Query 015933
Match_columns 398
No_of_seqs 322 out of 977
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 02:15:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015933.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015933hhsearch_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-56 9E-61 423.9 19.2 196 199-396 3-199 (353)
2 smart00483 POLXc DNA polymeras 100.0 4.3E-47 9.2E-52 377.7 21.6 190 208-397 1-193 (334)
3 cd00141 NT_POLXc Nucleotidyltr 100.0 1.9E-45 4.2E-50 362.1 20.3 184 212-396 2-188 (307)
4 PRK08609 hypothetical protein; 100.0 8.9E-43 1.9E-47 368.3 18.9 188 208-396 1-203 (570)
5 COG1796 POL4 DNA polymerase IV 100.0 4.1E-34 8.9E-39 275.4 16.2 189 207-396 2-208 (326)
6 PF14716 HHH_8: Helix-hairpin- 99.7 1.1E-17 2.4E-22 129.3 7.4 66 210-275 1-68 (68)
7 PF10391 DNA_pol_lambd_f: Fing 99.7 2.3E-17 4.9E-22 120.5 5.0 51 294-344 1-52 (52)
8 PF14792 DNA_pol_B_palm: DNA p 99.6 2E-16 4.4E-21 134.0 5.4 53 345-397 1-53 (112)
9 PRK07945 hypothetical protein; 99.6 4.7E-15 1E-19 148.2 8.7 102 213-324 3-118 (335)
10 PF00533 BRCT: BRCA1 C Terminu 99.1 1.1E-10 2.4E-15 90.7 6.4 75 16-95 3-78 (78)
11 smart00292 BRCT breast cancer 99.1 1.9E-10 4.1E-15 88.3 7.0 79 17-98 1-80 (80)
12 cd00027 BRCT Breast Cancer Sup 98.8 1E-08 2.2E-13 76.8 6.0 72 21-96 1-72 (72)
13 PF14520 HHH_5: Helix-hairpin- 98.2 1.2E-06 2.7E-11 65.8 3.4 52 293-344 3-56 (60)
14 TIGR00575 dnlj DNA ligase, NAD 98.2 7.4E-06 1.6E-10 88.8 10.1 130 254-394 466-630 (652)
15 PF12738 PTCB-BRCT: twin BRCT 98.0 5.4E-06 1.2E-10 62.5 3.5 63 22-90 1-63 (63)
16 KOG3226 DNA repair protein [Re 97.9 3.6E-06 7.9E-11 83.3 2.2 90 16-111 315-404 (508)
17 PLN03123 poly [ADP-ribose] pol 97.9 2.4E-05 5.1E-10 87.8 7.7 93 14-109 389-481 (981)
18 PLN03122 Poly [ADP-ribose] pol 97.6 8.2E-05 1.8E-09 82.0 6.8 95 13-110 184-279 (815)
19 PF14520 HHH_5: Helix-hairpin- 97.5 0.00012 2.6E-09 54.9 4.2 52 254-313 5-56 (60)
20 COG1555 ComEA DNA uptake prote 97.3 0.00033 7.2E-09 62.4 5.0 51 252-314 95-146 (149)
21 PF12826 HHH_2: Helix-hairpin- 97.3 0.00037 8.1E-09 53.1 4.5 48 257-313 6-53 (64)
22 PRK07956 ligA NAD-dependent DN 97.3 0.0014 3.1E-08 71.4 10.5 131 254-394 479-636 (665)
23 PF11731 Cdd1: Pathogenicity l 97.2 0.00036 7.7E-09 57.1 4.1 36 290-325 7-42 (93)
24 TIGR01259 comE comEA protein. 97.2 0.00063 1.4E-08 58.4 5.5 50 252-313 66-116 (120)
25 PF12836 HHH_3: Helix-hairpin- 97.1 0.00069 1.5E-08 51.7 4.5 48 252-311 12-60 (65)
26 PRK14351 ligA NAD-dependent DN 97.1 0.0022 4.7E-08 70.2 9.9 131 254-394 496-655 (689)
27 KOG0966 ATP-dependent DNA liga 96.9 0.0014 3.1E-08 70.9 6.2 91 12-107 627-720 (881)
28 PF14229 DUF4332: Domain of un 96.8 0.0075 1.6E-07 51.9 8.9 66 260-325 1-83 (122)
29 KOG2481 Protein required for n 96.8 0.00092 2E-08 69.1 3.4 86 12-109 321-416 (570)
30 PRK02515 psbU photosystem II c 96.7 0.0023 5E-08 55.3 4.8 47 252-313 59-105 (132)
31 TIGR00084 ruvA Holliday juncti 96.7 0.0013 2.7E-08 61.1 3.2 50 292-343 69-124 (191)
32 TIGR00084 ruvA Holliday juncti 96.7 0.0029 6.2E-08 58.7 5.5 53 254-312 72-124 (191)
33 TIGR00426 competence protein C 96.7 0.0039 8.6E-08 47.9 5.4 50 253-314 15-66 (69)
34 PRK12766 50S ribosomal protein 96.6 0.00081 1.8E-08 63.6 1.6 52 296-347 4-57 (232)
35 KOG4362 Transcriptional regula 96.6 0.0022 4.9E-08 68.9 4.5 79 30-111 485-565 (684)
36 PF00633 HHH: Helix-hairpin-he 96.5 0.0024 5.1E-08 41.4 2.5 23 251-273 8-30 (30)
37 PRK14605 ruvA Holliday junctio 96.4 0.0039 8.4E-08 57.9 4.2 52 254-312 73-125 (194)
38 PRK07956 ligA NAD-dependent DN 96.3 0.0021 4.6E-08 70.1 2.4 48 299-346 449-499 (665)
39 PRK00116 ruvA Holliday junctio 96.2 0.0086 1.9E-07 55.5 5.8 54 254-314 73-127 (192)
40 PRK13901 ruvA Holliday junctio 96.2 0.0063 1.4E-07 56.6 4.7 54 254-313 72-125 (196)
41 PRK14601 ruvA Holliday junctio 96.2 0.0064 1.4E-07 56.0 4.6 54 254-313 73-126 (183)
42 PRK14973 DNA topoisomerase I; 96.0 0.0089 1.9E-07 67.6 5.7 91 254-345 835-929 (936)
43 PF00633 HHH: Helix-hairpin-he 96.0 0.006 1.3E-07 39.5 2.6 22 292-313 8-29 (30)
44 COG1555 ComEA DNA uptake prote 96.0 0.0068 1.5E-07 54.0 3.8 53 289-347 91-148 (149)
45 TIGR00575 dnlj DNA ligase, NAD 96.0 0.0036 7.8E-08 68.2 2.3 49 298-346 435-486 (652)
46 PRK14606 ruvA Holliday junctio 96.0 0.0091 2E-07 55.2 4.6 54 254-313 73-126 (188)
47 PRK14602 ruvA Holliday junctio 96.0 0.0084 1.8E-07 56.1 4.4 54 254-313 74-127 (203)
48 PRK14604 ruvA Holliday junctio 95.9 0.0099 2.1E-07 55.3 4.5 54 254-313 73-126 (195)
49 PRK14603 ruvA Holliday junctio 95.9 0.01 2.2E-07 55.3 4.6 54 254-313 72-125 (197)
50 PRK02362 ski2-like helicase; P 95.9 0.0089 1.9E-07 66.1 4.8 60 284-346 642-703 (737)
51 PRK14350 ligA NAD-dependent DN 95.9 0.024 5.2E-07 61.9 7.9 132 254-394 470-639 (669)
52 TIGR01259 comE comEA protein. 95.8 0.011 2.3E-07 50.8 4.1 51 290-346 63-118 (120)
53 PF12836 HHH_3: Helix-hairpin- 95.7 0.012 2.6E-07 44.8 3.5 50 291-346 10-64 (65)
54 PF11798 IMS_HHH: IMS family H 95.5 0.0073 1.6E-07 39.6 1.6 20 297-316 13-32 (32)
55 KOG1929 Nucleotide excision re 95.5 0.023 5.1E-07 62.8 6.1 89 17-110 102-190 (811)
56 PRK00116 ruvA Holliday junctio 95.4 0.01 2.2E-07 55.0 2.7 51 293-343 71-125 (192)
57 TIGR00426 competence protein C 95.4 0.023 5E-07 43.6 4.2 46 295-346 16-67 (69)
58 COG0272 Lig NAD-dependent DNA 95.4 0.068 1.5E-06 57.8 8.9 84 254-347 479-564 (667)
59 PRK14605 ruvA Holliday junctio 95.3 0.01 2.3E-07 55.1 2.3 51 291-341 69-123 (194)
60 PRK02515 psbU photosystem II c 95.2 0.033 7.2E-07 48.2 5.0 41 291-337 57-98 (132)
61 KOG2043 Signaling protein SWIF 95.2 0.019 4.1E-07 64.4 4.3 68 38-109 672-739 (896)
62 COG0632 RuvA Holliday junction 95.2 0.024 5.1E-07 53.0 4.3 54 254-313 73-126 (201)
63 cd05397 NT_Pol-beta-like Nucle 95.2 0.041 8.9E-07 39.5 4.6 28 365-392 14-42 (49)
64 PF12826 HHH_2: Helix-hairpin- 95.1 0.018 3.9E-07 43.8 2.7 45 299-344 7-53 (64)
65 KOG0966 ATP-dependent DNA liga 95.1 0.058 1.3E-06 58.9 7.4 91 16-107 782-881 (881)
66 KOG1929 Nucleotide excision re 95.1 0.024 5.2E-07 62.7 4.6 93 11-109 486-578 (811)
67 PRK14600 ruvA Holliday junctio 95.0 0.024 5.2E-07 52.4 3.8 53 254-313 73-125 (186)
68 PRK00254 ski2-like helicase; P 94.9 0.042 9.1E-07 60.7 6.1 69 276-345 623-697 (720)
69 COG5163 NOP7 Protein required 94.7 0.025 5.4E-07 57.2 3.3 86 12-109 344-440 (591)
70 PRK14606 ruvA Holliday junctio 94.4 0.022 4.7E-07 52.7 1.9 51 291-343 69-125 (188)
71 PRK14601 ruvA Holliday junctio 94.4 0.023 4.9E-07 52.4 2.0 51 291-343 69-125 (183)
72 PRK14603 ruvA Holliday junctio 94.3 0.024 5.2E-07 52.8 1.9 51 291-343 68-124 (197)
73 PRK12766 50S ribosomal protein 94.3 0.071 1.5E-06 50.6 5.0 54 253-314 2-55 (232)
74 PRK14602 ruvA Holliday junctio 94.1 0.028 6.1E-07 52.6 2.1 51 291-343 70-126 (203)
75 PRK14604 ruvA Holliday junctio 94.0 0.029 6.3E-07 52.2 1.9 51 291-343 69-125 (195)
76 PRK13901 ruvA Holliday junctio 93.9 0.034 7.4E-07 51.7 2.0 51 291-343 68-124 (196)
77 PRK14351 ligA NAD-dependent DN 93.3 0.043 9.4E-07 60.2 1.9 49 298-346 465-516 (689)
78 PRK04301 radA DNA repair and r 93.2 0.08 1.7E-06 52.6 3.6 47 297-343 8-56 (317)
79 PRK14600 ruvA Holliday junctio 93.1 0.055 1.2E-06 50.0 2.0 50 291-343 69-124 (186)
80 TIGR01448 recD_rel helicase, p 93.1 0.47 1E-05 52.6 9.6 83 253-346 116-201 (720)
81 PF01909 NTP_transf_2: Nucleot 92.8 0.22 4.7E-06 39.6 5.0 31 366-396 12-43 (93)
82 PF04994 TfoX_C: TfoX C-termin 92.7 0.082 1.8E-06 42.2 2.4 30 297-326 5-34 (81)
83 smart00278 HhH1 Helix-hairpin- 92.7 0.077 1.7E-06 32.9 1.7 18 296-313 2-19 (26)
84 PRK08097 ligB NAD-dependent DN 92.2 0.26 5.6E-06 52.9 6.0 88 253-353 458-547 (562)
85 TIGR02236 recomb_radA DNA repa 92.2 0.11 2.4E-06 51.2 3.1 37 298-334 2-40 (310)
86 COG1796 POL4 DNA polymerase IV 92.1 0.38 8.3E-06 47.7 6.5 97 207-322 59-155 (326)
87 COG3743 Uncharacterized conser 92.0 0.17 3.7E-06 43.8 3.5 53 295-350 67-119 (133)
88 TIGR01448 recD_rel helicase, p 91.6 0.099 2.2E-06 57.8 2.2 46 300-345 89-136 (720)
89 COG1948 MUS81 ERCC4-type nucle 91.6 0.25 5.5E-06 47.6 4.6 49 256-313 184-232 (254)
90 PRK01172 ski2-like helicase; P 91.4 0.43 9.3E-06 52.3 6.8 57 285-342 603-661 (674)
91 PRK03352 DNA polymerase IV; Va 90.7 0.26 5.7E-06 49.4 4.1 30 297-326 179-208 (346)
92 KOG2841 Structure-specific end 90.4 0.32 6.9E-06 46.2 3.9 49 256-313 197-245 (254)
93 TIGR00588 ogg 8-oxoguanine DNA 90.2 0.8 1.7E-05 45.6 6.9 64 255-320 177-245 (310)
94 PRK14670 uvrC excinuclease ABC 90.1 0.6 1.3E-05 50.3 6.3 52 254-314 514-565 (574)
95 PRK01216 DNA polymerase IV; Va 89.9 0.33 7.2E-06 49.1 3.9 40 297-336 180-219 (351)
96 PRK03858 DNA polymerase IV; Va 89.8 0.32 6.9E-06 49.7 3.8 28 298-325 176-203 (396)
97 PRK14133 DNA polymerase IV; Pr 89.7 0.84 1.8E-05 45.8 6.7 45 298-342 176-223 (347)
98 smart00279 HhH2 Helix-hairpin- 89.0 0.27 5.8E-06 33.1 1.7 16 299-314 20-35 (36)
99 COG0632 RuvA Holliday junction 89.0 0.26 5.7E-06 46.0 2.3 52 292-343 70-125 (201)
100 PRK14666 uvrC excinuclease ABC 88.9 0.26 5.7E-06 53.9 2.4 50 294-344 636-687 (694)
101 cd00080 HhH2_motif Helix-hairp 88.6 0.37 8E-06 37.8 2.5 28 297-325 24-51 (75)
102 PF14490 HHH_4: Helix-hairpin- 88.5 0.57 1.2E-05 38.2 3.7 53 293-346 11-66 (94)
103 COG1948 MUS81 ERCC4-type nucle 88.4 0.62 1.3E-05 45.0 4.4 54 290-344 177-232 (254)
104 cd01701 PolY_Rev1 DNA polymera 88.3 0.5 1.1E-05 48.6 4.1 30 297-326 224-253 (404)
105 PRK14667 uvrC excinuclease ABC 88.3 0.92 2E-05 48.9 6.1 51 254-314 514-564 (567)
106 PRK03609 umuC DNA polymerase V 88.1 0.5 1.1E-05 48.9 3.9 29 298-326 182-210 (422)
107 PRK08097 ligB NAD-dependent DN 88.1 0.23 5.1E-06 53.2 1.5 49 298-346 428-479 (562)
108 PRK07758 hypothetical protein; 87.7 0.36 7.8E-06 39.6 1.9 45 300-344 39-85 (95)
109 TIGR01083 nth endonuclease III 87.5 2.9 6.2E-05 38.5 8.2 24 293-316 104-127 (191)
110 cd05402 NT_PAP_TUTase Nucleoti 87.4 1.3 2.9E-05 36.7 5.4 39 354-396 9-48 (114)
111 PRK03348 DNA polymerase IV; Pr 87.4 0.55 1.2E-05 49.2 3.7 29 297-325 182-210 (454)
112 TIGR03252 uncharacterized HhH- 87.3 0.9 2E-05 41.6 4.5 49 261-312 75-132 (177)
113 cd01703 PolY_Pol_iota DNA Poly 87.2 0.61 1.3E-05 47.7 3.8 30 297-326 174-203 (379)
114 smart00278 HhH1 Helix-hairpin- 87.1 0.55 1.2E-05 29.0 2.2 20 255-274 2-21 (26)
115 PF11731 Cdd1: Pathogenicity l 86.7 1 2.2E-05 36.9 4.2 48 252-303 10-57 (93)
116 PRK10308 3-methyl-adenine DNA 86.3 1.6 3.4E-05 43.0 6.0 65 254-322 167-234 (283)
117 COG0122 AlkA 3-methyladenine D 86.1 3.3 7.3E-05 40.8 8.2 49 268-317 172-220 (285)
118 PRK14672 uvrC excinuclease ABC 86.1 1.3 2.7E-05 48.6 5.6 54 254-316 608-661 (691)
119 PRK01810 DNA polymerase IV; Va 86.0 0.83 1.8E-05 46.9 4.1 29 297-325 181-209 (407)
120 cd01700 PolY_Pol_V_umuC umuC s 86.0 0.62 1.3E-05 46.7 3.1 29 297-325 178-206 (344)
121 PRK02406 DNA polymerase IV; Va 85.8 0.61 1.3E-05 46.7 3.0 29 297-325 170-198 (343)
122 PRK00558 uvrC excinuclease ABC 85.8 1.4 3E-05 47.9 5.8 52 254-314 543-594 (598)
123 PF01367 5_3_exonuc: 5'-3' exo 85.8 0.066 1.4E-06 44.6 -3.3 25 299-325 22-47 (101)
124 PRK14666 uvrC excinuclease ABC 85.8 1.2 2.6E-05 48.8 5.3 51 254-313 637-687 (694)
125 PTZ00205 DNA polymerase kappa; 85.7 0.84 1.8E-05 49.0 4.0 29 297-325 311-339 (571)
126 COG0353 RecR Recombinational D 85.7 0.56 1.2E-05 43.5 2.3 22 292-313 9-30 (198)
127 PRK13482 DNA integrity scannin 85.3 1.2 2.5E-05 45.1 4.6 51 254-313 287-337 (352)
128 PRK08609 hypothetical protein; 85.1 1.2 2.5E-05 48.2 4.9 56 252-313 86-141 (570)
129 KOG3548 DNA damage checkpoint 84.7 0.97 2.1E-05 50.5 4.0 92 17-111 924-1038(1176)
130 PRK09482 flap endonuclease-lik 84.7 0.69 1.5E-05 44.9 2.6 25 299-325 186-211 (256)
131 smart00475 53EXOc 5'-3' exonuc 84.7 0.7 1.5E-05 44.9 2.6 25 299-325 190-215 (259)
132 PRK03103 DNA polymerase IV; Re 84.5 1.1 2.4E-05 46.0 4.2 29 298-326 184-212 (409)
133 PRK02794 DNA polymerase IV; Pr 84.5 0.73 1.6E-05 47.6 2.9 29 297-325 211-239 (419)
134 cd00424 PolY Y-family of DNA p 84.4 0.84 1.8E-05 45.8 3.2 29 298-326 176-204 (343)
135 cd01702 PolY_Pol_eta DNA Polym 84.0 1.2 2.6E-05 45.2 4.1 29 297-325 184-213 (359)
136 PRK14976 5'-3' exonuclease; Pr 84.0 0.76 1.6E-05 45.2 2.6 26 299-325 195-220 (281)
137 PRK06063 DNA polymerase III su 83.5 4.5 9.8E-05 40.3 7.9 73 17-93 231-303 (313)
138 cd00008 53EXOc 5'-3' exonuclea 82.5 0.98 2.1E-05 43.2 2.7 26 299-325 187-212 (240)
139 cd00056 ENDO3c endonuclease II 82.4 0.88 1.9E-05 40.1 2.2 27 291-317 79-105 (158)
140 TIGR03671 cca_archaeal CCA-add 82.1 2.7 5.9E-05 43.4 5.8 44 351-394 23-68 (408)
141 PRK14670 uvrC excinuclease ABC 82.1 0.81 1.8E-05 49.3 2.1 47 296-343 515-563 (574)
142 PRK14350 ligA NAD-dependent DN 81.9 3.5 7.6E-05 45.4 6.9 73 16-93 591-663 (669)
143 cd03468 PolY_like DNA Polymera 81.7 1.6 3.4E-05 43.3 3.9 27 299-325 174-200 (335)
144 PRK10702 endonuclease III; Pro 81.6 3.4 7.3E-05 38.9 5.8 43 232-274 85-129 (211)
145 PRK10702 endonuclease III; Pro 81.5 5.6 0.00012 37.4 7.3 25 292-316 106-130 (211)
146 PRK14667 uvrC excinuclease ABC 81.1 1.1 2.3E-05 48.4 2.6 47 295-343 514-562 (567)
147 TIGR00615 recR recombination p 81.0 1.3 2.8E-05 41.2 2.7 21 292-312 8-28 (195)
148 PRK00076 recR recombination pr 80.9 1.3 2.8E-05 41.3 2.7 22 292-313 8-29 (196)
149 COG0389 DinP Nucleotidyltransf 80.5 1.6 3.6E-05 44.1 3.6 28 297-324 178-205 (354)
150 TIGR01084 mutY A/G-specific ad 80.4 3.7 8E-05 40.3 5.8 78 219-303 68-147 (275)
151 PF14229 DUF4332: Domain of un 80.0 1.8 4E-05 37.1 3.2 25 301-325 1-25 (122)
152 PRK01229 N-glycosylase/DNA lya 79.9 2.3 5E-05 40.0 4.1 53 262-317 85-142 (208)
153 PRK13844 recombination protein 79.6 1.5 3.3E-05 40.9 2.7 21 292-312 12-32 (200)
154 PRK06195 DNA polymerase III su 79.5 4.6 0.0001 40.1 6.3 48 17-65 219-266 (309)
155 KOG2534 DNA polymerase IV (fam 79.5 1.6 3.5E-05 43.3 3.0 54 290-343 51-114 (353)
156 PRK14671 uvrC excinuclease ABC 79.4 1.9 4.1E-05 47.1 3.8 48 293-343 567-616 (621)
157 COG1708 Predicted nucleotidylt 79.1 5.1 0.00011 33.1 5.6 26 368-393 26-52 (128)
158 PRK10880 adenine DNA glycosyla 79.0 3.8 8.2E-05 41.6 5.6 65 232-303 85-151 (350)
159 PRK14669 uvrC excinuclease ABC 78.8 1.2 2.7E-05 48.4 2.2 47 295-344 552-600 (624)
160 KOG3524 Predicted guanine nucl 78.7 2.1 4.6E-05 46.5 3.8 79 15-101 115-193 (850)
161 cd03586 PolY_Pol_IV_kappa DNA 78.5 1.8 3.8E-05 43.0 3.0 28 298-325 174-201 (334)
162 smart00478 ENDO3c endonuclease 78.1 5 0.00011 34.9 5.5 26 293-318 70-95 (149)
163 cd05400 NT_2-5OAS_ClassI-CCAas 77.9 5.8 0.00013 34.2 5.8 28 368-395 27-56 (143)
164 cd05403 NT_KNTase_like Nucleot 77.9 5.4 0.00012 31.1 5.2 27 370-396 20-47 (93)
165 COG0258 Exo 5'-3' exonuclease 77.9 1.6 3.6E-05 43.2 2.6 25 299-325 202-227 (310)
166 KOG3524 Predicted guanine nucl 77.4 1.4 3.1E-05 47.8 2.1 86 17-109 209-294 (850)
167 PRK14672 uvrC excinuclease ABC 77.0 1.4 3.1E-05 48.2 2.0 58 296-354 609-668 (691)
168 PF11798 IMS_HHH: IMS family H 76.3 1.3 2.8E-05 28.9 0.9 18 255-272 12-29 (32)
169 cd00056 ENDO3c endonuclease II 76.3 5.1 0.00011 35.2 5.1 78 219-303 43-125 (158)
170 PF03118 RNA_pol_A_CTD: Bacter 76.3 3.8 8.3E-05 31.3 3.7 22 254-275 44-65 (66)
171 COG0177 Nth Predicted EndoIII- 76.2 3.6 7.8E-05 38.8 4.2 94 261-360 80-181 (211)
172 PRK13913 3-methyladenine DNA g 75.9 3.3 7.2E-05 39.2 3.9 22 292-313 118-139 (218)
173 PRK13766 Hef nuclease; Provisi 75.9 3.3 7E-05 46.1 4.5 49 256-313 717-765 (773)
174 PF14579 HHH_6: Helix-hairpin- 75.5 7.5 0.00016 31.2 5.4 50 256-316 29-78 (90)
175 PF03118 RNA_pol_A_CTD: Bacter 75.4 1.1 2.3E-05 34.4 0.4 44 301-344 17-62 (66)
176 PRK13910 DNA glycosylase MutY; 75.1 6.3 0.00014 38.9 5.8 68 232-306 48-117 (289)
177 TIGR03252 uncharacterized HhH- 75.0 9.5 0.00021 35.0 6.5 44 232-275 80-136 (177)
178 TIGR03491 RecB family nuclease 75.0 2.7 5.9E-05 44.0 3.4 30 297-326 209-238 (457)
179 PRK00254 ski2-like helicase; P 74.8 15 0.00032 40.8 9.3 52 255-314 646-697 (720)
180 TIGR00615 recR recombination p 74.6 2.2 4.7E-05 39.7 2.3 37 249-285 5-42 (195)
181 PF00416 Ribosomal_S13: Riboso 74.4 3.1 6.7E-05 34.8 3.0 26 293-318 13-39 (107)
182 PRK14668 uvrC excinuclease ABC 74.4 4.2 9.1E-05 44.0 4.7 49 295-344 525-575 (577)
183 PRK04301 radA DNA repair and r 74.2 7 0.00015 38.8 6.0 52 255-314 7-58 (317)
184 KOG2875 8-oxoguanine DNA glyco 73.4 5.1 0.00011 39.2 4.5 68 255-323 175-246 (323)
185 PRK13300 tRNA CCA-pyrophosphor 73.4 6.9 0.00015 41.0 5.9 42 354-395 27-70 (447)
186 COG1746 CCA1 tRNA nucleotidylt 73.3 7.6 0.00016 40.2 5.9 45 352-396 29-75 (443)
187 PRK00076 recR recombination pr 72.6 2.5 5.4E-05 39.4 2.2 37 249-285 5-42 (196)
188 PF02371 Transposase_20: Trans 72.3 2.4 5.1E-05 34.0 1.7 20 295-314 2-21 (87)
189 PRK00558 uvrC excinuclease ABC 72.2 2.7 6E-05 45.6 2.7 50 293-343 541-592 (598)
190 PRK13844 recombination protein 72.1 2.5 5.5E-05 39.5 2.1 38 249-286 9-47 (200)
191 KOG0323 TFIIF-interacting CTD 71.9 1.5 3.3E-05 47.6 0.7 89 17-109 440-531 (635)
192 PRK14973 DNA topoisomerase I; 71.9 5.5 0.00012 45.5 5.1 42 295-336 802-845 (936)
193 PRK14668 uvrC excinuclease ABC 70.8 3.8 8.2E-05 44.4 3.3 20 327-346 526-545 (577)
194 cd00141 NT_POLXc Nucleotidyltr 70.5 2.2 4.8E-05 42.4 1.4 52 292-343 42-102 (307)
195 KOG2093 Translesion DNA polyme 70.1 6.6 0.00014 43.9 5.0 86 14-108 43-130 (1016)
196 PRK14671 uvrC excinuclease ABC 70.0 6.1 0.00013 43.2 4.8 49 254-313 569-617 (621)
197 PRK12278 50S ribosomal protein 69.9 3.4 7.4E-05 39.2 2.5 30 295-324 158-187 (221)
198 COG2251 Predicted nuclease (Re 69.4 3.5 7.5E-05 42.9 2.5 27 299-325 229-255 (474)
199 TIGR01954 nusA_Cterm_rpt trans 69.3 5.7 0.00012 27.8 3.0 33 303-335 1-35 (50)
200 PF04919 DUF655: Protein of un 69.0 20 0.00042 33.0 7.0 42 248-289 109-151 (181)
201 PRK03980 flap endonuclease-1; 68.6 3.8 8.3E-05 40.5 2.6 25 299-324 193-217 (292)
202 TIGR00593 pola DNA polymerase 68.4 3.6 7.7E-05 46.8 2.7 24 299-324 189-213 (887)
203 PF14716 HHH_8: Helix-hairpin- 68.2 4.2 9.1E-05 31.0 2.2 24 290-313 41-65 (68)
204 PF14579 HHH_6: Helix-hairpin- 67.8 7 0.00015 31.4 3.6 31 296-326 28-62 (90)
205 COG0177 Nth Predicted EndoIII- 67.7 14 0.00031 34.8 6.1 32 242-273 96-128 (211)
206 PRK14669 uvrC excinuclease ABC 67.3 8.2 0.00018 42.2 5.0 50 254-314 552-601 (624)
207 COG1491 Predicted RNA-binding 66.9 4.7 0.0001 37.1 2.6 40 248-287 123-163 (202)
208 PRK10917 ATP-dependent DNA hel 66.5 4.8 0.0001 44.4 3.1 28 297-324 11-38 (681)
209 PTZ00217 flap endonuclease-1; 66.1 4.5 9.8E-05 41.7 2.7 26 298-324 238-263 (393)
210 TIGR01083 nth endonuclease III 65.6 15 0.00033 33.7 5.9 54 219-272 68-124 (191)
211 PRK13482 DNA integrity scannin 64.9 4.6 0.0001 40.9 2.4 54 288-343 280-336 (352)
212 KOG1921 Endonuclease III [Repl 64.8 8.5 0.00018 37.1 4.0 36 283-319 148-183 (286)
213 PF02889 Sec63: Sec63 Brl doma 64.7 12 0.00026 36.6 5.3 29 296-324 149-177 (314)
214 KOG2093 Translesion DNA polyme 64.6 7.7 0.00017 43.4 4.2 52 256-317 551-604 (1016)
215 PRK02362 ski2-like helicase; P 64.6 47 0.001 36.9 10.5 52 254-315 652-704 (737)
216 PRK07758 hypothetical protein; 64.5 6.8 0.00015 32.2 2.9 23 254-276 67-89 (95)
217 smart00611 SEC63 Domain of unk 63.6 6.3 0.00014 38.6 3.1 29 297-325 153-181 (312)
218 TIGR03674 fen_arch flap struct 63.4 5.5 0.00012 40.2 2.7 27 298-325 239-265 (338)
219 COG0322 UvrC Nuclease subunit 63.3 12 0.00027 40.5 5.4 50 254-313 530-579 (581)
220 PRK12311 rpsB 30S ribosomal pr 63.2 5.3 0.00012 40.1 2.5 32 293-324 261-292 (326)
221 PRK05755 DNA polymerase I; Pro 62.8 5.2 0.00011 45.5 2.6 24 299-324 191-215 (880)
222 cd01703 PolY_Pol_iota DNA Poly 62.0 16 0.00035 37.4 5.8 58 255-318 173-243 (379)
223 COG4277 Predicted DNA-binding 61.5 6 0.00013 39.3 2.4 39 294-332 329-371 (404)
224 CHL00137 rps13 ribosomal prote 60.8 5.7 0.00012 34.2 1.9 25 293-317 15-40 (122)
225 COG0272 Lig NAD-dependent DNA 60.6 22 0.00048 39.0 6.7 73 17-94 593-665 (667)
226 PRK05179 rpsM 30S ribosomal pr 60.3 5.7 0.00012 34.2 1.8 24 294-317 16-40 (122)
227 smart00483 POLXc DNA polymeras 60.2 6.1 0.00013 39.8 2.3 52 291-342 44-105 (334)
228 KOG1921 Endonuclease III [Repl 60.1 14 0.00031 35.6 4.6 29 245-273 149-178 (286)
229 smart00478 ENDO3c endonuclease 59.6 23 0.0005 30.7 5.6 42 232-273 48-91 (149)
230 COG1669 Predicted nucleotidylt 59.1 7.5 0.00016 32.2 2.2 29 367-395 22-52 (97)
231 KOG1918 3-methyladenine DNA gl 58.5 7.7 0.00017 36.8 2.5 58 254-312 122-182 (254)
232 TIGR00588 ogg 8-oxoguanine DNA 58.4 15 0.00033 36.6 4.7 77 223-305 177-265 (310)
233 KOG4362 Transcriptional regula 58.3 11 0.00025 41.2 4.0 93 3-99 573-679 (684)
234 PRK13913 3-methyladenine DNA g 57.8 21 0.00045 33.9 5.3 91 218-316 78-178 (218)
235 COG1204 Superfamily II helicas 57.7 9.7 0.00021 42.7 3.6 91 259-350 634-733 (766)
236 COG1725 Predicted transcriptio 57.4 15 0.00033 31.8 3.9 87 262-361 12-102 (125)
237 PF14490 HHH_4: Helix-hairpin- 57.2 18 0.0004 29.2 4.3 55 261-322 19-74 (94)
238 TIGR03631 bact_S13 30S ribosom 56.7 6.9 0.00015 33.2 1.7 25 293-317 13-38 (113)
239 TIGR00194 uvrC excinuclease AB 56.1 9.2 0.0002 41.4 3.0 30 295-325 541-570 (574)
240 TIGR02236 recomb_radA DNA repa 55.8 20 0.00044 35.2 5.2 50 256-313 1-50 (310)
241 COG5067 DBF4 Protein kinase es 55.1 8.1 0.00018 39.5 2.1 46 16-63 120-165 (468)
242 PRK13766 Hef nuclease; Provisi 54.7 10 0.00022 42.2 3.2 47 296-343 716-764 (773)
243 PF06514 PsbU: Photosystem II 54.2 6.7 0.00015 32.1 1.2 51 293-343 21-72 (93)
244 PRK01216 DNA polymerase IV; Va 54.1 44 0.00096 33.8 7.4 52 256-317 180-233 (351)
245 COG1194 MutY A/G-specific DNA 53.7 28 0.0006 35.3 5.6 57 219-275 76-134 (342)
246 PRK12373 NADH dehydrogenase su 53.2 11 0.00023 39.0 2.7 34 291-324 319-352 (400)
247 TIGR00596 rad1 DNA repair prot 52.5 20 0.00043 40.5 4.9 32 293-325 755-786 (814)
248 COG0353 RecR Recombinational D 52.4 9.9 0.00022 35.4 2.1 36 249-284 6-42 (198)
249 TIGR01084 mutY A/G-specific ad 51.4 11 0.00025 36.8 2.5 24 293-316 103-126 (275)
250 PTZ00134 40S ribosomal protein 50.8 10 0.00022 34.0 1.9 25 293-317 28-53 (154)
251 TIGR00596 rad1 DNA repair prot 50.3 23 0.0005 40.0 5.0 47 256-313 759-806 (814)
252 PF02961 BAF: Barrier to autoi 50.1 13 0.00027 30.3 2.1 45 278-324 4-48 (89)
253 PRK03352 DNA polymerase IV; Va 49.8 30 0.00066 34.6 5.4 55 256-320 179-235 (346)
254 PRK02794 DNA polymerase IV; Pr 49.7 61 0.0013 33.4 7.8 52 256-318 211-264 (419)
255 COG1491 Predicted RNA-binding 49.3 35 0.00075 31.6 5.0 55 269-324 103-163 (202)
256 COG0099 RpsM Ribosomal protein 49.3 13 0.00029 31.9 2.2 23 295-317 17-40 (121)
257 TIGR01446 DnaD_dom DnaD and ph 48.8 15 0.00033 27.9 2.4 19 305-323 54-72 (73)
258 PRK04053 rps13p 30S ribosomal 48.4 13 0.00028 33.2 2.1 25 293-317 23-48 (149)
259 COG0322 UvrC Nuclease subunit 48.2 14 0.0003 40.1 2.7 45 296-342 531-577 (581)
260 PF04919 DUF655: Protein of un 48.0 15 0.00032 33.8 2.5 59 266-324 86-149 (181)
261 KOG3548 DNA damage checkpoint 47.4 39 0.00084 38.5 5.9 69 32-103 1082-1160(1176)
262 TIGR03629 arch_S13P archaeal r 47.0 13 0.00029 32.9 2.0 24 294-317 20-44 (144)
263 cd00128 XPG Xeroderma pigmento 46.9 12 0.00025 37.2 1.9 23 298-321 226-248 (316)
264 PTZ00035 Rad51 protein; Provis 46.3 25 0.00053 35.5 4.1 50 293-343 22-73 (337)
265 PRK01229 N-glycosylase/DNA lya 46.2 29 0.00063 32.7 4.2 19 253-271 117-136 (208)
266 COG1200 RecG RecG-like helicas 45.8 17 0.00036 39.9 2.9 28 296-323 11-38 (677)
267 PRK10308 3-methyl-adenine DNA 45.5 37 0.0008 33.4 5.1 44 228-271 173-224 (283)
268 PRK03858 DNA polymerase IV; Va 44.8 40 0.00086 34.4 5.4 52 256-317 175-228 (396)
269 PLN03187 meiotic recombination 44.7 24 0.00053 35.7 3.8 52 291-343 28-81 (344)
270 PRK05007 PII uridylyl-transfer 44.5 42 0.0009 38.4 6.0 30 367-396 79-109 (884)
271 PF04994 TfoX_C: TfoX C-termin 43.9 19 0.00042 28.6 2.3 30 254-287 3-32 (81)
272 PRK13910 DNA glycosylase MutY; 43.5 16 0.00036 36.0 2.3 23 293-315 70-92 (289)
273 PHA00439 exonuclease 43.5 17 0.00037 35.9 2.3 26 299-325 192-219 (286)
274 PRK10880 adenine DNA glycosyla 43.1 17 0.00038 36.9 2.4 25 292-316 106-130 (350)
275 TIGR02238 recomb_DMC1 meiotic 42.5 24 0.00052 35.2 3.3 43 301-343 7-51 (313)
276 COG2231 Uncharacterized protei 41.7 42 0.00091 31.6 4.5 20 293-312 113-132 (215)
277 COG1031 Uncharacterized Fe-S o 39.7 24 0.00051 37.2 2.7 32 293-324 514-546 (560)
278 cd00424 PolY Y-family of DNA p 39.4 78 0.0017 31.6 6.4 53 256-318 175-229 (343)
279 PRK01759 glnD PII uridylyl-tra 39.1 60 0.0013 37.0 6.1 47 350-396 34-85 (854)
280 KOG2841 Structure-specific end 39.0 53 0.0011 31.6 4.7 51 292-343 192-244 (254)
281 COG5275 BRCT domain type II [G 37.6 65 0.0014 30.6 5.1 50 17-67 155-204 (276)
282 PRK03348 DNA polymerase IV; Pr 37.2 68 0.0015 33.6 5.8 53 256-318 182-236 (454)
283 PRK04374 PII uridylyl-transfer 36.2 67 0.0015 36.7 5.9 42 354-395 55-100 (869)
284 TIGR00207 fliG flagellar motor 36.2 2.6E+02 0.0057 28.1 9.6 87 236-323 144-245 (338)
285 cd01701 PolY_Rev1 DNA polymera 36.0 66 0.0014 33.1 5.4 53 256-318 224-280 (404)
286 COG2844 GlnD UTP:GlnB (protein 34.8 37 0.00081 38.1 3.5 29 368-396 66-95 (867)
287 PTZ00418 Poly(A) polymerase; P 34.5 75 0.0016 34.6 5.6 30 366-395 124-154 (593)
288 TIGR02239 recomb_RAD51 DNA rep 34.5 95 0.0021 30.9 6.1 25 301-325 7-31 (316)
289 PLN03186 DNA repair protein RA 34.2 91 0.002 31.5 6.0 42 293-335 27-70 (342)
290 KOG2875 8-oxoguanine DNA glyco 33.1 55 0.0012 32.3 3.9 48 224-271 176-235 (323)
291 cd01702 PolY_Pol_eta DNA Polym 32.9 63 0.0014 32.8 4.7 54 256-318 184-241 (359)
292 TIGR02922 conserved hypothetic 32.2 21 0.00045 27.1 0.7 22 370-391 34-59 (67)
293 TIGR00600 rad2 DNA excision re 31.9 35 0.00076 39.5 2.8 26 298-323 869-895 (1034)
294 PLN03187 meiotic recombination 30.6 1.5E+02 0.0033 30.0 6.8 82 253-343 31-119 (344)
295 PRK03059 PII uridylyl-transfer 29.5 1.1E+02 0.0023 35.0 6.2 30 367-396 60-90 (856)
296 cd04761 HTH_MerR-SF Helix-Turn 29.0 53 0.0012 22.4 2.4 23 295-317 4-26 (49)
297 cd05401 NT_GlnE_GlnD_like Nucl 28.7 1E+02 0.0023 27.2 4.9 29 368-396 55-84 (172)
298 PF15101 DUF4557: Domain of un 28.6 66 0.0014 30.2 3.5 85 19-113 1-92 (212)
299 PRK00275 glnD PII uridylyl-tra 28.5 1.1E+02 0.0024 35.1 6.0 28 368-395 78-106 (895)
300 PF07261 DnaB_2: Replication i 28.4 23 0.0005 26.9 0.5 21 305-325 54-74 (77)
301 KOG1715 Mitochondrial/chloropl 27.8 1.3E+02 0.0027 27.9 5.1 58 281-361 123-180 (187)
302 PF05559 DUF763: Protein of un 27.7 53 0.0012 32.9 2.9 20 293-312 267-286 (319)
303 COG1623 Predicted nucleic-acid 26.4 66 0.0014 32.0 3.3 76 232-318 272-347 (349)
304 COG1415 Uncharacterized conser 26.2 61 0.0013 32.9 3.1 21 293-313 276-296 (373)
305 PF14635 HHH_7: Helix-hairpin- 26.0 43 0.00094 28.0 1.7 21 293-313 48-68 (104)
306 PF12482 DUF3701: Phage integr 25.8 63 0.0014 26.7 2.6 39 304-342 22-66 (96)
307 PRK07945 hypothetical protein; 25.7 36 0.00077 34.3 1.4 30 296-325 50-83 (335)
308 PRK03381 PII uridylyl-transfer 24.8 1.5E+02 0.0034 33.3 6.3 27 369-395 58-85 (774)
309 PRK09202 nusA transcription el 24.6 90 0.002 33.1 4.2 53 292-344 353-407 (470)
310 PF00416 Ribosomal_S13: Riboso 24.5 66 0.0014 26.7 2.6 34 254-287 15-48 (107)
311 cd01104 HTH_MlrA-CarA Helix-Tu 24.5 1.6E+02 0.0036 21.5 4.6 25 294-318 3-28 (68)
312 PRK00024 hypothetical protein; 24.4 79 0.0017 29.9 3.4 41 266-313 43-84 (224)
313 KOG2379 Endonuclease MUS81 [Re 24.1 68 0.0015 34.0 3.1 43 232-274 35-77 (501)
314 cd04762 HTH_MerR-trunc Helix-T 22.9 87 0.0019 20.8 2.6 21 296-316 5-25 (49)
315 PF13838 Clathrin_H_link: Clat 22.5 1.6E+02 0.0035 22.6 4.1 44 258-301 1-50 (66)
316 TIGR00608 radc DNA repair prot 22.3 95 0.0021 29.4 3.5 42 263-311 30-76 (218)
317 PRK02406 DNA polymerase IV; Va 22.0 1.8E+02 0.0038 29.0 5.5 52 256-318 170-223 (343)
318 TIGR01764 excise DNA binding d 21.8 81 0.0018 21.1 2.2 20 296-315 6-25 (49)
319 PF09558 DUF2375: Protein of u 21.5 34 0.00075 26.3 0.3 22 369-390 35-60 (71)
320 PF03445 DUF294: Putative nucl 21.4 1.8E+02 0.0038 25.2 4.8 27 369-395 50-77 (138)
321 COG2003 RadC DNA repair protei 21.4 1E+02 0.0022 29.4 3.4 43 263-311 40-82 (224)
322 PRK03103 DNA polymerase IV; Re 20.6 1.7E+02 0.0038 29.9 5.3 51 256-317 183-235 (409)
323 PRK00024 hypothetical protein; 20.3 65 0.0014 30.5 1.9 27 252-278 64-90 (224)
324 PRK01810 DNA polymerase IV; Va 20.1 1.8E+02 0.004 29.6 5.4 52 256-318 181-234 (407)
No 1
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=100.00 E-value=4.1e-56 Score=423.86 Aligned_cols=196 Identities=37% Similarity=0.652 Sum_probs=188.7
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCC
Q 015933 199 DPSLLYNPPDLNKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGK 278 (398)
Q Consensus 199 ~~~~~~~~~~~N~~ia~~L~~la~~~e~~g~~~r~~aY~rAa~~l~~l~~~i~s~~~l~~lpgIG~~ia~kI~Eil~tG~ 278 (398)
++++| ..++|..|+++|+.||+.+++.|+.+|+++|++||++|+++|++|+|++|+++|||||++|+++|+|||+||+
T Consensus 3 qrkTp--lt~~N~~~~~aleiLa~~~ev~g~~~r~~~y~~Aasvlk~~p~~I~S~~ea~~lP~iG~kia~ki~EiletG~ 80 (353)
T KOG2534|consen 3 QRKTP--LTNNNQIFTEALEILAEAYEVEGEEDRARAYRRAASVLKSLPFPITSGEEAEKLPGIGPKIAEKIQEILETGV 80 (353)
T ss_pred CCCCc--cccccHHHHHHHHHHHHhhcccccHHHHHHHHHHHHHHHhCCCCcccHHHhcCCCCCCHHHHHHHHHHHHcCC
Confidence 33554 3689999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhh-ccCchhhhHhcHHhHHhhhcCCCHHHHHHHHHH
Q 015933 279 LSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN-EDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERL 357 (398)
Q Consensus 279 ~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~-~~~l~~~q~~Glk~~ed~~~~i~r~ea~~~~~~ 357 (398)
++++|++++|+.+++|++|++|||||++||++||++|+|||+|+++ ..++|.+|++|++||+||..+|+|+||.++.++
T Consensus 81 l~ele~v~~de~~~~lklFtnifGvG~ktA~~Wy~~GfrTled~Rk~~~kft~qqk~Gl~yy~Df~~~v~ReE~~~i~~~ 160 (353)
T KOG2534|consen 81 LRELEAVRNDERSQSLKLFTNIFGVGLKTAEKWYREGFRTLEDVRKKPDKFTRQQKAGLKYYEDFLKRVTREEATAIQQT 160 (353)
T ss_pred chhHHHHhcchhHHHHHHHHHHhccCHHHHHHHHHhhhhHHHHHHhCHHHHHHHHHHhHHHHHHHhhhccHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999994 458999999999999999999999999999999
Q ss_pred HHHHhhhcCCCeEEEEechhhcCCcccCCeeEEEecCCC
Q 015933 358 LQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPDR 396 (398)
Q Consensus 358 v~~~~~~~~p~~~v~~~Gs~RRgke~~gDvDiLit~~~~ 396 (398)
|++++..++|++.|+++|||||||++|||||||||||..
