Query 009281
Match_columns 538
No_of_seqs 312 out of 941
Neff 6.8
Searched_HMMs 46136
Date Thu Mar 28 22:38:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009281.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009281hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2534 DNA polymerase IV (fam 100.0 4.1E-88 8.9E-93 666.5 27.0 322 207-538 9-353 (353)
2 cd00141 NT_POLXc Nucleotidyltr 100.0 9.6E-74 2.1E-78 587.7 30.3 303 212-536 2-307 (307)
3 smart00483 POLXc DNA polymeras 100.0 5.7E-73 1.2E-77 588.0 26.7 309 208-537 1-334 (334)
4 PRK08609 hypothetical protein; 100.0 6.6E-68 1.4E-72 584.5 28.3 299 208-537 1-314 (570)
5 COG1796 POL4 DNA polymerase IV 100.0 5.8E-57 1.3E-61 449.9 23.7 298 208-537 3-318 (326)
6 PF14792 DNA_pol_B_palm: DNA p 99.9 1.1E-25 2.4E-30 198.5 9.9 105 345-459 1-112 (112)
7 PF14791 DNA_pol_B_thumb: DNA 99.9 1.4E-24 3E-29 171.8 3.1 63 465-537 1-63 (64)
8 PF14716 HHH_8: Helix-hairpin- 99.7 9E-17 2E-21 129.3 7.3 66 210-275 1-68 (68)
9 PF10391 DNA_pol_lambd_f: Fing 99.6 1.9E-16 4.2E-21 119.9 3.6 51 294-344 1-52 (52)
10 PRK07945 hypothetical protein; 99.6 9.9E-15 2.1E-19 152.4 11.5 102 213-324 3-118 (335)
11 smart00292 BRCT breast cancer 98.9 2.5E-09 5.4E-14 85.9 6.8 79 17-98 1-80 (80)
12 PF00533 BRCT: BRCA1 C Terminu 98.9 2.7E-09 5.9E-14 86.6 6.6 76 15-95 2-78 (78)
13 cd00027 BRCT Breast Cancer Sup 98.5 1.8E-07 3.9E-12 73.2 5.9 72 21-96 1-72 (72)
14 TIGR00575 dnlj DNA ligase, NAD 98.0 2.6E-05 5.6E-10 88.5 9.4 83 254-347 466-551 (652)
15 PF14520 HHH_5: Helix-hairpin- 97.9 8E-06 1.7E-10 63.9 2.7 51 293-343 3-55 (60)
16 PF14520 HHH_5: Helix-hairpin- 97.4 0.00021 4.6E-09 55.8 4.3 52 254-313 5-56 (60)
17 KOG3226 DNA repair protein [Re 97.3 0.00015 3.2E-09 74.7 3.7 88 16-110 315-403 (508)
18 PF12738 PTCB-BRCT: twin BRCT 97.1 0.00034 7.4E-09 54.9 2.9 51 36-90 13-63 (63)
19 PF11731 Cdd1: Pathogenicity l 97.0 0.00097 2.1E-08 56.7 4.2 35 291-325 8-42 (93)
20 COG1555 ComEA DNA uptake prote 96.9 0.0012 2.5E-08 61.4 5.1 50 252-313 95-145 (149)
21 KOG2481 Protein required for n 96.9 0.00029 6.2E-09 75.6 0.7 87 11-109 320-416 (570)
22 PF12826 HHH_2: Helix-hairpin- 96.9 0.0015 3.2E-08 51.9 4.6 48 257-313 6-53 (64)
23 PRK07956 ligA NAD-dependent DN 96.9 0.0041 8.9E-08 70.9 9.8 114 254-377 479-602 (665)
24 TIGR01259 comE comEA protein. 96.8 0.0023 4.9E-08 57.4 5.5 50 252-313 66-116 (120)
25 PF12836 HHH_3: Helix-hairpin- 96.7 0.002 4.4E-08 51.2 4.4 48 252-311 12-60 (65)
26 PLN03123 poly [ADP-ribose] pol 96.7 0.0031 6.8E-08 74.3 7.5 89 16-109 391-481 (981)
27 PRK14351 ligA NAD-dependent DN 96.5 0.0082 1.8E-07 68.7 9.0 87 254-350 496-584 (689)
28 KOG0966 ATP-dependent DNA liga 96.5 0.0039 8.4E-08 70.3 6.1 92 12-108 627-721 (881)
29 PRK02515 psbU photosystem II c 96.5 0.0042 9E-08 55.9 4.8 47 252-313 59-105 (132)
30 TIGR00084 ruvA Holliday juncti 96.3 0.0056 1.2E-07 59.3 5.3 53 254-312 72-124 (191)
31 TIGR00426 competence protein C 96.1 0.013 2.8E-07 47.0 5.4 50 253-314 15-66 (69)
32 PLN03122 Poly [ADP-ribose] pol 96.1 0.012 2.6E-07 68.1 7.2 93 14-111 185-280 (815)
33 PRK14605 ruvA Holliday junctio 96.1 0.0068 1.5E-07 58.8 4.4 52 254-312 73-125 (194)
34 PF00633 HHH: Helix-hairpin-he 96.0 0.0052 1.1E-07 41.3 2.4 23 251-273 8-30 (30)
35 PF14229 DUF4332: Domain of un 96.0 0.024 5.2E-07 50.9 7.5 67 260-326 1-84 (122)
36 PRK13901 ruvA Holliday junctio 95.9 0.01 2.3E-07 57.5 4.8 54 254-313 72-125 (196)
37 TIGR00084 ruvA Holliday juncti 95.8 0.0055 1.2E-07 59.3 2.7 50 292-343 69-124 (191)
38 PRK14601 ruvA Holliday junctio 95.8 0.011 2.4E-07 56.7 4.7 54 254-313 73-126 (183)
39 PRK00116 ruvA Holliday junctio 95.8 0.011 2.5E-07 57.2 4.7 54 254-314 73-127 (192)
40 PRK12766 50S ribosomal protein 95.6 0.0036 7.9E-08 61.6 0.5 51 296-346 4-56 (232)
41 PRK14602 ruvA Holliday junctio 95.6 0.013 2.8E-07 57.3 4.3 54 254-313 74-127 (203)
42 KOG4362 Transcriptional regula 95.6 0.013 2.8E-07 65.9 4.8 76 30-111 485-565 (684)
43 PRK14606 ruvA Holliday junctio 95.6 0.016 3.4E-07 56.0 4.7 54 254-313 73-126 (188)
44 PRK14603 ruvA Holliday junctio 95.5 0.017 3.7E-07 56.2 4.7 54 254-313 72-125 (197)
45 PRK14604 ruvA Holliday junctio 95.5 0.018 3.9E-07 55.9 4.7 54 254-313 73-126 (195)
46 PF00633 HHH: Helix-hairpin-he 95.4 0.015 3.2E-07 39.2 2.6 22 292-313 8-29 (30)
47 KOG0966 ATP-dependent DNA liga 95.3 0.044 9.5E-07 62.1 7.7 92 16-107 782-881 (881)
48 COG5163 NOP7 Protein required 95.3 0.015 3.1E-07 61.0 3.6 87 11-109 343-440 (591)
49 PRK07956 ligA NAD-dependent DN 95.2 0.0082 1.8E-07 68.5 1.7 61 299-359 449-512 (665)
50 PTZ00418 Poly(A) polymerase; P 95.0 0.23 5.1E-06 55.6 12.0 51 367-417 125-176 (593)
51 cd05397 NT_Pol-beta-like Nucle 94.8 0.052 1.1E-06 40.7 4.5 28 365-392 14-42 (49)
52 PRK14350 ligA NAD-dependent DN 94.7 0.065 1.4E-06 61.3 7.0 84 254-346 470-561 (669)
53 TIGR00575 dnlj DNA ligase, NAD 94.7 0.013 2.9E-07 66.7 1.5 63 298-360 435-500 (652)
54 COG0632 RuvA Holliday junction 94.7 0.037 8.1E-07 53.9 4.4 54 254-313 73-126 (201)
55 COG1555 ComEA DNA uptake prote 94.7 0.025 5.3E-07 52.6 3.0 51 291-347 93-148 (149)
56 PRK14973 DNA topoisomerase I; 94.7 0.038 8.3E-07 65.4 5.2 90 254-344 835-928 (936)
57 PF11798 IMS_HHH: IMS family H 94.5 0.022 4.8E-07 38.9 1.6 20 297-316 13-32 (32)
58 PRK14600 ruvA Holliday junctio 94.4 0.041 8.9E-07 53.1 3.9 53 254-313 73-125 (186)
59 PRK02515 psbU photosystem II c 94.3 0.05 1.1E-06 49.1 3.9 32 293-324 59-91 (132)
60 PRK02362 ski2-like helicase; P 94.3 0.031 6.8E-07 64.9 3.3 56 284-342 642-699 (737)
61 COG0272 Lig NAD-dependent DNA 94.3 0.12 2.6E-06 58.3 7.6 49 256-313 513-561 (667)
62 TIGR01259 comE comEA protein. 94.2 0.045 9.7E-07 49.0 3.4 47 293-345 66-117 (120)
63 cd05402 NT_PAP_TUTase Nucleoti 94.0 0.22 4.7E-06 43.5 7.4 59 353-415 8-68 (114)
64 PRK00116 ruvA Holliday junctio 93.7 0.036 7.9E-07 53.7 2.0 51 293-343 71-125 (192)
65 TIGR00426 competence protein C 93.6 0.078 1.7E-06 42.4 3.5 44 296-345 17-66 (69)
66 PRK14605 ruvA Holliday junctio 93.6 0.034 7.3E-07 54.0 1.6 52 291-342 69-124 (194)
67 PF12836 HHH_3: Helix-hairpin- 93.5 0.069 1.5E-06 42.4 3.0 47 293-345 12-63 (65)
68 PF12826 HHH_2: Helix-hairpin- 93.2 0.063 1.4E-06 42.5 2.4 43 299-342 7-51 (64)
69 PRK00254 ski2-like helicase; P 92.8 0.12 2.7E-06 59.8 4.9 66 276-342 623-694 (720)
70 KOG1929 Nucleotide excision re 92.5 0.19 4.2E-06 58.1 5.8 89 17-110 102-190 (811)
71 KOG2043 Signaling protein SWIF 92.5 0.12 2.7E-06 60.6 4.3 68 38-109 672-739 (896)
72 PRK12766 50S ribosomal protein 92.4 0.24 5.2E-06 49.1 5.6 54 253-314 2-55 (232)
73 PRK14606 ruvA Holliday junctio 91.3 0.11 2.3E-06 50.3 1.7 50 291-342 69-124 (188)
74 PRK14601 ruvA Holliday junctio 91.1 0.11 2.5E-06 49.9 1.7 50 291-342 69-124 (183)
75 PRK14603 ruvA Holliday junctio 91.0 0.1 2.2E-06 50.8 1.3 50 291-342 68-123 (197)
76 PF01909 NTP_transf_2: Nucleot 90.8 0.33 7.2E-06 40.4 4.1 32 366-397 12-44 (93)
77 smart00278 HhH1 Helix-hairpin- 90.8 0.17 3.6E-06 32.7 1.7 18 296-313 2-19 (26)
78 PRK14602 ruvA Holliday junctio 90.7 0.14 3E-06 50.1 1.9 50 291-342 70-125 (203)
79 PRK14604 ruvA Holliday junctio 90.5 0.13 2.9E-06 49.9 1.7 50 291-342 69-124 (195)
80 PF04994 TfoX_C: TfoX C-termin 90.2 0.22 4.9E-06 41.4 2.5 30 297-326 5-34 (81)
81 PRK13901 ruvA Holliday junctio 90.1 0.16 3.5E-06 49.3 1.8 50 291-342 68-123 (196)
82 PRK14351 ligA NAD-dependent DN 90.0 0.14 3E-06 58.9 1.4 64 298-361 465-531 (689)
83 COG3743 Uncharacterized conser 89.8 0.29 6.2E-06 44.2 3.0 53 295-350 67-119 (133)
84 TIGR01448 recD_rel helicase, p 89.5 1.3 2.8E-05 51.5 8.9 83 253-346 116-201 (720)
85 COG1948 MUS81 ERCC4-type nucle 89.5 0.47 1E-05 47.7 4.6 49 256-313 184-232 (254)
86 PRK04301 radA DNA repair and r 89.4 0.2 4.3E-06 52.2 1.9 46 297-342 8-55 (317)
87 TIGR03671 cca_archaeal CCA-add 88.9 1.8 3.9E-05 46.7 8.8 47 352-398 24-72 (408)
88 TIGR03252 uncharacterized HhH- 88.7 1.1 2.3E-05 42.9 6.2 49 261-312 75-132 (177)
89 PRK14600 ruvA Holliday junctio 88.6 0.22 4.8E-06 48.0 1.5 49 291-342 69-123 (186)
90 PRK08097 ligB NAD-dependent DN 88.3 0.58 1.2E-05 52.5 4.7 86 253-351 458-545 (562)
91 COG1796 POL4 DNA polymerase IV 87.8 1.4 3E-05 45.7 6.7 96 207-321 59-154 (326)
92 TIGR02236 recomb_radA DNA repa 87.7 0.36 7.9E-06 49.9 2.6 29 298-326 2-30 (310)
93 TIGR01448 recD_rel helicase, p 87.6 0.27 5.8E-06 57.1 1.6 54 291-344 78-135 (720)
94 KOG1929 Nucleotide excision re 87.5 0.7 1.5E-05 53.7 4.9 93 12-110 487-579 (811)
95 PRK14350 ligA NAD-dependent DN 87.2 0.75 1.6E-05 52.8 4.9 61 249-313 497-559 (669)
96 KOG0323 TFIIF-interacting CTD 87.1 0.26 5.6E-06 55.6 1.2 91 17-111 440-533 (635)
97 TIGR00588 ogg 8-oxoguanine DNA 86.8 1.6 3.5E-05 45.5 6.8 63 255-319 177-244 (310)
98 smart00279 HhH2 Helix-hairpin- 86.5 0.47 1E-05 33.3 1.7 16 299-314 20-35 (36)
99 cd00080 HhH2_motif Helix-hairp 86.2 0.64 1.4E-05 38.0 2.7 28 297-325 24-51 (75)
100 PRK01172 ski2-like helicase; P 85.5 1 2.3E-05 51.7 5.1 39 286-325 604-642 (674)
101 KOG2841 Structure-specific end 85.1 1 2.2E-05 44.6 3.9 50 255-313 196-245 (254)
102 PRK03352 DNA polymerase IV; Va 85.0 0.66 1.4E-05 48.8 2.9 29 297-325 179-207 (346)
103 PF11731 Cdd1: Pathogenicity l 84.9 1.4 3E-05 37.7 4.2 47 253-303 11-57 (93)
104 PRK14670 uvrC excinuclease ABC 84.8 2.1 4.5E-05 48.3 6.8 52 254-314 514-565 (574)
105 PRK08609 hypothetical protein; 84.7 1.2 2.5E-05 50.4 4.8 54 252-311 86-139 (570)
106 cd05400 NT_2-5OAS_ClassI-CCAas 83.9 4.7 0.0001 36.5 7.7 46 368-413 27-79 (143)
107 PRK03858 DNA polymerase IV; Va 83.6 0.8 1.7E-05 49.1 2.9 29 297-325 175-203 (396)
108 smart00278 HhH1 Helix-hairpin- 83.3 1 2.2E-05 29.0 2.1 20 255-274 2-21 (26)
109 PRK01216 DNA polymerase IV; Va 82.7 0.88 1.9E-05 48.2 2.6 30 297-326 180-209 (351)
110 PRK03609 umuC DNA polymerase V 82.4 0.92 2E-05 49.2 2.7 29 297-325 181-209 (422)
111 COG0353 RecR Recombinational D 82.2 0.97 2.1E-05 43.7 2.5 22 291-312 8-29 (198)
112 COG1708 Predicted nucleotidylt 82.2 5.9 0.00013 34.4 7.4 29 367-395 25-54 (128)
113 PRK10880 adenine DNA glycosyla 82.0 5.7 0.00012 42.2 8.4 65 232-303 85-151 (350)
114 PRK14667 uvrC excinuclease ABC 81.9 3.1 6.7E-05 46.9 6.7 51 254-314 514-564 (567)
115 PRK00227 glnD PII uridylyl-tra 81.4 4.1 8.9E-05 47.1 7.5 65 348-415 8-74 (693)
116 COG0122 AlkA 3-methyladenine D 81.3 6.1 0.00013 40.7 8.1 47 270-317 174-220 (285)
117 PRK14666 uvrC excinuclease ABC 81.1 0.79 1.7E-05 52.4 1.7 46 295-342 637-685 (694)
118 smart00478 ENDO3c endonuclease 80.8 4.5 9.8E-05 36.9 6.4 26 292-317 69-94 (149)
119 smart00475 53EXOc 5'-3' exonuc 80.7 1.2 2.7E-05 45.1 2.8 26 298-325 189-215 (259)
120 PF01367 5_3_exonuc: 5'-3' exo 80.6 0.13 2.9E-06 44.6 -3.7 24 299-324 22-46 (101)
121 PRK09482 flap endonuclease-lik 80.5 1.3 2.8E-05 45.0 2.8 25 299-325 186-211 (256)
122 cd01703 PolY_Pol_iota DNA Poly 80.4 1.1 2.5E-05 47.9 2.5 30 297-326 174-203 (379)
123 PF14490 HHH_4: Helix-hairpin- 80.4 1.6 3.6E-05 37.1 3.0 55 292-347 10-67 (94)
124 PRK08097 ligB NAD-dependent DN 80.4 0.67 1.5E-05 52.0 0.8 64 298-361 428-494 (562)
125 PRK14666 uvrC excinuclease ABC 80.4 2.7 6E-05 48.1 5.6 66 233-313 622-687 (694)
126 PRK01810 DNA polymerase IV; Va 80.1 1.3 2.8E-05 47.8 2.8 29 297-325 181-209 (407)
127 cd01701 PolY_Rev1 DNA polymera 79.9 1.3 2.8E-05 47.8 2.8 30 297-326 224-253 (404)
128 PRK13482 DNA integrity scannin 79.7 2.9 6.3E-05 44.2 5.2 60 245-313 276-337 (352)
129 PRK14976 5'-3' exonuclease; Pr 79.6 1.4 2.9E-05 45.4 2.7 24 299-324 195-219 (281)
130 PRK00558 uvrC excinuclease ABC 79.5 3.5 7.6E-05 46.9 6.2 52 254-314 543-594 (598)
131 cd01700 PolY_Pol_V_umuC umuC s 79.4 1.3 2.9E-05 46.4 2.7 29 297-325 178-206 (344)
132 cd00056 ENDO3c endonuclease II 79.3 1.2 2.5E-05 41.2 1.9 27 291-317 79-105 (158)
133 PRK02406 DNA polymerase IV; Va 79.2 1.3 2.9E-05 46.4 2.5 29 297-325 170-198 (343)
134 PRK03348 DNA polymerase IV; Pr 79.1 1.3 2.8E-05 48.7 2.5 29 297-325 182-210 (454)
135 COG1746 CCA1 tRNA nucleotidylt 78.8 4.6 9.9E-05 43.5 6.3 49 351-399 28-78 (443)
136 PRK10308 3-methyl-adenine DNA 78.5 2.1 4.6E-05 44.0 3.7 64 254-321 167-233 (283)
137 COG0632 RuvA Holliday junction 78.4 1.2 2.6E-05 43.5 1.7 51 292-342 70-124 (201)
138 PRK14672 uvrC excinuclease ABC 78.1 4.3 9.4E-05 46.5 6.3 54 254-316 608-661 (691)
139 PRK03103 DNA polymerase IV; Re 78.1 1.6 3.5E-05 47.0 2.9 29 297-325 183-211 (409)
140 PRK02794 DNA polymerase IV; Pr 77.8 1.5 3.2E-05 47.5 2.5 29 297-325 211-239 (419)
141 cd00424 PolY Y-family of DNA p 77.7 1.7 3.7E-05 45.7 2.8 28 298-325 176-203 (343)
142 cd00008 53EXOc 5'-3' exonuclea 77.7 1.8 3.9E-05 43.4 2.8 27 298-325 186-212 (240)
143 PRK14133 DNA polymerase IV; Pr 77.4 1.6 3.5E-05 45.9 2.6 29 297-325 175-203 (347)
144 PRK07758 hypothetical protein; 77.4 1.1 2.4E-05 38.3 1.0 45 300-344 39-85 (95)
145 TIGR01083 nth endonuclease III 76.1 5.8 0.00013 38.2 5.8 25 292-316 103-127 (191)
146 PRK00076 recR recombination pr 76.0 2.1 4.6E-05 41.6 2.7 21 292-312 8-28 (196)
147 TIGR00615 recR recombination p 76.0 2.1 4.6E-05 41.5 2.7 20 292-311 8-27 (195)
148 PRK13844 recombination protein 74.8 2.4 5.2E-05 41.3 2.7 22 291-312 11-32 (200)
149 PRK01229 N-glycosylase/DNA lya 74.7 3.4 7.3E-05 40.6 3.8 53 262-317 85-142 (208)
150 PTZ00205 DNA polymerase kappa; 74.5 2.1 4.6E-05 48.0 2.5 29 297-325 311-339 (571)
151 PRK10702 endonuclease III; Pro 74.2 5.6 0.00012 39.1 5.2 25 292-316 106-130 (211)
152 PRK13300 tRNA CCA-pyrophosphor 74.0 11 0.00024 41.3 7.9 46 354-399 27-74 (447)
153 PRK00254 ski2-like helicase; P 74.0 15 0.00032 42.7 9.5 53 254-314 645-697 (720)
154 PF14229 DUF4332: Domain of un 74.0 3.3 7.1E-05 37.1 3.2 26 301-326 1-26 (122)
155 COG1948 MUS81 ERCC4-type nucle 73.8 4.2 9.2E-05 41.0 4.3 55 288-343 175-231 (254)
156 cd01702 PolY_Pol_eta DNA Polym 72.8 2.8 6.1E-05 44.6 2.9 29 297-325 184-213 (359)
157 PRK10702 endonuclease III; Pro 72.7 7.7 0.00017 38.2 5.7 43 232-274 85-129 (211)
158 cd05403 NT_KNTase_like Nucleot 72.6 7.8 0.00017 31.6 5.0 29 370-398 20-49 (93)
159 cd03468 PolY_like DNA Polymera 72.6 2.9 6.2E-05 43.5 2.9 28 299-326 174-201 (335)
160 TIGR01084 mutY A/G-specific ad 72.3 7.6 0.00016 39.8 5.8 66 231-303 80-147 (275)
161 COG0258 Exo 5'-3' exonuclease 71.3 3.1 6.6E-05 43.3 2.7 25 299-325 202-227 (310)
162 PRK13913 3-methyladenine DNA g 70.9 4.9 0.00011 39.8 3.9 22 292-313 118-139 (218)
163 KOG2875 8-oxoguanine DNA glyco 70.7 6 0.00013 40.3 4.5 67 255-322 175-245 (323)
164 PF03118 RNA_pol_A_CTD: Bacter 70.3 5.8 0.00013 31.6 3.5 38 238-275 22-65 (66)
165 PF11798 IMS_HHH: IMS family H 69.6 2.2 4.9E-05 29.0 0.9 18 255-272 12-29 (32)
166 KOG2093 Translesion DNA polyme 69.4 6.5 0.00014 45.8 4.9 89 13-110 42-132 (1016)
167 cd03586 PolY_Pol_IV_kappa DNA 69.4 3.4 7.3E-05 43.0 2.6 28 298-325 174-201 (334)
168 COG0389 DinP Nucleotidyltransf 68.0 3.6 7.9E-05 43.6 2.5 28 297-324 178-205 (354)
169 cd00056 ENDO3c endonuclease II 67.6 9.8 0.00021 35.0 5.0 67 230-303 54-125 (158)
170 COG0177 Nth Predicted EndoIII- 67.5 11 0.00025 37.0 5.6 86 261-354 80-175 (211)
171 KOG3524 Predicted guanine nucl 66.7 6.6 0.00014 44.6 4.2 79 14-100 114-192 (850)
172 PRK13766 Hef nuclease; Provisi 66.7 6.4 0.00014 46.0 4.4 17 297-313 749-765 (773)
173 PF04919 DUF655: Protein of un 66.4 20 0.00042 34.4 6.7 52 231-289 99-151 (181)
174 PF00416 Ribosomal_S13: Riboso 66.3 5.9 0.00013 34.7 3.0 26 293-318 13-39 (107)
175 PRK13910 DNA glycosylase MutY; 65.8 12 0.00026 38.7 5.7 68 232-306 48-117 (289)
176 KOG2245 Poly(A) polymerase and 65.8 13 0.00028 41.0 6.0 86 331-418 41-140 (562)
177 PF02371 Transposase_20: Trans 65.2 4.1 8.8E-05 34.1 1.8 20 295-314 2-21 (87)
178 COG2251 Predicted nuclease (Re 63.3 5.3 0.00011 43.3 2.6 27 299-325 229-255 (474)
179 PF14579 HHH_6: Helix-hairpin- 63.0 18 0.0004 30.3 5.4 49 256-315 29-77 (90)
180 TIGR03252 uncharacterized HhH- 62.6 22 0.00049 34.0 6.4 44 232-275 80-136 (177)
181 TIGR00615 recR recombination p 62.5 5.3 0.00011 38.8 2.2 31 254-284 11-41 (195)
182 PRK05007 PII uridylyl-transfer 62.0 25 0.00054 42.0 8.2 49 367-415 79-130 (884)
183 PRK12278 50S ribosomal protein 61.7 6 0.00013 39.2 2.5 29 296-324 159-187 (221)
184 PRK03980 flap endonuclease-1; 61.6 6.3 0.00014 40.8 2.8 25 299-324 193-217 (292)
185 PRK14973 DNA topoisomerase I; 61.6 9.9 0.00022 45.5 4.7 40 296-335 803-844 (936)
186 KOG2534 DNA polymerase IV (fam 61.2 5.4 0.00012 41.4 2.1 54 290-343 51-114 (353)
187 COG0177 Nth Predicted EndoIII- 60.7 21 0.00045 35.2 6.0 32 242-273 96-128 (211)
188 PRK14668 uvrC excinuclease ABC 60.7 9.7 0.00021 43.1 4.3 51 254-313 525-575 (577)
189 TIGR00593 pola DNA polymerase 60.6 6.1 0.00013 47.0 2.8 24 299-324 189-213 (887)
190 cd05401 NT_GlnE_GlnD_like Nucl 60.6 31 0.00067 32.2 7.1 50 368-417 55-110 (172)
191 PF14579 HHH_6: Helix-hairpin- 60.6 11 0.00024 31.7 3.6 30 297-326 29-62 (90)
192 PRK01759 glnD PII uridylyl-tra 60.1 29 0.00062 41.4 8.2 68 348-415 32-106 (854)
193 COG1669 Predicted nucleotidylt 60.0 28 0.00062 30.0 6.0 30 367-396 22-53 (97)
194 PRK02362 ski2-like helicase; P 59.8 58 0.0013 38.0 10.6 52 254-315 652-704 (737)
195 PRK14671 uvrC excinuclease ABC 59.8 7.2 0.00016 44.6 3.0 32 293-325 567-598 (621)
196 PRK14671 uvrC excinuclease ABC 59.4 12 0.00027 42.7 4.8 49 254-313 569-617 (621)
197 TIGR03491 RecB family nuclease 59.4 7.6 0.00016 42.7 3.1 28 299-326 211-238 (457)
198 PF14716 HHH_8: Helix-hairpin- 59.1 7.4 0.00016 31.0 2.2 22 292-313 43-65 (68)
199 PRK14670 uvrC excinuclease ABC 58.9 5.7 0.00012 44.9 2.0 29 296-325 515-543 (574)
200 PRK00076 recR recombination pr 58.9 6.3 0.00014 38.3 2.1 31 254-284 11-41 (196)
201 PRK14667 uvrC excinuclease ABC 58.5 5 0.00011 45.3 1.5 29 296-325 515-543 (567)
202 COG4277 Predicted DNA-binding 58.5 8.4 0.00018 39.8 2.9 40 294-333 329-372 (404)
203 PRK07758 hypothetical protein; 58.1 9.9 0.00021 32.6 2.8 23 254-276 67-89 (95)
204 PRK13844 recombination protein 57.7 6.6 0.00014 38.3 2.0 32 254-285 15-46 (200)
205 smart00611 SEC63 Domain of unk 57.6 20 0.00043 36.9 5.7 29 297-325 153-181 (312)
206 PTZ00217 flap endonuclease-1; 57.5 7.9 0.00017 41.7 2.8 26 298-324 238-263 (393)
207 PF03118 RNA_pol_A_CTD: Bacter 57.3 3 6.5E-05 33.3 -0.4 45 300-344 16-62 (66)
208 PF14490 HHH_4: Helix-hairpin- 57.3 11 0.00024 32.0 3.1 56 261-323 19-75 (94)
209 PRK12311 rpsB 30S ribosomal pr 57.0 7.7 0.00017 40.7 2.5 31 294-324 262-292 (326)
210 PRK03352 DNA polymerase IV; Va 56.9 32 0.00068 36.1 7.1 56 255-320 178-235 (346)
211 PRK10917 ATP-dependent DNA hel 56.8 8.8 0.00019 44.4 3.2 27 297-323 11-37 (681)
212 TIGR03674 fen_arch flap struct 55.4 9.3 0.0002 40.3 2.8 27 298-325 239-265 (338)
213 KOG4362 Transcriptional regula 54.4 13 0.00029 42.5 3.9 96 3-100 573-680 (684)
214 PRK04374 PII uridylyl-transfer 54.3 42 0.0009 40.1 8.2 62 354-415 55-122 (869)
215 PRK05755 DNA polymerase I; Pro 54.1 9.1 0.0002 45.6 2.8 25 298-324 190-215 (880)
216 PRK06063 DNA polymerase III su 53.9 35 0.00075 35.6 6.7 48 17-66 231-278 (313)
217 TIGR01083 nth endonuclease III 53.0 31 0.00067 33.2 5.8 42 232-273 82-125 (191)
218 CHL00137 rps13 ribosomal prote 52.8 9.3 0.0002 34.4 2.0 25 293-317 15-40 (122)
219 TIGR02236 recomb_radA DNA repa 52.4 14 0.00031 38.0 3.7 50 256-313 1-50 (310)
220 PRK14672 uvrC excinuclease ABC 51.9 6.7 0.00014 45.0 1.1 48 296-344 609-658 (691)
221 PRK05179 rpsM 30S ribosomal pr 51.7 9.6 0.00021 34.3 1.9 24 294-317 16-40 (122)
222 PRK14669 uvrC excinuclease ABC 51.6 6.1 0.00013 45.1 0.8 30 295-325 552-581 (624)
223 KOG3548 DNA damage checkpoint 50.6 21 0.00046 42.0 4.8 89 17-111 924-1038(1176)
224 smart00478 ENDO3c endonuclease 50.4 36 0.00077 31.0 5.6 43 232-274 48-92 (149)
225 PRK13482 DNA integrity scannin 49.6 9.2 0.0002 40.5 1.6 52 288-341 280-334 (352)
226 PRK14669 uvrC excinuclease ABC 49.4 30 0.00065 39.6 5.8 50 254-314 552-601 (624)
227 COG5067 DBF4 Protein kinase es 48.7 12 0.00026 39.8 2.2 49 13-63 117-165 (468)
228 cd00141 NT_POLXc Nucleotidyltr 48.4 7.5 0.00016 40.4 0.8 51 293-343 43-102 (307)
229 KOG1921 Endonuclease III [Repl 48.1 28 0.0006 35.1 4.6 30 245-274 149-179 (286)
230 TIGR01954 nusA_Cterm_rpt trans 48.0 16 0.00034 26.7 2.3 31 303-333 1-33 (50)
231 TIGR01084 mutY A/G-specific ad 48.0 25 0.00054 36.0 4.5 24 292-315 102-125 (275)
232 TIGR03631 bact_S13 30S ribosom 47.9 11 0.00025 33.3 1.7 24 294-317 14-38 (113)
233 KOG2093 Translesion DNA polyme 47.7 31 0.00068 40.4 5.5 53 256-318 551-605 (1016)
234 cd01703 PolY_Pol_iota DNA Poly 47.7 36 0.00078 36.5 5.9 58 255-318 173-243 (379)
235 COG5186 PAP1 Poly(A) polymeras 47.3 76 0.0017 33.9 7.8 51 369-419 82-133 (552)
236 COG1491 Predicted RNA-binding 46.9 19 0.00041 34.6 3.1 40 248-287 123-163 (202)
237 PRK01216 DNA polymerase IV; Va 46.9 63 0.0014 34.3 7.5 52 256-317 180-233 (351)
238 COG2231 Uncharacterized protei 46.6 29 0.00064 34.0 4.4 20 293-312 113-132 (215)
239 PF02889 Sec63: Sec63 Brl doma 46.0 24 0.00052 36.2 4.1 28 297-324 150-177 (314)
240 PRK00275 glnD PII uridylyl-tra 45.8 69 0.0015 38.4 8.3 48 368-415 78-128 (895)
241 TIGR00588 ogg 8-oxoguanine DNA 45.8 29 0.00064 36.1 4.7 73 227-305 181-265 (310)
242 COG0322 UvrC Nuclease subunit 45.7 35 0.00077 38.7 5.6 84 209-313 496-579 (581)
243 KOG1921 Endonuclease III [Repl 45.7 14 0.0003 37.1 2.1 31 283-314 148-178 (286)
244 COG1194 MutY A/G-specific DNA 44.9 42 0.00091 35.5 5.6 61 222-282 79-141 (342)
245 PRK13913 3-methyladenine DNA g 44.7 40 0.00087 33.4 5.2 57 252-316 119-178 (218)
246 PRK12373 NADH dehydrogenase su 44.6 17 0.00037 39.2 2.7 33 292-324 320-352 (400)
247 TIGR00596 rad1 DNA repair prot 44.5 29 0.00062 41.1 4.8 32 293-325 755-786 (814)
248 PRK06195 DNA polymerase III su 44.4 49 0.0011 34.3 6.1 48 17-65 219-266 (309)
249 PRK02794 DNA polymerase IV; Pr 43.9 1.3E+02 0.0028 32.6 9.5 52 256-318 211-264 (419)
250 COG0099 RpsM Ribosomal protein 43.8 18 0.00039 32.3 2.3 22 296-317 18-40 (121)
251 PRK13746 aminoglycoside resist 43.4 1.2E+02 0.0026 31.0 8.5 27 370-397 30-58 (262)
252 PRK00558 uvrC excinuclease ABC 43.4 16 0.00034 41.7 2.4 43 294-337 542-586 (598)
253 PRK04301 radA DNA repair and r 43.2 39 0.00085 35.0 5.2 52 255-314 7-58 (317)
254 PTZ00134 40S ribosomal protein 42.5 16 0.00035 34.2 2.0 25 293-317 28-53 (154)
255 PF06514 PsbU: Photosystem II 42.4 7 0.00015 33.3 -0.4 51 293-343 21-72 (93)
256 cd01701 PolY_Rev1 DNA polymera 42.4 54 0.0012 35.3 6.3 53 256-318 224-280 (404)
257 COG0272 Lig NAD-dependent DNA 41.7 12 0.00027 42.6 1.2 48 299-346 449-499 (667)
258 KOG1918 3-methyladenine DNA gl 41.6 15 0.00032 36.4 1.6 58 254-312 122-182 (254)
259 PRK04053 rps13p 30S ribosomal 41.1 19 0.00042 33.5 2.2 24 294-317 24-48 (149)
260 TIGR01693 UTase_glnD [Protein- 40.9 72 0.0016 38.0 7.5 49 368-416 43-94 (850)
261 PF02961 BAF: Barrier to autoi 40.8 21 0.00045 30.2 2.1 27 297-323 21-47 (89)
262 smart00483 POLXc DNA polymeras 40.3 13 0.00029 39.0 1.2 52 292-343 45-106 (334)
263 TIGR00596 rad1 DNA repair prot 40.2 47 0.001 39.3 5.7 15 211-225 644-658 (814)
264 COG1204 Superfamily II helicas 40.2 21 0.00045 41.9 2.8 110 232-344 609-727 (766)
265 TIGR01446 DnaD_dom DnaD and ph 40.1 24 0.00053 28.1 2.4 18 306-323 55-72 (73)
266 PF04919 DUF655: Protein of un 40.1 22 0.00048 34.1 2.4 59 266-324 86-149 (181)
267 PRK03059 PII uridylyl-transfer 40.0 77 0.0017 37.8 7.5 65 351-415 42-111 (856)
268 TIGR03629 arch_S13P archaeal r 39.6 20 0.00044 33.2 2.1 45 295-360 21-66 (144)
269 COG1491 Predicted RNA-binding 39.3 58 0.0012 31.4 5.0 56 269-324 103-163 (202)
270 PF09970 DUF2204: Nucleotidyl 39.2 66 0.0014 30.8 5.6 40 367-406 15-59 (181)
271 PRK14668 uvrC excinuclease ABC 39.1 20 0.00044 40.6 2.4 43 295-338 525-569 (577)
272 PRK13766 Hef nuclease; Provisi 38.8 21 0.00046 41.7 2.7 45 296-341 716-762 (773)
273 PRK10308 3-methyl-adenine DNA 38.2 49 0.0011 34.0 4.9 45 228-272 173-225 (283)
274 cd00128 XPG Xeroderma pigmento 38.1 19 0.00042 37.4 1.9 24 298-322 226-249 (316)
275 TIGR00194 uvrC excinuclease AB 37.7 25 0.00055 39.9 2.9 29 296-325 542-570 (574)
276 KOG3524 Predicted guanine nucl 37.0 23 0.00051 40.4 2.4 86 17-109 209-294 (850)
277 COG1725 Predicted transcriptio 36.5 92 0.002 28.2 5.7 88 262-362 12-103 (125)
278 PTZ00035 Rad51 protein; Provis 36.2 62 0.0013 34.1 5.4 50 293-343 22-73 (337)
279 COG1200 RecG RecG-like helicas 36.2 28 0.00062 39.8 3.0 27 297-323 12-38 (677)
280 COG0353 RecR Recombinational D 35.5 33 0.00073 33.3 2.9 22 254-275 12-33 (198)
281 COG2844 GlnD UTP:GlnB (protein 35.3 63 0.0014 37.9 5.5 48 368-415 66-116 (867)
282 PRK10880 adenine DNA glycosyla 34.7 28 0.0006 37.1 2.4 23 292-314 106-128 (350)
283 PRK13910 DNA glycosylase MutY; 34.3 27 0.00059 36.1 2.3 22 293-314 70-91 (289)
284 PF11774 Lsr2: Lsr2 ; InterPr 33.9 26 0.00057 30.9 1.8 28 470-497 73-100 (110)
285 PHA01806 hypothetical protein 33.8 69 0.0015 31.1 4.7 49 345-397 14-67 (200)
286 PRK03858 DNA polymerase IV; Va 33.8 70 0.0015 34.1 5.5 52 256-317 175-228 (396)
287 PHA00439 exonuclease 33.7 28 0.00062 35.9 2.3 27 298-325 191-219 (286)
288 PLN03187 meiotic recombination 33.5 70 0.0015 33.9 5.2 43 292-335 29-73 (344)
289 cd01702 PolY_Pol_eta DNA Polym 32.8 1E+02 0.0023 32.7 6.5 54 256-318 184-241 (359)
290 TIGR03135 malonate_mdcG holo-A 32.5 78 0.0017 31.0 5.0 32 367-398 107-145 (202)
291 COG1031 Uncharacterized Fe-S o 32.3 38 0.00083 37.1 3.0 31 294-324 515-546 (560)
292 PRK03381 PII uridylyl-transfer 32.3 1.2E+02 0.0025 35.9 7.3 46 369-414 58-106 (774)
293 PRK01229 N-glycosylase/DNA lya 31.6 49 0.0011 32.6 3.4 20 252-271 116-136 (208)
294 cd00424 PolY Y-family of DNA p 30.9 1.2E+02 0.0026 31.7 6.5 53 256-318 175-229 (343)
295 PF04994 TfoX_C: TfoX C-termin 29.8 40 0.00086 28.0 2.1 36 254-293 3-38 (81)
296 COG5275 BRCT domain type II [G 28.5 1.2E+02 0.0027 30.0 5.5 50 17-67 155-204 (276)
297 cd05398 NT_ClassII-CCAase Nucl 28.5 1.2E+02 0.0025 27.7 5.2 38 354-394 4-45 (139)
298 PRK03348 DNA polymerase IV; Pr 27.6 1.2E+02 0.0025 33.5 5.9 53 256-318 182-236 (454)
299 PF02371 Transposase_20: Trans 26.6 54 0.0012 27.2 2.4 42 255-307 3-44 (87)
300 TIGR02238 recomb_DMC1 meiotic 25.5 45 0.00098 34.8 2.1 43 300-342 6-50 (313)
301 PRK14133 DNA polymerase IV; Pr 25.1 1.7E+02 0.0037 30.6 6.5 52 256-318 175-228 (347)
302 PLN03187 meiotic recombination 25.1 2E+02 0.0044 30.4 7.0 103 254-383 32-141 (344)
303 TIGR00600 rad2 DNA excision re 23.4 62 0.0013 39.2 2.9 26 298-323 869-895 (1034)
304 KOG2841 Structure-specific end 22.7 1.3E+02 0.0028 30.2 4.5 47 292-339 192-240 (254)
305 TIGR02922 conserved hypothetic 22.4 34 0.00073 27.0 0.3 15 370-384 34-48 (67)
306 TIGR00207 fliG flagellar motor 22.3 4.3E+02 0.0092 27.9 8.7 87 236-323 144-245 (338)
307 cd07749 NT_Pol-beta-like_1 Nuc 21.8 3.6E+02 0.0078 25.4 7.1 37 367-403 16-56 (156)
308 PF05559 DUF763: Protein of un 21.5 77 0.0017 33.1 2.8 20 293-312 267-286 (319)
309 KOG2875 8-oxoguanine DNA glyco 21.4 1.2E+02 0.0026 31.3 4.0 18 254-271 218-235 (323)
310 PRK07945 hypothetical protein; 21.3 50 0.0011 34.8 1.5 28 297-324 51-82 (335)
311 PF12482 DUF3701: Phage integr 21.1 86 0.0019 27.0 2.6 21 304-324 22-42 (96)
312 PRK00024 hypothetical protein; 20.7 1.2E+02 0.0026 30.1 4.0 44 235-278 43-90 (224)
313 PF00416 Ribosomal_S13: Riboso 20.5 95 0.0021 27.0 2.9 44 254-297 15-58 (107)
314 COG2176 PolC DNA polymerase II 20.1 2.3E+02 0.005 35.0 6.6 90 234-330 1294-1420(1444)
315 PRK14109 bifunctional glutamin 20.0 2.5E+02 0.0055 34.2 7.2 45 369-413 216-266 (1007)
No 1
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=100.00 E-value=4.1e-88 Score=666.49 Aligned_cols=322 Identities=36% Similarity=0.640 Sum_probs=295.4
Q ss_pred CCCcHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHH
Q 009281 207 PDLNKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFE 286 (538)
Q Consensus 207 ~~~N~~ia~~L~~la~~~e~~g~~~r~~aY~rAa~~l~~l~~~i~~~~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~ 286 (538)
.|+|..++++|+.||+.|++.|+.+|+++|++||++|+++|++|+|++|+++|||||++||.+|+|||+||.+++||+++
T Consensus 9 t~~N~~~~~aleiLa~~~ev~g~~~r~~~y~~Aasvlk~~p~~I~S~~ea~~lP~iG~kia~ki~EiletG~l~ele~v~ 88 (353)
T KOG2534|consen 9 TNNNQIFTEALEILAEAYEVEGEEDRARAYRRAASVLKSLPFPITSGEEAEKLPGIGPKIAEKIQEILETGVLRELEAVR 88 (353)
T ss_pred ccccHHHHHHHHHHHHhhcccccHHHHHHHHHHHHHHHhCCCCcccHHHhcCCCCCCHHHHHHHHHHHHcCCchhHHHHh
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhchhHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhh-ccCcchhhhccccchhhhccCcCHHHHHHHHHHHHHHhhhc
Q 009281 287 KDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN-EDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEV 365 (538)
Q Consensus 287 ~~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~-~~~L~~~q~~Glk~~ed~~~~i~r~ea~~i~~iv~~~~~~~ 365 (538)
+|+.+++|++|++|||||++||++||++|+|||+|+++ ..++|++|++||+||+||+.+|+|+||.+|.++|++++..+
T Consensus 89 ~de~~~~lklFtnifGvG~ktA~~Wy~~GfrTled~Rk~~~kft~qqk~Gl~yy~Df~~~v~ReE~~~i~~~V~~av~~~ 168 (353)
T KOG2534|consen 89 NDERSQSLKLFTNIFGVGLKTAEKWYREGFRTLEDVRKKPDKFTRQQKAGLKYYEDFLKRVTREEATAIQQTVQEAVWAF 168 (353)
T ss_pred cchhHHHHHHHHHHhccCHHHHHHHHHhhhhHHHHHHhCHHHHHHHHHHhHHHHHHHhhhccHHHHHHHHHHHHHHHhhc
Confidence 99999999999999999999999999999999999994 45899999999999999999999999999999999999999
Q ss_pred CCCeEEEecccccccCCcCCCeeEEEecCCcch-hhhhHHHHHHHHHHcCccceeeeeccccCCCC----CC---cceee
Q 009281 366 LPEVIILCGGSYRRGKASCGDLDVVIMHPDRKS-HKGFLSKYVKKLKEMKFLREDLIFSTHSEEGT----DS---GVDTY 437 (538)
Q Consensus 366 ~p~~~v~~~Gs~RRgke~~~DvDiLIt~~~~~~-~~~~l~~~v~~L~~~g~l~~~l~~s~~~~~~~----~~---~~~~~ 437 (538)
+|++.|++||||||||++|||||||||||...+ +.+++..|+..|.+.|++.......+..+... .+ -..++
T Consensus 169 ~p~~~vt~~GsfRRGk~~ggDvD~LithP~~~s~~~~~~~~l~~~le~~g~il~~~~~~S~~Ek~~l~~~~s~~~~~~~~ 248 (353)
T KOG2534|consen 169 DPEAFVTVTGSFRRGKKMGGDVDFLITHPGSTSTEAKLLQLLMILLEKKGLLLYYDQLHSCGEKLRLPSRKSALDHFKKF 248 (353)
T ss_pred CCCcEEEEeccccCCcccCCCeeEEEeCCCCCchhhhHHHHHHHHHHhcCeEEEEeeeccccccccccchhhhHhhhhhE
Confidence 999999999999999999999999999999887 77899999999999999983322111110000 01 12468
Q ss_pred eeeeecC-------------CCcc-ceeeeEEEecCchhHHHHHHhhccHHHHHHHHHHHHHcCCccCCCCCcccCCCCC
Q 009281 438 FGLCTYP-------------GREL-RHRIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATHGSG 503 (538)
Q Consensus 438 ~g~~~~~-------------~~~~-~~rVDl~~~p~~~~~~aLl~~TGS~~fnr~lR~~A~~kg~~L~~~gL~~~~~~~~ 503 (538)
||+|++| +++| +|||||+|||+++|||||||||||+.|||+||++|.+|||+||+||||+.+.
T Consensus 249 mgv~~LPr~~~~~~~~S~n~~~~~~~rRvDivv~P~~~~~~alLgwTGS~~FnR~lR~~A~~kG~~l~~h~L~~~~~--- 325 (353)
T KOG2534|consen 249 MGVFRLPRQRVDSDQSSWNEGKGWKARRVDIVVCPYDEFGFALLGWTGSKEFNRDLRRYATHKGFSLDEHALFDLTV--- 325 (353)
T ss_pred EEEEEcCcccccccccccCCCCCCceeeeEEEEechHHcceeeeeecchHHHHHHHHHHHHhcCceecccccccCCc---
Confidence 9999999 5544 5899999999999999999999999999999999999999999999998653
Q ss_pred CcccccccCCCCCCCHHHHHhhcCCCCCCCCCcCC
Q 009281 504 GKQGVRARTSLKFDTEKEVFDFLGFPWLEPHERNL 538 (538)
Q Consensus 504 g~~~~~~~~~~~~~tEedIF~~LGL~yipPe~Rn~ 538 (538)
..++++.+|+|||++|||+||||++||.
T Consensus 326 -------~~~l~~~sEkdIFr~l~L~Y~EP~~Rn~ 353 (353)
T KOG2534|consen 326 -------RIFLPVESEKDIFRYLGLKYIEPKERNA 353 (353)
T ss_pred -------ceecCCccHHHHHHHhCCccCChhhcCC
Confidence 3689999999999999999999999995
No 2
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=100.00 E-value=9.6e-74 Score=587.73 Aligned_cols=303 Identities=40% Similarity=0.677 Sum_probs=278.2
Q ss_pred HHHHHHHHHHHHHHHcCC-ChhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhch
Q 009281 212 NITEIFGKLINIYRALGE-DRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEK 290 (538)
Q Consensus 212 ~ia~~L~~la~~~e~~g~-~~r~~aY~rAa~~l~~l~~~i~~~~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~ 290 (538)
+|+++|++||++++++|+ .||++||++||++|+++|++|+++.++.+|||||++|+++|.||++||+++++|+++++ .
