Query 009742
Match_columns 527
No_of_seqs 282 out of 851
Neff 6.4
Searched_HMMs 46136
Date Thu Mar 28 16:47:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009742.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009742hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2534 DNA polymerase IV (fam 100.0 5.4E-89 1.2E-93 674.9 26.8 321 196-527 9-353 (353)
2 cd00141 NT_POLXc Nucleotidyltr 100.0 4.8E-74 1.1E-78 589.3 30.5 303 201-525 2-307 (307)
3 smart00483 POLXc DNA polymeras 100.0 2.5E-73 5.3E-78 590.1 27.3 318 197-526 1-334 (334)
4 PRK08609 hypothetical protein; 100.0 7.7E-68 1.7E-72 583.1 28.5 299 197-526 1-314 (570)
5 COG1796 POL4 DNA polymerase IV 100.0 2.1E-56 4.5E-61 447.0 23.6 299 196-526 2-318 (326)
6 PF14792 DNA_pol_B_palm: DNA p 99.9 6.3E-26 1.4E-30 200.3 9.9 105 334-448 1-112 (112)
7 PF14791 DNA_pol_B_thumb: DNA 99.9 1.8E-24 4E-29 171.8 3.1 63 454-526 1-63 (64)
8 PF14716 HHH_8: Helix-hairpin- 99.7 8.9E-17 1.9E-21 129.6 7.3 66 199-264 1-68 (68)
9 PF10391 DNA_pol_lambd_f: Fing 99.6 2.3E-16 5E-21 120.1 3.6 51 283-333 1-52 (52)
10 PRK07945 hypothetical protein; 99.6 8.6E-15 1.9E-19 152.7 11.7 91 202-302 3-98 (335)
11 PF00533 BRCT: BRCA1 C Terminu 98.8 1.7E-08 3.7E-13 81.7 8.0 67 16-84 3-78 (78)
12 smart00292 BRCT breast cancer 98.7 1.7E-08 3.7E-13 80.7 6.1 70 17-87 1-80 (80)
13 cd00027 BRCT Breast Cancer Sup 98.3 1.5E-06 3.2E-11 67.7 5.2 64 21-85 1-72 (72)
14 TIGR00575 dnlj DNA ligase, NAD 97.9 3.4E-05 7.4E-10 87.4 9.3 82 243-335 466-550 (652)
15 PF14520 HHH_5: Helix-hairpin- 97.8 9.7E-06 2.1E-10 63.6 2.6 51 282-332 3-55 (60)
16 KOG3226 DNA repair protein [Re 97.6 4.3E-05 9.3E-10 78.9 3.4 82 16-100 315-404 (508)
17 PF12738 PTCB-BRCT: twin BRCT 97.4 0.00014 3E-09 57.2 3.5 55 23-79 2-63 (63)
18 PF14520 HHH_5: Helix-hairpin- 97.3 0.00025 5.5E-09 55.5 4.2 52 243-302 5-56 (60)
19 PLN03123 poly [ADP-ribose] pol 97.0 0.0012 2.5E-08 77.8 7.5 81 16-98 391-481 (981)
20 PF11731 Cdd1: Pathogenicity l 97.0 0.00083 1.8E-08 57.4 4.2 35 280-314 8-42 (93)
21 PF12826 HHH_2: Helix-hairpin- 96.9 0.0014 3.1E-08 52.1 4.6 48 246-302 6-53 (64)
22 COG1555 ComEA DNA uptake prote 96.8 0.002 4.3E-08 60.0 5.0 50 241-302 95-145 (149)
23 PLN03122 Poly [ADP-ribose] pol 96.7 0.0033 7.1E-08 72.7 7.7 85 13-100 184-280 (815)
24 PRK07956 ligA NAD-dependent DN 96.7 0.0065 1.4E-07 69.3 9.9 85 243-337 479-565 (665)
25 TIGR01259 comE comEA protein. 96.6 0.0033 7.1E-08 56.4 5.4 50 241-302 66-116 (120)
26 TIGR00084 ruvA Holliday juncti 96.5 0.0042 9.2E-08 60.2 5.4 53 243-301 72-124 (191)
27 PF12836 HHH_3: Helix-hairpin- 96.5 0.0039 8.6E-08 49.7 4.3 48 241-300 12-60 (65)
28 KOG0966 ATP-dependent DNA liga 96.5 0.004 8.7E-08 70.3 5.7 86 13-98 628-722 (881)
29 PRK14351 ligA NAD-dependent DN 96.4 0.011 2.4E-07 67.6 9.1 87 243-339 496-584 (689)
30 PRK02515 psbU photosystem II c 96.3 0.0061 1.3E-07 55.0 4.8 47 241-302 59-105 (132)
31 KOG4362 Transcriptional regula 96.2 0.0052 1.1E-07 69.0 5.1 80 17-100 473-565 (684)
32 PF14229 DUF4332: Domain of un 96.2 0.019 4.2E-07 51.6 7.7 67 249-315 1-84 (122)
33 PRK14605 ruvA Holliday junctio 96.1 0.0062 1.3E-07 59.2 4.3 52 243-301 73-125 (194)
34 TIGR00426 competence protein C 96.0 0.014 3E-07 46.9 5.1 50 242-303 15-66 (69)
35 PRK13901 ruvA Holliday junctio 96.0 0.0089 1.9E-07 58.0 4.7 53 243-301 72-124 (196)
36 PRK00116 ruvA Holliday junctio 95.9 0.014 3E-07 56.6 5.9 53 243-302 73-126 (192)
37 PRK14601 ruvA Holliday junctio 95.9 0.0097 2.1E-07 57.3 4.6 53 243-301 73-125 (183)
38 PF00633 HHH: Helix-hairpin-he 95.9 0.0067 1.5E-07 41.1 2.4 23 240-262 8-30 (30)
39 PRK14602 ruvA Holliday junctio 95.7 0.011 2.4E-07 57.9 4.3 53 243-301 74-126 (203)
40 PRK14606 ruvA Holliday junctio 95.7 0.013 2.8E-07 56.6 4.6 53 243-301 73-125 (188)
41 TIGR00084 ruvA Holliday juncti 95.7 0.0069 1.5E-07 58.7 2.7 50 281-332 69-124 (191)
42 PRK14603 ruvA Holliday junctio 95.6 0.015 3.2E-07 56.7 4.6 53 243-301 72-124 (197)
43 PRK14604 ruvA Holliday junctio 95.6 0.015 3.3E-07 56.5 4.6 53 243-301 73-125 (195)
44 PRK12766 50S ribosomal protein 95.5 0.0043 9.3E-08 61.3 0.5 51 285-335 4-56 (232)
45 PF00633 HHH: Helix-hairpin-he 95.3 0.015 3.3E-07 39.4 2.6 22 281-302 8-29 (30)
46 COG1555 ComEA DNA uptake prote 95.1 0.016 3.5E-07 53.9 3.0 51 279-335 92-147 (149)
47 PRK07956 ligA NAD-dependent DN 95.0 0.011 2.4E-07 67.5 1.7 61 288-348 449-512 (665)
48 COG0632 RuvA Holliday junction 94.8 0.033 7E-07 54.4 4.3 54 243-302 73-126 (201)
49 cd05397 NT_Pol-beta-like Nucle 94.8 0.054 1.2E-06 40.7 4.5 28 354-381 14-42 (49)
50 PF11798 IMS_HHH: IMS family H 94.7 0.018 4E-07 39.5 1.6 19 287-305 14-32 (32)
51 PRK14973 DNA topoisomerase I; 94.6 0.039 8.4E-07 65.3 5.1 90 243-333 835-928 (936)
52 PRK14600 ruvA Holliday junctio 94.6 0.034 7.3E-07 53.7 3.8 52 243-301 73-124 (186)
53 PRK14350 ligA NAD-dependent DN 94.4 0.087 1.9E-06 60.2 7.0 84 243-335 470-561 (669)
54 PRK02362 ski2-like helicase; P 94.4 0.03 6.5E-07 64.8 3.4 55 273-330 642-698 (737)
55 TIGR00575 dnlj DNA ligase, NAD 94.3 0.018 3.9E-07 65.6 1.5 63 287-349 435-500 (652)
56 COG0272 Lig NAD-dependent DNA 94.3 0.12 2.6E-06 58.3 7.8 49 245-302 513-561 (667)
57 PTZ00418 Poly(A) polymerase; P 94.2 0.36 7.8E-06 54.2 11.2 51 356-406 125-176 (593)
58 cd05402 NT_PAP_TUTase Nucleoti 94.1 0.19 4.2E-06 43.8 7.4 60 341-404 7-68 (114)
59 TIGR01259 comE comEA protein. 93.9 0.053 1.1E-06 48.6 3.4 48 281-334 65-117 (120)
60 PRK02515 psbU photosystem II c 93.9 0.067 1.4E-06 48.5 3.9 32 282-313 59-91 (132)
61 PRK00116 ruvA Holliday junctio 93.5 0.042 9.1E-07 53.3 2.0 51 282-332 71-125 (192)
62 KOG2481 Protein required for n 93.3 0.054 1.2E-06 58.8 2.7 82 13-98 322-416 (570)
63 PF12836 HHH_3: Helix-hairpin- 93.3 0.077 1.7E-06 42.2 2.9 47 282-334 12-63 (65)
64 TIGR00426 competence protein C 93.2 0.099 2.2E-06 41.9 3.5 43 285-333 17-65 (69)
65 PRK14605 ruvA Holliday junctio 93.2 0.043 9.4E-07 53.3 1.6 52 280-331 69-124 (194)
66 PRK00254 ski2-like helicase; P 92.7 0.14 3E-06 59.3 5.0 75 255-330 608-693 (720)
67 COG5163 NOP7 Protein required 92.6 0.11 2.4E-06 54.8 3.8 82 13-98 345-440 (591)
68 KOG1929 Nucleotide excision re 92.4 0.2 4.3E-06 58.1 5.8 82 17-100 102-191 (811)
69 PRK12766 50S ribosomal protein 92.4 0.24 5.3E-06 49.2 5.6 54 242-303 2-55 (232)
70 PF12826 HHH_2: Helix-hairpin- 92.4 0.097 2.1E-06 41.6 2.3 43 288-331 7-51 (64)
71 KOG2043 Signaling protein SWIF 91.2 0.18 3.9E-06 59.2 3.8 61 37-98 671-739 (896)
72 PF01909 NTP_transf_2: Nucleot 90.8 0.34 7.3E-06 40.3 4.1 32 355-386 12-44 (93)
73 smart00278 HhH1 Helix-hairpin- 90.7 0.17 3.6E-06 32.9 1.7 18 285-302 2-19 (26)
74 PF04994 TfoX_C: TfoX C-termin 90.4 0.21 4.6E-06 41.7 2.6 30 286-315 5-34 (81)
75 PRK14601 ruvA Holliday junctio 90.4 0.12 2.7E-06 49.7 1.3 50 280-331 69-124 (183)
76 PRK14606 ruvA Holliday junctio 90.4 0.14 3.1E-06 49.5 1.6 50 280-331 69-124 (188)
77 PRK14603 ruvA Holliday junctio 90.0 0.14 2.9E-06 50.0 1.2 50 280-331 68-123 (197)
78 PRK14602 ruvA Holliday junctio 89.9 0.16 3.4E-06 49.8 1.5 50 280-331 70-125 (203)
79 PRK14604 ruvA Holliday junctio 89.8 0.15 3.2E-06 49.7 1.2 50 280-331 69-124 (195)
80 PRK04301 radA DNA repair and r 89.3 0.29 6.2E-06 50.9 3.1 30 286-315 8-37 (317)
81 PRK13901 ruvA Holliday junctio 89.2 0.18 3.9E-06 49.1 1.3 50 280-331 68-123 (196)
82 COG1796 POL4 DNA polymerase IV 89.1 0.99 2.1E-05 46.9 6.7 95 196-309 59-153 (326)
83 TIGR01448 recD_rel helicase, p 89.0 1.1 2.3E-05 52.1 7.7 82 242-334 116-200 (720)
84 PRK14351 ligA NAD-dependent DN 89.0 0.18 3.9E-06 57.9 1.4 64 287-350 465-531 (689)
85 TIGR03671 cca_archaeal CCA-add 88.9 1.9 4E-05 46.6 8.8 46 341-386 24-71 (408)
86 COG1948 MUS81 ERCC4-type nucle 88.8 0.55 1.2E-05 47.4 4.5 49 245-302 184-232 (254)
87 COG3743 Uncharacterized conser 88.7 0.39 8.4E-06 43.6 3.0 53 284-339 67-119 (133)
88 TIGR02236 recomb_radA DNA repa 88.5 0.31 6.6E-06 50.4 2.6 29 287-315 2-30 (310)
89 TIGR03252 uncharacterized HhH- 88.1 1.3 2.7E-05 42.5 6.3 49 250-301 75-132 (177)
90 PRK13482 DNA integrity scannin 87.5 0.87 1.9E-05 48.1 5.2 70 221-302 266-337 (352)
91 PRK14600 ruvA Holliday junctio 87.3 0.29 6.2E-06 47.3 1.5 49 280-331 69-123 (186)
92 TIGR00588 ogg 8-oxoguanine DNA 87.3 1.5 3.2E-05 45.7 6.8 61 244-306 177-242 (310)
93 KOG1929 Nucleotide excision re 87.1 0.7 1.5E-05 53.7 4.6 82 15-98 490-578 (811)
94 PRK08097 ligB NAD-dependent DN 87.0 0.79 1.7E-05 51.4 4.9 85 242-339 458-544 (562)
95 TIGR01448 recD_rel helicase, p 86.9 0.29 6.4E-06 56.6 1.5 53 281-333 79-135 (720)
96 PRK01172 ski2-like helicase; P 86.5 1.1 2.3E-05 51.5 5.8 40 274-314 603-642 (674)
97 PF11731 Cdd1: Pathogenicity l 86.3 1.1 2.3E-05 38.6 4.2 47 242-292 11-57 (93)
98 PRK03352 DNA polymerase IV; Va 86.2 0.54 1.2E-05 49.4 2.9 28 287-314 180-207 (346)
99 smart00279 HhH2 Helix-hairpin- 85.9 0.52 1.1E-05 33.3 1.8 16 288-303 20-35 (36)
100 cd00080 HhH2_motif Helix-hairp 85.6 0.72 1.6E-05 37.8 2.7 27 287-314 25-51 (75)
101 cd05400 NT_2-5OAS_ClassI-CCAas 85.6 3.4 7.3E-05 37.4 7.5 46 357-402 27-79 (143)
102 PRK14350 ligA NAD-dependent DN 85.4 1.5 3.3E-05 50.3 6.2 61 238-302 497-559 (669)
103 KOG0966 ATP-dependent DNA liga 85.2 1.7 3.6E-05 50.0 6.2 80 17-96 783-881 (881)
104 PRK14670 uvrC excinuclease ABC 84.9 2.2 4.7E-05 48.2 7.0 66 221-303 500-565 (574)
105 PRK03858 DNA polymerase IV; Va 84.8 0.68 1.5E-05 49.5 2.9 28 287-314 176-203 (396)
106 PRK01216 DNA polymerase IV; Va 84.1 0.72 1.6E-05 48.9 2.7 29 287-315 181-209 (351)
107 PRK03609 umuC DNA polymerase V 83.8 0.76 1.6E-05 49.7 2.8 28 287-314 182-209 (422)
108 COG1708 Predicted nucleotidylt 83.1 5.2 0.00011 34.7 7.4 29 356-384 25-54 (128)
109 cd00424 PolY Y-family of DNA p 82.6 3.3 7.2E-05 43.4 6.9 28 287-314 176-203 (343)
110 KOG2841 Structure-specific end 82.6 1.5 3.2E-05 43.7 3.9 50 244-302 196-245 (254)
111 PRK08609 hypothetical protein; 81.9 1.8 3.9E-05 48.9 4.9 54 241-300 86-139 (570)
112 smart00278 HhH1 Helix-hairpin- 81.9 1.2 2.7E-05 28.8 2.1 20 244-263 2-21 (26)
113 cd01703 PolY_Pol_iota DNA Poly 81.7 0.98 2.1E-05 48.4 2.6 30 286-315 174-203 (379)
114 COG0353 RecR Recombinational D 81.7 1 2.3E-05 43.6 2.5 20 281-300 9-28 (198)
115 COG0272 Lig NAD-dependent DNA 81.7 2.6 5.5E-05 48.0 5.9 135 243-387 479-644 (667)
116 PRK01810 DNA polymerase IV; Va 81.6 1.1 2.3E-05 48.3 2.8 28 287-314 182-209 (407)
117 cd01701 PolY_Rev1 DNA polymera 81.5 1.1 2.3E-05 48.4 2.8 29 287-315 225-253 (404)
118 cd01700 PolY_Pol_V_umuC umuC s 81.2 1.1 2.4E-05 47.0 2.7 28 287-314 179-206 (344)
119 smart00478 ENDO3c endonuclease 81.1 4.4 9.5E-05 37.0 6.4 26 281-306 69-94 (149)
120 PF14490 HHH_4: Helix-hairpin- 80.9 2.6 5.6E-05 35.9 4.4 54 281-335 10-66 (94)
121 PRK03348 DNA polymerase IV; Pr 80.9 1.1 2.3E-05 49.3 2.5 28 287-314 183-210 (454)
122 PRK02406 DNA polymerase IV; Va 80.8 1.1 2.4E-05 47.0 2.6 28 287-314 171-198 (343)
123 PRK10880 adenine DNA glycosyla 80.7 6.7 0.00015 41.7 8.3 65 221-292 85-151 (350)
124 PRK10308 3-methyl-adenine DNA 80.6 3.3 7.1E-05 42.6 5.9 63 243-309 167-232 (283)
125 smart00475 53EXOc 5'-3' exonuc 80.5 1.3 2.8E-05 45.0 2.8 26 287-314 189-215 (259)
126 PRK00227 glnD PII uridylyl-tra 80.4 4.7 0.0001 46.6 7.5 65 337-404 8-74 (693)
127 PRK09482 flap endonuclease-lik 80.0 1.3 2.9E-05 44.9 2.8 26 287-314 185-211 (256)
128 PF01367 5_3_exonuc: 5'-3' exo 79.9 0.14 3.1E-06 44.6 -3.7 24 288-313 22-46 (101)
129 PRK14667 uvrC excinuclease ABC 79.9 4 8.6E-05 46.1 6.6 67 221-303 498-564 (567)
130 PRK03103 DNA polymerase IV; Re 79.7 1.4 3E-05 47.5 2.9 28 287-314 184-211 (409)
131 PRK02794 DNA polymerase IV; Pr 79.5 1.2 2.7E-05 48.0 2.5 28 287-314 212-239 (419)
132 PRK14666 uvrC excinuclease ABC 79.4 0.96 2.1E-05 51.8 1.6 46 284-331 637-685 (694)
133 PRK14133 DNA polymerase IV; Pr 79.4 1.3 2.9E-05 46.5 2.6 28 287-314 176-203 (347)
134 PRK14976 5'-3' exonuclease; Pr 79.3 1.4 3.1E-05 45.3 2.7 25 287-313 194-219 (281)
135 cd00056 ENDO3c endonuclease II 79.2 1.2 2.6E-05 41.1 2.0 27 280-306 79-105 (158)
136 PRK01229 N-glycosylase/DNA lya 78.5 2.1 4.6E-05 42.1 3.6 53 251-306 85-142 (208)
137 PRK00558 uvrC excinuclease ABC 78.1 3.2 7E-05 47.1 5.4 52 243-303 543-594 (598)
138 PRK08097 ligB NAD-dependent DN 77.8 0.89 1.9E-05 51.0 0.8 64 287-350 428-494 (562)
139 PRK14666 uvrC excinuclease ABC 77.7 3.7 8E-05 47.2 5.6 67 221-302 621-687 (694)
140 cd00008 53EXOc 5'-3' exonuclea 77.5 1.8 3.9E-05 43.3 2.8 27 287-314 186-212 (240)
141 COG0122 AlkA 3-methyladenine D 77.4 2.8 6E-05 43.2 4.2 48 257-305 172-219 (285)
142 KOG2245 Poly(A) polymerase and 77.2 6.9 0.00015 43.1 7.1 87 319-407 40-140 (562)
143 PTZ00205 DNA polymerase kappa; 76.1 1.8 3.9E-05 48.6 2.6 28 287-314 312-339 (571)
144 PRK00076 recR recombination pr 76.1 2.1 4.6E-05 41.7 2.7 21 281-301 8-28 (196)
145 TIGR00615 recR recombination p 75.9 2.2 4.7E-05 41.6 2.7 20 281-300 8-27 (195)
146 PRK13300 tRNA CCA-pyrophosphor 75.8 9.4 0.0002 41.9 7.9 46 343-388 27-74 (447)
147 COG1746 CCA1 tRNA nucleotidylt 75.8 9.6 0.00021 41.3 7.7 49 340-388 28-78 (443)
148 TIGR01083 nth endonuclease III 75.7 6.1 0.00013 38.1 5.8 25 281-305 103-127 (191)
149 PRK14672 uvrC excinuclease ABC 75.4 5.7 0.00012 45.6 6.2 54 243-305 608-661 (691)
150 cd03468 PolY_like DNA Polymera 74.8 2.3 5.1E-05 44.0 2.9 28 288-315 174-201 (335)
151 PRK13844 recombination protein 74.4 2.5 5.4E-05 41.3 2.7 21 281-301 12-32 (200)
152 COG0632 RuvA Holliday junction 74.2 1.7 3.8E-05 42.5 1.6 50 282-331 71-124 (201)
153 cd01702 PolY_Pol_eta DNA Polym 74.2 2.5 5.4E-05 44.9 3.0 28 287-314 185-213 (359)
154 PRK07758 hypothetical protein; 74.1 1.5 3.3E-05 37.7 1.0 44 289-332 39-84 (95)
155 PRK00254 ski2-like helicase; P 73.9 15 0.00032 42.7 9.4 53 243-303 645-697 (720)
156 PF14229 DUF4332: Domain of un 73.8 3.3 7.2E-05 37.2 3.2 26 290-315 1-26 (122)
157 cd05403 NT_KNTase_like Nucleot 73.4 7.6 0.00017 31.7 5.2 29 359-387 20-49 (93)
158 PRK06063 DNA polymerase III su 73.4 8.3 0.00018 40.2 6.5 47 17-65 231-277 (313)
159 TIGR01084 mutY A/G-specific ad 72.4 7.5 0.00016 39.9 5.8 66 220-292 80-147 (275)
160 PRK10702 endonuclease III; Pro 72.3 6.6 0.00014 38.7 5.2 23 281-303 106-128 (211)
161 cd03586 PolY_Pol_IV_kappa DNA 71.6 2.9 6.2E-05 43.4 2.6 28 287-314 174-201 (334)
162 PRK10702 endonuclease III; Pro 71.6 8.4 0.00018 37.9 5.7 43 221-263 85-129 (211)
163 COG0258 Exo 5'-3' exonuclease 71.0 3.1 6.8E-05 43.2 2.7 25 288-314 202-227 (310)
164 COG0389 DinP Nucleotidyltransf 70.9 2.9 6.3E-05 44.3 2.5 27 287-313 179-205 (354)
165 KOG2875 8-oxoguanine DNA glyco 70.9 6 0.00013 40.5 4.5 67 244-311 175-245 (323)
166 COG1948 MUS81 ERCC4-type nucle 70.5 5.5 0.00012 40.3 4.2 53 278-331 176-230 (254)
167 PRK13913 3-methyladenine DNA g 70.5 5.1 0.00011 39.8 3.9 21 282-302 119-139 (218)
168 KOG2093 Translesion DNA polyme 70.4 6.5 0.00014 45.9 5.2 85 14-100 43-133 (1016)
169 KOG3524 Predicted guanine nucl 70.2 4.7 0.0001 45.8 4.0 73 14-89 114-192 (850)
170 cd00056 ENDO3c endonuclease II 67.0 10 0.00022 34.9 5.0 67 219-292 54-125 (158)
171 PRK13910 DNA glycosylase MutY; 66.3 11 0.00025 38.9 5.6 68 221-295 48-117 (289)
172 PF00416 Ribosomal_S13: Riboso 66.0 6 0.00013 34.7 3.1 25 282-306 13-38 (107)
173 PF03118 RNA_pol_A_CTD: Bacter 65.8 8.1 0.00018 30.9 3.5 22 243-264 44-65 (66)
174 PRK04301 radA DNA repair and r 65.6 12 0.00027 38.7 5.9 52 244-303 7-58 (317)
175 COG0177 Nth Predicted EndoIII- 65.4 8.2 0.00018 38.1 4.2 86 250-343 80-175 (211)
176 PF11798 IMS_HHH: IMS family H 65.4 3.1 6.7E-05 28.5 0.9 18 244-261 12-29 (32)
177 PRK13766 Hef nuclease; Provisi 65.3 8.3 0.00018 45.0 5.0 49 245-302 717-765 (773)
178 COG2251 Predicted nuclease (Re 64.8 4.7 0.0001 43.8 2.6 27 288-314 229-255 (474)
179 PF02371 Transposase_20: Trans 64.2 4.4 9.5E-05 33.9 1.8 20 284-303 2-21 (87)
180 PRK06195 DNA polymerase III su 63.7 15 0.00032 38.2 6.0 48 17-65 219-266 (309)
181 PRK14973 DNA topoisomerase I; 63.7 8.4 0.00018 46.1 4.6 31 285-315 803-833 (936)
182 TIGR00615 recR recombination p 63.5 5.1 0.00011 39.0 2.3 37 238-274 5-42 (195)
183 PRK05007 PII uridylyl-transfer 63.0 24 0.00051 42.2 8.2 63 342-404 61-130 (884)
184 TIGR03252 uncharacterized HhH- 63.0 22 0.00047 34.2 6.5 44 221-264 80-136 (177)
185 KOG3548 DNA damage checkpoint 62.1 6.9 0.00015 45.9 3.4 81 17-100 924-1038(1176)
186 cd05401 NT_GlnE_GlnD_like Nucl 61.9 29 0.00062 32.4 7.1 49 358-406 56-110 (172)
187 PRK03980 flap endonuclease-1; 61.3 6.4 0.00014 40.7 2.8 26 287-313 192-217 (292)
188 TIGR03491 RecB family nuclease 61.1 6.8 0.00015 43.0 3.1 28 288-315 211-238 (457)
189 PF04919 DUF655: Protein of un 61.0 28 0.0006 33.6 6.7 52 220-278 99-151 (181)
190 PRK12278 50S ribosomal protein 61.0 6.3 0.00014 39.2 2.5 30 284-313 158-187 (221)
191 PRK01759 glnD PII uridylyl-tra 61.0 27 0.00059 41.5 8.2 68 337-404 32-106 (854)
192 TIGR00593 pola DNA polymerase 60.1 6.4 0.00014 46.9 2.8 24 288-313 189-213 (887)
193 PRK00076 recR recombination pr 60.1 6.1 0.00013 38.6 2.2 32 243-274 11-42 (196)
194 PF14716 HHH_8: Helix-hairpin- 60.0 7.2 0.00016 31.1 2.2 24 279-302 41-65 (68)
195 PRK14668 uvrC excinuclease ABC 59.9 14 0.0003 42.0 5.3 41 285-326 526-568 (577)
196 smart00611 SEC63 Domain of unk 59.8 18 0.00038 37.2 5.7 29 286-314 153-181 (312)
197 PF14579 HHH_6: Helix-hairpin- 59.3 12 0.00026 31.5 3.6 30 286-315 29-62 (90)
198 PRK02362 ski2-like helicase; P 59.2 65 0.0014 37.5 10.8 52 243-304 652-704 (737)
199 PRK13844 recombination protein 59.0 6.3 0.00014 38.5 2.1 32 243-274 15-46 (200)
200 KOG2534 DNA polymerase IV (fam 58.7 6.3 0.00014 41.0 2.1 54 279-332 51-114 (353)
201 PRK10917 ATP-dependent DNA hel 58.0 8.2 0.00018 44.6 3.2 27 286-312 11-37 (681)
202 PRK14670 uvrC excinuclease ABC 57.8 6.1 0.00013 44.7 2.0 29 285-314 515-543 (574)
203 PTZ00217 flap endonuclease-1; 57.7 7.9 0.00017 41.8 2.8 26 287-313 238-263 (393)
204 PRK14671 uvrC excinuclease ABC 57.4 8.4 0.00018 44.1 3.0 32 282-314 567-598 (621)
205 PRK14671 uvrC excinuclease ABC 57.2 14 0.0003 42.3 4.8 49 243-302 569-617 (621)
206 PRK14667 uvrC excinuclease ABC 56.8 5.6 0.00012 45.0 1.5 29 285-314 515-543 (567)
207 COG4277 Predicted DNA-binding 56.2 9.6 0.00021 39.5 2.9 39 283-321 329-371 (404)
208 PRK12311 rpsB 30S ribosomal pr 55.8 8.2 0.00018 40.6 2.5 32 282-313 261-292 (326)
209 TIGR02236 recomb_radA DNA repa 55.5 12 0.00026 38.6 3.6 50 245-302 1-50 (310)
210 PRK04374 PII uridylyl-transfer 55.1 40 0.00087 40.2 8.3 62 343-404 55-122 (869)
211 KOG1921 Endonuclease III [Repl 55.0 13 0.00027 37.5 3.5 32 272-304 148-179 (286)
212 PRK14669 uvrC excinuclease ABC 54.3 16 0.00036 41.7 4.7 30 284-314 552-581 (624)
213 TIGR03674 fen_arch flap struct 54.3 9.9 0.00022 40.1 2.8 27 287-314 239-265 (338)
214 PRK05755 DNA polymerase I; Pro 54.1 9.1 0.0002 45.6 2.8 25 287-313 190-215 (880)
215 PRK07758 hypothetical protein; 53.5 13 0.00028 32.0 2.9 23 243-265 67-89 (95)
216 PF03118 RNA_pol_A_CTD: Bacter 53.2 3.8 8.2E-05 32.8 -0.4 44 290-333 17-62 (66)
217 COG0177 Nth Predicted EndoIII- 53.2 29 0.00062 34.3 5.6 33 230-262 95-128 (211)
218 TIGR01083 nth endonuclease III 52.7 30 0.00065 33.3 5.6 42 221-262 82-125 (191)
219 PRK14672 uvrC excinuclease ABC 52.6 6.3 0.00014 45.2 1.1 50 285-335 609-660 (691)
220 COG5186 PAP1 Poly(A) polymeras 52.5 56 0.0012 35.0 7.8 52 357-408 81-133 (552)
221 CHL00137 rps13 ribosomal prote 52.1 9.7 0.00021 34.3 2.0 24 283-306 16-40 (122)
222 COG1669 Predicted nucleotidylt 51.7 73 0.0016 27.7 7.2 30 356-385 22-53 (97)
223 PF14579 HHH_6: Helix-hairpin- 51.7 37 0.0008 28.5 5.4 50 245-305 29-78 (90)
224 TIGR01084 mutY A/G-specific ad 51.2 23 0.00049 36.4 4.7 22 282-303 103-124 (275)
225 PRK05179 rpsM 30S ribosomal pr 51.1 10 0.00022 34.3 1.9 23 284-306 17-40 (122)
226 KOG1921 Endonuclease III [Repl 50.3 24 0.00053 35.6 4.6 29 234-262 149-178 (286)
227 PRK01216 DNA polymerase IV; Va 49.5 53 0.0012 34.8 7.4 52 245-306 180-233 (351)
228 smart00478 ENDO3c endonuclease 49.4 38 0.00082 30.8 5.6 42 221-262 48-91 (149)
229 cd00141 NT_POLXc Nucleotidyltr 48.5 7.4 0.00016 40.5 0.8 51 282-332 43-102 (307)
230 COG0322 UvrC Nuclease subunit 48.3 30 0.00065 39.3 5.5 83 199-302 497-579 (581)
231 cd01703 PolY_Pol_iota DNA Poly 48.1 35 0.00077 36.6 5.9 58 244-307 173-243 (379)
232 PF02889 Sec63: Sec63 Brl doma 47.6 22 0.00049 36.3 4.2 29 285-313 149-177 (314)
233 KOG0323 TFIIF-interacting CTD 47.4 6 0.00013 45.1 -0.2 59 42-100 467-533 (635)
234 TIGR03631 bact_S13 30S ribosom 47.2 12 0.00026 33.3 1.8 23 284-306 15-38 (113)
235 PRK00275 glnD PII uridylyl-tra 47.0 65 0.0014 38.6 8.3 48 357-404 78-128 (895)
236 KOG1918 3-methyladenine DNA gl 46.4 11 0.00024 37.3 1.5 46 256-301 137-182 (254)
237 KOG2093 Translesion DNA polyme 45.8 34 0.00074 40.2 5.4 81 12-96 155-243 (1016)
238 PF14490 HHH_4: Helix-hairpin- 45.7 22 0.00048 30.2 3.2 54 250-310 19-73 (94)
239 PRK02794 DNA polymerase IV; Pr 45.1 1.2E+02 0.0025 32.8 9.4 52 245-307 211-264 (419)
240 PRK12373 NADH dehydrogenase su 44.2 17 0.00038 39.2 2.7 33 281-313 320-352 (400)
241 COG1194 MutY A/G-specific DNA 44.0 44 0.00096 35.4 5.6 60 210-269 78-139 (342)
242 PRK13482 DNA integrity scannin 43.9 12 0.00027 39.6 1.6 52 277-330 280-334 (352)
243 PRK14669 uvrC excinuclease ABC 43.9 41 0.0009 38.5 5.8 66 221-303 536-601 (624)
244 PRK13913 3-methyladenine DNA g 43.8 42 0.00092 33.3 5.2 57 241-305 119-178 (218)
245 PF03445 DUF294: Putative nucl 43.3 60 0.0013 29.6 5.8 51 358-408 50-107 (138)
246 TIGR00588 ogg 8-oxoguanine DNA 42.6 35 0.00076 35.6 4.7 73 216-294 181-265 (310)
247 TIGR01693 UTase_glnD [Protein- 42.1 68 0.0015 38.1 7.5 49 357-405 43-94 (850)
248 PRK13746 aminoglycoside resist 42.0 1.3E+02 0.0028 30.8 8.5 27 359-386 30-58 (262)
249 PRK00558 uvrC excinuclease ABC 41.9 17 0.00037 41.4 2.4 30 284-314 543-572 (598)
250 PTZ00134 40S ribosomal protein 41.8 17 0.00037 34.1 2.0 46 283-349 29-75 (154)
251 TIGR01954 nusA_Cterm_rpt trans 41.5 28 0.00062 25.4 2.8 31 292-322 1-33 (50)
252 COG0099 RpsM Ribosomal protein 41.5 20 0.00044 32.2 2.3 22 285-306 18-40 (121)
253 TIGR01446 DnaD_dom DnaD and ph 41.2 23 0.00049 28.3 2.4 19 294-312 54-72 (73)
254 TIGR00596 rad1 DNA repair prot 41.0 36 0.00078 40.3 4.9 32 282-314 755-786 (814)
255 PRK03352 DNA polymerase IV; Va 40.3 49 0.0011 34.6 5.4 56 244-309 178-235 (346)
256 smart00483 POLXc DNA polymeras 40.2 13 0.00029 39.1 1.1 51 281-331 45-105 (334)
257 PRK04053 rps13p 30S ribosomal 40.0 21 0.00045 33.4 2.2 24 283-306 24-48 (149)
258 PRK03059 PII uridylyl-transfer 39.9 78 0.0017 37.8 7.5 64 340-403 42-110 (856)
259 COG1491 Predicted RNA-binding 39.9 28 0.0006 33.7 3.1 40 237-276 123-163 (202)
260 PF09970 DUF2204: Nucleotidyl 39.1 66 0.0014 30.8 5.6 39 357-395 16-59 (181)
261 TIGR00194 uvrC excinuclease AB 39.0 23 0.00051 40.1 2.9 29 285-314 542-570 (574)
262 TIGR00596 rad1 DNA repair prot 38.9 51 0.0011 39.1 5.7 16 199-214 643-658 (814)
263 TIGR03629 arch_S13P archaeal r 38.6 21 0.00046 33.1 2.1 44 285-349 22-66 (144)
264 PRK14668 uvrC excinuclease ABC 38.4 20 0.00043 40.7 2.2 20 316-335 526-545 (577)
265 PF02961 BAF: Barrier to autoi 38.3 24 0.00052 30.1 2.1 27 286-312 21-47 (89)
266 cd01702 PolY_Pol_eta DNA Polym 38.3 59 0.0013 34.6 5.7 54 245-307 184-241 (359)
267 COG2231 Uncharacterized protei 37.8 69 0.0015 31.6 5.5 19 282-300 113-131 (215)
268 cd00128 XPG Xeroderma pigmento 37.8 20 0.00043 37.3 1.9 24 287-311 226-249 (316)
269 COG1725 Predicted transcriptio 37.7 85 0.0018 28.5 5.7 88 251-351 12-103 (125)
270 COG1200 RecG RecG-like helicas 37.0 27 0.00059 40.0 2.9 27 286-312 12-38 (677)
271 PRK13766 Hef nuclease; Provisi 36.5 24 0.00053 41.1 2.6 44 285-329 716-761 (773)
272 PTZ00035 Rad51 protein; Provis 36.0 64 0.0014 34.0 5.4 48 282-330 22-71 (337)
273 PRK03858 DNA polymerase IV; Va 35.6 64 0.0014 34.4 5.5 52 245-306 175-228 (396)
274 PRK10308 3-methyl-adenine DNA 35.4 60 0.0013 33.4 5.0 44 217-260 173-224 (283)
275 COG1491 Predicted RNA-binding 34.8 76 0.0016 30.8 5.1 56 258-313 103-163 (202)
276 PF06514 PsbU: Photosystem II 34.4 11 0.00025 32.2 -0.4 51 282-332 21-72 (93)
277 COG1204 Superfamily II helicas 34.0 30 0.00065 40.7 2.8 108 222-332 610-726 (766)
278 PRK10880 adenine DNA glycosyla 33.8 29 0.00063 36.9 2.4 23 281-303 106-128 (350)
279 PLN03187 meiotic recombination 33.8 69 0.0015 34.0 5.3 34 280-314 28-61 (344)
280 PF04919 DUF655: Protein of un 33.6 33 0.00071 33.1 2.5 59 255-313 86-149 (181)
281 PRK03381 PII uridylyl-transfer 33.5 1.1E+02 0.0023 36.2 7.3 46 358-403 58-106 (774)
282 PHA00439 exonuclease 33.5 29 0.00064 35.8 2.3 27 287-314 191-219 (286)
283 COG0353 RecR Recombinational D 33.5 39 0.00084 33.0 3.0 27 238-264 6-33 (198)
284 PRK13910 DNA glycosylase MutY; 33.3 29 0.00062 35.9 2.3 22 282-303 70-91 (289)
285 COG2844 GlnD UTP:GlnB (protein 32.2 76 0.0016 37.4 5.5 48 357-404 66-116 (867)
286 COG1031 Uncharacterized Fe-S o 32.1 36 0.00077 37.4 2.7 32 282-313 514-546 (560)
287 PF11774 Lsr2: Lsr2 ; InterPr 31.9 31 0.00068 30.5 1.9 28 459-486 73-100 (110)
288 cd01701 PolY_Rev1 DNA polymera 31.4 83 0.0018 33.9 5.5 53 245-307 224-280 (404)
289 cd00424 PolY Y-family of DNA p 31.1 1.2E+02 0.0025 31.8 6.5 53 245-307 175-229 (343)
290 COG5067 DBF4 Protein kinase es 30.9 33 0.00071 36.8 2.2 49 13-63 117-165 (468)
291 PRK01229 N-glycosylase/DNA lya 30.9 65 0.0014 31.8 4.2 20 241-260 116-136 (208)
292 TIGR03135 malonate_mdcG holo-A 29.9 2E+02 0.0044 28.1 7.4 32 356-387 107-145 (202)
293 PHA01806 hypothetical protein 29.7 89 0.0019 30.5 4.7 49 334-386 14-67 (200)
294 PF04994 TfoX_C: TfoX C-termin 29.6 40 0.00087 28.1 2.1 35 243-281 3-37 (81)
295 KOG3524 Predicted guanine nucl 28.5 39 0.00084 38.9 2.3 79 17-98 209-294 (850)
296 PRK03348 DNA polymerase IV; Pr 28.1 1.1E+02 0.0024 33.5 5.9 53 245-307 182-236 (454)
297 PRK11072 bifunctional glutamin 25.9 2.5E+02 0.0053 34.1 8.6 27 358-384 155-182 (943)
298 TIGR00207 fliG flagellar motor 24.8 4.1E+02 0.0088 28.1 9.2 86 226-312 145-245 (338)
299 PLN03187 meiotic recombination 24.6 3.1E+02 0.0067 29.1 8.2 104 242-372 31-141 (344)
300 cd05398 NT_ClassII-CCAase Nucl 24.6 1.5E+02 0.0032 27.0 5.2 38 343-383 4-45 (139)
301 KOG4362 Transcriptional regula 24.3 1.3E+02 0.0028 34.9 5.5 83 3-87 573-678 (684)
302 TIGR02238 recomb_DMC1 meiotic 24.2 50 0.0011 34.5 2.1 36 289-324 6-43 (313)
303 TIGR00600 rad2 DNA excision re 23.1 63 0.0014 39.2 2.9 26 287-312 869-895 (1034)
304 PRK07945 hypothetical protein; 22.8 45 0.00098 35.1 1.5 28 286-313 51-82 (335)
305 COG2176 PolC DNA polymerase II 22.2 1.9E+02 0.0042 35.6 6.5 90 223-319 1294-1420(1444)
306 PF14091 DUF4269: Domain of un 22.1 6.5E+02 0.014 23.7 8.8 26 362-387 20-46 (152)
307 PF04439 Adenyl_transf: Strept 20.4 7.1E+02 0.015 25.6 9.7 48 337-386 2-53 (282)
No 1
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=100.00 E-value=5.4e-89 Score=674.88 Aligned_cols=321 Identities=36% Similarity=0.640 Sum_probs=295.5
Q ss_pred CCCcHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHH
Q 009742 196 PDLNKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFE 275 (527)
Q Consensus 196 ~~~N~~ia~~L~~la~~~e~~g~~~r~~aY~rAa~~l~~l~~~i~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~ 275 (527)
.++|..|+++|+.||+.+++.|+.+|+++|++||++|+++|++|+|++|+++|||||++|+.+|+|||+||++++||+++
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 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhchhHHHHHHhhccCcCHHHHHHHHHhCCCCHHHHhh-ccCcchhhhccccchhhhccCcCHHHHHHHHHHHHHHhhhc
Q 009742 276 KDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN-EDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEV 354 (527)
Q Consensus 276 ~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~-~~~L~~~q~~Glk~yed~~~~i~r~Ea~~i~~iv~~~~~~~ 354 (527)
+|+.+++|++|++|||||++||++||++|+|||+|+++ ..++|++|++|++||+||..+|+|+||.+|.++|++++..+
T Consensus 89 ~de~~~~lklFtnifGvG~ktA~~Wy~~GfrTled~Rk~~~kft~qqk~Gl~yy~Df~~~v~ReE~~~i~~~V~~av~~~ 168 (353)
T KOG2534|consen 89 NDERSQSLKLFTNIFGVGLKTAEKWYREGFRTLEDVRKKPDKFTRQQKAGLKYYEDFLKRVTREEATAIQQTVQEAVWAF 168 (353)
T ss_pred cchhHHHHHHHHHHhccCHHHHHHHHHhhhhHHHHHHhCHHHHHHHHHHhHHHHHHHhhhccHHHHHHHHHHHHHHHhhc
Confidence 99999999999999999999999999999999999994 45899999999999999999999999999999999999999
Q ss_pred CCCeEEEecccccccCCccCCeeEEEecCCcch-hhhhHHHHHHHHHHcCcccceee-eccccCCC----CCC---ccee
Q 009742 355 LPEVIILCGGSYRRGKASCGDLDVVIMHPDRKS-HKGFLSKYVKKLKEMKFLREDLI-FSTHSEEG----TDS---GVDT 425 (527)
Q Consensus 355 ~p~~~v~~~GsyRRGke~~gDVDiLIt~~~~~~-~~~~l~~lv~~L~~~g~l~~~l~-~s~~~~~~----~~~---~~~~ 425 (527)
+|++.|++||||||||++|||||||||||...+ +.+++..|+..|.+.|++..... .|.- +.. ..+ -...
T Consensus 169 ~p~~~vt~~GsfRRGk~~ggDvD~LithP~~~s~~~~~~~~l~~~le~~g~il~~~~~~S~~-Ek~~l~~~~s~~~~~~~ 247 (353)
T KOG2534|consen 169 DPEAFVTVTGSFRRGKKMGGDVDFLITHPGSTSTEAKLLQLLMILLEKKGLLLYYDQLHSCG-EKLRLPSRKSALDHFKK 247 (353)
T ss_pred CCCcEEEEeccccCCcccCCCeeEEEeCCCCCchhhhHHHHHHHHHHhcCeEEEEeeecccc-ccccccchhhhHhhhhh
Confidence 999999999999999999999999999999887 77899999999999999983222 1210 000 001 1346
Q ss_pred eeeeeecC-------------CCcc-ceeeeEEEecCchhHHHHHHhcccHHHHHHHHHHHHHcCCccCCCCCcccccCC
Q 009742 426 YFGLCTYP-------------GREL-RHRIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGS 491 (527)
Q Consensus 426 ~~g~~~~~-------------~~~~-~~RVDl~v~p~~~f~~aLl~~TGS~~fnr~LR~~A~~kg~~L~~~GL~~~~~~~ 491 (527)
+||+|++| +++| +|||||+|||+++|||||||||||+.|||+||++|.+|||+||+||||+.+.
T Consensus 248 ~mgv~~LPr~~~~~~~~S~n~~~~~~~rRvDivv~P~~~~~~alLgwTGS~~FnR~lR~~A~~kG~~l~~h~L~~~~~-- 325 (353)
T KOG2534|consen 248 FMGVFRLPRQRVDSDQSSWNEGKGWKARRVDIVVCPYDEFGFALLGWTGSKEFNRDLRRYATHKGFSLDEHALFDLTV-- 325 (353)
T ss_pred EEEEEEcCcccccccccccCCCCCCceeeeEEEEechHHcceeeeeecchHHHHHHHHHHHHhcCceecccccccCCc--
Confidence 89999999 5544 5899999999999999999999999999999999999999999999998753
Q ss_pred CCccccccccCCCCCCHHHHHHhcCCCCCCCCCcCC
Q 009742 492 GGKQGVRARTSLKFDTEKEVFDFLGFPWLEPHERNL 527 (527)
Q Consensus 492 ~g~~~~~~~~~~~~~tEedIF~~LGL~YipPe~Rn~ 527 (527)
..++++++|+|||++|||+||||++||.
T Consensus 326 --------~~~l~~~sEkdIFr~l~L~Y~EP~~Rn~ 353 (353)
T KOG2534|consen 326 --------RIFLPVESEKDIFRYLGLKYIEPKERNA 353 (353)
T ss_pred --------ceecCCccHHHHHHHhCCccCChhhcCC
Confidence 3689999999999999999999999995
No 2
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=100.00 E-value=4.8e-74 Score=589.28 Aligned_cols=303 Identities=40% Similarity=0.680 Sum_probs=278.7
Q ss_pred HHHHHHHHHHHHHHHcCCC-hhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhch
Q 009742 201 NITEIFGKLINIYRALGED-RRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEK 279 (527)
Q Consensus 201 ~ia~~L~~la~~~e~~g~~-~r~~aY~rAa~~l~~l~~~i~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~ 279 (527)
+|+++|++||++++++|+| ||++||++||++|+++|++|++++++.+|||||++|+++|.||++||+++++|+++++ .
T Consensus 2 ~ia~~L~~ia~~~e~~~~~~~r~~aY~~Aa~~l~~l~~~i~~~~~~~~ipgiG~~ia~kI~E~~~tG~~~~le~l~~~-~ 80 (307)
T cd00141 2 EIADILEELADLLELLGGNPFRVRAYRKAARALESLPEPIESLEEAKKLPGIGKKIAEKIEEILETGKLRKLEELRED-V 80 (307)
T ss_pred hHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHhCCcccCCHHHhcCCCCccHHHHHHHHHHHHcCCHHHHHHHhcc-c
Confidence 6999999999999999655 8999999999999999999999999999999999999999999999999999999998 4
Q ss_pred hHHHHHHhhccCcCHHHHHHHHHhCCCCHHHHhhc--cCcchhhhccccchhhhccCcCHHHHHHHHHHHHHHhhhcCCC
Q 009742 280 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPE 357 (527)
Q Consensus 280 ~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~--~~L~~~q~~Glk~yed~~~~i~r~Ea~~i~~iv~~~~~~~~p~ 357 (527)
+..+..|++|||||||||++||++||+||+||+.+ .+++..|..|++||+|+.++|||+||+++.+.|.+.++.+.|+
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 55666666999999999999997799999999987 4899999999999999999999999999999998888888888
Q ss_pred eEEEecccccccCCccCCeeEEEecCCcchhhhhHHHHHHHHHHcCcccceeeeccccCCCCCCcceeeeeeeecCCCcc
Q 009742 358 VIILCGGSYRRGKASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCTYPGREL 437 (527)
Q Consensus 358 ~~v~~~GsyRRGke~~gDVDiLIt~~~~~~~~~~l~~lv~~L~~~g~l~~~l~~s~~~~~~~~~~~~~~~g~~~~~~~~~ 437 (527)
+.|++|||||||+++||||||||+|++... .+++.+|++.|.+.|++.+.+. .+..+|+|+|++|+.+.
