Query 009303
Match_columns 538
No_of_seqs 326 out of 950
Neff 6.8
Searched_HMMs 46136
Date Thu Mar 28 22:55:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009303.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009303hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2534 DNA polymerase IV (fam 100.0 5.6E-89 1.2E-93 672.8 26.9 321 207-538 9-353 (353)
2 cd00141 NT_POLXc Nucleotidyltr 100.0 3.5E-74 7.6E-79 591.0 30.5 303 212-536 2-307 (307)
3 smart00483 POLXc DNA polymeras 100.0 2.3E-73 5.1E-78 590.9 26.9 318 208-537 1-334 (334)
4 PRK08609 hypothetical protein; 100.0 6E-68 1.3E-72 584.8 28.4 299 208-537 1-314 (570)
5 COG1796 POL4 DNA polymerase IV 100.0 1.1E-56 2.4E-61 447.9 23.5 298 208-537 3-318 (326)
6 PF14792 DNA_pol_B_palm: DNA p 99.9 6.3E-26 1.4E-30 200.1 10.0 105 345-459 1-112 (112)
7 PF14791 DNA_pol_B_thumb: DNA 99.9 1.2E-24 2.5E-29 172.2 3.1 63 465-537 1-63 (64)
8 PF14716 HHH_8: Helix-hairpin- 99.7 8.4E-17 1.8E-21 129.5 7.3 66 210-275 1-68 (68)
9 PF10391 DNA_pol_lambd_f: Fing 99.6 1.5E-16 3.2E-21 120.6 3.7 51 294-344 1-52 (52)
10 PRK07945 hypothetical protein; 99.6 8.4E-15 1.8E-19 152.9 11.6 102 213-324 3-118 (335)
11 smart00292 BRCT breast cancer 98.9 2.4E-09 5.3E-14 85.9 6.8 79 17-98 1-80 (80)
12 PF00533 BRCT: BRCA1 C Terminu 98.9 2.6E-09 5.7E-14 86.7 6.6 76 15-95 2-78 (78)
13 cd00027 BRCT Breast Cancer Sup 98.5 1.8E-07 3.9E-12 73.2 5.9 72 21-96 1-72 (72)
14 TIGR00575 dnlj DNA ligase, NAD 97.9 2.9E-05 6.3E-10 88.0 9.4 83 254-347 466-551 (652)
15 PF14520 HHH_5: Helix-hairpin- 97.9 8.4E-06 1.8E-10 63.8 2.7 51 293-343 3-55 (60)
16 PF14520 HHH_5: Helix-hairpin- 97.4 0.0002 4.3E-09 56.0 4.4 52 254-313 5-56 (60)
17 KOG3226 DNA repair protein [Re 97.4 0.00014 3.1E-09 74.9 3.7 88 16-110 315-403 (508)
18 PF12738 PTCB-BRCT: twin BRCT 97.1 0.00034 7.3E-09 55.0 2.8 62 23-90 2-63 (63)
19 COG1555 ComEA DNA uptake prote 97.0 0.00096 2.1E-08 62.0 5.1 50 252-313 95-145 (149)
20 PF11731 Cdd1: Pathogenicity l 97.0 0.00086 1.9E-08 57.1 4.2 35 291-325 8-42 (93)
21 PF12826 HHH_2: Helix-hairpin- 96.9 0.0013 2.9E-08 52.2 4.6 48 257-313 6-53 (64)
22 KOG2481 Protein required for n 96.9 0.00027 5.9E-09 75.7 0.7 87 11-109 320-416 (570)
23 PRK07956 ligA NAD-dependent DN 96.8 0.0043 9.4E-08 70.8 9.5 115 254-378 479-603 (665)
24 TIGR01259 comE comEA protein. 96.8 0.0022 4.7E-08 57.5 5.5 50 252-313 66-116 (120)
25 PF12836 HHH_3: Helix-hairpin- 96.8 0.0018 4E-08 51.5 4.4 48 252-311 12-60 (65)
26 PLN03123 poly [ADP-ribose] pol 96.7 0.0035 7.5E-08 73.9 7.5 90 15-109 390-481 (981)
27 PRK02515 psbU photosystem II c 96.5 0.0039 8.5E-08 56.0 4.8 47 252-313 59-105 (132)
28 PRK14351 ligA NAD-dependent DN 96.5 0.0096 2.1E-07 68.1 9.1 87 254-350 496-584 (689)
29 KOG0966 ATP-dependent DNA liga 96.4 0.0046 1E-07 69.7 5.9 92 12-108 627-722 (881)
30 TIGR00084 ruvA Holliday juncti 96.3 0.0065 1.4E-07 58.8 5.3 53 254-312 72-124 (191)
31 PF14229 DUF4332: Domain of un 96.2 0.02 4.3E-07 51.4 7.6 67 260-326 1-84 (122)
32 TIGR00426 competence protein C 96.2 0.011 2.5E-07 47.3 5.4 50 253-314 15-66 (69)
33 PLN03122 Poly [ADP-ribose] pol 96.1 0.012 2.7E-07 68.0 7.1 93 14-111 185-280 (815)
34 PRK14605 ruvA Holliday junctio 96.0 0.007 1.5E-07 58.7 4.4 52 254-312 73-125 (194)
35 PF00633 HHH: Helix-hairpin-he 95.9 0.0065 1.4E-07 40.9 2.4 23 251-273 8-30 (30)
36 PRK13901 ruvA Holliday junctio 95.9 0.01 2.3E-07 57.5 4.8 54 254-313 72-125 (196)
37 PRK00116 ruvA Holliday junctio 95.9 0.0098 2.1E-07 57.6 4.6 54 254-314 73-127 (192)
38 PRK14601 ruvA Holliday junctio 95.8 0.011 2.4E-07 56.7 4.7 54 254-313 73-126 (183)
39 TIGR00084 ruvA Holliday juncti 95.7 0.0066 1.4E-07 58.8 2.7 50 292-343 69-124 (191)
40 PRK12766 50S ribosomal protein 95.7 0.0033 7.1E-08 62.0 0.6 51 296-346 4-56 (232)
41 PRK14606 ruvA Holliday junctio 95.6 0.015 3.3E-07 56.1 4.7 54 254-313 73-126 (188)
42 PRK14602 ruvA Holliday junctio 95.6 0.013 2.9E-07 57.2 4.3 54 254-313 74-127 (203)
43 PRK14603 ruvA Holliday junctio 95.5 0.017 3.6E-07 56.3 4.7 54 254-313 72-125 (197)
44 KOG4362 Transcriptional regula 95.5 0.015 3.2E-07 65.4 4.8 76 30-111 485-565 (684)
45 PRK14604 ruvA Holliday junctio 95.5 0.018 3.8E-07 56.0 4.7 54 254-313 73-126 (195)
46 PF00633 HHH: Helix-hairpin-he 95.4 0.014 3E-07 39.3 2.6 22 292-313 8-29 (30)
47 COG5163 NOP7 Protein required 95.3 0.015 3.2E-07 60.9 3.6 86 12-109 344-440 (591)
48 KOG0966 ATP-dependent DNA liga 95.2 0.048 1E-06 61.8 7.7 90 17-107 783-881 (881)
49 COG1555 ComEA DNA uptake prote 95.0 0.019 4.1E-07 53.4 3.1 52 290-347 92-148 (149)
50 PRK07956 ligA NAD-dependent DN 95.0 0.011 2.5E-07 67.4 1.8 52 298-349 448-502 (665)
51 cd05397 NT_Pol-beta-like Nucle 94.9 0.044 9.6E-07 41.0 4.3 28 365-392 14-42 (49)
52 COG0632 RuvA Holliday junction 94.7 0.038 8.2E-07 53.8 4.4 54 254-313 73-126 (201)
53 PTZ00418 Poly(A) polymerase; P 94.6 0.33 7.1E-06 54.4 12.0 52 366-417 124-176 (593)
54 PRK14973 DNA topoisomerase I; 94.6 0.037 7.9E-07 65.5 4.7 90 254-344 835-928 (936)
55 PF11798 IMS_HHH: IMS family H 94.5 0.021 4.5E-07 39.0 1.6 20 297-316 13-32 (32)
56 COG0272 Lig NAD-dependent DNA 94.5 0.1 2.3E-06 58.7 7.8 49 256-313 513-561 (667)
57 TIGR01259 comE comEA protein. 94.5 0.036 7.7E-07 49.7 3.4 48 292-345 65-117 (120)
58 PRK14350 ligA NAD-dependent DN 94.5 0.073 1.6E-06 60.8 6.7 84 254-346 470-561 (669)
59 PRK14600 ruvA Holliday junctio 94.5 0.04 8.6E-07 53.2 3.9 53 254-313 73-125 (186)
60 TIGR00575 dnlj DNA ligase, NAD 94.4 0.018 3.9E-07 65.7 1.6 62 298-359 435-499 (652)
61 PRK02515 psbU photosystem II c 94.3 0.051 1.1E-06 49.0 3.9 32 293-324 59-91 (132)
62 PRK02362 ski2-like helicase; P 94.2 0.034 7.4E-07 64.5 3.4 56 284-342 642-699 (737)
63 cd05402 NT_PAP_TUTase Nucleoti 94.1 0.19 4.2E-06 43.8 7.4 59 353-415 8-68 (114)
64 TIGR00426 competence protein C 93.8 0.068 1.5E-06 42.8 3.5 44 296-345 17-66 (69)
65 PF12836 HHH_3: Helix-hairpin- 93.8 0.056 1.2E-06 42.9 3.0 47 293-345 12-63 (65)
66 PRK00116 ruvA Holliday junctio 93.6 0.039 8.4E-07 53.5 2.0 51 293-343 71-125 (192)
67 PRK14605 ruvA Holliday junctio 93.5 0.036 7.8E-07 53.8 1.6 52 291-342 69-124 (194)
68 PF12826 HHH_2: Helix-hairpin- 93.0 0.065 1.4E-06 42.5 2.1 43 299-342 7-51 (64)
69 PRK00254 ski2-like helicase; P 92.8 0.13 2.7E-06 59.7 5.0 76 266-342 608-694 (720)
70 PRK12766 50S ribosomal protein 92.7 0.22 4.7E-06 49.4 5.6 54 253-314 2-55 (232)
71 KOG2043 Signaling protein SWIF 92.2 0.13 2.9E-06 60.3 4.1 68 38-109 672-739 (896)
72 KOG1929 Nucleotide excision re 91.9 0.25 5.5E-06 57.2 5.8 89 17-110 102-190 (811)
73 PRK14606 ruvA Holliday junctio 91.1 0.11 2.5E-06 50.1 1.7 50 291-342 69-124 (188)
74 smart00278 HhH1 Helix-hairpin- 91.0 0.15 3.3E-06 32.9 1.7 19 296-314 2-20 (26)
75 PF01909 NTP_transf_2: Nucleot 91.0 0.31 6.8E-06 40.5 4.1 32 366-397 12-44 (93)
76 PRK14601 ruvA Holliday junctio 90.9 0.12 2.7E-06 49.6 1.7 50 291-342 69-124 (183)
77 PRK14603 ruvA Holliday junctio 90.7 0.11 2.4E-06 50.5 1.3 50 291-342 68-123 (197)
78 PRK14602 ruvA Holliday junctio 90.4 0.15 3.3E-06 49.8 1.9 50 291-342 70-125 (203)
79 PRK14604 ruvA Holliday junctio 90.3 0.15 3.1E-06 49.7 1.7 50 291-342 69-124 (195)
80 PF04994 TfoX_C: TfoX C-termin 90.2 0.22 4.9E-06 41.4 2.5 30 297-326 5-34 (81)
81 PRK13901 ruvA Holliday junctio 89.9 0.17 3.8E-06 49.1 1.8 49 291-341 68-122 (196)
82 TIGR01448 recD_rel helicase, p 89.5 1.3 2.8E-05 51.4 9.0 82 253-345 116-200 (720)
83 TIGR03671 cca_archaeal CCA-add 89.4 1.7 3.6E-05 46.9 8.9 46 352-397 24-71 (408)
84 COG3743 Uncharacterized conser 89.2 0.34 7.3E-06 43.8 3.0 53 295-350 67-119 (133)
85 COG1948 MUS81 ERCC4-type nucle 89.2 0.51 1.1E-05 47.5 4.6 49 256-313 184-232 (254)
86 PRK14351 ligA NAD-dependent DN 89.0 0.18 4E-06 57.9 1.4 64 298-361 465-531 (689)
87 PRK04301 radA DNA repair and r 88.8 0.33 7.1E-06 50.5 3.1 38 297-334 8-47 (317)
88 TIGR03252 uncharacterized HhH- 88.6 1.1 2.4E-05 42.8 6.2 49 261-312 75-132 (177)
89 COG1796 POL4 DNA polymerase IV 88.3 1.2 2.6E-05 46.1 6.7 95 207-320 59-153 (326)
90 PRK14600 ruvA Holliday junctio 88.2 0.24 5.2E-06 47.8 1.5 49 291-342 69-123 (186)
91 TIGR02236 recomb_radA DNA repa 88.0 0.35 7.5E-06 50.1 2.6 29 298-326 2-30 (310)
92 PRK08097 ligB NAD-dependent DN 87.8 0.68 1.5E-05 52.0 4.9 85 253-350 458-544 (562)
93 TIGR01448 recD_rel helicase, p 87.4 0.28 6.1E-06 56.9 1.7 53 292-344 79-135 (720)
94 TIGR00588 ogg 8-oxoguanine DNA 86.9 1.6 3.5E-05 45.5 6.8 62 255-318 177-243 (310)
95 KOG1929 Nucleotide excision re 86.7 0.83 1.8E-05 53.1 4.9 93 12-110 487-579 (811)
96 smart00279 HhH2 Helix-hairpin- 86.6 0.45 9.9E-06 33.4 1.7 16 299-314 20-35 (36)
97 cd00080 HhH2_motif Helix-hairp 86.4 0.63 1.4E-05 38.1 2.7 27 297-324 24-50 (75)
98 PRK14350 ligA NAD-dependent DN 86.3 1.2 2.6E-05 51.1 5.9 62 249-314 497-560 (669)
99 KOG0323 TFIIF-interacting CTD 86.1 0.31 6.8E-06 55.0 1.1 90 17-110 440-532 (635)
100 KOG2841 Structure-specific end 86.1 0.85 1.8E-05 45.2 3.9 50 255-313 196-245 (254)
101 PRK01172 ski2-like helicase; P 85.7 1 2.2E-05 51.8 5.1 39 286-325 604-642 (674)
102 PRK03352 DNA polymerase IV; Va 85.1 0.65 1.4E-05 48.8 2.9 29 297-325 179-207 (346)
103 TIGR00615 recR recombination p 85.0 1.7 3.8E-05 42.1 5.5 45 292-364 8-52 (195)
104 cd05400 NT_2-5OAS_ClassI-CCAas 85.0 3.7 8E-05 37.2 7.4 46 368-413 27-79 (143)
105 PRK13844 recombination protein 84.6 1.9 4.2E-05 42.0 5.6 45 292-364 12-56 (200)
106 PF11731 Cdd1: Pathogenicity l 84.1 1.6 3.4E-05 37.4 4.2 47 253-303 11-57 (93)
107 PRK14670 uvrC excinuclease ABC 83.9 2.4 5.3E-05 47.8 6.8 52 254-314 514-565 (574)
108 PRK03858 DNA polymerase IV; Va 83.9 0.8 1.7E-05 49.1 2.9 29 297-325 175-203 (396)
109 smart00278 HhH1 Helix-hairpin- 83.0 1.1 2.3E-05 28.9 2.1 20 255-274 2-21 (26)
110 PRK01216 DNA polymerase IV; Va 82.9 0.82 1.8E-05 48.5 2.5 30 297-326 180-209 (351)
111 PRK08609 hypothetical protein; 82.9 1.5 3.3E-05 49.5 4.8 54 252-311 86-139 (570)
112 COG1708 Predicted nucleotidylt 82.8 5.4 0.00012 34.6 7.4 29 367-395 25-54 (128)
113 PRK03609 umuC DNA polymerase V 82.2 0.95 2.1E-05 49.1 2.8 29 297-325 181-209 (422)
114 COG0122 AlkA 3-methyladenine D 82.1 5.5 0.00012 41.0 8.1 47 270-317 174-220 (285)
115 COG0353 RecR Recombinational D 82.0 0.99 2.2E-05 43.6 2.5 21 292-312 9-29 (198)
116 smart00478 ENDO3c endonuclease 81.7 4.1 8.8E-05 37.3 6.4 26 292-317 69-94 (149)
117 COG0272 Lig NAD-dependent DNA 81.4 2.6 5.6E-05 47.9 5.8 135 254-398 479-644 (667)
118 PF14490 HHH_4: Helix-hairpin- 81.2 1.5 3.3E-05 37.3 3.1 54 292-346 10-66 (94)
119 PRK14667 uvrC excinuclease ABC 81.1 3.5 7.5E-05 46.5 6.7 67 232-314 498-564 (567)
120 PRK14666 uvrC excinuclease ABC 81.0 0.81 1.8E-05 52.3 1.7 46 295-342 637-685 (694)
121 PF01367 5_3_exonuc: 5'-3' exo 80.8 0.13 2.8E-06 44.7 -3.7 24 299-324 22-46 (101)
122 smart00475 53EXOc 5'-3' exonuc 80.8 1.2 2.7E-05 45.1 2.8 26 298-325 189-215 (259)
123 PRK13482 DNA integrity scannin 80.5 2.6 5.7E-05 44.5 5.2 60 245-313 276-337 (352)
124 PRK09482 flap endonuclease-lik 80.5 1.3 2.8E-05 45.0 2.8 26 298-325 185-211 (256)
125 cd01703 PolY_Pol_iota DNA Poly 80.4 1.1 2.5E-05 47.9 2.6 30 297-326 174-203 (379)
126 PRK00227 glnD PII uridylyl-tra 80.2 4.7 0.0001 46.6 7.5 65 348-415 8-74 (693)
127 PRK01810 DNA polymerase IV; Va 80.2 1.3 2.8E-05 47.8 2.8 29 297-325 181-209 (407)
128 cd01701 PolY_Rev1 DNA polymera 80.1 1.3 2.8E-05 47.9 2.8 30 297-326 224-253 (404)
129 COG1746 CCA1 tRNA nucleotidylt 79.9 4 8.7E-05 44.0 6.3 48 352-399 29-78 (443)
130 PRK10880 adenine DNA glycosyla 79.7 7.6 0.00016 41.2 8.4 65 232-303 85-151 (350)
131 PRK10308 3-methyl-adenine DNA 79.7 1.9 4E-05 44.4 3.7 64 254-321 167-233 (283)
132 cd01700 PolY_Pol_V_umuC umuC s 79.7 1.3 2.9E-05 46.5 2.7 29 297-325 178-206 (344)
133 PRK14976 5'-3' exonuclease; Pr 79.5 1.4 3E-05 45.3 2.7 25 298-324 194-219 (281)
134 PRK03348 DNA polymerase IV; Pr 79.4 1.2 2.7E-05 48.7 2.5 29 297-325 182-210 (454)
135 PRK02406 DNA polymerase IV; Va 79.2 1.3 2.9E-05 46.4 2.6 29 297-325 170-198 (343)
136 COG0632 RuvA Holliday junction 78.9 1.1 2.4E-05 43.7 1.7 51 292-342 70-124 (201)
137 cd00056 ENDO3c endonuclease II 78.9 1.2 2.6E-05 41.1 1.9 27 291-317 79-105 (158)
138 PRK14666 uvrC excinuclease ABC 78.6 3.6 7.8E-05 47.2 5.8 68 232-314 621-688 (694)
139 PRK00558 uvrC excinuclease ABC 78.4 4.2 9.2E-05 46.2 6.4 52 254-314 543-594 (598)
140 PRK03103 DNA polymerase IV; Re 78.1 1.6 3.6E-05 46.9 2.9 29 297-325 183-211 (409)
141 PRK02794 DNA polymerase IV; Pr 77.9 1.5 3.2E-05 47.5 2.5 29 297-325 211-239 (419)
142 cd00008 53EXOc 5'-3' exonuclea 77.7 1.8 3.8E-05 43.4 2.8 27 298-325 186-212 (240)
143 cd00424 PolY Y-family of DNA p 77.7 1.7 3.7E-05 45.7 2.8 28 298-325 176-203 (343)
144 PRK14133 DNA polymerase IV; Pr 77.6 1.6 3.5E-05 46.0 2.6 29 297-325 175-203 (347)
145 PRK14672 uvrC excinuclease ABC 77.6 4.6 9.9E-05 46.3 6.3 54 254-316 608-661 (691)
146 PRK08097 ligB NAD-dependent DN 77.2 0.96 2.1E-05 50.8 0.8 64 298-361 428-494 (562)
147 PRK07758 hypothetical protein; 76.3 1.3 2.8E-05 37.9 1.1 44 300-343 39-84 (95)
148 TIGR01083 nth endonuclease III 76.1 5.9 0.00013 38.2 5.8 25 292-316 103-127 (191)
149 PRK00076 recR recombination pr 75.8 2.2 4.7E-05 41.5 2.7 21 292-312 8-28 (196)
150 PRK01229 N-glycosylase/DNA lya 75.5 3.2 6.9E-05 40.8 3.8 53 262-317 85-142 (208)
151 PRK13300 tRNA CCA-pyrophosphor 75.0 10 0.00022 41.6 7.9 45 355-399 28-74 (447)
152 PTZ00205 DNA polymerase kappa; 74.3 2.1 4.7E-05 48.0 2.5 29 297-325 311-339 (571)
153 PRK10702 endonuclease III; Pro 74.1 5.7 0.00012 39.1 5.2 25 292-316 106-130 (211)
154 cd05403 NT_KNTase_like Nucleot 73.9 6.9 0.00015 32.0 5.0 29 370-398 20-49 (93)
155 PRK00254 ski2-like helicase; P 73.6 15 0.00034 42.6 9.5 53 254-314 645-697 (720)
156 cd03468 PolY_like DNA Polymera 73.1 2.8 6E-05 43.6 2.9 37 299-335 174-210 (335)
157 TIGR01084 mutY A/G-specific ad 73.0 6 0.00013 40.5 5.3 69 228-303 77-147 (275)
158 cd01702 PolY_Pol_eta DNA Polym 72.9 2.8 6.1E-05 44.6 3.0 29 297-325 184-213 (359)
159 PF14229 DUF4332: Domain of un 72.7 3.7 8E-05 36.8 3.2 26 301-326 1-26 (122)
160 COG1948 MUS81 ERCC4-type nucle 72.5 3.8 8.2E-05 41.4 3.6 53 289-342 176-230 (254)
161 KOG2093 Translesion DNA polyme 71.6 5.2 0.00011 46.5 4.8 89 13-110 42-132 (1016)
162 COG0258 Exo 5'-3' exonuclease 71.3 3 6.6E-05 43.3 2.7 25 299-325 202-227 (310)
163 PRK13913 3-methyladenine DNA g 70.7 5 0.00011 39.7 3.9 22 292-313 118-139 (218)
164 PRK10702 endonuclease III; Pro 70.5 9.2 0.0002 37.6 5.7 43 232-274 85-129 (211)
165 cd03586 PolY_Pol_IV_kappa DNA 69.7 3.3 7.2E-05 43.0 2.6 29 297-325 173-201 (334)
166 COG0389 DinP Nucleotidyltransf 68.5 3.5 7.7E-05 43.7 2.5 28 297-324 178-205 (354)
167 PF03118 RNA_pol_A_CTD: Bacter 68.2 6.8 0.00015 31.2 3.5 22 254-275 44-65 (66)
168 COG0177 Nth Predicted EndoIII- 67.9 6.6 0.00014 38.7 4.1 86 261-354 80-175 (211)
169 KOG2875 8-oxoguanine DNA glyco 67.8 7.5 0.00016 39.7 4.5 67 255-322 175-245 (323)
170 PF11798 IMS_HHH: IMS family H 67.3 2.7 5.8E-05 28.6 0.9 18 255-272 12-29 (32)
171 PF00416 Ribosomal_S13: Riboso 66.8 5.6 0.00012 34.8 3.0 26 293-318 13-39 (107)
172 KOG3524 Predicted guanine nucl 66.7 7.9 0.00017 44.0 4.8 79 14-100 114-192 (850)
173 PF14579 HHH_6: Helix-hairpin- 66.4 15 0.00032 30.9 5.4 49 256-315 29-77 (90)
174 PF04919 DUF655: Protein of un 66.2 20 0.00043 34.4 6.7 53 229-288 97-150 (181)
175 PRK13766 Hef nuclease; Provisi 66.0 6.7 0.00014 45.9 4.4 10 56-65 440-449 (773)
176 cd00056 ENDO3c endonuclease II 65.9 11 0.00024 34.7 5.0 67 230-303 54-125 (158)
177 COG2251 Predicted nuclease (Re 64.7 4.8 0.0001 43.6 2.6 27 299-325 229-255 (474)
178 PF02371 Transposase_20: Trans 63.8 4.5 9.7E-05 33.8 1.8 20 295-314 2-21 (87)
179 PRK13910 DNA glycosylase MutY; 63.4 14 0.00031 38.1 5.7 68 232-306 48-117 (289)
180 PRK14973 DNA topoisomerase I; 62.7 8.9 0.00019 45.9 4.6 40 295-334 802-843 (936)
181 KOG2245 Poly(A) polymerase and 62.6 16 0.00035 40.3 6.0 86 331-418 41-140 (562)
182 KOG2534 DNA polymerase IV (fam 62.1 5.2 0.00011 41.5 2.2 55 290-344 51-115 (353)
183 COG1669 Predicted nucleotidylt 61.9 27 0.00058 30.2 6.1 30 367-396 22-53 (97)
184 PRK03980 flap endonuclease-1; 61.7 6.3 0.00014 40.8 2.8 25 299-324 193-217 (292)
185 PF14716 HHH_8: Helix-hairpin- 60.9 6.6 0.00014 31.3 2.2 24 290-313 41-65 (68)
186 TIGR03491 RecB family nuclease 60.9 6.2 0.00013 43.4 2.7 29 298-326 210-238 (457)
187 PRK14670 uvrC excinuclease ABC 60.9 5.1 0.00011 45.3 2.1 29 296-325 515-543 (574)
188 TIGR00615 recR recombination p 60.7 6 0.00013 38.5 2.2 37 249-285 5-42 (195)
189 PRK14668 uvrC excinuclease ABC 60.6 13 0.00029 42.1 5.3 43 295-338 525-569 (577)
190 PRK12278 50S ribosomal protein 60.6 6.4 0.00014 39.0 2.5 30 295-324 158-187 (221)
191 cd05401 NT_GlnE_GlnD_like Nucl 60.5 32 0.00069 32.2 7.2 50 368-417 55-110 (172)
192 TIGR00593 pola DNA polymerase 60.5 6.3 0.00014 47.0 2.8 24 299-324 189-213 (887)
193 TIGR03252 uncharacterized HhH- 60.3 26 0.00057 33.6 6.4 44 232-275 80-136 (177)
194 PF14579 HHH_6: Helix-hairpin- 60.2 11 0.00024 31.6 3.6 30 297-326 29-62 (90)
195 PRK14667 uvrC excinuclease ABC 60.2 4.6 9.9E-05 45.6 1.6 29 296-325 515-543 (567)
196 PRK14671 uvrC excinuclease ABC 59.1 7.6 0.00016 44.4 3.1 32 293-325 567-598 (621)
197 PRK05007 PII uridylyl-transfer 59.0 31 0.00067 41.3 8.2 49 367-415 79-130 (884)
198 PRK02362 ski2-like helicase; P 58.8 63 0.0014 37.8 10.6 52 254-315 652-704 (737)
199 PRK14671 uvrC excinuclease ABC 58.6 13 0.00028 42.6 4.8 49 254-313 569-617 (621)
200 PTZ00217 flap endonuclease-1; 57.8 7.8 0.00017 41.8 2.8 26 298-324 238-263 (393)
201 COG4277 Predicted DNA-binding 56.8 9.3 0.0002 39.5 2.9 39 294-332 329-371 (404)
202 PRK00076 recR recombination pr 56.7 7.3 0.00016 37.9 2.1 32 254-285 11-42 (196)
203 PRK01759 glnD PII uridylyl-tra 56.6 36 0.00078 40.5 8.2 68 348-415 32-106 (854)
204 PF14490 HHH_4: Helix-hairpin- 56.5 12 0.00025 31.9 3.1 55 261-322 19-74 (94)
205 PF03118 RNA_pol_A_CTD: Bacter 56.1 3.3 7.2E-05 33.0 -0.3 45 300-344 16-62 (66)
206 PRK13844 recombination protein 55.9 7.4 0.00016 38.0 2.0 32 254-285 15-46 (200)
207 smart00611 SEC63 Domain of unk 55.8 22 0.00048 36.5 5.7 29 297-325 153-181 (312)
208 PRK10917 ATP-dependent DNA hel 55.8 9.4 0.0002 44.2 3.2 27 297-323 11-37 (681)
209 PRK03352 DNA polymerase IV; Va 55.7 34 0.00074 35.9 7.2 55 256-320 179-235 (346)
210 PRK12311 rpsB 30S ribosomal pr 55.6 8.4 0.00018 40.5 2.5 32 293-324 261-292 (326)
211 TIGR03674 fen_arch flap struct 55.6 9.2 0.0002 40.4 2.8 27 298-325 239-265 (338)
212 PRK07758 hypothetical protein; 55.5 12 0.00025 32.2 2.8 23 254-276 67-89 (95)
213 KOG1921 Endonuclease III [Repl 55.3 12 0.00026 37.6 3.3 32 283-315 148-179 (286)
214 PRK14672 uvrC excinuclease ABC 54.8 5.7 0.00012 45.6 1.1 51 296-347 609-661 (691)
215 PRK14669 uvrC excinuclease ABC 54.7 16 0.00035 41.8 4.8 30 295-325 552-581 (624)
216 cd00141 NT_POLXc Nucleotidyltr 54.7 5.3 0.00011 41.6 0.8 51 293-343 43-102 (307)
217 PRK05755 DNA polymerase I; Pro 54.4 8.9 0.00019 45.7 2.8 25 298-324 190-215 (880)
218 CHL00137 rps13 ribosomal prote 53.8 8.8 0.00019 34.5 2.0 25 293-317 15-40 (122)
219 PRK06063 DNA polymerase III su 53.4 36 0.00077 35.5 6.7 48 17-66 231-278 (313)
220 KOG4362 Transcriptional regula 53.0 14 0.00031 42.2 3.9 96 3-100 573-680 (684)
221 PRK05179 rpsM 30S ribosomal pr 53.0 8.9 0.00019 34.5 1.9 23 295-317 17-40 (122)
222 COG0177 Nth Predicted EndoIII- 52.3 30 0.00066 34.1 5.6 31 243-273 97-128 (211)
223 PRK04374 PII uridylyl-transfer 51.6 50 0.0011 39.5 8.3 62 354-415 55-122 (869)
224 TIGR02236 recomb_radA DNA repa 51.3 15 0.00033 37.8 3.7 50 256-313 1-50 (310)
225 TIGR01083 nth endonuclease III 50.7 35 0.00076 32.8 5.8 42 232-273 82-125 (191)
226 PRK04301 radA DNA repair and r 49.8 35 0.00076 35.4 6.0 52 255-314 7-58 (317)
227 TIGR01084 mutY A/G-specific ad 49.8 25 0.00054 36.1 4.8 25 292-316 102-126 (275)
228 COG5067 DBF4 Protein kinase es 49.3 12 0.00026 39.9 2.3 49 13-63 117-165 (468)
229 TIGR03631 bact_S13 30S ribosom 49.0 11 0.00023 33.5 1.7 24 294-317 14-38 (113)
230 KOG3548 DNA damage checkpoint 48.5 20 0.00044 42.1 4.2 28 84-111 1011-1038(1176)
231 PRK13482 DNA integrity scannin 48.4 10 0.00022 40.2 1.7 52 288-341 280-334 (352)
232 COG2231 Uncharacterized protei 47.6 27 0.0006 34.2 4.4 38 270-312 95-132 (215)
233 smart00478 ENDO3c endonuclease 47.2 43 0.00093 30.4 5.6 43 232-274 48-92 (149)
234 PF03445 DUF294: Putative nucl 46.9 50 0.0011 30.0 5.9 51 369-419 50-107 (138)
235 TIGR01954 nusA_Cterm_rpt trans 46.6 17 0.00037 26.5 2.3 31 303-333 1-33 (50)
236 cd01703 PolY_Pol_iota DNA Poly 46.1 40 0.00086 36.2 5.9 58 255-318 173-243 (379)
237 KOG1921 Endonuclease III [Repl 45.7 32 0.00069 34.7 4.6 30 245-274 149-179 (286)
238 PRK01216 DNA polymerase IV; Va 45.6 68 0.0015 34.0 7.5 52 256-317 180-233 (351)
239 PRK14669 uvrC excinuclease ABC 45.4 38 0.00082 38.8 5.8 50 254-314 552-601 (624)
240 PRK06195 DNA polymerase III su 45.0 43 0.00093 34.8 5.8 48 17-65 219-266 (309)
241 COG0099 RpsM Ribosomal protein 44.7 17 0.00037 32.5 2.3 22 296-317 18-40 (121)
242 smart00483 POLXc DNA polymeras 44.7 11 0.00023 39.8 1.3 52 292-343 45-106 (334)
243 PRK00558 uvrC excinuclease ABC 44.7 15 0.00032 41.9 2.4 42 294-336 542-585 (598)
244 PRK02794 DNA polymerase IV; Pr 44.2 1.2E+02 0.0026 32.7 9.4 52 256-318 211-264 (419)
245 PF02889 Sec63: Sec63 Brl doma 44.1 28 0.0006 35.8 4.2 29 296-324 149-177 (314)
246 PRK13746 aminoglycoside resist 44.0 1.2E+02 0.0025 31.1 8.5 27 370-397 30-58 (262)
247 KOG2093 Translesion DNA polyme 43.8 39 0.00084 39.7 5.5 53 256-318 551-605 (1016)
248 PRK12373 NADH dehydrogenase su 43.5 18 0.00039 39.0 2.7 33 292-324 320-352 (400)
249 PTZ00134 40S ribosomal protein 43.4 15 0.00034 34.3 2.0 46 294-360 29-75 (154)
250 COG5186 PAP1 Poly(A) polymeras 43.4 95 0.002 33.2 7.8 52 368-419 81-133 (552)
251 COG0322 UvrC Nuclease subunit 43.1 41 0.00089 38.2 5.6 84 209-313 496-579 (581)
252 PF04919 DUF655: Protein of un 43.1 19 0.0004 34.6 2.4 59 266-324 86-149 (181)
253 PRK00275 glnD PII uridylyl-tra 43.1 82 0.0018 37.8 8.4 48 368-415 78-128 (895)
254 PRK13913 3-methyladenine DNA g 42.7 45 0.00098 33.0 5.2 76 232-316 93-178 (218)
255 COG1725 Predicted transcriptio 42.6 66 0.0014 29.1 5.8 88 262-362 12-103 (125)
256 COG1491 Predicted RNA-binding 42.5 23 0.00051 34.0 3.0 40 248-287 123-163 (202)
257 TIGR00588 ogg 8-oxoguanine DNA 42.5 35 0.00077 35.5 4.7 76 224-305 178-265 (310)
258 TIGR00596 rad1 DNA repair prot 42.4 32 0.0007 40.7 4.8 32 293-325 755-786 (814)
259 PRK04053 rps13p 30S ribosomal 42.0 18 0.0004 33.7 2.2 24 294-317 24-48 (149)
260 KOG1918 3-methyladenine DNA gl 41.9 15 0.00031 36.4 1.6 58 254-312 122-182 (254)
261 PF06514 PsbU: Photosystem II 41.8 7.5 0.00016 33.2 -0.4 51 293-343 21-72 (93)
262 COG1491 Predicted RNA-binding 41.4 51 0.0011 31.8 5.0 57 268-324 102-163 (202)
263 cd01701 PolY_Rev1 DNA polymera 41.0 59 0.0013 35.1 6.3 53 256-318 224-280 (404)
264 COG1194 MutY A/G-specific DNA 40.8 53 0.0011 34.7 5.6 62 221-282 78-141 (342)
265 PRK14668 uvrC excinuclease ABC 40.8 18 0.00038 41.1 2.3 20 327-346 526-545 (577)
266 TIGR03629 arch_S13P archaeal r 40.3 19 0.00042 33.3 2.1 44 296-360 22-66 (144)
267 TIGR00194 uvrC excinuclease AB 40.1 23 0.0005 40.2 3.0 29 296-325 542-570 (574)
268 TIGR01446 DnaD_dom DnaD and ph 39.9 25 0.00053 28.0 2.4 18 306-323 55-72 (73)
269 PF02961 BAF: Barrier to autoi 39.5 23 0.00049 30.1 2.1 28 296-323 20-47 (89)
270 KOG3524 Predicted guanine nucl 39.1 21 0.00045 40.8 2.4 86 17-109 209-294 (850)
271 TIGR01693 UTase_glnD [Protein- 38.9 82 0.0018 37.5 7.5 49 368-416 43-94 (850)
272 cd00128 XPG Xeroderma pigmento 38.5 19 0.00041 37.4 1.9 23 298-321 226-248 (316)
273 TIGR00596 rad1 DNA repair prot 38.1 54 0.0012 38.9 5.7 16 210-225 643-658 (814)
274 COG1204 Superfamily II helicas 37.7 25 0.00054 41.3 2.9 109 233-344 610-727 (766)
275 PRK13766 Hef nuclease; Provisi 37.4 23 0.00051 41.4 2.7 45 296-341 716-762 (773)
276 PRK03059 PII uridylyl-transfer 37.2 92 0.002 37.2 7.5 65 351-415 42-111 (856)
277 PF09970 DUF2204: Nucleotidyl 36.7 73 0.0016 30.5 5.5 39 368-406 16-59 (181)
278 COG2844 GlnD UTP:GlnB (protein 35.9 61 0.0013 38.1 5.5 48 368-415 66-116 (867)
279 COG1200 RecG RecG-like helicas 35.0 31 0.00066 39.6 3.0 27 297-323 12-38 (677)
280 PHA01806 hypothetical protein 34.7 65 0.0014 31.3 4.7 49 345-397 14-67 (200)
281 PHA00439 exonuclease 34.2 28 0.00061 35.9 2.3 27 298-325 191-219 (286)
282 PRK10308 3-methyl-adenine DNA 34.2 63 0.0014 33.3 4.9 45 228-272 173-225 (283)
283 PF11774 Lsr2: Lsr2 ; InterPr 34.2 26 0.00057 30.9 1.8 28 470-497 73-100 (110)
284 PRK10880 adenine DNA glycosyla 34.0 29 0.00062 36.9 2.4 24 292-315 106-129 (350)
285 PTZ00035 Rad51 protein; Provis 33.7 73 0.0016 33.6 5.4 50 293-343 22-73 (337)
286 PRK13910 DNA glycosylase MutY; 33.1 29 0.00064 35.8 2.3 23 293-315 70-92 (289)
287 COG1031 Uncharacterized Fe-S o 33.0 34 0.00074 37.5 2.8 32 293-324 514-546 (560)
288 COG5275 BRCT domain type II [G 32.5 95 0.0021 30.8 5.4 50 17-67 155-204 (276)
289 cd01702 PolY_Pol_eta DNA Polym 32.4 1.1E+02 0.0023 32.6 6.5 54 256-318 184-241 (359)
290 PRK03858 DNA polymerase IV; Va 32.2 78 0.0017 33.8 5.5 52 256-317 175-228 (396)
291 PLN03187 meiotic recombination 31.5 80 0.0017 33.5 5.3 33 292-325 29-61 (344)
292 PF05559 DUF763: Protein of un 31.3 1.8E+02 0.0039 30.5 7.5 21 292-312 266-286 (319)
293 TIGR02238 recomb_DMC1 meiotic 31.0 68 0.0015 33.5 4.6 43 300-342 6-50 (313)
294 cd00424 PolY Y-family of DNA p 31.0 1.2E+02 0.0026 31.7 6.6 53 256-318 175-229 (343)
295 COG0353 RecR Recombinational D 31.0 44 0.00095 32.5 2.9 22 254-275 12-33 (198)
296 TIGR03135 malonate_mdcG holo-A 30.4 1.9E+02 0.0041 28.3 7.3 32 367-398 107-145 (202)
297 PRK03381 PII uridylyl-transfer 29.5 1.4E+02 0.003 35.3 7.3 46 369-414 58-106 (774)
298 cd05398 NT_ClassII-CCAase Nucl 29.4 1.1E+02 0.0024 27.9 5.2 38 354-394 4-45 (139)
299 PRK01229 N-glycosylase/DNA lya 28.5 59 0.0013 32.0 3.4 20 252-271 116-136 (208)
300 PF04994 TfoX_C: TfoX C-termin 26.0 50 0.0011 27.4 2.1 36 254-293 3-38 (81)
301 PF02371 Transposase_20: Trans 25.6 58 0.0013 27.0 2.4 42 255-307 3-44 (87)
302 PRK03348 DNA polymerase IV; Pr 25.6 1.3E+02 0.0029 33.0 5.9 53 256-318 182-236 (454)
303 PLN03187 meiotic recombination 24.8 2.1E+02 0.0045 30.4 7.0 104 253-383 31-141 (344)
304 cd07749 NT_Pol-beta-like_1 Nuc 24.1 3E+02 0.0065 25.9 7.0 37 367-403 16-56 (156)
305 PRK14133 DNA polymerase IV; Pr 24.1 1.9E+02 0.004 30.4 6.5 52 256-318 175-228 (347)
306 TIGR00600 rad2 DNA excision re 23.4 62 0.0013 39.3 2.9 26 298-323 869-895 (1034)
307 TIGR02922 conserved hypothetic 22.2 34 0.00074 27.0 0.4 15 370-384 34-48 (67)
308 KOG2841 Structure-specific end 22.1 1.4E+02 0.003 30.1 4.5 46 292-338 192-239 (254)
309 PRK07945 hypothetical protein; 21.9 48 0.001 34.9 1.5 28 297-324 51-82 (335)
310 COG0322 UvrC Nuclease subunit 21.8 50 0.0011 37.5 1.7 28 297-325 532-559 (581)
311 cd04761 HTH_MerR-SF Helix-Turn 21.6 86 0.0019 22.3 2.4 22 295-316 4-25 (49)
312 TIGR00207 fliG flagellar motor 20.7 5E+02 0.011 27.4 8.8 87 236-323 144-245 (338)
313 PF00416 Ribosomal_S13: Riboso 20.7 91 0.002 27.1 2.8 44 254-297 15-58 (107)
314 PF14091 DUF4269: Domain of un 20.5 7.1E+02 0.015 23.3 8.8 27 372-398 19-46 (152)
315 PRK14109 bifunctional glutamin 20.4 2.5E+02 0.0055 34.2 7.3 46 368-413 215-266 (1007)
No 1
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=100.00 E-value=5.6e-89 Score=672.75 Aligned_cols=321 Identities=36% Similarity=0.649 Sum_probs=295.4
Q ss_pred CCCcHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHH
Q 009303 207 PDLNKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFE 286 (538)
Q Consensus 207 ~~~N~~ia~~l~~la~~~e~~g~~~r~~aY~rAa~~l~~l~~~i~~~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~ 286 (538)
.++|..|+++|+.||+.|++.|+.+|+++|++||++|+++|++|+|++|+++|||||++|+.+|+|||+||++++||+++
T Consensus 9 t~~N~~~~~aleiLa~~~ev~g~~~r~~~y~~Aasvlk~~p~~I~S~~ea~~lP~iG~kia~ki~EiletG~l~ele~v~ 88 (353)
T KOG2534|consen 9 TNNNQIFTEALEILAEAYEVEGEEDRARAYRRAASVLKSLPFPITSGEEAEKLPGIGPKIAEKIQEILETGVLRELEAVR 88 (353)
T ss_pred ccccHHHHHHHHHHHHhhcccccHHHHHHHHHHHHHHHhCCCCcccHHHhcCCCCCCHHHHHHHHHHHHcCCchhHHHHh
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhchhHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhh-ccCcchhhhccccchhhhccCcCHHHHHHHHHHHHHHhhhc
Q 009303 287 KDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN-EDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEV 365 (538)
Q Consensus 287 ~~~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~-~~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~iv~~~~~~~ 365 (538)
+|+.+++|++|++|||||++||++||++|+|||+|+++ ..++|++|++|++||+||..+|+|+||.++.++|++++..+
T Consensus 89 ~de~~~~lklFtnifGvG~ktA~~Wy~~GfrTled~Rk~~~kft~qqk~Gl~yy~Df~~~v~ReE~~~i~~~V~~av~~~ 168 (353)
T KOG2534|consen 89 NDERSQSLKLFTNIFGVGLKTAEKWYREGFRTLEDVRKKPDKFTRQQKAGLKYYEDFLKRVTREEATAIQQTVQEAVWAF 168 (353)
T ss_pred cchhHHHHHHHHHHhccCHHHHHHHHHhhhhHHHHHHhCHHHHHHHHHHhHHHHHHHhhhccHHHHHHHHHHHHHHHhhc
Confidence 99999999999999999999999999999999999994 45899999999999999999999999999999999999999
Q ss_pred CCCeEEEecccccccCCcCCCeeEEEecCCcch-hhhhHHHHHHHHHHcCcccceeeeccccCC--------CCCCccee
Q 009303 366 LPEVIILCGGSYRRGKASCGDLDVVIMHPDRKS-HKGFLSKYVKKLKEMKFLREDLIFSTHSEE--------GTDSGVDT 436 (538)
Q Consensus 366 ~p~~~v~~~Gs~RRgke~~~DVDiLit~~~~~~-~~~~l~~vv~~L~~~g~l~~~l~~s~~~~~--------~~~~~~~~ 436 (538)
+|++.|++||||||||++|||||||||||...+ +.+++..|+..|.+.|++.......+..+. .++ -..+
T Consensus 169 ~p~~~vt~~GsfRRGk~~ggDvD~LithP~~~s~~~~~~~~l~~~le~~g~il~~~~~~S~~Ek~~l~~~~s~~~-~~~~ 247 (353)
T KOG2534|consen 169 DPEAFVTVTGSFRRGKKMGGDVDFLITHPGSTSTEAKLLQLLMILLEKKGLLLYYDQLHSCGEKLRLPSRKSALD-HFKK 247 (353)
T ss_pred CCCcEEEEeccccCCcccCCCeeEEEeCCCCCchhhhHHHHHHHHHHhcCeEEEEeeeccccccccccchhhhHh-hhhh
Confidence 999999999999999999999999999999887 788999999999999999833221111000 011 1346
Q ss_pred eeeeeecC-------------CCcc-ceeeeEEEecCchhHHHHHHhhccHHHHHHHHHHHHHcCCccCCCCCcccccCC
Q 009303 437 YFGLCTYP-------------GREL-RHRIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGS 502 (538)
Q Consensus 437 ~~g~~~~~-------------~~~~-~~RVDl~~~p~~~~~~aLl~~TGS~~fnr~lR~~A~~kg~~L~~~gL~~~~~~~ 502 (538)
+||+|++| +++| +|||||+|||+++|||||||||||++|||+||++|.+|||+||+||||+.+.
T Consensus 248 ~mgv~~LPr~~~~~~~~S~n~~~~~~~rRvDivv~P~~~~~~alLgwTGS~~FnR~lR~~A~~kG~~l~~h~L~~~~~-- 325 (353)
T KOG2534|consen 248 FMGVFRLPRQRVDSDQSSWNEGKGWKARRVDIVVCPYDEFGFALLGWTGSKEFNRDLRRYATHKGFSLDEHALFDLTV-- 325 (353)
T ss_pred EEEEEEcCcccccccccccCCCCCCceeeeEEEEechHHcceeeeeecchHHHHHHHHHHHHhcCceecccccccCCc--
Confidence 89999999 5544 5899999999999999999999999999999999999999999999998643
Q ss_pred CCcccccccCCCCCCCHHHHHhhcCCCCCCCCCcCC
Q 009303 503 GGKQGVRARTSLKFDTEKEVFDFLGFPWLEPHERNL 538 (538)
Q Consensus 503 ~g~~~~~~~~~~~~~tEedIF~~LGL~yipPe~Rn~ 538 (538)
..++++.+|+|||++|||+|+||++||.
T Consensus 326 --------~~~l~~~sEkdIFr~l~L~Y~EP~~Rn~ 353 (353)
T KOG2534|consen 326 --------RIFLPVESEKDIFRYLGLKYIEPKERNA 353 (353)
T ss_pred --------ceecCCccHHHHHHHhCCccCChhhcCC
Confidence 3689999999999999999999999995
No 2
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=100.00 E-value=3.5e-74 Score=591.02 Aligned_cols=303 Identities=40% Similarity=0.680 Sum_probs=279.2
Q ss_pred HHHHHHHHHHHHHHHcCCC-hhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhch
Q 009303 212 NITEIFGKLINIYRALGED-RRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEK 290 (538)
Q Consensus 212 ~ia~~l~~la~~~e~~g~~-~r~~aY~rAa~~l~~l~~~i~~~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~ 290 (538)
+|+++|++||++|+++|+| ||++||++||++|+++|++|++++++.+|||||++|+++|.||++||+++++|+++++ .
T Consensus 2 ~ia~~L~~ia~~~e~~~~~~~r~~aY~~Aa~~l~~l~~~i~~~~~~~~ipgiG~~ia~kI~E~~~tG~~~~le~l~~~-~ 80 (307)
T cd00141 2 EIADILEELADLLELLGGNPFRVRAYRKAARALESLPEPIESLEEAKKLPGIGKKIAEKIEEILETGKLRKLEELRED-V 80 (307)
T ss_pred hHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHhCCcccCCHHHhcCCCCccHHHHHHHHHHHHcCCHHHHHHHhcc-c
Confidence 6999999999999999655 8999999999999999999999999999999999999999999999999999999998 5
Q ss_pred hHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhc--cCcchhhhccccchhhhccCcCHHHHHHHHHHHHHHhhhcCCC
Q 009303 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPE 368 (538)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~--~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~iv~~~~~~~~p~ 368 (538)
+..+..|++|||||||||++||+.||+||+||+.+ .+++..|..|++||+|+.++|||+||+++.+.|.+.++.+.|+
T Consensus 81 ~~~l~~l~~i~GiGpk~a~~l~~lGi~sl~dL~~a~g~k~~~~i~~gl~~~~~~~~ri~r~ea~~~a~~i~~~l~~~~~~ 160 (307)
T cd00141 81 PPGLLLLLRVPGVGPKTARKLYELGIRTLEDLRKAAGAKLEQNILIGLEYYEDFQQRIPREEALAIAEIIKEALREVDPV 160 (307)
T ss_pred hHHHHHHHcCCCCCHHHHHHHHHcCCCCHHHHHHHhccccHHHHHHHHHHHHHhcCCeEHHHHHHHHHHHHHHHHhCCCc
Confidence 56677777999999999999997799999999987 4899999999999999999999999999999888888878888
Q ss_pred eEEEecccccccCCcCCCeeEEEecCCcchhhhhHHHHHHHHHHcCcccceeeeccccCCCCCCcceeeeeeeecCCCcc
Q 009303 369 VIILCGGSYRRGKASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCTYPGREL 448 (538)
Q Consensus 369 ~~v~~~Gs~RRgke~~~DVDiLit~~~~~~~~~~l~~vv~~L~~~g~l~~~l~~s~~~~~~~~~~~~~~~g~~~~~~~~~ 448 (538)
+.|++|||||||+++||||||||+|++... ..++.++++.|.+.|++.+.+. .+..+|+|.|++|+...