T Consensus 161 V~~av~~~~p~~~vt~~GsfRRGk~~ggDvD~LithP~~ 199 (353)
T KOG2534|consen 161 VQEAVWAFDPEAFVTVTGSFRRGKKMGGDVDFLITHPGS 199 (353)
T ss_pred HHHHHhhcCCCcEEEEeccccCCcccCCCeeEEEeCCCC
Confidence 999999999999999999999999999999999999975
No 2
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=100.00 E-value=4.3e-47 Score=377.66 Aligned_cols=190 Identities=40% Similarity=0.720 Sum_probs=176.9
Q ss_pred CCCHHHHHHHHHHHHHHHHcCCC-hhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHH
Q 015933 208 DLNKNITEIFGKLINIYRALGED-RRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFE 286 (398)
Q Consensus 208 ~~N~~ia~~L~~la~~~e~~g~~-~r~~aY~rAa~~l~~l~~~i~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~ 286 (398)
++|++|+++|++||++|++.|+| +|++||++||++|+++|++|++++++.+|||||++|++||.||++||++.++.+..
T Consensus 1 ~~N~~I~~~L~~la~l~el~gen~~k~~ay~~Aa~~i~~l~~~i~~~~~l~~lpgIG~~ia~kI~Eil~tG~~~~~~e~l 80 (334)
T smart00483 1 NLNRGIIDALEILAENYEVFGENKRKCSYFRKAASVLKSLPFPINSMKDLKGLPGIGDKIKKKIEEIIETGKSSKVLEIL 80 (334)
T ss_pred CCcHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhCCCCCCCHHHHhcCCCccHHHHHHHHHHHHhCcHHHHHHHh
Confidence 46999999999999999999998 58999999999999999999999999999999999999999999999999666666
Q ss_pred hhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhHhcHHhHHhhhcCCCHHHHHHHHHHHHHHhhh
Q 015933 287 KDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEE 364 (398)
Q Consensus 287 ~~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~~--~l~~~q~~Glk~~ed~~~~i~r~ea~~~~~~v~~~~~~ 364 (398)
.++.+..+..|++|||||||||++||+.||+||+||+.+. +|+..|.+|++||+++.++|||+||..+.++|......
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 6666778888889999999999999999999999999753 69999999999999999999999999999999888877
Q ss_pred cCCCeEEEEechhhcCCcccCCeeEEEecCCCC
Q 015933 365 VLPEVIILCGGSYRRGKASCGDLDVVIMHPDRK 397 (398)
Q Consensus 365 ~~p~~~v~~~Gs~RRgke~~gDvDiLit~~~~~ 397 (398)
+.|.+.|++||||||||++||||||||+|++..
T Consensus 161 ~~~~~~v~i~GSyRRgket~gDIDili~~~~~~ 193 (334)
T smart00483 161 ILPDAIVTLTGSFRRGKETGHDVDFLITSPHPA 193 (334)
T ss_pred hCCCcEEEEecccccCCCcCCCeeEEEecCCcc
Confidence 888889999999999999999999999999864
No 3
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=100.00 E-value=1.9e-45 Score=362.06 Aligned_cols=184 Identities=42% Similarity=0.706 Sum_probs=173.5
Q ss_pred HHHHHHHHHHHHHHHcCC-ChhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhch
Q 015933 212 NITEIFGKLINIYRALGE-DRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEK 290 (398)
Q Consensus 212 ~ia~~L~~la~~~e~~g~-~~r~~aY~rAa~~l~~l~~~i~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~ 290 (398)
+|+++|++||+++++.|+ .||++||++||++|+++|++|+++.++.+|||||++|+++|.||++||+++++|+++++ .
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 58999999999999999999999999999999999999999999999999999999998 5
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhc--cCchhhhHhcHHhHHhhhcCCCHHHHHHHHHHHHHHhhhcCCC
Q 015933 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPE 368 (398)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~--~~l~~~q~~Glk~~ed~~~~i~r~ea~~~~~~v~~~~~~~~p~ 368 (398)
+..+..|++||||||+||++||+.||+||+||+.+ .+++..|..|++||+++.++|||+||.++.+.|......+.|+
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 66777777999999999999997799999999987 4899999999999999999999999999988888887777888
Q ss_pred eEEEEechhhcCCcccCCeeEEEecCCC
Q 015933 369 VIILCGGSYRRGKASCGDLDVVIMHPDR 396 (398)
Q Consensus 369 ~~v~~~Gs~RRgke~~gDvDiLit~~~~ 396 (398)
+.|++|||||||+++||||||||+|++.
T Consensus 161 ~~v~i~GS~RRg~et~gDiDilv~~~~~ 188 (307)
T cd00141 161 LQVEIAGSYRRGKETVGDIDILVTHPDA 188 (307)
T ss_pred eEEEEcccccCCCCccCCEEEEEecCCc
Confidence 8999999999999999999999999873
No 4
>PRK08609 hypothetical protein; Provisional
Probab=100.00 E-value=8.9e-43 Score=368.33 Aligned_cols=188 Identities=22% Similarity=0.329 Sum_probs=169.1
Q ss_pred CCCHHHHHHHHHHHHHHHHcCCC-hhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHH
Q 015933 208 DLNKNITEIFGKLINIYRALGED-RRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFE 286 (398)
Q Consensus 208 ~~N~~ia~~L~~la~~~e~~g~~-~r~~aY~rAa~~l~~l~~~i~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~ 286 (398)
|+|++|+++|++||+++++.|+| ||++||++||++|+++|++|+++.++.+|||||++|++||+||++||++++||+|+
T Consensus 1 m~n~~ia~~l~~~A~~le~~g~n~fr~~aYr~Aa~~i~~l~~~i~~~~~l~~ipgIG~~ia~kI~Eil~tG~~~~le~l~ 80 (570)
T PRK08609 1 MNKKDVIKLLETIATYMELKGENPFKISAFRKAAQALELDERSLSEIDDFTKLKGIGKGTAEVIQEYRETGESSVLQELK 80 (570)
T ss_pred CChHHHHHHHHHHHHHHHhcCCCcHHHHHHHHHHHHHHhCchhhhhhhhhccCCCcCHHHHHHHHHHHHhCChHHHHHHH
Confidence 56999999999999999999987 89999999999999999999999999999999999999999999999999999999
Q ss_pred hhchhHHHHHhhhccCcCHHHHHHHHHc-CCCCHHHhhh---ccCchhhhHhc----------HHhHHhhhcCCCHHHHH
Q 015933 287 KDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKN---EDSLTHSQRLG----------LKYFDDIKTRIPRHEVE 352 (398)
Q Consensus 287 ~~~~~~~l~lf~~I~GvGpktA~~l~~~-GirtledL~~---~~~l~~~q~~G----------lk~~ed~~~~i~r~ea~ 352 (398)
++.|..+++++ +|||||||||++||++ ||+||+||+. +++++.+++|| +++|+++.+|||+.||.
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 98766666555 9999999999999975 9999999995 46788777775 55556667899999999
Q ss_pred HHHHHHHHHhhhcCCCeEEEEechhhcCCcccCCeeEEEecCCC
Q 015933 353 QMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPDR 396 (398)
Q Consensus 353 ~~~~~v~~~~~~~~p~~~v~~~Gs~RRgke~~gDvDiLit~~~~ 396 (398)
.+.+.|....+.+.+...|++||||||||+||||||||||++++
T Consensus 160 ~~a~~i~~~l~~~~~~~~v~~~GS~RR~~et~gDiDili~~~~~ 203 (570)
T PRK08609 160 PIAQEIEEYLATIDEIIRFSRAGSLRRARETVKDLDFIIATDEP 203 (570)
T ss_pred HHHHHHHHHHHhCCCccEEEeccchhccccccCCeeEEEecCCH
Confidence 99888887776665666899999999999999999999999874
No 5
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=100.00 E-value=4.1e-34 Score=275.43 Aligned_cols=189 Identities=28% Similarity=0.456 Sum_probs=168.0
Q ss_pred CCCCHHHHHHHHHHHHHHHHcCCC-hhHHHHHHHHHHHhcCCccccchhh---hcCCCCCCHHHHHHHHHHHHhCCchhh
Q 015933 207 PDLNKNITEIFGKLINIYRALGED-RRSFSYYKAIPVIEKLPFKIESADQ---VKGLPGIGKSMQDHIQEIVTTGKLSKL 282 (398)
Q Consensus 207 ~~~N~~ia~~L~~la~~~e~~g~~-~r~~aY~rAa~~l~~l~~~i~s~~~---l~~lpgIG~~ia~kI~Eil~tG~~~~l 282 (398)
.|.|+.|+.+|+++|++|++.|+| ||++|||+||++|+.+.+++.++.+ +..|||||++||.+|.+|++||+++.+
T Consensus 2 ~~~n~~ia~~le~iA~~me~~Gen~fk~~aYr~Aa~sle~~~e~~~ei~e~~~~t~l~gIGk~ia~~I~e~l~tG~~~~l 81 (326)
T COG1796 2 AMNNHDIARLLERIADYMELEGENPFKIRAYRKAAQSLENLTEDLEEIEERGRLTELPGIGKGIAEKISEYLDTGEVKKL 81 (326)
T ss_pred CcchHHHHHHHHHHHHHHHhcCCCccchHHHHHHHHhhhhcccchHHHHhhcccCCCCCccHHHHHHHHHHHHcCccHHH
Confidence 367999999999999999999999 8999999999999999999999865 469999999999999999999999999
Q ss_pred HHHHhhchhHHHHHhhhccCcCHHHHHHHHHc-CCCCHHHhhhc---cCchhhhHhcHHhHHhhh----------cCCCH
Q 015933 283 EHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNE---DSLTHSQRLGLKYFDDIK----------TRIPR 348 (398)
Q Consensus 283 e~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~-GirtledL~~~---~~l~~~q~~Glk~~ed~~----------~~i~r 348 (398)
+.|+...|.+...|+ .|+|+|||+...||++ ||.++++|+++ +++..+.|||-++.++|. +|+|.
T Consensus 82 e~lk~~~P~gl~~Ll-~v~GlGpkKi~~Ly~elgi~~~e~l~~a~~~~~~~~l~GfG~kse~~il~~i~~~~~~~~R~~l 160 (326)
T COG1796 82 EALKKEVPEGLEPLL-KVPGLGPKKIVSLYKELGIKDLEELQEALENGKIRGLRGFGKKSEAKILENIEFAEESPERIPL 160 (326)
T ss_pred HHHHHhCCcchHHHh-hCCCCCcHHHHHHHHHHCcccHHHHHHHHHhCCccccCCccchhHHHHHHHHHHHhhhhhhcch
Confidence 999999999988877 9999999999999998 99999999964 678899999999999987 47788
Q ss_pred HHHHHHHHHHHHHhhhcCCCeEEEEechhhcCCcccCCeeEEEecCCC
Q 015933 349 HEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPDR 396 (398)
Q Consensus 349 ~ea~~~~~~v~~~~~~~~p~~~v~~~Gs~RRgke~~gDvDiLit~~~~ 396 (398)
.++..+..-+......+.+-.++.++||+||+|+|++|||+||+..++
T Consensus 161 ~~~l~ia~ei~~yl~~~~~~~~~~~aGs~RR~retv~DiD~~~s~~~~ 208 (326)
T COG1796 161 SFTLPIAQEIEGYLEELTPIIQASIAGSLRRGRETVGDIDILISTSHP 208 (326)
T ss_pred HHHHHHHHHHHHHHHhccchheeeeccchhhccccccceeeEeccCCc
Confidence 888777555554444445545799999999999999999999987654
No 6
>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=99.72 E-value=1.1e-17 Score=129.30 Aligned_cols=66 Identities=36% Similarity=0.688 Sum_probs=62.4
Q ss_pred CHHHHHHHHHHHHHHHHc-CCChhHHHHHHHHHHHhcCCccccchhh-hcCCCCCCHHHHHHHHHHHH
Q 015933 210 NKNITEIFGKLINIYRAL-GEDRRSFSYYKAIPVIEKLPFKIESADQ-VKGLPGIGKSMQDHIQEIVT 275 (398)
Q Consensus 210 N~~ia~~L~~la~~~e~~-g~~~r~~aY~rAa~~l~~l~~~i~s~~~-l~~lpgIG~~ia~kI~Eil~ 275 (398)
|++|+++|++|++++++. |+.||++||++||++|++||++|+++++ +.+|||||++|+.+|.|||+
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 7
>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=99.69 E-value=2.3e-17 Score=120.48 Aligned_cols=51 Identities=49% Similarity=1.009 Sum_probs=42.2
Q ss_pred HHHhhhccCcCHHHHHHHHHcCCCCHHHhhh-ccCchhhhHhcHHhHHhhhc
Q 015933 294 ISLFGEVWGIGPATAQKLYEKGHRTLDDLKN-EDSLTHSQRLGLKYFDDIKT 344 (398)
Q Consensus 294 l~lf~~I~GvGpktA~~l~~~GirtledL~~-~~~l~~~q~~Glk~~ed~~~ 344 (398)
|++|++||||||+||++||++|+|||+||++ ...|+..|++|++||+||++
T Consensus 1 l~~f~~I~GVG~~tA~~w~~~G~rtl~Dl~~~~~~Lt~~Q~iGl~yyeD~~q 52 (52)
T PF10391_consen 1 LKLFTGIWGVGPKTARKWYAKGIRTLEDLRKSKSKLTWQQQIGLKYYEDFQQ 52 (52)
T ss_dssp HHHHHTSTT--HHHHHHHHHTT--SHHHHHHGGCGS-HHHHHHHHTHHHHH-
T ss_pred CcchhhcccccHHHHHHHHHhCCCCHHHHhhhhccCCHHHHHHHHHHHHhcC
Confidence 6799999999999999999999999999986 45899999999999999974
No 8
>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=99.64 E-value=2e-16 Score=134.00 Aligned_cols=53 Identities=47% Similarity=0.846 Sum_probs=48.3
Q ss_pred CCCHHHHHHHHHHHHHHhhhcCCCeEEEEechhhcCCcccCCeeEEEecCCCC
Q 015933 345 RIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPDRK 397 (398)
Q Consensus 345 ~i~r~ea~~~~~~v~~~~~~~~p~~~v~~~Gs~RRgke~~gDvDiLit~~~~~ 397 (398)
||||+||++++++|.+.+..++|++.+++||||||||++|||||||||||+..
T Consensus 1 rIPR~Ev~~i~~~V~~~~~~i~p~~~v~i~GSyRRGK~~~gDiDiLIt~~~~~ 53 (112)
T PF14792_consen 1 RIPRDEVEEIEEIVKEALEKIDPGLEVEICGSYRRGKETSGDIDILITHPDPS 53 (112)
T ss_dssp -EEHHHHHHHHHHHHHHHHCCSTT-EEEEEHHHHTT-SEESSEEEEEEETTCS
T ss_pred CCCHHHHHHHHHHHHHHHHhcCCCcEEEEccccccCCCcCCCeEEEEeCCCcC
Confidence 69999999999999999999999999999999999999999999999999864
No 9
>PRK07945 hypothetical protein; Provisional
Probab=99.57 E-value=4.7e-15 Score=148.16 Aligned_cols=102 Identities=19% Similarity=0.274 Sum_probs=88.8
Q ss_pred HHHHHHHHHHHHHHcCCC-hhHHHHHHHHHHHhcCCcc-ccchh---hhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHh
Q 015933 213 ITEIFGKLINIYRALGED-RRSFSYYKAIPVIEKLPFK-IESAD---QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEK 287 (398)
Q Consensus 213 ia~~L~~la~~~e~~g~~-~r~~aY~rAa~~l~~l~~~-i~s~~---~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~ 287 (398)
-+++|+++|++||++|+| ||++|||+||.+|+.++.+ +..+. +|.+|||||+++|+||.||++||+++.|++|+.
T Consensus 3 ~~~~l~~~a~lle~~~~n~frv~ayr~aa~~~~~~~~~~~~~~~~~g~l~~~~giG~~~a~~i~e~~~tg~~~~l~~l~~ 82 (335)
T PRK07945 3 PVAALRRIAFLLERARADTYRVRAFRRAADVVEALDAAERARRARAGSLTSLPGIGPKTAKVIAQALAGRVPDYLAELRA 82 (335)
T ss_pred HHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHhcChhHHHHHHhcCCcccCCCcCHHHHHHHHHHHhcCCHHHHHHHHH
Confidence 468999999999999999 7999999999999999999 88774 799999999999999999999999999999998
Q ss_pred hchhHHHHHhhhccCcCHHHHHHHHHc---------CCCCHHHhhh
Q 015933 288 DEKVRTISLFGEVWGIGPATAQKLYEK---------GHRTLDDLKN 324 (398)
Q Consensus 288 ~~~~~~l~lf~~I~GvGpktA~~l~~~---------GirtledL~~ 324 (398)
+..+. | |+..+.++.-. |-.|++|..+
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 66433 7 99999998742 4455666653
No 10
>PF00533 BRCT: BRCA1 C Terminus (BRCT) domain; InterPro: IPR001357 The BRCT domain (after the C_terminal domain of a breast cancer susceptibility protein) is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage [], for example as found in the breast cancer DNA-repair protein BRCA1. The domain is an approximately 100 amino acid tandem repeat, which appears to act as a phospho-protein binding domain []. A chitin biosynthesis protein from yeast also seems to belong to this group. ; GO: 0005622 intracellular; PDB: 3L46_A 3AL3_A 3AL2_A 1WF6_A 3II6_X 2NTE_B 3FA2_A 2R1Z_A 2COK_A 2K7F_A ....
Probab=99.13 E-value=1.1e-10 Score=90.74 Aligned_cols=75 Identities=23% Similarity=0.348 Sum_probs=59.3
Q ss_pred CCCCCCcEEEEccCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCC-hHHHHHHHHHhhhccCccccccchHHHH
Q 015933 16 NGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDL-EALLQQVSKQHLARFKGSVIRYQWLEDS 94 (398)
Q Consensus 16 ~~~F~g~~iy~~~~~~g~~r~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~~-~~~l~~l~~~~~~~~~~~lV~~~Wl~es 94 (398)
..+|+||.+|| .+.....++.+.++++++||++.+.++..+||||+.+. ....+ .......+.++|+.+||.+|
T Consensus 3 ~~~F~g~~f~i--~~~~~~~~~~l~~~i~~~GG~v~~~~~~~~thvI~~~~~~~~~k---~~~~~~~~i~iV~~~Wi~~c 77 (78)
T PF00533_consen 3 PKIFEGCTFCI--SGFDSDEREELEQLIKKHGGTVSNSFSKKTTHVIVGNPNKRTKK---YKAAIANGIPIVSPDWIEDC 77 (78)
T ss_dssp TTTTTTEEEEE--SSTSSSHHHHHHHHHHHTTEEEESSSSTTSSEEEESSSHCCCHH---HHHHHHTTSEEEETHHHHHH
T ss_pred CCCCCCEEEEE--ccCCCCCHHHHHHHHHHcCCEEEeecccCcEEEEeCCCCCccHH---HHHHHHCCCeEecHHHHHHh
Confidence 46999999999 45666677789999999999999999999999999876 21111 11222347899999999999
Q ss_pred H
Q 015933 95 L 95 (398)
Q Consensus 95 ~ 95 (398)
+
T Consensus 78 i 78 (78)
T PF00533_consen 78 I 78 (78)
T ss_dssp H
T ss_pred C
Confidence 7
No 11
>smart00292 BRCT breast cancer carboxy-terminal domain.
Probab=99.11 E-value=1.9e-10 Score=88.26 Aligned_cols=79 Identities=19% Similarity=0.279 Sum_probs=61.8
Q ss_pred CCCCCcEEEEccCCCCchHHHHHHHHHHhcCCEEEeecCC-CccEEEEcCChHHHHHHHHHhhhccCccccccchHHHHH
Q 015933 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSK-KVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSL 95 (398)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~r~~~l~~li~~~Gg~V~~~ls~-~VTHVV~~~~~~~l~~l~~~~~~~~~~~lV~~~Wl~es~ 95 (398)
.+|+|+++||.+ .+....++.+.+++..+||++...++. .+||||+.+.+..... .......+.++|+.+||.+|+
T Consensus 1 ~~f~g~~~~~~g-~~~~~~~~~l~~~i~~~Gg~~~~~~~~~~~thvi~~~~~~~~~~--~~~~~~~~~~iV~~~Wi~~~~ 77 (80)
T smart00292 1 KLFKGKVFVITG-KFDKNERDELKELIEALGGKVTSSLSSKTTTHVIVGSPEGGKLE--LLLAIALGIPIVTEDWLLDCL 77 (80)
T ss_pred CccCCeEEEEeC-CCCCccHHHHHHHHHHcCCEEecccCccceeEEEEcCCCCccHH--HHHHHHcCCCCccHHHHHHHH
Confidence 379999999986 356667789999999999999999988 9999999775532111 111223468999999999999
Q ss_pred hcC
Q 015933 96 RLG 98 (398)
Q Consensus 96 k~g 98 (398)
+++
T Consensus 78 ~~~ 80 (80)
T smart00292 78 KAG 80 (80)
T ss_pred HCc
Confidence 875
No 12
>cd00027 BRCT Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks.
Probab=98.80 E-value=1e-08 Score=76.77 Aligned_cols=72 Identities=18% Similarity=0.289 Sum_probs=54.7
Q ss_pred CcEEEEccCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccchHHHHHh
Q 015933 21 GMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSLR 96 (398)
Q Consensus 21 g~~iy~~~~~~g~~r~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~~~~~l~~l~~~~~~~~~~~lV~~~Wl~es~k 96 (398)
||.+||.+.-.+ ..+..|.+++..+||++.+.++..+||||+.+...... .......+.++|+.+||.+|++
T Consensus 1 ~~~~~i~g~~~~-~~~~~l~~~i~~~Gg~v~~~~~~~~thvI~~~~~~~~~---~~~~~~~~~~iV~~~Wi~~~~~ 72 (72)
T cd00027 1 GLTFVITGDLPS-EERDELKELIEKLGGKVTSSVSKKTTHVIVGSDAGPKK---LLKAIKLGIPIVTPEWLLDCLK 72 (72)
T ss_pred CCEEEEEecCCC-cCHHHHHHHHHHcCCEEeccccCCceEEEECCCCCchH---HHHHHHcCCeEecHHHHHHHhC
Confidence 678888864323 45568999999999999999999999999987653221 1122234789999999999985
No 13
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=98.20 E-value=1.2e-06 Score=65.76 Aligned_cols=52 Identities=37% Similarity=0.538 Sum_probs=44.9
Q ss_pred HHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhc--cCchhhhHhcHHhHHhhhc
Q 015933 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDIKT 344 (398)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~GirtledL~~~--~~l~~~q~~Glk~~ed~~~ 344 (398)
+...|++|+||||++|++||+.||.|++||... ..|..+.++|.+..+.|..
T Consensus 3 ~~~~L~~I~Gig~~~a~~L~~~G~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~ 56 (60)
T PF14520_consen 3 VFDDLLSIPGIGPKRAEKLYEAGIKTLEDLANADPEELAEIPGIGEKTAEKIIE 56 (60)
T ss_dssp HHHHHHTSTTCHHHHHHHHHHTTCSSHHHHHTSHHHHHHTSTTSSHHHHHHHHH
T ss_pred HHHhhccCCCCCHHHHHHHHhcCCCcHHHHHcCCHHHHhcCCCCCHHHHHHHHH
Confidence 455677999999999999999999999999865 3688899999998888753
No 14
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=98.17 E-value=7.4e-06 Score=88.80 Aligned_cols=130 Identities=20% Similarity=0.272 Sum_probs=94.9
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc-CCCCHHHhhhcc--Cchh
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED--SLTH 330 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~-GirtledL~~~~--~l~~ 330 (398)
++|..|||+|++++++|.+.++.++...+++ .+..| .|+|||+++|+.|++. | |+++|..+. .|..
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 5788999999999999999999988776654 44455 9999999999999986 5 999998653 5888
Q ss_pred hhHhcHHhHHhhhcCCCHHHHHH-HHHHHHH-H-----------h--hhcCCCeEEEEechhhcC---------------
Q 015933 331 SQRLGLKYFDDIKTRIPRHEVEQ-MERLLQK-A-----------G--EEVLPEVIILCGGSYRRG--------------- 380 (398)
Q Consensus 331 ~q~~Glk~~ed~~~~i~r~ea~~-~~~~v~~-~-----------~--~~~~p~~~v~~~Gs~RRg--------------- 380 (398)
+.+||.+..+.|..-+.-.+..+ +..+... + . ...+.|-.+++||++...
T Consensus 535 i~GIG~~~A~~I~~ff~~~~~~~~i~~L~~~gv~~~~~~~~~~~~~~~~~l~gk~~v~TG~l~~~~R~~~~~~i~~~G~~ 614 (652)
T TIGR00575 535 VEGVGPKVAESIVNFFHDPNNRQLIKKLEELGVEMESLPEKVNAELAGSPLAGKTFVLTGTLSQMSRDEAKELLENLGGK 614 (652)
T ss_pred CCCcCHHHHHHHHHHHhhhhHHHHHHHHHHcCCCcccccccccccccCCCccCcEEEEeccCCCCCHHHHHHHHHHcCCE
Confidence 88999999888876554433332 2322221 0 0 011335578999998643
Q ss_pred --CcccCCeeEEEecC
Q 015933 381 --KASCGDLDVVIMHP 394 (398)
Q Consensus 381 --ke~~gDvDiLit~~ 394 (398)
...+...|+||.-.
T Consensus 615 v~~sVs~kt~~lv~G~ 630 (652)
T TIGR00575 615 VASSVSKKTDYVIAGE 630 (652)
T ss_pred EeCCcCCCccEEEECC
Confidence 45567889999754
No 15
>PF12738 PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2WT8_C 3EF1_A 3EF0_A.
Probab=98.00 E-value=5.4e-06 Score=62.51 Aligned_cols=63 Identities=17% Similarity=0.343 Sum_probs=42.7
Q ss_pred cEEEEccCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccch
Q 015933 22 MRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQW 90 (398)
Q Consensus 22 ~~iy~~~~~~g~~r~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~~~~~l~~l~~~~~~~~~~~lV~~~W 90 (398)
|+|.|. |+....++.+.++++.+||++.+.++..+||+|+.+..- .+...+..++.+||+++|
T Consensus 1 ~~i~~s--g~~~~~~~~l~~~i~~~Gg~~~~~lt~~~THLI~~~~~~----~K~~~A~~~gi~vV~~~W 63 (63)
T PF12738_consen 1 VVICFS--GFSGKERSQLRKLIEALGGKYSKDLTKKTTHLICSSPEG----KKYRKAKEWGIPVVSPDW 63 (63)
T ss_dssp -EEEEE--EB-TTTCCHHHHHHHCTT-EEESSSSTT-SEEEEES--H----HHHHHHHHCTSEEEEHHH
T ss_pred CEEEEC--CCCHHHHHHHHHHHHHCCCEEeccccCCceEEEEeCCCc----HHHHHHHHCCCcEECCCC
Confidence 355554 343333567999999999999999999999999965432 223334445789999999
No 16
>KOG3226 consensus DNA repair protein [Replication, recombination and repair]
Probab=97.95 E-value=3.6e-06 Score=83.25 Aligned_cols=90 Identities=16% Similarity=0.293 Sum_probs=72.7
Q ss_pred CCCCCCcEEEEccCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccchHHHHH
Q 015933 16 NGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSL 95 (398)
Q Consensus 16 ~~~F~g~~iy~~~~~~g~~r~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~~~~~l~~l~~~~~~~~~~~lV~~~Wl~es~ 95 (398)
+.+++|+++.|. |+...-+.-|+..+..+||+.-.+++.+.||.|+.=.+ .-++.+....+..||+-+||++|.
T Consensus 315 ~klL~GVV~VlS--GfqNP~Rs~LRskAl~LGAkY~pDW~~gsThLICAF~N----TPKy~QV~g~Gg~IV~keWI~~Cy 388 (508)
T KOG3226|consen 315 SKLLEGVVFVLS--GFQNPERSTLRSKALTLGAKYQPDWNAGSTHLICAFPN----TPKYRQVEGNGGTIVSKEWITECY 388 (508)
T ss_pred HHhhhceEEEEe--cccCchHHHHHHHHHhhcccccCCcCCCceeEEEecCC----CcchhhcccCCceEeeHHHHHHHH
Confidence 478999998886 67766777899999999999999999999999985211 112223333467999999999999
Q ss_pred hcCCCCCccccccccC
Q 015933 96 RLGEKVSEDLYRIKLD 111 (398)
Q Consensus 96 k~g~lv~ee~y~l~~~ 111 (398)
..+++||..+|.+.-+
T Consensus 389 ~~kk~lp~rrYlm~~~ 404 (508)
T KOG3226|consen 389 AQKKLLPIRRYLMHAG 404 (508)
T ss_pred HHHhhccHHHHHhcCC
Confidence 9999999999998643
No 17
>PLN03123 poly [ADP-ribose] polymerase; Provisional
Probab=97.90 E-value=2.4e-05 Score=87.84 Aligned_cols=93 Identities=16% Similarity=0.356 Sum_probs=72.9
Q ss_pred CCCCCCCCcEEEEccCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccchHHH
Q 015933 14 DSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLED 93 (398)
Q Consensus 14 ~~~~~F~g~~iy~~~~~~g~~r~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~~~~~l~~l~~~~~~~~~~~lV~~~Wl~e 93 (398)
+....|.++.|.+.+. ++.. ...|++.|..+||+|...++..+||+|+.. +...+..++..+...+.+||+.+||+|
T Consensus 389 ~~~~~l~~~~i~i~G~-~~~~-~~~~k~~Ie~~GG~~s~~v~~~~t~l~tt~-e~~k~~~kv~qAk~~~ipIVsedwL~d 465 (981)
T PLN03123 389 SESEFLGDLKVSIVGA-SKEK-VTEWKAKIEEAGGVFHATVKKDTNCLVVCG-ELDDEDAEMRKARRMKIPIVREDYLVD 465 (981)
T ss_pred ccCCCcCCeEEEEecC-CCCc-HHHHHHHHHhcCCEEeeeccCCceEEEccH-HhhhcchHHHHHHhcCCCcccHHHHHH
Confidence 3447899999999986 3433 368999999999999999999999999875 222222333344455789999999999
Q ss_pred HHhcCCCCCccccccc
Q 015933 94 SLRLGEKVSEDLYRIK 109 (398)
Q Consensus 94 s~k~g~lv~ee~y~l~ 109 (398)
|.+.+.++|...|.+.
T Consensus 466 s~~~~~~~p~~~y~~~ 481 (981)
T PLN03123 466 CFKKKKKLPFDKYKLE 481 (981)
T ss_pred HHhccccCcchhhhhc
Confidence 9999999999888664
No 18
>PLN03122 Poly [ADP-ribose] polymerase; Provisional
Probab=97.65 E-value=8.2e-05 Score=81.99 Aligned_cols=95 Identities=20% Similarity=0.277 Sum_probs=72.8
Q ss_pred CCCCCCCCCcEEEEccCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHH-HHHHHhhhccCccccccchH
Q 015933 13 LDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQ-QVSKQHLARFKGSVIRYQWL 91 (398)
Q Consensus 13 ~~~~~~F~g~~iy~~~~~~g~~r~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~~~~~l~-~l~~~~~~~~~~~lV~~~Wl 91 (398)
..+...|.|++|.|.++ +.. .+..+++++..+||+|.+.+ .+.||+|+...+.... .-+...+...+++||+.+||
T Consensus 184 ~~~~kpL~G~~fviTGt-l~~-sr~elK~~Ie~~GGkvsssV-s~~T~lIvt~~ev~k~gsSKlkkAk~lgIpIVsEd~L 260 (815)
T PLN03122 184 GAPGKPFSGMMISLSGR-LSR-THQYWKKDIEKHGGKVANSV-EGVTCLVVSPAERERGGSSKIAEAMERGIPVVREAWL 260 (815)
T ss_pred cccCCCcCCcEEEEeCC-CCC-CHHHHHHHHHHcCCEEcccc-ccceEEEEcCccccccCccHHHHHHHcCCcCccHHHH
Confidence 34556799999999985 333 45689999999999999999 6788999866442110 11223344568899999999
Q ss_pred HHHHhcCCCCCcccccccc
Q 015933 92 EDSLRLGEKVSEDLYRIKL 110 (398)
Q Consensus 92 ~es~k~g~lv~ee~y~l~~ 110 (398)
.+|++.++++++..|.+..
T Consensus 261 ~d~i~~~k~~~~~~y~l~~ 279 (815)
T PLN03122 261 IDSIEKQEAQPLEAYDVVS 279 (815)
T ss_pred HHHHhcCCcccchhhhhcc
Confidence 9999999999999998853
No 19
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=97.52 E-value=0.00012 Score=54.88 Aligned_cols=52 Identities=33% Similarity=0.571 Sum_probs=40.9
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (398)
.+|.+|||||+.++.++.+. | +..++.+..- ..+.+.+|+|+|+++|++|.+
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-IKTLEDLANA----DPEELAEIPGIGEKTAEKIIE 56 (60)
T ss_dssp HHHHTSTTCHHHHHHHHHHT---T-CSSHHHHHTS----HHHHHHTSTTSSHHHHHHHHH
T ss_pred HhhccCCCCCHHHHHHHHhc---C-CCcHHHHHcC----CHHHHhcCCCCCHHHHHHHHH
Confidence 56889999999999887654 7 5667777653 234566999999999999986
No 20
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=97.30 E-value=0.00033 Score=62.38 Aligned_cols=51 Identities=33% Similarity=0.573 Sum_probs=40.8
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHH-hCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc
Q 015933 252 SADQVKGLPGIGKSMQDHIQEIVT-TGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (398)
Q Consensus 252 s~~~l~~lpgIG~~ia~kI~Eil~-tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~ 314 (398)
+.+||..|||||++.|++|.++.+ .|.+.-+| .|.+|.|||+++.++|-..
T Consensus 95 s~eeL~~lpgIG~~kA~aIi~yRe~~G~f~sv~------------dL~~v~GiG~~~~ekl~~~ 146 (149)
T COG1555 95 SAEELQALPGIGPKKAQAIIDYREENGPFKSVD------------DLAKVKGIGPKTLEKLKDY 146 (149)
T ss_pred CHHHHHHCCCCCHHHHHHHHHHHHHcCCCCcHH------------HHHhccCCCHHHHHHHHhh
Confidence 347899999999999999999874 44555444 4558999999999998653
No 21
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=97.29 E-value=0.00037 Score=53.06 Aligned_cols=48 Identities=29% Similarity=0.627 Sum_probs=32.3
Q ss_pred cCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 015933 257 KGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (398)
Q Consensus 257 ~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (398)
.+|||||+..++.+.+ ++.-++.+.+- ..+.|++|+||||++|+.+|+
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 5789999999998876 44456666542 456778999999999998886
No 22
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=97.27 E-value=0.0014 Score=71.38 Aligned_cols=131 Identities=17% Similarity=0.287 Sum_probs=89.3
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--Cchhh
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHS 331 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~~--~l~~~ 331 (398)
++|..|||+|++.+++|.+-++.-+-..| ...+--+ .|+|||+++|+.|.+. +.|+++|.++. .|..+
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 57999999999999999876652221222 2344455 9999999999999874 48899998653 58888
Q ss_pred hHhcHHhHHhhhcCCCHHHHHH-HHHHHHHHhh-------hcCCCeEEEEechhhc---C--------------CcccCC
Q 015933 332 QRLGLKYFDDIKTRIPRHEVEQ-MERLLQKAGE-------EVLPEVIILCGGSYRR---G--------------KASCGD 386 (398)
Q Consensus 332 q~~Glk~~ed~~~~i~r~ea~~-~~~~v~~~~~-------~~~p~~~v~~~Gs~RR---g--------------ke~~gD 386 (398)
.++|.+..+.|..-+.-.+..+ +..+...-.. ..+.|-.+++||.+-. . ...+..
T Consensus 549 ~GIG~~~A~sI~~ff~~~~~~~~i~~L~~~gv~~~~~~~~~~~~g~~~v~TG~l~~~~R~e~~~~i~~~G~~v~~sVs~k 628 (665)
T PRK07956 549 EGVGEVVAQSIVEFFAVEENRELIDELLEAGVNMEYKGEEVDLAGKTVVLTGTLEQLSRDEAKEKLEALGAKVSGSVSKK 628 (665)
T ss_pred CCcCHHHHHHHHHHHhhhhHHHHHHHHHHcCCCccccccCCCccccEEEEeCCCCCCCHHHHHHHHHHcCCEEeCcccCC
Confidence 8999999888877665444333 2333321010 0144668999999843 2 346678
Q ss_pred eeEEEecC
Q 015933 387 LDVVIMHP 394 (398)
Q Consensus 387 vDiLit~~ 394 (398)
.|+||+.+
T Consensus 629 t~~lv~G~ 636 (665)
T PRK07956 629 TDLVVAGE 636 (665)
T ss_pred CCEEEECC
Confidence 89999754
No 23
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=97.24 E-value=0.00036 Score=57.08 Aligned_cols=36 Identities=36% Similarity=0.373 Sum_probs=32.3
Q ss_pred hhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhc
Q 015933 290 KVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (398)
Q Consensus 290 ~~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~ 325 (398)
....+..|+.|||||+++|+.|+..||+|++||+..
T Consensus 7 ~~~~~~~L~~iP~IG~a~a~DL~~LGi~s~~~L~g~ 42 (93)
T PF11731_consen 7 KRAGLSDLTDIPNIGKATAEDLRLLGIRSPADLKGR 42 (93)
T ss_pred HHHHHHHHhcCCCccHHHHHHHHHcCCCCHHHHhCC
Confidence 345788899999999999999999999999999954
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=97.20 E-value=0.00063 Score=58.40 Aligned_cols=50 Identities=30% Similarity=0.515 Sum_probs=40.5
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHHh-CCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 015933 252 SADQVKGLPGIGKSMQDHIQEIVTT-GKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (398)
Q Consensus 252 s~~~l~~lpgIG~~ia~kI~Eil~t-G~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (398)
+.++|..|||||++.|.+|-++.+. |.+. .++.|.+|+|||++++.+|.+
T Consensus 66 ~~~eL~~lpGIG~~~A~~Ii~~R~~~g~f~------------s~eeL~~V~GIg~k~~~~i~~ 116 (120)
T TIGR01259 66 SLEELQALPGIGPAKAKAIIEYREENGAFK------------SVDDLTKVSGIGEKSLEKLKD 116 (120)
T ss_pred CHHHHhcCCCCCHHHHHHHHHHHHhcCCcC------------CHHHHHcCCCCCHHHHHHHHh
Confidence 3478999999999999999999864 5443 344456899999999999875
No 25
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=97.13 E-value=0.00069 Score=51.69 Aligned_cols=48 Identities=44% Similarity=0.685 Sum_probs=35.0
Q ss_pred chhhhcCCCCCCHHHHHHHHHHH-HhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHH
Q 015933 252 SADQVKGLPGIGKSMQDHIQEIV-TTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKL 311 (398)
Q Consensus 252 s~~~l~~lpgIG~~ia~kI~Eil-~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l 311 (398)
+.++|..+||||...|+.|.++- +.|.+..+++|. .|+|+|+++..+|
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 45889999999999999999998 567777776654 8999999999886
No 26
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=97.12 E-value=0.0022 Score=70.16 Aligned_cols=131 Identities=16% Similarity=0.299 Sum_probs=89.7
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--Cchhh
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHS 331 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~~--~l~~~ 331 (398)
+++..|+|+|++.+++|.+=++.-+-..|+ ..+--| .|+|||+++|++|.+ .+.|+++|..+. .|..+
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 568999999999999987766532222222 245556 999999999999986 668899998653 57888
Q ss_pred hHhcHHhHHhhhcCCCHHHHHH-HHHHHHHHh---------hhcCCCeEEEEechhhc-----------------CCccc
Q 015933 332 QRLGLKYFDDIKTRIPRHEVEQ-MERLLQKAG---------EEVLPEVIILCGGSYRR-----------------GKASC 384 (398)
Q Consensus 332 q~~Glk~~ed~~~~i~r~ea~~-~~~~v~~~~---------~~~~p~~~v~~~Gs~RR-----------------gke~~ 384 (398)
.++|.+..+.|.+-+.-.+..+ +..++..-. ...+.|-.+++||.+-. ....+
T Consensus 566 ~GIG~k~A~sI~~ff~~~~n~~~i~~L~~~Gv~~~~~~~~~~~~l~g~~~v~TG~l~~~~R~~~~~~i~~~Gg~v~~sVs 645 (689)
T PRK14351 566 DDVGPTVAEEIREFFDSERNRAVIDDLLDHGVDPQPAESEGGDALDGLTFVFTGSLSGYTRSEAQELVEAHGGNATGSVS 645 (689)
T ss_pred CCcCHHHHHHHHHHHhhhHHHHHHHHHHhcccccccccccCCCCCCCcEEEEccCCCCCCHHHHHHHHHHcCCEEcCCcC
Confidence 8899999988877665444333 333333101 01244568899999843 23456
Q ss_pred CCeeEEEecC
Q 015933 385 GDLDVVIMHP 394 (398)
Q Consensus 385 gDvDiLit~~ 394 (398)
...|+||.-.
T Consensus 646 ~kt~~Lv~G~ 655 (689)
T PRK14351 646 GNTDYLVVGE 655 (689)
T ss_pred CCccEEEEcC
Confidence 7779998754
No 27
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]
Probab=96.93 E-value=0.0014 Score=70.90 Aligned_cols=91 Identities=14% Similarity=0.197 Sum_probs=70.4
Q ss_pred CCCCCCCCCCcEEEEccCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEc--CCh-HHHHHHHHHhhhccCcccccc
Q 015933 12 ALDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAM--DLE-ALLQQVSKQHLARFKGSVIRY 88 (398)
Q Consensus 12 ~~~~~~~F~g~~iy~~~~~~g~~r~~~l~~li~~~Gg~V~~~ls~~VTHVV~~--~~~-~~l~~l~~~~~~~~~~~lV~~ 88 (398)
.++...+|.|+-+++.....+..+...|++.+..+||.++..+.++.||.|+. ..+ .... ..+.+ ..-||++
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 VAKISNIFDGLEFCVLSGTSETHTKAKLEEIIVENGGKIVQNVGPSDTLCIATAGKETTRVKA----QAIKR-SCDVLKP 701 (881)
T ss_pred ccchhhhhcCeeEEEecCCcccccHHHHHHHHHHcCCEEEEcCCCCCcceEEeccccchHHHH----HHHhc-cCceeeH
Confidence 45556899999999987666666677899999999999999999999999962 222 2211 12222 6689999
Q ss_pred chHHHHHhcCCCCCccccc
Q 015933 89 QWLEDSLRLGEKVSEDLYR 107 (398)
Q Consensus 89 ~Wl~es~k~g~lv~ee~y~ 107 (398)
+||.+|.+..++++..++-
T Consensus 702 ~Wlldcc~~~~l~p~~P~~ 720 (881)
T KOG0966|consen 702 AWLLDCCKKQRLLPWLPRD 720 (881)
T ss_pred HHHHHHHhhhhccccccHH
Confidence 9999999999999976543
No 28
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=96.84 E-value=0.0075 Score=51.89 Aligned_cols=66 Identities=24% Similarity=0.356 Sum_probs=44.1
Q ss_pred CCCCHHHHHHH--------HHHHHhCCchhhH-HHHhhc--------hhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHh
Q 015933 260 PGIGKSMQDHI--------QEIVTTGKLSKLE-HFEKDE--------KVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL 322 (398)
Q Consensus 260 pgIG~~ia~kI--------~Eil~tG~~~~le-~l~~~~--------~~~~l~lf~~I~GvGpktA~~l~~~GirtledL 322 (398)
||||+..+.+. .++++.|.-..-. +|.... ....+-.|+.|+|||+..|.-|...||+|+++|
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 67777777764 4556555433322 122111 122344555999999999999999999999999
Q ss_pred hhc
Q 015933 323 KNE 325 (398)
Q Consensus 323 ~~~ 325 (398)
.+.
T Consensus 81 A~~ 83 (122)
T PF14229_consen 81 AQR 83 (122)
T ss_pred HhC
Confidence 854
No 29
>KOG2481 consensus Protein required for normal rRNA processing [RNA processing and modification]
Probab=96.80 E-value=0.00092 Score=69.11 Aligned_cols=86 Identities=19% Similarity=0.271 Sum_probs=63.4
Q ss_pred CCCCCCCCCCcEEEEccCCCCchHHHHHHHHHHhcCCEEEee-c---------CCCccEEEEcCChHHHHHHHHHhhhcc
Q 015933 12 ALDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEK-L---------SKKVTHVLAMDLEALLQQVSKQHLARF 81 (398)
Q Consensus 12 ~~~~~~~F~g~~iy~~~~~~g~~r~~~l~~li~~~Gg~V~~~-l---------s~~VTHVV~~~~~~~l~~l~~~~~~~~ 81 (398)
.+....+|+||++|+.. ... ++.|.-+|++.||.|.-+ + +..|||=|++-..... . . .
T Consensus 321 ~s~~kslF~glkFfl~r-eVP---resL~fiI~s~GG~V~wd~~~~g~~~~~~d~~ITH~IvDrP~~~~---~--v---~ 388 (570)
T KOG2481|consen 321 QSSHKSLFSGLKFFLNR-EVP---RESLEFIIRSFGGKVSWDPLGIGATYDESDERITHQIVDRPGQQT---S--V---I 388 (570)
T ss_pred hhhHHHHhhcceeeeec-cCc---hHHHHHHHHHcCCceecCccCCCCcccccccceeeeeecccCccc---e--e---e
Confidence 34445899999999974 222 467889999999999855 1 2358998886433210 0 0 1
Q ss_pred CccccccchHHHHHhcCCCCCccccccc
Q 015933 82 KGSVIRYQWLEDSLRLGEKVSEDLYRIK 109 (398)
Q Consensus 82 ~~~lV~~~Wl~es~k~g~lv~ee~y~l~ 109 (398)
+-..|-++||-||+.+|.+++.+.|.+.
T Consensus 389 gR~YvQPQWvfDsvNar~llpt~~Y~~G 416 (570)
T KOG2481|consen 389 GRTYVQPQWVFDSVNARLLLPTEKYFPG 416 (570)
T ss_pred eeeeecchhhhhhccchhhccHhhhCCC
Confidence 3357999999999999999999999886
No 30
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=96.73 E-value=0.0023 Score=55.30 Aligned_cols=47 Identities=13% Similarity=0.210 Sum_probs=35.4
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 015933 252 SADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (398)
Q Consensus 252 s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (398)
+..++..|||||+..|++|. ..|-+. .++.+.+|+|||+++.+.|-+
T Consensus 59 ~~~el~~lpGigP~~A~~IV---~nGpf~------------sveDL~~V~GIgekqk~~l~k 105 (132)
T PRK02515 59 SVRAFRQFPGMYPTLAGKIV---KNAPYD------------SVEDVLNLPGLSERQKELLEA 105 (132)
T ss_pred CHHHHHHCCCCCHHHHHHHH---HCCCCC------------CHHHHHcCCCCCHHHHHHHHH
Confidence 34679999999999999988 355444 444455899999988777765
No 31
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=96.69 E-value=0.0013 Score=61.05 Aligned_cols=50 Identities=16% Similarity=0.230 Sum_probs=41.3
Q ss_pred HHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhc------cCchhhhHhcHHhHHhhh
Q 015933 292 RTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE------DSLTHSQRLGLKYFDDIK 343 (398)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~------~~l~~~q~~Glk~~ed~~ 343 (398)
..+.+|.+|+|||||+|..+ .+.-|+++|.++ +.|+.++|||.|..+.|.