T Consensus 2 ~ia~~L~~ia~~~e~~~~~~~r~~aY~~Aa~~l~~l~~~i~~~~~~~~ipgiG~~ia~kI~E~~~tG~~~~le~l~~~-~ 80 (307)
T cd00141 2 EIADILEELADLLELLGGNPFRVRAYRKAARALESLPEPIESLEEAKKLPGIGKKIAEKIEEILETGKLRKLEELRED-V 80 (307)
T ss_pred hHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHhCCcccCCHHHhcCCCCccHHHHHHHHHHHHcCCHHHHHHHhcc-c
Confidence 699999999999999965 48999999999999999999999999999999999999999999999999999999998 4
Q ss_pred hHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhc--cCcchhhhccccchhhhccCcCHHHHHHHHHHHHHHhhhcCCC
Q 009281 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPE 368 (538)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~--~~L~~~q~~Glk~~ed~~~~i~r~ea~~i~~iv~~~~~~~~p~ 368 (538)
+..+..|++|||||||||++||+.||+||+||+.+ .+++..|..|++||+|+.++|||+||+++.+.|.+.++.+.|+
T Consensus 81 ~~~l~~l~~i~GiGpk~a~~l~~lGi~sl~dL~~a~g~k~~~~i~~gl~~~~~~~~ri~r~ea~~~a~~i~~~l~~~~~~ 160 (307)
T cd00141 81 PPGLLLLLRVPGVGPKTARKLYELGIRTLEDLRKAAGAKLEQNILIGLEYYEDFQQRIPREEALAIAEIIKEALREVDPV 160 (307)
T ss_pred hHHHHHHHcCCCCCHHHHHHHHHcCCCCHHHHHHHhccccHHHHHHHHHHHHHhcCCeEHHHHHHHHHHHHHHHHhCCCc
Confidence 55666666999999999999997799999999987 4899999999999999999999999999999888888877888
Q ss_pred eEEEecccccccCCcCCCeeEEEecCCcchhhhhHHHHHHHHHHcCccceeeeeccccCCCCCCcceeeeeeeecCCCcc
Q 009281 369 VIILCGGSYRRGKASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCTYPGREL 448 (538)
Q Consensus 369 ~~v~~~Gs~RRgke~~~DvDiLIt~~~~~~~~~~l~~~v~~L~~~g~l~~~l~~s~~~~~~~~~~~~~~~g~~~~~~~~~ 448 (538)
++|++|||||||+++||||||||+|++... .+++.+|++.|.+.|++.+.+. .+..+|+|+|++|+...
T Consensus 161 ~~v~i~GS~RRg~et~gDiDilv~~~~~~~-~~~~~~v~~~l~~~~~~~~~~~----------~g~~k~~~~~~~~~~~~ 229 (307)
T cd00141 161 LQVEIAGSYRRGKETVGDIDILVTHPDATS-RGLLEKVVDALVELGFVTEVLS----------KGDTKASGILKLPGGWK 229 (307)
T ss_pred eEEEEcccccCCCCccCCEEEEEecCCccc-cccHHHHHHHHHhCCCeehhhh----------CCCceEEEEEecCCCCC
Confidence 899999999999999999999999998764 6778889999999999976432 23458999999987667
Q ss_pred ceeeeEEEecCchhHHHHHHhhccHHHHHHHHHHHHHcCCccCCCCCcccCCCCCCcccccccCCCCCCCHHHHHhhcCC
Q 009281 449 RHRIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATHGSGGKQGVRARTSLKFDTEKEVFDFLGF 528 (538)
Q Consensus 449 ~~rVDl~~~p~~~~~~aLl~~TGS~~fnr~lR~~A~~kg~~L~~~gL~~~~~~~~g~~~~~~~~~~~~~tEedIF~~LGL 528 (538)
++||||++||+++||+||+|||||++|||.||.+|.++||+||+||||+.. .+..+++.+|+|||++|||
T Consensus 230 ~~rVDl~~~p~~~~~~all~fTGs~~~nr~lR~~A~~~G~~L~~~GL~~~~----------~~~~~~~~~E~~If~~Lgl 299 (307)
T cd00141 230 GRRVDLRVVPPEEFGAALLYFTGSKQFNRALRRLAKEKGLKLNEYGLFDGV----------DGERLPGETEEEIFEALGL 299 (307)
T ss_pred ceEEEEEEeCHHHHHHHHHHhhCCHHHHHHHHHHHHHcCCeeeccccccCC----------CCCCccCCCHHHHHHHcCC
Confidence 799999999999999999999999999999999999999999999999843 1357999999999999999
Q ss_pred CCCCCCCc
Q 009281 529 PWLEPHER 536 (538)
Q Consensus 529 ~yipPe~R 536 (538)
||||||+|
T Consensus 300 ~yipPe~R 307 (307)
T cd00141 300 PYIEPELR 307 (307)
T ss_pred CCCCCCCC
Confidence 99999998
No 3
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=100.00 E-value=5.7e-73 Score=587.97 Aligned_cols=309 Identities=37% Similarity=0.614 Sum_probs=264.9
Q ss_pred CCcHHHHHHHHHHHHHHHHcCCC-hhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHH
Q 009281 208 DLNKNITEIFGKLINIYRALGED-RRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFE 286 (538)
Q Consensus 208 ~~N~~ia~~L~~la~~~e~~g~~-~r~~aY~rAa~~l~~l~~~i~~~~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~ 286 (538)
|+|++|+++|++||++||++|+| +|++||++||++|+++|++|++++++.+|||||++|++||.||++||++.++.+..
T Consensus 1 ~~N~~I~~~L~~la~l~el~gen~~k~~ay~~Aa~~i~~l~~~i~~~~~l~~lpgIG~~ia~kI~Eil~tG~~~~~~e~l 80 (334)
T smart00483 1 NLNRGIIDALEILAENYEVFGENKRKCSYFRKAASVLKSLPFPINSMKDLKGLPGIGDKIKKKIEEIIETGKSSKVLEIL 80 (334)
T ss_pred CCcHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhCCCCCCCHHHHhcCCCccHHHHHHHHHHHHhCcHHHHHHHh
Confidence 46999999999999999999999 58999999999999999999999999999999999999999999999999665555
Q ss_pred hhchhHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhcc--CcchhhhccccchhhhccCcCHHHHHHHHHHHHHHhhh
Q 009281 287 KDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEE 364 (538)
Q Consensus 287 ~~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~~--~L~~~q~~Glk~~ed~~~~i~r~ea~~i~~iv~~~~~~ 364 (538)
.++.+..+..|++|||||||||++||+.||+||+||+++. +|+..|.+|++||+|+.++|||+||+.+.++|....+.
T Consensus 81 ~~~~p~~l~~l~~i~GiGpk~a~~l~~lGi~tl~eL~~a~~~~l~~~q~~gl~~~~~~~~ri~r~e~~~i~~~i~~~l~~ 160 (334)
T smart00483 81 NDEVYKSLKLFTNVFGVGPKTAAKWYRKGIRTLEELKKNKELKLTKQQKAGLKYYEDILKKVSRAEAFAVEYIVKRAVRK 160 (334)
T ss_pred cCcHHHHHHHHHccCCcCHHHHHHHHHhCCCCHHHHHhcccccCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHh
Confidence 5555667777779999999999999999999999999754 69999999999999999999999999999999888888
Q ss_pred cCCCeEEEecccccccCCcCCCeeEEEecCCcchhhhhHHHHHHHHH---------HcCccceeeeeccccCCCCCCcce
Q 009281 365 VLPEVIILCGGSYRRGKASCGDLDVVIMHPDRKSHKGFLSKYVKKLK---------EMKFLREDLIFSTHSEEGTDSGVD 435 (538)
Q Consensus 365 ~~p~~~v~~~Gs~RRgke~~~DvDiLIt~~~~~~~~~~l~~~v~~L~---------~~g~l~~~l~~s~~~~~~~~~~~~ 435 (538)
+.|.+.|++||||||||++||||||||+|+++.. +++.++++.|. .-+++.+. ...+-.
T Consensus 161 ~~~~~~v~i~GSyRRgket~gDIDili~~~~~~~--~~~~~v~~~~~l~~~~~~~~~~~~~~~~----------~~~g~~ 228 (334)
T smart00483 161 ILPDAIVTLTGSFRRGKETGHDVDFLITSPHPAK--EKELEVLDLLLLESTFEELQLPSIRVAT----------LDHGQK 228 (334)
T ss_pred hCCCcEEEEecccccCCCcCCCeeEEEecCCccc--hhHHHHHHHHHHHHHHHHHhcccchhhh----------hhcCCC
Confidence 8888899999999999999999999999999773 44444543331 11111111 122334
Q ss_pred eeeeeeecCCC-------------ccceeeeEEEecCchhHHHHHHhhccHHHHHHHHHHHHHcCCccCCCCCcccCCCC
Q 009281 436 TYFGLCTYPGR-------------ELRHRIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATHGS 502 (538)
Q Consensus 436 ~~~g~~~~~~~-------------~~~~rVDl~~~p~~~~~~aLl~~TGS~~fnr~lR~~A~~kg~~L~~~gL~~~~~~~ 502 (538)
+|+++|..|.. +.++||||++||+++||+||+|||||++|||.||.+|.++| +||+||||+....
T Consensus 229 ~~~~v~~~~~~~~~~~~g~~~~~~~~~rrVDl~~~~~~~~g~aLl~fTGS~~fnr~lR~~A~~~g-~L~~~gl~~~~~~- 306 (334)
T smart00483 229 KFMILKLSPSREDKEKSGKPDEKGWKARRVDIVLCPEDQYPTALLGWTGSKQFNRDLRRYATSKF-KLMLDGHELYDKT- 306 (334)
T ss_pred EEEEEEeCCccccccccccccCCCCcceEEEEEEechHHheeEEEEEeCchhHHHHHHHHHHHcC-CcCcccCccccCC-
Confidence 67888766421 23589999999999999999999999999999999999999 9999999975321
Q ss_pred CCcccccccCCCCCCCHHHHHhhcCCCCCCCCCcC
Q 009281 503 GGKQGVRARTSLKFDTEKEVFDFLGFPWLEPHERN 537 (538)
Q Consensus 503 ~g~~~~~~~~~~~~~tEedIF~~LGL~yipPe~Rn 537 (538)
.+..+++.+|+|||++|||||||||+||
T Consensus 307 -------~~~~i~~~~E~~If~~LGl~yipPe~Rn 334 (334)
T smart00483 307 -------KEKFLKVESEEDIFDHLGLPYIEPEERN 334 (334)
T ss_pred -------CCeeccCCCHHHHHHHhCCCCCCcccCC
Confidence 1357889999999999999999999998
No 4
>PRK08609 hypothetical protein; Provisional
Probab=100.00 E-value=6.6e-68 Score=584.49 Aligned_cols=299 Identities=22% Similarity=0.346 Sum_probs=261.0
Q ss_pred CCcHHHHHHHHHHHHHHHHcCCC-hhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHH
Q 009281 208 DLNKNITEIFGKLINIYRALGED-RRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFE 286 (538)
Q Consensus 208 ~~N~~ia~~L~~la~~~e~~g~~-~r~~aY~rAa~~l~~l~~~i~~~~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~ 286 (538)
|+|++|+++|++||++++++|+| ||++||++||++|+++|++|++++++.+|||||++||+||+||++||++++||+|+
T Consensus 1 m~n~~ia~~l~~~A~~le~~g~n~fr~~aYr~Aa~~i~~l~~~i~~~~~l~~ipgIG~~ia~kI~Eil~tG~~~~le~l~ 80 (570)
T PRK08609 1 MNKKDVIKLLETIATYMELKGENPFKISAFRKAAQALELDERSLSEIDDFTKLKGIGKGTAEVIQEYRETGESSVLQELK 80 (570)
T ss_pred CChHHHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHhCchhhhhhhhhccCCCcCHHHHHHHHHHHHhCChHHHHHHH
Confidence 56999999999999999999988 79999999999999999999999999999999999999999999999999999999
Q ss_pred hhchhHHHHHHhhccCCCHHHHHHHHHh-CCCCHHHHhhc---cCcchhhhc----------cccchhhhccCcCHHHHH
Q 009281 287 KDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNE---DSLTHSQRL----------GLKYFDDIKTRIPRHEVE 352 (538)
Q Consensus 287 ~~~~~~~l~lf~~I~GvGpktA~~l~~~-GirtledL~~~---~~L~~~q~~----------Glk~~ed~~~~i~r~ea~ 352 (538)
++.|..+++|+ +|||||||||++||++ ||+||+||+++ ++++.+++| |+++|+++.+|||++||.
T Consensus 81 ~~~p~~~~~l~-~i~GiGpk~a~~l~~~lGi~tl~~L~~a~~~~~~~~~~gfg~k~~~~il~~i~~~~~~~~R~~~~~a~ 159 (570)
T PRK08609 81 KEVPEGLLPLL-KLPGLGGKKIAKLYKELGVVDKESLKEACENGKVQALAGFGKKTEEKILEAVKELGKRPERLPIAQVL 159 (570)
T ss_pred hhCcHHHHHHh-cCCCCCHHHHHHHHHHhCCCCHHHHHHHHHhCChhhccCcchhHHHHHHHHHHHHhcccccEEHHHHH
Confidence 98877777666 9999999999999975 99999999964 578877777 566777788999999999
Q ss_pred HHHHHHHHHhhhcCCCeEEEecccccccCCcCCCeeEEEecCCcchhhhhHHHHHHHHHHcCccceeeeeccccCCCCCC
Q 009281 353 QMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLREDLIFSTHSEEGTDS 432 (538)
Q Consensus 353 ~i~~iv~~~~~~~~p~~~v~~~Gs~RRgke~~~DvDiLIt~~~~~~~~~~l~~~v~~L~~~g~l~~~l~~s~~~~~~~~~ 432 (538)
.+.+.|.+..+.+.|...|++||||||||+||||||||||++++.. +++.|.+.+++.+.+..
T Consensus 160 ~~a~~i~~~l~~~~~~~~v~~~GS~RR~~et~gDiDili~~~~~~~-------~~~~l~~~~~v~~~~~~---------- 222 (570)
T PRK08609 160 PIAQEIEEYLATIDEIIRFSRAGSLRRARETVKDLDFIIATDEPEA-------VREQLLQLPNIVEVIAA---------- 222 (570)
T ss_pred HHHHHHHHHHHhCCCccEEEeccchhccccccCCeeEEEecCCHHH-------HHHHHHcCccHHHHHhc----------
Confidence 9988888777766666699999999999999999999999998754 34556666666544321
Q ss_pred cceeeeeeeecCCCccceeeeEEEecCchhHHHHHHhhccHHHHHHHHHHHHHcCCccCCCCCcccCCCCCCcccccccC
Q 009281 433 GVDTYFGLCTYPGRELRHRIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATHGSGGKQGVRART 512 (538)
Q Consensus 433 ~~~~~~g~~~~~~~~~~~rVDl~~~p~~~~~~aLl~~TGS~~fnr~lR~~A~~kg~~L~~~gL~~~~~~~~g~~~~~~~~ 512 (538)
+..++++.|.++ .++||||++||+++||+||+|||||++||+.||.+|.++||+||+||||+.. .+.
T Consensus 223 g~~~~~~~~~~~---~~~~vDl~~v~~~~~~~aL~yfTGS~~hn~~lr~~A~~~g~~l~e~gl~~~~----------~~~ 289 (570)
T PRK08609 223 GDTKVSVELEYE---YTISVDFRLVEPEAFATTLHHFTGSKDHNVRMRQLAKERGEKISEYGVEQAD----------TGE 289 (570)
T ss_pred CCceEEEEEecC---CCeEEEEEEeCHHHHHHHHHHHhccHHHHHHHHHHHHHcCCcccccccccCC----------CCc
Confidence 223555555431 2479999999999999999999999999999999999999999999999742 135
Q ss_pred CCCCCCHHHHHhhcCCCCCCCCCcC
Q 009281 513 SLKFDTEKEVFDFLGFPWLEPHERN 537 (538)
Q Consensus 513 ~~~~~tEedIF~~LGL~yipPe~Rn 537 (538)
.+++.||++||++|||||||||+||
T Consensus 290 ~~~~~~E~~iy~~Lgl~yipPelRe 314 (570)
T PRK08609 290 VKTFESEEAFFAHFGLPFIPPEVRE 314 (570)
T ss_pred cCCCCCHHHHHHHcCCCCCCccccC
Confidence 6889999999999999999999997
No 5
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=100.00 E-value=5.8e-57 Score=449.89 Aligned_cols=298 Identities=28% Similarity=0.477 Sum_probs=250.7
Q ss_pred CCcHHHHHHHHHHHHHHHHcCCC-hhHHHHHHHHHHHhcCCccccchhhh---cCCCCCCHHHHHHHHHHHHhCCcchhH
Q 009281 208 DLNKNITEIFGKLINIYRALGED-RRSFSYYKAIPVIEKLPFKIESADQV---KGLPGIGKSMQDHIQEIVTTGKLSKLE 283 (538)
Q Consensus 208 ~~N~~ia~~L~~la~~~e~~g~~-~r~~aY~rAa~~l~~l~~~i~~~~~l---~~lpgiG~~ia~~I~Eil~tG~~~~le 283 (538)
|.|+.|+.+|+++|++|++.|+| ||++|||+||.+|+.+.+++.++.+. ..|||||++||++|.||++||+++.++
T Consensus 3 ~~n~~ia~~le~iA~~me~~Gen~fk~~aYr~Aa~sle~~~e~~~ei~e~~~~t~l~gIGk~ia~~I~e~l~tG~~~~le 82 (326)
T COG1796 3 MNNHDIARLLERIADYMELEGENPFKIRAYRKAAQSLENLTEDLEEIEERGRLTELPGIGKGIAEKISEYLDTGEVKKLE 82 (326)
T ss_pred cchHHHHHHHHHHHHHHHhcCCCccchHHHHHHHHhhhhcccchHHHHhhcccCCCCCccHHHHHHHHHHHHcCccHHHH
Confidence 67999999999999999999999 89999999999999999999998664 599999999999999999999999999
Q ss_pred HHHhhchhHHHHHHhhccCCCHHHHHHHHHh-CCCCHHHHhhc---cCcchhhhccccchhhhc----------cCcCHH
Q 009281 284 HFEKDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNE---DSLTHSQRLGLKYFDDIK----------TRIPRH 349 (538)
Q Consensus 284 ~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~-GirtledL~~~---~~L~~~q~~Glk~~ed~~----------~~i~r~ 349 (538)
.++...|.+.+.|+ .|+|+|||+...||++ ||.++++|+++ +++..+.|||-++..+|. +|+|..
T Consensus 83 ~lk~~~P~gl~~Ll-~v~GlGpkKi~~Ly~elgi~~~e~l~~a~~~~~~~~l~GfG~kse~~il~~i~~~~~~~~R~~l~ 161 (326)
T COG1796 83 ALKKEVPEGLEPLL-KVPGLGPKKIVSLYKELGIKDLEELQEALENGKIRGLRGFGKKSEAKILENIEFAEESPERIPLS 161 (326)
T ss_pred HHHHhCCcchHHHh-hCCCCCcHHHHHHHHHHCcccHHHHHHHHHhCCccccCCccchhHHHHHHHHHHHhhhhhhcchH
Confidence 99999999988888 9999999999999998 99999999965 468899999988888876 566777
Q ss_pred HHHHHHHHHHHHhhhcCCCeEEEecccccccCCcCCCeeEEEecCCcchhhhhHHHHHHHHHHcCccceeeeeccccCCC
Q 009281 350 EVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLREDLIFSTHSEEG 429 (538)
Q Consensus 350 ea~~i~~iv~~~~~~~~p~~~v~~~Gs~RRgke~~~DvDiLIt~~~~~~~~~~l~~~v~~L~~~g~l~~~l~~s~~~~~~ 429 (538)
++-.+..-+.....++.+-.++.++||+||+++|++|||++|+..++.+ +++.|.+...+++....
T Consensus 162 ~~l~ia~ei~~yl~~~~~~~~~~~aGs~RR~retv~DiD~~~s~~~~~~-------v~~~~~~~~~~~~vi~~------- 227 (326)
T COG1796 162 FTLPIAQEIEGYLEELTPIIQASIAGSLRRGRETVGDIDILISTSHPES-------VLEELLEMPNVQEVIAK------- 227 (326)
T ss_pred HHHHHHHHHHHHHHhccchheeeeccchhhccccccceeeEeccCCcHH-------HHHHHhcCCCcceeeec-------
Confidence 7766644444443445554588999999999999999999998887765 45666665555444321
Q ss_pred CCCcceeeeeeeecCCCccceeeeEEEecCchhHHHHHHhhccHHHHHHHHHHHHHcCCccCCCCCcccCCCCCCccccc
Q 009281 430 TDSGVDTYFGLCTYPGRELRHRIDFKVYPRDIYAFGLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATHGSGGKQGVR 509 (538)
Q Consensus 430 ~~~~~~~~~g~~~~~~~~~~~rVDl~~~p~~~~~~aLl~~TGS~~fnr~lR~~A~~kg~~L~~~gL~~~~~~~~g~~~~~ 509 (538)
.+.++.....+ ..| ..|||+|||++.||+||+|||||++||+.||.+|+.+||+||+||||..
T Consensus 228 G~~k~s~~~~~--~~~----~svD~r~v~~e~fGaal~~fTGSkehNi~iR~lA~~kg~klseyGl~~~----------- 290 (326)
T COG1796 228 GETKVSMLLIL--DEG----TSVDFRVVPPEAFGAALQHFTGSKEHNIKIRQLAKAKGEKLSEYGLFRD----------- 290 (326)
T ss_pred CCceeeEEEEe--cCC----CeeEEEEcCHHHhhhhhhhcccchhhhHHHHHHHHHhCcchhhcceecc-----------
Confidence 11111110111 122 4699999999999999999999999999999999999999999999973
Q ss_pred ccCCCCCCCHHHHHhhcCCCCCCCCCcC
Q 009281 510 ARTSLKFDTEKEVFDFLGFPWLEPHERN 537 (538)
Q Consensus 510 ~~~~~~~~tEedIF~~LGL~yipPe~Rn 537 (538)
++..++..||++||++|||+|||||+|+
T Consensus 291 ~~e~i~~~tE~~i~~~l~l~yipPE~RE 318 (326)
T COG1796 291 SGEIIAGKTEEKIYEHLGLPYIPPELRE 318 (326)
T ss_pred CCceecCCcHhHHHHHcCCCCCChhhcc
Confidence 1357899999999999999999999997
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=1.1e-25 Score=198.52 Aligned_cols=105 Identities=44% Similarity=0.795 Sum_probs=91.6
Q ss_pred CcCHHHHHHHHHHHHHHhhhcCCCeEEEecccccccCCcCCCeeEEEecCCcchh----hhhHHHHHHHHHHcCccceee
Q 009281 345 RIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPDRKSH----KGFLSKYVKKLKEMKFLREDL 420 (538)
Q Consensus 345 ~i~r~ea~~i~~iv~~~~~~~~p~~~v~~~Gs~RRgke~~~DvDiLIt~~~~~~~----~~~l~~~v~~L~~~g~l~~~l 420 (538)
||||+|++++.++|++++..+.|++.+++||||||||++|||||||||||+.... .++|.++++.|+++|+|+++|
T Consensus 1 rIPR~Ev~~i~~~V~~~~~~i~p~~~v~i~GSyRRGK~~~gDiDiLIt~~~~~~~~~~~~~~l~~lv~~L~~~g~i~~~L 80 (112)
T PF14792_consen 1 RIPRDEVEEIEEIVKEALEKIDPGLEVEICGSYRRGKETSGDIDILITHPDPSSVSKKLEGLLEKLVKRLEEKGFITDDL 80 (112)
T ss_dssp -EEHHHHHHHHHHHHHHHHCCSTT-EEEEEHHHHTT-SEESSEEEEEEETTCSTTTCSTTCHHHHHHHHHHHTTSEEEEE
T ss_pred CCCHHHHHHHHHHHHHHHHhcCCCcEEEEccccccCCCcCCCeEEEEeCCCcCcchhhHHHHHHHHHHHHHhCCeEEEec
Confidence 6999999999999999999999999999999999999999999999999998774 789999999999999999998
Q ss_pred eeccccCCCCCCcceeeeeeeecCCC---ccceeeeEEEecC
Q 009281 421 IFSTHSEEGTDSGVDTYFGLCTYPGR---ELRHRIDFKVYPR 459 (538)
Q Consensus 421 ~~s~~~~~~~~~~~~~~~g~~~~~~~---~~~~rVDl~~~p~ 459 (538)
..+ ..+|+|+|++|+. ..+|||||+++|+
T Consensus 81 ~~~----------~~~~~G~~~l~~~~~~~~~RRiDi~~~P~ 112 (112)
T PF14792_consen 81 SLG----------PTKYMGVCRLPGNDNKSPHRRIDIIVVPY 112 (112)
T ss_dssp EEC----------SSEEEEEEE-SSTSST--EEEEEEEEEEG
T ss_pred ccC----------CceeeeEeecCCCCCCCCeeeEEEEEeCC
Confidence 542 1589999999987 6789999999995
No 7
>PF14791 DNA_pol_B_thumb: DNA polymerase beta thumb ; PDB: 1HUZ_A 3K75_D 1HUO_A 2BPC_A 1RPL_A 1NOM_A 1ZQX_A 1ZQU_A 1ZQZ_A 1ZQV_A ....
Probab=99.90 E-value=1.4e-24 Score=171.76 Aligned_cols=63 Identities=35% Similarity=0.696 Sum_probs=52.7
Q ss_pred HHHHhhccHHHHHHHHHHHHHcCCccCCCCCcccCCCCCCcccccccCCCCCCCHHHHHhhcCCCCCCCCCcC
Q 009281 465 GLIAWTGNDVLNRRLRLLAESKGYRLDDTGLFPATHGSGGKQGVRARTSLKFDTEKEVFDFLGFPWLEPHERN 537 (538)
Q Consensus 465 aLl~~TGS~~fnr~lR~~A~~kg~~L~~~gL~~~~~~~~g~~~~~~~~~~~~~tEedIF~~LGL~yipPe~Rn 537 (538)
||+|||||++|||+||.+|+++||+||+|||++... +..+++.+|+|||++|||||||||+||
T Consensus 1 All~~TGs~~fnr~lR~~A~~~g~~L~~~Gl~~~~~----------~~~~~~~~E~dif~~Lgl~yipPe~R~ 63 (64)
T PF14791_consen 1 ALLYFTGSKEFNRDLRQYAKKKGMKLSEYGLFKRET----------GELVPVESEEDIFDALGLPYIPPELRE 63 (64)
T ss_dssp HHHHHHS-HHHHHHHHHHHHHTTEEEESSEEEETTC----------EEEEE-SSHHHHHHHTTS----GGGCT
T ss_pred CcccccCCHHHHHHHHHHHHHcCCeeCccccccccc----------ceeecCCCHHHHHHHcCCCCCChhhcC
Confidence 799999999999999999999999999999998532 357899999999999999999999998
No 8
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=99.68 E-value=9e-17 Score=129.30 Aligned_cols=66 Identities=36% Similarity=0.688 Sum_probs=62.3
Q ss_pred cHHHHHHHHHHHHHHHHc-CCChhHHHHHHHHHHHhcCCccccchhh-hcCCCCCCHHHHHHHHHHHH
Q 009281 210 NKNITEIFGKLINIYRAL-GEDRRSFSYYKAIPVIEKLPFKIESADQ-VKGLPGIGKSMQDHIQEIVT 275 (538)
Q Consensus 210 N~~ia~~L~~la~~~e~~-g~~~r~~aY~rAa~~l~~l~~~i~~~~~-l~~lpgiG~~ia~~I~Eil~ 275 (538)
|++|+++|++||+++++. ++.+|++||++||++|+++|++|++++| +.+|||||++|+.+|.|||+
T Consensus 1 N~~i~~~L~~la~~~~~~~~~~~r~~aY~~Aa~~i~~l~~~i~~~~~~~~~l~gIG~~ia~kI~E~le 68 (68)
T PF14716_consen 1 NQEIADALEELADLYELQGGDPFRARAYRRAAAAIKALPYPITSGEEDLKKLPGIGKSIAKKIDEILE 68 (68)
T ss_dssp THHHHHHHHHHHHHHHHTSTSHHHHHHHHHHHHHHHHSSS-HHSHHHHHCTSTTTTHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHhhCCcHHHHHHHHHHHHHHhCCHhHhhHHHHHhhCCCCCHHHHHHHHHHHC
Confidence 899999999999999999 5668999999999999999999999987 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=1.9e-16 Score=119.95 Aligned_cols=51 Identities=49% Similarity=1.009 Sum_probs=42.1
Q ss_pred HHHHhhccCCCHHHHHHHHHhCCCCHHHHhh-ccCcchhhhccccchhhhcc
Q 009281 294 ISLFGEVWGIGPATAQKLYEKGHRTLDDLKN-EDSLTHSQRLGLKYFDDIKT 344 (538)
Q Consensus 294 l~lf~~I~GvGpktA~~l~~~GirtledL~~-~~~L~~~q~~Glk~~ed~~~ 344 (538)
|++|++||||||+||++||++|+|||+||++ ...|+..|++|++||+||++
T Consensus 1 l~~f~~I~GVG~~tA~~w~~~G~rtl~Dl~~~~~~Lt~~Q~iGl~yyeD~~q 52 (52)
T PF10391_consen 1 LKLFTGIWGVGPKTARKWYAKGIRTLEDLRKSKSKLTWQQQIGLKYYEDFQQ 52 (52)
T ss_dssp HHHHHTSTT--HHHHHHHHHTT--SHHHHHHGGCGS-HHHHHHHHTHHHHH-
T ss_pred CcchhhcccccHHHHHHHHHhCCCCHHHHhhhhccCCHHHHHHHHHHHHhcC
Confidence 6789999999999999999999999999986 45899999999999999974
No 10
>PRK07945 hypothetical protein; Provisional
Probab=99.57 E-value=9.9e-15 Score=152.39 Aligned_cols=102 Identities=19% Similarity=0.274 Sum_probs=88.8
Q ss_pred HHHHHHHHHHHHHHcCCC-hhHHHHHHHHHHHhcCCcc-ccchh---hhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHh
Q 009281 213 ITEIFGKLINIYRALGED-RRSFSYYKAIPVIEKLPFK-IESAD---QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEK 287 (538)
Q Consensus 213 ia~~L~~la~~~e~~g~~-~r~~aY~rAa~~l~~l~~~-i~~~~---~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~ 287 (538)
-+++|+++|+++|++|+| ||++|||+||.+|+.++.+ +..+. +|.+|||||+++|.||.||++||+++.||+|+.
T Consensus 3 ~~~~l~~~a~lle~~~~n~frv~ayr~aa~~~~~~~~~~~~~~~~~g~l~~~~giG~~~a~~i~e~~~tg~~~~l~~l~~ 82 (335)
T PRK07945 3 PVAALRRIAFLLERARADTYRVRAFRRAADVVEALDAAERARRARAGSLTSLPGIGPKTAKVIAQALAGRVPDYLAELRA 82 (335)
T ss_pred HHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHhcChhHHHHHHhcCCcccCCCcCHHHHHHHHHHHhcCCHHHHHHHHH
Confidence 468999999999999999 6999999999999999999 88774 799999999999999999999999999999998
Q ss_pred hchhHHHHHHhhccCCCHHHHHHHHHh---------CCCCHHHHhh
Q 009281 288 DEKVRTISLFGEVWGIGPATAQKLYEK---------GHRTLDDLKN 324 (538)
Q Consensus 288 ~~~~~~l~lf~~I~GvGpktA~~l~~~---------GirtledL~~ 324 (538)
+..+- | |+..+.++.-. |-.|++|...
T Consensus 83 ~~~~~---------~-g~~l~~~~~~D~H~HT~~Sdg~~~~ee~v~ 118 (335)
T PRK07945 83 DAEPL---------G-GGALRAALRGDLHTHSDWSDGGSPIEEMAR 118 (335)
T ss_pred hhcCC---------c-cHHHHHHHhhhcccccCCCCCCCCHHHHHH
Confidence 76442 7 99999998742 4455666554
No 11
>smart00292 BRCT breast cancer carboxy-terminal domain.
Probab=98.92 E-value=2.5e-09 Score=85.88 Aligned_cols=79 Identities=19% Similarity=0.292 Sum_probs=60.2
Q ss_pred CCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecCC-CccEEEEcCChHHHHHHHHhhhccCCccccccchHHHHH
Q 009281 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSK-KVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSL 95 (538)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls~-~VTHVV~~~~~~~~~~l~~~~~~~~~~~lV~~~Wl~eci 95 (538)
.+|+|+++||.+ .+....+..+.+++..+||++...++. .+||||+.+.......... ....+..+|+.+||.||+
T Consensus 1 ~~f~g~~~~~~g-~~~~~~~~~l~~~i~~~Gg~~~~~~~~~~~thvi~~~~~~~~~~~~~--~~~~~~~iV~~~Wi~~~~ 77 (80)
T smart00292 1 KLFKGKVFVITG-KFDKNERDELKELIEALGGKVTSSLSSKTTTHVIVGSPEGGKLELLL--AIALGIPIVTEDWLLDCL 77 (80)
T ss_pred CccCCeEEEEeC-CCCCccHHHHHHHHHHcCCEEecccCccceeEEEEcCCCCccHHHHH--HHHcCCCCccHHHHHHHH
Confidence 379999999987 455566788899999999999999988 9999999765421111111 112347899999999999
Q ss_pred hcC
Q 009281 96 RLG 98 (538)
Q Consensus 96 k~g 98 (538)
+++
T Consensus 78 ~~~ 80 (80)
T smart00292 78 KAG 80 (80)
T ss_pred HCc
Confidence 875
No 12
>PF00533 BRCT: BRCA1 C Terminus (BRCT) domain; InterPro: IPR001357 The BRCT domain (after the C_terminal domain of a breast cancer susceptibility protein) is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage [], for example as found in the breast cancer DNA-repair protein BRCA1. The domain is an approximately 100 amino acid tandem repeat, which appears to act as a phospho-protein binding domain []. A chitin biosynthesis protein from yeast also seems to belong to this group. ; GO: 0005622 intracellular; PDB: 3L46_A 3AL3_A 3AL2_A 1WF6_A 3II6_X 2NTE_B 3FA2_A 2R1Z_A 2COK_A 2K7F_A ....
Probab=98.91 E-value=2.7e-09 Score=86.63 Aligned_cols=76 Identities=22% Similarity=0.340 Sum_probs=58.8
Q ss_pred CCCCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEcCC-hHHHHHHHHhhhccCCccccccchHHH
Q 009281 15 SNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDL-EALLQQVSKQHLARFKGSVIRYQWLED 93 (538)
Q Consensus 15 ~~~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~~~~-~~~~~~l~~~~~~~~~~~lV~~~Wl~e 93 (538)
...+|+|+++|| .+.....++.+.++++++||.|...+++.+||||+.+. ....+... .......+|+.+||.|
T Consensus 2 ~~~~F~g~~f~i--~~~~~~~~~~l~~~i~~~GG~v~~~~~~~~thvI~~~~~~~~~k~~~---~~~~~i~iV~~~Wi~~ 76 (78)
T PF00533_consen 2 KPKIFEGCTFCI--SGFDSDEREELEQLIKKHGGTVSNSFSKKTTHVIVGNPNKRTKKYKA---AIANGIPIVSPDWIED 76 (78)
T ss_dssp STTTTTTEEEEE--SSTSSSHHHHHHHHHHHTTEEEESSSSTTSSEEEESSSHCCCHHHHH---HHHTTSEEEETHHHHH
T ss_pred CCCCCCCEEEEE--ccCCCCCHHHHHHHHHHcCCEEEeecccCcEEEEeCCCCCccHHHHH---HHHCCCeEecHHHHHH
Confidence 357999999999 66666667778999999999999999999999999765 22222221 1122478999999999
Q ss_pred HH
Q 009281 94 SL 95 (538)
Q Consensus 94 ci 95 (538)
||
T Consensus 77 ci 78 (78)
T PF00533_consen 77 CI 78 (78)
T ss_dssp HH
T ss_pred hC
Confidence 97
No 13
>cd00027 BRCT Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks.
Probab=98.52 E-value=1.8e-07 Score=73.24 Aligned_cols=72 Identities=19% Similarity=0.316 Sum_probs=52.8
Q ss_pred CcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHhhhccCCccccccchHHHHHh
Q 009281 21 GMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSLR 96 (538)
Q Consensus 21 g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~~~~~~~~~~l~~~~~~~~~~~lV~~~Wl~ecik 96 (538)
|+.+||.....+ ..+..+.+++..+||++.+.++..+||||+.+...... ... ....+..+|+.+|+.||++
T Consensus 1 ~~~~~i~g~~~~-~~~~~l~~~i~~~Gg~v~~~~~~~~thvI~~~~~~~~~-~~~--~~~~~~~iV~~~Wi~~~~~ 72 (72)
T cd00027 1 GLTFVITGDLPS-EERDELKELIEKLGGKVTSSVSKKTTHVIVGSDAGPKK-LLK--AIKLGIPIVTPEWLLDCLK 72 (72)
T ss_pred CCEEEEEecCCC-cCHHHHHHHHHHcCCEEeccccCCceEEEECCCCCchH-HHH--HHHcCCeEecHHHHHHHhC
Confidence 577888765434 44677889999999999999999999999976543211 111 1123478999999999985
No 14
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=97.95 E-value=2.6e-05 Score=88.45 Aligned_cols=83 Identities=23% Similarity=0.350 Sum_probs=68.9
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh-CCCCHHHHhhcc--Ccch
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED--SLTH 330 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~-GirtledL~~~~--~L~~ 330 (538)
++|.+|||+|++++++|.+.++.++...+++ .+..| +|+|||+++|+.|++. | |+++|.++. .|..
T Consensus 466 ~~L~~L~GfG~Ksa~nIl~~Ie~sk~~~l~r--------~L~aL-gIpgVG~~~ak~L~~~f~--sl~~l~~As~eeL~~ 534 (652)
T TIGR00575 466 EDLLELEGFGEKSAQNLLNAIEKSKEKPLAR--------LLFAL-GIRHVGEVTAKNLAKHFG--TLDKLKAASLEELLS 534 (652)
T ss_pred HHHhhccCccHHHHHHHHHHHHHhccCcHHH--------HHhhc-cCCCcCHHHHHHHHHHhC--CHHHHHhCCHHHHhc
Confidence 5789999999999999999999988776654 45556 9999999999999987 6 999998653 5888
Q ss_pred hhhccccchhhhccCcC
Q 009281 331 SQRLGLKYFDDIKTRIP 347 (538)
Q Consensus 331 ~q~~Glk~~ed~~~~i~ 347 (538)
..++|.+..+.+..-+.
T Consensus 535 i~GIG~~~A~~I~~ff~ 551 (652)
T TIGR00575 535 VEGVGPKVAESIVNFFH 551 (652)
T ss_pred CCCcCHHHHHHHHHHHh
Confidence 88899887777765443
No 15
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=97.88 E-value=8e-06 Score=63.93 Aligned_cols=51 Identities=37% Similarity=0.549 Sum_probs=42.6
Q ss_pred HHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhc--cCcchhhhccccchhhhc
Q 009281 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDIK 343 (538)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~GirtledL~~~--~~L~~~q~~Glk~~ed~~ 343 (538)
+...|++|+||||++|++||+.||.|++||.+. ..|....++|-+..+.|.
T Consensus 3 ~~~~L~~I~Gig~~~a~~L~~~G~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~ 55 (60)
T PF14520_consen 3 VFDDLLSIPGIGPKRAEKLYEAGIKTLEDLANADPEELAEIPGIGEKTAEKII 55 (60)
T ss_dssp HHHHHHTSTTCHHHHHHHHHHTTCSSHHHHHTSHHHHHHTSTTSSHHHHHHHH
T ss_pred HHHhhccCCCCCHHHHHHHHhcCCCcHHHHHcCCHHHHhcCCCCCHHHHHHHH
Confidence 345567999999999999999999999999865 368888888887766654
No 16
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=97.40 E-value=0.00021 Score=55.85 Aligned_cols=52 Identities=33% Similarity=0.601 Sum_probs=41.0
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (538)
.++.+|||||+.++.++.+. | +..++.+.+-.+ +.|.+|+|+|+++|++|.+
T Consensus 5 ~~L~~I~Gig~~~a~~L~~~---G-~~t~~~l~~a~~----~~L~~i~Gig~~~a~~i~~ 56 (60)
T PF14520_consen 5 DDLLSIPGIGPKRAEKLYEA---G-IKTLEDLANADP----EELAEIPGIGEKTAEKIIE 56 (60)
T ss_dssp HHHHTSTTCHHHHHHHHHHT---T-CSSHHHHHTSHH----HHHHTSTTSSHHHHHHHHH
T ss_pred HhhccCCCCCHHHHHHHHhc---C-CCcHHHHHcCCH----HHHhcCCCCCHHHHHHHHH
Confidence 57889999999999887654 6 566788765432 3466999999999999986
No 17
>KOG3226 consensus DNA repair protein [Replication, recombination and repair]
Probab=97.35 E-value=0.00015 Score=74.74 Aligned_cols=88 Identities=17% Similarity=0.324 Sum_probs=69.5
Q ss_pred CCCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEc-CChHHHHHHHHhhhccCCccccccchHHHH
Q 009281 16 NGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAM-DLEALLQQVSKQHLARFKGSVIRYQWLEDS 94 (538)
Q Consensus 16 ~~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~~-~~~~~~~~l~~~~~~~~~~~lV~~~Wl~ec 94 (538)
+.+++|+|+.+ .|+...-+.-|+..|...||..-.+|..+-||.|.. .++...+. ......+||+-+||++|
T Consensus 315 ~klL~GVV~Vl--SGfqNP~Rs~LRskAl~LGAkY~pDW~~gsThLICAF~NTPKy~Q-----V~g~Gg~IV~keWI~~C 387 (508)
T KOG3226|consen 315 SKLLEGVVFVL--SGFQNPERSTLRSKALTLGAKYQPDWNAGSTHLICAFPNTPKYRQ-----VEGNGGTIVSKEWITEC 387 (508)
T ss_pred HHhhhceEEEE--ecccCchHHHHHHHHHhhcccccCCcCCCceeEEEecCCCcchhh-----cccCCceEeeHHHHHHH
Confidence 58999999877 677545556678999999999999999999999973 33322111 11223689999999999
Q ss_pred HhcCcccCcccccccc
Q 009281 95 LRLGEKVSEDLYRIKL 110 (538)
Q Consensus 95 ik~g~lv~e~~y~l~~ 110 (538)
-..+++||+.+|.+.-
T Consensus 388 y~~kk~lp~rrYlm~~ 403 (508)
T KOG3226|consen 388 YAQKKLLPIRRYLMHA 403 (508)
T ss_pred HHHHhhccHHHHHhcC
Confidence 9999999999999864
No 18
>PF12738 PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2WT8_C 3EF1_A 3EF0_A.
Probab=97.13 E-value=0.00034 Score=54.92 Aligned_cols=51 Identities=20% Similarity=0.325 Sum_probs=34.8
Q ss_pred HHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHhhhccCCccccccch
Q 009281 36 LQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQW 90 (538)
Q Consensus 36 ~~~l~~~~~~~G~~V~~~ls~~VTHVV~~~~~~~~~~l~~~~~~~~~~~lV~~~W 90 (538)
+.-+.++++.+||.+.+.++.++||+|+.+... .++... ...+..+|+++|
T Consensus 13 ~~~l~~~i~~~Gg~~~~~lt~~~THLI~~~~~~-~K~~~A---~~~gi~vV~~~W 63 (63)
T PF12738_consen 13 RSQLRKLIEALGGKYSKDLTKKTTHLICSSPEG-KKYRKA---KEWGIPVVSPDW 63 (63)
T ss_dssp CCHHHHHHHCTT-EEESSSSTT-SEEEEES--H-HHHHHH---HHCTSEEEEHHH
T ss_pred HHHHHHHHHHCCCEEeccccCCceEEEEeCCCc-HHHHHH---HHCCCcEECCCC
Confidence 556779999999999999999999999955432 122221 122378999999
No 19
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=96.96 E-value=0.00097 Score=56.73 Aligned_cols=35 Identities=34% Similarity=0.353 Sum_probs=31.7
Q ss_pred hHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009281 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~ 325 (538)
...+..|+.|||||+++|+.|+..||+|++||+..
T Consensus 8 ~~~~~~L~~iP~IG~a~a~DL~~LGi~s~~~L~g~ 42 (93)
T PF11731_consen 8 RAGLSDLTDIPNIGKATAEDLRLLGIRSPADLKGR 42 (93)
T ss_pred HHHHHHHhcCCCccHHHHHHHHHcCCCCHHHHhCC
Confidence 44678899999999999999999999999999954
No 20
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=96.94 E-value=0.0012 Score=61.42 Aligned_cols=50 Identities=34% Similarity=0.627 Sum_probs=40.6
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHH-hCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009281 252 SADQVKGLPGIGKSMQDHIQEIVT-TGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 252 ~~~~l~~lpgiG~~ia~~I~Eil~-tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (538)
+.+||+.|||||++.|++|.++-+ .|.+.-+|+ |.+|+|||+++.++|-.
T Consensus 95 s~eeL~~lpgIG~~kA~aIi~yRe~~G~f~sv~d------------L~~v~GiG~~~~ekl~~ 145 (149)
T COG1555 95 SAEELQALPGIGPKKAQAIIDYREENGPFKSVDD------------LAKVKGIGPKTLEKLKD 145 (149)
T ss_pred CHHHHHHCCCCCHHHHHHHHHHHHHcCCCCcHHH------------HHhccCCCHHHHHHHHh
Confidence 347899999999999999999874 445555554 55899999999999854
No 21
>KOG2481 consensus Protein required for normal rRNA processing [RNA processing and modification]
Probab=96.90 E-value=0.00029 Score=75.58 Aligned_cols=87 Identities=17% Similarity=0.276 Sum_probs=63.7
Q ss_pred CCCCCCCCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEee-c---------CCCccEEEEcCChHHHHHHHHhhhcc
Q 009281 11 PALDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEK-L---------SKKVTHVLAMDLEALLQQVSKQHLAR 80 (538)
Q Consensus 11 ~~~~~~~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~-l---------s~~VTHVV~~~~~~~~~~l~~~~~~~ 80 (538)
..+....+|+|+++|+. +.++ ++.|.-.|++.||.|.-. + +..|||=|++-....... .
T Consensus 320 ~~s~~kslF~glkFfl~-reVP---resL~fiI~s~GG~V~wd~~~~g~~~~~~d~~ITH~IvDrP~~~~~v-----~-- 388 (570)
T KOG2481|consen 320 EQSSHKSLFSGLKFFLN-REVP---RESLEFIIRSFGGKVSWDPLGIGATYDESDERITHQIVDRPGQQTSV-----I-- 388 (570)
T ss_pred hhhhHHHHhhcceeeee-ccCc---hHHHHHHHHHcCCceecCccCCCCcccccccceeeeeecccCcccee-----e--
Confidence 34566799999999874 3444 455667899999999855 1 246999998654321111 1
Q ss_pred CCccccccchHHHHHhcCcccCccccccc
Q 009281 81 FKGSVIRYQWLEDSLRLGEKVSEDLYRIK 109 (538)
Q Consensus 81 ~~~~lV~~~Wl~ecik~g~lv~e~~y~l~ 109 (538)
.-..|.++||-||+.+|.+++.+.|.+-
T Consensus 389 -gR~YvQPQWvfDsvNar~llpt~~Y~~G 416 (570)
T KOG2481|consen 389 -GRTYVQPQWVFDSVNARLLLPTEKYFPG 416 (570)
T ss_pred -eeeeecchhhhhhccchhhccHhhhCCC
Confidence 1257999999999999999999999875
No 22
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=96.89 E-value=0.0015 Score=51.91 Aligned_cols=48 Identities=29% Similarity=0.627 Sum_probs=32.8
Q ss_pred cCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009281 257 KGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 257 ~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (538)
.+|||||+..|+.+.+ ++..++.+.+. ..+.|++|+||||++|+.+++
T Consensus 6 LGI~~VG~~~ak~L~~-----~f~sl~~l~~a----~~e~L~~i~gIG~~~A~si~~ 53 (64)
T PF12826_consen 6 LGIPGVGEKTAKLLAK-----HFGSLEALMNA----SVEELSAIPGIGPKIAQSIYE 53 (64)
T ss_dssp CTSTT--HHHHHHHHH-----CCSCHHHHCC------HHHHCTSTT--HHHHHHHHH
T ss_pred CCCCCccHHHHHHHHH-----HcCCHHHHHHc----CHHHHhccCCcCHHHHHHHHH
Confidence 5899999999998875 44556666543 456678999999999999885
No 23
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=96.88 E-value=0.0041 Score=70.94 Aligned_cols=114 Identities=18% Similarity=0.302 Sum_probs=74.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchh
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHS 331 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~~--~L~~~ 331 (538)
+++..|||+|++.+++|.+-++.-+-..| .+.+--+ .|+|||+++|+.|.+. +.|+++|.++. .|...