T Consensus 161 ~~v~i~GS~RRg~et~gDiDilv~~~~~~~-~~~~~~v~~~l~~~~~~~~~~~----------~g~~k~~~~~~~~~~~~ 229 (307)
T cd00141 161 LQVEIAGSYRRGKETVGDIDILVTHPDATS-RGLLEKVVDALVELGFVTEVLS----------KGDTKASGILKLPGGWK 229 (307)
T ss_pred eEEEEcccccCCCCccCCEEEEEecCCccc-cccHHHHHHHHHhCCCeehhhh----------CCCceEEEEEecCCCCC
Confidence 999999999999999999999999998764 6778899999999999976432 23458999999987767
Q ss_pred ceeeeEEEecCchhHHHHHHhhccHHHHHHHHHHHHHcCCccCCCCCcccccCCCCcccccccCCCCCCCHHHHHhhcCC
Q 009303 449 RHRIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGSGGKQGVRARTSLKFDTEKEVFDFLGF 528 (538)
Q Consensus 449 ~~RVDl~~~p~~~~~~aLl~~TGS~~fnr~lR~~A~~kg~~L~~~gL~~~~~~~~g~~~~~~~~~~~~~tEedIF~~LGL 528 (538)
++||||++||+++||+||+|||||++|||.||.+|.++||+||+||||+.. .+..+++.+|+|||++|||
T Consensus 230 ~~rVDl~~~p~~~~~~all~fTGs~~~nr~lR~~A~~~G~~L~~~GL~~~~----------~~~~~~~~~E~~If~~Lgl 299 (307)
T cd00141 230 GRRVDLRVVPPEEFGAALLYFTGSKQFNRALRRLAKEKGLKLNEYGLFDGV----------DGERLPGETEEEIFEALGL 299 (307)
T ss_pred ceEEEEEEeCHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCeeeccccccCC----------CCCCccCCCHHHHHHHcCC
Confidence 899999999999999999999999999999999999999999999999743 1368999999999999999
Q ss_pred CCCCCCCc
Q 009303 529 PWLEPHER 536 (538)
Q Consensus 529 ~yipPe~R 536 (538)
||||||+|
T Consensus 300 ~yipPe~R 307 (307)
T cd00141 300 PYIEPELR 307 (307)
T ss_pred CCCCCCCC
Confidence 99999998
No 3
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=100.00 E-value=2.3e-73 Score=590.91 Aligned_cols=318 Identities=36% Similarity=0.597 Sum_probs=266.6
Q ss_pred CCcHHHHHHHHHHHHHHHHcCCC-hhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHH
Q 009303 208 DLNKNITEIFGKLINIYRALGED-RRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFE 286 (538)
Q Consensus 208 ~~N~~ia~~l~~la~~~e~~g~~-~r~~aY~rAa~~l~~l~~~i~~~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~ 286 (538)
|+|++|+++|++||++||++|+| +|++||++||++|+++|++|++++++.+|||||++|++||.||++||++.++.+..
T Consensus 1 ~~N~~I~~~L~~la~l~el~gen~~k~~ay~~Aa~~i~~l~~~i~~~~~l~~lpgIG~~ia~kI~Eil~tG~~~~~~e~l 80 (334)
T smart00483 1 NLNRGIIDALEILAENYEVFGENKRKCSYFRKAASVLKSLPFPINSMKDLKGLPGIGDKIKKKIEEIIETGKSSKVLEIL 80 (334)
T ss_pred CCcHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhCCCCCCCHHHHhcCCCccHHHHHHHHHHHHhCcHHHHHHHh
Confidence 46999999999999999999999 58999999999999999999999999999999999999999999999999666655
Q ss_pred hhchhHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhcc--CcchhhhccccchhhhccCcCHHHHHHHHHHHHHHhhh
Q 009303 287 KDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEE 364 (538)
Q Consensus 287 ~~~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~~--~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~iv~~~~~~ 364 (538)
.++.+..+..|++|||||||||++||+.||+||+||+++. +|+..|.+|++||+|+.++|||+||+++.++|....+.
T Consensus 81 ~~~~p~~l~~l~~i~GiGpk~a~~l~~lGi~tl~eL~~a~~~~l~~~q~~gl~~~~~~~~ri~r~e~~~i~~~i~~~l~~ 160 (334)
T smart00483 81 NDEVYKSLKLFTNVFGVGPKTAAKWYRKGIRTLEELKKNKELKLTKQQKAGLKYYEDILKKVSRAEAFAVEYIVKRAVRK 160 (334)
T ss_pred cCcHHHHHHHHHccCCcCHHHHHHHHHhCCCCHHHHHhcccccCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHh
Confidence 6666677777779999999999999999999999999653 69999999999999999999999999999999888888
Q ss_pred cCCCeEEEecccccccCCcCCCeeEEEecCCcchhhhhHHHHHHHHHHcCcccceeeeccccCCCCCCcceeeeeeeecC
Q 009303 365 VLPEVIILCGGSYRRGKASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCTYP 444 (538)
Q Consensus 365 ~~p~~~v~~~Gs~RRgke~~~DVDiLit~~~~~~~~~~l~~vv~~L~~~g~l~~~l~~s~~~~~~~~~~~~~~~g~~~~~ 444 (538)
+.|.+.|++||||||||++||||||||+|+++.. +++.++++.|.-. .+...+............+..+|+++|..|
T Consensus 161 ~~~~~~v~i~GSyRRgket~gDIDili~~~~~~~--~~~~~v~~~~~l~-~~~~~~~~~~~~~~~~~~g~~~~~~v~~~~ 237 (334)
T smart00483 161 ILPDAIVTLTGSFRRGKETGHDVDFLITSPHPAK--EKELEVLDLLLLE-STFEELQLPSIRVATLDHGQKKFMILKLSP 237 (334)
T ss_pred hCCCcEEEEecccccCCCcCCCeeEEEecCCccc--hhHHHHHHHHHHH-HHHHHHhcccchhhhhhcCCCEEEEEEeCC
Confidence 8888899999999999999999999999999763 4455554333100 000000000000011123334678888764
Q ss_pred CC-------------ccceeeeEEEecCchhHHHHHHhhccHHHHHHHHHHHHHcCCccCCCCCcccccCCCCccccccc
Q 009303 445 GR-------------ELRHRIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGSGGKQGVRAR 511 (538)
Q Consensus 445 ~~-------------~~~~RVDl~~~p~~~~~~aLl~~TGS~~fnr~lR~~A~~kg~~L~~~gL~~~~~~~~g~~~~~~~ 511 (538)
.. +.++||||++||+++||+||+|||||++|||.||.+|.++| +||+||||+.... .+
T Consensus 238 ~~~~~~~~g~~~~~~~~~rrVDl~~~~~~~~g~aLl~fTGS~~fnr~lR~~A~~~g-~L~~~gl~~~~~~--------~~ 308 (334)
T smart00483 238 SREDKEKSGKPDEKGWKARRVDIVLCPEDQYPTALLGWTGSKQFNRDLRRYATSKF-KLMLDGHELYDKT--------KE 308 (334)
T ss_pred ccccccccccccCCCCcceEEEEEEechHHheeEEEEEeCchhHHHHHHHHHHHcC-CcCcccCccccCC--------CC
Confidence 21 23589999999999999999999999999999999999999 9999999974321 13
Q ss_pred CCCCCCCHHHHHhhcCCCCCCCCCcC
Q 009303 512 TSLKFDTEKEVFDFLGFPWLEPHERN 537 (538)
Q Consensus 512 ~~~~~~tEedIF~~LGL~yipPe~Rn 537 (538)
..+++.+|+|||++|||||||||+||
T Consensus 309 ~~i~~~~E~~If~~LGl~yipPe~Rn 334 (334)
T smart00483 309 KFLKVESEEDIFDHLGLPYIEPEERN 334 (334)
T ss_pred eeccCCCHHHHHHHhCCCCCCcccCC
Confidence 57889999999999999999999998
No 4
>PRK08609 hypothetical protein; Provisional
Probab=100.00 E-value=6e-68 Score=584.85 Aligned_cols=299 Identities=22% Similarity=0.347 Sum_probs=260.7
Q ss_pred CCcHHHHHHHHHHHHHHHHcCCC-hhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHH
Q 009303 208 DLNKNITEIFGKLINIYRALGED-RRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFE 286 (538)
Q Consensus 208 ~~N~~ia~~l~~la~~~e~~g~~-~r~~aY~rAa~~l~~l~~~i~~~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~ 286 (538)
|+|++|+++|++||++++++|+| ||++||+|||++|+++|++|++++++.+|||||++||+||+||++||++++||+|+
T Consensus 1 m~n~~ia~~l~~~A~~le~~g~n~fr~~aYr~Aa~~i~~l~~~i~~~~~l~~ipgIG~~ia~kI~Eil~tG~~~~le~l~ 80 (570)
T PRK08609 1 MNKKDVIKLLETIATYMELKGENPFKISAFRKAAQALELDERSLSEIDDFTKLKGIGKGTAEVIQEYRETGESSVLQELK 80 (570)
T ss_pred CChHHHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHhCchhhhhhhhhccCCCcCHHHHHHHHHHHHhCChHHHHHHH
Confidence 56999999999999999999988 79999999999999999999999999999999999999999999999999999999
Q ss_pred hhchhHHHHHHhhccCCCHHHHHHHHHh-CCCCHHHHhhc---cCcchhhhc----------cccchhhhccCcCHHHHH
Q 009303 287 KDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNE---DSLTHSQRL----------GLKYFDDIKTRIPRHEVE 352 (538)
Q Consensus 287 ~~~~~~~l~lf~~I~GvGpktA~~ly~~-GirtledL~~~---~~L~~~q~~----------Glk~~ed~~~~i~r~Ea~ 352 (538)
++.|..+++|+ +|||||||||++||+. ||+||+||+++ ++++.+++| |+++|+++.+|||++||.
T Consensus 81 ~~~p~~~~~l~-~i~GiGpk~a~~l~~~lGi~tl~~L~~a~~~~~~~~~~gfg~k~~~~il~~i~~~~~~~~R~~~~~a~ 159 (570)
T PRK08609 81 KEVPEGLLPLL-KLPGLGGKKIAKLYKELGVVDKESLKEACENGKVQALAGFGKKTEEKILEAVKELGKRPERLPIAQVL 159 (570)
T ss_pred hhCcHHHHHHh-cCCCCCHHHHHHHHHHhCCCCHHHHHHHHHhCChhhccCcchhHHHHHHHHHHHHhcccccEEHHHHH
Confidence 98777666655 9999999999999975 99999999954 578877777 567777888999999999
Q ss_pred HHHHHHHHHhhhcCCCeEEEecccccccCCcCCCeeEEEecCCcchhhhhHHHHHHHHHHcCcccceeeeccccCCCCCC
Q 009303 353 QMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLREDLIFSTHSEEGTDS 432 (538)
Q Consensus 353 ~i~~iv~~~~~~~~p~~~v~~~Gs~RRgke~~~DVDiLit~~~~~~~~~~l~~vv~~L~~~g~l~~~l~~s~~~~~~~~~ 432 (538)
.+.+.|.+..+.+.|...|++||||||||+||||||||||++++.. +++.|.+.+++.+.+. .
T Consensus 160 ~~a~~i~~~l~~~~~~~~v~~~GS~RR~~et~gDiDili~~~~~~~-------~~~~l~~~~~v~~~~~----------~ 222 (570)
T PRK08609 160 PIAQEIEEYLATIDEIIRFSRAGSLRRARETVKDLDFIIATDEPEA-------VREQLLQLPNIVEVIA----------A 222 (570)
T ss_pred HHHHHHHHHHHhCCCccEEEeccchhccccccCCeeEEEecCCHHH-------HHHHHHcCccHHHHHh----------c
Confidence 9988888777766666799999999999999999999999998754 3455666666654432 1
Q ss_pred cceeeeeeeecCCCccceeeeEEEecCchhHHHHHHhhccHHHHHHHHHHHHHcCCccCCCCCcccccCCCCcccccccC
Q 009303 433 GVDTYFGLCTYPGRELRHRIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGSGGKQGVRART 512 (538)
Q Consensus 433 ~~~~~~g~~~~~~~~~~~RVDl~~~p~~~~~~aLl~~TGS~~fnr~lR~~A~~kg~~L~~~gL~~~~~~~~g~~~~~~~~ 512 (538)
|..++++.|.++ .++||||++||+++||+||+|||||++|||.||.+|.+|||+||+||||+... +.
T Consensus 223 g~~~~~~~~~~~---~~~~vDl~~v~~~~~~~aL~yfTGS~~hn~~lr~~A~~~g~~l~e~gl~~~~~----------~~ 289 (570)
T PRK08609 223 GDTKVSVELEYE---YTISVDFRLVEPEAFATTLHHFTGSKDHNVRMRQLAKERGEKISEYGVEQADT----------GE 289 (570)
T ss_pred CCceEEEEEecC---CCeEEEEEEeCHHHHHHHHHHHhccHHHHHHHHHHHHHcCCcccccccccCCC----------Cc
Confidence 223555555431 24799999999999999999999999999999999999999999999997421 35
Q ss_pred CCCCCCHHHHHhhcCCCCCCCCCcC
Q 009303 513 SLKFDTEKEVFDFLGFPWLEPHERN 537 (538)
Q Consensus 513 ~~~~~tEedIF~~LGL~yipPe~Rn 537 (538)
.+++.||+|||++|||||||||+||
T Consensus 290 ~~~~~~E~~iy~~Lgl~yipPelRe 314 (570)
T PRK08609 290 VKTFESEEAFFAHFGLPFIPPEVRE 314 (570)
T ss_pred cCCCCCHHHHHHHcCCCCCCccccC
Confidence 7889999999999999999999997
No 5
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.1e-56 Score=447.95 Aligned_cols=298 Identities=28% Similarity=0.469 Sum_probs=249.8
Q ss_pred CCcHHHHHHHHHHHHHHHHcCCC-hhHHHHHHHHHHHhcCCccccchhhh---cCCCCCCHHHHHHHHHHHHhCCcchhH
Q 009303 208 DLNKNITEIFGKLINIYRALGED-RRSFSYYKAIPVIEKLPFKIESADQV---KGLPGIGKSMQDHIQEIVTTGKLSKLE 283 (538)
Q Consensus 208 ~~N~~ia~~l~~la~~~e~~g~~-~r~~aY~rAa~~l~~l~~~i~~~~~l---~~lpgIG~~ia~kI~Eil~tG~~~~le 283 (538)
|+|+.|+.+|+++|++|++.|+| ||++|||+||.+|+.+.+++.++.+. ..|||||+++|++|.||++||+++.++
T Consensus 3 ~~n~~ia~~le~iA~~me~~Gen~fk~~aYr~Aa~sle~~~e~~~ei~e~~~~t~l~gIGk~ia~~I~e~l~tG~~~~le 82 (326)
T COG1796 3 MNNHDIARLLERIADYMELEGENPFKIRAYRKAAQSLENLTEDLEEIEERGRLTELPGIGKGIAEKISEYLDTGEVKKLE 82 (326)
T ss_pred cchHHHHHHHHHHHHHHHhcCCCccchHHHHHHHHhhhhcccchHHHHhhcccCCCCCccHHHHHHHHHHHHcCccHHHH
Confidence 67999999999999999999999 89999999999999999999998765 599999999999999999999999999
Q ss_pred HHHhhchhHHHHHHhhccCCCHHHHHHHHHh-CCCCHHHHhhc---cCcchhhhccccchhhhc----------cCcCHH
Q 009303 284 HFEKDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNE---DSLTHSQRLGLKYFDDIK----------TRIPRH 349 (538)
Q Consensus 284 ~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~-GirtledL~~~---~~L~~~q~~Glk~~ed~~----------~~i~r~ 349 (538)
.++...|.+...|+ +|+|+|||+...||++ ||.++++|+++ +++..+.|||-++..+|. +|+|..
T Consensus 83 ~lk~~~P~gl~~Ll-~v~GlGpkKi~~Ly~elgi~~~e~l~~a~~~~~~~~l~GfG~kse~~il~~i~~~~~~~~R~~l~ 161 (326)
T COG1796 83 ALKKEVPEGLEPLL-KVPGLGPKKIVSLYKELGIKDLEELQEALENGKIRGLRGFGKKSEAKILENIEFAEESPERIPLS 161 (326)
T ss_pred HHHHhCCcchHHHh-hCCCCCcHHHHHHHHHHCcccHHHHHHHHHhCCccccCCccchhHHHHHHHHHHHhhhhhhcchH
Confidence 99999999988888 9999999999999998 99999999965 468889999988877776 566777
Q ss_pred HHHHHHHHHHHHhhhcCCCeEEEecccccccCCcCCCeeEEEecCCcchhhhhHHHHHHHHHHcCcccceeeeccccCCC
Q 009303 350 EVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLREDLIFSTHSEEG 429 (538)
Q Consensus 350 Ea~~i~~iv~~~~~~~~p~~~v~~~Gs~RRgke~~~DVDiLit~~~~~~~~~~l~~vv~~L~~~g~l~~~l~~s~~~~~~ 429 (538)
++-.+..-+.....++.|-.++.++||+||+++|++|||++|+..++.+ +++.|.+...+++....
T Consensus 162 ~~l~ia~ei~~yl~~~~~~~~~~~aGs~RR~retv~DiD~~~s~~~~~~-------v~~~~~~~~~~~~vi~~------- 227 (326)
T COG1796 162 FTLPIAQEIEGYLEELTPIIQASIAGSLRRGRETVGDIDILISTSHPES-------VLEELLEMPNVQEVIAK------- 227 (326)
T ss_pred HHHHHHHHHHHHHHhccchheeeeccchhhccccccceeeEeccCCcHH-------HHHHHhcCCCcceeeec-------
Confidence 7766644444444445565678899999999999999999998877765 45555555544433211
Q ss_pred CCCcceeeeeeeecCCCccceeeeEEEecCchhHHHHHHhhccHHHHHHHHHHHHHcCCccCCCCCcccccCCCCccccc
Q 009303 430 TDSGVDTYFGLCTYPGRELRHRIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGSGGKQGVR 509 (538)
Q Consensus 430 ~~~~~~~~~g~~~~~~~~~~~RVDl~~~p~~~~~~aLl~~TGS~~fnr~lR~~A~~kg~~L~~~gL~~~~~~~~g~~~~~ 509 (538)
.+.++.. +..+. ....|||+|||++.||+||+|||||++||+.||.+|+.+||+||+||||..
T Consensus 228 G~~k~s~---~~~~~---~~~svD~r~v~~e~fGaal~~fTGSkehNi~iR~lA~~kg~klseyGl~~~----------- 290 (326)
T COG1796 228 GETKVSM---LLILD---EGTSVDFRVVPPEAFGAALQHFTGSKEHNIKIRQLAKAKGEKLSEYGLFRD----------- 290 (326)
T ss_pred CCceeeE---EEEec---CCCeeEEEEcCHHHhhhhhhhcccchhhhHHHHHHHHHhCcchhhcceecc-----------
Confidence 1111111 11111 124699999999999999999999999999999999999999999999963
Q ss_pred ccCCCCCCCHHHHHhhcCCCCCCCCCcC
Q 009303 510 ARTSLKFDTEKEVFDFLGFPWLEPHERN 537 (538)
Q Consensus 510 ~~~~~~~~tEedIF~~LGL~yipPe~Rn 537 (538)
++..++..||++||++|||+|||||+|+
T Consensus 291 ~~e~i~~~tE~~i~~~l~l~yipPE~RE 318 (326)
T COG1796 291 SGEIIAGKTEEKIYEHLGLPYIPPELRE 318 (326)
T ss_pred CCceecCCcHhHHHHHcCCCCCChhhcc
Confidence 1367899999999999999999999997
No 6
>PF14792 DNA_pol_B_palm: DNA polymerase beta palm ; PDB: 1RZT_A 3PML_A 2PFN_A 3HX0_K 3HWT_A 2GWS_E 2BCQ_A 3UPQ_A 2BCS_A 3UQ2_A ....
Probab=99.93 E-value=6.3e-26 Score=200.08 Aligned_cols=105 Identities=44% Similarity=0.795 Sum_probs=91.7
Q ss_pred CcCHHHHHHHHHHHHHHhhhcCCCeEEEecccccccCCcCCCeeEEEecCCcchh----hhhHHHHHHHHHHcCccccee
Q 009303 345 RIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPDRKSH----KGFLSKYVKKLKEMKFLREDL 420 (538)
Q Consensus 345 ~i~r~Ea~~i~~iv~~~~~~~~p~~~v~~~Gs~RRgke~~~DVDiLit~~~~~~~----~~~l~~vv~~L~~~g~l~~~l 420 (538)
||||+|+++++++|++++..+.|++.+++||||||||++|||||||||||+.... .++|.++++.|+++|+|+++|
T Consensus 1 rIPR~Ev~~i~~~V~~~~~~i~p~~~v~i~GSyRRGK~~~gDiDiLIt~~~~~~~~~~~~~~l~~lv~~L~~~g~i~~~L 80 (112)
T PF14792_consen 1 RIPRDEVEEIEEIVKEALEKIDPGLEVEICGSYRRGKETSGDIDILITHPDPSSVSKKLEGLLEKLVKRLEEKGFITDDL 80 (112)
T ss_dssp -EEHHHHHHHHHHHHHHHHCCSTT-EEEEEHHHHTT-SEESSEEEEEEETTCSTTTCSTTCHHHHHHHHHHHTTSEEEEE
T ss_pred CCCHHHHHHHHHHHHHHHHhcCCCcEEEEccccccCCCcCCCeEEEEeCCCcCcchhhHHHHHHHHHHHHHhCCeEEEec
Confidence 6999999999999999999999999999999999999999999999999998774 789999999999999999998
Q ss_pred eeccccCCCCCCcceeeeeeeecCCC---ccceeeeEEEecC
Q 009303 421 IFSTHSEEGTDSGVDTYFGLCTYPGR---ELRHRIDFKVYPR 459 (538)
Q Consensus 421 ~~s~~~~~~~~~~~~~~~g~~~~~~~---~~~~RVDl~~~p~ 459 (538)
..+ ..+|+|+|++|+. ..+|||||+++|+
T Consensus 81 ~~~----------~~~~~G~~~l~~~~~~~~~RRiDi~~~P~ 112 (112)
T PF14792_consen 81 SLG----------PTKYMGVCRLPGNDNKSPHRRIDIIVVPY 112 (112)
T ss_dssp EEC----------SSEEEEEEE-SSTSST--EEEEEEEEEEG
T ss_pred ccC----------CceeeeEeecCCCCCCCCeeeEEEEEeCC
Confidence 542 2589999999987 6789999999995
No 7
>PF14791 DNA_pol_B_thumb: DNA polymerase beta thumb ; PDB: 1HUZ_A 3K75_D 1HUO_A 2BPC_A 1RPL_A 1NOM_A 1ZQX_A 1ZQU_A 1ZQZ_A 1ZQV_A ....
Probab=99.90 E-value=1.2e-24 Score=172.23 Aligned_cols=63 Identities=35% Similarity=0.688 Sum_probs=52.7
Q ss_pred HHHHhhccHHHHHHHHHHHHHcCCccCCCCCcccccCCCCcccccccCCCCCCCHHHHHhhcCCCCCCCCCcC
Q 009303 465 GLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGSGGKQGVRARTSLKFDTEKEVFDFLGFPWLEPHERN 537 (538)
Q Consensus 465 aLl~~TGS~~fnr~lR~~A~~kg~~L~~~gL~~~~~~~~g~~~~~~~~~~~~~tEedIF~~LGL~yipPe~Rn 537 (538)
||+|||||++|||+||.+|+++||+||+|||++... +..+++.+|+|||++|||||||||+||
T Consensus 1 All~~TGs~~fnr~lR~~A~~~g~~L~~~Gl~~~~~----------~~~~~~~~E~dif~~Lgl~yipPe~R~ 63 (64)
T PF14791_consen 1 ALLYFTGSKEFNRDLRQYAKKKGMKLSEYGLFKRET----------GELVPVESEEDIFDALGLPYIPPELRE 63 (64)
T ss_dssp HHHHHHS-HHHHHHHHHHHHHTTEEEESSEEEETTC----------EEEEE-SSHHHHHHHTTS----GGGCT
T ss_pred CcccccCCHHHHHHHHHHHHHcCCeeCccccccccc----------ceeecCCCHHHHHHHcCCCCCChhhcC
Confidence 799999999999999999999999999999998532 357899999999999999999999998
No 8
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=99.68 E-value=8.4e-17 Score=129.50 Aligned_cols=66 Identities=36% Similarity=0.688 Sum_probs=62.3
Q ss_pred cHHHHHHHHHHHHHHHHc-CCChhHHHHHHHHHHHhcCCccccchhh-hcCCCCCCHHHHHHHHHHHH
Q 009303 210 NKNITEIFGKLINIYRAL-GEDRRSFSYYKAIPVIEKLPFKIESADQ-VKGLPGIGKSMQDHIQEIVT 275 (538)
Q Consensus 210 N~~ia~~l~~la~~~e~~-g~~~r~~aY~rAa~~l~~l~~~i~~~~~-l~~lpgIG~~ia~kI~Eil~ 275 (538)
|++|+++|++||+++++. |+.+|++||++||++|+++|++|++++| +.+|||||++|+.+|.|||+
T Consensus 1 N~~i~~~L~~la~~~~~~~~~~~r~~aY~~Aa~~i~~l~~~i~~~~~~~~~l~gIG~~ia~kI~E~le 68 (68)
T PF14716_consen 1 NQEIADALEELADLYELQGGDPFRARAYRRAAAAIKALPYPITSGEEDLKKLPGIGKSIAKKIDEILE 68 (68)
T ss_dssp THHHHHHHHHHHHHHHHTSTSHHHHHHHHHHHHHHHHSSS-HHSHHHHHCTSTTTTHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHhhCCcHHHHHHHHHHHHHHhCCHhHhhHHHHHhhCCCCCHHHHHHHHHHHC
Confidence 899999999999999999 5568999999999999999999999987 99999999999999999986
No 9
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. This entry represents the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone []. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1KDH_A 1KEJ_A 1JMS_A 2IHM_A 3OGU_A 1MQ2_A 2P66_A 7ICI_A 1ZQN_A 1ZQK_A ....
Probab=99.63 E-value=1.5e-16 Score=120.62 Aligned_cols=51 Identities=49% Similarity=1.009 Sum_probs=42.1
Q ss_pred HHHHhhccCCCHHHHHHHHHhCCCCHHHHhh-ccCcchhhhccccchhhhcc
Q 009303 294 ISLFGEVWGIGPATAQKLYEKGHRTLDDLKN-EDSLTHSQRLGLKYFDDIKT 344 (538)
Q Consensus 294 l~lf~~I~GvGpktA~~ly~~GirtledL~~-~~~L~~~q~~Glk~~ed~~~ 344 (538)
|++|++||||||+||++||++|+|||+||++ ...|+..|++|++||+||++
T Consensus 1 l~~f~~I~GVG~~tA~~w~~~G~rtl~Dl~~~~~~Lt~~Q~iGl~yyeD~~q 52 (52)
T PF10391_consen 1 LKLFTGIWGVGPKTARKWYAKGIRTLEDLRKSKSKLTWQQQIGLKYYEDFQQ 52 (52)
T ss_dssp HHHHHTSTT--HHHHHHHHHTT--SHHHHHHGGCGS-HHHHHHHHTHHHHH-
T ss_pred CcchhhcccccHHHHHHHHHhCCCCHHHHhhhhccCCHHHHHHHHHHHHhcC
Confidence 6789999999999999999999999999986 45899999999999999974
No 10
>PRK07945 hypothetical protein; Provisional
Probab=99.58 E-value=8.4e-15 Score=152.94 Aligned_cols=102 Identities=19% Similarity=0.274 Sum_probs=88.6
Q ss_pred HHHHHHHHHHHHHHcCCC-hhHHHHHHHHHHHhcCCcc-ccchh---hhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHh
Q 009303 213 ITEIFGKLINIYRALGED-RRSFSYYKAIPVIEKLPFK-IESAD---QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEK 287 (538)
Q Consensus 213 ia~~l~~la~~~e~~g~~-~r~~aY~rAa~~l~~l~~~-i~~~~---~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~ 287 (538)
-+++|+++|+++|++|+| ||++|||+||.+|+.++.+ +..+. +|.+|||||+++|.||.||++||+++.||+|+.
T Consensus 3 ~~~~l~~~a~lle~~~~n~frv~ayr~aa~~~~~~~~~~~~~~~~~g~l~~~~giG~~~a~~i~e~~~tg~~~~l~~l~~ 82 (335)
T PRK07945 3 PVAALRRIAFLLERARADTYRVRAFRRAADVVEALDAAERARRARAGSLTSLPGIGPKTAKVIAQALAGRVPDYLAELRA 82 (335)
T ss_pred HHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHhcChhHHHHHHhcCCcccCCCcCHHHHHHHHHHHhcCCHHHHHHHHH
Confidence 468999999999999999 6999999999999999999 88774 799999999999999999999999999999998
Q ss_pred hchhHHHHHHhhccCCCHHHHHHHHHh---------CCCCHHHHhh
Q 009303 288 DEKVRTISLFGEVWGIGPATAQKLYEK---------GHRTLDDLKN 324 (538)
Q Consensus 288 ~~~~~~l~lf~~I~GvGpktA~~ly~~---------GirtledL~~ 324 (538)
+..+- | |+..+.++.-. |-.|++|...
T Consensus 83 ~~~~~---------~-g~~l~~~~~~D~H~HT~~Sdg~~~~ee~v~ 118 (335)
T PRK07945 83 DAEPL---------G-GGALRAALRGDLHTHSDWSDGGSPIEEMAR 118 (335)
T ss_pred hhcCC---------c-cHHHHHHHhhhcccccCCCCCCCCHHHHHH
Confidence 76442 7 99999998742 3445666554
No 11
>smart00292 BRCT breast cancer carboxy-terminal domain.
Probab=98.92 E-value=2.4e-09 Score=85.94 Aligned_cols=79 Identities=19% Similarity=0.293 Sum_probs=60.4
Q ss_pred CCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecCC-CccEEEEcCChHHHHHHHHhhhcccCccccccchHHHHH
Q 009303 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSK-KVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSL 95 (538)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls~-~VTHVV~~~~~~~~~~l~~~~~~~~~~~lV~~~Wl~eci 95 (538)
.+|+|+++||.+ .+....+..+.+++.++||++...++. .+||||+.+......... .....+..+|+.+||.+|+
T Consensus 1 ~~f~g~~~~~~g-~~~~~~~~~l~~~i~~~Gg~~~~~~~~~~~thvi~~~~~~~~~~~~--~~~~~~~~iV~~~Wi~~~~ 77 (80)
T smart00292 1 KLFKGKVFVITG-KFDKNERDELKELIEALGGKVTSSLSSKTTTHVIVGSPEGGKLELL--LAIALGIPIVTEDWLLDCL 77 (80)
T ss_pred CccCCeEEEEeC-CCCCccHHHHHHHHHHcCCEEecccCccceeEEEEcCCCCccHHHH--HHHHcCCCCccHHHHHHHH
Confidence 379999999987 455666788899999999999999988 999999976542111111 1112347899999999999
Q ss_pred hcC
Q 009303 96 RLG 98 (538)
Q Consensus 96 k~g 98 (538)
+++
T Consensus 78 ~~~ 80 (80)
T smart00292 78 KAG 80 (80)
T ss_pred HCc
Confidence 875
No 12
>PF00533 BRCT: BRCA1 C Terminus (BRCT) domain; InterPro: IPR001357 The BRCT domain (after the C_terminal domain of a breast cancer susceptibility protein) is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage [], for example as found in the breast cancer DNA-repair protein BRCA1. The domain is an approximately 100 amino acid tandem repeat, which appears to act as a phospho-protein binding domain []. A chitin biosynthesis protein from yeast also seems to belong to this group. ; GO: 0005622 intracellular; PDB: 3L46_A 3AL3_A 3AL2_A 1WF6_A 3II6_X 2NTE_B 3FA2_A 2R1Z_A 2COK_A 2K7F_A ....
Probab=98.91 E-value=2.6e-09 Score=86.73 Aligned_cols=76 Identities=22% Similarity=0.340 Sum_probs=59.0
Q ss_pred CCCCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEcCC-hHHHHHHHHhhhcccCccccccchHHH
Q 009303 15 SNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDL-EALLQQVSKQHLARFKGSVIRYQWLED 93 (538)
Q Consensus 15 ~~~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~~~~-~~~~~~l~~~~~~~~~~~lV~~~Wl~e 93 (538)
...+|+|+++|| .+.....++.+.++++++||.|...+++.+||||+.+. ....+... .......+|+.+||.|
T Consensus 2 ~~~~F~g~~f~i--~~~~~~~~~~l~~~i~~~GG~v~~~~~~~~thvI~~~~~~~~~k~~~---~~~~~i~iV~~~Wi~~ 76 (78)
T PF00533_consen 2 KPKIFEGCTFCI--SGFDSDEREELEQLIKKHGGTVSNSFSKKTTHVIVGNPNKRTKKYKA---AIANGIPIVSPDWIED 76 (78)
T ss_dssp STTTTTTEEEEE--SSTSSSHHHHHHHHHHHTTEEEESSSSTTSSEEEESSSHCCCHHHHH---HHHTTSEEEETHHHHH
T ss_pred CCCCCCCEEEEE--ccCCCCCHHHHHHHHHHcCCEEEeecccCcEEEEeCCCCCccHHHHH---HHHCCCeEecHHHHHH
Confidence 357999999999 66666667778999999999999999999999999765 22222211 1122478999999999
Q ss_pred HH
Q 009303 94 SL 95 (538)
Q Consensus 94 ci 95 (538)
||
T Consensus 77 ci 78 (78)
T PF00533_consen 77 CI 78 (78)
T ss_dssp HH
T ss_pred hC
Confidence 97
No 13
>cd00027 BRCT Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks.
Probab=98.52 E-value=1.8e-07 Score=73.23 Aligned_cols=72 Identities=19% Similarity=0.316 Sum_probs=52.9
Q ss_pred CcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHhhhcccCccccccchHHHHHh
Q 009303 21 GMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSLR 96 (538)
Q Consensus 21 g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~~~~~~~~~~l~~~~~~~~~~~lV~~~Wl~ecik 96 (538)
|+.+||.....+ ..+..+.+++..+||++.+.+++.+||||+.+...... ... ....+..+|+.+|+.||++
T Consensus 1 ~~~~~i~g~~~~-~~~~~l~~~i~~~Gg~v~~~~~~~~thvI~~~~~~~~~-~~~--~~~~~~~iV~~~Wi~~~~~ 72 (72)
T cd00027 1 GLTFVITGDLPS-EERDELKELIEKLGGKVTSSVSKKTTHVIVGSDAGPKK-LLK--AIKLGIPIVTPEWLLDCLK 72 (72)
T ss_pred CCEEEEEecCCC-cCHHHHHHHHHHcCCEEeccccCCceEEEECCCCCchH-HHH--HHHcCCeEecHHHHHHHhC
Confidence 577888665434 44677889999999999999999999999976543211 111 1123478999999999985
No 14
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=97.93 E-value=2.9e-05 Score=88.04 Aligned_cols=83 Identities=23% Similarity=0.350 Sum_probs=68.3
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh-CCCCHHHHhhcc--Ccch
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED--SLTH 330 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~-GirtledL~~~~--~L~~ 330 (538)
++|.+|||+|++++++|.+.+++++...+++ .+..| +|+|||+++|+.|++. | |+++|.++. .|..
T Consensus 466 ~~L~~L~GfG~Ksa~nIl~~Ie~sk~~~l~r--------~L~aL-gIpgVG~~~ak~L~~~f~--sl~~l~~As~eeL~~ 534 (652)
T TIGR00575 466 EDLLELEGFGEKSAQNLLNAIEKSKEKPLAR--------LLFAL-GIRHVGEVTAKNLAKHFG--TLDKLKAASLEELLS 534 (652)
T ss_pred HHHhhccCccHHHHHHHHHHHHHhccCcHHH--------HHhhc-cCCCcCHHHHHHHHHHhC--CHHHHHhCCHHHHhc
Confidence 5789999999999999999999988776664 44555 9999999999999987 6 899998653 5788
Q ss_pred hhhccccchhhhccCcC
Q 009303 331 SQRLGLKYFDDIKTRIP 347 (538)
Q Consensus 331 ~q~~Glk~~ed~~~~i~ 347 (538)
+.+||-+..+.+..-+.
T Consensus 535 i~GIG~~~A~~I~~ff~ 551 (652)
T TIGR00575 535 VEGVGPKVAESIVNFFH 551 (652)
T ss_pred CCCcCHHHHHHHHHHHh
Confidence 88899777777665443
No 15
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=97.88 E-value=8.4e-06 Score=63.81 Aligned_cols=51 Identities=37% Similarity=0.549 Sum_probs=42.4
Q ss_pred HHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhc--cCcchhhhccccchhhhc
Q 009303 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDIK 343 (538)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~GirtledL~~~--~~L~~~q~~Glk~~ed~~ 343 (538)
+...|++|+||||++|++||+.||.|++||.+. ..|..+.++|-+..+.|.
T Consensus 3 ~~~~L~~I~Gig~~~a~~L~~~G~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~ 55 (60)
T PF14520_consen 3 VFDDLLSIPGIGPKRAEKLYEAGIKTLEDLANADPEELAEIPGIGEKTAEKII 55 (60)
T ss_dssp HHHHHHTSTTCHHHHHHHHHHTTCSSHHHHHTSHHHHHHTSTTSSHHHHHHHH
T ss_pred HHHhhccCCCCCHHHHHHHHhcCCCcHHHHHcCCHHHHhcCCCCCHHHHHHHH
Confidence 455677999999999999999999999999864 358888888877766554
No 16
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=97.41 E-value=0.0002 Score=55.99 Aligned_cols=52 Identities=33% Similarity=0.588 Sum_probs=41.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (538)
+++.+|||||+.++.++.+. | +..++++.+-. .+.|.+|+|+|+++|++|.+
T Consensus 5 ~~L~~I~Gig~~~a~~L~~~---G-~~t~~~l~~a~----~~~L~~i~Gig~~~a~~i~~ 56 (60)
T PF14520_consen 5 DDLLSIPGIGPKRAEKLYEA---G-IKTLEDLANAD----PEELAEIPGIGEKTAEKIIE 56 (60)
T ss_dssp HHHHTSTTCHHHHHHHHHHT---T-CSSHHHHHTSH----HHHHHTSTTSSHHHHHHHHH
T ss_pred HhhccCCCCCHHHHHHHHhc---C-CCcHHHHHcCC----HHHHhcCCCCCHHHHHHHHH
Confidence 57889999999999887654 7 66688876532 23466999999999999986
No 17
>KOG3226 consensus DNA repair protein [Replication, recombination and repair]
Probab=97.36 E-value=0.00014 Score=74.93 Aligned_cols=88 Identities=17% Similarity=0.324 Sum_probs=70.1
Q ss_pred CCCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEc-CChHHHHHHHHhhhcccCccccccchHHHH
Q 009303 16 NGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAM-DLEALLQQVSKQHLARFKGSVIRYQWLEDS 94 (538)
Q Consensus 16 ~~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~~-~~~~~~~~l~~~~~~~~~~~lV~~~Wl~ec 94 (538)
+.++.|||+.+ .|+...-+.-|+..|...||..-.+|..+-||.|.. .++...+. ......+||+-+||++|
T Consensus 315 ~klL~GVV~Vl--SGfqNP~Rs~LRskAl~LGAkY~pDW~~gsThLICAF~NTPKy~Q-----V~g~Gg~IV~keWI~~C 387 (508)
T KOG3226|consen 315 SKLLEGVVFVL--SGFQNPERSTLRSKALTLGAKYQPDWNAGSTHLICAFPNTPKYRQ-----VEGNGGTIVSKEWITEC 387 (508)
T ss_pred HHhhhceEEEE--ecccCchHHHHHHHHHhhcccccCCcCCCceeEEEecCCCcchhh-----cccCCceEeeHHHHHHH
Confidence 58999999887 777655567788999999999999999999999973 33322111 11223689999999999
Q ss_pred HhcCcccCcccccccc
Q 009303 95 LRLGEKVSEDLYRIKL 110 (538)
Q Consensus 95 ik~g~lv~e~~y~l~~ 110 (538)
-..+++||+.+|.+.-
T Consensus 388 y~~kk~lp~rrYlm~~ 403 (508)
T KOG3226|consen 388 YAQKKLLPIRRYLMHA 403 (508)
T ss_pred HHHHhhccHHHHHhcC
Confidence 9999999999999864
No 18
>PF12738 PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2WT8_C 3EF1_A 3EF0_A.
Probab=97.13 E-value=0.00034 Score=54.96 Aligned_cols=62 Identities=18% Similarity=0.332 Sum_probs=38.8
Q ss_pred EEEEecCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHhhhcccCccccccch
Q 009303 23 RVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQW 90 (538)
Q Consensus 23 ~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~~~~~~~~~~l~~~~~~~~~~~lV~~~W 90 (538)
+|.+ +++....+.-+.+++..+||.+.+.++.++||+|+.+.... ++.. ....+..+|+++|
T Consensus 2 ~i~~--sg~~~~~~~~l~~~i~~~Gg~~~~~lt~~~THLI~~~~~~~-K~~~---A~~~gi~vV~~~W 63 (63)
T PF12738_consen 2 VICF--SGFSGKERSQLRKLIEALGGKYSKDLTKKTTHLICSSPEGK-KYRK---AKEWGIPVVSPDW 63 (63)
T ss_dssp EEEE--EEB-TTTCCHHHHHHHCTT-EEESSSSTT-SEEEEES--HH-HHHH---HHHCTSEEEEHHH
T ss_pred EEEE--CCCCHHHHHHHHHHHHHCCCEEeccccCCceEEEEeCCCcH-HHHH---HHHCCCcEECCCC
Confidence 4444 33433335667799999999999999999999999554321 2211 1122378999999
No 19
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=97.00 E-value=0.00096 Score=62.01 Aligned_cols=50 Identities=34% Similarity=0.627 Sum_probs=40.7
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHH-hCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009303 252 SADQVKGLPGIGKSMQDHIQEIVT-TGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 252 ~~~~l~~lpgIG~~ia~kI~Eil~-tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (538)
+.+||+.|||||++.|.+|.++-+ .|.+.-+|+ |.+|.|||+++.++|-.
T Consensus 95 s~eeL~~lpgIG~~kA~aIi~yRe~~G~f~sv~d------------L~~v~GiG~~~~ekl~~ 145 (149)
T COG1555 95 SAEELQALPGIGPKKAQAIIDYREENGPFKSVDD------------LAKVKGIGPKTLEKLKD 145 (149)
T ss_pred CHHHHHHCCCCCHHHHHHHHHHHHHcCCCCcHHH------------HHhccCCCHHHHHHHHh
Confidence 357899999999999999999874 445555554 55899999999999854
No 20
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=96.99 E-value=0.00086 Score=57.06 Aligned_cols=35 Identities=34% Similarity=0.353 Sum_probs=31.8
Q ss_pred hHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009303 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~ 325 (538)
...+..|+.|||||+++|+.|+..||+|++||+..
T Consensus 8 ~~~~~~L~~iP~IG~a~a~DL~~LGi~s~~~L~g~ 42 (93)
T PF11731_consen 8 RAGLSDLTDIPNIGKATAEDLRLLGIRSPADLKGR 42 (93)
T ss_pred HHHHHHHhcCCCccHHHHHHHHHcCCCCHHHHhCC
Confidence 44788899999999999999999999999999954
No 21
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=96.92 E-value=0.0013 Score=52.16 Aligned_cols=48 Identities=29% Similarity=0.627 Sum_probs=33.0
Q ss_pred cCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009303 257 KGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 257 ~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (538)
.+|||||+..++.+.+ ++..++.+.+. ..+.|++|+||||++|+.+++
T Consensus 6 LGI~~VG~~~ak~L~~-----~f~sl~~l~~a----~~e~L~~i~gIG~~~A~si~~ 53 (64)
T PF12826_consen 6 LGIPGVGEKTAKLLAK-----HFGSLEALMNA----SVEELSAIPGIGPKIAQSIYE 53 (64)
T ss_dssp CTSTT--HHHHHHHHH-----CCSCHHHHCC------HHHHCTSTT--HHHHHHHHH
T ss_pred CCCCCccHHHHHHHHH-----HcCCHHHHHHc----CHHHHhccCCcCHHHHHHHHH
Confidence 5899999999998875 44556666543 456788999999999999886
No 22
>KOG2481 consensus Protein required for normal rRNA processing [RNA processing and modification]
Probab=96.92 E-value=0.00027 Score=75.73 Aligned_cols=87 Identities=17% Similarity=0.276 Sum_probs=63.7
Q ss_pred CCCCCCCCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEee-c---------CCCccEEEEcCChHHHHHHHHhhhcc
Q 009303 11 PALDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEK-L---------SKKVTHVLAMDLEALLQQVSKQHLAR 80 (538)
Q Consensus 11 ~~~~~~~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~-l---------s~~VTHVV~~~~~~~~~~l~~~~~~~ 80 (538)
..+....+|+|+++|+. +.++ ++.|.-.|++.||.|.-. + +..|||=|++-....... .
T Consensus 320 ~~s~~kslF~glkFfl~-reVP---resL~fiI~s~GG~V~wd~~~~g~~~~~~d~~ITH~IvDrP~~~~~v-----~-- 388 (570)
T KOG2481|consen 320 EQSSHKSLFSGLKFFLN-REVP---RESLEFIIRSFGGKVSWDPLGIGATYDESDERITHQIVDRPGQQTSV-----I-- 388 (570)
T ss_pred hhhhHHHHhhcceeeee-ccCc---hHHHHHHHHHcCCceecCccCCCCcccccccceeeeeecccCcccee-----e--
Confidence 34566799999999884 3455 455666899999999855 1 246999998654321111 1
Q ss_pred cCccccccchHHHHHhcCcccCccccccc
Q 009303 81 FKGSVIRYQWLEDSLRLGEKVSEDLYRIK 109 (538)
Q Consensus 81 ~~~~lV~~~Wl~ecik~g~lv~e~~y~l~ 109 (538)
.-..|.++||-||+.+|.+++.+.|.+-
T Consensus 389 -gR~YvQPQWvfDsvNar~llpt~~Y~~G 416 (570)
T KOG2481|consen 389 -GRTYVQPQWVFDSVNARLLLPTEKYFPG 416 (570)
T ss_pred -eeeeecchhhhhhccchhhccHhhhCCC
Confidence 1257999999999999999999999875
No 23
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=96.83 E-value=0.0043 Score=70.78 Aligned_cols=115 Identities=17% Similarity=0.300 Sum_probs=73.8
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchh
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHS 331 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~~--~L~~~ 331 (538)
+++..|||+|++.+++|.+=++.-+-..|+ +.+--+ .|+|||+++|+.|.+. +.|+++|.++. .|..+
T Consensus 479 ~~L~~l~gfG~Ksa~~ll~~Ie~sk~~~l~--------R~l~al-gi~~IG~~~ak~L~~~-f~sl~~l~~As~eeL~~i 548 (665)
T PRK07956 479 EDLLGLEGFGEKSAQNLLDAIEKSKETSLA--------RFLYAL-GIRHVGEKAAKALARH-FGSLEALRAASEEELAAV 548 (665)
T ss_pred HHHhcCcCcchHHHHHHHHHHHHhhcCCHH--------HhhHhh-hccCcCHHHHHHHHHH-cCCHHHHHhCCHHHHhcc
Confidence 578999999999999988766532222222 344445 9999999999998864 47899998653 57788
Q ss_pred hhccccchhhhccCcCHHHHHH-HHHHHHHHhh-------hcCCCeEEEeccccc
Q 009303 332 QRLGLKYFDDIKTRIPRHEVEQ-MERLLQKAGE-------EVLPEVIILCGGSYR 378 (538)
Q Consensus 332 q~~Glk~~ed~~~~i~r~Ea~~-i~~iv~~~~~-------~~~p~~~v~~~Gs~R 378 (538)
.++|-+..+.+..-+.-.+..+ +..+...-+. ..+.|..+++||.+.
T Consensus 549 ~GIG~~~A~sI~~ff~~~~~~~~i~~L~~~gv~~~~~~~~~~~~g~~~v~TG~l~ 603 (665)
T PRK07956 549 EGVGEVVAQSIVEFFAVEENRELIDELLEAGVNMEYKGEEVDLAGKTVVLTGTLE 603 (665)
T ss_pred CCcCHHHHHHHHHHHhhhhHHHHHHHHHHcCCCccccccCCCccccEEEEeCCCC
Confidence 8899777776665544333222 2333221010 013355677777763
No 24
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=96.81 E-value=0.0022 Score=57.49 Aligned_cols=50 Identities=30% Similarity=0.505 Sum_probs=40.4
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHHh-CCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009303 252 SADQVKGLPGIGKSMQDHIQEIVTT-GKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 252 ~~~~l~~lpgIG~~ia~kI~Eil~t-G~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (538)
+.++|..|||||+..|.+|-++.+. |.+.. ++.|.+|+|||++++.+|.+
T Consensus 66 ~~~eL~~lpGIG~~~A~~Ii~~R~~~g~f~s------------~eeL~~V~GIg~k~~~~i~~ 116 (120)
T TIGR01259 66 SLEELQALPGIGPAKAKAIIEYREENGAFKS------------VDDLTKVSGIGEKSLEKLKD 116 (120)
T ss_pred CHHHHhcCCCCCHHHHHHHHHHHHhcCCcCC------------HHHHHcCCCCCHHHHHHHHh
Confidence 3578999999999999999999864 54443 34456899999999999865
No 25
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=96.79 E-value=0.0018 Score=51.48 Aligned_cols=48 Identities=44% Similarity=0.685 Sum_probs=35.7
Q ss_pred chhhhcCCCCCCHHHHHHHHHHH-HhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHH
Q 009303 252 SADQVKGLPGIGKSMQDHIQEIV-TTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKL 311 (538)
Q Consensus 252 ~~~~l~~lpgIG~~ia~kI~Eil-~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l 311 (538)
+.++|..+||||+..|..|.++- +.|.+..+++|. .|+|+|+++..+|
T Consensus 12 s~~eL~~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL~------------~v~gi~~~~~~~l 60 (65)
T PF12836_consen 12 SAEELQALPGIGPKQAKAIVEYREKNGPFKSLEDLK------------EVPGIGPKTYEKL 60 (65)
T ss_dssp -HHHHHTSTT--HHHHHHHHHHHHHH-S-SSGGGGG------------GSTT--HHHHHHH
T ss_pred CHHHHHHcCCCCHHHHHHHHHHHHhCcCCCCHHHHh------------hCCCCCHHHHHHH
Confidence 46899999999999999999998 677877777754 8999999999887
No 26
>PLN03123 poly [ADP-ribose] polymerase; Provisional
Probab=96.68 E-value=0.0035 Score=73.91 Aligned_cols=90 Identities=16% Similarity=0.338 Sum_probs=67.9
Q ss_pred CCCCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChH--HHHHHHHhhhcccCccccccchHH
Q 009303 15 SNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEA--LLQQVSKQHLARFKGSVIRYQWLE 92 (538)
Q Consensus 15 ~~~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~~~~~~--~~~~l~~~~~~~~~~~lV~~~Wl~ 92 (538)
....|.+++|.+... .+.. ..-|++.+..+||.|....++.+||+|+...-. ..++.+.. ..+.+||+.+||+
T Consensus 390 ~~~~l~~~~i~i~G~-~~~~-~~~~k~~Ie~~GG~~s~~v~~~~t~l~tt~e~~k~~~kv~qAk---~~~ipIVsedwL~ 464 (981)
T PLN03123 390 ESEFLGDLKVSIVGA-SKEK-VTEWKAKIEEAGGVFHATVKKDTNCLVVCGELDDEDAEMRKAR---RMKIPIVREDYLV 464 (981)
T ss_pred cCCCcCCeEEEEecC-CCCc-HHHHHHHHHhcCCEEeeeccCCceEEEccHHhhhcchHHHHHH---hcCCCcccHHHHH
Confidence 346799999999876 3333 367899999999999999999999999864211 11122221 2247899999999
Q ss_pred HHHhcCcccCccccccc
Q 009303 93 DSLRLGEKVSEDLYRIK 109 (538)
Q Consensus 93 ecik~g~lv~e~~y~l~ 109 (538)
||.+.++++|...|.+.
T Consensus 465 ds~~~~~~~p~~~y~~~ 481 (981)
T PLN03123 465 DCFKKKKKLPFDKYKLE 481 (981)
T ss_pred HHHhccccCcchhhhhc
Confidence 99999999999888664
No 27
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=96.49 E-value=0.0039 Score=56.02 Aligned_cols=47 Identities=15% Similarity=0.246 Sum_probs=36.6
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009303 252 SADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 252 ~~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (538)
+..+++.+||||+..|++|. ..|-+..+|+ +.+|+|||+++.+.+-+
T Consensus 59 ~~~el~~lpGigP~~A~~IV---~nGpf~sveD------------L~~V~GIgekqk~~l~k 105 (132)
T PRK02515 59 SVRAFRQFPGMYPTLAGKIV---KNAPYDSVED------------VLNLPGLSERQKELLEA 105 (132)
T ss_pred CHHHHHHCCCCCHHHHHHHH---HCCCCCCHHH------------HHcCCCCCHHHHHHHHH
Confidence 45789999999999999998 3555555554 44899999998877755
No 28
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=96.47 E-value=0.0096 Score=68.12 Aligned_cols=87 Identities=16% Similarity=0.306 Sum_probs=63.3
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchh
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHS 331 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~~--~L~~~ 331 (538)
+++..|+|+|++.+++|.+=++.-+-..|+ ..+--| +|+|||+++|++|.+ .+.|+++|..+. .|...