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 556778888732 469999999999999874
No 32
>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=96.67 E-value=0.0029 Score=58.66 Aligned_cols=53 Identities=17% Similarity=0.285 Sum_probs=38.4
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHH
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLY 312 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~ 312 (398)
..|.++||||+++|-.| |.+-..+++.+.-.+. -...|++|||||+|||+++.
T Consensus 72 ~~L~~V~GIGpK~Al~i---L~~~~~~el~~aI~~~---d~~~L~~ipGiGkKtAerIi 124 (191)
T TIGR00084 72 KELIKVNGVGPKLALAI---LSNMSPEEFVYAIETE---EVKALVKIPGVGKKTAERLL 124 (191)
T ss_pred HHHhCCCCCCHHHHHHH---HhcCCHHHHHHHHHhC---CHHHHHhCCCCCHHHHHHHH
Confidence 46899999999999888 5554554544332211 23456699999999999997
No 33
>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=96.67 E-value=0.0039 Score=47.88 Aligned_cols=50 Identities=22% Similarity=0.341 Sum_probs=39.4
Q ss_pred hhhhcC-CCCCCHHHHHHHHHHHH-hCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc
Q 015933 253 ADQVKG-LPGIGKSMQDHIQEIVT-TGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (398)
Q Consensus 253 ~~~l~~-lpgIG~~ia~kI~Eil~-tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~ 314 (398)
.++|.. +||||...+..|-++.. .|.+. .+..|.+|+|||.++++++++.
T Consensus 15 ~~~L~~~ipgig~~~a~~Il~~R~~~g~~~------------s~~dL~~v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 15 AEELQRAMNGVGLKKAEAIVSYREEYGPFK------------TVEDLKQVPGIGNSLVEKNLAV 66 (69)
T ss_pred HHHHHhHCCCCCHHHHHHHHHHHHHcCCcC------------CHHHHHcCCCCCHHHHHHHHhh
Confidence 467888 99999999999988875 45443 4455568999999999999863
No 34
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=96.65 E-value=0.00081 Score=63.56 Aligned_cols=52 Identities=25% Similarity=0.500 Sum_probs=44.3
Q ss_pred HhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhHhcHHhHHhhhcCCC
Q 015933 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIKTRIP 347 (398)
Q Consensus 296 lf~~I~GvGpktA~~l~~~GirtledL~~~~--~l~~~q~~Glk~~ed~~~~i~ 347 (398)
.|..|+|||++++++||+.||.|+++|..+. .|..+.++|.+..+.|...+.
T Consensus 4 ~L~~IpGIG~krakkLl~~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l~ 57 (232)
T PRK12766 4 ELEDISGVGPSKAEALREAGFESVEDVRAADQSELAEVDGIGNALAARIKADVG 57 (232)
T ss_pred ccccCCCcCHHHHHHHHHcCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHHhc
Confidence 4669999999999999999999999999764 588888899888887765543
No 35
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=96.57 E-value=0.0022 Score=68.91 Aligned_cols=79 Identities=28% Similarity=0.393 Sum_probs=57.8
Q ss_pred CCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEc-CChH-HHHHHHHHhhhccCccccccchHHHHHhcCCCCCccccc
Q 015933 30 GVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAM-DLEA-LLQQVSKQHLARFKGSVIRYQWLEDSLRLGEKVSEDLYR 107 (398)
Q Consensus 30 ~~g~~r~~~l~~li~~~Gg~V~~~ls~~VTHVV~~-~~~~-~l~~l~~~~~~~~~~~lV~~~Wl~es~k~g~lv~ee~y~ 107 (398)
+....-.+.+..+++. ++...+...|||||+. +.+. -.++++.......+.+|+++.|+.+||+++++++|+.|.
T Consensus 485 ~l~p~ek~~v~~~a~~---t~~k~~~~~~thvi~~~~~~g~c~rTlk~~~gil~gkwi~~~~w~~~s~k~~~~~~eepfE 561 (684)
T KOG4362|consen 485 GLTPSEKQLVEKFAVD---TISKFWIEPVTHVIASTDLEGACLRTLKVLMGILRGKWILSYDWVLASLKLRKWVSEEPFE 561 (684)
T ss_pred cCCcchHHHHHHHHHH---HHhhccCCCceeeeeecccccchhhhHHHHHHhhcCceeeeHHHHHHHHHhcCCCCCCCee
Confidence 3344556677777776 6666778999999984 3332 235555433223367999999999999999999999999
Q ss_pred cccC
Q 015933 108 IKLD 111 (398)
Q Consensus 108 l~~~ 111 (398)
|.++
T Consensus 562 l~~d 565 (684)
T KOG4362|consen 562 LQID 565 (684)
T ss_pred Eeec
Confidence 9764
No 36
>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=96.48 E-value=0.0024 Score=41.38 Aligned_cols=23 Identities=30% Similarity=0.546 Sum_probs=19.5
Q ss_pred cchhhhcCCCCCCHHHHHHHHHH
Q 015933 251 ESADQVKGLPGIGKSMQDHIQEI 273 (398)
Q Consensus 251 ~s~~~l~~lpgIG~~ia~kI~Ei 273 (398)
.++++|..|||||+.+|..|.+|
T Consensus 8 as~eeL~~lpGIG~~tA~~I~~~ 30 (30)
T PF00633_consen 8 ASIEELMKLPGIGPKTANAILSF 30 (30)
T ss_dssp SSHHHHHTSTT-SHHHHHHHHHH
T ss_pred CCHHHHHhCCCcCHHHHHHHHhC
Confidence 46789999999999999999875
No 37
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.36 E-value=0.0039 Score=57.94 Aligned_cols=52 Identities=17% Similarity=0.290 Sum_probs=37.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchh-hHHHHhhchhHHHHHhhhccCcCHHHHHHHH
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSK-LEHFEKDEKVRTISLFGEVWGIGPATAQKLY 312 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~-le~l~~~~~~~~l~lf~~I~GvGpktA~~l~ 312 (398)
..|.+++|||+++|-.|-.-+. .++ .+.+.+ +=.+.|++|||||+|||+++.
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 4589999999999998876443 233 233322 224567799999999999944
No 38
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=96.29 E-value=0.0021 Score=70.07 Aligned_cols=48 Identities=23% Similarity=0.322 Sum_probs=41.8
Q ss_pred hccCcCHHHHHHHHHc-CCCCHHHhhh--ccCchhhhHhcHHhHHhhhcCC
Q 015933 299 EVWGIGPATAQKLYEK-GHRTLDDLKN--EDSLTHSQRLGLKYFDDIKTRI 346 (398)
Q Consensus 299 ~I~GvGpktA~~l~~~-GirtledL~~--~~~l~~~q~~Glk~~ed~~~~i 346 (398)
+|+|+||+++++||+. +|++++||.. .+.|..+.+||.|..+.|.+.|
T Consensus 449 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~ll~~I 499 (665)
T PRK07956 449 DIDGLGEKIIEQLFEKGLIHDPADLFKLTAEDLLGLEGFGEKSAQNLLDAI 499 (665)
T ss_pred CCCCcCHHHHHHHHHcCCCCCHHHHHhcCHHHHhcCcCcchHHHHHHHHHH
Confidence 7999999999999998 7899999984 3468888999999999987544
No 39
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=96.24 E-value=0.0086 Score=55.49 Aligned_cols=54 Identities=19% Similarity=0.317 Sum_probs=37.9
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhh-HHHHhhchhHHHHHhhhccCcCHHHHHHHHHc
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKL-EHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~l-e~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~ 314 (398)
..|..+||||+++|.+|.+.+. . ..+ +.+.+. -.+.+++|||||+|+|++++..
T Consensus 73 ~~L~~i~GIGpk~A~~il~~fg--~-~~l~~~i~~~----d~~~L~~v~Gig~k~A~~I~~~ 127 (192)
T PRK00116 73 RLLISVSGVGPKLALAILSGLS--P-EELVQAIANG----DVKALTKVPGIGKKTAERIVLE 127 (192)
T ss_pred HHHhcCCCCCHHHHHHHHHhCC--H-HHHHHHHHhC----CHHHHHhCCCCCHHHHHHHHHH
Confidence 4688899999999999854332 2 333 233332 2334569999999999999963
No 40
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.20 E-value=0.0063 Score=56.56 Aligned_cols=54 Identities=24% Similarity=0.378 Sum_probs=38.0
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (398)
..|.++.|||+++|=.|- .+-..+++ ..-...+=.+.|++|||||+|||+++.=
T Consensus 72 ~~LisVsGIGPK~ALaIL---s~~~~~el---~~aI~~~D~~~L~~vpGIGkKtAeRIIl 125 (196)
T PRK13901 72 EELIGVDGIGPRAALRVL---SGIKYNEF---RDAIDREDIELISKVKGIGNKMAGKIFL 125 (196)
T ss_pred HHHhCcCCcCHHHHHHHH---cCCCHHHH---HHHHHhCCHHHHhhCCCCCHHHHHHHHH
Confidence 458899999999997654 33333333 2222333466788999999999999984
No 41
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.17 E-value=0.0064 Score=55.97 Aligned_cols=54 Identities=19% Similarity=0.304 Sum_probs=38.3
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (398)
..|.++.|||+++|=.|- .+-...++-.. ...+=.+.|++|||||+|||+++.=
T Consensus 73 ~~Li~VsGIGpK~Al~IL---s~~~~~el~~a---I~~~D~~~L~~vpGIGkKtAeRIil 126 (183)
T PRK14601 73 EMLLKVNGIGANTAMAVC---SSLDVNSFYKA---LSLGDESVLKKVPGIGPKSAKRIIA 126 (183)
T ss_pred HHHhccCCccHHHHHHHH---cCCCHHHHHHH---HHhCCHHHHhhCCCCCHHHHHHHHH
Confidence 458899999999987654 44444444332 2233466788999999999999983
No 42
>PRK14973 DNA topoisomerase I; Provisional
Probab=96.03 E-value=0.0089 Score=67.57 Aligned_cols=91 Identities=19% Similarity=0.154 Sum_probs=61.5
Q ss_pred hhhcCCCCCCHHHHHHHHHHHH-h-CCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--Cch
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVT-T-GKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLT 329 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~-t-G~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~~--~l~ 329 (398)
++|..+|||...+......... . +.-..-...+.....+.-+ |.+|.|||++|+.+|+..|+.|.|||.++. +|+
T Consensus 835 ~~La~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e-l~~vkg~ge~t~~~l~~ag~~~~e~l~~~d~~~la 913 (936)
T PRK14973 835 AYLALKTGISPETICRHAKLVCEKLGRPVPEKISKAAFERGRAE-LLSVPGLGETTLEKLYLAGVYDGDLLVSADPKKLA 913 (936)
T ss_pred HHHhcCCCCChhhHHHHHHHHHHHhcCCCchhhhhhhhcccchh-hhhccCCCHHHHHHHHHcCCCCHHHhccCCHHHHh
Confidence 4678888888777666654443 2 1111111111111112223 459999999999999999999999999764 688
Q ss_pred hhhHhcHHhHHhhhcC
Q 015933 330 HSQRLGLKYFDDIKTR 345 (398)
Q Consensus 330 ~~q~~Glk~~ed~~~~ 345 (398)
..-+++.+....|+..
T Consensus 914 ~~~~i~~k~~~~~~~~ 929 (936)
T PRK14973 914 KVTGIDEKKLRNLQAY 929 (936)
T ss_pred hhcCCCHHHHHHHHHH
Confidence 8888999888887754
No 43
>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=96.03 E-value=0.006 Score=39.48 Aligned_cols=22 Identities=32% Similarity=0.477 Sum_probs=17.4
Q ss_pred HHHHHhhhccCcCHHHHHHHHH
Q 015933 292 RTISLFGEVWGIGPATAQKLYE 313 (398)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~ 313 (398)
..++.|++||||||+||..+..
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 3577788999999999998764
No 44
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=96.02 E-value=0.0068 Score=54.01 Aligned_cols=53 Identities=25% Similarity=0.429 Sum_probs=42.8
Q ss_pred chhHHHHHhhhccCcCHHHHHHHHH---c--CCCCHHHhhhccCchhhhHhcHHhHHhhhcCCC
Q 015933 289 EKVRTISLFGEVWGIGPATAQKLYE---K--GHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIP 347 (398)
Q Consensus 289 ~~~~~l~lf~~I~GvGpktA~~l~~---~--GirtledL~~~~~l~~~q~~Glk~~ed~~~~i~ 347 (398)
......+.|..+||||+++|+++.+ + .|+|+|||.+ .+++|-+.++.+..+|.
T Consensus 91 iNtAs~eeL~~lpgIG~~kA~aIi~yRe~~G~f~sv~dL~~------v~GiG~~~~ekl~~~i~ 148 (149)
T COG1555 91 INTASAEELQALPGIGPKKAQAIIDYREENGPFKSVDDLAK------VKGIGPKTLEKLKDYIT 148 (149)
T ss_pred ccccCHHHHHHCCCCCHHHHHHHHHHHHHcCCCCcHHHHHh------ccCCCHHHHHHHHhhcc
Confidence 3445566668999999999999985 2 4899999986 57899999999887654
No 45
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=95.98 E-value=0.0036 Score=68.21 Aligned_cols=49 Identities=24% Similarity=0.392 Sum_probs=42.2
Q ss_pred hhccCcCHHHHHHHHHc-CCCCHHHhhh--ccCchhhhHhcHHhHHhhhcCC
Q 015933 298 GEVWGIGPATAQKLYEK-GHRTLDDLKN--EDSLTHSQRLGLKYFDDIKTRI 346 (398)
Q Consensus 298 ~~I~GvGpktA~~l~~~-GirtledL~~--~~~l~~~q~~Glk~~ed~~~~i 346 (398)
++|+|+|++++.+||+. +|++++||.. .+.|..+.+||.+..+.|.+.|
T Consensus 435 l~I~GLG~k~i~~L~~~g~I~~~~Dl~~L~~~~L~~L~GfG~Ksa~nIl~~I 486 (652)
T TIGR00575 435 MDIEGLGDKVIEQLFEKKLVRSVADLYALKKEDLLELEGFGEKSAQNLLNAI 486 (652)
T ss_pred cCCCCcCHHHHHHHHHcCCcCCHHHHHhcCHHHHhhccCccHHHHHHHHHHH
Confidence 37999999999999998 7899999983 3568889999999999987544
No 46
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.97 E-value=0.0091 Score=55.21 Aligned_cols=54 Identities=13% Similarity=0.122 Sum_probs=37.8
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (398)
..|.++.|||+++|=.|-. +-..+++ ..-...+=...|++|||||+|||+++.-
T Consensus 73 ~~Li~V~GIGpK~AL~iLs---~~~~~el---~~aI~~~D~~~L~~vpGIGkKtAerIil 126 (188)
T PRK14606 73 LSLTKVSRLGPKTALKIIS---NEDAETL---VTMIASQDVEGLSKLPGISKKTAERIVM 126 (188)
T ss_pred HHHhccCCccHHHHHHHHc---CCCHHHH---HHHHHhCCHHHHhhCCCCCHHHHHHHHH
Confidence 3588999999999976653 3233333 3223334467888999999999999983
No 47
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.97 E-value=0.0084 Score=56.11 Aligned_cols=54 Identities=19% Similarity=0.212 Sum_probs=38.5
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (398)
..|.+++|||+++|=.|- .+-...++ ..-...+-...|++|||||+|||+++.-
T Consensus 74 ~~Li~V~GIGpK~Al~iL---s~~~~~~l---~~aI~~~D~~~L~~ipGIGkKtAerIil 127 (203)
T PRK14602 74 IVLISISKVGAKTALAIL---SQFRPDDL---RRLVAEEDVAALTRVSGIGKKTAQHIFL 127 (203)
T ss_pred HHHhCCCCcCHHHHHHHH---hhCCHHHH---HHHHHhCCHHHHhcCCCcCHHHHHHHHH
Confidence 458899999999997754 44344433 2222334467888999999999999983
No 48
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.90 E-value=0.0099 Score=55.29 Aligned_cols=54 Identities=20% Similarity=0.354 Sum_probs=38.8
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (398)
..|.++.|||+++|=.| |.+....++-.. ...+=...|++|||||+|||+++.-
T Consensus 73 ~~Li~V~GIGpK~Al~i---Ls~~~~~el~~a---I~~~D~~~L~kvpGIGkKtAerIil 126 (195)
T PRK14604 73 ELLIGVSGVGPKAALNL---LSSGTPDELQLA---IAGGDVARLARVPGIGKKTAERIVL 126 (195)
T ss_pred HHHhCcCCcCHHHHHHH---HcCCCHHHHHHH---HHhCCHHHHhhCCCCCHHHHHHHHH
Confidence 45889999999998765 444454544332 2233466788999999999999984
No 49
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.90 E-value=0.01 Score=55.32 Aligned_cols=54 Identities=15% Similarity=0.222 Sum_probs=38.4
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (398)
..|.++.|||+++|=.| |.+.+..++-.. ...+=...|++|||||+|||+++.-
T Consensus 72 ~~L~~V~GIGpK~AL~i---Ls~~~~~~l~~a---I~~~D~~~L~kvpGIGkKtAerIil 125 (197)
T PRK14603 72 ELLLGVSGVGPKLALAL---LSALPPALLARA---LLEGDARLLTSASGVGKKLAERIAL 125 (197)
T ss_pred HHHhCcCCcCHHHHHHH---HcCCCHHHHHHH---HHhCCHHHHhhCCCCCHHHHHHHHH
Confidence 45889999999998765 444444444332 2233466788999999999999883
No 50
>PRK02362 ski2-like helicase; Provisional
Probab=95.88 E-value=0.0089 Score=66.12 Aligned_cols=60 Identities=23% Similarity=0.385 Sum_probs=47.9
Q ss_pred HHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhc--cCchhhhHhcHHhHHhhhcCC
Q 015933 284 HFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDIKTRI 346 (398)
Q Consensus 284 ~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~--~~l~~~q~~Glk~~ed~~~~i 346 (398)
.+....+...+.|+ +|||||+++|++||+.||+|++||... ..|..+ ||.+..+.|.+.+
T Consensus 642 ~l~~gv~~~~~~L~-~ip~i~~~~a~~l~~~gi~s~~dl~~~~~~~l~~~--~g~~~~~~i~~~~ 703 (737)
T PRK02362 642 RVEYGVREELLDLV-GLRGVGRVRARRLYNAGIESRADLRAADKSVVLAI--LGEKIAENILEQA 703 (737)
T ss_pred HHHhCCCHHHHHHh-CCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHHH--HCHHHHHHHHHHh
Confidence 44555666677777 999999999999999999999999943 356666 8988888877543
No 51
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=95.86 E-value=0.024 Score=61.94 Aligned_cols=132 Identities=14% Similarity=0.171 Sum_probs=87.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhc--------
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE-------- 325 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~-------- 325 (398)
++|.+|+|+|++.+++|.+=++.-+-..| ...|--| .|++||.++|+.|-+..+.|++.|.+.
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 57889999999999888765443222222 2355566 899999999999987788999988752
Q ss_pred cCchhhhHhcHHhHHhhhcCCCHHHHHH-HHHHHHHHh------------hhcCCCeEEEEechh---hcC---------
Q 015933 326 DSLTHSQRLGLKYFDDIKTRIPRHEVEQ-MERLLQKAG------------EEVLPEVIILCGGSY---RRG--------- 380 (398)
Q Consensus 326 ~~l~~~q~~Glk~~ed~~~~i~r~ea~~-~~~~v~~~~------------~~~~p~~~v~~~Gs~---RRg--------- 380 (398)
..|..+.+||.+..+.|.+-+.-.+... ++.+...-. ...+.|-.+++||++ .|.
T Consensus 541 e~l~~i~giG~~~a~si~~ff~~~~~~~~i~~l~~~gv~~~~~~~~~~~~~~~l~gktfV~TG~l~~~~R~e~~~lie~~ 620 (669)
T PRK14350 541 SKLLKIKGIGEKIALNIIEAFNDKIILDKFNFFKNLGFKMEEDSINIDVENSFLFGKKFCITGSFNGYSRSVLIDKLTKK 620 (669)
T ss_pred HHHhhCCCccHHHHHHHHHHHcCHHHHHHHHHHHHcCCCcccccccccccCCccCCcEEEEecccCCCCHHHHHHHHHHc
Confidence 1477888899888888876554333222 333322100 112446689999987 332
Q ss_pred -----CcccCCeeEEEecC
Q 015933 381 -----KASCGDLDVVIMHP 394 (398)
Q Consensus 381 -----ke~~gDvDiLit~~ 394 (398)
-..+...|+||+-.
T Consensus 621 Ggkv~ssVSkktd~LV~G~ 639 (669)
T PRK14350 621 GAIFNTCVTKYLDFLLVGE 639 (669)
T ss_pred CCEEeccccCCCcEEEECC
Confidence 24566779988753
No 52
>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=95.82 E-value=0.011 Score=50.76 Aligned_cols=51 Identities=25% Similarity=0.456 Sum_probs=40.9
Q ss_pred hhHHHHHhhhccCcCHHHHHHHHHc-----CCCCHHHhhhccCchhhhHhcHHhHHhhhcCC
Q 015933 290 KVRTISLFGEVWGIGPATAQKLYEK-----GHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRI 346 (398)
Q Consensus 290 ~~~~l~lf~~I~GvGpktA~~l~~~-----GirtledL~~~~~l~~~q~~Glk~~ed~~~~i 346 (398)
..-..+.|+.+||||+++|+++++. ++.|++||.+ ..++|.+.++.|...+
T Consensus 63 NtA~~~eL~~lpGIG~~~A~~Ii~~R~~~g~f~s~eeL~~------V~GIg~k~~~~i~~~l 118 (120)
T TIGR01259 63 NAASLEELQALPGIGPAKAKAIIEYREENGAFKSVDDLTK------VSGIGEKSLEKLKDYA 118 (120)
T ss_pred CcCCHHHHhcCCCCCHHHHHHHHHHHHhcCCcCCHHHHHc------CCCCCHHHHHHHHhce
Confidence 3446777779999999999999963 5899999964 5678888888887654
No 53
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=95.71 E-value=0.012 Score=44.84 Aligned_cols=50 Identities=26% Similarity=0.499 Sum_probs=35.3
Q ss_pred hHHHHHhhhccCcCHHHHHHHHH-c----CCCCHHHhhhccCchhhhHhcHHhHHhhhcCC
Q 015933 291 VRTISLFGEVWGIGPATAQKLYE-K----GHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRI 346 (398)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~-~----GirtledL~~~~~l~~~q~~Glk~~ed~~~~i 346 (398)
..+.+.|.++||||++.|+++.+ + +++|++||.. ..++|.+.|+.|...|
T Consensus 10 ~as~~eL~~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL~~------v~gi~~~~~~~l~~~l 64 (65)
T PF12836_consen 10 TASAEELQALPGIGPKQAKAIVEYREKNGPFKSLEDLKE------VPGIGPKTYEKLKPYL 64 (65)
T ss_dssp TS-HHHHHTSTT--HHHHHHHHHHHHHH-S-SSGGGGGG------STT--HHHHHHHCCCE
T ss_pred cCCHHHHHHcCCCCHHHHHHHHHHHHhCcCCCCHHHHhh------CCCCCHHHHHHHHhhc
Confidence 34566777999999999999985 2 8899999986 5678888888876543
No 54
>PF11798 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 This helix-hairpin-helix motif is found in proteins belonging to the type-Y family of DNA polymerases []. This type of polymerases are thought to be involved in UV protection and mutation [, ]. ; PDB: 3PZP_B 2OH2_B 2W7O_B 3IN5_B 1T94_A 2W7P_B 2W8K_A 2AGQ_A 1RYR_A 3RAX_A ....
Probab=95.55 E-value=0.0073 Score=39.63 Aligned_cols=20 Identities=45% Similarity=0.790 Sum_probs=16.2
Q ss_pred hhhccCcCHHHHHHHHHcCC
Q 015933 297 FGEVWGIGPATAQKLYEKGH 316 (398)
Q Consensus 297 f~~I~GvGpktA~~l~~~Gi 316 (398)
+.++||||++|+++|.+.||
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 45899999999999998886
No 55
>KOG1929 consensus Nucleotide excision repair factor NEF2, RAD4/CUT5 component [Replication, recombination and repair]
Probab=95.48 E-value=0.023 Score=62.77 Aligned_cols=89 Identities=18% Similarity=0.230 Sum_probs=71.7
Q ss_pred CCCCCcEEEEccCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccchHHHHHh
Q 015933 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSLR 96 (398)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~r~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~~~~~l~~l~~~~~~~~~~~lV~~~Wl~es~k 96 (398)
..|.+|.|.. +|+....+..+++++..|||+....++..|+||+.-....- .++.++..+..++|+.+|+.+|+.
T Consensus 102 p~~~~~~Vc~--tgl~~~eK~ei~~~v~k~gg~~~~~L~s~v~~~~~~~~~~~---~kYe~al~wn~~v~~~~w~~~s~~ 176 (811)
T KOG1929|consen 102 PGFFGLKVCL--TGLSGDEKSEIKILVPKHGGTLHRSLSSDVNSLKILPEVKT---EKYEQALKWNIPVVSDDWLFDSIE 176 (811)
T ss_pred CcccceEEEe--cccchHHHHHHHHHhhhcccEEehhhhhhhheeeeccccch---HHHHHHHhhCCccccHHHHhhhhc
Confidence 4567777766 46777778889999999999999999999999998654321 333444445789999999999999
Q ss_pred cCCCCCcccccccc
Q 015933 97 LGEKVSEDLYRIKL 110 (398)
Q Consensus 97 ~g~lv~ee~y~l~~ 110 (398)
.+..+++..|.+..
T Consensus 177 ~~~~~~~~~~e~~~ 190 (811)
T KOG1929|consen 177 KTAVLETKPYEGAP 190 (811)
T ss_pred cccccccccccccc
Confidence 99999999998865
No 56
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=95.43 E-value=0.01 Score=55.02 Aligned_cols=51 Identities=24% Similarity=0.277 Sum_probs=40.2
Q ss_pred HHHHhhhccCcCHHHHHHHHHc-CCCCHHHhhhc---cCchhhhHhcHHhHHhhh
Q 015933 293 TISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNE---DSLTHSQRLGLKYFDDIK 343 (398)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~-GirtledL~~~---~~l~~~q~~Glk~~ed~~ 343 (398)
....|.+|+|||||+|.++.+. |..++.+.... ..|+.++++|.+..+.|.
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 3556679999999999999987 88777654432 268889999988888776
No 57
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=95.43 E-value=0.023 Score=43.60 Aligned_cols=46 Identities=20% Similarity=0.291 Sum_probs=36.5
Q ss_pred HHhhh-ccCcCHHHHHHHHHc-----CCCCHHHhhhccCchhhhHhcHHhHHhhhcCC
Q 015933 295 SLFGE-VWGIGPATAQKLYEK-----GHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRI 346 (398)
Q Consensus 295 ~lf~~-I~GvGpktA~~l~~~-----GirtledL~~~~~l~~~q~~Glk~~ed~~~~i 346 (398)
..|.. ++|||+++|+++.+. ++++++||.+ ..++|.+.++.|...|
T Consensus 16 ~~L~~~ipgig~~~a~~Il~~R~~~g~~~s~~dL~~------v~gi~~~~~~~i~~~~ 67 (69)
T TIGR00426 16 EELQRAMNGVGLKKAEAIVSYREEYGPFKTVEDLKQ------VPGIGNSLVEKNLAVI 67 (69)
T ss_pred HHHHhHCCCCCHHHHHHHHHHHHHcCCcCCHHHHHc------CCCCCHHHHHHHHhhc
Confidence 35557 999999999999975 5999999975 4678888888776543
No 58
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=95.37 E-value=0.068 Score=57.77 Aligned_cols=84 Identities=18% Similarity=0.256 Sum_probs=43.5
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--Cchhh
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHS 331 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~~--~l~~~ 331 (398)
+++..|+++|++.+++|-.-++.-+-..|+. .+--| .|+.||.++|+.|-+ .+.|++.|..+. .|..+
T Consensus 479 ~~l~~l~~~~~ks~~nLl~aIe~sK~~~l~r--------~l~aL-GIr~VG~~~Ak~La~-~f~sl~~l~~a~~e~l~~i 548 (667)
T COG0272 479 EDLLSLEGFGEKSAENLLNAIEKSKKQPLAR--------FLYAL-GIRHVGETTAKSLAR-HFGTLEALLAASEEELASI 548 (667)
T ss_pred HHHhhccchhhhHHHHHHHHHHHhccCCHHH--------HHHHc-CCchhhHHHHHHHHH-HhhhHHHHHhcCHHHHhhc
Confidence 4566666666666655554333222222221 23333 666666666666666 666666666442 35556
Q ss_pred hHhcHHhHHhhhcCCC
Q 015933 332 QRLGLKYFDDIKTRIP 347 (398)
Q Consensus 332 q~~Glk~~ed~~~~i~ 347 (398)
.++|-+-...+..-+.
T Consensus 549 ~giG~~vA~si~~ff~ 564 (667)
T COG0272 549 PGIGEVVARSIIEFFA 564 (667)
T ss_pred cchhHHHHHHHHHHHc
Confidence 6666555555544333
No 59
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.29 E-value=0.01 Score=55.09 Aligned_cols=51 Identities=18% Similarity=0.234 Sum_probs=40.0
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHc-CCCCHHHhh-hc--cCchhhhHhcHHhHHh
Q 015933 291 VRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLK-NE--DSLTHSQRLGLKYFDD 341 (398)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~-GirtledL~-~~--~~l~~~q~~Glk~~ed 341 (398)
-..+++|.+|+|||||+|..+... +...|-+.. +. ..|++.+|+|.|..+.
T Consensus 69 r~lF~~Li~V~GIGpK~Al~ILs~~~~~~l~~aI~~~D~~~L~~vpGIGkKtAer 123 (194)
T PRK14605 69 LSLFETLIDVSGIGPKLGLAMLSAMNAEALASAIISGNAELLSTIPGIGKKTASR 123 (194)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHH
Confidence 357888889999999999999996 665533322 22 3699999999999998
No 60
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=95.22 E-value=0.033 Score=48.21 Aligned_cols=41 Identities=20% Similarity=0.286 Sum_probs=33.5
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHc-CCCCHHHhhhccCchhhhHhcHH
Q 015933 291 VRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNEDSLTHSQRLGLK 337 (398)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~-GirtledL~~~~~l~~~q~~Glk 337 (398)
....+.|.++|||||++|+++.+- .++|+|||.+ ..++|.+
T Consensus 57 ~A~~~el~~lpGigP~~A~~IV~nGpf~sveDL~~------V~GIgek 98 (132)
T PRK02515 57 NSSVRAFRQFPGMYPTLAGKIVKNAPYDSVEDVLN------LPGLSER 98 (132)
T ss_pred ccCHHHHHHCCCCCHHHHHHHHHCCCCCCHHHHHc------CCCCCHH
Confidence 335667889999999999999987 6999999986 4566643
No 61
>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=95.18 E-value=0.019 Score=64.35 Aligned_cols=68 Identities=24% Similarity=0.355 Sum_probs=52.4
Q ss_pred HHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccchHHHHHhcCCCCCccccccc
Q 015933 38 IWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSLRLGEKVSEDLYRIK 109 (398)
Q Consensus 38 ~l~~li~~~Gg~V~~~ls~~VTHVV~~~~~~~l~~l~~~~~~~~~~~lV~~~Wl~es~k~g~lv~ee~y~l~ 109 (398)
-+++.+++.|+.++... ...||+|+..--+-.+.+. .-..+..||+..||.+|.++|..+|+..|.+.
T Consensus 672 ~~k~~~k~lg~s~~ss~-~e~Th~i~~rirRT~k~Le---ai~~G~~ivT~~wL~s~~k~g~~~dek~yil~ 739 (896)
T KOG2043|consen 672 NYKLAKKFLGGSVASSD-SEATHFIADRIRRTLKFLE---AISSGKPLVTPQWLVSSLKSGEKLDEKPYILH 739 (896)
T ss_pred hhhhHHhhccceeeccc-ccceeeeehhhhccHHHHh---hhccCCcccchHHHHHHhhccccccCcccccc
Confidence 47889999998887775 4589999985433222222 11236799999999999999999999999885
No 62
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=95.18 E-value=0.024 Score=52.98 Aligned_cols=54 Identities=19% Similarity=0.265 Sum_probs=40.0
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (398)
..|.++.|||+++|=.| |.+....++-..- ..+=...|+++||||.|||+++.-
T Consensus 73 ~~LisVnGIGpK~ALai---Ls~~~~~~l~~aI---~~~d~~~L~k~PGIGkKtAerivl 126 (201)
T COG0632 73 RLLISVNGIGPKLALAI---LSNLDPEELAQAI---ANEDVKALSKIPGIGKKTAERIVL 126 (201)
T ss_pred HHHHccCCccHHHHHHH---HcCCCHHHHHHHH---HhcChHhhhcCCCCCHHHHHHHHH
Confidence 46899999999998764 4555555554332 233466788999999999999984
No 63
>cd05397 NT_Pol-beta-like Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins. This superfamily includes the NT domains of DNA polymerase beta and other family X DNA polymerases, as well as the NT domains of Class I and Class II CCA-adding enzymes, RelA- and SpoT-like ppGpp synthetases and hydrolases, 2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), poly (A) polymerases, terminal uridylyl transferases, and Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. The Escherichia coli CCA-adding enzyme belongs to this superfamily but is not included as this enzyme lacks the N-terminal helix conserved in the remainder of the superfamily. In the majority of the Pol beta-like superfamily NTs, two carboxylates, Dx[D/E], together with a third more distal carboxylate coordinate two divalent metal cations that are essential for catalysis. These divalent metal ions are
Probab=95.17 E-value=0.041 Score=39.52 Aligned_cols=28 Identities=29% Similarity=0.458 Sum_probs=23.1
Q ss_pred cCCCeEEEEechhhcCCc-ccCCeeEEEe
Q 015933 365 VLPEVIILCGGSYRRGKA-SCGDLDVVIM 392 (398)
Q Consensus 365 ~~p~~~v~~~Gs~RRgke-~~gDvDiLit 392 (398)
..+...+.+.|||.||.. ..+||||++.
T Consensus 14 ~~~~~~v~lfGS~arg~~~~~SDIDi~v~ 42 (49)
T cd05397 14 LVPGYEIVVYGSLVRGLLKKSSDIDLACV 42 (49)
T ss_pred hcCCcEEEEECCcCCCCCCCCCCEEEEEE
Confidence 345668999999999977 6789999985
No 64
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=95.12 E-value=0.018 Score=43.80 Aligned_cols=45 Identities=27% Similarity=0.333 Sum_probs=32.3
Q ss_pred hccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhHhcHHhHHhhhc
Q 015933 299 EVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIKT 344 (398)
Q Consensus 299 ~I~GvGpktA~~l~~~GirtledL~~~~--~l~~~q~~Glk~~ed~~~ 344 (398)
.|+|||+++|+.|-+ .+.|++.|.++. .|....++|.+..+.|..
T Consensus 7 GI~~VG~~~ak~L~~-~f~sl~~l~~a~~e~L~~i~gIG~~~A~si~~ 53 (64)
T PF12826_consen 7 GIPGVGEKTAKLLAK-HFGSLEALMNASVEELSAIPGIGPKIAQSIYE 53 (64)
T ss_dssp TSTT--HHHHHHHHH-CCSCHHHHCC--HHHHCTSTT--HHHHHHHHH
T ss_pred CCCCccHHHHHHHHH-HcCCHHHHHHcCHHHHhccCCcCHHHHHHHHH
Confidence 899999999999986 555999998653 578888888887777654
No 65
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]
Probab=95.09 E-value=0.058 Score=58.88 Aligned_cols=91 Identities=18% Similarity=0.250 Sum_probs=58.4
Q ss_pred CCCCCCcEEEEccCCCCchHHHHHHHHHHhcCCEEEeec------CCCccEEEEcC--ChHHH-HHHHHHhhhccCcccc
Q 015933 16 NGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKL------SKKVTHVLAMD--LEALL-QQVSKQHLARFKGSVI 86 (398)
Q Consensus 16 ~~~F~g~~iy~~~~~~g~~r~~~l~~li~~~Gg~V~~~l------s~~VTHVV~~~--~~~~l-~~l~~~~~~~~~~~lV 86 (398)
.+.|..|++|.+.++.=.+-..+..-.+...|+++++.- ...+||+|+.. .+-.. ...+...+-..+ +||
T Consensus 782 ~~~~~~~~~f~~~~~~~~se~~~~~l~~k~~g~~i~~~~~~~~~~~~~~t~~v~~~i~~~h~~~~~~~~~~lt~~r-kv~ 860 (881)
T KOG0966|consen 782 SLFLSSLRMFYVLRRKLSSEEVIIELKLKNFGGRITDAQSECNNIGAKYTHCVLRCIDEDHEKIKEQKKASLTIKR-KVV 860 (881)
T ss_pred ccccccceeeecccccccHHHHHHHHHHHHhcceeeeccchhhhcccceeeeeeeecchHHHHHHHHHHHHhcccc-ccc
Confidence 356777777777665443433344444445599998764 35689999863 22222 112221111112 999
Q ss_pred ccchHHHHHhcCCCCCccccc
Q 015933 87 RYQWLEDSLRLGEKVSEDLYR 107 (398)
Q Consensus 87 ~~~Wl~es~k~g~lv~ee~y~ 107 (398)
..+||.+|+.++.+++|+.|.
T Consensus 861 ~~~wv~~s~~~~~~~~e~~~~ 881 (881)
T KOG0966|consen 861 APSWVDHSINENCLLPEEDFP 881 (881)
T ss_pred CHHHHHHhhcccccCccccCC
Confidence 999999999999999999884
No 66
>KOG1929 consensus Nucleotide excision repair factor NEF2, RAD4/CUT5 component [Replication, recombination and repair]
Probab=95.07 E-value=0.024 Score=62.68 Aligned_cols=93 Identities=12% Similarity=0.191 Sum_probs=72.9
Q ss_pred CCCCCCCCCCCcEEEEccCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccch
Q 015933 11 PALDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQW 90 (398)
Q Consensus 11 ~~~~~~~~F~g~~iy~~~~~~g~~r~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~~~~~l~~l~~~~~~~~~~~lV~~~W 90 (398)
|.+.+..+|.+|++++.. ..-.+++.+.++++..|+.+...+....||||....... .......+...+|+++|
T Consensus 486 p~~~l~~~~e~~~~~~s~--~~~~~~e~ln~~~~~~gas~~~~f~r~~~~l~~~~~k~s----~~~~~~kw~ip~vT~~w 559 (811)
T KOG1929|consen 486 PAAALSQPFENLTISNSQ--SAEAEREKLNNLANDLGASNVKTFTRKSTTLLTTSAKGS----KYEIAGKWSIPIVTPDW 559 (811)
T ss_pred hhhcccccccCceEEeee--chHHHHHHHhHhhhhccccccceeeecccEEeccccccc----hhhhccccCCCccChhH
Confidence 455566789999999974 344678999999999999999999766699998652211 11122334789999999
Q ss_pred HHHHHhcCCCCCccccccc
Q 015933 91 LEDSLRLGEKVSEDLYRIK 109 (398)
Q Consensus 91 l~es~k~g~lv~ee~y~l~ 109 (398)
|.+|.++++.++.+.|...
T Consensus 560 L~e~~rq~~~~~~e~~l~~ 578 (811)
T KOG1929|consen 560 LYECVRQNKGERNEGFLNG 578 (811)
T ss_pred HHhhccccCcccceeeccc
Confidence 9999999999999999875
No 67
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.03 E-value=0.024 Score=52.37 Aligned_cols=53 Identities=13% Similarity=0.117 Sum_probs=36.7
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (398)
..|.++.|||+++|=.| |.+-...++-..-. .+=.+.| +|||||+|||+++.-
T Consensus 73 ~~LisV~GIGpK~Al~i---Ls~~~~~~l~~aI~---~~D~~~L-~vpGIGkKtAerIil 125 (186)
T PRK14600 73 RMLVKVSGVNYKTAMSI---LSKLTPEQLFSAIV---NEDKAAL-KVNGIGEKLINRIIT 125 (186)
T ss_pred HHHhCcCCcCHHHHHHH---HccCCHHHHHHHHH---cCCHhhe-ECCCCcHHHHHHHHH
Confidence 45889999999998765 44444444433222 2224667 899999999999983
No 68
>PRK00254 ski2-like helicase; Provisional
Probab=94.91 E-value=0.042 Score=60.67 Aligned_cols=69 Identities=25% Similarity=0.397 Sum_probs=51.0
Q ss_pred hCCchhhHHHH----hhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhc--cCchhhhHhcHHhHHhhhcC
Q 015933 276 TGKLSKLEHFE----KDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDIKTR 345 (398)
Q Consensus 276 tG~~~~le~l~----~~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~--~~l~~~q~~Glk~~ed~~~~ 345 (398)
.|.+..+.+|. ...+...+.|. +|||||+++|++||+.|+.|++||..+ ..|..+.++|.+..+.|.+.
T Consensus 623 ~~~~~~l~~l~~rl~~g~~~~~~~L~-~ipgig~~~~~~l~~~g~~s~~~i~~a~~~el~~~~gi~~~~a~~i~~~ 697 (720)
T PRK00254 623 QEVLDYLETLHLRVKHGVREELLELM-RLPMIGRKRARALYNAGFRSIEDIVNAKPSELLKVEGIGAKIVEGIFKH 697 (720)
T ss_pred hhHHHHHHHHHHHHHcCCCHHHhhhh-cCCCCCHHHHHHHHHccCCCHHHHHhCCHHHHhcCCCCCHHHHHHHHHH
Confidence 34444444333 44444455555 999999999999999999999999865 35888888888887776643
No 69
>COG5163 NOP7 Protein required for biogenesis of the 60S ribosomal subunit [Translation, ribosomal structure and biogenesis]
Probab=94.74 E-value=0.025 Score=57.18 Aligned_cols=86 Identities=19% Similarity=0.320 Sum_probs=62.9
Q ss_pred CCCCCCCCCCcEEEEccCCCCchHHHHHHHHHHhcCCEEEeec-----------CCCccEEEEcCChHHHHHHHHHhhhc
Q 015933 12 ALDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKL-----------SKKVTHVLAMDLEALLQQVSKQHLAR 80 (398)
Q Consensus 12 ~~~~~~~F~g~~iy~~~~~~g~~r~~~l~~li~~~Gg~V~~~l-----------s~~VTHVV~~~~~~~l~~l~~~~~~~ 80 (398)
.++-..+|+|.++|+...-.+ +.|+-+|...||.|..+. +..|||-|++-. .+.. ..
T Consensus 344 ~Ss~~slFS~f~FyisreVp~----dsLefiilscGG~V~~~p~~~~i~~~~~vD~~vth~i~drp--~~~~----kv-- 411 (591)
T COG5163 344 CSSLKSLFSGFKFYISREVPG----DSLEFIILSCGGSVVGSPCEADIHVSEKVDEKVTHQIVDRP--VMKN----KV-- 411 (591)
T ss_pred CcchhhhhhceEEEEeccccc----hHHHHHHHHcCCcccCchhhccCCchhhccchhhhhhccch--hhhh----hh--
Confidence 455568999999999743333 568889999999998652 345888887532 1111 00
Q ss_pred cCccccccchHHHHHhcCCCCCccccccc
Q 015933 81 FKGSVIRYQWLEDSLRLGEKVSEDLYRIK 109 (398)
Q Consensus 81 ~~~~lV~~~Wl~es~k~g~lv~ee~y~l~ 109 (398)
-+.-.+.++||-||+..|.+++.+.|.+.
T Consensus 412 egrtYiQPQw~fDsiNkG~l~~~~~Y~~G 440 (591)
T COG5163 412 EGRTYIQPQWLFDSINKGKLACVENYCVG 440 (591)
T ss_pred cceeeechHHHHhhhccccchhhhhcccc
Confidence 13457899999999999999999999986
No 70
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.43 E-value=0.022 Score=52.75 Aligned_cols=51 Identities=20% Similarity=0.245 Sum_probs=39.6
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhh---c---cCchhhhHhcHHhHHhhh
Q 015933 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDIK 343 (398)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~---~---~~l~~~q~~Glk~~ed~~ 343 (398)
...+++|.+|.|||||+|-.+... -+.++|.+ . ..|++++|+|.|..+.|.
T Consensus 69 r~lF~~Li~V~GIGpK~AL~iLs~--~~~~el~~aI~~~D~~~L~~vpGIGkKtAerIi 125 (188)
T PRK14606 69 KELFLSLTKVSRLGPKTALKIISN--EDAETLVTMIASQDVEGLSKLPGISKKTAERIV 125 (188)
T ss_pred HHHHHHHhccCCccHHHHHHHHcC--CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 347888889999999999999864 25555543 2 258999999999988763
No 71
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.39 E-value=0.023 Score=52.38 Aligned_cols=51 Identities=20% Similarity=0.236 Sum_probs=39.9
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhh---c---cCchhhhHhcHHhHHhhh
Q 015933 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDIK 343 (398)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~---~---~~l~~~q~~Glk~~ed~~ 343 (398)
...+++|.+|.|||||+|-.+... -+.++|.. . ..|++.+|+|-|..+.|.
T Consensus 69 r~lF~~Li~VsGIGpK~Al~ILs~--~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIi 125 (183)
T PRK14601 69 QKMFEMLLKVNGIGANTAMAVCSS--LDVNSFYKALSLGDESVLKKVPGIGPKSAKRII 125 (183)
T ss_pred HHHHHHHhccCCccHHHHHHHHcC--CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 357888889999999999998864 25666653 2 358999999999988764
No 72
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.28 E-value=0.024 Score=52.80 Aligned_cols=51 Identities=27% Similarity=0.299 Sum_probs=39.8
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhh---c---cCchhhhHhcHHhHHhhh
Q 015933 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDIK 343 (398)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~---~---~~l~~~q~~Glk~~ed~~ 343 (398)
-..+++|.+|.|||||+|-.+... -|+++|.+ . ..|++.+++|.|..+.|.
