Query 012388
Match_columns 464
No_of_seqs 342 out of 971
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 02:07:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012388.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012388hhsearch_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 8.4E-68 1.8E-72 515.4 24.0 264 198-463 2-288 (353)
2 cd00141 NT_POLXc Nucleotidyltr 100.0 1.1E-54 2.5E-59 437.9 24.6 240 212-463 2-244 (307)
3 smart00483 POLXc DNA polymeras 100.0 3E-54 6.4E-59 439.4 25.6 253 208-463 1-269 (334)
4 PRK08609 hypothetical protein; 100.0 2.6E-47 5.5E-52 412.7 21.4 235 208-463 1-250 (570)
5 COG1796 POL4 DNA polymerase IV 100.0 2.7E-35 5.8E-40 290.3 19.4 236 207-463 2-255 (326)
6 PF14792 DNA_pol_B_palm: DNA p 100.0 2.1E-32 4.5E-37 237.3 9.4 105 345-459 1-112 (112)
7 PF14716 HHH_8: Helix-hairpin- 99.7 2.4E-17 5.1E-22 130.6 7.5 66 210-275 1-68 (68)
8 PF10391 DNA_pol_lambd_f: Fing 99.7 1.6E-17 3.4E-22 124.3 5.0 51 294-344 1-52 (52)
9 PRK07945 hypothetical protein; 99.5 1.7E-14 3.7E-19 147.7 8.7 91 213-313 3-98 (335)
10 smart00292 BRCT breast cancer 99.0 8.8E-10 1.9E-14 86.6 7.1 79 17-98 1-80 (80)
11 PF00533 BRCT: BRCA1 C Terminu 99.0 7E-10 1.5E-14 88.3 6.6 75 16-95 3-78 (78)
12 cd00027 BRCT Breast Cancer Sup 98.7 4.1E-08 9E-13 75.2 6.1 72 21-96 1-72 (72)
13 TIGR00575 dnlj DNA ligase, NAD 98.1 1.4E-05 3.1E-10 88.8 10.0 133 254-397 466-633 (652)
14 PF14520 HHH_5: Helix-hairpin- 98.0 4.3E-06 9.3E-11 64.4 3.0 51 293-343 3-55 (60)
15 PF12738 PTCB-BRCT: twin BRCT 97.8 2.4E-05 5.2E-10 60.4 3.8 63 22-90 1-63 (63)
16 KOG3226 DNA repair protein [Re 97.6 2.4E-05 5.3E-10 79.3 2.5 89 16-111 315-404 (508)
17 PLN03123 poly [ADP-ribose] pol 97.6 0.00011 2.3E-09 84.7 7.9 93 14-109 389-481 (981)
18 PF14520 HHH_5: Helix-hairpin- 97.5 0.00015 3.3E-09 55.7 4.3 52 254-313 5-56 (60)
19 PLN03122 Poly [ADP-ribose] pol 97.4 0.00039 8.4E-09 78.7 7.4 95 13-110 184-279 (815)
20 PF11731 Cdd1: Pathogenicity l 97.1 0.00064 1.4E-08 57.0 4.2 37 290-326 7-43 (93)
21 PRK07956 ligA NAD-dependent DN 97.1 0.0027 5.9E-08 71.0 10.5 134 254-397 479-639 (665)
22 PF12826 HHH_2: Helix-hairpin- 97.0 0.0012 2.6E-08 51.5 4.8 49 256-313 5-53 (64)
23 COG1555 ComEA DNA uptake prote 97.0 0.0011 2.4E-08 60.5 5.0 50 252-313 95-145 (149)
24 TIGR01259 comE comEA protein. 96.9 0.0018 3.8E-08 57.1 5.5 50 252-313 66-116 (120)
25 PF12836 HHH_3: Helix-hairpin- 96.8 0.0019 4.1E-08 50.5 4.5 49 251-311 11-60 (65)
26 PRK14351 ligA NAD-dependent DN 96.8 0.0053 1.1E-07 68.9 9.7 134 254-397 496-658 (689)
27 PF14229 DUF4332: Domain of un 96.7 0.011 2.5E-07 52.1 9.2 67 260-326 1-84 (122)
28 TIGR00084 ruvA Holliday juncti 96.6 0.0037 8E-08 59.4 5.5 53 254-312 72-124 (191)
29 PRK02515 psbU photosystem II c 96.5 0.0042 9.2E-08 55.0 4.9 47 252-313 59-105 (132)
30 KOG0966 ATP-dependent DNA liga 96.5 0.0052 1.1E-07 68.2 6.6 91 12-107 627-720 (881)
31 TIGR00426 competence protein C 96.3 0.009 1.9E-07 47.1 5.4 51 252-314 14-66 (69)
32 PRK12766 50S ribosomal protein 96.2 0.0019 4.1E-08 62.7 1.4 52 296-347 4-57 (232)
33 PRK14605 ruvA Holliday junctio 96.2 0.0051 1.1E-07 58.6 4.2 52 254-312 73-125 (194)
34 PF00633 HHH: Helix-hairpin-he 96.2 0.0043 9.3E-08 41.2 2.5 23 251-273 8-30 (30)
35 PRK00116 ruvA Holliday junctio 96.1 0.0068 1.5E-07 57.6 4.3 54 254-314 73-127 (192)
36 TIGR00084 ruvA Holliday juncti 96.1 0.0042 9.2E-08 59.0 2.9 50 292-343 69-124 (191)
37 KOG2481 Protein required for n 96.0 0.0031 6.7E-08 66.9 1.7 86 12-109 321-416 (570)
38 PRK14604 ruvA Holliday junctio 96.0 0.011 2.3E-07 56.4 5.2 54 254-313 73-126 (195)
39 PRK13901 ruvA Holliday junctio 95.9 0.01 2.2E-07 56.6 4.7 54 254-313 72-125 (196)
40 PRK14601 ruvA Holliday junctio 95.9 0.011 2.3E-07 55.9 4.6 54 254-313 73-126 (183)
41 PRK14603 ruvA Holliday junctio 95.8 0.014 3E-07 55.8 5.2 54 254-313 72-125 (197)
42 PRK14602 ruvA Holliday junctio 95.8 0.0099 2.2E-07 57.0 4.2 54 254-313 74-127 (203)
43 PRK14606 ruvA Holliday junctio 95.7 0.014 3.1E-07 55.3 4.6 54 254-313 73-126 (188)
44 KOG4362 Transcriptional regula 95.5 0.016 3.5E-07 64.0 4.9 77 32-111 487-565 (684)
45 PF00633 HHH: Helix-hairpin-he 95.5 0.013 2.9E-07 38.9 2.6 22 292-313 8-29 (30)
46 PRK14973 DNA topoisomerase I; 95.4 0.019 4.1E-07 66.6 5.3 91 254-345 835-929 (936)
47 cd05397 NT_Pol-beta-like Nucle 95.4 0.027 5.8E-07 41.6 4.3 28 365-392 14-42 (49)
48 PRK07956 ligA NAD-dependent DN 95.4 0.008 1.7E-07 67.3 2.1 52 298-349 448-502 (665)
49 PRK14350 ligA NAD-dependent DN 95.3 0.043 9.3E-07 61.5 7.7 87 254-349 470-564 (669)
50 COG0272 Lig NAD-dependent DNA 95.3 0.051 1.1E-06 60.1 8.0 83 254-346 479-563 (667)
51 COG1555 ComEA DNA uptake prote 95.3 0.016 3.5E-07 52.9 3.5 52 290-347 92-148 (149)
52 PRK02362 ski2-like helicase; P 95.2 0.021 4.5E-07 64.9 4.9 58 284-344 642-701 (737)
53 cd05402 NT_PAP_TUTase Nucleoti 95.2 0.075 1.6E-06 45.5 7.2 58 354-415 9-68 (114)
54 PF11798 IMS_HHH: IMS family H 95.2 0.011 2.5E-07 39.7 1.6 20 297-316 13-32 (32)
55 PRK02515 psbU photosystem II c 95.0 0.044 9.5E-07 48.7 5.2 33 293-325 59-92 (132)
56 PRK14600 ruvA Holliday junctio 95.0 0.031 6.7E-07 53.0 4.5 53 254-313 73-125 (186)
57 TIGR01259 comE comEA protein. 94.9 0.027 5.9E-07 49.5 3.8 50 291-346 64-118 (120)
58 TIGR00575 dnlj DNA ligase, NAD 94.9 0.013 2.8E-07 65.5 2.0 62 298-359 435-499 (652)
59 COG0632 RuvA Holliday junction 94.8 0.033 7.2E-07 53.3 4.3 54 254-313 73-126 (201)
60 KOG2043 Signaling protein SWIF 94.6 0.034 7.4E-07 63.9 4.3 68 38-109 672-739 (896)
61 KOG0966 ATP-dependent DNA liga 94.5 0.12 2.5E-06 57.9 8.0 90 17-107 783-881 (881)
62 PF12836 HHH_3: Helix-hairpin- 94.4 0.045 9.7E-07 42.7 3.5 49 292-346 11-64 (65)
63 PRK00116 ruvA Holliday junctio 94.3 0.027 5.9E-07 53.5 2.4 51 293-343 71-125 (192)
64 TIGR00426 competence protein C 94.2 0.061 1.3E-06 42.3 3.9 45 296-346 17-67 (69)
65 PRK14605 ruvA Holliday junctio 94.1 0.027 5.9E-07 53.7 2.0 52 291-342 69-124 (194)
66 PF12826 HHH_2: Helix-hairpin- 94.1 0.038 8.2E-07 43.1 2.5 44 299-343 7-52 (64)
67 KOG1929 Nucleotide excision re 94.1 0.086 1.9E-06 59.9 6.2 89 17-110 102-190 (811)
68 PRK00254 ski2-like helicase; P 94.0 0.078 1.7E-06 60.1 5.6 67 276-343 623-695 (720)
69 KOG1929 Nucleotide excision re 93.9 0.062 1.4E-06 61.0 4.6 94 10-109 485-578 (811)
70 COG5163 NOP7 Protein required 93.4 0.076 1.6E-06 55.1 3.7 87 11-109 343-440 (591)
71 PRK12766 50S ribosomal protein 92.6 0.21 4.5E-06 48.7 5.4 54 253-314 2-55 (232)
72 PRK14606 ruvA Holliday junctio 92.3 0.08 1.7E-06 50.2 2.1 50 291-342 69-124 (188)
73 PRK14601 ruvA Holliday junctio 92.0 0.09 1.9E-06 49.7 2.1 50 291-342 69-124 (183)
74 TIGR01448 recD_rel helicase, p 91.9 0.68 1.5E-05 52.7 9.2 83 253-346 116-201 (720)
75 PF04994 TfoX_C: TfoX C-termin 91.7 0.13 2.8E-06 42.1 2.4 30 297-326 5-34 (81)
76 PRK03858 DNA polymerase IV; Va 91.7 0.23 5.1E-06 52.0 5.0 108 297-424 175-286 (396)
77 PRK14603 ruvA Holliday junctio 91.6 0.1 2.2E-06 49.8 2.1 50 291-342 68-123 (197)
78 PRK14602 ruvA Holliday junctio 91.6 0.11 2.4E-06 49.9 2.2 50 291-342 70-125 (203)
79 PRK04301 radA DNA repair and r 91.6 0.12 2.7E-06 52.6 2.7 30 297-326 8-37 (317)
80 PF01909 NTP_transf_2: Nucleot 91.5 0.3 6.5E-06 39.8 4.5 32 366-397 12-44 (93)
81 smart00278 HhH1 Helix-hairpin- 91.5 0.13 2.9E-06 32.7 1.8 18 296-313 2-19 (26)
82 PRK14604 ruvA Holliday junctio 91.4 0.11 2.4E-06 49.6 2.0 50 291-342 69-124 (195)
83 PRK13901 ruvA Holliday junctio 91.3 0.12 2.7E-06 49.2 2.1 50 291-342 68-123 (196)
84 COG1796 POL4 DNA polymerase IV 90.9 0.57 1.2E-05 47.7 6.6 97 207-323 59-156 (326)
85 PRK08097 ligB NAD-dependent DN 90.9 0.36 7.9E-06 53.1 5.6 88 253-353 458-547 (562)
86 TIGR03252 uncharacterized HhH- 90.5 0.7 1.5E-05 43.4 6.3 49 261-312 75-132 (177)
87 COG1948 MUS81 ERCC4-type nucle 90.4 0.38 8.3E-06 47.6 4.7 49 256-313 184-232 (254)
88 TIGR02236 recomb_radA DNA repa 90.2 0.2 4.4E-06 50.7 2.7 28 298-325 2-29 (310)
89 PRK14133 DNA polymerase IV; Pr 90.2 1.1 2.3E-05 46.2 8.1 29 297-325 175-203 (347)
90 PRK14351 ligA NAD-dependent DN 90.1 0.14 3.1E-06 57.7 1.6 63 298-360 465-530 (689)
91 TIGR01448 recD_rel helicase, p 90.1 0.15 3.3E-06 57.8 1.9 53 292-344 79-135 (720)
92 COG3743 Uncharacterized conser 89.7 0.41 8.9E-06 42.6 3.9 53 295-350 67-119 (133)
93 PRK03352 DNA polymerase IV; Va 89.5 0.36 7.9E-06 49.7 4.0 40 297-336 179-218 (346)
94 PRK14600 ruvA Holliday junctio 89.4 0.21 4.5E-06 47.4 1.9 49 291-342 69-123 (186)
95 PRK02406 DNA polymerase IV; Va 89.4 0.86 1.9E-05 46.8 6.6 29 297-325 170-198 (343)
96 cd00424 PolY Y-family of DNA p 89.3 1.7 3.6E-05 44.8 8.6 106 298-427 176-289 (343)
97 PRK01172 ski2-like helicase; P 89.1 0.72 1.6E-05 51.9 6.3 40 285-325 603-642 (674)
98 cd05400 NT_2-5OAS_ClassI-CCAas 88.9 1.8 3.9E-05 38.4 7.5 46 368-413 27-79 (143)
99 PRK01216 DNA polymerase IV; Va 88.7 0.44 9.5E-06 49.5 3.9 40 297-336 180-219 (351)
100 TIGR00588 ogg 8-oxoguanine DNA 88.7 1.2 2.5E-05 45.6 6.9 62 255-318 177-243 (310)
101 PTZ00418 Poly(A) polymerase; P 88.0 2.6 5.7E-05 46.6 9.4 53 366-418 124-177 (593)
102 PF11731 Cdd1: Pathogenicity l 87.9 0.77 1.7E-05 38.7 4.1 47 253-303 11-57 (93)
103 smart00279 HhH2 Helix-hairpin- 87.7 0.37 8E-06 33.3 1.7 16 299-314 20-35 (36)
104 PF14490 HHH_4: Helix-hairpin- 87.6 1.1 2.3E-05 37.6 4.9 54 292-346 10-66 (94)
105 cd00080 HhH2_motif Helix-hairp 87.5 0.48 1E-05 38.1 2.6 28 297-325 24-51 (75)
106 KOG2245 Poly(A) polymerase and 87.2 1.3 2.7E-05 47.7 6.2 82 368-460 89-176 (562)
107 PRK08609 hypothetical protein; 87.2 0.77 1.7E-05 50.8 4.9 54 252-311 86-139 (570)
108 PRK03609 umuC DNA polymerase V 87.2 0.59 1.3E-05 49.6 3.8 30 297-326 181-210 (422)
109 cd01701 PolY_Rev1 DNA polymera 86.7 0.67 1.5E-05 49.0 4.0 30 297-326 224-253 (404)
110 PRK14670 uvrC excinuclease ABC 86.7 1.4 3E-05 48.9 6.4 52 254-314 514-565 (574)
111 PRK13844 recombination protein 86.0 1.5 3.3E-05 42.0 5.5 22 291-312 11-32 (200)
112 KOG2841 Structure-specific end 85.9 0.88 1.9E-05 44.4 3.9 50 255-313 196-245 (254)
113 cd03468 PolY_like DNA Polymera 85.8 0.83 1.8E-05 46.5 4.0 109 299-426 174-284 (335)
114 PRK03348 DNA polymerase IV; Pr 85.7 0.74 1.6E-05 49.5 3.7 29 297-325 182-210 (454)
115 COG1708 Predicted nucleotidylt 85.6 3.4 7.4E-05 35.1 7.2 30 366-395 24-54 (128)
116 cd01703 PolY_Pol_iota DNA Poly 85.6 0.81 1.8E-05 48.1 3.8 30 297-326 174-203 (379)
117 TIGR01083 nth endonuclease III 85.0 4.4 9.5E-05 38.3 8.2 25 292-316 103-127 (191)
118 cd01700 PolY_Pol_V_umuC umuC s 84.9 0.75 1.6E-05 47.3 3.2 29 297-325 178-206 (344)
119 PRK01810 DNA polymerase IV; Va 84.7 0.96 2.1E-05 47.6 3.9 29 297-325 181-209 (407)
120 PRK14666 uvrC excinuclease ABC 84.5 0.55 1.2E-05 52.7 2.1 49 294-344 636-687 (694)
121 smart00278 HhH1 Helix-hairpin- 84.5 0.87 1.9E-05 28.9 2.2 20 255-274 2-21 (26)
122 COG0353 RecR Recombinational D 84.1 0.74 1.6E-05 43.8 2.5 21 292-312 9-29 (198)
123 COG1948 MUS81 ERCC4-type nucle 84.1 1.3 2.7E-05 44.0 4.1 55 288-343 175-231 (254)
124 TIGR03671 cca_archaeal CCA-add 84.1 3.5 7.6E-05 43.7 7.7 59 353-411 25-88 (408)
125 PTZ00205 DNA polymerase kappa; 84.0 1.1 2.4E-05 49.3 4.0 29 297-325 311-339 (571)
126 PRK10880 adenine DNA glycosyla 83.9 4.4 9.6E-05 42.2 8.3 64 232-303 85-151 (350)
127 PF01367 5_3_exonuc: 5'-3' exo 83.8 0.089 1.9E-06 45.0 -3.5 25 299-325 22-47 (101)
128 PRK03103 DNA polymerase IV; Re 83.2 1.2 2.6E-05 46.9 3.9 29 298-326 184-212 (409)
129 PRK00227 glnD PII uridylyl-tra 83.2 3.3 7.1E-05 47.0 7.5 65 348-415 8-74 (693)
130 PRK02794 DNA polymerase IV; Pr 83.2 0.89 1.9E-05 48.2 2.9 29 297-325 211-239 (419)
131 PRK09482 flap endonuclease-lik 82.8 0.93 2E-05 45.1 2.7 25 299-325 186-211 (256)
132 smart00475 53EXOc 5'-3' exonuc 82.7 0.95 2.1E-05 45.1 2.7 26 298-325 189-215 (259)
133 smart00478 ENDO3c endonuclease 82.6 3.7 8E-05 36.7 6.3 26 292-317 69-94 (149)
134 PRK14667 uvrC excinuclease ABC 82.5 2.4 5.3E-05 46.8 6.1 51 254-314 514-564 (567)
135 PRK10308 3-methyl-adenine DNA 82.4 1.4 3E-05 44.5 3.9 62 254-319 167-231 (283)
136 PRK14976 5'-3' exonuclease; Pr 82.2 0.99 2.1E-05 45.5 2.7 26 299-325 195-220 (281)
137 COG0122 AlkA 3-methyladenine D 82.2 4.2 9.1E-05 41.1 7.2 46 270-316 174-219 (285)
138 PRK00558 uvrC excinuclease ABC 82.1 1.9 4.2E-05 48.0 5.1 52 254-314 543-594 (598)
139 cd01702 PolY_Pol_eta DNA Polym 81.7 1.6 3.5E-05 45.4 4.1 29 297-325 184-213 (359)
140 cd00056 ENDO3c endonuclease II 81.5 0.96 2.1E-05 40.9 2.1 27 291-317 79-105 (158)
141 PRK08097 ligB NAD-dependent DN 81.2 0.67 1.5E-05 51.0 1.1 63 298-360 428-493 (562)
142 PRK07758 hypothetical protein; 80.9 0.93 2E-05 38.2 1.6 45 300-344 39-85 (95)
143 COG0632 RuvA Holliday junction 80.8 0.98 2.1E-05 43.3 1.9 51 292-342 70-124 (201)
144 cd00008 53EXOc 5'-3' exonuclea 80.5 1.3 2.8E-05 43.5 2.8 26 299-325 187-212 (240)
145 PRK13300 tRNA CCA-pyrophosphor 79.7 6.3 0.00014 42.4 7.8 45 355-399 28-74 (447)
146 PRK14666 uvrC excinuclease ABC 79.5 3.1 6.8E-05 46.8 5.6 51 254-313 637-687 (694)
147 PRK14672 uvrC excinuclease ABC 79.4 3.2 6.9E-05 46.7 5.6 55 254-317 608-662 (691)
148 PRK13482 DNA integrity scannin 79.0 3 6.6E-05 43.3 5.0 59 246-313 277-337 (352)
149 COG1746 CCA1 tRNA nucleotidylt 78.3 7.6 0.00017 41.2 7.7 49 352-400 29-79 (443)
150 COG0389 DinP Nucleotidyltransf 78.3 2.1 4.4E-05 44.6 3.6 28 297-324 178-205 (354)
151 PRK01229 N-glycosylase/DNA lya 78.1 2.7 5.8E-05 40.6 4.0 53 262-317 85-142 (208)
152 PRK00076 recR recombination pr 78.1 1.7 3.8E-05 41.5 2.7 21 292-312 8-28 (196)
153 TIGR00615 recR recombination p 78.0 1.8 3.8E-05 41.4 2.7 21 292-312 8-28 (195)
154 PRK10702 endonuclease III; Pro 77.5 5.1 0.00011 38.7 5.8 44 231-274 84-129 (211)
155 PRK04301 radA DNA repair and r 77.5 6.6 0.00014 39.9 7.0 88 254-350 6-103 (317)
156 cd05403 NT_KNTase_like Nucleot 77.4 5.9 0.00013 31.7 5.4 29 370-398 20-49 (93)
157 PF14229 DUF4332: Domain of un 77.2 2.5 5.4E-05 37.2 3.3 26 301-326 1-26 (122)
158 cd03586 PolY_Pol_IV_kappa DNA 76.8 2.1 4.6E-05 43.5 3.1 28 298-325 174-201 (334)
159 TIGR01084 mutY A/G-specific ad 76.4 5.5 0.00012 40.1 5.9 66 231-303 80-147 (275)
160 PRK00254 ski2-like helicase; P 76.2 13 0.00028 42.3 9.6 53 254-314 645-697 (720)
161 PRK06063 DNA polymerase III su 76.1 10 0.00022 38.7 7.9 71 17-91 231-301 (313)
162 COG0258 Exo 5'-3' exonuclease 74.9 2.2 4.8E-05 43.4 2.7 25 299-325 202-227 (310)
163 PRK13913 3-methyladenine DNA g 73.1 4.2 9.2E-05 39.5 4.0 22 292-313 118-139 (218)
164 PRK06195 DNA polymerase III su 73.0 8.3 0.00018 39.3 6.3 48 17-65 219-266 (309)
165 KOG2875 8-oxoguanine DNA glyco 72.9 5.2 0.00011 40.2 4.6 67 255-322 175-245 (323)
166 COG0177 Nth Predicted EndoIII- 72.8 4.8 0.0001 39.0 4.2 88 261-356 80-177 (211)
167 PF03118 RNA_pol_A_CTD: Bacter 72.7 5.2 0.00011 31.4 3.7 22 254-275 44-65 (66)
168 PF03445 DUF294: Putative nucl 72.3 13 0.00029 33.2 6.7 52 368-419 49-107 (138)
169 PRK14671 uvrC excinuclease ABC 72.0 3.6 7.8E-05 46.1 3.6 47 293-342 567-615 (621)
170 PRK14670 uvrC excinuclease ABC 71.8 2.1 4.5E-05 47.4 1.7 43 295-338 514-558 (574)
171 PF00416 Ribosomal_S13: Riboso 71.8 3.3 7.2E-05 35.6 2.6 26 293-318 13-39 (107)
172 PRK14667 uvrC excinuclease ABC 71.7 2.5 5.4E-05 46.8 2.3 45 295-341 514-560 (567)
173 cd00056 ENDO3c endonuclease II 71.5 7.6 0.00016 35.0 5.1 77 220-303 44-125 (158)
174 cd05401 NT_GlnE_GlnD_like Nucl 71.1 16 0.00034 33.5 7.2 52 368-419 55-112 (172)
175 KOG2534 DNA polymerase IV (fam 71.0 3.5 7.5E-05 42.1 2.9 54 290-343 51-114 (353)
176 KOG3548 DNA damage checkpoint 70.9 4.7 0.0001 46.4 4.1 91 17-111 924-1038(1176)
177 PF11798 IMS_HHH: IMS family H 70.9 2.1 4.5E-05 28.7 0.9 18 255-272 12-29 (32)
178 PRK13910 DNA glycosylase MutY; 70.7 8.9 0.00019 38.9 5.8 68 232-306 48-117 (289)
179 KOG3524 Predicted guanine nucl 70.6 4.1 8.8E-05 45.5 3.5 77 17-101 117-193 (850)
180 PRK13766 Hef nuclease; Provisi 69.9 4.8 0.0001 46.0 4.2 49 256-313 717-765 (773)
181 TIGR03491 RecB family nuclease 69.6 3.9 8.6E-05 43.9 3.2 29 298-326 210-238 (457)
182 PRK14669 uvrC excinuclease ABC 69.4 3.1 6.6E-05 46.6 2.4 31 294-325 551-581 (624)
183 PRK10702 endonuclease III; Pro 69.2 6.2 0.00014 38.1 4.2 24 292-315 106-129 (211)
184 PRK14350 ligA NAD-dependent DN 68.5 12 0.00027 42.2 6.9 73 16-93 591-663 (669)
185 PRK14973 DNA topoisomerase I; 68.0 6.5 0.00014 46.1 4.7 42 294-335 801-844 (936)
186 PRK05007 PII uridylyl-transfer 67.7 17 0.00037 42.5 8.1 50 367-416 79-131 (884)
187 COG2251 Predicted nuclease (Re 67.7 3.9 8.5E-05 43.6 2.6 27 299-325 229-255 (474)
188 PF02371 Transposase_20: Trans 67.3 3.5 7.6E-05 33.8 1.8 20 295-314 2-21 (87)
189 TIGR03252 uncharacterized HhH- 67.2 17 0.00037 34.2 6.5 44 232-275 80-136 (177)
190 PRK12278 50S ribosomal protein 67.0 4.3 9.2E-05 39.6 2.5 29 296-324 159-187 (221)
191 COG1669 Predicted nucleotidylt 67.0 28 0.00061 29.6 7.1 30 368-397 23-54 (97)
192 smart00611 SEC63 Domain of unk 66.8 13 0.00028 37.4 6.1 29 297-325 153-181 (312)
193 PRK02362 ski2-like helicase; P 66.6 42 0.00091 38.3 10.9 52 254-315 652-704 (737)
194 PF14579 HHH_6: Helix-hairpin- 65.7 8.3 0.00018 31.8 3.7 30 297-326 29-62 (90)
195 PHA01806 hypothetical protein 65.5 22 0.00048 33.9 6.8 49 345-397 14-67 (200)
196 TIGR00615 recR recombination p 65.2 4.7 0.0001 38.6 2.4 32 254-285 11-42 (195)
197 PF04919 DUF655: Protein of un 65.0 24 0.00053 33.3 7.0 41 248-288 109-150 (181)
198 TIGR00593 pola DNA polymerase 64.9 4.6 0.0001 47.1 2.7 25 299-325 189-214 (887)
199 PRK03980 flap endonuclease-1; 64.6 5.2 0.00011 40.6 2.7 25 299-324 193-217 (292)
200 PRK14672 uvrC excinuclease ABC 64.2 3.7 8.1E-05 46.2 1.7 53 295-348 608-662 (691)
201 PRK14668 uvrC excinuclease ABC 64.1 8.7 0.00019 42.7 4.6 50 255-313 526-575 (577)
202 PRK01759 glnD PII uridylyl-tra 63.5 23 0.00051 41.2 8.1 67 349-415 33-106 (854)
203 PF03118 RNA_pol_A_CTD: Bacter 63.2 2.7 5.8E-05 33.0 0.3 44 301-344 17-62 (66)
204 PF14716 HHH_8: Helix-hairpin- 62.8 6.2 0.00014 30.9 2.3 24 290-313 41-65 (68)
205 PRK00076 recR recombination pr 62.2 5.4 0.00012 38.2 2.2 32 254-285 11-42 (196)
206 PF14490 HHH_4: Helix-hairpin- 61.9 9.7 0.00021 31.7 3.5 55 261-322 19-74 (94)
207 PF14579 HHH_6: Helix-hairpin- 61.8 21 0.00046 29.4 5.5 50 256-316 29-78 (90)
208 PRK10917 ATP-dependent DNA hel 61.6 6.7 0.00014 44.4 3.2 28 297-324 11-38 (681)
209 PRK04374 PII uridylyl-transfer 61.4 27 0.00058 40.8 8.1 63 354-416 55-123 (869)
210 PTZ00217 flap endonuclease-1; 61.4 6.3 0.00014 41.7 2.7 26 298-324 238-263 (393)
211 COG5186 PAP1 Poly(A) polymeras 61.3 21 0.00046 37.3 6.3 81 368-459 81-167 (552)
212 TIGR01083 nth endonuclease III 61.2 16 0.00034 34.5 5.2 41 232-272 82-124 (191)
213 PRK02794 DNA polymerase IV; Pr 61.0 38 0.00082 35.9 8.6 52 256-318 211-264 (419)
214 PRK12311 rpsB 30S ribosomal pr 61.0 6 0.00013 40.8 2.5 31 294-324 262-292 (326)
215 PRK14671 uvrC excinuclease ABC 61.0 11 0.00024 42.3 4.7 49 254-313 569-617 (621)
216 PRK07758 hypothetical protein; 60.6 12 0.00025 31.7 3.6 23 254-276 67-89 (95)
217 TIGR03674 fen_arch flap struct 60.5 6.7 0.00015 40.6 2.7 27 298-325 239-265 (338)
218 KOG3524 Predicted guanine nucl 60.5 5 0.00011 44.9 1.8 86 17-109 209-294 (850)
219 COG0177 Nth Predicted EndoIII- 60.1 23 0.0005 34.3 6.1 31 243-273 97-128 (211)
220 TIGR02236 recomb_radA DNA repa 60.1 14 0.00031 37.2 5.0 50 256-313 1-50 (310)
221 PRK13844 recombination protein 59.8 6.1 0.00013 37.9 2.1 32 254-285 15-46 (200)
222 PF04919 DUF655: Protein of un 59.7 8.1 0.00017 36.4 2.8 59 266-324 86-149 (181)
223 cd00141 NT_POLXc Nucleotidyltr 59.4 4.3 9.3E-05 41.4 1.1 51 293-343 43-102 (307)
224 cd01703 PolY_Pol_iota DNA Poly 59.3 18 0.0004 37.9 5.8 54 255-318 173-243 (379)
225 PRK05755 DNA polymerase I; Pro 59.2 6.6 0.00014 45.8 2.7 26 298-325 190-216 (880)
226 TIGR01954 nusA_Cterm_rpt trans 58.4 10 0.00022 27.2 2.7 31 303-333 1-33 (50)
227 PF02889 Sec63: Sec63 Brl doma 57.8 18 0.00038 36.3 5.2 29 296-324 149-177 (314)
228 PRK01216 DNA polymerase IV; Va 57.5 34 0.00074 35.5 7.4 52 256-317 180-233 (351)
229 PRK00558 uvrC excinuclease ABC 56.9 7.1 0.00015 43.6 2.4 48 293-341 541-590 (598)
230 KOG1921 Endonuclease III [Repl 56.5 17 0.00038 35.9 4.6 29 245-273 149-178 (286)
231 CHL00137 rps13 ribosomal prote 56.4 7.5 0.00016 34.4 2.0 24 294-317 16-40 (122)
232 KOG1921 Endonuclease III [Repl 56.4 12 0.00026 37.0 3.5 33 283-316 148-180 (286)
233 PRK05179 rpsM 30S ribosomal pr 56.4 7.3 0.00016 34.5 1.9 23 295-317 17-40 (122)
234 KOG0323 TFIIF-interacting CTD 56.0 4.5 9.7E-05 45.2 0.6 89 17-109 440-531 (635)
235 PRK13482 DNA integrity scannin 53.6 8.3 0.00018 40.1 2.0 52 288-341 280-334 (352)
236 KOG2093 Translesion DNA polyme 53.5 19 0.00042 41.4 5.0 87 13-108 42-130 (1016)
237 PRK14668 uvrC excinuclease ABC 53.5 11 0.00023 42.0 3.0 48 294-342 524-573 (577)
238 TIGR03631 bact_S13 30S ribosom 53.2 8.5 0.00018 33.6 1.7 24 294-317 14-38 (113)
239 COG1204 Superfamily II helicas 52.8 22 0.00048 40.9 5.5 89 259-348 634-731 (766)
240 PRK00275 glnD PII uridylyl-tra 52.1 49 0.0011 38.9 8.2 49 368-416 78-129 (895)
241 TIGR00588 ogg 8-oxoguanine DNA 51.6 22 0.00048 36.3 4.8 75 225-305 179-265 (310)
242 PRK13746 aminoglycoside resist 51.2 74 0.0016 31.8 8.3 27 370-397 30-58 (262)
243 TIGR01084 mutY A/G-specific ad 51.2 23 0.00051 35.6 4.8 23 292-314 102-124 (275)
244 PF06514 PsbU: Photosystem II 50.1 12 0.00027 31.4 2.1 51 293-343 21-72 (93)
245 TIGR00596 rad1 DNA repair prot 49.8 29 0.00064 40.2 5.8 32 293-325 755-786 (814)
246 PRK12373 NADH dehydrogenase su 49.8 13 0.00028 39.4 2.7 56 292-350 320-375 (400)
247 COG0322 UvrC Nuclease subunit 49.8 29 0.00062 38.7 5.5 83 210-313 497-579 (581)
248 PRK14669 uvrC excinuclease ABC 49.6 31 0.00068 38.8 5.9 50 254-314 552-601 (624)
249 TIGR01446 DnaD_dom DnaD and ph 49.5 15 0.00031 28.8 2.4 19 305-323 54-72 (73)
250 COG4277 Predicted DNA-binding 49.5 12 0.00027 38.1 2.4 32 294-325 329-363 (404)
251 smart00483 POLXc DNA polymeras 49.2 10 0.00022 39.1 1.9 52 292-343 45-106 (334)
252 PRK03352 DNA polymerase IV; Va 49.0 31 0.00066 35.4 5.4 56 255-320 178-235 (346)
253 COG1491 Predicted RNA-binding 49.0 17 0.00037 34.4 3.1 40 248-287 123-163 (202)
254 TIGR00596 rad1 DNA repair prot 48.8 24 0.00052 40.9 5.0 48 256-314 759-807 (814)
255 PRK13913 3-methyladenine DNA g 48.7 34 0.00073 33.3 5.3 77 232-316 93-178 (218)
256 KOG2093 Translesion DNA polyme 48.5 26 0.00056 40.5 4.9 53 256-318 551-605 (1016)
257 KOG1918 3-methyladenine DNA gl 48.4 10 0.00022 37.0 1.5 58 254-312 122-182 (254)
258 smart00478 ENDO3c endonuclease 48.4 36 0.00079 30.2 5.2 42 232-273 48-91 (149)
259 COG0099 RpsM Ribosomal protein 47.9 14 0.0003 32.6 2.2 22 296-317 18-40 (121)
260 TIGR01693 UTase_glnD [Protein- 47.3 62 0.0013 37.7 8.1 50 367-416 42-94 (850)
261 PTZ00134 40S ribosomal protein 47.0 13 0.00028 34.3 1.9 25 293-317 28-53 (154)
262 PRK03059 PII uridylyl-transfer 46.4 64 0.0014 37.7 8.0 63 353-415 44-111 (856)
263 KOG4362 Transcriptional regula 45.9 29 0.00063 39.1 4.8 95 3-99 573-679 (684)
264 TIGR00194 uvrC excinuclease AB 45.8 17 0.00038 40.3 3.2 30 295-325 541-570 (574)
265 COG2844 GlnD UTP:GlnB (protein 45.8 35 0.00076 39.3 5.5 48 368-415 66-116 (867)
266 PF02961 BAF: Barrier to autoi 45.2 17 0.00036 30.4 2.2 27 297-323 21-47 (89)
267 COG0272 Lig NAD-dependent DNA 45.0 55 0.0012 36.9 6.8 72 17-93 593-664 (667)
268 PRK04053 rps13p 30S ribosomal 44.9 15 0.00032 33.7 2.0 25 293-317 23-48 (149)
269 PRK13766 Hef nuclease; Provisi 44.7 16 0.00035 41.7 2.8 46 296-342 716-763 (773)
270 PRK03858 DNA polymerase IV; Va 44.2 40 0.00086 35.3 5.4 53 255-317 174-228 (396)
271 PF09970 DUF2204: Nucleotidyl 44.0 51 0.0011 31.0 5.6 39 368-406 16-59 (181)
272 COG1194 MutY A/G-specific DNA 43.7 52 0.0011 34.2 5.9 77 220-303 77-155 (342)
273 COG5067 DBF4 Protein kinase es 43.5 15 0.00032 38.6 2.0 48 14-63 118-165 (468)
274 cd01702 PolY_Pol_eta DNA Polym 43.2 58 0.0013 33.9 6.4 55 255-318 183-241 (359)
275 TIGR03629 arch_S13P archaeal r 42.7 17 0.00037 33.1 2.0 22 296-317 22-44 (144)
276 cd00128 XPG Xeroderma pigmento 41.8 16 0.00034 37.2 1.9 24 298-322 226-249 (316)
277 cd01701 PolY_Rev1 DNA polymera 41.5 46 0.001 35.1 5.5 54 255-318 223-280 (404)
278 PRK03381 PII uridylyl-transfer 41.1 73 0.0016 36.8 7.3 48 368-415 57-107 (774)
279 cd00424 PolY Y-family of DNA p 40.6 69 0.0015 32.8 6.5 53 256-318 175-229 (343)
280 PRK01229 N-glycosylase/DNA lya 40.6 39 0.00085 32.6 4.3 21 251-271 115-136 (208)
281 PHA00439 exonuclease 40.4 20 0.00044 36.3 2.4 27 298-325 191-219 (286)
282 cd00080 HhH2_motif Helix-hairp 40.2 26 0.00056 28.0 2.5 29 254-284 22-50 (75)
283 COG1200 RecG RecG-like helicas 40.1 23 0.0005 39.9 2.9 27 297-323 12-38 (677)
284 PRK10308 3-methyl-adenine DNA 39.9 49 0.0011 33.4 5.1 44 228-271 173-224 (283)
285 COG1491 Predicted RNA-binding 39.6 58 0.0013 30.9 5.1 57 268-324 102-163 (202)
286 PTZ00035 Rad51 protein; Provis 39.4 32 0.0007 35.5 3.8 31 294-325 23-53 (337)
287 COG2231 Uncharacterized protei 38.1 49 0.0011 32.0 4.4 37 270-311 95-131 (215)
288 PLN03187 meiotic recombination 38.0 31 0.00068 35.8 3.4 31 293-324 30-60 (344)
289 PF02371 Transposase_20: Trans 36.9 28 0.00061 28.4 2.3 43 254-307 2-44 (87)
290 PRK03348 DNA polymerase IV; Pr 35.9 71 0.0015 34.4 5.8 54 255-318 181-236 (454)
291 TIGR02238 recomb_DMC1 meiotic 35.8 31 0.00068 35.3 3.0 24 301-324 7-30 (313)
292 TIGR00207 fliG flagellar motor 35.7 3.1E+02 0.0067 28.4 10.3 87 236-323 144-245 (338)
293 PRK10880 adenine DNA glycosyla 35.0 28 0.0006 36.4 2.5 23 292-314 106-128 (350)
294 COG1031 Uncharacterized Fe-S o 34.9 33 0.00072 37.0 3.0 33 293-325 514-547 (560)
295 COG0353 RecR Recombinational D 34.9 38 0.00083 32.4 3.2 22 254-275 12-33 (198)
296 COG1725 Predicted transcriptio 34.6 53 0.0011 29.2 3.8 61 263-336 13-73 (125)
297 PRK13910 DNA glycosylase MutY; 34.0 28 0.00061 35.3 2.3 22 293-314 70-91 (289)
298 COG0322 UvrC Nuclease subunit 33.2 29 0.00064 38.6 2.4 29 296-325 531-559 (581)
299 TIGR02239 recomb_RAD51 DNA rep 31.8 1E+02 0.0022 31.5 6.0 25 301-325 7-31 (316)
300 PLN03186 DNA repair protein RA 31.6 97 0.0021 32.2 5.8 33 293-326 27-59 (342)
301 KOG1906 DNA polymerase sigma [ 31.0 1.7E+02 0.0036 32.3 7.6 39 358-396 91-130 (514)
302 KOG3548 DNA damage checkpoint 30.9 99 0.0022 36.2 6.0 67 32-103 1082-1160(1176)
303 PRK09482 flap endonuclease-lik 29.4 1.3E+02 0.0029 29.9 6.1 27 254-282 182-208 (256)
304 PRK14109 bifunctional glutamin 29.3 2.2E+02 0.0048 34.0 8.9 46 368-413 215-266 (1007)
305 COG2185 Sbm Methylmalonyl-CoA 29.2 81 0.0018 28.7 4.1 58 356-415 30-92 (143)
306 cd05398 NT_ClassII-CCAase Nucl 28.8 1.2E+02 0.0025 27.2 5.2 37 355-394 5-45 (139)
307 PF14907 NTP_transf_5: Unchara 28.2 47 0.001 31.9 2.7 33 380-419 90-122 (249)
308 cd07749 NT_Pol-beta-like_1 Nuc 28.0 2.4E+02 0.0052 26.1 7.1 65 367-446 16-84 (156)
309 TIGR00600 rad2 DNA excision re 27.6 47 0.001 39.5 3.0 26 298-323 869-895 (1034)
310 PF04994 TfoX_C: TfoX C-termin 27.4 46 0.00099 27.2 2.1 40 254-297 3-42 (81)
311 PF07261 DnaB_2: Replication i 26.9 24 0.00052 27.6 0.3 21 305-325 54-74 (77)
312 PF04439 Adenyl_transf: Strept 26.6 2.6E+02 0.0056 28.2 7.7 48 348-397 2-53 (282)
313 KOG2875 8-oxoguanine DNA glyco 25.6 88 0.0019 31.7 4.0 44 228-271 180-235 (323)
314 TIGR02922 conserved hypothetic 25.4 26 0.00056 27.3 0.2 21 370-390 34-58 (67)
315 smart00611 SEC63 Domain of unk 24.6 6.6E+02 0.014 25.0 10.4 52 254-313 151-202 (312)
316 PRK07945 hypothetical protein; 24.4 40 0.00086 34.8 1.5 29 297-325 51-83 (335)
317 PLN03187 meiotic recombination 24.4 3E+02 0.0065 28.7 7.9 81 260-348 37-125 (344)
318 PF03710 GlnE: Glutamate-ammon 24.2 2.7E+02 0.0058 27.3 7.2 44 368-411 127-178 (247)
319 PF12482 DUF3701: Phage integr 23.1 75 0.0016 27.0 2.6 35 304-338 22-62 (96)
320 PRK05092 PII uridylyl-transfer 22.9 1.4E+02 0.0029 35.4 5.6 48 368-415 105-155 (931)
321 cd04761 HTH_MerR-SF Helix-Turn 22.8 76 0.0016 22.2 2.3 22 295-316 4-25 (49)
322 cd01104 HTH_MlrA-CarA Helix-Tu 22.8 1.9E+02 0.0041 21.7 4.7 24 295-318 4-28 (68)
323 COG5275 BRCT domain type II [G 22.6 1.7E+02 0.0036 28.7 5.1 50 17-67 155-204 (276)
324 KOG1715 Mitochondrial/chloropl 22.3 1.2E+02 0.0025 28.9 4.0 58 281-361 123-180 (187)
325 TIGR02884 spore_pdaA delta-lac 22.2 87 0.0019 30.2 3.3 33 388-420 188-220 (224)
326 PRK02406 DNA polymerase IV; Va 22.1 1.7E+02 0.0036 29.9 5.6 53 255-318 169-223 (343)
327 KOG2379 Endonuclease MUS81 [Re 21.6 74 0.0016 34.6 2.8 43 232-274 35-77 (501)
328 PF02889 Sec63: Sec63 Brl doma 21.5 5.4E+02 0.012 25.6 9.0 56 235-297 132-187 (314)
329 PF00416 Ribosomal_S13: Riboso 21.1 82 0.0018 26.9 2.5 44 254-297 15-58 (107)
330 COG2019 AdkA Archaeal adenylat 21.0 1.7E+02 0.0038 27.7 4.7 53 297-354 9-67 (189)
331 PRK00024 hypothetical protein; 20.9 99 0.0022 30.1 3.4 42 263-311 40-82 (224)
332 PF05984 Cytomega_UL20A: Cytom 20.9 91 0.002 25.8 2.5 31 369-399 50-81 (100)
333 PF00542 Ribosomal_L12: Riboso 20.4 1.2E+02 0.0025 24.0 3.1 51 287-360 10-60 (68)
334 PF13838 Clathrin_H_link: Clat 20.4 1.8E+02 0.0039 23.0 4.0 44 258-301 1-50 (66)
335 PRK11072 bifunctional glutamin 20.2 1.3E+03 0.028 27.5 12.8 44 368-411 154-207 (943)
336 PRK01810 DNA polymerase IV; Va 20.0 1.8E+02 0.0039 30.5 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=8.4e-68 Score=515.44 Aligned_cols=264 Identities=31% Similarity=0.526 Sum_probs=239.8
Q ss_pred CCCCCCCCCCCCcHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhC
Q 012388 198 TDPSLLYNPPDLNKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTG 277 (464)
Q Consensus 198 ~~~~~~~~~~~~N~~ia~~l~~la~~~e~~g~~~r~~aY~rAa~~l~~lp~~I~s~~~l~~lpgIG~~ia~kI~Eil~tG 277 (464)
|++++| ..++|..|+++|+.||+.|++.|+.+|+++|++||++|+++|++|+|++|+++|||||++|+++|+|||+||
T Consensus 2 cqrkTp--lt~~N~~~~~aleiLa~~~ev~g~~~r~~~y~~Aasvlk~~p~~I~S~~ea~~lP~iG~kia~ki~EiletG 79 (353)
T KOG2534|consen 2 CQRKTP--LTNNNQIFTEALEILAEAYEVEGEEDRARAYRRAASVLKSLPFPITSGEEAEKLPGIGPKIAEKIQEILETG 79 (353)
T ss_pred CCCCCc--cccccHHHHHHHHHHHHhhcccccHHHHHHHHHHHHHHHhCCCCcccHHHhcCCCCCCHHHHHHHHHHHHcC
Confidence 344554 378999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHHhhc-cCcchHHHhhHhhHHhhccCCCHHHHHHHHH
Q 012388 278 KLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE-DSLTHSQRLGLKYFDDIKTRIPRHEVEQMER 356 (464)
Q Consensus 278 ~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~-~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~ 356 (464)
++++||++++|+.++.|++|++|||||++||++||++|+|||+|++++ .++|.+|++|++||+||..+|+|+||.+|.+
T Consensus 80 ~l~ele~v~~de~~~~lklFtnifGvG~ktA~~Wy~~GfrTled~Rk~~~kft~qqk~Gl~yy~Df~~~v~ReE~~~i~~ 159 (353)
T KOG2534|consen 80 VLRELEAVRNDERSQSLKLFTNIFGVGLKTAEKWYREGFRTLEDVRKKPDKFTRQQKAGLKYYEDFLKRVTREEATAIQQ 159 (353)
T ss_pred CchhHHHHhcchhHHHHHHHHHHhccCHHHHHHHHHhhhhHHHHHHhCHHHHHHHHHHhHHHHHHHhhhccHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999944 5899999999999999999999999999999
Q ss_pred HHHHHhhhcCCCEEEEEcccccccCCcCCCccEEEeCCCcch-hhhHHHHHHHHHHhcccccccccccccCCCCC-----
Q 012388 357 LLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPDRKS-HKGFLSKYVKKLKEMKFLREDLIFSTHSEEGT----- 430 (464)
Q Consensus 357 iv~~~~~~~~p~~~v~~~GsyRRgke~~gDvDiLit~~d~~~-~~~~l~~lv~~L~~~g~l~~~L~~~~~~~~~~----- 430 (464)
+|++++..++|++.|++||||||||++|||||||||||...+ +.+++..|+..|++.|+|.......+.-+...
T Consensus 160 ~V~~av~~~~p~~~vt~~GsfRRGk~~ggDvD~LithP~~~s~~~~~~~~l~~~le~~g~il~~~~~~S~~Ek~~l~~~~ 239 (353)
T KOG2534|consen 160 TVQEAVWAFDPEAFVTVTGSFRRGKKMGGDVDFLITHPGSTSTEAKLLQLLMILLEKKGLLLYYDQLHSCGEKLRLPSRK 239 (353)
T ss_pred HHHHHHhhcCCCcEEEEeccccCCcccCCCeeEEEeCCCCCchhhhHHHHHHHHHHhcCeEEEEeeeccccccccccchh
Confidence 999999999999999999999999999999999999999887 78899999999999999996554322211110
Q ss_pred --CCCCceEEEEeecC-------------CCC-cceeeeEEEecCcccc
Q 012388 431 --DSGVDTYFGLCTYP-------------GRE-LRHRIDFKVLASLSLI 463 (464)
Q Consensus 431 --~~~~~~~~g~~~~p-------------~~~-~~rRiDi~~~P~~~~~ 463 (464)
-+-..+|||||+|| +++ .+|||||+|+||++|.
T Consensus 240 s~~~~~~~~mgv~~LPr~~~~~~~~S~n~~~~~~~rRvDivv~P~~~~~ 288 (353)
T KOG2534|consen 240 SALDHFKKFMGVFRLPRQRVDSDQSSWNEGKGWKARRVDIVVCPYDEFG 288 (353)
T ss_pred hhHhhhhhEEEEEEcCcccccccccccCCCCCCceeeeEEEEechHHcc
Confidence 01136799999999 544 7899999999999874
No 2
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=100.00 E-value=1.1e-54 Score=437.86 Aligned_cols=240 Identities=39% Similarity=0.646 Sum_probs=223.4
Q ss_pred HHHHHHHHHHHHHHHcC-CChhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhch
Q 012388 212 NITEIFGKLINIYRALG-EDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEK 290 (464)
Q Consensus 212 ~ia~~l~~la~~~e~~g-~~~r~~aY~rAa~~l~~lp~~I~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~ 290 (464)
+|+++|++||++|+++| |.||++||++||++|+++|++|+++.++.+|||||++|+++|+||++||++++||+++++ .