T Consensus 496 ~~L~~l~g~g~Ksa~~Ll~~Ie~sk~~~l~--------r~l~AL-gIpgIG~~~ak~L~~-~F~si~~L~~As~eeL~~i 565 (689)
T PRK14351 496 ADLAELEGWGETSAENLLAELEASREPPLA--------DFLVAL-GIPEVGPTTARNLAR-EFGTFEAIMDADEEALRAV 565 (689)
T ss_pred HHHhcCcCcchhHHHHHHHHHHHHccCCHH--------HHHHHc-CCCCcCHHHHHHHHH-HhCCHHHHHhCCHHHHhcc
Confidence 578999999999999987766533323333 244446 999999999999975 568899998653 57778
Q ss_pred hhccccchhhhccCcCHHH
Q 009303 332 QRLGLKYFDDIKTRIPRHE 350 (538)
Q Consensus 332 q~~Glk~~ed~~~~i~r~E 350 (538)
.++|-+..+.+.+-+.-.+
T Consensus 566 ~GIG~k~A~sI~~ff~~~~ 584 (689)
T PRK14351 566 DDVGPTVAEEIREFFDSER 584 (689)
T ss_pred CCcCHHHHHHHHHHHhhhH
Confidence 8888777777765554443
No 29
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]
Probab=96.42 E-value=0.0046 Score=69.73 Aligned_cols=92 Identities=14% Similarity=0.191 Sum_probs=72.4
Q ss_pred CCCCCCCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEE-cC--ChHHHHHHHHhhhcccCcccccc
Q 009303 12 ALDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLA-MD--LEALLQQVSKQHLARFKGSVIRY 88 (538)
Q Consensus 12 ~~~~~~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~-~~--~~~~~~~l~~~~~~~~~~~lV~~ 88 (538)
+...+.+|.|+-+++.+.....-+..-|.+.++.+||.++....+..||-|+ .+ +.++... .+.+ ...||++
T Consensus 627 ~~~~s~if~gl~f~Vlsgt~~~~tk~~le~~ivenGG~iv~nv~p~~~~ci~~a~~et~~vk~~----~~~~-~cdVl~p 701 (881)
T KOG0966|consen 627 VAKISNIFDGLEFCVLSGTSETHTKAKLEEIIVENGGKIVQNVGPSDTLCIATAGKETTRVKAQ----AIKR-SCDVLKP 701 (881)
T ss_pred ccchhhhhcCeeEEEecCCcccccHHHHHHHHHHcCCEEEEcCCCCCcceEEeccccchHHHHH----HHhc-cCceeeH
Confidence 4666799999999999988877777889999999999999999988999995 22 2233221 2222 3679999
Q ss_pred chHHHHHhcCcccCccc-ccc
Q 009303 89 QWLEDSLRLGEKVSEDL-YRI 108 (538)
Q Consensus 89 ~Wl~ecik~g~lv~e~~-y~l 108 (538)
+||.+|.+..+++++.+ |.+
T Consensus 702 ~Wlldcc~~~~l~p~~P~~~f 722 (881)
T KOG0966|consen 702 AWLLDCCKKQRLLPWLPRDLF 722 (881)
T ss_pred HHHHHHHhhhhccccccHHHH
Confidence 99999999999999755 444
No 30
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=96.26 E-value=0.0065 Score=58.81 Aligned_cols=53 Identities=15% Similarity=0.265 Sum_probs=37.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHH
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLY 312 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly 312 (538)
.+|.++||||+++|-.| |.+-...++.+.-. .+-...|++|||||+|||+++.
T Consensus 72 ~~L~~V~GIGpK~Al~i---L~~~~~~el~~aI~---~~d~~~L~~ipGiGkKtAerIi 124 (191)
T TIGR00084 72 KELIKVNGVGPKLALAI---LSNMSPEEFVYAIE---TEEVKALVKIPGVGKKTAERLL 124 (191)
T ss_pred HHHhCCCCCCHHHHHHH---HhcCCHHHHHHHHH---hCCHHHHHhCCCCCHHHHHHHH
Confidence 46889999999999888 55444444443222 1223456789999999999997
No 31
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=96.17 E-value=0.02 Score=51.44 Aligned_cols=67 Identities=22% Similarity=0.346 Sum_probs=44.3
Q ss_pred CCCCHHHHHHH--------HHHHHhCCcchhH-HHHhhc--h------hHHHHHHhhccCCCHHHHHHHHHhCCCCHHHH
Q 009303 260 PGIGKSMQDHI--------QEIVTTGKLSKLE-HFEKDE--K------VRTISLFGEVWGIGPATAQKLYEKGHRTLDDL 322 (538)
Q Consensus 260 pgIG~~ia~kI--------~Eil~tG~~~~le-~l~~~~--~------~~~l~lf~~I~GvGpktA~~ly~~GirtledL 322 (538)
||||+..+.+. .++++.|..+.-. ++..+. . ...+--|..|+|||+..|.-|...||+|+++|
T Consensus 1 pgi~~~~~~~L~~~GI~t~~~Ll~~~~~~~~r~~La~~~~i~~~~l~~w~~~AdL~ri~gi~~~~a~LL~~AGv~Tv~~L 80 (122)
T PF14229_consen 1 PGIGPKEAAKLKAAGIKTTGDLLEAGDTPLGRKALAKKLGISERNLLKWVNQADLMRIPGIGPQYAELLEHAGVDTVEEL 80 (122)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHHcCCCHHHHHHHHHhcCCCHHHHHHHHhHHHhhhcCCCCHHHHHHHHHhCcCcHHHH
Confidence 67787777764 4566655543322 121111 1 12233455999999999999999999999999
Q ss_pred hhcc
Q 009303 323 KNED 326 (538)
Q Consensus 323 ~~~~ 326 (538)
.+..
T Consensus 81 A~~~ 84 (122)
T PF14229_consen 81 AQRN 84 (122)
T ss_pred HhCC
Confidence 8643
No 32
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=96.15 E-value=0.011 Score=47.33 Aligned_cols=50 Identities=22% Similarity=0.341 Sum_probs=39.5
Q ss_pred hhhhcC-CCCCCHHHHHHHHHHHH-hCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh
Q 009303 253 ADQVKG-LPGIGKSMQDHIQEIVT-TGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (538)
Q Consensus 253 ~~~l~~-lpgIG~~ia~kI~Eil~-tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 314 (538)
.++|.. +||||...+.+|-+... .|.+. .++.|.+|+|||.++++++++.
T Consensus 15 ~~~L~~~ipgig~~~a~~Il~~R~~~g~~~------------s~~dL~~v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 15 AEELQRAMNGVGLKKAEAIVSYREEYGPFK------------TVEDLKQVPGIGNSLVEKNLAV 66 (69)
T ss_pred HHHHHhHCCCCCHHHHHHHHHHHHHcCCcC------------CHHHHHcCCCCCHHHHHHHHhh
Confidence 467888 99999999999988875 45444 4445668999999999999764
No 33
>PLN03122 Poly [ADP-ribose] polymerase; Provisional
Probab=96.06 E-value=0.012 Score=68.05 Aligned_cols=93 Identities=22% Similarity=0.330 Sum_probs=67.8
Q ss_pred CCCCCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEcCCh--HH-HHHHHHhhhcccCccccccch
Q 009303 14 DSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLE--AL-LQQVSKQHLARFKGSVIRYQW 90 (538)
Q Consensus 14 ~~~~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~~~~~--~~-~~~l~~~~~~~~~~~lV~~~W 90 (538)
.+...|.|++|.|-..- ..+ +.-+++++..+||+|.... .+.||+|+.... .. ...++.. ......||+.+|
T Consensus 185 ~~~kpL~G~~fviTGtl-~~s-r~elK~~Ie~~GGkvsssV-s~~T~lIvt~~ev~k~gsSKlkkA--k~lgIpIVsEd~ 259 (815)
T PLN03122 185 APGKPFSGMMISLSGRL-SRT-HQYWKKDIEKHGGKVANSV-EGVTCLVVSPAERERGGSSKIAEA--MERGIPVVREAW 259 (815)
T ss_pred ccCCCcCCcEEEEeCCC-CCC-HHHHHHHHHHcCCEEcccc-ccceEEEEcCccccccCccHHHHH--HHcCCcCccHHH
Confidence 44567999999997653 334 5678999999999999998 668899874422 11 0112211 122478999999
Q ss_pred HHHHHhcCcccCccccccccC
Q 009303 91 LEDSLRLGEKVSEDLYRIKLD 111 (538)
Q Consensus 91 l~ecik~g~lv~e~~y~l~~~ 111 (538)
|.+|++.++++++..|.+..+
T Consensus 260 L~d~i~~~k~~~~~~y~l~~~ 280 (815)
T PLN03122 260 LIDSIEKQEAQPLEAYDVVSD 280 (815)
T ss_pred HHHHHhcCCcccchhhhhccc
Confidence 999999999999999988533
No 34
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.04 E-value=0.007 Score=58.73 Aligned_cols=52 Identities=17% Similarity=0.283 Sum_probs=37.7
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcch-hHHHHhhchhHHHHHHhhccCCCHHHHHHHH
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSK-LEHFEKDEKVRTISLFGEVWGIGPATAQKLY 312 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~-le~l~~~~~~~~l~lf~~I~GvGpktA~~ly 312 (538)
..|.+++|||+++|-.|-.-+. ..+ .+.+. .+-.+.|++|||||+|||+++.
T Consensus 73 ~~Li~V~GIGpK~Al~ILs~~~---~~~l~~aI~----~~D~~~L~~vpGIGkKtAerIi 125 (194)
T PRK14605 73 ETLIDVSGIGPKLGLAMLSAMN---AEALASAII----SGNAELLSTIPGIGKKTASRIV 125 (194)
T ss_pred HHHhCCCCCCHHHHHHHHHhCC---HHHHHHHHH----hCCHHHHHhCCCCCHHHHHHHH
Confidence 4689999999999998876442 233 22332 2335567899999999999964
No 35
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=95.91 E-value=0.0065 Score=40.88 Aligned_cols=23 Identities=30% Similarity=0.546 Sum_probs=19.5
Q ss_pred cchhhhcCCCCCCHHHHHHHHHH
Q 009303 251 ESADQVKGLPGIGKSMQDHIQEI 273 (538)
Q Consensus 251 ~~~~~l~~lpgIG~~ia~kI~Ei 273 (538)
.+.++|.+|||||+.+|+.|.+|
T Consensus 8 as~eeL~~lpGIG~~tA~~I~~~ 30 (30)
T PF00633_consen 8 ASIEELMKLPGIGPKTANAILSF 30 (30)
T ss_dssp SSHHHHHTSTT-SHHHHHHHHHH
T ss_pred CCHHHHHhCCCcCHHHHHHHHhC
Confidence 36789999999999999999875
No 36
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.90 E-value=0.01 Score=57.48 Aligned_cols=54 Identities=26% Similarity=0.404 Sum_probs=39.3
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (538)
..|.++.|||+++|=.|- .+-... ++..-...+-.+.|++|||||+|||+++.-
T Consensus 72 ~~LisVsGIGPK~ALaIL---s~~~~~---el~~aI~~~D~~~L~~vpGIGkKtAeRIIl 125 (196)
T PRK13901 72 EELIGVDGIGPRAALRVL---SGIKYN---EFRDAIDREDIELISKVKGIGNKMAGKIFL 125 (196)
T ss_pred HHHhCcCCcCHHHHHHHH---cCCCHH---HHHHHHHhCCHHHHhhCCCCCHHHHHHHHH
Confidence 468899999999998764 333333 333333444577889999999999999973
No 37
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=95.88 E-value=0.0098 Score=57.63 Aligned_cols=54 Identities=19% Similarity=0.284 Sum_probs=37.8
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhH-HHHhhchhHHHHHHhhccCCCHHHHHHHHHh
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLE-HFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le-~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 314 (538)
..|..+||||+++|.+|-+... ...+. .+.+. -.+.|++|||||+|+|++++..
T Consensus 73 ~~L~~i~GIGpk~A~~il~~fg---~~~l~~~i~~~----d~~~L~~v~Gig~k~A~~I~~~ 127 (192)
T PRK00116 73 RLLISVSGVGPKLALAILSGLS---PEELVQAIANG----DVKALTKVPGIGKKTAERIVLE 127 (192)
T ss_pred HHHhcCCCCCHHHHHHHHHhCC---HHHHHHHHHhC----CHHHHHhCCCCCHHHHHHHHHH
Confidence 4688899999999999854332 23332 23332 2344669999999999999863
No 38
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.83 E-value=0.011 Score=56.75 Aligned_cols=54 Identities=19% Similarity=0.316 Sum_probs=39.1
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (538)
..|.++.|||+++|=.|- .+-...++-. -...+-.+.|++|||||+|||+++.-
T Consensus 73 ~~Li~VsGIGpK~Al~IL---s~~~~~el~~---aI~~~D~~~L~~vpGIGkKtAeRIil 126 (183)
T PRK14601 73 EMLLKVNGIGANTAMAVC---SSLDVNSFYK---ALSLGDESVLKKVPGIGPKSAKRIIA 126 (183)
T ss_pred HHHhccCCccHHHHHHHH---cCCCHHHHHH---HHHhCCHHHHhhCCCCCHHHHHHHHH
Confidence 468899999999997654 4434444433 23344567889999999999999973
No 39
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=95.74 E-value=0.0066 Score=58.80 Aligned_cols=50 Identities=16% Similarity=0.230 Sum_probs=40.7
Q ss_pred HHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhc------cCcchhhhccccchhhhc
Q 009303 292 RTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE------DSLTHSQRLGLKYFDDIK 343 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~------~~L~~~q~~Glk~~ed~~ 343 (538)
..+.+|.+|+|||||+|..+ .+.-|+++|.++ ++|+.++|||-|..+.|.
T Consensus 69 ~lF~~L~~V~GIGpK~Al~i--L~~~~~~el~~aI~~~d~~~L~~ipGiGkKtAerIi 124 (191)
T TIGR00084 69 ELFKELIKVNGVGPKLALAI--LSNMSPEEFVYAIETEEVKALVKIPGVGKKTAERLL 124 (191)
T ss_pred HHHHHHhCCCCCCHHHHHHH--HhcCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHH
Confidence 46777889999999999999 566678888732 469999999999877654
No 40
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=95.73 E-value=0.0033 Score=61.97 Aligned_cols=51 Identities=25% Similarity=0.520 Sum_probs=41.0
Q ss_pred HHhhccCCCHHHHHHHHHhCCCCHHHHhhcc--CcchhhhccccchhhhccCc
Q 009303 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIKTRI 346 (538)
Q Consensus 296 lf~~I~GvGpktA~~ly~~GirtledL~~~~--~L~~~q~~Glk~~ed~~~~i 346 (538)
.|..|+|||++++++||+.||.|+++|..+. .|..+.++|-+..+.|...+
T Consensus 4 ~L~~IpGIG~krakkLl~~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l 56 (232)
T PRK12766 4 ELEDISGVGPSKAEALREAGFESVEDVRAADQSELAEVDGIGNALAARIKADV 56 (232)
T ss_pred ccccCCCcCHHHHHHHHHcCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHHh
Confidence 4668999999999999999999999999764 57777788866655554443
No 41
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.60 E-value=0.015 Score=56.08 Aligned_cols=54 Identities=13% Similarity=0.128 Sum_probs=39.0
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (538)
..|.++.|||+++|=.|-. +-.. +++..-...+-.+.|++|||||+|||+++.-
T Consensus 73 ~~Li~V~GIGpK~AL~iLs---~~~~---~el~~aI~~~D~~~L~~vpGIGkKtAerIil 126 (188)
T PRK14606 73 LSLTKVSRLGPKTALKIIS---NEDA---ETLVTMIASQDVEGLSKLPGISKKTAERIVM 126 (188)
T ss_pred HHHhccCCccHHHHHHHHc---CCCH---HHHHHHHHhCCHHHHhhCCCCCHHHHHHHHH
Confidence 4588999999999987653 3233 3333333445577889999999999999963
No 42
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.60 E-value=0.013 Score=57.23 Aligned_cols=54 Identities=19% Similarity=0.212 Sum_probs=39.6
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (538)
..|.++.|||+++|-.|- .+-...++ ..-...+-.+.|++|||||+|||+++.-
T Consensus 74 ~~Li~V~GIGpK~Al~iL---s~~~~~~l---~~aI~~~D~~~L~~ipGIGkKtAerIil 127 (203)
T PRK14602 74 IVLISISKVGAKTALAIL---SQFRPDDL---RRLVAEEDVAALTRVSGIGKKTAQHIFL 127 (203)
T ss_pred HHHhCCCCcCHHHHHHHH---hhCCHHHH---HHHHHhCCHHHHhcCCCcCHHHHHHHHH
Confidence 468999999999998764 33333333 3333444577899999999999999963
No 43
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.54 E-value=0.017 Score=56.28 Aligned_cols=54 Identities=15% Similarity=0.247 Sum_probs=38.4
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (538)
..|.++.|||+++|=.| |.+....++ ..-...+-.+.|++|||||+|||+++.-
T Consensus 72 ~~L~~V~GIGpK~AL~i---Ls~~~~~~l---~~aI~~~D~~~L~kvpGIGkKtAerIil 125 (197)
T PRK14603 72 ELLLGVSGVGPKLALAL---LSALPPALL---ARALLEGDARLLTSASGVGKKLAERIAL 125 (197)
T ss_pred HHHhCcCCcCHHHHHHH---HcCCCHHHH---HHHHHhCCHHHHhhCCCCCHHHHHHHHH
Confidence 46889999999999765 444444443 3323344567788999999999999963
No 44
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=95.51 E-value=0.015 Score=65.40 Aligned_cols=76 Identities=30% Similarity=0.458 Sum_probs=55.4
Q ss_pred CCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEc-CCh----HHHHHHHHhhhcccCccccccchHHHHHhcCcccCcc
Q 009303 30 GVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAM-DLE----ALLQQVSKQHLARFKGSVIRYQWLEDSLRLGEKVSED 104 (538)
Q Consensus 30 ~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~~-~~~----~~~~~l~~~~~~~~~~~lV~~~Wl~ecik~g~lv~e~ 104 (538)
+..+.-.+.+..+++. ++...+.+.|||||+. +.+ +.++.+.. .+. +.+|++..|+.+||+++++|+|+
T Consensus 485 ~l~p~ek~~v~~~a~~---t~~k~~~~~~thvi~~~~~~g~c~rTlk~~~g-il~--gkwi~~~~w~~~s~k~~~~~~ee 558 (684)
T KOG4362|consen 485 GLTPSEKQLVEKFAVD---TISKFWIEPVTHVIASTDLEGACLRTLKVLMG-ILR--GKWILSYDWVLASLKLRKWVSEE 558 (684)
T ss_pred cCCcchHHHHHHHHHH---HHhhccCCCceeeeeecccccchhhhHHHHHH-hhc--CceeeeHHHHHHHHHhcCCCCCC
Confidence 3334556777777777 6777788999999983 322 34443321 222 25899999999999999999999
Q ss_pred ccccccC
Q 009303 105 LYRIKLD 111 (538)
Q Consensus 105 ~y~l~~~ 111 (538)
.|-|.++
T Consensus 559 pfEl~~d 565 (684)
T KOG4362|consen 559 PFELQID 565 (684)
T ss_pred CeeEeec
Confidence 9999875
No 45
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.48 E-value=0.018 Score=55.99 Aligned_cols=54 Identities=20% Similarity=0.346 Sum_probs=39.0
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (538)
..|.++.|||+++|=.|- .+....++-. -...+-.+.|++|||||+|||+++.-
T Consensus 73 ~~Li~V~GIGpK~Al~iL---s~~~~~el~~---aI~~~D~~~L~kvpGIGkKtAerIil 126 (195)
T PRK14604 73 ELLIGVSGVGPKAALNLL---SSGTPDELQL---AIAGGDVARLARVPGIGKKTAERIVL 126 (195)
T ss_pred HHHhCcCCcCHHHHHHHH---cCCCHHHHHH---HHHhCCHHHHhhCCCCCHHHHHHHHH
Confidence 468899999999997654 4444444433 23334567788999999999999963
No 46
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=95.41 E-value=0.014 Score=39.27 Aligned_cols=22 Identities=32% Similarity=0.477 Sum_probs=17.3
Q ss_pred HHHHHHhhccCCCHHHHHHHHH
Q 009303 292 RTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~ 313 (538)
..++.|++||||||+||..+..
T Consensus 8 as~eeL~~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 8 ASIEELMKLPGIGPKTANAILS 29 (30)
T ss_dssp SSHHHHHTSTT-SHHHHHHHHH
T ss_pred CCHHHHHhCCCcCHHHHHHHHh
Confidence 3567778999999999998764
No 47
>COG5163 NOP7 Protein required for biogenesis of the 60S ribosomal subunit [Translation, ribosomal structure and biogenesis]
Probab=95.28 E-value=0.015 Score=60.88 Aligned_cols=86 Identities=20% Similarity=0.347 Sum_probs=60.3
Q ss_pred CCCCCCCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeec-----------CCCccEEEEcCChHHHHHHHHhhhcc
Q 009303 12 ALDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKL-----------SKKVTHVLAMDLEALLQQVSKQHLAR 80 (538)
Q Consensus 12 ~~~~~~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~l-----------s~~VTHVV~~~~~~~~~~l~~~~~~~ 80 (538)
.++-..+|+++++|+-. .++ ...|.-.++..||.|...- +..|||-|++.. +++ ++...
T Consensus 344 ~Ss~~slFS~f~Fyisr-eVp---~dsLefiilscGG~V~~~p~~~~i~~~~~vD~~vth~i~drp--~~~----~kveg 413 (591)
T COG5163 344 CSSLKSLFSGFKFYISR-EVP---GDSLEFIILSCGGSVVGSPCEADIHVSEKVDEKVTHQIVDRP--VMK----NKVEG 413 (591)
T ss_pred CcchhhhhhceEEEEec-ccc---chHHHHHHHHcCCcccCchhhccCCchhhccchhhhhhccch--hhh----hhhcc
Confidence 45556999999998843 333 2345567999999987532 345888887543 211 11111
Q ss_pred cCccccccchHHHHHhcCcccCccccccc
Q 009303 81 FKGSVIRYQWLEDSLRLGEKVSEDLYRIK 109 (538)
Q Consensus 81 ~~~~lV~~~Wl~ecik~g~lv~e~~y~l~ 109 (538)
.-.+.++|+-|||..|.+++.+.|.+-
T Consensus 414 --rtYiQPQw~fDsiNkG~l~~~~~Y~~G 440 (591)
T COG5163 414 --RTYIQPQWLFDSINKGKLACVENYCVG 440 (591)
T ss_pred --eeeechHHHHhhhccccchhhhhcccc
Confidence 357999999999999999999999874
No 48
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]
Probab=95.25 E-value=0.048 Score=61.82 Aligned_cols=90 Identities=20% Similarity=0.263 Sum_probs=59.8
Q ss_pred CCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecC------CCccEEEEc--CChHHHHHHHHh-hhcccCccccc
Q 009303 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLS------KKVTHVLAM--DLEALLQQVSKQ-HLARFKGSVIR 87 (538)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls------~~VTHVV~~--~~~~~~~~l~~~-~~~~~~~~lV~ 87 (538)
..|..+++|.+.++.-.+-..+..-.+...|++|.+.-+ ..+||+|+. +.+-...++... .+... -+||.
T Consensus 783 ~~~~~~~~f~~~~~~~~se~~~~~l~~k~~g~~i~~~~~~~~~~~~~~t~~v~~~i~~~h~~~~~~~~~~lt~~-rkv~~ 861 (881)
T KOG0966|consen 783 LFLSSLRMFYVLRRKLSSEEVIIELKLKNFGGRITDAQSECNNIGAKYTHCVLRCIDEDHEKIKEQKKASLTIK-RKVVA 861 (881)
T ss_pred cccccceeeecccccccHHHHHHHHHHHHhcceeeeccchhhhcccceeeeeeeecchHHHHHHHHHHHHhccc-ccccC
Confidence 556667777666655444455555556666999998653 458999985 332222233322 22222 38999
Q ss_pred cchHHHHHhcCcccCccccc
Q 009303 88 YQWLEDSLRLGEKVSEDLYR 107 (538)
Q Consensus 88 ~~Wl~ecik~g~lv~e~~y~ 107 (538)
.+||.+|+.++.+++|+.|.
T Consensus 862 ~~wv~~s~~~~~~~~e~~~~ 881 (881)
T KOG0966|consen 862 PSWVDHSINENCLLPEEDFP 881 (881)
T ss_pred HHHHHHhhcccccCccccCC
Confidence 99999999999999999883
No 49
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=95.00 E-value=0.019 Score=53.42 Aligned_cols=52 Identities=27% Similarity=0.507 Sum_probs=41.0
Q ss_pred hhHHHHHHhhccCCCHHHHHHHHH---h-C-CCCHHHHhhccCcchhhhccccchhhhccCcC
Q 009303 290 KVRTISLFGEVWGIGPATAQKLYE---K-G-HRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIP 347 (538)
Q Consensus 290 ~~~~l~lf~~I~GvGpktA~~ly~---~-G-irtledL~~~~~L~~~q~~Glk~~ed~~~~i~ 347 (538)
..-..+.|..+||||+++|+.+.+ + | |+|+|||.+ .+++|-+.++.+..+|.
T Consensus 92 NtAs~eeL~~lpgIG~~kA~aIi~yRe~~G~f~sv~dL~~------v~GiG~~~~ekl~~~i~ 148 (149)
T COG1555 92 NTASAEELQALPGIGPKKAQAIIDYREENGPFKSVDDLAK------VKGIGPKTLEKLKDYIT 148 (149)
T ss_pred cccCHHHHHHCCCCCHHHHHHHHHHHHHcCCCCcHHHHHh------ccCCCHHHHHHHHhhcc
Confidence 344556668999999999999985 2 4 899999986 57889888888776553
No 50
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=94.96 E-value=0.011 Score=67.42 Aligned_cols=52 Identities=21% Similarity=0.287 Sum_probs=43.6
Q ss_pred hhccCCCHHHHHHHHHh-CCCCHHHHhh--ccCcchhhhccccchhhhccCcCHH
Q 009303 298 GEVWGIGPATAQKLYEK-GHRTLDDLKN--EDSLTHSQRLGLKYFDDIKTRIPRH 349 (538)
Q Consensus 298 ~~I~GvGpktA~~ly~~-GirtledL~~--~~~L~~~q~~Glk~~ed~~~~i~r~ 349 (538)
++|+|+||+++++||+. +|++++||.. .++|..+.+||-+..+.+.+.|-..
T Consensus 448 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~ll~~Ie~s 502 (665)
T PRK07956 448 MDIDGLGEKIIEQLFEKGLIHDPADLFKLTAEDLLGLEGFGEKSAQNLLDAIEKS 502 (665)
T ss_pred cCCCCcCHHHHHHHHHcCCCCCHHHHHhcCHHHHhcCcCcchHHHHHHHHHHHHh
Confidence 37999999999999998 7899999984 3468888999999998887655444
No 51
>cd05397 NT_Pol-beta-like Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins. This superfamily includes the NT domains of DNA polymerase beta and other family X DNA polymerases, as well as the NT domains of Class I and Class II CCA-adding enzymes, RelA- and SpoT-like ppGpp synthetases and hydrolases, 2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), poly (A) polymerases, terminal uridylyl transferases, and Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. The Escherichia coli CCA-adding enzyme belongs to this superfamily but is not included as this enzyme lacks the N-terminal helix conserved in the remainder of the superfamily. In the majority of the Pol beta-like superfamily NTs, two carboxylates, Dx[D/E], together with a third more distal carboxylate coordinate two divalent metal cations that are essential for catalysis. These divalent metal ions are
Probab=94.91 E-value=0.044 Score=41.04 Aligned_cols=28 Identities=29% Similarity=0.458 Sum_probs=23.5
Q ss_pred cCCCeEEEecccccccCC-cCCCeeEEEe
Q 009303 365 VLPEVIILCGGSYRRGKA-SCGDLDVVIM 392 (538)
Q Consensus 365 ~~p~~~v~~~Gs~RRgke-~~~DVDiLit 392 (538)
..+...+.+.|||.||.. ..+|||+++.
T Consensus 14 ~~~~~~v~lfGS~arg~~~~~SDIDi~v~ 42 (49)
T cd05397 14 LVPGYEIVVYGSLVRGLLKKSSDIDLACV 42 (49)
T ss_pred hcCCcEEEEECCcCCCCCCCCCCEEEEEE
Confidence 345668999999999977 6789999986
No 52
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=94.68 E-value=0.038 Score=53.84 Aligned_cols=54 Identities=19% Similarity=0.265 Sum_probs=40.3
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (538)
..|.++.|||+++|=.| |.+....++-.. ...+-...|+++||||+|||+++.-
T Consensus 73 ~~LisVnGIGpK~ALai---Ls~~~~~~l~~a---I~~~d~~~L~k~PGIGkKtAerivl 126 (201)
T COG0632 73 RLLISVNGIGPKLALAI---LSNLDPEELAQA---IANEDVKALSKIPGIGKKTAERIVL 126 (201)
T ss_pred HHHHccCCccHHHHHHH---HcCCCHHHHHHH---HHhcChHhhhcCCCCCHHHHHHHHH
Confidence 46899999999999765 444444444433 3344567889999999999999974
No 53
>PTZ00418 Poly(A) polymerase; Provisional
Probab=94.61 E-value=0.33 Score=54.42 Aligned_cols=52 Identities=23% Similarity=0.381 Sum_probs=42.2
Q ss_pred CCCeEEEecccccccCCc-CCCeeEEEecCCcchhhhhHHHHHHHHHHcCccc
Q 009303 366 LPEVIILCGGSYRRGKAS-CGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLR 417 (538)
Q Consensus 366 ~p~~~v~~~Gs~RRgke~-~~DVDiLit~~~~~~~~~~l~~vv~~L~~~g~l~ 417 (538)
..+.++...||||-|.-. +.|||.|+-.|..-....||..+.+.|.+..-++
T Consensus 124 ~~~g~I~tfGSYrLGV~~pgSDID~L~V~P~~vtredFF~~f~~~L~~~~~V~ 176 (593)
T PTZ00418 124 QISGKLFTFGSYRLGVVAPGSDIDTLCLAPRHITRESFFSDFYAKLQQDPNIT 176 (593)
T ss_pred cCCeEEEEeccccccCCCCCCcccEEEECCCCCCHHHHHHHHHHHHhcCCCcc
Confidence 356788889999999876 6799999999876666789998989888876554
No 54
>PRK14973 DNA topoisomerase I; Provisional
Probab=94.56 E-value=0.037 Score=65.52 Aligned_cols=90 Identities=19% Similarity=0.162 Sum_probs=58.6
Q ss_pred hhhcCCCCCCHHHHHHHHHHHH-h-CCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccc
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVT-T-GKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLT 329 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~-t-G~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~~--~L~ 329 (538)
++|..+|||...+.......+. . +.-..-...+.....+.-+ |..|.|||++|+..++..|+.|.|||.+++ +|+
T Consensus 835 ~~La~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e-l~~vkg~ge~t~~~l~~ag~~~~e~l~~~d~~~la 913 (936)
T PRK14973 835 AYLALKTGISPETICRHAKLVCEKLGRPVPEKISKAAFERGRAE-LLSVPGLGETTLEKLYLAGVYDGDLLVSADPKKLA 913 (936)
T ss_pred HHHhcCCCCChhhHHHHHHHHHHHhcCCCchhhhhhhhcccchh-hhhccCCCHHHHHHHHHcCCCCHHHhccCCHHHHh
Confidence 5678888888776666654443 1 1111111111111112223 449999999999999999999999999764 577
Q ss_pred hhhhccccchhhhcc
Q 009303 330 HSQRLGLKYFDDIKT 344 (538)
Q Consensus 330 ~~q~~Glk~~ed~~~ 344 (538)
..-+++.+....|..
T Consensus 914 ~~~~i~~k~~~~~~~ 928 (936)
T PRK14973 914 KVTGIDEKKLRNLQA 928 (936)
T ss_pred hhcCCCHHHHHHHHH
Confidence 777788777666654
No 55
>PF11798 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 This helix-hairpin-helix motif is found in proteins belonging to the type-Y family of DNA polymerases []. This type of polymerases are thought to be involved in UV protection and mutation [, ]. ; PDB: 3PZP_B 2OH2_B 2W7O_B 3IN5_B 1T94_A 2W7P_B 2W8K_A 2AGQ_A 1RYR_A 3RAX_A ....
Probab=94.53 E-value=0.021 Score=38.98 Aligned_cols=20 Identities=45% Similarity=0.790 Sum_probs=16.3
Q ss_pred HhhccCCCHHHHHHHHHhCC
Q 009303 297 FGEVWGIGPATAQKLYEKGH 316 (538)
Q Consensus 297 f~~I~GvGpktA~~ly~~Gi 316 (538)
+.++||||++|+++|.+.||
T Consensus 13 i~~~~GIG~kt~~kL~~~GI 32 (32)
T PF11798_consen 13 IRKFWGIGKKTAKKLNKLGI 32 (32)
T ss_dssp GGGSTTS-HHHHHHHHCTT-
T ss_pred HHhhCCccHHHHHHHHHccC
Confidence 46899999999999988886
No 56
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=94.51 E-value=0.1 Score=58.73 Aligned_cols=49 Identities=18% Similarity=0.310 Sum_probs=27.5
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009303 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (538)
..+||+||+.+|..+..... .++.+.. ...+.+..|+|||++.|+.+++
T Consensus 513 aLGIr~VG~~~Ak~La~~f~-----sl~~l~~----a~~e~l~~i~giG~~vA~si~~ 561 (667)
T COG0272 513 ALGIRHVGETTAKSLARHFG-----TLEALLA----ASEEELASIPGIGEVVARSIIE 561 (667)
T ss_pred HcCCchhhHHHHHHHHHHhh-----hHHHHHh----cCHHHHhhccchhHHHHHHHHH
Confidence 46677777777766665222 2444332 1344455677777777766654
No 57
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=94.50 E-value=0.036 Score=49.68 Aligned_cols=48 Identities=27% Similarity=0.483 Sum_probs=37.6
Q ss_pred HHHHHHhhccCCCHHHHHHHHHh-----CCCCHHHHhhccCcchhhhccccchhhhccC
Q 009303 292 RTISLFGEVWGIGPATAQKLYEK-----GHRTLDDLKNEDSLTHSQRLGLKYFDDIKTR 345 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~-----GirtledL~~~~~L~~~q~~Glk~~ed~~~~ 345 (538)
-..+.|+++||||+++|+++++. ++.|++||.+ ..++|.+.++.+...
T Consensus 65 A~~~eL~~lpGIG~~~A~~Ii~~R~~~g~f~s~eeL~~------V~GIg~k~~~~i~~~ 117 (120)
T TIGR01259 65 ASLEELQALPGIGPAKAKAIIEYREENGAFKSVDDLTK------VSGIGEKSLEKLKDY 117 (120)
T ss_pred CCHHHHhcCCCCCHHHHHHHHHHHHhcCCcCCHHHHHc------CCCCCHHHHHHHHhc
Confidence 35666779999999999999964 5899999965 567787777776554
No 58
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=94.48 E-value=0.073 Score=60.83 Aligned_cols=84 Identities=14% Similarity=0.224 Sum_probs=60.7
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhc--------
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE-------- 325 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~-------- 325 (538)
+++.+|+|+|++.+++|.+=++.-+-..|+ +.|--| +|++||.++|+.|-+..+.|++.|.+.
T Consensus 470 ~~l~~l~g~geksa~nl~~~Ie~sk~~~l~--------r~l~AL-GI~~vG~~~ak~La~~~f~~~~~l~~~~~~~~~~~ 540 (669)
T PRK14350 470 DRLINLKGFKDKRINNLKRSIEASKKRPFS--------KLLLSM-GIKDLGENTILLLINNNLNSFDKISTLCQDREFAL 540 (669)
T ss_pred HHHhhccCccHHHHHHHHHHHHHHhCCCHH--------HHHHHc-CCCchhHHHHHHHHHHhhCCHHHHHhhhhccCCCH
Confidence 688899999999888877655433322232 345556 899999999999887788999988752
Q ss_pred cCcchhhhccccchhhhccCc
Q 009303 326 DSLTHSQRLGLKYFDDIKTRI 346 (538)
Q Consensus 326 ~~L~~~q~~Glk~~ed~~~~i 346 (538)
..|..+.+||-...+.+.+-+
T Consensus 541 e~l~~i~giG~~~a~si~~ff 561 (669)
T PRK14350 541 SKLLKIKGIGEKIALNIIEAF 561 (669)
T ss_pred HHHhhCCCccHHHHHHHHHHH
Confidence 147778888877666665544
No 59
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.46 E-value=0.04 Score=53.17 Aligned_cols=53 Identities=13% Similarity=0.096 Sum_probs=37.4
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (538)
..|.++.|||+++|=.|- .+-...++-.. ...+-.+.| +|||||+|||+++.-
T Consensus 73 ~~LisV~GIGpK~Al~iL---s~~~~~~l~~a---I~~~D~~~L-~vpGIGkKtAerIil 125 (186)
T PRK14600 73 RMLVKVSGVNYKTAMSIL---SKLTPEQLFSA---IVNEDKAAL-KVNGIGEKLINRIIT 125 (186)
T ss_pred HHHhCcCCcCHHHHHHHH---ccCCHHHHHHH---HHcCCHhhe-ECCCCcHHHHHHHHH
Confidence 468899999999997654 44444444332 223335677 899999999999963
No 60
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=94.38 E-value=0.018 Score=65.75 Aligned_cols=62 Identities=24% Similarity=0.392 Sum_probs=47.3
Q ss_pred hhccCCCHHHHHHHHHh-CCCCHHHHhh--ccCcchhhhccccchhhhccCcCHHHHHHHHHHHH
Q 009303 298 GEVWGIGPATAQKLYEK-GHRTLDDLKN--EDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQ 359 (538)
Q Consensus 298 ~~I~GvGpktA~~ly~~-GirtledL~~--~~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~iv~ 359 (538)
++|+|+|++++++||++ +|++++||.. ..+|..+.+||-+..+.|.+.|-...-..+.+++.
T Consensus 435 l~I~GLG~k~i~~L~~~g~I~~~~Dl~~L~~~~L~~L~GfG~Ksa~nIl~~Ie~sk~~~l~r~L~ 499 (652)
T TIGR00575 435 MDIEGLGDKVIEQLFEKKLVRSVADLYALKKEDLLELEGFGEKSAQNLLNAIEKSKEKPLARLLF 499 (652)
T ss_pred cCCCCcCHHHHHHHHHcCCcCCHHHHHhcCHHHHhhccCccHHHHHHHHHHHHHhccCcHHHHHh
Confidence 47999999999999998 6899999984 35688889999998888876554443333334433
No 61
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=94.30 E-value=0.051 Score=48.98 Aligned_cols=32 Identities=22% Similarity=0.380 Sum_probs=28.4
Q ss_pred HHHHHhhccCCCHHHHHHHHHh-CCCCHHHHhh
Q 009303 293 TISLFGEVWGIGPATAQKLYEK-GHRTLDDLKN 324 (538)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~-GirtledL~~ 324 (538)
..+.|.++|||||++|+++.+. .++|+|||.+
T Consensus 59 ~~~el~~lpGigP~~A~~IV~nGpf~sveDL~~ 91 (132)
T PRK02515 59 SVRAFRQFPGMYPTLAGKIVKNAPYDSVEDVLN 91 (132)
T ss_pred CHHHHHHCCCCCHHHHHHHHHCCCCCCHHHHHc
Confidence 4566779999999999999987 6999999986
No 62
>PRK02362 ski2-like helicase; Provisional
Probab=94.21 E-value=0.034 Score=64.55 Aligned_cols=56 Identities=25% Similarity=0.421 Sum_probs=41.5
Q ss_pred HHHhhchhHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhc--cCcchhhhccccchhhh
Q 009303 284 HFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDI 342 (538)
Q Consensus 284 ~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~--~~L~~~q~~Glk~~ed~ 342 (538)
.+....+...+.|+ +|||||+++|+++|+.||+|++||.+. .+|..+ ||-+..+.+
T Consensus 642 ~l~~gv~~~~~~L~-~ip~i~~~~a~~l~~~gi~s~~dl~~~~~~~l~~~--~g~~~~~~i 699 (737)
T PRK02362 642 RVEYGVREELLDLV-GLRGVGRVRARRLYNAGIESRADLRAADKSVVLAI--LGEKIAENI 699 (737)
T ss_pred HHHhCCCHHHHHHh-CCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHHH--HCHHHHHHH
Confidence 34455566677777 899999999999999999999999953 245544 665544433
No 63
>cd05402 NT_PAP_TUTase Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases. Poly(A) polymerases (PAPs) catalyze mRNA poly(A) tail synthesis, and terminal uridylyl transferases (TUTases) uridylate RNA. PAPs in this subgroup include human PAP alpha, mouse testis-specific cytoplasmic PAP beta, human nuclear PAP gamma, Saccharomyces cerevisiae PAP1, TRF4 and-5, Schizosaccharomyces pombe caffeine-induced death proteins -1, and -14, Caenorhabditis elegans Germ Line Development-2, and Chlamydomonas reinhardtii MUT68. This family also includes human U6 snRNA-specific TUTase1, and Trypanosoma brucei 3'-TUTase-1,-2, and 4. This family belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. For the majority of proteins in this family, these carboxyla
Probab=94.14 E-value=0.19 Score=43.83 Aligned_cols=59 Identities=25% Similarity=0.449 Sum_probs=45.2
Q ss_pred HHHHHHHHHhhhcCCCeEEEecccccccCC-cCCCeeEEEecCCc-chhhhhHHHHHHHHHHcCc
Q 009303 353 QMERLLQKAGEEVLPEVIILCGGSYRRGKA-SCGDLDVVIMHPDR-KSHKGFLSKYVKKLKEMKF 415 (538)
Q Consensus 353 ~i~~iv~~~~~~~~p~~~v~~~Gs~RRgke-~~~DVDiLit~~~~-~~~~~~l~~vv~~L~~~g~ 415 (538)
.+++++++ ..|++.+.+-||++.|.. ..+|||+.|..++. .....++..+-+.|++.+.
T Consensus 8 ~l~~~i~~----~~~~~~v~~fGS~~~g~~~~~SDiDl~i~~~~~~~~~~~~l~~l~~~l~~~~~ 68 (114)
T cd05402 8 RLQELIKE----WFPGAKLYPFGSYVTGLGLPGSDIDLCLLGPNHRVDREDFLRKLAKLLKKSGE 68 (114)
T ss_pred HHHHHHHH----HCCCCEEEEecccccCCCCCCCCeeEEEEeCCCCccHHHHHHHHHHHHHhCCC
Confidence 34555554 578999999999999954 46899999998876 4556788888888888774
No 64
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=93.84 E-value=0.068 Score=42.80 Aligned_cols=44 Identities=18% Similarity=0.272 Sum_probs=33.6
Q ss_pred HHhh-ccCCCHHHHHHHHHh-----CCCCHHHHhhccCcchhhhccccchhhhccC
Q 009303 296 LFGE-VWGIGPATAQKLYEK-----GHRTLDDLKNEDSLTHSQRLGLKYFDDIKTR 345 (538)
Q Consensus 296 lf~~-I~GvGpktA~~ly~~-----GirtledL~~~~~L~~~q~~Glk~~ed~~~~ 345 (538)
.|.. ++|||+++|+++.+. ++++++||.+ ..++|.+.++.+...
T Consensus 17 ~L~~~ipgig~~~a~~Il~~R~~~g~~~s~~dL~~------v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 17 ELQRAMNGVGLKKAEAIVSYREEYGPFKTVEDLKQ------VPGIGNSLVEKNLAV 66 (69)
T ss_pred HHHhHCCCCCHHHHHHHHHHHHHcCCcCCHHHHHc------CCCCCHHHHHHHHhh
Confidence 4556 999999999999975 5999999975 456777666665543
No 65
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=93.82 E-value=0.056 Score=42.91 Aligned_cols=47 Identities=30% Similarity=0.519 Sum_probs=32.5
Q ss_pred HHHHHhhccCCCHHHHHHHHH---h--CCCCHHHHhhccCcchhhhccccchhhhccC
Q 009303 293 TISLFGEVWGIGPATAQKLYE---K--GHRTLDDLKNEDSLTHSQRLGLKYFDDIKTR 345 (538)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~---~--GirtledL~~~~~L~~~q~~Glk~~ed~~~~ 345 (538)
..+.|.++||||++.|+++++ + +++|++||.. ..++|.+.|+.+...
T Consensus 12 s~~eL~~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL~~------v~gi~~~~~~~l~~~ 63 (65)
T PF12836_consen 12 SAEELQALPGIGPKQAKAIVEYREKNGPFKSLEDLKE------VPGIGPKTYEKLKPY 63 (65)
T ss_dssp -HHHHHTSTT--HHHHHHHHHHHHHH-S-SSGGGGGG------STT--HHHHHHHCCC
T ss_pred CHHHHHHcCCCCHHHHHHHHHHHHhCcCCCCHHHHhh------CCCCCHHHHHHHHhh
Confidence 556677999999999999985 2 7999999986 567777777776654
No 66
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=93.61 E-value=0.039 Score=53.48 Aligned_cols=51 Identities=24% Similarity=0.275 Sum_probs=38.3
Q ss_pred HHHHHhhccCCCHHHHHHHHHh-CCCCHHHHhhcc---Ccchhhhccccchhhhc
Q 009303 293 TISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED---SLTHSQRLGLKYFDDIK 343 (538)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~-GirtledL~~~~---~L~~~q~~Glk~~ed~~ 343 (538)
.+..|.+|+|||||+|.++.+. |..++.+....+ .|+..+|+|.+..+.+.
T Consensus 71 ~f~~L~~i~GIGpk~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~ 125 (192)
T PRK00116 71 LFRLLISVSGVGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIV 125 (192)
T ss_pred HHHHHhcCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHH
Confidence 4656779999999999999987 887776544322 58888888877765544
No 67
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.50 E-value=0.036 Score=53.81 Aligned_cols=52 Identities=19% Similarity=0.255 Sum_probs=39.9
Q ss_pred hHHHHHHhhccCCCHHHHHHHHHh-CCCCHHHHh-hc--cCcchhhhccccchhhh
Q 009303 291 VRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLK-NE--DSLTHSQRLGLKYFDDI 342 (538)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~-GirtledL~-~~--~~L~~~q~~Glk~~ed~ 342 (538)
...+++|.+|+|||||+|..+... +...|-+.. +. ..|++.+|+|-|..+.+
T Consensus 69 r~lF~~Li~V~GIGpK~Al~ILs~~~~~~l~~aI~~~D~~~L~~vpGIGkKtAerI 124 (194)
T PRK14605 69 LSLFETLIDVSGIGPKLGLAMLSAMNAEALASAIISGNAELLSTIPGIGKKTASRI 124 (194)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHH
Confidence 357888899999999999999986 766633333 22 35899999999887653
No 68
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=92.96 E-value=0.065 Score=42.46 Aligned_cols=43 Identities=28% Similarity=0.365 Sum_probs=28.6
Q ss_pred hccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhccccchhhh
Q 009303 299 EVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDI 342 (538)
Q Consensus 299 ~I~GvGpktA~~ly~~GirtledL~~~~--~L~~~q~~Glk~~ed~ 342 (538)
+|+|||+++|+.|-+ .+.|++.|.++. .|+...++|.+.-+.+
T Consensus 7 GI~~VG~~~ak~L~~-~f~sl~~l~~a~~e~L~~i~gIG~~~A~si 51 (64)
T PF12826_consen 7 GIPGVGEKTAKLLAK-HFGSLEALMNASVEELSAIPGIGPKIAQSI 51 (64)
T ss_dssp TSTT--HHHHHHHHH-CCSCHHHHCC--HHHHCTSTT--HHHHHHH
T ss_pred CCCCccHHHHHHHHH-HcCCHHHHHHcCHHHHhccCCcCHHHHHHH
Confidence 899999999999975 455999999653 5777777776554443
No 69
>PRK00254 ski2-like helicase; Provisional
Probab=92.78 E-value=0.13 Score=59.71 Aligned_cols=76 Identities=24% Similarity=0.395 Sum_probs=50.7
Q ss_pred HHHHHHHHHH-----hCCcchhHHHH----hhchhHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhc--cCcchhhhc
Q 009303 266 MQDHIQEIVT-----TGKLSKLEHFE----KDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRL 334 (538)
Q Consensus 266 ia~kI~Eil~-----tG~~~~le~l~----~~~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~--~~L~~~q~~ 334 (538)
++.-+.+|+. .|.+..+.++. ...+...+.|. +|||||+++|+++|+.|+.|++||.++ ..|....++
T Consensus 608 l~~a~~~i~~~~~~~~~~~~~l~~l~~rl~~g~~~~~~~L~-~ipgig~~~~~~l~~~g~~s~~~i~~a~~~el~~~~gi 686 (720)
T PRK00254 608 LMYSLIELYKLFEPKQEVLDYLETLHLRVKHGVREELLELM-RLPMIGRKRARALYNAGFRSIEDIVNAKPSELLKVEGI 686 (720)
T ss_pred HHHHHHHHHHHhCcchhHHHHHHHHHHHHHcCCCHHHhhhh-cCCCCCHHHHHHHHHccCCCHHHHHhCCHHHHhcCCCC
Confidence 3344444543 34444544333 44444456666 999999999999999999999999864 357666667
Q ss_pred cccchhhh
Q 009303 335 GLKYFDDI 342 (538)
Q Consensus 335 Glk~~ed~ 342 (538)
|-+..+.+
T Consensus 687 ~~~~a~~i 694 (720)
T PRK00254 687 GAKIVEGI 694 (720)
T ss_pred CHHHHHHH
Confidence 76554443
No 70
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=92.66 E-value=0.22 Score=49.36 Aligned_cols=54 Identities=24% Similarity=0.435 Sum_probs=41.4
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh
Q 009303 253 ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (538)
Q Consensus 253 ~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 314 (538)
++.|..|||||+..+.++ ++.| +.-++.+... ..+.|.+|+|||.++|.++++.
T Consensus 2 ~~~L~~IpGIG~krakkL---l~~G-F~Sve~Ik~A----S~eEL~~V~GIg~k~AekI~e~ 55 (232)
T PRK12766 2 PEELEDISGVGPSKAEAL---REAG-FESVEDVRAA----DQSELAEVDGIGNALAARIKAD 55 (232)
T ss_pred ccccccCCCcCHHHHHHH---HHcC-CCCHHHHHhC----CHHHHHHccCCCHHHHHHHHHH
Confidence 356889999999888775 5566 5666766543 3455679999999999999986
No 71
>KOG2043 consensus Signaling protein SWIFT and related BRCT domain proteins [Transcription; Signal transduction mechanisms; Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]
Probab=92.17 E-value=0.13 Score=60.31 Aligned_cols=68 Identities=25% Similarity=0.406 Sum_probs=52.9
Q ss_pred HHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHhhhcccCccccccchHHHHHhcCcccCccccccc
Q 009303 38 IWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSLRLGEKVSEDLYRIK 109 (538)
Q Consensus 38 ~l~~~~~~~G~~V~~~ls~~VTHVV~~~~~~~~~~l~~~~~~~~~~~lV~~~Wl~ecik~g~lv~e~~y~l~ 109 (538)
-+++.+++.|+.|+.... ..||+|+....+....|.. +.. ..-||+..|+.+|.++|..+|+..|.+.