T Consensus 68 r~lF~~L~~V~GIGpK~AL~iLs~--~~~~~l~~aI~~~D~~~L~kvpGIGkKtAerIi 124 (197)
T PRK14603 68 LELFELLLGVSGVGPKLALALLSA--LPPALLARALLEGDARLLTSASGVGKKLAERIA 124 (197)
T ss_pred HHHHHHHhCcCCcCHHHHHHHHcC--CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 347888889999999999999874 25666653 2 358999999999988763
No 73
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=94.26 E-value=0.071 Score=50.60 Aligned_cols=54 Identities=24% Similarity=0.435 Sum_probs=41.2
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc
Q 015933 253 ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (398)
Q Consensus 253 ~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~ 314 (398)
++.|..|||||+..+.++ ++.| +.-++.+... ..+.+..|+|||.++|.++++.
T Consensus 2 ~~~L~~IpGIG~krakkL---l~~G-F~Sve~Ik~A----S~eEL~~V~GIg~k~AekI~e~ 55 (232)
T PRK12766 2 PEELEDISGVGPSKAEAL---REAG-FESVEDVRAA----DQSELAEVDGIGNALAARIKAD 55 (232)
T ss_pred ccccccCCCcCHHHHHHH---HHcC-CCCHHHHHhC----CHHHHHHccCCCHHHHHHHHHH
Confidence 356889999999888776 5555 5556666542 3456679999999999999985
No 74
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.12 E-value=0.028 Score=52.58 Aligned_cols=51 Identities=25% Similarity=0.296 Sum_probs=39.6
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhh---c---cCchhhhHhcHHhHHhhh
Q 015933 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDIK 343 (398)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~---~---~~l~~~q~~Glk~~ed~~ 343 (398)
...+++|.+|.|||||+|-.+... -+.++|.+ . ..|++++|+|-|..+.|.
T Consensus 70 r~lF~~Li~V~GIGpK~Al~iLs~--~~~~~l~~aI~~~D~~~L~~ipGIGkKtAerIi 126 (203)
T PRK14602 70 RQTFIVLISISKVGAKTALAILSQ--FRPDDLRRLVAEEDVAALTRVSGIGKKTAQHIF 126 (203)
T ss_pred HHHHHHHhCCCCcCHHHHHHHHhh--CCHHHHHHHHHhCCHHHHhcCCCcCHHHHHHHH
Confidence 347888889999999999999985 25555542 2 358999999999988763
No 75
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.02 E-value=0.029 Score=52.19 Aligned_cols=51 Identities=27% Similarity=0.346 Sum_probs=40.3
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhc------cCchhhhHhcHHhHHhhh
Q 015933 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE------DSLTHSQRLGLKYFDDIK 343 (398)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~------~~l~~~q~~Glk~~ed~~ 343 (398)
-..+++|.+|.|||||+|-.+... -|+++|..+ ..|++++|+|.|..+.|.
T Consensus 69 r~lF~~Li~V~GIGpK~Al~iLs~--~~~~el~~aI~~~D~~~L~kvpGIGkKtAerIi 125 (195)
T PRK14604 69 RQLFELLIGVSGVGPKAALNLLSS--GTPDELQLAIAGGDVARLARVPGIGKKTAERIV 125 (195)
T ss_pred HHHHHHHhCcCCcCHHHHHHHHcC--CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 347888889999999999999884 366666532 358999999999988763
No 76
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.85 E-value=0.034 Score=51.71 Aligned_cols=51 Identities=18% Similarity=0.288 Sum_probs=40.0
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhc------cCchhhhHhcHHhHHhhh
Q 015933 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE------DSLTHSQRLGLKYFDDIK 343 (398)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~------~~l~~~q~~Glk~~ed~~ 343 (398)
...+++|.+|.|||||+|-.+... -+.++|..+ ..|++.+|+|.|..+.|.
T Consensus 68 r~lF~~LisVsGIGPK~ALaILs~--~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRII 124 (196)
T PRK13901 68 REVFEELIGVDGIGPRAALRVLSG--IKYNEFRDAIDREDIELISKVKGIGNKMAGKIF 124 (196)
T ss_pred HHHHHHHhCcCCcCHHHHHHHHcC--CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 347788889999999999999864 356666532 258999999999988763
No 77
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=93.25 E-value=0.043 Score=60.18 Aligned_cols=49 Identities=18% Similarity=0.275 Sum_probs=40.9
Q ss_pred hhccCcCHHHHHHHHHc-CCCCHHHhhh--ccCchhhhHhcHHhHHhhhcCC
Q 015933 298 GEVWGIGPATAQKLYEK-GHRTLDDLKN--EDSLTHSQRLGLKYFDDIKTRI 346 (398)
Q Consensus 298 ~~I~GvGpktA~~l~~~-GirtledL~~--~~~l~~~q~~Glk~~ed~~~~i 346 (398)
++|.|+|++++.+||+. +++++.||.. ...|..+.+||-|..+.|.+.|
T Consensus 465 l~I~GLG~k~i~~L~~~g~V~~~~Dl~~L~~~~L~~l~g~g~Ksa~~Ll~~I 516 (689)
T PRK14351 465 LDIEGLGEERVQQLVDAGLVESLADLYDLTVADLAELEGWGETSAENLLAEL 516 (689)
T ss_pred cCCCCcCHHHHHHHHHcCCCCCHHHHHHcCHHHHhcCcCcchhHHHHHHHHH
Confidence 37999999999999999 5699999985 2347778889999999887654
No 78
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=93.19 E-value=0.08 Score=52.58 Aligned_cols=47 Identities=30% Similarity=0.457 Sum_probs=35.3
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhHhcHHhHHhhh
Q 015933 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIK 343 (398)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~~--~l~~~q~~Glk~~ed~~ 343 (398)
+..+||||+++|++|.+.||.|++||.... .|....+++.+..+.|.
T Consensus 8 l~~l~gIg~~~a~~L~~~Gi~t~~dl~~~~~~~L~~~~g~~~~~a~~l~ 56 (317)
T PRK04301 8 LEDLPGVGPATAEKLREAGYDTVEAIAVASPKELSEAAGIGESTAAKII 56 (317)
T ss_pred HhhcCCCCHHHHHHHHHcCCCCHHHHHcCCHHHHHHhcCCCHHHHHHHH
Confidence 558999999999999999999999998643 35555454444544444
No 79
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.06 E-value=0.055 Score=50.00 Aligned_cols=50 Identities=22% Similarity=0.286 Sum_probs=39.1
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhh---c---cCchhhhHhcHHhHHhhh
Q 015933 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDIK 343 (398)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~---~---~~l~~~q~~Glk~~ed~~ 343 (398)
...+++|.+|.|||||+|-.+-.. -|+++|.. . ..| +++|+|-|..+.|.
T Consensus 69 r~lF~~LisV~GIGpK~Al~iLs~--~~~~~l~~aI~~~D~~~L-~vpGIGkKtAerIi 124 (186)
T PRK14600 69 QDCLRMLVKVSGVNYKTAMSILSK--LTPEQLFSAIVNEDKAAL-KVNGIGEKLINRII 124 (186)
T ss_pred HHHHHHHhCcCCcCHHHHHHHHcc--CCHHHHHHHHHcCCHhhe-ECCCCcHHHHHHHH
Confidence 347888889999999999999874 25666653 2 358 89999999988764
No 80
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=93.06 E-value=0.47 Score=52.62 Aligned_cols=83 Identities=20% Similarity=0.350 Sum_probs=64.2
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc-CCCCHHHhhhcc-Cch-
Q 015933 253 ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED-SLT- 329 (398)
Q Consensus 253 ~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~-GirtledL~~~~-~l~- 329 (398)
.+.|..+||||+..++.|.+-++. .+ ....++..| .=+|++++.|.++|+. |-.+++.|+++. .|.
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 457899999999999999876631 11 122355455 8899999999999998 999999999765 555
Q ss_pred hhhHhcHHhHHhhhcCC
Q 015933 330 HSQRLGLKYFDDIKTRI 346 (398)
Q Consensus 330 ~~q~~Glk~~ed~~~~i 346 (398)
...++|++..+.|..++
T Consensus 185 ~i~gigF~~aD~iA~~~ 201 (720)
T TIGR01448 185 DVKGIGFLTADQLAQAL 201 (720)
T ss_pred hcCCCCHHHHHHHHHHc
Confidence 57889999999986543
No 81
>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=92.84 E-value=0.22 Score=39.58 Aligned_cols=31 Identities=29% Similarity=0.460 Sum_probs=25.3
Q ss_pred CCCeEEEEechhhcCCcc-cCCeeEEEecCCC
Q 015933 366 LPEVIILCGGSYRRGKAS-CGDLDVVIMHPDR 396 (398)
Q Consensus 366 ~p~~~v~~~Gs~RRgke~-~gDvDiLit~~~~ 396 (398)
.+...+.+.|||.||..+ .+|||++|..++.
T Consensus 12 ~~~~~v~lfGS~a~g~~~~~SDIDl~i~~~~~ 43 (93)
T PF01909_consen 12 FGVAEVYLFGSYARGDATPDSDIDLLIILDEP 43 (93)
T ss_dssp HTTEEEEEEHHHHHTSSCTTSCEEEEEEESST
T ss_pred CCCCEEEEECCcccCcCCCCCCEEEEEEeCCc
Confidence 446689999999999965 6999999976654
No 82
>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=92.75 E-value=0.082 Score=42.20 Aligned_cols=30 Identities=27% Similarity=0.480 Sum_probs=23.4
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhcc
Q 015933 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (398)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~~ 326 (398)
+..+|.+||+..+.|++-||.|++||+.-|
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 458899999999999999999999999755
No 83
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=92.74 E-value=0.077 Score=32.90 Aligned_cols=18 Identities=50% Similarity=0.648 Sum_probs=16.0
Q ss_pred HhhhccCcCHHHHHHHHH
Q 015933 296 LFGEVWGIGPATAQKLYE 313 (398)
Q Consensus 296 lf~~I~GvGpktA~~l~~ 313 (398)
.|++|+|||+++|+++.+
T Consensus 2 ~L~~i~GiG~k~A~~il~ 19 (26)
T smart00278 2 ELLKVPGIGPKTAEKILE 19 (26)
T ss_pred hhhhCCCCCHHHHHHHHH
Confidence 356999999999999997
No 84
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=92.22 E-value=0.26 Score=52.91 Aligned_cols=88 Identities=15% Similarity=0.194 Sum_probs=66.8
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--Cchh
Q 015933 253 ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTH 330 (398)
Q Consensus 253 ~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~~--~l~~ 330 (398)
.+++.+|+|+|++.+++|.+-++.-+-..|+ ..+--| .|++||..+|+. .+.|+++|..+. .|..
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 3579999999999999998766644333333 355567 999999998887 678899998543 5888
Q ss_pred hhHhcHHhHHhhhcCCCHHHHHH
Q 015933 331 SQRLGLKYFDDIKTRIPRHEVEQ 353 (398)
Q Consensus 331 ~q~~Glk~~ed~~~~i~r~ea~~ 353 (398)
+.+||.+..+.|.+-+.-.+..+
T Consensus 525 i~gIG~~~a~si~~~f~~~~~~~ 547 (562)
T PRK08097 525 LPGIGEGRARQLIAFLQHPEVKA 547 (562)
T ss_pred CCCchHHHHHHHHHHHcCHHHHH
Confidence 89999999999887776555433
No 85
>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=92.19 E-value=0.11 Score=51.24 Aligned_cols=37 Identities=32% Similarity=0.521 Sum_probs=29.6
Q ss_pred hhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhHh
Q 015933 298 GEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRL 334 (398)
Q Consensus 298 ~~I~GvGpktA~~l~~~GirtledL~~~~--~l~~~q~~ 334 (398)
..+||||++++++|++.||.|++||.... .|....++
T Consensus 2 ~~i~gig~~~~~~L~~~Gi~ti~dl~~~~~~~L~~~~g~ 40 (310)
T TIGR02236 2 EDLPGVGPATAEKLREAGYDTFEAIAVASPKELSEIAGI 40 (310)
T ss_pred cccCCCCHHHHHHHHHcCCCCHHHHHcCCHHHHHhccCC
Confidence 47899999999999999999999998653 34444343
No 86
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=92.08 E-value=0.38 Score=47.74 Aligned_cols=97 Identities=15% Similarity=0.251 Sum_probs=63.4
Q ss_pred CCCCHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHH
Q 015933 207 PDLNKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFE 286 (398)
Q Consensus 207 ~~~N~~ia~~L~~la~~~e~~g~~~r~~aY~rAa~~l~~l~~~i~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~ 286 (398)
+.=++.|++.++++.+-=++. +.....+.+|.. +.+|..+||+|.+-..+..+.|- +..+++|+
T Consensus 59 ~gIGk~ia~~I~e~l~tG~~~----------~le~lk~~~P~g---l~~Ll~v~GlGpkKi~~Ly~elg---i~~~e~l~ 122 (326)
T COG1796 59 PGIGKGIAEKISEYLDTGEVK----------KLEALKKEVPEG---LEPLLKVPGLGPKKIVSLYKELG---IKDLEELQ 122 (326)
T ss_pred CCccHHHHHHHHHHHHcCccH----------HHHHHHHhCCcc---hHHHhhCCCCCcHHHHHHHHHHC---cccHHHHH
Confidence 566889998766554432221 344455567766 66899999999954444444333 66677776
Q ss_pred hhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHh
Q 015933 287 KDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL 322 (398)
Q Consensus 287 ~~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL 322 (398)
.... .-.|..++|+|.|.+.+|++.+....+.-
T Consensus 123 ~a~~---~~~~~~l~GfG~kse~~il~~i~~~~~~~ 155 (326)
T COG1796 123 EALE---NGKIRGLRGFGKKSEAKILENIEFAEESP 155 (326)
T ss_pred HHHH---hCCccccCCccchhHHHHHHHHHHHhhhh
Confidence 5332 44577999999999999998644444433
No 87
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=91.98 E-value=0.17 Score=43.84 Aligned_cols=53 Identities=23% Similarity=0.316 Sum_probs=38.5
Q ss_pred HHhhhccCcCHHHHHHHHHcCCCCHHHhhhccCchhhhHhcHHhHHhhhcCCCHHH
Q 015933 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIPRHE 350 (398)
Q Consensus 295 ~lf~~I~GvGpktA~~l~~~GirtledL~~~~~l~~~q~~Glk~~ed~~~~i~r~e 350 (398)
.-|+.|-||||+.+..|...||.|+.+|-. ++..-..-+..|-.|..||-|+.
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 467799999999999999999999999974 22222233444555666777764
No 88
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=91.62 E-value=0.099 Score=57.84 Aligned_cols=46 Identities=17% Similarity=0.376 Sum_probs=39.3
Q ss_pred ccCcCHHHHHHHHHc-CCCCHHHhhhcc-CchhhhHhcHHhHHhhhcC
Q 015933 300 VWGIGPATAQKLYEK-GHRTLDDLKNED-SLTHSQRLGLKYFDDIKTR 345 (398)
Q Consensus 300 I~GvGpktA~~l~~~-GirtledL~~~~-~l~~~q~~Glk~~ed~~~~ 345 (398)
++||||+||+++++. |.++++-|.++. +|...+++|.+..+.|...
T Consensus 89 ~~GIG~~~A~~iv~~fg~~~~~~i~~~~~~L~~v~gi~~~~~~~i~~~ 136 (720)
T TIGR01448 89 IKGVGKKLAQRIVKTFGEAAFDVLDDDPEKLLEVPGISKANLEKFVSQ 136 (720)
T ss_pred CCCcCHHHHHHHHHHhCHhHHHHHHhCHHHHhcCCCCCHHHHHHHHHH
Confidence 899999999999998 999999998664 5888888888888777653
No 89
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=91.61 E-value=0.25 Score=47.62 Aligned_cols=49 Identities=22% Similarity=0.481 Sum_probs=35.5
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 015933 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (398)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (398)
+..|||||..++..+-.. -|++..+ .+ .....++.|+|||+++|..+|+
T Consensus 184 l~s~pgig~~~a~~ll~~--fgS~~~~---~t----as~~eL~~v~gig~k~A~~I~~ 232 (254)
T COG1948 184 LESIPGIGPKLAERLLKK--FGSVEDV---LT----ASEEELMKVKGIGEKKAREIYR 232 (254)
T ss_pred HHcCCCccHHHHHHHHHH--hcCHHHH---hh----cCHHHHHHhcCccHHHHHHHHH
Confidence 789999999999876542 3444333 22 1225666999999999999997
No 90
>PRK01172 ski2-like helicase; Provisional
Probab=91.42 E-value=0.43 Score=52.30 Aligned_cols=57 Identities=19% Similarity=0.362 Sum_probs=41.1
Q ss_pred HHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhc--cCchhhhHhcHHhHHhh
Q 015933 285 FEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDI 342 (398)
Q Consensus 285 l~~~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~--~~l~~~q~~Glk~~ed~ 342 (398)
+....+...+.|+ +|||+|..+|++||+.|++|+.||... ..+..+-++|-+..+.|
T Consensus 603 l~~gv~~~~~~L~-~ip~~~~~~a~~l~~~g~~~~~di~~~~~~~~~~i~~~~~~~~~~i 661 (674)
T PRK01172 603 IKEGIREDLIDLV-LIPKVGRVRARRLYDAGFKTVDDIARSSPERIKKIYGFSDTLANAI 661 (674)
T ss_pred HHcCCCHHHHhhc-CCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHHHhccCHHHHHHH
Confidence 3444555567777 899999999999999999999999854 24555545555444443
No 91
>PRK03352 DNA polymerase IV; Validated
Probab=90.74 E-value=0.26 Score=49.41 Aligned_cols=30 Identities=40% Similarity=0.746 Sum_probs=26.5
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhcc
Q 015933 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (398)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~~ 326 (398)
+..+||||++++++|...||+|+.||..-.
T Consensus 179 l~~l~gig~~~~~~L~~~Gi~ti~dl~~l~ 208 (346)
T PRK03352 179 TDALWGVGPKTAKRLAALGITTVADLAAAD 208 (346)
T ss_pred HHHcCCCCHHHHHHHHHcCCccHHHHhcCC
Confidence 357899999999999999999999998643
No 92
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=90.37 E-value=0.32 Score=46.25 Aligned_cols=49 Identities=22% Similarity=0.468 Sum_probs=36.8
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 015933 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (398)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (398)
|+.||||+|.=|..+-. ++.-|+.+-+ .....|.+|+|+||.+|++||+
T Consensus 197 Lt~i~~VnKtda~~LL~-----~FgsLq~~~~----AS~~ele~~~G~G~~kak~l~~ 245 (254)
T KOG2841|consen 197 LTTIPGVNKTDAQLLLQ-----KFGSLQQISN----ASEGELEQCPGLGPAKAKRLHK 245 (254)
T ss_pred HHhCCCCCcccHHHHHH-----hcccHHHHHh----cCHhHHHhCcCcCHHHHHHHHH
Confidence 88999999987765432 4444555543 3567788999999999999997
No 93
>TIGR00588 ogg 8-oxoguanine DNA-glycosylase (ogg). All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is distantly realted to the Nth-MutY superfamily.
Probab=90.16 E-value=0.8 Score=45.60 Aligned_cols=64 Identities=19% Similarity=0.243 Sum_probs=41.3
Q ss_pred hhcCCCCCCHHHHHHHHHHH---HhCCc--hhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHH
Q 015933 255 QVKGLPGIGKSMQDHIQEIV---TTGKL--SKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLD 320 (398)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil---~tG~~--~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~Girtle 320 (398)
+|+.+ |+|-+ ++-|.++. ..|.. ..++.|..-....+.+.|++++||||+||.-+-=.|+.-.+
T Consensus 177 ~Lr~~-G~g~R-a~~I~~~A~~i~~~~~~~~~l~~l~~~~~~~~~~~L~~l~GIG~~tAd~vll~~l~~~d 245 (310)
T TIGR00588 177 HLRKL-GLGYR-ARYIRETARALLEEQGGRAWLQQIRGASYEDAREALCELPGVGPKVADCICLMGLDKPQ 245 (310)
T ss_pred HHHHc-CCHHH-HHHHHHHHHHHHhccCCchhHHhhccCChHHHHHHHHhCCCccHHHHHHHHHHhCCCCC
Confidence 45554 66765 44444333 34443 34666655444558899999999999999987765665443
No 94
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=90.11 E-value=0.6 Score=50.34 Aligned_cols=52 Identities=17% Similarity=0.142 Sum_probs=38.7
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~ 314 (398)
..|.+|||||++...++-+ ++.-++.+++ .+++.+.+|+|+|.+.|+.+|+.
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 3789999999988776654 3344445443 35677789999999999999873
No 95
>PRK01216 DNA polymerase IV; Validated
Probab=89.87 E-value=0.33 Score=49.14 Aligned_cols=40 Identities=28% Similarity=0.260 Sum_probs=29.9
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhccCchhhhHhcH
Q 015933 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGL 336 (398)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~~~l~~~q~~Gl 336 (398)
+..+||||++++++|.+.||+|+.||.+-..-.-.++||.
T Consensus 180 i~~l~giG~~~~~~L~~~Gi~TigdL~~~~~~~L~~rfG~ 219 (351)
T PRK01216 180 IADIPGIGDITAEKLKKLGVNKLVDTLRIEFDELKGIIGE 219 (351)
T ss_pred cccccCCCHHHHHHHHHcCCCcHHHHhcCCHHHHHHHHCH
Confidence 3478999999999999999999999986432122334553
No 96
>PRK03858 DNA polymerase IV; Validated
Probab=89.82 E-value=0.32 Score=49.71 Aligned_cols=28 Identities=39% Similarity=0.749 Sum_probs=25.5
Q ss_pred hhccCcCHHHHHHHHHcCCCCHHHhhhc
Q 015933 298 GEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (398)
Q Consensus 298 ~~I~GvGpktA~~l~~~GirtledL~~~ 325 (398)
..+||||++++++|.+.||+|+.||.+-
T Consensus 176 ~~l~Gig~~~~~~L~~~Gi~t~~dl~~l 203 (396)
T PRK03858 176 RRLWGVGPVTAAKLRAHGITTVGDVAEL 203 (396)
T ss_pred hhcCCCCHHHHHHHHHhCCCcHHHHhcC
Confidence 4779999999999999999999999854
No 97
>PRK14133 DNA polymerase IV; Provisional
Probab=89.68 E-value=0.84 Score=45.82 Aligned_cols=45 Identities=27% Similarity=0.426 Sum_probs=32.1
Q ss_pred hhccCcCHHHHHHHHHcCCCCHHHhhhccCchhhhHh---cHHhHHhh
Q 015933 298 GEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRL---GLKYFDDI 342 (398)
Q Consensus 298 ~~I~GvGpktA~~l~~~GirtledL~~~~~l~~~q~~---Glk~~ed~ 342 (398)
..+||||++++++|.+.||+|+.||.+-..-.-..+| |..+++.+
T Consensus 176 ~~l~gig~~~~~~L~~~Gi~ti~dl~~l~~~~L~~rfG~~g~~l~~~a 223 (347)
T PRK14133 176 SKVHGIGKKSVEKLNNIGIYTIEDLLKLSREFLIEYFGKFGVEIYERI 223 (347)
T ss_pred cccCCCCHHHHHHHHHcCCccHHHHhhCCHHHHHHHHhHHHHHHHHHh
Confidence 4789999999999999999999999864321112223 45555554
No 98
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=89.01 E-value=0.27 Score=33.13 Aligned_cols=16 Identities=56% Similarity=0.742 Sum_probs=14.3
Q ss_pred hccCcCHHHHHHHHHc
Q 015933 299 EVWGIGPATAQKLYEK 314 (398)
Q Consensus 299 ~I~GvGpktA~~l~~~ 314 (398)
.|+|||+|||.+|.++
T Consensus 20 Gv~giG~ktA~~ll~~ 35 (36)
T smart00279 20 GVKGIGPKTALKLLRE 35 (36)
T ss_pred CCCcccHHHHHHHHHh
Confidence 7999999999999763
No 99
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=88.98 E-value=0.26 Score=46.03 Aligned_cols=52 Identities=23% Similarity=0.294 Sum_probs=38.6
Q ss_pred HHHHHhhhccCcCHHHHHHHHHc-CCCCHHHhhhc---cCchhhhHhcHHhHHhhh
Q 015933 292 RTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNE---DSLTHSQRLGLKYFDDIK 343 (398)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~~-GirtledL~~~---~~l~~~q~~Glk~~ed~~ 343 (398)
..+..|.+|.|||||+|-.+..- ....|-+.... ..|++.+++|-|..+.|.
T Consensus 70 ~lF~~LisVnGIGpK~ALaiLs~~~~~~l~~aI~~~d~~~L~k~PGIGkKtAeriv 125 (201)
T COG0632 70 ELFRLLISVNGIGPKLALAILSNLDPEELAQAIANEDVKALSKIPGIGKKTAERIV 125 (201)
T ss_pred HHHHHHHccCCccHHHHHHHHcCCCHHHHHHHHHhcChHhhhcCCCCCHHHHHHHH
Confidence 36677779999999999999874 44444443322 258899999999988764
No 100
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=88.86 E-value=0.26 Score=53.87 Aligned_cols=50 Identities=26% Similarity=0.387 Sum_probs=39.0
Q ss_pred HHHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhHhcHHhHHhhhc
Q 015933 294 ISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIKT 344 (398)
Q Consensus 294 l~lf~~I~GvGpktA~~l~~~GirtledL~~~~--~l~~~q~~Glk~~ed~~~ 344 (398)
-..|..|+||||+++++|++. +.|+++|..+. .|....++|.+..+.|.+
T Consensus 636 ~s~L~~IPGIGpkr~k~LL~~-FGSle~I~~AS~eELa~V~Gig~k~Ae~I~~ 687 (694)
T PRK14666 636 TGELQRVEGIGPATARLLWER-FGSLQAMAAAGEEGLAAVPGIGPARAAALHE 687 (694)
T ss_pred HhHHhhCCCCCHHHHHHHHHH-hCCHHHHHhcCHHHHHhcCCcCHHHHHHHHH
Confidence 345669999999999999997 33999999753 476777788877777654
No 101
>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=88.59 E-value=0.37 Score=37.76 Aligned_cols=28 Identities=39% Similarity=0.539 Sum_probs=22.8
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhc
Q 015933 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (398)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~ 325 (398)
+..|+|||||||.+|..+ +.|++.+...
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 102
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=88.49 E-value=0.57 Score=38.20 Aligned_cols=53 Identities=28% Similarity=0.561 Sum_probs=41.3
Q ss_pred HHHHhhhccCcCHHHHHHHHHc-CCCCHHHhhhcc-Cchh-hhHhcHHhHHhhhcCC
Q 015933 293 TISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED-SLTH-SQRLGLKYFDDIKTRI 346 (398)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~-GirtledL~~~~-~l~~-~q~~Glk~~ed~~~~i 346 (398)
++..| .-+|++++.|.++|+. |-.+++-|+++. .|.. ..++|++..+.|..++
T Consensus 11 ~~~~L-~~~gl~~~~a~kl~~~yg~~ai~~l~~nPY~L~~~i~gi~F~~aD~iA~~~ 66 (94)
T PF14490_consen 11 LMAFL-QEYGLSPKLAMKLYKKYGDDAIEILKENPYRLIEDIDGIGFKTADKIALKL 66 (94)
T ss_dssp HHHHH-HHTT--HHHHHHHHHHH-TTHHHHHHH-STCCCB-SSSSBHHHHHHHHHTT
T ss_pred HHHHH-HHcCCCHHHHHHHHHHHhHHHHHHHHHChHHHHHHccCCCHHHHHHHHHHc
Confidence 45555 8899999999999998 999999998765 5555 8999999999998765
No 103
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=88.44 E-value=0.62 Score=44.98 Aligned_cols=54 Identities=22% Similarity=0.370 Sum_probs=43.3
Q ss_pred hhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhHhcHHhHHhhhc
Q 015933 290 KVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIKT 344 (398)
Q Consensus 290 ~~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~~--~l~~~q~~Glk~~ed~~~ 344 (398)
...-+.++.++||||+++|..+.+ -+.|++++.++. .|....++|.+....|..
T Consensus 177 ~e~q~~il~s~pgig~~~a~~ll~-~fgS~~~~~tas~~eL~~v~gig~k~A~~I~~ 232 (254)
T COG1948 177 KELQLYILESIPGIGPKLAERLLK-KFGSVEDVLTASEEELMKVKGIGEKKAREIYR 232 (254)
T ss_pred HHHHHHHHHcCCCccHHHHHHHHH-HhcCHHHHhhcCHHHHHHhcCccHHHHHHHHH
Confidence 344677788999999999999998 566899998764 588888888888776654
No 104
>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=88.34 E-value=0.5 Score=48.64 Aligned_cols=30 Identities=27% Similarity=0.328 Sum_probs=26.7
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhcc
Q 015933 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (398)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~~ 326 (398)
+..+||||++++++|...||+|+.||.+..
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 105
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=88.34 E-value=0.92 Score=48.89 Aligned_cols=51 Identities=24% Similarity=0.367 Sum_probs=38.1
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~ 314 (398)
..|.+|||||++...++-. ++.-++.+++ .+++.+.+| |||+++|+++|+.
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 3344445543 356777899 9999999999873
No 106
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=88.13 E-value=0.5 Score=48.85 Aligned_cols=29 Identities=38% Similarity=0.674 Sum_probs=26.3
Q ss_pred hhccCcCHHHHHHHHHcCCCCHHHhhhcc
Q 015933 298 GEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (398)
Q Consensus 298 ~~I~GvGpktA~~l~~~GirtledL~~~~ 326 (398)
..+||||++++++|.+.||+|+.||.+..
T Consensus 182 ~~l~GiG~~~~~~L~~lGi~TigdL~~~~ 210 (422)
T PRK03609 182 EEVWGVGRRISKKLNAMGIKTALDLADTN 210 (422)
T ss_pred hhcCCccHHHHHHHHHcCCCcHHHHhcCC
Confidence 58899999999999999999999998643
No 107
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=88.10 E-value=0.23 Score=53.19 Aligned_cols=49 Identities=18% Similarity=0.208 Sum_probs=41.3
Q ss_pred hhccCcCHHHHHHHHHcCC-CCHHHhhh--ccCchhhhHhcHHhHHhhhcCC
Q 015933 298 GEVWGIGPATAQKLYEKGH-RTLDDLKN--EDSLTHSQRLGLKYFDDIKTRI 346 (398)
Q Consensus 298 ~~I~GvGpktA~~l~~~Gi-rtledL~~--~~~l~~~q~~Glk~~ed~~~~i 346 (398)
++|-|+|++++.+|++.|+ +++.||.. ...|..+.+||-|..+.|...|
T Consensus 428 mdI~GlGe~~i~~L~~~G~i~~~~Diy~L~~~~l~~l~gfgeks~~nll~aI 479 (562)
T PRK08097 428 LGLDGIGEGTWRALHQTGLFEHLFSWLALTPEQLANTPGIGKARAEQLWHQF 479 (562)
T ss_pred cCCCCcCHHHHHHHHHcCCcCCHHHHhcCCHHHHhcCcCccHHHHHHHHHHH
Confidence 4899999999999999974 99999974 3457778899999999987544
No 108
>PRK07758 hypothetical protein; Provisional
Probab=87.66 E-value=0.36 Score=39.62 Aligned_cols=45 Identities=13% Similarity=0.280 Sum_probs=38.6
Q ss_pred ccCcCHHHHHHHHHcCCCCHHHhhh--ccCchhhhHhcHHhHHhhhc
Q 015933 300 VWGIGPATAQKLYEKGHRTLDDLKN--EDSLTHSQRLGLKYFDDIKT 344 (398)
Q Consensus 300 I~GvGpktA~~l~~~GirtledL~~--~~~l~~~q~~Glk~~ed~~~ 344 (398)
.++++......|...||.|++||.. ...|..+.+||.+..+.|.+
T Consensus 39 ~~~LSvRA~N~Lk~AGI~TL~dLv~~te~ELl~iknlGkKSL~EIke 85 (95)
T PRK07758 39 LSLLSAPARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRK 85 (95)
T ss_pred CccccHHHHHHHHHcCCCcHHHHHcCCHHHHHHccCCCHHHHHHHHH
Confidence 4688999999999999999999984 34688899999999888764
No 109
>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=87.55 E-value=2.9 Score=38.51 Aligned_cols=24 Identities=17% Similarity=0.169 Sum_probs=20.1
Q ss_pred HHHHhhhccCcCHHHHHHHHHcCC
Q 015933 293 TISLFGEVWGIGPATAQKLYEKGH 316 (398)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~Gi 316 (398)
.++.|++++|||++||..+--.++
T Consensus 104 ~~~~L~~l~GIG~ktA~~ill~~~ 127 (191)
T TIGR01083 104 DREELVKLPGVGRKTANVVLNVAF 127 (191)
T ss_pred HHHHHHhCCCCcHHHHHHHHHHHc
Confidence 567888999999999998876554
No 110
>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=87.42 E-value=1.3 Score=36.68 Aligned_cols=39 Identities=23% Similarity=0.513 Sum_probs=30.1
Q ss_pred HHHHHHHHhhhcCCCeEEEEechhhcCCc-ccCCeeEEEecCCC
Q 015933 354 MERLLQKAGEEVLPEVIILCGGSYRRGKA-SCGDLDVVIMHPDR 396 (398)
Q Consensus 354 ~~~~v~~~~~~~~p~~~v~~~Gs~RRgke-~~gDvDiLit~~~~ 396 (398)
++.+++. ..|++.+.+-||++.|.- ..+|||+.|..++.
T Consensus 9 l~~~i~~----~~~~~~v~~fGS~~~g~~~~~SDiDl~i~~~~~ 48 (114)
T cd05402 9 LQELIKE----WFPGAKLYPFGSYVTGLGLPGSDIDLCLLGPNH 48 (114)
T ss_pred HHHHHHH----HCCCCEEEEecccccCCCCCCCCeeEEEEeCCC
Confidence 4555544 578999999999999853 46799999988763
No 111
>PRK03348 DNA polymerase IV; Provisional
Probab=87.41 E-value=0.55 Score=49.20 Aligned_cols=29 Identities=41% Similarity=0.728 Sum_probs=26.1
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhc
Q 015933 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (398)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~ 325 (398)
+..+||||++++++|.+.||+|+.||.+-
T Consensus 182 v~~L~GIG~~t~~~L~~lGI~TigDLa~l 210 (454)
T PRK03348 182 VRRLWGIGPVTEEKLHRLGIETIGDLAAL 210 (454)
T ss_pred ccccCCCCHHHHHHHHHcCCccHHHHhcC
Confidence 35789999999999999999999999854
No 112
>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=87.27 E-value=0.9 Score=41.63 Aligned_cols=49 Identities=14% Similarity=0.218 Sum_probs=30.2
Q ss_pred CCCHHHHHHHHHHHH------hCCchhhHHHHh---hchhHHHHHhhhccCcCHHHHHHHH
Q 015933 261 GIGKSMQDHIQEIVT------TGKLSKLEHFEK---DEKVRTISLFGEVWGIGPATAQKLY 312 (398)
Q Consensus 261 gIG~~ia~kI~Eil~------tG~~~~le~l~~---~~~~~~l~lf~~I~GvGpktA~~l~ 312 (398)
|.-..-|+.|.++.+ .|.+..+ .. -.....++.|+++||||||||.-..
T Consensus 75 Gfy~~KAk~Lk~~a~~iie~y~G~v~~L---~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL 132 (177)
T TIGR03252 75 RFPGSMAKRVQALAQYVVDTYDGDATAV---WTEGDPDGKELLRRLKALPGFGKQKAKIFL 132 (177)
T ss_pred CchHHHHHHHHHHHHHHHHHhCCChhhh---hcccCCCcHHHHHHHHcCCCCCHHHHHHHH
Confidence 455566666665544 2444433 32 1123356788899999999998654
No 113
>cd01703 PolY_Pol_iota DNA Polymerase iota. Pol iota, also called Rad30B, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol iota is thought to be one of the least efficient polymerases, particularly when opposite pyrimidines; it can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine, and prefers to insert guanosine instead of adenosine opposite thymidine. Pol iota is believed to use Hoogsteen rather than Watson-Crick base pairing, which may explain the varying efficiency for different template nucleotides.
Probab=87.20 E-value=0.61 Score=47.72 Aligned_cols=30 Identities=33% Similarity=0.431 Sum_probs=26.7
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhcc
Q 015933 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (398)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~~ 326 (398)
+..+||||++|+++|.+.||.|+.||.+..
T Consensus 174 v~~l~GiG~~~~~kL~~~GI~tigdl~~~~ 203 (379)
T cd01703 174 LRKIPGIGYKTAAKLEAHGISSVRDLQEFS 203 (379)
T ss_pred ccccCCcCHHHHHHHHHcCCCcHHHHHhCC
Confidence 458899999999999999999999997543
No 114
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=87.08 E-value=0.55 Score=29.00 Aligned_cols=20 Identities=30% Similarity=0.573 Sum_probs=17.2
Q ss_pred hhcCCCCCCHHHHHHHHHHH
Q 015933 255 QVKGLPGIGKSMQDHIQEIV 274 (398)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil 274 (398)
+|..|||||+++++.|.++.
T Consensus 2 ~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred hhhhCCCCCHHHHHHHHHhc
Confidence 57899999999999988744
No 115
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=86.74 E-value=1 Score=36.92 Aligned_cols=48 Identities=10% Similarity=0.252 Sum_probs=36.2
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCc
Q 015933 252 SADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGI 303 (398)
Q Consensus 252 s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~Gv 303 (398)
.+.+|..|||||+++++-...| -+..+++|+...|.....-++.+-|.
T Consensus 10 ~~~~L~~iP~IG~a~a~DL~~L----Gi~s~~~L~g~dP~~Ly~~lc~~~G~ 57 (93)
T PF11731_consen 10 GLSDLTDIPNIGKATAEDLRLL----GIRSPADLKGRDPEELYERLCALTGQ 57 (93)
T ss_pred HHHHHhcCCCccHHHHHHHHHc----CCCCHHHHhCCCHHHHHHHHHHHcCC
Confidence 3568999999999999877643 34667788887787777777666664
No 116
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=86.33 E-value=1.6 Score=43.00 Aligned_cols=65 Identities=18% Similarity=0.209 Sum_probs=40.4
Q ss_pred hhhcCCCCCCHHHHHHHH---HHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHh
Q 015933 254 DQVKGLPGIGKSMQDHIQ---EIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL 322 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~---Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL 322 (398)
++|..+ |++..=++-|. +.+..|.+..- ... ....+++.|++|+||||+||..+--.|+.-.|-+
T Consensus 167 ~eL~~~-Gl~~~Ra~~L~~lA~~i~~g~l~l~-~~~--~~~~~~~~L~~LpGIGpwTA~~vllr~lg~~D~f 234 (283)
T PRK10308 167 QALKAL-GMPLKRAEALIHLANAALEGTLPLT-IPG--DVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVF 234 (283)
T ss_pred HHHHHC-CCCHHHHHHHHHHHHHHHcCCCCcc-ccC--CHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCCCC
Confidence 456665 77764344333 34446777532 211 1234778888999999999998766566555443
No 117
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=86.09 E-value=3.3 Score=40.76 Aligned_cols=49 Identities=20% Similarity=0.237 Sum_probs=34.6
Q ss_pred HHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCC
Q 015933 268 DHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHR 317 (398)
Q Consensus 268 ~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~Gir 317 (398)
.-+.+.+..|.+.. ..+..-....+++.|++|+||||+||+.+--.|+.
T Consensus 172 ~~~A~~~~~g~~~~-~~l~~~~~e~a~e~L~~i~GIG~WTAe~~llf~lg 220 (285)
T COG0122 172 ISLARAAAEGELDL-SELKPLSDEEAIEELTALKGIGPWTAEMFLLFGLG 220 (285)
T ss_pred HHHHHHHHcCCccH-HHhccCCHHHHHHHHHcCCCcCHHHHHHHHHHcCC
Confidence 34556666786443 34444445679999999999999999988765444
No 118
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=86.09 E-value=1.3 Score=48.61 Aligned_cols=54 Identities=13% Similarity=0.182 Sum_probs=34.5
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCC
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGH 316 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~Gi 316 (398)
..|.+|||||+..+.++-. ++.-++.+++ .+++.+.+|+|||++.|+.+|...-
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 3567888888877666543 2233334432 2455667888888888888887633
No 119
>PRK01810 DNA polymerase IV; Validated
Probab=86.02 E-value=0.83 Score=46.90 Aligned_cols=29 Identities=45% Similarity=0.691 Sum_probs=25.9
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhc
Q 015933 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (398)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~ 325 (398)
+..+||||++++++|...||+|+.||...
T Consensus 181 v~~l~giG~~~~~~L~~~Gi~tigdL~~~ 209 (407)
T PRK01810 181 VGEMHGIGEKTAEKLKDIGIQTIGDLAKA 209 (407)
T ss_pred HhhcCCcCHHHHHHHHHcCCCcHHHHHhC
Confidence 34689999999999999999999999864
No 120
>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=85.96 E-value=0.62 Score=46.68 Aligned_cols=29 Identities=48% Similarity=0.792 Sum_probs=25.7
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhc
Q 015933 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (398)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~ 325 (398)
+..+||||+++.++|.+.||+|+.||.+-
T Consensus 178 l~~l~gig~~~~~~L~~~Gi~ti~dL~~~ 206 (344)
T cd01700 178 VGDVWGIGRRTAKKLNAMGIHTAGDLAQA 206 (344)
T ss_pred hhhcCccCHHHHHHHHHcCCCcHHHHhcC
Confidence 34679999999999999999999999853
No 121
>PRK02406 DNA polymerase IV; Validated
Probab=85.84 E-value=0.61 Score=46.71 Aligned_cols=29 Identities=34% Similarity=0.409 Sum_probs=25.9
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhc
Q 015933 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (398)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~ 325 (398)
+..+||||++++++|-..||+|+.||.+-
T Consensus 170 i~~l~giG~~~~~~L~~~Gi~ti~dl~~l 198 (343)
T PRK02406 170 VEKIPGVGKVTAEKLHALGIYTCADLQKY 198 (343)
T ss_pred cchhcCCCHHHHHHHHHcCCCcHHHHHhC
Confidence 35789999999999998999999999864
No 122
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=85.83 E-value=1.4 Score=47.92 Aligned_cols=52 Identities=23% Similarity=0.469 Sum_probs=38.6
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~ 314 (398)
..|.+|||||+..+.+|.+.. |++. .+... ..+.+.+|+|||+++|..+++.
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--GSLK---AIKEA----SVEELAKVPGISKKLAEAIYEA 594 (598)
T ss_pred hhHhhCCCcCHHHHHHHHHHc--CCHH---HHHhC----CHHHHhhcCCcCHHHHHHHHHH
Confidence 468999999999999877644 4444 44431 2345679999999999999873
No 123
>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=85.80 E-value=0.066 Score=44.61 Aligned_cols=25 Identities=44% Similarity=0.735 Sum_probs=19.8
Q ss_pred hccCcCHHHHHHHHHc-CCCCHHHhhhc
Q 015933 299 EVWGIGPATAQKLYEK-GHRTLDDLKNE 325 (398)
Q Consensus 299 ~I~GvGpktA~~l~~~-GirtledL~~~ 325 (398)
.|+|||||||.+|.++ | |||.+..+
T Consensus 22 GV~GIG~KtA~~LL~~yg--sle~i~~~ 47 (101)
T PF01367_consen 22 GVPGIGPKTAAKLLQEYG--SLENILAN 47 (101)
T ss_dssp --TTSTCHCCCCCHHHHT--SCHCCCCC
T ss_pred CCCCCCHHHHHHHHHHcC--CHHHHHHh
Confidence 7999999999999997 6 88888743
No 124
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=85.77 E-value=1.2 Score=48.84 Aligned_cols=51 Identities=29% Similarity=0.386 Sum_probs=38.3
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (398)
..|..|||||++.+.++.+- -|++ +.+.+. ..+.+.+|+|+|+++|+.+++
T Consensus 637 s~L~~IPGIGpkr~k~LL~~--FGSl---e~I~~A----S~eELa~V~Gig~k~Ae~I~~ 687 (694)
T PRK14666 637 GELQRVEGIGPATARLLWER--FGSL---QAMAAA----GEEGLAAVPGIGPARAAALHE 687 (694)
T ss_pred hHHhhCCCCCHHHHHHHHHH--hCCH---HHHHhc----CHHHHHhcCCcCHHHHHHHHH
Confidence 57899999999998887663 3444 444432 344567899999999999987
No 125
>PTZ00205 DNA polymerase kappa; Provisional
Probab=85.69 E-value=0.84 Score=49.00 Aligned_cols=29 Identities=34% Similarity=0.408 Sum_probs=26.0
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhc
Q 015933 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (398)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~ 325 (398)
+..|||||++++++|-..||.|+.||.+.
T Consensus 311 V~ki~GIG~~t~~~L~~~GI~TigDLa~~ 339 (571)
T PTZ00205 311 LRSVPGVGKVTEALLKGLGITTLSDIYNR 339 (571)
T ss_pred cceeCCcCHHHHHHHHHcCCCcHHHHhcC
Confidence 45899999999999999999999999753
No 126
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=85.69 E-value=0.56 Score=43.47 Aligned_cols=22 Identities=32% Similarity=0.520 Sum_probs=19.3
Q ss_pred HHHHHhhhccCcCHHHHHHHHH
Q 015933 292 RTISLFGEVWGIGPATAQKLYE 313 (398)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~ 313 (398)
+.++.|.++||||||+|++|--
T Consensus 9 ~LI~~l~kLPGvG~KsA~R~Af 30 (198)
T COG0353 9 KLIDALKKLPGVGPKSAQRLAF 30 (198)
T ss_pred HHHHHHhhCCCCChhHHHHHHH
Confidence 3688899999999999999863
No 127
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=85.28 E-value=1.2 Score=45.14 Aligned_cols=51 Identities=24% Similarity=0.365 Sum_probs=33.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (398)
.=|.+||+|++.+++.+-+ +-|+++ .+.+ ...+.|.+|.|||+++|+.+++
T Consensus 287 RiLs~IPrl~k~iAk~Ll~--~FGSL~---~Il~----As~eeL~~VeGIGe~rA~~I~e 337 (352)
T PRK13482 287 RLLSKIPRLPSAVIENLVE--HFGSLQ---GLLA----ASIEDLDEVEGIGEVRARAIRE 337 (352)
T ss_pred HHHhcCCCCCHHHHHHHHH--HcCCHH---HHHc----CCHHHHhhCCCcCHHHHHHHHH
Confidence 3478888888888777654 224443 3332 1345567888888888888554
No 128
>PRK08609 hypothetical protein; Provisional
Probab=85.12 E-value=1.2 Score=48.15 Aligned_cols=56 Identities=18% Similarity=0.219 Sum_probs=39.4
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 015933 252 SADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (398)
Q Consensus 252 s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (398)
.+.++.+|||||.+.+.++.+-+---++++|+....+ -+ +..++|+|+||.+.+-+
T Consensus 86 ~~~~l~~i~GiGpk~a~~l~~~lGi~tl~~L~~a~~~-----~~-~~~~~gfg~k~~~~il~ 141 (570)
T PRK08609 86 GLLPLLKLPGLGGKKIAKLYKELGVVDKESLKEACEN-----GK-VQALAGFGKKTEEKILE 141 (570)
T ss_pred HHHHHhcCCCCCHHHHHHHHHHhCCCCHHHHHHHHHh-----CC-hhhccCcchhHHHHHHH
Confidence 3557899999999999888766655555555543221 11 33889999999998843
No 129
>KOG3548 consensus DNA damage checkpoint protein RHP9/CRB2/53BP1 [Replication, recombination and repair]
Probab=84.74 E-value=0.97 Score=50.46 Aligned_cols=92 Identities=14% Similarity=0.058 Sum_probs=56.7
Q ss_pred CCCCCcEEEEccCCCCchHHHHHHHHHHhcCCEEEee-cCCCccEEEEcCCh--HH--------------------HHHH
Q 015933 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEK-LSKKVTHVLAMDLE--AL--------------------LQQV 73 (398)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~r~~~l~~li~~~Gg~V~~~-ls~~VTHVV~~~~~--~~--------------------l~~l 73 (398)
.+|.||++.|-... .....+++-+..|||.|.+. |..--+|=...... +. .+..
