Query 010406
Match_columns 511
No_of_seqs 338 out of 983
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 00:09:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010406.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010406hhsearch_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 9.6E-83 2.1E-87 623.8 24.5 295 207-511 9-353 (353)
2 cd00141 NT_POLXc Nucleotidyltr 100.0 1.3E-69 2.9E-74 552.8 27.6 286 212-509 2-307 (307)
3 smart00483 POLXc DNA polymeras 100.0 2.3E-69 5E-74 556.6 26.0 292 208-510 1-334 (334)
4 PRK08609 hypothetical protein; 100.0 3.7E-66 8.1E-71 566.2 27.8 292 208-510 1-314 (570)
5 COG1796 POL4 DNA polymerase IV 100.0 7.5E-57 1.6E-61 445.8 21.1 291 208-510 3-318 (326)
6 PF14791 DNA_pol_B_thumb: DNA 99.9 5.2E-25 1.1E-29 172.8 3.1 63 438-510 1-63 (64)
7 PF14792 DNA_pol_B_palm: DNA p 99.8 3.8E-19 8.3E-24 155.7 7.2 79 345-423 1-83 (112)
8 PF14716 HHH_8: Helix-hairpin- 99.7 5.8E-17 1.3E-21 129.4 7.4 66 210-275 1-68 (68)
9 PF10391 DNA_pol_lambd_f: Fing 99.6 1.1E-16 2.3E-21 120.4 3.9 51 294-344 1-52 (52)
10 PRK07945 hypothetical protein; 99.6 5.9E-15 1.3E-19 152.9 11.5 103 213-325 3-119 (335)
11 PF00533 BRCT: BRCA1 C Terminu 99.0 6.1E-10 1.3E-14 89.8 7.8 75 16-95 3-78 (78)
12 smart00292 BRCT breast cancer 99.0 8.9E-10 1.9E-14 87.8 7.2 78 18-98 2-80 (80)
13 cd00027 BRCT Breast Cancer Sup 98.7 3.2E-08 6.9E-13 76.9 6.4 72 21-96 1-72 (72)
14 TIGR00575 dnlj DNA ligase, NAD 98.0 1.5E-05 3.2E-10 89.7 9.4 133 254-397 466-633 (652)
15 PF14520 HHH_5: Helix-hairpin- 97.9 5.6E-06 1.2E-10 64.3 2.7 51 293-343 3-55 (60)
16 KOG3226 DNA repair protein [Re 97.7 3.1E-05 6.7E-10 79.0 3.9 88 16-110 315-403 (508)
17 PF12738 PTCB-BRCT: twin BRCT 97.6 6.1E-05 1.3E-09 58.7 3.7 63 22-90 1-63 (63)
18 PLN03123 poly [ADP-ribose] pol 97.5 0.00017 3.7E-09 84.0 7.8 90 15-109 390-481 (981)
19 PF14520 HHH_5: Helix-hairpin- 97.5 0.00014 3.1E-09 56.4 4.3 52 254-313 5-56 (60)
20 PLN03122 Poly [ADP-ribose] pol 97.3 0.00055 1.2E-08 78.3 7.5 93 13-111 184-280 (815)
21 COG1555 ComEA DNA uptake prote 97.0 0.00082 1.8E-08 61.9 5.0 49 253-313 96-145 (149)
22 PF12826 HHH_2: Helix-hairpin- 97.0 0.001 2.2E-08 52.4 4.6 48 257-313 6-53 (64)
23 PRK07956 ligA NAD-dependent DN 97.0 0.0027 5.8E-08 71.9 9.6 133 254-396 479-638 (665)
24 PF11731 Cdd1: Pathogenicity l 97.0 0.00095 2.1E-08 56.3 4.3 35 291-325 8-42 (93)
25 TIGR01259 comE comEA protein. 96.9 0.0015 3.3E-08 58.0 5.6 50 252-313 66-116 (120)
26 PF12836 HHH_3: Helix-hairpin- 96.9 0.0015 3.2E-08 51.6 4.5 48 252-311 12-60 (65)
27 KOG2481 Protein required for n 96.8 0.00039 8.4E-09 74.0 0.8 88 11-110 320-417 (570)
28 PRK14351 ligA NAD-dependent DN 96.7 0.0051 1.1E-07 69.7 9.2 88 254-351 496-585 (689)
29 KOG0966 ATP-dependent DNA liga 96.6 0.0036 7.7E-08 70.1 6.2 94 12-109 627-723 (881)
30 TIGR00084 ruvA Holliday juncti 96.5 0.0039 8.5E-08 59.8 5.5 53 254-312 72-124 (191)
31 PRK02515 psbU photosystem II c 96.5 0.0038 8.3E-08 55.6 4.9 47 252-313 59-105 (132)
32 PF14229 DUF4332: Domain of un 96.5 0.012 2.6E-07 52.5 7.8 67 260-326 1-84 (122)
33 KOG4362 Transcriptional regula 96.3 0.0039 8.4E-08 69.4 4.7 76 33-111 488-565 (684)
34 TIGR00426 competence protein C 96.3 0.0088 1.9E-07 47.6 5.5 50 253-314 15-66 (69)
35 PF00633 HHH: Helix-hairpin-he 96.3 0.0036 7.7E-08 41.8 2.5 23 251-273 8-30 (30)
36 PRK14605 ruvA Holliday junctio 96.3 0.0046 1E-07 59.5 4.3 52 254-312 73-125 (194)
37 PRK00116 ruvA Holliday junctio 96.2 0.0061 1.3E-07 58.6 4.6 54 254-314 73-127 (192)
38 PRK13901 ruvA Holliday junctio 96.1 0.0077 1.7E-07 57.9 4.8 54 254-313 72-125 (196)
39 TIGR00084 ruvA Holliday juncti 96.1 0.004 8.8E-08 59.7 2.8 51 291-343 68-124 (191)
40 PRK14601 ruvA Holliday junctio 96.0 0.0086 1.9E-07 57.0 4.7 54 254-313 73-126 (183)
41 COG5163 NOP7 Protein required 96.0 0.0059 1.3E-07 63.3 3.7 87 11-109 343-440 (591)
42 PRK12766 50S ribosomal protein 95.9 0.0028 6E-08 62.0 0.7 52 296-347 4-57 (232)
43 PRK14602 ruvA Holliday junctio 95.8 0.0097 2.1E-07 57.7 4.3 54 254-313 74-127 (203)
44 PRK14606 ruvA Holliday junctio 95.8 0.012 2.6E-07 56.4 4.7 54 254-313 73-126 (188)
45 PRK14603 ruvA Holliday junctio 95.7 0.013 2.8E-07 56.6 4.7 54 254-313 72-125 (197)
46 PRK14604 ruvA Holliday junctio 95.7 0.014 3E-07 56.3 4.6 54 254-313 73-126 (195)
47 PF00633 HHH: Helix-hairpin-he 95.5 0.012 2.6E-07 39.2 2.6 22 292-313 8-29 (30)
48 PRK07956 ligA NAD-dependent DN 95.4 0.0075 1.6E-07 68.3 2.0 52 298-349 448-502 (665)
49 COG1555 ComEA DNA uptake prote 95.2 0.015 3.2E-07 53.7 3.1 52 290-347 92-148 (149)
50 COG0272 Lig NAD-dependent DNA 95.2 0.054 1.2E-06 60.5 7.9 15 384-398 630-644 (667)
51 KOG0966 ATP-dependent DNA liga 95.0 0.056 1.2E-06 60.8 7.3 91 16-107 782-881 (881)
52 PRK14973 DNA topoisomerase I; 95.0 0.023 5.1E-07 66.6 4.7 90 254-344 835-928 (936)
53 PRK14350 ligA NAD-dependent DN 95.0 0.054 1.2E-06 61.4 7.2 86 254-348 470-563 (669)
54 COG0632 RuvA Holliday junction 95.0 0.03 6.4E-07 54.1 4.4 54 254-313 73-126 (201)
55 TIGR00575 dnlj DNA ligase, NAD 94.9 0.012 2.6E-07 66.6 1.7 63 298-360 435-500 (652)
56 PRK14600 ruvA Holliday junctio 94.9 0.029 6.3E-07 53.6 4.0 53 254-313 73-125 (186)
57 TIGR01259 comE comEA protein. 94.8 0.028 6.1E-07 49.9 3.6 50 291-346 64-118 (120)
58 cd05397 NT_Pol-beta-like Nucle 94.8 0.048 1E-06 40.5 4.2 28 365-392 14-42 (49)
59 PRK02362 ski2-like helicase; P 94.7 0.025 5.3E-07 65.2 3.7 57 284-343 642-700 (737)
60 PF11798 IMS_HHH: IMS family H 94.7 0.019 4.1E-07 38.8 1.6 20 297-316 13-32 (32)
61 PRK02515 psbU photosystem II c 94.4 0.049 1.1E-06 48.7 4.0 32 293-324 59-91 (132)
62 PRK14605 ruvA Holliday junctio 94.3 0.022 4.7E-07 54.9 1.7 52 291-342 69-124 (194)
63 PRK00116 ruvA Holliday junctio 94.3 0.026 5.6E-07 54.3 2.2 51 293-343 71-125 (192)
64 TIGR00426 competence protein C 94.2 0.054 1.2E-06 43.0 3.6 45 295-345 16-66 (69)
65 KOG2043 Signaling protein SWIF 94.0 0.049 1.1E-06 63.3 4.2 69 37-109 671-739 (896)
66 PF12836 HHH_3: Helix-hairpin- 94.0 0.046 1E-06 43.0 2.8 48 293-346 12-64 (65)
67 cd05402 NT_PAP_TUTase Nucleoti 94.0 0.22 4.8E-06 43.1 7.3 58 354-415 9-68 (114)
68 PF12826 HHH_2: Helix-hairpin- 93.6 0.048 1E-06 42.9 2.2 44 299-343 7-52 (64)
69 KOG1929 Nucleotide excision re 93.5 0.085 1.8E-06 60.5 4.7 94 12-111 487-580 (811)
70 KOG1929 Nucleotide excision re 93.3 0.14 3.1E-06 58.7 6.2 89 17-110 102-190 (811)
71 PRK00254 ski2-like helicase; P 93.3 0.11 2.3E-06 59.8 5.2 67 276-343 623-695 (720)
72 PRK12766 50S ribosomal protein 93.1 0.14 3E-06 50.2 4.9 54 253-314 2-55 (232)
73 PRK14601 ruvA Holliday junctio 92.6 0.055 1.2E-06 51.6 1.4 50 291-342 69-124 (183)
74 PRK14606 ruvA Holliday junctio 92.6 0.063 1.4E-06 51.4 1.8 52 291-342 69-124 (188)
75 PRK14603 ruvA Holliday junctio 92.4 0.06 1.3E-06 52.0 1.4 50 291-342 68-123 (197)
76 PRK14602 ruvA Holliday junctio 92.1 0.072 1.6E-06 51.7 1.6 52 291-342 70-125 (203)
77 PRK14604 ruvA Holliday junctio 92.0 0.07 1.5E-06 51.4 1.3 50 291-342 69-124 (195)
78 PRK13901 ruvA Holliday junctio 91.7 0.094 2E-06 50.5 1.9 50 291-342 68-123 (196)
79 smart00278 HhH1 Helix-hairpin- 91.4 0.14 3E-06 32.8 1.8 19 296-314 2-20 (26)
80 TIGR01448 recD_rel helicase, p 91.1 0.6 1.3E-05 53.7 7.8 83 253-346 116-201 (720)
81 PF04994 TfoX_C: TfoX C-termin 90.9 0.19 4E-06 41.6 2.6 30 297-326 5-34 (81)
82 COG1796 POL4 DNA polymerase IV 90.9 0.61 1.3E-05 47.9 6.8 95 207-320 59-153 (326)
83 KOG0323 TFIIF-interacting CTD 90.6 0.075 1.6E-06 59.3 0.0 90 17-110 440-532 (635)
84 PRK14600 ruvA Holliday junctio 90.6 0.13 2.8E-06 49.3 1.6 49 291-342 69-123 (186)
85 PRK14351 ligA NAD-dependent DN 90.4 0.13 2.8E-06 58.7 1.6 190 298-500 465-683 (689)
86 PF01909 NTP_transf_2: Nucleot 90.3 0.33 7.2E-06 40.0 3.7 32 366-397 12-44 (93)
87 PRK08097 ligB NAD-dependent DN 90.3 0.38 8.3E-06 53.4 5.1 86 253-351 458-545 (562)
88 COG1948 MUS81 ERCC4-type nucle 90.2 0.39 8.4E-06 48.0 4.6 49 256-313 184-232 (254)
89 PRK04301 radA DNA repair and r 89.8 0.18 4E-06 52.0 2.1 30 297-326 8-37 (317)
90 PF11731 Cdd1: Pathogenicity l 89.6 0.49 1.1E-05 40.1 4.1 47 253-303 11-57 (93)
91 COG3743 Uncharacterized conser 89.0 0.37 8E-06 43.2 3.1 53 295-350 67-119 (133)
92 TIGR03252 uncharacterized HhH- 88.9 1.1 2.4E-05 42.4 6.4 49 261-312 75-132 (177)
93 PTZ00418 Poly(A) polymerase; P 88.3 4.8 0.0001 45.0 11.7 50 367-416 125-175 (593)
94 TIGR02236 recomb_radA DNA repa 88.3 0.34 7.3E-06 49.7 2.7 29 298-326 2-30 (310)
95 PRK13482 DNA integrity scannin 88.3 0.77 1.7E-05 48.0 5.3 60 245-313 276-337 (352)
96 KOG2245 Poly(A) polymerase and 88.2 3.2 7E-05 45.1 10.0 85 331-417 41-139 (562)
97 smart00279 HhH2 Helix-hairpin- 87.8 0.37 8E-06 33.5 1.8 16 299-314 20-35 (36)
98 PRK01172 ski2-like helicase; P 87.7 0.9 2E-05 51.8 6.0 40 285-325 603-642 (674)
99 TIGR00588 ogg 8-oxoguanine DNA 87.6 1.4 3.1E-05 45.5 6.9 62 255-318 177-243 (310)
100 KOG2841 Structure-specific end 87.5 0.65 1.4E-05 45.6 3.9 50 255-313 196-245 (254)
101 TIGR01448 recD_rel helicase, p 87.4 0.29 6.2E-06 56.3 1.8 53 292-344 79-135 (720)
102 cd00080 HhH2_motif Helix-hairp 87.3 0.55 1.2E-05 38.1 2.8 27 298-325 25-51 (75)
103 PRK14670 uvrC excinuclease ABC 86.6 1.6 3.4E-05 48.9 6.9 52 254-314 514-565 (574)
104 smart00278 HhH1 Helix-hairpin- 85.6 0.71 1.5E-05 29.5 2.1 20 255-274 2-21 (26)
105 cd05400 NT_2-5OAS_ClassI-CCAas 85.4 4.1 8.8E-05 36.6 7.9 46 368-413 27-79 (143)
106 PRK03352 DNA polymerase IV; Va 85.0 0.68 1.5E-05 48.3 3.0 28 298-325 180-207 (346)
107 PF14490 HHH_4: Helix-hairpin- 84.8 1.5 3.3E-05 36.9 4.5 53 293-346 11-66 (94)
108 PRK03858 DNA polymerase IV; Va 84.5 0.74 1.6E-05 48.9 3.0 27 298-324 176-202 (396)
109 PRK14667 uvrC excinuclease ABC 84.3 2.2 4.8E-05 47.7 6.7 52 253-314 513-564 (567)
110 COG0632 RuvA Holliday junction 83.6 0.61 1.3E-05 45.1 1.7 51 292-342 70-124 (201)
111 PRK01216 DNA polymerase IV; Va 83.4 0.82 1.8E-05 48.1 2.7 28 298-325 181-208 (351)
112 PRK10880 adenine DNA glycosyla 83.3 4.6 9.9E-05 42.5 8.2 64 232-303 85-151 (350)
113 PRK14666 uvrC excinuclease ABC 83.0 0.63 1.4E-05 52.7 1.8 47 295-343 637-686 (694)
114 cd00424 PolY Y-family of DNA p 83.0 4.4 9.6E-05 42.2 8.0 29 298-326 176-204 (343)
115 PRK03609 umuC DNA polymerase V 82.5 0.94 2E-05 48.7 2.8 28 298-325 182-209 (422)
116 PRK14666 uvrC excinuclease ABC 82.4 2.2 4.7E-05 48.6 5.7 52 254-314 637-688 (694)
117 COG0122 AlkA 3-methyladenine D 82.0 5.9 0.00013 40.5 8.3 47 270-317 174-220 (285)
118 smart00475 53EXOc 5'-3' exonuc 82.0 1.1 2.4E-05 45.1 2.9 26 298-325 189-215 (259)
119 PRK09482 flap endonuclease-lik 82.0 1.1 2.4E-05 45.1 2.9 25 299-325 186-211 (256)
120 PRK14672 uvrC excinuclease ABC 82.0 2.8 6E-05 47.6 6.3 54 254-316 608-661 (691)
121 COG0353 RecR Recombinational D 81.9 1 2.2E-05 43.2 2.5 21 292-312 9-29 (198)
122 smart00478 ENDO3c endonuclease 81.6 4.3 9.3E-05 36.8 6.5 26 292-317 69-94 (149)
123 PRK00558 uvrC excinuclease ABC 81.6 2.2 4.7E-05 48.1 5.4 53 253-314 542-594 (598)
124 PRK06195 DNA polymerase III su 81.3 6.4 0.00014 40.6 8.4 48 17-65 219-266 (309)
125 PRK14976 5'-3' exonuclease; Pr 81.1 1.2 2.6E-05 45.4 2.8 25 298-324 194-219 (281)
126 cd01703 PolY_Pol_iota DNA Poly 81.0 1.1 2.4E-05 47.6 2.7 30 297-326 174-203 (379)
127 PRK10308 3-methyl-adenine DNA 80.9 1.6 3.5E-05 44.5 3.7 63 254-320 167-232 (283)
128 PRK08609 hypothetical protein; 80.9 2.1 4.6E-05 48.0 5.0 54 252-311 86-139 (570)
129 PRK14350 ligA NAD-dependent DN 80.9 4 8.6E-05 46.6 7.1 73 16-93 591-663 (669)
130 cd00056 ENDO3c endonuclease II 80.7 1.1 2.3E-05 41.1 2.2 27 291-317 79-105 (158)
131 cd01701 PolY_Rev1 DNA polymera 80.7 1.2 2.6E-05 47.7 2.8 29 298-326 225-253 (404)
132 PRK08097 ligB NAD-dependent DN 80.6 0.69 1.5E-05 51.5 1.0 64 298-361 428-494 (562)
133 TIGR03671 cca_archaeal CCA-add 80.5 3.8 8.2E-05 43.9 6.4 45 353-397 25-71 (408)
134 PRK00227 glnD PII uridylyl-tra 80.4 4.5 9.8E-05 46.4 7.4 66 348-416 8-75 (693)
135 PRK01810 DNA polymerase IV; Va 80.1 1.3 2.9E-05 47.2 2.9 28 298-325 182-209 (407)
136 KOG3524 Predicted guanine nucl 80.1 2 4.4E-05 48.2 4.2 81 13-101 113-193 (850)
137 PRK04301 radA DNA repair and r 79.7 3.5 7.6E-05 42.5 5.8 86 255-349 7-102 (317)
138 cd01700 PolY_Pol_V_umuC umuC s 79.5 1.4 3E-05 45.9 2.8 28 298-325 179-206 (344)
139 PRK02406 DNA polymerase IV; Va 79.5 1.3 2.9E-05 46.0 2.6 28 298-325 171-198 (343)
140 PRK03348 DNA polymerase IV; Pr 79.3 1.3 2.9E-05 48.2 2.6 27 298-324 183-209 (454)
141 cd00008 53EXOc 5'-3' exonuclea 79.3 1.6 3.4E-05 43.5 2.9 27 298-325 186-212 (240)
142 PRK06063 DNA polymerase III su 79.1 8.2 0.00018 39.9 8.3 72 17-93 231-303 (313)
143 KOG3548 DNA damage checkpoint 79.1 2.2 4.9E-05 49.2 4.3 89 17-111 924-1038(1176)
144 PRK07758 hypothetical protein; 78.4 1.1 2.3E-05 38.1 1.2 45 300-344 39-85 (95)
145 PRK03103 DNA polymerase IV; Re 78.1 1.7 3.6E-05 46.5 3.0 28 298-325 184-211 (409)
146 PRK02794 DNA polymerase IV; Pr 78.0 1.5 3.3E-05 47.1 2.6 29 297-325 211-239 (419)
147 PRK14133 DNA polymerase IV; Pr 77.9 1.7 3.6E-05 45.4 2.8 28 298-325 176-203 (347)
148 TIGR01084 mutY A/G-specific ad 77.5 4 8.8E-05 41.5 5.3 75 222-303 71-147 (275)
149 PF04919 DUF655: Protein of un 77.1 5.9 0.00013 37.6 5.9 54 228-288 96-150 (181)
150 COG1708 Predicted nucleotidylt 76.9 11 0.00024 32.4 7.4 28 368-395 26-54 (128)
151 TIGR01083 nth endonuclease III 76.7 5.7 0.00012 37.9 5.9 25 292-316 103-127 (191)
152 PRK00254 ski2-like helicase; P 76.5 12 0.00027 43.1 9.6 53 254-314 645-697 (720)
153 PRK00076 recR recombination pr 76.3 2.1 4.5E-05 41.3 2.7 21 292-312 8-28 (196)
154 TIGR00615 recR recombination p 76.3 2.1 4.5E-05 41.2 2.7 20 292-311 8-27 (195)
155 KOG2875 8-oxoguanine DNA glyco 75.8 4.1 8.8E-05 41.2 4.6 68 255-323 175-246 (323)
156 PRK10702 endonuclease III; Pro 75.4 5.2 0.00011 39.0 5.3 25 292-316 106-130 (211)
157 PTZ00205 DNA polymerase kappa; 75.4 2.1 4.5E-05 47.7 2.7 29 297-325 311-339 (571)
158 PRK01229 N-glycosylase/DNA lya 75.2 3.5 7.7E-05 40.1 4.0 53 262-317 85-142 (208)
159 PRK13844 recombination protein 75.0 2.3 5.1E-05 41.0 2.7 21 292-312 12-32 (200)
160 PRK10702 endonuclease III; Pro 74.7 6.6 0.00014 38.3 5.8 43 232-274 85-129 (211)
161 PF14229 DUF4332: Domain of un 74.1 3.4 7.3E-05 36.7 3.3 26 301-326 1-26 (122)
162 COG0258 Exo 5'-3' exonuclease 73.9 2.5 5.5E-05 43.5 2.8 25 299-325 202-227 (310)
163 COG0177 Nth Predicted EndoIII- 73.8 4.9 0.00011 39.3 4.6 86 261-354 80-175 (211)
164 COG1948 MUS81 ERCC4-type nucle 73.6 3.6 7.7E-05 41.2 3.6 54 289-343 176-231 (254)
165 cd03468 PolY_like DNA Polymera 73.4 2.5 5.5E-05 43.5 2.7 28 299-326 174-201 (335)
166 PF11798 IMS_HHH: IMS family H 73.1 1.7 3.7E-05 29.3 0.9 18 255-272 12-29 (32)
167 cd01702 PolY_Pol_eta DNA Polym 72.9 2.8 6.1E-05 44.2 2.9 28 298-325 185-213 (359)
168 cd00056 ENDO3c endonuclease II 72.1 7 0.00015 35.7 5.1 77 220-303 44-125 (158)
169 PRK13913 3-methyladenine DNA g 71.7 4.7 0.0001 39.6 4.0 22 292-313 118-139 (218)
170 PF01367 5_3_exonuc: 5'-3' exo 71.6 0.5 1.1E-05 40.7 -2.5 24 299-324 22-46 (101)
171 PF14579 HHH_6: Helix-hairpin- 71.3 10 0.00022 31.6 5.4 49 256-315 29-77 (90)
172 cd05403 NT_KNTase_like Nucleot 70.6 9.8 0.00021 30.8 5.2 29 370-398 20-49 (93)
173 PRK13910 DNA glycosylase MutY; 70.6 8.3 0.00018 39.5 5.6 68 232-306 48-117 (289)
174 KOG2093 Translesion DNA polyme 70.4 4.4 9.6E-05 46.7 3.9 90 12-110 41-132 (1016)
175 TIGR03252 uncharacterized HhH- 70.2 13 0.00029 35.2 6.5 44 232-275 80-136 (177)
176 PRK13300 tRNA CCA-pyrophosphor 70.0 17 0.00036 39.6 8.0 31 368-398 41-73 (447)
177 cd03586 PolY_Pol_IV_kappa DNA 70.0 3.4 7.3E-05 42.6 2.7 28 298-325 174-201 (334)
178 PF03118 RNA_pol_A_CTD: Bacter 69.2 6.5 0.00014 31.1 3.6 36 238-275 22-65 (66)
179 COG0389 DinP Nucleotidyltransf 69.2 3.4 7.3E-05 43.5 2.5 27 298-324 179-205 (354)
180 PRK13766 Hef nuclease; Provisi 69.0 6.4 0.00014 45.6 5.0 49 256-313 717-765 (773)
181 PF00416 Ribosomal_S13: Riboso 68.6 5 0.00011 34.8 3.1 26 293-318 13-39 (107)
182 PF14490 HHH_4: Helix-hairpin- 68.3 5.4 0.00012 33.6 3.1 54 261-321 19-73 (94)
183 PF02371 Transposase_20: Trans 68.0 3.5 7.5E-05 34.2 1.9 20 295-314 2-21 (87)
184 COG1746 CCA1 tRNA nucleotidylt 67.9 12 0.00025 40.2 6.1 47 352-398 29-77 (443)
185 PRK14670 uvrC excinuclease ABC 65.6 3.1 6.7E-05 46.6 1.5 42 296-338 515-558 (574)
186 COG2251 Predicted nuclease (Re 65.4 4.7 0.0001 43.3 2.6 27 299-325 229-255 (474)
187 TIGR02236 recomb_radA DNA repa 65.1 11 0.00023 38.7 5.2 61 256-324 1-69 (310)
188 TIGR00615 recR recombination p 65.1 4.6 0.0001 38.9 2.3 32 254-285 11-42 (195)
189 KOG2534 DNA polymerase IV (fam 64.9 4.5 9.7E-05 41.6 2.3 54 290-343 51-114 (353)
190 PRK02362 ski2-like helicase; P 64.4 48 0.001 38.4 10.9 52 254-315 652-704 (737)
191 PRK14671 uvrC excinuclease ABC 64.4 4.9 0.00011 45.5 2.7 32 293-325 567-598 (621)
192 PRK03980 flap endonuclease-1; 64.2 5.5 0.00012 40.8 2.9 25 299-324 193-217 (292)
193 PRK14671 uvrC excinuclease ABC 64.1 8.7 0.00019 43.5 4.7 49 254-313 569-617 (621)
194 TIGR03491 RecB family nuclease 63.9 5.4 0.00012 43.5 2.9 29 298-326 210-238 (457)
195 PRK14667 uvrC excinuclease ABC 63.8 3.8 8.2E-05 45.9 1.7 29 296-325 515-543 (567)
196 PRK14668 uvrC excinuclease ABC 63.5 8.9 0.00019 43.1 4.6 51 254-313 525-575 (577)
197 KOG4362 Transcriptional regula 63.5 10 0.00022 43.0 5.0 96 3-100 573-680 (684)
198 COG4277 Predicted DNA-binding 63.4 6.2 0.00013 40.4 2.9 33 294-326 329-364 (404)
199 PF04919 DUF655: Protein of un 63.3 6.7 0.00015 37.2 3.0 59 266-324 86-149 (181)
200 TIGR00593 pola DNA polymerase 63.2 5.4 0.00012 47.1 2.9 24 299-324 189-213 (887)
201 PRK05007 PII uridylyl-transfer 62.2 24 0.00053 41.8 8.1 50 367-416 79-131 (884)
202 PRK12278 50S ribosomal protein 62.2 6.1 0.00013 38.8 2.6 30 295-324 158-187 (221)
203 PF14716 HHH_8: Helix-hairpin- 61.9 6.6 0.00014 31.0 2.3 23 291-313 42-65 (68)
204 PF14579 HHH_6: Helix-hairpin- 61.7 11 0.00023 31.5 3.7 31 296-326 28-62 (90)
205 PRK13844 recombination protein 60.9 5.6 0.00012 38.4 2.1 32 254-285 15-46 (200)
206 PTZ00217 flap endonuclease-1; 60.5 6.9 0.00015 41.9 2.9 26 298-324 238-263 (393)
207 COG0272 Lig NAD-dependent DNA 59.8 23 0.00049 40.3 6.8 73 17-94 593-665 (667)
208 PF03118 RNA_pol_A_CTD: Bacter 59.2 2.8 6.1E-05 33.1 -0.2 45 300-344 16-62 (66)
209 PRK14973 DNA topoisomerase I; 59.0 9.9 0.00021 45.2 4.1 41 295-335 802-844 (936)
210 cd01703 PolY_Pol_iota DNA Poly 58.9 19 0.00041 38.3 5.9 54 255-318 173-243 (379)
211 COG0177 Nth Predicted EndoIII- 58.7 21 0.00046 34.9 5.6 31 243-273 97-128 (211)
212 TIGR03674 fen_arch flap struct 58.2 8.1 0.00018 40.4 2.9 27 298-325 239-265 (338)
213 TIGR01083 nth endonuclease III 57.6 24 0.00052 33.6 5.9 42 232-273 82-125 (191)
214 PRK01759 glnD PII uridylyl-tra 57.4 34 0.00074 40.4 8.2 68 349-416 33-107 (854)
215 PRK01216 DNA polymerase IV; Va 57.3 35 0.00075 35.9 7.5 52 256-317 180-233 (351)
216 PRK14669 uvrC excinuclease ABC 57.3 4.8 0.0001 45.6 1.1 30 295-325 552-581 (624)
217 KOG1921 Endonuclease III [Repl 57.0 11 0.00024 37.5 3.4 32 283-315 148-179 (286)
218 PRK14672 uvrC excinuclease ABC 56.9 5.6 0.00012 45.3 1.5 52 296-348 609-662 (691)
219 PRK05755 DNA polymerase I; Pro 56.8 7.9 0.00017 45.7 2.9 24 298-323 190-214 (880)
220 PRK10917 ATP-dependent DNA hel 56.8 8.9 0.00019 44.0 3.2 27 297-323 11-37 (681)
221 smart00611 SEC63 Domain of unk 56.7 23 0.0005 36.1 6.0 29 297-325 153-181 (312)
222 COG1669 Predicted nucleotidylt 56.6 39 0.00085 28.9 6.2 31 367-397 22-54 (97)
223 CHL00137 rps13 ribosomal prote 56.2 7.8 0.00017 34.6 2.0 25 293-317 15-40 (122)
224 KOG3524 Predicted guanine nucl 56.2 6.9 0.00015 44.1 2.0 86 17-109 209-294 (850)
225 cd00141 NT_POLXc Nucleotidyltr 56.1 5.1 0.00011 41.3 1.0 51 293-343 43-102 (307)
226 KOG2093 Translesion DNA polyme 56.0 19 0.00041 41.8 5.4 53 256-318 551-605 (1016)
227 PRK07758 hypothetical protein; 55.9 15 0.00034 31.2 3.6 23 254-276 67-89 (95)
228 PRK00076 recR recombination pr 55.8 11 0.00024 36.4 3.1 32 254-285 11-42 (196)
229 PRK05179 rpsM 30S ribosomal pr 55.7 7.8 0.00017 34.6 1.9 24 294-317 16-40 (122)
230 PRK12311 rpsB 30S ribosomal pr 55.4 8.5 0.00018 40.1 2.5 32 293-324 261-292 (326)
231 COG1491 Predicted RNA-binding 55.3 13 0.00027 35.5 3.3 40 248-287 123-163 (202)
232 cd05401 NT_GlnE_GlnD_like Nucl 54.9 42 0.00091 31.0 6.9 50 368-417 55-110 (172)
233 PRK02794 DNA polymerase IV; Pr 54.7 1.1E+02 0.0025 32.7 11.1 52 256-318 211-264 (419)
234 PRK14669 uvrC excinuclease ABC 54.5 23 0.0005 40.2 5.9 50 254-314 552-601 (624)
235 smart00478 ENDO3c endonuclease 53.2 27 0.00058 31.5 5.2 42 232-273 48-91 (149)
236 PRK13913 3-methyladenine DNA g 52.3 27 0.00058 34.3 5.2 77 232-316 93-178 (218)
237 TIGR03631 bact_S13 30S ribosom 52.3 9.3 0.0002 33.6 1.9 24 294-317 14-38 (113)
238 KOG1921 Endonuclease III [Repl 50.7 24 0.00053 35.2 4.6 29 245-273 149-178 (286)
239 COG0322 UvrC Nuclease subunit 50.7 26 0.00056 39.4 5.5 84 209-313 496-579 (581)
240 COG1725 Predicted transcriptio 50.4 50 0.0011 29.6 6.2 88 262-362 12-103 (125)
241 PRK04374 PII uridylyl-transfer 50.3 52 0.0011 39.0 8.1 63 354-416 55-123 (869)
242 COG2231 Uncharacterized protei 50.1 25 0.00054 34.2 4.5 37 271-312 96-132 (215)
243 TIGR01954 nusA_Cterm_rpt trans 49.9 15 0.00032 26.6 2.4 31 303-333 1-33 (50)
244 TIGR00588 ogg 8-oxoguanine DNA 49.5 24 0.00053 36.4 4.7 76 224-305 178-265 (310)
245 PRK13482 DNA integrity scannin 49.2 9.9 0.00021 39.9 1.8 52 288-341 280-334 (352)
246 PRK03352 DNA polymerase IV; Va 48.4 32 0.00068 35.8 5.5 56 255-320 178-235 (346)
247 TIGR00596 rad1 DNA repair prot 48.0 25 0.00054 41.2 5.0 32 293-325 755-786 (814)
248 PRK00558 uvrC excinuclease ABC 47.9 11 0.00023 42.7 2.0 44 294-338 542-587 (598)
249 TIGR01084 mutY A/G-specific ad 47.8 26 0.00056 35.7 4.5 25 292-316 102-126 (275)
250 COG0099 RpsM Ribosomal protein 47.3 15 0.00032 32.6 2.3 22 296-317 18-40 (121)
251 PRK13746 aminoglycoside resist 47.3 96 0.0021 31.4 8.4 27 370-397 30-58 (262)
252 PF02889 Sec63: Sec63 Brl doma 46.8 25 0.00054 35.8 4.3 29 296-324 149-177 (314)
253 PTZ00134 40S ribosomal protein 46.5 13 0.00029 34.5 2.0 25 293-317 28-53 (154)
254 COG1194 MutY A/G-specific DNA 46.3 40 0.00086 35.3 5.6 59 220-278 77-137 (342)
255 cd01702 PolY_Pol_eta DNA Polym 46.3 38 0.00083 35.7 5.7 54 256-318 184-241 (359)
256 PRK00275 glnD PII uridylyl-tra 46.0 68 0.0015 38.2 8.2 49 368-416 78-129 (895)
257 COG5067 DBF4 Protein kinase es 45.2 14 0.0003 39.1 2.1 49 13-63 117-165 (468)
258 PRK14668 uvrC excinuclease ABC 44.7 15 0.00032 41.4 2.4 44 295-339 525-570 (577)
259 PF03445 DUF294: Putative nucl 44.5 61 0.0013 29.2 6.0 51 369-419 50-107 (138)
260 PRK04053 rps13p 30S ribosomal 44.5 16 0.00035 33.7 2.3 25 293-317 23-48 (149)
261 COG1491 Predicted RNA-binding 44.3 45 0.00097 31.9 5.1 57 268-324 102-163 (202)
262 PRK12373 NADH dehydrogenase su 43.8 18 0.00039 38.7 2.8 33 292-324 320-352 (400)
263 COG1204 Superfamily II helicas 43.2 24 0.00052 41.1 3.8 109 233-344 610-727 (766)
264 TIGR03629 arch_S13P archaeal r 42.9 17 0.00037 33.4 2.1 23 295-317 21-44 (144)
265 PF02961 BAF: Barrier to autoi 42.9 19 0.00042 30.2 2.2 28 296-323 20-47 (89)
266 PRK03858 DNA polymerase IV; Va 42.8 43 0.00092 35.5 5.5 52 256-317 175-228 (396)
267 TIGR01693 UTase_glnD [Protein- 42.6 66 0.0014 38.0 7.4 49 368-416 43-94 (850)
268 COG2844 GlnD UTP:GlnB (protein 42.1 77 0.0017 37.0 7.5 49 368-416 66-117 (867)
269 cd00128 XPG Xeroderma pigmento 42.0 16 0.00034 37.7 2.0 17 298-314 226-242 (316)
270 cd01701 PolY_Rev1 DNA polymera 41.8 46 0.001 35.6 5.6 53 256-318 224-280 (404)
271 smart00483 POLXc DNA polymeras 41.7 15 0.00032 38.4 1.7 51 292-342 45-105 (334)
272 TIGR00194 uvrC excinuclease AB 41.6 22 0.00047 40.0 3.1 29 296-325 542-570 (574)
273 PF11774 Lsr2: Lsr2 ; InterPr 41.6 17 0.00037 31.8 1.8 28 443-470 73-100 (110)
274 TIGR01446 DnaD_dom DnaD and ph 41.2 23 0.0005 27.9 2.4 19 305-323 54-72 (73)
275 PRK10308 3-methyl-adenine DNA 41.2 43 0.00092 34.2 4.9 45 228-272 173-225 (283)
276 PRK13766 Hef nuclease; Provisi 40.8 20 0.00043 41.6 2.8 46 296-342 716-763 (773)
277 cd00424 PolY Y-family of DNA p 40.1 71 0.0015 33.2 6.6 53 256-318 175-229 (343)
278 KOG1918 3-methyladenine DNA gl 39.8 16 0.00035 35.8 1.5 58 254-312 122-182 (254)
279 PF06514 PsbU: Photosystem II 39.5 12 0.00025 31.7 0.4 51 293-343 21-72 (93)
280 PHA00439 exonuclease 39.3 22 0.00047 36.4 2.4 27 298-325 191-219 (286)
281 PRK03059 PII uridylyl-transfer 39.1 78 0.0017 37.5 7.3 63 353-415 44-111 (856)
282 TIGR00596 rad1 DNA repair prot 38.3 54 0.0012 38.5 5.7 14 212-225 645-658 (814)
283 COG0353 RecR Recombinational D 36.5 33 0.00071 33.1 3.0 22 254-275 12-33 (198)
284 PRK03348 DNA polymerase IV; Pr 36.3 69 0.0015 34.9 5.9 53 256-318 182-236 (454)
285 PRK01229 N-glycosylase/DNA lya 36.2 38 0.00082 33.0 3.5 20 252-271 116-136 (208)
286 PRK10880 adenine DNA glycosyla 36.0 26 0.00057 36.9 2.5 25 292-316 106-130 (350)
287 PF09970 DUF2204: Nucleotidyl 35.8 76 0.0016 30.1 5.4 39 368-406 16-59 (181)
288 PRK13910 DNA glycosylase MutY; 35.3 26 0.00056 35.9 2.3 23 293-315 70-92 (289)
289 COG1200 RecG RecG-like helicas 35.1 30 0.00066 39.3 2.9 28 296-323 11-38 (677)
290 COG5275 BRCT domain type II [G 35.1 1.2E+02 0.0026 29.9 6.5 50 17-67 155-204 (276)
291 PF05559 DUF763: Protein of un 34.9 1.5E+02 0.0032 30.9 7.5 21 292-312 266-286 (319)
292 COG1031 Uncharacterized Fe-S o 32.6 37 0.00081 36.9 3.0 31 294-324 515-546 (560)
293 PRK03381 PII uridylyl-transfer 32.0 1.1E+02 0.0024 35.7 7.1 47 369-415 58-107 (774)
294 COG5186 PAP1 Poly(A) polymeras 31.4 4.4E+02 0.0094 28.2 10.3 48 369-416 82-130 (552)
295 cd00080 HhH2_motif Helix-hairp 30.7 33 0.00071 27.6 1.7 28 255-284 23-50 (75)
296 PTZ00035 Rad51 protein; Provis 30.5 43 0.00093 35.0 3.0 49 293-342 22-72 (337)
297 PHA01806 hypothetical protein 29.9 80 0.0017 30.4 4.4 49 345-397 14-67 (200)
298 PLN03187 meiotic recombination 28.4 45 0.00097 35.1 2.7 32 292-324 29-60 (344)
299 PF04994 TfoX_C: TfoX C-termin 27.9 42 0.00092 27.6 2.0 30 254-287 3-32 (81)
300 TIGR00600 rad2 DNA excision re 27.8 47 0.001 39.9 3.0 26 298-323 869-895 (1034)
301 TIGR02238 recomb_DMC1 meiotic 26.5 45 0.00098 34.5 2.3 41 300-340 6-48 (313)
302 KOG2841 Structure-specific end 26.0 89 0.0019 31.1 4.0 49 292-341 192-242 (254)
303 TIGR00207 fliG flagellar motor 24.6 3.5E+02 0.0075 28.3 8.5 87 236-323 144-245 (338)
304 COG0322 UvrC Nuclease subunit 24.4 44 0.00095 37.7 1.9 28 297-325 532-559 (581)
305 TIGR02922 conserved hypothetic 24.1 28 0.0006 27.2 0.2 21 370-390 34-58 (67)
306 PF12482 DUF3701: Phage integr 21.8 83 0.0018 26.9 2.6 21 304-324 22-42 (96)
307 PRK02406 DNA polymerase IV; Va 21.8 1.7E+02 0.0037 30.3 5.6 52 256-318 170-223 (343)
308 cd05398 NT_ClassII-CCAase Nucl 21.6 1.7E+02 0.0037 26.3 4.9 38 354-394 4-45 (139)
309 PF00416 Ribosomal_S13: Riboso 21.6 84 0.0018 27.1 2.7 44 254-297 15-58 (107)
310 PRK07945 hypothetical protein; 21.4 52 0.0011 34.4 1.6 28 297-324 51-82 (335)
311 PF14635 HHH_7: Helix-hairpin- 21.2 62 0.0013 28.1 1.8 21 293-313 48-68 (104)
312 PLN03187 meiotic recombination 21.0 3.5E+02 0.0076 28.5 7.7 75 260-342 37-118 (344)
313 COG2176 PolC DNA polymerase II 21.0 2.2E+02 0.0048 34.9 6.6 90 234-330 1294-1420(1444)
314 cd04761 HTH_MerR-SF Helix-Turn 20.8 84 0.0018 22.2 2.2 22 295-316 4-25 (49)
315 PF08103 Antimicrobial_8: Uper 20.6 87 0.0019 18.1 1.7 12 235-246 5-16 (17)
316 PRK00024 hypothetical protein; 20.4 1E+02 0.0023 30.2 3.5 42 263-311 40-82 (224)
317 KOG2875 8-oxoguanine DNA glyco 20.4 1.3E+02 0.0028 30.7 4.1 18 254-271 218-235 (323)
318 PRK09482 flap endonuclease-lik 20.3 1.1E+02 0.0024 30.8 3.6 25 254-280 182-206 (256)
No 1
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=100.00 E-value=9.6e-83 Score=623.82 Aligned_cols=295 Identities=37% Similarity=0.650 Sum_probs=275.7
Q ss_pred CCCcHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHH
Q 010406 207 PDLNKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFE 286 (511)
Q Consensus 207 ~~~N~~ia~~l~~la~~~e~~g~~~r~~aY~rAa~~l~~l~~~i~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~ 286 (511)
.|+|..++++|+.||+.|++.|+.+|+++|++||++|+++|++|+|++|+++|||||++|+++|+|||+||++++||+++
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 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhchhHHHHHHhcccCCCHHHHHHHHHhCCCCHHHHhh-ccCcchhhhhcccchhhhccCcCHHHHHHHHHHHHHHhhhc
Q 010406 287 KDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN-EDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEV 365 (511)
Q Consensus 287 ~~~~~~~l~lf~~I~GvGpktA~~l~~~Gi~tledL~~-~~~L~~~q~~Glk~~~d~~~~i~r~ea~~~~~iv~~~~~~~ 365 (511)
+|+.+++|++|++|||||++||++||++|+|||+|+++ ..++|++|++|++||+||+.+|+|+||.++.++|++++..+
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 CCCeEEEEccceeecCCccCCeeEEEecCCcch-hhhHHHHHHHHHHHhcceee--eeEee-------------------
Q 010406 366 LPEVIILCGGSYRRGKASCGDLDVVIMHPDRKS-HKGFLSKYVKKLKEMKFLRE--DLIFS------------------- 423 (511)
Q Consensus 366 ~p~~~v~~~Gs~RRgke~~gDvDiLit~~~~~~-~~~~l~~~v~~l~~~g~l~~--~l~~~------------------- 423 (511)
+|++.|++||||||||++|||||||||||...+ +.+++..+...|.+.|++.. ++...