T Consensus 479 ~~L~~l~gfG~Ksa~~ll~~Ie~sk~~~l--------~R~l~al-gi~~IG~~~ak~L~~~-f~sl~~l~~As~eeL~~i 548 (665)
T PRK07956 479 EDLLGLEGFGEKSAQNLLDAIEKSKETSL--------ARFLYAL-GIRHVGEKAAKALARH-FGSLEALRAASEEELAAV 548 (665)
T ss_pred HHHhcCcCcchHHHHHHHHHHHHhhcCCH--------HHhhHhh-hccCcCHHHHHHHHHH-cCCHHHHHhCCHHHHhcc
Confidence 57899999999999998876653222222 2344555 8999999999998864 47899998653 57888
Q ss_pred hhccccchhhhccCcCHHHHHH-HHHHHHHHhh-------hcCCCeEEEecccc
Q 009281 332 QRLGLKYFDDIKTRIPRHEVEQ-MERLLQKAGE-------EVLPEVIILCGGSY 377 (538)
Q Consensus 332 q~~Glk~~ed~~~~i~r~ea~~-i~~iv~~~~~-------~~~p~~~v~~~Gs~ 377 (538)
.++|-+..+.+..-+.-.+..+ +..+...-+. ..+.|..+++||.+
T Consensus 549 ~GIG~~~A~sI~~ff~~~~~~~~i~~L~~~gv~~~~~~~~~~~~g~~~v~TG~l 602 (665)
T PRK07956 549 EGVGEVVAQSIVEFFAVEENRELIDELLEAGVNMEYKGEEVDLAGKTVVLTGTL 602 (665)
T ss_pred CCcCHHHHHHHHHHHhhhhHHHHHHHHHHcCCCccccccCCCccccEEEEeCCC
Confidence 8899877777765554333222 2333221010 01335567778876
No 24
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=96.79 E-value=0.0023 Score=57.36 Aligned_cols=50 Identities=30% Similarity=0.497 Sum_probs=40.3
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHHh-CCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009281 252 SADQVKGLPGIGKSMQDHIQEIVTT-GKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 252 ~~~~l~~lpgiG~~ia~~I~Eil~t-G~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (538)
+.++|..|||||++.|.+|-++.+. |.+..+ +.|.+|+|||++++.+|.+
T Consensus 66 ~~~eL~~lpGIG~~~A~~Ii~~R~~~g~f~s~------------eeL~~V~GIg~k~~~~i~~ 116 (120)
T TIGR01259 66 SLEELQALPGIGPAKAKAIIEYREENGAFKSV------------DDLTKVSGIGEKSLEKLKD 116 (120)
T ss_pred CHHHHhcCCCCCHHHHHHHHHHHHhcCCcCCH------------HHHHcCCCCCHHHHHHHHh
Confidence 3578999999999999999998864 554433 4445899999999999865
No 25
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=96.75 E-value=0.002 Score=51.19 Aligned_cols=48 Identities=44% Similarity=0.685 Sum_probs=35.7
Q ss_pred chhhhcCCCCCCHHHHHHHHHHH-HhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHH
Q 009281 252 SADQVKGLPGIGKSMQDHIQEIV-TTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKL 311 (538)
Q Consensus 252 ~~~~l~~lpgiG~~ia~~I~Eil-~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l 311 (538)
+.++|..+||||+..|+.|-++- +.|.+..+++|. .|+|+|+++..+|
T Consensus 12 s~~eL~~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL~------------~v~gi~~~~~~~l 60 (65)
T PF12836_consen 12 SAEELQALPGIGPKQAKAIVEYREKNGPFKSLEDLK------------EVPGIGPKTYEKL 60 (65)
T ss_dssp -HHHHHTSTT--HHHHHHHHHHHHHH-S-SSGGGGG------------GSTT--HHHHHHH
T ss_pred CHHHHHHcCCCCHHHHHHHHHHHHhCcCCCCHHHHh------------hCCCCCHHHHHHH
Confidence 56899999999999999999998 677777777654 7999999999887
No 26
>PLN03123 poly [ADP-ribose] polymerase; Provisional
Probab=96.72 E-value=0.0031 Score=74.25 Aligned_cols=89 Identities=16% Similarity=0.341 Sum_probs=67.6
Q ss_pred CCCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChH--HHHHHHHhhhccCCccccccchHHH
Q 009281 16 NGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEA--LLQQVSKQHLARFKGSVIRYQWLED 93 (538)
Q Consensus 16 ~~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~~~~~~--~~~~l~~~~~~~~~~~lV~~~Wl~e 93 (538)
...|.+++|.+... .+.. ..-|++.+..+||.+....++.+||+|+...-. ..++.+.. ..+.+||+.+||+|
T Consensus 391 ~~~l~~~~i~i~G~-~~~~-~~~~k~~Ie~~GG~~s~~v~~~~t~l~tt~e~~k~~~kv~qAk---~~~ipIVsedwL~d 465 (981)
T PLN03123 391 SEFLGDLKVSIVGA-SKEK-VTEWKAKIEEAGGVFHATVKKDTNCLVVCGELDDEDAEMRKAR---RMKIPIVREDYLVD 465 (981)
T ss_pred CCCcCCeEEEEecC-CCCc-HHHHHHHHHhcCCEEeeeccCCceEEEccHHhhhcchHHHHHH---hcCCCcccHHHHHH
Confidence 46799999999876 3333 367889999999999999999999999864211 11122211 22478999999999
Q ss_pred HHhcCcccCccccccc
Q 009281 94 SLRLGEKVSEDLYRIK 109 (538)
Q Consensus 94 cik~g~lv~e~~y~l~ 109 (538)
|.+.+++++...|.+.
T Consensus 466 s~~~~~~~p~~~y~~~ 481 (981)
T PLN03123 466 CFKKKKKLPFDKYKLE 481 (981)
T ss_pred HHhccccCcchhhhhc
Confidence 9999999999888664
No 27
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=96.53 E-value=0.0082 Score=68.68 Aligned_cols=87 Identities=16% Similarity=0.306 Sum_probs=63.7
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchh
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHS 331 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~~--~L~~~ 331 (538)
+++..|+|+|++.+++|.+=++.-+-..|+ ..|--| +|+|||+++|++|.+ .+.|+++|..+. .|...
T Consensus 496 ~~L~~l~g~g~Ksa~~Ll~~Ie~sk~~~l~--------r~l~AL-gIpgIG~~~ak~L~~-~F~si~~L~~As~eeL~~i 565 (689)
T PRK14351 496 ADLAELEGWGETSAENLLAELEASREPPLA--------DFLVAL-GIPEVGPTTARNLAR-EFGTFEAIMDADEEALRAV 565 (689)
T ss_pred HHHhcCcCcchhHHHHHHHHHHHHccCCHH--------HHHHHc-CCCCcCHHHHHHHHH-HhCCHHHHHhCCHHHHhcc
Confidence 578999999999999887666532222232 345556 899999999999975 558899998653 57788
Q ss_pred hhccccchhhhccCcCHHH
Q 009281 332 QRLGLKYFDDIKTRIPRHE 350 (538)
Q Consensus 332 q~~Glk~~ed~~~~i~r~e 350 (538)
.++|-+..+.+.+-+.-.+
T Consensus 566 ~GIG~k~A~sI~~ff~~~~ 584 (689)
T PRK14351 566 DDVGPTVAEEIREFFDSER 584 (689)
T ss_pred CCcCHHHHHHHHHHHhhhH
Confidence 8889888777766554443
No 28
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]
Probab=96.52 E-value=0.0039 Score=70.30 Aligned_cols=92 Identities=14% Similarity=0.208 Sum_probs=72.2
Q ss_pred CCCCCCCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEE-cC--ChHHHHHHHHhhhccCCcccccc
Q 009281 12 ALDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLA-MD--LEALLQQVSKQHLARFKGSVIRY 88 (538)
Q Consensus 12 ~~~~~~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~-~~--~~~~~~~l~~~~~~~~~~~lV~~ 88 (538)
+.+.+.+|.|+-+++.+...+.-++.-|.+.+..+||.++....++.||-|+ .+ +.++... .+.+ ...||++
T Consensus 627 ~~~~s~if~gl~f~Vlsgt~~~~tk~~le~~ivenGG~iv~nv~p~~~~ci~~a~~et~~vk~~----~~~~-~cdVl~p 701 (881)
T KOG0966|consen 627 VAKISNIFDGLEFCVLSGTSETHTKAKLEEIIVENGGKIVQNVGPSDTLCIATAGKETTRVKAQ----AIKR-SCDVLKP 701 (881)
T ss_pred ccchhhhhcCeeEEEecCCcccccHHHHHHHHHHcCCEEEEcCCCCCcceEEeccccchHHHHH----HHhc-cCceeeH
Confidence 4566799999999999988877777889999999999999999988999995 22 2233221 1222 3679999
Q ss_pred chHHHHHhcCcccCcccccc
Q 009281 89 QWLEDSLRLGEKVSEDLYRI 108 (538)
Q Consensus 89 ~Wl~ecik~g~lv~e~~y~l 108 (538)
+||.+|.+..+++++.++-+
T Consensus 702 ~Wlldcc~~~~l~p~~P~~~ 721 (881)
T KOG0966|consen 702 AWLLDCCKKQRLLPWLPRDL 721 (881)
T ss_pred HHHHHHHhhhhccccccHHH
Confidence 99999999999999755433
No 29
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=96.47 E-value=0.0042 Score=55.85 Aligned_cols=47 Identities=15% Similarity=0.246 Sum_probs=36.6
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009281 252 SADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 252 ~~~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (538)
+..+++.+||||+..|++|. ..|-+..+|+ +.+|+|||+++.+.+-+
T Consensus 59 ~~~el~~lpGigP~~A~~IV---~nGpf~sveD------------L~~V~GIgekqk~~l~k 105 (132)
T PRK02515 59 SVRAFRQFPGMYPTLAGKIV---KNAPYDSVED------------VLNLPGLSERQKELLEA 105 (132)
T ss_pred CHHHHHHCCCCCHHHHHHHH---HCCCCCCHHH------------HHcCCCCCHHHHHHHHH
Confidence 45789999999999999988 3555555554 44899999998877754
No 30
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=96.33 E-value=0.0056 Score=59.27 Aligned_cols=53 Identities=15% Similarity=0.265 Sum_probs=37.1
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHH
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLY 312 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~ 312 (538)
..|.++||||+++|-.| |.+-...++.+.-. .+-...|++|||||+|||+++.
T Consensus 72 ~~L~~V~GIGpK~Al~i---L~~~~~~el~~aI~---~~d~~~L~~ipGiGkKtAerIi 124 (191)
T TIGR00084 72 KELIKVNGVGPKLALAI---LSNMSPEEFVYAIE---TEEVKALVKIPGVGKKTAERLL 124 (191)
T ss_pred HHHhCCCCCCHHHHHHH---HhcCCHHHHHHHHH---hCCHHHHHhCCCCCHHHHHHHH
Confidence 46889999999999888 54444444443222 1223456789999999999997
No 31
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=96.09 E-value=0.013 Score=47.03 Aligned_cols=50 Identities=22% Similarity=0.341 Sum_probs=39.3
Q ss_pred hhhhcC-CCCCCHHHHHHHHHHHH-hCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh
Q 009281 253 ADQVKG-LPGIGKSMQDHIQEIVT-TGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (538)
Q Consensus 253 ~~~l~~-lpgiG~~ia~~I~Eil~-tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~ 314 (538)
.++|.. +||||...|..|-+... .|.+. .++.|.+|+|||.++++++++.
T Consensus 15 ~~~L~~~ipgig~~~a~~Il~~R~~~g~~~------------s~~dL~~v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 15 AEELQRAMNGVGLKKAEAIVSYREEYGPFK------------TVEDLKQVPGIGNSLVEKNLAV 66 (69)
T ss_pred HHHHHhHCCCCCHHHHHHHHHHHHHcCCcC------------CHHHHHcCCCCCHHHHHHHHhh
Confidence 468888 99999999999988875 45444 3444568999999999999764
No 32
>PLN03122 Poly [ADP-ribose] polymerase; Provisional
Probab=96.07 E-value=0.012 Score=68.08 Aligned_cols=93 Identities=22% Similarity=0.330 Sum_probs=67.8
Q ss_pred CCCCCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEcCCh--HH-HHHHHHhhhccCCccccccch
Q 009281 14 DSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLE--AL-LQQVSKQHLARFKGSVIRYQW 90 (538)
Q Consensus 14 ~~~~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~~~~~--~~-~~~l~~~~~~~~~~~lV~~~W 90 (538)
.+...|.|++|.|-..- ..+ +.-+++++..+||+|.... ...||+|+.... .. ...++.. ......||+.+|
T Consensus 185 ~~~kpL~G~~fviTGtl-~~s-r~elK~~Ie~~GGkvsssV-s~~T~lIvt~~ev~k~gsSKlkkA--k~lgIpIVsEd~ 259 (815)
T PLN03122 185 APGKPFSGMMISLSGRL-SRT-HQYWKKDIEKHGGKVANSV-EGVTCLVVSPAERERGGSSKIAEA--MERGIPVVREAW 259 (815)
T ss_pred ccCCCcCCcEEEEeCCC-CCC-HHHHHHHHHHcCCEEcccc-ccceEEEEcCccccccCccHHHHH--HHcCCcCccHHH
Confidence 44567999999997653 334 5677999999999999998 668899874422 11 0112211 122478999999
Q ss_pred HHHHHhcCcccCccccccccC
Q 009281 91 LEDSLRLGEKVSEDLYRIKLD 111 (538)
Q Consensus 91 l~ecik~g~lv~e~~y~l~~~ 111 (538)
|.+|++.++++++..|.+..+
T Consensus 260 L~d~i~~~k~~~~~~y~l~~~ 280 (815)
T PLN03122 260 LIDSIEKQEAQPLEAYDVVSD 280 (815)
T ss_pred HHHHHhcCCcccchhhhhccc
Confidence 999999999999999988543
No 33
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.06 E-value=0.0068 Score=58.82 Aligned_cols=52 Identities=17% Similarity=0.290 Sum_probs=37.6
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcch-hHHHHhhchhHHHHHHhhccCCCHHHHHHHH
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSK-LEHFEKDEKVRTISLFGEVWGIGPATAQKLY 312 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~tG~~~~-le~l~~~~~~~~l~lf~~I~GvGpktA~~l~ 312 (538)
..|.+++|||+++|-.|-.-+. ... .+.+.+ +-.+.|++|||||+|||+++.
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 4689999999999998876443 233 233322 234567799999999999964
No 34
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=96.04 E-value=0.0052 Score=41.32 Aligned_cols=23 Identities=30% Similarity=0.546 Sum_probs=19.5
Q ss_pred cchhhhcCCCCCCHHHHHHHHHH
Q 009281 251 ESADQVKGLPGIGKSMQDHIQEI 273 (538)
Q Consensus 251 ~~~~~l~~lpgiG~~ia~~I~Ei 273 (538)
.+.++|.+|||||+.+|+.|.+|
T Consensus 8 as~eeL~~lpGIG~~tA~~I~~~ 30 (30)
T PF00633_consen 8 ASIEELMKLPGIGPKTANAILSF 30 (30)
T ss_dssp SSHHHHHTSTT-SHHHHHHHHHH
T ss_pred CCHHHHHhCCCcCHHHHHHHHhC
Confidence 36789999999999999999875
No 35
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=96.04 E-value=0.024 Score=50.92 Aligned_cols=67 Identities=22% Similarity=0.350 Sum_probs=44.3
Q ss_pred CCCCHHHHHHH--------HHHHHhCCcchhH-HHHhhc--hh------HHHHHHhhccCCCHHHHHHHHHhCCCCHHHH
Q 009281 260 PGIGKSMQDHI--------QEIVTTGKLSKLE-HFEKDE--KV------RTISLFGEVWGIGPATAQKLYEKGHRTLDDL 322 (538)
Q Consensus 260 pgiG~~ia~~I--------~Eil~tG~~~~le-~l~~~~--~~------~~l~lf~~I~GvGpktA~~l~~~GirtledL 322 (538)
||||+..+.+. .++++.|.-+.-. +|..+. .. ..+--|..|+|||+..|.-|...||+|+++|
T Consensus 1 pgi~~~~~~~L~~~GI~t~~~Ll~~~~~~~~r~~La~~~~i~~~~l~~w~~~AdL~ri~gi~~~~a~LL~~AGv~Tv~~L 80 (122)
T PF14229_consen 1 PGIGPKEAAKLKAAGIKTTGDLLEAGDTPLGRKALAKKLGISERNLLKWVNQADLMRIPGIGPQYAELLEHAGVDTVEEL 80 (122)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHHcCCCHHHHHHHHHhcCCCHHHHHHHHhHHHhhhcCCCCHHHHHHHHHhCcCcHHHH
Confidence 77888777774 4556655433322 122211 11 1233455999999999999999999999999
Q ss_pred hhcc
Q 009281 323 KNED 326 (538)
Q Consensus 323 ~~~~ 326 (538)
.+..
T Consensus 81 A~~~ 84 (122)
T PF14229_consen 81 AQRN 84 (122)
T ss_pred HhCC
Confidence 8643
No 36
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.90 E-value=0.01 Score=57.45 Aligned_cols=54 Identities=26% Similarity=0.409 Sum_probs=39.0
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (538)
..|.++.|||+++|=.|- .+-...+ +..-...+-.+.|++|||||+|||+++.-
T Consensus 72 ~~LisVsGIGPK~ALaIL---s~~~~~e---l~~aI~~~D~~~L~~vpGIGkKtAeRIIl 125 (196)
T PRK13901 72 EELIGVDGIGPRAALRVL---SGIKYNE---FRDAIDREDIELISKVKGIGNKMAGKIFL 125 (196)
T ss_pred HHHhCcCCcCHHHHHHHH---cCCCHHH---HHHHHHhCCHHHHhhCCCCCHHHHHHHHH
Confidence 468899999999998765 3333333 33333344567788999999999999963
No 37
>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=95.85 E-value=0.0055 Score=59.29 Aligned_cols=50 Identities=16% Similarity=0.230 Sum_probs=40.9
Q ss_pred HHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhc------cCcchhhhccccchhhhc
Q 009281 292 RTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE------DSLTHSQRLGLKYFDDIK 343 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~------~~L~~~q~~Glk~~ed~~ 343 (538)
..+.+|.+|+|||||+|..+ .+.-|+++|.++ ++|++++|||-|..+.|.
T Consensus 69 ~lF~~L~~V~GIGpK~Al~i--L~~~~~~el~~aI~~~d~~~L~~ipGiGkKtAerIi 124 (191)
T TIGR00084 69 ELFKELIKVNGVGPKLALAI--LSNMSPEEFVYAIETEEVKALVKIPGVGKKTAERLL 124 (191)
T ss_pred HHHHHHhCCCCCCHHHHHHH--HhcCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHH
Confidence 46777779999999999999 666788888732 469999999999877765
No 38
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.83 E-value=0.011 Score=56.73 Aligned_cols=54 Identities=19% Similarity=0.316 Sum_probs=38.9
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (538)
..|.++.|||+++|=.|- .+-...++-. -...+-.+.|++|||||+|||+++.-
T Consensus 73 ~~Li~VsGIGpK~Al~IL---s~~~~~el~~---aI~~~D~~~L~~vpGIGkKtAeRIil 126 (183)
T PRK14601 73 EMLLKVNGIGANTAMAVC---SSLDVNSFYK---ALSLGDESVLKKVPGIGPKSAKRIIA 126 (183)
T ss_pred HHHhccCCccHHHHHHHH---cCCCHHHHHH---HHHhCCHHHHhhCCCCCHHHHHHHHH
Confidence 468899999999997654 4434444333 23334467789999999999999963
No 39
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=95.82 E-value=0.011 Score=57.18 Aligned_cols=54 Identities=19% Similarity=0.284 Sum_probs=37.6
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhH-HHHhhchhHHHHHHhhccCCCHHHHHHHHHh
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLE-HFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~tG~~~~le-~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~ 314 (538)
..|..+||||+++|.+|-+... ...+. .+.+. -.+.|++|||||+|+|++++..
T Consensus 73 ~~L~~i~GIGpk~A~~il~~fg---~~~l~~~i~~~----d~~~L~~v~Gig~k~A~~I~~~ 127 (192)
T PRK00116 73 RLLISVSGVGPKLALAILSGLS---PEELVQAIANG----DVKALTKVPGIGKKTAERIVLE 127 (192)
T ss_pred HHHhcCCCCCHHHHHHHHHhCC---HHHHHHHHHhC----CHHHHHhCCCCCHHHHHHHHHH
Confidence 4688899999999999854332 23332 33332 2334569999999999999853
No 40
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=95.64 E-value=0.0036 Score=61.65 Aligned_cols=51 Identities=25% Similarity=0.520 Sum_probs=40.7
Q ss_pred HHhhccCCCHHHHHHHHHhCCCCHHHHhhcc--CcchhhhccccchhhhccCc
Q 009281 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIKTRI 346 (538)
Q Consensus 296 lf~~I~GvGpktA~~l~~~GirtledL~~~~--~L~~~q~~Glk~~ed~~~~i 346 (538)
.|..|+|||++++++|++.||.|+++|..+. .|....++|.+..+.|...+
T Consensus 4 ~L~~IpGIG~krakkLl~~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l 56 (232)
T PRK12766 4 ELEDISGVGPSKAEALREAGFESVEDVRAADQSELAEVDGIGNALAARIKADV 56 (232)
T ss_pred ccccCCCcCHHHHHHHHHcCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHHh
Confidence 3568999999999999999999999999764 57777777766655554433
No 41
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.63 E-value=0.013 Score=57.33 Aligned_cols=54 Identities=19% Similarity=0.204 Sum_probs=39.4
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (538)
..|.++.|||+++|=.|-. +-...++ ..-...+-.+.|++|||||+|||+++.-
T Consensus 74 ~~Li~V~GIGpK~Al~iLs---~~~~~~l---~~aI~~~D~~~L~~ipGIGkKtAerIil 127 (203)
T PRK14602 74 IVLISISKVGAKTALAILS---QFRPDDL---RRLVAEEDVAALTRVSGIGKKTAQHIFL 127 (203)
T ss_pred HHHhCCCCcCHHHHHHHHh---hCCHHHH---HHHHHhCCHHHHhcCCCcCHHHHHHHHH
Confidence 4689999999999987654 3333333 3333344577889999999999999963
No 42
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=95.62 E-value=0.013 Score=65.89 Aligned_cols=76 Identities=30% Similarity=0.458 Sum_probs=55.9
Q ss_pred CCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEc-CCh----HHHHHHHHhhhccCCccccccchHHHHHhcCcccCcc
Q 009281 30 GVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAM-DLE----ALLQQVSKQHLARFKGSVIRYQWLEDSLRLGEKVSED 104 (538)
Q Consensus 30 ~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~~-~~~----~~~~~l~~~~~~~~~~~lV~~~Wl~ecik~g~lv~e~ 104 (538)
+..+.-.+.+..+++. ++...+.+.|||||+. +.+ +.++.+.. .+. +.+|+++.|+.+||+.+++|+|+
T Consensus 485 ~l~p~ek~~v~~~a~~---t~~k~~~~~~thvi~~~~~~g~c~rTlk~~~g-il~--gkwi~~~~w~~~s~k~~~~~~ee 558 (684)
T KOG4362|consen 485 GLTPSEKQLVEKFAVD---TISKFWIEPVTHVIASTDLEGACLRTLKVLMG-ILR--GKWILSYDWVLASLKLRKWVSEE 558 (684)
T ss_pred cCCcchHHHHHHHHHH---HHhhccCCCceeeeeecccccchhhhHHHHHH-hhc--CceeeeHHHHHHHHHhcCCCCCC
Confidence 3334556777778877 7777888999999983 322 34444331 122 25899999999999999999999
Q ss_pred ccccccC
Q 009281 105 LYRIKLD 111 (538)
Q Consensus 105 ~y~l~~~ 111 (538)
.|-|.++
T Consensus 559 pfEl~~d 565 (684)
T KOG4362|consen 559 PFELQID 565 (684)
T ss_pred CeeEeec
Confidence 9999875
No 43
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.59 E-value=0.016 Score=56.03 Aligned_cols=54 Identities=11% Similarity=0.107 Sum_probs=38.7
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (538)
..|.++.|||+++|=.|-. +-... ++..-...+-.+.|++|||||+|||+++.-
T Consensus 73 ~~Li~V~GIGpK~AL~iLs---~~~~~---el~~aI~~~D~~~L~~vpGIGkKtAerIil 126 (188)
T PRK14606 73 LSLTKVSRLGPKTALKIIS---NEDAE---TLVTMIASQDVEGLSKLPGISKKTAERIVM 126 (188)
T ss_pred HHHhccCCccHHHHHHHHc---CCCHH---HHHHHHHhCCHHHHhhCCCCCHHHHHHHHH
Confidence 4588999999999987653 32333 333333344577889999999999999963
No 44
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.52 E-value=0.017 Score=56.19 Aligned_cols=54 Identities=15% Similarity=0.213 Sum_probs=38.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (538)
..|.++.|||+++|=.|- .+....++-+ -...+=...|++|||||+|||+++.-
T Consensus 72 ~~L~~V~GIGpK~AL~iL---s~~~~~~l~~---aI~~~D~~~L~kvpGIGkKtAerIil 125 (197)
T PRK14603 72 ELLLGVSGVGPKLALALL---SALPPALLAR---ALLEGDARLLTSASGVGKKLAERIAL 125 (197)
T ss_pred HHHhCcCCcCHHHHHHHH---cCCCHHHHHH---HHHhCCHHHHhhCCCCCHHHHHHHHH
Confidence 468899999999997654 4444444332 23334467788999999999999963
No 45
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.48 E-value=0.018 Score=55.95 Aligned_cols=54 Identities=20% Similarity=0.346 Sum_probs=38.9
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (538)
..|.++.|||+++|=.|- .+....++-. -...+-...|++|||||+|||+++.-
T Consensus 73 ~~Li~V~GIGpK~Al~iL---s~~~~~el~~---aI~~~D~~~L~kvpGIGkKtAerIil 126 (195)
T PRK14604 73 ELLIGVSGVGPKAALNLL---SSGTPDELQL---AIAGGDVARLARVPGIGKKTAERIVL 126 (195)
T ss_pred HHHhCcCCcCHHHHHHHH---cCCCHHHHHH---HHHhCCHHHHhhCCCCCHHHHHHHHH
Confidence 468899999999997754 4444444433 23334467788999999999999963
No 46
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=95.38 E-value=0.015 Score=39.16 Aligned_cols=22 Identities=32% Similarity=0.477 Sum_probs=17.2
Q ss_pred HHHHHHhhccCCCHHHHHHHHH
Q 009281 292 RTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~ 313 (538)
..++.|++||||||+||..+..
T Consensus 8 as~eeL~~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 8 ASIEELMKLPGIGPKTANAILS 29 (30)
T ss_dssp SSHHHHHTSTT-SHHHHHHHHH
T ss_pred CCHHHHHhCCCcCHHHHHHHHh
Confidence 3567777999999999998764
No 47
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]
Probab=95.33 E-value=0.044 Score=62.13 Aligned_cols=92 Identities=20% Similarity=0.265 Sum_probs=61.5
Q ss_pred CCCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecC------CCccEEEEc--CChHHHHHHHHhhhccCCccccc
Q 009281 16 NGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLS------KKVTHVLAM--DLEALLQQVSKQHLARFKGSVIR 87 (538)
Q Consensus 16 ~~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls------~~VTHVV~~--~~~~~~~~l~~~~~~~~~~~lV~ 87 (538)
...|..+++|.+.++.-.+-..+..-.+...|++|.+.-+ ..+||+|+. +.+-...++......-.+-+||.
T Consensus 782 ~~~~~~~~~f~~~~~~~~se~~~~~l~~k~~g~~i~~~~~~~~~~~~~~t~~v~~~i~~~h~~~~~~~~~~lt~~rkv~~ 861 (881)
T KOG0966|consen 782 SLFLSSLRMFYVLRRKLSSEEVIIELKLKNFGGRITDAQSECNNIGAKYTHCVLRCIDEDHEKIKEQKKASLTIKRKVVA 861 (881)
T ss_pred ccccccceeeecccccccHHHHHHHHHHHHhcceeeeccchhhhcccceeeeeeeecchHHHHHHHHHHHHhcccccccC
Confidence 3566777777777665445555555566666999998653 468999985 33222223332211111238999
Q ss_pred cchHHHHHhcCcccCccccc
Q 009281 88 YQWLEDSLRLGEKVSEDLYR 107 (538)
Q Consensus 88 ~~Wl~ecik~g~lv~e~~y~ 107 (538)
.+||.+|+.++.+++|+.|.
T Consensus 862 ~~wv~~s~~~~~~~~e~~~~ 881 (881)
T KOG0966|consen 862 PSWVDHSINENCLLPEEDFP 881 (881)
T ss_pred HHHHHHhhcccccCccccCC
Confidence 99999999999999999883
No 48
>COG5163 NOP7 Protein required for biogenesis of the 60S ribosomal subunit [Translation, ribosomal structure and biogenesis]
Probab=95.31 E-value=0.015 Score=60.96 Aligned_cols=87 Identities=21% Similarity=0.381 Sum_probs=60.7
Q ss_pred CCCCCCCCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeec-----------CCCccEEEEcCChHHHHHHHHhhhc
Q 009281 11 PALDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKL-----------SKKVTHVLAMDLEALLQQVSKQHLA 79 (538)
Q Consensus 11 ~~~~~~~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~l-----------s~~VTHVV~~~~~~~~~~l~~~~~~ 79 (538)
+.++-..+|+++++|+- +.++ ...|.-.++..||.|...- +..|||-|++.. +++ ++..
T Consensus 343 ~~Ss~~slFS~f~Fyis-reVp---~dsLefiilscGG~V~~~p~~~~i~~~~~vD~~vth~i~drp--~~~----~kve 412 (591)
T COG5163 343 PCSSLKSLFSGFKFYIS-REVP---GDSLEFIILSCGGSVVGSPCEADIHVSEKVDEKVTHQIVDRP--VMK----NKVE 412 (591)
T ss_pred cCcchhhhhhceEEEEe-cccc---chHHHHHHHHcCCcccCchhhccCCchhhccchhhhhhccch--hhh----hhhc
Confidence 34556699999999884 3333 2445567999999997532 345788877543 211 1111
Q ss_pred cCCccccccchHHHHHhcCcccCccccccc
Q 009281 80 RFKGSVIRYQWLEDSLRLGEKVSEDLYRIK 109 (538)
Q Consensus 80 ~~~~~lV~~~Wl~ecik~g~lv~e~~y~l~ 109 (538)
. .-.+.++|+-|||..|.+++.+.|.+.
T Consensus 413 g--rtYiQPQw~fDsiNkG~l~~~~~Y~~G 440 (591)
T COG5163 413 G--RTYIQPQWLFDSINKGKLACVENYCVG 440 (591)
T ss_pred c--eeeechHHHHhhhccccchhhhhcccc
Confidence 1 347899999999999999999999874
No 49
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=95.25 E-value=0.0082 Score=68.54 Aligned_cols=61 Identities=21% Similarity=0.325 Sum_probs=47.4
Q ss_pred hccCCCHHHHHHHHHh-CCCCHHHHhh--ccCcchhhhccccchhhhccCcCHHHHHHHHHHHH
Q 009281 299 EVWGIGPATAQKLYEK-GHRTLDDLKN--EDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQ 359 (538)
Q Consensus 299 ~I~GvGpktA~~l~~~-GirtledL~~--~~~L~~~q~~Glk~~ed~~~~i~r~ea~~i~~iv~ 359 (538)
+|+|+||+++++||+. +|++++||.. .++|..+.+||-+..+.+.+.|-......+..++-
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 8899999984 34688889999999998876665443333334333
No 50
>PTZ00418 Poly(A) polymerase; Provisional
Probab=95.00 E-value=0.23 Score=55.56 Aligned_cols=51 Identities=24% Similarity=0.399 Sum_probs=42.2
Q ss_pred CCeEEEecccccccCCc-CCCeeEEEecCCcchhhhhHHHHHHHHHHcCccc
Q 009281 367 PEVIILCGGSYRRGKAS-CGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLR 417 (538)
Q Consensus 367 p~~~v~~~Gs~RRgke~-~~DvDiLIt~~~~~~~~~~l~~~v~~L~~~g~l~ 417 (538)
.+.++...||||-|.-. +.|||.|+..|..-....+|..+.+.|.+..-++
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 46688889999999876 6799999999976666789998989888876554
No 51
>cd05397 NT_Pol-beta-like Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins. This superfamily includes the NT domains of DNA polymerase beta and other family X DNA polymerases, as well as the NT domains of Class I and Class II CCA-adding enzymes, RelA- and SpoT-like ppGpp synthetases and hydrolases, 2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), poly (A) polymerases, terminal uridylyl transferases, and Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. The Escherichia coli CCA-adding enzyme belongs to this superfamily but is not included as this enzyme lacks the N-terminal helix conserved in the remainder of the superfamily. In the majority of the Pol beta-like superfamily NTs, two carboxylates, Dx[D/E], together with a third more distal carboxylate coordinate two divalent metal cations that are essential for catalysis. These divalent metal ions are
Probab=94.83 E-value=0.052 Score=40.66 Aligned_cols=28 Identities=29% Similarity=0.458 Sum_probs=23.4
Q ss_pred cCCCeEEEecccccccCC-cCCCeeEEEe
Q 009281 365 VLPEVIILCGGSYRRGKA-SCGDLDVVIM 392 (538)
Q Consensus 365 ~~p~~~v~~~Gs~RRgke-~~~DvDiLIt 392 (538)
..+...+.+.|||.||.. ..+|||+++.
T Consensus 14 ~~~~~~v~lfGS~arg~~~~~SDIDi~v~ 42 (49)
T cd05397 14 LVPGYEIVVYGSLVRGLLKKSSDIDLACV 42 (49)
T ss_pred hcCCcEEEEECCcCCCCCCCCCCEEEEEE
Confidence 345668999999999987 6789999986
No 52
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=94.71 E-value=0.065 Score=61.26 Aligned_cols=84 Identities=14% Similarity=0.219 Sum_probs=61.0
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhc--------
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE-------- 325 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~-------- 325 (538)
+++.+|+|+|++.+++|..=++.-+-..| .+.|--| +|++||.++|+.|-+..+.|++.|.+.
T Consensus 470 ~~l~~l~g~geksa~nl~~~Ie~sk~~~l--------~r~l~AL-GI~~vG~~~ak~La~~~f~~~~~l~~~~~~~~~~~ 540 (669)
T PRK14350 470 DRLINLKGFKDKRINNLKRSIEASKKRPF--------SKLLLSM-GIKDLGENTILLLINNNLNSFDKISTLCQDREFAL 540 (669)
T ss_pred HHHhhccCccHHHHHHHHHHHHHHhCCCH--------HHHHHHc-CCCchhHHHHHHHHHHhhCCHHHHHhhhhccCCCH
Confidence 68889999999888887765543222222 3455566 899999999998887788999988752
Q ss_pred cCcchhhhccccchhhhccCc
Q 009281 326 DSLTHSQRLGLKYFDDIKTRI 346 (538)
Q Consensus 326 ~~L~~~q~~Glk~~ed~~~~i 346 (538)
..|..+.++|-...+.+.+-+
T Consensus 541 e~l~~i~giG~~~a~si~~ff 561 (669)
T PRK14350 541 SKLLKIKGIGEKIALNIIEAF 561 (669)
T ss_pred HHHhhCCCccHHHHHHHHHHH
Confidence 147778888877776666544
No 53
>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=94.71 E-value=0.013 Score=66.74 Aligned_cols=63 Identities=24% Similarity=0.383 Sum_probs=48.6
Q ss_pred hhccCCCHHHHHHHHHh-CCCCHHHHhh--ccCcchhhhccccchhhhccCcCHHHHHHHHHHHHH
Q 009281 298 GEVWGIGPATAQKLYEK-GHRTLDDLKN--EDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQK 360 (538)
Q Consensus 298 ~~I~GvGpktA~~l~~~-GirtledL~~--~~~L~~~q~~Glk~~ed~~~~i~r~ea~~i~~iv~~ 360 (538)
++|+|+|++++.+||++ +|++++||.. .++|..+.+||-+..+.|.+.|....-..+.+++..
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 7899999984 357888999999998888766654443334444443
No 54
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=94.70 E-value=0.037 Score=53.88 Aligned_cols=54 Identities=19% Similarity=0.265 Sum_probs=40.1
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (538)
..|.++.|||+++|=.| |.+....++-.. ...+-...|+++||||+|||+++.-
T Consensus 73 ~~LisVnGIGpK~ALai---Ls~~~~~~l~~a---I~~~d~~~L~k~PGIGkKtAerivl 126 (201)
T COG0632 73 RLLISVNGIGPKLALAI---LSNLDPEELAQA---IANEDVKALSKIPGIGKKTAERIVL 126 (201)
T ss_pred HHHHccCCccHHHHHHH---HcCCCHHHHHHH---HHhcChHhhhcCCCCCHHHHHHHHH
Confidence 47899999999999765 444444444333 3334467789999999999999964
No 55
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=94.70 E-value=0.025 Score=52.64 Aligned_cols=51 Identities=27% Similarity=0.512 Sum_probs=39.9
Q ss_pred hHHHHHHhhccCCCHHHHHHHHH---h-C-CCCHHHHhhccCcchhhhccccchhhhccCcC
Q 009281 291 VRTISLFGEVWGIGPATAQKLYE---K-G-HRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIP 347 (538)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~---~-G-irtledL~~~~~L~~~q~~Glk~~ed~~~~i~ 347 (538)
.-..+.|..+||||+++|+++.+ + | ++|+|||.+ .+++|-+.++.+..+|.
T Consensus 93 tAs~eeL~~lpgIG~~kA~aIi~yRe~~G~f~sv~dL~~------v~GiG~~~~ekl~~~i~ 148 (149)
T COG1555 93 TASAEELQALPGIGPKKAQAIIDYREENGPFKSVDDLAK------VKGIGPKTLEKLKDYIT 148 (149)
T ss_pred ccCHHHHHHCCCCCHHHHHHHHHHHHHcCCCCcHHHHHh------ccCCCHHHHHHHHhhcc
Confidence 33455567999999999999985 2 4 899999986 46788888888776553
No 56
>PRK14973 DNA topoisomerase I; Provisional
Probab=94.67 E-value=0.038 Score=65.38 Aligned_cols=90 Identities=20% Similarity=0.193 Sum_probs=58.6
Q ss_pred hhhcCCCCCCHHHHHHHHHHHH-h-CCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccc
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVT-T-GKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLT 329 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~-t-G~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~~--~L~ 329 (538)
++|..+|||...++......+. . +.-..-...+.....+.-+++ +|.|||++|+.+++..||.|.|||.+++ +|+
T Consensus 835 ~~La~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~el~-~vkg~ge~t~~~l~~ag~~~~e~l~~~d~~~la 913 (936)
T PRK14973 835 AYLALKTGISPETICRHAKLVCEKLGRPVPEKISKAAFERGRAELL-SVPGLGETTLEKLYLAGVYDGDLLVSADPKKLA 913 (936)
T ss_pred HHHhcCCCCChhhHHHHHHHHHHHhcCCCchhhhhhhhcccchhhh-hccCCCHHHHHHHHHcCCCCHHHhccCCHHHHh
Confidence 5677888888776666654443 1 111111111111112223344 9999999999999999999999999764 677
Q ss_pred hhhhccccchhhhcc
Q 009281 330 HSQRLGLKYFDDIKT 344 (538)
Q Consensus 330 ~~q~~Glk~~ed~~~ 344 (538)
..-+++.+....|..
T Consensus 914 ~~~~i~~k~~~~~~~ 928 (936)
T PRK14973 914 KVTGIDEKKLRNLQA 928 (936)
T ss_pred hhcCCCHHHHHHHHH
Confidence 777788777666654
No 57
>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=94.47 E-value=0.022 Score=38.86 Aligned_cols=20 Identities=45% Similarity=0.790 Sum_probs=16.3
Q ss_pred HhhccCCCHHHHHHHHHhCC
Q 009281 297 FGEVWGIGPATAQKLYEKGH 316 (538)
Q Consensus 297 f~~I~GvGpktA~~l~~~Gi 316 (538)
+.++||||++|+++|.+.||
T Consensus 13 i~~~~GIG~kt~~kL~~~GI 32 (32)
T PF11798_consen 13 IRKFWGIGKKTAKKLNKLGI 32 (32)
T ss_dssp GGGSTTS-HHHHHHHHCTT-
T ss_pred HHhhCCccHHHHHHHHHccC
Confidence 46899999999999988886
No 58
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.42 E-value=0.041 Score=53.05 Aligned_cols=53 Identities=13% Similarity=0.096 Sum_probs=37.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (538)
..|.++.|||+++|=.|- .+-...++-.. ...+-.+.| +|||||+|||+++.-
T Consensus 73 ~~LisV~GIGpK~Al~iL---s~~~~~~l~~a---I~~~D~~~L-~vpGIGkKtAerIil 125 (186)
T PRK14600 73 RMLVKVSGVNYKTAMSIL---SKLTPEQLFSA---IVNEDKAAL-KVNGIGEKLINRIIT 125 (186)
T ss_pred HHHhCcCCcCHHHHHHHH---ccCCHHHHHHH---HHcCCHhhe-ECCCCcHHHHHHHHH
Confidence 468899999999997654 44344444332 222334677 899999999999963
No 59
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=94.32 E-value=0.05 Score=49.05 Aligned_cols=32 Identities=22% Similarity=0.380 Sum_probs=28.3
Q ss_pred HHHHHhhccCCCHHHHHHHHHh-CCCCHHHHhh
Q 009281 293 TISLFGEVWGIGPATAQKLYEK-GHRTLDDLKN 324 (538)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~-GirtledL~~ 324 (538)
..+.|+++|||||++|+++.+. .++|+|||.+
T Consensus 59 ~~~el~~lpGigP~~A~~IV~nGpf~sveDL~~ 91 (132)
T PRK02515 59 SVRAFRQFPGMYPTLAGKIVKNAPYDSVEDVLN 91 (132)
T ss_pred CHHHHHHCCCCCHHHHHHHHHCCCCCCHHHHHc
Confidence 4556779999999999999987 6999999986
No 60
>PRK02362 ski2-like helicase; Provisional
Probab=94.29 E-value=0.031 Score=64.85 Aligned_cols=56 Identities=25% Similarity=0.421 Sum_probs=41.9
Q ss_pred HHHhhchhHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhc--cCcchhhhccccchhhh
Q 009281 284 HFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDI 342 (538)
Q Consensus 284 ~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~--~~L~~~q~~Glk~~ed~ 342 (538)
.+....+...+.|+ +|||||+++|+++|+.||+|++||... .+|..+ ||-+..+.+
T Consensus 642 ~l~~gv~~~~~~L~-~ip~i~~~~a~~l~~~gi~s~~dl~~~~~~~l~~~--~g~~~~~~i 699 (737)
T PRK02362 642 RVEYGVREELLDLV-GLRGVGRVRARRLYNAGIESRADLRAADKSVVLAI--LGEKIAENI 699 (737)
T ss_pred HHHhCCCHHHHHHh-CCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHHH--HCHHHHHHH
Confidence 34455566678887 899999999999999999999999953 345555 665554443
No 61
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=94.27 E-value=0.12 Score=58.31 Aligned_cols=49 Identities=18% Similarity=0.310 Sum_probs=25.7
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009281 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 256 l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (538)
..+||+||+.+|..+..... .++.|.. ...+.+..|+|||++.|..+.+
T Consensus 513 aLGIr~VG~~~Ak~La~~f~-----sl~~l~~----a~~e~l~~i~giG~~vA~si~~ 561 (667)
T COG0272 513 ALGIRHVGETTAKSLARHFG-----TLEALLA----ASEEELASIPGIGEVVARSIIE 561 (667)
T ss_pred HcCCchhhHHHHHHHHHHhh-----hHHHHHh----cCHHHHhhccchhHHHHHHHHH
Confidence 45666666666666555222 2333332 1234444666666666666554
No 62
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=94.21 E-value=0.045 Score=49.04 Aligned_cols=47 Identities=28% Similarity=0.498 Sum_probs=36.9
Q ss_pred HHHHHhhccCCCHHHHHHHHHh-----CCCCHHHHhhccCcchhhhccccchhhhccC
Q 009281 293 TISLFGEVWGIGPATAQKLYEK-----GHRTLDDLKNEDSLTHSQRLGLKYFDDIKTR 345 (538)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~-----GirtledL~~~~~L~~~q~~Glk~~ed~~~~ 345 (538)
..+.|+.+||||+++|+++++. ++.|++||.+ ..++|.+.++.+...
T Consensus 66 ~~~eL~~lpGIG~~~A~~Ii~~R~~~g~f~s~eeL~~------V~GIg~k~~~~i~~~ 117 (120)
T TIGR01259 66 SLEELQALPGIGPAKAKAIIEYREENGAFKSVDDLTK------VSGIGEKSLEKLKDY 117 (120)
T ss_pred CHHHHhcCCCCCHHHHHHHHHHHHhcCCcCCHHHHHc------CCCCCHHHHHHHHhc
Confidence 5666779999999999999963 5899999964 456777777776554
No 63
>cd05402 NT_PAP_TUTase Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases. Poly(A) polymerases (PAPs) catalyze mRNA poly(A) tail synthesis, and terminal uridylyl transferases (TUTases) uridylate RNA. PAPs in this subgroup include human PAP alpha, mouse testis-specific cytoplasmic PAP beta, human nuclear PAP gamma, Saccharomyces cerevisiae PAP1, TRF4 and-5, Schizosaccharomyces pombe caffeine-induced death proteins -1, and -14, Caenorhabditis elegans Germ Line Development-2, and Chlamydomonas reinhardtii MUT68. This family also includes human U6 snRNA-specific TUTase1, and Trypanosoma brucei 3'-TUTase-1,-2, and 4. This family belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. For the majority of proteins in this family, these carboxyla
Probab=94.01 E-value=0.22 Score=43.54 Aligned_cols=59 Identities=25% Similarity=0.449 Sum_probs=45.2
Q ss_pred HHHHHHHHHhhhcCCCeEEEecccccccCC-cCCCeeEEEecCCc-chhhhhHHHHHHHHHHcCc
Q 009281 353 QMERLLQKAGEEVLPEVIILCGGSYRRGKA-SCGDLDVVIMHPDR-KSHKGFLSKYVKKLKEMKF 415 (538)
Q Consensus 353 ~i~~iv~~~~~~~~p~~~v~~~Gs~RRgke-~~~DvDiLIt~~~~-~~~~~~l~~~v~~L~~~g~ 415 (538)
.++++++. ..|++.+.+-||++.|.. ..+|||+.|..++. .....++..+-+.|++.+.
T Consensus 8 ~l~~~i~~----~~~~~~v~~fGS~~~g~~~~~SDiDl~i~~~~~~~~~~~~l~~l~~~l~~~~~ 68 (114)
T cd05402 8 RLQELIKE----WFPGAKLYPFGSYVTGLGLPGSDIDLCLLGPNHRVDREDFLRKLAKLLKKSGE 68 (114)
T ss_pred HHHHHHHH----HCCCCEEEEecccccCCCCCCCCeeEEEEeCCCCccHHHHHHHHHHHHHhCCC
Confidence 34555554 578999999999999954 46899999998876 4556778888888888774
No 64
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=93.69 E-value=0.036 Score=53.65 Aligned_cols=51 Identities=24% Similarity=0.275 Sum_probs=38.4
Q ss_pred HHHHHhhccCCCHHHHHHHHHh-CCCCHHHHhhcc---Ccchhhhccccchhhhc
Q 009281 293 TISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED---SLTHSQRLGLKYFDDIK 343 (538)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~-GirtledL~~~~---~L~~~q~~Glk~~ed~~ 343 (538)
....|.+|+|||||+|.++.+. |..++.+....+ .|+...|+|.+..+.+.
T Consensus 71 ~f~~L~~i~GIGpk~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~ 125 (192)
T PRK00116 71 LFRLLISVSGVGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIV 125 (192)
T ss_pred HHHHHhcCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHH
Confidence 3556779999999999999987 887776544322 58888888887755544
No 65
>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=93.62 E-value=0.078 Score=42.44 Aligned_cols=44 Identities=18% Similarity=0.272 Sum_probs=33.4
Q ss_pred HHhh-ccCCCHHHHHHHHHh-----CCCCHHHHhhccCcchhhhccccchhhhccC
Q 009281 296 LFGE-VWGIGPATAQKLYEK-----GHRTLDDLKNEDSLTHSQRLGLKYFDDIKTR 345 (538)
Q Consensus 296 lf~~-I~GvGpktA~~l~~~-----GirtledL~~~~~L~~~q~~Glk~~ed~~~~ 345 (538)
.|.. ++|||+++|+++.+. ++++++||.+ ..++|.+.++.+...