T Consensus 2 ~ia~~L~~ia~~~e~~~~~~~r~~aY~~Aa~~l~~l~~~i~~~~~~~~ipgiG~~ia~kI~E~~~tG~~~~le~l~~~-~ 80 (307)
T cd00141 2 EIADILEELADLLELLGGNPFRVRAYRKAARALESLPEPIESLEEAKKLPGIGKKIAEKIEEILETGKLRKLEELRED-V 80 (307)
T ss_pred hHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHhCCcccCCHHHhcCCCCccHHHHHHHHHHHHcCCHHHHHHHhcc-c
Confidence 69999999999999996 559999999999999999999999999999999999999999999999999999999998 5
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHcCCCCHHHHhhc--cCcchHHHhhHhhHHhhccCCCHHHHHHHHHHHHHHhhhcCCC
Q 012388 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPE 368 (464)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~--~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~iv~~~~~~~~p~ 368 (464)
+..+..|++||||||+||++||+.||+||+||+.+ .+++..|..|++||+|+.++|||+||+++.+.|.+.+..+.|+
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 56666777999999999999997799999999987 4899999999999999999999999999999999888888889
Q ss_pred EEEEEcccccccCCcCCCccEEEeCCCcchhhhHHHHHHHHHHhcccccccccccccCCCCCCCCCceEEEEeecCCCCc
Q 012388 369 VIILCGGSYRRGKASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCTYPGREL 448 (464)
Q Consensus 369 ~~v~~~GsyRRgke~~gDvDiLit~~d~~~~~~~l~~lv~~L~~~g~l~~~L~~~~~~~~~~~~~~~~~~g~~~~p~~~~ 448 (464)
+.|++|||||||+++||||||||+|++... .+++.+|++.|.+.|++++.+. +|..+|||+|++|+...
T Consensus 161 ~~v~i~GS~RRg~et~gDiDilv~~~~~~~-~~~~~~v~~~l~~~~~~~~~~~----------~g~~k~~~~~~~~~~~~ 229 (307)
T cd00141 161 LQVEIAGSYRRGKETVGDIDILVTHPDATS-RGLLEKVVDALVELGFVTEVLS----------KGDTKASGILKLPGGWK 229 (307)
T ss_pred eEEEEcccccCCCCccCCEEEEEecCCccc-cccHHHHHHHHHhCCCeehhhh----------CCCceEEEEEecCCCCC
Confidence 999999999999999999999999999865 7889999999999999988653 25589999999999889
Q ss_pred ceeeeEEEecCcccc
Q 012388 449 RHRIDFKVLASLSLI 463 (464)
Q Consensus 449 ~rRiDi~~~P~~~~~ 463 (464)
+|||||+++|+++|.
T Consensus 230 ~~rVDl~~~p~~~~~ 244 (307)
T cd00141 230 GRRVDLRVVPPEEFG 244 (307)
T ss_pred ceEEEEEEeCHHHHH
Confidence 999999999999874
No 3
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=100.00 E-value=3e-54 Score=439.38 Aligned_cols=253 Identities=34% Similarity=0.559 Sum_probs=212.9
Q ss_pred CCcHHHHHHHHHHHHHHHHcCCC-hhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHH
Q 012388 208 DLNKNITEIFGKLINIYRALGED-RRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFE 286 (464)
Q Consensus 208 ~~N~~ia~~l~~la~~~e~~g~~-~r~~aY~rAa~~l~~lp~~I~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~ 286 (464)
|+|++|+++|++||++||+.|+| ||++||++||++|+++|++|++++++.+|||||++|++||+||++||++.++.+..
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 69999999999999999999999999999999999999999999999999666656
Q ss_pred hhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHHhhcc--CcchHHHhhHhhHHhhccCCCHHHHHHHHHHHHHHhhh
Q 012388 287 KDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEE 364 (464)
Q Consensus 287 ~~~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~~--~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~iv~~~~~~ 364 (464)
.++.+..+..|++|||||||||++||+.||+||+||+++. +|+..|.+|++||+|+.++|||+||+.++++|......
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 6666777777789999999999999999999999999754 69999999999999999999999999999999988888
Q ss_pred cCCCEEEEEcccccccCCcCCCccEEEeCCCcchhhhHHHHHHHHHHhcccccccccccccCCCCCCCCCceEEEEeecC
Q 012388 365 VLPEVIILCGGSYRRGKASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCTYP 444 (464)
Q Consensus 365 ~~p~~~v~~~GsyRRgke~~gDvDiLit~~d~~~~~~~l~~lv~~L~~~g~l~~~L~~~~~~~~~~~~~~~~~~g~~~~p 444 (464)
+.|.+.|++||||||||++||||||||+|+++.. +++.++++.|.- +.++..+.++........+|..+|||||..|
T Consensus 161 ~~~~~~v~i~GSyRRgket~gDIDili~~~~~~~--~~~~~v~~~~~l-~~~~~~~~~~~~~~~~~~~g~~~~~~v~~~~ 237 (334)
T smart00483 161 ILPDAIVTLTGSFRRGKETGHDVDFLITSPHPAK--EKELEVLDLLLL-ESTFEELQLPSIRVATLDHGQKKFMILKLSP 237 (334)
T ss_pred hCCCcEEEEecccccCCCcCCCeeEEEecCCccc--hhHHHHHHHHHH-HHHHHHHhcccchhhhhhcCCCEEEEEEeCC
Confidence 8899999999999999999999999999999773 455555544421 1111111111110111234567999999986
Q ss_pred CC-------------CcceeeeEEEecCcccc
Q 012388 445 GR-------------ELRHRIDFKVLASLSLI 463 (464)
Q Consensus 445 ~~-------------~~~rRiDi~~~P~~~~~ 463 (464)
.. ..||||||+++|+++|.
T Consensus 238 ~~~~~~~~g~~~~~~~~~rrVDl~~~~~~~~g 269 (334)
T smart00483 238 SREDKEKSGKPDEKGWKARRVDIVLCPEDQYP 269 (334)
T ss_pred ccccccccccccCCCCcceEEEEEEechHHhe
Confidence 32 26799999999999985
No 4
>PRK08609 hypothetical protein; Provisional
Probab=100.00 E-value=2.6e-47 Score=412.68 Aligned_cols=235 Identities=20% Similarity=0.292 Sum_probs=207.3
Q ss_pred CCcHHHHHHHHHHHHHHHHcCCC-hhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHH
Q 012388 208 DLNKNITEIFGKLINIYRALGED-RRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFE 286 (464)
Q Consensus 208 ~~N~~ia~~l~~la~~~e~~g~~-~r~~aY~rAa~~l~~lp~~I~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~ 286 (464)
|+|++|+++|++||++++++|+| ||++||++||++|+++|++|++++++.+|||||++||+||+||++||++++||+|+
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 46999999999999999999987 89999999999999999999999999999999999999999999999999999999
Q ss_pred hhchhHHHHHhhhccCcCHHHHHHHHHc-CCCCHHHHhhc---cCcchHHHh----------hHhhHHhhccCCCHHHHH
Q 012388 287 KDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNE---DSLTHSQRL----------GLKYFDDIKTRIPRHEVE 352 (464)
Q Consensus 287 ~~~~~~~l~lf~~I~GvGpktA~~ly~~-GirtledL~~~---~~L~~~q~~----------Glk~~ed~~~~i~r~Ea~ 352 (464)
++.|.++++|+ +|||||||||++||+. ||+||+||+++ ++++.+++| |+++|+++.+|||+.||.
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 98877777665 9999999999999975 99999999964 567666555 677788889999999999
Q ss_pred HHHHHHHHHhhhcCCCEEEEEcccccccCCcCCCccEEEeCCCcchhhhHHHHHHHHHHhcccccccccccccCCCCCCC
Q 012388 353 QMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLREDLIFSTHSEEGTDS 432 (464)
Q Consensus 353 ~i~~iv~~~~~~~~p~~~v~~~GsyRRgke~~gDvDiLit~~d~~~~~~~l~~lv~~L~~~g~l~~~L~~~~~~~~~~~~ 432 (464)
.+.+.|.+.+..+.|...|++||||||||+||||||||||++++.. +++.|...+++++.+. .
T Consensus 160 ~~a~~i~~~l~~~~~~~~v~~~GS~RR~~et~gDiDili~~~~~~~-------~~~~l~~~~~v~~~~~----------~ 222 (570)
T PRK08609 160 PIAQEIEEYLATIDEIIRFSRAGSLRRARETVKDLDFIIATDEPEA-------VREQLLQLPNIVEVIA----------A 222 (570)
T ss_pred HHHHHHHHHHHhCCCccEEEeccchhccccccCCeeEEEecCCHHH-------HHHHHHcCccHHHHHh----------c
Confidence 9988888877776667799999999999999999999999998754 5677777788876653 2
Q ss_pred CCceEEEEeecCCCCcceeeeEEEecCcccc
Q 012388 433 GVDTYFGLCTYPGRELRHRIDFKVLASLSLI 463 (464)
Q Consensus 433 ~~~~~~g~~~~p~~~~~rRiDi~~~P~~~~~ 463 (464)
|..++++.|.++ .++||||+|||+++|.
T Consensus 223 g~~~~~~~~~~~---~~~~vDl~~v~~~~~~ 250 (570)
T PRK08609 223 GDTKVSVELEYE---YTISVDFRLVEPEAFA 250 (570)
T ss_pred CCceEEEEEecC---CCeEEEEEEeCHHHHH
Confidence 457899888762 3689999999999874
No 5
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=100.00 E-value=2.7e-35 Score=290.29 Aligned_cols=236 Identities=26% Similarity=0.404 Sum_probs=196.6
Q ss_pred CCCcHHHHHHHHHHHHHHHHcCCC-hhHHHHHHHHHHHhcCCccccchhhh---cCCCCCCHHHHHHHHHHHHhCCchhh
Q 012388 207 PDLNKNITEIFGKLINIYRALGED-RRSFSYYKAIPVIEKLPFKIESADQV---KGLPGIGKSMQDHIQEIVTTGKLSKL 282 (464)
Q Consensus 207 ~~~N~~ia~~l~~la~~~e~~g~~-~r~~aY~rAa~~l~~lp~~I~s~~~l---~~lpgIG~~ia~kI~Eil~tG~~~~l 282 (464)
.++|+.|+.+|+++|++|++.|+| ||++|||+||++|+.+.+++.++.+. ..|||||++||.+|+||++||+++.+
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 99999999999999999999998765 59999999999999999999999999
Q ss_pred HHHHhhchhHHHHHhhhccCcCHHHHHHHHHc-CCCCHHHHhhc---cCcchHHHhhHhhHHhhcc----------CCCH
Q 012388 283 EHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNE---DSLTHSQRLGLKYFDDIKT----------RIPR 348 (464)
Q Consensus 283 e~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~-GirtledL~~~---~~L~~~q~~Glk~~ed~~~----------~i~r 348 (464)
+.++...|.+...|+ +|+|+|||+...||++ ||.++++|+++ +++..+.+||-++.++|.+ |+|.
T Consensus 82 e~lk~~~P~gl~~Ll-~v~GlGpkKi~~Ly~elgi~~~e~l~~a~~~~~~~~l~GfG~kse~~il~~i~~~~~~~~R~~l 160 (326)
T COG1796 82 EALKKEVPEGLEPLL-KVPGLGPKKIVSLYKELGIKDLEELQEALENGKIRGLRGFGKKSEAKILENIEFAEESPERIPL 160 (326)
T ss_pred HHHHHhCCcchHHHh-hCCCCCcHHHHHHHHHHCcccHHHHHHHHHhCCccccCCccchhHHHHHHHHHHHhhhhhhcch
Confidence 999999999988888 9999999999999998 99999999975 5788899999888888864 5677
Q ss_pred HHHHHHHHHHHHHhhhcCCCEEEEEcccccccCCcCCCccEEEeCCCcchhhhHHHHHHHHHHhcccccccccccccCCC
Q 012388 349 HEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLREDLIFSTHSEE 428 (464)
Q Consensus 349 ~Ea~~i~~iv~~~~~~~~p~~~v~~~GsyRRgke~~gDvDiLit~~d~~~~~~~l~~lv~~L~~~g~l~~~L~~~~~~~~ 428 (464)
.++..+..-+.....++.+-.++.++||+||+|+|++|||++|+..++.+ +++.|.+...++.....
T Consensus 161 ~~~l~ia~ei~~yl~~~~~~~~~~~aGs~RR~retv~DiD~~~s~~~~~~-------v~~~~~~~~~~~~vi~~------ 227 (326)
T COG1796 161 SFTLPIAQEIEGYLEELTPIIQASIAGSLRRGRETVGDIDILISTSHPES-------VLEELLEMPNVQEVIAK------ 227 (326)
T ss_pred HHHHHHHHHHHHHHHhccchheeeeccchhhccccccceeeEeccCCcHH-------HHHHHhcCCCcceeeec------
Confidence 77766655555544455554588999999999999999999999887765 77777777766655432
Q ss_pred CCCCCCceEEEEeecCCCCcceeeeEEEecCcccc
Q 012388 429 GTDSGVDTYFGLCTYPGRELRHRIDFKVLASLSLI 463 (464)
Q Consensus 429 ~~~~~~~~~~g~~~~p~~~~~rRiDi~~~P~~~~~ 463 (464)
|..|+--+-.+...- -+||+|||+++|-
T Consensus 228 ----G~~k~s~~~~~~~~~---svD~r~v~~e~fG 255 (326)
T COG1796 228 ----GETKVSMLLILDEGT---SVDFRVVPPEAFG 255 (326)
T ss_pred ----CCceeeEEEEecCCC---eeEEEEcCHHHhh
Confidence 334554333333221 2999999999873
No 6
>PF14792 DNA_pol_B_palm: DNA polymerase beta palm ; PDB: 1RZT_A 3PML_A 2PFN_A 3HX0_K 3HWT_A 2GWS_E 2BCQ_A 3UPQ_A 2BCS_A 3UQ2_A ....
Probab=99.97 E-value=2.1e-32 Score=237.28 Aligned_cols=105 Identities=43% Similarity=0.781 Sum_probs=93.4
Q ss_pred CCCHHHHHHHHHHHHHHhhhcCCCEEEEEcccccccCCcCCCccEEEeCCCcchh----hhHHHHHHHHHHhcccccccc
Q 012388 345 RIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYRRGKASCGDLDVVIMHPDRKSH----KGFLSKYVKKLKEMKFLREDL 420 (464)
Q Consensus 345 ~i~r~Ea~~i~~iv~~~~~~~~p~~~v~~~GsyRRgke~~gDvDiLit~~d~~~~----~~~l~~lv~~L~~~g~l~~~L 420 (464)
||||+||++++++|++++.+++|++.+++||||||||++|||||||||||+.... .++|.+|+..|+++|||+++|
T Consensus 1 rIPR~Ev~~i~~~V~~~~~~i~p~~~v~i~GSyRRGK~~~gDiDiLIt~~~~~~~~~~~~~~l~~lv~~L~~~g~i~~~L 80 (112)
T PF14792_consen 1 RIPRDEVEEIEEIVKEALEKIDPGLEVEICGSYRRGKETSGDIDILITHPDPSSVSKKLEGLLEKLVKRLEEKGFITDDL 80 (112)
T ss_dssp -EEHHHHHHHHHHHHHHHHCCSTT-EEEEEHHHHTT-SEESSEEEEEEETTCSTTTCSTTCHHHHHHHHHHHTTSEEEEE
T ss_pred CCCHHHHHHHHHHHHHHHHhcCCCcEEEEccccccCCCcCCCeEEEEeCCCcCcchhhHHHHHHHHHHHHHhCCeEEEec
Confidence 6999999999999999999999999999999999999999999999999998774 789999999999999999999
Q ss_pred cccccCCCCCCCCCceEEEEeecCCC---CcceeeeEEEecC
Q 012388 421 IFSTHSEEGTDSGVDTYFGLCTYPGR---ELRHRIDFKVLAS 459 (464)
Q Consensus 421 ~~~~~~~~~~~~~~~~~~g~~~~p~~---~~~rRiDi~~~P~ 459 (464)
+.+ ..+|||+|+||+. .+||||||+|||+
T Consensus 81 ~~~----------~~~~~G~~~l~~~~~~~~~RRiDi~~~P~ 112 (112)
T PF14792_consen 81 SLG----------PTKYMGVCRLPGNDNKSPHRRIDIIVVPY 112 (112)
T ss_dssp EEC----------SSEEEEEEE-SSTSST--EEEEEEEEEEG
T ss_pred ccC----------CceeeeEeecCCCCCCCCeeeEEEEEeCC
Confidence 652 3799999999998 7999999999996
No 7
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=99.71 E-value=2.4e-17 Score=130.58 Aligned_cols=66 Identities=36% Similarity=0.688 Sum_probs=62.6
Q ss_pred cHHHHHHHHHHHHHHHHc-CCChhHHHHHHHHHHHhcCCccccchhh-hcCCCCCCHHHHHHHHHHHH
Q 012388 210 NKNITEIFGKLINIYRAL-GEDRRSFSYYKAIPVIEKLPFKIESADQ-VKGLPGIGKSMQDHIQEIVT 275 (464)
Q Consensus 210 N~~ia~~l~~la~~~e~~-g~~~r~~aY~rAa~~l~~lp~~I~s~~~-l~~lpgIG~~ia~kI~Eil~ 275 (464)
|++|+++|++||++|++. |+.||++||++||++|+++|++|++++| +.+|||||++|+.+|.|||+
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 6669999999999999999999999987 99999999999999999986
No 8
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. This entry represents the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone []. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1KDH_A 1KEJ_A 1JMS_A 2IHM_A 3OGU_A 1MQ2_A 2P66_A 7ICI_A 1ZQN_A 1ZQK_A ....
Probab=99.70 E-value=1.6e-17 Score=124.27 Aligned_cols=51 Identities=49% Similarity=1.009 Sum_probs=42.2
Q ss_pred HHHhhhccCcCHHHHHHHHHcCCCCHHHHhh-ccCcchHHHhhHhhHHhhcc
Q 012388 294 ISLFGEVWGIGPATAQKLYEKGHRTLDDLKN-EDSLTHSQRLGLKYFDDIKT 344 (464)
Q Consensus 294 l~lf~~I~GvGpktA~~ly~~GirtledL~~-~~~L~~~q~~Glk~~ed~~~ 344 (464)
|++|++||||||+||++||++|+|||+||++ ...|+..|++|++||+||++
T Consensus 1 l~~f~~I~GVG~~tA~~w~~~G~rtl~Dl~~~~~~Lt~~Q~iGl~yyeD~~q 52 (52)
T PF10391_consen 1 LKLFTGIWGVGPKTARKWYAKGIRTLEDLRKSKSKLTWQQQIGLKYYEDFQQ 52 (52)
T ss_dssp HHHHHTSTT--HHHHHHHHHTT--SHHHHHHGGCGS-HHHHHHHHTHHHHH-
T ss_pred CcchhhcccccHHHHHHHHHhCCCCHHHHhhhhccCCHHHHHHHHHHHHhcC
Confidence 6789999999999999999999999999986 45899999999999999974
No 9
>PRK07945 hypothetical protein; Provisional
Probab=99.53 E-value=1.7e-14 Score=147.68 Aligned_cols=91 Identities=20% Similarity=0.247 Sum_probs=83.2
Q ss_pred HHHHHHHHHHHHHHcCCC-hhHHHHHHHHHHHhcCCcc-ccchh---hhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHh
Q 012388 213 ITEIFGKLINIYRALGED-RRSFSYYKAIPVIEKLPFK-IESAD---QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEK 287 (464)
Q Consensus 213 ia~~l~~la~~~e~~g~~-~r~~aY~rAa~~l~~lp~~-I~s~~---~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~ 287 (464)
-+++|+++|+++|++|+| ||++|||+||.+|+.++.+ +..+. ++.+|||||+++|+||.||++||+++.||+|+.
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 8999999999999999999 88774 799999999999999999999999999999988
Q ss_pred hchhHHHHHhhhccCcCHHHHHHHHH
Q 012388 288 DEKVRTISLFGEVWGIGPATAQKLYE 313 (464)
Q Consensus 288 ~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (464)
+..+. | |+..+.++.-
T Consensus 83 ~~~~~---------~-g~~l~~~~~~ 98 (335)
T PRK07945 83 DAEPL---------G-GGALRAALRG 98 (335)
T ss_pred hhcCC---------c-cHHHHHHHhh
Confidence 76443 7 9999999874
No 10
>smart00292 BRCT breast cancer carboxy-terminal domain.
Probab=99.01 E-value=8.8e-10 Score=86.56 Aligned_cols=79 Identities=19% Similarity=0.279 Sum_probs=61.7
Q ss_pred CCCCCeEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCC-CccEEEEcCChHHHHHHHHHhhhccCccccccchHHHHH
Q 012388 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSK-KVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSL 95 (464)
Q Consensus 17 ~~F~g~~vy~~~~~~g~~R~~~l~~~i~~~Gg~V~~~ls~-~VTHVV~~~~~~~~~~l~~~~~~~~~~~iV~~~Wl~ec~ 95 (464)
.+|+|+++||.+ .+.......+.+++..+||++...++. .+||||+.+.+..... .........++|+.+||.+|+
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 379999999996 356667788999999999999999988 9999999776532111 112223467999999999999
Q ss_pred hcC
Q 012388 96 RLG 98 (464)
Q Consensus 96 k~g 98 (464)
+++
T Consensus 78 ~~~ 80 (80)
T smart00292 78 KAG 80 (80)
T ss_pred HCc
Confidence 875
No 11
>PF00533 BRCT: BRCA1 C Terminus (BRCT) domain; InterPro: IPR001357 The BRCT domain (after the C_terminal domain of a breast cancer susceptibility protein) is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage [], for example as found in the breast cancer DNA-repair protein BRCA1. The domain is an approximately 100 amino acid tandem repeat, which appears to act as a phospho-protein binding domain []. A chitin biosynthesis protein from yeast also seems to belong to this group. ; GO: 0005622 intracellular; PDB: 3L46_A 3AL3_A 3AL2_A 1WF6_A 3II6_X 2NTE_B 3FA2_A 2R1Z_A 2COK_A 2K7F_A ....
Probab=99.01 E-value=7e-10 Score=88.30 Aligned_cols=75 Identities=23% Similarity=0.348 Sum_probs=59.2
Q ss_pred CCCCCCeEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCC-hHHHHHHHHHhhhccCccccccchHHHH
Q 012388 16 NGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDL-EALLQQVSKQHLARFKGSVIRYQWLEDS 94 (464)
Q Consensus 16 ~~~F~g~~vy~~~~~~g~~R~~~l~~~i~~~Gg~V~~~ls~~VTHVV~~~~-~~~~~~l~~~~~~~~~~~iV~~~Wl~ec 94 (464)
..+|+||.+|| .+.....++.++++++++||++.+.+++.+||||+.+. +.... .......+..+|+.+||.+|
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 46899999999 45666677788999999999999999999999999876 22111 12222346899999999999
Q ss_pred H
Q 012388 95 L 95 (464)
Q Consensus 95 ~ 95 (464)
+
T Consensus 78 i 78 (78)
T PF00533_consen 78 I 78 (78)
T ss_dssp H
T ss_pred C
Confidence 6
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=98.68 E-value=4.1e-08 Score=75.19 Aligned_cols=72 Identities=18% Similarity=0.289 Sum_probs=54.3
Q ss_pred CeEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccchHHHHHh
Q 012388 21 GMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSLR 96 (464)
Q Consensus 21 g~~vy~~~~~~g~~R~~~l~~~i~~~Gg~V~~~ls~~VTHVV~~~~~~~~~~l~~~~~~~~~~~iV~~~Wl~ec~k 96 (464)
||.+||.+.-.+ ..+..|++++..+||++.+.++..+||||+.+...... .......+.++|+.+||.+|++
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 578888864323 34568999999999999999999999999976653221 1112234689999999999985
No 13
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=98.07 E-value=1.4e-05 Score=88.76 Aligned_cols=133 Identities=20% Similarity=0.260 Sum_probs=95.3
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc-CCCCHHHHhhcc--Ccch
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED--SLTH 330 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~-GirtledL~~~~--~L~~ 330 (464)
+++..|||+|++.+++|.+.++.++...|++ .+..| +|+|||+++|+.|++. | |+++|.++. .|..
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 5788999999999999999999988776664 45556 9999999999999986 6 999998753 5777
Q ss_pred HHHhhHhhHHhhccCCCHHHHHH-HHHHHHH------H------h--hhcCCCEEEEEccccccc---------------
Q 012388 331 SQRLGLKYFDDIKTRIPRHEVEQ-MERLLQK------A------G--EEVLPEVIILCGGSYRRG--------------- 380 (464)
Q Consensus 331 ~q~~Glk~~ed~~~~i~r~Ea~~-i~~iv~~------~------~--~~~~p~~~v~~~GsyRRg--------------- 380 (464)
..+||.+..+.|..-+.-.+..+ +..+... . . ...+.|-.+++||++...
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 88899888887776554333322 2222221 0 0 011335578899987643
Q ss_pred --CCcCCCccEEEeCCCcc
Q 012388 381 --KASCGDLDVVIMHPDRK 397 (464)
Q Consensus 381 --ke~~gDvDiLit~~d~~ 397 (464)
...+...|+||..++..
T Consensus 615 v~~sVs~kt~~lv~G~~~g 633 (652)
T TIGR00575 615 VASSVSKKTDYVIAGEKAG 633 (652)
T ss_pred EeCCcCCCccEEEECCCCC
Confidence 45567789999876544
No 14
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=98.00 E-value=4.3e-06 Score=64.39 Aligned_cols=51 Identities=37% Similarity=0.549 Sum_probs=43.5
Q ss_pred HHHHhhhccCcCHHHHHHHHHcCCCCHHHHhhc--cCcchHHHhhHhhHHhhc
Q 012388 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDIK 343 (464)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~GirtledL~~~--~~L~~~q~~Glk~~ed~~ 343 (464)
+...|++|+||||++|++||+.||.|++||.+. ..|....++|-+..+.|.
T Consensus 3 ~~~~L~~I~Gig~~~a~~L~~~G~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~ 55 (60)
T PF14520_consen 3 VFDDLLSIPGIGPKRAEKLYEAGIKTLEDLANADPEELAEIPGIGEKTAEKII 55 (60)
T ss_dssp HHHHHHTSTTCHHHHHHHHHHTTCSSHHHHHTSHHHHHHTSTTSSHHHHHHHH
T ss_pred HHHhhccCCCCCHHHHHHHHhcCCCcHHHHHcCCHHHHhcCCCCCHHHHHHHH
Confidence 455677999999999999999999999999875 358888899988877765
No 15
>PF12738 PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2WT8_C 3EF1_A 3EF0_A.
Probab=97.78 E-value=2.4e-05 Score=60.44 Aligned_cols=63 Identities=17% Similarity=0.343 Sum_probs=42.1
Q ss_pred eEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccch
Q 012388 22 MRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQW 90 (464)
Q Consensus 22 ~~vy~~~~~~g~~R~~~l~~~i~~~Gg~V~~~ls~~VTHVV~~~~~~~~~~l~~~~~~~~~~~iV~~~W 90 (464)
|+|.+. ++....+..+.++++.+||++.+.++.++||+|+.+..- .+...+...+.++|+.+|
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 345554 343333567899999999999999999999999965432 223334445789999999
No 16
>KOG3226 consensus DNA repair protein [Replication, recombination and repair]
Probab=97.64 E-value=2.4e-05 Score=79.33 Aligned_cols=89 Identities=16% Similarity=0.312 Sum_probs=72.4
Q ss_pred CCCCCCeEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEc-CChHHHHHHHHHhhhccCccccccchHHHH
Q 012388 16 NGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAM-DLEALLQQVSKQHLARFKGSVIRYQWLEDS 94 (464)
Q Consensus 16 ~~~F~g~~vy~~~~~~g~~R~~~l~~~i~~~Gg~V~~~ls~~VTHVV~~-~~~~~~~~l~~~~~~~~~~~iV~~~Wl~ec 94 (464)
+.++.|+++.+. |+...-+.-|+..+..+||+.-.+++.+.||.|+. .+.. +..+....+..||+-+||++|
T Consensus 315 ~klL~GVV~VlS--GfqNP~Rs~LRskAl~LGAkY~pDW~~gsThLICAF~NTP-----Ky~QV~g~Gg~IV~keWI~~C 387 (508)
T KOG3226|consen 315 SKLLEGVVFVLS--GFQNPERSTLRSKALTLGAKYQPDWNAGSTHLICAFPNTP-----KYRQVEGNGGTIVSKEWITEC 387 (508)
T ss_pred HHhhhceEEEEe--cccCchHHHHHHHHHhhcccccCCcCCCceeEEEecCCCc-----chhhcccCCceEeeHHHHHHH
Confidence 478999988886 67766667899999999999999999999999984 2222 223333446799999999999
Q ss_pred HhcCCCCCccccccccC
Q 012388 95 LRLGEKVSEDLYRIKLD 111 (464)
Q Consensus 95 ~k~g~lvdee~y~l~~~ 111 (464)
...+++||..+|.+.-+
T Consensus 388 y~~kk~lp~rrYlm~~~ 404 (508)
T KOG3226|consen 388 YAQKKLLPIRRYLMHAG 404 (508)
T ss_pred HHHHhhccHHHHHhcCC
Confidence 99999999999998643
No 17
>PLN03123 poly [ADP-ribose] polymerase; Provisional
Probab=97.64 E-value=0.00011 Score=84.68 Aligned_cols=93 Identities=16% Similarity=0.356 Sum_probs=72.8
Q ss_pred CCCCCCCCeEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccchHHH
Q 012388 14 DSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLED 93 (464)
Q Consensus 14 ~~~~~F~g~~vy~~~~~~g~~R~~~l~~~i~~~Gg~V~~~ls~~VTHVV~~~~~~~~~~l~~~~~~~~~~~iV~~~Wl~e 93 (464)
+....|.++.|.+.++ ++.. ..-|++.+..+||++...+++.+||+|+.. +......++..+...+.+||+.+||++
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 3446799999999986 3433 367999999999999999999999999875 222222334444455789999999999
Q ss_pred HHhcCCCCCccccccc
Q 012388 94 SLRLGEKVSEDLYRIK 109 (464)
Q Consensus 94 c~k~g~lvdee~y~l~ 109 (464)
|.+.+++++.+.|.+.
T Consensus 466 s~~~~~~~p~~~y~~~ 481 (981)
T PLN03123 466 CFKKKKKLPFDKYKLE 481 (981)
T ss_pred HHhccccCcchhhhhc
Confidence 9999999998888664
No 18
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=97.47 E-value=0.00015 Score=55.73 Aligned_cols=52 Identities=33% Similarity=0.610 Sum_probs=40.7
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (464)
.++.+|||||+.++.++.+ .| +..++++.+..+ +.+.+|+|||+++|++|.+
T Consensus 5 ~~L~~I~Gig~~~a~~L~~---~G-~~t~~~l~~a~~----~~L~~i~Gig~~~a~~i~~ 56 (60)
T PF14520_consen 5 DDLLSIPGIGPKRAEKLYE---AG-IKTLEDLANADP----EELAEIPGIGEKTAEKIIE 56 (60)
T ss_dssp HHHHTSTTCHHHHHHHHHH---TT-CSSHHHHHTSHH----HHHHTSTTSSHHHHHHHHH
T ss_pred HhhccCCCCCHHHHHHHHh---cC-CCcHHHHHcCCH----HHHhcCCCCCHHHHHHHHH
Confidence 5788999999999887655 47 566788765322 3466999999999999976
No 19
>PLN03122 Poly [ADP-ribose] polymerase; Provisional
Probab=97.35 E-value=0.00039 Score=78.66 Aligned_cols=95 Identities=20% Similarity=0.277 Sum_probs=72.4
Q ss_pred CCCCCCCCCeEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHH-HHHHHhhhccCccccccchH
Q 012388 13 LDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQ-QVSKQHLARFKGSVIRYQWL 91 (464)
Q Consensus 13 ~~~~~~F~g~~vy~~~~~~g~~R~~~l~~~i~~~Gg~V~~~ls~~VTHVV~~~~~~~~~-~l~~~~~~~~~~~iV~~~Wl 91 (464)
..+...|.|++|.|.++ +..+ +.-+++++..+||+|.+.+ .+.||+|+...+.... .-+...+...+.+||+.+||
T Consensus 184 ~~~~kpL~G~~fviTGt-l~~s-r~elK~~Ie~~GGkvsssV-s~~T~lIvt~~ev~k~gsSKlkkAk~lgIpIVsEd~L 260 (815)
T PLN03122 184 GAPGKPFSGMMISLSGR-LSRT-HQYWKKDIEKHGGKVANSV-EGVTCLVVSPAERERGGSSKIAEAMERGIPVVREAWL 260 (815)
T ss_pred cccCCCcCCcEEEEeCC-CCCC-HHHHHHHHHHcCCEEcccc-ccceEEEEcCccccccCccHHHHHHHcCCcCccHHHH
Confidence 35556799999999986 3333 4578999999999999999 6788999866442110 12233344457899999999
Q ss_pred HHHHhcCCCCCcccccccc
Q 012388 92 EDSLRLGEKVSEDLYRIKL 110 (464)
Q Consensus 92 ~ec~k~g~lvdee~y~l~~ 110 (464)
.+|++.++++++..|.+..
T Consensus 261 ~d~i~~~k~~~~~~y~l~~ 279 (815)
T PLN03122 261 IDSIEKQEAQPLEAYDVVS 279 (815)
T ss_pred HHHHhcCCcccchhhhhcc
Confidence 9999999999999998853
No 20
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=97.09 E-value=0.00064 Score=57.00 Aligned_cols=37 Identities=38% Similarity=0.405 Sum_probs=32.6
Q ss_pred hhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHHhhcc
Q 012388 290 KVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (464)
Q Consensus 290 ~~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~~ 326 (464)
....+..|+.|||||+++|+.|+..||+|++||+...
T Consensus 7 ~~~~~~~L~~iP~IG~a~a~DL~~LGi~s~~~L~g~d 43 (93)
T PF11731_consen 7 KRAGLSDLTDIPNIGKATAEDLRLLGIRSPADLKGRD 43 (93)
T ss_pred HHHHHHHHhcCCCccHHHHHHHHHcCCCCHHHHhCCC
Confidence 3457788999999999999999999999999999653
No 21
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=97.08 E-value=0.0027 Score=70.97 Aligned_cols=134 Identities=16% Similarity=0.276 Sum_probs=89.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHHhhcc--CcchH
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHS 331 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~~--~L~~~ 331 (464)
+++..|||+|++.+++|.+=++.-+-..| ...+--+ +|+|||+++|+.|.+. +.|+++|.++. .|...
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 57899999999999998766553222222 2344445 9999999999999864 48899998653 57778
Q ss_pred HHhhHhhHHhhccCCCHHHHHH-HHHHHHHHhh-------hcCCCEEEEEcccccc---c--------------CCcCCC
Q 012388 332 QRLGLKYFDDIKTRIPRHEVEQ-MERLLQKAGE-------EVLPEVIILCGGSYRR---G--------------KASCGD 386 (464)
Q Consensus 332 q~~Glk~~ed~~~~i~r~Ea~~-i~~iv~~~~~-------~~~p~~~v~~~GsyRR---g--------------ke~~gD 386 (464)
.++|-+..+.|..-+.-.+..+ +..+...-.. ..+.|-.+++||.+.. . ...+..
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 8899888887776665443333 2333221010 0144668889998842 2 446678
Q ss_pred ccEEEeCCCcc
Q 012388 387 LDVVIMHPDRK 397 (464)
Q Consensus 387 vDiLit~~d~~ 397 (464)
.|+||..+...
T Consensus 629 t~~lv~G~~~g 639 (665)
T PRK07956 629 TDLVVAGEAAG 639 (665)
T ss_pred CCEEEECCCCC
Confidence 89999876543
No 22
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=96.98 E-value=0.0012 Score=51.53 Aligned_cols=49 Identities=29% Similarity=0.615 Sum_probs=32.0
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012388 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (464)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (464)
..+|||||+..|+.+-+ ++..++.+.+. ..+.|++|+|||+++|+.+|+
T Consensus 5 aLGI~~VG~~~ak~L~~-----~f~sl~~l~~a----~~e~L~~i~gIG~~~A~si~~ 53 (64)
T PF12826_consen 5 ALGIPGVGEKTAKLLAK-----HFGSLEALMNA----SVEELSAIPGIGPKIAQSIYE 53 (64)
T ss_dssp HCTSTT--HHHHHHHHH-----CCSCHHHHCC------HHHHCTSTT--HHHHHHHHH
T ss_pred eCCCCCccHHHHHHHHH-----HcCCHHHHHHc----CHHHHhccCCcCHHHHHHHHH
Confidence 35899999999998865 33445555432 455678999999999999875
No 23
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=96.96 E-value=0.0011 Score=60.52 Aligned_cols=50 Identities=34% Similarity=0.627 Sum_probs=40.6
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHH-hCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012388 252 SADQVKGLPGIGKSMQDHIQEIVT-TGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (464)
Q Consensus 252 s~~~l~~lpgIG~~ia~kI~Eil~-tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (464)
+.+||..|||||++.|++|.++-+ .|.+.-+|+ |.+|.|||+++.++|-.
T Consensus 95 s~eeL~~lpgIG~~kA~aIi~yRe~~G~f~sv~d------------L~~v~GiG~~~~ekl~~ 145 (149)
T COG1555 95 SAEELQALPGIGPKKAQAIIDYREENGPFKSVDD------------LAKVKGIGPKTLEKLKD 145 (149)
T ss_pred CHHHHHHCCCCCHHHHHHHHHHHHHcCCCCcHHH------------HHhccCCCHHHHHHHHh
Confidence 457899999999999999999874 445555554 56999999999999854
No 24
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=96.89 E-value=0.0018 Score=57.06 Aligned_cols=50 Identities=30% Similarity=0.505 Sum_probs=40.3
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHHh-CCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012388 252 SADQVKGLPGIGKSMQDHIQEIVTT-GKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (464)
Q Consensus 252 s~~~l~~lpgIG~~ia~kI~Eil~t-G~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (464)
+.++|..|||||++.|.+|-++.+. |.+.. ++.|.+|+|||++++++|.+
T Consensus 66 ~~~eL~~lpGIG~~~A~~Ii~~R~~~g~f~s------------~eeL~~V~GIg~k~~~~i~~ 116 (120)
T TIGR01259 66 SLEELQALPGIGPAKAKAIIEYREENGAFKS------------VDDLTKVSGIGEKSLEKLKD 116 (120)
T ss_pred CHHHHhcCCCCCHHHHHHHHHHHHhcCCcCC------------HHHHHcCCCCCHHHHHHHHh
Confidence 4578999999999999999998864 44433 44456899999999999865
No 25
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=96.80 E-value=0.0019 Score=50.54 Aligned_cols=49 Identities=43% Similarity=0.655 Sum_probs=35.7
Q ss_pred cchhhhcCCCCCCHHHHHHHHHHH-HhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHH
Q 012388 251 ESADQVKGLPGIGKSMQDHIQEIV-TTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKL 311 (464)
Q Consensus 251 ~s~~~l~~lpgIG~~ia~kI~Eil-~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l 311 (464)
.+.+||..+||||+..|+.|.++- +.|.+..+++| ..|+|+|+++..+|
T Consensus 11 as~~eL~~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL------------~~v~gi~~~~~~~l 60 (65)
T PF12836_consen 11 ASAEELQALPGIGPKQAKAIVEYREKNGPFKSLEDL------------KEVPGIGPKTYEKL 60 (65)
T ss_dssp S-HHHHHTSTT--HHHHHHHHHHHHHH-S-SSGGGG------------GGSTT--HHHHHHH
T ss_pred CCHHHHHHcCCCCHHHHHHHHHHHHhCcCCCCHHHH------------hhCCCCCHHHHHHH
Confidence 356899999999999999999998 56777777765 48999999999887
No 26
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=96.80 E-value=0.0053 Score=68.90 Aligned_cols=134 Identities=16% Similarity=0.293 Sum_probs=90.3
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHHhhcc--CcchH
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHS 331 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~~--~L~~~ 331 (464)
+++..|+|+|++.+++|.+=++.-+-..|+ ..+--| +|+|||+++|++|.+ .+.|+++|..+. .|...
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 578899999999999887665533322333 345556 999999999999975 568899998653 47778
Q ss_pred HHhhHhhHHhhccCCCHHHHHH-HHHHHHHHh---------hhcCCCEEEEEcccccc-----------------cCCcC
Q 012388 332 QRLGLKYFDDIKTRIPRHEVEQ-MERLLQKAG---------EEVLPEVIILCGGSYRR-----------------GKASC 384 (464)
Q Consensus 332 q~~Glk~~ed~~~~i~r~Ea~~-i~~iv~~~~---------~~~~p~~~v~~~GsyRR-----------------gke~~ 384 (464)
.++|.+..+.|.+-+.-.+..+ +..++..-. ...+.|..+++||++-. ....+
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 8889888888776665444333 233332100 01134567889998743 23456
Q ss_pred CCccEEEeCCCcc
Q 012388 385 GDLDVVIMHPDRK 397 (464)
Q Consensus 385 gDvDiLit~~d~~ 397 (464)
...|+||....+.
T Consensus 646 ~kt~~Lv~G~~~g 658 (689)
T PRK14351 646 GNTDYLVVGENPG 658 (689)
T ss_pred CCccEEEEcCCCC
Confidence 7789999876544
No 27
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=96.70 E-value=0.011 Score=52.05 Aligned_cols=67 Identities=24% Similarity=0.362 Sum_probs=44.2
Q ss_pred CCCCHHHHHHH--------HHHHHhCCchhhH-HHHhhc--------hhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHH
Q 012388 260 PGIGKSMQDHI--------QEIVTTGKLSKLE-HFEKDE--------KVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL 322 (464)
Q Consensus 260 pgIG~~ia~kI--------~Eil~tG~~~~le-~l~~~~--------~~~~l~lf~~I~GvGpktA~~ly~~GirtledL 322 (464)
||||+..+++. .++++.|..+.-. ++.... ....+.-|+.|+|||+..|.-|...||+|+++|
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 67777776663 4556555433222 121111 122444566999999999999999999999999
Q ss_pred hhcc
Q 012388 323 KNED 326 (464)
Q Consensus 323 ~~~~ 326 (464)
....
T Consensus 81 A~~~ 84 (122)
T PF14229_consen 81 AQRN 84 (122)
T ss_pred HhCC
Confidence 8653
No 28
>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=96.56 E-value=0.0037 Score=59.44 Aligned_cols=53 Identities=17% Similarity=0.285 Sum_probs=38.7
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHH
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLY 312 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly 312 (464)
.+|.++||||+++|-.| |.+-+.+++.+.-.+. -...|++|||||+|||+++.
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 57899999999999888 5554555554433222 23456799999999999997
No 29
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=96.47 E-value=0.0042 Score=55.04 Aligned_cols=47 Identities=15% Similarity=0.246 Sum_probs=36.1
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012388 252 SADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (464)
Q Consensus 252 s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (464)
+..++..+||||+..|++|- ..|-+..+|+ +.+|+|||+++.+.+-+
T Consensus 59 ~~~el~~lpGigP~~A~~IV---~nGpf~sveD------------L~~V~GIgekqk~~l~k 105 (132)
T PRK02515 59 SVRAFRQFPGMYPTLAGKIV---KNAPYDSVED------------VLNLPGLSERQKELLEA 105 (132)
T ss_pred CHHHHHHCCCCCHHHHHHHH---HCCCCCCHHH------------HHcCCCCCHHHHHHHHH
Confidence 45788999999999999887 4665555554 44899999988777754
No 30
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]
Probab=96.46 E-value=0.0052 Score=68.22 Aligned_cols=91 Identities=14% Similarity=0.194 Sum_probs=70.7
Q ss_pred CCCCCCCCCCeEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEE--cCC-hHHHHHHHHHhhhccCcccccc
Q 012388 12 ALDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLA--MDL-EALLQQVSKQHLARFKGSVIRY 88 (464)
Q Consensus 12 ~~~~~~~F~g~~vy~~~~~~g~~R~~~l~~~i~~~Gg~V~~~ls~~VTHVV~--~~~-~~~~~~l~~~~~~~~~~~iV~~ 88 (464)
..+.+.+|.|+-+++.....+..+...|.+.+..+||.++..+.++.||.|+ ... .+. +...+.+ ..-||+.
T Consensus 627 ~~~~s~if~gl~f~Vlsgt~~~~tk~~le~~ivenGG~iv~nv~p~~~~ci~~a~~et~~v----k~~~~~~-~cdVl~p 701 (881)
T KOG0966|consen 627 VAKISNIFDGLEFCVLSGTSETHTKAKLEEIIVENGGKIVQNVGPSDTLCIATAGKETTRV----KAQAIKR-SCDVLKP 701 (881)
T ss_pred ccchhhhhcCeeEEEecCCcccccHHHHHHHHHHcCCEEEEcCCCCCcceEEeccccchHH----HHHHHhc-cCceeeH
Confidence 3566789999999998766666667789999999999999999999999996 222 222 2222223 6789999
Q ss_pred chHHHHHhcCCCCCccccc
Q 012388 89 QWLEDSLRLGEKVSEDLYR 107 (464)
Q Consensus 89 ~Wl~ec~k~g~lvdee~y~ 107 (464)
+||.+|.+..++++..++-
T Consensus 702 ~Wlldcc~~~~l~p~~P~~ 720 (881)
T KOG0966|consen 702 AWLLDCCKKQRLLPWLPRD 720 (881)
T ss_pred HHHHHHHhhhhccccccHH
Confidence 9999999999999975543
No 31
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=96.30 E-value=0.009 Score=47.08 Aligned_cols=51 Identities=22% Similarity=0.344 Sum_probs=39.5
Q ss_pred chhhhcC-CCCCCHHHHHHHHHHHH-hCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc
Q 012388 252 SADQVKG-LPGIGKSMQDHIQEIVT-TGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (464)
Q Consensus 252 s~~~l~~-lpgIG~~ia~kI~Eil~-tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 314 (464)
+.++|.. +||||...+..|-+... .|.+. .++.|.+|+|||.++|++++..
T Consensus 14 ~~~~L~~~ipgig~~~a~~Il~~R~~~g~~~------------s~~dL~~v~gi~~~~~~~i~~~ 66 (69)
T TIGR00426 14 TAEELQRAMNGVGLKKAEAIVSYREEYGPFK------------TVEDLKQVPGIGNSLVEKNLAV 66 (69)
T ss_pred CHHHHHhHCCCCCHHHHHHHHHHHHHcCCcC------------CHHHHHcCCCCCHHHHHHHHhh
Confidence 3467888 99999999999888875 45444 3444568999999999999763
No 32
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=96.22 E-value=0.0019 Score=62.65 Aligned_cols=52 Identities=25% Similarity=0.500 Sum_probs=42.8
Q ss_pred HhhhccCcCHHHHHHHHHcCCCCHHHHhhcc--CcchHHHhhHhhHHhhccCCC
Q 012388 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIKTRIP 347 (464)
Q Consensus 296 lf~~I~GvGpktA~~ly~~GirtledL~~~~--~L~~~q~~Glk~~ed~~~~i~ 347 (464)
.|..|+|||++++++||+.||.|+++|..+. .|..+.+||-+..+.|...+.
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 577777888777666655544
No 33
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.21 E-value=0.0051 Score=58.64 Aligned_cols=52 Identities=17% Similarity=0.292 Sum_probs=37.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchh-hHHHHhhchhHHHHHhhhccCcCHHHHHHHH
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSK-LEHFEKDEKVRTISLFGEVWGIGPATAQKLY 312 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~-le~l~~~~~~~~l~lf~~I~GvGpktA~~ly 312 (464)
..|.+++|||+++|-.|-.-+ ..++ .+.+.+ +-.+.|++|||||+|||+++.
T Consensus 73 ~~Li~V~GIGpK~Al~ILs~~---~~~~l~~aI~~----~D~~~L~~vpGIGkKtAerIi 125 (194)
T PRK14605 73 ETLIDVSGIGPKLGLAMLSAM---NAEALASAIIS----GNAELLSTIPGIGKKTASRIV 125 (194)
T ss_pred HHHhCCCCCCHHHHHHHHHhC---CHHHHHHHHHh----CCHHHHHhCCCCCHHHHHHHH
Confidence 568999999999999876543 2333 233322 234557799999999999964
No 34
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=96.18 E-value=0.0043 Score=41.22 Aligned_cols=23 Identities=30% Similarity=0.546 Sum_probs=19.5
Q ss_pred cchhhhcCCCCCCHHHHHHHHHH
Q 012388 251 ESADQVKGLPGIGKSMQDHIQEI 273 (464)
Q Consensus 251 ~s~~~l~~lpgIG~~ia~kI~Ei 273 (464)
.+++||.+|||||+.+|..|.+|
T Consensus 8 as~eeL~~lpGIG~~tA~~I~~~ 30 (30)
T PF00633_consen 8 ASIEELMKLPGIGPKTANAILSF 30 (30)
T ss_dssp SSHHHHHTSTT-SHHHHHHHHHH
T ss_pred CCHHHHHhCCCcCHHHHHHHHhC
Confidence 46799999999999999999775
No 35
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=96.06 E-value=0.0068 Score=57.61 Aligned_cols=54 Identities=19% Similarity=0.276 Sum_probs=37.8
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhH-HHHhhchhHHHHHhhhccCcCHHHHHHHHHc
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLE-HFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le-~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 314 (464)
..+..+||||+++|.+|.+.+ ....+. .+.+. -.+.|++|+|||+|+|++++..
T Consensus 73 ~~L~~i~GIGpk~A~~il~~f---g~~~l~~~i~~~----d~~~L~~v~Gig~k~A~~I~~~ 127 (192)
T PRK00116 73 RLLISVSGVGPKLALAILSGL---SPEELVQAIANG----DVKALTKVPGIGKKTAERIVLE 127 (192)
T ss_pred HHHhcCCCCCHHHHHHHHHhC---CHHHHHHHHHhC----CHHHHHhCCCCCHHHHHHHHHH
Confidence 468889999999999885433 223343 23322 2334569999999999999863
No 36
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=96.06 E-value=0.0042 Score=59.02 Aligned_cols=50 Identities=16% Similarity=0.230 Sum_probs=41.1
Q ss_pred HHHHHhhhccCcCHHHHHHHHHcCCCCHHHHhhc------cCcchHHHhhHhhHHhhc
Q 012388 292 RTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE------DSLTHSQRLGLKYFDDIK 343 (464)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~------~~L~~~q~~Glk~~ed~~ 343 (464)
..+.+|.+|+|||||+|..+ .+.-|+++|.++ ..|+..++||-|..+.|.
T Consensus 69 ~lF~~L~~V~GIGpK~Al~i--L~~~~~~el~~aI~~~d~~~L~~ipGiGkKtAerIi 124 (191)
T TIGR00084 69 ELFKELIKVNGVGPKLALAI--LSNMSPEEFVYAIETEEVKALVKIPGVGKKTAERLL 124 (191)
T ss_pred HHHHHHhCCCCCCHHHHHHH--HhcCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHH
Confidence 46777789999999999999 566778888742 468999999999987765
No 37
>KOG2481 consensus Protein required for normal rRNA processing [RNA processing and modification]
Probab=95.98 E-value=0.0031 Score=66.90 Aligned_cols=86 Identities=17% Similarity=0.263 Sum_probs=63.1
Q ss_pred CCCCCCCCCCeEEEEecCCCCchHHHHHHHHHHhcCCEEEee-c---------CCCccEEEEcCChHHHHHHHHHhhhcc
Q 012388 12 ALDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEK-L---------SKKVTHVLAMDLEALLQQVSKQHLARF 81 (464)
Q Consensus 12 ~~~~~~~F~g~~vy~~~~~~g~~R~~~l~~~i~~~Gg~V~~~-l---------s~~VTHVV~~~~~~~~~~l~~~~~~~~ 81 (464)
.+....+|+||+.|+.. .+. ++.|.-+|++.||.|.-+ + +..|||=|++--..... . .
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---RESLEFIIRSFGGKVSWDPLGIGATYDESDERITHQIVDRPGQQTS-----V---I 388 (570)
T ss_pred hhhHHHHhhcceeeeec-cCc---hHHHHHHHHHcCCceecCccCCCCcccccccceeeeeecccCccce-----e---e
Confidence 44556899999999963 222 467889999999999865 1 24589988864332100 0 0
Q ss_pred CccccccchHHHHHhcCCCCCccccccc
Q 012388 82 KGSVIRYQWLEDSLRLGEKVSEDLYRIK 109 (464)
Q Consensus 82 ~~~iV~~~Wl~ec~k~g~lvdee~y~l~ 109 (464)
+-..|.++||-||+.+|.+++.+.|.+.
