Query 009729
Match_columns 527
No_of_seqs 227 out of 1577
Neff 5.4
Searched_HMMs 46136
Date Thu Mar 28 16:38:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009729.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009729hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01703 PolY_Pol_iota DNA Poly 100.0 2.2E-38 4.7E-43 333.8 22.4 230 2-239 122-379 (379)
2 cd01702 PolY_Pol_eta DNA Polym 100.0 1.5E-38 3.3E-43 332.9 20.6 219 2-239 135-359 (359)
3 PTZ00205 DNA polymerase kappa; 100.0 3.8E-38 8.3E-43 342.3 21.0 216 2-244 259-488 (571)
4 PRK03348 DNA polymerase IV; Pr 100.0 1.5E-37 3.3E-42 334.3 24.6 225 2-258 133-357 (454)
5 cd01701 PolY_Rev1 DNA polymera 100.0 7.5E-38 1.6E-42 331.9 21.8 220 2-240 175-404 (404)
6 PRK14133 DNA polymerase IV; Pr 100.0 1.3E-37 2.9E-42 323.1 22.3 222 2-254 126-347 (347)
7 cd00424 PolY Y-family of DNA p 100.0 2.1E-37 4.6E-42 321.1 21.7 217 2-238 125-343 (343)
8 PRK02794 DNA polymerase IV; Pr 100.0 8.4E-38 1.8E-42 332.7 18.1 225 2-256 162-386 (419)
9 PRK03609 umuC DNA polymerase V 100.0 2.2E-37 4.8E-42 329.7 20.4 231 2-256 126-363 (422)
10 PRK01810 DNA polymerase IV; Va 100.0 5E-37 1.1E-41 325.2 22.0 225 2-255 132-358 (407)
11 PRK01216 DNA polymerase IV; Va 100.0 4.3E-37 9.3E-42 321.1 20.9 212 2-243 131-342 (351)
12 PRK03858 DNA polymerase IV; Va 100.0 6.7E-37 1.4E-41 322.7 22.4 228 2-256 126-354 (396)
13 PRK03103 DNA polymerase IV; Re 100.0 9E-37 1.9E-41 323.4 22.5 227 2-256 131-362 (409)
14 PRK03352 DNA polymerase IV; Va 100.0 2.6E-36 5.6E-41 313.2 21.0 215 2-243 130-345 (346)
15 PRK02406 DNA polymerase IV; Va 100.0 5.5E-36 1.2E-40 310.4 21.3 213 2-244 121-335 (343)
16 cd03586 PolY_Pol_IV_kappa DNA 100.0 1.9E-35 4E-40 303.9 21.8 211 2-240 124-334 (334)
17 KOG2095 DNA polymerase iota/DN 100.0 3.2E-35 6.9E-40 318.3 22.2 167 2-168 209-375 (656)
18 cd01700 PolY_Pol_V_umuC umuC s 100.0 7.2E-35 1.6E-39 302.2 21.5 215 2-239 124-344 (344)
19 COG0389 DinP Nucleotidyltransf 100.0 2.9E-33 6.2E-38 292.5 20.9 217 2-243 129-347 (354)
20 KOG2094 Predicted DNA damage i 100.0 6.4E-32 1.4E-36 275.2 16.5 213 2-244 233-447 (490)
21 KOG2093 Translesion DNA polyme 100.0 7.5E-31 1.6E-35 289.1 12.0 237 1-256 501-748 (1016)
22 cd03468 PolY_like DNA Polymera 100.0 2.1E-28 4.6E-33 251.5 18.7 203 5-238 126-334 (335)
23 PF11799 IMS_C: impB/mucB/samB 99.5 5.9E-14 1.3E-18 123.7 8.5 124 106-254 1-127 (127)
24 PF11798 IMS_HHH: IMS family H 98.6 2.3E-08 4.9E-13 70.2 1.3 32 39-71 1-32 (32)
25 PRK04301 radA DNA repair and r 98.1 2.7E-06 5.7E-11 88.2 4.8 80 45-125 2-88 (317)
26 TIGR02236 recomb_radA DNA repa 97.6 9.7E-05 2.1E-09 76.1 5.5 74 51-125 1-81 (310)
27 PF14520 HHH_5: Helix-hairpin- 97.0 0.00091 2E-08 52.9 4.2 50 52-102 8-59 (60)
28 PF11731 Cdd1: Pathogenicity l 96.5 0.0016 3.5E-08 56.6 2.6 40 50-90 13-52 (93)
29 PRK12766 50S ribosomal protein 95.3 0.032 6.9E-07 56.0 5.8 56 50-106 4-61 (232)
30 PF04994 TfoX_C: TfoX C-termin 93.7 0.081 1.7E-06 44.9 3.9 34 49-83 3-36 (81)
31 PF10391 DNA_pol_lambd_f: Fing 93.4 0.075 1.6E-06 41.5 2.9 27 52-79 5-31 (52)
32 PRK02362 ski2-like helicase; P 93.0 0.11 2.3E-06 60.2 4.7 55 49-104 652-706 (737)
33 COG3743 Uncharacterized conser 92.4 0.16 3.4E-06 46.9 4.1 36 50-86 68-103 (133)
34 PF12826 HHH_2: Helix-hairpin- 91.6 0.18 3.8E-06 40.6 3.1 47 54-102 8-56 (64)
35 PF03118 RNA_pol_A_CTD: Bacter 91.6 0.27 5.9E-06 40.0 4.1 46 43-90 6-51 (66)
36 PF14229 DUF4332: Domain of un 90.7 0.19 4.2E-06 45.6 2.8 54 37-91 41-94 (122)
37 PRK00254 ski2-like helicase; P 89.0 0.47 1E-05 54.9 4.7 53 49-102 645-699 (720)
38 PRK01172 ski2-like helicase; P 88.7 0.59 1.3E-05 53.5 5.3 52 49-101 612-665 (674)
39 COG2251 Predicted nuclease (Re 86.3 0.83 1.8E-05 50.0 4.4 69 38-107 214-284 (474)
40 PF14229 DUF4332: Domain of un 86.0 1.4 3E-05 40.0 5.0 44 55-100 1-49 (122)
41 PRK14667 uvrC excinuclease ABC 84.4 1.3 2.8E-05 50.3 4.9 54 48-103 513-567 (567)
42 PRK00116 ruvA Holliday junctio 82.7 1.3 2.8E-05 43.2 3.6 56 50-105 74-132 (192)
43 PRK08609 hypothetical protein; 82.3 0.93 2E-05 51.3 2.8 31 51-81 90-120 (570)
44 smart00483 POLXc DNA polymeras 82.2 1.1 2.4E-05 47.4 3.1 30 51-81 91-120 (334)
45 TIGR00596 rad1 DNA repair prot 81.7 1.6 3.4E-05 51.5 4.5 52 51-104 759-811 (814)
46 smart00611 SEC63 Domain of unk 80.3 4.2 9.2E-05 41.7 6.6 62 48-110 150-213 (312)
47 TIGR03491 RecB family nuclease 80.3 1.4 3.1E-05 48.3 3.3 60 42-102 200-261 (457)
48 PF02889 Sec63: Sec63 Brl doma 79.7 3.1 6.6E-05 42.7 5.3 60 49-109 148-209 (314)
49 PF14377 DUF4414: Domain of un 78.8 1.3 2.9E-05 39.2 2.1 25 479-503 42-66 (108)
50 PF14377 DUF4414: Domain of un 78.4 0.97 2.1E-05 40.1 1.0 21 482-502 1-21 (108)
51 PRK14671 uvrC excinuclease ABC 78.3 3.3 7.2E-05 47.5 5.5 51 49-101 569-619 (621)
52 cd00141 NT_POLXc Nucleotidyltr 77.5 1.6 3.5E-05 45.5 2.5 29 51-80 87-115 (307)
53 PF02961 BAF: Barrier to autoi 76.9 2.2 4.8E-05 37.0 2.7 33 46-79 16-48 (89)
54 PRK07758 hypothetical protein; 76.2 4.9 0.00011 35.3 4.7 38 54-92 39-78 (95)
55 PRK07956 ligA NAD-dependent DN 75.7 3.8 8.3E-05 47.4 5.1 54 48-101 444-499 (665)
56 TIGR00575 dnlj DNA ligase, NAD 75.2 4.1 8.9E-05 47.0 5.2 55 48-102 431-487 (652)
57 PRK14666 uvrC excinuclease ABC 74.9 3.7 8.1E-05 47.5 4.7 51 49-101 637-689 (694)
58 PTZ00035 Rad51 protein; Provis 74.4 4.6 9.9E-05 42.8 4.9 55 49-104 21-79 (337)
59 PRK14669 uvrC excinuclease ABC 73.4 4.9 0.00011 46.2 5.2 55 48-104 551-605 (624)
60 PRK10917 ATP-dependent DNA hel 71.1 3.1 6.6E-05 48.1 2.9 31 49-80 9-39 (681)
61 PRK14672 uvrC excinuclease ABC 70.7 5.6 0.00012 46.1 4.8 62 48-111 607-670 (691)
62 TIGR02239 recomb_RAD51 DNA rep 69.4 6 0.00013 41.5 4.4 36 56-92 8-43 (316)
63 PLN03187 meiotic recombination 68.7 5 0.00011 42.8 3.7 56 48-104 28-87 (344)
64 PRK14670 uvrC excinuclease ABC 68.1 6.6 0.00014 44.7 4.7 53 48-102 513-567 (574)
65 PLN03186 DNA repair protein RA 67.9 2.2 4.7E-05 45.4 0.8 44 48-92 25-70 (342)
66 PF00633 HHH: Helix-hairpin-he 67.8 2.7 5.8E-05 29.2 1.0 16 51-66 13-28 (30)
67 PRK12278 50S ribosomal protein 67.0 5.9 0.00013 39.8 3.6 37 49-86 158-194 (221)
68 TIGR02238 recomb_DMC1 meiotic 66.6 11 0.00023 39.7 5.6 50 52-102 2-55 (313)
69 PRK14351 ligA NAD-dependent DN 66.3 8.6 0.00019 44.7 5.2 55 48-102 461-517 (689)
70 TIGR01954 nusA_Cterm_rpt trans 66.3 13 0.00029 27.5 4.7 34 57-91 1-34 (50)
71 PRK14973 DNA topoisomerase I; 64.5 10 0.00022 45.6 5.6 79 21-103 851-932 (936)
72 COG1948 MUS81 ERCC4-type nucle 64.2 8.6 0.00019 39.4 4.2 50 51-102 184-235 (254)
73 COG1200 RecG RecG-like helicas 63.0 5.2 0.00011 46.0 2.6 31 49-80 10-40 (677)
74 PRK12311 rpsB 30S ribosomal pr 62.9 5.9 0.00013 42.0 2.9 36 50-86 264-299 (326)
75 COG0632 RuvA Holliday junction 62.1 4.2 9.1E-05 40.3 1.5 43 14-66 80-125 (201)
76 PRK14601 ruvA Holliday junctio 61.4 3.9 8.5E-05 39.9 1.1 43 14-66 80-125 (183)
77 PRK00558 uvrC excinuclease ABC 58.7 13 0.00029 42.5 4.9 53 48-102 542-596 (598)
78 TIGR00575 dnlj DNA ligase, NAD 58.5 13 0.00028 43.0 4.9 16 51-66 468-483 (652)
79 PRK14606 ruvA Holliday junctio 58.2 4.6 0.0001 39.5 1.0 43 14-66 80-125 (188)
80 PRK12373 NADH dehydrogenase su 54.9 12 0.00026 40.8 3.5 36 50-86 324-359 (400)
81 PF07887 Calmodulin_bind: Calm 53.9 16 0.00035 38.4 4.1 49 51-100 164-217 (299)
82 PRK14604 ruvA Holliday junctio 52.5 6.8 0.00015 38.5 1.2 43 14-66 80-125 (195)
83 PRK14603 ruvA Holliday junctio 52.5 6.9 0.00015 38.5 1.2 43 14-66 79-124 (197)
84 PRK13766 Hef nuclease; Provisi 52.4 18 0.00038 42.2 4.7 50 51-102 717-768 (773)
85 TIGR00084 ruvA Holliday juncti 52.3 17 0.00037 35.5 3.9 51 51-104 74-130 (191)
86 PRK13901 ruvA Holliday junctio 51.7 6.6 0.00014 38.8 0.9 16 51-66 109-124 (196)
87 smart00278 HhH1 Helix-hairpin- 51.4 10 0.00022 25.1 1.5 16 51-66 3-18 (26)
88 PRK14602 ruvA Holliday junctio 50.4 8.7 0.00019 38.0 1.5 28 39-66 96-126 (203)
89 PTZ00134 40S ribosomal protein 48.8 13 0.00029 35.4 2.5 40 51-90 32-74 (154)
90 TIGR00426 competence protein C 46.3 22 0.00047 28.6 3.0 30 51-80 18-52 (69)
91 KOG2534 DNA polymerase IV (fam 46.2 23 0.0005 37.6 3.8 32 52-85 100-131 (353)
92 CHL00137 rps13 ribosomal prote 45.4 17 0.00037 33.3 2.5 39 50-88 18-59 (122)
93 PF00416 Ribosomal_S13: Riboso 44.9 17 0.00036 32.3 2.3 29 51-79 17-48 (107)
94 TIGR02027 rpoA DNA-directed RN 44.9 23 0.00049 37.1 3.7 54 46-101 232-287 (297)
95 TIGR03631 bact_S13 30S ribosom 44.9 20 0.00044 32.3 2.9 37 51-87 17-56 (113)
96 TIGR00084 ruvA Holliday juncti 44.2 8.8 0.00019 37.6 0.5 43 14-66 79-124 (191)
97 PRK14605 ruvA Holliday junctio 43.9 25 0.00055 34.5 3.6 53 52-104 76-131 (194)
98 COG5018 KapD Inhibitor of the 43.4 6.9 0.00015 38.1 -0.4 39 476-514 24-62 (210)
99 PRK14600 ruvA Holliday junctio 41.8 14 0.0003 36.1 1.4 14 53-66 111-124 (186)
100 PRK04053 rps13p 30S ribosomal 41.0 20 0.00044 33.9 2.4 41 50-90 26-69 (149)
101 PRK08097 ligB NAD-dependent DN 40.9 39 0.00084 38.6 4.9 50 51-101 427-479 (562)
102 TIGR00615 recR recombination p 40.1 25 0.00055 34.8 2.9 16 51-66 13-28 (195)
103 PRK14351 ligA NAD-dependent DN 40.0 40 0.00086 39.4 5.0 45 54-100 533-579 (689)
104 PRK05182 DNA-directed RNA poly 39.5 32 0.00069 36.2 3.8 51 46-98 246-298 (310)
105 PRK14668 uvrC excinuclease ABC 38.5 29 0.00062 39.7 3.5 49 48-98 524-574 (577)
106 PRK00076 recR recombination pr 38.5 27 0.00059 34.5 2.9 16 51-66 13-28 (196)
107 PRK13844 recombination protein 37.9 28 0.00061 34.6 2.9 16 51-66 17-32 (200)
108 PRK13482 DNA integrity scannin 37.1 48 0.0011 35.7 4.7 39 51-91 289-327 (352)
109 PRK05179 rpsM 30S ribosomal pr 36.6 34 0.00075 31.3 3.1 39 50-88 18-59 (122)
110 COG0322 UvrC Nuclease subunit 36.5 35 0.00075 39.1 3.7 50 47-99 528-579 (581)
111 TIGR01259 comE comEA protein. 36.5 34 0.00073 31.0 3.0 30 51-80 70-103 (120)
112 PRK07956 ligA NAD-dependent DN 36.2 47 0.001 38.6 4.8 16 51-66 481-496 (665)
113 CHL00013 rpoA RNA polymerase a 34.5 42 0.00091 35.7 3.7 55 45-101 259-315 (327)
114 PRK14350 ligA NAD-dependent DN 33.5 59 0.0013 37.9 5.0 52 50-101 437-490 (669)
115 TIGR03629 arch_S13P archaeal r 33.0 38 0.00082 31.9 2.8 40 50-89 22-64 (144)
116 TIGR01448 recD_rel helicase, p 32.5 58 0.0013 38.1 4.8 42 41-86 79-120 (720)
117 TIGR03252 uncharacterized HhH- 32.4 49 0.0011 32.3 3.5 57 51-138 117-173 (177)
118 COG0099 RpsM Ribosomal protein 31.0 61 0.0013 29.8 3.7 39 50-88 18-56 (121)
119 PRK02515 psbU photosystem II c 30.4 40 0.00088 31.4 2.4 53 18-81 40-93 (132)
120 PRK07945 hypothetical protein; 29.9 90 0.002 33.1 5.4 57 42-103 42-98 (335)
