Query 035092
Match_columns 73
No_of_seqs 120 out of 1100
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 09:07:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035092.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035092hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01367 5_3_exonuc: 5'-3' exo 99.8 6E-24 1.3E-28 135.7 -10.2 65 5-69 18-82 (101)
2 PRK09482 flap endonuclease-lik 99.8 4.7E-20 1E-24 133.1 6.4 64 5-69 182-245 (256)
3 smart00475 53EXOc 5'-3' exonuc 99.8 1.8E-19 3.9E-24 129.5 6.4 64 5-69 186-249 (259)
4 PRK14976 5'-3' exonuclease; Pr 99.8 1.8E-19 4E-24 130.7 6.2 64 5-69 191-254 (281)
5 TIGR00593 pola DNA polymerase 99.7 2.8E-18 6E-23 139.5 6.7 65 5-69 185-249 (887)
6 cd00008 53EXOc 5'-3' exonuclea 99.7 2.9E-17 6.4E-22 116.3 6.7 58 5-63 183-240 (240)
7 PRK05755 DNA polymerase I; Pro 99.6 2.2E-16 4.7E-21 127.5 6.4 64 5-69 187-250 (880)
8 COG0258 Exo 5'-3' exonuclease 99.5 5.9E-15 1.3E-19 107.2 5.2 64 5-69 198-261 (310)
9 cd00080 HhH2_motif Helix-hairp 99.5 3.3E-14 7.1E-19 85.9 6.0 53 5-60 22-74 (75)
10 smart00279 HhH2 Helix-hairpin- 98.9 1.7E-09 3.6E-14 57.8 2.3 22 4-25 15-36 (36)
11 PF12826 HHH_2: Helix-hairpin- 98.8 9.4E-09 2E-13 60.2 5.4 48 8-55 6-59 (64)
12 PTZ00217 flap endonuclease-1; 98.7 2.1E-08 4.5E-13 76.1 4.0 34 5-38 235-268 (393)
13 PRK03980 flap endonuclease-1; 98.6 3.2E-08 7E-13 72.5 3.6 31 5-35 189-219 (292)
14 TIGR03674 fen_arch flap struct 98.6 4.4E-08 9.6E-13 72.7 3.7 31 6-37 238-268 (338)
15 cd00128 XPG Xeroderma pigmento 98.5 1.1E-07 2.4E-12 69.2 3.9 31 5-35 223-253 (316)
16 PRK14670 uvrC excinuclease ABC 98.5 2.1E-07 4.5E-12 73.8 5.6 49 5-53 514-568 (574)
17 PRK14667 uvrC excinuclease ABC 98.5 2.5E-07 5.4E-12 73.2 5.2 48 4-51 513-565 (567)
18 PHA00439 exonuclease 98.4 2.9E-07 6.3E-12 67.9 4.6 29 5-34 188-219 (286)
19 PRK14669 uvrC excinuclease ABC 98.4 5.3E-07 1.1E-11 72.1 4.6 48 5-52 552-603 (624)
20 PF14520 HHH_5: Helix-hairpin- 98.3 3.9E-06 8.4E-11 48.1 5.6 45 7-51 7-58 (60)
21 PRK14671 uvrC excinuclease ABC 98.1 3.4E-06 7.3E-11 67.3 4.8 48 4-51 568-619 (621)
22 PRK14666 uvrC excinuclease ABC 98.1 4.6E-06 9.9E-11 67.6 5.3 51 4-54 636-692 (694)
23 PRK14672 uvrC excinuclease ABC 98.1 4.3E-06 9.3E-11 67.8 5.0 46 4-49 607-658 (691)
24 COG0322 UvrC Nuclease subunit 98.1 5.2E-06 1.1E-10 66.1 4.5 48 3-50 528-580 (581)
25 PRK12766 50S ribosomal protein 98.0 1.1E-05 2.3E-10 58.4 5.0 48 5-52 3-57 (232)
26 TIGR00194 uvrC excinuclease AB 98.0 3.7E-06 8E-11 66.7 2.6 30 5-34 541-570 (574)
27 PRK00116 ruvA Holliday junctio 98.0 9.9E-06 2.2E-10 56.0 4.4 49 5-53 73-130 (192)
28 PRK00558 uvrC excinuclease ABC 97.9 1.1E-05 2.4E-10 64.0 4.4 48 4-51 542-595 (598)
29 PRK14668 uvrC excinuclease ABC 97.9 2.4E-05 5.1E-10 62.2 4.9 46 5-50 525-576 (577)
30 TIGR00575 dnlj DNA ligase, NAD 97.8 6E-05 1.3E-09 60.5 6.8 56 8-63 501-562 (652)
31 PRK14351 ligA NAD-dependent DN 97.8 8.7E-05 1.9E-09 60.1 6.8 57 8-64 531-593 (689)
32 PRK07956 ligA NAD-dependent DN 97.7 0.00014 3E-09 58.6 6.5 55 9-63 515-575 (665)
33 TIGR00084 ruvA Holliday juncti 97.3 0.00038 8.3E-09 48.4 4.5 42 6-48 73-124 (191)
34 PF00633 HHH: Helix-hairpin-he 97.2 0.0003 6.4E-09 36.1 2.0 17 7-23 13-29 (30)
35 COG0272 Lig NAD-dependent DNA 97.2 0.001 2.2E-08 54.1 5.8 56 8-63 514-575 (667)
36 TIGR00600 rad2 DNA excision re 97.1 0.00042 9.1E-09 58.5 3.5 27 6-32 867-895 (1034)
37 COG1948 MUS81 ERCC4-type nucle 97.1 0.0011 2.4E-08 48.5 5.1 45 7-51 184-234 (254)
38 PRK13766 Hef nuclease; Provisi 97.1 0.0013 2.8E-08 52.5 5.5 46 7-52 717-768 (773)
39 TIGR00596 rad1 DNA repair prot 97.0 0.0013 2.9E-08 54.3 4.9 46 7-52 759-809 (814)
40 PRK14602 ruvA Holliday junctio 96.9 0.002 4.3E-08 45.2 4.7 42 7-49 76-127 (203)
41 PRK13482 DNA integrity scannin 96.9 0.0032 6.9E-08 47.9 5.8 50 4-53 286-341 (352)
42 TIGR01259 comE comEA protein. 96.8 0.0017 3.7E-08 42.1 3.8 40 7-50 70-117 (120)
43 PRK02515 psbU photosystem II c 96.8 0.0019 4E-08 43.4 3.6 45 8-54 64-110 (132)
44 PRK14603 ruvA Holliday junctio 96.8 0.0024 5.1E-08 44.7 4.1 43 6-49 73-125 (197)
45 PRK14605 ruvA Holliday junctio 96.7 0.0027 5.9E-08 44.2 4.4 26 7-33 75-100 (194)
46 smart00278 HhH1 Helix-hairpin- 96.7 0.0011 2.5E-08 32.4 1.8 19 7-25 3-21 (26)
47 PRK13901 ruvA Holliday junctio 96.7 0.0027 5.9E-08 44.8 4.2 42 7-49 74-125 (196)
48 PRK00254 ski2-like helicase; P 96.7 0.0027 5.8E-08 50.9 4.4 46 7-52 647-699 (720)
49 PRK14601 ruvA Holliday junctio 96.7 0.0031 6.8E-08 43.8 4.2 42 7-49 75-126 (183)
50 PRK14604 ruvA Holliday junctio 96.6 0.0041 8.9E-08 43.5 4.8 43 6-49 74-126 (195)
51 PRK14600 ruvA Holliday junctio 96.6 0.0034 7.3E-08 43.7 4.3 42 7-49 75-125 (186)
52 KOG2841 Structure-specific end 96.6 0.0023 5E-08 46.8 3.6 49 8-56 198-252 (254)
53 PRK14606 ruvA Holliday junctio 96.6 0.0039 8.4E-08 43.4 4.1 42 7-49 75-126 (188)
54 PRK14350 ligA NAD-dependent DN 96.5 0.0074 1.6E-07 49.0 6.1 46 8-53 505-563 (669)
55 TIGR00426 competence protein C 96.5 0.0041 8.8E-08 36.2 3.4 39 10-50 22-66 (69)
56 PF02371 Transposase_20: Trans 96.1 0.0056 1.2E-07 37.2 2.4 27 6-32 3-29 (87)
57 TIGR01448 recD_rel helicase, p 96.0 0.022 4.7E-07 46.3 6.2 46 7-52 86-138 (720)
58 PF11798 IMS_HHH: IMS family H 95.9 0.005 1.1E-07 31.7 1.5 16 6-21 12-27 (32)
59 PF10391 DNA_pol_lambd_f: Fing 95.9 0.028 6.1E-07 31.9 4.7 33 8-40 5-38 (52)
60 KOG2519 5'-3' exonuclease [Rep 95.8 0.0078 1.7E-07 47.2 2.9 28 6-33 230-257 (449)
61 cd00141 NT_POLXc Nucleotidyltr 95.7 0.02 4.3E-07 42.1 4.5 29 7-35 87-116 (307)
62 PRK08609 hypothetical protein; 95.7 0.024 5.3E-07 44.9 5.2 48 7-54 90-146 (570)
63 TIGR02236 recomb_radA DNA repa 95.6 0.033 7.2E-07 40.1 5.4 32 7-38 1-34 (310)
64 COG1555 ComEA DNA uptake prote 95.4 0.027 5.9E-07 37.9 3.9 25 8-32 100-130 (149)
65 PF12826 HHH_2: Helix-hairpin- 95.2 0.014 3.1E-07 33.8 2.0 25 7-31 37-61 (64)
66 PRK08097 ligB NAD-dependent DN 95.0 0.057 1.2E-06 43.3 5.4 55 8-65 494-554 (562)
67 PRK07956 ligA NAD-dependent DN 94.9 0.067 1.5E-06 43.4 5.5 54 2-55 441-503 (665)
68 PRK14601 ruvA Holliday junctio 94.8 0.017 3.7E-07 40.1 1.7 20 7-26 110-129 (183)
69 PRK14600 ruvA Holliday junctio 94.7 0.017 3.6E-07 40.2 1.5 18 9-26 111-128 (186)
70 PF04919 DUF655: Protein of un 94.7 0.095 2.1E-06 36.8 5.1 30 9-38 120-154 (181)
71 COG0632 RuvA Holliday junction 94.6 0.057 1.2E-06 38.2 4.0 41 8-49 76-126 (201)
72 COG1491 Predicted RNA-binding 94.6 0.085 1.8E-06 37.6 4.8 42 8-49 133-181 (202)
73 KOG2518 5'-3' exonuclease [Rep 94.6 0.056 1.2E-06 43.4 4.3 29 6-34 226-254 (556)
74 PRK13901 ruvA Holliday junctio 94.5 0.019 4.1E-07 40.5 1.4 20 7-26 109-128 (196)
75 PRK14604 ruvA Holliday junctio 94.5 0.022 4.8E-07 39.8 1.7 21 7-27 110-130 (195)
76 PRK14606 ruvA Holliday junctio 94.4 0.024 5.1E-07 39.5 1.7 20 7-26 110-129 (188)
77 PRK14602 ruvA Holliday junctio 94.4 0.022 4.8E-07 39.9 1.6 20 7-26 111-130 (203)
78 PF14520 HHH_5: Helix-hairpin- 94.3 0.042 9E-07 31.1 2.3 19 7-25 40-58 (60)
79 PRK14603 ruvA Holliday junctio 94.3 0.026 5.5E-07 39.5 1.6 21 7-27 109-129 (197)
80 TIGR00575 dnlj DNA ligase, NAD 94.3 0.11 2.4E-06 42.1 5.3 54 2-55 428-490 (652)
81 smart00483 POLXc DNA polymeras 93.9 0.056 1.2E-06 40.2 2.9 27 7-34 91-119 (334)
82 TIGR00084 ruvA Holliday juncti 93.1 0.06 1.3E-06 37.4 1.8 19 7-25 109-127 (191)
83 TIGR00615 recR recombination p 93.0 0.074 1.6E-06 37.6 2.1 52 6-64 12-63 (195)
84 PRK14605 ruvA Holliday junctio 92.9 0.056 1.2E-06 37.6 1.5 18 7-24 110-127 (194)
85 PRK00076 recR recombination pr 92.9 0.079 1.7E-06 37.4 2.2 52 6-64 12-63 (196)
86 PRK04301 radA DNA repair and r 92.5 0.25 5.5E-06 35.9 4.5 27 7-33 8-35 (317)
87 PRK13844 recombination protein 92.4 0.11 2.4E-06 36.9 2.3 51 6-63 16-66 (200)
88 TIGR03252 uncharacterized HhH- 91.9 0.091 2E-06 36.6 1.5 25 7-31 117-141 (177)
89 COG0632 RuvA Holliday junction 91.8 0.1 2.2E-06 36.9 1.7 21 7-27 110-130 (201)
90 COG0353 RecR Recombinational D 91.5 0.14 3.1E-06 36.4 2.1 51 6-64 13-64 (198)
91 PRK14351 ligA NAD-dependent DN 91.5 0.43 9.4E-06 39.1 5.1 53 2-54 458-519 (689)
92 PF14716 HHH_8: Helix-hairpin- 91.1 0.15 3.3E-06 29.6 1.6 16 7-22 49-64 (68)
93 PRK00116 ruvA Holliday junctio 91.0 0.14 3E-06 35.4 1.6 21 7-27 110-130 (192)
94 PRK01229 N-glycosylase/DNA lya 90.2 0.22 4.9E-06 35.3 2.1 19 9-27 123-141 (208)
95 PF14579 HHH_6: Helix-hairpin- 90.0 0.83 1.8E-05 27.7 4.3 33 7-39 29-66 (90)
96 COG1796 POL4 DNA polymerase IV 89.7 1.1 2.3E-05 34.2 5.5 56 8-63 96-160 (326)
97 PRK10702 endonuclease III; Pro 89.3 0.24 5.1E-06 34.9 1.7 17 8-24 112-128 (211)
98 COG0177 Nth Predicted EndoIII- 89.2 0.28 6E-06 35.1 2.0 21 8-28 112-133 (211)
99 cd00056 ENDO3c endonuclease II 89.1 0.28 6E-06 31.9 1.8 19 7-25 85-103 (158)
100 PRK13913 3-methyladenine DNA g 89.0 0.28 6E-06 35.0 1.8 17 8-24 124-140 (218)
101 KOG2520 5'-3' exonuclease [Rep 88.9 0.5 1.1E-05 39.6 3.5 31 7-37 562-595 (815)
102 PF00416 Ribosomal_S13: Riboso 88.4 0.33 7.2E-06 30.7 1.7 24 3-26 13-36 (107)
103 smart00478 ENDO3c endonuclease 88.1 0.35 7.6E-06 31.1 1.8 17 8-24 75-91 (149)
104 TIGR01083 nth endonuclease III 87.9 0.36 7.7E-06 33.0 1.8 17 8-24 109-125 (191)
105 PRK02362 ski2-like helicase; P 86.9 1.5 3.2E-05 35.5 4.9 44 8-51 655-703 (737)
106 PF11731 Cdd1: Pathogenicity l 86.5 0.56 1.2E-05 29.7 1.9 27 6-32 13-40 (93)
107 PRK13910 DNA glycosylase MutY; 85.8 0.55 1.2E-05 34.7 1.9 20 7-26 74-94 (289)
108 PRK10736 hypothetical protein; 85.5 0.73 1.6E-05 35.4 2.5 25 7-31 10-34 (374)
109 TIGR01084 mutY A/G-specific ad 85.0 0.59 1.3E-05 34.2 1.7 17 7-23 107-123 (275)
110 PRK10880 adenine DNA glycosyla 83.5 0.8 1.7E-05 34.7 1.9 20 7-26 111-131 (350)
111 PF14635 HHH_7: Helix-hairpin- 83.0 0.35 7.5E-06 31.1 -0.2 32 7-38 52-83 (104)
112 PRK08097 ligB NAD-dependent DN 83.0 3.4 7.4E-05 33.3 5.4 54 2-55 421-483 (562)
113 PF12836 HHH_3: Helix-hairpin- 82.4 1.3 2.8E-05 25.4 2.2 17 8-24 17-33 (65)
114 PF13052 DUF3913: Protein of u 81.7 0.61 1.3E-05 26.8 0.6 27 3-31 17-43 (57)
115 PF14229 DUF4332: Domain of un 81.5 4.1 9E-05 26.2 4.5 24 11-34 1-25 (122)
116 COG1936 Predicted nucleotide k 81.3 1.2 2.7E-05 31.2 2.1 21 6-26 4-24 (180)
117 PRK10308 3-methyl-adenine DNA 79.9 1.2 2.6E-05 32.6 1.7 25 7-31 209-234 (283)
118 COG1623 Predicted nucleic-acid 79.7 4.1 8.8E-05 31.2 4.5 50 4-53 292-347 (349)
119 TIGR00375 conserved hypothetic 79.6 1.8 3.9E-05 33.3 2.6 46 3-48 293-354 (374)
120 PRK14350 ligA NAD-dependent DN 79.1 6 0.00013 32.5 5.6 53 2-54 432-493 (669)
121 TIGR00588 ogg 8-oxoguanine DNA 78.7 1.4 3E-05 32.6 1.7 22 8-29 223-245 (310)
122 cd01702 PolY_Pol_eta DNA Polym 77.3 1.5 3.2E-05 32.9 1.6 27 7-33 184-212 (359)
123 TIGR01448 recD_rel helicase, p 77.3 4.2 9E-05 33.3 4.2 42 7-49 119-165 (720)
124 PRK12766 50S ribosomal protein 76.5 1.4 3.1E-05 32.0 1.3 25 6-30 37-61 (232)
125 PF12482 DUF3701: Phage integr 74.4 2.9 6.2E-05 26.5 2.1 27 8-34 53-79 (96)
126 COG0272 Lig NAD-dependent DNA 74.4 8.9 0.00019 31.8 5.4 54 2-55 441-503 (667)
127 COG1796 POL4 DNA polymerase IV 73.7 4.6 9.9E-05 30.8 3.4 49 6-54 129-177 (326)
128 COG4277 Predicted DNA-binding 73.6 2.4 5.1E-05 32.8 1.8 19 6-24 331-349 (404)
129 KOG1921 Endonuclease III [Repl 73.5 2.7 5.9E-05 31.4 2.1 23 9-31 163-186 (286)
130 PRK01172 ski2-like helicase; P 73.2 10 0.00022 30.3 5.4 42 9-50 616-664 (674)
131 TIGR03631 bact_S13 30S ribosom 72.9 2.8 6.2E-05 27.0 1.9 23 5-27 15-37 (113)
132 CHL00137 rps13 ribosomal prote 69.7 4 8.8E-05 26.7 2.1 22 5-26 17-38 (122)
133 PTZ00134 40S ribosomal protein 69.6 3.9 8.4E-05 27.9 2.0 22 5-26 30-51 (154)
134 PRK05179 rpsM 30S ribosomal pr 69.6 4.1 8.8E-05 26.6 2.1 22 5-26 17-38 (122)
135 TIGR03629 arch_S13P archaeal r 69.0 3.9 8.4E-05 27.5 1.9 23 4-26 20-42 (144)
136 COG1194 MutY A/G-specific DNA 68.3 8.5 0.00018 29.5 3.8 32 7-38 115-155 (342)
137 COG0122 AlkA 3-methyladenine D 67.9 3.7 7.9E-05 30.2 1.7 17 8-24 201-217 (285)
138 PRK00024 hypothetical protein; 67.2 35 0.00076 24.1 6.6 47 9-55 37-90 (224)
139 KOG2534 DNA polymerase IV (fam 65.5 5.8 0.00013 30.5 2.4 30 9-38 101-131 (353)
140 PRK04053 rps13p 30S ribosomal 65.5 5.5 0.00012 27.0 2.1 23 4-26 24-46 (149)
141 PRK07373 DNA polymerase III su 64.9 15 0.00033 28.7 4.7 32 4-35 113-150 (449)
142 cd00141 NT_POLXc Nucleotidyltr 62.9 5.1 0.00011 29.5 1.7 25 7-31 47-73 (307)
143 COG2003 RadC DNA repair protei 62.0 29 0.00063 25.2 5.4 22 17-38 46-68 (224)
144 PRK05672 dnaE2 error-prone DNA 61.9 16 0.00035 31.5 4.7 31 5-35 816-851 (1046)
145 COG1948 MUS81 ERCC4-type nucle 61.2 6.6 0.00014 28.9 2.0 27 8-34 217-243 (254)
146 PF02961 BAF: Barrier to autoi 60.7 6.2 0.00013 24.9 1.5 18 7-24 21-38 (89)
147 PF13238 AAA_18: AAA domain; P 60.4 6.2 0.00013 23.5 1.5 20 7-26 3-22 (129)
148 KOG2534 DNA polymerase IV (fam 58.5 6.5 0.00014 30.3 1.6 15 7-21 58-72 (353)
149 PF13207 AAA_17: AAA domain; P 58.5 7 0.00015 23.5 1.5 20 6-25 3-22 (121)
150 PF02742 Fe_dep_repr_C: Iron d 58.3 11 0.00024 21.7 2.3 25 14-38 4-28 (71)
151 cd01703 PolY_Pol_iota DNA Poly 58.2 6.6 0.00014 29.7 1.6 18 7-24 174-191 (379)
152 COG2019 AdkA Archaeal adenylat 57.6 7.7 0.00017 27.6 1.8 20 5-24 7-26 (189)
153 cd01700 PolY_Pol_V_umuC umuC s 57.4 23 0.00049 25.8 4.3 25 7-32 178-204 (344)
154 cd01080 NAD_bind_m-THF_DH_Cycl 57.0 10 0.00023 25.6 2.3 20 6-25 143-163 (168)
155 smart00483 POLXc DNA polymeras 56.7 7.2 0.00016 29.0 1.6 26 7-32 50-77 (334)
156 PRK02406 DNA polymerase IV; Va 56.4 26 0.00056 25.5 4.5 26 7-33 170-197 (343)
157 TIGR01405 polC_Gram_pos DNA po 56.0 24 0.00052 31.1 4.8 40 8-49 1153-1197(1213)
158 PRK00254 ski2-like helicase; P 54.6 9.5 0.00021 30.8 2.1 22 7-28 680-701 (720)
159 PRK14133 DNA polymerase IV; Pr 54.4 37 0.0008 24.8 5.0 26 7-33 175-202 (347)
160 PF03118 RNA_pol_A_CTD: Bacter 54.2 12 0.00026 21.7 2.0 18 7-24 46-63 (66)
161 PF07726 AAA_3: ATPase family 54.2 7.3 0.00016 26.0 1.2 19 7-25 4-22 (131)
162 KOG2379 Endonuclease MUS81 [Re 54.1 9.5 0.00021 30.7 1.9 30 7-36 432-461 (501)
163 TIGR00608 radc DNA repair prot 53.5 76 0.0016 22.5 6.3 48 9-56 27-85 (218)
164 PRK07945 hypothetical protein; 52.7 11 0.00024 28.0 2.0 23 7-29 51-75 (335)
165 cd00424 PolY Y-family of DNA p 52.4 28 0.00061 25.4 4.1 25 7-32 175-201 (343)
166 KOG2841 Structure-specific end 52.0 12 0.00026 27.7 2.0 20 7-26 229-248 (254)
167 PTZ00205 DNA polymerase kappa; 51.2 8.8 0.00019 31.2 1.4 25 7-32 311-337 (571)
168 KOG2457 A/G-specific adenine D 51.0 5.9 0.00013 31.6 0.4 25 8-32 209-234 (555)
169 PRK01184 hypothetical protein; 50.0 16 0.00035 23.8 2.3 20 7-26 6-25 (184)
170 COG1415 Uncharacterized conser 49.9 10 0.00022 29.5 1.5 13 9-21 282-294 (373)
171 TIGR00041 DTMP_kinase thymidyl 49.4 14 0.0003 24.2 1.9 20 6-25 7-26 (195)
172 PRK00625 shikimate kinase; Pro 48.9 71 0.0015 21.4 5.4 27 7-33 5-36 (173)
173 PRK00448 polC DNA polymerase I 48.4 37 0.0008 30.5 4.8 27 8-34 1376-1407(1437)
174 PF01798 Nop: Putative snoRNA 48.0 18 0.00039 24.3 2.3 20 13-32 38-57 (150)
175 PRK01810 DNA polymerase IV; Va 47.8 40 0.00087 25.2 4.4 24 9-33 183-208 (407)
176 PRK10792 bifunctional 5,10-met 47.4 17 0.00038 26.9 2.3 20 5-24 254-274 (285)
177 COG3743 Uncharacterized conser 47.3 12 0.00027 25.1 1.4 19 6-25 68-86 (133)
178 PRK13973 thymidylate kinase; P 46.8 16 0.00035 24.9 2.0 19 7-25 8-26 (213)
179 PRK08609 hypothetical protein; 46.2 13 0.00029 29.6 1.7 25 7-31 50-76 (570)
180 PF05559 DUF763: Protein of un 44.3 15 0.00032 28.0 1.6 14 8-21 272-285 (319)
181 COG2231 Uncharacterized protei 44.1 14 0.00031 26.7 1.4 17 8-24 118-134 (215)
182 PRK03103 DNA polymerase IV; Re 44.0 37 0.0008 25.4 3.7 24 8-32 184-209 (409)
183 PRK00558 uvrC excinuclease ABC 43.7 16 0.00035 29.5 1.8 21 7-27 577-597 (598)
184 COG0099 RpsM Ribosomal protein 43.5 18 0.00039 24.0 1.7 24 7-30 19-42 (121)
185 PRK06826 dnaE DNA polymerase I 43.3 48 0.001 29.1 4.6 32 4-35 823-860 (1151)
186 COG1031 Uncharacterized Fe-S o 43.2 20 0.00043 29.1 2.2 28 7-34 518-547 (560)
187 COG3547 Transposase and inacti 42.9 27 0.00059 24.4 2.7 25 9-33 192-219 (303)
188 PF14842 FliG_N: FliG N-termin 42.7 62 0.0014 20.1 4.1 40 13-52 18-62 (108)
189 PF14490 HHH_4: Helix-hairpin- 42.5 29 0.00063 21.0 2.5 23 4-26 45-67 (94)
190 PRK02794 DNA polymerase IV; Pr 42.2 51 0.0011 24.9 4.2 26 7-33 211-238 (419)
191 TIGR01359 UMP_CMP_kin_fam UMP- 42.1 26 0.00055 22.7 2.3 20 7-26 4-24 (183)
192 PRK05686 fliG flagellar motor 41.4 47 0.001 24.7 3.8 52 13-64 202-259 (339)
193 PRK06920 dnaE DNA polymerase I 41.3 57 0.0012 28.6 4.8 32 4-35 801-837 (1107)
194 smart00611 SEC63 Domain of unk 40.7 80 0.0017 22.4 4.9 28 7-34 153-181 (312)
195 KOG4747 Two-component phosphor 40.6 99 0.0021 21.2 5.0 49 2-52 80-136 (150)
196 PF15608 PELOTA_1: PELOTA RNA 40.1 18 0.00039 23.2 1.3 11 11-21 42-52 (100)
197 KOG0442 Structure-specific end 40.1 69 0.0015 27.7 4.9 49 6-54 822-875 (892)
198 cd01701 PolY_Rev1 DNA polymera 39.8 17 0.00037 27.4 1.3 25 8-32 225-250 (404)
199 PRK07279 dnaE DNA polymerase I 39.8 27 0.00058 30.3 2.6 32 4-35 749-782 (1034)
200 PRK14666 uvrC excinuclease ABC 39.7 14 0.00031 30.7 0.9 23 6-28 670-692 (694)
201 PRK03352 DNA polymerase IV; Va 39.5 15 0.00033 26.8 1.0 26 7-33 179-206 (346)
202 PLN02924 thymidylate kinase 39.4 24 0.00053 24.6 2.0 20 6-25 20-39 (220)
203 PRK07374 dnaE DNA polymerase I 39.4 59 0.0013 28.6 4.6 32 4-35 834-871 (1170)
204 KOG1514 Origin recognition com 39.4 30 0.00066 29.3 2.8 19 5-23 425-444 (767)
205 PF02777 Sod_Fe_C: Iron/mangan 38.8 66 0.0014 19.7 3.7 22 15-36 5-26 (106)
206 PF00004 AAA: ATPase family as 38.8 33 0.00072 20.3 2.3 21 7-27 3-23 (132)
207 PF04994 TfoX_C: TfoX C-termin 38.8 28 0.00061 20.9 2.0 27 6-32 4-31 (81)
208 PRK03858 DNA polymerase IV; Va 38.6 18 0.00039 26.9 1.3 25 7-32 175-201 (396)
209 PRK14552 C/D box methylation g 38.4 28 0.00061 27.1 2.3 25 6-32 265-289 (414)
210 PRK14175 bifunctional 5,10-met 38.3 30 0.00065 25.6 2.4 19 6-24 254-273 (286)
211 cd01672 TMPK Thymidine monopho 37.7 28 0.0006 22.3 1.9 20 6-25 4-23 (200)
212 COG0190 FolD 5,10-methylene-te 37.6 27 0.00058 26.1 2.0 18 7-24 253-271 (283)
213 PRK12339 2-phosphoglycerate ki 37.2 27 0.00059 24.0 1.9 20 6-25 7-26 (197)
214 TIGR00207 fliG flagellar motor 36.9 63 0.0014 24.2 3.9 53 13-65 199-257 (338)
215 cd01673 dNK Deoxyribonucleosid 36.6 29 0.00063 22.7 2.0 20 6-25 3-22 (193)
216 PRK05673 dnaE DNA polymerase I 36.5 41 0.00089 29.4 3.2 32 4-35 819-856 (1135)
217 PRK14670 uvrC excinuclease ABC 36.3 22 0.00047 28.9 1.5 20 7-26 548-567 (574)
218 PRK03839 putative kinase; Prov 36.2 30 0.00064 22.5 1.9 19 7-25 5-23 (180)
219 PRK07135 dnaE DNA polymerase I 35.9 79 0.0017 27.4 4.8 32 4-35 752-789 (973)
220 PTZ00035 Rad51 protein; Provis 35.9 1.2E+02 0.0026 22.6 5.3 28 6-33 22-52 (337)
221 PRK14178 bifunctional 5,10-met 35.6 34 0.00075 25.3 2.3 19 6-24 247-266 (279)
222 TIGR03191 benz_CoA_bzdO benzoy 35.2 1.9E+02 0.0041 22.4 6.4 58 13-70 152-211 (430)
223 PRK03609 umuC DNA polymerase V 34.7 23 0.0005 26.8 1.3 25 7-32 181-207 (422)
224 COG1321 TroR Mn-dependent tran 34.5 1E+02 0.0022 20.6 4.3 26 13-38 67-92 (154)
225 TIGR00594 polc DNA-directed DN 33.9 85 0.0019 27.2 4.7 31 5-35 824-860 (1022)
226 PRK01216 DNA polymerase IV; Va 33.8 28 0.0006 26.1 1.6 26 7-33 180-207 (351)
227 cd02021 GntK Gluconate kinase 33.5 39 0.00085 21.1 2.1 19 7-25 4-22 (150)
228 PRK13976 thymidylate kinase; P 33.2 35 0.00076 23.6 2.0 20 6-25 4-23 (209)
229 PRK01151 rps17E 30S ribosomal 33.2 1E+02 0.0022 17.9 3.8 37 15-51 9-53 (58)
230 KOG2875 8-oxoguanine DNA glyco 33.1 18 0.0004 27.5 0.6 22 9-30 222-244 (323)
231 PRK13975 thymidylate kinase; P 32.9 39 0.00085 22.0 2.1 20 6-25 6-25 (196)
232 cd03468 PolY_like DNA Polymera 32.8 86 0.0019 22.4 4.0 25 9-33 174-199 (335)
233 PF05427 FIBP: Acidic fibrobla 32.3 30 0.00065 26.8 1.6 40 9-49 118-160 (361)
234 KOG3152 TBP-binding protein, a 32.0 21 0.00045 26.8 0.7 30 3-34 78-107 (278)
235 COG0125 Tmk Thymidylate kinase 31.1 40 0.00086 23.7 2.0 20 6-25 7-26 (208)
236 PRK05898 dnaE DNA polymerase I 31.0 63 0.0014 28.1 3.4 31 4-34 751-786 (971)
237 PRK10917 ATP-dependent DNA hel 30.9 31 0.00067 28.0 1.5 28 5-33 9-38 (681)
238 PRK04040 adenylate kinase; Pro 30.2 44 0.00095 22.6 2.0 18 7-24 7-24 (188)
239 COG1536 FliG Flagellar motor s 30.1 1.8E+02 0.004 22.1 5.5 49 8-56 197-250 (339)
240 PF02764 Diphtheria_T: Diphthe 29.7 82 0.0018 21.8 3.3 54 16-69 15-70 (180)
241 PRK06369 nac nascent polypepti 29.4 55 0.0012 21.4 2.3 18 9-26 1-18 (115)
242 PRK14180 bifunctional 5,10-met 29.2 46 0.00099 24.7 2.1 19 6-24 253-272 (282)
243 PF13543 KSR1-SAM: SAM like do 29.1 1.5E+02 0.0032 19.7 4.3 31 10-40 75-106 (129)
244 PF02223 Thymidylate_kin: Thym 29.0 39 0.00084 22.0 1.6 19 7-25 1-19 (186)
245 PRK07758 hypothetical protein; 28.8 50 0.0011 21.0 2.0 18 7-24 69-86 (95)
246 PRK10925 superoxide dismutase; 28.3 83 0.0018 22.0 3.2 23 13-35 95-117 (206)
247 PRK08356 hypothetical protein; 28.3 50 0.0011 22.0 2.0 22 5-26 8-29 (195)
248 TIGR00255 conserved hypothetic 28.3 1.4E+02 0.0031 22.1 4.6 22 14-35 152-173 (291)
249 COG1379 PHP family phosphoeste 28.0 78 0.0017 24.8 3.2 41 12-52 315-365 (403)
250 TIGR01954 nusA_Cterm_rpt trans 27.9 66 0.0014 16.6 2.1 17 8-24 29-45 (50)
251 PRK11820 hypothetical protein; 27.6 1.4E+02 0.0031 22.0 4.5 24 14-37 150-173 (288)
252 TIGR00615 recR recombination p 27.4 1.5E+02 0.0032 21.0 4.3 45 27-71 5-57 (195)
253 COG5241 RAD10 Nucleotide excis 27.4 59 0.0013 23.5 2.3 26 7-32 169-194 (224)
254 PLN02685 iron superoxide dismu 26.9 84 0.0018 23.6 3.2 22 14-35 139-160 (299)
255 PRK14194 bifunctional 5,10-met 26.8 53 0.0012 24.6 2.1 18 7-24 259-277 (301)
256 PTZ00078 Superoxide dismutase 26.6 87 0.0019 21.6 3.0 21 15-35 86-106 (193)
257 PRK03348 DNA polymerase IV; Pr 26.5 44 0.00095 25.8 1.7 25 7-32 182-208 (454)
258 COG0703 AroK Shikimate kinase 26.4 1.3E+02 0.0027 20.8 3.8 48 8-58 8-60 (172)
259 TIGR01366 serC_3 phosphoserine 26.4 1.3E+02 0.0028 22.2 4.0 44 5-49 235-279 (361)
260 PF02889 Sec63: Sec63 Brl doma 26.3 1.9E+02 0.0041 20.4 4.8 28 7-34 150-178 (314)
261 PF02845 CUE: CUE domain; Int 26.2 1E+02 0.0023 15.8 3.8 25 10-34 12-37 (42)
262 cd02020 CMPK Cytidine monophos 26.1 61 0.0013 19.7 2.0 19 6-24 3-21 (147)
263 PRK14181 bifunctional 5,10-met 25.9 59 0.0013 24.2 2.2 19 6-24 258-277 (287)
264 TIGR03574 selen_PSTK L-seryl-t 25.7 63 0.0014 22.3 2.2 19 7-25 4-22 (249)
265 PRK10869 recombination and rep 25.2 2.7E+02 0.0059 22.2 5.9 19 19-37 309-328 (553)
266 PRK13947 shikimate kinase; Pro 25.0 69 0.0015 20.4 2.2 18 7-24 6-23 (171)
267 PRK14973 DNA topoisomerase I; 24.9 1.2E+02 0.0027 26.0 4.1 32 7-38 879-912 (936)
268 COG1139 Uncharacterized conser 24.8 1.9E+02 0.004 23.3 4.8 36 18-54 35-70 (459)
269 COG0714 MoxR-like ATPases [Gen 23.8 60 0.0013 23.5 1.9 21 7-27 48-68 (329)
270 KOG1856 Transcription elongati 23.8 29 0.00064 30.9 0.3 32 7-38 808-839 (1299)
271 cd03586 PolY_Pol_IV_kappa DNA 23.8 57 0.0012 23.4 1.7 24 8-32 174-199 (334)
272 PRK14955 DNA polymerase III su 23.5 70 0.0015 24.1 2.2 19 7-25 43-61 (397)
273 PRK08306 dipicolinate synthase 23.3 70 0.0015 23.2 2.1 24 8-33 263-287 (296)
274 COG0055 AtpD F0F1-type ATP syn 22.7 1.1E+02 0.0025 24.5 3.3 25 16-40 364-390 (468)
275 PF13234 rRNA_proc-arch: rRNA- 22.6 89 0.0019 22.1 2.5 30 41-70 239-268 (268)
276 PLN03187 meiotic recombination 22.5 2.8E+02 0.0061 20.9 5.3 28 6-33 30-60 (344)
277 PF13030 DUF3891: Protein of u 22.2 75 0.0016 22.5 2.1 13 1-13 105-117 (221)
278 COG2256 MGS1 ATPase related to 22.0 77 0.0017 25.2 2.3 20 9-28 55-74 (436)
279 PF09374 PG_binding_3: Predict 22.0 1.8E+02 0.0038 16.9 3.8 21 13-35 22-42 (72)
280 COG0389 DinP Nucleotidyltransf 21.9 1.9E+02 0.0041 21.5 4.2 25 7-33 178-202 (354)
281 PRK07933 thymidylate kinase; V 21.8 73 0.0016 21.9 1.9 19 7-25 5-23 (213)
282 PRK14964 DNA polymerase III su 21.7 75 0.0016 25.3 2.2 18 7-24 40-57 (491)
283 COG1498 SIK1 Protein implicate 21.5 84 0.0018 24.6 2.4 20 13-32 248-267 (395)
284 PF04336 DUF479: Protein of un 21.5 1.9E+02 0.0041 17.8 3.6 21 19-39 49-69 (106)
285 KOG1350 F0F1-type ATP synthase 21.4 1.9E+02 0.0041 23.1 4.2 25 16-40 414-440 (521)
286 PF11697 DUF3293: Protein of u 21.3 86 0.0019 18.3 1.9 17 10-26 53-69 (73)
287 cd02022 DPCK Dephospho-coenzym 21.3 83 0.0018 20.7 2.0 20 7-26 4-23 (179)
288 smart00511 ORANGE Orange domai 21.3 53 0.0011 17.2 0.9 21 7-27 18-38 (45)
289 PHA03134 thymidine kinase; Pro 21.3 80 0.0017 24.2 2.2 23 5-27 16-38 (340)
290 PRK00698 tmk thymidylate kinas 21.3 81 0.0018 20.5 2.0 19 6-24 7-25 (205)
291 KOG0991 Replication factor C, 21.2 72 0.0016 24.3 1.9 19 6-24 52-70 (333)
292 PF10392 COG5: Golgi transport 21.1 2.4E+02 0.0051 18.0 5.8 47 18-64 57-113 (132)
293 PRK00131 aroK shikimate kinase 21.0 92 0.002 19.4 2.2 19 7-25 9-27 (175)
294 PRK14021 bifunctional shikimat 20.9 2.9E+02 0.0064 21.9 5.3 28 7-34 11-43 (542)
295 cd02019 NK Nucleoside/nucleoti 20.9 91 0.002 17.4 1.9 19 7-25 4-22 (69)
296 PF14048 MBD_C: C-terminal dom 20.9 1.2E+02 0.0026 19.0 2.6 41 7-49 53-94 (96)
297 PLN02184 superoxide dismutase 20.8 1.2E+02 0.0025 21.4 2.8 22 14-35 103-124 (212)
298 PF14894 Lsm_C: Lsm C-terminal 20.7 59 0.0013 19.3 1.1 18 8-25 39-58 (64)
299 PHA03135 thymidine kinase; Pro 20.7 83 0.0018 24.2 2.1 22 5-26 13-34 (343)
300 COG0237 CoaE Dephospho-CoA kin 20.5 93 0.002 21.6 2.2 19 7-25 7-25 (201)
301 PF08839 CDT1: DNA replication 20.5 2E+02 0.0043 19.1 3.8 54 19-72 6-63 (163)
302 PF13276 HTH_21: HTH-like doma 20.5 93 0.002 16.9 1.9 15 12-26 37-51 (60)
303 PRK06762 hypothetical protein; 20.5 93 0.002 19.7 2.1 20 6-25 6-25 (166)
304 KOG2093 Translesion DNA polyme 20.5 1.7E+02 0.0036 25.8 4.0 43 7-49 551-598 (1016)
305 PF13877 RPAP3_C: Potential Mo 20.4 1.5E+02 0.0032 17.5 2.9 51 15-65 4-58 (94)
306 PTZ00046 rifin; Provisional 20.4 1.6E+02 0.0035 22.8 3.6 29 42-70 93-126 (358)
307 PRK00889 adenylylsulfate kinas 20.3 99 0.0022 19.9 2.2 19 7-25 9-27 (175)
308 PF09674 DUF2400: Protein of u 20.3 2.3E+02 0.005 20.4 4.3 17 17-33 83-99 (232)
No 1
>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=99.82 E-value=6e-24 Score=135.72 Aligned_cols=65 Identities=29% Similarity=0.412 Sum_probs=52.1
Q ss_pred cccCCCCcccHHHHHHHHHHhCCHHHHHHHhhhhhhHHHHHHHHHhHHHHHHHHHhhhHhhcCcc
Q 035092 5 FINAGVEGTGDVCAVQLITKFGSLENLLQCVYQVEEERTRKALITFADQAVLSKNLVIIIAFSST 69 (73)
Q Consensus 5 ~~I~gVpGIG~KtA~~LL~~fgsle~i~~~~~~l~~~k~~~~L~~~~e~a~ls~~L~~L~~~~~~ 69 (73)
-|||||||||||||.+||++|||+|+|+++++++++++++++|.++.|++++||+|++|++++|-
T Consensus 18 DNIPGV~GIG~KtA~~LL~~ygsle~i~~~~~~~~~~k~~~~l~~~~e~a~ls~~L~tl~~dv~l 82 (101)
T PF01367_consen 18 DNIPGVPGIGPKTAAKLLQEYGSLENILANLDEIKGKKIREKLRENKEQALLSRKLATLKTDVPL 82 (101)
T ss_dssp CTB---TTSTCHCCCCCHHHHTSCHCCCCC-SSS-TSCCCHHHHTSCCCCCCHHHHH-H-S----
T ss_pred cCCCCCCCCCHHHHHHHHHHcCCHHHHHHhHHhccccHHHHHHHHHHHHHHHhHHHhhhhcCCCC
Confidence 59999999999999999999999999999999998767899999999999999999999999874
No 2
>PRK09482 flap endonuclease-like protein; Provisional
Probab=99.81 E-value=4.7e-20 Score=133.07 Aligned_cols=64 Identities=28% Similarity=0.351 Sum_probs=61.2
Q ss_pred cccCCCCcccHHHHHHHHHHhCCHHHHHHHhhhhhhHHHHHHHHHhHHHHHHHHHhhhHhhcCcc
Q 035092 5 FINAGVEGTGDVCAVQLITKFGSLENLLQCVYQVEEERTRKALITFADQAVLSKNLVIIIAFSST 69 (73)
Q Consensus 5 ~~I~gVpGIG~KtA~~LL~~fgsle~i~~~~~~l~~~k~~~~L~~~~e~a~ls~~L~~L~~~~~~ 69 (73)
-|||||||||||||.+||++|||+|+|+++++++++ +++++|.++.+++++||+|++|++++|-
T Consensus 182 DnIpGVpGIG~KtA~~LL~~~gsle~i~~~~~~~~~-~~~~~L~~~~~~a~lsr~L~~l~~dv~l 245 (256)
T PRK09482 182 SKIPGVAGIGPKSAAELLNQFRSLENIYESLDALPE-KWRKKLEEHKEMARLCRKLAQLQTDLPL 245 (256)
T ss_pred cCCCCCCCcChHHHHHHHHHhCCHHHHHHhHHHhhH-HHHHHHHHhHHHHHHHHhhheEeeCCCC
Confidence 599999999999999999999999999999999976 8999999999999999999999999874
No 3
>smart00475 53EXOc 5'-3' exonuclease.