T Consensus 169 ~p~~~vt~~GsfRRGk~~ggDvD~LithP~~~s~~~~~~~~l~~~le~~g~il~~~~~~S~~Ek~~l~~~~s~~~~~~~~ 248 (353)
T KOG2534|consen 169 DPEAFVTVTGSFRRGKKMGGDVDFLITHPGSTSTEAKLLQLLMILLEKKGLLLYYDQLHSCGEKLRLPSRKSALDHFKKF 248 (353)
T ss_pred CCCcEEEEeccccCCcccCCCeeEEEeCCCCCchhhhHHHHHHHHHHhcCeEEEEeeeccccccccccchhhhHhhhhhE
Confidence 999999999999999999999999999999888 67888999999999999862 11000
Q ss_pred -----cc----------------------cccccCcchHHHHHHHhcCcHHHHHHHHHHHHHcCCccCCCCCcccccCCC
Q 010406 424 -----TH----------------------SEEVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGSG 476 (511)
Q Consensus 424 -----~~----------------------~~~~~p~~~~~~aLl~~TGS~~fnr~lR~~A~~kg~~L~~~gL~~~~~~~~ 476 (511)
.. +..+||+++|||||||||||++|||+||++|.+|||+||+||||+.+.
T Consensus 249 mgv~~LPr~~~~~~~~S~n~~~~~~~rRvDivv~P~~~~~~alLgwTGS~~FnR~lR~~A~~kG~~l~~h~L~~~~~--- 325 (353)
T KOG2534|consen 249 MGVFRLPRQRVDSDQSSWNEGKGWKARRVDIVVCPYDEFGFALLGWTGSKEFNRDLRRYATHKGFSLDEHALFDLTV--- 325 (353)
T ss_pred EEEEEcCcccccccccccCCCCCCceeeeEEEEechHHcceeeeeecchHHHHHHHHHHHHhcCceecccccccCCc---
Confidence 00 011999999999999999999999999999999999999999998753
Q ss_pred CcccccccccCCCCCHHHHHhhcCCCCCCCCCcCC
Q 010406 477 GKQGVRARTSLKFDTEKEVFDFLGFPWLEPHERNL 511 (511)
Q Consensus 477 ~~~~~~~~~~~~~~tEedIf~~LGL~yipPe~Rn~ 511 (511)
..++++++|+|||++|||+||||++||.
T Consensus 326 -------~~~l~~~sEkdIFr~l~L~Y~EP~~Rn~ 353 (353)
T KOG2534|consen 326 -------RIFLPVESEKDIFRYLGLKYIEPKERNA 353 (353)
T ss_pred -------ceecCCccHHHHHHHhCCccCChhhcCC
Confidence 2689999999999999999999999995
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=1.3e-69 Score=552.75 Aligned_cols=286 Identities=41% Similarity=0.684 Sum_probs=258.9
Q ss_pred HHHHHHHHHHHHHHHcCC-ChhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhch
Q 010406 212 NITEIFGKLINIYRALGE-DRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEK 290 (511)
Q Consensus 212 ~ia~~l~~la~~~e~~g~-~~r~~aY~rAa~~l~~l~~~i~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~ 290 (511)
+|+++|++||++|+++|+ .+|++||++||++|+++|++|+++.++.+|||||++|+++|.||++||+++++|+++++ .
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 699999999999999965 57999999999999999999999999999999999999999999999999999999998 5
Q ss_pred hHHHHHHhcccCCCHHHHHHHHHhCCCCHHHHhhc--cCcchhhhhcccchhhhccCcCHHHHHHHHHHHHHHhhhcCCC
Q 010406 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPE 368 (511)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~Gi~tledL~~~--~~L~~~q~~Glk~~~d~~~~i~r~ea~~~~~iv~~~~~~~~p~ 368 (511)
+..+..|++|||||||||++||+.||+||+||+.+ .+++..|..|++||+|+.++|||+||+++.+.|...+..+.|+
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 4899999999999999999999999999988888877777788
Q ss_pred eEEEEccceeecCCccCCeeEEEecCCcchhhhHHHHHHHHHHHhcceeeee---------Eeec--------ccccccC
Q 010406 369 VIILCGGSYRRGKASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLREDL---------IFST--------HSEEVYP 431 (511)
Q Consensus 369 ~~v~~~Gs~RRgke~~gDvDiLit~~~~~~~~~~l~~~v~~l~~~g~l~~~l---------~~~~--------~~~~~~p 431 (511)
++|++|||||||+++||||||||+|++... ..++.++++.|.+.|++.+.+ .+.. .+..+||
T Consensus 161 ~~v~i~GS~RRg~et~gDiDilv~~~~~~~-~~~~~~v~~~l~~~~~~~~~~~~g~~k~~~~~~~~~~~~~~rVDl~~~p 239 (307)
T cd00141 161 LQVEIAGSYRRGKETVGDIDILVTHPDATS-RGLLEKVVDALVELGFVTEVLSKGDTKASGILKLPGGWKGRRVDLRVVP 239 (307)
T ss_pred eEEEEcccccCCCCccCCEEEEEecCCccc-cccHHHHHHHHHhCCCeehhhhCCCceEEEEEecCCCCCceEEEEEEeC
Confidence 899999999999999999999999998764 667888999999999885421 1111 1345999
Q ss_pred cchHHHHHHHhcCcHHHHHHHHHHHHHcCCccCCCCCcccccCCCCcccccccccCCCCCHHHHHhhcCCCCCCCCCc
Q 010406 432 RDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGSGGKQGVRARTSLKFDTEKEVFDFLGFPWLEPHER 509 (511)
Q Consensus 432 ~~~~~~aLl~~TGS~~fnr~lR~~A~~kg~~L~~~gL~~~~~~~~~~~~~~~~~~~~~~tEedIf~~LGL~yipPe~R 509 (511)
+++||+||+|||||++|||.||.+|.++||+||+||||+.. .+..+++.+|++||++|||||||||+|
T Consensus 240 ~~~~~~all~fTGs~~~nr~lR~~A~~~G~~L~~~GL~~~~----------~~~~~~~~~E~~If~~Lgl~yipPe~R 307 (307)
T cd00141 240 PEEFGAALLYFTGSKQFNRALRRLAKEKGLKLNEYGLFDGV----------DGERLPGETEEEIFEALGLPYIEPELR 307 (307)
T ss_pred HHHHHHHHHHhhCCHHHHHHHHHHHHHcCCeeeccccccCC----------CCCCccCCCHHHHHHHcCCCCCCCCCC
Confidence 99999999999999999999999999999999999999753 135789999999999999999999998
No 3
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=100.00 E-value=2.3e-69 Score=556.64 Aligned_cols=292 Identities=37% Similarity=0.615 Sum_probs=249.4
Q ss_pred CCcHHHHHHHHHHHHHHHHcCCCh-hHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHH
Q 010406 208 DLNKNITEIFGKLINIYRALGEDR-RSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFE 286 (511)
Q Consensus 208 ~~N~~ia~~l~~la~~~e~~g~~~-r~~aY~rAa~~l~~l~~~i~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~ 286 (511)
|+|++|+++|++||++||+.|+|+ |++||++||++|+++|++|++++++.+|||||++|++||.||++||++.++.+..
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 469999999999999999999995 8999999999999999999999999999999999999999999999999666655
Q ss_pred hhchhHHHHHHhcccCCCHHHHHHHHHhCCCCHHHHhhcc--CcchhhhhcccchhhhccCcCHHHHHHHHHHHHHHhhh
Q 010406 287 KDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEE 364 (511)
Q Consensus 287 ~~~~~~~l~lf~~I~GvGpktA~~l~~~Gi~tledL~~~~--~L~~~q~~Glk~~~d~~~~i~r~ea~~~~~iv~~~~~~ 364 (511)
.++.+..+..|++|||||||||++||+.||+||+||+.+. +|+..|.+|++||+|+.++|||+||+.+.++|......
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 5666677777779999999999999999999999999753 69999999999999999999999999999988888777
Q ss_pred cCCCeEEEEccceeecCCccCCeeEEEecCCcchhhhHHHHHH---------HHHHHhccee----------eeeEee--
Q 010406 365 VLPEVIILCGGSYRRGKASCGDLDVVIMHPDRKSHKGFLSKYV---------KKLKEMKFLR----------EDLIFS-- 423 (511)
Q Consensus 365 ~~p~~~v~~~Gs~RRgke~~gDvDiLit~~~~~~~~~~l~~~v---------~~l~~~g~l~----------~~l~~~-- 423 (511)
+.|.+.|++||||||||++||||||||+|+++.. +++..++ ..+...++.. ..+.+.
T Consensus 161 ~~~~~~v~i~GSyRRgket~gDIDili~~~~~~~--~~~~~v~~~~~l~~~~~~~~~~~~~~~~~~~g~~~~~~v~~~~~ 238 (334)
T smart00483 161 ILPDAIVTLTGSFRRGKETGHDVDFLITSPHPAK--EKELEVLDLLLLESTFEELQLPSIRVATLDHGQKKFMILKLSPS 238 (334)
T ss_pred hCCCcEEEEecccccCCCcCCCeeEEEecCCccc--hhHHHHHHHHHHHHHHHHHhcccchhhhhhcCCCEEEEEEeCCc
Confidence 8888899999999999999999999999999762 2222222 1111111110 011110
Q ss_pred ------------------cccccccCcchHHHHHHHhcCcHHHHHHHHHHHHHcCCccCCCCCcccccCCCCcccccccc
Q 010406 424 ------------------THSEEVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGSGGKQGVRART 485 (511)
Q Consensus 424 ------------------~~~~~~~p~~~~~~aLl~~TGS~~fnr~lR~~A~~kg~~L~~~gL~~~~~~~~~~~~~~~~~ 485 (511)
..+..+||+++||+||+|||||++|||.||.+|.++| +||+||||+.... .+.
T Consensus 239 ~~~~~~~g~~~~~~~~~rrVDl~~~~~~~~g~aLl~fTGS~~fnr~lR~~A~~~g-~L~~~gl~~~~~~--------~~~ 309 (334)
T smart00483 239 REDKEKSGKPDEKGWKARRVDIVLCPEDQYPTALLGWTGSKQFNRDLRRYATSKF-KLMLDGHELYDKT--------KEK 309 (334)
T ss_pred cccccccccccCCCCcceEEEEEEechHHheeEEEEEeCchhHHHHHHHHHHHcC-CcCcccCccccCC--------CCe
Confidence 0134589999999999999999999999999999999 9999999975321 135
Q ss_pred cCCCCCHHHHHhhcCCCCCCCCCcC
Q 010406 486 SLKFDTEKEVFDFLGFPWLEPHERN 510 (511)
Q Consensus 486 ~~~~~tEedIf~~LGL~yipPe~Rn 510 (511)
.+++.+|++||++|||||||||+||
T Consensus 310 ~i~~~~E~~If~~LGl~yipPe~Rn 334 (334)
T smart00483 310 FLKVESEEDIFDHLGLPYIEPEERN 334 (334)
T ss_pred eccCCCHHHHHHHhCCCCCCcccCC
Confidence 7889999999999999999999998
No 4
>PRK08609 hypothetical protein; Provisional
Probab=100.00 E-value=3.7e-66 Score=566.20 Aligned_cols=292 Identities=21% Similarity=0.329 Sum_probs=253.0
Q ss_pred CCcHHHHHHHHHHHHHHHHcCCC-hhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHH
Q 010406 208 DLNKNITEIFGKLINIYRALGED-RRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFE 286 (511)
Q Consensus 208 ~~N~~ia~~l~~la~~~e~~g~~-~r~~aY~rAa~~l~~l~~~i~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~ 286 (511)
|+|++|+++|++||++||++|+| +|++||++||++|+++|++|+++.++.+|||||++||+||+||++||++++||+|+
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 hhchhHHHHHHhcccCCCHHHHHHHHHh-CCCCHHHHhh---ccCcchhhhhc----------ccchhhhccCcCHHHHH
Q 010406 287 KDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKN---EDSLTHSQRLG----------LKYFDDIKTRIPRHEVE 352 (511)
Q Consensus 287 ~~~~~~~l~lf~~I~GvGpktA~~l~~~-Gi~tledL~~---~~~L~~~q~~G----------lk~~~d~~~~i~r~ea~ 352 (511)
++.|..+++|+ +|||||||||++||++ ||+||+||+. +++++.+++|| +++|+++.+|||+.||.
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 98777677655 9999999999999976 9999999996 45788887775 66677778999999999
Q ss_pred HHHHHHHHHhhhcCCCeEEEEccceeecCCccCCeeEEEecCCcchhhhHHHHH--HHHHHHhcceeeeeEeec-----c
Q 010406 353 QMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPDRKSHKGFLSKY--VKKLKEMKFLREDLIFST-----H 425 (511)
Q Consensus 353 ~~~~iv~~~~~~~~p~~~v~~~Gs~RRgke~~gDvDiLit~~~~~~~~~~l~~~--v~~l~~~g~l~~~l~~~~-----~ 425 (511)
.+.+.|....+.+.|..+|++||||||||+||||||||||++++..+...|.++ +..+...|..+..+.+.. .
T Consensus 160 ~~a~~i~~~l~~~~~~~~v~~~GS~RR~~et~gDiDili~~~~~~~~~~~l~~~~~v~~~~~~g~~~~~~~~~~~~~~~v 239 (570)
T PRK08609 160 PIAQEIEEYLATIDEIIRFSRAGSLRRARETVKDLDFIIATDEPEAVREQLLQLPNIVEVIAAGDTKVSVELEYEYTISV 239 (570)
T ss_pred HHHHHHHHHHHhCCCccEEEeccchhccccccCCeeEEEecCCHHHHHHHHHcCccHHHHHhcCCceEEEEEecCCCeEE
Confidence 998877777666656669999999999999999999999999987665555422 344455665544333321 2
Q ss_pred cccccCcchHHHHHHHhcCcHHHHHHHHHHHHHcCCccCCCCCcccccCCCCcccccccccCCCCCHHHHHhhcCCCCCC
Q 010406 426 SEEVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGSGGKQGVRARTSLKFDTEKEVFDFLGFPWLE 505 (511)
Q Consensus 426 ~~~~~p~~~~~~aLl~~TGS~~fnr~lR~~A~~kg~~L~~~gL~~~~~~~~~~~~~~~~~~~~~~tEedIf~~LGL~yip 505 (511)
+..+||+++||+||+|||||++|||+||.+|.+|||+||+||||+... +..+++.+|++||++|||||||
T Consensus 240 Dl~~v~~~~~~~aL~yfTGS~~hn~~lr~~A~~~g~~l~e~gl~~~~~----------~~~~~~~~E~~iy~~Lgl~yip 309 (570)
T PRK08609 240 DFRLVEPEAFATTLHHFTGSKDHNVRMRQLAKERGEKISEYGVEQADT----------GEVKTFESEEAFFAHFGLPFIP 309 (570)
T ss_pred EEEEeCHHHHHHHHHHHhccHHHHHHHHHHHHHcCCcccccccccCCC----------CccCCCCCHHHHHHHcCCCCCC
Confidence 345999999999999999999999999999999999999999997421 3468899999999999999999
Q ss_pred CCCcC
Q 010406 506 PHERN 510 (511)
Q Consensus 506 Pe~Rn 510 (511)
||+|+
T Consensus 310 PelRe 314 (570)
T PRK08609 310 PEVRE 314 (570)
T ss_pred ccccC
Confidence 99997
No 5
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=100.00 E-value=7.5e-57 Score=445.75 Aligned_cols=291 Identities=26% Similarity=0.443 Sum_probs=241.9
Q ss_pred CCcHHHHHHHHHHHHHHHHcCCC-hhHHHHHHHHHHHhcCCccccchhh---hcCCCCCCHHHHHHHHHHHHhCCchhhH
Q 010406 208 DLNKNITEIFGKLINIYRALGED-RRSFSYYKAIPVIEKLPFKIESADQ---VKGLPGIGKSMQDHIQEIVTTGKLSKLE 283 (511)
Q Consensus 208 ~~N~~ia~~l~~la~~~e~~g~~-~r~~aY~rAa~~l~~l~~~i~s~~~---l~~lpgIG~~ia~kI~Eil~tG~~~~le 283 (511)
|.|+.|+.+|+++|++|++.|+| +|++|||+||++|+.+.+++..+.+ +..|||||++||++|.||++||+++.++
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 7999999999999999999999866 4699999999999999999999999999
Q ss_pred HHHhhchhHHHHHHhcccCCCHHHHHHHHHh-CCCCHHHHhhc---cCcchhhhhcccchhhhc----------cCcCHH
Q 010406 284 HFEKDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNE---DSLTHSQRLGLKYFDDIK----------TRIPRH 349 (511)
Q Consensus 284 ~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~-Gi~tledL~~~---~~L~~~q~~Glk~~~d~~----------~~i~r~ 349 (511)
.++...|.+...|+ .|+|+|||+...||++ ||.++++|+++ +++..+.|||-++..+|+ +|+|..
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 99999999988887 9999999999999998 99999999965 578899999998888886 477777
Q ss_pred HHHHHHHHHHHHhhhcCCCeEEEEccceeecCCccCCeeEEEecCCcchhhhHHHHH--HHHHHHhcceeeeeEee----
Q 010406 350 EVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPDRKSHKGFLSKY--VKKLKEMKFLREDLIFS---- 423 (511)
Q Consensus 350 ea~~~~~iv~~~~~~~~p~~~v~~~Gs~RRgke~~gDvDiLit~~~~~~~~~~l~~~--v~~l~~~g~l~~~l~~~---- 423 (511)
++..+..-+.....++.+-.++.++||+||+++|++|||++|+..++.++...|..+ +..+..+|--.....+.
T Consensus 162 ~~l~ia~ei~~yl~~~~~~~~~~~aGs~RR~retv~DiD~~~s~~~~~~v~~~~~~~~~~~~vi~~G~~k~s~~~~~~~~ 241 (326)
T COG1796 162 FTLPIAQEIEGYLEELTPIIQASIAGSLRRGRETVGDIDILISTSHPESVLEELLEMPNVQEVIAKGETKVSMLLILDEG 241 (326)
T ss_pred HHHHHHHHHHHHHHhccchheeeeccchhhccccccceeeEeccCCcHHHHHHHhcCCCcceeeecCCceeeEEEEecCC
Confidence 777664433333334455458899999999999999999999988887632222221 11111111111110011
Q ss_pred -cccccccCcchHHHHHHHhcCcHHHHHHHHHHHHHcCCccCCCCCcccccCCCCcccccccccCCCCCHHHHHhhcCCC
Q 010406 424 -THSEEVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGSGGKQGVRARTSLKFDTEKEVFDFLGFP 502 (511)
Q Consensus 424 -~~~~~~~p~~~~~~aLl~~TGS~~fnr~lR~~A~~kg~~L~~~gL~~~~~~~~~~~~~~~~~~~~~~tEedIf~~LGL~ 502 (511)
..+..+||++.||+||+|||||++||+.||.+|+.+||+||+||||.. ++..++..||++||++|||+
T Consensus 242 ~svD~r~v~~e~fGaal~~fTGSkehNi~iR~lA~~kg~klseyGl~~~-----------~~e~i~~~tE~~i~~~l~l~ 310 (326)
T COG1796 242 TSVDFRVVPPEAFGAALQHFTGSKEHNIKIRQLAKAKGEKLSEYGLFRD-----------SGEIIAGKTEEKIYEHLGLP 310 (326)
T ss_pred CeeEEEEcCHHHhhhhhhhcccchhhhHHHHHHHHHhCcchhhcceecc-----------CCceecCCcHhHHHHHcCCC
Confidence 134569999999999999999999999999999999999999999953 13578999999999999999
Q ss_pred CCCCCCcC
Q 010406 503 WLEPHERN 510 (511)
Q Consensus 503 yipPe~Rn 510 (511)
|||||+|+
T Consensus 311 yipPE~RE 318 (326)
T COG1796 311 YIPPELRE 318 (326)
T ss_pred CCChhhcc
Confidence 99999997
No 6
>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=5.2e-25 Score=172.82 Aligned_cols=63 Identities=35% Similarity=0.688 Sum_probs=52.6
Q ss_pred HHHHhcCcHHHHHHHHHHHHHcCCccCCCCCcccccCCCCcccccccccCCCCCHHHHHhhcCCCCCCCCCcC
Q 010406 438 GLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGSGGKQGVRARTSLKFDTEKEVFDFLGFPWLEPHERN 510 (511)
Q Consensus 438 aLl~~TGS~~fnr~lR~~A~~kg~~L~~~gL~~~~~~~~~~~~~~~~~~~~~~tEedIf~~LGL~yipPe~Rn 510 (511)
||+|||||++|||+||.+|+++||+||+|||++... +..+++.+|+|||++|||||||||+||
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 799999999999999999999999999999997532 347899999999999999999999998
No 7
>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=99.77 E-value=3.8e-19 Score=155.69 Aligned_cols=79 Identities=46% Similarity=0.798 Sum_probs=71.5
Q ss_pred CcCHHHHHHHHHHHHHHhhhcCCCeEEEEccceeecCCccCCeeEEEecCCcchh----hhHHHHHHHHHHHhcceeeee
Q 010406 345 RIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPDRKSH----KGFLSKYVKKLKEMKFLREDL 420 (511)
Q Consensus 345 ~i~r~ea~~~~~iv~~~~~~~~p~~~v~~~Gs~RRgke~~gDvDiLit~~~~~~~----~~~l~~~v~~l~~~g~l~~~l 420 (511)
||||+||++++++|.+.+..+.|++.+++||||||||++|||||||||||+.... .++|.+++..|+++|+|+++|
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 6999999999999999999999999999999999999999999999999998874 689999999999999999988
Q ss_pred Eee
Q 010406 421 IFS 423 (511)
Q Consensus 421 ~~~ 423 (511)
..+
T Consensus 81 ~~~ 83 (112)
T PF14792_consen 81 SLG 83 (112)
T ss_dssp EEC
T ss_pred ccC
Confidence 654
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=99.69 E-value=5.8e-17 Score=129.40 Aligned_cols=66 Identities=36% Similarity=0.688 Sum_probs=62.2
Q ss_pred cHHHHHHHHHHHHHHHHc-CCChhHHHHHHHHHHHhcCCccccchhh-hcCCCCCCHHHHHHHHHHHH
Q 010406 210 NKNITEIFGKLINIYRAL-GEDRRSFSYYKAIPVIEKLPFKIESADQ-VKGLPGIGKSMQDHIQEIVT 275 (511)
Q Consensus 210 N~~ia~~l~~la~~~e~~-g~~~r~~aY~rAa~~l~~l~~~i~s~~~-l~~lpgIG~~ia~kI~Eil~ 275 (511)
|++|+++|++|+++|++. |+.+|++||++|+++|+++|++|++++| +.+|||||++|+.+|.|||+
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 5567999999999999999999999987 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=99.64 E-value=1.1e-16 Score=120.37 Aligned_cols=51 Identities=49% Similarity=1.009 Sum_probs=42.1
Q ss_pred HHHHhcccCCCHHHHHHHHHhCCCCHHHHhh-ccCcchhhhhcccchhhhcc
Q 010406 294 ISLFGEVWGIGPATAQKLYEKGHRTLDDLKN-EDSLTHSQRLGLKYFDDIKT 344 (511)
Q Consensus 294 l~lf~~I~GvGpktA~~l~~~Gi~tledL~~-~~~L~~~q~~Glk~~~d~~~ 344 (511)
|++|++||||||+||++||++|+|||+||++ ...|+..|++|++||+||++
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 6799999999999999999999999999986 45899999999999999974
No 10
>PRK07945 hypothetical protein; Provisional
Probab=99.59 E-value=5.9e-15 Score=152.86 Aligned_cols=103 Identities=18% Similarity=0.271 Sum_probs=89.2
Q ss_pred HHHHHHHHHHHHHHcCCC-hhHHHHHHHHHHHhcCCcc-ccchh---hhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHh
Q 010406 213 ITEIFGKLINIYRALGED-RRSFSYYKAIPVIEKLPFK-IESAD---QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEK 287 (511)
Q Consensus 213 ia~~l~~la~~~e~~g~~-~r~~aY~rAa~~l~~l~~~-i~s~~---~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~ 287 (511)
-+++|+++|++||++|+| +|++|||+||.+|+.++.+ +..+. +|.+|||||+++|+||.||++||+++.|++|+.
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 5999999999999999999 88774 799999999999999999999999999999998
Q ss_pred hchhHHHHHHhcccCCCHHHHHHHHHh---------CCCCHHHHhhc
Q 010406 288 DEKVRTISLFGEVWGIGPATAQKLYEK---------GHRTLDDLKNE 325 (511)
Q Consensus 288 ~~~~~~l~lf~~I~GvGpktA~~l~~~---------Gi~tledL~~~ 325 (511)
+..+. | |+..+.++.-. |-.|++|....
T Consensus 83 ~~~~~---------~-g~~l~~~~~~D~H~HT~~Sdg~~~~ee~v~~ 119 (335)
T PRK07945 83 DAEPL---------G-GGALRAALRGDLHTHSDWSDGGSPIEEMART 119 (335)
T ss_pred hhcCC---------c-cHHHHHHHhhhcccccCCCCCCCCHHHHHHH
Confidence 76432 7 99999998752 44556666543
No 11
>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=99.05 E-value=6.1e-10 Score=89.78 Aligned_cols=75 Identities=23% Similarity=0.343 Sum_probs=58.9
Q ss_pred CCCCCCeEEEEecCCCcchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCC-hHHHHHHHHHhhhccCCcccccchHHHH
Q 010406 16 NGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDL-EALLQQVSKQHLARFKGSVIRYQWLEDS 94 (511)
Q Consensus 16 ~~~F~g~~iy~~~~~~g~~r~~~l~~~~~~~Gg~v~~~~s~~VTHVV~~~~-s~~~~~l~~~~~~~~~~~iV~~~Wl~ec 94 (511)
..+|+||.+|| .+.....++.+.++++.+||.+.+.+++.+||||+.+. +...+..... ....+||+.+||.||
T Consensus 3 ~~~F~g~~f~i--~~~~~~~~~~l~~~i~~~GG~v~~~~~~~~thvI~~~~~~~~~k~~~~~---~~~i~iV~~~Wi~~c 77 (78)
T PF00533_consen 3 PKIFEGCTFCI--SGFDSDEREELEQLIKKHGGTVSNSFSKKTTHVIVGNPNKRTKKYKAAI---ANGIPIVSPDWIEDC 77 (78)
T ss_dssp TTTTTTEEEEE--SSTSSSHHHHHHHHHHHTTEEEESSSSTTSSEEEESSSHCCCHHHHHHH---HTTSEEEETHHHHHH
T ss_pred CCCCCCEEEEE--ccCCCCCHHHHHHHHHHcCCEEEeecccCcEEEEeCCCCCccHHHHHHH---HCCCeEecHHHHHHh
Confidence 46999999999 55555556778999999999999999999999999766 2222322221 236899999999999
Q ss_pred H
Q 010406 95 L 95 (511)
Q Consensus 95 i 95 (511)
+
T Consensus 78 i 78 (78)
T PF00533_consen 78 I 78 (78)
T ss_dssp H
T ss_pred C
Confidence 7
No 12
>smart00292 BRCT breast cancer carboxy-terminal domain.
Probab=99.01 E-value=8.9e-10 Score=87.83 Aligned_cols=78 Identities=19% Similarity=0.301 Sum_probs=60.1
Q ss_pred CCCCeEEEEecCCCcchHHHHHHHHHHhcCCEEEeecCC-CccEEEEcCChHHHHHHHHHhhhccCCcccccchHHHHHh
Q 010406 18 IFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSK-KVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSLR 96 (511)
Q Consensus 18 ~F~g~~iy~~~~~~g~~r~~~l~~~~~~~Gg~v~~~~s~-~VTHVV~~~~s~~~~~l~~~~~~~~~~~iV~~~Wl~ecik 96 (511)
+|+|+++||.+ .+.....+.+.+++..+||++...++. .+||||+.+.+........ ......+||+.+||.+|++
T Consensus 2 ~f~g~~~~~~g-~~~~~~~~~l~~~i~~~Gg~~~~~~~~~~~thvi~~~~~~~~~~~~~--~~~~~~~iV~~~Wi~~~~~ 78 (80)
T smart00292 2 LFKGKVFVITG-KFDKNERDELKELIEALGGKVTSSLSSKTTTHVIVGSPEGGKLELLL--AIALGIPIVTEDWLLDCLK 78 (80)
T ss_pred ccCCeEEEEeC-CCCCccHHHHHHHHHHcCCEEecccCccceeEEEEcCCCCccHHHHH--HHHcCCCCccHHHHHHHHH
Confidence 79999999987 344455688899999999999999998 9999999765432111111 1123679999999999998
Q ss_pred cC
Q 010406 97 LG 98 (511)
Q Consensus 97 ~g 98 (511)
++
T Consensus 79 ~~ 80 (80)
T smart00292 79 AG 80 (80)
T ss_pred Cc
Confidence 75
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=98.71 E-value=3.2e-08 Score=76.95 Aligned_cols=72 Identities=18% Similarity=0.307 Sum_probs=54.2
Q ss_pred CeEEEEecCCCcchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCCcccccchHHHHHh
Q 010406 21 GMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSLR 96 (511)
Q Consensus 21 g~~iy~~~~~~g~~r~~~l~~~~~~~Gg~v~~~~s~~VTHVV~~~~s~~~~~l~~~~~~~~~~~iV~~~Wl~ecik 96 (511)
|+.|||.+...+.. +..|++++..+||++.+.+++.+||||+.+......... ....+.+||+.+|+.+|++
T Consensus 1 ~~~~~i~g~~~~~~-~~~l~~~i~~~Gg~v~~~~~~~~thvI~~~~~~~~~~~~---~~~~~~~iV~~~Wi~~~~~ 72 (72)
T cd00027 1 GLTFVITGDLPSEE-RDELKELIEKLGGKVTSSVSKKTTHVIVGSDAGPKKLLK---AIKLGIPIVTPEWLLDCLK 72 (72)
T ss_pred CCEEEEEecCCCcC-HHHHHHHHHHcCCEEeccccCCceEEEECCCCCchHHHH---HHHcCCeEecHHHHHHHhC
Confidence 57888877543433 477899999999999999999999999976543221111 1123689999999999985
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=98.04 E-value=1.5e-05 Score=89.70 Aligned_cols=133 Identities=20% Similarity=0.258 Sum_probs=94.5
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHh-CCCCHHHHhhcc--Ccch
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED--SLTH 330 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~-Gi~tledL~~~~--~L~~ 330 (511)
++|.+|||+|++++++|.+.++.++...+++ .+..| +|+|||+++|+.|++. | |+++|.++. .|..
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 5789999999999999999999988777664 34455 9999999999999987 6 899998653 5778
Q ss_pred hhhhcccchhhhccCcCHHHHHH-HHHHHHHHh--------------hhcCCCeEEEEccceeec---------------
Q 010406 331 SQRLGLKYFDDIKTRIPRHEVEQ-MERLLQKAG--------------EEVLPEVIILCGGSYRRG--------------- 380 (511)
Q Consensus 331 ~q~~Glk~~~d~~~~i~r~ea~~-~~~iv~~~~--------------~~~~p~~~v~~~Gs~RRg--------------- 380 (511)
..+||.+..+.|.+-+.-.+..+ +..+...-. ...+.|-.+++||++...
T Consensus 535 i~GIG~~~A~~I~~ff~~~~~~~~i~~L~~~gv~~~~~~~~~~~~~~~~~l~gk~~v~TG~l~~~~R~~~~~~i~~~G~~ 614 (652)
T TIGR00575 535 VEGVGPKVAESIVNFFHDPNNRQLIKKLEELGVEMESLPEKVNAELAGSPLAGKTFVLTGTLSQMSRDEAKELLENLGGK 614 (652)
T ss_pred CCCcCHHHHHHHHHHHhhhhHHHHHHHHHHcCCCcccccccccccccCCCccCcEEEEeccCCCCCHHHHHHHHHHcCCE
Confidence 88899888877766554433322 232222100 001234578889987542
Q ss_pred --CCccCCeeEEEecCCcc
Q 010406 381 --KASCGDLDVVIMHPDRK 397 (511)
Q Consensus 381 --ke~~gDvDiLit~~~~~ 397 (511)
...+...|+||.-++..
T Consensus 615 v~~sVs~kt~~lv~G~~~g 633 (652)
T TIGR00575 615 VASSVSKKTDYVIAGEKAG 633 (652)
T ss_pred EeCCcCCCccEEEECCCCC
Confidence 45567778888866544
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=97.94 E-value=5.6e-06 Score=64.28 Aligned_cols=51 Identities=37% Similarity=0.549 Sum_probs=43.0
Q ss_pred HHHHHhcccCCCHHHHHHHHHhCCCCHHHHhhc--cCcchhhhhcccchhhhc
Q 010406 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDIK 343 (511)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~Gi~tledL~~~--~~L~~~q~~Glk~~~d~~ 343 (511)
+...|++|+||||++|++||+.||.|++||... ..|....++|.+..+.|.
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 455677999999999999999999999999865 358888898888776654
No 16
>KOG3226 consensus DNA repair protein [Replication, recombination and repair]
Probab=97.68 E-value=3.1e-05 Score=79.03 Aligned_cols=88 Identities=16% Similarity=0.305 Sum_probs=68.3
Q ss_pred CCCCCCeEEEEecCCCcchHHHHHHHHHHhcCCEEEeecCCCccEEEEc-CChHHHHHHHHHhhhccCCcccccchHHHH
Q 010406 16 NGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAM-DLEALLQQVSKQHLARFKGSVIRYQWLEDS 94 (511)
Q Consensus 16 ~~~F~g~~iy~~~~~~g~~r~~~l~~~~~~~Gg~v~~~~s~~VTHVV~~-~~s~~~~~l~~~~~~~~~~~iV~~~Wl~ec 94 (511)
..+++|+|+.+. |+..--+.-|+..+..+||..-.+|..+.||.|+. .+.. ++-+ +...+..||+-+||++|
T Consensus 315 ~klL~GVV~VlS--GfqNP~Rs~LRskAl~LGAkY~pDW~~gsThLICAF~NTP--Ky~Q---V~g~Gg~IV~keWI~~C 387 (508)
T KOG3226|consen 315 SKLLEGVVFVLS--GFQNPERSTLRSKALTLGAKYQPDWNAGSTHLICAFPNTP--KYRQ---VEGNGGTIVSKEWITEC 387 (508)
T ss_pred HHhhhceEEEEe--cccCchHHHHHHHHHhhcccccCCcCCCceeEEEecCCCc--chhh---cccCCceEeeHHHHHHH
Confidence 478999998884 45333346688999999999999999999999985 2221 1211 11236799999999999
Q ss_pred HhcCCCCCcccccccc
Q 010406 95 LRLGEKVSEDLYRIKL 110 (511)
Q Consensus 95 ik~g~lvde~~y~l~~ 110 (511)
-..+++||..+|.+.-
T Consensus 388 y~~kk~lp~rrYlm~~ 403 (508)
T KOG3226|consen 388 YAQKKLLPIRRYLMHA 403 (508)
T ss_pred HHHHhhccHHHHHhcC
Confidence 9999999999999864
No 17
>PF12738 PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2WT8_C 3EF1_A 3EF0_A.
Probab=97.60 E-value=6.1e-05 Score=58.73 Aligned_cols=63 Identities=16% Similarity=0.269 Sum_probs=40.1
Q ss_pred eEEEEecCCCcchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCCcccccch
Q 010406 22 MRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQW 90 (511)
Q Consensus 22 ~~iy~~~~~~g~~r~~~l~~~~~~~Gg~v~~~~s~~VTHVV~~~~s~~~~~l~~~~~~~~~~~iV~~~W 90 (511)
|+|.|.+ +....+..+.++++.+||++.+.++.++||+|+.+.. -.++..+ ...+.+||+++|
T Consensus 1 ~~i~~sg--~~~~~~~~l~~~i~~~Gg~~~~~lt~~~THLI~~~~~-~~K~~~A---~~~gi~vV~~~W 63 (63)
T PF12738_consen 1 VVICFSG--FSGKERSQLRKLIEALGGKYSKDLTKKTTHLICSSPE-GKKYRKA---KEWGIPVVSPDW 63 (63)
T ss_dssp -EEEEEE--B-TTTCCHHHHHHHCTT-EEESSSSTT-SEEEEES---HHHHHHH---HHCTSEEEEHHH
T ss_pred CEEEECC--CCHHHHHHHHHHHHHCCCEEeccccCCceEEEEeCCC-cHHHHHH---HHCCCcEECCCC
Confidence 3455543 3222245678999999999999999999999995543 2233222 223689999999
No 18
>PLN03123 poly [ADP-ribose] polymerase; Provisional
Probab=97.54 E-value=0.00017 Score=84.00 Aligned_cols=90 Identities=16% Similarity=0.344 Sum_probs=70.0
Q ss_pred CCCCCCCeEEEEecCCCcchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChH--HHHHHHHHhhhccCCcccccchHH
Q 010406 15 SNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEA--LLQQVSKQHLARFKGSVIRYQWLE 92 (511)
Q Consensus 15 ~~~~F~g~~iy~~~~~~g~~r~~~l~~~~~~~Gg~v~~~~s~~VTHVV~~~~s~--~~~~l~~~~~~~~~~~iV~~~Wl~ 92 (511)
....|.+++|.++++- +.. ..-|++.+..+||+|...+++.+||+|+...-. ..+..++. ..+.+||+.+||+
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 ESEFLGDLKVSIVGAS-KEK-VTEWKAKIEEAGGVFHATVKKDTNCLVVCGELDDEDAEMRKAR---RMKIPIVREDYLV 464 (981)
T ss_pred cCCCcCCeEEEEecCC-CCc-HHHHHHHHHhcCCEEeeeccCCceEEEccHHhhhcchHHHHHH---hcCCCcccHHHHH
Confidence 3467999999999874 323 377899999999999999999999999874211 12222222 2368999999999
Q ss_pred HHHhcCCCCCccccccc
Q 010406 93 DSLRLGEKVSEDLYRIK 109 (511)
Q Consensus 93 ecik~g~lvde~~y~l~ 109 (511)
||.+.+++++...|.+.
T Consensus 465 ds~~~~~~~p~~~y~~~ 481 (981)
T PLN03123 465 DCFKKKKKLPFDKYKLE 481 (981)
T ss_pred HHHhccccCcchhhhhc
Confidence 99999999999888664
No 19
>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=97.49 E-value=0.00014 Score=56.35 Aligned_cols=52 Identities=33% Similarity=0.588 Sum_probs=41.3
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHH
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (511)
++|.+|||||+.++.++.+. | +..++++.+.. .+.|.+|+|+|+++|++|.+
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 6 56678876532 23466999999999999976
No 20
>PLN03122 Poly [ADP-ribose] polymerase; Provisional
Probab=97.27 E-value=0.00055 Score=78.29 Aligned_cols=93 Identities=22% Similarity=0.304 Sum_probs=71.6
Q ss_pred CCCCCCCCCeEEEEecCCCcchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChH----HHHHHHHHhhhccCCccccc
Q 010406 13 LDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEA----LLQQVSKQHLARFKGSVIRY 88 (511)
Q Consensus 13 ~~~~~~F~g~~iy~~~~~~g~~r~~~l~~~~~~~Gg~v~~~~s~~VTHVV~~~~s~----~~~~l~~~~~~~~~~~iV~~ 88 (511)
..+...|.|++|.|.++--. +| ..+++++..+||+|+..+ .+.||+|+...+. ..+..++. ..+++||+.
T Consensus 184 ~~~~kpL~G~~fviTGtl~~-sr-~elK~~Ie~~GGkvsssV-s~~T~lIvt~~ev~k~gsSKlkkAk---~lgIpIVsE 257 (815)
T PLN03122 184 GAPGKPFSGMMISLSGRLSR-TH-QYWKKDIEKHGGKVANSV-EGVTCLVVSPAERERGGSSKIAEAM---ERGIPVVRE 257 (815)
T ss_pred cccCCCcCCcEEEEeCCCCC-CH-HHHHHHHHHcCCEEcccc-ccceEEEEcCccccccCccHHHHHH---HcCCcCccH
Confidence 34456799999999887433 44 678999999999999999 6788999865431 12222322 337899999
Q ss_pred chHHHHHhcCCCCCccccccccC
Q 010406 89 QWLEDSLRLGEKVSEDLYRIKLD 111 (511)
Q Consensus 89 ~Wl~ecik~g~lvde~~y~l~~~ 111 (511)
+||.+|++.++++++..|.+..+
T Consensus 258 d~L~d~i~~~k~~~~~~y~l~~~ 280 (815)
T PLN03122 258 AWLIDSIEKQEAQPLEAYDVVSD 280 (815)
T ss_pred HHHHHHHhcCCcccchhhhhccc
Confidence 99999999999999999988643
No 21
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=97.05 E-value=0.00082 Score=61.94 Aligned_cols=49 Identities=33% Similarity=0.595 Sum_probs=39.8
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHH-hCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHH
Q 010406 253 ADQVKGLPGIGKSMQDHIQEIVT-TGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (511)
Q Consensus 253 ~~~l~~lpgIG~~ia~kI~Eil~-tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (511)
.+||+.|||||++.|.+|.++-+ .|.+.-++ -|.+|.|||+++.++|-.
T Consensus 96 ~eeL~~lpgIG~~kA~aIi~yRe~~G~f~sv~------------dL~~v~GiG~~~~ekl~~ 145 (149)
T COG1555 96 AEELQALPGIGPKKAQAIIDYREENGPFKSVD------------DLAKVKGIGPKTLEKLKD 145 (149)
T ss_pred HHHHHHCCCCCHHHHHHHHHHHHHcCCCCcHH------------HHHhccCCCHHHHHHHHh
Confidence 47899999999999999999874 44454444 456999999999999854
No 22
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=97.01 E-value=0.001 Score=52.36 Aligned_cols=48 Identities=29% Similarity=0.627 Sum_probs=32.8
Q ss_pred cCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHH
Q 010406 257 KGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (511)
Q Consensus 257 ~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (511)
.+|||||+..|+.+.+ ++..++.+.+. ..+.|++|+||||++|+.+++
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 34456666543 456778999999999999875
No 23
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=97.00 E-value=0.0027 Score=71.87 Aligned_cols=133 Identities=17% Similarity=0.289 Sum_probs=86.3
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchh
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHS 331 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~Gi~tledL~~~~--~L~~~ 331 (511)
++|..|||+|++.+++|.+=++.-+-..| .+.+--| .|+|||+++|+.|.+. +.|+++|.++. .|...
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 EDLLGLEGFGEKSAQNLLDAIEKSKETSL--------ARFLYAL-GIRHVGEKAAKALARH-FGSLEALRAASEEELAAV 548 (665)
T ss_pred HHHhcCcCcchHHHHHHHHHHHHhhcCCH--------HHhhHhh-hccCcCHHHHHHHHHH-cCCHHHHHhCCHHHHhcc
Confidence 57899999999999999876653222222 2344455 9999999999998865 47899998653 57788
Q ss_pred hhhcccchhhhccCcCHHHHHH-HHHHHHHHhh-------hcCCCeEEEEcccee---ec--------------CCccCC
Q 010406 332 QRLGLKYFDDIKTRIPRHEVEQ-MERLLQKAGE-------EVLPEVIILCGGSYR---RG--------------KASCGD 386 (511)
Q Consensus 332 q~~Glk~~~d~~~~i~r~ea~~-~~~iv~~~~~-------~~~p~~~v~~~Gs~R---Rg--------------ke~~gD 386 (511)
.++|-+..+.|.+-+.-.+..+ +..+...-.. ..+.|..+++||.+. |. ...+..
T Consensus 549 ~GIG~~~A~sI~~ff~~~~~~~~i~~L~~~gv~~~~~~~~~~~~g~~~v~TG~l~~~~R~e~~~~i~~~G~~v~~sVs~k 628 (665)
T PRK07956 549 EGVGEVVAQSIVEFFAVEENRELIDELLEAGVNMEYKGEEVDLAGKTVVLTGTLEQLSRDEAKEKLEALGAKVSGSVSKK 628 (665)
T ss_pred CCcCHHHHHHHHHHHhhhhHHHHHHHHHHcCCCccccccCCCccccEEEEeCCCCCCCHHHHHHHHHHcCCEEeCcccCC
Confidence 8899888777766554433322 2333221010 013456788888873 22 345567
Q ss_pred eeEEEecCCc
Q 010406 387 LDVVIMHPDR 396 (511)
Q Consensus 387 vDiLit~~~~ 396 (511)
.|+||+.+..
T Consensus 629 t~~lv~G~~~ 638 (665)
T PRK07956 629 TDLVVAGEAA 638 (665)
T ss_pred CCEEEECCCC
Confidence 7888876544
No 24
>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=96.97 E-value=0.00095 Score=56.31 Aligned_cols=35 Identities=34% Similarity=0.353 Sum_probs=31.8
Q ss_pred hHHHHHHhcccCCCHHHHHHHHHhCCCCHHHHhhc
Q 010406 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (511)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~Gi~tledL~~~ 325 (511)
...+..|+.|||||+++|+.|+..||+|++||+..