T Consensus 389 gR~YvQPQWvfDsvNar~llpt~~Y~~G 416 (570)
T KOG2481|consen 389 GRTYVQPQWVFDSVNARLLLPTEKYFPG 416 (570)
T ss_pred eeeeecchhhhhhccchhhccHhhhCCC
Confidence 2357999999999999999999999886
No 38
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.97 E-value=0.011 Score=56.45 Aligned_cols=54 Identities=20% Similarity=0.354 Sum_probs=40.1
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (464)
..|.++.|||+++|-.| |.+.+..++-..- ..+-.+.|++|||||+|||+++.-
T Consensus 73 ~~Li~V~GIGpK~Al~i---Ls~~~~~el~~aI---~~~D~~~L~kvpGIGkKtAerIil 126 (195)
T PRK14604 73 ELLIGVSGVGPKAALNL---LSSGTPDELQLAI---AGGDVARLARVPGIGKKTAERIVL 126 (195)
T ss_pred HHHhCcCCcCHHHHHHH---HcCCCHHHHHHHH---HhCCHHHHhhCCCCCHHHHHHHHH
Confidence 56899999999999755 5555555554432 333467788999999999999963
No 39
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.92 E-value=0.01 Score=56.64 Aligned_cols=54 Identities=24% Similarity=0.399 Sum_probs=39.4
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (464)
..|.++.|||+++|-.| |.+-..+++-. -...+-.+.|++|||||+|||+++.-
T Consensus 72 ~~LisVsGIGPK~ALaI---Ls~~~~~el~~---aI~~~D~~~L~~vpGIGkKtAeRIIl 125 (196)
T PRK13901 72 EELIGVDGIGPRAALRV---LSGIKYNEFRD---AIDREDIELISKVKGIGNKMAGKIFL 125 (196)
T ss_pred HHHhCcCCcCHHHHHHH---HcCCCHHHHHH---HHHhCCHHHHhhCCCCCHHHHHHHHH
Confidence 56899999999999765 44444444433 23334467788999999999999963
No 40
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.86 E-value=0.011 Score=55.95 Aligned_cols=54 Identities=19% Similarity=0.319 Sum_probs=39.8
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (464)
..|.++.|||+++|=.| |.+-...++-.. ...+-.+.|++|||||+|||+++.-
T Consensus 73 ~~Li~VsGIGpK~Al~I---Ls~~~~~el~~a---I~~~D~~~L~~vpGIGkKtAeRIil 126 (183)
T PRK14601 73 EMLLKVNGIGANTAMAV---CSSLDVNSFYKA---LSLGDESVLKKVPGIGPKSAKRIIA 126 (183)
T ss_pred HHHhccCCccHHHHHHH---HcCCCHHHHHHH---HHhCCHHHHhhCCCCCHHHHHHHHH
Confidence 56889999999999755 555555555433 2333467788999999999999963
No 41
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.81 E-value=0.014 Score=55.81 Aligned_cols=54 Identities=15% Similarity=0.222 Sum_probs=39.7
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (464)
..|.++.|||+++|=.| |.+.+..++-+. ...+=.+.|++|||||+|||+++.-
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 56889999999999754 555555555433 2333467788999999999999863
No 42
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.81 E-value=0.0099 Score=57.04 Aligned_cols=54 Identities=19% Similarity=0.220 Sum_probs=39.7
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (464)
..|.++.|||+++|-.| |.+-..+++-. -...+-.+.|++|||||+|||+++.-
T Consensus 74 ~~Li~V~GIGpK~Al~i---Ls~~~~~~l~~---aI~~~D~~~L~~ipGIGkKtAerIil 127 (203)
T PRK14602 74 IVLISISKVGAKTALAI---LSQFRPDDLRR---LVAEEDVAALTRVSGIGKKTAQHIFL 127 (203)
T ss_pred HHHhCCCCcCHHHHHHH---HhhCCHHHHHH---HHHhCCHHHHhcCCCcCHHHHHHHHH
Confidence 56899999999999765 45444444433 23344567789999999999999963
No 43
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=95.66 E-value=0.014 Score=55.33 Aligned_cols=54 Identities=13% Similarity=0.130 Sum_probs=39.0
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (464)
..|.++.|||+++|=.|- .+-...++- .-...+-.+.|++|||||+|||+++.-
T Consensus 73 ~~Li~V~GIGpK~AL~iL---s~~~~~el~---~aI~~~D~~~L~~vpGIGkKtAerIil 126 (188)
T PRK14606 73 LSLTKVSRLGPKTALKII---SNEDAETLV---TMIASQDVEGLSKLPGISKKTAERIVM 126 (188)
T ss_pred HHHhccCCccHHHHHHHH---cCCCHHHHH---HHHHhCCHHHHhhCCCCCHHHHHHHHH
Confidence 468899999999997654 443444443 333344567789999999999999963
No 44
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=95.49 E-value=0.016 Score=64.04 Aligned_cols=77 Identities=27% Similarity=0.367 Sum_probs=55.9
Q ss_pred CchHHHHHHHHHHhcCCEEEeecCCCccEEEEc-CChH-HHHHHHHHhhhccCccccccchHHHHHhcCCCCCccccccc
Q 012388 32 QNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAM-DLEA-LLQQVSKQHLARFKGSVIRYQWLEDSLRLGEKVSEDLYRIK 109 (464)
Q Consensus 32 g~~R~~~l~~~i~~~Gg~V~~~ls~~VTHVV~~-~~~~-~~~~l~~~~~~~~~~~iV~~~Wl~ec~k~g~lvdee~y~l~ 109 (464)
...-...+..+++. ++...+.+.|||||+. +.+. -.+.++.......+.+|+++.|+.+|++++++|+|+.|-|.
T Consensus 487 ~p~ek~~v~~~a~~---t~~k~~~~~~thvi~~~~~~g~c~rTlk~~~gil~gkwi~~~~w~~~s~k~~~~~~eepfEl~ 563 (684)
T KOG4362|consen 487 TPSEKQLVEKFAVD---TISKFWIEPVTHVIASTDLEGACLRTLKVLMGILRGKWILSYDWVLASLKLRKWVSEEPFELQ 563 (684)
T ss_pred CcchHHHHHHHHHH---HHhhccCCCceeeeeecccccchhhhHHHHHHhhcCceeeeHHHHHHHHHhcCCCCCCCeeEe
Confidence 34456677777776 6666778999999984 3332 23444433222236789999999999999999999999987
Q ss_pred cC
Q 012388 110 LD 111 (464)
Q Consensus 110 ~~ 111 (464)
++
T Consensus 564 ~d 565 (684)
T KOG4362|consen 564 ID 565 (684)
T ss_pred ec
Confidence 64
No 45
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=95.48 E-value=0.013 Score=38.89 Aligned_cols=22 Identities=32% Similarity=0.477 Sum_probs=17.2
Q ss_pred HHHHHhhhccCcCHHHHHHHHH
Q 012388 292 RTISLFGEVWGIGPATAQKLYE 313 (464)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~ 313 (464)
..++.|++|||||++||..+..
T Consensus 8 as~eeL~~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 8 ASIEELMKLPGIGPKTANAILS 29 (30)
T ss_dssp SSHHHHHTSTT-SHHHHHHHHH
T ss_pred CCHHHHHhCCCcCHHHHHHHHh
Confidence 3567778999999999998763
No 46
>PRK14973 DNA topoisomerase I; Provisional
Probab=95.41 E-value=0.019 Score=66.59 Aligned_cols=91 Identities=19% Similarity=0.154 Sum_probs=59.3
Q ss_pred hhhcCCCCCCHHHHHHHHHHHH-h-CCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHHhhcc--Ccc
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVT-T-GKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLT 329 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~-t-G~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~~--~L~ 329 (464)
++|..+|||...++......+. . +.-..-...+.....+.-+ |.+|.|||++|+.+++..|++|.|||.+++ +|+
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 5677888888766655544433 1 1111000001111112223 459999999999999999999999999874 688
Q ss_pred hHHHhhHhhHHhhccC
Q 012388 330 HSQRLGLKYFDDIKTR 345 (464)
Q Consensus 330 ~~q~~Glk~~ed~~~~ 345 (464)
..-+++.+....|+..
T Consensus 914 ~~~~i~~k~~~~~~~~ 929 (936)
T PRK14973 914 KVTGIDEKKLRNLQAY 929 (936)
T ss_pred hhcCCCHHHHHHHHHH
Confidence 8888888887777654
No 47
>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=95.39 E-value=0.027 Score=41.58 Aligned_cols=28 Identities=29% Similarity=0.458 Sum_probs=23.5
Q ss_pred cCCCEEEEEcccccccCC-cCCCccEEEe
Q 012388 365 VLPEVIILCGGSYRRGKA-SCGDLDVVIM 392 (464)
Q Consensus 365 ~~p~~~v~~~GsyRRgke-~~gDvDiLit 392 (464)
..+...+.+.|||.||.. ..+|||+++.
T Consensus 14 ~~~~~~v~lfGS~arg~~~~~SDIDi~v~ 42 (49)
T cd05397 14 LVPGYEIVVYGSLVRGLLKKSSDIDLACV 42 (49)
T ss_pred hcCCcEEEEECCcCCCCCCCCCCEEEEEE
Confidence 455668999999999977 6789999986
No 48
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=95.36 E-value=0.008 Score=67.32 Aligned_cols=52 Identities=21% Similarity=0.287 Sum_probs=43.8
Q ss_pred hhccCcCHHHHHHHHHc-CCCCHHHHhh--ccCcchHHHhhHhhHHhhccCCCHH
Q 012388 298 GEVWGIGPATAQKLYEK-GHRTLDDLKN--EDSLTHSQRLGLKYFDDIKTRIPRH 349 (464)
Q Consensus 298 ~~I~GvGpktA~~ly~~-GirtledL~~--~~~L~~~q~~Glk~~ed~~~~i~r~ 349 (464)
++|+|+||+++++||+. ++++++||.. ..+|..+.+||-|..+.|.+.|-..
T Consensus 448 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~ll~~Ie~s 502 (665)
T PRK07956 448 MDIDGLGEKIIEQLFEKGLIHDPADLFKLTAEDLLGLEGFGEKSAQNLLDAIEKS 502 (665)
T ss_pred cCCCCcCHHHHHHHHHcCCCCCHHHHHhcCHHHHhcCcCcchHHHHHHHHHHHHh
Confidence 37999999999999998 7899999984 2468888899999999987766443
No 49
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=95.35 E-value=0.043 Score=61.50 Aligned_cols=87 Identities=14% Similarity=0.210 Sum_probs=63.3
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHHhhc--------
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE-------- 325 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~-------- 325 (464)
+++.+|+|+|++.+++|.+=++.-+-..| ...|--| +|++||.++|+.|-+..+.|++.|.+.
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 68889999999988887764443222222 3455666 899999999999887789999998752
Q ss_pred cCcchHHHhhHhhHHhhccCCCHH
Q 012388 326 DSLTHSQRLGLKYFDDIKTRIPRH 349 (464)
Q Consensus 326 ~~L~~~q~~Glk~~ed~~~~i~r~ 349 (464)
..|..+.+||-+..+.|.+-+.-.
T Consensus 541 e~l~~i~giG~~~a~si~~ff~~~ 564 (669)
T PRK14350 541 SKLLKIKGIGEKIALNIIEAFNDK 564 (669)
T ss_pred HHHhhCCCccHHHHHHHHHHHcCH
Confidence 147778888988777776655433
No 50
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=95.32 E-value=0.051 Score=60.10 Aligned_cols=83 Identities=19% Similarity=0.274 Sum_probs=44.4
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHHhhcc--CcchH
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHS 331 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~~--~L~~~ 331 (464)
+++..|+++|++.+++|-.-++.-+-..|+ ..+--| +|+.||.++|+.|-+ .+.|++.|..+. .|..+
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 EDLLSLEGFGEKSAENLLNAIEKSKKQPLA--------RFLYAL-GIRHVGETTAKSLAR-HFGTLEALLAASEEELASI 548 (667)
T ss_pred HHHhhccchhhhHHHHHHHHHHHhccCCHH--------HHHHHc-CCchhhHHHHHHHHH-HhhhHHHHHhcCHHHHhhc
Confidence 456666666666666554433332222222 223333 666666666666666 666666666543 35556
Q ss_pred HHhhHhhHHhhccCC
Q 012388 332 QRLGLKYFDDIKTRI 346 (464)
Q Consensus 332 q~~Glk~~ed~~~~i 346 (464)
.++|-.-.+.+..-.
T Consensus 549 ~giG~~vA~si~~ff 563 (667)
T COG0272 549 PGIGEVVARSIIEFF 563 (667)
T ss_pred cchhHHHHHHHHHHH
Confidence 666655554444433
No 51
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=95.30 E-value=0.016 Score=52.91 Aligned_cols=52 Identities=27% Similarity=0.507 Sum_probs=41.0
Q ss_pred hhHHHHHhhhccCcCHHHHHHHHH---c-C-CCCHHHHhhccCcchHHHhhHhhHHhhccCCC
Q 012388 290 KVRTISLFGEVWGIGPATAQKLYE---K-G-HRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIP 347 (464)
Q Consensus 290 ~~~~l~lf~~I~GvGpktA~~ly~---~-G-irtledL~~~~~L~~~q~~Glk~~ed~~~~i~ 347 (464)
.....+.|..+||||+++|+++.+ + | |+|+|||.+ .+++|-+.+|.+..+|.
T Consensus 92 NtAs~eeL~~lpgIG~~kA~aIi~yRe~~G~f~sv~dL~~------v~GiG~~~~ekl~~~i~ 148 (149)
T COG1555 92 NTASAEELQALPGIGPKKAQAIIDYREENGPFKSVDDLAK------VKGIGPKTLEKLKDYIT 148 (149)
T ss_pred cccCHHHHHHCCCCCHHHHHHHHHHHHHcCCCCcHHHHHh------ccCCCHHHHHHHHhhcc
Confidence 334455568999999999999985 2 4 899999986 46899999988877653
No 52
>PRK02362 ski2-like helicase; Provisional
Probab=95.22 E-value=0.021 Score=64.87 Aligned_cols=58 Identities=24% Similarity=0.394 Sum_probs=45.5
Q ss_pred HHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHHhhc--cCcchHHHhhHhhHHhhcc
Q 012388 284 HFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDIKT 344 (464)
Q Consensus 284 ~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~--~~L~~~q~~Glk~~ed~~~ 344 (464)
.+....+...+.|+ +|||||+++|+++|+.||+|++||... .+|..+ ||-+..+.|.+
T Consensus 642 ~l~~gv~~~~~~L~-~ip~i~~~~a~~l~~~gi~s~~dl~~~~~~~l~~~--~g~~~~~~i~~ 701 (737)
T PRK02362 642 RVEYGVREELLDLV-GLRGVGRVRARRLYNAGIESRADLRAADKSVVLAI--LGEKIAENILE 701 (737)
T ss_pred HHHhCCCHHHHHHh-CCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHHH--HCHHHHHHHHH
Confidence 45556677788887 999999999999999999999999953 345555 78777665543
No 53
>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=95.18 E-value=0.075 Score=45.54 Aligned_cols=58 Identities=26% Similarity=0.438 Sum_probs=46.1
Q ss_pred HHHHHHHHhhhcCCCEEEEEcccccccC-CcCCCccEEEeCCCc-chhhhHHHHHHHHHHhccc
Q 012388 354 MERLLQKAGEEVLPEVIILCGGSYRRGK-ASCGDLDVVIMHPDR-KSHKGFLSKYVKKLKEMKF 415 (464)
Q Consensus 354 i~~iv~~~~~~~~p~~~v~~~GsyRRgk-e~~gDvDiLit~~d~-~~~~~~l~~lv~~L~~~g~ 415 (464)
++.+++. ..|++.+.+-|||+.|. ...+|||+.|..++. .....+|.++-+.|++.+.
T Consensus 9 l~~~i~~----~~~~~~v~~fGS~~~g~~~~~SDiDl~i~~~~~~~~~~~~l~~l~~~l~~~~~ 68 (114)
T cd05402 9 LQELIKE----WFPGAKLYPFGSYVTGLGLPGSDIDLCLLGPNHRVDREDFLRKLAKLLKKSGE 68 (114)
T ss_pred HHHHHHH----HCCCCEEEEecccccCCCCCCCCeeEEEEeCCCCccHHHHHHHHHHHHHhCCC
Confidence 4444444 57899999999999984 346799999999876 5567889999999988875
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=95.18 E-value=0.011 Score=39.74 Aligned_cols=20 Identities=45% Similarity=0.790 Sum_probs=16.3
Q ss_pred hhhccCcCHHHHHHHHHcCC
Q 012388 297 FGEVWGIGPATAQKLYEKGH 316 (464)
Q Consensus 297 f~~I~GvGpktA~~ly~~Gi 316 (464)
+.++||||++|+++|.+.||
T Consensus 13 i~~~~GIG~kt~~kL~~~GI 32 (32)
T PF11798_consen 13 IRKFWGIGKKTAKKLNKLGI 32 (32)
T ss_dssp GGGSTTS-HHHHHHHHCTT-
T ss_pred HHhhCCccHHHHHHHHHccC
Confidence 46999999999999988886
No 55
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=95.00 E-value=0.044 Score=48.69 Aligned_cols=33 Identities=21% Similarity=0.341 Sum_probs=28.9
Q ss_pred HHHHhhhccCcCHHHHHHHHHc-CCCCHHHHhhc
Q 012388 293 TISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNE 325 (464)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~-GirtledL~~~ 325 (464)
..+.|+++|||||++|+++.+- .++|+|||.+-
T Consensus 59 ~~~el~~lpGigP~~A~~IV~nGpf~sveDL~~V 92 (132)
T PRK02515 59 SVRAFRQFPGMYPTLAGKIVKNAPYDSVEDVLNL 92 (132)
T ss_pred CHHHHHHCCCCCHHHHHHHHHCCCCCCHHHHHcC
Confidence 4566789999999999999987 69999999864
No 56
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.99 E-value=0.031 Score=52.96 Aligned_cols=53 Identities=13% Similarity=0.145 Sum_probs=38.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (464)
..|.++.|||+++|=.| |.+-+..++-..-.. +=.+.| +|||||+|||+++.-
T Consensus 73 ~~LisV~GIGpK~Al~i---Ls~~~~~~l~~aI~~---~D~~~L-~vpGIGkKtAerIil 125 (186)
T PRK14600 73 RMLVKVSGVNYKTAMSI---LSKLTPEQLFSAIVN---EDKAAL-KVNGIGEKLINRIIT 125 (186)
T ss_pred HHHhCcCCcCHHHHHHH---HccCCHHHHHHHHHc---CCHhhe-ECCCCcHHHHHHHHH
Confidence 56899999999999755 555555555443222 234667 899999999999863
No 57
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=94.94 E-value=0.027 Score=49.52 Aligned_cols=50 Identities=26% Similarity=0.460 Sum_probs=39.0
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHc-----CCCCHHHHhhccCcchHHHhhHhhHHhhccCC
Q 012388 291 VRTISLFGEVWGIGPATAQKLYEK-----GHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRI 346 (464)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~-----GirtledL~~~~~L~~~q~~Glk~~ed~~~~i 346 (464)
.-..+.|+++||||+++|+++++. ++.|++||.+ ..++|.+.++.|...+
T Consensus 64 tA~~~eL~~lpGIG~~~A~~Ii~~R~~~g~f~s~eeL~~------V~GIg~k~~~~i~~~l 118 (120)
T TIGR01259 64 AASLEELQALPGIGPAKAKAIIEYREENGAFKSVDDLTK------VSGIGEKSLEKLKDYA 118 (120)
T ss_pred cCCHHHHhcCCCCCHHHHHHHHHHHHhcCCcCCHHHHHc------CCCCCHHHHHHHHhce
Confidence 345666779999999999999864 6899999964 4567888888776543
No 58
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=94.89 E-value=0.013 Score=65.54 Aligned_cols=62 Identities=24% Similarity=0.392 Sum_probs=47.5
Q ss_pred hhccCcCHHHHHHHHHc-CCCCHHHHhh--ccCcchHHHhhHhhHHhhccCCCHHHHHHHHHHHH
Q 012388 298 GEVWGIGPATAQKLYEK-GHRTLDDLKN--EDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQ 359 (464)
Q Consensus 298 ~~I~GvGpktA~~ly~~-GirtledL~~--~~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~iv~ 359 (464)
++|+|+|++++++||++ ++++++||.. ..+|..+.+||-+..+.|.+.|-...-..+..++.
T Consensus 435 l~I~GLG~k~i~~L~~~g~I~~~~Dl~~L~~~~L~~L~GfG~Ksa~nIl~~Ie~sk~~~l~r~L~ 499 (652)
T TIGR00575 435 MDIEGLGDKVIEQLFEKKLVRSVADLYALKKEDLLELEGFGEKSAQNLLNAIEKSKEKPLARLLF 499 (652)
T ss_pred cCCCCcCHHHHHHHHHcCCcCCHHHHHhcCHHHHhhccCccHHHHHHHHHHHHHhccCcHHHHHh
Confidence 37999999999999998 7899999984 34688888999999999877664433333333333
No 59
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=94.81 E-value=0.033 Score=53.30 Aligned_cols=54 Identities=19% Similarity=0.265 Sum_probs=41.0
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (464)
..|.++.|||+++|=.| |.+....++-..- ..+-...|+++||||.|||+++.-
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 57899999999999754 5665666554433 333467789999999999999964
No 60
>KOG2043 consensus Signaling protein SWIFT and related BRCT domain proteins [Transcription; Signal transduction mechanisms; Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]
Probab=94.56 E-value=0.034 Score=63.92 Aligned_cols=68 Identities=24% Similarity=0.355 Sum_probs=52.5
Q ss_pred HHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccchHHHHHhcCCCCCccccccc
Q 012388 38 IWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSLRLGEKVSEDLYRIK 109 (464)
Q Consensus 38 ~l~~~i~~~Gg~V~~~ls~~VTHVV~~~~~~~~~~l~~~~~~~~~~~iV~~~Wl~ec~k~g~lvdee~y~l~ 109 (464)
-+++.+++.|+.++... ...||+|+..--+-...+. .-..+..||+.+||.+|.++|..+|++.|.+.
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 47899999999988776 4589999984333222222 11236799999999999999999999999985
No 61
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]
Probab=94.47 E-value=0.12 Score=57.94 Aligned_cols=90 Identities=20% Similarity=0.274 Sum_probs=58.3
Q ss_pred CCCCCeEEEEecCCCCchHHHHHHHHHHhcCCEEEeec------CCCccEEEEc--CChHHHHHHH-HHhhhccCccccc
Q 012388 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKL------SKKVTHVLAM--DLEALLQQVS-KQHLARFKGSVIR 87 (464)
Q Consensus 17 ~~F~g~~vy~~~~~~g~~R~~~l~~~i~~~Gg~V~~~l------s~~VTHVV~~--~~~~~~~~l~-~~~~~~~~~~iV~ 87 (464)
..|..|++|.+.++.=.+-..+..-.+...|+++.+.- ...+||+|+. +.+-...++. ...+-- .-+||.
T Consensus 783 ~~~~~~~~f~~~~~~~~se~~~~~l~~k~~g~~i~~~~~~~~~~~~~~t~~v~~~i~~~h~~~~~~~~~~lt~-~rkv~~ 861 (881)
T KOG0966|consen 783 LFLSSLRMFYVLRRKLSSEEVIIELKLKNFGGRITDAQSECNNIGAKYTHCVLRCIDEDHEKIKEQKKASLTI-KRKVVA 861 (881)
T ss_pred cccccceeeecccccccHHHHHHHHHHHHhcceeeeccchhhhcccceeeeeeeecchHHHHHHHHHHHHhcc-cccccC
Confidence 55677777777665544444444555555599998763 3568999985 3222111211 111111 229999
Q ss_pred cchHHHHHhcCCCCCccccc
Q 012388 88 YQWLEDSLRLGEKVSEDLYR 107 (464)
Q Consensus 88 ~~Wl~ec~k~g~lvdee~y~ 107 (464)
.+||.+|+.++.+++|+.|.
T Consensus 862 ~~wv~~s~~~~~~~~e~~~~ 881 (881)
T KOG0966|consen 862 PSWVDHSINENCLLPEEDFP 881 (881)
T ss_pred HHHHHHhhcccccCccccCC
Confidence 99999999999999999884
No 62
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=94.41 E-value=0.045 Score=42.72 Aligned_cols=49 Identities=29% Similarity=0.513 Sum_probs=33.7
Q ss_pred HHHHHhhhccCcCHHHHHHHHH---c--CCCCHHHHhhccCcchHHHhhHhhHHhhccCC
Q 012388 292 RTISLFGEVWGIGPATAQKLYE---K--GHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRI 346 (464)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~---~--GirtledL~~~~~L~~~q~~Glk~~ed~~~~i 346 (464)
...+.|.++||||++.|+++.+ + +++|++||.+ ..++|.+.|+.+...|
T Consensus 11 as~~eL~~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL~~------v~gi~~~~~~~l~~~l 64 (65)
T PF12836_consen 11 ASAEELQALPGIGPKQAKAIVEYREKNGPFKSLEDLKE------VPGIGPKTYEKLKPYL 64 (65)
T ss_dssp S-HHHHHTSTT--HHHHHHHHHHHHHH-S-SSGGGGGG------STT--HHHHHHHCCCE
T ss_pred CCHHHHHHcCCCCHHHHHHHHHHHHhCcCCCCHHHHhh------CCCCCHHHHHHHHhhc
Confidence 3556677999999999999985 2 8899999986 4567888888776543
No 63
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=94.29 E-value=0.027 Score=53.52 Aligned_cols=51 Identities=24% Similarity=0.275 Sum_probs=38.6
Q ss_pred HHHHhhhccCcCHHHHHHHHHc-CCCCHHHHhhcc---CcchHHHhhHhhHHhhc
Q 012388 293 TISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED---SLTHSQRLGLKYFDDIK 343 (464)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~-GirtledL~~~~---~L~~~q~~Glk~~ed~~ 343 (464)
.+..|.+|+|||||+|.++.+. |..++.+..... .|+...++|.+..+.|.
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 3666779999999999999986 887776544332 57888888888766554
No 64
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=94.23 E-value=0.061 Score=42.30 Aligned_cols=45 Identities=20% Similarity=0.296 Sum_probs=34.7
Q ss_pred Hhhh-ccCcCHHHHHHHHHc-----CCCCHHHHhhccCcchHHHhhHhhHHhhccCC
Q 012388 296 LFGE-VWGIGPATAQKLYEK-----GHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRI 346 (464)
Q Consensus 296 lf~~-I~GvGpktA~~ly~~-----GirtledL~~~~~L~~~q~~Glk~~ed~~~~i 346 (464)
.|.. ++|||+++|+++.+. ++++++||.+ ..++|.+.++.|...|
T Consensus 17 ~L~~~ipgig~~~a~~Il~~R~~~g~~~s~~dL~~------v~gi~~~~~~~i~~~~ 67 (69)
T TIGR00426 17 ELQRAMNGVGLKKAEAIVSYREEYGPFKTVEDLKQ------VPGIGNSLVEKNLAVI 67 (69)
T ss_pred HHHhHCCCCCHHHHHHHHHHHHHcCCcCCHHHHHc------CCCCCHHHHHHHHhhc
Confidence 4556 999999999999975 5999999975 3567777777766543
No 65
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.13 E-value=0.027 Score=53.68 Aligned_cols=52 Identities=19% Similarity=0.281 Sum_probs=40.1
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHc-CCCCHHH-Hhhc--cCcchHHHhhHhhHHhh
Q 012388 291 VRTISLFGEVWGIGPATAQKLYEK-GHRTLDD-LKNE--DSLTHSQRLGLKYFDDI 342 (464)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~-Girtled-L~~~--~~L~~~q~~Glk~~ed~ 342 (464)
...+++|.+|.|||||+|..+... +...|-+ +.+. ..|++.+++|-|..+.|
T Consensus 69 r~lF~~Li~V~GIGpK~Al~ILs~~~~~~l~~aI~~~D~~~L~~vpGIGkKtAerI 124 (194)
T PRK14605 69 LSLFETLIDVSGIGPKLGLAMLSAMNAEALASAIISGNAELLSTIPGIGKKTASRI 124 (194)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHH
Confidence 457888889999999999999986 7666333 3232 35899999999997764
No 66
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=94.13 E-value=0.038 Score=43.09 Aligned_cols=44 Identities=27% Similarity=0.341 Sum_probs=30.1
Q ss_pred hccCcCHHHHHHHHHcCCCCHHHHhhcc--CcchHHHhhHhhHHhhc
Q 012388 299 EVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIK 343 (464)
Q Consensus 299 ~I~GvGpktA~~ly~~GirtledL~~~~--~L~~~q~~Glk~~ed~~ 343 (464)
+|+|||+++|+.|.+ .+.|++.|.++. .|+...++|.+..+.+.
T Consensus 7 GI~~VG~~~ak~L~~-~f~sl~~l~~a~~e~L~~i~gIG~~~A~si~ 52 (64)
T PF12826_consen 7 GIPGVGEKTAKLLAK-HFGSLEALMNASVEELSAIPGIGPKIAQSIY 52 (64)
T ss_dssp TSTT--HHHHHHHHH-CCSCHHHHCC--HHHHCTSTT--HHHHHHHH
T ss_pred CCCCccHHHHHHHHH-HcCCHHHHHHcCHHHHhccCCcCHHHHHHHH
Confidence 999999999999975 555999999763 57777778876655554
No 67
>KOG1929 consensus Nucleotide excision repair factor NEF2, RAD4/CUT5 component [Replication, recombination and repair]
Probab=94.10 E-value=0.086 Score=59.88 Aligned_cols=89 Identities=18% Similarity=0.230 Sum_probs=70.5
Q ss_pred CCCCCeEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccchHHHHHh
Q 012388 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSLR 96 (464)
Q Consensus 17 ~~F~g~~vy~~~~~~g~~R~~~l~~~i~~~Gg~V~~~ls~~VTHVV~~~~~~~~~~l~~~~~~~~~~~iV~~~Wl~ec~k 96 (464)
..|.+|.|.. +|+...++.-+++++.+|||+....++..|+||+.-..... -+.+++..+..++|+.+|+.+|+.
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 3566776665 46777777889999999999999999999999997654431 233344445779999999999999
Q ss_pred cCCCCCcccccccc
Q 012388 97 LGEKVSEDLYRIKL 110 (464)
Q Consensus 97 ~g~lvdee~y~l~~ 110 (464)
.+..+++..|.+..
T Consensus 177 ~~~~~~~~~~e~~~ 190 (811)
T KOG1929|consen 177 KTAVLETKPYEGAP 190 (811)
T ss_pred cccccccccccccc
Confidence 99999999998864
No 68
>PRK00254 ski2-like helicase; Provisional
Probab=93.97 E-value=0.078 Score=60.11 Aligned_cols=67 Identities=25% Similarity=0.400 Sum_probs=48.4
Q ss_pred hCCchhhHH----HHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHHhhc--cCcchHHHhhHhhHHhhc
Q 012388 276 TGKLSKLEH----FEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDIK 343 (464)
Q Consensus 276 tG~~~~le~----l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~--~~L~~~q~~Glk~~ed~~ 343 (464)
.|.+..+.+ +....+...+.|. +|+|||+++|+++|+.|+.|++||.++ ..|....++|.+..+.+.
T Consensus 623 ~~~~~~l~~l~~rl~~g~~~~~~~L~-~ipgig~~~~~~l~~~g~~s~~~i~~a~~~el~~~~gi~~~~a~~i~ 695 (720)
T PRK00254 623 QEVLDYLETLHLRVKHGVREELLELM-RLPMIGRKRARALYNAGFRSIEDIVNAKPSELLKVEGIGAKIVEGIF 695 (720)
T ss_pred hhHHHHHHHHHHHHHcCCCHHHhhhh-cCCCCCHHHHHHHHHccCCCHHHHHhCCHHHHhcCCCCCHHHHHHHH
Confidence 344444443 3345555566666 999999999999999999999999875 357667677776655544
No 69
>KOG1929 consensus Nucleotide excision repair factor NEF2, RAD4/CUT5 component [Replication, recombination and repair]
Probab=93.89 E-value=0.062 Score=60.98 Aligned_cols=94 Identities=12% Similarity=0.193 Sum_probs=73.3
Q ss_pred CCCCCCCCCCCCeEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccc
Q 012388 10 TPALDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQ 89 (464)
Q Consensus 10 ~~~~~~~~~F~g~~vy~~~~~~g~~R~~~l~~~i~~~Gg~V~~~ls~~VTHVV~~~~~~~~~~l~~~~~~~~~~~iV~~~ 89 (464)
.|.+.+...|.+|++++... .-.+++.+.+.++..|+.+...+....||||....... .......+...+|+++
T Consensus 485 vp~~~l~~~~e~~~~~~s~~--~~~~~e~ln~~~~~~gas~~~~f~r~~~~l~~~~~k~s----~~~~~~kw~ip~vT~~ 558 (811)
T KOG1929|consen 485 VPAAALSQPFENLTISNSQS--AEAEREKLNNLANDLGASNVKTFTRKSTTLLTTSAKGS----KYEIAGKWSIPIVTPD 558 (811)
T ss_pred chhhcccccccCceEEeeec--hHHHHHHHhHhhhhccccccceeeecccEEeccccccc----hhhhccccCCCccChh
Confidence 34566677899999999742 34578999999999999999998766699998652221 1122333478999999
Q ss_pred hHHHHHhcCCCCCccccccc
Q 012388 90 WLEDSLRLGEKVSEDLYRIK 109 (464)
Q Consensus 90 Wl~ec~k~g~lvdee~y~l~ 109 (464)
||.+|.++++-++.+.|...
T Consensus 559 wL~e~~rq~~~~~~e~~l~~ 578 (811)
T KOG1929|consen 559 WLYECVRQNKGERNEGFLNG 578 (811)
T ss_pred HHHhhccccCcccceeeccc
Confidence 99999999999999999875
No 70
>COG5163 NOP7 Protein required for biogenesis of the 60S ribosomal subunit [Translation, ribosomal structure and biogenesis]
Probab=93.37 E-value=0.076 Score=55.05 Aligned_cols=87 Identities=20% Similarity=0.331 Sum_probs=62.8
Q ss_pred CCCCCCCCCCCeEEEEecCCCCchHHHHHHHHHHhcCCEEEeec-----------CCCccEEEEcCChHHHHHHHHHhhh
Q 012388 11 PALDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKL-----------SKKVTHVLAMDLEALLQQVSKQHLA 79 (464)
Q Consensus 11 ~~~~~~~~F~g~~vy~~~~~~g~~R~~~l~~~i~~~Gg~V~~~l-----------s~~VTHVV~~~~~~~~~~l~~~~~~ 79 (464)
+.++-..+|.++++|+...-.+ +.|+-+|+..||.|..+. +..|||-|++..- +.. ..
T Consensus 343 ~~Ss~~slFS~f~FyisreVp~----dsLefiilscGG~V~~~p~~~~i~~~~~vD~~vth~i~drp~--~~~----kv- 411 (591)
T COG5163 343 PCSSLKSLFSGFKFYISREVPG----DSLEFIILSCGGSVVGSPCEADIHVSEKVDEKVTHQIVDRPV--MKN----KV- 411 (591)
T ss_pred cCcchhhhhhceEEEEeccccc----hHHHHHHHHcCCcccCchhhccCCchhhccchhhhhhccchh--hhh----hh-
Confidence 3455678999999999743333 468889999999998653 3447777765321 110 11
Q ss_pred ccCccccccchHHHHHhcCCCCCccccccc
Q 012388 80 RFKGSVIRYQWLEDSLRLGEKVSEDLYRIK 109 (464)
Q Consensus 80 ~~~~~iV~~~Wl~ec~k~g~lvdee~y~l~ 109 (464)
-+.-.+.++||-+|+..|.++..+.|.+.
T Consensus 412 -egrtYiQPQw~fDsiNkG~l~~~~~Y~~G 440 (591)
T COG5163 412 -EGRTYIQPQWLFDSINKGKLACVENYCVG 440 (591)
T ss_pred -cceeeechHHHHhhhccccchhhhhcccc
Confidence 13356899999999999999999999885
No 71
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=92.65 E-value=0.21 Score=48.67 Aligned_cols=54 Identities=24% Similarity=0.435 Sum_probs=40.7
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc
Q 012388 253 ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (464)
Q Consensus 253 ~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 314 (464)
+++|..|||||+..+.++ ++.| +.-++.+... ..+.|.+|+|||.++|.++++.
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 356889999999887765 5666 5666666543 2444569999999999999986
No 72
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.27 E-value=0.08 Score=50.24 Aligned_cols=50 Identities=20% Similarity=0.261 Sum_probs=38.4
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHcCCCCHHHHhh---c---cCcchHHHhhHhhHHhh
Q 012388 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDI 342 (464)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~---~---~~L~~~q~~Glk~~ed~ 342 (464)
...+++|.+|.|||||+|-.+... -+.++|.. . ..|++.+++|-|..+.|
T Consensus 69 r~lF~~Li~V~GIGpK~AL~iLs~--~~~~el~~aI~~~D~~~L~~vpGIGkKtAerI 124 (188)
T PRK14606 69 KELFLSLTKVSRLGPKTALKIISN--EDAETLVTMIASQDVEGLSKLPGISKKTAERI 124 (188)
T ss_pred HHHHHHHhccCCccHHHHHHHHcC--CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHH
Confidence 357888899999999999998754 35555553 2 25899999999987654
No 73
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.05 E-value=0.09 Score=49.70 Aligned_cols=50 Identities=20% Similarity=0.274 Sum_probs=38.6
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHcCCCCHHHHhhc------cCcchHHHhhHhhHHhh
Q 012388 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE------DSLTHSQRLGLKYFDDI 342 (464)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~------~~L~~~q~~Glk~~ed~ 342 (464)
...+++|.+|.|||||+|-.+... -+.++|..+ ..|++.+++|-|..+.|
T Consensus 69 r~lF~~Li~VsGIGpK~Al~ILs~--~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRI 124 (183)
T PRK14601 69 QKMFEMLLKVNGIGANTAMAVCSS--LDVNSFYKALSLGDESVLKKVPGIGPKSAKRI 124 (183)
T ss_pred HHHHHHHhccCCccHHHHHHHHcC--CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHH
Confidence 457888889999999999988753 356666532 35889999999986654
No 74
>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=91.87 E-value=0.68 Score=52.66 Aligned_cols=83 Identities=20% Similarity=0.350 Sum_probs=63.4
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc-CCCCHHHHhhcc-Ccc-
Q 012388 253 ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED-SLT- 329 (464)
Q Consensus 253 ~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~-GirtledL~~~~-~L~- 329 (464)
.+.|.++||||++.++.|.+-++. .. .-..++..| .=+|++++.|.++|+. |-.+++.|+++. .|.
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 467889999999999998876532 11 123456555 8899999999999998 999999999764 455
Q ss_pred hHHHhhHhhHHhhccCC
Q 012388 330 HSQRLGLKYFDDIKTRI 346 (464)
Q Consensus 330 ~~q~~Glk~~ed~~~~i 346 (464)
...++|++..|.|..++
T Consensus 185 ~i~gigF~~aD~iA~~~ 201 (720)
T TIGR01448 185 DVKGIGFLTADQLAQAL 201 (720)
T ss_pred hcCCCCHHHHHHHHHHc
Confidence 47788888888876443
No 75
>PF04994 TfoX_C: TfoX C-terminal domain; InterPro: IPR007077 This domain is found in a number of bacterial proteins including the TfoX gene product of Haemophilus influenzae. TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes []. This family corresponds to the C-terminal presumed domain of TfoX. The domain is found in association with the N-terminal domain in some, but not all members of this group, suggesting this is an autonomous and functionally unrelated domain. For example it is found associated with Q9JZR1 from SWISSPROT in IPR002125 from INTERPRO.; PDB: 3BQT_A 3MAB_A.
Probab=91.72 E-value=0.13 Score=42.13 Aligned_cols=30 Identities=27% Similarity=0.480 Sum_probs=23.3
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHHhhcc
Q 012388 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (464)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~~ 326 (464)
+..+|++|++..+.|++-||.|++||+.-+
T Consensus 5 l~~LpNig~~~e~~L~~vGI~t~~~L~~~G 34 (81)
T PF04994_consen 5 LKDLPNIGPKSERMLAKVGIHTVEDLRELG 34 (81)
T ss_dssp GCGSTT--HHHHHHHHHTT--SHHHHHHHH
T ss_pred hhhCCCCCHHHHHHHHHcCCCCHHHHHHhC
Confidence 457899999999999999999999999755
No 76
>PRK03858 DNA polymerase IV; Validated
Probab=91.72 E-value=0.23 Score=52.00 Aligned_cols=108 Identities=15% Similarity=0.216 Sum_probs=60.2
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHHhhccCcchHHHhhHhhHHhhccCCCHHHHHHHHHHHHHHhhhcCCCEEEEEccc
Q 012388 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGS 376 (464)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~iv~~~~~~~~p~~~v~~~Gs 376 (464)
+..+||||++++++|.+.||+|+.||.+-..-.-..+||....+.+ ...+.-+++. .+ -.
T Consensus 175 l~~l~Gig~~~~~~L~~~Gi~t~~dl~~l~~~~L~~~fG~~~~~~l----------------~~~a~G~d~~-~v---~~ 234 (396)
T PRK03858 175 VRRLWGVGPVTAAKLRAHGITTVGDVAELPESALVSLLGPAAGRHL----------------HALAHNRDPR-RV---ET 234 (396)
T ss_pred hhhcCCCCHHHHHHHHHhCCCcHHHHhcCCHHHHHHHhCcHHHHHH----------------HHHhCCCCCC-CC---CC
Confidence 3578999999999999999999999986432222334554221111 1111111111 11 11
Q ss_pred ccccCCcCCCccEEEeCCCcc----hhhhHHHHHHHHHHhcccccccccccc
Q 012388 377 YRRGKASCGDLDVVIMHPDRK----SHKGFLSKYVKKLKEMKFLREDLIFST 424 (464)
Q Consensus 377 yRRgke~~gDvDiLit~~d~~----~~~~~l~~lv~~L~~~g~l~~~L~~~~ 424 (464)
++.-|..+....|----.+.. ....++.+|..+|.+.|.....+++.-
T Consensus 235 ~~~~ksi~~~~t~~~~~~~~~~l~~~l~~L~~~l~~rLr~~~~~~~~l~l~l 286 (396)
T PRK03858 235 GRRRRSVGAQRALGRGPNSPAEVDAVVVALVDRVARRMRAAGRTGRTVVLRL 286 (396)
T ss_pred CCCCccccceeEcCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCcceEEEEE
Confidence 333344444433321001111 134678888999999999988876644
No 77
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=91.65 E-value=0.1 Score=49.84 Aligned_cols=50 Identities=26% Similarity=0.284 Sum_probs=38.8
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHcCCCCHHHHhhc------cCcchHHHhhHhhHHhh
Q 012388 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE------DSLTHSQRLGLKYFDDI 342 (464)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~------~~L~~~q~~Glk~~ed~ 342 (464)
...+++|.+|.|||||+|-.+... -|.++|... ..|++.+++|-|..+.|
T Consensus 68 r~lF~~L~~V~GIGpK~AL~iLs~--~~~~~l~~aI~~~D~~~L~kvpGIGkKtAerI 123 (197)
T PRK14603 68 LELFELLLGVSGVGPKLALALLSA--LPPALLARALLEGDARLLTSASGVGKKLAERI 123 (197)
T ss_pred HHHHHHHhCcCCcCHHHHHHHHcC--CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHH
Confidence 357888889999999999998764 356666532 35899999999996654
No 78
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=91.60 E-value=0.11 Score=49.90 Aligned_cols=50 Identities=26% Similarity=0.324 Sum_probs=38.5
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHcCCCCHHHHhh---c---cCcchHHHhhHhhHHhh
Q 012388 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKN---E---DSLTHSQRLGLKYFDDI 342 (464)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~---~---~~L~~~q~~Glk~~ed~ 342 (464)
...+.+|.+|.|||||+|-.+... -+.++|.. . ..|++.+++|-|..+.|
T Consensus 70 r~lF~~Li~V~GIGpK~Al~iLs~--~~~~~l~~aI~~~D~~~L~~ipGIGkKtAerI 125 (203)
T PRK14602 70 RQTFIVLISISKVGAKTALAILSQ--FRPDDLRRLVAEEDVAALTRVSGIGKKTAQHI 125 (203)
T ss_pred HHHHHHHhCCCCcCHHHHHHHHhh--CCHHHHHHHHHhCCHHHHhcCCCcCHHHHHHH
Confidence 357888889999999999999874 25555553 2 35899999999986654
No 79
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=91.59 E-value=0.12 Score=52.60 Aligned_cols=30 Identities=37% Similarity=0.597 Sum_probs=27.2
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHHhhcc
Q 012388 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (464)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~~ 326 (464)
+..+||||+++|++|.+.||.|++||....
T Consensus 8 l~~l~gIg~~~a~~L~~~Gi~t~~dl~~~~ 37 (317)
T PRK04301 8 LEDLPGVGPATAEKLREAGYDTVEAIAVAS 37 (317)
T ss_pred HhhcCCCCHHHHHHHHHcCCCCHHHHHcCC
Confidence 568999999999999999999999998643
No 80
>PF01909 NTP_transf_2: Nucleotidyltransferase domain A subset of this Pfam family; InterPro: IPR002934 A small region that overlaps with a nuclear localization signal and binds to the RNA primer contains three aspartates that are essential for catalysis. Sequence and secondary structure comparisons of regions surrounding these aspartates with sequences of other polymerases revealed a significant homology to the palm structure of DNA polymerase beta, terminal deoxynucleotidyltransferase and DNA polymerase IV of Saccharomyces cerevisiae, all members of the family X of polymerases. This homology extends as far as cca: tRNA nucleotidyltransferase and streptomycin adenylyltransferase, an antibiotic resistance factor [, ]. Proteins containing this domain include kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTase inactivates antibiotics by catalysing the addition of a nucleotidyl group onto the drug. In experiments, Mn2+ strongly stimulated this reaction due to a 50-fold lower Ki for 8-azido-ATP in the presence of Mn2+. Mutations of the highly conserved Asp residues 113, 115, and 167, critical for metal binding in the catalytic domain of bovine poly(A) polymerase, led to a strong reduction of cross-linking efficiency, and Mn2+ no longer stimulated the reaction. Mutations in the region of the "helical turn motif" (a domain binding the triphosphate moiety of the nucleotide) and in the suspected nucleotide-binding helix of bovine poly(A) polymerase impaired ATP binding and catalysis. The results indicate that ATP is bound in part by the helical turn motif and in part by a region that may be a structural analogue of the fingers domain found in many polymerases.; GO: 0016779 nucleotidyltransferase activity; PDB: 4EBK_B 4EBJ_A 1KNY_A 2B4V_A 2B56_A 2B51_A 1NO5_B 1Q79_A 1Q78_A 1F5A_A ....
Probab=91.51 E-value=0.3 Score=39.78 Aligned_cols=32 Identities=28% Similarity=0.458 Sum_probs=26.5
Q ss_pred CCCEEEEEcccccccCCc-CCCccEEEeCCCcc
Q 012388 366 LPEVIILCGGSYRRGKAS-CGDLDVVIMHPDRK 397 (464)
Q Consensus 366 ~p~~~v~~~GsyRRgke~-~gDvDiLit~~d~~ 397 (464)
.+...+.+.|||.||..+ ..|||++|..++..
T Consensus 12 ~~~~~v~lfGS~a~g~~~~~SDIDl~i~~~~~~ 44 (93)
T PF01909_consen 12 FGVAEVYLFGSYARGDATPDSDIDLLIILDEPE 44 (93)
T ss_dssp HTTEEEEEEHHHHHTSSCTTSCEEEEEEESSTS
T ss_pred CCCCEEEEECCcccCcCCCCCCEEEEEEeCCcc
Confidence 446789999999999965 69999999877664
No 81
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=91.48 E-value=0.13 Score=32.71 Aligned_cols=18 Identities=50% Similarity=0.648 Sum_probs=15.9
Q ss_pred HhhhccCcCHHHHHHHHH
Q 012388 296 LFGEVWGIGPATAQKLYE 313 (464)
Q Consensus 296 lf~~I~GvGpktA~~ly~ 313 (464)
.|++|+|||+++|+++.+
T Consensus 2 ~L~~i~GiG~k~A~~il~ 19 (26)
T smart00278 2 ELLKVPGIGPKTAEKILE 19 (26)
T ss_pred hhhhCCCCCHHHHHHHHH
Confidence 356999999999999986
No 82
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=91.44 E-value=0.11 Score=49.56 Aligned_cols=50 Identities=28% Similarity=0.365 Sum_probs=39.2
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHcCCCCHHHHhhc------cCcchHHHhhHhhHHhh
Q 012388 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE------DSLTHSQRLGLKYFDDI 342 (464)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~------~~L~~~q~~Glk~~ed~ 342 (464)
...+.+|.+|.|||||+|-.+... -|.++|... ..|++.+++|.|..+.|
T Consensus 69 r~lF~~Li~V~GIGpK~Al~iLs~--~~~~el~~aI~~~D~~~L~kvpGIGkKtAerI 124 (195)
T PRK14604 69 RQLFELLIGVSGVGPKAALNLLSS--GTPDELQLAIAGGDVARLARVPGIGKKTAERI 124 (195)
T ss_pred HHHHHHHhCcCCcCHHHHHHHHcC--CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHH
Confidence 357888889999999999999774 366676632 35899999999986654
No 83
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=91.27 E-value=0.12 Score=49.23 Aligned_cols=50 Identities=18% Similarity=0.316 Sum_probs=38.7
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHcCCCCHHHHhhc------cCcchHHHhhHhhHHhh
Q 012388 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE------DSLTHSQRLGLKYFDDI 342 (464)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~------~~L~~~q~~Glk~~ed~ 342 (464)
...+++|.+|.|||||+|-.+... -+.++|..+ ..|++.+++|-|..+.|
T Consensus 68 r~lF~~LisVsGIGPK~ALaILs~--~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRI 123 (196)
T PRK13901 68 REVFEELIGVDGIGPRAALRVLSG--IKYNEFRDAIDREDIELISKVKGIGNKMAGKI 123 (196)
T ss_pred HHHHHHHhCcCCcCHHHHHHHHcC--CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHH
Confidence 357888889999999999998754 366666632 25889999999986654
No 84
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=90.95 E-value=0.57 Score=47.69 Aligned_cols=97 Identities=16% Similarity=0.295 Sum_probs=64.2
Q ss_pred CCCcHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhcCCccccchhhhcCCCCCCH-HHHHHHHHHHHhCCchhhHHH
Q 012388 207 PDLNKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGK-SMQDHIQEIVTTGKLSKLEHF 285 (464)
Q Consensus 207 ~~~N~~ia~~l~~la~~~e~~g~~~r~~aY~rAa~~l~~lp~~I~s~~~l~~lpgIG~-~ia~kI~Eil~tG~~~~le~l 285 (464)
+.=++.|++.++++.+-=++ .+.....+.+|.. ..+|..+||+|+ +|+..-+|+ - +..+++|
T Consensus 59 ~gIGk~ia~~I~e~l~tG~~----------~~le~lk~~~P~g---l~~Ll~v~GlGpkKi~~Ly~el-g---i~~~e~l 121 (326)
T COG1796 59 PGIGKGIAEKISEYLDTGEV----------KKLEALKKEVPEG---LEPLLKVPGLGPKKIVSLYKEL-G---IKDLEEL 121 (326)
T ss_pred CCccHHHHHHHHHHHHcCcc----------HHHHHHHHhCCcc---hHHHhhCCCCCcHHHHHHHHHH-C---cccHHHH
Confidence 66689999888776443221 1445555667776 678999999999 444433333 2 5666666
Q ss_pred HhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHHh
Q 012388 286 EKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLK 323 (464)
Q Consensus 286 ~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL~ 323 (464)
+.... .-.+.+++|+|.|.+.+|++.+....+.-+
T Consensus 122 ~~a~~---~~~~~~l~GfG~kse~~il~~i~~~~~~~~ 156 (326)
T COG1796 122 QEALE---NGKIRGLRGFGKKSEAKILENIEFAEESPE 156 (326)
T ss_pred HHHHH---hCCccccCCccchhHHHHHHHHHHHhhhhh
Confidence 64333 334679999999999999986554444443
No 85
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=90.92 E-value=0.36 Score=53.07 Aligned_cols=88 Identities=15% Similarity=0.194 Sum_probs=66.4
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHHhhcc--Ccch
Q 012388 253 ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTH 330 (464)
Q Consensus 253 ~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~~--~L~~ 330 (464)
.+++.+++|+|++.+++|.+=++.-+-..|+ ..|--| +|++||.++|+. .+.|+++|.... .|..