Probab=99.79 E-value=1.8e-19 Score=129.49 Aligned_cols=64 Identities=31% Similarity=0.471 Sum_probs=61.0
Q ss_pred cccCCCCcccHHHHHHHHHHhCCHHHHHHHhhhhhhHHHHHHHHHhHHHHHHHHHhhhHhhcCcc
Q 035092 5 FINAGVEGTGDVCAVQLITKFGSLENLLQCVYQVEEERTRKALITFADQAVLSKNLVIIIAFSST 69 (73)
Q Consensus 5 ~~I~gVpGIG~KtA~~LL~~fgsle~i~~~~~~l~~~k~~~~L~~~~e~a~ls~~L~~L~~~~~~ 69 (73)
-|||||||||||||.+||++|||+|+|+++++++++ +++++|.++.+++++|++|++|++++|.
T Consensus 186 DnipGV~GIG~KtA~~Ll~~ygsle~i~~~~~~~~~-~~~~~l~~~~~~~~ls~~L~~l~~d~~l 249 (259)
T smart00475 186 DNIPGVPGIGEKTAAKLLKEFGSLENILENLDKLKK-KLREKLLAHKEDAKLSRKLATIETDVPL 249 (259)
T ss_pred cCCCCCCCCCHHHHHHHHHHhCCHHHHHHHHHHHHH-HHHHHHHhcHHHHHHhhhhheeeeCCCC
Confidence 589999999999999999999999999999999986 8999999999999999999999999884
No 4
>PRK14976 5'-3' exonuclease; Provisional
Probab=99.79 E-value=1.8e-19 Score=130.68 Aligned_cols=64 Identities=27% Similarity=0.436 Sum_probs=61.2
Q ss_pred cccCCCCcccHHHHHHHHHHhCCHHHHHHHhhhhhhHHHHHHHHHhHHHHHHHHHhhhHhhcCcc
Q 035092 5 FINAGVEGTGDVCAVQLITKFGSLENLLQCVYQVEEERTRKALITFADQAVLSKNLVIIIAFSST 69 (73)
Q Consensus 5 ~~I~gVpGIG~KtA~~LL~~fgsle~i~~~~~~l~~~k~~~~L~~~~e~a~ls~~L~~L~~~~~~ 69 (73)
-|||||||||||||.+||++|||+|+|+++++++++ +++++|.++.+++++|++|++|++++|-
T Consensus 191 DnipGVpGIG~KtA~~LL~~~gsle~i~~~~~~~~~-~~~~~L~~~~~~~~~s~~L~~l~~d~~l 254 (281)
T PRK14976 191 DNIKGVKGIGPKTAIKLLNKYGNIENIYENIDKIKK-KIKNKLSEAKEKALLSKKLATIKTDVPL 254 (281)
T ss_pred CCCCCCCcccHHHHHHHHHHcCCHHHHHHhHHHHhH-HHHHHHHHhHHHHHHhhhhhEEeecCCC
Confidence 599999999999999999999999999999999986 7999999999999999999999999874
No 5
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.74 E-value=2.8e-18 Score=139.54 Aligned_cols=65 Identities=34% Similarity=0.511 Sum_probs=61.8
Q ss_pred cccCCCCcccHHHHHHHHHHhCCHHHHHHHhhhhhhHHHHHHHHHhHHHHHHHHHhhhHhhcCcc
Q 035092 5 FINAGVEGTGDVCAVQLITKFGSLENLLQCVYQVEEERTRKALITFADQAVLSKNLVIIIAFSST 69 (73)
Q Consensus 5 ~~I~gVpGIG~KtA~~LL~~fgsle~i~~~~~~l~~~k~~~~L~~~~e~a~ls~~L~~L~~~~~~ 69 (73)
-|||||||||||||.+||++|||+|+|+++++++++++++++|.++.|++++||+|++|++++|-
T Consensus 185 DnIpGVpGIG~KtA~kLL~~ygsle~i~~~~~~i~~~k~~~~L~~~~e~a~ls~~L~ti~~d~~l 249 (887)
T TIGR00593 185 DNIPGVKGIGEKTAAKLLQEFGSLENIYENLDQIKSAKMREKLIAHKEDAFLSKELATIVTDVPL 249 (887)
T ss_pred cCCCCCCCcCHHHHHHHHHHcCCHHHHHHHHHHhccHHHHHHHHHhHHHHHHHHHhheeecCCCC
Confidence 59999999999999999999999999999999997657999999999999999999999999874
No 6
>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=99.70 E-value=2.9e-17 Score=116.30 Aligned_cols=58 Identities=33% Similarity=0.469 Sum_probs=55.3
Q ss_pred cccCCCCcccHHHHHHHHHHhCCHHHHHHHhhhhhhHHHHHHHHHhHHHHHHHHHhhhH
Q 035092 5 FINAGVEGTGDVCAVQLITKFGSLENLLQCVYQVEEERTRKALITFADQAVLSKNLVII 63 (73)
Q Consensus 5 ~~I~gVpGIG~KtA~~LL~~fgsle~i~~~~~~l~~~k~~~~L~~~~e~a~ls~~L~~L 63 (73)
-|||||||||||||.+||++|||+|+|+++++++++ +++++|.++.|++++|++|++|
T Consensus 183 DnipGv~GiG~ktA~~Ll~~~gsle~i~~~~~~~~~-~~~~~l~~~~~~~~~s~~L~~l 240 (240)
T cd00008 183 DNIPGVPGIGEKTAAKLLKEYGSLEGILENLDKIKG-KLREKLEEGKEMAFLSKRLATI 240 (240)
T ss_pred cCCCCCCccCHHHHHHHHHHhCCHHHHHHhHHHHhH-HHHHHHHHhHHHHHHHHHhhcC
Confidence 589999999999999999999999999999999876 8999999999999999999986
No 7
>PRK05755 DNA polymerase I; Provisional
Probab=99.65 E-value=2.2e-16 Score=127.49 Aligned_cols=64 Identities=28% Similarity=0.399 Sum_probs=60.5
Q ss_pred cccCCCCcccHHHHHHHHHHhCCHHHHHHHhhhhhhHHHHHHHHHhHHHHHHHHHhhhHhhcCcc
Q 035092 5 FINAGVEGTGDVCAVQLITKFGSLENLLQCVYQVEEERTRKALITFADQAVLSKNLVIIIAFSST 69 (73)
Q Consensus 5 ~~I~gVpGIG~KtA~~LL~~fgsle~i~~~~~~l~~~k~~~~L~~~~e~a~ls~~L~~L~~~~~~ 69 (73)
-|||||||||||||.+||++|||+|+|+++++++++ +++++|.++.|++++|++|++|+++.|-
T Consensus 187 DnipGv~GiG~ktA~~Ll~~~gsle~i~~~~~~~~~-~~~~~l~~~~~~~~ls~~l~~l~~d~~~ 250 (880)
T PRK05755 187 DNIPGVPGIGEKTAAKLLQEYGSLEGLYENLDEIKG-KKKEKLRENKEQAFLSRKLATIKTDVPL 250 (880)
T ss_pred CCCCCCCCccHHHHHHHHHHcCCHHHHHHhHHHhch-HHHHHHHHhHHHHHhhhhhheeeeCCCC
Confidence 589999999999999999999999999999999987 7899999999999999999999998873
No 8
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=99.55 E-value=5.9e-15 Score=107.25 Aligned_cols=64 Identities=31% Similarity=0.420 Sum_probs=59.5
Q ss_pred cccCCCCcccHHHHHHHHHHhCCHHHHHHHhhhhhhHHHHHHHHHhHHHHHHHHHhhhHhhcCcc
Q 035092 5 FINAGVEGTGDVCAVQLITKFGSLENLLQCVYQVEEERTRKALITFADQAVLSKNLVIIIAFSST 69 (73)
Q Consensus 5 ~~I~gVpGIG~KtA~~LL~~fgsle~i~~~~~~l~~~k~~~~L~~~~e~a~ls~~L~~L~~~~~~ 69 (73)
.|||||||||||||.+||++|||++.++++++.+++ +.++++.++.+.+++|++|+++.++.+.
T Consensus 198 DnipGV~GIG~ktA~~Ll~~~gs~e~i~~~~~~~~~-~~~~~l~~~~~~afl~~~l~t~~~d~~l 261 (310)
T COG0258 198 DNIPGVKGIGPKTALKLLQEYGSLEGLYENLDIIKK-KTREKLLEDKEKAFLSKPLATIKTDVPL 261 (310)
T ss_pred cCCCCCCCcCHHHHHHHHHHhCCHHHHHHhhhhhcc-hhhHHHHHHHHHHhcCcccccccccccC
Confidence 599999999999999999999999999999987766 8999999999999999999999988653
No 9
>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=99.52 E-value=3.3e-14 Score=85.91 Aligned_cols=53 Identities=38% Similarity=0.528 Sum_probs=48.9
Q ss_pred cccCCCCcccHHHHHHHHHHhCCHHHHHHHhhhhhhHHHHHHHHHhHHHHHHHHHh
Q 035092 5 FINAGVEGTGDVCAVQLITKFGSLENLLQCVYQVEEERTRKALITFADQAVLSKNL 60 (73)
Q Consensus 5 ~~I~gVpGIG~KtA~~LL~~fgsle~i~~~~~~l~~~k~~~~L~~~~e~a~ls~~L 60 (73)
.|+|||||||+|+|.+||++|+|+++++++.++++ +++++.++.+.++++++|
T Consensus 22 D~i~gv~giG~k~A~~ll~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~l 74 (75)
T cd00080 22 DNIPGVPGIGPKTALKLLKEYGSLENLLENLDKIK---LREKLLEHKELAKLSKLL 74 (75)
T ss_pred ccCCCCCcccHHHHHHHHHHhCCHHHHHHHHHHHh---HHHhhhccHHHHHHHHhh
Confidence 58999999999999999999999999999988874 788999999999999886
No 10
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=98.85 E-value=1.7e-09 Score=57.80 Aligned_cols=22 Identities=32% Similarity=0.451 Sum_probs=20.3
Q ss_pred ccccCCCCcccHHHHHHHHHHh
Q 035092 4 YFINAGVEGTGDVCAVQLITKF 25 (73)
Q Consensus 4 ~~~I~gVpGIG~KtA~~LL~~f 25 (73)
-.|||||||||+|+|.+||++|
T Consensus 15 ~dni~Gv~giG~ktA~~ll~~~ 36 (36)
T smart00279 15 SDNIPGVKGIGPKTALKLLREF 36 (36)
T ss_pred CCCCCCCCcccHHHHHHHHHhC
Confidence 3589999999999999999987
No 11
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=98.84 E-value=9.4e-09 Score=60.25 Aligned_cols=48 Identities=27% Similarity=0.479 Sum_probs=36.3
Q ss_pred CCCCcccHHHHHHHHHHhCCHHHHHH-Hhhhh---hh--HHHHHHHHHhHHHHH
Q 035092 8 AGVEGTGDVCAVQLITKFGSLENLLQ-CVYQV---EE--ERTRKALITFADQAV 55 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~~fgsle~i~~-~~~~l---~~--~k~~~~L~~~~e~a~ 55 (73)
-||||||+++|+.|+++|+|++++.+ +.+++ ++ ++.++.+.++.+.-.
T Consensus 6 LGI~~VG~~~ak~L~~~f~sl~~l~~a~~e~L~~i~gIG~~~A~si~~ff~~~~ 59 (64)
T PF12826_consen 6 LGIPGVGEKTAKLLAKHFGSLEALMNASVEELSAIPGIGPKIAQSIYEFFQDPE 59 (64)
T ss_dssp CTSTT--HHHHHHHHHCCSCHHHHCC--HHHHCTSTT--HHHHHHHHHHHH-HH
T ss_pred CCCCCccHHHHHHHHHHcCCHHHHHHcCHHHHhccCCcCHHHHHHHHHHHCCHH
Confidence 49999999999999999999999984 34554 33 788999998877644
No 12
>PTZ00217 flap endonuclease-1; Provisional
Probab=98.67 E-value=2.1e-08 Score=76.11 Aligned_cols=34 Identities=26% Similarity=0.402 Sum_probs=31.2
Q ss_pred cccCCCCcccHHHHHHHHHHhCCHHHHHHHhhhh
Q 035092 5 FINAGVEGTGDVCAVQLITKFGSLENLLQCVYQV 38 (73)
Q Consensus 5 ~~I~gVpGIG~KtA~~LL~~fgsle~i~~~~~~l 38 (73)
.|+|||||||||+|.+||++|+|+|++++++++.
T Consensus 235 Dy~pgi~GIG~ktA~~Li~~~gsle~il~~~~~~ 268 (393)
T PTZ00217 235 DYCDTIKGIGPKTAYKLIKKYKSIEEILEHLDKT 268 (393)
T ss_pred CCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhc
Confidence 4789999999999999999999999999987654
No 13
>PRK03980 flap endonuclease-1; Provisional
Probab=98.61 E-value=3.2e-08 Score=72.49 Aligned_cols=31 Identities=39% Similarity=0.585 Sum_probs=28.6
Q ss_pred cccCCCCcccHHHHHHHHHHhCCHHHHHHHh
Q 035092 5 FINAGVEGTGDVCAVQLITKFGSLENLLQCV 35 (73)
Q Consensus 5 ~~I~gVpGIG~KtA~~LL~~fgsle~i~~~~ 35 (73)
-|+|||||||||||.+|+++|+|+|++++..
T Consensus 189 Dy~~GI~GIG~ktA~kLi~~~~sle~i~~~~ 219 (292)
T PRK03980 189 DYNPGIKGIGPKTALKLIKKHGDLEKVLEER 219 (292)
T ss_pred CCCCCCCCccHHHHHHHHHHCCCHHHHHHhc
Confidence 4789999999999999999999999999853
No 14
>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=98.59 E-value=4.4e-08 Score=72.74 Aligned_cols=31 Identities=35% Similarity=0.560 Sum_probs=28.5
Q ss_pred ccCCCCcccHHHHHHHHHHhCCHHHHHHHhhh
Q 035092 6 INAGVEGTGDVCAVQLITKFGSLENLLQCVYQ 37 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~fgsle~i~~~~~~ 37 (73)
| |||||||||||.+|+++|||+|+++++++.
T Consensus 238 n-~Gv~GIG~ktA~kli~~~gsie~il~~~~~ 268 (338)
T TIGR03674 238 N-EGVKGIGPKTALKLIKEHGDLEKVLKARGE 268 (338)
T ss_pred C-CCCCCccHHHHHHHHHHcCCHHHHHHhhcC
Confidence 5 999999999999999999999999987543
No 15
>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=98.51 E-value=1.1e-07 Score=69.15 Aligned_cols=31 Identities=32% Similarity=0.600 Sum_probs=28.3
Q ss_pred cccCCCCcccHHHHHHHHHHhCCHHHHHHHh
Q 035092 5 FINAGVEGTGDVCAVQLITKFGSLENLLQCV 35 (73)
Q Consensus 5 ~~I~gVpGIG~KtA~~LL~~fgsle~i~~~~ 35 (73)
.|+|||||||+|||.+|+++|+|++++++++
T Consensus 223 Dy~~gv~giG~k~A~~li~~~~~~~~~~~~l 253 (316)
T cd00128 223 DYTEGIPGIGPVTALKLIKKYGDIEKDIERL 253 (316)
T ss_pred CCCCCCCCccHHHHHHHHHHcCChHHHHHHH
Confidence 4789999999999999999999998888765
No 16
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=98.50 E-value=2.1e-07 Score=73.77 Aligned_cols=49 Identities=16% Similarity=0.361 Sum_probs=40.3
Q ss_pred cccCCCCcccHHHHHHHHHHhCCHHHHHHH-hhhh---hh--HHHHHHHHHhHHH
Q 035092 5 FINAGVEGTGDVCAVQLITKFGSLENLLQC-VYQV---EE--ERTRKALITFADQ 53 (73)
Q Consensus 5 ~~I~gVpGIG~KtA~~LL~~fgsle~i~~~-~~~l---~~--~k~~~~L~~~~e~ 53 (73)
|.+.+|||||||+..+||++|||+++|.++ .++| ++ ++++++|.+++..
T Consensus 514 s~L~~I~GiG~kr~~~LL~~Fgs~~~I~~As~eeL~~v~gi~~~~A~~I~~~l~~ 568 (574)
T PRK14670 514 LNYTKIKGIGEKKAKKILKSLGTYKDILLLNEDEIAEKMKINIKMAKKIKKFAEK 568 (574)
T ss_pred cccccCCCCCHHHHHHHHHHhCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 567899999999999999999999999864 5665 22 6788888887643
No 17
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=98.46 E-value=2.5e-07 Score=73.20 Aligned_cols=48 Identities=15% Similarity=0.254 Sum_probs=39.2
Q ss_pred ccccCCCCcccHHHHHHHHHHhCCHHHHHHH-hhhhh----hHHHHHHHHHhH
Q 035092 4 YFINAGVEGTGDVCAVQLITKFGSLENLLQC-VYQVE----EERTRKALITFA 51 (73)
Q Consensus 4 ~~~I~gVpGIG~KtA~~LL~~fgsle~i~~~-~~~l~----~~k~~~~L~~~~ 51 (73)
-|-+.+|||||||++.+||++|||+++|.++ +++|. +++++++|.++.
T Consensus 513 ~S~Ld~I~GiG~kr~~~Ll~~Fgs~~~ik~As~eeL~~vgi~~~~A~~I~~~l 565 (567)
T PRK14667 513 KDILDKIKGIGEVKKEIIYRNFKTLYDFLKADDEELKKLGIPPSVKQEVKKYL 565 (567)
T ss_pred cCccccCCCCCHHHHHHHHHHhCCHHHHHhCCHHHHHHcCCCHHHHHHHHHHh
Confidence 3667899999999999999999999999964 56553 257888887764
No 18
>PHA00439 exonuclease
Probab=98.44 E-value=2.9e-07 Score=67.92 Aligned_cols=29 Identities=24% Similarity=0.369 Sum_probs=26.8
Q ss_pred cccCCCCcccHHHHHHHHHH---hCCHHHHHHH
Q 035092 5 FINAGVEGTGDVCAVQLITK---FGSLENLLQC 34 (73)
Q Consensus 5 ~~I~gVpGIG~KtA~~LL~~---fgsle~i~~~ 34 (73)
-||||||||| |||.+||++ |..++..+.+
T Consensus 188 DNIPGVpGIG-KTA~kLL~~~~~~~~~~~~~~s 219 (286)
T PHA00439 188 DGYSGIPGWG-DTAEAFLENPYIFEQVEKVLKS 219 (286)
T ss_pred cCCCCCCCcC-HHHHHHHhCccccchhhHHhhc
Confidence 5999999999 999999999 8888888876
No 19
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=98.35 E-value=5.3e-07 Score=72.08 Aligned_cols=48 Identities=23% Similarity=0.295 Sum_probs=39.2
Q ss_pred cccCCCCcccHHHHHHHHHHhCCHHHHHHH-hhhhh---hHHHHHHHHHhHH
Q 035092 5 FINAGVEGTGDVCAVQLITKFGSLENLLQC-VYQVE---EERTRKALITFAD 52 (73)
Q Consensus 5 ~~I~gVpGIG~KtA~~LL~~fgsle~i~~~-~~~l~---~~k~~~~L~~~~e 52 (73)
|-+.+|||||||++.+||++|||+++|.++ .++|. +.+.++.|.++..
T Consensus 552 S~L~~IpGIG~kr~~~LL~~FgSi~~I~~As~eeL~~vi~~k~A~~I~~~l~ 603 (624)
T PRK14669 552 SELLEIPGVGAKTVQRLLKHFGSLERVRAATETQLAAVVGRAAAEAIIAHFT 603 (624)
T ss_pred HHHhcCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHHHHhCHHHHHHHHHHhc
Confidence 567899999999999999999999999964 66663 3567777777654
No 20
>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=98.26 E-value=3.9e-06 Score=48.07 Aligned_cols=45 Identities=24% Similarity=0.340 Sum_probs=34.9
Q ss_pred cCCCCcccHHHHHHHHHH-hCCHHHHHHH----hhhhhh--HHHHHHHHHhH
Q 035092 7 NAGVEGTGDVCAVQLITK-FGSLENLLQC----VYQVEE--ERTRKALITFA 51 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~-fgsle~i~~~----~~~l~~--~k~~~~L~~~~ 51 (73)
+.+||||||++|..|.+. |.|++++... +.++++ ++.+++|.+..
T Consensus 7 L~~I~Gig~~~a~~L~~~G~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~ 58 (60)
T PF14520_consen 7 LLSIPGIGPKRAEKLYEAGIKTLEDLANADPEELAEIPGIGEKTAEKIIEAA 58 (60)
T ss_dssp HHTSTTCHHHHHHHHHHTTCSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHHH
T ss_pred hccCCCCCHHHHHHHHhcCCCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHHH
Confidence 457999999999999999 9999999842 344444 66777776644
No 21
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=98.14 E-value=3.4e-06 Score=67.35 Aligned_cols=48 Identities=19% Similarity=0.374 Sum_probs=38.6
Q ss_pred ccccCCCCcccHHHHHHHHHHhCCHHHHHHH-hhhh---hhHHHHHHHHHhH
Q 035092 4 YFINAGVEGTGDVCAVQLITKFGSLENLLQC-VYQV---EEERTRKALITFA 51 (73)
Q Consensus 4 ~~~I~gVpGIG~KtA~~LL~~fgsle~i~~~-~~~l---~~~k~~~~L~~~~ 51 (73)
.+.+.||||||||+|..|+++|||+++|..+ .+++ -++++++.|.+++
T Consensus 568 ~s~L~~I~GIG~k~a~~Ll~~Fgs~~~i~~As~eeL~~vig~k~A~~I~~~~ 619 (621)
T PRK14671 568 QTELTDIAGIGEKTAEKLLEHFGSVEKVAKASLEELAAVAGPKTAETIYRYY 619 (621)
T ss_pred hhhhhcCCCcCHHHHHHHHHHcCCHHHHHhCCHHHHHHHhCHHHHHHHHHHh
Confidence 4667899999999999999999999999854 5555 3457777777654
No 22
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=98.12 E-value=4.6e-06 Score=67.64 Aligned_cols=51 Identities=24% Similarity=0.175 Sum_probs=41.3
Q ss_pred ccccCCCCcccHHHHHHHHHHhCCHHHHHHH-hhhhh---h--HHHHHHHHHhHHHH
Q 035092 4 YFINAGVEGTGDVCAVQLITKFGSLENLLQC-VYQVE---E--ERTRKALITFADQA 54 (73)
Q Consensus 4 ~~~I~gVpGIG~KtA~~LL~~fgsle~i~~~-~~~l~---~--~k~~~~L~~~~e~a 54 (73)
-|.+..|||||||++.+||++|||+++|.++ .+++. + ++.+++|.+++..+
T Consensus 636 ~s~L~~IPGIGpkr~k~LL~~FGSle~I~~AS~eELa~V~Gig~k~Ae~I~~~L~~~ 692 (694)
T PRK14666 636 TGELQRVEGIGPATARLLWERFGSLQAMAAAGEEGLAAVPGIGPARAAALHEHLKTL 692 (694)
T ss_pred HhHHhhCCCCCHHHHHHHHHHhCCHHHHHhcCHHHHHhcCCcCHHHHHHHHHHHHHh
Confidence 3667899999999999999999999999964 55553 2 67888888877654
No 23
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=98.11 E-value=4.3e-06 Score=67.76 Aligned_cols=46 Identities=17% Similarity=0.281 Sum_probs=36.2
Q ss_pred ccccCCCCcccHHHHHHHHHHhCCHHHHHHH-hhhhhh-----HHHHHHHHH
Q 035092 4 YFINAGVEGTGDVCAVQLITKFGSLENLLQC-VYQVEE-----ERTRKALIT 49 (73)
Q Consensus 4 ~~~I~gVpGIG~KtA~~LL~~fgsle~i~~~-~~~l~~-----~k~~~~L~~ 49 (73)
-|-+.+|||||||++..||++|||+++|.++ +++|.. .+++++|.-
T Consensus 607 ~s~L~~IpGiG~kr~~~LL~~FgS~~~i~~As~eel~~v~gi~~~~A~~i~~ 658 (691)
T PRK14672 607 VLSFERLPHVGKVRAHRLLAHFGSFRSLQSATPQDIATAIHIPLTQAHTILH 658 (691)
T ss_pred ccccccCCCCCHHHHHHHHHHhcCHHHHHhCCHHHHHhCCCCCHHHHHHHHH
Confidence 3667899999999999999999999999964 666632 455655544
No 24
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=98.06 E-value=5.2e-06 Score=66.10 Aligned_cols=48 Identities=17% Similarity=0.271 Sum_probs=37.9
Q ss_pred cccccCCCCcccHHHHHHHHHHhCCHHHHHHH-hhhhhh----HHHHHHHHHh
Q 035092 3 FYFINAGVEGTGDVCAVQLITKFGSLENLLQC-VYQVEE----ERTRKALITF 50 (73)
Q Consensus 3 ~~~~I~gVpGIG~KtA~~LL~~fgsle~i~~~-~~~l~~----~k~~~~L~~~ 50 (73)
+-|-.++|||||||+.++||++|||+++|.++ .+++.. .++++++.++
T Consensus 528 ~~s~Ld~I~GiG~~r~~~LL~~Fgs~~~i~~As~eel~~vgi~~~~a~~i~~~ 580 (581)
T COG0322 528 LQSSLDDIPGIGPKRRKALLKHFGSLKGIKSASVEELAKVGISKKLAEKIYEA 580 (581)
T ss_pred hcCccccCCCcCHHHHHHHHHHhhCHHHHHhcCHHHHHHcCCCHHHHHHHHhh
Confidence 45667899999999999999999999999864 566532 4667766553
No 25
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=98.02 E-value=1.1e-05 Score=58.37 Aligned_cols=48 Identities=15% Similarity=0.115 Sum_probs=38.5
Q ss_pred cccCCCCcccHHHHHHHHHH-hCCHHHHHHH-hhhh---hh--HHHHHHHHHhHH
Q 035092 5 FINAGVEGTGDVCAVQLITK-FGSLENLLQC-VYQV---EE--ERTRKALITFAD 52 (73)
Q Consensus 5 ~~I~gVpGIG~KtA~~LL~~-fgsle~i~~~-~~~l---~~--~k~~~~L~~~~e 52 (73)
..+.+|||||++++.+|++. |+|+++|..+ .++| ++ .+.+++|.++..
T Consensus 3 ~~L~~IpGIG~krakkLl~~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l~ 57 (232)
T PRK12766 3 EELEDISGVGPSKAEALREAGFESVEDVRAADQSELAEVDGIGNALAARIKADVG 57 (232)
T ss_pred cccccCCCcCHHHHHHHHHcCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHHhc
Confidence 45789999999999999999 9999999854 4444 32 577888887755
No 26
>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=98.00 E-value=3.7e-06 Score=66.66 Aligned_cols=30 Identities=23% Similarity=0.367 Sum_probs=27.8
Q ss_pred cccCCCCcccHHHHHHHHHHhCCHHHHHHH
Q 035092 5 FINAGVEGTGDVCAVQLITKFGSLENLLQC 34 (73)
Q Consensus 5 ~~I~gVpGIG~KtA~~LL~~fgsle~i~~~ 34 (73)
|-+.+|||||||++.+||++|||+++|.++
T Consensus 541 S~Ld~I~GIG~kr~~~LL~~Fgs~~~i~~A 570 (574)
T TIGR00194 541 SPLLKIPGVGEKRVQKLLKYFGSLKGIKKA 570 (574)
T ss_pred HHHhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 567899999999999999999999999865
No 27
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=97.99 E-value=9.9e-06 Score=56.02 Aligned_cols=49 Identities=12% Similarity=0.248 Sum_probs=35.1
Q ss_pred cccCCCCcccHHHHHHHHHHhCC---HHHHHHH----hhhhhh--HHHHHHHHHhHHH
Q 035092 5 FINAGVEGTGDVCAVQLITKFGS---LENLLQC----VYQVEE--ERTRKALITFADQ 53 (73)
Q Consensus 5 ~~I~gVpGIG~KtA~~LL~~fgs---le~i~~~----~~~l~~--~k~~~~L~~~~e~ 53 (73)
+.+..|||||||+|.++|+.|++ .+.+.++ +.++++ ++.++++......
T Consensus 73 ~~L~~i~GIGpk~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~~~l~~ 130 (192)
T PRK00116 73 RLLISVSGVGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELKD 130 (192)
T ss_pred HHHhcCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 45678999999999999999998 6666642 334444 5677777764443
No 28
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=97.94 E-value=1.1e-05 Score=64.05 Aligned_cols=48 Identities=19% Similarity=0.262 Sum_probs=37.8
Q ss_pred ccccCCCCcccHHHHHHHHHHhCCHHHHHHH-hhhh---hh--HHHHHHHHHhH
Q 035092 4 YFINAGVEGTGDVCAVQLITKFGSLENLLQC-VYQV---EE--ERTRKALITFA 51 (73)
Q Consensus 4 ~~~I~gVpGIG~KtA~~LL~~fgsle~i~~~-~~~l---~~--~k~~~~L~~~~ 51 (73)
-+-+.+|||||++++..|+++|||+++|.++ .+++ ++ +++++.|.++.
T Consensus 542 ~s~L~~IpGIG~k~~k~Ll~~FgS~~~i~~As~eeL~~v~Gig~~~A~~I~~~l 595 (598)
T PRK00558 542 TSALDDIPGIGPKRRKALLKHFGSLKAIKEASVEELAKVPGISKKLAEAIYEAL 595 (598)
T ss_pred hhhHhhCCCcCHHHHHHHHHHcCCHHHHHhCCHHHHhhcCCcCHHHHHHHHHHh
Confidence 3566899999999999999999999999964 4444 22 67777777654
No 29
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=97.85 E-value=2.4e-05 Score=62.18 Aligned_cols=46 Identities=24% Similarity=0.377 Sum_probs=35.7
Q ss_pred cccCCCCcccHHHHHHHHHHhCCHHHHHHH-hhhh---hh--HHHHHHHHHh
Q 035092 5 FINAGVEGTGDVCAVQLITKFGSLENLLQC-VYQV---EE--ERTRKALITF 50 (73)
Q Consensus 5 ~~I~gVpGIG~KtA~~LL~~fgsle~i~~~-~~~l---~~--~k~~~~L~~~ 50 (73)
+.+..|||||++++.+||++|||+++|.++ .+++ ++ +++++.|.++
T Consensus 525 ~~L~~IpGIG~kr~~~LL~~FGS~~~I~~As~eeL~~vpGi~~~~A~~I~~~ 576 (577)
T PRK14668 525 TVLDDVPGVGPETRKRLLRRFGSVEGVREASVEDLRDVPGVGEKTAETIRER 576 (577)
T ss_pred hHHhcCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHh
Confidence 456899999999999999999999999964 4444 22 4666666543
No 30
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=97.83 E-value=6e-05 Score=60.52 Aligned_cols=56 Identities=20% Similarity=0.398 Sum_probs=41.9
Q ss_pred CCCCcccHHHHHHHHHHhCCHHHHHHH-hhhh---hh--HHHHHHHHHhHHHHHHHHHhhhH
Q 035092 8 AGVEGTGDVCAVQLITKFGSLENLLQC-VYQV---EE--ERTRKALITFADQAVLSKNLVII 63 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~~fgsle~i~~~-~~~l---~~--~k~~~~L~~~~e~a~ls~~L~~L 63 (73)
-||||||+++|..|+++|+|++++..+ .+++ ++ ++.++.|.+++..-.....+..|
T Consensus 501 LgIpgVG~~~ak~L~~~f~sl~~l~~As~eeL~~i~GIG~~~A~~I~~ff~~~~~~~~i~~L 562 (652)
T TIGR00575 501 LGIRHVGEVTAKNLAKHFGTLDKLKAASLEELLSVEGVGPKVAESIVNFFHDPNNRQLIKKL 562 (652)
T ss_pred ccCCCcCHHHHHHHHHHhCCHHHHHhCCHHHHhcCCCcCHHHHHHHHHHHhhhhHHHHHHHH
Confidence 489999999999999999999999853 3444 32 68889998877665444433333
No 31
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=97.76 E-value=8.7e-05 Score=60.08 Aligned_cols=57 Identities=16% Similarity=0.282 Sum_probs=42.9
Q ss_pred CCCCcccHHHHHHHHHHhCCHHHHHHH-hhhh---h--hHHHHHHHHHhHHHHHHHHHhhhHh
Q 035092 8 AGVEGTGDVCAVQLITKFGSLENLLQC-VYQV---E--EERTRKALITFADQAVLSKNLVIII 64 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~~fgsle~i~~~-~~~l---~--~~k~~~~L~~~~e~a~ls~~L~~L~ 64 (73)
-||||||+++|..|+++|+|++++..+ .+++ + +++.++.|.+++........+..|.
T Consensus 531 LgIpgIG~~~ak~L~~~F~si~~L~~As~eeL~~i~GIG~k~A~sI~~ff~~~~n~~~i~~L~ 593 (689)
T PRK14351 531 LGIPEVGPTTARNLAREFGTFEAIMDADEEALRAVDDVGPTVAEEIREFFDSERNRAVIDDLL 593 (689)
T ss_pred cCCCCcCHHHHHHHHHHhCCHHHHHhCCHHHHhccCCcCHHHHHHHHHHHhhhHHHHHHHHHH
Confidence 489999999999999999999999853 3444 2 3688889988876655444444443
No 32
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=97.66 E-value=0.00014 Score=58.60 Aligned_cols=55 Identities=24% Similarity=0.324 Sum_probs=41.6
Q ss_pred CCCcccHHHHHHHHHHhCCHHHHHHH-hhhh---h--hHHHHHHHHHhHHHHHHHHHhhhH
Q 035092 9 GVEGTGDVCAVQLITKFGSLENLLQC-VYQV---E--EERTRKALITFADQAVLSKNLVII 63 (73)
Q Consensus 9 gVpGIG~KtA~~LL~~fgsle~i~~~-~~~l---~--~~k~~~~L~~~~e~a~ls~~L~~L 63 (73)
||||||+++|..|+++|+|++++..+ .+++ + +++.++.|.+++..-.....+..|
T Consensus 515 gi~~IG~~~ak~L~~~f~sl~~l~~As~eeL~~i~GIG~~~A~sI~~ff~~~~~~~~i~~L 575 (665)
T PRK07956 515 GIRHVGEKAAKALARHFGSLEALRAASEEELAAVEGVGEVVAQSIVEFFAVEENRELIDEL 575 (665)
T ss_pred hccCcCHHHHHHHHHHcCCHHHHHhCCHHHHhccCCcCHHHHHHHHHHHhhhhHHHHHHHH
Confidence 89999999999999999999999853 3443 3 368899999988665444433333
No 33
>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=97.34 E-value=0.00038 Score=48.38 Aligned_cols=42 Identities=19% Similarity=0.346 Sum_probs=30.8
Q ss_pred ccCCCCcccHHHHHHHHHHhCCHHHHHHHhh--------hhhh--HHHHHHHH
Q 035092 6 INAGVEGTGDVCAVQLITKFGSLENLLQCVY--------QVEE--ERTRKALI 48 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~fgsle~i~~~~~--------~l~~--~k~~~~L~ 48 (73)
.+-+|||||||+|..+|..+ +++++.+++. ++++ +|.+++|.
