Query 012847
Match_columns 455
No_of_seqs 325 out of 970
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 06:55:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012847.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012847hhsearch_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 4.9E-58 1.1E-62 447.6 22.8 243 207-449 9-261 (353)
2 smart00483 POLXc DNA polymeras 100.0 2.8E-47 6.1E-52 387.5 21.8 199 208-408 1-202 (334)
3 cd00141 NT_POLXc Nucleotidyltr 100.0 3.9E-47 8.5E-52 382.5 21.8 208 212-421 2-212 (307)
4 PRK08609 hypothetical protein; 100.0 2.2E-43 4.8E-48 381.3 19.0 206 208-421 1-221 (570)
5 COG1796 POL4 DNA polymerase IV 100.0 7.7E-34 1.7E-38 280.2 17.1 206 208-421 3-226 (326)
6 PF14792 DNA_pol_B_palm: DNA p 99.8 8.6E-22 1.9E-26 170.8 6.4 91 345-435 1-95 (112)
7 PF14716 HHH_8: Helix-hairpin- 99.7 2.4E-17 5.2E-22 130.6 7.5 66 210-275 1-68 (68)
8 PF10391 DNA_pol_lambd_f: Fing 99.7 4.8E-17 1E-21 121.9 4.5 51 294-344 1-52 (52)
9 PRK07945 hypothetical protein; 99.5 9.1E-15 2E-19 149.4 8.7 91 213-313 3-98 (335)
10 PF00533 BRCT: BRCA1 C Terminu 99.0 4E-10 8.7E-15 89.5 6.4 75 16-95 3-78 (78)
11 smart00292 BRCT breast cancer 99.0 6.5E-10 1.4E-14 87.0 7.0 78 18-98 2-80 (80)
12 cd00027 BRCT Breast Cancer Sup 98.7 2.7E-08 5.9E-13 75.9 6.1 72 21-96 1-72 (72)
13 TIGR00575 dnlj DNA ligase, NAD 98.1 8.9E-06 1.9E-10 90.3 10.1 133 254-397 466-633 (652)
14 PF14520 HHH_5: Helix-hairpin- 98.1 2.7E-06 5.8E-11 65.5 2.9 51 293-343 3-55 (60)
15 PF12738 PTCB-BRCT: twin BRCT 97.9 1.2E-05 2.6E-10 62.1 3.7 62 23-90 2-63 (63)
16 KOG3226 DNA repair protein [Re 97.8 1.1E-05 2.4E-10 81.8 2.0 89 16-111 315-404 (508)
17 PLN03123 poly [ADP-ribose] pol 97.7 5.7E-05 1.2E-09 86.8 7.8 91 16-109 391-481 (981)
18 PF14520 HHH_5: Helix-hairpin- 97.5 0.00012 2.6E-09 56.3 4.2 52 254-313 5-56 (60)
19 PLN03122 Poly [ADP-ribose] pol 97.5 0.00022 4.9E-09 80.5 7.4 94 14-110 185-279 (815)
20 COG1555 ComEA DNA uptake prote 97.2 0.00048 1E-08 62.9 5.0 50 252-313 95-145 (149)
21 PRK07956 ligA NAD-dependent DN 97.2 0.002 4.4E-08 71.9 10.5 134 254-397 479-639 (665)
22 PF12826 HHH_2: Helix-hairpin- 97.1 0.00078 1.7E-08 52.7 4.6 48 257-313 6-53 (64)
23 TIGR01259 comE comEA protein. 97.1 0.00098 2.1E-08 58.7 5.5 50 252-313 66-116 (120)
24 PF11731 Cdd1: Pathogenicity l 97.1 0.0007 1.5E-08 56.9 4.2 36 290-325 7-42 (93)
25 PF12836 HHH_3: Helix-hairpin- 97.0 0.00095 2.1E-08 52.3 4.5 49 251-311 11-60 (65)
26 PRK14351 ligA NAD-dependent DN 96.9 0.0037 7.9E-08 70.1 9.9 134 254-397 496-658 (689)
27 PF14229 DUF4332: Domain of un 96.7 0.01 2.3E-07 52.3 8.6 32 294-325 52-83 (122)
28 PRK02515 psbU photosystem II c 96.6 0.0029 6.3E-08 56.2 4.9 47 252-313 59-105 (132)
29 KOG0966 ATP-dependent DNA liga 96.6 0.0036 7.9E-08 69.5 6.3 90 13-107 628-720 (881)
30 TIGR00426 competence protein C 96.5 0.0053 1.1E-07 48.4 5.4 51 252-314 14-66 (69)
31 TIGR00084 ruvA Holliday juncti 96.5 0.0041 8.9E-08 59.1 5.4 53 254-312 72-124 (191)
32 KOG2481 Protein required for n 96.4 0.0015 3.3E-08 69.2 1.7 86 12-109 321-416 (570)
33 PRK14605 ruvA Holliday junctio 96.4 0.0038 8.2E-08 59.5 4.2 52 254-312 73-125 (194)
34 TIGR00084 ruvA Holliday juncti 96.3 0.0024 5.3E-08 60.6 2.8 51 291-343 68-124 (191)
35 PF00633 HHH: Helix-hairpin-he 96.3 0.0036 7.8E-08 41.7 2.5 23 251-273 8-30 (30)
36 KOG4362 Transcriptional regula 96.2 0.0045 9.6E-08 68.3 4.5 76 33-111 488-565 (684)
37 PRK12766 50S ribosomal protein 96.2 0.0017 3.7E-08 63.0 1.1 52 296-347 4-57 (232)
38 PRK13901 ruvA Holliday junctio 96.2 0.0062 1.4E-07 58.0 4.7 54 254-313 72-125 (196)
39 PRK00116 ruvA Holliday junctio 96.2 0.0069 1.5E-07 57.5 4.9 54 254-314 73-127 (192)
40 PRK14601 ruvA Holliday junctio 96.1 0.0068 1.5E-07 57.2 4.6 54 254-313 73-126 (183)
41 PRK14602 ruvA Holliday junctio 96.0 0.0074 1.6E-07 57.9 4.2 54 254-313 74-127 (203)
42 PRK07956 ligA NAD-dependent DN 96.0 0.0034 7.4E-08 70.1 2.0 61 299-359 449-512 (665)
43 PRK14606 ruvA Holliday junctio 95.9 0.0092 2E-07 56.6 4.6 54 254-313 73-126 (188)
44 PRK14604 ruvA Holliday junctio 95.9 0.01 2.2E-07 56.6 4.5 54 254-313 73-126 (195)
45 PRK14603 ruvA Holliday junctio 95.9 0.01 2.2E-07 56.7 4.6 54 254-313 72-125 (197)
46 PRK02362 ski2-like helicase; P 95.8 0.0088 1.9E-07 67.7 4.3 59 283-344 641-701 (737)
47 PRK14973 DNA topoisomerase I; 95.6 0.016 3.6E-07 67.0 5.7 91 254-345 835-929 (936)
48 TIGR00575 dnlj DNA ligase, NAD 95.6 0.006 1.3E-07 68.1 1.9 62 299-360 436-500 (652)
49 PF00633 HHH: Helix-hairpin-he 95.6 0.012 2.6E-07 39.2 2.6 22 292-313 8-29 (30)
50 PRK14350 ligA NAD-dependent DN 95.5 0.034 7.3E-07 62.3 7.7 135 254-397 470-642 (669)
51 COG1555 ComEA DNA uptake prote 95.3 0.019 4.1E-07 52.5 3.8 51 291-347 93-148 (149)
52 COG0632 RuvA Holliday junction 95.2 0.022 4.8E-07 54.5 4.3 54 254-313 73-126 (201)
53 cd05397 NT_Pol-beta-like Nucle 95.1 0.04 8.6E-07 40.7 4.4 28 365-392 14-42 (49)
54 PF11798 IMS_HHH: IMS family H 95.0 0.013 2.9E-07 39.5 1.6 20 297-316 13-32 (32)
55 PRK14600 ruvA Holliday junctio 95.0 0.024 5.2E-07 53.7 3.8 53 254-313 73-125 (186)
56 TIGR01259 comE comEA protein. 95.0 0.026 5.6E-07 49.7 3.8 49 292-346 65-118 (120)
57 COG0272 Lig NAD-dependent DNA 95.0 0.081 1.8E-06 58.6 8.3 80 254-343 479-560 (667)
58 cd05402 NT_PAP_TUTase Nucleoti 94.9 0.1 2.3E-06 44.6 7.3 58 354-415 9-68 (114)
59 PRK02515 psbU photosystem II c 94.9 0.044 9.6E-07 48.8 4.9 32 293-324 59-91 (132)
60 PRK00116 ruvA Holliday junctio 94.8 0.018 3.9E-07 54.7 2.3 51 293-343 71-125 (192)
61 PF12836 HHH_3: Helix-hairpin- 94.7 0.039 8.5E-07 43.1 3.7 48 293-346 12-64 (65)
62 PRK14605 ruvA Holliday junctio 94.6 0.017 3.7E-07 55.0 1.9 52 291-342 69-124 (194)
63 KOG0966 ATP-dependent DNA liga 94.6 0.093 2E-06 58.7 7.6 91 16-107 782-881 (881)
64 KOG2043 Signaling protein SWIF 94.6 0.033 7.2E-07 64.0 4.3 68 38-109 672-739 (896)
65 PRK00254 ski2-like helicase; P 94.6 0.047 1E-06 61.7 5.5 67 276-343 623-695 (720)
66 KOG1929 Nucleotide excision re 94.4 0.049 1.1E-06 61.8 5.1 93 11-109 486-578 (811)
67 TIGR00426 competence protein C 94.4 0.05 1.1E-06 42.8 3.8 45 296-346 17-67 (69)
68 KOG1929 Nucleotide excision re 94.4 0.064 1.4E-06 60.9 5.9 88 18-110 103-190 (811)
69 PF12826 HHH_2: Helix-hairpin- 94.4 0.034 7.4E-07 43.4 2.7 47 295-343 4-52 (64)
70 PRK03858 DNA polymerase IV; Va 94.1 0.067 1.4E-06 56.0 4.9 113 297-429 175-291 (396)
71 COG5163 NOP7 Protein required 93.5 0.065 1.4E-06 55.6 3.5 87 11-109 343-440 (591)
72 PRK14606 ruvA Holliday junctio 93.1 0.053 1.1E-06 51.5 2.0 50 291-342 69-124 (188)
73 PRK14601 ruvA Holliday junctio 93.0 0.056 1.2E-06 51.1 2.1 50 291-342 69-124 (183)
74 PRK12766 50S ribosomal protein 93.0 0.18 3.9E-06 49.2 5.5 54 253-314 2-55 (232)
75 PRK14603 ruvA Holliday junctio 92.7 0.064 1.4E-06 51.3 2.0 50 291-342 68-123 (197)
76 PRK02406 DNA polymerase IV; Va 92.7 0.28 6.1E-06 50.3 6.9 112 297-429 170-287 (343)
77 cd00424 PolY Y-family of DNA p 92.7 0.35 7.5E-06 49.7 7.5 108 298-429 176-291 (343)
78 PRK14602 ruvA Holliday junctio 92.7 0.068 1.5E-06 51.3 2.2 50 291-342 70-125 (203)
79 PRK14604 ruvA Holliday junctio 92.5 0.07 1.5E-06 50.9 2.0 50 291-342 69-124 (195)
80 PRK14351 ligA NAD-dependent DN 92.5 0.052 1.1E-06 61.0 1.3 63 299-361 466-531 (689)
81 cd03468 PolY_like DNA Polymera 92.5 0.13 2.9E-06 52.1 4.2 121 299-438 174-296 (335)
82 PRK13901 ruvA Holliday junctio 92.3 0.082 1.8E-06 50.5 2.1 50 291-342 68-123 (196)
83 TIGR01448 recD_rel helicase, p 92.2 0.41 8.9E-06 54.3 8.0 83 253-346 116-201 (720)
84 PRK04301 radA DNA repair and r 92.0 0.097 2.1E-06 53.2 2.5 46 297-342 8-55 (317)
85 PF04994 TfoX_C: TfoX C-termin 91.9 0.12 2.6E-06 42.4 2.4 30 297-326 5-34 (81)
86 PRK03348 DNA polymerase IV; Pr 91.8 0.16 3.5E-06 54.4 4.0 115 297-430 182-299 (454)
87 smart00278 HhH1 Helix-hairpin- 91.8 0.12 2.5E-06 33.1 1.8 17 297-313 3-19 (26)
88 PF01909 NTP_transf_2: Nucleot 91.5 0.32 6.9E-06 39.6 4.5 32 366-397 12-44 (93)
89 COG1796 POL4 DNA polymerase IV 91.4 0.48 1E-05 48.3 6.6 97 207-323 59-156 (326)
90 cd01701 PolY_Rev1 DNA polymera 91.1 0.3 6.5E-06 51.5 5.1 110 297-426 224-339 (404)
91 COG1948 MUS81 ERCC4-type nucle 91.1 0.3 6.4E-06 48.4 4.6 49 256-313 184-232 (254)
92 TIGR01448 recD_rel helicase, p 91.0 0.12 2.5E-06 58.7 1.9 55 292-346 79-137 (720)
93 PRK14600 ruvA Holliday junctio 90.9 0.13 2.8E-06 48.8 1.9 49 291-342 69-123 (186)
94 PRK01172 ski2-like helicase; P 90.9 0.27 5.8E-06 55.2 4.7 51 285-336 603-655 (674)
95 TIGR03252 uncharacterized HhH- 90.9 0.64 1.4E-05 43.7 6.4 49 261-312 75-132 (177)
96 PRK08097 ligB NAD-dependent DN 90.8 0.38 8.2E-06 52.9 5.6 88 253-353 458-547 (562)
97 COG3743 Uncharacterized conser 90.8 0.28 6.2E-06 43.7 3.8 53 295-350 67-119 (133)
98 TIGR02236 recomb_radA DNA repa 90.7 0.16 3.5E-06 51.3 2.5 29 298-326 2-30 (310)
99 TIGR00588 ogg 8-oxoguanine DNA 90.2 0.78 1.7E-05 46.8 6.9 63 255-319 177-244 (310)
100 cd01700 PolY_Pol_V_umuC umuC s 90.0 0.92 2E-05 46.6 7.4 108 297-428 178-293 (344)
101 PF11731 Cdd1: Pathogenicity l 89.8 0.48 1E-05 40.0 4.1 48 252-303 10-57 (93)
102 PRK02794 DNA polymerase IV; Pr 89.8 0.66 1.4E-05 49.1 6.2 112 297-429 211-326 (419)
103 PTZ00205 DNA polymerase kappa; 89.7 0.61 1.3E-05 51.3 5.9 123 297-429 311-437 (571)
104 PRK01810 DNA polymerase IV; Va 89.6 0.45 9.7E-06 50.0 4.8 115 297-430 181-299 (407)
105 PRK03103 DNA polymerase IV; Re 89.5 0.66 1.4E-05 48.8 6.0 110 298-429 184-300 (409)
106 PRK03352 DNA polymerase IV; Va 89.3 0.35 7.6E-06 49.7 3.7 40 297-336 179-218 (346)
107 PRK14133 DNA polymerase IV; Pr 88.9 0.55 1.2E-05 48.3 4.8 109 297-429 175-290 (347)
108 PRK13482 DNA integrity scannin 88.8 0.66 1.4E-05 48.0 5.2 89 213-313 243-337 (352)
109 cd03586 PolY_Pol_IV_kappa DNA 88.8 1.2 2.6E-05 45.2 7.1 108 298-429 174-288 (334)
110 PF14490 HHH_4: Helix-hairpin- 88.5 0.79 1.7E-05 38.4 4.6 54 292-346 10-66 (94)
111 PRK01216 DNA polymerase IV; Va 88.3 0.43 9.4E-06 49.5 3.6 30 297-326 180-209 (351)
112 smart00279 HhH2 Helix-hairpin- 88.1 0.33 7.1E-06 33.7 1.7 16 299-314 20-35 (36)
113 PRK14670 uvrC excinuclease ABC 88.1 1 2.2E-05 49.8 6.4 52 254-314 514-565 (574)
114 cd00080 HhH2_motif Helix-hairp 87.6 0.47 1E-05 38.2 2.6 27 297-324 24-50 (75)
115 KOG2841 Structure-specific end 87.0 0.72 1.6E-05 45.1 3.9 50 255-313 196-245 (254)
116 PRK03609 umuC DNA polymerase V 86.8 0.59 1.3E-05 49.5 3.6 30 297-326 181-210 (422)
117 cd05400 NT_2-5OAS_ClassI-CCAas 86.7 2.8 6.2E-05 37.1 7.5 46 368-413 27-79 (143)
118 PRK08609 hypothetical protein; 86.2 0.88 1.9E-05 50.3 4.6 56 252-313 86-141 (570)
119 TIGR01083 nth endonuclease III 86.0 3.1 6.7E-05 39.3 7.7 25 292-316 103-127 (191)
120 PRK10880 adenine DNA glycosyla 85.9 3.2 6.9E-05 43.2 8.3 65 232-303 85-151 (350)
121 PRK14666 uvrC excinuclease ABC 85.9 0.42 9.1E-06 53.6 1.9 49 294-344 636-687 (694)
122 PRK10308 3-methyl-adenine DNA 85.7 1.7 3.7E-05 43.8 6.1 64 254-321 167-233 (283)
123 PRK08097 ligB NAD-dependent DN 85.6 0.35 7.6E-06 53.2 1.1 64 298-361 428-494 (562)
124 COG0122 AlkA 3-methyladenine D 85.5 3.6 7.7E-05 41.6 8.2 47 270-317 174-220 (285)
125 smart00278 HhH1 Helix-hairpin- 85.4 0.73 1.6E-05 29.3 2.1 20 255-274 2-21 (26)
126 COG0353 RecR Recombinational D 85.4 0.6 1.3E-05 44.4 2.5 31 292-322 9-40 (198)
127 COG1948 MUS81 ERCC4-type nucle 85.0 1.3 2.9E-05 43.9 4.7 55 288-343 175-231 (254)
128 cd01703 PolY_Pol_iota DNA Poly 85.0 0.81 1.7E-05 48.0 3.5 30 297-326 174-203 (379)
129 PRK07758 hypothetical protein; 84.9 0.49 1.1E-05 39.9 1.5 45 300-344 39-85 (95)
130 PF01367 5_3_exonuc: 5'-3' exo 84.8 0.08 1.7E-06 45.3 -3.4 25 299-325 22-47 (101)
131 COG0632 RuvA Holliday junction 84.6 0.57 1.2E-05 45.0 2.0 51 292-342 70-124 (201)
132 PRK14667 uvrC excinuclease ABC 84.5 1.8 4E-05 47.7 6.1 51 254-314 514-564 (567)
133 COG1708 Predicted nucleotidylt 84.3 4.5 9.7E-05 34.3 7.3 29 367-395 25-54 (128)
134 PRK14666 uvrC excinuclease ABC 83.9 1.8 3.9E-05 48.7 5.7 51 254-313 637-687 (694)
135 PRK09482 flap endonuclease-lik 83.6 0.81 1.8E-05 45.5 2.6 25 299-325 186-211 (256)
136 PRK10702 endonuclease III; Pro 83.5 1.1 2.4E-05 43.2 3.5 25 292-316 106-130 (211)
137 smart00475 53EXOc 5'-3' exonuc 83.4 0.84 1.8E-05 45.4 2.7 26 298-325 189-215 (259)
138 PRK00227 glnD PII uridylyl-tra 83.3 3.3 7.2E-05 46.9 7.6 65 348-415 8-74 (693)
139 PRK00558 uvrC excinuclease ABC 83.3 2.3 4.9E-05 47.4 6.2 52 254-314 543-594 (598)
140 PRK14976 5'-3' exonuclease; Pr 82.9 0.88 1.9E-05 45.8 2.6 25 299-324 195-219 (281)
141 TIGR03671 cca_archaeal CCA-add 82.7 4.2 9.1E-05 43.1 7.6 45 352-396 24-70 (408)
142 cd00056 ENDO3c endonuclease II 82.6 0.87 1.9E-05 41.2 2.2 28 290-317 78-105 (158)
143 PRK14672 uvrC excinuclease ABC 82.2 2.2 4.8E-05 47.9 5.6 54 254-316 608-661 (691)
144 PRK04301 radA DNA repair and r 81.9 4.5 9.7E-05 41.1 7.3 52 255-314 7-58 (317)
145 cd01702 PolY_Pol_eta DNA Polym 81.6 1.4 3.1E-05 45.8 3.6 29 297-325 184-213 (359)
146 PTZ00418 Poly(A) polymerase; P 81.6 5.1 0.00011 44.4 8.0 53 366-418 124-177 (593)
147 cd00008 53EXOc 5'-3' exonuclea 81.1 1.2 2.5E-05 43.8 2.7 26 299-325 187-212 (240)
148 COG1669 Predicted nucleotidylt 80.9 4.5 9.8E-05 34.4 5.8 46 367-413 22-69 (97)
149 PRK06063 DNA polymerase III su 80.9 5.8 0.00013 40.5 7.7 73 17-93 231-303 (313)
150 PRK01229 N-glycosylase/DNA lya 80.4 2.1 4.6E-05 41.3 4.1 53 262-317 85-142 (208)
151 PRK00076 recR recombination pr 80.3 1.3 2.9E-05 42.3 2.7 22 292-313 8-29 (196)
152 TIGR00615 recR recombination p 80.2 1.4 3E-05 42.1 2.7 21 292-312 8-28 (195)
153 PRK10702 endonuclease III; Pro 79.9 4 8.7E-05 39.4 5.9 43 231-273 84-128 (211)
154 PRK13844 recombination protein 79.1 1.6 3.4E-05 41.9 2.7 23 291-313 11-33 (200)
155 TIGR01084 mutY A/G-specific ad 78.9 4.2 9.2E-05 40.9 5.9 78 219-303 68-147 (275)
156 smart00478 ENDO3c endonuclease 78.6 4.2 9.1E-05 36.3 5.3 26 292-317 69-94 (149)
157 PF14229 DUF4332: Domain of un 77.9 2.3 5E-05 37.5 3.2 26 301-326 1-26 (122)
158 COG0177 Nth Predicted EndoIII- 77.7 3 6.5E-05 40.4 4.2 95 261-363 80-184 (211)
159 PRK00254 ski2-like helicase; P 77.5 12 0.00025 42.6 9.6 53 254-314 645-697 (720)
160 COG0389 DinP Nucleotidyltransf 77.3 2 4.4E-05 44.5 3.2 27 298-324 179-205 (354)
161 cd05403 NT_KNTase_like Nucleot 76.8 13 0.00029 29.5 7.4 29 370-398 20-49 (93)
162 PRK13300 tRNA CCA-pyrophosphor 76.6 8.6 0.00019 41.4 7.7 45 354-398 27-73 (447)
163 PRK14350 ligA NAD-dependent DN 76.5 5.8 0.00013 44.8 6.7 73 16-93 591-663 (669)
164 COG0258 Exo 5'-3' exonuclease 76.3 1.9 4.1E-05 43.8 2.6 25 299-325 202-227 (310)
165 KOG2875 8-oxoguanine DNA glyco 75.9 4 8.6E-05 41.1 4.6 69 254-323 174-246 (323)
166 cd00056 ENDO3c endonuclease II 75.4 5.4 0.00012 35.9 5.1 78 219-303 43-125 (158)
167 COG1746 CCA1 tRNA nucleotidylt 75.1 10 0.00022 40.3 7.6 47 352-398 29-77 (443)
168 KOG3524 Predicted guanine nucl 74.6 2.6 5.7E-05 47.0 3.2 77 17-101 117-193 (850)
169 PRK13913 3-methyladenine DNA g 74.3 3.8 8.2E-05 39.9 4.0 22 292-313 118-139 (218)
170 KOG3548 DNA damage checkpoint 74.3 3.2 7E-05 47.7 3.9 91 17-110 924-1037(1176)
171 PRK13910 DNA glycosylase MutY; 74.3 6.6 0.00014 39.8 5.8 68 232-306 48-117 (289)
172 PRK14670 uvrC excinuclease ABC 74.0 2.2 4.7E-05 47.3 2.5 45 296-341 515-561 (574)
173 PRK14667 uvrC excinuclease ABC 74.0 1.9 4.1E-05 47.7 2.0 46 295-342 514-561 (567)
174 PF03118 RNA_pol_A_CTD: Bacter 73.6 4.8 0.0001 31.6 3.7 36 238-275 22-65 (66)
175 PRK14671 uvrC excinuclease ABC 73.3 3.4 7.3E-05 46.3 3.8 47 293-342 567-615 (621)
176 PRK13766 Hef nuclease; Provisi 73.1 4.9 0.00011 45.8 5.1 44 297-341 717-762 (773)
177 PF00416 Ribosomal_S13: Riboso 72.9 3.4 7.5E-05 35.5 3.0 26 293-318 13-39 (107)
178 PF11798 IMS_HHH: IMS family H 72.3 1.8 4E-05 29.1 0.9 18 255-272 12-29 (32)
179 PRK03352 DNA polymerase IV; Va 71.8 11 0.00025 38.6 7.0 55 256-320 179-235 (346)
180 TIGR03252 uncharacterized HhH- 71.5 12 0.00027 35.2 6.5 44 232-275 80-136 (177)
181 PRK14669 uvrC excinuclease ABC 70.4 2.4 5.1E-05 47.4 1.7 30 295-325 552-581 (624)
182 PF03445 DUF294: Putative nucl 70.3 16 0.00034 32.8 6.7 51 369-419 50-107 (138)
183 PF02371 Transposase_20: Trans 70.2 2.7 6E-05 34.5 1.7 20 295-314 2-21 (87)
184 KOG2245 Poly(A) polymerase and 70.2 7.5 0.00016 42.1 5.3 88 330-419 40-141 (562)
185 PRK01216 DNA polymerase IV; Va 70.1 14 0.00031 38.3 7.3 86 209-317 146-233 (351)
186 PRK05007 PII uridylyl-transfer 69.9 15 0.00032 43.0 8.1 51 367-417 79-132 (884)
187 cd01701 PolY_Rev1 DNA polymera 69.7 9.8 0.00021 40.1 6.2 53 256-318 224-280 (404)
188 TIGR03491 RecB family nuclease 69.6 4.4 9.6E-05 43.5 3.6 29 298-326 210-238 (457)
189 TIGR00615 recR recombination p 69.2 3.4 7.4E-05 39.5 2.3 37 249-285 5-42 (195)
190 KOG2534 DNA polymerase IV (fam 69.2 3.8 8.2E-05 41.9 2.7 54 290-343 51-114 (353)
191 PRK14973 DNA topoisomerase I; 68.6 4.9 0.00011 47.1 3.9 41 295-335 802-844 (936)
192 PF03118 RNA_pol_A_CTD: Bacter 68.4 1.5 3.3E-05 34.5 -0.2 44 301-344 17-62 (66)
193 COG2251 Predicted nuclease (Re 68.3 3.7 8.1E-05 43.8 2.6 27 299-325 229-255 (474)
194 PRK14672 uvrC excinuclease ABC 67.8 2.9 6.2E-05 47.0 1.7 53 295-348 608-662 (691)
195 PF14579 HHH_6: Helix-hairpin- 67.7 14 0.00031 30.4 5.5 50 256-316 29-78 (90)
196 smart00611 SEC63 Domain of unk 67.3 13 0.00028 37.3 6.3 29 297-325 153-181 (312)
197 cd05401 NT_GlnE_GlnD_like Nucl 67.1 21 0.00045 32.7 7.1 52 368-419 55-112 (172)
198 PRK00076 recR recombination pr 66.9 3.9 8.4E-05 39.2 2.2 32 254-285 11-42 (196)
199 PRK14671 uvrC excinuclease ABC 66.8 7.5 0.00016 43.6 4.7 49 254-313 569-617 (621)
200 PRK02362 ski2-like helicase; P 66.6 41 0.0009 38.3 10.8 52 254-315 652-704 (737)
201 TIGR00593 pola DNA polymerase 66.4 4.1 8.8E-05 47.5 2.7 24 299-324 189-213 (887)
202 PRK03980 flap endonuclease-1; 66.2 4.5 9.7E-05 41.0 2.6 25 299-324 193-217 (292)
203 PRK03858 DNA polymerase IV; Va 66.1 12 0.00026 39.1 5.9 52 256-317 175-228 (396)
204 PRK12278 50S ribosomal protein 66.1 4.5 9.8E-05 39.4 2.5 30 295-324 158-187 (221)
205 COG0177 Nth Predicted EndoIII- 66.0 14 0.00031 35.7 5.9 31 243-273 97-128 (211)
206 TIGR02236 recomb_radA DNA repa 65.9 9.6 0.00021 38.4 5.0 50 256-313 1-50 (310)
207 PRK13844 recombination protein 65.5 4.2 9.1E-05 39.0 2.1 32 254-285 15-46 (200)
208 PRK14668 uvrC excinuclease ABC 65.5 9.6 0.00021 42.3 5.2 48 295-343 525-574 (577)
209 PRK01759 glnD PII uridylyl-tra 64.8 22 0.00048 41.4 8.2 67 349-415 33-106 (854)
210 PF04919 DUF655: Protein of un 64.6 10 0.00022 35.8 4.4 43 248-290 109-152 (181)
211 KOG1921 Endonuclease III [Repl 64.1 7 0.00015 38.7 3.4 31 283-314 148-178 (286)
212 PF14579 HHH_6: Helix-hairpin- 64.1 8.9 0.00019 31.7 3.6 30 297-326 29-62 (90)
213 PRK06195 DNA polymerase III su 63.6 17 0.00036 37.0 6.2 48 17-65 219-266 (309)
214 PTZ00217 flap endonuclease-1; 63.0 5.5 0.00012 42.1 2.7 26 298-324 238-263 (393)
215 PRK10917 ATP-dependent DNA hel 62.7 6.1 0.00013 44.6 3.2 27 297-323 11-37 (681)
216 cd01703 PolY_Pol_iota DNA Poly 62.5 15 0.00032 38.6 5.8 54 255-318 173-243 (379)
217 PF14716 HHH_8: Helix-hairpin- 62.3 6.5 0.00014 30.8 2.3 23 291-313 42-65 (68)
218 TIGR01083 nth endonuclease III 62.2 19 0.0004 34.0 5.9 54 219-272 68-124 (191)
219 PRK00558 uvrC excinuclease ABC 61.9 5.9 0.00013 44.2 2.8 49 293-342 541-591 (598)
220 KOG4362 Transcriptional regula 61.7 11 0.00025 42.2 4.9 93 3-97 573-677 (684)
221 KOG2093 Translesion DNA polyme 61.4 9.3 0.0002 43.9 4.1 85 15-108 44-130 (1016)
222 PRK04374 PII uridylyl-transfer 61.3 27 0.00058 40.8 8.0 63 354-416 55-123 (869)
223 KOG3524 Predicted guanine nucl 61.3 4.6 0.0001 45.1 1.7 86 17-109 209-294 (850)
224 TIGR01954 nusA_Cterm_rpt trans 61.3 8.4 0.00018 27.7 2.6 32 303-334 1-34 (50)
225 PRK07758 hypothetical protein; 61.2 8.5 0.00018 32.6 2.9 23 254-276 67-89 (95)
226 TIGR03674 fen_arch flap struct 60.5 6.6 0.00014 40.6 2.7 27 298-325 239-265 (338)
227 PRK05755 DNA polymerase I; Pro 60.5 6 0.00013 46.1 2.6 25 298-324 190-215 (880)
228 PRK12311 rpsB 30S ribosomal pr 60.2 6.3 0.00014 40.6 2.4 32 293-324 261-292 (326)
229 PRK14668 uvrC excinuclease ABC 60.0 6.7 0.00015 43.5 2.8 20 327-346 526-545 (577)
230 PRK02794 DNA polymerase IV; Pr 60.0 54 0.0012 34.6 9.6 52 256-318 211-264 (419)
231 COG1204 Superfamily II helicas 59.8 11 0.00024 43.2 4.6 112 232-346 609-729 (766)
232 COG4277 Predicted DNA-binding 59.3 6.8 0.00015 39.9 2.4 32 294-325 329-363 (404)
233 cd00141 NT_POLXc Nucleotidyltr 59.0 4.9 0.00011 40.9 1.4 51 293-343 43-102 (307)
234 KOG2093 Translesion DNA polyme 58.5 14 0.0003 42.5 4.9 27 298-324 552-578 (1016)
235 CHL00137 rps13 ribosomal prote 58.3 6.6 0.00014 34.8 1.9 25 293-317 15-40 (122)
236 PF02889 Sec63: Sec63 Brl doma 58.2 16 0.00035 36.6 5.0 29 296-324 149-177 (314)
237 PRK05179 rpsM 30S ribosomal pr 57.9 6.5 0.00014 34.8 1.8 24 294-317 16-40 (122)
238 PRK14669 uvrC excinuclease ABC 57.7 19 0.00042 40.3 5.9 50 254-314 552-601 (624)
239 TIGR00588 ogg 8-oxoguanine DNA 57.5 16 0.00034 37.4 4.7 77 223-305 177-265 (310)
240 COG0272 Lig NAD-dependent DNA 56.7 26 0.00057 39.4 6.6 72 17-93 593-664 (667)
241 PRK13482 DNA integrity scannin 56.2 6.8 0.00015 40.7 1.9 54 286-341 278-334 (352)
242 PRK13913 3-methyladenine DNA g 56.0 22 0.00048 34.6 5.3 91 218-316 78-178 (218)
243 smart00478 ENDO3c endonuclease 55.7 28 0.00061 30.9 5.7 42 232-273 48-91 (149)
244 PRK00275 glnD PII uridylyl-tra 54.8 41 0.0009 39.4 8.2 49 368-416 78-129 (895)
245 PF14490 HHH_4: Helix-hairpin- 54.8 11 0.00024 31.3 2.7 55 261-322 19-74 (94)
246 PRK03348 DNA polymerase IV; Pr 54.5 25 0.00054 37.8 6.0 53 256-318 182-236 (454)
247 TIGR03631 bact_S13 30S ribosom 54.1 7.9 0.00017 33.8 1.7 25 293-317 13-38 (113)
248 COG1491 Predicted RNA-binding 53.9 13 0.00028 35.3 3.2 40 248-287 123-163 (202)
249 KOG1921 Endonuclease III [Repl 53.9 20 0.00044 35.5 4.6 29 245-273 149-178 (286)
250 COG0322 UvrC Nuclease subunit 53.9 23 0.00049 39.5 5.5 83 210-313 497-579 (581)
251 TIGR00596 rad1 DNA repair prot 53.6 18 0.0004 41.8 5.0 47 293-342 755-804 (814)
252 PF04919 DUF655: Protein of un 53.5 12 0.00026 35.3 2.9 58 266-324 86-149 (181)
253 cd01702 PolY_Pol_eta DNA Polym 53.3 25 0.00054 36.6 5.6 54 256-318 184-241 (359)
254 KOG0323 TFIIF-interacting CTD 53.0 6.8 0.00015 43.8 1.4 89 17-109 440-531 (635)
255 TIGR01084 mutY A/G-specific ad 52.8 20 0.00043 36.1 4.6 25 292-316 102-126 (275)
256 TIGR00596 rad1 DNA repair prot 52.3 23 0.00051 41.0 5.5 19 328-346 759-777 (814)
257 TIGR01693 UTase_glnD [Protein- 52.2 35 0.00077 39.6 7.1 51 367-417 42-95 (850)
258 COG2844 GlnD UTP:GlnB (protein 51.7 25 0.00055 40.4 5.5 48 368-415 66-116 (867)
259 KOG1918 3-methyladenine DNA gl 51.6 8.3 0.00018 37.6 1.5 58 254-312 122-182 (254)
260 COG1194 MutY A/G-specific DNA 51.1 31 0.00067 35.8 5.7 58 219-276 76-135 (342)
261 COG5067 DBF4 Protein kinase es 50.1 11 0.00023 39.7 2.1 46 16-63 120-165 (468)
262 PLN03187 meiotic recombination 49.6 17 0.00036 37.8 3.5 50 291-341 28-79 (344)
263 PRK13766 Hef nuclease; Provisi 49.6 13 0.00028 42.4 3.0 18 296-313 748-765 (773)
264 TIGR00194 uvrC excinuclease AB 49.5 13 0.00029 41.2 3.0 30 295-325 541-570 (574)
265 PRK13746 aminoglycoside resist 49.1 87 0.0019 31.4 8.4 27 370-397 30-58 (262)
266 PRK12373 NADH dehydrogenase su 48.8 14 0.00029 39.2 2.7 35 290-324 318-352 (400)
267 PTZ00134 40S ribosomal protein 48.7 11 0.00025 34.7 1.9 25 293-317 28-53 (154)
268 PF06514 PsbU: Photosystem II 48.6 13 0.00028 31.4 2.0 51 293-343 21-72 (93)
269 TIGR01446 DnaD_dom DnaD and ph 48.6 15 0.00033 28.7 2.4 19 305-323 54-72 (73)
270 smart00483 POLXc DNA polymeras 47.4 12 0.00026 38.5 2.1 27 292-318 45-74 (334)
271 PRK03059 PII uridylyl-transfer 47.0 52 0.0011 38.4 7.3 49 367-415 60-111 (856)
272 COG0099 RpsM Ribosomal protein 47.0 14 0.00031 32.5 2.2 22 296-317 18-40 (121)
273 cd00424 PolY Y-family of DNA p 46.8 48 0.001 33.9 6.4 53 256-318 175-229 (343)
274 PRK10308 3-methyl-adenine DNA 46.1 34 0.00075 34.5 5.1 44 228-271 173-224 (283)
275 PRK04053 rps13p 30S ribosomal 45.9 14 0.0003 33.9 2.0 25 293-317 23-48 (149)
276 PF02961 BAF: Barrier to autoi 45.4 16 0.00035 30.5 2.1 27 297-323 21-47 (89)
277 COG1725 Predicted transcriptio 45.1 33 0.00073 30.5 4.2 87 262-361 12-102 (125)
278 PRK01229 N-glycosylase/DNA lya 44.7 31 0.00067 33.4 4.3 20 252-271 116-136 (208)
279 cd00128 XPG Xeroderma pigmento 44.6 13 0.00029 37.7 1.9 24 298-322 226-249 (316)
280 COG2231 Uncharacterized protei 44.4 35 0.00075 33.0 4.5 37 271-312 96-132 (215)
281 TIGR03629 arch_S13P archaeal r 44.4 15 0.00031 33.6 1.9 23 295-317 21-44 (144)
282 cd00080 HhH2_motif Helix-hairp 43.8 21 0.00046 28.6 2.6 29 254-284 22-50 (75)
283 KOG1906 DNA polymerase sigma [ 43.3 81 0.0017 34.7 7.6 38 358-395 91-129 (514)
284 PRK03381 PII uridylyl-transfer 42.2 68 0.0015 37.0 7.3 48 368-415 57-107 (774)
285 TIGR02238 recomb_DMC1 meiotic 42.0 36 0.00079 34.8 4.6 44 300-343 6-51 (313)
286 PRK14133 DNA polymerase IV; Pr 41.6 64 0.0014 33.1 6.4 52 256-318 175-228 (347)
287 KOG4132 Uroporphyrinogen III s 40.8 72 0.0016 31.5 6.0 117 293-441 84-209 (260)
288 COG0353 RecR Recombinational D 40.7 28 0.0006 33.4 3.2 28 249-276 6-34 (198)
289 PHA00439 exonuclease 40.5 20 0.00044 36.3 2.4 27 298-325 191-219 (286)
290 PF02371 Transposase_20: Trans 40.5 23 0.00049 29.0 2.3 43 254-307 2-44 (87)
291 COG1200 RecG RecG-like helicas 40.4 22 0.00048 40.0 2.9 27 297-323 12-38 (677)
292 PTZ00035 Rad51 protein; Provis 40.0 96 0.0021 32.0 7.4 50 293-343 22-73 (337)
293 PRK10880 adenine DNA glycosyla 39.7 21 0.00045 37.2 2.5 23 292-314 106-128 (350)
294 PRK13910 DNA glycosylase MutY; 39.1 21 0.00045 36.3 2.3 22 293-314 70-91 (289)
295 PF09970 DUF2204: Nucleotidyl 39.0 69 0.0015 30.1 5.6 36 368-403 16-56 (181)
296 PRK01810 DNA polymerase IV; Va 38.2 67 0.0015 33.7 6.0 52 256-318 181-234 (407)
297 COG1031 Uncharacterized Fe-S o 38.1 27 0.00059 37.7 3.0 32 293-324 514-546 (560)
298 COG0322 UvrC Nuclease subunit 34.4 26 0.00056 39.0 2.2 40 297-338 532-573 (581)
299 KOG3548 DNA damage checkpoint 34.2 79 0.0017 37.0 5.9 70 31-103 1081-1160(1176)
300 PLN03186 DNA repair protein RA 34.2 82 0.0018 32.7 5.8 33 293-326 27-59 (342)
301 TIGR02239 recomb_RAD51 DNA rep 33.7 86 0.0019 32.0 5.8 26 300-325 6-31 (316)
302 COG1491 Predicted RNA-binding 32.0 89 0.0019 29.8 5.0 55 269-324 103-163 (202)
303 KOG2094 Predicted DNA damage i 31.0 68 0.0015 33.7 4.4 108 299-427 286-396 (490)
304 PF14907 NTP_transf_5: Unchara 30.9 48 0.001 31.8 3.3 33 380-419 90-122 (249)
305 COG2185 Sbm Methylmalonyl-CoA 30.5 70 0.0015 29.2 4.0 50 366-415 38-92 (143)
306 cd03586 PolY_Pol_IV_kappa DNA 30.2 1.1E+02 0.0024 30.9 5.9 51 256-317 173-225 (334)
307 PHA01806 hypothetical protein 30.1 86 0.0019 30.1 4.6 49 345-397 14-67 (200)
308 PRK05092 PII uridylyl-transfer 30.0 86 0.0019 36.9 5.7 48 368-415 105-155 (931)
309 PF04994 TfoX_C: TfoX C-termin 29.3 43 0.00093 27.4 2.2 36 254-293 3-38 (81)
310 KOG2875 8-oxoguanine DNA glyco 29.2 69 0.0015 32.5 4.0 46 226-271 178-235 (323)
311 TIGR00207 fliG flagellar motor 28.7 4.4E+02 0.0095 27.2 10.0 87 236-323 144-245 (338)
312 KOG2841 Structure-specific end 28.4 87 0.0019 31.0 4.4 49 292-341 192-242 (254)
313 TIGR00600 rad2 DNA excision re 28.0 44 0.00096 39.7 2.8 26 298-323 869-895 (1034)
314 PRK14109 bifunctional glutamin 27.6 2.2E+02 0.0049 33.9 8.6 46 368-413 215-266 (1007)
315 smart00611 SEC63 Domain of unk 27.4 5.6E+02 0.012 25.5 10.4 52 254-313 151-202 (312)
316 PF07261 DnaB_2: Replication i 26.7 26 0.00056 27.4 0.5 20 305-324 54-73 (77)
317 COG5275 BRCT domain type II [G 26.0 2.1E+02 0.0045 28.1 6.4 50 17-67 155-204 (276)
318 TIGR02922 conserved hypothetic 24.8 25 0.00054 27.5 0.0 21 370-390 34-58 (67)
319 PF05559 DUF763: Protein of un 24.1 67 0.0015 33.0 3.0 19 294-312 268-286 (319)
320 PF12482 DUF3701: Phage integr 24.0 70 0.0015 27.2 2.6 35 304-338 22-62 (96)
321 PRK07945 hypothetical protein; 23.9 40 0.00087 34.7 1.4 28 297-324 51-82 (335)
322 PRK11072 bifunctional glutamin 23.5 1.3E+03 0.028 27.5 13.8 28 368-395 154-182 (943)
323 COG2019 AdkA Archaeal adenylat 23.1 1.1E+02 0.0024 29.0 3.9 53 297-354 9-67 (189)
324 COG5186 PAP1 Poly(A) polymeras 22.9 1.7E+02 0.0038 30.9 5.6 51 369-419 82-133 (552)
325 PF14635 HHH_7: Helix-hairpin- 22.7 54 0.0012 28.3 1.7 21 293-313 48-68 (104)
326 PRK02406 DNA polymerase IV; Va 22.6 1.6E+02 0.0035 30.0 5.5 52 256-318 170-223 (343)
327 cd04761 HTH_MerR-SF Helix-Turn 22.4 79 0.0017 22.1 2.3 22 296-317 5-26 (49)
328 cd05398 NT_ClassII-CCAase Nucl 22.4 1.9E+02 0.004 25.8 5.2 37 355-394 5-45 (139)
329 PRK01172 ski2-like helicase; P 21.9 1.5E+02 0.0032 33.4 5.5 52 255-314 613-664 (674)
330 PF00416 Ribosomal_S13: Riboso 21.8 78 0.0017 27.1 2.5 44 254-297 15-58 (107)
331 PRK03103 DNA polymerase IV; Re 21.8 1.5E+02 0.0033 31.0 5.3 51 256-317 183-235 (409)
332 COG1415 Uncharacterized conser 21.8 83 0.0018 32.8 3.1 30 283-313 267-296 (373)
333 PRK00024 hypothetical protein; 21.5 96 0.0021 30.2 3.4 41 266-313 43-84 (224)
334 PF13838 Clathrin_H_link: Clat 21.0 1.7E+02 0.0038 23.1 4.1 44 258-301 1-50 (66)
335 KOG2379 Endonuclease MUS81 [Re 20.6 80 0.0017 34.4 2.8 42 232-273 35-76 (501)
336 PF03710 GlnE: Glutamate-ammon 20.5 3.1E+02 0.0067 26.9 6.8 30 368-397 127-157 (247)
337 KOG0950 DNA polymerase theta/e 20.4 96 0.0021 36.5 3.5 35 291-326 891-925 (1008)
338 cd04885 ACT_ThrD-I Tandem C-te 20.4 2.6E+02 0.0056 21.3 5.1 44 368-416 22-65 (68)
339 PF00542 Ribosomal_L12: Riboso 20.4 1.5E+02 0.0032 23.5 3.6 51 287-360 10-60 (68)
340 PRK00024 hypothetical protein; 20.3 65 0.0014 31.4 1.9 27 252-278 64-90 (224)
341 cd01104 HTH_MlrA-CarA Helix-Tu 20.1 1.9E+02 0.004 21.8 4.2 22 296-317 5-27 (68)
342 PRK09482 flap endonuclease-lik 20.1 1.5E+02 0.0032 29.6 4.5 27 254-282 182-208 (256)
343 PF02889 Sec63: Sec63 Brl doma 20.1 6E+02 0.013 25.2 9.0 56 235-297 132-187 (314)
No 1
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=100.00 E-value=4.9e-58 Score=447.61 Aligned_cols=243 Identities=34% Similarity=0.561 Sum_probs=221.4
Q ss_pred CCCCHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHH
Q 012847 207 PDLNKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFE 286 (455)
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 (455)
.++|..|+++|+.||+.+++.|+.+|+++|++||++|+++|++|+|++|+++|||||++|+.+|+|||+||++++||+++
T Consensus 9 t~~N~~~~~aleiLa~~~ev~g~~~r~~~y~~Aasvlk~~p~~I~S~~ea~~lP~iG~kia~ki~EiletG~l~ele~v~ 88 (353)
T KOG2534|consen 9 TNNNQIFTEALEILAEAYEVEGEEDRARAYRRAASVLKSLPFPITSGEEAEKLPGIGPKIAEKIQEILETGVLRELEAVR 88 (353)
T ss_pred ccccHHHHHHHHHHHHhhcccccHHHHHHHHHHHHHHHhCCCCcccHHHhcCCCCCCHHHHHHHHHHHHcCCchhHHHHh
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhh-ccCchhhhhhchhhHhhhccCcCHHHHHHHHHHHHHHhhhc
Q 012847 287 KDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN-EDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEV 365 (455)
Q Consensus 287 ~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~-~~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~~v~~~~~~~ 365 (455)
+++.++.|++|++|||||++||++||++|+|||+|+++ ..++|.+|++|++||+||+.+|+|+||.++.++|++++..+
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 46899999999999999999999999999999999999999
Q ss_pred CCCeEEEEecccccCCCCCCCccEEEeCCCchh-hhhhHHHHHHHHHHcCceeeeecccccCCcch--------hhcccc
Q 012847 366 LPEVIILCGGSYRRGKASCGDLDVVIMHPDRKS-HKGFLSKYVKKLKEMKFLREDLIFSTHSEETV--------GIALQN 436 (455)
Q Consensus 366 ~p~~~v~~~Gs~RRgke~~gDvDiLit~~d~~~-~~~~l~~lv~~L~~~g~l~~~L~~~~~~~~~~--------~~~~~~ 436 (455)
+|++.|++||||||||++|||||||||||...+ +.+++..|+..|++.|||....-+-+..+.+. |.+=-.
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 999999999999999999999999999999887 78899999999999999996555333333331 222223
Q ss_pred cceeecccccccc
Q 012847 437 SMVYELPSVHVDS 449 (455)
Q Consensus 437 ~~~~~~~~~~~~~ 449 (455)
+.|.-||.--+|+
T Consensus 249 mgv~~LPr~~~~~ 261 (353)
T KOG2534|consen 249 MGVFRLPRQRVDS 261 (353)
T ss_pred EEEEEcCcccccc
Confidence 4467788555554
No 2
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=100.00 E-value=2.8e-47 Score=387.50 Aligned_cols=199 Identities=38% Similarity=0.677 Sum_probs=180.0
Q ss_pred CCCHHHHHHHHHHHHHHHHcCCC-hhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHH
Q 012847 208 DLNKNITEIFGKLINIYRALGED-RRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFE 286 (455)
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 (455)
|+|++|+++|++||++||+.|+| +|++||++||++|+++|++|++++++.+|||||++|++||+||++||++.++.+..
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 46999999999999999999998 68999999999999999999999999999999999999999999999999665555
Q ss_pred hhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhhhchhhHhhhccCcCHHHHHHHHHHHHHHhhh
Q 012847 287 KDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEE 364 (455)
Q Consensus 287 ~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~~v~~~~~~ 364 (455)
.++.+..+..|++|||||||||++||+.||+||+||+++. +|+..|.+|++||+|+.++|||+||+.+.++|.+....
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 5555667777779999999999999999999999999753 69999999999999999999999999999999988888
Q ss_pred cCCCeEEEEecccccCCCCCCCccEEEeCCCchhhhhhHHHHHH
Q 012847 365 VLPEVIILCGGSYRRGKASCGDLDVVIMHPDRKSHKGFLSKYVK 408 (455)
Q Consensus 365 ~~p~~~v~~~Gs~RRgke~~gDvDiLit~~d~~~~~~~l~~lv~ 408 (455)
+.|.+.|++||||||||++||||||||+|+++.. +++..+++
T Consensus 161 ~~~~~~v~i~GSyRRgket~gDIDili~~~~~~~--~~~~~v~~ 202 (334)
T smart00483 161 ILPDAIVTLTGSFRRGKETGHDVDFLITSPHPAK--EKELEVLD 202 (334)
T ss_pred hCCCcEEEEecccccCCCcCCCeeEEEecCCccc--hhHHHHHH
Confidence 8888899999999999999999999999999763 34444443
No 3
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=100.00 E-value=3.9e-47 Score=382.47 Aligned_cols=208 Identities=42% Similarity=0.695 Sum_probs=193.4
Q ss_pred HHHHHHHHHHHHHHHcC-CChhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhch
Q 012847 212 NITEIFGKLINIYRALG-EDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEK 290 (455)
Q Consensus 212 ~ia~~L~~la~~~e~~g-~~~r~~aY~rAa~~L~~l~~~i~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~ 290 (455)
+|+++|++||++++++| |.||++||++||++|+++|++|+++.++.+|||||++|+++|+||++||+++++|+++++ .