T Consensus 924 niFd~cvF~lTsa~---~sd~~~r~s~e~~gg~vle~gl~~~Fn~p~~g~~~~lr~Ln~~q~~ks~~qalLIsdth~Rt~ 1000 (1176)
T KOG3548|consen 924 NIFDGCVFMLTSAN---RSDSASRPSMEKHGGLVLEKGLMNLFNTPFKGGGIVLRQLNSFQERKSNYQALLISDTHYRTH 1000 (1176)
T ss_pred chhcceeEEEeccc---cchhhhhhhhhccCChhhhccccccccccccCCcchHHhhhHHhhhccccceeEeehhhhHHH
Confidence 78999999886432 22334555556699988765 33323443321110 00 1122
Q ss_pred HHHhhhccCccccccchHHHHHhcCCCCCccccccccC
Q 015933 74 SKQHLARFKGSVIRYQWLEDSLRLGEKVSEDLYRIKLD 111 (398)
Q Consensus 74 ~~~~~~~~~~~lV~~~Wl~es~k~g~lv~ee~y~l~~~ 111 (398)
++--.-+++..-|+..||.+|++.++.||-.+|+|.-.
T Consensus 1001 KYLeaLA~giPcVh~~fI~aC~e~nr~Vdy~~YLLpsG 1038 (1176)
T KOG3548|consen 1001 KYLEALARGIPCVHNTFIQACGEQNRCVDYTDYLLPSG 1038 (1176)
T ss_pred HHHHHHHcCCCcccHHHHHHHHhccccccchhhcccCc
Confidence 21111123678999999999999999999999998654
No 130
>PRK09482 flap endonuclease-like protein; Provisional
Probab=84.68 E-value=0.69 Score=44.86 Aligned_cols=25 Identities=32% Similarity=0.613 Sum_probs=21.9
Q ss_pred hccCcCHHHHHHHHHc-CCCCHHHhhhc
Q 015933 299 EVWGIGPATAQKLYEK-GHRTLDDLKNE 325 (398)
Q Consensus 299 ~I~GvGpktA~~l~~~-GirtledL~~~ 325 (398)
.|+|||||||.+|.++ | |+|.+.+.
T Consensus 186 GVpGIG~KtA~~LL~~~g--sle~i~~~ 211 (256)
T PRK09482 186 GVAGIGPKSAAELLNQFR--SLENIYES 211 (256)
T ss_pred CCCCcChHHHHHHHHHhC--CHHHHHHh
Confidence 5799999999999997 6 99998754
No 131
>smart00475 53EXOc 5'-3' exonuclease.
Probab=84.66 E-value=0.7 Score=44.86 Aligned_cols=25 Identities=40% Similarity=0.636 Sum_probs=21.8
Q ss_pred hccCcCHHHHHHHHHc-CCCCHHHhhhc
Q 015933 299 EVWGIGPATAQKLYEK-GHRTLDDLKNE 325 (398)
Q Consensus 299 ~I~GvGpktA~~l~~~-GirtledL~~~ 325 (398)
.|+|||||||.+|.++ | |+|.+.+.
T Consensus 190 GV~GIG~KtA~~Ll~~yg--sle~i~~~ 215 (259)
T smart00475 190 GVPGIGEKTAAKLLKEFG--SLENILEN 215 (259)
T ss_pred CCCCCCHHHHHHHHHHhC--CHHHHHHH
Confidence 6799999999999986 6 99998753
No 132
>PRK03103 DNA polymerase IV; Reviewed
Probab=84.50 E-value=1.1 Score=46.04 Aligned_cols=29 Identities=28% Similarity=0.534 Sum_probs=25.7
Q ss_pred hhccCcCHHHHHHHHHcCCCCHHHhhhcc
Q 015933 298 GEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (398)
Q Consensus 298 ~~I~GvGpktA~~l~~~GirtledL~~~~ 326 (398)
..+||||++++++|.+.||+|+.||.+-.
T Consensus 184 ~~l~gig~~~~~~L~~~Gi~tigdl~~~~ 212 (409)
T PRK03103 184 RKLFGVGSRMEKHLRRMGIRTIGQLANTP 212 (409)
T ss_pred hhcCCccHHHHHHHHHcCCCCHHHHhcCC
Confidence 46799999999999999999999998543
No 133
>PRK02794 DNA polymerase IV; Provisional
Probab=84.49 E-value=0.73 Score=47.62 Aligned_cols=29 Identities=48% Similarity=0.950 Sum_probs=26.2
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhc
Q 015933 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (398)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~ 325 (398)
+..+||||++++++|.+.||+|+.||.+-
T Consensus 211 l~~L~GiG~~~~~~L~~~GI~tigdL~~l 239 (419)
T PRK02794 211 VGIIWGVGPATAARLARDGIRTIGDLQRA 239 (419)
T ss_pred hhhhCCCCHHHHHHHHHhccchHHHHhhC
Confidence 45889999999999999999999999854
No 134
>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=84.41 E-value=0.84 Score=45.76 Aligned_cols=29 Identities=31% Similarity=0.452 Sum_probs=26.0
Q ss_pred hhccCcCHHHHHHHHHcCCCCHHHhhhcc
Q 015933 298 GEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (398)
Q Consensus 298 ~~I~GvGpktA~~l~~~GirtledL~~~~ 326 (398)
..+||||++++++|.+.||+|+.||.+-.
T Consensus 176 ~~l~giG~~~~~~L~~~Gi~ti~dl~~~~ 204 (343)
T cd00424 176 TDLPGIGAVTAKRLEAVGINPIGDLLAAS 204 (343)
T ss_pred hhcCCCCHHHHHHHHHcCCCcHHHHhcCC
Confidence 46899999999999999999999998644
No 135
>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=84.00 E-value=1.2 Score=45.24 Aligned_cols=29 Identities=17% Similarity=0.307 Sum_probs=24.5
Q ss_pred hhhccCcCHHHHHHHHH-cCCCCHHHhhhc
Q 015933 297 FGEVWGIGPATAQKLYE-KGHRTLDDLKNE 325 (398)
Q Consensus 297 f~~I~GvGpktA~~l~~-~GirtledL~~~ 325 (398)
+..+||||+++++++.+ .||+|+.||.+-
T Consensus 184 v~~l~GiG~~~~~~ll~~~Gi~ti~dl~~~ 213 (359)
T cd01702 184 ITSIRGLGGKLGEEIIDLLGLPTEGDVAGF 213 (359)
T ss_pred HHHhCCcCHHHHHHHHHHcCCcCHHHHHhc
Confidence 35789999999988765 699999999864
No 136
>PRK14976 5'-3' exonuclease; Provisional
Probab=83.97 E-value=0.76 Score=45.16 Aligned_cols=26 Identities=38% Similarity=0.581 Sum_probs=21.7
Q ss_pred hccCcCHHHHHHHHHcCCCCHHHhhhc
Q 015933 299 EVWGIGPATAQKLYEKGHRTLDDLKNE 325 (398)
Q Consensus 299 ~I~GvGpktA~~l~~~GirtledL~~~ 325 (398)
.|+|||||||.+|.++ +-|+|++.+.
T Consensus 195 GVpGIG~KtA~~LL~~-~gsle~i~~~ 220 (281)
T PRK14976 195 GVKGIGPKTAIKLLNK-YGNIENIYEN 220 (281)
T ss_pred CCCcccHHHHHHHHHH-cCCHHHHHHh
Confidence 5899999999999985 3399998753
No 137
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=83.51 E-value=4.5 Score=40.32 Aligned_cols=73 Identities=15% Similarity=0.211 Sum_probs=50.8
Q ss_pred CCCCCcEEEEccCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccchHHH
Q 015933 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLED 93 (398)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~r~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~~~~~l~~l~~~~~~~~~~~lV~~~Wl~e 93 (398)
.+|.|.+|.|-+. +.. .+.-+++++..+||.|.++++.+++.||+.+....-. +..++...+..|++-+=+.+
T Consensus 231 ~l~~g~~~v~TG~-l~~-~R~e~~~~~~~~G~~v~~sVs~~t~~lv~g~~~~~ss--K~~kA~~~gi~ii~e~~f~~ 303 (313)
T PRK06063 231 PLVQGMRVALSAE-VSR-THEELVERILHAGLAYSDSVDRDTSLVVCNDPAPEQG--KGYHARQLGVPVLDEAAFLE 303 (313)
T ss_pred cccCCCEEEEecC-CCC-CHHHHHHHHHHcCCEecCccccCccEEEECCCCCccc--HHHHHHHcCCccccHHHHHH
Confidence 4689999999875 333 4567999999999999999999999999975432100 11223344666766554443
No 138
>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=82.54 E-value=0.98 Score=43.22 Aligned_cols=26 Identities=35% Similarity=0.460 Sum_probs=22.3
Q ss_pred hccCcCHHHHHHHHHcCCCCHHHhhhc
Q 015933 299 EVWGIGPATAQKLYEKGHRTLDDLKNE 325 (398)
Q Consensus 299 ~I~GvGpktA~~l~~~GirtledL~~~ 325 (398)
.|+|||||||.+|.++ +.|+|++.+.
T Consensus 187 Gv~GiG~ktA~~Ll~~-~gsle~i~~~ 212 (240)
T cd00008 187 GVPGIGEKTAAKLLKE-YGSLEGILEN 212 (240)
T ss_pred CCCccCHHHHHHHHHH-hCCHHHHHHh
Confidence 5899999999999986 4499999864
No 139
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=82.44 E-value=0.88 Score=40.14 Aligned_cols=27 Identities=15% Similarity=0.004 Sum_probs=22.8
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHcCCC
Q 015933 291 VRTISLFGEVWGIGPATAQKLYEKGHR 317 (398)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~Gir 317 (398)
....+.|++++||||+||..+--.++.
T Consensus 79 ~~~~~~L~~l~GIG~~tA~~~l~~~~~ 105 (158)
T cd00056 79 PDAREELLALPGVGRKTANVVLLFALG 105 (158)
T ss_pred cccHHHHHcCCCCCHHHHHHHHHHHCC
Confidence 457888889999999999998876665
No 140
>TIGR03671 cca_archaeal CCA-adding enzyme.
Probab=82.10 E-value=2.7 Score=43.41 Aligned_cols=44 Identities=27% Similarity=0.410 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHhhhcCCCeEEEEechhhcCCccc--CCeeEEEecC
Q 015933 351 VEQMERLLQKAGEEVLPEVIILCGGSYRRGKASC--GDLDVVIMHP 394 (398)
Q Consensus 351 a~~~~~~v~~~~~~~~p~~~v~~~Gs~RRgke~~--gDvDiLit~~ 394 (398)
+..+...+++...+..+.+.|.+.|||.||.-.. .||||+|..|
T Consensus 23 ~~~l~~~l~~~~~e~~~~~~v~~~GS~ArgT~L~G~sDIDIfi~f~ 68 (408)
T TIGR03671 23 ADELIARLEEIIEELGVDAEVVLVGSYARGTWLKGDRDIDIFILFP 68 (408)
T ss_pred HHHHHHHHHHHHHhcCCcceEEEEeeEecCCccCCCCceeEEEEeC
Confidence 3334455555555555668999999999999886 5899988665
No 141
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=82.09 E-value=0.81 Score=49.35 Aligned_cols=47 Identities=21% Similarity=0.372 Sum_probs=35.3
Q ss_pred HhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhHhcHHhHHhhh
Q 015933 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIK 343 (398)
Q Consensus 296 lf~~I~GvGpktA~~l~~~GirtledL~~~~--~l~~~q~~Glk~~ed~~ 343 (398)
.|.+|+||||++.++|++ -|.|+++++++. .|....+++.+..+.|.
T Consensus 515 ~L~~I~GiG~kr~~~LL~-~Fgs~~~I~~As~eeL~~v~gi~~~~A~~I~ 563 (574)
T PRK14670 515 NYTKIKGIGEKKAKKILK-SLGTYKDILLLNEDEIAEKMKINIKMAKKIK 563 (574)
T ss_pred ccccCCCCCHHHHHHHHH-HhCCHHHHHhCCHHHHHhCCCCCHHHHHHHH
Confidence 555999999999999999 677999998763 45556566655555554
No 142
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=81.91 E-value=3.5 Score=45.37 Aligned_cols=73 Identities=12% Similarity=0.130 Sum_probs=54.4
Q ss_pred CCCCCCcEEEEccCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccchHHH
Q 015933 16 NGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLED 93 (398)
Q Consensus 16 ~~~F~g~~iy~~~~~~g~~r~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~~~~~l~~l~~~~~~~~~~~lV~~~Wl~e 93 (398)
+.+|.|.+|.|-++-.+. .|..+++++.++||.|.+++|.+++.+|+.++... +..++...++.|++-+.+.+
T Consensus 591 ~~~l~gktfV~TG~l~~~-~R~e~~~lie~~Ggkv~ssVSkktd~LV~G~~aGs----Kl~KA~~LGI~Ii~e~~f~~ 663 (669)
T PRK14350 591 NSFLFGKKFCITGSFNGY-SRSVLIDKLTKKGAIFNTCVTKYLDFLLVGEKAGL----KLKKANNLGIKIMSLFDIKS 663 (669)
T ss_pred CCccCCcEEEEecccCCC-CHHHHHHHHHHcCCEEeccccCCCcEEEECCCCCc----hHHHHHHcCCEEecHHHHHH
Confidence 457999999998753333 45679999999999999999999999999754321 12234455788888777655
No 143
>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=81.65 E-value=1.6 Score=43.26 Aligned_cols=27 Identities=33% Similarity=0.380 Sum_probs=24.8
Q ss_pred hccCcCHHHHHHHHHcCCCCHHHhhhc
Q 015933 299 EVWGIGPATAQKLYEKGHRTLDDLKNE 325 (398)
Q Consensus 299 ~I~GvGpktA~~l~~~GirtledL~~~ 325 (398)
.+||||++++.+|.+.||+|+.||.+-
T Consensus 174 ~~~gig~~~~~~L~~~Gi~t~~dl~~~ 200 (335)
T cd03468 174 AALRLPPETVELLARLGLRTLGDLAAL 200 (335)
T ss_pred hHhCCCHHHHHHHHHhCcccHHHHHhC
Confidence 578999999999999999999999864
No 144
>PRK10702 endonuclease III; Provisional
Probab=81.59 E-value=3.4 Score=38.92 Aligned_cols=43 Identities=12% Similarity=0.281 Sum_probs=31.4
Q ss_pred hHHHHHHHHHHHh-cCCcccc-chhhhcCCCCCCHHHHHHHHHHH
Q 015933 232 RSFSYYKAIPVIE-KLPFKIE-SADQVKGLPGIGKSMQDHIQEIV 274 (398)
Q Consensus 232 r~~aY~rAa~~l~-~l~~~i~-s~~~l~~lpgIG~~ia~kI~Eil 274 (398)
|+....+++..|. .+...+. +.++|..|||||.++|+.|.=+.
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 6666777777764 3344443 45789999999999999987544
No 145
>PRK10702 endonuclease III; Provisional
Probab=81.47 E-value=5.6 Score=37.41 Aligned_cols=25 Identities=16% Similarity=0.242 Sum_probs=20.0
Q ss_pred HHHHHhhhccCcCHHHHHHHHHcCC
Q 015933 292 RTISLFGEVWGIGPATAQKLYEKGH 316 (398)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~~Gi 316 (398)
..++.|+++||||+|||.-+---++
T Consensus 106 ~~~~~Ll~lpGVG~ktA~~ill~a~ 130 (211)
T PRK10702 106 EDRAALEALPGVGRKTANVVLNTAF 130 (211)
T ss_pred chHHHHhcCCcccHHHHHHHHHHHc
Confidence 4677888999999999998765444
No 146
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=81.15 E-value=1.1 Score=48.44 Aligned_cols=47 Identities=21% Similarity=0.401 Sum_probs=34.9
Q ss_pred HHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhHhcHHhHHhhh
Q 015933 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIK 343 (398)
Q Consensus 295 ~lf~~I~GvGpktA~~l~~~GirtledL~~~~--~l~~~q~~Glk~~ed~~ 343 (398)
..|.+|+||||++.++|++ -|.|++.++++. .|... ++|.+..+.|.
T Consensus 514 S~Ld~I~GiG~kr~~~Ll~-~Fgs~~~ik~As~eeL~~v-gi~~~~A~~I~ 562 (567)
T PRK14667 514 DILDKIKGIGEVKKEIIYR-NFKTLYDFLKADDEELKKL-GIPPSVKQEVK 562 (567)
T ss_pred CccccCCCCCHHHHHHHHH-HhCCHHHHHhCCHHHHHHc-CCCHHHHHHHH
Confidence 4456999999999999999 677899998653 35555 66666655554
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=80.96 E-value=1.3 Score=41.25 Aligned_cols=21 Identities=38% Similarity=0.602 Sum_probs=18.4
Q ss_pred HHHHHhhhccCcCHHHHHHHH
Q 015933 292 RTISLFGEVWGIGPATAQKLY 312 (398)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~ 312 (398)
..++.|.++||||+|+|+++-
T Consensus 8 ~Li~~l~~LPGIG~KsA~RlA 28 (195)
T TIGR00615 8 KLIESLKKLPGIGPKSAQRLA 28 (195)
T ss_pred HHHHHHHHCCCCCHHHHHHHH
Confidence 367889999999999999984
No 148
>PRK00076 recR recombination protein RecR; Reviewed
Probab=80.92 E-value=1.3 Score=41.31 Aligned_cols=22 Identities=36% Similarity=0.531 Sum_probs=19.0
Q ss_pred HHHHHhhhccCcCHHHHHHHHH
Q 015933 292 RTISLFGEVWGIGPATAQKLYE 313 (398)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~ 313 (398)
..++.|.++||||+|+|+++--
T Consensus 8 ~Li~~l~~LPGIG~KsA~Rla~ 29 (196)
T PRK00076 8 KLIEALRKLPGIGPKSAQRLAF 29 (196)
T ss_pred HHHHHHHHCCCCCHHHHHHHHH
Confidence 3678899999999999999863
No 149
>COG0389 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]
Probab=80.49 E-value=1.6 Score=44.13 Aligned_cols=28 Identities=43% Similarity=0.697 Sum_probs=25.9
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhh
Q 015933 297 FGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (398)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~ 324 (398)
+..+||||+.|+.+|...||.|+-||.+
T Consensus 178 v~~~~GvG~~~~~~l~~~Gi~ti~dl~~ 205 (354)
T COG0389 178 VLEFWGVGKVTAEKLRRLGISTIGDLAE 205 (354)
T ss_pred hhhhCCCCHHHHHHHHHcCChhHHHHHh
Confidence 3489999999999999999999999986
No 150
>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=80.36 E-value=3.7 Score=40.27 Aligned_cols=78 Identities=14% Similarity=0.260 Sum_probs=46.6
Q ss_pred HHHHHHHHcCCChhHHHHHHHHHHHhcC-Cccc-cchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHH
Q 015933 219 KLINIYRALGEDRRSFSYYKAIPVIEKL-PFKI-ESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISL 296 (398)
Q Consensus 219 ~la~~~e~~g~~~r~~aY~rAa~~l~~l-~~~i-~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~l 296 (398)
+|.++.+-.|--.|+..-.++|..|..- ...+ .+.++|.+|||||..+|+.|.-|. -|...-+ ....+.+.
T Consensus 68 eL~~~~~~lG~y~RAr~L~~~A~~i~~~~~g~~p~~~~~L~~LpGIG~~TA~~Il~~a-~~~~~~~------vD~~v~RV 140 (275)
T TIGR01084 68 EVLKLWEGLGYYARARNLHKAAQEVVEEFGGEFPQDFEDLAALPGVGRYTAGAILSFA-LNKPYPI------LDGNVKRV 140 (275)
T ss_pred HHHHHHHHCCcHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCCCHHHHHHHHHHH-CCCCCCc------chHhHHHH
Confidence 3444434334333777778888877541 1111 346789999999999999988554 3432211 22346666
Q ss_pred hhhccCc
Q 015933 297 FGEVWGI 303 (398)
Q Consensus 297 f~~I~Gv 303 (398)
+.+++|+
T Consensus 141 l~Rl~~~ 147 (275)
T TIGR01084 141 LSRLFAV 147 (275)
T ss_pred HHHHccC
Confidence 6666665
No 151
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=80.01 E-value=1.8 Score=37.08 Aligned_cols=25 Identities=44% Similarity=0.562 Sum_probs=23.0
Q ss_pred cCcCHHHHHHHHHcCCCCHHHhhhc
Q 015933 301 WGIGPATAQKLYEKGHRTLDDLKNE 325 (398)
Q Consensus 301 ~GvGpktA~~l~~~GirtledL~~~ 325 (398)
||+|++++.+|-+.||.|.+||.+.
T Consensus 1 pgi~~~~~~~L~~~GI~t~~~Ll~~ 25 (122)
T PF14229_consen 1 PGIGPKEAAKLKAAGIKTTGDLLEA 25 (122)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHHc
Confidence 7999999999988899999999854
No 152
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=79.90 E-value=2.3 Score=40.01 Aligned_cols=53 Identities=19% Similarity=0.253 Sum_probs=33.5
Q ss_pred CCHHHHHHHHHHHHh-CCchhhHHHH--hhchhHHHHHhh-hccCcCHHHHHHHHH-cCCC
Q 015933 262 IGKSMQDHIQEIVTT-GKLSKLEHFE--KDEKVRTISLFG-EVWGIGPATAQKLYE-KGHR 317 (398)
Q Consensus 262 IG~~ia~kI~Eil~t-G~~~~le~l~--~~~~~~~l~lf~-~I~GvGpktA~~l~~-~Gir 317 (398)
+-..=|+.|.++... |.+ +.+. ........+.|. ++||||+|||.-+-. .|++
T Consensus 85 f~~~KAk~I~~~~~~~~~l---~~~~~~~~~~~~~R~~Ll~~lpGIG~KTAd~vL~~~~~~ 142 (208)
T PRK01229 85 FYNKRAEYIVEARKLYGKL---KEIIKADKDQFEAREFLVKNIKGIGYKEASHFLRNVGYE 142 (208)
T ss_pred cHHHHHHHHHHHHHHHHHH---HHHHhccCCchHHHHHHHHcCCCCcHHHHHHHHHHccCC
Confidence 335555556555543 332 2222 223356888888 999999999999873 4663
No 153
>PRK13844 recombination protein RecR; Provisional
Probab=79.57 E-value=1.5 Score=40.92 Aligned_cols=21 Identities=24% Similarity=0.300 Sum_probs=18.6
Q ss_pred HHHHHhhhccCcCHHHHHHHH
Q 015933 292 RTISLFGEVWGIGPATAQKLY 312 (398)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~ 312 (398)
..++.|.++||||+|+|+++-
T Consensus 12 ~LI~~l~~LPGIG~KsA~Rla 32 (200)
T PRK13844 12 AVIESLRKLPTIGKKSSQRLA 32 (200)
T ss_pred HHHHHHHHCCCCCHHHHHHHH
Confidence 367889999999999999986
No 154
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=79.50 E-value=4.6 Score=40.07 Aligned_cols=48 Identities=17% Similarity=0.137 Sum_probs=40.0
Q ss_pred CCCCCcEEEEccCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcC
Q 015933 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMD 65 (398)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~r~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~ 65 (398)
..|.|.+|.|-+. +..-.+..+++++..+||.|.++++.++|.+|+.+
T Consensus 219 ~~l~g~~~vfTG~-l~~~~R~~~~~~~~~~Gg~v~~sVs~~t~~lV~G~ 266 (309)
T PRK06195 219 TAFKEEVVVFTGG-LASMTRDEAMILVRRLGGTVGSSVTKKTTYLVTNT 266 (309)
T ss_pred ccccCCEEEEccc-cCCCCHHHHHHHHHHhCCEecCCcccCceEEEECC
Confidence 5799999999875 32223567899999999999999999999999864
No 155
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=79.50 E-value=1.6 Score=43.31 Aligned_cols=54 Identities=28% Similarity=0.418 Sum_probs=40.7
Q ss_pred hhHHHHHhhhccCcCHHHHHHHHH---cCC-CCHHHhhhccC------chhhhHhcHHhHHhhh
Q 015933 290 KVRTISLFGEVWGIGPATAQKLYE---KGH-RTLDDLKNEDS------LTHSQRLGLKYFDDIK 343 (398)
Q Consensus 290 ~~~~l~lf~~I~GvGpktA~~l~~---~Gi-rtledL~~~~~------l~~~q~~Glk~~ed~~ 343 (398)
++.+++....+||||||.|++|-+ .|. +-+++++++.+ ++..-|+|.++.+.|.
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 445788889999999999999986 265 78888886431 5567777777777664
No 156
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=79.43 E-value=1.9 Score=47.08 Aligned_cols=48 Identities=25% Similarity=0.340 Sum_probs=35.0
Q ss_pred HHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhHhcHHhHHhhh
Q 015933 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIK 343 (398)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~GirtledL~~~~--~l~~~q~~Glk~~ed~~ 343 (398)
....|..|+||||++|+.|++ .+.|+++|.++. .|+.. +|.+..+.|.
T Consensus 567 ~~s~L~~I~GIG~k~a~~Ll~-~Fgs~~~i~~As~eeL~~v--ig~k~A~~I~ 616 (621)
T PRK14671 567 LQTELTDIAGIGEKTAEKLLE-HFGSVEKVAKASLEELAAV--AGPKTAETIY 616 (621)
T ss_pred hhhhhhcCCCcCHHHHHHHHH-HcCCHHHHHhCCHHHHHHH--hCHHHHHHHH
Confidence 445667999999999999998 555999998653 24443 6766666554
No 157
>COG1708 Predicted nucleotidyltransferases [General function prediction only]
Probab=79.09 E-value=5.1 Score=33.13 Aligned_cols=26 Identities=31% Similarity=0.603 Sum_probs=22.5
Q ss_pred CeEEEEechhhcCCccc-CCeeEEEec
Q 015933 368 EVIILCGGSYRRGKASC-GDLDVVIMH 393 (398)
Q Consensus 368 ~~~v~~~Gs~RRgke~~-gDvDiLit~ 393 (398)
...|.+-|||=||..+- +|||++|..
T Consensus 26 ~~~v~LfGS~arG~~~~~SDiDv~vv~ 52 (128)
T COG1708 26 DLLIYLFGSYARGDFVKESDIDLLVVS 52 (128)
T ss_pred CeEEEEEccCcccccccCCCeeEEEEc
Confidence 34799999999999876 899999975
No 158
>PRK10880 adenine DNA glycosylase; Provisional
Probab=79.02 E-value=3.8 Score=41.59 Aligned_cols=65 Identities=20% Similarity=0.289 Sum_probs=42.9
Q ss_pred hHHHHHHHHHHHh-cCCccc-cchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCc
Q 015933 232 RSFSYYKAIPVIE-KLPFKI-ESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGI 303 (398)
Q Consensus 232 r~~aY~rAa~~l~-~l~~~i-~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~Gv 303 (398)
|++...++|..|. .+...+ .+.++|..|||||..+|+.|.-|.- |...-+ ...-+.+.|.+++|+
T Consensus 85 RAr~L~~~A~~i~~~~~g~~p~~~~~L~~LpGIG~~TA~aIl~~af-~~~~~i------VD~nV~RV~~Rl~~i 151 (350)
T PRK10880 85 RARNLHKAAQQVATLHGGEFPETFEEVAALPGVGRSTAGAILSLSL-GKHFPI------LDGNVKRVLARCYAV 151 (350)
T ss_pred HHHHHHHHHHHHHHHhCCCchhhHHHHhcCCCccHHHHHHHHHHHC-CCCeec------ccHHHHHHHHHHhcc
Confidence 8888888888883 333322 3468899999999999999986653 331111 123356666666655
No 159
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=78.78 E-value=1.2 Score=48.40 Aligned_cols=47 Identities=23% Similarity=0.334 Sum_probs=32.4
Q ss_pred HHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhHhcHHhHHhhhc
Q 015933 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIKT 344 (398)
Q Consensus 295 ~lf~~I~GvGpktA~~l~~~GirtledL~~~~--~l~~~q~~Glk~~ed~~~ 344 (398)
..|.+|+||||+++++|++ -|.|+++++++. .|... +|.+..+.|..
T Consensus 552 S~L~~IpGIG~kr~~~LL~-~FgSi~~I~~As~eeL~~v--i~~k~A~~I~~ 600 (624)
T PRK14669 552 SELLEIPGVGAKTVQRLLK-HFGSLERVRAATETQLAAV--VGRAAAEAIIA 600 (624)
T ss_pred HHHhcCCCCCHHHHHHHHH-HcCCHHHHHhCCHHHHHHH--hCHHHHHHHHH
Confidence 4566999999999999999 577888888653 23322 45555444443
No 160
>KOG3524 consensus Predicted guanine nucleotide exchange factor (PEBBLE) [Signal transduction mechanisms]
Probab=78.66 E-value=2.1 Score=46.50 Aligned_cols=79 Identities=14% Similarity=0.236 Sum_probs=57.2
Q ss_pred CCCCCCCcEEEEccCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccchHHHH
Q 015933 15 SNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDS 94 (398)
Q Consensus 15 ~~~~F~g~~iy~~~~~~g~~r~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~~~~~l~~l~~~~~~~~~~~lV~~~Wl~es 94 (398)
....|++++.||-+ +-..-. -|-+++..+||.|--+...++||.|+-...... +. ...-...++.+.||.+|
T Consensus 115 y~~~m~~vvlcfTg--~rkk~e-~lv~lvh~mgg~irkd~nsktthli~n~s~gek--~~---~a~t~~~~~rp~wv~~a 186 (850)
T KOG3524|consen 115 YCELMKDVVMCFTG--ERKKKE-ELVDLVHYMGGSIRKDTNSKTTHLIANKVEGEK--QS---IALVGVPTMRPDWVTEA 186 (850)
T ss_pred cchhhcCceeeeec--cchhhH-HHHHHHHHhcceeEeeeccCceEEEeecccceE--EE---EEeeccceechHhhhhh
Confidence 34679999999963 433222 677899999999999999999999986654321 11 11113688999999999
Q ss_pred HhcCCCC
Q 015933 95 LRLGEKV 101 (398)
Q Consensus 95 ~k~g~lv 101 (398)
|+...-.
T Consensus 187 w~~rn~~ 193 (850)
T KOG3524|consen 187 WKHRNDS 193 (850)
T ss_pred hcCcchh
Confidence 9986554
No 161
>cd03586 PolY_Pol_IV_kappa DNA Polymerase IV/Kappa. Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Known primarily as Pol IV in prokaryotes and Pol kappa in eukaryotes, this polymerase has a propensity for generating frameshift mutations. The eukaryotic Pol kappa differs from Pol IV and Dpo4 by an N-terminal extension of ~75 residues known as the "N-clasp" region. The structure of Pol kappa shows DNA that is almost totally encircled by Pol kappa, with the N-clasp region augmenting the interactions between DNA and the polymerase. Pol kappa is more resistant than Pol eta and Pol iota to bulky guanine adducts and is efficient at catalyzing the incorporation of dCTP. Bacterial pol IV has a
Probab=78.47 E-value=1.8 Score=42.97 Aligned_cols=28 Identities=39% Similarity=0.550 Sum_probs=25.3
Q ss_pred hhccCcCHHHHHHHHHcCCCCHHHhhhc
Q 015933 298 GEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (398)
Q Consensus 298 ~~I~GvGpktA~~l~~~GirtledL~~~ 325 (398)
..+||||.+++++|...||+|+.||.+.
T Consensus 174 ~~l~gig~~~~~~L~~~Gi~ti~dl~~~ 201 (334)
T cd03586 174 RKIPGVGKVTAEKLKELGIKTIGDLAKL 201 (334)
T ss_pred hhhCCcCHHHHHHHHHcCCcCHHHHHcC
Confidence 4779999999999999999999999854
No 162
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=78.07 E-value=5 Score=34.94 Aligned_cols=26 Identities=15% Similarity=0.095 Sum_probs=20.4
Q ss_pred HHHHhhhccCcCHHHHHHHHHcCCCC
Q 015933 293 TISLFGEVWGIGPATAQKLYEKGHRT 318 (398)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~Girt 318 (398)
.++.|++++||||+||..+--.|+.-
T Consensus 70 ~~~~L~~l~GIG~~tA~~~l~~~~~~ 95 (149)
T smart00478 70 DREELLKLPGVGRKTANAVLSFALGK 95 (149)
T ss_pred HHHHHHcCCCCcHHHHHHHHHHHCCC
Confidence 56667799999999999887665543
No 163
>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=77.94 E-value=5.8 Score=34.19 Aligned_cols=28 Identities=39% Similarity=0.673 Sum_probs=22.3
Q ss_pred CeEEEEechhhcCCccc--CCeeEEEecCC
Q 015933 368 EVIILCGGSYRRGKASC--GDLDVVIMHPD 395 (398)
Q Consensus 368 ~~~v~~~Gs~RRgke~~--gDvDiLit~~~ 395 (398)
...+.+.|||.||...- .|||++|..+.
T Consensus 27 ~~~~~~~GS~a~~T~i~~~sDiD~~v~~~~ 56 (143)
T cd05400 27 VAEVFLQGSYARGTALRGDSDIDLVVVLPD 56 (143)
T ss_pred ccEEEEEcceeCCCCCCCCCceeEEEEEcC
Confidence 34789999999998654 89999996543
No 164
>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=77.94 E-value=5.4 Score=31.07 Aligned_cols=27 Identities=33% Similarity=0.567 Sum_probs=22.5
Q ss_pred EEEEechhhcCCcc-cCCeeEEEecCCC
Q 015933 370 IILCGGSYRRGKAS-CGDLDVVIMHPDR 396 (398)
Q Consensus 370 ~v~~~Gs~RRgke~-~gDvDiLit~~~~ 396 (398)
.+.+-||+=||..+ ..||||+|..++.
T Consensus 20 ~i~LfGS~arg~~~~~SDiDl~vi~~~~ 47 (93)
T cd05403 20 KVYLFGSYARGDARPDSDIDLLVIFDDP 47 (93)
T ss_pred EEEEEeeeecCCCCCCCCeeEEEEeCCC
Confidence 68899999999975 7899999866543
No 165
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=77.93 E-value=1.6 Score=43.22 Aligned_cols=25 Identities=48% Similarity=0.740 Sum_probs=21.9
Q ss_pred hccCcCHHHHHHHHHc-CCCCHHHhhhc
Q 015933 299 EVWGIGPATAQKLYEK-GHRTLDDLKNE 325 (398)
Q Consensus 299 ~I~GvGpktA~~l~~~-GirtledL~~~ 325 (398)
.|+|||||||.+|.++ | |++.|.+.
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 4999999999999998 8 88888753
No 166
>KOG3524 consensus Predicted guanine nucleotide exchange factor (PEBBLE) [Signal transduction mechanisms]
Probab=77.44 E-value=1.4 Score=47.83 Aligned_cols=86 Identities=19% Similarity=0.337 Sum_probs=64.1
Q ss_pred CCCCCcEEEEccCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccchHHHHHh
Q 015933 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSLR 96 (398)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~r~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~~~~~l~~l~~~~~~~~~~~lV~~~Wl~es~k 96 (398)
..|.||.++|. |+...-.+++-.-+.-.||..+. -...+||||+.+......-+ ..+..-++|+-+|+-=++.
T Consensus 209 ~~feg~~~~f~--gF~~ee~~~m~~sle~~gg~~a~-~d~~cthvvv~e~~~~~~p~----~~s~~~~~vk~ewfw~siq 281 (850)
T KOG3524|consen 209 GVFEGLSLFFH--GFKQEEIDDMLRSLENTGGKLAP-SDTLCTHVVVNEDNDEVEPL----AVSSNQVHVKKEWFWVSIQ 281 (850)
T ss_pred ccccCCeEeec--CCcHHHHHHHHHHHHhcCCcccC-CCCCceeEeecCCccccccc----cccccceeecccceEEEEe
Confidence 57999999997 57777778888999999999988 56789999997754321111 1122457888899888888
Q ss_pred cCCCCCccccccc
Q 015933 97 LGEKVSEDLYRIK 109 (398)
Q Consensus 97 ~g~lv~ee~y~l~ 109 (398)
.|..--|+.|...
T Consensus 282 ~g~~a~e~~yl~~ 294 (850)
T KOG3524|consen 282 RGCCAIEDNYLLP 294 (850)
T ss_pred cchhccccceecc
Confidence 8877777777664
No 167
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=76.96 E-value=1.4 Score=48.15 Aligned_cols=58 Identities=14% Similarity=0.220 Sum_probs=45.1
Q ss_pred HhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhHhcHHhHHhhhcCCCHHHHHHH
Q 015933 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIKTRIPRHEVEQM 354 (398)
Q Consensus 296 lf~~I~GvGpktA~~l~~~GirtledL~~~~--~l~~~q~~Glk~~ed~~~~i~r~ea~~~ 354 (398)
.|.+|+||||++.++|++ -|.|+++|+.+. .|....++|.+..+.|...-.|.....+
T Consensus 609 ~L~~IpGiG~kr~~~LL~-~FgS~~~i~~As~eel~~v~gi~~~~A~~i~~~~~~~~~~~~ 668 (691)
T PRK14672 609 SFERLPHVGKVRAHRLLA-HFGSFRSLQSATPQDIATAIHIPLTQAHTILHAATRSTTAPV 668 (691)
T ss_pred ccccCCCCCHHHHHHHHH-HhcCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHhhcccccch
Confidence 456999999999999998 677999998763 5777888888888888766555444333
No 168
>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=76.34 E-value=1.3 Score=28.94 Aligned_cols=18 Identities=22% Similarity=0.501 Sum_probs=14.3
Q ss_pred hhcCCCCCCHHHHHHHHH
Q 015933 255 QVKGLPGIGKSMQDHIQE 272 (398)
Q Consensus 255 ~l~~lpgIG~~ia~kI~E 272 (398)
.+.+++|||+++++++..
T Consensus 12 pi~~~~GIG~kt~~kL~~ 29 (32)
T PF11798_consen 12 PIRKFWGIGKKTAKKLNK 29 (32)
T ss_dssp BGGGSTTS-HHHHHHHHC
T ss_pred CHHhhCCccHHHHHHHHH
Confidence 478999999999998764
No 169
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=76.29 E-value=5.1 Score=35.21 Aligned_cols=78 Identities=17% Similarity=0.231 Sum_probs=45.7
Q ss_pred HHHHHHHHcCCChhHHHHHHHHHHHhcCCccc----c-chhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHH
Q 015933 219 KLINIYRALGEDRRSFSYYKAIPVIEKLPFKI----E-SADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRT 293 (398)
Q Consensus 219 ~la~~~e~~g~~~r~~aY~rAa~~l~~l~~~i----~-s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~ 293 (398)
+|.++..-.|-+.|+.....++..+..-.... . ..++|.+|||||..+|+.|.-+.- | . +.+-- ...+
T Consensus 43 ~l~~~~~~~G~~~kA~~i~~~a~~~~~~~~~~~~~~~~~~~~L~~l~GIG~~tA~~~l~~~~-~-~---~~~pv--D~~v 115 (158)
T cd00056 43 ELRELIRSLGYRRKAKYLKELARAIVEGFGGLVLDDPDAREELLALPGVGRKTANVVLLFAL-G-P---DAFPV--DTHV 115 (158)
T ss_pred HHHHHHHhcChHHHHHHHHHHHHHHHHHcCCccCCCcccHHHHHcCCCCCHHHHHHHHHHHC-C-C---CCCcc--chhH
Confidence 34444433443457777777777776533222 2 236799999999999999876532 2 2 22211 2346
Q ss_pred HHHhhhccCc
Q 015933 294 ISLFGEVWGI 303 (398)
Q Consensus 294 l~lf~~I~Gv 303 (398)
.+.+..+.++
T Consensus 116 ~r~~~~~~~~ 125 (158)
T cd00056 116 RRVLKRLGLI 125 (158)
T ss_pred HHHHHHhCCC
Confidence 6677666654
No 170
>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=76.25 E-value=3.8 Score=31.27 Aligned_cols=22 Identities=18% Similarity=0.376 Sum_probs=19.8
Q ss_pred hhhcCCCCCCHHHHHHHHHHHH
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVT 275 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~ 275 (398)
++|..+||+|++..+.|.+.|+
T Consensus 44 ~~L~~i~n~G~ksl~EI~~~L~ 65 (66)
T PF03118_consen 44 EDLLKIKNFGKKSLEEIKEKLK 65 (66)
T ss_dssp HHHHTSTTSHHHHHHHHHHHHH
T ss_pred HHHHhCCCCCHhHHHHHHHHHc
Confidence 5799999999999999998875
No 171
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=76.21 E-value=3.6 Score=38.80 Aligned_cols=94 Identities=20% Similarity=0.231 Sum_probs=53.2
Q ss_pred CCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhccCch-hhhHhc----
Q 015933 261 GIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLT-HSQRLG---- 335 (398)
Q Consensus 261 gIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~~~l~-~~q~~G---- 335 (398)
|+-..=|+.|.++.+ .-+|.... +....++.|.++||||+|||.-....++.=. -+-=+-.+. -..++|
T Consensus 80 Glyr~KAk~I~~~~~----~l~e~~~g-~vP~~~~eL~~LPGVGrKTAnvVL~~a~g~p-~i~VDTHV~Rvs~R~gl~~~ 153 (211)
T COG0177 80 GLYRNKAKNIKELAR----ILLEKFGG-EVPDTREELLSLPGVGRKTANVVLSFAFGIP-AIAVDTHVHRVSNRLGLVPG 153 (211)
T ss_pred CCcHHHHHHHHHHHH----HHHHHcCC-CCCchHHHHHhCCCcchHHHHHHHHhhcCCC-cccccchHHHHHHHhCCCCC
Confidence 555555666655443 22233333 3446788888999999999998877633222 222111111 122333
Q ss_pred ---HHhHHhhhcCCCHHHHHHHHHHHHH
Q 015933 336 ---LKYFDDIKTRIPRHEVEQMERLLQK 360 (398)
Q Consensus 336 ---lk~~ed~~~~i~r~ea~~~~~~v~~ 360 (398)
.+..+++.+.+|.+.=..+...+-.
T Consensus 154 ~~p~~ve~~L~~~iP~~~~~~~h~~lI~ 181 (211)
T COG0177 154 KTPEEVEEALMKLIPKELWTDLHHWLIL 181 (211)
T ss_pred CCHHHHHHHHHHHCCHHHHHHHHHHHHH
Confidence 4556677888998777665444433
No 172
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=75.94 E-value=3.3 Score=39.22 Aligned_cols=22 Identities=23% Similarity=0.210 Sum_probs=18.1
Q ss_pred HHHHHhhhccCcCHHHHHHHHH
Q 015933 292 RTISLFGEVWGIGPATAQKLYE 313 (398)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~ 313 (398)
...+.|++++|||++||..+--
T Consensus 118 ~~re~Ll~l~GIG~kTAd~iLl 139 (218)
T PRK13913 118 VTREWLLDQKGIGKESADAILC 139 (218)
T ss_pred hHHHHHHcCCCccHHHHHHHHH
Confidence 3567788999999999998764
No 173
>PRK13766 Hef nuclease; Provisional
Probab=75.88 E-value=3.3 Score=46.13 Aligned_cols=49 Identities=29% Similarity=0.425 Sum_probs=31.2
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 015933 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (398)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (398)
|..|||||...+.+|.+- -|.+.. +.+. ..+.|..++|+|+++|+.|++
T Consensus 717 L~~ipgig~~~a~~Ll~~--fgs~~~---i~~a----s~~~L~~i~Gig~~~a~~i~~ 765 (773)
T PRK13766 717 VESLPDVGPVLARNLLEH--FGSVEA---VMTA----SEEELMEVEGIGEKTAKRIRE 765 (773)
T ss_pred HhcCCCCCHHHHHHHHHH--cCCHHH---HHhC----CHHHHHhCCCCCHHHHHHHHH
Confidence 568888888877766553 244333 3221 123456788888888888876
No 174
>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=75.53 E-value=7.5 Score=31.24 Aligned_cols=50 Identities=22% Similarity=0.395 Sum_probs=33.5
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCC
Q 015933 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGH 316 (398)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~Gi 316 (398)
+..|+|||+.+++.|.+--+.|.+.-++++... +++|..+..+.|...|.
T Consensus 29 l~~Ikglg~~~a~~I~~~R~~g~f~s~~df~~R-----------~~~i~~~~le~Li~aGa 78 (90)
T PF14579_consen 29 LSAIKGLGEEVAEKIVEERENGPFKSLEDFIQR-----------LPKINKRQLEALIKAGA 78 (90)
T ss_dssp GGGSTTS-HHHHHHHHHHHHCSS-SSHHHHHHH-----------S-TS-HHHHHHHHHTTT
T ss_pred HhhcCCCCHHHHHHHHHhHhcCCCCCHHHHHHH-----------HhcCCHHHHHHHHHCCC
Confidence 678888888888888888877777777766542 22677777777777654
No 175
>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=75.43 E-value=1.1 Score=34.38 Aligned_cols=44 Identities=25% Similarity=0.367 Sum_probs=34.2
Q ss_pred cCcCHHHHHHHHHcCCCCHHHhhhc--cCchhhhHhcHHhHHhhhc
Q 015933 301 WGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDIKT 344 (398)
Q Consensus 301 ~GvGpktA~~l~~~GirtledL~~~--~~l~~~q~~Glk~~ed~~~ 344 (398)
-|+-+++...|-..||.|+.||..- ..|..+++||-+..++|.+
T Consensus 17 L~LS~Ra~n~L~~~~I~tv~dL~~~s~~~L~~i~n~G~ksl~EI~~ 62 (66)
T PF03118_consen 17 LGLSVRAYNCLKRAGIHTVGDLVKYSEEDLLKIKNFGKKSLEEIKE 62 (66)
T ss_dssp STSBHHHHHHHHCTT--BHHHHHCS-HHHHHTSTTSHHHHHHHHHH
T ss_pred hCCCHHHHHHHHHhCCcCHHHHHhCCHHHHHhCCCCCHhHHHHHHH
Confidence 3677888888888899999999853 4588899999999988865
No 176
>PRK13910 DNA glycosylase MutY; Provisional
Probab=75.08 E-value=6.3 Score=38.94 Aligned_cols=68 Identities=16% Similarity=0.197 Sum_probs=45.8
Q ss_pred hHHHHHHHHHHHh-cCCccc-cchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHH
Q 015933 232 RSFSYYKAIPVIE-KLPFKI-ESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPA 306 (398)
Q Consensus 232 r~~aY~rAa~~l~-~l~~~i-~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpk 306 (398)
|++.-.++|..|. .+...+ .+.++|.+|||||..+|..|.-|. -|.-.- -...-+.+.|.+++|+...
