus 19 Fi~lrD~~g~iQ~v~~~~~~~~~~~~~~~l~~~s~v~V~G~v~~~~~~~~~~Ei~~~~i~vl~ 81 (103)
T cd04319 19 FIVLRDSTGIVQAVFSKDLNEEAYREAKKVGIESSVIVEGAVKADPRAPGGAEVHGEKLEIIQ 81 (103)
T ss_pred EEEEecCCeeEEEEEeCCCCHHHHHHHhCCCCCCEEEEEEEEEECCCCCCCEEEEEEEEEEEe
Confidence 45789999989998865421 1111 1258899999999976653111112335556666664
No 286
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=31.94 E-value=15 Score=35.23 Aligned_cols=28 Identities=25% Similarity=0.591 Sum_probs=21.3
Q ss_pred eccccccccceecCC--CCeeecCcCCCCc
Q 006973 482 YRACKTCNKKVTDAL--GSGYWCEGCQKND 509 (623)
Q Consensus 482 Y~aC~~C~KKv~~~~--~~~~~C~kC~~~~ 509 (623)
|..||.|+-|++.+. .-.+.|++||...
T Consensus 113 ~y~C~~~~~r~sfdeA~~~~F~Cp~Cg~~L 142 (176)
T COG1675 113 YYVCPNCHVKYSFDEAMELGFTCPKCGEDL 142 (176)
T ss_pred ceeCCCCCCcccHHHHHHhCCCCCCCCchh
Confidence 667899999987531 2348999999865
No 287
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=31.86 E-value=24 Score=24.97 Aligned_cols=23 Identities=17% Similarity=0.445 Sum_probs=13.0
Q ss_pred ccccccceecCC---CCeeecCcCCC
Q 006973 485 CKTCNKKVTDAL---GSGYWCEGCQK 507 (623)
Q Consensus 485 C~~C~KKv~~~~---~~~~~C~kC~~ 507 (623)
||.|+..+.... -..+.|++|+-
T Consensus 2 CP~C~~~l~~~~~~~~~id~C~~C~G 27 (41)
T PF13453_consen 2 CPRCGTELEPVRLGDVEIDVCPSCGG 27 (41)
T ss_pred cCCCCcccceEEECCEEEEECCCCCe
Confidence 777776554321 13466777764
No 288
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=31.80 E-value=33 Score=23.52 Aligned_cols=24 Identities=17% Similarity=0.425 Sum_probs=13.0
Q ss_pred cccccccceec---C--CCCeeecCcCCC
Q 006973 484 ACKTCNKKVTD---A--LGSGYWCEGCQK 507 (623)
Q Consensus 484 aC~~C~KKv~~---~--~~~~~~C~kC~~ 507 (623)
=||.|+..+.. + .-..+.|+.|+.
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred ccccccChhhhhcCCCCCccceECCCCCC
Confidence 38999887753 1 234688999985
No 289
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=31.71 E-value=18 Score=27.04 Aligned_cols=26 Identities=27% Similarity=0.565 Sum_probs=18.5
Q ss_pred ccccccccceecC---CCCeeecCcCCCC
Q 006973 483 RACKTCNKKVTDA---LGSGYWCEGCQKN 508 (623)
Q Consensus 483 ~aC~~C~KKv~~~---~~~~~~C~kC~~~ 508 (623)
..|+.|||.+-.. ....-.|++|+.-
T Consensus 5 iRC~~CnklLa~~g~~~~leIKCpRC~ti 33 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVIELEIKCPRCKTI 33 (51)
T ss_pred eeccchhHHHhhhcCccEEEEECCCCCcc
Confidence 3699999998652 1235689999864
No 290
>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=31.59 E-value=20 Score=22.92 Aligned_cols=12 Identities=25% Similarity=0.681 Sum_probs=9.4
Q ss_pred ecccccccccee
Q 006973 482 YRACKTCNKKVT 493 (623)
Q Consensus 482 Y~aC~~C~KKv~ 493 (623)
+.+||.|+++|.
T Consensus 1 ~v~CPiC~~~v~ 12 (26)
T smart00734 1 LVQCPVCFREVP 12 (26)
T ss_pred CCcCCCCcCccc
Confidence 357999999884
No 291
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=31.41 E-value=40 Score=38.00 Aligned_cols=67 Identities=27% Similarity=0.376 Sum_probs=51.7
Q ss_pred eeeccccCCCCC-CeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHHhhcccCcEEEEee
Q 006973 174 VHPLVSLNPYQG-NWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFYDRFQLGKVYYISR 250 (623)
Q Consensus 174 ~~~I~~L~p~~~-~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~~l~eG~vy~is~ 250 (623)
.+.|.+|..+.. ..+|++.|++ +++-..+ .+ |+|.|++| .|.|.+|-+.--+-|+-++.|+++.+.+
T Consensus 202 r~~i~~id~~ig~tV~I~GeV~q---ikqT~GP----TV--FtltDetg-~i~aAAFe~aGvRAyP~IevGdiV~ViG 269 (715)
T COG1107 202 RTLIDDLDEMIGKTVRIEGEVTQ---IKQTSGP----TV--FTLTDETG-AIWAAAFEEAGVRAYPEIEVGDIVEVIG 269 (715)
T ss_pred cccHHHHHhhcCceEEEEEEEEE---EEEcCCC----EE--EEEecCCC-ceehhhhccCCcccCCCCCCCceEEEEE
Confidence 455677766543 5789999998 4443321 25 56799999 8999999988889999999999999985
No 292
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=31.08 E-value=31 Score=23.26 Aligned_cols=24 Identities=17% Similarity=0.484 Sum_probs=17.9
Q ss_pred cccccccceecCCCCeeecCcCCCC
Q 006973 484 ACKTCNKKVTDALGSGYWCEGCQKN 508 (623)
Q Consensus 484 aC~~C~KKv~~~~~~~~~C~kC~~~ 508 (623)
.|+.|+--.... ...|.|+.|+..
T Consensus 3 ~C~~CGy~y~~~-~~~~~CP~Cg~~ 26 (33)
T cd00350 3 VCPVCGYIYDGE-EAPWVCPVCGAP 26 (33)
T ss_pred ECCCCCCEECCC-cCCCcCcCCCCc
Confidence 588888776543 467999999864
No 293
>cd04317 EcAspRS_like_N EcAspRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli aspartyl-tRNA synthetase (AspRS), the human mitochondrial (mt) AspRS-2, the discriminating (D) Thermus thermophilus AspRS-1, and the nondiscriminating (ND) Helicobacter pylori AspRS. These homodimeric enzymes are class2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, wh
Probab=31.00 E-value=1e+02 Score=27.89 Aligned_cols=65 Identities=9% Similarity=0.156 Sum_probs=41.0
Q ss_pred ceEEEEEeCcccceeecccccccc-ccccCccceeeEEEEcceeeeccC-------CCceEEEEEEeeeeecc
Q 006973 40 NRYMFNASDGKKRLKAILPSNLSS-EVISGNIQNKGLIRLLDYALNEIP-------TKSEKYLIVTKCEVVSP 104 (623)
Q Consensus 40 ~ryr~~lSDG~~~~~~mlat~ln~-~v~~~~l~~~siirl~~y~~~~~~-------~~~~~vlii~~lev~~~ 104 (623)
.--=+.|.||...+++++....+. .-.-..|..||+|.+.......-. .++..=|.+.++++++.
T Consensus 31 k~~Fi~LrD~~g~~Q~v~~~~~~~~~~~~~~l~~gs~V~V~G~~~~~~~~~~~~~~~~~~~El~~~~i~vl~~ 103 (135)
T cd04317 31 GLIFIDLRDRYGIVQVVFDPEEAPEFELAEKLRNESVIQVTGKVRARPEGTVNPKLPTGEIEVVASELEVLNK 103 (135)
T ss_pred CEEEEEEecCCeeEEEEEeCCchhHHHHHhCCCCccEEEEEEEEECCCccccCCCCCCCcEEEEEeEEEEEEC
Confidence 333567899999999999655433 111135899999999997764211 01124456666766653
No 294
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=30.95 E-value=19 Score=37.53 Aligned_cols=26 Identities=27% Similarity=0.494 Sum_probs=21.7
Q ss_pred eccccccccceecCCCCeeecCcCCC
Q 006973 482 YRACKTCNKKVTDALGSGYWCEGCQK 507 (623)
Q Consensus 482 Y~aC~~C~KKv~~~~~~~~~C~kC~~ 507 (623)
-.-||.|+-||..-..|...||.|.-
T Consensus 15 ~ElCPVCGDkVSGYHYGLLTCESCKG 40 (475)
T KOG4218|consen 15 GELCPVCGDKVSGYHYGLLTCESCKG 40 (475)
T ss_pred ccccccccCccccceeeeeehhhhhh
Confidence 45699999999887778889999963
No 295
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=30.81 E-value=21 Score=31.30 Aligned_cols=27 Identities=22% Similarity=0.425 Sum_probs=17.9
Q ss_pred eccccccccceecCCCCeeecCcCCCCc
Q 006973 482 YRACKTCNKKVTDALGSGYWCEGCQKND 509 (623)
Q Consensus 482 Y~aC~~C~KKv~~~~~~~~~C~kC~~~~ 509 (623)
..-||+|+|--.-- +-...|..|++..