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 44788899999999999999999999999999964
No 25
>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=96.94 E-value=0.0015 Score=57.95 Aligned_cols=50 Identities=30% Similarity=0.515 Sum_probs=40.4
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHHh-CCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHH
Q 010406 252 SADQVKGLPGIGKSMQDHIQEIVTT-GKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (511)
Q Consensus 252 s~~~l~~lpgIG~~ia~kI~Eil~t-G~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (511)
+.++|..|||||++.|.+|.++.+. |.+. .++.|.+|+|||++++.+|.+
T Consensus 66 ~~~eL~~lpGIG~~~A~~Ii~~R~~~g~f~------------s~eeL~~V~GIg~k~~~~i~~ 116 (120)
T TIGR01259 66 SLEELQALPGIGPAKAKAIIEYREENGAFK------------SVDDLTKVSGIGEKSLEKLKD 116 (120)
T ss_pred CHHHHhcCCCCCHHHHHHHHHHHHhcCCcC------------CHHHHHcCCCCCHHHHHHHHh
Confidence 3578999999999999999999864 4443 344556999999999999865
No 26
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=96.89 E-value=0.0015 Score=51.58 Aligned_cols=48 Identities=44% Similarity=0.669 Sum_probs=35.1
Q ss_pred chhhhcCCCCCCHHHHHHHHHHH-HhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHH
Q 010406 252 SADQVKGLPGIGKSMQDHIQEIV-TTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKL 311 (511)
Q Consensus 252 s~~~l~~lpgIG~~ia~kI~Eil-~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l 311 (511)
+.++|..+||||+..|+.|.++- ..|.+..+++| ..|+|+|+++..+|
T Consensus 12 s~~eL~~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL------------~~v~gi~~~~~~~l 60 (65)
T PF12836_consen 12 SAEELQALPGIGPKQAKAIVEYREKNGPFKSLEDL------------KEVPGIGPKTYEKL 60 (65)
T ss_dssp -HHHHHTSTT--HHHHHHHHHHHHHH-S-SSGGGG------------GGSTT--HHHHHHH
T ss_pred CHHHHHHcCCCCHHHHHHHHHHHHhCcCCCCHHHH------------hhCCCCCHHHHHHH
Confidence 46899999999999999999998 56777766655 48999999999887
No 27
>KOG2481 consensus Protein required for normal rRNA processing [RNA processing and modification]
Probab=96.81 E-value=0.00039 Score=74.02 Aligned_cols=88 Identities=17% Similarity=0.256 Sum_probs=64.5
Q ss_pred CCCCCCCCCCCeEEEEecCCCcchHHHHHHHHHHhcCCEEEee-c---------CCCccEEEEcCChHHHHHHHHHhhhc
Q 010406 11 PALDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEK-L---------SKKVTHVLAMDLEALLQQVSKQHLAR 80 (511)
Q Consensus 11 ~~~~~~~~F~g~~iy~~~~~~g~~r~~~l~~~~~~~Gg~v~~~-~---------s~~VTHVV~~~~s~~~~~l~~~~~~~ 80 (511)
..+....+|+||++|+.. .++ ++.|.-+|++.||.|.-+ + +..|||=|++-......+ +
T Consensus 320 ~~s~~kslF~glkFfl~r-eVP---resL~fiI~s~GG~V~wd~~~~g~~~~~~d~~ITH~IvDrP~~~~~v-----~-- 388 (570)
T KOG2481|consen 320 EQSSHKSLFSGLKFFLNR-EVP---RESLEFIIRSFGGKVSWDPLGIGATYDESDERITHQIVDRPGQQTSV-----I-- 388 (570)
T ss_pred hhhhHHHHhhcceeeeec-cCc---hHHHHHHHHHcCCceecCccCCCCcccccccceeeeeecccCcccee-----e--
Confidence 355667899999998854 333 366778899999999755 1 235899998654321111 1
Q ss_pred cCCcccccchHHHHHhcCCCCCcccccccc
Q 010406 81 FKGSVIRYQWLEDSLRLGEKVSEDLYRIKL 110 (511)
Q Consensus 81 ~~~~iV~~~Wl~ecik~g~lvde~~y~l~~ 110 (511)
+-..|.++||-||+.+|.+++.+.|.+..
T Consensus 389 -gR~YvQPQWvfDsvNar~llpt~~Y~~G~ 417 (570)
T KOG2481|consen 389 -GRTYVQPQWVFDSVNARLLLPTEKYFPGK 417 (570)
T ss_pred -eeeeecchhhhhhccchhhccHhhhCCCc
Confidence 23579999999999999999999998864
No 28
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=96.75 E-value=0.0051 Score=69.74 Aligned_cols=88 Identities=16% Similarity=0.294 Sum_probs=65.0
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchh
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHS 331 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~Gi~tledL~~~~--~L~~~ 331 (511)
+++..|+|+|++.+++|.+=++.-+-..|+ ..+--| +|+|||+++|++|.+ .+.|+++|..+. .|...
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 578999999999999987766543333333 244455 999999999999975 558899998653 47778
Q ss_pred hhhcccchhhhccCcCHHHH
Q 010406 332 QRLGLKYFDDIKTRIPRHEV 351 (511)
Q Consensus 332 q~~Glk~~~d~~~~i~r~ea 351 (511)
.++|.+..+.|.+-+.-.+.
T Consensus 566 ~GIG~k~A~sI~~ff~~~~n 585 (689)
T PRK14351 566 DDVGPTVAEEIREFFDSERN 585 (689)
T ss_pred CCcCHHHHHHHHHHHhhhHH
Confidence 88998888877666544443
No 29
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]
Probab=96.58 E-value=0.0036 Score=70.05 Aligned_cols=94 Identities=13% Similarity=0.188 Sum_probs=72.2
Q ss_pred CCCCCCCCCCeEEEEecCCCcchHHHHHHHHHHhcCCEEEeecCCCccEEEEc-CC-hHHHHHHHHHhhhccCCcccccc
Q 010406 12 ALDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAM-DL-EALLQQVSKQHLARFKGSVIRYQ 89 (511)
Q Consensus 12 ~~~~~~~F~g~~iy~~~~~~g~~r~~~l~~~~~~~Gg~v~~~~s~~VTHVV~~-~~-s~~~~~l~~~~~~~~~~~iV~~~ 89 (511)
.++...+|.|+-+++.+.....-+.+-|++.+..+||.++..+....||-|+. +. +-..+... +.+ ..-||.++
T Consensus 627 ~~~~s~if~gl~f~Vlsgt~~~~tk~~le~~ivenGG~iv~nv~p~~~~ci~~a~~et~~vk~~~---~~~-~cdVl~p~ 702 (881)
T KOG0966|consen 627 VAKISNIFDGLEFCVLSGTSETHTKAKLEEIIVENGGKIVQNVGPSDTLCIATAGKETTRVKAQA---IKR-SCDVLKPA 702 (881)
T ss_pred ccchhhhhcCeeEEEecCCcccccHHHHHHHHHHcCCEEEEcCCCCCcceEEeccccchHHHHHH---Hhc-cCceeeHH
Confidence 56667999999999998777666678899999999999999999989999962 22 22222222 222 56899999
Q ss_pred hHHHHHhcCCCCCccc-cccc
Q 010406 90 WLEDSLRLGEKVSEDL-YRIK 109 (511)
Q Consensus 90 Wl~ecik~g~lvde~~-y~l~ 109 (511)
||.+|.+-.++++..+ |.+.
T Consensus 703 Wlldcc~~~~l~p~~P~~~fh 723 (881)
T KOG0966|consen 703 WLLDCCKKQRLLPWLPRDLFH 723 (881)
T ss_pred HHHHHHhhhhccccccHHHHh
Confidence 9999999999999755 4443
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=96.52 E-value=0.0039 Score=59.82 Aligned_cols=53 Identities=15% Similarity=0.265 Sum_probs=37.8
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHH
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLY 312 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~ 312 (511)
..|.++||||+++|-.| |.+-...++.+.-. .+-...|++|||||+|||+++.
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 46899999999999888 44444444443322 2223457799999999999997
No 31
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=96.52 E-value=0.0038 Score=55.62 Aligned_cols=47 Identities=13% Similarity=0.200 Sum_probs=35.8
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHH
Q 010406 252 SADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (511)
Q Consensus 252 s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (511)
+..+++.+||||+..|++|. ..|-+.. ++.+.+|+|||+++.+.+-+
T Consensus 59 ~~~el~~lpGigP~~A~~IV---~nGpf~s------------veDL~~V~GIgekqk~~l~k 105 (132)
T PRK02515 59 SVRAFRQFPGMYPTLAGKIV---KNAPYDS------------VEDVLNLPGLSERQKELLEA 105 (132)
T ss_pred CHHHHHHCCCCCHHHHHHHH---HCCCCCC------------HHHHHcCCCCCHHHHHHHHH
Confidence 35789999999999999988 3554444 44455999999998777755
No 32
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=96.47 E-value=0.012 Score=52.45 Aligned_cols=67 Identities=22% Similarity=0.346 Sum_probs=44.0
Q ss_pred CCCCHHHHHHH--------HHHHHhCCchhhH-HHHhhc--h------hHHHHHHhcccCCCHHHHHHHHHhCCCCHHHH
Q 010406 260 PGIGKSMQDHI--------QEIVTTGKLSKLE-HFEKDE--K------VRTISLFGEVWGIGPATAQKLYEKGHRTLDDL 322 (511)
Q Consensus 260 pgIG~~ia~kI--------~Eil~tG~~~~le-~l~~~~--~------~~~l~lf~~I~GvGpktA~~l~~~Gi~tledL 322 (511)
||||+..+.+. .++++.|.-..-. .|..+. . ...+-.|.+|+|||+..|.-|.+.||+|+++|
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 67888777774 3455555433322 121111 1 11233456999999999999999999999999
Q ss_pred hhcc
Q 010406 323 KNED 326 (511)
Q Consensus 323 ~~~~ 326 (511)
....
T Consensus 81 A~~~ 84 (122)
T PF14229_consen 81 AQRN 84 (122)
T ss_pred HhCC
Confidence 8643
No 33
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=96.34 E-value=0.0039 Score=69.39 Aligned_cols=76 Identities=28% Similarity=0.372 Sum_probs=55.3
Q ss_pred chHHHHHHHHHHhcCCEEEeecCCCccEEEEc-CChH-HHHHHHHHhhhccCCcccccchHHHHHhcCCCCCcccccccc
Q 010406 33 NRRLQIWRQKLVQMGATVEEKLSKKVTHVLAM-DLEA-LLQQVSKQHLARFKGSVIRYQWLEDSLRLGEKVSEDLYRIKL 110 (511)
Q Consensus 33 ~~r~~~l~~~~~~~Gg~v~~~~s~~VTHVV~~-~~s~-~~~~l~~~~~~~~~~~iV~~~Wl~ecik~g~lvde~~y~l~~ 110 (511)
+...+.+..+++. ++...+.+.|||||+. +.+. ..+.++.......+.+|+++.|+.+||+++++|+|+.|-|.+
T Consensus 488 p~ek~~v~~~a~~---t~~k~~~~~~thvi~~~~~~g~c~rTlk~~~gil~gkwi~~~~w~~~s~k~~~~~~eepfEl~~ 564 (684)
T KOG4362|consen 488 PSEKQLVEKFAVD---TISKFWIEPVTHVIASTDLEGACLRTLKVLMGILRGKWILSYDWVLASLKLRKWVSEEPFELQI 564 (684)
T ss_pred cchHHHHHHHHHH---HHhhccCCCceeeeeecccccchhhhHHHHHHhhcCceeeeHHHHHHHHHhcCCCCCCCeeEee
Confidence 3456677777777 6777888999999984 3332 233333221222367899999999999999999999999987
Q ss_pred C
Q 010406 111 D 111 (511)
Q Consensus 111 ~ 111 (511)
+
T Consensus 565 d 565 (684)
T KOG4362|consen 565 D 565 (684)
T ss_pred c
Confidence 5
No 34
>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=96.31 E-value=0.0088 Score=47.56 Aligned_cols=50 Identities=22% Similarity=0.341 Sum_probs=39.6
Q ss_pred hhhhcC-CCCCCHHHHHHHHHHHH-hCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHh
Q 010406 253 ADQVKG-LPGIGKSMQDHIQEIVT-TGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (511)
Q Consensus 253 ~~~l~~-lpgIG~~ia~kI~Eil~-tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~ 314 (511)
.++|.. +||||...+..|.+... .|.+. .++.|.+|+|||.++++++++.
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 45443 4455668999999999999764
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=96.27 E-value=0.0036 Score=41.77 Aligned_cols=23 Identities=30% Similarity=0.546 Sum_probs=19.5
Q ss_pred cchhhhcCCCCCCHHHHHHHHHH
Q 010406 251 ESADQVKGLPGIGKSMQDHIQEI 273 (511)
Q Consensus 251 ~s~~~l~~lpgIG~~ia~kI~Ei 273 (511)
.+.++|.+|||||+++|+.|.+|
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 46789999999999999999875
No 36
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.27 E-value=0.0046 Score=59.48 Aligned_cols=52 Identities=17% Similarity=0.283 Sum_probs=37.8
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchh-hHHHHhhchhHHHHHHhcccCCCHHHHHHHH
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSK-LEHFEKDEKVRTISLFGEVWGIGPATAQKLY 312 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~-le~l~~~~~~~~l~lf~~I~GvGpktA~~l~ 312 (511)
..|.+++|||+++|-.|-.-+. ... .+.+. .+-.+.|++|||||+|||+++.
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 2235567899999999999964
No 37
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=96.17 E-value=0.0061 Score=58.57 Aligned_cols=54 Identities=19% Similarity=0.284 Sum_probs=38.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhH-HHHhhchhHHHHHHhcccCCCHHHHHHHHHh
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLE-HFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le-~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~ 314 (511)
..|..+||||+++|.+|.+... ...+. .+.+. -.+.|++|||||+|+|++++..
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 4688899999999999954432 23333 23332 2345679999999999999864
No 38
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.08 E-value=0.0077 Score=57.90 Aligned_cols=54 Identities=26% Similarity=0.404 Sum_probs=39.5
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHH
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (511)
..|.++.|||+++|=.|- .+-... ++..-...+-.+.|++|||||+|||+++.-
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 468899999999997765 333333 333333444577889999999999999964
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=96.06 E-value=0.004 Score=59.74 Aligned_cols=51 Identities=16% Similarity=0.212 Sum_probs=41.3
Q ss_pred hHHHHHHhcccCCCHHHHHHHHHhCCCCHHHHhh---c---cCcchhhhhcccchhhhc
Q 010406 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDIK 343 (511)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~Gi~tledL~~---~---~~L~~~q~~Glk~~~d~~ 343 (511)
...+.+|.+|+|||||+|..+ .+.-|+++|.. + ++|++++|||-|..+.|.
T Consensus 68 r~lF~~L~~V~GIGpK~Al~i--L~~~~~~el~~aI~~~d~~~L~~ipGiGkKtAerIi 124 (191)
T TIGR00084 68 RELFKELIKVNGVGPKLALAI--LSNMSPEEFVYAIETEEVKALVKIPGVGKKTAERLL 124 (191)
T ss_pred HHHHHHHhCCCCCCHHHHHHH--HhcCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHH
Confidence 346778889999999999999 55667888873 2 469999999999988764
No 40
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.00 E-value=0.0086 Score=57.05 Aligned_cols=54 Identities=19% Similarity=0.316 Sum_probs=39.3
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHH
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (511)
..|.++.|||+++|=.|- .+-...++-. -...+-.+.|++|||||+|||+++.-
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 33344567889999999999999964
No 41
>COG5163 NOP7 Protein required for biogenesis of the 60S ribosomal subunit [Translation, ribosomal structure and biogenesis]
Probab=95.99 E-value=0.0059 Score=63.31 Aligned_cols=87 Identities=20% Similarity=0.360 Sum_probs=63.0
Q ss_pred CCCCCCCCCCCeEEEEecCCCcchHHHHHHHHHHhcCCEEEeec-----------CCCccEEEEcCChHHHHHHHHHhhh
Q 010406 11 PALDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKL-----------SKKVTHVLAMDLEALLQQVSKQHLA 79 (511)
Q Consensus 11 ~~~~~~~~F~g~~iy~~~~~~g~~r~~~l~~~~~~~Gg~v~~~~-----------s~~VTHVV~~~~s~~~~~l~~~~~~ 79 (511)
+.++-..+|+|+++|+..--.+ ..|.-+|+..||.|..+. +..|||-|++.. .++. +..
T Consensus 343 ~~Ss~~slFS~f~FyisreVp~----dsLefiilscGG~V~~~p~~~~i~~~~~vD~~vth~i~drp--~~~~----kve 412 (591)
T COG5163 343 PCSSLKSLFSGFKFYISREVPG----DSLEFIILSCGGSVVGSPCEADIHVSEKVDEKVTHQIVDRP--VMKN----KVE 412 (591)
T ss_pred cCcchhhhhhceEEEEeccccc----hHHHHHHHHcCCcccCchhhccCCchhhccchhhhhhccch--hhhh----hhc
Confidence 3556679999999998653333 456678999999998642 235888887542 2111 111
Q ss_pred ccCCcccccchHHHHHhcCCCCCccccccc
Q 010406 80 RFKGSVIRYQWLEDSLRLGEKVSEDLYRIK 109 (511)
Q Consensus 80 ~~~~~iV~~~Wl~ecik~g~lvde~~y~l~ 109 (511)
+.-.+.++|+-|||..|.++..+.|.+.
T Consensus 413 --grtYiQPQw~fDsiNkG~l~~~~~Y~~G 440 (591)
T COG5163 413 --GRTYIQPQWLFDSINKGKLACVENYCVG 440 (591)
T ss_pred --ceeeechHHHHhhhccccchhhhhcccc
Confidence 3357899999999999999999999885
No 42
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=95.88 E-value=0.0028 Score=61.95 Aligned_cols=52 Identities=25% Similarity=0.500 Sum_probs=42.0
Q ss_pred HHhcccCCCHHHHHHHHHhCCCCHHHHhhcc--CcchhhhhcccchhhhccCcC
Q 010406 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIKTRIP 347 (511)
Q Consensus 296 lf~~I~GvGpktA~~l~~~Gi~tledL~~~~--~L~~~q~~Glk~~~d~~~~i~ 347 (511)
.|..|+|||++++++|++.||.|+++|..+. .|....++|.+..+.|...+.
T Consensus 4 ~L~~IpGIG~krakkLl~~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l~ 57 (232)
T PRK12766 4 ELEDISGVGPSKAEALREAGFESVEDVRAADQSELAEVDGIGNALAARIKADVG 57 (232)
T ss_pred ccccCCCcCHHHHHHHHHcCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHHhc
Confidence 4569999999999999999999999999764 577777888766666554443
No 43
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.84 E-value=0.0097 Score=57.69 Aligned_cols=54 Identities=17% Similarity=0.191 Sum_probs=39.8
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHH
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (511)
..|.++.|||+++|=.|-. +-...+ +..-...+-.+.|++|||||+|||+++.-
T Consensus 74 ~~Li~V~GIGpK~Al~iLs---~~~~~~---l~~aI~~~D~~~L~~ipGIGkKtAerIil 127 (203)
T PRK14602 74 IVLISISKVGAKTALAILS---QFRPDD---LRRLVAEEDVAALTRVSGIGKKTAQHIFL 127 (203)
T ss_pred HHHhCCCCcCHHHHHHHHh---hCCHHH---HHHHHHhCCHHHHhcCCCcCHHHHHHHHH
Confidence 4689999999999987653 333333 33333444577889999999999999964
No 44
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.79 E-value=0.012 Score=56.39 Aligned_cols=54 Identities=13% Similarity=0.128 Sum_probs=39.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHH
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (511)
..|.++.|||+++|=.|-. +-.. +++..-...+-.+.|++|||||+|||+++.-
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 4588999999999977653 3233 3333334445577889999999999999964
No 45
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.73 E-value=0.013 Score=56.57 Aligned_cols=54 Identities=15% Similarity=0.213 Sum_probs=39.0
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHH
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (511)
..|.++.|||+++|=.|- .+....++-+ -...+-.+.|++|||||+|||+++.-
T Consensus 72 ~~L~~V~GIGpK~AL~iL---s~~~~~~l~~---aI~~~D~~~L~kvpGIGkKtAerIil 125 (197)
T PRK14603 72 ELLLGVSGVGPKLALALL---SALPPALLAR---ALLEGDARLLTSASGVGKKLAERIAL 125 (197)
T ss_pred HHHhCcCCcCHHHHHHHH---cCCCHHHHHH---HHHhCCHHHHhhCCCCCHHHHHHHHH
Confidence 468899999999997654 4444444433 33344567888999999999999964
No 46
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.68 E-value=0.014 Score=56.29 Aligned_cols=54 Identities=20% Similarity=0.346 Sum_probs=39.5
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHH
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (511)
..|.++.|||+++|=.|- .+....++-. -...+-.+.|++|||||+|||+++.-
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 23344467889999999999999964
No 47
>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=95.54 E-value=0.012 Score=39.20 Aligned_cols=22 Identities=32% Similarity=0.477 Sum_probs=17.3
Q ss_pred HHHHHHhcccCCCHHHHHHHHH
Q 010406 292 RTISLFGEVWGIGPATAQKLYE 313 (511)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~ 313 (511)
..++.|++||||||+||..+..
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 3567778999999999998763
No 48
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=95.38 E-value=0.0075 Score=68.31 Aligned_cols=52 Identities=21% Similarity=0.287 Sum_probs=43.7
Q ss_pred hcccCCCHHHHHHHHHh-CCCCHHHHhh--ccCcchhhhhcccchhhhccCcCHH
Q 010406 298 GEVWGIGPATAQKLYEK-GHRTLDDLKN--EDSLTHSQRLGLKYFDDIKTRIPRH 349 (511)
Q Consensus 298 ~~I~GvGpktA~~l~~~-Gi~tledL~~--~~~L~~~q~~Glk~~~d~~~~i~r~ 349 (511)
++|+|+||+++++||++ +|++++||.. .++|..+.+||-|..+.|.+.|-..
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 38999999999999998 7899999984 3468888999999999887655443
No 49
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=95.25 E-value=0.015 Score=53.70 Aligned_cols=52 Identities=27% Similarity=0.507 Sum_probs=41.3
Q ss_pred hhHHHHHHhcccCCCHHHHHHHHH---h-C-CCCHHHHhhccCcchhhhhcccchhhhccCcC
Q 010406 290 KVRTISLFGEVWGIGPATAQKLYE---K-G-HRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIP 347 (511)
Q Consensus 290 ~~~~l~lf~~I~GvGpktA~~l~~---~-G-i~tledL~~~~~L~~~q~~Glk~~~d~~~~i~ 347 (511)
.....+.|..+||||+++|+++.+ + | |+|++||.+ .+++|-+.++.+..+|.
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 344556668999999999999986 2 4 899999986 46899998888876653
No 50
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=95.23 E-value=0.054 Score=60.48 Aligned_cols=15 Identities=20% Similarity=0.189 Sum_probs=11.4
Q ss_pred cCCeeEEEecCCcch
Q 010406 384 CGDLDVVIMHPDRKS 398 (511)
Q Consensus 384 ~gDvDiLit~~~~~~ 398 (511)
+.-.|+||+-++..+
T Consensus 630 SkktD~vvaG~~aGS 644 (667)
T COG0272 630 SKKTDYVVAGENAGS 644 (667)
T ss_pred cccccEEEEcCCCCh
Confidence 455699998888776
No 51
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]
Probab=95.03 E-value=0.056 Score=60.84 Aligned_cols=91 Identities=21% Similarity=0.313 Sum_probs=61.2
Q ss_pred CCCCCCeEEEEecCCCcchHHHHHHHHHHhcCCEEEeecC------CCccEEEEc--CChHH-HHHHHHHhhhccCCccc
Q 010406 16 NGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLS------KKVTHVLAM--DLEAL-LQQVSKQHLARFKGSVI 86 (511)
Q Consensus 16 ~~~F~g~~iy~~~~~~g~~r~~~l~~~~~~~Gg~v~~~~s------~~VTHVV~~--~~s~~-~~~l~~~~~~~~~~~iV 86 (511)
...|..+++|.+.++.=.+.-.+..-.+...|++|++.-+ ..+||+|+. +.+-. .....+..+.. +-+||
T Consensus 782 ~~~~~~~~~f~~~~~~~~se~~~~~l~~k~~g~~i~~~~~~~~~~~~~~t~~v~~~i~~~h~~~~~~~~~~lt~-~rkv~ 860 (881)
T KOG0966|consen 782 SLFLSSLRMFYVLRRKLSSEEVIIELKLKNFGGRITDAQSECNNIGAKYTHCVLRCIDEDHEKIKEQKKASLTI-KRKVV 860 (881)
T ss_pred ccccccceeeecccccccHHHHHHHHHHHHhcceeeeccchhhhcccceeeeeeeecchHHHHHHHHHHHHhcc-ccccc
Confidence 3567778888777765444445555556666999997653 468999985 33222 22222222222 22899
Q ss_pred ccchHHHHHhcCCCCCccccc
Q 010406 87 RYQWLEDSLRLGEKVSEDLYR 107 (511)
Q Consensus 87 ~~~Wl~ecik~g~lvde~~y~ 107 (511)
..+||.+|+.++.+++|+.|.
T Consensus 861 ~~~wv~~s~~~~~~~~e~~~~ 881 (881)
T KOG0966|consen 861 APSWVDHSINENCLLPEEDFP 881 (881)
T ss_pred CHHHHHHhhcccccCccccCC
Confidence 999999999999999999884
No 52
>PRK14973 DNA topoisomerase I; Provisional
Probab=95.03 E-value=0.023 Score=66.58 Aligned_cols=90 Identities=19% Similarity=0.162 Sum_probs=59.1
Q ss_pred hhhcCCCCCCHHHHHHHHHHHH-h-CCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccc
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVT-T-GKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLT 329 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~-t-G~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~Gi~tledL~~~~--~L~ 329 (511)
++|..+|||...+.......+. . +.-..-...+.....+.-+ |..|.|||++|+.+++..|+.|.+||.+++ +|+
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 5677888888776666644443 1 1111111111111112223 459999999999999999999999999874 577
Q ss_pred hhhhhcccchhhhcc
Q 010406 330 HSQRLGLKYFDDIKT 344 (511)
Q Consensus 330 ~~q~~Glk~~~d~~~ 344 (511)
..-+++.+....|..
T Consensus 914 ~~~~i~~k~~~~~~~ 928 (936)
T PRK14973 914 KVTGIDEKKLRNLQA 928 (936)
T ss_pred hhcCCCHHHHHHHHH
Confidence 777888887777654
No 53
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=94.97 E-value=0.054 Score=61.37 Aligned_cols=86 Identities=14% Similarity=0.214 Sum_probs=63.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHhCCCCHHHHhhc--------
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE-------- 325 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~Gi~tledL~~~-------- 325 (511)
++|.+|+|+|++.+++|.+=++.-+-..|+ ..|--| +|++||.++|+.|-+..+.|++.|.+.
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 688999999999998887755533322232 345566 899999999999987788999988752
Q ss_pred cCcchhhhhcccchhhhccCcCH
Q 010406 326 DSLTHSQRLGLKYFDDIKTRIPR 348 (511)
Q Consensus 326 ~~L~~~q~~Glk~~~d~~~~i~r 348 (511)
..|..+.+||-+..+.|.+-+.-
T Consensus 541 e~l~~i~giG~~~a~si~~ff~~ 563 (669)
T PRK14350 541 SKLLKIKGIGEKIALNIIEAFND 563 (669)
T ss_pred HHHhhCCCccHHHHHHHHHHHcC
Confidence 14777888897777777655533
No 54
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=94.96 E-value=0.03 Score=54.10 Aligned_cols=54 Identities=19% Similarity=0.265 Sum_probs=40.5
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHH
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (511)
..|.++.|||+++|=.| |.+....++-.. ...+-...|+++||||+|||+++.-
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 455455554443 3344467889999999999999974
No 55
>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=94.88 E-value=0.012 Score=66.56 Aligned_cols=63 Identities=24% Similarity=0.383 Sum_probs=47.7
Q ss_pred hcccCCCHHHHHHHHHh-CCCCHHHHhh--ccCcchhhhhcccchhhhccCcCHHHHHHHHHHHHH
Q 010406 298 GEVWGIGPATAQKLYEK-GHRTLDDLKN--EDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQK 360 (511)
Q Consensus 298 ~~I~GvGpktA~~l~~~-Gi~tledL~~--~~~L~~~q~~Glk~~~d~~~~i~r~ea~~~~~iv~~ 360 (511)
++|+|+|++++++||++ +|++++||.. .++|..+.+||-+..+.|.+.|-...-..+..++..
T Consensus 435 l~I~GLG~k~i~~L~~~g~I~~~~Dl~~L~~~~L~~L~GfG~Ksa~nIl~~Ie~sk~~~l~r~L~a 500 (652)
T TIGR00575 435 MDIEGLGDKVIEQLFEKKLVRSVADLYALKKEDLLELEGFGEKSAQNLLNAIEKSKEKPLARLLFA 500 (652)
T ss_pred cCCCCcCHHHHHHHHHcCCcCCHHHHHhcCHHHHhhccCccHHHHHHHHHHHHHhccCcHHHHHhh
Confidence 47999999999999998 6899999984 356888899999999888765544333333344333
No 56
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.87 E-value=0.029 Score=53.65 Aligned_cols=53 Identities=13% Similarity=0.096 Sum_probs=37.9
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHH
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (511)
..|.++.|||+++|=.|- .+-...++-.. ...+-.+.| +|||||+|||+++.-
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 468999999999997654 44444444332 233345677 999999999999964
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=94.81 E-value=0.028 Score=49.88 Aligned_cols=50 Identities=26% Similarity=0.460 Sum_probs=39.0
Q ss_pred hHHHHHHhcccCCCHHHHHHHHHh-----CCCCHHHHhhccCcchhhhhcccchhhhccCc
Q 010406 291 VRTISLFGEVWGIGPATAQKLYEK-----GHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRI 346 (511)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~-----Gi~tledL~~~~~L~~~q~~Glk~~~d~~~~i 346 (511)
.-..+.|+.|||||+++|+++++. ++.|++||.+ ..++|.+.++.|...+
T Consensus 64 tA~~~eL~~lpGIG~~~A~~Ii~~R~~~g~f~s~eeL~~------V~GIg~k~~~~i~~~l 118 (120)
T TIGR01259 64 AASLEELQALPGIGPAKAKAIIEYREENGAFKSVDDLTK------VSGIGEKSLEKLKDYA 118 (120)
T ss_pred cCCHHHHhcCCCCCHHHHHHHHHHHHhcCCcCCHHHHHc------CCCCCHHHHHHHHhce
Confidence 335667779999999999999974 5899999964 5678888887776543
No 58
>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=94.77 E-value=0.048 Score=40.48 Aligned_cols=28 Identities=29% Similarity=0.458 Sum_probs=23.3
Q ss_pred cCCCeEEEEccceeecCC-ccCCeeEEEe
Q 010406 365 VLPEVIILCGGSYRRGKA-SCGDLDVVIM 392 (511)
Q Consensus 365 ~~p~~~v~~~Gs~RRgke-~~gDvDiLit 392 (511)
..+...+.+.|||.||.. ..+|||+++.
T Consensus 14 ~~~~~~v~lfGS~arg~~~~~SDIDi~v~ 42 (49)
T cd05397 14 LVPGYEIVVYGSLVRGLLKKSSDIDLACV 42 (49)
T ss_pred hcCCcEEEEECCcCCCCCCCCCCEEEEEE
Confidence 345668999999999977 6789999986
No 59
>PRK02362 ski2-like helicase; Provisional
Probab=94.70 E-value=0.025 Score=65.17 Aligned_cols=57 Identities=25% Similarity=0.401 Sum_probs=43.3
Q ss_pred HHHhhchhHHHHHHhcccCCCHHHHHHHHHhCCCCHHHHhhc--cCcchhhhhcccchhhhc
Q 010406 284 HFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDIK 343 (511)
Q Consensus 284 ~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~Gi~tledL~~~--~~L~~~q~~Glk~~~d~~ 343 (511)
.+....+...+.|+ +|||||+++|+++|+.||+|++||... .+|..+ ||-+..+.+.
T Consensus 642 ~l~~gv~~~~~~L~-~ip~i~~~~a~~l~~~gi~s~~dl~~~~~~~l~~~--~g~~~~~~i~ 700 (737)
T PRK02362 642 RVEYGVREELLDLV-GLRGVGRVRARRLYNAGIESRADLRAADKSVVLAI--LGEKIAENIL 700 (737)
T ss_pred HHHhCCCHHHHHHh-CCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHHH--HCHHHHHHHH
Confidence 34556666678887 999999999999999999999999953 345555 6766655443
No 60
>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=94.69 E-value=0.019 Score=38.84 Aligned_cols=20 Identities=45% Similarity=0.790 Sum_probs=16.1
Q ss_pred HhcccCCCHHHHHHHHHhCC
Q 010406 297 FGEVWGIGPATAQKLYEKGH 316 (511)
Q Consensus 297 f~~I~GvGpktA~~l~~~Gi 316 (511)
+..+||||++|+++|.+.||
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 36899999999999988886
No 61
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=94.41 E-value=0.049 Score=48.68 Aligned_cols=32 Identities=22% Similarity=0.380 Sum_probs=28.4
Q ss_pred HHHHHhcccCCCHHHHHHHHHh-CCCCHHHHhh
Q 010406 293 TISLFGEVWGIGPATAQKLYEK-GHRTLDDLKN 324 (511)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~-Gi~tledL~~ 324 (511)
..+.|.++|||||++|+++.+. .++|+|||.+
T Consensus 59 ~~~el~~lpGigP~~A~~IV~nGpf~sveDL~~ 91 (132)
T PRK02515 59 SVRAFRQFPGMYPTLAGKIVKNAPYDSVEDVLN 91 (132)
T ss_pred CHHHHHHCCCCCHHHHHHHHHCCCCCCHHHHHc
Confidence 4566779999999999999987 5999999986
No 62
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.29 E-value=0.022 Score=54.89 Aligned_cols=52 Identities=19% Similarity=0.255 Sum_probs=40.6
Q ss_pred hHHHHHHhcccCCCHHHHHHHHHh-CCCCHHHHh-hc--cCcchhhhhcccchhhh
Q 010406 291 VRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLK-NE--DSLTHSQRLGLKYFDDI 342 (511)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~-Gi~tledL~-~~--~~L~~~q~~Glk~~~d~ 342 (511)
...+++|.+|.|||||+|..+... +...|-+.. +. ..|++.+|+|-|..+.|
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 457888899999999999999996 766643332 32 36999999999987764
No 63
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=94.26 E-value=0.026 Score=54.25 Aligned_cols=51 Identities=24% Similarity=0.275 Sum_probs=38.9
Q ss_pred HHHHHhcccCCCHHHHHHHHHh-CCCCHHHHhhcc---Ccchhhhhcccchhhhc
Q 010406 293 TISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED---SLTHSQRLGLKYFDDIK 343 (511)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~-Gi~tledL~~~~---~L~~~q~~Glk~~~d~~ 343 (511)
.+..|..|+|||||+|.++.+. |..++.+....+ .|+..+|+|.+..+.|.
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 3656779999999999999987 887776544332 58888888888766553
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=94.20 E-value=0.054 Score=43.00 Aligned_cols=45 Identities=18% Similarity=0.268 Sum_probs=34.9
Q ss_pred HHHhc-ccCCCHHHHHHHHHh-----CCCCHHHHhhccCcchhhhhcccchhhhccC
Q 010406 295 SLFGE-VWGIGPATAQKLYEK-----GHRTLDDLKNEDSLTHSQRLGLKYFDDIKTR 345 (511)
Q Consensus 295 ~lf~~-I~GvGpktA~~l~~~-----Gi~tledL~~~~~L~~~q~~Glk~~~d~~~~ 345 (511)
+.|.. ++|||+++|+++.+. ++++++||.+ ..++|.+.++.+...
T Consensus 16 ~~L~~~ipgig~~~a~~Il~~R~~~g~~~s~~dL~~------v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 16 EELQRAMNGVGLKKAEAIVSYREEYGPFKTVEDLKQ------VPGIGNSLVEKNLAV 66 (69)
T ss_pred HHHHhHCCCCCHHHHHHHHHHHHHcCCcCCHHHHHc------CCCCCHHHHHHHHhh
Confidence 34557 999999999999975 5999999975 457777777766543
No 65
>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=94.05 E-value=0.049 Score=63.32 Aligned_cols=69 Identities=23% Similarity=0.356 Sum_probs=53.5
Q ss_pred HHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCCcccccchHHHHHhcCCCCCccccccc
Q 010406 37 QIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSLRLGEKVSEDLYRIK 109 (511)
Q Consensus 37 ~~l~~~~~~~Gg~v~~~~s~~VTHVV~~~~s~~~~~l~~~~~~~~~~~iV~~~Wl~ecik~g~lvde~~y~l~ 109 (511)
.-+++.+++.|++++... ...||+|+..--+..+.+.+- ..+..||+..||.+|.++|..+|++.|.+.
T Consensus 671 ~~~k~~~k~lg~s~~ss~-~e~Th~i~~rirRT~k~Leai---~~G~~ivT~~wL~s~~k~g~~~dek~yil~ 739 (896)
T KOG2043|consen 671 KNYKLAKKFLGGSVASSD-SEATHFIADRIRRTLKFLEAI---SSGKPLVTPQWLVSSLKSGEKLDEKPYILH 739 (896)
T ss_pred hhhhhHHhhccceeeccc-ccceeeeehhhhccHHHHhhh---ccCCcccchHHHHHHhhccccccCcccccc
Confidence 336788899998888775 468999998554444444321 236789999999999999999999999985
No 66
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=93.98 E-value=0.046 Score=42.99 Aligned_cols=48 Identities=29% Similarity=0.528 Sum_probs=33.2
Q ss_pred HHHHHhcccCCCHHHHHHHHH---h--CCCCHHHHhhccCcchhhhhcccchhhhccCc
Q 010406 293 TISLFGEVWGIGPATAQKLYE---K--GHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRI 346 (511)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~---~--Gi~tledL~~~~~L~~~q~~Glk~~~d~~~~i 346 (511)
..+.|.++||||++.|+++++ + +++|++||.. ..++|.+.|+.+...+
T Consensus 12 s~~eL~~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL~~------v~gi~~~~~~~l~~~l 64 (65)
T PF12836_consen 12 SAEELQALPGIGPKQAKAIVEYREKNGPFKSLEDLKE------VPGIGPKTYEKLKPYL 64 (65)
T ss_dssp -HHHHHTSTT--HHHHHHHHHHHHHH-S-SSGGGGGG------STT--HHHHHHHCCCE
T ss_pred CHHHHHHcCCCCHHHHHHHHHHHHhCcCCCCHHHHhh------CCCCCHHHHHHHHhhc
Confidence 566777999999999999985 2 7899999986 4677777777776543
No 67
>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=93.97 E-value=0.22 Score=43.10 Aligned_cols=58 Identities=26% Similarity=0.438 Sum_probs=44.3
Q ss_pred HHHHHHHHhhhcCCCeEEEEccceeecC-CccCCeeEEEecCCc-chhhhHHHHHHHHHHHhcc
Q 010406 354 MERLLQKAGEEVLPEVIILCGGSYRRGK-ASCGDLDVVIMHPDR-KSHKGFLSKYVKKLKEMKF 415 (511)
Q Consensus 354 ~~~iv~~~~~~~~p~~~v~~~Gs~RRgk-e~~gDvDiLit~~~~-~~~~~~l~~~v~~l~~~g~ 415 (511)
++.++++ ..|++.+.+-||++.|. ...+|||+.|..++. .....++..+-+.|++.+.
T Consensus 9 l~~~i~~----~~~~~~v~~fGS~~~g~~~~~SDiDl~i~~~~~~~~~~~~l~~l~~~l~~~~~ 68 (114)
T cd05402 9 LQELIKE----WFPGAKLYPFGSYVTGLGLPGSDIDLCLLGPNHRVDREDFLRKLAKLLKKSGE 68 (114)
T ss_pred HHHHHHH----HCCCCEEEEecccccCCCCCCCCeeEEEEeCCCCccHHHHHHHHHHHHHhCCC
Confidence 4555554 57899999999999984 346899999998876 4456777888888877774
No 68
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=93.60 E-value=0.048 Score=42.86 Aligned_cols=44 Identities=27% Similarity=0.341 Sum_probs=29.7
Q ss_pred cccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhhcccchhhhc
Q 010406 299 EVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIK 343 (511)
Q Consensus 299 ~I~GvGpktA~~l~~~Gi~tledL~~~~--~L~~~q~~Glk~~~d~~ 343 (511)
+|+|||+++|+.|.+ .+.|++.|.++. .|....++|.+..+.+.
T Consensus 7 GI~~VG~~~ak~L~~-~f~sl~~l~~a~~e~L~~i~gIG~~~A~si~ 52 (64)
T PF12826_consen 7 GIPGVGEKTAKLLAK-HFGSLEALMNASVEELSAIPGIGPKIAQSIY 52 (64)
T ss_dssp TSTT--HHHHHHHHH-CCSCHHHHCC--HHHHCTSTT--HHHHHHHH
T ss_pred CCCCccHHHHHHHHH-HcCCHHHHHHcCHHHHhccCCcCHHHHHHHH
Confidence 999999999999975 455999999653 57777788866655543
No 69
>KOG1929 consensus Nucleotide excision repair factor NEF2, RAD4/CUT5 component [Replication, recombination and repair]
Probab=93.45 E-value=0.085 Score=60.53 Aligned_cols=94 Identities=11% Similarity=0.170 Sum_probs=71.3
Q ss_pred CCCCCCCCCCeEEEEecCCCcchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCCcccccchH
Q 010406 12 ALDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWL 91 (511)
Q Consensus 12 ~~~~~~~F~g~~iy~~~~~~g~~r~~~l~~~~~~~Gg~v~~~~s~~VTHVV~~~~s~~~~~l~~~~~~~~~~~iV~~~Wl 91 (511)
..-.-..|.+|++++... .-.+++.|.+.+...|+.+...+....||||........... ...+...+|+++||
T Consensus 487 ~~~l~~~~e~~~~~~s~~--~~~~~e~ln~~~~~~gas~~~~f~r~~~~l~~~~~k~s~~~~----~~kw~ip~vT~~wL 560 (811)
T KOG1929|consen 487 AAALSQPFENLTISNSQS--AEAEREKLNNLANDLGASNVKTFTRKSTTLLTTSAKGSKYEI----AGKWSIPIVTPDWL 560 (811)
T ss_pred hhcccccccCceEEeeec--hHHHHHHHhHhhhhccccccceeeecccEEeccccccchhhh----ccccCCCccChhHH
Confidence 344457799999998543 335679999999999999999997766999986522111111 22346789999999
Q ss_pred HHHHhcCCCCCccccccccC
Q 010406 92 EDSLRLGEKVSEDLYRIKLD 111 (511)
Q Consensus 92 ~ecik~g~lvde~~y~l~~~ 111 (511)
.+|.++++.++.+.|.....
T Consensus 561 ~e~~rq~~~~~~e~~l~~~s 580 (811)
T KOG1929|consen 561 YECVRQNKGERNEGFLNGNS 580 (811)
T ss_pred HhhccccCcccceeeccccc
Confidence 99999999999999988643
No 70
>KOG1929 consensus Nucleotide excision repair factor NEF2, RAD4/CUT5 component [Replication, recombination and repair]
Probab=93.33 E-value=0.14 Score=58.74 Aligned_cols=89 Identities=18% Similarity=0.216 Sum_probs=68.7
Q ss_pred CCCCCeEEEEecCCCcchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCCcccccchHHHHHh
Q 010406 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSLR 96 (511)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~r~~~l~~~~~~~Gg~v~~~~s~~VTHVV~~~~s~~~~~l~~~~~~~~~~~iV~~~Wl~ecik 96 (511)
..|.+|.|.. +|+...++.-+++++-.|||.....++..|+||+.-......++.. ...+..++|+.+|+.+||.
T Consensus 102 p~~~~~~Vc~--tgl~~~eK~ei~~~v~k~gg~~~~~L~s~v~~~~~~~~~~~~kYe~---al~wn~~v~~~~w~~~s~~ 176 (811)
T KOG1929|consen 102 PGFFGLKVCL--TGLSGDEKSEIKILVPKHGGTLHRSLSSDVNSLKILPEVKTEKYEQ---ALKWNIPVVSDDWLFDSIE 176 (811)
T ss_pred CcccceEEEe--cccchHHHHHHHHHhhhcccEEehhhhhhhheeeeccccchHHHHH---HHhhCCccccHHHHhhhhc
Confidence 4567777766 5665555677889999999999999999999999865433222222 2233678999999999999
Q ss_pred cCCCCCcccccccc
Q 010406 97 LGEKVSEDLYRIKL 110 (511)
Q Consensus 97 ~g~lvde~~y~l~~ 110 (511)
.+..+++..|.+..