T Consensus 161 ~~v~i~GS~RRg~et~gDiDilv~~~~~~~-~~~~~~v~~~l~~~~~~~~~~~----------~g~~k~~~~~~~~~~~~ 229 (307)
T cd00141 161 LQVEIAGSYRRGKETVGDIDILVTHPDATS-RGLLEKVVDALVELGFVTEVLS----------KGDTKASGILKLPGGWK 229 (307)
T ss_pred eEEEEcccccCCCCccCCEEEEEecCCccc-cccHHHHHHHHHhCCCeehhhh----------CCCceEEEEEecCCCCC
Confidence 999999999999999999999999998754 6788899999999999976532 23468999999987777
Q ss_pred ceeeeEEEecCchhHHHHHHhcccHHHHHHHHHHHHHcCCccCCCCCcccccCCCCccccccccCCCCCCHHHHHHhcCC
Q 009742 438 RHRIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGSGGKQGVRARTSLKFDTEKEVFDFLGF 517 (527)
Q Consensus 438 ~~RVDl~v~p~~~f~~aLl~~TGS~~fnr~LR~~A~~kg~~L~~~GL~~~~~~~~g~~~~~~~~~~~~~tEedIF~~LGL 517 (527)
++||||++||+++|++||+|||||++|||.||.+|.++||+||+||||+.. .+..+++.+|+|||++|||
T Consensus 230 ~~rVDl~~~p~~~~~~all~fTGs~~~nr~lR~~A~~~G~~L~~~GL~~~~----------~~~~~~~~~E~~If~~Lgl 299 (307)
T cd00141 230 GRRVDLRVVPPEEFGAALLYFTGSKQFNRALRRLAKEKGLKLNEYGLFDGV----------DGERLPGETEEEIFEALGL 299 (307)
T ss_pred ceEEEEEEeCHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCeeeccccccCC----------CCCCccCCCHHHHHHHcCC
Confidence 899999999999999999999999999999999999999999999999753 1357899999999999999
Q ss_pred CCCCCCCc
Q 009742 518 PWLEPHER 525 (527)
Q Consensus 518 ~YipPe~R 525 (527)
||||||+|
T Consensus 300 ~yipPe~R 307 (307)
T cd00141 300 PYIEPELR 307 (307)
T ss_pred CCCCCCCC
Confidence 99999998
No 3
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=100.00 E-value=2.5e-73 Score=590.06 Aligned_cols=318 Identities=36% Similarity=0.597 Sum_probs=265.8
Q ss_pred CCcHHHHHHHHHHHHHHHHcCCC-hhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHH
Q 009742 197 DLNKNITEIFGKLINIYRALGED-RRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFE 275 (527)
Q Consensus 197 ~~N~~ia~~L~~la~~~e~~g~~-~r~~aY~rAa~~l~~l~~~i~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~ 275 (527)
|+|++|+++|++||++||+.|+| +|++||++||++|+++|++|++++++.+|||||++|++||.||++||++.++.+..
T Consensus 1 ~~N~~I~~~L~~la~l~el~gen~~k~~ay~~Aa~~i~~l~~~i~~~~~l~~lpgIG~~ia~kI~Eil~tG~~~~~~e~l 80 (334)
T smart00483 1 NLNRGIIDALEILAENYEVFGENKRKCSYFRKAASVLKSLPFPINSMKDLKGLPGIGDKIKKKIEEIIETGKSSKVLEIL 80 (334)
T ss_pred CCcHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhCCCCCCCHHHHhcCCCccHHHHHHHHHHHHhCcHHHHHHHh
Confidence 46999999999999999999999 58999999999999999999999999999999999999999999999999666555
Q ss_pred hhchhHHHHHHhhccCcCHHHHHHHHHhCCCCHHHHhhcc--CcchhhhccccchhhhccCcCHHHHHHHHHHHHHHhhh
Q 009742 276 KDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEE 353 (527)
Q Consensus 276 ~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~q~~Glk~yed~~~~i~r~Ea~~i~~iv~~~~~~ 353 (527)
.++.+..+..|++|||||||||++||+.||+||+||+++. +|+.+|.+|++||+|+.++|||+||+.+.++|...+..
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 5555666777779999999999999999999999999754 69999999999999999999999999999999888888
Q ss_pred cCCCeEEEecccccccCCccCCeeEEEecCCcchhhhhHHHHHHHHHHcCcccceeeeccccCCCCCCcceeeeeeeecC
Q 009742 354 VLPEVIILCGGSYRRGKASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCTYP 433 (527)
Q Consensus 354 ~~p~~~v~~~GsyRRGke~~gDVDiLIt~~~~~~~~~~l~~lv~~L~~~g~l~~~l~~s~~~~~~~~~~~~~~~g~~~~~ 433 (527)
+.|.+.|++||||||||++||||||||+|+++.. +++.++++.|.-. .+...+............+..+|+++|..|
T Consensus 161 ~~~~~~v~i~GSyRRgket~gDIDili~~~~~~~--~~~~~v~~~~~l~-~~~~~~~~~~~~~~~~~~g~~~~~~v~~~~ 237 (334)
T smart00483 161 ILPDAIVTLTGSFRRGKETGHDVDFLITSPHPAK--EKELEVLDLLLLE-STFEELQLPSIRVATLDHGQKKFMILKLSP 237 (334)
T ss_pred hCCCcEEEEecccccCCCcCCCeeEEEecCCccc--hhHHHHHHHHHHH-HHHHHHhcccchhhhhhcCCCEEEEEEeCC
Confidence 8888899999999999999999999999999763 4555554333100 000000000000011122334678887764
Q ss_pred CC-------------ccceeeeEEEecCchhHHHHHHhcccHHHHHHHHHHHHHcCCccCCCCCcccccCCCCccccccc
Q 009742 434 GR-------------ELRHRIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGSGGKQGVRAR 500 (527)
Q Consensus 434 ~~-------------~~~~RVDl~v~p~~~f~~aLl~~TGS~~fnr~LR~~A~~kg~~L~~~GL~~~~~~~~g~~~~~~~ 500 (527)
.. +.++||||++||+++||+||+|||||++|||.||.+|.++| +||+||||+.... .+
T Consensus 238 ~~~~~~~~g~~~~~~~~~rrVDl~~~~~~~~g~aLl~fTGS~~fnr~lR~~A~~~g-~L~~~gl~~~~~~--------~~ 308 (334)
T smart00483 238 SREDKEKSGKPDEKGWKARRVDIVLCPEDQYPTALLGWTGSKQFNRDLRRYATSKF-KLMLDGHELYDKT--------KE 308 (334)
T ss_pred ccccccccccccCCCCcceEEEEEEechHHheeEEEEEeCchhHHHHHHHHHHHcC-CcCcccCccccCC--------CC
Confidence 21 24589999999999999999999999999999999999999 9999999975321 13
Q ss_pred cCCCCCCHHHHHHhcCCCCCCCCCcC
Q 009742 501 TSLKFDTEKEVFDFLGFPWLEPHERN 526 (527)
Q Consensus 501 ~~~~~~tEedIF~~LGL~YipPe~Rn 526 (527)
..+++.+|+|||++|||||||||+||
T Consensus 309 ~~i~~~~E~~If~~LGl~yipPe~Rn 334 (334)
T smart00483 309 KFLKVESEEDIFDHLGLPYIEPEERN 334 (334)
T ss_pred eeccCCCHHHHHHHhCCCCCCcccCC
Confidence 57889999999999999999999998
No 4
>PRK08609 hypothetical protein; Provisional
Probab=100.00 E-value=7.7e-68 Score=583.10 Aligned_cols=299 Identities=22% Similarity=0.343 Sum_probs=260.8
Q ss_pred CCcHHHHHHHHHHHHHHHHcCCC-hhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHH
Q 009742 197 DLNKNITEIFGKLINIYRALGED-RRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFE 275 (527)
Q Consensus 197 ~~N~~ia~~L~~la~~~e~~g~~-~r~~aY~rAa~~l~~l~~~i~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~ 275 (527)
|+|++|+++|++||+++|+.|+| ||++||++||++|+++|++|++++++.+|||||++||+||+||++||++++||+|+
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 57999999999999999999988 79999999999999999999999999999999999999999999999999999999
Q ss_pred hhchhHHHHHHhhccCcCHHHHHHHHHh-CCCCHHHHhhc---cCcchhhhc----------cccchhhhccCcCHHHHH
Q 009742 276 KDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNE---DSLTHSQRL----------GLKYFDDIKTRIPRHEVE 341 (527)
Q Consensus 276 ~~~~~~~l~lf~~I~GvGpktA~~ly~~-GirTledL~~~---~~L~~~q~~----------Glk~yed~~~~i~r~Ea~ 341 (527)
++.|.++++|+ +|||||||||++||+. ||+||+||+++ ++++.+++| |+++|+++.+|||++||.
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 98877777666 9999999999999975 99999999964 568777777 567788888999999999
Q ss_pred HHHHHHHHHhhhcCCCeEEEecccccccCCccCCeeEEEecCCcchhhhhHHHHHHHHHHcCcccceeeeccccCCCCCC
Q 009742 342 QMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLREDLIFSTHSEEGTDS 421 (527)
Q Consensus 342 ~i~~iv~~~~~~~~p~~~v~~~GsyRRGke~~gDVDiLIt~~~~~~~~~~l~~lv~~L~~~g~l~~~l~~s~~~~~~~~~ 421 (527)
.+.+.|.+.++.+.|...|++||||||||+||||||||||++++.. +++.|.+.+++.+.+..
T Consensus 160 ~~a~~i~~~l~~~~~~~~v~~~GS~RR~~et~gDiDili~~~~~~~-------~~~~l~~~~~v~~~~~~---------- 222 (570)
T PRK08609 160 PIAQEIEEYLATIDEIIRFSRAGSLRRARETVKDLDFIIATDEPEA-------VREQLLQLPNIVEVIAA---------- 222 (570)
T ss_pred HHHHHHHHHHHhCCCccEEEeccchhccccccCCeeEEEecCCHHH-------HHHHHHcCccHHHHHhc----------
Confidence 9988888877776666789999999999999999999999998754 34555566666544321
Q ss_pred cceeeeeeeecCCCccceeeeEEEecCchhHHHHHHhcccHHHHHHHHHHHHHcCCccCCCCCcccccCCCCcccccccc
Q 009742 422 GVDTYFGLCTYPGRELRHRIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGSGGKQGVRART 501 (527)
Q Consensus 422 ~~~~~~g~~~~~~~~~~~RVDl~v~p~~~f~~aLl~~TGS~~fnr~LR~~A~~kg~~L~~~GL~~~~~~~~g~~~~~~~~ 501 (527)
+..++++.|.++ .++||||++||+++||+||+|||||++|||.||.+|.++||+||+||||+... +.
T Consensus 223 g~~~~~~~~~~~---~~~~vDl~~v~~~~~~~aL~yfTGS~~hn~~lr~~A~~~g~~l~e~gl~~~~~----------~~ 289 (570)
T PRK08609 223 GDTKVSVELEYE---YTISVDFRLVEPEAFATTLHHFTGSKDHNVRMRQLAKERGEKISEYGVEQADT----------GE 289 (570)
T ss_pred CCceEEEEEecC---CCeEEEEEEeCHHHHHHHHHHHhccHHHHHHHHHHHHHcCCcccccccccCCC----------Cc
Confidence 223455554431 25799999999999999999999999999999999999999999999997421 35
Q ss_pred CCCCCCHHHHHHhcCCCCCCCCCcC
Q 009742 502 SLKFDTEKEVFDFLGFPWLEPHERN 526 (527)
Q Consensus 502 ~~~~~tEedIF~~LGL~YipPe~Rn 526 (527)
.+++.||+|||++|||||||||+||
T Consensus 290 ~~~~~~E~~iy~~Lgl~yipPelRe 314 (570)
T PRK08609 290 VKTFESEEAFFAHFGLPFIPPEVRE 314 (570)
T ss_pred cCCCCCHHHHHHHcCCCCCCccccC
Confidence 6888999999999999999999997
No 5
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=100.00 E-value=2.1e-56 Score=447.04 Aligned_cols=299 Identities=28% Similarity=0.464 Sum_probs=250.1
Q ss_pred CCCcHHHHHHHHHHHHHHHHcCCC-hhHHHHHHHHHHHhcCCccccchhhh---cCCCCCCHHHHHHHHHHHHhCCchhh
Q 009742 196 PDLNKNITEIFGKLINIYRALGED-RRSFSYYKAIPVIEKLPFKIESADQV---KGLPGIGKSMQDHIQEIVTTGKLSKL 271 (527)
Q Consensus 196 ~~~N~~ia~~L~~la~~~e~~g~~-~r~~aY~rAa~~l~~l~~~i~s~~~l---~~lpgIG~~ia~kI~Eil~tG~~~~l 271 (527)
-|+|+.|+.+|+++|++|++.|+| ||++|||+||.+|+.+.+++.++.+. ..|||||++||++|.||++||+++.+
T Consensus 2 ~~~n~~ia~~le~iA~~me~~Gen~fk~~aYr~Aa~sle~~~e~~~ei~e~~~~t~l~gIGk~ia~~I~e~l~tG~~~~l 81 (326)
T COG1796 2 AMNNHDIARLLERIADYMELEGENPFKIRAYRKAAQSLENLTEDLEEIEERGRLTELPGIGKGIAEKISEYLDTGEVKKL 81 (326)
T ss_pred CcchHHHHHHHHHHHHHHHhcCCCccchHHHHHHHHhhhhcccchHHHHhhcccCCCCCccHHHHHHHHHHHHcCccHHH
Confidence 368999999999999999999999 89999999999999999999998665 59999999999999999999999999
Q ss_pred HHHHhhchhHHHHHHhhccCcCHHHHHHHHHh-CCCCHHHHhhc---cCcchhhhccccchhhhc----------cCcCH
Q 009742 272 EHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNE---DSLTHSQRLGLKYFDDIK----------TRIPR 337 (527)
Q Consensus 272 e~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~-GirTledL~~~---~~L~~~q~~Glk~yed~~----------~~i~r 337 (527)
+.++...|.+.+.|+ .|+|+|||+...||+. ||.++++|+++ +++..+.|||-+..++|. +|+|.
T Consensus 82 e~lk~~~P~gl~~Ll-~v~GlGpkKi~~Ly~elgi~~~e~l~~a~~~~~~~~l~GfG~kse~~il~~i~~~~~~~~R~~l 160 (326)
T COG1796 82 EALKKEVPEGLEPLL-KVPGLGPKKIVSLYKELGIKDLEELQEALENGKIRGLRGFGKKSEAKILENIEFAEESPERIPL 160 (326)
T ss_pred HHHHHhCCcchHHHh-hCCCCCcHHHHHHHHHHCcccHHHHHHHHHhCCccccCCccchhHHHHHHHHHHHhhhhhhcch
Confidence 999999999988888 9999999999999987 99999999965 468889999977777775 56677
Q ss_pred HHHHHHHHHHHHHhhhcCCCeEEEecccccccCCccCCeeEEEecCCcchhhhhHHHHHHHHHHcCcccceeeeccccCC
Q 009742 338 HEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLREDLIFSTHSEE 417 (527)
Q Consensus 338 ~Ea~~i~~iv~~~~~~~~p~~~v~~~GsyRRGke~~gDVDiLIt~~~~~~~~~~l~~lv~~L~~~g~l~~~l~~s~~~~~ 417 (527)
.++-.|..-+.....++.+-.++.++||+||+++|++|||++|+..++.+ +++.|.+...+.+.... +
T Consensus 161 ~~~l~ia~ei~~yl~~~~~~~~~~~aGs~RR~retv~DiD~~~s~~~~~~-------v~~~~~~~~~~~~vi~~-----G 228 (326)
T COG1796 161 SFTLPIAQEIEGYLEELTPIIQASIAGSLRRGRETVGDIDILISTSHPES-------VLEELLEMPNVQEVIAK-----G 228 (326)
T ss_pred HHHHHHHHHHHHHHHhccchheeeeccchhhccccccceeeEeccCCcHH-------HHHHHhcCCCcceeeec-----C
Confidence 77766655444444445554578899999999999999999999887765 45555555544443321 1
Q ss_pred CCCCcceeeeeeeecCCCccceeeeEEEecCchhHHHHHHhcccHHHHHHHHHHHHHcCCccCCCCCcccccCCCCcccc
Q 009742 418 GTDSGVDTYFGLCTYPGRELRHRIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGSGGKQGV 497 (527)
Q Consensus 418 ~~~~~~~~~~g~~~~~~~~~~~RVDl~v~p~~~f~~aLl~~TGS~~fnr~LR~~A~~kg~~L~~~GL~~~~~~~~g~~~~ 497 (527)
.+...+ ...+ .. ...|||+|||++.||+||+|||||++||+.||.+|+.+||+||+||||..
T Consensus 229 ~~k~s~--~~~~--~~----~~svD~r~v~~e~fGaal~~fTGSkehNi~iR~lA~~kg~klseyGl~~~---------- 290 (326)
T COG1796 229 ETKVSM--LLIL--DE----GTSVDFRVVPPEAFGAALQHFTGSKEHNIKIRQLAKAKGEKLSEYGLFRD---------- 290 (326)
T ss_pred CceeeE--EEEe--cC----CCeeEEEEcCHHHhhhhhhhcccchhhhHHHHHHHHHhCcchhhcceecc----------
Confidence 111110 0010 11 23699999999999999999999999999999999999999999999953
Q ss_pred ccccCCCCCCHHHHHHhcCCCCCCCCCcC
Q 009742 498 RARTSLKFDTEKEVFDFLGFPWLEPHERN 526 (527)
Q Consensus 498 ~~~~~~~~~tEedIF~~LGL~YipPe~Rn 526 (527)
++..++..||++||++|||+|||||+||
T Consensus 291 -~~e~i~~~tE~~i~~~l~l~yipPE~RE 318 (326)
T COG1796 291 -SGEIIAGKTEEKIYEHLGLPYIPPELRE 318 (326)
T ss_pred -CCceecCCcHhHHHHHcCCCCCChhhcc
Confidence 1357889999999999999999999997
No 6
>PF14792 DNA_pol_B_palm: DNA polymerase beta palm ; PDB: 1RZT_A 3PML_A 2PFN_A 3HX0_K 3HWT_A 2GWS_E 2BCQ_A 3UPQ_A 2BCS_A 3UQ2_A ....
Probab=99.93 E-value=6.3e-26 Score=200.35 Aligned_cols=105 Identities=44% Similarity=0.795 Sum_probs=91.8
Q ss_pred CcCHHHHHHHHHHHHHHhhhcCCCeEEEecccccccCCccCCeeEEEecCCcchh----hhhHHHHHHHHHHcCccccee
Q 009742 334 RIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPDRKSH----KGFLSKYVKKLKEMKFLREDL 409 (527)
Q Consensus 334 ~i~r~Ea~~i~~iv~~~~~~~~p~~~v~~~GsyRRGke~~gDVDiLIt~~~~~~~----~~~l~~lv~~L~~~g~l~~~l 409 (527)
+|||+|+++++++|++++.++.|++.+++||||||||++|||||||||||+.... .++|.+|++.|++.|+|+++|
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 6999999999999999999999999999999999999999999999999998764 689999999999999999998
Q ss_pred eeccccCCCCCCcceeeeeeeecCCC---ccceeeeEEEecC
Q 009742 410 IFSTHSEEGTDSGVDTYFGLCTYPGR---ELRHRIDFKVYPR 448 (527)
Q Consensus 410 ~~s~~~~~~~~~~~~~~~g~~~~~~~---~~~~RVDl~v~p~ 448 (527)
..+ ..+|||+|++|+. ..+|||||+++|+
T Consensus 81 ~~~----------~~~~~G~~~l~~~~~~~~~RRiDi~~~P~ 112 (112)
T PF14792_consen 81 SLG----------PTKYMGVCRLPGNDNKSPHRRIDIIVVPY 112 (112)
T ss_dssp EEC----------SSEEEEEEE-SSTSST--EEEEEEEEEEG
T ss_pred ccC----------CceeeeEeecCCCCCCCCeeeEEEEEeCC
Confidence 542 2689999999987 6789999999995
No 7
>PF14791 DNA_pol_B_thumb: DNA polymerase beta thumb ; PDB: 1HUZ_A 3K75_D 1HUO_A 2BPC_A 1RPL_A 1NOM_A 1ZQX_A 1ZQU_A 1ZQZ_A 1ZQV_A ....
Probab=99.89 E-value=1.8e-24 Score=171.75 Aligned_cols=63 Identities=35% Similarity=0.688 Sum_probs=52.7
Q ss_pred HHHHhcccHHHHHHHHHHHHHcCCccCCCCCcccccCCCCccccccccCCCCCCHHHHHHhcCCCCCCCCCcC
Q 009742 454 GLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATYGSGGKQGVRARTSLKFDTEKEVFDFLGFPWLEPHERN 526 (527)
Q Consensus 454 aLl~~TGS~~fnr~LR~~A~~kg~~L~~~GL~~~~~~~~g~~~~~~~~~~~~~tEedIF~~LGL~YipPe~Rn 526 (527)
||+|||||++|||+||.+|+++||+||+|||++... +..+++.+|+|||++|||||||||+||
T Consensus 1 All~~TGs~~fnr~lR~~A~~~g~~L~~~Gl~~~~~----------~~~~~~~~E~dif~~Lgl~yipPe~R~ 63 (64)
T PF14791_consen 1 ALLYFTGSKEFNRDLRQYAKKKGMKLSEYGLFKRET----------GELVPVESEEDIFDALGLPYIPPELRE 63 (64)
T ss_dssp HHHHHHS-HHHHHHHHHHHHHTTEEEESSEEEETTC----------EEEEE-SSHHHHHHHTTS----GGGCT
T ss_pred CcccccCCHHHHHHHHHHHHHcCCeeCccccccccc----------ceeecCCCHHHHHHHcCCCCCChhhcC
Confidence 799999999999999999999999999999997532 357899999999999999999999998
No 8
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=99.68 E-value=8.9e-17 Score=129.62 Aligned_cols=66 Identities=36% Similarity=0.688 Sum_probs=62.3
Q ss_pred cHHHHHHHHHHHHHHHHc-CCChhHHHHHHHHHHHhcCCccccchhh-hcCCCCCCHHHHHHHHHHHH
Q 009742 199 NKNITEIFGKLINIYRAL-GEDRRSFSYYKAIPVIEKLPFKIESADQ-VKGLPGIGKSMQDHIQEIVT 264 (527)
Q Consensus 199 N~~ia~~L~~la~~~e~~-g~~~r~~aY~rAa~~l~~l~~~i~s~~~-l~~lpgIG~~ia~kI~Eil~ 264 (527)
|++|+++|++||+++++. ++.+|++||++||++|+++|++|++++| +.+|||||++|+.+|.|||+
T Consensus 1 N~~i~~~L~~la~~~~~~~~~~~r~~aY~~Aa~~i~~l~~~i~~~~~~~~~l~gIG~~ia~kI~E~le 68 (68)
T PF14716_consen 1 NQEIADALEELADLYELQGGDPFRARAYRRAAAAIKALPYPITSGEEDLKKLPGIGKSIAKKIDEILE 68 (68)
T ss_dssp THHHHHHHHHHHHHHHHTSTSHHHHHHHHHHHHHHHHSSS-HHSHHHHHCTSTTTTHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHhhCCcHHHHHHHHHHHHHHhCCHhHhhHHHHHhhCCCCCHHHHHHHHHHHC
Confidence 899999999999999999 5568999999999999999999999987 99999999999999999986
No 9
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. This entry represents the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone []. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1KDH_A 1KEJ_A 1JMS_A 2IHM_A 3OGU_A 1MQ2_A 2P66_A 7ICI_A 1ZQN_A 1ZQK_A ....
Probab=99.62 E-value=2.3e-16 Score=120.12 Aligned_cols=51 Identities=49% Similarity=1.009 Sum_probs=42.0
Q ss_pred HHHHhhccCcCHHHHHHHHHhCCCCHHHHhh-ccCcchhhhccccchhhhcc
Q 009742 283 ISLFGEVWGIGPATAQKLYEKGHRTLDDLKN-EDSLTHSQRLGLKYFDDIKT 333 (527)
Q Consensus 283 l~lf~~I~GvGpktA~~ly~~GirTledL~~-~~~L~~~q~~Glk~yed~~~ 333 (527)
|++|++||||||+||++||++|+|||+||++ ...|+..|++|++||+||++
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 45899999999999999874
No 10
>PRK07945 hypothetical protein; Provisional
Probab=99.58 E-value=8.6e-15 Score=152.67 Aligned_cols=91 Identities=20% Similarity=0.247 Sum_probs=83.0
Q ss_pred HHHHHHHHHHHHHHcCCC-hhHHHHHHHHHHHhcCCcc-ccchh---hhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHh
Q 009742 202 ITEIFGKLINIYRALGED-RRSFSYYKAIPVIEKLPFK-IESAD---QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEK 276 (527)
Q Consensus 202 ia~~L~~la~~~e~~g~~-~r~~aY~rAa~~l~~l~~~-i~s~~---~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~ 276 (527)
-+++|+++|+++|++|+| ||++|||+||.+|+.++.+ +..+. +|.+|||||+++|.||.||++||+++.|++|+.
T Consensus 3 ~~~~l~~~a~lle~~~~n~frv~ayr~aa~~~~~~~~~~~~~~~~~g~l~~~~giG~~~a~~i~e~~~tg~~~~l~~l~~ 82 (335)
T PRK07945 3 PVAALRRIAFLLERARADTYRVRAFRRAADVVEALDAAERARRARAGSLTSLPGIGPKTAKVIAQALAGRVPDYLAELRA 82 (335)
T ss_pred HHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHhcChhHHHHHHhcCCcccCCCcCHHHHHHHHHHHhcCCHHHHHHHHH
Confidence 468999999999999999 6999999999999999999 88774 799999999999999999999999999999998
Q ss_pred hchhHHHHHHhhccCcCHHHHHHHHH
Q 009742 277 DEKVRTISLFGEVWGIGPATAQKLYE 302 (527)
Q Consensus 277 ~~~~~~l~lf~~I~GvGpktA~~ly~ 302 (527)
+..+- | |+..+.++.-
T Consensus 83 ~~~~~---------~-g~~l~~~~~~ 98 (335)
T PRK07945 83 DAEPL---------G-GGALRAALRG 98 (335)
T ss_pred hhcCC---------c-cHHHHHHHhh
Confidence 76432 7 9999999874
No 11
>PF00533 BRCT: BRCA1 C Terminus (BRCT) domain; InterPro: IPR001357 The BRCT domain (after the C_terminal domain of a breast cancer susceptibility protein) is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage [], for example as found in the breast cancer DNA-repair protein BRCA1. The domain is an approximately 100 amino acid tandem repeat, which appears to act as a phospho-protein binding domain []. A chitin biosynthesis protein from yeast also seems to belong to this group. ; GO: 0005622 intracellular; PDB: 3L46_A 3AL3_A 3AL2_A 1WF6_A 3II6_X 2NTE_B 3FA2_A 2R1Z_A 2COK_A 2K7F_A ....
Probab=98.81 E-value=1.7e-08 Score=81.74 Aligned_cols=67 Identities=25% Similarity=0.467 Sum_probs=56.5
Q ss_pred CCCcCCeEEEEeeCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEeCcH-H--H----HHh--ccccchHHHHHH
Q 009742 16 NGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLE-A--L----LQQ--SVIRYQWLEDSL 84 (527)
Q Consensus 16 ~~~f~~~~i~iv~~~~g~~r~~~l~~~~~~~G~~v~~~~s~~VTHVV~~~~~-~--~----l~~--~vv~~~Wl~ec~ 84 (527)
..+|+|+.+|| .+.....++.|+++|+++||.+...+++.+||||+.+.. . . ... .+|+.+||.+|+
T Consensus 3 ~~~F~g~~f~i--~~~~~~~~~~l~~~i~~~GG~v~~~~~~~~thvI~~~~~~~~~k~~~~~~~~i~iV~~~Wi~~ci 78 (78)
T PF00533_consen 3 PKIFEGCTFCI--SGFDSDEREELEQLIKKHGGTVSNSFSKKTTHVIVGNPNKRTKKYKAAIANGIPIVSPDWIEDCI 78 (78)
T ss_dssp TTTTTTEEEEE--SSTSSSHHHHHHHHHHHTTEEEESSSSTTSSEEEESSSHCCCHHHHHHHHTTSEEEETHHHHHHH
T ss_pred CCCCCCEEEEE--ccCCCCCHHHHHHHHHHcCCEEEeecccCcEEEEeCCCCCccHHHHHHHHCCCeEecHHHHHHhC
Confidence 47899999999 677888889999999999999999999999999987651 1 1 111 299999999997
No 12
>smart00292 BRCT breast cancer carboxy-terminal domain.
Probab=98.75 E-value=1.7e-08 Score=80.66 Aligned_cols=70 Identities=24% Similarity=0.422 Sum_probs=57.8
Q ss_pred CCcCCeEEEEeeCCCChhHHHHHHHHHHhcCCEEEeecCC-CccEEEEeCcHH--H-HH------hccccchHHHHHHhc
Q 009742 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSK-KVTHVLAMDLEA--L-LQ------QSVIRYQWLEDSLRL 86 (527)
Q Consensus 17 ~~f~~~~i~iv~~~~g~~r~~~l~~~~~~~G~~v~~~~s~-~VTHVV~~~~~~--~-l~------~~vv~~~Wl~ec~~~ 86 (527)
.+|+|+++|+.. .+....++.|.+++.++||++...+++ ++||||+.+.+. . .+ ..+|+++|+.+|+++
T Consensus 1 ~~f~g~~~~~~g-~~~~~~~~~l~~~i~~~Gg~~~~~~~~~~~thvi~~~~~~~~~~~~~~~~~~~~iV~~~Wi~~~~~~ 79 (80)
T smart00292 1 KLFKGKVFVITG-KFDKNERDELKELIEALGGKVTSSLSSKTTTHVIVGSPEGGKLELLLAIALGIPIVTEDWLLDCLKA 79 (80)
T ss_pred CccCCeEEEEeC-CCCCccHHHHHHHHHHcCCEEecccCccceeEEEEcCCCCccHHHHHHHHcCCCCccHHHHHHHHHC
Confidence 379999999975 377778899999999999999999998 999999876322 1 11 129999999999987
Q ss_pred C
Q 009742 87 G 87 (527)
Q Consensus 87 g 87 (527)
+
T Consensus 80 ~ 80 (80)
T smart00292 80 G 80 (80)
T ss_pred c
Confidence 5
No 13
>cd00027 BRCT Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks.
Probab=98.26 E-value=1.5e-06 Score=67.69 Aligned_cols=64 Identities=22% Similarity=0.366 Sum_probs=49.2
Q ss_pred CeEEEEeeCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEeCcHH-H-HH------hccccchHHHHHHh
Q 009742 21 GMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEA-L-LQ------QSVIRYQWLEDSLR 85 (527)
Q Consensus 21 ~~~i~iv~~~~g~~r~~~l~~~~~~~G~~v~~~~s~~VTHVV~~~~~~-~-l~------~~vv~~~Wl~ec~~ 85 (527)
|+.+||...-. ...+..|++++.++||.+...+++.+||||+.+... . +. ..+|+.+|+.+|++
T Consensus 1 ~~~~~i~g~~~-~~~~~~l~~~i~~~Gg~v~~~~~~~~thvI~~~~~~~~~~~~~~~~~~~iV~~~Wi~~~~~ 72 (72)
T cd00027 1 GLTFVITGDLP-SEERDELKELIEKLGGKVTSSVSKKTTHVIVGSDAGPKKLLKAIKLGIPIVTPEWLLDCLK 72 (72)
T ss_pred CCEEEEEecCC-CcCHHHHHHHHHHcCCEEeccccCCceEEEECCCCCchHHHHHHHcCCeEecHHHHHHHhC
Confidence 56778864322 445699999999999999999999999999876422 1 11 12999999999985
No 14
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=97.91 E-value=3.4e-05 Score=87.41 Aligned_cols=82 Identities=23% Similarity=0.359 Sum_probs=67.6
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHHh-CCCCHHHHhhcc--Ccch
Q 009742 243 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED--SLTH 319 (527)
Q Consensus 243 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~-GirTledL~~~~--~L~~ 319 (527)
++|..|||+|++++++|.+.+++++...+++ .+..| .|+|||+++|+.|++. | |+++|.++. .|..
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 5788999999999999999999988766654 45555 9999999999999987 6 899998653 5778
Q ss_pred hhhccccchhhhccCc
Q 009742 320 SQRLGLKYFDDIKTRI 335 (527)
Q Consensus 320 ~q~~Glk~yed~~~~i 335 (527)
..++|-+..+.+..-+
T Consensus 535 i~GIG~~~A~~I~~ff 550 (652)
T TIGR00575 535 VEGVGPKVAESIVNFF 550 (652)
T ss_pred CCCcCHHHHHHHHHHH
Confidence 8889977777766544
No 15
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=97.85 E-value=9.7e-06 Score=63.59 Aligned_cols=51 Identities=37% Similarity=0.549 Sum_probs=42.1
Q ss_pred HHHHHhhccCcCHHHHHHHHHhCCCCHHHHhhc--cCcchhhhccccchhhhc
Q 009742 282 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDIK 332 (527)
Q Consensus 282 ~l~lf~~I~GvGpktA~~ly~~GirTledL~~~--~~L~~~q~~Glk~yed~~ 332 (527)
+...|++|+||||++|++||+.||.|++||... ..|....++|-+..+.|.
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 455667999999999999999999999999965 358888888877666554
No 16
>KOG3226 consensus DNA repair protein [Replication, recombination and repair]
Probab=97.59 E-value=4.3e-05 Score=78.89 Aligned_cols=82 Identities=17% Similarity=0.351 Sum_probs=71.6
Q ss_pred CCCcCCeEEEEeeCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEe--CcHHHHHh------ccccchHHHHHHhcC
Q 009742 16 NGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAM--DLEALLQQ------SVIRYQWLEDSLRLG 87 (527)
Q Consensus 16 ~~~f~~~~i~iv~~~~g~~r~~~l~~~~~~~G~~v~~~~s~~VTHVV~~--~~~~~l~~------~vv~~~Wl~ec~~~g 87 (527)
+-++.||++.| .|++.+-|.-|+..|..+|+.....+..+.||.|+. |.. +++. -||+=+|+++|-..+
T Consensus 315 ~klL~GVV~Vl--SGfqNP~Rs~LRskAl~LGAkY~pDW~~gsThLICAF~NTP-Ky~QV~g~Gg~IV~keWI~~Cy~~k 391 (508)
T KOG3226|consen 315 SKLLEGVVFVL--SGFQNPERSTLRSKALTLGAKYQPDWNAGSTHLICAFPNTP-KYRQVEGNGGTIVSKEWITECYAQK 391 (508)
T ss_pred HHhhhceEEEE--ecccCchHHHHHHHHHhhcccccCCcCCCceeEEEecCCCc-chhhcccCCceEeeHHHHHHHHHHH
Confidence 37899999988 599999999999999999999999999999999975 333 3332 299999999999999
Q ss_pred CCcCCcccccccC
Q 009742 88 EKVSEDLYRIKLD 100 (527)
Q Consensus 88 ~~v~~~~~~l~~~ 100 (527)
++||+..|.+.-+
T Consensus 392 k~lp~rrYlm~~~ 404 (508)
T KOG3226|consen 392 KLLPIRRYLMHAG 404 (508)
T ss_pred hhccHHHHHhcCC
Confidence 9999999999754
No 17
>PF12738 PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2WT8_C 3EF1_A 3EF0_A.
Probab=97.41 E-value=0.00014 Score=57.23 Aligned_cols=55 Identities=20% Similarity=0.396 Sum_probs=40.0
Q ss_pred EEEEeeCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEeCcH-HHHHh---c---cccchH
Q 009742 23 RVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLE-ALLQQ---S---VIRYQW 79 (527)
Q Consensus 23 ~i~iv~~~~g~~r~~~l~~~~~~~G~~v~~~~s~~VTHVV~~~~~-~~l~~---~---vv~~~W 79 (527)
+|.+ .|+....++-+.+++.++||.+...++.++||+|+.+.. .+++. + +|+++|
T Consensus 2 ~i~~--sg~~~~~~~~l~~~i~~~Gg~~~~~lt~~~THLI~~~~~~~K~~~A~~~gi~vV~~~W 63 (63)
T PF12738_consen 2 VICF--SGFSGKERSQLRKLIEALGGKYSKDLTKKTTHLICSSPEGKKYRKAKEWGIPVVSPDW 63 (63)
T ss_dssp EEEE--EEB-TTTCCHHHHHHHCTT-EEESSSSTT-SEEEEES--HHHHHHHHHCTSEEEEHHH
T ss_pred EEEE--CCCCHHHHHHHHHHHHHCCCEEeccccCCceEEEEeCCCcHHHHHHHHCCCcEECCCC
Confidence 4444 466666678999999999999999999999999997643 33332 2 999999
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=97.34 E-value=0.00025 Score=55.54 Aligned_cols=52 Identities=33% Similarity=0.601 Sum_probs=40.9
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHH
Q 009742 243 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 302 (527)
Q Consensus 243 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 302 (527)
+++.+|||||+.++.++.+. | +..++.+.+-.+ +.|.+|+|||+++|++|.+
T Consensus 5 ~~L~~I~Gig~~~a~~L~~~---G-~~t~~~l~~a~~----~~L~~i~Gig~~~a~~i~~ 56 (60)
T PF14520_consen 5 DDLLSIPGIGPKRAEKLYEA---G-IKTLEDLANADP----EELAEIPGIGEKTAEKIIE 56 (60)
T ss_dssp HHHHTSTTCHHHHHHHHHHT---T-CSSHHHHHTSHH----HHHHTSTTSSHHHHHHHHH
T ss_pred HhhccCCCCCHHHHHHHHhc---C-CCcHHHHHcCCH----HHHhcCCCCCHHHHHHHHH
Confidence 57889999999999887654 6 566788765332 3456999999999999975
No 19
>PLN03123 poly [ADP-ribose] polymerase; Provisional
Probab=97.05 E-value=0.0012 Score=77.75 Aligned_cols=81 Identities=16% Similarity=0.428 Sum_probs=65.8
Q ss_pred CCCcCCeEEEEeeCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEeCc----HHHHHh------ccccchHHHHHHh
Q 009742 16 NGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDL----EALLQQ------SVIRYQWLEDSLR 85 (527)
Q Consensus 16 ~~~f~~~~i~iv~~~~g~~r~~~l~~~~~~~G~~v~~~~s~~VTHVV~~~~----~~~l~~------~vv~~~Wl~ec~~ 85 (527)
...|.+++|.++-+. +. ....|+++|..+||.|...+++.+||||+... ....+. .||+.+||.+|++
T Consensus 391 ~~~l~~~~i~i~G~~-~~-~~~~~k~~Ie~~GG~~s~~v~~~~t~l~tt~e~~k~~~kv~qAk~~~ipIVsedwL~ds~~ 468 (981)
T PLN03123 391 SEFLGDLKVSIVGAS-KE-KVTEWKAKIEEAGGVFHATVKKDTNCLVVCGELDDEDAEMRKARRMKIPIVREDYLVDCFK 468 (981)
T ss_pred CCCcCCeEEEEecCC-CC-cHHHHHHHHHhcCCEEeeeccCCceEEEccHHhhhcchHHHHHHhcCCCcccHHHHHHHHh
Confidence 366999999998653 33 34899999999999999999999999998652 112222 2999999999999
Q ss_pred cCCCcCCcccccc
Q 009742 86 LGEKVSEDLYRIK 98 (527)
Q Consensus 86 ~g~~v~~~~~~l~ 98 (527)
.++++|...|.+.
T Consensus 469 ~~~~~p~~~y~~~ 481 (981)
T PLN03123 469 KKKKLPFDKYKLE 481 (981)
T ss_pred ccccCcchhhhhc
Confidence 9999999888664
No 20
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=97.00 E-value=0.00083 Score=57.39 Aligned_cols=35 Identities=34% Similarity=0.353 Sum_probs=31.8
Q ss_pred hHHHHHHhhccCcCHHHHHHHHHhCCCCHHHHhhc
Q 009742 280 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 314 (527)
Q Consensus 280 ~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~ 314 (527)
...+..|+.|||||+++|+.|+..||+|++||+..
T Consensus 8 ~~~~~~L~~iP~IG~a~a~DL~~LGi~s~~~L~g~ 42 (93)
T PF11731_consen 8 RAGLSDLTDIPNIGKATAEDLRLLGIRSPADLKGR 42 (93)
T ss_pred HHHHHHHhcCCCccHHHHHHHHHcCCCCHHHHhCC
Confidence 45788889999999999999999999999999964
No 21
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=96.90 E-value=0.0014 Score=52.13 Aligned_cols=48 Identities=29% Similarity=0.627 Sum_probs=33.2
Q ss_pred cCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHH
Q 009742 246 KGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 302 (527)
Q Consensus 246 ~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 302 (527)
.+|||||+..++.+.+ ++..++.+.+. ..+.|++|+||||++|+.+++
T Consensus 6 LGI~~VG~~~ak~L~~-----~f~sl~~l~~a----~~e~L~~i~gIG~~~A~si~~ 53 (64)
T PF12826_consen 6 LGIPGVGEKTAKLLAK-----HFGSLEALMNA----SVEELSAIPGIGPKIAQSIYE 53 (64)
T ss_dssp CTSTT--HHHHHHHHH-----CCSCHHHHCC------HHHHCTSTT--HHHHHHHHH
T ss_pred CCCCCccHHHHHHHHH-----HcCCHHHHHHc----CHHHHhccCCcCHHHHHHHHH
Confidence 5899999999998875 44556666543 456778999999999999875
No 22
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=96.76 E-value=0.002 Score=60.04 Aligned_cols=50 Identities=34% Similarity=0.606 Sum_probs=40.4
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHH-hCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHH
Q 009742 241 SADQVKGLPGIGKSMQDHIQEIVT-TGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 302 (527)
Q Consensus 241 s~~~l~~lpgIG~~ia~kI~Eil~-tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 302 (527)
+.+||+.|||||++.|.+|.++-+ .| ++..++-|.+|.|||+++.++|-.
T Consensus 95 s~eeL~~lpgIG~~kA~aIi~yRe~~G------------~f~sv~dL~~v~GiG~~~~ekl~~ 145 (149)
T COG1555 95 SAEELQALPGIGPKKAQAIIDYREENG------------PFKSVDDLAKVKGIGPKTLEKLKD 145 (149)
T ss_pred CHHHHHHCCCCCHHHHHHHHHHHHHcC------------CCCcHHHHHhccCCCHHHHHHHHh
Confidence 347899999999999999998764 33 455556667999999999999854
No 23
>PLN03122 Poly [ADP-ribose] polymerase; Provisional
Probab=96.74 E-value=0.0033 Score=72.65 Aligned_cols=85 Identities=22% Similarity=0.404 Sum_probs=67.0
Q ss_pred CCCCCCcCCeEEEEeeCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEeCc------HHHHHh------ccccchHH
Q 009742 13 LDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDL------EALLQQ------SVIRYQWL 80 (527)
Q Consensus 13 ~~~~~~f~~~~i~iv~~~~g~~r~~~l~~~~~~~G~~v~~~~s~~VTHVV~~~~------~~~l~~------~vv~~~Wl 80 (527)
..+...|.|++|.|.-+ +.. .+..++++|.++||.|.+.+ .++||+|+... +.+++. -||+.+||
T Consensus 184 ~~~~kpL~G~~fviTGt-l~~-sr~elK~~Ie~~GGkvsssV-s~~T~lIvt~~ev~k~gsSKlkkAk~lgIpIVsEd~L 260 (815)
T PLN03122 184 GAPGKPFSGMMISLSGR-LSR-THQYWKKDIEKHGGKVANSV-EGVTCLVVSPAERERGGSSKIAEAMERGIPVVREAWL 260 (815)
T ss_pred cccCCCcCCcEEEEeCC-CCC-CHHHHHHHHHHcCCEEcccc-ccceEEEEcCccccccCccHHHHHHHcCCcCccHHHH
Confidence 34556799999999654 333 46899999999999999999 67888886441 234443 29999999
Q ss_pred HHHHhcCCCcCCcccccccC
Q 009742 81 EDSLRLGEKVSEDLYRIKLD 100 (527)
Q Consensus 81 ~ec~~~g~~v~~~~~~l~~~ 100 (527)
.+|++.+++++...|.+..+
T Consensus 261 ~d~i~~~k~~~~~~y~l~~~ 280 (815)
T PLN03122 261 IDSIEKQEAQPLEAYDVVSD 280 (815)
T ss_pred HHHHhcCCcccchhhhhccc
Confidence 99999999999999998643
No 24
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=96.73 E-value=0.0065 Score=69.33 Aligned_cols=85 Identities=18% Similarity=0.311 Sum_probs=61.5
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHHhCCCCHHHHhhcc--Ccchh
Q 009742 243 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHS 320 (527)
Q Consensus 243 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~ 320 (527)
+++..|||+|++.+++|.+-++.-+-..| ...+--+ .|+|||+++|+.|.+. +.|+++|.++. .|...
T Consensus 479 ~~L~~l~gfG~Ksa~~ll~~Ie~sk~~~l--------~R~l~al-gi~~IG~~~ak~L~~~-f~sl~~l~~As~eeL~~i 548 (665)
T PRK07956 479 EDLLGLEGFGEKSAQNLLDAIEKSKETSL--------ARFLYAL-GIRHVGEKAAKALARH-FGSLEALRAASEEELAAV 548 (665)
T ss_pred HHHhcCcCcchHHHHHHHHHHHHhhcCCH--------HHhhHhh-hccCcCHHHHHHHHHH-cCCHHHHHhCCHHHHhcc
Confidence 57899999999999998876653221222 2344445 8999999999999864 47899998653 57788
Q ss_pred hhccccchhhhccCcCH
Q 009742 321 QRLGLKYFDDIKTRIPR 337 (527)
Q Consensus 321 q~~Glk~yed~~~~i~r 337 (527)
.++|-+..+.+..-+.-
T Consensus 549 ~GIG~~~A~sI~~ff~~ 565 (665)
T PRK07956 549 EGVGEVVAQSIVEFFAV 565 (665)
T ss_pred CCcCHHHHHHHHHHHhh
Confidence 88887777766555443
No 25
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=96.64 E-value=0.0033 Score=56.44 Aligned_cols=50 Identities=30% Similarity=0.515 Sum_probs=40.2
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHHh-CCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHH
Q 009742 241 SADQVKGLPGIGKSMQDHIQEIVTT-GKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 302 (527)
Q Consensus 241 s~~~l~~lpgIG~~ia~kI~Eil~t-G~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 302 (527)
+.++|..|||||+..|.+|-++-+. |.+. .++.|.+|+|||++++.+|.+
T Consensus 66 ~~~eL~~lpGIG~~~A~~Ii~~R~~~g~f~------------s~eeL~~V~GIg~k~~~~i~~ 116 (120)
T TIGR01259 66 SLEELQALPGIGPAKAKAIIEYREENGAFK------------SVDDLTKVSGIGEKSLEKLKD 116 (120)
T ss_pred CHHHHhcCCCCCHHHHHHHHHHHHhcCCcC------------CHHHHHcCCCCCHHHHHHHHh
Confidence 3578999999999999999998764 4443 344556899999999999865
No 26
>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=96.48 E-value=0.0042 Score=60.16 Aligned_cols=53 Identities=15% Similarity=0.265 Sum_probs=37.9
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHH
Q 009742 243 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLY 301 (527)
Q Consensus 243 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly 301 (527)
.+|.++||||+++|-.| |.+-+..++.+.-.+ +-...|++|||||+|||+++.