T Consensus 69 ~V~CP~C~K~TKmL-Gr~D~CM~C~~pL 95 (114)
T PF11023_consen 69 QVECPNCGKQTKML-GRVDACMHCKEPL 95 (114)
T ss_pred eeECCCCCChHhhh-chhhccCcCCCcC
Confidence 34499999853221 3346899999765
No 296
>KOG3084 consensus NADH pyrophosphatase I of the Nudix family of hydrolases [Replication, recombination and repair]
Probab=30.67 E-value=43 Score=34.91 Aligned_cols=48 Identities=17% Similarity=0.356 Sum_probs=29.1
Q ss_pred EeccccccccceecCC-CCeeecC--cCC---CCccccceeEEEEEEEEeCCCcEE
Q 006973 481 WYRACKTCNKKVTDAL-GSGYWCE--GCQ---KNDEECSLRYIMVARVCDGSGEAW 530 (623)
Q Consensus 481 ~Y~aC~~C~KKv~~~~-~~~~~C~--kC~---~~~~~~~~ry~l~~~i~D~Tg~~~ 530 (623)
-|.-||.|+++...+. ++.-.|. .|. ..++... =.+-+.|.|++|+.-
T Consensus 149 kykFCp~CG~~tkp~e~g~k~~Cs~~~C~~~n~~yPr~d--PvVIm~li~~d~~~~ 202 (345)
T KOG3084|consen 149 KYKFCPGCGSPTKPEEAGTKLQCSDETCPSCNVIYPRTD--PVVIMLLIDHDGKHA 202 (345)
T ss_pred HhccCcccCCCcccccCCccceeecccCCcCCeeccCCC--CeEEEEEEcCCCCEe
Confidence 3999999998876542 3445555 354 3332222 235567888888753
No 297
>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=30.42 E-value=24 Score=26.53 Aligned_cols=25 Identities=32% Similarity=0.709 Sum_probs=12.6
Q ss_pred ccccccceecCC-----CCeeecCcCCCCc
Q 006973 485 CKTCNKKVTDAL-----GSGYWCEGCQKND 509 (623)
Q Consensus 485 C~~C~KKv~~~~-----~~~~~C~kC~~~~ 509 (623)
|-.|.+.+.... ...|+|++|+..+
T Consensus 2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~F 31 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKADSSRYRCPKCKNHF 31 (51)
T ss_dssp ETTTTEE-TTS-------EEE--TTTT--B
T ss_pred CccCCCCCCCcccccccCCeEECCCCCCcc
Confidence 556777776531 2579999998754
No 298
>cd03574 NTR_complement_C345C NTR/C345C domain; The NTR domains that are found in the C-termini of complement C3, C4 and C5, are also called C345C domains. In C5, the domain interacts with various partners during the formation of the membrane attack complex, a fundamental process in the mammalian defense against infection. It's role in component C3 and C4 is not well understood.
Probab=30.30 E-value=3.3e+02 Score=25.06 Aligned_cols=45 Identities=22% Similarity=0.279 Sum_probs=30.8
Q ss_pred HhhcccCcEEEEeeeEEEecCCCccccCCceEEEEccCcEEEEccCc
Q 006973 237 YDRFQLGKVYYISRGTLRVANKQFKTVQNDYEMNLNENSEVEEAVNE 283 (623)
Q Consensus 237 ~~~l~eG~vy~is~~~V~~a~~~~~~~~~~yei~f~~~T~I~~~~d~ 283 (623)
...|++|+.|.|.+-.....+. ......|.+.+++.|-|++.+..
T Consensus 76 ~~~l~~g~~YLImG~~~~~~~~--~~~~~~~~yvl~~~t~Ve~Wp~~ 120 (147)
T cd03574 76 PLRLKEGRHYLIMGSDGAFYDD--RNGEDRYQYVLDSNTWVEEWPTD 120 (147)
T ss_pred hhcCCCCCEEEEeccCcCcccc--cCCCcceEEEeCCCcEEEECCCh
Confidence 3568899999998763222110 01224589999999999998754
No 299
>PLN02221 asparaginyl-tRNA synthetase
Probab=30.22 E-value=3.7e+02 Score=30.85 Aligned_cols=83 Identities=16% Similarity=0.180 Sum_probs=52.6
Q ss_pred CCeEEEEEEEeeccccccccCCCccc--EEEEEEEeCC--CCeEEEEEechHHHHHHhhcccCcEEEEeeeEEEecCCCc
Q 006973 185 GNWTIKVRVTSKGNMRTYKNARGEGC--VFNVELTDED--GTQIQATMFNEAARKFYDRFQLGKVYYISRGTLRVANKQF 260 (623)
Q Consensus 185 ~~w~I~~RV~~K~~~r~~~~~~g~g~--~f~~~L~D~~--G~~I~at~~~~~~~kf~~~l~eG~vy~is~~~V~~a~~~~ 260 (623)
..-+|+|+|-+ +|. .|+ +.=++|.|.+ | .|++++-.+. ......|..|.++.+.+ .|+.....
T Consensus 51 ~~V~I~GWV~~---iR~------~Gk~~i~Fl~LRDgs~~g-~iQvVv~~~~-~~~~~~L~~ES~V~V~G-~V~~~~~~- 117 (572)
T PLN02221 51 QKVRIGGWVKT---GRE------QGKGTFAFLEVNDGSCPA-NLQVMVDSSL-YDLSTLVATGTCVTVDG-VLKVPPEG- 117 (572)
T ss_pred CEEEEEEEEEe---hhh------CCCceEEEEEEeCCcccc-cEEEEEcCch-hhHHhcCCCceEEEEEE-EEEeCCcc-
Confidence 46888888865 332 233 3346789998 6 7999886542 22223688999999976 44433221
Q ss_pred cccCCceEEEEccCcEEEEc
Q 006973 261 KTVQNDYEMNLNENSEVEEA 280 (623)
Q Consensus 261 ~~~~~~yei~f~~~T~I~~~ 280 (623)
...+..+||..+.-..+-++
T Consensus 118 ~~~~~~iEl~v~~i~vl~~a 137 (572)
T PLN02221 118 KGTKQKIELSVEKVIDVGTV 137 (572)
T ss_pred CCCCccEEEEEeEEEEEecC
Confidence 11345899988765555554
No 300
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=29.81 E-value=30 Score=33.43 Aligned_cols=30 Identities=23% Similarity=0.517 Sum_probs=20.5
Q ss_pred Eeccccccc-cce----ecC--CCCeeecCcCCCCcc
Q 006973 481 WYRACKTCN-KKV----TDA--LGSGYWCEGCQKNDE 510 (623)
Q Consensus 481 ~Y~aC~~C~-KKv----~~~--~~~~~~C~kC~~~~~ 510 (623)
.|.-||.|+ -.+ ... .+-.++|+.|+..++
T Consensus 5 iy~~Cp~Cg~eev~hEVik~~g~~~lvrC~eCG~V~~ 41 (201)
T COG1326 5 IYIECPSCGSEEVSHEVIKERGREPLVRCEECGTVHP 41 (201)
T ss_pred EEEECCCCCcchhhHHHHHhcCCceEEEccCCCcEee
Confidence 589999999 222 111 124789999998763
No 301
>cd04321 ScAspRS_mt_like_N ScAspRS_mt_like_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae mitochondrial (mt) aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this fungal group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Mutations in the gene for
Probab=29.54 E-value=1.3e+02 Score=24.92 Aligned_cols=60 Identities=8% Similarity=0.062 Sum_probs=34.8
Q ss_pred EEEeCccc-ceeeccccccccccccCccceeeEEEEcceeeeccCCC----ceEEEEEEeeeeec
Q 006973 44 FNASDGKK-RLKAILPSNLSSEVISGNIQNKGLIRLLDYALNEIPTK----SEKYLIVTKCEVVS 103 (623)
Q Consensus 44 ~~lSDG~~-~~~~mlat~ln~~v~~~~l~~~siirl~~y~~~~~~~~----~~~vlii~~lev~~ 103 (623)
+.|.||.. .+|.++......+-.-..|..||+|.++.-....-... +..-|.+.+++++.