121 COG1555 ComEA DNA uptake prote 29.0 56 0.0012 30.8 3.2 30 52-81 100-133 (149)
122 PF14716 HHH_8: Helix-hairpin- 28.5 36 0.00079 27.4 1.6 16 51-66 49-64 (68)
123 PRK14604 ruvA Holliday junctio 27.2 81 0.0017 31.1 4.1 50 52-104 76-131 (195)
124 COG0353 RecR Recombinational D 26.4 56 0.0012 32.4 2.8 16 51-66 14-29 (198)
125 PRK14602 ruvA Holliday junctio 25.7 78 0.0017 31.3 3.7 50 52-104 77-132 (203)
126 smart00483 POLXc DNA polymeras 25.7 91 0.002 33.0 4.5 55 51-107 50-113 (334)
127 COG1796 POL4 DNA polymerase IV 25.6 41 0.0009 35.7 1.8 34 49-82 93-126 (326)
128 cd00166 SAM Sterile alpha moti 25.3 1.1E+02 0.0023 23.1 3.7 46 38-93 3-48 (63)
129 smart00279 HhH2 Helix-hairpin- 25.2 65 0.0014 23.2 2.3 16 51-66 18-33 (36)
130 COG4380 Uncharacterized protei 25.0 82 0.0018 30.6 3.5 31 61-92 76-106 (216)
131 cd00080 HhH2_motif Helix-hairp 24.4 64 0.0014 26.7 2.4 24 53-78 26-49 (75)
132 PF00730 HhH-GPD: HhH-GPD supe 23.9 1.2E+02 0.0025 26.0 4.1 47 59-105 15-66 (108)
133 PRK14603 ruvA Holliday junctio 23.6 1E+02 0.0022 30.4 4.0 51 52-105 75-131 (197)
134 PF07647 SAM_2: SAM domain (St 23.2 52 0.0011 25.7 1.6 46 38-92 5-50 (66)
135 PRK13901 ruvA Holliday junctio 23.2 1.1E+02 0.0024 30.3 4.2 50 52-104 75-130 (196)
136 PF12937 F-box-like: F-box-lik 22.7 44 0.00094 24.5 1.0 18 487-504 1-18 (47)
137 PRK14601 ruvA Holliday junctio 22.7 1.1E+02 0.0024 29.8 4.1 50 52-104 76-131 (183)
138 PF12836 HHH_3: Helix-hairpin- 22.2 58 0.0013 26.0 1.7 29 52-80 17-49 (65)
139 PF05643 DUF799: Putative bact 22.1 1.4E+02 0.003 30.1 4.7 63 27-92 31-107 (215)
140 PRK14606 ruvA Holliday junctio 21.7 1.2E+02 0.0026 29.7 4.1 50 52-104 76-131 (188)
141 PRK08609 hypothetical protein; 21.2 2.1E+02 0.0045 32.7 6.5 56 50-106 49-112 (570)
142 cd00141 NT_POLXc Nucleotidyltr 21.1 1.6E+02 0.0034 30.9 5.1 54 51-106 47-108 (307)
143 COG0177 Nth Predicted EndoIII- 21.0 1.1E+02 0.0023 30.8 3.6 50 90-144 118-167 (211)
144 KOG3285 Spindle assembly check 20.7 46 0.001 32.6 1.0 32 133-170 57-88 (203)
145 PF03538 VRP1: Salmonella viru 20.5 1.4E+02 0.003 31.9 4.6 46 59-104 15-63 (325)
No 1
>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=100.00 E-value=2.2e-38 Score=333.82 Aligned_cols=230 Identities=27% Similarity=0.397 Sum_probs=193.1
Q ss_pred ccchhcCceEEEEEcccHHHHHHHhcCCCCCCeEEecc---CCHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHh
Q 009729 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPF---SSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLL 78 (527)
Q Consensus 2 ~I~~etGLt~SIGIA~NKlLAKLAS~~aKPnG~~vl~~---e~v~~fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa 78 (527)
+|+++||||||||||+||+|||||++++||+|+++|.+ +++.+||+++||++|||||++++++|. .+||.|+|||+
T Consensus 122 ~I~~~~Glt~siGIa~nk~lAKlas~~~KP~g~~~i~~~~~~~~~~fl~~lpv~~l~GiG~~~~~kL~-~~GI~tigdl~ 200 (379)
T cd01703 122 RIENELGLTCCAGIASNKLLAKLVGSVNKPNQQTTLLPPSCADLMDFMDLHDLRKIPGIGYKTAAKLE-AHGISSVRDLQ 200 (379)
T ss_pred HHHHHhCCeEEEEEcCCHHHHHHHhhhcCCCCeEEEcCCchHHHHHHhccCCccccCCcCHHHHHHHH-HcCCCcHHHHH
Confidence 57889999999999999999999999999999999876 466789999999999999999999995 99999999999
Q ss_pred hcC---------------HHHHHHHhccchHHHHHHHHcCCcCccc-cccCCCccccccccCCCCCCCCCHHHHHHHHHH
Q 009729 79 KFS---------------EDKLQESYGFNTGTWLWNIARGISGEEV-QARLLPKSHGSGKSFPGPRALKTVASVQHWLNQ 142 (527)
Q Consensus 79 ~~~---------------~~~L~~~FG~~~G~~L~~~arGiD~~~V-~~~~~~KSIs~erTF~~~~di~~~eel~~~L~~ 142 (527)
.++ ...|+++||...|.+||+.|+|+|+++| .+...+|||+.++||.. .++.+.++++.+|..
T Consensus 201 ~~~~~~~~~~~~~~~~~s~~~L~~~fG~~~g~~l~~~a~G~d~~~V~~~~~~~ksis~e~tf~~-~~~~~~~~~~~~l~~ 279 (379)
T cd01703 201 EFSNRNRQTVGAAPSLLELLLMVKEFGEGIGQRIWKLLFGRDTSPVKPASDFPQQISIEDSYKK-CSLEEIREARNKIEE 279 (379)
T ss_pred hCCcccccccccccccccHHHHHHHHCHHHHHHHHHHHCCCCCCccCCCCCCCceeEEeeccCC-CCCCCHHHHHHHHHH
Confidence 999 9999999997569999999999999999 55567899999999983 389999999999999
Q ss_pred HHHHHHHHHHHhHHh----cCceeeEEEEEEEeccCCCCCCCCCcCcceeeCCCchhh-h---H-HhHHHHHHHHHHHHh
Q 009729 143 LCEELSERLCSDLEQ----NKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAK-I---Q-EDTFNLFQAGLREFL 213 (527)
Q Consensus 143 LaeeLa~RLr~dl~~----~~~~a~tLtL~iR~~~~~df~~~~~~~SkS~~Lp~~T~~-i---~-~~a~~Lf~aal~Ll~ 213 (527)
|+++|+.||++++.+ .++.++||+|++|+.+. ..+|..+.+++++++.+++. + . .+...|++.++.||.
T Consensus 280 l~~~l~~rl~~~l~~~~~~~~~~~~tv~l~vr~~~~--~~~~~~~~sr~~~l~~~~~~~~~~~~~~~~~~i~~~~~~L~~ 357 (379)
T cd01703 280 LLASLLERMKQDLQEVKAGDGRRPHTLRLTLRRYTS--TKKHYNRESKQAPIPSHVFQKLTGGNEIAARPIEKILMRLFR 357 (379)
T ss_pred HHHHHHHHHHhhhhccchhcCeeeeEEEEEEEECCC--CCCccceeeeccccCchhhccccccchhhHHHHHHHHHHHHH
Confidence 999999999986533 68899999999999651 11112346899999988841 1 1 145679999999998
Q ss_pred cccCccccCCccCCcceeEEEEEecC
Q 009729 214 GSFGVKTQGSHYSGWRITALSVSASK 239 (527)
Q Consensus 214 ~~~~~k~~~~~~~~~~IR~lGVsls~ 239 (527)
..++. ....+.+||++||++++
T Consensus 358 ~~~~~----~~~~~~~irl~gv~~~~ 379 (379)
T cd01703 358 ELVPP----KNVKGFNLTLLNVCFTN 379 (379)
T ss_pred Hhccc----ccCCCCceEEEEEEeeC
Confidence 64321 00124589999999975
No 2
>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=100.00 E-value=1.5e-38 Score=332.88 Aligned_cols=219 Identities=43% Similarity=0.629 Sum_probs=189.8
Q ss_pred ccchhcCceEEEEEcccHHHHHHHhcCCCCCCeEEeccCCHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhc-
Q 009729 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKF- 80 (527)
Q Consensus 2 ~I~~etGLt~SIGIA~NKlLAKLAS~~aKPnG~~vl~~e~v~~fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~- 80 (527)
+|++++|||||||||+||+|||||++++||+|+++++++++.+||+++||++|||||++++++|.+.+||+|++||+++
T Consensus 135 ~I~~~~glt~SiGIa~nk~lAKlAs~~~KP~g~~v~~~~~~~~~L~~lpv~~l~GiG~~~~~~ll~~~Gi~ti~dl~~~~ 214 (359)
T cd01702 135 QVYDELGYTCSAGIAHNKMLAKLASGMNKPNAQTILRNDAVASFLSSLPITSIRGLGGKLGEEIIDLLGLPTEGDVAGFR 214 (359)
T ss_pred HHHHHhCccEEeeecCCHHHHHHHhcccCCCCeEEECHHHHHHHhhcCcHHHhCCcCHHHHHHHHHHcCCcCHHHHHhcc
Confidence 5789999999999999999999999999999999999999999999999999999999998775458999999999999
Q ss_pred -CHHHHHHHhccchHHHHHHHHcCCcCccccccCCCccccccccCCCCCCCCCH-HHHHHHHHHHHHHHHHHHHHhHHhc
Q 009729 81 -SEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTV-ASVQHWLNQLCEELSERLCSDLEQN 158 (527)
Q Consensus 81 -~~~~L~~~FG~~~G~~L~~~arGiD~~~V~~~~~~KSIs~erTF~~~~di~~~-eel~~~L~~LaeeLa~RLr~dl~~~ 158 (527)
+...|+++||.+.|.+||+.|+|+|+++|.+..++|||+.++||. .++.+. +++..+|..||++|+.||+.++..+
T Consensus 215 ~~~~~L~~~fG~~~g~~l~~~a~G~d~~~v~~~~~~ksi~~~~tf~--~~~~~~~~~l~~~l~~L~~~l~~rL~~~~~~~ 292 (359)
T cd01702 215 SSESDLQEHFGEKLGEWLYNLLRGIDHEPVKPRPLPKSMGSSKNFP--GKTALSTEDVQHWLLVLASELNSRLEDDRYEN 292 (359)
T ss_pred CCHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCCceeeeeeecC--CCCCChHHHHHHHHHHHHHHHHHHHHhhhhhc
Confidence 999999999965899999999999999999888899999999999 688887 9999999999999999999855556
Q ss_pred CceeeEEEEEEEeccCCCCCCCCCcCcceeeCCCchhhhHHhHHHHHHHHHHHHhcccCccccCCccC---CcceeEEEE
Q 009729 159 KRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYS---GWRITALSV 235 (527)
Q Consensus 159 ~~~a~tLtL~iR~~~~~df~~~~~~~SkS~~Lp~~T~~i~~~a~~Lf~aal~Ll~~~~~~k~~~~~~~---~~~IR~lGV 235 (527)
++.+++|+|++++.++ + .+.+++.+++.++ ...|+.++.+||...+.. ... +.+||+|||
T Consensus 293 ~~~~~~v~v~lr~~~~--~----~~~sr~~~~~~~~------~~~i~~~~~~l~~~~~~~-----~~~~~~~~~~rl~g~ 355 (359)
T cd01702 293 NRRPKTLVLSLRQRGD--G----VRRSRSCALPRYD------AQKIVKDAFKLIKAINEE-----GLGLAWNYPLTLLSL 355 (359)
T ss_pred CceeeEEEEEEEECCC--c----EEEEEEecCCCCC------HHHHHHHHHHHHHHhhhh-----ccccccCCCeEEEEE
Confidence 9999999999998642 1 2346777777655 445777777777754321 111 479999999
Q ss_pred EecC
Q 009729 236 SASK 239 (527)
Q Consensus 236 sls~ 239 (527)
++++
T Consensus 356 ~~~~ 359 (359)
T cd01702 356 SFTK 359 (359)
T ss_pred EecC
Confidence 9875
No 3
>PTZ00205 DNA polymerase kappa; Provisional
Probab=100.00 E-value=3.8e-38 Score=342.34 Aligned_cols=216 Identities=21% Similarity=0.229 Sum_probs=190.0
Q ss_pred ccchhcCceEEEEEcccHHHHHHHhcCCCCCCeEEe---ccCCHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHh
Q 009729 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTV---PFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLL 78 (527)
Q Consensus 2 ~I~~etGLt~SIGIA~NKlLAKLAS~~aKPnG~~vl---~~e~v~~fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa 78 (527)
+|+++||||||||||+||+||||||+++||||++++ +++++..||++|||++|||||++++++|. .+||+||+||+
T Consensus 259 ~I~~~tgLt~SiGIA~NklLAKiASd~~KPnG~~vl~l~~~~~v~~fL~~LpV~ki~GIG~~t~~~L~-~~GI~TigDLa 337 (571)
T PTZ00205 259 RVFGETKLTASAGIGPTAALAKIASNINKPNGQHDLNLHTRGDVMTYVRDLGLRSVPGVGKVTEALLK-GLGITTLSDIY 337 (571)
T ss_pred HHHHHHCCcEEEEEcCCHHHHHHhhhccCCCCCeEEecCCHHHHHHHHhCCCcceeCCcCHHHHHHHH-HcCCCcHHHHh
Confidence 588999999999999999999999999999999986 67899999999999999999999999995 99999999999
Q ss_pred hcCHH--------HHHHHhccchHHHHHHHHcCCcCcc-cc--ccCCCccccccccCCCCCCCCCHHHHHHHHHHHHHHH
Q 009729 79 KFSED--------KLQESYGFNTGTWLWNIARGISGEE-VQ--ARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEEL 147 (527)
Q Consensus 79 ~~~~~--------~L~~~FG~~~G~~L~~~arGiD~~~-V~--~~~~~KSIs~erTF~~~~di~~~eel~~~L~~LaeeL 147 (527)
+.+.. .|+..||...|.++|..++|+|.++ +. ....+||||+++||. . +.+.+++...|..||++|
T Consensus 338 ~~~~~l~~~f~~k~l~~llG~~~G~~l~~~a~G~d~~~~v~~~~~~~rKSIg~ErTF~--~-~~d~~el~~~L~~L~~~v 414 (571)
T PTZ00205 338 NRRVELCYILHNNLFRFLLGASIGIMQWPDAATAANTENCEGATGGQRKAISSERSFT--T-PRTKEGLQEMVDTVFNGA 414 (571)
T ss_pred cCCHHHHHHhHHHHHHHHhCchhhHHHHHHhcCCCCCCccCCCCCCCCceeEEeEeCC--C-CCCHHHHHHHHHHHHHHH
Confidence 98876 4778899767999999999999885 33 245689999999998 4 579999999999999999
Q ss_pred HHHHHHhHHhcCceeeEEEEEEEeccCCCCCCCCCcCcceeeCCCchhhhHHhHHHHHHHHHHHHhcccCccccCCccCC
Q 009729 148 SERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSG 227 (527)
Q Consensus 148 a~RLr~dl~~~~~~a~tLtL~iR~~~~~df~~~~~~~SkS~~Lp~~T~~i~~~a~~Lf~aal~Ll~~~~~~k~~~~~~~~ 227 (527)
+.||++ .++.|++|+|++|+.+ |.. .+++.+|+.||+ +...|+++|..||... .+..
T Consensus 415 ~~rLrk----~~l~artVtlKlK~~d---F~~----~trs~tL~~pT~----d~~~I~~aa~~Ll~~~--------~~~~ 471 (571)
T PTZ00205 415 YEEMRK----SELMCRQISLTIRWAS---YRY----QQYTKSLIQYSD----DSATLRRAVDGLLLPH--------AAKY 471 (571)
T ss_pred HHHHHh----cCCCccEEEEEEEECC---CCc----eEEEEECCCCcC----CHHHHHHHHHHHHHhc--------cccC
Confidence 999997 8999999999999854 343 377899999984 6778999999888642 1334
Q ss_pred cceeEEEEEecCCcccc
Q 009729 228 WRITALSVSASKIVPVL 244 (527)
Q Consensus 228 ~~IR~lGVsls~L~~~~ 244 (527)
.+||+|||++++|....