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 3689999999999999987766644433333 355566 999999998887 678999998653 5788
Q ss_pred HHHhhHhhHHhhccCCCHHHHHH
Q 012388 331 SQRLGLKYFDDIKTRIPRHEVEQ 353 (464)
Q Consensus 331 ~q~~Glk~~ed~~~~i~r~Ea~~ 353 (464)
..+||-+..+.|..-+.-.+..+
T Consensus 525 i~gIG~~~a~si~~~f~~~~~~~ 547 (562)
T PRK08097 525 LPGIGEGRARQLIAFLQHPEVKA 547 (562)
T ss_pred CCCchHHHHHHHHHHHcCHHHHH
Confidence 88999888888877776555444
No 86
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=90.51 E-value=0.7 Score=43.42 Aligned_cols=49 Identities=14% Similarity=0.218 Sum_probs=30.2
Q ss_pred CCCHHHHHHHHHHHH------hCCchhhHHHHh---hchhHHHHHhhhccCcCHHHHHHHH
Q 012388 261 GIGKSMQDHIQEIVT------TGKLSKLEHFEK---DEKVRTISLFGEVWGIGPATAQKLY 312 (464)
Q Consensus 261 gIG~~ia~kI~Eil~------tG~~~~le~l~~---~~~~~~l~lf~~I~GvGpktA~~ly 312 (464)
|.-..-|+.|.++.+ .|.+..+ .. -....+++.|++++|||+|||.-..
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 455566666665543 3433333 33 1223457788899999999999753
No 87
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=90.36 E-value=0.38 Score=47.59 Aligned_cols=49 Identities=22% Similarity=0.481 Sum_probs=35.8
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012388 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (464)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (464)
+..|||||..+|..+-. .-|+...+-.. ....|+.|+|||+++|..+|+
T Consensus 184 l~s~pgig~~~a~~ll~--~fgS~~~~~ta-------s~~eL~~v~gig~k~A~~I~~ 232 (254)
T COG1948 184 LESIPGIGPKLAERLLK--KFGSVEDVLTA-------SEEELMKVKGIGEKKAREIYR 232 (254)
T ss_pred HHcCCCccHHHHHHHHH--HhcCHHHHhhc-------CHHHHHHhcCccHHHHHHHHH
Confidence 68999999999987643 34444444321 125567999999999999987
No 88
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=90.22 E-value=0.2 Score=50.68 Aligned_cols=28 Identities=39% Similarity=0.612 Sum_probs=26.0
Q ss_pred hhccCcCHHHHHHHHHcCCCCHHHHhhc
Q 012388 298 GEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (464)
Q Consensus 298 ~~I~GvGpktA~~ly~~GirtledL~~~ 325 (464)
.++||||++++++|++.||.|++||...
T Consensus 2 ~~i~gig~~~~~~L~~~Gi~ti~dl~~~ 29 (310)
T TIGR02236 2 EDLPGVGPATAEKLREAGYDTFEAIAVA 29 (310)
T ss_pred cccCCCCHHHHHHHHHcCCCCHHHHHcC
Confidence 4789999999999999999999999864
No 89
>PRK14133 DNA polymerase IV; Provisional
Probab=90.15 E-value=1.1 Score=46.24 Aligned_cols=29 Identities=34% Similarity=0.512 Sum_probs=26.2
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHHhhc
Q 012388 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (464)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~ 325 (464)
+..+||||++++++|.+.||+|+.||.+-
T Consensus 175 v~~l~gig~~~~~~L~~~Gi~ti~dl~~l 203 (347)
T PRK14133 175 ISKVHGIGKKSVEKLNNIGIYTIEDLLKL 203 (347)
T ss_pred ccccCCCCHHHHHHHHHcCCccHHHHhhC
Confidence 35789999999999999999999999864
No 90
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=90.13 E-value=0.14 Score=57.66 Aligned_cols=63 Identities=16% Similarity=0.226 Sum_probs=46.4
Q ss_pred hhccCcCHHHHHHHHHc-CCCCHHHHhhc--cCcchHHHhhHhhHHhhccCCCHHHHHHHHHHHHH
Q 012388 298 GEVWGIGPATAQKLYEK-GHRTLDDLKNE--DSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQK 360 (464)
Q Consensus 298 ~~I~GvGpktA~~ly~~-GirtledL~~~--~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~iv~~ 360 (464)
++|.|+|++++++||+. +++++.||..- ..|..+.+||-|..+.|.+.|-..--..+..++..
T Consensus 465 l~I~GLG~k~i~~L~~~g~V~~~~Dl~~L~~~~L~~l~g~g~Ksa~~Ll~~Ie~sk~~~l~r~l~A 530 (689)
T PRK14351 465 LDIEGLGEERVQQLVDAGLVESLADLYDLTVADLAELEGWGETSAENLLAELEASREPPLADFLVA 530 (689)
T ss_pred cCCCCcCHHHHHHHHHcCCCCCHHHHHHcCHHHHhcCcCcchhHHHHHHHHHHHHccCCHHHHHHH
Confidence 37999999999999999 57999999853 34777778999999988776643322223444443
No 91
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=90.08 E-value=0.15 Score=57.83 Aligned_cols=53 Identities=15% Similarity=0.350 Sum_probs=40.8
Q ss_pred HHHHHhhh--ccCcCHHHHHHHHHc-CCCCHHHHhhcc-CcchHHHhhHhhHHhhcc
Q 012388 292 RTISLFGE--VWGIGPATAQKLYEK-GHRTLDDLKNED-SLTHSQRLGLKYFDDIKT 344 (464)
Q Consensus 292 ~~l~lf~~--I~GvGpktA~~ly~~-GirtledL~~~~-~L~~~q~~Glk~~ed~~~ 344 (464)
.++..|.+ ++||||++|+++++. |.++++-|.++. +|...+++|.+..+.|..
T Consensus 79 ~i~~yL~s~~~~GIG~~~A~~iv~~fg~~~~~~i~~~~~~L~~v~gi~~~~~~~i~~ 135 (720)
T TIGR01448 79 GIVAYLSSRSIKGVGKKLAQRIVKTFGEAAFDVLDDDPEKLLEVPGISKANLEKFVS 135 (720)
T ss_pred HHHHHHhcCCCCCcCHHHHHHHHHHhCHhHHHHHHhCHHHHhcCCCCCHHHHHHHHH
Confidence 34455543 899999999999998 999999998763 577777777776666654
No 92
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=89.72 E-value=0.41 Score=42.61 Aligned_cols=53 Identities=23% Similarity=0.293 Sum_probs=39.1
Q ss_pred HHhhhccCcCHHHHHHHHHcCCCCHHHHhhccCcchHHHhhHhhHHhhccCCCHHH
Q 012388 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIPRHE 350 (464)
Q Consensus 295 ~lf~~I~GvGpktA~~ly~~GirtledL~~~~~L~~~q~~Glk~~ed~~~~i~r~E 350 (464)
.-|+.|-||||+.++.|...||.|+.+|-.. +..--.-+..|=.|..||-|+.
T Consensus 67 DDLt~I~GIGPk~e~~Ln~~GI~tfaQIAAw---t~~di~~id~~l~f~GRi~RDd 119 (133)
T COG3743 67 DDLTRISGIGPKLEKVLNELGIFTFAQIAAW---TRADIAWIDDYLNFDGRIERDD 119 (133)
T ss_pred ccchhhcccCHHHHHHHHHcCCccHHHHHhc---CHHHHHHHHhhcCCcchhHHHH
Confidence 3467999999999999999999999999742 2222333455556677777764
No 93
>PRK03352 DNA polymerase IV; Validated
Probab=89.51 E-value=0.36 Score=49.65 Aligned_cols=40 Identities=33% Similarity=0.595 Sum_probs=30.6
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHHhhccCcchHHHhhH
Q 012388 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGL 336 (464)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~~~L~~~q~~Gl 336 (464)
+..+||||++++++|.+.||+|+.||.+-..-.-.++||.
T Consensus 179 l~~l~gig~~~~~~L~~~Gi~ti~dl~~l~~~~L~~~fG~ 218 (346)
T PRK03352 179 TDALWGVGPKTAKRLAALGITTVADLAAADPAELAATFGP 218 (346)
T ss_pred HHHcCCCCHHHHHHHHHcCCccHHHHhcCCHHHHHHHhCh
Confidence 3588999999999999999999999986432222344553
No 94
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=89.38 E-value=0.21 Score=47.35 Aligned_cols=49 Identities=22% Similarity=0.300 Sum_probs=37.8
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHcCCCCHHHHhhc------cCcchHHHhhHhhHHhh
Q 012388 291 VRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE------DSLTHSQRLGLKYFDDI 342 (464)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~------~~L~~~q~~Glk~~ed~ 342 (464)
...+++|.+|.|||||+|-.+... -|.++|... ..| +.+++|-|..+.|
T Consensus 69 r~lF~~LisV~GIGpK~Al~iLs~--~~~~~l~~aI~~~D~~~L-~vpGIGkKtAerI 123 (186)
T PRK14600 69 QDCLRMLVKVSGVNYKTAMSILSK--LTPEQLFSAIVNEDKAAL-KVNGIGEKLINRI 123 (186)
T ss_pred HHHHHHHhCcCCcCHHHHHHHHcc--CCHHHHHHHHHcCCHhhe-ECCCCcHHHHHHH
Confidence 457888889999999999999764 356666532 358 8999999986654
No 95
>PRK02406 DNA polymerase IV; Validated
Probab=89.36 E-value=0.86 Score=46.84 Aligned_cols=29 Identities=34% Similarity=0.409 Sum_probs=26.3
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHHhhc
Q 012388 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (464)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~ 325 (464)
+..+||||++++++|-+.||+|+.||.+-
T Consensus 170 i~~l~giG~~~~~~L~~~Gi~ti~dl~~l 198 (343)
T PRK02406 170 VEKIPGVGKVTAEKLHALGIYTCADLQKY 198 (343)
T ss_pred cchhcCCCHHHHHHHHHcCCCcHHHHHhC
Confidence 36889999999999998999999999864
No 96
>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=89.27 E-value=1.7 Score=44.77 Aligned_cols=106 Identities=16% Similarity=0.114 Sum_probs=59.8
Q ss_pred hhccCcCHHHHHHHHHcCCCCHHHHhhccCcchH-HHhh---HhhHHhhccCCCHHHHHHHHHHHHHHhhhcCCCEEEEE
Q 012388 298 GEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHS-QRLG---LKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILC 373 (464)
Q Consensus 298 ~~I~GvGpktA~~ly~~GirtledL~~~~~L~~~-q~~G---lk~~ed~~~~i~r~Ea~~i~~iv~~~~~~~~p~~~v~~ 373 (464)
..+||||++++++|.+.||+|+.||.+-.....+ ..|| ...|+.... +++. .+
T Consensus 176 ~~l~giG~~~~~~L~~~Gi~ti~dl~~~~~~~~l~~~fg~~~~~l~~~a~G--------------------~d~~-~v-- 232 (343)
T cd00424 176 TDLPGIGAVTAKRLEAVGINPIGDLLAASPDALLALWGGVSGERLWYALRG--------------------IDDE-PL-- 232 (343)
T ss_pred hhcCCCCHHHHHHHHHcCCCcHHHHhcCCHHHHHHHHhhHHHHHHHHHhCC--------------------cCCC-CC--
Confidence 4689999999999999999999999864311111 2233 222222221 1111 01
Q ss_pred cccccccCCcCCCccEEEeCCCcc----hhhhHHHHHHHHHHhcccccccccccccCC
Q 012388 374 GGSYRRGKASCGDLDVVIMHPDRK----SHKGFLSKYVKKLKEMKFLREDLIFSTHSE 427 (464)
Q Consensus 374 ~GsyRRgke~~gDvDiLit~~d~~----~~~~~l~~lv~~L~~~g~l~~~L~~~~~~~ 427 (464)
-.++.-|..+....|----.+.. ....++.+|..+|.++|.....|.+.-+..
T Consensus 233 -~~~~~~ksi~~~~tf~~~~~~~~~l~~~l~~l~~~l~~rL~~~~~~~~~l~l~lr~~ 289 (343)
T cd00424 233 -SPPRPRKSFSHERVLPRDSRNAEDARPLLRLLLEKLARRLRRDGRGATRLRLWLRTV 289 (343)
T ss_pred -CCCCCCCceeeeEECCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCceeEEEEEEEeC
Confidence 11222344444433311001111 134678888999999999998887765543
No 97
>PRK01172 ski2-like helicase; Provisional
Probab=89.10 E-value=0.72 Score=51.86 Aligned_cols=40 Identities=25% Similarity=0.484 Sum_probs=33.9
Q ss_pred HHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHHhhc
Q 012388 285 FEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (464)
Q Consensus 285 l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~ 325 (464)
+....+...+.|. +|||+|...|+++|+.|++|+.||.+.
T Consensus 603 l~~gv~~~~~~L~-~ip~~~~~~a~~l~~~g~~~~~di~~~ 642 (674)
T PRK01172 603 IKEGIREDLIDLV-LIPKVGRVRARRLYDAGFKTVDDIARS 642 (674)
T ss_pred HHcCCCHHHHhhc-CCCCCCHHHHHHHHHcCCCCHHHHHhC
Confidence 4445566677777 899999999999999999999999864
No 98
>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=88.86 E-value=1.8 Score=38.42 Aligned_cols=46 Identities=33% Similarity=0.509 Sum_probs=33.5
Q ss_pred CEEEEEcccccccCCcC--CCccEEEeCCCcc-----hhhhHHHHHHHHHHhc
Q 012388 368 EVIILCGGSYRRGKASC--GDLDVVIMHPDRK-----SHKGFLSKYVKKLKEM 413 (464)
Q Consensus 368 ~~~v~~~GsyRRgke~~--gDvDiLit~~d~~-----~~~~~l~~lv~~L~~~ 413 (464)
...+.+.|||.||...- .|||++|..+... ....++..|-+.|.+.
T Consensus 27 ~~~~~~~GS~a~~T~i~~~sDiD~~v~~~~~~~~~~~~~~~~~~~l~~~L~~~ 79 (143)
T cd05400 27 VAEVFLQGSYARGTALRGDSDIDLVVVLPDDTSFAEYGPAELLDELGEALKEY 79 (143)
T ss_pred ccEEEEEcceeCCCCCCCCCceeEEEEEcCcccccccCHHHHHHHHHHHHHHh
Confidence 35789999999998654 8999999655432 3456777777777654
No 99
>PRK01216 DNA polymerase IV; Validated
Probab=88.67 E-value=0.44 Score=49.51 Aligned_cols=40 Identities=28% Similarity=0.260 Sum_probs=30.3
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHHhhccCcchHHHhhH
Q 012388 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGL 336 (464)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~~~L~~~q~~Gl 336 (464)
+..+||||++++++|.+.||+|+.||.+...-.-.++||.
T Consensus 180 i~~l~giG~~~~~~L~~~Gi~TigdL~~~~~~~L~~rfG~ 219 (351)
T PRK01216 180 IADIPGIGDITAEKLKKLGVNKLVDTLRIEFDELKGIIGE 219 (351)
T ss_pred cccccCCCHHHHHHHHHcCCCcHHHHhcCCHHHHHHHHCH
Confidence 3578999999999999999999999986432122334553
No 100
>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=88.66 E-value=1.2 Score=45.64 Aligned_cols=62 Identities=19% Similarity=0.270 Sum_probs=40.0
Q ss_pred hhcCCCCCCHHHHHHHHHHH---HhCC--chhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCC
Q 012388 255 QVKGLPGIGKSMQDHIQEIV---TTGK--LSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRT 318 (464)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil---~tG~--~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~Girt 318 (464)
+|..+ |+|-+ |+.|.++. ..|. ...++.+..-....+.+.|++++||||+||.-+--.|+.-
T Consensus 177 ~Lr~~-G~g~R-a~~I~~~A~~i~~~~~~~~~l~~l~~~~~~~~~~~L~~l~GIG~~tAd~vll~~l~~ 243 (310)
T TIGR00588 177 HLRKL-GLGYR-ARYIRETARALLEEQGGRAWLQQIRGASYEDAREALCELPGVGPKVADCICLMGLDK 243 (310)
T ss_pred HHHHc-CCHHH-HHHHHHHHHHHHhccCCchhHHhhccCChHHHHHHHHhCCCccHHHHHHHHHHhCCC
Confidence 45554 66765 45454433 3443 3346666554455688999999999999999876545543
No 101
>PTZ00418 Poly(A) polymerase; Provisional
Probab=88.01 E-value=2.6 Score=46.60 Aligned_cols=53 Identities=23% Similarity=0.382 Sum_probs=43.7
Q ss_pred CCCEEEEEcccccccCCc-CCCccEEEeCCCcchhhhHHHHHHHHHHhcccccc
Q 012388 366 LPEVIILCGGSYRRGKAS-CGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLRE 418 (464)
Q Consensus 366 ~p~~~v~~~GsyRRgke~-~gDvDiLit~~d~~~~~~~l~~lv~~L~~~g~l~~ 418 (464)
..+.++...||||-|--. +.|||.|+-.|..-+...||..+.+.|.+..-+++
T Consensus 124 ~~~g~I~tfGSYrLGV~~pgSDID~L~V~P~~vtredFF~~f~~~L~~~~~V~e 177 (593)
T PTZ00418 124 QISGKLFTFGSYRLGVVAPGSDIDTLCLAPRHITRESFFSDFYAKLQQDPNITK 177 (593)
T ss_pred cCCeEEEEeccccccCCCCCCcccEEEECCCCCCHHHHHHHHHHHHhcCCCcce
Confidence 356778888999999866 67999999999776678899999999998766554
No 102
>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=87.92 E-value=0.77 Score=38.67 Aligned_cols=47 Identities=11% Similarity=0.254 Sum_probs=37.5
Q ss_pred hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCc
Q 012388 253 ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGI 303 (464)
Q Consensus 253 ~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~Gv 303 (464)
+.+|..|||||+++++-...| -+..+++|+...|....+-++.+-|.
T Consensus 11 ~~~L~~iP~IG~a~a~DL~~L----Gi~s~~~L~g~dP~~Ly~~lc~~~G~ 57 (93)
T PF11731_consen 11 LSDLTDIPNIGKATAEDLRLL----GIRSPADLKGRDPEELYERLCALTGQ 57 (93)
T ss_pred HHHHhcCCCccHHHHHHHHHc----CCCCHHHHhCCCHHHHHHHHHHHcCC
Confidence 578999999999999876644 35778888888888888877777664
No 103
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=87.67 E-value=0.37 Score=33.34 Aligned_cols=16 Identities=56% Similarity=0.742 Sum_probs=14.2
Q ss_pred hccCcCHHHHHHHHHc
Q 012388 299 EVWGIGPATAQKLYEK 314 (464)
Q Consensus 299 ~I~GvGpktA~~ly~~ 314 (464)
.|+|||+|||.+|.++
T Consensus 20 Gv~giG~ktA~~ll~~ 35 (36)
T smart00279 20 GVKGIGPKTALKLLRE 35 (36)
T ss_pred CCCcccHHHHHHHHHh
Confidence 7999999999999763
No 104
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=87.65 E-value=1.1 Score=37.57 Aligned_cols=54 Identities=28% Similarity=0.553 Sum_probs=41.6
Q ss_pred HHHHHhhhccCcCHHHHHHHHHc-CCCCHHHHhhcc-Ccch-HHHhhHhhHHhhccCC
Q 012388 292 RTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED-SLTH-SQRLGLKYFDDIKTRI 346 (464)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~-GirtledL~~~~-~L~~-~q~~Glk~~ed~~~~i 346 (464)
.++..| .=+|++++.|.++|+. |-.+++-|+++. .|.. ..++|++..+.|-.++
T Consensus 10 ~~~~~L-~~~gl~~~~a~kl~~~yg~~ai~~l~~nPY~L~~~i~gi~F~~aD~iA~~~ 66 (94)
T PF14490_consen 10 ELMAFL-QEYGLSPKLAMKLYKKYGDDAIEILKENPYRLIEDIDGIGFKTADKIALKL 66 (94)
T ss_dssp HHHHHH-HHTT--HHHHHHHHHHH-TTHHHHHHH-STCCCB-SSSSBHHHHHHHHHTT
T ss_pred HHHHHH-HHcCCCHHHHHHHHHHHhHHHHHHHHHChHHHHHHccCCCHHHHHHHHHHc
Confidence 355566 8899999999999998 999999998764 5554 8899999999997765
No 105
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=87.45 E-value=0.48 Score=38.08 Aligned_cols=28 Identities=39% Similarity=0.539 Sum_probs=22.8
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHHhhc
Q 012388 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (464)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~ 325 (464)
+.+|+|||+|||.+|..+ +.|++.+...
T Consensus 24 i~gv~giG~k~A~~ll~~-~~~~~~~~~~ 51 (75)
T cd00080 24 IPGVPGIGPKTALKLLKE-YGSLENLLEN 51 (75)
T ss_pred CCCCCcccHHHHHHHHHH-hCCHHHHHHH
Confidence 347999999999999976 5588888753
No 106
>KOG2245 consensus Poly(A) polymerase and related nucleotidyltransferases [RNA processing and modification]
Probab=87.20 E-value=1.3 Score=47.74 Aligned_cols=82 Identities=24% Similarity=0.332 Sum_probs=58.1
Q ss_pred CEEEEEcccccccCCcC-CCccEEEeCCCcchhhhHHHHHHHHHHhcccccccccccccCCCCCCCCCceEEEEee--cC
Q 012388 368 EVIILCGGSYRRGKASC-GDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCT--YP 444 (464)
Q Consensus 368 ~~~v~~~GsyRRgke~~-gDvDiLit~~d~~~~~~~l~~lv~~L~~~g~l~~~L~~~~~~~~~~~~~~~~~~g~~~--~p 444 (464)
|.++---||||-|--.. .|||=|.-.|.-.+..+||..+-+.|+++.-+|+--.+. |-|-=+.+ +.
T Consensus 89 ggkIftfGSYRLGVhg~GADIDtLcV~Prhv~R~DFF~sf~~mL~~~~eVteL~~V~-----------dAfVPiikfKf~ 157 (562)
T KOG2245|consen 89 GGKIFTFGSYRLGVHGPGADIDTLCVGPRHVSRSDFFTSFYDMLKERPEVTELHAVE-----------DAFVPIIKFKFD 157 (562)
T ss_pred CceEEeccceeecccCCCCCcceeeeccccccHHHHHHHHHHHHhcCcccccccccc-----------ccccceEEEEec
Confidence 45666679999998765 599999999988778899999999999999888743221 22222222 22
Q ss_pred CC---CcceeeeEEEecCc
Q 012388 445 GR---ELRHRIDFKVLASL 460 (464)
Q Consensus 445 ~~---~~~rRiDi~~~P~~ 460 (464)
|- -+.-|+.+.+||.+
T Consensus 158 GI~IDllfArL~l~~VP~d 176 (562)
T KOG2245|consen 158 GIEIDLLFARLALPVVPED 176 (562)
T ss_pred CeeeeeeehhcccccCCCc
Confidence 32 24558888888865
No 107
>PRK08609 hypothetical protein; Provisional
Probab=87.16 E-value=0.77 Score=50.81 Aligned_cols=54 Identities=19% Similarity=0.247 Sum_probs=38.6
Q ss_pred chhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHH
Q 012388 252 SADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKL 311 (464)
Q Consensus 252 s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l 311 (464)
.+.++.+|||||++.+.++.+=+---++++|+....+-+ +..++|+|+|+++.+
T Consensus 86 ~~~~l~~i~GiGpk~a~~l~~~lGi~tl~~L~~a~~~~~------~~~~~gfg~k~~~~i 139 (570)
T PRK08609 86 GLLPLLKLPGLGGKKIAKLYKELGVVDKESLKEACENGK------VQALAGFGKKTEEKI 139 (570)
T ss_pred HHHHHhcCCCCCHHHHHHHHHHhCCCCHHHHHHHHHhCC------hhhccCcchhHHHHH
Confidence 356789999999999998876555445555554332212 348899999999988
No 108
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=87.15 E-value=0.59 Score=49.61 Aligned_cols=30 Identities=37% Similarity=0.653 Sum_probs=26.9
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHHhhcc
Q 012388 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (464)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~~ 326 (464)
+..+||||++++++|.+.||+|+.||.+..
T Consensus 181 v~~l~GiG~~~~~~L~~lGi~TigdL~~~~ 210 (422)
T PRK03609 181 VEEVWGVGRRISKKLNAMGIKTALDLADTN 210 (422)
T ss_pred hhhcCCccHHHHHHHHHcCCCcHHHHhcCC
Confidence 368999999999999999999999998643
No 109
>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=86.75 E-value=0.67 Score=48.96 Aligned_cols=30 Identities=27% Similarity=0.328 Sum_probs=26.9
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHHhhcc
Q 012388 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (464)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~~ 326 (464)
+..+||||++++++|.+.||+|+.||.+..
T Consensus 224 v~~l~GIG~~~~~~L~~~Gi~t~~dl~~~~ 253 (404)
T cd01701 224 VGDLPGVGSSLAEKLVKLFGDTCGGLELRS 253 (404)
T ss_pred HhHhCCCCHHHHHHHHHcCCcchHHHHhCc
Confidence 357899999999999999999999998753
No 110
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=86.69 E-value=1.4 Score=48.85 Aligned_cols=52 Identities=17% Similarity=0.157 Sum_probs=37.8
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 314 (464)
..|.+|||||++...++-+ .-|++ +.+++ .+++.+.+|+|+|.+.|+.+|+.
T Consensus 514 s~L~~I~GiG~kr~~~LL~--~Fgs~---~~I~~----As~eeL~~v~gi~~~~A~~I~~~ 565 (574)
T PRK14670 514 LNYTKIKGIGEKKAKKILK--SLGTY---KDILL----LNEDEIAEKMKINIKMAKKIKKF 565 (574)
T ss_pred cccccCCCCCHHHHHHHHH--HhCCH---HHHHh----CCHHHHHhCCCCCHHHHHHHHHH
Confidence 3789999999988776543 23444 44432 24566789999999999999863
No 111
>PRK13844 recombination protein RecR; Provisional
Probab=86.01 E-value=1.5 Score=41.97 Aligned_cols=22 Identities=23% Similarity=0.271 Sum_probs=18.9
Q ss_pred hHHHHHhhhccCcCHHHHHHHH
Q 012388 291 VRTISLFGEVWGIGPATAQKLY 312 (464)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly 312 (464)
...++.|.++||||+|+|+++-
T Consensus 11 ~~LI~~l~~LPGIG~KsA~Rla 32 (200)
T PRK13844 11 SAVIESLRKLPTIGKKSSQRLA 32 (200)
T ss_pred HHHHHHHHHCCCCCHHHHHHHH
Confidence 3468889999999999999983
No 112
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=85.91 E-value=0.88 Score=44.40 Aligned_cols=50 Identities=22% Similarity=0.453 Sum_probs=35.7
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012388 255 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (464)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (464)
-|..||||+|.=|..+ |. ++.-|+++-+ .....+.+|+|+||.+|+++|+
T Consensus 196 ~Lt~i~~VnKtda~~L---L~--~FgsLq~~~~----AS~~ele~~~G~G~~kak~l~~ 245 (254)
T KOG2841|consen 196 FLTTIPGVNKTDAQLL---LQ--KFGSLQQISN----ASEGELEQCPGLGPAKAKRLHK 245 (254)
T ss_pred HHHhCCCCCcccHHHH---HH--hcccHHHHHh----cCHhHHHhCcCcCHHHHHHHHH
Confidence 3789999999877654 22 3444444432 2455678999999999999997
No 113
>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=85.85 E-value=0.83 Score=46.45 Aligned_cols=109 Identities=19% Similarity=0.120 Sum_probs=61.0
Q ss_pred hccCcCHHHHHHHHHcCCCCHHHHhhccCcchHHHhhHhhHHhhccCCCHHHHHHHHHHHHHHhhhcCCCEEEEEccccc
Q 012388 299 EVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQKAGEEVLPEVIILCGGSYR 378 (464)
Q Consensus 299 ~I~GvGpktA~~ly~~GirtledL~~~~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~iv~~~~~~~~p~~~v~~~GsyR 378 (464)
.+||||++++++|.+.||+|+.||.+-..-.-.++||.+...- ...+. -.++.. +.. -..+
T Consensus 174 ~~~gig~~~~~~L~~~Gi~t~~dl~~~~~~~l~~rfG~~~~~l----------------~~~~~-G~d~~~-~~~-~~~~ 234 (335)
T cd03468 174 AALRLPPETVELLARLGLRTLGDLAALPRAELARRFGLALLLR----------------LDQAY-GRDPEP-LLF-SPPP 234 (335)
T ss_pred hHhCCCHHHHHHHHHhCcccHHHHHhCChHHHHhhcCHHHHHH----------------HHHHC-CCCCCC-CCC-CCCC
Confidence 5789999999999999999999998644322334555432111 11110 011111 000 1112
Q ss_pred ccCCcCCCccEEEeCCC--cchhhhHHHHHHHHHHhcccccccccccccC
Q 012388 379 RGKASCGDLDVVIMHPD--RKSHKGFLSKYVKKLKEMKFLREDLIFSTHS 426 (464)
Q Consensus 379 Rgke~~gDvDiLit~~d--~~~~~~~l~~lv~~L~~~g~l~~~L~~~~~~ 426 (464)
..+..+.+..|-.-..+ ......++.++..+|...|.....+++.-+.
T Consensus 235 ~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~~L~~~~~~~~~l~l~l~~ 284 (335)
T cd03468 235 PAFDFRLELQLEEPIARGLLFPLRRLLEQLCAFLALRGLGARRLSLTLFR 284 (335)
T ss_pred CChhhhhhcCCCCCcchhHHHHHHHHHHHHHHHHHHcCCeeeEEEEEEEE
Confidence 22333333333221111 1234578889999999999999888765543
No 114
>PRK03348 DNA polymerase IV; Provisional
Probab=85.68 E-value=0.74 Score=49.47 Aligned_cols=29 Identities=41% Similarity=0.728 Sum_probs=26.4
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHHhhc
Q 012388 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (464)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~ 325 (464)
+..+||||++++++|.+.||+|+.||.+-
T Consensus 182 v~~L~GIG~~t~~~L~~lGI~TigDLa~l 210 (454)
T PRK03348 182 VRRLWGIGPVTEEKLHRLGIETIGDLAAL 210 (454)
T ss_pred ccccCCCCHHHHHHHHHcCCccHHHHhcC
Confidence 46889999999999999999999999864
No 115
>COG1708 Predicted nucleotidyltransferases [General function prediction only]
Probab=85.65 E-value=3.4 Score=35.13 Aligned_cols=30 Identities=30% Similarity=0.501 Sum_probs=24.5
Q ss_pred CCCEEEEEcccccccCCcC-CCccEEEeCCC
Q 012388 366 LPEVIILCGGSYRRGKASC-GDLDVVIMHPD 395 (464)
Q Consensus 366 ~p~~~v~~~GsyRRgke~~-gDvDiLit~~d 395 (464)
.....|.+-|||=||..+- +|||++|-.++
T Consensus 24 ~~~~~v~LfGS~arG~~~~~SDiDv~vv~~~ 54 (128)
T COG1708 24 GGDLLIYLFGSYARGDFVKESDIDLLVVSDD 54 (128)
T ss_pred CCCeEEEEEccCcccccccCCCeeEEEEcCC
Confidence 3345899999999999876 99999998644
No 116
>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=85.57 E-value=0.81 Score=48.07 Aligned_cols=30 Identities=33% Similarity=0.431 Sum_probs=26.8
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHHhhcc
Q 012388 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (464)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~~ 326 (464)
+..+||||++++++|.+.||.|+.||....
T Consensus 174 v~~l~GiG~~~~~kL~~~GI~tigdl~~~~ 203 (379)
T cd01703 174 LRKIPGIGYKTAAKLEAHGISSVRDLQEFS 203 (379)
T ss_pred ccccCCcCHHHHHHHHHcCCCcHHHHHhCC
Confidence 468899999999999999999999997543
No 117
>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=84.98 E-value=4.4 Score=38.27 Aligned_cols=25 Identities=16% Similarity=0.167 Sum_probs=20.2
Q ss_pred HHHHHhhhccCcCHHHHHHHHHcCC
Q 012388 292 RTISLFGEVWGIGPATAQKLYEKGH 316 (464)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~Gi 316 (464)
..++.|++++|||++||..+--.++
T Consensus 103 ~~~~~L~~l~GIG~ktA~~ill~~~ 127 (191)
T TIGR01083 103 EDREELVKLPGVGRKTANVVLNVAF 127 (191)
T ss_pred hHHHHHHhCCCCcHHHHHHHHHHHc
Confidence 3577888999999999999765544
No 118
>cd01700 PolY_Pol_V_umuC umuC subunit of DNA Polymerase V. umuC subunit of Pol V. Pol V is a bacterial translesion synthesis (TLS) polymerase that consists of the heterotrimer of one umuC and two umuD subunits. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol V, RecA, single stranded DNA-binding protein, beta sliding clamp, and gamma clamp loading complex are responsible for inducing the SOS response in bacteria to repair UV-induced DNA damage.
Probab=84.94 E-value=0.75 Score=47.29 Aligned_cols=29 Identities=48% Similarity=0.792 Sum_probs=26.1
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHHhhc
Q 012388 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (464)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~ 325 (464)
+..+||||++++++|.+.||+|+.||.+-
T Consensus 178 l~~l~gig~~~~~~L~~~Gi~ti~dL~~~ 206 (344)
T cd01700 178 VGDVWGIGRRTAKKLNAMGIHTAGDLAQA 206 (344)
T ss_pred hhhcCccCHHHHHHHHHcCCCcHHHHhcC
Confidence 35789999999999999999999999864
No 119
>PRK01810 DNA polymerase IV; Validated
Probab=84.69 E-value=0.96 Score=47.65 Aligned_cols=29 Identities=45% Similarity=0.691 Sum_probs=26.1
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHHhhc
Q 012388 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (464)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~ 325 (464)
+..+||||++++++|...||+|+.||...
T Consensus 181 v~~l~giG~~~~~~L~~~Gi~tigdL~~~ 209 (407)
T PRK01810 181 VGEMHGIGEKTAEKLKDIGIQTIGDLAKA 209 (407)
T ss_pred HhhcCCcCHHHHHHHHHcCCCcHHHHHhC
Confidence 35789999999999999999999999864
No 120
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=84.50 E-value=0.55 Score=52.68 Aligned_cols=49 Identities=29% Similarity=0.447 Sum_probs=37.0
Q ss_pred HHHhhhccCcCHHHHHHHHHc-CCCCHHHHhhcc--CcchHHHhhHhhHHhhcc
Q 012388 294 ISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED--SLTHSQRLGLKYFDDIKT 344 (464)
Q Consensus 294 l~lf~~I~GvGpktA~~ly~~-GirtledL~~~~--~L~~~q~~Glk~~ed~~~ 344 (464)
-..|..|+||||+++++|++. | |+++|.++. .|....++|.+..+.|.+
T Consensus 636 ~s~L~~IPGIGpkr~k~LL~~FG--Sle~I~~AS~eELa~V~Gig~k~Ae~I~~ 687 (694)
T PRK14666 636 TGELQRVEGIGPATARLLWERFG--SLQAMAAAGEEGLAAVPGIGPARAAALHE 687 (694)
T ss_pred HhHHhhCCCCCHHHHHHHHHHhC--CHHHHHhcCHHHHHhcCCcCHHHHHHHHH
Confidence 355679999999999999997 6 999999753 365666677666555543
No 121
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=84.48 E-value=0.87 Score=28.89 Aligned_cols=20 Identities=30% Similarity=0.573 Sum_probs=17.1
Q ss_pred hhcCCCCCCHHHHHHHHHHH
Q 012388 255 QVKGLPGIGKSMQDHIQEIV 274 (464)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil 274 (464)
++.+|||||+++|+.|.++.
T Consensus 2 ~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred hhhhCCCCCHHHHHHHHHhc
Confidence 57899999999999987643
No 122
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=84.14 E-value=0.74 Score=43.76 Aligned_cols=21 Identities=33% Similarity=0.607 Sum_probs=18.9
Q ss_pred HHHHHhhhccCcCHHHHHHHH
Q 012388 292 RTISLFGEVWGIGPATAQKLY 312 (464)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly 312 (464)
+.++.|.++||||||+|++|-
T Consensus 9 ~LI~~l~kLPGvG~KsA~R~A 29 (198)
T COG0353 9 KLIDALKKLPGVGPKSAQRLA 29 (198)
T ss_pred HHHHHHhhCCCCChhHHHHHH
Confidence 478889999999999999984
No 123
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=84.12 E-value=1.3 Score=44.02 Aligned_cols=55 Identities=22% Similarity=0.348 Sum_probs=42.5
Q ss_pred hchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHHhhcc--CcchHHHhhHhhHHhhc
Q 012388 288 DEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIK 343 (464)
Q Consensus 288 ~~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~~--~L~~~q~~Glk~~ed~~ 343 (464)
+....-+.++.++||||++.|+.+.+ -+.|++++.++. .|.+..++|.+....|.
T Consensus 175 t~~e~q~~il~s~pgig~~~a~~ll~-~fgS~~~~~tas~~eL~~v~gig~k~A~~I~ 231 (254)
T COG1948 175 TLKELQLYILESIPGIGPKLAERLLK-KFGSVEDVLTASEEELMKVKGIGEKKAREIY 231 (254)
T ss_pred chHHHHHHHHHcCCCccHHHHHHHHH-HhcCHHHHhhcCHHHHHHhcCccHHHHHHHH
Confidence 44455678888999999999999987 466888888764 57788888877755554
No 124
>TIGR03671 cca_archaeal CCA-adding enzyme.
Probab=84.11 E-value=3.5 Score=43.74 Aligned_cols=59 Identities=22% Similarity=0.295 Sum_probs=38.7
Q ss_pred HHHHHHHHHhhhcCCCEEEEEcccccccCCcC--CCccEEEeCCCcchh---hhHHHHHHHHHH
Q 012388 353 QMERLLQKAGEEVLPEVIILCGGSYRRGKASC--GDLDVVIMHPDRKSH---KGFLSKYVKKLK 411 (464)
Q Consensus 353 ~i~~iv~~~~~~~~p~~~v~~~GsyRRgke~~--gDvDiLit~~d~~~~---~~~l~~lv~~L~ 411 (464)
.+...+++.+.+..+.+.|.+.|||.||.-.. .||||+|..+...+. ..+...+...+-
T Consensus 25 ~l~~~l~~~~~e~~~~~~v~~~GS~ArgT~L~G~sDIDIfi~f~~~~~~e~l~~~gl~i~~~~~ 88 (408)
T TIGR03671 25 ELIARLEEIIEELGVDAEVVLVGSYARGTWLKGDRDIDIFILFPKDTSREELEEYGLEIGHEVL 88 (408)
T ss_pred HHHHHHHHHHHhcCCcceEEEEeeEecCCccCCCCceeEEEEeCCCCCHHHHHHHHHHHHHHHH
Confidence 34445555555555668999999999999886 599999987654332 233334444443
No 125
>PTZ00205 DNA polymerase kappa; Provisional
Probab=83.98 E-value=1.1 Score=49.34 Aligned_cols=29 Identities=34% Similarity=0.408 Sum_probs=26.3
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHHhhc
Q 012388 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (464)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~ 325 (464)
+.+|||||++++++|-..||.|+.||...
T Consensus 311 V~ki~GIG~~t~~~L~~~GI~TigDLa~~ 339 (571)
T PTZ00205 311 LRSVPGVGKVTEALLKGLGITTLSDIYNR 339 (571)
T ss_pred cceeCCcCHHHHHHHHHcCCCcHHHHhcC
Confidence 45899999999999999999999999854
No 126
>PRK10880 adenine DNA glycosylase; Provisional
Probab=83.87 E-value=4.4 Score=42.17 Aligned_cols=64 Identities=22% Similarity=0.344 Sum_probs=43.0
Q ss_pred hHHHHHHHHHHHh-cCCccc-cchhhhcCCCCCCHHHHHHHHHHHHhCC-chhhHHHHhhchhHHHHHhhhccCc
Q 012388 232 RSFSYYKAIPVIE-KLPFKI-ESADQVKGLPGIGKSMQDHIQEIVTTGK-LSKLEHFEKDEKVRTISLFGEVWGI 303 (464)
Q Consensus 232 r~~aY~rAa~~l~-~lp~~I-~s~~~l~~lpgIG~~ia~kI~Eil~tG~-~~~le~l~~~~~~~~l~lf~~I~Gv 303 (464)
|++...+||..|. .+...+ .+.++|.+|||||..+|+.|--|.- |. ..-+ ...+.+.+..++|+
T Consensus 85 RAr~L~~~A~~i~~~~~g~~p~~~~~L~~LpGIG~~TA~aIl~~af-~~~~~iV-------D~nV~RV~~Rl~~i 151 (350)
T PRK10880 85 RARNLHKAAQQVATLHGGEFPETFEEVAALPGVGRSTAGAILSLSL-GKHFPIL-------DGNVKRVLARCYAV 151 (350)
T ss_pred HHHHHHHHHHHHHHHhCCCchhhHHHHhcCCCccHHHHHHHHHHHC-CCCeecc-------cHHHHHHHHHHhcc
Confidence 8888888888883 333222 4568999999999999999987653 33 1111 23456666666655
No 127
>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=83.81 E-value=0.089 Score=44.98 Aligned_cols=25 Identities=44% Similarity=0.735 Sum_probs=19.8
Q ss_pred hccCcCHHHHHHHHHc-CCCCHHHHhhc
Q 012388 299 EVWGIGPATAQKLYEK-GHRTLDDLKNE 325 (464)
Q Consensus 299 ~I~GvGpktA~~ly~~-GirtledL~~~ 325 (464)
+|+|||+|||.+|.++ | |||.+..+
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 7999999999999987 6 88887753
No 128
>PRK03103 DNA polymerase IV; Reviewed
Probab=83.22 E-value=1.2 Score=46.93 Aligned_cols=29 Identities=28% Similarity=0.534 Sum_probs=26.0
Q ss_pred hhccCcCHHHHHHHHHcCCCCHHHHhhcc
Q 012388 298 GEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (464)
Q Consensus 298 ~~I~GvGpktA~~ly~~GirtledL~~~~ 326 (464)
..+||||++++++|.+.||+|+.||.+-.
T Consensus 184 ~~l~gig~~~~~~L~~~Gi~tigdl~~~~ 212 (409)
T PRK03103 184 RKLFGVGSRMEKHLRRMGIRTIGQLANTP 212 (409)
T ss_pred hhcCCccHHHHHHHHHcCCCCHHHHhcCC
Confidence 57899999999999999999999998643
No 129
>PRK00227 glnD PII uridylyl-transferase; Provisional
Probab=83.20 E-value=3.3 Score=46.97 Aligned_cols=65 Identities=22% Similarity=0.314 Sum_probs=45.8
Q ss_pred HHHHHH-HHHHHHHHhhhcCCCEEEEEcccccccCC-cCCCccEEEeCCCcchhhhHHHHHHHHHHhccc
Q 012388 348 RHEVEQ-MERLLQKAGEEVLPEVIILCGGSYRRGKA-SCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKF 415 (464)
Q Consensus 348 r~Ea~~-i~~iv~~~~~~~~p~~~v~~~GsyRRgke-~~gDvDiLit~~d~~~~~~~l~~lv~~L~~~g~ 415 (464)
|++|.+ ...+++... +.+++-+..+|||-||.- --.|||+||-|++... ..++.+++--|=+.|+
T Consensus 8 ~~~~~~~~~~~~~~~~--~~~~~aLvAvGGYGR~EL~P~SDIDLLiL~~~~~~-~~~i~~~~~~LWD~gL 74 (693)
T PRK00227 8 REDAEASALALLGSLQ--LPPGTALAATGSLARREMTPYSDLDLILLHPPGAT-PDGVEDLWYPIWDAKK 74 (693)
T ss_pred HHHHHHHHHHHHHhcC--CCCCeEEEEeccccccCcCCCcCceEEEEeCCccc-HHHHHHHHHHHHhcCC
Confidence 455554 355566543 335677888999988764 4579999999985543 6778888888887776
No 130
>PRK02794 DNA polymerase IV; Provisional
Probab=83.17 E-value=0.89 Score=48.21 Aligned_cols=29 Identities=48% Similarity=0.950 Sum_probs=26.5
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHHhhc
Q 012388 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (464)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~ 325 (464)
+..+||||++++++|.+.||+|+.||.+-
T Consensus 211 l~~L~GiG~~~~~~L~~~GI~tigdL~~l 239 (419)
T PRK02794 211 VGIIWGVGPATAARLARDGIRTIGDLQRA 239 (419)
T ss_pred hhhhCCCCHHHHHHHHHhccchHHHHhhC
Confidence 46899999999999999999999999864
No 131
>PRK09482 flap endonuclease-like protein; Provisional
Probab=82.85 E-value=0.93 Score=45.13 Aligned_cols=25 Identities=32% Similarity=0.613 Sum_probs=22.0
Q ss_pred hccCcCHHHHHHHHHc-CCCCHHHHhhc
Q 012388 299 EVWGIGPATAQKLYEK-GHRTLDDLKNE 325 (464)
Q Consensus 299 ~I~GvGpktA~~ly~~-GirtledL~~~ 325 (464)
+|+|||||||.+|.++ | |+|.+.+.
T Consensus 186 GVpGIG~KtA~~LL~~~g--sle~i~~~ 211 (256)
T PRK09482 186 GVAGIGPKSAAELLNQFR--SLENIYES 211 (256)
T ss_pred CCCCcChHHHHHHHHHhC--CHHHHHHh
Confidence 6799999999999997 7 99998754
No 132
>smart00475 53EXOc 5'-3' exonuclease.
Probab=82.71 E-value=0.95 Score=45.09 Aligned_cols=26 Identities=38% Similarity=0.592 Sum_probs=22.2
Q ss_pred hhccCcCHHHHHHHHHc-CCCCHHHHhhc
Q 012388 298 GEVWGIGPATAQKLYEK-GHRTLDDLKNE 325 (464)
Q Consensus 298 ~~I~GvGpktA~~ly~~-GirtledL~~~ 325 (464)
-+|+|||||||.+|.++ | |+|.+.+.
T Consensus 189 pGV~GIG~KtA~~Ll~~yg--sle~i~~~ 215 (259)
T smart00475 189 PGVPGIGEKTAAKLLKEFG--SLENILEN 215 (259)
T ss_pred CCCCCCCHHHHHHHHHHhC--CHHHHHHH
Confidence 36899999999999986 6 99998754
No 133
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=82.58 E-value=3.7 Score=36.74 Aligned_cols=26 Identities=15% Similarity=0.089 Sum_probs=20.3
Q ss_pred HHHHHhhhccCcCHHHHHHHHHcCCC
Q 012388 292 RTISLFGEVWGIGPATAQKLYEKGHR 317 (464)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~Gir 317 (464)
..++.|++++||||+||..+--.|+.
T Consensus 69 ~~~~~L~~l~GIG~~tA~~~l~~~~~ 94 (149)
T smart00478 69 DDREELLKLPGVGRKTANAVLSFALG 94 (149)
T ss_pred HHHHHHHcCCCCcHHHHHHHHHHHCC
Confidence 35666779999999999987665543
No 134
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=82.55 E-value=2.4 Score=46.84 Aligned_cols=51 Identities=24% Similarity=0.330 Sum_probs=37.0
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 314 (464)
..|.+|||||++...++-. .-|++ +.+++ ..++.+.+| |||+++|+++|+.
T Consensus 514 S~Ld~I~GiG~kr~~~Ll~--~Fgs~---~~ik~----As~eeL~~v-gi~~~~A~~I~~~ 564 (567)
T PRK14667 514 DILDKIKGIGEVKKEIIYR--NFKTL---YDFLK----ADDEELKKL-GIPPSVKQEVKKY 564 (567)
T ss_pred CccccCCCCCHHHHHHHHH--HhCCH---HHHHh----CCHHHHHHc-CCCHHHHHHHHHH
Confidence 5688999999988876643 33444 44432 345667799 9999999999874
No 135
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=82.45 E-value=1.4 Score=44.47 Aligned_cols=62 Identities=18% Similarity=0.221 Sum_probs=37.9
Q ss_pred hhhcCCCCCCHHHHHHHHHH---HHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCH
Q 012388 254 DQVKGLPGIGKSMQDHIQEI---VTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTL 319 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Ei---l~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~Girtl 319 (464)
++|..+ |++..=++-|.++ +..|.+.. +... ....+++.|++|+||||+||..+--.|+.-.
T Consensus 167 ~eL~~~-Gl~~~Ra~~L~~lA~~i~~g~l~l-~~~~--~~~~~~~~L~~LpGIGpwTA~~vllr~lg~~ 231 (283)
T PRK10308 167 QALKAL-GMPLKRAEALIHLANAALEGTLPL-TIPG--DVEQAMKTLQTFPGIGRWTANYFALRGWQAK 231 (283)
T ss_pred HHHHHC-CCCHHHHHHHHHHHHHHHcCCCCc-cccC--CHHHHHHHHhcCCCcCHHHHHHHHHHhCCCC
Confidence 456555 7776444444443 34577652 2111 2245788888999999999998755454443
No 136
>PRK14976 5'-3' exonuclease; Provisional
Probab=82.22 E-value=0.99 Score=45.51 Aligned_cols=26 Identities=38% Similarity=0.581 Sum_probs=21.7
Q ss_pred hccCcCHHHHHHHHHcCCCCHHHHhhc
Q 012388 299 EVWGIGPATAQKLYEKGHRTLDDLKNE 325 (464)
Q Consensus 299 ~I~GvGpktA~~ly~~GirtledL~~~ 325 (464)
+|+|||||||.+|.++ +-|+|++.+.
T Consensus 195 GVpGIG~KtA~~LL~~-~gsle~i~~~ 220 (281)
T PRK14976 195 GVKGIGPKTAIKLLNK-YGNIENIYEN 220 (281)
T ss_pred CCCcccHHHHHHHHHH-cCCHHHHHHh
Confidence 5899999999999976 3399998753
No 137
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=82.21 E-value=4.2 Score=41.13 Aligned_cols=46 Identities=24% Similarity=0.333 Sum_probs=32.4
Q ss_pred HHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCC
Q 012388 270 IQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGH 316 (464)
Q Consensus 270 I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~Gi 316 (464)
+-+.+..|.+. +..+..-....+++.|++|+||||.||+.+--.|.