T Consensus 21 i~LrD~~g~~iQvv~~~~~~~~~~~~~l~~~s~V~V~G~v~~~~~~~~~~~~~~Ei~~~~i~il~ 85 (86)
T cd04321 21 ADLRDPNGDIIQLVSTAKKDAFSLLKSITAESPVQVRGKLQLKEAKSSEKNDEWELVVDDIQTLN 85 (86)
T ss_pred EEEECCCCCEEEEEECCCHHHHHHHhcCCCCcEEEEEEEEEeCCCcCCCCCCCEEEEEEEEEEec
Confidence 57789988 47877744321111113478999999988766532100 12445566666653
No 302
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=29.31 E-value=18 Score=24.83 Aligned_cols=25 Identities=16% Similarity=0.385 Sum_probs=15.6
Q ss_pred cccccccceecCC--CCeeecCcCCCC
Q 006973 484 ACKTCNKKVTDAL--GSGYWCEGCQKN 508 (623)
Q Consensus 484 aC~~C~KKv~~~~--~~~~~C~kC~~~ 508 (623)
=||.|+.-+.... .+...|.+|+-.
T Consensus 3 FCp~C~nlL~p~~~~~~~~~C~~C~Y~ 29 (35)
T PF02150_consen 3 FCPECGNLLYPKEDKEKRVACRTCGYE 29 (35)
T ss_dssp BETTTTSBEEEEEETTTTEEESSSS-E
T ss_pred eCCCCCccceEcCCCccCcCCCCCCCc
Confidence 3899998775532 222369999854
No 303
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=29.23 E-value=71 Score=29.21 Aligned_cols=27 Identities=15% Similarity=0.352 Sum_probs=18.6
Q ss_pred eccccccccceecCC--------------------CCeeecCcCCCC
Q 006973 482 YRACKTCNKKVTDAL--------------------GSGYWCEGCQKN 508 (623)
Q Consensus 482 Y~aC~~C~KKv~~~~--------------------~~~~~C~kC~~~ 508 (623)
..-|+.|+....... ...+.|++|+..
T Consensus 70 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 70 VLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred EEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC
Confidence 567999997765431 234779999864
No 304
>COG5235 RFA2 Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair]
Probab=29.20 E-value=1.9e+02 Score=28.39 Aligned_cols=74 Identities=14% Similarity=0.180 Sum_probs=46.0
Q ss_pred EEEEEeCCCcEEEEEehHhHHHHhCCCHHHHHHHHhhcCCchhHHHHHHHhcCceEEEEEEEEeeecCceeeeEEEEEEe
Q 006973 519 VARVCDGSGEAWISIFNEEAERIIGCSADELNELKSQLGDDNSYQMKLKEVTWVPHLLRVSVAQQEYNNEKRQRVTVRAV 598 (623)
Q Consensus 519 ~~~i~D~Tg~~~~~~F~~~ae~llG~sA~el~~~~~~~~~~~~~~~~l~~~~~~~~~f~v~~k~~~y~~~~r~~~~v~~~ 598 (623)
.+.|.|+||++.++.|...+-.. ...++.+ - .-..||-.....|+|..-+.+++++.
T Consensus 86 ~~~iEDGTG~Ievr~W~~~~~~~--------e~~~d~~-------------~--~~yvkV~G~lk~F~GK~~I~~~~i~~ 142 (258)
T COG5235 86 MFVIEDGTGSIEVRFWPGNSYEE--------EQCKDLE-------------E--QNYVKVNGSLKTFNGKRSISASHISA 142 (258)
T ss_pred EEEEecCCceEEEEecCCCchHH--------Hhccccc-------------c--ccEEEEecceeeeCCeeEEehhheee
Confidence 35799999999999997655211 1111110 0 11456666677899966666666554
Q ss_pred eccCHHHHHHHHHHHHHh
Q 006973 599 APVDFAAESKFLLEEISK 616 (623)
Q Consensus 599 ~~vd~~~e~~~Ll~~i~~ 616 (623)
.+ |+.+---+.|+.|..
T Consensus 143 I~-d~NeV~~HfLe~I~~ 159 (258)
T COG5235 143 IE-DSNEVTYHFLECIYQ 159 (258)
T ss_pred cc-ccchhHHHHHHHHHH
Confidence 33 566666788888864
No 305
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=28.70 E-value=18 Score=36.21 Aligned_cols=27 Identities=19% Similarity=0.680 Sum_probs=10.4
Q ss_pred ccccccccc-eecCCC----CeeecCcCCCCc
Q 006973 483 RACKTCNKK-VTDALG----SGYWCEGCQKND 509 (623)
Q Consensus 483 ~aC~~C~KK-v~~~~~----~~~~C~kC~~~~ 509 (623)
..||.|+.+ +..-.+ ..+.|+.|+..+
T Consensus 32 ~yCP~Cg~~~L~~f~NN~PVaDF~C~~C~eey 63 (254)
T PF06044_consen 32 MYCPNCGSKPLSKFENNRPVADFYCPNCNEEY 63 (254)
T ss_dssp ---TTT--SS-EE--------EEE-TTT--EE
T ss_pred CcCCCCCChhHhhccCCCccceeECCCCchHH
Confidence 469999987 432111 248999998753
No 306
>COG4640 Predicted membrane protein [Function unknown]
Probab=28.28 E-value=29 Score=37.12 Aligned_cols=26 Identities=15% Similarity=0.484 Sum_probs=17.9
Q ss_pred ccccccccceecCCCCeeecCcCCCCccc
Q 006973 483 RACKTCNKKVTDALGSGYWCEGCQKNDEE 511 (623)
Q Consensus 483 ~aC~~C~KKv~~~~~~~~~C~kC~~~~~~ 511 (623)
..||.|++-=. .+.+.|..|+..+..
T Consensus 2 ~fC~kcG~qk~---Ed~~qC~qCG~~~t~ 27 (465)
T COG4640 2 KFCPKCGSQKA---EDDVQCTQCGHKFTS 27 (465)
T ss_pred Ccccccccccc---cccccccccCCcCCc
Confidence 35999995432 234669999987654
No 307
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=28.24 E-value=26 Score=36.33 Aligned_cols=14 Identities=36% Similarity=0.755 Sum_probs=11.0
Q ss_pred CeeecCcCCCCccc
Q 006973 498 SGYWCEGCQKNDEE 511 (623)
Q Consensus 498 ~~~~C~kC~~~~~~ 511 (623)
..|+||-|++.+.+
T Consensus 397 KPYrCevC~KRYKN 410 (423)
T COG5189 397 KPYRCEVCDKRYKN 410 (423)
T ss_pred Cceeccccchhhcc
Confidence 56999999986644
No 308
>PF13695 zf-3CxxC: Zinc-binding domain
Probab=27.97 E-value=72 Score=27.34 Aligned_cols=40 Identities=10% Similarity=0.381 Sum_probs=30.0
Q ss_pred CeeecCcCCCCccccceeEEEEEEEEeCCCcEEEEEehHhHHH
Q 006973 498 SGYWCEGCQKNDEECSLRYIMVARVCDGSGEAWISIFNEEAER 540 (623)
Q Consensus 498 ~~~~C~kC~~~~~~~~~ry~l~~~i~D~Tg~~~~~~F~~~ae~ 540 (623)
|.|.|.+|+.......-.-.+.+. ..|...+.+|++....
T Consensus 4 grF~C~~C~~~W~S~~v~i~f~~~---~~g~v~~rv~~Q~C~~ 43 (98)
T PF13695_consen 4 GRFQCSKCSRGWTSAKVWILFHMY---RGGQVNMRVFGQRCKK 43 (98)
T ss_pred EEEECCCCCCCCccCEEEEEEEEc---CCCeEEEEEECCCCCC
Confidence 679999999888665544444444 6688999999988764
No 309
>PF08696 Dna2: DNA replication factor Dna2; InterPro: IPR014808 Dna2 is a DNA replication factor with single-stranded DNA-dependent ATPase, ATP-dependent nuclease, (5'-flap endonuclease) and helicase activities. It is required for Okazaki fragment processing and is involved in DNA repair pathways []. ; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication
Probab=27.92 E-value=1.7e+02 Score=28.87 Aligned_cols=55 Identities=18% Similarity=0.327 Sum_probs=37.0
Q ss_pred EEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEEeeeccce--eeecccceEEEEcCCh
Q 006973 339 ITVADETKRTVTVSLWNELATNVGQELLDNADKSPIVAIKSLKVGDFQGI--SLSTLGRSTVLVSPDL 404 (623)
Q Consensus 339 i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~kV~~f~G~--~Ls~~~~S~i~iNPd~ 404 (623)
++..|.++....|.|||+.+... +..|++|-+-+ +|.+. .+-.....-++++||.