T Consensus 472 ~~vRLlGV~ls~L~~~~ 488 (571)
T PTZ00205 472 SEMCLLGVRFLDLISAK 488 (571)
T ss_pred CCEEEEEEEEcccCcHH
Confidence 68999999999998864
No 4
>PRK03348 DNA polymerase IV; Provisional
Probab=100.00 E-value=1.5e-37 Score=334.29 Aligned_cols=225 Identities=28% Similarity=0.375 Sum_probs=203.4
Q ss_pred ccchhcCceEEEEEcccHHHHHHHhcCCCCCCeEEeccCCHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcC
Q 009729 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFS 81 (527)
Q Consensus 2 ~I~~etGLt~SIGIA~NKlLAKLAS~~aKPnG~~vl~~e~v~~fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~ 81 (527)
+|++++|||||||||+||+|||||++++||+|+++++++++.+||++|||++|||||++++++|. .+||+||+||++++
T Consensus 133 ~I~~~~Gl~~SvGIa~nk~lAKlAs~~aKP~G~~vi~~~~~~~~L~~LPv~~L~GIG~~t~~~L~-~lGI~TigDLa~l~ 211 (454)
T PRK03348 133 RVREETGLPASVGAGSGKQIAKIASGLAKPDGIRVVPPGEERELLAPLPVRRLWGIGPVTEEKLH-RLGIETIGDLAALS 211 (454)
T ss_pred HHHHHHCCCeEEEEcCCHHHHHHhhccCCCCcEEEEEchHHHHHHHhCCccccCCCCHHHHHHHH-HcCCccHHHHhcCC
Confidence 47789999999999999999999999999999999999999999999999999999999999995 99999999999999
Q ss_pred HHHHHHHhccchHHHHHHHHcCCcCccccccCCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhHHhcCce
Q 009729 82 EDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRI 161 (527)
Q Consensus 82 ~~~L~~~FG~~~G~~L~~~arGiD~~~V~~~~~~KSIs~erTF~~~~di~~~eel~~~L~~LaeeLa~RLr~dl~~~~~~ 161 (527)
...|.++||...|.+||++|+|+|+++|.+..++|+|+.+++|+ .++.+.++++.+|..|+++|+.||++ .++.
T Consensus 212 ~~~L~~~fG~~~g~~L~~~a~G~d~~pv~~~~~~ksis~e~tf~--~~i~~~~~l~~~L~~L~~~l~~rL~~----~g~~ 285 (454)
T PRK03348 212 EAEVANLLGATVGPALHRLARGIDDRPVAERAEAKQISAESTFA--VDLTTRAQLREAIERIAEHAHRRLLK----DGRG 285 (454)
T ss_pred HHHHHHHHCHHHHHHHHHHHcCCCCCCcccCCCCceEEEEEECC--CCCCCHHHHHHHHHHHHHHHHHHHHH----cCCC
Confidence 99999999965899999999999999999888899999999998 78999999999999999999999997 8999
Q ss_pred eeEEEEEEEeccCCCCCCCCCcCcceeeCCCchhhhHHhHHHHHHHHHHHHhcccCccccCCccCCcceeEEEEEecCCc
Q 009729 162 AHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIV 241 (527)
Q Consensus 162 a~tLtL~iR~~~~~df~~~~~~~SkS~~Lp~~T~~i~~~a~~Lf~aal~Ll~~~~~~k~~~~~~~~~~IR~lGVsls~L~ 241 (527)
+++|+|++++.+ +.. .+++.+++++|+ +...|++.+..+|... +...+||++||++++|.
T Consensus 286 ~r~v~l~l~~~d---~~~----~srs~~l~~pt~----d~~~L~~la~~ll~~~---------~~~~~vRllgV~~s~l~ 345 (454)
T PRK03348 286 ARTVTVKLRKSD---FST----LTRSATLPYATD----DAAVLAATARRLLLDP---------DEIGPIRLVGVGFSGLS 345 (454)
T ss_pred ccEEEEEEEeCC---CCc----cEEEEECCCCCC----CHHHHHHHHHHHHHhh---------ccCCCeEEEEEEECCCC
Confidence 999999999854 333 478999999985 6777888888888743 23458999999999997
Q ss_pred cccCCccccccccCCCC
Q 009729 242 PVLSGTCSIMKYFNGPD 258 (527)
Q Consensus 242 ~~~~g~~sq~~lF~~~~ 258 (527)
+. .|.+||...+
T Consensus 346 ~~-----~q~~LF~~~~ 357 (454)
T PRK03348 346 DV-----RQESLFPELD 357 (454)
T ss_pred cc-----hhhccCCCcc
Confidence 52 5789997544
No 5
>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=100.00 E-value=7.5e-38 Score=331.94 Aligned_cols=220 Identities=25% Similarity=0.295 Sum_probs=195.7
Q ss_pred ccchhcCceEEEEEcccHHHHHHHhcCCCCCCeEEeccCCHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcC
Q 009729 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFS 81 (527)
Q Consensus 2 ~I~~etGLt~SIGIA~NKlLAKLAS~~aKPnG~~vl~~e~v~~fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~ 81 (527)
+|++++|||||||||+||++||||++++||+|++++.++++..||++|||++|||||++++++|. .+||+|++||+.++
T Consensus 175 ~I~~~~gl~~siGia~nk~lAKlAs~~aKP~g~~~i~~~~~~~~L~~lPv~~l~GIG~~~~~~L~-~~Gi~t~~dl~~~~ 253 (404)
T cd01701 175 EIRETTGCSASVGIGPNILLARLATRKAKPDGQYHLSAEKVEEFLSQLKVGDLPGVGSSLAEKLV-KLFGDTCGGLELRS 253 (404)
T ss_pred HHHHHHCCCEEEEEcCCHHHHHHHhcccCCCcEEEECHHHHHHHhhcCCHhHhCCCCHHHHHHHH-HcCCcchHHHHhCc
Confidence 47889999999999999999999999999999999999999999999999999999999999995 99999999999999
Q ss_pred --HHHHHHHhccchHHHHHHHHcCCcCccccccCCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhHHhcC
Q 009729 82 --EDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNK 159 (527)
Q Consensus 82 --~~~L~~~FG~~~G~~L~~~arGiD~~~V~~~~~~KSIs~erTF~~~~di~~~eel~~~L~~LaeeLa~RLr~dl~~~~ 159 (527)
...|+++||...|.+||+.|+|+|+++|.+..++|||+.++||+ .++.+.+++..+|..|+++|+.||+. ++
T Consensus 254 ~~~~~L~~~fG~~~g~~L~~~a~G~d~~~v~~~~~~ksi~~~~tf~--~~~~~~~~l~~~l~~L~~~l~~rLr~----~~ 327 (404)
T cd01701 254 KTKEKLQKVLGPKTGEKLYDYCRGIDDRPVTGEKERKSVSAEINYG--IRFTNVDDVEQFLQRLSEELSKRLEE----SN 327 (404)
T ss_pred ccHHHHHHHHCHHHHHHHHHHhCCcCCCCCCCCCCCccccceeeCC--CCCCCHHHHHHHHHHHHHHHHHHHHH----cC
Confidence 99999999975799999999999999998888899999999998 78999999999999999999999997 89
Q ss_pred ceeeEEEEEEEecc--CC----CCCCC--CCcCcceeeCCCchhhhHHhHHHHHHHHHHHHhcccCccccCCccCCccee
Q 009729 160 RIAHTLTLHASAFK--SS----DSDSR--KKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRIT 231 (527)
Q Consensus 160 ~~a~tLtL~iR~~~--~~----df~~~--~~~~SkS~~Lp~~T~~i~~~a~~Lf~aal~Ll~~~~~~k~~~~~~~~~~IR 231 (527)
+.+++|+|+++|.. +. .+.++ .+..+++.+|+.||+ +...|+++|.+||...+ ..+.+||
T Consensus 328 ~~~~~l~l~l~~~~~~~~~~~~~y~g~~~~~~~~~~~~l~~pT~----d~~~i~~~a~~ll~~~~--------~~~~~vR 395 (404)
T cd01701 328 VTGRQITLKLMKRAPGAPIEPPKYMGHGICDSFSKSSTLGVATD----DSGVIGTEAKKLFRDLS--------IPPEELR 395 (404)
T ss_pred CceeeEEEEEEeccccCccccccccccCCCcEEeeeeECCCCCC----CHHHHHHHHHHHHHhcc--------CCCCCee
Confidence 99999999999732 11 11111 124578999999995 77789999999997531 2356899
Q ss_pred EEEEEecCC
Q 009729 232 ALSVSASKI 240 (527)
Q Consensus 232 ~lGVsls~L 240 (527)
+|||++++|
T Consensus 396 ~lgv~~~~l 404 (404)
T cd01701 396 GVGIQVTKL 404 (404)
T ss_pred EEEEEEecC
Confidence 999999986
No 6
>PRK14133 DNA polymerase IV; Provisional
Probab=100.00 E-value=1.3e-37 Score=323.13 Aligned_cols=222 Identities=27% Similarity=0.340 Sum_probs=201.3
Q ss_pred ccchhcCceEEEEEcccHHHHHHHhcCCCCCCeEEeccCCHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcC
Q 009729 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFS 81 (527)
Q Consensus 2 ~I~~etGLt~SIGIA~NKlLAKLAS~~aKPnG~~vl~~e~v~~fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~ 81 (527)
+|++++|||||||||+||++||||++++||+|+++++++++..||+++||++|||||+++.++|. .+||+|++||++++
T Consensus 126 ~i~~~~gl~~siGia~n~~~Aklas~~~kp~g~~~~~~~~~~~~L~~lpv~~l~gig~~~~~~L~-~~Gi~ti~dl~~l~ 204 (347)
T PRK14133 126 KVKKETGLTLSVGISYNKFLAKLASDWNKPDGIKIITEDMIPDILKPLPISKVHGIGKKSVEKLN-NIGIYTIEDLLKLS 204 (347)
T ss_pred HHHHHHCCcEEEEEcCcHHHHHHHhccCCCCceEEECHHHHHHHHHhCCccccCCCCHHHHHHHH-HcCCccHHHHhhCC
Confidence 57899999999999999999999999999999999999999999999999999999999999995 99999999999999
Q ss_pred HHHHHHHhccchHHHHHHHHcCCcCccccccCCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhHHhcCce
Q 009729 82 EDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRI 161 (527)
Q Consensus 82 ~~~L~~~FG~~~G~~L~~~arGiD~~~V~~~~~~KSIs~erTF~~~~di~~~eel~~~L~~LaeeLa~RLr~dl~~~~~~ 161 (527)
...|.++||. .|.++|+.++|+|+.+|.+..++|||+.+++|. .++.+.+++..+|..|+++|+.||++ +++.
T Consensus 205 ~~~L~~rfG~-~g~~l~~~a~G~d~~~v~~~~~~ksi~~~~~~~--~~~~~~~~l~~~l~~L~~~l~~rL~~----~~~~ 277 (347)
T PRK14133 205 REFLIEYFGK-FGVEIYERIRGIDYREVEVSRERKSIGKETTLK--KDTKDKEELKKYLKDFSNIISEELKK----RNLY 277 (347)
T ss_pred HHHHHHHHhH-HHHHHHHHhCCCCCCCCCCCCCCcceEeeEEcC--CCCCCHHHHHHHHHHHHHHHHHHHHh----cCCC
Confidence 9999999997 799999999999999999888899999999998 78999999999999999999999997 8999
Q ss_pred eeEEEEEEEeccCCCCCCCCCcCcceeeCCCchhhhHHhHHHHHHHHHHHHhcccCccccCCccCCcceeEEEEEecCCc
Q 009729 162 AHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIV 241 (527)
Q Consensus 162 a~tLtL~iR~~~~~df~~~~~~~SkS~~Lp~~T~~i~~~a~~Lf~aal~Ll~~~~~~k~~~~~~~~~~IR~lGVsls~L~ 241 (527)
+++|+|++++.+ +.. .+++++++.+|+ +...|++.+..+|... +.+.+||.|||++++|.
T Consensus 278 ~~~l~l~l~~~~---~~~----~~~~~~l~~~t~----~~~~l~~l~~~lle~~---------~~~~~vr~lgl~~~~l~ 337 (347)
T PRK14133 278 GKTVTVKIKTSD---FQT----HTKSKTLNDYIR----DKEEIYNVACEILEHI---------NIKEPIRLIGLSVSNLS 337 (347)
T ss_pred cceEEEEEEECC---CCe----eEEEEECCCCcC----CHHHHHHHHHHHHHhc---------cCCCCEEEEEEEEecCC
Confidence 999999999853 333 367899999884 6778899888888753 34679999999999999
Q ss_pred cccCCcccccccc
Q 009729 242 PVLSGTCSIMKYF 254 (527)
Q Consensus 242 ~~~~g~~sq~~lF 254 (527)
+.. ..|.+||
T Consensus 338 ~~~---~~q~~l~ 347 (347)
T PRK14133 338 ENK---IEQLSFL 347 (347)
T ss_pred CCc---ccccCCC
Confidence 752 4467776
No 7
>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=100.00 E-value=2.1e-37 Score=321.14 Aligned_cols=217 Identities=28% Similarity=0.393 Sum_probs=190.9
Q ss_pred ccchhcC-ceEEEEEcccHHHHHHHhcCCCCCCeEEeccCCHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhc
Q 009729 2 QVLKETE-FTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKF 80 (527)
Q Consensus 2 ~I~~etG-Lt~SIGIA~NKlLAKLAS~~aKPnG~~vl~~e~v~~fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~ 80 (527)
+|++++| ||||||||+||++||||++++||+|+++++++++.+||+++||++|||||++++++|. .+||+|++||+++
T Consensus 125 ~i~~~~ggl~~siGia~n~~lAKlAs~~~KP~g~~v~~~~~~~~~L~~lpi~~l~giG~~~~~~L~-~~Gi~ti~dl~~~ 203 (343)
T cd00424 125 HIAEQLGGITASIGIASNKLLAKLAAKYAKPDGLTILDPEDLPGFLSKLPLTDLPGIGAVTAKRLE-AVGINPIGDLLAA 203 (343)
T ss_pred HHHHHhCCceEEEeecccHHHHHHHhccCCCCCEEEEcHHHHHHHHhcCChhhcCCCCHHHHHHHH-HcCCCcHHHHhcC
Confidence 5778998 9999999999999999999999999999999999999999999999999999999995 9999999999999
Q ss_pred C-HHHHHHHhccchHHHHHHHHcCCcCccccccCCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhHHhcC
Q 009729 81 S-EDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNK 159 (527)
Q Consensus 81 ~-~~~L~~~FG~~~G~~L~~~arGiD~~~V~~~~~~KSIs~erTF~~~~di~~~eel~~~L~~LaeeLa~RLr~dl~~~~ 159 (527)
+ ...|+++||+ .|.++|+.|+|+|+++|.+..++|||+.++||+ .++.+.+++..+|..|+++|+.||+. .+
T Consensus 204 ~~~~~l~~~fg~-~~~~l~~~a~G~d~~~v~~~~~~ksi~~~~tf~--~~~~~~~~l~~~l~~l~~~l~~rL~~----~~ 276 (343)
T cd00424 204 SPDALLALWGGV-SGERLWYALRGIDDEPLSPPRPRKSFSHERVLP--RDSRNAEDARPLLRLLLEKLARRLRR----DG 276 (343)
T ss_pred CHHHHHHHHhhH-HHHHHHHHhCCcCCCCCCCCCCCCceeeeEECC--CCCCCHHHHHHHHHHHHHHHHHHHHH----cC
Confidence 9 8889999997 799999999999999998888899999999999 78999999999999999999999997 79
Q ss_pred ceeeEEEEEEEeccCCCCCCCCCcCcceeeCCCchhhhHHhHHHHHHHHHHHHhcccCccccCCccCCcceeEEEEEec
Q 009729 160 RIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSAS 238 (527)
Q Consensus 160 ~~a~tLtL~iR~~~~~df~~~~~~~SkS~~Lp~~T~~i~~~a~~Lf~aal~Ll~~~~~~k~~~~~~~~~~IR~lGVsls 238 (527)
+.+++|+|++++.+... .++..+.+++++++.+| +...|++++.+||...++ ...+.+||+|||+++
T Consensus 277 ~~~~~l~l~lr~~~~~~-~~~~~~~~~~~~l~~~t-----~~~~l~~~~~~l~~~~~~------~~~~~~ir~~gv~~~ 343 (343)
T cd00424 277 RGATRLRLWLRTVDGRW-SGHADIPSRSAPRPIST-----EDGELLHALDKLWRALLD------DKGPRRLRRLGVRLS 343 (343)
T ss_pred CceeEEEEEEEeCCCcc-cccceeeeeeeeCCCCC-----CHHHHHHHHHHHHHhhhh------ccCCCCeeEEEEEeC
Confidence 99999999999865311 01112358899999887 345788888888875321 013578999999874
No 8
>PRK02794 DNA polymerase IV; Provisional
Probab=100.00 E-value=8.4e-38 Score=332.68 Aligned_cols=225 Identities=24% Similarity=0.326 Sum_probs=203.0
Q ss_pred ccchhcCceEEEEEcccHHHHHHHhcCCCCCCeEEeccCCHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcC
Q 009729 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFS 81 (527)
Q Consensus 2 ~I~~etGLt~SIGIA~NKlLAKLAS~~aKPnG~~vl~~e~v~~fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~ 81 (527)
+|++++|||||||||+||++||||++.+||+|++++.++++.+||+++||++|||||+++.++|. .+||+|++||++++
T Consensus 162 ~i~~~~gl~~svGIa~n~~lAKlas~~~KP~g~~ii~~~~~~~~L~~lPl~~L~GiG~~~~~~L~-~~GI~tigdL~~l~ 240 (419)
T PRK02794 162 RVEREIGITVSVGLSYNKFLAKIASDLDKPRGFSVIGRAEALAFLAPKPVGIIWGVGPATAARLA-RDGIRTIGDLQRAD 240 (419)
T ss_pred HHHHHHCCceEEEEcCCHHHHHHHHhhhCCCCeEecCHHHHHHHHhcCChhhhCCCCHHHHHHHH-HhccchHHHHhhCC
Confidence 47789999999999999999999999999999999999999999999999999999999999995 99999999999999
Q ss_pred HHHHHHHhccchHHHHHHHHcCCcCccccccCCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhHHhcCce
Q 009729 82 EDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRI 161 (527)
Q Consensus 82 ~~~L~~~FG~~~G~~L~~~arGiD~~~V~~~~~~KSIs~erTF~~~~di~~~eel~~~L~~LaeeLa~RLr~dl~~~~~~ 161 (527)
...|+++||. .|.++|+.++|+|+.+|.+..++|||+.+++|+ .++.+.+++..+|..|+++|+.||+. .++.