T Consensus 73 ~L~~V~GIGpK~Al~iL~~~-~~~el~~aI~~~d~~~L~~ipGiGkKtAerIi 124 (191)
T TIGR00084 73 ELIKVNGVGPKLALAILSNM-SPEEFVYAIETEEVKALVKIPGVGKKTAERLL 124 (191)
T ss_pred HHhCCCCCCHHHHHHHHhcC-CHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHH
Confidence 34689999999999999986 5777765543 3444 67777765
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=97.19 E-value=0.0003 Score=36.05 Aligned_cols=17 Identities=18% Similarity=0.262 Sum_probs=13.6
Q ss_pred cCCCCcccHHHHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLIT 23 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~ 23 (73)
+..+||||||+|..++.
T Consensus 13 L~~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 13 LMKLPGIGPKTANAILS 29 (30)
T ss_dssp HHTSTT-SHHHHHHHHH
T ss_pred HHhCCCcCHHHHHHHHh
Confidence 34799999999999875
No 35
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=97.16 E-value=0.001 Score=54.09 Aligned_cols=56 Identities=23% Similarity=0.351 Sum_probs=42.6
Q ss_pred CCCCcccHHHHHHHHHHhCCHHHHHHH-hhhh---h--hHHHHHHHHHhHHHHHHHHHhhhH
Q 035092 8 AGVEGTGDVCAVQLITKFGSLENLLQC-VYQV---E--EERTRKALITFADQAVLSKNLVII 63 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~~fgsle~i~~~-~~~l---~--~~k~~~~L~~~~e~a~ls~~L~~L 63 (73)
-|||+||+++|+.|.++|+|+++++.+ .+++ + |+.+++.|.++++....-.-+..|
T Consensus 514 LGIr~VG~~~Ak~La~~f~sl~~l~~a~~e~l~~i~giG~~vA~si~~ff~~~~~~~li~~L 575 (667)
T COG0272 514 LGIRHVGETTAKSLARHFGTLEALLAASEEELASIPGIGEVVARSIIEFFANEENRELIDEL 575 (667)
T ss_pred cCCchhhHHHHHHHHHHhhhHHHHHhcCHHHHhhccchhHHHHHHHHHHHcCHHHHHHHHHH
Confidence 599999999999999999999999854 4444 3 378899999877765544333333
No 36
>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=97.13 E-value=0.00042 Score=58.50 Aligned_cols=27 Identities=33% Similarity=0.628 Sum_probs=23.7
Q ss_pred ccCCCCcccHHHHHHHHHHhC--CHHHHH
Q 035092 6 INAGVEGTGDVCAVQLITKFG--SLENLL 32 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~fg--sle~i~ 32 (73)
+.+||||||||+|.+||++|+ +++++.
T Consensus 867 Y~~GI~GIGpktAl~li~~~~~~~le~L~ 895 (1034)
T TIGR00600 867 YTEGIPTVGPVSAMEILNEFPGDGLEPLL 895 (1034)
T ss_pred CCCCCCcccHHHHHHHHHHcCCCCHHHHH
Confidence 469999999999999999999 467665
No 37
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=97.11 E-value=0.0011 Score=48.53 Aligned_cols=45 Identities=27% Similarity=0.490 Sum_probs=33.9
Q ss_pred cCCCCcccHHHHHHHHHHhCCHHHHHHH-hhhh---h--hHHHHHHHHHhH
Q 035092 7 NAGVEGTGDVCAVQLITKFGSLENLLQC-VYQV---E--EERTRKALITFA 51 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fgsle~i~~~-~~~l---~--~~k~~~~L~~~~ 51 (73)
+..+||||++.|..||++|||+++++.+ .+++ . +++.+..|....
T Consensus 184 l~s~pgig~~~a~~ll~~fgS~~~~~tas~~eL~~v~gig~k~A~~I~~~~ 234 (254)
T COG1948 184 LESIPGIGPKLAERLLKKFGSVEDVLTASEEELMKVKGIGEKKAREIYRFL 234 (254)
T ss_pred HHcCCCccHHHHHHHHHHhcCHHHHhhcCHHHHHHhcCccHHHHHHHHHHH
Confidence 4578899999999999999999999964 4554 2 245566665543
No 38
>PRK13766 Hef nuclease; Provisional
Probab=97.07 E-value=0.0013 Score=52.53 Aligned_cols=46 Identities=28% Similarity=0.410 Sum_probs=35.3
Q ss_pred cCCCCcccHHHHHHHHHHhCCHHHHHHH-hh---hhhh--HHHHHHHHHhHH
Q 035092 7 NAGVEGTGDVCAVQLITKFGSLENLLQC-VY---QVEE--ERTRKALITFAD 52 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fgsle~i~~~-~~---~l~~--~k~~~~L~~~~e 52 (73)
+.++||||+++|.+|+++|||+++++.+ .+ ++++ ++.++.+.+..+
T Consensus 717 L~~ipgig~~~a~~Ll~~fgs~~~i~~as~~~L~~i~Gig~~~a~~i~~~~~ 768 (773)
T PRK13766 717 VESLPDVGPVLARNLLEHFGSVEAVMTASEEELMEVEGIGEKTAKRIREVVT 768 (773)
T ss_pred HhcCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHh
Confidence 5789999999999999999999999853 33 3322 566777766544
No 39
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=96.97 E-value=0.0013 Score=54.26 Aligned_cols=46 Identities=20% Similarity=0.151 Sum_probs=35.9
Q ss_pred cCCCCcccHHHHHHHHHHhCCHHHHHHH-hhhh---hh-HHHHHHHHHhHH
Q 035092 7 NAGVEGTGDVCAVQLITKFGSLENLLQC-VYQV---EE-ERTRKALITFAD 52 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fgsle~i~~~-~~~l---~~-~k~~~~L~~~~e 52 (73)
+-.+||||++.|..||.+|||++++..+ .+++ -| ++.+++|.+...
T Consensus 759 L~~lPgI~~~~a~~ll~~f~si~~l~~as~eeL~~~iG~~~~A~~i~~fl~ 809 (814)
T TIGR00596 759 LLKLPGVTKKNYRNLRKKVKSIRELAKLSQNELNELIGDEEAAKRLYDFLR 809 (814)
T ss_pred HHHCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHHHHhCCHHHHHHHHHHhc
Confidence 4589999999999999999999999864 4555 33 566777766543
No 40
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.89 E-value=0.002 Score=45.22 Aligned_cols=42 Identities=17% Similarity=0.331 Sum_probs=30.4
Q ss_pred cCCCCcccHHHHHHHHHHhCCHHHHHHHh--------hhhhh--HHHHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITKFGSLENLLQCV--------YQVEE--ERTRKALIT 49 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fgsle~i~~~~--------~~l~~--~k~~~~L~~ 49 (73)
+-+|.|||||+|..+|+.+ +++++.+++ ..+++ +|.+++|.-
T Consensus 76 Li~V~GIGpK~Al~iLs~~-~~~~l~~aI~~~D~~~L~~ipGIGkKtAerIil 127 (203)
T PRK14602 76 LISISKVGAKTALAILSQF-RPDDLRRLVAEEDVAALTRVSGIGKKTAQHIFL 127 (203)
T ss_pred HhCCCCcCHHHHHHHHhhC-CHHHHHHHHHhCCHHHHhcCCCcCHHHHHHHHH
Confidence 4689999999999999996 677776543 22343 677776654
No 41
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=96.86 E-value=0.0032 Score=47.94 Aligned_cols=50 Identities=22% Similarity=0.316 Sum_probs=37.0
Q ss_pred ccccCCCCcccHHHHHHHHHHhCCHHHHHHH-hhhh---hh--HHHHHHHHHhHHH
Q 035092 4 YFINAGVEGTGDVCAVQLITKFGSLENLLQC-VYQV---EE--ERTRKALITFADQ 53 (73)
Q Consensus 4 ~~~I~gVpGIG~KtA~~LL~~fgsle~i~~~-~~~l---~~--~k~~~~L~~~~e~ 53 (73)
|-.+..||+||+..|..|+++|||+.+++++ .+++ ++ ++.++.+.+....
T Consensus 286 yRiLs~IPrl~k~iAk~Ll~~FGSL~~Il~As~eeL~~VeGIGe~rA~~I~e~l~R 341 (352)
T PRK13482 286 YRLLSKIPRLPSAVIENLVEHFGSLQGLLAASIEDLDEVEGIGEVRARAIREGLSR 341 (352)
T ss_pred HHHHhcCCCCCHHHHHHHHHHcCCHHHHHcCCHHHHhhCCCcCHHHHHHHHHHHHH
Confidence 4455689999999999999999999999964 4454 33 5556666654443
No 42
>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=96.85 E-value=0.0017 Score=42.10 Aligned_cols=40 Identities=23% Similarity=0.312 Sum_probs=26.9
Q ss_pred cCCCCcccHHHHHHHHHHh------CCHHHHHHHhhhhhh--HHHHHHHHHh
Q 035092 7 NAGVEGTGDVCAVQLITKF------GSLENLLQCVYQVEE--ERTRKALITF 50 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f------gsle~i~~~~~~l~~--~k~~~~L~~~ 50 (73)
+..+||||+++|.++++.+ .|++++ .++++ ++..++|..+
T Consensus 70 L~~lpGIG~~~A~~Ii~~R~~~g~f~s~eeL----~~V~GIg~k~~~~i~~~ 117 (120)
T TIGR01259 70 LQALPGIGPAKAKAIIEYREENGAFKSVDDL----TKVSGIGEKSLEKLKDY 117 (120)
T ss_pred HhcCCCCCHHHHHHHHHHHHhcCCcCCHHHH----HcCCCCCHHHHHHHHhc
Confidence 4579999999999999996 455554 23322 3555555543
No 43
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=96.77 E-value=0.0019 Score=43.40 Aligned_cols=45 Identities=20% Similarity=0.273 Sum_probs=32.8
Q ss_pred CCCCcccHHHHHHHHH--HhCCHHHHHHHhhhhhhHHHHHHHHHhHHHH
Q 035092 8 AGVEGTGDVCAVQLIT--KFGSLENLLQCVYQVEEERTRKALITFADQA 54 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~--~fgsle~i~~~~~~l~~~k~~~~L~~~~e~a 54 (73)
..+|||||+.|.++++ -|.|+|++++ +..+.+ +..+.++++++..
T Consensus 64 ~~lpGigP~~A~~IV~nGpf~sveDL~~-V~GIge-kqk~~l~k~~~~f 110 (132)
T PRK02515 64 RQFPGMYPTLAGKIVKNAPYDSVEDVLN-LPGLSE-RQKELLEANLDNF 110 (132)
T ss_pred HHCCCCCHHHHHHHHHCCCCCCHHHHHc-CCCCCH-HHHHHHHHhhcce
Confidence 4689999999999998 4889988854 344433 5666777776653
No 44
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.75 E-value=0.0024 Score=44.72 Aligned_cols=43 Identities=16% Similarity=0.271 Sum_probs=30.7
Q ss_pred ccCCCCcccHHHHHHHHHHhCCHHHHHHHh--------hhhhh--HHHHHHHHH
Q 035092 6 INAGVEGTGDVCAVQLITKFGSLENLLQCV--------YQVEE--ERTRKALIT 49 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~fgsle~i~~~~--------~~l~~--~k~~~~L~~ 49 (73)
.+-+|.|||||+|..+|+.+ +++++.+++ ..+++ +|.+++|.-
T Consensus 73 ~L~~V~GIGpK~AL~iLs~~-~~~~l~~aI~~~D~~~L~kvpGIGkKtAerIil 125 (197)
T PRK14603 73 LLLGVSGVGPKLALALLSAL-PPALLARALLEGDARLLTSASGVGKKLAERIAL 125 (197)
T ss_pred HHhCcCCcCHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHH
Confidence 34589999999999999985 777777543 22343 666666653
No 45
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.75 E-value=0.0027 Score=44.22 Aligned_cols=26 Identities=19% Similarity=0.316 Sum_probs=21.4
Q ss_pred cCCCCcccHHHHHHHHHHhCCHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITKFGSLENLLQ 33 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fgsle~i~~ 33 (73)
+-+|+|||||+|..+|+.|+ .+.+.+
T Consensus 75 Li~V~GIGpK~Al~ILs~~~-~~~l~~ 100 (194)
T PRK14605 75 LIDVSGIGPKLGLAMLSAMN-AEALAS 100 (194)
T ss_pred HhCCCCCCHHHHHHHHHhCC-HHHHHH
Confidence 45899999999999999985 666543
No 46
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=96.73 E-value=0.0011 Score=32.35 Aligned_cols=19 Identities=21% Similarity=0.260 Sum_probs=16.2
Q ss_pred cCCCCcccHHHHHHHHHHh
Q 035092 7 NAGVEGTGDVCAVQLITKF 25 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f 25 (73)
+..|||||+|+|..+++..
T Consensus 3 L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 3 LLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred hhhCCCCCHHHHHHHHHhc
Confidence 4689999999999999743
No 47
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.71 E-value=0.0027 Score=44.75 Aligned_cols=42 Identities=14% Similarity=0.351 Sum_probs=30.3
Q ss_pred cCCCCcccHHHHHHHHHHhCCHHHHHHHh--------hhhhh--HHHHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITKFGSLENLLQCV--------YQVEE--ERTRKALIT 49 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fgsle~i~~~~--------~~l~~--~k~~~~L~~ 49 (73)
+-+|.|||||+|..+|+.+ +++++..++ ..++| +|.+++|.-
T Consensus 74 LisVsGIGPK~ALaILs~~-~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIIl 125 (196)
T PRK13901 74 LIGVDGIGPRAALRVLSGI-KYNEFRDAIDREDIELISKVKGIGNKMAGKIFL 125 (196)
T ss_pred HhCcCCcCHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHH
Confidence 4589999999999999996 777777543 22343 666766653
No 48
>PRK00254 ski2-like helicase; Provisional
Probab=96.66 E-value=0.0027 Score=50.86 Aligned_cols=46 Identities=15% Similarity=0.206 Sum_probs=36.8
Q ss_pred cCCCCcccHHHHHHHHHH-hCCHHHHHHH-hhhh---h--hHHHHHHHHHhHH
Q 035092 7 NAGVEGTGDVCAVQLITK-FGSLENLLQC-VYQV---E--EERTRKALITFAD 52 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~-fgsle~i~~~-~~~l---~--~~k~~~~L~~~~e 52 (73)
+..|||||+++|.+|++. |+|+++|.++ .+++ + +++.++++.++..
T Consensus 647 L~~ipgig~~~~~~l~~~g~~s~~~i~~a~~~el~~~~gi~~~~a~~i~~~~~ 699 (720)
T PRK00254 647 LMRLPMIGRKRARALYNAGFRSIEDIVNAKPSELLKVEGIGAKIVEGIFKHLG 699 (720)
T ss_pred hhcCCCCCHHHHHHHHHccCCCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHhc
Confidence 458999999999999999 9999999864 4444 2 2678888877644
No 49
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.66 E-value=0.0031 Score=43.85 Aligned_cols=42 Identities=17% Similarity=0.328 Sum_probs=30.0
Q ss_pred cCCCCcccHHHHHHHHHHhCCHHHHHHHh--------hhhhh--HHHHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITKFGSLENLLQCV--------YQVEE--ERTRKALIT 49 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fgsle~i~~~~--------~~l~~--~k~~~~L~~ 49 (73)
+-+|.|||||+|..+|+.+ +++++..++ ..+++ +|.+++|.-
T Consensus 75 Li~VsGIGpK~Al~ILs~~-~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIil 126 (183)
T PRK14601 75 LLKVNGIGANTAMAVCSSL-DVNSFYKALSLGDESVLKKVPGIGPKSAKRIIA 126 (183)
T ss_pred HhccCCccHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHH
Confidence 3579999999999999996 777877543 22343 666666553
No 50
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.65 E-value=0.0041 Score=43.49 Aligned_cols=43 Identities=21% Similarity=0.375 Sum_probs=31.0
Q ss_pred ccCCCCcccHHHHHHHHHHhCCHHHHHHHh--------hhhhh--HHHHHHHHH
Q 035092 6 INAGVEGTGDVCAVQLITKFGSLENLLQCV--------YQVEE--ERTRKALIT 49 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~fgsle~i~~~~--------~~l~~--~k~~~~L~~ 49 (73)
.+-+|.|||||+|..+|+.+ +++++..++ ..++| +|.+++|.-
T Consensus 74 ~Li~V~GIGpK~Al~iLs~~-~~~el~~aI~~~D~~~L~kvpGIGkKtAerIil 126 (195)
T PRK14604 74 LLIGVSGVGPKAALNLLSSG-TPDELQLAIAGGDVARLARVPGIGKKTAERIVL 126 (195)
T ss_pred HHhCcCCcCHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHH
Confidence 34589999999999999985 778877543 22343 677776654
No 51
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.64 E-value=0.0034 Score=43.70 Aligned_cols=42 Identities=24% Similarity=0.377 Sum_probs=29.9
Q ss_pred cCCCCcccHHHHHHHHHHhCCHHHHHHHhh-------hhhh--HHHHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITKFGSLENLLQCVY-------QVEE--ERTRKALIT 49 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fgsle~i~~~~~-------~l~~--~k~~~~L~~ 49 (73)
.-+|.|||||+|..+|+.+ +++++..++. .+++ +|.+++|.-
T Consensus 75 LisV~GIGpK~Al~iLs~~-~~~~l~~aI~~~D~~~L~vpGIGkKtAerIil 125 (186)
T PRK14600 75 LVKVSGVNYKTAMSILSKL-TPEQLFSAIVNEDKAALKVNGIGEKLINRIIT 125 (186)
T ss_pred HhCcCCcCHHHHHHHHccC-CHHHHHHHHHcCCHhheECCCCcHHHHHHHHH
Confidence 4589999999999999996 6777764431 3343 666666653
No 52
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=96.64 E-value=0.0023 Score=46.82 Aligned_cols=49 Identities=29% Similarity=0.360 Sum_probs=39.0
Q ss_pred CCCCcccHHHHHHHHHHhCCHHHHHHH-h---hhhh--hHHHHHHHHHhHHHHHH
Q 035092 8 AGVEGTGDVCAVQLITKFGSLENLLQC-V---YQVE--EERTRKALITFADQAVL 56 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~~fgsle~i~~~-~---~~l~--~~k~~~~L~~~~e~a~l 56 (73)
-.||||++.-|..||.+|||+++|..+ . ++++ |+..+++|.++..+-++
T Consensus 198 t~i~~VnKtda~~LL~~FgsLq~~~~AS~~ele~~~G~G~~kak~l~~~l~~pf~ 252 (254)
T KOG2841|consen 198 TTIPGVNKTDAQLLLQKFGSLQQISNASEGELEQCPGLGPAKAKRLHKFLHQPFL 252 (254)
T ss_pred HhCCCCCcccHHHHHHhcccHHHHHhcCHhHHHhCcCcCHHHHHHHHHHHhcccc
Confidence 358999999999999999999999853 3 4455 47788888887766544
No 53
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=96.56 E-value=0.0039 Score=43.41 Aligned_cols=42 Identities=17% Similarity=0.282 Sum_probs=30.1
Q ss_pred cCCCCcccHHHHHHHHHHhCCHHHHHHHhh--------hhhh--HHHHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITKFGSLENLLQCVY--------QVEE--ERTRKALIT 49 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fgsle~i~~~~~--------~l~~--~k~~~~L~~ 49 (73)
+-+|.|||||+|..+|..+ +++++.+++. .+++ +|.+++|.-
T Consensus 75 Li~V~GIGpK~AL~iLs~~-~~~el~~aI~~~D~~~L~~vpGIGkKtAerIil 126 (188)
T PRK14606 75 LTKVSRLGPKTALKIISNE-DAETLVTMIASQDVEGLSKLPGISKKTAERIVM 126 (188)
T ss_pred HhccCCccHHHHHHHHcCC-CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHH
Confidence 3589999999999999986 7778775532 2333 666666653
No 54
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=96.52 E-value=0.0074 Score=48.99 Aligned_cols=46 Identities=15% Similarity=0.366 Sum_probs=36.0
Q ss_pred CCCCcccHHHHHHHH-HHhCCHHHHHH-------H---hhhhh--hHHHHHHHHHhHHH
Q 035092 8 AGVEGTGDVCAVQLI-TKFGSLENLLQ-------C---VYQVE--EERTRKALITFADQ 53 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL-~~fgsle~i~~-------~---~~~l~--~~k~~~~L~~~~e~ 53 (73)
-|||+||+++|..|. ++|++++++.+ + +.+++ |+.+++.|.+++..
T Consensus 505 LGI~~vG~~~ak~La~~~f~~~~~l~~~~~~~~~~~e~l~~i~giG~~~a~si~~ff~~ 563 (669)
T PRK14350 505 MGIKDLGENTILLLINNNLNSFDKISTLCQDREFALSKLLKIKGIGEKIALNIIEAFND 563 (669)
T ss_pred cCCCchhHHHHHHHHHHhhCCHHHHHhhhhccCCCHHHHhhCCCccHHHHHHHHHHHcC
Confidence 489999999999999 89999999875 2 23344 36888888886643
No 55
>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=96.51 E-value=0.0041 Score=36.15 Aligned_cols=39 Identities=18% Similarity=0.278 Sum_probs=25.2
Q ss_pred CCcccHHHHHHHHHH---hCC---HHHHHHHhhhhhhHHHHHHHHHh
Q 035092 10 VEGTGDVCAVQLITK---FGS---LENLLQCVYQVEEERTRKALITF 50 (73)
Q Consensus 10 VpGIG~KtA~~LL~~---fgs---le~i~~~~~~l~~~k~~~~L~~~ 50 (73)
+||||+++|.+|++. +|+ ++++. .+..+. .+.+++|..+
T Consensus 22 ipgig~~~a~~Il~~R~~~g~~~s~~dL~-~v~gi~-~~~~~~i~~~ 66 (69)
T TIGR00426 22 MNGVGLKKAEAIVSYREEYGPFKTVEDLK-QVPGIG-NSLVEKNLAV 66 (69)
T ss_pred CCCCCHHHHHHHHHHHHHcCCcCCHHHHH-cCCCCC-HHHHHHHHhh
Confidence 899999999999999 564 44442 122333 3556666543
No 56
>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=96.06 E-value=0.0056 Score=37.18 Aligned_cols=27 Identities=19% Similarity=0.498 Sum_probs=23.9
Q ss_pred ccCCCCcccHHHHHHHHHHhCCHHHHH
Q 035092 6 INAGVEGTGDVCAVQLITKFGSLENLL 32 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~fgsle~i~ 32 (73)
.+..|||||+.+|..|+.+.++++++-
T Consensus 3 ~l~sipGig~~~a~~llaeigd~~rF~ 29 (87)
T PF02371_consen 3 LLTSIPGIGPITAATLLAEIGDISRFK 29 (87)
T ss_pred hhcCCCCccHHHHHHHHHHHcCchhcc
Confidence 456899999999999999999997764
No 57
>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=96.00 E-value=0.022 Score=46.26 Aligned_cols=46 Identities=15% Similarity=0.276 Sum_probs=28.8
Q ss_pred cCCCCcccHHHHHHHHHHhCC--HHHHHHHhh---hhhh--HHHHHHHHHhHH
Q 035092 7 NAGVEGTGDVCAVQLITKFGS--LENLLQCVY---QVEE--ERTRKALITFAD 52 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fgs--le~i~~~~~---~l~~--~k~~~~L~~~~e 52 (73)
-+.+||||||+|.+|.+.||. ++-|.++.+ ++++ ++.++.+.+..+
T Consensus 86 s~~~~GIG~~~A~~iv~~fg~~~~~~i~~~~~~L~~v~gi~~~~~~~i~~~~~ 138 (720)
T TIGR01448 86 SRSIKGVGKKLAQRIVKTFGEAAFDVLDDDPEKLLEVPGISKANLEKFVSQWS 138 (720)
T ss_pred cCCCCCcCHHHHHHHHHHhCHhHHHHHHhCHHHHhcCCCCCHHHHHHHHHHHH
Confidence 356999999999999999973 333333333 3333 344555555443
No 58
>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=95.92 E-value=0.005 Score=31.66 Aligned_cols=16 Identities=25% Similarity=0.123 Sum_probs=12.6
Q ss_pred ccCCCCcccHHHHHHH
Q 035092 6 INAGVEGTGDVCAVQL 21 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~L 21 (73)
.|..++|||+||+.+|
T Consensus 12 pi~~~~GIG~kt~~kL 27 (32)
T PF11798_consen 12 PIRKFWGIGKKTAKKL 27 (32)
T ss_dssp BGGGSTTS-HHHHHHH
T ss_pred CHHhhCCccHHHHHHH
Confidence 3569999999999985
No 59
>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=95.88 E-value=0.028 Score=31.89 Aligned_cols=33 Identities=24% Similarity=0.311 Sum_probs=22.0
Q ss_pred CCCCcccHHHHHHHHHH-hCCHHHHHHHhhhhhh
Q 035092 8 AGVEGTGDVCAVQLITK-FGSLENLLQCVYQVEE 40 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~~-fgsle~i~~~~~~l~~ 40 (73)
-+|-||||+||.++.+. |.|++++...-..+..
T Consensus 5 ~~I~GVG~~tA~~w~~~G~rtl~Dl~~~~~~Lt~ 38 (52)
T PF10391_consen 5 TGIWGVGPKTARKWYAKGIRTLEDLRKSKSKLTW 38 (52)
T ss_dssp HTSTT--HHHHHHHHHTT--SHHHHHHGGCGS-H
T ss_pred hhcccccHHHHHHHHHhCCCCHHHHhhhhccCCH
Confidence 47899999999999985 6899999764335543
No 60
>KOG2519 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=95.83 E-value=0.0078 Score=47.16 Aligned_cols=28 Identities=32% Similarity=0.576 Sum_probs=26.4
Q ss_pred ccCCCCcccHHHHHHHHHHhCCHHHHHH
Q 035092 6 INAGVEGTGDVCAVQLITKFGSLENLLQ 33 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~fgsle~i~~ 33 (73)
+.++|.||||++|.+|+++|+|+++|++
T Consensus 230 Yc~~I~Gig~~~al~lir~~~~i~~ile 257 (449)
T KOG2519|consen 230 YCPTIRGIGPKKALKLIRQHGDIENILE 257 (449)
T ss_pred ccccccccChHHHHHHHHHhcCHHHHhh
Confidence 4688999999999999999999999997
No 61
>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=95.73 E-value=0.02 Score=42.11 Aligned_cols=29 Identities=28% Similarity=0.314 Sum_probs=23.4
Q ss_pred cCCCCcccHHHHHHHHH-HhCCHHHHHHHh
Q 035092 7 NAGVEGTGDVCAVQLIT-KFGSLENLLQCV 35 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~-~fgsle~i~~~~ 35 (73)
.-+|||||||+|.+|.+ .+.|++++..+.
T Consensus 87 l~~i~GiGpk~a~~l~~lGi~sl~dL~~a~ 116 (307)
T cd00141 87 LLRVPGVGPKTARKLYELGIRTLEDLRKAA 116 (307)
T ss_pred HHcCCCCCHHHHHHHHHcCCCCHHHHHHHh
Confidence 34799999999999993 358899888653
No 62
>PRK08609 hypothetical protein; Provisional
Probab=95.68 E-value=0.024 Score=44.92 Aligned_cols=48 Identities=13% Similarity=0.160 Sum_probs=33.4
Q ss_pred cCCCCcccHHHHHHHHHH--hCCHHHHHHHhh-----hhhh--HHHHHHHHHhHHHH
Q 035092 7 NAGVEGTGDVCAVQLITK--FGSLENLLQCVY-----QVEE--ERTRKALITFADQA 54 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~--fgsle~i~~~~~-----~l~~--~k~~~~L~~~~e~a 54 (73)
.-.|||||||+|.+|-++ ..|++++.++.+ .+++ +|..++|....+..
T Consensus 90 l~~i~GiGpk~a~~l~~~lGi~tl~~L~~a~~~~~~~~~~gfg~k~~~~il~~i~~~ 146 (570)
T PRK08609 90 LLKLPGLGGKKIAKLYKELGVVDKESLKEACENGKVQALAGFGKKTEEKILEAVKEL 146 (570)
T ss_pred HhcCCCCCHHHHHHHHHHhCCCCHHHHHHHHHhCChhhccCcchhHHHHHHHHHHHH
Confidence 347999999999999975 478999986543 3333 45566665555443
No 63
>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=95.64 E-value=0.033 Score=40.09 Aligned_cols=32 Identities=16% Similarity=0.270 Sum_probs=27.1
Q ss_pred cCCCCcccHHHHHHHHHH-hCCHHHHHHH-hhhh
Q 035092 7 NAGVEGTGDVCAVQLITK-FGSLENLLQC-VYQV 38 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~-fgsle~i~~~-~~~l 38 (73)
+..+||||++++.+|.+. |.|++++... .+++
T Consensus 1 l~~i~gig~~~~~~L~~~Gi~ti~dl~~~~~~~L 34 (310)
T TIGR02236 1 LEDLPGVGPATAEKLREAGYDTFEAIAVASPKEL 34 (310)
T ss_pred CcccCCCCHHHHHHHHHcCCCCHHHHHcCCHHHH
Confidence 467999999999999999 9999999853 4444
No 64
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=95.39 E-value=0.027 Score=37.87 Aligned_cols=25 Identities=28% Similarity=0.428 Sum_probs=20.4
Q ss_pred CCCCcccHHHHHHHHHH------hCCHHHHH
Q 035092 8 AGVEGTGDVCAVQLITK------FGSLENLL 32 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~~------fgsle~i~ 32 (73)
..+||||+|+|.++++. |.|++++.
T Consensus 100 ~~lpgIG~~kA~aIi~yRe~~G~f~sv~dL~ 130 (149)
T COG1555 100 QALPGIGPKKAQAIIDYREENGPFKSVDDLA 130 (149)
T ss_pred HHCCCCCHHHHHHHHHHHHHcCCCCcHHHHH
Confidence 46899999999999973 67777763
No 65
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=95.25 E-value=0.014 Score=33.80 Aligned_cols=25 Identities=24% Similarity=0.262 Sum_probs=18.8
Q ss_pred cCCCCcccHHHHHHHHHHhCCHHHH
Q 035092 7 NAGVEGTGDVCAVQLITKFGSLENL 31 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fgsle~i 31 (73)
+..||||||++|..+.+-|.+.++.
T Consensus 37 L~~i~gIG~~~A~si~~ff~~~~n~ 61 (64)
T PF12826_consen 37 LSAIPGIGPKIAQSIYEFFQDPENR 61 (64)
T ss_dssp HCTSTT--HHHHHHHHHHHH-HHHH
T ss_pred HhccCCcCHHHHHHHHHHHCCHHhh
Confidence 4679999999999999999887664
No 66
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=95.04 E-value=0.057 Score=43.27 Aligned_cols=55 Identities=18% Similarity=0.123 Sum_probs=39.3
Q ss_pred CCCCcccHHHHHHHHHHhCCHHHHHHH-hhh---hh--hHHHHHHHHHhHHHHHHHHHhhhHhh
Q 035092 8 AGVEGTGDVCAVQLITKFGSLENLLQC-VYQ---VE--EERTRKALITFADQAVLSKNLVIIIA 65 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~~fgsle~i~~~-~~~---l~--~~k~~~~L~~~~e~a~ls~~L~~L~~ 65 (73)
-|||+||+++|+. .|+|++++.++ .++ +. |+++++.|.+++..-.....+..|..
T Consensus 494 LGI~~vG~~~ak~---~~~~i~~l~~a~~e~l~~i~gIG~~~a~si~~~f~~~~~~~~i~~L~~ 554 (562)
T PRK08097 494 LGIPLPQAALNAL---DDRSWQQLLSRSEQQWQQLPGIGEGRARQLIAFLQHPEVKALADWLAA 554 (562)
T ss_pred cCCccHHHHHHHH---hcCCHHHHHcCCHHHHhcCCCchHHHHHHHHHHHcCHHHHHHHHHHHH
Confidence 4899999988876 99999999743 343 33 37889999998866555444444543
No 67
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=94.89 E-value=0.067 Score=43.42 Aligned_cols=54 Identities=20% Similarity=0.314 Sum_probs=39.1
Q ss_pred ccccc-cCCCCcccHHHHHHHHHHh--CCHHHHHH----Hhhhhhh--HHHHHHHHHhHHHHH
Q 035092 2 HFYFI-NAGVEGTGDVCAVQLITKF--GSLENLLQ----CVYQVEE--ERTRKALITFADQAV 55 (73)
Q Consensus 2 ~~~~~-I~gVpGIG~KtA~~LL~~f--gsle~i~~----~~~~l~~--~k~~~~L~~~~e~a~ 55 (73)
||-|- --+|||+|||++.+|.++- .+++++++ .+..+++ +|.+++|.+..+.++
T Consensus 441 hf~sr~al~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~ll~~Ie~sk 503 (665)
T PRK07956 441 HFVSRNAMDIDGLGEKIIEQLFEKGLIHDPADLFKLTAEDLLGLEGFGEKSAQNLLDAIEKSK 503 (665)
T ss_pred HhhcccccCCCCcCHHHHHHHHHcCCCCCHHHHHhcCHHHHhcCcCcchHHHHHHHHHHHHhh
Confidence 66653 4689999999999999875 58889884 2334443 567778877776554
No 68
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.80 E-value=0.017 Score=40.14 Aligned_cols=20 Identities=25% Similarity=0.366 Sum_probs=16.5
Q ss_pred cCCCCcccHHHHHHHHHHhC
Q 035092 7 NAGVEGTGDVCAVQLITKFG 26 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fg 26 (73)
+-.+||||+|||.+++-+.+
T Consensus 110 L~~vpGIGkKtAeRIilELk 129 (183)
T PRK14601 110 LKKVPGIGPKSAKRIIAELS 129 (183)
T ss_pred HhhCCCCCHHHHHHHHHHHH
Confidence 35799999999999986653
No 69
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.73 E-value=0.017 Score=40.24 Aligned_cols=18 Identities=28% Similarity=0.469 Sum_probs=15.6
Q ss_pred CCCcccHHHHHHHHHHhC
Q 035092 9 GVEGTGDVCAVQLITKFG 26 (73)
Q Consensus 9 gVpGIG~KtA~~LL~~fg 26 (73)
.+||||+|||.+++-+.+
T Consensus 111 ~vpGIGkKtAerIilELk 128 (186)
T PRK14600 111 KVNGIGEKLINRIITELQ 128 (186)
T ss_pred ECCCCcHHHHHHHHHHHH
Confidence 799999999999996653
No 70
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=94.67 E-value=0.095 Score=36.83 Aligned_cols=30 Identities=20% Similarity=0.340 Sum_probs=21.1
Q ss_pred CCCcccHHHHHHHHHH-----hCCHHHHHHHhhhh
Q 035092 9 GVEGTGDVCAVQLITK-----FGSLENLLQCVYQV 38 (73)
Q Consensus 9 gVpGIG~KtA~~LL~~-----fgsle~i~~~~~~l 38 (73)
=+||||.|+..++|.+ |.|.++|-+.+.-+
T Consensus 120 LLPGIGKK~m~~ILeERkkkpFeSFeDi~~Rv~gl 154 (181)
T PF04919_consen 120 LLPGIGKKTMWKILEERKKKPFESFEDIEERVKGL 154 (181)
T ss_dssp GSTT--HHHHHHHHHHHHHS---SHHHHHHHSTT-
T ss_pred hcccccHHHHHHHHHHHccCCCCCHHHHHHHhccC
Confidence 3799999999999975 89999998776544
No 71
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=94.62 E-value=0.057 Score=38.24 Aligned_cols=41 Identities=20% Similarity=0.354 Sum_probs=28.2
Q ss_pred CCCCcccHHHHHHHHHHhCCHHHHHHHhh--h------hhh--HHHHHHHHH
Q 035092 8 AGVEGTGDVCAVQLITKFGSLENLLQCVY--Q------VEE--ERTRKALIT 49 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~~fgsle~i~~~~~--~------l~~--~k~~~~L~~ 49 (73)
-.|.|||||+|..+|+. -+++++..+++ + +++ +|.++++.-
T Consensus 76 isVnGIGpK~ALaiLs~-~~~~~l~~aI~~~d~~~L~k~PGIGkKtAerivl 126 (201)
T COG0632 76 ISVNGIGPKLALAILSN-LDPEELAQAIANEDVKALSKIPGIGKKTAERIVL 126 (201)
T ss_pred HccCCccHHHHHHHHcC-CCHHHHHHHHHhcChHhhhcCCCCCHHHHHHHHH
Confidence 36899999999999998 56777765432 2 233 566666544
No 72
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=94.61 E-value=0.085 Score=37.58 Aligned_cols=42 Identities=14% Similarity=0.268 Sum_probs=31.1
Q ss_pred CCCCcccHHHHHHHHHH-----hCCHHHHHHHhhhh--hhHHHHHHHHH
Q 035092 8 AGVEGTGDVCAVQLITK-----FGSLENLLQCVYQV--EEERTRKALIT 49 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~~-----fgsle~i~~~~~~l--~~~k~~~~L~~ 49 (73)
.=.||||.|++..+|.+ |.|.++|.+.+..+ +.+-+++.+.+
T Consensus 133 ELLpGiGkK~m~~ILeERkkkpFeSFeDi~~Rv~~~~~p~~~I~~RIl~ 181 (202)
T COG1491 133 ELLPGIGKKTMWAILEERKKKPFESFEDIKERVKGLHDPAKMIAERILD 181 (202)
T ss_pred HhcccccHHHHHHHHHHHhcCCCcCHHHHHHHhcCCCCHHHHHHHHHHH
Confidence 34799999999999986 89999998877666 33344444444
No 73
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=94.59 E-value=0.056 Score=43.40 Aligned_cols=29 Identities=17% Similarity=0.367 Sum_probs=26.4
Q ss_pred ccCCCCcccHHHHHHHHHHhCCHHHHHHH
Q 035092 6 INAGVEGTGDVCAVQLITKFGSLENLLQC 34 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~fgsle~i~~~ 34 (73)
+.+||||||=+||.+++++|.+++.++..