T Consensus 2 l~~~~~~~~~~~v~L~~~W~~t~-------v~~Gd~I~ii~----~~~~~~~~~v~~~~~~lIl~PD~ 58 (209)
T PF08696_consen 2 LVCSESSGETRTVILRDEWCETP-------VSPGDIIHIIG----EFDDDDPCIVDNDSNLLILHPDI 58 (209)
T ss_pred eEeecCCCCeEEEEEeCCcccCC-------CcCCCEEEEEE----EeCCCCCEEEeCCCCEEEEcCCc
Confidence 45667788899999999988653 45688887655 44432 2222233378889984
No 310
>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=27.90 E-value=39 Score=22.46 Aligned_cols=25 Identities=24% Similarity=0.562 Sum_probs=13.6
Q ss_pred cccccccceecCCC-CeeecCcCCCC
Q 006973 484 ACKTCNKKVTDALG-SGYWCEGCQKN 508 (623)
Q Consensus 484 aC~~C~KKv~~~~~-~~~~C~kC~~~ 508 (623)
=|+.|+-++..... -.-.|+.|+..
T Consensus 5 fC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 5 FCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp B-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred ccCcCCccccCCCCcCEeECCCCcCE
Confidence 48999988766533 35689999864
No 311
>KOG1885 consensus Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=26.81 E-value=2.3e+02 Score=31.39 Aligned_cols=92 Identities=15% Similarity=0.185 Sum_probs=55.2
Q ss_pred CeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEech------HHHHHHhhcccCcEEEEeeeEEEecCCC
Q 006973 186 NWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNE------AARKFYDRFQLGKVYYISRGTLRVANKQ 259 (623)
Q Consensus 186 ~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~------~~~kf~~~l~eG~vy~is~~~V~~a~~~ 259 (623)
..+|.|||..| |.. .+|++=++|.++ |.++++.+-.. ......+.|+-||++-+++.- ++
T Consensus 106 ~~svaGRI~s~---R~s-----GsKL~Fydl~~~-g~klQvm~~~~~~~~~~~F~~~~~~lkrGDiig~~G~p-----gr 171 (560)
T KOG1885|consen 106 IVSVAGRIHSK---RES-----GSKLVFYDLHGD-GVKLQVMANAKKITSEEDFEQLHKFLKRGDIIGVSGYP-----GR 171 (560)
T ss_pred eeeeeeeEeee---ecc-----CCceEEEEEecC-CeEEEEEEehhhcCCHHHHHHHHhhhhccCEEeeecCC-----Cc
Confidence 57899999874 332 126666777776 55899887542 356677889999999887631 11
Q ss_pred ccccCCceEEEEccCcEEEEccCcCCCCCCCcccccc
Q 006973 260 FKTVQNDYEMNLNENSEVEEAVNETAFIPQTKFNFVP 296 (623)
Q Consensus 260 ~~~~~~~yei~f~~~T~I~~~~d~~~~iP~~~~~f~~ 296 (623)
+-+. |+++-.+..+...+.. ..+|..+|.+..
T Consensus 172 --t~~g--ELSi~~~~~~lLspcL-h~lP~~~~gLkD 203 (560)
T KOG1885|consen 172 --TKSG--ELSIIPNEIILLSPCL-HMLPHEHFGLKD 203 (560)
T ss_pred --CCCc--eEEEeecchheecchh-ccCChhhcCCCc
Confidence 1112 5555544443332222 457755555544
No 312
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=26.68 E-value=44 Score=24.73 Aligned_cols=26 Identities=19% Similarity=0.525 Sum_probs=17.4
Q ss_pred ecccc--ccccce-ecCCCCeeecCcCCC
Q 006973 482 YRACK--TCNKKV-TDALGSGYWCEGCQK 507 (623)
Q Consensus 482 Y~aC~--~C~KKv-~~~~~~~~~C~kC~~ 507 (623)
-.-|| .|+.-| -.+..+.|.|-||+-
T Consensus 18 rk~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 18 RKECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp SEE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred hhcCCCcccCCceEeeecCCCccCCCccc
Confidence 34688 898875 223467899999974
No 313
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=26.44 E-value=32 Score=30.50 Aligned_cols=26 Identities=23% Similarity=0.461 Sum_probs=18.2
Q ss_pred eccccccccceecCCCCeeecCcCCCC
Q 006973 482 YRACKTCNKKVTDALGSGYWCEGCQKN 508 (623)
Q Consensus 482 Y~aC~~C~KKv~~~~~~~~~C~kC~~~ 508 (623)
.--|..|+.-+..+ ...|+|++|+..
T Consensus 70 ~~~C~~C~~~~~~e-~~~~~CP~C~s~ 95 (115)
T COG0375 70 ECWCLDCGQEVELE-ELDYRCPKCGSI 95 (115)
T ss_pred EEEeccCCCeecch-hheeECCCCCCC
Confidence 44588888777765 456779999853
No 314
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=26.31 E-value=24 Score=31.22 Aligned_cols=26 Identities=15% Similarity=0.538 Sum_probs=18.0
Q ss_pred eccccccccceecCCCCeeecCcCCCC
Q 006973 482 YRACKTCNKKVTDALGSGYWCEGCQKN 508 (623)
Q Consensus 482 Y~aC~~C~KKv~~~~~~~~~C~kC~~~ 508 (623)
--.|..|++....+ ...+.|+.|+..
T Consensus 70 ~~~C~~Cg~~~~~~-~~~~~CP~Cgs~ 95 (113)
T PF01155_consen 70 RARCRDCGHEFEPD-EFDFSCPRCGSP 95 (113)
T ss_dssp EEEETTTS-EEECH-HCCHH-SSSSSS
T ss_pred cEECCCCCCEEecC-CCCCCCcCCcCC
Confidence 55699999988765 344889999975
No 315
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=26.27 E-value=1.3e+02 Score=25.19 Aligned_cols=56 Identities=13% Similarity=0.200 Sum_probs=43.5
Q ss_pred ceEEEEEeCcccceeeccccccccccccCccceeeEEEEcceeeeccCCCceEEEEEE
Q 006973 40 NRYMFNASDGKKRLKAILPSNLSSEVISGNIQNKGLIRLLDYALNEIPTKSEKYLIVT 97 (623)
Q Consensus 40 ~ryr~~lSDG~~~~~~mlat~ln~~v~~~~l~~~siirl~~y~~~~~~~~~~~vlii~ 97 (623)
.=+.++|.|-...|.|.+.-.+=+- ..+.|..|+++=|++..+..-.. ..++|+|.
T Consensus 19 ~D~~v~l~DpTG~i~~tiH~~v~~~-y~~~l~~GavLlLk~V~Vf~ps~-~~~yLnIt 74 (86)
T PF15072_consen 19 EDAFVVLKDPTGEIRGTIHRKVLEE-YGDELSPGAVLLLKDVTVFSPSP-RSHYLNIT 74 (86)
T ss_pred CCeEEEEECCCCcEEEEEeHHHHhh-cCCccccCEEEEEeeeeEEecCC-CccEEEEe
Confidence 4568999999999999997555443 46789999999999999876543 36777665
No 316
>PF04057 Rep-A_N: Replication factor-A protein 1, N-terminal domain; InterPro: IPR007199 Replication factor-a protein 1 (RPA1) forms a multiprotein complex with RPA2 and RPA3 that binds single-stranded DNA and functions in the recognition of DNA damage for nucleotide excision repair. The complex binds to single-stranded DNA sequences participating in DNA replication in addition to those mediating transcriptional repression and activation, and stimulates the activity of cognate strand exchange protein Sep1. It cooperates with T-AG and DNA topoisomerase I to unwind template DNA containing the Simian Virus 40 origin of replication [].; GO: 0003677 DNA binding, 0006260 DNA replication, 0005634 nucleus; PDB: 1EWI_A 2B3G_A 2B29_A.
Probab=26.08 E-value=4e+02 Score=22.87 Aligned_cols=50 Identities=18% Similarity=0.206 Sum_probs=37.2
Q ss_pred CcccEEEEEEEeCCCCeEEEEEechHHHHHHh-hcccCcEEEEeeeEEEecC
Q 006973 207 GEGCVFNVELTDEDGTQIQATMFNEAARKFYD-RFQLGKVYYISRGTLRVAN 257 (623)
Q Consensus 207 g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~~-~l~eG~vy~is~~~V~~a~ 257 (623)
+....|.+.|-|..- .++|.+-..+.+...+ .|+.|.++.+.++.+..-+
T Consensus 35 ~~~~RyR~~lSDG~~-~~~amLatqln~lv~~g~l~~~siirl~~y~~n~v~ 85 (101)
T PF04057_consen 35 GGSDRYRLVLSDGVH-SIQAMLATQLNHLVESGELQKGSIIRLKQYTCNTVK 85 (101)
T ss_dssp TS--EEEEEEESSSE-EEEEEESGGGHHHHHTTSSSTT-EEEEEEEEEEEST
T ss_pred CCCceEEEEEEChHH-HHHHHhHHHhHHHHhcCCcccCCEEEEeEEEEeecc
Confidence 345689999999877 6999887777776655 7999999999998775543
No 317
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=25.78 E-value=6.1e+02 Score=24.45 Aligned_cols=35 Identities=20% Similarity=0.247 Sum_probs=25.1
Q ss_pred EEEEEEechhhhhhhhHhhhcCCCCcEEEEE-eEEeeecc
Q 006973 348 TVTVSLWNELATNVGQELLDNADKSPIVAIK-SLKVGDFQ 386 (623)
Q Consensus 348 ~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~-~~kV~~f~ 386 (623)
-++|++||..|+.+.+. +..|.-|+|. .++...|.