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 69999999999999996 458999999999999999999999999999999999999999999999999999999998 4
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhc--cCchhhhhhchhhHhhhccCcCHHHHHHHHHHHHHHhhhcCCC
Q 012847 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPE 368 (455)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~--~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~~v~~~~~~~~p~ 368 (455)
+..+..|++|||||||||++||+.||+||+||+.+ .+++..|..|++||+++.++|||+||+++.+.|.+.+..+.|+
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 45666666999999999999997799999999987 4899999999999999999999999999999999888888888
Q ss_pred eEEEEecccccCCCCCCCccEEEeCCCchhhhhhHHHHHHHHHHcCceeeeec
Q 012847 369 VIILCGGSYRRGKASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLREDLI 421 (455)
Q Consensus 369 ~~v~~~Gs~RRgke~~gDvDiLit~~d~~~~~~~l~~lv~~L~~~g~l~~~L~ 421 (455)
++|++|||||||+++||||||||+|++... .+++.++++.|.+.|++++.+.
T Consensus 161 ~~v~i~GS~RRg~et~gDiDilv~~~~~~~-~~~~~~v~~~l~~~~~~~~~~~ 212 (307)
T cd00141 161 LQVEIAGSYRRGKETVGDIDILVTHPDATS-RGLLEKVVDALVELGFVTEVLS 212 (307)
T ss_pred eEEEEcccccCCCCccCCEEEEEecCCccc-cccHHHHHHHHHhCCCeehhhh
Confidence 899999999999999999999999998764 6788999999999999988554
No 4
>PRK08609 hypothetical protein; Provisional
Probab=100.00 E-value=2.2e-43 Score=381.28 Aligned_cols=206 Identities=21% Similarity=0.304 Sum_probs=182.1
Q ss_pred CCCHHHHHHHHHHHHHHHHcCCC-hhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHH
Q 012847 208 DLNKNITEIFGKLINIYRALGED-RRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFE 286 (455)
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 (455)
|+|++|+++|++||+++++.|+| ||++||+|||++|+++|++|++++++.+|||||++||+||+||++||++++||+|+
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 56999999999999999999987 89999999999999999999999999999999999999999999999999999999
Q ss_pred hhchhHHHHHhhhccCcCHHHHHHHHHc-CCCCHHHhhh---ccCchhhhhh----------chhhHhhhccCcCHHHHH
Q 012847 287 KDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKN---EDSLTHSQRL----------GLKYFDDIKTRIPRHEVE 352 (455)
Q Consensus 287 ~~~~~~~l~lf~~I~GvGpktA~~ly~~-GirTledL~~---~~~L~~~q~~----------Glk~~ed~~~~i~r~Ea~ 352 (455)
++.|.++++|+ +|||||||||++||++ ||+||+||++ +++++.+++| |+++|+++.+|||+.||.
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 98888777766 9999999999999975 9999999995 3578777666 566777778999999999
Q ss_pred HHHHHHHHHhhhcCCCeEEEEecccccCCCCCCCccEEEeCCCchhhhhhHHHHHHHHHHcCceeeeec
Q 012847 353 QMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLREDLI 421 (455)
Q Consensus 353 ~i~~~v~~~~~~~~p~~~v~~~Gs~RRgke~~gDvDiLit~~d~~~~~~~l~~lv~~L~~~g~l~~~L~ 421 (455)
.+.+.|.+....+.|...|++||||||||+||||||||||++++.. +++.|...+++++.+.
T Consensus 160 ~~a~~i~~~l~~~~~~~~v~~~GS~RR~~et~gDiDili~~~~~~~-------~~~~l~~~~~v~~~~~ 221 (570)
T PRK08609 160 PIAQEIEEYLATIDEIIRFSRAGSLRRARETVKDLDFIIATDEPEA-------VREQLLQLPNIVEVIA 221 (570)
T ss_pred HHHHHHHHHHHhCCCccEEEeccchhccccccCCeeEEEecCCHHH-------HHHHHHcCccHHHHHh
Confidence 9988888877766666699999999999999999999999998755 4455555566655443
No 5
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=100.00 E-value=7.7e-34 Score=280.15 Aligned_cols=206 Identities=28% Similarity=0.448 Sum_probs=180.3
Q ss_pred CCCHHHHHHHHHHHHHHHHcCCC-hhHHHHHHHHHHHhcCCccccchhh---hcCCCCCCHHHHHHHHHHHHhCCchhhH
Q 012847 208 DLNKNITEIFGKLINIYRALGED-RRSFSYYKAIPVIEKLPFKIESADQ---VKGLPGIGKSMQDHIQEIVTTGKLSKLE 283 (455)
Q Consensus 208 ~~N~~ia~~L~~la~~~e~~g~~-~r~~aY~rAa~~L~~l~~~i~s~~~---l~~lpgIG~~ia~kI~Eil~tG~~~~le 283 (455)
++|+.|+.+|+++|++|++.|+| ||++|||+||++|+.+.+++.++.+ +..|||||+++|.+|.||++||++++++
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 57999999999999999999999 8999999999999999999999865 4699999999999999999999999999
Q ss_pred HHHhhchhHHHHHhhhccCcCHHHHHHHHHc-CCCCHHHhhhc---cCchhhhhhchhhHhhhc----------cCcCHH
Q 012847 284 HFEKDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNE---DSLTHSQRLGLKYFDDIK----------TRIPRH 349 (455)
Q Consensus 284 ~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~-GirTledL~~~---~~L~~~q~~Glk~~ed~~----------~~i~r~ 349 (455)
+|+...|.+...|+ .|+|+|||+...||++ ||+++++|+++ +++..+.|||-++.++|+ +|+|..
T Consensus 83 ~lk~~~P~gl~~Ll-~v~GlGpkKi~~Ly~elgi~~~e~l~~a~~~~~~~~l~GfG~kse~~il~~i~~~~~~~~R~~l~ 161 (326)
T COG1796 83 ALKKEVPEGLEPLL-KVPGLGPKKIVSLYKELGIKDLEELQEALENGKIRGLRGFGKKSEAKILENIEFAEESPERIPLS 161 (326)
T ss_pred HHHHhCCcchHHHh-hCCCCCcHHHHHHHHHHCcccHHHHHHHHHhCCccccCCccchhHHHHHHHHHHHhhhhhhcchH
Confidence 99999999988888 9999999999999998 99999999965 578899999988888886 466777
Q ss_pred HHHHHHHHHHHHhhhcCCCeEEEEecccccCCCCCCCccEEEeCCCchhhhhhHHHHHHHHHHcCceeeeec
Q 012847 350 EVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLREDLI 421 (455)
Q Consensus 350 Ea~~i~~~v~~~~~~~~p~~~v~~~Gs~RRgke~~gDvDiLit~~d~~~~~~~l~~lv~~L~~~g~l~~~L~ 421 (455)
++..+..-+.....++.+-.++.++||+||+|+|++|||++|+..++.. +++.|.+...++....
T Consensus 162 ~~l~ia~ei~~yl~~~~~~~~~~~aGs~RR~retv~DiD~~~s~~~~~~-------v~~~~~~~~~~~~vi~ 226 (326)
T COG1796 162 FTLPIAQEIEGYLEELTPIIQASIAGSLRRGRETVGDIDILISTSHPES-------VLEELLEMPNVQEVIA 226 (326)
T ss_pred HHHHHHHHHHHHHHhccchheeeeccchhhccccccceeeEeccCCcHH-------HHHHHhcCCCcceeee
Confidence 7777755555555555565689999999999999999999998877765 6777777666665544
No 6
>PF14792 DNA_pol_B_palm: DNA polymerase beta palm ; PDB: 1RZT_A 3PML_A 2PFN_A 3HX0_K 3HWT_A 2GWS_E 2BCQ_A 3UPQ_A 2BCS_A 3UQ2_A ....
Probab=99.85 E-value=8.6e-22 Score=170.83 Aligned_cols=91 Identities=41% Similarity=0.651 Sum_probs=78.0
Q ss_pred CcCHHHHHHHHHHHHHHhhhcCCCeEEEEecccccCCCCCCCccEEEeCCCchhh----hhhHHHHHHHHHHcCceeeee
Q 012847 345 RIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPDRKSH----KGFLSKYVKKLKEMKFLREDL 420 (455)
Q Consensus 345 ~i~r~Ea~~i~~~v~~~~~~~~p~~~v~~~Gs~RRgke~~gDvDiLit~~d~~~~----~~~l~~lv~~L~~~g~l~~~L 420 (455)
||||+||++++++|.+.+.+++|++.+++||||||||++|||||||||||+.... .++|.++++.|+++|||+++|
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 6999999999999999999999999999999999999999999999999998763 789999999999999999999
Q ss_pred cccccCCcchhhccc
Q 012847 421 IFSTHSEETVGIALQ 435 (455)
Q Consensus 421 ~~~~~~~~~~~~~~~ 435 (455)
..+....+|...+.+
T Consensus 81 ~~~~~~~~G~~~l~~ 95 (112)
T PF14792_consen 81 SLGPTKYMGVCRLPG 95 (112)
T ss_dssp EECSSEEEEEEE-SS
T ss_pred ccCCceeeeEeecCC
Confidence 876544455444433
No 7
>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=99.71 E-value=2.4e-17 Score=130.55 Aligned_cols=66 Identities=36% Similarity=0.688 Sum_probs=62.5
Q ss_pred CHHHHHHHHHHHHHHHHc-CCChhHHHHHHHHHHHhcCCccccchhh-hcCCCCCCHHHHHHHHHHHH
Q 012847 210 NKNITEIFGKLINIYRAL-GEDRRSFSYYKAIPVIEKLPFKIESADQ-VKGLPGIGKSMQDHIQEIVT 275 (455)
Q Consensus 210 N~~ia~~L~~la~~~e~~-g~~~r~~aY~rAa~~L~~l~~~i~s~~~-l~~lpgIG~~ia~kI~Eil~ 275 (455)
|++|+++|++||+++++. |+.||++||++||++|+++|++|++++| +.+|||||++|+.+|.|||+
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 6668999999999999999999999987 99999999999999999986
No 8
>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=99.67 E-value=4.8e-17 Score=121.94 Aligned_cols=51 Identities=49% Similarity=1.009 Sum_probs=42.1
Q ss_pred HHHhhhccCcCHHHHHHHHHcCCCCHHHhhh-ccCchhhhhhchhhHhhhcc
Q 012847 294 ISLFGEVWGIGPATAQKLYEKGHRTLDDLKN-EDSLTHSQRLGLKYFDDIKT 344 (455)
Q Consensus 294 l~lf~~I~GvGpktA~~ly~~GirTledL~~-~~~L~~~q~~Glk~~ed~~~ 344 (455)
|++|++||||||+||++||++|+|||+||++ ...|+..|++|++||+||++
T Consensus 1 l~~f~~I~GVG~~tA~~w~~~G~rtl~Dl~~~~~~Lt~~Q~iGl~yyeD~~q 52 (52)
T PF10391_consen 1 LKLFTGIWGVGPKTARKWYAKGIRTLEDLRKSKSKLTWQQQIGLKYYEDFQQ 52 (52)
T ss_dssp HHHHHTSTT--HHHHHHHHHTT--SHHHHHHGGCGS-HHHHHHHHTHHHHH-
T ss_pred CcchhhcccccHHHHHHHHHhCCCCHHHHhhhhccCCHHHHHHHHHHHHhcC
Confidence 6789999999999999999999999999986 45899999999999999974
No 9
>PRK07945 hypothetical protein; Provisional
Probab=99.55 E-value=9.1e-15 Score=149.44 Aligned_cols=91 Identities=20% Similarity=0.247 Sum_probs=83.5
Q ss_pred HHHHHHHHHHHHHHcCCC-hhHHHHHHHHHHHhcCCcc-ccchh---hhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHh
Q 012847 213 ITEIFGKLINIYRALGED-RRSFSYYKAIPVIEKLPFK-IESAD---QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEK 287 (455)
Q Consensus 213 ia~~L~~la~~~e~~g~~-~r~~aY~rAa~~L~~l~~~-i~s~~---~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~ 287 (455)
-+++|+++|+++|++|+| ||++|||+||.+|++++.+ +..+. +|.+|||||+++|+||.||++||++++||+|+.
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 7999999999999999999 88774 799999999999999999999999999999998
Q ss_pred hchhHHHHHhhhccCcCHHHHHHHHH
Q 012847 288 DEKVRTISLFGEVWGIGPATAQKLYE 313 (455)
Q Consensus 288 ~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (455)
+..+. | |+..+.++.-
T Consensus 83 ~~~~~---------~-g~~l~~~~~~ 98 (335)
T PRK07945 83 DAEPL---------G-GGALRAALRG 98 (335)
T ss_pred hhcCC---------c-cHHHHHHHhh
Confidence 77543 7 9999999874
No 10
>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=99.04 E-value=4e-10 Score=89.47 Aligned_cols=75 Identities=23% Similarity=0.342 Sum_probs=59.2
Q ss_pred CCCCCCcEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCC-hHHHHHHHHHhhhccCccccccchHHHH
Q 012847 16 NGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDL-EALLQQVSKQHLARFKGSVIRYQWLEDS 94 (455)
Q Consensus 16 ~~~F~g~~iy~~~~~~g~~R~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~~-~~~l~~l~~~~~~~~~~~lV~~~Wl~es 94 (455)
..+|+||.+|| .+.....++.++++++++||++...+++.+||||+.+. .... +...+...+.++|+.+||.+|
T Consensus 3 ~~~F~g~~f~i--~~~~~~~~~~l~~~i~~~GG~v~~~~~~~~thvI~~~~~~~~~---k~~~~~~~~i~iV~~~Wi~~c 77 (78)
T PF00533_consen 3 PKIFEGCTFCI--SGFDSDEREELEQLIKKHGGTVSNSFSKKTTHVIVGNPNKRTK---KYKAAIANGIPIVSPDWIEDC 77 (78)
T ss_dssp TTTTTTEEEEE--SSTSSSHHHHHHHHHHHTTEEEESSSSTTSSEEEESSSHCCCH---HHHHHHHTTSEEEETHHHHHH
T ss_pred CCCCCCEEEEE--ccCCCCCHHHHHHHHHHcCCEEEeecccCcEEEEeCCCCCccH---HHHHHHHCCCeEecHHHHHHh
Confidence 46999999999 56666667788999999999999999999999999876 1111 111222347899999999999
Q ss_pred H
Q 012847 95 L 95 (455)
Q Consensus 95 ~ 95 (455)
+
T Consensus 78 i 78 (78)
T PF00533_consen 78 I 78 (78)
T ss_dssp H
T ss_pred C
Confidence 6
No 11
>smart00292 BRCT breast cancer carboxy-terminal domain.
Probab=99.03 E-value=6.5e-10 Score=87.02 Aligned_cols=78 Identities=19% Similarity=0.287 Sum_probs=61.3
Q ss_pred CCCCcEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCC-CccEEEEcCChHHHHHHHHHhhhccCccccccchHHHHHh
Q 012847 18 IFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSK-KVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSLR 96 (455)
Q Consensus 18 ~F~g~~iy~~~~~~g~~R~~~l~~li~~~Gg~V~~~ls~-~VTHVV~~~~~~~l~~l~~~~~~~~~~~lV~~~Wl~es~k 96 (455)
+|+|+++||.+ .+....++.+.+++..+||++...++. .+||||+.+.+..... .......+.++|+.+||.+|++
T Consensus 2 ~f~g~~~~~~g-~~~~~~~~~l~~~i~~~Gg~~~~~~~~~~~thvi~~~~~~~~~~--~~~~~~~~~~iV~~~Wi~~~~~ 78 (80)
T smart00292 2 LFKGKVFVITG-KFDKNERDELKELIEALGGKVTSSLSSKTTTHVIVGSPEGGKLE--LLLAIALGIPIVTEDWLLDCLK 78 (80)
T ss_pred ccCCeEEEEeC-CCCCccHHHHHHHHHHcCCEEecccCccceeEEEEcCCCCccHH--HHHHHHcCCCCccHHHHHHHHH
Confidence 79999999986 355567788999999999999999988 9999999775432111 1122234689999999999998
Q ss_pred cC
Q 012847 97 LG 98 (455)
Q Consensus 97 ~g 98 (455)
++
T Consensus 79 ~~ 80 (80)
T smart00292 79 AG 80 (80)
T ss_pred Cc
Confidence 75
No 12
>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=2.7e-08 Score=75.95 Aligned_cols=72 Identities=18% Similarity=0.289 Sum_probs=54.6
Q ss_pred CcEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccchHHHHHh
Q 012847 21 GMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSLR 96 (455)
Q Consensus 21 g~~iy~~~~~~g~~R~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~~~~~l~~l~~~~~~~~~~~lV~~~Wl~es~k 96 (455)
||.+||.+...+ ..+..|++++..+||++.+.++..+||||+.+...... ...+...+.++|+.+|+.+|++
T Consensus 1 ~~~~~i~g~~~~-~~~~~l~~~i~~~Gg~v~~~~~~~~thvI~~~~~~~~~---~~~~~~~~~~iV~~~Wi~~~~~ 72 (72)
T cd00027 1 GLTFVITGDLPS-EERDELKELIEKLGGKVTSSVSKKTTHVIVGSDAGPKK---LLKAIKLGIPIVTPEWLLDCLK 72 (72)
T ss_pred CCEEEEEecCCC-cCHHHHHHHHHHcCCEEeccccCCceEEEECCCCCchH---HHHHHHcCCeEecHHHHHHHhC
Confidence 578888854333 44568999999999999999999999999986653221 1122234789999999999985
No 13
>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=98.14 E-value=8.9e-06 Score=90.25 Aligned_cols=133 Identities=20% Similarity=0.263 Sum_probs=95.9
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc-CCCCHHHhhhcc--Cchh
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED--SLTH 330 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~-GirTledL~~~~--~L~~ 330 (455)
++|.+|||+|++.+++|.+.++.++...+++ .+..| +|+|||+++|+.|++. | |+++|..+. .|..
T Consensus 466 ~~L~~L~GfG~Ksa~nIl~~Ie~sk~~~l~r--------~L~aL-gIpgVG~~~ak~L~~~f~--sl~~l~~As~eeL~~ 534 (652)
T TIGR00575 466 EDLLELEGFGEKSAQNLLNAIEKSKEKPLAR--------LLFAL-GIRHVGEVTAKNLAKHFG--TLDKLKAASLEELLS 534 (652)
T ss_pred HHHhhccCccHHHHHHHHHHHHHhccCcHHH--------HHhhc-cCCCcCHHHHHHHHHHhC--CHHHHHhCCHHHHhc
Confidence 5789999999999999999999988776664 55556 9999999999999986 6 999998653 5778
Q ss_pred hhhhchhhHhhhccCcCHHHHHH-HHHHHHH-H-----------h--hhcCCCeEEEEecccccC---------------
Q 012847 331 SQRLGLKYFDDIKTRIPRHEVEQ-MERLLQK-A-----------G--EEVLPEVIILCGGSYRRG--------------- 380 (455)
Q Consensus 331 ~q~~Glk~~ed~~~~i~r~Ea~~-i~~~v~~-~-----------~--~~~~p~~~v~~~Gs~RRg--------------- 380 (455)
+.+||.+..+.|.+-+.-.+..+ +..+... + . ...+.|-.+++||++...
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 88899888887766553333322 2222211 0 0 011334578999998643
Q ss_pred --CCCCCCccEEEeCCCch
Q 012847 381 --KASCGDLDVVIMHPDRK 397 (455)
Q Consensus 381 --ke~~gDvDiLit~~d~~ 397 (455)
...+...|+||.-.+.+
T Consensus 615 v~~sVs~kt~~lv~G~~~g 633 (652)
T TIGR00575 615 VASSVSKKTDYVIAGEKAG 633 (652)
T ss_pred EeCCcCCCccEEEECCCCC
Confidence 45677889999866543
No 14
>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=98.06 E-value=2.7e-06 Score=65.53 Aligned_cols=51 Identities=37% Similarity=0.549 Sum_probs=43.6
Q ss_pred HHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhc--cCchhhhhhchhhHhhhc
Q 012847 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDIK 343 (455)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~GirTledL~~~--~~L~~~q~~Glk~~ed~~ 343 (455)
+...|++|+||||++|++||+.||.|++||... ..|..+.++|.+..+.|.
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 455667999999999999999999999999865 368889999988877664
No 15
>PF12738 PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2WT8_C 3EF1_A 3EF0_A.
Probab=97.88 E-value=1.2e-05 Score=62.06 Aligned_cols=62 Identities=18% Similarity=0.340 Sum_probs=42.5
Q ss_pred EEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccch
Q 012847 23 RVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQW 90 (455)
Q Consensus 23 ~iy~~~~~~g~~R~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~~~~~l~~l~~~~~~~~~~~lV~~~W 90 (455)
+|.+. ++....++.+.++++.+||++...++.++||+|+.+... .+...+...+.++|+++|
T Consensus 2 ~i~~s--g~~~~~~~~l~~~i~~~Gg~~~~~lt~~~THLI~~~~~~----~K~~~A~~~gi~vV~~~W 63 (63)
T PF12738_consen 2 VICFS--GFSGKERSQLRKLIEALGGKYSKDLTKKTTHLICSSPEG----KKYRKAKEWGIPVVSPDW 63 (63)
T ss_dssp EEEEE--EB-TTTCCHHHHHHHCTT-EEESSSSTT-SEEEEES--H----HHHHHHHHCTSEEEEHHH
T ss_pred EEEEC--CCCHHHHHHHHHHHHHCCCEEeccccCCceEEEEeCCCc----HHHHHHHHCCCcEECCCC
Confidence 45554 443333567899999999999999999999999965432 233344445789999999
No 16
>KOG3226 consensus DNA repair protein [Replication, recombination and repair]
Probab=97.76 E-value=1.1e-05 Score=81.83 Aligned_cols=89 Identities=16% Similarity=0.312 Sum_probs=72.1
Q ss_pred CCCCCCcEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEc-CChHHHHHHHHHhhhccCccccccchHHHH
Q 012847 16 NGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAM-DLEALLQQVSKQHLARFKGSVIRYQWLEDS 94 (455)
Q Consensus 16 ~~~F~g~~iy~~~~~~g~~R~~~l~~li~~~Gg~V~~~ls~~VTHVV~~-~~~~~l~~l~~~~~~~~~~~lV~~~Wl~es 94 (455)
+.++.|+++.+. |+...-+.-|+..+..+||+.-.+++.+.||.|+. .+.. ++.+....+..||+-+||++|
T Consensus 315 ~klL~GVV~VlS--GfqNP~Rs~LRskAl~LGAkY~pDW~~gsThLICAF~NTP-----Ky~QV~g~Gg~IV~keWI~~C 387 (508)
T KOG3226|consen 315 SKLLEGVVFVLS--GFQNPERSTLRSKALTLGAKYQPDWNAGSTHLICAFPNTP-----KYRQVEGNGGTIVSKEWITEC 387 (508)
T ss_pred HHhhhceEEEEe--cccCchHHHHHHHHHhhcccccCCcCCCceeEEEecCCCc-----chhhcccCCceEeeHHHHHHH
Confidence 478999988776 77766667899999999999999999999999984 2222 222333346799999999999
Q ss_pred HhcCCCCCccccccccC
Q 012847 95 LRLGEKVSEDLYRIKLD 111 (455)
Q Consensus 95 ~k~g~lvdee~y~l~~~ 111 (455)
...+++||..+|.+.-+
T Consensus 388 y~~kk~lp~rrYlm~~~ 404 (508)
T KOG3226|consen 388 YAQKKLLPIRRYLMHAG 404 (508)
T ss_pred HHHHhhccHHHHHhcCC
Confidence 99999999999998643
No 17
>PLN03123 poly [ADP-ribose] polymerase; Provisional
Probab=97.75 E-value=5.7e-05 Score=86.82 Aligned_cols=91 Identities=16% Similarity=0.366 Sum_probs=72.3
Q ss_pred CCCCCCcEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccchHHHHH
Q 012847 16 NGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSL 95 (455)
Q Consensus 16 ~~~F~g~~iy~~~~~~g~~R~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~~~~~l~~l~~~~~~~~~~~lV~~~Wl~es~ 95 (455)
...|.+++|.+.++. +.. ...|+++|..+||++...++..+||+|+.. +......++..+...+.+||+.+||++|.
T Consensus 391 ~~~l~~~~i~i~G~~-~~~-~~~~k~~Ie~~GG~~s~~v~~~~t~l~tt~-e~~k~~~kv~qAk~~~ipIVsedwL~ds~ 467 (981)
T PLN03123 391 SEFLGDLKVSIVGAS-KEK-VTEWKAKIEEAGGVFHATVKKDTNCLVVCG-ELDDEDAEMRKARRMKIPIVREDYLVDCF 467 (981)
T ss_pred CCCcCCeEEEEecCC-CCc-HHHHHHHHHhcCCEEeeeccCCceEEEccH-HhhhcchHHHHHHhcCCCcccHHHHHHHH
Confidence 467999999999764 322 368999999999999999999999999875 22222334444555579999999999999
Q ss_pred hcCCCCCccccccc
Q 012847 96 RLGEKVSEDLYRIK 109 (455)
Q Consensus 96 k~g~lvdee~y~l~ 109 (455)
+.++++|...|.+.
T Consensus 468 ~~~~~~p~~~y~~~ 481 (981)
T PLN03123 468 KKKKKLPFDKYKLE 481 (981)
T ss_pred hccccCcchhhhhc
Confidence 99999998888663
No 18
>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=97.51 E-value=0.00012 Score=56.27 Aligned_cols=52 Identities=33% Similarity=0.610 Sum_probs=40.9
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (455)
.+|.+|||||+.++.++.+ .| +..++++....+ +.|.+|+|+|+++|++|.+
T Consensus 5 ~~L~~I~Gig~~~a~~L~~---~G-~~t~~~l~~a~~----~~L~~i~Gig~~~a~~i~~ 56 (60)
T PF14520_consen 5 DDLLSIPGIGPKRAEKLYE---AG-IKTLEDLANADP----EELAEIPGIGEKTAEKIIE 56 (60)
T ss_dssp HHHHTSTTCHHHHHHHHHH---TT-CSSHHHHHTSHH----HHHHTSTTSSHHHHHHHHH
T ss_pred HhhccCCCCCHHHHHHHHh---cC-CCcHHHHHcCCH----HHHhcCCCCCHHHHHHHHH
Confidence 5788999999999987765 47 566788765322 3456999999999999986
No 19
>PLN03122 Poly [ADP-ribose] polymerase; Provisional
Probab=97.47 E-value=0.00022 Score=80.48 Aligned_cols=94 Identities=20% Similarity=0.274 Sum_probs=72.2
Q ss_pred CCCCCCCCcEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHH-HHHHHhhhccCccccccchHH
Q 012847 14 DSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQ-QVSKQHLARFKGSVIRYQWLE 92 (455)
Q Consensus 14 ~~~~~F~g~~iy~~~~~~g~~R~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~~~~~l~-~l~~~~~~~~~~~lV~~~Wl~ 92 (455)
.+...|.|++|.|.++. .. .+..++++|..+||+|.+.+ .+.||+|+.+.+.... .-+...+...+++||+.+||.
T Consensus 185 ~~~kpL~G~~fviTGtl-~~-sr~elK~~Ie~~GGkvsssV-s~~T~lIvt~~ev~k~gsSKlkkAk~lgIpIVsEd~L~ 261 (815)
T PLN03122 185 APGKPFSGMMISLSGRL-SR-THQYWKKDIEKHGGKVANSV-EGVTCLVVSPAERERGGSSKIAEAMERGIPVVREAWLI 261 (815)
T ss_pred ccCCCcCCcEEEEeCCC-CC-CHHHHHHHHHHcCCEEcccc-ccceEEEEcCccccccCccHHHHHHHcCCcCccHHHHH
Confidence 44567999999998764 33 34578999999999999999 6788999866442111 122334445689999999999
Q ss_pred HHHhcCCCCCcccccccc
Q 012847 93 DSLRLGEKVSEDLYRIKL 110 (455)
Q Consensus 93 es~k~g~lvdee~y~l~~ 110 (455)
+|++.++++++..|.+..
T Consensus 262 d~i~~~k~~~~~~y~l~~ 279 (815)
T PLN03122 262 DSIEKQEAQPLEAYDVVS 279 (815)
T ss_pred HHHhcCCcccchhhhhcc
Confidence 999999999999998853
No 20
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=97.20 E-value=0.00048 Score=62.88 Aligned_cols=50 Identities=34% Similarity=0.627 Sum_probs=40.9
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHH-hCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012847 252 SADQVKGLPGIGKSMQDHIQEIVT-TGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (455)
Q Consensus 252 s~~~l~~lpgIG~~ia~kI~Eil~-tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (455)
+.+||+.|||||++.|++|.++.+ .|.+.-+|+ |.+|.|||+++.++|-.
T Consensus 95 s~eeL~~lpgIG~~kA~aIi~yRe~~G~f~sv~d------------L~~v~GiG~~~~ekl~~ 145 (149)
T COG1555 95 SAEELQALPGIGPKKAQAIIDYREENGPFKSVDD------------LAKVKGIGPKTLEKLKD 145 (149)
T ss_pred CHHHHHHCCCCCHHHHHHHHHHHHHcCCCCcHHH------------HHhccCCCHHHHHHHHh
Confidence 358999999999999999999874 455555555 45999999999999854
No 21
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=97.17 E-value=0.002 Score=71.90 Aligned_cols=134 Identities=16% Similarity=0.271 Sum_probs=90.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--Cchhh
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHS 331 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~ 331 (455)
++|..|||+|++.+++|.+-++.-+-..| ...+--+ +|+|||+++|+.|.+ -+.|+++|..+. .|..+
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-GIRHVGEKAAKALAR-HFGSLEALRAASEEELAAV 548 (665)
T ss_pred HHHhcCcCcchHHHHHHHHHHHHhhcCCH--------HHhhHhh-hccCcCHHHHHHHHH-HcCCHHHHHhCCHHHHhcc
Confidence 57999999999999998776653222222 2345555 999999999999987 448899998653 57888
Q ss_pred hhhchhhHhhhccCcCHHHHHH-HHHHHHHHhh-------hcCCCeEEEEeccccc---C--------------CCCCCC
Q 012847 332 QRLGLKYFDDIKTRIPRHEVEQ-MERLLQKAGE-------EVLPEVIILCGGSYRR---G--------------KASCGD 386 (455)
Q Consensus 332 q~~Glk~~ed~~~~i~r~Ea~~-i~~~v~~~~~-------~~~p~~~v~~~Gs~RR---g--------------ke~~gD 386 (455)
.++|-+..+.|.+-+.-.+..+ +..+...-.. ..+.|-.+++||.+.. . ...+..
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 8899888877766554433333 2333221010 0144668999999843 2 456788
Q ss_pred ccEEEeCCCch
Q 012847 387 LDVVIMHPDRK 397 (455)
Q Consensus 387 vDiLit~~d~~ 397 (455)
.|+||.-+..+
T Consensus 629 t~~lv~G~~~g 639 (665)
T PRK07956 629 TDLVVAGEAAG 639 (665)
T ss_pred CCEEEECCCCC
Confidence 89999866543
No 22
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=97.10 E-value=0.00078 Score=52.68 Aligned_cols=48 Identities=29% Similarity=0.627 Sum_probs=31.9
Q ss_pred cCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012847 257 KGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (455)
Q Consensus 257 ~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (455)
.+|||||+..++.+.+ ++..++.+.+. ..+.|++|+|||+++|+.+|+
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 5799999999998865 34445666542 445677999999999999886
No 23
>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=97.07 E-value=0.00098 Score=58.68 Aligned_cols=50 Identities=30% Similarity=0.497 Sum_probs=40.4
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHHh-CCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012847 252 SADQVKGLPGIGKSMQDHIQEIVTT-GKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (455)
Q Consensus 252 s~~~l~~lpgIG~~ia~kI~Eil~t-G~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (455)
+.++|..|||||++.|++|-++.+. |.+.-. +.|.+|+|||++++.+|.+
T Consensus 66 ~~~eL~~lpGIG~~~A~~Ii~~R~~~g~f~s~------------eeL~~V~GIg~k~~~~i~~ 116 (120)
T TIGR01259 66 SLEELQALPGIGPAKAKAIIEYREENGAFKSV------------DDLTKVSGIGEKSLEKLKD 116 (120)
T ss_pred CHHHHhcCCCCCHHHHHHHHHHHHhcCCcCCH------------HHHHcCCCCCHHHHHHHHh
Confidence 4578999999999999999999864 554433 3445899999999999875
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=97.05 E-value=0.0007 Score=56.87 Aligned_cols=36 Identities=36% Similarity=0.373 Sum_probs=32.1
Q ss_pred hhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhc
Q 012847 290 KVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (455)
Q Consensus 290 ~~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~ 325 (455)
....+..|+.|||||+++|+.|+..||+|++||+..
T Consensus 7 ~~~~~~~L~~iP~IG~a~a~DL~~LGi~s~~~L~g~ 42 (93)
T PF11731_consen 7 KRAGLSDLTDIPNIGKATAEDLRLLGIRSPADLKGR 42 (93)
T ss_pred HHHHHHHHhcCCCccHHHHHHHHHcCCCCHHHHhCC
Confidence 345778889999999999999999999999999964
No 25
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=97.03 E-value=0.00095 Score=52.26 Aligned_cols=49 Identities=43% Similarity=0.655 Sum_probs=36.0
Q ss_pred cchhhhcCCCCCCHHHHHHHHHHH-HhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHH
Q 012847 251 ESADQVKGLPGIGKSMQDHIQEIV-TTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKL 311 (455)
Q Consensus 251 ~s~~~l~~lpgIG~~ia~kI~Eil-~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l 311 (455)
.+.++|..+||||+..|+.|.++- +.|.+..+++| ..|+|+|+++..+|
T Consensus 11 as~~eL~~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL------------~~v~gi~~~~~~~l 60 (65)
T PF12836_consen 11 ASAEELQALPGIGPKQAKAIVEYREKNGPFKSLEDL------------KEVPGIGPKTYEKL 60 (65)
T ss_dssp S-HHHHHTSTT--HHHHHHHHHHHHHH-S-SSGGGG------------GGSTT--HHHHHHH
T ss_pred CCHHHHHHcCCCCHHHHHHHHHHHHhCcCCCCHHHH------------hhCCCCCHHHHHHH
Confidence 356899999999999999999998 56777777765 48999999999887
No 26
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=96.95 E-value=0.0037 Score=70.06 Aligned_cols=134 Identities=16% Similarity=0.293 Sum_probs=91.4
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--Cchhh
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHS 331 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~ 331 (455)
+++..|+|+|++.+++|.+=++.-+-..|+ ..+--| +|+|||+++|++|.+ .+.|+++|..+. .|...
T Consensus 496 ~~L~~l~g~g~Ksa~~Ll~~Ie~sk~~~l~--------r~l~AL-gIpgIG~~~ak~L~~-~F~si~~L~~As~eeL~~i 565 (689)
T PRK14351 496 ADLAELEGWGETSAENLLAELEASREPPLA--------DFLVAL-GIPEVGPTTARNLAR-EFGTFEAIMDADEEALRAV 565 (689)
T ss_pred HHHhcCcCcchhHHHHHHHHHHHHccCCHH--------HHHHHc-CCCCcCHHHHHHHHH-HhCCHHHHHhCCHHHHhcc
Confidence 578999999999999987766533323333 345556 999999999999986 668899998653 57778
Q ss_pred hhhchhhHhhhccCcCHHHHHH-HHHHHHHHh---------hhcCCCeEEEEeccccc-----------------CCCCC
Q 012847 332 QRLGLKYFDDIKTRIPRHEVEQ-MERLLQKAG---------EEVLPEVIILCGGSYRR-----------------GKASC 384 (455)
Q Consensus 332 q~~Glk~~ed~~~~i~r~Ea~~-i~~~v~~~~---------~~~~p~~~v~~~Gs~RR-----------------gke~~ 384 (455)
.++|.+..+.|.+-+.-.+..+ +..++..-. ...+.|-.+++||.+-. ....+
T Consensus 566 ~GIG~k~A~sI~~ff~~~~n~~~i~~L~~~Gv~~~~~~~~~~~~l~g~~~v~TG~l~~~~R~~~~~~i~~~Gg~v~~sVs 645 (689)
T PRK14351 566 DDVGPTVAEEIREFFDSERNRAVIDDLLDHGVDPQPAESEGGDALDGLTFVFTGSLSGYTRSEAQELVEAHGGNATGSVS 645 (689)
T ss_pred CCcCHHHHHHHHHHHhhhHHHHHHHHHHhcccccccccccCCCCCCCcEEEEccCCCCCCHHHHHHHHHHcCCEEcCCcC
Confidence 8899888887766654444333 233332100 01234568899998843 23566
Q ss_pred CCccEEEeCCCch
Q 012847 385 GDLDVVIMHPDRK 397 (455)
Q Consensus 385 gDvDiLit~~d~~ 397 (455)
...|+||.-..++
T Consensus 646 ~kt~~Lv~G~~~g 658 (689)
T PRK14351 646 GNTDYLVVGENPG 658 (689)
T ss_pred CCccEEEEcCCCC
Confidence 7889999865544
No 27
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=96.65 E-value=0.01 Score=52.31 Aligned_cols=32 Identities=28% Similarity=0.386 Sum_probs=27.9
Q ss_pred HHHhhhccCcCHHHHHHHHHcCCCCHHHhhhc
Q 012847 294 ISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (455)
Q Consensus 294 l~lf~~I~GvGpktA~~ly~~GirTledL~~~ 325 (455)
+--|+.|+|||+..|.-|.+.||+|+++|.+.
T Consensus 52 ~AdL~ri~gi~~~~a~LL~~AGv~Tv~~LA~~ 83 (122)
T PF14229_consen 52 QADLMRIPGIGPQYAELLEHAGVDTVEELAQR 83 (122)
T ss_pred HHHhhhcCCCCHHHHHHHHHhCcCcHHHHHhC
Confidence 33345999999999999999999999999864
No 28
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=96.63 E-value=0.0029 Score=56.16 Aligned_cols=47 Identities=15% Similarity=0.246 Sum_probs=36.9
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012847 252 SADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (455)
Q Consensus 252 s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (455)
+.++++.+||||+..|++|. ..|-+..+|+| .+|+|||+++.+.+-+
T Consensus 59 ~~~el~~lpGigP~~A~~IV---~nGpf~sveDL------------~~V~GIgekqk~~l~k 105 (132)
T PRK02515 59 SVRAFRQFPGMYPTLAGKIV---KNAPYDSVEDV------------LNLPGLSERQKELLEA 105 (132)
T ss_pred CHHHHHHCCCCCHHHHHHHH---HCCCCCCHHHH------------HcCCCCCHHHHHHHHH
Confidence 45789999999999999987 46655555544 4899999998877765
No 29
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]
Probab=96.58 E-value=0.0036 Score=69.47 Aligned_cols=90 Identities=14% Similarity=0.203 Sum_probs=70.4
Q ss_pred CCCCCCCCCcEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEc-C--ChHHHHHHHHHhhhccCccccccc
Q 012847 13 LDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAM-D--LEALLQQVSKQHLARFKGSVIRYQ 89 (455)
Q Consensus 13 ~~~~~~F~g~~iy~~~~~~g~~R~~~l~~li~~~Gg~V~~~ls~~VTHVV~~-~--~~~~l~~l~~~~~~~~~~~lV~~~ 89 (455)
...+.+|.|+-+++.....+..+...|++.+..+||.++..+.+..||.|+. + +.++.. ..+.+ ..-||+++
T Consensus 628 ~~~s~if~gl~f~Vlsgt~~~~tk~~le~~ivenGG~iv~nv~p~~~~ci~~a~~et~~vk~----~~~~~-~cdVl~p~ 702 (881)
T KOG0966|consen 628 AKISNIFDGLEFCVLSGTSETHTKAKLEEIIVENGGKIVQNVGPSDTLCIATAGKETTRVKA----QAIKR-SCDVLKPA 702 (881)
T ss_pred cchhhhhcCeeEEEecCCcccccHHHHHHHHHHcCCEEEEcCCCCCcceEEeccccchHHHH----HHHhc-cCceeeHH
Confidence 4446899999999998777766678899999999999999999999999962 2 223322 12222 56899999
Q ss_pred hHHHHHhcCCCCCccccc
Q 012847 90 WLEDSLRLGEKVSEDLYR 107 (455)
Q Consensus 90 Wl~es~k~g~lvdee~y~ 107 (455)
||.+|.+..++++..++-
T Consensus 703 Wlldcc~~~~l~p~~P~~ 720 (881)
T KOG0966|consen 703 WLLDCCKKQRLLPWLPRD 720 (881)
T ss_pred HHHHHHhhhhccccccHH
Confidence 999999999999976543
No 30
>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=96.54 E-value=0.0053 Score=48.41 Aligned_cols=51 Identities=22% Similarity=0.344 Sum_probs=39.9
Q ss_pred chhhhcC-CCCCCHHHHHHHHHHHH-hCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc
Q 012847 252 SADQVKG-LPGIGKSMQDHIQEIVT-TGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (455)
Q Consensus 252 s~~~l~~-lpgIG~~ia~kI~Eil~-tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 314 (455)
+.++|.. +||||...+..|-+... .|.+. .++.|.+|+|||.++|+++++.
T Consensus 14 ~~~~L~~~ipgig~~~a~~Il~~R~~~g~~~------------s~~dL~~v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 14 TAEELQRAMNGVGLKKAEAIVSYREEYGPFK------------TVEDLKQVPGIGNSLVEKNLAV 66 (69)
T ss_pred CHHHHHhHCCCCCHHHHHHHHHHHHHcCCcC------------CHHHHHcCCCCCHHHHHHHHhh
Confidence 3468888 99999999999988875 45444 3444568999999999999864
No 31
>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=96.51 E-value=0.0041 Score=59.09 Aligned_cols=53 Identities=15% Similarity=0.265 Sum_probs=37.4
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHH
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLY 312 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly 312 (455)
..|.++||||+++|-.| |.+-...++.+.-. .+=...|++|||||+|||+++.
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 56899999999999888 55444444433222 1223446799999999999997
No 32
>KOG2481 consensus Protein required for normal rRNA processing [RNA processing and modification]
Probab=96.36 E-value=0.0015 Score=69.17 Aligned_cols=86 Identities=17% Similarity=0.246 Sum_probs=63.3
Q ss_pred CCCCCCCCCCcEEEEecCCCCchHHHHHHHHHHhcCCEEEeec----------CCCccEEEEcCChHHHHHHHHHhhhcc
Q 012847 12 ALDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKL----------SKKVTHVLAMDLEALLQQVSKQHLARF 81 (455)
Q Consensus 12 ~~~~~~~F~g~~iy~~~~~~g~~R~~~l~~li~~~Gg~V~~~l----------s~~VTHVV~~~~~~~l~~l~~~~~~~~ 81 (455)
.+....+|+||++|+.. .+. ++.|.-+|++.||.|.-.- +..|||=|++-..... . . .
T Consensus 321 ~s~~kslF~glkFfl~r-eVP---resL~fiI~s~GG~V~wd~~~~g~~~~~~d~~ITH~IvDrP~~~~---~--v---~ 388 (570)
T KOG2481|consen 321 QSSHKSLFSGLKFFLNR-EVP---RESLEFIIRSFGGKVSWDPLGIGATYDESDERITHQIVDRPGQQT---S--V---I 388 (570)
T ss_pred hhhHHHHhhcceeeeec-cCc---hHHHHHHHHHcCCceecCccCCCCcccccccceeeeeecccCccc---e--e---e
Confidence 34445899999999973 333 3578899999999998651 2458998886432210 0 0 1
Q ss_pred CccccccchHHHHHhcCCCCCccccccc
Q 012847 82 KGSVIRYQWLEDSLRLGEKVSEDLYRIK 109 (455)
Q Consensus 82 ~~~lV~~~Wl~es~k~g~lvdee~y~l~ 109 (455)
+-..|.++||-||+.+|.+++.+.|.+.
T Consensus 389 gR~YvQPQWvfDsvNar~llpt~~Y~~G 416 (570)
T KOG2481|consen 389 GRTYVQPQWVFDSVNARLLLPTEKYFPG 416 (570)
T ss_pred eeeeecchhhhhhccchhhccHhhhCCC
Confidence 3367999999999999999999999886
No 33
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.35 E-value=0.0038 Score=59.48 Aligned_cols=52 Identities=17% Similarity=0.290 Sum_probs=37.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchh-hHHHHhhchhHHHHHhhhccCcCHHHHHHHH
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSK-LEHFEKDEKVRTISLFGEVWGIGPATAQKLY 312 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~-le~l~~~~~~~~l~lf~~I~GvGpktA~~ly 312 (455)
..|.+++|||+++|-.|-.-+. ..+ .+.+.+ +=.+.|++|||||+|||+++.
T Consensus 73 ~~Li~V~GIGpK~Al~ILs~~~---~~~l~~aI~~----~D~~~L~~vpGIGkKtAerIi 125 (194)
T PRK14605 73 ETLIDVSGIGPKLGLAMLSAMN---AEALASAIIS----GNAELLSTIPGIGKKTASRIV 125 (194)
T ss_pred HHHhCCCCCCHHHHHHHHHhCC---HHHHHHHHHh----CCHHHHHhCCCCCHHHHHHHH
Confidence 5689999999999998866432 233 233322 234557799999999999954
No 34
>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=96.34 E-value=0.0024 Score=60.62 Aligned_cols=51 Identities=16% Similarity=0.212 Sum_probs=41.6
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhc------cCchhhhhhchhhHhhhc
Q 012847 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE------DSLTHSQRLGLKYFDDIK 343 (455)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~------~~L~~~q~~Glk~~ed~~ 343 (455)
...+.+|.+|+|||||+|..+ .+.-|+++|.++ ++|++++|+|-|..+.|.
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 347777889999999999999 566778888742 469999999999977765
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=96.28 E-value=0.0036 Score=41.74 Aligned_cols=23 Identities=30% Similarity=0.546 Sum_probs=19.5
Q ss_pred cchhhhcCCCCCCHHHHHHHHHH
Q 012847 251 ESADQVKGLPGIGKSMQDHIQEI 273 (455)
Q Consensus 251 ~s~~~l~~lpgIG~~ia~kI~Ei 273 (455)
.+.++|.+|||||+++|..|.+|
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 46799999999999999999775
No 36
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=96.24 E-value=0.0045 Score=68.30 Aligned_cols=76 Identities=28% Similarity=0.373 Sum_probs=57.0
Q ss_pred chHHHHHHHHHHhcCCEEEeecCCCccEEEEc-CChHH-HHHHHHHhhhccCccccccchHHHHHhcCCCCCcccccccc
Q 012847 33 NRRLQIWRQKLVQMGATVEEKLSKKVTHVLAM-DLEAL-LQQVSKQHLARFKGSVIRYQWLEDSLRLGEKVSEDLYRIKL 110 (455)
Q Consensus 33 ~~R~~~l~~li~~~Gg~V~~~ls~~VTHVV~~-~~~~~-l~~l~~~~~~~~~~~lV~~~Wl~es~k~g~lvdee~y~l~~ 110 (455)
..-.+.+..+++. ++...+...|||||+. +.+.+ .+.+++......+.+|+++.|+.+|++++++|+|+.|-+.+
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 3455667777766 6667778999999984 33332 35555544333477999999999999999999999999976
Q ss_pred C
Q 012847 111 D 111 (455)
Q Consensus 111 ~ 111 (455)
+
T Consensus 565 d 565 (684)
T KOG4362|consen 565 D 565 (684)
T ss_pred c
Confidence 4
No 37
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=96.24 E-value=0.0017 Score=63.02 Aligned_cols=52 Identities=25% Similarity=0.500 Sum_probs=42.8
Q ss_pred HhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhhhchhhHhhhccCcC
Q 012847 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIKTRIP 347 (455)
Q Consensus 296 lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~q~~Glk~~ed~~~~i~ 347 (455)
.|..|+|||++++++||+.||.|+++|..+. .|..+.++|.+..+.|...+.
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 3569999999999999999999999999764 588888888777666655443
No 38
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.19 E-value=0.0062 Score=58.04 Aligned_cols=54 Identities=26% Similarity=0.409 Sum_probs=39.5
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (455)
..|.++.|||+++|=.|- .+-...+ |..-...+=.+.|++|||||+|||+++.-
T Consensus 72 ~~LisVsGIGPK~ALaIL---s~~~~~e---l~~aI~~~D~~~L~~vpGIGkKtAeRIIl 125 (196)
T PRK13901 72 EELIGVDGIGPRAALRVL---SGIKYNE---FRDAIDREDIELISKVKGIGNKMAGKIFL 125 (196)
T ss_pred HHHhCcCCcCHHHHHHHH---cCCCHHH---HHHHHHhCCHHHHhhCCCCCHHHHHHHHH
Confidence 568999999999998664 3333333 33333444567788999999999999974
No 39
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=96.16 E-value=0.0069 Score=57.52 Aligned_cols=54 Identities=19% Similarity=0.327 Sum_probs=37.7
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhh-HHHHhhchhHHHHHhhhccCcCHHHHHHHHHc
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKL-EHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~l-e~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 314 (455)
..|..+||||+++|.+|.+.+ |. ..+ +.+.+.. .+.|++|||||+|+|++++..