T Consensus 72 ~~L~~V~GIGpK~Al~i---L~~~~~~el~~aI~~---~d~~~L~~ipGiGkKtAerIi 124 (191)
T TIGR00084 72 KELIKVNGVGPKLALAI---LSNMSPEEFVYAIET---EEVKALVKIPGVGKKTAERLL 124 (191)
T ss_pred HHHhCCCCCCHHHHHHH---HhcCCHHHHHHHHHh---CCHHHHHhCCCCCHHHHHHHH
Confidence 46899999999999888 554445454433222 123456789999999999996
No 27
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=96.48 E-value=0.0039 Score=49.67 Aligned_cols=48 Identities=44% Similarity=0.669 Sum_probs=34.4
Q ss_pred chhhhcCCCCCCHHHHHHHHHHH-HhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHH
Q 009742 241 SADQVKGLPGIGKSMQDHIQEIV-TTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKL 300 (527)
Q Consensus 241 s~~~l~~lpgIG~~ia~kI~Eil-~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l 300 (527)
+.++|..+||||+..|..|.++- +.|.+..+++| ..|+|+|+++..+|
T Consensus 12 s~~eL~~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL------------~~v~gi~~~~~~~l 60 (65)
T PF12836_consen 12 SAEELQALPGIGPKQAKAIVEYREKNGPFKSLEDL------------KEVPGIGPKTYEKL 60 (65)
T ss_dssp -HHHHHTSTT--HHHHHHHHHHHHHH-S-SSGGGG------------GGSTT--HHHHHHH
T ss_pred CHHHHHHcCCCCHHHHHHHHHHHHhCcCCCCHHHH------------hhCCCCCHHHHHHH
Confidence 45899999999999999999987 56666666554 48999999999887
No 28
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]
Probab=96.46 E-value=0.004 Score=70.30 Aligned_cols=86 Identities=13% Similarity=0.201 Sum_probs=71.1
Q ss_pred CCCCCCcCCeEEEEeeCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEe-C--cHH----HHHh-c-cccchHHHHH
Q 009742 13 LDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAM-D--LEA----LLQQ-S-VIRYQWLEDS 83 (527)
Q Consensus 13 ~~~~~~f~~~~i~iv~~~~g~~r~~~l~~~~~~~G~~v~~~~s~~VTHVV~~-~--~~~----~l~~-~-vv~~~Wl~ec 83 (527)
...+.+|.|+.+++++.-.+..+++-|++.|+.+||.|+.-+.+.+||-|+. . +.+ .++. + ||+++||.+|
T Consensus 628 ~~~s~if~gl~f~Vlsgt~~~~tk~~le~~ivenGG~iv~nv~p~~~~ci~~a~~et~~vk~~~~~~~cdVl~p~Wlldc 707 (881)
T KOG0966|consen 628 AKISNIFDGLEFCVLSGTSETHTKAKLEEIIVENGGKIVQNVGPSDTLCIATAGKETTRVKAQAIKRSCDVLKPAWLLDC 707 (881)
T ss_pred cchhhhhcCeeEEEecCCcccccHHHHHHHHHHcCCEEEEcCCCCCcceEEeccccchHHHHHHHhccCceeeHHHHHHH
Confidence 4556899999999999888888899999999999999999999999999952 2 111 2222 3 9999999999
Q ss_pred HhcCCCcCCcccccc
Q 009742 84 LRLGEKVSEDLYRIK 98 (527)
Q Consensus 84 ~~~g~~v~~~~~~l~ 98 (527)
.+-.+++|+.++-+.
T Consensus 708 c~~~~l~p~~P~~~f 722 (881)
T KOG0966|consen 708 CKKQRLLPWLPRDLF 722 (881)
T ss_pred HhhhhccccccHHHH
Confidence 999999998765443
No 29
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=96.41 E-value=0.011 Score=67.61 Aligned_cols=87 Identities=16% Similarity=0.306 Sum_probs=62.6
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHHhCCCCHHHHhhcc--Ccchh
Q 009742 243 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHS 320 (527)
Q Consensus 243 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~ 320 (527)
+++..|+|+|++.+.+|.+=++.-+-..| ...+--| .|+|||+++|++|.+ .+.|+++|..+. .|...
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 ADLAELEGWGETSAENLLAELEASREPPL--------ADFLVAL-GIPEVGPTTARNLAR-EFGTFEAIMDADEEALRAV 565 (689)
T ss_pred HHHhcCcCcchhHHHHHHHHHHHHccCCH--------HHHHHHc-CCCCcCHHHHHHHHH-HhCCHHHHHhCCHHHHhcc
Confidence 57899999999999988776653222222 2345555 899999999999975 557899998653 47777
Q ss_pred hhccccchhhhccCcCHHH
Q 009742 321 QRLGLKYFDDIKTRIPRHE 339 (527)
Q Consensus 321 q~~Glk~yed~~~~i~r~E 339 (527)
.++|-+..+.+..-+.-.+
T Consensus 566 ~GIG~k~A~sI~~ff~~~~ 584 (689)
T PRK14351 566 DDVGPTVAEEIREFFDSER 584 (689)
T ss_pred CCcCHHHHHHHHHHHhhhH
Confidence 8888777777665554333
No 30
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=96.28 E-value=0.0061 Score=55.05 Aligned_cols=47 Identities=13% Similarity=0.197 Sum_probs=36.3
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHH
Q 009742 241 SADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 302 (527)
Q Consensus 241 s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 302 (527)
+..+++.+||||+..|++|. .+|- +..++-+.+|+|||+++.+.+-+
T Consensus 59 ~~~el~~lpGigP~~A~~IV---~nGp------------f~sveDL~~V~GIgekqk~~l~k 105 (132)
T PRK02515 59 SVRAFRQFPGMYPTLAGKIV---KNAP------------YDSVEDVLNLPGLSERQKELLEA 105 (132)
T ss_pred CHHHHHHCCCCCHHHHHHHH---HCCC------------CCCHHHHHcCCCCCHHHHHHHHH
Confidence 45789999999999999998 3554 44444455899999998887754
No 31
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=96.24 E-value=0.0052 Score=69.04 Aligned_cols=80 Identities=30% Similarity=0.455 Sum_probs=62.0
Q ss_pred CCcCCeEEEEeeCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEeC-c----HHHHH--------hccccchHHHHH
Q 009742 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMD-L----EALLQ--------QSVIRYQWLEDS 83 (527)
Q Consensus 17 ~~f~~~~i~iv~~~~g~~r~~~l~~~~~~~G~~v~~~~s~~VTHVV~~~-~----~~~l~--------~~vv~~~Wl~ec 83 (527)
..|+---.-++ .+..+.-.+.+.++++. ++...+...|||||+.. . .+.|+ .|++++.|+.+|
T Consensus 473 ~~~~kk~~~~~-s~l~p~ek~~v~~~a~~---t~~k~~~~~~thvi~~~~~~g~c~rTlk~~~gil~gkwi~~~~w~~~s 548 (684)
T KOG4362|consen 473 HRFKKKLVLLV-SGLTPSEKQLVEKFAVD---TISKFWIEPVTHVIASTDLEGACLRTLKVLMGILRGKWILSYDWVLAS 548 (684)
T ss_pred cCcccceeeee-ccCCcchHHHHHHHHHH---HHhhccCCCceeeeeecccccchhhhHHHHHHhhcCceeeeHHHHHHH
Confidence 44544334443 57888889999999998 66677788999999743 2 23333 369999999999
Q ss_pred HhcCCCcCCcccccccC
Q 009742 84 LRLGEKVSEDLYRIKLD 100 (527)
Q Consensus 84 ~~~g~~v~~~~~~l~~~ 100 (527)
|+++++|++++|.|.++
T Consensus 549 ~k~~~~~~eepfEl~~d 565 (684)
T KOG4362|consen 549 LKLRKWVSEEPFELQID 565 (684)
T ss_pred HHhcCCCCCCCeeEeec
Confidence 99999999999999875
No 32
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=96.19 E-value=0.019 Score=51.60 Aligned_cols=67 Identities=22% Similarity=0.350 Sum_probs=45.0
Q ss_pred CCCCHHHHHHH--------HHHHHhCCchhhH-HHHhhc--hh------HHHHHHhhccCcCHHHHHHHHHhCCCCHHHH
Q 009742 249 PGIGKSMQDHI--------QEIVTTGKLSKLE-HFEKDE--KV------RTISLFGEVWGIGPATAQKLYEKGHRTLDDL 311 (527)
Q Consensus 249 pgIG~~ia~kI--------~Eil~tG~~~~le-~l~~~~--~~------~~l~lf~~I~GvGpktA~~ly~~GirTledL 311 (527)
||||+..+.+. .++++.|..+.-. +|..+. .. ..+--|..|+|||+..|.-|...||+|+++|
T Consensus 1 pgi~~~~~~~L~~~GI~t~~~Ll~~~~~~~~r~~La~~~~i~~~~l~~w~~~AdL~ri~gi~~~~a~LL~~AGv~Tv~~L 80 (122)
T PF14229_consen 1 PGIGPKEAAKLKAAGIKTTGDLLEAGDTPLGRKALAKKLGISERNLLKWVNQADLMRIPGIGPQYAELLEHAGVDTVEEL 80 (122)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHHcCCCHHHHHHHHHhcCCCHHHHHHHHhHHHhhhcCCCCHHHHHHHHHhCcCcHHHH
Confidence 67888777774 4566665544332 122211 11 1233355999999999999999999999999
Q ss_pred hhcc
Q 009742 312 KNED 315 (527)
Q Consensus 312 ~~~~ 315 (527)
.+..
T Consensus 81 A~~~ 84 (122)
T PF14229_consen 81 AQRN 84 (122)
T ss_pred HhCC
Confidence 8653
No 33
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.11 E-value=0.0062 Score=59.15 Aligned_cols=52 Identities=17% Similarity=0.290 Sum_probs=37.6
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchh-hHHHHhhchhHHHHHHhhccCcCHHHHHHHH
Q 009742 243 DQVKGLPGIGKSMQDHIQEIVTTGKLSK-LEHFEKDEKVRTISLFGEVWGIGPATAQKLY 301 (527)
Q Consensus 243 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~-le~l~~~~~~~~l~lf~~I~GvGpktA~~ly 301 (527)
..|.+++|||+++|-.|-.-+. ... .+.+.+ +-.+.|++|||||+|||+++.
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 5689999999999998876442 233 223322 234567799999999999964
No 34
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=95.98 E-value=0.014 Score=46.91 Aligned_cols=50 Identities=22% Similarity=0.341 Sum_probs=39.0
Q ss_pred hhhhcC-CCCCCHHHHHHHHHHHH-hCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHHh
Q 009742 242 ADQVKG-LPGIGKSMQDHIQEIVT-TGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 303 (527)
Q Consensus 242 ~~~l~~-lpgIG~~ia~kI~Eil~-tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 303 (527)
.++|.. +||||...+.+|-+... .|.+. .++.|.+|+|||.+++++++..
T Consensus 15 ~~~L~~~ipgig~~~a~~Il~~R~~~g~~~------------s~~dL~~v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 15 AEELQRAMNGVGLKKAEAIVSYREEYGPFK------------TVEDLKQVPGIGNSLVEKNLAV 66 (69)
T ss_pred HHHHHhHCCCCCHHHHHHHHHHHHHcCCcC------------CHHHHHcCCCCCHHHHHHHHhh
Confidence 467888 99999999999888764 44333 4555668999999999999763
No 35
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.98 E-value=0.0089 Score=58.04 Aligned_cols=53 Identities=26% Similarity=0.434 Sum_probs=38.8
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHH
Q 009742 243 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLY 301 (527)
Q Consensus 243 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly 301 (527)
..|.++.|||+++|=.|- .+-...+ +..-...+-.+.|++|||||+|||+++.
T Consensus 72 ~~LisVsGIGPK~ALaIL---s~~~~~e---l~~aI~~~D~~~L~~vpGIGkKtAeRII 124 (196)
T PRK13901 72 EELIGVDGIGPRAALRVL---SGIKYNE---FRDAIDREDIELISKVKGIGNKMAGKIF 124 (196)
T ss_pred HHHhCcCCcCHHHHHHHH---cCCCHHH---HHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 568899999999998765 3333333 3333334456788899999999999996
No 36
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=95.93 E-value=0.014 Score=56.56 Aligned_cols=53 Identities=19% Similarity=0.299 Sum_probs=37.3
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhH-HHHhhchhHHHHHHhhccCcCHHHHHHHHH
Q 009742 243 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLE-HFEKDEKVRTISLFGEVWGIGPATAQKLYE 302 (527)
Q Consensus 243 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le-~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 302 (527)
..|..+||||+++|.+|-+... ...+. .+.+.. .+.|++|||||+|+|++++.
T Consensus 73 ~~L~~i~GIGpk~A~~il~~fg---~~~l~~~i~~~d----~~~L~~v~Gig~k~A~~I~~ 126 (192)
T PRK00116 73 RLLISVSGVGPKLALAILSGLS---PEELVQAIANGD----VKALTKVPGIGKKTAERIVL 126 (192)
T ss_pred HHHhcCCCCCHHHHHHHHHhCC---HHHHHHHHHhCC----HHHHHhCCCCCHHHHHHHHH
Confidence 4688899999999999854332 23332 233322 33456999999999999985
No 37
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.91 E-value=0.0097 Score=57.27 Aligned_cols=53 Identities=19% Similarity=0.322 Sum_probs=38.8
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHH
Q 009742 243 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLY 301 (527)
Q Consensus 243 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly 301 (527)
..|.++.|||+++|=.|- .+-+..++-. -...+-.+.|++|||||+|||+++.
T Consensus 73 ~~Li~VsGIGpK~Al~IL---s~~~~~el~~---aI~~~D~~~L~~vpGIGkKtAeRIi 125 (183)
T PRK14601 73 EMLLKVNGIGANTAMAVC---SSLDVNSFYK---ALSLGDESVLKKVPGIGPKSAKRII 125 (183)
T ss_pred HHHhccCCccHHHHHHHH---cCCCHHHHHH---HHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 468899999999997654 4444444433 2333446788999999999999996
No 38
>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=95.89 E-value=0.0067 Score=41.08 Aligned_cols=23 Identities=30% Similarity=0.546 Sum_probs=19.5
Q ss_pred cchhhhcCCCCCCHHHHHHHHHH
Q 009742 240 ESADQVKGLPGIGKSMQDHIQEI 262 (527)
Q Consensus 240 ~s~~~l~~lpgIG~~ia~kI~Ei 262 (527)
.+.++|..|||||+.+|+.|.+|
T Consensus 8 as~eeL~~lpGIG~~tA~~I~~~ 30 (30)
T PF00633_consen 8 ASIEELMKLPGIGPKTANAILSF 30 (30)
T ss_dssp SSHHHHHTSTT-SHHHHHHHHHH
T ss_pred CCHHHHHhCCCcCHHHHHHHHhC
Confidence 36789999999999999999875
No 39
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.74 E-value=0.011 Score=57.88 Aligned_cols=53 Identities=19% Similarity=0.225 Sum_probs=39.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHH
Q 009742 243 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLY 301 (527)
Q Consensus 243 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly 301 (527)
..|.+++|||+++|-.|-. +-...++ ..-...+-.+.|++|||||+|||+++.
T Consensus 74 ~~Li~V~GIGpK~Al~iLs---~~~~~~l---~~aI~~~D~~~L~~ipGIGkKtAerIi 126 (203)
T PRK14602 74 IVLISISKVGAKTALAILS---QFRPDDL---RRLVAEEDVAALTRVSGIGKKTAQHIF 126 (203)
T ss_pred HHHhCCCCcCHHHHHHHHh---hCCHHHH---HHHHHhCCHHHHhcCCCcCHHHHHHHH
Confidence 4689999999999987654 3333333 333334457788999999999999996
No 40
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.70 E-value=0.013 Score=56.65 Aligned_cols=53 Identities=11% Similarity=0.122 Sum_probs=38.6
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHH
Q 009742 243 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLY 301 (527)
Q Consensus 243 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly 301 (527)
..|.++.|||+++|=.|-. +-..+ ++..-...+-.+.|++|||||+|||+++.
T Consensus 73 ~~Li~V~GIGpK~AL~iLs---~~~~~---el~~aI~~~D~~~L~~vpGIGkKtAerIi 125 (188)
T PRK14606 73 LSLTKVSRLGPKTALKIIS---NEDAE---TLVTMIASQDVEGLSKLPGISKKTAERIV 125 (188)
T ss_pred HHHhccCCccHHHHHHHHc---CCCHH---HHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 4688999999999987653 32333 33333344457788999999999999996
No 41
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=95.69 E-value=0.0069 Score=58.70 Aligned_cols=50 Identities=16% Similarity=0.230 Sum_probs=40.9
Q ss_pred HHHHHHhhccCcCHHHHHHHHHhCCCCHHHHhhc------cCcchhhhccccchhhhc
Q 009742 281 RTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE------DSLTHSQRLGLKYFDDIK 332 (527)
Q Consensus 281 ~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~------~~L~~~q~~Glk~yed~~ 332 (527)
..+.+|.+|+|||||+|..+ .+.-|+++|.++ .+|++.+++|-|..+.|.
T Consensus 69 ~lF~~L~~V~GIGpK~Al~i--L~~~~~~el~~aI~~~d~~~L~~ipGiGkKtAerIi 124 (191)
T TIGR00084 69 ELFKELIKVNGVGPKLALAI--LSNMSPEEFVYAIETEEVKALVKIPGVGKKTAERLL 124 (191)
T ss_pred HHHHHHhCCCCCCHHHHHHH--HhcCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHH
Confidence 46777789999999999999 666788888742 469999999999877665
No 42
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.61 E-value=0.015 Score=56.72 Aligned_cols=53 Identities=15% Similarity=0.234 Sum_probs=38.4
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHH
Q 009742 243 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLY 301 (527)
Q Consensus 243 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly 301 (527)
..|.++.|||+++|=.|- .+.+..++-+ -...+=.+.|++|||||+|||+++.
T Consensus 72 ~~L~~V~GIGpK~AL~iL---s~~~~~~l~~---aI~~~D~~~L~kvpGIGkKtAerIi 124 (197)
T PRK14603 72 ELLLGVSGVGPKLALALL---SALPPALLAR---ALLEGDARLLTSASGVGKKLAERIA 124 (197)
T ss_pred HHHhCcCCcCHHHHHHHH---cCCCHHHHHH---HHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 468899999999997654 4444444433 2333446778899999999999995
No 43
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.57 E-value=0.015 Score=56.46 Aligned_cols=53 Identities=21% Similarity=0.357 Sum_probs=39.0
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHH
Q 009742 243 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLY 301 (527)
Q Consensus 243 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly 301 (527)
..|.++.|||+++|=.|- .+.+..++-.. ...+-.+.|++|||||+|||+++.
T Consensus 73 ~~Li~V~GIGpK~Al~iL---s~~~~~el~~a---I~~~D~~~L~kvpGIGkKtAerIi 125 (195)
T PRK14604 73 ELLIGVSGVGPKAALNLL---SSGTPDELQLA---IAGGDVARLARVPGIGKKTAERIV 125 (195)
T ss_pred HHHhCcCCcCHHHHHHHH---cCCCHHHHHHH---HHhCCHHHHhhCCCCCHHHHHHHH
Confidence 468899999999997754 44444444332 333446788899999999999996
No 44
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=95.51 E-value=0.0043 Score=61.30 Aligned_cols=51 Identities=25% Similarity=0.520 Sum_probs=40.3
Q ss_pred HHhhccCcCHHHHHHHHHhCCCCHHHHhhcc--CcchhhhccccchhhhccCc
Q 009742 285 LFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIKTRI 335 (527)
Q Consensus 285 lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~q~~Glk~yed~~~~i 335 (527)
.|..|+|||++++++||+.||.|+++|..+. .|....++|-+..+.+...+
T Consensus 4 ~L~~IpGIG~krakkLl~~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l 56 (232)
T PRK12766 4 ELEDISGVGPSKAEALREAGFESVEDVRAADQSELAEVDGIGNALAARIKADV 56 (232)
T ss_pred ccccCCCcCHHHHHHHHHcCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHHh
Confidence 4568999999999999999999999999764 47777777766555554433
No 45
>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=95.33 E-value=0.015 Score=39.37 Aligned_cols=22 Identities=32% Similarity=0.477 Sum_probs=17.1
Q ss_pred HHHHHHhhccCcCHHHHHHHHH
Q 009742 281 RTISLFGEVWGIGPATAQKLYE 302 (527)
Q Consensus 281 ~~l~lf~~I~GvGpktA~~ly~ 302 (527)
..++.|++||||||+||..+..
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 3566777999999999998763
No 46
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=95.11 E-value=0.016 Score=53.94 Aligned_cols=51 Identities=27% Similarity=0.516 Sum_probs=39.8
Q ss_pred hhHHHHHHhhccCcCHHHHHHHHH--h--C-CCCHHHHhhccCcchhhhccccchhhhccCc
Q 009742 279 KVRTISLFGEVWGIGPATAQKLYE--K--G-HRTLDDLKNEDSLTHSQRLGLKYFDDIKTRI 335 (527)
Q Consensus 279 ~~~~l~lf~~I~GvGpktA~~ly~--~--G-irTledL~~~~~L~~~q~~Glk~yed~~~~i 335 (527)
.....+.|..+||||+++|+++.+ + | ++|+|||.+ .+++|-+.++.+..+|
T Consensus 92 NtAs~eeL~~lpgIG~~kA~aIi~yRe~~G~f~sv~dL~~------v~GiG~~~~ekl~~~i 147 (149)
T COG1555 92 NTASAEELQALPGIGPKKAQAIIDYREENGPFKSVDDLAK------VKGIGPKTLEKLKDYI 147 (149)
T ss_pred cccCHHHHHHCCCCCHHHHHHHHHHHHHcCCCCcHHHHHh------ccCCCHHHHHHHHhhc
Confidence 344556668999999999999964 2 4 899999986 4678888888777654
No 47
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=94.96 E-value=0.011 Score=67.47 Aligned_cols=61 Identities=21% Similarity=0.325 Sum_probs=46.9
Q ss_pred hccCcCHHHHHHHHHh-CCCCHHHHhh--ccCcchhhhccccchhhhccCcCHHHHHHHHHHHH
Q 009742 288 EVWGIGPATAQKLYEK-GHRTLDDLKN--EDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQ 348 (527)
Q Consensus 288 ~I~GvGpktA~~ly~~-GirTledL~~--~~~L~~~q~~Glk~yed~~~~i~r~Ea~~i~~iv~ 348 (527)
+|+|+|||++++||+. +|++++||.. ..+|..+.+||-+..+.+.+.|-......+..++-
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 7899999994 34688888999999888876665443333334333
No 48
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=94.82 E-value=0.033 Score=54.40 Aligned_cols=54 Identities=19% Similarity=0.265 Sum_probs=40.3
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHH
Q 009742 243 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 302 (527)
Q Consensus 243 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 302 (527)
..|.++.|||+++|=.| |.+....++-.. ...+-...|+++||||.|||+++.-
T Consensus 73 ~~LisVnGIGpK~ALai---Ls~~~~~~l~~a---I~~~d~~~L~k~PGIGkKtAerivl 126 (201)
T COG0632 73 RLLISVNGIGPKLALAI---LSNLDPEELAQA---IANEDVKALSKIPGIGKKTAERIVL 126 (201)
T ss_pred HHHHccCCccHHHHHHH---HcCCCHHHHHHH---HHhcChHhhhcCCCCCHHHHHHHHH
Confidence 57899999999999765 455555554433 3334467889999999999999963
No 49
>cd05397 NT_Pol-beta-like Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins. This superfamily includes the NT domains of DNA polymerase beta and other family X DNA polymerases, as well as the NT domains of Class I and Class II CCA-adding enzymes, RelA- and SpoT-like ppGpp synthetases and hydrolases, 2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), poly (A) polymerases, terminal uridylyl transferases, and Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. The Escherichia coli CCA-adding enzyme belongs to this superfamily but is not included as this enzyme lacks the N-terminal helix conserved in the remainder of the superfamily. In the majority of the Pol beta-like superfamily NTs, two carboxylates, Dx[D/E], together with a third more distal carboxylate coordinate two divalent metal cations that are essential for catalysis. These divalent metal ions are
Probab=94.78 E-value=0.054 Score=40.73 Aligned_cols=28 Identities=29% Similarity=0.458 Sum_probs=23.4
Q ss_pred cCCCeEEEecccccccCC-ccCCeeEEEe
Q 009742 354 VLPEVIILCGGSYRRGKA-SCGDLDVVIM 381 (527)
Q Consensus 354 ~~p~~~v~~~GsyRRGke-~~gDVDiLIt 381 (527)
..+...+.+.|||.||.. ..+|||+++.
T Consensus 14 ~~~~~~v~lfGS~arg~~~~~SDIDi~v~ 42 (49)
T cd05397 14 LVPGYEIVVYGSLVRGLLKKSSDIDLACV 42 (49)
T ss_pred hcCCcEEEEECCcCCCCCCCCCCEEEEEE
Confidence 345668999999999977 6789999986
No 50
>PF11798 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 This helix-hairpin-helix motif is found in proteins belonging to the type-Y family of DNA polymerases []. This type of polymerases are thought to be involved in UV protection and mutation [, ]. ; PDB: 3PZP_B 2OH2_B 2W7O_B 3IN5_B 1T94_A 2W7P_B 2W8K_A 2AGQ_A 1RYR_A 3RAX_A ....
Probab=94.67 E-value=0.018 Score=39.50 Aligned_cols=19 Identities=47% Similarity=0.814 Sum_probs=15.8
Q ss_pred hhccCcCHHHHHHHHHhCC
Q 009742 287 GEVWGIGPATAQKLYEKGH 305 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~Gi 305 (527)
..+||||++|+++|.+.||
T Consensus 14 ~~~~GIG~kt~~kL~~~GI 32 (32)
T PF11798_consen 14 RKFWGIGKKTAKKLNKLGI 32 (32)
T ss_dssp GGSTTS-HHHHHHHHCTT-
T ss_pred HhhCCccHHHHHHHHHccC
Confidence 6899999999999988886
No 51
>PRK14973 DNA topoisomerase I; Provisional
Probab=94.64 E-value=0.039 Score=65.31 Aligned_cols=90 Identities=20% Similarity=0.170 Sum_probs=58.1
Q ss_pred hhhcCCCCCCHHHHHHHHHHHH-h-CCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHHhCCCCHHHHhhcc--Ccc
Q 009742 243 DQVKGLPGIGKSMQDHIQEIVT-T-GKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLT 318 (527)
Q Consensus 243 ~~l~~lpgIG~~ia~kI~Eil~-t-G~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~ 318 (527)
++|..+|||...++......+. . +.-..-...+.....+.-++ .+|.|||++|+..++..|+.|.|||.+++ +|+
T Consensus 835 ~~La~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~el-~~vkg~ge~t~~~l~~ag~~~~e~l~~~d~~~la 913 (936)
T PRK14973 835 AYLALKTGISPETICRHAKLVCEKLGRPVPEKISKAAFERGRAEL-LSVPGLGETTLEKLYLAGVYDGDLLVSADPKKLA 913 (936)
T ss_pred HHHhcCCCCChhhHHHHHHHHHHHhcCCCchhhhhhhhcccchhh-hhccCCCHHHHHHHHHcCCCCHHHhccCCHHHHh
Confidence 5677888888776666644443 1 11111111111111222334 49999999999999999999999999874 577
Q ss_pred hhhhccccchhhhcc
Q 009742 319 HSQRLGLKYFDDIKT 333 (527)
Q Consensus 319 ~~q~~Glk~yed~~~ 333 (527)
..-+++.+....+..
T Consensus 914 ~~~~i~~k~~~~~~~ 928 (936)
T PRK14973 914 KVTGIDEKKLRNLQA 928 (936)
T ss_pred hhcCCCHHHHHHHHH
Confidence 777777777666554
No 52
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.62 E-value=0.034 Score=53.71 Aligned_cols=52 Identities=13% Similarity=0.098 Sum_probs=37.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHH
Q 009742 243 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLY 301 (527)
Q Consensus 243 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly 301 (527)
..|.++.|||+++|=.|- .+-+..++-.. ...+=.+.| +|||||+|||+++.
T Consensus 73 ~~LisV~GIGpK~Al~iL---s~~~~~~l~~a---I~~~D~~~L-~vpGIGkKtAerIi 124 (186)
T PRK14600 73 RMLVKVSGVNYKTAMSIL---SKLTPEQLFSA---IVNEDKAAL-KVNGIGEKLINRII 124 (186)
T ss_pred HHHhCcCCcCHHHHHHHH---ccCCHHHHHHH---HHcCCHhhe-ECCCCcHHHHHHHH
Confidence 468899999999997754 44444444332 223335677 89999999999996
No 53
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=94.36 E-value=0.087 Score=60.23 Aligned_cols=84 Identities=14% Similarity=0.199 Sum_probs=60.5
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHHhCCCCHHHHhhc--------
Q 009742 243 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE-------- 314 (527)
Q Consensus 243 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~-------- 314 (527)
++|..|+|+|++.+++|.+=++.-+-. +-...|--| .|++||.++|+.|-+..+.|++.|.+.
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 DRLINLKGFKDKRINNLKRSIEASKKR--------PFSKLLLSM-GIKDLGENTILLLINNNLNSFDKISTLCQDREFAL 540 (669)
T ss_pred HHHhhccCccHHHHHHHHHHHHHHhCC--------CHHHHHHHc-CCCchhHHHHHHHHHHhhCCHHHHHhhhhccCCCH
Confidence 688899999999888877655432222 223355566 899999999999887788999988752
Q ss_pred cCcchhhhccccchhhhccCc
Q 009742 315 DSLTHSQRLGLKYFDDIKTRI 335 (527)
Q Consensus 315 ~~L~~~q~~Glk~yed~~~~i 335 (527)
..|....++|-...+.+.+-+
T Consensus 541 e~l~~i~giG~~~a~si~~ff 561 (669)
T PRK14350 541 SKLLKIKGIGEKIALNIIEAF 561 (669)
T ss_pred HHHhhCCCccHHHHHHHHHHH
Confidence 147777888877666665544
No 54
>PRK02362 ski2-like helicase; Provisional
Probab=94.36 E-value=0.03 Score=64.84 Aligned_cols=55 Identities=24% Similarity=0.404 Sum_probs=41.4
Q ss_pred HHHhhchhHHHHHHhhccCcCHHHHHHHHHhCCCCHHHHhhc--cCcchhhhccccchhh
Q 009742 273 HFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDD 330 (527)
Q Consensus 273 ~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~--~~L~~~q~~Glk~yed 330 (527)
++....+...+.|+ +|||||+++|+++|+.||+|++||... .+|..+ ||-+..+.
T Consensus 642 ~l~~gv~~~~~~L~-~ip~i~~~~a~~l~~~gi~s~~dl~~~~~~~l~~~--~g~~~~~~ 698 (737)
T PRK02362 642 RVEYGVREELLDLV-GLRGVGRVRARRLYNAGIESRADLRAADKSVVLAI--LGEKIAEN 698 (737)
T ss_pred HHHhCCCHHHHHHh-CCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHHH--HCHHHHHH
Confidence 34555666778887 899999999999999999999999953 244444 55544443
No 55
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=94.34 E-value=0.018 Score=65.64 Aligned_cols=63 Identities=24% Similarity=0.383 Sum_probs=47.7
Q ss_pred hhccCcCHHHHHHHHHh-CCCCHHHHhh--ccCcchhhhccccchhhhccCcCHHHHHHHHHHHHH
Q 009742 287 GEVWGIGPATAQKLYEK-GHRTLDDLKN--EDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQK 349 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~-GirTledL~~--~~~L~~~q~~Glk~yed~~~~i~r~Ea~~i~~iv~~ 349 (527)
++|+|+|++++++||+. +|++++||.. ..+|..+.+||-+..+.|.+.|....-..+.+++..
T Consensus 435 l~I~GLG~k~i~~L~~~g~I~~~~Dl~~L~~~~L~~L~GfG~Ksa~nIl~~Ie~sk~~~l~r~L~a 500 (652)
T TIGR00575 435 MDIEGLGDKVIEQLFEKKLVRSVADLYALKKEDLLELEGFGEKSAQNLLNAIEKSKEKPLARLLFA 500 (652)
T ss_pred cCCCCcCHHHHHHHHHcCCcCCHHHHHhcCHHHHhhccCccHHHHHHHHHHHHHhccCcHHHHHhh
Confidence 37999999999999998 7899999994 346888899999888888766554433333444433
No 56
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=94.29 E-value=0.12 Score=58.29 Aligned_cols=49 Identities=18% Similarity=0.312 Sum_probs=27.4
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHH
Q 009742 245 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 302 (527)
Q Consensus 245 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 302 (527)
..+||+||+.+|..+..... -++.|... ..+.+..|+|||++.|+.+.+
T Consensus 513 aLGIr~VG~~~Ak~La~~f~-----sl~~l~~a----~~e~l~~i~giG~~vA~si~~ 561 (667)
T COG0272 513 ALGIRHVGETTAKSLARHFG-----TLEALLAA----SEEELASIPGIGEVVARSIIE 561 (667)
T ss_pred HcCCchhhHHHHHHHHHHhh-----hHHHHHhc----CHHHHhhccchhHHHHHHHHH
Confidence 46677777777766665222 24444321 234445677777777766654
No 57
>PTZ00418 Poly(A) polymerase; Provisional
Probab=94.23 E-value=0.36 Score=54.17 Aligned_cols=51 Identities=24% Similarity=0.399 Sum_probs=41.8
Q ss_pred CCeEEEecccccccCCc-cCCeeEEEecCCcchhhhhHHHHHHHHHHcCccc
Q 009742 356 PEVIILCGGSYRRGKAS-CGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLR 406 (527)
Q Consensus 356 p~~~v~~~GsyRRGke~-~gDVDiLIt~~~~~~~~~~l~~lv~~L~~~g~l~ 406 (527)
.+.++...||||-|--. +.|||.|+..|..-+...||..+.+.|.+..-++
T Consensus 125 ~~g~I~tfGSYrLGV~~pgSDID~L~V~P~~vtredFF~~f~~~L~~~~~V~ 176 (593)
T PTZ00418 125 ISGKLFTFGSYRLGVVAPGSDIDTLCLAPRHITRESFFSDFYAKLQQDPNIT 176 (593)
T ss_pred CCeEEEEeccccccCCCCCCcccEEEECCCCCCHHHHHHHHHHHHhcCCCcc
Confidence 46678889999999876 6799999999976666789998888888876554
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=94.14 E-value=0.19 Score=43.80 Aligned_cols=60 Identities=25% Similarity=0.457 Sum_probs=45.8
Q ss_pred HHHHHHHHHHhhhcCCCeEEEecccccccCC-ccCCeeEEEecCCc-chhhhhHHHHHHHHHHcCc
Q 009742 341 EQMERLLQKAGEEVLPEVIILCGGSYRRGKA-SCGDLDVVIMHPDR-KSHKGFLSKYVKKLKEMKF 404 (527)
Q Consensus 341 ~~i~~iv~~~~~~~~p~~~v~~~GsyRRGke-~~gDVDiLIt~~~~-~~~~~~l~~lv~~L~~~g~ 404 (527)
+.+++++++ ..|++.+.+-||++.|.. ..+|||+.|..++. .....++..+-+.|++.+.
T Consensus 7 ~~l~~~i~~----~~~~~~v~~fGS~~~g~~~~~SDiDl~i~~~~~~~~~~~~l~~l~~~l~~~~~ 68 (114)
T cd05402 7 DRLQELIKE----WFPGAKLYPFGSYVTGLGLPGSDIDLCLLGPNHRVDREDFLRKLAKLLKKSGE 68 (114)
T ss_pred HHHHHHHHH----HCCCCEEEEecccccCCCCCCCCeeEEEEeCCCCccHHHHHHHHHHHHHhCCC
Confidence 334555554 578999999999999953 46899999998876 4566788888888888774
No 59
>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=93.95 E-value=0.053 Score=48.65 Aligned_cols=48 Identities=27% Similarity=0.483 Sum_probs=36.7
Q ss_pred HHHHHHhhccCcCHHHHHHHHHh-----CCCCHHHHhhccCcchhhhccccchhhhccC
Q 009742 281 RTISLFGEVWGIGPATAQKLYEK-----GHRTLDDLKNEDSLTHSQRLGLKYFDDIKTR 334 (527)
Q Consensus 281 ~~l~lf~~I~GvGpktA~~ly~~-----GirTledL~~~~~L~~~q~~Glk~yed~~~~ 334 (527)
-..+.|++|||||+++|+++++. ++.|++||.+ ..++|.+.++.+...
T Consensus 65 A~~~eL~~lpGIG~~~A~~Ii~~R~~~g~f~s~eeL~~------V~GIg~k~~~~i~~~ 117 (120)
T TIGR01259 65 ASLEELQALPGIGPAKAKAIIEYREENGAFKSVDDLTK------VSGIGEKSLEKLKDY 117 (120)
T ss_pred CCHHHHhcCCCCCHHHHHHHHHHHHhcCCcCCHHHHHc------CCCCCHHHHHHHHhc
Confidence 35666779999999999999853 6899999964 456777777766543
No 60
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=93.91 E-value=0.067 Score=48.45 Aligned_cols=32 Identities=22% Similarity=0.380 Sum_probs=28.5
Q ss_pred HHHHHhhccCcCHHHHHHHHHh-CCCCHHHHhh
Q 009742 282 TISLFGEVWGIGPATAQKLYEK-GHRTLDDLKN 313 (527)
Q Consensus 282 ~l~lf~~I~GvGpktA~~ly~~-GirTledL~~ 313 (527)
..+.|.++|||||++|+++.+. .++|+|||.+
T Consensus 59 ~~~el~~lpGigP~~A~~IV~nGpf~sveDL~~ 91 (132)
T PRK02515 59 SVRAFRQFPGMYPTLAGKIVKNAPYDSVEDVLN 91 (132)
T ss_pred CHHHHHHCCCCCHHHHHHHHHCCCCCCHHHHHc
Confidence 4566779999999999999987 6999999986
No 61
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=93.45 E-value=0.042 Score=53.26 Aligned_cols=51 Identities=24% Similarity=0.275 Sum_probs=37.9
Q ss_pred HHHHHhhccCcCHHHHHHHHHh-CCCCHHHHhhcc---Ccchhhhccccchhhhc
Q 009742 282 TISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED---SLTHSQRLGLKYFDDIK 332 (527)
Q Consensus 282 ~l~lf~~I~GvGpktA~~ly~~-GirTledL~~~~---~L~~~q~~Glk~yed~~ 332 (527)
.+..|.+|+|||||+|.++.+. |..++.+....+ .|+..+++|.+..+.+.
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 3556679999999999999986 887776544332 57788888877665543
No 62
>KOG2481 consensus Protein required for normal rRNA processing [RNA processing and modification]
Probab=93.30 E-value=0.054 Score=58.78 Aligned_cols=82 Identities=18% Similarity=0.302 Sum_probs=60.4
Q ss_pred CCCCCCcCCeEEEEeeCCCChhHHHHHHHHHHhcCCEEEee-c--------C-CCccEEEEeCcHH---HHHhccccchH
Q 009742 13 LDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEK-L--------S-KKVTHVLAMDLEA---LLQQSVIRYQW 79 (527)
Q Consensus 13 ~~~~~~f~~~~i~iv~~~~g~~r~~~l~~~~~~~G~~v~~~-~--------s-~~VTHVV~~~~~~---~l~~~vv~~~W 79 (527)
+.-..+|+|++.||.. . -+ ++.|.=+|+..||.|.-. + + ..+||=|..--.. ..-.+-|.++|
T Consensus 322 s~~kslF~glkFfl~r-e--VP-resL~fiI~s~GG~V~wd~~~~g~~~~~~d~~ITH~IvDrP~~~~~v~gR~YvQPQW 397 (570)
T KOG2481|consen 322 SSHKSLFSGLKFFLNR-E--VP-RESLEFIIRSFGGKVSWDPLGIGATYDESDERITHQIVDRPGQQTSVIGRTYVQPQW 397 (570)
T ss_pred hhHHHHhhcceeeeec-c--Cc-hHHHHHHHHHcCCceecCccCCCCcccccccceeeeeecccCccceeeeeeeecchh
Confidence 3444899999999953 2 22 377888999999999854 1 1 2478877543221 12235899999
Q ss_pred HHHHHhcCCCcCCcccccc
Q 009742 80 LEDSLRLGEKVSEDLYRIK 98 (527)
Q Consensus 80 l~ec~~~g~~v~~~~~~l~ 98 (527)
+-||+-+|.++|++.|...
T Consensus 398 vfDsvNar~llpt~~Y~~G 416 (570)
T KOG2481|consen 398 VFDSVNARLLLPTEKYFPG 416 (570)
T ss_pred hhhhccchhhccHhhhCCC
Confidence 9999999999999999875
No 63
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=93.27 E-value=0.077 Score=42.22 Aligned_cols=47 Identities=30% Similarity=0.519 Sum_probs=31.5
Q ss_pred HHHHHhhccCcCHHHHHHHHH---h--CCCCHHHHhhccCcchhhhccccchhhhccC
Q 009742 282 TISLFGEVWGIGPATAQKLYE---K--GHRTLDDLKNEDSLTHSQRLGLKYFDDIKTR 334 (527)
Q Consensus 282 ~l~lf~~I~GvGpktA~~ly~---~--GirTledL~~~~~L~~~q~~Glk~yed~~~~ 334 (527)
..+.|.++||||++.|+++.+ + +++|++||.+ ..++|.+.|+.+...
T Consensus 12 s~~eL~~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL~~------v~gi~~~~~~~l~~~ 63 (65)
T PF12836_consen 12 SAEELQALPGIGPKQAKAIVEYREKNGPFKSLEDLKE------VPGIGPKTYEKLKPY 63 (65)
T ss_dssp -HHHHHTSTT--HHHHHHHHHHHHHH-S-SSGGGGGG------STT--HHHHHHHCCC
T ss_pred CHHHHHHcCCCCHHHHHHHHHHHHhCcCCCCHHHHhh------CCCCCHHHHHHHHhh
Confidence 456677999999999999974 2 8899999986 456777777666543
No 64
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=93.17 E-value=0.099 Score=41.91 Aligned_cols=43 Identities=19% Similarity=0.294 Sum_probs=32.2
Q ss_pred HHhh-ccCcCHHHHHHHHHh-----CCCCHHHHhhccCcchhhhccccchhhhcc
Q 009742 285 LFGE-VWGIGPATAQKLYEK-----GHRTLDDLKNEDSLTHSQRLGLKYFDDIKT 333 (527)
Q Consensus 285 lf~~-I~GvGpktA~~ly~~-----GirTledL~~~~~L~~~q~~Glk~yed~~~ 333 (527)
.|.. ++|||+++|+++.+. ++++++||.+ ..++|.+.++.+..
T Consensus 17 ~L~~~ipgig~~~a~~Il~~R~~~g~~~s~~dL~~------v~gi~~~~~~~i~~ 65 (69)
T TIGR00426 17 ELQRAMNGVGLKKAEAIVSYREEYGPFKTVEDLKQ------VPGIGNSLVEKNLA 65 (69)
T ss_pred HHHhHCCCCCHHHHHHHHHHHHHcCCcCCHHHHHc------CCCCCHHHHHHHHh
Confidence 4456 999999999999864 5999999975 34666666665544
No 65
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.15 E-value=0.043 Score=53.31 Aligned_cols=52 Identities=19% Similarity=0.255 Sum_probs=39.7
Q ss_pred hHHHHHHhhccCcCHHHHHHHHHh-CCCCHHHHh-hc--cCcchhhhccccchhhh
Q 009742 280 VRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLK-NE--DSLTHSQRLGLKYFDDI 331 (527)
Q Consensus 280 ~~~l~lf~~I~GvGpktA~~ly~~-GirTledL~-~~--~~L~~~q~~Glk~yed~ 331 (527)
...+++|.+|+|||||+|..+... +...|-+.. +. ..|++.+++|-|..+.+
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 357888889999999999999985 766633332 32 35899999999887764
No 66
>PRK00254 ski2-like helicase; Provisional
Probab=92.65 E-value=0.14 Score=59.31 Aligned_cols=75 Identities=23% Similarity=0.382 Sum_probs=50.1
Q ss_pred HHHHHHHHHH-----hCCchhhHHHH----hhchhHHHHHHhhccCcCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhc
Q 009742 255 MQDHIQEIVT-----TGKLSKLEHFE----KDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRL 323 (527)
Q Consensus 255 ia~kI~Eil~-----tG~~~~le~l~----~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~q~~ 323 (527)
++.-+.+|+. .|.+..+.++. ...+...+.|. +|||||+++|+++|+.|+.|++||..+. .|....++
T Consensus 608 l~~a~~~i~~~~~~~~~~~~~l~~l~~rl~~g~~~~~~~L~-~ipgig~~~~~~l~~~g~~s~~~i~~a~~~el~~~~gi 686 (720)
T PRK00254 608 LMYSLIELYKLFEPKQEVLDYLETLHLRVKHGVREELLELM-RLPMIGRKRARALYNAGFRSIEDIVNAKPSELLKVEGI 686 (720)
T ss_pred HHHHHHHHHHHhCcchhHHHHHHHHHHHHHcCCCHHHhhhh-cCCCCCHHHHHHHHHccCCCHHHHHhCCHHHHhcCCCC
Confidence 3344444543 44445554333 44455556666 8999999999999999999999999753 46666666
Q ss_pred cccchhh
Q 009742 324 GLKYFDD 330 (527)
Q Consensus 324 Glk~yed 330 (527)
|-+..+.
T Consensus 687 ~~~~a~~ 693 (720)
T PRK00254 687 GAKIVEG 693 (720)
T ss_pred CHHHHHH
Confidence 6555433
No 67
>COG5163 NOP7 Protein required for biogenesis of the 60S ribosomal subunit [Translation, ribosomal structure and biogenesis]
Probab=92.63 E-value=0.11 Score=54.76 Aligned_cols=82 Identities=20% Similarity=0.312 Sum_probs=59.6
Q ss_pred CCCCCCcCCeEEEEeeCCCChhHHHHHHHHHHhcCCEEEeec-----------CCCccEEEEeCcHH--HHHh-ccccch
Q 009742 13 LDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKL-----------SKKVTHVLAMDLEA--LLQQ-SVIRYQ 78 (527)
Q Consensus 13 ~~~~~~f~~~~i~iv~~~~g~~r~~~l~~~~~~~G~~v~~~~-----------s~~VTHVV~~~~~~--~l~~-~vv~~~ 78 (527)
+.-.++|++++.||...-.| ..|.=+|.+.||.|...- +..|||-|+.---- ++.. ..+.++
T Consensus 345 Ss~~slFS~f~FyisreVp~----dsLefiilscGG~V~~~p~~~~i~~~~~vD~~vth~i~drp~~~~kvegrtYiQPQ 420 (591)
T COG5163 345 SSLKSLFSGFKFYISREVPG----DSLEFIILSCGGSVVGSPCEADIHVSEKVDEKVTHQIVDRPVMKNKVEGRTYIQPQ 420 (591)
T ss_pred cchhhhhhceEEEEeccccc----hHHHHHHHHcCCcccCchhhccCCchhhccchhhhhhccchhhhhhhcceeeechH
Confidence 44558999999999654443 567778999999997543 23577766533211 1111 288999
Q ss_pred HHHHHHhcCCCcCCcccccc
Q 009742 79 WLEDSLRLGEKVSEDLYRIK 98 (527)
Q Consensus 79 Wl~ec~~~g~~v~~~~~~l~ 98 (527)
|+-+|+-.|++++++.|...
T Consensus 421 w~fDsiNkG~l~~~~~Y~~G 440 (591)
T COG5163 421 WLFDSINKGKLACVENYCVG 440 (591)
T ss_pred HHHhhhccccchhhhhcccc
Confidence 99999999999999999885
No 68
>KOG1929 consensus Nucleotide excision repair factor NEF2, RAD4/CUT5 component [Replication, recombination and repair]
Probab=92.43 E-value=0.2 Score=58.10 Aligned_cols=82 Identities=22% Similarity=0.276 Sum_probs=70.1
Q ss_pred CCcCCeEEEEeeCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEeCc------HHHHHh--ccccchHHHHHHhcCC
Q 009742 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDL------EALLQQ--SVIRYQWLEDSLRLGE 88 (527)
Q Consensus 17 ~~f~~~~i~iv~~~~g~~r~~~l~~~~~~~G~~v~~~~s~~VTHVV~~~~------~~~l~~--~vv~~~Wl~ec~~~g~ 88 (527)
..|.++.|.. +|++..++.-+++++.+|||+.+..++..|+||+.-.. +.+++. .+|..+|+-+|+..+.
T Consensus 102 p~~~~~~Vc~--tgl~~~eK~ei~~~v~k~gg~~~~~L~s~v~~~~~~~~~~~~kYe~al~wn~~v~~~~w~~~s~~~~~ 179 (811)
T KOG1929|consen 102 PGFFGLKVCL--TGLSGDEKSEIKILVPKHGGTLHRSLSSDVNSLKILPEVKTEKYEQALKWNIPVVSDDWLFDSIEKTA 179 (811)
T ss_pred CcccceEEEe--cccchHHHHHHHHHhhhcccEEehhhhhhhheeeeccccchHHHHHHHhhCCccccHHHHhhhhcccc
Confidence 5677888887 89999999999999999999999999999999986443 223432 2999999999999999
Q ss_pred CcCCcccccccC
Q 009742 89 KVSEDLYRIKLD 100 (527)
Q Consensus 89 ~v~~~~~~l~~~ 100 (527)
.++++.|.+..+
T Consensus 180 ~~~~~~~e~~~~ 191 (811)
T KOG1929|consen 180 VLETKPYEGAPV 191 (811)
T ss_pred cccccccccccc
Confidence 999999999763
No 69
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=92.38 E-value=0.24 Score=49.15 Aligned_cols=54 Identities=24% Similarity=0.452 Sum_probs=41.0
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHHh
Q 009742 242 ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 303 (527)
Q Consensus 242 ~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 303 (527)
++.|..|||||+..+.++ ++.| +.-++.+.... .+.|.+|+|||.++|.++++.