T Consensus 241 ~~~L~~rfG~-~g~~l~~~a~G~d~~~v~~~~~~ksi~~~~tl~--~~~~~~~~l~~~l~~L~~~l~~rL~~----~~~~ 313 (419)
T PRK02794 241 EADLMRRFGS-MGLRLWRLARGIDDRKVSPDREAKSVSAETTFE--TDLSDFEDLEPILWRLSEKVSRRLKA----AGLA 313 (419)
T ss_pred HHHHHHHHhH-HHHHHHHHhCCCCCCCCccCCCCceeeeeEECC--CCCCCHHHHHHHHHHHHHHHHHHHHh----cCCC
Confidence 9999999998 799999999999999998888899999999999 78999999999999999999999997 8999
Q ss_pred eeEEEEEEEeccCCCCCCCCCcCcceeeCCCchhhhHHhHHHHHHHHHHHHhcccCccccCCccCCcceeEEEEEecCCc
Q 009729 162 AHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIV 241 (527)
Q Consensus 162 a~tLtL~iR~~~~~df~~~~~~~SkS~~Lp~~T~~i~~~a~~Lf~aal~Ll~~~~~~k~~~~~~~~~~IR~lGVsls~L~ 241 (527)
+++|+|++++.+ |.. .+++++++.||+ +...|++.+..+|... +.+.+||.|||++++|.
T Consensus 314 ~~~l~l~l~~~~---~~~----~~~~~~l~~pt~----~~~~l~~~~~~ll~~~---------~~~~~vr~igv~~~~l~ 373 (419)
T PRK02794 314 GRTVTLKLKTAD---FRL----RTRRRTLEDPTQ----LADRIFRTARELLEKE---------TDGTAFRLIGIGVSDLS 373 (419)
T ss_pred cceEEEEEEECC---CCc----eEEEEECCCCcC----CHHHHHHHHHHHHHhc---------ccCCCEEEEEEEEecCC
Confidence 999999999754 332 368889998884 6777888888888742 34678999999999999
Q ss_pred cccCCccccccccCC
Q 009729 242 PVLSGTCSIMKYFNG 256 (527)
Q Consensus 242 ~~~~g~~sq~~lF~~ 256 (527)
+.. ...|.+||+.
T Consensus 374 ~~~--~~~q~~LF~~ 386 (419)
T PRK02794 374 PAD--EADPPDLLDP 386 (419)
T ss_pred Ccc--ccccccccCc
Confidence 753 1247889974
No 9
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=100.00 E-value=2.2e-37 Score=329.74 Aligned_cols=231 Identities=18% Similarity=0.207 Sum_probs=200.2
Q ss_pred ccchhcCceEEEEEcccHHHHHHHhcCCCC-----CCeEEe-ccCCHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHH
Q 009729 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKP-----AQQTTV-PFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVG 75 (527)
Q Consensus 2 ~I~~etGLt~SIGIA~NKlLAKLAS~~aKP-----nG~~vl-~~e~v~~fL~~LPI~kLpGIG~k~~~kL~~~lGI~Tig 75 (527)
+|++++|||||||||+||++|||||+.+|| +|+++| +++++..||++|||++|||||+++.++|. .+||+|+|
T Consensus 126 ~I~~~~gl~~siGia~n~~lAK~As~~~k~~~k~~~g~~~i~~~~~~~~~L~~lPv~~l~GiG~~~~~~L~-~lGi~Tig 204 (422)
T PRK03609 126 TVLQRTHLTVGVGIAQTKTLAKLANHAAKKWQRQTGGVVDLSNLERQRKLLSLQPVEEVWGVGRRISKKLN-AMGIKTAL 204 (422)
T ss_pred HHHHHHCCceEEEecCCHHHHHHHHHHhCCCCCCCCcEEEcCCHHHHHHHhhcCChhhcCCccHHHHHHHH-HcCCCcHH
Confidence 478999999999999999999999987776 688888 68899999999999999999999999995 99999999
Q ss_pred HHhhcCHHHHHHHhccchHHHHHHHHcCCcCccccccCC-CccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Q 009729 76 DLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLL-PKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSD 154 (527)
Q Consensus 76 DLa~~~~~~L~~~FG~~~G~~L~~~arGiD~~~V~~~~~-~KSIs~erTF~~~~di~~~eel~~~L~~LaeeLa~RLr~d 154 (527)
||++++...|+++||+ .|.++|+.|+|+|+.++....+ +|+|+.++||+ .++.+.+++...+..|+++|+.||++
T Consensus 205 dL~~~~~~~L~~~fG~-~~~~l~~~a~G~~~~~~~~~~~~~ksi~~~~tf~--~~~~~~~~l~~~l~~l~~~l~~rLr~- 280 (422)
T PRK03609 205 DLADTNIRFIRKHFNV-VLERTVRELRGEPCLSLEEFAPTKQEIVCSRSFG--ERITDYESMRQAICSYAARAAEKLRG- 280 (422)
T ss_pred HHhcCCHHHHHHHHCH-HHHHHHHHhCCCCCCCccccCCCCceEEEeeECC--CCCCCHHHHHHHHHHHHHHHHHHHHH-
Confidence 9999999999999998 7999999999999999876655 47999999998 78999999999999999999999997
Q ss_pred HHhcCceeeEEEEEEEeccCCCCCCCCCcCcceeeCCCchhhhHHhHHHHHHHHHHHHhcccCccccCCccCCcceeEEE
Q 009729 155 LEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALS 234 (527)
Q Consensus 155 l~~~~~~a~tLtL~iR~~~~~df~~~~~~~SkS~~Lp~~T~~i~~~a~~Lf~aal~Ll~~~~~~k~~~~~~~~~~IR~lG 234 (527)
+++.+++|+|++||.++..... .+..+++.+++.||+ +...|++.+.++|...+ ..+.++|++|
T Consensus 281 ---~~~~~~~l~l~ir~~~~~~~~~-~~~~~~~~~l~~pt~----d~~~l~~~a~~ll~~~~--------~~~~~~r~~G 344 (422)
T PRK03609 281 ---EHQYCRFISTFVKTSPFALNEP-YYGNSASVKLLTPTQ----DSRDIIAAATRALDAIW--------RDGHRYQKAG 344 (422)
T ss_pred ---cCCcccEEEEEEEcCCccccCC-CcCceeEEeCCCCCC----CHHHHHHHHHHHHHHHh--------CCCCceEEee
Confidence 8999999999999965421000 123467788998884 67789999998887532 2356899999
Q ss_pred EEecCCccccCCccccccccCC
Q 009729 235 VSASKIVPVLSGTCSIMKYFNG 256 (527)
Q Consensus 235 Vsls~L~~~~~g~~sq~~lF~~ 256 (527)
|.+++|.+.. ..|.+||+.
T Consensus 345 V~~~~l~~~~---~~q~~LF~~ 363 (422)
T PRK03609 345 VMLGDFFSQG---VAQLNLFDD 363 (422)
T ss_pred EEEEeeccCC---CcCccCccc
Confidence 9999999752 457899974
No 10
>PRK01810 DNA polymerase IV; Validated
Probab=100.00 E-value=5e-37 Score=325.16 Aligned_cols=225 Identities=27% Similarity=0.400 Sum_probs=201.4
Q ss_pred ccchhcCceEEEEEcccHHHHHHHhcCCCCCCeEEeccCCHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcC
Q 009729 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFS 81 (527)
Q Consensus 2 ~I~~etGLt~SIGIA~NKlLAKLAS~~aKPnG~~vl~~e~v~~fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~ 81 (527)
+|++++|||||||||+||++||||++.+||+|++++.++++..||+++||++|||||+++.++|. .+||+|+|||+.++
T Consensus 132 ~i~~~~gl~~svGia~n~~lAklas~~~Kp~g~~vi~~~~~~~~L~~lpv~~l~giG~~~~~~L~-~~Gi~tigdL~~~~ 210 (407)
T PRK01810 132 RLLTELQLPCSIGIAPNKFLAKMASDMKKPLGITVLRKRDVPEMLWPLPVGEMHGIGEKTAEKLK-DIGIQTIGDLAKAD 210 (407)
T ss_pred HHHHHHCCceEEEEcCCHHHHHHHhcCCCCCCEEEECHHHHHHHHHhCCHhhcCCcCHHHHHHHH-HcCCCcHHHHHhCC
Confidence 47889999999999999999999999999999999999999999999999999999999999995 99999999999999
Q ss_pred HHHHHHHhccchHHHHHHHHcCCcCccccccC--CCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhHHhcC
Q 009729 82 EDKLQESYGFNTGTWLWNIARGISGEEVQARL--LPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNK 159 (527)
Q Consensus 82 ~~~L~~~FG~~~G~~L~~~arGiD~~~V~~~~--~~KSIs~erTF~~~~di~~~eel~~~L~~LaeeLa~RLr~dl~~~~ 159 (527)
...|+++||. .|.++|+.|+|+|+.+|.+.. .+|||+.+++|+ .++.+.+++..+|..|+++|+.||+. .+
T Consensus 211 ~~~L~~rfG~-~g~~l~~~a~G~d~~~v~~~~~~~~ksi~~~~~~~--~~~~~~~~l~~~l~~L~~~l~~rLr~----~~ 283 (407)
T PRK01810 211 EHILRAKLGI-NGVRLQRRANGIDDRPVDPEAIYQFKSVGNSTTLS--HDMDEEKELLDVLRRLSKSVSKRLQK----KT 283 (407)
T ss_pred HHHHHHHHhH-HHHHHHHHhcCCCCCCCCCCCCCCCceecceEECC--CCCCCHHHHHHHHHHHHHHHHHHHHH----cC
Confidence 9999999998 799999999999999998654 369999999999 78999999999999999999999997 89
Q ss_pred ceeeEEEEEEEeccCCCCCCCCCcCcceeeCCCchhhhHHhHHHHHHHHHHHHhcccCccccCCccCCcceeEEEEEecC
Q 009729 160 RIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASK 239 (527)
Q Consensus 160 ~~a~tLtL~iR~~~~~df~~~~~~~SkS~~Lp~~T~~i~~~a~~Lf~aal~Ll~~~~~~k~~~~~~~~~~IR~lGVsls~ 239 (527)
+.+++|+|++++.++ .. .+++.+++.||+ +...|+..+..+|... +.+.+||++||++++
T Consensus 284 ~~~~~l~l~lr~~~~---~~----~~~~~~l~~pt~----~~~~l~~~~~~ll~~~---------~~~~~vr~lgv~~~~ 343 (407)
T PRK01810 284 VVSYNVQIMIRYHDR---RT----ITRSKTLKNPIW----EKRDIFQAASRLFKQH---------WNGDPVRLLGVTATD 343 (407)
T ss_pred CccceeEEEEEECCC---Cc----eEEEEECCCCCC----CHHHHHHHHHHHHHhc---------cCCCCEEEEEEEEec
Confidence 999999999998543 22 368888999984 6778999999888753 345689999999999
Q ss_pred CccccCCccccccccC
Q 009729 240 IVPVLSGTCSIMKYFN 255 (527)
Q Consensus 240 L~~~~~g~~sq~~lF~ 255 (527)
|.+... ...|.+||+
T Consensus 344 l~~~~~-~~~q~~Lf~ 358 (407)
T PRK01810 344 LEWKTE-AVKQLDLFS 358 (407)
T ss_pred Cccccc-ccccccccc
Confidence 987531 245779997
No 11
>PRK01216 DNA polymerase IV; Validated
Probab=100.00 E-value=4.3e-37 Score=321.05 Aligned_cols=212 Identities=25% Similarity=0.374 Sum_probs=189.0
Q ss_pred ccchhcCceEEEEEcccHHHHHHHhcCCCCCCeEEeccCCHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcC
Q 009729 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFS 81 (527)
Q Consensus 2 ~I~~etGLt~SIGIA~NKlLAKLAS~~aKPnG~~vl~~e~v~~fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~ 81 (527)
+|++++|||||||||+||++|||||+++||+|+++++++++.+||++|||+++||||++++++|. .+||+|+|||++++
T Consensus 131 ~I~~~~glt~siGia~nk~lAKlas~~~KP~g~~vi~~~~~~~~L~~LPi~~l~giG~~~~~~L~-~~Gi~TigdL~~~~ 209 (351)
T PRK01216 131 KILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRFINELDIADIPGIGDITAEKLK-KLGVNKLVDTLRIE 209 (351)
T ss_pred HHHHHHCCcEEEEecCCHHHHHHHHhccCCCCEEEeCHHHHHHHHhcCCcccccCCCHHHHHHHH-HcCCCcHHHHhcCC
Confidence 47899999999999999999999999999999999999999999999999999999999999995 99999999999999
Q ss_pred HHHHHHHhccchHHHHHHHHcCCcCccccccCCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhHHhcCce
Q 009729 82 EDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRI 161 (527)
Q Consensus 82 ~~~L~~~FG~~~G~~L~~~arGiD~~~V~~~~~~KSIs~erTF~~~~di~~~eel~~~L~~LaeeLa~RLr~dl~~~~~~ 161 (527)
...|.++||...|.+||+.++|+|.++|.+ ..+||++.++||. .++.+.+++...|..|+++++.||+. .
T Consensus 210 ~~~L~~rfG~~~~~~L~~~a~G~d~~pv~~-~~~ksi~~~~tl~--~di~~~~~l~~~l~~L~~~~~~rl~~-------~ 279 (351)
T PRK01216 210 FDELKGIIGEAKAKYLFSLARNEYNEPVRA-RVRKSIGRYVTLP--RNTRDLEEIKPYLKRAIEEAYYKLDG-------I 279 (351)
T ss_pred HHHHHHHHCHHHHHHHHHHhCCCCCCCCCC-CCCCCCcCeEECC--CccCCHHHHHHHHHHHHHHHHHHHHh-------C
Confidence 999999999756999999999999999987 4569999999998 79999999999999999999999984 4
Q ss_pred eeEEEEEEEeccCCCCCCCCCcCcceeeCCCchhhhHHhHHHHHHHHHHHHhcccCccccCCccCCcceeEEEEEecCCc
Q 009729 162 AHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIV 241 (527)
Q Consensus 162 a~tLtL~iR~~~~~df~~~~~~~SkS~~Lp~~T~~i~~~a~~Lf~aal~Ll~~~~~~k~~~~~~~~~~IR~lGVsls~L~ 241 (527)
+++++++++|. +|.+ .+++.+++.+|+ ...|+++|.+||...+ .+.+.+||+|||++++|.
T Consensus 280 ~~~~~~~~~~~---df~~----~t~~~tl~~~~~-----~~~~~~~a~~Ll~~~~-------~~~~~~vRllGv~~~~l~ 340 (351)
T PRK01216 280 PKAIHVVAIME---DLDI----VSRGRTFTHGIS-----KETAYREAVRLLQKIL-------EEDERKIRRIGVRFSKII 340 (351)
T ss_pred CCEEEEEEEcC---CCCE----EEEEEECCCCCC-----HHHHHHHHHHHHHhhh-------hcCCCCeeEEEEEEeccc
Confidence 78899999974 4443 589999998883 3557899998887431 112458999999999998
Q ss_pred cc
Q 009729 242 PV 243 (527)
Q Consensus 242 ~~ 243 (527)
+.