T Consensus 17 ~L~~~ipgig~~~a~~Il~~R~~~g~~~s~~dL~~------v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 17 ELQRAMNGVGLKKAEAIVSYREEYGPFKTVEDLKQ------VPGIGNSLVEKNLAV 66 (69)
T ss_pred HHHhHCCCCCHHHHHHHHHHHHHcCCcCCHHHHHc------CCCCCHHHHHHHHhh
Confidence 4556 999999999999975 5999999975 356676666665543
No 66
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.61 E-value=0.034 Score=54.01 Aligned_cols=52 Identities=19% Similarity=0.255 Sum_probs=40.0
Q ss_pred hHHHHHHhhccCCCHHHHHHHHHh-CCCCHHHHh-hc--cCcchhhhccccchhhh
Q 009281 291 VRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLK-NE--DSLTHSQRLGLKYFDDI 342 (538)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~-GirtledL~-~~--~~L~~~q~~Glk~~ed~ 342 (538)
...+++|.+|.|||||+|..+... +...|-+.. +. ..|++.+|+|-|..+.|
T Consensus 69 r~lF~~Li~V~GIGpK~Al~ILs~~~~~~l~~aI~~~D~~~L~~vpGIGkKtAerI 124 (194)
T PRK14605 69 LSLFETLIDVSGIGPKLGLAMLSAMNAEALASAIISGNAELLSTIPGIGKKTASRI 124 (194)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHH
Confidence 457888889999999999999986 766633333 32 36899999999887664
No 67
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=93.48 E-value=0.069 Score=42.37 Aligned_cols=47 Identities=30% Similarity=0.519 Sum_probs=31.9
Q ss_pred HHHHHhhccCCCHHHHHHHHH---h--CCCCHHHHhhccCcchhhhccccchhhhccC
Q 009281 293 TISLFGEVWGIGPATAQKLYE---K--GHRTLDDLKNEDSLTHSQRLGLKYFDDIKTR 345 (538)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~---~--GirtledL~~~~~L~~~q~~Glk~~ed~~~~ 345 (538)
..+.|.++||||++.|+++.+ + +++|++||.. ..++|.+.|+.+...
T Consensus 12 s~~eL~~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL~~------v~gi~~~~~~~l~~~ 63 (65)
T PF12836_consen 12 SAEELQALPGIGPKQAKAIVEYREKNGPFKSLEDLKE------VPGIGPKTYEKLKPY 63 (65)
T ss_dssp -HHHHHTSTT--HHHHHHHHHHHHHH-S-SSGGGGGG------STT--HHHHHHHCCC
T ss_pred CHHHHHHcCCCCHHHHHHHHHHHHhCcCCCCHHHHhh------CCCCCHHHHHHHHhh
Confidence 456677999999999999985 2 8999999985 456777777766544
No 68
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=93.24 E-value=0.063 Score=42.53 Aligned_cols=43 Identities=28% Similarity=0.365 Sum_probs=28.8
Q ss_pred hccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhccccchhhh
Q 009281 299 EVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDI 342 (538)
Q Consensus 299 ~I~GvGpktA~~l~~~GirtledL~~~~--~L~~~q~~Glk~~ed~ 342 (538)
+|+|||+++|+.|-+ .+.|++.|.++. .|+...++|.+..+.+
T Consensus 7 GI~~VG~~~ak~L~~-~f~sl~~l~~a~~e~L~~i~gIG~~~A~si 51 (64)
T PF12826_consen 7 GIPGVGEKTAKLLAK-HFGSLEALMNASVEELSAIPGIGPKIAQSI 51 (64)
T ss_dssp TSTT--HHHHHHHHH-CCSCHHHHCC--HHHHCTSTT--HHHHHHH
T ss_pred CCCCccHHHHHHHHH-HcCCHHHHHHcCHHHHhccCCcCHHHHHHH
Confidence 899999999999975 455999999653 5777777776554444
No 69
>PRK00254 ski2-like helicase; Provisional
Probab=92.77 E-value=0.12 Score=59.77 Aligned_cols=66 Identities=26% Similarity=0.428 Sum_probs=46.5
Q ss_pred hCCcchhHHHH----hhchhHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhc--cCcchhhhccccchhhh
Q 009281 276 TGKLSKLEHFE----KDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDI 342 (538)
Q Consensus 276 tG~~~~le~l~----~~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~--~~L~~~q~~Glk~~ed~ 342 (538)
.|.+..+.++. ...+...+.|. +|||||+++|+++|+.|+.|++||..+ ..|....++|.+..+.+
T Consensus 623 ~~~~~~l~~l~~rl~~g~~~~~~~L~-~ipgig~~~~~~l~~~g~~s~~~i~~a~~~el~~~~gi~~~~a~~i 694 (720)
T PRK00254 623 QEVLDYLETLHLRVKHGVREELLELM-RLPMIGRKRARALYNAGFRSIEDIVNAKPSELLKVEGIGAKIVEGI 694 (720)
T ss_pred hhHHHHHHHHHHHHHcCCCHHHhhhh-cCCCCCHHHHHHHHHccCCCHHHHHhCCHHHHhcCCCCCHHHHHHH
Confidence 34444444333 44444556666 899999999999999999999999965 35766667776554443
No 70
>KOG1929 consensus Nucleotide excision repair factor NEF2, RAD4/CUT5 component [Replication, recombination and repair]
Probab=92.47 E-value=0.19 Score=58.13 Aligned_cols=89 Identities=18% Similarity=0.232 Sum_probs=68.6
Q ss_pred CCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHhhhccCCccccccchHHHHHh
Q 009281 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSLR 96 (538)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~~~~~~~~~~l~~~~~~~~~~~lV~~~Wl~ecik 96 (538)
..|.+|.|.. .|+...++.-+++++-.|||.....++..|+||++-......+ .++...++..+|..+|+-+||.
T Consensus 102 p~~~~~~Vc~--tgl~~~eK~ei~~~v~k~gg~~~~~L~s~v~~~~~~~~~~~~k---Ye~al~wn~~v~~~~w~~~s~~ 176 (811)
T KOG1929|consen 102 PGFFGLKVCL--TGLSGDEKSEIKILVPKHGGTLHRSLSSDVNSLKILPEVKTEK---YEQALKWNIPVVSDDWLFDSIE 176 (811)
T ss_pred CcccceEEEe--cccchHHHHHHHHHhhhcccEEehhhhhhhheeeeccccchHH---HHHHHhhCCccccHHHHhhhhc
Confidence 4566676666 7776666777789999999999999999999999855432211 1222233578999999999999
Q ss_pred cCcccCcccccccc
Q 009281 97 LGEKVSEDLYRIKL 110 (538)
Q Consensus 97 ~g~lv~e~~y~l~~ 110 (538)
.+..+++..|.+..
T Consensus 177 ~~~~~~~~~~e~~~ 190 (811)
T KOG1929|consen 177 KTAVLETKPYEGAP 190 (811)
T ss_pred cccccccccccccc
Confidence 99999999998865
No 71
>KOG2043 consensus Signaling protein SWIFT and related BRCT domain proteins [Transcription; Signal transduction mechanisms; Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]
Probab=92.45 E-value=0.12 Score=60.55 Aligned_cols=68 Identities=25% Similarity=0.406 Sum_probs=53.0
Q ss_pred HHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHhhhccCCccccccchHHHHHhcCcccCccccccc
Q 009281 38 IWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSLRLGEKVSEDLYRIK 109 (538)
Q Consensus 38 ~l~~~~~~~G~~V~~~ls~~VTHVV~~~~~~~~~~l~~~~~~~~~~~lV~~~Wl~ecik~g~lv~e~~y~l~ 109 (538)
-+++.+++.|+.|+...+ ..||+|+....+....|.. +.. ..-||+..|+.+|.++|..+|+..|.+.
T Consensus 672 ~~k~~~k~lg~s~~ss~~-e~Th~i~~rirRT~k~Lea--i~~-G~~ivT~~wL~s~~k~g~~~dek~yil~ 739 (896)
T KOG2043|consen 672 NYKLAKKFLGGSVASSDS-EATHFIADRIRRTLKFLEA--ISS-GKPLVTPQWLVSSLKSGEKLDEKPYILH 739 (896)
T ss_pred hhhhHHhhccceeecccc-cceeeeehhhhccHHHHhh--hcc-CCcccchHHHHHHhhccccccCcccccc
Confidence 367888999988887754 5899999865554444442 222 3579999999999999999999999986
No 72
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=92.45 E-value=0.24 Score=49.05 Aligned_cols=54 Identities=24% Similarity=0.452 Sum_probs=41.1
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh
Q 009281 253 ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (538)
Q Consensus 253 ~~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~ 314 (538)
++.|..|||||+..+.++ ++.| +.-++.+.... .+.|..|+|||.++|.++++.
T Consensus 2 ~~~L~~IpGIG~krakkL---l~~G-F~Sve~Ik~AS----~eEL~~V~GIg~k~AekI~e~ 55 (232)
T PRK12766 2 PEELEDISGVGPSKAEAL---REAG-FESVEDVRAAD----QSELAEVDGIGNALAARIKAD 55 (232)
T ss_pred ccccccCCCcCHHHHHHH---HHcC-CCCHHHHHhCC----HHHHHHccCCCHHHHHHHHHH
Confidence 356889999999988876 5555 56666665433 444569999999999999986
No 73
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=91.27 E-value=0.11 Score=50.31 Aligned_cols=50 Identities=20% Similarity=0.261 Sum_probs=38.0
Q ss_pred hHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhh---c---cCcchhhhccccchhhh
Q 009281 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDI 342 (538)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~---~---~~L~~~q~~Glk~~ed~ 342 (538)
...+++|.+|.|||||+|-.+... -+.++|.. . ..|++.+|+|-|..+.|
T Consensus 69 r~lF~~Li~V~GIGpK~AL~iLs~--~~~~el~~aI~~~D~~~L~~vpGIGkKtAerI 124 (188)
T PRK14606 69 KELFLSLTKVSRLGPKTALKIISN--EDAETLVTMIASQDVEGLSKLPGISKKTAERI 124 (188)
T ss_pred HHHHHHHhccCCccHHHHHHHHcC--CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHH
Confidence 357888899999999999999754 25555542 2 25899999999886554
No 74
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=91.11 E-value=0.11 Score=49.87 Aligned_cols=50 Identities=20% Similarity=0.255 Sum_probs=38.1
Q ss_pred hHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhh---c---cCcchhhhccccchhhh
Q 009281 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDI 342 (538)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~---~---~~L~~~q~~Glk~~ed~ 342 (538)
...+++|.+|.|||||+|-.+... -+.++|.. . ..|++.+|+|-|..+.|
T Consensus 69 r~lF~~Li~VsGIGpK~Al~ILs~--~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRI 124 (183)
T PRK14601 69 QKMFEMLLKVNGIGANTAMAVCSS--LDVNSFYKALSLGDESVLKKVPGIGPKSAKRI 124 (183)
T ss_pred HHHHHHHhccCCccHHHHHHHHcC--CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHH
Confidence 457888889999999999988754 35566653 2 35899999999886554
No 75
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=91.01 E-value=0.1 Score=50.82 Aligned_cols=50 Identities=28% Similarity=0.308 Sum_probs=38.5
Q ss_pred hHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhh---c---cCcchhhhccccchhhh
Q 009281 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDI 342 (538)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~---~---~~L~~~q~~Glk~~ed~ 342 (538)
...+++|.+|.|||||+|-.+... -|.++|.. . ..|++.+|+|-|..+.|
T Consensus 68 r~lF~~L~~V~GIGpK~AL~iLs~--~~~~~l~~aI~~~D~~~L~kvpGIGkKtAerI 123 (197)
T PRK14603 68 LELFELLLGVSGVGPKLALALLSA--LPPALLARALLEGDARLLTSASGVGKKLAERI 123 (197)
T ss_pred HHHHHHHhCcCCcCHHHHHHHHcC--CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHH
Confidence 357888889999999999999764 25666653 2 35899999999986654
No 76
>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=90.79 E-value=0.33 Score=40.35 Aligned_cols=32 Identities=28% Similarity=0.458 Sum_probs=26.5
Q ss_pred CCCeEEEecccccccCCc-CCCeeEEEecCCcc
Q 009281 366 LPEVIILCGGSYRRGKAS-CGDLDVVIMHPDRK 397 (538)
Q Consensus 366 ~p~~~v~~~Gs~RRgke~-~~DvDiLIt~~~~~ 397 (538)
.+...+.+.|||.||..+ .+|||++|..++..
T Consensus 12 ~~~~~v~lfGS~a~g~~~~~SDIDl~i~~~~~~ 44 (93)
T PF01909_consen 12 FGVAEVYLFGSYARGDATPDSDIDLLIILDEPE 44 (93)
T ss_dssp HTTEEEEEEHHHHHTSSCTTSCEEEEEEESSTS
T ss_pred CCCCEEEEECCcccCcCCCCCCEEEEEEeCCcc
Confidence 456689999999999966 69999999877664
No 77
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=90.77 E-value=0.17 Score=32.68 Aligned_cols=18 Identities=50% Similarity=0.648 Sum_probs=15.9
Q ss_pred HHhhccCCCHHHHHHHHH
Q 009281 296 LFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 296 lf~~I~GvGpktA~~l~~ 313 (538)
.|++|+|||+++|+++.+
T Consensus 2 ~L~~i~GiG~k~A~~il~ 19 (26)
T smart00278 2 ELLKVPGIGPKTAEKILE 19 (26)
T ss_pred hhhhCCCCCHHHHHHHHH
Confidence 356999999999999986
No 78
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=90.71 E-value=0.14 Score=50.12 Aligned_cols=50 Identities=26% Similarity=0.324 Sum_probs=38.2
Q ss_pred hHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhh---c---cCcchhhhccccchhhh
Q 009281 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDI 342 (538)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~---~---~~L~~~q~~Glk~~ed~ 342 (538)
...+++|.+|.|||||+|-.+... -+.++|.. . ..|++++|+|-|..+.|
T Consensus 70 r~lF~~Li~V~GIGpK~Al~iLs~--~~~~~l~~aI~~~D~~~L~~ipGIGkKtAerI 125 (203)
T PRK14602 70 RQTFIVLISISKVGAKTALAILSQ--FRPDDLRRLVAEEDVAALTRVSGIGKKTAQHI 125 (203)
T ss_pred HHHHHHHhCCCCcCHHHHHHHHhh--CCHHHHHHHHHhCCHHHHhcCCCcCHHHHHHH
Confidence 357888889999999999999875 25555542 2 35899999999886654
No 79
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=90.55 E-value=0.13 Score=49.90 Aligned_cols=50 Identities=28% Similarity=0.365 Sum_probs=39.0
Q ss_pred hHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhc------cCcchhhhccccchhhh
Q 009281 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE------DSLTHSQRLGLKYFDDI 342 (538)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~------~~L~~~q~~Glk~~ed~ 342 (538)
...+++|.+|.|||||+|-.+... -|.++|..+ ..|++++|+|.|..+.+
T Consensus 69 r~lF~~Li~V~GIGpK~Al~iLs~--~~~~el~~aI~~~D~~~L~kvpGIGkKtAerI 124 (195)
T PRK14604 69 RQLFELLIGVSGVGPKAALNLLSS--GTPDELQLAIAGGDVARLARVPGIGKKTAERI 124 (195)
T ss_pred HHHHHHHhCcCCcCHHHHHHHHcC--CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHH
Confidence 357888889999999999999874 366666532 35899999999986654
No 80
>PF04994 TfoX_C: TfoX C-terminal domain; InterPro: IPR007077 This domain is found in a number of bacterial proteins including the TfoX gene product of Haemophilus influenzae. TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes []. This family corresponds to the C-terminal presumed domain of TfoX. The domain is found in association with the N-terminal domain in some, but not all members of this group, suggesting this is an autonomous and functionally unrelated domain. For example it is found associated with Q9JZR1 from SWISSPROT in IPR002125 from INTERPRO.; PDB: 3BQT_A 3MAB_A.
Probab=90.24 E-value=0.22 Score=41.42 Aligned_cols=30 Identities=27% Similarity=0.480 Sum_probs=23.3
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhcc
Q 009281 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (538)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~~ 326 (538)
+..+|.+||+..+.|++-||.|++||+.-|
T Consensus 5 l~~LpNig~~~e~~L~~vGI~t~~~L~~~G 34 (81)
T PF04994_consen 5 LKDLPNIGPKSERMLAKVGIHTVEDLRELG 34 (81)
T ss_dssp GCGSTT--HHHHHHHHHTT--SHHHHHHHH
T ss_pred hhhCCCCCHHHHHHHHHcCCCCHHHHHHhC
Confidence 457899999999999999999999999755
No 81
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=90.07 E-value=0.16 Score=49.28 Aligned_cols=50 Identities=18% Similarity=0.318 Sum_probs=38.2
Q ss_pred hHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhh---c---cCcchhhhccccchhhh
Q 009281 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDI 342 (538)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~---~---~~L~~~q~~Glk~~ed~ 342 (538)
...+++|.+|.|||||+|-.+... -|.++|.. . ..|++.+|+|-|..+.|
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 357888889999999999999754 35666653 2 35899999999886543
No 82
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=90.00 E-value=0.14 Score=58.86 Aligned_cols=64 Identities=16% Similarity=0.221 Sum_probs=48.3
Q ss_pred hhccCCCHHHHHHHHHh-CCCCHHHHhh--ccCcchhhhccccchhhhccCcCHHHHHHHHHHHHHH
Q 009281 298 GEVWGIGPATAQKLYEK-GHRTLDDLKN--EDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKA 361 (538)
Q Consensus 298 ~~I~GvGpktA~~l~~~-GirtledL~~--~~~L~~~q~~Glk~~ed~~~~i~r~ea~~i~~iv~~~ 361 (538)
++|.|+|++++.+||+. +++++.||.. ...|..+.+||-+..+.+.+.|-.+--..+..++..+
T Consensus 465 l~I~GLG~k~i~~L~~~g~V~~~~Dl~~L~~~~L~~l~g~g~Ksa~~Ll~~Ie~sk~~~l~r~l~AL 531 (689)
T PRK14351 465 LDIEGLGEERVQQLVDAGLVESLADLYDLTVADLAELEGWGETSAENLLAELEASREPPLADFLVAL 531 (689)
T ss_pred cCCCCcCHHHHHHHHHcCCCCCHHHHHHcCHHHHhcCcCcchhHHHHHHHHHHHHccCCHHHHHHHc
Confidence 37999999999999999 6799999985 2347778899999998887766544333345555544
No 83
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=89.80 E-value=0.29 Score=44.21 Aligned_cols=53 Identities=23% Similarity=0.316 Sum_probs=39.3
Q ss_pred HHHhhccCCCHHHHHHHHHhCCCCHHHHhhccCcchhhhccccchhhhccCcCHHH
Q 009281 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIPRHE 350 (538)
Q Consensus 295 ~lf~~I~GvGpktA~~l~~~GirtledL~~~~~L~~~q~~Glk~~ed~~~~i~r~e 350 (538)
.-|+.|-||||+.+..|..+||.|+.+|-. ++..--.-+..|-.|..||-|+.
T Consensus 67 DDLt~I~GIGPk~e~~Ln~~GI~tfaQIAA---wt~~di~~id~~l~f~GRi~RDd 119 (133)
T COG3743 67 DDLTRISGIGPKLEKVLNELGIFTFAQIAA---WTRADIAWIDDYLNFDGRIERDD 119 (133)
T ss_pred ccchhhcccCHHHHHHHHHcCCccHHHHHh---cCHHHHHHHHhhcCCcchhHHHH
Confidence 447799999999999999999999999974 22222233445566677887774
No 84
>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=89.55 E-value=1.3 Score=51.49 Aligned_cols=83 Identities=20% Similarity=0.350 Sum_probs=62.9
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh-CCCCHHHHhhcc-Ccc-
Q 009281 253 ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED-SLT- 329 (538)
Q Consensus 253 ~~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~-GirtledL~~~~-~L~- 329 (538)
.+.|.++||||+..++.|.+-++. .. .-..++..| .-+|++++.|.++|+. |-.+++.|++.. +|.
T Consensus 116 ~~~L~~v~gi~~~~~~~i~~~~~~--------~~--~~~~~~~~L-~~~gi~~~~a~ki~~~yg~~~~~~i~~nPY~L~~ 184 (720)
T TIGR01448 116 PEKLLEVPGISKANLEKFVSQWSQ--------QG--DERRLLAGL-QGLGIGIKLAQRIYKFYQADTLDRVEKDPYLLAE 184 (720)
T ss_pred HHHHhcCCCCCHHHHHHHHHHHHH--------hH--HHHHHHHHH-HHcCCCHHHHHHHHHHHhHHHHHHHHhCchhhhh
Confidence 467899999999999999876632 11 123355555 8999999999999998 999999998764 555
Q ss_pred hhhhccccchhhhccCc
Q 009281 330 HSQRLGLKYFDDIKTRI 346 (538)
Q Consensus 330 ~~q~~Glk~~ed~~~~i 346 (538)
...++|++..+.+..++
T Consensus 185 ~i~gigF~~aD~iA~~~ 201 (720)
T TIGR01448 185 DVKGIGFLTADQLAQAL 201 (720)
T ss_pred hcCCCCHHHHHHHHHHc
Confidence 47788888888775443
No 85
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=89.46 E-value=0.47 Score=47.72 Aligned_cols=49 Identities=24% Similarity=0.485 Sum_probs=35.1
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009281 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 256 l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (538)
+..|||||..+|..+-.- -|+. +.+.+.. ...|+.|+|||+++|..+|+
T Consensus 184 l~s~pgig~~~a~~ll~~--fgS~---~~~~tas----~~eL~~v~gig~k~A~~I~~ 232 (254)
T COG1948 184 LESIPGIGPKLAERLLKK--FGSV---EDVLTAS----EEELMKVKGIGEKKAREIYR 232 (254)
T ss_pred HHcCCCccHHHHHHHHHH--hcCH---HHHhhcC----HHHHHHhcCccHHHHHHHHH
Confidence 689999999999876542 2333 3333211 25566999999999999986
No 86
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=89.37 E-value=0.2 Score=52.19 Aligned_cols=46 Identities=30% Similarity=0.482 Sum_probs=33.5
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhccccchhhh
Q 009281 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDI 342 (538)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~~--~L~~~q~~Glk~~ed~ 342 (538)
+..+||||+++|++|.+.||.|++||.... .|.+.-+++.+.-+.+
T Consensus 8 l~~l~gIg~~~a~~L~~~Gi~t~~dl~~~~~~~L~~~~g~~~~~a~~l 55 (317)
T PRK04301 8 LEDLPGVGPATAEKLREAGYDTVEAIAVASPKELSEAAGIGESTAAKI 55 (317)
T ss_pred HhhcCCCCHHHHHHHHHcCCCCHHHHHcCCHHHHHHhcCCCHHHHHHH
Confidence 558999999999999999999999998643 3444444333333333
No 87
>TIGR03671 cca_archaeal CCA-adding enzyme.
Probab=88.89 E-value=1.8 Score=46.66 Aligned_cols=47 Identities=28% Similarity=0.401 Sum_probs=34.0
Q ss_pred HHHHHHHHHHhhhcCCCeEEEecccccccCCcC--CCeeEEEecCCcch
Q 009281 352 EQMERLLQKAGEEVLPEVIILCGGSYRRGKASC--GDLDVVIMHPDRKS 398 (538)
Q Consensus 352 ~~i~~iv~~~~~~~~p~~~v~~~Gs~RRgke~~--~DvDiLIt~~~~~~ 398 (538)
..+...+++.+.+..+.+.|.+.|||.||.-.. .||||+|..|...+
T Consensus 24 ~~l~~~l~~~~~e~~~~~~v~~~GS~ArgT~L~G~sDIDIfi~f~~~~~ 72 (408)
T TIGR03671 24 DELIARLEEIIEELGVDAEVVLVGSYARGTWLKGDRDIDIFILFPKDTS 72 (408)
T ss_pred HHHHHHHHHHHHhcCCcceEEEEeeEecCCccCCCCceeEEEEeCCCCC
Confidence 334455555555555668999999999999886 69999998765443
No 88
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=88.73 E-value=1.1 Score=42.91 Aligned_cols=49 Identities=14% Similarity=0.216 Sum_probs=30.0
Q ss_pred CCCHHHHHHHHHHHH------hCCcchhHHHHhh---chhHHHHHHhhccCCCHHHHHHHH
Q 009281 261 GIGKSMQDHIQEIVT------TGKLSKLEHFEKD---EKVRTISLFGEVWGIGPATAQKLY 312 (538)
Q Consensus 261 giG~~ia~~I~Eil~------tG~~~~le~l~~~---~~~~~l~lf~~I~GvGpktA~~l~ 312 (538)
|.-..-|+.|.++.+ .|.+ +.+... ....+++.|+++||||||||....
T Consensus 75 Gfy~~KAk~Lk~~a~~iie~y~G~v---~~L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL 132 (177)
T TIGR03252 75 RFPGSMAKRVQALAQYVVDTYDGDA---TAVWTEGDPDGKELLRRLKALPGFGKQKAKIFL 132 (177)
T ss_pred CchHHHHHHHHHHHHHHHHHhCCCh---hhhhcccCCCcHHHHHHHHcCCCCCHHHHHHHH
Confidence 455566666665543 2433 333331 123357788899999999999764
No 89
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=88.58 E-value=0.22 Score=48.04 Aligned_cols=49 Identities=22% Similarity=0.306 Sum_probs=37.4
Q ss_pred hHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhh---c---cCcchhhhccccchhhh
Q 009281 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDI 342 (538)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~---~---~~L~~~q~~Glk~~ed~ 342 (538)
...+++|.+|.|||||+|-.+-.. -|.++|.. . ..| +.+|+|-|..+.|
T Consensus 69 r~lF~~LisV~GIGpK~Al~iLs~--~~~~~l~~aI~~~D~~~L-~vpGIGkKtAerI 123 (186)
T PRK14600 69 QDCLRMLVKVSGVNYKTAMSILSK--LTPEQLFSAIVNEDKAAL-KVNGIGEKLINRI 123 (186)
T ss_pred HHHHHHHhCcCCcCHHHHHHHHcc--CCHHHHHHHHHcCCHhhe-ECCCCcHHHHHHH
Confidence 357888889999999999999764 25666653 2 358 8999998886554
No 90
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=88.32 E-value=0.58 Score=52.50 Aligned_cols=86 Identities=15% Similarity=0.195 Sum_probs=63.8
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccch
Q 009281 253 ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTH 330 (538)
Q Consensus 253 ~~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~~--~L~~ 330 (538)
.+++.+++|+|++.+++|.+-++.-+-..|+ +.|--| +|++||.++|+. .+.|+++|..+. .|..
T Consensus 458 ~~~l~~l~gfgeks~~nll~aIe~sk~~~l~--------r~l~aL-GI~~vG~~~ak~----~~~~i~~l~~a~~e~l~~ 524 (562)
T PRK08097 458 PEQLANTPGIGKARAEQLWHQFNLARQQPFS--------RWLKAL-GIPLPQAALNAL----DDRSWQQLLSRSEQQWQQ 524 (562)
T ss_pred HHHHhcCcCccHHHHHHHHHHHHHHcCCCHH--------HHHHHc-CCccHHHHHHHH----hcCCHHHHHcCCHHHHhc
Confidence 3689999999999999988766644333333 355567 999999998886 678899998543 5888
Q ss_pred hhhccccchhhhccCcCHHHH
Q 009281 331 SQRLGLKYFDDIKTRIPRHEV 351 (538)
Q Consensus 331 ~q~~Glk~~ed~~~~i~r~ea 351 (538)
..++|-...+.+..-+.-.+.
T Consensus 525 i~gIG~~~a~si~~~f~~~~~ 545 (562)
T PRK08097 525 LPGIGEGRARQLIAFLQHPEV 545 (562)
T ss_pred CCCchHHHHHHHHHHHcCHHH
Confidence 888998777777665544443
No 91
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=87.78 E-value=1.4 Score=45.68 Aligned_cols=96 Identities=18% Similarity=0.315 Sum_probs=62.7
Q ss_pred CCCcHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHH
Q 009281 207 PDLNKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFE 286 (538)
Q Consensus 207 ~~~N~~ia~~L~~la~~~e~~g~~~r~~aY~rAa~~l~~l~~~i~~~~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~ 286 (538)
+.=|+.|++.++.+.+- |.-. +.....+.+|.. ..+|..+||+|++-..+..+.+- +..+++|+
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 56689999887666432 2211 444555667766 67899999999954444433333 66677776
Q ss_pred hhchhHHHHHHhhccCCCHHHHHHHHHhCCCCHHH
Q 009281 287 KDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDD 321 (538)
Q Consensus 287 ~~~~~~~l~lf~~I~GvGpktA~~l~~~Girtled 321 (538)
.... .-.+.+++|+|.|.+.+|++..-...+.
T Consensus 123 ~a~~---~~~~~~l~GfG~kse~~il~~i~~~~~~ 154 (326)
T COG1796 123 EALE---NGKIRGLRGFGKKSEAKILENIEFAEES 154 (326)
T ss_pred HHHH---hCCccccCCccchhHHHHHHHHHHHhhh
Confidence 5433 3346699999999999999864443333
No 92
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=87.73 E-value=0.36 Score=49.92 Aligned_cols=29 Identities=38% Similarity=0.597 Sum_probs=26.4
Q ss_pred hhccCCCHHHHHHHHHhCCCCHHHHhhcc
Q 009281 298 GEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (538)
Q Consensus 298 ~~I~GvGpktA~~l~~~GirtledL~~~~ 326 (538)
..+||||++++++|++.||.|++||....
T Consensus 2 ~~i~gig~~~~~~L~~~Gi~ti~dl~~~~ 30 (310)
T TIGR02236 2 EDLPGVGPATAEKLREAGYDTFEAIAVAS 30 (310)
T ss_pred cccCCCCHHHHHHHHHcCCCCHHHHHcCC
Confidence 47999999999999999999999998653
No 93
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=87.56 E-value=0.27 Score=57.06 Aligned_cols=54 Identities=15% Similarity=0.332 Sum_probs=41.9
Q ss_pred hHHHHHHhh--ccCCCHHHHHHHHHh-CCCCHHHHhhcc-Ccchhhhccccchhhhcc
Q 009281 291 VRTISLFGE--VWGIGPATAQKLYEK-GHRTLDDLKNED-SLTHSQRLGLKYFDDIKT 344 (538)
Q Consensus 291 ~~~l~lf~~--I~GvGpktA~~l~~~-GirtledL~~~~-~L~~~q~~Glk~~ed~~~ 344 (538)
..++..|.+ ++||||++|+++|+. |.++++-|.++. +|...+++|.+..+.|..
T Consensus 78 ~~i~~yL~s~~~~GIG~~~A~~iv~~fg~~~~~~i~~~~~~L~~v~gi~~~~~~~i~~ 135 (720)
T TIGR01448 78 EGIVAYLSSRSIKGVGKKLAQRIVKTFGEAAFDVLDDDPEKLLEVPGISKANLEKFVS 135 (720)
T ss_pred HHHHHHHhcCCCCCcCHHHHHHHHHHhCHhHHHHHHhCHHHHhcCCCCCHHHHHHHHH
Confidence 345555543 999999999999998 999999998653 577778888766666654
No 94
>KOG1929 consensus Nucleotide excision repair factor NEF2, RAD4/CUT5 component [Replication, recombination and repair]
Probab=87.51 E-value=0.7 Score=53.71 Aligned_cols=93 Identities=11% Similarity=0.160 Sum_probs=69.6
Q ss_pred CCCCCCCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHhhhccCCccccccchH
Q 009281 12 ALDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWL 91 (538)
Q Consensus 12 ~~~~~~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~~~~~~~~~~l~~~~~~~~~~~lV~~~Wl 91 (538)
..-....|.+|++++ ......+++.+.+.+...|+.+...+-...||||.-......... ...+..-+|+++||
T Consensus 487 ~~~l~~~~e~~~~~~--s~~~~~~~e~ln~~~~~~gas~~~~f~r~~~~l~~~~~k~s~~~~----~~kw~ip~vT~~wL 560 (811)
T KOG1929|consen 487 AAALSQPFENLTISN--SQSAEAEREKLNNLANDLGASNVKTFTRKSTTLLTTSAKGSKYEI----AGKWSIPIVTPDWL 560 (811)
T ss_pred hhcccccccCceEEe--eechHHHHHHHhHhhhhccccccceeeecccEEeccccccchhhh----ccccCCCccChhHH
Confidence 344557799999988 444457789999999999999999996666999974421111111 11223678999999
Q ss_pred HHHHhcCcccCcccccccc
Q 009281 92 EDSLRLGEKVSEDLYRIKL 110 (538)
Q Consensus 92 ~ecik~g~lv~e~~y~l~~ 110 (538)
.+|.++++.++.+.|....
T Consensus 561 ~e~~rq~~~~~~e~~l~~~ 579 (811)
T KOG1929|consen 561 YECVRQNKGERNEGFLNGN 579 (811)
T ss_pred HhhccccCcccceeecccc
Confidence 9999999999999998754
No 95
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=87.23 E-value=0.75 Score=52.77 Aligned_cols=61 Identities=15% Similarity=0.217 Sum_probs=40.0
Q ss_pred cccchhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhh--chhHHHHHHhhccCCCHHHHHHHHH
Q 009281 249 KIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKD--EKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 249 ~i~~~~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~--~~~~~l~lf~~I~GvGpktA~~l~~ 313 (538)
++...=-..+||+||.+.|+.|.. ..+..++++.+. .+....+.|++|+|||+++|..+++
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 333444467899999999998773 122334444321 0112455677999999999999986
No 96
>KOG0323 consensus TFIIF-interacting CTD phosphatases, including NLI-interacting factor [Transcription]
Probab=87.13 E-value=0.26 Score=55.61 Aligned_cols=91 Identities=23% Similarity=0.307 Sum_probs=63.3
Q ss_pred CCCcCcEEEEe---cCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHhhhccCCccccccchHHH
Q 009281 17 GIFAGMRVFLV---EKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLED 93 (538)
Q Consensus 17 ~~F~g~~iy~~---~~~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~~~~~~~~~~l~~~~~~~~~~~lV~~~Wl~e 93 (538)
..+++|.+.|. |.++...+.+++ ..+.+.|+.+....+..+||+|+.+...... .+.. ... ..+||...|+..
T Consensus 440 ~v~~~~~~vfSg~~P~~~~~~~s~~~-~~~~~~g~vs~~~~~~~~th~i~~~~gt~k~-~~a~-~~~-~~~Vv~~~wl~~ 515 (635)
T KOG0323|consen 440 KVLKGSQIVFSGLHPTGSTDESADIL-GVAQQLGAVSAPDVSDKTTHLIAANAGTKKV-YKAV-VSG-SAKVVNAAWLWR 515 (635)
T ss_pred HHhhccceeecccccCcCCcchhhhh-hhhhcccceecccccchhhhHHhhccCccee-eccc-ccc-ceeEechhHHHH
Confidence 56677777664 334443444444 5677889999999999999999977642211 1111 111 278999999999
Q ss_pred HHhcCcccCccccccccC
Q 009281 94 SLRLGEKVSEDLYRIKLD 111 (538)
Q Consensus 94 cik~g~lv~e~~y~l~~~ 111 (538)
|+..+..|++..|.+...
T Consensus 516 ~~e~w~~v~ek~~~l~~~ 533 (635)
T KOG0323|consen 516 SLEKWGKVEEKLEPLDDD 533 (635)
T ss_pred HHHHhcchhccccccccc
Confidence 999999999988877543
No 97
>TIGR00588 ogg 8-oxoguanine DNA-glycosylase (ogg). All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is distantly realted to the Nth-MutY superfamily.
Probab=86.82 E-value=1.6 Score=45.47 Aligned_cols=63 Identities=19% Similarity=0.254 Sum_probs=40.4
Q ss_pred hhcCCCCCCHHHHHHHHHHH---HhCC--cchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHhCCCCH
Q 009281 255 QVKGLPGIGKSMQDHIQEIV---TTGK--LSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTL 319 (538)
Q Consensus 255 ~l~~lpgiG~~ia~~I~Eil---~tG~--~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~Girtl 319 (538)
+|..+ |+|-+ |+-|.++. ..|. ...++++..-....+.+.|++++||||+||.-+--.|+.-.
T Consensus 177 ~Lr~~-G~g~R-a~~I~~~A~~i~~~~~~~~~l~~l~~~~~~~~~~~L~~l~GIG~~tAd~vll~~l~~~ 244 (310)
T TIGR00588 177 HLRKL-GLGYR-ARYIRETARALLEEQGGRAWLQQIRGASYEDAREALCELPGVGPKVADCICLMGLDKP 244 (310)
T ss_pred HHHHc-CCHHH-HHHHHHHHHHHHhccCCchhHHhhccCChHHHHHHHHhCCCccHHHHHHHHHHhCCCC
Confidence 45554 66765 45454433 3443 33466775544556889999999999999998765455433
No 98
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=86.46 E-value=0.47 Score=33.28 Aligned_cols=16 Identities=56% Similarity=0.742 Sum_probs=14.3
Q ss_pred hccCCCHHHHHHHHHh
Q 009281 299 EVWGIGPATAQKLYEK 314 (538)
Q Consensus 299 ~I~GvGpktA~~l~~~ 314 (538)
.|+|||+|||.+|.++
T Consensus 20 Gv~giG~ktA~~ll~~ 35 (36)
T smart00279 20 GVKGIGPKTALKLLRE 35 (36)
T ss_pred CCCcccHHHHHHHHHh
Confidence 7999999999999764
No 99
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=86.21 E-value=0.64 Score=37.99 Aligned_cols=28 Identities=39% Similarity=0.539 Sum_probs=22.8
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009281 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~ 325 (538)
+..|+|||||||.+|..+ +.|++.+...
T Consensus 24 i~gv~giG~k~A~~ll~~-~~~~~~~~~~ 51 (75)
T cd00080 24 IPGVPGIGPKTALKLLKE-YGSLENLLEN 51 (75)
T ss_pred CCCCCcccHHHHHHHHHH-hCCHHHHHHH
Confidence 347999999999999986 5588888753
No 100
>PRK01172 ski2-like helicase; Provisional
Probab=85.54 E-value=1 Score=51.71 Aligned_cols=39 Identities=26% Similarity=0.488 Sum_probs=32.6
Q ss_pred HhhchhHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009281 286 EKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 286 ~~~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~ 325 (538)
..-.+...+.|+ +|||+|...|+++|+.|++|+.||...
T Consensus 604 ~~gv~~~~~~L~-~ip~~~~~~a~~l~~~g~~~~~di~~~ 642 (674)
T PRK01172 604 KEGIREDLIDLV-LIPKVGRVRARRLYDAGFKTVDDIARS 642 (674)
T ss_pred HcCCCHHHHhhc-CCCCCCHHHHHHHHHcCCCCHHHHHhC
Confidence 334455567777 899999999999999999999999854
No 101
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=85.07 E-value=1 Score=44.62 Aligned_cols=50 Identities=22% Similarity=0.430 Sum_probs=36.8
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009281 255 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 255 ~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (538)
-|..||||+|.=|..+- . ++.-|+.+-+ .....|.+|+|+||.+|+++|+
T Consensus 196 ~Lt~i~~VnKtda~~LL---~--~FgsLq~~~~----AS~~ele~~~G~G~~kak~l~~ 245 (254)
T KOG2841|consen 196 FLTTIPGVNKTDAQLLL---Q--KFGSLQQISN----ASEGELEQCPGLGPAKAKRLHK 245 (254)
T ss_pred HHHhCCCCCcccHHHHH---H--hcccHHHHHh----cCHhHHHhCcCcCHHHHHHHHH
Confidence 37899999998776543 2 4555555543 2455677999999999999997
No 102
>PRK03352 DNA polymerase IV; Validated
Probab=85.00 E-value=0.66 Score=48.79 Aligned_cols=29 Identities=38% Similarity=0.717 Sum_probs=26.2
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009281 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~ 325 (538)
+..+||||++++++|...||+|+.||.+-
T Consensus 179 l~~l~gig~~~~~~L~~~Gi~ti~dl~~l 207 (346)
T PRK03352 179 TDALWGVGPKTAKRLAALGITTVADLAAA 207 (346)
T ss_pred HHHcCCCCHHHHHHHHHcCCccHHHHhcC
Confidence 35789999999999999999999999864
No 103
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=84.92 E-value=1.4 Score=37.71 Aligned_cols=47 Identities=11% Similarity=0.254 Sum_probs=37.2
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCC
Q 009281 253 ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGI 303 (538)
Q Consensus 253 ~~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~Gv 303 (538)
+.+|..|||||+++++-...| -+..+++|+...|....+-++.+-|.
T Consensus 11 ~~~L~~iP~IG~a~a~DL~~L----Gi~s~~~L~g~dP~~Ly~~lc~~~G~ 57 (93)
T PF11731_consen 11 LSDLTDIPNIGKATAEDLRLL----GIRSPADLKGRDPEELYERLCALTGQ 57 (93)
T ss_pred HHHHhcCCCccHHHHHHHHHc----CCCCHHHHhCCCHHHHHHHHHHHcCC
Confidence 578999999999999877643 35677888888888887777776664
No 104
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=84.85 E-value=2.1 Score=48.32 Aligned_cols=52 Identities=17% Similarity=0.142 Sum_probs=38.8
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~ 314 (538)
..|.+|||||+....++-. ++..++++++ -+++.+.+|+|++.+.|+.+|+.
T Consensus 514 s~L~~I~GiG~kr~~~LL~-----~Fgs~~~I~~----As~eeL~~v~gi~~~~A~~I~~~ 565 (574)
T PRK14670 514 LNYTKIKGIGEKKAKKILK-----SLGTYKDILL----LNEDEIAEKMKINIKMAKKIKKF 565 (574)
T ss_pred cccccCCCCCHHHHHHHHH-----HhCCHHHHHh----CCHHHHHhCCCCCHHHHHHHHHH
Confidence 3789999999998877654 2344555543 24666789999999999999863
No 105
>PRK08609 hypothetical protein; Provisional
Probab=84.68 E-value=1.2 Score=50.42 Aligned_cols=54 Identities=17% Similarity=0.228 Sum_probs=38.4
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHH
Q 009281 252 SADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKL 311 (538)
Q Consensus 252 ~~~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l 311 (538)
.+.++.+|||||++.+.++.+-+---++.+|+....+- + +..++|+|+|+.+.+
T Consensus 86 ~~~~l~~i~GiGpk~a~~l~~~lGi~tl~~L~~a~~~~-----~-~~~~~gfg~k~~~~i 139 (570)
T PRK08609 86 GLLPLLKLPGLGGKKIAKLYKELGVVDKESLKEACENG-----K-VQALAGFGKKTEEKI 139 (570)
T ss_pred HHHHHhcCCCCCHHHHHHHHHHhCCCCHHHHHHHHHhC-----C-hhhccCcchhHHHHH
Confidence 35578899999999999888655544555555432211 1 347999999999888
No 106
>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=83.91 E-value=4.7 Score=36.47 Aligned_cols=46 Identities=33% Similarity=0.509 Sum_probs=32.1
Q ss_pred CeEEEecccccccCCcC--CCeeEEEecCCcc-----hhhhhHHHHHHHHHHc
Q 009281 368 EVIILCGGSYRRGKASC--GDLDVVIMHPDRK-----SHKGFLSKYVKKLKEM 413 (538)
Q Consensus 368 ~~~v~~~Gs~RRgke~~--~DvDiLIt~~~~~-----~~~~~l~~~v~~L~~~ 413 (538)
...+.+.|||.||...- .|||++|..+... ....++..+-+.|.+.
T Consensus 27 ~~~~~~~GS~a~~T~i~~~sDiD~~v~~~~~~~~~~~~~~~~~~~l~~~L~~~ 79 (143)
T cd05400 27 VAEVFLQGSYARGTALRGDSDIDLVVVLPDDTSFAEYGPAELLDELGEALKEY 79 (143)
T ss_pred ccEEEEEcceeCCCCCCCCCceeEEEEEcCcccccccCHHHHHHHHHHHHHHh
Confidence 35788999999998754 8999999655432 2345566666655554
No 107
>PRK03858 DNA polymerase IV; Validated
Probab=83.64 E-value=0.8 Score=49.05 Aligned_cols=29 Identities=38% Similarity=0.724 Sum_probs=26.0
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009281 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~ 325 (538)
+..+||||++++++|.+.||+|+.||.+-
T Consensus 175 l~~l~Gig~~~~~~L~~~Gi~t~~dl~~l 203 (396)
T PRK03858 175 VRRLWGVGPVTAAKLRAHGITTVGDVAEL 203 (396)
T ss_pred hhhcCCCCHHHHHHHHHhCCCcHHHHhcC
Confidence 45789999999999999999999999853
No 108
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=83.25 E-value=1 Score=28.97 Aligned_cols=20 Identities=30% Similarity=0.573 Sum_probs=17.2
Q ss_pred hhcCCCCCCHHHHHHHHHHH
Q 009281 255 QVKGLPGIGKSMQDHIQEIV 274 (538)
Q Consensus 255 ~l~~lpgiG~~ia~~I~Eil 274 (538)
+|.+|||||+++|+.|.+..
T Consensus 2 ~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred hhhhCCCCCHHHHHHHHHhc
Confidence 57899999999999988643
No 109
>PRK01216 DNA polymerase IV; Validated
Probab=82.67 E-value=0.88 Score=48.23 Aligned_cols=30 Identities=33% Similarity=0.407 Sum_probs=26.5
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhcc
Q 009281 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (538)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~~ 326 (538)
+..+||||++++++|.+.||+|+.||.+-.
T Consensus 180 i~~l~giG~~~~~~L~~~Gi~TigdL~~~~ 209 (351)
T PRK01216 180 IADIPGIGDITAEKLKKLGVNKLVDTLRIE 209 (351)
T ss_pred cccccCCCHHHHHHHHHcCCCcHHHHhcCC
Confidence 457899999999999999999999998643
No 110
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=82.44 E-value=0.92 Score=49.19 Aligned_cols=29 Identities=38% Similarity=0.650 Sum_probs=26.2
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009281 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~ 325 (538)
+..+||||++++.+|.+.||+|+.||.+.
T Consensus 181 v~~l~GiG~~~~~~L~~lGi~TigdL~~~ 209 (422)
T PRK03609 181 VEEVWGVGRRISKKLNAMGIKTALDLADT 209 (422)
T ss_pred hhhcCCccHHHHHHHHHcCCCcHHHHhcC
Confidence 35899999999999999999999999854
No 111
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=82.24 E-value=0.97 Score=43.66 Aligned_cols=22 Identities=32% Similarity=0.551 Sum_probs=19.2
Q ss_pred hHHHHHHhhccCCCHHHHHHHH
Q 009281 291 VRTISLFGEVWGIGPATAQKLY 312 (538)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~ 312 (538)
.+.++.|.++||||||+|++|-
T Consensus 8 ~~LI~~l~kLPGvG~KsA~R~A 29 (198)
T COG0353 8 EKLIDALKKLPGVGPKSAQRLA 29 (198)
T ss_pred HHHHHHHhhCCCCChhHHHHHH
Confidence 3478889999999999999994
No 112
>COG1708 Predicted nucleotidyltransferases [General function prediction only]
Probab=82.21 E-value=5.9 Score=34.40 Aligned_cols=29 Identities=31% Similarity=0.568 Sum_probs=24.2
Q ss_pred CCeEEEecccccccCCcC-CCeeEEEecCC
Q 009281 367 PEVIILCGGSYRRGKASC-GDLDVVIMHPD 395 (538)
Q Consensus 367 p~~~v~~~Gs~RRgke~~-~DvDiLIt~~~ 395 (538)
....|.+-|||-||..+- +|||++|..++
T Consensus 25 ~~~~v~LfGS~arG~~~~~SDiDv~vv~~~ 54 (128)
T COG1708 25 GDLLIYLFGSYARGDFVKESDIDLLVVSDD 54 (128)
T ss_pred CCeEEEEEccCcccccccCCCeeEEEEcCC
Confidence 345789999999999876 99999998644
No 113
>PRK10880 adenine DNA glycosylase; Provisional
Probab=81.98 E-value=5.7 Score=42.15 Aligned_cols=65 Identities=18% Similarity=0.280 Sum_probs=42.7
Q ss_pred hHHHHHHHHHHHh-cCCccc-cchhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCC
Q 009281 232 RSFSYYKAIPVIE-KLPFKI-ESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGI 303 (538)
Q Consensus 232 r~~aY~rAa~~l~-~l~~~i-~~~~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~Gv 303 (538)
|++...+||..|. .....+ .+.++|.+|||||..+|+.|--|.-.-...-+ ...+.+.+.+++|+
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 322222 45689999999999999999877643222212 22355666666554
No 114
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=81.94 E-value=3.1 Score=46.94 Aligned_cols=51 Identities=24% Similarity=0.367 Sum_probs=38.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~ 314 (538)
..|.+|||||++...++-. ++.-++.+++ -.++.+.+| |||+++|+++++.