T Consensus 48 RAr~L~~~A~~i~~~~~g~~P~~~~~L~~LpGIG~kTA~aIl~~a-f~~~~~------~VD~nV~RVl~Rl~g~~~~ 117 (289)
T PRK13910 48 RAKNLKKSAEICVKEHHSQLPNDYQSLLKLPGIGAYTANAILCFG-FREKSA------CVDANIKRVLLRLFGLDPN 117 (289)
T ss_pred HHHHHHHHHHHHHHHhCCCCChhHHHHHhCCCCCHHHHHHHHHHH-CCCCcC------cccHHHHHHHHHHhcCCCC
Confidence 7777888888775 322222 246889999999999999997544 333111 1234578888888888643
No 177
>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=75.04 E-value=9.5 Score=34.99 Aligned_cols=44 Identities=14% Similarity=0.178 Sum_probs=30.6
Q ss_pred hHHHHHHHHHHH-hcCCccc--------c-c---hhhhcCCCCCCHHHHHHHHHHHH
Q 015933 232 RSFSYYKAIPVI-EKLPFKI--------E-S---ADQVKGLPGIGKSMQDHIQEIVT 275 (398)
Q Consensus 232 r~~aY~rAa~~l-~~l~~~i--------~-s---~~~l~~lpgIG~~ia~kI~Eil~ 275 (398)
++.....++..| +.+...+ . + .++|..|||||.++|..+--+|.
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 455555566665 4666554 1 1 36799999999999999876654
No 178
>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=75.02 E-value=2.7 Score=44.03 Aligned_cols=30 Identities=43% Similarity=0.574 Sum_probs=26.9
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhcc
Q 015933 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (398)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~~ 326 (398)
++-|+|||.+++..|++.||.|++||-...
T Consensus 209 lslv~gi~~~~~~~L~~~GI~ti~~La~~~ 238 (457)
T TIGR03491 209 LSLVPGIGPSRYRLLQELGIHTLEDLAAAD 238 (457)
T ss_pred eeecCCCCHHHHHHHHHcCCCcHHHHhcCC
Confidence 347999999999999999999999998654
No 179
>PRK00254 ski2-like helicase; Provisional
Probab=74.84 E-value=15 Score=40.76 Aligned_cols=52 Identities=21% Similarity=0.380 Sum_probs=37.7
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc
Q 015933 255 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (398)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~ 314 (398)
.|.+|||||...+.+ +++.| +.-++++..- ..+.+..|+|||.++|+++++.
T Consensus 646 ~L~~ipgig~~~~~~---l~~~g-~~s~~~i~~a----~~~el~~~~gi~~~~a~~i~~~ 697 (720)
T PRK00254 646 ELMRLPMIGRKRARA---LYNAG-FRSIEDIVNA----KPSELLKVEGIGAKIVEGIFKH 697 (720)
T ss_pred hhhcCCCCCHHHHHH---HHHcc-CCCHHHHHhC----CHHHHhcCCCCCHHHHHHHHHH
Confidence 478899999987776 45555 4445555432 2334569999999999999986
No 180
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=74.65 E-value=2.2 Score=39.73 Aligned_cols=37 Identities=22% Similarity=0.333 Sum_probs=26.9
Q ss_pred cccch-hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHH
Q 015933 249 KIESA-DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHF 285 (398)
Q Consensus 249 ~i~s~-~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l 285 (398)
++..+ +.+..|||||++.|+++.-+|-.-.-.+++.|
T Consensus 5 ~~~~Li~~l~~LPGIG~KsA~RlA~~ll~~~~~~~~~l 42 (195)
T TIGR00615 5 PISKLIESLKKLPGIGPKSAQRLAFHLLKRDPSEVLRL 42 (195)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHcCCHHHHHHH
Confidence 34444 67899999999999999877765544445444
No 181
>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a beta-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [, ].; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBN_M 2QBB_M 3I1M_M 3OFP_M 3OFX_M 3OFO_M 1VS5_M 3OAQ_M 2QAL_M 3J18_M ....
Probab=74.39 E-value=3.1 Score=34.84 Aligned_cols=26 Identities=23% Similarity=0.484 Sum_probs=21.8
Q ss_pred HHHHhhhccCcCHHHHHHHHHc-CCCC
Q 015933 293 TISLFGEVWGIGPATAQKLYEK-GHRT 318 (398)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~-Girt 318 (398)
+.-.|++|+|||+++|..+.+. |+..
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 5667789999999999999986 8854
No 182
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=74.38 E-value=4.2 Score=44.01 Aligned_cols=49 Identities=20% Similarity=0.458 Sum_probs=37.4
Q ss_pred HHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhHhcHHhHHhhhc
Q 015933 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIKT 344 (398)
Q Consensus 295 ~lf~~I~GvGpktA~~l~~~GirtledL~~~~--~l~~~q~~Glk~~ed~~~ 344 (398)
..|..|+|||++++++|++ -+-|++++.++. .|....++|.+..+.|.+
T Consensus 525 ~~L~~IpGIG~kr~~~LL~-~FGS~~~I~~As~eeL~~vpGi~~~~A~~I~~ 575 (577)
T PRK14668 525 TVLDDVPGVGPETRKRLLR-RFGSVEGVREASVEDLRDVPGVGEKTAETIRE 575 (577)
T ss_pred hHHhcCCCCCHHHHHHHHH-HcCCHHHHHhCCHHHHHhCCCCCHHHHHHHHH
Confidence 4566999999999999998 567888888653 466677778777776643
No 183
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=74.24 E-value=7 Score=38.75 Aligned_cols=52 Identities=27% Similarity=0.493 Sum_probs=37.1
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc
Q 015933 255 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (398)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~ 314 (398)
.+..|||||+.+++++.+ --+..+++|..-.+ ..+.+++|+++++|..||+.
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 478999999888776554 34555666654222 23448889999999999974
No 184
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=73.44 E-value=5.1 Score=39.24 Aligned_cols=68 Identities=18% Similarity=0.289 Sum_probs=49.1
Q ss_pred hhcCCCCCCH---HHHHHHHHHHH-hCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhh
Q 015933 255 QVKGLPGIGK---SMQDHIQEIVT-TGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLK 323 (398)
Q Consensus 255 ~l~~lpgIG~---~ia~kI~Eil~-tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL~ 323 (398)
+|..+ |+|= -|+.-.++|++ .|...-|..++...=..+.+.|+.+||||||.|.=+-=+|+.-+.-+.
T Consensus 175 ~LR~~-gfGYRAkYI~~ta~~l~~~~g~~~wLqsl~~~~yeear~~L~~lpGVG~KVADCI~Lm~l~~~~~VP 246 (323)
T KOG2875|consen 175 ELRKL-GFGYRAKYISATARALQEKQGGLAWLQSLRKSSYEEAREALCSLPGVGPKVADCICLMSLDKLSAVP 246 (323)
T ss_pred HHHHc-CcchhHHHHHHHHHHHHHhcccchHHHHHhcccHHHHHHHHhcCCCCcchHhhhhhhhhcCCCCccc
Confidence 45555 6764 46666777775 466677888887555559999999999999999977766666555443
No 185
>PRK13300 tRNA CCA-pyrophosphorylase; Provisional
Probab=73.40 E-value=6.9 Score=41.00 Aligned_cols=42 Identities=24% Similarity=0.311 Sum_probs=28.3
Q ss_pred HHHHHHHHhhhcCCCeEEEEechhhcCCccc--CCeeEEEecCC
Q 015933 354 MERLLQKAGEEVLPEVIILCGGSYRRGKASC--GDLDVVIMHPD 395 (398)
Q Consensus 354 ~~~~v~~~~~~~~p~~~v~~~Gs~RRgke~~--gDvDiLit~~~ 395 (398)
+...+++........+.|.+.|||.||.-.- +||||+|.-|+
T Consensus 27 l~~~L~~~~~~~~~~~~V~l~GS~ArgT~L~GdsDIDIFv~fp~ 70 (447)
T PRK13300 27 LIERLEEAIKELGLDAEVELVGSTARGTWLSGDRDIDIFVLFPK 70 (447)
T ss_pred HHHHHHHHHHhcCCceEEEEEeeecCCcccCCCCceeEEEEeCC
Confidence 3333444333322237899999999998776 48999987654
No 186
>COG1746 CCA1 tRNA nucleotidyltransferase (CCA-adding enzyme) [Translation, ribosomal structure and biogenesis]
Probab=73.27 E-value=7.6 Score=40.25 Aligned_cols=45 Identities=27% Similarity=0.380 Sum_probs=32.1
Q ss_pred HHHHHHHHHHhhhcCCCeEEEEechhhcCCccc--CCeeEEEecCCC
Q 015933 352 EQMERLLQKAGEEVLPEVIILCGGSYRRGKASC--GDLDVVIMHPDR 396 (398)
Q Consensus 352 ~~~~~~v~~~~~~~~p~~~v~~~Gs~RRgke~~--gDvDiLit~~~~ 396 (398)
+.+...+.+...+....+.+.++|||.||-=.. +|||+-|.-|..
T Consensus 29 e~l~~~~~~~~~e~~~~aev~lVGS~AkgTwL~gd~DIDvFi~Fp~d 75 (443)
T COG1746 29 EELRERINEIIEELGIDAEVVLVGSYAKGTWLRGDHDIDVFIAFPKD 75 (443)
T ss_pred HHHHHHHHHHHHhcCCcceEEEEeecccCcccCCCcceeEEEECCCC
Confidence 334444555555556788999999999997665 788888877653
No 187
>PRK00076 recR recombination protein RecR; Reviewed
Probab=72.60 E-value=2.5 Score=39.41 Aligned_cols=37 Identities=19% Similarity=0.331 Sum_probs=27.3
Q ss_pred cccch-hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHH
Q 015933 249 KIESA-DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHF 285 (398)
Q Consensus 249 ~i~s~-~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l 285 (398)
++..+ +.+..|||||++.|+++.-+|-.-.-.+++.|
T Consensus 5 ~~~~Li~~l~~LPGIG~KsA~Rla~~ll~~~~~~~~~l 42 (196)
T PRK00076 5 PIEKLIEALRKLPGIGPKSAQRLAFHLLQRDREDVLRL 42 (196)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHcCCHHHHHHH
Confidence 34443 67899999999999999988865554555544
No 188
>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=72.29 E-value=2.4 Score=33.96 Aligned_cols=20 Identities=40% Similarity=0.624 Sum_probs=17.9
Q ss_pred HHhhhccCcCHHHHHHHHHc
Q 015933 295 SLFGEVWGIGPATAQKLYEK 314 (398)
Q Consensus 295 ~lf~~I~GvGpktA~~l~~~ 314 (398)
++|++|||||+.||-.|..+
T Consensus 2 ~~l~sipGig~~~a~~llae 21 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAE 21 (87)
T ss_pred chhcCCCCccHHHHHHHHHH
Confidence 46789999999999999975
No 189
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=72.24 E-value=2.7 Score=45.62 Aligned_cols=50 Identities=22% Similarity=0.348 Sum_probs=36.3
Q ss_pred HHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhHhcHHhHHhhh
Q 015933 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIK 343 (398)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~GirtledL~~~~--~l~~~q~~Glk~~ed~~ 343 (398)
....|..|+|||++++++|++ .+.|++++.++. .|....++|.+..+.|.
T Consensus 541 ~~s~L~~IpGIG~k~~k~Ll~-~FgS~~~i~~As~eeL~~v~Gig~~~A~~I~ 592 (598)
T PRK00558 541 LTSALDDIPGIGPKRRKALLK-HFGSLKAIKEASVEELAKVPGISKKLAEAIY 592 (598)
T ss_pred hhhhHhhCCCcCHHHHHHHHH-HcCCHHHHHhCCHHHHhhcCCcCHHHHHHHH
Confidence 344567999999999999999 556788888653 35556666666655554
No 190
>PRK13844 recombination protein RecR; Provisional
Probab=72.13 E-value=2.5 Score=39.47 Aligned_cols=38 Identities=18% Similarity=0.287 Sum_probs=27.7
Q ss_pred cccch-hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHH
Q 015933 249 KIESA-DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFE 286 (398)
Q Consensus 249 ~i~s~-~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~ 286 (398)
++..+ +.+..|||||++.|+++.-++-.-.-.++++|-
T Consensus 9 ~~~~LI~~l~~LPGIG~KsA~Rla~~lL~~~~~~~~~la 47 (200)
T PRK13844 9 KISAVIESLRKLPTIGKKSSQRLALYLLDKSPETAIAIA 47 (200)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHcCCHHHHHHHH
Confidence 34443 568999999999999999888755545555543
No 191
>KOG0323 consensus TFIIF-interacting CTD phosphatases, including NLI-interacting factor [Transcription]
Probab=71.95 E-value=1.5 Score=47.56 Aligned_cols=89 Identities=21% Similarity=0.237 Sum_probs=60.1
Q ss_pred CCCCCcEEEEccC---CCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccchHHH
Q 015933 17 GIFAGMRVFLVEK---GVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLED 93 (398)
Q Consensus 17 ~~F~g~~iy~~~~---~~g~~r~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~~~~~l~~l~~~~~~~~~~~lV~~~Wl~e 93 (398)
..+++|.+.|++. ++...+. ..-....+.|+.+...++..+||+|+........... ... ...+||...|+..
T Consensus 440 ~v~~~~~~vfSg~~P~~~~~~~s-~~~~~~~~~g~vs~~~~~~~~th~i~~~~gt~k~~~a--~~~-~~~~Vv~~~wl~~ 515 (635)
T KOG0323|consen 440 KVLKGSQIVFSGLHPTGSTDESA-DILGVAQQLGAVSAPDVSDKTTHLIAANAGTKKVYKA--VVS-GSAKVVNAAWLWR 515 (635)
T ss_pred HHhhccceeecccccCcCCcchh-hhhhhhhcccceecccccchhhhHHhhccCcceeecc--ccc-cceeEechhHHHH
Confidence 4688999988763 2222222 2234556778999899999999999977553211111 111 1368999999999
Q ss_pred HHhcCCCCCccccccc
Q 015933 94 SLRLGEKVSEDLYRIK 109 (398)
Q Consensus 94 s~k~g~lv~ee~y~l~ 109 (398)
|+..=..++|..|.+.
T Consensus 516 ~~e~w~~v~ek~~~l~ 531 (635)
T KOG0323|consen 516 SLEKWGKVEEKLEPLD 531 (635)
T ss_pred HHHHhcchhccccccc
Confidence 9998888888777664
No 192
>PRK14973 DNA topoisomerase I; Provisional
Probab=71.91 E-value=5.5 Score=45.54 Aligned_cols=42 Identities=17% Similarity=0.115 Sum_probs=34.0
Q ss_pred HHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhHhcH
Q 015933 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGL 336 (398)
Q Consensus 295 ~lf~~I~GvGpktA~~l~~~GirtledL~~~~--~l~~~q~~Gl 336 (398)
+-|++++||=..+|+++|+.||+|++|+-.+. .|+...|+..
T Consensus 802 ~~~~~~~gv~~~~~~~~~~~G~~~~~d~~~a~p~~La~~~g~~~ 845 (936)
T PRK14973 802 ISRLKEIGVPAVSLKKYQEAGFDTPEDFCSVHPAYLALKTGISP 845 (936)
T ss_pred HHhhcccCCCHHHHHHHHHhcCCCHHHHHhcCHHHHhcCCCCCh
Confidence 34569999999999999999999999998653 4666666653
No 193
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=70.79 E-value=3.8 Score=44.38 Aligned_cols=20 Identities=15% Similarity=0.165 Sum_probs=14.1
Q ss_pred CchhhhHhcHHhHHhhhcCC
Q 015933 327 SLTHSQRLGLKYFDDIKTRI 346 (398)
Q Consensus 327 ~l~~~q~~Glk~~ed~~~~i 346 (398)
.|..+.++|.+....|...+
T Consensus 526 ~L~~IpGIG~kr~~~LL~~F 545 (577)
T PRK14668 526 VLDDVPGVGPETRKRLLRRF 545 (577)
T ss_pred HHhcCCCCCHHHHHHHHHHc
Confidence 46677788877777776654
No 194
>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=70.48 E-value=2.2 Score=42.40 Aligned_cols=52 Identities=25% Similarity=0.338 Sum_probs=35.5
Q ss_pred HHHHHhhhccCcCHHHHHHHHHc---C-CCCHHHhhhcc-----CchhhhHhcHHhHHhhh
Q 015933 292 RTISLFGEVWGIGPATAQKLYEK---G-HRTLDDLKNED-----SLTHSQRLGLKYFDDIK 343 (398)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~~---G-irtledL~~~~-----~l~~~q~~Glk~~ed~~ 343 (398)
..+..+++|||||+++|.++.+- | +..+++|+.+. .|..+.++|.+....|-
T Consensus 42 ~~~~~~~~ipgiG~~ia~kI~E~~~tG~~~~le~l~~~~~~~l~~l~~i~GiGpk~a~~l~ 102 (307)
T cd00141 42 ESLEEAKKLPGIGKKIAEKIEEILETGKLRKLEELREDVPPGLLLLLRVPGVGPKTARKLY 102 (307)
T ss_pred CCHHHhcCCCCccHHHHHHHHHHHHcCCHHHHHHHhccchHHHHHHHcCCCCCHHHHHHHH
Confidence 34555579999999999999873 4 35666666431 25567777777666654
No 195
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=70.08 E-value=6.6 Score=43.95 Aligned_cols=86 Identities=13% Similarity=0.188 Sum_probs=64.9
Q ss_pred CCCCCCCCcEEEEccCCCCchHHHHHHHHHHhcCCEEEeec-CCCccEEEEcCChHHH-HHHHHHhhhccCccccccchH
Q 015933 14 DSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKL-SKKVTHVLAMDLEALL-QQVSKQHLARFKGSVIRYQWL 91 (398)
Q Consensus 14 ~~~~~F~g~~iy~~~~~~g~~r~~~l~~li~~~Gg~V~~~l-s~~VTHVV~~~~~~~l-~~l~~~~~~~~~~~lV~~~Wl 91 (398)
.....|+++.+|..++.+.. ..-|+++-..+|+...... ..+.||+++.+..+.+ +.++ .+...+++|+
T Consensus 43 t~~s~fs~is~~~ngs~~e~--~nelk~~~~~~t~~~~~~~~rs~T~~ii~~~l~a~~vk~~~-------~~~~~~~e~i 113 (1016)
T KOG2093|consen 43 TGSSSFSGISISVNGSTDES--ANELKLQNMFHTGASAASYERSGTENIIAQGLPADLVKGFT-------IPKHISIEWI 113 (1016)
T ss_pred CCcceeeeeeeccCCccccc--hHHHhhhhhhcccccccccccccceeeecccchHHHhcccc-------chhhhcHHHH
Confidence 33478999999998765553 4567888899999998444 5789999999877542 2211 4677999999
Q ss_pred HHHHhcCCCCCcccccc
Q 015933 92 EDSLRLGEKVSEDLYRI 108 (398)
Q Consensus 92 ~es~k~g~lv~ee~y~l 108 (398)
.||.+.|..+.--.|.+
T Consensus 114 ie~~~~~~~~~~~~~~~ 130 (1016)
T KOG2093|consen 114 IECCENGMDVGYYPYQL 130 (1016)
T ss_pred HHHHhccCcccccccee
Confidence 99999999988666554
No 196
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=69.98 E-value=6.1 Score=43.16 Aligned_cols=49 Identities=27% Similarity=0.575 Sum_probs=34.8
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (398)
..|.+|||||++.+..|..-. |++ +.+++- ..+.+.+| ||+++|+.+++
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 458899999999999765532 333 444432 34455677 99999999986
No 197
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=69.87 E-value=3.4 Score=39.20 Aligned_cols=30 Identities=33% Similarity=0.531 Sum_probs=27.3
Q ss_pred HHhhhccCcCHHHHHHHHHcCCCCHHHhhh
Q 015933 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (398)
Q Consensus 295 ~lf~~I~GvGpktA~~l~~~GirtledL~~ 324 (398)
..|+.|.||||+.+.+|.+.|+.++++|-.
T Consensus 158 DDL~~I~GIGp~~a~~L~eaGi~tfaQIAa 187 (221)
T PRK12278 158 DDLTKITGVGPALAKKLNEAGVTTFAQIAA 187 (221)
T ss_pred chheeccccChHHHHHHHHcCCCCHHHhhC
Confidence 456799999999999999999999999974
No 198
>COG2251 Predicted nuclease (RecB family) [General function prediction only]
Probab=69.39 E-value=3.5 Score=42.89 Aligned_cols=27 Identities=37% Similarity=0.452 Sum_probs=24.8
Q ss_pred hccCcCHHHHHHHHHcCCCCHHHhhhc
Q 015933 299 EVWGIGPATAQKLYEKGHRTLDDLKNE 325 (398)
Q Consensus 299 ~I~GvGpktA~~l~~~GirtledL~~~ 325 (398)
=|+||||.+...|++.||+|++||-+.
T Consensus 229 Lv~Gi~~~r~~~l~~~GI~Ti~~LA~~ 255 (474)
T COG2251 229 LVPGITPSRYDVLEEVGITTIEDLADA 255 (474)
T ss_pred ccCCCCHHHHHHHHHcCcchHHHHHhc
Confidence 468999999999999999999999863
No 199
>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=69.35 E-value=5.7 Score=27.81 Aligned_cols=33 Identities=30% Similarity=0.355 Sum_probs=24.4
Q ss_pred cCHHHHHHHHHcCCCCHHHhhhcc--CchhhhHhc
Q 015933 303 IGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLG 335 (398)
Q Consensus 303 vGpktA~~l~~~GirtledL~~~~--~l~~~q~~G 335 (398)
|.+..+.+|++.|+.|+++|.... .|...++++
T Consensus 1 i~~~~~~~L~~~G~~s~e~la~~~~~eL~~i~g~~ 35 (50)
T TIGR01954 1 IDEEIAQLLVEEGFTTVEDLAYVPIDELLSIEGFD 35 (50)
T ss_pred CCHHHHHHHHHcCCCCHHHHHccCHHHHhcCCCCC
Confidence 467889999999999999998542 355554443
No 200
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=68.95 E-value=20 Score=33.03 Aligned_cols=42 Identities=26% Similarity=0.273 Sum_probs=28.8
Q ss_pred ccccc-hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhc
Q 015933 248 FKIES-ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDE 289 (398)
Q Consensus 248 ~~i~s-~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~ 289 (398)
.||+. +-.|.=|||||++++.+|-|=-+.+.+..++++.+-.
T Consensus 109 ~PIt~RlH~LeLLPGIGKK~m~~ILeERkkkpFeSFeDi~~Rv 151 (181)
T PF04919_consen 109 QPITLRLHSLELLPGIGKKTMWKILEERKKKPFESFEDIEERV 151 (181)
T ss_dssp --B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHS
T ss_pred CCChHHHHHHhhcccccHHHHHHHHHHHccCCCCCHHHHHHHh
Confidence 47775 4678899999999999999999999999888887633
No 201
>PRK03980 flap endonuclease-1; Provisional
Probab=68.61 E-value=3.8 Score=40.48 Aligned_cols=25 Identities=44% Similarity=0.670 Sum_probs=21.0
Q ss_pred hccCcCHHHHHHHHHcCCCCHHHhhh
Q 015933 299 EVWGIGPATAQKLYEKGHRTLDDLKN 324 (398)
Q Consensus 299 ~I~GvGpktA~~l~~~GirtledL~~ 324 (398)
.|+|||||||.+|.++ +.|||.+..
T Consensus 193 GI~GIG~ktA~kLi~~-~~sle~i~~ 217 (292)
T PRK03980 193 GIKGIGPKTALKLIKK-HGDLEKVLE 217 (292)
T ss_pred CCCCccHHHHHHHHHH-CCCHHHHHH
Confidence 7899999999999985 347888875
No 202
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=68.44 E-value=3.6 Score=46.83 Aligned_cols=24 Identities=42% Similarity=0.678 Sum_probs=20.9
Q ss_pred hccCcCHHHHHHHHHc-CCCCHHHhhh
Q 015933 299 EVWGIGPATAQKLYEK-GHRTLDDLKN 324 (398)
Q Consensus 299 ~I~GvGpktA~~l~~~-GirtledL~~ 324 (398)
.|+|||||||.+|.++ | |||.+..
T Consensus 189 GVpGIG~KtA~kLL~~yg--sle~i~~ 213 (887)
T TIGR00593 189 GVKGIGEKTAAKLLQEFG--SLENIYE 213 (887)
T ss_pred CCCCcCHHHHHHHHHHcC--CHHHHHH
Confidence 4899999999999996 6 8888874
No 203
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=68.20 E-value=4.2 Score=30.99 Aligned_cols=24 Identities=25% Similarity=0.326 Sum_probs=18.1
Q ss_pred hhHHHHH-hhhccCcCHHHHHHHHH
Q 015933 290 KVRTISL-FGEVWGIGPATAQKLYE 313 (398)
Q Consensus 290 ~~~~l~l-f~~I~GvGpktA~~l~~ 313 (398)
+...++. +.+|||||+++|.++.+
T Consensus 41 ~i~~~~~~~~~l~gIG~~ia~kI~E 65 (68)
T PF14716_consen 41 PITSGEEDLKKLPGIGKSIAKKIDE 65 (68)
T ss_dssp -HHSHHHHHCTSTTTTHHHHHHHHH
T ss_pred hHhhHHHHHhhCCCCCHHHHHHHHH
Confidence 3444554 78999999999998854
No 204
>PF14579 HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI_A 3E0D_A 3F2C_A 3F2B_A 3F2D_A 2HQA_A 2HNH_A.
Probab=67.77 E-value=7 Score=31.43 Aligned_cols=31 Identities=23% Similarity=0.408 Sum_probs=24.3
Q ss_pred HhhhccCcCHHHHHHHHHc----CCCCHHHhhhcc
Q 015933 296 LFGEVWGIGPATAQKLYEK----GHRTLDDLKNED 326 (398)
Q Consensus 296 lf~~I~GvGpktA~~l~~~----GirtledL~~~~ 326 (398)
=|+.|.|||..+|+++.+. .+.|++|+....
T Consensus 28 gl~~Ikglg~~~a~~I~~~R~~g~f~s~~df~~R~ 62 (90)
T PF14579_consen 28 GLSAIKGLGEEVAEKIVEERENGPFKSLEDFIQRL 62 (90)
T ss_dssp BGGGSTTS-HHHHHHHHHHHHCSS-SSHHHHHHHS
T ss_pred hHhhcCCCCHHHHHHHHHhHhcCCCCCHHHHHHHH
Confidence 3779999999999999963 789999987543
No 205
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=67.69 E-value=14 Score=34.79 Aligned_cols=32 Identities=19% Similarity=0.507 Sum_probs=23.8
Q ss_pred HHhcCCcccc-chhhhcCCCCCCHHHHHHHHHH
Q 015933 242 VIEKLPFKIE-SADQVKGLPGIGKSMQDHIQEI 273 (398)
Q Consensus 242 ~l~~l~~~i~-s~~~l~~lpgIG~~ia~kI~Ei 273 (398)
.++.+..++. +.++|.+|||||.++|..+--+
T Consensus 96 l~e~~~g~vP~~~~eL~~LPGVGrKTAnvVL~~ 128 (211)
T COG0177 96 LLEKFGGEVPDTREELLSLPGVGRKTANVVLSF 128 (211)
T ss_pred HHHHcCCCCCchHHHHHhCCCcchHHHHHHHHh
Confidence 3445665555 3578999999999999987643
No 206
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=67.30 E-value=8.2 Score=42.21 Aligned_cols=50 Identities=20% Similarity=0.427 Sum_probs=35.7
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~ 314 (398)
..|.+|||||++.+.++-+ ++.-++.+++ .+.+.+.+| ||.++|+++|+.
T Consensus 552 S~L~~IpGIG~kr~~~LL~-----~FgSi~~I~~----As~eeL~~v--i~~k~A~~I~~~ 601 (624)
T PRK14669 552 SELLEIPGVGAKTVQRLLK-----HFGSLERVRA----ATETQLAAV--VGRAAAEAIIAH 601 (624)
T ss_pred HHHhcCCCCCHHHHHHHHH-----HcCCHHHHHh----CCHHHHHHH--hCHHHHHHHHHH
Confidence 4688999999998887654 3444455543 234455566 999999999974
No 207
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=66.90 E-value=4.7 Score=37.12 Aligned_cols=40 Identities=28% Similarity=0.283 Sum_probs=32.1
Q ss_pred ccccc-hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHh
Q 015933 248 FKIES-ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEK 287 (398)
Q Consensus 248 ~~i~s-~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~ 287 (398)
.||+. +-+|.-|||||++++..|-|=-+..-+..++.+++
T Consensus 123 ~PIt~RLH~LELLpGiGkK~m~~ILeERkkkpFeSFeDi~~ 163 (202)
T COG1491 123 EPITLRLHQLELLPGIGKKTMWAILEERKKKPFESFEDIKE 163 (202)
T ss_pred CcchHHHHHHHhcccccHHHHHHHHHHHhcCCCcCHHHHHH
Confidence 57775 47899999999999999988777777777777765
No 208
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=66.53 E-value=4.8 Score=44.40 Aligned_cols=28 Identities=39% Similarity=0.565 Sum_probs=25.3
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhh
Q 015933 297 FGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (398)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~ 324 (398)
++.+.||||++|+.|-+.||.|+.||..
T Consensus 11 ~~~l~gvg~~~~~~l~~lgi~t~~dll~ 38 (681)
T PRK10917 11 LTSLKGVGPKTAEKLAKLGIHTVQDLLL 38 (681)
T ss_pred hhhcCCCCHHHHHHHHHcCCCCHHHHhh
Confidence 4578999999999999999999999973
No 209
>PTZ00217 flap endonuclease-1; Provisional
Probab=66.13 E-value=4.5 Score=41.69 Aligned_cols=26 Identities=35% Similarity=0.640 Sum_probs=21.6
Q ss_pred hhccCcCHHHHHHHHHcCCCCHHHhhh
Q 015933 298 GEVWGIGPATAQKLYEKGHRTLDDLKN 324 (398)
Q Consensus 298 ~~I~GvGpktA~~l~~~GirtledL~~ 324 (398)
-.|+|||||||.+|.++ +.|+|.+.+
T Consensus 238 pgi~GIG~ktA~~Li~~-~gsle~il~ 263 (393)
T PTZ00217 238 DTIKGIGPKTAYKLIKK-YKSIEEILE 263 (393)
T ss_pred CCCCCccHHHHHHHHHH-cCCHHHHHH
Confidence 37999999999999986 348888864
No 210
>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=65.60 E-value=15 Score=33.66 Aligned_cols=54 Identities=11% Similarity=0.284 Sum_probs=32.7
Q ss_pred HHHHHHHHcCCC-hhHHHHHHHHHHHh-cCCcccc-chhhhcCCCCCCHHHHHHHHH
Q 015933 219 KLINIYRALGED-RRSFSYYKAIPVIE-KLPFKIE-SADQVKGLPGIGKSMQDHIQE 272 (398)
Q Consensus 219 ~la~~~e~~g~~-~r~~aY~rAa~~l~-~l~~~i~-s~~~l~~lpgIG~~ia~kI~E 272 (398)
+|.++++-.|=. .|+..-.+.+..|. .+...+. ..++|..|||||..+|+.|-=
T Consensus 68 ~L~~~ir~~G~~~~Ka~~i~~~a~~i~~~~~~~~~~~~~~L~~l~GIG~ktA~~ill 124 (191)
T TIGR01083 68 ELEEYIKSIGLYRNKAKNIIALCRILVERYGGEVPEDREELVKLPGVGRKTANVVLN 124 (191)
T ss_pred HHHHHHHhcCChHHHHHHHHHHHHHHHHHcCCCCchHHHHHHhCCCCcHHHHHHHHH
Confidence 344444433432 35555566666553 3333333 346799999999999999863
No 211
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=64.85 E-value=4.6 Score=40.92 Aligned_cols=54 Identities=20% Similarity=0.265 Sum_probs=43.6
Q ss_pred hchhHHHHHhhhccCcCHHHHHHHHHc-CCCCHHHhhhcc--CchhhhHhcHHhHHhhh
Q 015933 288 DEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED--SLTHSQRLGLKYFDDIK 343 (398)
Q Consensus 288 ~~~~~~l~lf~~I~GvGpktA~~l~~~-GirtledL~~~~--~l~~~q~~Glk~~ed~~ 343 (398)
...+...+++.+||+||+..|++|.+. | ||..|..+. .|....++|.+....|.
T Consensus 280 ~v~prGyRiLs~IPrl~k~iAk~Ll~~FG--SL~~Il~As~eeL~~VeGIGe~rA~~I~ 336 (352)
T PRK13482 280 PVSPRGYRLLSKIPRLPSAVIENLVEHFG--SLQGLLAASIEDLDEVEGIGEVRARAIR 336 (352)
T ss_pred ccCCcHHHHHhcCCCCCHHHHHHHHHHcC--CHHHHHcCCHHHHhhCCCcCHHHHHHHH
Confidence 445668999999999999999999997 6 999988653 57778888877766643
No 212
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=64.79 E-value=8.5 Score=37.09 Aligned_cols=36 Identities=17% Similarity=0.278 Sum_probs=24.4
Q ss_pred HHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCH
Q 015933 283 EHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTL 319 (398)
Q Consensus 283 e~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~Girtl 319 (398)
+++..|.|.. ++.|.++||||||.|.--.+.++..+
T Consensus 148 d~f~gDIP~~-v~dLlsLPGVGPKMa~L~m~~AWn~i 183 (286)
T KOG1921|consen 148 DKFDGDIPDT-VEDLLSLPGVGPKMAHLTMQVAWNKI 183 (286)
T ss_pred HHhCCCCchh-HHHHhcCCCCchHHHHHHHHHHhccc
Confidence 4556666654 44445999999999987666544433
No 213
>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=64.66 E-value=12 Score=36.63 Aligned_cols=29 Identities=31% Similarity=0.470 Sum_probs=22.6
Q ss_pred HhhhccCcCHHHHHHHHHcCCCCHHHhhh
Q 015933 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (398)
Q Consensus 296 lf~~I~GvGpktA~~l~~~GirtledL~~ 324 (398)
.|.++||+|++.++++-+.|+.|+++|.+
T Consensus 149 ~L~Qlp~i~~~~~~~l~~~~i~~l~~l~~ 177 (314)
T PF02889_consen 149 PLLQLPHIGEESLKKLEKRGIKTLQDLRD 177 (314)
T ss_dssp GGGGSTT--HHHHHHHHHTT--SHHHHHH
T ss_pred hhhcCCCCCHHHHHHHhccCCCcHHHHhh
Confidence 45599999999999999999999999985
No 214
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=64.64 E-value=7.7 Score=43.43 Aligned_cols=52 Identities=27% Similarity=0.473 Sum_probs=34.9
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--CCC
Q 015933 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHR 317 (398)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~--Gir 317 (398)
+..|||+|-+|..|+...- +...-+|+ ..++.-+ .+-+|||++.++|.. |+.
T Consensus 551 v~~LPGVG~sm~~kL~s~~----i~tCgdLq----~~T~~kl--~k~~G~Klgq~i~~~CrG~D 604 (1016)
T KOG2093|consen 551 VDDLPGVGSSMKSKLVSQF----IQTCGDLQ----LITLIKL--RKVFGPKLGQKIYRGCRGID 604 (1016)
T ss_pred cccCCCccHHHHHHHHHhc----cchhHHHH----HHHHHHH--HhhhcccHHHHHHHhcCCCc
Confidence 7899999999999977654 33333333 2334444 233589999999983 663
No 215
>PRK02362 ski2-like helicase; Provisional
Probab=64.58 E-value=47 Score=36.94 Aligned_cols=52 Identities=19% Similarity=0.464 Sum_probs=38.0
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc-C
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-G 315 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~-G 315 (398)
-+|..|||||...+.++.+ .| +.-+++|.+-++.....+ +|.|+|+++.+. |
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 3588999999987776654 44 566677765445444444 699999999986 6
No 216
>PRK07758 hypothetical protein; Provisional
Probab=64.48 E-value=6.8 Score=32.23 Aligned_cols=23 Identities=13% Similarity=0.355 Sum_probs=20.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHh
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVTT 276 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~t 276 (398)
+||.+|+|+|++..+.|+|-|..
T Consensus 67 ~ELl~iknlGkKSL~EIkekL~E 89 (95)
T PRK07758 67 KEILKLHGMGPASLPKLRKALEE 89 (95)
T ss_pred HHHHHccCCCHHHHHHHHHHHHH
Confidence 57999999999999999988754
No 217
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=63.58 E-value=6.3 Score=38.64 Aligned_cols=29 Identities=17% Similarity=0.130 Sum_probs=26.2
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHhhhc
Q 015933 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (398)
Q Consensus 297 f~~I~GvGpktA~~l~~~GirtledL~~~ 325 (398)
|.++||+|+..++++.+.|+.|++||...
T Consensus 153 L~Qlp~i~~~~~~~l~~~~i~s~~~l~~~ 181 (312)
T smart00611 153 LLQLPHLPEEILKRLEKKKVLSLEDLLEL 181 (312)
T ss_pred cccCCCCCHHHHHHHHhCCCCCHHHHHhc
Confidence 44899999999999999999999999853
No 218
>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=63.37 E-value=5.5 Score=40.15 Aligned_cols=27 Identities=41% Similarity=0.588 Sum_probs=22.6
Q ss_pred hhccCcCHHHHHHHHHcCCCCHHHhhhc
Q 015933 298 GEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (398)
Q Consensus 298 ~~I~GvGpktA~~l~~~GirtledL~~~ 325 (398)
..|+|||||||.+|.++ +.|++.+.+.
T Consensus 239 ~Gv~GIG~ktA~kli~~-~gsie~il~~ 265 (338)
T TIGR03674 239 EGVKGIGPKTALKLIKE-HGDLEKVLKA 265 (338)
T ss_pred CCCCCccHHHHHHHHHH-cCCHHHHHHh
Confidence 38999999999999997 4588888753
No 219
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=63.30 E-value=12 Score=40.49 Aligned_cols=50 Identities=26% Similarity=0.528 Sum_probs=36.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (398)
..|.+|||||++...++-.. -|++..+ + ..+++.|..| ||+++.|+++|+
T Consensus 530 s~Ld~I~GiG~~r~~~LL~~--Fgs~~~i---~----~As~eel~~v-gi~~~~a~~i~~ 579 (581)
T COG0322 530 SSLDDIPGIGPKRRKALLKH--FGSLKGI---K----SASVEELAKV-GISKKLAEKIYE 579 (581)
T ss_pred CccccCCCcCHHHHHHHHHH--hhCHHHH---H----hcCHHHHHHc-CCCHHHHHHHHh
Confidence 35889999999887766442 2444333 2 2357788899 999999999986
No 220
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=63.16 E-value=5.3 Score=40.14 Aligned_cols=32 Identities=19% Similarity=0.239 Sum_probs=28.4
Q ss_pred HHHHhhhccCcCHHHHHHHHHcCCCCHHHhhh
Q 015933 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (398)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~GirtledL~~ 324 (398)
.-..|+.|.||||+.++.|.+.||.+++++-.
T Consensus 261 ~~DdL~~I~GiGp~~e~~L~~~Gi~~f~QiA~ 292 (326)
T PRK12311 261 APDDLKKLTGVSPQIEKKLNDLGIFHFWQLAE 292 (326)
T ss_pred CchhhhhhccCChhhhhhhhhcCCCCHHHhhC
Confidence 34567799999999999999999999999974
No 221
>PRK05755 DNA polymerase I; Provisional
Probab=62.76 E-value=5.2 Score=45.45 Aligned_cols=24 Identities=46% Similarity=0.645 Sum_probs=20.7
Q ss_pred hccCcCHHHHHHHHHc-CCCCHHHhhh
Q 015933 299 EVWGIGPATAQKLYEK-GHRTLDDLKN 324 (398)
Q Consensus 299 ~I~GvGpktA~~l~~~-GirtledL~~ 324 (398)
.|+|||||||.+|.++ | |+|.+.+
T Consensus 191 Gv~GiG~ktA~~Ll~~~g--sle~i~~ 215 (880)
T PRK05755 191 GVPGIGEKTAAKLLQEYG--SLEGLYE 215 (880)
T ss_pred CCCCccHHHHHHHHHHcC--CHHHHHH
Confidence 6899999999999986 5 8888864
No 222
>cd01703 PolY_Pol_iota DNA Polymerase iota. Pol iota, also called Rad30B, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol iota is thought to be one of the least efficient polymerases, particularly when opposite pyrimidines; it can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine, and prefers to insert guanosine instead of adenosine opposite thymidine. Pol iota is believed to use Hoogsteen rather than Watson-Crick base pairing, which may explain the varying efficiency for different template nucleotides.
Probab=62.05 E-value=16 Score=37.41 Aligned_cols=58 Identities=19% Similarity=0.453 Sum_probs=34.1
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhc----------h-hHHHHHhhhccCcCHHHHHHHHHc--CCCC
Q 015933 255 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDE----------K-VRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (398)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~----------~-~~~l~lf~~I~GvGpktA~~l~~~--Girt 318 (398)
.+..|||||.++.+++..+ | +..+-+|.+-. + .-....+.+.+ |.+++.+||+. |+.+
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 3788999999999998875 3 22223333222 0 00022333333 66778888875 8865
No 223
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=61.46 E-value=6 Score=39.27 Aligned_cols=39 Identities=28% Similarity=0.333 Sum_probs=27.5
Q ss_pred HHHhhhccCcCHHHHHHHHHc-CC--CCHHHhhhcc-Cchhhh
Q 015933 294 ISLFGEVWGIGPATAQKLYEK-GH--RTLDDLKNED-SLTHSQ 332 (398)
Q Consensus 294 l~lf~~I~GvGpktA~~l~~~-Gi--rtledL~~~~-~l~~~q 332 (398)
.+++.+|||+|+|.|+++... -. -++|+|++-| .+.+++
T Consensus 329 ~~~llRVPGiG~ksa~rIv~~Rr~~rl~~e~Lkk~GvvlkRak 371 (404)
T COG4277 329 YKELLRVPGIGVKSARRIVMTRRRTRLTLEDLKKLGVVLKRAK 371 (404)
T ss_pred HHHhcccCCCChHHHHHHHHHhhhcccCHHHHhhhceeeeccc
Confidence 455569999999999999974 33 4678887644 344443
No 224
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=60.84 E-value=5.7 Score=34.19 Aligned_cols=25 Identities=24% Similarity=0.383 Sum_probs=20.8
Q ss_pred HHHHhhhccCcCHHHHHHHHHc-CCC
Q 015933 293 TISLFGEVWGIGPATAQKLYEK-GHR 317 (398)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~-Gir 317 (398)
+.-.|+.|+|||+++|..+-+. ||.
T Consensus 15 v~~aLt~i~GIG~~~A~~ic~~lgi~ 40 (122)
T CHL00137 15 IEYALTYIYGIGLTSAKEILEKANID 40 (122)
T ss_pred eeeeecccccccHHHHHHHHHHcCcC
Confidence 3445689999999999999987 874
No 225
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=60.57 E-value=22 Score=38.99 Aligned_cols=73 Identities=19% Similarity=0.099 Sum_probs=54.5
Q ss_pred CCCCCcEEEEccCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccchHHHH
Q 015933 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDS 94 (398)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~r~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~~~~~l~~l~~~~~~~~~~~lV~~~Wl~es 94 (398)
..|.|.+|.|-++--+-+| +..+.++...||+|..++|.++.-||+.++-.. +..++...+++|++-+++.+-
T Consensus 593 ~~l~gkt~V~TGtL~~~sR-~eak~~le~lGakv~~SVSkktD~vvaG~~aGS----Kl~kA~eLgv~i~~E~~~~~l 665 (667)
T COG0272 593 SPLAGKTFVLTGTLEGMSR-DEAKALLEALGAKVSGSVSKKTDYVVAGENAGS----KLAKAQELGVKIIDEEEFLAL 665 (667)
T ss_pred cccCCCEEEEeccCCCCCH-HHHHHHHHHcCCEEeceecccccEEEEcCCCCh----HHHHHHHcCCeEecHHHHHHh
Confidence 6799999999876333444 567999999999999999999999998765321 222344568889888877653
No 226
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=60.34 E-value=5.7 Score=34.20 Aligned_cols=24 Identities=21% Similarity=0.470 Sum_probs=20.4
Q ss_pred HHHhhhccCcCHHHHHHHHHc-CCC
Q 015933 294 ISLFGEVWGIGPATAQKLYEK-GHR 317 (398)
Q Consensus 294 l~lf~~I~GvGpktA~~l~~~-Gir 317 (398)
.-.|+.|+|||+.+|..+.+. |+.