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 356889999999988775 5565 56666665433 445569999999999999986
No 70
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=92.37 E-value=0.097 Score=41.59 Aligned_cols=43 Identities=28% Similarity=0.365 Sum_probs=28.3
Q ss_pred hccCcCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhccccchhhh
Q 009742 288 EVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDI 331 (527)
Q Consensus 288 ~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~q~~Glk~yed~ 331 (527)
+|+|||+++|+.|-+ .+.|++.|.++. .|+...++|.+.-+.+
T Consensus 7 GI~~VG~~~ak~L~~-~f~sl~~l~~a~~e~L~~i~gIG~~~A~si 51 (64)
T PF12826_consen 7 GIPGVGEKTAKLLAK-HFGSLEALMNASVEELSAIPGIGPKIAQSI 51 (64)
T ss_dssp TSTT--HHHHHHHHH-CCSCHHHHCC--HHHHCTSTT--HHHHHHH
T ss_pred CCCCccHHHHHHHHH-HcCCHHHHHHcCHHHHhccCCcCHHHHHHH
Confidence 899999999999975 455999999653 4777777775554443
No 71
>KOG2043 consensus Signaling protein SWIFT and related BRCT domain proteins [Transcription; Signal transduction mechanisms; Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]
Probab=91.19 E-value=0.18 Score=59.22 Aligned_cols=61 Identities=26% Similarity=0.432 Sum_probs=49.9
Q ss_pred HHHHHHHHhcCCEEEeecCCCccEEEEeCcHHHHHh--------ccccchHHHHHHhcCCCcCCcccccc
Q 009742 37 QIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQ--------SVIRYQWLEDSLRLGEKVSEDLYRIK 98 (527)
Q Consensus 37 ~~l~~~~~~~G~~v~~~~s~~VTHVV~~~~~~~l~~--------~vv~~~Wl~ec~~~g~~v~~~~~~l~ 98 (527)
.-++++++..|+.++... .+.||+|+-..-+.++. +||+.+||.+|+++|..++++.|.|.
T Consensus 671 ~~~k~~~k~lg~s~~ss~-~e~Th~i~~rirRT~k~Leai~~G~~ivT~~wL~s~~k~g~~~dek~yil~ 739 (896)
T KOG2043|consen 671 KNYKLAKKFLGGSVASSD-SEATHFIADRIRRTLKFLEAISSGKPLVTPQWLVSSLKSGEKLDEKPYILH 739 (896)
T ss_pred hhhhhHHhhccceeeccc-ccceeeeehhhhccHHHHhhhccCCcccchHHHHHHhhccccccCcccccc
Confidence 457888999998888774 67999999854433332 39999999999999999999999995
No 72
>PF01909 NTP_transf_2: Nucleotidyltransferase domain A subset of this Pfam family; InterPro: IPR002934 A small region that overlaps with a nuclear localization signal and binds to the RNA primer contains three aspartates that are essential for catalysis. Sequence and secondary structure comparisons of regions surrounding these aspartates with sequences of other polymerases revealed a significant homology to the palm structure of DNA polymerase beta, terminal deoxynucleotidyltransferase and DNA polymerase IV of Saccharomyces cerevisiae, all members of the family X of polymerases. This homology extends as far as cca: tRNA nucleotidyltransferase and streptomycin adenylyltransferase, an antibiotic resistance factor [, ]. Proteins containing this domain include kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTase inactivates antibiotics by catalysing the addition of a nucleotidyl group onto the drug. In experiments, Mn2+ strongly stimulated this reaction due to a 50-fold lower Ki for 8-azido-ATP in the presence of Mn2+. Mutations of the highly conserved Asp residues 113, 115, and 167, critical for metal binding in the catalytic domain of bovine poly(A) polymerase, led to a strong reduction of cross-linking efficiency, and Mn2+ no longer stimulated the reaction. Mutations in the region of the "helical turn motif" (a domain binding the triphosphate moiety of the nucleotide) and in the suspected nucleotide-binding helix of bovine poly(A) polymerase impaired ATP binding and catalysis. The results indicate that ATP is bound in part by the helical turn motif and in part by a region that may be a structural analogue of the fingers domain found in many polymerases.; GO: 0016779 nucleotidyltransferase activity; PDB: 4EBK_B 4EBJ_A 1KNY_A 2B4V_A 2B56_A 2B51_A 1NO5_B 1Q79_A 1Q78_A 1F5A_A ....
Probab=90.77 E-value=0.34 Score=40.30 Aligned_cols=32 Identities=28% Similarity=0.458 Sum_probs=26.5
Q ss_pred CCCeEEEecccccccCCc-cCCeeEEEecCCcc
Q 009742 355 LPEVIILCGGSYRRGKAS-CGDLDVVIMHPDRK 386 (527)
Q Consensus 355 ~p~~~v~~~GsyRRGke~-~gDVDiLIt~~~~~ 386 (527)
.+...+.+.|||.||... .+|||++|..++..
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 69999999877654
No 73
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=90.75 E-value=0.17 Score=32.89 Aligned_cols=18 Identities=50% Similarity=0.648 Sum_probs=15.8
Q ss_pred HHhhccCcCHHHHHHHHH
Q 009742 285 LFGEVWGIGPATAQKLYE 302 (527)
Q Consensus 285 lf~~I~GvGpktA~~ly~ 302 (527)
.|++|+|||+++|+++.+
T Consensus 2 ~L~~i~GiG~k~A~~il~ 19 (26)
T smart00278 2 ELLKVPGIGPKTAEKILE 19 (26)
T ss_pred hhhhCCCCCHHHHHHHHH
Confidence 356999999999999986
No 74
>PF04994 TfoX_C: TfoX C-terminal domain; InterPro: IPR007077 This domain is found in a number of bacterial proteins including the TfoX gene product of Haemophilus influenzae. TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes []. This family corresponds to the C-terminal presumed domain of TfoX. The domain is found in association with the N-terminal domain in some, but not all members of this group, suggesting this is an autonomous and functionally unrelated domain. For example it is found associated with Q9JZR1 from SWISSPROT in IPR002125 from INTERPRO.; PDB: 3BQT_A 3MAB_A.
Probab=90.43 E-value=0.21 Score=41.70 Aligned_cols=30 Identities=27% Similarity=0.480 Sum_probs=23.2
Q ss_pred HhhccCcCHHHHHHHHHhCCCCHHHHhhcc
Q 009742 286 FGEVWGIGPATAQKLYEKGHRTLDDLKNED 315 (527)
Q Consensus 286 f~~I~GvGpktA~~ly~~GirTledL~~~~ 315 (527)
+..+|.+||+..+.|++-||.|++||++-+
T Consensus 5 l~~LpNig~~~e~~L~~vGI~t~~~L~~~G 34 (81)
T PF04994_consen 5 LKDLPNIGPKSERMLAKVGIHTVEDLRELG 34 (81)
T ss_dssp GCGSTT--HHHHHHHHHTT--SHHHHHHHH
T ss_pred hhhCCCCCHHHHHHHHHcCCCCHHHHHHhC
Confidence 457899999999999999999999999754
No 75
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=90.40 E-value=0.12 Score=49.72 Aligned_cols=50 Identities=20% Similarity=0.255 Sum_probs=38.1
Q ss_pred hHHHHHHhhccCcCHHHHHHHHHhCCCCHHHHhh---c---cCcchhhhccccchhhh
Q 009742 280 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDI 331 (527)
Q Consensus 280 ~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~---~---~~L~~~q~~Glk~yed~ 331 (527)
...+++|.+|.|||||+|-.+... -|.++|.. . ..|++.+++|-|..+.+
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 457888899999999999988753 35666653 2 25899999998886643
No 76
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=90.37 E-value=0.14 Score=49.53 Aligned_cols=50 Identities=20% Similarity=0.261 Sum_probs=38.0
Q ss_pred hHHHHHHhhccCcCHHHHHHHHHhCCCCHHHHhh---c---cCcchhhhccccchhhh
Q 009742 280 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDI 331 (527)
Q Consensus 280 ~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~---~---~~L~~~q~~Glk~yed~ 331 (527)
...+++|.+|.|||||+|-.+... -+.++|.+ . ..|++.+++|-|..+.+
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 357888899999999999999753 35555553 2 25899999998886654
No 77
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=90.04 E-value=0.14 Score=50.00 Aligned_cols=50 Identities=28% Similarity=0.308 Sum_probs=38.6
Q ss_pred hHHHHHHhhccCcCHHHHHHHHHhCCCCHHHHhh---c---cCcchhhhccccchhhh
Q 009742 280 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDI 331 (527)
Q Consensus 280 ~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~---~---~~L~~~q~~Glk~yed~ 331 (527)
...+++|.+|.|||||+|-.+... -|.++|.+ . ..|++.+++|-|..+.+
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 347888889999999999999764 35666653 2 25899999999886654
No 78
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=89.86 E-value=0.16 Score=49.83 Aligned_cols=50 Identities=26% Similarity=0.324 Sum_probs=38.2
Q ss_pred hHHHHHHhhccCcCHHHHHHHHHhCCCCHHHHhh---c---cCcchhhhccccchhhh
Q 009742 280 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDI 331 (527)
Q Consensus 280 ~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~---~---~~L~~~q~~Glk~yed~ 331 (527)
...+++|.+|.|||||+|-.+... -+.++|.+ . ..|++.+++|-|..+.+
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 347888889999999999999874 25555553 2 25899999999886654
No 79
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=89.76 E-value=0.15 Score=49.70 Aligned_cols=50 Identities=28% Similarity=0.365 Sum_probs=39.0
Q ss_pred hHHHHHHhhccCcCHHHHHHHHHhCCCCHHHHhhc------cCcchhhhccccchhhh
Q 009742 280 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE------DSLTHSQRLGLKYFDDI 331 (527)
Q Consensus 280 ~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~------~~L~~~q~~Glk~yed~ 331 (527)
...+++|.+|.|||||+|-.+... -|.++|..+ ..|++.+++|-|..+.+
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 347888889999999999999774 366676632 25899999999886654
No 80
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=89.30 E-value=0.29 Score=50.90 Aligned_cols=30 Identities=37% Similarity=0.597 Sum_probs=27.2
Q ss_pred HhhccCcCHHHHHHHHHhCCCCHHHHhhcc
Q 009742 286 FGEVWGIGPATAQKLYEKGHRTLDDLKNED 315 (527)
Q Consensus 286 f~~I~GvGpktA~~ly~~GirTledL~~~~ 315 (527)
+..+||||+++|++|.+.||.|++||....
T Consensus 8 l~~l~gIg~~~a~~L~~~Gi~t~~dl~~~~ 37 (317)
T PRK04301 8 LEDLPGVGPATAEKLREAGYDTVEAIAVAS 37 (317)
T ss_pred HhhcCCCCHHHHHHHHHcCCCCHHHHHcCC
Confidence 458999999999999999999999998653
No 81
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=89.16 E-value=0.18 Score=49.08 Aligned_cols=50 Identities=18% Similarity=0.316 Sum_probs=38.3
Q ss_pred hHHHHHHhhccCcCHHHHHHHHHhCCCCHHHHhhc------cCcchhhhccccchhhh
Q 009742 280 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE------DSLTHSQRLGLKYFDDI 331 (527)
Q Consensus 280 ~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~------~~L~~~q~~Glk~yed~ 331 (527)
...+++|.+|.|||||+|-.+... -|.++|..+ ..|++.+|+|-|..+.+
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 357888889999999999999753 366666632 25899999998886643
No 82
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=89.11 E-value=0.99 Score=46.87 Aligned_cols=95 Identities=18% Similarity=0.317 Sum_probs=62.9
Q ss_pred CCCcHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHH
Q 009742 196 PDLNKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFE 275 (527)
Q Consensus 196 ~~~N~~ia~~L~~la~~~e~~g~~~r~~aY~rAa~~l~~l~~~i~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~ 275 (527)
+.=|+.|++.++.+.+- |.-. +.....+.+|.+ ..+|..+||+|++-..+....+- +..+++|+
T Consensus 59 ~gIGk~ia~~I~e~l~t----G~~~------~le~lk~~~P~g---l~~Ll~v~GlGpkKi~~Ly~elg---i~~~e~l~ 122 (326)
T COG1796 59 PGIGKGIAEKISEYLDT----GEVK------KLEALKKEVPEG---LEPLLKVPGLGPKKIVSLYKELG---IKDLEELQ 122 (326)
T ss_pred CCccHHHHHHHHHHHHc----CccH------HHHHHHHhCCcc---hHHHhhCCCCCcHHHHHHHHHHC---cccHHHHH
Confidence 67789999987766443 2211 444555667766 77899999999943333333332 66677776
Q ss_pred hhchhHHHHHHhhccCcCHHHHHHHHHhCCCCHH
Q 009742 276 KDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLD 309 (527)
Q Consensus 276 ~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTle 309 (527)
.... .-.+.+++|+|.|.+.+|++......+
T Consensus 123 ~a~~---~~~~~~l~GfG~kse~~il~~i~~~~~ 153 (326)
T COG1796 123 EALE---NGKIRGLRGFGKKSEAKILENIEFAEE 153 (326)
T ss_pred HHHH---hCCccccCCccchhHHHHHHHHHHHhh
Confidence 5433 334569999999999999986444333
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=89.00 E-value=1.1 Score=52.07 Aligned_cols=82 Identities=21% Similarity=0.343 Sum_probs=61.9
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHHh-CCCCHHHHhhcc-Ccc-
Q 009742 242 ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED-SLT- 318 (527)
Q Consensus 242 ~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~-GirTledL~~~~-~L~- 318 (527)
.+.|..+||||+..++.|.+-++. .. .-..++..| .-+|++++.|.++|+. |-.+++.|++.. +|.
T Consensus 116 ~~~L~~v~gi~~~~~~~i~~~~~~--------~~--~~~~~~~~L-~~~gi~~~~a~ki~~~yg~~~~~~i~~nPY~L~~ 184 (720)
T TIGR01448 116 PEKLLEVPGISKANLEKFVSQWSQ--------QG--DERRLLAGL-QGLGIGIKLAQRIYKFYQADTLDRVEKDPYLLAE 184 (720)
T ss_pred HHHHhcCCCCCHHHHHHHHHHHHH--------hH--HHHHHHHHH-HHcCCCHHHHHHHHHHHhHHHHHHHHhCchhhhh
Confidence 467889999999999999876632 11 123355555 8999999999999997 999999998764 455
Q ss_pred hhhhccccchhhhccC
Q 009742 319 HSQRLGLKYFDDIKTR 334 (527)
Q Consensus 319 ~~q~~Glk~yed~~~~ 334 (527)
...++|++..+.+...
T Consensus 185 ~i~gigF~~aD~iA~~ 200 (720)
T TIGR01448 185 DVKGIGFLTADQLAQA 200 (720)
T ss_pred hcCCCCHHHHHHHHHH
Confidence 4678888887777543
No 84
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=88.96 E-value=0.18 Score=57.89 Aligned_cols=64 Identities=16% Similarity=0.216 Sum_probs=47.4
Q ss_pred hhccCcCHHHHHHHHHh-CCCCHHHHhhc--cCcchhhhccccchhhhccCcCHHHHHHHHHHHHHH
Q 009742 287 GEVWGIGPATAQKLYEK-GHRTLDDLKNE--DSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKA 350 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~-GirTledL~~~--~~L~~~q~~Glk~yed~~~~i~r~Ea~~i~~iv~~~ 350 (527)
++|.|+|++++.+||+. +++++.||..- ..|..+.+||-+..+.+...|-.+--..+..++..+
T Consensus 465 l~I~GLG~k~i~~L~~~g~V~~~~Dl~~L~~~~L~~l~g~g~Ksa~~Ll~~Ie~sk~~~l~r~l~AL 531 (689)
T PRK14351 465 LDIEGLGEERVQQLVDAGLVESLADLYDLTVADLAELEGWGETSAENLLAELEASREPPLADFLVAL 531 (689)
T ss_pred cCCCCcCHHHHHHHHHcCCCCCHHHHHHcCHHHHhcCcCcchhHHHHHHHHHHHHccCCHHHHHHHc
Confidence 37999999999999999 57999999852 347777889988888887666444323345555443
No 85
>TIGR03671 cca_archaeal CCA-adding enzyme.
Probab=88.86 E-value=1.9 Score=46.62 Aligned_cols=46 Identities=26% Similarity=0.394 Sum_probs=33.7
Q ss_pred HHHHHHHHHHhhhcCCCeEEEecccccccCCcc--CCeeEEEecCCcc
Q 009742 341 EQMERLLQKAGEEVLPEVIILCGGSYRRGKASC--GDLDVVIMHPDRK 386 (527)
Q Consensus 341 ~~i~~iv~~~~~~~~p~~~v~~~GsyRRGke~~--gDVDiLIt~~~~~ 386 (527)
..+...+++.+.+..+.+.+.+.|||.||.-+. +||||+|..+...
T Consensus 24 ~~l~~~l~~~~~e~~~~~~v~~~GS~ArgT~L~G~sDIDIfi~f~~~~ 71 (408)
T TIGR03671 24 DELIARLEEIIEELGVDAEVVLVGSYARGTWLKGDRDIDIFILFPKDT 71 (408)
T ss_pred HHHHHHHHHHHHhcCCcceEEEEeeEecCCccCCCCceeEEEEeCCCC
Confidence 334455555555555668999999999999886 6999999876543
No 86
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=88.85 E-value=0.55 Score=47.38 Aligned_cols=49 Identities=22% Similarity=0.470 Sum_probs=34.8
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHH
Q 009742 245 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 302 (527)
Q Consensus 245 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 302 (527)
+..|||||..+|..+-.- =|+.. .+.+. ....|+.|+|||+++|..+|+
T Consensus 184 l~s~pgig~~~a~~ll~~--fgS~~---~~~ta----s~~eL~~v~gig~k~A~~I~~ 232 (254)
T COG1948 184 LESIPGIGPKLAERLLKK--FGSVE---DVLTA----SEEELMKVKGIGEKKAREIYR 232 (254)
T ss_pred HHcCCCccHHHHHHHHHH--hcCHH---HHhhc----CHHHHHHhcCccHHHHHHHHH
Confidence 689999999999876542 23333 33321 124556999999999999986
No 87
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=88.69 E-value=0.39 Score=43.59 Aligned_cols=53 Identities=23% Similarity=0.293 Sum_probs=38.7
Q ss_pred HHHhhccCcCHHHHHHHHHhCCCCHHHHhhccCcchhhhccccchhhhccCcCHHH
Q 009742 284 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIPRHE 339 (527)
Q Consensus 284 ~lf~~I~GvGpktA~~ly~~GirTledL~~~~~L~~~q~~Glk~yed~~~~i~r~E 339 (527)
.-|+.|-||||+.+..|-++||.|+.+|-.. +..--.-+.-|-.|..||-|+.
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 2222223444555667777764
No 88
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=88.53 E-value=0.31 Score=50.37 Aligned_cols=29 Identities=38% Similarity=0.597 Sum_probs=26.5
Q ss_pred hhccCcCHHHHHHHHHhCCCCHHHHhhcc
Q 009742 287 GEVWGIGPATAQKLYEKGHRTLDDLKNED 315 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~GirTledL~~~~ 315 (527)
..+||||++++++|++.||.|++||....
T Consensus 2 ~~i~gig~~~~~~L~~~Gi~ti~dl~~~~ 30 (310)
T TIGR02236 2 EDLPGVGPATAEKLREAGYDTFEAIAVAS 30 (310)
T ss_pred cccCCCCHHHHHHHHHcCCCCHHHHHcCC
Confidence 47999999999999999999999998653
No 89
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=88.14 E-value=1.3 Score=42.54 Aligned_cols=49 Identities=14% Similarity=0.216 Sum_probs=29.3
Q ss_pred CCCHHHHHHHHHHHH------hCCchhhHHHHhh---chhHHHHHHhhccCcCHHHHHHHH
Q 009742 250 GIGKSMQDHIQEIVT------TGKLSKLEHFEKD---EKVRTISLFGEVWGIGPATAQKLY 301 (527)
Q Consensus 250 gIG~~ia~kI~Eil~------tG~~~~le~l~~~---~~~~~l~lf~~I~GvGpktA~~ly 301 (527)
|+-+.-|+.|.++.+ .|.+ +.+... ....+++.|+++||||||||.-..
T Consensus 75 Gfy~~KAk~Lk~~a~~iie~y~G~v---~~L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL 132 (177)
T TIGR03252 75 RFPGSMAKRVQALAQYVVDTYDGDA---TAVWTEGDPDGKELLRRLKALPGFGKQKAKIFL 132 (177)
T ss_pred CchHHHHHHHHHHHHHHHHHhCCCh---hhhhcccCCCcHHHHHHHHcCCCCCHHHHHHHH
Confidence 454555555555443 3333 333331 123356778899999999999763
No 90
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=87.47 E-value=0.87 Score=48.09 Aligned_cols=70 Identities=21% Similarity=0.337 Sum_probs=45.4
Q ss_pred hHHHHHHHHHHHhcCCccccch--hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHH
Q 009742 221 RSFSYYKAIPVIEKLPFKIESA--DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQ 298 (527)
Q Consensus 221 r~~aY~rAa~~l~~l~~~i~s~--~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~ 298 (527)
|+++|... ...++.+|... -=|.++|+|++.+|+.+-+ ++..+..+.+. ..+.|.+|+|||+++|+
T Consensus 266 ~~lGy~~~---~~~ld~~v~prGyRiLs~IPrl~k~iAk~Ll~-----~FGSL~~Il~A----s~eeL~~VeGIGe~rA~ 333 (352)
T PRK13482 266 RLLGYPGG---SEALDTPVSPRGYRLLSKIPRLPSAVIENLVE-----HFGSLQGLLAA----SIEDLDEVEGIGEVRAR 333 (352)
T ss_pred HHhCCCCC---CcccccccCCcHHHHHhcCCCCCHHHHHHHHH-----HcCCHHHHHcC----CHHHHhhCCCcCHHHHH
Confidence 55555322 23455555543 4589999999999888765 23344444432 24456799999999999
Q ss_pred HHHH
Q 009742 299 KLYE 302 (527)
Q Consensus 299 ~ly~ 302 (527)
.+.+
T Consensus 334 ~I~e 337 (352)
T PRK13482 334 AIRE 337 (352)
T ss_pred HHHH
Confidence 9654
No 91
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=87.34 E-value=0.29 Score=47.33 Aligned_cols=49 Identities=22% Similarity=0.300 Sum_probs=37.3
Q ss_pred hHHHHHHhhccCcCHHHHHHHHHhCCCCHHHHhhc------cCcchhhhccccchhhh
Q 009742 280 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE------DSLTHSQRLGLKYFDDI 331 (527)
Q Consensus 280 ~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~------~~L~~~q~~Glk~yed~ 331 (527)
...+++|.+|.|||||+|-.+... -|.++|..+ ..| +.+++|-|..+.+
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 357888889999999999999764 256666532 258 8999998886654
No 92
>TIGR00588 ogg 8-oxoguanine DNA-glycosylase (ogg). All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is distantly realted to the Nth-MutY superfamily.
Probab=87.30 E-value=1.5 Score=45.74 Aligned_cols=61 Identities=20% Similarity=0.271 Sum_probs=38.8
Q ss_pred hhcCCCCCCHHHHHHHHHH---HHhCCc--hhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHHhCCC
Q 009742 244 QVKGLPGIGKSMQDHIQEI---VTTGKL--SKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHR 306 (527)
Q Consensus 244 ~l~~lpgIG~~ia~kI~Ei---l~tG~~--~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~Gir 306 (527)
+|..+ |+|-+ |+.|.++ +..|.. ..++++..-....+.+.|++++||||+||.-+-=.|+.
T Consensus 177 ~Lr~~-G~g~R-a~~I~~~A~~i~~~~~~~~~l~~l~~~~~~~~~~~L~~l~GIG~~tAd~vll~~l~ 242 (310)
T TIGR00588 177 HLRKL-GLGYR-ARYIRETARALLEEQGGRAWLQQIRGASYEDAREALCELPGVGPKVADCICLMGLD 242 (310)
T ss_pred HHHHc-CCHHH-HHHHHHHHHHHHhccCCchhHHhhccCChHHHHHHHHhCCCccHHHHHHHHHHhCC
Confidence 45554 66755 4444433 334443 34666655444568889999999999999987544444
No 93
>KOG1929 consensus Nucleotide excision repair factor NEF2, RAD4/CUT5 component [Replication, recombination and repair]
Probab=87.13 E-value=0.7 Score=53.75 Aligned_cols=82 Identities=11% Similarity=0.148 Sum_probs=66.9
Q ss_pred CCCCcCCeEEEEeeCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEeCcHHH--HH--hc---cccchHHHHHHhcC
Q 009742 15 SNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEAL--LQ--QS---VIRYQWLEDSLRLG 87 (527)
Q Consensus 15 ~~~~f~~~~i~iv~~~~g~~r~~~l~~~~~~~G~~v~~~~s~~VTHVV~~~~~~~--l~--~~---vv~~~Wl~ec~~~g 87 (527)
.-..|.++++++- .---.+++.|..++...|..+..++....||||+...... .. .| +|.++||.+|.+++
T Consensus 490 l~~~~e~~~~~~s--~~~~~~~e~ln~~~~~~gas~~~~f~r~~~~l~~~~~k~s~~~~~~kw~ip~vT~~wL~e~~rq~ 567 (811)
T KOG1929|consen 490 LSQPFENLTISNS--QSAEAEREKLNNLANDLGASNVKTFTRKSTTLLTTSAKGSKYEIAGKWSIPIVTPDWLYECVRQN 567 (811)
T ss_pred ccccccCceEEee--echHHHHHHHhHhhhhccccccceeeecccEEeccccccchhhhccccCCCccChhHHHhhcccc
Confidence 3356999999984 5556688999999999999999999888899998753221 11 22 99999999999999
Q ss_pred CCcCCcccccc
Q 009742 88 EKVSEDLYRIK 98 (527)
Q Consensus 88 ~~v~~~~~~l~ 98 (527)
+-++.+.|...
T Consensus 568 ~~~~~e~~l~~ 578 (811)
T KOG1929|consen 568 KGERNEGFLNG 578 (811)
T ss_pred Ccccceeeccc
Confidence 99999998875
No 94
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=87.05 E-value=0.79 Score=51.44 Aligned_cols=85 Identities=14% Similarity=0.179 Sum_probs=62.4
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHHhCCCCHHHHhhcc--Ccch
Q 009742 242 ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTH 319 (527)
Q Consensus 242 ~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~ 319 (527)
.+++.+++|+|++.+++|.+-++.-+-..| ...+--| .|++||.++|+. .+.|+++|..+. .|..
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 PEQLANTPGIGKARAEQLWHQFNLARQQPF--------SRWLKAL-GIPLPQAALNAL----DDRSWQQLLSRSEQQWQQ 524 (562)
T ss_pred HHHHhcCcCccHHHHHHHHHHHHHHcCCCH--------HHHHHHc-CCccHHHHHHHH----hcCCHHHHHcCCHHHHhc
Confidence 368999999999999998877664333333 3355566 899999998886 678899998643 5778
Q ss_pred hhhccccchhhhccCcCHHH
Q 009742 320 SQRLGLKYFDDIKTRIPRHE 339 (527)
Q Consensus 320 ~q~~Glk~yed~~~~i~r~E 339 (527)
..++|-...+.+..-+.-.+
T Consensus 525 i~gIG~~~a~si~~~f~~~~ 544 (562)
T PRK08097 525 LPGIGEGRARQLIAFLQHPE 544 (562)
T ss_pred CCCchHHHHHHHHHHHcCHH
Confidence 88888777777666554444
No 95
>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=86.94 E-value=0.29 Score=56.65 Aligned_cols=53 Identities=15% Similarity=0.350 Sum_probs=40.7
Q ss_pred HHHHHHhh--ccCcCHHHHHHHHHh-CCCCHHHHhhcc-Ccchhhhccccchhhhcc
Q 009742 281 RTISLFGE--VWGIGPATAQKLYEK-GHRTLDDLKNED-SLTHSQRLGLKYFDDIKT 333 (527)
Q Consensus 281 ~~l~lf~~--I~GvGpktA~~ly~~-GirTledL~~~~-~L~~~q~~Glk~yed~~~ 333 (527)
.++..|.+ ++||||+||+++++. |.++++-|.++. +|...+++|.+..+.|..
T Consensus 79 ~i~~yL~s~~~~GIG~~~A~~iv~~fg~~~~~~i~~~~~~L~~v~gi~~~~~~~i~~ 135 (720)
T TIGR01448 79 GIVAYLSSRSIKGVGKKLAQRIVKTFGEAAFDVLDDDPEKLLEVPGISKANLEKFVS 135 (720)
T ss_pred HHHHHHhcCCCCCcCHHHHHHHHHHhCHhHHHHHHhCHHHHhcCCCCCHHHHHHHHH
Confidence 44555543 999999999999998 999999998754 577777777666666554
No 96
>PRK01172 ski2-like helicase; Provisional
Probab=86.55 E-value=1.1 Score=51.50 Aligned_cols=40 Identities=25% Similarity=0.484 Sum_probs=33.3
Q ss_pred HHhhchhHHHHHHhhccCcCHHHHHHHHHhCCCCHHHHhhc
Q 009742 274 FEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 314 (527)
Q Consensus 274 l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~ 314 (527)
+..-.+...+.|+ +|||+|...|+++|+.|++|+.||...
T Consensus 603 l~~gv~~~~~~L~-~ip~~~~~~a~~l~~~g~~~~~di~~~ 642 (674)
T PRK01172 603 IKEGIREDLIDLV-LIPKVGRVRARRLYDAGFKTVDDIARS 642 (674)
T ss_pred HHcCCCHHHHhhc-CCCCCCHHHHHHHHHcCCCCHHHHHhC
Confidence 3344555567777 899999999999999999999999864
No 97
>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=86.27 E-value=1.1 Score=38.56 Aligned_cols=47 Identities=11% Similarity=0.254 Sum_probs=37.6
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCc
Q 009742 242 ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGI 292 (527)
Q Consensus 242 ~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~Gv 292 (527)
+.+|..||+||+++++-...| -+..+++|+...|....+-++.+-|.
T Consensus 11 ~~~L~~iP~IG~a~a~DL~~L----Gi~s~~~L~g~dP~~Ly~~lc~~~G~ 57 (93)
T PF11731_consen 11 LSDLTDIPNIGKATAEDLRLL----GIRSPADLKGRDPEELYERLCALTGQ 57 (93)
T ss_pred HHHHhcCCCccHHHHHHHHHc----CCCCHHHHhCCCHHHHHHHHHHHcCC
Confidence 578999999999999987754 45778888888888877777766664
No 98
>PRK03352 DNA polymerase IV; Validated
Probab=86.18 E-value=0.54 Score=49.36 Aligned_cols=28 Identities=39% Similarity=0.769 Sum_probs=25.9
Q ss_pred hhccCcCHHHHHHHHHhCCCCHHHHhhc
Q 009742 287 GEVWGIGPATAQKLYEKGHRTLDDLKNE 314 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~GirTledL~~~ 314 (527)
..+||||++++++|.+.||+|+.||.+-
T Consensus 180 ~~l~gig~~~~~~L~~~Gi~ti~dl~~l 207 (346)
T PRK03352 180 DALWGVGPKTAKRLAALGITTVADLAAA 207 (346)
T ss_pred HHcCCCCHHHHHHHHHcCCccHHHHhcC
Confidence 5789999999999999999999999864
No 99
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=85.94 E-value=0.52 Score=33.28 Aligned_cols=16 Identities=56% Similarity=0.742 Sum_probs=14.2
Q ss_pred hccCcCHHHHHHHHHh
Q 009742 288 EVWGIGPATAQKLYEK 303 (527)
Q Consensus 288 ~I~GvGpktA~~ly~~ 303 (527)
.|+|||+|||.+|.++
T Consensus 20 Gv~giG~ktA~~ll~~ 35 (36)
T smart00279 20 GVKGIGPKTALKLLRE 35 (36)
T ss_pred CCCcccHHHHHHHHHh
Confidence 7999999999999753
No 100
>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=85.59 E-value=0.72 Score=37.82 Aligned_cols=27 Identities=41% Similarity=0.546 Sum_probs=22.3
Q ss_pred hhccCcCHHHHHHHHHhCCCCHHHHhhc
Q 009742 287 GEVWGIGPATAQKLYEKGHRTLDDLKNE 314 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~GirTledL~~~ 314 (527)
..|+|||||||.+|..+ +.|++.+...
T Consensus 25 ~gv~giG~k~A~~ll~~-~~~~~~~~~~ 51 (75)
T cd00080 25 PGVPGIGPKTALKLLKE-YGSLENLLEN 51 (75)
T ss_pred CCCCcccHHHHHHHHHH-hCCHHHHHHH
Confidence 47999999999999976 5588888753
No 101
>cd05400 NT_2-5OAS_ClassI-CCAase Nucleotidyltransferase (NT) domain of 2'5'-oligoadenylate (2-5A)synthetase (2-5OAS) and class I CCA-adding enzyme. In vertebrates, 2-5OASs are induced by interferon during the innate immune response to protect against RNA virus infections. In the presence of an RNA activator, 2-5OASs catalyze the oligomerization of ATP into 2-5A. 2-5A activates endoribonuclease L, which leads to degradation of the viral RNA. 2-5OASs are also implicated in cell growth control, differentiation, and apoptosis. This family includes human OAS1, -2, -3, and OASL. CCA-adding enzymes add the sequence [cytidine(C)-cytidine-adenosine (A)], one nucleotide at a time, onto the 3' end of tRNA, in a template-independent reaction. This class I group includes the archaeal Sulfolobus shibatae and Archeoglobus fulgidus CCA-adding enzymes. It belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more dis
Probab=85.55 E-value=3.4 Score=37.41 Aligned_cols=46 Identities=33% Similarity=0.509 Sum_probs=32.2
Q ss_pred CeEEEecccccccCCcc--CCeeEEEecCCcc-----hhhhhHHHHHHHHHHc
Q 009742 357 EVIILCGGSYRRGKASC--GDLDVVIMHPDRK-----SHKGFLSKYVKKLKEM 402 (527)
Q Consensus 357 ~~~v~~~GsyRRGke~~--gDVDiLIt~~~~~-----~~~~~l~~lv~~L~~~ 402 (527)
...+.+.|||.||...- .|||++|..+... ....++..+.+.|.+.
T Consensus 27 ~~~~~~~GS~a~~T~i~~~sDiD~~v~~~~~~~~~~~~~~~~~~~l~~~L~~~ 79 (143)
T cd05400 27 VAEVFLQGSYARGTALRGDSDIDLVVVLPDDTSFAEYGPAELLDELGEALKEY 79 (143)
T ss_pred ccEEEEEcceeCCCCCCCCCceeEEEEEcCcccccccCHHHHHHHHHHHHHHh
Confidence 35788999999998754 8999999655432 2345666666666554
No 102
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=85.44 E-value=1.5 Score=50.28 Aligned_cols=61 Identities=15% Similarity=0.217 Sum_probs=40.2
Q ss_pred cccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhh--chhHHHHHHhhccCcCHHHHHHHHH
Q 009742 238 KIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKD--EKVRTISLFGEVWGIGPATAQKLYE 302 (527)
Q Consensus 238 ~i~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~--~~~~~l~lf~~I~GvGpktA~~ly~ 302 (527)
++...=-..+||+||.+.|+.|.. ..+..++++.+. .+....+.|++|+|||+++|..+++
T Consensus 497 ~l~r~l~ALGI~~vG~~~ak~La~----~~f~~~~~l~~~~~~~~~~~e~l~~i~giG~~~a~si~~ 559 (669)
T PRK14350 497 PFSKLLLSMGIKDLGENTILLLIN----NNLNSFDKISTLCQDREFALSKLLKIKGIGEKIALNIIE 559 (669)
T ss_pred CHHHHHHHcCCCchhHHHHHHHHH----HhhCCHHHHHhhhhccCCCHHHHhhCCCccHHHHHHHHH
Confidence 444444567899999999998773 122223444321 0112455677999999999999986
No 103
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]
Probab=85.22 E-value=1.7 Score=49.98 Aligned_cols=80 Identities=21% Similarity=0.312 Sum_probs=55.1
Q ss_pred CCcCCeEEEEeeCCCChhHHHHHHHHHHhcCCEEEeecC------CCccEEEEe--CcH---HHHH--------hccccc
Q 009742 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLS------KKVTHVLAM--DLE---ALLQ--------QSVIRY 77 (527)
Q Consensus 17 ~~f~~~~i~iv~~~~g~~r~~~l~~~~~~~G~~v~~~~s------~~VTHVV~~--~~~---~~l~--------~~vv~~ 77 (527)
-.|..+++|.+.++.=.+-..+..=.+...|+++...-+ ..+||+|+. +.. -++. ..||..
T Consensus 783 ~~~~~~~~f~~~~~~~~se~~~~~l~~k~~g~~i~~~~~~~~~~~~~~t~~v~~~i~~~h~~~~~~~~~~lt~~rkv~~~ 862 (881)
T KOG0966|consen 783 LFLSSLRMFYVLRRKLSSEEVIIELKLKNFGGRITDAQSECNNIGAKYTHCVLRCIDEDHEKIKEQKKASLTIKRKVVAP 862 (881)
T ss_pred cccccceeeecccccccHHHHHHHHHHHHhcceeeeccchhhhcccceeeeeeeecchHHHHHHHHHHHHhcccccccCH
Confidence 345666777776666666444444445555999997654 368999976 222 1222 139999
Q ss_pred hHHHHHHhcCCCcCCcccc
Q 009742 78 QWLEDSLRLGEKVSEDLYR 96 (527)
Q Consensus 78 ~Wl~ec~~~g~~v~~~~~~ 96 (527)
+|+.+|+.++.++|++.|.
T Consensus 863 ~wv~~s~~~~~~~~e~~~~ 881 (881)
T KOG0966|consen 863 SWVDHSINENCLLPEEDFP 881 (881)
T ss_pred HHHHHhhcccccCccccCC
Confidence 9999999999999998873
No 104
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=84.92 E-value=2.2 Score=48.23 Aligned_cols=66 Identities=17% Similarity=0.181 Sum_probs=45.4
Q ss_pred hHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHH
Q 009742 221 RSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKL 300 (527)
Q Consensus 221 r~~aY~rAa~~l~~l~~~i~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l 300 (527)
.+..|.|-.+. ..+ ..|.+|||||++...++-+ ++..++.+++ -+++.+.+|+|++.+.|+.+
T Consensus 500 FAit~hRk~R~------k~~--s~L~~I~GiG~kr~~~LL~-----~Fgs~~~I~~----As~eeL~~v~gi~~~~A~~I 562 (574)
T PRK14670 500 KANGFNKKLRE------NIK--LNYTKIKGIGEKKAKKILK-----SLGTYKDILL----LNEDEIAEKMKINIKMAKKI 562 (574)
T ss_pred HHHHHHHHhhc------ccc--cccccCCCCCHHHHHHHHH-----HhCCHHHHHh----CCHHHHHhCCCCCHHHHHHH
Confidence 35566655432 333 3789999999998877654 2444555543 24667789999999999999
Q ss_pred HHh
Q 009742 301 YEK 303 (527)
Q Consensus 301 y~~ 303 (527)
|+.
T Consensus 563 ~~~ 565 (574)
T PRK14670 563 KKF 565 (574)
T ss_pred HHH
Confidence 863
No 105
>PRK03858 DNA polymerase IV; Validated
Probab=84.80 E-value=0.68 Score=49.53 Aligned_cols=28 Identities=39% Similarity=0.749 Sum_probs=25.6
Q ss_pred hhccCcCHHHHHHHHHhCCCCHHHHhhc
Q 009742 287 GEVWGIGPATAQKLYEKGHRTLDDLKNE 314 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~GirTledL~~~ 314 (527)
..+||||++++++|.+.||+|+.||.+-
T Consensus 176 ~~l~Gig~~~~~~L~~~Gi~t~~dl~~l 203 (396)
T PRK03858 176 RRLWGVGPVTAAKLRAHGITTVGDVAEL 203 (396)
T ss_pred hhcCCCCHHHHHHHHHhCCCcHHHHhcC
Confidence 5789999999999999999999999853
No 106
>PRK01216 DNA polymerase IV; Validated
Probab=84.13 E-value=0.72 Score=48.88 Aligned_cols=29 Identities=34% Similarity=0.409 Sum_probs=26.2
Q ss_pred hhccCcCHHHHHHHHHhCCCCHHHHhhcc
Q 009742 287 GEVWGIGPATAQKLYEKGHRTLDDLKNED 315 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~GirTledL~~~~ 315 (527)
..+||||++++++|.+.||+|+.||.+-.
T Consensus 181 ~~l~giG~~~~~~L~~~Gi~TigdL~~~~ 209 (351)
T PRK01216 181 ADIPGIGDITAEKLKKLGVNKLVDTLRIE 209 (351)
T ss_pred ccccCCCHHHHHHHHHcCCCcHHHHhcCC
Confidence 57899999999999999999999998643
No 107
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=83.80 E-value=0.76 Score=49.74 Aligned_cols=28 Identities=39% Similarity=0.672 Sum_probs=26.0
Q ss_pred hhccCcCHHHHHHHHHhCCCCHHHHhhc
Q 009742 287 GEVWGIGPATAQKLYEKGHRTLDDLKNE 314 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~GirTledL~~~ 314 (527)
..+||||++++++|.+.||+|+.||.+.
T Consensus 182 ~~l~GiG~~~~~~L~~lGi~TigdL~~~ 209 (422)
T PRK03609 182 EEVWGVGRRISKKLNAMGIKTALDLADT 209 (422)
T ss_pred hhcCCccHHHHHHHHHcCCCcHHHHhcC
Confidence 5899999999999999999999999854
No 108
>COG1708 Predicted nucleotidyltransferases [General function prediction only]
Probab=83.10 E-value=5.2 Score=34.66 Aligned_cols=29 Identities=31% Similarity=0.568 Sum_probs=24.1
Q ss_pred CCeEEEecccccccCCcc-CCeeEEEecCC
Q 009742 356 PEVIILCGGSYRRGKASC-GDLDVVIMHPD 384 (527)
Q Consensus 356 p~~~v~~~GsyRRGke~~-gDVDiLIt~~~ 384 (527)
....|.+-|||-||..+- +|||++|..++
T Consensus 25 ~~~~v~LfGS~arG~~~~~SDiDv~vv~~~ 54 (128)
T COG1708 25 GDLLIYLFGSYARGDFVKESDIDLLVVSDD 54 (128)
T ss_pred CCeEEEEEccCcccccccCCCeeEEEEcCC
Confidence 345788999999999876 99999998644
No 109
>cd00424 PolY Y-family of DNA polymerases. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Most TLS polymerases are members of the Y-family, including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is found exclusively in bacteria. In eukaryotes, the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in ord
Probab=82.61 E-value=3.3 Score=43.42 Aligned_cols=28 Identities=32% Similarity=0.462 Sum_probs=25.6
Q ss_pred hhccCcCHHHHHHHHHhCCCCHHHHhhc
Q 009742 287 GEVWGIGPATAQKLYEKGHRTLDDLKNE 314 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~GirTledL~~~ 314 (527)
..+||||++++++|.+.||+|+.||.+-
T Consensus 176 ~~l~giG~~~~~~L~~~Gi~ti~dl~~~ 203 (343)
T cd00424 176 TDLPGIGAVTAKRLEAVGINPIGDLLAA 203 (343)
T ss_pred hhcCCCCHHHHHHHHHcCCCcHHHHhcC
Confidence 4689999999999999999999999864
No 110
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=82.56 E-value=1.5 Score=43.67 Aligned_cols=50 Identities=22% Similarity=0.424 Sum_probs=37.3
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHH
Q 009742 244 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 302 (527)
Q Consensus 244 ~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 302 (527)
-|..||||+|.=|..+- +++.-|+++.+ .....|.+|+|+||.+|++||+
T Consensus 196 ~Lt~i~~VnKtda~~LL-----~~FgsLq~~~~----AS~~ele~~~G~G~~kak~l~~ 245 (254)
T KOG2841|consen 196 FLTTIPGVNKTDAQLLL-----QKFGSLQQISN----ASEGELEQCPGLGPAKAKRLHK 245 (254)
T ss_pred HHHhCCCCCcccHHHHH-----HhcccHHHHHh----cCHhHHHhCcCcCHHHHHHHHH
Confidence 47899999998776543 24555666543 2456677999999999999996
No 111
>PRK08609 hypothetical protein; Provisional
Probab=81.92 E-value=1.8 Score=48.87 Aligned_cols=54 Identities=17% Similarity=0.199 Sum_probs=38.3
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHH
Q 009742 241 SADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKL 300 (527)
Q Consensus 241 s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l 300 (527)
.+.++.+|||||++.+.++.+-+---++++|+.... .+ + +..++|+|+||++.+
T Consensus 86 ~~~~l~~i~GiGpk~a~~l~~~lGi~tl~~L~~a~~---~~--~-~~~~~gfg~k~~~~i 139 (570)
T PRK08609 86 GLLPLLKLPGLGGKKIAKLYKELGVVDKESLKEACE---NG--K-VQALAGFGKKTEEKI 139 (570)
T ss_pred HHHHHhcCCCCCHHHHHHHHHHhCCCCHHHHHHHHH---hC--C-hhhccCcchhHHHHH
Confidence 356789999999999998886555445555544322 11 1 247899999999888
No 112
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=81.91 E-value=1.2 Score=28.78 Aligned_cols=20 Identities=30% Similarity=0.573 Sum_probs=17.2
Q ss_pred hhcCCCCCCHHHHHHHHHHH
Q 009742 244 QVKGLPGIGKSMQDHIQEIV 263 (527)
Q Consensus 244 ~l~~lpgIG~~ia~kI~Eil 263 (527)
+|.+|||||+++|+.|.+..
T Consensus 2 ~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred hhhhCCCCCHHHHHHHHHhc
Confidence 67899999999999988643
No 113
>cd01703 PolY_Pol_iota DNA Polymerase iota. Pol iota, also called Rad30B, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol iota is thought to be one of the least efficient polymerases, particularly when opposite pyrimidines; it can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine, and prefers to insert guanosine instead of adenosine opposite thymidine. Pol iota is believed to use Hoogsteen rather than Watson-Crick base pairing, which may explain the varying efficiency for different template nucleotides.
Probab=81.73 E-value=0.98 Score=48.39 Aligned_cols=30 Identities=33% Similarity=0.431 Sum_probs=26.7
Q ss_pred HhhccCcCHHHHHHHHHhCCCCHHHHhhcc
Q 009742 286 FGEVWGIGPATAQKLYEKGHRTLDDLKNED 315 (527)
Q Consensus 286 f~~I~GvGpktA~~ly~~GirTledL~~~~ 315 (527)
+..+||||++|+++|.+.||.|+.||.+..
T Consensus 174 v~~l~GiG~~~~~kL~~~GI~tigdl~~~~ 203 (379)
T cd01703 174 LRKIPGIGYKTAAKLEAHGISSVRDLQEFS 203 (379)
T ss_pred ccccCCcCHHHHHHHHHcCCCcHHHHHhCC
Confidence 358899999999999999999999998543
No 114
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=81.69 E-value=1 Score=43.60 Aligned_cols=20 Identities=35% Similarity=0.674 Sum_probs=18.4
Q ss_pred HHHHHHhhccCcCHHHHHHH
Q 009742 281 RTISLFGEVWGIGPATAQKL 300 (527)
Q Consensus 281 ~~l~lf~~I~GvGpktA~~l 300 (527)
+.++.|.++||||||+|++|
T Consensus 9 ~LI~~l~kLPGvG~KsA~R~ 28 (198)
T COG0353 9 KLIDALKKLPGVGPKSAQRL 28 (198)
T ss_pred HHHHHHhhCCCCChhHHHHH
Confidence 47888999999999999999
No 115
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=81.69 E-value=2.6 Score=48.01 Aligned_cols=135 Identities=18% Similarity=0.247 Sum_probs=86.9
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHHhCCCCHHHHhhcc--Ccchh
Q 009742 243 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHS 320 (527)
Q Consensus 243 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~ 320 (527)
+++..|+++|++.+++|-.-++.-+-..+++ .+--| .|+.||.++|+.|-+ .+.|++.|..+. .|..+
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 7899999999999998876665443333332 34445 999999999999988 999999999764 47778
Q ss_pred hhccccchhhhccCcCHHHHHHH-HHHHHHHhh-----------hcCCCeEEEeccccc-------------ccCCc---
Q 009742 321 QRLGLKYFDDIKTRIPRHEVEQM-ERLLQKAGE-----------EVLPEVIILCGGSYR-------------RGKAS--- 372 (527)
Q Consensus 321 q~~Glk~yed~~~~i~r~Ea~~i-~~iv~~~~~-----------~~~p~~~v~~~GsyR-------------RGke~--- 372 (527)
.++|-.-...+..-..-++..++ ..+...-.. ..+.|-.+++||++- .|-..