T Consensus 341 ~~ 342 (351)
T PRK01216 341 EA 342 (351)
T ss_pred cc
Confidence 75
No 12
>PRK03858 DNA polymerase IV; Validated
Probab=100.00 E-value=6.7e-37 Score=322.71 Aligned_cols=228 Identities=23% Similarity=0.285 Sum_probs=201.7
Q ss_pred ccchhcCceEEEEEcccHHHHHHHhcCCCCCCeEEeccCCHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcC
Q 009729 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFS 81 (527)
Q Consensus 2 ~I~~etGLt~SIGIA~NKlLAKLAS~~aKPnG~~vl~~e~v~~fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~ 81 (527)
+|++++|||||||||+||++||||++++||+|+++++++++..||+++||++|||||++++++|. .+||+|++||++++
T Consensus 126 ~i~~~~gl~~svGia~n~~lAklas~~~Kp~g~~~i~~~~~~~~L~~lpl~~l~Gig~~~~~~L~-~~Gi~t~~dl~~l~ 204 (396)
T PRK03858 126 RVREEVGLPITVGVARTKFLAKVASQVAKPDGLLVVPPDRELAFLHPLPVRRLWGVGPVTAAKLR-AHGITTVGDVAELP 204 (396)
T ss_pred HHHHHHCCCeEEEEcCChHHHHHhhcccCCCceEEECcHHHHHHHhcCChhhcCCCCHHHHHHHH-HhCCCcHHHHhcCC
Confidence 57789999999999999999999999999999999999999999999999999999999999995 99999999999999
Q ss_pred HHHHHHHhccchHHHHHHHHcCCcCccccccCCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhHHhcCce
Q 009729 82 EDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRI 161 (527)
Q Consensus 82 ~~~L~~~FG~~~G~~L~~~arGiD~~~V~~~~~~KSIs~erTF~~~~di~~~eel~~~L~~LaeeLa~RLr~dl~~~~~~ 161 (527)
...|.++||...|++||+.++|+|+++|.+..++|||+.+++|+ .++.+.++++.+|..|+++|+.||++ .++.
T Consensus 205 ~~~L~~~fG~~~~~~l~~~a~G~d~~~v~~~~~~ksi~~~~t~~--~~~~~~~~l~~~l~~L~~~l~~rLr~----~~~~ 278 (396)
T PRK03858 205 ESALVSLLGPAAGRHLHALAHNRDPRRVETGRRRRSVGAQRALG--RGPNSPAEVDAVVVALVDRVARRMRA----AGRT 278 (396)
T ss_pred HHHHHHHhCcHHHHHHHHHhCCCCCCCCCCCCCCccccceeEcC--CCCCCHHHHHHHHHHHHHHHHHHHHh----cCCC
Confidence 99999999986799999999999999998877889999999998 78999999999999999999999997 7999
Q ss_pred eeEEEEEEEeccCCCCCCCCCcCcceeeCCCchhhhHHhHHHHHHHHHHHHhcccCccccCCccCCcceeEEEEEecCCc
Q 009729 162 AHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIV 241 (527)
Q Consensus 162 a~tLtL~iR~~~~~df~~~~~~~SkS~~Lp~~T~~i~~~a~~Lf~aal~Ll~~~~~~k~~~~~~~~~~IR~lGVsls~L~ 241 (527)
+++|+|++++.++ .. .+++++++.+|+ +...|++.+..+|...+. ...+.+||++||.+++|.
T Consensus 279 ~~~l~l~l~~~~~---~~----~~~~~~l~~~t~----~~~~l~~l~~~ll~~~~~------~~~~~~irligv~~~~l~ 341 (396)
T PRK03858 279 GRTVVLRLRFDDF---TR----ATRSHTLPRPTA----STATLLAAARDLVAAAAP------LIAERGLTLVGFAVSNLD 341 (396)
T ss_pred cceEEEEEEeCCC---CE----EEEEEECCCCcC----CHHHHHHHHHHHHHhhhh------ccCCCCeEEEEEEeecCC
Confidence 9999999998543 32 467889998885 566788888888865321 112468999999999998
Q ss_pred cccCCccccccc-cCC
Q 009729 242 PVLSGTCSIMKY-FNG 256 (527)
Q Consensus 242 ~~~~g~~sq~~l-F~~ 256 (527)
+.. ..|.+| |+.
T Consensus 342 ~~~---~~q~~L~f~~ 354 (396)
T PRK03858 342 DDG---AQQLELPFGL 354 (396)
T ss_pred ccc---ccccCCCccc
Confidence 752 446777 753
No 13
>PRK03103 DNA polymerase IV; Reviewed
Probab=100.00 E-value=9e-37 Score=323.38 Aligned_cols=227 Identities=25% Similarity=0.404 Sum_probs=203.0
Q ss_pred ccchhcCceEEEEEcccHHHHHHHhcC---CCCCCeEEeccCCHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHh
Q 009729 2 QVLKETEFTCSAGIAHNKMLAKLASGM---NKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLL 78 (527)
Q Consensus 2 ~I~~etGLt~SIGIA~NKlLAKLAS~~---aKPnG~~vl~~e~v~~fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa 78 (527)
+|++++|||||||||+||++||||+++ +||+|++++.++++..||+++||++|||||+++.++|. .+||+|+|||+
T Consensus 131 ~i~~~~gl~~svGia~n~~lAklas~~~~k~kp~g~~v~~~~~~~~~L~~lpi~~l~gig~~~~~~L~-~~Gi~tigdl~ 209 (409)
T PRK03103 131 RIMRETGVYARVGIGPNKLLAKMACDNFAKKNPDGLFTLDKEDVPADLWPLPVRKLFGVGSRMEKHLR-RMGIRTIGQLA 209 (409)
T ss_pred HHHHHHCceEEEeecCCHHHHHHHhcchhhcCCCcEEEECHHHHHHHHHcCCHhhcCCccHHHHHHHH-HcCCCCHHHHh
Confidence 477899999999999999999999998 99999999999999999999999999999999999995 99999999999
Q ss_pred hcCHHHHHHHhccchHHHHHHHHcCCcCccccccCC--CccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhHH
Q 009729 79 KFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLL--PKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLE 156 (527)
Q Consensus 79 ~~~~~~L~~~FG~~~G~~L~~~arGiD~~~V~~~~~--~KSIs~erTF~~~~di~~~eel~~~L~~LaeeLa~RLr~dl~ 156 (527)
+++...|+++||. .|.++|+.++|+|+++|.+..+ +|||+.+++|+ .++.+.+++...|..|+++|+.||++
T Consensus 210 ~~~~~~L~~~fG~-~~~~l~~~a~G~d~~~v~~~~~~~~ksi~~~~t~~--~~~~~~~~l~~~l~~L~~~l~~rLr~--- 283 (409)
T PRK03103 210 NTPLERLKKRWGI-NGEVLWRTANGIDYSPVTPHSLDRQKAIGHQMTLP--RDYRGFEEIKVVLLELCEEVCRRARA--- 283 (409)
T ss_pred cCCHHHHHHHHCH-HHHHHHHHhcCCCCCcCCcccCCCCCccCCCeECC--CCCCCHHHHHHHHHHHHHHHHHHHHH---
Confidence 9999999999997 7999999999999999987643 68999999998 78999999999999999999999997
Q ss_pred hcCceeeEEEEEEEeccCCCCCCCCCcCcceeeCCCchhhhHHhHHHHHHHHHHHHhcccCccccCCccCCcceeEEEEE
Q 009729 157 QNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVS 236 (527)
Q Consensus 157 ~~~~~a~tLtL~iR~~~~~df~~~~~~~SkS~~Lp~~T~~i~~~a~~Lf~aal~Ll~~~~~~k~~~~~~~~~~IR~lGVs 236 (527)
.++.+++|+|++++.++ +. .+..+++++++.||+ +...|+..+..+|.. .+.+.+||+|||+
T Consensus 284 -~~~~~~~l~l~lr~~~~---~~-~~~~~~~~~l~~pt~----~~~~l~~~~~~ll~~---------~~~~~~vr~lgv~ 345 (409)
T PRK03103 284 -KGYMGRTVSVSLRGADF---DW-PTGFSRQMTLPEPTN----LAMEVYEAACKLFHR---------HWDGKPVRRVGVT 345 (409)
T ss_pred -hCCceeEEEEEEEeCCC---cC-CCCcceeeecCCCCC----CHHHHHHHHHHHHHh---------cccCCCceEEEEE
Confidence 79999999999998643 22 123578889998884 677899998888875 2457899999999
Q ss_pred ecCCccccCCccccccccCC
Q 009729 237 ASKIVPVLSGTCSIMKYFNG 256 (527)
Q Consensus 237 ls~L~~~~~g~~sq~~lF~~ 256 (527)
+++|.+. ...|.+||+.
T Consensus 346 ~~~l~~~---~~~q~~LF~~ 362 (409)
T PRK03103 346 LSNLVSD---DVWQLSLFGD 362 (409)
T ss_pred EeCCCCC---cccCCCcccc
Confidence 9999975 3567899974
No 14
>PRK03352 DNA polymerase IV; Validated
Probab=100.00 E-value=2.6e-36 Score=313.18 Aligned_cols=215 Identities=27% Similarity=0.362 Sum_probs=194.3
Q ss_pred ccchhcCceEEEEEcccHHHHHHHhcCCCCCCeEEeccCCHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcC
Q 009729 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFS 81 (527)
Q Consensus 2 ~I~~etGLt~SIGIA~NKlLAKLAS~~aKPnG~~vl~~e~v~~fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~ 81 (527)
+|++++|||||||||+||++||||++.+||+|++++.++++..||+++||++|||||+++.++|. .+||+|+|||+.++
T Consensus 130 ~i~~~~gl~~siGia~nk~lAklaa~~~Kp~g~~~~~~~~~~~~L~~lpl~~l~gig~~~~~~L~-~~Gi~ti~dl~~l~ 208 (346)
T PRK03352 130 AVLERTGLSCSVGIGDNKLRAKIATGFAKPAGVFRLTDANWMAVMGDRPTDALWGVGPKTAKRLA-ALGITTVADLAAAD 208 (346)
T ss_pred HHHHHHCCCEEEeecCCHHHHHHHHhhcCCCcEEEECHHHHHHHHhcCCHHHcCCCCHHHHHHHH-HcCCccHHHHhcCC
Confidence 57788999999999999999999999999999999999999999999999999999999999995 99999999999999
Q ss_pred HHHHHHHhccchHHHHHHHHcCCcCcccccc-CCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhHHhcCc
Q 009729 82 EDKLQESYGFNTGTWLWNIARGISGEEVQAR-LLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKR 160 (527)
Q Consensus 82 ~~~L~~~FG~~~G~~L~~~arGiD~~~V~~~-~~~KSIs~erTF~~~~di~~~eel~~~L~~LaeeLa~RLr~dl~~~~~ 160 (527)
...|.++||...|.+||+.++|+|.+++... ..+||++.+++|+ .++.+.+++..+|..|+++|+.||+. +++
T Consensus 209 ~~~L~~~fG~~~~~~l~~~a~G~d~~~~~~~~~~~ksi~~~~tf~--~~~~~~~~l~~~l~~L~~~l~~rLr~----~~~ 282 (346)
T PRK03352 209 PAELAATFGPTTGPWLLLLARGGGDTEVSAEPWVPRSRSREVTFP--QDLTDRAEVESAVRELARRVLDEVVA----EGR 282 (346)
T ss_pred HHHHHHHhChHHHHHHHHHhCCCCCCCCCCCCCCCceEEEEEECC--CCCCCHHHHHHHHHHHHHHHHHHHHH----cCC
Confidence 9999999997679999999999999998764 3579999999998 78999999999999999999999997 899
Q ss_pred eeeEEEEEEEeccCCCCCCCCCcCcceeeCCCchhhhHHhHHHHHHHHHHHHhcccCccccCCccCCcceeEEEEEecCC
Q 009729 161 IAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKI 240 (527)
Q Consensus 161 ~a~tLtL~iR~~~~~df~~~~~~~SkS~~Lp~~T~~i~~~a~~Lf~aal~Ll~~~~~~k~~~~~~~~~~IR~lGVsls~L 240 (527)
.+++|+|++++.++ .. .+++++++.||+ +...|+..+..+|.+. +.+.+||.|||++.+|
T Consensus 283 ~~~~l~l~l~~~~~---~~----~~~~~~l~~pt~----d~~~l~~~~~~ll~~~---------~~~~~vr~igl~~~~~ 342 (346)
T PRK03352 283 PVTRVAVKVRTATF---YT----RTKIRKLPEPTT----DPDVIEAAALDVLDRF---------ELDRPVRLLGVRLELA 342 (346)
T ss_pred ccceEEEEEEeCCC---ce----eEEEEECCCCcC----CHHHHHHHHHHHHHhc---------cCCCCEEEEEEEEecc
Confidence 99999999998543 22 367888998884 6778888888888742 3456899999999999
Q ss_pred ccc
Q 009729 241 VPV 243 (527)
Q Consensus 241 ~~~ 243 (527)
.+.
T Consensus 343 ~~~ 345 (346)
T PRK03352 343 MPD 345 (346)
T ss_pred CCC
Confidence 864
No 15
>PRK02406 DNA polymerase IV; Validated
Probab=100.00 E-value=5.5e-36 Score=310.40 Aligned_cols=213 Identities=27% Similarity=0.340 Sum_probs=189.7
Q ss_pred ccchhcCceEEEEEcccHHHHHHHhcCCCCCCeEEeccCCHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcC
Q 009729 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFS 81 (527)
Q Consensus 2 ~I~~etGLt~SIGIA~NKlLAKLAS~~aKPnG~~vl~~e~v~~fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~ 81 (527)
+|++++|||||||||+||++||||++++||+|+++++++++..||+++||++|||||+++.++|. .+||+|+|||++++
T Consensus 121 ~i~~~~gl~~siGia~n~~lAklas~~~Kp~g~~~~~~~~~~~~L~~lpi~~l~giG~~~~~~L~-~~Gi~ti~dl~~l~ 199 (343)
T PRK02406 121 DIFEELGLTASAGVAPNKFLAKIASDWNKPNGLFVITPEEVDAFLATLPVEKIPGVGKVTAEKLH-ALGIYTCADLQKYD 199 (343)
T ss_pred HHHHHHCCCeEEEeccCHHHHHHHhcCCCCCCEEEECHHHHHHHHHcCCcchhcCCCHHHHHHHH-HcCCCcHHHHHhCC
Confidence 47889999999999999999999999999999999999999999999999999999999999995 99999999999999
Q ss_pred HHHHHHHhccchHHHHHHHHcCCcCccccccCCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhHHhcC--
Q 009729 82 EDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNK-- 159 (527)
Q Consensus 82 ~~~L~~~FG~~~G~~L~~~arGiD~~~V~~~~~~KSIs~erTF~~~~di~~~eel~~~L~~LaeeLa~RLr~dl~~~~-- 159 (527)
...|.++||. .|.++|+.++|+|+.+|.+..++|+|+.+++|+ .++.+.+++..+|..|+++|+.||+. .+
T Consensus 200 ~~~L~~~fG~-~~~~l~~~a~G~d~~~v~~~~~~ksi~~~~~~~--~~~~~~~~l~~~l~~l~~~l~~rL~~----~~~~ 272 (343)
T PRK02406 200 LAELIRHFGK-FGRRLYERARGIDERPVKPDRERKSVGVERTFA--EDLYDLEACLAELPRLAEKLERRLER----AKPD 272 (343)
T ss_pred HHHHHHHHhH-HHHHHHHHhCCCCCCccccCCCCcceeeeeeCC--CCCCCHHHHHHHHHHHHHHHHHHHHh----cCCC
Confidence 9999999997 799999999999999998877899999999998 78999999999999999999999997 78
Q ss_pred ceeeEEEEEEEeccCCCCCCCCCcCcceeeCCCchhhhHHhHHHHHHHHHHHHhcccCccccCCccCCcceeEEEEEecC
Q 009729 160 RIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASK 239 (527)
Q Consensus 160 ~~a~tLtL~iR~~~~~df~~~~~~~SkS~~Lp~~T~~i~~~a~~Lf~aal~Ll~~~~~~k~~~~~~~~~~IR~lGVsls~ 239 (527)
+.+++|+|++++.+ +.. .+++.+ ..++ ++...|+..+.+|+.. .+ +.+||.|||++++
T Consensus 273 ~~~~~l~l~l~~~~---~~~----~~~~~~-~~~~----~~~~~l~~~~~~L~~~---------~~-~~~vr~lgv~~~~ 330 (343)
T PRK02406 273 KRIKTVGVKLKFAD---FQQ----TTKEHT-ADPL----DKADLIELLAQALLRR---------LG-GRGVRLLGVGVTL 330 (343)
T ss_pred ccceeEEEEEEeCC---CCe----EEEecC-CCCC----CcHHHHHHHHHHHHhh---------Cc-CCCEEEEEEEEec
Confidence 99999999999854 232 245555 4445 3555677777777763 23 6789999999999
Q ss_pred Ccccc
Q 009729 240 IVPVL 244 (527)
Q Consensus 240 L~~~~ 244 (527)
|.+..