T Consensus 226 Yl~slpGvGl~tA~k~l~k~~~~d~vi~~ 254 (556)
T KOG2518|consen 226 YLSSLPGVGLATAHKLLSKYNTPDRVIIS 254 (556)
T ss_pred ccccCccccHHHHHHHHHhcCcHHHHHHH
Confidence 56899999999999999999999999753
No 74
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.53 E-value=0.019 Score=40.48 Aligned_cols=20 Identities=25% Similarity=0.356 Sum_probs=16.5
Q ss_pred cCCCCcccHHHHHHHHHHhC
Q 035092 7 NAGVEGTGDVCAVQLITKFG 26 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fg 26 (73)
+..+||||+|||.+++-+.+
T Consensus 109 L~~vpGIGkKtAeRIIlELk 128 (196)
T PRK13901 109 ISKVKGIGNKMAGKIFLKLR 128 (196)
T ss_pred HhhCCCCCHHHHHHHHHHHH
Confidence 45799999999999986653
No 75
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.50 E-value=0.022 Score=39.81 Aligned_cols=21 Identities=24% Similarity=0.340 Sum_probs=17.5
Q ss_pred cCCCCcccHHHHHHHHHHhCC
Q 035092 7 NAGVEGTGDVCAVQLITKFGS 27 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fgs 27 (73)
+-.+||||+|||.+++-+.++
T Consensus 110 L~kvpGIGkKtAerIilELk~ 130 (195)
T PRK14604 110 LARVPGIGKKTAERIVLELKG 130 (195)
T ss_pred HhhCCCCCHHHHHHHHHHHHH
Confidence 457999999999999877644
No 76
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.44 E-value=0.024 Score=39.48 Aligned_cols=20 Identities=10% Similarity=0.209 Sum_probs=16.4
Q ss_pred cCCCCcccHHHHHHHHHHhC
Q 035092 7 NAGVEGTGDVCAVQLITKFG 26 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fg 26 (73)
+-.+||||+|||.+|+-+.+
T Consensus 110 L~~vpGIGkKtAerIilELk 129 (188)
T PRK14606 110 LSKLPGISKKTAERIVMELK 129 (188)
T ss_pred HhhCCCCCHHHHHHHHHHHH
Confidence 35799999999999986653
No 77
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.44 E-value=0.022 Score=39.94 Aligned_cols=20 Identities=20% Similarity=0.298 Sum_probs=16.6
Q ss_pred cCCCCcccHHHHHHHHHHhC
Q 035092 7 NAGVEGTGDVCAVQLITKFG 26 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fg 26 (73)
+-.+||||+|||.+++-+.+
T Consensus 111 L~~ipGIGkKtAerIilELk 130 (203)
T PRK14602 111 LTRVSGIGKKTAQHIFLELK 130 (203)
T ss_pred HhcCCCcCHHHHHHHHHHHH
Confidence 45799999999999986653
No 78
>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=94.34 E-value=0.042 Score=31.12 Aligned_cols=19 Identities=26% Similarity=0.357 Sum_probs=16.3
Q ss_pred cCCCCcccHHHHHHHHHHh
Q 035092 7 NAGVEGTGDVCAVQLITKF 25 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f 25 (73)
+..|||||+++|.+|+..+
T Consensus 40 L~~i~Gig~~~a~~i~~~~ 58 (60)
T PF14520_consen 40 LAEIPGIGEKTAEKIIEAA 58 (60)
T ss_dssp HHTSTTSSHHHHHHHHHHH
T ss_pred HhcCCCCCHHHHHHHHHHH
Confidence 3478999999999999875
No 79
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.29 E-value=0.026 Score=39.52 Aligned_cols=21 Identities=14% Similarity=0.224 Sum_probs=17.2
Q ss_pred cCCCCcccHHHHHHHHHHhCC
Q 035092 7 NAGVEGTGDVCAVQLITKFGS 27 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fgs 27 (73)
+-.+||||+|||.+++-+.++
T Consensus 109 L~kvpGIGkKtAerIilELkd 129 (197)
T PRK14603 109 LTSASGVGKKLAERIALELKG 129 (197)
T ss_pred HhhCCCCCHHHHHHHHHHHHH
Confidence 457999999999999966543
No 80
>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=94.28 E-value=0.11 Score=42.11 Aligned_cols=54 Identities=26% Similarity=0.379 Sum_probs=39.3
Q ss_pred ccccc-cCCCCcccHHHHHHHHHHh--CCHHHHHH----Hhhhhhh--HHHHHHHHHhHHHHH
Q 035092 2 HFYFI-NAGVEGTGDVCAVQLITKF--GSLENLLQ----CVYQVEE--ERTRKALITFADQAV 55 (73)
Q Consensus 2 ~~~~~-I~gVpGIG~KtA~~LL~~f--gsle~i~~----~~~~l~~--~k~~~~L~~~~e~a~ 55 (73)
||.|- --+|+|+|||++.+|.++- .++.++++ .+.++++ ++.+++|.+..+..+
T Consensus 428 hf~sr~al~I~GLG~k~i~~L~~~g~I~~~~Dl~~L~~~~L~~L~GfG~Ksa~nIl~~Ie~sk 490 (652)
T TIGR00575 428 HFASRNAMDIEGLGDKVIEQLFEKKLVRSVADLYALKKEDLLELEGFGEKSAQNLLNAIEKSK 490 (652)
T ss_pred HhhcCCccCCCCcCHHHHHHHHHcCCcCCHHHHHhcCHHHHhhccCccHHHHHHHHHHHHHhc
Confidence 66654 4689999999999999875 58888884 2344543 677778877777554
No 81
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=93.92 E-value=0.056 Score=40.23 Aligned_cols=27 Identities=26% Similarity=0.217 Sum_probs=22.8
Q ss_pred cCCCCcccHHHHHHHHHHh--CCHHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITKF--GSLENLLQC 34 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f--gsle~i~~~ 34 (73)
+-.|||||||+|..|.+ . .|++++.++
T Consensus 91 l~~i~GiGpk~a~~l~~-lGi~tl~eL~~a 119 (334)
T smart00483 91 FTNVFGVGPKTAAKWYR-KGIRTLEELKKN 119 (334)
T ss_pred HHccCCcCHHHHHHHHH-hCCCCHHHHHhc
Confidence 45799999999999998 5 688888764
No 82
>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=93.15 E-value=0.06 Score=37.42 Aligned_cols=19 Identities=21% Similarity=0.366 Sum_probs=15.8
Q ss_pred cCCCCcccHHHHHHHHHHh
Q 035092 7 NAGVEGTGDVCAVQLITKF 25 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f 25 (73)
+-.|||||+|||.+++-+.
T Consensus 109 L~~ipGiGkKtAerIileL 127 (191)
T TIGR00084 109 LVKIPGVGKKTAERLLLEL 127 (191)
T ss_pred HHhCCCCCHHHHHHHHHHH
Confidence 4579999999999998543
No 83
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=92.97 E-value=0.074 Score=37.62 Aligned_cols=52 Identities=19% Similarity=0.056 Sum_probs=31.3
Q ss_pred ccCCCCcccHHHHHHHHHHhCCHHHHHHHhhhhhhHHHHHHHHHhHHHHHHHHHhhhHh
Q 035092 6 INAGVEGTGDVCAVQLITKFGSLENLLQCVYQVEEERTRKALITFADQAVLSKNLVIII 64 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~fgsle~i~~~~~~l~~~k~~~~L~~~~e~a~ls~~L~~L~ 64 (73)
.+..+||||+|+|.++--. ++...++-. ..+++.|.+-.+.+..+...-.+.
T Consensus 12 ~l~~LPGIG~KsA~RlA~~------ll~~~~~~~-~~la~ai~~~~~~i~~C~~C~~ls 63 (195)
T TIGR00615 12 SLKKLPGIGPKSAQRLAFH------LLKRDPSEV-LRLAQALLEAKENLRTCSVCGAIS 63 (195)
T ss_pred HHHHCCCCCHHHHHHHHHH------HHcCCHHHH-HHHHHHHHHHHHcCCcCCCCCCCC
Confidence 3457899999999998543 333222211 246667777666666665554443
No 84
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.94 E-value=0.056 Score=37.63 Aligned_cols=18 Identities=17% Similarity=0.357 Sum_probs=14.4
Q ss_pred cCCCCcccHHHHHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITK 24 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~ 24 (73)
+-.|||||+|||.+++-+
T Consensus 110 L~~vpGIGkKtAerIilE 127 (194)
T PRK14605 110 LSTIPGIGKKTASRIVLE 127 (194)
T ss_pred HHhCCCCCHHHHHHHHHH
Confidence 347999999999996533
No 85
>PRK00076 recR recombination protein RecR; Reviewed
Probab=92.93 E-value=0.079 Score=37.44 Aligned_cols=52 Identities=19% Similarity=0.038 Sum_probs=31.3
Q ss_pred ccCCCCcccHHHHHHHHHHhCCHHHHHHHhhhhhhHHHHHHHHHhHHHHHHHHHhhhHh
Q 035092 6 INAGVEGTGDVCAVQLITKFGSLENLLQCVYQVEEERTRKALITFADQAVLSKNLVIII 64 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~fgsle~i~~~~~~l~~~k~~~~L~~~~e~a~ls~~L~~L~ 64 (73)
.+..+||||+|+|.++--+ ++...++-. ..+++.|.+-.+.+..+...-.+.
T Consensus 12 ~l~~LPGIG~KsA~Rla~~------ll~~~~~~~-~~la~~i~~~~~~i~~C~~C~~ls 63 (196)
T PRK00076 12 ALRKLPGIGPKSAQRLAFH------LLQRDREDV-LRLAQALEEAKEKIKHCSVCGNLT 63 (196)
T ss_pred HHHHCCCCCHHHHHHHHHH------HHcCCHHHH-HHHHHHHHHHHHcCCcCCCCCCcC
Confidence 3457899999999998654 332211111 246666766666666665554443
No 86
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=92.53 E-value=0.25 Score=35.87 Aligned_cols=27 Identities=19% Similarity=0.316 Sum_probs=24.7
Q ss_pred cCCCCcccHHHHHHHHHH-hCCHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITK-FGSLENLLQ 33 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~-fgsle~i~~ 33 (73)
+..+||||+++|.+|.+. |.|++++..
T Consensus 8 l~~l~gIg~~~a~~L~~~Gi~t~~dl~~ 35 (317)
T PRK04301 8 LEDLPGVGPATAEKLREAGYDTVEAIAV 35 (317)
T ss_pred HhhcCCCCHHHHHHHHHcCCCCHHHHHc
Confidence 468999999999999999 999999975
No 87
>PRK13844 recombination protein RecR; Provisional
Probab=92.35 E-value=0.11 Score=36.92 Aligned_cols=51 Identities=10% Similarity=-0.014 Sum_probs=30.5
Q ss_pred ccCCCCcccHHHHHHHHHHhCCHHHHHHHhhhhhhHHHHHHHHHhHHHHHHHHHhhhH
Q 035092 6 INAGVEGTGDVCAVQLITKFGSLENLLQCVYQVEEERTRKALITFADQAVLSKNLVII 63 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~fgsle~i~~~~~~l~~~k~~~~L~~~~e~a~ls~~L~~L 63 (73)
.+..+||||+|+|.++--. ++...++-. ..+++.|.+-.+.+..++..-.+
T Consensus 16 ~l~~LPGIG~KsA~Rla~~------lL~~~~~~~-~~la~~i~~~~~~i~~C~~C~~l 66 (200)
T PRK13844 16 SLRKLPTIGKKSSQRLALY------LLDKSPETA-IAIANSLLDATANIKKCVYCQAL 66 (200)
T ss_pred HHHHCCCCCHHHHHHHHHH------HHcCCHHHH-HHHHHHHHHHHHhCCcCCCCCCC
Confidence 4557899999999988644 333222111 24666666666666665554444
No 88
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=91.92 E-value=0.091 Score=36.65 Aligned_cols=25 Identities=16% Similarity=0.191 Sum_probs=19.8
Q ss_pred cCCCCcccHHHHHHHHHHhCCHHHH
Q 035092 7 NAGVEGTGDVCAVQLITKFGSLENL 31 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fgsle~i 31 (73)
.-.+||||+|||--.|..+++--.+
T Consensus 117 Ll~LpGVG~KTAnvVL~~l~~~~~~ 141 (177)
T TIGR03252 117 LKALPGFGKQKAKIFLALLGKQLGV 141 (177)
T ss_pred HHcCCCCCHHHHHHHHHHHHHHhCC
Confidence 4578999999999999887654444
No 89
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=91.83 E-value=0.1 Score=36.92 Aligned_cols=21 Identities=14% Similarity=0.313 Sum_probs=17.3
Q ss_pred cCCCCcccHHHHHHHHHHhCC
Q 035092 7 NAGVEGTGDVCAVQLITKFGS 27 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fgs 27 (73)
+-.+||||+|+|.+++-+-.+
T Consensus 110 L~k~PGIGkKtAerivleLk~ 130 (201)
T COG0632 110 LSKIPGIGKKTAERIVLELKG 130 (201)
T ss_pred hhcCCCCCHHHHHHHHHHHhh
Confidence 457999999999999876643
No 90
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=91.54 E-value=0.14 Score=36.39 Aligned_cols=51 Identities=25% Similarity=0.176 Sum_probs=32.7
Q ss_pred ccCCCCcccHHHHHHHHHHhCCHHHHHHH-hhhhhhHHHHHHHHHhHHHHHHHHHhhhHh
Q 035092 6 INAGVEGTGDVCAVQLITKFGSLENLLQC-VYQVEEERTRKALITFADQAVLSKNLVIII 64 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~fgsle~i~~~-~~~l~~~k~~~~L~~~~e~a~ls~~L~~L~ 64 (73)
....+||||||+|.++-=+ ++.. .+++ .++++.|.+..+.+..+...-.+.
T Consensus 13 ~l~kLPGvG~KsA~R~Afh------LL~~~~~~~--~~la~al~~a~~~i~~C~~C~~~t 64 (198)
T COG0353 13 ALKKLPGVGPKSAQRLAFH------LLQRDREDV--ERLAKALLEAKENIKHCSVCGNLT 64 (198)
T ss_pred HHhhCCCCChhHHHHHHHH------HHccCHHHH--HHHHHHHHHHHhcCccccccCCcC
Confidence 4567899999999987433 2222 1222 357778888777776666555543
No 91
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=91.47 E-value=0.43 Score=39.07 Aligned_cols=53 Identities=23% Similarity=0.307 Sum_probs=37.2
Q ss_pred ccccc-cCCCCcccHHHHHHHHHHh--CCHHHHHH----Hhhhhhh--HHHHHHHHHhHHHH
Q 035092 2 HFYFI-NAGVEGTGDVCAVQLITKF--GSLENLLQ----CVYQVEE--ERTRKALITFADQA 54 (73)
Q Consensus 2 ~~~~~-I~gVpGIG~KtA~~LL~~f--gsle~i~~----~~~~l~~--~k~~~~L~~~~e~a 54 (73)
||-|. --+|+|+||++..+|.+.- .++.+++. .+.++++ ++.+++|.+..+.+
T Consensus 458 hf~sr~al~I~GLG~k~i~~L~~~g~V~~~~Dl~~L~~~~L~~l~g~g~Ksa~~Ll~~Ie~s 519 (689)
T PRK14351 458 HYASRDALDIEGLGEERVQQLVDAGLVESLADLYDLTVADLAELEGWGETSAENLLAELEAS 519 (689)
T ss_pred HHhcccccCCCCcCHHHHHHHHHcCCCCCHHHHHHcCHHHHhcCcCcchhHHHHHHHHHHHH
Confidence 66653 4689999999999999885 57888874 2344432 56677777766655
No 92
>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=91.05 E-value=0.15 Score=29.60 Aligned_cols=16 Identities=19% Similarity=0.190 Sum_probs=13.8
Q ss_pred cCCCCcccHHHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLI 22 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL 22 (73)
..++||||+++|.++-
T Consensus 49 ~~~l~gIG~~ia~kI~ 64 (68)
T PF14716_consen 49 LKKLPGIGKSIAKKID 64 (68)
T ss_dssp HCTSTTTTHHHHHHHH
T ss_pred HhhCCCCCHHHHHHHH
Confidence 5789999999998873
No 93
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=91.03 E-value=0.14 Score=35.39 Aligned_cols=21 Identities=19% Similarity=0.311 Sum_probs=17.9
Q ss_pred cCCCCcccHHHHHHHHHHhCC
Q 035092 7 NAGVEGTGDVCAVQLITKFGS 27 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fgs 27 (73)
+..|||||+|+|.+++.++.+
T Consensus 110 L~~v~Gig~k~A~~I~~~l~~ 130 (192)
T PRK00116 110 LTKVPGIGKKTAERIVLELKD 130 (192)
T ss_pred HHhCCCCCHHHHHHHHHHHHH
Confidence 457999999999999988753
No 94
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=90.21 E-value=0.22 Score=35.29 Aligned_cols=19 Identities=21% Similarity=0.398 Sum_probs=15.8
Q ss_pred CCCcccHHHHHHHHHHhCC
Q 035092 9 GVEGTGDVCAVQLITKFGS 27 (73)
Q Consensus 9 gVpGIG~KtA~~LL~~fgs 27 (73)
.+||||+|||--+|...+.
T Consensus 123 ~lpGIG~KTAd~vL~~~~~ 141 (208)
T PRK01229 123 NIKGIGYKEASHFLRNVGY 141 (208)
T ss_pred cCCCCcHHHHHHHHHHccC
Confidence 7999999999999964443
No 95
>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=89.98 E-value=0.83 Score=27.71 Aligned_cols=33 Identities=24% Similarity=0.508 Sum_probs=23.7
Q ss_pred cCCCCcccHHHHHHHHH-----HhCCHHHHHHHhhhhh
Q 035092 7 NAGVEGTGDVCAVQLIT-----KFGSLENLLQCVYQVE 39 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~-----~fgsle~i~~~~~~l~ 39 (73)
.-.|+|||+..|.++++ .|.|++++....+.+.
T Consensus 29 l~~Ikglg~~~a~~I~~~R~~g~f~s~~df~~R~~~i~ 66 (90)
T PF14579_consen 29 LSAIKGLGEEVAEKIVEERENGPFKSLEDFIQRLPKIN 66 (90)
T ss_dssp GGGSTTS-HHHHHHHHHHHHCSS-SSHHHHHHHS-TS-
T ss_pred HhhcCCCCHHHHHHHHHhHhcCCCCCHHHHHHHHhcCC
Confidence 34799999999999996 5789999887764333
No 96
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=89.67 E-value=1.1 Score=34.17 Aligned_cols=56 Identities=18% Similarity=0.200 Sum_probs=37.3
Q ss_pred CCCCcccHHHHHHHHHHh--CCHHHHHHHhhhh-----hh--HHHHHHHHHhHHHHHHHHHhhhH
Q 035092 8 AGVEGTGDVCAVQLITKF--GSLENLLQCVYQV-----EE--ERTRKALITFADQAVLSKNLVII 63 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~~f--gsle~i~~~~~~l-----~~--~k~~~~L~~~~e~a~ls~~L~~L 63 (73)
-+|||+|||+-..|-+++ .+++++.+++++. +| ++-..++.++...+..+.+...|
T Consensus 96 l~v~GlGpkKi~~Ly~elgi~~~e~l~~a~~~~~~~~l~GfG~kse~~il~~i~~~~~~~~R~~l 160 (326)
T COG1796 96 LKVPGLGPKKIVSLYKELGIKDLEELQEALENGKIRGLRGFGKKSEAKILENIEFAEESPERIPL 160 (326)
T ss_pred hhCCCCCcHHHHHHHHHHCcccHHHHHHHHHhCCccccCCccchhHHHHHHHHHHHhhhhhhcch
Confidence 479999999999999887 6777777665433 33 44556666666665555544433
No 97
>PRK10702 endonuclease III; Provisional
Probab=89.35 E-value=0.24 Score=34.89 Aligned_cols=17 Identities=18% Similarity=0.323 Sum_probs=14.1
Q ss_pred CCCCcccHHHHHHHHHH
Q 035092 8 AGVEGTGDVCAVQLITK 24 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~~ 24 (73)
-.+||||+|||--+|..
T Consensus 112 l~lpGVG~ktA~~ill~ 128 (211)
T PRK10702 112 EALPGVGRKTANVVLNT 128 (211)
T ss_pred hcCCcccHHHHHHHHHH
Confidence 46899999999988743
No 98
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=89.22 E-value=0.28 Score=35.06 Aligned_cols=21 Identities=24% Similarity=0.354 Sum_probs=17.4
Q ss_pred CCCCcccHHHHHHHHHH-hCCH
Q 035092 8 AGVEGTGDVCAVQLITK-FGSL 28 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~~-fgsl 28 (73)
-.+||||+|||.-.|.. ||-.
T Consensus 112 ~~LPGVGrKTAnvVL~~a~g~p 133 (211)
T COG0177 112 LSLPGVGRKTANVVLSFAFGIP 133 (211)
T ss_pred HhCCCcchHHHHHHHHhhcCCC
Confidence 46899999999999998 6544
No 99
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=89.14 E-value=0.28 Score=31.88 Aligned_cols=19 Identities=16% Similarity=0.085 Sum_probs=15.5
Q ss_pred cCCCCcccHHHHHHHHHHh
Q 035092 7 NAGVEGTGDVCAVQLITKF 25 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f 25 (73)
+..+||||||+|.-++.--
T Consensus 85 L~~l~GIG~~tA~~~l~~~ 103 (158)
T cd00056 85 LLALPGVGRKTANVVLLFA 103 (158)
T ss_pred HHcCCCCCHHHHHHHHHHH
Confidence 3579999999999887644
No 100
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=88.97 E-value=0.28 Score=34.99 Aligned_cols=17 Identities=18% Similarity=0.241 Sum_probs=14.6
Q ss_pred CCCCcccHHHHHHHHHH
Q 035092 8 AGVEGTGDVCAVQLITK 24 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~~ 24 (73)
-.+||||++||-.+|--
T Consensus 124 l~l~GIG~kTAd~iLly 140 (218)
T PRK13913 124 LDQKGIGKESADAILCY 140 (218)
T ss_pred HcCCCccHHHHHHHHHH
Confidence 46999999999998873
No 101
>KOG2520 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=88.91 E-value=0.5 Score=39.65 Aligned_cols=31 Identities=29% Similarity=0.559 Sum_probs=25.1
Q ss_pred cCCCCcccHHHHHHHHHHhC---CHHHHHHHhhh
Q 035092 7 NAGVEGTGDVCAVQLITKFG---SLENLLQCVYQ 37 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fg---sle~i~~~~~~ 37 (73)
-.|++||||.+|..+|.+|+ ++..+.+++++
T Consensus 562 t~Gl~giGpV~AlEil~Efp~~~~l~~f~~w~~~ 595 (815)
T KOG2520|consen 562 TEGLKGIGPVSALEILAEFPGDENLLKFKKWVQQ 595 (815)
T ss_pred ccCCCcccchHHHHHHHHcCCcchhHHHHHHHHH
Confidence 46999999999999999999 66666566543
No 102
>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=88.36 E-value=0.33 Score=30.69 Aligned_cols=24 Identities=29% Similarity=0.423 Sum_probs=20.3
Q ss_pred cccccCCCCcccHHHHHHHHHHhC
Q 035092 3 FYFINAGVEGTGDVCAVQLITKFG 26 (73)
Q Consensus 3 ~~~~I~gVpGIG~KtA~~LL~~fg 26 (73)
+++-...|.|||+++|..+++..|
T Consensus 13 i~~aLt~IyGIG~~~A~~Ic~~lg 36 (107)
T PF00416_consen 13 IYIALTKIYGIGRRKAKQICKKLG 36 (107)
T ss_dssp HHHHHTTSTTBCHHHHHHHHHHTT
T ss_pred hHhHHhhhhccCHHHHHHHHHHcC
Confidence 345567899999999999999985
No 103
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=88.08 E-value=0.35 Score=31.15 Aligned_cols=17 Identities=18% Similarity=0.247 Sum_probs=13.4
Q ss_pred CCCCcccHHHHHHHHHH
Q 035092 8 AGVEGTGDVCAVQLITK 24 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~~ 24 (73)
..+||||+|+|.-++..
T Consensus 75 ~~l~GIG~~tA~~~l~~ 91 (149)
T smart00478 75 LKLPGVGRKTANAVLSF 91 (149)
T ss_pred HcCCCCcHHHHHHHHHH
Confidence 46899999999776544
No 104
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=87.88 E-value=0.36 Score=32.98 Aligned_cols=17 Identities=18% Similarity=0.259 Sum_probs=14.3
Q ss_pred CCCCcccHHHHHHHHHH
Q 035092 8 AGVEGTGDVCAVQLITK 24 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~~ 24 (73)
..+||||+|||.-+|..
T Consensus 109 ~~l~GIG~ktA~~ill~ 125 (191)
T TIGR01083 109 VKLPGVGRKTANVVLNV 125 (191)
T ss_pred HhCCCCcHHHHHHHHHH
Confidence 47899999999987754
No 105
>PRK02362 ski2-like helicase; Provisional
Probab=86.87 E-value=1.5 Score=35.53 Aligned_cols=44 Identities=25% Similarity=0.296 Sum_probs=32.0
Q ss_pred CCCCcccHHHHHHHHHH-hCCHHHHHHH-hhhh---hhHHHHHHHHHhH
Q 035092 8 AGVEGTGDVCAVQLITK-FGSLENLLQC-VYQV---EEERTRKALITFA 51 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~~-fgsle~i~~~-~~~l---~~~k~~~~L~~~~ 51 (73)
-.|||||+++|.+|.+. +.|++++.+. .+++ -+++.+++|.+..
T Consensus 655 ~~ip~i~~~~a~~l~~~gi~s~~dl~~~~~~~l~~~~g~~~~~~i~~~~ 703 (737)
T PRK02362 655 VGLRGVGRVRARRLYNAGIESRADLRAADKSVVLAILGEKIAENILEQA 703 (737)
T ss_pred hCCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHHHHCHHHHHHHHHHh
Confidence 46899999999999874 5799999853 3343 3457777777653
No 106
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=86.49 E-value=0.56 Score=29.70 Aligned_cols=27 Identities=19% Similarity=0.096 Sum_probs=20.2
Q ss_pred ccCCCCcccHHHHHHHHH-HhCCHHHHH
Q 035092 6 INAGVEGTGDVCAVQLIT-KFGSLENLL 32 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~-~fgsle~i~ 32 (73)
..-.|||||+++|..|.. -+.|++++.
T Consensus 13 ~L~~iP~IG~a~a~DL~~LGi~s~~~L~ 40 (93)
T PF11731_consen 13 DLTDIPNIGKATAEDLRLLGIRSPADLK 40 (93)
T ss_pred HHhcCCCccHHHHHHHHHcCCCCHHHHh
Confidence 345799999999999875 345666654
No 107
>PRK13910 DNA glycosylase MutY; Provisional
Probab=85.77 E-value=0.55 Score=34.72 Aligned_cols=20 Identities=20% Similarity=0.280 Sum_probs=15.9
Q ss_pred cCCCCcccHHHHHHHHH-HhC
Q 035092 7 NAGVEGTGDVCAVQLIT-KFG 26 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~-~fg 26 (73)
+-.+||||+|||..+|. .|+
T Consensus 74 L~~LpGIG~kTA~aIl~~af~ 94 (289)
T PRK13910 74 LLKLPGIGAYTANAILCFGFR 94 (289)
T ss_pred HHhCCCCCHHHHHHHHHHHCC
Confidence 34689999999999887 443
No 108
>PRK10736 hypothetical protein; Provisional
Probab=85.49 E-value=0.73 Score=35.35 Aligned_cols=25 Identities=8% Similarity=-0.008 Sum_probs=22.1
Q ss_pred cCCCCcccHHHHHHHHHHhCCHHHH
Q 035092 7 NAGVEGTGDVCAVQLITKFGSLENL 31 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fgsle~i 31 (73)
...+||||+++..+|++.|++.++.
T Consensus 10 L~~~~giG~~~~~~L~~~~~~~~~~ 34 (374)
T PRK10736 10 LMSVSSLYGDKMVRIAHRLLAQSQI 34 (374)
T ss_pred HHhCCCCCHHHHHHHHHHhcChhhC
Confidence 3468999999999999999999954
No 109
>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=85.02 E-value=0.59 Score=34.20 Aligned_cols=17 Identities=24% Similarity=0.364 Sum_probs=14.2
Q ss_pred cCCCCcccHHHHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLIT 23 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~ 23 (73)
+-.+||||++||..++.
T Consensus 107 L~~LpGIG~~TA~~Il~ 123 (275)
T TIGR01084 107 LAALPGVGRYTAGAILS 123 (275)
T ss_pred HHhCCCCCHHHHHHHHH
Confidence 34689999999988776
No 110
>PRK10880 adenine DNA glycosylase; Provisional
Probab=83.55 E-value=0.8 Score=34.71 Aligned_cols=20 Identities=25% Similarity=0.469 Sum_probs=16.3
Q ss_pred cCCCCcccHHHHHHHHH-HhC
Q 035092 7 NAGVEGTGDVCAVQLIT-KFG 26 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~-~fg 26 (73)
+-.+||||+|||..+|. .|+
T Consensus 111 L~~LpGIG~~TA~aIl~~af~ 131 (350)
T PRK10880 111 VAALPGVGRSTAGAILSLSLG 131 (350)
T ss_pred HhcCCCccHHHHHHHHHHHCC
Confidence 34789999999999887 554
No 111
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A.
Probab=83.04 E-value=0.35 Score=31.13 Aligned_cols=32 Identities=22% Similarity=0.061 Sum_probs=18.3
Q ss_pred cCCCCcccHHHHHHHHHHhCCHHHHHHHhhhh
Q 035092 7 NAGVEGTGDVCAVQLITKFGSLENLLQCVYQV 38 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fgsle~i~~~~~~l 38 (73)
.+=|.|.||..|..|++........+++.+++
T Consensus 52 LqfV~GLGPRKA~~Ll~~l~~~g~~l~~R~~L 83 (104)
T PF14635_consen 52 LQFVCGLGPRKAQALLKALKQNGGRLENRSQL 83 (104)
T ss_dssp GGGSTT--HHHHHHHHHHHHHC-S----TTHH
T ss_pred HhHhcCCChHHHHHHHHHHHHcCCccccHHHH
Confidence 35689999999999999886443344444443
No 112
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=82.98 E-value=3.4 Score=33.34 Aligned_cols=54 Identities=15% Similarity=0.024 Sum_probs=36.7
Q ss_pred cccc-ccCCCCcccHHHHHHHHHHh--CCHHHHHH----Hhhhhhh--HHHHHHHHHhHHHHH
Q 035092 2 HFYF-INAGVEGTGDVCAVQLITKF--GSLENLLQ----CVYQVEE--ERTRKALITFADQAV 55 (73)
Q Consensus 2 ~~~~-~I~gVpGIG~KtA~~LL~~f--gsle~i~~----~~~~l~~--~k~~~~L~~~~e~a~ 55 (73)
||.| +--+|.|+|+++..+|++.- .++.+|+. .+.++++ ++-+++|.+..+..+
T Consensus 421 hf~Sr~amdI~GlGe~~i~~L~~~G~i~~~~Diy~L~~~~l~~l~gfgeks~~nll~aIe~sk 483 (562)
T PRK08097 421 WLSGKQGLGLDGIGEGTWRALHQTGLFEHLFSWLALTPEQLANTPGIGKARAEQLWHQFNLAR 483 (562)
T ss_pred hhhcccccCCCCcCHHHHHHHHHcCCcCCHHHHhcCCHHHHhcCcCccHHHHHHHHHHHHHHc
Confidence 6654 34689999999999999764 78888874 3344432 566667766655543
No 113
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=82.45 E-value=1.3 Score=25.37 Aligned_cols=17 Identities=18% Similarity=0.268 Sum_probs=12.9
Q ss_pred CCCCcccHHHHHHHHHH
Q 035092 8 AGVEGTGDVCAVQLITK 24 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~~ 24 (73)
..+||||++.|.++++.
T Consensus 17 ~~lpgi~~~~A~~Iv~~ 33 (65)
T PF12836_consen 17 QALPGIGPKQAKAIVEY 33 (65)
T ss_dssp HTSTT--HHHHHHHHHH
T ss_pred HHcCCCCHHHHHHHHHH
Confidence 46899999999999974
No 114
>PF13052 DUF3913: Protein of unknown function (DUF3913)
Probab=81.73 E-value=0.61 Score=26.79 Aligned_cols=27 Identities=4% Similarity=0.238 Sum_probs=20.5
Q ss_pred cccccCCCCcccHHHHHHHHHHhCCHHHH
Q 035092 3 FYFINAGVEGTGDVCAVQLITKFGSLENL 31 (73)
Q Consensus 3 ~~~~I~gVpGIG~KtA~~LL~~fgsle~i 31 (73)
...|+|-||.||+|. ++|+.-.++.+|
T Consensus 17 iwdnvptiprigekv--eilktirtvtdi 43 (57)
T PF13052_consen 17 IWDNVPTIPRIGEKV--EILKTIRTVTDI 43 (57)
T ss_pred hhccCCCccccchhh--hHHhhhheeeee
Confidence 357999999999985 567776666554
No 115
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=81.46 E-value=4.1 Score=26.21 Aligned_cols=24 Identities=25% Similarity=0.256 Sum_probs=19.4
Q ss_pred CcccHHHHHHHHHHh-CCHHHHHHH
Q 035092 11 EGTGDVCAVQLITKF-GSLENLLQC 34 (73)
Q Consensus 11 pGIG~KtA~~LL~~f-gsle~i~~~ 34 (73)
||||++.+.+|-+.- .|++++++.
T Consensus 1 pgi~~~~~~~L~~~GI~t~~~Ll~~ 25 (122)
T PF14229_consen 1 PGIGPKEAAKLKAAGIKTTGDLLEA 25 (122)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHHc
Confidence 899999999995443 688888865
No 116
>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]
Probab=81.26 E-value=1.2 Score=31.24 Aligned_cols=21 Identities=24% Similarity=0.545 Sum_probs=18.4
Q ss_pred ccCCCCcccHHHHHHHHHHhC
Q 035092 6 INAGVEGTGDVCAVQLITKFG 26 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~fg 26 (73)
.|-|-||+|+-|+.++|+++|
T Consensus 4 ~ITGTPGvGKTT~~~~L~~lg 24 (180)
T COG1936 4 AITGTPGVGKTTVCKLLRELG 24 (180)
T ss_pred EEeCCCCCchHHHHHHHHHhC
Confidence 367999999999999999664
No 117
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=79.88 E-value=1.2 Score=32.56 Aligned_cols=25 Identities=12% Similarity=0.143 Sum_probs=18.2
Q ss_pred cCCCCcccHHHHHHH-HHHhCCHHHH
Q 035092 7 NAGVEGTGDVCAVQL-ITKFGSLENL 31 (73)
Q Consensus 7 I~gVpGIG~KtA~~L-L~~fgsle~i 31 (73)
+-.+|||||+||.-+ |..|+..+-+
T Consensus 209 L~~LpGIGpwTA~~vllr~lg~~D~f 234 (283)
T PRK10308 209 LQTFPGIGRWTANYFALRGWQAKDVF 234 (283)
T ss_pred HhcCCCcCHHHHHHHHHHhCCCCCCC
Confidence 356999999999655 4567766554
No 118
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=79.67 E-value=4.1 Score=31.19 Aligned_cols=50 Identities=18% Similarity=0.263 Sum_probs=37.3
Q ss_pred ccccCCCCcccHHHHHHHHHHhCCHHHHHHH-hhhh---hh--HHHHHHHHHhHHH
Q 035092 4 YFINAGVEGTGDVCAVQLITKFGSLENLLQC-VYQV---EE--ERTRKALITFADQ 53 (73)
Q Consensus 4 ~~~I~gVpGIG~KtA~~LL~~fgsle~i~~~-~~~l---~~--~k~~~~L~~~~e~ 53 (73)
|.-..+||-+-..-...|.+.|+++++|+++ .+++ .| +.+++.+.+....
T Consensus 292 YR~l~kIpRlp~~iv~nlV~~F~~l~~il~As~edL~~VeGIGe~rAr~i~~Gl~r 347 (349)
T COG1623 292 YRLLNKIPRLPFAIVENLVRAFGTLDGILEASAEDLDAVEGIGEARARAIKEGLSR 347 (349)
T ss_pred hHHHhcCcCccHHHHHHHHHHHhhHHHHHHhcHhHHhhhcchhHHHHHHHHHhHhh
Confidence 3445678889899999999999999999964 4554 32 5677777765543
No 119
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=79.62 E-value=1.8 Score=33.26 Aligned_cols=46 Identities=15% Similarity=0.200 Sum_probs=32.5
Q ss_pred cccccC--CCCcccHHH----------HHHHHHHhCCHHHHHHH--hhhhhh--HHHHHHHH
Q 035092 3 FYFINA--GVEGTGDVC----------AVQLITKFGSLENLLQC--VYQVEE--ERTRKALI 48 (73)
Q Consensus 3 ~~~~I~--gVpGIG~Kt----------A~~LL~~fgsle~i~~~--~~~l~~--~k~~~~L~ 48 (73)
|++-|| .|+|+|+++ -.+|++.||+=-+|+.+ .++|.. +++++.|.
T Consensus 293 y~~~iPL~ei~~~~~~~~~~~k~v~~~~~~l~~~fG~E~~iL~~~~~eel~~~~~~~a~~I~ 354 (374)
T TIGR00375 293 YVHLIPLAEVIGVGPKKGIFTKAVQSLWEKLKKAFGTEIAVLHEAAEEDLARVVPKVAALIV 354 (374)
T ss_pred eeeeCCHHHHHhhhcCCCCccHHHHHHHHHHHHHhccHHHHHhcCCHHHHHHHHHHHHHHHH
Confidence 445554 788999988 89999999999999853 466643 34444443
No 120
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=79.06 E-value=6 Score=32.50 Aligned_cols=53 Identities=15% Similarity=0.105 Sum_probs=30.3
Q ss_pred ccccc-cCCCCcccHHHHHHHHHHh--CCHHHHHH----Hhhhhhh--HHHHHHHHHhHHHH
Q 035092 2 HFYFI-NAGVEGTGDVCAVQLITKF--GSLENLLQ----CVYQVEE--ERTRKALITFADQA 54 (73)
Q Consensus 2 ~~~~~-I~gVpGIG~KtA~~LL~~f--gsle~i~~----~~~~l~~--~k~~~~L~~~~e~a 54 (73)
||.|- --+|.|+|+++..+|++.- .++.+|+. .+.++++ ++-+++|.+..+..
T Consensus 432 hf~sr~aldI~GlG~~~i~~L~~~G~i~~~~Dly~L~~~~l~~l~g~geksa~nl~~~Ie~s 493 (669)
T PRK14350 432 YFCSKKCMNIVGLSDKTIEFLFEKKFISSEIDLYTFNFDRLINLKGFKDKRINNLKRSIEAS 493 (669)
T ss_pred eeccCCcccccCcCHHHHHHHHHcCCcCCHHHHhhCCHHHHhhccCccHHHHHHHHHHHHHH
Confidence 56654 3578888888888887653 55555553 2233332 44555555555443
No 121
>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=78.65 E-value=1.4 Score=32.56 Aligned_cols=22 Identities=14% Similarity=0.161 Sum_probs=15.7
Q ss_pred CCCCcccHHHHHHHH-HHhCCHH
Q 035092 8 AGVEGTGDVCAVQLI-TKFGSLE 29 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL-~~fgsle 29 (73)
-.+||||||||--++ ..|+-.+
T Consensus 223 ~~l~GIG~~tAd~vll~~l~~~d 245 (310)
T TIGR00588 223 CELPGVGPKVADCICLMGLDKPQ 245 (310)
T ss_pred HhCCCccHHHHHHHHHHhCCCCC
Confidence 358999999998765 4455443
No 122
>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=77.34 E-value=1.5 Score=32.90 Aligned_cols=27 Identities=15% Similarity=0.295 Sum_probs=20.5
Q ss_pred cCCCCcccHHHHHHHHHHhC--CHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITKFG--SLENLLQ 33 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fg--sle~i~~ 33 (73)
+..+||||++++.+||+.+| ++.++.+
T Consensus 184 v~~l~GiG~~~~~~ll~~~Gi~ti~dl~~ 212 (359)
T cd01702 184 ITSIRGLGGKLGEEIIDLLGLPTEGDVAG 212 (359)
T ss_pred HHHhCCcCHHHHHHHHHHcCCcCHHHHHh
Confidence 34899999999999998774 5555543
No 123
>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=77.33 E-value=4.2 Score=33.30 Aligned_cols=42 Identities=7% Similarity=0.112 Sum_probs=28.7
Q ss_pred cCCCCcccHHHHHHHHHHhCCHHHH---HHHhhhh--hhHHHHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITKFGSLENL---LQCVYQV--EEERTRKALIT 49 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fgsle~i---~~~~~~l--~~~k~~~~L~~ 49 (73)
+..|||||+|++..+.+.+..-... +..+++. + ++++.+|.+
T Consensus 119 L~~v~gi~~~~~~~i~~~~~~~~~~~~~~~~L~~~gi~-~~~a~ki~~ 165 (720)
T TIGR01448 119 LLEVPGISKANLEKFVSQWSQQGDERRLLAGLQGLGIG-IKLAQRIYK 165 (720)
T ss_pred HhcCCCCCHHHHHHHHHHHHHhHHHHHHHHHHHHcCCC-HHHHHHHHH
Confidence 4578999999999999998655543 3333332 3 356667666
No 124
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=76.52 E-value=1.4 Score=32.02 Aligned_cols=25 Identities=32% Similarity=0.450 Sum_probs=21.5
Q ss_pred ccCCCCcccHHHHHHHHHHhCCHHH
Q 035092 6 INAGVEGTGDVCAVQLITKFGSLEN 30 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~fgsle~ 30 (73)
.|-.|||||+++|.++++.++.++.