T Consensus 73 ~~L~~i~GIGpk~A~~il~~f--g~-~~l~~~i~~~d----~~~L~~v~Gig~k~A~~I~~~ 127 (192)
T PRK00116 73 RLLISVSGVGPKLALAILSGL--SP-EELVQAIANGD----VKALTKVPGIGKKTAERIVLE 127 (192)
T ss_pred HHHhcCCCCCHHHHHHHHHhC--CH-HHHHHHHHhCC----HHHHHhCCCCCHHHHHHHHHH
Confidence 468889999999999985433 22 333 2333322 234569999999999999963
No 40
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.12 E-value=0.0068 Score=57.25 Aligned_cols=54 Identities=20% Similarity=0.347 Sum_probs=39.3
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (455)
..|.++.|||+++|=.| |.+-...++ ..-...+=.+.|++|||||+|||+++.-
T Consensus 73 ~~Li~VsGIGpK~Al~I---Ls~~~~~el---~~aI~~~D~~~L~~vpGIGkKtAeRIil 126 (183)
T PRK14601 73 EMLLKVNGIGANTAMAV---CSSLDVNSF---YKALSLGDESVLKKVPGIGPKSAKRIIA 126 (183)
T ss_pred HHHhccCCccHHHHHHH---HcCCCHHHH---HHHHHhCCHHHHhhCCCCCHHHHHHHHH
Confidence 56889999999999765 444444444 3333344466788999999999999974
No 41
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.99 E-value=0.0074 Score=57.90 Aligned_cols=54 Identities=19% Similarity=0.212 Sum_probs=39.8
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (455)
..|.++.|||+++|=.|- .+-...++ ..-...+=.+.|++|||||+|||+++.-
T Consensus 74 ~~Li~V~GIGpK~Al~iL---s~~~~~~l---~~aI~~~D~~~L~~ipGIGkKtAerIil 127 (203)
T PRK14602 74 IVLISISKVGAKTALAIL---SQFRPDDL---RRLVAEEDVAALTRVSGIGKKTAQHIFL 127 (203)
T ss_pred HHHhCCCCcCHHHHHHHH---hhCCHHHH---HHHHHhCCHHHHhcCCCcCHHHHHHHHH
Confidence 568999999999998664 44344433 3333444567788999999999999974
No 42
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=95.96 E-value=0.0034 Score=70.13 Aligned_cols=61 Identities=21% Similarity=0.325 Sum_probs=47.7
Q ss_pred hccCcCHHHHHHHHHc-CCCCHHHhhh--ccCchhhhhhchhhHhhhccCcCHHHHHHHHHHHH
Q 012847 299 EVWGIGPATAQKLYEK-GHRTLDDLKN--EDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQ 359 (455)
Q Consensus 299 ~I~GvGpktA~~ly~~-GirTledL~~--~~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~~v~ 359 (455)
+|+|+||+++++||+. +|++++||.. .++|..+.+||-|..+.|.+.|-......+..++-
T Consensus 449 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~ll~~Ie~sk~~~l~R~l~ 512 (665)
T PRK07956 449 DIDGLGEKIIEQLFEKGLIHDPADLFKLTAEDLLGLEGFGEKSAQNLLDAIEKSKETSLARFLY 512 (665)
T ss_pred CCCCcCHHHHHHHHHcCCCCCHHHHHhcCHHHHhcCcCcchHHHHHHHHHHHHhhcCCHHHhhH
Confidence 7999999999999998 7899999984 34688889999999999877665443333334433
No 43
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.94 E-value=0.0092 Score=56.60 Aligned_cols=54 Identities=11% Similarity=0.115 Sum_probs=39.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (455)
..|.++.|||+++|=.|- .+-... +|..-...+=.+.|++|||||+|||+++.-
T Consensus 73 ~~Li~V~GIGpK~AL~iL---s~~~~~---el~~aI~~~D~~~L~~vpGIGkKtAerIil 126 (188)
T PRK14606 73 LSLTKVSRLGPKTALKII---SNEDAE---TLVTMIASQDVEGLSKLPGISKKTAERIVM 126 (188)
T ss_pred HHHhccCCccHHHHHHHH---cCCCHH---HHHHHHHhCCHHHHhhCCCCCHHHHHHHHH
Confidence 468899999999998664 332333 333334445567788999999999999974
No 44
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.87 E-value=0.01 Score=56.64 Aligned_cols=54 Identities=20% Similarity=0.366 Sum_probs=39.7
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (455)
..|.++.|||+++|=.| |.+....++- .-...+=.+.|++|||||+|||+++.-
T Consensus 73 ~~Li~V~GIGpK~Al~i---Ls~~~~~el~---~aI~~~D~~~L~kvpGIGkKtAerIil 126 (195)
T PRK14604 73 ELLIGVSGVGPKAALNL---LSSGTPDELQ---LAIAGGDVARLARVPGIGKKTAERIVL 126 (195)
T ss_pred HHHhCcCCcCHHHHHHH---HcCCCHHHHH---HHHHhCCHHHHhhCCCCCHHHHHHHHH
Confidence 56899999999999865 4454444443 333344466788999999999999974
No 45
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.87 E-value=0.01 Score=56.68 Aligned_cols=54 Identities=15% Similarity=0.247 Sum_probs=39.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (455)
..|.++.|||+++|=.| |.+....++ ..-...+=.+.|++|||||+|||+++.-
T Consensus 72 ~~L~~V~GIGpK~AL~i---Ls~~~~~~l---~~aI~~~D~~~L~kvpGIGkKtAerIil 125 (197)
T PRK14603 72 ELLLGVSGVGPKLALAL---LSALPPALL---ARALLEGDARLLTSASGVGKKLAERIAL 125 (197)
T ss_pred HHHhCcCCcCHHHHHHH---HcCCCHHHH---HHHHHhCCHHHHhhCCCCCHHHHHHHHH
Confidence 56889999999999765 454444444 3333344456788999999999999974
No 46
>PRK02362 ski2-like helicase; Provisional
Probab=95.77 E-value=0.0088 Score=67.69 Aligned_cols=59 Identities=24% Similarity=0.394 Sum_probs=47.0
Q ss_pred HHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhc--cCchhhhhhchhhHhhhcc
Q 012847 283 EHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDIKT 344 (455)
Q Consensus 283 e~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~--~~L~~~q~~Glk~~ed~~~ 344 (455)
.+|....+...+.|+ +|||||+++|++||+.||+|++||... ++|..+ ||-+..+.|.+
T Consensus 641 ~~l~~gv~~~~~~L~-~ip~i~~~~a~~l~~~gi~s~~dl~~~~~~~l~~~--~g~~~~~~i~~ 701 (737)
T PRK02362 641 KRVEYGVREELLDLV-GLRGVGRVRARRLYNAGIESRADLRAADKSVVLAI--LGEKIAENILE 701 (737)
T ss_pred HHHHhCCCHHHHHHh-CCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHHH--HCHHHHHHHHH
Confidence 455667777888888 999999999999999999999999953 356666 88777665543
No 47
>PRK14973 DNA topoisomerase I; Provisional
Probab=95.59 E-value=0.016 Score=67.00 Aligned_cols=91 Identities=20% Similarity=0.185 Sum_probs=59.8
Q ss_pred hhhcCCCCCCHHHHHHHHHHHH-h-CCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--Cch
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVT-T-GKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLT 329 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~-t-G~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~ 329 (455)
++|..+|||...++...+.... . +.-..-...+.....+.-+++ +|.|||++|+.+++..|++|.|||.+++ +|+
T Consensus 835 ~~La~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~el~-~vkg~ge~t~~~l~~ag~~~~e~l~~~d~~~la 913 (936)
T PRK14973 835 AYLALKTGISPETICRHAKLVCEKLGRPVPEKISKAAFERGRAELL-SVPGLGETTLEKLYLAGVYDGDLLVSADPKKLA 913 (936)
T ss_pred HHHhcCCCCChhhHHHHHHHHHHHhcCCCchhhhhhhhcccchhhh-hccCCCHHHHHHHHHcCCCCHHHhccCCHHHHh
Confidence 5678888888766665544433 1 111111111111122233344 9999999999999999999999999774 577
Q ss_pred hhhhhchhhHhhhccC
Q 012847 330 HSQRLGLKYFDDIKTR 345 (455)
Q Consensus 330 ~~q~~Glk~~ed~~~~ 345 (455)
..-+++.+....|...
T Consensus 914 ~~~~i~~k~~~~~~~~ 929 (936)
T PRK14973 914 KVTGIDEKKLRNLQAY 929 (936)
T ss_pred hhcCCCHHHHHHHHHH
Confidence 7778888887776543
No 48
>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=95.56 E-value=0.006 Score=68.11 Aligned_cols=62 Identities=24% Similarity=0.408 Sum_probs=48.4
Q ss_pred hccCcCHHHHHHHHHc-CCCCHHHhhh--ccCchhhhhhchhhHhhhccCcCHHHHHHHHHHHHH
Q 012847 299 EVWGIGPATAQKLYEK-GHRTLDDLKN--EDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQK 360 (455)
Q Consensus 299 ~I~GvGpktA~~ly~~-GirTledL~~--~~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~~v~~ 360 (455)
+|+|+|++++++||++ +|++++||.. .++|..+.+||-+..+.|.+.|.......+.+++..
T Consensus 436 ~I~GLG~k~i~~L~~~g~I~~~~Dl~~L~~~~L~~L~GfG~Ksa~nIl~~Ie~sk~~~l~r~L~a 500 (652)
T TIGR00575 436 DIEGLGDKVIEQLFEKKLVRSVADLYALKKEDLLELEGFGEKSAQNLLNAIEKSKEKPLARLLFA 500 (652)
T ss_pred CCCCcCHHHHHHHHHcCCcCCHHHHHhcCHHHHhhccCccHHHHHHHHHHHHHhccCcHHHHHhh
Confidence 7999999999999998 7899999984 356888999999999998876654443334444443
No 49
>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=95.55 E-value=0.012 Score=39.23 Aligned_cols=22 Identities=32% Similarity=0.477 Sum_probs=16.9
Q ss_pred HHHHHhhhccCcCHHHHHHHHH
Q 012847 292 RTISLFGEVWGIGPATAQKLYE 313 (455)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~ 313 (455)
..++.|++||||||+||..+..
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 3566677999999999998764
No 50
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=95.55 E-value=0.034 Score=62.28 Aligned_cols=135 Identities=13% Similarity=0.164 Sum_probs=87.7
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhc--------
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE-------- 325 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~-------- 325 (455)
++|.+|+|+|++.+++|.+=++.-+-..| ...|--| +|++||.++|+.|-+..+.|++.|.+.
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 DRLINLKGFKDKRINNLKRSIEASKKRPF--------SKLLLSM-GIKDLGENTILLLINNNLNSFDKISTLCQDREFAL 540 (669)
T ss_pred HHHhhccCccHHHHHHHHHHHHHHhCCCH--------HHHHHHc-CCCchhHHHHHHHHHHhhCCHHHHHhhhhccCCCH
Confidence 68889999999988887765543332222 3456666 899999999999886788999988752
Q ss_pred cCchhhhhhchhhHhhhccCcCHHHHHH-HHHHHHHHh------------hhcCCCeEEEEeccc---ccC---------
Q 012847 326 DSLTHSQRLGLKYFDDIKTRIPRHEVEQ-MERLLQKAG------------EEVLPEVIILCGGSY---RRG--------- 380 (455)
Q Consensus 326 ~~L~~~q~~Glk~~ed~~~~i~r~Ea~~-i~~~v~~~~------------~~~~p~~~v~~~Gs~---RRg--------- 380 (455)
..|..+.++|-+..+.|.+-+.-.+..+ ++.+.+.-. ...+.|-.+++||++ .|.
T Consensus 541 e~l~~i~giG~~~a~si~~ff~~~~~~~~i~~l~~~gv~~~~~~~~~~~~~~~l~gktfV~TG~l~~~~R~e~~~lie~~ 620 (669)
T PRK14350 541 SKLLKIKGIGEKIALNIIEAFNDKIILDKFNFFKNLGFKMEEDSINIDVENSFLFGKKFCITGSFNGYSRSVLIDKLTKK 620 (669)
T ss_pred HHHhhCCCccHHHHHHHHHHHcCHHHHHHHHHHHHcCCCcccccccccccCCccCCcEEEEecccCCCCHHHHHHHHHHc
Confidence 1477788889777777665443333222 233222100 112345688999977 332
Q ss_pred -----CCCCCCccEEEeCCCch
Q 012847 381 -----KASCGDLDVVIMHPDRK 397 (455)
Q Consensus 381 -----ke~~gDvDiLit~~d~~ 397 (455)
...+...|+||+-..++
T Consensus 621 Ggkv~ssVSkktd~LV~G~~aG 642 (669)
T PRK14350 621 GAIFNTCVTKYLDFLLVGEKAG 642 (669)
T ss_pred CCEEeccccCCCcEEEECCCCC
Confidence 34567779999865544
No 51
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=95.25 E-value=0.019 Score=52.47 Aligned_cols=51 Identities=27% Similarity=0.512 Sum_probs=40.2
Q ss_pred hHHHHHhhhccCcCHHHHHHHHH---c-C-CCCHHHhhhccCchhhhhhchhhHhhhccCcC
Q 012847 291 VRTISLFGEVWGIGPATAQKLYE---K-G-HRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIP 347 (455)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~---~-G-irTledL~~~~~L~~~q~~Glk~~ed~~~~i~ 347 (455)
....+.|..+||||+++|+++.+ + | |+|+|||.+ .+++|-+.++.+..+|.
T Consensus 93 tAs~eeL~~lpgIG~~kA~aIi~yRe~~G~f~sv~dL~~------v~GiG~~~~ekl~~~i~ 148 (149)
T COG1555 93 TASAEELQALPGIGPKKAQAIIDYREENGPFKSVDDLAK------VKGIGPKTLEKLKDYIT 148 (149)
T ss_pred ccCHHHHHHCCCCCHHHHHHHHHHHHHcCCCCcHHHHHh------ccCCCHHHHHHHHhhcc
Confidence 33455557999999999999985 2 4 899999986 46899999888877654
No 52
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=95.20 E-value=0.022 Score=54.52 Aligned_cols=54 Identities=19% Similarity=0.279 Sum_probs=40.4
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (455)
..|.++.|||+++|=.| |.+....++- +-...+=...|+++||||.|||+++.-
T Consensus 73 ~~LisVnGIGpK~ALai---Ls~~~~~~l~---~aI~~~d~~~L~k~PGIGkKtAerivl 126 (201)
T COG0632 73 RLLISVNGIGPKLALAI---LSNLDPEELA---QAIANEDVKALSKIPGIGKKTAERIVL 126 (201)
T ss_pred HHHHccCCccHHHHHHH---HcCCCHHHHH---HHHHhcChHhhhcCCCCCHHHHHHHHH
Confidence 57899999999999765 4555555443 333344566788999999999999975
No 53
>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=95.07 E-value=0.04 Score=40.70 Aligned_cols=28 Identities=29% Similarity=0.458 Sum_probs=23.5
Q ss_pred cCCCeEEEEecccccCCC-CCCCccEEEe
Q 012847 365 VLPEVIILCGGSYRRGKA-SCGDLDVVIM 392 (455)
Q Consensus 365 ~~p~~~v~~~Gs~RRgke-~~gDvDiLit 392 (455)
..+...+.+.|||.||.. ..+|||+++.
T Consensus 14 ~~~~~~v~lfGS~arg~~~~~SDIDi~v~ 42 (49)
T cd05397 14 LVPGYEIVVYGSLVRGLLKKSSDIDLACV 42 (49)
T ss_pred hcCCcEEEEECCcCCCCCCCCCCEEEEEE
Confidence 345668999999999977 6789999986
No 54
>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=95.02 E-value=0.013 Score=39.50 Aligned_cols=20 Identities=45% Similarity=0.790 Sum_probs=16.3
Q ss_pred hhhccCcCHHHHHHHHHcCC
Q 012847 297 FGEVWGIGPATAQKLYEKGH 316 (455)
Q Consensus 297 f~~I~GvGpktA~~ly~~Gi 316 (455)
+..+||||++|+++|.+.||
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 46999999999999988886
No 55
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.01 E-value=0.024 Score=53.71 Aligned_cols=53 Identities=13% Similarity=0.117 Sum_probs=37.7
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (455)
..|.++.|||+++|=.| |.+-...++-.. ...+=.+.| +|||||+|||+++.-
T Consensus 73 ~~LisV~GIGpK~Al~i---Ls~~~~~~l~~a---I~~~D~~~L-~vpGIGkKtAerIil 125 (186)
T PRK14600 73 RMLVKVSGVNYKTAMSI---LSKLTPEQLFSA---IVNEDKAAL-KVNGIGEKLINRIIT 125 (186)
T ss_pred HHHhCcCCcCHHHHHHH---HccCCHHHHHHH---HHcCCHhhe-ECCCCcHHHHHHHHH
Confidence 56899999999999865 444444444332 222334667 899999999999974
No 56
>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=94.99 E-value=0.026 Score=49.69 Aligned_cols=49 Identities=27% Similarity=0.468 Sum_probs=38.4
Q ss_pred HHHHHhhhccCcCHHHHHHHHHc-----CCCCHHHhhhccCchhhhhhchhhHhhhccCc
Q 012847 292 RTISLFGEVWGIGPATAQKLYEK-----GHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRI 346 (455)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~-----GirTledL~~~~~L~~~q~~Glk~~ed~~~~i 346 (455)
-..+.|+++||||+++|+++++. ++.|++||.+ ..++|.+.++.|...+
T Consensus 65 A~~~eL~~lpGIG~~~A~~Ii~~R~~~g~f~s~eeL~~------V~GIg~k~~~~i~~~l 118 (120)
T TIGR01259 65 ASLEELQALPGIGPAKAKAIIEYREENGAFKSVDDLTK------VSGIGEKSLEKLKDYA 118 (120)
T ss_pred CCHHHHhcCCCCCHHHHHHHHHHHHhcCCcCCHHHHHc------CCCCCHHHHHHHHhce
Confidence 35666779999999999999964 5899999964 4578888888776543
No 57
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=94.97 E-value=0.081 Score=58.59 Aligned_cols=80 Identities=19% Similarity=0.277 Sum_probs=38.0
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--Cchhh
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHS 331 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~ 331 (455)
+++..|+++|++.+++|-.-++.-+-..|++ .+--| +|+.||.++|+.|-+ .+.|++.|..+. .|..+
T Consensus 479 ~~l~~l~~~~~ks~~nLl~aIe~sK~~~l~r--------~l~aL-GIr~VG~~~Ak~La~-~f~sl~~l~~a~~e~l~~i 548 (667)
T COG0272 479 EDLLSLEGFGEKSAENLLNAIEKSKKQPLAR--------FLYAL-GIRHVGETTAKSLAR-HFGTLEALLAASEEELASI 548 (667)
T ss_pred HHHhhccchhhhHHHHHHHHHHHhccCCHHH--------HHHHc-CCchhhHHHHHHHHH-HhhhHHHHHhcCHHHHhhc
Confidence 4555555555555555444333222222221 22233 556666666655555 555555555432 34455
Q ss_pred hhhchhhHhhhc
Q 012847 332 QRLGLKYFDDIK 343 (455)
Q Consensus 332 q~~Glk~~ed~~ 343 (455)
.++|-.-...+.
T Consensus 549 ~giG~~vA~si~ 560 (667)
T COG0272 549 PGIGEVVARSII 560 (667)
T ss_pred cchhHHHHHHHH
Confidence 555544444433
No 58
>cd05402 NT_PAP_TUTase Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases. Poly(A) polymerases (PAPs) catalyze mRNA poly(A) tail synthesis, and terminal uridylyl transferases (TUTases) uridylate RNA. PAPs in this subgroup include human PAP alpha, mouse testis-specific cytoplasmic PAP beta, human nuclear PAP gamma, Saccharomyces cerevisiae PAP1, TRF4 and-5, Schizosaccharomyces pombe caffeine-induced death proteins -1, and -14, Caenorhabditis elegans Germ Line Development-2, and Chlamydomonas reinhardtii MUT68. This family also includes human U6 snRNA-specific TUTase1, and Trypanosoma brucei 3'-TUTase-1,-2, and 4. This family belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. For the majority of proteins in this family, these carboxyla
Probab=94.91 E-value=0.1 Score=44.55 Aligned_cols=58 Identities=26% Similarity=0.438 Sum_probs=46.1
Q ss_pred HHHHHHHHhhhcCCCeEEEEecccccCC-CCCCCccEEEeCCCc-hhhhhhHHHHHHHHHHcCc
Q 012847 354 MERLLQKAGEEVLPEVIILCGGSYRRGK-ASCGDLDVVIMHPDR-KSHKGFLSKYVKKLKEMKF 415 (455)
Q Consensus 354 i~~~v~~~~~~~~p~~~v~~~Gs~RRgk-e~~gDvDiLit~~d~-~~~~~~l~~lv~~L~~~g~ 415 (455)
++.+++. ..|.+.+.+-||++.|. ...+|||+.|..++. .....++..+-+.|++.+.
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 4444444 57999999999999984 346899999998876 4567789999999999885
No 59
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=94.89 E-value=0.044 Score=48.76 Aligned_cols=32 Identities=22% Similarity=0.380 Sum_probs=28.1
Q ss_pred HHHHhhhccCcCHHHHHHHHHc-CCCCHHHhhh
Q 012847 293 TISLFGEVWGIGPATAQKLYEK-GHRTLDDLKN 324 (455)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~-GirTledL~~ 324 (455)
..+.|+++|||||++|+++.+- .++|+|||.+
T Consensus 59 ~~~el~~lpGigP~~A~~IV~nGpf~sveDL~~ 91 (132)
T PRK02515 59 SVRAFRQFPGMYPTLAGKIVKNAPYDSVEDVLN 91 (132)
T ss_pred CHHHHHHCCCCCHHHHHHHHHCCCCCCHHHHHc
Confidence 4555778999999999999987 6999999986
No 60
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=94.76 E-value=0.018 Score=54.70 Aligned_cols=51 Identities=24% Similarity=0.275 Sum_probs=38.9
Q ss_pred HHHHhhhccCcCHHHHHHHHHc-CCCCHHHhhhcc---CchhhhhhchhhHhhhc
Q 012847 293 TISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED---SLTHSQRLGLKYFDDIK 343 (455)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~-GirTledL~~~~---~L~~~q~~Glk~~ed~~ 343 (455)
.+..|.+|+|||||+|.++.+. |..++.+....+ .|+..+|+|.+..+.|.
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 4656679999999999999987 887776544332 58888889988766554
No 61
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=94.69 E-value=0.039 Score=43.09 Aligned_cols=48 Identities=29% Similarity=0.528 Sum_probs=33.2
Q ss_pred HHHHhhhccCcCHHHHHHHHH---c--CCCCHHHhhhccCchhhhhhchhhHhhhccCc
Q 012847 293 TISLFGEVWGIGPATAQKLYE---K--GHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRI 346 (455)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~---~--GirTledL~~~~~L~~~q~~Glk~~ed~~~~i 346 (455)
..+.|.++||||++.|+++.+ + +++|++||.+ ..++|.+.|+.+...+
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 455667999999999999985 2 8899999985 4578888888776543
No 62
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.64 E-value=0.017 Score=54.99 Aligned_cols=52 Identities=19% Similarity=0.255 Sum_probs=40.1
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHc-CCCCHHHhh-hc--cCchhhhhhchhhHhhh
Q 012847 291 VRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLK-NE--DSLTHSQRLGLKYFDDI 342 (455)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~-GirTledL~-~~--~~L~~~q~~Glk~~ed~ 342 (455)
...+++|.+|+|||||+|..+... +...|-+.. +. ..|++.+|+|-|..+.|
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 458888899999999999999996 665533322 32 35899999999987763
No 63
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]
Probab=94.62 E-value=0.093 Score=58.70 Aligned_cols=91 Identities=19% Similarity=0.279 Sum_probs=59.1
Q ss_pred CCCCCCcEEEEecCCCCchHHHHHHHHHHhcCCEEEeec------CCCccEEEEc--CChHHH-HHHHHHhhhccCcccc
Q 012847 16 NGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKL------SKKVTHVLAM--DLEALL-QQVSKQHLARFKGSVI 86 (455)
Q Consensus 16 ~~~F~g~~iy~~~~~~g~~R~~~l~~li~~~Gg~V~~~l------s~~VTHVV~~--~~~~~l-~~l~~~~~~~~~~~lV 86 (455)
.+.|..|++|.+.++.=.+-..+..-.+...|+++.+.- ...+||+|+. +.+-.. ...+...+-..+ +||
T Consensus 782 ~~~~~~~~~f~~~~~~~~se~~~~~l~~k~~g~~i~~~~~~~~~~~~~~t~~v~~~i~~~h~~~~~~~~~~lt~~r-kv~ 860 (881)
T KOG0966|consen 782 SLFLSSLRMFYVLRRKLSSEEVIIELKLKNFGGRITDAQSECNNIGAKYTHCVLRCIDEDHEKIKEQKKASLTIKR-KVV 860 (881)
T ss_pred ccccccceeeecccccccHHHHHHHHHHHHhcceeeeccchhhhcccceeeeeeeecchHHHHHHHHHHHHhcccc-ccc
Confidence 356777777777665544444444445555599998763 3568999985 222111 111111111123 999
Q ss_pred ccchHHHHHhcCCCCCccccc
Q 012847 87 RYQWLEDSLRLGEKVSEDLYR 107 (455)
Q Consensus 87 ~~~Wl~es~k~g~lvdee~y~ 107 (455)
..+|+.+|+.++.+++|+.|.
T Consensus 861 ~~~wv~~s~~~~~~~~e~~~~ 881 (881)
T KOG0966|consen 861 APSWVDHSINENCLLPEEDFP 881 (881)
T ss_pred CHHHHHHhhcccccCccccCC
Confidence 999999999999999999884
No 64
>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=94.59 E-value=0.033 Score=63.97 Aligned_cols=68 Identities=24% Similarity=0.355 Sum_probs=52.4
Q ss_pred HHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccchHHHHHhcCCCCCccccccc
Q 012847 38 IWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSLRLGEKVSEDLYRIK 109 (455)
Q Consensus 38 ~l~~li~~~Gg~V~~~ls~~VTHVV~~~~~~~l~~l~~~~~~~~~~~lV~~~Wl~es~k~g~lvdee~y~l~ 109 (455)
-+++.+++.|+.+.... ...||+|+..--+-...+. +-..+..||+.+||.+|.++|..+|+..|.+.
T Consensus 672 ~~k~~~k~lg~s~~ss~-~e~Th~i~~rirRT~k~Le---ai~~G~~ivT~~wL~s~~k~g~~~dek~yil~ 739 (896)
T KOG2043|consen 672 NYKLAKKFLGGSVASSD-SEATHFIADRIRRTLKFLE---AISSGKPLVTPQWLVSSLKSGEKLDEKPYILH 739 (896)
T ss_pred hhhhHHhhccceeeccc-ccceeeeehhhhccHHHHh---hhccCCcccchHHHHHHhhccccccCcccccc
Confidence 47889999998888775 4589999984333222222 12237799999999999999999999999885
No 65
>PRK00254 ski2-like helicase; Provisional
Probab=94.58 E-value=0.047 Score=61.68 Aligned_cols=67 Identities=25% Similarity=0.405 Sum_probs=49.6
Q ss_pred hCCchhhH----HHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhc--cCchhhhhhchhhHhhhc
Q 012847 276 TGKLSKLE----HFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDIK 343 (455)
Q Consensus 276 tG~~~~le----~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~--~~L~~~q~~Glk~~ed~~ 343 (455)
.|.+..+. .+....+...+.|. +|||||+++|+++|+.|+.|++||..+ ..|....++|.+..+.+.
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 34444444 34455666677776 999999999999999999999999865 357777778877655443
No 66
>KOG1929 consensus Nucleotide excision repair factor NEF2, RAD4/CUT5 component [Replication, recombination and repair]
Probab=94.43 E-value=0.049 Score=61.79 Aligned_cols=93 Identities=12% Similarity=0.182 Sum_probs=72.5
Q ss_pred CCCCCCCCCCCcEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccch
Q 012847 11 PALDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQW 90 (455)
Q Consensus 11 ~~~~~~~~F~g~~iy~~~~~~g~~R~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~~~~~l~~l~~~~~~~~~~~lV~~~W 90 (455)
|...+...|.+|++++. ...-.+++.+.++++..|+.+...+....||||....... ....+..+..++|+++|
T Consensus 486 p~~~l~~~~e~~~~~~s--~~~~~~~e~ln~~~~~~gas~~~~f~r~~~~l~~~~~k~s----~~~~~~kw~ip~vT~~w 559 (811)
T KOG1929|consen 486 PAAALSQPFENLTISNS--QSAEAEREKLNNLANDLGASNVKTFTRKSTTLLTTSAKGS----KYEIAGKWSIPIVTPDW 559 (811)
T ss_pred hhhcccccccCceEEee--echHHHHHHHhHhhhhccccccceeeecccEEeccccccc----hhhhccccCCCccChhH
Confidence 44555678999999997 3444678999999999999999998766699998752221 11223334789999999
Q ss_pred HHHHHhcCCCCCccccccc
Q 012847 91 LEDSLRLGEKVSEDLYRIK 109 (455)
Q Consensus 91 l~es~k~g~lvdee~y~l~ 109 (455)
|.+|.++++.++.+.|...
T Consensus 560 L~e~~rq~~~~~~e~~l~~ 578 (811)
T KOG1929|consen 560 LYECVRQNKGERNEGFLNG 578 (811)
T ss_pred HHhhccccCcccceeeccc
Confidence 9999999999999999875
No 67
>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=94.43 E-value=0.05 Score=42.81 Aligned_cols=45 Identities=20% Similarity=0.296 Sum_probs=35.0
Q ss_pred Hhhh-ccCcCHHHHHHHHHc-----CCCCHHHhhhccCchhhhhhchhhHhhhccCc
Q 012847 296 LFGE-VWGIGPATAQKLYEK-----GHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRI 346 (455)
Q Consensus 296 lf~~-I~GvGpktA~~ly~~-----GirTledL~~~~~L~~~q~~Glk~~ed~~~~i 346 (455)
.|.. ++|||+++|+++.+. ++++++||.+ ..++|.+.++.|...|
T Consensus 17 ~L~~~ipgig~~~a~~Il~~R~~~g~~~s~~dL~~------v~gi~~~~~~~i~~~~ 67 (69)
T TIGR00426 17 ELQRAMNGVGLKKAEAIVSYREEYGPFKTVEDLKQ------VPGIGNSLVEKNLAVI 67 (69)
T ss_pred HHHhHCCCCCHHHHHHHHHHHHHcCCcCCHHHHHc------CCCCCHHHHHHHHhhc
Confidence 4446 999999999999975 5999999975 3577877777766543
No 68
>KOG1929 consensus Nucleotide excision repair factor NEF2, RAD4/CUT5 component [Replication, recombination and repair]
Probab=94.40 E-value=0.064 Score=60.87 Aligned_cols=88 Identities=18% Similarity=0.239 Sum_probs=70.4
Q ss_pred CCCCcEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccchHHHHHhc
Q 012847 18 IFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSLRL 97 (455)
Q Consensus 18 ~F~g~~iy~~~~~~g~~R~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~~~~~l~~l~~~~~~~~~~~lV~~~Wl~es~k~ 97 (455)
.|.+|.|.. +|+....+..+++++.++||+....++..|+||+.-..... .+++++..+..++|+.+|+-+|+..
T Consensus 103 ~~~~~~Vc~--tgl~~~eK~ei~~~v~k~gg~~~~~L~s~v~~~~~~~~~~~---~kYe~al~wn~~v~~~~w~~~s~~~ 177 (811)
T KOG1929|consen 103 GFFGLKVCL--TGLSGDEKSEIKILVPKHGGTLHRSLSSDVNSLKILPEVKT---EKYEQALKWNIPVVSDDWLFDSIEK 177 (811)
T ss_pred cccceEEEe--cccchHHHHHHHHHhhhcccEEehhhhhhhheeeeccccch---HHHHHHHhhCCccccHHHHhhhhcc
Confidence 466666655 47777777889999999999999999999999998654321 3344444457899999999999999
Q ss_pred CCCCCcccccccc
Q 012847 98 GEKVSEDLYRIKL 110 (455)
Q Consensus 98 g~lvdee~y~l~~ 110 (455)
+..+++..|.+..
T Consensus 178 ~~~~~~~~~e~~~ 190 (811)
T KOG1929|consen 178 TAVLETKPYEGAP 190 (811)
T ss_pred ccccccccccccc
Confidence 9999999998865
No 69
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=94.40 E-value=0.034 Score=43.39 Aligned_cols=47 Identities=26% Similarity=0.305 Sum_probs=31.5
Q ss_pred HHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhhhchhhHhhhc
Q 012847 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIK 343 (455)
Q Consensus 295 ~lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~q~~Glk~~ed~~ 343 (455)
--| +|+|||+++|+.|.+ -+.|++.|.++. .|....++|.+..+.+.
T Consensus 4 ~aL-GI~~VG~~~ak~L~~-~f~sl~~l~~a~~e~L~~i~gIG~~~A~si~ 52 (64)
T PF12826_consen 4 FAL-GIPGVGEKTAKLLAK-HFGSLEALMNASVEELSAIPGIGPKIAQSIY 52 (64)
T ss_dssp HHC-TSTT--HHHHHHHHH-CCSCHHHHCC--HHHHCTSTT--HHHHHHHH
T ss_pred eeC-CCCCccHHHHHHHHH-HcCCHHHHHHcCHHHHhccCCcCHHHHHHHH
Confidence 345 999999999999986 555999999653 57777888876655543
No 70
>PRK03858 DNA polymerase IV; Validated
Probab=94.06 E-value=0.067 Score=55.96 Aligned_cols=113 Identities=15% Similarity=0.213 Sum_probs=65.3
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhccCchhhhhhchhhHhhhccCcCHHHHHHHHHHHHHHhhhcCCCeEEEEecc
Q 012847 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGS 376 (455)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirTledL~~~~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~~v~~~~~~~~p~~~v~~~Gs 376 (455)
+..+||||++++++|.+.||+|+.||.+-..-.-..+||....+. +...+..+++. .+ -.
T Consensus 175 l~~l~Gig~~~~~~L~~~Gi~t~~dl~~l~~~~L~~~fG~~~~~~----------------l~~~a~G~d~~-~v---~~ 234 (396)
T PRK03858 175 VRRLWGVGPVTAAKLRAHGITTVGDVAELPESALVSLLGPAAGRH----------------LHALAHNRDPR-RV---ET 234 (396)
T ss_pred hhhcCCCCHHHHHHHHHhCCCcHHHHhcCCHHHHHHHhCcHHHHH----------------HHHHhCCCCCC-CC---CC
Confidence 357899999999999999999999998643222233455422111 11111111111 11 12
Q ss_pred cccCCCCCCCccEEEeCCCch----hhhhhHHHHHHHHHHcCceeeeecccccCCcc
Q 012847 377 YRRGKASCGDLDVVIMHPDRK----SHKGFLSKYVKKLKEMKFLREDLIFSTHSEET 429 (455)
Q Consensus 377 ~RRgke~~gDvDiLit~~d~~----~~~~~l~~lv~~L~~~g~l~~~L~~~~~~~~~ 429 (455)
++.-|..+....|---..+.. ....++..+..+|++.|.....+++..+..+|
T Consensus 235 ~~~~ksi~~~~t~~~~~~~~~~l~~~l~~L~~~l~~rLr~~~~~~~~l~l~l~~~~~ 291 (396)
T PRK03858 235 GRRRRSVGAQRALGRGPNSPAEVDAVVVALVDRVARRMRAAGRTGRTVVLRLRFDDF 291 (396)
T ss_pred CCCCccccceeEcCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCcceEEEEEEeCCC
Confidence 333344444444321111111 14567888999999999999999988755543
No 71
>COG5163 NOP7 Protein required for biogenesis of the 60S ribosomal subunit [Translation, ribosomal structure and biogenesis]
Probab=93.49 E-value=0.065 Score=55.62 Aligned_cols=87 Identities=20% Similarity=0.316 Sum_probs=63.1
Q ss_pred CCCCCCCCCCCcEEEEecCCCCchHHHHHHHHHHhcCCEEEeec-----------CCCccEEEEcCChHHHHHHHHHhhh
Q 012847 11 PALDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKL-----------SKKVTHVLAMDLEALLQQVSKQHLA 79 (455)
Q Consensus 11 ~~~~~~~~F~g~~iy~~~~~~g~~R~~~l~~li~~~Gg~V~~~l-----------s~~VTHVV~~~~~~~l~~l~~~~~~ 79 (455)
+.++-..+|+++++|+..--.+ ..|+-+|...||.|.... +..|||-|++-.- +.. ++
T Consensus 343 ~~Ss~~slFS~f~FyisreVp~----dsLefiilscGG~V~~~p~~~~i~~~~~vD~~vth~i~drp~--~~~-kv---- 411 (591)
T COG5163 343 PCSSLKSLFSGFKFYISREVPG----DSLEFIILSCGGSVVGSPCEADIHVSEKVDEKVTHQIVDRPV--MKN-KV---- 411 (591)
T ss_pred cCcchhhhhhceEEEEeccccc----hHHHHHHHHcCCcccCchhhccCCchhhccchhhhhhccchh--hhh-hh----
Confidence 3445568999999999743333 468889999999998652 3457887775321 111 11
Q ss_pred ccCccccccchHHHHHhcCCCCCccccccc
Q 012847 80 RFKGSVIRYQWLEDSLRLGEKVSEDLYRIK 109 (455)
Q Consensus 80 ~~~~~lV~~~Wl~es~k~g~lvdee~y~l~ 109 (455)
-+.-.+.++|+-+|+..|.+++.+.|.+.
T Consensus 412 -egrtYiQPQw~fDsiNkG~l~~~~~Y~~G 440 (591)
T COG5163 412 -EGRTYIQPQWLFDSINKGKLACVENYCVG 440 (591)
T ss_pred -cceeeechHHHHhhhccccchhhhhcccc
Confidence 13457899999999999999999999986
No 72
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.12 E-value=0.053 Score=51.47 Aligned_cols=50 Identities=20% Similarity=0.261 Sum_probs=38.7
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhh---c---cCchhhhhhchhhHhhh
Q 012847 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDI 342 (455)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~---~---~~L~~~q~~Glk~~ed~ 342 (455)
...+++|.+|.|||||+|-.+-.. -+.++|.. . ..|++.+|+|-|..+.|
T Consensus 69 r~lF~~Li~V~GIGpK~AL~iLs~--~~~~el~~aI~~~D~~~L~~vpGIGkKtAerI 124 (188)
T PRK14606 69 KELFLSLTKVSRLGPKTALKIISN--EDAETLVTMIASQDVEGLSKLPGISKKTAERI 124 (188)
T ss_pred HHHHHHHhccCCccHHHHHHHHcC--CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHH
Confidence 458888999999999999999864 35556653 2 25899999999987654
No 73
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.02 E-value=0.056 Score=51.06 Aligned_cols=50 Identities=20% Similarity=0.255 Sum_probs=38.9
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhh---c---cCchhhhhhchhhHhhh
Q 012847 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDI 342 (455)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~---~---~~L~~~q~~Glk~~ed~ 342 (455)
...+++|.+|.|||||+|-.+-.. -+.++|.. . ..|++.+|+|-|..+.|
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 458888999999999999988764 36666653 2 25889999999986654
No 74
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=92.97 E-value=0.18 Score=49.19 Aligned_cols=54 Identities=24% Similarity=0.452 Sum_probs=40.9
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc
Q 012847 253 ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (455)
Q Consensus 253 ~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 314 (455)
++.|..|||||+..+.++ ++.| +.-++.++... .+.+..|+|||.++|.++++.
T Consensus 2 ~~~L~~IpGIG~krakkL---l~~G-F~Sve~Ik~AS----~eEL~~V~GIg~k~AekI~e~ 55 (232)
T PRK12766 2 PEELEDISGVGPSKAEAL---REAG-FESVEDVRAAD----QSELAEVDGIGNALAARIKAD 55 (232)
T ss_pred ccccccCCCcCHHHHHHH---HHcC-CCCHHHHHhCC----HHHHHHccCCCHHHHHHHHHH
Confidence 356889999999988876 5566 55666665433 344569999999999999986
No 75
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.74 E-value=0.064 Score=51.27 Aligned_cols=50 Identities=28% Similarity=0.308 Sum_probs=39.1
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhh---c---cCchhhhhhchhhHhhh
Q 012847 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDI 342 (455)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~---~---~~L~~~q~~Glk~~ed~ 342 (455)
...+++|.+|.|||||+|-.+... -|.++|.. . ..|++.+|+|.|..+.|
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 358888899999999999999874 36666653 2 25899999999986654
No 76
>PRK02406 DNA polymerase IV; Validated
Probab=92.69 E-value=0.28 Score=50.33 Aligned_cols=112 Identities=18% Similarity=0.149 Sum_probs=62.0
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhccCchhhhhhchhhHhhhccCcCHHHHHHHHHHHHHHhhhcCCCeEEEEecc
Q 012847 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGS 376 (455)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirTledL~~~~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~~v~~~~~~~~p~~~v~~~Gs 376 (455)
+..+||||++++++|-+.||+|+.||.+-..=.-.++||.. ...+...+.. +.+. .+. .
T Consensus 170 i~~l~giG~~~~~~L~~~Gi~ti~dl~~l~~~~L~~~fG~~----------------~~~l~~~a~G-~d~~-~v~---~ 228 (343)
T PRK02406 170 VEKIPGVGKVTAEKLHALGIYTCADLQKYDLAELIRHFGKF----------------GRRLYERARG-IDER-PVK---P 228 (343)
T ss_pred cchhcCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHHHhHH----------------HHHHHHHhCC-CCCC-ccc---c
Confidence 35889999999999998899999999864321122345521 1111111111 1111 010 1
Q ss_pred cccCCCCCCCccEE--EeCCCc--hhhhhhHHHHHHHHHHcC--ceeeeecccccCCcc
Q 012847 377 YRRGKASCGDLDVV--IMHPDR--KSHKGFLSKYVKKLKEMK--FLREDLIFSTHSEET 429 (455)
Q Consensus 377 ~RRgke~~gDvDiL--it~~d~--~~~~~~l~~lv~~L~~~g--~l~~~L~~~~~~~~~ 429 (455)
++--|..+....|- +.+.+. .....++..+..+|++.| .....+++..+..++
T Consensus 229 ~~~~ksi~~~~~~~~~~~~~~~l~~~l~~l~~~l~~rL~~~~~~~~~~~l~l~l~~~~~ 287 (343)
T PRK02406 229 DRERKSVGVERTFAEDLYDLEACLAELPRLAEKLERRLERAKPDKRIKTVGVKLKFADF 287 (343)
T ss_pred CCCCcceeeeeeCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCccceeEEEEEEeCCC
Confidence 11112222222221 111111 124568889999999999 999999988865553
No 77
>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=92.68 E-value=0.35 Score=49.67 Aligned_cols=108 Identities=16% Similarity=0.136 Sum_probs=63.4
Q ss_pred hhccCcCHHHHHHHHHcCCCCHHHhhhccCchh-hhhhc---hhhHhhhccCcCHHHHHHHHHHHHHHhhhcCCCeEEEE
Q 012847 298 GEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTH-SQRLG---LKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILC 373 (455)
Q Consensus 298 ~~I~GvGpktA~~ly~~GirTledL~~~~~L~~-~q~~G---lk~~ed~~~~i~r~Ea~~i~~~v~~~~~~~~p~~~v~~ 373 (455)
..+||||++++++|.+.||+|+.||.+...... ...|| ...|+.... +.+. .+
T Consensus 176 ~~l~giG~~~~~~L~~~Gi~ti~dl~~~~~~~~l~~~fg~~~~~l~~~a~G--------------------~d~~-~v-- 232 (343)
T cd00424 176 TDLPGIGAVTAKRLEAVGINPIGDLLAASPDALLALWGGVSGERLWYALRG--------------------IDDE-PL-- 232 (343)
T ss_pred hhcCCCCHHHHHHHHHcCCCcHHHHhcCCHHHHHHHHhhHHHHHHHHHhCC--------------------cCCC-CC--
Confidence 468999999999999999999999986431111 12233 222222221 1111 01
Q ss_pred ecccccCCCCCCCccEEE--eCCCc--hhhhhhHHHHHHHHHHcCceeeeecccccCCcc
Q 012847 374 GGSYRRGKASCGDLDVVI--MHPDR--KSHKGFLSKYVKKLKEMKFLREDLIFSTHSEET 429 (455)
Q Consensus 374 ~Gs~RRgke~~gDvDiLi--t~~d~--~~~~~~l~~lv~~L~~~g~l~~~L~~~~~~~~~ 429 (455)
-.++.-|..+....|-- ++.+. .....++..+..+|++.|.....|.+..+..+|
T Consensus 233 -~~~~~~ksi~~~~tf~~~~~~~~~l~~~l~~l~~~l~~rL~~~~~~~~~l~l~lr~~~~ 291 (343)
T cd00424 233 -SPPRPRKSFSHERVLPRDSRNAEDARPLLRLLLEKLARRLRRDGRGATRLRLWLRTVDG 291 (343)
T ss_pred -CCCCCCCceeeeEECCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCceeEEEEEEEeCCC
Confidence 11232344444443321 11111 124567888999999999999999998876654
No 78
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.68 E-value=0.068 Score=51.31 Aligned_cols=50 Identities=26% Similarity=0.324 Sum_probs=38.8
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhh---c---cCchhhhhhchhhHhhh
Q 012847 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDI 342 (455)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~---~---~~L~~~q~~Glk~~ed~ 342 (455)
...+++|.+|.|||||+|-.+... -+.++|.. . ..|++++|+|-|..+.|
T Consensus 70 r~lF~~Li~V~GIGpK~Al~iLs~--~~~~~l~~aI~~~D~~~L~~ipGIGkKtAerI 125 (203)
T PRK14602 70 RQTFIVLISISKVGAKTALAILSQ--FRPDDLRRLVAEEDVAALTRVSGIGKKTAQHI 125 (203)
T ss_pred HHHHHHHhCCCCcCHHHHHHHHhh--CCHHHHHHHHHhCCHHHHhcCCCcCHHHHHHH
Confidence 358888889999999999999874 25556553 2 35899999999986654
No 79
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.55 E-value=0.07 Score=50.94 Aligned_cols=50 Identities=28% Similarity=0.365 Sum_probs=39.5
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhc------cCchhhhhhchhhHhhh
Q 012847 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE------DSLTHSQRLGLKYFDDI 342 (455)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~------~~L~~~q~~Glk~~ed~ 342 (455)
...+++|.+|.|||||+|-.+-.. -|.++|..+ ..|++++|+|.|..+.|
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 358888899999999999999874 366777632 25899999999986654
No 80
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=92.53 E-value=0.052 Score=61.04 Aligned_cols=63 Identities=16% Similarity=0.243 Sum_probs=47.9
Q ss_pred hccCcCHHHHHHHHHc-CCCCHHHhhhc--cCchhhhhhchhhHhhhccCcCHHHHHHHHHHHHHH
Q 012847 299 EVWGIGPATAQKLYEK-GHRTLDDLKNE--DSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKA 361 (455)
Q Consensus 299 ~I~GvGpktA~~ly~~-GirTledL~~~--~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~~v~~~ 361 (455)
+|.|+|++++++||+. +++++.||..- ..|..+.+||-|..+.|.+.|-..--..+..++..+
T Consensus 466 ~I~GLG~k~i~~L~~~g~V~~~~Dl~~L~~~~L~~l~g~g~Ksa~~Ll~~Ie~sk~~~l~r~l~AL 531 (689)
T PRK14351 466 DIEGLGEERVQQLVDAGLVESLADLYDLTVADLAELEGWGETSAENLLAELEASREPPLADFLVAL 531 (689)
T ss_pred CCCCcCHHHHHHHHHcCCCCCHHHHHHcCHHHHhcCcCcchhHHHHHHHHHHHHccCCHHHHHHHc
Confidence 7999999999999999 57999999852 347778899999999988776444333345555443
No 81
>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=92.50 E-value=0.13 Score=52.13 Aligned_cols=121 Identities=18% Similarity=0.091 Sum_probs=70.7
Q ss_pred hccCcCHHHHHHHHHcCCCCHHHhhhccCchhhhhhchhhHhhhccCcCHHHHHHHHHHHHHHhhhcCCCeEEEEecccc
Q 012847 299 EVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYR 378 (455)
Q Consensus 299 ~I~GvGpktA~~ly~~GirTledL~~~~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~~v~~~~~~~~p~~~v~~~Gs~R 378 (455)
.+||||++++++|.+.||+|+.||.+-..-.-.++||.+... +...+. -.++.. +. --..+
T Consensus 174 ~~~gig~~~~~~L~~~Gi~t~~dl~~~~~~~l~~rfG~~~~~----------------l~~~~~-G~d~~~-~~-~~~~~ 234 (335)
T cd03468 174 AALRLPPETVELLARLGLRTLGDLAALPRAELARRFGLALLL----------------RLDQAY-GRDPEP-LL-FSPPP 234 (335)
T ss_pred hHhCCCHHHHHHHHHhCcccHHHHHhCChHHHHhhcCHHHHH----------------HHHHHC-CCCCCC-CC-CCCCC
Confidence 578999999999999999999999864432233456643211 111110 011111 00 01122
Q ss_pred cCCCCCCCccEEEeCCC--chhhhhhHHHHHHHHHHcCceeeeecccccCCcchhhcccccc
Q 012847 379 RGKASCGDLDVVIMHPD--RKSHKGFLSKYVKKLKEMKFLREDLIFSTHSEETVGIALQNSM 438 (455)
Q Consensus 379 Rgke~~gDvDiLit~~d--~~~~~~~l~~lv~~L~~~g~l~~~L~~~~~~~~~~~~~~~~~~ 438 (455)
..+..+.+..|-.-..+ ......++..+..+|+..|.....+++..+..+|.....+..+
T Consensus 235 ~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~~L~~~~~~~~~l~l~l~~~~~~~~~~~~~~ 296 (335)
T cd03468 235 PAFDFRLELQLEEPIARGLLFPLRRLLEQLCAFLALRGLGARRLSLTLFREDGRVTRVLVGL 296 (335)
T ss_pred CChhhhhhcCCCCCcchhHHHHHHHHHHHHHHHHHHcCCeeeEEEEEEEEECCceEEEEEec
Confidence 22444444333221111 2235678899999999999999999998887777555444433
No 82
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.29 E-value=0.082 Score=50.47 Aligned_cols=50 Identities=18% Similarity=0.316 Sum_probs=39.0
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhc------cCchhhhhhchhhHhhh
Q 012847 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE------DSLTHSQRLGLKYFDDI 342 (455)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~------~~L~~~q~~Glk~~ed~ 342 (455)
...+++|.+|.|||||+|-.+... -+.++|..+ ..|++.+|+|-|..+.|
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 458888889999999999999764 366666632 25889999999986654
No 83
>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=92.22 E-value=0.41 Score=54.34 Aligned_cols=83 Identities=20% Similarity=0.350 Sum_probs=64.3
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc-CCCCHHHhhhcc-Cch-
Q 012847 253 ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED-SLT- 329 (455)
Q Consensus 253 ~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~-GirTledL~~~~-~L~- 329 (455)
.+.|.++||||++.++.|.+-++. .+ .-..++..| .=+|++++.|.++|+. |-.+++.|+++. +|.
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 467899999999999999876531 11 123466666 8899999999999997 999999999765 455
Q ss_pred hhhhhchhhHhhhccCc
Q 012847 330 HSQRLGLKYFDDIKTRI 346 (455)
Q Consensus 330 ~~q~~Glk~~ed~~~~i 346 (455)
...++|++..+.|..++
T Consensus 185 ~i~gigF~~aD~iA~~~ 201 (720)
T TIGR01448 185 DVKGIGFLTADQLAQAL 201 (720)
T ss_pred hcCCCCHHHHHHHHHHc
Confidence 47889999888886544
No 84
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=92.04 E-value=0.097 Score=53.22 Aligned_cols=46 Identities=30% Similarity=0.482 Sum_probs=33.6
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhhhchhhHhhh
Q 012847 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDI 342 (455)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~q~~Glk~~ed~ 342 (455)
+..+||||+++|++|.+.||.|++||.... .|.+.-+++.+..+.+
T Consensus 8 l~~l~gIg~~~a~~L~~~Gi~t~~dl~~~~~~~L~~~~g~~~~~a~~l 55 (317)
T PRK04301 8 LEDLPGVGPATAEKLREAGYDTVEAIAVASPKELSEAAGIGESTAAKI 55 (317)
T ss_pred HhhcCCCCHHHHHHHHHcCCCCHHHHHcCCHHHHHHhcCCCHHHHHHH
Confidence 468999999999999999999999998643 3444444333344433
No 85
>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=91.90 E-value=0.12 Score=42.38 Aligned_cols=30 Identities=27% Similarity=0.480 Sum_probs=23.3
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhcc
Q 012847 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (455)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirTledL~~~~ 326 (455)
+..+|.+||+..+.|++-||.|++||+.-|
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 86
>PRK03348 DNA polymerase IV; Provisional
Probab=91.81 E-value=0.16 Score=54.41 Aligned_cols=115 Identities=17% Similarity=0.189 Sum_probs=61.7
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhccCchhhhhhchhhHhh---hccCcCHHHHHHHHHHHHHHhhhcCCCeEEEE
Q 012847 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYFDD---IKTRIPRHEVEQMERLLQKAGEEVLPEVIILC 373 (455)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirTledL~~~~~L~~~q~~Glk~~ed---~~~~i~r~Ea~~i~~~v~~~~~~~~p~~~v~~ 373 (455)
+..+||||++++++|.+.||+|+.||.+-..-.-.+.||...... +...+....+.. ..+.-.+..
T Consensus 182 v~~L~GIG~~t~~~L~~lGI~TigDLa~l~~~~L~~~fG~~~g~~L~~~a~G~d~~pv~~-----------~~~~ksis~ 250 (454)
T PRK03348 182 VRRLWGIGPVTEEKLHRLGIETIGDLAALSEAEVANLLGATVGPALHRLARGIDDRPVAE-----------RAEAKQISA 250 (454)
T ss_pred ccccCCCCHHHHHHHHHcCCccHHHHhcCCHHHHHHHHCHHHHHHHHHHHcCCCCCCccc-----------CCCCceEEE
Confidence 358899999999999999999999998643212223344321111 111111000000 000001111
Q ss_pred ecccccCCCCCCCccEEEeCCCchhhhhhHHHHHHHHHHcCceeeeecccccCCcch
Q 012847 374 GGSYRRGKASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLREDLIFSTHSEETV 430 (455)
Q Consensus 374 ~Gs~RRgke~~gDvDiLit~~d~~~~~~~l~~lv~~L~~~g~l~~~L~~~~~~~~~~ 430 (455)
.=.|... +.|.+-| ......++..+..+|.+.|+....+++..+..++.