T Consensus 177 ~~~~~~~~~~e~~~ 190 (811)
T KOG1929|consen 177 KTAVLETKPYEGAP 190 (811)
T ss_pred cccccccccccccc
Confidence 99999999998865
No 71
>PRK00254 ski2-like helicase; Provisional
Probab=93.27 E-value=0.11 Score=59.83 Aligned_cols=67 Identities=25% Similarity=0.410 Sum_probs=47.7
Q ss_pred hCCchhhHHH----HhhchhHHHHHHhcccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhhcccchhhhc
Q 010406 276 TGKLSKLEHF----EKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIK 343 (511)
Q Consensus 276 tG~~~~le~l----~~~~~~~~l~lf~~I~GvGpktA~~l~~~Gi~tledL~~~~--~L~~~q~~Glk~~~d~~ 343 (511)
.|.+..+.++ ....+...+.|. +|||+|+++|+++|+.|+.|++||..+. .|....++|.+..+.+.
T Consensus 623 ~~~~~~l~~l~~rl~~g~~~~~~~L~-~ipgig~~~~~~l~~~g~~s~~~i~~a~~~el~~~~gi~~~~a~~i~ 695 (720)
T PRK00254 623 QEVLDYLETLHLRVKHGVREELLELM-RLPMIGRKRARALYNAGFRSIEDIVNAKPSELLKVEGIGAKIVEGIF 695 (720)
T ss_pred hhHHHHHHHHHHHHHcCCCHHHhhhh-cCCCCCHHHHHHHHHccCCCHHHHHhCCHHHHhcCCCCCHHHHHHHH
Confidence 3444444433 344455556666 9999999999999999999999998653 57777777766655443
No 72
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=93.06 E-value=0.14 Score=50.25 Aligned_cols=54 Identities=24% Similarity=0.435 Sum_probs=41.5
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHh
Q 010406 253 ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (511)
Q Consensus 253 ~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~ 314 (511)
++.|.+|||||+..+.++ ++.| +.-++.+... ..+.|..|+|||.++|.++++.
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 356889999999988876 4555 5666666543 2445679999999999999986
No 73
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.58 E-value=0.055 Score=51.57 Aligned_cols=50 Identities=20% Similarity=0.255 Sum_probs=38.5
Q ss_pred hHHHHHHhcccCCCHHHHHHHHHhCCCCHHHHhh---c---cCcchhhhhcccchhhh
Q 010406 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDI 342 (511)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~Gi~tledL~~---~---~~L~~~q~~Glk~~~d~ 342 (511)
...+++|.+|.|||||+|-.+... -+.++|.. . ..|++.+|+|-|..+.|
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 457888999999999999988764 25555552 2 35899999999987754
No 74
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.58 E-value=0.063 Score=51.44 Aligned_cols=52 Identities=21% Similarity=0.245 Sum_probs=38.5
Q ss_pred hHHHHHHhcccCCCHHHHHHHHHh-CCCCHHHHhhc---cCcchhhhhcccchhhh
Q 010406 291 VRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNE---DSLTHSQRLGLKYFDDI 342 (511)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~-Gi~tledL~~~---~~L~~~q~~Glk~~~d~ 342 (511)
...+++|.+|.|||||+|-.+... ....+-+.... ..|++.+|+|-|..+.|
T Consensus 69 r~lF~~Li~V~GIGpK~AL~iLs~~~~~el~~aI~~~D~~~L~~vpGIGkKtAerI 124 (188)
T PRK14606 69 KELFLSLTKVSRLGPKTALKIISNEDAETLVTMIASQDVEGLSKLPGISKKTAERI 124 (188)
T ss_pred HHHHHHHhccCCccHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHH
Confidence 447888899999999999999764 44433333322 25899999999987754
No 75
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.39 E-value=0.06 Score=51.98 Aligned_cols=50 Identities=28% Similarity=0.308 Sum_probs=38.8
Q ss_pred hHHHHHHhcccCCCHHHHHHHHHhCCCCHHHHhh---c---cCcchhhhhcccchhhh
Q 010406 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDI 342 (511)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~Gi~tledL~~---~---~~L~~~q~~Glk~~~d~ 342 (511)
...+++|.+|.|||||+|-.+... -|.++|.. . ..|++.+|+|-|..+.|
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 447888899999999999999774 25555553 2 35899999999987754
No 76
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.15 E-value=0.072 Score=51.66 Aligned_cols=52 Identities=23% Similarity=0.263 Sum_probs=38.8
Q ss_pred hHHHHHHhcccCCCHHHHHHHHHh-CCCCHHHHhhc---cCcchhhhhcccchhhh
Q 010406 291 VRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNE---DSLTHSQRLGLKYFDDI 342 (511)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~-Gi~tledL~~~---~~L~~~q~~Glk~~~d~ 342 (511)
...+++|.+|.|||||+|..+... +...|-+.... ..|++++|+|-|..+.|
T Consensus 70 r~lF~~Li~V~GIGpK~Al~iLs~~~~~~l~~aI~~~D~~~L~~ipGIGkKtAerI 125 (203)
T PRK14602 70 RQTFIVLISISKVGAKTALAILSQFRPDDLRRLVAEEDVAALTRVSGIGKKTAQHI 125 (203)
T ss_pred HHHHHHHhCCCCcCHHHHHHHHhhCCHHHHHHHHHhCCHHHHhcCCCcCHHHHHHH
Confidence 347888889999999999999875 44433333322 35899999999987754
No 77
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.00 E-value=0.07 Score=51.41 Aligned_cols=50 Identities=28% Similarity=0.359 Sum_probs=39.2
Q ss_pred hHHHHHHhcccCCCHHHHHHHHHhCCCCHHHHhh---c---cCcchhhhhcccchhhh
Q 010406 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDI 342 (511)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~Gi~tledL~~---~---~~L~~~q~~Glk~~~d~ 342 (511)
...+++|.+|.|||||+|-.+... -|.++|.. . ..|++++|+|.|..+.|
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 447888899999999999999874 25666653 2 35999999999987754
No 78
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=91.74 E-value=0.094 Score=50.49 Aligned_cols=50 Identities=18% Similarity=0.318 Sum_probs=38.6
Q ss_pred hHHHHHHhcccCCCHHHHHHHHHhCCCCHHHHhh---c---cCcchhhhhcccchhhh
Q 010406 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDI 342 (511)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~Gi~tledL~~---~---~~L~~~q~~Glk~~~d~ 342 (511)
...+++|.+|.|||||+|-.+... -+.++|.. . ..|++.+|+|-|..+.|
T Consensus 68 r~lF~~LisVsGIGPK~ALaILs~--~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRI 123 (196)
T PRK13901 68 REVFEELIGVDGIGPRAALRVLSG--IKYNEFRDAIDREDIELISKVKGIGNKMAGKI 123 (196)
T ss_pred HHHHHHHhCcCCcCHHHHHHHHcC--CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHH
Confidence 457888889999999999999764 35556653 2 35899999999987654
No 79
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=91.36 E-value=0.14 Score=32.78 Aligned_cols=19 Identities=47% Similarity=0.607 Sum_probs=16.3
Q ss_pred HHhcccCCCHHHHHHHHHh
Q 010406 296 LFGEVWGIGPATAQKLYEK 314 (511)
Q Consensus 296 lf~~I~GvGpktA~~l~~~ 314 (511)
.|++|+|||+++|+++.+.
T Consensus 2 ~L~~i~GiG~k~A~~il~~ 20 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEA 20 (26)
T ss_pred hhhhCCCCCHHHHHHHHHh
Confidence 3569999999999999863
No 80
>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=91.06 E-value=0.6 Score=53.74 Aligned_cols=83 Identities=20% Similarity=0.350 Sum_probs=63.2
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHh-CCCCHHHHhhcc-Ccc-
Q 010406 253 ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED-SLT- 329 (511)
Q Consensus 253 ~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~-Gi~tledL~~~~-~L~- 329 (511)
.+.|..+||||++.+++|.+-+.. .. ....++..| .=+|++++.|.++|+. |-.+++.|+++. +|.
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 467899999999999999876632 11 122355555 8999999999999998 999999998764 555
Q ss_pred hhhhhcccchhhhccCc
Q 010406 330 HSQRLGLKYFDDIKTRI 346 (511)
Q Consensus 330 ~~q~~Glk~~~d~~~~i 346 (511)
...++|++..+.|..++
T Consensus 185 ~i~gigF~~aD~iA~~~ 201 (720)
T TIGR01448 185 DVKGIGFLTADQLAQAL 201 (720)
T ss_pred hcCCCCHHHHHHHHHHc
Confidence 47888988888876443
No 81
>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=90.91 E-value=0.19 Score=41.55 Aligned_cols=30 Identities=27% Similarity=0.480 Sum_probs=23.3
Q ss_pred HhcccCCCHHHHHHHHHhCCCCHHHHhhcc
Q 010406 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (511)
Q Consensus 297 f~~I~GvGpktA~~l~~~Gi~tledL~~~~ 326 (511)
+..+|.+||+..+.|++-||.|++||+.-|
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 457899999999999999999999999755
No 82
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=90.91 E-value=0.61 Score=47.88 Aligned_cols=95 Identities=16% Similarity=0.262 Sum_probs=63.9
Q ss_pred CCCcHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHH
Q 010406 207 PDLNKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFE 286 (511)
Q Consensus 207 ~~~N~~ia~~l~~la~~~e~~g~~~r~~aY~rAa~~l~~l~~~i~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~ 286 (511)
+.-++.|++.++++.+-=+++ +.....+.+|.+ ..+|..+||+|++-..+..+.+- +..+++|+
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 577999999877664432221 444555667776 77899999999954444444333 66677776
Q ss_pred hhchhHHHHHHhcccCCCHHHHHHHHHhCCCCHH
Q 010406 287 KDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLD 320 (511)
Q Consensus 287 ~~~~~~~l~lf~~I~GvGpktA~~l~~~Gi~tle 320 (511)
.... .-.+.+++|+|.|.+.+|++..-...+
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 334669999999999999986444333
No 83
>KOG0323 consensus TFIIF-interacting CTD phosphatases, including NLI-interacting factor [Transcription]
Probab=90.64 E-value=0.075 Score=59.34 Aligned_cols=90 Identities=22% Similarity=0.243 Sum_probs=64.3
Q ss_pred CCCCCeEEEEecC---CCcchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCCcccccchHHH
Q 010406 17 GIFAGMRVFLVEK---GVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLED 93 (511)
Q Consensus 17 ~~F~g~~iy~~~~---~~g~~r~~~l~~~~~~~Gg~v~~~~s~~VTHVV~~~~s~~~~~l~~~~~~~~~~~iV~~~Wl~e 93 (511)
..+++|.+.|.+. ++...+.+++ ..+.+.|+.+....+..+||+|+.+...... .+.... ...+||...|+..
T Consensus 440 ~v~~~~~~vfSg~~P~~~~~~~s~~~-~~~~~~g~vs~~~~~~~~th~i~~~~gt~k~-~~a~~~--~~~~Vv~~~wl~~ 515 (635)
T KOG0323|consen 440 KVLKGSQIVFSGLHPTGSTDESADIL-GVAQQLGAVSAPDVSDKTTHLIAANAGTKKV-YKAVVS--GSAKVVNAAWLWR 515 (635)
T ss_pred HHhhccceeecccccCcCCcchhhhh-hhhhcccceecccccchhhhHHhhccCccee-eccccc--cceeEechhHHHH
Confidence 4678888887754 3333333443 5678889999999999999999977642211 111111 1378999999999
Q ss_pred HHhcCCCCCcccccccc
Q 010406 94 SLRLGEKVSEDLYRIKL 110 (511)
Q Consensus 94 cik~g~lvde~~y~l~~ 110 (511)
|+..+..+++..|.+..
T Consensus 516 ~~e~w~~v~ek~~~l~~ 532 (635)
T KOG0323|consen 516 SLEKWGKVEEKLEPLDD 532 (635)
T ss_pred HHHHhcchhcccccccc
Confidence 99999999998887754
No 84
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=90.61 E-value=0.13 Score=49.26 Aligned_cols=49 Identities=22% Similarity=0.306 Sum_probs=37.7
Q ss_pred hHHHHHHhcccCCCHHHHHHHHHhCCCCHHHHhh---c---cCcchhhhhcccchhhh
Q 010406 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDI 342 (511)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~Gi~tledL~~---~---~~L~~~q~~Glk~~~d~ 342 (511)
...+++|.+|.|||||+|-.+-.. -|.++|.. . ..| +.+|+|-|..+.|
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 447888899999999999999775 25556652 2 358 8999999987754
No 85
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=90.43 E-value=0.13 Score=58.67 Aligned_cols=190 Identities=17% Similarity=0.177 Sum_probs=98.4
Q ss_pred hcccCCCHHHHHHHHHh-CCCCHHHHhh--ccCcchhhhhcccchhhhccCcCHHHHHHHHHHHHHHhhhcCCCeEE---
Q 010406 298 GEVWGIGPATAQKLYEK-GHRTLDDLKN--EDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVII--- 371 (511)
Q Consensus 298 ~~I~GvGpktA~~l~~~-Gi~tledL~~--~~~L~~~q~~Glk~~~d~~~~i~r~ea~~~~~iv~~~~~~~~p~~~v--- 371 (511)
++|.|+|++++.+||+. +++++.||.. ...|..+.+||-|..+.|.+.|-.+--..+..++..+. .|++-.
T Consensus 465 l~I~GLG~k~i~~L~~~g~V~~~~Dl~~L~~~~L~~l~g~g~Ksa~~Ll~~Ie~sk~~~l~r~l~ALg---IpgIG~~~a 541 (689)
T PRK14351 465 LDIEGLGEERVQQLVDAGLVESLADLYDLTVADLAELEGWGETSAENLLAELEASREPPLADFLVALG---IPEVGPTTA 541 (689)
T ss_pred cCCCCcCHHHHHHHHHcCCCCCHHHHHHcCHHHHhcCcCcchhHHHHHHHHHHHHccCCHHHHHHHcC---CCCcCHHHH
Confidence 48999999999999999 5799999985 23477788999999988876664332223445544443 444310
Q ss_pred -EEc---cceeecCCccCCeeEEEecCCc-ch----hhhHH-----HHHHHHHHHhcceeeeeEeecccccccCcchHHH
Q 010406 372 -LCG---GSYRRGKASCGDLDVVIMHPDR-KS----HKGFL-----SKYVKKLKEMKFLREDLIFSTHSEEVYPRDIYAF 437 (511)
Q Consensus 372 -~~~---Gs~RRgke~~gDvDiLit~~~~-~~----~~~~l-----~~~v~~l~~~g~l~~~l~~~~~~~~~~p~~~~~~ 437 (511)
.++ ||+..-+. -+.+-|..-++- .. ...+| ..+++.|.+.|+-..... ..+...|.-
T Consensus 542 k~L~~~F~si~~L~~--As~eeL~~i~GIG~k~A~sI~~ff~~~~n~~~i~~L~~~Gv~~~~~~-------~~~~~~l~g 612 (689)
T PRK14351 542 RNLAREFGTFEAIMD--ADEEALRAVDDVGPTVAEEIREFFDSERNRAVIDDLLDHGVDPQPAE-------SEGGDALDG 612 (689)
T ss_pred HHHHHHhCCHHHHHh--CCHHHHhccCCcCHHHHHHHHHHHhhhHHHHHHHHHHhccccccccc-------ccCCCCCCC
Confidence 011 22211111 011112222221 11 11222 234555665554211100 011122333
Q ss_pred HHHHhcCcHH-HHH-HHHHHHHHcCCccCCCCCccccc----C-CCC-cccc-cccccCCCCCHHHHHhhcC
Q 010406 438 GLIAWTGNDV-LNR-RLRLLAESKGYRLDDTGLFPATY----G-SGG-KQGV-RARTSLKFDTEKEVFDFLG 500 (511)
Q Consensus 438 aLl~~TGS~~-fnr-~lR~~A~~kg~~L~~~gL~~~~~----~-~~~-~~~~-~~~~~~~~~tEedIf~~LG 500 (511)
.-+-|||+-. +.| .+..++++.|.+...- +...+. | ..| .|.. ....-+++-+|+++++.|.
T Consensus 613 ~~~v~TG~l~~~~R~~~~~~i~~~Gg~v~~s-Vs~kt~~Lv~G~~~g~sKl~kA~~lgi~ii~E~~f~~ll~ 683 (689)
T PRK14351 613 LTFVFTGSLSGYTRSEAQELVEAHGGNATGS-VSGNTDYLVVGENPGQSKRDDAEANDVPTLDEEEFEELLA 683 (689)
T ss_pred cEEEEccCCCCCCHHHHHHHHHHcCCEEcCC-cCCCccEEEEcCCCChhHHHHHHHCCCeEecHHHHHHHHH
Confidence 4566899853 333 3666777888777653 433321 1 112 1111 0112467778999988774
No 86
>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=90.33 E-value=0.33 Score=40.02 Aligned_cols=32 Identities=28% Similarity=0.458 Sum_probs=26.3
Q ss_pred CCCeEEEEccceeecCCc-cCCeeEEEecCCcc
Q 010406 366 LPEVIILCGGSYRRGKAS-CGDLDVVIMHPDRK 397 (511)
Q Consensus 366 ~p~~~v~~~Gs~RRgke~-~gDvDiLit~~~~~ 397 (511)
.+...+.+.|||.||... .+|||++|..++..
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 456689999999999965 69999999776654
No 87
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=90.27 E-value=0.38 Score=53.44 Aligned_cols=86 Identities=15% Similarity=0.195 Sum_probs=64.7
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccch
Q 010406 253 ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTH 330 (511)
Q Consensus 253 ~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~Gi~tledL~~~~--~L~~ 330 (511)
.+++.+++|+|++.+++|.+=++.-+-..|+ ..+--| +|++||.++|+. .+.|+++|..+. .|..
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 3689999999999999998777654434443 345566 999999998886 678899998643 5788
Q ss_pred hhhhcccchhhhccCcCHHHH
Q 010406 331 SQRLGLKYFDDIKTRIPRHEV 351 (511)
Q Consensus 331 ~q~~Glk~~~d~~~~i~r~ea 351 (511)
..++|-+..+.|.+-+.-++.
T Consensus 525 i~gIG~~~a~si~~~f~~~~~ 545 (562)
T PRK08097 525 LPGIGEGRARQLIAFLQHPEV 545 (562)
T ss_pred CCCchHHHHHHHHHHHcCHHH
Confidence 889998887777766655443
No 88
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=90.20 E-value=0.39 Score=47.95 Aligned_cols=49 Identities=22% Similarity=0.483 Sum_probs=35.5
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHH
Q 010406 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (511)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (511)
+..|||||..+|..+-.. -|+...+ ... ....|+.|+|||+++|..+|+
T Consensus 184 l~s~pgig~~~a~~ll~~--fgS~~~~---~ta----s~~eL~~v~gig~k~A~~I~~ 232 (254)
T COG1948 184 LESIPGIGPKLAERLLKK--FGSVEDV---LTA----SEEELMKVKGIGEKKAREIYR 232 (254)
T ss_pred HHcCCCccHHHHHHHHHH--hcCHHHH---hhc----CHHHHHHhcCccHHHHHHHHH
Confidence 789999999999887653 3333333 321 125566999999999999986
No 89
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=89.80 E-value=0.18 Score=52.00 Aligned_cols=30 Identities=37% Similarity=0.597 Sum_probs=27.1
Q ss_pred HhcccCCCHHHHHHHHHhCCCCHHHHhhcc
Q 010406 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (511)
Q Consensus 297 f~~I~GvGpktA~~l~~~Gi~tledL~~~~ 326 (511)
+..+||||+++|++|.+.||.|++||....
T Consensus 8 l~~l~gIg~~~a~~L~~~Gi~t~~dl~~~~ 37 (317)
T PRK04301 8 LEDLPGVGPATAEKLREAGYDTVEAIAVAS 37 (317)
T ss_pred HhhcCCCCHHHHHHHHHcCCCCHHHHHcCC
Confidence 468999999999999999999999998643
No 90
>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=89.60 E-value=0.49 Score=40.07 Aligned_cols=47 Identities=11% Similarity=0.254 Sum_probs=38.2
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCC
Q 010406 253 ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGI 303 (511)
Q Consensus 253 ~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~Gv 303 (511)
+.+|+.|||||+++++-...| -+..+++|+...|....+-++.+-|.
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 578999999999999987755 45778889888888887777776664
No 91
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=89.03 E-value=0.37 Score=43.17 Aligned_cols=53 Identities=23% Similarity=0.316 Sum_probs=38.3
Q ss_pred HHHhcccCCCHHHHHHHHHhCCCCHHHHhhccCcchhhhhcccchhhhccCcCHHH
Q 010406 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIPRHE 350 (511)
Q Consensus 295 ~lf~~I~GvGpktA~~l~~~Gi~tledL~~~~~L~~~q~~Glk~~~d~~~~i~r~e 350 (511)
.-|+.|-||||+.+..|...||.|+.+|-. +++.--.-+..|-.|..||-|+.
T Consensus 67 DDLt~I~GIGPk~e~~Ln~~GI~tfaQIAA---wt~~di~~id~~l~f~GRi~RDd 119 (133)
T COG3743 67 DDLTRISGIGPKLEKVLNELGIFTFAQIAA---WTRADIAWIDDYLNFDGRIERDD 119 (133)
T ss_pred ccchhhcccCHHHHHHHHHcCCccHHHHHh---cCHHHHHHHHhhcCCcchhHHHH
Confidence 456799999999999999999999999964 22222223344555667777764
No 92
>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=88.89 E-value=1.1 Score=42.45 Aligned_cols=49 Identities=14% Similarity=0.226 Sum_probs=29.8
Q ss_pred CCCHHHHHHHHHHHH------hCCchhhHHHHhh---chhHHHHHHhcccCCCHHHHHHHH
Q 010406 261 GIGKSMQDHIQEIVT------TGKLSKLEHFEKD---EKVRTISLFGEVWGIGPATAQKLY 312 (511)
Q Consensus 261 gIG~~ia~kI~Eil~------tG~~~~le~l~~~---~~~~~l~lf~~I~GvGpktA~~l~ 312 (511)
|+-..-|+.|.++.+ .|.+. .+..+ ....+++.|+++||||||||.-.-
T Consensus 75 Gfy~~KAk~Lk~~a~~iie~y~G~v~---~L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL 132 (177)
T TIGR03252 75 RFPGSMAKRVQALAQYVVDTYDGDAT---AVWTEGDPDGKELLRRLKALPGFGKQKAKIFL 132 (177)
T ss_pred CchHHHHHHHHHHHHHHHHHhCCChh---hhhcccCCCcHHHHHHHHcCCCCCHHHHHHHH
Confidence 455566666655543 23333 33331 123357788899999999999763
No 93
>PTZ00418 Poly(A) polymerase; Provisional
Probab=88.27 E-value=4.8 Score=45.04 Aligned_cols=50 Identities=24% Similarity=0.408 Sum_probs=39.4
Q ss_pred CCeEEEEccceeecCCc-cCCeeEEEecCCcchhhhHHHHHHHHHHHhcce
Q 010406 367 PEVIILCGGSYRRGKAS-CGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFL 416 (511)
Q Consensus 367 p~~~v~~~Gs~RRgke~-~gDvDiLit~~~~~~~~~~l~~~v~~l~~~g~l 416 (511)
.+.++...||||-|.-. ..|||.|+..|..-.-..+|..+.+.|.+..-+
T Consensus 125 ~~g~I~tfGSYrLGV~~pgSDID~L~V~P~~vtredFF~~f~~~L~~~~~V 175 (593)
T PTZ00418 125 ISGKLFTFGSYRLGVVAPGSDIDTLCLAPRHITRESFFSDFYAKLQQDPNI 175 (593)
T ss_pred CCeEEEEeccccccCCCCCCcccEEEECCCCCCHHHHHHHHHHHHhcCCCc
Confidence 46678889999999876 679999999886555567888888888776543
No 94
>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=88.27 E-value=0.34 Score=49.75 Aligned_cols=29 Identities=38% Similarity=0.597 Sum_probs=26.3
Q ss_pred hcccCCCHHHHHHHHHhCCCCHHHHhhcc
Q 010406 298 GEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (511)
Q Consensus 298 ~~I~GvGpktA~~l~~~Gi~tledL~~~~ 326 (511)
.++||||++++++|++.||.|++||....
T Consensus 2 ~~i~gig~~~~~~L~~~Gi~ti~dl~~~~ 30 (310)
T TIGR02236 2 EDLPGVGPATAEKLREAGYDTFEAIAVAS 30 (310)
T ss_pred cccCCCCHHHHHHHHHcCCCCHHHHHcCC
Confidence 47899999999999999999999998643
No 95
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=88.26 E-value=0.77 Score=47.97 Aligned_cols=60 Identities=22% Similarity=0.338 Sum_probs=41.3
Q ss_pred cCCccccch--hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHH
Q 010406 245 KLPFKIESA--DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (511)
Q Consensus 245 ~l~~~i~s~--~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (511)
.++.+|... .-|.+||+|++.+|+.+.+ +-|.+ ..+.+. ..+.|.+|+|||+++|+.+.+
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--HFGSL---QGLLAA----SIEDLDEVEGIGEVRARAIRE 337 (352)
T ss_pred ccccccCCcHHHHHhcCCCCCHHHHHHHHH--HcCCH---HHHHcC----CHHHHhhCCCcCHHHHHHHHH
Confidence 344555543 4589999999999988765 33444 444332 245677999999999999544
No 96
>KOG2245 consensus Poly(A) polymerase and related nucleotidyltransferases [RNA processing and modification]
Probab=88.23 E-value=3.2 Score=45.10 Aligned_cols=85 Identities=26% Similarity=0.378 Sum_probs=54.7
Q ss_pred hhhhcccchhhhccCcCHHHHHH-HHHHHHHHhhhc-----C-------CCeEEEEccceeecCCc-cCCeeEEEecCCc
Q 010406 331 SQRLGLKYFDDIKTRIPRHEVEQ-MERLLQKAGEEV-----L-------PEVIILCGGSYRRGKAS-CGDLDVVIMHPDR 396 (511)
Q Consensus 331 ~q~~Glk~~~d~~~~i~r~ea~~-~~~iv~~~~~~~-----~-------p~~~v~~~Gs~RRgke~-~gDvDiLit~~~~ 396 (511)
++.+|+ ||+-.+-..|.++.. +.++|++-+.++ + -|.++..-||||-|.-. +.|||=|+-.|.-
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 444443 455555556666654 455554432221 2 24467777999999876 4599999988876
Q ss_pred chhhhHHHHHHHHHHHhccee
Q 010406 397 KSHKGFLSKYVKKLKEMKFLR 417 (511)
Q Consensus 397 ~~~~~~l~~~v~~l~~~g~l~ 417 (511)
.+-..+|..|-+-|++..-++
T Consensus 119 v~R~DFF~sf~~mL~~~~eVt 139 (562)
T KOG2245|consen 119 VSRSDFFTSFYDMLKERPEVT 139 (562)
T ss_pred ccHHHHHHHHHHHHhcCcccc
Confidence 666688888888777665443
No 97
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=87.82 E-value=0.37 Score=33.51 Aligned_cols=16 Identities=56% Similarity=0.742 Sum_probs=14.4
Q ss_pred cccCCCHHHHHHHHHh
Q 010406 299 EVWGIGPATAQKLYEK 314 (511)
Q Consensus 299 ~I~GvGpktA~~l~~~ 314 (511)
.|+|||+|||.+|.++
T Consensus 20 Gv~giG~ktA~~ll~~ 35 (36)
T smart00279 20 GVKGIGPKTALKLLRE 35 (36)
T ss_pred CCCcccHHHHHHHHHh
Confidence 8999999999999764
No 98
>PRK01172 ski2-like helicase; Provisional
Probab=87.69 E-value=0.9 Score=51.81 Aligned_cols=40 Identities=25% Similarity=0.484 Sum_probs=33.2
Q ss_pred HHhhchhHHHHHHhcccCCCHHHHHHHHHhCCCCHHHHhhc
Q 010406 285 FEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (511)
Q Consensus 285 l~~~~~~~~l~lf~~I~GvGpktA~~l~~~Gi~tledL~~~ 325 (511)
+....+...+.|+ +|||+|..+|+++|+.|++|+.||...
T Consensus 603 l~~gv~~~~~~L~-~ip~~~~~~a~~l~~~g~~~~~di~~~ 642 (674)
T PRK01172 603 IKEGIREDLIDLV-LIPKVGRVRARRLYDAGFKTVDDIARS 642 (674)
T ss_pred HHcCCCHHHHhhc-CCCCCCHHHHHHHHHcCCCCHHHHHhC
Confidence 3444555567777 999999999999999999999999854
No 99
>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=87.62 E-value=1.4 Score=45.47 Aligned_cols=62 Identities=19% Similarity=0.270 Sum_probs=39.8
Q ss_pred hhcCCCCCCHHHHHHHHHHH---HhCC--chhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHhCCCC
Q 010406 255 QVKGLPGIGKSMQDHIQEIV---TTGK--LSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRT 318 (511)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil---~tG~--~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~Gi~t 318 (511)
+|..+ |+|-+ |+-|.++. ..|. ...++.+..-....+.+.|++++||||+||.-+--.|+.-
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 67765 45454333 3443 3346667554445688999999999999999875545443
No 100
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=87.49 E-value=0.65 Score=45.60 Aligned_cols=50 Identities=22% Similarity=0.424 Sum_probs=37.8
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHH
Q 010406 255 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (511)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (511)
-|+.||||+|.=|..+- +++.-|+++-+ .....|.+|+|+||.+|+++|+
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 37899999998776553 24555666543 2456778999999999999997
No 101
>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=87.43 E-value=0.29 Score=56.33 Aligned_cols=53 Identities=15% Similarity=0.350 Sum_probs=41.0
Q ss_pred HHHHHHhc--ccCCCHHHHHHHHHh-CCCCHHHHhhcc-Ccchhhhhcccchhhhcc
Q 010406 292 RTISLFGE--VWGIGPATAQKLYEK-GHRTLDDLKNED-SLTHSQRLGLKYFDDIKT 344 (511)
Q Consensus 292 ~~l~lf~~--I~GvGpktA~~l~~~-Gi~tledL~~~~-~L~~~q~~Glk~~~d~~~ 344 (511)
..+..|.+ ++||||++|+++|+. |.++++-|.++. +|...+++|.+..+.|..
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 34455543 999999999999998 999999998753 577777888776666654
No 102
>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=87.26 E-value=0.55 Score=38.08 Aligned_cols=27 Identities=41% Similarity=0.546 Sum_probs=22.2
Q ss_pred hcccCCCHHHHHHHHHhCCCCHHHHhhc
Q 010406 298 GEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (511)
Q Consensus 298 ~~I~GvGpktA~~l~~~Gi~tledL~~~ 325 (511)
..|+|||||||.+|..+ +.|++.+...
T Consensus 25 ~gv~giG~k~A~~ll~~-~~~~~~~~~~ 51 (75)
T cd00080 25 PGVPGIGPKTALKLLKE-YGSLENLLEN 51 (75)
T ss_pred CCCCcccHHHHHHHHHH-hCCHHHHHHH
Confidence 47999999999999987 5588877753
No 103
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=86.55 E-value=1.6 Score=48.90 Aligned_cols=52 Identities=17% Similarity=0.142 Sum_probs=39.6
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHh
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~ 314 (511)
..|.+|||||++...++-+ ++..++.+++ -+++.+..|+|++.+.|+.+|+.
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 4789999999998887655 2444555543 24667789999999999999874
No 104
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=85.63 E-value=0.71 Score=29.45 Aligned_cols=20 Identities=30% Similarity=0.573 Sum_probs=17.3
Q ss_pred hhcCCCCCCHHHHHHHHHHH
Q 010406 255 QVKGLPGIGKSMQDHIQEIV 274 (511)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil 274 (511)
+|.+|||||+++|+.|.++.
T Consensus 2 ~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred hhhhCCCCCHHHHHHHHHhc
Confidence 57899999999999988743
No 105
>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=85.38 E-value=4.1 Score=36.57 Aligned_cols=46 Identities=33% Similarity=0.509 Sum_probs=32.4
Q ss_pred CeEEEEccceeecCCcc--CCeeEEEecCCcc-----hhhhHHHHHHHHHHHh
Q 010406 368 EVIILCGGSYRRGKASC--GDLDVVIMHPDRK-----SHKGFLSKYVKKLKEM 413 (511)
Q Consensus 368 ~~~v~~~Gs~RRgke~~--gDvDiLit~~~~~-----~~~~~l~~~v~~l~~~ 413 (511)
...+.+.|||.||...- .|||++|..+... ....++..+.+.|.+.
T Consensus 27 ~~~~~~~GS~a~~T~i~~~sDiD~~v~~~~~~~~~~~~~~~~~~~l~~~L~~~ 79 (143)
T cd05400 27 VAEVFLQGSYARGTALRGDSDIDLVVVLPDDTSFAEYGPAELLDELGEALKEY 79 (143)
T ss_pred ccEEEEEcceeCCCCCCCCCceeEEEEEcCcccccccCHHHHHHHHHHHHHHh
Confidence 35789999999998654 8999999655432 2345666666666654
No 106
>PRK03352 DNA polymerase IV; Validated
Probab=84.98 E-value=0.68 Score=48.28 Aligned_cols=28 Identities=39% Similarity=0.769 Sum_probs=25.8
Q ss_pred hcccCCCHHHHHHHHHhCCCCHHHHhhc
Q 010406 298 GEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (511)
Q Consensus 298 ~~I~GvGpktA~~l~~~Gi~tledL~~~ 325 (511)
..+||||++++++|.+.||+|+.||..-
T Consensus 180 ~~l~gig~~~~~~L~~~Gi~ti~dl~~l 207 (346)
T PRK03352 180 DALWGVGPKTAKRLAALGITTVADLAAA 207 (346)
T ss_pred HHcCCCCHHHHHHHHHcCCccHHHHhcC
Confidence 5789999999999999999999999864
No 107
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=84.80 E-value=1.5 Score=36.93 Aligned_cols=53 Identities=28% Similarity=0.561 Sum_probs=41.0
Q ss_pred HHHHHhcccCCCHHHHHHHHHh-CCCCHHHHhhcc-Ccch-hhhhcccchhhhccCc
Q 010406 293 TISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED-SLTH-SQRLGLKYFDDIKTRI 346 (511)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~-Gi~tledL~~~~-~L~~-~q~~Glk~~~d~~~~i 346 (511)
++..| .-+|++++.|.++|+. |-.+++-|+++. .|.. ..++|++..+.|..++
T Consensus 11 ~~~~L-~~~gl~~~~a~kl~~~yg~~ai~~l~~nPY~L~~~i~gi~F~~aD~iA~~~ 66 (94)
T PF14490_consen 11 LMAFL-QEYGLSPKLAMKLYKKYGDDAIEILKENPYRLIEDIDGIGFKTADKIALKL 66 (94)
T ss_dssp HHHHH-HHTT--HHHHHHHHHHH-TTHHHHHHH-STCCCB-SSSSBHHHHHHHHHTT
T ss_pred HHHHH-HHcCCCHHHHHHHHHHHhHHHHHHHHHChHHHHHHccCCCHHHHHHHHHHc
Confidence 45555 8899999999999999 999999888764 5555 8899999999997665
No 108
>PRK03858 DNA polymerase IV; Validated
Probab=84.54 E-value=0.74 Score=48.92 Aligned_cols=27 Identities=41% Similarity=0.811 Sum_probs=25.1
Q ss_pred hcccCCCHHHHHHHHHhCCCCHHHHhh
Q 010406 298 GEVWGIGPATAQKLYEKGHRTLDDLKN 324 (511)
Q Consensus 298 ~~I~GvGpktA~~l~~~Gi~tledL~~ 324 (511)
..+||||++++++|.+.||+|+.||.+
T Consensus 176 ~~l~Gig~~~~~~L~~~Gi~t~~dl~~ 202 (396)
T PRK03858 176 RRLWGVGPVTAAKLRAHGITTVGDVAE 202 (396)
T ss_pred hhcCCCCHHHHHHHHHhCCCcHHHHhc
Confidence 578999999999999999999999985
No 109
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=84.26 E-value=2.2 Score=47.68 Aligned_cols=52 Identities=23% Similarity=0.357 Sum_probs=39.2
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHh
Q 010406 253 ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (511)
Q Consensus 253 ~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~ 314 (511)
-..|.+|||||++...++-. ++.-++.+++ -+++.+.+| |||+++|+++|+.
T Consensus 513 ~S~Ld~I~GiG~kr~~~Ll~-----~Fgs~~~ik~----As~eeL~~v-gi~~~~A~~I~~~ 564 (567)
T PRK14667 513 KDILDKIKGIGEVKKEIIYR-----NFKTLYDFLK----ADDEELKKL-GIPPSVKQEVKKY 564 (567)
T ss_pred cCccccCCCCCHHHHHHHHH-----HhCCHHHHHh----CCHHHHHHc-CCCHHHHHHHHHH
Confidence 35688999999999887755 2344555543 246677899 9999999999874
No 110
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=83.64 E-value=0.61 Score=45.11 Aligned_cols=51 Identities=24% Similarity=0.311 Sum_probs=37.7
Q ss_pred HHHHHHhcccCCCHHHHHHHHHh-CCCCHHHHhhc---cCcchhhhhcccchhhh
Q 010406 292 RTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNE---DSLTHSQRLGLKYFDDI 342 (511)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~~-Gi~tledL~~~---~~L~~~q~~Glk~~~d~ 342 (511)
..+..|.+|-|||||+|-.+... ....|.+.... ..|++..|+|-|..+.|
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 36777789999999999999875 44444444322 25889999999887654
No 111
>PRK01216 DNA polymerase IV; Validated
Probab=83.44 E-value=0.82 Score=48.07 Aligned_cols=28 Identities=36% Similarity=0.392 Sum_probs=25.7
Q ss_pred hcccCCCHHHHHHHHHhCCCCHHHHhhc
Q 010406 298 GEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (511)
Q Consensus 298 ~~I~GvGpktA~~l~~~Gi~tledL~~~ 325 (511)
..+||||++++++|.+.||+|+.||.+-
T Consensus 181 ~~l~giG~~~~~~L~~~Gi~TigdL~~~ 208 (351)
T PRK01216 181 ADIPGIGDITAEKLKKLGVNKLVDTLRI 208 (351)
T ss_pred ccccCCCHHHHHHHHHcCCCcHHHHhcC
Confidence 5789999999999999999999999864
No 112
>PRK10880 adenine DNA glycosylase; Provisional
Probab=83.30 E-value=4.6 Score=42.51 Aligned_cols=64 Identities=22% Similarity=0.344 Sum_probs=42.2
Q ss_pred hHHHHHHHHHHHh-cCCccc-cchhhhcCCCCCCHHHHHHHHHHHHhCC-chhhHHHHhhchhHHHHHHhcccCC
Q 010406 232 RSFSYYKAIPVIE-KLPFKI-ESADQVKGLPGIGKSMQDHIQEIVTTGK-LSKLEHFEKDEKVRTISLFGEVWGI 303 (511)
Q Consensus 232 r~~aY~rAa~~l~-~l~~~i-~s~~~l~~lpgIG~~ia~kI~Eil~tG~-~~~le~l~~~~~~~~l~lf~~I~Gv 303 (511)
|++...+||..|. .....+ .+.++|.+|||||..+|+.|.-|-- |+ ..-+ ..-+...+.+++|+
T Consensus 85 RAr~L~~~A~~i~~~~~g~~p~~~~~L~~LpGIG~~TA~aIl~~af-~~~~~iV-------D~nV~RV~~Rl~~i 151 (350)
T PRK10880 85 RARNLHKAAQQVATLHGGEFPETFEEVAALPGVGRSTAGAILSLSL-GKHFPIL-------DGNVKRVLARCYAV 151 (350)
T ss_pred HHHHHHHHHHHHHHHhCCCchhhHHHHhcCCCccHHHHHHHHHHHC-CCCeecc-------cHHHHHHHHHHhcc
Confidence 7888888888883 322222 4568899999999999999987653 33 1111 22355566666554
No 113
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=83.03 E-value=0.63 Score=52.74 Aligned_cols=47 Identities=30% Similarity=0.471 Sum_probs=35.7
Q ss_pred HHHhcccCCCHHHHHHHHHh-CCCCHHHHhhcc--Ccchhhhhcccchhhhc
Q 010406 295 SLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED--SLTHSQRLGLKYFDDIK 343 (511)
Q Consensus 295 ~lf~~I~GvGpktA~~l~~~-Gi~tledL~~~~--~L~~~q~~Glk~~~d~~ 343 (511)
..|..|+||||+++++|++. | |+++|.++. .|....++|.+..+.|.
T Consensus 637 s~L~~IPGIGpkr~k~LL~~FG--Sle~I~~AS~eELa~V~Gig~k~Ae~I~ 686 (694)
T PRK14666 637 GELQRVEGIGPATARLLWERFG--SLQAMAAAGEEGLAAVPGIGPARAAALH 686 (694)
T ss_pred hHHhhCCCCCHHHHHHHHHHhC--CHHHHHhcCHHHHHhcCCcCHHHHHHHH
Confidence 35669999999999999997 6 999999753 36666667766655543
No 114
>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=82.98 E-value=4.4 Score=42.17 Aligned_cols=29 Identities=31% Similarity=0.452 Sum_probs=25.9
Q ss_pred hcccCCCHHHHHHHHHhCCCCHHHHhhcc
Q 010406 298 GEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (511)
Q Consensus 298 ~~I~GvGpktA~~l~~~Gi~tledL~~~~ 326 (511)
..+||||++++++|.+.||+|+.||.+-.
T Consensus 176 ~~l~giG~~~~~~L~~~Gi~ti~dl~~~~ 204 (343)
T cd00424 176 TDLPGIGAVTAKRLEAVGINPIGDLLAAS 204 (343)
T ss_pred hhcCCCCHHHHHHHHHcCCCcHHHHhcCC
Confidence 46899999999999999999999998643
No 115
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=82.52 E-value=0.94 Score=48.69 Aligned_cols=28 Identities=39% Similarity=0.672 Sum_probs=25.8
Q ss_pred hcccCCCHHHHHHHHHhCCCCHHHHhhc
Q 010406 298 GEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (511)
Q Consensus 298 ~~I~GvGpktA~~l~~~Gi~tledL~~~ 325 (511)
..+||||++++++|.+.||+|+.||.+.
T Consensus 182 ~~l~GiG~~~~~~L~~lGi~TigdL~~~ 209 (422)
T PRK03609 182 EEVWGVGRRISKKLNAMGIKTALDLADT 209 (422)
T ss_pred hhcCCccHHHHHHHHHcCCCcHHHHhcC
Confidence 5889999999999999999999999854
No 116
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=82.41 E-value=2.2 Score=48.56 Aligned_cols=52 Identities=29% Similarity=0.382 Sum_probs=39.0
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHh
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~ 314 (511)
..|..|||||++.+.++.+- -| -++.+.+. ..+.+.+|+|+|+++|+++++.
T Consensus 637 s~L~~IPGIGpkr~k~LL~~--FG---Sle~I~~A----S~eELa~V~Gig~k~Ae~I~~~ 688 (694)
T PRK14666 637 GELQRVEGIGPATARLLWER--FG---SLQAMAAA----GEEGLAAVPGIGPARAAALHEH 688 (694)
T ss_pred hHHhhCCCCCHHHHHHHHHH--hC---CHHHHHhc----CHHHHHhcCCcCHHHHHHHHHH
Confidence 57999999999999887763 34 44555442 2344678999999999999863
No 117
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=82.05 E-value=5.9 Score=40.47 Aligned_cols=47 Identities=21% Similarity=0.275 Sum_probs=33.2
Q ss_pred HHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHhCCC
Q 010406 270 IQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHR 317 (511)
Q Consensus 270 I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~Gi~ 317 (511)
|.+.+..|.+.. ..+..-....+++.|++|+||||.||+.+---|..
T Consensus 174 ~A~~~~~g~~~~-~~l~~~~~e~a~e~L~~i~GIG~WTAe~~llf~lg 220 (285)
T COG0122 174 LARAAAEGELDL-SELKPLSDEEAIEELTALKGIGPWTAEMFLLFGLG 220 (285)
T ss_pred HHHHHHcCCccH-HHhccCCHHHHHHHHHcCCCcCHHHHHHHHHHcCC
Confidence 455566786333 34444455679999999999999999988654443
No 118
>smart00475 53EXOc 5'-3' exonuclease.