T Consensus 549 ~giG~~vA~si~~ff~~~~~~~li~~L~~~g~~~~~~~~~~~~~~~l~gkt~V~TGtL~~~sR~eak~~le~lGakv~~S 628 (667)
T COG0272 549 PGIGEVVARSIIEFFANEENRELIDELLAAGVKWEEEEKISIETSPLAGKTFVLTGTLEGMSRDEAKALLEALGAKVSGS 628 (667)
T ss_pred cchhHHHHHHHHHHHcCHHHHHHHHHHHHcCCCccccccccccccccCCCEEEEeccCCCCCHHHHHHHHHHcCCEEece
Confidence 88885555554433332222221 111111000 123445677888875 33333
Q ss_pred -cCCeeEEEecCCcch
Q 009742 373 -CGDLDVVIMHPDRKS 387 (527)
Q Consensus 373 -~gDVDiLIt~~~~~~ 387 (527)
+.-.|+||+-++.++
T Consensus 629 VSkktD~vvaG~~aGS 644 (667)
T COG0272 629 VSKKTDYVVAGENAGS 644 (667)
T ss_pred ecccccEEEEcCCCCh
Confidence 445599999888775
No 116
>PRK01810 DNA polymerase IV; Validated
Probab=81.59 E-value=1.1 Score=48.26 Aligned_cols=28 Identities=46% Similarity=0.715 Sum_probs=25.5
Q ss_pred hhccCcCHHHHHHHHHhCCCCHHHHhhc
Q 009742 287 GEVWGIGPATAQKLYEKGHRTLDDLKNE 314 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~GirTledL~~~ 314 (527)
..+||||++++++|...||+|+.||.+.
T Consensus 182 ~~l~giG~~~~~~L~~~Gi~tigdL~~~ 209 (407)
T PRK01810 182 GEMHGIGEKTAEKLKDIGIQTIGDLAKA 209 (407)
T ss_pred hhcCCcCHHHHHHHHHcCCCcHHHHHhC
Confidence 4789999999999999999999999853
No 117
>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=81.51 E-value=1.1 Score=48.40 Aligned_cols=29 Identities=28% Similarity=0.338 Sum_probs=26.5
Q ss_pred hhccCcCHHHHHHHHHhCCCCHHHHhhcc
Q 009742 287 GEVWGIGPATAQKLYEKGHRTLDDLKNED 315 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~GirTledL~~~~ 315 (527)
..|||||++++++|-+.||+|+.||.+..
T Consensus 225 ~~l~GIG~~~~~~L~~~Gi~t~~dl~~~~ 253 (404)
T cd01701 225 GDLPGVGSSLAEKLVKLFGDTCGGLELRS 253 (404)
T ss_pred hHhCCCCHHHHHHHHHcCCcchHHHHhCc
Confidence 57899999999999999999999998643
No 118
>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=81.19 E-value=1.1 Score=47.02 Aligned_cols=28 Identities=50% Similarity=0.819 Sum_probs=25.6
Q ss_pred hhccCcCHHHHHHHHHhCCCCHHHHhhc
Q 009742 287 GEVWGIGPATAQKLYEKGHRTLDDLKNE 314 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~GirTledL~~~ 314 (527)
..+||||++++++|.+.||+|+.||.+-
T Consensus 179 ~~l~gig~~~~~~L~~~Gi~ti~dL~~~ 206 (344)
T cd01700 179 GDVWGIGRRTAKKLNAMGIHTAGDLAQA 206 (344)
T ss_pred hhcCccCHHHHHHHHHcCCCcHHHHhcC
Confidence 5789999999999999999999999863
No 119
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=81.07 E-value=4.4 Score=37.02 Aligned_cols=26 Identities=15% Similarity=0.089 Sum_probs=20.1
Q ss_pred HHHHHHhhccCcCHHHHHHHHHhCCC
Q 009742 281 RTISLFGEVWGIGPATAQKLYEKGHR 306 (527)
Q Consensus 281 ~~l~lf~~I~GvGpktA~~ly~~Gir 306 (527)
..++.|++++||||+||..+--.++.
T Consensus 69 ~~~~~L~~l~GIG~~tA~~~l~~~~~ 94 (149)
T smart00478 69 DDREELLKLPGVGRKTANAVLSFALG 94 (149)
T ss_pred HHHHHHHcCCCCcHHHHHHHHHHHCC
Confidence 35666779999999999988665543
No 120
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=80.89 E-value=2.6 Score=35.93 Aligned_cols=54 Identities=28% Similarity=0.553 Sum_probs=41.2
Q ss_pred HHHHHHhhccCcCHHHHHHHHHh-CCCCHHHHhhcc-Ccch-hhhccccchhhhccCc
Q 009742 281 RTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED-SLTH-SQRLGLKYFDDIKTRI 335 (527)
Q Consensus 281 ~~l~lf~~I~GvGpktA~~ly~~-GirTledL~~~~-~L~~-~q~~Glk~yed~~~~i 335 (527)
.++..| .-+|++++.|.++|+. |-.+++-|+++. .|.. ..++|++..+.+..++
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 355566 8899999999999998 999998888764 5555 8899999999987665
No 121
>PRK03348 DNA polymerase IV; Provisional
Probab=80.86 E-value=1.1 Score=49.28 Aligned_cols=28 Identities=43% Similarity=0.752 Sum_probs=25.7
Q ss_pred hhccCcCHHHHHHHHHhCCCCHHHHhhc
Q 009742 287 GEVWGIGPATAQKLYEKGHRTLDDLKNE 314 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~GirTledL~~~ 314 (527)
..+||||++++++|.+.||+|+.||.+-
T Consensus 183 ~~L~GIG~~t~~~L~~lGI~TigDLa~l 210 (454)
T PRK03348 183 RRLWGIGPVTEEKLHRLGIETIGDLAAL 210 (454)
T ss_pred cccCCCCHHHHHHHHHcCCccHHHHhcC
Confidence 5889999999999999999999999853
No 122
>PRK02406 DNA polymerase IV; Validated
Probab=80.84 E-value=1.1 Score=46.97 Aligned_cols=28 Identities=36% Similarity=0.423 Sum_probs=25.8
Q ss_pred hhccCcCHHHHHHHHHhCCCCHHHHhhc
Q 009742 287 GEVWGIGPATAQKLYEKGHRTLDDLKNE 314 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~GirTledL~~~ 314 (527)
..+||||++++++|-+.||+|+.||.+-
T Consensus 171 ~~l~giG~~~~~~L~~~Gi~ti~dl~~l 198 (343)
T PRK02406 171 EKIPGVGKVTAEKLHALGIYTCADLQKY 198 (343)
T ss_pred chhcCCCHHHHHHHHHcCCCcHHHHHhC
Confidence 5789999999999998999999999864
No 123
>PRK10880 adenine DNA glycosylase; Provisional
Probab=80.66 E-value=6.7 Score=41.65 Aligned_cols=65 Identities=18% Similarity=0.280 Sum_probs=42.5
Q ss_pred hHHHHHHHHHHHh-cCCccc-cchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCc
Q 009742 221 RSFSYYKAIPVIE-KLPFKI-ESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGI 292 (527)
Q Consensus 221 r~~aY~rAa~~l~-~l~~~i-~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~Gv 292 (527)
|++...+||..|. .....+ .+.++|..|||||..+|+.|.-|.-.-...-+ ...+.+.+.+++|+
T Consensus 85 RAr~L~~~A~~i~~~~~g~~p~~~~~L~~LpGIG~~TA~aIl~~af~~~~~iV-------D~nV~RV~~Rl~~i 151 (350)
T PRK10880 85 RARNLHKAAQQVATLHGGEFPETFEEVAALPGVGRSTAGAILSLSLGKHFPIL-------DGNVKRVLARCYAV 151 (350)
T ss_pred HHHHHHHHHHHHHHHhCCCchhhHHHHhcCCCccHHHHHHHHHHHCCCCeecc-------cHHHHHHHHHHhcc
Confidence 7888888888883 332222 45689999999999999999876642211111 23356666666554
No 124
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=80.65 E-value=3.3 Score=42.63 Aligned_cols=63 Identities=19% Similarity=0.220 Sum_probs=38.0
Q ss_pred hhhcCCCCCCHHHHHHHH---HHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHHhCCCCHH
Q 009742 243 DQVKGLPGIGKSMQDHIQ---EIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLD 309 (527)
Q Consensus 243 ~~l~~lpgIG~~ia~kI~---Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTle 309 (527)
++|..+ |++..=++-|. +.+..|.+..- ... ....+++.|++|+||||+||..+--.|+.-.|
T Consensus 167 ~eL~~~-Gl~~~Ra~~L~~lA~~i~~g~l~l~-~~~--~~~~~~~~L~~LpGIGpwTA~~vllr~lg~~D 232 (283)
T PRK10308 167 QALKAL-GMPLKRAEALIHLANAALEGTLPLT-IPG--DVEQAMKTLQTFPGIGRWTANYFALRGWQAKD 232 (283)
T ss_pred HHHHHC-CCCHHHHHHHHHHHHHHHcCCCCcc-ccC--CHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCC
Confidence 456555 77754333333 34446776532 111 12347788889999999999987544554433
No 125
>smart00475 53EXOc 5'-3' exonuclease.
Probab=80.51 E-value=1.3 Score=45.05 Aligned_cols=26 Identities=38% Similarity=0.592 Sum_probs=22.3
Q ss_pred hhccCcCHHHHHHHHHh-CCCCHHHHhhc
Q 009742 287 GEVWGIGPATAQKLYEK-GHRTLDDLKNE 314 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~-GirTledL~~~ 314 (527)
-.|+|||||||.+|.++ | |++.+.+.
T Consensus 189 pGV~GIG~KtA~~Ll~~yg--sle~i~~~ 215 (259)
T smart00475 189 PGVPGIGEKTAAKLLKEFG--SLENILEN 215 (259)
T ss_pred CCCCCCCHHHHHHHHHHhC--CHHHHHHH
Confidence 46899999999999987 7 99998853
No 126
>PRK00227 glnD PII uridylyl-transferase; Provisional
Probab=80.39 E-value=4.7 Score=46.63 Aligned_cols=65 Identities=22% Similarity=0.311 Sum_probs=43.0
Q ss_pred HHHHHH-HHHHHHHHhhhcCCCeEEEecccccccC-CccCCeeEEEecCCcchhhhhHHHHHHHHHHcCc
Q 009742 337 RHEVEQ-MERLLQKAGEEVLPEVIILCGGSYRRGK-ASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKF 404 (527)
Q Consensus 337 r~Ea~~-i~~iv~~~~~~~~p~~~v~~~GsyRRGk-e~~gDVDiLIt~~~~~~~~~~l~~lv~~L~~~g~ 404 (527)
|++|.+ ...+++.+. +.+++.+..+|||=||. .--+|||+||-|++.. ...++..++.-|=+.|+
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 445544 355555543 23566788899996665 4568999999998543 25666777776766665
No 127
>PRK09482 flap endonuclease-like protein; Provisional
Probab=80.03 E-value=1.3 Score=44.85 Aligned_cols=26 Identities=31% Similarity=0.569 Sum_probs=22.5
Q ss_pred hhccCcCHHHHHHHHHh-CCCCHHHHhhc
Q 009742 287 GEVWGIGPATAQKLYEK-GHRTLDDLKNE 314 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~-GirTledL~~~ 314 (527)
-.|+|||||||.+|.++ | |++.+.+.
T Consensus 185 pGVpGIG~KtA~~LL~~~g--sle~i~~~ 211 (256)
T PRK09482 185 PGVAGIGPKSAAELLNQFR--SLENIYES 211 (256)
T ss_pred CCCCCcChHHHHHHHHHhC--CHHHHHHh
Confidence 46899999999999987 7 99998853
No 128
>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=79.93 E-value=0.14 Score=44.58 Aligned_cols=24 Identities=46% Similarity=0.753 Sum_probs=19.3
Q ss_pred hccCcCHHHHHHHHHh-CCCCHHHHhh
Q 009742 288 EVWGIGPATAQKLYEK-GHRTLDDLKN 313 (527)
Q Consensus 288 ~I~GvGpktA~~ly~~-GirTledL~~ 313 (527)
.|+|||||||.+|.++ | |||.+..
T Consensus 22 GV~GIG~KtA~~LL~~yg--sle~i~~ 46 (101)
T PF01367_consen 22 GVPGIGPKTAAKLLQEYG--SLENILA 46 (101)
T ss_dssp --TTSTCHCCCCCHHHHT--SCHCCCC
T ss_pred CCCCCCHHHHHHHHHHcC--CHHHHHH
Confidence 7999999999999987 6 7887774
No 129
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=79.85 E-value=4 Score=46.10 Aligned_cols=67 Identities=22% Similarity=0.324 Sum_probs=45.0
Q ss_pred hHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHH
Q 009742 221 RSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKL 300 (527)
Q Consensus 221 r~~aY~rAa~~l~~l~~~i~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l 300 (527)
.+.+|.|-.+.=. .--..|.+|||||++.+.++-. ++.-++.+++ -+++.+.+| |||+++|+.+
T Consensus 498 FAi~~hR~~r~k~------~~~S~Ld~I~GiG~kr~~~Ll~-----~Fgs~~~ik~----As~eeL~~v-gi~~~~A~~I 561 (567)
T PRK14667 498 FALSYNRKLREKE------GLKDILDKIKGIGEVKKEIIYR-----NFKTLYDFLK----ADDEELKKL-GIPPSVKQEV 561 (567)
T ss_pred HHHHHHHHHhhcc------cccCccccCCCCCHHHHHHHHH-----HhCCHHHHHh----CCHHHHHHc-CCCHHHHHHH
Confidence 3556666543322 2225688999999998887654 2344555543 246667799 9999999999
Q ss_pred HHh
Q 009742 301 YEK 303 (527)
Q Consensus 301 y~~ 303 (527)
|+.
T Consensus 562 ~~~ 564 (567)
T PRK14667 562 KKY 564 (567)
T ss_pred HHH
Confidence 873
No 130
>PRK03103 DNA polymerase IV; Reviewed
Probab=79.65 E-value=1.4 Score=47.45 Aligned_cols=28 Identities=29% Similarity=0.561 Sum_probs=25.4
Q ss_pred hhccCcCHHHHHHHHHhCCCCHHHHhhc
Q 009742 287 GEVWGIGPATAQKLYEKGHRTLDDLKNE 314 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~GirTledL~~~ 314 (527)
..+||||++++++|.+.||+|+.||.+-
T Consensus 184 ~~l~gig~~~~~~L~~~Gi~tigdl~~~ 211 (409)
T PRK03103 184 RKLFGVGSRMEKHLRRMGIRTIGQLANT 211 (409)
T ss_pred hhcCCccHHHHHHHHHcCCCCHHHHhcC
Confidence 4789999999999999999999999853
No 131
>PRK02794 DNA polymerase IV; Provisional
Probab=79.48 E-value=1.2 Score=48.04 Aligned_cols=28 Identities=50% Similarity=0.983 Sum_probs=25.8
Q ss_pred hhccCcCHHHHHHHHHhCCCCHHHHhhc
Q 009742 287 GEVWGIGPATAQKLYEKGHRTLDDLKNE 314 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~GirTledL~~~ 314 (527)
..+||||++++++|.+.||+|+.||.+-
T Consensus 212 ~~L~GiG~~~~~~L~~~GI~tigdL~~l 239 (419)
T PRK02794 212 GIIWGVGPATAARLARDGIRTIGDLQRA 239 (419)
T ss_pred hhhCCCCHHHHHHHHHhccchHHHHhhC
Confidence 6899999999999999999999999854
No 132
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=79.41 E-value=0.96 Score=51.79 Aligned_cols=46 Identities=30% Similarity=0.477 Sum_probs=33.9
Q ss_pred HHHhhccCcCHHHHHHHHHh-CCCCHHHHhhcc--Ccchhhhccccchhhh
Q 009742 284 SLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED--SLTHSQRLGLKYFDDI 331 (527)
Q Consensus 284 ~lf~~I~GvGpktA~~ly~~-GirTledL~~~~--~L~~~q~~Glk~yed~ 331 (527)
..|..||||||+++++|++. | |+++|.++. .|....++|.+..+.|
T Consensus 637 s~L~~IPGIGpkr~k~LL~~FG--Sle~I~~AS~eELa~V~Gig~k~Ae~I 685 (694)
T PRK14666 637 GELQRVEGIGPATARLLWERFG--SLQAMAAAGEEGLAAVPGIGPARAAAL 685 (694)
T ss_pred hHHhhCCCCCHHHHHHHHHHhC--CHHHHHhcCHHHHHhcCCcCHHHHHHH
Confidence 35669999999999999997 6 999999753 3555556665544443
No 133
>PRK14133 DNA polymerase IV; Provisional
Probab=79.39 E-value=1.3 Score=46.49 Aligned_cols=28 Identities=36% Similarity=0.519 Sum_probs=25.7
Q ss_pred hhccCcCHHHHHHHHHhCCCCHHHHhhc
Q 009742 287 GEVWGIGPATAQKLYEKGHRTLDDLKNE 314 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~GirTledL~~~ 314 (527)
..+||||++++++|.+.||+|+.||.+-
T Consensus 176 ~~l~gig~~~~~~L~~~Gi~ti~dl~~l 203 (347)
T PRK14133 176 SKVHGIGKKSVEKLNNIGIYTIEDLLKL 203 (347)
T ss_pred cccCCCCHHHHHHHHHcCCccHHHHhhC
Confidence 5789999999999999999999999864
No 134
>PRK14976 5'-3' exonuclease; Provisional
Probab=79.32 E-value=1.4 Score=45.26 Aligned_cols=25 Identities=44% Similarity=0.708 Sum_probs=21.7
Q ss_pred hhccCcCHHHHHHHHHh-CCCCHHHHhh
Q 009742 287 GEVWGIGPATAQKLYEK-GHRTLDDLKN 313 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~-GirTledL~~ 313 (527)
-.|||||||||.+|.++ | |++++.+
T Consensus 194 pGVpGIG~KtA~~LL~~~g--sle~i~~ 219 (281)
T PRK14976 194 KGVKGIGPKTAIKLLNKYG--NIENIYE 219 (281)
T ss_pred CCCCcccHHHHHHHHHHcC--CHHHHHH
Confidence 35899999999999976 6 9999885
No 135
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=79.22 E-value=1.2 Score=41.10 Aligned_cols=27 Identities=15% Similarity=0.004 Sum_probs=22.3
Q ss_pred hHHHHHHhhccCcCHHHHHHHHHhCCC
Q 009742 280 VRTISLFGEVWGIGPATAQKLYEKGHR 306 (527)
Q Consensus 280 ~~~l~lf~~I~GvGpktA~~ly~~Gir 306 (527)
..+.+.|++|+||||+||..+--.++.
T Consensus 79 ~~~~~~L~~l~GIG~~tA~~~l~~~~~ 105 (158)
T cd00056 79 PDAREELLALPGVGRKTANVVLLFALG 105 (158)
T ss_pred cccHHHHHcCCCCCHHHHHHHHHHHCC
Confidence 457888889999999999998766554
No 136
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=78.54 E-value=2.1 Score=42.08 Aligned_cols=53 Identities=19% Similarity=0.253 Sum_probs=33.3
Q ss_pred CCHHHHHHHHHHHHh-CCchhhHHHH--hhchhHHHHHHh-hccCcCHHHHHHHHH-hCCC
Q 009742 251 IGKSMQDHIQEIVTT-GKLSKLEHFE--KDEKVRTISLFG-EVWGIGPATAQKLYE-KGHR 306 (527)
Q Consensus 251 IG~~ia~kI~Eil~t-G~~~~le~l~--~~~~~~~l~lf~-~I~GvGpktA~~ly~-~Gir 306 (527)
+-..=|+.|.++... |. ++.+. ........+.|. ++||||+|||.-+-. .|++
T Consensus 85 f~~~KAk~I~~~~~~~~~---l~~~~~~~~~~~~~R~~Ll~~lpGIG~KTAd~vL~~~~~~ 142 (208)
T PRK01229 85 FYNKRAEYIVEARKLYGK---LKEIIKADKDQFEAREFLVKNIKGIGYKEASHFLRNVGYE 142 (208)
T ss_pred cHHHHHHHHHHHHHHHHH---HHHHHhccCCchHHHHHHHHcCCCCcHHHHHHHHHHccCC
Confidence 335555556555542 32 22222 233456888888 999999999999873 4553
No 137
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=78.15 E-value=3.2 Score=47.14 Aligned_cols=52 Identities=23% Similarity=0.476 Sum_probs=38.5
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHHh
Q 009742 243 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 303 (527)
Q Consensus 243 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 303 (527)
..|.+|||||+..+.+|.+.. |++ +.+.+. ..+.+.+|+|||+++|+.+++.
T Consensus 543 s~L~~IpGIG~k~~k~Ll~~F--gS~---~~i~~A----s~eeL~~v~Gig~~~A~~I~~~ 594 (598)
T PRK00558 543 SALDDIPGIGPKRRKALLKHF--GSL---KAIKEA----SVEELAKVPGISKKLAEAIYEA 594 (598)
T ss_pred hhHhhCCCcCHHHHHHHHHHc--CCH---HHHHhC----CHHHHhhcCCcCHHHHHHHHHH
Confidence 568999999999999877643 444 444432 2344679999999999999863
No 138
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=77.79 E-value=0.89 Score=51.04 Aligned_cols=64 Identities=17% Similarity=0.201 Sum_probs=47.3
Q ss_pred hhccCcCHHHHHHHHHhC-CCCHHHHhh--ccCcchhhhccccchhhhccCcCHHHHHHHHHHHHHH
Q 009742 287 GEVWGIGPATAQKLYEKG-HRTLDDLKN--EDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKA 350 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~G-irTledL~~--~~~L~~~q~~Glk~yed~~~~i~r~Ea~~i~~iv~~~ 350 (527)
++|-|+|++++.+|++.| ++++.||.+ ...|..+.+||-+..+.+...|-.+.-..+..++-.+
T Consensus 428 mdI~GlGe~~i~~L~~~G~i~~~~Diy~L~~~~l~~l~gfgeks~~nll~aIe~sk~~~l~r~l~aL 494 (562)
T PRK08097 428 LGLDGIGEGTWRALHQTGLFEHLFSWLALTPEQLANTPGIGKARAEQLWHQFNLARQQPFSRWLKAL 494 (562)
T ss_pred cCCCCcCHHHHHHHHHcCCcCCHHHHhcCCHHHHhcCcCccHHHHHHHHHHHHHHcCCCHHHHHHHc
Confidence 489999999999999997 599999984 3457777788988888777655444333345555544
No 139
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=77.70 E-value=3.7 Score=47.17 Aligned_cols=67 Identities=24% Similarity=0.279 Sum_probs=45.9
Q ss_pred hHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHH
Q 009742 221 RSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKL 300 (527)
Q Consensus 221 r~~aY~rAa~~l~~l~~~i~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l 300 (527)
.+..|.|-.+.=..+ -..|..|||||++.+.++.+- =| -++.+.+. ..+.+.+|+|+|+++|+.+
T Consensus 621 fAi~~hR~~r~k~~~------~s~L~~IPGIGpkr~k~LL~~--FG---Sle~I~~A----S~eELa~V~Gig~k~Ae~I 685 (694)
T PRK14666 621 YAIGRHRRARAGAAL------TGELQRVEGIGPATARLLWER--FG---SLQAMAAA----GEEGLAAVPGIGPARAAAL 685 (694)
T ss_pred HHHHHHHHHHHhhhh------HhHHhhCCCCCHHHHHHHHHH--hC---CHHHHHhc----CHHHHHhcCCcCHHHHHHH
Confidence 356777665443322 257899999999998887663 24 44555442 2344578999999999999
Q ss_pred HH
Q 009742 301 YE 302 (527)
Q Consensus 301 y~ 302 (527)
++
T Consensus 686 ~~ 687 (694)
T PRK14666 686 HE 687 (694)
T ss_pred HH
Confidence 86
No 140
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=77.54 E-value=1.8 Score=43.35 Aligned_cols=27 Identities=33% Similarity=0.423 Sum_probs=22.6
Q ss_pred hhccCcCHHHHHHHHHhCCCCHHHHhhc
Q 009742 287 GEVWGIGPATAQKLYEKGHRTLDDLKNE 314 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~GirTledL~~~ 314 (527)
-.|+|||||||.+|.++ +.|+|++.+.
T Consensus 186 pGv~GiG~ktA~~Ll~~-~gsle~i~~~ 212 (240)
T cd00008 186 PGVPGIGEKTAAKLLKE-YGSLEGILEN 212 (240)
T ss_pred CCCCccCHHHHHHHHHH-hCCHHHHHHh
Confidence 46899999999999987 3499999864
No 141
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=77.43 E-value=2.8 Score=43.25 Aligned_cols=48 Identities=21% Similarity=0.249 Sum_probs=33.2
Q ss_pred HHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHHhCC
Q 009742 257 DHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGH 305 (527)
Q Consensus 257 ~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~Gi 305 (527)
.-|.+.+..|.++. ..+..-....+++.|++|+||||+||+.+--.|.
T Consensus 172 ~~~A~~~~~g~~~~-~~l~~~~~e~a~e~L~~i~GIG~WTAe~~llf~l 219 (285)
T COG0122 172 ISLARAAAEGELDL-SELKPLSDEEAIEELTALKGIGPWTAEMFLLFGL 219 (285)
T ss_pred HHHHHHHHcCCccH-HHhccCCHHHHHHHHHcCCCcCHHHHHHHHHHcC
Confidence 33556667886333 3344444566999999999999999999864433
No 142
>KOG2245 consensus Poly(A) polymerase and related nucleotidyltransferases [RNA processing and modification]
Probab=77.15 E-value=6.9 Score=43.09 Aligned_cols=87 Identities=26% Similarity=0.382 Sum_probs=61.2
Q ss_pred hhhhccccchhhhccCcCHHHHHH-HHHHHHHHhhhc-----C-------CCeEEEecccccccCCc-cCCeeEEEecCC
Q 009742 319 HSQRLGLKYFDDIKTRIPRHEVEQ-MERLLQKAGEEV-----L-------PEVIILCGGSYRRGKAS-CGDLDVVIMHPD 384 (527)
Q Consensus 319 ~~q~~Glk~yed~~~~i~r~Ea~~-i~~iv~~~~~~~-----~-------p~~~v~~~GsyRRGke~-~gDVDiLIt~~~ 384 (527)
.++.+|+ ||+-.+-..|.++-. +.++|++-++++ + .|.++..-||||-|--. +.|||=|+..|.
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 566666666777643 566665543322 2 24567778999999865 559999999998
Q ss_pred cchhhhhHHHHHHHHHHcCcccc
Q 009742 385 RKSHKGFLSKYVKKLKEMKFLRE 407 (527)
Q Consensus 385 ~~~~~~~l~~lv~~L~~~g~l~~ 407 (527)
-.+-..+|..+-+.|+...-+++
T Consensus 118 hv~R~DFF~sf~~mL~~~~eVte 140 (562)
T KOG2245|consen 118 HVSRSDFFTSFYDMLKERPEVTE 140 (562)
T ss_pred cccHHHHHHHHHHHHhcCccccc
Confidence 77777999999999998877764
No 143
>PTZ00205 DNA polymerase kappa; Provisional
Probab=76.10 E-value=1.8 Score=48.57 Aligned_cols=28 Identities=36% Similarity=0.399 Sum_probs=25.9
Q ss_pred hhccCcCHHHHHHHHHhCCCCHHHHhhc
Q 009742 287 GEVWGIGPATAQKLYEKGHRTLDDLKNE 314 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~GirTledL~~~ 314 (527)
..|||||++++++|-..||.|+.||.+.
T Consensus 312 ~ki~GIG~~t~~~L~~~GI~TigDLa~~ 339 (571)
T PTZ00205 312 RSVPGVGKVTEALLKGLGITTLSDIYNR 339 (571)
T ss_pred ceeCCcCHHHHHHHHHcCCCcHHHHhcC
Confidence 6899999999999999999999999853
No 144
>PRK00076 recR recombination protein RecR; Reviewed
Probab=76.07 E-value=2.1 Score=41.72 Aligned_cols=21 Identities=38% Similarity=0.618 Sum_probs=18.6
Q ss_pred HHHHHHhhccCcCHHHHHHHH
Q 009742 281 RTISLFGEVWGIGPATAQKLY 301 (527)
Q Consensus 281 ~~l~lf~~I~GvGpktA~~ly 301 (527)
..++.|.++||||+|+|+++-
T Consensus 8 ~Li~~l~~LPGIG~KsA~Rla 28 (196)
T PRK00076 8 KLIEALRKLPGIGPKSAQRLA 28 (196)
T ss_pred HHHHHHHHCCCCCHHHHHHHH
Confidence 467889999999999999983
No 145
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=75.94 E-value=2.2 Score=41.60 Aligned_cols=20 Identities=40% Similarity=0.669 Sum_probs=18.1
Q ss_pred HHHHHHhhccCcCHHHHHHH
Q 009742 281 RTISLFGEVWGIGPATAQKL 300 (527)
Q Consensus 281 ~~l~lf~~I~GvGpktA~~l 300 (527)
..++.|.++||||+|+|+++
T Consensus 8 ~Li~~l~~LPGIG~KsA~Rl 27 (195)
T TIGR00615 8 KLIESLKKLPGIGPKSAQRL 27 (195)
T ss_pred HHHHHHHHCCCCCHHHHHHH
Confidence 46788999999999999998
No 146
>PRK13300 tRNA CCA-pyrophosphorylase; Provisional
Probab=75.83 E-value=9.4 Score=41.86 Aligned_cols=46 Identities=24% Similarity=0.303 Sum_probs=31.2
Q ss_pred HHHHHHHHhhhcCCCeEEEecccccccCCcc--CCeeEEEecCCcchh
Q 009742 343 MERLLQKAGEEVLPEVIILCGGSYRRGKASC--GDLDVVIMHPDRKSH 388 (527)
Q Consensus 343 i~~iv~~~~~~~~p~~~v~~~GsyRRGke~~--gDVDiLIt~~~~~~~ 388 (527)
+...+++.+.+....+.|.++|||.||.-.- +||||+|..|...+.
T Consensus 27 l~~~L~~~~~~~~~~~~V~l~GS~ArgT~L~GdsDIDIFv~fp~~~~~ 74 (447)
T PRK13300 27 LIERLEEAIKELGLDAEVELVGSTARGTWLSGDRDIDIFVLFPKDTSR 74 (447)
T ss_pred HHHHHHHHHHhcCCceEEEEEeeecCCcccCCCCceeEEEEeCCCCCH
Confidence 3334444433322237899999999999886 589999988765443
No 147
>COG1746 CCA1 tRNA nucleotidyltransferase (CCA-adding enzyme) [Translation, ribosomal structure and biogenesis]
Probab=75.80 E-value=9.6 Score=41.27 Aligned_cols=49 Identities=27% Similarity=0.368 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHhhhcCCCeEEEecccccccCCcc--CCeeEEEecCCcchh
Q 009742 340 VEQMERLLQKAGEEVLPEVIILCGGSYRRGKASC--GDLDVVIMHPDRKSH 388 (527)
Q Consensus 340 a~~i~~iv~~~~~~~~p~~~v~~~GsyRRGke~~--gDVDiLIt~~~~~~~ 388 (527)
++.|...+.+++.+...++.+.++|||.||--.. +|||+-|.-|...+.
T Consensus 28 ~e~l~~~~~~~~~e~~~~aev~lVGS~AkgTwL~gd~DIDvFi~Fp~d~~~ 78 (443)
T COG1746 28 AEELRERINEIIEELGIDAEVVLVGSYAKGTWLRGDHDIDVFIAFPKDTSE 78 (443)
T ss_pred HHHHHHHHHHHHHhcCCcceEEEEeecccCcccCCCcceeEEEECCCCCCH
Confidence 3445555555555556688999999999998765 789999988876543
No 148
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=75.73 E-value=6.1 Score=38.08 Aligned_cols=25 Identities=16% Similarity=0.167 Sum_probs=20.0
Q ss_pred HHHHHHhhccCcCHHHHHHHHHhCC
Q 009742 281 RTISLFGEVWGIGPATAQKLYEKGH 305 (527)
Q Consensus 281 ~~l~lf~~I~GvGpktA~~ly~~Gi 305 (527)
..++.|++++|||++||..+--.++
T Consensus 103 ~~~~~L~~l~GIG~ktA~~ill~~~ 127 (191)
T TIGR01083 103 EDREELVKLPGVGRKTANVVLNVAF 127 (191)
T ss_pred hHHHHHHhCCCCcHHHHHHHHHHHc
Confidence 3577788999999999999865443
No 149
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=75.36 E-value=5.7 Score=45.62 Aligned_cols=54 Identities=13% Similarity=0.182 Sum_probs=38.7
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHHhCC
Q 009742 243 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGH 305 (527)
Q Consensus 243 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~Gi 305 (527)
..|.+|||||+.-+.++-. ++.-++.+++ -.++.+.+|+|||++.|+.+|...-
T Consensus 608 s~L~~IpGiG~kr~~~LL~-----~FgS~~~i~~----As~eel~~v~gi~~~~A~~i~~~~~ 661 (691)
T PRK14672 608 LSFERLPHVGKVRAHRLLA-----HFGSFRSLQS----ATPQDIATAIHIPLTQAHTILHAAT 661 (691)
T ss_pred cccccCCCCCHHHHHHHHH-----HhcCHHHHHh----CCHHHHHhCCCCCHHHHHHHHHHhh
Confidence 4577999999988877644 2334444443 2456667999999999999998633
No 150
>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=74.77 E-value=2.3 Score=44.04 Aligned_cols=28 Identities=32% Similarity=0.359 Sum_probs=25.5
Q ss_pred hccCcCHHHHHHHHHhCCCCHHHHhhcc
Q 009742 288 EVWGIGPATAQKLYEKGHRTLDDLKNED 315 (527)
Q Consensus 288 ~I~GvGpktA~~ly~~GirTledL~~~~ 315 (527)
.+||||++++++|-+.||+|+.||.+-.
T Consensus 174 ~~~gig~~~~~~L~~~Gi~t~~dl~~~~ 201 (335)
T cd03468 174 AALRLPPETVELLARLGLRTLGDLAALP 201 (335)
T ss_pred hHhCCCHHHHHHHHHhCcccHHHHHhCC
Confidence 5899999999999999999999998643
No 151
>PRK13844 recombination protein RecR; Provisional
Probab=74.40 E-value=2.5 Score=41.32 Aligned_cols=21 Identities=24% Similarity=0.300 Sum_probs=18.6
Q ss_pred HHHHHHhhccCcCHHHHHHHH
Q 009742 281 RTISLFGEVWGIGPATAQKLY 301 (527)
Q Consensus 281 ~~l~lf~~I~GvGpktA~~ly 301 (527)
..++.|.++||||+|+|+++-
T Consensus 12 ~LI~~l~~LPGIG~KsA~Rla 32 (200)
T PRK13844 12 AVIESLRKLPTIGKKSSQRLA 32 (200)
T ss_pred HHHHHHHHCCCCCHHHHHHHH
Confidence 468889999999999999983
No 152
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=74.25 E-value=1.7 Score=42.46 Aligned_cols=50 Identities=24% Similarity=0.314 Sum_probs=35.6
Q ss_pred HHHHHhhccCcCHHHHHHHHHh-CCCCHHHHhhc---cCcchhhhccccchhhh
Q 009742 282 TISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNE---DSLTHSQRLGLKYFDDI 331 (527)
Q Consensus 282 ~l~lf~~I~GvGpktA~~ly~~-GirTledL~~~---~~L~~~q~~Glk~yed~ 331 (527)
.+..|.+|-|||||+|-.+..- ....|-+.... ..|++..++|-|..+.+
T Consensus 71 lF~~LisVnGIGpK~ALaiLs~~~~~~l~~aI~~~d~~~L~k~PGIGkKtAeri 124 (201)
T COG0632 71 LFRLLISVNGIGPKLALAILSNLDPEELAQAIANEDVKALSKIPGIGKKTAERI 124 (201)
T ss_pred HHHHHHccCCccHHHHHHHHcCCCHHHHHHHHHhcChHhhhcCCCCCHHHHHHH
Confidence 6777779999999999999764 44444443322 25888999998876543
No 153
>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=74.22 E-value=2.5 Score=44.93 Aligned_cols=28 Identities=18% Similarity=0.306 Sum_probs=24.2
Q ss_pred hhccCcCHHHHHHHHH-hCCCCHHHHhhc
Q 009742 287 GEVWGIGPATAQKLYE-KGHRTLDDLKNE 314 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~-~GirTledL~~~ 314 (527)
..+||||+++++++.+ .||+|+.||.+-
T Consensus 185 ~~l~GiG~~~~~~ll~~~Gi~ti~dl~~~ 213 (359)
T cd01702 185 TSIRGLGGKLGEEIIDLLGLPTEGDVAGF 213 (359)
T ss_pred HHhCCcCHHHHHHHHHHcCCcCHHHHHhc
Confidence 5789999999988765 699999999864
No 154
>PRK07758 hypothetical protein; Provisional
Probab=74.11 E-value=1.5 Score=37.65 Aligned_cols=44 Identities=14% Similarity=0.286 Sum_probs=35.5
Q ss_pred ccCcCHHHHHHHHHhCCCCHHHHhh--ccCcchhhhccccchhhhc
Q 009742 289 VWGIGPATAQKLYEKGHRTLDDLKN--EDSLTHSQRLGLKYFDDIK 332 (527)
Q Consensus 289 I~GvGpktA~~ly~~GirTledL~~--~~~L~~~q~~Glk~yed~~ 332 (527)
.++++......|...||.||+||.+ +..|..+++||-+..++|.
T Consensus 39 ~~~LSvRA~N~Lk~AGI~TL~dLv~~te~ELl~iknlGkKSL~EIk 84 (95)
T PRK07758 39 LSLLSAPARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLR 84 (95)
T ss_pred CccccHHHHHHHHHcCCCcHHHHHcCCHHHHHHccCCCHHHHHHHH
Confidence 4678889999999999999999985 3458888888888776655
No 155
>PRK00254 ski2-like helicase; Provisional
Probab=73.95 E-value=15 Score=42.67 Aligned_cols=53 Identities=21% Similarity=0.354 Sum_probs=38.1
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHHh
Q 009742 243 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 303 (527)
Q Consensus 243 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 303 (527)
-.|.+|||||+..+.+ +++.| +.-++++.+-. .+.+..|+|||+++|+++++.
T Consensus 645 ~~L~~ipgig~~~~~~---l~~~g-~~s~~~i~~a~----~~el~~~~gi~~~~a~~i~~~ 697 (720)
T PRK00254 645 LELMRLPMIGRKRARA---LYNAG-FRSIEDIVNAK----PSELLKVEGIGAKIVEGIFKH 697 (720)
T ss_pred hhhhcCCCCCHHHHHH---HHHcc-CCCHHHHHhCC----HHHHhcCCCCCHHHHHHHHHH
Confidence 3577899999987776 44555 45555555432 234469999999999999986
No 156
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=73.84 E-value=3.3 Score=37.17 Aligned_cols=26 Identities=42% Similarity=0.542 Sum_probs=23.6
Q ss_pred cCcCHHHHHHHHHhCCCCHHHHhhcc
Q 009742 290 WGIGPATAQKLYEKGHRTLDDLKNED 315 (527)
Q Consensus 290 ~GvGpktA~~ly~~GirTledL~~~~ 315 (527)
||+|++++.+|-+.||.|.+||.+.+
T Consensus 1 pgi~~~~~~~L~~~GI~t~~~Ll~~~ 26 (122)
T PF14229_consen 1 PGIGPKEAAKLKAAGIKTTGDLLEAG 26 (122)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHHcC
Confidence 79999999999888999999999654
No 157
>cd05403 NT_KNTase_like Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. S. aureus KNTase is a plasmid encoded enzyme which confers resistance to a wide range of aminoglycoside antibiotics which have a 4'- or 4''-hydroxyl group in the equatorial position, such as kanamycin A. This enzyme transfers a nucleoside monophosphate group from a nucleotide (ATP,GTP, or UTP) to the 4'-hydroxyl group of kanamycin A. This enzyme is a homodimer, having two NT active sites. The nucleotide and antibiotic binding sites of each active site include residues from each monomer. Included in this subgroup is Escherichia coli AadA5 which confers resistance to the antibiotic spectinomycin and is a putative aminoglycoside-3'-adenylyltransferase. It is part of the aadA5 cassette of a class 1 integron. This subgroup also includes Haemophilus influenzae HI0073 which forms a 2:2 heterotetramer with an unrelated protein HI0074. Structurally HI0074 is
Probab=73.38 E-value=7.6 Score=31.65 Aligned_cols=29 Identities=31% Similarity=0.510 Sum_probs=24.2
Q ss_pred EEEecccccccCCc-cCCeeEEEecCCcch
Q 009742 359 IILCGGSYRRGKAS-CGDLDVVIMHPDRKS 387 (527)
Q Consensus 359 ~v~~~GsyRRGke~-~gDVDiLIt~~~~~~ 387 (527)
.+.+-||+-||..+ .+||||+|..++...
T Consensus 20 ~i~LfGS~arg~~~~~SDiDl~vi~~~~~~ 49 (93)
T cd05403 20 KVYLFGSYARGDARPDSDIDLLVIFDDPLD 49 (93)
T ss_pred EEEEEeeeecCCCCCCCCeeEEEEeCCCCC
Confidence 68899999999975 789999997766543
No 158
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=73.37 E-value=8.3 Score=40.24 Aligned_cols=47 Identities=19% Similarity=0.362 Sum_probs=39.7
Q ss_pred CCcCCeEEEEeeCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEeC
Q 009742 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMD 65 (527)
Q Consensus 17 ~~f~~~~i~iv~~~~g~~r~~~l~~~~~~~G~~v~~~~s~~VTHVV~~~ 65 (527)
.+|.|.++.|-.. +.. .|..+++++.++||.|.+.+|++++.||+-+
T Consensus 231 ~l~~g~~~v~TG~-l~~-~R~e~~~~~~~~G~~v~~sVs~~t~~lv~g~ 277 (313)
T PRK06063 231 PLVQGMRVALSAE-VSR-THEELVERILHAGLAYSDSVDRDTSLVVCND 277 (313)
T ss_pred cccCCCEEEEecC-CCC-CHHHHHHHHHHcCCEecCccccCccEEEECC
Confidence 4589999999543 443 5689999999999999999999999999865
No 159
>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=72.41 E-value=7.5 Score=39.90 Aligned_cols=66 Identities=14% Similarity=0.209 Sum_probs=40.8
Q ss_pred hhHHHHHHHHHHHhcC-Cccc-cchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCc
Q 009742 220 RRSFSYYKAIPVIEKL-PFKI-ESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGI 292 (527)
Q Consensus 220 ~r~~aY~rAa~~l~~l-~~~i-~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~Gv 292 (527)
.|++.-.+||..|..- ...+ .+.++|.+|||||..+|+.|.-+.- |...-+ ....+.+.+.+++|+
T Consensus 80 ~RAr~L~~~A~~i~~~~~g~~p~~~~~L~~LpGIG~~TA~~Il~~a~-~~~~~~------vD~~v~RVl~Rl~~~ 147 (275)
T TIGR01084 80 ARARNLHKAAQEVVEEFGGEFPQDFEDLAALPGVGRYTAGAILSFAL-NKPYPI------LDGNVKRVLSRLFAV 147 (275)
T ss_pred HHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCCCHHHHHHHHHHHC-CCCCCc------chHhHHHHHHHHccC
Confidence 3677777888777541 1111 3468999999999999999986553 332111 122355566555554
No 160
>PRK10702 endonuclease III; Provisional
Probab=72.28 E-value=6.6 Score=38.68 Aligned_cols=23 Identities=17% Similarity=0.257 Sum_probs=18.9
Q ss_pred HHHHHHhhccCcCHHHHHHHHHh
Q 009742 281 RTISLFGEVWGIGPATAQKLYEK 303 (527)
Q Consensus 281 ~~l~lf~~I~GvGpktA~~ly~~ 303 (527)
..++.|+++||||+|||.-+---
T Consensus 106 ~~~~~Ll~lpGVG~ktA~~ill~ 128 (211)
T PRK10702 106 EDRAALEALPGVGRKTANVVLNT 128 (211)
T ss_pred chHHHHhcCCcccHHHHHHHHHH
Confidence 46777889999999999987543
No 161
>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=71.63 E-value=2.9 Score=43.44 Aligned_cols=28 Identities=39% Similarity=0.550 Sum_probs=25.5
Q ss_pred hhccCcCHHHHHHHHHhCCCCHHHHhhc
Q 009742 287 GEVWGIGPATAQKLYEKGHRTLDDLKNE 314 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~GirTledL~~~ 314 (527)
..+||||.+++++|.+.||+|+.||.+.
T Consensus 174 ~~l~gig~~~~~~L~~~Gi~ti~dl~~~ 201 (334)
T cd03586 174 RKIPGVGKVTAEKLKELGIKTIGDLAKL 201 (334)
T ss_pred hhhCCcCHHHHHHHHHcCCcCHHHHHcC
Confidence 5789999999999999999999999853
No 162
>PRK10702 endonuclease III; Provisional
Probab=71.55 E-value=8.4 Score=37.94 Aligned_cols=43 Identities=12% Similarity=0.281 Sum_probs=30.8
Q ss_pred hHHHHHHHHHHHh-cCCcccc-chhhhcCCCCCCHHHHHHHHHHH
Q 009742 221 RSFSYYKAIPVIE-KLPFKIE-SADQVKGLPGIGKSMQDHIQEIV 263 (527)
Q Consensus 221 r~~aY~rAa~~l~-~l~~~i~-s~~~l~~lpgIG~~ia~kI~Eil 263 (527)
|+....+++..|. .....+. +.++|..|||||+.+|+.|.=+.
T Consensus 85 kA~~l~~~a~~i~~~~~~~~p~~~~~Ll~lpGVG~ktA~~ill~a 129 (211)
T PRK10702 85 KAENVIKTCRILLEQHNGEVPEDRAALEALPGVGRKTANVVLNTA 129 (211)
T ss_pred HHHHHHHHHHHHHHHcCCCCCchHHHHhcCCcccHHHHHHHHHHH
Confidence 6666666676664 3333333 56899999999999999987554
No 163
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=70.97 E-value=3.1 Score=43.15 Aligned_cols=25 Identities=48% Similarity=0.740 Sum_probs=21.9
Q ss_pred hccCcCHHHHHHHHHh-CCCCHHHHhhc
Q 009742 288 EVWGIGPATAQKLYEK-GHRTLDDLKNE 314 (527)
Q Consensus 288 ~I~GvGpktA~~ly~~-GirTledL~~~ 314 (527)
.|+|||||||.+|.++ | |++.|.+.