T Consensus 50 fi~v~~fg~~AE~~~~~----l~KG~~V~VeGrL~~~~y~ 85 (182)
T PRK08486 50 FIDIRLFGRTAEIANQY----LSKGSKVLIEGRLTFESWM 85 (182)
T ss_pred EEEEEEEhHHHHHHHHH----cCCCCEEEEEEEEEeCcEE
Confidence 68999999999987554 4557766665 45556673
No 318
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=25.67 E-value=27 Score=20.85 Aligned_cols=11 Identities=36% Similarity=0.640 Sum_probs=8.2
Q ss_pred eecCcCCCCcc
Q 006973 500 YWCEGCQKNDE 510 (623)
Q Consensus 500 ~~C~kC~~~~~ 510 (623)
|.|+.|++.+.
T Consensus 1 y~C~~C~~~f~ 11 (23)
T PF00096_consen 1 YKCPICGKSFS 11 (23)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCccC
Confidence 67888887664
No 319
>COG4085 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=25.57 E-value=6.4e+02 Score=24.61 Aligned_cols=72 Identities=19% Similarity=0.236 Sum_probs=46.7
Q ss_pred CeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCCeEEEEEechHHHHHH-----hhcccCcEEEEeeeEEEecCCCc
Q 006973 186 NWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGTQIQATMFNEAARKFY-----DRFQLGKVYYISRGTLRVANKQF 260 (623)
Q Consensus 186 ~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~~I~at~~~~~~~kf~-----~~l~eG~vy~is~~~V~~a~~~~ 260 (623)
..++++-|++- .+..+. -..++.|.|.+| .|.+.+|.....-.. +.+.+|++..+.+ +|...
T Consensus 53 ~v~vkg~V~~~------~n~~~~-gi~~l~lndgtG-ti~vva~~~tee~l~~n~~~p~~~eGe~veVtG-rv~~y---- 119 (204)
T COG4085 53 EVTVKGEVTAD------QNAIGG-GIESLVLNDGTG-TITVVASRSTEETLELNEGMPVTVEGEIVEVTG-RVEEY---- 119 (204)
T ss_pred cceeeeEEEee------eccccc-ceEEEEEECCCC-cEEEEEecChhHhHhhcCCCCccccCcEEEEEE-EEEEe----
Confidence 35566666653 223333 356788999999 799999986544433 5788999998874 44332
Q ss_pred cccCCceEEEEcc
Q 006973 261 KTVQNDYEMNLNE 273 (623)
Q Consensus 261 ~~~~~~yei~f~~ 273 (623)
+..+++..+.
T Consensus 120 ---rG~~eVkvnq 129 (204)
T COG4085 120 ---RGSSEVKVNQ 129 (204)
T ss_pred ---CCCceeeccC
Confidence 2346666654
No 320
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=25.39 E-value=49 Score=22.95 Aligned_cols=28 Identities=14% Similarity=0.340 Sum_probs=18.4
Q ss_pred EeccccccccceecC----CCCeeecCcCCCC
Q 006973 481 WYRACKTCNKKVTDA----LGSGYWCEGCQKN 508 (623)
Q Consensus 481 ~Y~aC~~C~KKv~~~----~~~~~~C~kC~~~ 508 (623)
|-..|+.|++..... .+..-.|+.|+..
T Consensus 4 Y~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (41)
T smart00834 4 YEYRCEDCGHTFEVLQKISDDPLATCPECGGD 35 (41)
T ss_pred EEEEcCCCCCEEEEEEecCCCCCCCCCCCCCc
Confidence 445799999865421 1345679999873
No 321
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=25.10 E-value=31 Score=26.38 Aligned_cols=15 Identities=20% Similarity=0.459 Sum_probs=12.7
Q ss_pred eEeccccccccceec
Q 006973 480 MWYRACKTCNKKVTD 494 (623)
Q Consensus 480 ~~Y~aC~~C~KKv~~ 494 (623)
.-|.+||-|++++..
T Consensus 37 ~rYngCPfC~~~~~~ 51 (55)
T PF14447_consen 37 ERYNGCPFCGTPFEF 51 (55)
T ss_pred hhccCCCCCCCcccC
Confidence 459999999999864
No 322
>PRK05978 hypothetical protein; Provisional
Probab=24.82 E-value=37 Score=31.62 Aligned_cols=29 Identities=21% Similarity=0.455 Sum_probs=17.9
Q ss_pred eccccccccc-eecC-CCCeeecCcCCCCcc
Q 006973 482 YRACKTCNKK-VTDA-LGSGYWCEGCQKNDE 510 (623)
Q Consensus 482 Y~aC~~C~KK-v~~~-~~~~~~C~kC~~~~~ 510 (623)
--.||.|++. +-.. ..-.-+|+.|+..+.
T Consensus 33 ~grCP~CG~G~LF~g~Lkv~~~C~~CG~~~~ 63 (148)
T PRK05978 33 RGRCPACGEGKLFRAFLKPVDHCAACGEDFT 63 (148)
T ss_pred cCcCCCCCCCcccccccccCCCccccCCccc
Confidence 6679999863 2110 011247999998763
No 323
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=24.79 E-value=21 Score=26.92 Aligned_cols=25 Identities=36% Similarity=0.868 Sum_probs=17.7
Q ss_pred ccccccccceecCCCCee---ecCcCCC
Q 006973 483 RACKTCNKKVTDALGSGY---WCEGCQK 507 (623)
Q Consensus 483 ~aC~~C~KKv~~~~~~~~---~C~kC~~ 507 (623)
..|..|||-+...+...| .|++|..