T Consensus 16 ~~aL~~I~GIG~~~a~~i~~~lgi~ 40 (122)
T PRK05179 16 VIALTYIYGIGRTRAKEILAAAGID 40 (122)
T ss_pred EeeecccccccHHHHHHHHHHhCcC
Confidence 345689999999999999987 885
No 227
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=60.18 E-value=6.1 Score=39.77 Aligned_cols=52 Identities=19% Similarity=0.279 Sum_probs=32.0
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHc---CCCC-HHHhhhcc------CchhhhHhcHHhHHhh
Q 015933 291 VRTISLFGEVWGIGPATAQKLYEK---GHRT-LDDLKNED------SLTHSQRLGLKYFDDI 342 (398)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~---Girt-ledL~~~~------~l~~~q~~Glk~~ed~ 342 (398)
...+..+++|||||+++|.++.+- |--. +.++..+. .|.++.++|.+....|
T Consensus 44 i~~~~~l~~lpgIG~~ia~kI~Eil~tG~~~~~~e~l~~~~p~~l~~l~~i~GiGpk~a~~l 105 (334)
T smart00483 44 INSMKDLKGLPGIGDKIKKKIEEIIETGKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKW 105 (334)
T ss_pred CCCHHHHhcCCCccHHHHHHHHHHHHhCcHHHHHHHhcCcHHHHHHHHHccCCcCHHHHHHH
Confidence 345667789999999999999973 6544 33333221 2455555554444333
No 228
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=60.12 E-value=14 Score=35.59 Aligned_cols=29 Identities=24% Similarity=0.481 Sum_probs=22.4
Q ss_pred cCCcccc-chhhhcCCCCCCHHHHHHHHHH
Q 015933 245 KLPFKIE-SADQVKGLPGIGKSMQDHIQEI 273 (398)
Q Consensus 245 ~l~~~i~-s~~~l~~lpgIG~~ia~kI~Ei 273 (398)
.+..+|- ++++|..|||||.+||-.+..+
T Consensus 149 ~f~gDIP~~v~dLlsLPGVGPKMa~L~m~~ 178 (286)
T KOG1921|consen 149 KFDGDIPDTVEDLLSLPGVGPKMAHLTMQV 178 (286)
T ss_pred HhCCCCchhHHHHhcCCCCchHHHHHHHHH
Confidence 4555665 4689999999999999876554
No 229
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=59.57 E-value=23 Score=30.73 Aligned_cols=42 Identities=10% Similarity=0.282 Sum_probs=26.6
Q ss_pred hHHHHHHHHHHHhc-CCcccc-chhhhcCCCCCCHHHHHHHHHH
Q 015933 232 RSFSYYKAIPVIEK-LPFKIE-SADQVKGLPGIGKSMQDHIQEI 273 (398)
Q Consensus 232 r~~aY~rAa~~l~~-l~~~i~-s~~~l~~lpgIG~~ia~kI~Ei 273 (398)
|+..-...+..|.. +...+. ..+.|..|||||..+|+.|.=+
T Consensus 48 ka~~i~~~a~~~~~~~~~~~~~~~~~L~~l~GIG~~tA~~~l~~ 91 (149)
T smart00478 48 KAKYLIELARILVEEYGGEVPDDREELLKLPGVGRKTANAVLSF 91 (149)
T ss_pred HHHHHHHHHHHHHHHHCCCccHHHHHHHcCCCCcHHHHHHHHHH
Confidence 55555555555443 222222 3467899999999999987655
No 230
>COG1669 Predicted nucleotidyltransferases [General function prediction only]
Probab=59.11 E-value=7.5 Score=32.15 Aligned_cols=29 Identities=28% Similarity=0.418 Sum_probs=22.1
Q ss_pred CCe-EEEEechhhcCCcc-cCCeeEEEecCC
Q 015933 367 PEV-IILCGGSYRRGKAS-CGDLDVVIMHPD 395 (398)
Q Consensus 367 p~~-~v~~~Gs~RRgke~-~gDvDiLit~~~ 395 (398)
.|+ .+.+-|||=||... -.||||||-...
T Consensus 22 ~gv~~~~vFGS~aRgE~~~~SDIDILVef~~ 52 (97)
T COG1669 22 YGVKRVAVFGSYARGEQKPDSDIDILVEFEP 52 (97)
T ss_pred hCCceEEEeeeeecCCCCCCCCceeEEeecC
Confidence 355 68899999999643 389999996443
No 231
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]
Probab=58.48 E-value=7.7 Score=36.78 Aligned_cols=58 Identities=22% Similarity=0.302 Sum_probs=42.4
Q ss_pred hhhcCCCCCCHH---HHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHH
Q 015933 254 DQVKGLPGIGKS---MQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLY 312 (398)
Q Consensus 254 ~~l~~lpgIG~~---ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~ 312 (398)
+++..+ |+.+. -..-+.|....|.+...+.+..-.....++++|+|.|||+-|++++-
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 34333 33446667778988888877776677799999999999999998865
No 232
>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=58.38 E-value=15 Score=36.57 Aligned_cols=77 Identities=18% Similarity=0.196 Sum_probs=44.0
Q ss_pred HHHHcCCChhHHHHHHHHHHHhcCC--c----ccc------chhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhch
Q 015933 223 IYRALGEDRRSFSYYKAIPVIEKLP--F----KIE------SADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEK 290 (398)
Q Consensus 223 ~~e~~g~~~r~~aY~rAa~~l~~l~--~----~i~------s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~ 290 (398)
.++..|-.+|+..-..+|..|..-. . .+. ..++|..|||||..+|+-|.= ..-|... .+- ..
T Consensus 177 ~Lr~~G~g~Ra~~I~~~A~~i~~~~~~~~~l~~l~~~~~~~~~~~L~~l~GIG~~tAd~vll-~~l~~~d---~~P--vD 250 (310)
T TIGR00588 177 HLRKLGLGYRARYIRETARALLEEQGGRAWLQQIRGASYEDAREALCELPGVGPKVADCICL-MGLDKPQ---AVP--VD 250 (310)
T ss_pred HHHHcCCHHHHHHHHHHHHHHHhccCCchhHHhhccCChHHHHHHHHhCCCccHHHHHHHHH-HhCCCCC---cee--ec
Confidence 3444555467777777777665421 1 111 136799999999999998763 2333322 111 12
Q ss_pred hHHHHHhhhccCcCH
Q 015933 291 VRTISLFGEVWGIGP 305 (398)
Q Consensus 291 ~~~l~lf~~I~GvGp 305 (398)
..+.+.+.+++|+.+
T Consensus 251 ~~v~r~~~r~y~~~~ 265 (310)
T TIGR00588 251 VHVWRIANRDYPWHP 265 (310)
T ss_pred HHHHHHHHHHhcccc
Confidence 445666666666543
No 233
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=58.29 E-value=11 Score=41.22 Aligned_cols=93 Identities=16% Similarity=0.183 Sum_probs=54.9
Q ss_pred CCCCCCCCCCCCCCCCCCCcEEEEccCCCCchHHHHHHHHHHhcCCEEEeec------CCCccEEEEcC----ChHHHHH
Q 015933 3 PKTTRKPTPALDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKL------SKKVTHVLAMD----LEALLQQ 72 (398)
Q Consensus 3 pkr~r~~~~~~~~~~~F~g~~iy~~~~~~g~~r~~~l~~li~~~Gg~V~~~l------s~~VTHVV~~~----~~~~l~~ 72 (398)
|+.+|.+| -.....+|.|.-+||++.... .--+.|.+++...||++...- +..-|-|++.. ... .|
T Consensus 573 ~~~~~~~a-~s~~~kLf~gl~~~~~g~fs~-~p~~~l~~l~~~~gg~~l~~~~~~~~~~k~s~~~~~~~~~~~~~~--~~ 648 (684)
T KOG4362|consen 573 PKEKRLRA-ESYKPKLFEGLKFYFVGDFSN-PPKEQLQELVHLAGGTILQVPRVAYSDKKKSTIVVLSEKPVLDSI--LW 648 (684)
T ss_pred cccccccc-cccCcchhcCCcceeeccccc-CcHHHHHHHHhhcCcceeeccCcccccccccceeEeecccCCCch--hh
Confidence 34443333 344457999999999986443 234678999999999987542 12233333311 111 11
Q ss_pred HHHHhhh----ccCccccccchHHHHHhcCC
Q 015933 73 VSKQHLA----RFKGSVIRYQWLEDSLRLGE 99 (398)
Q Consensus 73 l~~~~~~----~~~~~lV~~~Wl~es~k~g~ 99 (398)
.+...+. .-+.++|+-.||.+++.--+
T Consensus 649 ~k~~~~ea~~~s~~a~~~~~~wvl~s~a~~~ 679 (684)
T KOG4362|consen 649 QKVNDAEALALSQRARAVSSSWVLDSIAGYQ 679 (684)
T ss_pred hhhccHHHHHHhcCCCccchhhhhcchhcee
Confidence 1111111 12678999999999986543
No 234
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=57.80 E-value=21 Score=33.89 Aligned_cols=91 Identities=22% Similarity=0.195 Sum_probs=48.7
Q ss_pred HHHHHHHHHcCCC-hhHHHHHHHHHHHhc-CCc-----cccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhch
Q 015933 218 GKLINIYRALGED-RRSFSYYKAIPVIEK-LPF-----KIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEK 290 (398)
Q Consensus 218 ~~la~~~e~~g~~-~r~~aY~rAa~~l~~-l~~-----~i~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~ 290 (398)
++|+++.+-.|=- .|+..-+..+..+.. +.. .-...++|..|||||..+|+.|-=+. -|+-. +- ..
T Consensus 78 eeL~~~Irp~Gf~~~KA~~Lk~la~~i~~~~g~~~~~~~~~~re~Ll~l~GIG~kTAd~iLlya-~~rp~----fv--VD 150 (218)
T PRK13913 78 SKLAECVRPSGFYNQKAKRLIDLSENILKDFGSFENFKQEVTREWLLDQKGIGKESADAILCYV-CAKEV----MV--VD 150 (218)
T ss_pred HHHHHHHHhcCCHHHHHHHHHHHHHHHHHHcCCchhccCchHHHHHHcCCCccHHHHHHHHHHH-cCCCc----cc--cc
Confidence 4455554444432 245455555555532 211 01233679999999999999987554 33211 11 12
Q ss_pred hHHHHHhhhccCcCH---HHHHHHHHcCC
Q 015933 291 VRTISLFGEVWGIGP---ATAQKLYEKGH 316 (398)
Q Consensus 291 ~~~l~lf~~I~GvGp---ktA~~l~~~Gi 316 (398)
.-+.++|.++ |+.+ ..++.|++.++
T Consensus 151 ty~~Rv~~Rl-G~~~~~y~~~~~~~~~~l 178 (218)
T PRK13913 151 KYSYLFLKKL-GIEIEDYDELQHFFEKGV 178 (218)
T ss_pred hhHHHHHHHc-CCCCCCHHHHHHHHHHhh
Confidence 3367777553 7754 34555555444
No 235
>COG1204 Superfamily II helicase [General function prediction only]
Probab=57.70 E-value=9.7 Score=42.67 Aligned_cols=91 Identities=25% Similarity=0.402 Sum_probs=59.8
Q ss_pred CCCCCHHHHHHHHHHHHhCCc--hhhHHHH----hhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhc---cCch
Q 015933 259 LPGIGKSMQDHIQEIVTTGKL--SKLEHFE----KDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE---DSLT 329 (398)
Q Consensus 259 lpgIG~~ia~kI~Eil~tG~~--~~le~l~----~~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~---~~l~ 329 (398)
+..+|. .+.++..++..|.. ..++.+. ...+...+..+..+.|+|-..|++||..|+++++++... ..+.
T Consensus 634 ~~~l~~-~~~r~~~~~~~~~~~~~~~~~~~~rie~gv~~e~~~~l~~i~~~grvrar~ly~~g~~~~~~~~~~~~~~~~~ 712 (766)
T COG1204 634 LLALGK-AAERLAKILGLGLHVLRKLEILSLRIEYGVRSEELLELVEIRGVGRVRARKLYNAGYKSLEDLRLIADPAELL 712 (766)
T ss_pred hhhhhh-hhhhhHhhhCCCccccccchhhhhhhhcCCChhhhcccccccccchhHHHHHHHhhhccHHHHHhhcChhhhh
Confidence 433444 44555556665543 3333332 233323444555999999999999999999999999843 3466
Q ss_pred hhhHhcHHhHHhhhcCCCHHH
Q 015933 330 HSQRLGLKYFDDIKTRIPRHE 350 (398)
Q Consensus 330 ~~q~~Glk~~ed~~~~i~r~e 350 (398)
...++|.+.++.|.....+..
T Consensus 713 ~~~~~~~~~~~~i~~~~~~~~ 733 (766)
T COG1204 713 PLTGIGERLVEAILESLGRDV 733 (766)
T ss_pred hhhhhHHHHHHHHHHHhhhhh
Confidence 777888888888876554433
No 236
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=57.42 E-value=15 Score=31.79 Aligned_cols=87 Identities=23% Similarity=0.441 Sum_probs=58.4
Q ss_pred CCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhccCchhhhHhcHHhHHh
Q 015933 262 IGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYFDD 341 (398)
Q Consensus 262 IG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~~~l~~~q~~Glk~~ed 341 (398)
|=+.|++.|.+-+-+|++..=+ +.++++.|..-.||-|.|+.+-|+ +|+++|-+....+.|----++
T Consensus 12 IY~QI~~qIk~~I~~g~l~pGd------kLPSvRelA~~~~VNpnTv~raY~-------eLE~eG~i~t~rg~G~fV~~~ 78 (125)
T COG1725 12 IYEQIANQIKEQIASGELKPGD------KLPSVRELAKDLGVNPNTVQRAYQ-------ELEREGIVETKRGKGTFVTED 78 (125)
T ss_pred HHHHHHHHHHHHHHhCCcCCCC------CCCcHHHHHHHhCCCHHHHHHHHH-------HHHHCCCEEEecCeeEEEcCC
Confidence 4456899999999999987644 456788888899999999999997 667776666666666433322
Q ss_pred ---hhcCCCHHHHHH-HHHHHHHH
Q 015933 342 ---IKTRIPRHEVEQ-MERLLQKA 361 (398)
Q Consensus 342 ---~~~~i~r~ea~~-~~~~v~~~ 361 (398)
+....-...+.. ++.+|.++
T Consensus 79 ~~~~~~~~~~~~~~~~l~~~I~~~ 102 (125)
T COG1725 79 AKEILDQLKRELAEEELEEFIEEA 102 (125)
T ss_pred chhhHHHHHHHHHHHHHHHHHHHH
Confidence 333333334433 35555543
No 237
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=57.19 E-value=18 Score=29.23 Aligned_cols=55 Identities=24% Similarity=0.314 Sum_probs=35.3
Q ss_pred CCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc-CCCCHHHh
Q 015933 261 GIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDL 322 (398)
Q Consensus 261 gIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~-GirtledL 322 (398)
||+.+++.+|.+...... ++.|+++ ||. |+..|.|||-++|.++... |+..-+.-
T Consensus 19 gl~~~~a~kl~~~yg~~a---i~~l~~n-PY~---L~~~i~gi~F~~aD~iA~~~g~~~~d~~ 74 (94)
T PF14490_consen 19 GLSPKLAMKLYKKYGDDA---IEILKEN-PYR---LIEDIDGIGFKTADKIALKLGIEPDDPR 74 (94)
T ss_dssp T--HHHHHHHHHHH-TTH---HHHHHH--STC---CCB-SSSSBHHHHHHHHHTTT--TT-HH
T ss_pred CCCHHHHHHHHHHHhHHH---HHHHHHC-hHH---HHHHccCCCHHHHHHHHHHcCCCCCCHH
Confidence 899999999999987643 4555554 553 4435899999999999997 88644433
No 238
>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=56.73 E-value=6.9 Score=33.23 Aligned_cols=25 Identities=32% Similarity=0.497 Sum_probs=20.8
Q ss_pred HHHHhhhccCcCHHHHHHHHHc-CCC
Q 015933 293 TISLFGEVWGIGPATAQKLYEK-GHR 317 (398)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~-Gir 317 (398)
+.-.|+.|+|||+++|..+.+. |+.
T Consensus 13 v~~aL~~i~GIG~~~a~~i~~~lgi~ 38 (113)
T TIGR03631 13 VEIALTYIYGIGRTRARKILEKAGID 38 (113)
T ss_pred EeeeeeeeecccHHHHHHHHHHhCcC
Confidence 3345689999999999999987 885
No 239
>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=56.13 E-value=9.2 Score=41.42 Aligned_cols=30 Identities=27% Similarity=0.346 Sum_probs=25.0
Q ss_pred HHhhhccCcCHHHHHHHHHcCCCCHHHhhhc
Q 015933 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (398)
Q Consensus 295 ~lf~~I~GvGpktA~~l~~~GirtledL~~~ 325 (398)
..|.+|+|||||+.+.|++ -|.|+++++++
T Consensus 541 S~Ld~I~GIG~kr~~~LL~-~Fgs~~~i~~A 570 (574)
T TIGR00194 541 SPLLKIPGVGEKRVQKLLK-YFGSLKGIKKA 570 (574)
T ss_pred HHHhcCCCCCHHHHHHHHH-HcCCHHHHHhC
Confidence 3566999999999999999 56788888754
No 240
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=55.80 E-value=20 Score=35.18 Aligned_cols=50 Identities=26% Similarity=0.502 Sum_probs=30.6
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 015933 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (398)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (398)
+..|||||+.+++++.+. | +..+++|..-. .+.+.+++|++.++|.+||+
T Consensus 1 l~~i~gig~~~~~~L~~~---G-i~ti~dl~~~~----~~~L~~~~g~~~~~a~~l~~ 50 (310)
T TIGR02236 1 LEDLPGVGPATAEKLREA---G-YDTFEAIAVAS----PKELSEIAGISEGTAAKIIQ 50 (310)
T ss_pred CcccCCCCHHHHHHHHHc---C-CCCHHHHHcCC----HHHHHhccCCCHHHHHHHHH
Confidence 457899999888877654 1 23344443321 22334667777777777774
No 241
>COG5067 DBF4 Protein kinase essential for the initiation of DNA replication [DNA replication, recombination, and repair / Cell division and chromosome partitioning]
Probab=55.08 E-value=8.1 Score=39.48 Aligned_cols=46 Identities=17% Similarity=0.315 Sum_probs=36.3
Q ss_pred CCCCCCcEEEEccCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEE
Q 015933 16 NGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLA 63 (398)
Q Consensus 16 ~~~F~g~~iy~~~~~~g~~r~~~l~~li~~~Gg~V~~~ls~~VTHVV~ 63 (398)
--.|+...+|+.. ....+...+++.+...||.|+.-++..||||+.
T Consensus 120 ~~aFp~f~fY~dn--~s~~~khRvk~gf~~LGa~v~tfF~~~VThfiT 165 (468)
T COG5067 120 CCAFPAFKFYKDN--KSGKRKHRVKEGFCELGAVVFTFFEEHVTHFIT 165 (468)
T ss_pred hcccchhhhhhcC--CCHHHHHHHHHHHHHhhhhhheeeccceEEEEE
Confidence 3568888888863 222334448999999999999999999999996
No 242
>PRK13766 Hef nuclease; Provisional
Probab=54.70 E-value=10 Score=42.18 Aligned_cols=47 Identities=19% Similarity=0.359 Sum_probs=35.9
Q ss_pred HhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhHhcHHhHHhhh
Q 015933 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIK 343 (398)
Q Consensus 296 lf~~I~GvGpktA~~l~~~GirtledL~~~~--~l~~~q~~Glk~~ed~~ 343 (398)
+|..|+|||+++|++|.+. +.|++++..+. .|....++|.+..+.|.
T Consensus 716 ~L~~ipgig~~~a~~Ll~~-fgs~~~i~~as~~~L~~i~Gig~~~a~~i~ 764 (773)
T PRK13766 716 IVESLPDVGPVLARNLLEH-FGSVEAVMTASEEELMEVEGIGEKTAKRIR 764 (773)
T ss_pred HHhcCCCCCHHHHHHHHHH-cCCHHHHHhCCHHHHHhCCCCCHHHHHHHH
Confidence 5789999999999999995 55899887643 46666677766666654
No 243
>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=54.16 E-value=6.7 Score=32.10 Aligned_cols=51 Identities=24% Similarity=0.337 Sum_probs=40.4
Q ss_pred HHHHhhhccCcCHHHHHHHHHc-CCCCHHHhhhccCchhhhHhcHHhHHhhh
Q 015933 293 TISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNEDSLTHSQRLGLKYFDDIK 343 (398)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~-GirtledL~~~~~l~~~q~~Glk~~ed~~ 343 (398)
.+..|++.||+=|..|.++..- -+.|++|+.+-..|+..|+-=++-|++--
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 5678899999999999999997 78999999988789988888888777643
No 244
>PRK01216 DNA polymerase IV; Validated
Probab=54.05 E-value=44 Score=33.80 Aligned_cols=52 Identities=23% Similarity=0.411 Sum_probs=34.1
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--CCC
Q 015933 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHR 317 (398)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~--Gir 317 (398)
+..|||||++++++...+ | +..+.+|.+-......+.| |+..+..||+. |+.
T Consensus 180 i~~l~giG~~~~~~L~~~---G-i~TigdL~~~~~~~L~~rf------G~~~~~~L~~~a~G~d 233 (351)
T PRK01216 180 IADIPGIGDITAEKLKKL---G-VNKLVDTLRIEFDELKGII------GEAKAKYLFSLARNEY 233 (351)
T ss_pred cccccCCCHHHHHHHHHc---C-CCcHHHHhcCCHHHHHHHH------CHHHHHHHHHHhCCCC
Confidence 677899999888877654 3 4556666653333344445 56778888883 754
No 245
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=53.66 E-value=28 Score=35.26 Aligned_cols=57 Identities=18% Similarity=0.278 Sum_probs=41.5
Q ss_pred HHHHHHHHcCCChhHHHHHHHHHHHhc-CCccccc-hhhhcCCCCCCHHHHHHHHHHHH
Q 015933 219 KLINIYRALGEDRRSFSYYKAIPVIEK-LPFKIES-ADQVKGLPGIGKSMQDHIQEIVT 275 (398)
Q Consensus 219 ~la~~~e~~g~~~r~~aY~rAa~~l~~-l~~~i~s-~~~l~~lpgIG~~ia~kI~Eil~ 275 (398)
++-.+.+-+|--.|++...+||..|.. +...+.+ .++|..|||||..++.-|.-|.=
T Consensus 76 evl~~W~gLGYysRArnL~~~A~~v~~~~~G~~P~~~~~l~~LpGiG~yTa~Ail~~a~ 134 (342)
T COG1194 76 EVLKAWEGLGYYSRARNLHKAAQEVVERHGGEFPDDEEELAALPGVGPYTAGAILSFAF 134 (342)
T ss_pred HHHHHHHhcChHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHhCCCCcHHHHHHHHHHHh
Confidence 344455556645588888888877765 4555553 57799999999999999987754
No 246
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=53.19 E-value=11 Score=38.98 Aligned_cols=34 Identities=24% Similarity=0.286 Sum_probs=29.6
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhh
Q 015933 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (398)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~ 324 (398)
.+.-.-|+.|.||||+.+.+|...||.+++++-.
T Consensus 319 ~g~aDDLk~I~GIGpk~e~~Ln~~Gi~~f~QIA~ 352 (400)
T PRK12373 319 PGGADDLKLISGVGPKIEATLNELGIFTFDQVAA 352 (400)
T ss_pred CCCchhhhhccCCChHHHHHHHhcCCCCHHHHhC
Confidence 3445677899999999999999999999999974
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=52.52 E-value=20 Score=40.54 Aligned_cols=32 Identities=13% Similarity=0.211 Sum_probs=27.4
Q ss_pred HHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhc
Q 015933 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (398)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~GirtledL~~~ 325 (398)
..+++.++|||||+.|+.|.+. +.|+++|.+.
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 4555669999999999999995 9999999864
No 248
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=52.40 E-value=9.9 Score=35.37 Aligned_cols=36 Identities=25% Similarity=0.396 Sum_probs=24.8
Q ss_pred cccch-hhhcCCCCCCHHHHHHHHHHHHhCCchhhHH
Q 015933 249 KIESA-DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEH 284 (398)
Q Consensus 249 ~i~s~-~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~ 284 (398)
+|..+ +.+..|||||.+.|.++.=.|-.-.-..++.
T Consensus 6 ~i~~LI~~l~kLPGvG~KsA~R~AfhLL~~~~~~~~~ 42 (198)
T COG0353 6 PIEKLIDALKKLPGVGPKSAQRLAFHLLQRDREDVER 42 (198)
T ss_pred HHHHHHHHHhhCCCCChhHHHHHHHHHHccCHHHHHH
Confidence 44444 6689999999999999987664433333333
No 249
>TIGR01084 mutY A/G-specific adenine glycosylase. This equivalog model identifies mutY members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=51.37 E-value=11 Score=36.85 Aligned_cols=24 Identities=17% Similarity=0.162 Sum_probs=19.4
Q ss_pred HHHHhhhccCcCHHHHHHHHHcCC
Q 015933 293 TISLFGEVWGIGPATAQKLYEKGH 316 (398)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~Gi 316 (398)
.++.|+++||||++||..+---++
T Consensus 103 ~~~~L~~LpGIG~~TA~~Il~~a~ 126 (275)
T TIGR01084 103 DFEDLAALPGVGRYTAGAILSFAL 126 (275)
T ss_pred HHHHHHhCCCCCHHHHHHHHHHHC
Confidence 577788999999999988775433
No 250
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=50.82 E-value=10 Score=34.00 Aligned_cols=25 Identities=24% Similarity=0.225 Sum_probs=20.8
Q ss_pred HHHHhhhccCcCHHHHHHHHHc-CCC
Q 015933 293 TISLFGEVWGIGPATAQKLYEK-GHR 317 (398)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~-Gir 317 (398)
+.-.|+.|+|||+.+|..+-.. ||.
T Consensus 28 v~~aLt~I~GIG~~~A~~I~~~lgi~ 53 (154)
T PTZ00134 28 VPYALTAIKGIGRRFAYLVCKKAGID 53 (154)
T ss_pred EEEeecccccccHHHHHHHHHHcCcC
Confidence 3445689999999999999987 884
No 251
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=50.30 E-value=23 Score=40.04 Aligned_cols=47 Identities=26% Similarity=0.483 Sum_probs=33.6
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcC-HHHHHHHHH
Q 015933 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIG-PATAQKLYE 313 (398)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvG-pktA~~l~~ 313 (398)
|..|||||...+..|.+ ..|++..+ .+- ..+.|+.+ || +++|+++|+
T Consensus 759 L~~lPgI~~~~a~~ll~--~f~si~~l---~~a----s~eeL~~~--iG~~~~A~~i~~ 806 (814)
T TIGR00596 759 LLKLPGVTKKNYRNLRK--KVKSIREL---AKL----SQNELNEL--IGDEEAAKRLYD 806 (814)
T ss_pred HHHCCCCCHHHHHHHHH--HcCCHHHH---HhC----CHHHHHHH--hCCHHHHHHHHH
Confidence 77999999999999876 34555444 332 23344453 88 999999997
No 252
>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=50.09 E-value=13 Score=30.30 Aligned_cols=45 Identities=27% Similarity=0.310 Sum_probs=25.8
Q ss_pred CchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhh
Q 015933 278 KLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (398)
Q Consensus 278 ~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~ 324 (398)
++.++..+-+ +|. .-+..+.|+||||..+.+|-+.|+.----|..
T Consensus 4 tSqKhr~Fv~-EPM-GeK~V~~laGIG~~lg~~L~~~GfdKAy~vLG 48 (89)
T PF02961_consen 4 TSQKHRNFVS-EPM-GEKPVTELAGIGPVLGKRLEEKGFDKAYVVLG 48 (89)
T ss_dssp S-HHHHHHTT-S---TT-BGGGSTT--HHHHHHHHHTT--BHHHHHH
T ss_pred cCHHHHHHhc-Ccc-CCCCccccCCcCHHHHHHHHHCCCcHHHHHhh
Confidence 3444444433 222 23445689999999999999999988766653
No 253
>PRK03352 DNA polymerase IV; Validated
Probab=49.76 E-value=30 Score=34.55 Aligned_cols=55 Identities=16% Similarity=0.331 Sum_probs=36.7
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--CCCCHH
Q 015933 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRTLD 320 (398)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~--Girtle 320 (398)
+..|||||+++++++..+ -+..+.+|.+-.+....+.| |++.+..||+. |+..-.
T Consensus 179 l~~l~gig~~~~~~L~~~----Gi~ti~dl~~l~~~~L~~~f------G~~~~~~l~~~a~G~d~~~ 235 (346)
T PRK03352 179 TDALWGVGPKTAKRLAAL----GITTVADLAAADPAELAATF------GPTTGPWLLLLARGGGDTE 235 (346)
T ss_pred HHHcCCCCHHHHHHHHHc----CCccHHHHhcCCHHHHHHHh------ChHHHHHHHHHhCCCCCCC
Confidence 688999999988886653 55666676654333344445 56678888875 775443
No 254
>PRK02794 DNA polymerase IV; Provisional
Probab=49.71 E-value=61 Score=33.41 Aligned_cols=52 Identities=12% Similarity=0.300 Sum_probs=32.0
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--CCCC
Q 015933 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (398)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~--Girt 318 (398)
+..|||||+.+.++...+ -+..+.+|.+-...... +.+| + .+..+|+. |+..
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 788999999988887643 35555565543322233 3444 3 56777764 7753
No 255
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=49.26 E-value=35 Score=31.59 Aligned_cols=55 Identities=20% Similarity=0.303 Sum_probs=33.3
Q ss_pred HHHHHHHhCCchhhHHHHhhchhHH--HHHhhhccCcCHHHHHHHHHc----CCCCHHHhhh
Q 015933 269 HIQEIVTTGKLSKLEHFEKDEKVRT--ISLFGEVWGIGPATAQKLYEK----GHRTLDDLKN 324 (398)
Q Consensus 269 kI~Eil~tG~~~~le~l~~~~~~~~--l~lf~~I~GvGpktA~~l~~~----GirtledL~~ 324 (398)
.+++|+....=..++ +-|+...-+ |-.|.=+||||-|+.+.+.++ -|.|++|+++
T Consensus 103 vve~iV~~~E~rFV~-fFN~A~PIt~RLH~LELLpGiGkK~m~~ILeERkkkpFeSFeDi~~ 163 (202)
T COG1491 103 VVEKIVKENEDRFVK-FFNEAEPITLRLHQLELLPGIGKKTMWAILEERKKKPFESFEDIKE 163 (202)
T ss_pred HHHHHHHhhhhHHHH-HhcccCcchHHHHHHHhcccccHHHHHHHHHHHhcCCCcCHHHHHH
Confidence 344555444333333 233322222 333445699999999999963 7889998875
No 256
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=49.26 E-value=13 Score=31.85 Aligned_cols=23 Identities=26% Similarity=0.491 Sum_probs=19.7
Q ss_pred HHhhhccCcCHHHHHHHHHc-CCC
Q 015933 295 SLFGEVWGIGPATAQKLYEK-GHR 317 (398)
Q Consensus 295 ~lf~~I~GvGpktA~~l~~~-Gir 317 (398)
--|+.|+|||..+|+.+.++ ||.
T Consensus 17 iALt~IyGIG~~~a~~I~~~~gi~ 40 (121)
T COG0099 17 IALTYIYGIGRRRAKEICKKAGID 40 (121)
T ss_pred ehhhhhccccHHHHHHHHHHcCCC
Confidence 34678999999999999987 874
No 257
>TIGR01446 DnaD_dom DnaD and phage-associated domain. This model represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria.
Probab=48.85 E-value=15 Score=27.90 Aligned_cols=19 Identities=21% Similarity=0.389 Sum_probs=16.7
Q ss_pred HHHHHHHHHcCCCCHHHhh
Q 015933 305 PATAQKLYEKGHRTLDDLK 323 (398)
Q Consensus 305 pktA~~l~~~GirtledL~ 323 (398)
-+.++.|++.||+|++|++
T Consensus 54 ~~Il~~W~~~gi~T~e~~~ 72 (73)
T TIGR01446 54 DAILNNWKNNGIKTVEDVE 72 (73)
T ss_pred HHHHHHHHHcCCCCHHHHh
Confidence 4678999999999999985
No 258
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=48.39 E-value=13 Score=33.20 Aligned_cols=25 Identities=28% Similarity=0.324 Sum_probs=20.9
Q ss_pred HHHHhhhccCcCHHHHHHHHHc-CCC
Q 015933 293 TISLFGEVWGIGPATAQKLYEK-GHR 317 (398)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~-Gir 317 (398)
+.-.|+.|+|||+++|..+-+. ||.
T Consensus 23 i~~aLt~IyGIG~~~a~~Ic~~lgi~ 48 (149)
T PRK04053 23 VEYALTGIKGIGRRTARAIARKLGLD 48 (149)
T ss_pred EeeeccccccccHHHHHHHHHHcCcC
Confidence 3445689999999999999987 885
No 259
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=48.22 E-value=14 Score=40.15 Aligned_cols=45 Identities=22% Similarity=0.403 Sum_probs=31.6
Q ss_pred HhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhHhcHHhHHhh
Q 015933 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDI 342 (398)
Q Consensus 296 lf~~I~GvGpktA~~l~~~GirtledL~~~~--~l~~~q~~Glk~~ed~ 342 (398)
.|-.|+||||++.++|.+ .+.|+++++.+. .|+.. +++.+..+.+
T Consensus 531 ~Ld~I~GiG~~r~~~LL~-~Fgs~~~i~~As~eel~~v-gi~~~~a~~i 577 (581)
T COG0322 531 SLDDIPGIGPKRRKALLK-HFGSLKGIKSASVEELAKV-GISKKLAEKI 577 (581)
T ss_pred ccccCCCcCHHHHHHHHH-HhhCHHHHHhcCHHHHHHc-CCCHHHHHHH
Confidence 345899999999999998 566788877652 35555 5555554444
No 260
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=48.00 E-value=15 Score=33.80 Aligned_cols=59 Identities=19% Similarity=0.353 Sum_probs=32.5
Q ss_pred HHHHHHHHHHhCCchhhHHHHhhchhH-HHHHhhhccCcCHHHHHHHHHc----CCCCHHHhhh
Q 015933 266 MQDHIQEIVTTGKLSKLEHFEKDEKVR-TISLFGEVWGIGPATAQKLYEK----GHRTLDDLKN 324 (398)
Q Consensus 266 ia~kI~Eil~tG~~~~le~l~~~~~~~-~l~lf~~I~GvGpktA~~l~~~----GirtledL~~ 324 (398)
+-..|++|+....-..++-+-...|.- -|-.|.=+||||-|+...+.++ -|.|++|+.+
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 455688888877755555443322222 1233445699999999999963 7777777764
No 261
>KOG3548 consensus DNA damage checkpoint protein RHP9/CRB2/53BP1 [Replication, recombination and repair]
Probab=47.42 E-value=39 Score=38.47 Aligned_cols=69 Identities=17% Similarity=0.281 Sum_probs=44.7
Q ss_pred CchHHHHHHHHHHhcCCEEEeecC-----C----CccEEEEcCCh-HHHHHHHHHhhhccCccccccchHHHHHhcCCCC
Q 015933 32 QNRRLQIWRQKLVQMGATVEEKLS-----K----KVTHVLAMDLE-ALLQQVSKQHLARFKGSVIRYQWLEDSLRLGEKV 101 (398)
Q Consensus 32 g~~r~~~l~~li~~~Gg~V~~~ls-----~----~VTHVV~~~~~-~~l~~l~~~~~~~~~~~lV~~~Wl~es~k~g~lv 101 (398)
+..-.++|...+..+|+-+++... . .+--||+.+.. .... + +.+...++++|+.+||.+|+-.|.-.
T Consensus 1082 ~~~f~e~~~e~le~G~aa~vd~~hada~~~D~~l~~fdvvl~d~~~~~sv-m--k~ad~l~~pvvs~EWvIQtiI~~~~i 1158 (1176)
T KOG3548|consen 1082 GGTFIEIWKEILELGGAAVVDGYHADAETLDETLLKFDVVLVDGTFRDSV-M--KYADTLGAPVVSSEWVIQTIILGKAI 1158 (1176)
T ss_pred CcchHHHHHHHHHhhchheecccccccccccccccceeEEEecCccHHHH-H--HHHHHhCCCccChhHhheeeeccccC
Confidence 456788999999999999998631 1 12334444433 2111 1 12233468999999999999887665
Q ss_pred Cc
Q 015933 102 SE 103 (398)
Q Consensus 102 ~e 103 (398)
..
T Consensus 1159 ~~ 1160 (1176)
T KOG3548|consen 1159 EP 1160 (1176)
T ss_pred Cc
Confidence 43
No 262
>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=46.95 E-value=13 Score=32.88 Aligned_cols=24 Identities=25% Similarity=0.271 Sum_probs=20.2
Q ss_pred HHHhhhccCcCHHHHHHHHHc-CCC
Q 015933 294 ISLFGEVWGIGPATAQKLYEK-GHR 317 (398)
Q Consensus 294 l~lf~~I~GvGpktA~~l~~~-Gir 317 (398)
.-.|+.|+|||+++|..+-+. ||.
T Consensus 20 ~~aLt~I~GIG~~~a~~I~~~lgi~ 44 (144)
T TIGR03629 20 EYALTGIKGIGRRFARAIARKLGVD 44 (144)
T ss_pred EEeecceeccCHHHHHHHHHHcCcC
Confidence 334679999999999999987 885
No 263
>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=46.94 E-value=12 Score=37.16 Aligned_cols=23 Identities=39% Similarity=0.557 Sum_probs=18.0
Q ss_pred hhccCcCHHHHHHHHHcCCCCHHH
Q 015933 298 GEVWGIGPATAQKLYEKGHRTLDD 321 (398)
Q Consensus 298 ~~I~GvGpktA~~l~~~Girtled 321 (398)
..|+|||||||.+|.++ +.|++.
T Consensus 226 ~gv~giG~k~A~~li~~-~~~~~~ 248 (316)
T cd00128 226 EGIPGIGPVTALKLIKK-YGDIEK 248 (316)
T ss_pred CCCCCccHHHHHHHHHH-cCChHH
Confidence 37999999999999997 334433
No 264
>PTZ00035 Rad51 protein; Provisional
Probab=46.34 E-value=25 Score=35.46 Aligned_cols=50 Identities=24% Similarity=0.307 Sum_probs=36.8
Q ss_pred HHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhHhcHHhHHhhh
Q 015933 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIK 343 (398)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~GirtledL~~~~--~l~~~q~~Glk~~ed~~ 343 (398)
.+..+ .-+||||.++.+|-+.||.|++||.... .|....+++....++|.
T Consensus 22 ~~~~l-~~~g~~~~~~~kL~~~g~~t~~~~~~~~~~~L~~~~gis~~~~~~i~ 73 (337)
T PTZ00035 22 EIEKL-QSAGINAADIKKLKEAGICTVESVAYATKKDLCNIKGISEAKVEKIK 73 (337)
T ss_pred cHHHH-hcCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhhCCCHHHHHHHH
Confidence 34445 3489999999999999999999998543 46566666666555655
No 265
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=46.22 E-value=29 Score=32.68 Aligned_cols=19 Identities=21% Similarity=0.372 Sum_probs=16.6
Q ss_pred hhhhc-CCCCCCHHHHHHHH
Q 015933 253 ADQVK-GLPGIGKSMQDHIQ 271 (398)
Q Consensus 253 ~~~l~-~lpgIG~~ia~kI~ 271 (398)
.++|. +|||||.++|+.|-
T Consensus 117 R~~Ll~~lpGIG~KTAd~vL 136 (208)
T PRK01229 117 REFLVKNIKGIGYKEASHFL 136 (208)
T ss_pred HHHHHHcCCCCcHHHHHHHH
Confidence 46788 99999999999976
No 266
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=45.79 E-value=17 Score=39.90 Aligned_cols=28 Identities=43% Similarity=0.599 Sum_probs=25.7
Q ss_pred HhhhccCcCHHHHHHHHHcCCCCHHHhh
Q 015933 296 LFGEVWGIGPATAQKLYEKGHRTLDDLK 323 (398)
Q Consensus 296 lf~~I~GvGpktA~~l~~~GirtledL~ 323 (398)
.+..+.||||++|.+|-+.|+.|+.||.
T Consensus 11 ~l~~l~gig~~~a~~l~~Lgi~tv~DLL 38 (677)
T COG1200 11 PLSTLKGIGPKTAEKLKKLGIHTVQDLL 38 (677)
T ss_pred chhhhcCcCHHHHHHHHHcCCCcHHHHH
Confidence 3558899999999999999999999997
No 267
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=45.50 E-value=37 Score=33.39 Aligned_cols=44 Identities=18% Similarity=0.329 Sum_probs=30.8
Q ss_pred CCC-hhHHHHHHHHHHHhc--CCcc-ccc----hhhhcCCCCCCHHHHHHHH
Q 015933 228 GED-RRSFSYYKAIPVIEK--LPFK-IES----ADQVKGLPGIGKSMQDHIQ 271 (398)
Q Consensus 228 g~~-~r~~aY~rAa~~l~~--l~~~-i~s----~~~l~~lpgIG~~ia~kI~ 271 (398)
|-. .|+..-..+|..+.+ ++.. ..+ .++|..|||||..+|+-|.
T Consensus 173 Gl~~~Ra~~L~~lA~~i~~g~l~l~~~~~~~~~~~~L~~LpGIGpwTA~~vl 224 (283)
T PRK10308 173 GMPLKRAEALIHLANAALEGTLPLTIPGDVEQAMKTLQTFPGIGRWTANYFA 224 (283)
T ss_pred CCCHHHHHHHHHHHHHHHcCCCCccccCCHHHHHHHHhcCCCcCHHHHHHHH
Confidence 544 377777788877754 4322 112 3679999999999999875
No 268
>PRK03858 DNA polymerase IV; Validated
Probab=44.80 E-value=40 Score=34.36 Aligned_cols=52 Identities=21% Similarity=0.382 Sum_probs=34.0
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--CCC
Q 015933 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHR 317 (398)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~--Gir 317 (398)
+..|||||+++++++..+ | +..+.+|.+-.+....+.| |+..++.||+. |+.
T Consensus 175 l~~l~Gig~~~~~~L~~~---G-i~t~~dl~~l~~~~L~~~f------G~~~~~~l~~~a~G~d 228 (396)
T PRK03858 175 VRRLWGVGPVTAAKLRAH---G-ITTVGDVAELPESALVSLL------GPAAGRHLHALAHNRD 228 (396)
T ss_pred hhhcCCCCHHHHHHHHHh---C-CCcHHHHhcCCHHHHHHHh------CcHHHHHHHHHhCCCC
Confidence 678899999999998764 3 4555555543333334444 56778888863 764
No 269
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=44.69 E-value=24 Score=35.69 Aligned_cols=52 Identities=25% Similarity=0.247 Sum_probs=35.5
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhHhcHHhHHhhh
Q 015933 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIK 343 (398)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~~--~l~~~q~~Glk~~ed~~ 343 (398)
+..+..+ .-.||+|.++++|-+.||.|++||.... .|....++.....+.|.
T Consensus 28 ~~~~~~l-~~~g~~~~~~~kL~~~g~~tv~~~~~~~~~~L~~~~g~s~~~~~ki~ 81 (344)
T PLN03187 28 FESIDKL-ISQGINAGDVKKLQDAGIYTCNGLMMHTKKNLTGIKGLSEAKVDKIC 81 (344)
T ss_pred ccCHHHH-hhCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHH
Confidence 3345555 3489999999999999999999997432 35555555544444443
No 270
>PRK05007 PII uridylyl-transferase; Provisional
Probab=44.46 E-value=42 Score=38.38 Aligned_cols=30 Identities=27% Similarity=0.696 Sum_probs=23.6
Q ss_pred CCeEEEEechhhcCC-cccCCeeEEEecCCC
Q 015933 367 PEVIILCGGSYRRGK-ASCGDLDVVIMHPDR 396 (398)
Q Consensus 367 p~~~v~~~Gs~RRgk-e~~gDvDiLit~~~~ 396 (398)
|++-++.+|||-||. .-..||||||-+++.
T Consensus 79 ~~~alvAvGgyGR~EL~p~SDiDll~l~~~~ 109 (884)
T PRK05007 79 PDLALVAVGGYGRGELHPLSDIDLLILSRKK 109 (884)
T ss_pred CceEEEecCCCCCcccCCcccceEEEEeCCC
Confidence 457788899997765 457899999998753
No 271
>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=43.95 E-value=19 Score=28.58 Aligned_cols=30 Identities=20% Similarity=0.458 Sum_probs=16.1
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHh
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEK 287 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~ 287 (398)
.+++.||+||..+.+...+ =-+.-+++|+.
T Consensus 3 ~~l~~LpNig~~~e~~L~~----vGI~t~~~L~~ 32 (81)
T PF04994_consen 3 NRLKDLPNIGPKSERMLAK----VGIHTVEDLRE 32 (81)
T ss_dssp --GCGSTT--HHHHHHHHH----TT--SHHHHHH
T ss_pred cchhhCCCCCHHHHHHHHH----cCCCCHHHHHH
Confidence 3689999999987765443 23455566664
No 272
>PRK13910 DNA glycosylase MutY; Provisional
Probab=43.52 E-value=16 Score=36.04 Aligned_cols=23 Identities=26% Similarity=0.242 Sum_probs=18.6
Q ss_pred HHHHhhhccCcCHHHHHHHHHcC
Q 015933 293 TISLFGEVWGIGPATAQKLYEKG 315 (398)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~G 315 (398)
..+.|+++||||++||..+---+
T Consensus 70 ~~~~L~~LpGIG~kTA~aIl~~a 92 (289)
T PRK13910 70 DYQSLLKLPGIGAYTANAILCFG 92 (289)
T ss_pred hHHHHHhCCCCCHHHHHHHHHHH
Confidence 35677799999999999877543
No 273
>PHA00439 exonuclease
Probab=43.45 E-value=17 Score=35.91 Aligned_cols=26 Identities=19% Similarity=0.290 Sum_probs=21.5
Q ss_pred hccCcCHHHHHHHHHc--CCCCHHHhhhc
Q 015933 299 EVWGIGPATAQKLYEK--GHRTLDDLKNE 325 (398)
Q Consensus 299 ~I~GvGpktA~~l~~~--GirtledL~~~ 325 (398)
.|+||| |||.+|.++ .+..++.....
T Consensus 192 GVpGIG-KTA~kLL~~~~~~~~~~~~~~s 219 (286)
T PHA00439 192 GIPGWG-DTAEAFLENPYIFEQVEKVLKS 219 (286)
T ss_pred CCCCcC-HHHHHHHhCccccchhhHHhhc
Confidence 799999 999999998 77777776644
No 274
>PRK10880 adenine DNA glycosylase; Provisional
Probab=43.13 E-value=17 Score=36.85 Aligned_cols=25 Identities=20% Similarity=0.243 Sum_probs=19.9
Q ss_pred HHHHHhhhccCcCHHHHHHHHHcCC
Q 015933 292 RTISLFGEVWGIGPATAQKLYEKGH 316 (398)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~~Gi 316 (398)
..++.|+++||||++||..+---++
T Consensus 106 ~~~~~L~~LpGIG~~TA~aIl~~af 130 (350)
T PRK10880 106 ETFEEVAALPGVGRSTAGAILSLSL 130 (350)
T ss_pred hhHHHHhcCCCccHHHHHHHHHHHC
Confidence 3567778999999999998876433
No 275
>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=42.54 E-value=24 Score=35.15 Aligned_cols=43 Identities=28% Similarity=0.313 Sum_probs=31.7
Q ss_pred cCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhHhcHHhHHhhh
Q 015933 301 WGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIK 343 (398)
Q Consensus 301 ~GvGpktA~~l~~~GirtledL~~~~--~l~~~q~~Glk~~ed~~ 343 (398)
.||||.++++|-+.||.|++||.... .|....+++....+++.
T Consensus 7 ~g~~~~~~~~L~~~g~~t~~~~~~~~~~~L~~~~gls~~~~~~i~ 51 (313)
T TIGR02238 7 HGINAADIKKLKSAGICTVNGVIMTTRRALCKIKGLSEAKVDKIK 51 (313)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHH
Confidence 67999999999999999999997543 35555555555555554
No 276
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=41.69 E-value=42 Score=31.62 Aligned_cols=20 Identities=25% Similarity=0.275 Sum_probs=16.5
Q ss_pred HHHHhhhccCcCHHHHHHHH
Q 015933 293 TISLFGEVWGIGPATAQKLY 312 (398)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~ 312 (398)
..+.|.+|.|||+-||..+.