T Consensus 37 EL~~V~GIg~k~AekI~e~l~~~~~ 61 (232)
T PRK12766 37 ELAEVDGIGNALAARIKADVGGLEV 61 (232)
T ss_pred HHHHccCCCHHHHHHHHHHhccccc
Confidence 3567899999999999999987765
No 125
>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=74.38 E-value=2.9 Score=26.53 Aligned_cols=27 Identities=22% Similarity=0.216 Sum_probs=20.7
Q ss_pred CCCCcccHHHHHHHHHHhCCHHHHHHH
Q 035092 8 AGVEGTGDVCAVQLITKFGSLENLLQC 34 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~~fgsle~i~~~ 34 (73)
-.|||||++.|..+..-|..-......
T Consensus 53 r~vpglG~~~A~~I~awLa~h~~~~~~ 79 (96)
T PF12482_consen 53 RAVPGLGAAGARRIEAWLAAHPALLGR 79 (96)
T ss_pred HhCcccchHHHHHHHHHHHHhHHHHhh
Confidence 359999999999988777666655543
No 126
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=74.37 E-value=8.9 Score=31.81 Aligned_cols=54 Identities=22% Similarity=0.357 Sum_probs=36.4
Q ss_pred cccccc-CCCCcccHHHHHHHHHHh--CCHHHHHH----Hhhhhhh--HHHHHHHHHhHHHHH
Q 035092 2 HFYFIN-AGVEGTGDVCAVQLITKF--GSLENLLQ----CVYQVEE--ERTRKALITFADQAV 55 (73)
Q Consensus 2 ~~~~~I-~gVpGIG~KtA~~LL~~f--gsle~i~~----~~~~l~~--~k~~~~L~~~~e~a~ 55 (73)
||.|-- -+|.|+|+|...+|+++- .++.+++. .+..+++ .+.+++|.+..+.++
T Consensus 441 hfvSr~AmdI~GLG~k~i~~L~e~~lI~~~~Dly~Lt~~~l~~l~~~~~ks~~nLl~aIe~sK 503 (667)
T COG0272 441 HFVSRNALDIDGLGEKIIEQLFEKGLIKDIADLYTLTEEDLLSLEGFGEKSAENLLNAIEKSK 503 (667)
T ss_pred eEecCCccCCCCcCHHHHHHHHHcCccCCHHHHHhCCHHHHhhccchhhhHHHHHHHHHHHhc
Confidence 666543 589999999999999873 67777762 2344443 455666766666544
No 127
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=73.67 E-value=4.6 Score=30.82 Aligned_cols=49 Identities=8% Similarity=0.091 Sum_probs=29.0
Q ss_pred ccCCCCcccHHHHHHHHHHhCCHHHHHHHhhhhhhHHHHHHHHHhHHHH
Q 035092 6 INAGVEGTGDVCAVQLITKFGSLENLLQCVYQVEEERTRKALITFADQA 54 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~fgsle~i~~~~~~l~~~k~~~~L~~~~e~a 54 (73)
.+-+++|.|+|.+.++|+.-.-.++-.+...-.....++..+..+.+++
T Consensus 129 ~~~~l~GfG~kse~~il~~i~~~~~~~~R~~l~~~l~ia~ei~~yl~~~ 177 (326)
T COG1796 129 KIRGLRGFGKKSEAKILENIEFAEESPERIPLSFTLPIAQEIEGYLEEL 177 (326)
T ss_pred CccccCCccchhHHHHHHHHHHHhhhhhhcchHHHHHHHHHHHHHHHhc
Confidence 4678999999999999986433332222211111234666666666543
No 128
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=73.57 E-value=2.4 Score=32.80 Aligned_cols=19 Identities=21% Similarity=0.184 Sum_probs=16.2
Q ss_pred ccCCCCcccHHHHHHHHHH
Q 035092 6 INAGVEGTGDVCAVQLITK 24 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~ 24 (73)
-+--|||||+|+|+.++..
T Consensus 331 ~llRVPGiG~ksa~rIv~~ 349 (404)
T COG4277 331 ELLRVPGIGVKSARRIVMT 349 (404)
T ss_pred HhcccCCCChHHHHHHHHH
Confidence 3557999999999999875
No 129
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=73.48 E-value=2.7 Score=31.36 Aligned_cols=23 Identities=13% Similarity=0.264 Sum_probs=18.2
Q ss_pred CCCcccHHHHHHHHHH-hCCHHHH
Q 035092 9 GVEGTGDVCAVQLITK-FGSLENL 31 (73)
Q Consensus 9 gVpGIG~KtA~~LL~~-fgsle~i 31 (73)
+.||||||.|.-.|+. ++.+..|
T Consensus 163 sLPGVGPKMa~L~m~~AWn~i~GI 186 (286)
T KOG1921|consen 163 SLPGVGPKMAHLTMQVAWNKIVGI 186 (286)
T ss_pred cCCCCchHHHHHHHHHHhccceeE
Confidence 6899999999988875 4666555
No 130
>PRK01172 ski2-like helicase; Provisional
Probab=73.22 E-value=10 Score=30.29 Aligned_cols=42 Identities=14% Similarity=0.250 Sum_probs=29.6
Q ss_pred CCCcccHHHHHHHHHH-hCCHHHHHHH-hhh---hh--hHHHHHHHHHh
Q 035092 9 GVEGTGDVCAVQLITK-FGSLENLLQC-VYQ---VE--EERTRKALITF 50 (73)
Q Consensus 9 gVpGIG~KtA~~LL~~-fgsle~i~~~-~~~---l~--~~k~~~~L~~~ 50 (73)
.|||+|+.+|++|.+. |.|+++|.+. .++ +. +++.++++.+.
T Consensus 616 ~ip~~~~~~a~~l~~~g~~~~~di~~~~~~~~~~i~~~~~~~~~~i~~~ 664 (674)
T PRK01172 616 LIPKVGRVRARRLYDAGFKTVDDIARSSPERIKKIYGFSDTLANAIVNR 664 (674)
T ss_pred CCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHHHhccCHHHHHHHHHH
Confidence 6899999999999984 6899999853 333 32 13555555554
No 131
>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=72.87 E-value=2.8 Score=27.00 Aligned_cols=23 Identities=22% Similarity=0.254 Sum_probs=19.4
Q ss_pred cccCCCCcccHHHHHHHHHHhCC
Q 035092 5 FINAGVEGTGDVCAVQLITKFGS 27 (73)
Q Consensus 5 ~~I~gVpGIG~KtA~~LL~~fgs 27 (73)
+-+-.|.|||+.+|..++...|-
T Consensus 15 ~aL~~i~GIG~~~a~~i~~~lgi 37 (113)
T TIGR03631 15 IALTYIYGIGRTRARKILEKAGI 37 (113)
T ss_pred eeeeeeecccHHHHHHHHHHhCc
Confidence 44567999999999999999863
No 132
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=69.74 E-value=4 Score=26.69 Aligned_cols=22 Identities=18% Similarity=0.247 Sum_probs=18.6
Q ss_pred cccCCCCcccHHHHHHHHHHhC
Q 035092 5 FINAGVEGTGDVCAVQLITKFG 26 (73)
Q Consensus 5 ~~I~gVpGIG~KtA~~LL~~fg 26 (73)
+-+-.|.|||+++|..+++..|
T Consensus 17 ~aLt~i~GIG~~~A~~ic~~lg 38 (122)
T CHL00137 17 YALTYIYGIGLTSAKEILEKAN 38 (122)
T ss_pred eeecccccccHHHHHHHHHHcC
Confidence 3456789999999999999975
No 133
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=69.59 E-value=3.9 Score=27.93 Aligned_cols=22 Identities=23% Similarity=0.368 Sum_probs=19.0
Q ss_pred cccCCCCcccHHHHHHHHHHhC
Q 035092 5 FINAGVEGTGDVCAVQLITKFG 26 (73)
Q Consensus 5 ~~I~gVpGIG~KtA~~LL~~fg 26 (73)
+-+-.|.|||+.+|..+++..|
T Consensus 30 ~aLt~I~GIG~~~A~~I~~~lg 51 (154)
T PTZ00134 30 YALTAIKGIGRRFAYLVCKKAG 51 (154)
T ss_pred EeecccccccHHHHHHHHHHcC
Confidence 3456799999999999999986
No 134
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=69.58 E-value=4.1 Score=26.64 Aligned_cols=22 Identities=18% Similarity=0.256 Sum_probs=18.8
Q ss_pred cccCCCCcccHHHHHHHHHHhC
Q 035092 5 FINAGVEGTGDVCAVQLITKFG 26 (73)
Q Consensus 5 ~~I~gVpGIG~KtA~~LL~~fg 26 (73)
+-+-.|-|||+.+|..++...|
T Consensus 17 ~aL~~I~GIG~~~a~~i~~~lg 38 (122)
T PRK05179 17 IALTYIYGIGRTRAKEILAAAG 38 (122)
T ss_pred eeecccccccHHHHHHHHHHhC
Confidence 3456799999999999999986
No 135
>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=68.98 E-value=3.9 Score=27.52 Aligned_cols=23 Identities=26% Similarity=0.485 Sum_probs=19.3
Q ss_pred ccccCCCCcccHHHHHHHHHHhC
Q 035092 4 YFINAGVEGTGDVCAVQLITKFG 26 (73)
Q Consensus 4 ~~~I~gVpGIG~KtA~~LL~~fg 26 (73)
++-+-.|.|||+++|..+++..|
T Consensus 20 ~~aLt~I~GIG~~~a~~I~~~lg 42 (144)
T TIGR03629 20 EYALTGIKGIGRRFARAIARKLG 42 (144)
T ss_pred EEeecceeccCHHHHHHHHHHcC
Confidence 34456799999999999999986
No 136
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=68.31 E-value=8.5 Score=29.50 Aligned_cols=32 Identities=22% Similarity=0.482 Sum_probs=23.2
Q ss_pred cCCCCcccHHHHHHHHHH-h--------CCHHHHHHHhhhh
Q 035092 7 NAGVEGTGDVCAVQLITK-F--------GSLENLLQCVYQV 38 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~-f--------gsle~i~~~~~~l 38 (73)
+..+||||+.||..++.- | |++.+++..+-.+
T Consensus 115 l~~LpGiG~yTa~Ail~~a~~~~~~~lDgNV~RVl~R~f~i 155 (342)
T COG1194 115 LAALPGVGPYTAGAILSFAFNQPEPVLDGNVKRVLSRLFAI 155 (342)
T ss_pred HHhCCCCcHHHHHHHHHHHhCCCCceeecchheeehhhhcc
Confidence 456899999999999874 3 6677766654333
No 137
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=67.89 E-value=3.7 Score=30.20 Aligned_cols=17 Identities=18% Similarity=0.249 Sum_probs=13.2
Q ss_pred CCCCcccHHHHHHHHHH
Q 035092 8 AGVEGTGDVCAVQLITK 24 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~~ 24 (73)
-.++||||+||.-+|--
T Consensus 201 ~~i~GIG~WTAe~~llf 217 (285)
T COG0122 201 TALKGIGPWTAEMFLLF 217 (285)
T ss_pred HcCCCcCHHHHHHHHHH
Confidence 35899999999876543
No 138
>PRK00024 hypothetical protein; Reviewed
Probab=67.16 E-value=35 Score=24.11 Aligned_cols=47 Identities=26% Similarity=0.393 Sum_probs=29.1
Q ss_pred CCCcccHH-HHHHHHHHhCCHHHHHHH-hhhh---hh--HHHHHHHHHhHHHHH
Q 035092 9 GVEGTGDV-CAVQLITKFGSLENLLQC-VYQV---EE--ERTRKALITFADQAV 55 (73)
Q Consensus 9 gVpGIG~K-tA~~LL~~fgsle~i~~~-~~~l---~~--~k~~~~L~~~~e~a~ 55 (73)
|+|+---+ .|.+||++|||+.++... .+++ +| +..+..|..-.|..+
T Consensus 37 g~~~~~~~~LA~~LL~~fgsL~~l~~as~~eL~~i~GIG~akA~~L~a~~El~~ 90 (224)
T PRK00024 37 GTKGKSVLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQLKAALELAR 90 (224)
T ss_pred CCCCCCHHHHHHHHHHHcCCHHHHHhCCHHHHhhccCccHHHHHHHHHHHHHHH
Confidence 45554443 788999999999999863 4554 33 334445555444433
No 139
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=65.54 E-value=5.8 Score=30.53 Aligned_cols=30 Identities=20% Similarity=0.207 Sum_probs=23.8
Q ss_pred CCCcccHHHHHHHHH-HhCCHHHHHHHhhhh
Q 035092 9 GVEGTGDVCAVQLIT-KFGSLENLLQCVYQV 38 (73)
Q Consensus 9 gVpGIG~KtA~~LL~-~fgsle~i~~~~~~l 38 (73)
.|=|||.|+|.++.+ -|.|++++.++.+++
T Consensus 101 nifGvG~ktA~~Wy~~GfrTled~Rk~~~kf 131 (353)
T KOG2534|consen 101 NIFGVGLKTAEKWYREGFRTLEDVRKKPDKF 131 (353)
T ss_pred HHhccCHHHHHHHHHhhhhHHHHHHhCHHHH
Confidence 356999999999976 489999998665554
No 140
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=65.54 E-value=5.5 Score=27.00 Aligned_cols=23 Identities=26% Similarity=0.489 Sum_probs=19.3
Q ss_pred ccccCCCCcccHHHHHHHHHHhC
Q 035092 4 YFINAGVEGTGDVCAVQLITKFG 26 (73)
Q Consensus 4 ~~~I~gVpGIG~KtA~~LL~~fg 26 (73)
++.+-.|-|||+++|..+++..|
T Consensus 24 ~~aLt~IyGIG~~~a~~Ic~~lg 46 (149)
T PRK04053 24 EYALTGIKGIGRRTARAIARKLG 46 (149)
T ss_pred eeeccccccccHHHHHHHHHHcC
Confidence 34456799999999999999986
No 141
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=64.86 E-value=15 Score=28.73 Aligned_cols=32 Identities=22% Similarity=0.316 Sum_probs=26.5
Q ss_pred ccccCCCCcccHHHHHHHHHH------hCCHHHHHHHh
Q 035092 4 YFINAGVEGTGDVCAVQLITK------FGSLENLLQCV 35 (73)
Q Consensus 4 ~~~I~gVpGIG~KtA~~LL~~------fgsle~i~~~~ 35 (73)
++-.-.|+|||+..+.+++++ |.|+.++...+
T Consensus 113 rfGL~aIKGVG~~~i~~Iv~eR~~~g~F~sl~DF~~Rv 150 (449)
T PRK07373 113 LFGLSAVRNLGEGAIESILKAREEGGEFKSLADFCDRV 150 (449)
T ss_pred EEcchhcCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHh
Confidence 345678999999999999963 89999998664
No 142
>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=62.87 E-value=5.1 Score=29.46 Aligned_cols=25 Identities=24% Similarity=0.369 Sum_probs=17.0
Q ss_pred cCCCCcccHHHHHHHHHHh--CCHHHH
Q 035092 7 NAGVEGTGDVCAVQLITKF--GSLENL 31 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f--gsle~i 31 (73)
..++||||+++|.++-.-. |++..+
T Consensus 47 ~~~ipgiG~~ia~kI~E~~~tG~~~~l 73 (307)
T cd00141 47 AKKLPGIGKKIAEKIEEILETGKLRKL 73 (307)
T ss_pred hcCCCCccHHHHHHHHHHHHcCCHHHH
Confidence 3589999999998764322 555444
No 143
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=62.05 E-value=29 Score=25.17 Aligned_cols=22 Identities=41% Similarity=0.664 Sum_probs=17.4
Q ss_pred HHHHHHHHhCCHHHHHHH-hhhh
Q 035092 17 CAVQLITKFGSLENLLQC-VYQV 38 (73)
Q Consensus 17 tA~~LL~~fgsle~i~~~-~~~l 38 (73)
.|..||++|||+.+++.+ .+++
T Consensus 46 la~~lL~~fg~L~~l~~a~~~el 68 (224)
T COG2003 46 LAKELLQEFGSLAELLKASVEEL 68 (224)
T ss_pred HHHHHHHHcccHHHHHhCCHHHH
Confidence 578899999999999854 4554
No 144
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=61.94 E-value=16 Score=31.48 Aligned_cols=31 Identities=26% Similarity=0.351 Sum_probs=26.0
Q ss_pred cccCCCCcccHHHHHHHHHH-----hCCHHHHHHHh
Q 035092 5 FINAGVEGTGDVCAVQLITK-----FGSLENLLQCV 35 (73)
Q Consensus 5 ~~I~gVpGIG~KtA~~LL~~-----fgsle~i~~~~ 35 (73)
+-+..|+|||+..|..++++ |.|++++....
T Consensus 816 ~gl~~Ikgvg~~~~~~Iv~~R~~g~f~s~~Df~~R~ 851 (1046)
T PRK05672 816 LGLRLVRGLGEEAAERIVAARARGPFTSVEDLARRA 851 (1046)
T ss_pred echhhcCCCCHHHHHHHHHHhhcCCCCCHHHHHHHh
Confidence 34567999999999999985 99999998654
No 145
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=61.22 E-value=6.6 Score=28.92 Aligned_cols=27 Identities=19% Similarity=0.262 Sum_probs=23.0
Q ss_pred CCCCcccHHHHHHHHHHhCCHHHHHHH
Q 035092 8 AGVEGTGDVCAVQLITKFGSLENLLQC 34 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~~fgsle~i~~~ 34 (73)
.-|+|||+|+|..+=..|.+.-...+.
T Consensus 217 ~~v~gig~k~A~~I~~~~~t~~~~~~~ 243 (254)
T COG1948 217 MKVKGIGEKKAREIYRFLRTEYKLIEA 243 (254)
T ss_pred HHhcCccHHHHHHHHHHHhchhhhhcc
Confidence 468999999999999999998776654
No 146
>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=60.69 E-value=6.2 Score=24.93 Aligned_cols=18 Identities=28% Similarity=0.333 Sum_probs=12.2
Q ss_pred cCCCCcccHHHHHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITK 24 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~ 24 (73)
+..+|||||..+.+|-.+
T Consensus 21 V~~laGIG~~lg~~L~~~ 38 (89)
T PF02961_consen 21 VTELAGIGPVLGKRLEEK 38 (89)
T ss_dssp GGGSTT--HHHHHHHHHT
T ss_pred ccccCCcCHHHHHHHHHC
Confidence 346899999998887654
No 147
>PF13238 AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB_A 3IIM_A 2AXP_A 3KB2_A 1KHT_A 1NKS_A 3H86_C ....
Probab=60.38 E-value=6.2 Score=23.51 Aligned_cols=20 Identities=15% Similarity=0.288 Sum_probs=17.4
Q ss_pred cCCCCcccHHHHHHHHHHhC
Q 035092 7 NAGVEGTGDVCAVQLITKFG 26 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fg 26 (73)
|-|.||.|+-|..+-|.+-.
T Consensus 3 i~G~~GsGKtTia~~L~~~~ 22 (129)
T PF13238_consen 3 ISGIPGSGKTTIAKELAERL 22 (129)
T ss_dssp EEESTTSSHHHHHHHHHHHH
T ss_pred EECCCCCCHHHHHHHHHHHH
Confidence 56999999999999888874
No 148
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=58.55 E-value=6.5 Score=30.26 Aligned_cols=15 Identities=20% Similarity=0.308 Sum_probs=12.5
Q ss_pred cCCCCcccHHHHHHH
Q 035092 7 NAGVEGTGDVCAVQL 21 (73)
Q Consensus 7 I~gVpGIG~KtA~~L 21 (73)
..++||||||.|.++
T Consensus 58 a~~lP~iG~kia~ki 72 (353)
T KOG2534|consen 58 AEKLPGIGPKIAEKI 72 (353)
T ss_pred hcCCCCCCHHHHHHH
Confidence 358999999999765
No 149
>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A ....
Probab=58.52 E-value=7 Score=23.50 Aligned_cols=20 Identities=20% Similarity=0.323 Sum_probs=17.2
Q ss_pred ccCCCCcccHHHHHHHHHHh
Q 035092 6 INAGVEGTGDVCAVQLITKF 25 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~f 25 (73)
.|-|.||.|+-|..+.|++.
T Consensus 3 ~I~G~~gsGKST~a~~La~~ 22 (121)
T PF13207_consen 3 IISGPPGSGKSTLAKELAER 22 (121)
T ss_dssp EEEESTTSSHHHHHHHHHHH
T ss_pred EEECCCCCCHHHHHHHHHHH
Confidence 36799999999999988884
No 150
>PF02742 Fe_dep_repr_C: Iron dependent repressor, metal binding and dimerisation domain; InterPro: IPR001367 The diphtheria toxin repressor protein (DTXR) is a member of this group []. In Corynebacterium diphtheriae where it has been studied in some detail this protein acts as an iron-binding repressor of dipheteria toxin gene expression and may serve as a global regulator of gene expression. The N terminus may be involved in iron binding and may associate with the Tox operator. Binding of DTXR to Tox operator requires a divalent metal ion such as cobalt, ferric, manganese and nickel whereas zinc shows weak activation [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005506 iron ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2X4H_D 2H09_A 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A 2F5D_A 3R61_A ....
Probab=58.33 E-value=11 Score=21.69 Aligned_cols=25 Identities=28% Similarity=0.352 Sum_probs=20.4
Q ss_pred cHHHHHHHHHHhCCHHHHHHHhhhh
Q 035092 14 GDVCAVQLITKFGSLENLLQCVYQV 38 (73)
Q Consensus 14 G~KtA~~LL~~fgsle~i~~~~~~l 38 (73)
|.+.|..+++.+.-++.++...=.+
T Consensus 4 G~~~A~~i~~rH~~le~fl~~~lgv 28 (71)
T PF02742_consen 4 GREIAERILRRHRILEEFLVEVLGV 28 (71)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTTT-
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 8899999999999999999553333
No 151
>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=58.23 E-value=6.6 Score=29.75 Aligned_cols=18 Identities=22% Similarity=0.224 Sum_probs=15.0
Q ss_pred cCCCCcccHHHHHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITK 24 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~ 24 (73)
+..+||||++++.+|-+.
T Consensus 174 v~~l~GiG~~~~~kL~~~ 191 (379)
T cd01703 174 LRKIPGIGYKTAAKLEAH 191 (379)
T ss_pred ccccCCcCHHHHHHHHHc
Confidence 458999999999888763
No 152
>COG2019 AdkA Archaeal adenylate kinase [Nucleotide transport and metabolism]
Probab=57.63 E-value=7.7 Score=27.56 Aligned_cols=20 Identities=25% Similarity=0.517 Sum_probs=15.6
Q ss_pred cccCCCCcccHHHHHHHHHH
Q 035092 5 FINAGVEGTGDVCAVQLITK 24 (73)
Q Consensus 5 ~~I~gVpGIG~KtA~~LL~~ 24 (73)
.-|-||||+|.-|..+...+
T Consensus 7 vvitGVpGvGKTTVl~~~~~ 26 (189)
T COG2019 7 VVITGVPGVGKTTVLKIALK 26 (189)
T ss_pred EEEEcCCCCChHHHHHHHHH
Confidence 35679999999987776654
No 153
>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=57.44 E-value=23 Score=25.85 Aligned_cols=25 Identities=24% Similarity=0.246 Sum_probs=17.5
Q ss_pred cCCCCcccHHHHHHHHHHh--CCHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITKF--GSLENLL 32 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f--gsle~i~ 32 (73)
|..+||||++++.+| +.+ .++.++.
T Consensus 178 l~~l~gig~~~~~~L-~~~Gi~ti~dL~ 204 (344)
T cd01700 178 VGDVWGIGRRTAKKL-NAMGIHTAGDLA 204 (344)
T ss_pred hhhcCccCHHHHHHH-HHcCCCcHHHHh
Confidence 347899999999986 555 3444444
No 154
>cd01080 NAD_bind_m-THF_DH_Cyclohyd NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase. NADP binding domain of the Methylene-Tetrahydrofolate Dehydrogenase/cyclohydrolase (m-THF DH/cyclohydrolase) bifunctional enzyme. Tetrahydrofolate is a versatile carrier of activated one-carbon units. The major one-carbon folate donors are N-5 methyltetrahydrofolate, N5,N10-m-THF, and N10-formayltetrahydrofolate. The oxidation of metabolic intermediate m-THF to m-THF requires the enzyme m-THF DH. In addition, most DHs also have an associated cyclohydrolase activity which catalyzes its hydrolysis to N10-formyltetrahydrofolate. m-THF DH is typically found as part of a multifunctional protein in eukaryotes. NADP-dependent m-THF DH in mammals, birds and yeast are components of a trifunctional enzyme with DH, cyclohydrolase, and synthetase activities. Certain eukaryotic cells also contain homodimeric bifunctional DH/cyclodrolase form. In bacteria, monofucntional DH, as well a
Probab=57.02 E-value=10 Score=25.62 Aligned_cols=20 Identities=20% Similarity=0.273 Sum_probs=15.1
Q ss_pred ccCCCC-cccHHHHHHHHHHh
Q 035092 6 INAGVE-GTGDVCAVQLITKF 25 (73)
Q Consensus 6 ~I~gVp-GIG~KtA~~LL~~f 25 (73)
+++++| ||||.|+..|++..
T Consensus 143 ~~~~~pggvgp~t~a~l~~n~ 163 (168)
T cd01080 143 AITPVPGGVGPMTVAMLMKNT 163 (168)
T ss_pred CcCCCCCcChHHHHHHHHHHH
Confidence 345555 69999999998763
No 155
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=56.74 E-value=7.2 Score=29.04 Aligned_cols=26 Identities=23% Similarity=0.371 Sum_probs=17.9
Q ss_pred cCCCCcccHHHHHHHHH--HhCCHHHHH
Q 035092 7 NAGVEGTGDVCAVQLIT--KFGSLENLL 32 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~--~fgsle~i~ 32 (73)
+.++||||++.|.++-. +=|++....
T Consensus 50 l~~lpgIG~~ia~kI~Eil~tG~~~~~~ 77 (334)
T smart00483 50 LKGLPGIGDKIKKKIEEIIETGKSSKVL 77 (334)
T ss_pred HhcCCCccHHHHHHHHHHHHhCcHHHHH
Confidence 45799999999987643 227766444
No 156
>PRK02406 DNA polymerase IV; Validated
Probab=56.41 E-value=26 Score=25.53 Aligned_cols=26 Identities=23% Similarity=0.326 Sum_probs=18.7
Q ss_pred cCCCCcccHHHHHHHHHHh--CCHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITKF--GSLENLLQ 33 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f--gsle~i~~ 33 (73)
|..+||||++++.+| +.+ .++.++..
T Consensus 170 i~~l~giG~~~~~~L-~~~Gi~ti~dl~~ 197 (343)
T PRK02406 170 VEKIPGVGKVTAEKL-HALGIYTCADLQK 197 (343)
T ss_pred cchhcCCCHHHHHHH-HHcCCCcHHHHHh
Confidence 458899999999996 564 45555543
No 157
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=56.02 E-value=24 Score=31.05 Aligned_cols=40 Identities=20% Similarity=0.304 Sum_probs=29.0
Q ss_pred CCCCcccHHHHHHHHHH-----hCCHHHHHHHhhhhhhHHHHHHHHH
Q 035092 8 AGVEGTGDVCAVQLITK-----FGSLENLLQCVYQVEEERTRKALIT 49 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~~-----fgsle~i~~~~~~l~~~k~~~~L~~ 49 (73)
..|+|||+..|..+++. |.|++++.... .+.. +.-+.|..
T Consensus 1153 ~aI~glg~~~a~~Iv~~R~~g~F~s~~Df~~R~-~v~k-~~le~L~~ 1197 (1213)
T TIGR01405 1153 NAIPGLGENVANSIVEARNEKPFLSKEDLKKRT-KISK-THIEKLDS 1197 (1213)
T ss_pred hhcCCCCHHHHHHHHHHHhhCCCCCHHHHHHHh-CCCH-HHHHHHHh
Confidence 47999999999999975 89999998763 3433 34444433
No 158
>PRK00254 ski2-like helicase; Provisional
Probab=54.56 E-value=9.5 Score=30.83 Aligned_cols=22 Identities=23% Similarity=0.270 Sum_probs=18.4
Q ss_pred cCCCCcccHHHHHHHHHHhCCH
Q 035092 7 NAGVEGTGDVCAVQLITKFGSL 28 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fgsl 28 (73)
+..+||||+|+|.++.+.+++-
T Consensus 680 l~~~~gi~~~~a~~i~~~~~~~ 701 (720)
T PRK00254 680 LLKVEGIGAKIVEGIFKHLGVE 701 (720)
T ss_pred HhcCCCCCHHHHHHHHHHhccc
Confidence 4568999999999999987744
No 159
>PRK14133 DNA polymerase IV; Provisional
Probab=54.37 E-value=37 Score=24.81 Aligned_cols=26 Identities=27% Similarity=0.438 Sum_probs=18.2
Q ss_pred cCCCCcccHHHHHHHHHHh--CCHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITKF--GSLENLLQ 33 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f--gsle~i~~ 33 (73)
|..+||||++++.+| +.+ .++.++.+
T Consensus 175 v~~l~gig~~~~~~L-~~~Gi~ti~dl~~ 202 (347)
T PRK14133 175 ISKVHGIGKKSVEKL-NNIGIYTIEDLLK 202 (347)
T ss_pred ccccCCCCHHHHHHH-HHcCCccHHHHhh
Confidence 347899999999986 566 34555543
No 160
>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=54.24 E-value=12 Score=21.67 Aligned_cols=18 Identities=11% Similarity=0.097 Sum_probs=13.9
Q ss_pred cCCCCcccHHHHHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITK 24 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~ 24 (73)
+-.+||+|+|+...+.+.
T Consensus 46 L~~i~n~G~ksl~EI~~~ 63 (66)
T PF03118_consen 46 LLKIKNFGKKSLEEIKEK 63 (66)
T ss_dssp HHTSTTSHHHHHHHHHHH
T ss_pred HHhCCCCCHhHHHHHHHH
Confidence 346899999998887654
No 161
>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model. AAA ATPases form a large, functionally diverse protein family belonging to the AAA+ superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent unfolding of macromolecules. AAA ATPases contain a P-loop NTPase domain, which is the most abundant class of NTP-binding protein fold, and is found throughout all kingdoms of life []. P-loop NTPase domains act to hydrolyse the beta-gamma phosphate bond of bound nucleoside triphosphate. There are two classes of P-loop domains: the KG (kinase-GTPase) division, and the ASCE division, the latter including the AAA+ group as well as several other ATPases. There are at least six major clades of AAA domains (metalloproteases, meiotic proteins, D1 and D2 domains of ATPases with two AAA domains, proteasome subunits, and BSC1), as well as several minor clades, some of which consist of hypothetical proteins []. The domain organisation of AAA ATPases consists of a non-ATPase N-terminal domain that acts in substrate recognition, followed by one or two AAA domains (D1 and D2), one of which may be degenerate.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 2R44_A.
Probab=54.18 E-value=7.3 Score=26.00 Aligned_cols=19 Identities=21% Similarity=0.391 Sum_probs=13.3
Q ss_pred cCCCCcccHHHHHHHHHHh
Q 035092 7 NAGVEGTGDVCAVQLITKF 25 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f 25 (73)
+.|+||+|+-+..+.|.+-
T Consensus 4 leg~PG~GKT~la~~lA~~ 22 (131)
T PF07726_consen 4 LEGVPGVGKTTLAKALARS 22 (131)
T ss_dssp EES---HHHHHHHHHHHHH
T ss_pred eECCCccHHHHHHHHHHHH
Confidence 5799999999999888764
No 162
>KOG2379 consensus Endonuclease MUS81 [Replication, recombination and repair]
Probab=54.13 E-value=9.5 Score=30.67 Aligned_cols=30 Identities=20% Similarity=0.262 Sum_probs=26.5
Q ss_pred cCCCCcccHHHHHHHHHHhCCHHHHHHHhh
Q 035092 7 NAGVEGTGDVCAVQLITKFGSLENLLQCVY 36 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fgsle~i~~~~~ 36 (73)
.--||||+.-+|.++...|.|+-.++.+.+
T Consensus 432 LMqvkg~S~erAiAI~d~YpTl~sLl~AY~ 461 (501)
T KOG2379|consen 432 LMQVKGMSLERAIAIADRYPTLRSLLSAYE 461 (501)
T ss_pred HHhccCccHHHHHHHHHhccCHHHHHHHHh
Confidence 456999999999999999999999987654
No 163
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=53.47 E-value=76 Score=22.46 Aligned_cols=48 Identities=21% Similarity=0.174 Sum_probs=29.8
Q ss_pred CCCcc-cH-HHHHHHHHHh---CCHHHHHHH-hhhh---hh--HHHHHHHHHhHHHHHH
Q 035092 9 GVEGT-GD-VCAVQLITKF---GSLENLLQC-VYQV---EE--ERTRKALITFADQAVL 56 (73)
Q Consensus 9 gVpGI-G~-KtA~~LL~~f---gsle~i~~~-~~~l---~~--~k~~~~L~~~~e~a~l 56 (73)
|+|+- .- -.|..||++| ||+.++.+. .+++ +| +..+..|..-.|..+.
T Consensus 27 g~~~~~~~~~lA~~ll~~f~~~g~l~~l~~a~~~eL~~i~GiG~aka~~l~a~~El~rR 85 (218)
T TIGR00608 27 GTPKGLDVLSLSKRLLDVFGRQDSLGHLLSAPPEELSSVPGIGEAKAIQLKAAVELAKR 85 (218)
T ss_pred CCCCCCCHHHHHHHHHHHhcccCCHHHHHhCCHHHHHhCcCCcHHHHHHHHHHHHHHHH
Confidence 55554 22 3788999999 999999864 4554 33 3344555554444433
No 164
>PRK07945 hypothetical protein; Provisional
Probab=52.72 E-value=11 Score=28.02 Aligned_cols=23 Identities=13% Similarity=0.150 Sum_probs=16.6
Q ss_pred cCCCCcccHHHHHHHHHHh--CCHH
Q 035092 7 NAGVEGTGDVCAVQLITKF--GSLE 29 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f--gsle 29 (73)
+..+||||+.+|.++-+-- |+++
T Consensus 51 l~~~~giG~~~a~~i~e~~~tg~~~ 75 (335)
T PRK07945 51 LTSLPGIGPKTAKVIAQALAGRVPD 75 (335)
T ss_pred cccCCCcCHHHHHHHHHHHhcCCHH
Confidence 5589999999998764432 5554
No 165
>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=52.35 E-value=28 Score=25.41 Aligned_cols=25 Identities=28% Similarity=0.407 Sum_probs=17.6
Q ss_pred cCCCCcccHHHHHHHHHHh--CCHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITKF--GSLENLL 32 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f--gsle~i~ 32 (73)
|..+||||++++.+|- ++ .++.++.
T Consensus 175 i~~l~giG~~~~~~L~-~~Gi~ti~dl~ 201 (343)
T cd00424 175 LTDLPGIGAVTAKRLE-AVGINPIGDLL 201 (343)
T ss_pred hhhcCCCCHHHHHHHH-HcCCCcHHHHh
Confidence 3479999999999974 55 3454443
No 166
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=51.99 E-value=12 Score=27.71 Aligned_cols=20 Identities=20% Similarity=0.092 Sum_probs=17.0
Q ss_pred cCCCCcccHHHHHHHHHHhC
Q 035092 7 NAGVEGTGDVCAVQLITKFG 26 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fg 26 (73)
+.-+||+||-.|.+|.+.|.
T Consensus 229 le~~~G~G~~kak~l~~~l~ 248 (254)
T KOG2841|consen 229 LEQCPGLGPAKAKRLHKFLH 248 (254)
T ss_pred HHhCcCcCHHHHHHHHHHHh
Confidence 45689999999999998764
No 167
>PTZ00205 DNA polymerase kappa; Provisional
Probab=51.21 E-value=8.8 Score=31.20 Aligned_cols=25 Identities=28% Similarity=0.496 Sum_probs=17.3
Q ss_pred cCCCCcccHHHHHHHHHHhC--CHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITKFG--SLENLL 32 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fg--sle~i~ 32 (73)
|..+||||++++.+| +.+| ++.++.
T Consensus 311 V~ki~GIG~~t~~~L-~~~GI~TigDLa 337 (571)
T PTZ00205 311 LRSVPGVGKVTEALL-KGLGITTLSDIY 337 (571)
T ss_pred cceeCCcCHHHHHHH-HHcCCCcHHHHh
Confidence 458999999999765 5664 344443
No 168
>KOG2457 consensus A/G-specific adenine DNA glycosylase [Replication, recombination and repair]
Probab=50.99 E-value=5.9 Score=31.61 Aligned_cols=25 Identities=24% Similarity=0.506 Sum_probs=18.8
Q ss_pred CCCCcccHHHHHHHHH-HhCCHHHHH
Q 035092 8 AGVEGTGDVCAVQLIT-KFGSLENLL 32 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~-~fgsle~i~ 32 (73)
.||||||+.||-.++. .|+-+..|.
T Consensus 209 kgvpGVG~YTAGAiaSIAf~q~tGiV 234 (555)
T KOG2457|consen 209 KGVPGVGQYTAGAIASIAFNQVTGIV 234 (555)
T ss_pred hhCCCCCccchhhhhhhhhcCccccc
Confidence 5799999999998876 465555443
No 169
>PRK01184 hypothetical protein; Provisional
Probab=50.03 E-value=16 Score=23.81 Aligned_cols=20 Identities=20% Similarity=0.400 Sum_probs=17.8
Q ss_pred cCCCCcccHHHHHHHHHHhC
Q 035092 7 NAGVEGTGDVCAVQLITKFG 26 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fg 26 (73)
+-|.||-|+-|...+++++|
T Consensus 6 l~G~~GsGKsT~a~~~~~~g 25 (184)
T PRK01184 6 VVGMPGSGKGEFSKIAREMG 25 (184)
T ss_pred EECCCCCCHHHHHHHHHHcC
Confidence 56999999999999998885
No 170
>COG1415 Uncharacterized conserved protein [Function unknown]
Probab=49.92 E-value=10 Score=29.46 Aligned_cols=13 Identities=31% Similarity=0.279 Sum_probs=10.7
Q ss_pred CCCcccHHHHHHH
Q 035092 9 GVEGTGDVCAVQL 21 (73)
Q Consensus 9 gVpGIG~KtA~~L 21 (73)
-+|||||+|.+.|
T Consensus 282 l~~GiGpstvRAL 294 (373)
T COG1415 282 LVPGIGPSTVRAL 294 (373)
T ss_pred hccCCCHHHHHHH
Confidence 4799999987765
No 171
>TIGR00041 DTMP_kinase thymidylate kinase. Function: phosphorylation of DTMP to form DTDP in both de novo and salvage pathways of DTTP synthesis. Catalytic activity: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate.
Probab=49.38 E-value=14 Score=24.16 Aligned_cols=20 Identities=25% Similarity=0.654 Sum_probs=17.6
Q ss_pred ccCCCCcccHHHHHHHHHHh
Q 035092 6 INAGVEGTGDVCAVQLITKF 25 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~f 25 (73)
-|.|+||.|+-|..++|.+.