T Consensus 331 l~~~~ 335 (343)
T PRK02406 331 LEPQL 335 (343)
T ss_pred CCcCc
Confidence 99753
No 16
>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=100.00 E-value=1.9e-35 Score=303.86 Aligned_cols=211 Identities=33% Similarity=0.457 Sum_probs=193.3
Q ss_pred ccchhcCceEEEEEcccHHHHHHHhcCCCCCCeEEeccCCHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcC
Q 009729 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFS 81 (527)
Q Consensus 2 ~I~~etGLt~SIGIA~NKlLAKLAS~~aKPnG~~vl~~e~v~~fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~ 81 (527)
+|++++||+||||||+|+++||||++.+||+|+++++++++..||+++||+++||||++++++|. .+||+|++||++++
T Consensus 124 ~i~~~~g~~~siGia~n~~lAklaa~~~kp~g~~i~~~~~~~~~L~~lpl~~l~gig~~~~~~L~-~~Gi~ti~dl~~~~ 202 (334)
T cd03586 124 RIREETGLTASAGIAPNKFLAKIASDLNKPNGLTVIPPEDVEEFLAPLPVRKIPGVGKVTAEKLK-ELGIKTIGDLAKLD 202 (334)
T ss_pred HHHHHHCCceEEEEhhcHHHHHHHhcCCCCCcEEEECHHHHHHHHhcCCchhhCCcCHHHHHHHH-HcCCcCHHHHHcCC
Confidence 46789999999999999999999999999999999999999999999999999999999999995 99999999999999
Q ss_pred HHHHHHHhccchHHHHHHHHcCCcCccccccCCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhHHhcCce
Q 009729 82 EDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRI 161 (527)
Q Consensus 82 ~~~L~~~FG~~~G~~L~~~arGiD~~~V~~~~~~KSIs~erTF~~~~di~~~eel~~~L~~LaeeLa~RLr~dl~~~~~~ 161 (527)
...|.++||. .|.++|+.++|+|+.+|.+..++|+|+.+++|+ .++.+.+++..+|..|+++|+.||+. .++.
T Consensus 203 ~~~L~~~~g~-~~~~l~~~~~G~~~~~v~~~~~~ks~~~~~~~~--~~~~~~~~l~~~l~~l~~~l~~rL~~----~~~~ 275 (334)
T cd03586 203 VELLKKLFGK-SGRRLYELARGIDNRPVEPDRERKSIGVERTFS--EDLTDPEELLEELLELAEELAERLRK----RGLK 275 (334)
T ss_pred HHHHHHHHhH-HHHHHHHHhCCCCCCCCCCCCCCCeeeeeEECC--CCCCCHHHHHHHHHHHHHHHHHHHHh----CCCC
Confidence 9999999997 899999999999999999888899999999998 78999999999999999999999997 7999
Q ss_pred eeEEEEEEEeccCCCCCCCCCcCcceeeCCCchhhhHHhHHHHHHHHHHHHhcccCccccCCccCCcceeEEEEEecCC
Q 009729 162 AHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKI 240 (527)
Q Consensus 162 a~tLtL~iR~~~~~df~~~~~~~SkS~~Lp~~T~~i~~~a~~Lf~aal~Ll~~~~~~k~~~~~~~~~~IR~lGVsls~L 240 (527)
+++|+|++++.++ . ..+++.+++.||+ +...|++.+..+|... +.+.+||+|||++++|
T Consensus 276 ~~~l~l~l~~~~~---~----~~~~~~~l~~~t~----~~~~l~~~~~~~l~~~---------~~~~~vr~igv~~~~l 334 (334)
T cd03586 276 GRTVTVKLKYADF---S----TRTRSRTLPEPTD----DAEDIYELALELLEEL---------LDGRPIRLLGVRLSGL 334 (334)
T ss_pred eEEEEEEEEECCC---C----eEEEEEECCCCCC----CHHHHHHHHHHHHHhc---------cCCCCEEEEEEEeecC
Confidence 9999999998542 2 2478888998884 6778899888888753 3347899999999986
No 17
>KOG2095 consensus DNA polymerase iota/DNA damage inducible protein [Replication, recombination and repair]
Probab=100.00 E-value=3.2e-35 Score=318.33 Aligned_cols=167 Identities=57% Similarity=0.877 Sum_probs=162.9
Q ss_pred ccchhcCceEEEEEcccHHHHHHHhcCCCCCCeEEeccCCHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcC
Q 009729 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFS 81 (527)
Q Consensus 2 ~I~~etGLt~SIGIA~NKlLAKLAS~~aKPnG~~vl~~e~v~~fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~ 81 (527)
+|+.+||||||+|||+||+|||||+.++|||.||+|++..+.+||..|||+++|++|+++++.|.+.|||.++|||++++
T Consensus 209 ~i~~elg~tCSAGIa~NKmLAKLvsg~nKPnqQTil~~~~v~~ll~slpi~k~~~lGGk~G~~lie~LGi~~vgdl~~fs 288 (656)
T KOG2095|consen 209 AIKLELGYTCSAGIAHNKMLAKLVSGRNKPNQQTILPNTYVQDLLDSLPITKIRTLGGKLGEELIEVLGIDSVGDLQQFS 288 (656)
T ss_pred HHHHHhCceeeccccccHHHHHHHhccCCCCcceecchHHHHHHHHhCCCceeeeccchHHHHHHHHhCCchHHHHHhcC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhccchHHHHHHHHcCCcCccccccCCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhHHhcCce
Q 009729 82 EDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRI 161 (527)
Q Consensus 82 ~~~L~~~FG~~~G~~L~~~arGiD~~~V~~~~~~KSIs~erTF~~~~di~~~eel~~~L~~LaeeLa~RLr~dl~~~~~~ 161 (527)
+.+|++.||.++|.|||..|+|||.++|.++..+|||+++++|++...+.+.+++..||..++++++.||..+.....+.
T Consensus 289 e~~L~~~fg~~~g~~l~~la~Gid~s~V~pr~~pkSig~~K~Fpg~~~~~~~~~l~~wl~~la~el~~Rl~~d~~en~r~ 368 (656)
T KOG2095|consen 289 ETQLQKKFGEKNGTWLRNLARGIDNSPVRPRGLPKSIGSEKNFPGKRSRKSLEELQRWLNQLAEELAERLGKDRNENKRR 368 (656)
T ss_pred HHHHHHhhCcchhHHHHHHhcccCCCccccCCCCcchhhhhcCCCccccccHHHHHHHHHHHHHHHHHHHHhhhhhhccc
Confidence 99999999988999999999999999999999999999999999878899999999999999999999999988888999
Q ss_pred eeEEEEE
Q 009729 162 AHTLTLH 168 (527)
Q Consensus 162 a~tLtL~ 168 (527)
+.+++++
T Consensus 369 as~l~~~ 375 (656)
T KOG2095|consen 369 ASTLVVS 375 (656)
T ss_pred cceEEee
Confidence 9999999
No 18
>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=100.00 E-value=7.2e-35 Score=302.17 Aligned_cols=215 Identities=27% Similarity=0.397 Sum_probs=186.1
Q ss_pred ccchhcCceEEEEEcccHHHHHHHhcCCCCC----CeEEeccCCHH-hhcccCCCCcccCCcHHHHHHHHHhcCCCcHHH
Q 009729 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPA----QQTTVPFSSVK-GLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGD 76 (527)
Q Consensus 2 ~I~~etGLt~SIGIA~NKlLAKLAS~~aKPn----G~~vl~~e~v~-~fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigD 76 (527)
+|++++|||||||||+||++||||++++||+ |++++++++.. .||+++||++|||||+++.++|. .+||+|+||
T Consensus 124 ~i~~~~gl~~s~Gia~~~~lAklas~~~kp~~~~~g~~~~~~~~~~~~~l~~lpl~~l~gig~~~~~~L~-~~Gi~ti~d 202 (344)
T cd01700 124 RILQETGIPVTVGIGPTKTLAKLANDLAKKKNPYGGVVDLTDEEVRDKLLKILPVGDVWGIGRRTAKKLN-AMGIHTAGD 202 (344)
T ss_pred HHHHHhCCceEEEecCCHHHHHHHHHHhcCCCCCCeEEEecChhHHHHHhccCChhhcCccCHHHHHHHH-HcCCCcHHH
Confidence 4788999999999999999999999999984 88888776665 99999999999999999999995 999999999
Q ss_pred HhhcCHHHHHHHhccchHHHHHHHHcCCcCccccccC-CCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhH
Q 009729 77 LLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARL-LPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDL 155 (527)
Q Consensus 77 La~~~~~~L~~~FG~~~G~~L~~~arGiD~~~V~~~~-~~KSIs~erTF~~~~di~~~eel~~~L~~LaeeLa~RLr~dl 155 (527)
|++++...|.++||. .|.++|+.++|+|+++|.... ++|||+.+++|. .++.+.+++..+|..|+++|+.||+.
T Consensus 203 L~~~~~~~L~~rfG~-~~~~l~~~a~G~d~~~v~~~~~~~ks~~~~~~~~--~~~~~~~~l~~~l~~L~~~l~~~L~~-- 277 (344)
T cd01700 203 LAQADPDLLRKKFGV-VGERLVRELNGIDCLPLEEYPPPKKSIGSSRSFG--RDVTDLDELKQALAEYAERAAEKLRR-- 277 (344)
T ss_pred HhcCCHHHHHHHHHH-HHHHHHHHhCCCCCCcCCCCCCCCcEEEEeeEcC--CCCCCHHHHHHHHHHHHHHHHHHHHH--
Confidence 999999999999997 799999999999999997544 459999999998 78999999999999999999999997
Q ss_pred HhcCceeeEEEEEEEeccCCCCCCCCCcCcceeeCCCchhhhHHhHHHHHHHHHHHHhcccCccccCCccCCcceeEEEE
Q 009729 156 EQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSV 235 (527)
Q Consensus 156 ~~~~~~a~tLtL~iR~~~~~df~~~~~~~SkS~~Lp~~T~~i~~~a~~Lf~aal~Ll~~~~~~k~~~~~~~~~~IR~lGV 235 (527)
+++.+++|+|++++.++ .......+.+.+++.||+ +...|+..++.+|...+ ..+.+||+|||
T Consensus 278 --~~~~~~~l~l~l~~~~~---~~~~~~~~~~~~~~~~t~----~~~~l~~~~~~ll~~~~--------~~~~~iR~iGV 340 (344)
T cd01700 278 --QKSVARTISVFIGTSGF---SRQPKYYSATNTLPYPTN----DTREIVKAALRLLYAIY--------RPGYAYRKAGV 340 (344)
T ss_pred --cCCcccEEEEEEEcCCC---CCCCCccccccccCCcch----hHHHHHHHHHHHHHHHh--------CCCCcEEEEEE
Confidence 89999999999998643 322122334456777884 67788999888887532 24678999999
Q ss_pred EecC
Q 009729 236 SASK 239 (527)
Q Consensus 236 sls~ 239 (527)
++++
T Consensus 341 ~~~~ 344 (344)
T cd01700 341 MLSD 344 (344)
T ss_pred EeeC
Confidence 9975
No 19
>COG0389 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]
Probab=100.00 E-value=2.9e-33 Score=292.54 Aligned_cols=217 Identities=30% Similarity=0.428 Sum_probs=194.7
Q ss_pred ccchhcCceEEEEEcccHHHHHHHhcCCCCCCeEEeccCCHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcC
Q 009729 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFS 81 (527)
Q Consensus 2 ~I~~etGLt~SIGIA~NKlLAKLAS~~aKPnG~~vl~~e~v~~fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~ 81 (527)
.|+.++|||||+|||+||++||||++++||+|++++.++++.+||++|||.++||||++++++|. .+||.||+||+..+
T Consensus 129 ~i~~~~~l~~s~Gi~~nk~laKiAs~~~kp~gi~~~~~~~~~~~l~~Lpv~~~~GvG~~~~~~l~-~~Gi~ti~dl~~~~ 207 (354)
T COG0389 129 GILLELGLTASVGISDNKFLAKIASDLNKPDGITVIEPEEVPALLWQLPVLEFWGVGKVTAEKLR-RLGISTIGDLAETD 207 (354)
T ss_pred HHHHhhCCEEEEEecCcHHHHHHHhcccCCCCEEEECHHHHHHHHhcCChhhhCCCCHHHHHHHH-HcCChhHHHHHhcC
Confidence 47899999999999999999999999999999999999999999999999999999999999995 99999999999999
Q ss_pred HHHHHHHhccchHHHHHHHHcCCcCccccccCCC-ccccccccCCCCCCCCCHHHHHHHHHH-HHHHHHHHHHHhHHhcC
Q 009729 82 EDKLQESYGFNTGTWLWNIARGISGEEVQARLLP-KSHGSGKSFPGPRALKTVASVQHWLNQ-LCEELSERLCSDLEQNK 159 (527)
Q Consensus 82 ~~~L~~~FG~~~G~~L~~~arGiD~~~V~~~~~~-KSIs~erTF~~~~di~~~eel~~~L~~-LaeeLa~RLr~dl~~~~ 159 (527)
.+.|.++||. .|.+||+.++|+|.++|.+.... ||++.+.||+ .++.+.+++...|.. |+++++.||+. .+
T Consensus 208 ~~~L~~~~g~-~~~~l~~~a~Gid~~~v~~~~~~~ksi~~~~t~~--~d~~~~~~~~~~l~~~l~e~~~~rl~~----~~ 280 (354)
T COG0389 208 LDALKKRFGK-LGERLYRLARGIDNRPVREQALRAKSIGAESTFE--EDLTDAEELIERLRARLGEEVVSRLRK----SG 280 (354)
T ss_pred HHHHHHHHhH-hHHHHHHHhcCCCccccccccccCccccceeecc--ccccCHHHHHHHHHHHHHHHHHHHHHH----hC
Confidence 9999999998 78999999999999999998877 9999999999 799999988888888 99999999997 78
Q ss_pred ceeeEEEEEEEeccCCCCCCCCCcCcceeeCCCchhhhHHhHHHHHHHHHHHHhcccCccccCCccCCcceeEEEEEecC
Q 009729 160 RIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASK 239 (527)
Q Consensus 160 ~~a~tLtL~iR~~~~~df~~~~~~~SkS~~Lp~~T~~i~~~a~~Lf~aal~Ll~~~~~~k~~~~~~~~~~IR~lGVsls~ 239 (527)
..+++|++++++.++ .+ .+++.+|+.|++ +..+++.++..+|...+. .+.+.++|++||++++
T Consensus 281 ~~~r~v~~~~~~~df---~~----~t~~~~l~~p~~----~~~~i~~~~~~l~~~~~~------~~~~~~~rl~gv~~~~ 343 (354)
T COG0389 281 RHGRTVSVKLKTADF---PT----NTRSRKLAQPTS----DPIEIYAAALPLLPPLLF------RGRGRRIRLLGVSGPE 343 (354)
T ss_pred CCceEEEEEEEecCC---Cc----ceeecccCCcCC----CHHHHHHHHHHHHHHhhc------cCCCceEEEEEEEecC
Confidence 889999999998654 33 578888998884 466788888888765321 1336789999999999
Q ss_pred Cccc
Q 009729 240 IVPV 243 (527)
Q Consensus 240 L~~~ 243 (527)
|.+.