T Consensus 672 ~~k~~~k~lg~s~~ss~~-e~Th~i~~rirRT~k~Lea--i~~-G~~ivT~~wL~s~~k~g~~~dek~yil~ 739 (896)
T KOG2043|consen 672 NYKLAKKFLGGSVASSDS-EATHFIADRIRRTLKFLEA--ISS-GKPLVTPQWLVSSLKSGEKLDEKPYILH 739 (896)
T ss_pred hhhhHHhhccceeecccc-cceeeeehhhhccHHHHhh--hcc-CCcccchHHHHHHhhccccccCcccccc
Confidence 367888999988887754 5899999865554444442 222 2579999999999999999999999985
No 72
>KOG1929 consensus Nucleotide excision repair factor NEF2, RAD4/CUT5 component [Replication, recombination and repair]
Probab=91.87 E-value=0.25 Score=57.23 Aligned_cols=89 Identities=18% Similarity=0.232 Sum_probs=68.9
Q ss_pred CCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHhhhcccCccccccchHHHHHh
Q 009303 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSLR 96 (538)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~~~~~~~~~~l~~~~~~~~~~~lV~~~Wl~ecik 96 (538)
..|.+|.|.. .++...++.-+++++-.|||.....++..|+||++-......+ .++...++..+|..+|+-+|+.
T Consensus 102 p~~~~~~Vc~--tgl~~~eK~ei~~~v~k~gg~~~~~L~s~v~~~~~~~~~~~~k---Ye~al~wn~~v~~~~w~~~s~~ 176 (811)
T KOG1929|consen 102 PGFFGLKVCL--TGLSGDEKSEIKILVPKHGGTLHRSLSSDVNSLKILPEVKTEK---YEQALKWNIPVVSDDWLFDSIE 176 (811)
T ss_pred CcccceEEEe--cccchHHHHHHHHHhhhcccEEehhhhhhhheeeeccccchHH---HHHHHhhCCccccHHHHhhhhc
Confidence 4566777666 7787666777889999999999999999999999855432211 1222233478999999999999
Q ss_pred cCcccCcccccccc
Q 009303 97 LGEKVSEDLYRIKL 110 (538)
Q Consensus 97 ~g~lv~e~~y~l~~ 110 (538)
.+..+++..|.+..
T Consensus 177 ~~~~~~~~~~e~~~ 190 (811)
T KOG1929|consen 177 KTAVLETKPYEGAP 190 (811)
T ss_pred cccccccccccccc
Confidence 99999999998865
No 73
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=91.07 E-value=0.11 Score=50.10 Aligned_cols=50 Identities=20% Similarity=0.261 Sum_probs=37.7
Q ss_pred hHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhh---c---cCcchhhhccccchhhh
Q 009303 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDI 342 (538)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~---~---~~L~~~q~~Glk~~ed~ 342 (538)
...+++|.+|.|||||+|-.+... -+.++|.+ . ..|++++|+|-|..+.+
T Consensus 69 r~lF~~Li~V~GIGpK~AL~iLs~--~~~~el~~aI~~~D~~~L~~vpGIGkKtAerI 124 (188)
T PRK14606 69 KELFLSLTKVSRLGPKTALKIISN--EDAETLVTMIASQDVEGLSKLPGISKKTAERI 124 (188)
T ss_pred HHHHHHHhccCCccHHHHHHHHcC--CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHH
Confidence 357888899999999999999754 25555542 2 25899999998886543
No 74
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=91.01 E-value=0.15 Score=32.86 Aligned_cols=19 Identities=47% Similarity=0.607 Sum_probs=16.3
Q ss_pred HHhhccCCCHHHHHHHHHh
Q 009303 296 LFGEVWGIGPATAQKLYEK 314 (538)
Q Consensus 296 lf~~I~GvGpktA~~ly~~ 314 (538)
.|++|+|||+++|+++.+.
T Consensus 2 ~L~~i~GiG~k~A~~il~~ 20 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEA 20 (26)
T ss_pred hhhhCCCCCHHHHHHHHHh
Confidence 3569999999999999863
No 75
>PF01909 NTP_transf_2: Nucleotidyltransferase domain A subset of this Pfam family; InterPro: IPR002934 A small region that overlaps with a nuclear localization signal and binds to the RNA primer contains three aspartates that are essential for catalysis. Sequence and secondary structure comparisons of regions surrounding these aspartates with sequences of other polymerases revealed a significant homology to the palm structure of DNA polymerase beta, terminal deoxynucleotidyltransferase and DNA polymerase IV of Saccharomyces cerevisiae, all members of the family X of polymerases. This homology extends as far as cca: tRNA nucleotidyltransferase and streptomycin adenylyltransferase, an antibiotic resistance factor [, ]. Proteins containing this domain include kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTase inactivates antibiotics by catalysing the addition of a nucleotidyl group onto the drug. In experiments, Mn2+ strongly stimulated this reaction due to a 50-fold lower Ki for 8-azido-ATP in the presence of Mn2+. Mutations of the highly conserved Asp residues 113, 115, and 167, critical for metal binding in the catalytic domain of bovine poly(A) polymerase, led to a strong reduction of cross-linking efficiency, and Mn2+ no longer stimulated the reaction. Mutations in the region of the "helical turn motif" (a domain binding the triphosphate moiety of the nucleotide) and in the suspected nucleotide-binding helix of bovine poly(A) polymerase impaired ATP binding and catalysis. The results indicate that ATP is bound in part by the helical turn motif and in part by a region that may be a structural analogue of the fingers domain found in many polymerases.; GO: 0016779 nucleotidyltransferase activity; PDB: 4EBK_B 4EBJ_A 1KNY_A 2B4V_A 2B56_A 2B51_A 1NO5_B 1Q79_A 1Q78_A 1F5A_A ....
Probab=90.97 E-value=0.31 Score=40.51 Aligned_cols=32 Identities=28% Similarity=0.458 Sum_probs=26.5
Q ss_pred CCCeEEEecccccccCCc-CCCeeEEEecCCcc
Q 009303 366 LPEVIILCGGSYRRGKAS-CGDLDVVIMHPDRK 397 (538)
Q Consensus 366 ~p~~~v~~~Gs~RRgke~-~~DVDiLit~~~~~ 397 (538)
.+...+.+.|||.||..+ .+|||++|..++..
T Consensus 12 ~~~~~v~lfGS~a~g~~~~~SDIDl~i~~~~~~ 44 (93)
T PF01909_consen 12 FGVAEVYLFGSYARGDATPDSDIDLLIILDEPE 44 (93)
T ss_dssp HTTEEEEEEHHHHHTSSCTTSCEEEEEEESSTS
T ss_pred CCCCEEEEECCcccCcCCCCCCEEEEEEeCCcc
Confidence 456689999999999966 69999999877654
No 76
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=90.88 E-value=0.12 Score=49.64 Aligned_cols=50 Identities=20% Similarity=0.255 Sum_probs=37.9
Q ss_pred hHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhh---c---cCcchhhhccccchhhh
Q 009303 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDI 342 (538)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~---~---~~L~~~q~~Glk~~ed~ 342 (538)
...+++|.+|.|||||+|-.+... -+.++|.. . ..|++.+|+|-|..+.+
T Consensus 69 r~lF~~Li~VsGIGpK~Al~ILs~--~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRI 124 (183)
T PRK14601 69 QKMFEMLLKVNGIGANTAMAVCSS--LDVNSFYKALSLGDESVLKKVPGIGPKSAKRI 124 (183)
T ss_pred HHHHHHHhccCCccHHHHHHHHcC--CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHH
Confidence 457888899999999999988754 25566653 2 35899999998886543
No 77
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=90.69 E-value=0.11 Score=50.50 Aligned_cols=50 Identities=28% Similarity=0.308 Sum_probs=38.4
Q ss_pred hHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhh---c---cCcchhhhccccchhhh
Q 009303 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDI 342 (538)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~---~---~~L~~~q~~Glk~~ed~ 342 (538)
...+++|.+|.|||||+|-.+... -|.++|.+ . ..|++.+|+|-|..+.+
T Consensus 68 r~lF~~L~~V~GIGpK~AL~iLs~--~~~~~l~~aI~~~D~~~L~kvpGIGkKtAerI 123 (197)
T PRK14603 68 LELFELLLGVSGVGPKLALALLSA--LPPALLARALLEGDARLLTSASGVGKKLAERI 123 (197)
T ss_pred HHHHHHHhCcCCcCHHHHHHHHcC--CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHH
Confidence 357888899999999999999764 25566653 2 35899999999886644
No 78
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=90.40 E-value=0.15 Score=49.82 Aligned_cols=50 Identities=26% Similarity=0.324 Sum_probs=38.0
Q ss_pred hHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhh---c---cCcchhhhccccchhhh
Q 009303 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDI 342 (538)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~---~---~~L~~~q~~Glk~~ed~ 342 (538)
...+++|.+|.|||||+|-.+... -+.++|.. . ..|++++|+|-|..+.+
T Consensus 70 r~lF~~Li~V~GIGpK~Al~iLs~--~~~~~l~~aI~~~D~~~L~~ipGIGkKtAerI 125 (203)
T PRK14602 70 RQTFIVLISISKVGAKTALAILSQ--FRPDDLRRLVAEEDVAALTRVSGIGKKTAQHI 125 (203)
T ss_pred HHHHHHHhCCCCcCHHHHHHHHhh--CCHHHHHHHHHhCCHHHHhcCCCcCHHHHHHH
Confidence 347888889999999999999875 24555542 2 35899999999886644
No 79
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=90.30 E-value=0.15 Score=49.67 Aligned_cols=50 Identities=28% Similarity=0.359 Sum_probs=38.8
Q ss_pred hHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhh---c---cCcchhhhccccchhhh
Q 009303 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDI 342 (538)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~---~---~~L~~~q~~Glk~~ed~ 342 (538)
...+++|.+|.|||||+|-.+... -|.++|.. . ..|++++|+|.|..+.+
T Consensus 69 r~lF~~Li~V~GIGpK~Al~iLs~--~~~~el~~aI~~~D~~~L~kvpGIGkKtAerI 124 (195)
T PRK14604 69 RQLFELLIGVSGVGPKAALNLLSS--GTPDELQLAIAGGDVARLARVPGIGKKTAERI 124 (195)
T ss_pred HHHHHHHhCcCCcCHHHHHHHHcC--CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHH
Confidence 357888899999999999999874 26666653 2 25899999999886644
No 80
>PF04994 TfoX_C: TfoX C-terminal domain; InterPro: IPR007077 This domain is found in a number of bacterial proteins including the TfoX gene product of Haemophilus influenzae. TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes []. This family corresponds to the C-terminal presumed domain of TfoX. The domain is found in association with the N-terminal domain in some, but not all members of this group, suggesting this is an autonomous and functionally unrelated domain. For example it is found associated with Q9JZR1 from SWISSPROT in IPR002125 from INTERPRO.; PDB: 3BQT_A 3MAB_A.
Probab=90.24 E-value=0.22 Score=41.43 Aligned_cols=30 Identities=27% Similarity=0.480 Sum_probs=23.3
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhcc
Q 009303 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (538)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~~ 326 (538)
+..+|.+||+..+.|++-||.|++||+.-+
T Consensus 5 l~~LpNig~~~e~~L~~vGI~t~~~L~~~G 34 (81)
T PF04994_consen 5 LKDLPNIGPKSERMLAKVGIHTVEDLRELG 34 (81)
T ss_dssp GCGSTT--HHHHHHHHHTT--SHHHHHHHH
T ss_pred hhhCCCCCHHHHHHHHHcCCCCHHHHHHhC
Confidence 457899999999999999999999999754
No 81
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=89.86 E-value=0.17 Score=49.10 Aligned_cols=49 Identities=16% Similarity=0.298 Sum_probs=37.7
Q ss_pred hHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhh---c---cCcchhhhccccchhh
Q 009303 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDD 341 (538)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~---~---~~L~~~q~~Glk~~ed 341 (538)
...+++|.+|.|||||+|-.+... -|.++|.. . ..|++.+|+|-|..+.
T Consensus 68 r~lF~~LisVsGIGPK~ALaILs~--~~~~el~~aI~~~D~~~L~~vpGIGkKtAeR 122 (196)
T PRK13901 68 REVFEELIGVDGIGPRAALRVLSG--IKYNEFRDAIDREDIELISKVKGIGNKMAGK 122 (196)
T ss_pred HHHHHHHhCcCCcCHHHHHHHHcC--CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHH
Confidence 357888889999999999999764 35666653 2 3589999999888654
No 82
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=89.54 E-value=1.3 Score=51.43 Aligned_cols=82 Identities=21% Similarity=0.343 Sum_probs=62.2
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh-CCCCHHHHhhcc-Ccc-
Q 009303 253 ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED-SLT- 329 (538)
Q Consensus 253 ~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~-GirtledL~~~~-~L~- 329 (538)
.+.|.++||||+..++.|.+-++. .. ....++..| .-+|++++.|.++|+. |-.+++.|++.. .|.
T Consensus 116 ~~~L~~v~gi~~~~~~~i~~~~~~--------~~--~~~~~~~~L-~~~gi~~~~a~ki~~~yg~~~~~~i~~nPY~L~~ 184 (720)
T TIGR01448 116 PEKLLEVPGISKANLEKFVSQWSQ--------QG--DERRLLAGL-QGLGIGIKLAQRIYKFYQADTLDRVEKDPYLLAE 184 (720)
T ss_pred HHHHhcCCCCCHHHHHHHHHHHHH--------hH--HHHHHHHHH-HHcCCCHHHHHHHHHHHhHHHHHHHHhCchhhhh
Confidence 467889999999999999876632 11 122355555 8999999999999998 999999998764 555
Q ss_pred hhhhccccchhhhccC
Q 009303 330 HSQRLGLKYFDDIKTR 345 (538)
Q Consensus 330 ~~q~~Glk~~ed~~~~ 345 (538)
...++|++..+.+..+
T Consensus 185 ~i~gigF~~aD~iA~~ 200 (720)
T TIGR01448 185 DVKGIGFLTADQLAQA 200 (720)
T ss_pred hcCCCCHHHHHHHHHH
Confidence 4778888888877543
No 83
>TIGR03671 cca_archaeal CCA-adding enzyme.
Probab=89.41 E-value=1.7 Score=46.93 Aligned_cols=46 Identities=26% Similarity=0.394 Sum_probs=33.4
Q ss_pred HHHHHHHHHHhhhcCCCeEEEecccccccCCcC--CCeeEEEecCCcc
Q 009303 352 EQMERLLQKAGEEVLPEVIILCGGSYRRGKASC--GDLDVVIMHPDRK 397 (538)
Q Consensus 352 ~~i~~iv~~~~~~~~p~~~v~~~Gs~RRgke~~--~DVDiLit~~~~~ 397 (538)
..+...+++.+.+..+.+.|.+.|||.||.-+. .||||+|..+...
T Consensus 24 ~~l~~~l~~~~~e~~~~~~v~~~GS~ArgT~L~G~sDIDIfi~f~~~~ 71 (408)
T TIGR03671 24 DELIARLEEIIEELGVDAEVVLVGSYARGTWLKGDRDIDIFILFPKDT 71 (408)
T ss_pred HHHHHHHHHHHHhcCCcceEEEEeeEecCCccCCCCceeEEEEeCCCC
Confidence 334444555554555668999999999999886 6999999876543
No 84
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=89.24 E-value=0.34 Score=43.78 Aligned_cols=53 Identities=23% Similarity=0.293 Sum_probs=39.0
Q ss_pred HHHhhccCCCHHHHHHHHHhCCCCHHHHhhccCcchhhhccccchhhhccCcCHHH
Q 009303 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIPRHE 350 (538)
Q Consensus 295 ~lf~~I~GvGpktA~~ly~~GirtledL~~~~~L~~~q~~Glk~~ed~~~~i~r~E 350 (538)
.-|+.|-||||+.+..|-..||.|+.+|-.- +..--.-+.-|-.|..||-|+.
T Consensus 67 DDLt~I~GIGPk~e~~Ln~~GI~tfaQIAAw---t~~di~~id~~l~f~GRi~RDd 119 (133)
T COG3743 67 DDLTRISGIGPKLEKVLNELGIFTFAQIAAW---TRADIAWIDDYLNFDGRIERDD 119 (133)
T ss_pred ccchhhcccCHHHHHHHHHcCCccHHHHHhc---CHHHHHHHHhhcCCcchhHHHH
Confidence 4577999999999999999999999999742 2222223445556677887774
No 85
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=89.17 E-value=0.51 Score=47.48 Aligned_cols=49 Identities=24% Similarity=0.493 Sum_probs=35.0
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009303 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (538)
+..|||||..+|..+-.- -|+. +.+.+- ....|+.|+|||+++|..+|+
T Consensus 184 l~s~pgig~~~a~~ll~~--fgS~---~~~~ta----s~~eL~~v~gig~k~A~~I~~ 232 (254)
T COG1948 184 LESIPGIGPKLAERLLKK--FGSV---EDVLTA----SEEELMKVKGIGEKKAREIYR 232 (254)
T ss_pred HHcCCCccHHHHHHHHHH--hcCH---HHHhhc----CHHHHHHhcCccHHHHHHHHH
Confidence 689999999999876542 2333 333321 125566999999999999987
No 86
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=88.98 E-value=0.18 Score=57.89 Aligned_cols=64 Identities=16% Similarity=0.221 Sum_probs=47.3
Q ss_pred hhccCCCHHHHHHHHHh-CCCCHHHHhh--ccCcchhhhccccchhhhccCcCHHHHHHHHHHHHHH
Q 009303 298 GEVWGIGPATAQKLYEK-GHRTLDDLKN--EDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKA 361 (538)
Q Consensus 298 ~~I~GvGpktA~~ly~~-GirtledL~~--~~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~iv~~~ 361 (538)
++|.|+|++++.+||+. +++++.||.. ...|..+.+||-+..+.+.+.|-.+--..+..++..+
T Consensus 465 l~I~GLG~k~i~~L~~~g~V~~~~Dl~~L~~~~L~~l~g~g~Ksa~~Ll~~Ie~sk~~~l~r~l~AL 531 (689)
T PRK14351 465 LDIEGLGEERVQQLVDAGLVESLADLYDLTVADLAELEGWGETSAENLLAELEASREPPLADFLVAL 531 (689)
T ss_pred cCCCCcCHHHHHHHHHcCCCCCHHHHHHcCHHHHhcCcCcchhHHHHHHHHHHHHccCCHHHHHHHc
Confidence 37999999999999999 5799999985 2347778889999888887666443322344544443
No 87
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=88.78 E-value=0.33 Score=50.54 Aligned_cols=38 Identities=32% Similarity=0.549 Sum_probs=30.5
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhc
Q 009303 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRL 334 (538)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~~--~L~~~q~~ 334 (538)
+..+||||+++|++|.+.||.|++||.... .|...-++
T Consensus 8 l~~l~gIg~~~a~~L~~~Gi~t~~dl~~~~~~~L~~~~g~ 47 (317)
T PRK04301 8 LEDLPGVGPATAEKLREAGYDTVEAIAVASPKELSEAAGI 47 (317)
T ss_pred HhhcCCCCHHHHHHHHHcCCCCHHHHHcCCHHHHHHhcCC
Confidence 568999999999999999999999998643 34444343
No 88
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=88.61 E-value=1.1 Score=42.81 Aligned_cols=49 Identities=14% Similarity=0.216 Sum_probs=30.0
Q ss_pred CCCHHHHHHHHHHHH------hCCcchhHHHHhh---chhHHHHHHhhccCCCHHHHHHHH
Q 009303 261 GIGKSMQDHIQEIVT------TGKLSKLEHFEKD---EKVRTISLFGEVWGIGPATAQKLY 312 (538)
Q Consensus 261 gIG~~ia~kI~Eil~------tG~~~~le~l~~~---~~~~~l~lf~~I~GvGpktA~~ly 312 (538)
|.-..-|+.|.++.+ .|.+ +.+..+ ....+++.|+++||||||||.-..
T Consensus 75 Gfy~~KAk~Lk~~a~~iie~y~G~v---~~L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL 132 (177)
T TIGR03252 75 RFPGSMAKRVQALAQYVVDTYDGDA---TAVWTEGDPDGKELLRRLKALPGFGKQKAKIFL 132 (177)
T ss_pred CchHHHHHHHHHHHHHHHHHhCCCh---hhhhcccCCCcHHHHHHHHcCCCCCHHHHHHHH
Confidence 455566666665544 2333 333331 123357788899999999999653
No 89
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=88.34 E-value=1.2 Score=46.11 Aligned_cols=95 Identities=16% Similarity=0.262 Sum_probs=62.7
Q ss_pred CCCcHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHH
Q 009303 207 PDLNKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFE 286 (538)
Q Consensus 207 ~~~N~~ia~~l~~la~~~e~~g~~~r~~aY~rAa~~l~~l~~~i~~~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~ 286 (538)
+.=|+.|++.++++.+-=+++ +.....+.+|.. ..+|..+||+|++-..+..+.+- +..+++|+
T Consensus 59 ~gIGk~ia~~I~e~l~tG~~~----------~le~lk~~~P~g---l~~Ll~v~GlGpkKi~~Ly~elg---i~~~e~l~ 122 (326)
T COG1796 59 PGIGKGIAEKISEYLDTGEVK----------KLEALKKEVPEG---LEPLLKVPGLGPKKIVSLYKELG---IKDLEELQ 122 (326)
T ss_pred CCccHHHHHHHHHHHHcCccH----------HHHHHHHhCCcc---hHHHhhCCCCCcHHHHHHHHHHC---cccHHHHH
Confidence 566899999877664432221 444555667766 77899999999954444433333 66677776
Q ss_pred hhchhHHHHHHhhccCCCHHHHHHHHHhCCCCHH
Q 009303 287 KDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLD 320 (538)
Q Consensus 287 ~~~~~~~l~lf~~I~GvGpktA~~ly~~Girtle 320 (538)
.... .-.+.+++|.|.|.+.+|++..-...+
T Consensus 123 ~a~~---~~~~~~l~GfG~kse~~il~~i~~~~~ 153 (326)
T COG1796 123 EALE---NGKIRGLRGFGKKSEAKILENIEFAEE 153 (326)
T ss_pred HHHH---hCCccccCCccchhHHHHHHHHHHHhh
Confidence 5433 334669999999999999986443333
No 90
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=88.22 E-value=0.24 Score=47.78 Aligned_cols=49 Identities=22% Similarity=0.306 Sum_probs=37.2
Q ss_pred hHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhh---c---cCcchhhhccccchhhh
Q 009303 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDI 342 (538)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~---~---~~L~~~q~~Glk~~ed~ 342 (538)
...+++|.+|.|||||+|-.+-.. -|.++|.. . ..| +++|+|-|..+.+
T Consensus 69 r~lF~~LisV~GIGpK~Al~iLs~--~~~~~l~~aI~~~D~~~L-~vpGIGkKtAerI 123 (186)
T PRK14600 69 QDCLRMLVKVSGVNYKTAMSILSK--LTPEQLFSAIVNEDKAAL-KVNGIGEKLINRI 123 (186)
T ss_pred HHHHHHHhCcCCcCHHHHHHHHcc--CCHHHHHHHHHcCCHhhe-ECCCCcHHHHHHH
Confidence 357888899999999999999774 25666653 2 358 8999998886643
No 91
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=87.97 E-value=0.35 Score=50.07 Aligned_cols=29 Identities=38% Similarity=0.597 Sum_probs=26.4
Q ss_pred hhccCCCHHHHHHHHHhCCCCHHHHhhcc
Q 009303 298 GEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (538)
Q Consensus 298 ~~I~GvGpktA~~ly~~GirtledL~~~~ 326 (538)
.++||||++++++|++.||.|++||....
T Consensus 2 ~~i~gig~~~~~~L~~~Gi~ti~dl~~~~ 30 (310)
T TIGR02236 2 EDLPGVGPATAEKLREAGYDTFEAIAVAS 30 (310)
T ss_pred cccCCCCHHHHHHHHHcCCCCHHHHHcCC
Confidence 47899999999999999999999998643
No 92
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=87.79 E-value=0.68 Score=51.96 Aligned_cols=85 Identities=14% Similarity=0.184 Sum_probs=62.8
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccch
Q 009303 253 ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTH 330 (538)
Q Consensus 253 ~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~~--~L~~ 330 (538)
.+++.+++|+|++.+++|.+-++.-+-..|+ +.|--| +|++||.++|+. .+.|+++|.++. .|..
T Consensus 458 ~~~l~~l~gfgeks~~nll~aIe~sk~~~l~--------r~l~aL-GI~~vG~~~ak~----~~~~i~~l~~a~~e~l~~ 524 (562)
T PRK08097 458 PEQLANTPGIGKARAEQLWHQFNLARQQPFS--------RWLKAL-GIPLPQAALNAL----DDRSWQQLLSRSEQQWQQ 524 (562)
T ss_pred HHHHhcCcCccHHHHHHHHHHHHHHcCCCHH--------HHHHHc-CCccHHHHHHHH----hcCCHHHHHcCCHHHHhc
Confidence 3689999999999999988776654433343 345556 999999998886 678899998543 5788
Q ss_pred hhhccccchhhhccCcCHHH
Q 009303 331 SQRLGLKYFDDIKTRIPRHE 350 (538)
Q Consensus 331 ~q~~Glk~~ed~~~~i~r~E 350 (538)
..++|-..-+.+..-+.-.+
T Consensus 525 i~gIG~~~a~si~~~f~~~~ 544 (562)
T PRK08097 525 LPGIGEGRARQLIAFLQHPE 544 (562)
T ss_pred CCCchHHHHHHHHHHHcCHH
Confidence 88899777777666554444
No 93
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=87.42 E-value=0.28 Score=56.89 Aligned_cols=53 Identities=15% Similarity=0.350 Sum_probs=41.1
Q ss_pred HHHHHHhh--ccCCCHHHHHHHHHh-CCCCHHHHhhcc-Ccchhhhccccchhhhcc
Q 009303 292 RTISLFGE--VWGIGPATAQKLYEK-GHRTLDDLKNED-SLTHSQRLGLKYFDDIKT 344 (538)
Q Consensus 292 ~~l~lf~~--I~GvGpktA~~ly~~-GirtledL~~~~-~L~~~q~~Glk~~ed~~~ 344 (538)
.++..|.+ ++||||++|+++|+. |.++++-|.++. +|...+++|.+..+.|..
T Consensus 79 ~i~~yL~s~~~~GIG~~~A~~iv~~fg~~~~~~i~~~~~~L~~v~gi~~~~~~~i~~ 135 (720)
T TIGR01448 79 GIVAYLSSRSIKGVGKKLAQRIVKTFGEAAFDVLDDDPEKLLEVPGISKANLEKFVS 135 (720)
T ss_pred HHHHHHhcCCCCCcCHHHHHHHHHHhCHhHHHHHHhCHHHHhcCCCCCHHHHHHHHH
Confidence 34555543 999999999999998 999999998654 577778887666666654
No 94
>TIGR00588 ogg 8-oxoguanine DNA-glycosylase (ogg). All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is distantly realted to the Nth-MutY superfamily.
Probab=86.85 E-value=1.6 Score=45.48 Aligned_cols=62 Identities=19% Similarity=0.258 Sum_probs=39.9
Q ss_pred hhcCCCCCCHHHHHHHHHHH---HhCCc--chhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHhCCCC
Q 009303 255 QVKGLPGIGKSMQDHIQEIV---TTGKL--SKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRT 318 (538)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil---~tG~~--~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~Girt 318 (538)
+|..+ |+|-+ |+.|.++. ..|.. ..++++..-....+.+.|++++||||+||.-+--.|+.-
T Consensus 177 ~Lr~~-G~g~R-a~~I~~~A~~i~~~~~~~~~l~~l~~~~~~~~~~~L~~l~GIG~~tAd~vll~~l~~ 243 (310)
T TIGR00588 177 HLRKL-GLGYR-ARYIRETARALLEEQGGRAWLQQIRGASYEDAREALCELPGVGPKVADCICLMGLDK 243 (310)
T ss_pred HHHHc-CCHHH-HHHHHHHHHHHHhccCCchhHHhhccCChHHHHHHHHhCCCccHHHHHHHHHHhCCC
Confidence 45554 66765 55554443 34433 346666554445588999999999999999876555543
No 95
>KOG1929 consensus Nucleotide excision repair factor NEF2, RAD4/CUT5 component [Replication, recombination and repair]
Probab=86.65 E-value=0.83 Score=53.12 Aligned_cols=93 Identities=11% Similarity=0.160 Sum_probs=69.8
Q ss_pred CCCCCCCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHhhhcccCccccccchH
Q 009303 12 ALDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWL 91 (538)
Q Consensus 12 ~~~~~~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~~~~~~~~~~l~~~~~~~~~~~lV~~~Wl 91 (538)
..-....|.++++++ ......+++.+.+.+...|+.+...+-...||||.-......... ...+..-+|.++||
T Consensus 487 ~~~l~~~~e~~~~~~--s~~~~~~~e~ln~~~~~~gas~~~~f~r~~~~l~~~~~k~s~~~~----~~kw~ip~vT~~wL 560 (811)
T KOG1929|consen 487 AAALSQPFENLTISN--SQSAEAEREKLNNLANDLGASNVKTFTRKSTTLLTTSAKGSKYEI----AGKWSIPIVTPDWL 560 (811)
T ss_pred hhcccccccCceEEe--eechHHHHHHHhHhhhhccccccceeeecccEEeccccccchhhh----ccccCCCccChhHH
Confidence 344557799999998 445557789999999999999999996666999975422111111 11223678999999
Q ss_pred HHHHhcCcccCcccccccc
Q 009303 92 EDSLRLGEKVSEDLYRIKL 110 (538)
Q Consensus 92 ~ecik~g~lv~e~~y~l~~ 110 (538)
.+|.++++.++.+.|....
T Consensus 561 ~e~~rq~~~~~~e~~l~~~ 579 (811)
T KOG1929|consen 561 YECVRQNKGERNEGFLNGN 579 (811)
T ss_pred HhhccccCcccceeecccc
Confidence 9999999999999998754
No 96
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=86.61 E-value=0.45 Score=33.35 Aligned_cols=16 Identities=56% Similarity=0.742 Sum_probs=14.3
Q ss_pred hccCCCHHHHHHHHHh
Q 009303 299 EVWGIGPATAQKLYEK 314 (538)
Q Consensus 299 ~I~GvGpktA~~ly~~ 314 (538)
.|+|||+|||.+|.++
T Consensus 20 Gv~giG~ktA~~ll~~ 35 (36)
T smart00279 20 GVKGIGPKTALKLLRE 35 (36)
T ss_pred CCCcccHHHHHHHHHh
Confidence 7999999999999764
No 97
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=86.35 E-value=0.63 Score=38.07 Aligned_cols=27 Identities=41% Similarity=0.548 Sum_probs=22.4
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhh
Q 009303 297 FGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (538)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~ 324 (538)
+..|+|||||||.+|..+ +.|++.+..
T Consensus 24 i~gv~giG~k~A~~ll~~-~~~~~~~~~ 50 (75)
T cd00080 24 IPGVPGIGPKTALKLLKE-YGSLENLLE 50 (75)
T ss_pred CCCCCcccHHHHHHHHHH-hCCHHHHHH
Confidence 347999999999999986 558888875
No 98
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=86.27 E-value=1.2 Score=51.11 Aligned_cols=62 Identities=15% Similarity=0.211 Sum_probs=40.6
Q ss_pred cccchhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhh--chhHHHHHHhhccCCCHHHHHHHHHh
Q 009303 249 KIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKD--EKVRTISLFGEVWGIGPATAQKLYEK 314 (538)
Q Consensus 249 ~i~~~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~--~~~~~l~lf~~I~GvGpktA~~ly~~ 314 (538)
++...=-..+||+||++.+..|.. ..+..++++.+. .+....+.|++|+|||+++|..+++-
T Consensus 497 ~l~r~l~ALGI~~vG~~~ak~La~----~~f~~~~~l~~~~~~~~~~~e~l~~i~giG~~~a~si~~f 560 (669)
T PRK14350 497 PFSKLLLSMGIKDLGENTILLLIN----NNLNSFDKISTLCQDREFALSKLLKIKGIGEKIALNIIEA 560 (669)
T ss_pred CHHHHHHHcCCCchhHHHHHHHHH----HhhCCHHHHHhhhhccCCCHHHHhhCCCccHHHHHHHHHH
Confidence 444444467899999999998773 122334444321 01124556789999999999999863
No 99
>KOG0323 consensus TFIIF-interacting CTD phosphatases, including NLI-interacting factor [Transcription]
Probab=86.14 E-value=0.31 Score=54.98 Aligned_cols=90 Identities=22% Similarity=0.289 Sum_probs=62.5
Q ss_pred CCCcCcEEEEe---cCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHhhhcccCccccccchHHH
Q 009303 17 GIFAGMRVFLV---EKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLED 93 (538)
Q Consensus 17 ~~F~g~~iy~~---~~~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~~~~~~~~~~l~~~~~~~~~~~lV~~~Wl~e 93 (538)
..+++|.+.|. |.++...+.+++ ..+.+.|+.+....+..+||+|+.++...... +. .... ..+||...|+..
T Consensus 440 ~v~~~~~~vfSg~~P~~~~~~~s~~~-~~~~~~g~vs~~~~~~~~th~i~~~~gt~k~~-~a-~~~~-~~~Vv~~~wl~~ 515 (635)
T KOG0323|consen 440 KVLKGSQIVFSGLHPTGSTDESADIL-GVAQQLGAVSAPDVSDKTTHLIAANAGTKKVY-KA-VVSG-SAKVVNAAWLWR 515 (635)
T ss_pred HHhhccceeecccccCcCCcchhhhh-hhhhcccceecccccchhhhHHhhccCcceee-cc-cccc-ceeEechhHHHH
Confidence 55667777664 333433334443 56778899999999999999999876422111 11 1111 278999999999
Q ss_pred HHhcCcccCcccccccc
Q 009303 94 SLRLGEKVSEDLYRIKL 110 (538)
Q Consensus 94 cik~g~lv~e~~y~l~~ 110 (538)
|+..+..|++..|.+..
T Consensus 516 ~~e~w~~v~ek~~~l~~ 532 (635)
T KOG0323|consen 516 SLEKWGKVEEKLEPLDD 532 (635)
T ss_pred HHHHhcchhcccccccc
Confidence 99999999998887754
No 100
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=86.08 E-value=0.85 Score=45.17 Aligned_cols=50 Identities=22% Similarity=0.424 Sum_probs=37.6
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009303 255 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (538)
-|..||||+|.=|..+- +++.-|+++.+ .....|.+|+|+||.+|+++|+
T Consensus 196 ~Lt~i~~VnKtda~~LL-----~~FgsLq~~~~----AS~~ele~~~G~G~~kak~l~~ 245 (254)
T KOG2841|consen 196 FLTTIPGVNKTDAQLLL-----QKFGSLQQISN----ASEGELEQCPGLGPAKAKRLHK 245 (254)
T ss_pred HHHhCCCCCcccHHHHH-----HhcccHHHHHh----cCHhHHHhCcCcCHHHHHHHHH
Confidence 47899999998776543 24556666543 2456678999999999999997
No 101
>PRK01172 ski2-like helicase; Provisional
Probab=85.66 E-value=1 Score=51.81 Aligned_cols=39 Identities=26% Similarity=0.488 Sum_probs=32.4
Q ss_pred HhhchhHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009303 286 EKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 286 ~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~ 325 (538)
..-.+...+.|+ +|||+|..+|+++|+.|++|+.||...
T Consensus 604 ~~gv~~~~~~L~-~ip~~~~~~a~~l~~~g~~~~~di~~~ 642 (674)
T PRK01172 604 KEGIREDLIDLV-LIPKVGRVRARRLYDAGFKTVDDIARS 642 (674)
T ss_pred HcCCCHHHHhhc-CCCCCCHHHHHHHHHcCCCCHHHHHhC
Confidence 334455567777 899999999999999999999999854
No 102
>PRK03352 DNA polymerase IV; Validated
Probab=85.15 E-value=0.65 Score=48.84 Aligned_cols=29 Identities=38% Similarity=0.717 Sum_probs=26.2
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009303 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~ 325 (538)
+..+||||++++++|.+.||+|+.||.+-
T Consensus 179 l~~l~gig~~~~~~L~~~Gi~ti~dl~~l 207 (346)
T PRK03352 179 TDALWGVGPKTAKRLAALGITTVADLAAA 207 (346)
T ss_pred HHHcCCCCHHHHHHHHHcCCccHHHHhcC
Confidence 35789999999999999999999999864
No 103
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=85.05 E-value=1.7 Score=42.13 Aligned_cols=45 Identities=29% Similarity=0.336 Sum_probs=31.9
Q ss_pred HHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhccCcchhhhccccchhhhccCcCHHHHHHHHHHHHHHhhh
Q 009303 292 RTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEE 364 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~iv~~~~~~ 364 (538)
..++.|.++||||+|+|+++-- ..-..+.+++..+.+.+.++...
T Consensus 8 ~Li~~l~~LPGIG~KsA~RlA~----------------------------~ll~~~~~~~~~la~ai~~~~~~ 52 (195)
T TIGR00615 8 KLIESLKKLPGIGPKSAQRLAF----------------------------HLLKRDPSEVLRLAQALLEAKEN 52 (195)
T ss_pred HHHHHHHHCCCCCHHHHHHHHH----------------------------HHHcCCHHHHHHHHHHHHHHHHc
Confidence 3678899999999999999832 11245667777776666666543
No 104
>cd05400 NT_2-5OAS_ClassI-CCAase Nucleotidyltransferase (NT) domain of 2'5'-oligoadenylate (2-5A)synthetase (2-5OAS) and class I CCA-adding enzyme. In vertebrates, 2-5OASs are induced by interferon during the innate immune response to protect against RNA virus infections. In the presence of an RNA activator, 2-5OASs catalyze the oligomerization of ATP into 2-5A. 2-5A activates endoribonuclease L, which leads to degradation of the viral RNA. 2-5OASs are also implicated in cell growth control, differentiation, and apoptosis. This family includes human OAS1, -2, -3, and OASL. CCA-adding enzymes add the sequence [cytidine(C)-cytidine-adenosine (A)], one nucleotide at a time, onto the 3' end of tRNA, in a template-independent reaction. This class I group includes the archaeal Sulfolobus shibatae and Archeoglobus fulgidus CCA-adding enzymes. It belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more dis
Probab=84.96 E-value=3.7 Score=37.18 Aligned_cols=46 Identities=33% Similarity=0.509 Sum_probs=32.3
Q ss_pred CeEEEecccccccCCcC--CCeeEEEecCCcc-----hhhhhHHHHHHHHHHc
Q 009303 368 EVIILCGGSYRRGKASC--GDLDVVIMHPDRK-----SHKGFLSKYVKKLKEM 413 (538)
Q Consensus 368 ~~~v~~~Gs~RRgke~~--~DVDiLit~~~~~-----~~~~~l~~vv~~L~~~ 413 (538)
...+.+.|||.||...- .|||++|..+... ....++..+.+.|.+.
T Consensus 27 ~~~~~~~GS~a~~T~i~~~sDiD~~v~~~~~~~~~~~~~~~~~~~l~~~L~~~ 79 (143)
T cd05400 27 VAEVFLQGSYARGTALRGDSDIDLVVVLPDDTSFAEYGPAELLDELGEALKEY 79 (143)
T ss_pred ccEEEEEcceeCCCCCCCCCceeEEEEEcCcccccccCHHHHHHHHHHHHHHh
Confidence 35788999999998754 8999999655432 2345666666666554
No 105
>PRK13844 recombination protein RecR; Provisional
Probab=84.58 E-value=1.9 Score=41.98 Aligned_cols=45 Identities=16% Similarity=0.093 Sum_probs=31.9
Q ss_pred HHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhccCcchhhhccccchhhhccCcCHHHHHHHHHHHHHHhhh
Q 009303 292 RTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEE 364 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~iv~~~~~~ 364 (538)
..++.|.++||||+|+|+++-- ..-..+.+++.++.+.+.++...
T Consensus 12 ~LI~~l~~LPGIG~KsA~Rla~----------------------------~lL~~~~~~~~~la~~i~~~~~~ 56 (200)
T PRK13844 12 AVIESLRKLPTIGKKSSQRLAL----------------------------YLLDKSPETAIAIANSLLDATAN 56 (200)
T ss_pred HHHHHHHHCCCCCHHHHHHHHH----------------------------HHHcCCHHHHHHHHHHHHHHHHh
Confidence 4678899999999999999832 11245667777776666665543
No 106
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=84.13 E-value=1.6 Score=37.37 Aligned_cols=47 Identities=11% Similarity=0.254 Sum_probs=37.1
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCC
Q 009303 253 ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGI 303 (538)
Q Consensus 253 ~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~Gv 303 (538)
+.+|..|||||+++++-...| -+..+++|+...|....+-++.+-|.
T Consensus 11 ~~~L~~iP~IG~a~a~DL~~L----Gi~s~~~L~g~dP~~Ly~~lc~~~G~ 57 (93)
T PF11731_consen 11 LSDLTDIPNIGKATAEDLRLL----GIRSPADLKGRDPEELYERLCALTGQ 57 (93)
T ss_pred HHHHhcCCCccHHHHHHHHHc----CCCCHHHHhCCCHHHHHHHHHHHcCC
Confidence 578999999999999876643 35778888888888877777776664
No 107
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=83.93 E-value=2.4 Score=47.81 Aligned_cols=52 Identities=17% Similarity=0.142 Sum_probs=39.0
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 314 (538)
..|.+|||||+.-..++-+ ++..++.+++ -+++.+.+|+|++.+.|+.+|+.
T Consensus 514 s~L~~I~GiG~kr~~~LL~-----~Fgs~~~I~~----As~eeL~~v~gi~~~~A~~I~~~ 565 (574)
T PRK14670 514 LNYTKIKGIGEKKAKKILK-----SLGTYKDILL----LNEDEIAEKMKINIKMAKKIKKF 565 (574)
T ss_pred cccccCCCCCHHHHHHHHH-----HhCCHHHHHh----CCHHHHHhCCCCCHHHHHHHHHH
Confidence 3789999999988776544 3444555543 24667789999999999999863
No 108
>PRK03858 DNA polymerase IV; Validated
Probab=83.86 E-value=0.8 Score=49.09 Aligned_cols=29 Identities=38% Similarity=0.724 Sum_probs=26.0
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009303 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~ 325 (538)
+..+||||++++++|.+.||+|+.||.+-
T Consensus 175 l~~l~Gig~~~~~~L~~~Gi~t~~dl~~l 203 (396)
T PRK03858 175 VRRLWGVGPVTAAKLRAHGITTVGDVAEL 203 (396)
T ss_pred hhhcCCCCHHHHHHHHHhCCCcHHHHhcC
Confidence 45789999999999999999999999853
No 109
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=83.00 E-value=1.1 Score=28.90 Aligned_cols=20 Identities=30% Similarity=0.573 Sum_probs=17.2
Q ss_pred hhcCCCCCCHHHHHHHHHHH
Q 009303 255 QVKGLPGIGKSMQDHIQEIV 274 (538)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil 274 (538)
+|.+|||||+++++.|.+..
T Consensus 2 ~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred hhhhCCCCCHHHHHHHHHhc
Confidence 67899999999999988643
No 110
>PRK01216 DNA polymerase IV; Validated
Probab=82.94 E-value=0.82 Score=48.46 Aligned_cols=30 Identities=33% Similarity=0.407 Sum_probs=26.5
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhcc
Q 009303 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (538)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~~ 326 (538)
+..+||||++++++|.+.||+|+.||.+-.
T Consensus 180 i~~l~giG~~~~~~L~~~Gi~TigdL~~~~ 209 (351)
T PRK01216 180 IADIPGIGDITAEKLKKLGVNKLVDTLRIE 209 (351)
T ss_pred cccccCCCHHHHHHHHHcCCCcHHHHhcCC
Confidence 457899999999999999999999998643
No 111
>PRK08609 hypothetical protein; Provisional
Probab=82.92 E-value=1.5 Score=49.50 Aligned_cols=54 Identities=17% Similarity=0.228 Sum_probs=38.2
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHH
Q 009303 252 SADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKL 311 (538)
Q Consensus 252 ~~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l 311 (538)
.+.++.+|||||++.+.++.+-+---++.+|+....+- + +..++|+|+|+.+.+
T Consensus 86 ~~~~l~~i~GiGpk~a~~l~~~lGi~tl~~L~~a~~~~-----~-~~~~~gfg~k~~~~i 139 (570)
T PRK08609 86 GLLPLLKLPGLGGKKIAKLYKELGVVDKESLKEACENG-----K-VQALAGFGKKTEEKI 139 (570)
T ss_pred HHHHHhcCCCCCHHHHHHHHHHhCCCCHHHHHHHHHhC-----C-hhhccCcchhHHHHH
Confidence 35578999999999999887655544455554432211 1 348999999999888
No 112
>COG1708 Predicted nucleotidyltransferases [General function prediction only]
Probab=82.82 E-value=5.4 Score=34.63 Aligned_cols=29 Identities=31% Similarity=0.568 Sum_probs=24.1
Q ss_pred CCeEEEecccccccCCcC-CCeeEEEecCC
Q 009303 367 PEVIILCGGSYRRGKASC-GDLDVVIMHPD 395 (538)
Q Consensus 367 p~~~v~~~Gs~RRgke~~-~DVDiLit~~~ 395 (538)
....|.+-||+-||..+- +|||++|-.++
T Consensus 25 ~~~~v~LfGS~arG~~~~~SDiDv~vv~~~ 54 (128)
T COG1708 25 GDLLIYLFGSYARGDFVKESDIDLLVVSDD 54 (128)
T ss_pred CCeEEEEEccCcccccccCCCeeEEEEcCC
Confidence 345789999999999876 99999998644
No 113
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=82.24 E-value=0.95 Score=49.07 Aligned_cols=29 Identities=38% Similarity=0.650 Sum_probs=26.3
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009303 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~ 325 (538)
+..+||||++++.+|.+.||+|+.||.+.
T Consensus 181 v~~l~GiG~~~~~~L~~lGi~TigdL~~~ 209 (422)
T PRK03609 181 VEEVWGVGRRISKKLNAMGIKTALDLADT 209 (422)
T ss_pred hhhcCCccHHHHHHHHHcCCCcHHHHhcC
Confidence 35899999999999999999999999854
No 114
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=82.07 E-value=5.5 Score=41.03 Aligned_cols=47 Identities=23% Similarity=0.319 Sum_probs=32.5
Q ss_pred HHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHhCCC
Q 009303 270 IQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHR 317 (538)
Q Consensus 270 I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~Gir 317 (538)
|.+.+..|.+. +..+..-....+++.|++|+||||.||+..--.|+.
T Consensus 174 ~A~~~~~g~~~-~~~l~~~~~e~a~e~L~~i~GIG~WTAe~~llf~lg 220 (285)
T COG0122 174 LARAAAEGELD-LSELKPLSDEEAIEELTALKGIGPWTAEMFLLFGLG 220 (285)
T ss_pred HHHHHHcCCcc-HHHhccCCHHHHHHHHHcCCCcCHHHHHHHHHHcCC
Confidence 44555677633 333444345569999999999999999988755444
No 115
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=82.04 E-value=0.99 Score=43.59 Aligned_cols=21 Identities=33% Similarity=0.607 Sum_probs=18.8
Q ss_pred HHHHHHhhccCCCHHHHHHHH
Q 009303 292 RTISLFGEVWGIGPATAQKLY 312 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly 312 (538)
+.++.|.++||||||+|++|-
T Consensus 9 ~LI~~l~kLPGvG~KsA~R~A 29 (198)
T COG0353 9 KLIDALKKLPGVGPKSAQRLA 29 (198)
T ss_pred HHHHHHhhCCCCChhHHHHHH
Confidence 478889999999999999994
No 116
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=81.70 E-value=4.1 Score=37.26 Aligned_cols=26 Identities=15% Similarity=0.089 Sum_probs=20.5
Q ss_pred HHHHHHhhccCCCHHHHHHHHHhCCC
Q 009303 292 RTISLFGEVWGIGPATAQKLYEKGHR 317 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~Gir 317 (538)
..++.|++++||||+||..+--.|+.
T Consensus 69 ~~~~~L~~l~GIG~~tA~~~l~~~~~ 94 (149)
T smart00478 69 DDREELLKLPGVGRKTANAVLSFALG 94 (149)
T ss_pred HHHHHHHcCCCCcHHHHHHHHHHHCC
Confidence 35666779999999999988766544
No 117
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=81.44 E-value=2.6 Score=47.90 Aligned_cols=135 Identities=18% Similarity=0.247 Sum_probs=87.9
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchh
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHS 331 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~~--~L~~~ 331 (538)
+++..|+++|++.+++|-.-++.-+-..|++ .+--| +|+.||.++|+.|-+ .+.|++.|..+. .|..+
T Consensus 479 ~~l~~l~~~~~ks~~nLl~aIe~sK~~~l~r--------~l~aL-GIr~VG~~~Ak~La~-~f~sl~~l~~a~~e~l~~i 548 (667)
T COG0272 479 EDLLSLEGFGEKSAENLLNAIEKSKKQPLAR--------FLYAL-GIRHVGETTAKSLAR-HFGTLEALLAASEEELASI 548 (667)
T ss_pred HHHhhccchhhhHHHHHHHHHHHhccCCHHH--------HHHHc-CCchhhHHHHHHHHH-HhhhHHHHHhcCHHHHhhc
Confidence 7899999999999998876665544333433 34445 999999999999998 999999999654 57778
Q ss_pred hhccccchhhhccCcCHHHHHHH-HHHHHHHhh-----------hcCCCeEEEeccccc-------------ccCCc---
Q 009303 332 QRLGLKYFDDIKTRIPRHEVEQM-ERLLQKAGE-----------EVLPEVIILCGGSYR-------------RGKAS--- 383 (538)
Q Consensus 332 q~~Glk~~ed~~~~i~r~Ea~~i-~~iv~~~~~-----------~~~p~~~v~~~Gs~R-------------Rgke~--- 383 (538)
.++|-.-...+..-..-++..++ ..+...-.. ..+.|-.+++||++- .|...
T Consensus 549 ~giG~~vA~si~~ff~~~~~~~li~~L~~~g~~~~~~~~~~~~~~~l~gkt~V~TGtL~~~sR~eak~~le~lGakv~~S 628 (667)
T COG0272 549 PGIGEVVARSIIEFFANEENRELIDELLAAGVKWEEEEKISIETSPLAGKTFVLTGTLEGMSRDEAKALLEALGAKVSGS 628 (667)
T ss_pred cchhHHHHHHHHHHHcCHHHHHHHHHHHHcCCCccccccccccccccCCCEEEEeccCCCCCHHHHHHHHHHcCCEEece
Confidence 88885555544433332222221 111111000 123455678888875 33333
Q ss_pred -CCCeeEEEecCCcch
Q 009303 384 -CGDLDVVIMHPDRKS 398 (538)
Q Consensus 384 -~~DVDiLit~~~~~~ 398 (538)
+.-.|+||+-+++++
T Consensus 629 VSkktD~vvaG~~aGS 644 (667)
T COG0272 629 VSKKTDYVVAGENAGS 644 (667)
T ss_pred ecccccEEEEcCCCCh
Confidence 445599999888775
No 118
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=81.18 E-value=1.5 Score=37.31 Aligned_cols=54 Identities=28% Similarity=0.553 Sum_probs=41.4
Q ss_pred HHHHHHhhccCCCHHHHHHHHHh-CCCCHHHHhhcc-Ccch-hhhccccchhhhccCc
Q 009303 292 RTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED-SLTH-SQRLGLKYFDDIKTRI 346 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~-GirtledL~~~~-~L~~-~q~~Glk~~ed~~~~i 346 (538)
.++..| .-+|++++.|.++|+. |-.+++-|+++. .|.. ..++|++..+.+..++
T Consensus 10 ~~~~~L-~~~gl~~~~a~kl~~~yg~~ai~~l~~nPY~L~~~i~gi~F~~aD~iA~~~ 66 (94)
T PF14490_consen 10 ELMAFL-QEYGLSPKLAMKLYKKYGDDAIEILKENPYRLIEDIDGIGFKTADKIALKL 66 (94)
T ss_dssp HHHHHH-HHTT--HHHHHHHHHHH-TTHHHHHHH-STCCCB-SSSSBHHHHHHHHHTT
T ss_pred HHHHHH-HHcCCCHHHHHHHHHHHhHHHHHHHHHChHHHHHHccCCCHHHHHHHHHHc
Confidence 355556 8999999999999998 999998888764 5655 8899999999988765
No 119
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=81.08 E-value=3.5 Score=46.55 Aligned_cols=67 Identities=22% Similarity=0.319 Sum_probs=44.9
Q ss_pred hHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHH
Q 009303 232 RSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKL 311 (538)
Q Consensus 232 r~~aY~rAa~~l~~l~~~i~~~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l 311 (538)
-+.+|.|-.+. .-..-..|.+|||||+....++-. ++..++.+++ -.++.+.+| |||+++|+++
T Consensus 498 FAi~~hR~~r~------k~~~~S~Ld~I~GiG~kr~~~Ll~-----~Fgs~~~ik~----As~eeL~~v-gi~~~~A~~I 561 (567)
T PRK14667 498 FALSYNRKLRE------KEGLKDILDKIKGIGEVKKEIIYR-----NFKTLYDFLK----ADDEELKKL-GIPPSVKQEV 561 (567)
T ss_pred HHHHHHHHHhh------cccccCccccCCCCCHHHHHHHHH-----HhCCHHHHHh----CCHHHHHHc-CCCHHHHHHH
Confidence 35566555432 222235688999999998887654 3444555543 246667899 9999999999
Q ss_pred HHh
Q 009303 312 YEK 314 (538)
Q Consensus 312 y~~ 314 (538)
|+.