T Consensus 7 vieG~~GsGKsT~~~~L~~~ 26 (195)
T TIGR00041 7 VIEGIDGAGKTTQANLLKKL 26 (195)
T ss_pred EEECCCCCCHHHHHHHHHHH
Confidence 46899999999999999865
No 172
>PRK00625 shikimate kinase; Provisional
Probab=48.95 E-value=71 Score=21.41 Aligned_cols=27 Identities=19% Similarity=0.298 Sum_probs=19.7
Q ss_pred cCCCCcccHHHHHHHHHHh-----CCHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITKF-----GSLENLLQ 33 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f-----gsle~i~~ 33 (73)
+=|+||.|+-|..+.|.+. =+.+.+.+
T Consensus 5 LiG~pGsGKTT~~k~La~~l~~~~id~D~~I~ 36 (173)
T PRK00625 5 LCGLPTVGKTSFGKALAKFLSLPFFDTDDLIV 36 (173)
T ss_pred EECCCCCCHHHHHHHHHHHhCCCEEEhhHHHH
Confidence 4599999999988888663 34555543
No 173
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=48.40 E-value=37 Score=30.52 Aligned_cols=27 Identities=26% Similarity=0.369 Sum_probs=24.1
Q ss_pred CCCCcccHHHHHHHHHH-----hCCHHHHHHH
Q 035092 8 AGVEGTGDVCAVQLITK-----FGSLENLLQC 34 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~~-----fgsle~i~~~ 34 (73)
..|+|+|+..|..+++. |.|++++...
T Consensus 1376 ~~I~glG~~~a~~Iv~~R~~g~F~s~~Df~~R 1407 (1437)
T PRK00448 1376 NALPGLGENVAKSIVEAREEGEFLSKEDLRKR 1407 (1437)
T ss_pred hhcCCCCHHHHHHHHHHHhcCCCCCHHHHHHH
Confidence 47999999999999986 9999999876
No 174
>PF01798 Nop: Putative snoRNA binding domain; InterPro: IPR002687 This domain is present in various pre-mRNA processing ribonucleoproteins. The function of the domain is unknown however it may be a common RNA or snoRNA or Nop1p binding domain. Proteins have been implicated in an expanding variety of functions during pre-mRNA splicing. Molecular cloning has identified genes encoding spliceosomal proteins that potentially act as novel RNA helicases, GTPases, or protein isomerases. Novel protein-protein and protein-RNA interactions that are required for functional spliceosome formation have also been described. Finally, growing evidence suggests that proteins may contribute directly to the spliceosome's active sites [].; PDB: 3GQX_B 3GQU_A 3NVM_A 3NMU_B 2NNW_C 3NVI_A 3NVK_A 2OZB_E 3SIU_B 3SIV_H ....
Probab=48.02 E-value=18 Score=24.33 Aligned_cols=20 Identities=45% Similarity=0.652 Sum_probs=18.9
Q ss_pred ccHHHHHHHHHHhCCHHHHH
Q 035092 13 TGDVCAVQLITKFGSLENLL 32 (73)
Q Consensus 13 IG~KtA~~LL~~fgsle~i~ 32 (73)
||+..|.+|+..-|+++++-
T Consensus 38 vG~~vaA~Li~~aGgL~~La 57 (150)
T PF01798_consen 38 VGSSVAARLISHAGGLENLA 57 (150)
T ss_dssp HHHHHHHHHHHHHTSHHHHH
T ss_pred HCcHHHHHHHHHcccHHHHH
Confidence 79999999999999999986
No 175
>PRK01810 DNA polymerase IV; Validated
Probab=47.83 E-value=40 Score=25.19 Aligned_cols=24 Identities=21% Similarity=0.430 Sum_probs=17.1
Q ss_pred CCCcccHHHHHHHHHHh--CCHHHHHH
Q 035092 9 GVEGTGDVCAVQLITKF--GSLENLLQ 33 (73)
Q Consensus 9 gVpGIG~KtA~~LL~~f--gsle~i~~ 33 (73)
.+||||++++.+| +.+ .++.++..
T Consensus 183 ~l~giG~~~~~~L-~~~Gi~tigdL~~ 208 (407)
T PRK01810 183 EMHGIGEKTAEKL-KDIGIQTIGDLAK 208 (407)
T ss_pred hcCCcCHHHHHHH-HHcCCCcHHHHHh
Confidence 6899999999886 565 35555543
No 176
>PRK10792 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=47.44 E-value=17 Score=26.92 Aligned_cols=20 Identities=20% Similarity=0.265 Sum_probs=15.9
Q ss_pred cccCCCC-cccHHHHHHHHHH
Q 035092 5 FINAGVE-GTGDVCAVQLITK 24 (73)
Q Consensus 5 ~~I~gVp-GIG~KtA~~LL~~ 24 (73)
+.|..|| ||||.|...||+.
T Consensus 254 ~~itPvPGGVGp~T~a~L~~N 274 (285)
T PRK10792 254 SWITPVPGGVGPMTVATLLEN 274 (285)
T ss_pred cCcCCCCCCChHHHHHHHHHH
Confidence 4566666 5999999999976
No 177
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=47.29 E-value=12 Score=25.15 Aligned_cols=19 Identities=16% Similarity=0.165 Sum_probs=14.2
Q ss_pred ccCCCCcccHHHHHHHHHHh
Q 035092 6 INAGVEGTGDVCAVQLITKF 25 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~f 25 (73)
++.-|.|||||-+..| +..
T Consensus 68 DLt~I~GIGPk~e~~L-n~~ 86 (133)
T COG3743 68 DLTRISGIGPKLEKVL-NEL 86 (133)
T ss_pred cchhhcccCHHHHHHH-HHc
Confidence 5667899999988765 443
No 178
>PRK13973 thymidylate kinase; Provisional
Probab=46.80 E-value=16 Score=24.93 Aligned_cols=19 Identities=26% Similarity=0.464 Sum_probs=17.5
Q ss_pred cCCCCcccHHHHHHHHHHh
Q 035092 7 NAGVEGTGDVCAVQLITKF 25 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f 25 (73)
+.|++|-|+-|..++|.++
T Consensus 8 iEG~dGsGKtTq~~~l~~~ 26 (213)
T PRK13973 8 FEGGEGAGKSTQIRLLAER 26 (213)
T ss_pred EEcCCCCCHHHHHHHHHHH
Confidence 5899999999999999887
No 179
>PRK08609 hypothetical protein; Provisional
Probab=46.18 E-value=13 Score=29.63 Aligned_cols=25 Identities=20% Similarity=0.134 Sum_probs=16.5
Q ss_pred cCCCCcccHHHHHHHHHHh--CCHHHH
Q 035092 7 NAGVEGTGDVCAVQLITKF--GSLENL 31 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f--gsle~i 31 (73)
..++||||++.|.++-.-. |++..+
T Consensus 50 l~~ipgIG~~ia~kI~Eil~tG~~~~l 76 (570)
T PRK08609 50 FTKLKGIGKGTAEVIQEYRETGESSVL 76 (570)
T ss_pred hccCCCcCHHHHHHHHHHHHhCChHHH
Confidence 4689999999997643221 555444
No 180
>PF05559 DUF763: Protein of unknown function (DUF763); InterPro: IPR008482 This family consists of several uncharacterised bacterial and archaeal proteins of unknown function.
Probab=44.29 E-value=15 Score=28.03 Aligned_cols=14 Identities=21% Similarity=0.247 Sum_probs=11.7
Q ss_pred CCCCcccHHHHHHH
Q 035092 8 AGVEGTGDVCAVQL 21 (73)
Q Consensus 8 ~gVpGIG~KtA~~L 21 (73)
-.+|||||+|.+.|
T Consensus 272 L~~~GvGp~TlRAL 285 (319)
T PF05559_consen 272 LLIKGVGPSTLRAL 285 (319)
T ss_pred HhcCCCCHHHHHHH
Confidence 45899999998776
No 181
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=44.13 E-value=14 Score=26.66 Aligned_cols=17 Identities=18% Similarity=0.317 Sum_probs=14.1
Q ss_pred CCCCcccHHHHHHHHHH
Q 035092 8 AGVEGTGDVCAVQLITK 24 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~~ 24 (73)
.+|+|||+-||-.+|--
T Consensus 118 L~iKGIG~ETaDsILlY 134 (215)
T COG2231 118 LSIKGIGKETADSILLY 134 (215)
T ss_pred HccCCcchhhHHHHHHH
Confidence 47899999999887754
No 182
>PRK03103 DNA polymerase IV; Reviewed
Probab=43.95 E-value=37 Score=25.40 Aligned_cols=24 Identities=21% Similarity=0.393 Sum_probs=17.0
Q ss_pred CCCCcccHHHHHHHHHHhC--CHHHHH
Q 035092 8 AGVEGTGDVCAVQLITKFG--SLENLL 32 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~~fg--sle~i~ 32 (73)
..+||||++++.+| +.+| ++.++.
T Consensus 184 ~~l~gig~~~~~~L-~~~Gi~tigdl~ 209 (409)
T PRK03103 184 RKLFGVGSRMEKHL-RRMGIRTIGQLA 209 (409)
T ss_pred hhcCCccHHHHHHH-HHcCCCCHHHHh
Confidence 36899999998885 5664 455544
No 183
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=43.68 E-value=16 Score=29.46 Aligned_cols=21 Identities=19% Similarity=0.121 Sum_probs=17.7
Q ss_pred cCCCCcccHHHHHHHHHHhCC
Q 035092 7 NAGVEGTGDVCAVQLITKFGS 27 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fgs 27 (73)
+..|||||++.|..|.+.|..
T Consensus 577 L~~v~Gig~~~A~~I~~~l~~ 597 (598)
T PRK00558 577 LAKVPGISKKLAEAIYEALHK 597 (598)
T ss_pred HhhcCCcCHHHHHHHHHHhcc
Confidence 456899999999999988753
No 184
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=43.54 E-value=18 Score=23.99 Aligned_cols=24 Identities=21% Similarity=0.137 Sum_probs=19.1
Q ss_pred cCCCCcccHHHHHHHHHHhCCHHH
Q 035092 7 NAGVEGTGDVCAVQLITKFGSLEN 30 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fgsle~ 30 (73)
.-.|.|||..+|.+++++-+=-.+
T Consensus 19 Lt~IyGIG~~~a~~I~~~~gi~~~ 42 (121)
T COG0099 19 LTYIYGIGRRRAKEICKKAGIDPD 42 (121)
T ss_pred hhhhccccHHHHHHHHHHcCCCHh
Confidence 345899999999999999764333
No 185
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=43.26 E-value=48 Score=29.10 Aligned_cols=32 Identities=25% Similarity=0.340 Sum_probs=26.2
Q ss_pred ccccCCCCcccHHHHHHHHHH------hCCHHHHHHHh
Q 035092 4 YFINAGVEGTGDVCAVQLITK------FGSLENLLQCV 35 (73)
Q Consensus 4 ~~~I~gVpGIG~KtA~~LL~~------fgsle~i~~~~ 35 (73)
++-+..|+|||+..+..++++ |.|++++....
T Consensus 823 r~gL~aIkgvg~~~~~~Iv~~R~~~g~f~s~~Df~~R~ 860 (1151)
T PRK06826 823 RFGLAAVKNVGENAIDSIVEEREKKGKFKSLVDFCERV 860 (1151)
T ss_pred EechhhcCCCCHHHHHHHHHHHHhCCCCCCHHHHHHHh
Confidence 344568999999999999963 89999998664
No 186
>COG1031 Uncharacterized Fe-S oxidoreductase [Energy production and conversion]
Probab=43.21 E-value=20 Score=29.13 Aligned_cols=28 Identities=21% Similarity=0.389 Sum_probs=23.2
Q ss_pred cCCCCcccHHHHHHHHHH--hCCHHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITK--FGSLENLLQC 34 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~--fgsle~i~~~ 34 (73)
+..|||||.|++.+++.+ |.|.|++++.
T Consensus 518 l~~ipgig~~~~~~I~~~Rp~~s~e~~l~~ 547 (560)
T COG1031 518 LRAIPGIGKKTLRKILAERPFKSSEEFLKL 547 (560)
T ss_pred HHhcccchhhhHHHHHhcCCccchHHHHhc
Confidence 457999999999999987 5788887754
No 187
>COG3547 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=42.93 E-value=27 Score=24.36 Aligned_cols=25 Identities=24% Similarity=0.476 Sum_probs=21.2
Q ss_pred CCCcccHHHHHHHH---HHhCCHHHHHH
Q 035092 9 GVEGTGDVCAVQLI---TKFGSLENLLQ 33 (73)
Q Consensus 9 gVpGIG~KtA~~LL---~~fgsle~i~~ 33 (73)
.+||||+.+|..+. ..|.+...+-+
T Consensus 192 ~~pgig~~~a~~i~~~~~~f~~~~~~~~ 219 (303)
T COG3547 192 SIPGIGELTAAAIADDVGRFPSARQLAA 219 (303)
T ss_pred hCCCccHHHHHHHHHHhccCCcHHHHHH
Confidence 58999999999999 67888877765
No 188
>PF14842 FliG_N: FliG N-terminal domain; PDB: 3HJL_A 3AJC_A 3USY_B.
Probab=42.66 E-value=62 Score=20.10 Aligned_cols=40 Identities=20% Similarity=0.350 Sum_probs=19.4
Q ss_pred ccHHHHHHHHHHhCC--HHHHHHH---hhhhhhHHHHHHHHHhHH
Q 035092 13 TGDVCAVQLITKFGS--LENLLQC---VYQVEEERTRKALITFAD 52 (73)
Q Consensus 13 IG~KtA~~LL~~fgs--le~i~~~---~~~l~~~k~~~~L~~~~e 52 (73)
+|+..|.++|+++.. ++.|-.. ++.++...+..-+.++.+
T Consensus 18 Lgee~Aa~vlk~l~~~ei~~i~~~ma~l~~v~~~~~~~Vl~EF~~ 62 (108)
T PF14842_consen 18 LGEEAAAEVLKHLDEEEIERISREMAKLGSVSPEEVEEVLEEFYD 62 (108)
T ss_dssp S-HHHHHHHHHHS-HHHHHHHHHHHHT-----HHHHHHHHHHHHH
T ss_pred HCHHHHHHHHccCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHHH
Confidence 688889999988843 4444433 344444344444444444
No 189
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=42.48 E-value=29 Score=21.00 Aligned_cols=23 Identities=26% Similarity=0.434 Sum_probs=17.2
Q ss_pred ccccCCCCcccHHHHHHHHHHhC
Q 035092 4 YFINAGVEGTGDVCAVQLITKFG 26 (73)
Q Consensus 4 ~~~I~gVpGIG~KtA~~LL~~fg 26 (73)
|.=+.+|+|||-|+|-++-.++|
T Consensus 45 Y~L~~~i~gi~F~~aD~iA~~~g 67 (94)
T PF14490_consen 45 YRLIEDIDGIGFKTADKIALKLG 67 (94)
T ss_dssp TCCCB-SSSSBHHHHHHHHHTTT
T ss_pred HHHHHHccCCCHHHHHHHHHHcC
Confidence 33455789999999999888874
No 190
>PRK02794 DNA polymerase IV; Provisional
Probab=42.18 E-value=51 Score=24.86 Aligned_cols=26 Identities=19% Similarity=0.259 Sum_probs=18.2
Q ss_pred cCCCCcccHHHHHHHHHHh--CCHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITKF--GSLENLLQ 33 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f--gsle~i~~ 33 (73)
|..+||||++++.+| +.+ .++.++.+
T Consensus 211 l~~L~GiG~~~~~~L-~~~GI~tigdL~~ 238 (419)
T PRK02794 211 VGIIWGVGPATAARL-ARDGIRTIGDLQR 238 (419)
T ss_pred hhhhCCCCHHHHHHH-HHhccchHHHHhh
Confidence 457899999999998 444 35555543
No 191
>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family. This subfamily of the adenylate kinase superfamily contains examples of UMP-CMP kinase, as well as others proteins with unknown specificity, some currently designated adenylate kinase. All known members are eukaryotic.
Probab=42.10 E-value=26 Score=22.66 Aligned_cols=20 Identities=25% Similarity=0.541 Sum_probs=15.2
Q ss_pred cCCCCcccHHHH-HHHHHHhC
Q 035092 7 NAGVEGTGDVCA-VQLITKFG 26 (73)
Q Consensus 7 I~gVpGIG~KtA-~~LL~~fg 26 (73)
|-|.||.|+-|. ..|.++|+
T Consensus 4 i~G~pGsGKst~a~~la~~~~ 24 (183)
T TIGR01359 4 VLGGPGSGKGTQCAKIVENFG 24 (183)
T ss_pred EECCCCCCHHHHHHHHHHHcC
Confidence 569999999996 55555665
No 192
>PRK05686 fliG flagellar motor switch protein G; Validated
Probab=41.37 E-value=47 Score=24.65 Aligned_cols=52 Identities=12% Similarity=0.319 Sum_probs=33.4
Q ss_pred ccHHHHHHHHHHhCCH--HHHHHHhhhhhh---HHHHHHHHHhHHHHHHHHH-hhhHh
Q 035092 13 TGDVCAVQLITKFGSL--ENLLQCVYQVEE---ERTRKALITFADQAVLSKN-LVIII 64 (73)
Q Consensus 13 IG~KtA~~LL~~fgsl--e~i~~~~~~l~~---~k~~~~L~~~~e~a~ls~~-L~~L~ 64 (73)
=|.+++..+|+.+..- +++++.+++..+ .++++++..+.+...+..+ +..+-
T Consensus 202 ~g~~~~a~Iln~~~~~~~~~il~~L~~~d~~~a~~Ir~~mF~Fedl~~l~~~~l~~ll 259 (339)
T PRK05686 202 GGVKTVAEILNNLDRQTEKTILESLEEEDPELAEKIKDLMFVFEDLVDLDDRSIQRLL 259 (339)
T ss_pred CcHHHHHHHHhcCCchHHHHHHHHHHhhCHHHHHHHHHHhcCHHHHhcCCHHHHHHHH
Confidence 4789999999999543 468888877654 3455555555555555443 44333
No 193
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=41.25 E-value=57 Score=28.57 Aligned_cols=32 Identities=13% Similarity=0.153 Sum_probs=26.3
Q ss_pred ccccCCCCcccHHHHHHHHHH-----hCCHHHHHHHh
Q 035092 4 YFINAGVEGTGDVCAVQLITK-----FGSLENLLQCV 35 (73)
Q Consensus 4 ~~~I~gVpGIG~KtA~~LL~~-----fgsle~i~~~~ 35 (73)
++-+..|+|||+..+..+++. |.|+.++....
T Consensus 801 r~gL~~Ikgvg~~~~~~Iv~~R~~g~f~s~~Df~~R~ 837 (1107)
T PRK06920 801 RYSLLSIRNIGMATVTALYEEREKKMFEDLFEFCLRM 837 (1107)
T ss_pred EechhhcCCCCHHHHHHHHHHhhcCCCCCHHHHHHHH
Confidence 344568999999999999976 99999987654
No 194
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=40.72 E-value=80 Score=22.39 Aligned_cols=28 Identities=25% Similarity=0.128 Sum_probs=22.2
Q ss_pred cCCCCcccHHHHHHHHHH-hCCHHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITK-FGSLENLLQC 34 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~-fgsle~i~~~ 34 (73)
.-.+||+|++.+.+|-+. ..|++++.+.
T Consensus 153 L~Qlp~i~~~~~~~l~~~~i~s~~~l~~~ 181 (312)
T smart00611 153 LLQLPHLPEEILKRLEKKKVLSLEDLLEL 181 (312)
T ss_pred cccCCCCCHHHHHHHHhCCCCCHHHHHhc
Confidence 447899999999999764 5788888754
No 195
>KOG4747 consensus Two-component phosphorelay intermediate involved in MAP kinase cascade regulation [Signal transduction mechanisms]
Probab=40.55 E-value=99 Score=21.24 Aligned_cols=49 Identities=22% Similarity=0.331 Sum_probs=28.3
Q ss_pred ccccccCCCCcccHHHHHHHHHHh------CCHHHHHHHhhhhhh--HHHHHHHHHhHH
Q 035092 2 HFYFINAGVEGTGDVCAVQLITKF------GSLENLLQCVYQVEE--ERTRKALITFAD 52 (73)
Q Consensus 2 ~~~~~I~gVpGIG~KtA~~LL~~f------gsle~i~~~~~~l~~--~k~~~~L~~~~e 52 (73)
||.-|... -||..+.++++..| +++|.....+++++- .-+++++.....
T Consensus 80 hqlkgsss--sIGa~kvk~~c~~~~~~~~~~n~egcvr~l~~v~ie~~~lkkkL~~~f~ 136 (150)
T KOG4747|consen 80 HQLKGSSS--SIGALKVKKVCVGFNEFCEAGNIEGCVRCLQQVKIEYSLLKKKLETLFQ 136 (150)
T ss_pred HHccCchh--hhhHHHHHHHHHHHHHHHhhccchhHhhchHHHHHHHHHHHHHHHHHHH
Confidence 44443332 38899999998887 444444444454432 345666666544
No 196
>PF15608 PELOTA_1: PELOTA RNA binding domain
Probab=40.13 E-value=18 Score=23.16 Aligned_cols=11 Identities=36% Similarity=0.595 Sum_probs=8.7
Q ss_pred CcccHHHHHHH
Q 035092 11 EGTGDVCAVQL 21 (73)
Q Consensus 11 pGIG~KtA~~L 21 (73)
|||||-|..-|
T Consensus 42 PGIgEaTRvLL 52 (100)
T PF15608_consen 42 PGIGEATRVLL 52 (100)
T ss_pred CChhHHHHHHH
Confidence 99999887543
No 197
>KOG0442 consensus Structure-specific endonuclease ERCC1-XPF, catalytic component XPF/ERCC4 [Replication, recombination and repair]
Probab=40.10 E-value=69 Score=27.68 Aligned_cols=49 Identities=20% Similarity=0.234 Sum_probs=35.8
Q ss_pred ccCCCCcccHHHHHHHHHHhCCHHHHHHH-hhhhh---h-HHHHHHHHHhHHHH
Q 035092 6 INAGVEGTGDVCAVQLITKFGSLENLLQC-VYQVE---E-ERTRKALITFADQA 54 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~fgsle~i~~~-~~~l~---~-~k~~~~L~~~~e~a 54 (73)
...++|||-.+....++.+|+|+..+... ++++. + ...++.|..+....
T Consensus 822 fll~lPgVs~~n~~~l~~k~ks~~~La~sS~~el~el~~~~~~a~~LYdFi~~~ 875 (892)
T KOG0442|consen 822 FLLSLPGVSYINYRNLRHKFKSLKELANSSQEELSELLGVHENAKLLYDFIHTE 875 (892)
T ss_pred HHhcCCCccHHHHHHHHHHhhHHHHHHhCcHHHHHHHhcchHHHHHHHHHHHHh
Confidence 34679999999999999999999999753 45553 2 44566666655543
No 198
>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=39.79 E-value=17 Score=27.44 Aligned_cols=25 Identities=24% Similarity=0.376 Sum_probs=18.1
Q ss_pred CCCCcccHHHHHHHHHHh-CCHHHHH
Q 035092 8 AGVEGTGDVCAVQLITKF-GSLENLL 32 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~~f-gsle~i~ 32 (73)
..+||||++++.+|-+-. .++.++.
T Consensus 225 ~~l~GIG~~~~~~L~~~Gi~t~~dl~ 250 (404)
T cd01701 225 GDLPGVGSSLAEKLVKLFGDTCGGLE 250 (404)
T ss_pred hHhCCCCHHHHHHHHHcCCcchHHHH
Confidence 478999999998887653 3554544
No 199
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=39.79 E-value=27 Score=30.34 Aligned_cols=32 Identities=25% Similarity=0.371 Sum_probs=27.2
Q ss_pred ccccCCCCcccHHHHHHHHHH--hCCHHHHHHHh
Q 035092 4 YFINAGVEGTGDVCAVQLITK--FGSLENLLQCV 35 (73)
Q Consensus 4 ~~~I~gVpGIG~KtA~~LL~~--fgsle~i~~~~ 35 (73)
++-+..|+|||+..+..++++ |.|++++...+
T Consensus 749 r~GL~aIkgvg~~~~~~I~~~R~f~s~~Df~~R~ 782 (1034)
T PRK07279 749 YLGLKNIKGLPRDLAYWIIENRPFSSIEDFLTRL 782 (1034)
T ss_pred EeehhhcCCCCHHHHHHHHHCCCCCCHHHHHHhc
Confidence 445678999999999999986 99999998664
No 200
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=39.73 E-value=14 Score=30.74 Aligned_cols=23 Identities=30% Similarity=0.278 Sum_probs=18.6
Q ss_pred ccCCCCcccHHHHHHHHHHhCCH
Q 035092 6 INAGVEGTGDVCAVQLITKFGSL 28 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~fgsl 28 (73)
.|..|+|||+++|..+++.+..+
T Consensus 670 ELa~V~Gig~k~Ae~I~~~L~~~ 692 (694)
T PRK14666 670 GLAAVPGIGPARAAALHEHLKTL 692 (694)
T ss_pred HHHhcCCcCHHHHHHHHHHHHHh
Confidence 35678999999999999887543
No 201
>PRK03352 DNA polymerase IV; Validated
Probab=39.50 E-value=15 Score=26.76 Aligned_cols=26 Identities=19% Similarity=0.308 Sum_probs=18.2
Q ss_pred cCCCCcccHHHHHHHHHHh--CCHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITKF--GSLENLLQ 33 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f--gsle~i~~ 33 (73)
|..+||||++++.+| +.+ .++.++.+
T Consensus 179 l~~l~gig~~~~~~L-~~~Gi~ti~dl~~ 206 (346)
T PRK03352 179 TDALWGVGPKTAKRL-AALGITTVADLAA 206 (346)
T ss_pred HHHcCCCCHHHHHHH-HHcCCccHHHHhc
Confidence 347899999999986 555 35555543
No 202
>PLN02924 thymidylate kinase
Probab=39.41 E-value=24 Score=24.60 Aligned_cols=20 Identities=15% Similarity=0.413 Sum_probs=17.8
Q ss_pred ccCCCCcccHHHHHHHHHHh
Q 035092 6 INAGVEGTGDVCAVQLITKF 25 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~f 25 (73)
-+.|++|-|+-|..++|.++
T Consensus 20 viEGiDGsGKsTq~~~L~~~ 39 (220)
T PLN02924 20 VLEGLDRSGKSTQCAKLVSF 39 (220)
T ss_pred EEECCCCCCHHHHHHHHHHH
Confidence 46899999999999999876
No 203
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=39.38 E-value=59 Score=28.64 Aligned_cols=32 Identities=28% Similarity=0.371 Sum_probs=26.0
Q ss_pred ccccCCCCcccHHHHHHHHHH------hCCHHHHHHHh
Q 035092 4 YFINAGVEGTGDVCAVQLITK------FGSLENLLQCV 35 (73)
Q Consensus 4 ~~~I~gVpGIG~KtA~~LL~~------fgsle~i~~~~ 35 (73)
++-+..|+|||+..+..++++ |.|++++....
T Consensus 834 r~GL~aIkgvg~~~~~~Iv~~R~~~g~f~s~~Df~~R~ 871 (1170)
T PRK07374 834 LFGLSAVKNLGDGAIRNIIAARDSDGPFKSLADLCDRL 871 (1170)
T ss_pred EechhhcCCCCHHHHHHHHHHHHhCCCCCCHHHHHHHh
Confidence 344568999999999999953 89999998664
No 204
>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]
Probab=39.38 E-value=30 Score=29.26 Aligned_cols=19 Identities=26% Similarity=0.569 Sum_probs=12.8
Q ss_pred cccCCCCcccHH-HHHHHHH
Q 035092 5 FINAGVEGTGDV-CAVQLIT 23 (73)
Q Consensus 5 ~~I~gVpGIG~K-tA~~LL~ 23 (73)
.+|.||||.|.- |...+++
T Consensus 425 mYIsGvPGtGKT~tV~~Vm~ 444 (767)
T KOG1514|consen 425 MYISGVPGTGKTATVLEVMK 444 (767)
T ss_pred EEEecCCCCCceehHHHHHH
Confidence 478999999963 3344444
No 205
>PF02777 Sod_Fe_C: Iron/manganese superoxide dismutases, C-terminal domain Note: SCOP classifies the two domains separately.; InterPro: IPR019832 Superoxide dismutases (SODs) (1.15.1.1 from EC) catalyse the conversion of superoxide radicals to molecular oxygen. Their function is to destroy the radicals that are normally produced within cells and are toxic to biological systems. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one [, , ]. This family includes both single metal-binding SODs and cambialistic SOD, which can bind either Mn or Fe. Fe/MnSODs are ubiquitous enzymes that are responsible for the majority of SOD activity in prokaryotes, fungi, blue-green algae and mitochondria. Fe/MnSODs are found as homodimers or homotetramers. The structure of Fe/MnSODs can be divided into two domains, an alpha N-terminal domain and an alpha/beta C-terminal domain, connected by a loop. The structure of the N-terminal domain consists of a two helices in an antiparallel hairpin, with a left-handed twist []. The structure of the C-terminal domain is of the alpha/beta type, and consists of a three-stranded antiparallel beta-sheet in the order 213, along with four helices in the arrangement alpha/beta(2)/alpha/beta/alpha(2) []. This entry represents the C-terminal domain of Manganese/iron superoxide dismutase. ; GO: 0004784 superoxide dismutase activity, 0046872 metal ion binding, 0006801 superoxide metabolic process, 0055114 oxidation-reduction process; PDB: 1KKC_Y 2GOJ_B 1UES_C 1UER_C 1QNN_A 1MY6_A 1MA1_F 1P7G_Q 3EVK_D 2GPC_A ....
Probab=38.85 E-value=66 Score=19.73 Aligned_cols=22 Identities=18% Similarity=0.218 Sum_probs=18.2
Q ss_pred HHHHHHHHHHhCCHHHHHHHhh
Q 035092 15 DVCAVQLITKFGSLENLLQCVY 36 (73)
Q Consensus 15 ~KtA~~LL~~fgsle~i~~~~~ 36 (73)
.+.+..|=+.|||+|++.+...
T Consensus 5 g~l~~~I~~~FGS~d~fk~~f~ 26 (106)
T PF02777_consen 5 GKLKKAIEEDFGSFDNFKAEFT 26 (106)
T ss_dssp HHHHHHHHHHHSSHHHHHHHHH
T ss_pred HHHHHHHHHHhCCHHHHHHHHH
Confidence 6778889999999999986643
No 206
>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....
Probab=38.84 E-value=33 Score=20.31 Aligned_cols=21 Identities=19% Similarity=0.341 Sum_probs=17.2
Q ss_pred cCCCCcccHHHHHHHHHHhCC
Q 035092 7 NAGVEGTGDVCAVQLITKFGS 27 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fgs 27 (73)
+-|.||.|+.+..+.+.+.-.
T Consensus 3 l~G~~G~GKT~l~~~la~~l~ 23 (132)
T PF00004_consen 3 LHGPPGTGKTTLARALAQYLG 23 (132)
T ss_dssp EESSTTSSHHHHHHHHHHHTT
T ss_pred EECcCCCCeeHHHHHHHhhcc
Confidence 358999999999888887743
No 207
>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=38.82 E-value=28 Score=20.94 Aligned_cols=27 Identities=15% Similarity=0.034 Sum_probs=17.0
Q ss_pred ccCCCCcccHHHHHHHHHHh-CCHHHHH
Q 035092 6 INAGVEGTGDVCAVQLITKF-GSLENLL 32 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~f-gsle~i~ 32 (73)
.|...|+||++....|-+-- .|++++.
T Consensus 4 ~l~~LpNig~~~e~~L~~vGI~t~~~L~ 31 (81)
T PF04994_consen 4 RLKDLPNIGPKSERMLAKVGIHTVEDLR 31 (81)
T ss_dssp -GCGSTT--HHHHHHHHHTT--SHHHHH
T ss_pred chhhCCCCCHHHHHHHHHcCCCCHHHHH
Confidence 46789999999998886653 4555554
No 208
>PRK03858 DNA polymerase IV; Validated
Probab=38.59 E-value=18 Score=26.88 Aligned_cols=25 Identities=20% Similarity=0.276 Sum_probs=17.4
Q ss_pred cCCCCcccHHHHHHHHHHh--CCHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITKF--GSLENLL 32 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f--gsle~i~ 32 (73)
|..+||||++++.+| +++ .++.++.
T Consensus 175 l~~l~Gig~~~~~~L-~~~Gi~t~~dl~ 201 (396)
T PRK03858 175 VRRLWGVGPVTAAKL-RAHGITTVGDVA 201 (396)
T ss_pred hhhcCCCCHHHHHHH-HHhCCCcHHHHh
Confidence 347899999999887 455 3444443
No 209
>PRK14552 C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional
Probab=38.41 E-value=28 Score=27.09 Aligned_cols=25 Identities=28% Similarity=0.348 Sum_probs=21.9
Q ss_pred ccCCCCcccHHHHHHHHHHhCCHHHHH
Q 035092 6 INAGVEGTGDVCAVQLITKFGSLENLL 32 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~fgsle~i~ 32 (73)
|+-.+ ||+.+|+.||.+-||+.++-
T Consensus 265 NLtaL--VG~~lAArLIa~AGsL~~La 289 (414)
T PRK14552 265 NLTAL--VGPSLGARLISLAGGLEELA 289 (414)
T ss_pred HHHHH--HhhHHHHHHHHHhCCHHHHh
Confidence 44555 99999999999999999986
No 210
>PRK14175 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=38.28 E-value=30 Score=25.65 Aligned_cols=19 Identities=16% Similarity=0.286 Sum_probs=14.9
Q ss_pred ccCCCC-cccHHHHHHHHHH
Q 035092 6 INAGVE-GTGDVCAVQLITK 24 (73)
Q Consensus 6 ~I~gVp-GIG~KtA~~LL~~ 24 (73)
.|..|| ||||.|...|++.
T Consensus 254 ~iTPVPGGVGp~T~a~L~~n 273 (286)
T PRK14175 254 AITPVPGGVGPLTITMVLNN 273 (286)
T ss_pred CcCCCCCCCHHHHHHHHHHH
Confidence 455555 6999999999976
No 211
>cd01672 TMPK Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).
Probab=37.74 E-value=28 Score=22.27 Aligned_cols=20 Identities=20% Similarity=0.587 Sum_probs=17.2
Q ss_pred ccCCCCcccHHHHHHHHHHh
Q 035092 6 INAGVEGTGDVCAVQLITKF 25 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~f 25 (73)
-|.|++|.|+-|..+.|.+.
T Consensus 4 ~ieG~~GsGKtT~~~~L~~~ 23 (200)
T cd01672 4 VFEGIDGAGKTTLIELLAER 23 (200)
T ss_pred EEECCCCCCHHHHHHHHHHH
Confidence 36799999999999999765
No 212
>COG0190 FolD 5,10-methylene-tetrahydrofolate dehydrogenase/Methenyl tetrahydrofolate cyclohydrolase [Coenzyme metabolism]
Probab=37.64 E-value=27 Score=26.13 Aligned_cols=18 Identities=22% Similarity=0.361 Sum_probs=14.7
Q ss_pred cCCCC-cccHHHHHHHHHH
Q 035092 7 NAGVE-GTGDVCAVQLITK 24 (73)
Q Consensus 7 I~gVp-GIG~KtA~~LL~~ 24 (73)
|-=|| ||||-|.+-||+.
T Consensus 253 iTPVPGGVGPmTvamLl~N 271 (283)
T COG0190 253 ITPVPGGVGPMTVAMLLEN 271 (283)
T ss_pred cCCCCCccCHHHHHHHHHH
Confidence 44577 9999999999874
No 213
>PRK12339 2-phosphoglycerate kinase; Provisional
Probab=37.22 E-value=27 Score=24.01 Aligned_cols=20 Identities=20% Similarity=0.436 Sum_probs=16.5
Q ss_pred ccCCCCcccHHHHHHHHHHh
Q 035092 6 INAGVEGTGDVCAVQLITKF 25 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~f 25 (73)
-|-|+||.|+-|....|.+.
T Consensus 7 ~i~G~~G~GKst~a~~l~~~ 26 (197)
T PRK12339 7 FIGGIPGVGKTSISGYIARH 26 (197)
T ss_pred EEECCCCCCHHHHHHHHHHh
Confidence 46799999999988877665
No 214
>TIGR00207 fliG flagellar motor switch protein FliG. The fliG protein along with fliM and fliN interact to form the switch complex of the bacterial flagellar motor located at the base of the basal body. This complex interacts with chemotaxis proteins (eg CHEY). In addition the complex interacts with other components of the motor that determine the direction of flagellar rotation. The model contains putative members of the fliG family at scores of less than 100 from Agrobacterium radiobacter and Sinorhizobium meliloti as well as fliG-like genes from treponema pallidum and Borrelia burgdorferi. That is why the suggested cutoff is set at 20 but was set at 100 to construct the family.
Probab=36.85 E-value=63 Score=24.16 Aligned_cols=53 Identities=13% Similarity=0.297 Sum_probs=33.3
Q ss_pred ccHHHHHHHHHHhCC--HHHHHHHhhhhhh---HHHHHHHHHhHHHHHHHHH-hhhHhh
Q 035092 13 TGDVCAVQLITKFGS--LENLLQCVYQVEE---ERTRKALITFADQAVLSKN-LVIIIA 65 (73)
Q Consensus 13 IG~KtA~~LL~~fgs--le~i~~~~~~l~~---~k~~~~L~~~~e~a~ls~~-L~~L~~ 65 (73)
=|.+.+..+|+.... -++|++.+++..+ ..+++.+..+.+...+..+ +..+-.
T Consensus 199 gG~~~~a~ILN~~~~~~~~~il~~L~~~dp~la~~Ir~~mF~Fedl~~ld~~~l~~llr 257 (338)
T TIGR00207 199 GGVRAVAEIINLMDRKTEKTIITSLEEFDPELAEEIKKEMFVFEDIVDLDDRSIQRVLR 257 (338)
T ss_pred ChHHHHHHHHHhCCchHHHHHHHHHHHhCHHHHHHHHHHccCHHHHhcCCHHHHHHHHH
Confidence 478999999999843 3468888876654 3455555555555555444 444433
No 215
>cd01673 dNK Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs). This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1.113), adenosine (EC 2.7.1.76), and thymidine (EC 2.7.1.21) kinases. They are key enzymes in the salvage of deoxyribonucleosides originating from extra- or intracellular breakdown of DNA.
Probab=36.61 E-value=29 Score=22.69 Aligned_cols=20 Identities=15% Similarity=0.293 Sum_probs=17.8
Q ss_pred ccCCCCcccHHHHHHHHHHh
Q 035092 6 INAGVEGTGDVCAVQLITKF 25 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~f 25 (73)
-|.|++|.|+-|..+.|+++
T Consensus 3 ~ieG~~GsGKSTl~~~L~~~ 22 (193)
T cd01673 3 VVEGNIGAGKSTLAKELAEH 22 (193)
T ss_pred EEECCCCCCHHHHHHHHHHH
Confidence 36899999999999999985
No 216
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=36.48 E-value=41 Score=29.42 Aligned_cols=32 Identities=16% Similarity=0.291 Sum_probs=26.1
Q ss_pred ccccCCCCcccHHHHHHHHHH------hCCHHHHHHHh
Q 035092 4 YFINAGVEGTGDVCAVQLITK------FGSLENLLQCV 35 (73)
Q Consensus 4 ~~~I~gVpGIG~KtA~~LL~~------fgsle~i~~~~ 35 (73)
++-+..|+|||+..+..++++ |.|++++....
T Consensus 819 ~~gL~~Ikgvg~~~~~~I~~~R~~~g~f~s~~Df~~R~ 856 (1135)
T PRK05673 819 RYGLGAIKGVGEGAVEAIVEAREEGGPFKDLFDFCARV 856 (1135)
T ss_pred EechhhcCCCCHHHHHHHHHHHHhCCCCCCHHHHHHHh
Confidence 344568999999999999963 89999998664
No 217
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=36.29 E-value=22 Score=28.86 Aligned_cols=20 Identities=10% Similarity=-0.263 Sum_probs=17.4
Q ss_pred cCCCCcccHHHHHHHHHHhC
Q 035092 7 NAGVEGTGDVCAVQLITKFG 26 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fg 26 (73)
|..|||||++.|.++.+.|.