T Consensus 251 e~tf~~~---i~~~~~l-----~~~L~~L~~~l~~rL~~~g~~~r~v~l~l~~~d~~ 299 (454)
T PRK03348 251 ESTFAVD---LTTRAQL-----REAIERIAEHAHRRLLKDGRGARTVTVKLRKSDFS 299 (454)
T ss_pred EEECCCC---CCCHHHH-----HHHHHHHHHHHHHHHHHcCCCccEEEEEEEeCCCC
Confidence 1123221 1111111 01245678889999999999999999888755543
No 87
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=91.78 E-value=0.12 Score=33.06 Aligned_cols=17 Identities=53% Similarity=0.741 Sum_probs=15.5
Q ss_pred hhhccCcCHHHHHHHHH
Q 012847 297 FGEVWGIGPATAQKLYE 313 (455)
Q Consensus 297 f~~I~GvGpktA~~ly~ 313 (455)
|++|+|||+++|+++.+
T Consensus 3 L~~i~GiG~k~A~~il~ 19 (26)
T smart00278 3 LLKVPGIGPKTAEKILE 19 (26)
T ss_pred hhhCCCCCHHHHHHHHH
Confidence 56999999999999987
No 88
>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=91.45 E-value=0.32 Score=39.57 Aligned_cols=32 Identities=28% Similarity=0.458 Sum_probs=26.2
Q ss_pred CCCeEEEEecccccCCCC-CCCccEEEeCCCch
Q 012847 366 LPEVIILCGGSYRRGKAS-CGDLDVVIMHPDRK 397 (455)
Q Consensus 366 ~p~~~v~~~Gs~RRgke~-~gDvDiLit~~d~~ 397 (455)
.+...+.+.|||.||..+ .+|||++|..++..
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 69999999776553
No 89
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=91.40 E-value=0.48 Score=48.26 Aligned_cols=97 Identities=16% Similarity=0.295 Sum_probs=64.4
Q ss_pred CCCCHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHH-HHHHHHHHHHhCCchhhHHH
Q 012847 207 PDLNKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKS-MQDHIQEIVTTGKLSKLEHF 285 (455)
Q Consensus 207 ~~~N~~ia~~L~~la~~~e~~g~~~r~~aY~rAa~~L~~l~~~i~s~~~l~~lpgIG~~-ia~kI~Eil~tG~~~~le~l 285 (455)
+.=++.|++.++++.+-=+++ +.-...+.+|.+ ..+|..+||+|++ |+..-.|+ - +..+++|
T Consensus 59 ~gIGk~ia~~I~e~l~tG~~~----------~le~lk~~~P~g---l~~Ll~v~GlGpkKi~~Ly~el-g---i~~~e~l 121 (326)
T COG1796 59 PGIGKGIAEKISEYLDTGEVK----------KLEALKKEVPEG---LEPLLKVPGLGPKKIVSLYKEL-G---IKDLEEL 121 (326)
T ss_pred CCccHHHHHHHHHHHHcCccH----------HHHHHHHhCCcc---hHHHhhCCCCCcHHHHHHHHHH-C---cccHHHH
Confidence 566899998876655432222 444555677766 6789999999994 44444433 2 6667777
Q ss_pred HhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhh
Q 012847 286 EKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLK 323 (455)
Q Consensus 286 ~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTledL~ 323 (455)
+.... .-.+.+++|+|.|.+.+|++.+....+.-+
T Consensus 122 ~~a~~---~~~~~~l~GfG~kse~~il~~i~~~~~~~~ 156 (326)
T COG1796 122 QEALE---NGKIRGLRGFGKKSEAKILENIEFAEESPE 156 (326)
T ss_pred HHHHH---hCCccccCCccchhHHHHHHHHHHHhhhhh
Confidence 65433 334669999999999999986444444333
No 90
>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=91.15 E-value=0.3 Score=51.52 Aligned_cols=110 Identities=15% Similarity=0.167 Sum_probs=61.7
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhhhchhhHhhhccCcCHHHHHHHHHHHHHHhhhcCCCeEEEEe
Q 012847 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCG 374 (455)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~~v~~~~~~~~p~~~v~~~ 374 (455)
+..+||||++++++|.+.||+|+.||.+.. .-.-.+.||.+..+.+ ...+. -+.+. .+.
T Consensus 224 v~~l~GIG~~~~~~L~~~Gi~t~~dl~~~~~~~~~L~~~fG~~~g~~L---------------~~~a~-G~d~~-~v~-- 284 (404)
T cd01701 224 VGDLPGVGSSLAEKLVKLFGDTCGGLELRSKTKEKLQKVLGPKTGEKL---------------YDYCR-GIDDR-PVT-- 284 (404)
T ss_pred HhHhCCCCHHHHHHHHHcCCcchHHHHhCcccHHHHHHHHCHHHHHHH---------------HHHhC-CcCCC-CCC--
Confidence 357899999999999999999999998644 2122234553221111 11111 01110 110
Q ss_pred cccccCCCCCCCccEE--EeCCCc--hhhhhhHHHHHHHHHHcCceeeeecccccC
Q 012847 375 GSYRRGKASCGDLDVV--IMHPDR--KSHKGFLSKYVKKLKEMKFLREDLIFSTHS 426 (455)
Q Consensus 375 Gs~RRgke~~gDvDiL--it~~d~--~~~~~~l~~lv~~L~~~g~l~~~L~~~~~~ 426 (455)
..+--|..+....|= +++.+. .....++.++..+|++.|.....+++..+.
T Consensus 285 -~~~~~ksi~~~~tf~~~~~~~~~l~~~l~~L~~~l~~rLr~~~~~~~~l~l~l~~ 339 (404)
T cd01701 285 -GEKERKSVSAEINYGIRFTNVDDVEQFLQRLSEELSKRLEESNVTGRQITLKLMK 339 (404)
T ss_pred -CCCCCccccceeeCCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCceeeEEEEEEe
Confidence 112123323222221 111111 124568888999999999999999988753
No 91
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=91.08 E-value=0.3 Score=48.39 Aligned_cols=49 Identities=22% Similarity=0.481 Sum_probs=35.6
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012847 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (455)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (455)
+..|||||..+|..+-. .-|+...+-.. ....|+.|+|||+++|..+|+
T Consensus 184 l~s~pgig~~~a~~ll~--~fgS~~~~~ta-------s~~eL~~v~gig~k~A~~I~~ 232 (254)
T COG1948 184 LESIPGIGPKLAERLLK--KFGSVEDVLTA-------SEEELMKVKGIGEKKAREIYR 232 (254)
T ss_pred HHcCCCccHHHHHHHHH--HhcCHHHHhhc-------CHHHHHHhcCccHHHHHHHHH
Confidence 78999999999987643 33554443221 114556999999999999997
No 92
>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=90.96 E-value=0.12 Score=58.66 Aligned_cols=55 Identities=15% Similarity=0.335 Sum_probs=42.3
Q ss_pred HHHHHhhh--ccCcCHHHHHHHHHc-CCCCHHHhhhcc-CchhhhhhchhhHhhhccCc
Q 012847 292 RTISLFGE--VWGIGPATAQKLYEK-GHRTLDDLKNED-SLTHSQRLGLKYFDDIKTRI 346 (455)
Q Consensus 292 ~~l~lf~~--I~GvGpktA~~ly~~-GirTledL~~~~-~L~~~q~~Glk~~ed~~~~i 346 (455)
.++..|.+ ++||||+||+++|+. |.++++-|.++. +|...+++|.+..+.|...+
T Consensus 79 ~i~~yL~s~~~~GIG~~~A~~iv~~fg~~~~~~i~~~~~~L~~v~gi~~~~~~~i~~~~ 137 (720)
T TIGR01448 79 GIVAYLSSRSIKGVGKKLAQRIVKTFGEAAFDVLDDDPEKLLEVPGISKANLEKFVSQW 137 (720)
T ss_pred HHHHHHhcCCCCCcCHHHHHHHHHHhCHhHHHHHHhCHHHHhcCCCCCHHHHHHHHHHH
Confidence 34455543 899999999999998 999999998653 57777888877777665543
No 93
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=90.94 E-value=0.13 Score=48.75 Aligned_cols=49 Identities=22% Similarity=0.306 Sum_probs=38.1
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhh---c---cCchhhhhhchhhHhhh
Q 012847 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDI 342 (455)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~---~---~~L~~~q~~Glk~~ed~ 342 (455)
...+++|.+|.|||||+|-.+-.. -|.++|.. . ..| +.+|+|-|..+.|
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 458888899999999999999874 36666653 2 358 8999999986654
No 94
>PRK01172 ski2-like helicase; Provisional
Probab=90.90 E-value=0.27 Score=55.18 Aligned_cols=51 Identities=20% Similarity=0.365 Sum_probs=39.5
Q ss_pred HHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--Cchhhhhhch
Q 012847 285 FEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGL 336 (455)
Q Consensus 285 l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~q~~Gl 336 (455)
+..-.+...+.|+ +|||+|...|+++|+.|++|+.||.... .+..+-++|-
T Consensus 603 l~~gv~~~~~~L~-~ip~~~~~~a~~l~~~g~~~~~di~~~~~~~~~~i~~~~~ 655 (674)
T PRK01172 603 IKEGIREDLIDLV-LIPKVGRVRARRLYDAGFKTVDDIARSSPERIKKIYGFSD 655 (674)
T ss_pred HHcCCCHHHHhhc-CCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHHHhccCH
Confidence 4556667788888 8999999999999999999999998542 3444444443
No 95
>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=90.86 E-value=0.64 Score=43.74 Aligned_cols=49 Identities=14% Similarity=0.218 Sum_probs=30.9
Q ss_pred CCCHHHHHHHHHHHH------hCCchhhHHHHh---hchhHHHHHhhhccCcCHHHHHHHH
Q 012847 261 GIGKSMQDHIQEIVT------TGKLSKLEHFEK---DEKVRTISLFGEVWGIGPATAQKLY 312 (455)
Q Consensus 261 gIG~~ia~kI~Eil~------tG~~~~le~l~~---~~~~~~l~lf~~I~GvGpktA~~ly 312 (455)
|.-+.-|+.|.++.+ .|.+..+ .. -....+++.|+++||||+|||.-.-
T Consensus 75 Gfy~~KAk~Lk~~a~~iie~y~G~v~~L---~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL 132 (177)
T TIGR03252 75 RFPGSMAKRVQALAQYVVDTYDGDATAV---WTEGDPDGKELLRRLKALPGFGKQKAKIFL 132 (177)
T ss_pred CchHHHHHHHHHHHHHHHHHhCCChhhh---hcccCCCcHHHHHHHHcCCCCCHHHHHHHH
Confidence 455666666666554 2444433 33 1223457788899999999998654
No 96
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=90.83 E-value=0.38 Score=52.90 Aligned_cols=88 Identities=15% Similarity=0.194 Sum_probs=66.3
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--Cchh
Q 012847 253 ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTH 330 (455)
Q Consensus 253 ~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~ 330 (455)
.+++.+++|+|++.+++|.+-++.-+-..|+ ..+--| +|++||.++|+. .+.|+++|..+. .|..
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 3689999999999999988766644433333 356667 999999998887 678899998543 5888
Q ss_pred hhhhchhhHhhhccCcCHHHHHH
Q 012847 331 SQRLGLKYFDDIKTRIPRHEVEQ 353 (455)
Q Consensus 331 ~q~~Glk~~ed~~~~i~r~Ea~~ 353 (455)
+.++|-+..+.|.+-+.-.+..+
T Consensus 525 i~gIG~~~a~si~~~f~~~~~~~ 547 (562)
T PRK08097 525 LPGIGEGRARQLIAFLQHPEVKA 547 (562)
T ss_pred CCCchHHHHHHHHHHHcCHHHHH
Confidence 88999888888777665555444
No 97
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=90.81 E-value=0.28 Score=43.70 Aligned_cols=53 Identities=23% Similarity=0.293 Sum_probs=39.5
Q ss_pred HHhhhccCcCHHHHHHHHHcCCCCHHHhhhccCchhhhhhchhhHhhhccCcCHHH
Q 012847 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIPRHE 350 (455)
Q Consensus 295 ~lf~~I~GvGpktA~~ly~~GirTledL~~~~~L~~~q~~Glk~~ed~~~~i~r~E 350 (455)
.-|+.|-||||+.+..|...||.|+.+|-.. +..--.-+.-|-.|..||-|+.
T Consensus 67 DDLt~I~GIGPk~e~~Ln~~GI~tfaQIAAw---t~~di~~id~~l~f~GRi~RDd 119 (133)
T COG3743 67 DDLTRISGIGPKLEKVLNELGIFTFAQIAAW---TRADIAWIDDYLNFDGRIERDD 119 (133)
T ss_pred ccchhhcccCHHHHHHHHHcCCccHHHHHhc---CHHHHHHHHhhcCCcchhHHHH
Confidence 4567999999999999999999999999742 2222233455666777777764
No 98
>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=90.74 E-value=0.16 Score=51.29 Aligned_cols=29 Identities=38% Similarity=0.597 Sum_probs=26.4
Q ss_pred hhccCcCHHHHHHHHHcCCCCHHHhhhcc
Q 012847 298 GEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (455)
Q Consensus 298 ~~I~GvGpktA~~ly~~GirTledL~~~~ 326 (455)
..+||||++++++|++.||.|++||....
T Consensus 2 ~~i~gig~~~~~~L~~~Gi~ti~dl~~~~ 30 (310)
T TIGR02236 2 EDLPGVGPATAEKLREAGYDTFEAIAVAS 30 (310)
T ss_pred cccCCCCHHHHHHHHHcCCCCHHHHHcCC
Confidence 47899999999999999999999998653
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=90.16 E-value=0.78 Score=46.83 Aligned_cols=63 Identities=19% Similarity=0.242 Sum_probs=41.6
Q ss_pred hhcCCCCCCHHHHHHHHHHH---HhCCc--hhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCH
Q 012847 255 QVKGLPGIGKSMQDHIQEIV---TTGKL--SKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTL 319 (455)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil---~tG~~--~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTl 319 (455)
.|+.+ |+|-+ |+.|.++. ..|.. ..++.|..-....+.+.|++++||||+||.-+-=.|+.-.
T Consensus 177 ~Lr~~-G~g~R-a~~I~~~A~~i~~~~~~~~~l~~l~~~~~~~~~~~L~~l~GIG~~tAd~vll~~l~~~ 244 (310)
T TIGR00588 177 HLRKL-GLGYR-ARYIRETARALLEEQGGRAWLQQIRGASYEDAREALCELPGVGPKVADCICLMGLDKP 244 (310)
T ss_pred HHHHc-CCHHH-HHHHHHHHHHHHhccCCchhHHhhccCChHHHHHHHHhCCCccHHHHHHHHHHhCCCC
Confidence 46655 67766 55554443 34443 3466776555566889999999999999998765555443
No 100
>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=90.04 E-value=0.92 Score=46.55 Aligned_cols=108 Identities=20% Similarity=0.277 Sum_probs=61.6
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhccCchhhhhhch---hhHhhhccCcCHHHHHHHHHHHHHHhhhcCCCeEEEE
Q 012847 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGL---KYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILC 373 (455)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirTledL~~~~~L~~~q~~Gl---k~~ed~~~~i~r~Ea~~i~~~v~~~~~~~~p~~~v~~ 373 (455)
+..+||||++++++|.+.||+|+.||.+-..-.-.++||. .+|+..... .+. .+.
T Consensus 178 l~~l~gig~~~~~~L~~~Gi~ti~dL~~~~~~~L~~rfG~~~~~l~~~a~G~--------------------d~~-~v~- 235 (344)
T cd01700 178 VGDVWGIGRRTAKKLNAMGIHTAGDLAQADPDLLRKKFGVVGERLVRELNGI--------------------DCL-PLE- 235 (344)
T ss_pred hhhcCccCHHHHHHHHHcCCCcHHHHhcCCHHHHHHHHHHHHHHHHHHhCCC--------------------CCC-cCC-
Confidence 3577999999999999999999999986432112234553 222222111 110 010
Q ss_pred ecccccC-CCCCCCccEEE--eCCCc--hhhhhhHHHHHHHHHHcCceeeeecccccCCc
Q 012847 374 GGSYRRG-KASCGDLDVVI--MHPDR--KSHKGFLSKYVKKLKEMKFLREDLIFSTHSEE 428 (455)
Q Consensus 374 ~Gs~RRg-ke~~gDvDiLi--t~~d~--~~~~~~l~~lv~~L~~~g~l~~~L~~~~~~~~ 428 (455)
-++.- |..+....|-- .+.+. .....++..+..+|++.|.....+++..+..+
T Consensus 236 --~~~~~~ks~~~~~~~~~~~~~~~~l~~~l~~L~~~l~~~L~~~~~~~~~l~l~l~~~~ 293 (344)
T cd01700 236 --EYPPPKKSIGSSRSFGRDVTDLDELKQALAEYAERAAEKLRRQKSVARTISVFIGTSG 293 (344)
T ss_pred --CCCCCCcEEEEeeEcCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCcccEEEEEEEcCC
Confidence 12221 22222222211 11111 12456888899999999999999999886544
No 101
>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=89.79 E-value=0.48 Score=39.98 Aligned_cols=48 Identities=10% Similarity=0.252 Sum_probs=38.9
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCc
Q 012847 252 SADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGI 303 (455)
Q Consensus 252 s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~Gv 303 (455)
.+.+|..|||||+++++-...| -+..+++|+...|....+-++.+-|.
T Consensus 10 ~~~~L~~iP~IG~a~a~DL~~L----Gi~s~~~L~g~dP~~Ly~~lc~~~G~ 57 (93)
T PF11731_consen 10 GLSDLTDIPNIGKATAEDLRLL----GIRSPADLKGRDPEELYERLCALTGQ 57 (93)
T ss_pred HHHHHhcCCCccHHHHHHHHHc----CCCCHHHHhCCCHHHHHHHHHHHcCC
Confidence 3578999999999999977655 45677889998998888888777765
No 102
>PRK02794 DNA polymerase IV; Provisional
Probab=89.76 E-value=0.66 Score=49.09 Aligned_cols=112 Identities=22% Similarity=0.316 Sum_probs=61.7
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhccCchhhhhhchhhHhhhccCcCHHHHHHHHHHHHHHhhhcCCCeEEEEecc
Q 012847 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGS 376 (455)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirTledL~~~~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~~v~~~~~~~~p~~~v~~~Gs 376 (455)
+..+||||++++++|.+.||+|+.||.+-..-.-.++||.. + ..+...+.. +.+. .+. .
T Consensus 211 l~~L~GiG~~~~~~L~~~GI~tigdL~~l~~~~L~~rfG~~-------------g---~~l~~~a~G-~d~~-~v~---~ 269 (419)
T PRK02794 211 VGIIWGVGPATAARLARDGIRTIGDLQRADEADLMRRFGSM-------------G---LRLWRLARG-IDDR-KVS---P 269 (419)
T ss_pred hhhhCCCCHHHHHHHHHhccchHHHHhhCCHHHHHHHHhHH-------------H---HHHHHHhCC-CCCC-CCc---c
Confidence 46889999999999999999999999864321122345521 1 111111111 1111 111 1
Q ss_pred cccCCCCCCCccEEE--eCCCc--hhhhhhHHHHHHHHHHcCceeeeecccccCCcc
Q 012847 377 YRRGKASCGDLDVVI--MHPDR--KSHKGFLSKYVKKLKEMKFLREDLIFSTHSEET 429 (455)
Q Consensus 377 ~RRgke~~gDvDiLi--t~~d~--~~~~~~l~~lv~~L~~~g~l~~~L~~~~~~~~~ 429 (455)
.+.-|..+....|-- .+.+. .....++.++..+|++.|+....|++.....++
T Consensus 270 ~~~~ksi~~~~tl~~~~~~~~~l~~~l~~L~~~l~~rL~~~~~~~~~l~l~l~~~~~ 326 (419)
T PRK02794 270 DREAKSVSAETTFETDLSDFEDLEPILWRLSEKVSRRLKAAGLAGRTVTLKLKTADF 326 (419)
T ss_pred CCCCceeeeeEECCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCcceEEEEEEECCC
Confidence 122232222222210 11111 113467888999999999999999888754443
No 103
>PTZ00205 DNA polymerase kappa; Provisional
Probab=89.66 E-value=0.61 Score=51.30 Aligned_cols=123 Identities=11% Similarity=0.057 Sum_probs=66.4
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhccCchhhhhhchhhHhhhccCcCHHHHHHHHHHHHHHhhhcCCCeEEEEecc
Q 012847 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGS 376 (455)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirTledL~~~~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~~v~~~~~~~~p~~~v~~~Gs 376 (455)
+..|||||++++++|-..||.|+.||.... ......||.+.+..+..... ...+...+..++.+-.+... .
T Consensus 311 V~ki~GIG~~t~~~L~~~GI~TigDLa~~~-~~l~~~f~~k~l~~llG~~~-------G~~l~~~a~G~d~~~~v~~~-~ 381 (571)
T PTZ00205 311 LRSVPGVGKVTEALLKGLGITTLSDIYNRR-VELCYILHNNLFRFLLGASI-------GIMQWPDAATAANTENCEGA-T 381 (571)
T ss_pred cceeCCcCHHHHHHHHHcCCCcHHHHhcCC-HHHHHHhHHHHHHHHhCchh-------hHHHHHHhcCCCCCCccCCC-C
Confidence 458999999999999999999999998542 11233456555555554310 00011111111211111100 0
Q ss_pred cccCCCCCCCccEEEeCCCch----hhhhhHHHHHHHHHHcCceeeeecccccCCcc
Q 012847 377 YRRGKASCGDLDVVIMHPDRK----SHKGFLSKYVKKLKEMKFLREDLIFSTHSEET 429 (455)
Q Consensus 377 ~RRgke~~gDvDiLit~~d~~----~~~~~l~~lv~~L~~~g~l~~~L~~~~~~~~~ 429 (455)
.+..|..++..-|=-. .+.. ....+..++..+|++.|++...+++.....+.
T Consensus 382 ~~~rKSIg~ErTF~~~-~d~~el~~~L~~L~~~v~~rLrk~~l~artVtlKlK~~dF 437 (571)
T PTZ00205 382 GGQRKAISSERSFTTP-RTKEGLQEMVDTVFNGAYEEMRKSELMCRQISLTIRWASY 437 (571)
T ss_pred CCCCceeEEeEeCCCC-CCHHHHHHHHHHHHHHHHHHHHhcCCCccEEEEEEEECCC
Confidence 1111333333222100 0111 13457777899999999999998887755443
No 104
>PRK01810 DNA polymerase IV; Validated
Probab=89.60 E-value=0.45 Score=50.03 Aligned_cols=115 Identities=19% Similarity=0.239 Sum_probs=63.0
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhccCchhhhhhchhhHhhhccCcCHHHHHHHHHHHHHHhhhcCCCeEEEEecc
Q 012847 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGS 376 (455)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirTledL~~~~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~~v~~~~~~~~p~~~v~~~Gs 376 (455)
+..+||||++++++|...||+|+.||.....-.-..+||... ..+...+.. +.+.- +.. ..
T Consensus 181 v~~l~giG~~~~~~L~~~Gi~tigdL~~~~~~~L~~rfG~~g----------------~~l~~~a~G-~d~~~-v~~-~~ 241 (407)
T PRK01810 181 VGEMHGIGEKTAEKLKDIGIQTIGDLAKADEHILRAKLGING----------------VRLQRRANG-IDDRP-VDP-EA 241 (407)
T ss_pred HhhcCCcCHHHHHHHHHcCCCcHHHHHhCCHHHHHHHHhHHH----------------HHHHHHhcC-CCCCC-CCC-CC
Confidence 357899999999999999999999998643212223455321 111111111 11110 100 00
Q ss_pred cccCCCCCCCccEE--EeCCCc--hhhhhhHHHHHHHHHHcCceeeeecccccCCcch
Q 012847 377 YRRGKASCGDLDVV--IMHPDR--KSHKGFLSKYVKKLKEMKFLREDLIFSTHSEETV 430 (455)
Q Consensus 377 ~RRgke~~gDvDiL--it~~d~--~~~~~~l~~lv~~L~~~g~l~~~L~~~~~~~~~~ 430 (455)
...-|..+.-..|- +++.+. .....++..+..+|++.+.....+.+..+..++.
T Consensus 242 ~~~~ksi~~~~~~~~~~~~~~~l~~~l~~L~~~l~~rLr~~~~~~~~l~l~lr~~~~~ 299 (407)
T PRK01810 242 IYQFKSVGNSTTLSHDMDEEKELLDVLRRLSKSVSKRLQKKTVVSYNVQIMIRYHDRR 299 (407)
T ss_pred CCCCceecceEECCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCccceeEEEEEECCCC
Confidence 00012222222221 111111 1245688889999999999999998888655543
No 105
>PRK03103 DNA polymerase IV; Reviewed
Probab=89.46 E-value=0.66 Score=48.82 Aligned_cols=110 Identities=14% Similarity=0.169 Sum_probs=61.6
Q ss_pred hhccCcCHHHHHHHHHcCCCCHHHhhhccCchhhhhhch---hhHhhhccCcCHHHHHHHHHHHHHHhhhcCCCeEEEEe
Q 012847 298 GEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGL---KYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCG 374 (455)
Q Consensus 298 ~~I~GvGpktA~~ly~~GirTledL~~~~~L~~~q~~Gl---k~~ed~~~~i~r~Ea~~i~~~v~~~~~~~~p~~~v~~~ 374 (455)
..+||||++++++|.+.||+|+.||.+-..-.-..+||. ..|+.... +.+.- +...
T Consensus 184 ~~l~gig~~~~~~L~~~Gi~tigdl~~~~~~~L~~~fG~~~~~l~~~a~G--------------------~d~~~-v~~~ 242 (409)
T PRK03103 184 RKLFGVGSRMEKHLRRMGIRTIGQLANTPLERLKKRWGINGEVLWRTANG--------------------IDYSP-VTPH 242 (409)
T ss_pred hhcCCccHHHHHHHHHcCCCCHHHHhcCCHHHHHHHHCHHHHHHHHHhcC--------------------CCCCc-CCcc
Confidence 577999999999999899999999986432222334553 22222221 11110 1000
Q ss_pred cccccCCCCCCCccEEEeCCCch----hhhhhHHHHHHHHHHcCceeeeecccccCCcc
Q 012847 375 GSYRRGKASCGDLDVVIMHPDRK----SHKGFLSKYVKKLKEMKFLREDLIFSTHSEET 429 (455)
Q Consensus 375 Gs~RRgke~~gDvDiLit~~d~~----~~~~~l~~lv~~L~~~g~l~~~L~~~~~~~~~ 429 (455)
..-..|..+..+.|-..-.+.. ....++..+..+|++.+.....+++..+..++
T Consensus 243 -~~~~~ksi~~~~t~~~~~~~~~~l~~~l~~L~~~l~~rLr~~~~~~~~l~l~lr~~~~ 300 (409)
T PRK03103 243 -SLDRQKAIGHQMTLPRDYRGFEEIKVVLLELCEEVCRRARAKGYMGRTVSVSLRGADF 300 (409)
T ss_pred -cCCCCCccCCCeECCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCceeEEEEEEEeCCC
Confidence 0000133333333311111111 24467788889999999999998887765543
No 106
>PRK03352 DNA polymerase IV; Validated
Probab=89.32 E-value=0.35 Score=49.68 Aligned_cols=40 Identities=33% Similarity=0.595 Sum_probs=30.6
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhccCchhhhhhch
Q 012847 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGL 336 (455)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirTledL~~~~~L~~~q~~Gl 336 (455)
+..+||||++++++|...||+|+.||..-..-.-.++||.
T Consensus 179 l~~l~gig~~~~~~L~~~Gi~ti~dl~~l~~~~L~~~fG~ 218 (346)
T PRK03352 179 TDALWGVGPKTAKRLAALGITTVADLAAADPAELAATFGP 218 (346)
T ss_pred HHHcCCCCHHHHHHHHHcCCccHHHHhcCCHHHHHHHhCh
Confidence 3578999999999999999999999986432222344554
No 107
>PRK14133 DNA polymerase IV; Provisional
Probab=88.93 E-value=0.55 Score=48.31 Aligned_cols=109 Identities=17% Similarity=0.225 Sum_probs=62.1
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhccCchhhhhhc---hhhHhhhccCcCHHHHHHHHHHHHHHhhhcCCCeEEEE
Q 012847 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLG---LKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILC 373 (455)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirTledL~~~~~L~~~q~~G---lk~~ed~~~~i~r~Ea~~i~~~v~~~~~~~~p~~~v~~ 373 (455)
+..+||||++++++|.+.||+|+.||.+-..-.-..+|| ...|+.....-+ .- +.
T Consensus 175 v~~l~gig~~~~~~L~~~Gi~ti~dl~~l~~~~L~~rfG~~g~~l~~~a~G~d~--------------------~~-v~- 232 (347)
T PRK14133 175 ISKVHGIGKKSVEKLNNIGIYTIEDLLKLSREFLIEYFGKFGVEIYERIRGIDY--------------------RE-VE- 232 (347)
T ss_pred ccccCCCCHHHHHHHHHcCCccHHHHhhCCHHHHHHHHhHHHHHHHHHhCCCCC--------------------CC-CC-
Confidence 357899999999999999999999998643211223354 333332222111 00 00
Q ss_pred ecccccCCCCCCCccEE--EeCCCc--hhhhhhHHHHHHHHHHcCceeeeecccccCCcc
Q 012847 374 GGSYRRGKASCGDLDVV--IMHPDR--KSHKGFLSKYVKKLKEMKFLREDLIFSTHSEET 429 (455)
Q Consensus 374 ~Gs~RRgke~~gDvDiL--it~~d~--~~~~~~l~~lv~~L~~~g~l~~~L~~~~~~~~~ 429 (455)
.++.-|..+....|- +++.+. .....++..+..+|++.|.....+.+..+..++
T Consensus 233 --~~~~~ksi~~~~~~~~~~~~~~~l~~~l~~L~~~l~~rL~~~~~~~~~l~l~l~~~~~ 290 (347)
T PRK14133 233 --VSRERKSIGKETTLKKDTKDKEELKKYLKDFSNIISEELKKRNLYGKTVTVKIKTSDF 290 (347)
T ss_pred --CCCCCcceEeeEEcCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCcceEEEEEEECCC
Confidence 011112222222221 111111 114567888999999999999999988764443
No 108
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=88.79 E-value=0.66 Score=48.05 Aligned_cols=89 Identities=24% Similarity=0.310 Sum_probs=52.6
Q ss_pred HHHHHHHHHHHH--HHcCCC--hhHHHHHHHHHHHhcCCccccc--hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHH
Q 012847 213 ITEIFGKLINIY--RALGED--RRSFSYYKAIPVIEKLPFKIES--ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFE 286 (455)
Q Consensus 213 ia~~L~~la~~~--e~~g~~--~r~~aY~rAa~~L~~l~~~i~s--~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~ 286 (455)
..++++.|.++- ++.... .|++.|... ...++.+|.. +.=|.++|+||+.+|+.+-+ +-|+++.+ .
T Consensus 243 ~~~~~~~l~~l~~~~lld~~~ia~~lGy~~~---~~~ld~~v~prGyRiLs~IPrl~k~iAk~Ll~--~FGSL~~I---l 314 (352)
T PRK13482 243 PEEILEELQELSSEELLDLSAIARLLGYPGG---SEALDTPVSPRGYRLLSKIPRLPSAVIENLVE--HFGSLQGL---L 314 (352)
T ss_pred HHHHHHHHHhCCHHHhcCHHHHHHHhCCCCC---CcccccccCCcHHHHHhcCCCCCHHHHHHHHH--HcCCHHHH---H
Confidence 445555555442 222222 255555322 1234444544 34689999999999988754 34555544 3
Q ss_pred hhchhHHHHHhhhccCcCHHHHHHHHH
Q 012847 287 KDEKVRTISLFGEVWGIGPATAQKLYE 313 (455)
Q Consensus 287 ~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (455)
+. ..+.|.+|+|||+++|+.+++
T Consensus 315 ~A----s~eeL~~VeGIGe~rA~~I~e 337 (352)
T PRK13482 315 AA----SIEDLDEVEGIGEVRARAIRE 337 (352)
T ss_pred cC----CHHHHhhCCCcCHHHHHHHHH
Confidence 21 234577999999999999654
No 109
>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=88.79 E-value=1.2 Score=45.20 Aligned_cols=108 Identities=17% Similarity=0.210 Sum_probs=61.0
Q ss_pred hhccCcCHHHHHHHHHcCCCCHHHhhhccCchhhhhhc---hhhHhhhccCcCHHHHHHHHHHHHHHhhhcCCCeEEEEe
Q 012847 298 GEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLG---LKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCG 374 (455)
Q Consensus 298 ~~I~GvGpktA~~ly~~GirTledL~~~~~L~~~q~~G---lk~~ed~~~~i~r~Ea~~i~~~v~~~~~~~~p~~~v~~~ 374 (455)
..+||||.+++++|...||+|+.||.+...-.-.+.|| .+.++.....-+ ..+.
T Consensus 174 ~~l~gig~~~~~~L~~~Gi~ti~dl~~~~~~~L~~~~g~~~~~l~~~~~G~~~-------------------~~v~---- 230 (334)
T cd03586 174 RKIPGVGKVTAEKLKELGIKTIGDLAKLDVELLKKLFGKSGRRLYELARGIDN-------------------RPVE---- 230 (334)
T ss_pred hhhCCcCHHHHHHHHHcCCcCHHHHHcCCHHHHHHHHhHHHHHHHHHhCCCCC-------------------CCCC----
Confidence 57899999999999999999999998543111111233 222222221111 0010
Q ss_pred cccccCCCCCCCccEE--EeCCCc--hhhhhhHHHHHHHHHHcCceeeeecccccCCcc
Q 012847 375 GSYRRGKASCGDLDVV--IMHPDR--KSHKGFLSKYVKKLKEMKFLREDLIFSTHSEET 429 (455)
Q Consensus 375 Gs~RRgke~~gDvDiL--it~~d~--~~~~~~l~~lv~~L~~~g~l~~~L~~~~~~~~~ 429 (455)
.++.-|..+....|- +.+.+. .....++..+..+|+..|.....|.+..+..++
T Consensus 231 -~~~~~ks~~~~~~~~~~~~~~~~l~~~l~~l~~~l~~rL~~~~~~~~~l~l~l~~~~~ 288 (334)
T cd03586 231 -PDRERKSIGVERTFSEDLTDPEELLEELLELAEELAERLRKRGLKGRTVTVKLKYADF 288 (334)
T ss_pred -CCCCCCeeeeeEECCCCCCCHHHHHHHHHHHHHHHHHHHHhCCCCeEEEEEEEEECCC
Confidence 111112222222211 111111 124568899999999999999999998865554
No 110
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=88.52 E-value=0.79 Score=38.36 Aligned_cols=54 Identities=28% Similarity=0.553 Sum_probs=41.9
Q ss_pred HHHHHhhhccCcCHHHHHHHHHc-CCCCHHHhhhcc-Cchh-hhhhchhhHhhhccCc
Q 012847 292 RTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED-SLTH-SQRLGLKYFDDIKTRI 346 (455)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~-GirTledL~~~~-~L~~-~q~~Glk~~ed~~~~i 346 (455)
.++..| .=+|++++.|.++|+. |-.+++-|+++. .|.. ..++|++..+.|..++
T Consensus 10 ~~~~~L-~~~gl~~~~a~kl~~~yg~~ai~~l~~nPY~L~~~i~gi~F~~aD~iA~~~ 66 (94)
T PF14490_consen 10 ELMAFL-QEYGLSPKLAMKLYKKYGDDAIEILKENPYRLIEDIDGIGFKTADKIALKL 66 (94)
T ss_dssp HHHHHH-HHTT--HHHHHHHHHHH-TTHHHHHHH-STCCCB-SSSSBHHHHHHHHHTT
T ss_pred HHHHHH-HHcCCCHHHHHHHHHHHhHHHHHHHHHChHHHHHHccCCCHHHHHHHHHHc
Confidence 456666 8899999999999998 999999998765 5554 8899999999998765
No 111
>PRK01216 DNA polymerase IV; Validated
Probab=88.32 E-value=0.43 Score=49.48 Aligned_cols=30 Identities=33% Similarity=0.407 Sum_probs=26.5
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhcc
Q 012847 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (455)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirTledL~~~~ 326 (455)
+..+||||++++++|.+.||+|+.||.+..
T Consensus 180 i~~l~giG~~~~~~L~~~Gi~TigdL~~~~ 209 (351)
T PRK01216 180 IADIPGIGDITAEKLKKLGVNKLVDTLRIE 209 (351)
T ss_pred cccccCCCHHHHHHHHHcCCCcHHHHhcCC
Confidence 357899999999999999999999998643
No 112
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=88.15 E-value=0.33 Score=33.70 Aligned_cols=16 Identities=56% Similarity=0.742 Sum_probs=14.3
Q ss_pred hccCcCHHHHHHHHHc
Q 012847 299 EVWGIGPATAQKLYEK 314 (455)
Q Consensus 299 ~I~GvGpktA~~ly~~ 314 (455)
.|+|||+|||.+|.++
T Consensus 20 Gv~giG~ktA~~ll~~ 35 (36)
T smart00279 20 GVKGIGPKTALKLLRE 35 (36)
T ss_pred CCCcccHHHHHHHHHh
Confidence 8999999999999763
No 113
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=88.11 E-value=1 Score=49.78 Aligned_cols=52 Identities=17% Similarity=0.157 Sum_probs=38.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 314 (455)
..|.+|||||++...++-+ .-|++ +.+++ -.++.+.+|+|+|.+.|+++|+.
T Consensus 514 s~L~~I~GiG~kr~~~LL~--~Fgs~---~~I~~----As~eeL~~v~gi~~~~A~~I~~~ 565 (574)
T PRK14670 514 LNYTKIKGIGEKKAKKILK--SLGTY---KDILL----LNEDEIAEKMKINIKMAKKIKKF 565 (574)
T ss_pred cccccCCCCCHHHHHHHHH--HhCCH---HHHHh----CCHHHHHhCCCCCHHHHHHHHHH
Confidence 3789999999998877643 23444 44443 24566679999999999999873
No 114
>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=87.59 E-value=0.47 Score=38.20 Aligned_cols=27 Identities=41% Similarity=0.548 Sum_probs=22.5
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhh
Q 012847 297 FGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (455)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirTledL~~ 324 (455)
+.+|+|||+|||.+|..+ +.|++.+..
T Consensus 24 i~gv~giG~k~A~~ll~~-~~~~~~~~~ 50 (75)
T cd00080 24 IPGVPGIGPKTALKLLKE-YGSLENLLE 50 (75)
T ss_pred CCCCCcccHHHHHHHHHH-hCCHHHHHH
Confidence 347999999999999986 558888875
No 115
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=87.00 E-value=0.72 Score=45.08 Aligned_cols=50 Identities=22% Similarity=0.430 Sum_probs=36.2
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012847 255 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (455)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (455)
-|..||||+|.=|..+- . ++.-|+.+-+ .....|.+|+|+||.+|+++|+
T Consensus 196 ~Lt~i~~VnKtda~~LL---~--~FgsLq~~~~----AS~~ele~~~G~G~~kak~l~~ 245 (254)
T KOG2841|consen 196 FLTTIPGVNKTDAQLLL---Q--KFGSLQQISN----ASEGELEQCPGLGPAKAKRLHK 245 (254)
T ss_pred HHHhCCCCCcccHHHHH---H--hcccHHHHHh----cCHhHHHhCcCcCHHHHHHHHH
Confidence 47899999998777553 2 3444444432 2455677999999999999997
No 116
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=86.77 E-value=0.59 Score=49.50 Aligned_cols=30 Identities=37% Similarity=0.653 Sum_probs=26.7
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhcc
Q 012847 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (455)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirTledL~~~~ 326 (455)
+..+||||++++++|.+.||+|+.||.+..
T Consensus 181 v~~l~GiG~~~~~~L~~lGi~TigdL~~~~ 210 (422)
T PRK03609 181 VEEVWGVGRRISKKLNAMGIKTALDLADTN 210 (422)
T ss_pred hhhcCCccHHHHHHHHHcCCCcHHHHhcCC
Confidence 358999999999999999999999998643
No 117
>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=86.73 E-value=2.8 Score=37.06 Aligned_cols=46 Identities=33% Similarity=0.494 Sum_probs=33.4
Q ss_pred CeEEEEecccccCCCCC--CCccEEEeCCCc-----hhhhhhHHHHHHHHHHc
Q 012847 368 EVIILCGGSYRRGKASC--GDLDVVIMHPDR-----KSHKGFLSKYVKKLKEM 413 (455)
Q Consensus 368 ~~~v~~~Gs~RRgke~~--gDvDiLit~~d~-----~~~~~~l~~lv~~L~~~ 413 (455)
...+.+.|||.||...- .|||++|..+.. .....++..|-+.|++.
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 899999965433 23456777777777764
No 118
>PRK08609 hypothetical protein; Provisional
Probab=86.21 E-value=0.88 Score=50.31 Aligned_cols=56 Identities=20% Similarity=0.259 Sum_probs=38.8
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012847 252 SADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (455)
Q Consensus 252 s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (455)
.+.++.+|||||++.+.++.+-+---++.+|+....+-+ +..++|+|+|+.+.+-+
T Consensus 86 ~~~~l~~i~GiGpk~a~~l~~~lGi~tl~~L~~a~~~~~------~~~~~gfg~k~~~~il~ 141 (570)
T PRK08609 86 GLLPLLKLPGLGGKKIAKLYKELGVVDKESLKEACENGK------VQALAGFGKKTEEKILE 141 (570)
T ss_pred HHHHHhcCCCCCHHHHHHHHHHhCCCCHHHHHHHHHhCC------hhhccCcchhHHHHHHH
Confidence 356789999999999998876554444555543322111 34889999999998843
No 119
>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=86.04 E-value=3.1 Score=39.25 Aligned_cols=25 Identities=16% Similarity=0.167 Sum_probs=20.4
Q ss_pred HHHHHhhhccCcCHHHHHHHHHcCC
Q 012847 292 RTISLFGEVWGIGPATAQKLYEKGH 316 (455)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~Gi 316 (455)
..++.|++++|||++||..+--.++
T Consensus 103 ~~~~~L~~l~GIG~ktA~~ill~~~ 127 (191)
T TIGR01083 103 EDREELVKLPGVGRKTANVVLNVAF 127 (191)
T ss_pred hHHHHHHhCCCCcHHHHHHHHHHHc
Confidence 3577788999999999999876544
No 120
>PRK10880 adenine DNA glycosylase; Provisional
Probab=85.94 E-value=3.2 Score=43.22 Aligned_cols=65 Identities=20% Similarity=0.289 Sum_probs=43.0
Q ss_pred hHHHHHHHHHHHh-cCCccc-cchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCc
Q 012847 232 RSFSYYKAIPVIE-KLPFKI-ESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGI 303 (455)
Q Consensus 232 r~~aY~rAa~~L~-~l~~~i-~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~Gv 303 (455)
|++...+||..|. .+...+ .+.++|.+|||||..+|+.|--|- -|...-+ ...-+.+.+.+++|+
T Consensus 85 RAr~L~~~A~~i~~~~~g~~p~~~~~L~~LpGIG~~TA~aIl~~a-f~~~~~i------VD~nV~RV~~Rl~~i 151 (350)
T PRK10880 85 RARNLHKAAQQVATLHGGEFPETFEEVAALPGVGRSTAGAILSLS-LGKHFPI------LDGNVKRVLARCYAV 151 (350)
T ss_pred HHHHHHHHHHHHHHHhCCCchhhHHHHhcCCCccHHHHHHHHHHH-CCCCeec------ccHHHHHHHHHHhcc
Confidence 8888888988883 333222 456899999999999999998664 3331111 123366666666655
No 121
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=85.90 E-value=0.42 Score=53.60 Aligned_cols=49 Identities=29% Similarity=0.447 Sum_probs=37.2
Q ss_pred HHHhhhccCcCHHHHHHHHHc-CCCCHHHhhhcc--CchhhhhhchhhHhhhcc
Q 012847 294 ISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED--SLTHSQRLGLKYFDDIKT 344 (455)
Q Consensus 294 l~lf~~I~GvGpktA~~ly~~-GirTledL~~~~--~L~~~q~~Glk~~ed~~~ 344 (455)
-..|..|+||||+++++|++. | |+++|.++. .|....++|.+..+.|.+
T Consensus 636 ~s~L~~IPGIGpkr~k~LL~~FG--Sle~I~~AS~eELa~V~Gig~k~Ae~I~~ 687 (694)
T PRK14666 636 TGELQRVEGIGPATARLLWERFG--SLQAMAAAGEEGLAAVPGIGPARAAALHE 687 (694)
T ss_pred HhHHhhCCCCCHHHHHHHHHHhC--CHHHHHhcCHHHHHhcCCcCHHHHHHHHH
Confidence 345669999999999999997 6 999999753 366666777766555543
No 122
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=85.75 E-value=1.7 Score=43.85 Aligned_cols=64 Identities=19% Similarity=0.224 Sum_probs=40.0
Q ss_pred hhhcCCCCCCHHHHHHHHHH---HHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHH
Q 012847 254 DQVKGLPGIGKSMQDHIQEI---VTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDD 321 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Ei---l~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTled 321 (455)
++|..+ |++..=++.|.++ +..|.+.. +... ....+++.|++|+||||+||..+--.|+.-.|-
T Consensus 167 ~eL~~~-Gl~~~Ra~~L~~lA~~i~~g~l~l-~~~~--~~~~~~~~L~~LpGIGpwTA~~vllr~lg~~D~ 233 (283)
T PRK10308 167 QALKAL-GMPLKRAEALIHLANAALEGTLPL-TIPG--DVEQAMKTLQTFPGIGRWTANYFALRGWQAKDV 233 (283)
T ss_pred HHHHHC-CCCHHHHHHHHHHHHHHHcCCCCc-cccC--CHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCC
Confidence 466666 7876444444444 34577653 2111 224577888899999999999876555544433
No 123
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=85.55 E-value=0.35 Score=53.17 Aligned_cols=64 Identities=17% Similarity=0.201 Sum_probs=48.5
Q ss_pred hhccCcCHHHHHHHHHcC-CCCHHHhhh--ccCchhhhhhchhhHhhhccCcCHHHHHHHHHHHHHH
Q 012847 298 GEVWGIGPATAQKLYEKG-HRTLDDLKN--EDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKA 361 (455)
Q Consensus 298 ~~I~GvGpktA~~ly~~G-irTledL~~--~~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~~v~~~ 361 (455)
++|-|+|++++.+|++.| ++++.||-+ ...|..+.+||-|..+.+...|-...-..+..++-.+
T Consensus 428 mdI~GlGe~~i~~L~~~G~i~~~~Diy~L~~~~l~~l~gfgeks~~nll~aIe~sk~~~l~r~l~aL 494 (562)
T PRK08097 428 LGLDGIGEGTWRALHQTGLFEHLFSWLALTPEQLANTPGIGKARAEQLWHQFNLARQQPFSRWLKAL 494 (562)
T ss_pred cCCCCcCHHHHHHHHHcCCcCCHHHHhcCCHHHHhcCcCccHHHHHHHHHHHHHHcCCCHHHHHHHc
Confidence 489999999999999997 599999974 3457777899999999987666444433345555443
No 124
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=85.52 E-value=3.6 Score=41.61 Aligned_cols=47 Identities=21% Similarity=0.275 Sum_probs=33.9
Q ss_pred HHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCC
Q 012847 270 IQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHR 317 (455)
Q Consensus 270 I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~Gir 317 (455)
|.+.+..|.+.. ..+..-....+++.|++|+||||+||+.+--.|..
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 455556786433 34555556779999999999999999988754443
No 125
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=85.42 E-value=0.73 Score=29.32 Aligned_cols=20 Identities=30% Similarity=0.573 Sum_probs=17.2
Q ss_pred hhcCCCCCCHHHHHHHHHHH
Q 012847 255 QVKGLPGIGKSMQDHIQEIV 274 (455)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil 274 (455)
+|.+|||||+++|+.|.++.
T Consensus 2 ~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred hhhhCCCCCHHHHHHHHHhc
Confidence 57899999999999988643
No 126
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=85.40 E-value=0.6 Score=44.43 Aligned_cols=31 Identities=29% Similarity=0.468 Sum_probs=23.1
Q ss_pred HHHHHhhhccCcCHHHHHHHHHc-CCCCHHHh
Q 012847 292 RTISLFGEVWGIGPATAQKLYEK-GHRTLDDL 322 (455)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~-GirTledL 322 (455)
+.++.|.++||||||+|++|--. --+.-+++
T Consensus 9 ~LI~~l~kLPGvG~KsA~R~AfhLL~~~~~~~ 40 (198)
T COG0353 9 KLIDALKKLPGVGPKSAQRLAFHLLQRDREDV 40 (198)
T ss_pred HHHHHHhhCCCCChhHHHHHHHHHHccCHHHH
Confidence 47888999999999999999643 33443333
No 127
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=84.99 E-value=1.3 Score=43.89 Aligned_cols=55 Identities=22% Similarity=0.348 Sum_probs=42.5
Q ss_pred hchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhhhchhhHhhhc
Q 012847 288 DEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIK 343 (455)
Q Consensus 288 ~~~~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~q~~Glk~~ed~~ 343 (455)
+....-+.++.++||||++.|+++.+ -+.|++++.++. .|....++|.+....|.
T Consensus 175 t~~e~q~~il~s~pgig~~~a~~ll~-~fgS~~~~~tas~~eL~~v~gig~k~A~~I~ 231 (254)
T COG1948 175 TLKELQLYILESIPGIGPKLAERLLK-KFGSVEDVLTASEEELMKVKGIGEKKAREIY 231 (254)
T ss_pred chHHHHHHHHHcCCCccHHHHHHHHH-HhcCHHHHhhcCHHHHHHhcCccHHHHHHHH
Confidence 34455677888999999999999998 466889988764 57888888877755443
No 128
>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=84.98 E-value=0.81 Score=48.01 Aligned_cols=30 Identities=33% Similarity=0.431 Sum_probs=26.7
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhcc
Q 012847 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (455)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirTledL~~~~ 326 (455)
+..+||||++++++|.+.||.|+.||....
T Consensus 174 v~~l~GiG~~~~~kL~~~GI~tigdl~~~~ 203 (379)
T cd01703 174 LRKIPGIGYKTAAKLEAHGISSVRDLQEFS 203 (379)
T ss_pred ccccCCcCHHHHHHHHHcCCCcHHHHHhCC
Confidence 458899999999999999999999998543
No 129
>PRK07758 hypothetical protein; Provisional
Probab=84.92 E-value=0.49 Score=39.94 Aligned_cols=45 Identities=13% Similarity=0.280 Sum_probs=38.0
Q ss_pred ccCcCHHHHHHHHHcCCCCHHHhhh--ccCchhhhhhchhhHhhhcc
Q 012847 300 VWGIGPATAQKLYEKGHRTLDDLKN--EDSLTHSQRLGLKYFDDIKT 344 (455)
Q Consensus 300 I~GvGpktA~~ly~~GirTledL~~--~~~L~~~q~~Glk~~ed~~~ 344 (455)
.++++......|...||.||+||.. ...|..+.+||-+..++|.+
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 4688999999999999999999984 35688899999998877654
No 130
>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=84.79 E-value=0.08 Score=45.31 Aligned_cols=25 Identities=44% Similarity=0.735 Sum_probs=19.9
Q ss_pred hccCcCHHHHHHHHHc-CCCCHHHhhhc
Q 012847 299 EVWGIGPATAQKLYEK-GHRTLDDLKNE 325 (455)
Q Consensus 299 ~I~GvGpktA~~ly~~-GirTledL~~~ 325 (455)
+|+|||+|||.+|.++ | |||.+...