T Consensus 174 ~A~~~~~g~~~-~~~l~~~~~e~a~e~L~~i~GIG~WTAe~~llf~l 219 (285)
T COG0122 174 LARAAAEGELD-LSELKPLSDEEAIEELTALKGIGPWTAEMFLLFGL 219 (285)
T ss_pred HHHHHHcCCcc-HHHhccCCHHHHHHHHHcCCCcCHHHHHHHHHHcC
Confidence 44555678633 33445445667999999999999999999764433
No 138
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=82.11 E-value=1.9 Score=48.02 Aligned_cols=52 Identities=23% Similarity=0.483 Sum_probs=38.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 314 (464)
..|.+|||||+..+.++.+.. |++..+ ... ..+.+.+|+|||+++|+.+++.
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--GSLKAI---KEA----SVEELAKVPGISKKLAEAIYEA 594 (598)
T ss_pred hhHhhCCCcCHHHHHHHHHHc--CCHHHH---HhC----CHHHHhhcCCcCHHHHHHHHHH
Confidence 568999999999999876643 554444 332 2334679999999999999863
No 139
>cd01702 PolY_Pol_eta DNA Polymerase eta. Pol eta, also called Rad30A, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Unlike other Y-family members, Pol eta can efficiently and accurately replicate DNA past UV-induced lesions. Its activity is initiated by two simultaneous interactions: the PIP box in pol eta interacting with PCNA, and the UBZ (ubiquitin-binding zinc finger) in pol eta interacting with monoubiquitin attached to PCNA. Pol eta is more efficient in copying damaged DNA than undamaged DNA and seems to recognize when a lesion has been passed, facilitating a lesion-dependent dissociation from the DNA.
Probab=81.66 E-value=1.6 Score=45.44 Aligned_cols=29 Identities=17% Similarity=0.307 Sum_probs=24.7
Q ss_pred hhhccCcCHHHHHHHHH-cCCCCHHHHhhc
Q 012388 297 FGEVWGIGPATAQKLYE-KGHRTLDDLKNE 325 (464)
Q Consensus 297 f~~I~GvGpktA~~ly~-~GirtledL~~~ 325 (464)
+..+||||+++++++.+ .||+|+.||.+-
T Consensus 184 v~~l~GiG~~~~~~ll~~~Gi~ti~dl~~~ 213 (359)
T cd01702 184 ITSIRGLGGKLGEEIIDLLGLPTEGDVAGF 213 (359)
T ss_pred HHHhCCcCHHHHHHHHHHcCCcCHHHHHhc
Confidence 35889999999988755 699999999865
No 140
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=81.50 E-value=0.96 Score=40.94 Aligned_cols=27 Identities=15% Similarity=0.004 Sum_probs=22.6
Q ss_pred hHHHHHhhhccCcCHHHHHHHHHcCCC
Q 012388 291 VRTISLFGEVWGIGPATAQKLYEKGHR 317 (464)
Q Consensus 291 ~~~l~lf~~I~GvGpktA~~ly~~Gir 317 (464)
..+.+.|++++||||+||..+--.++.
T Consensus 79 ~~~~~~L~~l~GIG~~tA~~~l~~~~~ 105 (158)
T cd00056 79 PDAREELLALPGVGRKTANVVLLFALG 105 (158)
T ss_pred cccHHHHHcCCCCCHHHHHHHHHHHCC
Confidence 457888899999999999998766555
No 141
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=81.23 E-value=0.67 Score=51.02 Aligned_cols=63 Identities=17% Similarity=0.211 Sum_probs=46.7
Q ss_pred hhccCcCHHHHHHHHHcC-CCCHHHHhh--ccCcchHHHhhHhhHHhhccCCCHHHHHHHHHHHHH
Q 012388 298 GEVWGIGPATAQKLYEKG-HRTLDDLKN--EDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQK 360 (464)
Q Consensus 298 ~~I~GvGpktA~~ly~~G-irtledL~~--~~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~iv~~ 360 (464)
++|-|+|++++.+|++.| ++++.||-+ ...|..+.+||-|..+.+...|-...-..+..++-.
T Consensus 428 mdI~GlGe~~i~~L~~~G~i~~~~Diy~L~~~~l~~l~gfgeks~~nll~aIe~sk~~~l~r~l~a 493 (562)
T PRK08097 428 LGLDGIGEGTWRALHQTGLFEHLFSWLALTPEQLANTPGIGKARAEQLWHQFNLARQQPFSRWLKA 493 (562)
T ss_pred cCCCCcCHHHHHHHHHcCCcCCHHHHhcCCHHHHhcCcCccHHHHHHHHHHHHHHcCCCHHHHHHH
Confidence 589999999999999997 599999974 335667778999999988766543333334444443
No 142
>PRK07758 hypothetical protein; Provisional
Probab=80.91 E-value=0.93 Score=38.20 Aligned_cols=45 Identities=11% Similarity=0.234 Sum_probs=37.5
Q ss_pred ccCcCHHHHHHHHHcCCCCHHHHhhc--cCcchHHHhhHhhHHhhcc
Q 012388 300 VWGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDIKT 344 (464)
Q Consensus 300 I~GvGpktA~~ly~~GirtledL~~~--~~L~~~q~~Glk~~ed~~~ 344 (464)
.++++......|...||.|++||..- ..|..+.+||-+..++|.+
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 35788999999999999999999853 4688889999998887764
No 143
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=80.77 E-value=0.98 Score=43.35 Aligned_cols=51 Identities=24% Similarity=0.311 Sum_probs=36.7
Q ss_pred HHHHHhhhccCcCHHHHHHHHHc-CCCCHHHHhhc---cCcchHHHhhHhhHHhh
Q 012388 292 RTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNE---DSLTHSQRLGLKYFDDI 342 (464)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~-GirtledL~~~---~~L~~~q~~Glk~~ed~ 342 (464)
..+..|.+|-|||||+|-.+..- ....|-+.... ..|++..++|-|..+.|
T Consensus 70 ~lF~~LisVnGIGpK~ALaiLs~~~~~~l~~aI~~~d~~~L~k~PGIGkKtAeri 124 (201)
T COG0632 70 ELFRLLISVNGIGPKLALAILSNLDPEELAQAIANEDVKALSKIPGIGKKTAERI 124 (201)
T ss_pred HHHHHHHccCCccHHHHHHHHcCCCHHHHHHHHHhcChHhhhcCCCCCHHHHHHH
Confidence 36777779999999999999764 44444443322 25888999999986554
No 144
>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=80.52 E-value=1.3 Score=43.52 Aligned_cols=26 Identities=35% Similarity=0.460 Sum_probs=22.3
Q ss_pred hccCcCHHHHHHHHHcCCCCHHHHhhc
Q 012388 299 EVWGIGPATAQKLYEKGHRTLDDLKNE 325 (464)
Q Consensus 299 ~I~GvGpktA~~ly~~GirtledL~~~ 325 (464)
+|+|||||||.+|.++ +.|+|++.+.
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 145
>PRK13300 tRNA CCA-pyrophosphorylase; Provisional
Probab=79.72 E-value=6.3 Score=42.37 Aligned_cols=45 Identities=24% Similarity=0.289 Sum_probs=31.0
Q ss_pred HHHHHHHhhhcCCCEEEEEcccccccCCcC--CCccEEEeCCCcchh
Q 012388 355 ERLLQKAGEEVLPEVIILCGGSYRRGKASC--GDLDVVIMHPDRKSH 399 (464)
Q Consensus 355 ~~iv~~~~~~~~p~~~v~~~GsyRRgke~~--gDvDiLit~~d~~~~ 399 (464)
...+++.+.+....+.|.+.|||.||.-.- +||||.|.-|+....
T Consensus 28 ~~~L~~~~~~~~~~~~V~l~GS~ArgT~L~GdsDIDIFv~fp~~~~~ 74 (447)
T PRK13300 28 IERLEEAIKELGLDAEVELVGSTARGTWLSGDRDIDIFVLFPKDTSR 74 (447)
T ss_pred HHHHHHHHHhcCCceEEEEEeeecCCcccCCCCceeEEEEeCCCCCH
Confidence 334444443322348899999999998776 489999988765543
No 146
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=79.50 E-value=3.1 Score=46.85 Aligned_cols=51 Identities=29% Similarity=0.386 Sum_probs=37.6
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (464)
..|..|||||++.+.++.+- -|++ +.+.+. ..+.+.+|+|+|+++|+++++
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 57899999999998877653 3544 444432 233457899999999999986
No 147
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=79.36 E-value=3.2 Score=46.71 Aligned_cols=55 Identities=16% Similarity=0.210 Sum_probs=37.9
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCC
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHR 317 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~Gir 317 (464)
..|.+|||||+.-+.++-. .-|++. .+++ ..++.+.+|+|||.+.|+++|...-|
T Consensus 608 s~L~~IpGiG~kr~~~LL~--~FgS~~---~i~~----As~eel~~v~gi~~~~A~~i~~~~~~ 662 (691)
T PRK14672 608 LSFERLPHVGKVRAHRLLA--HFGSFR---SLQS----ATPQDIATAIHIPLTQAHTILHAATR 662 (691)
T ss_pred cccccCCCCCHHHHHHHHH--HhcCHH---HHHh----CCHHHHHhCCCCCHHHHHHHHHHhhc
Confidence 4577999999987776533 334444 4332 24555679999999999999987433
No 148
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=78.97 E-value=3 Score=43.26 Aligned_cols=59 Identities=24% Similarity=0.351 Sum_probs=38.6
Q ss_pred CCccccch--hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012388 246 LPFKIESA--DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (464)
Q Consensus 246 lp~~I~s~--~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (464)
++.+|... .=+.++|+|++.+|+.+-+ +-|+++.+ .+. ..+.|.+|.|||+++|+.+++
T Consensus 277 ld~~v~prGyRiLs~IPrl~k~iAk~Ll~--~FGSL~~I---l~A----s~eeL~~VeGIGe~rA~~I~e 337 (352)
T PRK13482 277 LDTPVSPRGYRLLSKIPRLPSAVIENLVE--HFGSLQGL---LAA----SIEDLDEVEGIGEVRARAIRE 337 (352)
T ss_pred cccccCCcHHHHHhcCCCCCHHHHHHHHH--HcCCHHHH---HcC----CHHHHhhCCCcCHHHHHHHHH
Confidence 33444432 3578999999988887654 33555444 321 244577999999999998644
No 149
>COG1746 CCA1 tRNA nucleotidyltransferase (CCA-adding enzyme) [Translation, ribosomal structure and biogenesis]
Probab=78.30 E-value=7.6 Score=41.23 Aligned_cols=49 Identities=27% Similarity=0.375 Sum_probs=35.7
Q ss_pred HHHHHHHHHHhhhcCCCEEEEEcccccccCCcC--CCccEEEeCCCcchhh
Q 012388 352 EQMERLLQKAGEEVLPEVIILCGGSYRRGKASC--GDLDVVIMHPDRKSHK 400 (464)
Q Consensus 352 ~~i~~iv~~~~~~~~p~~~v~~~GsyRRgke~~--gDvDiLit~~d~~~~~ 400 (464)
+.+...+.+++.+....+.+.++|||.||-=-. +|||+-|.-|...+..
T Consensus 29 e~l~~~~~~~~~e~~~~aev~lVGS~AkgTwL~gd~DIDvFi~Fp~d~~~e 79 (443)
T COG1746 29 EELRERINEIIEELGIDAEVVLVGSYAKGTWLRGDHDIDVFIAFPKDTSEE 79 (443)
T ss_pred HHHHHHHHHHHHhcCCcceEEEEeecccCcccCCCcceeEEEECCCCCCHH
Confidence 334455555565566788999999999997554 7899999888765443
No 150
>COG0389 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]
Probab=78.27 E-value=2.1 Score=44.56 Aligned_cols=28 Identities=43% Similarity=0.697 Sum_probs=26.1
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHHhh
Q 012388 297 FGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (464)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~ 324 (464)
+..+||||+.+++++...||+|+-||.+
T Consensus 178 v~~~~GvG~~~~~~l~~~Gi~ti~dl~~ 205 (354)
T COG0389 178 VLEFWGVGKVTAEKLRRLGISTIGDLAE 205 (354)
T ss_pred hhhhCCCCHHHHHHHHHcCChhHHHHHh
Confidence 3489999999999999999999999987
No 151
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=78.07 E-value=2.7 Score=40.62 Aligned_cols=53 Identities=19% Similarity=0.253 Sum_probs=33.9
Q ss_pred CCHHHHHHHHHHHHh-CCchhhHHHH--hhchhHHHHHhh-hccCcCHHHHHHHHH-cCCC
Q 012388 262 IGKSMQDHIQEIVTT-GKLSKLEHFE--KDEKVRTISLFG-EVWGIGPATAQKLYE-KGHR 317 (464)
Q Consensus 262 IG~~ia~kI~Eil~t-G~~~~le~l~--~~~~~~~l~lf~-~I~GvGpktA~~ly~-~Gir 317 (464)
+-..=|+.|.++... |. ++.+. ........+.|. ++||||+|||.-+-. .|++
T Consensus 85 f~~~KAk~I~~~~~~~~~---l~~~~~~~~~~~~~R~~Ll~~lpGIG~KTAd~vL~~~~~~ 142 (208)
T PRK01229 85 FYNKRAEYIVEARKLYGK---LKEIIKADKDQFEAREFLVKNIKGIGYKEASHFLRNVGYE 142 (208)
T ss_pred cHHHHHHHHHHHHHHHHH---HHHHHhccCCchHHHHHHHHcCCCCcHHHHHHHHHHccCC
Confidence 445556666665543 33 22222 334457888888 999999999999773 4553
No 152
>PRK00076 recR recombination protein RecR; Reviewed
Probab=78.07 E-value=1.7 Score=41.48 Aligned_cols=21 Identities=38% Similarity=0.618 Sum_probs=18.6
Q ss_pred HHHHHhhhccCcCHHHHHHHH
Q 012388 292 RTISLFGEVWGIGPATAQKLY 312 (464)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly 312 (464)
..++.|.++||||+|+|+++-
T Consensus 8 ~Li~~l~~LPGIG~KsA~Rla 28 (196)
T PRK00076 8 KLIEALRKLPGIGPKSAQRLA 28 (196)
T ss_pred HHHHHHHHCCCCCHHHHHHHH
Confidence 467889999999999999984
No 153
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=78.01 E-value=1.8 Score=41.38 Aligned_cols=21 Identities=38% Similarity=0.602 Sum_probs=18.5
Q ss_pred HHHHHhhhccCcCHHHHHHHH
Q 012388 292 RTISLFGEVWGIGPATAQKLY 312 (464)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly 312 (464)
..++.|.++||||+|+|+++-
T Consensus 8 ~Li~~l~~LPGIG~KsA~RlA 28 (195)
T TIGR00615 8 KLIESLKKLPGIGPKSAQRLA 28 (195)
T ss_pred HHHHHHHHCCCCCHHHHHHHH
Confidence 467889999999999999983
No 154
>PRK10702 endonuclease III; Provisional
Probab=77.50 E-value=5.1 Score=38.66 Aligned_cols=44 Identities=14% Similarity=0.305 Sum_probs=31.8
Q ss_pred hhHHHHHHHHHHHh-cCCccc-cchhhhcCCCCCCHHHHHHHHHHH
Q 012388 231 RRSFSYYKAIPVIE-KLPFKI-ESADQVKGLPGIGKSMQDHIQEIV 274 (464)
Q Consensus 231 ~r~~aY~rAa~~l~-~lp~~I-~s~~~l~~lpgIG~~ia~kI~Eil 274 (464)
.|+....+++..|. .+...+ .+.++|.+|||||.++|+.|.-+.
T Consensus 84 ~kA~~l~~~a~~i~~~~~~~~p~~~~~Ll~lpGVG~ktA~~ill~a 129 (211)
T PRK10702 84 SKAENVIKTCRILLEQHNGEVPEDRAALEALPGVGRKTANVVLNTA 129 (211)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCchHHHHhcCCcccHHHHHHHHHHH
Confidence 36666777777764 334433 356889999999999999986543
No 155
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=77.46 E-value=6.6 Score=39.95 Aligned_cols=88 Identities=22% Similarity=0.353 Sum_probs=54.9
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--C---C---CCHHHHhhc
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--G---H---RTLDDLKNE 325 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--G---i---rtledL~~~ 325 (464)
..+..+||||+.++++..+ -.+..++++.+-.+ +.+.+++|+++++|..||+. | . .|.-++...
T Consensus 6 ~~l~~l~gIg~~~a~~L~~----~Gi~t~~dl~~~~~----~~L~~~~g~~~~~a~~l~~~a~~~~~~~~~~t~~~l~~~ 77 (317)
T PRK04301 6 KDLEDLPGVGPATAEKLRE----AGYDTVEAIAVASP----KELSEAAGIGESTAAKIIEAAREAADIGGFETALEVLER 77 (317)
T ss_pred ccHhhcCCCCHHHHHHHHH----cCCCCHHHHHcCCH----HHHHHhcCCCHHHHHHHHHHHHHhhccccCccHHHHHHh
Confidence 3578999999888776554 35566777755333 23347789999999999974 4 3 455555332
Q ss_pred -cCcchHHHhhHhhHHhhcc-CCCHHH
Q 012388 326 -DSLTHSQRLGLKYFDDIKT-RIPRHE 350 (464)
Q Consensus 326 -~~L~~~q~~Glk~~ed~~~-~i~r~E 350 (464)
.++.. -..|..-.+++.. .||...
T Consensus 78 ~ks~~~-~~Tg~~~lD~~l~GGi~~g~ 103 (317)
T PRK04301 78 RKNVGK-ITTGSKELDELLGGGIETQS 103 (317)
T ss_pred hccCCc-cCCCCHHHHHHhcCCccCCc
Confidence 22222 2346666677653 566544
No 156
>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=77.44 E-value=5.9 Score=31.67 Aligned_cols=29 Identities=31% Similarity=0.510 Sum_probs=24.5
Q ss_pred EEEEcccccccCCc-CCCccEEEeCCCcch
Q 012388 370 IILCGGSYRRGKAS-CGDLDVVIMHPDRKS 398 (464)
Q Consensus 370 ~v~~~GsyRRgke~-~gDvDiLit~~d~~~ 398 (464)
.+.+-|||-||..+ ..||||+|-.++...
T Consensus 20 ~i~LfGS~arg~~~~~SDiDl~vi~~~~~~ 49 (93)
T cd05403 20 KVYLFGSYARGDARPDSDIDLLVIFDDPLD 49 (93)
T ss_pred EEEEEeeeecCCCCCCCCeeEEEEeCCCCC
Confidence 78899999999975 789999998776654
No 157
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=77.17 E-value=2.5 Score=37.22 Aligned_cols=26 Identities=42% Similarity=0.542 Sum_probs=23.6
Q ss_pred cCcCHHHHHHHHHcCCCCHHHHhhcc
Q 012388 301 WGIGPATAQKLYEKGHRTLDDLKNED 326 (464)
Q Consensus 301 ~GvGpktA~~ly~~GirtledL~~~~ 326 (464)
||+|++++.+|-+.||.|.+||.+.+
T Consensus 1 pgi~~~~~~~L~~~GI~t~~~Ll~~~ 26 (122)
T PF14229_consen 1 PGIGPKEAAKLKAAGIKTTGDLLEAG 26 (122)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHHcC
Confidence 79999999999888999999998653
No 158
>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=76.78 E-value=2.1 Score=43.53 Aligned_cols=28 Identities=39% Similarity=0.550 Sum_probs=25.6
Q ss_pred hhccCcCHHHHHHHHHcCCCCHHHHhhc
Q 012388 298 GEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (464)
Q Consensus 298 ~~I~GvGpktA~~ly~~GirtledL~~~ 325 (464)
..+||||.+++++|.+.||+|+.||.+.
T Consensus 174 ~~l~gig~~~~~~L~~~Gi~ti~dl~~~ 201 (334)
T cd03586 174 RKIPGVGKVTAEKLKELGIKTIGDLAKL 201 (334)
T ss_pred hhhCCcCHHHHHHHHHcCCcCHHHHHcC
Confidence 5789999999999999999999999864
No 159
>TIGR01084 mutY A/G-specific adenine glycosylase. This equivalog model identifies mutY members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=76.43 E-value=5.5 Score=40.10 Aligned_cols=66 Identities=14% Similarity=0.233 Sum_probs=41.4
Q ss_pred hhHHHHHHHHHHHhc-CCccc-cchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCc
Q 012388 231 RRSFSYYKAIPVIEK-LPFKI-ESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGI 303 (464)
Q Consensus 231 ~r~~aY~rAa~~l~~-lp~~I-~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~Gv 303 (464)
.|++.-.+||..|.. ....+ .+.++|.+|||||..+|+.|.-|. -|...-+ ....+...+..++|+
T Consensus 80 ~RAr~L~~~A~~i~~~~~g~~p~~~~~L~~LpGIG~~TA~~Il~~a-~~~~~~~------vD~~v~RVl~Rl~~~ 147 (275)
T TIGR01084 80 ARARNLHKAAQEVVEEFGGEFPQDFEDLAALPGVGRYTAGAILSFA-LNKPYPI------LDGNVKRVLSRLFAV 147 (275)
T ss_pred HHHHHHHHHHHHHHHHcCCCCcHHHHHHHhCCCCCHHHHHHHHHHH-CCCCCCc------chHhHHHHHHHHccC
Confidence 377777888887754 11111 346889999999999999987554 3332111 223456666666555
No 160
>PRK00254 ski2-like helicase; Provisional
Probab=76.17 E-value=13 Score=42.26 Aligned_cols=53 Identities=21% Similarity=0.354 Sum_probs=38.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 314 (464)
-.|.+|||||+..+.+ +++.| +.-++++.... .+.+..|+|||.++|+++++.
T Consensus 645 ~~L~~ipgig~~~~~~---l~~~g-~~s~~~i~~a~----~~el~~~~gi~~~~a~~i~~~ 697 (720)
T PRK00254 645 LELMRLPMIGRKRARA---LYNAG-FRSIEDIVNAK----PSELLKVEGIGAKIVEGIFKH 697 (720)
T ss_pred hhhhcCCCCCHHHHHH---HHHcc-CCCHHHHHhCC----HHHHhcCCCCCHHHHHHHHHH
Confidence 3577899999987765 55555 45555555432 233469999999999999986
No 161
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=76.11 E-value=10 Score=38.74 Aligned_cols=71 Identities=15% Similarity=0.217 Sum_probs=48.8
Q ss_pred CCCCCeEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccchH
Q 012388 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWL 91 (464)
Q Consensus 17 ~~F~g~~vy~~~~~~g~~R~~~l~~~i~~~Gg~V~~~ls~~VTHVV~~~~~~~~~~l~~~~~~~~~~~iV~~~Wl 91 (464)
.+|.|.+|.|-+. +.. .+.-+++++..+||.|.+.++.+++.||+.+...... +.+++...+.+|++-+=|
T Consensus 231 ~l~~g~~~v~TG~-l~~-~R~e~~~~~~~~G~~v~~sVs~~t~~lv~g~~~~~ss--K~~kA~~~gi~ii~e~~f 301 (313)
T PRK06063 231 PLVQGMRVALSAE-VSR-THEELVERILHAGLAYSDSVDRDTSLVVCNDPAPEQG--KGYHARQLGVPVLDEAAF 301 (313)
T ss_pred cccCCCEEEEecC-CCC-CHHHHHHHHHHcCCEecCccccCccEEEECCCCCccc--HHHHHHHcCCccccHHHH
Confidence 4689999999875 443 3467899999999999999999999999975432101 122233345556654433
No 162
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=74.93 E-value=2.2 Score=43.38 Aligned_cols=25 Identities=48% Similarity=0.740 Sum_probs=21.9
Q ss_pred hccCcCHHHHHHHHHc-CCCCHHHHhhc
Q 012388 299 EVWGIGPATAQKLYEK-GHRTLDDLKNE 325 (464)
Q Consensus 299 ~I~GvGpktA~~ly~~-GirtledL~~~ 325 (464)
+|+|||||||.+|.++ | |++.|.+.
T Consensus 202 GV~GIG~ktA~~Ll~~~g--s~e~i~~~ 227 (310)
T COG0258 202 GVKGIGPKTALKLLQEYG--SLEGLYEN 227 (310)
T ss_pred CCCCcCHHHHHHHHHHhC--CHHHHHHh
Confidence 5999999999999998 8 88888754
No 163
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=73.07 E-value=4.2 Score=39.51 Aligned_cols=22 Identities=23% Similarity=0.210 Sum_probs=18.0
Q ss_pred HHHHHhhhccCcCHHHHHHHHH
Q 012388 292 RTISLFGEVWGIGPATAQKLYE 313 (464)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~ 313 (464)
...+.|++++|||++||..+.-
T Consensus 118 ~~re~Ll~l~GIG~kTAd~iLl 139 (218)
T PRK13913 118 VTREWLLDQKGIGKESADAILC 139 (218)
T ss_pred hHHHHHHcCCCccHHHHHHHHH
Confidence 3567788999999999998643
No 164
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=72.97 E-value=8.3 Score=39.26 Aligned_cols=48 Identities=17% Similarity=0.088 Sum_probs=39.6
Q ss_pred CCCCCeEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcC
Q 012388 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMD 65 (464)
Q Consensus 17 ~~F~g~~vy~~~~~~g~~R~~~l~~~i~~~Gg~V~~~ls~~VTHVV~~~ 65 (464)
..|.|.++.|-+.--+. .+..+++++..+||.|.++++.++|.+|+.+
T Consensus 219 ~~l~g~~~vfTG~l~~~-~R~~~~~~~~~~Gg~v~~sVs~~t~~lV~G~ 266 (309)
T PRK06195 219 TAFKEEVVVFTGGLASM-TRDEAMILVRRLGGTVGSSVTKKTTYLVTNT 266 (309)
T ss_pred ccccCCEEEEccccCCC-CHHHHHHHHHHhCCEecCCcccCceEEEECC
Confidence 47999999998753223 3456899999999999999999999999864
No 165
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=72.94 E-value=5.2 Score=40.17 Aligned_cols=67 Identities=18% Similarity=0.296 Sum_probs=48.9
Q ss_pred hhcCCCCCCH---HHHHHHHHHHH-hCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHH
Q 012388 255 QVKGLPGIGK---SMQDHIQEIVT-TGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDL 322 (464)
Q Consensus 255 ~l~~lpgIG~---~ia~kI~Eil~-tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL 322 (464)
+++++ |+|= -|++-.++|++ .|...-|..++..+-..+.+.|+.+||||||.|.=+-=+|+.-+.-+
T Consensus 175 ~LR~~-gfGYRAkYI~~ta~~l~~~~g~~~wLqsl~~~~yeear~~L~~lpGVG~KVADCI~Lm~l~~~~~V 245 (323)
T KOG2875|consen 175 ELRKL-GFGYRAKYISATARALQEKQGGLAWLQSLRKSSYEEAREALCSLPGVGPKVADCICLMSLDKLSAV 245 (323)
T ss_pred HHHHc-CcchhHHHHHHHHHHHHHhcccchHHHHHhcccHHHHHHHHhcCCCCcchHhhhhhhhhcCCCCcc
Confidence 45555 6774 35666667775 56678888888866677999999999999999997766555554444
No 166
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=72.81 E-value=4.8 Score=38.96 Aligned_cols=88 Identities=22% Similarity=0.280 Sum_probs=50.9
Q ss_pred CCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--CCCCHHHHhhccCc-chHHHhh--
Q 012388 261 GIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRTLDDLKNEDSL-THSQRLG-- 335 (464)
Q Consensus 261 gIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--GirtledL~~~~~L-~~~q~~G-- 335 (464)
|+-..=|+.|.++.+ .-+|+... +....++.|+++||||+|||.-.... |+-++ -=+.-+ .-..++|
T Consensus 80 Glyr~KAk~I~~~~~----~l~e~~~g-~vP~~~~eL~~LPGVGrKTAnvVL~~a~g~p~i---~VDTHV~Rvs~R~gl~ 151 (211)
T COG0177 80 GLYRNKAKNIKELAR----ILLEKFGG-EVPDTREELLSLPGVGRKTANVVLSFAFGIPAI---AVDTHVHRVSNRLGLV 151 (211)
T ss_pred CCcHHHHHHHHHHHH----HHHHHcCC-CCCchHHHHHhCCCcchHHHHHHHHhhcCCCcc---cccchHHHHHHHhCCC
Confidence 555555666665543 22333333 44567777889999999999987765 44322 111111 1123344
Q ss_pred -----HhhHHhhccCCCHHHHHHHHH
Q 012388 336 -----LKYFDDIKTRIPRHEVEQMER 356 (464)
Q Consensus 336 -----lk~~ed~~~~i~r~Ea~~i~~ 356 (464)
.+..+++.+.||++.-..+..
T Consensus 152 ~~~~p~~ve~~L~~~iP~~~~~~~h~ 177 (211)
T COG0177 152 PGKTPEEVEEALMKLIPKELWTDLHH 177 (211)
T ss_pred CCCCHHHHHHHHHHHCCHHHHHHHHH
Confidence 345667788888777666533
No 167
>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=72.67 E-value=5.2 Score=31.38 Aligned_cols=22 Identities=18% Similarity=0.376 Sum_probs=19.7
Q ss_pred hhhcCCCCCCHHHHHHHHHHHH
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVT 275 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~ 275 (464)
+++..+||+|++..+.|.+.|+
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 6799999999999999998775
No 168
>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=72.28 E-value=13 Score=33.22 Aligned_cols=52 Identities=25% Similarity=0.353 Sum_probs=38.2
Q ss_pred CEEEEEcccccccCCc-CCCccEEEeCCCcc--h----hhhHHHHHHHHHHhccccccc
Q 012388 368 EVIILCGGSYRRGKAS-CGDLDVVIMHPDRK--S----HKGFLSKYVKKLKEMKFLRED 419 (464)
Q Consensus 368 ~~~v~~~GsyRRgke~-~gDvDiLit~~d~~--~----~~~~l~~lv~~L~~~g~l~~~ 419 (464)
.+-..++|||=|+..+ ..|+|..|-+++.. . ...|..++++.|.+.||-.|.
T Consensus 49 ~~a~lalGS~GR~E~~~~sDqD~alv~~d~~~~~~~~~f~~~a~~~~~~L~~~G~~~C~ 107 (138)
T PF03445_consen 49 PFAWLALGSYGRREQTLYSDQDNALVFEDEESEEDRAYFEAFAERLVDALDECGFPPCP 107 (138)
T ss_pred CEEEEEECcccccCCCcCccccceeeecCccchhHHHHHHHHHHHHHHHHHHcCCCCCC
Confidence 3456678998777655 57999999998822 1 235678889999999997764
No 169
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=72.04 E-value=3.6 Score=46.10 Aligned_cols=47 Identities=26% Similarity=0.362 Sum_probs=33.1
Q ss_pred HHHHhhhccCcCHHHHHHHHHcCCCCHHHHhhcc--CcchHHHhhHhhHHhh
Q 012388 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDI 342 (464)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~GirtledL~~~~--~L~~~q~~Glk~~ed~ 342 (464)
....|.+|+||||++|+.|++ .+.|+++|.++. .|+.. +|.+..+.|
T Consensus 567 ~~s~L~~I~GIG~k~a~~Ll~-~Fgs~~~i~~As~eeL~~v--ig~k~A~~I 615 (621)
T PRK14671 567 LQTELTDIAGIGEKTAEKLLE-HFGSVEKVAKASLEELAAV--AGPKTAETI 615 (621)
T ss_pred hhhhhhcCCCcCHHHHHHHHH-HcCCHHHHHhCCHHHHHHH--hCHHHHHHH
Confidence 456678999999999999988 455899998752 23333 555554444
No 170
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=71.85 E-value=2.1 Score=47.42 Aligned_cols=43 Identities=19% Similarity=0.345 Sum_probs=30.3
Q ss_pred HHhhhccCcCHHHHHHHHHcCCCCHHHHhhcc--CcchHHHhhHhh
Q 012388 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKY 338 (464)
Q Consensus 295 ~lf~~I~GvGpktA~~ly~~GirtledL~~~~--~L~~~q~~Glk~ 338 (464)
..|.+|+||||++.++|++ -+.|+++++++. .|....+++.+.
T Consensus 514 s~L~~I~GiG~kr~~~LL~-~Fgs~~~I~~As~eeL~~v~gi~~~~ 558 (574)
T PRK14670 514 LNYTKIKGIGEKKAKKILK-SLGTYKDILLLNEDEIAEKMKINIKM 558 (574)
T ss_pred cccccCCCCCHHHHHHHHH-HhCCHHHHHhCCHHHHHhCCCCCHHH
Confidence 3566999999999999998 566888888753 244443444333
No 171
>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=71.77 E-value=3.3 Score=35.55 Aligned_cols=26 Identities=23% Similarity=0.484 Sum_probs=21.4
Q ss_pred HHHHhhhccCcCHHHHHHHHHc-CCCC
Q 012388 293 TISLFGEVWGIGPATAQKLYEK-GHRT 318 (464)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~-Girt 318 (464)
+.-.|++|+|||+++|..+.+. |+..
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 5566789999999999999986 8854
No 172
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=71.68 E-value=2.5 Score=46.79 Aligned_cols=45 Identities=20% Similarity=0.372 Sum_probs=31.4
Q ss_pred HHhhhccCcCHHHHHHHHHcCCCCHHHHhhcc--CcchHHHhhHhhHHh
Q 012388 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDD 341 (464)
Q Consensus 295 ~lf~~I~GvGpktA~~ly~~GirtledL~~~~--~L~~~q~~Glk~~ed 341 (464)
..|.+|+||||++.++|++ -+.|++.++++. .|... ++|.+..+.
T Consensus 514 S~Ld~I~GiG~kr~~~Ll~-~Fgs~~~ik~As~eeL~~v-gi~~~~A~~ 560 (567)
T PRK14667 514 DILDKIKGIGEVKKEIIYR-NFKTLYDFLKADDEELKKL-GIPPSVKQE 560 (567)
T ss_pred CccccCCCCCHHHHHHHHH-HhCCHHHHHhCCHHHHHHc-CCCHHHHHH
Confidence 4566999999999999998 566888888753 34444 444444333
No 173
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=71.45 E-value=7.6 Score=35.02 Aligned_cols=77 Identities=17% Similarity=0.242 Sum_probs=44.8
Q ss_pred HHHHHHHcCCChhHHHHHHHHHHHhcCCccc-----cchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHH
Q 012388 220 LINIYRALGEDRRSFSYYKAIPVIEKLPFKI-----ESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTI 294 (464)
Q Consensus 220 la~~~e~~g~~~r~~aY~rAa~~l~~lp~~I-----~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l 294 (464)
|.++..-.|-+.|+.....++..+..-.... +..++|.+|||||+.+|+.|.-+.- | . +.+-- ...+.
T Consensus 44 l~~~~~~~G~~~kA~~i~~~a~~~~~~~~~~~~~~~~~~~~L~~l~GIG~~tA~~~l~~~~-~-~---~~~pv--D~~v~ 116 (158)
T cd00056 44 LRELIRSLGYRRKAKYLKELARAIVEGFGGLVLDDPDAREELLALPGVGRKTANVVLLFAL-G-P---DAFPV--DTHVR 116 (158)
T ss_pred HHHHHHhcChHHHHHHHHHHHHHHHHHcCCccCCCcccHHHHHcCCCCCHHHHHHHHHHHC-C-C---CCCcc--chhHH
Confidence 3333333342457777777777775432221 2346799999999999998875532 2 1 22211 33466
Q ss_pred HHhhhccCc
Q 012388 295 SLFGEVWGI 303 (464)
Q Consensus 295 ~lf~~I~Gv 303 (464)
+.+..+.++
T Consensus 117 r~~~~~~~~ 125 (158)
T cd00056 117 RVLKRLGLI 125 (158)
T ss_pred HHHHHhCCC
Confidence 666666554
No 174
>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=71.10 E-value=16 Score=33.54 Aligned_cols=52 Identities=23% Similarity=0.291 Sum_probs=36.8
Q ss_pred CEEEEEcccccccCC-cCCCccEEEeCCCcch-----hhhHHHHHHHHHHhccccccc
Q 012388 368 EVIILCGGSYRRGKA-SCGDLDVVIMHPDRKS-----HKGFLSKYVKKLKEMKFLRED 419 (464)
Q Consensus 368 ~~~v~~~GsyRRgke-~~gDvDiLit~~d~~~-----~~~~l~~lv~~L~~~g~l~~~ 419 (464)
++-+...|||-|+.. -..|+|+++-+++... ...+-.++++.|...|+..+.
T Consensus 55 ~~~~la~Gs~GR~E~~~~SD~D~~~v~~~~~~~~~~~~~~l~~~i~~~L~~~g~~~~~ 112 (172)
T cd05401 55 PFALLALGSYGRGELNPSSDQDLLLLYDDDGDEVAAYFEELAERLIKILSEAGGPYCL 112 (172)
T ss_pred cEEEEEeCCcccCCcCCCcCcceEEEeCCCCchHHHHHHHHHHHHHHHHHhCCCCCCC
Confidence 356777899977655 4689999998876532 235666777778777776653
No 175
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=71.04 E-value=3.5 Score=42.10 Aligned_cols=54 Identities=28% Similarity=0.405 Sum_probs=40.5
Q ss_pred hhHHHHHhhhccCcCHHHHHHHHHc---CC-CCHHHHhhccC------cchHHHhhHhhHHhhc
Q 012388 290 KVRTISLFGEVWGIGPATAQKLYEK---GH-RTLDDLKNEDS------LTHSQRLGLKYFDDIK 343 (464)
Q Consensus 290 ~~~~l~lf~~I~GvGpktA~~ly~~---Gi-rtledL~~~~~------L~~~q~~Glk~~ed~~ 343 (464)
+....+...++||+||+.|++|-+- |. +-+++++++.+ ++..-++|.++.+.|.
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 4557788889999999999998862 65 77888886432 4566677777777764
No 176
>KOG3548 consensus DNA damage checkpoint protein RHP9/CRB2/53BP1 [Replication, recombination and repair]
Probab=70.89 E-value=4.7 Score=46.42 Aligned_cols=91 Identities=15% Similarity=0.112 Sum_probs=53.7
Q ss_pred CCCCCeEEEEecCCCCchHHHHHHHHHHhcCCEEEee-cCCCccEEEEcCChHHHHHHH---------------------
Q 012388 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEK-LSKKVTHVLAMDLEALLQQVS--------------------- 74 (464)
Q Consensus 17 ~~F~g~~vy~~~~~~g~~R~~~l~~~i~~~Gg~V~~~-ls~~VTHVV~~~~~~~~~~l~--------------------- 74 (464)
.+|.||++.|-...-. .....+-+..+||.|.+. |..=-+|=.... -..++.|.
T Consensus 924 niFd~cvF~lTsa~~s---d~~~r~s~e~~gg~vle~gl~~~Fn~p~~g~-~~~lr~Ln~~q~~ks~~qalLIsdth~Rt 999 (1176)
T KOG3548|consen 924 NIFDGCVFMLTSANRS---DSASRPSMEKHGGLVLEKGLMNLFNTPFKGG-GIVLRQLNSFQERKSNYQALLISDTHYRT 999 (1176)
T ss_pred chhcceeEEEeccccc---hhhhhhhhhccCChhhhccccccccccccCC-cchHHhhhHHhhhccccceeEeehhhhHH
Confidence 7899999888543211 223344445588888765 322234433211 11111111
Q ss_pred --HHhhhccCccccccchHHHHHhcCCCCCccccccccC
Q 012388 75 --KQHLARFKGSVIRYQWLEDSLRLGEKVSEDLYRIKLD 111 (464)
Q Consensus 75 --~~~~~~~~~~iV~~~Wl~ec~k~g~lvdee~y~l~~~ 111 (464)
.--.-+++..-|...||.+|++.++.||-.+|+|...
T Consensus 1000 ~KYLeaLA~giPcVh~~fI~aC~e~nr~Vdy~~YLLpsG 1038 (1176)
T KOG3548|consen 1000 HKYLEALARGIPCVHNTFIQACGEQNRCVDYTDYLLPSG 1038 (1176)
T ss_pred HHHHHHHHcCCCcccHHHHHHHHhccccccchhhcccCc
Confidence 1001123567899999999999999999999998643
No 177
>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=70.86 E-value=2.1 Score=28.72 Aligned_cols=18 Identities=22% Similarity=0.501 Sum_probs=14.4
Q ss_pred hhcCCCCCCHHHHHHHHH
Q 012388 255 QVKGLPGIGKSMQDHIQE 272 (464)
Q Consensus 255 ~l~~lpgIG~~ia~kI~E 272 (464)
.+.+++|||+++++++..
T Consensus 12 pi~~~~GIG~kt~~kL~~ 29 (32)
T PF11798_consen 12 PIRKFWGIGKKTAKKLNK 29 (32)
T ss_dssp BGGGSTTS-HHHHHHHHC
T ss_pred CHHhhCCccHHHHHHHHH
Confidence 478899999999998764
No 178
>PRK13910 DNA glycosylase MutY; Provisional
Probab=70.68 E-value=8.9 Score=38.89 Aligned_cols=68 Identities=16% Similarity=0.197 Sum_probs=45.7
Q ss_pred hHHHHHHHHHHHh-cCCccc-cchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHH
Q 012388 232 RSFSYYKAIPVIE-KLPFKI-ESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPA 306 (464)
Q Consensus 232 r~~aY~rAa~~l~-~lp~~I-~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpk 306 (464)
|++.-.++|..|. .+...+ .+.++|.+|||||+.+|+.|.-|. -|.-.- -....+..+|.+++|+...
T Consensus 48 RAr~L~~~A~~i~~~~~g~~P~~~~~L~~LpGIG~kTA~aIl~~a-f~~~~~------~VD~nV~RVl~Rl~g~~~~ 117 (289)
T PRK13910 48 RAKNLKKSAEICVKEHHSQLPNDYQSLLKLPGIGAYTANAILCFG-FREKSA------CVDANIKRVLLRLFGLDPN 117 (289)
T ss_pred HHHHHHHHHHHHHHHhCCCCChhHHHHHhCCCCCHHHHHHHHHHH-CCCCcC------cccHHHHHHHHHHhcCCCC
Confidence 7777888888775 222222 357899999999999999997554 332111 1234577888888888643
No 179
>KOG3524 consensus Predicted guanine nucleotide exchange factor (PEBBLE) [Signal transduction mechanisms]
Probab=70.56 E-value=4.1 Score=45.53 Aligned_cols=77 Identities=16% Similarity=0.307 Sum_probs=55.3
Q ss_pred CCCCCeEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccchHHHHHh
Q 012388 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSLR 96 (464)
Q Consensus 17 ~~F~g~~vy~~~~~~g~~R~~~l~~~i~~~Gg~V~~~ls~~VTHVV~~~~~~~~~~l~~~~~~~~~~~iV~~~Wl~ec~k 96 (464)
..|++++.||- ++-..-. -|-.++-.+||.|..+...++||.|+-..... + .....-...++...||.+||+
T Consensus 117 ~~m~~vvlcfT--g~rkk~e-~lv~lvh~mgg~irkd~nsktthli~n~s~ge----k-~~~a~t~~~~~rp~wv~~aw~ 188 (850)
T KOG3524|consen 117 ELMKDVVMCFT--GERKKKE-ELVDLVHYMGGSIRKDTNSKTTHLIANKVEGE----K-QSIALVGVPTMRPDWVTEAWK 188 (850)
T ss_pred hhhcCceeeee--ccchhhH-HHHHHHHHhcceeEeeeccCceEEEeecccce----E-EEEEeeccceechHhhhhhhc
Confidence 56899999996 3433322 57789999999999999999999998654421 0 001111368899999999998
Q ss_pred cCCCC
Q 012388 97 LGEKV 101 (464)
Q Consensus 97 ~g~lv 101 (464)
-+.-.
T Consensus 189 ~rn~~ 193 (850)
T KOG3524|consen 189 HRNDS 193 (850)
T ss_pred Ccchh
Confidence 76543
No 180
>PRK13766 Hef nuclease; Provisional
Probab=69.95 E-value=4.8 Score=45.96 Aligned_cols=49 Identities=29% Similarity=0.428 Sum_probs=32.2
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012388 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (464)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (464)
|..|||||...+.+|.+- -|++..+ .+.. .+.|..++|+|+++|+.+++
T Consensus 717 L~~ipgig~~~a~~Ll~~--fgs~~~i---~~as----~~~L~~i~Gig~~~a~~i~~ 765 (773)
T PRK13766 717 VESLPDVGPVLARNLLEH--FGSVEAV---MTAS----EEELMEVEGIGEKTAKRIRE 765 (773)
T ss_pred HhcCCCCCHHHHHHHHHH--cCCHHHH---HhCC----HHHHHhCCCCCHHHHHHHHH
Confidence 568899998887766553 3444433 2211 22356788999999988876
No 181
>TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Probab=69.64 E-value=3.9 Score=43.94 Aligned_cols=29 Identities=45% Similarity=0.571 Sum_probs=26.6
Q ss_pred hhccCcCHHHHHHHHHcCCCCHHHHhhcc
Q 012388 298 GEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (464)
Q Consensus 298 ~~I~GvGpktA~~ly~~GirtledL~~~~ 326 (464)
.-|+|||.+++.+|++.||.|++||-...
T Consensus 210 slv~gi~~~~~~~L~~~GI~ti~~La~~~ 238 (457)
T TIGR03491 210 SLVPGIGPSRYRLLQELGIHTLEDLAAAD 238 (457)
T ss_pred eecCCCCHHHHHHHHHcCCCcHHHHhcCC
Confidence 47999999999999999999999998764
No 182
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=69.37 E-value=3.1 Score=46.60 Aligned_cols=31 Identities=26% Similarity=0.400 Sum_probs=25.3
Q ss_pred HHHhhhccCcCHHHHHHHHHcCCCCHHHHhhc
Q 012388 294 ISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (464)
Q Consensus 294 l~lf~~I~GvGpktA~~ly~~GirtledL~~~ 325 (464)
-..|.+|+|||++++++|++ -+.|+++++++
T Consensus 551 ~S~L~~IpGIG~kr~~~LL~-~FgSi~~I~~A 581 (624)
T PRK14669 551 TSELLEIPGVGAKTVQRLLK-HFGSLERVRAA 581 (624)
T ss_pred HHHHhcCCCCCHHHHHHHHH-HcCCHHHHHhC
Confidence 34566999999999999998 46688888765
No 183
>PRK10702 endonuclease III; Provisional
Probab=69.16 E-value=6.2 Score=38.08 Aligned_cols=24 Identities=17% Similarity=0.253 Sum_probs=19.4
Q ss_pred HHHHHhhhccCcCHHHHHHHHHcC
Q 012388 292 RTISLFGEVWGIGPATAQKLYEKG 315 (464)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~G 315 (464)
..++.|+++||||+|||.-.---+
T Consensus 106 ~~~~~Ll~lpGVG~ktA~~ill~a 129 (211)
T PRK10702 106 EDRAALEALPGVGRKTANVVLNTA 129 (211)
T ss_pred chHHHHhcCCcccHHHHHHHHHHH
Confidence 467778899999999999865433
No 184
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=68.48 E-value=12 Score=42.24 Aligned_cols=73 Identities=12% Similarity=0.130 Sum_probs=53.1
Q ss_pred CCCCCCeEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccchHHH
Q 012388 16 NGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLED 93 (464)
Q Consensus 16 ~~~F~g~~vy~~~~~~g~~R~~~l~~~i~~~Gg~V~~~ls~~VTHVV~~~~~~~~~~l~~~~~~~~~~~iV~~~Wl~e 93 (464)
+..|.|.++.|-++--+. .+..+++++.++||.|.+++|..++.+|+.++.. . +..++...+.+|++-+.+.+
T Consensus 591 ~~~l~gktfV~TG~l~~~-~R~e~~~lie~~Ggkv~ssVSkktd~LV~G~~aG-s---Kl~KA~~LGI~Ii~e~~f~~ 663 (669)
T PRK14350 591 NSFLFGKKFCITGSFNGY-SRSVLIDKLTKKGAIFNTCVTKYLDFLLVGEKAG-L---KLKKANNLGIKIMSLFDIKS 663 (669)
T ss_pred CCccCCcEEEEecccCCC-CHHHHHHHHHHcCCEEeccccCCCcEEEECCCCC-c---hHHHHHHcCCEEecHHHHHH
Confidence 457999999997753333 3567899999999999999999999999965432 1 22233344677887766655
No 185
>PRK14973 DNA topoisomerase I; Provisional
Probab=67.96 E-value=6.5 Score=46.11 Aligned_cols=42 Identities=17% Similarity=0.111 Sum_probs=32.8
Q ss_pred HHHhhhccCcCHHHHHHHHHcCCCCHHHHhhcc--CcchHHHhh
Q 012388 294 ISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLG 335 (464)
Q Consensus 294 l~lf~~I~GvGpktA~~ly~~GirtledL~~~~--~L~~~q~~G 335 (464)
.+-|++++||=..+|+++|+.||+|++|+-... .|+..-++.
T Consensus 801 ~~~~~~~~gv~~~~~~~~~~~G~~~~~d~~~a~p~~La~~~g~~ 844 (936)
T PRK14973 801 NISRLKEIGVPAVSLKKYQEAGFDTPEDFCSVHPAYLALKTGIS 844 (936)
T ss_pred HHHhhcccCCCHHHHHHHHHhcCCCHHHHHhcCHHHHhcCCCCC
Confidence 334569999999999999999999999998653 355444444
No 186
>PRK05007 PII uridylyl-transferase; Provisional
Probab=67.71 E-value=17 Score=42.53 Aligned_cols=50 Identities=20% Similarity=0.468 Sum_probs=37.4
Q ss_pred CCEEEEEcccccccC-CcCCCccEEEeCCCcc--hhhhHHHHHHHHHHhcccc
Q 012388 367 PEVIILCGGSYRRGK-ASCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMKFL 416 (464)
Q Consensus 367 p~~~v~~~GsyRRgk-e~~gDvDiLit~~d~~--~~~~~l~~lv~~L~~~g~l 416 (464)
|++-++.+|||-||. .-..|||+||-+++.. ....++.+++..|-+.|+=
T Consensus 79 ~~~alvAvGgyGR~EL~p~SDiDll~l~~~~~~~~~~~~i~~~~~~lwD~gL~ 131 (884)
T PRK05007 79 PDLALVAVGGYGRGELHPLSDIDLLILSRKKLPDEQAQKVGELITLLWDLKLE 131 (884)
T ss_pred CceEEEecCCCCCcccCCcccceEEEEeCCCCChHHHHHHHHHHHHHHhcCCC
Confidence 467788899997765 4578999999998542 3456778888887777764
No 187
>COG2251 Predicted nuclease (RecB family) [General function prediction only]
Probab=67.68 E-value=3.9 Score=43.55 Aligned_cols=27 Identities=37% Similarity=0.452 Sum_probs=24.8
Q ss_pred hccCcCHHHHHHHHHcCCCCHHHHhhc
Q 012388 299 EVWGIGPATAQKLYEKGHRTLDDLKNE 325 (464)
Q Consensus 299 ~I~GvGpktA~~ly~~GirtledL~~~ 325 (464)
=|+||||.+.+.+++.||+|++||-+.