Probab=82.04 E-value=1.1 Score=45.14 Aligned_cols=26 Identities=38% Similarity=0.592 Sum_probs=22.2
Q ss_pred hcccCCCHHHHHHHHHh-CCCCHHHHhhc
Q 010406 298 GEVWGIGPATAQKLYEK-GHRTLDDLKNE 325 (511)
Q Consensus 298 ~~I~GvGpktA~~l~~~-Gi~tledL~~~ 325 (511)
-+|+|||||||.+|.++ | |++.+...
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 89888753
No 119
>PRK09482 flap endonuclease-like protein; Provisional
Probab=82.01 E-value=1.1 Score=45.07 Aligned_cols=25 Identities=32% Similarity=0.613 Sum_probs=21.9
Q ss_pred cccCCCHHHHHHHHHh-CCCCHHHHhhc
Q 010406 299 EVWGIGPATAQKLYEK-GHRTLDDLKNE 325 (511)
Q Consensus 299 ~I~GvGpktA~~l~~~-Gi~tledL~~~ 325 (511)
+|+|||||||.+|.++ | |++.+.+.
T Consensus 186 GVpGIG~KtA~~LL~~~g--sle~i~~~ 211 (256)
T PRK09482 186 GVAGIGPKSAAELLNQFR--SLENIYES 211 (256)
T ss_pred CCCCcChHHHHHHHHHhC--CHHHHHHh
Confidence 6899999999999998 7 88888753
No 120
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=82.01 E-value=2.8 Score=47.62 Aligned_cols=54 Identities=13% Similarity=0.182 Sum_probs=39.9
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHhCC
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGH 316 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~Gi 316 (511)
..|.+|||||++-+.++.. ++..++.+++ -.++.+..|+|||++.|+++|...-
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 4688999999998887654 2344445443 2456677999999999999998743
No 121
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=81.93 E-value=1 Score=43.16 Aligned_cols=21 Identities=33% Similarity=0.607 Sum_probs=18.7
Q ss_pred HHHHHHhcccCCCHHHHHHHH
Q 010406 292 RTISLFGEVWGIGPATAQKLY 312 (511)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~ 312 (511)
+.++.|.++||||||+|++|-
T Consensus 9 ~LI~~l~kLPGvG~KsA~R~A 29 (198)
T COG0353 9 KLIDALKKLPGVGPKSAQRLA 29 (198)
T ss_pred HHHHHHhhCCCCChhHHHHHH
Confidence 478889999999999999983
No 122
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=81.61 E-value=4.3 Score=36.76 Aligned_cols=26 Identities=15% Similarity=0.089 Sum_probs=20.4
Q ss_pred HHHHHHhcccCCCHHHHHHHHHhCCC
Q 010406 292 RTISLFGEVWGIGPATAQKLYEKGHR 317 (511)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~~Gi~ 317 (511)
..++.|++++||||+||..+--.|+.
T Consensus 69 ~~~~~L~~l~GIG~~tA~~~l~~~~~ 94 (149)
T smart00478 69 DDREELLKLPGVGRKTANAVLSFALG 94 (149)
T ss_pred HHHHHHHcCCCCcHHHHHHHHHHHCC
Confidence 35667779999999999988766543
No 123
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=81.56 E-value=2.2 Score=48.12 Aligned_cols=53 Identities=23% Similarity=0.471 Sum_probs=39.4
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHh
Q 010406 253 ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (511)
Q Consensus 253 ~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~ 314 (511)
...|.+|||||+..+.+|.+.. |+ ++.+.+. ..+.+.+|+|||+++|+.+++.
T Consensus 542 ~s~L~~IpGIG~k~~k~Ll~~F--gS---~~~i~~A----s~eeL~~v~Gig~~~A~~I~~~ 594 (598)
T PRK00558 542 TSALDDIPGIGPKRRKALLKHF--GS---LKAIKEA----SVEELAKVPGISKKLAEAIYEA 594 (598)
T ss_pred hhhHhhCCCcCHHHHHHHHHHc--CC---HHHHHhC----CHHHHhhcCCcCHHHHHHHHHH
Confidence 3568999999999999887743 44 4444432 2345679999999999999863
No 124
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=81.34 E-value=6.4 Score=40.55 Aligned_cols=48 Identities=19% Similarity=0.135 Sum_probs=39.5
Q ss_pred CCCCCeEEEEecCCCcchHHHHHHHHHHhcCCEEEeecCCCccEEEEcC
Q 010406 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMD 65 (511)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~r~~~l~~~~~~~Gg~v~~~~s~~VTHVV~~~ 65 (511)
..|.|.+|.|-+.--...| ..+++++..+||.|.++++..+|.+|+-+
T Consensus 219 ~~l~g~~~vfTG~l~~~~R-~~~~~~~~~~Gg~v~~sVs~~t~~lV~G~ 266 (309)
T PRK06195 219 TAFKEEVVVFTGGLASMTR-DEAMILVRRLGGTVGSSVTKKTTYLVTNT 266 (309)
T ss_pred ccccCCEEEEccccCCCCH-HHHHHHHHHhCCEecCCcccCceEEEECC
Confidence 4799999999776433344 55789999999999999999999999854
No 125
>PRK14976 5'-3' exonuclease; Provisional
Probab=81.05 E-value=1.2 Score=45.42 Aligned_cols=25 Identities=44% Similarity=0.708 Sum_probs=21.6
Q ss_pred hcccCCCHHHHHHHHHh-CCCCHHHHhh
Q 010406 298 GEVWGIGPATAQKLYEK-GHRTLDDLKN 324 (511)
Q Consensus 298 ~~I~GvGpktA~~l~~~-Gi~tledL~~ 324 (511)
-+|+|||||||.+|.++ | |++++.+
T Consensus 194 pGVpGIG~KtA~~LL~~~g--sle~i~~ 219 (281)
T PRK14976 194 KGVKGIGPKTAIKLLNKYG--NIENIYE 219 (281)
T ss_pred CCCCcccHHHHHHHHHHcC--CHHHHHH
Confidence 36899999999999986 6 9999875
No 126
>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=81.04 E-value=1.1 Score=47.55 Aligned_cols=30 Identities=33% Similarity=0.431 Sum_probs=26.7
Q ss_pred HhcccCCCHHHHHHHHHhCCCCHHHHhhcc
Q 010406 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (511)
Q Consensus 297 f~~I~GvGpktA~~l~~~Gi~tledL~~~~ 326 (511)
+..+||||++++++|.+.||.|+.||.+..
T Consensus 174 v~~l~GiG~~~~~kL~~~GI~tigdl~~~~ 203 (379)
T cd01703 174 LRKIPGIGYKTAAKLEAHGISSVRDLQEFS 203 (379)
T ss_pred ccccCCcCHHHHHHHHHcCCCcHHHHHhCC
Confidence 358899999999999999999999998543
No 127
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=80.94 E-value=1.6 Score=44.49 Aligned_cols=63 Identities=19% Similarity=0.243 Sum_probs=38.5
Q ss_pred hhhcCCCCCCHHHHHHHHHH---HHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHhCCCCHH
Q 010406 254 DQVKGLPGIGKSMQDHIQEI---VTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLD 320 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Ei---l~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~Gi~tle 320 (511)
++|..+ |++..=++-|.++ +..|.+.. +... ....+++.|++|+||||+||..+--.|+.-.|
T Consensus 167 ~eL~~~-Gl~~~Ra~~L~~lA~~i~~g~l~l-~~~~--~~~~~~~~L~~LpGIGpwTA~~vllr~lg~~D 232 (283)
T PRK10308 167 QALKAL-GMPLKRAEALIHLANAALEGTLPL-TIPG--DVEQAMKTLQTFPGIGRWTANYFALRGWQAKD 232 (283)
T ss_pred HHHHHC-CCCHHHHHHHHHHHHHHHcCCCCc-cccC--CHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCC
Confidence 456655 7776444444433 34577653 2211 12347788889999999999987554554443
No 128
>PRK08609 hypothetical protein; Provisional
Probab=80.92 E-value=2.1 Score=47.96 Aligned_cols=54 Identities=17% Similarity=0.178 Sum_probs=37.5
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHH
Q 010406 252 SADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKL 311 (511)
Q Consensus 252 s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l 311 (511)
.+.++.+|||||++.+.++.+=+---++.+|+... .. -+ +..++|+|+|+.+.+
T Consensus 86 ~~~~l~~i~GiGpk~a~~l~~~lGi~tl~~L~~a~---~~--~~-~~~~~gfg~k~~~~i 139 (570)
T PRK08609 86 GLLPLLKLPGLGGKKIAKLYKELGVVDKESLKEAC---EN--GK-VQALAGFGKKTEEKI 139 (570)
T ss_pred HHHHHhcCCCCCHHHHHHHHHHhCCCCHHHHHHHH---Hh--CC-hhhccCcchhHHHHH
Confidence 35578999999999999887655444444444322 21 11 238899999999887
No 129
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=80.91 E-value=4 Score=46.61 Aligned_cols=73 Identities=14% Similarity=0.143 Sum_probs=54.1
Q ss_pred CCCCCCeEEEEecCCCcchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCCcccccchHHH
Q 010406 16 NGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLED 93 (511)
Q Consensus 16 ~~~F~g~~iy~~~~~~g~~r~~~l~~~~~~~Gg~v~~~~s~~VTHVV~~~~s~~~~~l~~~~~~~~~~~iV~~~Wl~e 93 (511)
...|.|.+|.|-++-.+.+| ..+++++..+||.|.+++|..++.+|+-+.. -.+..+++. .++.|++.+.+.+
T Consensus 591 ~~~l~gktfV~TG~l~~~~R-~e~~~lie~~Ggkv~ssVSkktd~LV~G~~a-GsKl~KA~~---LGI~Ii~e~~f~~ 663 (669)
T PRK14350 591 NSFLFGKKFCITGSFNGYSR-SVLIDKLTKKGAIFNTCVTKYLDFLLVGEKA-GLKLKKANN---LGIKIMSLFDIKS 663 (669)
T ss_pred CCccCCcEEEEecccCCCCH-HHHHHHHHHcCCEEeccccCCCcEEEECCCC-CchHHHHHH---cCCEEecHHHHHH
Confidence 45799999999776444444 6689999999999999999999999996432 233333333 3678888777765
No 130
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=80.73 E-value=1.1 Score=41.13 Aligned_cols=27 Identities=15% Similarity=0.004 Sum_probs=22.5
Q ss_pred hHHHHHHhcccCCCHHHHHHHHHhCCC
Q 010406 291 VRTISLFGEVWGIGPATAQKLYEKGHR 317 (511)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~Gi~ 317 (511)
..+.+.|++++||||+||..+---++.
T Consensus 79 ~~~~~~L~~l~GIG~~tA~~~l~~~~~ 105 (158)
T cd00056 79 PDAREELLALPGVGRKTANVVLLFALG 105 (158)
T ss_pred cccHHHHHcCCCCCHHHHHHHHHHHCC
Confidence 457888899999999999998776555
No 131
>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=80.65 E-value=1.2 Score=47.72 Aligned_cols=29 Identities=28% Similarity=0.338 Sum_probs=26.4
Q ss_pred hcccCCCHHHHHHHHHhCCCCHHHHhhcc
Q 010406 298 GEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (511)
Q Consensus 298 ~~I~GvGpktA~~l~~~Gi~tledL~~~~ 326 (511)
..|||||++++++|-+.||+|+.||.+..
T Consensus 225 ~~l~GIG~~~~~~L~~~Gi~t~~dl~~~~ 253 (404)
T cd01701 225 GDLPGVGSSLAEKLVKLFGDTCGGLELRS 253 (404)
T ss_pred hHhCCCCHHHHHHHHHcCCcchHHHHhCc
Confidence 57899999999999999999999998643
No 132
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=80.57 E-value=0.69 Score=51.45 Aligned_cols=64 Identities=17% Similarity=0.201 Sum_probs=47.4
Q ss_pred hcccCCCHHHHHHHHHhC-CCCHHHHhh--ccCcchhhhhcccchhhhccCcCHHHHHHHHHHHHHH
Q 010406 298 GEVWGIGPATAQKLYEKG-HRTLDDLKN--EDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKA 361 (511)
Q Consensus 298 ~~I~GvGpktA~~l~~~G-i~tledL~~--~~~L~~~q~~Glk~~~d~~~~i~r~ea~~~~~iv~~~ 361 (511)
++|-|+|++++.+|++.| ++++.||.+ ...|..+.+||-|..+.+...|-..--..+..++-.+
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 599999984 3457777889988888887655433333345555544
No 133
>TIGR03671 cca_archaeal CCA-adding enzyme.
Probab=80.47 E-value=3.8 Score=43.89 Aligned_cols=45 Identities=27% Similarity=0.383 Sum_probs=32.6
Q ss_pred HHHHHHHHHhhhcCCCeEEEEccceeecCCcc--CCeeEEEecCCcc
Q 010406 353 QMERLLQKAGEEVLPEVIILCGGSYRRGKASC--GDLDVVIMHPDRK 397 (511)
Q Consensus 353 ~~~~iv~~~~~~~~p~~~v~~~Gs~RRgke~~--gDvDiLit~~~~~ 397 (511)
.+...+++.+.+..+.+.|.+.|||.||.-.. .||||+|..+...
T Consensus 25 ~l~~~l~~~~~e~~~~~~v~~~GS~ArgT~L~G~sDIDIfi~f~~~~ 71 (408)
T TIGR03671 25 ELIARLEEIIEELGVDAEVVLVGSYARGTWLKGDRDIDIFILFPKDT 71 (408)
T ss_pred HHHHHHHHHHHhcCCcceEEEEeeEecCCccCCCCceeEEEEeCCCC
Confidence 34444555554455567999999999999886 6999999776443
No 134
>PRK00227 glnD PII uridylyl-transferase; Provisional
Probab=80.42 E-value=4.5 Score=46.37 Aligned_cols=66 Identities=21% Similarity=0.305 Sum_probs=44.2
Q ss_pred HHHHHH-HHHHHHHHhhhcCCCeEEEEccceeecC-CccCCeeEEEecCCcchhhhHHHHHHHHHHHhcce
Q 010406 348 RHEVEQ-MERLLQKAGEEVLPEVIILCGGSYRRGK-ASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFL 416 (511)
Q Consensus 348 r~ea~~-~~~iv~~~~~~~~p~~~v~~~Gs~RRgk-e~~gDvDiLit~~~~~~~~~~l~~~v~~l~~~g~l 416 (511)
|.+|.+ ..++++.+. +.+++-+..+|||=||. .--+|||+||-+++... ...+..|+..|=+.|+-
T Consensus 8 ~~~~~~~~~~~~~~~~--~~~~~aLvAvGGYGR~EL~P~SDIDLLiL~~~~~~-~~~i~~~~~~LWD~gL~ 75 (693)
T PRK00227 8 REDAEASALALLGSLQ--LPPGTALAATGSLARREMTPYSDLDLILLHPPGAT-PDGVEDLWYPIWDAKKR 75 (693)
T ss_pred HHHHHHHHHHHHHhcC--CCCCeEEEEeccccccCcCCCcCceEEEEeCCccc-HHHHHHHHHHHHhcCCC
Confidence 445544 455666553 23566788899996654 55689999999985432 56677777777666663
No 135
>PRK01810 DNA polymerase IV; Validated
Probab=80.10 E-value=1.3 Score=47.23 Aligned_cols=28 Identities=46% Similarity=0.715 Sum_probs=25.4
Q ss_pred hcccCCCHHHHHHHHHhCCCCHHHHhhc
Q 010406 298 GEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (511)
Q Consensus 298 ~~I~GvGpktA~~l~~~Gi~tledL~~~ 325 (511)
..+||||++++++|...||+|+.||.+.
T Consensus 182 ~~l~giG~~~~~~L~~~Gi~tigdL~~~ 209 (407)
T PRK01810 182 GEMHGIGEKTAEKLKDIGIQTIGDLAKA 209 (407)
T ss_pred hhcCCcCHHHHHHHHHcCCCcHHHHHhC
Confidence 4789999999999999999999999853
No 136
>KOG3524 consensus Predicted guanine nucleotide exchange factor (PEBBLE) [Signal transduction mechanisms]
Probab=80.06 E-value=2 Score=48.18 Aligned_cols=81 Identities=14% Similarity=0.227 Sum_probs=56.9
Q ss_pred CCCCCCCCCeEEEEecCCCcchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCCcccccchHH
Q 010406 13 LDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLE 92 (511)
Q Consensus 13 ~~~~~~F~g~~iy~~~~~~g~~r~~~l~~~~~~~Gg~v~~~~s~~VTHVV~~~~s~~~~~l~~~~~~~~~~~iV~~~Wl~ 92 (511)
+-....|++++.||- ++-..-. -|-+++..+||.|..+...++||.|+...... .+..... ...++.+.||.
T Consensus 113 ply~~~m~~vvlcfT--g~rkk~e-~lv~lvh~mgg~irkd~nsktthli~n~s~ge--k~~~a~t---~~~~~rp~wv~ 184 (850)
T KOG3524|consen 113 PLYCELMKDVVMCFT--GERKKKE-ELVDLVHYMGGSIRKDTNSKTTHLIANKVEGE--KQSIALV---GVPTMRPDWVT 184 (850)
T ss_pred cccchhhcCceeeee--ccchhhH-HHHHHHHHhcceeEeeeccCceEEEeecccce--EEEEEee---ccceechHhhh
Confidence 345578999999994 4432222 45699999999999999999999998654321 0111111 35789999999
Q ss_pred HHHhcCCCC
Q 010406 93 DSLRLGEKV 101 (511)
Q Consensus 93 ecik~g~lv 101 (511)
+||+-+.-+
T Consensus 185 ~aw~~rn~~ 193 (850)
T KOG3524|consen 185 EAWKHRNDS 193 (850)
T ss_pred hhhcCcchh
Confidence 999876543
No 137
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=79.73 E-value=3.5 Score=42.50 Aligned_cols=86 Identities=22% Similarity=0.353 Sum_probs=53.9
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHh--C---C---CCHHHHhhc-
Q 010406 255 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--G---H---RTLDDLKNE- 325 (511)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~--G---i---~tledL~~~- 325 (511)
.+..|||||+.+++++.+. -+..++++.+-.+ +.+.+++|+++++|..||+. | . .|.-++...
T Consensus 7 ~l~~l~gIg~~~a~~L~~~----Gi~t~~dl~~~~~----~~L~~~~g~~~~~a~~l~~~a~~~~~~~~~~t~~~l~~~~ 78 (317)
T PRK04301 7 DLEDLPGVGPATAEKLREA----GYDTVEAIAVASP----KELSEAAGIGESTAAKIIEAAREAADIGGFETALEVLERR 78 (317)
T ss_pred cHhhcCCCCHHHHHHHHHc----CCCCHHHHHcCCH----HHHHHhcCCCHHHHHHHHHHHHHhhccccCccHHHHHHhh
Confidence 5789999999888876653 4566677755332 23448889999999999974 4 3 455555432
Q ss_pred cCcchhhhhcccchhhhcc-CcCHH
Q 010406 326 DSLTHSQRLGLKYFDDIKT-RIPRH 349 (511)
Q Consensus 326 ~~L~~~q~~Glk~~~d~~~-~i~r~ 349 (511)
.++.. -..|..-.++++. -+|..
T Consensus 79 ks~~~-~~Tg~~~lD~~l~GGi~~g 102 (317)
T PRK04301 79 KNVGK-ITTGSKELDELLGGGIETQ 102 (317)
T ss_pred ccCCc-cCCCCHHHHHHhcCCccCC
Confidence 12211 2345666666543 45553
No 138
>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=79.51 E-value=1.4 Score=45.94 Aligned_cols=28 Identities=50% Similarity=0.819 Sum_probs=25.5
Q ss_pred hcccCCCHHHHHHHHHhCCCCHHHHhhc
Q 010406 298 GEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (511)
Q Consensus 298 ~~I~GvGpktA~~l~~~Gi~tledL~~~ 325 (511)
..+||||++++++|.+.||+|+.||.+-
T Consensus 179 ~~l~gig~~~~~~L~~~Gi~ti~dL~~~ 206 (344)
T cd01700 179 GDVWGIGRRTAKKLNAMGIHTAGDLAQA 206 (344)
T ss_pred hhcCccCHHHHHHHHHcCCCcHHHHhcC
Confidence 5779999999999999999999999863
No 139
>PRK02406 DNA polymerase IV; Validated
Probab=79.46 E-value=1.3 Score=46.04 Aligned_cols=28 Identities=36% Similarity=0.423 Sum_probs=25.6
Q ss_pred hcccCCCHHHHHHHHHhCCCCHHHHhhc
Q 010406 298 GEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (511)
Q Consensus 298 ~~I~GvGpktA~~l~~~Gi~tledL~~~ 325 (511)
..+||||++++++|-+.||+|+.||.+-
T Consensus 171 ~~l~giG~~~~~~L~~~Gi~ti~dl~~l 198 (343)
T PRK02406 171 EKIPGVGKVTAEKLHALGIYTCADLQKY 198 (343)
T ss_pred chhcCCCHHHHHHHHHcCCCcHHHHHhC
Confidence 5889999999999988899999999864
No 140
>PRK03348 DNA polymerase IV; Provisional
Probab=79.31 E-value=1.3 Score=48.16 Aligned_cols=27 Identities=44% Similarity=0.815 Sum_probs=25.3
Q ss_pred hcccCCCHHHHHHHHHhCCCCHHHHhh
Q 010406 298 GEVWGIGPATAQKLYEKGHRTLDDLKN 324 (511)
Q Consensus 298 ~~I~GvGpktA~~l~~~Gi~tledL~~ 324 (511)
..+||||++++++|.+.||+|+.||.+
T Consensus 183 ~~L~GIG~~t~~~L~~lGI~TigDLa~ 209 (454)
T PRK03348 183 RRLWGIGPVTEEKLHRLGIETIGDLAA 209 (454)
T ss_pred cccCCCCHHHHHHHHHcCCccHHHHhc
Confidence 588999999999999999999999985
No 141
>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=79.27 E-value=1.6 Score=43.46 Aligned_cols=27 Identities=33% Similarity=0.423 Sum_probs=22.6
Q ss_pred hcccCCCHHHHHHHHHhCCCCHHHHhhc
Q 010406 298 GEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (511)
Q Consensus 298 ~~I~GvGpktA~~l~~~Gi~tledL~~~ 325 (511)
-+|+|||||||.+|.++ +.|++++.+.
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 3499999864
No 142
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=79.13 E-value=8.2 Score=39.92 Aligned_cols=72 Identities=13% Similarity=0.180 Sum_probs=49.8
Q ss_pred CCCCCeEEEEecCCCcchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHH-HHHHHHHhhhccCCcccccchHHH
Q 010406 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEAL-LQQVSKQHLARFKGSVIRYQWLED 93 (511)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~r~~~l~~~~~~~Gg~v~~~~s~~VTHVV~~~~s~~-~~~l~~~~~~~~~~~iV~~~Wl~e 93 (511)
.+|.|.+|.|-+.- ...| .-+++++..+||.|.++++.+++.||+-+.... .|..+++ ..++.|++.+=+.+
T Consensus 231 ~l~~g~~~v~TG~l-~~~R-~e~~~~~~~~G~~v~~sVs~~t~~lv~g~~~~~ssK~~kA~---~~gi~ii~e~~f~~ 303 (313)
T PRK06063 231 PLVQGMRVALSAEV-SRTH-EELVERILHAGLAYSDSVDRDTSLVVCNDPAPEQGKGYHAR---QLGVPVLDEAAFLE 303 (313)
T ss_pred cccCCCEEEEecCC-CCCH-HHHHHHHHHcCCEecCccccCccEEEECCCCCcccHHHHHH---HcCCccccHHHHHH
Confidence 46899999997763 2344 668899999999999999999999999654321 2222222 23566766554443
No 143
>KOG3548 consensus DNA damage checkpoint protein RHP9/CRB2/53BP1 [Replication, recombination and repair]
Probab=79.09 E-value=2.2 Score=49.22 Aligned_cols=89 Identities=12% Similarity=0.032 Sum_probs=54.1
Q ss_pred CCCCCeEEEEecCCCcchHHHHHHHHHHhcCCEEEeec-CCCccEEEE-------------------------cCChHHH
Q 010406 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKL-SKKVTHVLA-------------------------MDLEALL 70 (511)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~r~~~l~~~~~~~Gg~v~~~~-s~~VTHVV~-------------------------~~~s~~~ 70 (511)
.+|.||++.|-...-. ...+.+-+..|||.|.+.- ..--+|=.. ....+..
T Consensus 924 niFd~cvF~lTsa~~s---d~~~r~s~e~~gg~vle~gl~~~Fn~p~~g~~~~lr~Ln~~q~~ks~~qalLIsdth~Rt~ 1000 (1176)
T KOG3548|consen 924 NIFDGCVFMLTSANRS---DSASRPSMEKHGGLVLEKGLMNLFNTPFKGGGIVLRQLNSFQERKSNYQALLISDTHYRTH 1000 (1176)
T ss_pred chhcceeEEEeccccc---hhhhhhhhhccCChhhhccccccccccccCCcchHHhhhHHhhhccccceeEeehhhhHHH
Confidence 7999999998654321 1222233344888887653 222333322 1111223
Q ss_pred HHHHHHhhhccCCcccccchHHHHHhcCCCCCccccccccC
Q 010406 71 QQVSKQHLARFKGSVIRYQWLEDSLRLGEKVSEDLYRIKLD 111 (511)
Q Consensus 71 ~~l~~~~~~~~~~~iV~~~Wl~ecik~g~lvde~~y~l~~~ 111 (511)
++|..- +++..-|...||.+|+++++.||-.+|+|.-.
T Consensus 1001 KYLeaL---A~giPcVh~~fI~aC~e~nr~Vdy~~YLLpsG 1038 (1176)
T KOG3548|consen 1001 KYLEAL---ARGIPCVHNTFIQACGEQNRCVDYTDYLLPSG 1038 (1176)
T ss_pred HHHHHH---HcCCCcccHHHHHHHHhccccccchhhcccCc
Confidence 333211 23667899999999999999999999998643
No 144
>PRK07758 hypothetical protein; Provisional
Probab=78.35 E-value=1.1 Score=38.07 Aligned_cols=45 Identities=13% Similarity=0.280 Sum_probs=36.6
Q ss_pred ccCCCHHHHHHHHHhCCCCHHHHhh--ccCcchhhhhcccchhhhcc
Q 010406 300 VWGIGPATAQKLYEKGHRTLDDLKN--EDSLTHSQRLGLKYFDDIKT 344 (511)
Q Consensus 300 I~GvGpktA~~l~~~Gi~tledL~~--~~~L~~~q~~Glk~~~d~~~ 344 (511)
.++++......|...||.||+||.. +..|..+.+||-+..++|.+
T Consensus 39 ~~~LSvRA~N~Lk~AGI~TL~dLv~~te~ELl~iknlGkKSL~EIke 85 (95)
T PRK07758 39 LSLLSAPARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRK 85 (95)
T ss_pred CccccHHHHHHHHHcCCCcHHHHHcCCHHHHHHccCCCHHHHHHHHH
Confidence 3578889999999999999999974 34688889999888777653
No 145
>PRK03103 DNA polymerase IV; Reviewed
Probab=78.14 E-value=1.7 Score=46.48 Aligned_cols=28 Identities=29% Similarity=0.561 Sum_probs=25.2
Q ss_pred hcccCCCHHHHHHHHHhCCCCHHHHhhc
Q 010406 298 GEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (511)
Q Consensus 298 ~~I~GvGpktA~~l~~~Gi~tledL~~~ 325 (511)
..+||||++++++|.+.||+|+.||.+-
T Consensus 184 ~~l~gig~~~~~~L~~~Gi~tigdl~~~ 211 (409)
T PRK03103 184 RKLFGVGSRMEKHLRRMGIRTIGQLANT 211 (409)
T ss_pred hhcCCccHHHHHHHHHcCCCCHHHHhcC
Confidence 4779999999999998999999999853
No 146
>PRK02794 DNA polymerase IV; Provisional
Probab=78.01 E-value=1.5 Score=47.07 Aligned_cols=29 Identities=48% Similarity=0.950 Sum_probs=26.1
Q ss_pred HhcccCCCHHHHHHHHHhCCCCHHHHhhc
Q 010406 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (511)
Q Consensus 297 f~~I~GvGpktA~~l~~~Gi~tledL~~~ 325 (511)
+..+||||++++++|.+.||+|+.||.+-
T Consensus 211 l~~L~GiG~~~~~~L~~~GI~tigdL~~l 239 (419)
T PRK02794 211 VGIIWGVGPATAARLARDGIRTIGDLQRA 239 (419)
T ss_pred hhhhCCCCHHHHHHHHHhccchHHHHhhC
Confidence 36889999999999999999999999853
No 147
>PRK14133 DNA polymerase IV; Provisional
Probab=77.85 E-value=1.7 Score=45.45 Aligned_cols=28 Identities=36% Similarity=0.519 Sum_probs=25.6
Q ss_pred hcccCCCHHHHHHHHHhCCCCHHHHhhc
Q 010406 298 GEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (511)
Q Consensus 298 ~~I~GvGpktA~~l~~~Gi~tledL~~~ 325 (511)
..+||||++++++|.+.||+|+.||.+-
T Consensus 176 ~~l~gig~~~~~~L~~~Gi~ti~dl~~l 203 (347)
T PRK14133 176 SKVHGIGKKSVEKLNNIGIYTIEDLLKL 203 (347)
T ss_pred cccCCCCHHHHHHHHHcCCccHHHHhhC
Confidence 5789999999999999999999999864
No 148
>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=77.53 E-value=4 Score=41.46 Aligned_cols=75 Identities=15% Similarity=0.245 Sum_probs=44.2
Q ss_pred HHHHHcCCChhHHHHHHHHHHHhcC-Cccc-cchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhc
Q 010406 222 NIYRALGEDRRSFSYYKAIPVIEKL-PFKI-ESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGE 299 (511)
Q Consensus 222 ~~~e~~g~~~r~~aY~rAa~~l~~l-~~~i-~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~ 299 (511)
++.+-.|--.|++.-.+||..|..- ...+ .+.++|.+|||||..+|+.|.-+- -|+..-+ ....+...+.+
T Consensus 71 ~~~~~lG~y~RAr~L~~~A~~i~~~~~g~~p~~~~~L~~LpGIG~~TA~~Il~~a-~~~~~~~------vD~~v~RVl~R 143 (275)
T TIGR01084 71 KLWEGLGYYARARNLHKAAQEVVEEFGGEFPQDFEDLAALPGVGRYTAGAILSFA-LNKPYPI------LDGNVKRVLSR 143 (275)
T ss_pred HHHHHCCcHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCCCHHHHHHHHHHH-CCCCCCc------chHhHHHHHHH
Confidence 3333334333777778888877541 1111 346889999999999999988554 3332211 12235555655
Q ss_pred ccCC
Q 010406 300 VWGI 303 (511)
Q Consensus 300 I~Gv 303 (511)
++|+
T Consensus 144 l~~~ 147 (275)
T TIGR01084 144 LFAV 147 (275)
T ss_pred HccC
Confidence 5554
No 149
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=77.14 E-value=5.9 Score=37.58 Aligned_cols=54 Identities=22% Similarity=0.337 Sum_probs=33.8
Q ss_pred CCChhHHHHHHHHHHHhcCCccccc-hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhh
Q 010406 228 GEDRRSFSYYKAIPVIEKLPFKIES-ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKD 288 (511)
Q Consensus 228 g~~~r~~aY~rAa~~l~~l~~~i~s-~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~ 288 (511)
.++.|-.-|-+-|. ||+. +-+|.=|||||++++.+|.|=-+.+.+..++++.+-
T Consensus 96 ~~E~~FV~FfN~A~-------PIt~RlH~LeLLPGIGKK~m~~ILeERkkkpFeSFeDi~~R 150 (181)
T PF04919_consen 96 ENEERFVDFFNEAQ-------PITLRLHSLELLPGIGKKTMWKILEERKKKPFESFEDIEER 150 (181)
T ss_dssp TTHHHHHHHH------------B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHH
T ss_pred hChHHHHHHhhcCC-------CChHHHHHHhhcccccHHHHHHHHHHHccCCCCCHHHHHHH
Confidence 33345555555554 7776 578999999999999999999888988888888763
No 150
>COG1708 Predicted nucleotidyltransferases [General function prediction only]
Probab=76.93 E-value=11 Score=32.37 Aligned_cols=28 Identities=32% Similarity=0.608 Sum_probs=23.7
Q ss_pred CeEEEEccceeecCCcc-CCeeEEEecCC
Q 010406 368 EVIILCGGSYRRGKASC-GDLDVVIMHPD 395 (511)
Q Consensus 368 ~~~v~~~Gs~RRgke~~-gDvDiLit~~~ 395 (511)
...|.+-||+=||..+- +|||++|-.++
T Consensus 26 ~~~v~LfGS~arG~~~~~SDiDv~vv~~~ 54 (128)
T COG1708 26 DLLIYLFGSYARGDFVKESDIDLLVVSDD 54 (128)
T ss_pred CeEEEEEccCcccccccCCCeeEEEEcCC
Confidence 44889999999999876 99999998644
No 151
>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=76.66 E-value=5.7 Score=37.93 Aligned_cols=25 Identities=16% Similarity=0.167 Sum_probs=20.4
Q ss_pred HHHHHHhcccCCCHHHHHHHHHhCC
Q 010406 292 RTISLFGEVWGIGPATAQKLYEKGH 316 (511)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~~Gi 316 (511)
..++.|++++|||++||..+--.++
T Consensus 103 ~~~~~L~~l~GIG~ktA~~ill~~~ 127 (191)
T TIGR01083 103 EDREELVKLPGVGRKTANVVLNVAF 127 (191)
T ss_pred hHHHHHHhCCCCcHHHHHHHHHHHc
Confidence 3577888999999999999876544
No 152
>PRK00254 ski2-like helicase; Provisional
Probab=76.55 E-value=12 Score=43.08 Aligned_cols=53 Identities=21% Similarity=0.354 Sum_probs=38.6
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHh
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~ 314 (511)
..|.+|||||+..+.++ ++.| +..++++.... .+.+..|+|||+++|+++++.
T Consensus 645 ~~L~~ipgig~~~~~~l---~~~g-~~s~~~i~~a~----~~el~~~~gi~~~~a~~i~~~ 697 (720)
T PRK00254 645 LELMRLPMIGRKRARAL---YNAG-FRSIEDIVNAK----PSELLKVEGIGAKIVEGIFKH 697 (720)
T ss_pred hhhhcCCCCCHHHHHHH---HHcc-CCCHHHHHhCC----HHHHhcCCCCCHHHHHHHHHH
Confidence 34778999999987774 4554 45555555432 334569999999999999986
No 153
>PRK00076 recR recombination protein RecR; Reviewed
Probab=76.27 E-value=2.1 Score=41.32 Aligned_cols=21 Identities=38% Similarity=0.618 Sum_probs=18.6
Q ss_pred HHHHHHhcccCCCHHHHHHHH
Q 010406 292 RTISLFGEVWGIGPATAQKLY 312 (511)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~ 312 (511)
..++.|.++||||+|+|+++-
T Consensus 8 ~Li~~l~~LPGIG~KsA~Rla 28 (196)
T PRK00076 8 KLIEALRKLPGIGPKSAQRLA 28 (196)
T ss_pred HHHHHHHHCCCCCHHHHHHHH
Confidence 367889999999999999984
No 154
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=76.26 E-value=2.1 Score=41.23 Aligned_cols=20 Identities=40% Similarity=0.669 Sum_probs=18.1
Q ss_pred HHHHHHhcccCCCHHHHHHH
Q 010406 292 RTISLFGEVWGIGPATAQKL 311 (511)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l 311 (511)
..++.|.++||||+|+|+++
T Consensus 8 ~Li~~l~~LPGIG~KsA~Rl 27 (195)
T TIGR00615 8 KLIESLKKLPGIGPKSAQRL 27 (195)
T ss_pred HHHHHHHHCCCCCHHHHHHH
Confidence 36788999999999999998
No 155
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=75.75 E-value=4.1 Score=41.19 Aligned_cols=68 Identities=18% Similarity=0.289 Sum_probs=49.8
Q ss_pred hhcCCCCCCH---HHHHHHHHHHH-hCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHhCCCCHHHHh
Q 010406 255 QVKGLPGIGK---SMQDHIQEIVT-TGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLK 323 (511)
Q Consensus 255 ~l~~lpgIG~---~ia~kI~Eil~-tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~Gi~tledL~ 323 (511)
+|.++ |+|= -|+.-.++|++ .|...-|..++...-..+.+.|+.+||||||.|.=+-=+|+.-+.-+-
T Consensus 175 ~LR~~-gfGYRAkYI~~ta~~l~~~~g~~~wLqsl~~~~yeear~~L~~lpGVG~KVADCI~Lm~l~~~~~VP 246 (323)
T KOG2875|consen 175 ELRKL-GFGYRAKYISATARALQEKQGGLAWLQSLRKSSYEEAREALCSLPGVGPKVADCICLMSLDKLSAVP 246 (323)
T ss_pred HHHHc-CcchhHHHHHHHHHHHHHhcccchHHHHHhcccHHHHHHHHhcCCCCcchHhhhhhhhhcCCCCccc
Confidence 45555 6773 46666777775 566788889988666669999999999999999977666655554443
No 156
>PRK10702 endonuclease III; Provisional
Probab=75.39 E-value=5.2 Score=39.03 Aligned_cols=25 Identities=16% Similarity=0.242 Sum_probs=20.1
Q ss_pred HHHHHHhcccCCCHHHHHHHHHhCC
Q 010406 292 RTISLFGEVWGIGPATAQKLYEKGH 316 (511)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~~Gi 316 (511)
..++.|+++||||+|||.-+---++
T Consensus 106 ~~~~~Ll~lpGVG~ktA~~ill~a~ 130 (211)
T PRK10702 106 EDRAALEALPGVGRKTANVVLNTAF 130 (211)
T ss_pred chHHHHhcCCcccHHHHHHHHHHHc
Confidence 4677888999999999998755443
No 157
>PTZ00205 DNA polymerase kappa; Provisional
Probab=75.36 E-value=2.1 Score=47.73 Aligned_cols=29 Identities=34% Similarity=0.408 Sum_probs=26.2
Q ss_pred HhcccCCCHHHHHHHHHhCCCCHHHHhhc
Q 010406 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (511)
Q Consensus 297 f~~I~GvGpktA~~l~~~Gi~tledL~~~ 325 (511)
+..|||||++++++|-..||.|+.||.+.
T Consensus 311 V~ki~GIG~~t~~~L~~~GI~TigDLa~~ 339 (571)
T PTZ00205 311 LRSVPGVGKVTEALLKGLGITTLSDIYNR 339 (571)
T ss_pred cceeCCcCHHHHHHHHHcCCCcHHHHhcC
Confidence 35899999999999999999999999853
No 158
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=75.18 E-value=3.5 Score=40.15 Aligned_cols=53 Identities=19% Similarity=0.253 Sum_probs=33.5
Q ss_pred CCHHHHHHHHHHHHh-CCchhhHHHH--hhchhHHHHHHh-cccCCCHHHHHHHHH-hCCC
Q 010406 262 IGKSMQDHIQEIVTT-GKLSKLEHFE--KDEKVRTISLFG-EVWGIGPATAQKLYE-KGHR 317 (511)
Q Consensus 262 IG~~ia~kI~Eil~t-G~~~~le~l~--~~~~~~~l~lf~-~I~GvGpktA~~l~~-~Gi~ 317 (511)
+-..=|+.|.++... |. ++.+. ........+.|+ ++||||+|||.-+-. .|++
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 335555556555542 32 22222 233456888898 999999999999874 4553
No 159
>PRK13844 recombination protein RecR; Provisional
Probab=75.03 E-value=2.3 Score=41.04 Aligned_cols=21 Identities=24% Similarity=0.300 Sum_probs=18.5
Q ss_pred HHHHHHhcccCCCHHHHHHHH
Q 010406 292 RTISLFGEVWGIGPATAQKLY 312 (511)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~ 312 (511)
..++.|.++||||+|+|+++-
T Consensus 12 ~LI~~l~~LPGIG~KsA~Rla 32 (200)
T PRK13844 12 AVIESLRKLPTIGKKSSQRLA 32 (200)
T ss_pred HHHHHHHHCCCCCHHHHHHHH
Confidence 467889999999999999983
No 160
>PRK10702 endonuclease III; Provisional
Probab=74.69 E-value=6.6 Score=38.32 Aligned_cols=43 Identities=12% Similarity=0.281 Sum_probs=31.2
Q ss_pred hHHHHHHHHHHHh-cCCcccc-chhhhcCCCCCCHHHHHHHHHHH
Q 010406 232 RSFSYYKAIPVIE-KLPFKIE-SADQVKGLPGIGKSMQDHIQEIV 274 (511)
Q Consensus 232 r~~aY~rAa~~l~-~l~~~i~-s~~~l~~lpgIG~~ia~kI~Eil 274 (511)
|+....+++..|. ....++. +.++|.+|||||.++|+.|.=+.
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 6666677777664 3333333 46889999999999999987554
No 161
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=74.08 E-value=3.4 Score=36.74 Aligned_cols=26 Identities=42% Similarity=0.542 Sum_probs=23.6
Q ss_pred cCCCHHHHHHHHHhCCCCHHHHhhcc
Q 010406 301 WGIGPATAQKLYEKGHRTLDDLKNED 326 (511)
Q Consensus 301 ~GvGpktA~~l~~~Gi~tledL~~~~ 326 (511)
||+|++++.+|-+.||.|.+||.+.+
T Consensus 1 pgi~~~~~~~L~~~GI~t~~~Ll~~~ 26 (122)
T PF14229_consen 1 PGIGPKEAAKLKAAGIKTTGDLLEAG 26 (122)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHHcC
Confidence 79999999999888999999998654
No 162
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=73.88 E-value=2.5 Score=43.52 Aligned_cols=25 Identities=48% Similarity=0.740 Sum_probs=22.0
Q ss_pred cccCCCHHHHHHHHHh-CCCCHHHHhhc
Q 010406 299 EVWGIGPATAQKLYEK-GHRTLDDLKNE 325 (511)
Q Consensus 299 ~I~GvGpktA~~l~~~-Gi~tledL~~~ 325 (511)
+|+|||||||.+|.++ | |++.|...
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
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=73.79 E-value=4.9 Score=39.25 Aligned_cols=86 Identities=23% Similarity=0.308 Sum_probs=49.7
Q ss_pred CCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHh--CCCCHHHHhhccCcc-hhhhhcc-
Q 010406 261 GIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRTLDDLKNEDSLT-HSQRLGL- 336 (511)
Q Consensus 261 gIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~--Gi~tledL~~~~~L~-~~q~~Gl- 336 (511)
|+-..=|+.|.++.+ .-+|+... +.+..++.|+++||||+|||.-.... |+-++. =+-.+. -..++|+
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-EVPDTREELLSLPGVGRKTANVVLSFAFGIPAIA---VDTHVHRVSNRLGLV 151 (211)
T ss_pred CCcHHHHHHHHHHHH----HHHHHcCC-CCCchHHHHHhCCCcchHHHHHHHHhhcCCCccc---ccchHHHHHHHhCCC
Confidence 555666666665543 12333333 44567888889999999999988776 444321 111111 1233443
Q ss_pred ------cchhhhccCcCHHHHHHH
Q 010406 337 ------KYFDDIKTRIPRHEVEQM 354 (511)
Q Consensus 337 ------k~~~d~~~~i~r~ea~~~ 354 (511)
+..+++...+|.+.-..+
T Consensus 152 ~~~~p~~ve~~L~~~iP~~~~~~~ 175 (211)
T COG0177 152 PGKTPEEVEEALMKLIPKELWTDL 175 (211)
T ss_pred CCCCHHHHHHHHHHHCCHHHHHHH
Confidence 345566778887765554
No 164
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=73.56 E-value=3.6 Score=41.22 Aligned_cols=54 Identities=24% Similarity=0.381 Sum_probs=40.3
Q ss_pred chhHHHHHHhcccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhhcccchhhhc
Q 010406 289 EKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIK 343 (511)
Q Consensus 289 ~~~~~l~lf~~I~GvGpktA~~l~~~Gi~tledL~~~~--~L~~~q~~Glk~~~d~~ 343 (511)
....-+.++.++||||++.|..+.+. +.|++++.++. .|....++|.+....|.
T Consensus 176 ~~e~q~~il~s~pgig~~~a~~ll~~-fgS~~~~~tas~~eL~~v~gig~k~A~~I~ 231 (254)
T COG1948 176 LKELQLYILESIPGIGPKLAERLLKK-FGSVEDVLTASEEELMKVKGIGEKKAREIY 231 (254)
T ss_pred hHHHHHHHHHcCCCccHHHHHHHHHH-hcCHHHHhhcCHHHHHHhcCccHHHHHHHH
Confidence 34456778889999999999999875 55888888653 47777888876655543
No 165
>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=73.39 E-value=2.5 Score=43.54 Aligned_cols=28 Identities=32% Similarity=0.359 Sum_probs=25.3
Q ss_pred cccCCCHHHHHHHHHhCCCCHHHHhhcc
Q 010406 299 EVWGIGPATAQKLYEKGHRTLDDLKNED 326 (511)
Q Consensus 299 ~I~GvGpktA~~l~~~Gi~tledL~~~~ 326 (511)
.+||||++++++|-+.||+|+.||.+-.