T Consensus 514 S~Ld~I~GiG~kr~~~Ll~-----~Fgs~~~ik~----As~eeL~~v-gi~~~~A~~I~~~ 564 (567)
T PRK14667 514 DILDKIKGIGEVKKEIIYR-----NFKTLYDFLK----ADDEELKKL-GIPPSVKQEVKKY 564 (567)
T ss_pred CccccCCCCCHHHHHHHHH-----HhCCHHHHHh----CCHHHHHHc-CCCHHHHHHHHHH
Confidence 5688999999998887654 2344555543 246667799 9999999999874
No 115
>PRK00227 glnD PII uridylyl-transferase; Provisional
Probab=81.38 E-value=4.1 Score=47.06 Aligned_cols=65 Identities=22% Similarity=0.320 Sum_probs=44.0
Q ss_pred HHHHHH-HHHHHHHHhhhcCCCeEEEecccccccC-CcCCCeeEEEecCCcchhhhhHHHHHHHHHHcCc
Q 009281 348 RHEVEQ-MERLLQKAGEEVLPEVIILCGGSYRRGK-ASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKF 415 (538)
Q Consensus 348 r~ea~~-i~~iv~~~~~~~~p~~~v~~~Gs~RRgk-e~~~DvDiLIt~~~~~~~~~~l~~~v~~L~~~g~ 415 (538)
|++|.+ ...+++.+. +.+++-+..+|||=||. .--+|||+||-|++... ..++..++.-|=+.|+
T Consensus 8 ~~~~~~~~~~~~~~~~--~~~~~aLvAvGGYGR~EL~P~SDIDLLiL~~~~~~-~~~i~~~~~~LWD~gL 74 (693)
T PRK00227 8 REDAEASALALLGSLQ--LPPGTALAATGSLARREMTPYSDLDLILLHPPGAT-PDGVEDLWYPIWDAKK 74 (693)
T ss_pred HHHHHHHHHHHHHhcC--CCCCeEEEEeccccccCcCCCcCceEEEEeCCccc-HHHHHHHHHHHHhcCC
Confidence 445544 455666543 23566788899996654 55689999999985432 5667777777777765
No 116
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=81.28 E-value=6.1 Score=40.71 Aligned_cols=47 Identities=23% Similarity=0.319 Sum_probs=32.8
Q ss_pred HHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHhCCC
Q 009281 270 IQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHR 317 (538)
Q Consensus 270 I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~Gir 317 (538)
|.+.+..|.+. ++.+..-....+++.|++|+||||.||+..--.|..
T Consensus 174 ~A~~~~~g~~~-~~~l~~~~~e~a~e~L~~i~GIG~WTAe~~llf~lg 220 (285)
T COG0122 174 LARAAAEGELD-LSELKPLSDEEAIEELTALKGIGPWTAEMFLLFGLG 220 (285)
T ss_pred HHHHHHcCCcc-HHHhccCCHHHHHHHHHcCCCcCHHHHHHHHHHcCC
Confidence 44555677633 334444445679999999999999999988654443
No 117
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=81.11 E-value=0.79 Score=52.42 Aligned_cols=46 Identities=30% Similarity=0.477 Sum_probs=34.6
Q ss_pred HHHhhccCCCHHHHHHHHHh-CCCCHHHHhhcc--Ccchhhhccccchhhh
Q 009281 295 SLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED--SLTHSQRLGLKYFDDI 342 (538)
Q Consensus 295 ~lf~~I~GvGpktA~~l~~~-GirtledL~~~~--~L~~~q~~Glk~~ed~ 342 (538)
..|..||||||+++++|++. | |+++|.++. .|....++|.+..+.|
T Consensus 637 s~L~~IPGIGpkr~k~LL~~FG--Sle~I~~AS~eELa~V~Gig~k~Ae~I 685 (694)
T PRK14666 637 GELQRVEGIGPATARLLWERFG--SLQAMAAAGEEGLAAVPGIGPARAAAL 685 (694)
T ss_pred hHHhhCCCCCHHHHHHHHHHhC--CHHHHHhcCHHHHHhcCCcCHHHHHHH
Confidence 34669999999999999997 6 999999753 3666666665554444
No 118
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=80.81 E-value=4.5 Score=36.94 Aligned_cols=26 Identities=15% Similarity=0.089 Sum_probs=20.4
Q ss_pred HHHHHHhhccCCCHHHHHHHHHhCCC
Q 009281 292 RTISLFGEVWGIGPATAQKLYEKGHR 317 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~~Gir 317 (538)
..++.|++++||||+||..+--.|+.
T Consensus 69 ~~~~~L~~l~GIG~~tA~~~l~~~~~ 94 (149)
T smart00478 69 DDREELLKLPGVGRKTANAVLSFALG 94 (149)
T ss_pred HHHHHHHcCCCCcHHHHHHHHHHHCC
Confidence 35666779999999999988766544
No 119
>smart00475 53EXOc 5'-3' exonuclease.
Probab=80.70 E-value=1.2 Score=45.10 Aligned_cols=26 Identities=38% Similarity=0.592 Sum_probs=22.3
Q ss_pred hhccCCCHHHHHHHHHh-CCCCHHHHhhc
Q 009281 298 GEVWGIGPATAQKLYEK-GHRTLDDLKNE 325 (538)
Q Consensus 298 ~~I~GvGpktA~~l~~~-GirtledL~~~ 325 (538)
-+|+|||||||.+|.++ | |++.+.+.
T Consensus 189 pGV~GIG~KtA~~Ll~~yg--sle~i~~~ 215 (259)
T smart00475 189 PGVPGIGEKTAAKLLKEFG--SLENILEN 215 (259)
T ss_pred CCCCCCCHHHHHHHHHHhC--CHHHHHHH
Confidence 46899999999999987 7 99998753
No 120
>PF01367 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases. The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include: Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins []. 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [, ]. Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases []. Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair []. ; GO: 0003677 DNA binding, 0003824 catalytic activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B.
Probab=80.61 E-value=0.13 Score=44.64 Aligned_cols=24 Identities=46% Similarity=0.753 Sum_probs=19.5
Q ss_pred hccCCCHHHHHHHHHh-CCCCHHHHhh
Q 009281 299 EVWGIGPATAQKLYEK-GHRTLDDLKN 324 (538)
Q Consensus 299 ~I~GvGpktA~~l~~~-GirtledL~~ 324 (538)
.|+|||||||.+|.++ | |||.+..
T Consensus 22 GV~GIG~KtA~~LL~~yg--sle~i~~ 46 (101)
T PF01367_consen 22 GVPGIGPKTAAKLLQEYG--SLENILA 46 (101)
T ss_dssp --TTSTCHCCCCCHHHHT--SCHCCCC
T ss_pred CCCCCCHHHHHHHHHHcC--CHHHHHH
Confidence 7999999999999987 6 8888774
No 121
>PRK09482 flap endonuclease-like protein; Provisional
Probab=80.47 E-value=1.3 Score=44.96 Aligned_cols=25 Identities=32% Similarity=0.613 Sum_probs=22.1
Q ss_pred hccCCCHHHHHHHHHh-CCCCHHHHhhc
Q 009281 299 EVWGIGPATAQKLYEK-GHRTLDDLKNE 325 (538)
Q Consensus 299 ~I~GvGpktA~~l~~~-GirtledL~~~ 325 (538)
.|+|||||||.+|.++ | |++.+.+.
T Consensus 186 GVpGIG~KtA~~LL~~~g--sle~i~~~ 211 (256)
T PRK09482 186 GVAGIGPKSAAELLNQFR--SLENIYES 211 (256)
T ss_pred CCCCcChHHHHHHHHHhC--CHHHHHHh
Confidence 6899999999999997 7 99998853
No 122
>cd01703 PolY_Pol_iota DNA Polymerase iota. Pol iota, also called Rad30B, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol iota is thought to be one of the least efficient polymerases, particularly when opposite pyrimidines; it can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine, and prefers to insert guanosine instead of adenosine opposite thymidine. Pol iota is believed to use Hoogsteen rather than Watson-Crick base pairing, which may explain the varying efficiency for different template nucleotides.
Probab=80.43 E-value=1.1 Score=47.92 Aligned_cols=30 Identities=33% Similarity=0.431 Sum_probs=26.7
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhcc
Q 009281 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (538)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~~ 326 (538)
+..+||||++++++|.+.||.|+.||.+..
T Consensus 174 v~~l~GiG~~~~~kL~~~GI~tigdl~~~~ 203 (379)
T cd01703 174 LRKIPGIGYKTAAKLEAHGISSVRDLQEFS 203 (379)
T ss_pred ccccCCcCHHHHHHHHHcCCCcHHHHHhCC
Confidence 458899999999999999999999998543
No 123
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=80.40 E-value=1.6 Score=37.09 Aligned_cols=55 Identities=27% Similarity=0.533 Sum_probs=41.8
Q ss_pred HHHHHHhhccCCCHHHHHHHHHh-CCCCHHHHhhcc-Ccch-hhhccccchhhhccCcC
Q 009281 292 RTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED-SLTH-SQRLGLKYFDDIKTRIP 347 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~~-GirtledL~~~~-~L~~-~q~~Glk~~ed~~~~i~ 347 (538)
.++..| .-+|++++.|.++|+. |-.+++-|+++. .|.. ..++|++..+.+..++.
T Consensus 10 ~~~~~L-~~~gl~~~~a~kl~~~yg~~ai~~l~~nPY~L~~~i~gi~F~~aD~iA~~~g 67 (94)
T PF14490_consen 10 ELMAFL-QEYGLSPKLAMKLYKKYGDDAIEILKENPYRLIEDIDGIGFKTADKIALKLG 67 (94)
T ss_dssp HHHHHH-HHTT--HHHHHHHHHHH-TTHHHHHHH-STCCCB-SSSSBHHHHHHHHHTTT
T ss_pred HHHHHH-HHcCCCHHHHHHHHHHHhHHHHHHHHHChHHHHHHccCCCHHHHHHHHHHcC
Confidence 355666 8999999999999998 999998888764 5655 88999999999877653
No 124
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=80.38 E-value=0.67 Score=51.97 Aligned_cols=64 Identities=17% Similarity=0.201 Sum_probs=48.5
Q ss_pred hhccCCCHHHHHHHHHhC-CCCHHHHhh--ccCcchhhhccccchhhhccCcCHHHHHHHHHHHHHH
Q 009281 298 GEVWGIGPATAQKLYEKG-HRTLDDLKN--EDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKA 361 (538)
Q Consensus 298 ~~I~GvGpktA~~l~~~G-irtledL~~--~~~L~~~q~~Glk~~ed~~~~i~r~ea~~i~~iv~~~ 361 (538)
++|-|+|++++.+|++.| ++++.||.+ ...|..+.+||-+..+.+...|-.+.-..+..++-.+
T Consensus 428 mdI~GlGe~~i~~L~~~G~i~~~~Diy~L~~~~l~~l~gfgeks~~nll~aIe~sk~~~l~r~l~aL 494 (562)
T PRK08097 428 LGLDGIGEGTWRALHQTGLFEHLFSWLALTPEQLANTPGIGKARAEQLWHQFNLARQQPFSRWLKAL 494 (562)
T ss_pred cCCCCcCHHHHHHHHHcCCcCCHHHHhcCCHHHHhcCcCccHHHHHHHHHHHHHHcCCCHHHHHHHc
Confidence 489999999999999997 599999984 3467778889988888887665544433455555554
No 125
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=80.36 E-value=2.7 Score=48.14 Aligned_cols=66 Identities=24% Similarity=0.292 Sum_probs=44.6
Q ss_pred HHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHH
Q 009281 233 SFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLY 312 (538)
Q Consensus 233 ~~aY~rAa~~l~~l~~~i~~~~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~ 312 (538)
+..|.|-.+.=..+ -..|..|||||++.+.++.+- -| -++.+.+. ..+.+.+|+|+|+++|+.++
T Consensus 622 Ai~~hR~~r~k~~~------~s~L~~IPGIGpkr~k~LL~~--FG---Sle~I~~A----S~eELa~V~Gig~k~Ae~I~ 686 (694)
T PRK14666 622 AIGRHRRARAGAAL------TGELQRVEGIGPATARLLWER--FG---SLQAMAAA----GEEGLAAVPGIGPARAAALH 686 (694)
T ss_pred HHHHHHHHHHhhhh------HhHHhhCCCCCHHHHHHHHHH--hC---CHHHHHhc----CHHHHHhcCCcCHHHHHHHH
Confidence 45665554432222 257999999999998887663 34 44555442 23446789999999999998
Q ss_pred H
Q 009281 313 E 313 (538)
Q Consensus 313 ~ 313 (538)
+
T Consensus 687 ~ 687 (694)
T PRK14666 687 E 687 (694)
T ss_pred H
Confidence 6
No 126
>PRK01810 DNA polymerase IV; Validated
Probab=80.10 E-value=1.3 Score=47.76 Aligned_cols=29 Identities=45% Similarity=0.691 Sum_probs=25.9
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009281 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~ 325 (538)
+..+||||++++.+|...||+|+.||.+.
T Consensus 181 v~~l~giG~~~~~~L~~~Gi~tigdL~~~ 209 (407)
T PRK01810 181 VGEMHGIGEKTAEKLKDIGIQTIGDLAKA 209 (407)
T ss_pred HhhcCCcCHHHHHHHHHcCCCcHHHHHhC
Confidence 45789999999999999999999999853
No 127
>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=79.91 E-value=1.3 Score=47.82 Aligned_cols=30 Identities=27% Similarity=0.328 Sum_probs=26.8
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhcc
Q 009281 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (538)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~~ 326 (538)
+..|||||++++++|-+.||+|+.||.+..
T Consensus 224 v~~l~GIG~~~~~~L~~~Gi~t~~dl~~~~ 253 (404)
T cd01701 224 VGDLPGVGSSLAEKLVKLFGDTCGGLELRS 253 (404)
T ss_pred HhHhCCCCHHHHHHHHHcCCcchHHHHhCc
Confidence 357899999999999999999999998643
No 128
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=79.69 E-value=2.9 Score=44.15 Aligned_cols=60 Identities=22% Similarity=0.338 Sum_probs=38.6
Q ss_pred cCCccccch--hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009281 245 KLPFKIESA--DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 245 ~l~~~i~~~--~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (538)
.++.+|... -=|.++|+|++.+|+.+-+ +-|+ |..+.+- ..+.|.+|+|||+++|+.+.+
T Consensus 276 ~ld~~v~prGyRiLs~IPrl~k~iAk~Ll~--~FGS---L~~Il~A----s~eeL~~VeGIGe~rA~~I~e 337 (352)
T PRK13482 276 ALDTPVSPRGYRLLSKIPRLPSAVIENLVE--HFGS---LQGLLAA----SIEDLDEVEGIGEVRARAIRE 337 (352)
T ss_pred ccccccCCcHHHHHhcCCCCCHHHHHHHHH--HcCC---HHHHHcC----CHHHHhhCCCcCHHHHHHHHH
Confidence 344555543 3578899999988887654 2244 3443332 244577899999999988544
No 129
>PRK14976 5'-3' exonuclease; Provisional
Probab=79.65 E-value=1.4 Score=45.38 Aligned_cols=24 Identities=46% Similarity=0.753 Sum_probs=21.3
Q ss_pred hccCCCHHHHHHHHHh-CCCCHHHHhh
Q 009281 299 EVWGIGPATAQKLYEK-GHRTLDDLKN 324 (538)
Q Consensus 299 ~I~GvGpktA~~l~~~-GirtledL~~ 324 (538)
+|||||||||.+|.++ | |++++.+
T Consensus 195 GVpGIG~KtA~~LL~~~g--sle~i~~ 219 (281)
T PRK14976 195 GVKGIGPKTAIKLLNKYG--NIENIYE 219 (281)
T ss_pred CCCcccHHHHHHHHHHcC--CHHHHHH
Confidence 5899999999999976 6 9999875
No 130
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=79.50 E-value=3.5 Score=46.88 Aligned_cols=52 Identities=23% Similarity=0.476 Sum_probs=38.6
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~ 314 (538)
..|.+|||||+..+.+|.+.. |+ ++.+.+. ..+.+.+|+|||+++|+.+++.
T Consensus 543 s~L~~IpGIG~k~~k~Ll~~F--gS---~~~i~~A----s~eeL~~v~Gig~~~A~~I~~~ 594 (598)
T PRK00558 543 SALDDIPGIGPKRRKALLKHF--GS---LKAIKEA----SVEELAKVPGISKKLAEAIYEA 594 (598)
T ss_pred hhHhhCCCcCHHHHHHHHHHc--CC---HHHHHhC----CHHHHhhcCCcCHHHHHHHHHH
Confidence 568999999999999877643 44 4444432 2344679999999999999863
No 131
>cd01700 PolY_Pol_V_umuC umuC subunit of DNA Polymerase V. umuC subunit of Pol V. Pol V is a bacterial translesion synthesis (TLS) polymerase that consists of the heterotrimer of one umuC and two umuD subunits. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol V, RecA, single stranded DNA-binding protein, beta sliding clamp, and gamma clamp loading complex are responsible for inducing the SOS response in bacteria to repair UV-induced DNA damage.
Probab=79.42 E-value=1.3 Score=46.43 Aligned_cols=29 Identities=48% Similarity=0.792 Sum_probs=25.9
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009281 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~ 325 (538)
+..+||||++++++|.+.||+|+.||.+-
T Consensus 178 l~~l~gig~~~~~~L~~~Gi~ti~dL~~~ 206 (344)
T cd01700 178 VGDVWGIGRRTAKKLNAMGIHTAGDLAQA 206 (344)
T ss_pred hhhcCccCHHHHHHHHHcCCCcHHHHhcC
Confidence 35789999999999999999999999863
No 132
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=79.27 E-value=1.2 Score=41.24 Aligned_cols=27 Identities=15% Similarity=0.004 Sum_probs=22.7
Q ss_pred hHHHHHHhhccCCCHHHHHHHHHhCCC
Q 009281 291 VRTISLFGEVWGIGPATAQKLYEKGHR 317 (538)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~Gir 317 (538)
..+.+.|++++||||+||..+--.++.
T Consensus 79 ~~~~~~L~~l~GIG~~tA~~~l~~~~~ 105 (158)
T cd00056 79 PDAREELLALPGVGRKTANVVLLFALG 105 (158)
T ss_pred cccHHHHHcCCCCCHHHHHHHHHHHCC
Confidence 457888889999999999998776555
No 133
>PRK02406 DNA polymerase IV; Validated
Probab=79.16 E-value=1.3 Score=46.44 Aligned_cols=29 Identities=34% Similarity=0.409 Sum_probs=26.1
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009281 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~ 325 (538)
+..+||||++++++|-+.||+|+.||.+-
T Consensus 170 i~~l~giG~~~~~~L~~~Gi~ti~dl~~l 198 (343)
T PRK02406 170 VEKIPGVGKVTAEKLHALGIYTCADLQKY 198 (343)
T ss_pred cchhcCCCHHHHHHHHHcCCCcHHHHHhC
Confidence 45889999999999988899999999864
No 134
>PRK03348 DNA polymerase IV; Provisional
Probab=79.13 E-value=1.3 Score=48.68 Aligned_cols=29 Identities=41% Similarity=0.728 Sum_probs=26.1
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009281 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~ 325 (538)
+..+||||++++++|.+.||+|+.||.+-
T Consensus 182 v~~L~GIG~~t~~~L~~lGI~TigDLa~l 210 (454)
T PRK03348 182 VRRLWGIGPVTEEKLHRLGIETIGDLAAL 210 (454)
T ss_pred ccccCCCCHHHHHHHHHcCCccHHHHhcC
Confidence 45889999999999999999999999853
No 135
>COG1746 CCA1 tRNA nucleotidyltransferase (CCA-adding enzyme) [Translation, ribosomal structure and biogenesis]
Probab=78.78 E-value=4.6 Score=43.55 Aligned_cols=49 Identities=27% Similarity=0.368 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHhhhcCCCeEEEecccccccCCcC--CCeeEEEecCCcchh
Q 009281 351 VEQMERLLQKAGEEVLPEVIILCGGSYRRGKASC--GDLDVVIMHPDRKSH 399 (538)
Q Consensus 351 a~~i~~iv~~~~~~~~p~~~v~~~Gs~RRgke~~--~DvDiLIt~~~~~~~ 399 (538)
++.+...+.+++.+...++.|.++|||.||--.. +|||+-|.-|...+.
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 3444445555555556788999999999997665 789999988877543
No 136
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=78.51 E-value=2.1 Score=44.02 Aligned_cols=64 Identities=19% Similarity=0.224 Sum_probs=38.9
Q ss_pred hhhcCCCCCCHHHHHHHHHH---HHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHhCCCCHHH
Q 009281 254 DQVKGLPGIGKSMQDHIQEI---VTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDD 321 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Ei---l~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~Girtled 321 (538)
++|..+ |++..=++-|.++ +..|.+.. +... ....+++.|++|+||||+||..+--.|+.-.|-
T Consensus 167 ~eL~~~-Gl~~~Ra~~L~~lA~~i~~g~l~l-~~~~--~~~~~~~~L~~LpGIGpwTA~~vllr~lg~~D~ 233 (283)
T PRK10308 167 QALKAL-GMPLKRAEALIHLANAALEGTLPL-TIPG--DVEQAMKTLQTFPGIGRWTANYFALRGWQAKDV 233 (283)
T ss_pred HHHHHC-CCCHHHHHHHHHHHHHHHcCCCCc-cccC--CHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCC
Confidence 456555 7776444444443 34577652 2111 123477888899999999999876555554443
No 137
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=78.36 E-value=1.2 Score=43.53 Aligned_cols=51 Identities=24% Similarity=0.311 Sum_probs=36.5
Q ss_pred HHHHHHhhccCCCHHHHHHHHHh-CCCCHHHHhhc---cCcchhhhccccchhhh
Q 009281 292 RTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNE---DSLTHSQRLGLKYFDDI 342 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~~-GirtledL~~~---~~L~~~q~~Glk~~ed~ 342 (538)
..+..|.+|-|||||+|-.+..- ....|-+.... ..|++..++|-|..+.+
T Consensus 70 ~lF~~LisVnGIGpK~ALaiLs~~~~~~l~~aI~~~d~~~L~k~PGIGkKtAeri 124 (201)
T COG0632 70 ELFRLLISVNGIGPKLALAILSNLDPEELAQAIANEDVKALSKIPGIGKKTAERI 124 (201)
T ss_pred HHHHHHHccCCccHHHHHHHHcCCCHHHHHHHHHhcChHhhhcCCCCCHHHHHHH
Confidence 36777779999999999999764 44444444322 25889999998875544
No 138
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=78.11 E-value=4.3 Score=46.48 Aligned_cols=54 Identities=13% Similarity=0.182 Sum_probs=38.8
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHhCC
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGH 316 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~Gi 316 (538)
..|.+|||||+.-+.++-. ++..++.+++ -.++.+.+|+|||++.|+++|...-
T Consensus 608 s~L~~IpGiG~kr~~~LL~-----~FgS~~~i~~----As~eel~~v~gi~~~~A~~i~~~~~ 661 (691)
T PRK14672 608 LSFERLPHVGKVRAHRLLA-----HFGSFRSLQS----ATPQDIATAIHIPLTQAHTILHAAT 661 (691)
T ss_pred cccccCCCCCHHHHHHHHH-----HhcCHHHHHh----CCHHHHHhCCCCCHHHHHHHHHHhh
Confidence 4578999999988877644 2333444443 2456677999999999999998733
No 139
>PRK03103 DNA polymerase IV; Reviewed
Probab=78.05 E-value=1.6 Score=46.97 Aligned_cols=29 Identities=28% Similarity=0.543 Sum_probs=25.7
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009281 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~ 325 (538)
+..+||||++++++|.+.||+|+.||.+-
T Consensus 183 i~~l~gig~~~~~~L~~~Gi~tigdl~~~ 211 (409)
T PRK03103 183 VRKLFGVGSRMEKHLRRMGIRTIGQLANT 211 (409)
T ss_pred HhhcCCccHHHHHHHHHcCCCCHHHHhcC
Confidence 34789999999999998999999999853
No 140
>PRK02794 DNA polymerase IV; Provisional
Probab=77.85 E-value=1.5 Score=47.53 Aligned_cols=29 Identities=48% Similarity=0.950 Sum_probs=26.2
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009281 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~ 325 (538)
+..+||||++++++|.+.||+|+.||.+-
T Consensus 211 l~~L~GiG~~~~~~L~~~GI~tigdL~~l 239 (419)
T PRK02794 211 VGIIWGVGPATAARLARDGIRTIGDLQRA 239 (419)
T ss_pred hhhhCCCCHHHHHHHHHhccchHHHHhhC
Confidence 46899999999999999999999999853
No 141
>cd00424 PolY Y-family of DNA polymerases. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Most TLS polymerases are members of the Y-family, including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is found exclusively in bacteria. In eukaryotes, the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in ord
Probab=77.66 E-value=1.7 Score=45.68 Aligned_cols=28 Identities=32% Similarity=0.462 Sum_probs=25.5
Q ss_pred hhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009281 298 GEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 298 ~~I~GvGpktA~~l~~~GirtledL~~~ 325 (538)
..+||||++++++|.+.||+|+.||.+-
T Consensus 176 ~~l~giG~~~~~~L~~~Gi~ti~dl~~~ 203 (343)
T cd00424 176 TDLPGIGAVTAKRLEAVGINPIGDLLAA 203 (343)
T ss_pred hhcCCCCHHHHHHHHHcCCCcHHHHhcC
Confidence 4689999999999999999999999864
No 142
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=77.65 E-value=1.8 Score=43.39 Aligned_cols=27 Identities=33% Similarity=0.423 Sum_probs=22.6
Q ss_pred hhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009281 298 GEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 298 ~~I~GvGpktA~~l~~~GirtledL~~~ 325 (538)
-+|+|||||||.+|.++ +.|++++.+.
T Consensus 186 pGv~GiG~ktA~~Ll~~-~gsle~i~~~ 212 (240)
T cd00008 186 PGVPGIGEKTAAKLLKE-YGSLEGILEN 212 (240)
T ss_pred CCCCccCHHHHHHHHHH-hCCHHHHHHh
Confidence 36899999999999987 3499999854
No 143
>PRK14133 DNA polymerase IV; Provisional
Probab=77.44 E-value=1.6 Score=45.92 Aligned_cols=29 Identities=34% Similarity=0.512 Sum_probs=26.0
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009281 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~ 325 (538)
+..+||||++++++|.+.||+|+.||.+-
T Consensus 175 v~~l~gig~~~~~~L~~~Gi~ti~dl~~l 203 (347)
T PRK14133 175 ISKVHGIGKKSVEKLNNIGIYTIEDLLKL 203 (347)
T ss_pred ccccCCCCHHHHHHHHHcCCccHHHHhhC
Confidence 35789999999999999999999999864
No 144
>PRK07758 hypothetical protein; Provisional
Probab=77.40 E-value=1.1 Score=38.27 Aligned_cols=45 Identities=13% Similarity=0.280 Sum_probs=36.9
Q ss_pred ccCCCHHHHHHHHHhCCCCHHHHhh--ccCcchhhhccccchhhhcc
Q 009281 300 VWGIGPATAQKLYEKGHRTLDDLKN--EDSLTHSQRLGLKYFDDIKT 344 (538)
Q Consensus 300 I~GvGpktA~~l~~~GirtledL~~--~~~L~~~q~~Glk~~ed~~~ 344 (538)
.++++......|...||.|++||.. ...|..+++||-+..+.|.+
T Consensus 39 ~~~LSvRA~N~Lk~AGI~TL~dLv~~te~ELl~iknlGkKSL~EIke 85 (95)
T PRK07758 39 LSLLSAPARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRK 85 (95)
T ss_pred CccccHHHHHHHHHcCCCcHHHHHcCCHHHHHHccCCCHHHHHHHHH
Confidence 4688899999999999999999984 45688889999888776653
No 145
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=76.11 E-value=5.8 Score=38.17 Aligned_cols=25 Identities=16% Similarity=0.167 Sum_probs=20.3
Q ss_pred HHHHHHhhccCCCHHHHHHHHHhCC
Q 009281 292 RTISLFGEVWGIGPATAQKLYEKGH 316 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~~Gi 316 (538)
..++.|++++|||++||..+--.++
T Consensus 103 ~~~~~L~~l~GIG~ktA~~ill~~~ 127 (191)
T TIGR01083 103 EDREELVKLPGVGRKTANVVLNVAF 127 (191)
T ss_pred hHHHHHHhCCCCcHHHHHHHHHHHc
Confidence 3577788999999999999876544
No 146
>PRK00076 recR recombination protein RecR; Reviewed
Probab=76.04 E-value=2.1 Score=41.60 Aligned_cols=21 Identities=38% Similarity=0.618 Sum_probs=18.6
Q ss_pred HHHHHHhhccCCCHHHHHHHH
Q 009281 292 RTISLFGEVWGIGPATAQKLY 312 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~ 312 (538)
..++.|.++||||+|+|+++-
T Consensus 8 ~Li~~l~~LPGIG~KsA~Rla 28 (196)
T PRK00076 8 KLIEALRKLPGIGPKSAQRLA 28 (196)
T ss_pred HHHHHHHHCCCCCHHHHHHHH
Confidence 467889999999999999984
No 147
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=76.00 E-value=2.1 Score=41.51 Aligned_cols=20 Identities=40% Similarity=0.669 Sum_probs=18.1
Q ss_pred HHHHHHhhccCCCHHHHHHH
Q 009281 292 RTISLFGEVWGIGPATAQKL 311 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l 311 (538)
..++.|.++||||+|+|+++
T Consensus 8 ~Li~~l~~LPGIG~KsA~Rl 27 (195)
T TIGR00615 8 KLIESLKKLPGIGPKSAQRL 27 (195)
T ss_pred HHHHHHHHCCCCCHHHHHHH
Confidence 46788999999999999998
No 148
>PRK13844 recombination protein RecR; Provisional
Probab=74.79 E-value=2.4 Score=41.31 Aligned_cols=22 Identities=23% Similarity=0.271 Sum_probs=19.0
Q ss_pred hHHHHHHhhccCCCHHHHHHHH
Q 009281 291 VRTISLFGEVWGIGPATAQKLY 312 (538)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~ 312 (538)
...++.|.++||||+|+|+++-
T Consensus 11 ~~LI~~l~~LPGIG~KsA~Rla 32 (200)
T PRK13844 11 SAVIESLRKLPTIGKKSSQRLA 32 (200)
T ss_pred HHHHHHHHHCCCCCHHHHHHHH
Confidence 3467889999999999999983
No 149
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=74.75 E-value=3.4 Score=40.62 Aligned_cols=53 Identities=19% Similarity=0.253 Sum_probs=33.6
Q ss_pred CCHHHHHHHHHHHHh-CCcchhHHHH--hhchhHHHHHHh-hccCCCHHHHHHHHH-hCCC
Q 009281 262 IGKSMQDHIQEIVTT-GKLSKLEHFE--KDEKVRTISLFG-EVWGIGPATAQKLYE-KGHR 317 (538)
Q Consensus 262 iG~~ia~~I~Eil~t-G~~~~le~l~--~~~~~~~l~lf~-~I~GvGpktA~~l~~-~Gir 317 (538)
+-..=|+.|.++... |. ++++. ........+.|+ ++||||+|||.-+-. .|++
T Consensus 85 f~~~KAk~I~~~~~~~~~---l~~~~~~~~~~~~~R~~Ll~~lpGIG~KTAd~vL~~~~~~ 142 (208)
T PRK01229 85 FYNKRAEYIVEARKLYGK---LKEIIKADKDQFEAREFLVKNIKGIGYKEASHFLRNVGYE 142 (208)
T ss_pred cHHHHHHHHHHHHHHHHH---HHHHHhccCCchHHHHHHHHcCCCCcHHHHHHHHHHccCC
Confidence 435555556655542 32 33322 333457888888 999999999999873 4553
No 150
>PTZ00205 DNA polymerase kappa; Provisional
Probab=74.46 E-value=2.1 Score=48.01 Aligned_cols=29 Identities=34% Similarity=0.408 Sum_probs=26.2
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009281 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~ 325 (538)
+..|||||++++++|-..||.|+.||.+.
T Consensus 311 V~ki~GIG~~t~~~L~~~GI~TigDLa~~ 339 (571)
T PTZ00205 311 LRSVPGVGKVTEALLKGLGITTLSDIYNR 339 (571)
T ss_pred cceeCCcCHHHHHHHHHcCCCcHHHHhcC
Confidence 45899999999999999999999999853
No 151
>PRK10702 endonuclease III; Provisional
Probab=74.23 E-value=5.6 Score=39.14 Aligned_cols=25 Identities=16% Similarity=0.242 Sum_probs=19.9
Q ss_pred HHHHHHhhccCCCHHHHHHHHHhCC
Q 009281 292 RTISLFGEVWGIGPATAQKLYEKGH 316 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~~Gi 316 (538)
..++.|+++||||+|||.-+---++
T Consensus 106 ~~~~~Ll~lpGVG~ktA~~ill~a~ 130 (211)
T PRK10702 106 EDRAALEALPGVGRKTANVVLNTAF 130 (211)
T ss_pred chHHHHhcCCcccHHHHHHHHHHHc
Confidence 4677788999999999998754433
No 152
>PRK13300 tRNA CCA-pyrophosphorylase; Provisional
Probab=74.03 E-value=11 Score=41.25 Aligned_cols=46 Identities=24% Similarity=0.303 Sum_probs=31.3
Q ss_pred HHHHHHHHhhhcCCCeEEEecccccccCCcC--CCeeEEEecCCcchh
Q 009281 354 MERLLQKAGEEVLPEVIILCGGSYRRGKASC--GDLDVVIMHPDRKSH 399 (538)
Q Consensus 354 i~~iv~~~~~~~~p~~~v~~~Gs~RRgke~~--~DvDiLIt~~~~~~~ 399 (538)
+...+++.+.+....+.|.++|||.||.-.- +||||.|..|...+.
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 3333444433322237899999999998886 589999988765543
No 153
>PRK00254 ski2-like helicase; Provisional
Probab=74.02 E-value=15 Score=42.74 Aligned_cols=53 Identities=21% Similarity=0.354 Sum_probs=38.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~ 314 (538)
-.|.+|||||+..+.+ +++.| +.-++++..-. .+.+..|+|||+++|+++++.
T Consensus 645 ~~L~~ipgig~~~~~~---l~~~g-~~s~~~i~~a~----~~el~~~~gi~~~~a~~i~~~ 697 (720)
T PRK00254 645 LELMRLPMIGRKRARA---LYNAG-FRSIEDIVNAK----PSELLKVEGIGAKIVEGIFKH 697 (720)
T ss_pred hhhhcCCCCCHHHHHH---HHHcc-CCCHHHHHhCC----HHHHhcCCCCCHHHHHHHHHH
Confidence 3577899999998776 44554 45555555432 233469999999999999986
No 154
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=73.98 E-value=3.3 Score=37.14 Aligned_cols=26 Identities=42% Similarity=0.542 Sum_probs=23.6
Q ss_pred cCCCHHHHHHHHHhCCCCHHHHhhcc
Q 009281 301 WGIGPATAQKLYEKGHRTLDDLKNED 326 (538)
Q Consensus 301 ~GvGpktA~~l~~~GirtledL~~~~ 326 (538)
||+|++++.+|-+.||.|.+||.+.+
T Consensus 1 pgi~~~~~~~L~~~GI~t~~~Ll~~~ 26 (122)
T PF14229_consen 1 PGIGPKEAAKLKAAGIKTTGDLLEAG 26 (122)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHHcC
Confidence 79999999999888999999999654
No 155
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=73.81 E-value=4.2 Score=41.02 Aligned_cols=55 Identities=24% Similarity=0.374 Sum_probs=40.8
Q ss_pred hchhHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhccccchhhhc
Q 009281 288 DEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIK 343 (538)
Q Consensus 288 ~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~~--~L~~~q~~Glk~~ed~~ 343 (538)
+....-+.++.++||||++.|..+.+. +.|++++.++. .|.+..++|.+....|.
T Consensus 175 t~~e~q~~il~s~pgig~~~a~~ll~~-fgS~~~~~tas~~eL~~v~gig~k~A~~I~ 231 (254)
T COG1948 175 TLKELQLYILESIPGIGPKLAERLLKK-FGSVEDVLTASEEELMKVKGIGEKKAREIY 231 (254)
T ss_pred chHHHHHHHHHcCCCccHHHHHHHHHH-hcCHHHHhhcCHHHHHHhcCccHHHHHHHH
Confidence 344556778889999999999999874 55888888653 57777777766544443
No 156
>cd01702 PolY_Pol_eta DNA Polymerase eta. Pol eta, also called Rad30A, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Unlike other Y-family members, Pol eta can efficiently and accurately replicate DNA past UV-induced lesions. Its activity is initiated by two simultaneous interactions: the PIP box in pol eta interacting with PCNA, and the UBZ (ubiquitin-binding zinc finger) in pol eta interacting with monoubiquitin attached to PCNA. Pol eta is more efficient in copying damaged DNA than undamaged DNA and seems to recognize when a lesion has been passed, facilitating a lesion-dependent dissociation from the DNA.
Probab=72.81 E-value=2.8 Score=44.56 Aligned_cols=29 Identities=17% Similarity=0.307 Sum_probs=24.6
Q ss_pred HhhccCCCHHHHHHHHH-hCCCCHHHHhhc
Q 009281 297 FGEVWGIGPATAQKLYE-KGHRTLDDLKNE 325 (538)
Q Consensus 297 f~~I~GvGpktA~~l~~-~GirtledL~~~ 325 (538)
+..+||||++++.++.+ .||+|+.||.+-
T Consensus 184 v~~l~GiG~~~~~~ll~~~Gi~ti~dl~~~ 213 (359)
T cd01702 184 ITSIRGLGGKLGEEIIDLLGLPTEGDVAGF 213 (359)
T ss_pred HHHhCCcCHHHHHHHHHHcCCcCHHHHHhc
Confidence 45889999999988765 699999999864
No 157
>PRK10702 endonuclease III; Provisional
Probab=72.68 E-value=7.7 Score=38.18 Aligned_cols=43 Identities=12% Similarity=0.281 Sum_probs=31.2
Q ss_pred hHHHHHHHHHHHh-cCCcccc-chhhhcCCCCCCHHHHHHHHHHH
Q 009281 232 RSFSYYKAIPVIE-KLPFKIE-SADQVKGLPGIGKSMQDHIQEIV 274 (538)
Q Consensus 232 r~~aY~rAa~~l~-~l~~~i~-~~~~l~~lpgiG~~ia~~I~Eil 274 (538)
|+....+++..|. .....+. +.++|.+|||||+.+|+.|.-+.
T Consensus 85 kA~~l~~~a~~i~~~~~~~~p~~~~~Ll~lpGVG~ktA~~ill~a 129 (211)
T PRK10702 85 KAENVIKTCRILLEQHNGEVPEDRAALEALPGVGRKTANVVLNTA 129 (211)
T ss_pred HHHHHHHHHHHHHHHcCCCCCchHHHHhcCCcccHHHHHHHHHHH
Confidence 6666677777664 3333333 46899999999999999987554
No 158
>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=72.58 E-value=7.8 Score=31.63 Aligned_cols=29 Identities=31% Similarity=0.510 Sum_probs=24.3
Q ss_pred EEEecccccccCCc-CCCeeEEEecCCcch
Q 009281 370 IILCGGSYRRGKAS-CGDLDVVIMHPDRKS 398 (538)
Q Consensus 370 ~v~~~Gs~RRgke~-~~DvDiLIt~~~~~~ 398 (538)
.+.+-||+-||..+ .+||||+|..++...
T Consensus 20 ~i~LfGS~arg~~~~~SDiDl~vi~~~~~~ 49 (93)
T cd05403 20 KVYLFGSYARGDARPDSDIDLLVIFDDPLD 49 (93)
T ss_pred EEEEEeeeecCCCCCCCCeeEEEEeCCCCC
Confidence 78899999999985 789999997766553
No 159
>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=72.56 E-value=2.9 Score=43.50 Aligned_cols=28 Identities=32% Similarity=0.359 Sum_probs=25.4
Q ss_pred hccCCCHHHHHHHHHhCCCCHHHHhhcc
Q 009281 299 EVWGIGPATAQKLYEKGHRTLDDLKNED 326 (538)
Q Consensus 299 ~I~GvGpktA~~l~~~GirtledL~~~~ 326 (538)
.++|||++++++|-+.||+|+.||.+-.
T Consensus 174 ~~~gig~~~~~~L~~~Gi~t~~dl~~~~ 201 (335)
T cd03468 174 AALRLPPETVELLARLGLRTLGDLAALP 201 (335)
T ss_pred hHhCCCHHHHHHHHHhCcccHHHHHhCC
Confidence 5889999999999999999999998643
No 160
>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=72.28 E-value=7.6 Score=39.83 Aligned_cols=66 Identities=14% Similarity=0.209 Sum_probs=41.0
Q ss_pred hhHHHHHHHHHHHhcC-Cccc-cchhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCC
Q 009281 231 RRSFSYYKAIPVIEKL-PFKI-ESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGI 303 (538)
Q Consensus 231 ~r~~aY~rAa~~l~~l-~~~i-~~~~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~Gv 303 (538)
.|++.-.+||..|..- ...+ .+.++|.+|||||..+|+.|.-+.- |...-+ ....+.+.+.+++|+
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 3468899999999999999986553 332111 122355666555554
No 161
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=71.26 E-value=3.1 Score=43.28 Aligned_cols=25 Identities=48% Similarity=0.740 Sum_probs=22.0
Q ss_pred hccCCCHHHHHHHHHh-CCCCHHHHhhc
Q 009281 299 EVWGIGPATAQKLYEK-GHRTLDDLKNE 325 (538)
Q Consensus 299 ~I~GvGpktA~~l~~~-GirtledL~~~ 325 (538)
+|+|||||||.+|.++ | |++.|...
T Consensus 202 GV~GIG~ktA~~Ll~~~g--s~e~i~~~ 227 (310)
T COG0258 202 GVKGIGPKTALKLLQEYG--SLEGLYEN 227 (310)
T ss_pred CCCCcCHHHHHHHHHHhC--CHHHHHHh
Confidence 5999999999999998 8 88888753
No 162
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=70.91 E-value=4.9 Score=39.78 Aligned_cols=22 Identities=23% Similarity=0.210 Sum_probs=18.2
Q ss_pred HHHHHHhhccCCCHHHHHHHHH
Q 009281 292 RTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~ 313 (538)
...+.|+++||||++||..+--
T Consensus 118 ~~re~Ll~l~GIG~kTAd~iLl 139 (218)
T PRK13913 118 VTREWLLDQKGIGKESADAILC 139 (218)
T ss_pred hHHHHHHcCCCccHHHHHHHHH
Confidence 3567788999999999998754
No 163
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=70.69 E-value=6 Score=40.34 Aligned_cols=67 Identities=19% Similarity=0.322 Sum_probs=48.3
Q ss_pred hhcCCCCCC---HHHHHHHHHHHH-hCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHhCCCCHHHH
Q 009281 255 QVKGLPGIG---KSMQDHIQEIVT-TGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL 322 (538)
Q Consensus 255 ~l~~lpgiG---~~ia~~I~Eil~-tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL 322 (538)
+|.++ |+| +-|+.-.++|++ .|...-|..++..+-..+.++|+.+||||||.|.=+-=+|+.-+.-+
T Consensus 175 ~LR~~-gfGYRAkYI~~ta~~l~~~~g~~~wLqsl~~~~yeear~~L~~lpGVG~KVADCI~Lm~l~~~~~V 245 (323)
T KOG2875|consen 175 ELRKL-GFGYRAKYISATARALQEKQGGLAWLQSLRKSSYEEAREALCSLPGVGPKVADCICLMSLDKLSAV 245 (323)
T ss_pred HHHHc-CcchhHHHHHHHHHHHHHhcccchHHHHHhcccHHHHHHHHhcCCCCcchHhhhhhhhhcCCCCcc
Confidence 45554 666 446777777775 46667788888766666999999999999999997765555544443
No 164
>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=70.33 E-value=5.8 Score=31.63 Aligned_cols=38 Identities=16% Similarity=0.332 Sum_probs=26.2
Q ss_pred HHHHHHhcCCc-ccc-----chhhhcCCCCCCHHHHHHHHHHHH
Q 009281 238 KAIPVIEKLPF-KIE-----SADQVKGLPGIGKSMQDHIQEIVT 275 (538)
Q Consensus 238 rAa~~l~~l~~-~i~-----~~~~l~~lpgiG~~ia~~I~Eil~ 275 (538)
||.++|++..- .|. +.+++..+||+|++..+.|.+.|+
T Consensus 22 Ra~n~L~~~~I~tv~dL~~~s~~~L~~i~n~G~ksl~EI~~~L~ 65 (66)
T PF03118_consen 22 RAYNCLKRAGIHTVGDLVKYSEEDLLKIKNFGKKSLEEIKEKLK 65 (66)
T ss_dssp HHHHHHHCTT--BHHHHHCS-HHHHHTSTTSHHHHHHHHHHHHH
T ss_pred HHHHHHHHhCCcCHHHHHhCCHHHHHhCCCCCHhHHHHHHHHHc
Confidence 45566666532 111 226789999999999999998875
No 165
>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=69.64 E-value=2.2 Score=28.97 Aligned_cols=18 Identities=22% Similarity=0.501 Sum_probs=14.5
Q ss_pred hhcCCCCCCHHHHHHHHH
Q 009281 255 QVKGLPGIGKSMQDHIQE 272 (538)
Q Consensus 255 ~l~~lpgiG~~ia~~I~E 272 (538)
.+.+++|||+++++++..
T Consensus 12 pi~~~~GIG~kt~~kL~~ 29 (32)
T PF11798_consen 12 PIRKFWGIGKKTAKKLNK 29 (32)
T ss_dssp BGGGSTTS-HHHHHHHHC
T ss_pred CHHhhCCccHHHHHHHHH
Confidence 478899999999998764
No 166
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=69.41 E-value=6.5 Score=45.75 Aligned_cols=89 Identities=12% Similarity=0.165 Sum_probs=66.9
Q ss_pred CCCCCCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEe-ecCCCccEEEEcCChHHHHHHHHhhhccCC-ccccccch
Q 009281 13 LDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEE-KLSKKVTHVLAMDLEALLQQVSKQHLARFK-GSVIRYQW 90 (538)
Q Consensus 13 ~~~~~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~-~ls~~VTHVV~~~~~~~~~~l~~~~~~~~~-~~lV~~~W 90 (538)
......|+++.+|.+...+.. ..-+++.-..+|+..+. +..++.|||++.+..+. + +..++ +...++.|
T Consensus 42 ~t~~s~fs~is~~~ngs~~e~--~nelk~~~~~~t~~~~~~~~rs~T~~ii~~~l~a~---~----vk~~~~~~~~~~e~ 112 (1016)
T KOG2093|consen 42 ATGSSSFSGISISVNGSTDES--ANELKLQNMFHTGASAASYERSGTENIIAQGLPAD---L----VKGFTIPKHISIEW 112 (1016)
T ss_pred cCCcceeeeeeeccCCccccc--hHHHhhhhhhcccccccccccccceeeecccchHH---H----hccccchhhhcHHH
Confidence 344588999999998777753 35566788899999984 44678999999887643 1 12222 67899999
Q ss_pred HHHHHhcCcccCcccccccc
Q 009281 91 LEDSLRLGEKVSEDLYRIKL 110 (538)
Q Consensus 91 l~ecik~g~lv~e~~y~l~~ 110 (538)
+.||.+.|..|.--.|.+..