T Consensus 22 GV~GIG~KtA~~LL~~yg--sle~i~~~ 47 (101)
T PF01367_consen 22 GVPGIGPKTAAKLLQEYG--SLENILAN 47 (101)
T ss_dssp --TTSTCHCCCCCHHHHT--SCHCCCCC
T ss_pred CCCCCCHHHHHHHHHHcC--CHHHHHHh
Confidence 7999999999999997 6 88888753
No 131
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=84.62 E-value=0.57 Score=44.97 Aligned_cols=51 Identities=24% Similarity=0.311 Sum_probs=36.9
Q ss_pred HHHHHhhhccCcCHHHHHHHHHc-CCCCHHHhhhc---cCchhhhhhchhhHhhh
Q 012847 292 RTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNE---DSLTHSQRLGLKYFDDI 342 (455)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~-GirTledL~~~---~~L~~~q~~Glk~~ed~ 342 (455)
..+..|.+|-|||||+|-.+..- ....|-+.... ..|++.+++|-|..+.|
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 47777789999999999999874 44444443322 25889999999886554
No 132
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=84.46 E-value=1.8 Score=47.75 Aligned_cols=51 Identities=24% Similarity=0.330 Sum_probs=37.4
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 314 (455)
..|.+|||||++...++-. .-|++ +.+++ -.++.+.+| |||+++|+++|+.
T Consensus 514 S~Ld~I~GiG~kr~~~Ll~--~Fgs~---~~ik~----As~eeL~~v-gi~~~~A~~I~~~ 564 (567)
T PRK14667 514 DILDKIKGIGEVKKEIIYR--NFKTL---YDFLK----ADDEELKKL-GIPPSVKQEVKKY 564 (567)
T ss_pred CccccCCCCCHHHHHHHHH--HhCCH---HHHHh----CCHHHHHHc-CCCHHHHHHHHHH
Confidence 5688999999998887644 23444 44443 245566799 9999999999873
No 133
>COG1708 Predicted nucleotidyltransferases [General function prediction only]
Probab=84.27 E-value=4.5 Score=34.28 Aligned_cols=29 Identities=31% Similarity=0.568 Sum_probs=24.1
Q ss_pred CCeEEEEecccccCCCCC-CCccEEEeCCC
Q 012847 367 PEVIILCGGSYRRGKASC-GDLDVVIMHPD 395 (455)
Q Consensus 367 p~~~v~~~Gs~RRgke~~-gDvDiLit~~d 395 (455)
....|.+-|||=||..+- +|||++|..++
T Consensus 25 ~~~~v~LfGS~arG~~~~~SDiDv~vv~~~ 54 (128)
T COG1708 25 GDLLIYLFGSYARGDFVKESDIDLLVVSDD 54 (128)
T ss_pred CCeEEEEEccCcccccccCCCeeEEEEcCC
Confidence 344899999999999876 99999998643
No 134
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=83.89 E-value=1.8 Score=48.73 Aligned_cols=51 Identities=29% Similarity=0.386 Sum_probs=37.9
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (455)
..|..|||||++.+.++.+- -|++ +.+++. ..+.+.+|+|+|+++|+++++
T Consensus 637 s~L~~IPGIGpkr~k~LL~~--FGSl---e~I~~A----S~eELa~V~Gig~k~Ae~I~~ 687 (694)
T PRK14666 637 GELQRVEGIGPATARLLWER--FGSL---QAMAAA----GEEGLAAVPGIGPARAAALHE 687 (694)
T ss_pred hHHhhCCCCCHHHHHHHHHH--hCCH---HHHHhc----CHHHHHhcCCcCHHHHHHHHH
Confidence 57999999999999887653 3544 444442 233356899999999999987
No 135
>PRK09482 flap endonuclease-like protein; Provisional
Probab=83.59 E-value=0.81 Score=45.54 Aligned_cols=25 Identities=32% Similarity=0.613 Sum_probs=22.0
Q ss_pred hccCcCHHHHHHHHHc-CCCCHHHhhhc
Q 012847 299 EVWGIGPATAQKLYEK-GHRTLDDLKNE 325 (455)
Q Consensus 299 ~I~GvGpktA~~ly~~-GirTledL~~~ 325 (455)
+|+|||||||.+|.++ | |+|.+.+.
T Consensus 186 GVpGIG~KtA~~LL~~~g--sle~i~~~ 211 (256)
T PRK09482 186 GVAGIGPKSAAELLNQFR--SLENIYES 211 (256)
T ss_pred CCCCcChHHHHHHHHHhC--CHHHHHHh
Confidence 6899999999999997 6 99998753
No 136
>PRK10702 endonuclease III; Provisional
Probab=83.50 E-value=1.1 Score=43.19 Aligned_cols=25 Identities=16% Similarity=0.242 Sum_probs=19.0
Q ss_pred HHHHHhhhccCcCHHHHHHHHHcCC
Q 012847 292 RTISLFGEVWGIGPATAQKLYEKGH 316 (455)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~Gi 316 (455)
..++.|+++||||+|||.-+---++
T Consensus 106 ~~~~~Ll~lpGVG~ktA~~ill~a~ 130 (211)
T PRK10702 106 EDRAALEALPGVGRKTANVVLNTAF 130 (211)
T ss_pred chHHHHhcCCcccHHHHHHHHHHHc
Confidence 4677777999999999998754433
No 137
>smart00475 53EXOc 5'-3' exonuclease.
Probab=83.39 E-value=0.84 Score=45.43 Aligned_cols=26 Identities=38% Similarity=0.592 Sum_probs=22.1
Q ss_pred hhccCcCHHHHHHHHHc-CCCCHHHhhhc
Q 012847 298 GEVWGIGPATAQKLYEK-GHRTLDDLKNE 325 (455)
Q Consensus 298 ~~I~GvGpktA~~ly~~-GirTledL~~~ 325 (455)
-+|+|||||||.+|.++ | |+|.+.+.
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 36899999999999986 6 99998753
No 138
>PRK00227 glnD PII uridylyl-transferase; Provisional
Probab=83.34 E-value=3.3 Score=46.87 Aligned_cols=65 Identities=22% Similarity=0.311 Sum_probs=46.0
Q ss_pred HHHHHH-HHHHHHHHhhhcCCCeEEEEecccccCC-CCCCCccEEEeCCCchhhhhhHHHHHHHHHHcCc
Q 012847 348 RHEVEQ-MERLLQKAGEEVLPEVIILCGGSYRRGK-ASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKF 415 (455)
Q Consensus 348 r~Ea~~-i~~~v~~~~~~~~p~~~v~~~Gs~RRgk-e~~gDvDiLit~~d~~~~~~~l~~lv~~L~~~g~ 415 (455)
|.+|.+ ...+++.+. +.+++-+..+|||=||. .--.|||+||-|+++. ...++..++.-|=+.|+
T Consensus 8 ~~~~~~~~~~~~~~~~--~~~~~aLvAvGGYGR~EL~P~SDIDLLiL~~~~~-~~~~i~~~~~~LWD~gL 74 (693)
T PRK00227 8 REDAEASALALLGSLQ--LPPGTALAATGSLARREMTPYSDLDLILLHPPGA-TPDGVEDLWYPIWDAKK 74 (693)
T ss_pred HHHHHHHHHHHHHhcC--CCCCeEEEEeccccccCcCCCcCceEEEEeCCcc-cHHHHHHHHHHHHhcCC
Confidence 445554 355555543 33566788899997765 4567999999998543 36778888888888887
No 139
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=83.26 E-value=2.3 Score=47.37 Aligned_cols=52 Identities=23% Similarity=0.454 Sum_probs=38.3
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 314 (455)
..|.+|||||+..+.+|.+. -|++. .+... ..+.+.+|+|||+++|+.+++.
T Consensus 543 s~L~~IpGIG~k~~k~Ll~~--FgS~~---~i~~A----s~eeL~~v~Gig~~~A~~I~~~ 594 (598)
T PRK00558 543 SALDDIPGIGPKRRKALLKH--FGSLK---AIKEA----SVEELAKVPGISKKLAEAIYEA 594 (598)
T ss_pred hhHhhCCCcCHHHHHHHHHH--cCCHH---HHHhC----CHHHHhhcCCcCHHHHHHHHHH
Confidence 56899999999999987663 35544 44432 2234579999999999999863
No 140
>PRK14976 5'-3' exonuclease; Provisional
Probab=82.86 E-value=0.88 Score=45.84 Aligned_cols=25 Identities=40% Similarity=0.593 Sum_probs=21.4
Q ss_pred hccCcCHHHHHHHHHcCCCCHHHhhh
Q 012847 299 EVWGIGPATAQKLYEKGHRTLDDLKN 324 (455)
Q Consensus 299 ~I~GvGpktA~~ly~~GirTledL~~ 324 (455)
+|+|||||||.+|.++ +.|+|++.+
T Consensus 195 GVpGIG~KtA~~LL~~-~gsle~i~~ 219 (281)
T PRK14976 195 GVKGIGPKTAIKLLNK-YGNIENIYE 219 (281)
T ss_pred CCCcccHHHHHHHHHH-cCCHHHHHH
Confidence 5899999999999985 339999875
No 141
>TIGR03671 cca_archaeal CCA-adding enzyme.
Probab=82.68 E-value=4.2 Score=43.14 Aligned_cols=45 Identities=27% Similarity=0.402 Sum_probs=33.2
Q ss_pred HHHHHHHHHHhhhcCCCeEEEEecccccCCCCC--CCccEEEeCCCc
Q 012847 352 EQMERLLQKAGEEVLPEVIILCGGSYRRGKASC--GDLDVVIMHPDR 396 (455)
Q Consensus 352 ~~i~~~v~~~~~~~~p~~~v~~~Gs~RRgke~~--gDvDiLit~~d~ 396 (455)
..+...+++.+.+..+.+.|.+.|||.||.-.. .||||+|..+..
T Consensus 24 ~~l~~~l~~~~~e~~~~~~v~~~GS~ArgT~L~G~sDIDIfi~f~~~ 70 (408)
T TIGR03671 24 DELIARLEEIIEELGVDAEVVLVGSYARGTWLKGDRDIDIFILFPKD 70 (408)
T ss_pred HHHHHHHHHHHHhcCCcceEEEEeeEecCCccCCCCceeEEEEeCCC
Confidence 344555555555555668999999999999886 589999977643
No 142
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=82.60 E-value=0.87 Score=41.17 Aligned_cols=28 Identities=14% Similarity=0.010 Sum_probs=23.2
Q ss_pred hhHHHHHhhhccCcCHHHHHHHHHcCCC
Q 012847 290 KVRTISLFGEVWGIGPATAQKLYEKGHR 317 (455)
Q Consensus 290 ~~~~l~lf~~I~GvGpktA~~ly~~Gir 317 (455)
...+.+.|++++||||+||..+--.++.
T Consensus 78 ~~~~~~~L~~l~GIG~~tA~~~l~~~~~ 105 (158)
T cd00056 78 DPDAREELLALPGVGRKTANVVLLFALG 105 (158)
T ss_pred CcccHHHHHcCCCCCHHHHHHHHHHHCC
Confidence 3557888899999999999998876655
No 143
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=82.21 E-value=2.2 Score=47.91 Aligned_cols=54 Identities=15% Similarity=0.185 Sum_probs=37.8
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCC
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGH 316 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~Gi 316 (455)
..|.+|||||++-+.++-. .-|++. .+++ -.++.+.+|+|||++.|+++|...-
T Consensus 608 s~L~~IpGiG~kr~~~LL~--~FgS~~---~i~~----As~eel~~v~gi~~~~A~~i~~~~~ 661 (691)
T PRK14672 608 LSFERLPHVGKVRAHRLLA--HFGSFR---SLQS----ATPQDIATAIHIPLTQAHTILHAAT 661 (691)
T ss_pred cccccCCCCCHHHHHHHHH--HhcCHH---HHHh----CCHHHHHhCCCCCHHHHHHHHHHhh
Confidence 4578999999988876643 234444 4432 2445567899999999999998633
No 144
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=81.87 E-value=4.5 Score=41.11 Aligned_cols=52 Identities=27% Similarity=0.473 Sum_probs=38.0
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc
Q 012847 255 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (455)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 314 (455)
.+..|||||+.+++++.+. -+..+++|..-.+. .+.+++|+++++|..||+.
T Consensus 7 ~l~~l~gIg~~~a~~L~~~----Gi~t~~dl~~~~~~----~L~~~~g~~~~~a~~l~~~ 58 (317)
T PRK04301 7 DLEDLPGVGPATAEKLREA----GYDTVEAIAVASPK----ELSEAAGIGESTAAKIIEA 58 (317)
T ss_pred cHhhcCCCCHHHHHHHHHc----CCCCHHHHHcCCHH----HHHHhcCCCHHHHHHHHHH
Confidence 5789999999888776543 45666777653332 2347779999999999974
No 145
>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=81.64 E-value=1.4 Score=45.83 Aligned_cols=29 Identities=17% Similarity=0.307 Sum_probs=24.7
Q ss_pred hhhccCcCHHHHHHHHH-cCCCCHHHhhhc
Q 012847 297 FGEVWGIGPATAQKLYE-KGHRTLDDLKNE 325 (455)
Q Consensus 297 f~~I~GvGpktA~~ly~-~GirTledL~~~ 325 (455)
+..+||||+++++++.+ .||+|+.||.+-
T Consensus 184 v~~l~GiG~~~~~~ll~~~Gi~ti~dl~~~ 213 (359)
T cd01702 184 ITSIRGLGGKLGEEIIDLLGLPTEGDVAGF 213 (359)
T ss_pred HHHhCCcCHHHHHHHHHHcCCcCHHHHHhc
Confidence 35789999999988765 599999999864
No 146
>PTZ00418 Poly(A) polymerase; Provisional
Probab=81.61 E-value=5.1 Score=44.36 Aligned_cols=53 Identities=23% Similarity=0.382 Sum_probs=43.7
Q ss_pred CCCeEEEEecccccCCCC-CCCccEEEeCCCchhhhhhHHHHHHHHHHcCceee
Q 012847 366 LPEVIILCGGSYRRGKAS-CGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLRE 418 (455)
Q Consensus 366 ~p~~~v~~~Gs~RRgke~-~gDvDiLit~~d~~~~~~~l~~lv~~L~~~g~l~~ 418 (455)
..+.++...||||-|--. +.|||.|+..|.--+...||..+.+.|++..-+++
T Consensus 124 ~~~g~I~tfGSYrLGV~~pgSDID~L~V~P~~vtredFF~~f~~~L~~~~~V~e 177 (593)
T PTZ00418 124 QISGKLFTFGSYRLGVVAPGSDIDTLCLAPRHITRESFFSDFYAKLQQDPNITK 177 (593)
T ss_pred cCCeEEEEeccccccCCCCCCcccEEEECCCCCCHHHHHHHHHHHHhcCCCcce
Confidence 356788889999999866 67999999988766667899999999998776654
No 147
>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=81.13 E-value=1.2 Score=43.79 Aligned_cols=26 Identities=35% Similarity=0.460 Sum_probs=22.3
Q ss_pred hccCcCHHHHHHHHHcCCCCHHHhhhc
Q 012847 299 EVWGIGPATAQKLYEKGHRTLDDLKNE 325 (455)
Q Consensus 299 ~I~GvGpktA~~ly~~GirTledL~~~ 325 (455)
+|+|||||||.+|.++ +.|+|++.+.
T Consensus 187 Gv~GiG~ktA~~Ll~~-~gsle~i~~~ 212 (240)
T cd00008 187 GVPGIGEKTAAKLLKE-YGSLEGILEN 212 (240)
T ss_pred CCCccCHHHHHHHHHH-hCCHHHHHHh
Confidence 5899999999999986 4499999854
No 148
>COG1669 Predicted nucleotidyltransferases [General function prediction only]
Probab=80.93 E-value=4.5 Score=34.40 Aligned_cols=46 Identities=24% Similarity=0.372 Sum_probs=29.9
Q ss_pred CCe-EEEEecccccCCCC-CCCccEEEeCCCchhhhhhHHHHHHHHHHc
Q 012847 367 PEV-IILCGGSYRRGKAS-CGDLDVVIMHPDRKSHKGFLSKYVKKLKEM 413 (455)
Q Consensus 367 p~~-~v~~~Gs~RRgke~-~gDvDiLit~~d~~~~~~~l~~lv~~L~~~ 413 (455)
.|+ .+.+-|||=||... -.||||||-...+....+ +-.+.+.|.+.
T Consensus 22 ~gv~~~~vFGS~aRgE~~~~SDIDILVef~~~~~ll~-~~~l~~~L~~l 69 (97)
T COG1669 22 YGVKRVAVFGSYARGEQKPDSDIDILVEFEPGKTLLD-LVRLEDELSDL 69 (97)
T ss_pred hCCceEEEeeeeecCCCCCCCCceeEEeecCCccHHH-HHHHHHHHHHH
Confidence 455 78899999998643 389999997655533222 23355555543
No 149
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=80.86 E-value=5.8 Score=40.52 Aligned_cols=73 Identities=15% Similarity=0.200 Sum_probs=50.6
Q ss_pred CCCCCcEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccchHHH
Q 012847 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLED 93 (455)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~R~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~~~~~l~~l~~~~~~~~~~~lV~~~Wl~e 93 (455)
.+|.|.+|.|-+. +.. .+.-+++++..+||.|.++++.+++.||+.+..... -+.+++...+.+|++-+=|.+
T Consensus 231 ~l~~g~~~v~TG~-l~~-~R~e~~~~~~~~G~~v~~sVs~~t~~lv~g~~~~~s--sK~~kA~~~gi~ii~e~~f~~ 303 (313)
T PRK06063 231 PLVQGMRVALSAE-VSR-THEELVERILHAGLAYSDSVDRDTSLVVCNDPAPEQ--GKGYHARQLGVPVLDEAAFLE 303 (313)
T ss_pred cccCCCEEEEecC-CCC-CHHHHHHHHHHcCCEecCccccCccEEEECCCCCcc--cHHHHHHHcCCccccHHHHHH
Confidence 3689999999765 333 446789999999999999999999999997653210 112233344667776554433
No 150
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=80.41 E-value=2.1 Score=41.33 Aligned_cols=53 Identities=19% Similarity=0.253 Sum_probs=35.0
Q ss_pred CCHHHHHHHHHHHHh-CCchhhHHHH--hhchhHHHHHhh-hccCcCHHHHHHHHH-cCCC
Q 012847 262 IGKSMQDHIQEIVTT-GKLSKLEHFE--KDEKVRTISLFG-EVWGIGPATAQKLYE-KGHR 317 (455)
Q Consensus 262 IG~~ia~kI~Eil~t-G~~~~le~l~--~~~~~~~l~lf~-~I~GvGpktA~~ly~-~Gir 317 (455)
+-..=|+.|.++... |. ++++. ........+.|. ++||||+|||.-+-. .|++
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 446666666666643 33 23222 334467888888 999999999999874 4653
No 151
>PRK00076 recR recombination protein RecR; Reviewed
Probab=80.31 E-value=1.3 Score=42.25 Aligned_cols=22 Identities=36% Similarity=0.531 Sum_probs=19.3
Q ss_pred HHHHHhhhccCcCHHHHHHHHH
Q 012847 292 RTISLFGEVWGIGPATAQKLYE 313 (455)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~ 313 (455)
..++.|.++||||+|+|+++--
T Consensus 8 ~Li~~l~~LPGIG~KsA~Rla~ 29 (196)
T PRK00076 8 KLIEALRKLPGIGPKSAQRLAF 29 (196)
T ss_pred HHHHHHHHCCCCCHHHHHHHHH
Confidence 4778899999999999999864
No 152
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=80.20 E-value=1.4 Score=42.14 Aligned_cols=21 Identities=38% Similarity=0.602 Sum_probs=18.6
Q ss_pred HHHHHhhhccCcCHHHHHHHH
Q 012847 292 RTISLFGEVWGIGPATAQKLY 312 (455)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly 312 (455)
..++.|.++||||+|+|+++-
T Consensus 8 ~Li~~l~~LPGIG~KsA~RlA 28 (195)
T TIGR00615 8 KLIESLKKLPGIGPKSAQRLA 28 (195)
T ss_pred HHHHHHHHCCCCCHHHHHHHH
Confidence 477889999999999999984
No 153
>PRK10702 endonuclease III; Provisional
Probab=79.88 E-value=4 Score=39.40 Aligned_cols=43 Identities=12% Similarity=0.279 Sum_probs=31.3
Q ss_pred hhHHHHHHHHHHHh-cCCcccc-chhhhcCCCCCCHHHHHHHHHH
Q 012847 231 RRSFSYYKAIPVIE-KLPFKIE-SADQVKGLPGIGKSMQDHIQEI 273 (455)
Q Consensus 231 ~r~~aY~rAa~~L~-~l~~~i~-s~~~l~~lpgIG~~ia~kI~Ei 273 (455)
.|+....+++..|. .+...+. +.++|.+|||||.++|+.|.-+
T Consensus 84 ~kA~~l~~~a~~i~~~~~~~~p~~~~~Ll~lpGVG~ktA~~ill~ 128 (211)
T PRK10702 84 SKAENVIKTCRILLEQHNGEVPEDRAALEALPGVGRKTANVVLNT 128 (211)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCchHHHHhcCCcccHHHHHHHHHH
Confidence 36666777777764 3333333 4689999999999999998654
No 154
>PRK13844 recombination protein RecR; Provisional
Probab=79.11 E-value=1.6 Score=41.93 Aligned_cols=23 Identities=22% Similarity=0.219 Sum_probs=19.6
Q ss_pred hHHHHHhhhccCcCHHHHHHHHH
Q 012847 291 VRTISLFGEVWGIGPATAQKLYE 313 (455)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~ 313 (455)
...++.|.++||||+|+|+++--
T Consensus 11 ~~LI~~l~~LPGIG~KsA~Rla~ 33 (200)
T PRK13844 11 SAVIESLRKLPTIGKKSSQRLAL 33 (200)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHH
Confidence 34788899999999999999854
No 155
>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=78.88 E-value=4.2 Score=40.87 Aligned_cols=78 Identities=14% Similarity=0.260 Sum_probs=46.1
Q ss_pred HHHHHHHHcCCChhHHHHHHHHHHHhcC-Cccc-cchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHH
Q 012847 219 KLINIYRALGEDRRSFSYYKAIPVIEKL-PFKI-ESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISL 296 (455)
Q Consensus 219 ~la~~~e~~g~~~r~~aY~rAa~~L~~l-~~~i-~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~l 296 (455)
+|.++.+-.|=-.|++...+||..|..- ...+ .+.++|.+|||||..+|+.|.-+- -|...-+ ....+...
T Consensus 68 eL~~~~~~lG~y~RAr~L~~~A~~i~~~~~g~~p~~~~~L~~LpGIG~~TA~~Il~~a-~~~~~~~------vD~~v~RV 140 (275)
T TIGR01084 68 EVLKLWEGLGYYARARNLHKAAQEVVEEFGGEFPQDFEDLAALPGVGRYTAGAILSFA-LNKPYPI------LDGNVKRV 140 (275)
T ss_pred HHHHHHHHCCcHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCCCHHHHHHHHHHH-CCCCCCc------chHhHHHH
Confidence 3333333334333777778888877541 1111 346899999999999999987554 3432211 22335666
Q ss_pred hhhccCc
Q 012847 297 FGEVWGI 303 (455)
Q Consensus 297 f~~I~Gv 303 (455)
+.+++|+
T Consensus 141 l~Rl~~~ 147 (275)
T TIGR01084 141 LSRLFAV 147 (275)
T ss_pred HHHHccC
Confidence 6666555
No 156
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=78.58 E-value=4.2 Score=36.32 Aligned_cols=26 Identities=15% Similarity=0.089 Sum_probs=20.3
Q ss_pred HHHHHhhhccCcCHHHHHHHHHcCCC
Q 012847 292 RTISLFGEVWGIGPATAQKLYEKGHR 317 (455)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~Gir 317 (455)
..++.|++++||||+||.-+--.|+.
T Consensus 69 ~~~~~L~~l~GIG~~tA~~~l~~~~~ 94 (149)
T smart00478 69 DDREELLKLPGVGRKTANAVLSFALG 94 (149)
T ss_pred HHHHHHHcCCCCcHHHHHHHHHHHCC
Confidence 35666779999999999988765543
No 157
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=77.86 E-value=2.3 Score=37.45 Aligned_cols=26 Identities=42% Similarity=0.542 Sum_probs=23.5
Q ss_pred cCcCHHHHHHHHHcCCCCHHHhhhcc
Q 012847 301 WGIGPATAQKLYEKGHRTLDDLKNED 326 (455)
Q Consensus 301 ~GvGpktA~~ly~~GirTledL~~~~ 326 (455)
||+|++++.+|-+.||.|.+||.+.+
T Consensus 1 pgi~~~~~~~L~~~GI~t~~~Ll~~~ 26 (122)
T PF14229_consen 1 PGIGPKEAAKLKAAGIKTTGDLLEAG 26 (122)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHHcC
Confidence 79999999999888999999998653
No 158
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=77.71 E-value=3 Score=40.36 Aligned_cols=95 Identities=22% Similarity=0.278 Sum_probs=55.6
Q ss_pred CCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--CCCCHHHhhhccCch-hhhhhc--
Q 012847 261 GIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRTLDDLKNEDSLT-HSQRLG-- 335 (455)
Q Consensus 261 gIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--GirTledL~~~~~L~-~~q~~G-- 335 (455)
|+-..=|+.|.++.+ .-+|++.. +.+..++.|.++||||+|||.-.... |+-++ -=+-.+. -..++|
T Consensus 80 Glyr~KAk~I~~~~~----~l~e~~~g-~vP~~~~eL~~LPGVGrKTAnvVL~~a~g~p~i---~VDTHV~Rvs~R~gl~ 151 (211)
T COG0177 80 GLYRNKAKNIKELAR----ILLEKFGG-EVPDTREELLSLPGVGRKTANVVLSFAFGIPAI---AVDTHVHRVSNRLGLV 151 (211)
T ss_pred CCcHHHHHHHHHHHH----HHHHHcCC-CCCchHHHHHhCCCcchHHHHHHHHhhcCCCcc---cccchHHHHHHHhCCC
Confidence 666666666666544 22344433 44567777789999999999988765 44322 1111111 123334
Q ss_pred -----hhhHhhhccCcCHHHHHHHHHHHHHHhh
Q 012847 336 -----LKYFDDIKTRIPRHEVEQMERLLQKAGE 363 (455)
Q Consensus 336 -----lk~~ed~~~~i~r~Ea~~i~~~v~~~~~ 363 (455)
.+..+++.+.+|++.-..+...+-...+
T Consensus 152 ~~~~p~~ve~~L~~~iP~~~~~~~h~~lI~~GR 184 (211)
T COG0177 152 PGKTPEEVEEALMKLIPKELWTDLHHWLILHGR 184 (211)
T ss_pred CCCCHHHHHHHHHHHCCHHHHHHHHHHHHHhhh
Confidence 4456677788888777666444444433
No 159
>PRK00254 ski2-like helicase; Provisional
Probab=77.48 E-value=12 Score=42.60 Aligned_cols=53 Identities=21% Similarity=0.367 Sum_probs=38.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 314 (455)
-.|.+|||||+..+.+ +++.| +.-++++..-.. +.+..|+|||.++|+++++.
T Consensus 645 ~~L~~ipgig~~~~~~---l~~~g-~~s~~~i~~a~~----~el~~~~gi~~~~a~~i~~~ 697 (720)
T PRK00254 645 LELMRLPMIGRKRARA---LYNAG-FRSIEDIVNAKP----SELLKVEGIGAKIVEGIFKH 697 (720)
T ss_pred hhhhcCCCCCHHHHHH---HHHcc-CCCHHHHHhCCH----HHHhcCCCCCHHHHHHHHHH
Confidence 3578899999998776 44555 445555554332 33459999999999999986
No 160
>COG0389 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]
Probab=77.27 E-value=2 Score=44.50 Aligned_cols=27 Identities=44% Similarity=0.721 Sum_probs=25.6
Q ss_pred hhccCcCHHHHHHHHHcCCCCHHHhhh
Q 012847 298 GEVWGIGPATAQKLYEKGHRTLDDLKN 324 (455)
Q Consensus 298 ~~I~GvGpktA~~ly~~GirTledL~~ 324 (455)
..+||||+.++.++...||.|+-||.+
T Consensus 179 ~~~~GvG~~~~~~l~~~Gi~ti~dl~~ 205 (354)
T COG0389 179 LEFWGVGKVTAEKLRRLGISTIGDLAE 205 (354)
T ss_pred hhhCCCCHHHHHHHHHcCChhHHHHHh
Confidence 489999999999999999999999986
No 161
>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=76.79 E-value=13 Score=29.46 Aligned_cols=29 Identities=31% Similarity=0.510 Sum_probs=24.2
Q ss_pred EEEEecccccCCCC-CCCccEEEeCCCchh
Q 012847 370 IILCGGSYRRGKAS-CGDLDVVIMHPDRKS 398 (455)
Q Consensus 370 ~v~~~Gs~RRgke~-~gDvDiLit~~d~~~ 398 (455)
.+.+-|||-||..+ ..||||+|-.++...
T Consensus 20 ~i~LfGS~arg~~~~~SDiDl~vi~~~~~~ 49 (93)
T cd05403 20 KVYLFGSYARGDARPDSDIDLLVIFDDPLD 49 (93)
T ss_pred EEEEEeeeecCCCCCCCCeeEEEEeCCCCC
Confidence 78899999999975 889999997766543
No 162
>PRK13300 tRNA CCA-pyrophosphorylase; Provisional
Probab=76.58 E-value=8.6 Score=41.36 Aligned_cols=45 Identities=24% Similarity=0.305 Sum_probs=30.5
Q ss_pred HHHHHHHHhhhcCCCeEEEEecccccCCCCC--CCccEEEeCCCchh
Q 012847 354 MERLLQKAGEEVLPEVIILCGGSYRRGKASC--GDLDVVIMHPDRKS 398 (455)
Q Consensus 354 i~~~v~~~~~~~~p~~~v~~~Gs~RRgke~~--gDvDiLit~~d~~~ 398 (455)
+...+++.+.+....+.|.+.|||.||.-.- +||||.|..|+...
T Consensus 27 l~~~L~~~~~~~~~~~~V~l~GS~ArgT~L~GdsDIDIFv~fp~~~~ 73 (447)
T PRK13300 27 LIERLEEAIKELGLDAEVELVGSTARGTWLSGDRDIDIFVLFPKDTS 73 (447)
T ss_pred HHHHHHHHHHhcCCceEEEEEeeecCCcccCCCCceeEEEEeCCCCC
Confidence 3444444443322237899999999998876 58999998765443
No 163
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=76.50 E-value=5.8 Score=44.77 Aligned_cols=73 Identities=12% Similarity=0.130 Sum_probs=54.4
Q ss_pred CCCCCCcEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccchHHH
Q 012847 16 NGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLED 93 (455)
Q Consensus 16 ~~~F~g~~iy~~~~~~g~~R~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~~~~~l~~l~~~~~~~~~~~lV~~~Wl~e 93 (455)
+..|.|.++.|-++-.+.+ +..+++++.++||+|.++++..++.+|+.++.. . +..++...+++|++-+.+.+
T Consensus 591 ~~~l~gktfV~TG~l~~~~-R~e~~~lie~~Ggkv~ssVSkktd~LV~G~~aG-s---Kl~KA~~LGI~Ii~e~~f~~ 663 (669)
T PRK14350 591 NSFLFGKKFCITGSFNGYS-RSVLIDKLTKKGAIFNTCVTKYLDFLLVGEKAG-L---KLKKANNLGIKIMSLFDIKS 663 (669)
T ss_pred CCccCCcEEEEecccCCCC-HHHHHHHHHHcCCEEeccccCCCcEEEECCCCC-c---hHHHHHHcCCEEecHHHHHH
Confidence 4579999999976543433 567899999999999999999999999975433 1 22334455778888777655
No 164
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=76.30 E-value=1.9 Score=43.80 Aligned_cols=25 Identities=48% Similarity=0.740 Sum_probs=21.9
Q ss_pred hccCcCHHHHHHHHHc-CCCCHHHhhhc
Q 012847 299 EVWGIGPATAQKLYEK-GHRTLDDLKNE 325 (455)
Q Consensus 299 ~I~GvGpktA~~ly~~-GirTledL~~~ 325 (455)
+|+|||||||.+|.++ | |++.|.+.
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 165
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=75.91 E-value=4 Score=41.05 Aligned_cols=69 Identities=17% Similarity=0.283 Sum_probs=50.5
Q ss_pred hhhcCCCCCCH---HHHHHHHHHHH-hCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhh
Q 012847 254 DQVKGLPGIGK---SMQDHIQEIVT-TGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLK 323 (455)
Q Consensus 254 ~~l~~lpgIG~---~ia~kI~Eil~-tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTledL~ 323 (455)
++|+++ |+|= -|+...++|++ .|...-|..|+...-..+.+.|+.+||||||.|.=+-=.|+.-+.-+-
T Consensus 174 a~LR~~-gfGYRAkYI~~ta~~l~~~~g~~~wLqsl~~~~yeear~~L~~lpGVG~KVADCI~Lm~l~~~~~VP 246 (323)
T KOG2875|consen 174 AELRKL-GFGYRAKYISATARALQEKQGGLAWLQSLRKSSYEEAREALCSLPGVGPKVADCICLMSLDKLSAVP 246 (323)
T ss_pred HHHHHc-CcchhHHHHHHHHHHHHHhcccchHHHHHhcccHHHHHHHHhcCCCCcchHhhhhhhhhcCCCCccc
Confidence 356666 6774 46666777775 467788888888666679999999999999999977665555544443
No 166
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=75.43 E-value=5.4 Score=35.94 Aligned_cols=78 Identities=17% Similarity=0.244 Sum_probs=45.4
Q ss_pred HHHHHHHHcCCChhHHHHHHHHHHHhcCCccc-----cchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHH
Q 012847 219 KLINIYRALGEDRRSFSYYKAIPVIEKLPFKI-----ESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRT 293 (455)
Q Consensus 219 ~la~~~e~~g~~~r~~aY~rAa~~L~~l~~~i-----~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~ 293 (455)
+|.+...-.|-+.|+.....++..+..-.... +..++|.+|||||+.+|+.|.-+.- | . +.+-- ...+
T Consensus 43 ~l~~~~~~~G~~~kA~~i~~~a~~~~~~~~~~~~~~~~~~~~L~~l~GIG~~tA~~~l~~~~-~-~---~~~pv--D~~v 115 (158)
T cd00056 43 ELRELIRSLGYRRKAKYLKELARAIVEGFGGLVLDDPDAREELLALPGVGRKTANVVLLFAL-G-P---DAFPV--DTHV 115 (158)
T ss_pred HHHHHHHhcChHHHHHHHHHHHHHHHHHcCCccCCCcccHHHHHcCCCCCHHHHHHHHHHHC-C-C---CCCcc--chhH
Confidence 34444433343457777777777775432221 2347799999999999999875532 2 1 22211 2346
Q ss_pred HHHhhhccCc
Q 012847 294 ISLFGEVWGI 303 (455)
Q Consensus 294 l~lf~~I~Gv 303 (455)
.+.+..+.++
T Consensus 116 ~r~~~~~~~~ 125 (158)
T cd00056 116 RRVLKRLGLI 125 (158)
T ss_pred HHHHHHhCCC
Confidence 6666566554
No 167
>COG1746 CCA1 tRNA nucleotidyltransferase (CCA-adding enzyme) [Translation, ribosomal structure and biogenesis]
Probab=75.07 E-value=10 Score=40.29 Aligned_cols=47 Identities=28% Similarity=0.380 Sum_probs=34.3
Q ss_pred HHHHHHHHHHhhhcCCCeEEEEecccccCCCCC--CCccEEEeCCCchh
Q 012847 352 EQMERLLQKAGEEVLPEVIILCGGSYRRGKASC--GDLDVVIMHPDRKS 398 (455)
Q Consensus 352 ~~i~~~v~~~~~~~~p~~~v~~~Gs~RRgke~~--gDvDiLit~~d~~~ 398 (455)
+.+...+.+++.+....+.+.++|||.||-=.. +|||+-|.-|...+
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 344555555555556778999999999997665 78999998876643
No 168
>KOG3524 consensus Predicted guanine nucleotide exchange factor (PEBBLE) [Signal transduction mechanisms]
Probab=74.64 E-value=2.6 Score=47.00 Aligned_cols=77 Identities=16% Similarity=0.290 Sum_probs=56.3
Q ss_pred CCCCCcEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccchHHHHHh
Q 012847 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSLR 96 (455)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~R~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~~~~~l~~l~~~~~~~~~~~lV~~~Wl~es~k 96 (455)
..|++++.||- ++-..-. -|-+++..+||.|......++||.|+-...... +. ...-..+++...||.+||+
T Consensus 117 ~~m~~vvlcfT--g~rkk~e-~lv~lvh~mgg~irkd~nsktthli~n~s~gek--~~---~a~t~~~~~rp~wv~~aw~ 188 (850)
T KOG3524|consen 117 ELMKDVVMCFT--GERKKKE-ELVDLVHYMGGSIRKDTNSKTTHLIANKVEGEK--QS---IALVGVPTMRPDWVTEAWK 188 (850)
T ss_pred hhhcCceeeee--ccchhhH-HHHHHHHHhcceeEeeeccCceEEEeecccceE--EE---EEeeccceechHhhhhhhc
Confidence 57899999996 4443322 677899999999999999999999986554321 11 1111368899999999998
Q ss_pred cCCCC
Q 012847 97 LGEKV 101 (455)
Q Consensus 97 ~g~lv 101 (455)
...-.
T Consensus 189 ~rn~~ 193 (850)
T KOG3524|consen 189 HRNDS 193 (850)
T ss_pred Ccchh
Confidence 76543
No 169
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=74.33 E-value=3.8 Score=39.86 Aligned_cols=22 Identities=23% Similarity=0.210 Sum_probs=18.2
Q ss_pred HHHHHhhhccCcCHHHHHHHHH
Q 012847 292 RTISLFGEVWGIGPATAQKLYE 313 (455)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~ 313 (455)
...+.|++++|||++||..+--
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
>KOG3548 consensus DNA damage checkpoint protein RHP9/CRB2/53BP1 [Replication, recombination and repair]
Probab=74.30 E-value=3.2 Score=47.66 Aligned_cols=91 Identities=13% Similarity=0.034 Sum_probs=55.3
Q ss_pred CCCCCcEEEEecCCCCchHHHHHHHHHHhcCCEEEee-cCCCccEEEEcCCh--HH--------------------HHHH
Q 012847 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEK-LSKKVTHVLAMDLE--AL--------------------LQQV 73 (455)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~R~~~l~~li~~~Gg~V~~~-ls~~VTHVV~~~~~--~~--------------------l~~l 73 (455)
.+|.||++.|-...- .....++-+..+||.|.+. |..=-+|=...... +. .+..
T Consensus 924 niFd~cvF~lTsa~~---sd~~~r~s~e~~gg~vle~gl~~~Fn~p~~g~~~~lr~Ln~~q~~ks~~qalLIsdth~Rt~ 1000 (1176)
T KOG3548|consen 924 NIFDGCVFMLTSANR---SDSASRPSMEKHGGLVLEKGLMNLFNTPFKGGGIVLRQLNSFQERKSNYQALLISDTHYRTH 1000 (1176)
T ss_pred chhcceeEEEecccc---chhhhhhhhhccCChhhhccccccccccccCCcchHHhhhHHhhhccccceeEeehhhhHHH
Confidence 789999988853322 2234455555688888765 33223343321110 10 1122
Q ss_pred HHHhhhccCccccccchHHHHHhcCCCCCcccccccc
Q 012847 74 SKQHLARFKGSVIRYQWLEDSLRLGEKVSEDLYRIKL 110 (455)
Q Consensus 74 ~~~~~~~~~~~lV~~~Wl~es~k~g~lvdee~y~l~~ 110 (455)
++--.-+.+.+-|...||.+|.+.++.||-.+|.|.-
T Consensus 1001 KYLeaLA~giPcVh~~fI~aC~e~nr~Vdy~~YLLps 1037 (1176)
T KOG3548|consen 1001 KYLEALARGIPCVHNTFIQACGEQNRCVDYTDYLLPS 1037 (1176)
T ss_pred HHHHHHHcCCCcccHHHHHHHHhccccccchhhcccC
Confidence 2211112367889999999999999999999998864
No 171
>PRK13910 DNA glycosylase MutY; Provisional
Probab=74.27 E-value=6.6 Score=39.82 Aligned_cols=68 Identities=16% Similarity=0.197 Sum_probs=45.7
Q ss_pred hHHHHHHHHHHHh-cCCccc-cchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHH
Q 012847 232 RSFSYYKAIPVIE-KLPFKI-ESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPA 306 (455)
Q Consensus 232 r~~aY~rAa~~L~-~l~~~i-~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpk 306 (455)
|++.-.++|..|. .+...+ .+.++|.+|||||+.+|+.|.-+- -|.-.- -...-+.++|.+++|+...
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 7777888888775 222222 257899999999999999997553 333111 1234478888888888653
No 172
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=73.99 E-value=2.2 Score=47.25 Aligned_cols=45 Identities=18% Similarity=0.336 Sum_probs=32.4
Q ss_pred HhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhhhchhhHhh
Q 012847 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDD 341 (455)
Q Consensus 296 lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~q~~Glk~~ed 341 (455)
.|.+|+||||++.++|++ -+.|+++++++. .|....+++.+..+.
T Consensus 515 ~L~~I~GiG~kr~~~LL~-~Fgs~~~I~~As~eeL~~v~gi~~~~A~~ 561 (574)
T PRK14670 515 NYTKIKGIGEKKAKKILK-SLGTYKDILLLNEDEIAEKMKINIKMAKK 561 (574)
T ss_pred ccccCCCCCHHHHHHHHH-HhCCHHHHHhCCHHHHHhCCCCCHHHHHH
Confidence 456999999999999998 677999998753 354454555444333
No 173
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=73.98 E-value=1.9 Score=47.66 Aligned_cols=46 Identities=20% Similarity=0.387 Sum_probs=32.5
Q ss_pred HHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhhhchhhHhhh
Q 012847 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDI 342 (455)
Q Consensus 295 ~lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~q~~Glk~~ed~ 342 (455)
..|.+|+|||||+.++|++ -+.|++.++++. .|... |+|.+..+.|
T Consensus 514 S~Ld~I~GiG~kr~~~Ll~-~Fgs~~~ik~As~eeL~~v-gi~~~~A~~I 561 (567)
T PRK14667 514 DILDKIKGIGEVKKEIIYR-NFKTLYDFLKADDEELKKL-GIPPSVKQEV 561 (567)
T ss_pred CccccCCCCCHHHHHHHHH-HhCCHHHHHhCCHHHHHHc-CCCHHHHHHH
Confidence 4456999999999999998 577889988653 34444 4554444333
No 174
>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=73.59 E-value=4.8 Score=31.61 Aligned_cols=36 Identities=17% Similarity=0.353 Sum_probs=26.0
Q ss_pred HHHHHHhcCCccccc--------hhhhcCCCCCCHHHHHHHHHHHH
Q 012847 238 KAIPVIEKLPFKIES--------ADQVKGLPGIGKSMQDHIQEIVT 275 (455)
Q Consensus 238 rAa~~L~~l~~~i~s--------~~~l~~lpgIG~~ia~kI~Eil~ 275 (455)
||.++|+... |.+ .+++..+||+|++..+.|.+.|+
T Consensus 22 Ra~n~L~~~~--I~tv~dL~~~s~~~L~~i~n~G~ksl~EI~~~L~ 65 (66)
T PF03118_consen 22 RAYNCLKRAG--IHTVGDLVKYSEEDLLKIKNFGKKSLEEIKEKLK 65 (66)
T ss_dssp HHHHHHHCTT----BHHHHHCS-HHHHHTSTTSHHHHHHHHHHHHH
T ss_pred HHHHHHHHhC--CcCHHHHHhCCHHHHHhCCCCCHhHHHHHHHHHc
Confidence 4556666553 333 26799999999999999998875
No 175
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=73.34 E-value=3.4 Score=46.26 Aligned_cols=47 Identities=26% Similarity=0.362 Sum_probs=33.4
Q ss_pred HHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhhhchhhHhhh
Q 012847 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDI 342 (455)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~q~~Glk~~ed~ 342 (455)
....|.+|+||||++|+.|++ .+.|+++|.++. .|+.. +|.+..+.|
T Consensus 567 ~~s~L~~I~GIG~k~a~~Ll~-~Fgs~~~i~~As~eeL~~v--ig~k~A~~I 615 (621)
T PRK14671 567 LQTELTDIAGIGEKTAEKLLE-HFGSVEKVAKASLEELAAV--AGPKTAETI 615 (621)
T ss_pred hhhhhhcCCCcCHHHHHHHHH-HcCCHHHHHhCCHHHHHHH--hCHHHHHHH
Confidence 456677999999999999998 555999998653 24333 565554443
No 176
>PRK13766 Hef nuclease; Provisional
Probab=73.06 E-value=4.9 Score=45.79 Aligned_cols=44 Identities=18% Similarity=0.311 Sum_probs=20.1
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhhhchhhHhh
Q 012847 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDD 341 (455)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~q~~Glk~~ed 341 (455)
|..|+|||+++|++|.+. +.|++++..+. .|....++|.+..+.
T Consensus 717 L~~ipgig~~~a~~Ll~~-fgs~~~i~~as~~~L~~i~Gig~~~a~~ 762 (773)
T PRK13766 717 VESLPDVGPVLARNLLEH-FGSVEAVMTASEEELMEVEGIGEKTAKR 762 (773)
T ss_pred HhcCCCCCHHHHHHHHHH-cCCHHHHHhCCHHHHHhCCCCCHHHHHH
Confidence 445555555555555553 23455554321 233344444444333
No 177
>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=72.92 E-value=3.4 Score=35.48 Aligned_cols=26 Identities=23% Similarity=0.484 Sum_probs=21.6
Q ss_pred HHHHhhhccCcCHHHHHHHHHc-CCCC
Q 012847 293 TISLFGEVWGIGPATAQKLYEK-GHRT 318 (455)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~-GirT 318 (455)
+.-.|++|+|||+++|..+.+. |+..
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 5666789999999999999987 8854
No 178
>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=72.30 E-value=1.8 Score=29.06 Aligned_cols=18 Identities=22% Similarity=0.501 Sum_probs=14.3
Q ss_pred hhcCCCCCCHHHHHHHHH
Q 012847 255 QVKGLPGIGKSMQDHIQE 272 (455)
Q Consensus 255 ~l~~lpgIG~~ia~kI~E 272 (455)
.+.+++|||+++++++..
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 179
>PRK03352 DNA polymerase IV; Validated
Probab=71.77 E-value=11 Score=38.55 Aligned_cols=55 Identities=16% Similarity=0.331 Sum_probs=38.9
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--CCCCHH
Q 012847 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRTLD 320 (455)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--GirTle 320 (455)
+..|||||++++++...+ -+..+.+|.+-.+..+.+.| |++.+.+||+. |+..-.
T Consensus 179 l~~l~gig~~~~~~L~~~----Gi~ti~dl~~l~~~~L~~~f------G~~~~~~l~~~a~G~d~~~ 235 (346)
T PRK03352 179 TDALWGVGPKTAKRLAAL----GITTVADLAAADPAELAATF------GPTTGPWLLLLARGGGDTE 235 (346)
T ss_pred HHHcCCCCHHHHHHHHHc----CCccHHHHhcCCHHHHHHHh------ChHHHHHHHHHhCCCCCCC
Confidence 778999999998887654 56677777665555555566 67788888875 775443
No 180
>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=71.46 E-value=12 Score=35.19 Aligned_cols=44 Identities=14% Similarity=0.203 Sum_probs=30.3
Q ss_pred hHHHHHHHHHHH-hcCCccc---------cc---hhhhcCCCCCCHHHHHHHHHHHH
Q 012847 232 RSFSYYKAIPVI-EKLPFKI---------ES---ADQVKGLPGIGKSMQDHIQEIVT 275 (455)
Q Consensus 232 r~~aY~rAa~~L-~~l~~~i---------~s---~~~l~~lpgIG~~ia~kI~Eil~ 275 (455)
++.....++..| +.+...+ .+ .++|..|||||+++|..+--+|.
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 555555566665 4555554 11 36899999999999999876554
No 181
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=70.36 E-value=2.4 Score=47.44 Aligned_cols=30 Identities=27% Similarity=0.420 Sum_probs=25.2
Q ss_pred HHhhhccCcCHHHHHHHHHcCCCCHHHhhhc
Q 012847 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (455)
Q Consensus 295 ~lf~~I~GvGpktA~~ly~~GirTledL~~~ 325 (455)
..|.+|+||||+++++|++ -+.|+++++++
T Consensus 552 S~L~~IpGIG~kr~~~LL~-~FgSi~~I~~A 581 (624)
T PRK14669 552 SELLEIPGVGAKTVQRLLK-HFGSLERVRAA 581 (624)
T ss_pred HHHhcCCCCCHHHHHHHHH-HcCCHHHHHhC
Confidence 4566999999999999998 56788888865
No 182
>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=70.29 E-value=16 Score=32.75 Aligned_cols=51 Identities=25% Similarity=0.341 Sum_probs=37.2
Q ss_pred eEEEEecccccCCC-CCCCccEEEeCCCc---hh---hhhhHHHHHHHHHHcCceeee
Q 012847 369 VIILCGGSYRRGKA-SCGDLDVVIMHPDR---KS---HKGFLSKYVKKLKEMKFLRED 419 (455)
Q Consensus 369 ~~v~~~Gs~RRgke-~~gDvDiLit~~d~---~~---~~~~l~~lv~~L~~~g~l~~~ 419 (455)
+-..+.||+=|+.. ...|+|..|-+++. .. ...+..++++.|.+.||=.+.
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 35667888866554 56799999988872 11 345678899999999997653
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=70.22 E-value=2.7 Score=34.47 Aligned_cols=20 Identities=40% Similarity=0.624 Sum_probs=17.8
Q ss_pred HHhhhccCcCHHHHHHHHHc
Q 012847 295 SLFGEVWGIGPATAQKLYEK 314 (455)
Q Consensus 295 ~lf~~I~GvGpktA~~ly~~ 314 (455)
++|++|||||+.+|-.|..+
T Consensus 2 ~~l~sipGig~~~a~~llae 21 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAE 21 (87)
T ss_pred chhcCCCCccHHHHHHHHHH
Confidence 46789999999999999985
No 184
>KOG2245 consensus Poly(A) polymerase and related nucleotidyltransferases [RNA processing and modification]
Probab=70.20 E-value=7.5 Score=42.11 Aligned_cols=88 Identities=24% Similarity=0.312 Sum_probs=61.1
Q ss_pred hhhhhchhhHhhhccCcCHHHHHH-HHHHHHHHhhh------------cCCCeEEEEecccccCCCCC-CCccEEEeCCC
Q 012847 330 HSQRLGLKYFDDIKTRIPRHEVEQ-MERLLQKAGEE------------VLPEVIILCGGSYRRGKASC-GDLDVVIMHPD 395 (455)
Q Consensus 330 ~~q~~Glk~~ed~~~~i~r~Ea~~-i~~~v~~~~~~------------~~p~~~v~~~Gs~RRgke~~-gDvDiLit~~d 395 (455)
.++.+|+ ||+-.+-..|.++.. +.++|++-+.+ ...|.++---||||-|--.. .|||=|+-.|.