T Consensus 174 ~~~gig~~~~~~L~~~Gi~t~~dl~~~~ 201 (335)
T cd03468 174 AALRLPPETVELLARLGLRTLGDLAALP 201 (335)
T ss_pred hHhCCCHHHHHHHHHhCcccHHHHHhCC
Confidence 5889999999999999999999998643
No 166
>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=73.11 E-value=1.7 Score=29.28 Aligned_cols=18 Identities=22% Similarity=0.501 Sum_probs=14.5
Q ss_pred hhcCCCCCCHHHHHHHHH
Q 010406 255 QVKGLPGIGKSMQDHIQE 272 (511)
Q Consensus 255 ~l~~lpgIG~~ia~kI~E 272 (511)
.+.+++|||+++++++..
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 478899999999998764
No 167
>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=44.19 Aligned_cols=28 Identities=18% Similarity=0.306 Sum_probs=24.1
Q ss_pred hcccCCCHHHHHHHHH-hCCCCHHHHhhc
Q 010406 298 GEVWGIGPATAQKLYE-KGHRTLDDLKNE 325 (511)
Q Consensus 298 ~~I~GvGpktA~~l~~-~Gi~tledL~~~ 325 (511)
..+||||+++++++.+ .||+|+.||.+-
T Consensus 185 ~~l~GiG~~~~~~ll~~~Gi~ti~dl~~~ 213 (359)
T cd01702 185 TSIRGLGGKLGEEIIDLLGLPTEGDVAGF 213 (359)
T ss_pred HHhCCcCHHHHHHHHHHcCCcCHHHHHhc
Confidence 5889999999988765 599999999864
No 168
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=72.09 E-value=7 Score=35.69 Aligned_cols=77 Identities=16% Similarity=0.200 Sum_probs=44.5
Q ss_pred HHHHHHHcCCChhHHHHHHHHHHHhcCCccc-----cchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHH
Q 010406 220 LINIYRALGEDRRSFSYYKAIPVIEKLPFKI-----ESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTI 294 (511)
Q Consensus 220 la~~~e~~g~~~r~~aY~rAa~~l~~l~~~i-----~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l 294 (511)
|.++..-.|-+.|+.....++..+.+-.... +..++|.+|||||+.+|+.|.-+.-. .+ .+-- ...+.
T Consensus 44 l~~~~~~~G~~~kA~~i~~~a~~~~~~~~~~~~~~~~~~~~L~~l~GIG~~tA~~~l~~~~~--~~---~~pv--D~~v~ 116 (158)
T cd00056 44 LRELIRSLGYRRKAKYLKELARAIVEGFGGLVLDDPDAREELLALPGVGRKTANVVLLFALG--PD---AFPV--DTHVR 116 (158)
T ss_pred HHHHHHhcChHHHHHHHHHHHHHHHHHcCCccCCCcccHHHHHcCCCCCHHHHHHHHHHHCC--CC---CCcc--chhHH
Confidence 3333333342457777777777776532222 23467999999999999998765332 11 1111 23356
Q ss_pred HHHhcccCC
Q 010406 295 SLFGEVWGI 303 (511)
Q Consensus 295 ~lf~~I~Gv 303 (511)
+.+..+.++
T Consensus 117 r~~~~~~~~ 125 (158)
T cd00056 117 RVLKRLGLI 125 (158)
T ss_pred HHHHHhCCC
Confidence 666555554
No 169
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=71.68 E-value=4.7 Score=39.56 Aligned_cols=22 Identities=23% Similarity=0.210 Sum_probs=18.2
Q ss_pred HHHHHHhcccCCCHHHHHHHHH
Q 010406 292 RTISLFGEVWGIGPATAQKLYE 313 (511)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~ 313 (511)
...+.|++|+|||++||..+--
T Consensus 118 ~~re~Ll~l~GIG~kTAd~iLl 139 (218)
T PRK13913 118 VTREWLLDQKGIGKESADAILC 139 (218)
T ss_pred hHHHHHHcCCCccHHHHHHHHH
Confidence 3567788999999999998754
No 170
>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=71.56 E-value=0.5 Score=40.70 Aligned_cols=24 Identities=46% Similarity=0.753 Sum_probs=19.3
Q ss_pred cccCCCHHHHHHHHHh-CCCCHHHHhh
Q 010406 299 EVWGIGPATAQKLYEK-GHRTLDDLKN 324 (511)
Q Consensus 299 ~I~GvGpktA~~l~~~-Gi~tledL~~ 324 (511)
.|+|||||||.+|.++ | |||.+..
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 7999999999999997 6 7777764
No 171
>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=71.35 E-value=10 Score=31.62 Aligned_cols=49 Identities=22% Similarity=0.409 Sum_probs=32.3
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHhC
Q 010406 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKG 315 (511)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~G 315 (511)
+..|+|||+.+++.|.+--+.|.+.-++++... ++++..+..+.|...|
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 677888888888888887777777777766442 2266777777776665
No 172
>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=70.63 E-value=9.8 Score=30.75 Aligned_cols=29 Identities=31% Similarity=0.510 Sum_probs=24.2
Q ss_pred EEEEccceeecCCc-cCCeeEEEecCCcch
Q 010406 370 IILCGGSYRRGKAS-CGDLDVVIMHPDRKS 398 (511)
Q Consensus 370 ~v~~~Gs~RRgke~-~gDvDiLit~~~~~~ 398 (511)
.+.+-||+=||..+ .+||||+|-.++...
T Consensus 20 ~i~LfGS~arg~~~~~SDiDl~vi~~~~~~ 49 (93)
T cd05403 20 KVYLFGSYARGDARPDSDIDLLVIFDDPLD 49 (93)
T ss_pred EEEEEeeeecCCCCCCCCeeEEEEeCCCCC
Confidence 78899999999975 789999997766543
No 173
>PRK13910 DNA glycosylase MutY; Provisional
Probab=70.55 E-value=8.3 Score=39.49 Aligned_cols=68 Identities=18% Similarity=0.207 Sum_probs=44.8
Q ss_pred hHHHHHHHHHHHhc-CCccc-cchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHH
Q 010406 232 RSFSYYKAIPVIEK-LPFKI-ESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPA 306 (511)
Q Consensus 232 r~~aY~rAa~~l~~-l~~~i-~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpk 306 (511)
|++.-.++|..|.. ....+ .+.++|.+|||||..+|+.|.-+- -|.-.- -...-+..+|.+++|+...
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-FREKSA------CVDANIKRVLLRLFGLDPN 117 (289)
T ss_pred HHHHHHHHHHHHHHHhCCCCChhHHHHHhCCCCCHHHHHHHHHHH-CCCCcC------cccHHHHHHHHHHhcCCCC
Confidence 77777788877742 22222 247899999999999999997554 333111 1223467788788888643
No 174
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=70.44 E-value=4.4 Score=46.70 Aligned_cols=90 Identities=12% Similarity=0.147 Sum_probs=67.8
Q ss_pred CCCCCCCCCCeEEEEecCCCcchHHHHHHHHHHhcCCEEEe-ecCCCccEEEEcCChHH-HHHHHHHhhhccCCcccccc
Q 010406 12 ALDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEE-KLSKKVTHVLAMDLEAL-LQQVSKQHLARFKGSVIRYQ 89 (511)
Q Consensus 12 ~~~~~~~F~g~~iy~~~~~~g~~r~~~l~~~~~~~Gg~v~~-~~s~~VTHVV~~~~s~~-~~~l~~~~~~~~~~~iV~~~ 89 (511)
.......|+++.+|..+.-+... .-+++.-..+|+..+. ...++.||+++.+..+. ++.++ .+...+++
T Consensus 41 ~~t~~s~fs~is~~~ngs~~e~~--nelk~~~~~~t~~~~~~~~rs~T~~ii~~~l~a~~vk~~~-------~~~~~~~e 111 (1016)
T KOG2093|consen 41 AATGSSSFSGISISVNGSTDESA--NELKLQNMFHTGASAASYERSGTENIIAQGLPADLVKGFT-------IPKHISIE 111 (1016)
T ss_pred CcCCcceeeeeeeccCCccccch--HHHhhhhhhcccccccccccccceeeecccchHHHhcccc-------chhhhcHH
Confidence 33445789999999988877643 5567888899999984 44678999999887643 22222 46778999
Q ss_pred hHHHHHhcCCCCCcccccccc
Q 010406 90 WLEDSLRLGEKVSEDLYRIKL 110 (511)
Q Consensus 90 Wl~ecik~g~lvde~~y~l~~ 110 (511)
|+.||.+.|..+.--.|.+..
T Consensus 112 ~iie~~~~~~~~~~~~~~~~t 132 (1016)
T KOG2093|consen 112 WIIECCENGMDVGYYPYQLYT 132 (1016)
T ss_pred HHHHHHhccCccccccceeec
Confidence 999999999999877766543
No 175
>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=70.18 E-value=13 Score=35.22 Aligned_cols=44 Identities=16% Similarity=0.190 Sum_probs=30.4
Q ss_pred hHHHHHHHHHHH-hcCCccc------------cchhhhcCCCCCCHHHHHHHHHHHH
Q 010406 232 RSFSYYKAIPVI-EKLPFKI------------ESADQVKGLPGIGKSMQDHIQEIVT 275 (511)
Q Consensus 232 r~~aY~rAa~~l-~~l~~~i------------~s~~~l~~lpgIG~~ia~kI~Eil~ 275 (511)
|+.....++..| +.+...+ +-.++|..|||||+++|+.+.-++.
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 555555666655 4555554 1146799999999999999876654
No 176
>PRK13300 tRNA CCA-pyrophosphorylase; Provisional
Probab=69.99 E-value=17 Score=39.62 Aligned_cols=31 Identities=26% Similarity=0.410 Sum_probs=25.6
Q ss_pred CeEEEEccceeecCCcc--CCeeEEEecCCcch
Q 010406 368 EVIILCGGSYRRGKASC--GDLDVVIMHPDRKS 398 (511)
Q Consensus 368 ~~~v~~~Gs~RRgke~~--gDvDiLit~~~~~~ 398 (511)
.+.|.+.|||.||.-.- +||||.|..|...+
T Consensus 41 ~~~V~l~GS~ArgT~L~GdsDIDIFv~fp~~~~ 73 (447)
T PRK13300 41 DAEVELVGSTARGTWLSGDRDIDIFVLFPKDTS 73 (447)
T ss_pred ceEEEEEeeecCCcccCCCCceeEEEEeCCCCC
Confidence 37899999999998876 58999998876544
No 177
>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=69.96 E-value=3.4 Score=42.63 Aligned_cols=28 Identities=39% Similarity=0.550 Sum_probs=25.4
Q ss_pred hcccCCCHHHHHHHHHhCCCCHHHHhhc
Q 010406 298 GEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (511)
Q Consensus 298 ~~I~GvGpktA~~l~~~Gi~tledL~~~ 325 (511)
..+||||.+++++|.+.||+|+.||.+-
T Consensus 174 ~~l~gig~~~~~~L~~~Gi~ti~dl~~~ 201 (334)
T cd03586 174 RKIPGVGKVTAEKLKELGIKTIGDLAKL 201 (334)
T ss_pred hhhCCcCHHHHHHHHHcCCcCHHHHHcC
Confidence 5789999999999999999999999853
No 178
>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=69.24 E-value=6.5 Score=31.06 Aligned_cols=36 Identities=17% Similarity=0.359 Sum_probs=25.7
Q ss_pred HHHHHHhcCCccccch--------hhhcCCCCCCHHHHHHHHHHHH
Q 010406 238 KAIPVIEKLPFKIESA--------DQVKGLPGIGKSMQDHIQEIVT 275 (511)
Q Consensus 238 rAa~~l~~l~~~i~s~--------~~l~~lpgIG~~ia~kI~Eil~ 275 (511)
||.++|++. .|.++ +++..+||+|++..+.|.+.|+
T Consensus 22 Ra~n~L~~~--~I~tv~dL~~~s~~~L~~i~n~G~ksl~EI~~~L~ 65 (66)
T PF03118_consen 22 RAYNCLKRA--GIHTVGDLVKYSEEDLLKIKNFGKKSLEEIKEKLK 65 (66)
T ss_dssp HHHHHHHCT--T--BHHHHHCS-HHHHHTSTTSHHHHHHHHHHHHH
T ss_pred HHHHHHHHh--CCcCHHHHHhCCHHHHHhCCCCCHhHHHHHHHHHc
Confidence 455566655 33332 5789999999999999998875
No 179
>COG0389 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]
Probab=69.18 E-value=3.4 Score=43.50 Aligned_cols=27 Identities=44% Similarity=0.721 Sum_probs=25.6
Q ss_pred hcccCCCHHHHHHHHHhCCCCHHHHhh
Q 010406 298 GEVWGIGPATAQKLYEKGHRTLDDLKN 324 (511)
Q Consensus 298 ~~I~GvGpktA~~l~~~Gi~tledL~~ 324 (511)
+.+||||+.+++++...||.|+.||.+
T Consensus 179 ~~~~GvG~~~~~~l~~~Gi~ti~dl~~ 205 (354)
T COG0389 179 LEFWGVGKVTAEKLRRLGISTIGDLAE 205 (354)
T ss_pred hhhCCCCHHHHHHHHHcCChhHHHHHh
Confidence 489999999999999999999999987
No 180
>PRK13766 Hef nuclease; Provisional
Probab=69.05 E-value=6.4 Score=45.62 Aligned_cols=49 Identities=31% Similarity=0.437 Sum_probs=34.9
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHH
Q 010406 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (511)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (511)
|..|||||...+.+|.+- -|. ++++.+.. .+.|..++|+|+++|+.+++
T Consensus 717 L~~ipgig~~~a~~Ll~~--fgs---~~~i~~as----~~~L~~i~Gig~~~a~~i~~ 765 (773)
T PRK13766 717 VESLPDVGPVLARNLLEH--FGS---VEAVMTAS----EEELMEVEGIGEKTAKRIRE 765 (773)
T ss_pred HhcCCCCCHHHHHHHHHH--cCC---HHHHHhCC----HHHHHhCCCCCHHHHHHHHH
Confidence 678999999988877664 244 34433322 23456899999999999876
No 181
>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=68.56 E-value=5 Score=34.76 Aligned_cols=26 Identities=23% Similarity=0.484 Sum_probs=21.5
Q ss_pred HHHHHhcccCCCHHHHHHHHHh-CCCC
Q 010406 293 TISLFGEVWGIGPATAQKLYEK-GHRT 318 (511)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~-Gi~t 318 (511)
+.-.|++|+|||+++|..+.+. |+..
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 5667789999999999999987 8753
No 182
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=68.26 E-value=5.4 Score=33.60 Aligned_cols=54 Identities=24% Similarity=0.335 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHh-CCCCHHH
Q 010406 261 GIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDD 321 (511)
Q Consensus 261 gIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~-Gi~tled 321 (511)
||+.+++.+|.+.... .-++.|+++ ||. |+..|.|||-++|.++... |+..-+.
T Consensus 19 gl~~~~a~kl~~~yg~---~ai~~l~~n-PY~---L~~~i~gi~F~~aD~iA~~~g~~~~d~ 73 (94)
T PF14490_consen 19 GLSPKLAMKLYKKYGD---DAIEILKEN-PYR---LIEDIDGIGFKTADKIALKLGIEPDDP 73 (94)
T ss_dssp T--HHHHHHHHHHH-T---THHHHHHH--STC---CCB-SSSSBHHHHHHHHHTTT--TT-H
T ss_pred CCCHHHHHHHHHHHhH---HHHHHHHHC-hHH---HHHHccCCCHHHHHHHHHHcCCCCCCH
Confidence 8999999999998775 444555554 553 3434899999999999987 7764433
No 183
>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=67.99 E-value=3.5 Score=34.19 Aligned_cols=20 Identities=40% Similarity=0.624 Sum_probs=17.9
Q ss_pred HHHhcccCCCHHHHHHHHHh
Q 010406 295 SLFGEVWGIGPATAQKLYEK 314 (511)
Q Consensus 295 ~lf~~I~GvGpktA~~l~~~ 314 (511)
++|++|||||+.+|-.+..+
T Consensus 2 ~~l~sipGig~~~a~~llae 21 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAE 21 (87)
T ss_pred chhcCCCCccHHHHHHHHHH
Confidence 46789999999999999986
No 184
>COG1746 CCA1 tRNA nucleotidyltransferase (CCA-adding enzyme) [Translation, ribosomal structure and biogenesis]
Probab=67.91 E-value=12 Score=40.18 Aligned_cols=47 Identities=28% Similarity=0.380 Sum_probs=34.3
Q ss_pred HHHHHHHHHHhhhcCCCeEEEEccceeecCCcc--CCeeEEEecCCcch
Q 010406 352 EQMERLLQKAGEEVLPEVIILCGGSYRRGKASC--GDLDVVIMHPDRKS 398 (511)
Q Consensus 352 ~~~~~iv~~~~~~~~p~~~v~~~Gs~RRgke~~--gDvDiLit~~~~~~ 398 (511)
+.+...+.+++++....+.+.+.|||.||-=.. +|||+-|.-|...+
T Consensus 29 e~l~~~~~~~~~e~~~~aev~lVGS~AkgTwL~gd~DIDvFi~Fp~d~~ 77 (443)
T COG1746 29 EELRERINEIIEELGIDAEVVLVGSYAKGTWLRGDHDIDVFIAFPKDTS 77 (443)
T ss_pred HHHHHHHHHHHHhcCCcceEEEEeecccCcccCCCcceeEEEECCCCCC
Confidence 334444555555556678899999999987655 78999998887654
No 185
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=65.64 E-value=3.1 Score=46.61 Aligned_cols=42 Identities=19% Similarity=0.367 Sum_probs=29.5
Q ss_pred HHhcccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhhcccc
Q 010406 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKY 338 (511)
Q Consensus 296 lf~~I~GvGpktA~~l~~~Gi~tledL~~~~--~L~~~q~~Glk~ 338 (511)
.|.+|+||||++.++|++. +.|+++++++. .|....+++.+.
T Consensus 515 ~L~~I~GiG~kr~~~LL~~-Fgs~~~I~~As~eeL~~v~gi~~~~ 558 (574)
T PRK14670 515 NYTKIKGIGEKKAKKILKS-LGTYKDILLLNEDEIAEKMKINIKM 558 (574)
T ss_pred ccccCCCCCHHHHHHHHHH-hCCHHHHHhCCHHHHHhCCCCCHHH
Confidence 4569999999999999984 56888888653 244444444333
No 186
>COG2251 Predicted nuclease (RecB family) [General function prediction only]
Probab=65.38 E-value=4.7 Score=43.34 Aligned_cols=27 Identities=37% Similarity=0.452 Sum_probs=24.8
Q ss_pred cccCCCHHHHHHHHHhCCCCHHHHhhc
Q 010406 299 EVWGIGPATAQKLYEKGHRTLDDLKNE 325 (511)
Q Consensus 299 ~I~GvGpktA~~l~~~Gi~tledL~~~ 325 (511)
=|+||||.+.+.++..||+|++||-..
T Consensus 229 Lv~Gi~~~r~~~l~~~GI~Ti~~LA~~ 255 (474)
T COG2251 229 LVPGITPSRYDVLEEVGITTIEDLADA 255 (474)
T ss_pred ccCCCCHHHHHHHHHcCcchHHHHHhc
Confidence 468999999999999999999999864
No 187
>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=65.14 E-value=11 Score=38.69 Aligned_cols=61 Identities=25% Similarity=0.432 Sum_probs=41.2
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHh-----C---CCCHHHHhh
Q 010406 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-----G---HRTLDDLKN 324 (511)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~-----G---i~tledL~~ 324 (511)
+.+|||||+.+++++.+. -+..+++|..-. .+.+.+++|++.++|.+||+. | +.|..++..
T Consensus 1 l~~i~gig~~~~~~L~~~----Gi~ti~dl~~~~----~~~L~~~~g~~~~~a~~l~~~~~~~~~~~~~~t~~~~~~ 69 (310)
T TIGR02236 1 LEDLPGVGPATAEKLREA----GYDTFEAIAVAS----PKELSEIAGISEGTAAKIIQAARKAADLGGFETADDVLE 69 (310)
T ss_pred CcccCCCCHHHHHHHHHc----CCCCHHHHHcCC----HHHHHhccCCCHHHHHHHHHHHHHHhhccCCCCHHHHHH
Confidence 467999999999887765 234455655432 234458889999999999863 2 346656643
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=65.07 E-value=4.6 Score=38.90 Aligned_cols=32 Identities=22% Similarity=0.359 Sum_probs=23.6
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHH
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHF 285 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l 285 (511)
+.+..|||||++.|.++.-.+-.-.-.+++.|
T Consensus 11 ~~l~~LPGIG~KsA~RlA~~ll~~~~~~~~~l 42 (195)
T TIGR00615 11 ESLKKLPGIGPKSAQRLAFHLLKRDPSEVLRL 42 (195)
T ss_pred HHHHHCCCCCHHHHHHHHHHHHcCCHHHHHHH
Confidence 67899999999999999877654443444433
No 189
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=64.92 E-value=4.5 Score=41.61 Aligned_cols=54 Identities=28% Similarity=0.405 Sum_probs=41.0
Q ss_pred hhHHHHHHhcccCCCHHHHHHHHHh---CC-CCHHHHhhccC------cchhhhhcccchhhhc
Q 010406 290 KVRTISLFGEVWGIGPATAQKLYEK---GH-RTLDDLKNEDS------LTHSQRLGLKYFDDIK 343 (511)
Q Consensus 290 ~~~~l~lf~~I~GvGpktA~~l~~~---Gi-~tledL~~~~~------L~~~q~~Glk~~~d~~ 343 (511)
|...++....+||+|||.|++|-+- |. +-+++++++.+ ++..-|+|.++.+.|.
T Consensus 51 ~I~S~~ea~~lP~iG~kia~ki~EiletG~l~ele~v~~de~~~~lklFtnifGvG~ktA~~Wy 114 (353)
T KOG2534|consen 51 PITSGEEAEKLPGIGPKIAEKIQEILETGVLRELEAVRNDERSQSLKLFTNIFGVGLKTAEKWY 114 (353)
T ss_pred CcccHHHhcCCCCCCHHHHHHHHHHHHcCCchhHHHHhcchhHHHHHHHHHHhccCHHHHHHHH
Confidence 3446788889999999999999862 64 78888886432 5667778888877775
No 190
>PRK02362 ski2-like helicase; Provisional
Probab=64.44 E-value=48 Score=38.38 Aligned_cols=52 Identities=19% Similarity=0.464 Sum_probs=39.8
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHh-C
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-G 315 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~-G 315 (511)
-+|..|||||...+.++.+ .| +.-+++|.+-++..+..+ +|.|+|+++.+. |
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 4588999999998877664 44 677777776556555555 599999999997 6
No 191
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=64.40 E-value=4.9 Score=45.54 Aligned_cols=32 Identities=25% Similarity=0.423 Sum_probs=25.8
Q ss_pred HHHHHhcccCCCHHHHHHHHHhCCCCHHHHhhc
Q 010406 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (511)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~Gi~tledL~~~ 325 (511)
....|..|+||||++|+.|++. +.|+++|.++
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 3456679999999999999885 4488888864
No 192
>PRK03980 flap endonuclease-1; Provisional
Probab=64.17 E-value=5.5 Score=40.85 Aligned_cols=25 Identities=44% Similarity=0.670 Sum_probs=21.4
Q ss_pred cccCCCHHHHHHHHHhCCCCHHHHhh
Q 010406 299 EVWGIGPATAQKLYEKGHRTLDDLKN 324 (511)
Q Consensus 299 ~I~GvGpktA~~l~~~Gi~tledL~~ 324 (511)
+|+|||||||.+|.++ +.||+.+..
T Consensus 193 GI~GIG~ktA~kLi~~-~~sle~i~~ 217 (292)
T PRK03980 193 GIKGIGPKTALKLIKK-HGDLEKVLE 217 (292)
T ss_pred CCCCccHHHHHHHHHH-CCCHHHHHH
Confidence 7899999999999987 237888876
No 193
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=64.10 E-value=8.7 Score=43.55 Aligned_cols=49 Identities=27% Similarity=0.575 Sum_probs=35.0
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHH
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (511)
..|.+|||||++.+..|..-. |++ +.+.+. ..+.|.+| ||+++|+++++
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--GSV---EKVAKA----SLEELAAV--AGPKTAETIYR 617 (621)
T ss_pred hhhhcCCCcCHHHHHHHHHHc--CCH---HHHHhC----CHHHHHHH--hCHHHHHHHHH
Confidence 568899999999999776532 233 455442 34445577 99999999976
No 194
>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=63.86 E-value=5.4 Score=43.45 Aligned_cols=29 Identities=45% Similarity=0.571 Sum_probs=26.5
Q ss_pred hcccCCCHHHHHHHHHhCCCCHHHHhhcc
Q 010406 298 GEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (511)
Q Consensus 298 ~~I~GvGpktA~~l~~~Gi~tledL~~~~ 326 (511)
.-|+|||.+++.+|++.||.|++||-...
T Consensus 210 slv~gi~~~~~~~L~~~GI~ti~~La~~~ 238 (457)
T TIGR03491 210 SLVPGIGPSRYRLLQELGIHTLEDLAAAD 238 (457)
T ss_pred eecCCCCHHHHHHHHHcCCCcHHHHhcCC
Confidence 37999999999999999999999998654
No 195
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=63.84 E-value=3.8 Score=45.86 Aligned_cols=29 Identities=24% Similarity=0.521 Sum_probs=24.0
Q ss_pred HHhcccCCCHHHHHHHHHhCCCCHHHHhhc
Q 010406 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (511)
Q Consensus 296 lf~~I~GvGpktA~~l~~~Gi~tledL~~~ 325 (511)
.|.+|+|||||+.++|++. +.|+++++++
T Consensus 515 ~Ld~I~GiG~kr~~~Ll~~-Fgs~~~ik~A 543 (567)
T PRK14667 515 ILDKIKGIGEVKKEIIYRN-FKTLYDFLKA 543 (567)
T ss_pred ccccCCCCCHHHHHHHHHH-hCCHHHHHhC
Confidence 4569999999999999984 5588888765
No 196
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=63.53 E-value=8.9 Score=43.09 Aligned_cols=51 Identities=20% Similarity=0.416 Sum_probs=30.8
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHH
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (511)
..|..|||||+..+.++.+. -|++. .+.+. ..+.+..|||+|++.|+.+++
T Consensus 525 ~~L~~IpGIG~kr~~~LL~~--FGS~~---~I~~A----s~eeL~~vpGi~~~~A~~I~~ 575 (577)
T PRK14668 525 TVLDDVPGVGPETRKRLLRR--FGSVE---GVREA----SVEDLRDVPGVGEKTAETIRE 575 (577)
T ss_pred hHHhcCCCCCHHHHHHHHHH--cCCHH---HHHhC----CHHHHHhCCCCCHHHHHHHHH
Confidence 45778888888777766543 24333 33221 233445788888888887764
No 197
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=63.51 E-value=10 Score=42.95 Aligned_cols=96 Identities=16% Similarity=0.172 Sum_probs=55.8
Q ss_pred CCCCCCCCCCCCCCCCCCCeEEEEecCCCcchHHHHHHHHHHhcCCEEEeecC------CCccEEEEcC-Ch-HHHHHHH
Q 010406 3 PKTTRKPTPALDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLS------KKVTHVLAMD-LE-ALLQQVS 74 (511)
Q Consensus 3 p~r~~~~~~~~~~~~~F~g~~iy~~~~~~g~~r~~~l~~~~~~~Gg~v~~~~s------~~VTHVV~~~-~s-~~~~~l~ 74 (511)
|+.+|.++ -+.-..+|.|+.+||++.....- .+.|.+++..-||++...-+ ..-|-||... .. ....|.+
T Consensus 573 ~~~~~~~a-~s~~~kLf~gl~~~~~g~fs~~p-~~~l~~l~~~~gg~~l~~~~~~~~~~k~s~~~~~~~~~~~~~~~~~k 650 (684)
T KOG4362|consen 573 PKEKRLRA-ESYKPKLFEGLKFYFVGDFSNPP-KEQLQELVHLAGGTILQVPRVAYSDKKKSTIVVLSEKPVLDSILWQK 650 (684)
T ss_pred cccccccc-cccCcchhcCCcceeecccccCc-HHHHHHHHhhcCcceeeccCcccccccccceeEeecccCCCchhhhh
Confidence 44454433 33445899999999998755322 36688999999999886431 1223333211 00 0111222
Q ss_pred HHhhh----ccCCcccccchHHHHHhcCCC
Q 010406 75 KQHLA----RFKGSVIRYQWLEDSLRLGEK 100 (511)
Q Consensus 75 ~~~~~----~~~~~iV~~~Wl~ecik~g~l 100 (511)
...+. .-..+.|+-.||.+++.--+.
T Consensus 651 ~~~~ea~~~s~~a~~~~~~wvl~s~a~~~~ 680 (684)
T KOG4362|consen 651 VNDAEALALSQRARAVSSSWVLDSIAGYQI 680 (684)
T ss_pred hccHHHHHHhcCCCccchhhhhcchhceee
Confidence 21111 126789999999999865443
No 198
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=63.37 E-value=6.2 Score=40.39 Aligned_cols=33 Identities=30% Similarity=0.330 Sum_probs=25.2
Q ss_pred HHHHhcccCCCHHHHHHHHHh-CC--CCHHHHhhcc
Q 010406 294 ISLFGEVWGIGPATAQKLYEK-GH--RTLDDLKNED 326 (511)
Q Consensus 294 l~lf~~I~GvGpktA~~l~~~-Gi--~tledL~~~~ 326 (511)
.+++.+|||+|+|.|+++... -. -|+|+|++-|
T Consensus 329 ~~~llRVPGiG~ksa~rIv~~Rr~~rl~~e~Lkk~G 364 (404)
T COG4277 329 YKELLRVPGIGVKSARRIVMTRRRTRLTLEDLKKLG 364 (404)
T ss_pred HHHhcccCCCChHHHHHHHHHhhhcccCHHHHhhhc
Confidence 456669999999999999975 33 3677887644
No 199
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=63.31 E-value=6.7 Score=37.21 Aligned_cols=59 Identities=19% Similarity=0.353 Sum_probs=33.0
Q ss_pred HHHHHHHHHHhCCchhhHHHHhhchhH-HHHHHhcccCCCHHHHHHHHHh----CCCCHHHHhh
Q 010406 266 MQDHIQEIVTTGKLSKLEHFEKDEKVR-TISLFGEVWGIGPATAQKLYEK----GHRTLDDLKN 324 (511)
Q Consensus 266 ia~kI~Eil~tG~~~~le~l~~~~~~~-~l~lf~~I~GvGpktA~~l~~~----Gi~tledL~~ 324 (511)
+-..|++|+....-..++-+....|.- -|-.|.=+||||.|+...+.++ -+.|++|+.+
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 445688888887766666655433322 1222444699999999999863 5777777764
No 200
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=63.25 E-value=5.4 Score=47.12 Aligned_cols=24 Identities=42% Similarity=0.678 Sum_probs=20.1
Q ss_pred cccCCCHHHHHHHHHh-CCCCHHHHhh
Q 010406 299 EVWGIGPATAQKLYEK-GHRTLDDLKN 324 (511)
Q Consensus 299 ~I~GvGpktA~~l~~~-Gi~tledL~~ 324 (511)
+|+|||||||.+|.++ | |||.+..
T Consensus 189 GVpGIG~KtA~kLL~~yg--sle~i~~ 213 (887)
T TIGR00593 189 GVKGIGEKTAAKLLQEFG--SLENIYE 213 (887)
T ss_pred CCCCcCHHHHHHHHHHcC--CHHHHHH
Confidence 5899999999999987 6 7777653
No 201
>PRK05007 PII uridylyl-transferase; Provisional
Probab=62.25 E-value=24 Score=41.76 Aligned_cols=50 Identities=20% Similarity=0.446 Sum_probs=36.2
Q ss_pred CCeEEEEccceeec-CCccCCeeEEEecCCcc--hhhhHHHHHHHHHHHhcce
Q 010406 367 PEVIILCGGSYRRG-KASCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMKFL 416 (511)
Q Consensus 367 p~~~v~~~Gs~RRg-ke~~gDvDiLit~~~~~--~~~~~l~~~v~~l~~~g~l 416 (511)
|++-+..+|||=|| ..-.+||||||-+++.. .....+.+++..|-+.|+-
T Consensus 79 ~~~alvAvGgyGR~EL~p~SDiDll~l~~~~~~~~~~~~i~~~~~~lwD~gL~ 131 (884)
T PRK05007 79 PDLALVAVGGYGRGELHPLSDIDLLILSRKKLPDEQAQKVGELITLLWDLKLE 131 (884)
T ss_pred CceEEEecCCCCCcccCCcccceEEEEeCCCCChHHHHHHHHHHHHHHhcCCC
Confidence 45778889999665 46689999999987532 2455677777777777764
No 202
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=62.25 E-value=6.1 Score=38.84 Aligned_cols=30 Identities=33% Similarity=0.531 Sum_probs=27.2
Q ss_pred HHHhcccCCCHHHHHHHHHhCCCCHHHHhh
Q 010406 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (511)
Q Consensus 295 ~lf~~I~GvGpktA~~l~~~Gi~tledL~~ 324 (511)
.-|+.|.||||+.+.+|.+.||.++++|-.
T Consensus 158 DDL~~I~GIGp~~a~~L~eaGi~tfaQIAa 187 (221)
T PRK12278 158 DDLTKITGVGPALAKKLNEAGVTTFAQIAA 187 (221)
T ss_pred chheeccccChHHHHHHHHcCCCCHHHhhC
Confidence 356799999999999999999999999974
No 203
>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=61.90 E-value=6.6 Score=30.98 Aligned_cols=23 Identities=26% Similarity=0.349 Sum_probs=17.9
Q ss_pred hHHHHH-HhcccCCCHHHHHHHHH
Q 010406 291 VRTISL-FGEVWGIGPATAQKLYE 313 (511)
Q Consensus 291 ~~~l~l-f~~I~GvGpktA~~l~~ 313 (511)
...++. +.+|||||+++|.++.+
T Consensus 42 i~~~~~~~~~l~gIG~~ia~kI~E 65 (68)
T PF14716_consen 42 ITSGEEDLKKLPGIGKSIAKKIDE 65 (68)
T ss_dssp HHSHHHHHCTSTTTTHHHHHHHHH
T ss_pred HhhHHHHHhhCCCCCHHHHHHHHH
Confidence 334554 78999999999999854
No 204
>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=61.65 E-value=11 Score=31.45 Aligned_cols=31 Identities=23% Similarity=0.408 Sum_probs=24.4
Q ss_pred HHhcccCCCHHHHHHHHHh----CCCCHHHHhhcc
Q 010406 296 LFGEVWGIGPATAQKLYEK----GHRTLDDLKNED 326 (511)
Q Consensus 296 lf~~I~GvGpktA~~l~~~----Gi~tledL~~~~ 326 (511)
=|+.|.|||.+.|+++.++ .+.|++|+....
T Consensus 28 gl~~Ikglg~~~a~~I~~~R~~g~f~s~~df~~R~ 62 (90)
T PF14579_consen 28 GLSAIKGLGEEVAEKIVEERENGPFKSLEDFIQRL 62 (90)
T ss_dssp BGGGSTTS-HHHHHHHHHHHHCSS-SSHHHHHHHS
T ss_pred hHhhcCCCCHHHHHHHHHhHhcCCCCCHHHHHHHH
Confidence 3779999999999999973 689999988643
No 205
>PRK13844 recombination protein RecR; Provisional
Probab=60.91 E-value=5.6 Score=38.45 Aligned_cols=32 Identities=16% Similarity=0.251 Sum_probs=24.3
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHH
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHF 285 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l 285 (511)
+.+..|||||++.|.++.-.+-.-.-.++++|
T Consensus 15 ~~l~~LPGIG~KsA~Rla~~lL~~~~~~~~~l 46 (200)
T PRK13844 15 ESLRKLPTIGKKSSQRLALYLLDKSPETAIAI 46 (200)
T ss_pred HHHHHCCCCCHHHHHHHHHHHHcCCHHHHHHH
Confidence 57899999999999999887765444444444
No 206
>PTZ00217 flap endonuclease-1; Provisional
Probab=60.46 E-value=6.9 Score=41.87 Aligned_cols=26 Identities=35% Similarity=0.640 Sum_probs=21.9
Q ss_pred hcccCCCHHHHHHHHHhCCCCHHHHhh
Q 010406 298 GEVWGIGPATAQKLYEKGHRTLDDLKN 324 (511)
Q Consensus 298 ~~I~GvGpktA~~l~~~Gi~tledL~~ 324 (511)
-+|+|||||||.+|.++ +.|++.+..
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 238888864
No 207
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=59.76 E-value=23 Score=40.25 Aligned_cols=73 Identities=21% Similarity=0.101 Sum_probs=54.2
Q ss_pred CCCCCeEEEEecCCCcchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCCcccccchHHHH
Q 010406 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDS 94 (511)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~r~~~l~~~~~~~Gg~v~~~~s~~VTHVV~~~~s~~~~~l~~~~~~~~~~~iV~~~Wl~ec 94 (511)
..|.|.+|.|-++--+-+| ...+.+++..||.|+.++|..+.-||+-++- -.+..++. ..+++|++.+++.+-
T Consensus 593 ~~l~gkt~V~TGtL~~~sR-~eak~~le~lGakv~~SVSkktD~vvaG~~a-GSKl~kA~---eLgv~i~~E~~~~~l 665 (667)
T COG0272 593 SPLAGKTFVLTGTLEGMSR-DEAKALLEALGAKVSGSVSKKTDYVVAGENA-GSKLAKAQ---ELGVKIIDEEEFLAL 665 (667)
T ss_pred cccCCCEEEEeccCCCCCH-HHHHHHHHHcCCEEeceecccccEEEEcCCC-ChHHHHHH---HcCCeEecHHHHHHh
Confidence 6799999999777555555 5578999999999999999998888886542 22333322 237889988887653
No 208
>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=59.19 E-value=2.8 Score=33.13 Aligned_cols=45 Identities=24% Similarity=0.337 Sum_probs=33.1
Q ss_pred ccCCCHHHHHHHHHhCCCCHHHHhhc--cCcchhhhhcccchhhhcc
Q 010406 300 VWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDIKT 344 (511)
Q Consensus 300 I~GvGpktA~~l~~~Gi~tledL~~~--~~L~~~q~~Glk~~~d~~~ 344 (511)
--|+-+++...|-..||.|+.||..- ..|..+++||-+..++|.+
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 33667788888888899999999853 3588889999888877654
No 209
>PRK14973 DNA topoisomerase I; Provisional
Probab=59.02 E-value=9.9 Score=45.15 Aligned_cols=41 Identities=17% Similarity=0.136 Sum_probs=32.6
Q ss_pred HHHhcccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhhc
Q 010406 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLG 335 (511)
Q Consensus 295 ~lf~~I~GvGpktA~~l~~~Gi~tledL~~~~--~L~~~q~~G 335 (511)
+-|++++||=...|+++|+.||+|++|+..+. -|+..-|+.
T Consensus 802 ~~~~~~~gv~~~~~~~~~~~G~~~~~d~~~a~p~~La~~~g~~ 844 (936)
T PRK14973 802 ISRLKEIGVPAVSLKKYQEAGFDTPEDFCSVHPAYLALKTGIS 844 (936)
T ss_pred HHhhcccCCCHHHHHHHHHhcCCCHHHHHhcCHHHHhcCCCCC
Confidence 34569999999999999999999999998654 355444444
No 210
>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=58.86 E-value=19 Score=38.31 Aligned_cols=54 Identities=20% Similarity=0.484 Sum_probs=35.4
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhc---------------hhHHHHHHhcccCCCHHHHHHHHHh--CCC
Q 010406 255 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDE---------------KVRTISLFGEVWGIGPATAQKLYEK--GHR 317 (511)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~---------------~~~~l~lf~~I~GvGpktA~~l~~~--Gi~ 317 (511)
.+..|||||+++++++..+ | +..+-+|.+-. .....+.| |.+++.++|+. |+.
T Consensus 173 pv~~l~GiG~~~~~kL~~~---G-I~tigdl~~~~~~~~~~~~~~~~~~s~~~L~~~f------G~~~g~~l~~~a~G~d 242 (379)
T cd01703 173 DLRKIPGIGYKTAAKLEAH---G-ISSVRDLQEFSNRNRQTVGAAPSLLELLLMVKEF------GEGIGQRIWKLLFGRD 242 (379)
T ss_pred CccccCCcCHHHHHHHHHc---C-CCcHHHHHhCCcccccccccccccccHHHHHHHH------CHHHHHHHHHHHCCCC
Confidence 4788999999999999875 3 33333433322 22333444 67778888885 887
Q ss_pred C
Q 010406 318 T 318 (511)
Q Consensus 318 t 318 (511)
+
T Consensus 243 ~ 243 (379)
T cd01703 243 T 243 (379)
T ss_pred C
Confidence 5
No 211
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=58.67 E-value=21 Score=34.86 Aligned_cols=31 Identities=19% Similarity=0.504 Sum_probs=23.2
Q ss_pred HhcCCcccc-chhhhcCCCCCCHHHHHHHHHH
Q 010406 243 IEKLPFKIE-SADQVKGLPGIGKSMQDHIQEI 273 (511)
Q Consensus 243 l~~l~~~i~-s~~~l~~lpgIG~~ia~kI~Ei 273 (511)
++.+..++. ++++|.+|||||.++|..+.-.
T Consensus 97 ~e~~~g~vP~~~~eL~~LPGVGrKTAnvVL~~ 128 (211)
T COG0177 97 LEKFGGEVPDTREELLSLPGVGRKTANVVLSF 128 (211)
T ss_pred HHHcCCCCCchHHHHHhCCCcchHHHHHHHHh
Confidence 344555554 3688999999999999987654
No 212
>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=58.21 E-value=8.1 Score=40.44 Aligned_cols=27 Identities=41% Similarity=0.588 Sum_probs=23.0
Q ss_pred hcccCCCHHHHHHHHHhCCCCHHHHhhc
Q 010406 298 GEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (511)
Q Consensus 298 ~~I~GvGpktA~~l~~~Gi~tledL~~~ 325 (511)
-+|+|||||||.+|.++ +.|++.+.+.
T Consensus 239 ~Gv~GIG~ktA~kli~~-~gsie~il~~ 265 (338)
T TIGR03674 239 EGVKGIGPKTALKLIKE-HGDLEKVLKA 265 (338)
T ss_pred CCCCCccHHHHHHHHHH-cCCHHHHHHh
Confidence 48999999999999998 3488888754
No 213
>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=57.60 E-value=24 Score=33.60 Aligned_cols=42 Identities=10% Similarity=0.311 Sum_probs=27.9
Q ss_pred hHHHHHHHHHHHh-cCCcccc-chhhhcCCCCCCHHHHHHHHHH
Q 010406 232 RSFSYYKAIPVIE-KLPFKIE-SADQVKGLPGIGKSMQDHIQEI 273 (511)
Q Consensus 232 r~~aY~rAa~~l~-~l~~~i~-s~~~l~~lpgIG~~ia~kI~Ei 273 (511)
|+..-.+.+..+. .....+. ..++|.+|||||+.+|+.|-=+
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 5555556665553 2222222 3578999999999999998733
No 214
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=57.37 E-value=34 Score=40.38 Aligned_cols=68 Identities=16% Similarity=0.295 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHHHhhhcCC----CeEEEEccceeecC-CccCCeeEEEecCCcc--hhhhHHHHHHHHHHHhcce
Q 010406 349 HEVEQMERLLQKAGEEVLP----EVIILCGGSYRRGK-ASCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMKFL 416 (511)
Q Consensus 349 ~ea~~~~~iv~~~~~~~~p----~~~v~~~Gs~RRgk-e~~gDvDiLit~~~~~--~~~~~l~~~v~~l~~~g~l 416 (511)
.-+..+..+++.+-....+ ++-+..+|||=||. .--+||||||-+++.. .....+.+++..|=+.|+-
T Consensus 33 ~~~~~~D~~l~~l~~~~~~~~~~~iaLvAvGGYGR~eL~P~SDIDlliL~~~~~~~~~~~~i~~~~~~LWD~gl~ 107 (854)
T PRK01759 33 NRSDFYDQLLIHLWQQFGLEEQSDLALIAVGGYGRREMFPLSDLDILILTEQPPDEETEEKINQFFQFLWDCGFE 107 (854)
T ss_pred HHHHHHHHHHHHHHHHccCCCCCCeEEEEeCCcccccCCCcccceEEEEeCCCCChHHHHHHHHHHHHHHhcCCC
Confidence 3344455666655443322 35677889997664 4568999999887542 3456677777777677764
No 215
>PRK01216 DNA polymerase IV; Validated
Probab=57.30 E-value=35 Score=35.92 Aligned_cols=52 Identities=21% Similarity=0.362 Sum_probs=36.8
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHh--CCC
Q 010406 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHR 317 (511)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~--Gi~ 317 (511)
+..|||||+++++++..+ -+..+.+|.+-......+.| |+..+..||+. |+.