T Consensus 113 iie~~~~~~~~~~~~~~~~t 132 (1016)
T KOG2093|consen 113 IIECCENGMDVGYYPYQLYT 132 (1016)
T ss_pred HHHHHhccCccccccceeec
Confidence 99999999999877776654
No 167
>cd03586 PolY_Pol_IV_kappa DNA Polymerase IV/Kappa. Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Known primarily as Pol IV in prokaryotes and Pol kappa in eukaryotes, this polymerase has a propensity for generating frameshift mutations. The eukaryotic Pol kappa differs from Pol IV and Dpo4 by an N-terminal extension of ~75 residues known as the "N-clasp" region. The structure of Pol kappa shows DNA that is almost totally encircled by Pol kappa, with the N-clasp region augmenting the interactions between DNA and the polymerase. Pol kappa is more resistant than Pol eta and Pol iota to bulky guanine adducts and is efficient at catalyzing the incorporation of dCTP. Bacterial pol IV has a
Probab=69.40 E-value=3.4 Score=42.99 Aligned_cols=28 Identities=39% Similarity=0.550 Sum_probs=25.4
Q ss_pred hhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009281 298 GEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 298 ~~I~GvGpktA~~l~~~GirtledL~~~ 325 (538)
..+||||.+++++|...||+|+.||.+-
T Consensus 174 ~~l~gig~~~~~~L~~~Gi~ti~dl~~~ 201 (334)
T cd03586 174 RKIPGVGKVTAEKLKELGIKTIGDLAKL 201 (334)
T ss_pred hhhCCcCHHHHHHHHHcCCcCHHHHHcC
Confidence 5789999999999999999999999853
No 168
>COG0389 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]
Probab=67.96 E-value=3.6 Score=43.60 Aligned_cols=28 Identities=43% Similarity=0.697 Sum_probs=26.0
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhh
Q 009281 297 FGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (538)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~ 324 (538)
++.+||||+.++.++...||.|+.||.+
T Consensus 178 v~~~~GvG~~~~~~l~~~Gi~ti~dl~~ 205 (354)
T COG0389 178 VLEFWGVGKVTAEKLRRLGISTIGDLAE 205 (354)
T ss_pred hhhhCCCCHHHHHHHHHcCChhHHHHHh
Confidence 3489999999999999999999999987
No 169
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=67.58 E-value=9.8 Score=35.03 Aligned_cols=67 Identities=12% Similarity=0.138 Sum_probs=41.1
Q ss_pred ChhHHHHHHHHHHHhcCCccc-----cchhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCC
Q 009281 230 DRRSFSYYKAIPVIEKLPFKI-----ESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGI 303 (538)
Q Consensus 230 ~~r~~aY~rAa~~l~~l~~~i-----~~~~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~Gv 303 (538)
+.|+..-..++..+.+-.... +..++|.+|||||+.+|+.|.-+.-. .+ .+-- ...+.+.+..+.++
T Consensus 54 ~~kA~~i~~~a~~~~~~~~~~~~~~~~~~~~L~~l~GIG~~tA~~~l~~~~~--~~---~~pv--D~~v~r~~~~~~~~ 125 (158)
T cd00056 54 RRKAKYLKELARAIVEGFGGLVLDDPDAREELLALPGVGRKTANVVLLFALG--PD---AFPV--DTHVRRVLKRLGLI 125 (158)
T ss_pred HHHHHHHHHHHHHHHHHcCCccCCCcccHHHHHcCCCCCHHHHHHHHHHHCC--CC---CCcc--chhHHHHHHHhCCC
Confidence 457777777777765432221 23477999999999999998765432 21 1111 23466666555554
No 170
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=67.46 E-value=11 Score=37.05 Aligned_cols=86 Identities=23% Similarity=0.308 Sum_probs=48.3
Q ss_pred CCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh--CCCCHHHHhhccCc-chhhhccc-
Q 009281 261 GIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRTLDDLKNEDSL-THSQRLGL- 336 (538)
Q Consensus 261 giG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~--GirtledL~~~~~L-~~~q~~Gl- 336 (538)
|+-..=|+.|.++.+ .-+|+... +.+..++.|.++||||+|||.--... |+-++ -=+--+ .-..++|+
T Consensus 80 Glyr~KAk~I~~~~~----~l~e~~~g-~vP~~~~eL~~LPGVGrKTAnvVL~~a~g~p~i---~VDTHV~Rvs~R~gl~ 151 (211)
T COG0177 80 GLYRNKAKNIKELAR----ILLEKFGG-EVPDTREELLSLPGVGRKTANVVLSFAFGIPAI---AVDTHVHRVSNRLGLV 151 (211)
T ss_pred CCcHHHHHHHHHHHH----HHHHHcCC-CCCchHHHHHhCCCcchHHHHHHHHhhcCCCcc---cccchHHHHHHHhCCC
Confidence 555666666665543 22333333 44567888889999999999988765 44322 101001 11233343
Q ss_pred ------cchhhhccCcCHHHHHHH
Q 009281 337 ------KYFDDIKTRIPRHEVEQM 354 (538)
Q Consensus 337 ------k~~ed~~~~i~r~ea~~i 354 (538)
+..+++...||++.-..+
T Consensus 152 ~~~~p~~ve~~L~~~iP~~~~~~~ 175 (211)
T COG0177 152 PGKTPEEVEEALMKLIPKELWTDL 175 (211)
T ss_pred CCCCHHHHHHHHHHHCCHHHHHHH
Confidence 344556677777766554
No 171
>KOG3524 consensus Predicted guanine nucleotide exchange factor (PEBBLE) [Signal transduction mechanisms]
Probab=66.71 E-value=6.6 Score=44.61 Aligned_cols=79 Identities=14% Similarity=0.214 Sum_probs=54.6
Q ss_pred CCCCCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHhhhccCCccccccchHHH
Q 009281 14 DSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLED 93 (538)
Q Consensus 14 ~~~~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~~~~~~~~~~l~~~~~~~~~~~lV~~~Wl~e 93 (538)
-....|++++.|| .++-..-. -+=+++..+||.|-.....++||.|+...... .+.... -. ..++.+.||.+
T Consensus 114 ly~~~m~~vvlcf--Tg~rkk~e-~lv~lvh~mgg~irkd~nsktthli~n~s~ge--k~~~a~--t~-~~~~rp~wv~~ 185 (850)
T KOG3524|consen 114 LYCELMKDVVMCF--TGERKKKE-ELVDLVHYMGGSIRKDTNSKTTHLIANKVEGE--KQSIAL--VG-VPTMRPDWVTE 185 (850)
T ss_pred ccchhhcCceeee--eccchhhH-HHHHHHHHhcceeEeeeccCceEEEeecccce--EEEEEe--ec-cceechHhhhh
Confidence 3457899999999 55532323 34489999999999999999999998654321 011000 11 46788999999
Q ss_pred HHhcCcc
Q 009281 94 SLRLGEK 100 (538)
Q Consensus 94 cik~g~l 100 (538)
||+-..-
T Consensus 186 aw~~rn~ 192 (850)
T KOG3524|consen 186 AWKHRND 192 (850)
T ss_pred hhcCcch
Confidence 9987654
No 172
>PRK13766 Hef nuclease; Provisional
Probab=66.70 E-value=6.4 Score=46.02 Aligned_cols=17 Identities=47% Similarity=0.612 Sum_probs=9.3
Q ss_pred HhhccCCCHHHHHHHHH
Q 009281 297 FGEVWGIGPATAQKLYE 313 (538)
Q Consensus 297 f~~I~GvGpktA~~l~~ 313 (538)
|..++|+|+++|+.+++
T Consensus 749 L~~i~Gig~~~a~~i~~ 765 (773)
T PRK13766 749 LMEVEGIGEKTAKRIRE 765 (773)
T ss_pred HHhCCCCCHHHHHHHHH
Confidence 34555566655555544
No 173
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=66.38 E-value=20 Score=34.44 Aligned_cols=52 Identities=23% Similarity=0.305 Sum_probs=32.8
Q ss_pred hhHHHHHHHHHHHhcCCccccc-hhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhc
Q 009281 231 RRSFSYYKAIPVIEKLPFKIES-ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDE 289 (538)
Q Consensus 231 ~r~~aY~rAa~~l~~l~~~i~~-~~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~ 289 (538)
.|..-|-+-| .||+. +-+|.=||||||+++.+|-|=-+.+.+..++++.+-.
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 4555555544 57876 4789999999999999999999999999898887643
No 174
>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=66.27 E-value=5.9 Score=34.66 Aligned_cols=26 Identities=23% Similarity=0.484 Sum_probs=21.3
Q ss_pred HHHHHhhccCCCHHHHHHHHHh-CCCC
Q 009281 293 TISLFGEVWGIGPATAQKLYEK-GHRT 318 (538)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~-Girt 318 (538)
+.-.|++|+|||+++|..+.+. |+..
T Consensus 13 i~~aLt~IyGIG~~~A~~Ic~~lgi~~ 39 (107)
T PF00416_consen 13 IYIALTKIYGIGRRKAKQICKKLGINP 39 (107)
T ss_dssp HHHHHTTSTTBCHHHHHHHHHHTTS-S
T ss_pred hHhHHhhhhccCHHHHHHHHHHcCCCh
Confidence 5666789999999999999886 8753
No 175
>PRK13910 DNA glycosylase MutY; Provisional
Probab=65.83 E-value=12 Score=38.67 Aligned_cols=68 Identities=18% Similarity=0.207 Sum_probs=45.1
Q ss_pred hHHHHHHHHHHHhc-CCccc-cchhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHH
Q 009281 232 RSFSYYKAIPVIEK-LPFKI-ESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPA 306 (538)
Q Consensus 232 r~~aY~rAa~~l~~-l~~~i-~~~~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpk 306 (538)
|++.-.++|..|.. ....+ .+.++|.+|||||+.+|+.|.-+. -|.-.- -...-+.++|.+++|+...
T Consensus 48 RAr~L~~~A~~i~~~~~g~~P~~~~~L~~LpGIG~kTA~aIl~~a-f~~~~~------~VD~nV~RVl~Rl~g~~~~ 117 (289)
T PRK13910 48 RAKNLKKSAEICVKEHHSQLPNDYQSLLKLPGIGAYTANAILCFG-FREKSA------CVDANIKRVLLRLFGLDPN 117 (289)
T ss_pred HHHHHHHHHHHHHHHhCCCCChhHHHHHhCCCCCHHHHHHHHHHH-CCCCcC------cccHHHHHHHHHHhcCCCC
Confidence 77777788877753 22222 257899999999999999997654 333111 1234477788788888643
No 176
>KOG2245 consensus Poly(A) polymerase and related nucleotidyltransferases [RNA processing and modification]
Probab=65.81 E-value=13 Score=41.00 Aligned_cols=86 Identities=26% Similarity=0.361 Sum_probs=60.8
Q ss_pred hhhccccchhhhccCcCHHHHHH-HHHHHHHHhhhc------------CCCeEEEecccccccCCc-CCCeeEEEecCCc
Q 009281 331 SQRLGLKYFDDIKTRIPRHEVEQ-MERLLQKAGEEV------------LPEVIILCGGSYRRGKAS-CGDLDVVIMHPDR 396 (538)
Q Consensus 331 ~q~~Glk~~ed~~~~i~r~ea~~-i~~iv~~~~~~~------------~p~~~v~~~Gs~RRgke~-~~DvDiLIt~~~~ 396 (538)
++.+|+ ||+-.+-..|.++-. +.+||++-++++ ..|.++..-||||-|--. +.|||=|+..|.-
T Consensus 41 L~~~g~--fEs~eEt~~R~~VL~~L~~iVk~wVk~vs~~k~~p~~~~~~aggkIftfGSYRLGVhg~GADIDtLcV~Prh 118 (562)
T KOG2245|consen 41 LKNEGL--FESKEETQRREEVLGKLNQIVKEWVKKVSEQKGLPDGMIENAGGKIFTFGSYRLGVHGPGADIDTLCVGPRH 118 (562)
T ss_pred HHhcCC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCChhhhhhcCceEEeccceeecccCCCCCcceeeecccc
Confidence 455553 555556666777644 566665543322 234567778999999865 5599999999988
Q ss_pred chhhhhHHHHHHHHHHcCccce
Q 009281 397 KSHKGFLSKYVKKLKEMKFLRE 418 (538)
Q Consensus 397 ~~~~~~l~~~v~~L~~~g~l~~ 418 (538)
.+...+|..+-+.|+...-+++
T Consensus 119 v~R~DFF~sf~~mL~~~~eVte 140 (562)
T KOG2245|consen 119 VSRSDFFTSFYDMLKERPEVTE 140 (562)
T ss_pred ccHHHHHHHHHHHHhcCccccc
Confidence 7778999999998998877764
No 177
>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=65.23 E-value=4.1 Score=34.07 Aligned_cols=20 Identities=40% Similarity=0.624 Sum_probs=17.8
Q ss_pred HHHhhccCCCHHHHHHHHHh
Q 009281 295 SLFGEVWGIGPATAQKLYEK 314 (538)
Q Consensus 295 ~lf~~I~GvGpktA~~l~~~ 314 (538)
++|++|||||+.+|-.+..+
T Consensus 2 ~~l~sipGig~~~a~~llae 21 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAE 21 (87)
T ss_pred chhcCCCCccHHHHHHHHHH
Confidence 46789999999999999875
No 178
>COG2251 Predicted nuclease (RecB family) [General function prediction only]
Probab=63.30 E-value=5.3 Score=43.31 Aligned_cols=27 Identities=37% Similarity=0.452 Sum_probs=24.8
Q ss_pred hccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009281 299 EVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 299 ~I~GvGpktA~~l~~~GirtledL~~~ 325 (538)
=|+||||.+.+.+++.||+|++||-..
T Consensus 229 Lv~Gi~~~r~~~l~~~GI~Ti~~LA~~ 255 (474)
T COG2251 229 LVPGITPSRYDVLEEVGITTIEDLADA 255 (474)
T ss_pred ccCCCCHHHHHHHHHcCcchHHHHHhc
Confidence 378999999999999999999999864
No 179
>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=63.00 E-value=18 Score=30.31 Aligned_cols=49 Identities=22% Similarity=0.409 Sum_probs=28.6
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHhC
Q 009281 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKG 315 (538)
Q Consensus 256 l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~G 315 (538)
+..|+|||+.+++.|.+--+.|.+.-++++... ++++..+..+.|...|
T Consensus 29 l~~Ikglg~~~a~~I~~~R~~g~f~s~~df~~R-----------~~~i~~~~le~Li~aG 77 (90)
T PF14579_consen 29 LSAIKGLGEEVAEKIVEERENGPFKSLEDFIQR-----------LPKINKRQLEALIKAG 77 (90)
T ss_dssp GGGSTTS-HHHHHHHHHHHHCSS-SSHHHHHHH-----------S-TS-HHHHHHHHHTT
T ss_pred HhhcCCCCHHHHHHHHHhHhcCCCCCHHHHHHH-----------HhcCCHHHHHHHHHCC
Confidence 566777777777777777776666666665432 1255566666665554
No 180
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=62.57 E-value=22 Score=34.02 Aligned_cols=44 Identities=16% Similarity=0.190 Sum_probs=30.3
Q ss_pred hHHHHHHHHHHH-hcCCccc------------cchhhhcCCCCCCHHHHHHHHHHHH
Q 009281 232 RSFSYYKAIPVI-EKLPFKI------------ESADQVKGLPGIGKSMQDHIQEIVT 275 (538)
Q Consensus 232 r~~aY~rAa~~l-~~l~~~i------------~~~~~l~~lpgiG~~ia~~I~Eil~ 275 (538)
|+.....++..| +.+...+ +-.++|..|||||+++|+.+--++.
T Consensus 80 KAk~Lk~~a~~iie~y~G~v~~L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL~~l~ 136 (177)
T TIGR03252 80 MAKRVQALAQYVVDTYDGDATAVWTEGDPDGKELLRRLKALPGFGKQKAKIFLALLG 136 (177)
T ss_pred HHHHHHHHHHHHHHHhCCChhhhhcccCCCcHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 555555566555 4555544 1146899999999999999876654
No 181
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=62.47 E-value=5.3 Score=38.83 Aligned_cols=31 Identities=23% Similarity=0.349 Sum_probs=22.8
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHH
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEH 284 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~ 284 (538)
+.+..|||||++.|.++.-.+-.-.-.+++.
T Consensus 11 ~~l~~LPGIG~KsA~RlA~~ll~~~~~~~~~ 41 (195)
T TIGR00615 11 ESLKKLPGIGPKSAQRLAFHLLKRDPSEVLR 41 (195)
T ss_pred HHHHHCCCCCHHHHHHHHHHHHcCCHHHHHH
Confidence 6789999999999999987665433333333
No 182
>PRK05007 PII uridylyl-transferase; Provisional
Probab=61.99 E-value=25 Score=42.01 Aligned_cols=49 Identities=20% Similarity=0.474 Sum_probs=35.4
Q ss_pred CCeEEEeccccccc-CCcCCCeeEEEecCCcc--hhhhhHHHHHHHHHHcCc
Q 009281 367 PEVIILCGGSYRRG-KASCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMKF 415 (538)
Q Consensus 367 p~~~v~~~Gs~RRg-ke~~~DvDiLIt~~~~~--~~~~~l~~~v~~L~~~g~ 415 (538)
|++.++.+|||=|| ..-.+|||+||-+++.. .....+.+++..|-+.|+
T Consensus 79 ~~~alvAvGgyGR~EL~p~SDiDll~l~~~~~~~~~~~~i~~~~~~lwD~gL 130 (884)
T PRK05007 79 PDLALVAVGGYGRGELHPLSDIDLLILSRKKLPDEQAQKVGELITLLWDLKL 130 (884)
T ss_pred CceEEEecCCCCCcccCCcccceEEEEeCCCCChHHHHHHHHHHHHHHhcCC
Confidence 45778889999555 56689999999988532 244567777777777765
No 183
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=61.70 E-value=6 Score=39.23 Aligned_cols=29 Identities=34% Similarity=0.543 Sum_probs=26.7
Q ss_pred HHhhccCCCHHHHHHHHHhCCCCHHHHhh
Q 009281 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (538)
Q Consensus 296 lf~~I~GvGpktA~~l~~~GirtledL~~ 324 (538)
-|+.|.||||+.+.+|.+.||.++++|-.
T Consensus 159 DL~~I~GIGp~~a~~L~eaGi~tfaQIAa 187 (221)
T PRK12278 159 DLTKITGVGPALAKKLNEAGVTTFAQIAA 187 (221)
T ss_pred hheeccccChHHHHHHHHcCCCCHHHhhC
Confidence 36799999999999999999999999974
No 184
>PRK03980 flap endonuclease-1; Provisional
Probab=61.58 E-value=6.3 Score=40.76 Aligned_cols=25 Identities=44% Similarity=0.670 Sum_probs=21.5
Q ss_pred hccCCCHHHHHHHHHhCCCCHHHHhh
Q 009281 299 EVWGIGPATAQKLYEKGHRTLDDLKN 324 (538)
Q Consensus 299 ~I~GvGpktA~~l~~~GirtledL~~ 324 (538)
+|+|||||||.+|.++ +.||+.+..
T Consensus 193 GI~GIG~ktA~kLi~~-~~sle~i~~ 217 (292)
T PRK03980 193 GIKGIGPKTALKLIKK-HGDLEKVLE 217 (292)
T ss_pred CCCCccHHHHHHHHHH-CCCHHHHHH
Confidence 7899999999999986 238998886
No 185
>PRK14973 DNA topoisomerase I; Provisional
Probab=61.58 E-value=9.9 Score=45.51 Aligned_cols=40 Identities=18% Similarity=0.154 Sum_probs=31.8
Q ss_pred HHhhccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhcc
Q 009281 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLG 335 (538)
Q Consensus 296 lf~~I~GvGpktA~~l~~~GirtledL~~~~--~L~~~q~~G 335 (538)
-|++++||=...|+++|+.||+|++|+-.+. .|+..-|+.
T Consensus 803 ~~~~~~gv~~~~~~~~~~~G~~~~~d~~~a~p~~La~~~g~~ 844 (936)
T PRK14973 803 SRLKEIGVPAVSLKKYQEAGFDTPEDFCSVHPAYLALKTGIS 844 (936)
T ss_pred HhhcccCCCHHHHHHHHHhcCCCHHHHHhcCHHHHhcCCCCC
Confidence 4559999999999999999999999998653 355444443
No 186
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=61.19 E-value=5.4 Score=41.37 Aligned_cols=54 Identities=28% Similarity=0.405 Sum_probs=41.1
Q ss_pred hhHHHHHHhhccCCCHHHHHHHHHh---CC-CCHHHHhhccC------cchhhhccccchhhhc
Q 009281 290 KVRTISLFGEVWGIGPATAQKLYEK---GH-RTLDDLKNEDS------LTHSQRLGLKYFDDIK 343 (538)
Q Consensus 290 ~~~~l~lf~~I~GvGpktA~~l~~~---Gi-rtledL~~~~~------L~~~q~~Glk~~ed~~ 343 (538)
|..+++...++||+|||.|++|-+- |. +-+++++++.+ ++..-|+|.++.+.|.
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 4456788889999999999999862 54 77777776432 5677788888887775
No 187
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=60.72 E-value=21 Score=35.23 Aligned_cols=32 Identities=19% Similarity=0.507 Sum_probs=23.9
Q ss_pred HHhcCCcccc-chhhhcCCCCCCHHHHHHHHHH
Q 009281 242 VIEKLPFKIE-SADQVKGLPGIGKSMQDHIQEI 273 (538)
Q Consensus 242 ~l~~l~~~i~-~~~~l~~lpgiG~~ia~~I~Ei 273 (538)
.++.+..++. ++++|.+|||||.++|..+--+
T Consensus 96 l~e~~~g~vP~~~~eL~~LPGVGrKTAnvVL~~ 128 (211)
T COG0177 96 LLEKFGGEVPDTREELLSLPGVGRKTANVVLSF 128 (211)
T ss_pred HHHHcCCCCCchHHHHHhCCCcchHHHHHHHHh
Confidence 3445555554 4689999999999999987654
No 188
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=60.68 E-value=9.7 Score=43.14 Aligned_cols=51 Identities=20% Similarity=0.431 Sum_probs=28.9
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (538)
..|..|||||+..+.++-+.. |++. .+.+. ..+.+..+||+|++.|+.+++
T Consensus 525 ~~L~~IpGIG~kr~~~LL~~F--GS~~---~I~~A----s~eeL~~vpGi~~~~A~~I~~ 575 (577)
T PRK14668 525 TVLDDVPGVGPETRKRLLRRF--GSVE---GVREA----SVEDLRDVPGVGEKTAETIRE 575 (577)
T ss_pred hHHhcCCCCCHHHHHHHHHHc--CCHH---HHHhC----CHHHHHhCCCCCHHHHHHHHH
Confidence 356777777777766554422 3333 32221 223345777777777777754
No 189
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=60.64 E-value=6.1 Score=47.01 Aligned_cols=24 Identities=42% Similarity=0.678 Sum_probs=20.6
Q ss_pred hccCCCHHHHHHHHHh-CCCCHHHHhh
Q 009281 299 EVWGIGPATAQKLYEK-GHRTLDDLKN 324 (538)
Q Consensus 299 ~I~GvGpktA~~l~~~-GirtledL~~ 324 (538)
+|||||||||.+|.++ | |||.+..
T Consensus 189 GVpGIG~KtA~kLL~~yg--sle~i~~ 213 (887)
T TIGR00593 189 GVKGIGEKTAAKLLQEFG--SLENIYE 213 (887)
T ss_pred CCCCcCHHHHHHHHHHcC--CHHHHHH
Confidence 4999999999999987 6 8888763
No 190
>cd05401 NT_GlnE_GlnD_like Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins. Escherichia coli GlnD and -E participate in the Glutamine synthetase (GS)/Glutamate synthase (GOGAT) pathway for the assimilation of ammonium nitrogen. In nitrogen sufficiency, GlnE adenylates GS, reducing GS activity; when nitrogen is limiting, GlnE deadenylates GS-AMP, restoring GS activity. When nitrogen is limiting, GlnD uridylylates the nitrogen regulatory protein PII to PII-UTP, and in nitrogen sufficiency, it removes the modifying groups. The activity of Escherichia coli GlnE is modulated by PII-proteins. PII-UMP promotes GlnE deadenylation activity, and PII promotes GlnE adenylation activity. Escherichia coli GlnE has two separate NT domains. The N-terminal NT domain catalyzes the deadenylylation of GS, and the C-terminal NT domain the adenylylation reaction. The majority of proteins in this family conta
Probab=60.63 E-value=31 Score=32.22 Aligned_cols=50 Identities=24% Similarity=0.355 Sum_probs=31.1
Q ss_pred CeEEEecccccccC-CcCCCeeEEEecCCcch-----hhhhHHHHHHHHHHcCccc
Q 009281 368 EVIILCGGSYRRGK-ASCGDLDVVIMHPDRKS-----HKGFLSKYVKKLKEMKFLR 417 (538)
Q Consensus 368 ~~~v~~~Gs~RRgk-e~~~DvDiLIt~~~~~~-----~~~~l~~~v~~L~~~g~l~ 417 (538)
.+-+.+.|||=|+. ....|+|+++.+++... ...+-..+++.|...|+..
T Consensus 55 ~~~~la~Gs~GR~E~~~~SD~D~~~v~~~~~~~~~~~~~~l~~~i~~~L~~~g~~~ 110 (172)
T cd05401 55 PFALLALGSYGRGELNPSSDQDLLLLYDDDGDEVAAYFEELAERLIKILSEAGGPY 110 (172)
T ss_pred cEEEEEeCCcccCCcCCCcCcceEEEeCCCCchHHHHHHHHHHHHHHHHHhCCCCC
Confidence 34567789986654 56789999998876532 1233444555555555444
No 191
>PF14579 HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI_A 3E0D_A 3F2C_A 3F2B_A 3F2D_A 2HQA_A 2HNH_A.
Probab=60.61 E-value=11 Score=31.71 Aligned_cols=30 Identities=23% Similarity=0.470 Sum_probs=24.0
Q ss_pred HhhccCCCHHHHHHHHHh----CCCCHHHHhhcc
Q 009281 297 FGEVWGIGPATAQKLYEK----GHRTLDDLKNED 326 (538)
Q Consensus 297 f~~I~GvGpktA~~l~~~----GirtledL~~~~ 326 (538)
|+.|.|||.+.|+++.++ .++|++|+....
T Consensus 29 l~~Ikglg~~~a~~I~~~R~~g~f~s~~df~~R~ 62 (90)
T PF14579_consen 29 LSAIKGLGEEVAEKIVEERENGPFKSLEDFIQRL 62 (90)
T ss_dssp GGGSTTS-HHHHHHHHHHHHCSS-SSHHHHHHHS
T ss_pred HhhcCCCCHHHHHHHHHhHhcCCCCCHHHHHHHH
Confidence 779999999999999962 789999988643
No 192
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=60.13 E-value=29 Score=41.37 Aligned_cols=68 Identities=16% Similarity=0.320 Sum_probs=44.2
Q ss_pred HHHHHHHHHHHHHHhhhcCC----CeEEEecccccccC-CcCCCeeEEEecCCc--chhhhhHHHHHHHHHHcCc
Q 009281 348 RHEVEQMERLLQKAGEEVLP----EVIILCGGSYRRGK-ASCGDLDVVIMHPDR--KSHKGFLSKYVKKLKEMKF 415 (538)
Q Consensus 348 r~ea~~i~~iv~~~~~~~~p----~~~v~~~Gs~RRgk-e~~~DvDiLIt~~~~--~~~~~~l~~~v~~L~~~g~ 415 (538)
+.-+..+..+++.+.....+ ++-+..+|||=||. .--+|||+||-+++. .....++.+++..|=+.|+
T Consensus 32 ~~~~~~~D~~l~~l~~~~~~~~~~~iaLvAvGGYGR~eL~P~SDIDlliL~~~~~~~~~~~~i~~~~~~LWD~gl 106 (854)
T PRK01759 32 ENRSDFYDQLLIHLWQQFGLEEQSDLALIAVGGYGRREMFPLSDLDILILTEQPPDEETEEKINQFFQFLWDCGF 106 (854)
T ss_pred HHHHHHHHHHHHHHHHHccCCCCCCeEEEEeCCcccccCCCcccceEEEEeCCCCChHHHHHHHHHHHHHHhcCC
Confidence 33444456666655443322 35677889996654 556899999988753 2345677777777777775
No 193
>COG1669 Predicted nucleotidyltransferases [General function prediction only]
Probab=60.02 E-value=28 Score=30.02 Aligned_cols=30 Identities=27% Similarity=0.393 Sum_probs=23.3
Q ss_pred CCe-EEEecccccccCCc-CCCeeEEEecCCc
Q 009281 367 PEV-IILCGGSYRRGKAS-CGDLDVVIMHPDR 396 (538)
Q Consensus 367 p~~-~v~~~Gs~RRgke~-~~DvDiLIt~~~~ 396 (538)
.|+ .+.+-|||-||... -.||||||-...+
T Consensus 22 ~gv~~~~vFGS~aRgE~~~~SDIDILVef~~~ 53 (97)
T COG1669 22 YGVKRVAVFGSYARGEQKPDSDIDILVEFEPG 53 (97)
T ss_pred hCCceEEEeeeeecCCCCCCCCceeEEeecCC
Confidence 455 68899999999653 3899999976555
No 194
>PRK02362 ski2-like helicase; Provisional
Probab=59.82 E-value=58 Score=38.00 Aligned_cols=52 Identities=19% Similarity=0.464 Sum_probs=39.1
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh-C
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-G 315 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~-G 315 (538)
-+|..|||||...+.+..+ .| +.-++++.+-++..+..+ +|+|+|+++.+. |
T Consensus 652 ~~L~~ip~i~~~~a~~l~~---~g-i~s~~dl~~~~~~~l~~~------~g~~~~~~i~~~~~ 704 (737)
T PRK02362 652 LDLVGLRGVGRVRARRLYN---AG-IESRADLRAADKSVVLAI------LGEKIAENILEQAG 704 (737)
T ss_pred HHHhCCCCCCHHHHHHHHH---cC-CCCHHHHHhCCHHHHHHH------HCHHHHHHHHHHhC
Confidence 4688999999998877664 44 677777776555555554 699999999987 6
No 195
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=59.76 E-value=7.2 Score=44.58 Aligned_cols=32 Identities=25% Similarity=0.423 Sum_probs=25.8
Q ss_pred HHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009281 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~GirtledL~~~ 325 (538)
....|..|+||||++|+.|+.. +.|+++|.++
T Consensus 567 ~~s~L~~I~GIG~k~a~~Ll~~-Fgs~~~i~~A 598 (621)
T PRK14671 567 LQTELTDIAGIGEKTAEKLLEH-FGSVEKVAKA 598 (621)
T ss_pred hhhhhhcCCCcCHHHHHHHHHH-cCCHHHHHhC
Confidence 3456679999999999999875 4488999864
No 196
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=59.39 E-value=12 Score=42.74 Aligned_cols=49 Identities=27% Similarity=0.575 Sum_probs=34.6
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (538)
..|.+|||||++.+..|..-. |++ +.+.+- ..+.|.+| ||+++|+++++
T Consensus 569 s~L~~I~GIG~k~a~~Ll~~F--gs~---~~i~~A----s~eeL~~v--ig~k~A~~I~~ 617 (621)
T PRK14671 569 TELTDIAGIGEKTAEKLLEHF--GSV---EKVAKA----SLEELAAV--AGPKTAETIYR 617 (621)
T ss_pred hhhhcCCCcCHHHHHHHHHHc--CCH---HHHHhC----CHHHHHHH--hCHHHHHHHHH
Confidence 468899999999999765532 233 454432 34445577 99999999986
No 197
>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=59.38 E-value=7.6 Score=42.65 Aligned_cols=28 Identities=46% Similarity=0.586 Sum_probs=26.0
Q ss_pred hccCCCHHHHHHHHHhCCCCHHHHhhcc
Q 009281 299 EVWGIGPATAQKLYEKGHRTLDDLKNED 326 (538)
Q Consensus 299 ~I~GvGpktA~~l~~~GirtledL~~~~ 326 (538)
-|+|||.+++.+|++.||.|++||-...
T Consensus 211 lv~gi~~~~~~~L~~~GI~ti~~La~~~ 238 (457)
T TIGR03491 211 LVPGIGPSRYRLLQELGIHTLEDLAAAD 238 (457)
T ss_pred ecCCCCHHHHHHHHHcCCCcHHHHhcCC
Confidence 6999999999999999999999998654
No 198
>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=59.05 E-value=7.4 Score=30.96 Aligned_cols=22 Identities=27% Similarity=0.318 Sum_probs=17.4
Q ss_pred HHHHH-HhhccCCCHHHHHHHHH
Q 009281 292 RTISL-FGEVWGIGPATAQKLYE 313 (538)
Q Consensus 292 ~~l~l-f~~I~GvGpktA~~l~~ 313 (538)
..++. +.+|||||+++|.++.+
T Consensus 43 ~~~~~~~~~l~gIG~~ia~kI~E 65 (68)
T PF14716_consen 43 TSGEEDLKKLPGIGKSIAKKIDE 65 (68)
T ss_dssp HSHHHHHCTSTTTTHHHHHHHHH
T ss_pred hhHHHHHhhCCCCCHHHHHHHHH
Confidence 34454 77999999999999854
No 199
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=58.93 E-value=5.7 Score=44.88 Aligned_cols=29 Identities=24% Similarity=0.336 Sum_probs=24.3
Q ss_pred HHhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009281 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 296 lf~~I~GvGpktA~~l~~~GirtledL~~~ 325 (538)
.|.+||||||++.+.|++. +.|+++++++
T Consensus 515 ~L~~I~GiG~kr~~~LL~~-Fgs~~~I~~A 543 (574)
T PRK14670 515 NYTKIKGIGEKKAKKILKS-LGTYKDILLL 543 (574)
T ss_pred ccccCCCCCHHHHHHHHHH-hCCHHHHHhC
Confidence 4559999999999999984 5688888865
No 200
>PRK00076 recR recombination protein RecR; Reviewed
Probab=58.91 E-value=6.3 Score=38.35 Aligned_cols=31 Identities=16% Similarity=0.310 Sum_probs=23.4
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHH
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEH 284 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~ 284 (538)
+.+..|||||++.|.++.-.+-.-.-..++.
T Consensus 11 ~~l~~LPGIG~KsA~Rla~~ll~~~~~~~~~ 41 (196)
T PRK00076 11 EALRKLPGIGPKSAQRLAFHLLQRDREDVLR 41 (196)
T ss_pred HHHHHCCCCCHHHHHHHHHHHHcCCHHHHHH
Confidence 6789999999999999987775444344433
No 201
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=58.51 E-value=5 Score=45.30 Aligned_cols=29 Identities=24% Similarity=0.521 Sum_probs=24.1
Q ss_pred HHhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009281 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 296 lf~~I~GvGpktA~~l~~~GirtledL~~~ 325 (538)
.|.+|+|||||+.++|++. +.|++.++++
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 5688888865
No 202
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=58.45 E-value=8.4 Score=39.77 Aligned_cols=40 Identities=28% Similarity=0.317 Sum_probs=27.4
Q ss_pred HHHHhhccCCCHHHHHHHHHh-CC--CCHHHHhhcc-Ccchhhh
Q 009281 294 ISLFGEVWGIGPATAQKLYEK-GH--RTLDDLKNED-SLTHSQR 333 (538)
Q Consensus 294 l~lf~~I~GvGpktA~~l~~~-Gi--rtledL~~~~-~L~~~q~ 333 (538)
.+++.+|||+|+|.|+++... -. -++|+|++-| .+.+++-
T Consensus 329 ~~~llRVPGiG~ksa~rIv~~Rr~~rl~~e~Lkk~GvvlkRak~ 372 (404)
T COG4277 329 YKELLRVPGIGVKSARRIVMTRRRTRLTLEDLKKLGVVLKRAKP 372 (404)
T ss_pred HHHhcccCCCChHHHHHHHHHhhhcccCHHHHhhhceeeeccce
Confidence 445569999999999999865 33 4677777644 3444433
No 203
>PRK07758 hypothetical protein; Provisional
Probab=58.08 E-value=9.9 Score=32.60 Aligned_cols=23 Identities=13% Similarity=0.355 Sum_probs=20.3
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHh
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTT 276 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~t 276 (538)
+||.+|+|+|++..+.|+|-|..
T Consensus 67 ~ELl~iknlGkKSL~EIkekL~E 89 (95)
T PRK07758 67 KEILKLHGMGPASLPKLRKALEE 89 (95)
T ss_pred HHHHHccCCCHHHHHHHHHHHHH
Confidence 67999999999999999988754
No 204
>PRK13844 recombination protein RecR; Provisional
Probab=57.74 E-value=6.6 Score=38.30 Aligned_cols=32 Identities=16% Similarity=0.251 Sum_probs=23.7
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHH
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHF 285 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l 285 (538)
+.+..|||||++.|+++.-.+-.-.-.++++|
T Consensus 15 ~~l~~LPGIG~KsA~Rla~~lL~~~~~~~~~l 46 (200)
T PRK13844 15 ESLRKLPTIGKKSSQRLALYLLDKSPETAIAI 46 (200)
T ss_pred HHHHHCCCCCHHHHHHHHHHHHcCCHHHHHHH
Confidence 67899999999999999877764443444433
No 205
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=57.65 E-value=20 Score=36.85 Aligned_cols=29 Identities=17% Similarity=0.130 Sum_probs=26.2
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009281 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~ 325 (538)
|.++||+|+..++++.+.|+.|++||...
T Consensus 153 L~Qlp~i~~~~~~~l~~~~i~s~~~l~~~ 181 (312)
T smart00611 153 LLQLPHLPEEILKRLEKKKVLSLEDLLEL 181 (312)
T ss_pred cccCCCCCHHHHHHHHhCCCCCHHHHHhc
Confidence 44899999999999999999999999864
No 206
>PTZ00217 flap endonuclease-1; Provisional
Probab=57.55 E-value=7.9 Score=41.74 Aligned_cols=26 Identities=35% Similarity=0.640 Sum_probs=21.9
Q ss_pred hhccCCCHHHHHHHHHhCCCCHHHHhh
Q 009281 298 GEVWGIGPATAQKLYEKGHRTLDDLKN 324 (538)
Q Consensus 298 ~~I~GvGpktA~~l~~~GirtledL~~ 324 (538)
-+|+|||||||.+|.++ +.|++.+.+
T Consensus 238 pgi~GIG~ktA~~Li~~-~gsle~il~ 263 (393)
T PTZ00217 238 DTIKGIGPKTAYKLIKK-YKSIEEILE 263 (393)
T ss_pred CCCCCccHHHHHHHHHH-cCCHHHHHH
Confidence 47999999999999987 338888874
No 207
>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=57.35 E-value=3 Score=33.26 Aligned_cols=45 Identities=24% Similarity=0.337 Sum_probs=32.8
Q ss_pred ccCCCHHHHHHHHHhCCCCHHHHhhc--cCcchhhhccccchhhhcc
Q 009281 300 VWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDIKT 344 (538)
Q Consensus 300 I~GvGpktA~~l~~~GirtledL~~~--~~L~~~q~~Glk~~ed~~~ 344 (538)
--|+-+.+...|-..||.|++||..- ..|..+++||-+..+++.+
T Consensus 16 ~L~LS~Ra~n~L~~~~I~tv~dL~~~s~~~L~~i~n~G~ksl~EI~~ 62 (66)
T PF03118_consen 16 DLGLSVRAYNCLKRAGIHTVGDLVKYSEEDLLKIKNFGKKSLEEIKE 62 (66)
T ss_dssp GSTSBHHHHHHHHCTT--BHHHHHCS-HHHHHTSTTSHHHHHHHHHH
T ss_pred HhCCCHHHHHHHHHhCCcCHHHHHhCCHHHHHhCCCCCHhHHHHHHH
Confidence 33666777778878899999999853 4588889999888777654
No 208
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=57.34 E-value=11 Score=31.98 Aligned_cols=56 Identities=23% Similarity=0.326 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh-CCCCHHHHh
Q 009281 261 GIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLK 323 (538)
Q Consensus 261 giG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~-GirtledL~ 323 (538)
||+.+++.+|.+.... .-++.++++ ||. |+..|.|||-++|.++-.. |+..-+.-+
T Consensus 19 gl~~~~a~kl~~~yg~---~ai~~l~~n-PY~---L~~~i~gi~F~~aD~iA~~~g~~~~d~~R 75 (94)
T PF14490_consen 19 GLSPKLAMKLYKKYGD---DAIEILKEN-PYR---LIEDIDGIGFKTADKIALKLGIEPDDPRR 75 (94)
T ss_dssp T--HHHHHHHHHHH-T---THHHHHHH--STC---CCB-SSSSBHHHHHHHHHTTT--TT-HHH
T ss_pred CCCHHHHHHHHHHHhH---HHHHHHHHC-hHH---HHHHccCCCHHHHHHHHHHcCCCCCCHHH
Confidence 8899999999998776 444555554 553 3434899999999999987 876544433
No 209
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=57.03 E-value=7.7 Score=40.74 Aligned_cols=31 Identities=19% Similarity=0.241 Sum_probs=27.8
Q ss_pred HHHHhhccCCCHHHHHHHHHhCCCCHHHHhh
Q 009281 294 ISLFGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (538)
Q Consensus 294 l~lf~~I~GvGpktA~~l~~~GirtledL~~ 324 (538)
-.-|+.|.||||+.+++|.+.||.+++++-.
T Consensus 262 ~DdL~~I~GiGp~~e~~L~~~Gi~~f~QiA~ 292 (326)
T PRK12311 262 PDDLKKLTGVSPQIEKKLNDLGIFHFWQLAE 292 (326)
T ss_pred chhhhhhccCChhhhhhhhhcCCCCHHHhhC
Confidence 3557799999999999999999999999974
No 210
>PRK03352 DNA polymerase IV; Validated
Probab=56.89 E-value=32 Score=36.13 Aligned_cols=56 Identities=16% Similarity=0.324 Sum_probs=37.3
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh--CCCCHH
Q 009281 255 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRTLD 320 (538)
Q Consensus 255 ~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~--Girtle 320 (538)
.+..|||||+++++++..+ -+..+.+|..-.+....+.| |++.+..||+. |+..-.
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 3788999999998886653 56777777654433333444 56677888875 775443
No 211
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=56.79 E-value=8.8 Score=44.37 Aligned_cols=27 Identities=41% Similarity=0.623 Sum_probs=24.9
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHh
Q 009281 297 FGEVWGIGPATAQKLYEKGHRTLDDLK 323 (538)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~ 323 (538)
++.++||||++|+.|-+.||.|+.||.
T Consensus 11 ~~~l~gvg~~~~~~l~~lgi~t~~dll 37 (681)
T PRK10917 11 LTSLKGVGPKTAEKLAKLGIHTVQDLL 37 (681)
T ss_pred hhhcCCCCHHHHHHHHHcCCCCHHHHh
Confidence 457899999999999988999999998
No 212
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=55.38 E-value=9.3 Score=40.34 Aligned_cols=27 Identities=41% Similarity=0.588 Sum_probs=23.0
Q ss_pred hhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009281 298 GEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 298 ~~I~GvGpktA~~l~~~GirtledL~~~ 325 (538)
.+|+|||||||.+|.++ +.|++.+.+.
T Consensus 239 ~Gv~GIG~ktA~kli~~-~gsie~il~~ 265 (338)
T TIGR03674 239 EGVKGIGPKTALKLIKE-HGDLEKVLKA 265 (338)
T ss_pred CCCCCccHHHHHHHHHH-cCCHHHHHHh
Confidence 38999999999999998 4589998753
No 213
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=54.39 E-value=13 Score=42.45 Aligned_cols=96 Identities=16% Similarity=0.160 Sum_probs=55.4
Q ss_pred CCCCCCCCCCCCCCCCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecC------CCccEEEE-cCCh-HHHHHHH
Q 009281 3 PKTTRKPTPALDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLS------KKVTHVLA-MDLE-ALLQQVS 74 (538)
Q Consensus 3 ~~~~~~~~~~~~~~~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls------~~VTHVV~-~~~~-~~~~~l~ 74 (538)
|+.+|.++. +....+|.|+.+||+....... -+.|.+++..-||++...-+ ..-|-|+. +... ....|.+
T Consensus 573 ~~~~~~~a~-s~~~kLf~gl~~~~~g~fs~~p-~~~l~~l~~~~gg~~l~~~~~~~~~~k~s~~~~~~~~~~~~~~~~~k 650 (684)
T KOG4362|consen 573 PKEKRLRAE-SYKPKLFEGLKFYFVGDFSNPP-KEQLQELVHLAGGTILQVPRVAYSDKKKSTIVVLSEKPVLDSILWQK 650 (684)
T ss_pred ccccccccc-ccCcchhcCCcceeecccccCc-HHHHHHHHhhcCcceeeccCcccccccccceeEeecccCCCchhhhh
Confidence 455554433 4445999999999997754322 46678899999999876431 22333333 1110 0111222
Q ss_pred Hhhhc----cCCccccccchHHHHHhcCcc
Q 009281 75 KQHLA----RFKGSVIRYQWLEDSLRLGEK 100 (538)
Q Consensus 75 ~~~~~----~~~~~lV~~~Wl~ecik~g~l 100 (538)
..... ..+.++|+-.||.+++.--+.
T Consensus 651 ~~~~ea~~~s~~a~~~~~~wvl~s~a~~~~ 680 (684)
T KOG4362|consen 651 VNDAEALALSQRARAVSSSWVLDSIAGYQI 680 (684)
T ss_pred hccHHHHHHhcCCCccchhhhhcchhceee
Confidence 11111 113789999999999864433
No 214
>PRK04374 PII uridylyl-transferase; Provisional
Probab=54.29 E-value=42 Score=40.10 Aligned_cols=62 Identities=19% Similarity=0.405 Sum_probs=40.1
Q ss_pred HHHHHHHHhhhcCC---CeEEEeccccccc-CCcCCCeeEEEecCCc--chhhhhHHHHHHHHHHcCc
Q 009281 354 MERLLQKAGEEVLP---EVIILCGGSYRRG-KASCGDLDVVIMHPDR--KSHKGFLSKYVKKLKEMKF 415 (538)
Q Consensus 354 i~~iv~~~~~~~~p---~~~v~~~Gs~RRg-ke~~~DvDiLIt~~~~--~~~~~~l~~~v~~L~~~g~ 415 (538)
+..+++++.....| ++-++.+|||=|| ..-.+|||+||-+++. ......+.+++..|-+.|+
T Consensus 55 ~D~~l~~~~~~~~~~~~~~alvAvGgYGR~EL~p~SDIDLliL~~~~~~~~~~~~i~~~i~~LWD~gL 122 (869)
T PRK04374 55 VDQLMRNAWTRCIPADSGLSLHAVGGYGRGELFPRSDVDLLVLGETAAQQRHEQALARLFALLWDVGL 122 (869)
T ss_pred HHHHHHHHHHHhCCCcCCEEEEEcCCccccccCCcccceEEEEecCCCCchHHHHHHHHHHHHHhcCC
Confidence 44455544433334 3567788999554 5667899999988743 2344566777777766664
No 215
>PRK05755 DNA polymerase I; Provisional
Probab=54.06 E-value=9.1 Score=45.64 Aligned_cols=25 Identities=44% Similarity=0.598 Sum_probs=21.1
Q ss_pred hhccCCCHHHHHHHHHh-CCCCHHHHhh
Q 009281 298 GEVWGIGPATAQKLYEK-GHRTLDDLKN 324 (538)
Q Consensus 298 ~~I~GvGpktA~~l~~~-GirtledL~~ 324 (538)
-+|+|||||||.+|.++ | |+|.+.+
T Consensus 190 pGv~GiG~ktA~~Ll~~~g--sle~i~~ 215 (880)
T PRK05755 190 PGVPGIGEKTAAKLLQEYG--SLEGLYE 215 (880)
T ss_pred CCCCCccHHHHHHHHHHcC--CHHHHHH
Confidence 46899999999999987 6 7888763
No 216
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=53.89 E-value=35 Score=35.63 Aligned_cols=48 Identities=19% Similarity=0.338 Sum_probs=38.8
Q ss_pred CCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEcCC
Q 009281 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDL 66 (538)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~~~~ 66 (538)
.+|.|.+|.|-.. +... +.-+++++..+||.|.+..+.+++.||+-+.
T Consensus 231 ~l~~g~~~v~TG~-l~~~-R~e~~~~~~~~G~~v~~sVs~~t~~lv~g~~ 278 (313)
T PRK06063 231 PLVQGMRVALSAE-VSRT-HEELVERILHAGLAYSDSVDRDTSLVVCNDP 278 (313)
T ss_pred cccCCCEEEEecC-CCCC-HHHHHHHHHHcCCEecCccccCccEEEECCC
Confidence 4689999988654 3334 4667899999999999999999999999543
No 217
>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=53.04 E-value=31 Score=33.16 Aligned_cols=42 Identities=10% Similarity=0.311 Sum_probs=27.8
Q ss_pred hHHHHHHHHHHHh-cCCcccc-chhhhcCCCCCCHHHHHHHHHH
Q 009281 232 RSFSYYKAIPVIE-KLPFKIE-SADQVKGLPGIGKSMQDHIQEI 273 (538)
Q Consensus 232 r~~aY~rAa~~l~-~l~~~i~-~~~~l~~lpgiG~~ia~~I~Ei 273 (538)
|+..-.+++..+. .....+. ..++|.+|||||+.+|+.|--+
T Consensus 82 Ka~~i~~~a~~i~~~~~~~~~~~~~~L~~l~GIG~ktA~~ill~ 125 (191)
T TIGR01083 82 KAKNIIALCRILVERYGGEVPEDREELVKLPGVGRKTANVVLNV 125 (191)
T ss_pred HHHHHHHHHHHHHHHcCCCCchHHHHHHhCCCCcHHHHHHHHHH
Confidence 5555555665553 2322222 3578999999999999998733
No 218
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=52.79 E-value=9.3 Score=34.35 Aligned_cols=25 Identities=24% Similarity=0.383 Sum_probs=20.1
Q ss_pred HHHHHhhccCCCHHHHHHHHHh-CCC
Q 009281 293 TISLFGEVWGIGPATAQKLYEK-GHR 317 (538)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~-Gir 317 (538)
+.--|+.|+|||+++|..+-+. ||.
T Consensus 15 v~~aLt~i~GIG~~~A~~ic~~lgi~ 40 (122)
T CHL00137 15 IEYALTYIYGIGLTSAKEILEKANID 40 (122)
T ss_pred eeeeecccccccHHHHHHHHHHcCcC
Confidence 3344689999999999999876 764
No 219
>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=52.44 E-value=14 Score=38.00 Aligned_cols=50 Identities=24% Similarity=0.451 Sum_probs=35.3
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH
Q 009281 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 256 l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (538)
+.+|||||+.+++++.+. -+..+++|..-. .+.+.+++|+++++|.+||+
T Consensus 1 l~~i~gig~~~~~~L~~~----Gi~ti~dl~~~~----~~~L~~~~g~~~~~a~~l~~ 50 (310)
T TIGR02236 1 LEDLPGVGPATAEKLREA----GYDTFEAIAVAS----PKELSEIAGISEGTAAKIIQ 50 (310)
T ss_pred CcccCCCCHHHHHHHHHc----CCCCHHHHHcCC----HHHHHhccCCCHHHHHHHHH
Confidence 467999999998887664 234455554432 23345888999999999986
No 220
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=51.87 E-value=6.7 Score=45.02 Aligned_cols=48 Identities=15% Similarity=0.248 Sum_probs=34.5
Q ss_pred HHhhccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhccccchhhhcc
Q 009281 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIKT 344 (538)
Q Consensus 296 lf~~I~GvGpktA~~l~~~GirtledL~~~~--~L~~~q~~Glk~~ed~~~ 344 (538)
.|.+|+||||++.++|++. +.|+++|+++. .|....+++.+..+.+..