T Consensus 5 iRC~~CnKlLa~a~~~~yle~KCPrCK~ 32 (60)
T COG4416 5 IRCAKCNKLLAEAEGQAYLEKKCPRCKE 32 (60)
T ss_pred eehHHHhHHHHhcccceeeeecCCccce
Confidence 468999998876533334 6888865
No 324
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=24.60 E-value=42 Score=21.92 Aligned_cols=22 Identities=32% Similarity=0.818 Sum_probs=9.3
Q ss_pred cccccccceecCCCCeeecCcCCC
Q 006973 484 ACKTCNKKVTDALGSGYWCEGCQK 507 (623)
Q Consensus 484 aC~~C~KKv~~~~~~~~~C~kC~~ 507 (623)
-|..|+++... +-.|+|..|+=
T Consensus 2 ~C~~C~~~~~~--~~~Y~C~~Cdf 23 (30)
T PF07649_consen 2 RCDACGKPIDG--GWFYRCSECDF 23 (30)
T ss_dssp --TTTS----S----EEE-TTT--
T ss_pred cCCcCCCcCCC--CceEECccCCC
Confidence 37778888764 35899999973
No 325
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=24.48 E-value=27 Score=36.30 Aligned_cols=44 Identities=16% Similarity=0.221 Sum_probs=26.7
Q ss_pred eccccccccceecC--CCCeeecCcCCCCccccceeEEEEEEEEeCC
Q 006973 482 YRACKTCNKKVTDA--LGSGYWCEGCQKNDEECSLRYIMVARVCDGS 526 (623)
Q Consensus 482 Y~aC~~C~KKv~~~--~~~~~~C~kC~~~~~~~~~ry~l~~~i~D~T 526 (623)
+..||.|++-+... ....|.|++|+.++. ...|=++...+.++|
T Consensus 38 w~kc~~C~~~~~~~~l~~~~~vcp~c~~h~r-ltAreRI~~L~D~gS 83 (296)
T CHL00174 38 WVQCENCYGLNYKKFLKSKMNICEQCGYHLK-MSSSDRIELLIDPGT 83 (296)
T ss_pred eeECCCccchhhHHHHHHcCCCCCCCCCCcC-CCHHHHHHHHccCCc
Confidence 46699999877542 134689999998653 233444444444433
No 326
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=24.39 E-value=27 Score=36.20 Aligned_cols=42 Identities=12% Similarity=0.267 Sum_probs=26.0
Q ss_pred eccccccccceecC--CCCeeecCcCCCCccccceeEEEEEEEEe
Q 006973 482 YRACKTCNKKVTDA--LGSGYWCEGCQKNDEECSLRYIMVARVCD 524 (623)
Q Consensus 482 Y~aC~~C~KKv~~~--~~~~~~C~kC~~~~~~~~~ry~l~~~i~D 524 (623)
...||.|++-+... ....+-|++|+.++. ...|-++...+.+
T Consensus 26 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~r-l~areRi~~L~D~ 69 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELERNLEVCPKCDHHMR-MDARERIESLLDE 69 (285)
T ss_pred eeECCCCcchhhHHHHHhhCCCCCCCCCcCc-CCHHHHHHHceeC
Confidence 45699999877542 134589999998753 2334444444433
No 327
>PLN02603 asparaginyl-tRNA synthetase
Probab=24.00 E-value=7.3e+02 Score=28.48 Aligned_cols=92 Identities=12% Similarity=0.152 Sum_probs=58.0
Q ss_pred eeeccccCCC--------CCCeEEEEEEEeeccccccccCCCcccEEEEEEEeCCCC-eEEEEEechHHHHHHh----hc
Q 006973 174 VHPLVSLNPY--------QGNWTIKVRVTSKGNMRTYKNARGEGCVFNVELTDEDGT-QIQATMFNEAARKFYD----RF 240 (623)
Q Consensus 174 ~~~I~~L~p~--------~~~w~I~~RV~~K~~~r~~~~~~g~g~~f~~~L~D~~G~-~I~at~~~~~~~kf~~----~l 240 (623)
.+.|.++.+. ...-+|+|+|.+ +|. .|++.=++|.|.+|. .|++++-.+. ..|.. .|
T Consensus 89 ~~~~~~~~~~~~~~~~~~g~~V~v~GwV~~---iR~------~g~~~Fi~l~Dgs~~~~lQ~v~~~~~-~~~~~l~~~~l 158 (565)
T PLN02603 89 KLRIADVKGGEDEGLARVGKTLNVMGWVRT---LRA------QSSVTFIEVNDGSCLSNMQCVMTPDA-EGYDQVESGLI 158 (565)
T ss_pred ceEhhhcccccccccccCCCEEEEEEEEEE---EEe------CCCeEEEEEECCCCCEeEEEEEECcH-HHHHHHhhcCC
Confidence 3567776532 346788999865 442 234544678998873 7999985442 22222 37
Q ss_pred ccCcEEEEeeeEEEecCCCccccCCceEEEEccCcEEEEc
Q 006973 241 QLGKVYYISRGTLRVANKQFKTVQNDYEMNLNENSEVEEA 280 (623)
Q Consensus 241 ~eG~vy~is~~~V~~a~~~~~~~~~~yei~f~~~T~I~~~ 280 (623)
..|+++.+.+.-++... ....+||..+.-..+-++
T Consensus 159 ~~gs~V~V~G~v~~~~~-----~~~~~EL~v~~i~vlg~a 193 (565)
T PLN02603 159 TTGASVLVQGTVVSSQG-----GKQKVELKVSKIVVVGKS 193 (565)
T ss_pred CCCCEEEEEEEEEecCC-----CCccEEEEEeEEEEEECC
Confidence 89999999985443321 235688888765555554
No 328
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=23.71 E-value=55 Score=37.45 Aligned_cols=34 Identities=26% Similarity=0.517 Sum_probs=21.7
Q ss_pred CCeEeccccccccceec-------C-----CCCeeecCcCCCCccc
Q 006973 478 QAMWYRACKTCNKKVTD-------A-----LGSGYWCEGCQKNDEE 511 (623)
Q Consensus 478 ~~~~Y~aC~~C~KKv~~-------~-----~~~~~~C~kC~~~~~~ 511 (623)
+.-||..||.|+..-.. + ..-.|.|+.|+....+
T Consensus 196 qr~~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e 241 (557)
T PF05876_consen 196 QRRYYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEE 241 (557)
T ss_pred ceEEEccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCH
Confidence 35678888888754321 1 1235888888877654
No 329
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=23.67 E-value=28 Score=36.29 Aligned_cols=28 Identities=14% Similarity=0.432 Sum_probs=20.0
Q ss_pred eccccccccceecC--CCCeeecCcCCCCc
Q 006973 482 YRACKTCNKKVTDA--LGSGYWCEGCQKND 509 (623)
Q Consensus 482 Y~aC~~C~KKv~~~--~~~~~~C~kC~~~~ 509 (623)
+..||.|++-+... ....+-|++|+.++
T Consensus 27 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 27 WTKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred eeECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 57899999876432 12357999999765
No 330
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=23.65 E-value=44 Score=25.60 Aligned_cols=22 Identities=23% Similarity=0.696 Sum_probs=17.1
Q ss_pred ccccccceecCCCCeeecCcCCCC
Q 006973 485 CKTCNKKVTDALGSGYWCEGCQKN 508 (623)
Q Consensus 485 C~~C~KKv~~~~~~~~~C~kC~~~ 508 (623)
||.|+++... .-.|.|+.||-.
T Consensus 2 Cpv~~~~~~~--~v~~~Cp~cGip 23 (55)
T PF13824_consen 2 CPVCKKDLPA--HVNFECPDCGIP 23 (55)
T ss_pred CCCCcccccc--ccCCcCCCCCCc
Confidence 8999997643 356999999964
No 331
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=23.45 E-value=63 Score=23.87 Aligned_cols=26 Identities=27% Similarity=0.530 Sum_probs=17.7
Q ss_pred ccccccccceecCCCCeeecCcCCCC
Q 006973 483 RACKTCNKKVTDALGSGYWCEGCQKN 508 (623)
Q Consensus 483 ~aC~~C~KKv~~~~~~~~~C~kC~~~ 508 (623)
.-|..|++.+.......|+|+.|+..
T Consensus 12 ~~C~~C~~~i~g~~~~g~~C~~C~~~ 37 (53)
T PF00130_consen 12 TYCDVCGKFIWGLGKQGYRCSWCGLV 37 (53)
T ss_dssp EB-TTSSSBECSSSSCEEEETTTT-E
T ss_pred CCCcccCcccCCCCCCeEEECCCCCh
Confidence 35888999994333468999999853
No 332
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=23.43 E-value=1.2e+02 Score=31.02 Aligned_cols=28 Identities=18% Similarity=0.451 Sum_probs=20.5
Q ss_pred eccccccccceecC-CCCeeecCcCCCCc
Q 006973 482 YRACKTCNKKVTDA-LGSGYWCEGCQKND 509 (623)
Q Consensus 482 Y~aC~~C~KKv~~~-~~~~~~C~kC~~~~ 509 (623)
+.=||.|+.++... .+-...|++|+...
T Consensus 99 ~~fC~~CG~~~~~~~~~~~~~C~~c~~~~ 127 (256)
T PRK00241 99 HRFCGYCGHPMHPSKTEWAMLCPHCRERY 127 (256)
T ss_pred CccccccCCCCeecCCceeEECCCCCCEE
Confidence 66799999987543 23467899999654
No 333
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.66 E-value=46 Score=31.74 Aligned_cols=10 Identities=30% Similarity=0.664 Sum_probs=7.1
Q ss_pred eecCcCCCCc
Q 006973 500 YWCEGCQKND 509 (623)
Q Consensus 500 ~~C~kC~~~~ 509 (623)
|+|..|+.+.
T Consensus 50 YkC~~Cd~tW 59 (203)
T COG4332 50 YKCTHCDYTW 59 (203)
T ss_pred EEeeccCCcc
Confidence 6777777664
No 334
>PHA02768 hypothetical protein; Provisional
Probab=22.50 E-value=75 Score=24.35 Aligned_cols=27 Identities=11% Similarity=0.324 Sum_probs=20.1
Q ss_pred cccccccceecC---------CCCeeecCcCCCCcc
Q 006973 484 ACKTCNKKVTDA---------LGSGYWCEGCQKNDE 510 (623)
Q Consensus 484 aC~~C~KKv~~~---------~~~~~~C~kC~~~~~ 510 (623)
.|+.|+|..... ....|.|.+|++.+.
T Consensus 7 ~C~~CGK~Fs~~~~L~~H~r~H~k~~kc~~C~k~f~ 42 (55)
T PHA02768 7 ECPICGEIYIKRKSMITHLRKHNTNLKLSNCKRISL 42 (55)
T ss_pred CcchhCCeeccHHHHHHHHHhcCCcccCCcccceec
Confidence 799999987542 134789999998653
No 335
>TIGR03844 cysteate_syn cysteate synthase. Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M.