T Consensus 562 ~~~ 564 (567)
T PRK14667 562 KKY 564 (567)
T ss_pred HHH
Confidence 874
No 120
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=81.00 E-value=0.81 Score=52.32 Aligned_cols=46 Identities=30% Similarity=0.477 Sum_probs=34.5
Q ss_pred HHHhhccCCCHHHHHHHHHh-CCCCHHHHhhcc--Ccchhhhccccchhhh
Q 009303 295 SLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED--SLTHSQRLGLKYFDDI 342 (538)
Q Consensus 295 ~lf~~I~GvGpktA~~ly~~-GirtledL~~~~--~L~~~q~~Glk~~ed~ 342 (538)
..|..|+||||+++++|++. | |+++|.++. .|....++|.+..+.|
T Consensus 637 s~L~~IPGIGpkr~k~LL~~FG--Sle~I~~AS~eELa~V~Gig~k~Ae~I 685 (694)
T PRK14666 637 GELQRVEGIGPATARLLWERFG--SLQAMAAAGEEGLAAVPGIGPARAAAL 685 (694)
T ss_pred hHHhhCCCCCHHHHHHHHHHhC--CHHHHHhcCHHHHHhcCCcCHHHHHHH
Confidence 35669999999999999997 6 999999743 3655666665554444
No 121
>PF01367 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases. The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include: Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins []. 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [, ]. Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases []. Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair []. ; GO: 0003677 DNA binding, 0003824 catalytic activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B.
Probab=80.82 E-value=0.13 Score=44.71 Aligned_cols=24 Identities=46% Similarity=0.753 Sum_probs=19.3
Q ss_pred hccCCCHHHHHHHHHh-CCCCHHHHhh
Q 009303 299 EVWGIGPATAQKLYEK-GHRTLDDLKN 324 (538)
Q Consensus 299 ~I~GvGpktA~~ly~~-GirtledL~~ 324 (538)
.|+|||||||.+|.++ | |||.+..
T Consensus 22 GV~GIG~KtA~~LL~~yg--sle~i~~ 46 (101)
T PF01367_consen 22 GVPGIGPKTAAKLLQEYG--SLENILA 46 (101)
T ss_dssp --TTSTCHCCCCCHHHHT--SCHCCCC
T ss_pred CCCCCCHHHHHHHHHHcC--CHHHHHH
Confidence 7999999999999987 6 7777764
No 122
>smart00475 53EXOc 5'-3' exonuclease.
Probab=80.79 E-value=1.2 Score=45.15 Aligned_cols=26 Identities=38% Similarity=0.592 Sum_probs=22.2
Q ss_pred hhccCCCHHHHHHHHHh-CCCCHHHHhhc
Q 009303 298 GEVWGIGPATAQKLYEK-GHRTLDDLKNE 325 (538)
Q Consensus 298 ~~I~GvGpktA~~ly~~-GirtledL~~~ 325 (538)
-+|+|||||||.+|.++ | |++.+.+.
T Consensus 189 pGV~GIG~KtA~~Ll~~yg--sle~i~~~ 215 (259)
T smart00475 189 PGVPGIGEKTAAKLLKEFG--SLENILEN 215 (259)
T ss_pred CCCCCCCHHHHHHHHHHhC--CHHHHHHH
Confidence 46899999999999987 6 99998753
No 123
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=80.55 E-value=2.6 Score=44.47 Aligned_cols=60 Identities=20% Similarity=0.332 Sum_probs=38.9
Q ss_pred cCCccccch--hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009303 245 KLPFKIESA--DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 245 ~l~~~i~~~--~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (538)
.++.+|... -=|.+||+|++.+++.+-+ ++..+..+.+- ..+.|.+|+|||+++|+.+.+
T Consensus 276 ~ld~~v~prGyRiLs~IPrl~k~iAk~Ll~-----~FGSL~~Il~A----s~eeL~~VeGIGe~rA~~I~e 337 (352)
T PRK13482 276 ALDTPVSPRGYRLLSKIPRLPSAVIENLVE-----HFGSLQGLLAA----SIEDLDEVEGIGEVRARAIRE 337 (352)
T ss_pred ccccccCCcHHHHHhcCCCCCHHHHHHHHH-----HcCCHHHHHcC----CHHHHhhCCCcCHHHHHHHHH
Confidence 344555543 3578899999988887654 23344444332 244577899999999998544
No 124
>PRK09482 flap endonuclease-like protein; Provisional
Probab=80.51 E-value=1.3 Score=44.98 Aligned_cols=26 Identities=31% Similarity=0.569 Sum_probs=22.3
Q ss_pred hhccCCCHHHHHHHHHh-CCCCHHHHhhc
Q 009303 298 GEVWGIGPATAQKLYEK-GHRTLDDLKNE 325 (538)
Q Consensus 298 ~~I~GvGpktA~~ly~~-GirtledL~~~ 325 (538)
-+|+|||||||.+|.++ | |++.+.+.
T Consensus 185 pGVpGIG~KtA~~LL~~~g--sle~i~~~ 211 (256)
T PRK09482 185 PGVAGIGPKSAAELLNQFR--SLENIYES 211 (256)
T ss_pred CCCCCcChHHHHHHHHHhC--CHHHHHHh
Confidence 36899999999999997 7 89998753
No 125
>cd01703 PolY_Pol_iota DNA Polymerase iota. Pol iota, also called Rad30B, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol iota is thought to be one of the least efficient polymerases, particularly when opposite pyrimidines; it can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine, and prefers to insert guanosine instead of adenosine opposite thymidine. Pol iota is believed to use Hoogsteen rather than Watson-Crick base pairing, which may explain the varying efficiency for different template nucleotides.
Probab=80.42 E-value=1.1 Score=47.89 Aligned_cols=30 Identities=33% Similarity=0.431 Sum_probs=26.8
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhcc
Q 009303 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (538)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~~ 326 (538)
+..+||||++++++|.+.||.|+.||.+..
T Consensus 174 v~~l~GiG~~~~~kL~~~GI~tigdl~~~~ 203 (379)
T cd01703 174 LRKIPGIGYKTAAKLEAHGISSVRDLQEFS 203 (379)
T ss_pred ccccCCcCHHHHHHHHHcCCCcHHHHHhCC
Confidence 458899999999999999999999998543
No 126
>PRK00227 glnD PII uridylyl-transferase; Provisional
Probab=80.24 E-value=4.7 Score=46.59 Aligned_cols=65 Identities=22% Similarity=0.320 Sum_probs=43.4
Q ss_pred HHHHHH-HHHHHHHHhhhcCCCeEEEecccccccC-CcCCCeeEEEecCCcchhhhhHHHHHHHHHHcCc
Q 009303 348 RHEVEQ-MERLLQKAGEEVLPEVIILCGGSYRRGK-ASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKF 415 (538)
Q Consensus 348 r~Ea~~-i~~iv~~~~~~~~p~~~v~~~Gs~RRgk-e~~~DVDiLit~~~~~~~~~~l~~vv~~L~~~g~ 415 (538)
|++|.+ ...+++... +.+++-+..+|||=||. .--+|||+||-|++... ..++..++.-|=+.|+
T Consensus 8 ~~~~~~~~~~~~~~~~--~~~~~aLvAvGGYGR~EL~P~SDIDLLiL~~~~~~-~~~i~~~~~~LWD~gL 74 (693)
T PRK00227 8 REDAEASALALLGSLQ--LPPGTALAATGSLARREMTPYSDLDLILLHPPGAT-PDGVEDLWYPIWDAKK 74 (693)
T ss_pred HHHHHHHHHHHHHhcC--CCCCeEEEEeccccccCcCCCcCceEEEEeCCccc-HHHHHHHHHHHHhcCC
Confidence 445544 455666543 33566788899997765 45689999999985432 5666677666666665
No 127
>PRK01810 DNA polymerase IV; Validated
Probab=80.15 E-value=1.3 Score=47.76 Aligned_cols=29 Identities=45% Similarity=0.691 Sum_probs=25.9
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009303 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~ 325 (538)
+..+||||++++++|...||+|+.||.+.
T Consensus 181 v~~l~giG~~~~~~L~~~Gi~tigdL~~~ 209 (407)
T PRK01810 181 VGEMHGIGEKTAEKLKDIGIQTIGDLAKA 209 (407)
T ss_pred HhhcCCcCHHHHHHHHHcCCCcHHHHHhC
Confidence 45789999999999999999999999853
No 128
>cd01701 PolY_Rev1 DNA polymerase Rev1. Rev1 is a translesion synthesis (TLS) polymerase found in eukaryotes. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Rev1 has both structural and enzymatic roles. Structurally, it is believed to interact with other nonclassical polymerases and replication machinery to act as a scaffold. Enzymatically, it catalyzes the specific insertion of dCMP opposite abasic sites. Rev1 interacts with the Rev7 subunit of the B-family TLS polymerase Pol zeta (Rev3/Rev7). Rev1 is known to actively promote the introduction of mutations, potentially making it a significant target for cancer treatment.
Probab=80.11 E-value=1.3 Score=47.87 Aligned_cols=30 Identities=27% Similarity=0.328 Sum_probs=26.8
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhcc
Q 009303 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (538)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~~ 326 (538)
+..|||||++++++|-+.||+|+.||.+..
T Consensus 224 v~~l~GIG~~~~~~L~~~Gi~t~~dl~~~~ 253 (404)
T cd01701 224 VGDLPGVGSSLAEKLVKLFGDTCGGLELRS 253 (404)
T ss_pred HhHhCCCCHHHHHHHHHcCCcchHHHHhCc
Confidence 357899999999999999999999998643
No 129
>COG1746 CCA1 tRNA nucleotidyltransferase (CCA-adding enzyme) [Translation, ribosomal structure and biogenesis]
Probab=79.88 E-value=4 Score=43.97 Aligned_cols=48 Identities=27% Similarity=0.375 Sum_probs=35.4
Q ss_pred HHHHHHHHHHhhhcCCCeEEEecccccccCCcC--CCeeEEEecCCcchh
Q 009303 352 EQMERLLQKAGEEVLPEVIILCGGSYRRGKASC--GDLDVVIMHPDRKSH 399 (538)
Q Consensus 352 ~~i~~iv~~~~~~~~p~~~v~~~Gs~RRgke~~--~DVDiLit~~~~~~~ 399 (538)
+.+...+.+++.+....+.+.++||+.||--.. +|||+-|.-|...+.
T Consensus 29 e~l~~~~~~~~~e~~~~aev~lVGS~AkgTwL~gd~DIDvFi~Fp~d~~~ 78 (443)
T COG1746 29 EELRERINEIIEELGIDAEVVLVGSYAKGTWLRGDHDIDVFIAFPKDTSE 78 (443)
T ss_pred HHHHHHHHHHHHhcCCcceEEEEeecccCcccCCCcceeEEEECCCCCCH
Confidence 344445555555556788999999999997665 789999988877553
No 130
>PRK10880 adenine DNA glycosylase; Provisional
Probab=79.74 E-value=7.6 Score=41.24 Aligned_cols=65 Identities=18% Similarity=0.291 Sum_probs=42.6
Q ss_pred hHHHHHHHHHHHh-cCCccc-cchhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCC
Q 009303 232 RSFSYYKAIPVIE-KLPFKI-ESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGI 303 (538)
Q Consensus 232 r~~aY~rAa~~l~-~l~~~i-~~~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~Gv 303 (538)
|++...+||..|. .....+ .+.++|.+|||||..+|+.|--|.-.-...-+| ..+.+.+.+++|+
T Consensus 85 RAr~L~~~A~~i~~~~~g~~p~~~~~L~~LpGIG~~TA~aIl~~af~~~~~iVD-------~nV~RV~~Rl~~i 151 (350)
T PRK10880 85 RARNLHKAAQQVATLHGGEFPETFEEVAALPGVGRSTAGAILSLSLGKHFPILD-------GNVKRVLARCYAV 151 (350)
T ss_pred HHHHHHHHHHHHHHHhCCCchhhHHHHhcCCCccHHHHHHHHHHHCCCCeeccc-------HHHHHHHHHHhcc
Confidence 7888888888883 332222 456899999999999999998776432222122 2355556565554
No 131
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=79.71 E-value=1.9 Score=44.45 Aligned_cols=64 Identities=19% Similarity=0.224 Sum_probs=39.0
Q ss_pred hhhcCCCCCCHHHHHHHHHHH---HhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHhCCCCHHH
Q 009303 254 DQVKGLPGIGKSMQDHIQEIV---TTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDD 321 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil---~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~Girtled 321 (538)
++|..+ |++..=++-|.++. ..|.+.. +... ....+++.|++|+||||+||..+--.|+.-.|-
T Consensus 167 ~eL~~~-Gl~~~Ra~~L~~lA~~i~~g~l~l-~~~~--~~~~~~~~L~~LpGIGpwTA~~vllr~lg~~D~ 233 (283)
T PRK10308 167 QALKAL-GMPLKRAEALIHLANAALEGTLPL-TIPG--DVEQAMKTLQTFPGIGRWTANYFALRGWQAKDV 233 (283)
T ss_pred HHHHHC-CCCHHHHHHHHHHHHHHHcCCCCc-cccC--CHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCC
Confidence 456655 77764444444443 4577652 2111 123477888899999999999876555544433
No 132
>cd01700 PolY_Pol_V_umuC umuC subunit of DNA Polymerase V. umuC subunit of Pol V. Pol V is a bacterial translesion synthesis (TLS) polymerase that consists of the heterotrimer of one umuC and two umuD subunits. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol V, RecA, single stranded DNA-binding protein, beta sliding clamp, and gamma clamp loading complex are responsible for inducing the SOS response in bacteria to repair UV-induced DNA damage.
Probab=79.68 E-value=1.3 Score=46.50 Aligned_cols=29 Identities=48% Similarity=0.792 Sum_probs=25.9
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009303 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~ 325 (538)
+..+||||++++++|.+.||+|+.||.+-
T Consensus 178 l~~l~gig~~~~~~L~~~Gi~ti~dL~~~ 206 (344)
T cd01700 178 VGDVWGIGRRTAKKLNAMGIHTAGDLAQA 206 (344)
T ss_pred hhhcCccCHHHHHHHHHcCCCcHHHHhcC
Confidence 35789999999999999999999999863
No 133
>PRK14976 5'-3' exonuclease; Provisional
Probab=79.55 E-value=1.4 Score=45.33 Aligned_cols=25 Identities=44% Similarity=0.708 Sum_probs=21.6
Q ss_pred hhccCCCHHHHHHHHHh-CCCCHHHHhh
Q 009303 298 GEVWGIGPATAQKLYEK-GHRTLDDLKN 324 (538)
Q Consensus 298 ~~I~GvGpktA~~ly~~-GirtledL~~ 324 (538)
-+|+|||||||.+|.++ | |++++.+
T Consensus 194 pGVpGIG~KtA~~LL~~~g--sle~i~~ 219 (281)
T PRK14976 194 KGVKGIGPKTAIKLLNKYG--NIENIYE 219 (281)
T ss_pred CCCCcccHHHHHHHHHHcC--CHHHHHH
Confidence 35899999999999986 6 9999875
No 134
>PRK03348 DNA polymerase IV; Provisional
Probab=79.38 E-value=1.2 Score=48.75 Aligned_cols=29 Identities=41% Similarity=0.728 Sum_probs=26.1
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009303 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~ 325 (538)
+..+||||++++++|.+.||+|+.||.+-
T Consensus 182 v~~L~GIG~~t~~~L~~lGI~TigDLa~l 210 (454)
T PRK03348 182 VRRLWGIGPVTEEKLHRLGIETIGDLAAL 210 (454)
T ss_pred ccccCCCCHHHHHHHHHcCCccHHHHhcC
Confidence 45889999999999999999999999853
No 135
>PRK02406 DNA polymerase IV; Validated
Probab=79.16 E-value=1.3 Score=46.41 Aligned_cols=29 Identities=34% Similarity=0.409 Sum_probs=26.1
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009303 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~ 325 (538)
+..+||||++++++|-+.||+|+.||.+-
T Consensus 170 i~~l~giG~~~~~~L~~~Gi~ti~dl~~l 198 (343)
T PRK02406 170 VEKIPGVGKVTAEKLHALGIYTCADLQKY 198 (343)
T ss_pred cchhcCCCHHHHHHHHHcCCCcHHHHHhC
Confidence 45889999999999998899999999864
No 136
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=78.94 E-value=1.1 Score=43.72 Aligned_cols=51 Identities=24% Similarity=0.311 Sum_probs=36.6
Q ss_pred HHHHHHhhccCCCHHHHHHHHHh-CCCCHHHHhhc---cCcchhhhccccchhhh
Q 009303 292 RTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNE---DSLTHSQRLGLKYFDDI 342 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~-GirtledL~~~---~~L~~~q~~Glk~~ed~ 342 (538)
..+..|.+|-|||||+|-.+... ....|-+.... ..|++..|+|-|..+.+
T Consensus 70 ~lF~~LisVnGIGpK~ALaiLs~~~~~~l~~aI~~~d~~~L~k~PGIGkKtAeri 124 (201)
T COG0632 70 ELFRLLISVNGIGPKLALAILSNLDPEELAQAIANEDVKALSKIPGIGKKTAERI 124 (201)
T ss_pred HHHHHHHccCCccHHHHHHHHcCCCHHHHHHHHHhcChHhhhcCCCCCHHHHHHH
Confidence 36777789999999999999764 44444444322 25888999998875543
No 137
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=78.93 E-value=1.2 Score=41.14 Aligned_cols=27 Identities=15% Similarity=0.004 Sum_probs=22.6
Q ss_pred hHHHHHHhhccCCCHHHHHHHHHhCCC
Q 009303 291 VRTISLFGEVWGIGPATAQKLYEKGHR 317 (538)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~Gir 317 (538)
....+.|++++||||+||..+--.++.
T Consensus 79 ~~~~~~L~~l~GIG~~tA~~~l~~~~~ 105 (158)
T cd00056 79 PDAREELLALPGVGRKTANVVLLFALG 105 (158)
T ss_pred cccHHHHHcCCCCCHHHHHHHHHHHCC
Confidence 457888889999999999998776555
No 138
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=78.61 E-value=3.6 Score=47.22 Aligned_cols=68 Identities=24% Similarity=0.278 Sum_probs=45.7
Q ss_pred hHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHH
Q 009303 232 RSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKL 311 (538)
Q Consensus 232 r~~aY~rAa~~l~~l~~~i~~~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l 311 (538)
-+..|.|-.+.=..+ -..|..|||||++.+.++.+- -| -++.+.+. ..+.+.+|+|+|+++|+.+
T Consensus 621 fAi~~hR~~r~k~~~------~s~L~~IPGIGpkr~k~LL~~--FG---Sle~I~~A----S~eELa~V~Gig~k~Ae~I 685 (694)
T PRK14666 621 YAIGRHRRARAGAAL------TGELQRVEGIGPATARLLWER--FG---SLQAMAAA----GEEGLAAVPGIGPARAAAL 685 (694)
T ss_pred HHHHHHHHHHHhhhh------HhHHhhCCCCCHHHHHHHHHH--hC---CHHHHHhc----CHHHHHhcCCcCHHHHHHH
Confidence 355666555432222 257899999999998887663 34 44555442 2344678999999999999
Q ss_pred HHh
Q 009303 312 YEK 314 (538)
Q Consensus 312 y~~ 314 (538)
++.
T Consensus 686 ~~~ 688 (694)
T PRK14666 686 HEH 688 (694)
T ss_pred HHH
Confidence 863
No 139
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=78.44 E-value=4.2 Score=46.23 Aligned_cols=52 Identities=23% Similarity=0.476 Sum_probs=38.6
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 314 (538)
..|.+|||||+..+.+|.+.. |+ ++.+.+. ..+.+.+|+|||+++|+.+++.
T Consensus 543 s~L~~IpGIG~k~~k~Ll~~F--gS---~~~i~~A----s~eeL~~v~Gig~~~A~~I~~~ 594 (598)
T PRK00558 543 SALDDIPGIGPKRRKALLKHF--GS---LKAIKEA----SVEELAKVPGISKKLAEAIYEA 594 (598)
T ss_pred hhHhhCCCcCHHHHHHHHHHc--CC---HHHHHhC----CHHHHhhcCCcCHHHHHHHHHH
Confidence 568999999999999876643 44 4444432 2344679999999999999864
No 140
>PRK03103 DNA polymerase IV; Reviewed
Probab=78.08 E-value=1.6 Score=46.95 Aligned_cols=29 Identities=28% Similarity=0.543 Sum_probs=25.7
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009303 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~ 325 (538)
+..+||||++++++|-+.||+|+.||.+-
T Consensus 183 i~~l~gig~~~~~~L~~~Gi~tigdl~~~ 211 (409)
T PRK03103 183 VRKLFGVGSRMEKHLRRMGIRTIGQLANT 211 (409)
T ss_pred HhhcCCccHHHHHHHHHcCCCCHHHHhcC
Confidence 35789999999999998999999999853
No 141
>PRK02794 DNA polymerase IV; Provisional
Probab=77.85 E-value=1.5 Score=47.51 Aligned_cols=29 Identities=48% Similarity=0.950 Sum_probs=26.3
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009303 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~ 325 (538)
+..+||||++++++|.+.||+|+.||.+-
T Consensus 211 l~~L~GiG~~~~~~L~~~GI~tigdL~~l 239 (419)
T PRK02794 211 VGIIWGVGPATAARLARDGIRTIGDLQRA 239 (419)
T ss_pred hhhhCCCCHHHHHHHHHhccchHHHHhhC
Confidence 46899999999999999999999999853
No 142
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=77.74 E-value=1.8 Score=43.43 Aligned_cols=27 Identities=33% Similarity=0.423 Sum_probs=22.6
Q ss_pred hhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009303 298 GEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 298 ~~I~GvGpktA~~ly~~GirtledL~~~ 325 (538)
-+|+|||||||.+|.++ +.|++++.+.
T Consensus 186 pGv~GiG~ktA~~Ll~~-~gsle~i~~~ 212 (240)
T cd00008 186 PGVPGIGEKTAAKLLKE-YGSLEGILEN 212 (240)
T ss_pred CCCCccCHHHHHHHHHH-hCCHHHHHHh
Confidence 36899999999999987 3499999854
No 143
>cd00424 PolY Y-family of DNA polymerases. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Most TLS polymerases are members of the Y-family, including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is found exclusively in bacteria. In eukaryotes, the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in ord
Probab=77.72 E-value=1.7 Score=45.67 Aligned_cols=28 Identities=32% Similarity=0.462 Sum_probs=25.6
Q ss_pred hhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009303 298 GEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 298 ~~I~GvGpktA~~ly~~GirtledL~~~ 325 (538)
..+||||++++++|.+.||+|+.||.+-
T Consensus 176 ~~l~giG~~~~~~L~~~Gi~ti~dl~~~ 203 (343)
T cd00424 176 TDLPGIGAVTAKRLEAVGINPIGDLLAA 203 (343)
T ss_pred hhcCCCCHHHHHHHHHcCCCcHHHHhcC
Confidence 4689999999999999999999999864
No 144
>PRK14133 DNA polymerase IV; Provisional
Probab=77.64 E-value=1.6 Score=45.96 Aligned_cols=29 Identities=34% Similarity=0.512 Sum_probs=26.0
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009303 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~ 325 (538)
+..+||||++++++|.+.||+|+.||.+-
T Consensus 175 v~~l~gig~~~~~~L~~~Gi~ti~dl~~l 203 (347)
T PRK14133 175 ISKVHGIGKKSVEKLNNIGIYTIEDLLKL 203 (347)
T ss_pred ccccCCCCHHHHHHHHHcCCccHHHHhhC
Confidence 35789999999999999999999999864
No 145
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=77.58 E-value=4.6 Score=46.29 Aligned_cols=54 Identities=13% Similarity=0.182 Sum_probs=38.7
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHhCC
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGH 316 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~Gi 316 (538)
..|.+|||||+.-+.++-. ++..++.+++ -.++.+.+|+|||++.|+++|...-
T Consensus 608 s~L~~IpGiG~kr~~~LL~-----~FgS~~~i~~----As~eel~~v~gi~~~~A~~i~~~~~ 661 (691)
T PRK14672 608 LSFERLPHVGKVRAHRLLA-----HFGSFRSLQS----ATPQDIATAIHIPLTQAHTILHAAT 661 (691)
T ss_pred cccccCCCCCHHHHHHHHH-----HhcCHHHHHh----CCHHHHHhCCCCCHHHHHHHHHHhh
Confidence 4577999999988776543 2334444443 2456677999999999999998743
No 146
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=77.15 E-value=0.96 Score=50.77 Aligned_cols=64 Identities=17% Similarity=0.201 Sum_probs=47.2
Q ss_pred hhccCCCHHHHHHHHHhC-CCCHHHHhh--ccCcchhhhccccchhhhccCcCHHHHHHHHHHHHHH
Q 009303 298 GEVWGIGPATAQKLYEKG-HRTLDDLKN--EDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKA 361 (538)
Q Consensus 298 ~~I~GvGpktA~~ly~~G-irtledL~~--~~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~iv~~~ 361 (538)
++|-|+|++++.+|++.| ++++.||.+ ...|..+.+||-+..+.+...|-.+.-..+..++-.+
T Consensus 428 mdI~GlGe~~i~~L~~~G~i~~~~Diy~L~~~~l~~l~gfgeks~~nll~aIe~sk~~~l~r~l~aL 494 (562)
T PRK08097 428 LGLDGIGEGTWRALHQTGLFEHLFSWLALTPEQLANTPGIGKARAEQLWHQFNLARQQPFSRWLKAL 494 (562)
T ss_pred cCCCCcCHHHHHHHHHcCCcCCHHHHhcCCHHHHhcCcCccHHHHHHHHHHHHHHcCCCHHHHHHHc
Confidence 489999999999999997 599999974 3457777889988888777655443333345555443
No 147
>PRK07758 hypothetical protein; Provisional
Probab=76.29 E-value=1.3 Score=37.92 Aligned_cols=44 Identities=14% Similarity=0.286 Sum_probs=36.3
Q ss_pred ccCCCHHHHHHHHHhCCCCHHHHhh--ccCcchhhhccccchhhhc
Q 009303 300 VWGIGPATAQKLYEKGHRTLDDLKN--EDSLTHSQRLGLKYFDDIK 343 (538)
Q Consensus 300 I~GvGpktA~~ly~~GirtledL~~--~~~L~~~q~~Glk~~ed~~ 343 (538)
.++++.....-|...||.|++||.. ...|..+.+||-+..++|.
T Consensus 39 ~~~LSvRA~N~Lk~AGI~TL~dLv~~te~ELl~iknlGkKSL~EIk 84 (95)
T PRK07758 39 LSLLSAPARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLR 84 (95)
T ss_pred CccccHHHHHHHHHcCCCcHHHHHcCCHHHHHHccCCCHHHHHHHH
Confidence 4688889999999999999999974 4568888899988877665
No 148
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=76.12 E-value=5.9 Score=38.17 Aligned_cols=25 Identities=16% Similarity=0.167 Sum_probs=20.4
Q ss_pred HHHHHHhhccCCCHHHHHHHHHhCC
Q 009303 292 RTISLFGEVWGIGPATAQKLYEKGH 316 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~Gi 316 (538)
..++.|++++|||++||..+--.++
T Consensus 103 ~~~~~L~~l~GIG~ktA~~ill~~~ 127 (191)
T TIGR01083 103 EDREELVKLPGVGRKTANVVLNVAF 127 (191)
T ss_pred hHHHHHHhCCCCcHHHHHHHHHHHc
Confidence 3577788999999999999876544
No 149
>PRK00076 recR recombination protein RecR; Reviewed
Probab=75.81 E-value=2.2 Score=41.55 Aligned_cols=21 Identities=38% Similarity=0.618 Sum_probs=18.6
Q ss_pred HHHHHHhhccCCCHHHHHHHH
Q 009303 292 RTISLFGEVWGIGPATAQKLY 312 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly 312 (538)
..++.|.++||||+|+|+++-
T Consensus 8 ~Li~~l~~LPGIG~KsA~Rla 28 (196)
T PRK00076 8 KLIEALRKLPGIGPKSAQRLA 28 (196)
T ss_pred HHHHHHHHCCCCCHHHHHHHH
Confidence 467889999999999999984
No 150
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=75.46 E-value=3.2 Score=40.82 Aligned_cols=53 Identities=19% Similarity=0.253 Sum_probs=34.0
Q ss_pred CCHHHHHHHHHHHHh-CCcchhHHHH--hhchhHHHHHHh-hccCCCHHHHHHHHH-hCCC
Q 009303 262 IGKSMQDHIQEIVTT-GKLSKLEHFE--KDEKVRTISLFG-EVWGIGPATAQKLYE-KGHR 317 (538)
Q Consensus 262 IG~~ia~kI~Eil~t-G~~~~le~l~--~~~~~~~l~lf~-~I~GvGpktA~~ly~-~Gir 317 (538)
+-..=|+.|.++... |. +++.. ........+.|+ ++||||+|||.-+-. .|++
T Consensus 85 f~~~KAk~I~~~~~~~~~---l~~~~~~~~~~~~~R~~Ll~~lpGIG~KTAd~vL~~~~~~ 142 (208)
T PRK01229 85 FYNKRAEYIVEARKLYGK---LKEIIKADKDQFEAREFLVKNIKGIGYKEASHFLRNVGYE 142 (208)
T ss_pred cHHHHHHHHHHHHHHHHH---HHHHHhccCCchHHHHHHHHcCCCCcHHHHHHHHHHccCC
Confidence 445556666666543 32 23222 233456888888 999999999999874 4553
No 151
>PRK13300 tRNA CCA-pyrophosphorylase; Provisional
Probab=75.03 E-value=10 Score=41.55 Aligned_cols=45 Identities=24% Similarity=0.289 Sum_probs=30.8
Q ss_pred HHHHHHHhhhcCCCeEEEecccccccCCcC--CCeeEEEecCCcchh
Q 009303 355 ERLLQKAGEEVLPEVIILCGGSYRRGKASC--GDLDVVIMHPDRKSH 399 (538)
Q Consensus 355 ~~iv~~~~~~~~p~~~v~~~Gs~RRgke~~--~DVDiLit~~~~~~~ 399 (538)
...+++.+.+....+.|.++|||.||.-.- +||||.|..|...+.
T Consensus 28 ~~~L~~~~~~~~~~~~V~l~GS~ArgT~L~GdsDIDIFv~fp~~~~~ 74 (447)
T PRK13300 28 IERLEEAIKELGLDAEVELVGSTARGTWLSGDRDIDIFVLFPKDTSR 74 (447)
T ss_pred HHHHHHHHHhcCCceEEEEEeeecCCcccCCCCceeEEEEeCCCCCH
Confidence 333444333322237899999999998886 589999988765543
No 152
>PTZ00205 DNA polymerase kappa; Provisional
Probab=74.30 E-value=2.1 Score=47.97 Aligned_cols=29 Identities=34% Similarity=0.408 Sum_probs=26.2
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009303 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~ 325 (538)
+.+|||||++++++|-..||.|+.||.+.
T Consensus 311 V~ki~GIG~~t~~~L~~~GI~TigDLa~~ 339 (571)
T PTZ00205 311 LRSVPGVGKVTEALLKGLGITTLSDIYNR 339 (571)
T ss_pred cceeCCcCHHHHHHHHHcCCCcHHHHhcC
Confidence 46899999999999999999999999853
No 153
>PRK10702 endonuclease III; Provisional
Probab=74.10 E-value=5.7 Score=39.10 Aligned_cols=25 Identities=16% Similarity=0.242 Sum_probs=20.0
Q ss_pred HHHHHHhhccCCCHHHHHHHHHhCC
Q 009303 292 RTISLFGEVWGIGPATAQKLYEKGH 316 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~Gi 316 (538)
..++.|+++||||+|||.-+---++
T Consensus 106 ~~~~~Ll~lpGVG~ktA~~ill~a~ 130 (211)
T PRK10702 106 EDRAALEALPGVGRKTANVVLNTAF 130 (211)
T ss_pred chHHHHhcCCcccHHHHHHHHHHHc
Confidence 4677888999999999998754433
No 154
>cd05403 NT_KNTase_like Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. S. aureus KNTase is a plasmid encoded enzyme which confers resistance to a wide range of aminoglycoside antibiotics which have a 4'- or 4''-hydroxyl group in the equatorial position, such as kanamycin A. This enzyme transfers a nucleoside monophosphate group from a nucleotide (ATP,GTP, or UTP) to the 4'-hydroxyl group of kanamycin A. This enzyme is a homodimer, having two NT active sites. The nucleotide and antibiotic binding sites of each active site include residues from each monomer. Included in this subgroup is Escherichia coli AadA5 which confers resistance to the antibiotic spectinomycin and is a putative aminoglycoside-3'-adenylyltransferase. It is part of the aadA5 cassette of a class 1 integron. This subgroup also includes Haemophilus influenzae HI0073 which forms a 2:2 heterotetramer with an unrelated protein HI0074. Structurally HI0074 is
Probab=73.94 E-value=6.9 Score=31.95 Aligned_cols=29 Identities=31% Similarity=0.510 Sum_probs=24.2
Q ss_pred EEEecccccccCCc-CCCeeEEEecCCcch
Q 009303 370 IILCGGSYRRGKAS-CGDLDVVIMHPDRKS 398 (538)
Q Consensus 370 ~v~~~Gs~RRgke~-~~DVDiLit~~~~~~ 398 (538)
.+.+-||+-||..+ .+||||+|-.++...
T Consensus 20 ~i~LfGS~arg~~~~~SDiDl~vi~~~~~~ 49 (93)
T cd05403 20 KVYLFGSYARGDARPDSDIDLLVIFDDPLD 49 (93)
T ss_pred EEEEEeeeecCCCCCCCCeeEEEEeCCCCC
Confidence 78899999999975 789999997766543
No 155
>PRK00254 ski2-like helicase; Provisional
Probab=73.63 E-value=15 Score=42.61 Aligned_cols=53 Identities=21% Similarity=0.354 Sum_probs=38.5
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 314 (538)
-.|.+|||||+..+.+ +++.| +..++++..-. .+.+..|+|||+++|+++++.
T Consensus 645 ~~L~~ipgig~~~~~~---l~~~g-~~s~~~i~~a~----~~el~~~~gi~~~~a~~i~~~ 697 (720)
T PRK00254 645 LELMRLPMIGRKRARA---LYNAG-FRSIEDIVNAK----PSELLKVEGIGAKIVEGIFKH 697 (720)
T ss_pred hhhhcCCCCCHHHHHH---HHHcc-CCCHHHHHhCC----HHHHhcCCCCCHHHHHHHHHH
Confidence 3477899999987776 45555 45566655422 334569999999999999986
No 156
>cd03468 PolY_like DNA Polymerase Y-family. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in order to access the lesion. Because of their high error rates, TLS polymerases are potential targets for cancer treatment and prevention.
Probab=73.07 E-value=2.8 Score=43.62 Aligned_cols=37 Identities=30% Similarity=0.384 Sum_probs=28.6
Q ss_pred hccCCCHHHHHHHHHhCCCCHHHHhhccCcchhhhcc
Q 009303 299 EVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLG 335 (538)
Q Consensus 299 ~I~GvGpktA~~ly~~GirtledL~~~~~L~~~q~~G 335 (538)
.++|||++++++|-+.||+|+.||.+-..-.-.++||
T Consensus 174 ~~~gig~~~~~~L~~~Gi~t~~dl~~~~~~~l~~rfG 210 (335)
T cd03468 174 AALRLPPETVELLARLGLRTLGDLAALPRAELARRFG 210 (335)
T ss_pred hHhCCCHHHHHHHHHhCcccHHHHHhCChHHHHhhcC
Confidence 5889999999999999999999998643222233455
No 157
>TIGR01084 mutY A/G-specific adenine glycosylase. This equivalog model identifies mutY members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=73.05 E-value=6 Score=40.55 Aligned_cols=69 Identities=14% Similarity=0.205 Sum_probs=41.9
Q ss_pred CCChhHHHHHHHHHHHhcC-Cccc-cchhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCC
Q 009303 228 GEDRRSFSYYKAIPVIEKL-PFKI-ESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGI 303 (538)
Q Consensus 228 g~~~r~~aY~rAa~~l~~l-~~~i-~~~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~Gv 303 (538)
|--.|++.-.+||..|..- ...+ .+.++|.+|||||..+|+.|--+.- |+..-+ ....+.+.+.+++|+
T Consensus 77 G~y~RAr~L~~~A~~i~~~~~g~~p~~~~~L~~LpGIG~~TA~~Il~~a~-~~~~~~------vD~~v~RVl~Rl~~~ 147 (275)
T TIGR01084 77 GYYARARNLHKAAQEVVEEFGGEFPQDFEDLAALPGVGRYTAGAILSFAL-NKPYPI------LDGNVKRVLSRLFAV 147 (275)
T ss_pred CcHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCCCHHHHHHHHHHHC-CCCCCc------chHhHHHHHHHHccC
Confidence 4323777777888777541 1111 3468899999999999999886553 332111 122355556555554
No 158
>cd01702 PolY_Pol_eta DNA Polymerase eta. Pol eta, also called Rad30A, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Unlike other Y-family members, Pol eta can efficiently and accurately replicate DNA past UV-induced lesions. Its activity is initiated by two simultaneous interactions: the PIP box in pol eta interacting with PCNA, and the UBZ (ubiquitin-binding zinc finger) in pol eta interacting with monoubiquitin attached to PCNA. Pol eta is more efficient in copying damaged DNA than undamaged DNA and seems to recognize when a lesion has been passed, facilitating a lesion-dependent dissociation from the DNA.
Probab=72.86 E-value=2.8 Score=44.55 Aligned_cols=29 Identities=17% Similarity=0.307 Sum_probs=24.6
Q ss_pred HhhccCCCHHHHHHHHH-hCCCCHHHHhhc
Q 009303 297 FGEVWGIGPATAQKLYE-KGHRTLDDLKNE 325 (538)
Q Consensus 297 f~~I~GvGpktA~~ly~-~GirtledL~~~ 325 (538)
+..+||||+++++++.+ .||+|+.||.+-
T Consensus 184 v~~l~GiG~~~~~~ll~~~Gi~ti~dl~~~ 213 (359)
T cd01702 184 ITSIRGLGGKLGEEIIDLLGLPTEGDVAGF 213 (359)
T ss_pred HHHhCCcCHHHHHHHHHHcCCcCHHHHHhc
Confidence 45889999999988765 699999999864
No 159
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=72.68 E-value=3.7 Score=36.82 Aligned_cols=26 Identities=42% Similarity=0.542 Sum_probs=23.5
Q ss_pred cCCCHHHHHHHHHhCCCCHHHHhhcc
Q 009303 301 WGIGPATAQKLYEKGHRTLDDLKNED 326 (538)
Q Consensus 301 ~GvGpktA~~ly~~GirtledL~~~~ 326 (538)
||+|++++.+|-+.||.|.+||.+.+
T Consensus 1 pgi~~~~~~~L~~~GI~t~~~Ll~~~ 26 (122)
T PF14229_consen 1 PGIGPKEAAKLKAAGIKTTGDLLEAG 26 (122)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHHcC
Confidence 79999999999888999999998653
No 160
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=72.51 E-value=3.8 Score=41.39 Aligned_cols=53 Identities=25% Similarity=0.401 Sum_probs=39.4
Q ss_pred chhHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhccccchhhh
Q 009303 289 EKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDI 342 (538)
Q Consensus 289 ~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~~--~L~~~q~~Glk~~ed~ 342 (538)
....-+.++.++||||++.|..+.+. +.|++++.++. .|....++|.+....|
T Consensus 176 ~~e~q~~il~s~pgig~~~a~~ll~~-fgS~~~~~tas~~eL~~v~gig~k~A~~I 230 (254)
T COG1948 176 LKELQLYILESIPGIGPKLAERLLKK-FGSVEDVLTASEEELMKVKGIGEKKAREI 230 (254)
T ss_pred hHHHHHHHHHcCCCccHHHHHHHHHH-hcCHHHHhhcCHHHHHHhcCccHHHHHHH
Confidence 34456778889999999999999874 55888888653 5777777776654443
No 161
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=71.64 E-value=5.2 Score=46.51 Aligned_cols=89 Identities=12% Similarity=0.165 Sum_probs=67.3
Q ss_pred CCCCCCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEe-ecCCCccEEEEcCChHHHHHHHHhhhcccC-ccccccch
Q 009303 13 LDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEE-KLSKKVTHVLAMDLEALLQQVSKQHLARFK-GSVIRYQW 90 (538)
Q Consensus 13 ~~~~~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~-~ls~~VTHVV~~~~~~~~~~l~~~~~~~~~-~~lV~~~W 90 (538)
......|+++.+|.+.+.+.. ..-+++.-..+|+..+. +.-++.|||++.+..+. + +..++ ++..++.|
T Consensus 42 ~t~~s~fs~is~~~ngs~~e~--~nelk~~~~~~t~~~~~~~~rs~T~~ii~~~l~a~---~----vk~~~~~~~~~~e~ 112 (1016)
T KOG2093|consen 42 ATGSSSFSGISISVNGSTDES--ANELKLQNMFHTGASAASYERSGTENIIAQGLPAD---L----VKGFTIPKHISIEW 112 (1016)
T ss_pred cCCcceeeeeeeccCCccccc--hHHHhhhhhhcccccccccccccceeeecccchHH---H----hccccchhhhcHHH
Confidence 445689999999998877763 35566788899999984 44678999999887643 1 12222 67899999
Q ss_pred HHHHHhcCcccCcccccccc
Q 009303 91 LEDSLRLGEKVSEDLYRIKL 110 (538)
Q Consensus 91 l~ecik~g~lv~e~~y~l~~ 110 (538)
+.||.+.|..|.--.|.+..
T Consensus 113 iie~~~~~~~~~~~~~~~~t 132 (1016)
T KOG2093|consen 113 IIECCENGMDVGYYPYQLYT 132 (1016)
T ss_pred HHHHHhccCccccccceeec
Confidence 99999999999877776544
No 162
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=71.35 E-value=3 Score=43.31 Aligned_cols=25 Identities=48% Similarity=0.740 Sum_probs=22.0
Q ss_pred hccCCCHHHHHHHHHh-CCCCHHHHhhc
Q 009303 299 EVWGIGPATAQKLYEK-GHRTLDDLKNE 325 (538)
Q Consensus 299 ~I~GvGpktA~~ly~~-GirtledL~~~ 325 (538)
+|+|||||||.+|.++ | |++.|.+.
T Consensus 202 GV~GIG~ktA~~Ll~~~g--s~e~i~~~ 227 (310)
T COG0258 202 GVKGIGPKTALKLLQEYG--SLEGLYEN 227 (310)
T ss_pred CCCCcCHHHHHHHHHHhC--CHHHHHHh
Confidence 5999999999999998 8 88888753
No 163
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=70.67 E-value=5 Score=39.73 Aligned_cols=22 Identities=23% Similarity=0.210 Sum_probs=18.2
Q ss_pred HHHHHHhhccCCCHHHHHHHHH
Q 009303 292 RTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~ 313 (538)
...+.|++++|||++||..+--
T Consensus 118 ~~re~Ll~l~GIG~kTAd~iLl 139 (218)
T PRK13913 118 VTREWLLDQKGIGKESADAILC 139 (218)
T ss_pred hHHHHHHcCCCccHHHHHHHHH
Confidence 3567788999999999998754
No 164
>PRK10702 endonuclease III; Provisional
Probab=70.52 E-value=9.2 Score=37.64 Aligned_cols=43 Identities=12% Similarity=0.281 Sum_probs=31.3
Q ss_pred hHHHHHHHHHHHh-cCCcccc-chhhhcCCCCCCHHHHHHHHHHH
Q 009303 232 RSFSYYKAIPVIE-KLPFKIE-SADQVKGLPGIGKSMQDHIQEIV 274 (538)
Q Consensus 232 r~~aY~rAa~~l~-~l~~~i~-~~~~l~~lpgIG~~ia~kI~Eil 274 (538)
|+....+++..|. .....+. +.++|.+|||||..+|+.|-=+.
T Consensus 85 kA~~l~~~a~~i~~~~~~~~p~~~~~Ll~lpGVG~ktA~~ill~a 129 (211)
T PRK10702 85 KAENVIKTCRILLEQHNGEVPEDRAALEALPGVGRKTANVVLNTA 129 (211)
T ss_pred HHHHHHHHHHHHHHHcCCCCCchHHHHhcCCcccHHHHHHHHHHH
Confidence 6666677777764 3344333 46889999999999999987554
No 165
>cd03586 PolY_Pol_IV_kappa DNA Polymerase IV/Kappa. Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Known primarily as Pol IV in prokaryotes and Pol kappa in eukaryotes, this polymerase has a propensity for generating frameshift mutations. The eukaryotic Pol kappa differs from Pol IV and Dpo4 by an N-terminal extension of ~75 residues known as the "N-clasp" region. The structure of Pol kappa shows DNA that is almost totally encircled by Pol kappa, with the N-clasp region augmenting the interactions between DNA and the polymerase. Pol kappa is more resistant than Pol eta and Pol iota to bulky guanine adducts and is efficient at catalyzing the incorporation of dCTP. Bacterial pol IV has a
Probab=69.65 E-value=3.3 Score=43.03 Aligned_cols=29 Identities=38% Similarity=0.532 Sum_probs=25.8
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009303 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~ 325 (538)
+..+||||.+++++|...||+|+.||.+-
T Consensus 173 l~~l~gig~~~~~~L~~~Gi~ti~dl~~~ 201 (334)
T cd03586 173 VRKIPGVGKVTAEKLKELGIKTIGDLAKL 201 (334)
T ss_pred chhhCCcCHHHHHHHHHcCCcCHHHHHcC
Confidence 35789999999999999999999999853
No 166
>COG0389 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]
Probab=68.49 E-value=3.5 Score=43.70 Aligned_cols=28 Identities=43% Similarity=0.697 Sum_probs=26.0
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhh
Q 009303 297 FGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (538)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~ 324 (538)
++.+||||+.++.++...||.|+.||.+
T Consensus 178 v~~~~GvG~~~~~~l~~~Gi~ti~dl~~ 205 (354)
T COG0389 178 VLEFWGVGKVTAEKLRRLGISTIGDLAE 205 (354)
T ss_pred hhhhCCCCHHHHHHHHHcCChhHHHHHh
Confidence 3489999999999999999999999987
No 167
>PF03118 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha chain C terminal domain; InterPro: IPR011260 The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals. The alpha subunit (RpoA) initiates RNAP assembly by dimerising to form a platform on which the beta subunits can interact. The alpha subunit consists of a N-terminal domain (NTD) and a C-terminal domain (CTD), connected by a short linker. The NTD is essential for RNAP assembly, while the CTD is necessary for transcription regulation, interacting with transcription factors and promoter upstream elements. In Escherichia coli, the catabolite activator protein (CAP or CRP) was shown to exert its effect through its interactions with the CTD, where CAP binding to CTD promotes RNAP binding to promoter DNA, thereby stimulating transcription initiation at class I CAP-dependent promoters. At class II CAP-dependent promoters, the interaction of CAP with CTD is one of multiple interactions involved in activation []. The CTD has a compact structure of four helices and two long arms enclosing its hydrophobic core, making its folding topology distinct from most other binding proteins. The upstream promoter element-binding site is formed from helices 1 and 4 [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3N97_B 1XS9_D 3K4G_A 3N4M_B 1COO_A 1LB2_E 3IYD_A 1Z3E_B 3GFK_B 3IHQ_B ....
Probab=68.25 E-value=6.8 Score=31.23 Aligned_cols=22 Identities=18% Similarity=0.376 Sum_probs=19.8
Q ss_pred hhhcCCCCCCHHHHHHHHHHHH
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVT 275 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~ 275 (538)
+++..+||+|+...+.|.+.|+
T Consensus 44 ~~L~~i~n~G~ksl~EI~~~L~ 65 (66)
T PF03118_consen 44 EDLLKIKNFGKKSLEEIKEKLK 65 (66)
T ss_dssp HHHHTSTTSHHHHHHHHHHHHH
T ss_pred HHHHhCCCCCHhHHHHHHHHHc
Confidence 6789999999999999998875
No 168
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=67.91 E-value=6.6 Score=38.68 Aligned_cols=86 Identities=23% Similarity=0.308 Sum_probs=48.7
Q ss_pred CCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh--CCCCHHHHhhccCc-chhhhccc-
Q 009303 261 GIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRTLDDLKNEDSL-THSQRLGL- 336 (538)
Q Consensus 261 gIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--GirtledL~~~~~L-~~~q~~Gl- 336 (538)
|+-..=|..|.++.+ .-+|+... +.+..++.|+++||||+|||.--... |+-++ -=+--+ .-.+++|+
T Consensus 80 Glyr~KAk~I~~~~~----~l~e~~~g-~vP~~~~eL~~LPGVGrKTAnvVL~~a~g~p~i---~VDTHV~Rvs~R~gl~ 151 (211)
T COG0177 80 GLYRNKAKNIKELAR----ILLEKFGG-EVPDTREELLSLPGVGRKTANVVLSFAFGIPAI---AVDTHVHRVSNRLGLV 151 (211)
T ss_pred CCcHHHHHHHHHHHH----HHHHHcCC-CCCchHHHHHhCCCcchHHHHHHHHhhcCCCcc---cccchHHHHHHHhCCC
Confidence 555666666665543 22333333 44567888889999999999988765 44322 101001 11233443
Q ss_pred ------cchhhhccCcCHHHHHHH
Q 009303 337 ------KYFDDIKTRIPRHEVEQM 354 (538)
Q Consensus 337 ------k~~ed~~~~i~r~Ea~~i 354 (538)
+..+++...||++.-..+
T Consensus 152 ~~~~p~~ve~~L~~~iP~~~~~~~ 175 (211)
T COG0177 152 PGKTPEEVEEALMKLIPKELWTDL 175 (211)
T ss_pred CCCCHHHHHHHHHHHCCHHHHHHH
Confidence 344566677787766554
No 169
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=67.79 E-value=7.5 Score=39.66 Aligned_cols=67 Identities=18% Similarity=0.296 Sum_probs=48.3
Q ss_pred hhcCCCCCCH---HHHHHHHHHHH-hCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHhCCCCHHHH
Q 009303 255 QVKGLPGIGK---SMQDHIQEIVT-TGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL 322 (538)
Q Consensus 255 ~l~~lpgIG~---~ia~kI~Eil~-tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL 322 (538)
+|.++ |+|= -|+.-.++|++ .|...-|..++...-..+.+.|+.+||||||.|.=+-=+|+.-++-+
T Consensus 175 ~LR~~-gfGYRAkYI~~ta~~l~~~~g~~~wLqsl~~~~yeear~~L~~lpGVG~KVADCI~Lm~l~~~~~V 245 (323)
T KOG2875|consen 175 ELRKL-GFGYRAKYISATARALQEKQGGLAWLQSLRKSSYEEAREALCSLPGVGPKVADCICLMSLDKLSAV 245 (323)
T ss_pred HHHHc-CcchhHHHHHHHHHHHHHhcccchHHHHHhcccHHHHHHHHhcCCCCcchHhhhhhhhhcCCCCcc
Confidence 45554 6774 46666777775 56677788888755555999999999999999997766655554444
No 170
>PF11798 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 This helix-hairpin-helix motif is found in proteins belonging to the type-Y family of DNA polymerases []. This type of polymerases are thought to be involved in UV protection and mutation [, ]. ; PDB: 3PZP_B 2OH2_B 2W7O_B 3IN5_B 1T94_A 2W7P_B 2W8K_A 2AGQ_A 1RYR_A 3RAX_A ....