T Consensus 40 ~L~~~g~--fEs~eEt~~R~~VL~~L~~iVk~wVk~vs~~k~~p~~~~~~aggkIftfGSYRLGVhg~GADIDtLcV~Pr 117 (562)
T KOG2245|consen 40 TLKNEGL--FESKEETQRREEVLGKLNQIVKEWVKKVSEQKGLPDGMIENAGGKIFTFGSYRLGVHGPGADIDTLCVGPR 117 (562)
T ss_pred HHHhcCC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCChhhhhhcCceEEeccceeecccCCCCCcceeeeccc
Confidence 3455553 555556666666654 45555443221 12345666779999998664 59999998887
Q ss_pred chhhhhhHHHHHHHHHHcCceeee
Q 012847 396 RKSHKGFLSKYVKKLKEMKFLRED 419 (455)
Q Consensus 396 ~~~~~~~l~~lv~~L~~~g~l~~~ 419 (455)
-.+..+||..+-+-|+++.-||+-
T Consensus 118 hv~R~DFF~sf~~mL~~~~eVteL 141 (562)
T KOG2245|consen 118 HVSRSDFFTSFYDMLKERPEVTEL 141 (562)
T ss_pred cccHHHHHHHHHHHHhcCcccccc
Confidence 777779999999999999888873
No 185
>PRK01216 DNA polymerase IV; Validated
Probab=70.07 E-value=14 Score=38.30 Aligned_cols=86 Identities=19% Similarity=0.272 Sum_probs=50.9
Q ss_pred CCHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhh
Q 012847 209 LNKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKD 288 (455)
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 (455)
+|+.+|.++..+++ .+...+.........|..|| +..|||||++++++...+ -+..+.+|.+-
T Consensus 146 ~nk~lAKlas~~~K-----P~g~~vi~~~~~~~~L~~LP--------i~~l~giG~~~~~~L~~~----Gi~TigdL~~~ 208 (351)
T PRK01216 146 KNKVFAKIAADMAK-----PNGIKVIDDEEVKRFINELD--------IADIPGIGDITAEKLKKL----GVNKLVDTLRI 208 (351)
T ss_pred CCHHHHHHHHhccC-----CCCEEEeCHHHHHHHHhcCC--------cccccCCCHHHHHHHHHc----CCCcHHHHhcC
Confidence 36666666544331 12112222233344454443 667899999998877654 35666677665
Q ss_pred chhHHHHHhhhccCcCHHHHHHHHHc--CCC
Q 012847 289 EKVRTISLFGEVWGIGPATAQKLYEK--GHR 317 (455)
Q Consensus 289 ~~~~~l~lf~~I~GvGpktA~~ly~~--Gir 317 (455)
......+.| |+..+..||+. |+.
T Consensus 209 ~~~~L~~rf------G~~~~~~L~~~a~G~d 233 (351)
T PRK01216 209 EFDELKGII------GEAKAKYLFSLARNEY 233 (351)
T ss_pred CHHHHHHHH------CHHHHHHHHHHhCCCC
Confidence 545555566 67778889883 754
No 186
>PRK05007 PII uridylyl-transferase; Provisional
Probab=69.88 E-value=15 Score=42.99 Aligned_cols=51 Identities=20% Similarity=0.446 Sum_probs=38.4
Q ss_pred CCeEEEEecccccCC-CCCCCccEEEeCCCch--hhhhhHHHHHHHHHHcCcee
Q 012847 367 PEVIILCGGSYRRGK-ASCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMKFLR 417 (455)
Q Consensus 367 p~~~v~~~Gs~RRgk-e~~gDvDiLit~~d~~--~~~~~l~~lv~~L~~~g~l~ 417 (455)
|++-++.+|||=||. .-..|||+||-+++.. .....+..++..|-+.|+=.
T Consensus 79 ~~~alvAvGgyGR~EL~p~SDiDll~l~~~~~~~~~~~~i~~~~~~lwD~gL~~ 132 (884)
T PRK05007 79 PDLALVAVGGYGRGELHPLSDIDLLILSRKKLPDEQAQKVGELITLLWDLKLEV 132 (884)
T ss_pred CceEEEecCCCCCcccCCcccceEEEEeCCCCChHHHHHHHHHHHHHHhcCCCC
Confidence 467788899996664 5678999999987432 35567888888888888743
No 187
>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=69.69 E-value=9.8 Score=40.12 Aligned_cols=53 Identities=28% Similarity=0.488 Sum_probs=36.0
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhc--hhHHHHHhhhccCcCHHHHHHHHHc--CCCC
Q 012847 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDE--KVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (455)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~--~~~~l~lf~~I~GvGpktA~~ly~~--GirT 318 (455)
+..|||||+++++++..+ | +..+.+|.+-. +..+.+.| |++++..||+. |+..
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 44455666 78889998875 8764
No 188
>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=69.59 E-value=4.4 Score=43.50 Aligned_cols=29 Identities=45% Similarity=0.571 Sum_probs=26.4
Q ss_pred hhccCcCHHHHHHHHHcCCCCHHHhhhcc
Q 012847 298 GEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (455)
Q Consensus 298 ~~I~GvGpktA~~ly~~GirTledL~~~~ 326 (455)
.-|+|||.+++.+|++.||.|++||-...
T Consensus 210 slv~gi~~~~~~~L~~~GI~ti~~La~~~ 238 (457)
T TIGR03491 210 SLVPGIGPSRYRLLQELGIHTLEDLAAAD 238 (457)
T ss_pred eecCCCCHHHHHHHHHcCCCcHHHHhcCC
Confidence 37999999999999999999999998654
No 189
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=69.25 E-value=3.4 Score=39.48 Aligned_cols=37 Identities=22% Similarity=0.333 Sum_probs=26.0
Q ss_pred cccch-hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHH
Q 012847 249 KIESA-DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHF 285 (455)
Q Consensus 249 ~i~s~-~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l 285 (455)
++..+ +.+..|||||++.|+++.-.+-.-.-.+++.|
T Consensus 5 ~~~~Li~~l~~LPGIG~KsA~RlA~~ll~~~~~~~~~l 42 (195)
T TIGR00615 5 PISKLIESLKKLPGIGPKSAQRLAFHLLKRDPSEVLRL 42 (195)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHcCCHHHHHHH
Confidence 34443 67899999999999999877654444444444
No 190
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=69.24 E-value=3.8 Score=41.89 Aligned_cols=54 Identities=28% Similarity=0.418 Sum_probs=39.8
Q ss_pred hhHHHHHhhhccCcCHHHHHHHHH---cCC-CCHHHhhhccC------chhhhhhchhhHhhhc
Q 012847 290 KVRTISLFGEVWGIGPATAQKLYE---KGH-RTLDDLKNEDS------LTHSQRLGLKYFDDIK 343 (455)
Q Consensus 290 ~~~~l~lf~~I~GvGpktA~~ly~---~Gi-rTledL~~~~~------L~~~q~~Glk~~ed~~ 343 (455)
|....+...++||+|||.|++|-+ -|. +-+++++++.+ ++..=|+|.++.+.|.
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 455777888999999999999986 265 77888886432 4566677777776664
No 191
>PRK14973 DNA topoisomerase I; Provisional
Probab=68.64 E-value=4.9 Score=47.10 Aligned_cols=41 Identities=17% Similarity=0.136 Sum_probs=33.1
Q ss_pred HHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--Cchhhhhhc
Q 012847 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLG 335 (455)
Q Consensus 295 ~lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~q~~G 335 (455)
+-|++++||=..+|+++|+.||+|++|+-.++ .|+..-|+.
T Consensus 802 ~~~~~~~gv~~~~~~~~~~~G~~~~~d~~~a~p~~La~~~g~~ 844 (936)
T PRK14973 802 ISRLKEIGVPAVSLKKYQEAGFDTPEDFCSVHPAYLALKTGIS 844 (936)
T ss_pred HHhhcccCCCHHHHHHHHHhcCCCHHHHHhcCHHHHhcCCCCC
Confidence 34559999999999999999999999998653 355555555
No 192
>PF03118 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha chain C terminal domain; InterPro: IPR011260 The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals. The alpha subunit (RpoA) initiates RNAP assembly by dimerising to form a platform on which the beta subunits can interact. The alpha subunit consists of a N-terminal domain (NTD) and a C-terminal domain (CTD), connected by a short linker. The NTD is essential for RNAP assembly, while the CTD is necessary for transcription regulation, interacting with transcription factors and promoter upstream elements. In Escherichia coli, the catabolite activator protein (CAP or CRP) was shown to exert its effect through its interactions with the CTD, where CAP binding to CTD promotes RNAP binding to promoter DNA, thereby stimulating transcription initiation at class I CAP-dependent promoters. At class II CAP-dependent promoters, the interaction of CAP with CTD is one of multiple interactions involved in activation []. The CTD has a compact structure of four helices and two long arms enclosing its hydrophobic core, making its folding topology distinct from most other binding proteins. The upstream promoter element-binding site is formed from helices 1 and 4 [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3N97_B 1XS9_D 3K4G_A 3N4M_B 1COO_A 1LB2_E 3IYD_A 1Z3E_B 3GFK_B 3IHQ_B ....
Probab=68.41 E-value=1.5 Score=34.48 Aligned_cols=44 Identities=25% Similarity=0.367 Sum_probs=33.5
Q ss_pred cCcCHHHHHHHHHcCCCCHHHhhhc--cCchhhhhhchhhHhhhcc
Q 012847 301 WGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDIKT 344 (455)
Q Consensus 301 ~GvGpktA~~ly~~GirTledL~~~--~~L~~~q~~Glk~~ed~~~ 344 (455)
-|+-+++...|-..||.|+.||..- ..|..+++||-+..++|.+
T Consensus 17 L~LS~Ra~n~L~~~~I~tv~dL~~~s~~~L~~i~n~G~ksl~EI~~ 62 (66)
T PF03118_consen 17 LGLSVRAYNCLKRAGIHTVGDLVKYSEEDLLKIKNFGKKSLEEIKE 62 (66)
T ss_dssp STSBHHHHHHHHCTT--BHHHHHCS-HHHHHTSTTSHHHHHHHHHH
T ss_pred hCCCHHHHHHHHHhCCcCHHHHHhCCHHHHHhCCCCCHhHHHHHHH
Confidence 3667888888888899999999853 4588899999998887764
No 193
>COG2251 Predicted nuclease (RecB family) [General function prediction only]
Probab=68.28 E-value=3.7 Score=43.75 Aligned_cols=27 Identities=37% Similarity=0.452 Sum_probs=24.7
Q ss_pred hccCcCHHHHHHHHHcCCCCHHHhhhc
Q 012847 299 EVWGIGPATAQKLYEKGHRTLDDLKNE 325 (455)
Q Consensus 299 ~I~GvGpktA~~ly~~GirTledL~~~ 325 (455)
=|+||||.+.+.+++.||+|++||-..
T Consensus 229 Lv~Gi~~~r~~~l~~~GI~Ti~~LA~~ 255 (474)
T COG2251 229 LVPGITPSRYDVLEEVGITTIEDLADA 255 (474)
T ss_pred ccCCCCHHHHHHHHHcCcchHHHHHhc
Confidence 468999999999999999999999853
No 194
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=67.76 E-value=2.9 Score=47.04 Aligned_cols=53 Identities=15% Similarity=0.221 Sum_probs=39.9
Q ss_pred HHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhhhchhhHhhhccCcCH
Q 012847 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIKTRIPR 348 (455)
Q Consensus 295 ~lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~q~~Glk~~ed~~~~i~r 348 (455)
..|.+|+|||+++.++|++ -|-|+++|+++. .|....++|.+..+.|...-.|
T Consensus 608 s~L~~IpGiG~kr~~~LL~-~FgS~~~i~~As~eel~~v~gi~~~~A~~i~~~~~~ 662 (691)
T PRK14672 608 LSFERLPHVGKVRAHRLLA-HFGSFRSLQSATPQDIATAIHIPLTQAHTILHAATR 662 (691)
T ss_pred cccccCCCCCHHHHHHHHH-HhcCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHhhc
Confidence 3466999999999999998 567899998763 4666777777777666654443
No 195
>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=67.74 E-value=14 Score=30.44 Aligned_cols=50 Identities=22% Similarity=0.395 Sum_probs=33.4
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCC
Q 012847 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGH 316 (455)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~Gi 316 (455)
+..|+|||+.+++.|.+--+.|.+.-++++... ++++..+....|.+.|.
T Consensus 29 l~~Ikglg~~~a~~I~~~R~~g~f~s~~df~~R-----------~~~i~~~~le~Li~aGa 78 (90)
T PF14579_consen 29 LSAIKGLGEEVAEKIVEERENGPFKSLEDFIQR-----------LPKINKRQLEALIKAGA 78 (90)
T ss_dssp GGGSTTS-HHHHHHHHHHHHCSS-SSHHHHHHH-----------S-TS-HHHHHHHHHTTT
T ss_pred HhhcCCCCHHHHHHHHHhHhcCCCCCHHHHHHH-----------HhcCCHHHHHHHHHCCC
Confidence 677888888888888888777777777766532 22677777777777654
No 196
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=67.30 E-value=13 Score=37.27 Aligned_cols=29 Identities=17% Similarity=0.130 Sum_probs=26.3
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhc
Q 012847 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (455)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirTledL~~~ 325 (455)
|.++||+|...++++.+.|+.|++||...
T Consensus 153 L~Qlp~i~~~~~~~l~~~~i~s~~~l~~~ 181 (312)
T smart00611 153 LLQLPHLPEEILKRLEKKKVLSLEDLLEL 181 (312)
T ss_pred cccCCCCCHHHHHHHHhCCCCCHHHHHhc
Confidence 44899999999999999999999999864
No 197
>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=67.13 E-value=21 Score=32.70 Aligned_cols=52 Identities=23% Similarity=0.297 Sum_probs=36.2
Q ss_pred CeEEEEecccccCC-CCCCCccEEEeCCCchh-----hhhhHHHHHHHHHHcCceeee
Q 012847 368 EVIILCGGSYRRGK-ASCGDLDVVIMHPDRKS-----HKGFLSKYVKKLKEMKFLRED 419 (455)
Q Consensus 368 ~~~v~~~Gs~RRgk-e~~gDvDiLit~~d~~~-----~~~~l~~lv~~L~~~g~l~~~ 419 (455)
++-+.+.|||-|+. ....|+|+++-+++... ...+-.++++.|...|+..+.
T Consensus 55 ~~~~la~Gs~GR~E~~~~SD~D~~~v~~~~~~~~~~~~~~l~~~i~~~L~~~g~~~~~ 112 (172)
T cd05401 55 PFALLALGSYGRGELNPSSDQDLLLLYDDDGDEVAAYFEELAERLIKILSEAGGPYCL 112 (172)
T ss_pred cEEEEEeCCcccCCcCCCcCcceEEEeCCCCchHHHHHHHHHHHHHHHHHhCCCCCCC
Confidence 35677889986654 55789999998876532 345666778888877766543
No 198
>PRK00076 recR recombination protein RecR; Reviewed
Probab=66.88 E-value=3.9 Score=39.16 Aligned_cols=32 Identities=16% Similarity=0.321 Sum_probs=24.4
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHH
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHF 285 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l 285 (455)
+.+..|||||++.|+++.-.+-.-.-.+++.|
T Consensus 11 ~~l~~LPGIG~KsA~Rla~~ll~~~~~~~~~l 42 (196)
T PRK00076 11 EALRKLPGIGPKSAQRLAFHLLQRDREDVLRL 42 (196)
T ss_pred HHHHHCCCCCHHHHHHHHHHHHcCCHHHHHHH
Confidence 67899999999999999877765444444444
No 199
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=66.82 E-value=7.5 Score=43.56 Aligned_cols=49 Identities=27% Similarity=0.560 Sum_probs=34.6
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (455)
..|.+|||||++.+..|..- -|++ +.+++. ..+.+.+| ||+++|+++++
T Consensus 569 s~L~~I~GIG~k~a~~Ll~~--Fgs~---~~i~~A----s~eeL~~v--ig~k~A~~I~~ 617 (621)
T PRK14671 569 TELTDIAGIGEKTAEKLLEH--FGSV---EKVAKA----SLEELAAV--AGPKTAETIYR 617 (621)
T ss_pred hhhhcCCCcCHHHHHHHHHH--cCCH---HHHHhC----CHHHHHHH--hCHHHHHHHHH
Confidence 56889999999999976542 2344 444432 33445567 99999999986
No 200
>PRK02362 ski2-like helicase; Provisional
Probab=66.61 E-value=41 Score=38.31 Aligned_cols=52 Identities=19% Similarity=0.464 Sum_probs=40.0
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc-C
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-G 315 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~-G 315 (455)
-+|.+|||||...+.+..+ .| +.-+++|.+-++..+..+ +|.|+|+++.+. |
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 4688999999998877664 44 667777776666666665 599999999986 6
No 201
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=66.42 E-value=4.1 Score=47.49 Aligned_cols=24 Identities=42% Similarity=0.678 Sum_probs=20.9
Q ss_pred hccCcCHHHHHHHHHc-CCCCHHHhhh
Q 012847 299 EVWGIGPATAQKLYEK-GHRTLDDLKN 324 (455)
Q Consensus 299 ~I~GvGpktA~~ly~~-GirTledL~~ 324 (455)
+|||||||||.+|.++ | |||.+.+
T Consensus 189 GVpGIG~KtA~kLL~~yg--sle~i~~ 213 (887)
T TIGR00593 189 GVKGIGEKTAAKLLQEFG--SLENIYE 213 (887)
T ss_pred CCCCcCHHHHHHHHHHcC--CHHHHHH
Confidence 4999999999999996 6 8888874
No 202
>PRK03980 flap endonuclease-1; Provisional
Probab=66.23 E-value=4.5 Score=41.02 Aligned_cols=25 Identities=44% Similarity=0.670 Sum_probs=21.5
Q ss_pred hccCcCHHHHHHHHHcCCCCHHHhhh
Q 012847 299 EVWGIGPATAQKLYEKGHRTLDDLKN 324 (455)
Q Consensus 299 ~I~GvGpktA~~ly~~GirTledL~~ 324 (455)
+|+|||||||.+|.++ +.|||.+..
T Consensus 193 GI~GIG~ktA~kLi~~-~~sle~i~~ 217 (292)
T PRK03980 193 GIKGIGPKTALKLIKK-HGDLEKVLE 217 (292)
T ss_pred CCCCccHHHHHHHHHH-CCCHHHHHH
Confidence 7899999999999985 348998875
No 203
>PRK03858 DNA polymerase IV; Validated
Probab=66.14 E-value=12 Score=39.09 Aligned_cols=52 Identities=21% Similarity=0.382 Sum_probs=36.6
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--CCC
Q 012847 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHR 317 (455)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--Gir 317 (455)
+..|||||+++++++..+ | +..+.+|.+-.+....+.| |+..++.||+. |+.
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 677899999999998765 3 5556666654444455555 67788889863 763
No 204
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=66.11 E-value=4.5 Score=39.41 Aligned_cols=30 Identities=33% Similarity=0.531 Sum_probs=27.2
Q ss_pred HHhhhccCcCHHHHHHHHHcCCCCHHHhhh
Q 012847 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (455)
Q Consensus 295 ~lf~~I~GvGpktA~~ly~~GirTledL~~ 324 (455)
.-|+.|.||||+.+.+|.+.|+.++++|-.
T Consensus 158 DDL~~I~GIGp~~a~~L~eaGi~tfaQIAa 187 (221)
T PRK12278 158 DDLTKITGVGPALAKKLNEAGVTTFAQIAA 187 (221)
T ss_pred chheeccccChHHHHHHHHcCCCCHHHhhC
Confidence 346799999999999999999999999974
No 205
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=65.97 E-value=14 Score=35.75 Aligned_cols=31 Identities=19% Similarity=0.504 Sum_probs=23.1
Q ss_pred HhcCCcccc-chhhhcCCCCCCHHHHHHHHHH
Q 012847 243 IEKLPFKIE-SADQVKGLPGIGKSMQDHIQEI 273 (455)
Q Consensus 243 L~~l~~~i~-s~~~l~~lpgIG~~ia~kI~Ei 273 (455)
++.+...+. ++++|.+|||||.++|..+--+
T Consensus 97 ~e~~~g~vP~~~~eL~~LPGVGrKTAnvVL~~ 128 (211)
T COG0177 97 LEKFGGEVPDTREELLSLPGVGRKTANVVLSF 128 (211)
T ss_pred HHHcCCCCCchHHHHHhCCCcchHHHHHHHHh
Confidence 345555554 4589999999999999987543
No 206
>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=65.89 E-value=9.6 Score=38.39 Aligned_cols=50 Identities=24% Similarity=0.464 Sum_probs=33.5
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012847 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (455)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (455)
+.+|||||+.+++++.+. -+..+++|..-.+ +.+.+++|++.++|.+||+
T Consensus 1 l~~i~gig~~~~~~L~~~----Gi~ti~dl~~~~~----~~L~~~~g~~~~~a~~l~~ 50 (310)
T TIGR02236 1 LEDLPGVGPATAEKLREA----GYDTFEAIAVASP----KELSEIAGISEGTAAKIIQ 50 (310)
T ss_pred CcccCCCCHHHHHHHHHc----CCCCHHHHHcCCH----HHHHhccCCCHHHHHHHHH
Confidence 457899999998887654 2344555554332 2234777888888888885
No 207
>PRK13844 recombination protein RecR; Provisional
Probab=65.50 E-value=4.2 Score=39.05 Aligned_cols=32 Identities=16% Similarity=0.251 Sum_probs=24.7
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHH
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHF 285 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l 285 (455)
+.+..|||||++.|+++.-++-.-.-.++++|
T Consensus 15 ~~l~~LPGIG~KsA~Rla~~lL~~~~~~~~~l 46 (200)
T PRK13844 15 ESLRKLPTIGKKSSQRLALYLLDKSPETAIAI 46 (200)
T ss_pred HHHHHCCCCCHHHHHHHHHHHHcCCHHHHHHH
Confidence 67899999999999999887765444444444
No 208
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=65.48 E-value=9.6 Score=42.35 Aligned_cols=48 Identities=21% Similarity=0.468 Sum_probs=34.4
Q ss_pred HHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhhhchhhHhhhc
Q 012847 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIK 343 (455)
Q Consensus 295 ~lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~q~~Glk~~ed~~ 343 (455)
..|..|+|||++++++|++ -+-|++++.++. .|....++|.+-.+.|.
T Consensus 525 ~~L~~IpGIG~kr~~~LL~-~FGS~~~I~~As~eeL~~vpGi~~~~A~~I~ 574 (577)
T PRK14668 525 TVLDDVPGVGPETRKRLLR-RFGSVEGVREASVEDLRDVPGVGEKTAETIR 574 (577)
T ss_pred hHHhcCCCCCHHHHHHHHH-HcCCHHHHHhCCHHHHHhCCCCCHHHHHHHH
Confidence 4466999999999999998 456888887653 36666667766655553
No 209
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=64.80 E-value=22 Score=41.39 Aligned_cols=67 Identities=16% Similarity=0.322 Sum_probs=45.2
Q ss_pred HHHHHHHHHHHHHhhhcCC----CeEEEEecccccCC-CCCCCccEEEeCCCc--hhhhhhHHHHHHHHHHcCc
Q 012847 349 HEVEQMERLLQKAGEEVLP----EVIILCGGSYRRGK-ASCGDLDVVIMHPDR--KSHKGFLSKYVKKLKEMKF 415 (455)
Q Consensus 349 ~Ea~~i~~~v~~~~~~~~p----~~~v~~~Gs~RRgk-e~~gDvDiLit~~d~--~~~~~~l~~lv~~L~~~g~ 415 (455)
.-+.-+..+++.+-....+ ++-+..+|||=||. ---.|||+||-+++. .....++..++.-|=+.|+
T Consensus 33 ~~~~~~D~~l~~l~~~~~~~~~~~iaLvAvGGYGR~eL~P~SDIDlliL~~~~~~~~~~~~i~~~~~~LWD~gl 106 (854)
T PRK01759 33 NRSDFYDQLLIHLWQQFGLEEQSDLALIAVGGYGRREMFPLSDLDILILTEQPPDEETEEKINQFFQFLWDCGF 106 (854)
T ss_pred HHHHHHHHHHHHHHHHccCCCCCCeEEEEeCCcccccCCCcccceEEEEeCCCCChHHHHHHHHHHHHHHhcCC
Confidence 3344455555554433312 35677899997765 456899999988753 3356788888888888887
No 210
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=64.58 E-value=10 Score=35.80 Aligned_cols=43 Identities=28% Similarity=0.292 Sum_probs=29.6
Q ss_pred ccccc-hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhch
Q 012847 248 FKIES-ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEK 290 (455)
Q Consensus 248 ~~i~s-~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~ 290 (455)
.||+. +.+|.=|||||+++...|-|=-+.+.+..++++++..+
T Consensus 109 ~PIt~RlH~LeLLPGIGKK~m~~ILeERkkkpFeSFeDi~~Rv~ 152 (181)
T PF04919_consen 109 QPITLRLHSLELLPGIGKKTMWKILEERKKKPFESFEDIEERVK 152 (181)
T ss_dssp --B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHST
T ss_pred CCChHHHHHHhhcccccHHHHHHHHHHHccCCCCCHHHHHHHhc
Confidence 46775 47899999999999999999999999999998876443
No 211
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=64.13 E-value=7 Score=38.67 Aligned_cols=31 Identities=23% Similarity=0.366 Sum_probs=23.1
Q ss_pred HHHHhhchhHHHHHhhhccCcCHHHHHHHHHc
Q 012847 283 EHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (455)
Q Consensus 283 e~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 314 (455)
+++..|.|..+-+|+ ++||||||.|.--.+.
T Consensus 148 d~f~gDIP~~v~dLl-sLPGVGPKMa~L~m~~ 178 (286)
T KOG1921|consen 148 DKFDGDIPDTVEDLL-SLPGVGPKMAHLTMQV 178 (286)
T ss_pred HHhCCCCchhHHHHh-cCCCCchHHHHHHHHH
Confidence 556677787666666 9999999999765543
No 212
>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=64.12 E-value=8.9 Score=31.67 Aligned_cols=30 Identities=23% Similarity=0.470 Sum_probs=23.9
Q ss_pred hhhccCcCHHHHHHHHHc----CCCCHHHhhhcc
Q 012847 297 FGEVWGIGPATAQKLYEK----GHRTLDDLKNED 326 (455)
Q Consensus 297 f~~I~GvGpktA~~ly~~----GirTledL~~~~ 326 (455)
|+.|.|||.++|+++.++ .++|++|+....
T Consensus 29 l~~Ikglg~~~a~~I~~~R~~g~f~s~~df~~R~ 62 (90)
T PF14579_consen 29 LSAIKGLGEEVAEKIVEERENGPFKSLEDFIQRL 62 (90)
T ss_dssp GGGSTTS-HHHHHHHHHHHHCSS-SSHHHHHHHS
T ss_pred HhhcCCCCHHHHHHHHHhHhcCCCCCHHHHHHHH
Confidence 789999999999999963 789999987543
No 213
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=63.65 E-value=17 Score=37.01 Aligned_cols=48 Identities=17% Similarity=0.088 Sum_probs=39.7
Q ss_pred CCCCCcEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcC
Q 012847 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMD 65 (455)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~R~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~ 65 (455)
..|.|.+|.|-+.--+.. +..+++++..+||.|.++++.++|.+|+.+
T Consensus 219 ~~l~g~~~vfTG~l~~~~-R~~~~~~~~~~Gg~v~~sVs~~t~~lV~G~ 266 (309)
T PRK06195 219 TAFKEEVVVFTGGLASMT-RDEAMILVRRLGGTVGSSVTKKTTYLVTNT 266 (309)
T ss_pred ccccCCEEEEccccCCCC-HHHHHHHHHHhCCEecCCcccCceEEEECC
Confidence 469999999976532333 456899999999999999999999999864
No 214
>PTZ00217 flap endonuclease-1; Provisional
Probab=63.00 E-value=5.5 Score=42.10 Aligned_cols=26 Identities=35% Similarity=0.640 Sum_probs=21.8
Q ss_pred hhccCcCHHHHHHHHHcCCCCHHHhhh
Q 012847 298 GEVWGIGPATAQKLYEKGHRTLDDLKN 324 (455)
Q Consensus 298 ~~I~GvGpktA~~ly~~GirTledL~~ 324 (455)
-+|+|||||||.+|.++ +.|+|.+.+
T Consensus 238 pgi~GIG~ktA~~Li~~-~gsle~il~ 263 (393)
T PTZ00217 238 DTIKGIGPKTAYKLIKK-YKSIEEILE 263 (393)
T ss_pred CCCCCccHHHHHHHHHH-cCCHHHHHH
Confidence 37999999999999986 348888864
No 215
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=62.72 E-value=6.1 Score=44.61 Aligned_cols=27 Identities=41% Similarity=0.623 Sum_probs=25.0
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhh
Q 012847 297 FGEVWGIGPATAQKLYEKGHRTLDDLK 323 (455)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirTledL~ 323 (455)
++.+.||||++|+.|-+.||.|+.||.
T Consensus 11 ~~~l~gvg~~~~~~l~~lgi~t~~dll 37 (681)
T PRK10917 11 LTSLKGVGPKTAEKLAKLGIHTVQDLL 37 (681)
T ss_pred hhhcCCCCHHHHHHHHHcCCCCHHHHh
Confidence 457899999999999989999999998
No 216
>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=62.47 E-value=15 Score=38.60 Aligned_cols=54 Identities=20% Similarity=0.484 Sum_probs=35.3
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhc---------------hhHHHHHhhhccCcCHHHHHHHHHc--CCC
Q 012847 255 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDE---------------KVRTISLFGEVWGIGPATAQKLYEK--GHR 317 (455)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~---------------~~~~l~lf~~I~GvGpktA~~ly~~--Gir 317 (455)
.+..|||||+++++++..+ | +..+-+|.+-. ...+.+.| |.+++.++|+. |+.
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 3778899999999998875 3 33333443322 22344444 67778889875 886
Q ss_pred C
Q 012847 318 T 318 (455)
Q Consensus 318 T 318 (455)
+
T Consensus 243 ~ 243 (379)
T cd01703 243 T 243 (379)
T ss_pred C
Confidence 5
No 217
>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=62.31 E-value=6.5 Score=30.78 Aligned_cols=23 Identities=26% Similarity=0.349 Sum_probs=17.6
Q ss_pred hHHHHH-hhhccCcCHHHHHHHHH
Q 012847 291 VRTISL-FGEVWGIGPATAQKLYE 313 (455)
Q Consensus 291 ~~~l~l-f~~I~GvGpktA~~ly~ 313 (455)
...++. +.+|||||+++|.++.+
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 334454 77999999999999854
No 218
>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=62.20 E-value=19 Score=33.95 Aligned_cols=54 Identities=11% Similarity=0.300 Sum_probs=32.7
Q ss_pred HHHHHHHHcCC-ChhHHHHHHHHHHHh-cCCcccc-chhhhcCCCCCCHHHHHHHHH
Q 012847 219 KLINIYRALGE-DRRSFSYYKAIPVIE-KLPFKIE-SADQVKGLPGIGKSMQDHIQE 272 (455)
Q Consensus 219 ~la~~~e~~g~-~~r~~aY~rAa~~L~-~l~~~i~-s~~~l~~lpgIG~~ia~kI~E 272 (455)
+|++.++-.|= +.|+..-.+++..+. .+...+. ..++|.+|||||+.+|+.|--
T Consensus 68 ~L~~~ir~~G~~~~Ka~~i~~~a~~i~~~~~~~~~~~~~~L~~l~GIG~ktA~~ill 124 (191)
T TIGR01083 68 ELEEYIKSIGLYRNKAKNIIALCRILVERYGGEVPEDREELVKLPGVGRKTANVVLN 124 (191)
T ss_pred HHHHHHHhcCChHHHHHHHHHHHHHHHHHcCCCCchHHHHHHhCCCCcHHHHHHHHH
Confidence 34444333342 235656666666553 3332222 357899999999999999863
No 219
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=61.95 E-value=5.9 Score=44.15 Aligned_cols=49 Identities=22% Similarity=0.369 Sum_probs=33.7
Q ss_pred HHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhhhchhhHhhh
Q 012847 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDI 342 (455)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~q~~Glk~~ed~ 342 (455)
....|..|+|||++++++|++ -+.|++++..+. .|....++|.+..+.|
T Consensus 541 ~~s~L~~IpGIG~k~~k~Ll~-~FgS~~~i~~As~eeL~~v~Gig~~~A~~I 591 (598)
T PRK00558 541 LTSALDDIPGIGPKRRKALLK-HFGSLKAIKEASVEELAKVPGISKKLAEAI 591 (598)
T ss_pred hhhhHhhCCCcCHHHHHHHHH-HcCCHHHHHhCCHHHHhhcCCcCHHHHHHH
Confidence 344567999999999999998 556788888643 3555555555444333
No 220
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=61.70 E-value=11 Score=42.23 Aligned_cols=93 Identities=16% Similarity=0.221 Sum_probs=55.5
Q ss_pred CCCCCCCCCCCCCCCCCCCcEEEEecCCCCchHHHHHHHHHHhcCCEEEeec------CCCccEEEEcCCh--HHHHHHH
Q 012847 3 PKTTRKPTPALDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKL------SKKVTHVLAMDLE--ALLQQVS 74 (455)
Q Consensus 3 p~~~~~~~~~~~~~~~F~g~~iy~~~~~~g~~R~~~l~~li~~~Gg~V~~~l------s~~VTHVV~~~~~--~~l~~l~ 74 (455)
||.+|.++-+.. ..+|.|.-+||++.+.... -+.|.+++...||++...- +..-|-|++...- ....|.+
T Consensus 573 ~~~~~~~a~s~~-~kLf~gl~~~~~g~fs~~p-~~~l~~l~~~~gg~~l~~~~~~~~~~k~s~~~~~~~~~~~~~~~~~k 650 (684)
T KOG4362|consen 573 PKEKRLRAESYK-PKLFEGLKFYFVGDFSNPP-KEQLQELVHLAGGTILQVPRVAYSDKKKSTIVVLSEKPVLDSILWQK 650 (684)
T ss_pred cccccccccccC-cchhcCCcceeecccccCc-HHHHHHHHhhcCcceeeccCcccccccccceeEeecccCCCchhhhh
Confidence 455554444433 4799999999998765432 4678999999999987642 2223334432110 0001111
Q ss_pred HHhhh----ccCccccccchHHHHHhc
Q 012847 75 KQHLA----RFKGSVIRYQWLEDSLRL 97 (455)
Q Consensus 75 ~~~~~----~~~~~lV~~~Wl~es~k~ 97 (455)
...+. ..+.++|+-.||.+++.-
T Consensus 651 ~~~~ea~~~s~~a~~~~~~wvl~s~a~ 677 (684)
T KOG4362|consen 651 VNDAEALALSQRARAVSSSWVLDSIAG 677 (684)
T ss_pred hccHHHHHHhcCCCccchhhhhcchhc
Confidence 11111 126789999999999754
No 221
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=61.43 E-value=9.3 Score=43.89 Aligned_cols=85 Identities=13% Similarity=0.179 Sum_probs=62.9
Q ss_pred CCCCCCCcEEEEecCCCCchHHHHHHHHHHhcCCEEEee-cCCCccEEEEcCChHHH-HHHHHHhhhccCccccccchHH
Q 012847 15 SNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEK-LSKKVTHVLAMDLEALL-QQVSKQHLARFKGSVIRYQWLE 92 (455)
Q Consensus 15 ~~~~F~g~~iy~~~~~~g~~R~~~l~~li~~~Gg~V~~~-ls~~VTHVV~~~~~~~l-~~l~~~~~~~~~~~lV~~~Wl~ 92 (455)
....|+++.+|...+.+.. ..-++++-..+|+..... ...+.||+++.+..+.+ +.++ .+...+++|+.
T Consensus 44 ~~s~fs~is~~~ngs~~e~--~nelk~~~~~~t~~~~~~~~rs~T~~ii~~~l~a~~vk~~~-------~~~~~~~e~ii 114 (1016)
T KOG2093|consen 44 GSSSFSGISISVNGSTDES--ANELKLQNMFHTGASAASYERSGTENIIAQGLPADLVKGFT-------IPKHISIEWII 114 (1016)
T ss_pred CcceeeeeeeccCCccccc--hHHHhhhhhhcccccccccccccceeeecccchHHHhcccc-------chhhhcHHHHH
Confidence 3468999999988766654 345778888999998844 46789999998876542 2211 46778999999
Q ss_pred HHHhcCCCCCcccccc
Q 012847 93 DSLRLGEKVSEDLYRI 108 (455)
Q Consensus 93 es~k~g~lvdee~y~l 108 (455)
||.+.|..+.--.|.+
T Consensus 115 e~~~~~~~~~~~~~~~ 130 (1016)
T KOG2093|consen 115 ECCENGMDVGYYPYQL 130 (1016)
T ss_pred HHHhccCcccccccee
Confidence 9999999887555433
No 222
>PRK04374 PII uridylyl-transferase; Provisional
Probab=61.30 E-value=27 Score=40.81 Aligned_cols=63 Identities=19% Similarity=0.404 Sum_probs=41.6
Q ss_pred HHHHHHHHhhhcCC---CeEEEEecccccCC-CCCCCccEEEeCCCc--hhhhhhHHHHHHHHHHcCce
Q 012847 354 MERLLQKAGEEVLP---EVIILCGGSYRRGK-ASCGDLDVVIMHPDR--KSHKGFLSKYVKKLKEMKFL 416 (455)
Q Consensus 354 i~~~v~~~~~~~~p---~~~v~~~Gs~RRgk-e~~gDvDiLit~~d~--~~~~~~l~~lv~~L~~~g~l 416 (455)
+..++..+.....| ++-++.+|||=||. --..|||+||-+++. ......+.+++..|=+.|+=
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 34455544433334 35677899996654 567899999988743 23456678888888777663
No 223
>KOG3524 consensus Predicted guanine nucleotide exchange factor (PEBBLE) [Signal transduction mechanisms]
Probab=61.28 E-value=4.6 Score=45.14 Aligned_cols=86 Identities=19% Similarity=0.337 Sum_probs=60.9
Q ss_pred CCCCCcEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccchHHHHHh
Q 012847 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSLR 96 (455)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~R~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~~~~~l~~l~~~~~~~~~~~lV~~~Wl~es~k 96 (455)
.-|.|+.++|. |+...-.+++-......||.... -...+||||+.+....-.-+ ......++|+-+|+-=++.
T Consensus 209 ~~feg~~~~f~--gF~~ee~~~m~~sle~~gg~~a~-~d~~cthvvv~e~~~~~~p~----~~s~~~~~vk~ewfw~siq 281 (850)
T KOG3524|consen 209 GVFEGLSLFFH--GFKQEEIDDMLRSLENTGGKLAP-SDTLCTHVVVNEDNDEVEPL----AVSSNQVHVKKEWFWVSIQ 281 (850)
T ss_pred ccccCCeEeec--CCcHHHHHHHHHHHHhcCCcccC-CCCCceeEeecCCccccccc----cccccceeecccceEEEEe
Confidence 56999999998 67766677888888999999888 56889999997754321111 1122457888888877777
Q ss_pred cCCCCCccccccc
Q 012847 97 LGEKVSEDLYRIK 109 (455)
Q Consensus 97 ~g~lvdee~y~l~ 109 (455)
.|..--|+.|...
T Consensus 282 ~g~~a~e~~yl~~ 294 (850)
T KOG3524|consen 282 RGCCAIEDNYLLP 294 (850)
T ss_pred cchhccccceecc
Confidence 7766666666553
No 224
>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=61.26 E-value=8.4 Score=27.71 Aligned_cols=32 Identities=31% Similarity=0.365 Sum_probs=23.8
Q ss_pred cCHHHHHHHHHcCCCCHHHhhhcc--Cchhhhhh
Q 012847 303 IGPATAQKLYEKGHRTLDDLKNED--SLTHSQRL 334 (455)
Q Consensus 303 vGpktA~~ly~~GirTledL~~~~--~L~~~q~~ 334 (455)
|.+..+.+|++.|+.|+++|.... .|...+++
T Consensus 1 i~~~~~~~L~~~G~~s~e~la~~~~~eL~~i~g~ 34 (50)
T TIGR01954 1 IDEEIAQLLVEEGFTTVEDLAYVPIDELLSIEGF 34 (50)
T ss_pred CCHHHHHHHHHcCCCCHHHHHccCHHHHhcCCCC
Confidence 467889999999999999998542 35544443
No 225
>PRK07758 hypothetical protein; Provisional
Probab=61.20 E-value=8.5 Score=32.61 Aligned_cols=23 Identities=13% Similarity=0.355 Sum_probs=20.3
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHh
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTT 276 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~t 276 (455)
+||.+|+|+|++..+.|+|-|..
T Consensus 67 ~ELl~iknlGkKSL~EIkekL~E 89 (95)
T PRK07758 67 KEILKLHGMGPASLPKLRKALEE 89 (95)
T ss_pred HHHHHccCCCHHHHHHHHHHHHH
Confidence 68999999999999999987754
No 226
>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=60.52 E-value=6.6 Score=40.58 Aligned_cols=27 Identities=41% Similarity=0.588 Sum_probs=22.9
Q ss_pred hhccCcCHHHHHHHHHcCCCCHHHhhhc
Q 012847 298 GEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (455)
Q Consensus 298 ~~I~GvGpktA~~ly~~GirTledL~~~ 325 (455)
.+|+|||||||.+|.++ +.|+|.+.+.
T Consensus 239 ~Gv~GIG~ktA~kli~~-~gsie~il~~ 265 (338)
T TIGR03674 239 EGVKGIGPKTALKLIKE-HGDLEKVLKA 265 (338)
T ss_pred CCCCCccHHHHHHHHHH-cCCHHHHHHh
Confidence 38999999999999997 4589988753
No 227
>PRK05755 DNA polymerase I; Provisional
Probab=60.48 E-value=6 Score=46.06 Aligned_cols=25 Identities=44% Similarity=0.598 Sum_probs=21.3
Q ss_pred hhccCcCHHHHHHHHHc-CCCCHHHhhh
Q 012847 298 GEVWGIGPATAQKLYEK-GHRTLDDLKN 324 (455)
Q Consensus 298 ~~I~GvGpktA~~ly~~-GirTledL~~ 324 (455)
-+|+|||||||.+|.++ | |+|.+.+
T Consensus 190 pGv~GiG~ktA~~Ll~~~g--sle~i~~ 215 (880)
T PRK05755 190 PGVPGIGEKTAAKLLQEYG--SLEGLYE 215 (880)
T ss_pred CCCCCccHHHHHHHHHHcC--CHHHHHH
Confidence 36899999999999986 6 8888874
No 228
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=60.18 E-value=6.3 Score=40.63 Aligned_cols=32 Identities=19% Similarity=0.239 Sum_probs=28.5
Q ss_pred HHHHhhhccCcCHHHHHHHHHcCCCCHHHhhh
Q 012847 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (455)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~GirTledL~~ 324 (455)
.-.-|+.|.||||+.+++|.+.||.+++++-.
T Consensus 261 ~~DdL~~I~GiGp~~e~~L~~~Gi~~f~QiA~ 292 (326)
T PRK12311 261 APDDLKKLTGVSPQIEKKLNDLGIFHFWQLAE 292 (326)
T ss_pred CchhhhhhccCChhhhhhhhhcCCCCHHHhhC
Confidence 34557799999999999999999999999974
No 229
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=60.00 E-value=6.7 Score=43.52 Aligned_cols=20 Identities=15% Similarity=0.165 Sum_probs=12.2
Q ss_pred CchhhhhhchhhHhhhccCc
Q 012847 327 SLTHSQRLGLKYFDDIKTRI 346 (455)
Q Consensus 327 ~L~~~q~~Glk~~ed~~~~i 346 (455)
.|..+.++|.+....+...+
T Consensus 526 ~L~~IpGIG~kr~~~LL~~F 545 (577)
T PRK14668 526 VLDDVPGVGPETRKRLLRRF 545 (577)
T ss_pred HHhcCCCCCHHHHHHHHHHc
Confidence 35566677766666665544
No 230
>PRK02794 DNA polymerase IV; Provisional
Probab=59.96 E-value=54 Score=34.63 Aligned_cols=52 Identities=13% Similarity=0.317 Sum_probs=34.5
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--CCCC
Q 012847 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (455)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--GirT 318 (455)
+..|||||+.+.++...+ -+..+.+|.+-.+....+.| |+ .+..+|+. |+..
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 778999999998887643 35666666654444444445 44 57777775 8854
No 231
>COG1204 Superfamily II helicase [General function prediction only]
Probab=59.80 E-value=11 Score=43.22 Aligned_cols=112 Identities=23% Similarity=0.312 Sum_probs=64.0
Q ss_pred hHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCc--hhhHHH----HhhchhHHHHHhhhccCcCH
Q 012847 232 RSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKL--SKLEHF----EKDEKVRTISLFGEVWGIGP 305 (455)
Q Consensus 232 r~~aY~rAa~~L~~l~~~i~s~~~l~~lpgIG~~ia~kI~Eil~tG~~--~~le~l----~~~~~~~~l~lf~~I~GvGp 305 (455)
-..+|-.+...+...-....=. .+. +..+|.++ .++..++..|.. ..++.+ +...+...+..+..|.|+|.
T Consensus 609 i~~~~~~~~~dl~~~~~~a~w~-~~~-~~~l~~~~-~r~~~~~~~~~~~~~~~~~~~~rie~gv~~e~~~~l~~i~~~gr 685 (766)
T COG1204 609 ILNAYGVAPGDLLRIAETAEWL-SAD-LLALGKAA-ERLAKILGLGLHVLRKLEILSLRIEYGVRSEELLELVEIRGVGR 685 (766)
T ss_pred HHHHhCcchhhHHhhcchhhhh-hhh-hhhhhhhh-hhhHhhhCCCccccccchhhhhhhhcCCChhhhcccccccccch
Confidence 3445555555544433222212 122 44444444 444455555533 333332 33333233334459999999
Q ss_pred HHHHHHHHcCCCCHHHhhhc---cCchhhhhhchhhHhhhccCc
Q 012847 306 ATAQKLYEKGHRTLDDLKNE---DSLTHSQRLGLKYFDDIKTRI 346 (455)
Q Consensus 306 ktA~~ly~~GirTledL~~~---~~L~~~q~~Glk~~ed~~~~i 346 (455)
..|++||..|+++++++... ..+....++|.+.++.+....
T Consensus 686 vrar~ly~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~ 729 (766)
T COG1204 686 VRARKLYNAGYKSLEDLRLIADPAELLPLTGIGERLVEAILESL 729 (766)
T ss_pred hHHHHHHHhhhccHHHHHhhcChhhhhhhhhhHHHHHHHHHHHh
Confidence 99999999999999999943 245666777777776665443
No 232
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=59.29 E-value=6.8 Score=39.93 Aligned_cols=32 Identities=31% Similarity=0.339 Sum_probs=23.6
Q ss_pred HHHhhhccCcCHHHHHHHHHc-CC--CCHHHhhhc
Q 012847 294 ISLFGEVWGIGPATAQKLYEK-GH--RTLDDLKNE 325 (455)
Q Consensus 294 l~lf~~I~GvGpktA~~ly~~-Gi--rTledL~~~ 325 (455)
.+++.+|||+|+|.|+++... -. -|+|+|++-
T Consensus 329 ~~~llRVPGiG~ksa~rIv~~Rr~~rl~~e~Lkk~ 363 (404)
T COG4277 329 YKELLRVPGIGVKSARRIVMTRRRTRLTLEDLKKL 363 (404)
T ss_pred HHHhcccCCCChHHHHHHHHHhhhcccCHHHHhhh
Confidence 344559999999999999874 33 456777653
No 233
>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=59.01 E-value=4.9 Score=40.90 Aligned_cols=51 Identities=25% Similarity=0.342 Sum_probs=34.2
Q ss_pred HHHHhhhccCcCHHHHHHHHHc---C-CCCHHHhhhcc-----CchhhhhhchhhHhhhc
Q 012847 293 TISLFGEVWGIGPATAQKLYEK---G-HRTLDDLKNED-----SLTHSQRLGLKYFDDIK 343 (455)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~---G-irTledL~~~~-----~L~~~q~~Glk~~ed~~ 343 (455)
.+..+++|||||+++|+++.+- | +..+++|+++. .|..+.|+|.+....|-
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 3444579999999999998873 4 35666666431 25566777766665554
No 234
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=58.55 E-value=14 Score=42.53 Aligned_cols=27 Identities=26% Similarity=0.332 Sum_probs=21.4
Q ss_pred hhccCcCHHHHHHHHHcCCCCHHHhhh
Q 012847 298 GEVWGIGPATAQKLYEKGHRTLDDLKN 324 (455)
Q Consensus 298 ~~I~GvGpktA~~ly~~GirTledL~~ 324 (455)
..+||||-.+-.+|-..||.|..||+.
T Consensus 552 ~~LPGVG~sm~~kL~s~~i~tCgdLq~ 578 (1016)
T KOG2093|consen 552 DDLPGVGSSMKSKLVSQFIQTCGDLQL 578 (1016)
T ss_pred ccCCCccHHHHHHHHHhccchhHHHHH
Confidence 467888888888888888888888874
No 235
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=58.30 E-value=6.6 Score=34.77 Aligned_cols=25 Identities=24% Similarity=0.383 Sum_probs=20.6
Q ss_pred HHHHhhhccCcCHHHHHHHHHc-CCC
Q 012847 293 TISLFGEVWGIGPATAQKLYEK-GHR 317 (455)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~-Gir 317 (455)
+.-.|+.|+|||+++|.++-+. ||.
T Consensus 15 v~~aLt~i~GIG~~~A~~ic~~lgi~ 40 (122)
T CHL00137 15 IEYALTYIYGIGLTSAKEILEKANID 40 (122)
T ss_pred eeeeecccccccHHHHHHHHHHcCcC
Confidence 3344689999999999999987 874
No 236
>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=58.24 E-value=16 Score=36.56 Aligned_cols=29 Identities=31% Similarity=0.470 Sum_probs=22.5
Q ss_pred HhhhccCcCHHHHHHHHHcCCCCHHHhhh
Q 012847 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (455)
Q Consensus 296 lf~~I~GvGpktA~~ly~~GirTledL~~ 324 (455)
.|.++||+|++.++++-+.|+.|+++|.+
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 35599999999999999999999999995
No 237
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=57.93 E-value=6.5 Score=34.80 Aligned_cols=24 Identities=21% Similarity=0.470 Sum_probs=20.3
Q ss_pred HHHhhhccCcCHHHHHHHHHc-CCC
Q 012847 294 ISLFGEVWGIGPATAQKLYEK-GHR 317 (455)
Q Consensus 294 l~lf~~I~GvGpktA~~ly~~-Gir 317 (455)
.-.|+.|+|||+++|..+.+. |+.
T Consensus 16 ~~aL~~I~GIG~~~a~~i~~~lgi~ 40 (122)
T PRK05179 16 VIALTYIYGIGRTRAKEILAAAGID 40 (122)
T ss_pred EeeecccccccHHHHHHHHHHhCcC
Confidence 334689999999999999987 874
No 238
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=57.68 E-value=19 Score=40.34 Aligned_cols=50 Identities=18% Similarity=0.412 Sum_probs=34.5
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 314 (455)
..|.+|||||++.+.++-+ ++.-++.+++.. .+.+.+| ||.++|+++|+.
T Consensus 552 S~L~~IpGIG~kr~~~LL~-----~FgSi~~I~~As----~eeL~~v--i~~k~A~~I~~~ 601 (624)
T PRK14669 552 SELLEIPGVGAKTVQRLLK-----HFGSLERVRAAT----ETQLAAV--VGRAAAEAIIAH 601 (624)
T ss_pred HHHhcCCCCCHHHHHHHHH-----HcCCHHHHHhCC----HHHHHHH--hCHHHHHHHHHH
Confidence 5788999999998887644 334444554422 3333455 899999999874
No 239
>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=57.45 E-value=16 Score=37.40 Aligned_cols=77 Identities=18% Similarity=0.200 Sum_probs=44.2
Q ss_pred HHHHcCCChhHHHHHHHHHHHhcCC--c----ccc------chhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhch
Q 012847 223 IYRALGEDRRSFSYYKAIPVIEKLP--F----KIE------SADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEK 290 (455)
Q Consensus 223 ~~e~~g~~~r~~aY~rAa~~L~~l~--~----~i~------s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~ 290 (455)
.++..|-.+|+..-..+|..+..-. . .+. ..++|..|||||+.+|+-|.=+ .-|... .+- ..