T Consensus 548 L~~v~gi~~~~A~~I~~~l~ 567 (574)
T PRK14670 548 IAEKMKINIKMAKKIKKFAE 567 (574)
T ss_pred HHhCCCCCHHHHHHHHHHHH
Confidence 45799999999999998874
No 218
>PRK03839 putative kinase; Provisional
Probab=36.17 E-value=30 Score=22.52 Aligned_cols=19 Identities=21% Similarity=0.405 Sum_probs=16.1
Q ss_pred cCCCCcccHHHHHHHHHHh
Q 035092 7 NAGVEGTGDVCAVQLITKF 25 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f 25 (73)
+-|.||.|+-|..+.|.+-
T Consensus 5 l~G~pGsGKsT~~~~La~~ 23 (180)
T PRK03839 5 ITGTPGVGKTTVSKLLAEK 23 (180)
T ss_pred EECCCCCCHHHHHHHHHHH
Confidence 5699999999999888763
No 219
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=35.93 E-value=79 Score=27.39 Aligned_cols=32 Identities=16% Similarity=0.364 Sum_probs=26.1
Q ss_pred ccccCCCCcccHHHHHHHHH------HhCCHHHHHHHh
Q 035092 4 YFINAGVEGTGDVCAVQLIT------KFGSLENLLQCV 35 (73)
Q Consensus 4 ~~~I~gVpGIG~KtA~~LL~------~fgsle~i~~~~ 35 (73)
++-+..|+|||+..+..+++ .|.|++++....
T Consensus 752 r~gL~~Ikgvg~~~~~~Iv~~R~~~g~f~s~~Df~~R~ 789 (973)
T PRK07135 752 FLPLIMIKGLGSVAIKKIIDERNKNGKYKNFFDFILRL 789 (973)
T ss_pred EECccccCCcCHHHHHHHHHHHHhCCCCCCHHHHHHhc
Confidence 34456899999999999995 399999998664
No 220
>PTZ00035 Rad51 protein; Provisional
Probab=35.89 E-value=1.2e+02 Score=22.59 Aligned_cols=28 Identities=11% Similarity=0.054 Sum_probs=22.9
Q ss_pred ccCCC--CcccHHHHHHHHHH-hCCHHHHHH
Q 035092 6 INAGV--EGTGDVCAVQLITK-FGSLENLLQ 33 (73)
Q Consensus 6 ~I~gV--pGIG~KtA~~LL~~-fgsle~i~~ 33 (73)
.|..+ |||||..+.+|-+. |.|++++..
T Consensus 22 ~~~~l~~~g~~~~~~~kL~~~g~~t~~~~~~ 52 (337)
T PTZ00035 22 EIEKLQSAGINAADIKKLKEAGICTVESVAY 52 (337)
T ss_pred cHHHHhcCCCCHHHHHHHHHcCCCcHHHHHh
Confidence 34445 88999999999877 899999874
No 221
>PRK14178 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=35.58 E-value=34 Score=25.29 Aligned_cols=19 Identities=21% Similarity=0.324 Sum_probs=14.8
Q ss_pred ccCCCC-cccHHHHHHHHHH
Q 035092 6 INAGVE-GTGDVCAVQLITK 24 (73)
Q Consensus 6 ~I~gVp-GIG~KtA~~LL~~ 24 (73)
.|..|| ||||.|..-|++.
T Consensus 247 ~iTPVPGGVGp~T~a~L~~N 266 (279)
T PRK14178 247 AITPVPGGVGPMTIATLMEN 266 (279)
T ss_pred CcCCCCCCCHHHHHHHHHHH
Confidence 455555 5999999999876
No 222
>TIGR03191 benz_CoA_bzdO benzoyl-CoA reductase, bzd-type, O subunit. Members of this family are the O subunit of one of two related types of four-subunit ATP-dependent benzoyl-CoA reductase. This enzyme system catalyzes the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for a number of different aromatic compounds, such as phenol and toluene.
Probab=35.17 E-value=1.9e+02 Score=22.38 Aligned_cols=58 Identities=7% Similarity=-0.035 Sum_probs=39.4
Q ss_pred ccHHHHHHHHHHhCCHHHHHHHh--hhhhhHHHHHHHHHhHHHHHHHHHhhhHhhcCccc
Q 035092 13 TGDVCAVQLITKFGSLENLLQCV--YQVEEERTRKALITFADQAVLSKNLVIIIAFSSTC 70 (73)
Q Consensus 13 IG~KtA~~LL~~fgsle~i~~~~--~~l~~~k~~~~L~~~~e~a~ls~~L~~L~~~~~~~ 70 (73)
..+....-+.+++..+...++.. ..+...++++.+.+.......-+++..++..-|..
T Consensus 152 ~~~~~~~Y~~~ql~~l~~~LEe~tG~kit~e~L~eaI~n~nr~~~~~~e~~~l~~~~P~P 211 (430)
T TIGR03191 152 LTDARLDYVANQLHDGIEFVEKASGRKCDDELFIKAIKNEMRSTARWADICALNKAKPAP 211 (430)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCC
Confidence 46777777888877666666543 33445788888886555555666788887766653
No 223
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=34.73 E-value=23 Score=26.77 Aligned_cols=25 Identities=20% Similarity=0.187 Sum_probs=17.5
Q ss_pred cCCCCcccHHHHHHHHHHh--CCHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITKF--GSLENLL 32 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f--gsle~i~ 32 (73)
|..+||||++++.+| +++ .|+-++.
T Consensus 181 v~~l~GiG~~~~~~L-~~lGi~TigdL~ 207 (422)
T PRK03609 181 VEEVWGVGRRISKKL-NAMGIKTALDLA 207 (422)
T ss_pred hhhcCCccHHHHHHH-HHcCCCcHHHHh
Confidence 347899999999888 444 3555554
No 224
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=34.46 E-value=1e+02 Score=20.65 Aligned_cols=26 Identities=31% Similarity=0.310 Sum_probs=21.7
Q ss_pred ccHHHHHHHHHHhCCHHHHHHHhhhh
Q 035092 13 TGDVCAVQLITKFGSLENLLQCVYQV 38 (73)
Q Consensus 13 IG~KtA~~LL~~fgsle~i~~~~~~l 38 (73)
=|++.|..+++.+..++.++.+.-.+
T Consensus 67 ~G~~~a~~~~r~hrlle~fL~~~lg~ 92 (154)
T COG1321 67 KGREKAKELLRKHRLLERFLVDVLGL 92 (154)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 38999999999999999999764333
No 225
>TIGR00594 polc DNA-directed DNA polymerase III (polc). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=33.87 E-value=85 Score=27.15 Aligned_cols=31 Identities=23% Similarity=0.446 Sum_probs=25.3
Q ss_pred cccCCCCcccHHHHHHHHHH------hCCHHHHHHHh
Q 035092 5 FINAGVEGTGDVCAVQLITK------FGSLENLLQCV 35 (73)
Q Consensus 5 ~~I~gVpGIG~KtA~~LL~~------fgsle~i~~~~ 35 (73)
+-...|+|||+..+..++++ |.|++++....
T Consensus 824 ~gl~~Ikgig~~~~~~Iv~~R~~~~~f~s~~Df~~R~ 860 (1022)
T TIGR00594 824 YGLGAIKGVGESVVKSIIEERNKNGPFKSLFDFINRV 860 (1022)
T ss_pred echhhcCCCCHHHHHHHHHHHHhCCCCCCHHHHHHHh
Confidence 34567999999999999962 89999988654
No 226
>PRK01216 DNA polymerase IV; Validated
Probab=33.82 E-value=28 Score=26.09 Aligned_cols=26 Identities=35% Similarity=0.546 Sum_probs=18.1
Q ss_pred cCCCCcccHHHHHHHHHHh--CCHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITKF--GSLENLLQ 33 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f--gsle~i~~ 33 (73)
|..+||||++++.+| +.+ .++.++.+
T Consensus 180 i~~l~giG~~~~~~L-~~~Gi~TigdL~~ 207 (351)
T PRK01216 180 IADIPGIGDITAEKL-KKLGVNKLVDTLR 207 (351)
T ss_pred cccccCCCHHHHHHH-HHcCCCcHHHHhc
Confidence 458899999998766 555 45555543
No 227
>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.
Probab=33.53 E-value=39 Score=21.08 Aligned_cols=19 Identities=21% Similarity=0.344 Sum_probs=16.5
Q ss_pred cCCCCcccHHHHHHHHHHh
Q 035092 7 NAGVEGTGDVCAVQLITKF 25 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f 25 (73)
+-|.||.|+.|-.+.|.+.
T Consensus 4 l~G~~GsGKST~a~~l~~~ 22 (150)
T cd02021 4 VMGVSGSGKSTVGKALAER 22 (150)
T ss_pred EEcCCCCCHHHHHHHHHhh
Confidence 5699999999999888875
No 228
>PRK13976 thymidylate kinase; Provisional
Probab=33.24 E-value=35 Score=23.57 Aligned_cols=20 Identities=20% Similarity=0.624 Sum_probs=17.6
Q ss_pred ccCCCCcccHHHHHHHHHHh
Q 035092 6 INAGVEGTGDVCAVQLITKF 25 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~f 25 (73)
-+.|+.|-|+-|-.++|.++
T Consensus 4 v~EGiDGsGKsTq~~~L~~~ 23 (209)
T PRK13976 4 TFEGIDGSGKTTQSRLLAEY 23 (209)
T ss_pred EEECCCCCCHHHHHHHHHHH
Confidence 36899999999999998875
No 229
>PRK01151 rps17E 30S ribosomal protein S17e; Validated
Probab=33.23 E-value=1e+02 Score=17.85 Aligned_cols=37 Identities=19% Similarity=0.368 Sum_probs=22.3
Q ss_pred HHHHHHHHHHhCCHHH--------HHHHhhhhhhHHHHHHHHHhH
Q 035092 15 DVCAVQLITKFGSLEN--------LLQCVYQVEEERTRKALITFA 51 (73)
Q Consensus 15 ~KtA~~LL~~fgsle~--------i~~~~~~l~~~k~~~~L~~~~ 51 (73)
.+.|..|+++|.+.-. +++.+..++.++++.++..+.
T Consensus 9 Kr~a~~lieky~~~ft~DFe~NK~~v~e~a~i~SK~lRNrIAGYi 53 (58)
T PRK01151 9 KRTAEELLEKYPDLFTTDFETNKKLVEELTNIESKKVRNRIAGYI 53 (58)
T ss_pred HHHHHHHHHHhHHHhcccHHHHHHHHHHHhcCccHhHHHHHhhhh
Confidence 4678899999866321 222233344567787777654
No 230
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=33.09 E-value=18 Score=27.51 Aligned_cols=22 Identities=18% Similarity=0.252 Sum_probs=14.7
Q ss_pred CCCcccHHHHHH-HHHHhCCHHH
Q 035092 9 GVEGTGDVCAVQ-LITKFGSLEN 30 (73)
Q Consensus 9 gVpGIG~KtA~~-LL~~fgsle~ 30 (73)
-+||||+|.|-= +|..++..+.
T Consensus 222 ~lpGVG~KVADCI~Lm~l~~~~~ 244 (323)
T KOG2875|consen 222 SLPGVGPKVADCICLMSLDKLSA 244 (323)
T ss_pred cCCCCcchHhhhhhhhhcCCCCc
Confidence 479999999864 4455555443
No 231
>PRK13975 thymidylate kinase; Provisional
Probab=32.86 E-value=39 Score=22.03 Aligned_cols=20 Identities=20% Similarity=0.564 Sum_probs=17.6
Q ss_pred ccCCCCcccHHHHHHHHHHh
Q 035092 6 INAGVEGTGDVCAVQLITKF 25 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~f 25 (73)
-|.|++|.|+-|-.++|++.
T Consensus 6 ~ieG~~GsGKtT~~~~L~~~ 25 (196)
T PRK13975 6 VFEGIDGSGKTTQAKLLAEK 25 (196)
T ss_pred EEECCCCCCHHHHHHHHHHH
Confidence 46899999999999998875
No 232
>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=32.78 E-value=86 Score=22.38 Aligned_cols=25 Identities=12% Similarity=-0.109 Sum_probs=17.0
Q ss_pred CCCcccHHHHHHHHHHh-CCHHHHHH
Q 035092 9 GVEGTGDVCAVQLITKF-GSLENLLQ 33 (73)
Q Consensus 9 gVpGIG~KtA~~LL~~f-gsle~i~~ 33 (73)
+++|||++++.+|-+-- .++.++.+
T Consensus 174 ~~~gig~~~~~~L~~~Gi~t~~dl~~ 199 (335)
T cd03468 174 AALRLPPETVELLARLGLRTLGDLAA 199 (335)
T ss_pred hHhCCCHHHHHHHHHhCcccHHHHHh
Confidence 69999999988875431 34544443
No 233
>PF05427 FIBP: Acidic fibroblast growth factor binding (FIBP) ; InterPro: IPR008614 Acidic fibroblast growth factor (aFGF) intracellular binding protein (FIBP) is a protein found mainly in the nucleus that is thought to be involved in the intracellular function of aFGF [].; GO: 0017134 fibroblast growth factor binding
Probab=32.31 E-value=30 Score=26.76 Aligned_cols=40 Identities=10% Similarity=0.283 Sum_probs=30.9
Q ss_pred CCCcccHHHHHHHHH---HhCCHHHHHHHhhhhhhHHHHHHHHH
Q 035092 9 GVEGTGDVCAVQLIT---KFGSLENLLQCVYQVEEERTRKALIT 49 (73)
Q Consensus 9 gVpGIG~KtA~~LL~---~fgsle~i~~~~~~l~~~k~~~~L~~ 49 (73)
+..+|.+||...|-. +|.+++++....++++| .+...|.+
T Consensus 118 dLdevsekt~i~l~ScrRQfDN~kri~k~ved~~g-~~~~nIq~ 160 (361)
T PF05427_consen 118 DLDEVSEKTGIRLKSCRRQFDNLKRIFKAVEDMPG-PLVDNIQQ 160 (361)
T ss_pred cHHHHHHHhCCchhhhhhhhhcHHHHHHHHHhCCC-cHHHHHHH
Confidence 456677888777776 99999999999999988 35555544
No 234
>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]
Probab=31.96 E-value=21 Score=26.78 Aligned_cols=30 Identities=7% Similarity=0.120 Sum_probs=26.0
Q ss_pred cccccCCCCcccHHHHHHHHHHhCCHHHHHHH
Q 035092 3 FYFINAGVEGTGDVCAVQLITKFGSLENLLQC 34 (73)
Q Consensus 3 ~~~~I~gVpGIG~KtA~~LL~~fgsle~i~~~ 34 (73)
|+|||| |..-|.+.+.+|..||-+-+++-.
T Consensus 78 ylS~IP--p~m~~~rlReil~~yGeVGRvylq 107 (278)
T KOG3152|consen 78 YLSNIP--PYMDPVRLREILSQYGEVGRVYLQ 107 (278)
T ss_pred EeccCC--CccCHHHHHHHHHhccccceEEec
Confidence 578888 788899999999999999998733
No 235
>COG0125 Tmk Thymidylate kinase [Nucleotide transport and metabolism]
Probab=31.12 E-value=40 Score=23.66 Aligned_cols=20 Identities=20% Similarity=0.551 Sum_probs=17.8
Q ss_pred ccCCCCcccHHHHHHHHHHh
Q 035092 6 INAGVEGTGDVCAVQLITKF 25 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~f 25 (73)
-|.|+.|-|+-|..++|.++
T Consensus 7 ~iEGiDGaGKTT~~~~L~~~ 26 (208)
T COG0125 7 VIEGIDGAGKTTQAELLKER 26 (208)
T ss_pred EEECCCCCCHHHHHHHHHHH
Confidence 36899999999999999875
No 236
>PRK05898 dnaE DNA polymerase III DnaE; Validated
Probab=31.00 E-value=63 Score=28.05 Aligned_cols=31 Identities=16% Similarity=0.276 Sum_probs=24.4
Q ss_pred ccccCCCCcccHHHHHHHHHH-----hCCHHHHHHH
Q 035092 4 YFINAGVEGTGDVCAVQLITK-----FGSLENLLQC 34 (73)
Q Consensus 4 ~~~I~gVpGIG~KtA~~LL~~-----fgsle~i~~~ 34 (73)
++-+..|+|||+..+..+++. |.|+.++...
T Consensus 751 r~gL~~Ikgig~~~~~~I~~~R~~g~f~~~~df~~r 786 (971)
T PRK05898 751 RFGFNTIKGFGDELLKKIKSALQNKTFSDFISYIDA 786 (971)
T ss_pred EecchhcCCcCHHHHHHHHHHHhcCCCCCHHHHHHH
Confidence 344568999999999999974 8888777643
No 237
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=30.91 E-value=31 Score=27.99 Aligned_cols=28 Identities=25% Similarity=0.363 Sum_probs=19.7
Q ss_pred cccCCCCcccHHHHHHHHHHh--CCHHHHHH
Q 035092 5 FINAGVEGTGDVCAVQLITKF--GSLENLLQ 33 (73)
Q Consensus 5 ~~I~gVpGIG~KtA~~LL~~f--gsle~i~~ 33 (73)
..+..++|||||+|..| ++. .|+.+++-
T Consensus 9 ~~~~~l~gvg~~~~~~l-~~lgi~t~~dll~ 38 (681)
T PRK10917 9 APLTSLKGVGPKTAEKL-AKLGIHTVQDLLL 38 (681)
T ss_pred CChhhcCCCCHHHHHHH-HHcCCCCHHHHhh
Confidence 35667899999997766 455 46666654
No 238
>PRK04040 adenylate kinase; Provisional
Probab=30.18 E-value=44 Score=22.61 Aligned_cols=18 Identities=22% Similarity=0.385 Sum_probs=14.7
Q ss_pred cCCCCcccHHHHHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITK 24 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~ 24 (73)
+-|+||.|+-|..+.|.+
T Consensus 7 v~G~pG~GKtt~~~~l~~ 24 (188)
T PRK04040 7 VTGVPGVGKTTVLNKALE 24 (188)
T ss_pred EEeCCCCCHHHHHHHHHH
Confidence 469999999998876644
No 239
>COG1536 FliG Flagellar motor switch protein [Cell motility and secretion]
Probab=30.13 E-value=1.8e+02 Score=22.10 Aligned_cols=49 Identities=14% Similarity=0.266 Sum_probs=32.1
Q ss_pred CCCCcccHHHHHHHHHHhC--CHHHHHHHhhhhhh---HHHHHHHHHhHHHHHH
Q 035092 8 AGVEGTGDVCAVQLITKFG--SLENLLQCVYQVEE---ERTRKALITFADQAVL 56 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~~fg--sle~i~~~~~~l~~---~k~~~~L~~~~e~a~l 56 (73)
...+.-|.+++.++|+... +.+++++++++..+ .++++++..+.+...+
T Consensus 197 ~~~~~gg~~~~aeIlN~~d~~~e~~il~~l~~~~~~la~~I~~kmF~Fediv~l 250 (339)
T COG1536 197 DYSKLGGIKAAAEILNLLDRGTEKTILESLEEEDPELAEEIKEKMFVFEDIVLL 250 (339)
T ss_pred cccccccHhHHHHHHHhcchhHHHHHHHHHhhcCHHHHHHHHHHHhhHHHHHhc
Confidence 4556778899999999985 55667788766433 2455555545444444
No 240
>PF02764 Diphtheria_T: Diphtheria toxin, T domain; InterPro: IPR022405 Diphtheria toxin (2.4.2.36 from EC) is a 58 kDa protein secreted by lysogenic strains of Corynebacterium diphtheriae. The toxin causes the disease diphtheria in humans by gaining entry into the cell cytoplasm and inhibiting protein synthesis []. The mechanism of inhibition involves transfer of the ADP-ribose group of NAD to elongation factor-2 (EF-2), rendering EF-2 inactive. The catalysed reaction is as follows: NAD+ + peptide diphthamide = nicotinamide + peptide N-(ADP-D-ribosyl)diphthamide The crystal structure of the diphtheria toxin homodimer has been determined to 2.5A resolution []. The structure reveals a Y-shaped molecule of 3 domains, a catalytic domain (fragment A), whose fold is of the alpha + beta type; a transmembrane (TM) domain, which consists of 9 alpha-helices, 2 pairs of which may participate in pH-triggered membrane insertion and translocation; and a receptor-binding domain, which forms a flattened beta-barrel with a jelly-roll-like topology []. The TM- and receptor binding-domains together constitute fragment B. This entry represents the translocation domain (also known as the T domain) found as the central domain in the Diphtheria toxin protein. The T domain has a multi-helical globin-like fold with two additional helices at N-termini, but which has no counterpart to the first globin helix. This domain is thought to unfold in the membrane []. pH-induced conformational change in the T domain triggers insertion into the endosomal membrane and facilitates the transfer of the catalytic domain into the cytoplasm [, ].; PDB: 1MDT_B 1SGK_A 1F0L_B 1DDT_A 1TOX_B 4AE0_A 1XDT_T 4AE1_A.
Probab=29.68 E-value=82 Score=21.76 Aligned_cols=54 Identities=19% Similarity=0.298 Sum_probs=36.0
Q ss_pred HHHHHHHHHhCCHHHHHH-Hh-hhhhhHHHHHHHHHhHHHHHHHHHhhhHhhcCcc
Q 035092 16 VCAVQLITKFGSLENLLQ-CV-YQVEEERTRKALITFADQAVLSKNLVIIIAFSST 69 (73)
Q Consensus 16 KtA~~LL~~fgsle~i~~-~~-~~l~~~k~~~~L~~~~e~a~ls~~L~~L~~~~~~ 69 (73)
||..+-|+++|.+.+-+. +. ..++.++-++-++++-..+.--.+|..|+|-+-|
T Consensus 15 ktkieslkehgpiknkmsespnktvseekakqyleefhqtalehpelselktvtgt 70 (180)
T PF02764_consen 15 KTKIESLKEHGPIKNKMSESPNKTVSEEKAKQYLEEFHQTALEHPELSELKTVTGT 70 (180)
T ss_dssp HHHHHHHHH-HHHHHHHHTS--S---HHHHHHHHHHHHHHHTTSGGGHHHHHHTSS
T ss_pred HhHHHHHHhcCCcccccccCCcchhhHHHHHHHHHHHHHHHhcCchhhhhhhccCC
Confidence 455666888898888764 33 3456667777788877778778888888876654
No 241
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=29.40 E-value=55 Score=21.39 Aligned_cols=18 Identities=22% Similarity=0.440 Sum_probs=15.2
Q ss_pred CCCcccHHHHHHHHHHhC
Q 035092 9 GVEGTGDVCAVQLITKFG 26 (73)
Q Consensus 9 gVpGIG~KtA~~LL~~fg 26 (73)
+..|+.||.+++++++.|
T Consensus 1 ~~~~~nprk~rkmmkkmG 18 (115)
T PRK06369 1 GMGGMNPRKMKQMMKQMG 18 (115)
T ss_pred CCCCCCHHHHHHHHHHcC
Confidence 357889999999999987
No 242
>PRK14180 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=29.18 E-value=46 Score=24.69 Aligned_cols=19 Identities=21% Similarity=0.326 Sum_probs=15.4
Q ss_pred ccCCCC-cccHHHHHHHHHH
Q 035092 6 INAGVE-GTGDVCAVQLITK 24 (73)
Q Consensus 6 ~I~gVp-GIG~KtA~~LL~~ 24 (73)
.|-=|| ||||-|..-|++.
T Consensus 253 ~iTPVPGGVGp~T~a~L~~N 272 (282)
T PRK14180 253 AITPVPGGVGPMTITELLYN 272 (282)
T ss_pred EeccCCCChhHHHHHHHHHH
Confidence 455577 9999999999875
No 243
>PF13543 KSR1-SAM: SAM like domain present in kinase suppressor RAS 1
Probab=29.09 E-value=1.5e+02 Score=19.73 Aligned_cols=31 Identities=26% Similarity=0.304 Sum_probs=25.2
Q ss_pred CCcccHHHHHHHHHHhCCHHHHHH-Hhhhhhh
Q 035092 10 VEGTGDVCAVQLITKFGSLENLLQ-CVYQVEE 40 (73)
Q Consensus 10 VpGIG~KtA~~LL~~fgsle~i~~-~~~~l~~ 40 (73)
|-|+-|-....++.+.-|+|.+++ +.+++..
T Consensus 75 vVgl~~~~i~~i~~~~~tLe~Llemsd~el~~ 106 (129)
T PF13543_consen 75 VVGLRPESIQAILSKVLTLEALLEMSDEELKE 106 (129)
T ss_pred hcCCCHHHHHHHHHhhcCHHHHHhCCHHHHHH
Confidence 568999999999999999999986 3455544
No 244
>PF02223 Thymidylate_kin: Thymidylate kinase; InterPro: IPR018094 Thymidylate kinase (2.7.4.9 from EC; dTMP kinase) catalyzes the phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) in the presence of ATP and magnesium: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate Thymidylate kinase is an ubiquitous enzyme of about 25 Kd and is important in the dTTP synthesis pathway for DNA synthesis. The function of dTMP kinase in eukaryotes comes from the study of a cell cycle mutant, cdc8, in Saccharomyces cerevisiae. Structural and functional analyses suggest that the cDNA codes for authentic human dTMP kinase. The mRNA levels and enzyme activities corresponded to cell cycle progression and cell growth stages[]. ; GO: 0004798 thymidylate kinase activity, 0005524 ATP binding, 0006233 dTDP biosynthetic process; PDB: 2PLR_B 1NMX_A 1NN0_A 2XX3_A 1NN3_A 1E9F_A 1E2Q_A 1E2D_A 1E9A_A 1E99_A ....
Probab=29.03 E-value=39 Score=22.04 Aligned_cols=19 Identities=21% Similarity=0.609 Sum_probs=16.5
Q ss_pred cCCCCcccHHHHHHHHHHh
Q 035092 7 NAGVEGTGDVCAVQLITKF 25 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f 25 (73)
+.|+.|-|+-|..++|.+.
T Consensus 1 ~EGiDGsGKtT~~~~L~~~ 19 (186)
T PF02223_consen 1 FEGIDGSGKTTQIRLLAEA 19 (186)
T ss_dssp EEESTTSSHHHHHHHHHHH
T ss_pred CCCCCCCCHHHHHHHHHHH
Confidence 4799999999999998864
No 245
>PRK07758 hypothetical protein; Provisional
Probab=28.80 E-value=50 Score=21.01 Aligned_cols=18 Identities=17% Similarity=0.169 Sum_probs=13.2
Q ss_pred cCCCCcccHHHHHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITK 24 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~ 24 (73)
+..++|+|+|+..+|-++
T Consensus 69 Ll~iknlGkKSL~EIkek 86 (95)
T PRK07758 69 ILKLHGMGPASLPKLRKA 86 (95)
T ss_pred HHHccCCCHHHHHHHHHH
Confidence 456899999988776543
No 246
>PRK10925 superoxide dismutase; Provisional
Probab=28.32 E-value=83 Score=21.99 Aligned_cols=23 Identities=17% Similarity=0.208 Sum_probs=18.7
Q ss_pred ccHHHHHHHHHHhCCHHHHHHHh
Q 035092 13 TGDVCAVQLITKFGSLENLLQCV 35 (73)
Q Consensus 13 IG~KtA~~LL~~fgsle~i~~~~ 35 (73)
.+.+.+..+=+.|||+|++.+..
T Consensus 95 p~g~L~~~I~~~FGS~d~fk~~f 117 (206)
T PRK10925 95 LQGDLKAAIERDFGSVDNFKAEF 117 (206)
T ss_pred CCHHHHHHHHHHhCCHHHHHHHH
Confidence 35678888888999999998664
No 247
>PRK08356 hypothetical protein; Provisional
Probab=28.31 E-value=50 Score=21.97 Aligned_cols=22 Identities=14% Similarity=0.191 Sum_probs=18.7
Q ss_pred cccCCCCcccHHHHHHHHHHhC
Q 035092 5 FINAGVEGTGDVCAVQLITKFG 26 (73)
Q Consensus 5 ~~I~gVpGIG~KtA~~LL~~fg 26 (73)
..+-|-||-|+-|..+.|++++
T Consensus 8 i~~~G~~gsGK~t~a~~l~~~g 29 (195)
T PRK08356 8 VGVVGKIAAGKTTVAKFFEEKG 29 (195)
T ss_pred EEEECCCCCCHHHHHHHHHHCC
Confidence 3467999999999999998874
No 248
>TIGR00255 conserved hypothetical protein TIGR00255. The apparent ortholog from Aquifex aeolicus as reported is split into two consecutive reading frames.
Probab=28.26 E-value=1.4e+02 Score=22.06 Aligned_cols=22 Identities=14% Similarity=0.327 Sum_probs=11.6
Q ss_pred cHHHHHHHHHHhCCHHHHHHHh
Q 035092 14 GDVCAVQLITKFGSLENLLQCV 35 (73)
Q Consensus 14 G~KtA~~LL~~fgsle~i~~~~ 35 (73)
|+..+..|......+++.++.+
T Consensus 152 G~~L~~dl~~rl~~i~~~v~~i 173 (291)
T TIGR00255 152 GENLKSDIVQRLDLIEREVKKV 173 (291)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4455555555555555555443
No 249
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=27.98 E-value=78 Score=24.81 Aligned_cols=41 Identities=20% Similarity=0.416 Sum_probs=29.6
Q ss_pred ccc------HHHHHHHHHHhCCHHHHHH--Hhhhhhh--HHHHHHHHHhHH
Q 035092 12 GTG------DVCAVQLITKFGSLENLLQ--CVYQVEE--ERTRKALITFAD 52 (73)
Q Consensus 12 GIG------~KtA~~LL~~fgsle~i~~--~~~~l~~--~k~~~~L~~~~e 52 (73)
|.| +.+=.+|.++|||=-+++- .++++.. +++++.|..+++
T Consensus 315 g~gi~tK~V~~~we~lv~~FGtEi~vLi~a~~e~La~V~~~vA~aI~~~R~ 365 (403)
T COG1379 315 GKGITTKAVKRTWERLVRAFGTEIDVLIDAPIEELARVDPKVAEAIVAFRN 365 (403)
T ss_pred ccceechhHHHHHHHHHHHhcchhhhHhcCCHHHHhhhhHHHHHHHHHHhc
Confidence 888 8888999999999777762 2566643 467777666543
No 250
>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=27.86 E-value=66 Score=16.59 Aligned_cols=17 Identities=29% Similarity=0.477 Sum_probs=12.6
Q ss_pred CCCCcccHHHHHHHHHH
Q 035092 8 AGVEGTGDVCAVQLITK 24 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~~ 24 (73)
-+++|+++.++.+++..
T Consensus 29 ~~i~g~~~e~a~~ii~~ 45 (50)
T TIGR01954 29 LSIEGFDEETAKELINR 45 (50)
T ss_pred hcCCCCCHHHHHHHHHH
Confidence 35788888888887654
No 251
>PRK11820 hypothetical protein; Provisional
Probab=27.61 E-value=1.4e+02 Score=22.04 Aligned_cols=24 Identities=17% Similarity=0.380 Sum_probs=13.3
Q ss_pred cHHHHHHHHHHhCCHHHHHHHhhh
Q 035092 14 GDVCAVQLITKFGSLENLLQCVYQ 37 (73)
Q Consensus 14 G~KtA~~LL~~fgsle~i~~~~~~ 37 (73)
|+..+..|......++++.+.+++
T Consensus 150 G~~L~~dl~~rl~~i~~~~~~i~~ 173 (288)
T PRK11820 150 GAALKADLLQRLDAIEALVAKIEA 173 (288)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455555566666666655544433
No 252
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=27.35 E-value=1.5e+02 Score=21.01 Aligned_cols=45 Identities=13% Similarity=0.209 Sum_probs=31.5
Q ss_pred CHHHHHHHhhhhhh--HHHHHHHHH------hHHHHHHHHHhhhHhhcCcccc
Q 035092 27 SLENLLQCVYQVEE--ERTRKALIT------FADQAVLSKNLVIIIAFSSTCY 71 (73)
Q Consensus 27 sle~i~~~~~~l~~--~k~~~~L~~------~~e~a~ls~~L~~L~~~~~~~~ 71 (73)
+++++.+.+..+++ +|-++++.- ..+...+++.|..++.....|-
T Consensus 5 ~~~~Li~~l~~LPGIG~KsA~RlA~~ll~~~~~~~~~la~ai~~~~~~i~~C~ 57 (195)
T TIGR00615 5 PISKLIESLKKLPGIGPKSAQRLAFHLLKRDPSEVLRLAQALLEAKENLRTCS 57 (195)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHcCCcCC
Confidence 47778888888876 555555533 2345667888888888887773
No 253
>COG5241 RAD10 Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, and repair]
Probab=27.35 E-value=59 Score=23.52 Aligned_cols=26 Identities=8% Similarity=-0.077 Sum_probs=22.9
Q ss_pred cCCCCcccHHHHHHHHHHhCCHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITKFGSLENLL 32 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fgsle~i~ 32 (73)
.--|+||-..-+..+|..||+++...
T Consensus 169 l~~i~~Vnksds~~~L~d~g~L~rf~ 194 (224)
T COG5241 169 LILIFIVNKSDSEDTLNDIGKLCRFN 194 (224)
T ss_pred eEEEEeeccccHHHHHHHHHHHHHHh
Confidence 34578899999999999999999987
No 254
>PLN02685 iron superoxide dismutase
Probab=26.86 E-value=84 Score=23.62 Aligned_cols=22 Identities=18% Similarity=0.267 Sum_probs=18.2
Q ss_pred cHHHHHHHHHHhCCHHHHHHHh
Q 035092 14 GDVCAVQLITKFGSLENLLQCV 35 (73)
Q Consensus 14 G~KtA~~LL~~fgsle~i~~~~ 35 (73)
+.+.+..|-+.|||++++.+..
T Consensus 139 ~g~L~~aI~~~FGS~d~FK~~F 160 (299)
T PLN02685 139 SGELLQLIERDFGSFERFVEEF 160 (299)
T ss_pred CHHHHHHHHHHhCCHHHHHHHH
Confidence 4578888999999999998654
No 255
>PRK14194 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=26.80 E-value=53 Score=24.55 Aligned_cols=18 Identities=22% Similarity=0.313 Sum_probs=14.6
Q ss_pred cCCCC-cccHHHHHHHHHH
Q 035092 7 NAGVE-GTGDVCAVQLITK 24 (73)
Q Consensus 7 I~gVp-GIG~KtA~~LL~~ 24 (73)
|-=|| ||||-|..-|++.
T Consensus 259 iTPVPGGVGp~Tva~L~~N 277 (301)
T PRK14194 259 ITPVPGGVGPMTIAFLMKN 277 (301)
T ss_pred ecCCCCchhHHHHHHHHHH
Confidence 34467 9999999999875
No 256
>PTZ00078 Superoxide dismutase [Fe]; Provisional
Probab=26.61 E-value=87 Score=21.64 Aligned_cols=21 Identities=24% Similarity=0.325 Sum_probs=17.2
Q ss_pred HHHHHHHHHHhCCHHHHHHHh
Q 035092 15 DVCAVQLITKFGSLENLLQCV 35 (73)
Q Consensus 15 ~KtA~~LL~~fgsle~i~~~~ 35 (73)
.+.+..+=+.|||+|++.+..
T Consensus 86 g~L~~~I~~~FGS~d~fk~~f 106 (193)
T PTZ00078 86 GEIKEKIDEKFGSFDNFKNEF 106 (193)
T ss_pred hHHHHHHHHHhCCHHHHHHHH
Confidence 467788888899999998654
No 257
>PRK03348 DNA polymerase IV; Provisional
Probab=26.49 E-value=44 Score=25.82 Aligned_cols=25 Identities=20% Similarity=0.324 Sum_probs=17.8
Q ss_pred cCCCCcccHHHHHHHHHHh--CCHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITKF--GSLENLL 32 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f--gsle~i~ 32 (73)
+..+||||++++.+| +.+ .++.++.
T Consensus 182 v~~L~GIG~~t~~~L-~~lGI~TigDLa 208 (454)
T PRK03348 182 VRRLWGIGPVTEEKL-HRLGIETIGDLA 208 (454)
T ss_pred ccccCCCCHHHHHHH-HHcCCccHHHHh
Confidence 458899999999887 555 3555554
No 258
>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]
Probab=26.44 E-value=1.3e+02 Score=20.84 Aligned_cols=48 Identities=10% Similarity=0.086 Sum_probs=30.8
Q ss_pred CCCCcccHHHHHHHHHH-----hCCHHHHHHHhhhhhhHHHHHHHHHhHHHHHHHH
Q 035092 8 AGVEGTGDVCAVQLITK-----FGSLENLLQCVYQVEEERTRKALITFADQAVLSK 58 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~~-----fgsle~i~~~~~~l~~~k~~~~L~~~~e~a~ls~ 58 (73)
=|.+|.|+-|.-+.|.+ |-+.+..++... +..+++.+.++.|..+...
T Consensus 8 iG~mGaGKSTIGr~LAk~L~~~F~D~D~~Ie~~~---g~sI~eIF~~~GE~~FR~~ 60 (172)
T COG0703 8 IGFMGAGKSTIGRALAKALNLPFIDTDQEIEKRT---GMSIAEIFEEEGEEGFRRL 60 (172)
T ss_pred EcCCCCCHhHHHHHHHHHcCCCcccchHHHHHHH---CcCHHHHHHHHhHHHHHHH
Confidence 48999999999999975 455555554322 1235566666666655543
No 259
>TIGR01366 serC_3 phosphoserine aminotransferase, putative. This model represents a putative variant form of the serine biosynthesis enzyme phosphoserine aminotransferase, as found in Mycobacterium tuberculosis and related high-GC Gram-positive bacteria.
Probab=26.37 E-value=1.3e+02 Score=22.17 Aligned_cols=44 Identities=7% Similarity=-0.026 Sum_probs=28.5
Q ss_pred cccCCCCcc-cHHHHHHHHHHhCCHHHHHHHhhhhhhHHHHHHHHH
Q 035092 5 FINAGVEGT-GDVCAVQLITKFGSLENLLQCVYQVEEERTRKALIT 49 (73)
Q Consensus 5 ~~I~gVpGI-G~KtA~~LL~~fgsle~i~~~~~~l~~~k~~~~L~~ 49 (73)
.|.|++.++ |=..|.+.+.+-|.++++.+..+++.. .+.+.+.+
T Consensus 235 ~~tp~i~~i~~l~~al~~l~~~gg~e~~~~r~~~l~~-~l~~~l~~ 279 (361)
T TIGR01366 235 YNTPAIATLALLAEQIDWMNGNGGLDWAVARTADSSS-RLYSWAQE 279 (361)
T ss_pred CCCchHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHH-HHHHHHHh
Confidence 466677766 677788888887778888766555543 34434433
No 260
>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=26.35 E-value=1.9e+02 Score=20.40 Aligned_cols=28 Identities=14% Similarity=0.105 Sum_probs=18.7
Q ss_pred cCCCCcccHHHHHHHHHHh-CCHHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITKF-GSLENLLQC 34 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f-gsle~i~~~ 34 (73)
.--+||||++.+.+|-+.- .+++++.+.
T Consensus 150 L~Qlp~i~~~~~~~l~~~~i~~l~~l~~~ 178 (314)
T PF02889_consen 150 LLQLPHIGEESLKKLEKRGIKTLQDLRDL 178 (314)
T ss_dssp GGGSTT--HHHHHHHHHTT--SHHHHHHS
T ss_pred hhcCCCCCHHHHHHHhccCCCcHHHHhhC
Confidence 3468999999998888743 478888753
No 261
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=26.20 E-value=1e+02 Score=15.75 Aligned_cols=25 Identities=8% Similarity=0.132 Sum_probs=17.1
Q ss_pred CCcccHHHHHHHHHHh-CCHHHHHHH
Q 035092 10 VEGTGDVCAVQLITKF-GSLENLLQC 34 (73)
Q Consensus 10 VpGIG~KtA~~LL~~f-gsle~i~~~ 34 (73)
.|.+++......|+++ +++|...+.