Probab=67.29 E-value=2.7 Score=28.60 Aligned_cols=18 Identities=22% Similarity=0.501 Sum_probs=14.4
Q ss_pred hhcCCCCCCHHHHHHHHH
Q 009303 255 QVKGLPGIGKSMQDHIQE 272 (538)
Q Consensus 255 ~l~~lpgIG~~ia~kI~E 272 (538)
.+.+++|||+++++++..
T Consensus 12 pi~~~~GIG~kt~~kL~~ 29 (32)
T PF11798_consen 12 PIRKFWGIGKKTAKKLNK 29 (32)
T ss_dssp BGGGSTTS-HHHHHHHHC
T ss_pred CHHhhCCccHHHHHHHHH
Confidence 478999999999998764
No 171
>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a beta-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [, ].; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBN_M 2QBB_M 3I1M_M 3OFP_M 3OFX_M 3OFO_M 1VS5_M 3OAQ_M 2QAL_M 3J18_M ....
Probab=66.77 E-value=5.6 Score=34.76 Aligned_cols=26 Identities=23% Similarity=0.484 Sum_probs=21.3
Q ss_pred HHHHHhhccCCCHHHHHHHHHh-CCCC
Q 009303 293 TISLFGEVWGIGPATAQKLYEK-GHRT 318 (538)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~-Girt 318 (538)
+.-.|++|+|||+++|..+.+. |+..
T Consensus 13 i~~aLt~IyGIG~~~A~~Ic~~lgi~~ 39 (107)
T PF00416_consen 13 IYIALTKIYGIGRRKAKQICKKLGINP 39 (107)
T ss_dssp HHHHHTTSTTBCHHHHHHHHHHTTS-S
T ss_pred hHhHHhhhhccCHHHHHHHHHHcCCCh
Confidence 5666789999999999999886 7753
No 172
>KOG3524 consensus Predicted guanine nucleotide exchange factor (PEBBLE) [Signal transduction mechanisms]
Probab=66.72 E-value=7.9 Score=44.03 Aligned_cols=79 Identities=14% Similarity=0.214 Sum_probs=54.8
Q ss_pred CCCCCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHhhhcccCccccccchHHH
Q 009303 14 DSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLED 93 (538)
Q Consensus 14 ~~~~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~~~~~~~~~~l~~~~~~~~~~~lV~~~Wl~e 93 (538)
-....|++++.|| .++-..-. -+=+++..+||.|-.....++||.|+...... .+.... -. ..++.+.||.+
T Consensus 114 ly~~~m~~vvlcf--Tg~rkk~e-~lv~lvh~mgg~irkd~nsktthli~n~s~ge--k~~~a~--t~-~~~~rp~wv~~ 185 (850)
T KOG3524|consen 114 LYCELMKDVVMCF--TGERKKKE-ELVDLVHYMGGSIRKDTNSKTTHLIANKVEGE--KQSIAL--VG-VPTMRPDWVTE 185 (850)
T ss_pred ccchhhcCceeee--eccchhhH-HHHHHHHHhcceeEeeeccCceEEEeecccce--EEEEEe--ec-cceechHhhhh
Confidence 4457899999999 55532322 34489999999999999999999998655321 011000 11 46788999999
Q ss_pred HHhcCcc
Q 009303 94 SLRLGEK 100 (538)
Q Consensus 94 cik~g~l 100 (538)
||+-..-
T Consensus 186 aw~~rn~ 192 (850)
T KOG3524|consen 186 AWKHRND 192 (850)
T ss_pred hhcCcch
Confidence 9987644
No 173
>PF14579 HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI_A 3E0D_A 3F2C_A 3F2B_A 3F2D_A 2HQA_A 2HNH_A.
Probab=66.39 E-value=15 Score=30.94 Aligned_cols=49 Identities=22% Similarity=0.409 Sum_probs=30.4
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHhC
Q 009303 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKG 315 (538)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~G 315 (538)
+..|+|||+.+++.|.+--+.|.+.-++++... ++++..+..+.|...|
T Consensus 29 l~~Ikglg~~~a~~I~~~R~~g~f~s~~df~~R-----------~~~i~~~~le~Li~aG 77 (90)
T PF14579_consen 29 LSAIKGLGEEVAEKIVEERENGPFKSLEDFIQR-----------LPKINKRQLEALIKAG 77 (90)
T ss_dssp GGGSTTS-HHHHHHHHHHHHCSS-SSHHHHHHH-----------S-TS-HHHHHHHHHTT
T ss_pred HhhcCCCCHHHHHHHHHhHhcCCCCCHHHHHHH-----------HhcCCHHHHHHHHHCC
Confidence 567788888888887777777777776665432 2266666666666654
No 174
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=66.22 E-value=20 Score=34.43 Aligned_cols=53 Identities=23% Similarity=0.334 Sum_probs=33.1
Q ss_pred CChhHHHHHHHHHHHhcCCccccc-hhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhh
Q 009303 229 EDRRSFSYYKAIPVIEKLPFKIES-ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKD 288 (538)
Q Consensus 229 ~~~r~~aY~rAa~~l~~l~~~i~~-~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~ 288 (538)
++.+..-|-+-| .||+. +-+|.=||||||+++.+|-|=-+.+.+..++++.+-
T Consensus 97 ~E~~FV~FfN~A-------~PIt~RlH~LeLLPGIGKK~m~~ILeERkkkpFeSFeDi~~R 150 (181)
T PF04919_consen 97 NEERFVDFFNEA-------QPITLRLHSLELLPGIGKKTMWKILEERKKKPFESFEDIEER 150 (181)
T ss_dssp THHHHHHHH------------B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHH
T ss_pred ChHHHHHHhhcC-------CCChHHHHHHhhcccccHHHHHHHHHHHccCCCCCHHHHHHH
Confidence 334555555444 58886 468899999999999999999999999999888763
No 175
>PRK13766 Hef nuclease; Provisional
Probab=66.01 E-value=6.7 Score=45.86 Aligned_cols=10 Identities=20% Similarity=0.248 Sum_probs=6.6
Q ss_pred CCccEEEEcC
Q 009303 56 KKVTHVLAMD 65 (538)
Q Consensus 56 ~~VTHVV~~~ 65 (538)
+.++|||.-+
T Consensus 440 ~~~~~VI~yd 449 (773)
T PRK13766 440 PSVDLVIFYE 449 (773)
T ss_pred ccCCEEEEeC
Confidence 3578888744
No 176
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=65.91 E-value=11 Score=34.68 Aligned_cols=67 Identities=12% Similarity=0.149 Sum_probs=41.2
Q ss_pred ChhHHHHHHHHHHHhcCCccc-----cchhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCC
Q 009303 230 DRRSFSYYKAIPVIEKLPFKI-----ESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGI 303 (538)
Q Consensus 230 ~~r~~aY~rAa~~l~~l~~~i-----~~~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~Gv 303 (538)
+.|+.....++..+.+-.... +..++|.+|||||+.+|+.|.-+.-. . +.+-- ...+.+.+..+.++
T Consensus 54 ~~kA~~i~~~a~~~~~~~~~~~~~~~~~~~~L~~l~GIG~~tA~~~l~~~~~--~---~~~pv--D~~v~r~~~~~~~~ 125 (158)
T cd00056 54 RRKAKYLKELARAIVEGFGGLVLDDPDAREELLALPGVGRKTANVVLLFALG--P---DAFPV--DTHVRRVLKRLGLI 125 (158)
T ss_pred HHHHHHHHHHHHHHHHHcCCccCCCcccHHHHHcCCCCCHHHHHHHHHHHCC--C---CCCcc--chhHHHHHHHhCCC
Confidence 457777777777775432222 23467999999999999998765432 2 12211 23456666555554
No 177
>COG2251 Predicted nuclease (RecB family) [General function prediction only]
Probab=64.70 E-value=4.8 Score=43.63 Aligned_cols=27 Identities=37% Similarity=0.452 Sum_probs=24.7
Q ss_pred hccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009303 299 EVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 299 ~I~GvGpktA~~ly~~GirtledL~~~ 325 (538)
=|+||||.+.+.+++.||+|++||-..
T Consensus 229 Lv~Gi~~~r~~~l~~~GI~Ti~~LA~~ 255 (474)
T COG2251 229 LVPGITPSRYDVLEEVGITTIEDLADA 255 (474)
T ss_pred ccCCCCHHHHHHHHHcCcchHHHHHhc
Confidence 478999999999999999999999864
No 178
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=63.78 E-value=4.5 Score=33.81 Aligned_cols=20 Identities=40% Similarity=0.624 Sum_probs=17.8
Q ss_pred HHHhhccCCCHHHHHHHHHh
Q 009303 295 SLFGEVWGIGPATAQKLYEK 314 (538)
Q Consensus 295 ~lf~~I~GvGpktA~~ly~~ 314 (538)
++|++|||||+.+|-.|..+
T Consensus 2 ~~l~sipGig~~~a~~llae 21 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAE 21 (87)
T ss_pred chhcCCCCccHHHHHHHHHH
Confidence 46789999999999999875
No 179
>PRK13910 DNA glycosylase MutY; Provisional
Probab=63.35 E-value=14 Score=38.14 Aligned_cols=68 Identities=18% Similarity=0.203 Sum_probs=44.8
Q ss_pred hHHHHHHHHHHHhc-CCccc-cchhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHH
Q 009303 232 RSFSYYKAIPVIEK-LPFKI-ESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPA 306 (538)
Q Consensus 232 r~~aY~rAa~~l~~-l~~~i-~~~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpk 306 (538)
|++.-.++|..|.. ....+ .+.++|.+|||||..+|+.|--+. -|.-. . -...-+.+.|.+++|+...
T Consensus 48 RAr~L~~~A~~i~~~~~g~~P~~~~~L~~LpGIG~kTA~aIl~~a-f~~~~-~-----~VD~nV~RVl~Rl~g~~~~ 117 (289)
T PRK13910 48 RAKNLKKSAEICVKEHHSQLPNDYQSLLKLPGIGAYTANAILCFG-FREKS-A-----CVDANIKRVLLRLFGLDPN 117 (289)
T ss_pred HHHHHHHHHHHHHHHhCCCCChhHHHHHhCCCCCHHHHHHHHHHH-CCCCc-C-----cccHHHHHHHHHHhcCCCC
Confidence 77777788877742 22222 257899999999999999997654 23211 1 1223477788788887643
No 180
>PRK14973 DNA topoisomerase I; Provisional
Probab=62.74 E-value=8.9 Score=45.92 Aligned_cols=40 Identities=18% Similarity=0.136 Sum_probs=31.7
Q ss_pred HHHhhccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhc
Q 009303 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRL 334 (538)
Q Consensus 295 ~lf~~I~GvGpktA~~ly~~GirtledL~~~~--~L~~~q~~ 334 (538)
+-|++++||=...|+++|+.||+|++|+..+. .|+..-|+
T Consensus 802 ~~~~~~~gv~~~~~~~~~~~G~~~~~d~~~a~p~~La~~~g~ 843 (936)
T PRK14973 802 ISRLKEIGVPAVSLKKYQEAGFDTPEDFCSVHPAYLALKTGI 843 (936)
T ss_pred HHhhcccCCCHHHHHHHHHhcCCCHHHHHhcCHHHHhcCCCC
Confidence 34569999999999999999999999998653 35544443
No 181
>KOG2245 consensus Poly(A) polymerase and related nucleotidyltransferases [RNA processing and modification]
Probab=62.62 E-value=16 Score=40.28 Aligned_cols=86 Identities=26% Similarity=0.361 Sum_probs=60.0
Q ss_pred hhhccccchhhhccCcCHHHHHH-HHHHHHHHhhhc------------CCCeEEEecccccccCCc-CCCeeEEEecCCc
Q 009303 331 SQRLGLKYFDDIKTRIPRHEVEQ-MERLLQKAGEEV------------LPEVIILCGGSYRRGKAS-CGDLDVVIMHPDR 396 (538)
Q Consensus 331 ~q~~Glk~~ed~~~~i~r~Ea~~-i~~iv~~~~~~~------------~p~~~v~~~Gs~RRgke~-~~DVDiLit~~~~ 396 (538)
++.+|+ ||+-.+-..|.++-. +.+||++-++++ ..|.++..-||||-|--. +.|||=|+-.|.-
T Consensus 41 L~~~g~--fEs~eEt~~R~~VL~~L~~iVk~wVk~vs~~k~~p~~~~~~aggkIftfGSYRLGVhg~GADIDtLcV~Prh 118 (562)
T KOG2245|consen 41 LKNEGL--FESKEETQRREEVLGKLNQIVKEWVKKVSEQKGLPDGMIENAGGKIFTFGSYRLGVHGPGADIDTLCVGPRH 118 (562)
T ss_pred HHhcCC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCChhhhhhcCceEEeccceeecccCCCCCcceeeecccc
Confidence 455553 555555566666643 555655533321 234577778999999865 5599999998987
Q ss_pred chhhhhHHHHHHHHHHcCcccc
Q 009303 397 KSHKGFLSKYVKKLKEMKFLRE 418 (538)
Q Consensus 397 ~~~~~~l~~vv~~L~~~g~l~~ 418 (538)
.+...||..+-+.|+...-+++
T Consensus 119 v~R~DFF~sf~~mL~~~~eVte 140 (562)
T KOG2245|consen 119 VSRSDFFTSFYDMLKERPEVTE 140 (562)
T ss_pred ccHHHHHHHHHHHHhcCccccc
Confidence 7778999999999988877664
No 182
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=62.15 E-value=5.2 Score=41.51 Aligned_cols=55 Identities=27% Similarity=0.397 Sum_probs=41.9
Q ss_pred hhHHHHHHhhccCCCHHHHHHHHHh---C-CCCHHHHhhccC------cchhhhccccchhhhcc
Q 009303 290 KVRTISLFGEVWGIGPATAQKLYEK---G-HRTLDDLKNEDS------LTHSQRLGLKYFDDIKT 344 (538)
Q Consensus 290 ~~~~l~lf~~I~GvGpktA~~ly~~---G-irtledL~~~~~------L~~~q~~Glk~~ed~~~ 344 (538)
|..+++...++||+|||.|++|-+- | .+-+++++++.+ +++.-|+|.++.+.|.+
T Consensus 51 ~I~S~~ea~~lP~iG~kia~ki~EiletG~l~ele~v~~de~~~~lklFtnifGvG~ktA~~Wy~ 115 (353)
T KOG2534|consen 51 PITSGEEAEKLPGIGPKIAEKIQEILETGVLRELEAVRNDERSQSLKLFTNIFGVGLKTAEKWYR 115 (353)
T ss_pred CcccHHHhcCCCCCCHHHHHHHHHHHHcCCchhHHHHhcchhHHHHHHHHHHhccCHHHHHHHHH
Confidence 4457788889999999999999863 6 478888886432 56777888888777753
No 183
>COG1669 Predicted nucleotidyltransferases [General function prediction only]
Probab=61.88 E-value=27 Score=30.18 Aligned_cols=30 Identities=27% Similarity=0.393 Sum_probs=23.3
Q ss_pred CCe-EEEecccccccCCc-CCCeeEEEecCCc
Q 009303 367 PEV-IILCGGSYRRGKAS-CGDLDVVIMHPDR 396 (538)
Q Consensus 367 p~~-~v~~~Gs~RRgke~-~~DVDiLit~~~~ 396 (538)
.|+ .+.+-|||-||... -.||||||-...+
T Consensus 22 ~gv~~~~vFGS~aRgE~~~~SDIDILVef~~~ 53 (97)
T COG1669 22 YGVKRVAVFGSYARGEQKPDSDIDILVEFEPG 53 (97)
T ss_pred hCCceEEEeeeeecCCCCCCCCceeEEeecCC
Confidence 455 78899999999653 3899999976554
No 184
>PRK03980 flap endonuclease-1; Provisional
Probab=61.70 E-value=6.3 Score=40.79 Aligned_cols=25 Identities=44% Similarity=0.670 Sum_probs=21.4
Q ss_pred hccCCCHHHHHHHHHhCCCCHHHHhh
Q 009303 299 EVWGIGPATAQKLYEKGHRTLDDLKN 324 (538)
Q Consensus 299 ~I~GvGpktA~~ly~~GirtledL~~ 324 (538)
+|+|||||||.+|.++ +.||+.+..
T Consensus 193 GI~GIG~ktA~kLi~~-~~sle~i~~ 217 (292)
T PRK03980 193 GIKGIGPKTALKLIKK-HGDLEKVLE 217 (292)
T ss_pred CCCCccHHHHHHHHHH-CCCHHHHHH
Confidence 7899999999999986 238888876
No 185
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=60.92 E-value=6.6 Score=31.25 Aligned_cols=24 Identities=25% Similarity=0.326 Sum_probs=18.0
Q ss_pred hhHHHHH-HhhccCCCHHHHHHHHH
Q 009303 290 KVRTISL-FGEVWGIGPATAQKLYE 313 (538)
Q Consensus 290 ~~~~l~l-f~~I~GvGpktA~~ly~ 313 (538)
+...++. +.+|||||+++|.++.+
T Consensus 41 ~i~~~~~~~~~l~gIG~~ia~kI~E 65 (68)
T PF14716_consen 41 PITSGEEDLKKLPGIGKSIAKKIDE 65 (68)
T ss_dssp -HHSHHHHHCTSTTTTHHHHHHHHH
T ss_pred hHhhHHHHHhhCCCCCHHHHHHHHH
Confidence 3334554 78999999999999854
No 186
>TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Probab=60.91 E-value=6.2 Score=43.37 Aligned_cols=29 Identities=45% Similarity=0.571 Sum_probs=26.4
Q ss_pred hhccCCCHHHHHHHHHhCCCCHHHHhhcc
Q 009303 298 GEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (538)
Q Consensus 298 ~~I~GvGpktA~~ly~~GirtledL~~~~ 326 (538)
.-|+|||.+++.+|++.||.|++||-...
T Consensus 210 slv~gi~~~~~~~L~~~GI~ti~~La~~~ 238 (457)
T TIGR03491 210 SLVPGIGPSRYRLLQELGIHTLEDLAAAD 238 (457)
T ss_pred eecCCCCHHHHHHHHHcCCCcHHHHhcCC
Confidence 37999999999999999999999998654
No 187
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=60.87 E-value=5.1 Score=45.29 Aligned_cols=29 Identities=24% Similarity=0.339 Sum_probs=24.3
Q ss_pred HHhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009303 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 296 lf~~I~GvGpktA~~ly~~GirtledL~~~ 325 (538)
.|.+|+||||++.+.|++ -+.|+++++++
T Consensus 515 ~L~~I~GiG~kr~~~LL~-~Fgs~~~I~~A 543 (574)
T PRK14670 515 NYTKIKGIGEKKAKKILK-SLGTYKDILLL 543 (574)
T ss_pred ccccCCCCCHHHHHHHHH-HhCCHHHHHhC
Confidence 456999999999999998 46688888865
No 188
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=60.70 E-value=6 Score=38.49 Aligned_cols=37 Identities=22% Similarity=0.333 Sum_probs=25.5
Q ss_pred cccch-hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHH
Q 009303 249 KIESA-DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHF 285 (538)
Q Consensus 249 ~i~~~-~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l 285 (538)
++..+ +.+..|||||++.|.++.-.+-.-.-.+++.+
T Consensus 5 ~~~~Li~~l~~LPGIG~KsA~RlA~~ll~~~~~~~~~l 42 (195)
T TIGR00615 5 PISKLIESLKKLPGIGPKSAQRLAFHLLKRDPSEVLRL 42 (195)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHcCCHHHHHHH
Confidence 34443 67899999999999999876654443444433
No 189
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=60.62 E-value=13 Score=42.07 Aligned_cols=43 Identities=21% Similarity=0.496 Sum_probs=24.4
Q ss_pred HHHhhccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhccccc
Q 009303 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKY 338 (538)
Q Consensus 295 ~lf~~I~GvGpktA~~ly~~GirtledL~~~~--~L~~~q~~Glk~ 338 (538)
..|..|+|||++++++|++. +.|++++.++. .|....++|-+.
T Consensus 525 ~~L~~IpGIG~kr~~~LL~~-FGS~~~I~~As~eeL~~vpGi~~~~ 569 (577)
T PRK14668 525 TVLDDVPGVGPETRKRLLRR-FGSVEGVREASVEDLRDVPGVGEKT 569 (577)
T ss_pred hHHhcCCCCCHHHHHHHHHH-cCCHHHHHhCCHHHHHhCCCCCHHH
Confidence 33457777777777777764 34666665432 244444444433
No 190
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=60.62 E-value=6.4 Score=39.03 Aligned_cols=30 Identities=33% Similarity=0.531 Sum_probs=27.1
Q ss_pred HHHhhccCCCHHHHHHHHHhCCCCHHHHhh
Q 009303 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (538)
Q Consensus 295 ~lf~~I~GvGpktA~~ly~~GirtledL~~ 324 (538)
.-|+.|.||||+.+.+|.+.|+.++++|-.
T Consensus 158 DDL~~I~GIGp~~a~~L~eaGi~tfaQIAa 187 (221)
T PRK12278 158 DDLTKITGVGPALAKKLNEAGVTTFAQIAA 187 (221)
T ss_pred chheeccccChHHHHHHHHcCCCCHHHhhC
Confidence 346799999999999999999999999974
No 191
>cd05401 NT_GlnE_GlnD_like Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins. Escherichia coli GlnD and -E participate in the Glutamine synthetase (GS)/Glutamate synthase (GOGAT) pathway for the assimilation of ammonium nitrogen. In nitrogen sufficiency, GlnE adenylates GS, reducing GS activity; when nitrogen is limiting, GlnE deadenylates GS-AMP, restoring GS activity. When nitrogen is limiting, GlnD uridylylates the nitrogen regulatory protein PII to PII-UTP, and in nitrogen sufficiency, it removes the modifying groups. The activity of Escherichia coli GlnE is modulated by PII-proteins. PII-UMP promotes GlnE deadenylation activity, and PII promotes GlnE adenylation activity. Escherichia coli GlnE has two separate NT domains. The N-terminal NT domain catalyzes the deadenylylation of GS, and the C-terminal NT domain the adenylylation reaction. The majority of proteins in this family conta
Probab=60.50 E-value=32 Score=32.16 Aligned_cols=50 Identities=24% Similarity=0.355 Sum_probs=31.3
Q ss_pred CeEEEecccccccC-CcCCCeeEEEecCCcch-----hhhhHHHHHHHHHHcCccc
Q 009303 368 EVIILCGGSYRRGK-ASCGDLDVVIMHPDRKS-----HKGFLSKYVKKLKEMKFLR 417 (538)
Q Consensus 368 ~~~v~~~Gs~RRgk-e~~~DVDiLit~~~~~~-----~~~~l~~vv~~L~~~g~l~ 417 (538)
++-+...|||-|+. ....|+|+++-+++... ...+-..+++.|...|+..
T Consensus 55 ~~~~la~Gs~GR~E~~~~SD~D~~~v~~~~~~~~~~~~~~l~~~i~~~L~~~g~~~ 110 (172)
T cd05401 55 PFALLALGSYGRGELNPSSDQDLLLLYDDDGDEVAAYFEELAERLIKILSEAGGPY 110 (172)
T ss_pred cEEEEEeCCcccCCcCCCcCcceEEEeCCCCchHHHHHHHHHHHHHHHHHhCCCCC
Confidence 34567789986665 55789999998876532 1234444555555555443
No 192
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=60.49 E-value=6.3 Score=46.95 Aligned_cols=24 Identities=42% Similarity=0.678 Sum_probs=20.3
Q ss_pred hccCCCHHHHHHHHHh-CCCCHHHHhh
Q 009303 299 EVWGIGPATAQKLYEK-GHRTLDDLKN 324 (538)
Q Consensus 299 ~I~GvGpktA~~ly~~-GirtledL~~ 324 (538)
+|+|||||||.+|.++ | |||.+.+
T Consensus 189 GVpGIG~KtA~kLL~~yg--sle~i~~ 213 (887)
T TIGR00593 189 GVKGIGEKTAAKLLQEFG--SLENIYE 213 (887)
T ss_pred CCCCcCHHHHHHHHHHcC--CHHHHHH
Confidence 4999999999999987 6 7777763
No 193
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=60.27 E-value=26 Score=33.59 Aligned_cols=44 Identities=14% Similarity=0.203 Sum_probs=30.7
Q ss_pred hHHHHHHHHHHH-hcCCccc---------cc---hhhhcCCCCCCHHHHHHHHHHHH
Q 009303 232 RSFSYYKAIPVI-EKLPFKI---------ES---ADQVKGLPGIGKSMQDHIQEIVT 275 (538)
Q Consensus 232 r~~aY~rAa~~l-~~l~~~i---------~~---~~~l~~lpgIG~~ia~kI~Eil~ 275 (538)
|+...+.++..| +.+...+ .+ .++|..|||||+++|+.+--+|.
T Consensus 80 KAk~Lk~~a~~iie~y~G~v~~L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL~~l~ 136 (177)
T TIGR03252 80 MAKRVQALAQYVVDTYDGDATAVWTEGDPDGKELLRRLKALPGFGKQKAKIFLALLG 136 (177)
T ss_pred HHHHHHHHHHHHHHHhCCChhhhhcccCCCcHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 555556666666 4555554 11 46899999999999998876554
No 194
>PF14579 HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI_A 3E0D_A 3F2C_A 3F2B_A 3F2D_A 2HQA_A 2HNH_A.
Probab=60.20 E-value=11 Score=31.62 Aligned_cols=30 Identities=23% Similarity=0.470 Sum_probs=23.9
Q ss_pred HhhccCCCHHHHHHHHHh----CCCCHHHHhhcc
Q 009303 297 FGEVWGIGPATAQKLYEK----GHRTLDDLKNED 326 (538)
Q Consensus 297 f~~I~GvGpktA~~ly~~----GirtledL~~~~ 326 (538)
|+.|.|||.+.|+++.+. .++|++|+....
T Consensus 29 l~~Ikglg~~~a~~I~~~R~~g~f~s~~df~~R~ 62 (90)
T PF14579_consen 29 LSAIKGLGEEVAEKIVEERENGPFKSLEDFIQRL 62 (90)
T ss_dssp GGGSTTS-HHHHHHHHHHHHCSS-SSHHHHHHHS
T ss_pred HhhcCCCCHHHHHHHHHhHhcCCCCCHHHHHHHH
Confidence 779999999999999963 689999988643
No 195
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=60.19 E-value=4.6 Score=45.61 Aligned_cols=29 Identities=24% Similarity=0.517 Sum_probs=24.0
Q ss_pred HHhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009303 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 296 lf~~I~GvGpktA~~ly~~GirtledL~~~ 325 (538)
.|.+|+|||||+.+.|++ -+.|++.++++
T Consensus 515 ~Ld~I~GiG~kr~~~Ll~-~Fgs~~~ik~A 543 (567)
T PRK14667 515 ILDKIKGIGEVKKEIIYR-NFKTLYDFLKA 543 (567)
T ss_pred ccccCCCCCHHHHHHHHH-HhCCHHHHHhC
Confidence 456999999999999998 45688888864
No 196
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=59.14 E-value=7.6 Score=44.40 Aligned_cols=32 Identities=25% Similarity=0.423 Sum_probs=25.8
Q ss_pred HHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009303 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~GirtledL~~~ 325 (538)
....|.+|+||||++|+.|+.. +.|+++|.++
T Consensus 567 ~~s~L~~I~GIG~k~a~~Ll~~-Fgs~~~i~~A 598 (621)
T PRK14671 567 LQTELTDIAGIGEKTAEKLLEH-FGSVEKVAKA 598 (621)
T ss_pred hhhhhhcCCCcCHHHHHHHHHH-cCCHHHHHhC
Confidence 3456679999999999999874 4488988864
No 197
>PRK05007 PII uridylyl-transferase; Provisional
Probab=58.95 E-value=31 Score=41.26 Aligned_cols=49 Identities=20% Similarity=0.497 Sum_probs=34.9
Q ss_pred CCeEEEecccccccC-CcCCCeeEEEecCCcc--hhhhhHHHHHHHHHHcCc
Q 009303 367 PEVIILCGGSYRRGK-ASCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMKF 415 (538)
Q Consensus 367 p~~~v~~~Gs~RRgk-e~~~DVDiLit~~~~~--~~~~~l~~vv~~L~~~g~ 415 (538)
|++.++.+|||=||. .-.+|||+||-+++.. ....++.+++..|-+.|+
T Consensus 79 ~~~alvAvGgyGR~EL~p~SDiDll~l~~~~~~~~~~~~i~~~~~~lwD~gL 130 (884)
T PRK05007 79 PDLALVAVGGYGRGELHPLSDIDLLILSRKKLPDEQAQKVGELITLLWDLKL 130 (884)
T ss_pred CceEEEecCCCCCcccCCcccceEEEEeCCCCChHHHHHHHHHHHHHHhcCC
Confidence 467788899996664 5678999999988532 234566666666666664
No 198
>PRK02362 ski2-like helicase; Provisional
Probab=58.77 E-value=63 Score=37.76 Aligned_cols=52 Identities=19% Similarity=0.464 Sum_probs=38.9
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh-C
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-G 315 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~-G 315 (538)
-+|.+|||||...+.+..+ .| +..++++.+-++..+..+ +|.|+|+++.+. |
T Consensus 652 ~~L~~ip~i~~~~a~~l~~---~g-i~s~~dl~~~~~~~l~~~------~g~~~~~~i~~~~~ 704 (737)
T PRK02362 652 LDLVGLRGVGRVRARRLYN---AG-IESRADLRAADKSVVLAI------LGEKIAENILEQAG 704 (737)
T ss_pred HHHhCCCCCCHHHHHHHHH---cC-CCCHHHHHhCCHHHHHHH------HCHHHHHHHHHHhC
Confidence 4688999999998776664 44 677777775555545444 699999999987 6
No 199
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=58.61 E-value=13 Score=42.56 Aligned_cols=49 Identities=27% Similarity=0.575 Sum_probs=34.7
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (538)
..|.+|||||++.+..|-.-. |+ ++.+.+- ..+.+.+| ||+++|+.+++
T Consensus 569 s~L~~I~GIG~k~a~~Ll~~F--gs---~~~i~~A----s~eeL~~v--ig~k~A~~I~~ 617 (621)
T PRK14671 569 TELTDIAGIGEKTAEKLLEHF--GS---VEKVAKA----SLEELAAV--AGPKTAETIYR 617 (621)
T ss_pred hhhhcCCCcCHHHHHHHHHHc--CC---HHHHHhC----CHHHHHHH--hCHHHHHHHHH
Confidence 468899999999999765432 23 3455432 34445677 99999999986
No 200
>PTZ00217 flap endonuclease-1; Provisional
Probab=57.81 E-value=7.8 Score=41.80 Aligned_cols=26 Identities=35% Similarity=0.640 Sum_probs=21.9
Q ss_pred hhccCCCHHHHHHHHHhCCCCHHHHhh
Q 009303 298 GEVWGIGPATAQKLYEKGHRTLDDLKN 324 (538)
Q Consensus 298 ~~I~GvGpktA~~ly~~GirtledL~~ 324 (538)
-+|+|||||||.+|.++ +.|++.+.+
T Consensus 238 pgi~GIG~ktA~~Li~~-~gsle~il~ 263 (393)
T PTZ00217 238 DTIKGIGPKTAYKLIKK-YKSIEEILE 263 (393)
T ss_pred CCCCCccHHHHHHHHHH-cCCHHHHHH
Confidence 47999999999999987 338888874
No 201
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=56.77 E-value=9.3 Score=39.47 Aligned_cols=39 Identities=28% Similarity=0.333 Sum_probs=27.0
Q ss_pred HHHHhhccCCCHHHHHHHHHh-CC--CCHHHHhhcc-Ccchhh
Q 009303 294 ISLFGEVWGIGPATAQKLYEK-GH--RTLDDLKNED-SLTHSQ 332 (538)
Q Consensus 294 l~lf~~I~GvGpktA~~ly~~-Gi--rtledL~~~~-~L~~~q 332 (538)
.+++.+|||+|+|.|+++... -. -|+|+|++-+ .+.++|
T Consensus 329 ~~~llRVPGiG~ksa~rIv~~Rr~~rl~~e~Lkk~GvvlkRak 371 (404)
T COG4277 329 YKELLRVPGIGVKSARRIVMTRRRTRLTLEDLKKLGVVLKRAK 371 (404)
T ss_pred HHHhcccCCCChHHHHHHHHHhhhcccCHHHHhhhceeeeccc
Confidence 455669999999999999975 33 3677777543 234443
No 202
>PRK00076 recR recombination protein RecR; Reviewed
Probab=56.70 E-value=7.3 Score=37.95 Aligned_cols=32 Identities=16% Similarity=0.321 Sum_probs=24.0
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHH
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHF 285 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l 285 (538)
+.+..|||||++.|.++.-.+-.-.-.+++.|
T Consensus 11 ~~l~~LPGIG~KsA~Rla~~ll~~~~~~~~~l 42 (196)
T PRK00076 11 EALRKLPGIGPKSAQRLAFHLLQRDREDVLRL 42 (196)
T ss_pred HHHHHCCCCCHHHHHHHHHHHHcCCHHHHHHH
Confidence 67899999999999999877765443444443
No 203
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=56.60 E-value=36 Score=40.54 Aligned_cols=68 Identities=16% Similarity=0.320 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHHHHhhhcCC----CeEEEecccccccC-CcCCCeeEEEecCCc--chhhhhHHHHHHHHHHcCc
Q 009303 348 RHEVEQMERLLQKAGEEVLP----EVIILCGGSYRRGK-ASCGDLDVVIMHPDR--KSHKGFLSKYVKKLKEMKF 415 (538)
Q Consensus 348 r~Ea~~i~~iv~~~~~~~~p----~~~v~~~Gs~RRgk-e~~~DVDiLit~~~~--~~~~~~l~~vv~~L~~~g~ 415 (538)
+.-+..+..+++.+-....+ ++-+..+|||=||. .--+|||+||-+++. .....++.+++.-|=+.|+
T Consensus 32 ~~~~~~~D~~l~~l~~~~~~~~~~~iaLvAvGGYGR~eL~P~SDIDlliL~~~~~~~~~~~~i~~~~~~LWD~gl 106 (854)
T PRK01759 32 ENRSDFYDQLLIHLWQQFGLEEQSDLALIAVGGYGRREMFPLSDLDILILTEQPPDEETEEKINQFFQFLWDCGF 106 (854)
T ss_pred HHHHHHHHHHHHHHHHHccCCCCCCeEEEEeCCcccccCCCcccceEEEEeCCCCChHHHHHHHHHHHHHHhcCC
Confidence 34444456666655443322 35677889997775 456899999988753 2345667777777777765
No 204
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=56.50 E-value=12 Score=31.85 Aligned_cols=55 Identities=24% Similarity=0.316 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh-CCCCHHHH
Q 009303 261 GIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDL 322 (538)
Q Consensus 261 gIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~-GirtledL 322 (538)
||+.+++.+|.+.... .-++.++++ ||. |+..|.|||-++|.++-.. |+..-+.-
T Consensus 19 gl~~~~a~kl~~~yg~---~ai~~l~~n-PY~---L~~~i~gi~F~~aD~iA~~~g~~~~d~~ 74 (94)
T PF14490_consen 19 GLSPKLAMKLYKKYGD---DAIEILKEN-PYR---LIEDIDGIGFKTADKIALKLGIEPDDPR 74 (94)
T ss_dssp T--HHHHHHHHHHH-T---THHHHHHH--STC---CCB-SSSSBHHHHHHHHHTTT--TT-HH
T ss_pred CCCHHHHHHHHHHHhH---HHHHHHHHC-hHH---HHHHccCCCHHHHHHHHHHcCCCCCCHH
Confidence 8899999999998876 344555543 553 3434899999999999987 77644433
No 205
>PF03118 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha chain C terminal domain; InterPro: IPR011260 The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals. The alpha subunit (RpoA) initiates RNAP assembly by dimerising to form a platform on which the beta subunits can interact. The alpha subunit consists of a N-terminal domain (NTD) and a C-terminal domain (CTD), connected by a short linker. The NTD is essential for RNAP assembly, while the CTD is necessary for transcription regulation, interacting with transcription factors and promoter upstream elements. In Escherichia coli, the catabolite activator protein (CAP or CRP) was shown to exert its effect through its interactions with the CTD, where CAP binding to CTD promotes RNAP binding to promoter DNA, thereby stimulating transcription initiation at class I CAP-dependent promoters. At class II CAP-dependent promoters, the interaction of CAP with CTD is one of multiple interactions involved in activation []. The CTD has a compact structure of four helices and two long arms enclosing its hydrophobic core, making its folding topology distinct from most other binding proteins. The upstream promoter element-binding site is formed from helices 1 and 4 [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3N97_B 1XS9_D 3K4G_A 3N4M_B 1COO_A 1LB2_E 3IYD_A 1Z3E_B 3GFK_B 3IHQ_B ....
Probab=56.10 E-value=3.3 Score=33.02 Aligned_cols=45 Identities=24% Similarity=0.337 Sum_probs=32.6
Q ss_pred ccCCCHHHHHHHHHhCCCCHHHHhhc--cCcchhhhccccchhhhcc
Q 009303 300 VWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDIKT 344 (538)
Q Consensus 300 I~GvGpktA~~ly~~GirtledL~~~--~~L~~~q~~Glk~~ed~~~ 344 (538)
--|+-+.+...|-..||.|++||..- ..|..+++||-+..+++.+
T Consensus 16 ~L~LS~Ra~n~L~~~~I~tv~dL~~~s~~~L~~i~n~G~ksl~EI~~ 62 (66)
T PF03118_consen 16 DLGLSVRAYNCLKRAGIHTVGDLVKYSEEDLLKIKNFGKKSLEEIKE 62 (66)
T ss_dssp GSTSBHHHHHHHHCTT--BHHHHHCS-HHHHHTSTTSHHHHHHHHHH
T ss_pred HhCCCHHHHHHHHHhCCcCHHHHHhCCHHHHHhCCCCCHhHHHHHHH
Confidence 33666777777878899999999853 4588888999888777654
No 206
>PRK13844 recombination protein RecR; Provisional
Probab=55.94 E-value=7.4 Score=37.98 Aligned_cols=32 Identities=16% Similarity=0.251 Sum_probs=24.1
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHH
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHF 285 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l 285 (538)
+.+..|||||++.|+++.-.+-.-.-.+++++
T Consensus 15 ~~l~~LPGIG~KsA~Rla~~lL~~~~~~~~~l 46 (200)
T PRK13844 15 ESLRKLPTIGKKSSQRLALYLLDKSPETAIAI 46 (200)
T ss_pred HHHHHCCCCCHHHHHHHHHHHHcCCHHHHHHH
Confidence 67899999999999999887765443444443
No 207
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=55.83 E-value=22 Score=36.50 Aligned_cols=29 Identities=17% Similarity=0.130 Sum_probs=26.3
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009303 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~ 325 (538)
|.++||+|+..++++.+.|+.|++||...
T Consensus 153 L~Qlp~i~~~~~~~l~~~~i~s~~~l~~~ 181 (312)
T smart00611 153 LLQLPHLPEEILKRLEKKKVLSLEDLLEL 181 (312)
T ss_pred cccCCCCCHHHHHHHHhCCCCCHHHHHhc
Confidence 44899999999999999999999999864
No 208
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=55.79 E-value=9.4 Score=44.16 Aligned_cols=27 Identities=41% Similarity=0.623 Sum_probs=25.0
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHh
Q 009303 297 FGEVWGIGPATAQKLYEKGHRTLDDLK 323 (538)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~ 323 (538)
++.+.||||++|+.|-+.||.|+.||.
T Consensus 11 ~~~l~gvg~~~~~~l~~lgi~t~~dll 37 (681)
T PRK10917 11 LTSLKGVGPKTAEKLAKLGIHTVQDLL 37 (681)
T ss_pred hhhcCCCCHHHHHHHHHcCCCCHHHHh
Confidence 557899999999999988999999998
No 209
>PRK03352 DNA polymerase IV; Validated
Probab=55.69 E-value=34 Score=35.88 Aligned_cols=55 Identities=15% Similarity=0.312 Sum_probs=36.7
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh--CCCCHH
Q 009303 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRTLD 320 (538)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--Girtle 320 (538)
+..|||||++++++...+ -+..+.+|.+-.+.... +.+ |++.+.+||+. |+..-.
T Consensus 179 l~~l~gig~~~~~~L~~~----Gi~ti~dl~~l~~~~L~----~~f--G~~~~~~l~~~a~G~d~~~ 235 (346)
T PRK03352 179 TDALWGVGPKTAKRLAAL----GITTVADLAAADPAELA----ATF--GPTTGPWLLLLARGGGDTE 235 (346)
T ss_pred HHHcCCCCHHHHHHHHHc----CCccHHHHhcCCHHHHH----HHh--ChHHHHHHHHHhCCCCCCC
Confidence 788999999988876553 56777777654333333 444 46678888875 775443
No 210
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=55.62 E-value=8.4 Score=40.48 Aligned_cols=32 Identities=19% Similarity=0.239 Sum_probs=28.3
Q ss_pred HHHHHhhccCCCHHHHHHHHHhCCCCHHHHhh
Q 009303 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (538)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~GirtledL~~ 324 (538)
.-.-|+.|.||||+.+++|.+.||.+++++-+
T Consensus 261 ~~DdL~~I~GiGp~~e~~L~~~Gi~~f~QiA~ 292 (326)
T PRK12311 261 APDDLKKLTGVSPQIEKKLNDLGIFHFWQLAE 292 (326)
T ss_pred CchhhhhhccCChhhhhhhhhcCCCCHHHhhC
Confidence 33557799999999999999999999999974
No 211
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=55.56 E-value=9.2 Score=40.38 Aligned_cols=27 Identities=41% Similarity=0.588 Sum_probs=23.0
Q ss_pred hhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009303 298 GEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 298 ~~I~GvGpktA~~ly~~GirtledL~~~ 325 (538)
.+|+|||||||.+|.++ +.|++.+.+.
T Consensus 239 ~Gv~GIG~ktA~kli~~-~gsie~il~~ 265 (338)
T TIGR03674 239 EGVKGIGPKTALKLIKE-HGDLEKVLKA 265 (338)
T ss_pred CCCCCccHHHHHHHHHH-cCCHHHHHHh
Confidence 38999999999999998 4589988753
No 212
>PRK07758 hypothetical protein; Provisional
Probab=55.51 E-value=12 Score=32.20 Aligned_cols=23 Identities=13% Similarity=0.355 Sum_probs=20.3
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHh
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVTT 276 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~t 276 (538)
+||.+|+|+|++..+.|+|-|..
T Consensus 67 ~ELl~iknlGkKSL~EIkekL~E 89 (95)
T PRK07758 67 KEILKLHGMGPASLPKLRKALEE 89 (95)
T ss_pred HHHHHccCCCHHHHHHHHHHHHH
Confidence 67999999999999999988754
No 213
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=55.27 E-value=12 Score=37.61 Aligned_cols=32 Identities=22% Similarity=0.360 Sum_probs=22.1
Q ss_pred HHHHhhchhHHHHHHhhccCCCHHHHHHHHHhC
Q 009303 283 EHFEKDEKVRTISLFGEVWGIGPATAQKLYEKG 315 (538)
Q Consensus 283 e~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~G 315 (538)
+++..|.|..+-+|+ ++||||||.|.--.+.+
T Consensus 148 d~f~gDIP~~v~dLl-sLPGVGPKMa~L~m~~A 179 (286)
T KOG1921|consen 148 DKFDGDIPDTVEDLL-SLPGVGPKMAHLTMQVA 179 (286)
T ss_pred HHhCCCCchhHHHHh-cCCCCchHHHHHHHHHH
Confidence 455566666444445 99999999997665433
No 214
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=54.85 E-value=5.7 Score=45.57 Aligned_cols=51 Identities=14% Similarity=0.212 Sum_probs=36.2
Q ss_pred HHhhccCCCHHHHHHHHHhCCCCHHHHhhcc--CcchhhhccccchhhhccCcC
Q 009303 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIKTRIP 347 (538)
Q Consensus 296 lf~~I~GvGpktA~~ly~~GirtledL~~~~--~L~~~q~~Glk~~ed~~~~i~ 347 (538)
.|.+|+||||++.+.|++ -+.|+++|+++. .|....+++.+..+.+...-+
T Consensus 609 ~L~~IpGiG~kr~~~LL~-~FgS~~~i~~As~eel~~v~gi~~~~A~~i~~~~~ 661 (691)
T PRK14672 609 SFERLPHVGKVRAHRLLA-HFGSFRSLQSATPQDIATAIHIPLTQAHTILHAAT 661 (691)
T ss_pred ccccCCCCCHHHHHHHHH-HhcCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHhh
Confidence 456999999999999998 456888888653 465666666666555554333
No 215
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=54.70 E-value=16 Score=41.76 Aligned_cols=30 Identities=27% Similarity=0.442 Sum_probs=24.2
Q ss_pred HHHhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009303 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 295 ~lf~~I~GvGpktA~~ly~~GirtledL~~~ 325 (538)
..|.+|+||||+++++|++. +.|+++++++
T Consensus 552 S~L~~IpGIG~kr~~~LL~~-FgSi~~I~~A 581 (624)
T PRK14669 552 SELLEIPGVGAKTVQRLLKH-FGSLERVRAA 581 (624)
T ss_pred HHHhcCCCCCHHHHHHHHHH-cCCHHHHHhC
Confidence 34669999999999999984 5577777764
No 216
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=54.65 E-value=5.3 Score=41.56 Aligned_cols=51 Identities=25% Similarity=0.342 Sum_probs=35.7
Q ss_pred HHHHHhhccCCCHHHHHHHHHh---C-CCCHHHHhhcc-----Ccchhhhccccchhhhc
Q 009303 293 TISLFGEVWGIGPATAQKLYEK---G-HRTLDDLKNED-----SLTHSQRLGLKYFDDIK 343 (538)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~---G-irtledL~~~~-----~L~~~q~~Glk~~ed~~ 343 (538)
.+..+++|||||+++|+++.+- | +..+++|+++. .|....|+|.+....|-
T Consensus 43 ~~~~~~~ipgiG~~ia~kI~E~~~tG~~~~le~l~~~~~~~l~~l~~i~GiGpk~a~~l~ 102 (307)
T cd00141 43 SLEEAKKLPGIGKKIAEKIEEILETGKLRKLEELREDVPPGLLLLLRVPGVGPKTARKLY 102 (307)
T ss_pred CHHHhcCCCCccHHHHHHHHHHHHcCCHHHHHHHhccchHHHHHHHcCCCCCHHHHHHHH
Confidence 4445579999999999999873 4 56666666541 25667788876665554
No 217
>PRK05755 DNA polymerase I; Provisional
Probab=54.38 E-value=8.9 Score=45.72 Aligned_cols=25 Identities=44% Similarity=0.598 Sum_probs=20.9
Q ss_pred hhccCCCHHHHHHHHHh-CCCCHHHHhh
Q 009303 298 GEVWGIGPATAQKLYEK-GHRTLDDLKN 324 (538)
Q Consensus 298 ~~I~GvGpktA~~ly~~-GirtledL~~ 324 (538)
-+|+|||||||.+|.++ | |+|.+.+
T Consensus 190 pGv~GiG~ktA~~Ll~~~g--sle~i~~ 215 (880)
T PRK05755 190 PGVPGIGEKTAAKLLQEYG--SLEGLYE 215 (880)
T ss_pred CCCCCccHHHHHHHHHHcC--CHHHHHH
Confidence 46899999999999987 6 7777763
No 218
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=53.78 E-value=8.8 Score=34.52 Aligned_cols=25 Identities=24% Similarity=0.383 Sum_probs=20.1
Q ss_pred HHHHHhhccCCCHHHHHHHHHh-CCC
Q 009303 293 TISLFGEVWGIGPATAQKLYEK-GHR 317 (538)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~-Gir 317 (538)
+.--|+.|+|||+++|..+-+. ||.
T Consensus 15 v~~aLt~i~GIG~~~A~~ic~~lgi~ 40 (122)
T CHL00137 15 IEYALTYIYGIGLTSAKEILEKANID 40 (122)
T ss_pred eeeeecccccccHHHHHHHHHHcCcC
Confidence 3344689999999999999876 764
No 219
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=53.41 E-value=36 Score=35.54 Aligned_cols=48 Identities=19% Similarity=0.338 Sum_probs=38.9
Q ss_pred CCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEcCC
Q 009303 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDL 66 (538)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~~~~ 66 (538)
.+|.|.+|.|-.. +... +.-+++++..+||.|.+..+.+++.||+-+.
T Consensus 231 ~l~~g~~~v~TG~-l~~~-R~e~~~~~~~~G~~v~~sVs~~t~~lv~g~~ 278 (313)
T PRK06063 231 PLVQGMRVALSAE-VSRT-HEELVERILHAGLAYSDSVDRDTSLVVCNDP 278 (313)
T ss_pred cccCCCEEEEecC-CCCC-HHHHHHHHHHcCCEecCccccCccEEEECCC
Confidence 4689999988654 3334 4667899999999999999999999999653
No 220
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=52.99 E-value=14 Score=42.16 Aligned_cols=96 Identities=16% Similarity=0.171 Sum_probs=55.1
Q ss_pred CCCCCCCCCCCCCCCCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecC------CCccEEEE-cCCh-HHHHHHH
Q 009303 3 PKTTRKPTPALDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLS------KKVTHVLA-MDLE-ALLQQVS 74 (538)
Q Consensus 3 ~~~~~~~~~~~~~~~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls------~~VTHVV~-~~~~-~~~~~l~ 74 (538)
|+.+|.++.+ ....+|.|+.+||+...-... -+.|.+++..-||++...-+ ..-|-|+. +... ....|.+
T Consensus 573 ~~~~~~~a~s-~~~kLf~gl~~~~~g~fs~~p-~~~l~~l~~~~gg~~l~~~~~~~~~~k~s~~~~~~~~~~~~~~~~~k 650 (684)
T KOG4362|consen 573 PKEKRLRAES-YKPKLFEGLKFYFVGDFSNPP-KEQLQELVHLAGGTILQVPRVAYSDKKKSTIVVLSEKPVLDSILWQK 650 (684)
T ss_pred cccccccccc-cCcchhcCCcceeecccccCc-HHHHHHHHhhcCcceeeccCcccccccccceeEeecccCCCchhhhh
Confidence 4555544443 445899999999997744322 45677899999999876431 22333332 1110 0111222
Q ss_pred Hhhhc----ccCccccccchHHHHHhcCcc
Q 009303 75 KQHLA----RFKGSVIRYQWLEDSLRLGEK 100 (538)
Q Consensus 75 ~~~~~----~~~~~lV~~~Wl~ecik~g~l 100 (538)
..... ..+.++|+-.||.+++.--+.
T Consensus 651 ~~~~ea~~~s~~a~~~~~~wvl~s~a~~~~ 680 (684)
T KOG4362|consen 651 VNDAEALALSQRARAVSSSWVLDSIAGYQI 680 (684)
T ss_pred hccHHHHHHhcCCCccchhhhhcchhceee
Confidence 11111 114789999999999864443
No 221
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=52.98 E-value=8.9 Score=34.49 Aligned_cols=23 Identities=22% Similarity=0.446 Sum_probs=19.4
Q ss_pred HHHhhccCCCHHHHHHHHHh-CCC
Q 009303 295 SLFGEVWGIGPATAQKLYEK-GHR 317 (538)
Q Consensus 295 ~lf~~I~GvGpktA~~ly~~-Gir 317 (538)
--|+.|+|||+.+|..+.+. |+.