T Consensus 609 ~L~~IpGiG~kr~~~LL~~-FgS~~~i~~As~eel~~v~gi~~~~A~~i~~ 658 (691)
T PRK14672 609 SFERLPHVGKVRAHRLLAH-FGSFRSLQSATPQDIATAIHIPLTQAHTILH 658 (691)
T ss_pred ccccCCCCCHHHHHHHHHH-hcCHHHHHhCCHHHHHhCCCCCHHHHHHHHH
Confidence 4569999999999999984 55888888653 455565666555555443
No 221
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=51.74 E-value=9.6 Score=34.28 Aligned_cols=24 Identities=21% Similarity=0.470 Sum_probs=19.8
Q ss_pred HHHHhhccCCCHHHHHHHHHh-CCC
Q 009281 294 ISLFGEVWGIGPATAQKLYEK-GHR 317 (538)
Q Consensus 294 l~lf~~I~GvGpktA~~l~~~-Gir 317 (538)
.--|+.|+|||+.+|..+.+. |+.
T Consensus 16 ~~aL~~I~GIG~~~a~~i~~~lgi~ 40 (122)
T PRK05179 16 VIALTYIYGIGRTRAKEILAAAGID 40 (122)
T ss_pred EeeecccccccHHHHHHHHHHhCcC
Confidence 334689999999999999886 764
No 222
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=51.61 E-value=6.1 Score=45.11 Aligned_cols=30 Identities=27% Similarity=0.442 Sum_probs=24.2
Q ss_pred HHHhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009281 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 295 ~lf~~I~GvGpktA~~l~~~GirtledL~~~ 325 (538)
..|.+||||||+++++|++. +.|+++++++
T Consensus 552 S~L~~IpGIG~kr~~~LL~~-FgSi~~I~~A 581 (624)
T PRK14669 552 SELLEIPGVGAKTVQRLLKH-FGSLERVRAA 581 (624)
T ss_pred HHHhcCCCCCHHHHHHHHHH-cCCHHHHHhC
Confidence 34669999999999999984 5578888764
No 223
>KOG3548 consensus DNA damage checkpoint protein RHP9/CRB2/53BP1 [Replication, recombination and repair]
Probab=50.65 E-value=21 Score=42.00 Aligned_cols=89 Identities=13% Similarity=0.051 Sum_probs=51.7
Q ss_pred CCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeec-CCCccEEEEcC-------------------------ChHHH
Q 009281 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKL-SKKVTHVLAMD-------------------------LEALL 70 (538)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~l-s~~VTHVV~~~-------------------------~~~~~ 70 (538)
.+|-||++.|-...-. ...+.+-+..+||.|.+.. ..--+|=...+ ..|..
T Consensus 924 niFd~cvF~lTsa~~s---d~~~r~s~e~~gg~vle~gl~~~Fn~p~~g~~~~lr~Ln~~q~~ks~~qalLIsdth~Rt~ 1000 (1176)
T KOG3548|consen 924 NIFDGCVFMLTSANRS---DSASRPSMEKHGGLVLEKGLMNLFNTPFKGGGIVLRQLNSFQERKSNYQALLISDTHYRTH 1000 (1176)
T ss_pred chhcceeEEEeccccc---hhhhhhhhhccCChhhhccccccccccccCCcchHHhhhHHhhhccccceeEeehhhhHHH
Confidence 7999999887533221 1222233344888887643 33244443211 11112
Q ss_pred HHHHHhhhccCCccccccchHHHHHhcCcccCccccccccC
Q 009281 71 QQVSKQHLARFKGSVIRYQWLEDSLRLGEKVSEDLYRIKLD 111 (538)
Q Consensus 71 ~~l~~~~~~~~~~~lV~~~Wl~ecik~g~lv~e~~y~l~~~ 111 (538)
++|.. | .+..--|...||.+|+++++.||-.+|.|...
T Consensus 1001 KYLea--L-A~giPcVh~~fI~aC~e~nr~Vdy~~YLLpsG 1038 (1176)
T KOG3548|consen 1001 KYLEA--L-ARGIPCVHNTFIQACGEQNRCVDYTDYLLPSG 1038 (1176)
T ss_pred HHHHH--H-HcCCCcccHHHHHHHHhccccccchhhcccCc
Confidence 22211 1 11234689999999999999999999998643
No 224
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=50.42 E-value=36 Score=30.95 Aligned_cols=43 Identities=9% Similarity=0.301 Sum_probs=27.1
Q ss_pred hHHHHHHHHHHHhc-CCccc-cchhhhcCCCCCCHHHHHHHHHHH
Q 009281 232 RSFSYYKAIPVIEK-LPFKI-ESADQVKGLPGIGKSMQDHIQEIV 274 (538)
Q Consensus 232 r~~aY~rAa~~l~~-l~~~i-~~~~~l~~lpgiG~~ia~~I~Eil 274 (538)
|+..-...+..|.. ....+ ...+.|..|||||+.+|+.|.=+.
T Consensus 48 ka~~i~~~a~~~~~~~~~~~~~~~~~L~~l~GIG~~tA~~~l~~~ 92 (149)
T smart00478 48 KAKYLIELARILVEEYGGEVPDDREELLKLPGVGRKTANAVLSFA 92 (149)
T ss_pred HHHHHHHHHHHHHHHHCCCccHHHHHHHcCCCCcHHHHHHHHHHH
Confidence 55555555555433 12122 235778999999999999876553
No 225
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=49.64 E-value=9.2 Score=40.48 Aligned_cols=52 Identities=19% Similarity=0.232 Sum_probs=41.3
Q ss_pred hchhHHHHHHhhccCCCHHHHHHHHHh-CCCCHHHHhhcc--Ccchhhhccccchhh
Q 009281 288 DEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED--SLTHSQRLGLKYFDD 341 (538)
Q Consensus 288 ~~~~~~l~lf~~I~GvGpktA~~l~~~-GirtledL~~~~--~L~~~q~~Glk~~ed 341 (538)
...++...++.+||+|+++.|++|.+. | ||..|.++. .|....++|-+....
T Consensus 280 ~v~prGyRiLs~IPrl~k~iAk~Ll~~FG--SL~~Il~As~eeL~~VeGIGe~rA~~ 334 (352)
T PRK13482 280 PVSPRGYRLLSKIPRLPSAVIENLVEHFG--SLQGLLAASIEDLDEVEGIGEVRARA 334 (352)
T ss_pred ccCCcHHHHHhcCCCCCHHHHHHHHHHcC--CHHHHHcCCHHHHhhCCCcCHHHHHH
Confidence 345667899999999999999999997 7 899988653 577777888655444
No 226
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=49.36 E-value=30 Score=39.62 Aligned_cols=50 Identities=20% Similarity=0.429 Sum_probs=35.5
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~ 314 (538)
..|.+|||||+..+.++-+ ++..++.+++- .++.+.+| ||.++|+++++.
T Consensus 552 S~L~~IpGIG~kr~~~LL~-----~FgSi~~I~~A----s~eeL~~v--i~~k~A~~I~~~ 601 (624)
T PRK14669 552 SELLEIPGVGAKTVQRLLK-----HFGSLERVRAA----TETQLAAV--VGRAAAEAIIAH 601 (624)
T ss_pred HHHhcCCCCCHHHHHHHHH-----HcCCHHHHHhC----CHHHHHHH--hCHHHHHHHHHH
Confidence 5688999999998887654 34445555542 23444566 999999999874
No 227
>COG5067 DBF4 Protein kinase essential for the initiation of DNA replication [DNA replication, recombination, and repair / Cell division and chromosome partitioning]
Probab=48.68 E-value=12 Score=39.85 Aligned_cols=49 Identities=16% Similarity=0.268 Sum_probs=38.7
Q ss_pred CCCCCCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEE
Q 009281 13 LDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLA 63 (538)
Q Consensus 13 ~~~~~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~ 63 (538)
+..-..|..+.+|+.. ....|.+.+++.+..-||.|..-++..||||+.
T Consensus 117 R~Y~~aFp~f~fY~dn--~s~~~khRvk~gf~~LGa~v~tfF~~~VThfiT 165 (468)
T COG5067 117 RTYCCAFPAFKFYKDN--KSGKRKHRVKEGFCELGAVVFTFFEEHVTHFIT 165 (468)
T ss_pred hhhhcccchhhhhhcC--CCHHHHHHHHHHHHHhhhhhheeeccceEEEEE
Confidence 4445789999998853 223444458999999999999999999999996
No 228
>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=48.38 E-value=7.5 Score=40.42 Aligned_cols=51 Identities=25% Similarity=0.342 Sum_probs=34.5
Q ss_pred HHHHHhhccCCCHHHHHHHHHh---C-CCCHHHHhhcc-----Ccchhhhccccchhhhc
Q 009281 293 TISLFGEVWGIGPATAQKLYEK---G-HRTLDDLKNED-----SLTHSQRLGLKYFDDIK 343 (538)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~---G-irtledL~~~~-----~L~~~q~~Glk~~ed~~ 343 (538)
.+..+++|||||+++|.++.+- | +..+++|+++. .|....|+|.+....|-
T Consensus 43 ~~~~~~~ipgiG~~ia~kI~E~~~tG~~~~le~l~~~~~~~l~~l~~i~GiGpk~a~~l~ 102 (307)
T cd00141 43 SLEEAKKLPGIGKKIAEKIEEILETGKLRKLEELREDVPPGLLLLLRVPGVGPKTARKLY 102 (307)
T ss_pred CHHHhcCCCCccHHHHHHHHHHHHcCCHHHHHHHhccchHHHHHHHcCCCCCHHHHHHHH
Confidence 3444579999999999999873 3 35556665431 25667778876665554
No 229
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=48.07 E-value=28 Score=35.06 Aligned_cols=30 Identities=23% Similarity=0.467 Sum_probs=22.5
Q ss_pred cCCcccc-chhhhcCCCCCCHHHHHHHHHHH
Q 009281 245 KLPFKIE-SADQVKGLPGIGKSMQDHIQEIV 274 (538)
Q Consensus 245 ~l~~~i~-~~~~l~~lpgiG~~ia~~I~Eil 274 (538)
.+..+|- ++++|..|||||++||-....+.
T Consensus 149 ~f~gDIP~~v~dLlsLPGVGPKMa~L~m~~A 179 (286)
T KOG1921|consen 149 KFDGDIPDTVEDLLSLPGVGPKMAHLTMQVA 179 (286)
T ss_pred HhCCCCchhHHHHhcCCCCchHHHHHHHHHH
Confidence 3444554 47999999999999998766543
No 230
>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=47.98 E-value=16 Score=26.72 Aligned_cols=31 Identities=32% Similarity=0.355 Sum_probs=23.2
Q ss_pred CCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhh
Q 009281 303 IGPATAQKLYEKGHRTLDDLKNED--SLTHSQR 333 (538)
Q Consensus 303 vGpktA~~l~~~GirtledL~~~~--~L~~~q~ 333 (538)
|.+..+.+|++.|+.|+++|-... .|...++
T Consensus 1 i~~~~~~~L~~~G~~s~e~la~~~~~eL~~i~g 33 (50)
T TIGR01954 1 IDEEIAQLLVEEGFTTVEDLAYVPIDELLSIEG 33 (50)
T ss_pred CCHHHHHHHHHcCCCCHHHHHccCHHHHhcCCC
Confidence 457889999999999999998543 3554444
No 231
>TIGR01084 mutY A/G-specific adenine glycosylase. This equivalog model identifies mutY members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=47.98 E-value=25 Score=36.04 Aligned_cols=24 Identities=17% Similarity=0.209 Sum_probs=19.2
Q ss_pred HHHHHHhhccCCCHHHHHHHHHhC
Q 009281 292 RTISLFGEVWGIGPATAQKLYEKG 315 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~~G 315 (538)
..++.|+++||||++||..+---+
T Consensus 102 ~~~~~L~~LpGIG~~TA~~Il~~a 125 (275)
T TIGR01084 102 QDFEDLAALPGVGRYTAGAILSFA 125 (275)
T ss_pred HHHHHHHhCCCCCHHHHHHHHHHH
Confidence 357778899999999999876543
No 232
>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=47.92 E-value=11 Score=33.31 Aligned_cols=24 Identities=33% Similarity=0.517 Sum_probs=19.8
Q ss_pred HHHHhhccCCCHHHHHHHHHh-CCC
Q 009281 294 ISLFGEVWGIGPATAQKLYEK-GHR 317 (538)
Q Consensus 294 l~lf~~I~GvGpktA~~l~~~-Gir 317 (538)
.--|+.|+|||+++|..+.+. |+.
T Consensus 14 ~~aL~~i~GIG~~~a~~i~~~lgi~ 38 (113)
T TIGR03631 14 EIALTYIYGIGRTRARKILEKAGID 38 (113)
T ss_pred eeeeeeeecccHHHHHHHHHHhCcC
Confidence 334689999999999999886 774
No 233
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=47.73 E-value=31 Score=40.43 Aligned_cols=53 Identities=26% Similarity=0.464 Sum_probs=36.3
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh--CCCC
Q 009281 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (538)
Q Consensus 256 l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~--Girt 318 (538)
+..|||+|-+|..++...- +...-+|+ ..++.-+ .+=+|||+++++|.. ||..
T Consensus 551 v~~LPGVG~sm~~kL~s~~----i~tCgdLq----~~T~~kl--~k~~G~Klgq~i~~~CrG~Dd 605 (1016)
T KOG2093|consen 551 VDDLPGVGSSMKSKLVSQF----IQTCGDLQ----LITLIKL--RKVFGPKLGQKIYRGCRGIDD 605 (1016)
T ss_pred cccCCCccHHHHHHHHHhc----cchhHHHH----HHHHHHH--HhhhcccHHHHHHHhcCCCcC
Confidence 6789999999999977654 33333433 2344444 344589999999984 7744
No 234
>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=47.72 E-value=36 Score=36.50 Aligned_cols=58 Identities=19% Similarity=0.445 Sum_probs=35.1
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhc---------hhH--HHHHHhhccCCCHHHHHHHHHh--CCCC
Q 009281 255 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDE---------KVR--TISLFGEVWGIGPATAQKLYEK--GHRT 318 (538)
Q Consensus 255 ~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~---------~~~--~l~lf~~I~GvGpktA~~l~~~--Girt 318 (538)
.+.+|||||+++++++..+ | +..+-+|.+-. ... ....+.+.+ |.+++.++|+. |+.+
T Consensus 173 pv~~l~GiG~~~~~kL~~~---G-I~tigdl~~~~~~~~~~~~~~~~~~s~~~L~~~f--G~~~g~~l~~~a~G~d~ 243 (379)
T cd01703 173 DLRKIPGIGYKTAAKLEAH---G-ISSVRDLQEFSNRNRQTVGAAPSLLELLLMVKEF--GEGIGQRIWKLLFGRDT 243 (379)
T ss_pred CccccCCcCHHHHHHHHHc---C-CCcHHHHHhCCcccccccccccccccHHHHHHHH--CHHHHHHHHHHHCCCCC
Confidence 4788999999999998875 2 23333333222 000 023343444 56778888875 8875
No 235
>COG5186 PAP1 Poly(A) polymerase [RNA processing and modification]
Probab=47.29 E-value=76 Score=33.85 Aligned_cols=51 Identities=27% Similarity=0.460 Sum_probs=41.0
Q ss_pred eEEEecccccccCC-cCCCeeEEEecCCcchhhhhHHHHHHHHHHcCcccee
Q 009281 369 VIILCGGSYRRGKA-SCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLRED 419 (538)
Q Consensus 369 ~~v~~~Gs~RRgke-~~~DvDiLIt~~~~~~~~~~l~~~v~~L~~~g~l~~~ 419 (538)
-++.--||||-|-- -+.|||-|+..|..-+...+|..+-..|+...-+.+.
T Consensus 82 GKIFTyGSYRLGVhgpGsDIDtLvvVPkHVsR~dFFt~f~~~Lrer~ei~ev 133 (552)
T COG5186 82 GKIFTYGSYRLGVHGPGSDIDTLVVVPKHVSRSDFFTHFYEELRERPEIEEV 133 (552)
T ss_pred ceeeeecceeeeccCCCCCcceEEEecccccHHHHHHHHHHHhccCcchhhh
Confidence 36777799999975 5779999999998888888999888888877666543
No 236
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=46.93 E-value=19 Score=34.62 Aligned_cols=40 Identities=28% Similarity=0.283 Sum_probs=33.3
Q ss_pred ccccc-hhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHh
Q 009281 248 FKIES-ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEK 287 (538)
Q Consensus 248 ~~i~~-~~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~ 287 (538)
.||+. +-+|+-|||||++++..|-|=-+..-+..++.+++
T Consensus 123 ~PIt~RLH~LELLpGiGkK~m~~ILeERkkkpFeSFeDi~~ 163 (202)
T COG1491 123 EPITLRLHQLELLPGIGKKTMWAILEERKKKPFESFEDIKE 163 (202)
T ss_pred CcchHHHHHHHhcccccHHHHHHHHHHHhcCCCcCHHHHHH
Confidence 67776 47899999999999999988777777777777765
No 237
>PRK01216 DNA polymerase IV; Validated
Probab=46.86 E-value=63 Score=34.27 Aligned_cols=52 Identities=23% Similarity=0.388 Sum_probs=34.4
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh--CCC
Q 009281 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHR 317 (538)
Q Consensus 256 l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~--Gir 317 (538)
+..|||||++++++...+ | +..+.+|.+-...... +.+ |+..+..||+. |+.
T Consensus 180 i~~l~giG~~~~~~L~~~---G-i~TigdL~~~~~~~L~----~rf--G~~~~~~L~~~a~G~d 233 (351)
T PRK01216 180 IADIPGIGDITAEKLKKL---G-VNKLVDTLRIEFDELK----GII--GEAKAKYLFSLARNEY 233 (351)
T ss_pred cccccCCCHHHHHHHHHc---C-CCcHHHHhcCCHHHHH----HHH--CHHHHHHHHHHhCCCC
Confidence 678899999988877654 3 5666676654433333 444 46678888883 754
No 238
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=46.60 E-value=29 Score=33.99 Aligned_cols=20 Identities=25% Similarity=0.275 Sum_probs=16.8
Q ss_pred HHHHHhhccCCCHHHHHHHH
Q 009281 293 TISLFGEVWGIGPATAQKLY 312 (538)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~ 312 (538)
..+.|.+|.|||+-||..+.
T Consensus 113 ~R~~LL~iKGIG~ETaDsIL 132 (215)
T COG2231 113 LREELLSIKGIGKETADSIL 132 (215)
T ss_pred HHHHHHccCCcchhhHHHHH
Confidence 56777799999999998763
No 239
>PF02889 Sec63: Sec63 Brl domain; InterPro: IPR004179 This domain was named after the yeast Sec63 (or NPL1) (also known as the Brl domain) protein in which it was found. This protein is required for assembly of functional endoplasmic reticulum translocons [, ]. Other yeast proteins containing this domain include pre-mRNA splicing helicase BRR2, HFM1 protein and putative helicases. ; PDB: 3IM2_A 3IM1_A 3HIB_A 2Q0Z_X.
Probab=46.01 E-value=24 Score=36.21 Aligned_cols=28 Identities=32% Similarity=0.514 Sum_probs=22.2
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHhh
Q 009281 297 FGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (538)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~ 324 (538)
|.++||+|++.++++-+.|+.|+++|.+
T Consensus 150 L~Qlp~i~~~~~~~l~~~~i~~l~~l~~ 177 (314)
T PF02889_consen 150 LLQLPHIGEESLKKLEKRGIKTLQDLRD 177 (314)
T ss_dssp GGGSTT--HHHHHHHHHTT--SHHHHHH
T ss_pred hhcCCCCCHHHHHHHhccCCCcHHHHhh
Confidence 5599999999999999999999999995
No 240
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=45.81 E-value=69 Score=38.43 Aligned_cols=48 Identities=17% Similarity=0.453 Sum_probs=34.3
Q ss_pred CeEEEeccccccc-CCcCCCeeEEEecCCcc--hhhhhHHHHHHHHHHcCc
Q 009281 368 EVIILCGGSYRRG-KASCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMKF 415 (538)
Q Consensus 368 ~~~v~~~Gs~RRg-ke~~~DvDiLIt~~~~~--~~~~~l~~~v~~L~~~g~ 415 (538)
++.+..+|||=|| ..-.+|||+||-+++.. ....+...++..|-+.|+
T Consensus 78 ~~alvAvGgyGR~EL~p~SDiDll~l~~~~~~~~~~~~i~~~~~~LwD~gL 128 (895)
T PRK00275 78 DIALVAVGGYGRGELHPYSDIDLLILLDSADHEEFREPIERFLTLLWDIGL 128 (895)
T ss_pred CEEEEEcCCccccCcCCCCCceEEEEecCCCChHHHHHHHHHHHHHHhcCC
Confidence 4567789999665 45689999999887442 234567777777777765
No 241
>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=45.78 E-value=29 Score=36.13 Aligned_cols=73 Identities=18% Similarity=0.195 Sum_probs=41.7
Q ss_pred cCCChhHHHHHHHHHHHhcCCc------ccc------chhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHH
Q 009281 227 LGEDRRSFSYYKAIPVIEKLPF------KIE------SADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTI 294 (538)
Q Consensus 227 ~g~~~r~~aY~rAa~~l~~l~~------~i~------~~~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l 294 (538)
.|-.+|+..-..+|..+..-.. .+. ..++|..|||||+.+|+-|.=+ .-|+..- +-. ...+.
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 4444576666667776654211 111 2367999999999999988633 2333221 111 23456
Q ss_pred HHHhhccCCCH
Q 009281 295 SLFGEVWGIGP 305 (538)
Q Consensus 295 ~lf~~I~GvGp 305 (538)
+.+.+++|+.+
T Consensus 255 r~~~r~y~~~~ 265 (310)
T TIGR00588 255 RIANRDYPWHP 265 (310)
T ss_pred HHHHHHhcccc
Confidence 66666666543
No 242
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=45.69 E-value=35 Score=38.70 Aligned_cols=84 Identities=20% Similarity=0.349 Sum_probs=51.5
Q ss_pred CcHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhh
Q 009281 209 LNKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKD 288 (538)
Q Consensus 209 ~N~~ia~~L~~la~~~e~~g~~~r~~aY~rAa~~l~~l~~~i~~~~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~ 288 (538)
.|......|..+-+... .-+.+|.|.-+. +-.--..|.+|||||++-..++-.- -|++..+..
T Consensus 496 ~~~p~l~~lq~irDEaH-----rfAi~~hR~~R~------k~~~~s~Ld~I~GiG~~r~~~LL~~--Fgs~~~i~~---- 558 (581)
T COG0322 496 PNSPALYLLQRIRDEAH-----RFAITYHRKKRS------KAMLQSSLDDIPGIGPKRRKALLKH--FGSLKGIKS---- 558 (581)
T ss_pred CCCHHHHHHHHHHHHHH-----HHHHHHHHHHhh------hhhhcCccccCCCcCHHHHHHHHHH--hhCHHHHHh----
Confidence 35555555555543321 235666666432 1111245889999999988776442 234443332
Q ss_pred chhHHHHHHhhccCCCHHHHHHHHH
Q 009281 289 EKVRTISLFGEVWGIGPATAQKLYE 313 (538)
Q Consensus 289 ~~~~~l~lf~~I~GvGpktA~~l~~ 313 (538)
-+++.|..| ||+++.|+++|+
T Consensus 559 ---As~eel~~v-gi~~~~a~~i~~ 579 (581)
T COG0322 559 ---ASVEELAKV-GISKKLAEKIYE 579 (581)
T ss_pred ---cCHHHHHHc-CCCHHHHHHHHh
Confidence 356778899 999999999986
No 243
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=45.67 E-value=14 Score=37.14 Aligned_cols=31 Identities=23% Similarity=0.366 Sum_probs=21.6
Q ss_pred HHHHhhchhHHHHHHhhccCCCHHHHHHHHHh
Q 009281 283 EHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (538)
Q Consensus 283 e~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~ 314 (538)
+++..|.|..+=+|+ ++||||||.|.--.+.
T Consensus 148 d~f~gDIP~~v~dLl-sLPGVGPKMa~L~m~~ 178 (286)
T KOG1921|consen 148 DKFDGDIPDTVEDLL-SLPGVGPKMAHLTMQV 178 (286)
T ss_pred HHhCCCCchhHHHHh-cCCCCchHHHHHHHHH
Confidence 455566666555555 9999999999765443
No 244
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=44.95 E-value=42 Score=35.47 Aligned_cols=61 Identities=18% Similarity=0.220 Sum_probs=43.4
Q ss_pred HHHHHcCCChhHHHHHHHHHHHhcC-Ccccc-chhhhcCCCCCCHHHHHHHHHHHHhCCcchh
Q 009281 222 NIYRALGEDRRSFSYYKAIPVIEKL-PFKIE-SADQVKGLPGIGKSMQDHIQEIVTTGKLSKL 282 (538)
Q Consensus 222 ~~~e~~g~~~r~~aY~rAa~~l~~l-~~~i~-~~~~l~~lpgiG~~ia~~I~Eil~tG~~~~l 282 (538)
.+.+=.|-..|++.-.+||..+... ...+. +.+++..|||||..+|..|--|.-.-...-|
T Consensus 79 ~~W~gLGYysRArnL~~~A~~v~~~~~G~~P~~~~~l~~LpGiG~yTa~Ail~~a~~~~~~~l 141 (342)
T COG1194 79 KAWEGLGYYSRARNLHKAAQEVVERHGGEFPDDEEELAALPGVGPYTAGAILSFAFNQPEPVL 141 (342)
T ss_pred HHHHhcChHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHhCCCCcHHHHHHHHHHHhCCCCcee
Confidence 4455556556898888888777654 44444 4578999999999999999887654333333
No 245
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=44.68 E-value=40 Score=33.38 Aligned_cols=57 Identities=25% Similarity=0.292 Sum_probs=34.2
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCH---HHHHHHHHhCC
Q 009281 252 SADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGP---ATAQKLYEKGH 316 (538)
Q Consensus 252 ~~~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGp---ktA~~l~~~Gi 316 (538)
..++|.+|||||+.+|+.|-=+. -|+-. +- ...-+.++|.++ |+.+ ..++.|++.++
T Consensus 119 ~re~Ll~l~GIG~kTAd~iLlya-~~rp~----fv--VDty~~Rv~~Rl-G~~~~~y~~~~~~~~~~l 178 (218)
T PRK13913 119 TREWLLDQKGIGKESADAILCYV-CAKEV----MV--VDKYSYLFLKKL-GIEIEDYDELQHFFEKGV 178 (218)
T ss_pred HHHHHHcCCCccHHHHHHHHHHH-cCCCc----cc--cchhHHHHHHHc-CCCCCCHHHHHHHHHHhh
Confidence 34779999999999999987654 33311 11 122356667443 6644 34555555444
No 246
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=44.56 E-value=17 Score=39.15 Aligned_cols=33 Identities=24% Similarity=0.313 Sum_probs=28.7
Q ss_pred HHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhh
Q 009281 292 RTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~~GirtledL~~ 324 (538)
+.-.-|+.|.||||+.+.+|...||.+++++-.
T Consensus 320 g~aDDLk~I~GIGpk~e~~Ln~~Gi~~f~QIA~ 352 (400)
T PRK12373 320 GGADDLKLISGVGPKIEATLNELGIFTFDQVAA 352 (400)
T ss_pred CCchhhhhccCCChHHHHHHHhcCCCCHHHHhC
Confidence 334557799999999999999999999999974
No 247
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=44.46 E-value=29 Score=41.07 Aligned_cols=32 Identities=13% Similarity=0.211 Sum_probs=26.3
Q ss_pred HHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009281 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~GirtledL~~~ 325 (538)
..+++.++|||||+.|+.+.+. +.|+++|.++
T Consensus 755 ~q~~L~~lPgI~~~~a~~ll~~-f~si~~l~~a 786 (814)
T TIGR00596 755 PQDFLLKLPGVTKKNYRNLRKK-VKSIRELAKL 786 (814)
T ss_pred HHHHHHHCCCCCHHHHHHHHHH-cCCHHHHHhC
Confidence 3445669999999999999985 8899999864
No 248
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=44.40 E-value=49 Score=34.31 Aligned_cols=48 Identities=17% Similarity=0.088 Sum_probs=37.7
Q ss_pred CCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEcC
Q 009281 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMD 65 (538)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~~~ 65 (538)
..|.|.+|.|-..=-.-. +.-+++++..+||.|.+..+.++|.+|+-+
T Consensus 219 ~~l~g~~~vfTG~l~~~~-R~~~~~~~~~~Gg~v~~sVs~~t~~lV~G~ 266 (309)
T PRK06195 219 TAFKEEVVVFTGGLASMT-RDEAMILVRRLGGTVGSSVTKKTTYLVTNT 266 (309)
T ss_pred ccccCCEEEEccccCCCC-HHHHHHHHHHhCCEecCCcccCceEEEECC
Confidence 469999999855421223 455679999999999999999999999853
No 249
>PRK02794 DNA polymerase IV; Provisional
Probab=43.87 E-value=1.3e+02 Score=32.57 Aligned_cols=52 Identities=12% Similarity=0.300 Sum_probs=33.8
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh--CCCC
Q 009281 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (538)
Q Consensus 256 l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~--Girt 318 (538)
+..|||||+.+.++...+ -+..+.+|.+-.+...- +.+| + .+..+|+. |+..
T Consensus 211 l~~L~GiG~~~~~~L~~~----GI~tigdL~~l~~~~L~----~rfG--~-~g~~l~~~a~G~d~ 264 (419)
T PRK02794 211 VGIIWGVGPATAARLARD----GIRTIGDLQRADEADLM----RRFG--S-MGLRLWRLARGIDD 264 (419)
T ss_pred hhhhCCCCHHHHHHHHHh----ccchHHHHhhCCHHHHH----HHHh--H-HHHHHHHHhCCCCC
Confidence 688999999998887643 35666666653333333 4444 3 57778775 8864
No 250
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=43.77 E-value=18 Score=32.34 Aligned_cols=22 Identities=27% Similarity=0.540 Sum_probs=18.8
Q ss_pred HHhhccCCCHHHHHHHHHh-CCC
Q 009281 296 LFGEVWGIGPATAQKLYEK-GHR 317 (538)
Q Consensus 296 lf~~I~GvGpktA~~l~~~-Gir 317 (538)
-||.|+|||..+|+.+.++ ||.
T Consensus 18 ALt~IyGIG~~~a~~I~~~~gi~ 40 (121)
T COG0099 18 ALTYIYGIGRRRAKEICKKAGID 40 (121)
T ss_pred hhhhhccccHHHHHHHHHHcCCC
Confidence 4678999999999999886 764
No 251
>PRK13746 aminoglycoside resistance protein; Provisional
Probab=43.40 E-value=1.2e+02 Score=30.97 Aligned_cols=27 Identities=26% Similarity=0.249 Sum_probs=22.0
Q ss_pred EEEeccccccc--CCcCCCeeEEEecCCcc
Q 009281 370 IILCGGSYRRG--KASCGDLDVVIMHPDRK 397 (538)
Q Consensus 370 ~v~~~Gs~RRg--ke~~~DvDiLIt~~~~~ 397 (538)
-|.+-||+-+| ++ -+||||+|...++-
T Consensus 30 ~vyLfGS~~~G~~~p-~SDIDllvvv~~~l 58 (262)
T PRK13746 30 AIHLYGSAVDGGLKP-HSDIDLLVTVAVPL 58 (262)
T ss_pred EEEEECCcccCCCCC-CCceeEEEEeCCCC
Confidence 47799999998 44 79999999877654
No 252
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=43.38 E-value=16 Score=41.71 Aligned_cols=43 Identities=23% Similarity=0.414 Sum_probs=29.5
Q ss_pred HHHHhhccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhcccc
Q 009281 294 ISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLK 337 (538)
Q Consensus 294 l~lf~~I~GvGpktA~~l~~~GirtledL~~~~--~L~~~q~~Glk 337 (538)
...|..|+|||++++++|++. +.|++++.++. .|....++|-+
T Consensus 542 ~s~L~~IpGIG~k~~k~Ll~~-FgS~~~i~~As~eeL~~v~Gig~~ 586 (598)
T PRK00558 542 TSALDDIPGIGPKRRKALLKH-FGSLKAIKEASVEELAKVPGISKK 586 (598)
T ss_pred hhhHhhCCCcCHHHHHHHHHH-cCCHHHHHhCCHHHHhhcCCcCHH
Confidence 345679999999999999985 45688887642 24444444433
No 253
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=43.16 E-value=39 Score=35.04 Aligned_cols=52 Identities=27% Similarity=0.493 Sum_probs=37.8
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh
Q 009281 255 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (538)
Q Consensus 255 ~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~ 314 (538)
.+..|||||+.+++++.+ --+..++++.+-.+ +.+.+++|+++++|..||+.
T Consensus 7 ~l~~l~gIg~~~a~~L~~----~Gi~t~~dl~~~~~----~~L~~~~g~~~~~a~~l~~~ 58 (317)
T PRK04301 7 DLEDLPGVGPATAEKLRE----AGYDTVEAIAVASP----KELSEAAGIGESTAAKIIEA 58 (317)
T ss_pred cHhhcCCCCHHHHHHHHH----cCCCCHHHHHcCCH----HHHHHhcCCCHHHHHHHHHH
Confidence 578999999888776554 34566677654332 23448889999999999974
No 254
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=42.49 E-value=16 Score=34.16 Aligned_cols=25 Identities=24% Similarity=0.225 Sum_probs=19.9
Q ss_pred HHHHHhhccCCCHHHHHHHHHh-CCC
Q 009281 293 TISLFGEVWGIGPATAQKLYEK-GHR 317 (538)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~-Gir 317 (538)
+.--|+.|+|||+.+|..+-+. ||.
T Consensus 28 v~~aLt~I~GIG~~~A~~I~~~lgi~ 53 (154)
T PTZ00134 28 VPYALTAIKGIGRRFAYLVCKKAGID 53 (154)
T ss_pred EEEeecccccccHHHHHHHHHHcCcC
Confidence 3334689999999999999876 763
No 255
>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=42.37 E-value=7 Score=33.30 Aligned_cols=51 Identities=24% Similarity=0.337 Sum_probs=39.7
Q ss_pred HHHHHhhccCCCHHHHHHHHHh-CCCCHHHHhhccCcchhhhccccchhhhc
Q 009281 293 TISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNEDSLTHSQRLGLKYFDDIK 343 (538)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~-GirtledL~~~~~L~~~q~~Glk~~ed~~ 343 (538)
.+..|++.||+=|..|.++..- -+.|++|+.+-.-|+..|+-=++-|++.-
T Consensus 21 ~vr~f~~~pGmYPtlA~kIv~naPY~sveDvl~ipgLse~qK~~lk~~~~~F 72 (93)
T PF06514_consen 21 NVRAFRQFPGMYPTLAGKIVSNAPYKSVEDVLNIPGLSERQKALLKKYEDNF 72 (93)
T ss_dssp -GGGGCCSTTTTCCHHHHHHHS---SSGGGGCCSTT--HHHHHHHHHHGGGE
T ss_pred hHHHHHHCCCCCHHHHHHHHhCCCCCCHHHHHhccCCCHHHHHHHHHHhccc
Confidence 4566889999999999999997 88999999988789988888777777643
No 256
>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=42.36 E-value=54 Score=35.33 Aligned_cols=53 Identities=28% Similarity=0.488 Sum_probs=33.9
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhc--hhHHHHHHhhccCCCHHHHHHHHHh--CCCC
Q 009281 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDE--KVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (538)
Q Consensus 256 l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~--~~~~l~lf~~I~GvGpktA~~l~~~--Girt 318 (538)
+..|||||+++++++..+ | +..+.++.+-. +..+.+.| |++.+..||+. |+..
T Consensus 224 v~~l~GIG~~~~~~L~~~---G-i~t~~dl~~~~~~~~~L~~~f------G~~~g~~L~~~a~G~d~ 280 (404)
T cd01701 224 VGDLPGVGSSLAEKLVKL---F-GDTCGGLELRSKTKEKLQKVL------GPKTGEKLYDYCRGIDD 280 (404)
T ss_pred HhHhCCCCHHHHHHHHHc---C-CcchHHHHhCcccHHHHHHHH------CHHHHHHHHHHhCCcCC
Confidence 678899999998887754 3 33444444322 33344444 57788998875 8765
No 257
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=41.68 E-value=12 Score=42.61 Aligned_cols=48 Identities=25% Similarity=0.427 Sum_probs=36.0
Q ss_pred hccCCCHHHHHHHHHh-CCCCHHHHhh--ccCcchhhhccccchhhhccCc
Q 009281 299 EVWGIGPATAQKLYEK-GHRTLDDLKN--EDSLTHSQRLGLKYFDDIKTRI 346 (538)
Q Consensus 299 ~I~GvGpktA~~l~~~-GirtledL~~--~~~L~~~q~~Glk~~ed~~~~i 346 (538)
.|-|+|.|.+.+|++. =|+++.||.. ...|..+.++|-+..+.+...|
T Consensus 449 dI~GLG~k~i~~L~e~~lI~~~~Dly~Lt~~~l~~l~~~~~ks~~nLl~aI 499 (667)
T COG0272 449 DIDGLGEKIIEQLFEKGLIKDIADLYTLTEEDLLSLEGFGEKSAENLLNAI 499 (667)
T ss_pred CCCCcCHHHHHHHHHcCccCCHHHHHhCCHHHHhhccchhhhHHHHHHHHH
Confidence 8999999999999998 5799999973 3456666666655555554433
No 258
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]
Probab=41.64 E-value=15 Score=36.36 Aligned_cols=58 Identities=22% Similarity=0.303 Sum_probs=41.8
Q ss_pred hhhcCCCCCCHHHHH---HHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHH
Q 009281 254 DQVKGLPGIGKSMQD---HIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLY 312 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~---~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~ 312 (538)
+++.++ |+-+.=+. -+.|....|.+...+.+..-.....++++|+|.|||+=|++++-
T Consensus 122 ~~lrkc-G~S~rK~~yLh~lA~~~~ng~I~s~~~i~~mseEeL~~~LT~VKGIg~Wtv~Mfl 182 (254)
T KOG1918|consen 122 EELRKC-GFSKRKASYLHSLAEAYTNGYIPSKSGIEKMSEEELIERLTNVKGIGRWTVEMFL 182 (254)
T ss_pred HHHHHh-CcchhhHHHHHHHHHHHhcCCCCchHHHhhcCHHHHHHHHHhccCccceeeeeee
Confidence 455444 44444333 35556668888888877776677899999999999999988774
No 259
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=41.11 E-value=19 Score=33.50 Aligned_cols=24 Identities=29% Similarity=0.338 Sum_probs=19.7
Q ss_pred HHHHhhccCCCHHHHHHHHHh-CCC
Q 009281 294 ISLFGEVWGIGPATAQKLYEK-GHR 317 (538)
Q Consensus 294 l~lf~~I~GvGpktA~~l~~~-Gir 317 (538)
.--|+.|+|||+++|..+-+. ||.
T Consensus 24 ~~aLt~IyGIG~~~a~~Ic~~lgi~ 48 (149)
T PRK04053 24 EYALTGIKGIGRRTARAIARKLGLD 48 (149)
T ss_pred eeeccccccccHHHHHHHHHHcCcC
Confidence 334689999999999999876 764
No 260
>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=40.91 E-value=72 Score=37.96 Aligned_cols=49 Identities=20% Similarity=0.474 Sum_probs=35.2
Q ss_pred CeEEEeccccccc-CCcCCCeeEEEecCCcc--hhhhhHHHHHHHHHHcCcc
Q 009281 368 EVIILCGGSYRRG-KASCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMKFL 416 (538)
Q Consensus 368 ~~~v~~~Gs~RRg-ke~~~DvDiLIt~~~~~--~~~~~l~~~v~~L~~~g~l 416 (538)
++-+..+|||=|| ..-..|||++|-+++.. ....++.+++..|-+.|+-
T Consensus 43 ~~aliA~GgyGR~El~p~SDiDll~l~~~~~~~~~~~~~~~~~~~LwD~gl~ 94 (850)
T TIGR01693 43 GIALVAVGGYGRGELAPYSDIDLLFLHDGKPAEEVEPKIERFLYPLWDLGFE 94 (850)
T ss_pred CeEEEEeCCccccCcCCCCCCeEEEEeCCCCChHHHHHHHHHHHHHHhcCCC
Confidence 4567788999555 45688999999887532 2456777777777777754
No 261
>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=40.84 E-value=21 Score=30.25 Aligned_cols=27 Identities=33% Similarity=0.449 Sum_probs=19.9
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHh
Q 009281 297 FGEVWGIGPATAQKLYEKGHRTLDDLK 323 (538)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~ 323 (538)
-+.|+||||..+.+|-++|+.---.|.
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 568999999999999999998866665
No 262
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=40.31 E-value=13 Score=39.04 Aligned_cols=52 Identities=19% Similarity=0.245 Sum_probs=33.1
Q ss_pred HHHHHHhhccCCCHHHHHHHHHh---CCCC-HHHHhhcc------Ccchhhhccccchhhhc
Q 009281 292 RTISLFGEVWGIGPATAQKLYEK---GHRT-LDDLKNED------SLTHSQRLGLKYFDDIK 343 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~~---Girt-ledL~~~~------~L~~~q~~Glk~~ed~~ 343 (538)
..+..+++|||||+++|.++.+- |--. +.++.++. .|.+..|+|.+....|-
T Consensus 45 ~~~~~l~~lpgIG~~ia~kI~Eil~tG~~~~~~e~l~~~~p~~l~~l~~i~GiGpk~a~~l~ 106 (334)
T smart00483 45 NSMKDLKGLPGIGDKIKKKIEEIIETGKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKWY 106 (334)
T ss_pred CCHHHHhcCCCccHHHHHHHHHHHHhCcHHHHHHHhcCcHHHHHHHHHccCCcCHHHHHHHH
Confidence 34556779999999999999974 6544 33333221 35666777755544443
No 263
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=40.23 E-value=47 Score=39.34 Aligned_cols=15 Identities=13% Similarity=0.293 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHHHHH
Q 009281 211 KNITEIFGKLINIYR 225 (538)
Q Consensus 211 ~~ia~~L~~la~~~e 225 (538)
..+-+..+.|...|+
T Consensus 644 gRL~~Q~~~m~~~Y~ 658 (814)
T TIGR00596 644 GRLYNQCEKMLRYYA 658 (814)
T ss_pred chHHHHHHHHHHhcC
Confidence 346666677777666
No 264
>COG1204 Superfamily II helicase [General function prediction only]
Probab=40.19 E-value=21 Score=41.94 Aligned_cols=110 Identities=23% Similarity=0.294 Sum_probs=61.3
Q ss_pred hHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCc--chhHHHH----hhchhHHHHHHhhccCCCH
Q 009281 232 RSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKL--SKLEHFE----KDEKVRTISLFGEVWGIGP 305 (538)
Q Consensus 232 r~~aY~rAa~~l~~l~~~i~~~~~l~~lpgiG~~ia~~I~Eil~tG~~--~~le~l~----~~~~~~~l~lf~~I~GvGp 305 (538)
-+.+|-.+...+...-....=. .+. +..+|.++.+ +..++..|.. ..++.+. ...+...+..+..|.|+|-
T Consensus 609 i~~~~~~~~~dl~~~~~~a~w~-~~~-~~~l~~~~~r-~~~~~~~~~~~~~~~~~~~~rie~gv~~e~~~~l~~i~~~gr 685 (766)
T COG1204 609 ILNAYGVAPGDLLRIAETAEWL-SAD-LLALGKAAER-LAKILGLGLHVLRKLEILSLRIEYGVRSEELLELVEIRGVGR 685 (766)
T ss_pred HHHHhCcchhhHHhhcchhhhh-hhh-hhhhhhhhhh-hHhhhCCCccccccchhhhhhhhcCCChhhhcccccccccch
Confidence 3445555555544443322222 122 4444544444 4445554433 3333332 2223123334459999999
Q ss_pred HHHHHHHHhCCCCHHHHhhcc---Ccchhhhccccchhhhcc
Q 009281 306 ATAQKLYEKGHRTLDDLKNED---SLTHSQRLGLKYFDDIKT 344 (538)
Q Consensus 306 ktA~~l~~~GirtledL~~~~---~L~~~q~~Glk~~ed~~~ 344 (538)
..|++||..|+++++++.... .+....++|.+.++.+..
T Consensus 686 vrar~ly~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~ 727 (766)
T COG1204 686 VRARKLYNAGYKSLEDLRLIADPAELLPLTGIGERLVEAILE 727 (766)
T ss_pred hHHHHHHHhhhccHHHHHhhcChhhhhhhhhhHHHHHHHHHH
Confidence 999999999999999999432 355556666666555543
No 265
>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=40.11 E-value=24 Score=28.05 Aligned_cols=18 Identities=22% Similarity=0.423 Sum_probs=16.2
Q ss_pred HHHHHHHHhCCCCHHHHh
Q 009281 306 ATAQKLYEKGHRTLDDLK 323 (538)
Q Consensus 306 ktA~~l~~~GirtledL~ 323 (538)
+.++.|.+.||+|++|++
T Consensus 55 ~Il~~W~~~gi~T~e~~~ 72 (73)
T TIGR01446 55 AILNNWKNNGIKTVEDVE 72 (73)
T ss_pred HHHHHHHHcCCCCHHHHh
Confidence 678899999999999986
No 266
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=40.09 E-value=22 Score=34.10 Aligned_cols=59 Identities=19% Similarity=0.353 Sum_probs=32.4
Q ss_pred HHHHHHHHHHhCCcchhHHHHhhchhH-HHHHHhhccCCCHHHHHHHHHh----CCCCHHHHhh
Q 009281 266 MQDHIQEIVTTGKLSKLEHFEKDEKVR-TISLFGEVWGIGPATAQKLYEK----GHRTLDDLKN 324 (538)
Q Consensus 266 ia~~I~Eil~tG~~~~le~l~~~~~~~-~l~lf~~I~GvGpktA~~l~~~----GirtledL~~ 324 (538)
+-..|++|+....-..++-+....|.- -|-.|.=+||||.|+...+.++ -+.|++|+.+
T Consensus 86 L~~vv~~IV~~~E~~FV~FfN~A~PIt~RlH~LeLLPGIGKK~m~~ILeERkkkpFeSFeDi~~ 149 (181)
T PF04919_consen 86 LPYVVEEIVKENEERFVDFFNEAQPITLRLHSLELLPGIGKKTMWKILEERKKKPFESFEDIEE 149 (181)
T ss_dssp HHHHHHHHHHTTHHHHHHHH-----B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHH
T ss_pred HHHHHHHHHHhChHHHHHHhhcCCCChHHHHHHhhcccccHHHHHHHHHHHccCCCCCHHHHHH
Confidence 445688888877756666554433321 1222434699999999999863 6777777764
No 267
>PRK03059 PII uridylyl-transferase; Provisional
Probab=39.99 E-value=77 Score=37.84 Aligned_cols=65 Identities=15% Similarity=0.355 Sum_probs=38.3
Q ss_pred HHHHHHHHHHHhhhc--CCCeEEEeccccccc-CCcCCCeeEEEecCCcc--hhhhhHHHHHHHHHHcCc
Q 009281 351 VEQMERLLQKAGEEV--LPEVIILCGGSYRRG-KASCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMKF 415 (538)
Q Consensus 351 a~~i~~iv~~~~~~~--~p~~~v~~~Gs~RRg-ke~~~DvDiLIt~~~~~--~~~~~l~~~v~~L~~~g~ 415 (538)
+..+..+++.+.... ..++-+..+|||=|| ..-..|||+||-+++.. .....+..++..|-+.|+
T Consensus 42 s~l~d~~l~~~~~~~~~~~~~alvAvGgyGR~EL~p~SDiDll~l~~~~~~~~~~~~i~~~~~~lwD~gL 111 (856)
T PRK03059 42 SRLVDQALRRLWQECGLPAGAALVAVGGYGRGELFPYSDVDLLVLLPDAPDAALDARIERFIGLCWDLGL 111 (856)
T ss_pred HHHHHHHHHHHHHhcCCCCCeEEEEcCCCCCcccCCCCCCEEEEEecCCcchHHHHHHHHHHHhhhccCC
Confidence 333444444443222 235677788999554 56789999999887543 233455555555555553
No 268
>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=39.63 E-value=20 Score=33.18 Aligned_cols=45 Identities=22% Similarity=0.330 Sum_probs=30.8
Q ss_pred HHHhhccCCCHHHHHHHHHh-CCCCHHHHhhccCcchhhhccccchhhhccCcCHHHHHHHHHHHHH
Q 009281 295 SLFGEVWGIGPATAQKLYEK-GHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQK 360 (538)
Q Consensus 295 ~lf~~I~GvGpktA~~l~~~-GirtledL~~~~~L~~~q~~Glk~~ed~~~~i~r~ea~~i~~iv~~ 360 (538)
--|+.|+|||+++|..+-+. ||..-.-+ .-++-++.+.|..++..