T Consensus 180 i~~l~giG~~~~~~L~~~----Gi~TigdL~~~~~~~L~~rf------G~~~~~~L~~~a~G~d 233 (351)
T PRK01216 180 IADIPGIGDITAEKLKKL----GVNKLVDTLRIEFDELKGII------GEAKAKYLFSLARNEY 233 (351)
T ss_pred cccccCCCHHHHHHHHHc----CCCcHHHHhcCCHHHHHHHH------CHHHHHHHHHHhCCCC
Confidence 677899999998887754 35667777664444455556 67778889884 654
No 216
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=57.26 E-value=4.8 Score=45.60 Aligned_cols=30 Identities=27% Similarity=0.442 Sum_probs=24.1
Q ss_pred HHHhcccCCCHHHHHHHHHhCCCCHHHHhhc
Q 010406 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (511)
Q Consensus 295 ~lf~~I~GvGpktA~~l~~~Gi~tledL~~~ 325 (511)
..|.+|+||||+++++|++. +.|+++++++
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 35669999999999999984 5577777764
No 217
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=56.99 E-value=11 Score=37.50 Aligned_cols=32 Identities=19% Similarity=0.288 Sum_probs=22.1
Q ss_pred HHHHhhchhHHHHHHhcccCCCHHHHHHHHHhC
Q 010406 283 EHFEKDEKVRTISLFGEVWGIGPATAQKLYEKG 315 (511)
Q Consensus 283 e~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~G 315 (511)
+++..|.|.. ++.|.++||||||.|.--.+.+
T Consensus 148 d~f~gDIP~~-v~dLlsLPGVGPKMa~L~m~~A 179 (286)
T KOG1921|consen 148 DKFDGDIPDT-VEDLLSLPGVGPKMAHLTMQVA 179 (286)
T ss_pred HHhCCCCchh-HHHHhcCCCCchHHHHHHHHHH
Confidence 4555666654 4445599999999998665543
No 218
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=56.91 E-value=5.6 Score=45.26 Aligned_cols=52 Identities=15% Similarity=0.251 Sum_probs=37.4
Q ss_pred HHhcccCCCHHHHHHHHHhCCCCHHHHhhcc--CcchhhhhcccchhhhccCcCH
Q 010406 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIKTRIPR 348 (511)
Q Consensus 296 lf~~I~GvGpktA~~l~~~Gi~tledL~~~~--~L~~~q~~Glk~~~d~~~~i~r 348 (511)
.|.+|+||||++.++|++. |.|+++|+++. .|....++|.+..+.|...-.|
T Consensus 609 ~L~~IpGiG~kr~~~LL~~-FgS~~~i~~As~eel~~v~gi~~~~A~~i~~~~~~ 662 (691)
T PRK14672 609 SFERLPHVGKVRAHRLLAH-FGSFRSLQSATPQDIATAIHIPLTQAHTILHAATR 662 (691)
T ss_pred ccccCCCCCHHHHHHHHHH-hcCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHhhc
Confidence 4569999999999999984 55888888653 3666666676666666544433
No 219
>PRK05755 DNA polymerase I; Provisional
Probab=56.83 E-value=7.9 Score=45.74 Aligned_cols=24 Identities=46% Similarity=0.610 Sum_probs=20.2
Q ss_pred hcccCCCHHHHHHHHHh-CCCCHHHHh
Q 010406 298 GEVWGIGPATAQKLYEK-GHRTLDDLK 323 (511)
Q Consensus 298 ~~I~GvGpktA~~l~~~-Gi~tledL~ 323 (511)
-+|+|||||||.+|.++ | |++.+.
T Consensus 190 pGv~GiG~ktA~~Ll~~~g--sle~i~ 214 (880)
T PRK05755 190 PGVPGIGEKTAAKLLQEYG--SLEGLY 214 (880)
T ss_pred CCCCCccHHHHHHHHHHcC--CHHHHH
Confidence 47899999999999987 6 677765
No 220
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=56.81 E-value=8.9 Score=43.97 Aligned_cols=27 Identities=41% Similarity=0.623 Sum_probs=24.9
Q ss_pred HhcccCCCHHHHHHHHHhCCCCHHHHh
Q 010406 297 FGEVWGIGPATAQKLYEKGHRTLDDLK 323 (511)
Q Consensus 297 f~~I~GvGpktA~~l~~~Gi~tledL~ 323 (511)
++.+.||||++|+.|-+.||.|+.||.
T Consensus 11 ~~~l~gvg~~~~~~l~~lgi~t~~dll 37 (681)
T PRK10917 11 LTSLKGVGPKTAEKLAKLGIHTVQDLL 37 (681)
T ss_pred hhhcCCCCHHHHHHHHHcCCCCHHHHh
Confidence 457899999999999988999999997
No 221
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=56.70 E-value=23 Score=36.05 Aligned_cols=29 Identities=17% Similarity=0.130 Sum_probs=26.2
Q ss_pred HhcccCCCHHHHHHHHHhCCCCHHHHhhc
Q 010406 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (511)
Q Consensus 297 f~~I~GvGpktA~~l~~~Gi~tledL~~~ 325 (511)
|.++||+|+..++++.+.|+.|++||...
T Consensus 153 L~Qlp~i~~~~~~~l~~~~i~s~~~l~~~ 181 (312)
T smart00611 153 LLQLPHLPEEILKRLEKKKVLSLEDLLEL 181 (312)
T ss_pred cccCCCCCHHHHHHHHhCCCCCHHHHHhc
Confidence 44999999999999999999999999864
No 222
>COG1669 Predicted nucleotidyltransferases [General function prediction only]
Probab=56.55 E-value=39 Score=28.92 Aligned_cols=31 Identities=29% Similarity=0.415 Sum_probs=23.7
Q ss_pred CCe-EEEEccceeecCCc-cCCeeEEEecCCcc
Q 010406 367 PEV-IILCGGSYRRGKAS-CGDLDVVIMHPDRK 397 (511)
Q Consensus 367 p~~-~v~~~Gs~RRgke~-~gDvDiLit~~~~~ 397 (511)
.|+ .+.+-|||=||... -.||||||-...+.
T Consensus 22 ~gv~~~~vFGS~aRgE~~~~SDIDILVef~~~~ 54 (97)
T COG1669 22 YGVKRVAVFGSYARGEQKPDSDIDILVEFEPGK 54 (97)
T ss_pred hCCceEEEeeeeecCCCCCCCCceeEEeecCCc
Confidence 455 78899999998643 38999999765553
No 223
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=56.18 E-value=7.8 Score=34.56 Aligned_cols=25 Identities=24% Similarity=0.383 Sum_probs=20.5
Q ss_pred HHHHHhcccCCCHHHHHHHHHh-CCC
Q 010406 293 TISLFGEVWGIGPATAQKLYEK-GHR 317 (511)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~-Gi~ 317 (511)
+.--|+.|+|||+++|.++-+. ||.
T Consensus 15 v~~aLt~i~GIG~~~A~~ic~~lgi~ 40 (122)
T CHL00137 15 IEYALTYIYGIGLTSAKEILEKANID 40 (122)
T ss_pred eeeeecccccccHHHHHHHHHHcCcC
Confidence 3345689999999999999987 875
No 224
>KOG3524 consensus Predicted guanine nucleotide exchange factor (PEBBLE) [Signal transduction mechanisms]
Probab=56.17 E-value=6.9 Score=44.10 Aligned_cols=86 Identities=17% Similarity=0.317 Sum_probs=60.7
Q ss_pred CCCCCeEEEEecCCCcchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCCcccccchHHHHHh
Q 010406 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSLR 96 (511)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~r~~~l~~~~~~~Gg~v~~~~s~~VTHVV~~~~s~~~~~l~~~~~~~~~~~iV~~~Wl~ecik 96 (511)
..|.|+.++|.+ ....-.+.+-.-....||..+. -....||||+.+......-+. ....-++|.-+|+--++.
T Consensus 209 ~~feg~~~~f~g--F~~ee~~~m~~sle~~gg~~a~-~d~~cthvvv~e~~~~~~p~~----~s~~~~~vk~ewfw~siq 281 (850)
T KOG3524|consen 209 GVFEGLSLFFHG--FKQEEIDDMLRSLENTGGKLAP-SDTLCTHVVVNEDNDEVEPLA----VSSNQVHVKKEWFWVSIQ 281 (850)
T ss_pred ccccCCeEeecC--CcHHHHHHHHHHHHhcCCcccC-CCCCceeEeecCCcccccccc----ccccceeecccceEEEEe
Confidence 679999999954 5555566777888899999988 456899999976532211111 112456888899888888
Q ss_pred cCCCCCccccccc
Q 010406 97 LGEKVSEDLYRIK 109 (511)
Q Consensus 97 ~g~lvde~~y~l~ 109 (511)
.|..--|..|.+.
T Consensus 282 ~g~~a~e~~yl~~ 294 (850)
T KOG3524|consen 282 RGCCAIEDNYLLP 294 (850)
T ss_pred cchhccccceecc
Confidence 8877777777664
No 225
>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=56.09 E-value=5.1 Score=41.34 Aligned_cols=51 Identities=25% Similarity=0.342 Sum_probs=35.3
Q ss_pred HHHHHhcccCCCHHHHHHHHHh---C-CCCHHHHhhcc-----Ccchhhhhcccchhhhc
Q 010406 293 TISLFGEVWGIGPATAQKLYEK---G-HRTLDDLKNED-----SLTHSQRLGLKYFDDIK 343 (511)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~---G-i~tledL~~~~-----~L~~~q~~Glk~~~d~~ 343 (511)
.+..+++|||||+++|.++.+- | +..+++|+++. .|....|+|.+....|-
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 3445579999999999999873 4 46666666541 25567777776665554
No 226
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=56.01 E-value=19 Score=41.81 Aligned_cols=53 Identities=26% Similarity=0.513 Sum_probs=35.5
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHh--CCCC
Q 010406 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (511)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~--Gi~t 318 (511)
+..|||+|-+|..|+...- +...-+|+.-......+.| |||++.++|.. |+..
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----IQTCGDLQLITLIKLRKVF------GPKLGQKIYRGCRGIDD 605 (1016)
T ss_pred cccCCCccHHHHHHHHHhc----cchhHHHHHHHHHHHHhhh------cccHHHHHHHhcCCCcC
Confidence 7899999999999987654 3333344332222233334 99999999985 7754
No 227
>PRK07758 hypothetical protein; Provisional
Probab=55.90 E-value=15 Score=31.16 Aligned_cols=23 Identities=13% Similarity=0.355 Sum_probs=20.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHh
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVTT 276 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~t 276 (511)
+||.+|+|+|++..+.|+|-|..
T Consensus 67 ~ELl~iknlGkKSL~EIkekL~E 89 (95)
T PRK07758 67 KEILKLHGMGPASLPKLRKALEE 89 (95)
T ss_pred HHHHHccCCCHHHHHHHHHHHHH
Confidence 67899999999999999988754
No 228
>PRK00076 recR recombination protein RecR; Reviewed
Probab=55.77 E-value=11 Score=36.42 Aligned_cols=32 Identities=16% Similarity=0.321 Sum_probs=24.0
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHH
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHF 285 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l 285 (511)
+.+..|||||++.|.++.-.+-.-.-.+++.|
T Consensus 11 ~~l~~LPGIG~KsA~Rla~~ll~~~~~~~~~l 42 (196)
T PRK00076 11 EALRKLPGIGPKSAQRLAFHLLQRDREDVLRL 42 (196)
T ss_pred HHHHHCCCCCHHHHHHHHHHHHcCCHHHHHHH
Confidence 67899999999999999877765444444443
No 229
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=55.66 E-value=7.8 Score=34.56 Aligned_cols=24 Identities=21% Similarity=0.470 Sum_probs=20.2
Q ss_pred HHHHhcccCCCHHHHHHHHHh-CCC
Q 010406 294 ISLFGEVWGIGPATAQKLYEK-GHR 317 (511)
Q Consensus 294 l~lf~~I~GvGpktA~~l~~~-Gi~ 317 (511)
.--|+.|+|||+.+|..+.+. |+.
T Consensus 16 ~~aL~~I~GIG~~~a~~i~~~lgi~ 40 (122)
T PRK05179 16 VIALTYIYGIGRTRAKEILAAAGID 40 (122)
T ss_pred EeeecccccccHHHHHHHHHHhCcC
Confidence 334689999999999999987 875
No 230
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=55.37 E-value=8.5 Score=40.08 Aligned_cols=32 Identities=19% Similarity=0.239 Sum_probs=28.4
Q ss_pred HHHHHhcccCCCHHHHHHHHHhCCCCHHHHhh
Q 010406 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (511)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~Gi~tledL~~ 324 (511)
.-.-|+.|.||||+.+++|.+.||.+++++-.
T Consensus 261 ~~DdL~~I~GiGp~~e~~L~~~Gi~~f~QiA~ 292 (326)
T PRK12311 261 APDDLKKLTGVSPQIEKKLNDLGIFHFWQLAE 292 (326)
T ss_pred CchhhhhhccCChhhhhhhhhcCCCCHHHhhC
Confidence 34567899999999999999999999999974
No 231
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=55.29 E-value=13 Score=35.47 Aligned_cols=40 Identities=28% Similarity=0.283 Sum_probs=33.0
Q ss_pred ccccc-hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHh
Q 010406 248 FKIES-ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEK 287 (511)
Q Consensus 248 ~~i~s-~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~ 287 (511)
.||+. +-+|+-|||||++++..|.|=-+..-+..++++++
T Consensus 123 ~PIt~RLH~LELLpGiGkK~m~~ILeERkkkpFeSFeDi~~ 163 (202)
T COG1491 123 EPITLRLHQLELLPGIGKKTMWAILEERKKKPFESFEDIKE 163 (202)
T ss_pred CcchHHHHHHHhcccccHHHHHHHHHHHhcCCCcCHHHHHH
Confidence 47775 57899999999999999988777777777777765
No 232
>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=54.94 E-value=42 Score=31.03 Aligned_cols=50 Identities=24% Similarity=0.355 Sum_probs=33.0
Q ss_pred CeEEEEccceeecC-CccCCeeEEEecCCcch-----hhhHHHHHHHHHHHhccee
Q 010406 368 EVIILCGGSYRRGK-ASCGDLDVVIMHPDRKS-----HKGFLSKYVKKLKEMKFLR 417 (511)
Q Consensus 368 ~~~v~~~Gs~RRgk-e~~gDvDiLit~~~~~~-----~~~~l~~~v~~l~~~g~l~ 417 (511)
++-+.+.|||-|+. ....|+|+++-+++... ...+...+++.|...|+..
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 34667789996654 56789999998876532 2334455666676666654
No 233
>PRK02794 DNA polymerase IV; Provisional
Probab=54.69 E-value=1.1e+02 Score=32.71 Aligned_cols=52 Identities=13% Similarity=0.317 Sum_probs=34.5
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHh--CCCC
Q 010406 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (511)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~--Gi~t 318 (511)
+..|||||+.+.+++..+ -+..+.+|.+-.+...-+.| |+ .+..+|+. |+..
T Consensus 211 l~~L~GiG~~~~~~L~~~----GI~tigdL~~l~~~~L~~rf------G~-~g~~l~~~a~G~d~ 264 (419)
T PRK02794 211 VGIIWGVGPATAARLARD----GIRTIGDLQRADEADLMRRF------GS-MGLRLWRLARGIDD 264 (419)
T ss_pred hhhhCCCCHHHHHHHHHh----ccchHHHHhhCCHHHHHHHH------hH-HHHHHHHHhCCCCC
Confidence 788999999999887654 35666666654333344444 44 57777775 8764
No 234
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=54.50 E-value=23 Score=40.22 Aligned_cols=50 Identities=20% Similarity=0.429 Sum_probs=35.9
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHh
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~ 314 (511)
..|.+|||||++.+.++-+ ++..++.+++. ..+.+.+| ||.++|+++++.
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 5688999999999887765 34455555543 23344566 899999999874
No 235
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=53.19 E-value=27 Score=31.50 Aligned_cols=42 Identities=10% Similarity=0.307 Sum_probs=26.8
Q ss_pred hHHHHHHHHHHHhc-CCccc-cchhhhcCCCCCCHHHHHHHHHH
Q 010406 232 RSFSYYKAIPVIEK-LPFKI-ESADQVKGLPGIGKSMQDHIQEI 273 (511)
Q Consensus 232 r~~aY~rAa~~l~~-l~~~i-~s~~~l~~lpgIG~~ia~kI~Ei 273 (511)
|+..-...+..|.. ....+ ...+.|..|||||+.+|+.|.=+
T Consensus 48 ka~~i~~~a~~~~~~~~~~~~~~~~~L~~l~GIG~~tA~~~l~~ 91 (149)
T smart00478 48 KAKYLIELARILVEEYGGEVPDDREELLKLPGVGRKTANAVLSF 91 (149)
T ss_pred HHHHHHHHHHHHHHHHCCCccHHHHHHHcCCCCcHHHHHHHHHH
Confidence 55555555555443 12122 23567999999999999987655
No 236
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=52.32 E-value=27 Score=34.34 Aligned_cols=77 Identities=21% Similarity=0.155 Sum_probs=42.3
Q ss_pred hHHHHHHHHHHHhcCCccc------cchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCH
Q 010406 232 RSFSYYKAIPVIEKLPFKI------ESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGP 305 (511)
Q Consensus 232 r~~aY~rAa~~l~~l~~~i------~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGp 305 (511)
|+..-+..+..+..--..+ ...++|.+|||||..+|+.|-=+. -|+-.-+ ...-+..+|.++ |+.+
T Consensus 93 KA~~Lk~la~~i~~~~g~~~~~~~~~~re~Ll~l~GIG~kTAd~iLlya-~~rp~fv------VDty~~Rv~~Rl-G~~~ 164 (218)
T PRK13913 93 KAKRLIDLSENILKDFGSFENFKQEVTREWLLDQKGIGKESADAILCYV-CAKEVMV------VDKYSYLFLKKL-GIEI 164 (218)
T ss_pred HHHHHHHHHHHHHHHcCCchhccCchHHHHHHcCCCccHHHHHHHHHHH-cCCCccc------cchhHHHHHHHc-CCCC
Confidence 4555555555553211111 234679999999999999987654 3331111 112356666443 6644
Q ss_pred ---HHHHHHHHhCC
Q 010406 306 ---ATAQKLYEKGH 316 (511)
Q Consensus 306 ---ktA~~l~~~Gi 316 (511)
..+++|+..++
T Consensus 165 ~~y~~~~~~~~~~l 178 (218)
T PRK13913 165 EDYDELQHFFEKGV 178 (218)
T ss_pred CCHHHHHHHHHHhh
Confidence 44555555444
No 237
>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=52.30 E-value=9.3 Score=33.59 Aligned_cols=24 Identities=33% Similarity=0.517 Sum_probs=20.2
Q ss_pred HHHHhcccCCCHHHHHHHHHh-CCC
Q 010406 294 ISLFGEVWGIGPATAQKLYEK-GHR 317 (511)
Q Consensus 294 l~lf~~I~GvGpktA~~l~~~-Gi~ 317 (511)
.--|+.|+|||+++|..+-+. |+.
T Consensus 14 ~~aL~~i~GIG~~~a~~i~~~lgi~ 38 (113)
T TIGR03631 14 EIALTYIYGIGRTRARKILEKAGID 38 (113)
T ss_pred eeeeeeeecccHHHHHHHHHHhCcC
Confidence 334689999999999999987 875
No 238
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=50.73 E-value=24 Score=35.16 Aligned_cols=29 Identities=24% Similarity=0.481 Sum_probs=22.4
Q ss_pred cCCcccc-chhhhcCCCCCCHHHHHHHHHH
Q 010406 245 KLPFKIE-SADQVKGLPGIGKSMQDHIQEI 273 (511)
Q Consensus 245 ~l~~~i~-s~~~l~~lpgIG~~ia~kI~Ei 273 (511)
.+..+|- ++++|.+|||||++||-....+
T Consensus 149 ~f~gDIP~~v~dLlsLPGVGPKMa~L~m~~ 178 (286)
T KOG1921|consen 149 KFDGDIPDTVEDLLSLPGVGPKMAHLTMQV 178 (286)
T ss_pred HhCCCCchhHHHHhcCCCCchHHHHHHHHH
Confidence 3445554 4789999999999999877654
No 239
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=50.71 E-value=26 Score=39.42 Aligned_cols=84 Identities=20% Similarity=0.346 Sum_probs=51.9
Q ss_pred CcHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhh
Q 010406 209 LNKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKD 288 (511)
Q Consensus 209 ~N~~ia~~l~~la~~~e~~g~~~r~~aY~rAa~~l~~l~~~i~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~ 288 (511)
.|......|..+-+... .-+.+|.|.-+. .-.--..|.+|||||++-..++-.. -|++..+.
T Consensus 496 ~~~p~l~~lq~irDEaH-----rfAi~~hR~~R~------k~~~~s~Ld~I~GiG~~r~~~LL~~--Fgs~~~i~----- 557 (581)
T COG0322 496 PNSPALYLLQRIRDEAH-----RFAITYHRKKRS------KAMLQSSLDDIPGIGPKRRKALLKH--FGSLKGIK----- 557 (581)
T ss_pred CCCHHHHHHHHHHHHHH-----HHHHHHHHHHhh------hhhhcCccccCCCcCHHHHHHHHHH--hhCHHHHH-----
Confidence 45555555555433221 245666666442 1111246889999999988876543 23333332
Q ss_pred chhHHHHHHhcccCCCHHHHHHHHH
Q 010406 289 EKVRTISLFGEVWGIGPATAQKLYE 313 (511)
Q Consensus 289 ~~~~~l~lf~~I~GvGpktA~~l~~ 313 (511)
.-+++.|..| ||+++.|+++|+
T Consensus 558 --~As~eel~~v-gi~~~~a~~i~~ 579 (581)
T COG0322 558 --SASVEELAKV-GISKKLAEKIYE 579 (581)
T ss_pred --hcCHHHHHHc-CCCHHHHHHHHh
Confidence 2357788899 999999999986
No 240
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=50.37 E-value=50 Score=29.62 Aligned_cols=88 Identities=23% Similarity=0.432 Sum_probs=60.5
Q ss_pred CCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHhCCCCHHHHhhccCcchhhhhcccchhh
Q 010406 262 IGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYFDD 341 (511)
Q Consensus 262 IG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~Gi~tledL~~~~~L~~~q~~Glk~~~d 341 (511)
|=..|++.|.+-+.+|++..=+ +.+++..|..--||-|.|+.+-|+ +|+++|-+....+.|----+|
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 3456899999999999987644 445677777889999999999997 677777777777777544443
Q ss_pred ---hccCcCHHHHHH-HHHHHHHHh
Q 010406 342 ---IKTRIPRHEVEQ-MERLLQKAG 362 (511)
Q Consensus 342 ---~~~~i~r~ea~~-~~~iv~~~~ 362 (511)
+.....+..+.+ ++.+|.++.
T Consensus 79 ~~~~~~~~~~~~~~~~l~~~I~~~~ 103 (125)
T COG1725 79 AKEILDQLKRELAEEELEEFIEEAK 103 (125)
T ss_pred chhhHHHHHHHHHHHHHHHHHHHHH
Confidence 333333444443 455555543
No 241
>PRK04374 PII uridylyl-transferase; Provisional
Probab=50.34 E-value=52 Score=38.98 Aligned_cols=63 Identities=19% Similarity=0.376 Sum_probs=40.3
Q ss_pred HHHHHHHHhhhcCC---CeEEEEccceeec-CCccCCeeEEEecCCcc--hhhhHHHHHHHHHHHhcce
Q 010406 354 MERLLQKAGEEVLP---EVIILCGGSYRRG-KASCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMKFL 416 (511)
Q Consensus 354 ~~~iv~~~~~~~~p---~~~v~~~Gs~RRg-ke~~gDvDiLit~~~~~--~~~~~l~~~v~~l~~~g~l 416 (511)
+..+++++-....| ++-+..+|||=|| ..-.+||||||-+++.. .....+.+++..|=+.|+-
T Consensus 55 ~D~~l~~~~~~~~~~~~~~alvAvGgYGR~EL~p~SDIDLliL~~~~~~~~~~~~i~~~i~~LWD~gL~ 123 (869)
T PRK04374 55 VDQLMRNAWTRCIPADSGLSLHAVGGYGRGELFPRSDVDLLVLGETAAQQRHEQALARLFALLWDVGLP 123 (869)
T ss_pred HHHHHHHHHHHhCCCcCCEEEEEcCCccccccCCcccceEEEEecCCCCchHHHHHHHHHHHHHhcCCC
Confidence 44455554433334 3567788999555 56678999999887432 2445667777766666654
No 242
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=50.11 E-value=25 Score=34.16 Aligned_cols=37 Identities=22% Similarity=0.293 Sum_probs=23.6
Q ss_pred HHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHH
Q 010406 271 QEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLY 312 (511)
Q Consensus 271 ~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~ 312 (511)
.+++.+ +..++.+.. .-.-+.|.+|.|||+-||..+.
T Consensus 96 k~l~~~--~~~~~~~~~---~~~R~~LL~iKGIG~ETaDsIL 132 (215)
T COG2231 96 KNLAKF--FINLESFKS---EVLREELLSIKGIGKETADSIL 132 (215)
T ss_pred HHHHHH--hhhhhccch---HHHHHHHHccCCcchhhHHHHH
Confidence 555443 334444432 2256777799999999998763
No 243
>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=49.85 E-value=15 Score=26.63 Aligned_cols=31 Identities=32% Similarity=0.355 Sum_probs=23.1
Q ss_pred CCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhh
Q 010406 303 IGPATAQKLYEKGHRTLDDLKNED--SLTHSQR 333 (511)
Q Consensus 303 vGpktA~~l~~~Gi~tledL~~~~--~L~~~q~ 333 (511)
|.+..+.+|++.|+.|+++|-... .|...++
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 467889999999999999998543 3544444
No 244
>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=49.48 E-value=24 Score=36.42 Aligned_cols=76 Identities=18% Similarity=0.222 Sum_probs=43.1
Q ss_pred HHHcCCChhHHHHHHHHHHHhcCC--c----ccc------chhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchh
Q 010406 224 YRALGEDRRSFSYYKAIPVIEKLP--F----KIE------SADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKV 291 (511)
Q Consensus 224 ~e~~g~~~r~~aY~rAa~~l~~l~--~----~i~------s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~ 291 (511)
+...|-.+|+..-..+|..+..-. . .+. ..++|..|||||+.+|+-|.=+ .-|+..-+ -- ..
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-GLDKPQAV---PV--DV 251 (310)
T ss_pred HHHcCCHHHHHHHHHHHHHHHhccCCchhHHhhccCChHHHHHHHHhCCCccHHHHHHHHHH-hCCCCCce---ee--cH
Confidence 333454457766677777665421 1 111 2367999999999999987633 33332211 11 23
Q ss_pred HHHHHHhcccCCCH
Q 010406 292 RTISLFGEVWGIGP 305 (511)
Q Consensus 292 ~~l~lf~~I~GvGp 305 (511)
.+.+.+.+++|+.+
T Consensus 252 ~v~r~~~r~y~~~~ 265 (310)
T TIGR00588 252 HVWRIANRDYPWHP 265 (310)
T ss_pred HHHHHHHHHhcccc
Confidence 45666666666543
No 245
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=49.22 E-value=9.9 Score=39.91 Aligned_cols=52 Identities=19% Similarity=0.232 Sum_probs=41.1
Q ss_pred hchhHHHHHHhcccCCCHHHHHHHHHh-CCCCHHHHhhcc--Ccchhhhhcccchhh
Q 010406 288 DEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED--SLTHSQRLGLKYFDD 341 (511)
Q Consensus 288 ~~~~~~l~lf~~I~GvGpktA~~l~~~-Gi~tledL~~~~--~L~~~q~~Glk~~~d 341 (511)
...++...++.+||+|+++.|++|.+. | ||..+.++. .|....++|.+....
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 345667889999999999999999998 7 888888653 477777888665554
No 246
>PRK03352 DNA polymerase IV; Validated
Probab=48.39 E-value=32 Score=35.81 Aligned_cols=56 Identities=16% Similarity=0.324 Sum_probs=39.3
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHh--CCCCHH
Q 010406 255 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRTLD 320 (511)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~--Gi~tle 320 (511)
.+..|||||+++++++..+ -+..+.+|.+-.+....+.| |++.+.+||+. |+....
T Consensus 178 pl~~l~gig~~~~~~L~~~----Gi~ti~dl~~l~~~~L~~~f------G~~~~~~l~~~a~G~d~~~ 235 (346)
T PRK03352 178 PTDALWGVGPKTAKRLAAL----GITTVADLAAADPAELAATF------GPTTGPWLLLLARGGGDTE 235 (346)
T ss_pred CHHHcCCCCHHHHHHHHHc----CCccHHHHhcCCHHHHHHHh------ChHHHHHHHHHhCCCCCCC
Confidence 3788999999998887654 56777777764444455555 67788888875 775443
No 247
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=48.04 E-value=25 Score=41.20 Aligned_cols=32 Identities=13% Similarity=0.211 Sum_probs=26.0
Q ss_pred HHHHHhcccCCCHHHHHHHHHhCCCCHHHHhhc
Q 010406 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (511)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~Gi~tledL~~~ 325 (511)
..+++.++|||||+.|+++.+. +.|+++|.+.
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 3445669999999999999985 8888888864
No 248
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=47.86 E-value=11 Score=42.66 Aligned_cols=44 Identities=23% Similarity=0.405 Sum_probs=30.1
Q ss_pred HHHHhcccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhhcccc
Q 010406 294 ISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKY 338 (511)
Q Consensus 294 l~lf~~I~GvGpktA~~l~~~Gi~tledL~~~~--~L~~~q~~Glk~ 338 (511)
...|..|+|||++++++|++. +.|++++.++. .|....++|.+.
T Consensus 542 ~s~L~~IpGIG~k~~k~Ll~~-FgS~~~i~~As~eeL~~v~Gig~~~ 587 (598)
T PRK00558 542 TSALDDIPGIGPKRRKALLKH-FGSLKAIKEASVEELAKVPGISKKL 587 (598)
T ss_pred hhhHhhCCCcCHHHHHHHHHH-cCCHHHHHhCCHHHHhhcCCcCHHH
Confidence 345679999999999999985 45688887642 244444455443
No 249
>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=47.82 E-value=26 Score=35.67 Aligned_cols=25 Identities=16% Similarity=0.175 Sum_probs=19.7
Q ss_pred HHHHHHhcccCCCHHHHHHHHHhCC
Q 010406 292 RTISLFGEVWGIGPATAQKLYEKGH 316 (511)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~~Gi 316 (511)
..++.|+++||||++||..+---++
T Consensus 102 ~~~~~L~~LpGIG~~TA~~Il~~a~ 126 (275)
T TIGR01084 102 QDFEDLAALPGVGRYTAGAILSFAL 126 (275)
T ss_pred HHHHHHHhCCCCCHHHHHHHHHHHC
Confidence 3577888999999999988765433
No 250
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=47.32 E-value=15 Score=32.61 Aligned_cols=22 Identities=27% Similarity=0.540 Sum_probs=19.1
Q ss_pred HHhcccCCCHHHHHHHHHh-CCC
Q 010406 296 LFGEVWGIGPATAQKLYEK-GHR 317 (511)
Q Consensus 296 lf~~I~GvGpktA~~l~~~-Gi~ 317 (511)
-|+.|+|||..+|+.+.++ ||.
T Consensus 18 ALt~IyGIG~~~a~~I~~~~gi~ 40 (121)
T COG0099 18 ALTYIYGIGRRRAKEICKKAGID 40 (121)
T ss_pred hhhhhccccHHHHHHHHHHcCCC
Confidence 4679999999999999987 874
No 251
>PRK13746 aminoglycoside resistance protein; Provisional
Probab=47.31 E-value=96 Score=31.36 Aligned_cols=27 Identities=26% Similarity=0.249 Sum_probs=22.0
Q ss_pred EEEEccceeec--CCccCCeeEEEecCCcc
Q 010406 370 IILCGGSYRRG--KASCGDLDVVIMHPDRK 397 (511)
Q Consensus 370 ~v~~~Gs~RRg--ke~~gDvDiLit~~~~~ 397 (511)
-|.+-||+-+| ++ -+||||+|...++-
T Consensus 30 ~vyLfGS~~~G~~~p-~SDIDllvvv~~~l 58 (262)
T PRK13746 30 AIHLYGSAVDGGLKP-HSDIDLLVTVAVPL 58 (262)
T ss_pred EEEEECCcccCCCCC-CCceeEEEEeCCCC
Confidence 57899999998 44 79999999877654
No 252
>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=46.81 E-value=25 Score=35.79 Aligned_cols=29 Identities=31% Similarity=0.470 Sum_probs=22.6
Q ss_pred HHhcccCCCHHHHHHHHHhCCCCHHHHhh
Q 010406 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (511)
Q Consensus 296 lf~~I~GvGpktA~~l~~~Gi~tledL~~ 324 (511)
.|.++||+|++.++++-+.|+.|+++|.+
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 45599999999999999999999999985
No 253
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=46.47 E-value=13 Score=34.45 Aligned_cols=25 Identities=24% Similarity=0.225 Sum_probs=20.0
Q ss_pred HHHHHhcccCCCHHHHHHHHHh-CCC
Q 010406 293 TISLFGEVWGIGPATAQKLYEK-GHR 317 (511)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~-Gi~ 317 (511)
+.--|+.|+|||+.+|.++-+. ||.
T Consensus 28 v~~aLt~I~GIG~~~A~~I~~~lgi~ 53 (154)
T PTZ00134 28 VPYALTAIKGIGRRFAYLVCKKAGID 53 (154)
T ss_pred EEEeecccccccHHHHHHHHHHcCcC
Confidence 3344689999999999999876 764
No 254
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=46.31 E-value=40 Score=35.33 Aligned_cols=59 Identities=17% Similarity=0.254 Sum_probs=42.8
Q ss_pred HHHHHHHcCCChhHHHHHHHHHHHhcC-Ccccc-chhhhcCCCCCCHHHHHHHHHHHHhCC
Q 010406 220 LINIYRALGEDRRSFSYYKAIPVIEKL-PFKIE-SADQVKGLPGIGKSMQDHIQEIVTTGK 278 (511)
Q Consensus 220 la~~~e~~g~~~r~~aY~rAa~~l~~l-~~~i~-s~~~l~~lpgIG~~ia~kI~Eil~tG~ 278 (511)
+-.+++=.|--.|++...+||..+... ...+. +.+++..|||||..+|..|.-|.-.-.
T Consensus 77 vl~~W~gLGYysRArnL~~~A~~v~~~~~G~~P~~~~~l~~LpGiG~yTa~Ail~~a~~~~ 137 (342)
T COG1194 77 VLKAWEGLGYYSRARNLHKAAQEVVERHGGEFPDDEEELAALPGVGPYTAGAILSFAFNQP 137 (342)
T ss_pred HHHHHHhcChHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHhCCCCcHHHHHHHHHHHhCCC
Confidence 335555566556899888999877654 44444 357899999999999999988765433
No 255
>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=46.30 E-value=38 Score=35.67 Aligned_cols=54 Identities=17% Similarity=0.305 Sum_probs=34.3
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhh--chhHHHHHHhcccCCCHHHHHHHHHh--CCCC
Q 010406 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKD--EKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (511)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~--~~~~~l~lf~~I~GvGpktA~~l~~~--Gi~t 318 (511)
+..|||||++++.++.+-+ .+..+.+|.+- .+....+.| |.+.+..+|+. |+..
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 7788999998876653322 23444455432 233345556 77889999875 8764
No 256
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=46.03 E-value=68 Score=38.18 Aligned_cols=49 Identities=16% Similarity=0.447 Sum_probs=34.6
Q ss_pred CeEEEEccceeecC-CccCCeeEEEecCCcc--hhhhHHHHHHHHHHHhcce
Q 010406 368 EVIILCGGSYRRGK-ASCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMKFL 416 (511)
Q Consensus 368 ~~~v~~~Gs~RRgk-e~~gDvDiLit~~~~~--~~~~~l~~~v~~l~~~g~l 416 (511)
++.+..+|||=||. .-.+||||||-+++.. ....+...++..|-+.|+-
T Consensus 78 ~~alvAvGgyGR~EL~p~SDiDll~l~~~~~~~~~~~~i~~~~~~LwD~gL~ 129 (895)
T PRK00275 78 DIALVAVGGYGRGELHPYSDIDLLILLDSADHEEFREPIERFLTLLWDIGLE 129 (895)
T ss_pred CEEEEEcCCccccCcCCCCCceEEEEecCCCChHHHHHHHHHHHHHHhcCCC
Confidence 46778899996654 5689999999887542 2445666777766666664
No 257
>COG5067 DBF4 Protein kinase essential for the initiation of DNA replication [DNA replication, recombination, and repair / Cell division and chromosome partitioning]
Probab=45.19 E-value=14 Score=39.07 Aligned_cols=49 Identities=18% Similarity=0.284 Sum_probs=37.4
Q ss_pred CCCCCCCCCeEEEEecCCCcchHHHHHHHHHHhcCCEEEeecCCCccEEEE
Q 010406 13 LDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLA 63 (511)
Q Consensus 13 ~~~~~~F~g~~iy~~~~~~g~~r~~~l~~~~~~~Gg~v~~~~s~~VTHVV~ 63 (511)
...--.|..+.+|+... .+ .+..-+++.+...||.|..-++..||||+.
T Consensus 117 R~Y~~aFp~f~fY~dn~-s~-~~khRvk~gf~~LGa~v~tfF~~~VThfiT 165 (468)
T COG5067 117 RTYCCAFPAFKFYKDNK-SG-KRKHRVKEGFCELGAVVFTFFEEHVTHFIT 165 (468)
T ss_pred hhhhcccchhhhhhcCC-CH-HHHHHHHHHHHHhhhhhheeeccceEEEEE
Confidence 33446788888888543 22 233338999999999999999999999996
No 258
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=44.74 E-value=15 Score=41.36 Aligned_cols=44 Identities=20% Similarity=0.468 Sum_probs=30.2
Q ss_pred HHHhcccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhhcccch
Q 010406 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYF 339 (511)
Q Consensus 295 ~lf~~I~GvGpktA~~l~~~Gi~tledL~~~~--~L~~~q~~Glk~~ 339 (511)
..|..|+|||++++++|++. +.|++++.++. .|....++|-+..
T Consensus 525 ~~L~~IpGIG~kr~~~LL~~-FGS~~~I~~As~eeL~~vpGi~~~~A 570 (577)
T PRK14668 525 TVLDDVPGVGPETRKRLLRR-FGSVEGVREASVEDLRDVPGVGEKTA 570 (577)
T ss_pred hHHhcCCCCCHHHHHHHHHH-cCCHHHHHhCCHHHHHhCCCCCHHHH
Confidence 44669999999999999985 45777777543 2444445554433
No 259
>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=44.48 E-value=61 Score=29.20 Aligned_cols=51 Identities=25% Similarity=0.343 Sum_probs=35.1
Q ss_pred eEEEEccceeecCC-ccCCeeEEEecCCcc--hh----hhHHHHHHHHHHHhcceeee
Q 010406 369 VIILCGGSYRRGKA-SCGDLDVVIMHPDRK--SH----KGFLSKYVKKLKEMKFLRED 419 (511)
Q Consensus 369 ~~v~~~Gs~RRgke-~~gDvDiLit~~~~~--~~----~~~l~~~v~~l~~~g~l~~~ 419 (511)
+-..+.||+=|+.. ...|+|..|-+++.. .. ..+...++..|.+.|+-.|.
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 35667899866655 467999999888822 12 33446678888888887653
No 260
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=44.47 E-value=16 Score=33.68 Aligned_cols=25 Identities=28% Similarity=0.324 Sum_probs=20.2
Q ss_pred HHHHHhcccCCCHHHHHHHHHh-CCC
Q 010406 293 TISLFGEVWGIGPATAQKLYEK-GHR 317 (511)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~-Gi~ 317 (511)
+.--|+.|+|||+++|.++-+. ||.
T Consensus 23 i~~aLt~IyGIG~~~a~~Ic~~lgi~ 48 (149)
T PRK04053 23 VEYALTGIKGIGRRTARAIARKLGLD 48 (149)
T ss_pred EeeeccccccccHHHHHHHHHHcCcC
Confidence 3345689999999999999886 764
No 261
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=44.27 E-value=45 Score=31.88 Aligned_cols=57 Identities=19% Similarity=0.325 Sum_probs=35.3
Q ss_pred HHHHHHHHhCCchhhHHHHhhchhH-HHHHHhcccCCCHHHHHHHHHh----CCCCHHHHhh
Q 010406 268 DHIQEIVTTGKLSKLEHFEKDEKVR-TISLFGEVWGIGPATAQKLYEK----GHRTLDDLKN 324 (511)
Q Consensus 268 ~kI~Eil~tG~~~~le~l~~~~~~~-~l~lf~~I~GvGpktA~~l~~~----Gi~tledL~~ 324 (511)
..+++|+....=..++-+....|.- -|-.|.=+||||.|+.+.+.++ -+.|++|+++
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 3466666655544444443333322 1223444599999999999864 6888888875
No 262
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=43.78 E-value=18 Score=38.66 Aligned_cols=33 Identities=24% Similarity=0.313 Sum_probs=28.9
Q ss_pred HHHHHHhcccCCCHHHHHHHHHhCCCCHHHHhh
Q 010406 292 RTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (511)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~~Gi~tledL~~ 324 (511)
+.-.-|+.|.||||+.+.+|...||.+++++-.
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 263
>COG1204 Superfamily II helicase [General function prediction only]
Probab=43.16 E-value=24 Score=41.12 Aligned_cols=109 Identities=23% Similarity=0.307 Sum_probs=61.5
Q ss_pred HHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCc--hhhHHHH----hhchhHHHHHHhcccCCCHH
Q 010406 233 SFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKL--SKLEHFE----KDEKVRTISLFGEVWGIGPA 306 (511)
Q Consensus 233 ~~aY~rAa~~l~~l~~~i~s~~~l~~lpgIG~~ia~kI~Eil~tG~~--~~le~l~----~~~~~~~l~lf~~I~GvGpk 306 (511)
..+|-.+...+...-....=. .+. +..+|.++. ++..++..|.. ..++.+. ...+...+..+..|.|+|-.
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 445555555444333222212 122 444454444 44445555433 3333332 22331233445599999999
Q ss_pred HHHHHHHhCCCCHHHHhhcc---Ccchhhhhcccchhhhcc
Q 010406 307 TAQKLYEKGHRTLDDLKNED---SLTHSQRLGLKYFDDIKT 344 (511)
Q Consensus 307 tA~~l~~~Gi~tledL~~~~---~L~~~q~~Glk~~~d~~~ 344 (511)
.|++||..|+.+++++.... .+....++|.+.++.+..
T Consensus 687 rar~ly~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~ 727 (766)
T COG1204 687 RARKLYNAGYKSLEDLRLIADPAELLPLTGIGERLVEAILE 727 (766)
T ss_pred HHHHHHHhhhccHHHHHhhcChhhhhhhhhhHHHHHHHHHH
Confidence 99999999999999999432 355556667666665544
No 264
>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=42.90 E-value=17 Score=33.35 Aligned_cols=23 Identities=26% Similarity=0.322 Sum_probs=19.2
Q ss_pred HHHhcccCCCHHHHHHHHHh-CCC
Q 010406 295 SLFGEVWGIGPATAQKLYEK-GHR 317 (511)
Q Consensus 295 ~lf~~I~GvGpktA~~l~~~-Gi~ 317 (511)
--|+.|+|||+++|..+-+. ||.
T Consensus 21 ~aLt~I~GIG~~~a~~I~~~lgi~ 44 (144)
T TIGR03629 21 YALTGIKGIGRRFARAIARKLGVD 44 (144)
T ss_pred EeecceeccCHHHHHHHHHHcCcC
Confidence 34679999999999999876 764
No 265
>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=42.87 E-value=19 Score=30.21 Aligned_cols=28 Identities=32% Similarity=0.406 Sum_probs=20.0
Q ss_pred HHhcccCCCHHHHHHHHHhCCCCHHHHh
Q 010406 296 LFGEVWGIGPATAQKLYEKGHRTLDDLK 323 (511)
Q Consensus 296 lf~~I~GvGpktA~~l~~~Gi~tledL~ 323 (511)
.-+.|+||||..+.+|-++|+.----|.