T Consensus 229 Lv~Gi~~~r~~~l~~~GI~Ti~~LA~~ 255 (474)
T COG2251 229 LVPGITPSRYDVLEEVGITTIEDLADA 255 (474)
T ss_pred ccCCCCHHHHHHHHHcCcchHHHHHhc
Confidence 468999999999999999999999864
No 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=67.26 E-value=3.5 Score=33.83 Aligned_cols=20 Identities=40% Similarity=0.624 Sum_probs=17.8
Q ss_pred HHhhhccCcCHHHHHHHHHc
Q 012388 295 SLFGEVWGIGPATAQKLYEK 314 (464)
Q Consensus 295 ~lf~~I~GvGpktA~~ly~~ 314 (464)
++|++|||||+.+|-.|..+
T Consensus 2 ~~l~sipGig~~~a~~llae 21 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAE 21 (87)
T ss_pred chhcCCCCccHHHHHHHHHH
Confidence 46789999999999999875
No 189
>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=67.21 E-value=17 Score=34.22 Aligned_cols=44 Identities=14% Similarity=0.203 Sum_probs=30.7
Q ss_pred hHHHHHHHHHHH-hcCCccc---------cc---hhhhcCCCCCCHHHHHHHHHHHH
Q 012388 232 RSFSYYKAIPVI-EKLPFKI---------ES---ADQVKGLPGIGKSMQDHIQEIVT 275 (464)
Q Consensus 232 r~~aY~rAa~~l-~~lp~~I---------~s---~~~l~~lpgIG~~ia~kI~Eil~ 275 (464)
++.....++..| +.+...+ .+ .++|..|||||+++|..+--+|.
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 555556666666 4566554 11 36899999999999998876554
No 190
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=67.04 E-value=4.3 Score=39.58 Aligned_cols=29 Identities=34% Similarity=0.543 Sum_probs=26.8
Q ss_pred HhhhccCcCHHHHHHHHHcCCCCHHHHhh
Q 012388 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (464)
Q Consensus 296 lf~~I~GvGpktA~~ly~~GirtledL~~ 324 (464)
-|+.|.||||+.+.+|.+.|+.++++|-.
T Consensus 159 DL~~I~GIGp~~a~~L~eaGi~tfaQIAa 187 (221)
T PRK12278 159 DLTKITGVGPALAKKLNEAGVTTFAQIAA 187 (221)
T ss_pred hheeccccChHHHHHHHHcCCCCHHHhhC
Confidence 36799999999999999999999999975
No 191
>COG1669 Predicted nucleotidyltransferases [General function prediction only]
Probab=67.00 E-value=28 Score=29.59 Aligned_cols=30 Identities=30% Similarity=0.463 Sum_probs=23.4
Q ss_pred CE-EEEEcccccccCCc-CCCccEEEeCCCcc
Q 012388 368 EV-IILCGGSYRRGKAS-CGDLDVVIMHPDRK 397 (464)
Q Consensus 368 ~~-~v~~~GsyRRgke~-~gDvDiLit~~d~~ 397 (464)
|+ .+.+-|||=||... -.||||||-...+.
T Consensus 23 gv~~~~vFGS~aRgE~~~~SDIDILVef~~~~ 54 (97)
T COG1669 23 GVKRVAVFGSYARGEQKPDSDIDILVEFEPGK 54 (97)
T ss_pred CCceEEEeeeeecCCCCCCCCceeEEeecCCc
Confidence 55 78899999998643 38999999765553
No 192
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=66.84 E-value=13 Score=37.41 Aligned_cols=29 Identities=17% Similarity=0.130 Sum_probs=26.4
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHHhhc
Q 012388 297 FGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (464)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~~ 325 (464)
|.++||+|...++++.+.|+.|++||...
T Consensus 153 L~Qlp~i~~~~~~~l~~~~i~s~~~l~~~ 181 (312)
T smart00611 153 LLQLPHLPEEILKRLEKKKVLSLEDLLEL 181 (312)
T ss_pred cccCCCCCHHHHHHHHhCCCCCHHHHHhc
Confidence 44899999999999999999999999864
No 193
>PRK02362 ski2-like helicase; Provisional
Probab=66.62 E-value=42 Score=38.32 Aligned_cols=52 Identities=19% Similarity=0.464 Sum_probs=39.8
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc-C
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-G 315 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~-G 315 (464)
-+|.+|||||...+.+..+ .| +.-++++.+-++..+..+ +|.|+|+++.+. |
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 4688999999998776654 44 677777776566666655 599999999986 6
No 194
>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=65.70 E-value=8.3 Score=31.83 Aligned_cols=30 Identities=23% Similarity=0.470 Sum_probs=23.9
Q ss_pred hhhccCcCHHHHHHHHHc----CCCCHHHHhhcc
Q 012388 297 FGEVWGIGPATAQKLYEK----GHRTLDDLKNED 326 (464)
Q Consensus 297 f~~I~GvGpktA~~ly~~----GirtledL~~~~ 326 (464)
|+.|.|||.++|+++.+. .++|++|+....
T Consensus 29 l~~Ikglg~~~a~~I~~~R~~g~f~s~~df~~R~ 62 (90)
T PF14579_consen 29 LSAIKGLGEEVAEKIVEERENGPFKSLEDFIQRL 62 (90)
T ss_dssp GGGSTTS-HHHHHHHHHHHHCSS-SSHHHHHHHS
T ss_pred HhhcCCCCHHHHHHHHHhHhcCCCCCHHHHHHHH
Confidence 789999999999999963 789999987654
No 195
>PHA01806 hypothetical protein
Probab=65.45 E-value=22 Score=33.92 Aligned_cols=49 Identities=18% Similarity=0.238 Sum_probs=31.4
Q ss_pred CCCHHHHHH-HHHHHHHHhhhcCCCEEEEEcccccc----cCCcCCCccEEEeCCCcc
Q 012388 345 RIPRHEVEQ-MERLLQKAGEEVLPEVIILCGGSYRR----GKASCGDLDVVIMHPDRK 397 (464)
Q Consensus 345 ~i~r~Ea~~-i~~iv~~~~~~~~p~~~v~~~GsyRR----gke~~gDvDiLit~~d~~ 397 (464)
.|++..... ...++..+. .-+.++.++|||=| |+ .+.|+||++....+.
T Consensus 14 ~I~~~~is~~al~v~~~l~---~~g~~aYlVGG~VRD~Llgr-~~kDiDivt~~~~pe 67 (200)
T PHA01806 14 EIPEGLIAKALLLRLYSDA---RHSEGVALAGGAARDLMHGA-EPKDIDIALYGMDDR 67 (200)
T ss_pred ccChhHcCHHHHHHHHHHH---HCCcEEEEECchHHHHHcCC-CCCceEEEccCCCHH
Confidence 456655543 334444443 35778888888877 66 889999977555444
No 196
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=65.23 E-value=4.7 Score=38.56 Aligned_cols=32 Identities=22% Similarity=0.359 Sum_probs=23.7
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHH
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHF 285 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l 285 (464)
+.+..|||||++.|+++.-.+-.-.-.+++.|
T Consensus 11 ~~l~~LPGIG~KsA~RlA~~ll~~~~~~~~~l 42 (195)
T TIGR00615 11 ESLKKLPGIGPKSAQRLAFHLLKRDPSEVLRL 42 (195)
T ss_pred HHHHHCCCCCHHHHHHHHHHHHcCCHHHHHHH
Confidence 67899999999999999776654443444443
No 197
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=64.97 E-value=24 Score=33.29 Aligned_cols=41 Identities=27% Similarity=0.295 Sum_probs=28.1
Q ss_pred ccccc-hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhh
Q 012388 248 FKIES-ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKD 288 (464)
Q Consensus 248 ~~I~s-~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~ 288 (464)
.||+. +.+|.=|||||++++.+|-|=-+.+.+..++++.+-
T Consensus 109 ~PIt~RlH~LeLLPGIGKK~m~~ILeERkkkpFeSFeDi~~R 150 (181)
T PF04919_consen 109 QPITLRLHSLELLPGIGKKTMWKILEERKKKPFESFEDIEER 150 (181)
T ss_dssp --B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHH
T ss_pred CCChHHHHHHhhcccccHHHHHHHHHHHccCCCCCHHHHHHH
Confidence 47776 478899999999999999998888888888888753
No 198
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=64.95 E-value=4.6 Score=47.11 Aligned_cols=25 Identities=40% Similarity=0.663 Sum_probs=21.3
Q ss_pred hccCcCHHHHHHHHHc-CCCCHHHHhhc
Q 012388 299 EVWGIGPATAQKLYEK-GHRTLDDLKNE 325 (464)
Q Consensus 299 ~I~GvGpktA~~ly~~-GirtledL~~~ 325 (464)
+|+|||||||.+|.++ | |||.+.+.
T Consensus 189 GVpGIG~KtA~kLL~~yg--sle~i~~~ 214 (887)
T TIGR00593 189 GVKGIGEKTAAKLLQEFG--SLENIYEN 214 (887)
T ss_pred CCCCcCHHHHHHHHHHcC--CHHHHHHH
Confidence 4899999999999986 6 88888743
No 199
>PRK03980 flap endonuclease-1; Provisional
Probab=64.59 E-value=5.2 Score=40.60 Aligned_cols=25 Identities=44% Similarity=0.670 Sum_probs=21.4
Q ss_pred hccCcCHHHHHHHHHcCCCCHHHHhh
Q 012388 299 EVWGIGPATAQKLYEKGHRTLDDLKN 324 (464)
Q Consensus 299 ~I~GvGpktA~~ly~~GirtledL~~ 324 (464)
+|+|||||||.+|.++ +.|||.+..
T Consensus 193 GI~GIG~ktA~kLi~~-~~sle~i~~ 217 (292)
T PRK03980 193 GIKGIGPKTALKLIKK-HGDLEKVLE 217 (292)
T ss_pred CCCCccHHHHHHHHHH-CCCHHHHHH
Confidence 7899999999999986 348888876
No 200
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=64.17 E-value=3.7 Score=46.16 Aligned_cols=53 Identities=15% Similarity=0.221 Sum_probs=38.7
Q ss_pred HHhhhccCcCHHHHHHHHHcCCCCHHHHhhcc--CcchHHHhhHhhHHhhccCCCH
Q 012388 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDIKTRIPR 348 (464)
Q Consensus 295 ~lf~~I~GvGpktA~~ly~~GirtledL~~~~--~L~~~q~~Glk~~ed~~~~i~r 348 (464)
..|.+|+|||+++.++|++ -|-|+++|+++. .|....++|.+..+.|...-.|
T Consensus 608 s~L~~IpGiG~kr~~~LL~-~FgS~~~i~~As~eel~~v~gi~~~~A~~i~~~~~~ 662 (691)
T PRK14672 608 LSFERLPHVGKVRAHRLLA-HFGSFRSLQSATPQDIATAIHIPLTQAHTILHAATR 662 (691)
T ss_pred cccccCCCCCHHHHHHHHH-HhcCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHhhc
Confidence 3566999999999999998 566888888763 4666666676666666554433
No 201
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=64.15 E-value=8.7 Score=42.70 Aligned_cols=50 Identities=20% Similarity=0.419 Sum_probs=22.9
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012388 255 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (464)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (464)
.|..|||||+..+.++-+. -|++..+-.. ..+.+.+++|+|++.|+.+++
T Consensus 526 ~L~~IpGIG~kr~~~LL~~--FGS~~~I~~A-------s~eeL~~vpGi~~~~A~~I~~ 575 (577)
T PRK14668 526 VLDDVPGVGPETRKRLLRR--FGSVEGVREA-------SVEDLRDVPGVGEKTAETIRE 575 (577)
T ss_pred HHhcCCCCCHHHHHHHHHH--cCCHHHHHhC-------CHHHHHhCCCCCHHHHHHHHH
Confidence 3556666666555544332 2333322211 122234566666666665543
No 202
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=63.46 E-value=23 Score=41.24 Aligned_cols=67 Identities=16% Similarity=0.330 Sum_probs=45.1
Q ss_pred HHHHHHHHHHHHHhhhcCC----CEEEEEcccccccCC-cCCCccEEEeCCCc--chhhhHHHHHHHHHHhccc
Q 012388 349 HEVEQMERLLQKAGEEVLP----EVIILCGGSYRRGKA-SCGDLDVVIMHPDR--KSHKGFLSKYVKKLKEMKF 415 (464)
Q Consensus 349 ~Ea~~i~~iv~~~~~~~~p----~~~v~~~GsyRRgke-~~gDvDiLit~~d~--~~~~~~l~~lv~~L~~~g~ 415 (464)
.-+..+..+++.+.....+ ++-+..+|||-||.- --.|||+||-+++. .....++.+++.-|=+.|+
T Consensus 33 ~~~~~~D~~l~~l~~~~~~~~~~~iaLvAvGGYGR~eL~P~SDIDlliL~~~~~~~~~~~~i~~~~~~LWD~gl 106 (854)
T PRK01759 33 NRSDFYDQLLIHLWQQFGLEEQSDLALIAVGGYGRREMFPLSDLDILILTEQPPDEETEEKINQFFQFLWDCGF 106 (854)
T ss_pred HHHHHHHHHHHHHHHHccCCCCCCeEEEEeCCcccccCCCcccceEEEEeCCCCChHHHHHHHHHHHHHHhcCC
Confidence 3344455566655443322 356778899988764 45799999998754 3356778888888888776
No 203
>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=63.15 E-value=2.7 Score=33.02 Aligned_cols=44 Identities=25% Similarity=0.367 Sum_probs=33.4
Q ss_pred cCcCHHHHHHHHHcCCCCHHHHhhc--cCcchHHHhhHhhHHhhcc
Q 012388 301 WGIGPATAQKLYEKGHRTLDDLKNE--DSLTHSQRLGLKYFDDIKT 344 (464)
Q Consensus 301 ~GvGpktA~~ly~~GirtledL~~~--~~L~~~q~~Glk~~ed~~~ 344 (464)
-|+-+.+...|-..||.|+.||..- ..|..+.+||-+..++|.+
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 3667788888888899999999854 3588888999999888764
No 204
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=62.78 E-value=6.2 Score=30.85 Aligned_cols=24 Identities=25% Similarity=0.326 Sum_probs=17.8
Q ss_pred hhHHHHH-hhhccCcCHHHHHHHHH
Q 012388 290 KVRTISL-FGEVWGIGPATAQKLYE 313 (464)
Q Consensus 290 ~~~~l~l-f~~I~GvGpktA~~ly~ 313 (464)
+...++- +.+|||||+++|.++.+
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 3344454 78999999999999854
No 205
>PRK00076 recR recombination protein RecR; Reviewed
Probab=62.18 E-value=5.4 Score=38.15 Aligned_cols=32 Identities=16% Similarity=0.321 Sum_probs=24.0
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHH
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHF 285 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l 285 (464)
+.+..|||||++.|+++.-++-.-.-.+++.|
T Consensus 11 ~~l~~LPGIG~KsA~Rla~~ll~~~~~~~~~l 42 (196)
T PRK00076 11 EALRKLPGIGPKSAQRLAFHLLQRDREDVLRL 42 (196)
T ss_pred HHHHHCCCCCHHHHHHHHHHHHcCCHHHHHHH
Confidence 67899999999999999877754444444443
No 206
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=61.87 E-value=9.7 Score=31.74 Aligned_cols=55 Identities=24% Similarity=0.306 Sum_probs=34.6
Q ss_pred CCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc-CCCCHHHH
Q 012388 261 GIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDL 322 (464)
Q Consensus 261 gIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~-GirtledL 322 (464)
||+.+++.+|.+...... ++.++. .||. |+..|.|||-++|.++... |+..-+.-
T Consensus 19 gl~~~~a~kl~~~yg~~a---i~~l~~-nPY~---L~~~i~gi~F~~aD~iA~~~g~~~~d~~ 74 (94)
T PF14490_consen 19 GLSPKLAMKLYKKYGDDA---IEILKE-NPYR---LIEDIDGIGFKTADKIALKLGIEPDDPR 74 (94)
T ss_dssp T--HHHHHHHHHHH-TTH---HHHHHH--STC---CCB-SSSSBHHHHHHHHHTTT--TT-HH
T ss_pred CCCHHHHHHHHHHHhHHH---HHHHHH-ChHH---HHHHccCCCHHHHHHHHHHcCCCCCCHH
Confidence 899999999999877643 444444 4553 3434899999999999987 87644443
No 207
>PF14579 HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI_A 3E0D_A 3F2C_A 3F2B_A 3F2D_A 2HQA_A 2HNH_A.
Probab=61.79 E-value=21 Score=29.39 Aligned_cols=50 Identities=22% Similarity=0.395 Sum_probs=37.0
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCC
Q 012388 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGH 316 (464)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~Gi 316 (464)
+..|+|||+.+++.|.+--+.|.+.-++++... ++++..+..+.|...|.
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 778999999999999998888888888876532 22778888888887754
No 208
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=61.57 E-value=6.7 Score=44.41 Aligned_cols=28 Identities=39% Similarity=0.565 Sum_probs=25.4
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHHhh
Q 012388 297 FGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (464)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~~ 324 (464)
++.+.||||++|+.|-+.||.|+.||..
T Consensus 11 ~~~l~gvg~~~~~~l~~lgi~t~~dll~ 38 (681)
T PRK10917 11 LTSLKGVGPKTAEKLAKLGIHTVQDLLL 38 (681)
T ss_pred hhhcCCCCHHHHHHHHHcCCCCHHHHhh
Confidence 4578999999999999899999999983
No 209
>PRK04374 PII uridylyl-transferase; Provisional
Probab=61.44 E-value=27 Score=40.85 Aligned_cols=63 Identities=19% Similarity=0.404 Sum_probs=41.8
Q ss_pred HHHHHHHHhhhcCC---CEEEEEcccccccC-CcCCCccEEEeCCCc--chhhhHHHHHHHHHHhcccc
Q 012388 354 MERLLQKAGEEVLP---EVIILCGGSYRRGK-ASCGDLDVVIMHPDR--KSHKGFLSKYVKKLKEMKFL 416 (464)
Q Consensus 354 i~~iv~~~~~~~~p---~~~v~~~GsyRRgk-e~~gDvDiLit~~d~--~~~~~~l~~lv~~L~~~g~l 416 (464)
+..+++.+.....| ++-++.+|||-||. --..|||+||-+++. .....++.+++..|-+.|+=
T Consensus 55 ~D~~l~~~~~~~~~~~~~~alvAvGgYGR~EL~p~SDIDLliL~~~~~~~~~~~~i~~~i~~LWD~gL~ 123 (869)
T PRK04374 55 VDQLMRNAWTRCIPADSGLSLHAVGGYGRGELFPRSDVDLLVLGETAAQQRHEQALARLFALLWDVGLP 123 (869)
T ss_pred HHHHHHHHHHHhCCCcCCEEEEEcCCccccccCCcccceEEEEecCCCCchHHHHHHHHHHHHHhcCCC
Confidence 44455554443334 35677889997765 456899999988743 23456778888888766653
No 210
>PTZ00217 flap endonuclease-1; Provisional
Probab=61.35 E-value=6.3 Score=41.70 Aligned_cols=26 Identities=35% Similarity=0.640 Sum_probs=21.8
Q ss_pred hhccCcCHHHHHHHHHcCCCCHHHHhh
Q 012388 298 GEVWGIGPATAQKLYEKGHRTLDDLKN 324 (464)
Q Consensus 298 ~~I~GvGpktA~~ly~~GirtledL~~ 324 (464)
-+|+|||||||.+|.++ +.|+|.+.+
T Consensus 238 pgi~GIG~ktA~~Li~~-~gsle~il~ 263 (393)
T PTZ00217 238 DTIKGIGPKTAYKLIKK-YKSIEEILE 263 (393)
T ss_pred CCCCCccHHHHHHHHHH-cCCHHHHHH
Confidence 47999999999999987 348888864
No 211
>COG5186 PAP1 Poly(A) polymerase [RNA processing and modification]
Probab=61.29 E-value=21 Score=37.33 Aligned_cols=81 Identities=22% Similarity=0.368 Sum_probs=57.4
Q ss_pred CEEEEEcccccccCC-cCCCccEEEeCCCcchhhhHHHHHHHHHHhcccccccccccccCCCCCCCCCceEEEEeecC--
Q 012388 368 EVIILCGGSYRRGKA-SCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCTYP-- 444 (464)
Q Consensus 368 ~~~v~~~GsyRRgke-~~gDvDiLit~~d~~~~~~~l~~lv~~L~~~g~l~~~L~~~~~~~~~~~~~~~~~~g~~~~p-- 444 (464)
|-++---||||-|-- -+.|||-|+.-|.--+..+||..+-..|++..-|++.-.+ +|-|.-+.++.
T Consensus 81 GGKIFTyGSYRLGVhgpGsDIDtLvvVPkHVsR~dFFt~f~~~Lrer~ei~eva~v-----------pDAfVPIIK~KF~ 149 (552)
T COG5186 81 GGKIFTYGSYRLGVHGPGSDIDTLVVVPKHVSRSDFFTHFYEELRERPEIEEVAKV-----------PDAFVPIIKLKFQ 149 (552)
T ss_pred CceeeeecceeeeccCCCCCcceEEEecccccHHHHHHHHHHHhccCcchhhhccC-----------CcccceeEEEEec
Confidence 345666799999975 4679999999998888889999999999998888765433 24454444432
Q ss_pred CC---CcceeeeEEEecC
Q 012388 445 GR---ELRHRIDFKVLAS 459 (464)
Q Consensus 445 ~~---~~~rRiDi~~~P~ 459 (464)
|- -+.-|+||-+||.
T Consensus 150 GIsIDLifARLs~P~Vp~ 167 (552)
T COG5186 150 GISIDLIFARLSIPVVPD 167 (552)
T ss_pred CccceeeeeeccCCcCCC
Confidence 22 2445777777764
No 212
>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=61.25 E-value=16 Score=34.47 Aligned_cols=41 Identities=10% Similarity=0.293 Sum_probs=27.7
Q ss_pred hHHHHHHHHHHHh-cCCcccc-chhhhcCCCCCCHHHHHHHHH
Q 012388 232 RSFSYYKAIPVIE-KLPFKIE-SADQVKGLPGIGKSMQDHIQE 272 (464)
Q Consensus 232 r~~aY~rAa~~l~-~lp~~I~-s~~~l~~lpgIG~~ia~kI~E 272 (464)
|+..-.+++..+. .+...+. ..++|.+|||||+.+|+.|--
T Consensus 82 Ka~~i~~~a~~i~~~~~~~~~~~~~~L~~l~GIG~ktA~~ill 124 (191)
T TIGR01083 82 KAKNIIALCRILVERYGGEVPEDREELVKLPGVGRKTANVVLN 124 (191)
T ss_pred HHHHHHHHHHHHHHHcCCCCchHHHHHHhCCCCcHHHHHHHHH
Confidence 5655666666553 3332222 357899999999999999863
No 213
>PRK02794 DNA polymerase IV; Provisional
Probab=61.04 E-value=38 Score=35.90 Aligned_cols=52 Identities=13% Similarity=0.317 Sum_probs=34.6
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--CCCC
Q 012388 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (464)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--Girt 318 (464)
+..|||||+.+.++...+ .+..+.+|.+-.+....+.| |+ .+..+|+. |+..
T Consensus 211 l~~L~GiG~~~~~~L~~~----GI~tigdL~~l~~~~L~~rf------G~-~g~~l~~~a~G~d~ 264 (419)
T PRK02794 211 VGIIWGVGPATAARLARD----GIRTIGDLQRADEADLMRRF------GS-MGLRLWRLARGIDD 264 (419)
T ss_pred hhhhCCCCHHHHHHHHHh----ccchHHHHhhCCHHHHHHHH------hH-HHHHHHHHhCCCCC
Confidence 678999999988877543 46666676654444444445 44 57777775 8854
No 214
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=61.02 E-value=6 Score=40.79 Aligned_cols=31 Identities=19% Similarity=0.241 Sum_probs=27.9
Q ss_pred HHHhhhccCcCHHHHHHHHHcCCCCHHHHhh
Q 012388 294 ISLFGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (464)
Q Consensus 294 l~lf~~I~GvGpktA~~ly~~GirtledL~~ 324 (464)
-.-|+.|.||||+.+++|.+.||.+++++-+
T Consensus 262 ~DdL~~I~GiGp~~e~~L~~~Gi~~f~QiA~ 292 (326)
T PRK12311 262 PDDLKKLTGVSPQIEKKLNDLGIFHFWQLAE 292 (326)
T ss_pred chhhhhhccCChhhhhhhhhcCCCCHHHhhC
Confidence 3457799999999999999999999999975
No 215
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=61.00 E-value=11 Score=42.26 Aligned_cols=49 Identities=27% Similarity=0.560 Sum_probs=34.1
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (464)
..|.+|||||++.+..|-.- -|++ +.+.+. ..+.+.+| ||+++|+.+++
T Consensus 569 s~L~~I~GIG~k~a~~Ll~~--Fgs~---~~i~~A----s~eeL~~v--ig~k~A~~I~~ 617 (621)
T PRK14671 569 TELTDIAGIGEKTAEKLLEH--FGSV---EKVAKA----SLEELAAV--AGPKTAETIYR 617 (621)
T ss_pred hhhhcCCCcCHHHHHHHHHH--cCCH---HHHHhC----CHHHHHHH--hCHHHHHHHHH
Confidence 56889999999999866542 2344 444432 34445567 99999999976
No 216
>PRK07758 hypothetical protein; Provisional
Probab=60.62 E-value=12 Score=31.73 Aligned_cols=23 Identities=13% Similarity=0.355 Sum_probs=20.2
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHh
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTT 276 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~t 276 (464)
+||.+|+|+|++..+.|+|-|..
T Consensus 67 ~ELl~iknlGkKSL~EIkekL~E 89 (95)
T PRK07758 67 KEILKLHGMGPASLPKLRKALEE 89 (95)
T ss_pred HHHHHccCCCHHHHHHHHHHHHH
Confidence 67999999999999999987754
No 217
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=60.54 E-value=6.7 Score=40.59 Aligned_cols=27 Identities=41% Similarity=0.588 Sum_probs=23.0
Q ss_pred hhccCcCHHHHHHHHHcCCCCHHHHhhc
Q 012388 298 GEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (464)
Q Consensus 298 ~~I~GvGpktA~~ly~~GirtledL~~~ 325 (464)
.+|+|||||||.+|.++ +.|++.+.+.
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 4589988754
No 218
>KOG3524 consensus Predicted guanine nucleotide exchange factor (PEBBLE) [Signal transduction mechanisms]
Probab=60.46 E-value=5 Score=44.86 Aligned_cols=86 Identities=19% Similarity=0.337 Sum_probs=61.3
Q ss_pred CCCCCeEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccchHHHHHh
Q 012388 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLEDSLR 96 (464)
Q Consensus 17 ~~F~g~~vy~~~~~~g~~R~~~l~~~i~~~Gg~V~~~ls~~VTHVV~~~~~~~~~~l~~~~~~~~~~~iV~~~Wl~ec~k 96 (464)
.-|.||.++|. |+...-.+++-.-+...||..+. -....||||+.++.....-+ ..+...++|+-+|+-=++.
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 57999999998 57767778888899999999888 45789999997654311111 1122457788888877777
Q ss_pred cCCCCCccccccc
Q 012388 97 LGEKVSEDLYRIK 109 (464)
Q Consensus 97 ~g~lvdee~y~l~ 109 (464)
.|.---|+.|...
T Consensus 282 ~g~~a~e~~yl~~ 294 (850)
T KOG3524|consen 282 RGCCAIEDNYLLP 294 (850)
T ss_pred cchhccccceecc
Confidence 7766666666553
No 219
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=60.15 E-value=23 Score=34.33 Aligned_cols=31 Identities=19% Similarity=0.504 Sum_probs=23.4
Q ss_pred HhcCCcccc-chhhhcCCCCCCHHHHHHHHHH
Q 012388 243 IEKLPFKIE-SADQVKGLPGIGKSMQDHIQEI 273 (464)
Q Consensus 243 l~~lp~~I~-s~~~l~~lpgIG~~ia~kI~Ei 273 (464)
++.+...+. ++++|.+|||||.++|..+--+
T Consensus 97 ~e~~~g~vP~~~~eL~~LPGVGrKTAnvVL~~ 128 (211)
T COG0177 97 LEKFGGEVPDTREELLSLPGVGRKTANVVLSF 128 (211)
T ss_pred HHHcCCCCCchHHHHHhCCCcchHHHHHHHHh
Confidence 345555554 4689999999999999987543
No 220
>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=60.07 E-value=14 Score=37.20 Aligned_cols=50 Identities=24% Similarity=0.464 Sum_probs=32.3
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012388 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (464)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (464)
+.+|||||+.+++++.+. -+..++++..-.+ +.+.+++|++.++|.+||+
T Consensus 1 l~~i~gig~~~~~~L~~~----Gi~ti~dl~~~~~----~~L~~~~g~~~~~a~~l~~ 50 (310)
T TIGR02236 1 LEDLPGVGPATAEKLREA----GYDTFEAIAVASP----KELSEIAGISEGTAAKIIQ 50 (310)
T ss_pred CcccCCCCHHHHHHHHHc----CCCCHHHHHcCCH----HHHHhccCCCHHHHHHHHH
Confidence 357899999888876654 2344555543222 2334677888888888775
No 221
>PRK13844 recombination protein RecR; Provisional
Probab=59.77 E-value=6.1 Score=37.92 Aligned_cols=32 Identities=16% Similarity=0.251 Sum_probs=24.3
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHH
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHF 285 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l 285 (464)
+.+..|||||++.|+++.-++-.-.-.++++|
T Consensus 15 ~~l~~LPGIG~KsA~Rla~~lL~~~~~~~~~l 46 (200)
T PRK13844 15 ESLRKLPTIGKKSSQRLALYLLDKSPETAIAI 46 (200)
T ss_pred HHHHHCCCCCHHHHHHHHHHHHcCCHHHHHHH
Confidence 67899999999999999877765444444444
No 222
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=59.70 E-value=8.1 Score=36.43 Aligned_cols=59 Identities=19% Similarity=0.353 Sum_probs=32.1
Q ss_pred HHHHHHHHHHhCCchhhHHHHhhchhH-HHHHhhhccCcCHHHHHHHHHc----CCCCHHHHhh
Q 012388 266 MQDHIQEIVTTGKLSKLEHFEKDEKVR-TISLFGEVWGIGPATAQKLYEK----GHRTLDDLKN 324 (464)
Q Consensus 266 ia~kI~Eil~tG~~~~le~l~~~~~~~-~l~lf~~I~GvGpktA~~ly~~----GirtledL~~ 324 (464)
+-..|++|+....-..++-+-...|.. -|-.|.=+||||.|+...+.++ -+.|++|+.+
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 446688888877756665543333322 1222444699999999999863 6777777764
No 223
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=59.42 E-value=4.3 Score=41.40 Aligned_cols=51 Identities=25% Similarity=0.342 Sum_probs=35.4
Q ss_pred HHHHhhhccCcCHHHHHHHHHc---C-CCCHHHHhhcc-----CcchHHHhhHhhHHhhc
Q 012388 293 TISLFGEVWGIGPATAQKLYEK---G-HRTLDDLKNED-----SLTHSQRLGLKYFDDIK 343 (464)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~---G-irtledL~~~~-----~L~~~q~~Glk~~ed~~ 343 (464)
.+..+++|||||+++|+++.+- | +..+++|+++. .|..+.++|.+....|-
T Consensus 43 ~~~~~~~ipgiG~~ia~kI~E~~~tG~~~~le~l~~~~~~~l~~l~~i~GiGpk~a~~l~ 102 (307)
T cd00141 43 SLEEAKKLPGIGKKIAEKIEEILETGKLRKLEELREDVPPGLLLLLRVPGVGPKTARKLY 102 (307)
T ss_pred CHHHhcCCCCccHHHHHHHHHHHHcCCHHHHHHHhccchHHHHHHHcCCCCCHHHHHHHH
Confidence 3444579999999999998873 4 35666666541 25567778877776665
No 224
>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=59.26 E-value=18 Score=37.95 Aligned_cols=54 Identities=20% Similarity=0.484 Sum_probs=35.7
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhc---------------hhHHHHHhhhccCcCHHHHHHHHHc--CCC
Q 012388 255 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDE---------------KVRTISLFGEVWGIGPATAQKLYEK--GHR 317 (464)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~---------------~~~~l~lf~~I~GvGpktA~~ly~~--Gir 317 (464)
.+..|||||+++++++..+ | +..+-++.+-. .....+.| |.+++.++|+. |+.
T Consensus 173 pv~~l~GiG~~~~~kL~~~---G-I~tigdl~~~~~~~~~~~~~~~~~~s~~~L~~~f------G~~~g~~l~~~a~G~d 242 (379)
T cd01703 173 DLRKIPGIGYKTAAKLEAH---G-ISSVRDLQEFSNRNRQTVGAAPSLLELLLMVKEF------GEGIGQRIWKLLFGRD 242 (379)
T ss_pred CccccCCcCHHHHHHHHHc---C-CCcHHHHHhCCcccccccccccccccHHHHHHHH------CHHHHHHHHHHHCCCC
Confidence 4788999999999998875 3 33344443323 33344444 67778888875 887
Q ss_pred C
Q 012388 318 T 318 (464)
Q Consensus 318 t 318 (464)
+
T Consensus 243 ~ 243 (379)
T cd01703 243 T 243 (379)
T ss_pred C
Confidence 5
No 225
>PRK05755 DNA polymerase I; Provisional
Probab=59.22 E-value=6.6 Score=45.79 Aligned_cols=26 Identities=42% Similarity=0.587 Sum_probs=21.8
Q ss_pred hhccCcCHHHHHHHHHc-CCCCHHHHhhc
Q 012388 298 GEVWGIGPATAQKLYEK-GHRTLDDLKNE 325 (464)
Q Consensus 298 ~~I~GvGpktA~~ly~~-GirtledL~~~ 325 (464)
-+|+|||||||.+|.++ | |+|.+.+.
T Consensus 190 pGv~GiG~ktA~~Ll~~~g--sle~i~~~ 216 (880)
T PRK05755 190 PGVPGIGEKTAAKLLQEYG--SLEGLYEN 216 (880)
T ss_pred CCCCCccHHHHHHHHHHcC--CHHHHHHh
Confidence 36899999999999986 6 88888743
No 226
>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=58.43 E-value=10 Score=27.24 Aligned_cols=31 Identities=32% Similarity=0.355 Sum_probs=23.1
Q ss_pred cCHHHHHHHHHcCCCCHHHHhhcc--CcchHHH
Q 012388 303 IGPATAQKLYEKGHRTLDDLKNED--SLTHSQR 333 (464)
Q Consensus 303 vGpktA~~ly~~GirtledL~~~~--~L~~~q~ 333 (464)
|.+..+.+|++.|+.|+++|.... .|...++
T Consensus 1 i~~~~~~~L~~~G~~s~e~la~~~~~eL~~i~g 33 (50)
T TIGR01954 1 IDEEIAQLLVEEGFTTVEDLAYVPIDELLSIEG 33 (50)
T ss_pred CCHHHHHHHHHcCCCCHHHHHccCHHHHhcCCC
Confidence 467889999999999999998643 3444433
No 227
>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=57.77 E-value=18 Score=36.35 Aligned_cols=29 Identities=31% Similarity=0.470 Sum_probs=22.6
Q ss_pred HhhhccCcCHHHHHHHHHcCCCCHHHHhh
Q 012388 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (464)
Q Consensus 296 lf~~I~GvGpktA~~ly~~GirtledL~~ 324 (464)
.|.++||+|++.++++-+.|+.|+++|.+
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 35699999999999999999999999995
No 228
>PRK01216 DNA polymerase IV; Validated
Probab=57.48 E-value=34 Score=35.53 Aligned_cols=52 Identities=21% Similarity=0.362 Sum_probs=36.9
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--CCC
Q 012388 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHR 317 (464)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--Gir 317 (464)
+..|||||++++++...+ .+..+.+|.+-......+.| |+..+..||+. |+.
T Consensus 180 i~~l~giG~~~~~~L~~~----Gi~TigdL~~~~~~~L~~rf------G~~~~~~L~~~a~G~d 233 (351)
T PRK01216 180 IADIPGIGDITAEKLKKL----GVNKLVDTLRIEFDELKGII------GEAKAKYLFSLARNEY 233 (351)
T ss_pred cccccCCCHHHHHHHHHc----CCCcHHHHhcCCHHHHHHHH------CHHHHHHHHHHhCCCC
Confidence 677899999888777654 46667777665555555566 67778888883 754
No 229
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=56.92 E-value=7.1 Score=43.57 Aligned_cols=48 Identities=21% Similarity=0.349 Sum_probs=32.4
Q ss_pred HHHHhhhccCcCHHHHHHHHHcCCCCHHHHhhcc--CcchHHHhhHhhHHh
Q 012388 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDD 341 (464)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~GirtledL~~~~--~L~~~q~~Glk~~ed 341 (464)
....|..|+|||++++++|++ -+.|++++.++. .|....++|-+..+.
T Consensus 541 ~~s~L~~IpGIG~k~~k~Ll~-~FgS~~~i~~As~eeL~~v~Gig~~~A~~ 590 (598)
T PRK00558 541 LTSALDDIPGIGPKRRKALLK-HFGSLKAIKEASVEELAKVPGISKKLAEA 590 (598)
T ss_pred hhhhHhhCCCcCHHHHHHHHH-HcCCHHHHHhCCHHHHhhcCCcCHHHHHH
Confidence 345567999999999999998 455688887642 244444455444333
No 230
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=56.52 E-value=17 Score=35.91 Aligned_cols=29 Identities=24% Similarity=0.481 Sum_probs=22.2
Q ss_pred cCCcccc-chhhhcCCCCCCHHHHHHHHHH
Q 012388 245 KLPFKIE-SADQVKGLPGIGKSMQDHIQEI 273 (464)
Q Consensus 245 ~lp~~I~-s~~~l~~lpgIG~~ia~kI~Ei 273 (464)
.+..+|- ++++|..|||||++||-....+
T Consensus 149 ~f~gDIP~~v~dLlsLPGVGPKMa~L~m~~ 178 (286)
T KOG1921|consen 149 KFDGDIPDTVEDLLSLPGVGPKMAHLTMQV 178 (286)
T ss_pred HhCCCCchhHHHHhcCCCCchHHHHHHHHH
Confidence 4555554 5799999999999999876544
No 231
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=56.43 E-value=7.5 Score=34.38 Aligned_cols=24 Identities=25% Similarity=0.407 Sum_probs=19.9
Q ss_pred HHHhhhccCcCHHHHHHHHHc-CCC
Q 012388 294 ISLFGEVWGIGPATAQKLYEK-GHR 317 (464)
Q Consensus 294 l~lf~~I~GvGpktA~~ly~~-Gir 317 (464)
.--|+.|+|||+++|..+-+. ||.
T Consensus 16 ~~aLt~i~GIG~~~A~~ic~~lgi~ 40 (122)
T CHL00137 16 EYALTYIYGIGLTSAKEILEKANID 40 (122)
T ss_pred eeeecccccccHHHHHHHHHHcCcC
Confidence 334689999999999999886 874
No 232
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=56.40 E-value=12 Score=36.97 Aligned_cols=33 Identities=21% Similarity=0.341 Sum_probs=23.4
Q ss_pred HHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCC
Q 012388 283 EHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGH 316 (464)
Q Consensus 283 e~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~Gi 316 (464)
+++..|.|..+-+|+ ++||||||.|.--.+.++
T Consensus 148 d~f~gDIP~~v~dLl-sLPGVGPKMa~L~m~~AW 180 (286)
T KOG1921|consen 148 DKFDGDIPDTVEDLL-SLPGVGPKMAHLTMQVAW 180 (286)
T ss_pred HHhCCCCchhHHHHh-cCCCCchHHHHHHHHHHh
Confidence 456667776555555 999999999986655433
No 233
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=56.35 E-value=7.3 Score=34.46 Aligned_cols=23 Identities=22% Similarity=0.446 Sum_probs=19.6
Q ss_pred HHhhhccCcCHHHHHHHHHc-CCC
Q 012388 295 SLFGEVWGIGPATAQKLYEK-GHR 317 (464)
Q Consensus 295 ~lf~~I~GvGpktA~~ly~~-Gir 317 (464)
--|+.|+|||+.+|..+.+. |+.
T Consensus 17 ~aL~~I~GIG~~~a~~i~~~lgi~ 40 (122)
T PRK05179 17 IALTYIYGIGRTRAKEILAAAGID 40 (122)
T ss_pred eeecccccccHHHHHHHHHHhCcC
Confidence 34689999999999999986 874
No 234
>KOG0323 consensus TFIIF-interacting CTD phosphatases, including NLI-interacting factor [Transcription]
Probab=56.02 E-value=4.5 Score=45.19 Aligned_cols=89 Identities=21% Similarity=0.237 Sum_probs=59.2
Q ss_pred CCCCCeEEEEecC---CCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccchHHH
Q 012388 17 GIFAGMRVFLVEK---GVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLED 93 (464)
Q Consensus 17 ~~F~g~~vy~~~~---~~g~~R~~~l~~~i~~~Gg~V~~~ls~~VTHVV~~~~~~~~~~l~~~~~~~~~~~iV~~~Wl~e 93 (464)
..+++|.+.|++. ++...+. ..-....+.|+.+....+..+||+|+........... ... ...+||...|+..
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 4678888888753 2221222 2224456778998889999999999876543211111 111 1379999999999
Q ss_pred HHhcCCCCCccccccc
Q 012388 94 SLRLGEKVSEDLYRIK 109 (464)
Q Consensus 94 c~k~g~lvdee~y~l~ 109 (464)
|+..=.-+++..|.+.
T Consensus 516 ~~e~w~~v~ek~~~l~ 531 (635)
T KOG0323|consen 516 SLEKWGKVEEKLEPLD 531 (635)
T ss_pred HHHHhcchhccccccc
Confidence 9998888888777664
No 235
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=53.62 E-value=8.3 Score=40.10 Aligned_cols=52 Identities=19% Similarity=0.232 Sum_probs=41.3
Q ss_pred hchhHHHHHhhhccCcCHHHHHHHHHc-CCCCHHHHhhcc--CcchHHHhhHhhHHh
Q 012388 288 DEKVRTISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNED--SLTHSQRLGLKYFDD 341 (464)
Q Consensus 288 ~~~~~~l~lf~~I~GvGpktA~~ly~~-GirtledL~~~~--~L~~~q~~Glk~~ed 341 (464)
.....-..++.+||+||+..|+.|.+. | ||..|.++. .|....++|-+....
T Consensus 280 ~v~prGyRiLs~IPrl~k~iAk~Ll~~FG--SL~~Il~As~eeL~~VeGIGe~rA~~ 334 (352)
T PRK13482 280 PVSPRGYRLLSKIPRLPSAVIENLVEHFG--SLQGLLAASIEDLDEVEGIGEVRARA 334 (352)
T ss_pred ccCCcHHHHHhcCCCCCHHHHHHHHHHcC--CHHHHHcCCHHHHhhCCCcCHHHHHH
Confidence 345668899999999999999999997 7 888888753 477777788666554
No 236
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=53.49 E-value=19 Score=41.39 Aligned_cols=87 Identities=14% Similarity=0.190 Sum_probs=64.9
Q ss_pred CCCCCCCCCeEEEEecCCCCchHHHHHHHHHHhcCCEEEee-cCCCccEEEEcCChHHHHHHHHHhhhcc-Cccccccch
Q 012388 13 LDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEK-LSKKVTHVLAMDLEALLQQVSKQHLARF-KGSVIRYQW 90 (464)
Q Consensus 13 ~~~~~~F~g~~vy~~~~~~g~~R~~~l~~~i~~~Gg~V~~~-ls~~VTHVV~~~~~~~~~~l~~~~~~~~-~~~iV~~~W 90 (464)
......|+++.+|..++-+.. ..-++++-..+|+..... ...+.||+++.+..+.+ +..+ .+...++.|
T Consensus 42 ~t~~s~fs~is~~~ngs~~e~--~nelk~~~~~~t~~~~~~~~rs~T~~ii~~~l~a~~-------vk~~~~~~~~~~e~ 112 (1016)
T KOG2093|consen 42 ATGSSSFSGISISVNGSTDES--ANELKLQNMFHTGASAASYERSGTENIIAQGLPADL-------VKGFTIPKHISIEW 112 (1016)
T ss_pred cCCcceeeeeeeccCCccccc--hHHHhhhhhhcccccccccccccceeeecccchHHH-------hccccchhhhcHHH
Confidence 344578999999998765554 345788888999998844 45789999999877531 1112 467899999
Q ss_pred HHHHHhcCCCCCcccccc
Q 012388 91 LEDSLRLGEKVSEDLYRI 108 (464)
Q Consensus 91 l~ec~k~g~lvdee~y~l 108 (464)
+.||.+.|..+.--.|.+
T Consensus 113 iie~~~~~~~~~~~~~~~ 130 (1016)
T KOG2093|consen 113 IIECCENGMDVGYYPYQL 130 (1016)
T ss_pred HHHHHhccCcccccccee
Confidence 999999999988666544
No 237
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=53.46 E-value=11 Score=42.05 Aligned_cols=48 Identities=21% Similarity=0.463 Sum_probs=32.9
Q ss_pred HHHhhhccCcCHHHHHHHHHcCCCCHHHHhhcc--CcchHHHhhHhhHHhh
Q 012388 294 ISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDI 342 (464)
Q Consensus 294 l~lf~~I~GvGpktA~~ly~~GirtledL~~~~--~L~~~q~~Glk~~ed~ 342 (464)
-..|..|+|||++++++|++. +-|++++.++. .|....++|-+..+.|
T Consensus 524 ~~~L~~IpGIG~kr~~~LL~~-FGS~~~I~~As~eeL~~vpGi~~~~A~~I 573 (577)
T PRK14668 524 STVLDDVPGVGPETRKRLLRR-FGSVEGVREASVEDLRDVPGVGEKTAETI 573 (577)
T ss_pred HhHHhcCCCCCHHHHHHHHHH-cCCHHHHHhCCHHHHHhCCCCCHHHHHHH
Confidence 345679999999999999984 56888887653 3444445555544443
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=53.19 E-value=8.5 Score=33.56 Aligned_cols=24 Identities=33% Similarity=0.517 Sum_probs=19.9
Q ss_pred HHHhhhccCcCHHHHHHHHHc-CCC
Q 012388 294 ISLFGEVWGIGPATAQKLYEK-GHR 317 (464)
Q Consensus 294 l~lf~~I~GvGpktA~~ly~~-Gir 317 (464)
.--|++|+|||+.+|..+-+. |+.
T Consensus 14 ~~aL~~i~GIG~~~a~~i~~~lgi~ 38 (113)
T TIGR03631 14 EIALTYIYGIGRTRARKILEKAGID 38 (113)
T ss_pred eeeeeeeecccHHHHHHHHHHhCcC
Confidence 334689999999999999886 874
No 239
>COG1204 Superfamily II helicase [General function prediction only]
Probab=52.78 E-value=22 Score=40.91 Aligned_cols=89 Identities=27% Similarity=0.434 Sum_probs=55.8
Q ss_pred CCCCCHHHHHHHHHHHHhCCc--hhhHHH----HhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHHhhc---cCcc
Q 012388 259 LPGIGKSMQDHIQEIVTTGKL--SKLEHF----EKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE---DSLT 329 (464)
Q Consensus 259 lpgIG~~ia~kI~Eil~tG~~--~~le~l----~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~---~~L~ 329 (464)
+..+|.++ .++..++..|.. ..++.+ +...+...+..+..|.|+|-..|++||..|+++++++... ..+.
T Consensus 634 ~~~l~~~~-~r~~~~~~~~~~~~~~~~~~~~rie~gv~~e~~~~l~~i~~~grvrar~ly~~g~~~~~~~~~~~~~~~~~ 712 (766)
T COG1204 634 LLALGKAA-ERLAKILGLGLHVLRKLEILSLRIEYGVRSEELLELVEIRGVGRVRARKLYNAGYKSLEDLRLIADPAELL 712 (766)
T ss_pred hhhhhhhh-hhhHhhhCCCccccccchhhhhhhhcCCChhhhcccccccccchhHHHHHHHhhhccHHHHHhhcChhhhh
Confidence 34445444 444455555533 233222 2233323344455999999999999999999999999943 2466
Q ss_pred hHHHhhHhhHHhhccCCCH
Q 012388 330 HSQRLGLKYFDDIKTRIPR 348 (464)
Q Consensus 330 ~~q~~Glk~~ed~~~~i~r 348 (464)
...++|.+.++.+....-+
T Consensus 713 ~~~~~~~~~~~~i~~~~~~ 731 (766)
T COG1204 713 PLTGIGERLVEAILESLGR 731 (766)
T ss_pred hhhhhHHHHHHHHHHHhhh
Confidence 6777788877776654433
No 240
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=52.08 E-value=49 Score=38.88 Aligned_cols=49 Identities=16% Similarity=0.445 Sum_probs=35.6
Q ss_pred CEEEEEcccccccCC-cCCCccEEEeCCCcc--hhhhHHHHHHHHHHhcccc
Q 012388 368 EVIILCGGSYRRGKA-SCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMKFL 416 (464)
Q Consensus 368 ~~~v~~~GsyRRgke-~~gDvDiLit~~d~~--~~~~~l~~lv~~L~~~g~l 416 (464)
++-+..+|||-||.- -..|||+||-+++.. ....++.+++..|-+.|+=
T Consensus 78 ~~alvAvGgyGR~EL~p~SDiDll~l~~~~~~~~~~~~i~~~~~~LwD~gL~ 129 (895)
T PRK00275 78 DIALVAVGGYGRGELHPYSDIDLLILLDSADHEEFREPIERFLTLLWDIGLE 129 (895)
T ss_pred CEEEEEcCCccccCcCCCCCceEEEEecCCCChHHHHHHHHHHHHHHhcCCC
Confidence 467788999988754 578999999887542 3456777777777666653
No 241
>TIGR00588 ogg 8-oxoguanine DNA-glycosylase (ogg). All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is distantly realted to the Nth-MutY superfamily.
Probab=51.60 E-value=22 Score=36.32 Aligned_cols=75 Identities=19% Similarity=0.206 Sum_probs=43.4
Q ss_pred HHcCCChhHHHHHHHHHHHhcCCc------ccc------chhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhH
Q 012388 225 RALGEDRRSFSYYKAIPVIEKLPF------KIE------SADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVR 292 (464)
Q Consensus 225 e~~g~~~r~~aY~rAa~~l~~lp~------~I~------s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~ 292 (464)
+..|-.+|+..-..+|..+..-.. .+. ..++|..|||||+.+|+-|.=+ .-|... .+- ....