T Consensus 177 ~Lr~~G~g~Ra~~I~~~A~~i~~~~~~~~~l~~l~~~~~~~~~~~L~~l~GIG~~tAd~vll~-~l~~~d---~~P--vD 250 (310)
T TIGR00588 177 HLRKLGLGYRARYIRETARALLEEQGGRAWLQQIRGASYEDAREALCELPGVGPKVADCICLM-GLDKPQ---AVP--VD 250 (310)
T ss_pred HHHHcCCHHHHHHHHHHHHHHHhccCCchhHHhhccCChHHHHHHHHhCCCccHHHHHHHHHH-hCCCCC---cee--ec
Confidence 3344455467777777777765421 1 111 2368999999999999988533 333322 111 12
Q ss_pred hHHHHHhhhccCcCH
Q 012847 291 VRTISLFGEVWGIGP 305 (455)
Q Consensus 291 ~~~l~lf~~I~GvGp 305 (455)
..+.+.+.+++|+.+
T Consensus 251 ~~v~r~~~r~y~~~~ 265 (310)
T TIGR00588 251 VHVWRIANRDYPWHP 265 (310)
T ss_pred HHHHHHHHHHhcccc
Confidence 446666666666543
No 240
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=56.72 E-value=26 Score=39.38 Aligned_cols=72 Identities=19% Similarity=0.087 Sum_probs=54.7
Q ss_pred CCCCCcEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccchHHH
Q 012847 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLED 93 (455)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~R~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~~~~~l~~l~~~~~~~~~~~lV~~~Wl~e 93 (455)
..|.|.+|.|-++--+-+|. ..+.++...||+|..++|.++.-||+.++-.- +..++...+++|++-+|+.+
T Consensus 593 ~~l~gkt~V~TGtL~~~sR~-eak~~le~lGakv~~SVSkktD~vvaG~~aGS----Kl~kA~eLgv~i~~E~~~~~ 664 (667)
T COG0272 593 SPLAGKTFVLTGTLEGMSRD-EAKALLEALGAKVSGSVSKKTDYVVAGENAGS----KLAKAQELGVKIIDEEEFLA 664 (667)
T ss_pred cccCCCEEEEeccCCCCCHH-HHHHHHHHcCCEEeceecccccEEEEcCCCCh----HHHHHHHcCCeEecHHHHHH
Confidence 67999999997765555554 57999999999999999999999998765331 22334455788888887765
No 241
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=56.21 E-value=6.8 Score=40.75 Aligned_cols=54 Identities=19% Similarity=0.241 Sum_probs=42.7
Q ss_pred HhhchhHHHHHhhhccCcCHHHHHHHHHc-CCCCHHHhhhcc--CchhhhhhchhhHhh
Q 012847 286 EKDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED--SLTHSQRLGLKYFDD 341 (455)
Q Consensus 286 ~~~~~~~~l~lf~~I~GvGpktA~~ly~~-GirTledL~~~~--~L~~~q~~Glk~~ed 341 (455)
.....+.-..++.+||+||+..|++|.+. | ||..|.++. .|....++|-+....
T Consensus 278 d~~v~prGyRiLs~IPrl~k~iAk~Ll~~FG--SL~~Il~As~eeL~~VeGIGe~rA~~ 334 (352)
T PRK13482 278 DTPVSPRGYRLLSKIPRLPSAVIENLVEHFG--SLQGLLAASIEDLDEVEGIGEVRARA 334 (352)
T ss_pred ccccCCcHHHHHhcCCCCCHHHHHHHHHHcC--CHHHHHcCCHHHHhhCCCcCHHHHHH
Confidence 34455678899999999999999999997 6 898888653 477777888766554
No 242
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=56.01 E-value=22 Score=34.58 Aligned_cols=91 Identities=22% Similarity=0.216 Sum_probs=48.4
Q ss_pred HHHHHHHHHcCC-ChhHHHHHHHHHHHhc-CCc-----cccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhch
Q 012847 218 GKLINIYRALGE-DRRSFSYYKAIPVIEK-LPF-----KIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEK 290 (455)
Q Consensus 218 ~~la~~~e~~g~-~~r~~aY~rAa~~L~~-l~~-----~i~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~ 290 (455)
++|+++..-.|= +.|+..-+..+..+.. +.. .-...++|.+|||||..+|+.|-=+. -|+-.-+ ..
T Consensus 78 eeL~~~Irp~Gf~~~KA~~Lk~la~~i~~~~g~~~~~~~~~~re~Ll~l~GIG~kTAd~iLlya-~~rp~fv------VD 150 (218)
T PRK13913 78 SKLAECVRPSGFYNQKAKRLIDLSENILKDFGSFENFKQEVTREWLLDQKGIGKESADAILCYV-CAKEVMV------VD 150 (218)
T ss_pred HHHHHHHHhcCCHHHHHHHHHHHHHHHHHHcCCchhccCchHHHHHHcCCCccHHHHHHHHHHH-cCCCccc------cc
Confidence 444444443342 1245555555555532 211 01234789999999999999987553 3331111 12
Q ss_pred hHHHHHhhhccCcCH---HHHHHHHHcCC
Q 012847 291 VRTISLFGEVWGIGP---ATAQKLYEKGH 316 (455)
Q Consensus 291 ~~~l~lf~~I~GvGp---ktA~~ly~~Gi 316 (455)
.-+.++|.++ |+.+ ..+++|+..++
T Consensus 151 ty~~Rv~~Rl-G~~~~~y~~~~~~~~~~l 178 (218)
T PRK13913 151 KYSYLFLKKL-GIEIEDYDELQHFFEKGV 178 (218)
T ss_pred hhHHHHHHHc-CCCCCCHHHHHHHHHHhh
Confidence 2366677543 7644 44555555444
No 243
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=55.65 E-value=28 Score=30.93 Aligned_cols=42 Identities=10% Similarity=0.307 Sum_probs=26.8
Q ss_pred hHHHHHHHHHHHhc-CCccc-cchhhhcCCCCCCHHHHHHHHHH
Q 012847 232 RSFSYYKAIPVIEK-LPFKI-ESADQVKGLPGIGKSMQDHIQEI 273 (455)
Q Consensus 232 r~~aY~rAa~~L~~-l~~~i-~s~~~l~~lpgIG~~ia~kI~Ei 273 (455)
|+..-...+..|.. +...+ ...+.|..|||||+.+|+.|.=+
T Consensus 48 ka~~i~~~a~~~~~~~~~~~~~~~~~L~~l~GIG~~tA~~~l~~ 91 (149)
T smart00478 48 KAKYLIELARILVEEYGGEVPDDREELLKLPGVGRKTANAVLSF 91 (149)
T ss_pred HHHHHHHHHHHHHHHHCCCccHHHHHHHcCCCCcHHHHHHHHHH
Confidence 55555555555543 22222 23477999999999999987644
No 244
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=54.82 E-value=41 Score=39.41 Aligned_cols=49 Identities=16% Similarity=0.447 Sum_probs=35.9
Q ss_pred CeEEEEecccccCC-CCCCCccEEEeCCCch--hhhhhHHHHHHHHHHcCce
Q 012847 368 EVIILCGGSYRRGK-ASCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMKFL 416 (455)
Q Consensus 368 ~~~v~~~Gs~RRgk-e~~gDvDiLit~~d~~--~~~~~l~~lv~~L~~~g~l 416 (455)
++-+..+|||=||. --..|||+||-+++.. ....++..++..|=+.|+=
T Consensus 78 ~~alvAvGgyGR~EL~p~SDiDll~l~~~~~~~~~~~~i~~~~~~LwD~gL~ 129 (895)
T PRK00275 78 DIALVAVGGYGRGELHPYSDIDLLILLDSADHEEFREPIERFLTLLWDIGLE 129 (895)
T ss_pred CEEEEEcCCccccCcCCCCCceEEEEecCCCChHHHHHHHHHHHHHHhcCCC
Confidence 46778899997765 5678999999887432 2456777888877777763
No 245
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=54.79 E-value=11 Score=31.35 Aligned_cols=55 Identities=24% Similarity=0.306 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc-CCCCHHHh
Q 012847 261 GIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDL 322 (455)
Q Consensus 261 gIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~-GirTledL 322 (455)
||+.+++.+|.+......+ +.|++ .||. |+..|.|||-++|.++... |+.--+.-
T Consensus 19 gl~~~~a~kl~~~yg~~ai---~~l~~-nPY~---L~~~i~gi~F~~aD~iA~~~g~~~~d~~ 74 (94)
T PF14490_consen 19 GLSPKLAMKLYKKYGDDAI---EILKE-NPYR---LIEDIDGIGFKTADKIALKLGIEPDDPR 74 (94)
T ss_dssp T--HHHHHHHHHHH-TTHH---HHHHH--STC---CCB-SSSSBHHHHHHHHHTTT--TT-HH
T ss_pred CCCHHHHHHHHHHHhHHHH---HHHHH-ChHH---HHHHccCCCHHHHHHHHHHcCCCCCCHH
Confidence 8999999999998776443 44443 5664 3334899999999999987 88644433
No 246
>PRK03348 DNA polymerase IV; Provisional
Probab=54.53 E-value=25 Score=37.77 Aligned_cols=53 Identities=17% Similarity=0.334 Sum_probs=39.1
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--CCCC
Q 012847 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (455)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--GirT 318 (455)
+..|||||+.+.++...+ -+..+.+|.+-.+..+.+.| |++.+..||+. |+..
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 678899999988887654 45666666665566677777 77888899874 8754
No 247
>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=54.14 E-value=7.9 Score=33.79 Aligned_cols=25 Identities=32% Similarity=0.497 Sum_probs=20.6
Q ss_pred HHHHhhhccCcCHHHHHHHHHc-CCC
Q 012847 293 TISLFGEVWGIGPATAQKLYEK-GHR 317 (455)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~-Gir 317 (455)
+.-.|+.|+|||+++|..+-+. |+.
T Consensus 13 v~~aL~~i~GIG~~~a~~i~~~lgi~ 38 (113)
T TIGR03631 13 VEIALTYIYGIGRTRARKILEKAGID 38 (113)
T ss_pred EeeeeeeeecccHHHHHHHHHHhCcC
Confidence 3344689999999999999987 884
No 248
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=53.94 E-value=13 Score=35.26 Aligned_cols=40 Identities=28% Similarity=0.283 Sum_probs=33.2
Q ss_pred ccccc-hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHh
Q 012847 248 FKIES-ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEK 287 (455)
Q Consensus 248 ~~i~s-~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~ 287 (455)
.||+. +.+|.-|||||++++..|-|=-+..-+..++++++
T Consensus 123 ~PIt~RLH~LELLpGiGkK~m~~ILeERkkkpFeSFeDi~~ 163 (202)
T COG1491 123 EPITLRLHQLELLPGIGKKTMWAILEERKKKPFESFEDIKE 163 (202)
T ss_pred CcchHHHHHHHhcccccHHHHHHHHHHHhcCCCcCHHHHHH
Confidence 57775 58999999999999999988777777887777765
No 249
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=53.94 E-value=20 Score=35.51 Aligned_cols=29 Identities=24% Similarity=0.481 Sum_probs=22.0
Q ss_pred cCCcccc-chhhhcCCCCCCHHHHHHHHHH
Q 012847 245 KLPFKIE-SADQVKGLPGIGKSMQDHIQEI 273 (455)
Q Consensus 245 ~l~~~i~-s~~~l~~lpgIG~~ia~kI~Ei 273 (455)
.+..+|- ++++|..|||||++||-....+
T Consensus 149 ~f~gDIP~~v~dLlsLPGVGPKMa~L~m~~ 178 (286)
T KOG1921|consen 149 KFDGDIPDTVEDLLSLPGVGPKMAHLTMQV 178 (286)
T ss_pred HhCCCCchhHHHHhcCCCCchHHHHHHHHH
Confidence 3455554 4699999999999999876544
No 250
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=53.89 E-value=23 Score=39.49 Aligned_cols=83 Identities=19% Similarity=0.371 Sum_probs=50.5
Q ss_pred CHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhc
Q 012847 210 NKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDE 289 (455)
Q Consensus 210 N~~ia~~L~~la~~~e~~g~~~r~~aY~rAa~~L~~l~~~i~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~ 289 (455)
|......|..|-+... .-+.+|.|.-+.=. .+ -..|.+|||||++-.+++-. .-|++..+.
T Consensus 497 ~~p~l~~lq~irDEaH-----rfAi~~hR~~R~k~----~~--~s~Ld~I~GiG~~r~~~LL~--~Fgs~~~i~------ 557 (581)
T COG0322 497 NSPALYLLQRIRDEAH-----RFAITYHRKKRSKA----ML--QSSLDDIPGIGPKRRKALLK--HFGSLKGIK------ 557 (581)
T ss_pred CCHHHHHHHHHHHHHH-----HHHHHHHHHHhhhh----hh--cCccccCCCcCHHHHHHHHH--HhhCHHHHH------
Confidence 5555555444433221 24566766643211 11 14688999999998887643 234544443
Q ss_pred hhHHHHHhhhccCcCHHHHHHHHH
Q 012847 290 KVRTISLFGEVWGIGPATAQKLYE 313 (455)
Q Consensus 290 ~~~~l~lf~~I~GvGpktA~~ly~ 313 (455)
.-+++.|..| ||+++.|+++|+
T Consensus 558 -~As~eel~~v-gi~~~~a~~i~~ 579 (581)
T COG0322 558 -SASVEELAKV-GISKKLAEKIYE 579 (581)
T ss_pred -hcCHHHHHHc-CCCHHHHHHHHh
Confidence 2356677799 999999999986
No 251
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=53.57 E-value=18 Score=41.77 Aligned_cols=47 Identities=13% Similarity=0.214 Sum_probs=33.4
Q ss_pred HHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--Cchhhhhhc-hhhHhhh
Q 012847 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLG-LKYFDDI 342 (455)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~q~~G-lk~~ed~ 342 (455)
..+++.++|||||+.|+++.+. +.|+++|.+.. .|... +| -+..+.|
T Consensus 755 ~q~~L~~lPgI~~~~a~~ll~~-f~si~~l~~as~eeL~~~--iG~~~~A~~i 804 (814)
T TIGR00596 755 PQDFLLKLPGVTKKNYRNLRKK-VKSIRELAKLSQNELNEL--IGDEEAAKRL 804 (814)
T ss_pred HHHHHHHCCCCCHHHHHHHHHH-cCCHHHHHhCCHHHHHHH--hCCHHHHHHH
Confidence 3445669999999999999994 89999998653 34442 66 5444444
No 252
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=53.52 E-value=12 Score=35.34 Aligned_cols=58 Identities=21% Similarity=0.346 Sum_probs=32.0
Q ss_pred HHHHHHHHHHhCCchhhHHHHhhchhHHHH--HhhhccCcCHHHHHHHHHc----CCCCHHHhhh
Q 012847 266 MQDHIQEIVTTGKLSKLEHFEKDEKVRTIS--LFGEVWGIGPATAQKLYEK----GHRTLDDLKN 324 (455)
Q Consensus 266 ia~kI~Eil~tG~~~~le~l~~~~~~~~l~--lf~~I~GvGpktA~~ly~~----GirTledL~~ 324 (455)
+-..|++|+....-..++-+ |+..+-+++ .|.=+||||.|+...+.++ -+.|++|+.+
T Consensus 86 L~~vv~~IV~~~E~~FV~Ff-N~A~PIt~RlH~LeLLPGIGKK~m~~ILeERkkkpFeSFeDi~~ 149 (181)
T PF04919_consen 86 LPYVVEEIVKENEERFVDFF-NEAQPITLRLHSLELLPGIGKKTMWKILEERKKKPFESFEDIEE 149 (181)
T ss_dssp HHHHHHHHHHTTHHHHHHHH------B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHH
T ss_pred HHHHHHHHHHhChHHHHHHh-hcCCCChHHHHHHhhcccccHHHHHHHHHHHccCCCCCHHHHHH
Confidence 44568888887776666544 333333322 2444699999999999863 6677777764
No 253
>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=53.29 E-value=25 Score=36.58 Aligned_cols=54 Identities=19% Similarity=0.353 Sum_probs=34.3
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhh--chhHHHHHhhhccCcCHHHHHHHHHc--CCCC
Q 012847 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKD--EKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (455)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~--~~~~~l~lf~~I~GvGpktA~~ly~~--GirT 318 (455)
+..|||||++++.++.+-+ | +..+.+|.+- .+..+.+.| |.+.+..+|+. |+..
T Consensus 184 v~~l~GiG~~~~~~ll~~~--G-i~ti~dl~~~~~~~~~L~~~f------G~~~g~~l~~~a~G~d~ 241 (359)
T cd01702 184 ITSIRGLGGKLGEEIIDLL--G-LPTEGDVAGFRSSESDLQEHF------GEKLGEWLYNLLRGIDH 241 (359)
T ss_pred HHHhCCcCHHHHHHHHHHc--C-CcCHHHHHhccCCHHHHHHHH------HHHHHHHHHHHhCCCCC
Confidence 6788999998876553322 2 3444455443 344455556 77889999875 8754
No 254
>KOG0323 consensus TFIIF-interacting CTD phosphatases, including NLI-interacting factor [Transcription]
Probab=52.98 E-value=6.8 Score=43.77 Aligned_cols=89 Identities=21% Similarity=0.232 Sum_probs=58.7
Q ss_pred CCCCCcEEEEecC---CCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccchHHH
Q 012847 17 GIFAGMRVFLVEK---GVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLED 93 (455)
Q Consensus 17 ~~F~g~~iy~~~~---~~g~~R~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~~~~~l~~l~~~~~~~~~~~lV~~~Wl~e 93 (455)
..+++|.+.|.+. ++...+. ..-....+.|+.+....+..+||+|+........... .. ....+||...|+..
T Consensus 440 ~v~~~~~~vfSg~~P~~~~~~~s-~~~~~~~~~g~vs~~~~~~~~th~i~~~~gt~k~~~a--~~-~~~~~Vv~~~wl~~ 515 (635)
T KOG0323|consen 440 KVLKGSQIVFSGLHPTGSTDESA-DILGVAQQLGAVSAPDVSDKTTHLIAANAGTKKVYKA--VV-SGSAKVVNAAWLWR 515 (635)
T ss_pred HHhhccceeecccccCcCCcchh-hhhhhhhcccceecccccchhhhHHhhccCcceeecc--cc-ccceeEechhHHHH
Confidence 4678888888643 2222222 2223456778888889999999999977543211111 01 11379999999999
Q ss_pred HHhcCCCCCccccccc
Q 012847 94 SLRLGEKVSEDLYRIK 109 (455)
Q Consensus 94 s~k~g~lvdee~y~l~ 109 (455)
|+..=..+++..|.+.
T Consensus 516 ~~e~w~~v~ek~~~l~ 531 (635)
T KOG0323|consen 516 SLEKWGKVEEKLEPLD 531 (635)
T ss_pred HHHHhcchhccccccc
Confidence 9998888888777664
No 255
>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=52.79 E-value=20 Score=36.07 Aligned_cols=25 Identities=16% Similarity=0.175 Sum_probs=19.5
Q ss_pred HHHHHhhhccCcCHHHHHHHHHcCC
Q 012847 292 RTISLFGEVWGIGPATAQKLYEKGH 316 (455)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~Gi 316 (455)
..++.|+++||||++||..+---++
T Consensus 102 ~~~~~L~~LpGIG~~TA~~Il~~a~ 126 (275)
T TIGR01084 102 QDFEDLAALPGVGRYTAGAILSFAL 126 (275)
T ss_pred HHHHHHHhCCCCCHHHHHHHHHHHC
Confidence 3577788999999999988765433
No 256
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=52.28 E-value=23 Score=40.96 Aligned_cols=19 Identities=11% Similarity=0.331 Sum_probs=10.0
Q ss_pred chhhhhhchhhHhhhccCc
Q 012847 328 LTHSQRLGLKYFDDIKTRI 346 (455)
Q Consensus 328 L~~~q~~Glk~~ed~~~~i 346 (455)
|..++++|.+.+..+..++
T Consensus 759 L~~lPgI~~~~a~~ll~~f 777 (814)
T TIGR00596 759 LLKLPGVTKKNYRNLRKKV 777 (814)
T ss_pred HHHCCCCCHHHHHHHHHHc
Confidence 3445555555555555443
No 257
>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=52.17 E-value=35 Score=39.59 Aligned_cols=51 Identities=20% Similarity=0.467 Sum_probs=37.7
Q ss_pred CCeEEEEecccccCC-CCCCCccEEEeCCCch--hhhhhHHHHHHHHHHcCcee
Q 012847 367 PEVIILCGGSYRRGK-ASCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMKFLR 417 (455)
Q Consensus 367 p~~~v~~~Gs~RRgk-e~~gDvDiLit~~d~~--~~~~~l~~lv~~L~~~g~l~ 417 (455)
.++-+..+|||=||. .-..|||++|-+++.. ....++.+++..|-+.|+=.
T Consensus 42 ~~~aliA~GgyGR~El~p~SDiDll~l~~~~~~~~~~~~~~~~~~~LwD~gl~~ 95 (850)
T TIGR01693 42 SGIALVAVGGYGRGELAPYSDIDLLFLHDGKPAEEVEPKIERFLYPLWDLGFEV 95 (850)
T ss_pred CCeEEEEeCCccccCcCCCCCCeEEEEeCCCCChHHHHHHHHHHHHHHhcCCCC
Confidence 355677889996654 5678999999887532 35577888888888888753
No 258
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=51.69 E-value=25 Score=40.38 Aligned_cols=48 Identities=17% Similarity=0.479 Sum_probs=35.4
Q ss_pred CeEEEEecccccCC-CCCCCccEEEeCCCchh--hhhhHHHHHHHHHHcCc
Q 012847 368 EVIILCGGSYRRGK-ASCGDLDVVIMHPDRKS--HKGFLSKYVKKLKEMKF 415 (455)
Q Consensus 368 ~~~v~~~Gs~RRgk-e~~gDvDiLit~~d~~~--~~~~l~~lv~~L~~~g~ 415 (455)
++-++.+|||-||. --+.|||+||-+|...+ ....+..++.-|=+.||
T Consensus 66 ~~aLvAVGGyGRgEL~P~SDiDlL~L~p~~~~~~~e~~ie~~l~~LWD~gl 116 (867)
T COG2844 66 GLALVAVGGYGRGELHPLSDIDLLLLSPQKLTDWLEQKIERFLYLLWDLGL 116 (867)
T ss_pred ceEEEEeccccccccCCCccceEEEecCCCCChHHHHHHHHHHHHHHhcCc
Confidence 35677899998876 46899999999987654 34556667777777776
No 259
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]
Probab=51.59 E-value=8.3 Score=37.56 Aligned_cols=58 Identities=22% Similarity=0.303 Sum_probs=43.1
Q ss_pred hhhcCCCCCCHHHHH---HHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHH
Q 012847 254 DQVKGLPGIGKSMQD---HIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLY 312 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~---kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly 312 (455)
+++.++ |+-+.=+. -+.|....|.+...+.+..-....+++++|+|.|||+-|+..+-
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 566655 44443333 35566668988888888777778899999999999999998774
No 260
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=51.09 E-value=31 Score=35.82 Aligned_cols=58 Identities=17% Similarity=0.276 Sum_probs=42.1
Q ss_pred HHHHHHHHcCCChhHHHHHHHHHHHhc-CCcccc-chhhhcCCCCCCHHHHHHHHHHHHh
Q 012847 219 KLINIYRALGEDRRSFSYYKAIPVIEK-LPFKIE-SADQVKGLPGIGKSMQDHIQEIVTT 276 (455)
Q Consensus 219 ~la~~~e~~g~~~r~~aY~rAa~~L~~-l~~~i~-s~~~l~~lpgIG~~ia~kI~Eil~t 276 (455)
++-.+.+-.|--.|++...+||..+.. +...+. +.++|..|||||..+|..|--|.=.
T Consensus 76 evl~~W~gLGYysRArnL~~~A~~v~~~~~G~~P~~~~~l~~LpGiG~yTa~Ail~~a~~ 135 (342)
T COG1194 76 EVLKAWEGLGYYSRARNLHKAAQEVVERHGGEFPDDEEELAALPGVGPYTAGAILSFAFN 135 (342)
T ss_pred HHHHHHHhcChHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHhCCCCcHHHHHHHHHHHhC
Confidence 344455555645589889999887765 444444 4578999999999999999877543
No 261
>COG5067 DBF4 Protein kinase essential for the initiation of DNA replication [DNA replication, recombination, and repair / Cell division and chromosome partitioning]
Probab=50.07 E-value=11 Score=39.69 Aligned_cols=46 Identities=20% Similarity=0.332 Sum_probs=36.3
Q ss_pred CCCCCCcEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEE
Q 012847 16 NGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLA 63 (455)
Q Consensus 16 ~~~F~g~~iy~~~~~~g~~R~~~l~~li~~~Gg~V~~~ls~~VTHVV~ 63 (455)
-..|+....|+... .| .+...+++.+-..||.|++-++..||||+.
T Consensus 120 ~~aFp~f~fY~dn~-s~-~~khRvk~gf~~LGa~v~tfF~~~VThfiT 165 (468)
T COG5067 120 CCAFPAFKFYKDNK-SG-KRKHRVKEGFCELGAVVFTFFEEHVTHFIT 165 (468)
T ss_pred hcccchhhhhhcCC-CH-HHHHHHHHHHHHhhhhhheeeccceEEEEE
Confidence 35688888888632 22 333348999999999999999999999996
No 262
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=49.61 E-value=17 Score=37.82 Aligned_cols=50 Identities=24% Similarity=0.248 Sum_probs=33.4
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhhhchhhHhh
Q 012847 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDD 341 (455)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~q~~Glk~~ed 341 (455)
+..++.+ .-.||+|+++++|-+.||.|++||.... .|....++...-.++
T Consensus 28 ~~~~~~l-~~~g~~~~~~~kL~~~g~~tv~~~~~~~~~~L~~~~g~s~~~~~k 79 (344)
T PLN03187 28 FESIDKL-ISQGINAGDVKKLQDAGIYTCNGLMMHTKKNLTGIKGLSEAKVDK 79 (344)
T ss_pred ccCHHHH-hhCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHH
Confidence 3345555 4489999999999999999999997432 244444444333333
No 263
>PRK13766 Hef nuclease; Provisional
Probab=49.61 E-value=13 Score=42.41 Aligned_cols=18 Identities=44% Similarity=0.527 Sum_probs=14.8
Q ss_pred HhhhccCcCHHHHHHHHH
Q 012847 296 LFGEVWGIGPATAQKLYE 313 (455)
Q Consensus 296 lf~~I~GvGpktA~~ly~ 313 (455)
.|..++|+|+++|+.+++
T Consensus 748 ~L~~i~Gig~~~a~~i~~ 765 (773)
T PRK13766 748 ELMEVEGIGEKTAKRIRE 765 (773)
T ss_pred HHHhCCCCCHHHHHHHHH
Confidence 456889999999999876
No 264
>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=49.52 E-value=13 Score=41.18 Aligned_cols=30 Identities=27% Similarity=0.346 Sum_probs=24.9
Q ss_pred HHhhhccCcCHHHHHHHHHcCCCCHHHhhhc
Q 012847 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (455)
Q Consensus 295 ~lf~~I~GvGpktA~~ly~~GirTledL~~~ 325 (455)
..|.+|+|||||+.+.|++ -+.|+++++++
T Consensus 541 S~Ld~I~GIG~kr~~~LL~-~Fgs~~~i~~A 570 (574)
T TIGR00194 541 SPLLKIPGVGEKRVQKLLK-YFGSLKGIKKA 570 (574)
T ss_pred HHHhcCCCCCHHHHHHHHH-HcCCHHHHHhC
Confidence 3566999999999999998 56688888754
No 265
>PRK13746 aminoglycoside resistance protein; Provisional
Probab=49.07 E-value=87 Score=31.37 Aligned_cols=27 Identities=26% Similarity=0.249 Sum_probs=21.8
Q ss_pred EEEEecccccC--CCCCCCccEEEeCCCch
Q 012847 370 IILCGGSYRRG--KASCGDLDVVIMHPDRK 397 (455)
Q Consensus 370 ~v~~~Gs~RRg--ke~~gDvDiLit~~d~~ 397 (455)
-|.+-||+-+| ++ -+||||+|...++-
T Consensus 30 ~vyLfGS~~~G~~~p-~SDIDllvvv~~~l 58 (262)
T PRK13746 30 AIHLYGSAVDGGLKP-HSDIDLLVTVAVPL 58 (262)
T ss_pred EEEEECCcccCCCCC-CCceeEEEEeCCCC
Confidence 47899999998 44 79999999876653
No 266
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=48.84 E-value=14 Score=39.24 Aligned_cols=35 Identities=23% Similarity=0.303 Sum_probs=30.0
Q ss_pred hhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhh
Q 012847 290 KVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (455)
Q Consensus 290 ~~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~ 324 (455)
+.+.-.-|+.|.||||+.+.+|...||.+++++-.
T Consensus 318 r~g~aDDLk~I~GIGpk~e~~Ln~~Gi~~f~QIA~ 352 (400)
T PRK12373 318 RPGGADDLKLISGVGPKIEATLNELGIFTFDQVAA 352 (400)
T ss_pred CCCCchhhhhccCCChHHHHHHHhcCCCCHHHHhC
Confidence 33445667899999999999999999999999975
No 267
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=48.68 E-value=11 Score=34.65 Aligned_cols=25 Identities=24% Similarity=0.225 Sum_probs=20.4
Q ss_pred HHHHhhhccCcCHHHHHHHHHc-CCC
Q 012847 293 TISLFGEVWGIGPATAQKLYEK-GHR 317 (455)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~-Gir 317 (455)
+.-.|+.|+|||+++|.++-+. ||.
T Consensus 28 v~~aLt~I~GIG~~~A~~I~~~lgi~ 53 (154)
T PTZ00134 28 VPYALTAIKGIGRRFAYLVCKKAGID 53 (154)
T ss_pred EEEeecccccccHHHHHHHHHHcCcC
Confidence 3444689999999999999986 874
No 268
>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=48.63 E-value=13 Score=31.37 Aligned_cols=51 Identities=24% Similarity=0.337 Sum_probs=40.0
Q ss_pred HHHHhhhccCcCHHHHHHHHHc-CCCCHHHhhhccCchhhhhhchhhHhhhc
Q 012847 293 TISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNEDSLTHSQRLGLKYFDDIK 343 (455)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~-GirTledL~~~~~L~~~q~~Glk~~ed~~ 343 (455)
.+..|++.||+=|..|.++..- -+.|++|+.+-..|+..|+-=++.|++.-
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 4566889999999999999997 78999999988789998888888777643
No 269
>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=48.57 E-value=15 Score=28.70 Aligned_cols=19 Identities=21% Similarity=0.389 Sum_probs=16.8
Q ss_pred HHHHHHHHHcCCCCHHHhh
Q 012847 305 PATAQKLYEKGHRTLDDLK 323 (455)
Q Consensus 305 pktA~~ly~~GirTledL~ 323 (455)
-+.++.|++.||+|++|++
T Consensus 54 ~~Il~~W~~~gi~T~e~~~ 72 (73)
T TIGR01446 54 DAILNNWKNNGIKTVEDVE 72 (73)
T ss_pred HHHHHHHHHcCCCCHHHHh
Confidence 4678999999999999986
No 270
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=47.39 E-value=12 Score=38.55 Aligned_cols=27 Identities=22% Similarity=0.337 Sum_probs=21.0
Q ss_pred HHHHHhhhccCcCHHHHHHHHHc---CCCC
Q 012847 292 RTISLFGEVWGIGPATAQKLYEK---GHRT 318 (455)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~---GirT 318 (455)
..+..+++|||||+++|+++.+- |--.
T Consensus 45 ~~~~~l~~lpgIG~~ia~kI~Eil~tG~~~ 74 (334)
T smart00483 45 NSMKDLKGLPGIGDKIKKKIEEIIETGKSS 74 (334)
T ss_pred CCHHHHhcCCCccHHHHHHHHHHHHhCcHH
Confidence 34556779999999999999973 6544
No 271
>PRK03059 PII uridylyl-transferase; Provisional
Probab=46.97 E-value=52 Score=38.42 Aligned_cols=49 Identities=16% Similarity=0.413 Sum_probs=33.1
Q ss_pred CCeEEEEecccccC-CCCCCCccEEEeCCCch--hhhhhHHHHHHHHHHcCc
Q 012847 367 PEVIILCGGSYRRG-KASCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMKF 415 (455)
Q Consensus 367 p~~~v~~~Gs~RRg-ke~~gDvDiLit~~d~~--~~~~~l~~lv~~L~~~g~ 415 (455)
.++-+..+|||=|| ..-..|||+||-+++.. .....+..++..|=+.|+
T Consensus 60 ~~~alvAvGgyGR~EL~p~SDiDll~l~~~~~~~~~~~~i~~~~~~lwD~gL 111 (856)
T PRK03059 60 AGAALVAVGGYGRGELFPYSDVDLLVLLPDAPDAALDARIERFIGLCWDLGL 111 (856)
T ss_pred CCeEEEEcCCCCCcccCCCCCCEEEEEecCCcchHHHHHHHHHHHhhhccCC
Confidence 45677889999665 45689999999987543 234556666655555554
No 272
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=46.96 E-value=14 Score=32.54 Aligned_cols=22 Identities=27% Similarity=0.540 Sum_probs=19.1
Q ss_pred HhhhccCcCHHHHHHHHHc-CCC
Q 012847 296 LFGEVWGIGPATAQKLYEK-GHR 317 (455)
Q Consensus 296 lf~~I~GvGpktA~~ly~~-Gir 317 (455)
-||.|+|||..+|+.+.++ ||.
T Consensus 18 ALt~IyGIG~~~a~~I~~~~gi~ 40 (121)
T COG0099 18 ALTYIYGIGRRRAKEICKKAGID 40 (121)
T ss_pred hhhhhccccHHHHHHHHHHcCCC
Confidence 4679999999999999987 874
No 273
>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=46.75 E-value=48 Score=33.91 Aligned_cols=53 Identities=19% Similarity=0.456 Sum_probs=33.4
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--CCCC
Q 012847 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (455)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--GirT 318 (455)
+..|||||+++.+++..+ | +..+.+|.+-.....+..+ + | +.+..+|+. |+..
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 677899999999988754 3 4556666543313333322 2 2 567777775 8754
No 274
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=46.14 E-value=34 Score=34.46 Aligned_cols=44 Identities=18% Similarity=0.329 Sum_probs=31.1
Q ss_pred CCC-hhHHHHHHHHHHHhc--CCcc-ccc----hhhhcCCCCCCHHHHHHHH
Q 012847 228 GED-RRSFSYYKAIPVIEK--LPFK-IES----ADQVKGLPGIGKSMQDHIQ 271 (455)
Q Consensus 228 g~~-~r~~aY~rAa~~L~~--l~~~-i~s----~~~l~~lpgIG~~ia~kI~ 271 (455)
|-. .|+..-..+|..+.+ ++.. ..+ .++|..|||||+.+|+-|.
T Consensus 173 Gl~~~Ra~~L~~lA~~i~~g~l~l~~~~~~~~~~~~L~~LpGIGpwTA~~vl 224 (283)
T PRK10308 173 GMPLKRAEALIHLANAALEGTLPLTIPGDVEQAMKTLQTFPGIGRWTANYFA 224 (283)
T ss_pred CCCHHHHHHHHHHHHHHHcCCCCccccCCHHHHHHHHhcCCCcCHHHHHHHH
Confidence 444 477777888888754 4322 112 4689999999999999875
No 275
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=45.92 E-value=14 Score=33.92 Aligned_cols=25 Identities=28% Similarity=0.324 Sum_probs=20.4
Q ss_pred HHHHhhhccCcCHHHHHHHHHc-CCC
Q 012847 293 TISLFGEVWGIGPATAQKLYEK-GHR 317 (455)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~-Gir 317 (455)
+.-.|+.|+|||+++|.++-+. ||.
T Consensus 23 i~~aLt~IyGIG~~~a~~Ic~~lgi~ 48 (149)
T PRK04053 23 VEYALTGIKGIGRRTARAIARKLGLD 48 (149)
T ss_pred EeeeccccccccHHHHHHHHHHcCcC
Confidence 3344689999999999999986 875
No 276
>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=45.45 E-value=16 Score=30.54 Aligned_cols=27 Identities=33% Similarity=0.449 Sum_probs=19.9
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhh
Q 012847 297 FGEVWGIGPATAQKLYEKGHRTLDDLK 323 (455)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirTledL~ 323 (455)
-+.|+||||..+.+|-++|+.---.|.
T Consensus 21 V~~laGIG~~lg~~L~~~GfdKAy~vL 47 (89)
T PF02961_consen 21 VTELAGIGPVLGKRLEEKGFDKAYVVL 47 (89)
T ss_dssp GGGSTT--HHHHHHHHHTT--BHHHHH
T ss_pred ccccCCcCHHHHHHHHHCCCcHHHHHh
Confidence 468999999999999999998866665
No 277
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=45.06 E-value=33 Score=30.52 Aligned_cols=87 Identities=22% Similarity=0.432 Sum_probs=58.9
Q ss_pred CCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhccCchhhhhhchhhHhh
Q 012847 262 IGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYFDD 341 (455)
Q Consensus 262 IG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~~~L~~~q~~Glk~~ed 341 (455)
|=..|++.|.+-+-+|++..=+.| ..+..|..-.||-|-|+++-|+ +|+++|-+....+.|.---++
T Consensus 12 IY~QI~~qIk~~I~~g~l~pGdkL------PSvRelA~~~~VNpnTv~raY~-------eLE~eG~i~t~rg~G~fV~~~ 78 (125)
T COG1725 12 IYEQIANQIKEQIASGELKPGDKL------PSVRELAKDLGVNPNTVQRAYQ-------ELEREGIVETKRGKGTFVTED 78 (125)
T ss_pred HHHHHHHHHHHHHHhCCcCCCCCC------CcHHHHHHHhCCCHHHHHHHHH-------HHHHCCCEEEecCeeEEEcCC
Confidence 446789999999999998765543 4666677888999999999997 677777676667777433333
Q ss_pred ---hccCcCHHHHHH-HHHHHHHH
Q 012847 342 ---IKTRIPRHEVEQ-MERLLQKA 361 (455)
Q Consensus 342 ---~~~~i~r~Ea~~-i~~~v~~~ 361 (455)
+....-+..+.+ ++.+|.++
T Consensus 79 ~~~~~~~~~~~~~~~~l~~~I~~~ 102 (125)
T COG1725 79 AKEILDQLKRELAEEELEEFIEEA 102 (125)
T ss_pred chhhHHHHHHHHHHHHHHHHHHHH
Confidence 333333344443 35555554
No 278
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=44.71 E-value=31 Score=33.37 Aligned_cols=20 Identities=20% Similarity=0.371 Sum_probs=17.2
Q ss_pred chhhhc-CCCCCCHHHHHHHH
Q 012847 252 SADQVK-GLPGIGKSMQDHIQ 271 (455)
Q Consensus 252 s~~~l~-~lpgIG~~ia~kI~ 271 (455)
..++|. +|||||.++|+.|-
T Consensus 116 ~R~~Ll~~lpGIG~KTAd~vL 136 (208)
T PRK01229 116 AREFLVKNIKGIGYKEASHFL 136 (208)
T ss_pred HHHHHHHcCCCCcHHHHHHHH
Confidence 347788 99999999999975
No 279
>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=44.55 E-value=13 Score=37.69 Aligned_cols=24 Identities=38% Similarity=0.479 Sum_probs=18.5
Q ss_pred hhccCcCHHHHHHHHHcCCCCHHHh
Q 012847 298 GEVWGIGPATAQKLYEKGHRTLDDL 322 (455)
Q Consensus 298 ~~I~GvGpktA~~ly~~GirTledL 322 (455)
.+|+|||||||.+|.++ +.|++..
T Consensus 226 ~gv~giG~k~A~~li~~-~~~~~~~ 249 (316)
T cd00128 226 EGIPGIGPVTALKLIKK-YGDIEKD 249 (316)
T ss_pred CCCCCccHHHHHHHHHH-cCChHHH
Confidence 47999999999999997 3354333
No 280
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=44.37 E-value=35 Score=33.04 Aligned_cols=37 Identities=22% Similarity=0.293 Sum_probs=23.6
Q ss_pred HHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHH
Q 012847 271 QEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLY 312 (455)
Q Consensus 271 ~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly 312 (455)
.+++.. +..++.+. +....+.|.+|.|||+-||..+.
T Consensus 96 k~l~~~--~~~~~~~~---~~~~R~~LL~iKGIG~ETaDsIL 132 (215)
T COG2231 96 KNLAKF--FINLESFK---SEVLREELLSIKGIGKETADSIL 132 (215)
T ss_pred HHHHHH--hhhhhccc---hHHHHHHHHccCCcchhhHHHHH
Confidence 555543 33344443 22256677799999999998764
No 281
>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=44.37 E-value=15 Score=33.56 Aligned_cols=23 Identities=26% Similarity=0.322 Sum_probs=19.5
Q ss_pred HHhhhccCcCHHHHHHHHHc-CCC
Q 012847 295 SLFGEVWGIGPATAQKLYEK-GHR 317 (455)
Q Consensus 295 ~lf~~I~GvGpktA~~ly~~-Gir 317 (455)
-.|+.|+|||+++|..+-+. ||.
T Consensus 21 ~aLt~I~GIG~~~a~~I~~~lgi~ 44 (144)
T TIGR03629 21 YALTGIKGIGRRFARAIARKLGVD 44 (144)
T ss_pred EeecceeccCHHHHHHHHHHcCcC
Confidence 34679999999999999986 874
No 282
>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=43.78 E-value=21 Score=28.55 Aligned_cols=29 Identities=31% Similarity=0.543 Sum_probs=21.5
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHH
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEH 284 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~ 284 (455)
+-+.++||||.+.|.+|- .+.|.+..+-.
T Consensus 22 D~i~gv~giG~k~A~~ll--~~~~~~~~~~~ 50 (75)
T cd00080 22 DNIPGVPGIGPKTALKLL--KEYGSLENLLE 50 (75)
T ss_pred ccCCCCCcccHHHHHHHH--HHhCCHHHHHH
Confidence 347799999999999874 46677666543
No 283
>KOG1906 consensus DNA polymerase sigma [Replication, recombination and repair]
Probab=43.34 E-value=81 Score=34.66 Aligned_cols=38 Identities=18% Similarity=0.301 Sum_probs=29.5
Q ss_pred HHHHhhhcCCCeEEEEecccccCC-CCCCCccEEEeCCC
Q 012847 358 LQKAGEEVLPEVIILCGGSYRRGK-ASCGDLDVVIMHPD 395 (455)
Q Consensus 358 v~~~~~~~~p~~~v~~~Gs~RRgk-e~~gDvDiLit~~d 395 (455)
++.++.+..|.+.+.+-|||+-|- -..+|||++|..++
T Consensus 91 i~~~v~~~~~~a~v~~FGS~~tglyLP~sDIDl~v~~~~ 129 (514)
T KOG1906|consen 91 IRDVVKQKWPDASVYVFGSVPTGLYLPDSDIDLVVLSKF 129 (514)
T ss_pred HHHHHHHhcccceeEEeeeeeccccccccceEEEEeccc
Confidence 333444578999999999999986 45789999997763
No 284
>PRK03381 PII uridylyl-transferase; Provisional
Probab=42.22 E-value=68 Score=37.01 Aligned_cols=48 Identities=21% Similarity=0.306 Sum_probs=33.1
Q ss_pred CeEEEEecccccCC-CCCCCccEEEeCCCch--hhhhhHHHHHHHHHHcCc
Q 012847 368 EVIILCGGSYRRGK-ASCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMKF 415 (455)
Q Consensus 368 ~~~v~~~Gs~RRgk-e~~gDvDiLit~~d~~--~~~~~l~~lv~~L~~~g~ 415 (455)
.+-++.+|||-||. .-..|||+||-+++.. ....+...++.-|-+.|+
T Consensus 57 ~~alvAvg~~gr~el~p~SD~Dll~l~~~~~~~~~~~~~~~~~~~LwD~gl 107 (774)
T PRK03381 57 GVALVAVGGLGRRELLPYSDLDLVLLHDGRPADDVAEVADRLWYPLWDAGI 107 (774)
T ss_pred CeEEEEeCCcCCcCcCCCCCCeEEEEeCCCCchHHHHHHHHHhhhcccCCC
Confidence 35677889996654 5678999999887432 244566667766666665
No 285
>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=41.97 E-value=36 Score=34.76 Aligned_cols=44 Identities=27% Similarity=0.307 Sum_probs=31.1
Q ss_pred ccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhhhchhhHhhhc
Q 012847 300 VWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIK 343 (455)
Q Consensus 300 I~GvGpktA~~ly~~GirTledL~~~~--~L~~~q~~Glk~~ed~~ 343 (455)
-.|||+.++++|-+.||.|++||.... .|....++.....+++.
T Consensus 6 ~~g~~~~~~~~L~~~g~~t~~~~~~~~~~~L~~~~gls~~~~~~i~ 51 (313)
T TIGR02238 6 AHGINAADIKKLKSAGICTVNGVIMTTRRALCKIKGLSEAKVDKIK 51 (313)
T ss_pred cCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHH
Confidence 368999999999999999999998543 35555555544444443
No 286
>PRK14133 DNA polymerase IV; Provisional
Probab=41.65 E-value=64 Score=33.05 Aligned_cols=52 Identities=25% Similarity=0.437 Sum_probs=33.8
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--CCCC
Q 012847 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (455)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--GirT 318 (455)
+..|||||++++++...+ -+..+.+|.+-.+..+.+.| |+ ....+|+. |+..
T Consensus 175 v~~l~gig~~~~~~L~~~----Gi~ti~dl~~l~~~~L~~rf------G~-~g~~l~~~a~G~d~ 228 (347)
T PRK14133 175 ISKVHGIGKKSVEKLNNI----GIYTIEDLLKLSREFLIEYF------GK-FGVEIYERIRGIDY 228 (347)
T ss_pred ccccCCCCHHHHHHHHHc----CCccHHHHhhCCHHHHHHHH------hH-HHHHHHHHhCCCCC
Confidence 677899999999987654 35666666654444444555 44 45556653 8764
No 287
>KOG4132 consensus Uroporphyrinogen III synthase UROS/HEM4 [Coenzyme transport and metabolism]
Probab=40.82 E-value=72 Score=31.45 Aligned_cols=117 Identities=21% Similarity=0.244 Sum_probs=64.9
Q ss_pred HHHHhhhccCcCHHHHHHHHHc-CCCCHHHhhhccCchhhhhhchhhHhhhccCcCHHHHHHHHHHHHHHh--hhcCCCe
Q 012847 293 TISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAG--EEVLPEV 369 (455)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~-GirTledL~~~~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~~v~~~~--~~~~p~~ 369 (455)
...+. .|+-|||.|+..|... ++.|.. +..+. |+.+.++|.+.. ...+|
T Consensus 84 ~w~a~-~vYtVG~aT~~si~~~~~l~T~G--e~~gN-----------------------a~~LaD~Ive~~~~~~alP-- 135 (260)
T KOG4132|consen 84 AWLAK-HVYTVGPATHASIRRLGFLNTHG--EDAGN-----------------------AEILADLIVETFTDKRALP-- 135 (260)
T ss_pred HHhhc-ceeeeccccHHHHHHhcCccccc--ccccc-----------------------HHHHhHhhhhcCCCcccCc--
Confidence 44444 8999999999888776 555554 21111 223333333311 01123
Q ss_pred EEEEecccccC------CCCCCCccEEEeCCCchhhhhhHHHHHHHHHHcCceeeeecccccCCcchhhcccccceee
Q 012847 370 IILCGGSYRRG------KASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLREDLIFSTHSEETVGIALQNSMVYE 441 (455)
Q Consensus 370 ~v~~~Gs~RRg------ke~~gDvDiLit~~d~~~~~~~l~~lv~~L~~~g~l~~~L~~~~~~~~~~~~~~~~~~~~~ 441 (455)
....||-.||- ++.+=-||=++.-.. ..+.+++.++...|+.+|++.-...|| +-|+-+.+|.|--|.
T Consensus 136 LLfpcGn~~rdil~kkL~~~G~~Vds~~VY~T-~~hp~~~~~~~~alk~~~~~d~ivfFS---Psgv~~~lq~f~~~~ 209 (260)
T KOG4132|consen 136 LLFPCGNLRRDILPKKLHDKGIRVDSCEVYET-REHPDGFKQFIHALKECGFIDWIVFFS---PSGVKSSLQYFGDSN 209 (260)
T ss_pred eEEEcccchhHHHHHHHHhCCceeeEEEEEee-eecccHHHHHHHHHHhcCCcceEEEEC---cchHHHHHHHHHHhc
Confidence 34566766662 222224555543221 125566778999999999665555544 677777777665443
No 288
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=40.69 E-value=28 Score=33.37 Aligned_cols=28 Identities=29% Similarity=0.461 Sum_probs=21.2
Q ss_pred cccch-hhhcCCCCCCHHHHHHHHHHHHh
Q 012847 249 KIESA-DQVKGLPGIGKSMQDHIQEIVTT 276 (455)
Q Consensus 249 ~i~s~-~~l~~lpgIG~~ia~kI~Eil~t 276 (455)
+|+.+ +.+..|||||++.|.++.=.|-.
T Consensus 6 ~i~~LI~~l~kLPGvG~KsA~R~AfhLL~ 34 (198)
T COG0353 6 PIEKLIDALKKLPGVGPKSAQRLAFHLLQ 34 (198)
T ss_pred HHHHHHHHHhhCCCCChhHHHHHHHHHHc
Confidence 34443 67899999999999999765543
No 289
>PHA00439 exonuclease
Probab=40.50 E-value=20 Score=36.33 Aligned_cols=27 Identities=19% Similarity=0.284 Sum_probs=21.5
Q ss_pred hhccCcCHHHHHHHHHc--CCCCHHHhhhc
Q 012847 298 GEVWGIGPATAQKLYEK--GHRTLDDLKNE 325 (455)
Q Consensus 298 ~~I~GvGpktA~~ly~~--GirTledL~~~ 325 (455)
-+|+||| |||.+|.++ .+..++...+.
T Consensus 191 PGVpGIG-KTA~kLL~~~~~~~~~~~~~~s 219 (286)
T PHA00439 191 SGIPGWG-DTAEAFLENPYIFEQVEKVLKS 219 (286)
T ss_pred CCCCCcC-HHHHHHHhCccccchhhHHhhc
Confidence 3799999 999999998 66666666543
No 290
>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=40.47 E-value=23 Score=28.97 Aligned_cols=43 Identities=19% Similarity=0.441 Sum_probs=27.4
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHH
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPAT 307 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpkt 307 (455)
+-|..|||||.-++..|. .+.|.+..+..- +-|.+-.|+-|..
T Consensus 2 ~~l~sipGig~~~a~~ll--aeigd~~rF~~~---------~~l~~~~Gl~P~~ 44 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLL--AEIGDISRFKSA---------KQLASYAGLAPRP 44 (87)
T ss_pred chhcCCCCccHHHHHHHH--HHHcCchhcccc---------hhhhhcccccccc
Confidence 347899999999988774 333666544322 2245566776654
No 291
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=40.39 E-value=22 Score=39.96 Aligned_cols=27 Identities=44% Similarity=0.650 Sum_probs=25.2
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhh
Q 012847 297 FGEVWGIGPATAQKLYEKGHRTLDDLK 323 (455)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirTledL~ 323 (455)
+..+.||||++|.+|-+.||.|+.||.
T Consensus 12 l~~l~gig~~~a~~l~~Lgi~tv~DLL 38 (677)
T COG1200 12 LSTLKGIGPKTAEKLKKLGIHTVQDLL 38 (677)
T ss_pred hhhhcCcCHHHHHHHHHcCCCcHHHHH
Confidence 468899999999999999999999997
No 292
>PTZ00035 Rad51 protein; Provisional
Probab=40.01 E-value=96 Score=32.02 Aligned_cols=50 Identities=24% Similarity=0.307 Sum_probs=35.3
Q ss_pred HHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhhhchhhHhhhc
Q 012847 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIK 343 (455)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~q~~Glk~~ed~~ 343 (455)
.++.+ .-+||||.++++|-+.||.|++||.... .|....+++....+++.