T Consensus 12 FP~~~~~~I~~~L~~~~~~ve~ai~~ 37 (42)
T PF02845_consen 12 FPDLDREVIEAVLQANNGDVEAAIDA 37 (42)
T ss_dssp SSSS-HHHHHHHHHHTTTTHHHHHHH
T ss_pred CCCCCHHHHHHHHHHcCCCHHHHHHH
Confidence 4778888888888555 577776655
No 262
>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor.
Probab=26.05 E-value=61 Score=19.69 Aligned_cols=19 Identities=26% Similarity=0.473 Sum_probs=14.5
Q ss_pred ccCCCCcccHHHHHHHHHH
Q 035092 6 INAGVEGTGDVCAVQLITK 24 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~ 24 (73)
.|-|.||-|..|..+.|.+
T Consensus 3 ~i~G~~GsGKst~a~~la~ 21 (147)
T cd02020 3 AIDGPAGSGKSTVAKLLAK 21 (147)
T ss_pred EEECCCCCCHHHHHHHHHH
Confidence 3679999999996665554
No 263
>PRK14181 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=25.95 E-value=59 Score=24.19 Aligned_cols=19 Identities=21% Similarity=0.321 Sum_probs=15.3
Q ss_pred ccCCCC-cccHHHHHHHHHH
Q 035092 6 INAGVE-GTGDVCAVQLITK 24 (73)
Q Consensus 6 ~I~gVp-GIG~KtA~~LL~~ 24 (73)
.|-=|| ||||-|..-|++.
T Consensus 258 ~iTPVPGGVGp~T~a~L~~N 277 (287)
T PRK14181 258 AITPVPGGVGPMTVAMLMRN 277 (287)
T ss_pred cccCCCCchHHHHHHHHHHH
Confidence 344567 9999999999876
No 264
>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents archaeal proteins with this activity.
Probab=25.66 E-value=63 Score=22.31 Aligned_cols=19 Identities=21% Similarity=0.289 Sum_probs=16.2
Q ss_pred cCCCCcccHHHHHHHHHHh
Q 035092 7 NAGVEGTGDVCAVQLITKF 25 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f 25 (73)
+-|.||-|+-|..+.|+++
T Consensus 4 l~G~pGSGKST~a~~La~~ 22 (249)
T TIGR03574 4 LTGLPGVGKSTFSKELAKK 22 (249)
T ss_pred EEcCCCCCHHHHHHHHHHH
Confidence 5699999999999888764
No 265
>PRK10869 recombination and repair protein; Provisional
Probab=25.22 E-value=2.7e+02 Score=22.21 Aligned_cols=19 Identities=37% Similarity=0.256 Sum_probs=13.5
Q ss_pred HHHHHHhC-CHHHHHHHhhh
Q 035092 19 VQLITKFG-SLENLLQCVYQ 37 (73)
Q Consensus 19 ~~LL~~fg-sle~i~~~~~~ 37 (73)
..|-++|| |++++++..++
T Consensus 309 ~~L~rKyg~~~~~~~~~~~~ 328 (553)
T PRK10869 309 ISLARKHHVSPEELPQHHQQ 328 (553)
T ss_pred HHHHHHhCCCHHHHHHHHHH
Confidence 46778888 88888755443
No 266
>PRK13947 shikimate kinase; Provisional
Probab=24.97 E-value=69 Score=20.35 Aligned_cols=18 Identities=22% Similarity=0.307 Sum_probs=15.9
Q ss_pred cCCCCcccHHHHHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITK 24 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~ 24 (73)
+-|.||.|..|..+.|.+
T Consensus 6 l~G~~GsGKst~a~~La~ 23 (171)
T PRK13947 6 LIGFMGTGKTTVGKRVAT 23 (171)
T ss_pred EEcCCCCCHHHHHHHHHH
Confidence 459999999999999877
No 267
>PRK14973 DNA topoisomerase I; Provisional
Probab=24.90 E-value=1.2e+02 Score=26.04 Aligned_cols=32 Identities=16% Similarity=0.109 Sum_probs=23.7
Q ss_pred cCCCCcccHHHHHHHHH-HhCCHHHHHHH-hhhh
Q 035092 7 NAGVEGTGDVCAVQLIT-KFGSLENLLQC-VYQV 38 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~-~fgsle~i~~~-~~~l 38 (73)
...|+|+||+|..+|-. .+.++|.+..+ +++|
T Consensus 879 l~~vkg~ge~t~~~l~~ag~~~~e~l~~~d~~~l 912 (936)
T PRK14973 879 LLSVPGLGETTLEKLYLAGVYDGDLLVSADPKKL 912 (936)
T ss_pred hhhccCCCHHHHHHHHHcCCCCHHHhccCCHHHH
Confidence 34689999999977744 45788888754 5555
No 268
>COG1139 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]
Probab=24.81 E-value=1.9e+02 Score=23.30 Aligned_cols=36 Identities=11% Similarity=0.184 Sum_probs=23.8
Q ss_pred HHHHHHHhCCHHHHHHHhhhhhhHHHHHHHHHhHHHH
Q 035092 18 AVQLITKFGSLENLLQCVYQVEEERTRKALITFADQA 54 (73)
Q Consensus 18 A~~LL~~fgsle~i~~~~~~l~~~k~~~~L~~~~e~a 54 (73)
..+.+++|+.++++.+...+++. +..+.|-++.++.
T Consensus 35 r~~~~~~~~~~~elr~~~~eik~-~~lenLd~~l~~~ 70 (459)
T COG1139 35 REKVLDELPDWEELRDLAREIKL-HVLENLDEYLEQL 70 (459)
T ss_pred HHHHHhcchhHHHHHHHHHHHHH-HHHHhHHHHHHHH
Confidence 45667778888888777777765 4555565555543
No 269
>COG0714 MoxR-like ATPases [General function prediction only]
Probab=23.85 E-value=60 Score=23.51 Aligned_cols=21 Identities=14% Similarity=0.200 Sum_probs=15.9
Q ss_pred cCCCCcccHHHHHHHHHHhCC
Q 035092 7 NAGVEGTGDVCAVQLITKFGS 27 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fgs 27 (73)
+.|.||+|+-+..+-+.+.-+
T Consensus 48 l~G~PG~gKT~la~~lA~~l~ 68 (329)
T COG0714 48 LEGPPGVGKTLLARALARALG 68 (329)
T ss_pred EECCCCccHHHHHHHHHHHhC
Confidence 579999999887777766533
No 270
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=23.82 E-value=29 Score=30.87 Aligned_cols=32 Identities=16% Similarity=0.095 Sum_probs=23.2
Q ss_pred cCCCCcccHHHHHHHHHHhCCHHHHHHHhhhh
Q 035092 7 NAGVEGTGDVCAVQLITKFGSLENLLQCVYQV 38 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fgsle~i~~~~~~l 38 (73)
++=|+|+||..|..||+.-..-.+.+.+..+|
T Consensus 808 LqyI~GlGpRKa~~lLKsl~~~~~~i~~R~qL 839 (1299)
T KOG1856|consen 808 LQYICGLGPRKATSLLKSLKRNNRRIENRSQL 839 (1299)
T ss_pred HHHhcCCCcccHHHHHHHHHHcCchhhhHHHH
Confidence 36689999999999999876555444444443
No 271
>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=23.78 E-value=57 Score=23.36 Aligned_cols=24 Identities=25% Similarity=0.476 Sum_probs=16.6
Q ss_pred CCCCcccHHHHHHHHHHh--CCHHHHH
Q 035092 8 AGVEGTGDVCAVQLITKF--GSLENLL 32 (73)
Q Consensus 8 ~gVpGIG~KtA~~LL~~f--gsle~i~ 32 (73)
..+||||++++.+| +.+ .++.++.
T Consensus 174 ~~l~gig~~~~~~L-~~~Gi~ti~dl~ 199 (334)
T cd03586 174 RKIPGVGKVTAEKL-KELGIKTIGDLA 199 (334)
T ss_pred hhhCCcCHHHHHHH-HHcCCcCHHHHH
Confidence 37899999998876 454 4555554
No 272
>PRK14955 DNA polymerase III subunits gamma and tau; Provisional
Probab=23.53 E-value=70 Score=24.05 Aligned_cols=19 Identities=26% Similarity=0.497 Sum_probs=15.9
Q ss_pred cCCCCcccHHHHHHHHHHh
Q 035092 7 NAGVEGTGDVCAVQLITKF 25 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f 25 (73)
+-|-||+|..+.+.++.+.
T Consensus 43 f~Gp~G~GKtt~A~~~a~~ 61 (397)
T PRK14955 43 FSGLRGVGKTTAARVFAKA 61 (397)
T ss_pred EECCCCCCHHHHHHHHHHH
Confidence 3689999999999888764
No 273
>PRK08306 dipicolinate synthase subunit A; Reviewed
Probab=23.27 E-value=70 Score=23.23 Aligned_cols=24 Identities=25% Similarity=0.351 Sum_probs=17.9
Q ss_pred CCCC-cccHHHHHHHHHHhCCHHHHHH
Q 035092 8 AGVE-GTGDVCAVQLITKFGSLENLLQ 33 (73)
Q Consensus 8 ~gVp-GIG~KtA~~LL~~fgsle~i~~ 33 (73)
+|+| ++||++|..++.+ .+.++++
T Consensus 263 ~~lpg~vap~ta~~~~~~--~i~~~l~ 287 (296)
T PRK08306 263 PGLPGKVAPKTAGQILAN--VLSQLLA 287 (296)
T ss_pred CCCCccCCHHHHHHHHHH--HHHHHHH
Confidence 7888 5779999999965 4555553
No 274
>COG0055 AtpD F0F1-type ATP synthase, beta subunit [Energy production and conversion]
Probab=22.71 E-value=1.1e+02 Score=24.45 Aligned_cols=25 Identities=8% Similarity=0.329 Sum_probs=20.4
Q ss_pred HHHHHHHHHhCCHHHHHHH--hhhhhh
Q 035092 16 VCAVQLITKFGSLENLLQC--VYQVEE 40 (73)
Q Consensus 16 KtA~~LL~~fgsle~i~~~--~~~l~~ 40 (73)
+..+++|++|+++++|.+- .++|+.
T Consensus 364 ~~vq~iLqrYkeLqDIIaILGmdELse 390 (468)
T COG0055 364 REVQSILQRYKELQDIIAILGMDELSE 390 (468)
T ss_pred HHHHHHHHHHHHHHHHHHHhCchhcCh
Confidence 4567899999999999875 478865
No 275
>PF13234 rRNA_proc-arch: rRNA-processing arch domain; PDB: 4A4K_E 4A4Z_A 2XGJ_B 3L9O_A.
Probab=22.56 E-value=89 Score=22.09 Aligned_cols=30 Identities=10% Similarity=0.107 Sum_probs=22.3
Q ss_pred HHHHHHHHHhHHHHHHHHHhhhHhhcCccc
Q 035092 41 ERTRKALITFADQAVLSKNLVIIIAFSSTC 70 (73)
Q Consensus 41 ~k~~~~L~~~~e~a~ls~~L~~L~~~~~~~ 70 (73)
+.+.+.+..+.+...+-.++..|+...+.|
T Consensus 239 ~~~~~~~~~~~~k~~l~~~i~~Lk~~l~~a 268 (268)
T PF13234_consen 239 PDFEEHYALYHEKAELQEEIKALKRQLSDA 268 (268)
T ss_dssp SSHHHHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 346677777888888888888888776655
No 276
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=22.47 E-value=2.8e+02 Score=20.93 Aligned_cols=28 Identities=11% Similarity=0.036 Sum_probs=22.8
Q ss_pred ccCCC--CcccHHHHHHHHHH-hCCHHHHHH
Q 035092 6 INAGV--EGTGDVCAVQLITK-FGSLENLLQ 33 (73)
Q Consensus 6 ~I~gV--pGIG~KtA~~LL~~-fgsle~i~~ 33 (73)
.|..+ +||+|..+.+|-+. |.|++++..
T Consensus 30 ~~~~l~~~g~~~~~~~kL~~~g~~tv~~~~~ 60 (344)
T PLN03187 30 SIDKLISQGINAGDVKKLQDAGIYTCNGLMM 60 (344)
T ss_pred CHHHHhhCCCCHHHHHHHHHcCCCcHHHHHh
Confidence 34445 78999999999977 899999874
No 277
>PF13030 DUF3891: Protein of unknown function (DUF3891)
Probab=22.23 E-value=75 Score=22.48 Aligned_cols=13 Identities=31% Similarity=0.687 Sum_probs=8.5
Q ss_pred CccccccCCCCcc
Q 035092 1 MHFYFINAGVEGT 13 (73)
Q Consensus 1 ~~~~~~I~gVpGI 13 (73)
||+.|-+.+..|.
T Consensus 105 ~H~~~ly~~~~~~ 117 (221)
T PF13030_consen 105 MHYSFLYENRTGQ 117 (221)
T ss_pred HHHHHHcCCCcCC
Confidence 5666666666666
No 278
>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]
Probab=22.04 E-value=77 Score=25.22 Aligned_cols=20 Identities=30% Similarity=0.406 Sum_probs=17.2
Q ss_pred CCCcccHHHHHHHHHHhCCH
Q 035092 9 GVEGTGDVCAVQLITKFGSL 28 (73)
Q Consensus 9 gVpGIG~KtA~~LL~~fgsl 28 (73)
|-||+|+-|-+.+|....+.
T Consensus 55 GPPG~GKTTlA~liA~~~~~ 74 (436)
T COG2256 55 GPPGTGKTTLARLIAGTTNA 74 (436)
T ss_pred CCCCCCHHHHHHHHHHhhCC
Confidence 89999999999999986443
No 279
>PF09374 PG_binding_3: Predicted Peptidoglycan domain; InterPro: IPR018537 This family contains a potential peptidoglycan binding domain. ; PDB: 2IKB_B 2IS5_A 2NR7_A.
Probab=22.02 E-value=1.8e+02 Score=16.91 Aligned_cols=21 Identities=14% Similarity=0.246 Sum_probs=12.8
Q ss_pred ccHHHHHHHHHHhCCHHHHHHHh
Q 035092 13 TGDVCAVQLITKFGSLENLLQCV 35 (73)
Q Consensus 13 IG~KtA~~LL~~fgsle~i~~~~ 35 (73)
|||+|...+ .-.+...+...+
T Consensus 22 iGp~Tl~Al--~~~~~~~l~~~~ 42 (72)
T PF09374_consen 22 IGPKTLAAL--NAADPRDLINAL 42 (72)
T ss_dssp -SHHHHHHH--HHS-HHHHHHHH
T ss_pred cCHHHHHHH--hhCCHHHHHHHH
Confidence 799999998 445555555443
No 280
>COG0389 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]
Probab=21.86 E-value=1.9e+02 Score=21.53 Aligned_cols=25 Identities=24% Similarity=0.254 Sum_probs=15.9
Q ss_pred cCCCCcccHHHHHHHHHHhCCHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITKFGSLENLLQ 33 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fgsle~i~~ 33 (73)
+..++|||+.++.+|-.- | +..|-+
T Consensus 178 v~~~~GvG~~~~~~l~~~-G-i~ti~d 202 (354)
T COG0389 178 VLEFWGVGKVTAEKLRRL-G-ISTIGD 202 (354)
T ss_pred hhhhCCCCHHHHHHHHHc-C-ChhHHH
Confidence 457899996666665444 4 555543
No 281
>PRK07933 thymidylate kinase; Validated
Probab=21.77 E-value=73 Score=21.87 Aligned_cols=19 Identities=21% Similarity=0.368 Sum_probs=16.5
Q ss_pred cCCCCcccHHHHHHHHHHh
Q 035092 7 NAGVEGTGDVCAVQLITKF 25 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f 25 (73)
+.|+.|.|+-|-.++|.++
T Consensus 5 iEG~dGsGKST~~~~L~~~ 23 (213)
T PRK07933 5 IEGVDGAGKRTLTEALRAA 23 (213)
T ss_pred EEcCCCCCHHHHHHHHHHH
Confidence 6899999999988888775
No 282
>PRK14964 DNA polymerase III subunits gamma and tau; Provisional
Probab=21.72 E-value=75 Score=25.25 Aligned_cols=18 Identities=22% Similarity=0.473 Sum_probs=15.9
Q ss_pred cCCCCcccHHHHHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITK 24 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~ 24 (73)
+-|.||+|+.|.+.++.+
T Consensus 40 f~Gp~G~GKTT~ArilAk 57 (491)
T PRK14964 40 LVGASGVGKTTCARIISL 57 (491)
T ss_pred EECCCCccHHHHHHHHHH
Confidence 459999999999999986
No 283
>COG1498 SIK1 Protein implicated in ribosomal biogenesis, Nop56p homolog [Translation, ribosomal structure and biogenesis]
Probab=21.48 E-value=84 Score=24.65 Aligned_cols=20 Identities=35% Similarity=0.529 Sum_probs=19.0
Q ss_pred ccHHHHHHHHHHhCCHHHHH
Q 035092 13 TGDVCAVQLITKFGSLENLL 32 (73)
Q Consensus 13 IG~KtA~~LL~~fgsle~i~ 32 (73)
|||..++.|+..=|++.++-
T Consensus 248 VG~~lgARLIs~AGgL~~LA 267 (395)
T COG1498 248 VGPVLGARLISHAGGLTRLA 267 (395)
T ss_pred HhHHHHHHHHHHhcCHHHHH
Confidence 79999999999999999986
No 284
>PF04336 DUF479: Protein of unknown function, DUF479; InterPro: IPR007431 This entry contains the Escherichia coli gene yajB, now renamed acpH, which encodes an ACP hydrolase. AcpH converts holo-ACP to apo-ACP by hydrolytic cleavage of the phosphopantetheine prosthetic group from ACP []. A mutant E. coli strain having a total deletion of the acpH grows normally, showing that phosphodiesterase activity is not essential for growth, although it is required for turnover of the ACP prosthetic group in vivo. AcpH is found only in Gram-negative organisms suggesting that it plays a role in some aspect of lipid metabolism that is unique to these organisms. The most obvious of which is biosynthesis of lipid A. Because AcpH is a hydrolase, it could possibly be an editing enzyme that intercepts acyl-ACPs that would give an inappropriate lipid A structure if used as acyl donors []. ; GO: 0008770 [acyl-carrier-protein] phosphodiesterase activity, 0006633 fatty acid biosynthetic process
Probab=21.47 E-value=1.9e+02 Score=17.82 Aligned_cols=21 Identities=10% Similarity=0.344 Sum_probs=16.6
Q ss_pred HHHHHHhCCHHHHHHHhhhhh
Q 035092 19 VQLITKFGSLENLLQCVYQVE 39 (73)
Q Consensus 19 ~~LL~~fgsle~i~~~~~~l~ 39 (73)
..+|..|+++++|-.+++.+.
T Consensus 49 ~dWL~~Y~~~egi~~al~~m~ 69 (106)
T PF04336_consen 49 HDWLSSYRTLEGIERALQRMS 69 (106)
T ss_pred hCHHHHcCCHHHHHHHHHHHH
Confidence 347888999999987777664
No 285
>KOG1350 consensus F0F1-type ATP synthase, beta subunit [Energy production and conversion]
Probab=21.42 E-value=1.9e+02 Score=23.06 Aligned_cols=25 Identities=12% Similarity=0.303 Sum_probs=20.0
Q ss_pred HHHHHHHHHhCCHHHHHHH--hhhhhh
Q 035092 16 VCAVQLITKFGSLENLLQC--VYQVEE 40 (73)
Q Consensus 16 KtA~~LL~~fgsle~i~~~--~~~l~~ 40 (73)
...++.|+.|+|+.+|.+- .++++.
T Consensus 414 ~~Vqk~LQ~YKsLQDIIAILGmDELSE 440 (521)
T KOG1350|consen 414 RGVQKTLQDYKSLQDIIAILGMDELSE 440 (521)
T ss_pred HHHHHHHHHHHHHHHHHHHhCchhhch
Confidence 3567899999999999875 477765
No 286
>PF11697 DUF3293: Protein of unknown function (DUF3293); InterPro: IPR021710 This bacterial family of proteins has no known function.
Probab=21.33 E-value=86 Score=18.34 Aligned_cols=17 Identities=41% Similarity=0.384 Sum_probs=15.0
Q ss_pred CCcccHHHHHHHHHHhC
Q 035092 10 VEGTGDVCAVQLITKFG 26 (73)
Q Consensus 10 VpGIG~KtA~~LL~~fg 26 (73)
|+||.+-.|..|-++|+
T Consensus 53 V~~i~~~~A~~Lg~~f~ 69 (73)
T PF11697_consen 53 VLGISLEEAIALGRKFG 69 (73)
T ss_pred EcCCCHHHHHHHHHHhC
Confidence 67899999999999986
No 287
>cd02022 DPCK Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis.
Probab=21.30 E-value=83 Score=20.66 Aligned_cols=20 Identities=25% Similarity=0.506 Sum_probs=17.7
Q ss_pred cCCCCcccHHHHHHHHHHhC
Q 035092 7 NAGVEGTGDVCAVQLITKFG 26 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fg 26 (73)
|-|-||-|+-|..+.|.++|
T Consensus 4 itG~~gsGKst~~~~l~~~g 23 (179)
T cd02022 4 LTGGIGSGKSTVAKLLKELG 23 (179)
T ss_pred EECCCCCCHHHHHHHHHHCC
Confidence 56899999999999999865
No 288
>smart00511 ORANGE Orange domain. This domain confers specificity among members of the Hairy/E(SPL) family.
Probab=21.30 E-value=53 Score=17.24 Aligned_cols=21 Identities=14% Similarity=0.262 Sum_probs=14.1
Q ss_pred cCCCCcccHHHHHHHHHHhCC
Q 035092 7 NAGVEGTGDVCAVQLITKFGS 27 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~fgs 27 (73)
+...||+.+.....||+++.+
T Consensus 18 Ls~~~~~~~~~~~~Ll~HL~~ 38 (45)
T smart00511 18 LSQLPGTDPDVRARLLSHLQT 38 (45)
T ss_pred HhcCCCCChHHHHHHHHHHHH
Confidence 345566777778888877654
No 289
>PHA03134 thymidine kinase; Provisional
Probab=21.26 E-value=80 Score=24.22 Aligned_cols=23 Identities=17% Similarity=0.245 Sum_probs=19.5
Q ss_pred cccCCCCcccHHHHHHHHHHhCC
Q 035092 5 FINAGVEGTGDVCAVQLITKFGS 27 (73)
Q Consensus 5 ~~I~gVpGIG~KtA~~LL~~fgs 27 (73)
-+++|.-|||+-|..+.|...++
T Consensus 16 vYlDG~~GvGKTT~~~~l~~~~~ 38 (340)
T PHA03134 16 IYLDGAYGIGKSTTGRVMASAAS 38 (340)
T ss_pred EEEeCCCcCCHHHHHHHHHHhcc
Confidence 36799999999999999997543
No 290
>PRK00698 tmk thymidylate kinase; Validated
Probab=21.26 E-value=81 Score=20.49 Aligned_cols=19 Identities=21% Similarity=0.606 Sum_probs=17.0
Q ss_pred ccCCCCcccHHHHHHHHHH
Q 035092 6 INAGVEGTGDVCAVQLITK 24 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~ 24 (73)
-|.|++|-|+-|-.+.|.+
T Consensus 7 ~ieG~~gsGKsT~~~~L~~ 25 (205)
T PRK00698 7 TIEGIDGAGKSTQIELLKE 25 (205)
T ss_pred EEECCCCCCHHHHHHHHHH
Confidence 4689999999999999976
No 291
>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]
Probab=21.21 E-value=72 Score=24.27 Aligned_cols=19 Identities=26% Similarity=0.518 Sum_probs=15.8
Q ss_pred ccCCCCcccHHHHHHHHHH
Q 035092 6 INAGVEGTGDVCAVQLITK 24 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~ 24 (73)
.|.|-||+|+-|....|.+
T Consensus 52 iisGpPG~GKTTsi~~LAr 70 (333)
T KOG0991|consen 52 IISGPPGTGKTTSILCLAR 70 (333)
T ss_pred EeeCCCCCchhhHHHHHHH
Confidence 3679999999998887776
No 292
>PF10392 COG5: Golgi transport complex subunit 5; InterPro: IPR019465 The conserved oligomeric Golgi (COG) complex is a peripheral membrane complex involved in intra-Golgi protein trafficking. Subunit 5 is located in the smaller, B lobe, together with subunits 6-8, and has been shown to bind subunits 1 and 7 [].
Probab=21.14 E-value=2.4e+02 Score=18.03 Aligned_cols=47 Identities=23% Similarity=0.343 Sum_probs=25.6
Q ss_pred HHHHHHHhCCHHHHHHHhhhh-------hh--HHHHHHHHH-hHHHHHHHHHhhhHh
Q 035092 18 AVQLITKFGSLENLLQCVYQV-------EE--ERTRKALIT-FADQAVLSKNLVIII 64 (73)
Q Consensus 18 A~~LL~~fgsle~i~~~~~~l-------~~--~k~~~~L~~-~~e~a~ls~~L~~L~ 64 (73)
...||+++.++++.-...+.+ .. .+++..+.+ |...-....+|..+.
T Consensus 57 ~~~LL~q~~~~~~~~~~l~~v~~~v~~L~~s~~RL~~eV~~Py~~~~~~~~~L~rl~ 113 (132)
T PF10392_consen 57 HEDLLSQASSIEELESVLQAVRSSVESLQSSYERLRSEVIEPYEKIQKLTSQLERLH 113 (132)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence 346777777666654333333 21 567777766 444444455555544
No 293
>PRK00131 aroK shikimate kinase; Reviewed
Probab=21.03 E-value=92 Score=19.43 Aligned_cols=19 Identities=26% Similarity=0.326 Sum_probs=16.3
Q ss_pred cCCCCcccHHHHHHHHHHh
Q 035092 7 NAGVEGTGDVCAVQLITKF 25 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f 25 (73)
+-|.||-|.-|..+.|.+.
T Consensus 9 l~G~~GsGKstla~~La~~ 27 (175)
T PRK00131 9 LIGFMGAGKSTIGRLLAKR 27 (175)
T ss_pred EEcCCCCCHHHHHHHHHHH
Confidence 4699999999999988773
No 294
>PRK14021 bifunctional shikimate kinase/3-dehydroquinate synthase; Provisional
Probab=20.93 E-value=2.9e+02 Score=21.88 Aligned_cols=28 Identities=14% Similarity=0.266 Sum_probs=21.9
Q ss_pred cCCCCcccHHHHHHHHHH-----hCCHHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITK-----FGSLENLLQC 34 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~-----fgsle~i~~~ 34 (73)
+=|.||-|+-|..++|.+ |=+.+..++.
T Consensus 11 LiG~~GaGKttvg~~LA~~L~~~fiD~D~~ie~ 43 (542)
T PRK14021 11 IIGMMGAGKTRVGKEVAQMMRLPFADADVEIER 43 (542)
T ss_pred EECCCCCCHHHHHHHHHHHhCCCEEEchHHHHH
Confidence 359999999999999987 5566766544
No 295
>cd02019 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate.
Probab=20.92 E-value=91 Score=17.39 Aligned_cols=19 Identities=16% Similarity=0.293 Sum_probs=15.9
Q ss_pred cCCCCcccHHHHHHHHHHh
Q 035092 7 NAGVEGTGDVCAVQLITKF 25 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f 25 (73)
|-|-||.|+.|..+.|.+.
T Consensus 4 i~G~~gsGKst~~~~l~~~ 22 (69)
T cd02019 4 ITGGSGSGKSTVAKKLAEQ 22 (69)
T ss_pred EECCCCCCHHHHHHHHHHH
Confidence 4699999999988888765
No 296
>PF14048 MBD_C: C-terminal domain of methyl-CpG binding protein 2 and 3; PDB: 2L2L_B.
Probab=20.92 E-value=1.2e+02 Score=19.01 Aligned_cols=41 Identities=22% Similarity=0.186 Sum_probs=12.4
Q ss_pred cCCCCcccHHHHHHHHHHh-CCHHHHHHHhhhhhhHHHHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITKF-GSLENLLQCVYQVEEERTRKALIT 49 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f-gsle~i~~~~~~l~~~k~~~~L~~ 49 (73)
+.-+||+|--.-.-|.+.| =|-++|....+.++. .|++|.+
T Consensus 53 ~e~~P~~~~~~~QPLc~~~~VT~eDIr~QE~rVk~--aR~RLae 94 (96)
T PF14048_consen 53 LEKNPGVGLNPPQPLCKQFVVTEEDIRRQERRVKK--ARKRLAE 94 (96)
T ss_dssp ----------------T-----HHHHHHHHHHHHH--HHHHHHH
T ss_pred hccCcccccCCCcccccCCccCHHHHHHHHHHHHH--HHHHHHH
Confidence 3456778877778888888 677777766555543 4555544
No 297
>PLN02184 superoxide dismutase [Fe]
Probab=20.76 E-value=1.2e+02 Score=21.41 Aligned_cols=22 Identities=18% Similarity=0.143 Sum_probs=17.2
Q ss_pred cHHHHHHHHHHhCCHHHHHHHh
Q 035092 14 GDVCAVQLITKFGSLENLLQCV 35 (73)
Q Consensus 14 G~KtA~~LL~~fgsle~i~~~~ 35 (73)
+.+.+..+=+.|||+|++.+..
T Consensus 103 ~g~L~~~I~~~FGS~d~fk~~F 124 (212)
T PLN02184 103 SGELLALLERDFTSYEKFYEEF 124 (212)
T ss_pred CHHHHHHHHHHhhhHHHHHHHH
Confidence 3567778888899999998654
No 298
>PF14894 Lsm_C: Lsm C-terminal; PDB: 1M5Q_1.
Probab=20.73 E-value=59 Score=19.34 Aligned_cols=18 Identities=33% Similarity=0.684 Sum_probs=9.5
Q ss_pred CCCCcccHH--HHHHHHHHh
Q 035092 8 AGVEGTGDV--CAVQLITKF 25 (73)
Q Consensus 8 ~gVpGIG~K--tA~~LL~~f 25 (73)
.||.|.||- ++..|.++|
T Consensus 39 ~GVEGsGPlAerv~~ly~ey 58 (64)
T PF14894_consen 39 NGVEGSGPLAERVYDLYNEY 58 (64)
T ss_dssp TEEE--SHHHHHHHHHHHHH
T ss_pred cccccCChHHHHHHHHHHHH
Confidence 488899984 344455444
No 299
>PHA03135 thymidine kinase; Provisional
Probab=20.71 E-value=83 Score=24.17 Aligned_cols=22 Identities=14% Similarity=0.193 Sum_probs=19.5
Q ss_pred cccCCCCcccHHHHHHHHHHhC
Q 035092 5 FINAGVEGTGDVCAVQLITKFG 26 (73)
Q Consensus 5 ~~I~gVpGIG~KtA~~LL~~fg 26 (73)
-.++|.-|||+-|..+.|.+..
T Consensus 13 IYlDG~~GvGKTT~~~~l~~~~ 34 (343)
T PHA03135 13 VYLDGPFGIGKTSMLNEMPDHS 34 (343)
T ss_pred EEEECCCCCCHHHHHHHHHHhc
Confidence 4689999999999999999863
No 300
>COG0237 CoaE Dephospho-CoA kinase [Coenzyme metabolism]
Probab=20.54 E-value=93 Score=21.64 Aligned_cols=19 Identities=16% Similarity=0.405 Sum_probs=17.2
Q ss_pred cCCCCcccHHHHHHHHHHh
Q 035092 7 NAGVEGTGDVCAVQLITKF 25 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f 25 (73)
+-|-||-|+-|+.++++++
T Consensus 7 lTG~igsGKStva~~~~~~ 25 (201)
T COG0237 7 LTGGIGSGKSTVAKILAEL 25 (201)
T ss_pred EecCCCCCHHHHHHHHHHc
Confidence 4688999999999999996
No 301
>PF08839 CDT1: DNA replication factor CDT1 like; InterPro: IPR014939 CDT1 is a component of the replication licensing system and promotes the loading of the mini-chromosome maintenance complex onto chromatin. Geminin is an inhibitor of CDT1 and prevents inappropriate re-initiation of replication on an already fired origin. This region of CDT1 binds to Geminin []. ; PDB: 2WVR_C 2ZXX_F.
Probab=20.51 E-value=2e+02 Score=19.13 Aligned_cols=54 Identities=11% Similarity=0.209 Sum_probs=30.6
Q ss_pred HHHHHHhCCHHHHHHHh---hhhhh-HHHHHHHHHhHHHHHHHHHhhhHhhcCccccc
Q 035092 19 VQLITKFGSLENLLQCV---YQVEE-ERTRKALITFADQAVLSKNLVIIIAFSSTCYL 72 (73)
Q Consensus 19 ~~LL~~fgsle~i~~~~---~~l~~-~k~~~~L~~~~e~a~ls~~L~~L~~~~~~~~~ 72 (73)
..|.+-|..++.++.-. .+..- .++...+++....-+.-..|++|+.-.|.+|-
T Consensus 6 ~~L~~~F~~ldtv~~~l~~R~~~~tf~~i~~~Ve~~~kr~F~~~~LaQI~~i~P~a~~ 63 (163)
T PF08839_consen 6 EFLAELFRALDTVVSMLRNRKETPTFQKIKPSVENMTKRRFTEEHLAQIKYIYPEAYS 63 (163)
T ss_dssp HHHHHHHHHHHHHHHHHHHTT---BHHHHHHHHHHHHSS---HHHHHHHHHH-GGGEE
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCccHHHHHHHHHHHhcCCcCHHHHHHHHHhCcccEE
Confidence 45667777777766422 12111 45666666655555556778888888888774
No 302
>PF13276 HTH_21: HTH-like domain
Probab=20.49 E-value=93 Score=16.89 Aligned_cols=15 Identities=13% Similarity=0.235 Sum_probs=12.5
Q ss_pred cccHHHHHHHHHHhC
Q 035092 12 GTGDVCAVQLITKFG 26 (73)
Q Consensus 12 GIG~KtA~~LL~~fg 26 (73)
-||.|+...|+++.|
T Consensus 37 ~v~~krV~RlM~~~g 51 (60)
T PF13276_consen 37 RVSRKRVRRLMREMG 51 (60)
T ss_pred cccHHHHHHHHHHcC
Confidence 489999999998865
No 303
>PRK06762 hypothetical protein; Provisional
Probab=20.49 E-value=93 Score=19.74 Aligned_cols=20 Identities=20% Similarity=0.333 Sum_probs=16.2
Q ss_pred ccCCCCcccHHHHHHHHHHh
Q 035092 6 INAGVEGTGDVCAVQLITKF 25 (73)
Q Consensus 6 ~I~gVpGIG~KtA~~LL~~f 25 (73)
-|-|.||-|+-|..+.|.+.
T Consensus 6 ~i~G~~GsGKST~A~~L~~~ 25 (166)
T PRK06762 6 IIRGNSGSGKTTIAKQLQER 25 (166)
T ss_pred EEECCCCCCHHHHHHHHHHH
Confidence 45799999999988877654
No 304
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=20.48 E-value=1.7e+02 Score=25.76 Aligned_cols=43 Identities=16% Similarity=0.293 Sum_probs=25.6
Q ss_pred cCCCCcccHHHHHHHHHHh----CCHHHHH-HHhhhhhhHHHHHHHHH
Q 035092 7 NAGVEGTGDVCAVQLITKF----GSLENLL-QCVYQVEEERTRKALIT 49 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f----gsle~i~-~~~~~l~~~k~~~~L~~ 49 (73)
+...||||-.+..+|-+.| |++..+- +.++..-++++++++..
T Consensus 551 v~~LPGVG~sm~~kL~s~~i~tCgdLq~~T~~kl~k~~G~Klgq~i~~ 598 (1016)
T KOG2093|consen 551 VDDLPGVGSSMKSKLVSQFIQTCGDLQLITLIKLRKVFGPKLGQKIYR 598 (1016)
T ss_pred cccCCCccHHHHHHHHHhccchhHHHHHHHHHHHHhhhcccHHHHHHH
Confidence 4688999999988888887 3333221 12233334566666554
No 305
>PF13877 RPAP3_C: Potential Monad-binding region of RPAP3
Probab=20.42 E-value=1.5e+02 Score=17.54 Aligned_cols=51 Identities=12% Similarity=0.111 Sum_probs=27.2
Q ss_pred HHHHHHHHHHhCCH----HHHHHHhhhhhhHHHHHHHHHhHHHHHHHHHhhhHhh
Q 035092 15 DVCAVQLITKFGSL----ENLLQCVYQVEEERTRKALITFADQAVLSKNLVIIIA 65 (73)
Q Consensus 15 ~KtA~~LL~~fgsl----e~i~~~~~~l~~~k~~~~L~~~~e~a~ls~~L~~L~~ 65 (73)
|+++.+..+.+.++ +...+=+..+++..+.+-+.+..+.-.++.-|..+..
T Consensus 4 P~~~~eF~~~w~~~~~~~~~~~~yL~~i~p~~l~~if~~~l~~~~L~~il~~l~~ 58 (94)
T PF13877_consen 4 PKNSYEFERDWRRLKKDPEERYEYLKSIPPDSLPKIFKNSLEPEFLSEILEALNE 58 (94)
T ss_pred CCCHHHHHHHHHHHcCCHHHHHHHHHhCChHHHHHHHHccCCHHHHHHHHHHHHH
Confidence 44555555555444 3333334555555566666666666566555555554
No 306
>PTZ00046 rifin; Provisional
Probab=20.41 E-value=1.6e+02 Score=22.83 Aligned_cols=29 Identities=14% Similarity=0.181 Sum_probs=20.6
Q ss_pred HHHHHHHHhHHHHHHHHHhhhHhhcC-----ccc
Q 035092 42 RTRKALITFADQAVLSKNLVIIIAFS-----STC 70 (73)
Q Consensus 42 k~~~~L~~~~e~a~ls~~L~~L~~~~-----~~~ 70 (73)
.+++.+...+=+=.+..++++|.|+- |||
T Consensus 93 eIQKIILKDKlEKeL~ekf~tL~TdI~tddIPTC 126 (358)
T PTZ00046 93 EIQKIILKDKLEKELMEKFATLQTDIQSDAIPTC 126 (358)
T ss_pred HHHHHHHHHHHHHHHHhhhhhcccCCccccCccc
Confidence 46666666555557788999998864 666
No 307
>PRK00889 adenylylsulfate kinase; Provisional
Probab=20.34 E-value=99 Score=19.89 Aligned_cols=19 Identities=16% Similarity=0.366 Sum_probs=15.5
Q ss_pred cCCCCcccHHHHHHHHHHh
Q 035092 7 NAGVEGTGDVCAVQLITKF 25 (73)
Q Consensus 7 I~gVpGIG~KtA~~LL~~f 25 (73)
+-|.||.|+-|..+.|...
T Consensus 9 ~~G~~GsGKST~a~~la~~ 27 (175)
T PRK00889 9 FTGLSGAGKTTIARALAEK 27 (175)
T ss_pred EECCCCCCHHHHHHHHHHH
Confidence 4599999999988877653
No 308
>PF09674 DUF2400: Protein of unknown function (DUF2400); InterPro: IPR014127 Members of this uncharacterised protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighbourhoods show little conservation.
Probab=20.28 E-value=2.3e+02 Score=20.40 Aligned_cols=17 Identities=24% Similarity=0.499 Sum_probs=14.7
Q ss_pred HHHHHHHHhCCHHHHHH
Q 035092 17 CAVQLITKFGSLENLLQ 33 (73)
Q Consensus 17 tA~~LL~~fgsle~i~~ 33 (73)
+-+.++++|||+|+++.
T Consensus 83 ~l~~i~~~~gsLe~~f~ 99 (232)
T PF09674_consen 83 ALKRIYQEYGSLEEAFA 99 (232)
T ss_pred HHHHHHHccCCHHHHHH
Confidence 45788999999999987
Done!