Probab=22.40 E-value=41 Score=36.74 Aligned_cols=24 Identities=13% Similarity=0.217 Sum_probs=18.9
Q ss_pred EeccccccccceecCCCCeeecCcCC
Q 006973 481 WYRACKTCNKKVTDALGSGYWCEGCQ 506 (623)
Q Consensus 481 ~Y~aC~~C~KKv~~~~~~~~~C~kC~ 506 (623)
|+.-|+.|++... + ...|+|+.|+
T Consensus 1 ~~l~C~~Cg~~~~-~-~~~~~C~~c~ 24 (398)
T TIGR03844 1 YTLRCPGCGEVLP-D-HYTLSCPLDC 24 (398)
T ss_pred CEEEeCCCCCccC-C-ccccCCCCCC
Confidence 4667999999986 3 3479999986
No 336
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=21.88 E-value=1e+02 Score=23.84 Aligned_cols=29 Identities=14% Similarity=0.407 Sum_probs=19.6
Q ss_pred CCCeEeccccccccceec------CCCCeeecCcCC
Q 006973 477 DQAMWYRACKTCNKKVTD------ALGSGYWCEGCQ 506 (623)
Q Consensus 477 d~~~~Y~aC~~C~KKv~~------~~~~~~~C~kC~ 506 (623)
+++.+|.-|| |+-+..- ++...-+|+.|.
T Consensus 17 e~~~ftyPCP-CGDRFeIsLeDl~~GE~VArCPSCS 51 (67)
T COG5216 17 EEKTFTYPCP-CGDRFEISLEDLRNGEVVARCPSCS 51 (67)
T ss_pred CCceEEecCC-CCCEeEEEHHHhhCCceEEEcCCce
Confidence 4467788899 8876532 234467899985
No 337
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=21.79 E-value=30 Score=40.69 Aligned_cols=20 Identities=25% Similarity=0.386 Sum_probs=0.0
Q ss_pred EEEEEeC---CCCeEEEEEechH
Q 006973 213 NVELTDE---DGTQIQATMFNEA 232 (623)
Q Consensus 213 ~~~L~D~---~G~~I~at~~~~~ 232 (623)
.|.|+|+ .|++|+..-++..
T Consensus 350 tM~ild~FiAvGTQlK~ErPGKa 372 (900)
T PF03833_consen 350 TMHILDDFIAVGTQLKVERPGKA 372 (900)
T ss_dssp -----------------------
T ss_pred HHHHHhhheeeceeeeeccCCCc
Confidence 5677776 4788887777653
No 338
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=21.69 E-value=68 Score=29.29 Aligned_cols=27 Identities=30% Similarity=0.806 Sum_probs=18.4
Q ss_pred eccccccccc---eecCCCCe--eecCcCCCCc
Q 006973 482 YRACKTCNKK---VTDALGSG--YWCEGCQKND 509 (623)
Q Consensus 482 Y~aC~~C~KK---v~~~~~~~--~~C~kC~~~~ 509 (623)
|.-|+.|+.- +..+ +.. ..|..|+...
T Consensus 97 yVlC~~C~sPdT~l~k~-~r~~~l~C~ACGa~~ 128 (133)
T TIGR00311 97 YVICRECNRPDTRIIKE-GRVSLLKCEACGAKA 128 (133)
T ss_pred eEECCCCCCCCcEEEEe-CCeEEEecccCCCCC
Confidence 8999999863 3332 333 4899999754
No 339
>KOG3108 consensus Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [Replication, recombination and repair]
Probab=21.68 E-value=2.8e+02 Score=28.51 Aligned_cols=71 Identities=21% Similarity=0.340 Sum_probs=40.9
Q ss_pred eeEEEEEEEEeCCceEEEEccCCceeeEEEEEEEeCCccEEEEEEechhhhhhhhHhhhcCCCCcEEEEEeEEeeeccce
Q 006973 309 LVDIIGVVQNVSPTMSIRRKSNNEMVPKRDITVADETKRTVTVSLWNELATNVGQELLDNADKSPIVAIKSLKVGDFQGI 388 (623)
Q Consensus 309 ~vDVIGvV~~v~~~~~i~~k~~g~~~~kr~i~l~D~sg~~I~vtLWg~~A~~~~~~~~~~~~~~~Vv~i~~~kV~~f~G~ 388 (623)
.|-++|+|..+... .....++|.|.+| .|+|..|-.......+. ..+..+..|-+ ...++.|+|+
T Consensus 70 ~v~~VGivr~~e~~-----------~t~i~y~I~D~tg-~id~r~W~~~~~~~~e~--~~l~~~~yVkv-~G~Lk~f~Gk 134 (265)
T KOG3108|consen 70 AVSIVGIVRNIEKS-----------ATNITYEIEDGTG-QIDVRQWFHDNAESEEM--PALETGTYVKV-YGHLKPFQGK 134 (265)
T ss_pred EEEEEEEEEeceec-----------CcceEEEEecCcc-cEEEEEeccccchhhhC--cccccCcEEEe-eecccCCCCc
Confidence 46777777766422 3456789999999 69999998765442110 01222333322 2334568774
Q ss_pred -eeeccc
Q 006973 389 -SLSTLG 394 (623)
Q Consensus 389 -~Ls~~~ 394 (623)
+|....
T Consensus 135 ~sl~~fk 141 (265)
T KOG3108|consen 135 KSLQVFK 141 (265)
T ss_pred eeEEEEe
Confidence 665443
No 340
>PRK12495 hypothetical protein; Provisional
Probab=21.58 E-value=57 Score=32.22 Aligned_cols=32 Identities=22% Similarity=0.499 Sum_probs=24.8
Q ss_pred CeEeccccccccceecCCCCeeecCcCCCCccc
Q 006973 479 AMWYRACKTCNKKVTDALGSGYWCEGCQKNDEE 511 (623)
Q Consensus 479 ~~~Y~aC~~C~KKv~~~~~~~~~C~kC~~~~~~ 511 (623)
.+...-|+.|+.-+... .|.-+|..|+..+..
T Consensus 39 tmsa~hC~~CG~PIpa~-pG~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 39 TMTNAHCDECGDPIFRH-DGQEFCPTCQQPVTE 70 (226)
T ss_pred ccchhhcccccCcccCC-CCeeECCCCCCcccc
Confidence 34567899999988754 788899999976543
No 341
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=21.53 E-value=48 Score=34.33 Aligned_cols=23 Identities=26% Similarity=0.619 Sum_probs=17.8
Q ss_pred eccccccccceecCCCCeeecCcCCCCc
Q 006973 482 YRACKTCNKKVTDALGSGYWCEGCQKND 509 (623)
Q Consensus 482 Y~aC~~C~KKv~~~~~~~~~C~kC~~~~ 509 (623)
..+|+.|++.-. .|.|++||--+
T Consensus 7 ~~~C~ic~vq~~-----~YtCPRCn~~Y 29 (383)
T KOG4317|consen 7 FLACGICGVQKR-----EYTCPRCNLLY 29 (383)
T ss_pred eeeccccccccc-----cccCCCCCccc
Confidence 568999987643 39999999654
No 342
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=21.32 E-value=1.2e+02 Score=27.35 Aligned_cols=27 Identities=7% Similarity=0.052 Sum_probs=15.5
Q ss_pred eecCcCCCCc---cccceeEEEEEEEEeCC
Q 006973 500 YWCEGCQKND---EECSLRYIMVARVCDGS 526 (623)
Q Consensus 500 ~~C~kC~~~~---~~~~~ry~l~~~i~D~T 526 (623)
+.|++|+... ..-.--|+-++.+.++.
T Consensus 93 ~~CP~Cgs~~~~i~~G~El~i~~Ieve~~~ 122 (124)
T PRK00762 93 IECPVCGNKRAHILGGRECNVKNIKIEKED 122 (124)
T ss_pred CcCcCCCCCCCEEecCCeEEEEEEEEecCC
Confidence 5688887432 12234566677776544
No 343
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=21.32 E-value=67 Score=33.48 Aligned_cols=26 Identities=19% Similarity=0.431 Sum_probs=19.8
Q ss_pred eEeccccccccceecCCCCeeecCcCCCCc
Q 006973 480 MWYRACKTCNKKVTDALGSGYWCEGCQKND 509 (623)
Q Consensus 480 ~~Y~aC~~C~KKv~~~~~~~~~C~kC~~~~ 509 (623)
....-||.|+. . ....|.|+.|+...