T Consensus 344 ~~~~ 347 (354)
T COG0389 344 LIDS 347 (354)
T ss_pred cccc
Confidence 9875
No 20
>KOG2094 consensus Predicted DNA damage inducible protein [Replication, recombination and repair]
Probab=99.98 E-value=6.4e-32 Score=275.23 Aligned_cols=213 Identities=25% Similarity=0.331 Sum_probs=183.3
Q ss_pred ccchhcCceEEEEEcccHHHHHHHhcCCCCCCeEEeccC--CHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhh
Q 009729 2 QVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFS--SVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLK 79 (527)
Q Consensus 2 ~I~~etGLt~SIGIA~NKlLAKLAS~~aKPnG~~vl~~e--~v~~fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~ 79 (527)
+|+++||+|||+|||+|++|||++|+++|||||++|+++ .+..||..|||+++-|||+.++..|. .|||.||||+.+
T Consensus 233 rV~qeTglT~SaGIAaN~lLAKicSd~nKPNgQf~i~~dr~aim~F~kdLPvRkV~GIGrV~E~qLk-al~IkTcgdm~~ 311 (490)
T KOG2094|consen 233 RVEQETGLTCSAGIAANKLLAKICSDKNKPNGQFVIPNDRIAIMKFMKDLPVRKVSGIGRVTEQQLK-ALGIKTCGDMQQ 311 (490)
T ss_pred HHHHhcCceeeccccHhHHHHHHhccccCCCCceEecccHHHHHHHHhcCCcccccchhHHHHHHHH-hcCceeHHHHHH
Confidence 578999999999999999999999999999999999754 57899999999999999999999995 999999999987
Q ss_pred cCHHHHHHHhccchHHHHHHHHcCCcCccccccCCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhHHhcC
Q 009729 80 FSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNK 159 (527)
Q Consensus 80 ~~~~~L~~~FG~~~G~~L~~~arGiD~~~V~~~~~~KSIs~erTF~~~~di~~~eel~~~L~~LaeeLa~RLr~dl~~~~ 159 (527)
- ...|--.|.+...+.+.+.+.|...+++.....+|||++++||. ++.+...+...+.+||+.|++-|+. .|
T Consensus 312 k-~~ll~~lFsp~S~~~fLr~slG~g~t~~~~~~eRKsis~ErTFs---~~sd~~il~~k~qel~~~lsedlqK----~g 383 (490)
T KOG2094|consen 312 K-LVLLSLLFSPKSFQNFLRCSLGLGTTILDEDGERKSISSERTFS---STSDPSILYSKLQELCQMLSEDLQK----EG 383 (490)
T ss_pred h-hhHHHHHhCchhHHHHHHHhhcCCCCcCccccccccccceeeec---ccCCHHHHHHHHHHHHHHHHHHHHh----cC
Confidence 4 34677789987788899999999999888888899999999998 5899999998888988888887776 89
Q ss_pred ceeeEEEEEEEeccCCCCCCCCCcCcceeeCCCchhhhHHhHHHHHHHHHHHHhcccCccccCCccCCcceeEEEEEecC
Q 009729 160 RIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASK 239 (527)
Q Consensus 160 ~~a~tLtL~iR~~~~~df~~~~~~~SkS~~Lp~~T~~i~~~a~~Lf~aal~Ll~~~~~~k~~~~~~~~~~IR~lGVsls~ 239 (527)
+.++||||++++..| +.| +|+.++..-. ....+|++.|++||... .+..||++||+++.
T Consensus 384 lv~rtvtiKlK~ssF---ev~----Tr~~t~s~vv----~S~edi~k~aleLLk~e----------~~~~iRLlGvR~sq 442 (490)
T KOG2094|consen 384 LVGRTVTIKLKTSSF---EVH----TRQKTISQVV----HSEEDILKPALELLKQE----------YPMTIRLLGVRASQ 442 (490)
T ss_pred cccceEEEEEeccce---eee----eccCchhhhh----ccHHHHHHHHHHHHHhh----------cCceEeeeeeeHhh
Confidence 999999999998543 443 5555543322 35667999999999864 26799999999999
Q ss_pred Ccccc
Q 009729 240 IVPVL 244 (527)
Q Consensus 240 L~~~~ 244 (527)
|+...
T Consensus 443 lv~ee 447 (490)
T KOG2094|consen 443 LVSEE 447 (490)
T ss_pred ccchh
Confidence 99874
No 21
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=99.97 E-value=7.5e-31 Score=289.14 Aligned_cols=237 Identities=22% Similarity=0.284 Sum_probs=202.1
Q ss_pred CccchhcCceEEEEEcccHHHHHHHhcCCCCCCeEEeccCCHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhc
Q 009729 1 MQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKF 80 (527)
Q Consensus 1 ~~I~~etGLt~SIGIA~NKlLAKLAS~~aKPnG~~vl~~e~v~~fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~ 80 (527)
++|++.|||+||||||.|++||+||++.||||||+++.++.+.+||.+++|.+|||||..|..+|. .+||+|||||+..
T Consensus 501 qEI~e~TgC~aS~Gig~t~LLARlATr~AKP~Gq~~l~a~~veeFis~~~v~~LPGVG~sm~~kL~-s~~i~tCgdLq~~ 579 (1016)
T KOG2093|consen 501 QEILEKTGCPASAGIGGTMLLARLATRVAKPNGQFYLSAEKVEEFISQLKVDDLPGVGSSMKSKLV-SQFIQTCGDLQLI 579 (1016)
T ss_pred HHHHhccCCceeeccchHHHHHHHHHhhcCCCceeeecHHHHHHHhhhcccccCCCccHHHHHHHH-HhccchhHHHHHH
Confidence 479999999999999999999999999999999999999999999999999999999999999995 9999999999999
Q ss_pred CHHHHHHHhccchHHHHHHHHcCCcCccccccCCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhHHhcCc
Q 009729 81 SEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKR 160 (527)
Q Consensus 81 ~~~~L~~~FG~~~G~~L~~~arGiD~~~V~~~~~~KSIs~erTF~~~~di~~~eel~~~L~~LaeeLa~RLr~dl~~~~~ 160 (527)
+...|++.||++.|..+|+.|||+|++|+.....|||++.+.+|+ .+++++.++...|..++++|-+||.+ -++
T Consensus 580 T~~kl~k~~G~Klgq~i~~~CrG~Dd~P~~~~~~RKSvS~dIN~G--IRFtn~~ev~~fl~~~~eEl~rkL~e----i~k 653 (1016)
T KOG2093|consen 580 TLIKLRKVFGPKLGQKIYRGCRGIDDDPRSIEQVRKSVSADINYG--IRFTNIKEVEQFLCLLSEELRRKLLE----ISK 653 (1016)
T ss_pred HHHHHHhhhcccHHHHHHHhcCCCcCChHHHhhhhcceeeeeecc--eeeccHHHHHHHHHHHHHHHHHHHHH----hhc
Confidence 999999999999999999999999999987666799999999999 89999999999999999999999987 789
Q ss_pred eeeEEEEEEEec--c----CCCCCCCC--CcCcceeeCCCchhhhHHhHHHHHHHHHHHHhcccCccccCCccCCcceeE
Q 009729 161 IAHTLTLHASAF--K----SSDSDSRK--KFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITA 232 (527)
Q Consensus 161 ~a~tLtL~iR~~--~----~~df~~~~--~~~SkS~~Lp~~T~~i~~~a~~Lf~aal~Ll~~~~~~k~~~~~~~~~~IR~ 232 (527)
.++.++|+++.. + ++.|-+|+ +..+|++.|.++|+ ...-|...+++|+... -.+.-.+|+
T Consensus 654 ~~~sitLKlMvR~~~APietaK~mGhGiCD~~~rs~~l~~~Td----~~~iItt~~~~L~~t~--------~~~~~elRG 721 (1016)
T KOG2093|consen 654 TASSITLKLMVRTAKAPIETAKYMGHGICDDFVRSSKLREPTD----CNRIITTEVLRLYETN--------SEPPSELRG 721 (1016)
T ss_pred cccchhHHHHhhcCCCCCccccccceeeccchhhhhhccCccc----cccchHHHHHHHHHhc--------CCChHHhcc
Confidence 999999998642 1 13444554 45689999999996 3445566666766542 234667999
Q ss_pred EEEEec-CCccccC--CccccccccCC
Q 009729 233 LSVSAS-KIVPVLS--GTCSIMKYFNG 256 (527)
Q Consensus 233 lGVsls-~L~~~~~--g~~sq~~lF~~ 256 (527)
+||+++ +|.+... ...-+..+|..
T Consensus 722 ~gi~~ntkL~~~~~~~~~~~l~e~Fgt 748 (1016)
T KOG2093|consen 722 LGIHSNTKLMDVLENLPPELLSEMFGT 748 (1016)
T ss_pred chhhccccccccccCCcHHHHHhhccc
Confidence 999995 8887642 12334455653
No 22
>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=99.96 E-value=2.1e-28 Score=251.46 Aligned_cols=203 Identities=18% Similarity=0.102 Sum_probs=172.4
Q ss_pred hhcCceEEEEEcccHHHHHHHhcCCCCCCeEEeccCCHHh-hcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHH
Q 009729 5 KETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKG-LLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSED 83 (527)
Q Consensus 5 ~etGLt~SIGIA~NKlLAKLAS~~aKPnG~~vl~~e~v~~-fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~ 83 (527)
.++|++||||||+||++||||++.+||+|++.+....... ||+++|| ++||||+++.++|. .+||+|++||++++..
T Consensus 126 ~~~gl~~siGia~n~~~Aklas~~~kp~~~~~~~~~~~~~~~l~~lp~-~~~gig~~~~~~L~-~~Gi~t~~dl~~~~~~ 203 (335)
T cd03468 126 ATLGLSARAGIADTPGAAWLLARAGGGRGVLRREALAAALVLLAPLPV-AALRLPPETVELLA-RLGLRTLGDLAALPRA 203 (335)
T ss_pred HHcCCeEEEEecCCHHHHHHHhccCCCCccCCchHHHHHhhccCCCCh-hHhCCCHHHHHHHH-HhCcccHHHHHhCChH
Confidence 4689999999999999999999999999998776665554 8999999 59999999999995 9999999999999999
Q ss_pred HHHHHhccchHHHHHHHHcCCcCccc--cccCCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhHHhcCce
Q 009729 84 KLQESYGFNTGTWLWNIARGISGEEV--QARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRI 161 (527)
Q Consensus 84 ~L~~~FG~~~G~~L~~~arGiD~~~V--~~~~~~KSIs~erTF~~~~di~~~eel~~~L~~LaeeLa~RLr~dl~~~~~~ 161 (527)
.|.++||. .|.++|+.++|+|+.++ .....+|+++.+.+|+ .+..+.+ ...+..|+++++.||+. +++.
T Consensus 204 ~l~~rfG~-~~~~l~~~~~G~d~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~--~~~l~~l~~~l~~~L~~----~~~~ 274 (335)
T cd03468 204 ELARRFGL-ALLLRLDQAYGRDPEPLLFSPPPPAFDFRLELQLE--EPIARGL--LFPLRRLLEQLCAFLAL----RGLG 274 (335)
T ss_pred HHHhhcCH-HHHHHHHHHCCCCCCCCCCCCCCCChhhhhhcCCC--CCcchhH--HHHHHHHHHHHHHHHHH----cCCe
Confidence 99999998 69999999999999999 4556789999999999 5666655 88999999999999997 8999
Q ss_pred eeEEEEEEEeccCCCCCCCCCcCcceeeCCCchhhhHHhHHHHHHHHHHHHhcccCccccCCccCC---cceeEEEEEec
Q 009729 162 AHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSG---WRITALSVSAS 238 (527)
Q Consensus 162 a~tLtL~iR~~~~~df~~~~~~~SkS~~Lp~~T~~i~~~a~~Lf~aal~Ll~~~~~~k~~~~~~~~---~~IR~lGVsls 238 (527)
+++|+|++++.++ .. .+.+.++..+++ +...|++.+..+|.+ .+.+ .+||.++|++.
T Consensus 275 ~~~l~l~l~~~~~---~~----~~~~~~~~~~~~----~~~~l~~l~~~~l~~---------~~~~~~~~~v~~~~v~~~ 334 (335)
T cd03468 275 ARRLSLTLFREDG---RV----TRVLVGLARPSR----DDLPLLRLLRERLER---------LALPRGIAPVRLLALTAE 334 (335)
T ss_pred eeEEEEEEEEECC---ce----EEEEEeccCCcc----CHHHHHHHHHhhhhc---------cCCCCCeeeEEEEEeecc
Confidence 9999999998542 32 356777887774 455577777766653 2334 68999999874
No 23
>PF11799 IMS_C: impB/mucB/samB family C-terminal domain; InterPro: IPR017961 This entry represents the little finger domain found in Y-family (lesion bypass) DNA polymerases. Y-family polymerases were originally known as UmuC/DinB/Rev1/Rad30 after each branch of the family. These enzymes are characterised by their low-fidelity synthesis on undamaged DNA templates and by their ability to traverse replication-blocking lesions. By contrast, high-fidelity polymerases (such as DNA polymerase III) are sensitive to distortions in the DNA template. As a result, Y-family polymerases can extend primer strands across DNA strand lesions that would otherwise stall replicative polymerases. To minimize mutations through their low fidelity synthesis, these enzymes are regulated, and are thought to interact with processivity factors, beta-clamp or proliferating cell nuclear antigen (PCNA), which are also essential for the function of replicative DNA polymerases []. Organisms can contain more than one Y-family polymerase, each with a unique DNA damage bypass and fidelity profile. For example, humans posses four Y-family polymerases: DNA polymerases kappa, iota, eta and Rev1. Y-family polymerases show no homology to DNA polymerases from the A-, B-, C-, D- or X-families []. The Y-family of DNA polymerases includes the following enzymes: Prokaryotic DNA polymerase IV (DinB) []. Archaeal DinB homologue DNA polymerase IV []. Eukaryotic DinB homologue DNA polymerase kappa []. Prokarytoic DNA repair proteins UmuC and UmuD []. Eukaryotic Rad30 homologues DNA polymerase eta and iota [, ]. Eukaryotic DNA repair protein Rev1 []. Human DNA polymerase kappa is a right-handed shaped molecule with palm, fingers, thumb, little finger and wrist subdomains []. This entry represents the little finger domain.; GO: 0003684 damaged DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006281 DNA repair; PDB: 3PZP_B 2OH2_B 2W7O_B 3IN5_B 1T94_A 2W7P_B 3GV8_B 3G6V_A 4EBC_A 3GV5_B ....
Probab=99.50 E-value=5.9e-14 Score=123.70 Aligned_cols=124 Identities=31% Similarity=0.445 Sum_probs=91.6
Q ss_pred Ccccc-ccCCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhHHhcCceeeEEEEEEEeccCCCCCCCCCcC
Q 009729 106 GEEVQ-ARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFP 184 (527)
Q Consensus 106 ~~~V~-~~~~~KSIs~erTF~~~~di~~~eel~~~L~~LaeeLa~RLr~dl~~~~~~a~tLtL~iR~~~~~df~~~~~~~ 184 (527)
++||. +...+|||+++++|+ .++.+.+++..+|..|+++|+.||++ +++.|++|+|+++|.++ .. ....