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 164
>COG0389 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]
Probab=70.88 E-value=2.9 Score=44.30 Aligned_cols=27 Identities=44% Similarity=0.721 Sum_probs=25.7
Q ss_pred hhccCcCHHHHHHHHHhCCCCHHHHhh
Q 009742 287 GEVWGIGPATAQKLYEKGHRTLDDLKN 313 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~GirTledL~~ 313 (527)
+.+||||+.|+.++...||.|+.||.+
T Consensus 179 ~~~~GvG~~~~~~l~~~Gi~ti~dl~~ 205 (354)
T COG0389 179 LEFWGVGKVTAEKLRRLGISTIGDLAE 205 (354)
T ss_pred hhhCCCCHHHHHHHHHcCChhHHHHHh
Confidence 489999999999999999999999997
No 165
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=70.87 E-value=6 Score=40.48 Aligned_cols=67 Identities=18% Similarity=0.296 Sum_probs=47.4
Q ss_pred hhcCCCCCCH---HHHHHHHHHHH-hCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHHhCCCCHHHH
Q 009742 244 QVKGLPGIGK---SMQDHIQEIVT-TGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL 311 (527)
Q Consensus 244 ~l~~lpgIG~---~ia~kI~Eil~-tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTledL 311 (527)
+|..+ |+|= -|+.-.++|++ .|...-|..++...-..+.+.|+.+||||||.|.=+-=+|+.-+.-+
T Consensus 175 ~LR~~-gfGYRAkYI~~ta~~l~~~~g~~~wLqsl~~~~yeear~~L~~lpGVG~KVADCI~Lm~l~~~~~V 245 (323)
T KOG2875|consen 175 ELRKL-GFGYRAKYISATARALQEKQGGLAWLQSLRKSSYEEAREALCSLPGVGPKVADCICLMSLDKLSAV 245 (323)
T ss_pred HHHHc-CcchhHHHHHHHHHHHHHhcccchHHHHHhcccHHHHHHHHhcCCCCcchHhhhhhhhhcCCCCcc
Confidence 34444 6664 46666777775 55667788888755566999999999999999997765555444443
No 166
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=70.52 E-value=5.5 Score=40.32 Aligned_cols=53 Identities=25% Similarity=0.401 Sum_probs=38.8
Q ss_pred chhHHHHHHhhccCcCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhccccchhhh
Q 009742 278 EKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDI 331 (527)
Q Consensus 278 ~~~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~q~~Glk~yed~ 331 (527)
....-+.++.++||||+++|..+.+. +.|++++.++. .|....++|.+....|
T Consensus 176 ~~e~q~~il~s~pgig~~~a~~ll~~-fgS~~~~~tas~~eL~~v~gig~k~A~~I 230 (254)
T COG1948 176 LKELQLYILESIPGIGPKLAERLLKK-FGSVEDVLTASEEELMKVKGIGEKKAREI 230 (254)
T ss_pred hHHHHHHHHHcCCCccHHHHHHHHHH-hcCHHHHhhcCHHHHHHhcCccHHHHHHH
Confidence 34456778889999999999999874 55888888653 4677777776554443
No 167
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=70.52 E-value=5.1 Score=39.76 Aligned_cols=21 Identities=24% Similarity=0.251 Sum_probs=17.5
Q ss_pred HHHHHhhccCcCHHHHHHHHH
Q 009742 282 TISLFGEVWGIGPATAQKLYE 302 (527)
Q Consensus 282 ~l~lf~~I~GvGpktA~~ly~ 302 (527)
..+.|++|||||++||..+.-
T Consensus 119 ~re~Ll~l~GIG~kTAd~iLl 139 (218)
T PRK13913 119 TREWLLDQKGIGKESADAILC 139 (218)
T ss_pred HHHHHHcCCCccHHHHHHHHH
Confidence 557778999999999998743
No 168
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=70.36 E-value=6.5 Score=45.87 Aligned_cols=85 Identities=14% Similarity=0.229 Sum_probs=69.5
Q ss_pred CCCCCcCCeEEEEeeCCCChhHHHHHHHHHHhcCCEEE-eecCCCccEEEEeCcHH-HHHhc----cccchHHHHHHhcC
Q 009742 14 DSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVE-EKLSKKVTHVLAMDLEA-LLQQS----VIRYQWLEDSLRLG 87 (527)
Q Consensus 14 ~~~~~f~~~~i~iv~~~~g~~r~~~l~~~~~~~G~~v~-~~~s~~VTHVV~~~~~~-~l~~~----vv~~~Wl~ec~~~g 87 (527)
.....|+++.+|. +|-.-.-..-|+++-.-||+..+ .+.-...|||++.+..+ +++.+ ..++.|..||.+.|
T Consensus 43 t~~s~fs~is~~~--ngs~~e~~nelk~~~~~~t~~~~~~~~rs~T~~ii~~~l~a~~vk~~~~~~~~~~e~iie~~~~~ 120 (1016)
T KOG2093|consen 43 TGSSSFSGISISV--NGSTDESANELKLQNMFHTGASAASYERSGTENIIAQGLPADLVKGFTIPKHISIEWIIECCENG 120 (1016)
T ss_pred CCcceeeeeeecc--CCccccchHHHhhhhhhcccccccccccccceeeecccchHHHhccccchhhhcHHHHHHHHhcc
Confidence 3447899999988 56666667788999999999999 55567899999999885 56654 88999999999999
Q ss_pred CCcCCcccccccC
Q 009742 88 EKVSEDLYRIKLD 100 (527)
Q Consensus 88 ~~v~~~~~~l~~~ 100 (527)
..|.--+|.+...
T Consensus 121 ~~~~~~~~~~~t~ 133 (1016)
T KOG2093|consen 121 MDVGYYPYQLYTG 133 (1016)
T ss_pred Cccccccceeecc
Confidence 9999888777544
No 169
>KOG3524 consensus Predicted guanine nucleotide exchange factor (PEBBLE) [Signal transduction mechanisms]
Probab=70.23 E-value=4.7 Score=45.84 Aligned_cols=73 Identities=14% Similarity=0.275 Sum_probs=57.1
Q ss_pred CCCCCcCCeEEEEeeCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEeCcHHH-HH-----hccccchHHHHHHhcC
Q 009742 14 DSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEAL-LQ-----QSVIRYQWLEDSLRLG 87 (527)
Q Consensus 14 ~~~~~f~~~~i~iv~~~~g~~r~~~l~~~~~~~G~~v~~~~s~~VTHVV~~~~~~~-l~-----~~vv~~~Wl~ec~~~g 87 (527)
-+...|++++.|+ +||-+.-. -|=.++..|||.|......++||.|+.+.... ++ .-++.+.|+.+|.+-.
T Consensus 114 ly~~~m~~vvlcf--Tg~rkk~e-~lv~lvh~mgg~irkd~nsktthli~n~s~gek~~~a~t~~~~~rp~wv~~aw~~r 190 (850)
T KOG3524|consen 114 LYCELMKDVVMCF--TGERKKKE-ELVDLVHYMGGSIRKDTNSKTTHLIANKVEGEKQSIALVGVPTMRPDWVTEAWKHR 190 (850)
T ss_pred ccchhhcCceeee--eccchhhH-HHHHHHHHhcceeEeeeccCceEEEeecccceEEEEEeeccceechHhhhhhhcCc
Confidence 3457899999999 67766543 67789999999999999999999999876542 11 1288999999998765
Q ss_pred CC
Q 009742 88 EK 89 (527)
Q Consensus 88 ~~ 89 (527)
.-
T Consensus 191 n~ 192 (850)
T KOG3524|consen 191 ND 192 (850)
T ss_pred ch
Confidence 43
No 170
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=66.98 E-value=10 Score=34.88 Aligned_cols=67 Identities=12% Similarity=0.138 Sum_probs=41.1
Q ss_pred ChhHHHHHHHHHHHhcCCccc-----cchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCc
Q 009742 219 DRRSFSYYKAIPVIEKLPFKI-----ESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGI 292 (527)
Q Consensus 219 ~~r~~aY~rAa~~l~~l~~~i-----~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~Gv 292 (527)
+.|+.....++..+.+-.... +..++|.+|||||+.+|+.|.-+.-. .+ .+-- ...+.+.+..+.++
T Consensus 54 ~~kA~~i~~~a~~~~~~~~~~~~~~~~~~~~L~~l~GIG~~tA~~~l~~~~~--~~---~~pv--D~~v~r~~~~~~~~ 125 (158)
T cd00056 54 RRKAKYLKELARAIVEGFGGLVLDDPDAREELLALPGVGRKTANVVLLFALG--PD---AFPV--DTHVRRVLKRLGLI 125 (158)
T ss_pred HHHHHHHHHHHHHHHHHcCCccCCCcccHHHHHcCCCCCHHHHHHHHHHHCC--CC---CCcc--chhHHHHHHHhCCC
Confidence 457777777777775433222 23477999999999999998765332 11 1111 23456666555554
No 171
>PRK13910 DNA glycosylase MutY; Provisional
Probab=66.31 E-value=11 Score=38.88 Aligned_cols=68 Identities=18% Similarity=0.203 Sum_probs=44.8
Q ss_pred hHHHHHHHHHHHhc-CCccc-cchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHH
Q 009742 221 RSFSYYKAIPVIEK-LPFKI-ESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPA 295 (527)
Q Consensus 221 r~~aY~rAa~~l~~-l~~~i-~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpk 295 (527)
|++.-.++|..|.. ....+ .+.++|.+|||||+.+|+.|.-+.- |.-. . -...-+.++|.+++|+...
T Consensus 48 RAr~L~~~A~~i~~~~~g~~P~~~~~L~~LpGIG~kTA~aIl~~af-~~~~-~-----~VD~nV~RVl~Rl~g~~~~ 117 (289)
T PRK13910 48 RAKNLKKSAEICVKEHHSQLPNDYQSLLKLPGIGAYTANAILCFGF-REKS-A-----CVDANIKRVLLRLFGLDPN 117 (289)
T ss_pred HHHHHHHHHHHHHHHhCCCCChhHHHHHhCCCCCHHHHHHHHHHHC-CCCc-C-----cccHHHHHHHHHHhcCCCC
Confidence 77777778877742 22212 2578999999999999999976542 2211 1 1234477788888888643
No 172
>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a beta-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [, ].; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBN_M 2QBB_M 3I1M_M 3OFP_M 3OFX_M 3OFO_M 1VS5_M 3OAQ_M 2QAL_M 3J18_M ....
Probab=66.02 E-value=6 Score=34.66 Aligned_cols=25 Identities=24% Similarity=0.502 Sum_probs=20.7
Q ss_pred HHHHHhhccCcCHHHHHHHHHh-CCC
Q 009742 282 TISLFGEVWGIGPATAQKLYEK-GHR 306 (527)
Q Consensus 282 ~l~lf~~I~GvGpktA~~ly~~-Gir 306 (527)
+.-.|++|+|||+++|..+.+. ||.
T Consensus 13 i~~aLt~IyGIG~~~A~~Ic~~lgi~ 38 (107)
T PF00416_consen 13 IYIALTKIYGIGRRKAKQICKKLGIN 38 (107)
T ss_dssp HHHHHTTSTTBCHHHHHHHHHHTTS-
T ss_pred hHhHHhhhhccCHHHHHHHHHHcCCC
Confidence 5566789999999999999875 774
No 173
>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=65.76 E-value=8.1 Score=30.90 Aligned_cols=22 Identities=18% Similarity=0.376 Sum_probs=19.9
Q ss_pred hhhcCCCCCCHHHHHHHHHHHH
Q 009742 243 DQVKGLPGIGKSMQDHIQEIVT 264 (527)
Q Consensus 243 ~~l~~lpgIG~~ia~kI~Eil~ 264 (527)
+++..+||+|++..+.|.+.|+
T Consensus 44 ~~L~~i~n~G~ksl~EI~~~L~ 65 (66)
T PF03118_consen 44 EDLLKIKNFGKKSLEEIKEKLK 65 (66)
T ss_dssp HHHHTSTTSHHHHHHHHHHHHH
T ss_pred HHHHhCCCCCHhHHHHHHHHHc
Confidence 6799999999999999998875
No 174
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=65.63 E-value=12 Score=38.72 Aligned_cols=52 Identities=27% Similarity=0.493 Sum_probs=38.1
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHHh
Q 009742 244 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 303 (527)
Q Consensus 244 ~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 303 (527)
.+..|||||+.+++++.+ --+..++++.+-.+ +.+.+++|+++++|..||+.
T Consensus 7 ~l~~l~gIg~~~a~~L~~----~Gi~t~~dl~~~~~----~~L~~~~g~~~~~a~~l~~~ 58 (317)
T PRK04301 7 DLEDLPGVGPATAEKLRE----AGYDTVEAIAVASP----KELSEAAGIGESTAAKIIEA 58 (317)
T ss_pred cHhhcCCCCHHHHHHHHH----cCCCCHHHHHcCCH----HHHHHhcCCCHHHHHHHHHH
Confidence 578999999888776554 34566777755332 23348889999999999974
No 175
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=65.36 E-value=8.2 Score=38.12 Aligned_cols=86 Identities=23% Similarity=0.294 Sum_probs=46.4
Q ss_pred CCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHHh--CCCCHHHHhhccC-cchhhhccc-
Q 009742 250 GIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRTLDDLKNEDS-LTHSQRLGL- 325 (527)
Q Consensus 250 gIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--GirTledL~~~~~-L~~~q~~Gl- 325 (527)
|+-..=|+.|.++.+ .-+|+... +.+..++.|.++||||+|||.--... |+-++ -=+-. ..-..++|+
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 455555555555433 12233333 44567877889999999999988765 44322 10100 111233343
Q ss_pred ------cchhhhccCcCHHHHHHH
Q 009742 326 ------KYFDDIKTRIPRHEVEQM 343 (527)
Q Consensus 326 ------k~yed~~~~i~r~Ea~~i 343 (527)
+..+++...+|++.-..+
T Consensus 152 ~~~~p~~ve~~L~~~iP~~~~~~~ 175 (211)
T COG0177 152 PGKTPEEVEEALMKLIPKELWTDL 175 (211)
T ss_pred CCCCHHHHHHHHHHHCCHHHHHHH
Confidence 334456667777665554
No 176
>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=65.36 E-value=3.1 Score=28.48 Aligned_cols=18 Identities=22% Similarity=0.501 Sum_probs=14.4
Q ss_pred hhcCCCCCCHHHHHHHHH
Q 009742 244 QVKGLPGIGKSMQDHIQE 261 (527)
Q Consensus 244 ~l~~lpgIG~~ia~kI~E 261 (527)
.+.+++|||+++++++..
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 177
>PRK13766 Hef nuclease; Provisional
Probab=65.29 E-value=8.3 Score=44.95 Aligned_cols=49 Identities=31% Similarity=0.452 Sum_probs=33.4
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHH
Q 009742 245 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 302 (527)
Q Consensus 245 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 302 (527)
|..|||||...+.+|.+-. |+ ++++.+.. .+.|..++|+|+++|+.+++
T Consensus 717 L~~ipgig~~~a~~Ll~~f--gs---~~~i~~as----~~~L~~i~Gig~~~a~~i~~ 765 (773)
T PRK13766 717 VESLPDVGPVLARNLLEHF--GS---VEAVMTAS----EEELMEVEGIGEKTAKRIRE 765 (773)
T ss_pred HhcCCCCCHHHHHHHHHHc--CC---HHHHHhCC----HHHHHhCCCCCHHHHHHHHH
Confidence 5789999999887776532 44 33433322 23456889999999999876
No 178
>COG2251 Predicted nuclease (RecB family) [General function prediction only]
Probab=64.81 E-value=4.7 Score=43.76 Aligned_cols=27 Identities=37% Similarity=0.452 Sum_probs=24.8
Q ss_pred hccCcCHHHHHHHHHhCCCCHHHHhhc
Q 009742 288 EVWGIGPATAQKLYEKGHRTLDDLKNE 314 (527)
Q Consensus 288 ~I~GvGpktA~~ly~~GirTledL~~~ 314 (527)
=|+||||.+.+.+++.||+|++||-..
T Consensus 229 Lv~Gi~~~r~~~l~~~GI~Ti~~LA~~ 255 (474)
T COG2251 229 LVPGITPSRYDVLEEVGITTIEDLADA 255 (474)
T ss_pred ccCCCCHHHHHHHHHcCcchHHHHHhc
Confidence 378999999999999999999999864
No 179
>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=64.20 E-value=4.4 Score=33.94 Aligned_cols=20 Identities=40% Similarity=0.624 Sum_probs=17.6
Q ss_pred HHHhhccCcCHHHHHHHHHh
Q 009742 284 SLFGEVWGIGPATAQKLYEK 303 (527)
Q Consensus 284 ~lf~~I~GvGpktA~~ly~~ 303 (527)
++|++|||||+.+|-.|..+
T Consensus 2 ~~l~sipGig~~~a~~llae 21 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAE 21 (87)
T ss_pred chhcCCCCccHHHHHHHHHH
Confidence 46789999999999999874
No 180
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=63.67 E-value=15 Score=38.15 Aligned_cols=48 Identities=17% Similarity=0.137 Sum_probs=39.8
Q ss_pred CCcCCeEEEEeeCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEeC
Q 009742 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMD 65 (527)
Q Consensus 17 ~~f~~~~i~iv~~~~g~~r~~~l~~~~~~~G~~v~~~~s~~VTHVV~~~ 65 (527)
..|.|.++.|--. +..-.|..+++++.++||.|.+.+|+++|.+|+-+
T Consensus 219 ~~l~g~~~vfTG~-l~~~~R~~~~~~~~~~Gg~v~~sVs~~t~~lV~G~ 266 (309)
T PRK06195 219 TAFKEEVVVFTGG-LASMTRDEAMILVRRLGGTVGSSVTKKTTYLVTNT 266 (309)
T ss_pred ccccCCEEEEccc-cCCCCHHHHHHHHHHhCCEecCCcccCceEEEECC
Confidence 5799999999543 32334688899999999999999999999999854
No 181
>PRK14973 DNA topoisomerase I; Provisional
Probab=63.66 E-value=8.4 Score=46.10 Aligned_cols=31 Identities=19% Similarity=0.165 Sum_probs=27.9
Q ss_pred HHhhccCcCHHHHHHHHHhCCCCHHHHhhcc
Q 009742 285 LFGEVWGIGPATAQKLYEKGHRTLDDLKNED 315 (527)
Q Consensus 285 lf~~I~GvGpktA~~ly~~GirTledL~~~~ 315 (527)
-|++++||=..+|+++|+.||+|++|+..+.
T Consensus 803 ~~~~~~gv~~~~~~~~~~~G~~~~~d~~~a~ 833 (936)
T PRK14973 803 SRLKEIGVPAVSLKKYQEAGFDTPEDFCSVH 833 (936)
T ss_pred HhhcccCCCHHHHHHHHHhcCCCHHHHHhcC
Confidence 3559999999999999999999999999654
No 182
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=63.47 E-value=5.1 Score=39.03 Aligned_cols=37 Identities=22% Similarity=0.333 Sum_probs=25.5
Q ss_pred cccch-hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHH
Q 009742 238 KIESA-DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHF 274 (527)
Q Consensus 238 ~i~s~-~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l 274 (527)
++..+ +.+..|||||++.|.++.-.+-.-.-.+++.|
T Consensus 5 ~~~~Li~~l~~LPGIG~KsA~RlA~~ll~~~~~~~~~l 42 (195)
T TIGR00615 5 PISKLIESLKKLPGIGPKSAQRLAFHLLKRDPSEVLRL 42 (195)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHcCCHHHHHHH
Confidence 34443 67899999999999999876654443334333
No 183
>PRK05007 PII uridylyl-transferase; Provisional
Probab=63.02 E-value=24 Score=42.18 Aligned_cols=63 Identities=22% Similarity=0.454 Sum_probs=40.5
Q ss_pred HHHHHHHHHhhhc----CCCeEEEeccccccc-CCccCCeeEEEecCCcc--hhhhhHHHHHHHHHHcCc
Q 009742 342 QMERLLQKAGEEV----LPEVIILCGGSYRRG-KASCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMKF 404 (527)
Q Consensus 342 ~i~~iv~~~~~~~----~p~~~v~~~GsyRRG-ke~~gDVDiLIt~~~~~--~~~~~l~~lv~~L~~~g~ 404 (527)
.+.+++..+.... .|++.++.+|||=|| ..-.+|||+||-+++.. .....+.+++..|-+.|+
T Consensus 61 ~~D~~l~~l~~~~~~~~~~~~alvAvGgyGR~EL~p~SDiDll~l~~~~~~~~~~~~i~~~~~~lwD~gL 130 (884)
T PRK05007 61 FIDQLLQRLWIEAGFDQIPDLALVAVGGYGRGELHPLSDIDLLILSRKKLPDEQAQKVGELITLLWDLKL 130 (884)
T ss_pred HHHHHHHHHHHHccCCCcCceEEEecCCCCCcccCCcccceEEEEeCCCCChHHHHHHHHHHHHHHhcCC
Confidence 3444444443322 245778889999665 45688999999988532 244566667766666664
No 184
>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=63.00 E-value=22 Score=34.20 Aligned_cols=44 Identities=14% Similarity=0.203 Sum_probs=30.7
Q ss_pred hHHHHHHHHHHH-hcCCccc---------cc---hhhhcCCCCCCHHHHHHHHHHHH
Q 009742 221 RSFSYYKAIPVI-EKLPFKI---------ES---ADQVKGLPGIGKSMQDHIQEIVT 264 (527)
Q Consensus 221 r~~aY~rAa~~l-~~l~~~i---------~s---~~~l~~lpgIG~~ia~kI~Eil~ 264 (527)
|+...+.++..| +.+...+ .+ .++|..|||||+++|+.+--++.
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 555556666665 4565554 11 46899999999999999876554
No 185
>KOG3548 consensus DNA damage checkpoint protein RHP9/CRB2/53BP1 [Replication, recombination and repair]
Probab=62.10 E-value=6.9 Score=45.89 Aligned_cols=81 Identities=14% Similarity=0.088 Sum_probs=52.9
Q ss_pred CCcCCeEEEEeeCCCChhHHHHHHHHHHhcCCEEEeec-CCCccEEEEeC-------cHH---------------HHHh-
Q 009742 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKL-SKKVTHVLAMD-------LEA---------------LLQQ- 72 (527)
Q Consensus 17 ~~f~~~~i~iv~~~~g~~r~~~l~~~~~~~G~~v~~~~-s~~VTHVV~~~-------~~~---------------~l~~- 72 (527)
.+|-||+..| ++.... .....+-+..|||.|.+.. ..-.+|=++-. ++. .+|.
T Consensus 924 niFd~cvF~l--Tsa~~s-d~~~r~s~e~~gg~vle~gl~~~Fn~p~~g~~~~lr~Ln~~q~~ks~~qalLIsdth~Rt~ 1000 (1176)
T KOG3548|consen 924 NIFDGCVFML--TSANRS-DSASRPSMEKHGGLVLEKGLMNLFNTPFKGGGIVLRQLNSFQERKSNYQALLISDTHYRTH 1000 (1176)
T ss_pred chhcceeEEE--eccccc-hhhhhhhhhccCChhhhccccccccccccCCcchHHhhhHHhhhccccceeEeehhhhHHH
Confidence 6899998777 344444 3555666666999887543 33244443211 000 1111
Q ss_pred ---------c-cccchHHHHHHhcCCCcCCcccccccC
Q 009742 73 ---------S-VIRYQWLEDSLRLGEKVSEDLYRIKLD 100 (527)
Q Consensus 73 ---------~-vv~~~Wl~ec~~~g~~v~~~~~~l~~~ 100 (527)
+ -|+..|+.+|+++++.|+..+|.|...
T Consensus 1001 KYLeaLA~giPcVh~~fI~aC~e~nr~Vdy~~YLLpsG 1038 (1176)
T KOG3548|consen 1001 KYLEALARGIPCVHNTFIQACGEQNRCVDYTDYLLPSG 1038 (1176)
T ss_pred HHHHHHHcCCCcccHHHHHHHHhccccccchhhcccCc
Confidence 1 789999999999999999999999543
No 186
>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=61.95 E-value=29 Score=32.43 Aligned_cols=49 Identities=24% Similarity=0.353 Sum_probs=30.3
Q ss_pred eEEEecccccccC-CccCCeeEEEecCCcch-h----hhhHHHHHHHHHHcCccc
Q 009742 358 VIILCGGSYRRGK-ASCGDLDVVIMHPDRKS-H----KGFLSKYVKKLKEMKFLR 406 (527)
Q Consensus 358 ~~v~~~GsyRRGk-e~~gDVDiLIt~~~~~~-~----~~~l~~lv~~L~~~g~l~ 406 (527)
+-+...|||-|+. ....|+|+++.+++... . ..+-..+++.|...|+..
T Consensus 56 ~~~la~Gs~GR~E~~~~SD~D~~~v~~~~~~~~~~~~~~l~~~i~~~L~~~g~~~ 110 (172)
T cd05401 56 FALLALGSYGRGELNPSSDQDLLLLYDDDGDEVAAYFEELAERLIKILSEAGGPY 110 (172)
T ss_pred EEEEEeCCcccCCcCCCcCcceEEEeCCCCchHHHHHHHHHHHHHHHHHhCCCCC
Confidence 4566789986665 55789999998876432 1 233344455555555443
No 187
>PRK03980 flap endonuclease-1; Provisional
Probab=61.34 E-value=6.4 Score=40.73 Aligned_cols=26 Identities=42% Similarity=0.624 Sum_probs=21.8
Q ss_pred hhccCcCHHHHHHHHHhCCCCHHHHhh
Q 009742 287 GEVWGIGPATAQKLYEKGHRTLDDLKN 313 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~GirTledL~~ 313 (527)
..|+|||||||.+|.++ +.||+.+..
T Consensus 192 ~GI~GIG~ktA~kLi~~-~~sle~i~~ 217 (292)
T PRK03980 192 PGIKGIGPKTALKLIKK-HGDLEKVLE 217 (292)
T ss_pred CCCCCccHHHHHHHHHH-CCCHHHHHH
Confidence 37899999999999986 238998886
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=61.06 E-value=6.8 Score=42.98 Aligned_cols=28 Identities=46% Similarity=0.586 Sum_probs=26.1
Q ss_pred hccCcCHHHHHHHHHhCCCCHHHHhhcc
Q 009742 288 EVWGIGPATAQKLYEKGHRTLDDLKNED 315 (527)
Q Consensus 288 ~I~GvGpktA~~ly~~GirTledL~~~~ 315 (527)
-|+|||++++..|++.||+|++||-...
T Consensus 211 lv~gi~~~~~~~L~~~GI~ti~~La~~~ 238 (457)
T TIGR03491 211 LVPGIGPSRYRLLQELGIHTLEDLAAAD 238 (457)
T ss_pred ecCCCCHHHHHHHHHcCCCcHHHHhcCC
Confidence 6999999999999999999999999754
No 189
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=61.04 E-value=28 Score=33.57 Aligned_cols=52 Identities=23% Similarity=0.305 Sum_probs=32.1
Q ss_pred hhHHHHHHHHHHHhcCCccccc-hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhc
Q 009742 220 RRSFSYYKAIPVIEKLPFKIES-ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDE 278 (527)
Q Consensus 220 ~r~~aY~rAa~~l~~l~~~i~s-~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~ 278 (527)
.+..-|-+-| .||+. +-+|.=|||||++++.+|-|==+.+.+..++++.+-.
T Consensus 99 ~~FV~FfN~A-------~PIt~RlH~LeLLPGIGKK~m~~ILeERkkkpFeSFeDi~~Rv 151 (181)
T PF04919_consen 99 ERFVDFFNEA-------QPITLRLHSLELLPGIGKKTMWKILEERKKKPFESFEDIEERV 151 (181)
T ss_dssp HHHHHHH------------B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHS
T ss_pred HHHHHHhhcC-------CCChHHHHHHhhcccccHHHHHHHHHHHccCCCCCHHHHHHHh
Confidence 4544444444 58876 4789999999999999999988888888888887533
No 190
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=61.04 E-value=6.3 Score=39.18 Aligned_cols=30 Identities=33% Similarity=0.531 Sum_probs=27.3
Q ss_pred HHHhhccCcCHHHHHHHHHhCCCCHHHHhh
Q 009742 284 SLFGEVWGIGPATAQKLYEKGHRTLDDLKN 313 (527)
Q Consensus 284 ~lf~~I~GvGpktA~~ly~~GirTledL~~ 313 (527)
.-|+.|.||||+.+.+|.+.||.+.++|-.
T Consensus 158 DDL~~I~GIGp~~a~~L~eaGi~tfaQIAa 187 (221)
T PRK12278 158 DDLTKITGVGPALAKKLNEAGVTTFAQIAA 187 (221)
T ss_pred chheeccccChHHHHHHHHcCCCCHHHhhC
Confidence 356799999999999999999999999974
No 191
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=61.01 E-value=27 Score=41.52 Aligned_cols=68 Identities=16% Similarity=0.320 Sum_probs=43.9
Q ss_pred HHHHHHHHHHHHHHhhhcCC----CeEEEecccccccC-CccCCeeEEEecCCc--chhhhhHHHHHHHHHHcCc
Q 009742 337 RHEVEQMERLLQKAGEEVLP----EVIILCGGSYRRGK-ASCGDLDVVIMHPDR--KSHKGFLSKYVKKLKEMKF 404 (527)
Q Consensus 337 r~Ea~~i~~iv~~~~~~~~p----~~~v~~~GsyRRGk-e~~gDVDiLIt~~~~--~~~~~~l~~lv~~L~~~g~ 404 (527)
+.-+..+..+++++.....+ ++.+..+|||=||. ---+|||+||-+++. .....++.+++..|=+.|+
T Consensus 32 ~~~~~~~D~~l~~l~~~~~~~~~~~iaLvAvGGYGR~eL~P~SDIDlliL~~~~~~~~~~~~i~~~~~~LWD~gl 106 (854)
T PRK01759 32 ENRSDFYDQLLIHLWQQFGLEEQSDLALIAVGGYGRREMFPLSDLDILILTEQPPDEETEEKINQFFQFLWDCGF 106 (854)
T ss_pred HHHHHHHHHHHHHHHHHccCCCCCCeEEEEeCCcccccCCCcccceEEEEeCCCCChHHHHHHHHHHHHHHhcCC
Confidence 33444456666655443322 35677889996665 456899999998753 2345667777777777765
No 192
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=60.14 E-value=6.4 Score=46.87 Aligned_cols=24 Identities=42% Similarity=0.678 Sum_probs=20.3
Q ss_pred hccCcCHHHHHHHHHh-CCCCHHHHhh
Q 009742 288 EVWGIGPATAQKLYEK-GHRTLDDLKN 313 (527)
Q Consensus 288 ~I~GvGpktA~~ly~~-GirTledL~~ 313 (527)
.|||||||||.+|.++ | |||.+.+
T Consensus 189 GVpGIG~KtA~kLL~~yg--sle~i~~ 213 (887)
T TIGR00593 189 GVKGIGEKTAAKLLQEFG--SLENIYE 213 (887)
T ss_pred CCCCcCHHHHHHHHHHcC--CHHHHHH
Confidence 4999999999999986 6 7777763
No 193
>PRK00076 recR recombination protein RecR; Reviewed
Probab=60.11 E-value=6.1 Score=38.58 Aligned_cols=32 Identities=16% Similarity=0.321 Sum_probs=23.9
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHH
Q 009742 243 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHF 274 (527)
Q Consensus 243 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l 274 (527)
+.+..|||||++.|.++.-.+-.-.-.+++.|
T Consensus 11 ~~l~~LPGIG~KsA~Rla~~ll~~~~~~~~~l 42 (196)
T PRK00076 11 EALRKLPGIGPKSAQRLAFHLLQRDREDVLRL 42 (196)
T ss_pred HHHHHCCCCCHHHHHHHHHHHHcCCHHHHHHH
Confidence 67899999999999999877754443444433
No 194
>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=59.98 E-value=7.2 Score=31.15 Aligned_cols=24 Identities=25% Similarity=0.326 Sum_probs=17.8
Q ss_pred hhHHHHH-HhhccCcCHHHHHHHHH
Q 009742 279 KVRTISL-FGEVWGIGPATAQKLYE 302 (527)
Q Consensus 279 ~~~~l~l-f~~I~GvGpktA~~ly~ 302 (527)
+...++. +.+|||||+++|.++.+
T Consensus 41 ~i~~~~~~~~~l~gIG~~ia~kI~E 65 (68)
T PF14716_consen 41 PITSGEEDLKKLPGIGKSIAKKIDE 65 (68)
T ss_dssp -HHSHHHHHCTSTTTTHHHHHHHHH
T ss_pred hHhhHHHHHhhCCCCCHHHHHHHHH
Confidence 3334454 78999999999999854
No 195
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=59.94 E-value=14 Score=41.96 Aligned_cols=41 Identities=22% Similarity=0.524 Sum_probs=22.2
Q ss_pred HHhhccCcCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhcccc
Q 009742 285 LFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLK 326 (527)
Q Consensus 285 lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~q~~Glk 326 (527)
.|..|+|||++++++|++. +-|++++.++. .|....++|-+
T Consensus 526 ~L~~IpGIG~kr~~~LL~~-FGS~~~I~~As~eeL~~vpGi~~~ 568 (577)
T PRK14668 526 VLDDVPGVGPETRKRLLRR-FGSVEGVREASVEDLRDVPGVGEK 568 (577)
T ss_pred HHhcCCCCCHHHHHHHHHH-cCCHHHHHhCCHHHHHhCCCCCHH
Confidence 3446777777777777763 34555555432 24344444433
No 196
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=59.82 E-value=18 Score=37.19 Aligned_cols=29 Identities=17% Similarity=0.130 Sum_probs=26.2
Q ss_pred HhhccCcCHHHHHHHHHhCCCCHHHHhhc
Q 009742 286 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 314 (527)
Q Consensus 286 f~~I~GvGpktA~~ly~~GirTledL~~~ 314 (527)
|.++||+|+..++++.+.|+.|++||...
T Consensus 153 L~Qlp~i~~~~~~~l~~~~i~s~~~l~~~ 181 (312)
T smart00611 153 LLQLPHLPEEILKRLEKKKVLSLEDLLEL 181 (312)
T ss_pred cccCCCCCHHHHHHHHhCCCCCHHHHHhc
Confidence 34899999999999999999999999864
No 197
>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=59.28 E-value=12 Score=31.54 Aligned_cols=30 Identities=23% Similarity=0.486 Sum_probs=23.9
Q ss_pred HhhccCcCHHHHHHHHH-h---CCCCHHHHhhcc
Q 009742 286 FGEVWGIGPATAQKLYE-K---GHRTLDDLKNED 315 (527)
Q Consensus 286 f~~I~GvGpktA~~ly~-~---GirTledL~~~~ 315 (527)
|+.|.|||.++|+++.+ . .++|++|+....
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 67999999999999985 2 789999988643
No 198
>PRK02362 ski2-like helicase; Provisional
Probab=59.22 E-value=65 Score=37.55 Aligned_cols=52 Identities=19% Similarity=0.464 Sum_probs=39.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHHh-C
Q 009742 243 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-G 304 (527)
Q Consensus 243 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~-G 304 (527)
-+|..|||||...+.+..+ .| +.-++++.+-++..+..+ +|+|+|+++.+. |
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 677777776555555555 599999999986 6
No 199
>PRK13844 recombination protein RecR; Provisional
Probab=59.02 E-value=6.3 Score=38.54 Aligned_cols=32 Identities=16% Similarity=0.251 Sum_probs=24.1
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHH
Q 009742 243 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHF 274 (527)
Q Consensus 243 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l 274 (527)
+.+..|||||++.|.++.-.+-.-.-.++++|
T Consensus 15 ~~l~~LPGIG~KsA~Rla~~lL~~~~~~~~~l 46 (200)
T PRK13844 15 ESLRKLPTIGKKSSQRLALYLLDKSPETAIAI 46 (200)
T ss_pred HHHHHCCCCCHHHHHHHHHHHHcCCHHHHHHH
Confidence 67899999999999999887765444444443
No 200
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=58.71 E-value=6.3 Score=41.01 Aligned_cols=54 Identities=28% Similarity=0.418 Sum_probs=40.8
Q ss_pred hhHHHHHHhhccCcCHHHHHHHHH---hCC-CCHHHHhhccC------cchhhhccccchhhhc
Q 009742 279 KVRTISLFGEVWGIGPATAQKLYE---KGH-RTLDDLKNEDS------LTHSQRLGLKYFDDIK 332 (527)
Q Consensus 279 ~~~~l~lf~~I~GvGpktA~~ly~---~Gi-rTledL~~~~~------L~~~q~~Glk~yed~~ 332 (527)
|..+.+...++||||||.|++|-+ -|. +-+++++++.+ +++.-|+|.++.+.|.
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 445677888999999999999976 265 77888886432 5667778888877765
No 201
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=58.03 E-value=8.2 Score=44.59 Aligned_cols=27 Identities=41% Similarity=0.623 Sum_probs=24.9
Q ss_pred HhhccCcCHHHHHHHHHhCCCCHHHHh
Q 009742 286 FGEVWGIGPATAQKLYEKGHRTLDDLK 312 (527)
Q Consensus 286 f~~I~GvGpktA~~ly~~GirTledL~ 312 (527)
++.+.||||++|+.|-+.||.|+.||.
T Consensus 11 ~~~l~gvg~~~~~~l~~lgi~t~~dll 37 (681)
T PRK10917 11 LTSLKGVGPKTAEKLAKLGIHTVQDLL 37 (681)
T ss_pred hhhcCCCCHHHHHHHHHcCCCCHHHHh
Confidence 457899999999999989999999998
No 202
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=57.85 E-value=6.1 Score=44.69 Aligned_cols=29 Identities=24% Similarity=0.339 Sum_probs=24.1
Q ss_pred HHhhccCcCHHHHHHHHHhCCCCHHHHhhc
Q 009742 285 LFGEVWGIGPATAQKLYEKGHRTLDDLKNE 314 (527)
Q Consensus 285 lf~~I~GvGpktA~~ly~~GirTledL~~~ 314 (527)
.|.+||||||++.+.|++ -+.|+++++++
T Consensus 515 ~L~~I~GiG~kr~~~LL~-~Fgs~~~I~~A 543 (574)
T PRK14670 515 NYTKIKGIGEKKAKKILK-SLGTYKDILLL 543 (574)
T ss_pred ccccCCCCCHHHHHHHHH-HhCCHHHHHhC
Confidence 456999999999999998 45688888865
No 203
>PTZ00217 flap endonuclease-1; Provisional
Probab=57.67 E-value=7.9 Score=41.77 Aligned_cols=26 Identities=35% Similarity=0.640 Sum_probs=21.9
Q ss_pred hhccCcCHHHHHHHHHhCCCCHHHHhh
Q 009742 287 GEVWGIGPATAQKLYEKGHRTLDDLKN 313 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~GirTledL~~ 313 (527)
-+|+|||||||.+|.++ +.|++.+.+
T Consensus 238 pgi~GIG~ktA~~Li~~-~gsle~il~ 263 (393)
T PTZ00217 238 DTIKGIGPKTAYKLIKK-YKSIEEILE 263 (393)
T ss_pred CCCCCccHHHHHHHHHH-cCCHHHHHH
Confidence 47999999999999987 338888875
No 204
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=57.36 E-value=8.4 Score=44.06 Aligned_cols=32 Identities=25% Similarity=0.423 Sum_probs=25.7
Q ss_pred HHHHHhhccCcCHHHHHHHHHhCCCCHHHHhhc
Q 009742 282 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 314 (527)
Q Consensus 282 ~l~lf~~I~GvGpktA~~ly~~GirTledL~~~ 314 (527)
....|..|+|||||+|+.|++. +.|+++|.++
T Consensus 567 ~~s~L~~I~GIG~k~a~~Ll~~-Fgs~~~i~~A 598 (621)
T PRK14671 567 LQTELTDIAGIGEKTAEKLLEH-FGSVEKVAKA 598 (621)
T ss_pred hhhhhhcCCCcCHHHHHHHHHH-cCCHHHHHhC
Confidence 3456679999999999999874 4488888864
No 205
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=57.25 E-value=14 Score=42.32 Aligned_cols=49 Identities=27% Similarity=0.575 Sum_probs=34.5
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHH
Q 009742 243 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 302 (527)
Q Consensus 243 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 302 (527)
..|.+|||||++.+..|..-. |++ +.+.+- ..+.+.+| ||+++|+.+++
T Consensus 569 s~L~~I~GIG~k~a~~Ll~~F--gs~---~~i~~A----s~eeL~~v--ig~k~A~~I~~ 617 (621)
T PRK14671 569 TELTDIAGIGEKTAEKLLEHF--GSV---EKVAKA----SLEELAAV--AGPKTAETIYR 617 (621)
T ss_pred hhhhcCCCcCHHHHHHHHHHc--CCH---HHHHhC----CHHHHHHH--hCHHHHHHHHH
Confidence 468899999999999765532 233 444432 34445577 99999999976
No 206
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=56.81 E-value=5.6 Score=44.96 Aligned_cols=29 Identities=24% Similarity=0.521 Sum_probs=23.9
Q ss_pred HHhhccCcCHHHHHHHHHhCCCCHHHHhhc
Q 009742 285 LFGEVWGIGPATAQKLYEKGHRTLDDLKNE 314 (527)
Q Consensus 285 lf~~I~GvGpktA~~ly~~GirTledL~~~ 314 (527)
.|.+|+|||||+.+.|++. +-|++.++++
T Consensus 515 ~Ld~I~GiG~kr~~~Ll~~-Fgs~~~ik~A 543 (567)
T PRK14667 515 ILDKIKGIGEVKKEIIYRN-FKTLYDFLKA 543 (567)
T ss_pred ccccCCCCCHHHHHHHHHH-hCCHHHHHhC
Confidence 4569999999999999984 5588888865
No 207
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=56.22 E-value=9.6 Score=39.52 Aligned_cols=39 Identities=28% Similarity=0.333 Sum_probs=27.0
Q ss_pred HHHHhhccCcCHHHHHHHHHh-CC--CCHHHHhhcc-Ccchhh
Q 009742 283 ISLFGEVWGIGPATAQKLYEK-GH--RTLDDLKNED-SLTHSQ 321 (527)
Q Consensus 283 l~lf~~I~GvGpktA~~ly~~-Gi--rTledL~~~~-~L~~~q 321 (527)
.+++.+|||+|+|.|+++... -. -|+|+|++-+ .+.+++
T Consensus 329 ~~~llRVPGiG~ksa~rIv~~Rr~~rl~~e~Lkk~GvvlkRak 371 (404)
T COG4277 329 YKELLRVPGIGVKSARRIVMTRRRTRLTLEDLKKLGVVLKRAK 371 (404)
T ss_pred HHHhcccCCCChHHHHHHHHHhhhcccCHHHHhhhceeeeccc
Confidence 445569999999999999864 33 3678887643 244443
No 208
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=55.83 E-value=8.2 Score=40.58 Aligned_cols=32 Identities=19% Similarity=0.239 Sum_probs=28.4
Q ss_pred HHHHHhhccCcCHHHHHHHHHhCCCCHHHHhh
Q 009742 282 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKN 313 (527)
Q Consensus 282 ~l~lf~~I~GvGpktA~~ly~~GirTledL~~ 313 (527)
.-.-|+.|.||||+.++.|.+.||.+.+++-+
T Consensus 261 ~~DdL~~I~GiGp~~e~~L~~~Gi~~f~QiA~ 292 (326)
T PRK12311 261 APDDLKKLTGVSPQIEKKLNDLGIFHFWQLAE 292 (326)
T ss_pred CchhhhhhccCChhhhhhhhhcCCCCHHHhhC
Confidence 33566899999999999999999999999974
No 209
>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=55.52 E-value=12 Score=38.61 Aligned_cols=50 Identities=24% Similarity=0.451 Sum_probs=35.6
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHH
Q 009742 245 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 302 (527)
Q Consensus 245 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 302 (527)
+..|||||+.+++++.+. -+..+++|..-. .+.+.+++|++.++|.+||+
T Consensus 1 l~~i~gig~~~~~~L~~~----Gi~ti~dl~~~~----~~~L~~~~g~~~~~a~~l~~ 50 (310)
T TIGR02236 1 LEDLPGVGPATAEKLREA----GYDTFEAIAVAS----PKELSEIAGISEGTAAKIIQ 50 (310)
T ss_pred CcccCCCCHHHHHHHHHc----CCCCHHHHHcCC----HHHHHhccCCCHHHHHHHHH
Confidence 457999999998887764 234455655432 23445888999999999986
No 210
>PRK04374 PII uridylyl-transferase; Provisional
Probab=55.10 E-value=40 Score=40.22 Aligned_cols=62 Identities=19% Similarity=0.405 Sum_probs=39.7
Q ss_pred HHHHHHHHhhhcCC---CeEEEeccccccc-CCccCCeeEEEecCCc--chhhhhHHHHHHHHHHcCc
Q 009742 343 MERLLQKAGEEVLP---EVIILCGGSYRRG-KASCGDLDVVIMHPDR--KSHKGFLSKYVKKLKEMKF 404 (527)
Q Consensus 343 i~~iv~~~~~~~~p---~~~v~~~GsyRRG-ke~~gDVDiLIt~~~~--~~~~~~l~~lv~~L~~~g~ 404 (527)
+..++.++.....| ++.+..+|||=|| ..-.+|||+||-+++. ........+++..|=+.|+
T Consensus 55 ~D~~l~~~~~~~~~~~~~~alvAvGgYGR~EL~p~SDIDLliL~~~~~~~~~~~~i~~~i~~LWD~gL 122 (869)
T PRK04374 55 VDQLMRNAWTRCIPADSGLSLHAVGGYGRGELFPRSDVDLLVLGETAAQQRHEQALARLFALLWDVGL 122 (869)
T ss_pred HHHHHHHHHHHhCCCcCCEEEEEcCCccccccCCcccceEEEEecCCCCchHHHHHHHHHHHHHhcCC
Confidence 45555554443334 3567788999555 5667899999988743 2344566777776666654
No 211
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=55.01 E-value=13 Score=37.54 Aligned_cols=32 Identities=22% Similarity=0.360 Sum_probs=22.7
Q ss_pred HHHHhhchhHHHHHHhhccCcCHHHHHHHHHhC
Q 009742 272 EHFEKDEKVRTISLFGEVWGIGPATAQKLYEKG 304 (527)
Q Consensus 272 e~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~G 304 (527)
+++..|.|..+=+|+ ++||||||.|.--.+.+
T Consensus 148 d~f~gDIP~~v~dLl-sLPGVGPKMa~L~m~~A 179 (286)
T KOG1921|consen 148 DKFDGDIPDTVEDLL-SLPGVGPKMAHLTMQVA 179 (286)
T ss_pred HHhCCCCchhHHHHh-cCCCCchHHHHHHHHHH
Confidence 455667776555555 99999999998765533
No 212
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=54.32 E-value=16 Score=41.74 Aligned_cols=30 Identities=27% Similarity=0.442 Sum_probs=24.1
Q ss_pred HHHhhccCcCHHHHHHHHHhCCCCHHHHhhc
Q 009742 284 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 314 (527)
Q Consensus 284 ~lf~~I~GvGpktA~~ly~~GirTledL~~~ 314 (527)
..|.+||||||+++++|++. +.|+++++++
T Consensus 552 S~L~~IpGIG~kr~~~LL~~-FgSi~~I~~A 581 (624)
T PRK14669 552 SELLEIPGVGAKTVQRLLKH-FGSLERVRAA 581 (624)
T ss_pred HHHhcCCCCCHHHHHHHHHH-cCCHHHHHhC
Confidence 34569999999999999984 5577777764
No 213
>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=54.31 E-value=9.9 Score=40.12 Aligned_cols=27 Identities=41% Similarity=0.588 Sum_probs=23.0
Q ss_pred hhccCcCHHHHHHHHHhCCCCHHHHhhc
Q 009742 287 GEVWGIGPATAQKLYEKGHRTLDDLKNE 314 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~GirTledL~~~ 314 (527)
.+|+|||||||.+|.++ +.|++.+.+.
T Consensus 239 ~Gv~GIG~ktA~kli~~-~gsie~il~~ 265 (338)
T TIGR03674 239 EGVKGIGPKTALKLIKE-HGDLEKVLKA 265 (338)
T ss_pred CCCCCccHHHHHHHHHH-cCCHHHHHHh
Confidence 48999999999999987 4489998754
No 214
>PRK05755 DNA polymerase I; Provisional
Probab=54.11 E-value=9.1 Score=45.57 Aligned_cols=25 Identities=44% Similarity=0.598 Sum_probs=20.9
Q ss_pred hhccCcCHHHHHHHHHh-CCCCHHHHhh
Q 009742 287 GEVWGIGPATAQKLYEK-GHRTLDDLKN 313 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~-GirTledL~~ 313 (527)
-.|+|||||||.+|.++ | |+|.+.+
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 46899999999999986 6 7777763
No 215
>PRK07758 hypothetical protein; Provisional
Probab=53.51 E-value=13 Score=32.04 Aligned_cols=23 Identities=13% Similarity=0.355 Sum_probs=20.3
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHh
Q 009742 243 DQVKGLPGIGKSMQDHIQEIVTT 265 (527)
Q Consensus 243 ~~l~~lpgIG~~ia~kI~Eil~t 265 (527)
+||.+|+|+|++..+.|+|-|..
T Consensus 67 ~ELl~iknlGkKSL~EIkekL~E 89 (95)
T PRK07758 67 KEILKLHGMGPASLPKLRKALEE 89 (95)
T ss_pred HHHHHccCCCHHHHHHHHHHHHH
Confidence 68999999999999999988754
No 216
>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=53.20 E-value=3.8 Score=32.81 Aligned_cols=44 Identities=25% Similarity=0.367 Sum_probs=32.1
Q ss_pred cCcCHHHHHHHHHhCCCCHHHHhhc--cCcchhhhccccchhhhcc
Q 009742 290 WGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDIKT 333 (527)
Q Consensus 290 ~GvGpktA~~ly~~GirTledL~~~--~~L~~~q~~Glk~yed~~~ 333 (527)
-|+-+++...|-..||.|++||..- ..|...++||-+..+++..