T Consensus 17 ~aL~~I~GIG~~~a~~i~~~lgi~ 40 (122)
T PRK05179 17 IALTYIYGIGRTRAKEILAAAGID 40 (122)
T ss_pred eeecccccccHHHHHHHHHHhCcC
Confidence 34689999999999999886 764
No 222
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=52.27 E-value=30 Score=34.09 Aligned_cols=31 Identities=19% Similarity=0.504 Sum_probs=23.5
Q ss_pred HhcCCcccc-chhhhcCCCCCCHHHHHHHHHH
Q 009303 243 IEKLPFKIE-SADQVKGLPGIGKSMQDHIQEI 273 (538)
Q Consensus 243 l~~l~~~i~-~~~~l~~lpgIG~~ia~kI~Ei 273 (538)
++.+..++. ++++|.+|||||.++|..+--+
T Consensus 97 ~e~~~g~vP~~~~eL~~LPGVGrKTAnvVL~~ 128 (211)
T COG0177 97 LEKFGGEVPDTREELLSLPGVGRKTANVVLSF 128 (211)
T ss_pred HHHcCCCCCchHHHHHhCCCcchHHHHHHHHh
Confidence 345555554 4689999999999999987644
No 223
>PRK04374 PII uridylyl-transferase; Provisional
Probab=51.55 E-value=50 Score=39.47 Aligned_cols=62 Identities=19% Similarity=0.405 Sum_probs=39.8
Q ss_pred HHHHHHHHhhhcCC---CeEEEeccccccc-CCcCCCeeEEEecCCc--chhhhhHHHHHHHHHHcCc
Q 009303 354 MERLLQKAGEEVLP---EVIILCGGSYRRG-KASCGDLDVVIMHPDR--KSHKGFLSKYVKKLKEMKF 415 (538)
Q Consensus 354 i~~iv~~~~~~~~p---~~~v~~~Gs~RRg-ke~~~DVDiLit~~~~--~~~~~~l~~vv~~L~~~g~ 415 (538)
+..+++++.....| ++-++.+|||=|| ..-.+|||+||-+++. ........+++..|-+.|+
T Consensus 55 ~D~~l~~~~~~~~~~~~~~alvAvGgYGR~EL~p~SDIDLliL~~~~~~~~~~~~i~~~i~~LWD~gL 122 (869)
T PRK04374 55 VDQLMRNAWTRCIPADSGLSLHAVGGYGRGELFPRSDVDLLVLGETAAQQRHEQALARLFALLWDVGL 122 (869)
T ss_pred HHHHHHHHHHHhCCCcCCEEEEEcCCccccccCCcccceEEEEecCCCCchHHHHHHHHHHHHHhcCC
Confidence 44555554443334 3567788999665 4567899999988743 2344566777776666654
No 224
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=51.33 E-value=15 Score=37.81 Aligned_cols=50 Identities=24% Similarity=0.451 Sum_probs=35.4
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009303 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (538)
+.+|||||+.+++++.+. -+..++++..-. .+.+.+++|++.++|.+||+
T Consensus 1 l~~i~gig~~~~~~L~~~----Gi~ti~dl~~~~----~~~L~~~~g~~~~~a~~l~~ 50 (310)
T TIGR02236 1 LEDLPGVGPATAEKLREA----GYDTFEAIAVAS----PKELSEIAGISEGTAAKIIQ 50 (310)
T ss_pred CcccCCCCHHHHHHHHHc----CCCCHHHHHcCC----HHHHHhccCCCHHHHHHHHH
Confidence 467999999988877654 234556654422 33345888999999999986
No 225
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=50.75 E-value=35 Score=32.76 Aligned_cols=42 Identities=10% Similarity=0.311 Sum_probs=28.1
Q ss_pred hHHHHHHHHHHHh-cCCcccc-chhhhcCCCCCCHHHHHHHHHH
Q 009303 232 RSFSYYKAIPVIE-KLPFKIE-SADQVKGLPGIGKSMQDHIQEI 273 (538)
Q Consensus 232 r~~aY~rAa~~l~-~l~~~i~-~~~~l~~lpgIG~~ia~kI~Ei 273 (538)
|+..-.+++..+. .....+. ..++|.+|||||..+|+.|-=+
T Consensus 82 Ka~~i~~~a~~i~~~~~~~~~~~~~~L~~l~GIG~ktA~~ill~ 125 (191)
T TIGR01083 82 KAKNIIALCRILVERYGGEVPEDREELVKLPGVGRKTANVVLNV 125 (191)
T ss_pred HHHHHHHHHHHHHHHcCCCCchHHHHHHhCCCCcHHHHHHHHHH
Confidence 5655666665553 3322222 3578999999999999998633
No 226
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=49.83 E-value=35 Score=35.40 Aligned_cols=52 Identities=27% Similarity=0.493 Sum_probs=37.9
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh
Q 009303 255 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (538)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 314 (538)
.+..|||||+.+++++.+ --+..++++.+-.+ +.+.+++|+++++|..||+.
T Consensus 7 ~l~~l~gIg~~~a~~L~~----~Gi~t~~dl~~~~~----~~L~~~~g~~~~~a~~l~~~ 58 (317)
T PRK04301 7 DLEDLPGVGPATAEKLRE----AGYDTVEAIAVASP----KELSEAAGIGESTAAKIIEA 58 (317)
T ss_pred cHhhcCCCCHHHHHHHHH----cCCCCHHHHHcCCH----HHHHHhcCCCHHHHHHHHHH
Confidence 578999999888776554 34566777754322 23448889999999999974
No 227
>TIGR01084 mutY A/G-specific adenine glycosylase. This equivalog model identifies mutY members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=49.77 E-value=25 Score=36.10 Aligned_cols=25 Identities=16% Similarity=0.175 Sum_probs=19.6
Q ss_pred HHHHHHhhccCCCHHHHHHHHHhCC
Q 009303 292 RTISLFGEVWGIGPATAQKLYEKGH 316 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~Gi 316 (538)
..++.|+++||||++||..+---++
T Consensus 102 ~~~~~L~~LpGIG~~TA~~Il~~a~ 126 (275)
T TIGR01084 102 QDFEDLAALPGVGRYTAGAILSFAL 126 (275)
T ss_pred HHHHHHHhCCCCCHHHHHHHHHHHC
Confidence 3577788999999999988765433
No 228
>COG5067 DBF4 Protein kinase essential for the initiation of DNA replication [DNA replication, recombination, and repair / Cell division and chromosome partitioning]
Probab=49.27 E-value=12 Score=39.88 Aligned_cols=49 Identities=16% Similarity=0.255 Sum_probs=38.4
Q ss_pred CCCCCCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEE
Q 009303 13 LDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLA 63 (538)
Q Consensus 13 ~~~~~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~ 63 (538)
...-..|..+.+|+.. ..+ .|.+.+++.+..-||.|..-++..||||+.
T Consensus 117 R~Y~~aFp~f~fY~dn-~s~-~~khRvk~gf~~LGa~v~tfF~~~VThfiT 165 (468)
T COG5067 117 RTYCCAFPAFKFYKDN-KSG-KRKHRVKEGFCELGAVVFTFFEEHVTHFIT 165 (468)
T ss_pred hhhhcccchhhhhhcC-CCH-HHHHHHHHHHHHhhhhhheeeccceEEEEE
Confidence 4445788888888853 223 444448999999999999999999999996
No 229
>TIGR03631 bact_S13 30S ribosomal protein S13. This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type.
Probab=48.99 E-value=11 Score=33.48 Aligned_cols=24 Identities=33% Similarity=0.517 Sum_probs=19.7
Q ss_pred HHHHhhccCCCHHHHHHHHHh-CCC
Q 009303 294 ISLFGEVWGIGPATAQKLYEK-GHR 317 (538)
Q Consensus 294 l~lf~~I~GvGpktA~~ly~~-Gir 317 (538)
.--|++|+|||+++|..+.+. |+.
T Consensus 14 ~~aL~~i~GIG~~~a~~i~~~lgi~ 38 (113)
T TIGR03631 14 EIALTYIYGIGRTRARKILEKAGID 38 (113)
T ss_pred eeeeeeeecccHHHHHHHHHHhCcC
Confidence 334689999999999999886 764
No 230
>KOG3548 consensus DNA damage checkpoint protein RHP9/CRB2/53BP1 [Replication, recombination and repair]
Probab=48.49 E-value=20 Score=42.15 Aligned_cols=28 Identities=7% Similarity=0.074 Sum_probs=24.6
Q ss_pred cccccchHHHHHhcCcccCccccccccC
Q 009303 84 SVIRYQWLEDSLRLGEKVSEDLYRIKLD 111 (538)
Q Consensus 84 ~lV~~~Wl~ecik~g~lv~e~~y~l~~~ 111 (538)
--|...||.+|+++++.||-.+|.|.-.
T Consensus 1011 PcVh~~fI~aC~e~nr~Vdy~~YLLpsG 1038 (1176)
T KOG3548|consen 1011 PCVHNTFIQACGEQNRCVDYTDYLLPSG 1038 (1176)
T ss_pred CcccHHHHHHHHhccccccchhhcccCc
Confidence 4689999999999999999999998643
No 231
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=48.42 E-value=10 Score=40.20 Aligned_cols=52 Identities=19% Similarity=0.232 Sum_probs=41.1
Q ss_pred hchhHHHHHHhhccCCCHHHHHHHHHh-CCCCHHHHhhcc--Ccchhhhccccchhh
Q 009303 288 DEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED--SLTHSQRLGLKYFDD 341 (538)
Q Consensus 288 ~~~~~~l~lf~~I~GvGpktA~~ly~~-GirtledL~~~~--~L~~~q~~Glk~~ed 341 (538)
...++...++.+||+|+++.|++|.+. | ||..|.++. .|....++|-+....
T Consensus 280 ~v~prGyRiLs~IPrl~k~iAk~Ll~~FG--SL~~Il~As~eeL~~VeGIGe~rA~~ 334 (352)
T PRK13482 280 PVSPRGYRLLSKIPRLPSAVIENLVEHFG--SLQGLLAASIEDLDEVEGIGEVRARA 334 (352)
T ss_pred ccCCcHHHHHhcCCCCCHHHHHHHHHHcC--CHHHHHcCCHHHHhhCCCcCHHHHHH
Confidence 345668899999999999999999997 7 888888653 477777888655444
No 232
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=47.65 E-value=27 Score=34.19 Aligned_cols=38 Identities=21% Similarity=0.270 Sum_probs=24.1
Q ss_pred HHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHH
Q 009303 270 IQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLY 312 (538)
Q Consensus 270 I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly 312 (538)
+.+++.+ +..++.+.. .-..+.|.+|.|||+-||..+.
T Consensus 95 ~k~l~~~--~~~~~~~~~---~~~R~~LL~iKGIG~ETaDsIL 132 (215)
T COG2231 95 SKNLAKF--FINLESFKS---EVLREELLSIKGIGKETADSIL 132 (215)
T ss_pred HHHHHHH--hhhhhccch---HHHHHHHHccCCcchhhHHHHH
Confidence 3555543 333444332 2256777799999999998763
No 233
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=47.23 E-value=43 Score=30.42 Aligned_cols=43 Identities=9% Similarity=0.301 Sum_probs=27.2
Q ss_pred hHHHHHHHHHHHhc-CCccc-cchhhhcCCCCCCHHHHHHHHHHH
Q 009303 232 RSFSYYKAIPVIEK-LPFKI-ESADQVKGLPGIGKSMQDHIQEIV 274 (538)
Q Consensus 232 r~~aY~rAa~~l~~-l~~~i-~~~~~l~~lpgIG~~ia~kI~Eil 274 (538)
|+..-...+..|.. ....+ ...+.|.+|||||+.+|+.|.=+.
T Consensus 48 ka~~i~~~a~~~~~~~~~~~~~~~~~L~~l~GIG~~tA~~~l~~~ 92 (149)
T smart00478 48 KAKYLIELARILVEEYGGEVPDDREELLKLPGVGRKTANAVLSFA 92 (149)
T ss_pred HHHHHHHHHHHHHHHHCCCccHHHHHHHcCCCCcHHHHHHHHHHH
Confidence 55555555555433 22222 235778999999999999876553
No 234
>PF03445 DUF294: Putative nucleotidyltransferase DUF294; InterPro: IPR005105 This domain is found associated with an N-terminal cyclic nucleotide-binding domain (IPR000595 from INTERPRO) and two CBS domains (IPR000644 from INTERPRO). This domain, normally represents the C-terminal region, is uncharacterised; however, it seems to be similar to the nucleotidyltransferase domain (IPR002934 from INTERPRO), conserving the DXD motif, which strongly suggests that proteins containing this domain are also nucleotidyltransferases.; GO: 0008773 [protein-PII] uridylyltransferase activity
Probab=46.92 E-value=50 Score=30.04 Aligned_cols=51 Identities=25% Similarity=0.366 Sum_probs=35.5
Q ss_pred eEEEecccccccCCc-CCCeeEEEecCCcc--hh----hhhHHHHHHHHHHcCcccce
Q 009303 369 VIILCGGSYRRGKAS-CGDLDVVIMHPDRK--SH----KGFLSKYVKKLKEMKFLRED 419 (538)
Q Consensus 369 ~~v~~~Gs~RRgke~-~~DVDiLit~~~~~--~~----~~~l~~vv~~L~~~g~l~~~ 419 (538)
+-+.+.||+=|+..+ ..|+|..|-+++.. .. ..+..++++.|...||-.|.
T Consensus 50 ~a~lalGS~GR~E~~~~sDqD~alv~~d~~~~~~~~~f~~~a~~~~~~L~~~G~~~C~ 107 (138)
T PF03445_consen 50 FAWLALGSYGRREQTLYSDQDNALVFEDEESEEDRAYFEAFAERLVDALDECGFPPCP 107 (138)
T ss_pred EEEEEECcccccCCCcCccccceeeecCccchhHHHHHHHHHHHHHHHHHHcCCCCCC
Confidence 356678888776654 67999999888821 22 33456778888888887654
No 235
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication. NusA is a bacterial transcription termination factor. It is named for its interaction with phage lambda protein N, as part of the N utilization substance. Some members of the NusA family have a long C-terminal extension. This model represents an acidic 50-residue region found in two copies toward the C-terminus of most Proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic.
Probab=46.56 E-value=17 Score=26.51 Aligned_cols=31 Identities=32% Similarity=0.355 Sum_probs=23.1
Q ss_pred CCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhh
Q 009303 303 IGPATAQKLYEKGHRTLDDLKNED--SLTHSQR 333 (538)
Q Consensus 303 vGpktA~~ly~~GirtledL~~~~--~L~~~q~ 333 (538)
|.+..+.+|++.|+.|+++|-... .|...++
T Consensus 1 i~~~~~~~L~~~G~~s~e~la~~~~~eL~~i~g 33 (50)
T TIGR01954 1 IDEEIAQLLVEEGFTTVEDLAYVPIDELLSIEG 33 (50)
T ss_pred CCHHHHHHHHHcCCCCHHHHHccCHHHHhcCCC
Confidence 457889999999999999998542 3554444
No 236
>cd01703 PolY_Pol_iota DNA Polymerase iota. Pol iota, also called Rad30B, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol iota is thought to be one of the least efficient polymerases, particularly when opposite pyrimidines; it can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine, and prefers to insert guanosine instead of adenosine opposite thymidine. Pol iota is believed to use Hoogsteen rather than Watson-Crick base pairing, which may explain the varying efficiency for different template nucleotides.
Probab=46.14 E-value=40 Score=36.20 Aligned_cols=58 Identities=19% Similarity=0.453 Sum_probs=35.2
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhc----------h-hHHHHHHhhccCCCHHHHHHHHHh--CCCC
Q 009303 255 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDE----------K-VRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (538)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~----------~-~~~l~lf~~I~GvGpktA~~ly~~--Girt 318 (538)
.+..|||||+++.+++..+ | +..+-++.+-. + .-....+.+.+ |.+++.++|+. |+.+
T Consensus 173 pv~~l~GiG~~~~~kL~~~---G-I~tigdl~~~~~~~~~~~~~~~~~~s~~~L~~~f--G~~~g~~l~~~a~G~d~ 243 (379)
T cd01703 173 DLRKIPGIGYKTAAKLEAH---G-ISSVRDLQEFSNRNRQTVGAAPSLLELLLMVKEF--GEGIGQRIWKLLFGRDT 243 (379)
T ss_pred CccccCCcCHHHHHHHHHc---C-CCcHHHHHhCCcccccccccccccccHHHHHHHH--CHHHHHHHHHHHCCCCC
Confidence 4788999999999998875 3 33333333222 0 00023343444 56778888875 8875
No 237
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=45.72 E-value=32 Score=34.66 Aligned_cols=30 Identities=23% Similarity=0.467 Sum_probs=22.7
Q ss_pred cCCcccc-chhhhcCCCCCCHHHHHHHHHHH
Q 009303 245 KLPFKIE-SADQVKGLPGIGKSMQDHIQEIV 274 (538)
Q Consensus 245 ~l~~~i~-~~~~l~~lpgIG~~ia~kI~Eil 274 (538)
.+..+|- ++++|..|||||++||-..-.+.
T Consensus 149 ~f~gDIP~~v~dLlsLPGVGPKMa~L~m~~A 179 (286)
T KOG1921|consen 149 KFDGDIPDTVEDLLSLPGVGPKMAHLTMQVA 179 (286)
T ss_pred HhCCCCchhHHHHhcCCCCchHHHHHHHHHH
Confidence 4455554 47999999999999998766543
No 238
>PRK01216 DNA polymerase IV; Validated
Probab=45.61 E-value=68 Score=34.02 Aligned_cols=52 Identities=23% Similarity=0.388 Sum_probs=34.3
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh--CCC
Q 009303 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHR 317 (538)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--Gir 317 (538)
+..|||||++++++...+ | +..+.+|.+-...... +.+ |+..+..||+. |+.
T Consensus 180 i~~l~giG~~~~~~L~~~---G-i~TigdL~~~~~~~L~----~rf--G~~~~~~L~~~a~G~d 233 (351)
T PRK01216 180 IADIPGIGDITAEKLKKL---G-VNKLVDTLRIEFDELK----GII--GEAKAKYLFSLARNEY 233 (351)
T ss_pred cccccCCCHHHHHHHHHc---C-CCcHHHHhcCCHHHHH----HHH--CHHHHHHHHHHhCCCC
Confidence 677899999988877654 3 5667777654333333 444 46678888883 754
No 239
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=45.41 E-value=38 Score=38.84 Aligned_cols=50 Identities=20% Similarity=0.429 Sum_probs=35.6
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 314 (538)
..|.+|||||+..+.++-+ ++..++.+++- .++.+.+| ||.++|+++++.
T Consensus 552 S~L~~IpGIG~kr~~~LL~-----~FgSi~~I~~A----s~eeL~~v--i~~k~A~~I~~~ 601 (624)
T PRK14669 552 SELLEIPGVGAKTVQRLLK-----HFGSLERVRAA----TETQLAAV--VGRAAAEAIIAH 601 (624)
T ss_pred HHHhcCCCCCHHHHHHHHH-----HcCCHHHHHhC----CHHHHHHH--hCHHHHHHHHHH
Confidence 5688999999998887654 34455555542 34445566 999999999874
No 240
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=45.02 E-value=43 Score=34.76 Aligned_cols=48 Identities=17% Similarity=0.137 Sum_probs=37.8
Q ss_pred CCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEcC
Q 009303 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMD 65 (538)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~~~ 65 (538)
..|.|.+|.|-.. +..-.+.-+++++..+||.|.+..+.++|.+|+-+
T Consensus 219 ~~l~g~~~vfTG~-l~~~~R~~~~~~~~~~Gg~v~~sVs~~t~~lV~G~ 266 (309)
T PRK06195 219 TAFKEEVVVFTGG-LASMTRDEAMILVRRLGGTVGSSVTKKTTYLVTNT 266 (309)
T ss_pred ccccCCEEEEccc-cCCCCHHHHHHHHHHhCCEecCCcccCceEEEECC
Confidence 4699999998554 22223555679999999999999999999999853
No 241
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=44.72 E-value=17 Score=32.49 Aligned_cols=22 Identities=27% Similarity=0.540 Sum_probs=18.8
Q ss_pred HHhhccCCCHHHHHHHHHh-CCC
Q 009303 296 LFGEVWGIGPATAQKLYEK-GHR 317 (538)
Q Consensus 296 lf~~I~GvGpktA~~ly~~-Gir 317 (538)
-||.|+|||..+|+.+.+. ||.
T Consensus 18 ALt~IyGIG~~~a~~I~~~~gi~ 40 (121)
T COG0099 18 ALTYIYGIGRRRAKEICKKAGID 40 (121)
T ss_pred hhhhhccccHHHHHHHHHHcCCC
Confidence 4678999999999999886 764
No 242
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=44.68 E-value=11 Score=39.79 Aligned_cols=52 Identities=19% Similarity=0.245 Sum_probs=33.5
Q ss_pred HHHHHHhhccCCCHHHHHHHHHh---CCCC-HHHHhhcc------Ccchhhhccccchhhhc
Q 009303 292 RTISLFGEVWGIGPATAQKLYEK---GHRT-LDDLKNED------SLTHSQRLGLKYFDDIK 343 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~---Girt-ledL~~~~------~L~~~q~~Glk~~ed~~ 343 (538)
..+..+++|||||+++|.++.+- |--. +.++..+. .|.+..|+|.+....|-
T Consensus 45 ~~~~~l~~lpgIG~~ia~kI~Eil~tG~~~~~~e~l~~~~p~~l~~l~~i~GiGpk~a~~l~ 106 (334)
T smart00483 45 NSMKDLKGLPGIGDKIKKKIEEIIETGKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKWY 106 (334)
T ss_pred CCHHHHhcCCCccHHHHHHHHHHHHhCcHHHHHHHhcCcHHHHHHHHHccCCcCHHHHHHHH
Confidence 34556789999999999999974 5544 33333221 36667777755544443
No 243
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=44.67 E-value=15 Score=41.95 Aligned_cols=42 Identities=21% Similarity=0.399 Sum_probs=29.0
Q ss_pred HHHHhhccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhccc
Q 009303 294 ISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGL 336 (538)
Q Consensus 294 l~lf~~I~GvGpktA~~ly~~GirtledL~~~~--~L~~~q~~Gl 336 (538)
...|..|+|||++++++|++. +.|++++.++. .|....++|-
T Consensus 542 ~s~L~~IpGIG~k~~k~Ll~~-FgS~~~i~~As~eeL~~v~Gig~ 585 (598)
T PRK00558 542 TSALDDIPGIGPKRRKALLKH-FGSLKAIKEASVEELAKVPGISK 585 (598)
T ss_pred hhhHhhCCCcCHHHHHHHHHH-cCCHHHHHhCCHHHHhhcCCcCH
Confidence 345679999999999999984 45688887542 2444444443
No 244
>PRK02794 DNA polymerase IV; Provisional
Probab=44.17 E-value=1.2e+02 Score=32.74 Aligned_cols=52 Identities=12% Similarity=0.262 Sum_probs=33.7
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh--CCCC
Q 009303 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (538)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--Girt 318 (538)
+..|||||+.+.++...+ -+..+.+|.+-.+... .+.+| + .+..+|+. |+..
T Consensus 211 l~~L~GiG~~~~~~L~~~----GI~tigdL~~l~~~~L----~~rfG--~-~g~~l~~~a~G~d~ 264 (419)
T PRK02794 211 VGIIWGVGPATAARLARD----GIRTIGDLQRADEADL----MRRFG--S-MGLRLWRLARGIDD 264 (419)
T ss_pred hhhhCCCCHHHHHHHHHh----ccchHHHHhhCCHHHH----HHHHh--H-HHHHHHHHhCCCCC
Confidence 688999999988887643 3566666665332223 34445 3 57778875 8864
No 245
>PF02889 Sec63: Sec63 Brl domain; InterPro: IPR004179 This domain was named after the yeast Sec63 (or NPL1) (also known as the Brl domain) protein in which it was found. This protein is required for assembly of functional endoplasmic reticulum translocons [, ]. Other yeast proteins containing this domain include pre-mRNA splicing helicase BRR2, HFM1 protein and putative helicases. ; PDB: 3IM2_A 3IM1_A 3HIB_A 2Q0Z_X.
Probab=44.14 E-value=28 Score=35.76 Aligned_cols=29 Identities=31% Similarity=0.470 Sum_probs=22.5
Q ss_pred HHhhccCCCHHHHHHHHHhCCCCHHHHhh
Q 009303 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (538)
Q Consensus 296 lf~~I~GvGpktA~~ly~~GirtledL~~ 324 (538)
.|.++||+|++.++++-+.|+.|+++|.+
T Consensus 149 ~L~Qlp~i~~~~~~~l~~~~i~~l~~l~~ 177 (314)
T PF02889_consen 149 PLLQLPHIGEESLKKLEKRGIKTLQDLRD 177 (314)
T ss_dssp GGGGSTT--HHHHHHHHHTT--SHHHHHH
T ss_pred hhhcCCCCCHHHHHHHhccCCCcHHHHhh
Confidence 35699999999999999999999999995
No 246
>PRK13746 aminoglycoside resistance protein; Provisional
Probab=43.99 E-value=1.2e+02 Score=31.07 Aligned_cols=27 Identities=26% Similarity=0.249 Sum_probs=21.9
Q ss_pred EEEeccccccc--CCcCCCeeEEEecCCcc
Q 009303 370 IILCGGSYRRG--KASCGDLDVVIMHPDRK 397 (538)
Q Consensus 370 ~v~~~Gs~RRg--ke~~~DVDiLit~~~~~ 397 (538)
-|.+-||+-+| ++ -+||||+|...++-
T Consensus 30 ~vyLfGS~~~G~~~p-~SDIDllvvv~~~l 58 (262)
T PRK13746 30 AIHLYGSAVDGGLKP-HSDIDLLVTVAVPL 58 (262)
T ss_pred EEEEECCcccCCCCC-CCceeEEEEeCCCC
Confidence 47799999998 44 79999999877654
No 247
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=43.78 E-value=39 Score=39.72 Aligned_cols=53 Identities=26% Similarity=0.464 Sum_probs=36.2
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh--CCCC
Q 009303 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (538)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--Girt 318 (538)
+..|||+|-+|..|+...- +...-+|+ ..++.-| .+=+|||+++++|.. |+..
T Consensus 551 v~~LPGVG~sm~~kL~s~~----i~tCgdLq----~~T~~kl--~k~~G~Klgq~i~~~CrG~Dd 605 (1016)
T KOG2093|consen 551 VDDLPGVGSSMKSKLVSQF----IQTCGDLQ----LITLIKL--RKVFGPKLGQKIYRGCRGIDD 605 (1016)
T ss_pred cccCCCccHHHHHHHHHhc----cchhHHHH----HHHHHHH--HhhhcccHHHHHHHhcCCCcC
Confidence 6899999999999977544 33333333 3344444 344589999999985 7754
No 248
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=43.53 E-value=18 Score=38.97 Aligned_cols=33 Identities=24% Similarity=0.313 Sum_probs=28.9
Q ss_pred HHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhh
Q 009303 292 RTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~GirtledL~~ 324 (538)
+.-.-|+.|.||||+.+.+|...||.++++|-.
T Consensus 320 g~aDDLk~I~GIGpk~e~~Ln~~Gi~~f~QIA~ 352 (400)
T PRK12373 320 GGADDLKLISGVGPKIEATLNELGIFTFDQVAA 352 (400)
T ss_pred CCchhhhhccCCChHHHHHHHhcCCCCHHHHhC
Confidence 344567899999999999999999999999974
No 249
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=43.44 E-value=15 Score=34.32 Aligned_cols=46 Identities=17% Similarity=0.249 Sum_probs=30.9
Q ss_pred HHHHhhccCCCHHHHHHHHHh-CCCCHHHHhhccCcchhhhccccchhhhccCcCHHHHHHHHHHHHH
Q 009303 294 ISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQK 360 (538)
Q Consensus 294 l~lf~~I~GvGpktA~~ly~~-GirtledL~~~~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~iv~~ 360 (538)
.--|+.|+|||+.+|..+-.. ||..-. ...-++-+|++.+..+|..
T Consensus 29 ~~aLt~I~GIG~~~A~~I~~~lgi~~~~---------------------~~~~Lt~~qi~~l~~~i~~ 75 (154)
T PTZ00134 29 PYALTAIKGIGRRFAYLVCKKAGIDVTK---------------------RAGELTAEEIEKIVEIIAN 75 (154)
T ss_pred EEeecccccccHHHHHHHHHHcCcCcCC---------------------CcccCCHHHHHHHHHHHhc
Confidence 334689999999999999876 753211 1123345677777777765
No 250
>COG5186 PAP1 Poly(A) polymerase [RNA processing and modification]
Probab=43.36 E-value=95 Score=33.19 Aligned_cols=52 Identities=27% Similarity=0.447 Sum_probs=41.3
Q ss_pred CeEEEecccccccCC-cCCCeeEEEecCCcchhhhhHHHHHHHHHHcCcccce
Q 009303 368 EVIILCGGSYRRGKA-SCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLRED 419 (538)
Q Consensus 368 ~~~v~~~Gs~RRgke-~~~DVDiLit~~~~~~~~~~l~~vv~~L~~~g~l~~~ 419 (538)
|-++.--||||-|-- -+.|||-|+..|..-+...+|..+-..|+...-+.+.
T Consensus 81 GGKIFTyGSYRLGVhgpGsDIDtLvvVPkHVsR~dFFt~f~~~Lrer~ei~ev 133 (552)
T COG5186 81 GGKIFTYGSYRLGVHGPGSDIDTLVVVPKHVSRSDFFTHFYEELRERPEIEEV 133 (552)
T ss_pred CceeeeecceeeeccCCCCCcceEEEecccccHHHHHHHHHHHhccCcchhhh
Confidence 336777899999975 4779999999998877888999888888877666543
No 251
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=43.10 E-value=41 Score=38.22 Aligned_cols=84 Identities=20% Similarity=0.358 Sum_probs=51.5
Q ss_pred CcHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhh
Q 009303 209 LNKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKD 288 (538)
Q Consensus 209 ~N~~ia~~l~~la~~~e~~g~~~r~~aY~rAa~~l~~l~~~i~~~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~ 288 (538)
.|...-..|..+-+... .-+.+|.|.-+.=..+ -..|.+|||||++-..++-.. -|++..+..
T Consensus 496 ~~~p~l~~lq~irDEaH-----rfAi~~hR~~R~k~~~------~s~Ld~I~GiG~~r~~~LL~~--Fgs~~~i~~---- 558 (581)
T COG0322 496 PNSPALYLLQRIRDEAH-----RFAITYHRKKRSKAML------QSSLDDIPGIGPKRRKALLKH--FGSLKGIKS---- 558 (581)
T ss_pred CCCHHHHHHHHHHHHHH-----HHHHHHHHHHhhhhhh------cCccccCCCcCHHHHHHHHHH--hhCHHHHHh----
Confidence 45555555555533321 2466676664321111 245889999999988766442 234433332
Q ss_pred chhHHHHHHhhccCCCHHHHHHHHH
Q 009303 289 EKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 289 ~~~~~l~lf~~I~GvGpktA~~ly~ 313 (538)
-+++.|..| ||+++.|+++|+
T Consensus 559 ---As~eel~~v-gi~~~~a~~i~~ 579 (581)
T COG0322 559 ---ASVEELAKV-GISKKLAEKIYE 579 (581)
T ss_pred ---cCHHHHHHc-CCCHHHHHHHHh
Confidence 356778899 999999999986
No 252
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=43.07 E-value=19 Score=34.61 Aligned_cols=59 Identities=19% Similarity=0.353 Sum_probs=32.9
Q ss_pred HHHHHHHHHHhCCcchhHHHHhhchhH-HHHHHhhccCCCHHHHHHHHHh----CCCCHHHHhh
Q 009303 266 MQDHIQEIVTTGKLSKLEHFEKDEKVR-TISLFGEVWGIGPATAQKLYEK----GHRTLDDLKN 324 (538)
Q Consensus 266 ia~kI~Eil~tG~~~~le~l~~~~~~~-~l~lf~~I~GvGpktA~~ly~~----GirtledL~~ 324 (538)
+-..|++|+....-..++-+....|.. -|-.|.=+||||.|+...+.++ -+.|++|+.+
T Consensus 86 L~~vv~~IV~~~E~~FV~FfN~A~PIt~RlH~LeLLPGIGKK~m~~ILeERkkkpFeSFeDi~~ 149 (181)
T PF04919_consen 86 LPYVVEEIVKENEERFVDFFNEAQPITLRLHSLELLPGIGKKTMWKILEERKKKPFESFEDIEE 149 (181)
T ss_dssp HHHHHHHHHHTTHHHHHHHH-----B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHH
T ss_pred HHHHHHHHHHhChHHHHHHhhcCCCChHHHHHHhhcccccHHHHHHHHHHHccCCCCCHHHHHH
Confidence 446688888877766666554433332 1223444699999999999863 5777777764
No 253
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=43.05 E-value=82 Score=37.81 Aligned_cols=48 Identities=17% Similarity=0.476 Sum_probs=33.9
Q ss_pred CeEEEecccccccC-CcCCCeeEEEecCCcc--hhhhhHHHHHHHHHHcCc
Q 009303 368 EVIILCGGSYRRGK-ASCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMKF 415 (538)
Q Consensus 368 ~~~v~~~Gs~RRgk-e~~~DVDiLit~~~~~--~~~~~l~~vv~~L~~~g~ 415 (538)
++.+..+|||=||. .-.+|||+||-+++.. ....+...++..|-+.|+
T Consensus 78 ~~alvAvGgyGR~EL~p~SDiDll~l~~~~~~~~~~~~i~~~~~~LwD~gL 128 (895)
T PRK00275 78 DIALVAVGGYGRGELHPYSDIDLLILLDSADHEEFREPIERFLTLLWDIGL 128 (895)
T ss_pred CEEEEEcCCccccCcCCCCCceEEEEecCCCChHHHHHHHHHHHHHHhcCC
Confidence 45677899997765 5688999999887432 234566667766666664
No 254
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=42.68 E-value=45 Score=33.04 Aligned_cols=76 Identities=21% Similarity=0.218 Sum_probs=42.1
Q ss_pred hHHHHHHHHHHHhc-CCc-----cccchhhhcCCCCCCHHHHHHHHHHHHhCC-cchhHHHHhhchhHHHHHHhhccCCC
Q 009303 232 RSFSYYKAIPVIEK-LPF-----KIESADQVKGLPGIGKSMQDHIQEIVTTGK-LSKLEHFEKDEKVRTISLFGEVWGIG 304 (538)
Q Consensus 232 r~~aY~rAa~~l~~-l~~-----~i~~~~~l~~lpgIG~~ia~kI~Eil~tG~-~~~le~l~~~~~~~~l~lf~~I~GvG 304 (538)
|+..-+..+..+.. ... .-...++|.+|||||..+|+.|-=+.- |+ .--++ .-+.++|.+ .|+.
T Consensus 93 KA~~Lk~la~~i~~~~g~~~~~~~~~~re~Ll~l~GIG~kTAd~iLlya~-~rp~fvVD-------ty~~Rv~~R-lG~~ 163 (218)
T PRK13913 93 KAKRLIDLSENILKDFGSFENFKQEVTREWLLDQKGIGKESADAILCYVC-AKEVMVVD-------KYSYLFLKK-LGIE 163 (218)
T ss_pred HHHHHHHHHHHHHHHcCCchhccCchHHHHHHcCCCccHHHHHHHHHHHc-CCCccccc-------hhHHHHHHH-cCCC
Confidence 55555555555532 211 112347799999999999999876542 32 11111 235666644 3664
Q ss_pred H---HHHHHHHHhCC
Q 009303 305 P---ATAQKLYEKGH 316 (538)
Q Consensus 305 p---ktA~~ly~~Gi 316 (538)
+ ..++.|++.++
T Consensus 164 ~~~y~~~~~~~~~~l 178 (218)
T PRK13913 164 IEDYDELQHFFEKGV 178 (218)
T ss_pred CCCHHHHHHHHHHhh
Confidence 4 34555555444
No 255
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=42.57 E-value=66 Score=29.10 Aligned_cols=88 Identities=23% Similarity=0.432 Sum_probs=60.7
Q ss_pred CCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhccCcchhhhccccchhh
Q 009303 262 IGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYFDD 341 (538)
Q Consensus 262 IG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~~~L~~~q~~Glk~~ed 341 (538)
|=+.|++.|.+-+-+|++..=+ +.++++.|..-.||-|-|+++-|+ +|++++-+....+.|.---+|
T Consensus 12 IY~QI~~qIk~~I~~g~l~pGd------kLPSvRelA~~~~VNpnTv~raY~-------eLE~eG~i~t~rg~G~fV~~~ 78 (125)
T COG1725 12 IYEQIANQIKEQIASGELKPGD------KLPSVRELAKDLGVNPNTVQRAYQ-------ELEREGIVETKRGKGTFVTED 78 (125)
T ss_pred HHHHHHHHHHHHHHhCCcCCCC------CCCcHHHHHHHhCCCHHHHHHHHH-------HHHHCCCEEEecCeeEEEcCC
Confidence 3456899999999999987554 445677788899999999999997 677777777777777544444
Q ss_pred ---hccCcCHHHHHH-HHHHHHHHh
Q 009303 342 ---IKTRIPRHEVEQ-MERLLQKAG 362 (538)
Q Consensus 342 ---~~~~i~r~Ea~~-i~~iv~~~~ 362 (538)
+....-++.+.+ ++.+|.++.
T Consensus 79 ~~~~~~~~~~~~~~~~l~~~I~~~~ 103 (125)
T COG1725 79 AKEILDQLKRELAEEELEEFIEEAK 103 (125)
T ss_pred chhhHHHHHHHHHHHHHHHHHHHHH
Confidence 333333344433 455555543
No 256
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=42.50 E-value=23 Score=34.03 Aligned_cols=40 Identities=28% Similarity=0.283 Sum_probs=33.2
Q ss_pred ccccc-hhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHh
Q 009303 248 FKIES-ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEK 287 (538)
Q Consensus 248 ~~i~~-~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~ 287 (538)
.||+. +-+|+-|||||++++..|-|=-+..-+..++++++
T Consensus 123 ~PIt~RLH~LELLpGiGkK~m~~ILeERkkkpFeSFeDi~~ 163 (202)
T COG1491 123 EPITLRLHQLELLPGIGKKTMWAILEERKKKPFESFEDIKE 163 (202)
T ss_pred CcchHHHHHHHhcccccHHHHHHHHHHHhcCCCcCHHHHHH
Confidence 67776 47899999999999999988777777777777765
No 257
>TIGR00588 ogg 8-oxoguanine DNA-glycosylase (ogg). All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is distantly realted to the Nth-MutY superfamily.
Probab=42.47 E-value=35 Score=35.53 Aligned_cols=76 Identities=18% Similarity=0.206 Sum_probs=42.6
Q ss_pred HHHcCCChhHHHHHHHHHHHhcCCc------ccc------chhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchh
Q 009303 224 YRALGEDRRSFSYYKAIPVIEKLPF------KIE------SADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKV 291 (538)
Q Consensus 224 ~e~~g~~~r~~aY~rAa~~l~~l~~------~i~------~~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~ 291 (538)
+...|-.+|+..-..+|..+..-.. .+. ..++|..|||||+.+|+-|.=+ .-|+..- +-. ..
T Consensus 178 Lr~~G~g~Ra~~I~~~A~~i~~~~~~~~~l~~l~~~~~~~~~~~L~~l~GIG~~tAd~vll~-~l~~~d~---~Pv--D~ 251 (310)
T TIGR00588 178 LRKLGLGYRARYIRETARALLEEQGGRAWLQQIRGASYEDAREALCELPGVGPKVADCICLM-GLDKPQA---VPV--DV 251 (310)
T ss_pred HHHcCCHHHHHHHHHHHHHHHhccCCchhHHhhccCChHHHHHHHHhCCCccHHHHHHHHHH-hCCCCCc---eee--cH
Confidence 3334544576666677776654211 111 2467999999999999987633 2233211 111 23
Q ss_pred HHHHHHhhccCCCH
Q 009303 292 RTISLFGEVWGIGP 305 (538)
Q Consensus 292 ~~l~lf~~I~GvGp 305 (538)
.+.+.+.+++|+.+
T Consensus 252 ~v~r~~~r~y~~~~ 265 (310)
T TIGR00588 252 HVWRIANRDYPWHP 265 (310)
T ss_pred HHHHHHHHHhcccc
Confidence 45666666666543
No 258
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=42.44 E-value=32 Score=40.66 Aligned_cols=32 Identities=13% Similarity=0.211 Sum_probs=26.2
Q ss_pred HHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009303 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~GirtledL~~~ 325 (538)
..+++.++|||||+.|+.+.+. +.|+++|.+.
T Consensus 755 ~q~~L~~lPgI~~~~a~~ll~~-f~si~~l~~a 786 (814)
T TIGR00596 755 PQDFLLKLPGVTKKNYRNLRKK-VKSIRELAKL 786 (814)
T ss_pred HHHHHHHCCCCCHHHHHHHHHH-cCCHHHHHhC
Confidence 3444669999999999999985 8899998864
No 259
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=42.02 E-value=18 Score=33.66 Aligned_cols=24 Identities=29% Similarity=0.338 Sum_probs=19.6
Q ss_pred HHHHhhccCCCHHHHHHHHHh-CCC
Q 009303 294 ISLFGEVWGIGPATAQKLYEK-GHR 317 (538)
Q Consensus 294 l~lf~~I~GvGpktA~~ly~~-Gir 317 (538)
.--|+.|+|||+++|..+-+. ||.
T Consensus 24 ~~aLt~IyGIG~~~a~~Ic~~lgi~ 48 (149)
T PRK04053 24 EYALTGIKGIGRRTARAIARKLGLD 48 (149)
T ss_pred eeeccccccccHHHHHHHHHHcCcC
Confidence 334689999999999999876 764
No 260
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]
Probab=41.92 E-value=15 Score=36.41 Aligned_cols=58 Identities=22% Similarity=0.303 Sum_probs=41.6
Q ss_pred hhhcCCCCCCHHHH---HHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHH
Q 009303 254 DQVKGLPGIGKSMQ---DHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLY 312 (538)
Q Consensus 254 ~~l~~lpgIG~~ia---~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly 312 (538)
+++.++ |+-+.=+ .-+.|....|.+...+.+..-.....++++|+|.|||+=|++++-
T Consensus 122 ~~lrkc-G~S~rK~~yLh~lA~~~~ng~I~s~~~i~~mseEeL~~~LT~VKGIg~Wtv~Mfl 182 (254)
T KOG1918|consen 122 EELRKC-GFSKRKASYLHSLAEAYTNGYIPSKSGIEKMSEEELIERLTNVKGIGRWTVEMFL 182 (254)
T ss_pred HHHHHh-CcchhhHHHHHHHHHHHhcCCCCchHHHhhcCHHHHHHHHHhccCccceeeeeee
Confidence 455444 4444333 335566678888888777766667799999999999999998774
No 261
>PF06514 PsbU: Photosystem II 12 kDa extrinsic protein (PsbU); InterPro: IPR010527 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. In PSII, the oxygen-evolving complex (OEC) is responsible for catalysing the splitting of water to O(2) and 4H+. The OEC is composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ), PsbU and PsbV having been lost during the evolution of green plants []. This family represents the PSII extrinsic protein PsbU, which forms part of the OEC in cyanobacteria and red algae. PsbU acts to stabilise the oxygen-evolving machinery of PSII against heat-induced inactivation, which is crucial for cellular thermo-tolerance [].; GO: 0015979 photosynthesis, 0042549 photosystem II stabilization, 0009523 photosystem II, 0009654 oxygen evolving complex, 0019898 extrinsic to membrane; PDB: 3BZ1_U 3KZI_U 3PRQ_U 2AXT_u 3BZ2_U 4FBY_U 3PRR_U 1S5L_U 3A0H_U 3ARC_U ....
Probab=41.79 E-value=7.5 Score=33.16 Aligned_cols=51 Identities=24% Similarity=0.337 Sum_probs=39.8
Q ss_pred HHHHHhhccCCCHHHHHHHHHh-CCCCHHHHhhccCcchhhhccccchhhhc
Q 009303 293 TISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNEDSLTHSQRLGLKYFDDIK 343 (538)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~-GirtledL~~~~~L~~~q~~Glk~~ed~~ 343 (538)
.+..|++.||+=|..|.++..- -+.|++|+.+-.-|+..|+-=++-|++.-
T Consensus 21 ~vr~f~~~pGmYPtlA~kIv~naPY~sveDvl~ipgLse~qK~~lk~~~~~F 72 (93)
T PF06514_consen 21 NVRAFRQFPGMYPTLAGKIVSNAPYKSVEDVLNIPGLSERQKALLKKYEDNF 72 (93)
T ss_dssp -GGGGCCSTTTTCCHHHHHHHS---SSGGGGCCSTT--HHHHHHHHHHGGGE
T ss_pred hHHHHHHCCCCCHHHHHHHHhCCCCCCHHHHHhccCCCHHHHHHHHHHhccc
Confidence 4566889999999999999998 69999999988789988888777777643
No 262
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=41.36 E-value=51 Score=31.76 Aligned_cols=57 Identities=19% Similarity=0.325 Sum_probs=35.0
Q ss_pred HHHHHHHHhCCcchhHHHHhhchhH-HHHHHhhccCCCHHHHHHHHHh----CCCCHHHHhh
Q 009303 268 DHIQEIVTTGKLSKLEHFEKDEKVR-TISLFGEVWGIGPATAQKLYEK----GHRTLDDLKN 324 (538)
Q Consensus 268 ~kI~Eil~tG~~~~le~l~~~~~~~-~l~lf~~I~GvGpktA~~ly~~----GirtledL~~ 324 (538)
..+++|+....=..++-+..-.|.. -|-.|.=+||||.|+...+.++ -+.|++|+++
T Consensus 102 yvve~iV~~~E~rFV~fFN~A~PIt~RLH~LELLpGiGkK~m~~ILeERkkkpFeSFeDi~~ 163 (202)
T COG1491 102 YVVEKIVKENEDRFVKFFNEAEPITLRLHQLELLPGIGKKTMWAILEERKKKPFESFEDIKE 163 (202)
T ss_pred HHHHHHHHhhhhHHHHHhcccCcchHHHHHHHhcccccHHHHHHHHHHHhcCCCcCHHHHHH
Confidence 3455666554444444443323322 2333445699999999999863 6888888875
No 263
>cd01701 PolY_Rev1 DNA polymerase Rev1. Rev1 is a translesion synthesis (TLS) polymerase found in eukaryotes. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Rev1 has both structural and enzymatic roles. Structurally, it is believed to interact with other nonclassical polymerases and replication machinery to act as a scaffold. Enzymatically, it catalyzes the specific insertion of dCMP opposite abasic sites. Rev1 interacts with the Rev7 subunit of the B-family TLS polymerase Pol zeta (Rev3/Rev7). Rev1 is known to actively promote the introduction of mutations, potentially making it a significant target for cancer treatment.
Probab=40.96 E-value=59 Score=35.06 Aligned_cols=53 Identities=28% Similarity=0.488 Sum_probs=33.8
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhc--hhHHHHHHhhccCCCHHHHHHHHHh--CCCC
Q 009303 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDE--KVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (538)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~--~~~~l~lf~~I~GvGpktA~~ly~~--Girt 318 (538)
+..|||||+++++++..+ | +..+.++.+-. +....+.| |++.+..||+. |+..
T Consensus 224 v~~l~GIG~~~~~~L~~~---G-i~t~~dl~~~~~~~~~L~~~f------G~~~g~~L~~~a~G~d~ 280 (404)
T cd01701 224 VGDLPGVGSSLAEKLVKL---F-GDTCGGLELRSKTKEKLQKVL------GPKTGEKLYDYCRGIDD 280 (404)
T ss_pred HhHhCCCCHHHHHHHHHc---C-CcchHHHHhCcccHHHHHHHH------CHHHHHHHHHHhCCcCC
Confidence 678899999988877653 3 34444444322 23333444 57789998875 8764
No 264
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=40.82 E-value=53 Score=34.73 Aligned_cols=62 Identities=18% Similarity=0.232 Sum_probs=44.2
Q ss_pred HHHHHHcCCChhHHHHHHHHHHHhcC-Ccccc-chhhhcCCCCCCHHHHHHHHHHHHhCCcchh
Q 009303 221 INIYRALGEDRRSFSYYKAIPVIEKL-PFKIE-SADQVKGLPGIGKSMQDHIQEIVTTGKLSKL 282 (538)
Q Consensus 221 a~~~e~~g~~~r~~aY~rAa~~l~~l-~~~i~-~~~~l~~lpgIG~~ia~kI~Eil~tG~~~~l 282 (538)
-.+++=.|-..|++--.+||..+... ...+. +.+++..|||||..+|..|--|.-.-...-|
T Consensus 78 l~~W~gLGYysRArnL~~~A~~v~~~~~G~~P~~~~~l~~LpGiG~yTa~Ail~~a~~~~~~~l 141 (342)
T COG1194 78 LKAWEGLGYYSRARNLHKAAQEVVERHGGEFPDDEEELAALPGVGPYTAGAILSFAFNQPEPVL 141 (342)
T ss_pred HHHHHhcChHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHhCCCCcHHHHHHHHHHHhCCCCcee
Confidence 34555556556898888888877654 44444 3578999999999999999887754443433
No 265
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=40.78 E-value=18 Score=41.10 Aligned_cols=20 Identities=15% Similarity=0.165 Sum_probs=11.8
Q ss_pred CcchhhhccccchhhhccCc
Q 009303 327 SLTHSQRLGLKYFDDIKTRI 346 (538)
Q Consensus 327 ~L~~~q~~Glk~~ed~~~~i 346 (538)
.|..+.++|.+....+...+
T Consensus 526 ~L~~IpGIG~kr~~~LL~~F 545 (577)
T PRK14668 526 VLDDVPGVGPETRKRLLRRF 545 (577)
T ss_pred HHhcCCCCCHHHHHHHHHHc
Confidence 46667777755555555443
No 266
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=40.34 E-value=19 Score=33.30 Aligned_cols=44 Identities=23% Similarity=0.352 Sum_probs=30.4
Q ss_pred HHhhccCCCHHHHHHHHHh-CCCCHHHHhhccCcchhhhccccchhhhccCcCHHHHHHHHHHHHH
Q 009303 296 LFGEVWGIGPATAQKLYEK-GHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQK 360 (538)
Q Consensus 296 lf~~I~GvGpktA~~ly~~-GirtledL~~~~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~iv~~ 360 (538)
-|+.|+|||+++|..+-+. ||..-.-+ .-++-++++.+..+|..
T Consensus 22 aLt~I~GIG~~~a~~I~~~lgi~~~~~~---------------------~~Lt~~qi~~l~~~i~~ 66 (144)
T TIGR03629 22 ALTGIKGIGRRFARAIARKLGVDPNAKL---------------------GYLDDEEIEKLEEAVEN 66 (144)
T ss_pred eecceeccCHHHHHHHHHHcCcCCCCCc---------------------ccCCHHHHHHHHHHHHh
Confidence 4679999999999999876 76421111 12445677778777776
No 267
>TIGR00194 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.
Probab=40.14 E-value=23 Score=40.20 Aligned_cols=29 Identities=24% Similarity=0.354 Sum_probs=23.8
Q ss_pred HHhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009303 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 296 lf~~I~GvGpktA~~ly~~GirtledL~~~ 325 (538)
.|.+|+|||||+.+.|++. +.|+++++++
T Consensus 542 ~Ld~I~GIG~kr~~~LL~~-Fgs~~~i~~A 570 (574)
T TIGR00194 542 PLLKIPGVGEKRVQKLLKY-FGSLKGIKKA 570 (574)
T ss_pred HHhcCCCCCHHHHHHHHHH-cCCHHHHHhC
Confidence 4569999999999999984 5688888754
No 268
>TIGR01446 DnaD_dom DnaD and phage-associated domain. This model represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria.
Probab=39.93 E-value=25 Score=28.03 Aligned_cols=18 Identities=22% Similarity=0.423 Sum_probs=16.2
Q ss_pred HHHHHHHHhCCCCHHHHh
Q 009303 306 ATAQKLYEKGHRTLDDLK 323 (538)
Q Consensus 306 ktA~~ly~~GirtledL~ 323 (538)
+.++.|.+.||+|++|++
T Consensus 55 ~Il~~W~~~gi~T~e~~~ 72 (73)
T TIGR01446 55 AILNNWKNNGIKTVEDVE 72 (73)
T ss_pred HHHHHHHHcCCCCHHHHh
Confidence 678999999999999986
No 269
>PF02961 BAF: Barrier to autointegration factor; InterPro: IPR004122 Barrier-to-autointegration factor (BAF) is an essential protein that is highly conserved in metazoan evolution, and which may act as a DNA-bridging protein []. BAF binds directly to double-stranded DNA, to transcription activators, and to inner nuclear membrane proteins, including lamin A filament proteins that anchor nuclear-pore complexes in place, and nuclear LEM-domain proteins that bind to laminins filaments and chromatin. New findings suggest that BAF has structural roles in nuclear assembly and chromatin organisation, represses gene expression and might interlink chromatin structure, nuclear architecture and gene regulation in metazoans []. BAF can be exploited by retroviruses to act as a host component of pre-integration complexes, which promote the integration of the retroviral DNA into the host chromosome by preventing autointegration of retroviral DNA []. BAF might contribute to the assembly or activity of retroviral pre-integration complexes through direct binding to the retroviral proteins p55 Gag and matrix, as well as to DNA.; GO: 0003677 DNA binding; PDB: 2ODG_A 2BZF_A 2EZX_B 2EZY_B 1QCK_B 1CI4_B 2EZZ_B.