T Consensus 113 ~R~~LL~iKGIG~ETaDsIL 132 (215)
T COG2231 113 LREELLSIKGIGKETADSIL 132 (215)
T ss_pred HHHHHHccCCcchhhHHHHH
Confidence 56677799999999998754
No 277
>COG1031 Uncharacterized Fe-S oxidoreductase [Energy production and conversion]
Probab=39.67 E-value=24 Score=37.18 Aligned_cols=32 Identities=16% Similarity=0.350 Sum_probs=29.3
Q ss_pred HHHHhhhccCcCHHHHHHHHHc-CCCCHHHhhh
Q 015933 293 TISLFGEVWGIGPATAQKLYEK-GHRTLDDLKN 324 (398)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~-GirtledL~~ 324 (398)
....+..|||||.+++.+++.. ++.|.||+++
T Consensus 514 s~~vl~~ipgig~~~~~~I~~~Rp~~s~e~~l~ 546 (560)
T COG1031 514 SKDVLRAIPGIGKKTLRKILAERPFKSSEEFLK 546 (560)
T ss_pred cHHHHHhcccchhhhHHHHHhcCCccchHHHHh
Confidence 4788999999999999999987 9999999985
No 278
>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=39.36 E-value=78 Score=31.60 Aligned_cols=53 Identities=17% Similarity=0.375 Sum_probs=32.6
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--CCCC
Q 015933 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (398)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~--Girt 318 (398)
+..|||||+++.+++..+ | +..+.+|.+-.....+. ..+| +.+..+|+. |+..
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 4 44555665432133332 2233 567777775 8754
No 279
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=39.11 E-value=60 Score=36.96 Aligned_cols=47 Identities=19% Similarity=0.368 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHhhhcC-C---CeEEEEechhhcCCc-ccCCeeEEEecCCC
Q 015933 350 EVEQMERLLQKAGEEVL-P---EVIILCGGSYRRGKA-SCGDLDVVIMHPDR 396 (398)
Q Consensus 350 ea~~~~~~v~~~~~~~~-p---~~~v~~~Gs~RRgke-~~gDvDiLit~~~~ 396 (398)
-+.-+..++..+-.... | ++-++.+|||-||.- --.||||||-+++.
T Consensus 34 ~~~~~D~~l~~l~~~~~~~~~~~iaLvAvGGYGR~eL~P~SDIDlliL~~~~ 85 (854)
T PRK01759 34 RSDFYDQLLIHLWQQFGLEEQSDLALIAVGGYGRREMFPLSDLDILILTEQP 85 (854)
T ss_pred HHHHHHHHHHHHHHHccCCCCCCeEEEEeCCcccccCCCcccceEEEEeCCC
Confidence 33445555555443331 2 356788999977754 45799999988753
No 280
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=38.95 E-value=53 Score=31.58 Aligned_cols=51 Identities=18% Similarity=0.293 Sum_probs=40.8
Q ss_pred HHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhc--cCchhhhHhcHHhHHhhh
Q 015933 292 RTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDIK 343 (398)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~--~~l~~~q~~Glk~~ed~~ 343 (398)
..+.-+|+|+||+...|..|.. -|-||+.+..+ +.|.+.+|+|....+.|-
T Consensus 192 ~~~~~Lt~i~~VnKtda~~LL~-~FgsLq~~~~AS~~ele~~~G~G~~kak~l~ 244 (254)
T KOG2841|consen 192 SLLGFLTTIPGVNKTDAQLLLQ-KFGSLQQISNASEGELEQCPGLGPAKAKRLH 244 (254)
T ss_pred HHHHHHHhCCCCCcccHHHHHH-hcccHHHHHhcCHhHHHhCcCcCHHHHHHHH
Confidence 4677889999999999999988 45589988865 568889999976655543
No 281
>COG5275 BRCT domain type II [General function prediction only]
Probab=37.60 E-value=65 Score=30.61 Aligned_cols=50 Identities=14% Similarity=0.077 Sum_probs=39.8
Q ss_pred CCCCCcEEEEccCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCCh
Q 015933 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLE 67 (398)
Q Consensus 17 ~~F~g~~iy~~~~~~g~~r~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~~~ 67 (398)
..+.|.++.|-+. +..-.++--+.++..+||+|.-..+...|-||..|+-
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 5688999988652 3334456678999999999999999999999987764
No 282
>PRK03348 DNA polymerase IV; Provisional
Probab=37.21 E-value=68 Score=33.63 Aligned_cols=53 Identities=17% Similarity=0.334 Sum_probs=36.3
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--CCCC
Q 015933 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (398)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~--Girt 318 (398)
+..|||||+.+.+++..+ -+..+.+|.+-.+....+.| |+.....||+. |+..
T Consensus 182 v~~L~GIG~~t~~~L~~l----GI~TigDLa~l~~~~L~~~f------G~~~g~~L~~~a~G~d~ 236 (454)
T PRK03348 182 VRRLWGIGPVTEEKLHRL----GIETIGDLAALSEAEVANLL------GATVGPALHRLARGIDD 236 (454)
T ss_pred ccccCCCCHHHHHHHHHc----CCccHHHHhcCCHHHHHHHH------CHHHHHHHHHHHcCCCC
Confidence 678899999988887654 44555566554444455566 67788888874 7743
No 283
>PRK04374 PII uridylyl-transferase; Provisional
Probab=36.20 E-value=67 Score=36.69 Aligned_cols=42 Identities=21% Similarity=0.498 Sum_probs=27.6
Q ss_pred HHHHHHHHhhhcCC---CeEEEEechhhcCC-cccCCeeEEEecCC
Q 015933 354 MERLLQKAGEEVLP---EVIILCGGSYRRGK-ASCGDLDVVIMHPD 395 (398)
Q Consensus 354 ~~~~v~~~~~~~~p---~~~v~~~Gs~RRgk-e~~gDvDiLit~~~ 395 (398)
+..++..+-....| ++-++.+|||-||. --..||||||-+++
T Consensus 55 ~D~~l~~~~~~~~~~~~~~alvAvGgYGR~EL~p~SDIDLliL~~~ 100 (869)
T PRK04374 55 VDQLMRNAWTRCIPADSGLSLHAVGGYGRGELFPRSDVDLLVLGET 100 (869)
T ss_pred HHHHHHHHHHHhCCCcCCEEEEEcCCccccccCCcccceEEEEecC
Confidence 34444444333334 35678899996665 45689999998874
No 284
>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=36.17 E-value=2.6e+02 Score=28.13 Aligned_cols=87 Identities=9% Similarity=0.200 Sum_probs=52.8
Q ss_pred HHHHHHHHhcCCccccc--hhhhcCCCCCCHHHHHHHHHHHHh------------CCchhhHHHHhhchhHHH-HHhhhc
Q 015933 236 YYKAIPVIEKLPFKIES--ADQVKGLPGIGKSMQDHIQEIVTT------------GKLSKLEHFEKDEKVRTI-SLFGEV 300 (398)
Q Consensus 236 Y~rAa~~l~~l~~~i~s--~~~l~~lpgIG~~ia~kI~Eil~t------------G~~~~le~l~~~~~~~~l-~lf~~I 300 (398)
-..||.+|..||..... +.++..+..|...+.+.|.++|+. |-...+-++.+..+...- .+|..+
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 35789999999975443 356778888888877777555541 222334445444444433 455555
Q ss_pred cCcCHHHHHHHHHcCCCCHHHhh
Q 015933 301 WGIGPATAQKLYEKGHRTLDDLK 323 (398)
Q Consensus 301 ~GvGpktA~~l~~~GirtledL~ 323 (398)
--.-|..|..+-+ -+-+++||.
T Consensus 224 ~~~dp~la~~Ir~-~mF~Fedl~ 245 (338)
T TIGR00207 224 EEFDPELAEEIKK-EMFVFEDIV 245 (338)
T ss_pred HHhCHHHHHHHHH-HccCHHHHh
Confidence 5566777766644 455666664
No 285
>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=36.03 E-value=66 Score=33.08 Aligned_cols=53 Identities=28% Similarity=0.488 Sum_probs=33.9
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhc--hhHHHHHhhhccCcCHHHHHHHHHc--CCCC
Q 015933 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDE--KVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (398)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~--~~~~l~lf~~I~GvGpktA~~l~~~--Girt 318 (398)
+..|||||+++++++..+ | +..+.+|.+-. +....+.| |++++..||+. |+..
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 678899999988877753 3 23333443322 33344455 67889998875 8764
No 286
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=34.82 E-value=37 Score=38.15 Aligned_cols=29 Identities=24% Similarity=0.676 Sum_probs=23.3
Q ss_pred CeEEEEechhhcCCc-ccCCeeEEEecCCC
Q 015933 368 EVIILCGGSYRRGKA-SCGDLDVVIMHPDR 396 (398)
Q Consensus 368 ~~~v~~~Gs~RRgke-~~gDvDiLit~~~~ 396 (398)
++-++.+|||-||.- -+.|||+||-+|..
T Consensus 66 ~~aLvAVGGyGRgEL~P~SDiDlL~L~p~~ 95 (867)
T COG2844 66 GLALVAVGGYGRGELHPLSDIDLLLLSPQK 95 (867)
T ss_pred ceEEEEeccccccccCCCccceEEEecCCC
Confidence 356788999988764 58999999988865
No 287
>PTZ00418 Poly(A) polymerase; Provisional
Probab=34.50 E-value=75 Score=34.61 Aligned_cols=30 Identities=27% Similarity=0.396 Sum_probs=24.4
Q ss_pred CCCeEEEEechhhcCCcc-cCCeeEEEecCC
Q 015933 366 LPEVIILCGGSYRRGKAS-CGDLDVVIMHPD 395 (398)
Q Consensus 366 ~p~~~v~~~Gs~RRgke~-~gDvDiLit~~~ 395 (398)
..+.++...||||-|--. +.|||.|+..|.
T Consensus 124 ~~~g~I~tfGSYrLGV~~pgSDID~L~V~P~ 154 (593)
T PTZ00418 124 QISGKLFTFGSYRLGVVAPGSDIDTLCLAPR 154 (593)
T ss_pred cCCeEEEEeccccccCCCCCCcccEEEECCC
Confidence 356788889999999865 679999998773
No 288
>TIGR02239 recomb_RAD51 DNA repair protein RAD51. This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).
Probab=34.46 E-value=95 Score=30.93 Aligned_cols=25 Identities=32% Similarity=0.412 Sum_probs=21.6
Q ss_pred cCcCHHHHHHHHHcCCCCHHHhhhc
Q 015933 301 WGIGPATAQKLYEKGHRTLDDLKNE 325 (398)
Q Consensus 301 ~GvGpktA~~l~~~GirtledL~~~ 325 (398)
.||+|.++.+|-+.||.|++||...
T Consensus 7 ~~~~~~~~~~l~~~g~~t~~~~~~~ 31 (316)
T TIGR02239 7 NGITAADIKKLQEAGLHTVESVAYA 31 (316)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHhC
Confidence 5699999999999999999999854
No 289
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=34.18 E-value=91 Score=31.54 Aligned_cols=42 Identities=21% Similarity=0.333 Sum_probs=30.7
Q ss_pred HHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhHhc
Q 015933 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLG 335 (398)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~~GirtledL~~~~--~l~~~q~~G 335 (398)
.++.+ .-.||++..+.+|-+.||.|++||.... .|..+.++.
T Consensus 27 ~~~~l-~~~gi~~~~i~kL~~~g~~T~~~~~~~~~~~L~~i~~is 70 (342)
T PLN03186 27 PIEQL-QASGIAALDIKKLKDAGIHTVESLAYAPKKDLLQIKGIS 70 (342)
T ss_pred cHHHH-HhCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCC
Confidence 45555 4489999999999999999999998543 344444443
No 290
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=33.14 E-value=55 Score=32.31 Aligned_cols=48 Identities=23% Similarity=0.302 Sum_probs=29.4
Q ss_pred HHHcCCChhHHHHHHHHHHHhcCCcc---ccc-----h----hhhcCCCCCCHHHHHHHH
Q 015933 224 YRALGEDRRSFSYYKAIPVIEKLPFK---IES-----A----DQVKGLPGIGKSMQDHIQ 271 (398)
Q Consensus 224 ~e~~g~~~r~~aY~rAa~~l~~l~~~---i~s-----~----~~l~~lpgIG~~ia~kI~ 271 (398)
++-.|=.+|++--..+|+.|-.=+-. +.+ + +.|..|||||.++|+=|-
T Consensus 176 LR~~gfGYRAkYI~~ta~~l~~~~g~~~wLqsl~~~~yeear~~L~~lpGVG~KVADCI~ 235 (323)
T KOG2875|consen 176 LRKLGFGYRAKYISATARALQEKQGGLAWLQSLRKSSYEEAREALCSLPGVGPKVADCIC 235 (323)
T ss_pred HHHcCcchhHHHHHHHHHHHHHhcccchHHHHHhcccHHHHHHHHhcCCCCcchHhhhhh
Confidence 34445556666555566665543332 222 2 458899999999999664
No 291
>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=32.92 E-value=63 Score=32.77 Aligned_cols=54 Identities=19% Similarity=0.353 Sum_probs=32.5
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhh--chhHHHHHhhhccCcCHHHHHHHHHc--CCCC
Q 015933 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKD--EKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (398)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~--~~~~~l~lf~~I~GvGpktA~~l~~~--Girt 318 (398)
+..|||||.++..++.+-+ | +..+.+|.+- .+....+.| |.+.+..+|+. |+..
T Consensus 184 v~~l~GiG~~~~~~ll~~~--G-i~ti~dl~~~~~~~~~L~~~f------G~~~g~~l~~~a~G~d~ 241 (359)
T cd01702 184 ITSIRGLGGKLGEEIIDLL--G-LPTEGDVAGFRSSESDLQEHF------GEKLGEWLYNLLRGIDH 241 (359)
T ss_pred HHHhCCcCHHHHHHHHHHc--C-CcCHHHHHhccCCHHHHHHHH------HHHHHHHHHHHhCCCCC
Confidence 6788999998876653322 2 3333444332 223344445 67888999875 8754
No 292
>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=32.19 E-value=21 Score=27.09 Aligned_cols=22 Identities=18% Similarity=0.527 Sum_probs=17.6
Q ss_pred EEEEechhhcCCccc----CCeeEEE
Q 015933 370 IILCGGSYRRGKASC----GDLDVVI 391 (398)
Q Consensus 370 ~v~~~Gs~RRgke~~----gDvDiLi 391 (398)
.|++--+|||||..+ ||+|||=
T Consensus 34 rvmiPqeFkrGKsIiAV~EGe~~ilN 59 (67)
T TIGR02922 34 RVMIPQEFKRGKSIIAVCEGEITILN 59 (67)
T ss_pred cEEcchHHcCCCeEEEEEecceeehh
Confidence 577777999999876 7888774
No 293
>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=31.90 E-value=35 Score=39.50 Aligned_cols=26 Identities=19% Similarity=0.326 Sum_probs=21.1
Q ss_pred hhccCcCHHHHHHHHHc-CCCCHHHhh
Q 015933 298 GEVWGIGPATAQKLYEK-GHRTLDDLK 323 (398)
Q Consensus 298 ~~I~GvGpktA~~l~~~-GirtledL~ 323 (398)
..|+||||+||.+|... |-.+|+.|.
T Consensus 869 ~GI~GIGpktAl~li~~~~~~~le~L~ 895 (1034)
T TIGR00600 869 EGIPTVGPVSAMEILNEFPGDGLEPLL 895 (1034)
T ss_pred CCCCcccHHHHHHHHHHcCCCCHHHHH
Confidence 36999999999999998 645666665
No 294
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=30.56 E-value=1.5e+02 Score=30.04 Aligned_cols=82 Identities=17% Similarity=0.206 Sum_probs=47.4
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH-------cCCCCHHHhhhc
Q 015933 253 ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE-------KGHRTLDDLKNE 325 (398)
Q Consensus 253 ~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~-------~GirtledL~~~ 325 (398)
+++|.+ +||+..+.+|+++ .-+.-++.+..-.+ +.|.++-|+...+|.++.+ .|+.|-.++...
T Consensus 31 ~~~l~~-~g~~~~~~~kL~~----~g~~tv~~~~~~~~----~~L~~~~g~s~~~~~ki~~~a~~~~~~~~~ta~~~~~~ 101 (344)
T PLN03187 31 IDKLIS-QGINAGDVKKLQD----AGIYTCNGLMMHTK----KNLTGIKGLSEAKVDKICEAAEKLLNQGFITGSDALLK 101 (344)
T ss_pred HHHHhh-CCCCHHHHHHHHH----cCCCcHHHHHhCCH----HHHHHhcCCCHHHHHHHHHHHHHhhcccCCcHHHHHhh
Confidence 334444 5799887776553 34455555543332 2344888999999998774 277777777643
Q ss_pred cCchhhhHhcHHhHHhhh
Q 015933 326 DSLTHSQRLGLKYFDDIK 343 (398)
Q Consensus 326 ~~l~~~q~~Glk~~ed~~ 343 (398)
.+-......|.+-.++++
T Consensus 102 ~~~~~~isTG~~~LD~lL 119 (344)
T PLN03187 102 RKSVVRITTGSQALDELL 119 (344)
T ss_pred hccCceecCCcHhHHhhc
Confidence 211111224666655554
No 295
>PRK03059 PII uridylyl-transferase; Provisional
Probab=29.55 E-value=1.1e+02 Score=34.96 Aligned_cols=30 Identities=27% Similarity=0.616 Sum_probs=23.1
Q ss_pred CCeEEEEechhhcCC-cccCCeeEEEecCCC
Q 015933 367 PEVIILCGGSYRRGK-ASCGDLDVVIMHPDR 396 (398)
Q Consensus 367 p~~~v~~~Gs~RRgk-e~~gDvDiLit~~~~ 396 (398)
.++-++.+|||-||. --..|||+|+-+++.
T Consensus 60 ~~~alvAvGgyGR~EL~p~SDiDll~l~~~~ 90 (856)
T PRK03059 60 AGAALVAVGGYGRGELFPYSDVDLLVLLPDA 90 (856)
T ss_pred CCeEEEEcCCCCCcccCCCCCCEEEEEecCC
Confidence 456788899996664 567899999988753
No 296
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=29.04 E-value=53 Score=22.36 Aligned_cols=23 Identities=17% Similarity=0.251 Sum_probs=18.6
Q ss_pred HHhhhccCcCHHHHHHHHHcCCC
Q 015933 295 SLFGEVWGIGPATAQKLYEKGHR 317 (398)
Q Consensus 295 ~lf~~I~GvGpktA~~l~~~Gir 317 (398)
..+....||-+.|.+.|.++|.=
T Consensus 4 ~e~a~~~gv~~~tlr~~~~~g~l 26 (49)
T cd04761 4 GELAKLTGVSPSTLRYYERIGLL 26 (49)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCC
Confidence 34557789999999999998763
No 297
>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=28.72 E-value=1e+02 Score=27.24 Aligned_cols=29 Identities=31% Similarity=0.552 Sum_probs=21.7
Q ss_pred CeEEEEechhhcCCc-ccCCeeEEEecCCC
Q 015933 368 EVIILCGGSYRRGKA-SCGDLDVVIMHPDR 396 (398)
Q Consensus 368 ~~~v~~~Gs~RRgke-~~gDvDiLit~~~~ 396 (398)
++-+.+.|||-|+.- ...|+|+++.+++.
T Consensus 55 ~~~~la~Gs~GR~E~~~~SD~D~~~v~~~~ 84 (172)
T cd05401 55 PFALLALGSYGRGELNPSSDQDLLLLYDDD 84 (172)
T ss_pred cEEEEEeCCcccCCcCCCcCcceEEEeCCC
Confidence 356778899966654 57899999988754
No 298
>PF15101 DUF4557: Domain of unknown function (DUF4557)
Probab=28.57 E-value=66 Score=30.16 Aligned_cols=85 Identities=21% Similarity=0.257 Sum_probs=55.1
Q ss_pred CCCcEEEEccCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCC-----hHHHHHHHHHhhhccCccccccchHHH
Q 015933 19 FAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDL-----EALLQQVSKQHLARFKGSVIRYQWLED 93 (398)
Q Consensus 19 F~g~~iy~~~~~~g~~r~~~l~~li~~~Gg~V~~~ls~~VTHVV~~~~-----~~~l~~l~~~~~~~~~~~lV~~~Wl~e 93 (398)
|+|++..|..+... -++++-..+||.+++-- ..--+...|. -+....+.... ...-|-...||..
T Consensus 1 F~~q~aWFs~SVs~-----~~~~~Wv~~GG~isd~~--~AdFLFS~DAshpDT~~iy~S~dY~~---d~aTVFha~yl~a 70 (212)
T PF15101_consen 1 FQGQRAWFSGSVSQ-----DLRQFWVKEGGTISDWD--AADFLFSCDASHPDTARIYQSLDYIE---DRATVFHASYLSA 70 (212)
T ss_pred CCCceeeeecCcch-----HHHHHHHhcCCccCChh--hcceeeecCCCCcchHhhhhhhhhhh---cCeeeeeHHHHHH
Confidence 88999999754222 46788889999999832 1222333222 22334443321 2567899999999
Q ss_pred HHhcCCCCC--ccccccccCCC
Q 015933 94 SLRLGEKVS--EDLYRIKLDPE 113 (398)
Q Consensus 94 s~k~g~lv~--ee~y~l~~~~~ 113 (398)
|..+...-+ -..|.|..|++
T Consensus 71 ~~na~s~~sV~LGhyVL~~PP~ 92 (212)
T PF15101_consen 71 VANAESKNSVALGHYVLNTPPE 92 (212)
T ss_pred HhhhhhcCCccccceEecCCHH
Confidence 999987755 57788876665
No 299
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=28.51 E-value=1.1e+02 Score=35.11 Aligned_cols=28 Identities=25% Similarity=0.633 Sum_probs=22.3
Q ss_pred CeEEEEechhhcCC-cccCCeeEEEecCC
Q 015933 368 EVIILCGGSYRRGK-ASCGDLDVVIMHPD 395 (398)
Q Consensus 368 ~~~v~~~Gs~RRgk-e~~gDvDiLit~~~ 395 (398)
++-++.+|||-||. --..||||||-+++
T Consensus 78 ~~alvAvGgyGR~EL~p~SDiDll~l~~~ 106 (895)
T PRK00275 78 DIALVAVGGYGRGELHPYSDIDLLILLDS 106 (895)
T ss_pred CEEEEEcCCccccCcCCCCCceEEEEecC
Confidence 45778899997765 45789999998874
No 300
>PF07261 DnaB_2: Replication initiation and membrane attachment; InterPro: IPR006343 This entry represents a domain found in several bacterial replication initiation and membrane attachment proteins, DnaB and DnaD. The DnaD protein is a component of the PriA primosome. The PriA primosome functions to recruit the replication fork helicase onto the DNA []. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria []. The DnaB protein is essential for both replication initiation and membrane attachment of the origin region of the chromosome and Plasmid pUB110 in Bacillus subtilis. It is known that there are two different classes (DnaBI and DnaBII) in the DnaB mutants; DnaBI is essential for both chromosome and pUB110 replication, whereas DnaBII is necessary only for chromosome replication []. This domain tends to be found towards the C terminus of DnaB and DnaD proteins and is alpha helical in nature.; PDB: 2I5U_A 2ZC2_A.
Probab=28.44 E-value=23 Score=26.94 Aligned_cols=21 Identities=19% Similarity=0.286 Sum_probs=15.1
Q ss_pred HHHHHHHHHcCCCCHHHhhhc
Q 015933 305 PATAQKLYEKGHRTLDDLKNE 325 (398)
Q Consensus 305 pktA~~l~~~GirtledL~~~ 325 (398)
-+.+..|.+.|+.|++|+.+.
T Consensus 54 ~~Il~~W~~~gi~t~e~~~~~ 74 (77)
T PF07261_consen 54 EKILNNWKQKGIKTVEDAEEY 74 (77)
T ss_dssp HHHHHHHHHCT--SCCCCT--
T ss_pred HHHHHHHHHcCCCCHHHHHHH
Confidence 477899999999999998753
No 301
>KOG1715 consensus Mitochondrial/chloroplast ribosomal protein L12 [Translation, ribosomal structure and biogenesis]
Probab=27.82 E-value=1.3e+02 Score=27.91 Aligned_cols=58 Identities=31% Similarity=0.459 Sum_probs=44.6
Q ss_pred hhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhccCchhhhHhcHHhHHhhhcCCCHHHHHHHHHHHHH
Q 015933 281 KLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQK 360 (398)
Q Consensus 281 ~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~~~l~~~q~~Glk~~ed~~~~i~r~ea~~~~~~v~~ 360 (398)
+|+.+....+..+++....+.|+|-+=|++|.+. .-.-+.+.++.+||++|-..++.
T Consensus 123 kL~~fda~~KIkVIKEVR~~tgL~LkeAKklVE~-----------------------aP~ilKegvtKeEAEkik~kLea 179 (187)
T KOG1715|consen 123 KLEKFDASSKIKVIKEVRALTGLGLKEAKKLVEK-----------------------APKILKEGVTKEEAEEIKEKLEA 179 (187)
T ss_pred EEeecCccchhHHHHHHHHhccccHHHHHHHHHh-----------------------ccHHHHcCCCHHHHHHHHHHHHH
Confidence 4566666778889999999999999999999872 11125567899999998777776
Q ss_pred H
Q 015933 361 A 361 (398)
Q Consensus 361 ~ 361 (398)
+
T Consensus 180 ~ 180 (187)
T KOG1715|consen 180 A 180 (187)
T ss_pred c
Confidence 4
No 302
>PF05559 DUF763: Protein of unknown function (DUF763); InterPro: IPR008482 This family consists of several uncharacterised bacterial and archaeal proteins of unknown function.
Probab=27.66 E-value=53 Score=32.87 Aligned_cols=20 Identities=25% Similarity=0.368 Sum_probs=15.9
Q ss_pred HHHHhhhccCcCHHHHHHHH
Q 015933 293 TISLFGEVWGIGPATAQKLY 312 (398)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~ 312 (398)
-++.|..++||||+|.+.|.
T Consensus 267 ~feeLL~~~GvGp~TlRALa 286 (319)
T PF05559_consen 267 DFEELLLIKGVGPSTLRALA 286 (319)
T ss_pred CHHHHHhcCCCCHHHHHHHH
Confidence 44455589999999999886
No 303
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=26.42 E-value=66 Score=31.95 Aligned_cols=76 Identities=18% Similarity=0.239 Sum_probs=46.5
Q ss_pred hHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHH
Q 015933 232 RSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKL 311 (398)
Q Consensus 232 r~~aY~rAa~~l~~l~~~i~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l 311 (398)
|++.|-.+..+...+=.| .-+.-+.+||-+-..+.+++-.- -|.++ .+. ....+.|..|.|||...|+.+
T Consensus 272 kvlGY~~~~~~~d~~vsp-RGYR~l~kIpRlp~~iv~nlV~~--F~~l~---~il----~As~edL~~VeGIGe~rAr~i 341 (349)
T COG1623 272 KVLGYPKTTEADDSLVSP-RGYRLLNKIPRLPFAIVENLVRA--FGTLD---GIL----EASAEDLDAVEGIGEARARAI 341 (349)
T ss_pred HHhCCCCcchhcccccCc-hhhHHHhcCcCccHHHHHHHHHH--HhhHH---HHH----HhcHhHHhhhcchhHHHHHHH
Confidence 677776665443222110 11344788998888888776542 23333 332 235678889999999999987
Q ss_pred HHcCCCC
Q 015933 312 YEKGHRT 318 (398)
Q Consensus 312 ~~~Girt 318 (398)
-+ |+..
T Consensus 342 ~~-Gl~r 347 (349)
T COG1623 342 KE-GLSR 347 (349)
T ss_pred HH-hHhh
Confidence 54 5443
No 304
>COG1415 Uncharacterized conserved protein [Function unknown]
Probab=26.24 E-value=61 Score=32.86 Aligned_cols=21 Identities=33% Similarity=0.322 Sum_probs=16.7
Q ss_pred HHHHhhhccCcCHHHHHHHHH
Q 015933 293 TISLFGEVWGIGPATAQKLYE 313 (398)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~ 313 (398)
-++.|.-++||||+|++.|.=
T Consensus 276 Df~elLl~~GiGpstvRALal 296 (373)
T COG1415 276 DFEELLLVPGIGPSTVRALAL 296 (373)
T ss_pred cHHHHHhccCCCHHHHHHHHH
Confidence 445555899999999999874
No 305
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A.
Probab=26.01 E-value=43 Score=28.05 Aligned_cols=21 Identities=38% Similarity=0.561 Sum_probs=15.0
Q ss_pred HHHHhhhccCcCHHHHHHHHH
Q 015933 293 TISLFGEVWGIGPATAQKLYE 313 (398)
Q Consensus 293 ~l~lf~~I~GvGpktA~~l~~ 313 (398)
.-.++.=|.|+||++|..|.+
T Consensus 48 ~~~~LqfV~GLGPRKA~~Ll~ 68 (104)
T PF14635_consen 48 LANLLQFVCGLGPRKAQALLK 68 (104)
T ss_dssp HHGGGGGSTT--HHHHHHHHH
T ss_pred HHhhHhHhcCCChHHHHHHHH
Confidence 344555699999999999986
No 306
>PF12482 DUF3701: Phage integrase protein; InterPro: IPR022169 This domain family is found in bacteria, and is approximately 100 amino acids in length. The family is found in association with PF00589 from PFAM.
Probab=25.85 E-value=63 Score=26.70 Aligned_cols=39 Identities=31% Similarity=0.347 Sum_probs=28.0
Q ss_pred CHHHHHHHHHcCCCCHHHhhhc----c-C-chhhhHhcHHhHHhh
Q 015933 304 GPATAQKLYEKGHRTLDDLKNE----D-S-LTHSQRLGLKYFDDI 342 (398)
Q Consensus 304 GpktA~~l~~~GirtledL~~~----~-~-l~~~q~~Glk~~ed~ 342 (398)
.|..|++|-..||+||.||..- + + ...+.++|......|
T Consensus 22 ~p~va~~L~aaGi~TL~dL~~~i~~rg~~Wwr~vpglG~~~A~~I 66 (96)
T PF12482_consen 22 PPRVARRLAAAGIRTLADLVDRINRRGGRWWRAVPGLGAAGARRI 66 (96)
T ss_pred CHHHHHHHHHcCCchHHHHHHHHHHccchHHHhCcccchHHHHHH
Confidence 5999999999999999999742 2 2 345666665554443
No 307
>PRK07945 hypothetical protein; Provisional
Probab=25.73 E-value=36 Score=34.26 Aligned_cols=30 Identities=27% Similarity=0.423 Sum_probs=23.7
Q ss_pred HhhhccCcCHHHHHHHHHc---C-CCCHHHhhhc
Q 015933 296 LFGEVWGIGPATAQKLYEK---G-HRTLDDLKNE 325 (398)
Q Consensus 296 lf~~I~GvGpktA~~l~~~---G-irtledL~~~ 325 (398)
-|++|||||..+|.++.+. | +.-|++|+.+
T Consensus 50 ~l~~~~giG~~~a~~i~e~~~tg~~~~l~~l~~~ 83 (335)
T PRK07945 50 SLTSLPGIGPKTAKVIAQALAGRVPDYLAELRAD 83 (335)
T ss_pred CcccCCCcCHHHHHHHHHHHhcCCHHHHHHHHHh
Confidence 3559999999999999873 5 4678888753
No 308
>PRK03381 PII uridylyl-transferase; Provisional
Probab=24.81 E-value=1.5e+02 Score=33.31 Aligned_cols=27 Identities=30% Similarity=0.544 Sum_probs=21.1
Q ss_pred eEEEEechhhcCC-cccCCeeEEEecCC
Q 015933 369 VIILCGGSYRRGK-ASCGDLDVVIMHPD 395 (398)
Q Consensus 369 ~~v~~~Gs~RRgk-e~~gDvDiLit~~~ 395 (398)
+-++.+|||-||. .-..|||+||-+++
T Consensus 58 ~alvAvg~~gr~el~p~SD~Dll~l~~~ 85 (774)
T PRK03381 58 VALVAVGGLGRRELLPYSDLDLVLLHDG 85 (774)
T ss_pred eEEEEeCCcCCcCcCCCCCCeEEEEeCC
Confidence 5677889996665 45689999998874
No 309
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=24.58 E-value=90 Score=33.06 Aligned_cols=53 Identities=23% Similarity=0.347 Sum_probs=40.7
Q ss_pred HHHHHhhhccCcCHHHHHHHHHcCCCCHHHhhhcc--CchhhhHhcHHhHHhhhc
Q 015933 292 RTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIKT 344 (398)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~l~~~GirtledL~~~~--~l~~~q~~Glk~~ed~~~ 344 (398)
..+.+|....++....|..|++.|+.|+++|.... .|..+.++.-...+.+..
T Consensus 353 ~~~~~f~~~~~ide~~~~~l~~~g~~~~e~~~~~~~~el~~i~~~~ee~~~~l~~ 407 (470)
T PRK09202 353 AILDLFMEALDIDEEIAQLLVEEGFSSLEELAYVPVEELLEIEGFDEETVEELRE 407 (470)
T ss_pred hHHHHHhhhccccHHHHHHHHHcCcccHHHHhcCCHHHHhhccCCCHHHHHHHHH
Confidence 35678899999999999999999999999998542 355566666555555554
No 310
>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=24.48 E-value=66 Score=26.75 Aligned_cols=34 Identities=15% Similarity=0.211 Sum_probs=25.3
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHh
Q 015933 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEK 287 (398)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~ 287 (398)
-.|..|.|||...|..|...+.=.....+..|..
T Consensus 15 ~aLt~IyGIG~~~A~~Ic~~lgi~~~~~~~~Ls~ 48 (107)
T PF00416_consen 15 IALTKIYGIGRRKAKQICKKLGINPNKKVGDLSD 48 (107)
T ss_dssp HHHTTSTTBCHHHHHHHHHHTTS-SSSBTTTSTH
T ss_pred hHHhhhhccCHHHHHHHHHHcCCChhhhcccCCH
Confidence 3589999999999999998887555555555543
No 311
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=24.46 E-value=1.6e+02 Score=21.45 Aligned_cols=25 Identities=20% Similarity=0.354 Sum_probs=19.3
Q ss_pred HHHhhhccCcCHHHHHHHHHc-CCCC
Q 015933 294 ISLFGEVWGIGPATAQKLYEK-GHRT 318 (398)
Q Consensus 294 l~lf~~I~GvGpktA~~l~~~-Girt 318 (398)
+..+.+..||.+.|.+.|.++ |+-.
T Consensus 3 ~~eva~~~gvs~~tlr~w~~~~g~~~ 28 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWERRYGLPA 28 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHhCCCCC
Confidence 345567789999999999986 7643
No 312
>PRK00024 hypothetical protein; Reviewed
Probab=24.40 E-value=79 Score=29.95 Aligned_cols=41 Identities=29% Similarity=0.437 Sum_probs=24.6
Q ss_pred HHHHHHHHHH-hCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 015933 266 MQDHIQEIVT-TGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (398)
Q Consensus 266 ia~kI~Eil~-tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~ 313 (398)
....-.++++ -|.+..+-.. ..+.|.+|+|||+.+|..|..
T Consensus 43 ~~~LA~~LL~~fgsL~~l~~a-------s~~eL~~i~GIG~akA~~L~a 84 (224)
T PRK00024 43 VLDLARELLQRFGSLRGLLDA-------SLEELQSIKGIGPAKAAQLKA 84 (224)
T ss_pred HHHHHHHHHHHcCCHHHHHhC-------CHHHHhhccCccHHHHHHHHH
Confidence 3344444453 3555544332 244566999999999987753
No 313
>KOG2379 consensus Endonuclease MUS81 [Replication, recombination and repair]
Probab=24.13 E-value=68 Score=34.02 Aligned_cols=43 Identities=19% Similarity=0.220 Sum_probs=37.1
Q ss_pred hHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHH
Q 015933 232 RSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIV 274 (398)
Q Consensus 232 r~~aY~rAa~~l~~l~~~i~s~~~l~~lpgIG~~ia~kI~Eil 274 (398)
-...|.+|...|...+++|.++.++..+.|+|+...-++.|..
T Consensus 35 ~~~s~~ka~r~l~~~~~~l~tl~dl~~ikG~G~~~~~k~~~~~ 77 (501)
T KOG2379|consen 35 SEYSLKKALRNLCKAKDPLMTLPDLSSIKGFGKKWIVKLMEAY 77 (501)
T ss_pred hcccHHHHHHHhhcccCcccchhhcccccCccchhHHHHHhHH
Confidence 3468999999999999999999999999999997777776544
No 314
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=22.90 E-value=87 Score=20.75 Aligned_cols=21 Identities=24% Similarity=0.512 Sum_probs=17.0
Q ss_pred HhhhccCcCHHHHHHHHHcCC
Q 015933 296 LFGEVWGIGPATAQKLYEKGH 316 (398)
Q Consensus 296 lf~~I~GvGpktA~~l~~~Gi 316 (398)
.+.+..||.+.|+.+|.+.|.
T Consensus 5 e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 5 EAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred HHHHHHCcCHHHHHHHHHcCC
Confidence 444667999999999999864
No 315
>PF13838 Clathrin_H_link: Clathrin-H-link; PDB: 2XZG_A 3GD1_I 1BPO_C 1C9I_B 1C9L_A.
Probab=22.51 E-value=1.6e+02 Score=22.62 Aligned_cols=44 Identities=20% Similarity=0.342 Sum_probs=31.7
Q ss_pred CCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhH------HHHHhhhcc
Q 015933 258 GLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVR------TISLFGEVW 301 (398)
Q Consensus 258 ~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~------~l~lf~~I~ 301 (398)
+|||.-+-..++-.+++..|...+.-++-.+.|-+ +|.-|.+++
T Consensus 1 ~lpGad~l~~~~F~~l~~~g~y~eAA~~AA~sP~giLRt~~Ti~rFk~~p 50 (66)
T PF13838_consen 1 NLPGADDLYVQQFNELFSQGQYEEAAKVAANSPRGILRTPETINRFKQVP 50 (66)
T ss_dssp T-SS-HHHHHHHHHHHHHTT-HHHHHHHHHHSGGGTT-SHHHHHHHHTS-
T ss_pred CCccHHHHHHHHHHHHHHcCCHHHHHHHHHhCccchhcCHHHHHHHHcCC
Confidence 58899999999999999999999988887777643 555555444
No 316
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.32 E-value=95 Score=29.37 Aligned_cols=42 Identities=21% Similarity=0.213 Sum_probs=0.0
Q ss_pred CH-HHHHHHHHHHHh----CCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHH
Q 015933 263 GK-SMQDHIQEIVTT----GKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKL 311 (398)
Q Consensus 263 G~-~ia~kI~Eil~t----G~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l 311 (398)
++ .+.+.-+++++. |.+..+-.. ..+.|++|+|||+.+|..+
T Consensus 30 ~~~~~~~lA~~ll~~f~~~g~l~~l~~a-------~~~eL~~i~GiG~aka~~l 76 (218)
T TIGR00608 30 KGLDVLSLSKRLLDVFGRQDSLGHLLSA-------PPEELSSVPGIGEAKAIQL 76 (218)
T ss_pred CCCCHHHHHHHHHHHhcccCCHHHHHhC-------CHHHHHhCcCCcHHHHHHH
No 317
>PRK02406 DNA polymerase IV; Validated
Probab=21.96 E-value=1.8e+02 Score=29.00 Aligned_cols=52 Identities=23% Similarity=0.520 Sum_probs=32.6
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--CCCC
Q 015933 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (398)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~--Girt 318 (398)
+..|||||+.+.+++..+ -+..+.+|.+-.+.... +.+| . ....+|+. |+..
T Consensus 170 i~~l~giG~~~~~~L~~~----Gi~ti~dl~~l~~~~L~----~~fG--~-~~~~l~~~a~G~d~ 223 (343)
T PRK02406 170 VEKIPGVGKVTAEKLHAL----GIYTCADLQKYDLAELI----RHFG--K-FGRRLYERARGIDE 223 (343)
T ss_pred cchhcCCCHHHHHHHHHc----CCCcHHHHHhCCHHHHH----HHHh--H-HHHHHHHHhCCCCC
Confidence 678899999999887654 34556666553333333 4444 3 56667764 8754
No 318
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=21.76 E-value=81 Score=21.07 Aligned_cols=20 Identities=25% Similarity=0.360 Sum_probs=15.9
Q ss_pred HhhhccCcCHHHHHHHHHcC
Q 015933 296 LFGEVWGIGPATAQKLYEKG 315 (398)
Q Consensus 296 lf~~I~GvGpktA~~l~~~G 315 (398)
......||++.|+.+|.+.|
T Consensus 6 e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 6 EAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred HHHHHHCCCHHHHHHHHHcC
Confidence 34456699999999999875
No 319
>PF09558 DUF2375: Protein of unknown function (DUF2375); InterPro: IPR014271 Two members of this family are found in Colwellia psychrerythraea (strain 34H / ATCC BAA-681) 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 IPR013424 from INTERPRO.
Probab=21.55 E-value=34 Score=26.32 Aligned_cols=22 Identities=27% Similarity=0.522 Sum_probs=17.5
Q ss_pred eEEEEechhhcCCccc----CCeeEE
Q 015933 369 VIILCGGSYRRGKASC----GDLDVV 390 (398)
Q Consensus 369 ~~v~~~Gs~RRgke~~----gDvDiL 390 (398)
-.|++--+|||||..+ ||++||
T Consensus 35 grv~iP~~Fr~GKsIiAVleGe~~iL 60 (71)
T PF09558_consen 35 GRVMIPQSFRRGKSIIAVLEGECKIL 60 (71)
T ss_pred ccEEChHHHcCCceEEEEEcCceehh
Confidence 3677778999999875 777776
No 320
>PF03445 DUF294: Putative nucleotidyltransferase DUF294; InterPro: IPR005105 This domain is found associated with an N-terminal cyclic nucleotide-binding domain (IPR000595 from INTERPRO) and two CBS domains (IPR000644 from INTERPRO). This domain, normally represents the C-terminal region, is uncharacterised; however, it seems to be similar to the nucleotidyltransferase domain (IPR002934 from INTERPRO), conserving the DXD motif, which strongly suggests that proteins containing this domain are also nucleotidyltransferases.; GO: 0008773 [protein-PII] uridylyltransferase activity
Probab=21.43 E-value=1.8e+02 Score=25.22 Aligned_cols=27 Identities=30% Similarity=0.415 Sum_probs=20.7
Q ss_pred eEEEEechhhcCCcc-cCCeeEEEecCC
Q 015933 369 VIILCGGSYRRGKAS-CGDLDVVIMHPD 395 (398)
Q Consensus 369 ~~v~~~Gs~RRgke~-~gDvDiLit~~~ 395 (398)
+-+.+.||+=|+..+ ..|+|..|-+++
T Consensus 50 ~a~lalGS~GR~E~~~~sDqD~alv~~d 77 (138)
T PF03445_consen 50 FAWLALGSYGRREQTLYSDQDNALVFED 77 (138)
T ss_pred EEEEEECcccccCCCcCccccceeeecC
Confidence 356778998776654 579999998877
No 321
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=21.38 E-value=1e+02 Score=29.41 Aligned_cols=43 Identities=28% Similarity=0.453 Sum_probs=0.0
Q ss_pred CHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHH
Q 015933 263 GKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKL 311 (398)
Q Consensus 263 G~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l 311 (398)
|.++...=.++|+ ++..|..+.. ..++.|+.|+|+|+.+|-++
T Consensus 40 ~~~~~~la~~lL~--~fg~L~~l~~----a~~~el~~v~GiG~aka~~l 82 (224)
T COG2003 40 GESVLDLAKELLQ--EFGSLAELLK----ASVEELSSVKGIGLAKAIQI 82 (224)
T ss_pred CCCHHHHHHHHHH--HcccHHHHHh----CCHHHHhhCCCccHHHHHHH
No 322
>PRK03103 DNA polymerase IV; Reviewed
Probab=20.60 E-value=1.7e+02 Score=29.86 Aligned_cols=51 Identities=24% Similarity=0.532 Sum_probs=31.8
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--CCC
Q 015933 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHR 317 (398)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~--Gir 317 (398)
+..|||||.++.++... -| +..+.+|.+-.+.... +.+| . .+..+|+. |+.
T Consensus 183 i~~l~gig~~~~~~L~~---~G-i~tigdl~~~~~~~L~----~~fG--~-~~~~l~~~a~G~d 235 (409)
T PRK03103 183 VRKLFGVGSRMEKHLRR---MG-IRTIGQLANTPLERLK----KRWG--I-NGEVLWRTANGID 235 (409)
T ss_pred HhhcCCccHHHHHHHHH---cC-CCCHHHHhcCCHHHHH----HHHC--H-HHHHHHHHhcCCC
Confidence 67789999998887664 35 5666666653333233 4444 3 46777764 773
No 323
>PRK00024 hypothetical protein; Reviewed
Probab=20.31 E-value=65 Score=30.54 Aligned_cols=27 Identities=15% Similarity=0.438 Sum_probs=23.5
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHHhCC
Q 015933 252 SADQVKGLPGIGKSMQDHIQEIVTTGK 278 (398)
Q Consensus 252 s~~~l~~lpgIG~~ia~kI~Eil~tG~ 278 (398)
+.++|..++|||+..+..|.-+++-|+
T Consensus 64 s~~eL~~i~GIG~akA~~L~a~~El~~ 90 (224)
T PRK00024 64 SLEELQSIKGIGPAKAAQLKAALELAR 90 (224)
T ss_pred CHHHHhhccCccHHHHHHHHHHHHHHH
Confidence 457899999999999999988888765
No 324
>PRK01810 DNA polymerase IV; Validated
Probab=20.15 E-value=1.8e+02 Score=29.64 Aligned_cols=52 Identities=19% Similarity=0.394 Sum_probs=31.3
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--CCCC
Q 015933 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (398)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l~~~--Girt 318 (398)
+..|||||+.+++++..+ | +..+-+|.+-...... +.+| + ....+|+. |+..
T Consensus 181 v~~l~giG~~~~~~L~~~---G-i~tigdL~~~~~~~L~----~rfG--~-~g~~l~~~a~G~d~ 234 (407)
T PRK01810 181 VGEMHGIGEKTAEKLKDI---G-IQTIGDLAKADEHILR----AKLG--I-NGVRLQRRANGIDD 234 (407)
T ss_pred HhhcCCcCHHHHHHHHHc---C-CCcHHHHHhCCHHHHH----HHHh--H-HHHHHHHHhcCCCC
Confidence 677899999998887643 4 4555555543333233 4444 3 46667764 7653
Done!