T Consensus 179 r~~G~g~Ra~~I~~~A~~i~~~~~~~~~l~~l~~~~~~~~~~~L~~l~GIG~~tAd~vll~-~l~~~d---~~P--vD~~ 252 (310)
T TIGR00588 179 RKLGLGYRARYIRETARALLEEQGGRAWLQQIRGASYEDAREALCELPGVGPKVADCICLM-GLDKPQ---AVP--VDVH 252 (310)
T ss_pred HHcCCHHHHHHHHHHHHHHHhccCCchhHHhhccCChHHHHHHHHhCCCccHHHHHHHHHH-hCCCCC---cee--ecHH
Confidence 334544677677777777654211 111 2367999999999999987533 223322 121 1244
Q ss_pred HHHHhhhccCcCH
Q 012388 293 TISLFGEVWGIGP 305 (464)
Q Consensus 293 ~l~lf~~I~GvGp 305 (464)
+.+.+.+++|+.+
T Consensus 253 v~r~~~r~y~~~~ 265 (310)
T TIGR00588 253 VWRIANRDYPWHP 265 (310)
T ss_pred HHHHHHHHhcccc
Confidence 6666666666644
No 242
>PRK13746 aminoglycoside resistance protein; Provisional
Probab=51.25 E-value=74 Score=31.84 Aligned_cols=27 Identities=26% Similarity=0.249 Sum_probs=22.1
Q ss_pred EEEEccccccc--CCcCCCccEEEeCCCcc
Q 012388 370 IILCGGSYRRG--KASCGDLDVVIMHPDRK 397 (464)
Q Consensus 370 ~v~~~GsyRRg--ke~~gDvDiLit~~d~~ 397 (464)
-|.+-||+-+| ++ -.||||+|...++-
T Consensus 30 ~vyLfGS~~~G~~~p-~SDIDllvvv~~~l 58 (262)
T PRK13746 30 AIHLYGSAVDGGLKP-HSDIDLLVTVAVPL 58 (262)
T ss_pred EEEEECCcccCCCCC-CCceeEEEEeCCCC
Confidence 57789999998 44 79999999877654
No 243
>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=51.21 E-value=23 Score=35.59 Aligned_cols=23 Identities=17% Similarity=0.211 Sum_probs=18.7
Q ss_pred HHHHHhhhccCcCHHHHHHHHHc
Q 012388 292 RTISLFGEVWGIGPATAQKLYEK 314 (464)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~ 314 (464)
..++.|+++||||++||...---
T Consensus 102 ~~~~~L~~LpGIG~~TA~~Il~~ 124 (275)
T TIGR01084 102 QDFEDLAALPGVGRYTAGAILSF 124 (275)
T ss_pred HHHHHHHhCCCCCHHHHHHHHHH
Confidence 35777889999999999986654
No 244
>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=50.07 E-value=12 Score=31.42 Aligned_cols=51 Identities=24% Similarity=0.337 Sum_probs=40.6
Q ss_pred HHHHhhhccCcCHHHHHHHHHc-CCCCHHHHhhccCcchHHHhhHhhHHhhc
Q 012388 293 TISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNEDSLTHSQRLGLKYFDDIK 343 (464)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~-GirtledL~~~~~L~~~q~~Glk~~ed~~ 343 (464)
.+..|++.||+=|..|.++..- -+.|++|+.+-..|+..|+-=++-|++.-
T Consensus 21 ~vr~f~~~pGmYPtlA~kIv~naPY~sveDvl~ipgLse~qK~~lk~~~~~F 72 (93)
T PF06514_consen 21 NVRAFRQFPGMYPTLAGKIVSNAPYKSVEDVLNIPGLSERQKALLKKYEDNF 72 (93)
T ss_dssp -GGGGCCSTTTTCCHHHHHHHS---SSGGGGCCSTT--HHHHHHHHHHGGGE
T ss_pred hHHHHHHCCCCCHHHHHHHHhCCCCCCHHHHHhccCCCHHHHHHHHHHhccc
Confidence 4667889999999999999997 78999999988889999998888877744
No 245
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=49.84 E-value=29 Score=40.21 Aligned_cols=32 Identities=13% Similarity=0.211 Sum_probs=27.5
Q ss_pred HHHHhhhccCcCHHHHHHHHHcCCCCHHHHhhc
Q 012388 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (464)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~GirtledL~~~ 325 (464)
..+++.++||||++.|+.+.+. +.|+++|.+.
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 4555679999999999999985 9999999875
No 246
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=49.84 E-value=13 Score=39.40 Aligned_cols=56 Identities=23% Similarity=0.303 Sum_probs=37.8
Q ss_pred HHHHHhhhccCcCHHHHHHHHHcCCCCHHHHhhccCcchHHHhhHhhHHhhccCCCHHH
Q 012388 292 RTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIPRHE 350 (464)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~~~L~~~q~~Glk~~ed~~~~i~r~E 350 (464)
+.-.-|+.|.||||+.+++|...||.++++|-... ...-.-+.-+-.+..+|.|+.
T Consensus 320 g~aDDLk~I~GIGpk~e~~Ln~~Gi~~f~QIA~wt---~~eia~vd~~l~f~Gri~rd~ 375 (400)
T PRK12373 320 GGADDLKLISGVGPKIEATLNELGIFTFDQVAAWK---KAERAWVDGYLNFKGRIERDD 375 (400)
T ss_pred CCchhhhhccCCChHHHHHHHhcCCCCHHHHhCCC---HHHhHHhhhcccCCCCcCcch
Confidence 34455779999999999999999999999997532 111111222223566776654
No 247
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=49.78 E-value=29 Score=38.70 Aligned_cols=83 Identities=20% Similarity=0.379 Sum_probs=50.6
Q ss_pred cHHHHHHHHHHHHHHHHcCCChhHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhc
Q 012388 210 NKNITEIFGKLINIYRALGEDRRSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDE 289 (464)
Q Consensus 210 N~~ia~~l~~la~~~e~~g~~~r~~aY~rAa~~l~~lp~~I~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~ 289 (464)
|......|..+-+... .-+.+|.|.-+.=..+ -..|.+|||||++...++-. .-|++..+..
T Consensus 497 ~~p~l~~lq~irDEaH-----rfAi~~hR~~R~k~~~------~s~Ld~I~GiG~~r~~~LL~--~Fgs~~~i~~----- 558 (581)
T COG0322 497 NSPALYLLQRIRDEAH-----RFAITYHRKKRSKAML------QSSLDDIPGIGPKRRKALLK--HFGSLKGIKS----- 558 (581)
T ss_pred CCHHHHHHHHHHHHHH-----HHHHHHHHHHhhhhhh------cCccccCCCcCHHHHHHHHH--HhhCHHHHHh-----
Confidence 5555555555433221 2456666654311111 14588999999988776543 2344444432
Q ss_pred hhHHHHHhhhccCcCHHHHHHHHH
Q 012388 290 KVRTISLFGEVWGIGPATAQKLYE 313 (464)
Q Consensus 290 ~~~~l~lf~~I~GvGpktA~~ly~ 313 (464)
.+++.|..| ||+.+.|+++|+
T Consensus 559 --As~eel~~v-gi~~~~a~~i~~ 579 (581)
T COG0322 559 --ASVEELAKV-GISKKLAEKIYE 579 (581)
T ss_pred --cCHHHHHHc-CCCHHHHHHHHh
Confidence 356778899 999999999986
No 248
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=49.61 E-value=31 Score=38.77 Aligned_cols=50 Identities=20% Similarity=0.423 Sum_probs=34.0
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK 314 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~ 314 (464)
..|.+|||||++.+.++-+ . +.-++.+++. .++.+.+| ||.++|+++|+.
T Consensus 552 S~L~~IpGIG~kr~~~LL~--~---FgSi~~I~~A----s~eeL~~v--i~~k~A~~I~~~ 601 (624)
T PRK14669 552 SELLEIPGVGAKTVQRLLK--H---FGSLERVRAA----TETQLAAV--VGRAAAEAIIAH 601 (624)
T ss_pred HHHhcCCCCCHHHHHHHHH--H---cCCHHHHHhC----CHHHHHHH--hCHHHHHHHHHH
Confidence 5688999999988876643 2 3344444432 23334456 899999999874
No 249
>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=49.50 E-value=15 Score=28.82 Aligned_cols=19 Identities=21% Similarity=0.389 Sum_probs=16.7
Q ss_pred HHHHHHHHHcCCCCHHHHh
Q 012388 305 PATAQKLYEKGHRTLDDLK 323 (464)
Q Consensus 305 pktA~~ly~~GirtledL~ 323 (464)
-+.++.|++.||+|++|++
T Consensus 54 ~~Il~~W~~~gi~T~e~~~ 72 (73)
T TIGR01446 54 DAILNNWKNNGIKTVEDVE 72 (73)
T ss_pred HHHHHHHHHcCCCCHHHHh
Confidence 4678999999999999986
No 250
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=49.46 E-value=12 Score=38.07 Aligned_cols=32 Identities=31% Similarity=0.339 Sum_probs=23.3
Q ss_pred HHHhhhccCcCHHHHHHHHHc-CC--CCHHHHhhc
Q 012388 294 ISLFGEVWGIGPATAQKLYEK-GH--RTLDDLKNE 325 (464)
Q Consensus 294 l~lf~~I~GvGpktA~~ly~~-Gi--rtledL~~~ 325 (464)
.+.+.+|||+|+|.|+++... -. -|+|+|++-
T Consensus 329 ~~~llRVPGiG~ksa~rIv~~Rr~~rl~~e~Lkk~ 363 (404)
T COG4277 329 YKELLRVPGIGVKSARRIVMTRRRTRLTLEDLKKL 363 (404)
T ss_pred HHHhcccCCCChHHHHHHHHHhhhcccCHHHHhhh
Confidence 445569999999999999864 33 356777653
No 251
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=49.25 E-value=10 Score=39.12 Aligned_cols=52 Identities=19% Similarity=0.245 Sum_probs=33.0
Q ss_pred HHHHHhhhccCcCHHHHHHHHHc---CCCC-HHHHhhcc------CcchHHHhhHhhHHhhc
Q 012388 292 RTISLFGEVWGIGPATAQKLYEK---GHRT-LDDLKNED------SLTHSQRLGLKYFDDIK 343 (464)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~---Girt-ledL~~~~------~L~~~q~~Glk~~ed~~ 343 (464)
..+..+++|||||+++|+++.+- |--. +.++..+. .|..+.++|.+....|-
T Consensus 45 ~~~~~l~~lpgIG~~ia~kI~Eil~tG~~~~~~e~l~~~~p~~l~~l~~i~GiGpk~a~~l~ 106 (334)
T smart00483 45 NSMKDLKGLPGIGDKIKKKIEEIIETGKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKWY 106 (334)
T ss_pred CCHHHHhcCCCccHHHHHHHHHHHHhCcHHHHHHHhcCcHHHHHHHHHccCCcCHHHHHHHH
Confidence 34556779999999999999874 6544 33333221 35566666665555443
No 252
>PRK03352 DNA polymerase IV; Validated
Probab=48.99 E-value=31 Score=35.44 Aligned_cols=56 Identities=16% Similarity=0.324 Sum_probs=39.6
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--CCCCHH
Q 012388 255 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRTLD 320 (464)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--Girtle 320 (464)
.+..|||||++++++...+ .+..+.+|.+-.+....+.| |++.+..||+. |+....
T Consensus 178 pl~~l~gig~~~~~~L~~~----Gi~ti~dl~~l~~~~L~~~f------G~~~~~~l~~~a~G~d~~~ 235 (346)
T PRK03352 178 PTDALWGVGPKTAKRLAAL----GITTVADLAAADPAELAATF------GPTTGPWLLLLARGGGDTE 235 (346)
T ss_pred CHHHcCCCCHHHHHHHHHc----CCccHHHHhcCCHHHHHHHh------ChHHHHHHHHHhCCCCCCC
Confidence 3778999999988876543 56777777765555555566 67788888875 775443
No 253
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=48.98 E-value=17 Score=34.41 Aligned_cols=40 Identities=28% Similarity=0.283 Sum_probs=31.8
Q ss_pred ccccc-hhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHh
Q 012388 248 FKIES-ADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEK 287 (464)
Q Consensus 248 ~~I~s-~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~ 287 (464)
.||+. +.+|.-|||||++++..|-|=-+..-+..++++++
T Consensus 123 ~PIt~RLH~LELLpGiGkK~m~~ILeERkkkpFeSFeDi~~ 163 (202)
T COG1491 123 EPITLRLHQLELLPGIGKKTMWAILEERKKKPFESFEDIKE 163 (202)
T ss_pred CcchHHHHHHHhcccccHHHHHHHHHHHhcCCCcCHHHHHH
Confidence 57765 47899999999999999888777777777776654
No 254
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=48.84 E-value=24 Score=40.90 Aligned_cols=48 Identities=25% Similarity=0.441 Sum_probs=33.5
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcC-HHHHHHHHHc
Q 012388 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIG-PATAQKLYEK 314 (464)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvG-pktA~~ly~~ 314 (464)
+..|||||...|..|.+ .-|++.+| .+-. .+.|+.+ || +++|+++|+-
T Consensus 759 L~~lPgI~~~~a~~ll~--~f~si~~l---~~as----~eeL~~~--iG~~~~A~~i~~f 807 (814)
T TIGR00596 759 LLKLPGVTKKNYRNLRK--KVKSIREL---AKLS----QNELNEL--IGDEEAAKRLYDF 807 (814)
T ss_pred HHHCCCCCHHHHHHHHH--HcCCHHHH---HhCC----HHHHHHH--hCCHHHHHHHHHH
Confidence 67999999999998866 45555544 3322 2223343 78 9999999973
No 255
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=48.65 E-value=34 Score=33.30 Aligned_cols=77 Identities=21% Similarity=0.177 Sum_probs=42.6
Q ss_pred hHHHHHHHHHHHhc-CCc-----cccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCH
Q 012388 232 RSFSYYKAIPVIEK-LPF-----KIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGP 305 (464)
Q Consensus 232 r~~aY~rAa~~l~~-lp~-----~I~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGp 305 (464)
|+..-+..+..+.. +.. .-...++|.+|||||..+|+.|-=+. -|+-. +- ...-+.++|.+ .|+.+
T Consensus 93 KA~~Lk~la~~i~~~~g~~~~~~~~~~re~Ll~l~GIG~kTAd~iLlya-~~rp~----fv--VDty~~Rv~~R-lG~~~ 164 (218)
T PRK13913 93 KAKRLIDLSENILKDFGSFENFKQEVTREWLLDQKGIGKESADAILCYV-CAKEV----MV--VDKYSYLFLKK-LGIEI 164 (218)
T ss_pred HHHHHHHHHHHHHHHcCCchhccCchHHHHHHcCCCccHHHHHHHHHHH-cCCCc----cc--cchhHHHHHHH-cCCCC
Confidence 45555555555532 211 11234679999999999999987554 33311 11 12336667754 36644
Q ss_pred ---HHHHHHHHcCC
Q 012388 306 ---ATAQKLYEKGH 316 (464)
Q Consensus 306 ---ktA~~ly~~Gi 316 (464)
..+++|+..++
T Consensus 165 ~~y~~~~~~~~~~l 178 (218)
T PRK13913 165 EDYDELQHFFEKGV 178 (218)
T ss_pred CCHHHHHHHHHHhh
Confidence 34555555444
No 256
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=48.50 E-value=26 Score=40.46 Aligned_cols=53 Identities=26% Similarity=0.446 Sum_probs=34.7
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--CCCC
Q 012388 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (464)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--Girt 318 (464)
+..|||||-+|..|....- +...-+|+. .++.-+. +-+|||++.++|.. |+..
T Consensus 551 v~~LPGVG~sm~~kL~s~~----i~tCgdLq~----~T~~kl~--k~~G~Klgq~i~~~CrG~Dd 605 (1016)
T KOG2093|consen 551 VDDLPGVGSSMKSKLVSQF----IQTCGDLQL----ITLIKLR--KVFGPKLGQKIYRGCRGIDD 605 (1016)
T ss_pred cccCCCccHHHHHHHHHhc----cchhHHHHH----HHHHHHH--hhhcccHHHHHHHhcCCCcC
Confidence 6789999999999876543 333333332 2333332 23499999999984 6643
No 257
>KOG1918 consensus 3-methyladenine DNA glycosidase [Replication, recombination and repair]
Probab=48.42 E-value=10 Score=36.96 Aligned_cols=58 Identities=22% Similarity=0.303 Sum_probs=42.1
Q ss_pred hhhcCCCCCCHHHHH---HHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHH
Q 012388 254 DQVKGLPGIGKSMQD---HIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLY 312 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~---kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly 312 (464)
+++.++ |+.+.=+. -+.|....|.+...+.+..-.....++++|+|.|||+=|++++.
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 455544 44443333 34555668888888887777777899999999999999999874
No 258
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=48.40 E-value=36 Score=30.25 Aligned_cols=42 Identities=10% Similarity=0.307 Sum_probs=26.7
Q ss_pred hHHHHHHHHHHHhc-CCccc-cchhhhcCCCCCCHHHHHHHHHH
Q 012388 232 RSFSYYKAIPVIEK-LPFKI-ESADQVKGLPGIGKSMQDHIQEI 273 (464)
Q Consensus 232 r~~aY~rAa~~l~~-lp~~I-~s~~~l~~lpgIG~~ia~kI~Ei 273 (464)
|+..-...+..|.. +...+ ...++|..|||||+.+|+.|.=+
T Consensus 48 ka~~i~~~a~~~~~~~~~~~~~~~~~L~~l~GIG~~tA~~~l~~ 91 (149)
T smart00478 48 KAKYLIELARILVEEYGGEVPDDREELLKLPGVGRKTANAVLSF 91 (149)
T ss_pred HHHHHHHHHHHHHHHHCCCccHHHHHHHcCCCCcHHHHHHHHHH
Confidence 55555555555542 22222 23577899999999999987654
No 259
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=47.87 E-value=14 Score=32.56 Aligned_cols=22 Identities=27% Similarity=0.540 Sum_probs=18.7
Q ss_pred HhhhccCcCHHHHHHHHHc-CCC
Q 012388 296 LFGEVWGIGPATAQKLYEK-GHR 317 (464)
Q Consensus 296 lf~~I~GvGpktA~~ly~~-Gir 317 (464)
-|+.|+|||..+|+.+.++ ||.
T Consensus 18 ALt~IyGIG~~~a~~I~~~~gi~ 40 (121)
T COG0099 18 ALTYIYGIGRRRAKEICKKAGID 40 (121)
T ss_pred hhhhhccccHHHHHHHHHHcCCC
Confidence 3678999999999999886 764
No 260
>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase. This model describes GlnD, the uridylyltransferase/uridylyl-removing enzyme for the nitrogen regulatory protein PII. Not all homologs of PII share the property of uridylyltransferase modification on the characteristic Tyr residue (see Prosite pattern PS00496 and document PDOC00439), but the modification site is preserved in the PII homolog of all species with a member of this family.
Probab=47.30 E-value=62 Score=37.70 Aligned_cols=50 Identities=18% Similarity=0.466 Sum_probs=37.0
Q ss_pred CCEEEEEcccccccCC-cCCCccEEEeCCCcc--hhhhHHHHHHHHHHhcccc
Q 012388 367 PEVIILCGGSYRRGKA-SCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMKFL 416 (464)
Q Consensus 367 p~~~v~~~GsyRRgke-~~gDvDiLit~~d~~--~~~~~l~~lv~~L~~~g~l 416 (464)
.++-+..+|||-||.- -..|||++|-+++.. ....++.+++..|-+.|+=
T Consensus 42 ~~~aliA~GgyGR~El~p~SDiDll~l~~~~~~~~~~~~~~~~~~~LwD~gl~ 94 (850)
T TIGR01693 42 SGIALVAVGGYGRGELAPYSDIDLLFLHDGKPAEEVEPKIERFLYPLWDLGFE 94 (850)
T ss_pred CCeEEEEeCCccccCcCCCCCCeEEEEeCCCCChHHHHHHHHHHHHHHhcCCC
Confidence 3566778899977654 578999999887543 3456788888888877764
No 261
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=47.00 E-value=13 Score=34.31 Aligned_cols=25 Identities=24% Similarity=0.225 Sum_probs=20.0
Q ss_pred HHHHhhhccCcCHHHHHHHHHc-CCC
Q 012388 293 TISLFGEVWGIGPATAQKLYEK-GHR 317 (464)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~-Gir 317 (464)
+.--|+.|+|||+.+|..+-+. ||.
T Consensus 28 v~~aLt~I~GIG~~~A~~I~~~lgi~ 53 (154)
T PTZ00134 28 VPYALTAIKGIGRRFAYLVCKKAGID 53 (154)
T ss_pred EEEeecccccccHHHHHHHHHHcCcC
Confidence 3344689999999999999876 764
No 262
>PRK03059 PII uridylyl-transferase; Provisional
Probab=46.35 E-value=64 Score=37.70 Aligned_cols=63 Identities=16% Similarity=0.387 Sum_probs=39.2
Q ss_pred HHHHHHHHHhhhc--CCCEEEEEcccccccC-CcCCCccEEEeCCCcc--hhhhHHHHHHHHHHhccc
Q 012388 353 QMERLLQKAGEEV--LPEVIILCGGSYRRGK-ASCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMKF 415 (464)
Q Consensus 353 ~i~~iv~~~~~~~--~p~~~v~~~GsyRRgk-e~~gDvDiLit~~d~~--~~~~~l~~lv~~L~~~g~ 415 (464)
.+..+++.+.... ..++-+..+|||-||. --..|||+||-+++.. .....+..++..|-+.|+
T Consensus 44 l~d~~l~~~~~~~~~~~~~alvAvGgyGR~EL~p~SDiDll~l~~~~~~~~~~~~i~~~~~~lwD~gL 111 (856)
T PRK03059 44 LVDQALRRLWQECGLPAGAALVAVGGYGRGELFPYSDVDLLVLLPDAPDAALDARIERFIGLCWDLGL 111 (856)
T ss_pred HHHHHHHHHHHhcCCCCCeEEEEcCCCCCcccCCCCCCEEEEEecCCcchHHHHHHHHHHHhhhccCC
Confidence 3444444443222 2456778899997765 4578999999987543 234556666665555554
No 263
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=45.89 E-value=29 Score=39.12 Aligned_cols=95 Identities=16% Similarity=0.200 Sum_probs=54.5
Q ss_pred CCCCCCCCCCCCCCCCCCCeEEEEecCCCCchHHHHHHHHHHhcCCEEEeec------CCCccEEEEcCC--hHHHHHHH
Q 012388 3 PKTTRKPTPALDSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKL------SKKVTHVLAMDL--EALLQQVS 74 (464)
Q Consensus 3 p~r~~~~~~~~~~~~~F~g~~vy~~~~~~g~~R~~~l~~~i~~~Gg~V~~~l------s~~VTHVV~~~~--~~~~~~l~ 74 (464)
|+.+|.++-+.. ..+|.|.-+||++..... --+.|.+++...||++...- ...-|-||+... -....|.+
T Consensus 573 ~~~~~~~a~s~~-~kLf~gl~~~~~g~fs~~-p~~~l~~l~~~~gg~~l~~~~~~~~~~k~s~~~~~~~~~~~~~~~~~k 650 (684)
T KOG4362|consen 573 PKEKRLRAESYK-PKLFEGLKFYFVGDFSNP-PKEQLQELVHLAGGTILQVPRVAYSDKKKSTIVVLSEKPVLDSILWQK 650 (684)
T ss_pred cccccccccccC-cchhcCCcceeecccccC-cHHHHHHHHhhcCcceeeccCcccccccccceeEeecccCCCchhhhh
Confidence 344444333333 379999999999864432 34678999999999987542 222333333211 00011222
Q ss_pred HHhhh----ccCccccccchHHHHHhcCC
Q 012388 75 KQHLA----RFKGSVIRYQWLEDSLRLGE 99 (464)
Q Consensus 75 ~~~~~----~~~~~iV~~~Wl~ec~k~g~ 99 (464)
...+. ....++|+-.||.+++.--+
T Consensus 651 ~~~~ea~~~s~~a~~~~~~wvl~s~a~~~ 679 (684)
T KOG4362|consen 651 VNDAEALALSQRARAVSSSWVLDSIAGYQ 679 (684)
T ss_pred hccHHHHHHhcCCCccchhhhhcchhcee
Confidence 11111 12578999999999986433
No 264
>TIGR00194 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.
Probab=45.79 E-value=17 Score=40.33 Aligned_cols=30 Identities=27% Similarity=0.346 Sum_probs=24.7
Q ss_pred HHhhhccCcCHHHHHHHHHcCCCCHHHHhhc
Q 012388 295 SLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (464)
Q Consensus 295 ~lf~~I~GvGpktA~~ly~~GirtledL~~~ 325 (464)
..|.+|+|||||+.+.|++ -+.|+++++++
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 4566999999999999998 46688888764
No 265
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=45.77 E-value=35 Score=39.27 Aligned_cols=48 Identities=17% Similarity=0.493 Sum_probs=33.7
Q ss_pred CEEEEEcccccccCC-cCCCccEEEeCCCcchh--hhHHHHHHHHHHhccc
Q 012388 368 EVIILCGGSYRRGKA-SCGDLDVVIMHPDRKSH--KGFLSKYVKKLKEMKF 415 (464)
Q Consensus 368 ~~~v~~~GsyRRgke-~~gDvDiLit~~d~~~~--~~~l~~lv~~L~~~g~ 415 (464)
++-++.+|||-||.- -+.|||+||-+|...+. ..-+..++--|=+.||
T Consensus 66 ~~aLvAVGGyGRgEL~P~SDiDlL~L~p~~~~~~~e~~ie~~l~~LWD~gl 116 (867)
T COG2844 66 GLALVAVGGYGRGELHPLSDIDLLLLSPQKLTDWLEQKIERFLYLLWDLGL 116 (867)
T ss_pred ceEEEEeccccccccCCCccceEEEecCCCCChHHHHHHHHHHHHHHhcCc
Confidence 456778899988864 58899999999876542 3445555555555555
No 266
>PF02961 BAF: Barrier to autointegration factor; InterPro: IPR004122 Barrier-to-autointegration factor (BAF) is an essential protein that is highly conserved in metazoan evolution, and which may act as a DNA-bridging protein []. BAF binds directly to double-stranded DNA, to transcription activators, and to inner nuclear membrane proteins, including lamin A filament proteins that anchor nuclear-pore complexes in place, and nuclear LEM-domain proteins that bind to laminins filaments and chromatin. New findings suggest that BAF has structural roles in nuclear assembly and chromatin organisation, represses gene expression and might interlink chromatin structure, nuclear architecture and gene regulation in metazoans []. BAF can be exploited by retroviruses to act as a host component of pre-integration complexes, which promote the integration of the retroviral DNA into the host chromosome by preventing autointegration of retroviral DNA []. BAF might contribute to the assembly or activity of retroviral pre-integration complexes through direct binding to the retroviral proteins p55 Gag and matrix, as well as to DNA.; GO: 0003677 DNA binding; PDB: 2ODG_A 2BZF_A 2EZX_B 2EZY_B 1QCK_B 1CI4_B 2EZZ_B.
Probab=45.16 E-value=17 Score=30.41 Aligned_cols=27 Identities=33% Similarity=0.449 Sum_probs=19.9
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHHh
Q 012388 297 FGEVWGIGPATAQKLYEKGHRTLDDLK 323 (464)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~ 323 (464)
-+.++||||..+++|-++|+.---.|.
T Consensus 21 V~~laGIG~~lg~~L~~~GfdKAy~vL 47 (89)
T PF02961_consen 21 VTELAGIGPVLGKRLEEKGFDKAYVVL 47 (89)
T ss_dssp GGGSTT--HHHHHHHHHTT--BHHHHH
T ss_pred ccccCCcCHHHHHHHHHCCCcHHHHHh
Confidence 468999999999999999998766665
No 267
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=44.96 E-value=55 Score=36.94 Aligned_cols=72 Identities=19% Similarity=0.110 Sum_probs=53.2
Q ss_pred CCCCCeEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCChHHHHHHHHHhhhccCccccccchHHH
Q 012388 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLEALLQQVSKQHLARFKGSVIRYQWLED 93 (464)
Q Consensus 17 ~~F~g~~vy~~~~~~g~~R~~~l~~~i~~~Gg~V~~~ls~~VTHVV~~~~~~~~~~l~~~~~~~~~~~iV~~~Wl~e 93 (464)
..|.|.++.|-++--+-+| +..+.++...||.|..++|..+.-||+.++--. +..++...+.+|++-+++.+
T Consensus 593 ~~l~gkt~V~TGtL~~~sR-~eak~~le~lGakv~~SVSkktD~vvaG~~aGS----Kl~kA~eLgv~i~~E~~~~~ 664 (667)
T COG0272 593 SPLAGKTFVLTGTLEGMSR-DEAKALLEALGAKVSGSVSKKTDYVVAGENAGS----KLAKAQELGVKIIDEEEFLA 664 (667)
T ss_pred cccCCCEEEEeccCCCCCH-HHHHHHHHHcCCEEeceecccccEEEEcCCCCh----HHHHHHHcCCeEecHHHHHH
Confidence 6799999999876444455 467999999999999999999988888665321 22233345778888777765
No 268
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=44.91 E-value=15 Score=33.68 Aligned_cols=25 Identities=28% Similarity=0.324 Sum_probs=20.1
Q ss_pred HHHHhhhccCcCHHHHHHHHHc-CCC
Q 012388 293 TISLFGEVWGIGPATAQKLYEK-GHR 317 (464)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~-Gir 317 (464)
+.--|+.|+|||+++|..+-+. ||.
T Consensus 23 i~~aLt~IyGIG~~~a~~Ic~~lgi~ 48 (149)
T PRK04053 23 VEYALTGIKGIGRRTARAIARKLGLD 48 (149)
T ss_pred EeeeccccccccHHHHHHHHHHcCcC
Confidence 3334689999999999999886 865
No 269
>PRK13766 Hef nuclease; Provisional
Probab=44.69 E-value=16 Score=41.69 Aligned_cols=46 Identities=20% Similarity=0.347 Sum_probs=33.6
Q ss_pred HhhhccCcCHHHHHHHHHcCCCCHHHHhhcc--CcchHHHhhHhhHHhh
Q 012388 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKNED--SLTHSQRLGLKYFDDI 342 (464)
Q Consensus 296 lf~~I~GvGpktA~~ly~~GirtledL~~~~--~L~~~q~~Glk~~ed~ 342 (464)
+|..|+|||+++|++|.+. +.|++++.... .|....++|.+..+.|
T Consensus 716 ~L~~ipgig~~~a~~Ll~~-fgs~~~i~~as~~~L~~i~Gig~~~a~~i 763 (773)
T PRK13766 716 IVESLPDVGPVLARNLLEH-FGSVEAVMTASEEELMEVEGIGEKTAKRI 763 (773)
T ss_pred HHhcCCCCCHHHHHHHHHH-cCCHHHHHhCCHHHHHhCCCCCHHHHHHH
Confidence 5789999999999999985 45888887643 3555556665555444
No 270
>PRK03858 DNA polymerase IV; Validated
Probab=44.25 E-value=40 Score=35.28 Aligned_cols=53 Identities=19% Similarity=0.325 Sum_probs=37.4
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--CCC
Q 012388 255 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHR 317 (464)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--Gir 317 (464)
.+..|||||+++++++..+ .+..+.+|.+-.+....+.| |+..++.||+. |+.
T Consensus 174 pl~~l~Gig~~~~~~L~~~----Gi~t~~dl~~l~~~~L~~~f------G~~~~~~l~~~a~G~d 228 (396)
T PRK03858 174 PVRRLWGVGPVTAAKLRAH----GITTVGDVAELPESALVSLL------GPAAGRHLHALAHNRD 228 (396)
T ss_pred ChhhcCCCCHHHHHHHHHh----CCCcHHHHhcCCHHHHHHHh------CcHHHHHHHHHhCCCC
Confidence 3677899999999988764 35666666654444455556 67788888863 764
No 271
>PF09970 DUF2204: Nucleotidyl transferase of unknown function (DUF2204); InterPro: IPR018700 This family of hypothetical prokaryotic proteins has no known function.
Probab=44.05 E-value=51 Score=30.98 Aligned_cols=39 Identities=18% Similarity=0.211 Sum_probs=25.7
Q ss_pred CEEEEEcccc-----cccCCcCCCccEEEeCCCcchhhhHHHHH
Q 012388 368 EVIILCGGSY-----RRGKASCGDLDVVIMHPDRKSHKGFLSKY 406 (464)
Q Consensus 368 ~~~v~~~Gsy-----RRgke~~gDvDiLit~~d~~~~~~~l~~l 406 (464)
|+.+.+.||+ -..+.+.+|||+.|..++......++..+
T Consensus 16 gv~~~ivGG~av~l~~g~~r~T~DIDlfi~~~~~~~~~~~~~~~ 59 (181)
T PF09970_consen 16 GVEYVIVGGAAVNLAYGRRRTTKDIDLFIENPSPNLEADALREV 59 (181)
T ss_pred CCeEEEECHHHHHHHhCCCCCCCCeEEEeCCCchHHHHHHHHHH
Confidence 5666666763 24567899999999877665444444333
No 272
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=43.72 E-value=52 Score=34.21 Aligned_cols=77 Identities=16% Similarity=0.248 Sum_probs=50.1
Q ss_pred HHHHHHHcCCChhHHHHHHHHHHHhc-CCcccc-chhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHh
Q 012388 220 LINIYRALGEDRRSFSYYKAIPVIEK-LPFKIE-SADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLF 297 (464)
Q Consensus 220 la~~~e~~g~~~r~~aY~rAa~~l~~-lp~~I~-s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf 297 (464)
+-.+++=.|--.|++...+||..+.. +...+. +.+++..|||||..+|..|--|.=.-...-|+ -.++..|
T Consensus 77 vl~~W~gLGYysRArnL~~~A~~v~~~~~G~~P~~~~~l~~LpGiG~yTa~Ail~~a~~~~~~~lD-------gNV~RVl 149 (342)
T COG1194 77 VLKAWEGLGYYSRARNLHKAAQEVVERHGGEFPDDEEELAALPGVGPYTAGAILSFAFNQPEPVLD-------GNVKRVL 149 (342)
T ss_pred HHHHHHhcChHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHhCCCCcHHHHHHHHHHHhCCCCceee-------cchheee
Confidence 33555555655688888898887764 454554 45789999999999999998776443333333 1244445
Q ss_pred hhccCc
Q 012388 298 GEVWGI 303 (464)
Q Consensus 298 ~~I~Gv 303 (464)
.++++|
T Consensus 150 ~R~f~i 155 (342)
T COG1194 150 SRLFAI 155 (342)
T ss_pred hhhhcc
Confidence 555554
No 273
>COG5067 DBF4 Protein kinase essential for the initiation of DNA replication [DNA replication, recombination, and repair / Cell division and chromosome partitioning]
Probab=43.53 E-value=15 Score=38.60 Aligned_cols=48 Identities=19% Similarity=0.305 Sum_probs=37.0
Q ss_pred CCCCCCCCeEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEE
Q 012388 14 DSNGIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLA 63 (464)
Q Consensus 14 ~~~~~F~g~~vy~~~~~~g~~R~~~l~~~i~~~Gg~V~~~ls~~VTHVV~ 63 (464)
..-..|+.+..|+... -+ .+...+++.+-..||.|+.-++..||||+.
T Consensus 118 ~Y~~aFp~f~fY~dn~-s~-~~khRvk~gf~~LGa~v~tfF~~~VThfiT 165 (468)
T COG5067 118 TYCCAFPAFKFYKDNK-SG-KRKHRVKEGFCELGAVVFTFFEEHVTHFIT 165 (468)
T ss_pred hhhcccchhhhhhcCC-CH-HHHHHHHHHHHHhhhhhheeeccceEEEEE
Confidence 3346788888888642 22 233348999999999999999999999996
No 274
>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=43.21 E-value=58 Score=33.91 Aligned_cols=55 Identities=16% Similarity=0.299 Sum_probs=34.8
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhh--chhHHHHHhhhccCcCHHHHHHHHHc--CCCC
Q 012388 255 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKD--EKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (464)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~--~~~~~l~lf~~I~GvGpktA~~ly~~--Girt 318 (464)
.+..|||||++++.++.+-+ .+..+.+|.+- .+....+.| |.+.+..+|+. |+..
T Consensus 183 pv~~l~GiG~~~~~~ll~~~---Gi~ti~dl~~~~~~~~~L~~~f------G~~~g~~l~~~a~G~d~ 241 (359)
T cd01702 183 PITSIRGLGGKLGEEIIDLL---GLPTEGDVAGFRSSESDLQEHF------GEKLGEWLYNLLRGIDH 241 (359)
T ss_pred cHHHhCCcCHHHHHHHHHHc---CCcCHHHHHhccCCHHHHHHHH------HHHHHHHHHHHhCCCCC
Confidence 36788999998876543322 24445555443 344455556 77888999875 8764
No 275
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=42.72 E-value=17 Score=33.11 Aligned_cols=22 Identities=27% Similarity=0.365 Sum_probs=18.8
Q ss_pred HhhhccCcCHHHHHHHHHc-CCC
Q 012388 296 LFGEVWGIGPATAQKLYEK-GHR 317 (464)
Q Consensus 296 lf~~I~GvGpktA~~ly~~-Gir 317 (464)
-|+.|+|||+++|..+-+. ||.
T Consensus 22 aLt~I~GIG~~~a~~I~~~lgi~ 44 (144)
T TIGR03629 22 ALTGIKGIGRRFARAIARKLGVD 44 (144)
T ss_pred eecceeccCHHHHHHHHHHcCcC
Confidence 4579999999999999876 764
No 276
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=41.82 E-value=16 Score=37.22 Aligned_cols=24 Identities=38% Similarity=0.479 Sum_probs=18.4
Q ss_pred hhccCcCHHHHHHHHHcCCCCHHHH
Q 012388 298 GEVWGIGPATAQKLYEKGHRTLDDL 322 (464)
Q Consensus 298 ~~I~GvGpktA~~ly~~GirtledL 322 (464)
.+|+|||||||.+|.++ +.|++.+
T Consensus 226 ~gv~giG~k~A~~li~~-~~~~~~~ 249 (316)
T cd00128 226 EGIPGIGPVTALKLIKK-YGDIEKD 249 (316)
T ss_pred CCCCCccHHHHHHHHHH-cCChHHH
Confidence 47999999999999987 3354333
No 277
>cd01701 PolY_Rev1 DNA polymerase Rev1. Rev1 is a translesion synthesis (TLS) polymerase found in eukaryotes. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Rev1 has both structural and enzymatic roles. Structurally, it is believed to interact with other nonclassical polymerases and replication machinery to act as a scaffold. Enzymatically, it catalyzes the specific insertion of dCMP opposite abasic sites. Rev1 interacts with the Rev7 subunit of the B-family TLS polymerase Pol zeta (Rev3/Rev7). Rev1 is known to actively promote the introduction of mutations, potentially making it a significant target for cancer treatment.
Probab=41.50 E-value=46 Score=35.12 Aligned_cols=54 Identities=28% Similarity=0.488 Sum_probs=36.4
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhc--hhHHHHHhhhccCcCHHHHHHHHHc--CCCC
Q 012388 255 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDE--KVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (464)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~--~~~~l~lf~~I~GvGpktA~~ly~~--Girt 318 (464)
.+..|||||+++++++..+ | +..+.++.+-. +....+.| |++.+..||+. |+..
T Consensus 223 Pv~~l~GIG~~~~~~L~~~---G-i~t~~dl~~~~~~~~~L~~~f------G~~~g~~L~~~a~G~d~ 280 (404)
T cd01701 223 KVGDLPGVGSSLAEKLVKL---F-GDTCGGLELRSKTKEKLQKVL------GPKTGEKLYDYCRGIDD 280 (404)
T ss_pred CHhHhCCCCHHHHHHHHHc---C-CcchHHHHhCcccHHHHHHHH------CHHHHHHHHHHhCCcCC
Confidence 3678899999988877653 3 34444544433 44455666 78889998875 8765
No 278
>PRK03381 PII uridylyl-transferase; Provisional
Probab=41.06 E-value=73 Score=36.80 Aligned_cols=48 Identities=21% Similarity=0.306 Sum_probs=33.7
Q ss_pred CEEEEEcccccccCC-cCCCccEEEeCCCcc--hhhhHHHHHHHHHHhccc
Q 012388 368 EVIILCGGSYRRGKA-SCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMKF 415 (464)
Q Consensus 368 ~~~v~~~GsyRRgke-~~gDvDiLit~~d~~--~~~~~l~~lv~~L~~~g~ 415 (464)
.+-++.+|||-||.- -..|||+||-+++.. ....++..++--|-+.|+
T Consensus 57 ~~alvAvg~~gr~el~p~SD~Dll~l~~~~~~~~~~~~~~~~~~~LwD~gl 107 (774)
T PRK03381 57 GVALVAVGGLGRRELLPYSDLDLVLLHDGRPADDVAEVADRLWYPLWDAGI 107 (774)
T ss_pred CeEEEEeCCcCCcCcCCCCCCeEEEEeCCCCchHHHHHHHHHhhhcccCCC
Confidence 356778899977654 567999999987543 345667777776666665
No 279
>cd00424 PolY Y-family of DNA polymerases. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Most TLS polymerases are members of the Y-family, including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is found exclusively in bacteria. In eukaryotes, the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in ord
Probab=40.65 E-value=69 Score=32.83 Aligned_cols=53 Identities=19% Similarity=0.456 Sum_probs=33.6
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--CCCC
Q 012388 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (464)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--Girt 318 (464)
+..|||||+++.+++..+ | +..+.+|.+-.....+..+ + | +.+..+|+. |+..
T Consensus 175 i~~l~giG~~~~~~L~~~---G-i~ti~dl~~~~~~~~l~~~---f--g-~~~~~l~~~a~G~d~ 229 (343)
T cd00424 175 LTDLPGIGAVTAKRLEAV---G-INPIGDLLAASPDALLALW---G--G-VSGERLWYALRGIDD 229 (343)
T ss_pred hhhcCCCCHHHHHHHHHc---C-CCcHHHHhcCCHHHHHHHH---h--h-HHHHHHHHHhCCcCC
Confidence 677899999999987754 3 5566666553313333332 2 3 567777765 8754
No 280
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=40.61 E-value=39 Score=32.65 Aligned_cols=21 Identities=24% Similarity=0.411 Sum_probs=17.6
Q ss_pred cchhhhc-CCCCCCHHHHHHHH
Q 012388 251 ESADQVK-GLPGIGKSMQDHIQ 271 (464)
Q Consensus 251 ~s~~~l~-~lpgIG~~ia~kI~ 271 (464)
...++|. +|||||.++|+.|-
T Consensus 115 ~~R~~Ll~~lpGIG~KTAd~vL 136 (208)
T PRK01229 115 EAREFLVKNIKGIGYKEASHFL 136 (208)
T ss_pred HHHHHHHHcCCCCcHHHHHHHH
Confidence 3447788 99999999999865
No 281
>PHA00439 exonuclease
Probab=40.42 E-value=20 Score=36.29 Aligned_cols=27 Identities=19% Similarity=0.284 Sum_probs=21.6
Q ss_pred hhccCcCHHHHHHHHHc--CCCCHHHHhhc
Q 012388 298 GEVWGIGPATAQKLYEK--GHRTLDDLKNE 325 (464)
Q Consensus 298 ~~I~GvGpktA~~ly~~--GirtledL~~~ 325 (464)
-+|+||| |||.+|.++ .+..++...+.
T Consensus 191 PGVpGIG-KTA~kLL~~~~~~~~~~~~~~s 219 (286)
T PHA00439 191 SGIPGWG-DTAEAFLENPYIFEQVEKVLKS 219 (286)
T ss_pred CCCCCcC-HHHHHHHhCccccchhhHHhhc
Confidence 3799999 999999998 66777666544
No 282
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=40.18 E-value=26 Score=28.02 Aligned_cols=29 Identities=31% Similarity=0.543 Sum_probs=21.5
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHH
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEH 284 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~ 284 (464)
+-+.++||||++.|.+|- .+.|++..+-.
T Consensus 22 D~i~gv~giG~k~A~~ll--~~~~~~~~~~~ 50 (75)
T cd00080 22 DNIPGVPGIGPKTALKLL--KEYGSLENLLE 50 (75)
T ss_pred ccCCCCCcccHHHHHHHH--HHhCCHHHHHH
Confidence 346799999999998873 56677666543
No 283
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=40.05 E-value=23 Score=39.85 Aligned_cols=27 Identities=44% Similarity=0.650 Sum_probs=25.3
Q ss_pred hhhccCcCHHHHHHHHHcCCCCHHHHh
Q 012388 297 FGEVWGIGPATAQKLYEKGHRTLDDLK 323 (464)
Q Consensus 297 f~~I~GvGpktA~~ly~~GirtledL~ 323 (464)
+..+.||||++|.++-+.||+|+.||.
T Consensus 12 l~~l~gig~~~a~~l~~Lgi~tv~DLL 38 (677)
T COG1200 12 LSTLKGIGPKTAEKLKKLGIHTVQDLL 38 (677)
T ss_pred hhhhcCcCHHHHHHHHHcCCCcHHHHH
Confidence 568899999999999999999999998
No 284
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=39.92 E-value=49 Score=33.37 Aligned_cols=44 Identities=20% Similarity=0.384 Sum_probs=30.7
Q ss_pred CCC-hhHHHHHHHHHHHhc--CCccc-c----chhhhcCCCCCCHHHHHHHH
Q 012388 228 GED-RRSFSYYKAIPVIEK--LPFKI-E----SADQVKGLPGIGKSMQDHIQ 271 (464)
Q Consensus 228 g~~-~r~~aY~rAa~~l~~--lp~~I-~----s~~~l~~lpgIG~~ia~kI~ 271 (464)
|-. .|+..-..+|.++.+ ++... . ..++|..|||||+.+|+-|.
T Consensus 173 Gl~~~Ra~~L~~lA~~i~~g~l~l~~~~~~~~~~~~L~~LpGIGpwTA~~vl 224 (283)
T PRK10308 173 GMPLKRAEALIHLANAALEGTLPLTIPGDVEQAMKTLQTFPGIGRWTANYFA 224 (283)
T ss_pred CCCHHHHHHHHHHHHHHHcCCCCccccCCHHHHHHHHhcCCCcCHHHHHHHH
Confidence 444 477777788877754 43221 1 24679999999999999775
No 285
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=39.58 E-value=58 Score=30.94 Aligned_cols=57 Identities=19% Similarity=0.325 Sum_probs=34.0
Q ss_pred HHHHHHHHhCCchhhHHHHhhchhH-HHHHhhhccCcCHHHHHHHHHc----CCCCHHHHhh
Q 012388 268 DHIQEIVTTGKLSKLEHFEKDEKVR-TISLFGEVWGIGPATAQKLYEK----GHRTLDDLKN 324 (464)
Q Consensus 268 ~kI~Eil~tG~~~~le~l~~~~~~~-~l~lf~~I~GvGpktA~~ly~~----GirtledL~~ 324 (464)
..+++|+..-.=..++-+-..+|.. -|-.|.=+||||-|+.+.+.++ -+.|++|+++
T Consensus 102 yvve~iV~~~E~rFV~fFN~A~PIt~RLH~LELLpGiGkK~m~~ILeERkkkpFeSFeDi~~ 163 (202)
T COG1491 102 YVVEKIVKENEDRFVKFFNEAEPITLRLHQLELLPGIGKKTMWAILEERKKKPFESFEDIKE 163 (202)
T ss_pred HHHHHHHHhhhhHHHHHhcccCcchHHHHHHHhcccccHHHHHHHHHHHhcCCCcCHHHHHH
Confidence 3455666554434444332222221 1233445699999999999863 7888888875
No 286
>PTZ00035 Rad51 protein; Provisional
Probab=39.41 E-value=32 Score=35.54 Aligned_cols=31 Identities=29% Similarity=0.363 Sum_probs=22.6
Q ss_pred HHHhhhccCcCHHHHHHHHHcCCCCHHHHhhc
Q 012388 294 ISLFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (464)
Q Consensus 294 l~lf~~I~GvGpktA~~ly~~GirtledL~~~ 325 (464)
++.+ .-+||||.++++|-+.||.|++||...
T Consensus 23 ~~~l-~~~g~~~~~~~kL~~~g~~t~~~~~~~ 53 (337)
T PTZ00035 23 IEKL-QSAGINAADIKKLKEAGICTVESVAYA 53 (337)
T ss_pred HHHH-hcCCCCHHHHHHHHHcCCCcHHHHHhC
Confidence 4444 337888888888888888888888743
No 287
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=38.06 E-value=49 Score=31.97 Aligned_cols=37 Identities=22% Similarity=0.277 Sum_probs=23.9
Q ss_pred HHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHH
Q 012388 270 IQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKL 311 (464)
Q Consensus 270 I~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l 311 (464)
+.+++.. +..++.+. +....+.|.+|.|||+-||..+
T Consensus 95 ~k~l~~~--~~~~~~~~---~~~~R~~LL~iKGIG~ETaDsI 131 (215)
T COG2231 95 SKNLAKF--FINLESFK---SEVLREELLSIKGIGKETADSI 131 (215)
T ss_pred HHHHHHH--hhhhhccc---hHHHHHHHHccCCcchhhHHHH
Confidence 3666543 33444433 2226677779999999999875
No 288
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=38.04 E-value=31 Score=35.85 Aligned_cols=31 Identities=26% Similarity=0.292 Sum_probs=23.3
Q ss_pred HHHHhhhccCcCHHHHHHHHHcCCCCHHHHhh
Q 012388 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKN 324 (464)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~GirtledL~~ 324 (464)
.++.+ .-.||+|+++++|-+.||.|++||..
T Consensus 30 ~~~~l-~~~g~~~~~~~kL~~~g~~tv~~~~~ 60 (344)
T PLN03187 30 SIDKL-ISQGINAGDVKKLQDAGIYTCNGLMM 60 (344)
T ss_pred CHHHH-hhCCCCHHHHHHHHHcCCCcHHHHHh
Confidence 34445 33788888888888888888888864
No 289
>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=36.85 E-value=28 Score=28.41 Aligned_cols=43 Identities=19% Similarity=0.441 Sum_probs=27.1
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHH
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPAT 307 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpkt 307 (464)
+-|..|||||.-++..|- .+.|.+.....- +-|.+-.|+-|..
T Consensus 2 ~~l~sipGig~~~a~~ll--aeigd~~rF~~~---------~~l~~~~Gl~P~~ 44 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLL--AEIGDISRFKSA---------KQLASYAGLAPRP 44 (87)
T ss_pred chhcCCCCccHHHHHHHH--HHHcCchhcccc---------hhhhhcccccccc
Confidence 347899999999888763 344666554432 2245556666654
No 290
>PRK03348 DNA polymerase IV; Provisional
Probab=35.90 E-value=71 Score=34.40 Aligned_cols=54 Identities=17% Similarity=0.327 Sum_probs=39.7
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--CCCC
Q 012388 255 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (464)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--Girt 318 (464)
.+..|||||+.+.++...+ .+..+.+|.+-.+..+.+.| |.+.+..||+. |+..
T Consensus 181 Pv~~L~GIG~~t~~~L~~l----GI~TigDLa~l~~~~L~~~f------G~~~g~~L~~~a~G~d~ 236 (454)
T PRK03348 181 PVRRLWGIGPVTEEKLHRL----GIETIGDLAALSEAEVANLL------GATVGPALHRLARGIDD 236 (454)
T ss_pred CccccCCCCHHHHHHHHHc----CCccHHHHhcCCHHHHHHHH------CHHHHHHHHHHHcCCCC
Confidence 3678899999988876544 55667777665566677777 77888899874 8754
No 291
>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=35.80 E-value=31 Score=35.25 Aligned_cols=24 Identities=29% Similarity=0.346 Sum_probs=16.2
Q ss_pred cCcCHHHHHHHHHcCCCCHHHHhh
Q 012388 301 WGIGPATAQKLYEKGHRTLDDLKN 324 (464)
Q Consensus 301 ~GvGpktA~~ly~~GirtledL~~ 324 (464)
.|||+.++++|-+.||.|++||..