Probab=39.54 E-value=23 Score=30.07 Aligned_cols=28 Identities=32% Similarity=0.406 Sum_probs=20.4
Q ss_pred HHhhccCCCHHHHHHHHHhCCCCHHHHh
Q 009303 296 LFGEVWGIGPATAQKLYEKGHRTLDDLK 323 (538)
Q Consensus 296 lf~~I~GvGpktA~~ly~~GirtledL~ 323 (538)
..+.++||||..+.+|-+.|+.---.|.
T Consensus 20 ~V~~laGIG~~lg~~L~~~GfdKAy~vL 47 (89)
T PF02961_consen 20 PVTELAGIGPVLGKRLEEKGFDKAYVVL 47 (89)
T ss_dssp BGGGSTT--HHHHHHHHHTT--BHHHHH
T ss_pred CccccCCcCHHHHHHHHHCCCcHHHHHh
Confidence 3568999999999999999998866665
No 270
>KOG3524 consensus Predicted guanine nucleotide exchange factor (PEBBLE) [Signal transduction mechanisms]
Probab=39.14 E-value=21 Score=40.84 Aligned_cols=86 Identities=19% Similarity=0.346 Sum_probs=60.2
Q ss_pred CCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHhhhcccCccccccchHHHHHh
Q 009303 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSLR 96 (538)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~~~~~~~~~~l~~~~~~~~~~~lV~~~Wl~ecik 96 (538)
.-|.|+.++|. +....--+.+-.-....||..+. -+..-||||+.+......-+. ...+-++|.-.|+-=+|.
T Consensus 209 ~~feg~~~~f~--gF~~ee~~~m~~sle~~gg~~a~-~d~~cthvvv~e~~~~~~p~~----~s~~~~~vk~ewfw~siq 281 (850)
T KOG3524|consen 209 GVFEGLSLFFH--GFKQEEIDDMLRSLENTGGKLAP-SDTLCTHVVVNEDNDEVEPLA----VSSNQVHVKKEWFWVSIQ 281 (850)
T ss_pred ccccCCeEeec--CCcHHHHHHHHHHHHhcCCcccC-CCCCceeEeecCCcccccccc----ccccceeecccceEEEEe
Confidence 67999999994 45555567777888899999988 567899999976532211111 112356888888888888
Q ss_pred cCcccCccccccc
Q 009303 97 LGEKVSEDLYRIK 109 (538)
Q Consensus 97 ~g~lv~e~~y~l~ 109 (538)
.|..--|+.|.+.
T Consensus 282 ~g~~a~e~~yl~~ 294 (850)
T KOG3524|consen 282 RGCCAIEDNYLLP 294 (850)
T ss_pred cchhccccceecc
Confidence 8777777777653
No 271
>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase. This model describes GlnD, the uridylyltransferase/uridylyl-removing enzyme for the nitrogen regulatory protein PII. Not all homologs of PII share the property of uridylyltransferase modification on the characteristic Tyr residue (see Prosite pattern PS00496 and document PDOC00439), but the modification site is preserved in the PII homolog of all species with a member of this family.
Probab=38.86 E-value=82 Score=37.49 Aligned_cols=49 Identities=20% Similarity=0.497 Sum_probs=35.0
Q ss_pred CeEEEecccccccC-CcCCCeeEEEecCCcc--hhhhhHHHHHHHHHHcCcc
Q 009303 368 EVIILCGGSYRRGK-ASCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMKFL 416 (538)
Q Consensus 368 ~~~v~~~Gs~RRgk-e~~~DVDiLit~~~~~--~~~~~l~~vv~~L~~~g~l 416 (538)
++-+..+|||=||. .-..|||++|-+++.. ....++.+++..|-+.|+-
T Consensus 43 ~~aliA~GgyGR~El~p~SDiDll~l~~~~~~~~~~~~~~~~~~~LwD~gl~ 94 (850)
T TIGR01693 43 GIALVAVGGYGRGELAPYSDIDLLFLHDGKPAEEVEPKIERFLYPLWDLGFE 94 (850)
T ss_pred CeEEEEeCCccccCcCCCCCCeEEEEeCCCCChHHHHHHHHHHHHHHhcCCC
Confidence 45677889996665 5678999999887532 2456677777777777753
No 272
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=38.51 E-value=19 Score=37.44 Aligned_cols=23 Identities=39% Similarity=0.557 Sum_probs=18.2
Q ss_pred hhccCCCHHHHHHHHHhCCCCHHH
Q 009303 298 GEVWGIGPATAQKLYEKGHRTLDD 321 (538)
Q Consensus 298 ~~I~GvGpktA~~ly~~Girtled 321 (538)
.+|+|||||||.+|.++ +.|++.
T Consensus 226 ~gv~giG~k~A~~li~~-~~~~~~ 248 (316)
T cd00128 226 EGIPGIGPVTALKLIKK-YGDIEK 248 (316)
T ss_pred CCCCCccHHHHHHHHHH-cCChHH
Confidence 48999999999999988 334433
No 273
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=38.07 E-value=54 Score=38.86 Aligned_cols=16 Identities=19% Similarity=0.353 Sum_probs=10.0
Q ss_pred cHHHHHHHHHHHHHHH
Q 009303 210 NKNITEIFGKLINIYR 225 (538)
Q Consensus 210 N~~ia~~l~~la~~~e 225 (538)
|..+-+..+.|...|+
T Consensus 643 ~gRL~~Q~~~m~~~Y~ 658 (814)
T TIGR00596 643 NGRLYNQCEKMLRYYA 658 (814)
T ss_pred cchHHHHHHHHHHhcC
Confidence 3346666677777666
No 274
>COG1204 Superfamily II helicase [General function prediction only]
Probab=37.67 E-value=25 Score=41.35 Aligned_cols=109 Identities=23% Similarity=0.307 Sum_probs=60.0
Q ss_pred HHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCc--chhHHHH----hhchhHHHHHHhhccCCCHH
Q 009303 233 SFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKL--SKLEHFE----KDEKVRTISLFGEVWGIGPA 306 (538)
Q Consensus 233 ~~aY~rAa~~l~~l~~~i~~~~~l~~lpgIG~~ia~kI~Eil~tG~~--~~le~l~----~~~~~~~l~lf~~I~GvGpk 306 (538)
..+|-.+...+...-....=. .+. +..+|.++. ++..++..|.. ..++.+. ...+...+..+..|.|+|-.
T Consensus 610 ~~~~~~~~~dl~~~~~~a~w~-~~~-~~~l~~~~~-r~~~~~~~~~~~~~~~~~~~~rie~gv~~e~~~~l~~i~~~grv 686 (766)
T COG1204 610 LNAYGVAPGDLLRIAETAEWL-SAD-LLALGKAAE-RLAKILGLGLHVLRKLEILSLRIEYGVRSEELLELVEIRGVGRV 686 (766)
T ss_pred HHHhCcchhhHHhhcchhhhh-hhh-hhhhhhhhh-hhHhhhCCCccccccchhhhhhhhcCCChhhhcccccccccchh
Confidence 345555544444332222212 122 444454444 44445555433 3333332 22231233445599999999
Q ss_pred HHHHHHHhCCCCHHHHhhcc---Ccchhhhccccchhhhcc
Q 009303 307 TAQKLYEKGHRTLDDLKNED---SLTHSQRLGLKYFDDIKT 344 (538)
Q Consensus 307 tA~~ly~~GirtledL~~~~---~L~~~q~~Glk~~ed~~~ 344 (538)
.|++||..|+++++++.... .+....++|.+.++.+..
T Consensus 687 rar~ly~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~ 727 (766)
T COG1204 687 RARKLYNAGYKSLEDLRLIADPAELLPLTGIGERLVEAILE 727 (766)
T ss_pred HHHHHHHhhhccHHHHHhhcChhhhhhhhhhHHHHHHHHHH
Confidence 99999999999999999432 355555666666555443
No 275
>PRK13766 Hef nuclease; Provisional
Probab=37.38 E-value=23 Score=41.36 Aligned_cols=45 Identities=18% Similarity=0.325 Sum_probs=32.5
Q ss_pred HHhhccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhccccchhh
Q 009303 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDD 341 (538)
Q Consensus 296 lf~~I~GvGpktA~~ly~~GirtledL~~~~--~L~~~q~~Glk~~ed 341 (538)
+|..|+|||+++|++|.+. +.|++++..+. .|....++|.+..+.
T Consensus 716 ~L~~ipgig~~~a~~Ll~~-fgs~~~i~~as~~~L~~i~Gig~~~a~~ 762 (773)
T PRK13766 716 IVESLPDVGPVLARNLLEH-FGSVEAVMTASEEELMEVEGIGEKTAKR 762 (773)
T ss_pred HHhcCCCCCHHHHHHHHHH-cCCHHHHHhCCHHHHHhCCCCCHHHHHH
Confidence 5789999999999999986 45788887543 355555666444333
No 276
>PRK03059 PII uridylyl-transferase; Provisional
Probab=37.16 E-value=92 Score=37.20 Aligned_cols=65 Identities=15% Similarity=0.355 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHhhhc--CCCeEEEeccccccc-CCcCCCeeEEEecCCcc--hhhhhHHHHHHHHHHcCc
Q 009303 351 VEQMERLLQKAGEEV--LPEVIILCGGSYRRG-KASCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMKF 415 (538)
Q Consensus 351 a~~i~~iv~~~~~~~--~p~~~v~~~Gs~RRg-ke~~~DVDiLit~~~~~--~~~~~l~~vv~~L~~~g~ 415 (538)
+..+..+++.+.... ..++.+..+|||=|| ..-..|||+||-+++.. .....+..++..|-+.|+
T Consensus 42 s~l~d~~l~~~~~~~~~~~~~alvAvGgyGR~EL~p~SDiDll~l~~~~~~~~~~~~i~~~~~~lwD~gL 111 (856)
T PRK03059 42 SRLVDQALRRLWQECGLPAGAALVAVGGYGRGELFPYSDVDLLVLLPDAPDAALDARIERFIGLCWDLGL 111 (856)
T ss_pred HHHHHHHHHHHHHhcCCCCCeEEEEcCCCCCcccCCCCCCEEEEEecCCcchHHHHHHHHHHHhhhccCC
Confidence 333444454443222 235677789999665 46689999999887543 233445555544444443
No 277
>PF09970 DUF2204: Nucleotidyl transferase of unknown function (DUF2204); InterPro: IPR018700 This family of hypothetical prokaryotic proteins has no known function.
Probab=36.71 E-value=73 Score=30.47 Aligned_cols=39 Identities=18% Similarity=0.211 Sum_probs=25.9
Q ss_pred CeEEEecccc-----cccCCcCCCeeEEEecCCcchhhhhHHHH
Q 009303 368 EVIILCGGSY-----RRGKASCGDLDVVIMHPDRKSHKGFLSKY 406 (538)
Q Consensus 368 ~~~v~~~Gs~-----RRgke~~~DVDiLit~~~~~~~~~~l~~v 406 (538)
|+...+.||+ -..+.+.+|||++|..++......++..+
T Consensus 16 gv~~~ivGG~av~l~~g~~r~T~DIDlfi~~~~~~~~~~~~~~~ 59 (181)
T PF09970_consen 16 GVEYVIVGGAAVNLAYGRRRTTKDIDLFIENPSPNLEADALREV 59 (181)
T ss_pred CCeEEEECHHHHHHHhCCCCCCCCeEEEeCCCchHHHHHHHHHH
Confidence 6666667773 25667789999999877665444344333
No 278
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=35.93 E-value=61 Score=38.06 Aligned_cols=48 Identities=17% Similarity=0.495 Sum_probs=32.4
Q ss_pred CeEEEecccccccC-CcCCCeeEEEecCCcchh--hhhHHHHHHHHHHcCc
Q 009303 368 EVIILCGGSYRRGK-ASCGDLDVVIMHPDRKSH--KGFLSKYVKKLKEMKF 415 (538)
Q Consensus 368 ~~~v~~~Gs~RRgk-e~~~DVDiLit~~~~~~~--~~~l~~vv~~L~~~g~ 415 (538)
++-++.+|||=||. --+.|||+||-+|...+. ..-+..++..|=+.|+
T Consensus 66 ~~aLvAVGGyGRgEL~P~SDiDlL~L~p~~~~~~~e~~ie~~l~~LWD~gl 116 (867)
T COG2844 66 GLALVAVGGYGRGELHPLSDIDLLLLSPQKLTDWLEQKIERFLYLLWDLGL 116 (867)
T ss_pred ceEEEEeccccccccCCCccceEEEecCCCCChHHHHHHHHHHHHHHhcCc
Confidence 35677899998875 458999999999876542 2334444554555554
No 279
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=35.04 E-value=31 Score=39.59 Aligned_cols=27 Identities=44% Similarity=0.650 Sum_probs=25.3
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHh
Q 009303 297 FGEVWGIGPATAQKLYEKGHRTLDDLK 323 (538)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~ 323 (538)
+..+.||||++|.++-+.||.|+.||.
T Consensus 12 l~~l~gig~~~a~~l~~Lgi~tv~DLL 38 (677)
T COG1200 12 LSTLKGIGPKTAEKLKKLGIHTVQDLL 38 (677)
T ss_pred hhhhcCcCHHHHHHHHHcCCCcHHHHH
Confidence 568999999999999999999999997
No 280
>PHA01806 hypothetical protein
Probab=34.74 E-value=65 Score=31.31 Aligned_cols=49 Identities=18% Similarity=0.238 Sum_probs=31.3
Q ss_pred CcCHHHHHH-HHHHHHHHhhhcCCCeEEEecccccc----cCCcCCCeeEEEecCCcc
Q 009303 345 RIPRHEVEQ-MERLLQKAGEEVLPEVIILCGGSYRR----GKASCGDLDVVIMHPDRK 397 (538)
Q Consensus 345 ~i~r~Ea~~-i~~iv~~~~~~~~p~~~v~~~Gs~RR----gke~~~DVDiLit~~~~~ 397 (538)
.|++..... ...++..+. .-+..+.++||+=| |+ .+.|+||++....+.
T Consensus 14 ~I~~~~is~~al~v~~~l~---~~g~~aYlVGG~VRD~Llgr-~~kDiDivt~~~~pe 67 (200)
T PHA01806 14 EIPEGLIAKALLLRLYSDA---RHSEGVALAGGAARDLMHGA-EPKDIDIALYGMDDR 67 (200)
T ss_pred ccChhHcCHHHHHHHHHHH---HCCcEEEEECchHHHHHcCC-CCCceEEEccCCCHH
Confidence 456665433 344444443 35778888899877 55 789999976444444
No 281
>PHA00439 exonuclease
Probab=34.22 E-value=28 Score=35.91 Aligned_cols=27 Identities=19% Similarity=0.284 Sum_probs=21.9
Q ss_pred hhccCCCHHHHHHHHHh--CCCCHHHHhhc
Q 009303 298 GEVWGIGPATAQKLYEK--GHRTLDDLKNE 325 (538)
Q Consensus 298 ~~I~GvGpktA~~ly~~--GirtledL~~~ 325 (538)
-+|+||| |||.+|.++ .+..++...+.
T Consensus 191 PGVpGIG-KTA~kLL~~~~~~~~~~~~~~s 219 (286)
T PHA00439 191 SGIPGWG-DTAEAFLENPYIFEQVEKVLKS 219 (286)
T ss_pred CCCCCcC-HHHHHHHhCccccchhhHHhhc
Confidence 4799999 999999998 66777776644
No 282
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=34.17 E-value=63 Score=33.27 Aligned_cols=45 Identities=20% Similarity=0.350 Sum_probs=31.3
Q ss_pred CCC-hhHHHHHHHHHHHhc--CCccc-cc----hhhhcCCCCCCHHHHHHHHH
Q 009303 228 GED-RRSFSYYKAIPVIEK--LPFKI-ES----ADQVKGLPGIGKSMQDHIQE 272 (538)
Q Consensus 228 g~~-~r~~aY~rAa~~l~~--l~~~i-~~----~~~l~~lpgIG~~ia~kI~E 272 (538)
|-. .|+..-..+|.++.+ ++... .+ .++|..|||||+.+|+-|.=
T Consensus 173 Gl~~~Ra~~L~~lA~~i~~g~l~l~~~~~~~~~~~~L~~LpGIGpwTA~~vll 225 (283)
T PRK10308 173 GMPLKRAEALIHLANAALEGTLPLTIPGDVEQAMKTLQTFPGIGRWTANYFAL 225 (283)
T ss_pred CCCHHHHHHHHHHHHHHHcCCCCccccCCHHHHHHHHhcCCCcCHHHHHHHHH
Confidence 444 477777888877754 43221 12 46799999999999998763
No 283
>PF11774 Lsr2: Lsr2 ; InterPro: IPR024412 This entry represents Lsr2, which is a small, basic DNA-bridging protein present in Mycobacterium and related actinomycetes. It is a functional homologue of the H-NS-like proteins []. H-NS proteins play a role in nucleoid organisation and also function as a pleiotropic regulator of gene expression [, ].; PDB: 4E1R_B 4E1P_B 2KNG_A.
Probab=34.16 E-value=26 Score=30.90 Aligned_cols=28 Identities=25% Similarity=0.426 Sum_probs=17.6
Q ss_pred hccHHHHHHHHHHHHHcCCccCCCCCcc
Q 009303 470 TGNDVLNRRLRLLAESKGYRLDDTGLFP 497 (538)
Q Consensus 470 TGS~~fnr~lR~~A~~kg~~L~~~gL~~ 497 (538)
+.++..++.+|.||++.||.+++.|-..
T Consensus 73 ~~~~~~~~~IR~WA~~nG~~Vs~RGRIp 100 (110)
T PF11774_consen 73 AAPREDTAAIREWARENGYEVSDRGRIP 100 (110)
T ss_dssp --SSTHHHHHHHHHHHTT----SSS---
T ss_pred CCCccchHHHHHHHHHcCCcCCCCCcCC
Confidence 5567789999999999999999998653
No 284
>PRK10880 adenine DNA glycosylase; Provisional
Probab=33.98 E-value=29 Score=36.91 Aligned_cols=24 Identities=21% Similarity=0.279 Sum_probs=19.6
Q ss_pred HHHHHHhhccCCCHHHHHHHHHhC
Q 009303 292 RTISLFGEVWGIGPATAQKLYEKG 315 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~G 315 (538)
..++.|+++||||++||..+---+
T Consensus 106 ~~~~~L~~LpGIG~~TA~aIl~~a 129 (350)
T PRK10880 106 ETFEEVAALPGVGRSTAGAILSLS 129 (350)
T ss_pred hhHHHHhcCCCccHHHHHHHHHHH
Confidence 456778899999999999887643
No 285
>PTZ00035 Rad51 protein; Provisional
Probab=33.69 E-value=73 Score=33.61 Aligned_cols=50 Identities=24% Similarity=0.307 Sum_probs=34.5
Q ss_pred HHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhccccchhhhc
Q 009303 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIK 343 (538)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~GirtledL~~~~--~L~~~q~~Glk~~ed~~ 343 (538)
.++.+ .-+||+|.++++|-+.||.|++||.... .|....+++....+++.
T Consensus 22 ~~~~l-~~~g~~~~~~~kL~~~g~~t~~~~~~~~~~~L~~~~gis~~~~~~i~ 73 (337)
T PTZ00035 22 EIEKL-QSAGINAADIKKLKEAGICTVESVAYATKKDLCNIKGISEAKVEKIK 73 (337)
T ss_pred cHHHH-hcCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhhCCCHHHHHHHH
Confidence 35555 3489999999999999999999998543 35544444444334443
No 286
>PRK13910 DNA glycosylase MutY; Provisional
Probab=33.05 E-value=29 Score=35.84 Aligned_cols=23 Identities=26% Similarity=0.242 Sum_probs=18.5
Q ss_pred HHHHHhhccCCCHHHHHHHHHhC
Q 009303 293 TISLFGEVWGIGPATAQKLYEKG 315 (538)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~G 315 (538)
..+.|+++||||++||..+---+
T Consensus 70 ~~~~L~~LpGIG~kTA~aIl~~a 92 (289)
T PRK13910 70 DYQSLLKLPGIGAYTANAILCFG 92 (289)
T ss_pred hHHHHHhCCCCCHHHHHHHHHHH
Confidence 46677799999999999876543
No 287
>COG1031 Uncharacterized Fe-S oxidoreductase [Energy production and conversion]
Probab=33.01 E-value=34 Score=37.50 Aligned_cols=32 Identities=16% Similarity=0.350 Sum_probs=29.2
Q ss_pred HHHHHhhccCCCHHHHHHHHHh-CCCCHHHHhh
Q 009303 293 TISLFGEVWGIGPATAQKLYEK-GHRTLDDLKN 324 (538)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~-GirtledL~~ 324 (538)
..+.++.|||||.+++.+++.. .+.|.||+++
T Consensus 514 s~~vl~~ipgig~~~~~~I~~~Rp~~s~e~~l~ 546 (560)
T COG1031 514 SKDVLRAIPGIGKKTLRKILAERPFKSSEEFLK 546 (560)
T ss_pred cHHHHHhcccchhhhHHHHHhcCCccchHHHHh
Confidence 4778999999999999999987 9999999985
No 288
>COG5275 BRCT domain type II [General function prediction only]
Probab=32.54 E-value=95 Score=30.75 Aligned_cols=50 Identities=14% Similarity=0.074 Sum_probs=36.8
Q ss_pred CCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEcCCh
Q 009303 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLE 67 (538)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~~~~~ 67 (538)
.-+.|.+|.|-. -|..-.++-.+-++..+||+|....|...|-||.-++-
T Consensus 155 ~cL~G~~fVfTG-~l~TlsR~~a~~lvk~yGgrvT~~pSskTtflvlGdna 204 (276)
T COG5275 155 ECLKGKVFVFTG-DLKTLSRDDAKTLVKVYGGRVTAVPSSKTTFLVLGDNA 204 (276)
T ss_pred ccccccEEEEec-ccccccchhHHHHHHHhCCeeecccccceeEEEecCCC
Confidence 456788877732 22323455667899999999999999999999987664
No 289
>cd01702 PolY_Pol_eta DNA Polymerase eta. Pol eta, also called Rad30A, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Unlike other Y-family members, Pol eta can efficiently and accurately replicate DNA past UV-induced lesions. Its activity is initiated by two simultaneous interactions: the PIP box in pol eta interacting with PCNA, and the UBZ (ubiquitin-binding zinc finger) in pol eta interacting with monoubiquitin attached to PCNA. Pol eta is more efficient in copying damaged DNA than undamaged DNA and seems to recognize when a lesion has been passed, facilitating a lesion-dependent dissociation from the DNA.
Probab=32.41 E-value=1.1e+02 Score=32.63 Aligned_cols=54 Identities=17% Similarity=0.305 Sum_probs=32.5
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhh--chhHHHHHHhhccCCCHHHHHHHHHh--CCCC
Q 009303 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKD--EKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (538)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~--~~~~~l~lf~~I~GvGpktA~~ly~~--Girt 318 (538)
+..|||||++++.++.+-+ .+..+.+|.+- .+....+.| |.+.+..+|+. |+..
T Consensus 184 v~~l~GiG~~~~~~ll~~~---Gi~ti~dl~~~~~~~~~L~~~f------G~~~g~~l~~~a~G~d~ 241 (359)
T cd01702 184 ITSIRGLGGKLGEEIIDLL---GLPTEGDVAGFRSSESDLQEHF------GEKLGEWLYNLLRGIDH 241 (359)
T ss_pred HHHhCCcCHHHHHHHHHHc---CCcCHHHHHhccCCHHHHHHHH------HHHHHHHHHHHhCCCCC
Confidence 6788999988876543322 23444454432 222333444 67788999875 8764
No 290
>PRK03858 DNA polymerase IV; Validated
Probab=32.21 E-value=78 Score=33.81 Aligned_cols=52 Identities=17% Similarity=0.338 Sum_probs=34.9
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh--CCC
Q 009303 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHR 317 (538)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--Gir 317 (538)
+..|||||+++++++..+ | +..+.+|.+-.+...- +.+ |+..++.||+. |+.
T Consensus 175 l~~l~Gig~~~~~~L~~~---G-i~t~~dl~~l~~~~L~----~~f--G~~~~~~l~~~a~G~d 228 (396)
T PRK03858 175 VRRLWGVGPVTAAKLRAH---G-ITTVGDVAELPESALV----SLL--GPAAGRHLHALAHNRD 228 (396)
T ss_pred hhhcCCCCHHHHHHHHHh---C-CCcHHHHhcCCHHHHH----HHh--CcHHHHHHHHHhCCCC
Confidence 678899999999998764 3 5666666543333333 444 56778888863 764
No 291
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=31.51 E-value=80 Score=33.50 Aligned_cols=33 Identities=24% Similarity=0.282 Sum_probs=27.1
Q ss_pred HHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009303 292 RTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~ 325 (538)
..++.+ .-.||+|+++++|-+.||.|++||...
T Consensus 29 ~~~~~l-~~~g~~~~~~~kL~~~g~~tv~~~~~~ 61 (344)
T PLN03187 29 ESIDKL-ISQGINAGDVKKLQDAGIYTCNGLMMH 61 (344)
T ss_pred cCHHHH-hhCCCCHHHHHHHHHcCCCcHHHHHhC
Confidence 345555 448999999999999999999999743
No 292
>PF05559 DUF763: Protein of unknown function (DUF763); InterPro: IPR008482 This family consists of several uncharacterised bacterial and archaeal proteins of unknown function.
Probab=31.30 E-value=1.8e+02 Score=30.52 Aligned_cols=21 Identities=24% Similarity=0.347 Sum_probs=16.0
Q ss_pred HHHHHHhhccCCCHHHHHHHH
Q 009303 292 RTISLFGEVWGIGPATAQKLY 312 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly 312 (538)
.-++.|..++||||+|++.|.
T Consensus 266 ~~feeLL~~~GvGp~TlRALa 286 (319)
T PF05559_consen 266 SDFEELLLIKGVGPSTLRALA 286 (319)
T ss_pred cCHHHHHhcCCCCHHHHHHHH
Confidence 344455589999999999884
No 293
>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1. This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.
Probab=31.04 E-value=68 Score=33.47 Aligned_cols=43 Identities=26% Similarity=0.289 Sum_probs=30.3
Q ss_pred ccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhccccchhhh
Q 009303 300 VWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDI 342 (538)
Q Consensus 300 I~GvGpktA~~ly~~GirtledL~~~~--~L~~~q~~Glk~~ed~ 342 (538)
-.||||.++++|-+.||.|++||.... .|....++.....+.+
T Consensus 6 ~~g~~~~~~~~L~~~g~~t~~~~~~~~~~~L~~~~gls~~~~~~i 50 (313)
T TIGR02238 6 AHGINAADIKKLKSAGICTVNGVIMTTRRALCKIKGLSEAKVDKI 50 (313)
T ss_pred cCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHH
Confidence 368999999999999999999998543 3544444443333333
No 294
>cd00424 PolY Y-family of DNA polymerases. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Most TLS polymerases are members of the Y-family, including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is found exclusively in bacteria. In eukaryotes, the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in ord
Probab=31.01 E-value=1.2e+02 Score=31.72 Aligned_cols=53 Identities=17% Similarity=0.375 Sum_probs=33.5
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh--CCCC
Q 009303 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (538)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--Girt 318 (538)
+..|||||+++.+++..+ | +..+.+|.+-.....+. ..+| +.+..+|+. |+..
T Consensus 175 i~~l~giG~~~~~~L~~~---G-i~ti~dl~~~~~~~~l~---~~fg---~~~~~l~~~a~G~d~ 229 (343)
T cd00424 175 LTDLPGIGAVTAKRLEAV---G-INPIGDLLAASPDALLA---LWGG---VSGERLWYALRGIDD 229 (343)
T ss_pred hhhcCCCCHHHHHHHHHc---C-CCcHHHHhcCCHHHHHH---HHhh---HHHHHHHHHhCCcCC
Confidence 678899999999988754 3 45566665432133332 3333 567777775 8754
No 295
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=31.01 E-value=44 Score=32.53 Aligned_cols=22 Identities=27% Similarity=0.496 Sum_probs=18.9
Q ss_pred hhhcCCCCCCHHHHHHHHHHHH
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVT 275 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~ 275 (538)
+.+..|||||++.|.++.=.|-
T Consensus 12 ~~l~kLPGvG~KsA~R~AfhLL 33 (198)
T COG0353 12 DALKKLPGVGPKSAQRLAFHLL 33 (198)
T ss_pred HHHhhCCCCChhHHHHHHHHHH
Confidence 6789999999999999986554
No 296
>TIGR03135 malonate_mdcG holo-ACP synthase, malonate decarboxylase-specific. Malonate decarboxylase, like citrate lyase, has a unique acyl carrier protein subunit with a prosthetic group derived from, and distinct from, coenzyme A. Members of this protein family are the phosphoribosyl-dephospho-CoA transferase specific to the malonate decarboxylase system. This enzyme can also be designated holo-ACP synthase (2.7.7.61). The corresponding component of the citrate lyase system, CitX, shows little or no sequence similarity to this family.
Probab=30.45 E-value=1.9e+02 Score=28.28 Aligned_cols=32 Identities=28% Similarity=0.227 Sum_probs=23.8
Q ss_pred CCeEEEecccc----cccC---CcCCCeeEEEecCCcch
Q 009303 367 PEVIILCGGSY----RRGK---ASCGDLDVVIMHPDRKS 398 (538)
Q Consensus 367 p~~~v~~~Gs~----RRgk---e~~~DVDiLit~~~~~~ 398 (538)
-++.+-++||+ =+|- ...+|+|+||-.++...
T Consensus 107 ~~~~~gv~GS~~~qlaTg~~~~~~~SDLDLLi~~~~~~~ 145 (202)
T TIGR03135 107 LGVPWGVYGSAGWQLLTGLPYLHASSDLDLLLRAPSPLS 145 (202)
T ss_pred CCCcEEEecchHHHHhcCCcccCCCCCeeEEEcCCChhh
Confidence 35677789999 5665 45689999998876543
No 297
>PRK03381 PII uridylyl-transferase; Provisional
Probab=29.49 E-value=1.4e+02 Score=35.28 Aligned_cols=46 Identities=22% Similarity=0.317 Sum_probs=28.7
Q ss_pred eEEEecccccccC-CcCCCeeEEEecCCcc--hhhhhHHHHHHHHHHcC
Q 009303 369 VIILCGGSYRRGK-ASCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMK 414 (538)
Q Consensus 369 ~~v~~~Gs~RRgk-e~~~DVDiLit~~~~~--~~~~~l~~vv~~L~~~g 414 (538)
+-++.+|||-||. .-..|||+||-+++.. ....+...++--|-+.|
T Consensus 58 ~alvAvg~~gr~el~p~SD~Dll~l~~~~~~~~~~~~~~~~~~~LwD~g 106 (774)
T PRK03381 58 VALVAVGGLGRRELLPYSDLDLVLLHDGRPADDVAEVADRLWYPLWDAG 106 (774)
T ss_pred eEEEEeCCcCCcCcCCCCCCeEEEEeCCCCchHHHHHHHHHhhhcccCC
Confidence 4677789996654 5678999999887432 23344444444444443
No 298
>cd05398 NT_ClassII-CCAase Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes. CCA-adding enzymes add the sequence [cytidine(C)-cytidine-adenosine (A)], one nucleotide at a time, onto the 3' end of tRNA, in a template-independent reaction. This Class II group is comprised mainly of eubacterial and eukaryotic enzymes and includes Bacillus stearothermophilus CCAase, Escherichia coli poly(A) polymerase I, human mitochondrial CCAase, and Saccharomyces cerevisiae CCAase (CCA1). CCA-adding enzymes have a single catalytic pocket, which recognizes both ATP and CTP substrates. Included in this subgroup are CC- and A-adding enzymes from various ancient species of bacteria such as Aquifex aeolicus; these enzymes collaborate to add CCA to tRNAs. This family belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal io
Probab=29.35 E-value=1.1e+02 Score=27.88 Aligned_cols=38 Identities=18% Similarity=0.194 Sum_probs=25.7
Q ss_pred HHHHHHHHhhhcCCCeEEEecccccc----cCCcCCCeeEEEecC
Q 009303 354 MERLLQKAGEEVLPEVIILCGGSYRR----GKASCGDLDVVIMHP 394 (538)
Q Consensus 354 i~~iv~~~~~~~~p~~~v~~~Gs~RR----gke~~~DVDiLit~~ 394 (538)
+..+++.+.. ..+..+.++||+=| |+ .++|+||++...
T Consensus 4 ~~~il~~l~~--~~g~~~ylVGG~VRD~Llg~-~~~DiDi~v~~~ 45 (139)
T cd05398 4 LLKLLRELKK--ALGYEAYLVGGAVRDLLLGR-PPKDIDIATDAD 45 (139)
T ss_pred HHHHHHHHHh--ccCceEEEECChHHHHHcCC-CCCCceEEEeCC
Confidence 3445555442 14778888898776 55 579999988664
No 299
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=28.55 E-value=59 Score=32.01 Aligned_cols=20 Identities=20% Similarity=0.371 Sum_probs=17.3
Q ss_pred chhhhc-CCCCCCHHHHHHHH
Q 009303 252 SADQVK-GLPGIGKSMQDHIQ 271 (538)
Q Consensus 252 ~~~~l~-~lpgIG~~ia~kI~ 271 (538)
..++|. +|||||.++|+.|-
T Consensus 116 ~R~~Ll~~lpGIG~KTAd~vL 136 (208)
T PRK01229 116 AREFLVKNIKGIGYKEASHFL 136 (208)
T ss_pred HHHHHHHcCCCCcHHHHHHHH
Confidence 357788 99999999999965
No 300
>PF04994 TfoX_C: TfoX C-terminal domain; InterPro: IPR007077 This domain is found in a number of bacterial proteins including the TfoX gene product of Haemophilus influenzae. TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes []. This family corresponds to the C-terminal presumed domain of TfoX. The domain is found in association with the N-terminal domain in some, but not all members of this group, suggesting this is an autonomous and functionally unrelated domain. For example it is found associated with Q9JZR1 from SWISSPROT in IPR002125 from INTERPRO.; PDB: 3BQT_A 3MAB_A.
Probab=26.05 E-value=50 Score=27.38 Aligned_cols=36 Identities=19% Similarity=0.433 Sum_probs=19.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHH
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRT 293 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~ 293 (538)
.++..||+||..+.....++ -+.-+++|+.--...+
T Consensus 3 ~~l~~LpNig~~~e~~L~~v----GI~t~~~L~~~Ga~~a 38 (81)
T PF04994_consen 3 NRLKDLPNIGPKSERMLAKV----GIHTVEDLRELGAVEA 38 (81)
T ss_dssp --GCGSTT--HHHHHHHHHT----T--SHHHHHHHHHHHH
T ss_pred cchhhCCCCCHHHHHHHHHc----CCCCHHHHHHhCHHHH
Confidence 36889999999877654432 4566677765333333
No 301
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=25.64 E-value=58 Score=27.05 Aligned_cols=42 Identities=19% Similarity=0.438 Sum_probs=26.0
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHH
Q 009303 255 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPAT 307 (538)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpkt 307 (538)
-|..|||||.-++..|.--+ |.+.....- +-|.+-.|+-|..
T Consensus 3 ~l~sipGig~~~a~~llaei--gd~~rF~~~---------~~l~~~~Gl~P~~ 44 (87)
T PF02371_consen 3 LLTSIPGIGPITAATLLAEI--GDISRFKSA---------KQLASYAGLAPRP 44 (87)
T ss_pred hhcCCCCccHHHHHHHHHHH--cCchhcccc---------hhhhhcccccccc
Confidence 47899999999887764333 665444322 2255566665543
No 302
>PRK03348 DNA polymerase IV; Provisional
Probab=25.62 E-value=1.3e+02 Score=32.99 Aligned_cols=53 Identities=17% Similarity=0.334 Sum_probs=36.9
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh--CCCC
Q 009303 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (538)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--Girt 318 (538)
+..|||||+.+.++...+ -+..+.+|.+-.+..+.+.| |++....||+. |+..
T Consensus 182 v~~L~GIG~~t~~~L~~l----GI~TigDLa~l~~~~L~~~f------G~~~g~~L~~~a~G~d~ 236 (454)
T PRK03348 182 VRRLWGIGPVTEEKLHRL----GIETIGDLAALSEAEVANLL------GATVGPALHRLARGIDD 236 (454)
T ss_pred ccccCCCCHHHHHHHHHc----CCccHHHHhcCCHHHHHHHH------CHHHHHHHHHHHcCCCC
Confidence 688999999988886644 45666666654444455555 67788889874 8754
No 303
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=24.77 E-value=2.1e+02 Score=30.38 Aligned_cols=104 Identities=18% Similarity=0.235 Sum_probs=58.6
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH-------hCCCCHHHHhhc
Q 009303 253 ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE-------KGHRTLDDLKNE 325 (538)
Q Consensus 253 ~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~-------~GirtledL~~~ 325 (538)
+++|.+ +||+..+.+|+++ ..+.-++.+..-.+ .+ |.++.|+...+|.++.+ .|+.|-.++...
T Consensus 31 ~~~l~~-~g~~~~~~~kL~~----~g~~tv~~~~~~~~---~~-L~~~~g~s~~~~~ki~~~a~~~~~~~~~ta~~~~~~ 101 (344)
T PLN03187 31 IDKLIS-QGINAGDVKKLQD----AGIYTCNGLMMHTK---KN-LTGIKGLSEAKVDKICEAAEKLLNQGFITGSDALLK 101 (344)
T ss_pred HHHHhh-CCCCHHHHHHHHH----cCCCcHHHHHhCCH---HH-HHHhcCCCHHHHHHHHHHHHHhhcccCCcHHHHHhh
Confidence 333433 6799887776553 44556666654333 23 44899999999998774 266677776532
Q ss_pred cCcchhhhccccchhhhccCcCHHHHHHHHHHHHHHhhhcCCCeEEEecccccccCCc
Q 009303 326 DSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKAS 383 (538)
Q Consensus 326 ~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~iv~~~~~~~~p~~~v~~~Gs~RRgke~ 383 (538)
.+-..-...|.+-.++++. .-+..|...+++|.+.=||.+
T Consensus 102 ~~~~~~isTG~~~LD~lLg------------------GGi~~G~ItEI~G~~GsGKTq 141 (344)
T PLN03187 102 RKSVVRITTGSQALDELLG------------------GGIETRCITEAFGEFRSGKTQ 141 (344)
T ss_pred hccCceecCCcHhHHhhcC------------------CCCCCCeEEEEecCCCCChhH
Confidence 2111111234444333221 112334456688888888876
No 304
>cd07749 NT_Pol-beta-like_1 Nucleotidyltransferase (NT) domain of an uncharacterized subgroup of the Pol beta-like NT superfamily. The Pol beta-like NT superfamily includes DNA polymerase beta and other family X DNA Polymerases, as well as Class I and Class II CCA-adding enzymes, RelA- and SpoT-like ppGpp synthetases and hydrolases, 2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), poly(A) polymerases, terminal uridylyl transferases, Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. Proteins belonging to this subgroup are uncharacterized. In the majority of the Pol beta-like superfamily NTs, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations essential for catalysis. These divalent metal ions are involved in a two-metal ion mechanism of nucleotide addition. These carboxylate residues are conserved in this subgroup.
Probab=24.08 E-value=3e+02 Score=25.89 Aligned_cols=37 Identities=16% Similarity=0.135 Sum_probs=24.6
Q ss_pred CCeEEEeccccc---cc-CCcCCCeeEEEecCCcchhhhhH
Q 009303 367 PEVIILCGGSYR---RG-KASCGDLDVVIMHPDRKSHKGFL 403 (538)
Q Consensus 367 p~~~v~~~Gs~R---Rg-ke~~~DVDiLit~~~~~~~~~~l 403 (538)
-++...++||+. +| ...-+||||++-..+......+|
T Consensus 16 ~~i~W~lgGS~~L~l~Gl~~~p~DIDI~~D~~d~e~i~~il 56 (156)
T cd07749 16 INVNWALTGSLSFALQGVPVEPHDIDIQTDNEGAYEIERIF 56 (156)
T ss_pred CCceEEehhhHHHHHcCCCCCCCcceEEEchhhHHHHHHHH
Confidence 356778999964 34 35679999998766655433433
No 305
>PRK14133 DNA polymerase IV; Provisional
Probab=24.07 E-value=1.9e+02 Score=30.35 Aligned_cols=52 Identities=23% Similarity=0.397 Sum_probs=32.9
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh--CCCC
Q 009303 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (538)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--Girt 318 (538)
+..|||||++++++...+ -+..+.++.+-.+.. +.+.+| + ....+|+. |+..
T Consensus 175 v~~l~gig~~~~~~L~~~----Gi~ti~dl~~l~~~~----L~~rfG--~-~g~~l~~~a~G~d~ 228 (347)
T PRK14133 175 ISKVHGIGKKSVEKLNNI----GIYTIEDLLKLSREF----LIEYFG--K-FGVEIYERIRGIDY 228 (347)
T ss_pred ccccCCCCHHHHHHHHHc----CCccHHHHhhCCHHH----HHHHHh--H-HHHHHHHHhCCCCC
Confidence 678899999999987653 466677766533333 334444 3 45566654 8764
No 306
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.44 E-value=62 Score=39.26 Aligned_cols=26 Identities=19% Similarity=0.326 Sum_probs=21.5
Q ss_pred hhccCCCHHHHHHHHHh-CCCCHHHHh
Q 009303 298 GEVWGIGPATAQKLYEK-GHRTLDDLK 323 (538)
Q Consensus 298 ~~I~GvGpktA~~ly~~-GirtledL~ 323 (538)
.+|+||||+||.++... |=.+|+.|.
T Consensus 869 ~GI~GIGpktAl~li~~~~~~~le~L~ 895 (1034)
T TIGR00600 869 EGIPTVGPVSAMEILNEFPGDGLEPLL 895 (1034)
T ss_pred CCCCcccHHHHHHHHHHcCCCCHHHHH
Confidence 47999999999999998 655677665
No 307
>TIGR02922 conserved hypothetical protein TIGR02922. Two members of this family are found in Colwellia psychrerythraea 34H and one each in various other species of Colwellia and Shewanella. One member from C. psychrerythraea is of special interest because it is preceded by the same cis-regulatory site as a number of genes that have the PEP-CTERM domain described by TIGR02595.
Probab=22.15 E-value=34 Score=26.98 Aligned_cols=15 Identities=20% Similarity=0.457 Sum_probs=12.4
Q ss_pred EEEecccccccCCcC
Q 009303 370 IILCGGSYRRGKASC 384 (538)
Q Consensus 370 ~v~~~Gs~RRgke~~ 384 (538)
.|++--+|||||..+
T Consensus 34 rvmiPqeFkrGKsIi 48 (67)
T TIGR02922 34 RVMIPQEFKRGKSII 48 (67)
T ss_pred cEEcchHHcCCCeEE
Confidence 577778999999864
No 308
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=22.08 E-value=1.4e+02 Score=30.07 Aligned_cols=46 Identities=22% Similarity=0.346 Sum_probs=36.5
Q ss_pred HHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhc--cCcchhhhccccc
Q 009303 292 RTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKY 338 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~--~~L~~~q~~Glk~ 338 (538)
.++..+|+|+||+...|..|... +-||+.+.++ +.|.+.+|+|-.-
T Consensus 192 ~~~~~Lt~i~~VnKtda~~LL~~-FgsLq~~~~AS~~ele~~~G~G~~k 239 (254)
T KOG2841|consen 192 SLLGFLTTIPGVNKTDAQLLLQK-FGSLQQISNASEGELEQCPGLGPAK 239 (254)
T ss_pred HHHHHHHhCCCCCcccHHHHHHh-cccHHHHHhcCHhHHHhCcCcCHHH
Confidence 46778999999999999999764 5588888865 4688888888543
No 309
>PRK07945 hypothetical protein; Provisional
Probab=21.92 E-value=48 Score=34.93 Aligned_cols=28 Identities=29% Similarity=0.446 Sum_probs=23.4
Q ss_pred HhhccCCCHHHHHHHHHh---C-CCCHHHHhh
Q 009303 297 FGEVWGIGPATAQKLYEK---G-HRTLDDLKN 324 (538)
Q Consensus 297 f~~I~GvGpktA~~ly~~---G-irtledL~~ 324 (538)
|++|||||..+|.++.+. | +.-|++|+.
T Consensus 51 l~~~~giG~~~a~~i~e~~~tg~~~~l~~l~~ 82 (335)
T PRK07945 51 LTSLPGIGPKTAKVIAQALAGRVPDYLAELRA 82 (335)
T ss_pred cccCCCcCHHHHHHHHHHHhcCCHHHHHHHHH
Confidence 569999999999999874 6 677888874
No 310
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=21.79 E-value=50 Score=37.53 Aligned_cols=28 Identities=25% Similarity=0.516 Sum_probs=21.8
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009303 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~ 325 (538)
|-+|+||||++.++|.+ .+.|++.++.+
T Consensus 532 Ld~I~GiG~~r~~~LL~-~Fgs~~~i~~A 559 (581)
T COG0322 532 LDDIPGIGPKRRKALLK-HFGSLKGIKSA 559 (581)
T ss_pred cccCCCcCHHHHHHHHH-HhhCHHHHHhc
Confidence 45899999999999987 45566666653
No 311
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=21.63 E-value=86 Score=22.33 Aligned_cols=22 Identities=18% Similarity=0.296 Sum_probs=18.3
Q ss_pred HHHhhccCCCHHHHHHHHHhCC
Q 009303 295 SLFGEVWGIGPATAQKLYEKGH 316 (538)
Q Consensus 295 ~lf~~I~GvGpktA~~ly~~Gi 316 (538)
..+.++.||-+.|.+.|.++|.
T Consensus 4 ~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 4 GELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred HHHHHHHCcCHHHHHHHHHCCC
Confidence 4456788999999999998875
No 312
>TIGR00207 fliG flagellar motor switch protein FliG. The fliG protein along with fliM and fliN interact to form the switch complex of the bacterial flagellar motor located at the base of the basal body. This complex interacts with chemotaxis proteins (eg CHEY). In addition the complex interacts with other components of the motor that determine the direction of flagellar rotation. The model contains putative members of the fliG family at scores of less than 100 from Agrobacterium radiobacter and Sinorhizobium meliloti as well as fliG-like genes from treponema pallidum and Borrelia burgdorferi. That is why the suggested cutoff is set at 20 but was set at 100 to construct the family.
Probab=20.71 E-value=5e+02 Score=27.40 Aligned_cols=87 Identities=9% Similarity=0.200 Sum_probs=52.6
Q ss_pred HHHHHHHHhcCCccccc--hhhhcCCCCCCHHHHHHHHHHHHh------------CCcchhHHHHhhchhHHH-HHHhhc
Q 009303 236 YYKAIPVIEKLPFKIES--ADQVKGLPGIGKSMQDHIQEIVTT------------GKLSKLEHFEKDEKVRTI-SLFGEV 300 (538)
Q Consensus 236 Y~rAa~~l~~l~~~i~~--~~~l~~lpgIG~~ia~kI~Eil~t------------G~~~~le~l~~~~~~~~l-~lf~~I 300 (538)
-..||.+|..||..... ...+.++..|.+.+.+.|.++|+. |....+-++.+..+...- .+|..+
T Consensus 144 p~~AA~VL~~Lp~~~~~ei~~ria~l~~vs~~~i~~ie~~L~~~~~~~~~~~~~~gG~~~~a~ILN~~~~~~~~~il~~L 223 (338)
T TIGR00207 144 PAQAADILSLFPEEVQAEVARRIATMGRTSPEVVAEVERVLEGKLDSLNSDYTKMGGVRAVAEIINLMDRKTEKTIITSL 223 (338)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhhccccccCChHHHHHHHHHhCCchHHHHHHHHH
Confidence 35789999999976443 356778888888887777655541 222334445554444433 455555
Q ss_pred cCCCHHHHHHHHHhCCCCHHHHh
Q 009303 301 WGIGPATAQKLYEKGHRTLDDLK 323 (538)
Q Consensus 301 ~GvGpktA~~ly~~GirtledL~ 323 (538)
--.-|..|..+-+ -+=+++||.
T Consensus 224 ~~~dp~la~~Ir~-~mF~Fedl~ 245 (338)
T TIGR00207 224 EEFDPELAEEIKK-EMFVFEDIV 245 (338)
T ss_pred HHhCHHHHHHHHH-HccCHHHHh
Confidence 5556666666533 444566664
No 313
>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a beta-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [, ].; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBN_M 2QBB_M 3I1M_M 3OFP_M 3OFX_M 3OFO_M 1VS5_M 3OAQ_M 2QAL_M 3J18_M ....
Probab=20.70 E-value=91 Score=27.14 Aligned_cols=44 Identities=11% Similarity=0.181 Sum_probs=29.9
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHH
Q 009303 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLF 297 (538)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf 297 (538)
-.|..|.|||...|..|...+.=.....+.+|..++-....+.+
T Consensus 15 ~aLt~IyGIG~~~A~~Ic~~lgi~~~~~~~~Ls~~~i~~l~~~i 58 (107)
T PF00416_consen 15 IALTKIYGIGRRKAKQICKKLGINPNKKVGDLSDEQIDKLRKII 58 (107)
T ss_dssp HHHTTSTTBCHHHHHHHHHHTTS-SSSBTTTSTHHHHHHHHHHH
T ss_pred hHHhhhhccCHHHHHHHHHHcCCChhhhcccCCHHHHHHHHHHH
Confidence 45899999999999999998876555555555443333344444
No 314
>PF14091 DUF4269: Domain of unknown function (DUF4269)
Probab=20.46 E-value=7.1e+02 Score=23.32 Aligned_cols=27 Identities=26% Similarity=0.412 Sum_probs=17.7
Q ss_pred EecccccccCC-cCCCeeEEEecCCcch
Q 009303 372 LCGGSYRRGKA-SCGDLDVVIMHPDRKS 398 (538)
Q Consensus 372 ~~~Gs~RRgke-~~~DVDiLit~~~~~~ 398 (538)
++||-+==|-. ..+|+||+..++|...
T Consensus 19 iL~GTiPi~Idi~~SDLDIic~~~d~~~ 46 (152)
T PF14091_consen 19 ILVGTIPIGIDIPGSDLDIICEVPDPEA 46 (152)
T ss_pred EEecccccccCCCCCCccEEEEeCCHHH
Confidence 34555443332 2579999999998664
No 315
>PRK14109 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Provisional
Probab=20.36 E-value=2.5e+02 Score=34.21 Aligned_cols=46 Identities=13% Similarity=0.273 Sum_probs=31.2
Q ss_pred CeEEEecccc-cccCCcCCCeeEEEecCCcc-----hhhhhHHHHHHHHHHc
Q 009303 368 EVIILCGGSY-RRGKASCGDLDVVIMHPDRK-----SHKGFLSKYVKKLKEM 413 (538)
Q Consensus 368 ~~~v~~~Gs~-RRgke~~~DVDiLit~~~~~-----~~~~~l~~vv~~L~~~ 413 (538)
++.|...|+| |+-...+.|||+++.+++.. ....++.++.+.|...
T Consensus 215 ~~aviamGklG~~EL~~~SDiDLi~ly~~~~~~~~~~~~~~~~rl~q~l~~~ 266 (1007)
T PRK14109 215 RLAVIAMGKCGARELNYVSDVDVIFVAEPAEGVDEAAALAVATRLASELMRI 266 (1007)
T ss_pred CeEEEEeccccccccCCccCCCEEEEeCCCCCcccccHHHHHHHHHHHHHHH
Confidence 3466778888 45567789999999886432 1134567777777665
Done!