T Consensus 307 ~tS~~C~~cg~---~-~~r~~~C~~cg~~~ 332 (364)
T COG0675 307 YTSKTCPCCGH---L-SGRLFKCPRCGFVH 332 (364)
T ss_pred CCcccccccCC---c-cceeEECCCCCCee
Confidence 34578999999 2 25689999999754
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=21.30 E-value=13 Score=28.84 Aligned_cols=24 Identities=21% Similarity=0.731 Sum_probs=17.1
Q ss_pred ccccccccceecCCCCeeec-CcCCCCc
Q 006973 483 RACKTCNKKVTDALGSGYWC-EGCQKND 509 (623)
Q Consensus 483 ~aC~~C~KKv~~~~~~~~~C-~kC~~~~ 509 (623)
..|+.|++.+..+ .-+| ++|.+.+
T Consensus 4 kHC~~CG~~Ip~~---~~fCS~~C~~~~ 28 (59)
T PF09889_consen 4 KHCPVCGKPIPPD---ESFCSPKCREEY 28 (59)
T ss_pred CcCCcCCCcCCcc---hhhhCHHHHHHH
Confidence 3699999988754 4578 4787654
No 345
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=21.30 E-value=52 Score=24.96 Aligned_cols=24 Identities=17% Similarity=0.599 Sum_probs=18.5
Q ss_pred cccccccceecC-------CCCeeecCcCCC
Q 006973 484 ACKTCNKKVTDA-------LGSGYWCEGCQK 507 (623)
Q Consensus 484 aC~~C~KKv~~~-------~~~~~~C~kC~~ 507 (623)
.|..|+-++..+ .+...+|+.|++
T Consensus 24 ~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgR 54 (56)
T PF02591_consen 24 TCSGCHMELPPQELNEIRKGDEIVFCPNCGR 54 (56)
T ss_pred ccCCCCEEcCHHHHHHHHcCCCeEECcCCCc
Confidence 788998887642 256789999986
No 346
>cd04487 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB folds corresponding to the second OB fold (OBF2) of archaeal-specific proteins with similarity to eubacterial RecJ. RecJ is an ssDNA-specific exonuclease. Although the overall sequence similarity of these proteins to eubacterial RecJ proteins is marginal, they appear to carry motifs, which have been shown to be essential for nuclease function in Escherichia coli RecJ. In addition to this OB fold, most proteins in this subfamily contain: i) an N-terminal OB fold belonging to a different domain family (the ribosomal S1-like RNA-binding family); and ii) a domain, C-terminal to OBF2, characteristic of DHH family proteins. DHH family proteins include E. coli RecJ, and are predicted to have a phosphoesterase function.
Probab=21.29 E-value=3.2e+02 Score=21.96 Aligned_cols=58 Identities=12% Similarity=0.087 Sum_probs=38.1
Q ss_pred ceEEEEEeCcccceee-ccccccccccccCccceeeEEEEcceeeeccCCCceEEEEEEeeeee
Q 006973 40 NRYMFNASDGKKRLKA-ILPSNLSSEVISGNIQNKGLIRLLDYALNEIPTKSEKYLIVTKCEVV 102 (623)
Q Consensus 40 ~ryr~~lSDG~~~~~~-mlat~ln~~v~~~~l~~~siirl~~y~~~~~~~~~~~vlii~~lev~ 102 (623)
+=..+.|.|+...+.+ |+.+.... ..-.++.|+.|.+..-.- +. +++--+++.+++|+
T Consensus 15 GHvyfsLkD~~a~i~cv~f~~~~~~--~~~~l~~Gd~V~v~G~v~--~~-~G~~ql~v~~i~~~ 73 (73)
T cd04487 15 GPTIFTLRDETGTVWAAAFEEAGVR--AYPEVEVGDIVRVTGEVE--PR-DGQLQIEVESLEVL 73 (73)
T ss_pred CCEEEEEEcCCEEEEEEEEchhccC--CcCCCCCCCEEEEEEEEe--cC-CeEEEEEEeeEEEC
Confidence 3367889999888875 55443322 245689999888877643 22 33566788888764
No 347
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=21.14 E-value=49 Score=33.22 Aligned_cols=26 Identities=23% Similarity=0.631 Sum_probs=16.9
Q ss_pred ccccccceecC------CCCeeecCcCCCCcc
Q 006973 485 CKTCNKKVTDA------LGSGYWCEGCQKNDE 510 (623)
Q Consensus 485 C~~C~KKv~~~------~~~~~~C~kC~~~~~ 510 (623)
|..|+|+.... +-+.|+|.+|+..+.
T Consensus 135 Cr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~ 166 (278)
T PF15135_consen 135 CRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFR 166 (278)
T ss_pred ccccccccCCCccccccceeeeecccccccch
Confidence 44688875331 235689999987653
No 348
>COG4085 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=21.06 E-value=1.1e+02 Score=29.71 Aligned_cols=26 Identities=19% Similarity=0.197 Sum_probs=23.0
Q ss_pred EEEEEEEeCCCcEEEEEehHhHHHHh
Q 006973 517 IMVARVCDGSGEAWISIFNEEAERII 542 (623)
Q Consensus 517 ~l~~~i~D~Tg~~~~~~F~~~ae~ll 542 (623)
+.++.+.|+||++.|.+|...++.|.
T Consensus 71 i~~l~lndgtGti~vva~~~tee~l~ 96 (204)
T COG4085 71 IESLVLNDGTGTITVVASRSTEETLE 96 (204)
T ss_pred eEEEEEECCCCcEEEEEecChhHhHh
Confidence 45678999999999999999998876
No 349
>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=21.03 E-value=51 Score=25.46 Aligned_cols=24 Identities=25% Similarity=0.697 Sum_probs=11.6
Q ss_pred ccccccccceecCCCCee--ecC-cCC
Q 006973 483 RACKTCNKKVTDALGSGY--WCE-GCQ 506 (623)
Q Consensus 483 ~aC~~C~KKv~~~~~~~~--~C~-kC~ 506 (623)
..||.|+|.+....+..| +|. +|.
T Consensus 3 v~CP~C~k~~~~~~~n~~rPFCS~RCk 29 (57)
T PF03884_consen 3 VKCPICGKPVEWSPENPFRPFCSERCK 29 (57)
T ss_dssp EE-TTT--EEE-SSSSS--SSSSHHHH
T ss_pred ccCCCCCCeecccCCCCcCCcccHhhc
Confidence 579999999987423333 464 363
No 350
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=20.92 E-value=32 Score=40.46 Aligned_cols=22 Identities=23% Similarity=0.675 Sum_probs=0.0
Q ss_pred eccccccccceecCCCCeeecCcCCCC
Q 006973 482 YRACKTCNKKVTDALGSGYWCEGCQKN 508 (623)
Q Consensus 482 Y~aC~~C~KKv~~~~~~~~~C~kC~~~ 508 (623)
+..||.|+..+... .|++|+..
T Consensus 680 ~~~Cp~C~~~~~~~-----~C~~C~~~ 701 (900)
T PF03833_consen 680 VYVCPDCGIEVEED-----ECPKCGRE 701 (900)
T ss_dssp ---------------------------
T ss_pred ceeccccccccCcc-----cccccccc
Confidence 33455555555432 56666654
No 351
>cd01759 PLAT_PL PLAT/LH2 domain of pancreatic triglyceride lipase. Lipases hydrolyze phospholipids and triglycerides to generate fatty acids for energy production or for storage and to release inositol phosphates that act as second messengers. The central role of triglyceride lipases is in energy production. The proposed function of PLAT/LH2 domains is to mediate interaction with lipids or membrane bound proteins.
Probab=20.63 E-value=91 Score=27.61 Aligned_cols=26 Identities=15% Similarity=0.418 Sum_probs=21.9
Q ss_pred eeEEEEEEEEe---CCCcEEEEEehHhHH
Q 006973 514 LRYIMVARVCD---GSGEAWISIFNEEAE 539 (623)
Q Consensus 514 ~ry~l~~~i~D---~Tg~~~~~~F~~~ae 539 (623)
|||++++.+++ -+|.+.+.+++..++
T Consensus 1 ~~Yqv~V~~s~~~~~~g~~~vsL~G~~g~ 29 (113)
T cd01759 1 WRYKVSVTLSGKKKVTGTILVSLYGNKGN 29 (113)
T ss_pred CeEEEEEEEecccccCceEEEEEEcCCCC
Confidence 69999999988 678899999976664
No 352
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=20.35 E-value=52 Score=25.83 Aligned_cols=26 Identities=35% Similarity=0.604 Sum_probs=16.2
Q ss_pred eccccccccceecCCCCee--ecC-cCCC
Q 006973 482 YRACKTCNKKVTDALGSGY--WCE-GCQK 507 (623)
Q Consensus 482 Y~aC~~C~KKv~~~~~~~~--~C~-kC~~ 507 (623)
-..||.|+|.+.......| +|. +|..
T Consensus 6 ~v~CP~C~k~~~w~~~~~~rPFCS~RCk~ 34 (62)
T PRK00418 6 TVNCPTCGKPVEWGEISPFRPFCSKRCQL 34 (62)
T ss_pred cccCCCCCCcccccCCCCcCCcccHHHHh
Confidence 4679999999864322233 564 4753
Done!