T Consensus 22 ~~~~l-~~~g~~~~~~~kL~~~g~~t~~~~~~~~~~~L~~~~gis~~~~~~i~ 73 (337)
T PTZ00035 22 EIEKL-QSAGINAADIKKLKEAGICTVESVAYATKKDLCNIKGISEAKVEKIK 73 (337)
T ss_pred cHHHH-hcCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhhCCCHHHHHHHH
Confidence 34445 3489999999999999999999998543 35555555544444444
No 293
>PRK10880 adenine DNA glycosylase; Provisional
Probab=39.73 E-value=21 Score=37.22 Aligned_cols=23 Identities=22% Similarity=0.286 Sum_probs=19.1
Q ss_pred HHHHHhhhccCcCHHHHHHHHHc
Q 012847 292 RTISLFGEVWGIGPATAQKLYEK 314 (455)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~ 314 (455)
..++.|+++||||++||..+---
T Consensus 106 ~~~~~L~~LpGIG~~TA~aIl~~ 128 (350)
T PRK10880 106 ETFEEVAALPGVGRSTAGAILSL 128 (350)
T ss_pred hhHHHHhcCCCccHHHHHHHHHH
Confidence 46677789999999999988754
No 294
>PRK13910 DNA glycosylase MutY; Provisional
Probab=39.08 E-value=21 Score=36.25 Aligned_cols=22 Identities=23% Similarity=0.153 Sum_probs=18.0
Q ss_pred HHHHhhhccCcCHHHHHHHHHc
Q 012847 293 TISLFGEVWGIGPATAQKLYEK 314 (455)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~ 314 (455)
..+.|+++||||++||..+---
T Consensus 70 ~~~~L~~LpGIG~kTA~aIl~~ 91 (289)
T PRK13910 70 DYQSLLKLPGIGAYTANAILCF 91 (289)
T ss_pred hHHHHHhCCCCCHHHHHHHHHH
Confidence 4566779999999999987654
No 295
>PF09970 DUF2204: Nucleotidyl transferase of unknown function (DUF2204); InterPro: IPR018700 This family of hypothetical prokaryotic proteins has no known function.
Probab=38.97 E-value=69 Score=30.07 Aligned_cols=36 Identities=19% Similarity=0.230 Sum_probs=24.4
Q ss_pred CeEEEEeccc-----ccCCCCCCCccEEEeCCCchhhhhhH
Q 012847 368 EVIILCGGSY-----RRGKASCGDLDVVIMHPDRKSHKGFL 403 (455)
Q Consensus 368 ~~~v~~~Gs~-----RRgke~~gDvDiLit~~d~~~~~~~l 403 (455)
|+.+.+.||+ =..+.+.+|||++|..++......++
T Consensus 16 gv~~~ivGG~av~l~~g~~r~T~DIDlfi~~~~~~~~~~~~ 56 (181)
T PF09970_consen 16 GVEYVIVGGAAVNLAYGRRRTTKDIDLFIENPSPNLEADAL 56 (181)
T ss_pred CCeEEEECHHHHHHHhCCCCCCCCeEEEeCCCchHHHHHHH
Confidence 5677777773 25567899999999877655433333
No 296
>PRK01810 DNA polymerase IV; Validated
Probab=38.20 E-value=67 Score=33.68 Aligned_cols=52 Identities=19% Similarity=0.416 Sum_probs=33.6
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--CCCC
Q 012847 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (455)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--GirT 318 (455)
+..|||||++++++...+ | +..+-+|.+-.+..+.+.| |+ ....+|+. |+..
T Consensus 181 v~~l~giG~~~~~~L~~~---G-i~tigdL~~~~~~~L~~rf------G~-~g~~l~~~a~G~d~ 234 (407)
T PRK01810 181 VGEMHGIGEKTAEKLKDI---G-IQTIGDLAKADEHILRAKL------GI-NGVRLQRRANGIDD 234 (407)
T ss_pred HhhcCCcCHHHHHHHHHc---C-CCcHHHHHhCCHHHHHHHH------hH-HHHHHHHHhcCCCC
Confidence 667899999999887643 4 5566666654444444445 44 46667764 8754
No 297
>COG1031 Uncharacterized Fe-S oxidoreductase [Energy production and conversion]
Probab=38.09 E-value=27 Score=37.67 Aligned_cols=32 Identities=16% Similarity=0.350 Sum_probs=29.3
Q ss_pred HHHHhhhccCcCHHHHHHHHHc-CCCCHHHhhh
Q 012847 293 TISLFGEVWGIGPATAQKLYEK-GHRTLDDLKN 324 (455)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~-GirTledL~~ 324 (455)
..+.++.|||||.+++.+++.+ +++|.||+++
T Consensus 514 s~~vl~~ipgig~~~~~~I~~~Rp~~s~e~~l~ 546 (560)
T COG1031 514 SKDVLRAIPGIGKKTLRKILAERPFKSSEEFLK 546 (560)
T ss_pred cHHHHHhcccchhhhHHHHHhcCCccchHHHHh
Confidence 4778999999999999999987 9999999985
No 298
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=34.37 E-value=26 Score=39.04 Aligned_cols=40 Identities=23% Similarity=0.430 Sum_probs=27.8
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhcc--Cchhhhhhchhh
Q 012847 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKY 338 (455)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~q~~Glk~ 338 (455)
|-.|+|||+++.++|.+ -+.|+++++.+. .|+.. +++.+-
T Consensus 532 Ld~I~GiG~~r~~~LL~-~Fgs~~~i~~As~eel~~v-gi~~~~ 573 (581)
T COG0322 532 LDDIPGIGPKRRKALLK-HFGSLKGIKSASVEELAKV-GISKKL 573 (581)
T ss_pred cccCCCcCHHHHHHHHH-HhhCHHHHHhcCHHHHHHc-CCCHHH
Confidence 45899999999999998 566777777542 24444 444433
No 299
>KOG3548 consensus DNA damage checkpoint protein RHP9/CRB2/53BP1 [Replication, recombination and repair]
Probab=34.23 E-value=79 Score=37.03 Aligned_cols=70 Identities=17% Similarity=0.266 Sum_probs=44.5
Q ss_pred CCchHHHHHHHHHHhcCCEEEeecC-----CC----ccEEEEcCCh-HHHHHHHHHhhhccCccccccchHHHHHhcCCC
Q 012847 31 VQNRRLQIWRQKLVQMGATVEEKLS-----KK----VTHVLAMDLE-ALLQQVSKQHLARFKGSVIRYQWLEDSLRLGEK 100 (455)
Q Consensus 31 ~g~~R~~~l~~li~~~Gg~V~~~ls-----~~----VTHVV~~~~~-~~l~~l~~~~~~~~~~~lV~~~Wl~es~k~g~l 100 (455)
.+..-.++|...+..+|+-+++... .+ +--||+.+.. .... .+.+...++++|+.+||.+|+-.|.-
T Consensus 1081 p~~~f~e~~~e~le~G~aa~vd~~hada~~~D~~l~~fdvvl~d~~~~~sv---mk~ad~l~~pvvs~EWvIQtiI~~~~ 1157 (1176)
T KOG3548|consen 1081 PGGTFIEIWKEILELGGAAVVDGYHADAETLDETLLKFDVVLVDGTFRDSV---MKYADTLGAPVVSSEWVIQTIILGKA 1157 (1176)
T ss_pred CCcchHHHHHHHHHhhchheecccccccccccccccceeEEEecCccHHHH---HHHHHHhCCCccChhHhheeeecccc
Confidence 3456788999999999999988631 11 2234443332 2111 11222346899999999999988766
Q ss_pred CCc
Q 012847 101 VSE 103 (455)
Q Consensus 101 vde 103 (455)
...
T Consensus 1158 i~~ 1160 (1176)
T KOG3548|consen 1158 IEP 1160 (1176)
T ss_pred CCc
Confidence 543
No 300
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=34.23 E-value=82 Score=32.72 Aligned_cols=33 Identities=24% Similarity=0.360 Sum_probs=26.8
Q ss_pred HHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc
Q 012847 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (455)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~GirTledL~~~~ 326 (455)
.++.+ .-.||++..+++|-+.||.|++||....
T Consensus 27 ~~~~l-~~~gi~~~~i~kL~~~g~~T~~~~~~~~ 59 (342)
T PLN03186 27 PIEQL-QASGIAALDIKKLKDAGIHTVESLAYAP 59 (342)
T ss_pred cHHHH-HhCCCCHHHHHHHHHcCCCcHHHHHhCC
Confidence 45555 4489999999999999999999998543
No 301
>TIGR02239 recomb_RAD51 DNA repair protein RAD51. This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).
Probab=33.71 E-value=86 Score=32.05 Aligned_cols=26 Identities=31% Similarity=0.354 Sum_probs=21.8
Q ss_pred ccCcCHHHHHHHHHcCCCCHHHhhhc
Q 012847 300 VWGIGPATAQKLYEKGHRTLDDLKNE 325 (455)
Q Consensus 300 I~GvGpktA~~ly~~GirTledL~~~ 325 (455)
=.||+|.++.+|-+.||+|++||...
T Consensus 6 ~~~~~~~~~~~l~~~g~~t~~~~~~~ 31 (316)
T TIGR02239 6 GNGITAADIKKLQEAGLHTVESVAYA 31 (316)
T ss_pred cCCCCHHHHHHHHHcCCCcHHHHHhC
Confidence 35699999999999999999998854
No 302
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=32.05 E-value=89 Score=29.80 Aligned_cols=55 Identities=20% Similarity=0.303 Sum_probs=33.7
Q ss_pred HHHHHHHhCCchhhHHHHhhchhHHHH--HhhhccCcCHHHHHHHHHc----CCCCHHHhhh
Q 012847 269 HIQEIVTTGKLSKLEHFEKDEKVRTIS--LFGEVWGIGPATAQKLYEK----GHRTLDDLKN 324 (455)
Q Consensus 269 kI~Eil~tG~~~~le~l~~~~~~~~l~--lf~~I~GvGpktA~~ly~~----GirTledL~~ 324 (455)
.+++|+..-.=..++ +-|+..+-++. .|.=+||||-|+.+.+.++ -+.|++|+++
T Consensus 103 vve~iV~~~E~rFV~-fFN~A~PIt~RLH~LELLpGiGkK~m~~ILeERkkkpFeSFeDi~~ 163 (202)
T COG1491 103 VVEKIVKENEDRFVK-FFNEAEPITLRLHQLELLPGIGKKTMWAILEERKKKPFESFEDIKE 163 (202)
T ss_pred HHHHHHHhhhhHHHH-HhcccCcchHHHHHHHhcccccHHHHHHHHHHHhcCCCcCHHHHHH
Confidence 345555544433333 33433333322 2445699999999999863 7888888875
No 303
>KOG2094 consensus Predicted DNA damage inducible protein [Replication, recombination and repair]
Probab=31.05 E-value=68 Score=33.73 Aligned_cols=108 Identities=14% Similarity=0.106 Sum_probs=67.1
Q ss_pred hccCcCHHHHHHHHHcCCCCHHHhhhccCchhhhhhchhhHhhhccCcCHHHHHHHHHHHHHHhhhcCCCeEEEEecccc
Q 012847 299 EVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYR 378 (455)
Q Consensus 299 ~I~GvGpktA~~ly~~GirTledL~~~~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~~v~~~~~~~~p~~~v~~~Gs~R 378 (455)
+|-|||..|-++|-..||.|-.|+.....|-.+ -|-.+.++.|+ .- .-|+--++.-+++
T Consensus 286 kV~GIGrV~E~qLkal~IkTcgdm~~k~~ll~~-lFsp~S~~~fL---------------r~-----slG~g~t~~~~~~ 344 (490)
T KOG2094|consen 286 KVSGIGRVTEQQLKALGIKTCGDMQQKLVLLSL-LFSPKSFQNFL---------------RC-----SLGLGTTILDEDG 344 (490)
T ss_pred cccchhHHHHHHHHhcCceeHHHHHHhhhHHHH-HhCchhHHHHH---------------HH-----hhcCCCCcCcccc
Confidence 578999999999998899999999865432211 12233333322 11 1122222334677
Q ss_pred cCCCCCCCccEEEeCCCc---hhhhhhHHHHHHHHHHcCceeeeecccccCC
Q 012847 379 RGKASCGDLDVVIMHPDR---KSHKGFLSKYVKKLKEMKFLREDLIFSTHSE 427 (455)
Q Consensus 379 Rgke~~gDvDiLit~~d~---~~~~~~l~~lv~~L~~~g~l~~~L~~~~~~~ 427 (455)
+.|..+..--|--+.... ..+..+...|-+.|++.|++...+++..-..
T Consensus 345 eRKsis~ErTFs~~sd~~il~~k~qel~~~lsedlqK~glv~rtvtiKlK~s 396 (490)
T KOG2094|consen 345 ERKSISSERTFSSTSDPSILYSKLQELCQMLSEDLQKEGLVGRTVTIKLKTS 396 (490)
T ss_pred ccccccceeeecccCCHHHHHHHHHHHHHHHHHHHHhcCcccceEEEEEecc
Confidence 777777665554432211 1255677888899999999999888765433
No 304
>PF14907 NTP_transf_5: Uncharacterised nucleotidyltransferase
Probab=30.86 E-value=48 Score=31.75 Aligned_cols=33 Identities=30% Similarity=0.525 Sum_probs=25.5
Q ss_pred CCCCCCCccEEEeCCCchhhhhhHHHHHHHHHHcCceeee
Q 012847 380 GKASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLRED 419 (455)
Q Consensus 380 gke~~gDvDiLit~~d~~~~~~~l~~lv~~L~~~g~l~~~ 419 (455)
+.=.++||||||...+ +.++++.|.+.||....
T Consensus 90 ~~R~~~DiDlLV~~~d-------~~~a~~~L~~~Gy~~~~ 122 (249)
T PF14907_consen 90 GLRPMGDIDLLVPPED-------LERAVELLEELGYRIES 122 (249)
T ss_pred CCCCCCCeEEEEeCCc-------HHHHHHHHHHcCCEecc
Confidence 4457899999997433 45688999999997665
No 305
>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]
Probab=30.45 E-value=70 Score=29.18 Aligned_cols=50 Identities=16% Similarity=0.196 Sum_probs=39.9
Q ss_pred CCCeEEEEecccccCCCC-----CCCccEEEeCCCchhhhhhHHHHHHHHHHcCc
Q 012847 366 LPEVIILCGGSYRRGKAS-----CGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKF 415 (455)
Q Consensus 366 ~p~~~v~~~Gs~RRgke~-----~gDvDiLit~~d~~~~~~~l~~lv~~L~~~g~ 415 (455)
.-|+.|...|.++-..|. -+|+|+++-+.-...+..+++.+++.|++.|.
T Consensus 38 d~GfeVi~~g~~~tp~e~v~aA~~~dv~vIgvSsl~g~h~~l~~~lve~lre~G~ 92 (143)
T COG2185 38 DAGFEVINLGLFQTPEEAVRAAVEEDVDVIGVSSLDGGHLTLVPGLVEALREAGV 92 (143)
T ss_pred hCCceEEecCCcCCHHHHHHHHHhcCCCEEEEEeccchHHHHHHHHHHHHHHhCC
Confidence 567888888877665443 48999998766666689999999999999986
No 306
>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=30.22 E-value=1.1e+02 Score=30.89 Aligned_cols=51 Identities=25% Similarity=0.516 Sum_probs=32.2
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--CCC
Q 012847 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHR 317 (455)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--Gir 317 (455)
+..|||||+++++++..+ -+..+.+|.+-.+....+.| .+.+..+|+. |+.
T Consensus 173 l~~l~gig~~~~~~L~~~----Gi~ti~dl~~~~~~~L~~~~-------g~~~~~l~~~~~G~~ 225 (334)
T cd03586 173 VRKIPGVGKVTAEKLKEL----GIKTIGDLAKLDVELLKKLF-------GKSGRRLYELARGID 225 (334)
T ss_pred chhhCCcCHHHHHHHHHc----CCcCHHHHHcCCHHHHHHHH-------hHHHHHHHHHhCCCC
Confidence 567899999988876643 45666666654444444444 3566677764 764
No 307
>PHA01806 hypothetical protein
Probab=30.07 E-value=86 Score=30.07 Aligned_cols=49 Identities=18% Similarity=0.238 Sum_probs=31.2
Q ss_pred CcCHHHHHH-HHHHHHHHhhhcCCCeEEEEeccccc----CCCCCCCccEEEeCCCch
Q 012847 345 RIPRHEVEQ-MERLLQKAGEEVLPEVIILCGGSYRR----GKASCGDLDVVIMHPDRK 397 (455)
Q Consensus 345 ~i~r~Ea~~-i~~~v~~~~~~~~p~~~v~~~Gs~RR----gke~~gDvDiLit~~d~~ 397 (455)
.|++..... ...++..+. .-+.++.++||+=| |+ .+.|+||++....+.
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 455555433 344455443 35778888888877 55 789999977444443
No 308
>PRK05092 PII uridylyl-transferase; Provisional
Probab=29.99 E-value=86 Score=36.95 Aligned_cols=48 Identities=21% Similarity=0.412 Sum_probs=33.2
Q ss_pred CeEEEEecccccC-CCCCCCccEEEeCCCch--hhhhhHHHHHHHHHHcCc
Q 012847 368 EVIILCGGSYRRG-KASCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMKF 415 (455)
Q Consensus 368 ~~~v~~~Gs~RRg-ke~~gDvDiLit~~d~~--~~~~~l~~lv~~L~~~g~ 415 (455)
++-+..+|||=|| ..-..|||+||-+++.. .....+..++..|-+.|+
T Consensus 105 ~~alvA~GgyGr~EL~p~SDiDLl~l~~~~~~~~~~~~i~~~~~~lwD~gl 155 (931)
T PRK05092 105 RLAVLAVGGYGRGELAPGSDIDLLFLLPYKQTAWAESVVEYMLYMLWDLGL 155 (931)
T ss_pred ceEEEEecCcCCcccCCCCCceEEEEeCCCCcchHHHHHHHHHHHHHHcCC
Confidence 3567788999665 56689999999887432 233456667766766666
No 309
>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=29.30 E-value=43 Score=27.36 Aligned_cols=36 Identities=19% Similarity=0.433 Sum_probs=19.7
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHH
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRT 293 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~ 293 (455)
.++..||+||.++.+...++ -+.-+++|+.--...+
T Consensus 3 ~~l~~LpNig~~~e~~L~~v----GI~t~~~L~~~Ga~~a 38 (81)
T PF04994_consen 3 NRLKDLPNIGPKSERMLAKV----GIHTVEDLRELGAVEA 38 (81)
T ss_dssp --GCGSTT--HHHHHHHHHT----T--SHHHHHHHHHHHH
T ss_pred cchhhCCCCCHHHHHHHHHc----CCCCHHHHHHhCHHHH
Confidence 46889999999987765544 4455666765333333
No 310
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=29.16 E-value=69 Score=32.51 Aligned_cols=46 Identities=22% Similarity=0.281 Sum_probs=28.0
Q ss_pred HcCCChhHHHHHHHHHHHhcCCcc---ccc-----h----hhhcCCCCCCHHHHHHHH
Q 012847 226 ALGEDRRSFSYYKAIPVIEKLPFK---IES-----A----DQVKGLPGIGKSMQDHIQ 271 (455)
Q Consensus 226 ~~g~~~r~~aY~rAa~~L~~l~~~---i~s-----~----~~l~~lpgIG~~ia~kI~ 271 (455)
-.|=.+|++--..+|++|-.=+-. +.+ + +.|..|||||.++|+=|-
T Consensus 178 ~~gfGYRAkYI~~ta~~l~~~~g~~~wLqsl~~~~yeear~~L~~lpGVG~KVADCI~ 235 (323)
T KOG2875|consen 178 KLGFGYRAKYISATARALQEKQGGLAWLQSLRKSSYEEAREALCSLPGVGPKVADCIC 235 (323)
T ss_pred HcCcchhHHHHHHHHHHHHHhcccchHHHHHhcccHHHHHHHHhcCCCCcchHhhhhh
Confidence 334445665555566665443322 111 2 458899999999999664
No 311
>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=28.67 E-value=4.4e+02 Score=27.25 Aligned_cols=87 Identities=9% Similarity=0.200 Sum_probs=54.4
Q ss_pred HHHHHHHHhcCCccccc--hhhhcCCCCCCHHHHHHHHHHHHh------------CCchhhHHHHhhchhHHH-HHhhhc
Q 012847 236 YYKAIPVIEKLPFKIES--ADQVKGLPGIGKSMQDHIQEIVTT------------GKLSKLEHFEKDEKVRTI-SLFGEV 300 (455)
Q Consensus 236 Y~rAa~~L~~l~~~i~s--~~~l~~lpgIG~~ia~kI~Eil~t------------G~~~~le~l~~~~~~~~l-~lf~~I 300 (455)
-..||.+|..||..... ...+..+..|.+.+.+.|.++|+. |-...+-++.+..+...- .+|..+
T Consensus 144 p~~AA~VL~~Lp~~~~~ei~~ria~l~~vs~~~i~~ie~~L~~~~~~~~~~~~~~gG~~~~a~ILN~~~~~~~~~il~~L 223 (338)
T TIGR00207 144 PAQAADILSLFPEEVQAEVARRIATMGRTSPEVVAEVERVLEGKLDSLNSDYTKMGGVRAVAEIINLMDRKTEKTIITSL 223 (338)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhhccccccCChHHHHHHHHHhCCchHHHHHHHHH
Confidence 35789999999976443 356778888888888777665541 222334445554444433 455555
Q ss_pred cCcCHHHHHHHHHcCCCCHHHhh
Q 012847 301 WGIGPATAQKLYEKGHRTLDDLK 323 (455)
Q Consensus 301 ~GvGpktA~~ly~~GirTledL~ 323 (455)
--.-|..|..+-+ -+-+++||.
T Consensus 224 ~~~dp~la~~Ir~-~mF~Fedl~ 245 (338)
T TIGR00207 224 EEFDPELAEEIKK-EMFVFEDIV 245 (338)
T ss_pred HHhCHHHHHHHHH-HccCHHHHh
Confidence 5666777766643 556677775
No 312
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=28.42 E-value=87 Score=30.99 Aligned_cols=49 Identities=18% Similarity=0.282 Sum_probs=38.8
Q ss_pred HHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhc--cCchhhhhhchhhHhh
Q 012847 292 RTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDD 341 (455)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~--~~L~~~q~~Glk~~ed 341 (455)
.++..+|+|+||+...|..|.. -+-||+.+..+ +.|.+.+|+|....+.
T Consensus 192 ~~~~~Lt~i~~VnKtda~~LL~-~FgsLq~~~~AS~~ele~~~G~G~~kak~ 242 (254)
T KOG2841|consen 192 SLLGFLTTIPGVNKTDAQLLLQ-KFGSLQQISNASEGELEQCPGLGPAKAKR 242 (254)
T ss_pred HHHHHHHhCCCCCcccHHHHHH-hcccHHHHHhcCHhHHHhCcCcCHHHHHH
Confidence 4777789999999999999987 45589988865 5688888888655443
No 313
>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=28.04 E-value=44 Score=39.68 Aligned_cols=26 Identities=19% Similarity=0.326 Sum_probs=21.4
Q ss_pred hhccCcCHHHHHHHHHc-CCCCHHHhh
Q 012847 298 GEVWGIGPATAQKLYEK-GHRTLDDLK 323 (455)
Q Consensus 298 ~~I~GvGpktA~~ly~~-GirTledL~ 323 (455)
.+|+||||+||-++..+ |-.+|+.|.
T Consensus 869 ~GI~GIGpktAl~li~~~~~~~le~L~ 895 (1034)
T TIGR00600 869 EGIPTVGPVSAMEILNEFPGDGLEPLL 895 (1034)
T ss_pred CCCCcccHHHHHHHHHHcCCCCHHHHH
Confidence 36999999999999998 655677665
No 314
>PRK14109 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Provisional
Probab=27.60 E-value=2.2e+02 Score=33.92 Aligned_cols=46 Identities=13% Similarity=0.273 Sum_probs=31.6
Q ss_pred CeEEEEeccc-ccCCCCCCCccEEEeCCCch-----hhhhhHHHHHHHHHHc
Q 012847 368 EVIILCGGSY-RRGKASCGDLDVVIMHPDRK-----SHKGFLSKYVKKLKEM 413 (455)
Q Consensus 368 ~~~v~~~Gs~-RRgke~~gDvDiLit~~d~~-----~~~~~l~~lv~~L~~~ 413 (455)
++-|..+|+| ||-...+.|||+++.+++.. ....++.++.+.|...
T Consensus 215 ~~aviamGklG~~EL~~~SDiDLi~ly~~~~~~~~~~~~~~~~rl~q~l~~~ 266 (1007)
T PRK14109 215 RLAVIAMGKCGARELNYVSDVDVIFVAEPAEGVDEAAALAVATRLASELMRI 266 (1007)
T ss_pred CeEEEEeccccccccCCccCCCEEEEeCCCCCcccccHHHHHHHHHHHHHHH
Confidence 3567778888 55567789999999886431 1234567777777765
No 315
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=27.40 E-value=5.6e+02 Score=25.46 Aligned_cols=52 Identities=19% Similarity=0.312 Sum_probs=33.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (455)
..+.+||+||+..+.++. .+.+..+++|..-.+...-.+ -|.+++.+..+++
T Consensus 151 ~~L~Qlp~i~~~~~~~l~----~~~i~s~~~l~~~~~~~~~~l----l~~~~~~~~~i~~ 202 (312)
T smart00611 151 SPLLQLPHLPEEILKRLE----KKKVLSLEDLLELEDEERGEL----LGLLDAEGERVYK 202 (312)
T ss_pred CccccCCCCCHHHHHHHH----hCCCCCHHHHHhcCHHHHHHH----HcCCHHHHHHHHH
Confidence 468999999998888775 334455556654443333333 3677777777765
No 316
>PF07261 DnaB_2: Replication initiation and membrane attachment; InterPro: IPR006343 This entry represents a domain found in several bacterial replication initiation and membrane attachment proteins, DnaB and DnaD. The DnaD protein is a component of the PriA primosome. The PriA primosome functions to recruit the replication fork helicase onto the DNA []. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria []. The DnaB protein is essential for both replication initiation and membrane attachment of the origin region of the chromosome and Plasmid pUB110 in Bacillus subtilis. It is known that there are two different classes (DnaBI and DnaBII) in the DnaB mutants; DnaBI is essential for both chromosome and pUB110 replication, whereas DnaBII is necessary only for chromosome replication []. This domain tends to be found towards the C terminus of DnaB and DnaD proteins and is alpha helical in nature.; PDB: 2I5U_A 2ZC2_A.
Probab=26.68 E-value=26 Score=27.37 Aligned_cols=20 Identities=20% Similarity=0.345 Sum_probs=15.2
Q ss_pred HHHHHHHHHcCCCCHHHhhh
Q 012847 305 PATAQKLYEKGHRTLDDLKN 324 (455)
Q Consensus 305 pktA~~ly~~GirTledL~~ 324 (455)
-+.++.|.+.|++|++|+++
T Consensus 54 ~~Il~~W~~~gi~t~e~~~~ 73 (77)
T PF07261_consen 54 EKILNNWKQKGIKTVEDAEE 73 (77)
T ss_dssp HHHHHHHHHCT--SCCCCT-
T ss_pred HHHHHHHHHcCCCCHHHHHH
Confidence 47889999999999999875
No 317
>COG5275 BRCT domain type II [General function prediction only]
Probab=25.99 E-value=2.1e+02 Score=28.12 Aligned_cols=50 Identities=14% Similarity=0.074 Sum_probs=38.6
Q ss_pred CCCCCcEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCCh
Q 012847 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLE 67 (455)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~R~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~~~ 67 (455)
..+.|.++.|-+ -+..-.++-.+.++..+||+|....+...|-||..++-
T Consensus 155 ~cL~G~~fVfTG-~l~TlsR~~a~~lvk~yGgrvT~~pSskTtflvlGdna 204 (276)
T COG5275 155 ECLKGKVFVFTG-DLKTLSRDDAKTLVKVYGGRVTAVPSSKTTFLVLGDNA 204 (276)
T ss_pred ccccccEEEEec-ccccccchhHHHHHHHhCCeeecccccceeEEEecCCC
Confidence 567888887753 23333445678999999999999999999999998764
No 318
>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=24.77 E-value=25 Score=27.50 Aligned_cols=21 Identities=19% Similarity=0.596 Sum_probs=15.7
Q ss_pred EEEEecccccCCCCC----CCccEE
Q 012847 370 IILCGGSYRRGKASC----GDLDVV 390 (455)
Q Consensus 370 ~v~~~Gs~RRgke~~----gDvDiL 390 (455)
+|++--+|||||..+ ||+|||
T Consensus 34 rvmiPqeFkrGKsIiAV~EGe~~il 58 (67)
T TIGR02922 34 RVMIPQEFKRGKSIIAVCEGEITIL 58 (67)
T ss_pred cEEcchHHcCCCeEEEEEecceeeh
Confidence 677778999999864 555554
No 319
>PF05559 DUF763: Protein of unknown function (DUF763); InterPro: IPR008482 This family consists of several uncharacterised bacterial and archaeal proteins of unknown function.
Probab=24.12 E-value=67 Score=33.03 Aligned_cols=19 Identities=26% Similarity=0.387 Sum_probs=15.0
Q ss_pred HHHhhhccCcCHHHHHHHH
Q 012847 294 ISLFGEVWGIGPATAQKLY 312 (455)
Q Consensus 294 l~lf~~I~GvGpktA~~ly 312 (455)
++.|..++||||+|.+.|.
T Consensus 268 feeLL~~~GvGp~TlRALa 286 (319)
T PF05559_consen 268 FEELLLIKGVGPSTLRALA 286 (319)
T ss_pred HHHHHhcCCCCHHHHHHHH
Confidence 3334489999999999885
No 320
>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=23.97 E-value=70 Score=27.20 Aligned_cols=35 Identities=31% Similarity=0.376 Sum_probs=25.8
Q ss_pred CHHHHHHHHHcCCCCHHHhhhc----c-C-chhhhhhchhh
Q 012847 304 GPATAQKLYEKGHRTLDDLKNE----D-S-LTHSQRLGLKY 338 (455)
Q Consensus 304 GpktA~~ly~~GirTledL~~~----~-~-L~~~q~~Glk~ 338 (455)
.|..|++|-..||+||.||..- + + ...+.++|..-
T Consensus 22 ~p~va~~L~aaGi~TL~dL~~~i~~rg~~Wwr~vpglG~~~ 62 (96)
T PF12482_consen 22 PPRVARRLAAAGIRTLADLVDRINRRGGRWWRAVPGLGAAG 62 (96)
T ss_pred CHHHHHHHHHcCCchHHHHHHHHHHccchHHHhCcccchHH
Confidence 6999999999999999999732 2 2 34456666544
No 321
>PRK07945 hypothetical protein; Provisional
Probab=23.87 E-value=40 Score=34.75 Aligned_cols=28 Identities=29% Similarity=0.446 Sum_probs=23.0
Q ss_pred hhhccCcCHHHHHHHHHc---C-CCCHHHhhh
Q 012847 297 FGEVWGIGPATAQKLYEK---G-HRTLDDLKN 324 (455)
Q Consensus 297 f~~I~GvGpktA~~ly~~---G-irTledL~~ 324 (455)
|++|||||..+|.++.+. | +.-|++|+.
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 467888874
No 322
>PRK11072 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed
Probab=23.50 E-value=1.3e+03 Score=27.48 Aligned_cols=28 Identities=25% Similarity=0.443 Sum_probs=21.1
Q ss_pred CeEEEEecccc-cCCCCCCCccEEEeCCC
Q 012847 368 EVIILCGGSYR-RGKASCGDLDVVIMHPD 395 (455)
Q Consensus 368 ~~~v~~~Gs~R-Rgke~~gDvDiLit~~d 395 (455)
++.|..+|.|= |-...+.|||+++.+++
T Consensus 154 ~~aViamGKlG~~ELn~~SDIDLifly~~ 182 (943)
T PRK11072 154 PLLILGMGKLGGRELNFSSDIDLIFTYPE 182 (943)
T ss_pred CEEEEEeccccCccCCCccCCceEEEeCC
Confidence 35677788875 45677999999998763
No 323
>COG2019 AdkA Archaeal adenylate kinase [Nucleotide transport and metabolism]
Probab=23.06 E-value=1.1e+02 Score=29.02 Aligned_cols=53 Identities=23% Similarity=0.375 Sum_probs=34.5
Q ss_pred hhhccCcCHHHHHHHHHcCC-----CCHHHhhhccCchhhhhhc-hhhHhhhccCcCHHHHHHH
Q 012847 297 FGEVWGIGPATAQKLYEKGH-----RTLDDLKNEDSLTHSQRLG-LKYFDDIKTRIPRHEVEQM 354 (455)
Q Consensus 297 f~~I~GvGpktA~~ly~~Gi-----rTledL~~~~~L~~~q~~G-lk~~ed~~~~i~r~Ea~~i 354 (455)
.++|||+|..|+-+...++. -+..||. |..+.+.| .++.+++. ++|.++-..+
T Consensus 9 itGVpGvGKTTVl~~~~~~l~~~~ivNyG~~M----le~A~k~glve~rD~~R-klp~e~Q~~l 67 (189)
T COG2019 9 ITGVPGVGKTTVLKIALKELVKHKIVNYGDLM----LEIAKKKGLVEHRDEMR-KLPLENQREL 67 (189)
T ss_pred EEcCCCCChHHHHHHHHHHHhhceeeeHhHHH----HHHHHHhCCcccHHHHh-cCCHHHHHHH
Confidence 46899999999998887655 2222222 34444544 66666666 8888775554
No 324
>COG5186 PAP1 Poly(A) polymerase [RNA processing and modification]
Probab=22.93 E-value=1.7e+02 Score=30.90 Aligned_cols=51 Identities=27% Similarity=0.460 Sum_probs=41.2
Q ss_pred eEEEEecccccCCC-CCCCccEEEeCCCchhhhhhHHHHHHHHHHcCceeee
Q 012847 369 VIILCGGSYRRGKA-SCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLRED 419 (455)
Q Consensus 369 ~~v~~~Gs~RRgke-~~gDvDiLit~~d~~~~~~~l~~lv~~L~~~g~l~~~ 419 (455)
-++---||||-|-- -+.|||-|+.-|.--+..++|..+-..|++..-|++.
T Consensus 82 GKIFTyGSYRLGVhgpGsDIDtLvvVPkHVsR~dFFt~f~~~Lrer~ei~ev 133 (552)
T COG5186 82 GKIFTYGSYRLGVHGPGSDIDTLVVVPKHVSRSDFFTHFYEELRERPEIEEV 133 (552)
T ss_pred ceeeeecceeeeccCCCCCcceEEEecccccHHHHHHHHHHHhccCcchhhh
Confidence 35556799999965 4679999999888777888999999999987776653
No 325
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A.
Probab=22.73 E-value=54 Score=28.25 Aligned_cols=21 Identities=38% Similarity=0.561 Sum_probs=15.6
Q ss_pred HHHHhhhccCcCHHHHHHHHH
Q 012847 293 TISLFGEVWGIGPATAQKLYE 313 (455)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~ 313 (455)
.-.+|.=|.|+||++|..+.+
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 326
>PRK02406 DNA polymerase IV; Validated
Probab=22.65 E-value=1.6e+02 Score=30.01 Aligned_cols=52 Identities=25% Similarity=0.539 Sum_probs=34.0
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--CCCC
Q 012847 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (455)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--GirT 318 (455)
+..|||||+++++++..+ -+..+.+|.+-.+..+.+.| | . ...++|+. |+..
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 677899999999987654 35666666654444444444 4 3 56667764 8754
No 327
>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=22.36 E-value=79 Score=22.10 Aligned_cols=22 Identities=18% Similarity=0.256 Sum_probs=17.7
Q ss_pred HhhhccCcCHHHHHHHHHcCCC
Q 012847 296 LFGEVWGIGPATAQKLYEKGHR 317 (455)
Q Consensus 296 lf~~I~GvGpktA~~ly~~Gir 317 (455)
.+.+..||-+.|.+.|.++|.=
T Consensus 5 e~a~~~gv~~~tlr~~~~~g~l 26 (49)
T cd04761 5 ELAKLTGVSPSTLRYYERIGLL 26 (49)
T ss_pred HHHHHHCcCHHHHHHHHHCCCC
Confidence 3446779999999999998763
No 328
>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=22.35 E-value=1.9e+02 Score=25.83 Aligned_cols=37 Identities=19% Similarity=0.174 Sum_probs=24.7
Q ss_pred HHHHHHHhhhcCCCeEEEEeccccc----CCCCCCCccEEEeCC
Q 012847 355 ERLLQKAGEEVLPEVIILCGGSYRR----GKASCGDLDVVIMHP 394 (455)
Q Consensus 355 ~~~v~~~~~~~~p~~~v~~~Gs~RR----gke~~gDvDiLit~~ 394 (455)
..+++.+.. ..+..+.++||+=| |+ .++|+||++...
T Consensus 5 ~~il~~l~~--~~g~~~ylVGG~VRD~Llg~-~~~DiDi~v~~~ 45 (139)
T cd05398 5 LKLLRELKK--ALGYEAYLVGGAVRDLLLGR-PPKDIDIATDAD 45 (139)
T ss_pred HHHHHHHHh--ccCceEEEECChHHHHHcCC-CCCCceEEEeCC
Confidence 344444432 14778888888766 54 789999988653
No 329
>PRK01172 ski2-like helicase; Provisional
Probab=21.86 E-value=1.5e+02 Score=33.39 Aligned_cols=52 Identities=12% Similarity=0.379 Sum_probs=36.9
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc
Q 012847 255 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (455)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 314 (455)
.|.+|||||+..|++.. +.| +.-++++..-++... .+|.|+|.+.|++++++
T Consensus 613 ~L~~ip~~~~~~a~~l~---~~g-~~~~~di~~~~~~~~----~~i~~~~~~~~~~i~~~ 664 (674)
T PRK01172 613 DLVLIPKVGRVRARRLY---DAG-FKTVDDIARSSPERI----KKIYGFSDTLANAIVNR 664 (674)
T ss_pred hhcCCCCCCHHHHHHHH---HcC-CCCHHHHHhCCHHHH----HHHhccCHHHHHHHHHH
Confidence 58899999999888654 445 455566655444433 35669999999999874
No 330
>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=21.82 E-value=78 Score=27.09 Aligned_cols=44 Identities=11% Similarity=0.181 Sum_probs=29.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHh
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLF 297 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf 297 (455)
-.|..|.|||...|..|-..+.=..-..+..|..+.-..+.+.+
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 46899999999999999888765554555555443333344444
No 331
>PRK03103 DNA polymerase IV; Reviewed
Probab=21.79 E-value=1.5e+02 Score=31.05 Aligned_cols=51 Identities=22% Similarity=0.474 Sum_probs=34.0
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--CCC
Q 012847 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHR 317 (455)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--Gir 317 (455)
+..|||||++++++...+ | +..+.+|.+-.+..+.+.| |. .+..+|+. |+.
T Consensus 183 i~~l~gig~~~~~~L~~~---G-i~tigdl~~~~~~~L~~~f------G~-~~~~l~~~a~G~d 235 (409)
T PRK03103 183 VRKLFGVGSRMEKHLRRM---G-IRTIGQLANTPLERLKKRW------GI-NGEVLWRTANGID 235 (409)
T ss_pred HhhcCCccHHHHHHHHHc---C-CCCHHHHhcCCHHHHHHHH------CH-HHHHHHHHhcCCC
Confidence 667899999988887643 5 5667777654444444444 44 46777775 873
No 332
>COG1415 Uncharacterized conserved protein [Function unknown]
Probab=21.76 E-value=83 Score=32.80 Aligned_cols=30 Identities=27% Similarity=0.225 Sum_probs=19.6
Q ss_pred HHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012847 283 EHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (455)
Q Consensus 283 e~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (455)
+.+....|...-+++ -++||||+|++.|.=
T Consensus 267 ~~~ye~~p~Df~elL-l~~GiGpstvRALal 296 (373)
T COG1415 267 RRLYELNPDDFEELL-LVPGIGPSTVRALAL 296 (373)
T ss_pred HhhhhcCcccHHHHH-hccCCCHHHHHHHHH
Confidence 344333343333444 899999999999874
No 333
>PRK00024 hypothetical protein; Reviewed
Probab=21.46 E-value=96 Score=30.18 Aligned_cols=41 Identities=29% Similarity=0.437 Sum_probs=24.6
Q ss_pred HHHHHHHHHH-hCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012847 266 MQDHIQEIVT-TGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (455)
Q Consensus 266 ia~kI~Eil~-tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (455)
....-.++++ -|.+..+-.. ..+.|++|+|||+.+|..|..
T Consensus 43 ~~~LA~~LL~~fgsL~~l~~a-------s~~eL~~i~GIG~akA~~L~a 84 (224)
T PRK00024 43 VLDLARELLQRFGSLRGLLDA-------SLEELQSIKGIGPAKAAQLKA 84 (224)
T ss_pred HHHHHHHHHHHcCCHHHHHhC-------CHHHHhhccCccHHHHHHHHH
Confidence 3334444553 3655554332 233456999999999988753
No 334
>PF13838 Clathrin_H_link: Clathrin-H-link; PDB: 2XZG_A 3GD1_I 1BPO_C 1C9I_B 1C9L_A.
Probab=20.97 E-value=1.7e+02 Score=23.13 Aligned_cols=44 Identities=20% Similarity=0.342 Sum_probs=32.2
Q ss_pred CCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhH------HHHHhhhcc
Q 012847 258 GLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVR------TISLFGEVW 301 (455)
Q Consensus 258 ~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~------~l~lf~~I~ 301 (455)
+|||.-+-..++..+++..|...+.-++-.+.|.+ +|+-|.+++
T Consensus 1 ~lpGad~l~~~~F~~l~~~g~y~eAA~~AA~sP~giLRt~~Ti~rFk~~p 50 (66)
T PF13838_consen 1 NLPGADDLYVQQFNELFSQGQYEEAAKVAANSPRGILRTPETINRFKQVP 50 (66)
T ss_dssp T-SS-HHHHHHHHHHHHHTT-HHHHHHHHHHSGGGTT-SHHHHHHHHTS-
T ss_pred CCccHHHHHHHHHHHHHHcCCHHHHHHHHHhCccchhcCHHHHHHHHcCC
Confidence 57899999999999999999999998888877744 555555444
No 335
>KOG2379 consensus Endonuclease MUS81 [Replication, recombination and repair]
Probab=20.56 E-value=80 Score=34.39 Aligned_cols=42 Identities=19% Similarity=0.234 Sum_probs=36.1
Q ss_pred hHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHH
Q 012847 232 RSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEI 273 (455)
Q Consensus 232 r~~aY~rAa~~L~~l~~~i~s~~~l~~lpgIG~~ia~kI~Ei 273 (455)
-...|.+|...|...+++|.++.++..+.|+|+...-++.|.
T Consensus 35 ~~~s~~ka~r~l~~~~~~l~tl~dl~~ikG~G~~~~~k~~~~ 76 (501)
T KOG2379|consen 35 SEYSLKKALRNLCKAKDPLMTLPDLSSIKGFGKKWIVKLMEA 76 (501)
T ss_pred hcccHHHHHHHhhcccCcccchhhcccccCccchhHHHHHhH
Confidence 345899999999999999999999999999999666666643
No 336
>PF03710 GlnE: Glutamate-ammonia ligase adenylyltransferase; InterPro: IPR005190 This is a conserved repeated domain found in GlnE proteins. These proteins adenylate and deadenylate glutamine synthases: ATP + {L-Glutamate:ammonia ligase (ADP-forming)} = Diphosphate + Adenylyl-{L-Glutamate:Ammonia ligase (ADP-forming)}. The domain is related to the nucleotidyltransferase domain IPR002934 from INTERPRO.; GO: 0008882 [glutamate-ammonia-ligase] adenylyltransferase activity; PDB: 1V4A_A 3K7D_A.
Probab=20.51 E-value=3.1e+02 Score=26.86 Aligned_cols=30 Identities=13% Similarity=0.245 Sum_probs=15.5
Q ss_pred CeEEEEecccc-cCCCCCCCccEEEeCCCch
Q 012847 368 EVIILCGGSYR-RGKASCGDLDVVIMHPDRK 397 (455)
Q Consensus 368 ~~~v~~~Gs~R-Rgke~~gDvDiLit~~d~~ 397 (455)
++.|...|.|= |-...+.|||+++-+++..
T Consensus 127 ~~~ViamGKlGg~ELny~SDiDLifvy~~~~ 157 (247)
T PF03710_consen 127 GFAVIAMGKLGGRELNYSSDIDLIFVYDPDG 157 (247)
T ss_dssp SEEEEE-HHHHTT---TT--EEEEEEE---T
T ss_pred CeEEEEeccccccccCCccCCceEEEecccc
Confidence 45677777764 4566789999999776533
No 337
>KOG0950 consensus DNA polymerase theta/eta, DEAD-box superfamily [General function prediction only]
Probab=20.43 E-value=96 Score=36.45 Aligned_cols=35 Identities=20% Similarity=0.400 Sum_probs=30.5
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc
Q 012847 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (455)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~~ 326 (455)
..++.|+ +|||+-..+|+++|..|++|+-++.++.
T Consensus 891 ~eL~~Lm-rv~~~~~~RAr~lf~Agf~tv~~iA~a~ 925 (1008)
T KOG0950|consen 891 AELIPLM-RVPDVKAERARQLFKAGFTSVGSIANAT 925 (1008)
T ss_pred hhhhhhh-cCchhHHHHHHHHHHhhccchHHHhcCC
Confidence 4466666 9999999999999999999999998754
No 338
>cd04885 ACT_ThrD-I Tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes each of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=20.37 E-value=2.6e+02 Score=21.27 Aligned_cols=44 Identities=23% Similarity=0.204 Sum_probs=28.0
Q ss_pred CeEEEEecccccCCCCCCCccEEEeCCCchhhhhhHHHHHHHHHHcCce
Q 012847 368 EVIILCGGSYRRGKASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFL 416 (455)
Q Consensus 368 ~~~v~~~Gs~RRgke~~gDvDiLit~~d~~~~~~~l~~lv~~L~~~g~l 416 (455)
++.|+-. .|||-...-..|.+.|-.++. +.+..+++.|++.||-
T Consensus 22 ~~nI~~~-~~~~~~~~~~~v~v~ie~~~~----~~~~~i~~~L~~~G~~ 65 (68)
T cd04885 22 PRNITEF-HYRNQGGDEARVLVGIQVPDR----EDLAELKERLEALGYP 65 (68)
T ss_pred CCcEEEE-EEEcCCCCceEEEEEEEeCCH----HHHHHHHHHHHHcCCC
Confidence 6654432 588876444445555544443 3567899999999984
No 339
>PF00542 Ribosomal_L12: Ribosomal protein L7/L12 C-terminal domain; InterPro: IPR013823 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the C-terminal domain of the large subunit ribosomal proteins, known as the L7/L12 family. L7/L12 is present in each 50S subunit in four copies organised as two dimers. The L8 protein complex consisting of two dimers of L7/L12 and L10 in Escherichia coli ribosomes is assembled on the conserved region of 23 S rRNA termed the GTPase-associated domain []. The L7/L12 dimer probably interacts with EF-Tu. L7 and L12 only differ in a single post translational modification of the addition of an acetyl group to the N terminus of L7.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1DD4_B 1DD3_A 1RQU_B 2GYA_5 2GYC_5 1RQS_A 1RQV_A 1CTF_A 2XUX_L.
Probab=20.36 E-value=1.5e+02 Score=23.46 Aligned_cols=51 Identities=27% Similarity=0.462 Sum_probs=33.1
Q ss_pred hhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhccCchhhhhhchhhHhhhccCcCHHHHHHHHHHHHH
Q 012847 287 KDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQK 360 (455)
Q Consensus 287 ~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~~v~~ 360 (455)
.+.+..+++....+.|+|-+-|+.+.+. + -..+...++++||+++...++.
T Consensus 10 ~~~ki~vIK~vR~~tgl~L~eAK~~vd~-------------~----------p~~ik~~v~keeAe~ik~~Le~ 60 (68)
T PF00542_consen 10 GEKKIKVIKEVREITGLGLKEAKKLVDS-------------L----------PKVIKEGVSKEEAEEIKKKLEA 60 (68)
T ss_dssp TTGHHHHHHHHHHHC---HHHHHHHHCT-------------T----------TEEEEEEE-HHHHHHHHHHHHC
T ss_pred ccchHHHHHHHHHHhCCcHHHHHHHHHh-------------C----------CHHHHcCCCHHHHHHHHHHHHH
Confidence 4456678888888889999999888762 0 1124556888999888777665
No 340
>PRK00024 hypothetical protein; Reviewed
Probab=20.26 E-value=65 Score=31.35 Aligned_cols=27 Identities=15% Similarity=0.438 Sum_probs=23.6
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHHhCC
Q 012847 252 SADQVKGLPGIGKSMQDHIQEIVTTGK 278 (455)
Q Consensus 252 s~~~l~~lpgIG~~ia~kI~Eil~tG~ 278 (455)
+.++|.+++|||+..+..|.-+++-|+
T Consensus 64 s~~eL~~i~GIG~akA~~L~a~~El~~ 90 (224)
T PRK00024 64 SLEELQSIKGIGPAKAAQLKAALELAR 90 (224)
T ss_pred CHHHHhhccCccHHHHHHHHHHHHHHH
Confidence 468899999999999999988888765
No 341
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=20.13 E-value=1.9e+02 Score=21.76 Aligned_cols=22 Identities=18% Similarity=0.326 Sum_probs=17.6
Q ss_pred HhhhccCcCHHHHHHHHHc-CCC
Q 012847 296 LFGEVWGIGPATAQKLYEK-GHR 317 (455)
Q Consensus 296 lf~~I~GvGpktA~~ly~~-Gir 317 (455)
.+.+..||.+.|.+.|.++ |+-
T Consensus 5 eva~~~gvs~~tlr~w~~~~g~~ 27 (68)
T cd01104 5 AVARLTGVSPDTLRAWERRYGLP 27 (68)
T ss_pred HHHHHHCcCHHHHHHHHHhCCCC
Confidence 3456779999999999986 763
No 342
>PRK09482 flap endonuclease-like protein; Provisional
Probab=20.12 E-value=1.5e+02 Score=29.62 Aligned_cols=27 Identities=19% Similarity=0.398 Sum_probs=19.7
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhh
Q 012847 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKL 282 (455)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~l 282 (455)
+-+.++||||++.|.++- -+-|++..+
T Consensus 182 DnIpGVpGIG~KtA~~LL--~~~gsle~i 208 (256)
T PRK09482 182 SKIPGVAGIGPKSAAELL--NQFRSLENI 208 (256)
T ss_pred cCCCCCCCcChHHHHHHH--HHhCCHHHH
Confidence 568899999999998763 355665543
No 343
>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=20.08 E-value=6e+02 Score=25.17 Aligned_cols=56 Identities=14% Similarity=0.195 Sum_probs=30.6
Q ss_pred HHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHh
Q 012847 235 SYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLF 297 (455)
Q Consensus 235 aY~rAa~~L~~l~~~i~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf 297 (455)
++.-+-....++. + +...+.+|||||+..+.++.. ..+.-++.|..-.+.+.-.++
T Consensus 132 ~l~l~q~i~q~~w-~--~~~~L~Qlp~i~~~~~~~l~~----~~i~~l~~l~~~~~~e~~~ll 187 (314)
T PF02889_consen 132 ALELSQCIVQALW-D--SDSPLLQLPHIGEESLKKLEK----RGIKTLQDLRDLSPEELEELL 187 (314)
T ss_dssp HHHHHHHHHHTS--T--TS-GGGGSTT--HHHHHHHHH----TT--SHHHHHHS-HHHHHHHH
T ss_pred HHHHHHHHHhhcC-C--CCChhhcCCCCCHHHHHHHhc----cCCCcHHHHhhCCHHHHHHHH
Confidence 3444444555565 2 336799999999999888776 344556666654455455555
Done!