T Consensus 21 ~aLt~I~GIG~~~a~~I~~~lgi~~~~~~---------------------~~Lt~~qi~~l~~~i~~ 66 (144)
T TIGR03629 21 YALTGIKGIGRRFARAIARKLGVDPNAKL---------------------GYLDDEEIEKLEEAVEN 66 (144)
T ss_pred EeecceeccCHHHHHHHHHHcCcCCCCCc---------------------ccCCHHHHHHHHHHHHh
Confidence 34679999999999999876 76421111 12345677778777776
No 269
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=39.30 E-value=58 Score=31.43 Aligned_cols=56 Identities=20% Similarity=0.347 Sum_probs=34.2
Q ss_pred HHHHHHHhCCcchhHHHHhhchhH-HHHHHhhccCCCHHHHHHHHHh----CCCCHHHHhh
Q 009281 269 HIQEIVTTGKLSKLEHFEKDEKVR-TISLFGEVWGIGPATAQKLYEK----GHRTLDDLKN 324 (538)
Q Consensus 269 ~I~Eil~tG~~~~le~l~~~~~~~-~l~lf~~I~GvGpktA~~l~~~----GirtledL~~ 324 (538)
.+++|+....=..++-+..-.|.- -|-.|.=+||||.|+...+.++ -+.|++|+++
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 456666555434444333222221 1223445699999999999863 7888888875
No 270
>PF09970 DUF2204: Nucleotidyl transferase of unknown function (DUF2204); InterPro: IPR018700 This family of hypothetical prokaryotic proteins has no known function.
Probab=39.16 E-value=66 Score=30.77 Aligned_cols=40 Identities=18% Similarity=0.199 Sum_probs=26.3
Q ss_pred CCeEEEecccc-----cccCCcCCCeeEEEecCCcchhhhhHHHH
Q 009281 367 PEVIILCGGSY-----RRGKASCGDLDVVIMHPDRKSHKGFLSKY 406 (538)
Q Consensus 367 p~~~v~~~Gs~-----RRgke~~~DvDiLIt~~~~~~~~~~l~~~ 406 (538)
-++.+.+.||+ -..+.+.+|||++|..++......++..+
T Consensus 15 ~gv~~~ivGG~av~l~~g~~r~T~DIDlfi~~~~~~~~~~~~~~~ 59 (181)
T PF09970_consen 15 RGVEYVIVGGAAVNLAYGRRRTTKDIDLFIENPSPNLEADALREV 59 (181)
T ss_pred cCCeEEEECHHHHHHHhCCCCCCCCeEEEeCCCchHHHHHHHHHH
Confidence 36666666773 25567889999999877665444444333
No 271
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=39.10 E-value=20 Score=40.65 Aligned_cols=43 Identities=21% Similarity=0.496 Sum_probs=29.8
Q ss_pred HHHhhccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhccccc
Q 009281 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKY 338 (538)
Q Consensus 295 ~lf~~I~GvGpktA~~l~~~GirtledL~~~~--~L~~~q~~Glk~ 338 (538)
..|..|+|||++++++|++. +-|++++.++. .|....++|-+.
T Consensus 525 ~~L~~IpGIG~kr~~~LL~~-FGS~~~I~~As~eeL~~vpGi~~~~ 569 (577)
T PRK14668 525 TVLDDVPGVGPETRKRLLRR-FGSVEGVREASVEDLRDVPGVGEKT 569 (577)
T ss_pred hHHhcCCCCCHHHHHHHHHH-cCCHHHHHhCCHHHHHhCCCCCHHH
Confidence 44669999999999999985 46788887543 344444444433
No 272
>PRK13766 Hef nuclease; Provisional
Probab=38.81 E-value=21 Score=41.68 Aligned_cols=45 Identities=18% Similarity=0.325 Sum_probs=32.7
Q ss_pred HHhhccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhccccchhh
Q 009281 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDD 341 (538)
Q Consensus 296 lf~~I~GvGpktA~~l~~~GirtledL~~~~--~L~~~q~~Glk~~ed 341 (538)
+|..|+|||+++|++|.+. +.|++++..+. .|....++|.+..+.
T Consensus 716 ~L~~ipgig~~~a~~Ll~~-fgs~~~i~~as~~~L~~i~Gig~~~a~~ 762 (773)
T PRK13766 716 IVESLPDVGPVLARNLLEH-FGSVEAVMTASEEELMEVEGIGEKTAKR 762 (773)
T ss_pred HHhcCCCCCHHHHHHHHHH-cCCHHHHHhCCHHHHHhCCCCCHHHHHH
Confidence 5789999999999999986 45899888643 355555666444433
No 273
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=38.19 E-value=49 Score=34.01 Aligned_cols=45 Identities=20% Similarity=0.350 Sum_probs=31.3
Q ss_pred CCC-hhHHHHHHHHHHHhc--CCccc-cc----hhhhcCCCCCCHHHHHHHHH
Q 009281 228 GED-RRSFSYYKAIPVIEK--LPFKI-ES----ADQVKGLPGIGKSMQDHIQE 272 (538)
Q Consensus 228 g~~-~r~~aY~rAa~~l~~--l~~~i-~~----~~~l~~lpgiG~~ia~~I~E 272 (538)
|-. .|+.+-..+|.++.+ ++... .+ .++|..|||||+.+|+.|.=
T Consensus 173 Gl~~~Ra~~L~~lA~~i~~g~l~l~~~~~~~~~~~~L~~LpGIGpwTA~~vll 225 (283)
T PRK10308 173 GMPLKRAEALIHLANAALEGTLPLTIPGDVEQAMKTLQTFPGIGRWTANYFAL 225 (283)
T ss_pred CCCHHHHHHHHHHHHHHHcCCCCccccCCHHHHHHHHhcCCCcCHHHHHHHHH
Confidence 443 377777788877754 43221 12 46899999999999998763
No 274
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=38.14 E-value=19 Score=37.37 Aligned_cols=24 Identities=38% Similarity=0.479 Sum_probs=18.6
Q ss_pred hhccCCCHHHHHHHHHhCCCCHHHH
Q 009281 298 GEVWGIGPATAQKLYEKGHRTLDDL 322 (538)
Q Consensus 298 ~~I~GvGpktA~~l~~~GirtledL 322 (538)
.+|+|||||||.+|.++ +.|++..
T Consensus 226 ~gv~giG~k~A~~li~~-~~~~~~~ 249 (316)
T cd00128 226 EGIPGIGPVTALKLIKK-YGDIEKD 249 (316)
T ss_pred CCCCCccHHHHHHHHHH-cCChHHH
Confidence 48999999999999987 3354433
No 275
>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=37.73 E-value=25 Score=39.85 Aligned_cols=29 Identities=24% Similarity=0.354 Sum_probs=23.8
Q ss_pred HHhhccCCCHHHHHHHHHhCCCCHHHHhhc
Q 009281 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (538)
Q Consensus 296 lf~~I~GvGpktA~~l~~~GirtledL~~~ 325 (538)
.|.+|+|||||+.+.|++. +.|+++++++
T Consensus 542 ~Ld~I~GIG~kr~~~LL~~-Fgs~~~i~~A 570 (574)
T TIGR00194 542 PLLKIPGVGEKRVQKLLKY-FGSLKGIKKA 570 (574)
T ss_pred HHhcCCCCCHHHHHHHHHH-cCCHHHHHhC
Confidence 4569999999999999984 5588888754
No 276
>KOG3524 consensus Predicted guanine nucleotide exchange factor (PEBBLE) [Signal transduction mechanisms]
Probab=37.02 E-value=23 Score=40.42 Aligned_cols=86 Identities=17% Similarity=0.317 Sum_probs=60.0
Q ss_pred CCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHhhhccCCccccccchHHHHHh
Q 009281 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSLR 96 (538)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~~~~~~~~~~l~~~~~~~~~~~lV~~~Wl~ecik 96 (538)
.-|.|+.++|.+ ....--+.+-.-....||..+. -+..-||||+.+......-+. ...+.++|+-.|+-=+|.
T Consensus 209 ~~feg~~~~f~g--F~~ee~~~m~~sle~~gg~~a~-~d~~cthvvv~e~~~~~~p~~----~s~~~~~vk~ewfw~siq 281 (850)
T KOG3524|consen 209 GVFEGLSLFFHG--FKQEEIDDMLRSLENTGGKLAP-SDTLCTHVVVNEDNDEVEPLA----VSSNQVHVKKEWFWVSIQ 281 (850)
T ss_pred ccccCCeEeecC--CcHHHHHHHHHHHHhcCCcccC-CCCCceeEeecCCcccccccc----ccccceeecccceEEEEe
Confidence 679999999954 5545556666788889999888 567899999976532211111 112357888999888888
Q ss_pred cCcccCccccccc
Q 009281 97 LGEKVSEDLYRIK 109 (538)
Q Consensus 97 ~g~lv~e~~y~l~ 109 (538)
.|..--|+.|.+.
T Consensus 282 ~g~~a~e~~yl~~ 294 (850)
T KOG3524|consen 282 RGCCAIEDNYLLP 294 (850)
T ss_pred cchhccccceecc
Confidence 8877777777664
No 277
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=36.50 E-value=92 Score=28.17 Aligned_cols=88 Identities=22% Similarity=0.422 Sum_probs=60.7
Q ss_pred CCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhccCcchhhhccccchhh
Q 009281 262 IGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYFDD 341 (538)
Q Consensus 262 iG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~~~L~~~q~~Glk~~ed 341 (538)
|=..|++.|.+-+.+|.+..=+. .++++.|..-.||-|-|+++-|+ +|+++|-+....+.|.---+|
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 34677777899999999999997 677777777777777555444
Q ss_pred ---hccCcCHHHHHH-HHHHHHHHh
Q 009281 342 ---IKTRIPRHEVEQ-MERLLQKAG 362 (538)
Q Consensus 342 ---~~~~i~r~ea~~-i~~iv~~~~ 362 (538)
+....-+..+.+ ++.+|.++.
T Consensus 79 ~~~~~~~~~~~~~~~~l~~~I~~~~ 103 (125)
T COG1725 79 AKEILDQLKRELAEEELEEFIEEAK 103 (125)
T ss_pred chhhHHHHHHHHHHHHHHHHHHHHH
Confidence 333333444433 455555543
No 278
>PTZ00035 Rad51 protein; Provisional
Probab=36.24 E-value=62 Score=34.12 Aligned_cols=50 Identities=24% Similarity=0.307 Sum_probs=34.9
Q ss_pred HHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhccccchhhhc
Q 009281 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIK 343 (538)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~GirtledL~~~~--~L~~~q~~Glk~~ed~~ 343 (538)
.++.+ .-+||+|.++++|-+.||.|++||.... .|....+++....+++.
T Consensus 22 ~~~~l-~~~g~~~~~~~kL~~~g~~t~~~~~~~~~~~L~~~~gis~~~~~~i~ 73 (337)
T PTZ00035 22 EIEKL-QSAGINAADIKKLKEAGICTVESVAYATKKDLCNIKGISEAKVEKIK 73 (337)
T ss_pred cHHHH-hcCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhhCCCHHHHHHHH
Confidence 34555 3499999999999999999999998543 35555555444444443
No 279
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=36.23 E-value=28 Score=39.82 Aligned_cols=27 Identities=44% Similarity=0.650 Sum_probs=25.3
Q ss_pred HhhccCCCHHHHHHHHHhCCCCHHHHh
Q 009281 297 FGEVWGIGPATAQKLYEKGHRTLDDLK 323 (538)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~ 323 (538)
+..+.||||++|.++-+.||.|+.||.
T Consensus 12 l~~l~gig~~~a~~l~~Lgi~tv~DLL 38 (677)
T COG1200 12 LSTLKGIGPKTAEKLKKLGIHTVQDLL 38 (677)
T ss_pred hhhhcCcCHHHHHHHHHcCCCcHHHHH
Confidence 558999999999999999999999997
No 280
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=35.46 E-value=33 Score=33.31 Aligned_cols=22 Identities=27% Similarity=0.496 Sum_probs=18.9
Q ss_pred hhhcCCCCCCHHHHHHHHHHHH
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVT 275 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~ 275 (538)
+.+..|||||++.|.++.=.|-
T Consensus 12 ~~l~kLPGvG~KsA~R~AfhLL 33 (198)
T COG0353 12 DALKKLPGVGPKSAQRLAFHLL 33 (198)
T ss_pred HHHhhCCCCChhHHHHHHHHHH
Confidence 6789999999999999986554
No 281
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=35.32 E-value=63 Score=37.95 Aligned_cols=48 Identities=17% Similarity=0.495 Sum_probs=33.2
Q ss_pred CeEEEecccccccC-CcCCCeeEEEecCCcchh--hhhHHHHHHHHHHcCc
Q 009281 368 EVIILCGGSYRRGK-ASCGDLDVVIMHPDRKSH--KGFLSKYVKKLKEMKF 415 (538)
Q Consensus 368 ~~~v~~~Gs~RRgk-e~~~DvDiLIt~~~~~~~--~~~l~~~v~~L~~~g~ 415 (538)
++-++.+|||=||. .-++|||+||-+|...+. ...+..++..|=+.|+
T Consensus 66 ~~aLvAVGGyGRgEL~P~SDiDlL~L~p~~~~~~~e~~ie~~l~~LWD~gl 116 (867)
T COG2844 66 GLALVAVGGYGRGELHPLSDIDLLLLSPQKLTDWLEQKIERFLYLLWDLGL 116 (867)
T ss_pred ceEEEEeccccccccCCCccceEEEecCCCCChHHHHHHHHHHHHHHhcCc
Confidence 35677889997775 568999999999876543 2344455555555655
No 282
>PRK10880 adenine DNA glycosylase; Provisional
Probab=34.72 E-value=28 Score=37.05 Aligned_cols=23 Identities=22% Similarity=0.286 Sum_probs=19.1
Q ss_pred HHHHHHhhccCCCHHHHHHHHHh
Q 009281 292 RTISLFGEVWGIGPATAQKLYEK 314 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~~ 314 (538)
..++.|+++||||++||..+---
T Consensus 106 ~~~~~L~~LpGIG~~TA~aIl~~ 128 (350)
T PRK10880 106 ETFEEVAALPGVGRSTAGAILSL 128 (350)
T ss_pred hhHHHHhcCCCccHHHHHHHHHH
Confidence 45677789999999999988764
No 283
>PRK13910 DNA glycosylase MutY; Provisional
Probab=34.32 E-value=27 Score=36.07 Aligned_cols=22 Identities=23% Similarity=0.153 Sum_probs=18.1
Q ss_pred HHHHHhhccCCCHHHHHHHHHh
Q 009281 293 TISLFGEVWGIGPATAQKLYEK 314 (538)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~ 314 (538)
..+.|+++||||++||..+---
T Consensus 70 ~~~~L~~LpGIG~kTA~aIl~~ 91 (289)
T PRK13910 70 DYQSLLKLPGIGAYTANAILCF 91 (289)
T ss_pred hHHHHHhCCCCCHHHHHHHHHH
Confidence 4567779999999999987654
No 284
>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=33.88 E-value=26 Score=30.91 Aligned_cols=28 Identities=25% Similarity=0.426 Sum_probs=17.6
Q ss_pred hccHHHHHHHHHHHHHcCCccCCCCCcc
Q 009281 470 TGNDVLNRRLRLLAESKGYRLDDTGLFP 497 (538)
Q Consensus 470 TGS~~fnr~lR~~A~~kg~~L~~~gL~~ 497 (538)
+.++..++.+|.||++.||..++.|=+.
T Consensus 73 ~~~~~~~~~IR~WA~~nG~~Vs~RGRIp 100 (110)
T PF11774_consen 73 AAPREDTAAIREWARENGYEVSDRGRIP 100 (110)
T ss_dssp --SSTHHHHHHHHHHHTT----SSS---
T ss_pred CCCccchHHHHHHHHHcCCcCCCCCcCC
Confidence 4567789999999999999999998653
No 285
>PHA01806 hypothetical protein
Probab=33.85 E-value=69 Score=31.14 Aligned_cols=49 Identities=18% Similarity=0.238 Sum_probs=31.2
Q ss_pred CcCHHHHHH-HHHHHHHHhhhcCCCeEEEecccccc----cCCcCCCeeEEEecCCcc
Q 009281 345 RIPRHEVEQ-MERLLQKAGEEVLPEVIILCGGSYRR----GKASCGDLDVVIMHPDRK 397 (538)
Q Consensus 345 ~i~r~ea~~-i~~iv~~~~~~~~p~~~v~~~Gs~RR----gke~~~DvDiLIt~~~~~ 397 (538)
.|++..... +..++..+. .-+.++.++||+=| |+ .+.|+||++....+.
T Consensus 14 ~I~~~~is~~al~v~~~l~---~~g~~aYlVGG~VRD~Llgr-~~kDiDivt~~~~pe 67 (200)
T PHA01806 14 EIPEGLIAKALLLRLYSDA---RHSEGVALAGGAARDLMHGA-EPKDIDIALYGMDDR 67 (200)
T ss_pred ccChhHcCHHHHHHHHHHH---HCCcEEEEECchHHHHHcCC-CCCceEEEccCCCHH
Confidence 455655432 344444443 35778888888877 55 789999976555554
No 286
>PRK03858 DNA polymerase IV; Validated
Probab=33.78 E-value=70 Score=34.14 Aligned_cols=52 Identities=17% Similarity=0.338 Sum_probs=34.9
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh--CCC
Q 009281 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHR 317 (538)
Q Consensus 256 l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~--Gir 317 (538)
+..|||||+++++++..+ | +..+.+|.+-.+...- +.+ |+..++.||+. |+.
T Consensus 175 l~~l~Gig~~~~~~L~~~---G-i~t~~dl~~l~~~~L~----~~f--G~~~~~~l~~~a~G~d 228 (396)
T PRK03858 175 VRRLWGVGPVTAAKLRAH---G-ITTVGDVAELPESALV----SLL--GPAAGRHLHALAHNRD 228 (396)
T ss_pred hhhcCCCCHHHHHHHHHh---C-CCcHHHHhcCCHHHHH----HHh--CcHHHHHHHHHhCCCC
Confidence 678899999999998764 3 5566666543333333 344 56778888863 764
No 287
>PHA00439 exonuclease
Probab=33.66 E-value=28 Score=35.88 Aligned_cols=27 Identities=19% Similarity=0.284 Sum_probs=22.0
Q ss_pred hhccCCCHHHHHHHHHh--CCCCHHHHhhc
Q 009281 298 GEVWGIGPATAQKLYEK--GHRTLDDLKNE 325 (538)
Q Consensus 298 ~~I~GvGpktA~~l~~~--GirtledL~~~ 325 (538)
-.|+||| |||.+|.++ .+..++...+.
T Consensus 191 PGVpGIG-KTA~kLL~~~~~~~~~~~~~~s 219 (286)
T PHA00439 191 SGIPGWG-DTAEAFLENPYIFEQVEKVLKS 219 (286)
T ss_pred CCCCCcC-HHHHHHHhCccccchhhHHhhc
Confidence 4799999 999999998 77777776644
No 288
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=33.53 E-value=70 Score=33.92 Aligned_cols=43 Identities=26% Similarity=0.288 Sum_probs=31.1
Q ss_pred HHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhcc
Q 009281 292 RTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLG 335 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~~--~L~~~q~~G 335 (538)
..++.+ .-.||+|+++++|-+.||.|++||.... .|....++.
T Consensus 29 ~~~~~l-~~~g~~~~~~~kL~~~g~~tv~~~~~~~~~~L~~~~g~s 73 (344)
T PLN03187 29 ESIDKL-ISQGINAGDVKKLQDAGIYTCNGLMMHTKKNLTGIKGLS 73 (344)
T ss_pred cCHHHH-hhCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCC
Confidence 345555 4489999999999999999999997532 344444443
No 289
>cd01702 PolY_Pol_eta DNA Polymerase eta. Pol eta, also called Rad30A, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Unlike other Y-family members, Pol eta can efficiently and accurately replicate DNA past UV-induced lesions. Its activity is initiated by two simultaneous interactions: the PIP box in pol eta interacting with PCNA, and the UBZ (ubiquitin-binding zinc finger) in pol eta interacting with monoubiquitin attached to PCNA. Pol eta is more efficient in copying damaged DNA than undamaged DNA and seems to recognize when a lesion has been passed, facilitating a lesion-dependent dissociation from the DNA.
Probab=32.79 E-value=1e+02 Score=32.71 Aligned_cols=54 Identities=17% Similarity=0.305 Sum_probs=32.6
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhh--chhHHHHHHhhccCCCHHHHHHHHHh--CCCC
Q 009281 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKD--EKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (538)
Q Consensus 256 l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~--~~~~~l~lf~~I~GvGpktA~~l~~~--Girt 318 (538)
+..|||||++++.++.+-+ .+..+.+|.+- .+....+.| |.+.+..+|+. |+..
T Consensus 184 v~~l~GiG~~~~~~ll~~~---Gi~ti~dl~~~~~~~~~L~~~f------G~~~g~~l~~~a~G~d~ 241 (359)
T cd01702 184 ITSIRGLGGKLGEEIIDLL---GLPTEGDVAGFRSSESDLQEHF------GEKLGEWLYNLLRGIDH 241 (359)
T ss_pred HHHhCCcCHHHHHHHHHHc---CCcCHHHHHhccCCHHHHHHHH------HHHHHHHHHHHhCCCCC
Confidence 6788999998876553322 23444444432 233333444 67788899875 8764
No 290
>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=32.48 E-value=78 Score=30.97 Aligned_cols=32 Identities=28% Similarity=0.227 Sum_probs=23.6
Q ss_pred CCeEEEecccc----cccC---CcCCCeeEEEecCCcch
Q 009281 367 PEVIILCGGSY----RRGK---ASCGDLDVVIMHPDRKS 398 (538)
Q Consensus 367 p~~~v~~~Gs~----RRgk---e~~~DvDiLIt~~~~~~ 398 (538)
-++.+-++||+ =+|- ...+|+|+||-.++...
T Consensus 107 ~~~~~gv~GS~~~qlaTg~~~~~~~SDLDLLi~~~~~~~ 145 (202)
T TIGR03135 107 LGVPWGVYGSAGWQLLTGLPYLHASSDLDLLLRAPSPLS 145 (202)
T ss_pred CCCcEEEecchHHHHhcCCcccCCCCCeeEEEcCCChhh
Confidence 35567789998 5565 56689999998876543
No 291
>COG1031 Uncharacterized Fe-S oxidoreductase [Energy production and conversion]
Probab=32.32 E-value=38 Score=37.12 Aligned_cols=31 Identities=16% Similarity=0.345 Sum_probs=28.8
Q ss_pred HHHHhhccCCCHHHHHHHHHh-CCCCHHHHhh
Q 009281 294 ISLFGEVWGIGPATAQKLYEK-GHRTLDDLKN 324 (538)
Q Consensus 294 l~lf~~I~GvGpktA~~l~~~-GirtledL~~ 324 (538)
.+.++.|||||.+++.+++.. .++|.||+++
T Consensus 515 ~~vl~~ipgig~~~~~~I~~~Rp~~s~e~~l~ 546 (560)
T COG1031 515 KDVLRAIPGIGKKTLRKILAERPFKSSEEFLK 546 (560)
T ss_pred HHHHHhcccchhhhHHHHHhcCCccchHHHHh
Confidence 778999999999999999987 9999999985
No 292
>PRK03381 PII uridylyl-transferase; Provisional
Probab=32.31 E-value=1.2e+02 Score=35.94 Aligned_cols=46 Identities=22% Similarity=0.294 Sum_probs=29.2
Q ss_pred eEEEeccccccc-CCcCCCeeEEEecCCcc--hhhhhHHHHHHHHHHcC
Q 009281 369 VIILCGGSYRRG-KASCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMK 414 (538)
Q Consensus 369 ~~v~~~Gs~RRg-ke~~~DvDiLIt~~~~~--~~~~~l~~~v~~L~~~g 414 (538)
+-++.+|||=|| ..-..|||+||-+++.. ....+...++.-|-+.|
T Consensus 58 ~alvAvg~~gr~el~p~SD~Dll~l~~~~~~~~~~~~~~~~~~~LwD~g 106 (774)
T PRK03381 58 VALVAVGGLGRRELLPYSDLDLVLLHDGRPADDVAEVADRLWYPLWDAG 106 (774)
T ss_pred eEEEEeCCcCCcCcCCCCCCeEEEEeCCCCchHHHHHHHHHhhhcccCC
Confidence 467778999555 56678999999887432 23344455544444444
No 293
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=31.58 E-value=49 Score=32.59 Aligned_cols=20 Identities=20% Similarity=0.371 Sum_probs=17.3
Q ss_pred chhhhc-CCCCCCHHHHHHHH
Q 009281 252 SADQVK-GLPGIGKSMQDHIQ 271 (538)
Q Consensus 252 ~~~~l~-~lpgiG~~ia~~I~ 271 (538)
..++|. +|||||.++|+.|-
T Consensus 116 ~R~~Ll~~lpGIG~KTAd~vL 136 (208)
T PRK01229 116 AREFLVKNIKGIGYKEASHFL 136 (208)
T ss_pred HHHHHHHcCCCCcHHHHHHHH
Confidence 347788 99999999999976
No 294
>cd00424 PolY Y-family of DNA polymerases. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Most TLS polymerases are members of the Y-family, including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is found exclusively in bacteria. In eukaryotes, the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in ord
Probab=30.89 E-value=1.2e+02 Score=31.71 Aligned_cols=53 Identities=17% Similarity=0.375 Sum_probs=33.4
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh--CCCC
Q 009281 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (538)
Q Consensus 256 l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~--Girt 318 (538)
+..|||||+++.+++..+ | +..+.+|.+-.....+. ..+| +.+..+|+. |+..
T Consensus 175 i~~l~giG~~~~~~L~~~---G-i~ti~dl~~~~~~~~l~---~~fg---~~~~~l~~~a~G~d~ 229 (343)
T cd00424 175 LTDLPGIGAVTAKRLEAV---G-INPIGDLLAASPDALLA---LWGG---VSGERLWYALRGIDD 229 (343)
T ss_pred hhhcCCCCHHHHHHHHHc---C-CCcHHHHhcCCHHHHHH---HHhh---HHHHHHHHHhCCcCC
Confidence 678899999999988754 3 45566665432133332 3333 567777775 8754
No 295
>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=29.79 E-value=40 Score=27.99 Aligned_cols=36 Identities=19% Similarity=0.433 Sum_probs=19.1
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHH
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRT 293 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~ 293 (538)
.++..||+||..+.+...++ -+.-+++|+.--+..+
T Consensus 3 ~~l~~LpNig~~~e~~L~~v----GI~t~~~L~~~Ga~~a 38 (81)
T PF04994_consen 3 NRLKDLPNIGPKSERMLAKV----GIHTVEDLRELGAVEA 38 (81)
T ss_dssp --GCGSTT--HHHHHHHHHT----T--SHHHHHHHHHHHH
T ss_pred cchhhCCCCCHHHHHHHHHc----CCCCHHHHHHhCHHHH
Confidence 36889999999887765443 3455666665333333
No 296
>COG5275 BRCT domain type II [General function prediction only]
Probab=28.53 E-value=1.2e+02 Score=29.98 Aligned_cols=50 Identities=14% Similarity=0.077 Sum_probs=36.3
Q ss_pred CCCcCcEEEEecCCCChhHHHHHHHHHHhcCCEEEeecCCCccEEEEcCCh
Q 009281 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLE 67 (538)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~R~~~l~~~~~~~G~~V~~~ls~~VTHVV~~~~~ 67 (538)
.-+.|.+|.|-.- |..-.++-.+-++..+||+|....|...|-||.-++-
T Consensus 155 ~cL~G~~fVfTG~-l~TlsR~~a~~lvk~yGgrvT~~pSskTtflvlGdna 204 (276)
T COG5275 155 ECLKGKVFVFTGD-LKTLSRDDAKTLVKVYGGRVTAVPSSKTTFLVLGDNA 204 (276)
T ss_pred ccccccEEEEecc-cccccchhHHHHHHHhCCeeecccccceeEEEecCCC
Confidence 4567888777322 2323345567899999999999999999999886653
No 297
>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=28.46 E-value=1.2e+02 Score=27.71 Aligned_cols=38 Identities=18% Similarity=0.194 Sum_probs=25.5
Q ss_pred HHHHHHHHhhhcCCCeEEEecccccc----cCCcCCCeeEEEecC
Q 009281 354 MERLLQKAGEEVLPEVIILCGGSYRR----GKASCGDLDVVIMHP 394 (538)
Q Consensus 354 i~~iv~~~~~~~~p~~~v~~~Gs~RR----gke~~~DvDiLIt~~ 394 (538)
+..+++.+.. ..+.++.++||+=| |+ .++|+||++...
T Consensus 4 ~~~il~~l~~--~~g~~~ylVGG~VRD~Llg~-~~~DiDi~v~~~ 45 (139)
T cd05398 4 LLKLLRELKK--ALGYEAYLVGGAVRDLLLGR-PPKDIDIATDAD 45 (139)
T ss_pred HHHHHHHHHh--ccCceEEEECChHHHHHcCC-CCCCceEEEeCC
Confidence 3445555442 14778888888776 44 679999988664
No 298
>PRK03348 DNA polymerase IV; Provisional
Probab=27.62 E-value=1.2e+02 Score=33.45 Aligned_cols=53 Identities=17% Similarity=0.334 Sum_probs=37.1
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh--CCCC
Q 009281 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (538)
Q Consensus 256 l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~--Girt 318 (538)
+..|||||+.+.+++..+ -+..+.+|.+-.+..+.+.| |++....||+. |+..
T Consensus 182 v~~L~GIG~~t~~~L~~l----GI~TigDLa~l~~~~L~~~f------G~~~g~~L~~~a~G~d~ 236 (454)
T PRK03348 182 VRRLWGIGPVTEEKLHRL----GIETIGDLAALSEAEVANLL------GATVGPALHRLARGIDD 236 (454)
T ss_pred ccccCCCCHHHHHHHHHc----CCccHHHHhcCCHHHHHHHH------CHHHHHHHHHHHcCCCC
Confidence 678999999988887654 45666666654444555555 67788889874 8754
No 299
>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=26.60 E-value=54 Score=27.22 Aligned_cols=42 Identities=19% Similarity=0.438 Sum_probs=26.1
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHH
Q 009281 255 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPAT 307 (538)
Q Consensus 255 ~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpkt 307 (538)
-|..|||||.-++..|---+ |.+.....- +-|.+-.|+-|..
T Consensus 3 ~l~sipGig~~~a~~llaei--gd~~rF~~~---------~~l~~~~Gl~P~~ 44 (87)
T PF02371_consen 3 LLTSIPGIGPITAATLLAEI--GDISRFKSA---------KQLASYAGLAPRP 44 (87)
T ss_pred hhcCCCCccHHHHHHHHHHH--cCchhcccc---------hhhhhcccccccc
Confidence 47899999999888764333 666544332 2244556665543
No 300
>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=25.48 E-value=45 Score=34.78 Aligned_cols=43 Identities=26% Similarity=0.289 Sum_probs=30.3
Q ss_pred ccCCCHHHHHHHHHhCCCCHHHHhhcc--Ccchhhhccccchhhh
Q 009281 300 VWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDI 342 (538)
Q Consensus 300 I~GvGpktA~~l~~~GirtledL~~~~--~L~~~q~~Glk~~ed~ 342 (538)
-.||||.++++|-+.||.|++||.... .|....++.....+.+
T Consensus 6 ~~g~~~~~~~~L~~~g~~t~~~~~~~~~~~L~~~~gls~~~~~~i 50 (313)
T TIGR02238 6 AHGINAADIKKLKSAGICTVNGVIMTTRRALCKIKGLSEAKVDKI 50 (313)
T ss_pred cCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHH
Confidence 368999999999999999999998543 3544444444433333
No 301
>PRK14133 DNA polymerase IV; Provisional
Probab=25.14 E-value=1.7e+02 Score=30.61 Aligned_cols=52 Identities=25% Similarity=0.430 Sum_probs=33.0
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHHh--CCCC
Q 009281 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (538)
Q Consensus 256 l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~--Girt 318 (538)
+..|||||++++++...+ -+..+.+|.+-.+...- +.+| + ....+|+. |+..
T Consensus 175 v~~l~gig~~~~~~L~~~----Gi~ti~dl~~l~~~~L~----~rfG--~-~g~~l~~~a~G~d~ 228 (347)
T PRK14133 175 ISKVHGIGKKSVEKLNNI----GIYTIEDLLKLSREFLI----EYFG--K-FGVEIYERIRGIDY 228 (347)
T ss_pred ccccCCCCHHHHHHHHHc----CCccHHHHhhCCHHHHH----HHHh--H-HHHHHHHHhCCCCC
Confidence 678899999999987654 35666666654333333 4444 3 45666653 8764
No 302
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=25.13 E-value=2e+02 Score=30.45 Aligned_cols=103 Identities=18% Similarity=0.240 Sum_probs=58.0
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHHhhccCCCHHHHHHHHH-------hCCCCHHHHhhcc
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE-------KGHRTLDDLKNED 326 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~-------~GirtledL~~~~ 326 (538)
++|.+ +||++.+.+|+++ ..+.-++.+..-.+ .+ |.++.|+...+|.++.+ .|+.|-.++....
T Consensus 32 ~~l~~-~g~~~~~~~kL~~----~g~~tv~~~~~~~~---~~-L~~~~g~s~~~~~ki~~~a~~~~~~~~~ta~~~~~~~ 102 (344)
T PLN03187 32 DKLIS-QGINAGDVKKLQD----AGIYTCNGLMMHTK---KN-LTGIKGLSEAKVDKICEAAEKLLNQGFITGSDALLKR 102 (344)
T ss_pred HHHhh-CCCCHHHHHHHHH----cCCCcHHHHHhCCH---HH-HHHhcCCCHHHHHHHHHHHHHhhcccCCcHHHHHhhh
Confidence 33433 6799888777554 34555666554333 23 44889999999998764 2666777765322
Q ss_pred CcchhhhccccchhhhccCcCHHHHHHHHHHHHHHhhhcCCCeEEEecccccccCCc
Q 009281 327 SLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKAS 383 (538)
Q Consensus 327 ~L~~~q~~Glk~~ed~~~~i~r~ea~~i~~iv~~~~~~~~p~~~v~~~Gs~RRgke~ 383 (538)
+-......|.+-.++++. .-+..|...+++|.+.=||.+
T Consensus 103 ~~~~~isTG~~~LD~lLg------------------GGi~~G~ItEI~G~~GsGKTq 141 (344)
T PLN03187 103 KSVVRITTGSQALDELLG------------------GGIETRCITEAFGEFRSGKTQ 141 (344)
T ss_pred ccCceecCCcHhHHhhcC------------------CCCCCCeEEEEecCCCCChhH
Confidence 111111234444333321 112334456688888888876
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=23.37 E-value=62 Score=39.24 Aligned_cols=26 Identities=19% Similarity=0.326 Sum_probs=21.5
Q ss_pred hhccCCCHHHHHHHHHh-CCCCHHHHh
Q 009281 298 GEVWGIGPATAQKLYEK-GHRTLDDLK 323 (538)
Q Consensus 298 ~~I~GvGpktA~~l~~~-GirtledL~ 323 (538)
.+|+||||+||.++..+ |=.+++.|.
T Consensus 869 ~GI~GIGpktAl~li~~~~~~~le~L~ 895 (1034)
T TIGR00600 869 EGIPTVGPVSAMEILNEFPGDGLEPLL 895 (1034)
T ss_pred CCCCcccHHHHHHHHHHcCCCCHHHHH
Confidence 47999999999999998 655677665
No 304
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=22.68 E-value=1.3e+02 Score=30.22 Aligned_cols=47 Identities=21% Similarity=0.323 Sum_probs=36.7
Q ss_pred HHHHHHhhccCCCHHHHHHHHHhCCCCHHHHhhc--cCcchhhhccccch
Q 009281 292 RTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYF 339 (538)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~--~~L~~~q~~Glk~~ 339 (538)
.++..+|+|+||+...|..|... +-||+.+.++ +.|.+.+|+|-.-.
T Consensus 192 ~~~~~Lt~i~~VnKtda~~LL~~-FgsLq~~~~AS~~ele~~~G~G~~ka 240 (254)
T KOG2841|consen 192 SLLGFLTTIPGVNKTDAQLLLQK-FGSLQQISNASEGELEQCPGLGPAKA 240 (254)
T ss_pred HHHHHHHhCCCCCcccHHHHHHh-cccHHHHHhcCHhHHHhCcCcCHHHH
Confidence 56778999999999999999764 4488888864 46888888885443
No 305
>TIGR02922 conserved hypothetical protein TIGR02922. Two members of this family are found in Colwellia psychrerythraea 34H and one each in various other species of Colwellia and Shewanella. One member from C. psychrerythraea is of special interest because it is preceded by the same cis-regulatory site as a number of genes that have the PEP-CTERM domain described by TIGR02595.
Probab=22.40 E-value=34 Score=27.02 Aligned_cols=15 Identities=20% Similarity=0.457 Sum_probs=12.5
Q ss_pred EEEecccccccCCcC
Q 009281 370 IILCGGSYRRGKASC 384 (538)
Q Consensus 370 ~v~~~Gs~RRgke~~ 384 (538)
.|++--+|||||..+
T Consensus 34 rvmiPqeFkrGKsIi 48 (67)
T TIGR02922 34 RVMIPQEFKRGKSII 48 (67)
T ss_pred cEEcchHHcCCCeEE
Confidence 577788999999874
No 306
>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=22.33 E-value=4.3e+02 Score=27.90 Aligned_cols=87 Identities=9% Similarity=0.200 Sum_probs=54.0
Q ss_pred HHHHHHHHhcCCccccc--hhhhcCCCCCCHHHHHHHHHHHHh------------CCcchhHHHHhhchhHHH-HHHhhc
Q 009281 236 YYKAIPVIEKLPFKIES--ADQVKGLPGIGKSMQDHIQEIVTT------------GKLSKLEHFEKDEKVRTI-SLFGEV 300 (538)
Q Consensus 236 Y~rAa~~l~~l~~~i~~--~~~l~~lpgiG~~ia~~I~Eil~t------------G~~~~le~l~~~~~~~~l-~lf~~I 300 (538)
-..||.+|..||..... +..+..+..|.+.+.+.|.++|+. |....+-++.+..+...- .+|..+
T Consensus 144 p~~AA~VL~~Lp~~~~~ei~~ria~l~~vs~~~i~~ie~~L~~~~~~~~~~~~~~gG~~~~a~ILN~~~~~~~~~il~~L 223 (338)
T TIGR00207 144 PAQAADILSLFPEEVQAEVARRIATMGRTSPEVVAEVERVLEGKLDSLNSDYTKMGGVRAVAEIINLMDRKTEKTIITSL 223 (338)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhhccccccCChHHHHHHHHHhCCchHHHHHHHHH
Confidence 35789999999976443 356778888888888877665541 222334445554444433 455555
Q ss_pred cCCCHHHHHHHHHhCCCCHHHHh
Q 009281 301 WGIGPATAQKLYEKGHRTLDDLK 323 (538)
Q Consensus 301 ~GvGpktA~~l~~~GirtledL~ 323 (538)
--.-|..|..+-+ -+=+++||.
T Consensus 224 ~~~dp~la~~Ir~-~mF~Fedl~ 245 (338)
T TIGR00207 224 EEFDPELAEEIKK-EMFVFEDIV 245 (338)
T ss_pred HHhCHHHHHHHHH-HccCHHHHh
Confidence 5666777766633 455666665
No 307
>cd07749 NT_Pol-beta-like_1 Nucleotidyltransferase (NT) domain of an uncharacterized subgroup of the Pol beta-like NT superfamily. The Pol beta-like NT superfamily includes DNA polymerase beta and other family X DNA Polymerases, as well as Class I and Class II CCA-adding enzymes, RelA- and SpoT-like ppGpp synthetases and hydrolases, 2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), poly(A) polymerases, terminal uridylyl transferases, Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. Proteins belonging to this subgroup are uncharacterized. In the majority of the Pol beta-like superfamily NTs, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations essential for catalysis. These divalent metal ions are involved in a two-metal ion mechanism of nucleotide addition. These carboxylate residues are conserved in this subgroup.
Probab=21.79 E-value=3.6e+02 Score=25.40 Aligned_cols=37 Identities=16% Similarity=0.135 Sum_probs=24.3
Q ss_pred CCeEEEeccccc---cc-CCcCCCeeEEEecCCcchhhhhH
Q 009281 367 PEVIILCGGSYR---RG-KASCGDLDVVIMHPDRKSHKGFL 403 (538)
Q Consensus 367 p~~~v~~~Gs~R---Rg-ke~~~DvDiLIt~~~~~~~~~~l 403 (538)
-++...++||+. +| ...-+||||++-..+......+|
T Consensus 16 ~~i~W~lgGS~~L~l~Gl~~~p~DIDI~~D~~d~e~i~~il 56 (156)
T cd07749 16 INVNWALTGSLSFALQGVPVEPHDIDIQTDNEGAYEIERIF 56 (156)
T ss_pred CCceEEehhhHHHHHcCCCCCCCcceEEEchhhHHHHHHHH
Confidence 355677899954 33 35679999998666655433333
No 308
>PF05559 DUF763: Protein of unknown function (DUF763); InterPro: IPR008482 This family consists of several uncharacterised bacterial and archaeal proteins of unknown function.
Probab=21.47 E-value=77 Score=33.15 Aligned_cols=20 Identities=25% Similarity=0.368 Sum_probs=15.3
Q ss_pred HHHHHhhccCCCHHHHHHHH
Q 009281 293 TISLFGEVWGIGPATAQKLY 312 (538)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~ 312 (538)
-++.|..++||||+|++.|.
T Consensus 267 ~feeLL~~~GvGp~TlRALa 286 (319)
T PF05559_consen 267 DFEELLLIKGVGPSTLRALA 286 (319)
T ss_pred CHHHHHhcCCCCHHHHHHHH
Confidence 34444489999999999884
No 309
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=21.40 E-value=1.2e+02 Score=31.30 Aligned_cols=18 Identities=33% Similarity=0.661 Sum_probs=15.6
Q ss_pred hhhcCCCCCCHHHHHHHH
Q 009281 254 DQVKGLPGIGKSMQDHIQ 271 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~ 271 (538)
+.|..|||||.++|+-|-
T Consensus 218 ~~L~~lpGVG~KVADCI~ 235 (323)
T KOG2875|consen 218 EALCSLPGVGPKVADCIC 235 (323)
T ss_pred HHHhcCCCCcchHhhhhh
Confidence 458899999999999765
No 310
>PRK07945 hypothetical protein; Provisional
Probab=21.30 E-value=50 Score=34.77 Aligned_cols=28 Identities=29% Similarity=0.446 Sum_probs=23.0
Q ss_pred HhhccCCCHHHHHHHHHh---C-CCCHHHHhh
Q 009281 297 FGEVWGIGPATAQKLYEK---G-HRTLDDLKN 324 (538)
Q Consensus 297 f~~I~GvGpktA~~l~~~---G-irtledL~~ 324 (538)
|++|||||..+|.++.+. | +.-|++|+.
T Consensus 51 l~~~~giG~~~a~~i~e~~~tg~~~~l~~l~~ 82 (335)
T PRK07945 51 LTSLPGIGPKTAKVIAQALAGRVPDYLAELRA 82 (335)
T ss_pred cccCCCcCHHHHHHHHHHHhcCCHHHHHHHHH
Confidence 569999999999999873 5 567888874
No 311
>PF12482 DUF3701: Phage integrase protein; InterPro: IPR022169 This domain family is found in bacteria, and is approximately 100 amino acids in length. The family is found in association with PF00589 from PFAM.
Probab=21.08 E-value=86 Score=27.04 Aligned_cols=21 Identities=43% Similarity=0.602 Sum_probs=19.3
Q ss_pred CHHHHHHHHHhCCCCHHHHhh
Q 009281 304 GPATAQKLYEKGHRTLDDLKN 324 (538)
Q Consensus 304 GpktA~~l~~~GirtledL~~ 324 (538)
.|..|++|-..||+||.||..
T Consensus 22 ~p~va~~L~aaGi~TL~dL~~ 42 (96)
T PF12482_consen 22 PPRVARRLAAAGIRTLADLVD 42 (96)
T ss_pred CHHHHHHHHHcCCchHHHHHH
Confidence 589999999999999999983
No 312
>PRK00024 hypothetical protein; Reviewed
Probab=20.69 E-value=1.2e+02 Score=30.08 Aligned_cols=44 Identities=11% Similarity=0.227 Sum_probs=30.3
Q ss_pred HHHHHHHHHhcCCc----cccchhhhcCCCCCCHHHHHHHHHHHHhCC
Q 009281 235 SYYKAIPVIEKLPF----KIESADQVKGLPGIGKSMQDHIQEIVTTGK 278 (538)
Q Consensus 235 aY~rAa~~l~~l~~----~i~~~~~l~~lpgiG~~ia~~I~Eil~tG~ 278 (538)
+..-|-..|+.+.. --.+.++|..++|||+..|..|.-+++-|+
T Consensus 43 ~~~LA~~LL~~fgsL~~l~~as~~eL~~i~GIG~akA~~L~a~~El~~ 90 (224)
T PRK00024 43 VLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQLKAALELAR 90 (224)
T ss_pred HHHHHHHHHHHcCCHHHHHhCCHHHHhhccCccHHHHHHHHHHHHHHH
Confidence 44445555554431 112457899999999999999988888765
No 313
>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a beta-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [, ].; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBN_M 2QBB_M 3I1M_M 3OFP_M 3OFX_M 3OFO_M 1VS5_M 3OAQ_M 2QAL_M 3J18_M ....
Probab=20.53 E-value=95 Score=27.03 Aligned_cols=44 Identities=11% Similarity=0.181 Sum_probs=30.3
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCcchhHHHHhhchhHHHHHH
Q 009281 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLF 297 (538)
Q Consensus 254 ~~l~~lpgiG~~ia~~I~Eil~tG~~~~le~l~~~~~~~~l~lf 297 (538)
-.|..|.|||...|..|-..+.=.....+.+|..+.-..+.+.+
T Consensus 15 ~aLt~IyGIG~~~A~~Ic~~lgi~~~~~~~~Ls~~~i~~l~~~i 58 (107)
T PF00416_consen 15 IALTKIYGIGRRKAKQICKKLGINPNKKVGDLSDEQIDKLRKII 58 (107)
T ss_dssp HHHTTSTTBCHHHHHHHHHHTTS-SSSBTTTSTHHHHHHHHHHH
T ss_pred hHHhhhhccCHHHHHHHHHHcCCChhhhcccCCHHHHHHHHHHH
Confidence 35889999999999999988876555555555544434444444
No 314
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=20.09 E-value=2.3e+02 Score=34.96 Aligned_cols=90 Identities=22% Similarity=0.322 Sum_probs=0.0
Q ss_pred HHHHHHHHHHhcCCccccchhhhcCCCCCC-HHHHHHHHHHHHh--CCcchhHHHHhhchhHHHHHH-------------
Q 009281 234 FSYYKAIPVIEKLPFKIESADQVKGLPGIG-KSMQDHIQEIVTT--GKLSKLEHFEKDEKVRTISLF------------- 297 (538)
Q Consensus 234 ~aY~rAa~~l~~l~~~i~~~~~l~~lpgiG-~~ia~~I~Eil~t--G~~~~le~l~~~~~~~~l~lf------------- 297 (538)
++|.-|-..+++-.+++..+.. | ..+.++++||-.- -..+--|.=.-..-+-+++|+
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 009281 298 -----------------GEVWGIGPATAQKLYEK----GHRTLDDLKNEDSLTH 330 (538)
Q Consensus 298 -----------------~~I~GvGpktA~~l~~~----GirtledL~~~~~L~~ 330 (538)
-.|+|+|-..|+.+++. -+.|++||++.+.+++
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 315
>PRK14109 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Provisional
Probab=20.00 E-value=2.5e+02 Score=34.22 Aligned_cols=45 Identities=13% Similarity=0.276 Sum_probs=30.9
Q ss_pred eEEEecccc-cccCCcCCCeeEEEecCCcc-----hhhhhHHHHHHHHHHc
Q 009281 369 VIILCGGSY-RRGKASCGDLDVVIMHPDRK-----SHKGFLSKYVKKLKEM 413 (538)
Q Consensus 369 ~~v~~~Gs~-RRgke~~~DvDiLIt~~~~~-----~~~~~l~~~v~~L~~~ 413 (538)
+.|...|+| |+-...+.|||+++.+++.. ....++.++.+.|...
T Consensus 216 ~aviamGklG~~EL~~~SDiDLi~ly~~~~~~~~~~~~~~~~rl~q~l~~~ 266 (1007)
T PRK14109 216 LAVIAMGKCGARELNYVSDVDVIFVAEPAEGVDEAAALAVATRLASELMRI 266 (1007)
T ss_pred eEEEEeccccccccCCccCCCEEEEeCCCCCcccccHHHHHHHHHHHHHHH
Confidence 456778888 56667899999999886432 1134566777776665
Done!