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 3666777788878899999999853 3588888999888777654
No 217
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=53.16 E-value=29 Score=34.35 Aligned_cols=33 Identities=18% Similarity=0.466 Sum_probs=24.3
Q ss_pred HHHhcCCcccc-chhhhcCCCCCCHHHHHHHHHH
Q 009742 230 PVIEKLPFKIE-SADQVKGLPGIGKSMQDHIQEI 262 (527)
Q Consensus 230 ~~l~~l~~~i~-s~~~l~~lpgIG~~ia~kI~Ei 262 (527)
..++.+..+|. ++++|.+|||||.++|..+--+
T Consensus 95 ~l~e~~~g~vP~~~~eL~~LPGVGrKTAnvVL~~ 128 (211)
T COG0177 95 ILLEKFGGEVPDTREELLSLPGVGRKTANVVLSF 128 (211)
T ss_pred HHHHHcCCCCCchHHHHHhCCCcchHHHHHHHHh
Confidence 33445555554 4689999999999999987643
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=52.69 E-value=30 Score=33.26 Aligned_cols=42 Identities=10% Similarity=0.311 Sum_probs=27.7
Q ss_pred hHHHHHHHHHHHh-cCCcccc-chhhhcCCCCCCHHHHHHHHHH
Q 009742 221 RSFSYYKAIPVIE-KLPFKIE-SADQVKGLPGIGKSMQDHIQEI 262 (527)
Q Consensus 221 r~~aY~rAa~~l~-~l~~~i~-s~~~l~~lpgIG~~ia~kI~Ei 262 (527)
|+..-.+.+..|. .....+. ..++|..|||||+.+|+.|-=+
T Consensus 82 Ka~~i~~~a~~i~~~~~~~~~~~~~~L~~l~GIG~ktA~~ill~ 125 (191)
T TIGR01083 82 KAKNIIALCRILVERYGGEVPEDREELVKLPGVGRKTANVVLNV 125 (191)
T ss_pred HHHHHHHHHHHHHHHcCCCCchHHHHHHhCCCCcHHHHHHHHHH
Confidence 5555555555553 3322222 3578999999999999998733
No 219
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=52.62 E-value=6.3 Score=45.23 Aligned_cols=50 Identities=14% Similarity=0.229 Sum_probs=35.0
Q ss_pred HHhhccCcCHHHHHHHHHhCCCCHHHHhhcc--CcchhhhccccchhhhccCc
Q 009742 285 LFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIKTRI 335 (527)
Q Consensus 285 lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~q~~Glk~yed~~~~i 335 (527)
.|.+|+||||++.+.|++. +-|+++|+++. .|....+++.+..+.+...-
T Consensus 609 ~L~~IpGiG~kr~~~LL~~-FgS~~~i~~As~eel~~v~gi~~~~A~~i~~~~ 660 (691)
T PRK14672 609 SFERLPHVGKVRAHRLLAH-FGSFRSLQSATPQDIATAIHIPLTQAHTILHAA 660 (691)
T ss_pred ccccCCCCCHHHHHHHHHH-hcCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHh
Confidence 4569999999999999984 55888888653 35555556655555554433
No 220
>COG5186 PAP1 Poly(A) polymerase [RNA processing and modification]
Probab=52.54 E-value=56 Score=34.96 Aligned_cols=52 Identities=27% Similarity=0.447 Sum_probs=41.5
Q ss_pred CeEEEecccccccCC-ccCCeeEEEecCCcchhhhhHHHHHHHHHHcCcccce
Q 009742 357 EVIILCGGSYRRGKA-SCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLRED 408 (527)
Q Consensus 357 ~~~v~~~GsyRRGke-~~gDVDiLIt~~~~~~~~~~l~~lv~~L~~~g~l~~~ 408 (527)
|-++.--||||-|-- -+.|||-|+..|.--+-.++|..+-..|+...-+.+.
T Consensus 81 GGKIFTyGSYRLGVhgpGsDIDtLvvVPkHVsR~dFFt~f~~~Lrer~ei~ev 133 (552)
T COG5186 81 GGKIFTYGSYRLGVHGPGSDIDTLVVVPKHVSRSDFFTHFYEELRERPEIEEV 133 (552)
T ss_pred CceeeeecceeeeccCCCCCcceEEEecccccHHHHHHHHHHHhccCcchhhh
Confidence 346777799999975 4779999999998777788999988888887666543
No 221
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=52.12 E-value=9.7 Score=34.35 Aligned_cols=24 Identities=25% Similarity=0.407 Sum_probs=19.5
Q ss_pred HHHHhhccCcCHHHHHHHHHh-CCC
Q 009742 283 ISLFGEVWGIGPATAQKLYEK-GHR 306 (527)
Q Consensus 283 l~lf~~I~GvGpktA~~ly~~-Gir 306 (527)
.--|+.|+|||+++|..+-+. ||.
T Consensus 16 ~~aLt~i~GIG~~~A~~ic~~lgi~ 40 (122)
T CHL00137 16 EYALTYIYGIGLTSAKEILEKANID 40 (122)
T ss_pred eeeecccccccHHHHHHHHHHcCcC
Confidence 334689999999999999875 764
No 222
>COG1669 Predicted nucleotidyltransferases [General function prediction only]
Probab=51.69 E-value=73 Score=27.66 Aligned_cols=30 Identities=27% Similarity=0.393 Sum_probs=23.2
Q ss_pred CCe-EEEecccccccCCc-cCCeeEEEecCCc
Q 009742 356 PEV-IILCGGSYRRGKAS-CGDLDVVIMHPDR 385 (527)
Q Consensus 356 p~~-~v~~~GsyRRGke~-~gDVDiLIt~~~~ 385 (527)
.|+ .+.+-|||-||... -+||||||-...+
T Consensus 22 ~gv~~~~vFGS~aRgE~~~~SDIDILVef~~~ 53 (97)
T COG1669 22 YGVKRVAVFGSYARGEQKPDSDIDILVEFEPG 53 (97)
T ss_pred hCCceEEEeeeeecCCCCCCCCceeEEeecCC
Confidence 455 68899999999653 3899999976554
No 223
>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=51.69 E-value=37 Score=28.53 Aligned_cols=50 Identities=22% Similarity=0.365 Sum_probs=35.7
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHHhCC
Q 009742 245 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGH 305 (527)
Q Consensus 245 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~Gi 305 (527)
+..|+|||+.+++.|.+--+.|.+.-++++.... +++..+..+.|...|.
T Consensus 29 l~~Ikglg~~~a~~I~~~R~~g~f~s~~df~~R~-----------~~i~~~~le~Li~aGa 78 (90)
T PF14579_consen 29 LSAIKGLGEEVAEKIVEERENGPFKSLEDFIQRL-----------PKINKRQLEALIKAGA 78 (90)
T ss_dssp GGGSTTS-HHHHHHHHHHHHCSS-SSHHHHHHHS------------TS-HHHHHHHHHTTT
T ss_pred HhhcCCCCHHHHHHHHHhHhcCCCCCHHHHHHHH-----------hcCCHHHHHHHHHCCC
Confidence 6789999999999999988888888777765422 2677777777776653
No 224
>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=51.18 E-value=23 Score=36.43 Aligned_cols=22 Identities=18% Similarity=0.197 Sum_probs=18.3
Q ss_pred HHHHHhhccCcCHHHHHHHHHh
Q 009742 282 TISLFGEVWGIGPATAQKLYEK 303 (527)
Q Consensus 282 ~l~lf~~I~GvGpktA~~ly~~ 303 (527)
.++.|+++||||++||..+---
T Consensus 103 ~~~~L~~LpGIG~~TA~~Il~~ 124 (275)
T TIGR01084 103 DFEDLAALPGVGRYTAGAILSF 124 (275)
T ss_pred HHHHHHhCCCCCHHHHHHHHHH
Confidence 5677889999999999987643
No 225
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=51.10 E-value=10 Score=34.27 Aligned_cols=23 Identities=22% Similarity=0.446 Sum_probs=19.2
Q ss_pred HHHhhccCcCHHHHHHHHHh-CCC
Q 009742 284 SLFGEVWGIGPATAQKLYEK-GHR 306 (527)
Q Consensus 284 ~lf~~I~GvGpktA~~ly~~-Gir 306 (527)
--|+.|+|||+.+|..+.+. |+.
T Consensus 17 ~aL~~I~GIG~~~a~~i~~~lgi~ 40 (122)
T PRK05179 17 IALTYIYGIGRTRAKEILAAAGID 40 (122)
T ss_pred eeecccccccHHHHHHHHHHhCcC
Confidence 34589999999999999875 764
No 226
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=50.28 E-value=24 Score=35.60 Aligned_cols=29 Identities=24% Similarity=0.481 Sum_probs=22.1
Q ss_pred cCCcccc-chhhhcCCCCCCHHHHHHHHHH
Q 009742 234 KLPFKIE-SADQVKGLPGIGKSMQDHIQEI 262 (527)
Q Consensus 234 ~l~~~i~-s~~~l~~lpgIG~~ia~kI~Ei 262 (527)
.++.+|- ++++|.+|||||++||-....+
T Consensus 149 ~f~gDIP~~v~dLlsLPGVGPKMa~L~m~~ 178 (286)
T KOG1921|consen 149 KFDGDIPDTVEDLLSLPGVGPKMAHLTMQV 178 (286)
T ss_pred HhCCCCchhHHHHhcCCCCchHHHHHHHHH
Confidence 4455554 4799999999999999876543
No 227
>PRK01216 DNA polymerase IV; Validated
Probab=49.50 E-value=53 Score=34.81 Aligned_cols=52 Identities=21% Similarity=0.362 Sum_probs=35.8
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHHh--CCC
Q 009742 245 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHR 306 (527)
Q Consensus 245 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--Gir 306 (527)
+..|||||++++++...+ -+..+.+|.+-.+....+.| |+..+..||+. |+.
T Consensus 180 i~~l~giG~~~~~~L~~~----Gi~TigdL~~~~~~~L~~rf------G~~~~~~L~~~a~G~d 233 (351)
T PRK01216 180 IADIPGIGDITAEKLKKL----GVNKLVDTLRIEFDELKGII------GEAKAKYLFSLARNEY 233 (351)
T ss_pred cccccCCCHHHHHHHHHc----CCCcHHHHhcCCHHHHHHHH------CHHHHHHHHHHhCCCC
Confidence 677899999988877654 35667777654444444455 67778888883 754
No 228
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=49.39 E-value=38 Score=30.77 Aligned_cols=42 Identities=10% Similarity=0.307 Sum_probs=26.8
Q ss_pred hHHHHHHHHHHHhc-CCccc-cchhhhcCCCCCCHHHHHHHHHH
Q 009742 221 RSFSYYKAIPVIEK-LPFKI-ESADQVKGLPGIGKSMQDHIQEI 262 (527)
Q Consensus 221 r~~aY~rAa~~l~~-l~~~i-~s~~~l~~lpgIG~~ia~kI~Ei 262 (527)
|+..-...+..|.. ....+ ...+.|..|||||+.+|+.|.=+
T Consensus 48 ka~~i~~~a~~~~~~~~~~~~~~~~~L~~l~GIG~~tA~~~l~~ 91 (149)
T smart00478 48 KAKYLIELARILVEEYGGEVPDDREELLKLPGVGRKTANAVLSF 91 (149)
T ss_pred HHHHHHHHHHHHHHHHCCCccHHHHHHHcCCCCcHHHHHHHHHH
Confidence 55555555555432 12222 23577999999999999987655
No 229
>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=48.49 E-value=7.4 Score=40.46 Aligned_cols=51 Identities=25% Similarity=0.342 Sum_probs=34.5
Q ss_pred HHHHHhhccCcCHHHHHHHHHh---C-CCCHHHHhhcc-----Ccchhhhccccchhhhc
Q 009742 282 TISLFGEVWGIGPATAQKLYEK---G-HRTLDDLKNED-----SLTHSQRLGLKYFDDIK 332 (527)
Q Consensus 282 ~l~lf~~I~GvGpktA~~ly~~---G-irTledL~~~~-----~L~~~q~~Glk~yed~~ 332 (527)
.+..+++|||||+++|.++.+. | +..+++|+++. .|....++|.+....|-
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 3445579999999999999863 4 35566666431 25667777766655554
No 230
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=48.32 E-value=30 Score=39.30 Aligned_cols=83 Identities=20% Similarity=0.378 Sum_probs=50.7
Q ss_pred cHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhc
Q 009742 199 NKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDE 278 (527)
Q Consensus 199 N~~ia~~L~~la~~~e~~g~~~r~~aY~rAa~~l~~l~~~i~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~ 278 (527)
|......|..+-+... ..+.+|.|.-+.=..+ -..|.+|||||++...++-.-. |++..+ +
T Consensus 497 ~~p~l~~lq~irDEaH-----rfAi~~hR~~R~k~~~------~s~Ld~I~GiG~~r~~~LL~~F--gs~~~i---~--- 557 (581)
T COG0322 497 NSPALYLLQRIRDEAH-----RFAITYHRKKRSKAML------QSSLDDIPGIGPKRRKALLKHF--GSLKGI---K--- 557 (581)
T ss_pred CCHHHHHHHHHHHHHH-----HHHHHHHHHHhhhhhh------cCccccCCCcCHHHHHHHHHHh--hCHHHH---H---
Confidence 5555555544433211 2466777765321111 2458899999999888765432 333333 2
Q ss_pred hhHHHHHHhhccCcCHHHHHHHHH
Q 009742 279 KVRTISLFGEVWGIGPATAQKLYE 302 (527)
Q Consensus 279 ~~~~l~lf~~I~GvGpktA~~ly~ 302 (527)
.-+++.|..| ||+++.|+++|+
T Consensus 558 -~As~eel~~v-gi~~~~a~~i~~ 579 (581)
T COG0322 558 -SASVEELAKV-GISKKLAEKIYE 579 (581)
T ss_pred -hcCHHHHHHc-CCCHHHHHHHHh
Confidence 2356777899 999999999986
No 231
>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=48.05 E-value=35 Score=36.56 Aligned_cols=58 Identities=19% Similarity=0.452 Sum_probs=34.8
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhch---------hH--HHHHHhhccCcCHHHHHHHHHh--CCCC
Q 009742 244 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEK---------VR--TISLFGEVWGIGPATAQKLYEK--GHRT 307 (527)
Q Consensus 244 ~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~---------~~--~l~lf~~I~GvGpktA~~ly~~--GirT 307 (527)
.+..|||||+++++++..+ | +..+-+|.+... .. ....+.+.+ |.+++.++|+. |+.+
T Consensus 173 pv~~l~GiG~~~~~kL~~~---G-I~tigdl~~~~~~~~~~~~~~~~~~s~~~L~~~f--G~~~g~~l~~~a~G~d~ 243 (379)
T cd01703 173 DLRKIPGIGYKTAAKLEAH---G-ISSVRDLQEFSNRNRQTVGAAPSLLELLLMVKEF--GEGIGQRIWKLLFGRDT 243 (379)
T ss_pred CccccCCcCHHHHHHHHHc---C-CCcHHHHHhCCcccccccccccccccHHHHHHHH--CHHHHHHHHHHHCCCCC
Confidence 4788999999999998875 2 333333332220 00 022233333 67778888875 8875
No 232
>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=47.59 E-value=22 Score=36.35 Aligned_cols=29 Identities=31% Similarity=0.470 Sum_probs=22.5
Q ss_pred HHhhccCcCHHHHHHHHHhCCCCHHHHhh
Q 009742 285 LFGEVWGIGPATAQKLYEKGHRTLDDLKN 313 (527)
Q Consensus 285 lf~~I~GvGpktA~~ly~~GirTledL~~ 313 (527)
.|.++||+|++.++++-+.|+.|+++|.+
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 34599999999999999999999999995
No 233
>KOG0323 consensus TFIIF-interacting CTD phosphatases, including NLI-interacting factor [Transcription]
Probab=47.37 E-value=6 Score=45.05 Aligned_cols=59 Identities=31% Similarity=0.367 Sum_probs=47.5
Q ss_pred HHHhcCCEEEeecCCCccEEEEeCcHHH--HH------hccccchHHHHHHhcCCCcCCcccccccC
Q 009742 42 KLVQMGATVEEKLSKKVTHVLAMDLEAL--LQ------QSVIRYQWLEDSLRLGEKVSEDLYRIKLD 100 (527)
Q Consensus 42 ~~~~~G~~v~~~~s~~VTHVV~~~~~~~--l~------~~vv~~~Wl~ec~~~g~~v~~~~~~l~~~ 100 (527)
.+.+.|+.+.+..+..+||+|+.++... .+ ..||...|+..|+..=.-|++..|.+...
T Consensus 467 ~~~~~g~vs~~~~~~~~th~i~~~~gt~k~~~a~~~~~~~Vv~~~wl~~~~e~w~~v~ek~~~l~~~ 533 (635)
T KOG0323|consen 467 VAQQLGAVSAPDVSDKTTHLIAANAGTKKVYKAVVSGSAKVVNAAWLWRSLEKWGKVEEKLEPLDDD 533 (635)
T ss_pred hhhcccceecccccchhhhHHhhccCcceeeccccccceeEechhHHHHHHHHhcchhccccccccc
Confidence 4567889999999999999999886532 11 13999999999999999999888877543
No 234
>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=47.22 E-value=12 Score=33.28 Aligned_cols=23 Identities=35% Similarity=0.579 Sum_probs=19.2
Q ss_pred HHHhhccCcCHHHHHHHHHh-CCC
Q 009742 284 SLFGEVWGIGPATAQKLYEK-GHR 306 (527)
Q Consensus 284 ~lf~~I~GvGpktA~~ly~~-Gir 306 (527)
--|++|+|||+++|..+-+. |+.
T Consensus 15 ~aL~~i~GIG~~~a~~i~~~lgi~ 38 (113)
T TIGR03631 15 IALTYIYGIGRTRARKILEKAGID 38 (113)
T ss_pred eeeeeeecccHHHHHHHHHHhCcC
Confidence 34589999999999999875 764
No 235
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=47.01 E-value=65 Score=38.61 Aligned_cols=48 Identities=17% Similarity=0.476 Sum_probs=33.8
Q ss_pred CeEEEecccccccC-CccCCeeEEEecCCcc--hhhhhHHHHHHHHHHcCc
Q 009742 357 EVIILCGGSYRRGK-ASCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMKF 404 (527)
Q Consensus 357 ~~~v~~~GsyRRGk-e~~gDVDiLIt~~~~~--~~~~~l~~lv~~L~~~g~ 404 (527)
++.+..+|||=||. .-.+|||+||-+++.. ....+...++..|-+.|+
T Consensus 78 ~~alvAvGgyGR~EL~p~SDiDll~l~~~~~~~~~~~~i~~~~~~LwD~gL 128 (895)
T PRK00275 78 DIALVAVGGYGRGELHPYSDIDLLILLDSADHEEFREPIERFLTLLWDIGL 128 (895)
T ss_pred CEEEEEcCCccccCcCCCCCceEEEEecCCCChHHHHHHHHHHHHHHhcCC
Confidence 45677899996664 5689999999887532 244566677776666664
No 236
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]
Probab=46.37 E-value=11 Score=37.34 Aligned_cols=46 Identities=24% Similarity=0.256 Sum_probs=37.0
Q ss_pred HHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHH
Q 009742 256 QDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLY 301 (527)
Q Consensus 256 a~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly 301 (527)
..-+.|....|.+...+.+..-.....++++|+|.|||+=|++++.
T Consensus 137 Lh~lA~~~~ng~I~s~~~i~~mseEeL~~~LT~VKGIg~Wtv~Mfl 182 (254)
T KOG1918|consen 137 LHSLAEAYTNGYIPSKSGIEKMSEEELIERLTNVKGIGRWTVEMFL 182 (254)
T ss_pred HHHHHHHHhcCCCCchHHHhhcCHHHHHHHHHhccCccceeeeeee
Confidence 3446667778988888777766667799999999999999998873
No 237
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=45.81 E-value=34 Score=40.23 Aligned_cols=81 Identities=19% Similarity=0.192 Sum_probs=48.3
Q ss_pred CCCCCCCcCCeEEEEeeCCCChhHHHHHH-HHHHhcCCEEEeec--CCCccEEEEeCcHHHHH-----hccccchHHHHH
Q 009742 12 ALDSNGIFAGMRVFLVEKGVQNRRLQIWR-QKLVQMGATVEEKL--SKKVTHVLAMDLEALLQ-----QSVIRYQWLEDS 83 (527)
Q Consensus 12 ~~~~~~~f~~~~i~iv~~~~g~~r~~~l~-~~~~~~G~~v~~~~--s~~VTHVV~~~~~~~l~-----~~vv~~~Wl~ec 83 (527)
+..+..+|...+|+| +|+..+..-.|+ -.++-|+....+.. -+.|+|.++-+. .+. -..+++.|+.+.
T Consensus 155 ~~~~~ki~~~n~iki--nG~~E~~~~dlepp~gv~~d~~~~~~~~~rd~v~~~l~~~~--l~n~~f~n~~~~sP~~~~~k 230 (1016)
T KOG2093|consen 155 SSQSSKIFKNNVIKI--NGYNEPESLDLEPPSGVLHDKAEDDSTSARDHVDHELAGNL--LLNKRFVNIENTSPDWIVDK 230 (1016)
T ss_pred cccchhccccceeee--cCCCCccccccCCCcccccchhhhhhhhHHHHHHHHhcccc--ccccccceeeecCchhhhhh
Confidence 455668999999999 566655332222 11111222222222 234666666541 111 128899999999
Q ss_pred HhcCCCcCCcccc
Q 009742 84 LRLGEKVSEDLYR 96 (527)
Q Consensus 84 ~~~g~~v~~~~~~ 96 (527)
+..-+..+++.|.
T Consensus 231 ~~~a~~~~~~~~S 243 (1016)
T KOG2093|consen 231 ELTAHTGTGQNYS 243 (1016)
T ss_pred hhhhccCCccccc
Confidence 9999988888877
No 238
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=45.74 E-value=22 Score=30.16 Aligned_cols=54 Identities=24% Similarity=0.327 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHHh-CCCCHHH
Q 009742 250 GIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDD 310 (527)
Q Consensus 250 gIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~-GirTled 310 (527)
||+.+++.+|.+.... .-++.+++ .||. |+..|.|||=++|.++... |+..-+.
T Consensus 19 gl~~~~a~kl~~~yg~---~ai~~l~~-nPY~---L~~~i~gi~F~~aD~iA~~~g~~~~d~ 73 (94)
T PF14490_consen 19 GLSPKLAMKLYKKYGD---DAIEILKE-NPYR---LIEDIDGIGFKTADKIALKLGIEPDDP 73 (94)
T ss_dssp T--HHHHHHHHHHH-T---THHHHHHH--STC---CCB-SSSSBHHHHHHHHHTTT--TT-H
T ss_pred CCCHHHHHHHHHHHhH---HHHHHHHH-ChHH---HHHHccCCCHHHHHHHHHHcCCCCCCH
Confidence 8899999999998776 33455554 4664 3334899999999999886 8764443
No 239
>PRK02794 DNA polymerase IV; Provisional
Probab=45.09 E-value=1.2e+02 Score=32.83 Aligned_cols=52 Identities=12% Similarity=0.300 Sum_probs=33.8
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHHh--CCCC
Q 009742 245 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 307 (527)
Q Consensus 245 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--GirT 307 (527)
+..|||||+.+.++...+ -+..+.+|.+-.+.... +.+| + .+..+|+. |+..
T Consensus 211 l~~L~GiG~~~~~~L~~~----GI~tigdL~~l~~~~L~----~rfG--~-~g~~l~~~a~G~d~ 264 (419)
T PRK02794 211 VGIIWGVGPATAARLARD----GIRTIGDLQRADEADLM----RRFG--S-MGLRLWRLARGIDD 264 (419)
T ss_pred hhhhCCCCHHHHHHHHHh----ccchHHHHhhCCHHHHH----HHHh--H-HHHHHHHHhCCCCC
Confidence 678999999988887643 45666666654333333 3444 4 57777764 8864
No 240
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=44.23 E-value=17 Score=39.18 Aligned_cols=33 Identities=24% Similarity=0.313 Sum_probs=29.0
Q ss_pred HHHHHHhhccCcCHHHHHHHHHhCCCCHHHHhh
Q 009742 281 RTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN 313 (527)
Q Consensus 281 ~~l~lf~~I~GvGpktA~~ly~~GirTledL~~ 313 (527)
+.-.-|+.|.||||+.+.+|.+.||.+.++|-.
T Consensus 320 g~aDDLk~I~GIGpk~e~~Ln~~Gi~~f~QIA~ 352 (400)
T PRK12373 320 GGADDLKLISGVGPKIEATLNELGIFTFDQVAA 352 (400)
T ss_pred CCchhhhhccCCChHHHHHHHhcCCCCHHHHhC
Confidence 344567899999999999999999999999975
No 241
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=43.98 E-value=44 Score=35.38 Aligned_cols=60 Identities=17% Similarity=0.227 Sum_probs=42.4
Q ss_pred HHHHHHcCCChhHHHHHHHHHHHhcC-Ccccc-chhhhcCCCCCCHHHHHHHHHHHHhCCch
Q 009742 210 INIYRALGEDRRSFSYYKAIPVIEKL-PFKIE-SADQVKGLPGIGKSMQDHIQEIVTTGKLS 269 (527)
Q Consensus 210 a~~~e~~g~~~r~~aY~rAa~~l~~l-~~~i~-s~~~l~~lpgIG~~ia~kI~Eil~tG~~~ 269 (527)
-.+++=.|--.|++-..+||..|... ...+. +.+++..|||||..+|..|.-|.-.-...
T Consensus 78 l~~W~gLGYysRArnL~~~A~~v~~~~~G~~P~~~~~l~~LpGiG~yTa~Ail~~a~~~~~~ 139 (342)
T COG1194 78 LKAWEGLGYYSRARNLHKAAQEVVERHGGEFPDDEEELAALPGVGPYTAGAILSFAFNQPEP 139 (342)
T ss_pred HHHHHhcChHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHhCCCCcHHHHHHHHHHHhCCCCc
Confidence 34455556555888888888777654 44444 45789999999999999998876543333
No 242
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=43.89 E-value=12 Score=39.60 Aligned_cols=52 Identities=19% Similarity=0.232 Sum_probs=40.3
Q ss_pred hchhHHHHHHhhccCcCHHHHHHHHHh-CCCCHHHHhhcc--Ccchhhhccccchhh
Q 009742 277 DEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED--SLTHSQRLGLKYFDD 330 (527)
Q Consensus 277 ~~~~~~l~lf~~I~GvGpktA~~ly~~-GirTledL~~~~--~L~~~q~~Glk~yed 330 (527)
...+....++.+||+|+++.|++|.+. | ||..|.++. .|....++|-+....
T Consensus 280 ~v~prGyRiLs~IPrl~k~iAk~Ll~~FG--SL~~Il~As~eeL~~VeGIGe~rA~~ 334 (352)
T PRK13482 280 PVSPRGYRLLSKIPRLPSAVIENLVEHFG--SLQGLLAASIEDLDEVEGIGEVRARA 334 (352)
T ss_pred ccCCcHHHHHhcCCCCCHHHHHHHHHHcC--CHHHHHcCCHHHHhhCCCcCHHHHHH
Confidence 344567889999999999999999997 7 888888653 467777777555443
No 243
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=43.88 E-value=41 Score=38.55 Aligned_cols=66 Identities=15% Similarity=0.321 Sum_probs=42.2
Q ss_pred hHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHH
Q 009742 221 RSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKL 300 (527)
Q Consensus 221 r~~aY~rAa~~l~~l~~~i~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l 300 (527)
.+.+|.|-.+.=+.+ -..|.+|||||++.+.++-+ ++.-++.+++- .++.+.+| ||.++|+++
T Consensus 536 FAIt~hRk~R~k~~~------~S~L~~IpGIG~kr~~~LL~-----~FgSi~~I~~A----s~eeL~~v--i~~k~A~~I 598 (624)
T PRK14669 536 FAITFHRKRRETRDR------TSELLEIPGVGAKTVQRLLK-----HFGSLERVRAA----TETQLAAV--VGRAAAEAI 598 (624)
T ss_pred HHHHHhHHHhhHHHH------HHHHhcCCCCCHHHHHHHHH-----HcCCHHHHHhC----CHHHHHHH--hCHHHHHHH
Confidence 355666654332222 24688999999998887654 34445555542 23344566 899999999
Q ss_pred HHh
Q 009742 301 YEK 303 (527)
Q Consensus 301 y~~ 303 (527)
|+.
T Consensus 599 ~~~ 601 (624)
T PRK14669 599 IAH 601 (624)
T ss_pred HHH
Confidence 874
No 244
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=43.83 E-value=42 Score=33.29 Aligned_cols=57 Identities=25% Similarity=0.292 Sum_probs=33.9
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCH---HHHHHHHHhCC
Q 009742 241 SADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGP---ATAQKLYEKGH 305 (527)
Q Consensus 241 s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGp---ktA~~ly~~Gi 305 (527)
..++|.+|||||+.+|+.|-=+.- |+-. +- ...-+.++|.++ |+.+ ..++.|++.++
T Consensus 119 ~re~Ll~l~GIG~kTAd~iLlya~-~rp~----fv--VDty~~Rv~~Rl-G~~~~~y~~~~~~~~~~l 178 (218)
T PRK13913 119 TREWLLDQKGIGKESADAILCYVC-AKEV----MV--VDKYSYLFLKKL-GIEIEDYDELQHFFEKGV 178 (218)
T ss_pred HHHHHHcCCCccHHHHHHHHHHHc-CCCc----cc--cchhHHHHHHHc-CCCCCCHHHHHHHHHHhh
Confidence 347899999999999999875542 2211 11 112356677543 6644 34555555444
No 245
>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=43.31 E-value=60 Score=29.57 Aligned_cols=51 Identities=25% Similarity=0.376 Sum_probs=34.5
Q ss_pred eEEEecccccccCCc-cCCeeEEEecCCc--chhh----hhHHHHHHHHHHcCcccce
Q 009742 358 VIILCGGSYRRGKAS-CGDLDVVIMHPDR--KSHK----GFLSKYVKKLKEMKFLRED 408 (527)
Q Consensus 358 ~~v~~~GsyRRGke~-~gDVDiLIt~~~~--~~~~----~~l~~lv~~L~~~g~l~~~ 408 (527)
+...+.||+=|+..+ ..|+|..|-+++. .... .+...+++.|...||-.+.
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 345677888766654 6799999998882 1223 3446667778888876653
No 246
>TIGR00588 ogg 8-oxoguanine DNA-glycosylase (ogg). All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is distantly realted to the Nth-MutY superfamily.
Probab=42.63 E-value=35 Score=35.57 Aligned_cols=73 Identities=18% Similarity=0.195 Sum_probs=41.5
Q ss_pred cCCChhHHHHHHHHHHHhcCCc------ccc------chhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHH
Q 009742 216 LGEDRRSFSYYKAIPVIEKLPF------KIE------SADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTI 283 (527)
Q Consensus 216 ~g~~~r~~aY~rAa~~l~~l~~------~i~------s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l 283 (527)
.|-.+|+..-..+|..|..=.. .+. ..++|..|||||+.+|+-|.=+ .-|...- +-. ...+.
T Consensus 181 ~G~g~Ra~~I~~~A~~i~~~~~~~~~l~~l~~~~~~~~~~~L~~l~GIG~~tAd~vll~-~l~~~d~---~Pv--D~~v~ 254 (310)
T TIGR00588 181 LGLGYRARYIRETARALLEEQGGRAWLQQIRGASYEDAREALCELPGVGPKVADCICLM-GLDKPQA---VPV--DVHVW 254 (310)
T ss_pred cCCHHHHHHHHHHHHHHHhccCCchhHHhhccCChHHHHHHHHhCCCccHHHHHHHHHH-hCCCCCc---eee--cHHHH
Confidence 4544576666667776654211 111 2367999999999999988633 2222211 111 23456
Q ss_pred HHHhhccCcCH
Q 009742 284 SLFGEVWGIGP 294 (527)
Q Consensus 284 ~lf~~I~GvGp 294 (527)
+.+.+++|+.+
T Consensus 255 r~~~r~y~~~~ 265 (310)
T TIGR00588 255 RIANRDYPWHP 265 (310)
T ss_pred HHHHHHhcccc
Confidence 66666666543
No 247
>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase. This model describes GlnD, the uridylyltransferase/uridylyl-removing enzyme for the nitrogen regulatory protein PII. Not all homologs of PII share the property of uridylyltransferase modification on the characteristic Tyr residue (see Prosite pattern PS00496 and document PDOC00439), but the modification site is preserved in the PII homolog of all species with a member of this family.
Probab=42.07 E-value=68 Score=38.11 Aligned_cols=49 Identities=20% Similarity=0.497 Sum_probs=34.6
Q ss_pred CeEEEecccccccC-CccCCeeEEEecCCcc--hhhhhHHHHHHHHHHcCcc
Q 009742 357 EVIILCGGSYRRGK-ASCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMKFL 405 (527)
Q Consensus 357 ~~~v~~~GsyRRGk-e~~gDVDiLIt~~~~~--~~~~~l~~lv~~L~~~g~l 405 (527)
++-+..+|||=||. .-..|||++|-+++.. ....++.+++..|-+.|+-
T Consensus 43 ~~aliA~GgyGR~El~p~SDiDll~l~~~~~~~~~~~~~~~~~~~LwD~gl~ 94 (850)
T TIGR01693 43 GIALVAVGGYGRGELAPYSDIDLLFLHDGKPAEEVEPKIERFLYPLWDLGFE 94 (850)
T ss_pred CeEEEEeCCccccCcCCCCCCeEEEEeCCCCChHHHHHHHHHHHHHHhcCCC
Confidence 45677889996654 5678999999887532 2456677777777777753
No 248
>PRK13746 aminoglycoside resistance protein; Provisional
Probab=42.00 E-value=1.3e+02 Score=30.77 Aligned_cols=27 Identities=26% Similarity=0.249 Sum_probs=21.8
Q ss_pred EEEeccccccc--CCccCCeeEEEecCCcc
Q 009742 359 IILCGGSYRRG--KASCGDLDVVIMHPDRK 386 (527)
Q Consensus 359 ~v~~~GsyRRG--ke~~gDVDiLIt~~~~~ 386 (527)
-|.+-||+-+| ++ -+||||+|...++-
T Consensus 30 ~vyLfGS~~~G~~~p-~SDIDllvvv~~~l 58 (262)
T PRK13746 30 AIHLYGSAVDGGLKP-HSDIDLLVTVAVPL 58 (262)
T ss_pred EEEEECCcccCCCCC-CCceeEEEEeCCCC
Confidence 46789999998 44 79999999877653
No 249
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=41.86 E-value=17 Score=41.43 Aligned_cols=30 Identities=27% Similarity=0.511 Sum_probs=24.1
Q ss_pred HHHhhccCcCHHHHHHHHHhCCCCHHHHhhc
Q 009742 284 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 314 (527)
Q Consensus 284 ~lf~~I~GvGpktA~~ly~~GirTledL~~~ 314 (527)
..|..|+|||++++++|++. +-|++++.++
T Consensus 543 s~L~~IpGIG~k~~k~Ll~~-FgS~~~i~~A 572 (598)
T PRK00558 543 SALDDIPGIGPKRRKALLKH-FGSLKAIKEA 572 (598)
T ss_pred hhHhhCCCcCHHHHHHHHHH-cCCHHHHHhC
Confidence 45579999999999999984 4568888764
No 250
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=41.79 E-value=17 Score=34.15 Aligned_cols=46 Identities=17% Similarity=0.249 Sum_probs=31.0
Q ss_pred HHHHhhccCcCHHHHHHHHHh-CCCCHHHHhhccCcchhhhccccchhhhccCcCHHHHHHHHHHHHH
Q 009742 283 ISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQK 349 (527)
Q Consensus 283 l~lf~~I~GvGpktA~~ly~~-GirTledL~~~~~L~~~q~~Glk~yed~~~~i~r~Ea~~i~~iv~~ 349 (527)
.--|+.|+|||+.+|..+-.. ||..-. ...-++-+|++.|..+|..
T Consensus 29 ~~aLt~I~GIG~~~A~~I~~~lgi~~~~---------------------~~~~Lt~~qi~~l~~~i~~ 75 (154)
T PTZ00134 29 PYALTAIKGIGRRFAYLVCKKAGIDVTK---------------------RAGELTAEEIEKIVEIIAN 75 (154)
T ss_pred EEeecccccccHHHHHHHHHHcCcCcCC---------------------CcccCCHHHHHHHHHHHhc
Confidence 334589999999999999875 763211 1123455677788777765
No 251
>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=41.51 E-value=28 Score=25.37 Aligned_cols=31 Identities=32% Similarity=0.355 Sum_probs=23.5
Q ss_pred cCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhh
Q 009742 292 IGPATAQKLYEKGHRTLDDLKNED--SLTHSQR 322 (527)
Q Consensus 292 vGpktA~~ly~~GirTledL~~~~--~L~~~q~ 322 (527)
|.+..+.+|++.|+.|+++|-... .|...++
T Consensus 1 i~~~~~~~L~~~G~~s~e~la~~~~~eL~~i~g 33 (50)
T TIGR01954 1 IDEEIAQLLVEEGFTTVEDLAYVPIDELLSIEG 33 (50)
T ss_pred CCHHHHHHHHHcCCCCHHHHHccCHHHHhcCCC
Confidence 467889999999999999998643 3444433
No 252
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=41.51 E-value=20 Score=32.17 Aligned_cols=22 Identities=27% Similarity=0.540 Sum_probs=18.6
Q ss_pred HHhhccCcCHHHHHHHHHh-CCC
Q 009742 285 LFGEVWGIGPATAQKLYEK-GHR 306 (527)
Q Consensus 285 lf~~I~GvGpktA~~ly~~-Gir 306 (527)
-||.|+|||..+|+.+.+. ||.
T Consensus 18 ALt~IyGIG~~~a~~I~~~~gi~ 40 (121)
T COG0099 18 ALTYIYGIGRRRAKEICKKAGID 40 (121)
T ss_pred hhhhhccccHHHHHHHHHHcCCC
Confidence 4678999999999999876 764
No 253
>TIGR01446 DnaD_dom DnaD and phage-associated domain. This model represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria.
Probab=41.22 E-value=23 Score=28.27 Aligned_cols=19 Identities=21% Similarity=0.389 Sum_probs=16.5
Q ss_pred HHHHHHHHHhCCCCHHHHh
Q 009742 294 PATAQKLYEKGHRTLDDLK 312 (527)
Q Consensus 294 pktA~~ly~~GirTledL~ 312 (527)
-+.++.|++.||+|++|++
T Consensus 54 ~~Il~~W~~~gi~T~e~~~ 72 (73)
T TIGR01446 54 DAILNNWKNNGIKTVEDVE 72 (73)
T ss_pred HHHHHHHHHcCCCCHHHHh
Confidence 3668899999999999986
No 254
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=41.05 E-value=36 Score=40.26 Aligned_cols=32 Identities=13% Similarity=0.211 Sum_probs=26.4
Q ss_pred HHHHHhhccCcCHHHHHHHHHhCCCCHHHHhhc
Q 009742 282 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 314 (527)
Q Consensus 282 ~l~lf~~I~GvGpktA~~ly~~GirTledL~~~ 314 (527)
..+++.++|||||+.|+.+.+. +.|+++|.+.
T Consensus 755 ~q~~L~~lPgI~~~~a~~ll~~-f~si~~l~~a 786 (814)
T TIGR00596 755 PQDFLLKLPGVTKKNYRNLRKK-VKSIRELAKL 786 (814)
T ss_pred HHHHHHHCCCCCHHHHHHHHHH-cCCHHHHHhC
Confidence 3445669999999999999985 8899999864
No 255
>PRK03352 DNA polymerase IV; Validated
Probab=40.26 E-value=49 Score=34.61 Aligned_cols=56 Identities=16% Similarity=0.324 Sum_probs=38.3
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHHh--CCCCHH
Q 009742 244 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRTLD 309 (527)
Q Consensus 244 ~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--GirTle 309 (527)
.+..|||||++++++...+ -+..+.+|.+-.+....+.| |++.+..||+. |+..-.
T Consensus 178 pl~~l~gig~~~~~~L~~~----Gi~ti~dl~~l~~~~L~~~f------G~~~~~~l~~~a~G~d~~~ 235 (346)
T PRK03352 178 PTDALWGVGPKTAKRLAAL----GITTVADLAAADPAELAATF------GPTTGPWLLLLARGGGDTE 235 (346)
T ss_pred CHHHcCCCCHHHHHHHHHc----CCccHHHHhcCCHHHHHHHh------ChHHHHHHHHHhCCCCCCC
Confidence 3788999999988886654 56777777664444444455 66778888874 775443
No 256
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=40.20 E-value=13 Score=39.07 Aligned_cols=51 Identities=20% Similarity=0.264 Sum_probs=32.6
Q ss_pred HHHHHHhhccCcCHHHHHHHHHh---CCCC-HHHHhhcc------Ccchhhhccccchhhh
Q 009742 281 RTISLFGEVWGIGPATAQKLYEK---GHRT-LDDLKNED------SLTHSQRLGLKYFDDI 331 (527)
Q Consensus 281 ~~l~lf~~I~GvGpktA~~ly~~---GirT-ledL~~~~------~L~~~q~~Glk~yed~ 331 (527)
..+..+++|||||+++|.++.+- |--. +.++..+. .|.+..++|.+....|
T Consensus 45 ~~~~~l~~lpgIG~~ia~kI~Eil~tG~~~~~~e~l~~~~p~~l~~l~~i~GiGpk~a~~l 105 (334)
T smart00483 45 NSMKDLKGLPGIGDKIKKKIEEIIETGKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKW 105 (334)
T ss_pred CCHHHHhcCCCccHHHHHHHHHHHHhCcHHHHHHHhcCcHHHHHHHHHccCCcCHHHHHHH
Confidence 34556779999999999999873 5544 33333221 3566667775554444
No 257
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=39.99 E-value=21 Score=33.42 Aligned_cols=24 Identities=29% Similarity=0.338 Sum_probs=19.5
Q ss_pred HHHHhhccCcCHHHHHHHHHh-CCC
Q 009742 283 ISLFGEVWGIGPATAQKLYEK-GHR 306 (527)
Q Consensus 283 l~lf~~I~GvGpktA~~ly~~-Gir 306 (527)
.--|+.|+|||+++|..+-+. ||.
T Consensus 24 ~~aLt~IyGIG~~~a~~Ic~~lgi~ 48 (149)
T PRK04053 24 EYALTGIKGIGRRTARAIARKLGLD 48 (149)
T ss_pred eeeccccccccHHHHHHHHHHcCcC
Confidence 334589999999999999875 764
No 258
>PRK03059 PII uridylyl-transferase; Provisional
Probab=39.90 E-value=78 Score=37.76 Aligned_cols=64 Identities=16% Similarity=0.350 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHhhhc--CCCeEEEeccccccc-CCccCCeeEEEecCCcc--hhhhhHHHHHHHHHHcC
Q 009742 340 VEQMERLLQKAGEEV--LPEVIILCGGSYRRG-KASCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMK 403 (527)
Q Consensus 340 a~~i~~iv~~~~~~~--~p~~~v~~~GsyRRG-ke~~gDVDiLIt~~~~~--~~~~~l~~lv~~L~~~g 403 (527)
+..+..+++.+.... ..++.+..+|||=|| ..-.+|||+||-+++.. .....+..++..|=+.|
T Consensus 42 s~l~d~~l~~~~~~~~~~~~~alvAvGgyGR~EL~p~SDiDll~l~~~~~~~~~~~~i~~~~~~lwD~g 110 (856)
T PRK03059 42 SRLVDQALRRLWQECGLPAGAALVAVGGYGRGELFPYSDVDLLVLLPDAPDAALDARIERFIGLCWDLG 110 (856)
T ss_pred HHHHHHHHHHHHHhcCCCCCeEEEEcCCCCCcccCCCCCCEEEEEecCCcchHHHHHHHHHHHhhhccC
Confidence 333444444443222 235677788999555 56789999999987542 23344555554444444
No 259
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=39.87 E-value=28 Score=33.66 Aligned_cols=40 Identities=28% Similarity=0.283 Sum_probs=32.2
Q ss_pred ccccc-hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHh
Q 009742 237 FKIES-ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEK 276 (527)
Q Consensus 237 ~~i~s-~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~ 276 (527)
.||+. +-+|+-|||||++++..|-|=-+..-+..++.+++
T Consensus 123 ~PIt~RLH~LELLpGiGkK~m~~ILeERkkkpFeSFeDi~~ 163 (202)
T COG1491 123 EPITLRLHQLELLPGIGKKTMWAILEERKKKPFESFEDIKE 163 (202)
T ss_pred CcchHHHHHHHhcccccHHHHHHHHHHHhcCCCcCHHHHHH
Confidence 67775 57899999999999999988777777777776654
No 260
>PF09970 DUF2204: Nucleotidyl transferase of unknown function (DUF2204); InterPro: IPR018700 This family of hypothetical prokaryotic proteins has no known function.
Probab=39.13 E-value=66 Score=30.82 Aligned_cols=39 Identities=18% Similarity=0.211 Sum_probs=26.2
Q ss_pred CeEEEecccc-----cccCCccCCeeEEEecCCcchhhhhHHHH
Q 009742 357 EVIILCGGSY-----RRGKASCGDLDVVIMHPDRKSHKGFLSKY 395 (527)
Q Consensus 357 ~~~v~~~Gsy-----RRGke~~gDVDiLIt~~~~~~~~~~l~~l 395 (527)
++.+.++||+ -..+...+|||++|..++......++..+
T Consensus 16 gv~~~ivGG~av~l~~g~~r~T~DIDlfi~~~~~~~~~~~~~~~ 59 (181)
T PF09970_consen 16 GVEYVIVGGAAVNLAYGRRRTTKDIDLFIENPSPNLEADALREV 59 (181)
T ss_pred CCeEEEECHHHHHHHhCCCCCCCCeEEEeCCCchHHHHHHHHHH
Confidence 6677777774 25667789999999877665444444333
No 261
>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=39.04 E-value=23 Score=40.13 Aligned_cols=29 Identities=24% Similarity=0.354 Sum_probs=23.8
Q ss_pred HHhhccCcCHHHHHHHHHhCCCCHHHHhhc
Q 009742 285 LFGEVWGIGPATAQKLYEKGHRTLDDLKNE 314 (527)
Q Consensus 285 lf~~I~GvGpktA~~ly~~GirTledL~~~ 314 (527)
.|.+|+|||||+.+.|++. +.|+++++++
T Consensus 542 ~Ld~I~GIG~kr~~~LL~~-Fgs~~~i~~A 570 (574)
T TIGR00194 542 PLLKIPGVGEKRVQKLLKY-FGSLKGIKKA 570 (574)
T ss_pred HHhcCCCCCHHHHHHHHHH-cCCHHHHHhC
Confidence 4569999999999999984 5588888754
No 262
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=38.92 E-value=51 Score=39.07 Aligned_cols=16 Identities=19% Similarity=0.353 Sum_probs=10.6
Q ss_pred cHHHHHHHHHHHHHHH
Q 009742 199 NKNITEIFGKLINIYR 214 (527)
Q Consensus 199 N~~ia~~L~~la~~~e 214 (527)
|..+-++.+.|...|+
T Consensus 643 ~gRL~~Q~~~m~~~Y~ 658 (814)
T TIGR00596 643 NGRLYNQCEKMLRYYA 658 (814)
T ss_pred cchHHHHHHHHHHhcC
Confidence 3446667777777776
No 263
>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=38.62 E-value=21 Score=33.10 Aligned_cols=44 Identities=23% Similarity=0.352 Sum_probs=30.5
Q ss_pred HHhhccCcCHHHHHHHHHh-CCCCHHHHhhccCcchhhhccccchhhhccCcCHHHHHHHHHHHHH
Q 009742 285 LFGEVWGIGPATAQKLYEK-GHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQK 349 (527)
Q Consensus 285 lf~~I~GvGpktA~~ly~~-GirTledL~~~~~L~~~q~~Glk~yed~~~~i~r~Ea~~i~~iv~~ 349 (527)
-|+.|+|||+++|..+-+. ||..-.-+ .-++-++++.|..+|..
T Consensus 22 aLt~I~GIG~~~a~~I~~~lgi~~~~~~---------------------~~Lt~~qi~~l~~~i~~ 66 (144)
T TIGR03629 22 ALTGIKGIGRRFARAIARKLGVDPNAKL---------------------GYLDDEEIEKLEEAVEN 66 (144)
T ss_pred eecceeccCHHHHHHHHHHcCcCCCCCc---------------------ccCCHHHHHHHHHHHHh
Confidence 4579999999999999875 76421111 12455677788887776
No 264
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=38.44 E-value=20 Score=40.71 Aligned_cols=20 Identities=15% Similarity=0.165 Sum_probs=11.9
Q ss_pred CcchhhhccccchhhhccCc
Q 009742 316 SLTHSQRLGLKYFDDIKTRI 335 (527)
Q Consensus 316 ~L~~~q~~Glk~yed~~~~i 335 (527)
.|..+.++|.+....+...+
T Consensus 526 ~L~~IpGIG~kr~~~LL~~F 545 (577)
T PRK14668 526 VLDDVPGVGPETRKRLLRRF 545 (577)
T ss_pred HHhcCCCCCHHHHHHHHHHc
Confidence 46667777765555555443
No 265
>PF02961 BAF: Barrier to autointegration factor; InterPro: IPR004122 Barrier-to-autointegration factor (BAF) is an essential protein that is highly conserved in metazoan evolution, and which may act as a DNA-bridging protein []. BAF binds directly to double-stranded DNA, to transcription activators, and to inner nuclear membrane proteins, including lamin A filament proteins that anchor nuclear-pore complexes in place, and nuclear LEM-domain proteins that bind to laminins filaments and chromatin. New findings suggest that BAF has structural roles in nuclear assembly and chromatin organisation, represses gene expression and might interlink chromatin structure, nuclear architecture and gene regulation in metazoans []. BAF can be exploited by retroviruses to act as a host component of pre-integration complexes, which promote the integration of the retroviral DNA into the host chromosome by preventing autointegration of retroviral DNA []. BAF might contribute to the assembly or activity of retroviral pre-integration complexes through direct binding to the retroviral proteins p55 Gag and matrix, as well as to DNA.; GO: 0003677 DNA binding; PDB: 2ODG_A 2BZF_A 2EZX_B 2EZY_B 1QCK_B 1CI4_B 2EZZ_B.