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 3469999999999999999998766655
No 266
>PRK03858 DNA polymerase IV; Validated
Probab=42.80 E-value=43 Score=35.52 Aligned_cols=52 Identities=21% Similarity=0.382 Sum_probs=36.6
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHh--CCC
Q 010406 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHR 317 (511)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~--Gi~ 317 (511)
+..|||||+++++++..+ | +..+.+|.+-.+...-+.| |+..++.||+. |+.
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-ITTVGDVAELPESALVSLL------GPAAGRHLHALAHNRD 228 (396)
T ss_pred hhhcCCCCHHHHHHHHHh---C-CCcHHHHhcCCHHHHHHHh------CcHHHHHHHHHhCCCC
Confidence 678899999999998865 3 5566666654444444555 67788899873 764
No 267
>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=42.56 E-value=66 Score=37.98 Aligned_cols=49 Identities=20% Similarity=0.474 Sum_probs=35.3
Q ss_pred CeEEEEccceeec-CCccCCeeEEEecCCcc--hhhhHHHHHHHHHHHhcce
Q 010406 368 EVIILCGGSYRRG-KASCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMKFL 416 (511)
Q Consensus 368 ~~~v~~~Gs~RRg-ke~~gDvDiLit~~~~~--~~~~~l~~~v~~l~~~g~l 416 (511)
++-+..+|||=|| ..-..|||++|-+++.. ....++.+++..|-+.|+-
T Consensus 43 ~~aliA~GgyGR~El~p~SDiDll~l~~~~~~~~~~~~~~~~~~~LwD~gl~ 94 (850)
T TIGR01693 43 GIALVAVGGYGRGELAPYSDIDLLFLHDGKPAEEVEPKIERFLYPLWDLGFE 94 (850)
T ss_pred CeEEEEeCCccccCcCCCCCCeEEEEeCCCCChHHHHHHHHHHHHHHhcCCC
Confidence 4567788999665 45678999999887543 2456677777777777764
No 268
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=42.14 E-value=77 Score=36.96 Aligned_cols=49 Identities=16% Similarity=0.451 Sum_probs=34.0
Q ss_pred CeEEEEccceeecC-CccCCeeEEEecCCcch--hhhHHHHHHHHHHHhcce
Q 010406 368 EVIILCGGSYRRGK-ASCGDLDVVIMHPDRKS--HKGFLSKYVKKLKEMKFL 416 (511)
Q Consensus 368 ~~~v~~~Gs~RRgk-e~~gDvDiLit~~~~~~--~~~~l~~~v~~l~~~g~l 416 (511)
++-++.+|||=||. .-++|||+||-+|...+ ....+..++..|=+.|+-
T Consensus 66 ~~aLvAVGGyGRgEL~P~SDiDlL~L~p~~~~~~~e~~ie~~l~~LWD~gl~ 117 (867)
T COG2844 66 GLALVAVGGYGRGELHPLSDIDLLLLSPQKLTDWLEQKIERFLYLLWDLGLE 117 (867)
T ss_pred ceEEEEeccccccccCCCccceEEEecCCCCChHHHHHHHHHHHHHHhcCcc
Confidence 35677889997775 56899999999987654 234455566555555553
No 269
>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=41.98 E-value=16 Score=37.66 Aligned_cols=17 Identities=53% Similarity=0.698 Sum_probs=15.9
Q ss_pred hcccCCCHHHHHHHHHh
Q 010406 298 GEVWGIGPATAQKLYEK 314 (511)
Q Consensus 298 ~~I~GvGpktA~~l~~~ 314 (511)
.+|+|||||||.+|.++
T Consensus 226 ~gv~giG~k~A~~li~~ 242 (316)
T cd00128 226 EGIPGIGPVTALKLIKK 242 (316)
T ss_pred CCCCCccHHHHHHHHHH
Confidence 48999999999999998
No 270
>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=41.79 E-value=46 Score=35.59 Aligned_cols=53 Identities=28% Similarity=0.488 Sum_probs=36.0
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhc--hhHHHHHHhcccCCCHHHHHHHHHh--CCCC
Q 010406 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDE--KVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (511)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~--~~~~l~lf~~I~GvGpktA~~l~~~--Gi~t 318 (511)
+..|||||+++++++..+ | +..+.++.+-. +....+.| |++.+..||+. |+..
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 678899999998887754 3 34444444433 34455566 78889998885 8764
No 271
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=41.75 E-value=15 Score=38.44 Aligned_cols=51 Identities=20% Similarity=0.264 Sum_probs=32.3
Q ss_pred HHHHHHhcccCCCHHHHHHHHHh---CCCC-HHHHhhcc------Ccchhhhhcccchhhh
Q 010406 292 RTISLFGEVWGIGPATAQKLYEK---GHRT-LDDLKNED------SLTHSQRLGLKYFDDI 342 (511)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~~---Gi~t-ledL~~~~------~L~~~q~~Glk~~~d~ 342 (511)
..+..+++|||||+++|+++.+- |--. +.++..+. .|.+..|+|.+....|
T Consensus 45 ~~~~~l~~lpgIG~~ia~kI~Eil~tG~~~~~~e~l~~~~p~~l~~l~~i~GiGpk~a~~l 105 (334)
T smart00483 45 NSMKDLKGLPGIGDKIKKKIEEIIETGKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKW 105 (334)
T ss_pred CCHHHHhcCCCccHHHHHHHHHHHHhCcHHHHHHHhcCcHHHHHHHHHccCCcCHHHHHHH
Confidence 34556779999999999999973 5544 33333221 3556666665554444
No 272
>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=41.64 E-value=22 Score=40.04 Aligned_cols=29 Identities=24% Similarity=0.354 Sum_probs=23.7
Q ss_pred HHhcccCCCHHHHHHHHHhCCCCHHHHhhc
Q 010406 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (511)
Q Consensus 296 lf~~I~GvGpktA~~l~~~Gi~tledL~~~ 325 (511)
.|.+|+|||||+.++|++. +.|+++++++
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 5578887754
No 273
>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=41.56 E-value=17 Score=31.81 Aligned_cols=28 Identities=25% Similarity=0.426 Sum_probs=17.7
Q ss_pred cCcHHHHHHHHHHHHHcCCccCCCCCcc
Q 010406 443 TGNDVLNRRLRLLAESKGYRLDDTGLFP 470 (511)
Q Consensus 443 TGS~~fnr~lR~~A~~kg~~L~~~gL~~ 470 (511)
+.++..++.+|.||++.||..++.|-.+
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 5566789999999999999999999653
No 274
>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=41.19 E-value=23 Score=27.92 Aligned_cols=19 Identities=21% Similarity=0.389 Sum_probs=16.5
Q ss_pred HHHHHHHHHhCCCCHHHHh
Q 010406 305 PATAQKLYEKGHRTLDDLK 323 (511)
Q Consensus 305 pktA~~l~~~Gi~tledL~ 323 (511)
-+.++.|.+.||+|++|++
T Consensus 54 ~~Il~~W~~~gi~T~e~~~ 72 (73)
T TIGR01446 54 DAILNNWKNNGIKTVEDVE 72 (73)
T ss_pred HHHHHHHHHcCCCCHHHHh
Confidence 3668899999999999986
No 275
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=41.15 E-value=43 Score=34.19 Aligned_cols=45 Identities=20% Similarity=0.350 Sum_probs=31.4
Q ss_pred CCC-hhHHHHHHHHHHHhc--CCccc-cc----hhhhcCCCCCCHHHHHHHHH
Q 010406 228 GED-RRSFSYYKAIPVIEK--LPFKI-ES----ADQVKGLPGIGKSMQDHIQE 272 (511)
Q Consensus 228 g~~-~r~~aY~rAa~~l~~--l~~~i-~s----~~~l~~lpgIG~~ia~kI~E 272 (511)
|-. .|+..-..+|.++.+ ++... .+ .++|..|||||+.+|+-|.=
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 544 377777888887754 43221 12 46799999999999998763
No 276
>PRK13766 Hef nuclease; Provisional
Probab=40.78 E-value=20 Score=41.57 Aligned_cols=46 Identities=20% Similarity=0.347 Sum_probs=33.4
Q ss_pred HHhcccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhhcccchhhh
Q 010406 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDI 342 (511)
Q Consensus 296 lf~~I~GvGpktA~~l~~~Gi~tledL~~~~--~L~~~q~~Glk~~~d~ 342 (511)
+|..|+|||+++|++|.+. +.|++++..+. .|....++|.+..+.+
T Consensus 716 ~L~~ipgig~~~a~~Ll~~-fgs~~~i~~as~~~L~~i~Gig~~~a~~i 763 (773)
T PRK13766 716 IVESLPDVGPVLARNLLEH-FGSVEAVMTASEEELMEVEGIGEKTAKRI 763 (773)
T ss_pred HHhcCCCCCHHHHHHHHHH-cCCHHHHHhCCHHHHHhCCCCCHHHHHHH
Confidence 5789999999999999996 45788887643 3555566665544443
No 277
>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=40.10 E-value=71 Score=33.16 Aligned_cols=53 Identities=19% Similarity=0.456 Sum_probs=33.8
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHh--CCCC
Q 010406 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (511)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~--Gi~t 318 (511)
+..|||||+++.+++..+ | +..+.+|.+-.....+..+ + | +.+..+|+. |+..
T Consensus 175 i~~l~giG~~~~~~L~~~---G-i~ti~dl~~~~~~~~l~~~---f--g-~~~~~l~~~a~G~d~ 229 (343)
T cd00424 175 LTDLPGIGAVTAKRLEAV---G-INPIGDLLAASPDALLALW---G--G-VSGERLWYALRGIDD 229 (343)
T ss_pred hhhcCCCCHHHHHHHHHc---C-CCcHHHHhcCCHHHHHHHH---h--h-HHHHHHHHHhCCcCC
Confidence 678899999999998764 3 5556666553313333322 2 2 567777775 8754
No 278
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]
Probab=39.82 E-value=16 Score=35.78 Aligned_cols=58 Identities=22% Similarity=0.303 Sum_probs=41.8
Q ss_pred hhhcCCCCCCHHHH---HHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHH
Q 010406 254 DQVKGLPGIGKSMQ---DHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLY 312 (511)
Q Consensus 254 ~~l~~lpgIG~~ia---~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~ 312 (511)
+++.++ |+-+.=+ .-+.|....|.+...+.+..-.....++++|+|.|||+=|++++-
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 345566678888888887776777899999999999999988763
No 279
>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=39.48 E-value=12 Score=31.75 Aligned_cols=51 Identities=24% Similarity=0.337 Sum_probs=39.6
Q ss_pred HHHHHhcccCCCHHHHHHHHHh-CCCCHHHHhhccCcchhhhhcccchhhhc
Q 010406 293 TISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNEDSLTHSQRLGLKYFDDIK 343 (511)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~-Gi~tledL~~~~~L~~~q~~Glk~~~d~~ 343 (511)
.+..|++.||+=|..|.++... -+.|++|+.+-.-|+..|+-=++-|++.-
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 4567889999999999999998 68999999988788988887777776643
No 280
>PHA00439 exonuclease
Probab=39.29 E-value=22 Score=36.41 Aligned_cols=27 Identities=19% Similarity=0.284 Sum_probs=22.3
Q ss_pred hcccCCCHHHHHHHHHh--CCCCHHHHhhc
Q 010406 298 GEVWGIGPATAQKLYEK--GHRTLDDLKNE 325 (511)
Q Consensus 298 ~~I~GvGpktA~~l~~~--Gi~tledL~~~ 325 (511)
-+|+||| |||.+|.++ .+..++...+.
T Consensus 191 PGVpGIG-KTA~kLL~~~~~~~~~~~~~~s 219 (286)
T PHA00439 191 SGIPGWG-DTAEAFLENPYIFEQVEKVLKS 219 (286)
T ss_pred CCCCCcC-HHHHHHHhCccccchhhHHhhc
Confidence 4799999 999999998 67777776654
No 281
>PRK03059 PII uridylyl-transferase; Provisional
Probab=39.13 E-value=78 Score=37.49 Aligned_cols=63 Identities=16% Similarity=0.370 Sum_probs=37.6
Q ss_pred HHHHHHHHHhhhc--CCCeEEEEccceeec-CCccCCeeEEEecCCcc--hhhhHHHHHHHHHHHhcc
Q 010406 353 QMERLLQKAGEEV--LPEVIILCGGSYRRG-KASCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMKF 415 (511)
Q Consensus 353 ~~~~iv~~~~~~~--~p~~~v~~~Gs~RRg-ke~~gDvDiLit~~~~~--~~~~~l~~~v~~l~~~g~ 415 (511)
.+..+++.+-... ..++-+..+|||=|| ..-.+|||+|+-+++.. .....+..++..|=+.|+
T Consensus 44 l~d~~l~~~~~~~~~~~~~alvAvGgyGR~EL~p~SDiDll~l~~~~~~~~~~~~i~~~~~~lwD~gL 111 (856)
T PRK03059 44 LVDQALRRLWQECGLPAGAALVAVGGYGRGELFPYSDVDLLVLLPDAPDAALDARIERFIGLCWDLGL 111 (856)
T ss_pred HHHHHHHHHHHhcCCCCCeEEEEcCCCCCcccCCCCCCEEEEEecCCcchHHHHHHHHHHHhhhccCC
Confidence 3444444443221 235677888999555 56789999999887543 233455555554545544
No 282
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=38.31 E-value=54 Score=38.51 Aligned_cols=14 Identities=14% Similarity=0.339 Sum_probs=8.9
Q ss_pred HHHHHHHHHHHHHH
Q 010406 212 NITEIFGKLINIYR 225 (511)
Q Consensus 212 ~ia~~l~~la~~~e 225 (511)
.+-+..+.|...|+
T Consensus 645 RL~~Q~~~m~~~Y~ 658 (814)
T TIGR00596 645 RLYNQCEKMLRYYA 658 (814)
T ss_pred hHHHHHHHHHHhcC
Confidence 46666666766666
No 283
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=36.48 E-value=33 Score=33.10 Aligned_cols=22 Identities=27% Similarity=0.496 Sum_probs=18.9
Q ss_pred hhhcCCCCCCHHHHHHHHHHHH
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVT 275 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~ 275 (511)
+.+..|||||++.|.++.=.|-
T Consensus 12 ~~l~kLPGvG~KsA~R~AfhLL 33 (198)
T COG0353 12 DALKKLPGVGPKSAQRLAFHLL 33 (198)
T ss_pred HHHhhCCCCChhHHHHHHHHHH
Confidence 6689999999999999986554
No 284
>PRK03348 DNA polymerase IV; Provisional
Probab=36.33 E-value=69 Score=34.92 Aligned_cols=53 Identities=17% Similarity=0.334 Sum_probs=39.2
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHh--CCCC
Q 010406 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (511)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~--Gi~t 318 (511)
+..|||||+.+.+++..+ -+..+.+|.+-.+..+.+.| |++....||+. |+..
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 678899999998887654 45666666655555566677 77888999884 8754
No 285
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=36.17 E-value=38 Score=33.05 Aligned_cols=20 Identities=20% Similarity=0.371 Sum_probs=17.3
Q ss_pred chhhhc-CCCCCCHHHHHHHH
Q 010406 252 SADQVK-GLPGIGKSMQDHIQ 271 (511)
Q Consensus 252 s~~~l~-~lpgIG~~ia~kI~ 271 (511)
..++|. +|||||.++|+.|-
T Consensus 116 ~R~~Ll~~lpGIG~KTAd~vL 136 (208)
T PRK01229 116 AREFLVKNIKGIGYKEASHFL 136 (208)
T ss_pred HHHHHHHcCCCCcHHHHHHHH
Confidence 346788 99999999999976
No 286
>PRK10880 adenine DNA glycosylase; Provisional
Probab=35.98 E-value=26 Score=36.90 Aligned_cols=25 Identities=20% Similarity=0.243 Sum_probs=20.1
Q ss_pred HHHHHHhcccCCCHHHHHHHHHhCC
Q 010406 292 RTISLFGEVWGIGPATAQKLYEKGH 316 (511)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~~Gi 316 (511)
..++.|+++||||++||..+---++
T Consensus 106 ~~~~~L~~LpGIG~~TA~aIl~~af 130 (350)
T PRK10880 106 ETFEEVAALPGVGRSTAGAILSLSL 130 (350)
T ss_pred hhHHHHhcCCCccHHHHHHHHHHHC
Confidence 4567788999999999999876433
No 287
>PF09970 DUF2204: Nucleotidyl transferase of unknown function (DUF2204); InterPro: IPR018700 This family of hypothetical prokaryotic proteins has no known function.
Probab=35.82 E-value=76 Score=30.11 Aligned_cols=39 Identities=18% Similarity=0.211 Sum_probs=25.6
Q ss_pred CeEEEEccce-----eecCCccCCeeEEEecCCcchhhhHHHHH
Q 010406 368 EVIILCGGSY-----RRGKASCGDLDVVIMHPDRKSHKGFLSKY 406 (511)
Q Consensus 368 ~~~v~~~Gs~-----RRgke~~gDvDiLit~~~~~~~~~~l~~~ 406 (511)
|+.+.+.||+ -..+.+.+|||++|..++.......+..+
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 6666666763 25567789999999877665444444444
No 288
>PRK13910 DNA glycosylase MutY; Provisional
Probab=35.28 E-value=26 Score=35.93 Aligned_cols=23 Identities=26% Similarity=0.242 Sum_probs=18.7
Q ss_pred HHHHHhcccCCCHHHHHHHHHhC
Q 010406 293 TISLFGEVWGIGPATAQKLYEKG 315 (511)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~G 315 (511)
..+.|+++||||++||..+---+
T Consensus 70 ~~~~L~~LpGIG~kTA~aIl~~a 92 (289)
T PRK13910 70 DYQSLLKLPGIGAYTANAILCFG 92 (289)
T ss_pred hHHHHHhCCCCCHHHHHHHHHHH
Confidence 46777799999999999876543
No 289
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=35.12 E-value=30 Score=39.29 Aligned_cols=28 Identities=43% Similarity=0.599 Sum_probs=25.6
Q ss_pred HHhcccCCCHHHHHHHHHhCCCCHHHHh
Q 010406 296 LFGEVWGIGPATAQKLYEKGHRTLDDLK 323 (511)
Q Consensus 296 lf~~I~GvGpktA~~l~~~Gi~tledL~ 323 (511)
-+..+.||||++|.++-+.||.|+.||.
T Consensus 11 ~l~~l~gig~~~a~~l~~Lgi~tv~DLL 38 (677)
T COG1200 11 PLSTLKGIGPKTAEKLKKLGIHTVQDLL 38 (677)
T ss_pred chhhhcCcCHHHHHHHHHcCCCcHHHHH
Confidence 3568999999999999999999999997
No 290
>COG5275 BRCT domain type II [General function prediction only]
Probab=35.08 E-value=1.2e+02 Score=29.86 Aligned_cols=50 Identities=16% Similarity=0.052 Sum_probs=37.5
Q ss_pred CCCCCeEEEEecCCCcchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCCh
Q 010406 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLE 67 (511)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~r~~~l~~~~~~~Gg~v~~~~s~~VTHVV~~~~s 67 (511)
.-+.|.+|.|-+---.-.| +-.+-++..+||+|....+...|-||.-++-
T Consensus 155 ~cL~G~~fVfTG~l~TlsR-~~a~~lvk~yGgrvT~~pSskTtflvlGdna 204 (276)
T COG5275 155 ECLKGKVFVFTGDLKTLSR-DDAKTLVKVYGGRVTAVPSSKTTFLVLGDNA 204 (276)
T ss_pred ccccccEEEEecccccccc-hhHHHHHHHhCCeeecccccceeEEEecCCC
Confidence 5678888888442112233 5578999999999999999999998887653
No 291
>PF05559 DUF763: Protein of unknown function (DUF763); InterPro: IPR008482 This family consists of several uncharacterised bacterial and archaeal proteins of unknown function.
Probab=34.87 E-value=1.5e+02 Score=30.86 Aligned_cols=21 Identities=24% Similarity=0.347 Sum_probs=16.5
Q ss_pred HHHHHHhcccCCCHHHHHHHH
Q 010406 292 RTISLFGEVWGIGPATAQKLY 312 (511)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~ 312 (511)
.-++.|..++||||+|.+.|.
T Consensus 266 ~~feeLL~~~GvGp~TlRALa 286 (319)
T PF05559_consen 266 SDFEELLLIKGVGPSTLRALA 286 (319)
T ss_pred cCHHHHHhcCCCCHHHHHHHH
Confidence 345555699999999999874
No 292
>COG1031 Uncharacterized Fe-S oxidoreductase [Energy production and conversion]
Probab=32.64 E-value=37 Score=36.89 Aligned_cols=31 Identities=16% Similarity=0.345 Sum_probs=28.8
Q ss_pred HHHHhcccCCCHHHHHHHHHh-CCCCHHHHhh
Q 010406 294 ISLFGEVWGIGPATAQKLYEK-GHRTLDDLKN 324 (511)
Q Consensus 294 l~lf~~I~GvGpktA~~l~~~-Gi~tledL~~ 324 (511)
.+.+..|||||.+++.+++.+ .+.|.||+++
T Consensus 515 ~~vl~~ipgig~~~~~~I~~~Rp~~s~e~~l~ 546 (560)
T COG1031 515 KDVLRAIPGIGKKTLRKILAERPFKSSEEFLK 546 (560)
T ss_pred HHHHHhcccchhhhHHHHHhcCCccchHHHHh
Confidence 778999999999999999998 9999999985
No 293
>PRK03381 PII uridylyl-transferase; Provisional
Probab=31.99 E-value=1.1e+02 Score=35.71 Aligned_cols=47 Identities=21% Similarity=0.299 Sum_probs=29.9
Q ss_pred eEEEEccceeec-CCccCCeeEEEecCCcch--hhhHHHHHHHHHHHhcc
Q 010406 369 VIILCGGSYRRG-KASCGDLDVVIMHPDRKS--HKGFLSKYVKKLKEMKF 415 (511)
Q Consensus 369 ~~v~~~Gs~RRg-ke~~gDvDiLit~~~~~~--~~~~l~~~v~~l~~~g~ 415 (511)
+-+..+|||=|| ..-..|||+||-+++... ...+...++..|-+.|+
T Consensus 58 ~alvAvg~~gr~el~p~SD~Dll~l~~~~~~~~~~~~~~~~~~~LwD~gl 107 (774)
T PRK03381 58 VALVAVGGLGRRELLPYSDLDLVLLHDGRPADDVAEVADRLWYPLWDAGI 107 (774)
T ss_pred eEEEEeCCcCCcCcCCCCCCeEEEEeCCCCchHHHHHHHHHhhhcccCCC
Confidence 467778999555 566789999998874332 33445555554444444
No 294
>COG5186 PAP1 Poly(A) polymerase [RNA processing and modification]
Probab=31.40 E-value=4.4e+02 Score=28.18 Aligned_cols=48 Identities=27% Similarity=0.481 Sum_probs=36.2
Q ss_pred eEEEEccceeecCC-ccCCeeEEEecCCcchhhhHHHHHHHHHHHhcce
Q 010406 369 VIILCGGSYRRGKA-SCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFL 416 (511)
Q Consensus 369 ~~v~~~Gs~RRgke-~~gDvDiLit~~~~~~~~~~l~~~v~~l~~~g~l 416 (511)
-++.--||||-|.- -+.|||-|+..|..-+-.++|..+-..|++..-+
T Consensus 82 GKIFTyGSYRLGVhgpGsDIDtLvvVPkHVsR~dFFt~f~~~Lrer~ei 130 (552)
T COG5186 82 GKIFTYGSYRLGVHGPGSDIDTLVVVPKHVSRSDFFTHFYEELRERPEI 130 (552)
T ss_pred ceeeeecceeeeccCCCCCcceEEEecccccHHHHHHHHHHHhccCcch
Confidence 35666799999975 4679999999887766677888777777655433
No 295
>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=30.70 E-value=33 Score=27.64 Aligned_cols=28 Identities=29% Similarity=0.507 Sum_probs=20.5
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCchhhHH
Q 010406 255 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEH 284 (511)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil~tG~~~~le~ 284 (511)
-+.++||||+++|.+|. .+.|.+..+-.
T Consensus 23 ~i~gv~giG~k~A~~ll--~~~~~~~~~~~ 50 (75)
T cd00080 23 NIPGVPGIGPKTALKLL--KEYGSLENLLE 50 (75)
T ss_pred cCCCCCcccHHHHHHHH--HHhCCHHHHHH
Confidence 47799999999999875 35666655433
No 296
>PTZ00035 Rad51 protein; Provisional
Probab=30.46 E-value=43 Score=35.03 Aligned_cols=49 Identities=22% Similarity=0.291 Sum_probs=33.2
Q ss_pred HHHHHhcccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhhcccchhhh
Q 010406 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDI 342 (511)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~Gi~tledL~~~~--~L~~~q~~Glk~~~d~ 342 (511)
.++.+ .-+||+|.++++|-+.||.|++||.... .|....+++..-.+++
T Consensus 22 ~~~~l-~~~g~~~~~~~kL~~~g~~t~~~~~~~~~~~L~~~~gis~~~~~~i 72 (337)
T PTZ00035 22 EIEKL-QSAGINAADIKKLKEAGICTVESVAYATKKDLCNIKGISEAKVEKI 72 (337)
T ss_pred cHHHH-hcCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhhCCCHHHHHHH
Confidence 34455 4489999999999999999999997543 3444444444433443
No 297
>PHA01806 hypothetical protein
Probab=29.85 E-value=80 Score=30.44 Aligned_cols=49 Identities=18% Similarity=0.238 Sum_probs=31.1
Q ss_pred CcCHHHHHH-HHHHHHHHhhhcCCCeEEEEccceee----cCCccCCeeEEEecCCcc
Q 010406 345 RIPRHEVEQ-MERLLQKAGEEVLPEVIILCGGSYRR----GKASCGDLDVVIMHPDRK 397 (511)
Q Consensus 345 ~i~r~ea~~-~~~iv~~~~~~~~p~~~v~~~Gs~RR----gke~~gDvDiLit~~~~~ 397 (511)
.|++..... ...++..+. .-+..+.++||+=| |+ .+.|+||++....+.
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 455555432 344444443 35778888888877 55 789999976445444
No 298
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=28.36 E-value=45 Score=35.06 Aligned_cols=32 Identities=25% Similarity=0.287 Sum_probs=25.9
Q ss_pred HHHHHHhcccCCCHHHHHHHHHhCCCCHHHHhh
Q 010406 292 RTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (511)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~~Gi~tledL~~ 324 (511)
..++.+ .-.||+|+++++|-+.||.|++||..
T Consensus 29 ~~~~~l-~~~g~~~~~~~kL~~~g~~tv~~~~~ 60 (344)
T PLN03187 29 ESIDKL-ISQGINAGDVKKLQDAGIYTCNGLMM 60 (344)
T ss_pred cCHHHH-hhCCCCHHHHHHHHHcCCCcHHHHHh
Confidence 345555 44889999999999999999999874
No 299
>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=27.87 E-value=42 Score=27.57 Aligned_cols=30 Identities=20% Similarity=0.529 Sum_probs=17.6
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHh
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEK 287 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~ 287 (511)
.++.+||+||.++.....++ -+.-+++|+.
T Consensus 3 ~~l~~LpNig~~~e~~L~~v----GI~t~~~L~~ 32 (81)
T PF04994_consen 3 NRLKDLPNIGPKSERMLAKV----GIHTVEDLRE 32 (81)
T ss_dssp --GCGSTT--HHHHHHHHHT----T--SHHHHHH
T ss_pred cchhhCCCCCHHHHHHHHHc----CCCCHHHHHH
Confidence 36889999999888766554 4555666665
No 300
>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=27.81 E-value=47 Score=39.88 Aligned_cols=26 Identities=19% Similarity=0.326 Sum_probs=21.6
Q ss_pred hcccCCCHHHHHHHHHh-CCCCHHHHh
Q 010406 298 GEVWGIGPATAQKLYEK-GHRTLDDLK 323 (511)
Q Consensus 298 ~~I~GvGpktA~~l~~~-Gi~tledL~ 323 (511)
.+|+||||+||.++..+ |-.+|+.|.
T Consensus 869 ~GI~GIGpktAl~li~~~~~~~le~L~ 895 (1034)
T TIGR00600 869 EGIPTVGPVSAMEILNEFPGDGLEPLL 895 (1034)
T ss_pred CCCCcccHHHHHHHHHHcCCCCHHHHH
Confidence 47999999999999998 655676665
No 301
>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=26.53 E-value=45 Score=34.50 Aligned_cols=41 Identities=24% Similarity=0.267 Sum_probs=27.1
Q ss_pred ccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhhcccchh
Q 010406 300 VWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFD 340 (511)
Q Consensus 300 I~GvGpktA~~l~~~Gi~tledL~~~~--~L~~~q~~Glk~~~ 340 (511)
-.||||.++++|-+.||.|++||.... .|....+++....+
T Consensus 6 ~~g~~~~~~~~L~~~g~~t~~~~~~~~~~~L~~~~gls~~~~~ 48 (313)
T TIGR02238 6 AHGINAADIKKLKSAGICTVNGVIMTTRRALCKIKGLSEAKVD 48 (313)
T ss_pred cCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHH
Confidence 357889999999888999998887543 24444444433333
No 302
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=25.97 E-value=89 Score=31.09 Aligned_cols=49 Identities=20% Similarity=0.311 Sum_probs=37.3
Q ss_pred HHHHHHhcccCCCHHHHHHHHHhCCCCHHHHhhc--cCcchhhhhcccchhh
Q 010406 292 RTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDD 341 (511)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~~Gi~tledL~~~--~~L~~~q~~Glk~~~d 341 (511)
.++.-+|+|+||+...|..|... +-||+.+.++ +.|.+.+|+|..-.+.
T Consensus 192 ~~~~~Lt~i~~VnKtda~~LL~~-FgsLq~~~~AS~~ele~~~G~G~~kak~ 242 (254)
T KOG2841|consen 192 SLLGFLTTIPGVNKTDAQLLLQK-FGSLQQISNASEGELEQCPGLGPAKAKR 242 (254)
T ss_pred HHHHHHHhCCCCCcccHHHHHHh-cccHHHHHhcCHhHHHhCcCcCHHHHHH
Confidence 46778899999999999999775 4488888764 4688888888554433
No 303
>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=24.59 E-value=3.5e+02 Score=28.34 Aligned_cols=87 Identities=9% Similarity=0.200 Sum_probs=51.9
Q ss_pred HHHHHHHHhcCCccccc--hhhhcCCCCCCHHHHHHHHHHHHh------------CCchhhHHHHhhchhHHH-HHHhcc
Q 010406 236 YYKAIPVIEKLPFKIES--ADQVKGLPGIGKSMQDHIQEIVTT------------GKLSKLEHFEKDEKVRTI-SLFGEV 300 (511)
Q Consensus 236 Y~rAa~~l~~l~~~i~s--~~~l~~lpgIG~~ia~kI~Eil~t------------G~~~~le~l~~~~~~~~l-~lf~~I 300 (511)
-..||.+|..||..... ...+..+..|.+.+.+.|.++|+. |....+-++.+..+...- .+|..+
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 35899999999976544 356778888888888777665541 222334444444443333 344455
Q ss_pred cCCCHHHHHHHHHhCCCCHHHHh
Q 010406 301 WGIGPATAQKLYEKGHRTLDDLK 323 (511)
Q Consensus 301 ~GvGpktA~~l~~~Gi~tledL~ 323 (511)
--.-|..|..+-+ -+=+++||.
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 304
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=24.35 E-value=44 Score=37.68 Aligned_cols=28 Identities=25% Similarity=0.516 Sum_probs=21.8
Q ss_pred HhcccCCCHHHHHHHHHhCCCCHHHHhhc
Q 010406 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (511)
Q Consensus 297 f~~I~GvGpktA~~l~~~Gi~tledL~~~ 325 (511)
|-.|+||||++.++|.+ .+.|+++++.+
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 45566666654
No 305
>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=24.14 E-value=28 Score=27.23 Aligned_cols=21 Identities=19% Similarity=0.596 Sum_probs=15.7
Q ss_pred EEEEccceeecCCcc----CCeeEE
Q 010406 370 IILCGGSYRRGKASC----GDLDVV 390 (511)
Q Consensus 370 ~v~~~Gs~RRgke~~----gDvDiL 390 (511)
+|++--+|||||..+ ||+|||
T Consensus 34 rvmiPqeFkrGKsIiAV~EGe~~il 58 (67)
T TIGR02922 34 RVMIPQEFKRGKSIIAVCEGEITIL 58 (67)
T ss_pred cEEcchHHcCCCeEEEEEecceeeh
Confidence 677778999999875 555554
No 306
>PF12482 DUF3701: Phage integrase protein; InterPro: IPR022169 This domain family is found in bacteria, and is approximately 100 amino acids in length. The family is found in association with PF00589 from PFAM.
Probab=21.85 E-value=83 Score=26.91 Aligned_cols=21 Identities=43% Similarity=0.602 Sum_probs=19.4
Q ss_pred CHHHHHHHHHhCCCCHHHHhh
Q 010406 304 GPATAQKLYEKGHRTLDDLKN 324 (511)
Q Consensus 304 GpktA~~l~~~Gi~tledL~~ 324 (511)
.|..|++|-..||+||.||..
T Consensus 22 ~p~va~~L~aaGi~TL~dL~~ 42 (96)
T PF12482_consen 22 PPRVARRLAAAGIRTLADLVD 42 (96)
T ss_pred CHHHHHHHHHcCCchHHHHHH
Confidence 699999999999999999974
No 307
>PRK02406 DNA polymerase IV; Validated
Probab=21.81 E-value=1.7e+02 Score=30.30 Aligned_cols=52 Identities=25% Similarity=0.539 Sum_probs=33.9
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHHh--CCCC
Q 010406 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (511)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~--Gi~t 318 (511)
+..|||||+.+.+++..+ -+..+.+|.+-.+...-+.| | + ...++|+. |+..
T Consensus 170 i~~l~giG~~~~~~L~~~----Gi~ti~dl~~l~~~~L~~~f----G--~-~~~~l~~~a~G~d~ 223 (343)
T PRK02406 170 VEKIPGVGKVTAEKLHAL----GIYTCADLQKYDLAELIRHF----G--K-FGRRLYERARGIDE 223 (343)
T ss_pred cchhcCCCHHHHHHHHHc----CCCcHHHHHhCCHHHHHHHH----h--H-HHHHHHHHhCCCCC
Confidence 678899999999987754 35666666654333344444 4 3 56667764 8754
No 308
>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=21.64 E-value=1.7e+02 Score=26.34 Aligned_cols=38 Identities=18% Similarity=0.194 Sum_probs=25.4
Q ss_pred HHHHHHHHhhhcCCCeEEEEccceee----cCCccCCeeEEEecC
Q 010406 354 MERLLQKAGEEVLPEVIILCGGSYRR----GKASCGDLDVVIMHP 394 (511)
Q Consensus 354 ~~~iv~~~~~~~~p~~~v~~~Gs~RR----gke~~gDvDiLit~~ 394 (511)
+..+++.+.. ..+..+.++||+=| |+ .+.|+||++...
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 14778888888766 44 679999988754
No 309
>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=21.64 E-value=84 Score=27.11 Aligned_cols=44 Identities=11% Similarity=0.181 Sum_probs=29.7
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHH
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLF 297 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf 297 (511)
-.|..|.|||...|..|-..+.=.....+.+|..++-....+.+
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 46899999999999999988875555555555544333344444
No 310
>PRK07945 hypothetical protein; Provisional
Probab=21.42 E-value=52 Score=34.38 Aligned_cols=28 Identities=29% Similarity=0.446 Sum_probs=23.0
Q ss_pred HhcccCCCHHHHHHHHHh---C-CCCHHHHhh
Q 010406 297 FGEVWGIGPATAQKLYEK---G-HRTLDDLKN 324 (511)
Q Consensus 297 f~~I~GvGpktA~~l~~~---G-i~tledL~~ 324 (511)
|++|||||..+|.++.+- | +.-|++|+.
T Consensus 51 l~~~~giG~~~a~~i~e~~~tg~~~~l~~l~~ 82 (335)
T PRK07945 51 LTSLPGIGPKTAKVIAQALAGRVPDYLAELRA 82 (335)
T ss_pred cccCCCcCHHHHHHHHHHHhcCCHHHHHHHHH
Confidence 569999999999999873 6 567888874
No 311
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A.
Probab=21.19 E-value=62 Score=28.07 Aligned_cols=21 Identities=38% Similarity=0.561 Sum_probs=15.4
Q ss_pred HHHHHhcccCCCHHHHHHHHH
Q 010406 293 TISLFGEVWGIGPATAQKLYE 313 (511)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~ 313 (511)
.-.+|.=|.|+||+||..+.+
T Consensus 48 ~~~~LqfV~GLGPRKA~~Ll~ 68 (104)
T PF14635_consen 48 LANLLQFVCGLGPRKAQALLK 68 (104)
T ss_dssp HHGGGGGSTT--HHHHHHHHH
T ss_pred HHhhHhHhcCCChHHHHHHHH
Confidence 455666799999999999976
No 312
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=21.02 E-value=3.5e+02 Score=28.45 Aligned_cols=75 Identities=17% Similarity=0.200 Sum_probs=44.8
Q ss_pred CCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHHHH-------hCCCCHHHHhhccCcchhh
Q 010406 260 PGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE-------KGHRTLDDLKNEDSLTHSQ 332 (511)
Q Consensus 260 pgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~-------~Gi~tledL~~~~~L~~~q 332 (511)
+||+..+.+|+++ ..+.-++.+..-.+ . .|.++.|+...+|.++.+ .|+.|-.++....+-..--
T Consensus 37 ~g~~~~~~~kL~~----~g~~tv~~~~~~~~---~-~L~~~~g~s~~~~~ki~~~a~~~~~~~~~ta~~~~~~~~~~~~i 108 (344)
T PLN03187 37 QGINAGDVKKLQD----AGIYTCNGLMMHTK---K-NLTGIKGLSEAKVDKICEAAEKLLNQGFITGSDALLKRKSVVRI 108 (344)
T ss_pred CCCCHHHHHHHHH----cCCCcHHHHHhCCH---H-HHHHhcCCCHHHHHHHHHHHHHhhcccCCcHHHHHhhhccCcee
Confidence 6799888877654 34555666554333 2 344889999999998764 2667777776432111112
Q ss_pred hhcccchhhh
Q 010406 333 RLGLKYFDDI 342 (511)
Q Consensus 333 ~~Glk~~~d~ 342 (511)
..|.+-.+++
T Consensus 109 sTG~~~LD~l 118 (344)
T PLN03187 109 TTGSQALDEL 118 (344)
T ss_pred cCCcHhHHhh
Confidence 2455555544
No 313
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=20.99 E-value=2.2e+02 Score=34.86 Aligned_cols=90 Identities=22% Similarity=0.322 Sum_probs=0.0
Q ss_pred HHHHHHHHHHhcCCccccchhhhcCCCCCC-HHHHHHHHHHHHh--CCchhhHHHHhhchhHHHHHH-------------
Q 010406 234 FSYYKAIPVIEKLPFKIESADQVKGLPGIG-KSMQDHIQEIVTT--GKLSKLEHFEKDEKVRTISLF------------- 297 (511)
Q Consensus 234 ~aY~rAa~~l~~l~~~i~s~~~l~~lpgIG-~~ia~kI~Eil~t--G~~~~le~l~~~~~~~~l~lf------------- 297 (511)
++|.-|--.+++-.+++..+.. | ..+.++++||-.- -.....|.=.-..-+-+++|+
T Consensus 1294 l~YYAayfSira~~FDi~~m~~-------Gke~ik~k~~Ei~~~~~~~~~~kEk~l~t~lEi~~EM~aRGf~f~~idly~ 1366 (1444)
T COG2176 1294 LEYYAAYFSIRADDFDIETMSK-------GKEAIKAKMEEINKRKGNKASPKEKNLLTVLEIVLEMLARGFKFQKIDLYK 1366 (1444)
T ss_pred HHHHHHHheeehhhcCHHHHhc-------cHHHHHHHHHHHhhcccccCChhhhhhHhHHHHHHHHHHccCcccCceeee
Q ss_pred -----------------hcccCCCHHHHHHHHHh----CCCCHHHHhhccCcch
Q 010406 298 -----------------GEVWGIGPATAQKLYEK----GHRTLDDLKNEDSLTH 330 (511)
Q Consensus 298 -----------------~~I~GvGpktA~~l~~~----Gi~tledL~~~~~L~~ 330 (511)
-.|+|+|-..|+.+++. -+-|++||++.+++++
T Consensus 1367 S~At~Fvid~~~LipPFi~i~GlGe~vA~~IV~AR~Ek~FlS~eDlkkRtkis~ 1420 (1444)
T COG2176 1367 SDATEFVIDGDTLIPPFIAIPGLGENVAKSIVEAREEKEFLSKEDLKKRTKISK 1420 (1444)
T ss_pred ccCeEEEEeCCeecCceeccCChhHHHHHHHHHHhhcCCcCCHHHHHHhcCccH
No 314
>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=20.85 E-value=84 Score=22.16 Aligned_cols=22 Identities=18% Similarity=0.296 Sum_probs=18.0
Q ss_pred HHHhcccCCCHHHHHHHHHhCC
Q 010406 295 SLFGEVWGIGPATAQKLYEKGH 316 (511)
Q Consensus 295 ~lf~~I~GvGpktA~~l~~~Gi 316 (511)
..+.+..||-++|.+.|.++|.
T Consensus 4 ~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 4 GELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred HHHHHHHCcCHHHHHHHHHCCC
Confidence 3455778999999999998875
No 315
>PF08103 Antimicrobial_8: Uperin family; InterPro: IPR012527 This family consists of the uperin family of antimicrobial peptides. Uperin is a wide-spectrum antibiotic peptide isolated from the Australian toadlet, Uperoleia mjobergii. Being only 17 amino acid residues long, it is smaller than most other wide-spectrum antibiotic peptides isolated from amphibians. Uperin adopts a well-defined amphipathic alpha-helix with distinct hydrophilic and hydrophobic faces [].; GO: 0005576 extracellular region
Probab=20.61 E-value=87 Score=18.11 Aligned_cols=12 Identities=25% Similarity=0.437 Sum_probs=10.0
Q ss_pred HHHHHHHHHhcC
Q 010406 235 SYYKAIPVIEKL 246 (511)
Q Consensus 235 aY~rAa~~l~~l 246 (511)
+|++++++|+++
T Consensus 5 ~~rKivs~iKNv 16 (17)
T PF08103_consen 5 AIRKIVSVIKNV 16 (17)
T ss_pred HHHHHHHHHHhc
Confidence 688999999875
No 316
>PRK00024 hypothetical protein; Reviewed
Probab=20.39 E-value=1e+02 Score=30.24 Aligned_cols=42 Identities=36% Similarity=0.554 Sum_probs=0.0
Q ss_pred CHHHHHHHHHHHHh-CCchhhHHHHhhchhHHHHHHhcccCCCHHHHHHH
Q 010406 263 GKSMQDHIQEIVTT-GKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKL 311 (511)
Q Consensus 263 G~~ia~kI~Eil~t-G~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l 311 (511)
++.+...-.++++. |.+..+-.. ..+.|++|+|||+.+|..|
T Consensus 40 ~~~~~~LA~~LL~~fgsL~~l~~a-------s~~eL~~i~GIG~akA~~L 82 (224)
T PRK00024 40 GKSVLDLARELLQRFGSLRGLLDA-------SLEELQSIKGIGPAKAAQL 82 (224)
T ss_pred CCCHHHHHHHHHHHcCCHHHHHhC-------CHHHHhhccCccHHHHHHH
No 317
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=20.35 E-value=1.3e+02 Score=30.74 Aligned_cols=18 Identities=33% Similarity=0.661 Sum_probs=15.2
Q ss_pred hhhcCCCCCCHHHHHHHH
Q 010406 254 DQVKGLPGIGKSMQDHIQ 271 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~ 271 (511)
+.|..|||||.++|+=|-
T Consensus 218 ~~L~~lpGVG~KVADCI~ 235 (323)
T KOG2875|consen 218 EALCSLPGVGPKVADCIC 235 (323)
T ss_pred HHHhcCCCCcchHhhhhh
Confidence 458999999999999654
No 318
>PRK09482 flap endonuclease-like protein; Provisional
Probab=20.30 E-value=1.1e+02 Score=30.83 Aligned_cols=25 Identities=20% Similarity=0.422 Sum_probs=18.3
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCch
Q 010406 254 DQVKGLPGIGKSMQDHIQEIVTTGKLS 280 (511)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~ 280 (511)
+-+.++||||+++|.++-. +.|++.
T Consensus 182 DnIpGVpGIG~KtA~~LL~--~~gsle 206 (256)
T PRK09482 182 SKIPGVAGIGPKSAAELLN--QFRSLE 206 (256)
T ss_pred cCCCCCCCcChHHHHHHHH--HhCCHH
Confidence 4588999999999988643 445443
Done!