T Consensus 7 ~g~~~~~~~~L~~~g~~t~~~~~~ 30 (313)
T TIGR02238 7 HGINAADIKKLKSAGICTVNGVIM 30 (313)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHh
Confidence 456777777776667777776653
No 292
>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=35.74 E-value=3.1e+02 Score=28.36 Aligned_cols=87 Identities=10% Similarity=0.208 Sum_probs=54.7
Q ss_pred HHHHHHHHhcCCccccc--hhhhcCCCCCCHHHHHHHHHHHHh------------CCchhhHHHHhhchhHHH-HHhhhc
Q 012388 236 YYKAIPVIEKLPFKIES--ADQVKGLPGIGKSMQDHIQEIVTT------------GKLSKLEHFEKDEKVRTI-SLFGEV 300 (464)
Q Consensus 236 Y~rAa~~l~~lp~~I~s--~~~l~~lpgIG~~ia~kI~Eil~t------------G~~~~le~l~~~~~~~~l-~lf~~I 300 (464)
-..||.+|..||..... ...+.++..|.+.+.+.|.++|+. |....+-++.+..+...- .+|..+
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 45799999999976443 356788888888888877555541 222334444444444433 455555
Q ss_pred cCcCHHHHHHHHHcCCCCHHHHh
Q 012388 301 WGIGPATAQKLYEKGHRTLDDLK 323 (464)
Q Consensus 301 ~GvGpktA~~ly~~GirtledL~ 323 (464)
--.-|..|..+- .-+-+++||.
T Consensus 224 ~~~dp~la~~Ir-~~mF~Fedl~ 245 (338)
T TIGR00207 224 EEFDPELAEEIK-KEMFVFEDIV 245 (338)
T ss_pred HHhCHHHHHHHH-HHccCHHHHh
Confidence 556677777663 3566777776
No 293
>PRK10880 adenine DNA glycosylase; Provisional
Probab=35.01 E-value=28 Score=36.36 Aligned_cols=23 Identities=22% Similarity=0.286 Sum_probs=19.0
Q ss_pred HHHHHhhhccCcCHHHHHHHHHc
Q 012388 292 RTISLFGEVWGIGPATAQKLYEK 314 (464)
Q Consensus 292 ~~l~lf~~I~GvGpktA~~ly~~ 314 (464)
..++.|+++||||++||..+---
T Consensus 106 ~~~~~L~~LpGIG~~TA~aIl~~ 128 (350)
T PRK10880 106 ETFEEVAALPGVGRSTAGAILSL 128 (350)
T ss_pred hhHHHHhcCCCccHHHHHHHHHH
Confidence 45677889999999999987654
No 294
>COG1031 Uncharacterized Fe-S oxidoreductase [Energy production and conversion]
Probab=34.93 E-value=33 Score=37.01 Aligned_cols=33 Identities=15% Similarity=0.312 Sum_probs=29.6
Q ss_pred HHHHhhhccCcCHHHHHHHHHc-CCCCHHHHhhc
Q 012388 293 TISLFGEVWGIGPATAQKLYEK-GHRTLDDLKNE 325 (464)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~-GirtledL~~~ 325 (464)
..+.++.|||||.+++.+++.. .++|.||+++.
T Consensus 514 s~~vl~~ipgig~~~~~~I~~~Rp~~s~e~~l~~ 547 (560)
T COG1031 514 SKDVLRAIPGIGKKTLRKILAERPFKSSEEFLKL 547 (560)
T ss_pred cHHHHHhcccchhhhHHHHHhcCCccchHHHHhc
Confidence 4788999999999999999987 99999999853
No 295
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=34.88 E-value=38 Score=32.39 Aligned_cols=22 Identities=27% Similarity=0.496 Sum_probs=18.7
Q ss_pred hhhcCCCCCCHHHHHHHHHHHH
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVT 275 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~ 275 (464)
+.+..|||||++.|.++.=.|-
T Consensus 12 ~~l~kLPGvG~KsA~R~AfhLL 33 (198)
T COG0353 12 DALKKLPGVGPKSAQRLAFHLL 33 (198)
T ss_pred HHHhhCCCCChhHHHHHHHHHH
Confidence 6789999999999999976553
No 296
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=34.59 E-value=53 Score=29.24 Aligned_cols=61 Identities=20% Similarity=0.424 Sum_probs=45.6
Q ss_pred CHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHHhhccCcchHHHhhH
Q 012388 263 GKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGL 336 (464)
Q Consensus 263 G~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~~~L~~~q~~Gl 336 (464)
=..|++.|.+-+-+|.+..=+. ..++..|..-.||-|.|+++-|+ +|++++-+....+.|.
T Consensus 13 Y~QI~~qIk~~I~~g~l~pGdk------LPSvRelA~~~~VNpnTv~raY~-------eLE~eG~i~t~rg~G~ 73 (125)
T COG1725 13 YEQIANQIKEQIASGELKPGDK------LPSVRELAKDLGVNPNTVQRAYQ-------ELEREGIVETKRGKGT 73 (125)
T ss_pred HHHHHHHHHHHHHhCCcCCCCC------CCcHHHHHHHhCCCHHHHHHHHH-------HHHHCCCEEEecCeeE
Confidence 3568999999999999876554 34566677888999999999997 5666665555555553
No 297
>PRK13910 DNA glycosylase MutY; Provisional
Probab=34.04 E-value=28 Score=35.33 Aligned_cols=22 Identities=23% Similarity=0.153 Sum_probs=17.9
Q ss_pred HHHHhhhccCcCHHHHHHHHHc
Q 012388 293 TISLFGEVWGIGPATAQKLYEK 314 (464)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~ 314 (464)
..+.|+++||||++||..+---
T Consensus 70 ~~~~L~~LpGIG~kTA~aIl~~ 91 (289)
T PRK13910 70 DYQSLLKLPGIGAYTANAILCF 91 (289)
T ss_pred hHHHHHhCCCCCHHHHHHHHHH
Confidence 4667779999999999987654
No 298
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=33.18 E-value=29 Score=38.61 Aligned_cols=29 Identities=24% Similarity=0.474 Sum_probs=22.9
Q ss_pred HhhhccCcCHHHHHHHHHcCCCCHHHHhhc
Q 012388 296 LFGEVWGIGPATAQKLYEKGHRTLDDLKNE 325 (464)
Q Consensus 296 lf~~I~GvGpktA~~ly~~GirtledL~~~ 325 (464)
-|-+|+|||+++.++|.+ .+.|+++++++
T Consensus 531 ~Ld~I~GiG~~r~~~LL~-~Fgs~~~i~~A 559 (581)
T COG0322 531 SLDDIPGIGPKRRKALLK-HFGSLKGIKSA 559 (581)
T ss_pred ccccCCCcCHHHHHHHHH-HhhCHHHHHhc
Confidence 355899999999999987 45577777754
No 299
>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=31.77 E-value=1e+02 Score=31.52 Aligned_cols=25 Identities=32% Similarity=0.412 Sum_probs=21.5
Q ss_pred cCcCHHHHHHHHHcCCCCHHHHhhc
Q 012388 301 WGIGPATAQKLYEKGHRTLDDLKNE 325 (464)
Q Consensus 301 ~GvGpktA~~ly~~GirtledL~~~ 325 (464)
.||++.++.+|-+.||+|++||...
T Consensus 7 ~~~~~~~~~~l~~~g~~t~~~~~~~ 31 (316)
T TIGR02239 7 NGITAADIKKLQEAGLHTVESVAYA 31 (316)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHhC
Confidence 4689999999999999999998854
No 300
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=31.58 E-value=97 Score=32.19 Aligned_cols=33 Identities=24% Similarity=0.360 Sum_probs=26.8
Q ss_pred HHHHhhhccCcCHHHHHHHHHcCCCCHHHHhhcc
Q 012388 293 TISLFGEVWGIGPATAQKLYEKGHRTLDDLKNED 326 (464)
Q Consensus 293 ~l~lf~~I~GvGpktA~~ly~~GirtledL~~~~ 326 (464)
.++.+ .-.||++..+++|-+.||.|++||....
T Consensus 27 ~~~~l-~~~gi~~~~i~kL~~~g~~T~~~~~~~~ 59 (342)
T PLN03186 27 PIEQL-QASGIAALDIKKLKDAGIHTVESLAYAP 59 (342)
T ss_pred cHHHH-HhCCCCHHHHHHHHHcCCCcHHHHHhCC
Confidence 45555 4489999999999999999999998543
No 301
>KOG1906 consensus DNA polymerase sigma [Replication, recombination and repair]
Probab=30.95 E-value=1.7e+02 Score=32.29 Aligned_cols=39 Identities=18% Similarity=0.274 Sum_probs=30.2
Q ss_pred HHHHhhhcCCCEEEEEcccccccC-CcCCCccEEEeCCCc
Q 012388 358 LQKAGEEVLPEVIILCGGSYRRGK-ASCGDLDVVIMHPDR 396 (464)
Q Consensus 358 v~~~~~~~~p~~~v~~~GsyRRgk-e~~gDvDiLit~~d~ 396 (464)
++..+.+.-|.+.+.+-|||+-|- -..+|||++|..++-
T Consensus 91 i~~~v~~~~~~a~v~~FGS~~tglyLP~sDIDl~v~~~~~ 130 (514)
T KOG1906|consen 91 IRDVVKQKWPDASVYVFGSVPTGLYLPDSDIDLVVLSKFL 130 (514)
T ss_pred HHHHHHHhcccceeEEeeeeeccccccccceEEEEecccc
Confidence 334444578999999999999986 357899999987743
No 302
>KOG3548 consensus DNA damage checkpoint protein RHP9/CRB2/53BP1 [Replication, recombination and repair]
Probab=30.88 E-value=99 Score=36.23 Aligned_cols=67 Identities=18% Similarity=0.344 Sum_probs=43.9
Q ss_pred CchHHHHHHHHHHhcCCEEEeecC-----C----CccEEEEcCCh-H--HHHHHHHHhhhccCccccccchHHHHHhcCC
Q 012388 32 QNRRLQIWRQKLVQMGATVEEKLS-----K----KVTHVLAMDLE-A--LLQQVSKQHLARFKGSVIRYQWLEDSLRLGE 99 (464)
Q Consensus 32 g~~R~~~l~~~i~~~Gg~V~~~ls-----~----~VTHVV~~~~~-~--~~~~l~~~~~~~~~~~iV~~~Wl~ec~k~g~ 99 (464)
+.+-.++|...+..+|+-+++... . .+--||+.+.. . +++. +...++++|+.+||.+|+-.|.
T Consensus 1082 ~~~f~e~~~e~le~G~aa~vd~~hada~~~D~~l~~fdvvl~d~~~~~svmk~-----ad~l~~pvvs~EWvIQtiI~~~ 1156 (1176)
T KOG3548|consen 1082 GGTFIEIWKEILELGGAAVVDGYHADAETLDETLLKFDVVLVDGTFRDSVMKY-----ADTLGAPVVSSEWVIQTIILGK 1156 (1176)
T ss_pred CcchHHHHHHHHHhhchheecccccccccccccccceeEEEecCccHHHHHHH-----HHHhCCCccChhHhheeeeccc
Confidence 455688999999999999988631 1 12234444332 1 2222 2223579999999999998876
Q ss_pred CCCc
Q 012388 100 KVSE 103 (464)
Q Consensus 100 lvde 103 (464)
-...
T Consensus 1157 ~i~~ 1160 (1176)
T KOG3548|consen 1157 AIEP 1160 (1176)
T ss_pred cCCc
Confidence 6544
No 303
>PRK09482 flap endonuclease-like protein; Provisional
Probab=29.40 E-value=1.3e+02 Score=29.94 Aligned_cols=27 Identities=19% Similarity=0.398 Sum_probs=19.5
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhh
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKL 282 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~l 282 (464)
+-+.++||||++.|.++- -+.|++..+
T Consensus 182 DnIpGVpGIG~KtA~~LL--~~~gsle~i 208 (256)
T PRK09482 182 SKIPGVAGIGPKSAAELL--NQFRSLENI 208 (256)
T ss_pred cCCCCCCCcChHHHHHHH--HHhCCHHHH
Confidence 458899999999998763 355665543
No 304
>PRK14109 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Provisional
Probab=29.33 E-value=2.2e+02 Score=34.02 Aligned_cols=46 Identities=11% Similarity=0.231 Sum_probs=31.4
Q ss_pred CEEEEEccccccc-CCcCCCccEEEeCCCcc-----hhhhHHHHHHHHHHhc
Q 012388 368 EVIILCGGSYRRG-KASCGDLDVVIMHPDRK-----SHKGFLSKYVKKLKEM 413 (464)
Q Consensus 368 ~~~v~~~GsyRRg-ke~~gDvDiLit~~d~~-----~~~~~l~~lv~~L~~~ 413 (464)
++-|..+|+|=|+ -.-+.|||+++.+++.. ....++.++.+.|...
T Consensus 215 ~~aviamGklG~~EL~~~SDiDLi~ly~~~~~~~~~~~~~~~~rl~q~l~~~ 266 (1007)
T PRK14109 215 RLAVIAMGKCGARELNYVSDVDVIFVAEPAEGVDEAAALAVATRLASELMRI 266 (1007)
T ss_pred CeEEEEeccccccccCCccCCCEEEEeCCCCCcccccHHHHHHHHHHHHHHH
Confidence 3567778898655 45688999999886432 1234667777777754
No 305
>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]
Probab=29.21 E-value=81 Score=28.74 Aligned_cols=58 Identities=16% Similarity=0.214 Sum_probs=43.0
Q ss_pred HHHHHHhhhcCCCEEEEEcccccccCCc-----CCCccEEEeCCCcchhhhHHHHHHHHHHhccc
Q 012388 356 RLLQKAGEEVLPEVIILCGGSYRRGKAS-----CGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKF 415 (464)
Q Consensus 356 ~iv~~~~~~~~p~~~v~~~GsyRRgke~-----~gDvDiLit~~d~~~~~~~l~~lv~~L~~~g~ 415 (464)
.++..+.. +-|++|...|.++-..|. -+|+|+++-+--...+..+++.+++.|++.|.
T Consensus 30 kvia~~l~--d~GfeVi~~g~~~tp~e~v~aA~~~dv~vIgvSsl~g~h~~l~~~lve~lre~G~ 92 (143)
T COG2185 30 KVIARALA--DAGFEVINLGLFQTPEEAVRAAVEEDVDVIGVSSLDGGHLTLVPGLVEALREAGV 92 (143)
T ss_pred HHHHHHHH--hCCceEEecCCcCCHHHHHHHHHhcCCCEEEEEeccchHHHHHHHHHHHHHHhCC
Confidence 34444432 568888888877665443 48999998766556688999999999999886
No 306
>cd05398 NT_ClassII-CCAase Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes. CCA-adding enzymes add the sequence [cytidine(C)-cytidine-adenosine (A)], one nucleotide at a time, onto the 3' end of tRNA, in a template-independent reaction. This Class II group is comprised mainly of eubacterial and eukaryotic enzymes and includes Bacillus stearothermophilus CCAase, Escherichia coli poly(A) polymerase I, human mitochondrial CCAase, and Saccharomyces cerevisiae CCAase (CCA1). CCA-adding enzymes have a single catalytic pocket, which recognizes both ATP and CTP substrates. Included in this subgroup are CC- and A-adding enzymes from various ancient species of bacteria such as Aquifex aeolicus; these enzymes collaborate to add CCA to tRNAs. This family belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal io
Probab=28.81 E-value=1.2e+02 Score=27.16 Aligned_cols=37 Identities=19% Similarity=0.185 Sum_probs=25.0
Q ss_pred HHHHHHHhhhcCCCEEEEEcccccc----cCCcCCCccEEEeCC
Q 012388 355 ERLLQKAGEEVLPEVIILCGGSYRR----GKASCGDLDVVIMHP 394 (464)
Q Consensus 355 ~~iv~~~~~~~~p~~~v~~~GsyRR----gke~~gDvDiLit~~ 394 (464)
..+++.+... .+.++.++||+=| |+ .++|+||.+...
T Consensus 5 ~~il~~l~~~--~g~~~ylVGG~VRD~Llg~-~~~DiDi~v~~~ 45 (139)
T cd05398 5 LKLLRELKKA--LGYEAYLVGGAVRDLLLGR-PPKDIDIATDAD 45 (139)
T ss_pred HHHHHHHHhc--cCceEEEECChHHHHHcCC-CCCCceEEEeCC
Confidence 3444444321 4778888888766 55 789999998764
No 307
>PF14907 NTP_transf_5: Uncharacterised nucleotidyltransferase
Probab=28.16 E-value=47 Score=31.90 Aligned_cols=33 Identities=30% Similarity=0.525 Sum_probs=24.9
Q ss_pred cCCcCCCccEEEeCCCcchhhhHHHHHHHHHHhccccccc
Q 012388 380 GKASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLRED 419 (464)
Q Consensus 380 gke~~gDvDiLit~~d~~~~~~~l~~lv~~L~~~g~l~~~ 419 (464)
+.=.++||||||...+ +.++++.|.+.||....
T Consensus 90 ~~R~~~DiDlLV~~~d-------~~~a~~~L~~~Gy~~~~ 122 (249)
T PF14907_consen 90 GLRPMGDIDLLVPPED-------LERAVELLEELGYRIES 122 (249)
T ss_pred CCCCCCCeEEEEeCCc-------HHHHHHHHHHcCCEecc
Confidence 3457899999998444 34588889999997654
No 308
>cd07749 NT_Pol-beta-like_1 Nucleotidyltransferase (NT) domain of an uncharacterized subgroup of the Pol beta-like NT superfamily. The Pol beta-like NT superfamily includes DNA polymerase beta and other family X DNA Polymerases, as well as Class I and Class II CCA-adding enzymes, RelA- and SpoT-like ppGpp synthetases and hydrolases, 2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), poly(A) polymerases, terminal uridylyl transferases, Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. Proteins belonging to this subgroup are uncharacterized. In the majority of the Pol beta-like superfamily NTs, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations essential for catalysis. These divalent metal ions are involved in a two-metal ion mechanism of nucleotide addition. These carboxylate residues are conserved in this subgroup.
Probab=27.96 E-value=2.4e+02 Score=26.08 Aligned_cols=65 Identities=18% Similarity=0.286 Sum_probs=38.1
Q ss_pred CCEEEEEccccc---cc-CCcCCCccEEEeCCCcchhhhHHHHHHHHHHhcccccccccccccCCCCCCCCCceEEEEee
Q 012388 367 PEVIILCGGSYR---RG-KASCGDLDVVIMHPDRKSHKGFLSKYVKKLKEMKFLREDLIFSTHSEEGTDSGVDTYFGLCT 442 (464)
Q Consensus 367 p~~~v~~~GsyR---Rg-ke~~gDvDiLit~~d~~~~~~~l~~lv~~L~~~g~l~~~L~~~~~~~~~~~~~~~~~~g~~~ 442 (464)
-++...++||+. +| ...-+||||++-..+......+|... +++.-.. + ...+..+|||.+.
T Consensus 16 ~~i~W~lgGS~~L~l~Gl~~~p~DIDI~~D~~d~e~i~~il~~~---------~~~~~~~---~---~~~~~ts~F~e~~ 80 (156)
T cd07749 16 INVNWALTGSLSFALQGVPVEPHDIDIQTDNEGAYEIERIFHEF---------VNTEVRF---S---ESEGIRSHFGELQ 80 (156)
T ss_pred CCceEEehhhHHHHHcCCCCCCCcceEEEchhhHHHHHHHHHHh---------ccCCCcc---C---CCCceeeeeeEEE
Confidence 356778899954 33 46679999998766665444444332 2222211 1 1124578888777
Q ss_pred cCCC
Q 012388 443 YPGR 446 (464)
Q Consensus 443 ~p~~ 446 (464)
..|-
T Consensus 81 I~gv 84 (156)
T cd07749 81 IDGI 84 (156)
T ss_pred ECCE
Confidence 7653
No 309
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=27.57 E-value=47 Score=39.46 Aligned_cols=26 Identities=19% Similarity=0.326 Sum_probs=21.5
Q ss_pred hhccCcCHHHHHHHHHc-CCCCHHHHh
Q 012388 298 GEVWGIGPATAQKLYEK-GHRTLDDLK 323 (464)
Q Consensus 298 ~~I~GvGpktA~~ly~~-GirtledL~ 323 (464)
.+|+||||+||-++..+ |=.+|+.|.
T Consensus 869 ~GI~GIGpktAl~li~~~~~~~le~L~ 895 (1034)
T TIGR00600 869 EGIPTVGPVSAMEILNEFPGDGLEPLL 895 (1034)
T ss_pred CCCCcccHHHHHHHHHHcCCCCHHHHH
Confidence 46999999999999998 655677665
No 310
>PF04994 TfoX_C: TfoX C-terminal domain; InterPro: IPR007077 This domain is found in a number of bacterial proteins including the TfoX gene product of Haemophilus influenzae. TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes []. This family corresponds to the C-terminal presumed domain of TfoX. The domain is found in association with the N-terminal domain in some, but not all members of this group, suggesting this is an autonomous and functionally unrelated domain. For example it is found associated with Q9JZR1 from SWISSPROT in IPR002125 from INTERPRO.; PDB: 3BQT_A 3MAB_A.
Probab=27.36 E-value=46 Score=27.15 Aligned_cols=40 Identities=18% Similarity=0.365 Sum_probs=20.5
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHh
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLF 297 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf 297 (464)
.++..||+||..+.+...++ -+.-+++|+.--...+...+
T Consensus 3 ~~l~~LpNig~~~e~~L~~v----GI~t~~~L~~~Ga~~a~~~L 42 (81)
T PF04994_consen 3 NRLKDLPNIGPKSERMLAKV----GIHTVEDLRELGAVEAYLRL 42 (81)
T ss_dssp --GCGSTT--HHHHHHHHHT----T--SHHHHHHHHHHHHHHHH
T ss_pred cchhhCCCCCHHHHHHHHHc----CCCCHHHHHHhCHHHHHHHH
Confidence 46889999999876654433 45666676653333333333
No 311
>PF07261 DnaB_2: Replication initiation and membrane attachment; InterPro: IPR006343 This entry represents a domain found in several bacterial replication initiation and membrane attachment proteins, DnaB and DnaD. The DnaD protein is a component of the PriA primosome. The PriA primosome functions to recruit the replication fork helicase onto the DNA []. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria []. The DnaB protein is essential for both replication initiation and membrane attachment of the origin region of the chromosome and Plasmid pUB110 in Bacillus subtilis. It is known that there are two different classes (DnaBI and DnaBII) in the DnaB mutants; DnaBI is essential for both chromosome and pUB110 replication, whereas DnaBII is necessary only for chromosome replication []. This domain tends to be found towards the C terminus of DnaB and DnaD proteins and is alpha helical in nature.; PDB: 2I5U_A 2ZC2_A.
Probab=26.86 E-value=24 Score=27.60 Aligned_cols=21 Identities=19% Similarity=0.286 Sum_probs=15.0
Q ss_pred HHHHHHHHHcCCCCHHHHhhc
Q 012388 305 PATAQKLYEKGHRTLDDLKNE 325 (464)
Q Consensus 305 pktA~~ly~~GirtledL~~~ 325 (464)
-+.++.|.++|++|++|+++.
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 467899999999999998753
No 312
>PF04439 Adenyl_transf: Streptomycin adenylyltransferase; InterPro: IPR007530 Also known as aminoglycoside 6-adenylyltransferase (2.7.7 from EC), this protein confers resistance to aminoglycoside antibiotics.; PDB: 2PBE_A.
Probab=26.63 E-value=2.6e+02 Score=28.22 Aligned_cols=48 Identities=27% Similarity=0.315 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHHhhhcCCCEE-EEEccccccc---CCcCCCccEEEeCCCcc
Q 012388 348 RHEVEQMERLLQKAGEEVLPEVI-ILCGGSYRRG---KASCGDLDVVIMHPDRK 397 (464)
Q Consensus 348 r~Ea~~i~~iv~~~~~~~~p~~~-v~~~GsyRRg---ke~~gDvDiLit~~d~~ 397 (464)
|.|.+-+..|+.-+. .++.++ |.+.||.-+- +..=.|.||++-..+..
T Consensus 2 rte~em~~~Il~~A~--~d~rIraV~l~GSR~n~~~~~D~fqDyDIv~~v~d~~ 53 (282)
T PF04439_consen 2 RTEQEMMDLILEFAK--QDERIRAVILNGSRANPNAPKDEFQDYDIVYVVTDIE 53 (282)
T ss_dssp --HHHHHHHHHHHHH--H-TTEEEEEE----------------EEEEEEES-HH
T ss_pred CCHHHHHHHHHHHHh--cCCcEEEEEEecCCCCCCCCccccccccEEEEecchh
Confidence 345554555555443 388995 6789987663 45677899988766643
No 313
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=25.65 E-value=88 Score=31.72 Aligned_cols=44 Identities=20% Similarity=0.266 Sum_probs=26.9
Q ss_pred CCChhHHHHHHHHHHHhcCCcc---ccc-----h----hhhcCCCCCCHHHHHHHH
Q 012388 228 GEDRRSFSYYKAIPVIEKLPFK---IES-----A----DQVKGLPGIGKSMQDHIQ 271 (464)
Q Consensus 228 g~~~r~~aY~rAa~~l~~lp~~---I~s-----~----~~l~~lpgIG~~ia~kI~ 271 (464)
|=.+|++--..+|++|..=+.. +.+ + +.+..|||||.++|+=|-
T Consensus 180 gfGYRAkYI~~ta~~l~~~~g~~~wLqsl~~~~yeear~~L~~lpGVG~KVADCI~ 235 (323)
T KOG2875|consen 180 GFGYRAKYISATARALQEKQGGLAWLQSLRKSSYEEAREALCSLPGVGPKVADCIC 235 (323)
T ss_pred CcchhHHHHHHHHHHHHHhcccchHHHHHhcccHHHHHHHHhcCCCCcchHhhhhh
Confidence 4445665555566666543333 111 2 457889999999999664
No 314
>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=25.35 E-value=26 Score=27.30 Aligned_cols=21 Identities=19% Similarity=0.596 Sum_probs=16.0
Q ss_pred EEEEcccccccCCcC----CCccEE
Q 012388 370 IILCGGSYRRGKASC----GDLDVV 390 (464)
Q Consensus 370 ~v~~~GsyRRgke~~----gDvDiL 390 (464)
.|++--+|||||..+ ||+|||
T Consensus 34 rvmiPqeFkrGKsIiAV~EGe~~il 58 (67)
T TIGR02922 34 RVMIPQEFKRGKSIIAVCEGEITIL 58 (67)
T ss_pred cEEcchHHcCCCeEEEEEecceeeh
Confidence 677778999999864 566665
No 315
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=24.63 E-value=6.6e+02 Score=24.97 Aligned_cols=52 Identities=19% Similarity=0.312 Sum_probs=31.9
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE 313 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~ 313 (464)
..+.+||+||+..+.++. .+.+..++++..-.+...-.+ -|.+++.+..+++
T Consensus 151 ~~L~Qlp~i~~~~~~~l~----~~~i~s~~~l~~~~~~~~~~l----l~~~~~~~~~i~~ 202 (312)
T smart00611 151 SPLLQLPHLPEEILKRLE----KKKVLSLEDLLELEDEERGEL----LGLLDAEGERVYK 202 (312)
T ss_pred CccccCCCCCHHHHHHHH----hCCCCCHHHHHhcCHHHHHHH----HcCCHHHHHHHHH
Confidence 468999999998877765 334445555554333222222 3667777777655
No 316
>PRK07945 hypothetical protein; Provisional
Probab=24.42 E-value=40 Score=34.82 Aligned_cols=29 Identities=28% Similarity=0.462 Sum_probs=23.5
Q ss_pred hhhccCcCHHHHHHHHHc---C-CCCHHHHhhc
Q 012388 297 FGEVWGIGPATAQKLYEK---G-HRTLDDLKNE 325 (464)
Q Consensus 297 f~~I~GvGpktA~~ly~~---G-irtledL~~~ 325 (464)
|++|||||..+|.++.+. | +.-+++|+.+
T Consensus 51 l~~~~giG~~~a~~i~e~~~tg~~~~l~~l~~~ 83 (335)
T PRK07945 51 LTSLPGIGPKTAKVIAQALAGRVPDYLAELRAD 83 (335)
T ss_pred cccCCCcCHHHHHHHHHHHhcCCHHHHHHHHHh
Confidence 569999999999998874 5 5678888843
No 317
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=24.37 E-value=3e+02 Score=28.65 Aligned_cols=81 Identities=17% Similarity=0.199 Sum_probs=50.2
Q ss_pred CCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHH-------cCCCCHHHHhhccCcchHH
Q 012388 260 PGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYE-------KGHRTLDDLKNEDSLTHSQ 332 (464)
Q Consensus 260 pgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~-------~GirtledL~~~~~L~~~q 332 (464)
+||+..+.+|.++ ..+.-++.+..-.+. + |.++-|+...+|.++.+ .|+.|-.++....+-...-
T Consensus 37 ~g~~~~~~~kL~~----~g~~tv~~~~~~~~~---~-L~~~~g~s~~~~~ki~~~a~~~~~~~~~ta~~~~~~~~~~~~i 108 (344)
T PLN03187 37 QGINAGDVKKLQD----AGIYTCNGLMMHTKK---N-LTGIKGLSEAKVDKICEAAEKLLNQGFITGSDALLKRKSVVRI 108 (344)
T ss_pred CCCCHHHHHHHHH----cCCCcHHHHHhCCHH---H-HHHhcCCCHHHHHHHHHHHHHhhcccCCcHHHHHhhhccCcee
Confidence 6799888776543 445666666544433 2 34788999999998763 3778888876432211122
Q ss_pred HhhHhhHHhhcc-CCCH
Q 012388 333 RLGLKYFDDIKT-RIPR 348 (464)
Q Consensus 333 ~~Glk~~ed~~~-~i~r 348 (464)
..|.+-.|+++. .|+.
T Consensus 109 sTG~~~LD~lLgGGi~~ 125 (344)
T PLN03187 109 TTGSQALDELLGGGIET 125 (344)
T ss_pred cCCcHhHHhhcCCCCCC
Confidence 357777777653 4544
No 318
>PF03710 GlnE: Glutamate-ammonia ligase adenylyltransferase; InterPro: IPR005190 This is a conserved repeated domain found in GlnE proteins. These proteins adenylate and deadenylate glutamine synthases: ATP + {L-Glutamate:ammonia ligase (ADP-forming)} = Diphosphate + Adenylyl-{L-Glutamate:Ammonia ligase (ADP-forming)}. The domain is related to the nucleotidyltransferase domain IPR002934 from INTERPRO.; GO: 0008882 [glutamate-ammonia-ligase] adenylyltransferase activity; PDB: 1V4A_A 3K7D_A.
Probab=24.24 E-value=2.7e+02 Score=27.33 Aligned_cols=44 Identities=11% Similarity=0.274 Sum_probs=23.2
Q ss_pred CEEEEEccccccc-CCcCCCccEEEeCCCcchh-------hhHHHHHHHHHH
Q 012388 368 EVIILCGGSYRRG-KASCGDLDVVIMHPDRKSH-------KGFLSKYVKKLK 411 (464)
Q Consensus 368 ~~~v~~~GsyRRg-ke~~gDvDiLit~~d~~~~-------~~~l~~lv~~L~ 411 (464)
++.|+-+|.|=.+ --.+.|||+++-+++.... ..++.++.+++.
T Consensus 127 ~~~ViamGKlGg~ELny~SDiDLifvy~~~~~~~~~~~~~~~~~~rl~~~~~ 178 (247)
T PF03710_consen 127 GFAVIAMGKLGGRELNYSSDIDLIFVYDPDGETGRRSISNQEFFTRLAQRLI 178 (247)
T ss_dssp SEEEEE-HHHHTT---TT--EEEEEEE---TT-SSS-SBHHHHHHHHHHHHH
T ss_pred CeEEEEeccccccccCCccCCceEEEeccccccccChhhHHHHHHHHHHHHH
Confidence 5667777877543 4568899999987654332 356666655554
No 319
>PF12482 DUF3701: Phage integrase protein; InterPro: IPR022169 This domain family is found in bacteria, and is approximately 100 amino acids in length. The family is found in association with PF00589 from PFAM.
Probab=23.15 E-value=75 Score=26.97 Aligned_cols=35 Identities=31% Similarity=0.376 Sum_probs=25.5
Q ss_pred CHHHHHHHHHcCCCCHHHHhhc----c-C-cchHHHhhHhh
Q 012388 304 GPATAQKLYEKGHRTLDDLKNE----D-S-LTHSQRLGLKY 338 (464)
Q Consensus 304 GpktA~~ly~~GirtledL~~~----~-~-L~~~q~~Glk~ 338 (464)
.|..|++|-..||+||.||... + + ...+.++|..-
T Consensus 22 ~p~va~~L~aaGi~TL~dL~~~i~~rg~~Wwr~vpglG~~~ 62 (96)
T PF12482_consen 22 PPRVARRLAAAGIRTLADLVDRINRRGGRWWRAVPGLGAAG 62 (96)
T ss_pred CHHHHHHHHHcCCchHHHHHHHHHHccchHHHhCcccchHH
Confidence 6999999999999999999842 1 1 23455565444
No 320
>PRK05092 PII uridylyl-transferase; Provisional
Probab=22.85 E-value=1.4e+02 Score=35.38 Aligned_cols=48 Identities=21% Similarity=0.434 Sum_probs=32.4
Q ss_pred CEEEEEcccccccC-CcCCCccEEEeCCCcc--hhhhHHHHHHHHHHhccc
Q 012388 368 EVIILCGGSYRRGK-ASCGDLDVVIMHPDRK--SHKGFLSKYVKKLKEMKF 415 (464)
Q Consensus 368 ~~~v~~~GsyRRgk-e~~gDvDiLit~~d~~--~~~~~l~~lv~~L~~~g~ 415 (464)
++-+..+|||-||. --..|||+||-+++.. ....++..++-.|-+.|+
T Consensus 105 ~~alvA~GgyGr~EL~p~SDiDLl~l~~~~~~~~~~~~i~~~~~~lwD~gl 155 (931)
T PRK05092 105 RLAVLAVGGYGRGELAPGSDIDLLFLLPYKQTAWAESVVEYMLYMLWDLGL 155 (931)
T ss_pred ceEEEEecCcCCcccCCCCCceEEEEeCCCCcchHHHHHHHHHHHHHHcCC
Confidence 35677889997765 4578999999887432 233456666666655554
No 321
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=22.79 E-value=76 Score=22.17 Aligned_cols=22 Identities=18% Similarity=0.296 Sum_probs=18.0
Q ss_pred HHhhhccCcCHHHHHHHHHcCC
Q 012388 295 SLFGEVWGIGPATAQKLYEKGH 316 (464)
Q Consensus 295 ~lf~~I~GvGpktA~~ly~~Gi 316 (464)
..+.+..||-+.|.+.|.++|.
T Consensus 4 ~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 4 GELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred HHHHHHHCcCHHHHHHHHHCCC
Confidence 3455778999999999999876
No 322
>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=22.77 E-value=1.9e+02 Score=21.73 Aligned_cols=24 Identities=17% Similarity=0.313 Sum_probs=18.8
Q ss_pred HHhhhccCcCHHHHHHHHHc-CCCC
Q 012388 295 SLFGEVWGIGPATAQKLYEK-GHRT 318 (464)
Q Consensus 295 ~lf~~I~GvGpktA~~ly~~-Girt 318 (464)
..+.+..||.+.|.+.|.++ |+-.
T Consensus 4 ~eva~~~gvs~~tlr~w~~~~g~~~ 28 (68)
T cd01104 4 GAVARLTGVSPDTLRAWERRYGLPA 28 (68)
T ss_pred HHHHHHHCcCHHHHHHHHHhCCCCC
Confidence 44567789999999999986 7643
No 323
>COG5275 BRCT domain type II [General function prediction only]
Probab=22.57 E-value=1.7e+02 Score=28.66 Aligned_cols=50 Identities=14% Similarity=0.077 Sum_probs=38.5
Q ss_pred CCCCCeEEEEecCCCCchHHHHHHHHHHhcCCEEEeecCCCccEEEEcCCh
Q 012388 17 GIFAGMRVFLVEKGVQNRRLQIWRQKLVQMGATVEEKLSKKVTHVLAMDLE 67 (464)
Q Consensus 17 ~~F~g~~vy~~~~~~g~~R~~~l~~~i~~~Gg~V~~~ls~~VTHVV~~~~~ 67 (464)
..+.|.++.|-+- +..-.++--+.++..+||+|....+...|-||..|+-
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 5678888887542 3333345678999999999999999999999987764
No 324
>KOG1715 consensus Mitochondrial/chloroplast ribosomal protein L12 [Translation, ribosomal structure and biogenesis]
Probab=22.32 E-value=1.2e+02 Score=28.86 Aligned_cols=58 Identities=31% Similarity=0.459 Sum_probs=45.3
Q ss_pred hhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHHhhccCcchHHHhhHhhHHhhccCCCHHHHHHHHHHHHH
Q 012388 281 KLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQK 360 (464)
Q Consensus 281 ~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~iv~~ 360 (464)
+|+.+....+..+++....+.|+|-+-|++|.+. .=.-+.+.|+.+||++|-..+++
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 4666777778889999999999999999999762 11225578899999999877776
Q ss_pred H
Q 012388 361 A 361 (464)
Q Consensus 361 ~ 361 (464)
+
T Consensus 180 ~ 180 (187)
T KOG1715|consen 180 A 180 (187)
T ss_pred c
Confidence 5
No 325
>TIGR02884 spore_pdaA delta-lactam-biosynthetic de-N-acetylase. Muramic delta-lactam is an unusual constituent of peptidoglycan, found only in bacterial spores in the peptidoglycan wall, or spore cortex. The proteins in this family are PdaA (yfjS), a member of a larger family of polysaccharide deacetylases, and are specificially involved in delta-lactam biosynthesis. PdaA acts immediately after CwlD, an N-acetylmuramoyl-L-alanine amidase and performs a de-N-acetylation. PdaA may also perform the following transpeptidation for lactam ring formation, as heterologous expression in E. coli of CwlD and PdaA together is sufficient for delta-lactam production.
Probab=22.18 E-value=87 Score=30.15 Aligned_cols=33 Identities=27% Similarity=0.441 Sum_probs=25.1
Q ss_pred cEEEeCCCcchhhhHHHHHHHHHHhcccccccc
Q 012388 388 DVVIMHPDRKSHKGFLSKYVKKLKEMKFLREDL 420 (464)
Q Consensus 388 DiLit~~d~~~~~~~l~~lv~~L~~~g~l~~~L 420 (464)
+||+.|.........|+.+++.|+++||=--+|
T Consensus 188 ~IiLlHd~~~~t~~aL~~ii~~lk~~Gy~fvtl 220 (224)
T TIGR02884 188 AILLLHAVSKDNAEALDKIIKDLKEQGYTFKSL 220 (224)
T ss_pred cEEEEECCCCCHHHHHHHHHHHHHHCCCEEEEh
Confidence 577778754445679999999999999854433
No 326
>PRK02406 DNA polymerase IV; Validated
Probab=22.13 E-value=1.7e+02 Score=29.94 Aligned_cols=53 Identities=25% Similarity=0.527 Sum_probs=34.4
Q ss_pred hhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--CCCC
Q 012388 255 QVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (464)
Q Consensus 255 ~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--Girt 318 (464)
.+..|||||++++++...+ .+..+.++.+-.+....+.| |. ...++|+. |+..
T Consensus 169 pi~~l~giG~~~~~~L~~~----Gi~ti~dl~~l~~~~L~~~f------G~-~~~~l~~~a~G~d~ 223 (343)
T PRK02406 169 PVEKIPGVGKVTAEKLHAL----GIYTCADLQKYDLAELIRHF------GK-FGRRLYERARGIDE 223 (343)
T ss_pred CcchhcCCCHHHHHHHHHc----CCCcHHHHHhCCHHHHHHHH------hH-HHHHHHHHhCCCCC
Confidence 3678899999998887654 45667777654444444445 43 56666664 8754
No 327
>KOG2379 consensus Endonuclease MUS81 [Replication, recombination and repair]
Probab=21.58 E-value=74 Score=34.63 Aligned_cols=43 Identities=19% Similarity=0.220 Sum_probs=36.7
Q ss_pred hHHHHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHH
Q 012388 232 RSFSYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIV 274 (464)
Q Consensus 232 r~~aY~rAa~~l~~lp~~I~s~~~l~~lpgIG~~ia~kI~Eil 274 (464)
-...|.+|...|...+++|.++.++..+.|+|+...-++.|..
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 3458999999999999999999999999999997666666443
No 328
>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=21.50 E-value=5.4e+02 Score=25.55 Aligned_cols=56 Identities=14% Similarity=0.195 Sum_probs=30.1
Q ss_pred HHHHHHHHHhcCCccccchhhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHh
Q 012388 235 SYYKAIPVIEKLPFKIESADQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLF 297 (464)
Q Consensus 235 aY~rAa~~l~~lp~~I~s~~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf 297 (464)
++.-+-....++. + +...+.+|||||+..+.++.. ..+.-++++..-.+.+.-.++
T Consensus 132 ~l~l~q~i~q~~w-~--~~~~L~Qlp~i~~~~~~~l~~----~~i~~l~~l~~~~~~e~~~ll 187 (314)
T PF02889_consen 132 ALELSQCIVQALW-D--SDSPLLQLPHIGEESLKKLEK----RGIKTLQDLRDLSPEELEELL 187 (314)
T ss_dssp HHHHHHHHHHTS--T--TS-GGGGSTT--HHHHHHHHH----TT--SHHHHHHS-HHHHHHHH
T ss_pred HHHHHHHHHhhcC-C--CCChhhcCCCCCHHHHHHHhc----cCCCcHHHHhhCCHHHHHHHH
Confidence 3444444555665 3 346799999999999887776 444556666554444444444
No 329
>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a beta-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [, ].; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBN_M 2QBB_M 3I1M_M 3OFP_M 3OFX_M 3OFO_M 1VS5_M 3OAQ_M 2QAL_M 3J18_M ....
Probab=21.11 E-value=82 Score=26.93 Aligned_cols=44 Identities=11% Similarity=0.181 Sum_probs=29.7
Q ss_pred hhhcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHh
Q 012388 254 DQVKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLF 297 (464)
Q Consensus 254 ~~l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf 297 (464)
-.|..|.|||...|..|-..+.=.....+.+|..++-....+.+
T Consensus 15 ~aLt~IyGIG~~~A~~Ic~~lgi~~~~~~~~Ls~~~i~~l~~~i 58 (107)
T PF00416_consen 15 IALTKIYGIGRRKAKQICKKLGINPNKKVGDLSDEQIDKLRKII 58 (107)
T ss_dssp HHHTTSTTBCHHHHHHHHHHTTS-SSSBTTTSTHHHHHHHHHHH
T ss_pred hHHhhhhccCHHHHHHHHHHcCCChhhhcccCCHHHHHHHHHHH
Confidence 35889999999999999888775555555555444433444444
No 330
>COG2019 AdkA Archaeal adenylate kinase [Nucleotide transport and metabolism]
Probab=20.97 E-value=1.7e+02 Score=27.68 Aligned_cols=53 Identities=23% Similarity=0.375 Sum_probs=34.6
Q ss_pred hhhccCcCHHHHHHHHHcCC-----CCHHHHhhccCcchHHHhh-HhhHHhhccCCCHHHHHHH
Q 012388 297 FGEVWGIGPATAQKLYEKGH-----RTLDDLKNEDSLTHSQRLG-LKYFDDIKTRIPRHEVEQM 354 (464)
Q Consensus 297 f~~I~GvGpktA~~ly~~Gi-----rtledL~~~~~L~~~q~~G-lk~~ed~~~~i~r~Ea~~i 354 (464)
.++|||||..|+-+...++. -+..||. |..+.+.| .++.+++. ++|.++-..+
T Consensus 9 itGVpGvGKTTVl~~~~~~l~~~~ivNyG~~M----le~A~k~glve~rD~~R-klp~e~Q~~l 67 (189)
T COG2019 9 ITGVPGVGKTTVLKIALKELVKHKIVNYGDLM----LEIAKKKGLVEHRDEMR-KLPLENQREL 67 (189)
T ss_pred EEcCCCCChHHHHHHHHHHHhhceeeeHhHHH----HHHHHHhCCcccHHHHh-cCCHHHHHHH
Confidence 46899999999988877654 2223332 33444444 66777777 8888775554
No 331
>PRK00024 hypothetical protein; Reviewed
Probab=20.92 E-value=99 Score=30.09 Aligned_cols=42 Identities=36% Similarity=0.554 Sum_probs=0.0
Q ss_pred CHHHHHHHHHHHHh-CCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHH
Q 012388 263 GKSMQDHIQEIVTT-GKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKL 311 (464)
Q Consensus 263 G~~ia~kI~Eil~t-G~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~l 311 (464)
++.....-+++++. |.+..+-.. ..+.|++|+|||+.+|..|
T Consensus 40 ~~~~~~LA~~LL~~fgsL~~l~~a-------s~~eL~~i~GIG~akA~~L 82 (224)
T PRK00024 40 GKSVLDLARELLQRFGSLRGLLDA-------SLEELQSIKGIGPAKAAQL 82 (224)
T ss_pred CCCHHHHHHHHHHHcCCHHHHHhC-------CHHHHhhccCccHHHHHHH
No 332
>PF05984 Cytomega_UL20A: Cytomegalovirus UL20A protein; InterPro: IPR009245 This family consists of several Cytomegalovirus UL20A proteins. UL20A is thought to be a glycoprotein [].
Probab=20.90 E-value=91 Score=25.80 Aligned_cols=31 Identities=39% Similarity=0.597 Sum_probs=23.7
Q ss_pred EEEEEcccccccCCc-CCCccEEEeCCCcchh
Q 012388 369 VIILCGGSYRRGKAS-CGDLDVVIMHPDRKSH 399 (464)
Q Consensus 369 ~~v~~~GsyRRgke~-~gDvDiLit~~d~~~~ 399 (464)
+...-.|||--|.|. +||.|+|||..|+..+
T Consensus 50 vtlsqgGsttDg~EdysgdYDVLItd~dG~~h 81 (100)
T PF05984_consen 50 VTLSQGGSTTDGNEDYSGDYDVLITDGDGSEH 81 (100)
T ss_pred eEEcCCCccCCCcccccccccEEEecCCCCcC
Confidence 345567999988775 8999999987776543
No 333
>PF00542 Ribosomal_L12: Ribosomal protein L7/L12 C-terminal domain; InterPro: IPR013823 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the C-terminal domain of the large subunit ribosomal proteins, known as the L7/L12 family. L7/L12 is present in each 50S subunit in four copies organised as two dimers. The L8 protein complex consisting of two dimers of L7/L12 and L10 in Escherichia coli ribosomes is assembled on the conserved region of 23 S rRNA termed the GTPase-associated domain []. The L7/L12 dimer probably interacts with EF-Tu. L7 and L12 only differ in a single post translational modification of the addition of an acetyl group to the N terminus of L7.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1DD4_B 1DD3_A 1RQU_B 2GYA_5 2GYC_5 1RQS_A 1RQV_A 1CTF_A 2XUX_L.
Probab=20.41 E-value=1.2e+02 Score=24.00 Aligned_cols=51 Identities=27% Similarity=0.462 Sum_probs=32.7
Q ss_pred hhchhHHHHHhhhccCcCHHHHHHHHHcCCCCHHHHhhccCcchHHHhhHhhHHhhccCCCHHHHHHHHHHHHH
Q 012388 287 KDEKVRTISLFGEVWGIGPATAQKLYEKGHRTLDDLKNEDSLTHSQRLGLKYFDDIKTRIPRHEVEQMERLLQK 360 (464)
Q Consensus 287 ~~~~~~~l~lf~~I~GvGpktA~~ly~~GirtledL~~~~~L~~~q~~Glk~~ed~~~~i~r~Ea~~i~~iv~~ 360 (464)
.+.+..+++....+.|+|-+-|+.+.+. + -..+...++++||+++...+..
T Consensus 10 ~~~ki~vIK~vR~~tgl~L~eAK~~vd~-------------~----------p~~ik~~v~keeAe~ik~~Le~ 60 (68)
T PF00542_consen 10 GEKKIKVIKEVREITGLGLKEAKKLVDS-------------L----------PKVIKEGVSKEEAEEIKKKLEA 60 (68)
T ss_dssp TTGHHHHHHHHHHHC---HHHHHHHHCT-------------T----------TEEEEEEE-HHHHHHHHHHHHC
T ss_pred ccchHHHHHHHHHHhCCcHHHHHHHHHh-------------C----------CHHHHcCCCHHHHHHHHHHHHH
Confidence 4456778888888889999999988652 0 0124567889999888766664
No 334
>PF13838 Clathrin_H_link: Clathrin-H-link; PDB: 2XZG_A 3GD1_I 1BPO_C 1C9I_B 1C9L_A.
Probab=20.38 E-value=1.8e+02 Score=23.00 Aligned_cols=44 Identities=20% Similarity=0.342 Sum_probs=31.8
Q ss_pred CCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhH------HHHHhhhcc
Q 012388 258 GLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVR------TISLFGEVW 301 (464)
Q Consensus 258 ~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~------~l~lf~~I~ 301 (464)
+|||.-.-..++..+++..|...+.-.+..+.|.+ +|+-|.+++
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 57899999999999999999999988887777744 555555444
No 335
>PRK11072 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Reviewed
Probab=20.19 E-value=1.3e+03 Score=27.52 Aligned_cols=44 Identities=18% Similarity=0.389 Sum_probs=28.9
Q ss_pred CEEEEEccccccc-CCcCCCccEEEeCCCc-c--------hhhhHHHHHHHHHH
Q 012388 368 EVIILCGGSYRRG-KASCGDLDVVIMHPDR-K--------SHKGFLSKYVKKLK 411 (464)
Q Consensus 368 ~~~v~~~GsyRRg-ke~~gDvDiLit~~d~-~--------~~~~~l~~lv~~L~ 411 (464)
++.|..+|.|=++ -..+.|||+|+.+++. . ....++.+|.+.|-
T Consensus 154 ~~aViamGKlG~~ELn~~SDIDLifly~~~~~~~~~~~~~~~~~~f~rl~q~li 207 (943)
T PRK11072 154 PLLILGMGKLGGRELNFSSDIDLIFTYPEHGETQGGRRSIDNQQFFTRLGQRLI 207 (943)
T ss_pred CEEEEEeccccCccCCCccCCceEEEeCCCCCCCCCcccchHHHHHHHHHHHHH
Confidence 3567778888655 4578999999987632 1 23356666655554
No 336
>PRK01810 DNA polymerase IV; Validated
Probab=20.01 E-value=1.8e+02 Score=30.52 Aligned_cols=52 Identities=19% Similarity=0.416 Sum_probs=33.7
Q ss_pred hcCCCCCCHHHHHHHHHHHHhCCchhhHHHHhhchhHHHHHhhhccCcCHHHHHHHHHc--CCCC
Q 012388 256 VKGLPGIGKSMQDHIQEIVTTGKLSKLEHFEKDEKVRTISLFGEVWGIGPATAQKLYEK--GHRT 318 (464)
Q Consensus 256 l~~lpgIG~~ia~kI~Eil~tG~~~~le~l~~~~~~~~l~lf~~I~GvGpktA~~ly~~--Girt 318 (464)
+..|||||++++++...+ | +..+-+|.+-.+....+.| |+ ....+|+. |+..
T Consensus 181 v~~l~giG~~~~~~L~~~---G-i~tigdL~~~~~~~L~~rf------G~-~g~~l~~~a~G~d~ 234 (407)
T PRK01810 181 VGEMHGIGEKTAEKLKDI---G-IQTIGDLAKADEHILRAKL------GI-NGVRLQRRANGIDD 234 (407)
T ss_pred HhhcCCcCHHHHHHHHHc---C-CCcHHHHHhCCHHHHHHHH------hH-HHHHHHHHhcCCCC
Confidence 667899999998877643 3 5666666654444444455 44 46667764 8754
Done!