Probab=38.33 E-value=24 Score=30.05 Aligned_cols=27 Identities=33% Similarity=0.449 Sum_probs=20.0
Q ss_pred HhhccCcCHHHHHHHHHhCCCCHHHHh
Q 009742 286 FGEVWGIGPATAQKLYEKGHRTLDDLK 312 (527)
Q Consensus 286 f~~I~GvGpktA~~ly~~GirTledL~ 312 (527)
-+.++||||..+.+|-+.|+.---.|.
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 468999999999999999998876665
No 266
>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=38.26 E-value=59 Score=34.57 Aligned_cols=54 Identities=17% Similarity=0.305 Sum_probs=33.3
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhh--chhHHHHHHhhccCcCHHHHHHHHHh--CCCC
Q 009742 245 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKD--EKVRTISLFGEVWGIGPATAQKLYEK--GHRT 307 (527)
Q Consensus 245 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~--~~~~~l~lf~~I~GvGpktA~~ly~~--GirT 307 (527)
+..|||||++++.++.+-+ .+..+.+|.+- .+....+.| |.+.+..+|+. |+..
T Consensus 184 v~~l~GiG~~~~~~ll~~~---Gi~ti~dl~~~~~~~~~L~~~f------G~~~g~~l~~~a~G~d~ 241 (359)
T cd01702 184 ITSIRGLGGKLGEEIIDLL---GLPTEGDVAGFRSSESDLQEHF------GEKLGEWLYNLLRGIDH 241 (359)
T ss_pred HHHhCCcCHHHHHHHHHHc---CCcCHHHHHhccCCHHHHHHHH------HHHHHHHHHHHhCCCCC
Confidence 6788999998876653322 23444444432 233344455 77888999874 8764
No 267
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=37.78 E-value=69 Score=31.61 Aligned_cols=19 Identities=26% Similarity=0.289 Sum_probs=16.2
Q ss_pred HHHHHhhccCcCHHHHHHH
Q 009742 282 TISLFGEVWGIGPATAQKL 300 (527)
Q Consensus 282 ~l~lf~~I~GvGpktA~~l 300 (527)
..+.|.+|.|||+-||..+
T Consensus 113 ~R~~LL~iKGIG~ETaDsI 131 (215)
T COG2231 113 LREELLSIKGIGKETADSI 131 (215)
T ss_pred HHHHHHccCCcchhhHHHH
Confidence 5666779999999999876
No 268
>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=37.77 E-value=20 Score=37.25 Aligned_cols=24 Identities=38% Similarity=0.479 Sum_probs=18.4
Q ss_pred hhccCcCHHHHHHHHHhCCCCHHHH
Q 009742 287 GEVWGIGPATAQKLYEKGHRTLDDL 311 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~GirTledL 311 (527)
..|+|||||||.+|.++ +.|++..
T Consensus 226 ~gv~giG~k~A~~li~~-~~~~~~~ 249 (316)
T cd00128 226 EGIPGIGPVTALKLIKK-YGDIEKD 249 (316)
T ss_pred CCCCCccHHHHHHHHHH-cCChHHH
Confidence 57999999999999987 3344333
No 269
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=37.68 E-value=85 Score=28.52 Aligned_cols=88 Identities=22% Similarity=0.422 Sum_probs=60.0
Q ss_pred CCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHHhCCCCHHHHhhccCcchhhhccccchhh
Q 009742 251 IGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYFDD 330 (527)
Q Consensus 251 IG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~~~L~~~q~~Glk~yed 330 (527)
|=..|++.|.+-+.+|.+..=+. ..+++.|....||-|-|+++-|+ +|++++-+....+.|.---+|
T Consensus 12 IY~QI~~qIk~~I~~g~l~pGdk------LPSvRelA~~~~VNpnTv~raY~-------eLE~eG~i~t~rg~G~fV~~~ 78 (125)
T COG1725 12 IYEQIANQIKEQIASGELKPGDK------LPSVRELAKDLGVNPNTVQRAYQ-------ELEREGIVETKRGKGTFVTED 78 (125)
T ss_pred HHHHHHHHHHHHHHhCCcCCCCC------CCcHHHHHHHhCCCHHHHHHHHH-------HHHHCCCEEEecCeeEEEcCC
Confidence 34578999999999999875544 44677777889999999999997 677777777777777554444
Q ss_pred ---hccCcCHHHHHH-HHHHHHHHh
Q 009742 331 ---IKTRIPRHEVEQ-MERLLQKAG 351 (527)
Q Consensus 331 ---~~~~i~r~Ea~~-i~~iv~~~~ 351 (527)
+....-+..+.+ ++.+|.++.
T Consensus 79 ~~~~~~~~~~~~~~~~l~~~I~~~~ 103 (125)
T COG1725 79 AKEILDQLKRELAEEELEEFIEEAK 103 (125)
T ss_pred chhhHHHHHHHHHHHHHHHHHHHHH
Confidence 332223334433 455555543
No 270
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=36.95 E-value=27 Score=40.05 Aligned_cols=27 Identities=44% Similarity=0.650 Sum_probs=25.2
Q ss_pred HhhccCcCHHHHHHHHHhCCCCHHHHh
Q 009742 286 FGEVWGIGPATAQKLYEKGHRTLDDLK 312 (527)
Q Consensus 286 f~~I~GvGpktA~~ly~~GirTledL~ 312 (527)
+..+.||||++|.++-+.||.|+.||.
T Consensus 12 l~~l~gig~~~a~~l~~Lgi~tv~DLL 38 (677)
T COG1200 12 LSTLKGIGPKTAEKLKKLGIHTVQDLL 38 (677)
T ss_pred hhhhcCcCHHHHHHHHHcCCCcHHHHH
Confidence 458999999999999999999999997
No 271
>PRK13766 Hef nuclease; Provisional
Probab=36.51 E-value=24 Score=41.13 Aligned_cols=44 Identities=18% Similarity=0.335 Sum_probs=31.7
Q ss_pred HHhhccCcCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhccccchh
Q 009742 285 LFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFD 329 (527)
Q Consensus 285 lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~q~~Glk~ye 329 (527)
+|..|+|||+++|++|.+. +.|++++..+. .|....++|-+..+
T Consensus 716 ~L~~ipgig~~~a~~Ll~~-fgs~~~i~~as~~~L~~i~Gig~~~a~ 761 (773)
T PRK13766 716 IVESLPDVGPVLARNLLEH-FGSVEAVMTASEEELMEVEGIGEKTAK 761 (773)
T ss_pred HHhcCCCCCHHHHHHHHHH-cCCHHHHHhCCHHHHHhCCCCCHHHHH
Confidence 5789999999999999985 45788888643 35555556644433
No 272
>PTZ00035 Rad51 protein; Provisional
Probab=35.97 E-value=64 Score=34.04 Aligned_cols=48 Identities=21% Similarity=0.270 Sum_probs=33.1
Q ss_pred HHHHHhhccCcCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhccccchhh
Q 009742 282 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDD 330 (527)
Q Consensus 282 ~l~lf~~I~GvGpktA~~ly~~GirTledL~~~~--~L~~~q~~Glk~yed 330 (527)
.++.+ .-+||+|.++++|-+.||.|++||.... .|....++...-.++
T Consensus 22 ~~~~l-~~~g~~~~~~~kL~~~g~~t~~~~~~~~~~~L~~~~gis~~~~~~ 71 (337)
T PTZ00035 22 EIEKL-QSAGINAADIKKLKEAGICTVESVAYATKKDLCNIKGISEAKVEK 71 (337)
T ss_pred cHHHH-hcCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhhCCCHHHHHH
Confidence 35555 3489999999999999999999998543 344444443333333
No 273
>PRK03858 DNA polymerase IV; Validated
Probab=35.57 E-value=64 Score=34.43 Aligned_cols=52 Identities=19% Similarity=0.333 Sum_probs=35.8
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHHh--CCC
Q 009742 245 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHR 306 (527)
Q Consensus 245 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--Gir 306 (527)
+..|||||+++++++..+ -+..+.+|.+-.+...-+.| |+..++.||+. |+.
T Consensus 175 l~~l~Gig~~~~~~L~~~----Gi~t~~dl~~l~~~~L~~~f------G~~~~~~l~~~a~G~d 228 (396)
T PRK03858 175 VRRLWGVGPVTAAKLRAH----GITTVGDVAELPESALVSLL------GPAAGRHLHALAHNRD 228 (396)
T ss_pred hhhcCCCCHHHHHHHHHh----CCCcHHHHhcCCHHHHHHHh------CcHHHHHHHHHhCCCC
Confidence 678899999999998765 35566666554433344444 66788889863 774
No 274
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=35.38 E-value=60 Score=33.40 Aligned_cols=44 Identities=20% Similarity=0.379 Sum_probs=30.9
Q ss_pred CCC-hhHHHHHHHHHHHhc--CCccc-cc----hhhhcCCCCCCHHHHHHHH
Q 009742 217 GED-RRSFSYYKAIPVIEK--LPFKI-ES----ADQVKGLPGIGKSMQDHIQ 260 (527)
Q Consensus 217 g~~-~r~~aY~rAa~~l~~--l~~~i-~s----~~~l~~lpgIG~~ia~kI~ 260 (527)
|-. .|+.+-..+|..+.+ ++... .+ .++|..|||||+.+|+-|.
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 377777888877754 43221 12 4689999999999999876
No 275
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=34.82 E-value=76 Score=30.78 Aligned_cols=56 Identities=20% Similarity=0.347 Sum_probs=33.5
Q ss_pred HHHHHHHhCCchhhHHHHhhchhH-HHHHHhhccCcCHHHHHHHHHh----CCCCHHHHhh
Q 009742 258 HIQEIVTTGKLSKLEHFEKDEKVR-TISLFGEVWGIGPATAQKLYEK----GHRTLDDLKN 313 (527)
Q Consensus 258 kI~Eil~tG~~~~le~l~~~~~~~-~l~lf~~I~GvGpktA~~ly~~----GirTledL~~ 313 (527)
.+++|+....=..++-+-.-+|.. -|-.|.=+||||-|+...+.++ -+.|++|+++
T Consensus 103 vve~iV~~~E~rFV~fFN~A~PIt~RLH~LELLpGiGkK~m~~ILeERkkkpFeSFeDi~~ 163 (202)
T COG1491 103 VVEKIVKENEDRFVKFFNEAEPITLRLHQLELLPGIGKKTMWAILEERKKKPFESFEDIKE 163 (202)
T ss_pred HHHHHHHhhhhHHHHHhcccCcchHHHHHHHhcccccHHHHHHHHHHHhcCCCcCHHHHHH
Confidence 355555544433343332222221 2333445799999999999853 7888888885
No 276
>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=34.41 E-value=11 Score=32.23 Aligned_cols=51 Identities=24% Similarity=0.337 Sum_probs=39.9
Q ss_pred HHHHHhhccCcCHHHHHHHHHh-CCCCHHHHhhccCcchhhhccccchhhhc
Q 009742 282 TISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNEDSLTHSQRLGLKYFDDIK 332 (527)
Q Consensus 282 ~l~lf~~I~GvGpktA~~ly~~-GirTledL~~~~~L~~~q~~Glk~yed~~ 332 (527)
.+..|++.||+=|..|.++..- -+.|++|+.+-.-|+..|+.=++-|++.-
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 4667889999999999999997 78999999988789988888877777643
No 277
>COG1204 Superfamily II helicase [General function prediction only]
Probab=33.97 E-value=30 Score=40.68 Aligned_cols=108 Identities=23% Similarity=0.313 Sum_probs=59.5
Q ss_pred HHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCc--hhhHHHH----hhchhHHHHHHhhccCcCHH
Q 009742 222 SFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKL--SKLEHFE----KDEKVRTISLFGEVWGIGPA 295 (527)
Q Consensus 222 ~~aY~rAa~~l~~l~~~i~s~~~l~~lpgIG~~ia~kI~Eil~tG~~--~~le~l~----~~~~~~~l~lf~~I~GvGpk 295 (527)
..+|-.+...+...-....=. .+. +..+|.++ .++..++..|.. ..++.+. ...+...+..+..|.|+|-.
T Consensus 610 ~~~~~~~~~dl~~~~~~a~w~-~~~-~~~l~~~~-~r~~~~~~~~~~~~~~~~~~~~rie~gv~~e~~~~l~~i~~~grv 686 (766)
T COG1204 610 LNAYGVAPGDLLRIAETAEWL-SAD-LLALGKAA-ERLAKILGLGLHVLRKLEILSLRIEYGVRSEELLELVEIRGVGRV 686 (766)
T ss_pred HHHhCcchhhHHhhcchhhhh-hhh-hhhhhhhh-hhhHhhhCCCccccccchhhhhhhhcCCChhhhcccccccccchh
Confidence 345555554444433322222 122 44444444 444445555433 3333332 22331233344599999999
Q ss_pred HHHHHHHhCCCCHHHHhhcc---Ccchhhhccccchhhhc
Q 009742 296 TAQKLYEKGHRTLDDLKNED---SLTHSQRLGLKYFDDIK 332 (527)
Q Consensus 296 tA~~ly~~GirTledL~~~~---~L~~~q~~Glk~yed~~ 332 (527)
.|++||..|+++++++.... .+....++|.+.++.+.
T Consensus 687 rar~ly~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~ 726 (766)
T COG1204 687 RARKLYNAGYKSLEDLRLIADPAELLPLTGIGERLVEAIL 726 (766)
T ss_pred HHHHHHHhhhccHHHHHhhcChhhhhhhhhhHHHHHHHHH
Confidence 99999999999999999432 34455556665555444
No 278
>PRK10880 adenine DNA glycosylase; Provisional
Probab=33.79 E-value=29 Score=36.91 Aligned_cols=23 Identities=22% Similarity=0.286 Sum_probs=18.9
Q ss_pred HHHHHHhhccCcCHHHHHHHHHh
Q 009742 281 RTISLFGEVWGIGPATAQKLYEK 303 (527)
Q Consensus 281 ~~l~lf~~I~GvGpktA~~ly~~ 303 (527)
..++.|+++||||++||..+---
T Consensus 106 ~~~~~L~~LpGIG~~TA~aIl~~ 128 (350)
T PRK10880 106 ETFEEVAALPGVGRSTAGAILSL 128 (350)
T ss_pred hhHHHHhcCCCccHHHHHHHHHH
Confidence 45677779999999999998654
No 279
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=33.78 E-value=69 Score=33.99 Aligned_cols=34 Identities=24% Similarity=0.275 Sum_probs=27.6
Q ss_pred hHHHHHHhhccCcCHHHHHHHHHhCCCCHHHHhhc
Q 009742 280 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 314 (527)
Q Consensus 280 ~~~l~lf~~I~GvGpktA~~ly~~GirTledL~~~ 314 (527)
+..++.+ .-.||+|+++++|-+.||.|++||...
T Consensus 28 ~~~~~~l-~~~g~~~~~~~kL~~~g~~tv~~~~~~ 61 (344)
T PLN03187 28 FESIDKL-ISQGINAGDVKKLQDAGIYTCNGLMMH 61 (344)
T ss_pred ccCHHHH-hhCCCCHHHHHHHHHcCCCcHHHHHhC
Confidence 3345555 448999999999999999999999754
No 280
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=33.57 E-value=33 Score=33.06 Aligned_cols=59 Identities=19% Similarity=0.353 Sum_probs=32.4
Q ss_pred HHHHHHHHHHhCCchhhHHHHhhchhH-HHHHHhhccCcCHHHHHHHHHh----CCCCHHHHhh
Q 009742 255 MQDHIQEIVTTGKLSKLEHFEKDEKVR-TISLFGEVWGIGPATAQKLYEK----GHRTLDDLKN 313 (527)
Q Consensus 255 ia~kI~Eil~tG~~~~le~l~~~~~~~-~l~lf~~I~GvGpktA~~ly~~----GirTledL~~ 313 (527)
+-..|++|+....-..++-+-...|.. -|-.|.=+||||-|+...+.++ -+.|++|+.+
T Consensus 86 L~~vv~~IV~~~E~~FV~FfN~A~PIt~RlH~LeLLPGIGKK~m~~ILeERkkkpFeSFeDi~~ 149 (181)
T PF04919_consen 86 LPYVVEEIVKENEERFVDFFNEAQPITLRLHSLELLPGIGKKTMWKILEERKKKPFESFEDIEE 149 (181)
T ss_dssp HHHHHHHHHHTTHHHHHHHH-----B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHH
T ss_pred HHHHHHHHHHhChHHHHHHhhcCCCChHHHHHHhhcccccHHHHHHHHHHHccCCCCCHHHHHH
Confidence 445688888877755565543333321 1223444799999999999852 6777777775
No 281
>PRK03381 PII uridylyl-transferase; Provisional
Probab=33.54 E-value=1.1e+02 Score=36.16 Aligned_cols=46 Identities=22% Similarity=0.294 Sum_probs=28.9
Q ss_pred eEEEeccccccc-CCccCCeeEEEecCCcc--hhhhhHHHHHHHHHHcC
Q 009742 358 VIILCGGSYRRG-KASCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMK 403 (527)
Q Consensus 358 ~~v~~~GsyRRG-ke~~gDVDiLIt~~~~~--~~~~~l~~lv~~L~~~g 403 (527)
+-+..+|||=|| ..-..|||+||-+++.. ....+...++..|-+.|
T Consensus 58 ~alvAvg~~gr~el~p~SD~Dll~l~~~~~~~~~~~~~~~~~~~LwD~g 106 (774)
T PRK03381 58 VALVAVGGLGRRELLPYSDLDLVLLHDGRPADDVAEVADRLWYPLWDAG 106 (774)
T ss_pred eEEEEeCCcCCcCcCCCCCCeEEEEeCCCCchHHHHHHHHHhhhcccCC
Confidence 467778999555 45678999999887432 23344444444444443
No 282
>PHA00439 exonuclease
Probab=33.53 E-value=29 Score=35.84 Aligned_cols=27 Identities=19% Similarity=0.284 Sum_probs=21.9
Q ss_pred hhccCcCHHHHHHHHHh--CCCCHHHHhhc
Q 009742 287 GEVWGIGPATAQKLYEK--GHRTLDDLKNE 314 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~--GirTledL~~~ 314 (527)
-.|+||| |||.+|.++ .+..++...+.
T Consensus 191 PGVpGIG-KTA~kLL~~~~~~~~~~~~~~s 219 (286)
T PHA00439 191 SGIPGWG-DTAEAFLENPYIFEQVEKVLKS 219 (286)
T ss_pred CCCCCcC-HHHHHHHhCccccchhhHHhhc
Confidence 4799999 999999987 66777776654
No 283
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=33.48 E-value=39 Score=33.01 Aligned_cols=27 Identities=30% Similarity=0.478 Sum_probs=20.8
Q ss_pred cccch-hhhcCCCCCCHHHHHHHHHHHH
Q 009742 238 KIESA-DQVKGLPGIGKSMQDHIQEIVT 264 (527)
Q Consensus 238 ~i~s~-~~l~~lpgIG~~ia~kI~Eil~ 264 (527)
+|+.+ +.+..|||||++.|.++.=.|-
T Consensus 6 ~i~~LI~~l~kLPGvG~KsA~R~AfhLL 33 (198)
T COG0353 6 PIEKLIDALKKLPGVGPKSAQRLAFHLL 33 (198)
T ss_pred HHHHHHHHHhhCCCCChhHHHHHHHHHH
Confidence 34443 6789999999999999986553
No 284
>PRK13910 DNA glycosylase MutY; Provisional
Probab=33.33 E-value=29 Score=35.95 Aligned_cols=22 Identities=23% Similarity=0.153 Sum_probs=17.9
Q ss_pred HHHHHhhccCcCHHHHHHHHHh
Q 009742 282 TISLFGEVWGIGPATAQKLYEK 303 (527)
Q Consensus 282 ~l~lf~~I~GvGpktA~~ly~~ 303 (527)
..+.|+++||||++||..+---
T Consensus 70 ~~~~L~~LpGIG~kTA~aIl~~ 91 (289)
T PRK13910 70 DYQSLLKLPGIGAYTANAILCF 91 (289)
T ss_pred hHHHHHhCCCCCHHHHHHHHHH
Confidence 3567779999999999988643
No 285
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=32.23 E-value=76 Score=37.38 Aligned_cols=48 Identities=17% Similarity=0.495 Sum_probs=32.0
Q ss_pred CeEEEecccccccC-CccCCeeEEEecCCcchh--hhhHHHHHHHHHHcCc
Q 009742 357 EVIILCGGSYRRGK-ASCGDLDVVIMHPDRKSH--KGFLSKYVKKLKEMKF 404 (527)
Q Consensus 357 ~~~v~~~GsyRRGk-e~~gDVDiLIt~~~~~~~--~~~l~~lv~~L~~~g~ 404 (527)
++-++.+|||=||. --++|||+||-+|...+. ..-+..++..|=+.|+
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 35677899998775 468999999999876532 2334444544445554
No 286
>COG1031 Uncharacterized Fe-S oxidoreductase [Energy production and conversion]
Probab=32.10 E-value=36 Score=37.45 Aligned_cols=32 Identities=16% Similarity=0.350 Sum_probs=29.0
Q ss_pred HHHHHhhccCcCHHHHHHHHHh-CCCCHHHHhh
Q 009742 282 TISLFGEVWGIGPATAQKLYEK-GHRTLDDLKN 313 (527)
Q Consensus 282 ~l~lf~~I~GvGpktA~~ly~~-GirTledL~~ 313 (527)
..+.++.|||||.+++.+++.. .++|.||+++
T Consensus 514 s~~vl~~ipgig~~~~~~I~~~Rp~~s~e~~l~ 546 (560)
T COG1031 514 SKDVLRAIPGIGKKTLRKILAERPFKSSEEFLK 546 (560)
T ss_pred cHHHHHhcccchhhhHHHHHhcCCccchHHHHh
Confidence 3778899999999999999987 9999999985
No 287
>PF11774 Lsr2: Lsr2 ; InterPro: IPR024412 This entry represents Lsr2, which is a small, basic DNA-bridging protein present in Mycobacterium and related actinomycetes. It is a functional homologue of the H-NS-like proteins []. H-NS proteins play a role in nucleoid organisation and also function as a pleiotropic regulator of gene expression [, ].; PDB: 4E1R_B 4E1P_B 2KNG_A.
Probab=31.89 E-value=31 Score=30.51 Aligned_cols=28 Identities=25% Similarity=0.426 Sum_probs=17.7
Q ss_pred cccHHHHHHHHHHHHHcCCccCCCCCcc
Q 009742 459 TGNDVLNRRLRLLAESKGYRLDDTGLFP 486 (527)
Q Consensus 459 TGS~~fnr~LR~~A~~kg~~L~~~GL~~ 486 (527)
+.++..++.+|.||++.||..++.|-++
T Consensus 73 ~~~~~~~~~IR~WA~~nG~~Vs~RGRIp 100 (110)
T PF11774_consen 73 AAPREDTAAIREWARENGYEVSDRGRIP 100 (110)
T ss_dssp --SSTHHHHHHHHHHHTT----SSS---
T ss_pred CCCccchHHHHHHHHHcCCcCCCCCcCC
Confidence 5567889999999999999999998653
No 288
>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=31.40 E-value=83 Score=33.90 Aligned_cols=53 Identities=28% Similarity=0.488 Sum_probs=34.9
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhc--hhHHHHHHhhccCcCHHHHHHHHHh--CCCC
Q 009742 245 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDE--KVRTISLFGEVWGIGPATAQKLYEK--GHRT 307 (527)
Q Consensus 245 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~--~~~~l~lf~~I~GvGpktA~~ly~~--GirT 307 (527)
+..|||||+++++++..+ | +..+.++.+-. +....+.| |++++..||+. |+..
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 2 33444444333 33344555 77889998875 8864
No 289
>cd00424 PolY Y-family of DNA polymerases. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Most TLS polymerases are members of the Y-family, including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is found exclusively in bacteria. In eukaryotes, the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in ord
Probab=31.12 E-value=1.2e+02 Score=31.78 Aligned_cols=53 Identities=19% Similarity=0.417 Sum_probs=33.3
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHHh--CCCC
Q 009742 245 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 307 (527)
Q Consensus 245 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--GirT 307 (527)
+..|||||+++.+++..+ | +..+.+|.+-.....+.. .+| +.+..+|+. |+..
T Consensus 175 i~~l~giG~~~~~~L~~~---G-i~ti~dl~~~~~~~~l~~---~fg---~~~~~l~~~a~G~d~ 229 (343)
T cd00424 175 LTDLPGIGAVTAKRLEAV---G-INPIGDLLAASPDALLAL---WGG---VSGERLWYALRGIDD 229 (343)
T ss_pred hhhcCCCCHHHHHHHHHc---C-CCcHHHHhcCCHHHHHHH---Hhh---HHHHHHHHHhCCcCC
Confidence 677899999999988764 3 455666654331333332 222 567777764 8754
No 290
>COG5067 DBF4 Protein kinase essential for the initiation of DNA replication [DNA replication, recombination, and repair / Cell division and chromosome partitioning]
Probab=30.92 E-value=33 Score=36.79 Aligned_cols=49 Identities=16% Similarity=0.279 Sum_probs=39.0
Q ss_pred CCCCCCcCCeEEEEeeCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEE
Q 009742 13 LDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLA 63 (527)
Q Consensus 13 ~~~~~~f~~~~i~iv~~~~g~~r~~~l~~~~~~~G~~v~~~~s~~VTHVV~ 63 (527)
..+--.|+.+..|.- ++-|..++. +++.+.+.|+.|..-++..||||++
T Consensus 117 R~Y~~aFp~f~fY~d-n~s~~~khR-vk~gf~~LGa~v~tfF~~~VThfiT 165 (468)
T COG5067 117 RTYCCAFPAFKFYKD-NKSGKRKHR-VKEGFCELGAVVFTFFEEHVTHFIT 165 (468)
T ss_pred hhhhcccchhhhhhc-CCCHHHHHH-HHHHHHHhhhhhheeeccceEEEEE
Confidence 444577888888884 344554443 9999999999999999999999995
No 291
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=30.89 E-value=65 Score=31.77 Aligned_cols=20 Identities=20% Similarity=0.371 Sum_probs=17.3
Q ss_pred chhhhc-CCCCCCHHHHHHHH
Q 009742 241 SADQVK-GLPGIGKSMQDHIQ 260 (527)
Q Consensus 241 s~~~l~-~lpgIG~~ia~kI~ 260 (527)
..++|. +|||||.++|+.|-
T Consensus 116 ~R~~Ll~~lpGIG~KTAd~vL 136 (208)
T PRK01229 116 AREFLVKNIKGIGYKEASHFL 136 (208)
T ss_pred HHHHHHHcCCCCcHHHHHHHH
Confidence 347788 99999999999975
No 292
>TIGR03135 malonate_mdcG holo-ACP synthase, malonate decarboxylase-specific. Malonate decarboxylase, like citrate lyase, has a unique acyl carrier protein subunit with a prosthetic group derived from, and distinct from, coenzyme A. Members of this protein family are the phosphoribosyl-dephospho-CoA transferase specific to the malonate decarboxylase system. This enzyme can also be designated holo-ACP synthase (2.7.7.61). The corresponding component of the citrate lyase system, CitX, shows little or no sequence similarity to this family.
Probab=29.85 E-value=2e+02 Score=28.11 Aligned_cols=32 Identities=28% Similarity=0.227 Sum_probs=23.6
Q ss_pred CCeEEEecccc----cccC---CccCCeeEEEecCCcch
Q 009742 356 PEVIILCGGSY----RRGK---ASCGDLDVVIMHPDRKS 387 (527)
Q Consensus 356 p~~~v~~~Gsy----RRGk---e~~gDVDiLIt~~~~~~ 387 (527)
-++.+-++||+ =+|- ...+|+|+||-.++..+
T Consensus 107 ~~~~~gv~GS~~~qlaTg~~~~~~~SDLDLLi~~~~~~~ 145 (202)
T TIGR03135 107 LGVPWGVYGSAGWQLLTGLPYLHASSDLDLLLRAPSPLS 145 (202)
T ss_pred CCCcEEEecchHHHHhcCCcccCCCCCeeEEEcCCChhh
Confidence 35567789999 5565 45689999998876543
No 293
>PHA01806 hypothetical protein
Probab=29.67 E-value=89 Score=30.53 Aligned_cols=49 Identities=18% Similarity=0.238 Sum_probs=31.0
Q ss_pred CcCHHHHHH-HHHHHHHHhhhcCCCeEEEecccccc----cCCccCCeeEEEecCCcc
Q 009742 334 RIPRHEVEQ-MERLLQKAGEEVLPEVIILCGGSYRR----GKASCGDLDVVIMHPDRK 386 (527)
Q Consensus 334 ~i~r~Ea~~-i~~iv~~~~~~~~p~~~v~~~GsyRR----Gke~~gDVDiLIt~~~~~ 386 (527)
.|++..... ...++..+. .-+.++.++||+=| |+ .+.|+||++....+.
T Consensus 14 ~I~~~~is~~al~v~~~l~---~~g~~aYlVGG~VRD~Llgr-~~kDiDivt~~~~pe 67 (200)
T PHA01806 14 EIPEGLIAKALLLRLYSDA---RHSEGVALAGGAARDLMHGA-EPKDIDIALYGMDDR 67 (200)
T ss_pred ccChhHcCHHHHHHHHHHH---HCCcEEEEECchHHHHHcCC-CCCceEEEccCCCHH
Confidence 455555432 344444443 35778888888877 55 789999977555544
No 294
>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=29.58 E-value=40 Score=28.07 Aligned_cols=35 Identities=20% Similarity=0.440 Sum_probs=19.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhH
Q 009742 243 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVR 281 (527)
Q Consensus 243 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~ 281 (527)
.++..||+||..+.....++ -+.-+++|+.--+..
T Consensus 3 ~~l~~LpNig~~~e~~L~~v----GI~t~~~L~~~Ga~~ 37 (81)
T PF04994_consen 3 NRLKDLPNIGPKSERMLAKV----GIHTVEDLRELGAVE 37 (81)
T ss_dssp --GCGSTT--HHHHHHHHHT----T--SHHHHHHHHHHH
T ss_pred cchhhCCCCCHHHHHHHHHc----CCCCHHHHHHhCHHH
Confidence 36889999999887765543 455666766533333
No 295
>KOG3524 consensus Predicted guanine nucleotide exchange factor (PEBBLE) [Signal transduction mechanisms]
Probab=28.46 E-value=39 Score=38.85 Aligned_cols=79 Identities=22% Similarity=0.400 Sum_probs=60.9
Q ss_pred CCcCCeEEEEeeCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEeCcHHHHH-------hccccchHHHHHHhcCCC
Q 009742 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQ-------QSVIRYQWLEDSLRLGEK 89 (527)
Q Consensus 17 ~~f~~~~i~iv~~~~g~~r~~~l~~~~~~~G~~v~~~~s~~VTHVV~~~~~~~l~-------~~vv~~~Wl~ec~~~g~~ 89 (527)
+-|.|+.+++ .|....-.+++-.-...+||..+. -...+||||..+....-. ..+|.-.|+--++..|..
T Consensus 209 ~~feg~~~~f--~gF~~ee~~~m~~sle~~gg~~a~-~d~~cthvvv~e~~~~~~p~~~s~~~~~vk~ewfw~siq~g~~ 285 (850)
T KOG3524|consen 209 GVFEGLSLFF--HGFKQEEIDDMLRSLENTGGKLAP-SDTLCTHVVVNEDNDEVEPLAVSSNQVHVKKEWFWVSIQRGCC 285 (850)
T ss_pred ccccCCeEee--cCCcHHHHHHHHHHHHhcCCcccC-CCCCceeEeecCCccccccccccccceeecccceEEEEecchh
Confidence 7799999999 578888889999999999999999 567899999866432111 238888888888887766
Q ss_pred cCCcccccc
Q 009742 90 VSEDLYRIK 98 (527)
Q Consensus 90 v~~~~~~l~ 98 (527)
--++.|.+.
T Consensus 286 a~e~~yl~~ 294 (850)
T KOG3524|consen 286 AIEDNYLLP 294 (850)
T ss_pred ccccceecc
Confidence 666666653
No 296
>PRK03348 DNA polymerase IV; Provisional
Probab=28.12 E-value=1.1e+02 Score=33.53 Aligned_cols=53 Identities=17% Similarity=0.334 Sum_probs=38.1
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHHh--CCCC
Q 009742 245 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 307 (527)
Q Consensus 245 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--GirT 307 (527)
+..|||||+.+.++...+ -+..+.+|.+-.+..+.+.| |++....||+. |+..
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 45666666654555566666 77788899874 8754
No 297
>PRK11072 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed
Probab=25.88 E-value=2.5e+02 Score=34.07 Aligned_cols=27 Identities=26% Similarity=0.465 Sum_probs=20.8
Q ss_pred eEEEecccc-cccCCccCCeeEEEecCC
Q 009742 358 VIILCGGSY-RRGKASCGDLDVVIMHPD 384 (527)
Q Consensus 358 ~~v~~~Gsy-RRGke~~gDVDiLIt~~~ 384 (527)
+.|..+|.| +|-...++|||+++.+++
T Consensus 155 ~aViamGKlG~~ELn~~SDIDLifly~~ 182 (943)
T PRK11072 155 LLILGMGKLGGRELNFSSDIDLIFTYPE 182 (943)
T ss_pred EEEEEeccccCccCCCccCCceEEEeCC
Confidence 456677887 555678999999998763
No 298
>TIGR00207 fliG flagellar motor switch protein FliG. The fliG protein along with fliM and fliN interact to form the switch complex of the bacterial flagellar motor located at the base of the basal body. This complex interacts with chemotaxis proteins (eg CHEY). In addition the complex interacts with other components of the motor that determine the direction of flagellar rotation. The model contains putative members of the fliG family at scores of less than 100 from Agrobacterium radiobacter and Sinorhizobium meliloti as well as fliG-like genes from treponema pallidum and Borrelia burgdorferi. That is why the suggested cutoff is set at 20 but was set at 100 to construct the family.
Probab=24.80 E-value=4.1e+02 Score=28.07 Aligned_cols=86 Identities=9% Similarity=0.214 Sum_probs=51.8
Q ss_pred HHHHHHHhcCCccccc--hhhhcCCCCCCHHHHHHHHHHHHh------------CCchhhHHHHhhchhHHH-HHHhhcc
Q 009742 226 YKAIPVIEKLPFKIES--ADQVKGLPGIGKSMQDHIQEIVTT------------GKLSKLEHFEKDEKVRTI-SLFGEVW 290 (527)
Q Consensus 226 ~rAa~~l~~l~~~i~s--~~~l~~lpgIG~~ia~kI~Eil~t------------G~~~~le~l~~~~~~~~l-~lf~~I~ 290 (527)
..||.+|..||..... +..+..+..|.+.+.+.|.++|+. |....+-++.+..+...- .+|..+-
T Consensus 145 ~~AA~VL~~Lp~~~~~ei~~ria~l~~vs~~~i~~ie~~L~~~~~~~~~~~~~~gG~~~~a~ILN~~~~~~~~~il~~L~ 224 (338)
T TIGR00207 145 AQAADILSLFPEEVQAEVARRIATMGRTSPEVVAEVERVLEGKLDSLNSDYTKMGGVRAVAEIINLMDRKTEKTIITSLE 224 (338)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhhccccccCChHHHHHHHHHhCCchHHHHHHHHHH
Confidence 5789999999976443 366788888888888777555541 222334445444444333 3455555
Q ss_pred CcCHHHHHHHHHhCCCCHHHHh
Q 009742 291 GIGPATAQKLYEKGHRTLDDLK 312 (527)
Q Consensus 291 GvGpktA~~ly~~GirTledL~ 312 (527)
-.-|..|..+-+ -+=+++||.
T Consensus 225 ~~dp~la~~Ir~-~mF~Fedl~ 245 (338)
T TIGR00207 225 EFDPELAEEIKK-EMFVFEDIV 245 (338)
T ss_pred HhCHHHHHHHHH-HccCHHHHh
Confidence 556666666633 444566664
No 299
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=24.62 E-value=3.1e+02 Score=29.14 Aligned_cols=104 Identities=19% Similarity=0.242 Sum_probs=58.7
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHHhhccCcCHHHHHHHHH-------hCCCCHHHHhhc
Q 009742 242 ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE-------KGHRTLDDLKNE 314 (527)
Q Consensus 242 ~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~-------~GirTledL~~~ 314 (527)
+++|.+ +||++.+.+|+++ .-+.-++.+..-.+ .+| .+|.|+...+|.++.+ .|+.|-.++...
T Consensus 31 ~~~l~~-~g~~~~~~~kL~~----~g~~tv~~~~~~~~---~~L-~~~~g~s~~~~~ki~~~a~~~~~~~~~ta~~~~~~ 101 (344)
T PLN03187 31 IDKLIS-QGINAGDVKKLQD----AGIYTCNGLMMHTK---KNL-TGIKGLSEAKVDKICEAAEKLLNQGFITGSDALLK 101 (344)
T ss_pred HHHHhh-CCCCHHHHHHHHH----cCCCcHHHHHhCCH---HHH-HHhcCCCHHHHHHHHHHHHHhhcccCCcHHHHHhh
Confidence 334433 6799888777554 34555666554333 233 4889999999998764 266777776643
Q ss_pred cCcchhhhccccchhhhccCcCHHHHHHHHHHHHHHhhhcCCCeEEEecccccccCCc
Q 009742 315 DSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKAS 372 (527)
Q Consensus 315 ~~L~~~q~~Glk~yed~~~~i~r~Ea~~i~~iv~~~~~~~~p~~~v~~~GsyRRGke~ 372 (527)
.+-......|.+-.++++. .-+..|...+++|.+.=||.+
T Consensus 102 ~~~~~~isTG~~~LD~lLg------------------GGi~~G~ItEI~G~~GsGKTq 141 (344)
T PLN03187 102 RKSVVRITTGSQALDELLG------------------GGIETRCITEAFGEFRSGKTQ 141 (344)
T ss_pred hccCceecCCcHhHHhhcC------------------CCCCCCeEEEEecCCCCChhH
Confidence 2111111234433333221 112334456688888888876
No 300
>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=24.56 E-value=1.5e+02 Score=27.01 Aligned_cols=38 Identities=18% Similarity=0.194 Sum_probs=25.2
Q ss_pred HHHHHHHHhhhcCCCeEEEecccccc----cCCccCCeeEEEecC
Q 009742 343 MERLLQKAGEEVLPEVIILCGGSYRR----GKASCGDLDVVIMHP 383 (527)
Q Consensus 343 i~~iv~~~~~~~~p~~~v~~~GsyRR----Gke~~gDVDiLIt~~ 383 (527)
+..+++.+.. ..+..+.++||+=| |+ .++|+||++...
T Consensus 4 ~~~il~~l~~--~~g~~~ylVGG~VRD~Llg~-~~~DiDi~v~~~ 45 (139)
T cd05398 4 LLKLLRELKK--ALGYEAYLVGGAVRDLLLGR-PPKDIDIATDAD 45 (139)
T ss_pred HHHHHHHHHh--ccCceEEEECChHHHHHcCC-CCCCceEEEeCC
Confidence 3444554432 13778888888766 55 579999988664
No 301
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=24.34 E-value=1.3e+02 Score=34.87 Aligned_cols=83 Identities=18% Similarity=0.263 Sum_probs=54.9
Q ss_pred CCCCCCCCCCCCCCCCcCCeEEEEeeCCCChhHHHHHHHHHHhcCCEEEeec----C-CCccEE-E-Ee----CcHHHHH
Q 009742 3 PKTTRKPTPALDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKL----S-KKVTHV-L-AM----DLEALLQ 71 (527)
Q Consensus 3 ~~~~~~~~~~~~~~~~f~~~~i~iv~~~~g~~r~~~l~~~~~~~G~~v~~~~----s-~~VTHV-V-~~----~~~~~l~ 71 (527)
|+.+|.++.+-.+ -+|.|..+|++-.+-... .+.|.+++..-||++...- + .+.+-| | .+ +..+|-|
T Consensus 573 ~~~~~~~a~s~~~-kLf~gl~~~~~g~fs~~p-~~~l~~l~~~~gg~~l~~~~~~~~~~k~s~~~~~~~~~~~~~~~~~k 650 (684)
T KOG4362|consen 573 PKEKRLRAESYKP-KLFEGLKFYFVGDFSNPP-KEQLQELVHLAGGTILQVPRVAYSDKKKSTIVVLSEKPVLDSILWQK 650 (684)
T ss_pred cccccccccccCc-chhcCCcceeecccccCc-HHHHHHHHhhcCcceeeccCcccccccccceeEeecccCCCchhhhh
Confidence 4556555555554 799999999987776666 6899999999999987432 1 122222 2 11 2333433
Q ss_pred h------------ccccchHHHHHHhcC
Q 009742 72 Q------------SVIRYQWLEDSLRLG 87 (527)
Q Consensus 72 ~------------~vv~~~Wl~ec~~~g 87 (527)
. -+|+-+|+.+++.--
T Consensus 651 ~~~~ea~~~s~~a~~~~~~wvl~s~a~~ 678 (684)
T KOG4362|consen 651 VNDAEALALSQRARAVSSSWVLDSIAGY 678 (684)
T ss_pred hccHHHHHHhcCCCccchhhhhcchhce
Confidence 2 199999999987543
No 302
>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=24.20 E-value=50 Score=34.50 Aligned_cols=36 Identities=25% Similarity=0.308 Sum_probs=26.7
Q ss_pred ccCcCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhcc
Q 009742 289 VWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLG 324 (527)
Q Consensus 289 I~GvGpktA~~ly~~GirTledL~~~~--~L~~~q~~G 324 (527)
-.||||.++++|-+.||.|++||.... .|....++.
T Consensus 6 ~~g~~~~~~~~L~~~g~~t~~~~~~~~~~~L~~~~gls 43 (313)
T TIGR02238 6 AHGINAADIKKLKSAGICTVNGVIMTTRRALCKIKGLS 43 (313)
T ss_pred cCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCC
Confidence 368999999999999999999998543 244443433
No 303
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.06 E-value=63 Score=39.17 Aligned_cols=26 Identities=19% Similarity=0.326 Sum_probs=21.4
Q ss_pred hhccCcCHHHHHHHHHh-CCCCHHHHh
Q 009742 287 GEVWGIGPATAQKLYEK-GHRTLDDLK 312 (527)
Q Consensus 287 ~~I~GvGpktA~~ly~~-GirTledL~ 312 (527)
.+|+||||+||.++... |=.+|+.|.
T Consensus 869 ~GI~GIGpktAl~li~~~~~~~le~L~ 895 (1034)
T TIGR00600 869 EGIPTVGPVSAMEILNEFPGDGLEPLL 895 (1034)
T ss_pred CCCCcccHHHHHHHHHHcCCCCHHHHH
Confidence 47999999999999998 645666665
No 304
>PRK07945 hypothetical protein; Provisional
Probab=22.83 E-value=45 Score=35.12 Aligned_cols=28 Identities=29% Similarity=0.446 Sum_probs=23.0
Q ss_pred HhhccCcCHHHHHHHHHh---C-CCCHHHHhh
Q 009742 286 FGEVWGIGPATAQKLYEK---G-HRTLDDLKN 313 (527)
Q Consensus 286 f~~I~GvGpktA~~ly~~---G-irTledL~~ 313 (527)
|++|||||..+|.++.+. | +.-|++|+.
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 5 567888884
No 305
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=22.24 E-value=1.9e+02 Score=35.63 Aligned_cols=90 Identities=22% Similarity=0.322 Sum_probs=0.0
Q ss_pred HHHHHHHHHHhcCCccccchhhhcCCCCCC-HHHHHHHHHHHHh--CCchhhHHHHhhchhHHHHHH-------------
Q 009742 223 FSYYKAIPVIEKLPFKIESADQVKGLPGIG-KSMQDHIQEIVTT--GKLSKLEHFEKDEKVRTISLF------------- 286 (527)
Q Consensus 223 ~aY~rAa~~l~~l~~~i~s~~~l~~lpgIG-~~ia~kI~Eil~t--G~~~~le~l~~~~~~~~l~lf------------- 286 (527)
++|.-|-.++++-.+++..+.. | ..+.++++||-.- -..+-.|.=.-..-+-+++|+
T Consensus 1294 l~YYAayfSira~~FDi~~m~~-------Gke~ik~k~~Ei~~~~~~~~~~kEk~l~t~lEi~~EM~aRGf~f~~idly~ 1366 (1444)
T COG2176 1294 LEYYAAYFSIRADDFDIETMSK-------GKEAIKAKMEEINKRKGNKASPKEKNLLTVLEIVLEMLARGFKFQKIDLYK 1366 (1444)
T ss_pred HHHHHHHheeehhhcCHHHHhc-------cHHHHHHHHHHHhhcccccCChhhhhhHhHHHHHHHHHHccCcccCceeee
Q ss_pred -----------------hhccCcCHHHHHHHHHh----CCCCHHHHhhccCcch
Q 009742 287 -----------------GEVWGIGPATAQKLYEK----GHRTLDDLKNEDSLTH 319 (527)
Q Consensus 287 -----------------~~I~GvGpktA~~ly~~----GirTledL~~~~~L~~ 319 (527)
-.|+|+|...|+.+++. -+-|++||++..++++
T Consensus 1367 S~At~Fvid~~~LipPFi~i~GlGe~vA~~IV~AR~Ek~FlS~eDlkkRtkis~ 1420 (1444)
T COG2176 1367 SDATEFVIDGDTLIPPFIAIPGLGENVAKSIVEAREEKEFLSKEDLKKRTKISK 1420 (1444)
T ss_pred ccCeEEEEeCCeecCceeccCChhHHHHHHHHHHhhcCCcCCHHHHHHhcCccH
No 306
>PF14091 DUF4269: Domain of unknown function (DUF4269)
Probab=22.10 E-value=6.5e+02 Score=23.69 Aligned_cols=26 Identities=27% Similarity=0.392 Sum_probs=16.9
Q ss_pred ecccccccCC-ccCCeeEEEecCCcch
Q 009742 362 CGGSYRRGKA-SCGDLDVVIMHPDRKS 387 (527)
Q Consensus 362 ~~GsyRRGke-~~gDVDiLIt~~~~~~ 387 (527)
+||-+==|-. ..+|+||+..++|...
T Consensus 20 L~GTiPi~Idi~~SDLDIic~~~d~~~ 46 (152)
T PF14091_consen 20 LVGTIPIGIDIPGSDLDIICEVPDPEA 46 (152)
T ss_pred EecccccccCCCCCCccEEEEeCCHHH
Confidence 3454433332 2579999999998654
No 307
>PF04439 Adenyl_transf: Streptomycin adenylyltransferase; InterPro: IPR007530 Also known as aminoglycoside 6-adenylyltransferase (2.7.7 from EC), this protein confers resistance to aminoglycoside antibiotics.; PDB: 2PBE_A.
Probab=20.36 E-value=7.1e+02 Score=25.58 Aligned_cols=48 Identities=27% Similarity=0.315 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHHHHhhhcCCCeE-EEeccccccc---CCccCCeeEEEecCCcc
Q 009742 337 RHEVEQMERLLQKAGEEVLPEVI-ILCGGSYRRG---KASCGDLDVVIMHPDRK 386 (527)
Q Consensus 337 r~Ea~~i~~iv~~~~~~~~p~~~-v~~~GsyRRG---ke~~gDVDiLIt~~~~~ 386 (527)
|.|.+-+..|+.-+. ..+.++ |.+.||.-+. +-.=.|.||++-..+..
T Consensus 2 rte~em~~~Il~~A~--~d~rIraV~l~GSR~n~~~~~D~fqDyDIv~~v~d~~ 53 (282)
T PF04439_consen 2 RTEQEMMDLILEFAK--QDERIRAVILNGSRANPNAPKDEFQDYDIVYVVTDIE 53 (282)
T ss_dssp --HHHHHHHHHHHHH--H-TTEEEEEE----------------EEEEEEES-HH
T ss_pred CCHHHHHHHHHHHHh--cCCcEEEEEEecCCCCCCCCccccccccEEEEecchh
Confidence 445555555555443 378885 6789996553 34567889998776654
Done!