T Consensus 1 ~~pV~~~~~~~ksi~~~~t~~--~~~~~~~~i~~~l~~l~~~l~~rL~~----~~~~~~~i~l~l~~~~~---~~-~~~~ 70 (127)
T PF11799_consen 1 DEPVQQPRPPPKSIGSERTFP--EPISDREEIEEWLRELAEELAERLRE----RGLAARTITLKLRYSDF---GR-CSSR 70 (127)
T ss_dssp ------SCSS-SEEEEEEEEC--EEESSHHHHHHHHHHHHHHHHHHHHH----CTEEEEEEEEEEEETTS---CS-CEEE
T ss_pred CCCCCCCCCCCCEEEEEEECC--CCCCCHHHHHHHHHHHHHHHHHHHHh----hCcCCceEEEEEEecCC---cc-ccee
Confidence 46787 778899999999998 68999999999999999999999997 89999999999998643 21 1134
Q ss_pred cceeeCCCchhhhHHhHHHHHHHHHHHHhcccCccccCCcc-CCcceeEEEEEecCCc-cccCCcccccccc
Q 009729 185 SKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHY-SGWRITALSVSASKIV-PVLSGTCSIMKYF 254 (527)
Q Consensus 185 SkS~~Lp~~T~~i~~~a~~Lf~aal~Ll~~~~~~k~~~~~~-~~~~IR~lGVsls~L~-~~~~g~~sq~~lF 254 (527)
+++++++.|++ ++..|++++..+|... .+ .+.+||+|||++++|. +. ...|.+||
T Consensus 71 ~~~~~l~~p~~----~~~~l~~~~~~l~~~~--------~~~~~~~vr~igv~~~~l~~~~---~~~q~~lF 127 (127)
T PF11799_consen 71 SRSIRLPFPTN----DADELLKAARELLERL--------LYDPGFPVRLIGVSASDLIEPA---GQRQLDLF 127 (127)
T ss_dssp EEEEEECCCEH----CHHHHHHHHHHHHHHH--------HHHTTCGEEEEEEEEEEEEEC-------B----
T ss_pred eEEEeccCCcC----CHHHHHHHHHHHHHHH--------hcCCCCCEEEEEEEECCCcCCC---CCcccccC
Confidence 77899998885 5667888888888432 12 3678999999999999 44 36778887
No 24
>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=98.55 E-value=2.3e-08 Score=70.21 Aligned_cols=32 Identities=34% Similarity=0.513 Sum_probs=28.0
Q ss_pred cCCHHhhcccCCCCcccCCcHHHHHHHHHhcCC
Q 009729 39 FSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGV 71 (527)
Q Consensus 39 ~e~v~~fL~~LPI~kLpGIG~k~~~kL~~~lGI 71 (527)
|+++.+||++|||+++||||++++++|. .+||
T Consensus 1 pe~v~~~l~~lpi~~~~GIG~kt~~kL~-~~GI 32 (32)
T PF11798_consen 1 PEDVPEFLWPLPIRKFWGIGKKTAKKLN-KLGI 32 (32)
T ss_dssp CHHHHHHHHCSBGGGSTTS-HHHHHHHH-CTT-
T ss_pred ChHHHHHHhcCCHHhhCCccHHHHHHHH-HccC
Confidence 5788999999999999999999999994 9997
No 25
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=98.10 E-value=2.7e-06 Score=88.18 Aligned_cols=80 Identities=20% Similarity=0.218 Sum_probs=66.7
Q ss_pred hcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhcc--chHHHHHHHHcC---Cc--CccccccCCCcc
Q 009729 45 LLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF--NTGTWLWNIARG---IS--GEEVQARLLPKS 117 (527)
Q Consensus 45 fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~FG~--~~G~~L~~~arG---iD--~~~V~~~~~~KS 117 (527)
.|.++||.++||||++++++|. ..||.|++||+.++++.|.+++|. +.+..+|..++| .+ .+++.....+++
T Consensus 2 ~~~~~~l~~l~gIg~~~a~~L~-~~Gi~t~~dl~~~~~~~L~~~~g~~~~~a~~l~~~a~~~~~~~~~~t~~~l~~~~ks 80 (317)
T PRK04301 2 KMKEKDLEDLPGVGPATAEKLR-EAGYDTVEAIAVASPKELSEAAGIGESTAAKIIEAAREAADIGGFETALEVLERRKN 80 (317)
T ss_pred CcccccHhhcCCCCHHHHHHHH-HcCCCCHHHHHcCCHHHHHHhcCCCHHHHHHHHHHHHHhhccccCccHHHHHHhhcc
Confidence 4789999999999999999995 999999999999999999999995 479999999998 53 444443345677
Q ss_pred ccccccCC
Q 009729 118 HGSGKSFP 125 (527)
Q Consensus 118 Is~erTF~ 125 (527)
++...|+.
T Consensus 81 ~~~~~Tg~ 88 (317)
T PRK04301 81 VGKITTGS 88 (317)
T ss_pred CCccCCCC
Confidence 77766664
No 26
>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=97.55 E-value=9.7e-05 Score=76.08 Aligned_cols=74 Identities=19% Similarity=0.189 Sum_probs=61.5
Q ss_pred CCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhccc--hHHHHHHHHc---CCc--CccccccCCCcccccccc
Q 009729 51 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN--TGTWLWNIAR---GIS--GEEVQARLLPKSHGSGKS 123 (527)
Q Consensus 51 I~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~FG~~--~G~~L~~~ar---GiD--~~~V~~~~~~KSIs~erT 123 (527)
|.++||||++++++|. ..||.|++||+.++.+.|.+.+|.. .+..+|..++ |.+ .+.+.....+++++...|
T Consensus 1 l~~i~gig~~~~~~L~-~~Gi~ti~dl~~~~~~~L~~~~g~~~~~a~~l~~~~~~~~~~~~~~t~~~~~~~~~s~~~~~T 79 (310)
T TIGR02236 1 LEDLPGVGPATAEKLR-EAGYDTFEAIAVASPKELSEIAGISEGTAAKIIQAARKAADLGGFETADDVLERRKTIGKITT 79 (310)
T ss_pred CcccCCCCHHHHHHHH-HcCCCCHHHHHcCCHHHHHhccCCCHHHHHHHHHHHHHHhhccCCCCHHHHHHhhccCCeecC
Confidence 5689999999999995 9999999999999999999999963 5899999998 887 555544445677777776
Q ss_pred CC
Q 009729 124 FP 125 (527)
Q Consensus 124 F~ 125 (527)
+.
T Consensus 80 g~ 81 (310)
T TIGR02236 80 GS 81 (310)
T ss_pred CC
Confidence 65
No 27
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=97.00 E-value=0.00091 Score=52.94 Aligned_cols=50 Identities=28% Similarity=0.349 Sum_probs=42.3
Q ss_pred CcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hccchHHHHHHHHc
Q 009729 52 KKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 102 (527)
Q Consensus 52 ~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~--FG~~~G~~L~~~ar 102 (527)
.+++|||++++.+|. ..|+.|+.||+..+.+.|..+ +|.+.++.+...++
T Consensus 8 ~~I~Gig~~~a~~L~-~~G~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 8 LSIPGIGPKRAEKLY-EAGIKTLEDLANADPEELAEIPGIGEKTAEKIIEAAR 59 (60)
T ss_dssp HTSTTCHHHHHHHHH-HTTCSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHHHH
T ss_pred ccCCCCCHHHHHHHH-hcCCCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHHHh
Confidence 368999999999996 889999999999999999888 56666777766654
No 28
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=96.53 E-value=0.0016 Score=56.58 Aligned_cols=40 Identities=20% Similarity=0.327 Sum_probs=35.3
Q ss_pred CCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhc
Q 009729 50 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYG 90 (527)
Q Consensus 50 PI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~FG 90 (527)
.+.+|||||+++++-|. .+||+++.||+..++..|..++-
T Consensus 13 ~L~~iP~IG~a~a~DL~-~LGi~s~~~L~g~dP~~Ly~~lc 52 (93)
T PF11731_consen 13 DLTDIPNIGKATAEDLR-LLGIRSPADLKGRDPEELYERLC 52 (93)
T ss_pred HHhcCCCccHHHHHHHH-HcCCCCHHHHhCCCHHHHHHHHH
Confidence 46789999999999995 99999999999999987766654
No 29
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=95.28 E-value=0.032 Score=55.98 Aligned_cols=56 Identities=18% Similarity=0.262 Sum_probs=50.5
Q ss_pred CCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hccchHHHHHHHHcCCcC
Q 009729 50 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIARGISG 106 (527)
Q Consensus 50 PI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~--FG~~~G~~L~~~arGiD~ 106 (527)
++.+|+|||++.+++|. ..|+.|+.+|+.++.+.|..+ +|...+..++..+.+.+.
T Consensus 4 ~L~~IpGIG~krakkLl-~~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l~~~~~ 61 (232)
T PRK12766 4 ELEDISGVGPSKAEALR-EAGFESVEDVRAADQSELAEVDGIGNALAARIKADVGGLEV 61 (232)
T ss_pred ccccCCCcCHHHHHHHH-HcCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHHhccccc
Confidence 57889999999999996 999999999999999999999 887789999999886544
No 30
>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=93.70 E-value=0.081 Score=44.85 Aligned_cols=34 Identities=26% Similarity=0.398 Sum_probs=25.2
Q ss_pred CCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHH
Q 009729 49 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSED 83 (527)
Q Consensus 49 LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~ 83 (527)
-.|+++|+||.++++.|. +.||+|+.||..+...
T Consensus 3 ~~l~~LpNig~~~e~~L~-~vGI~t~~~L~~~Ga~ 36 (81)
T PF04994_consen 3 NRLKDLPNIGPKSERMLA-KVGIHTVEDLRELGAV 36 (81)
T ss_dssp --GCGSTT--HHHHHHHH-HTT--SHHHHHHHHHH
T ss_pred cchhhCCCCCHHHHHHHH-HcCCCCHHHHHHhCHH
Confidence 468999999999999995 9999999999997543
No 31
>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=93.35 E-value=0.075 Score=41.47 Aligned_cols=27 Identities=26% Similarity=0.302 Sum_probs=20.7
Q ss_pred CcccCCcHHHHHHHHHhcCCCcHHHHhh
Q 009729 52 KKMKQLGGKLGTSLQNELGVTTVGDLLK 79 (527)
Q Consensus 52 ~kLpGIG~k~~~kL~~~lGI~TigDLa~ 79 (527)
..+||||+++++++- ..|++|+.||..
T Consensus 5 ~~I~GVG~~tA~~w~-~~G~rtl~Dl~~ 31 (52)
T PF10391_consen 5 TGIWGVGPKTARKWY-AKGIRTLEDLRK 31 (52)
T ss_dssp HTSTT--HHHHHHHH-HTT--SHHHHHH
T ss_pred hhcccccHHHHHHHH-HhCCCCHHHHhh
Confidence 468999999999996 899999999975
No 32
>PRK02362 ski2-like helicase; Provisional
Probab=92.98 E-value=0.11 Score=60.22 Aligned_cols=55 Identities=15% Similarity=0.151 Sum_probs=50.2
Q ss_pred CCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhccchHHHHHHHHcCC
Q 009729 49 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGI 104 (527)
Q Consensus 49 LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~FG~~~G~~L~~~arGi 104 (527)
+|+-.|||||++.+++|. .+||.|+.||+.+..+.|.+.||.+.++.+...++..
T Consensus 652 ~~L~~ip~i~~~~a~~l~-~~gi~s~~dl~~~~~~~l~~~~g~~~~~~i~~~~~~~ 706 (737)
T PRK02362 652 LDLVGLRGVGRVRARRLY-NAGIESRADLRAADKSVVLAILGEKIAENILEQAGRR 706 (737)
T ss_pred HHHhCCCCCCHHHHHHHH-HcCCCCHHHHHhCCHHHHHHHHCHHHHHHHHHHhCcc
Confidence 567789999999999996 8999999999999999999999999999999888844
No 33
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=92.45 E-value=0.16 Score=46.90 Aligned_cols=36 Identities=25% Similarity=0.521 Sum_probs=31.6
Q ss_pred CCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHH
Q 009729 50 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQ 86 (527)
Q Consensus 50 PI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~ 86 (527)
.++.|-|||++++..| +.+||+|..||+.++...+.
T Consensus 68 DLt~I~GIGPk~e~~L-n~~GI~tfaQIAAwt~~di~ 103 (133)
T COG3743 68 DLTRISGIGPKLEKVL-NELGIFTFAQIAAWTRADIA 103 (133)
T ss_pred cchhhcccCHHHHHHH-HHcCCccHHHHHhcCHHHHH
Confidence 5778899999999999 59999999999999876544
No 34
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=91.61 E-value=0.18 Score=40.64 Aligned_cols=47 Identities=17% Similarity=0.314 Sum_probs=33.4
Q ss_pred ccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hccchHHHHHHHHc
Q 009729 54 MKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 102 (527)
Q Consensus 54 LpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~--FG~~~G~~L~~~ar 102 (527)
|||||.++++.|.+.+| ++..|...+.+.|... +|...++.++.+..
T Consensus 8 I~~VG~~~ak~L~~~f~--sl~~l~~a~~e~L~~i~gIG~~~A~si~~ff~ 56 (64)
T PF12826_consen 8 IPGVGEKTAKLLAKHFG--SLEALMNASVEELSAIPGIGPKIAQSIYEFFQ 56 (64)
T ss_dssp STT--HHHHHHHHHCCS--CHHHHCC--HHHHCTSTT--HHHHHHHHHHHH
T ss_pred CCCccHHHHHHHHHHcC--CHHHHHHcCHHHHhccCCcCHHHHHHHHHHHC
Confidence 68999999999976666 9999999999999887 67666777776654
No 35
>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=91.56 E-value=0.27 Score=40.03 Aligned_cols=46 Identities=33% Similarity=0.476 Sum_probs=36.5
Q ss_pred HhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhc
Q 009729 43 KGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYG 90 (527)
Q Consensus 43 ~~fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~FG 90 (527)
...+...||.+| |+..++...|. ..||+|++||..++...|.+.-|
T Consensus 6 ~~~~~~~~I~~L-~LS~Ra~n~L~-~~~I~tv~dL~~~s~~~L~~i~n 51 (66)
T PF03118_consen 6 EEELLDTPIEDL-GLSVRAYNCLK-RAGIHTVGDLVKYSEEDLLKIKN 51 (66)
T ss_dssp -HHHHCSBGGGS-TSBHHHHHHHH-CTT--BHHHHHCS-HHHHHTSTT
T ss_pred hHHHhcCcHHHh-CCCHHHHHHHH-HhCCcCHHHHHhCCHHHHHhCCC
Confidence 445667899999 89999999995 99999999999999998877655
No 36
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=90.73 E-value=0.19 Score=45.58 Aligned_cols=54 Identities=17% Similarity=0.306 Sum_probs=46.6
Q ss_pred eccCCHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhcc
Q 009729 37 VPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF 91 (527)
Q Consensus 37 l~~e~v~~fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~FG~ 91 (527)
++...+.++..--.+-.++|||...+..|. ..||.|+.+|+..++..|...++.
T Consensus 41 i~~~~l~~w~~~AdL~ri~gi~~~~a~LL~-~AGv~Tv~~LA~~~p~~L~~~l~~ 94 (122)
T PF14229_consen 41 ISERNLLKWVNQADLMRIPGIGPQYAELLE-HAGVDTVEELAQRNPQNLHQKLGR 94 (122)
T ss_pred CCHHHHHHHHhHHHhhhcCCCCHHHHHHHH-HhCcCcHHHHHhCCHHHHHHHHHH
Confidence 456677777776677789999999999995 999999999999999999888774
No 37
>PRK00254 ski2-like helicase; Provisional
Probab=88.96 E-value=0.47 Score=54.88 Aligned_cols=53 Identities=15% Similarity=0.271 Sum_probs=48.5
Q ss_pred CCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hccchHHHHHHHHc
Q 009729 49 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 102 (527)
Q Consensus 49 LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~--FG~~~G~~L~~~ar 102 (527)
+|+..+||||++.+++|. ..|+.|+.||..++.+.|.+. +|.+.++.++..++
T Consensus 645 ~~L~~ipgig~~~~~~l~-~~g~~s~~~i~~a~~~el~~~~gi~~~~a~~i~~~~~ 699 (720)
T PRK00254 645 LELMRLPMIGRKRARALY-NAGFRSIEDIVNAKPSELLKVEGIGAKIVEGIFKHLG 699 (720)
T ss_pred hhhhcCCCCCHHHHHHHH-HccCCCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHhc
Confidence 677789999999999996 999999999999999999999 77778999988876
No 38
>PRK01172 ski2-like helicase; Provisional
Probab=88.69 E-value=0.59 Score=53.54 Aligned_cols=52 Identities=17% Similarity=0.279 Sum_probs=43.5
Q ss_pred CCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hccchHHHHHHHH
Q 009729 49 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIA 101 (527)
Q Consensus 49 LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~--FG~~~G~~L~~~a 101 (527)
+|+-.|||||+..+++|. ..||+|+.||+.++.+.+.+. ||.+.+..++..|
T Consensus 612 ~~L~~ip~~~~~~a~~l~-~~g~~~~~di~~~~~~~~~~i~~~~~~~~~~i~~~~ 665 (674)
T PRK01172 612 IDLVLIPKVGRVRARRLY-DAGFKTVDDIARSSPERIKKIYGFSDTLANAIVNRA 665 (674)
T ss_pred HhhcCCCCCCHHHHHHHH-HcCCCCHHHHHhCCHHHHHHHhccCHHHHHHHHHHH
Confidence 678889999999999995 999999999999999999888 5554555555554
No 39
>COG2251 Predicted nuclease (RecB family) [General function prediction only]
Probab=86.32 E-value=0.83 Score=49.98 Aligned_cols=69 Identities=20% Similarity=0.092 Sum_probs=57.7
Q ss_pred ccCCHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhc--cchHHHHHHHHcCCcCc
Q 009729 38 PFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYG--FNTGTWLWNIARGISGE 107 (527)
Q Consensus 38 ~~e~v~~fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~FG--~~~G~~L~~~arGiD~~ 107 (527)
.|.....++..-.+.=++||++.....|. ..||+|+.||++.+...+...+| ...+..+...|+-....
T Consensus 214 ~p~C~~~a~e~~~L~Lv~Gi~~~r~~~l~-~~GI~Ti~~LA~~~~~~~~~~~ga~~~~~~~l~~qa~~~~e~ 284 (474)
T COG2251 214 EPQCESEALEEDDLSLVPGITPSRYDVLE-EVGITTIEDLADASLPILELVAGALTALAAQLVLQARARVEG 284 (474)
T ss_pred chhhhHHHhhccceeccCCCCHHHHHHHH-HcCcchHHHHHhccccchhhhhhhHHHHHHHHHHHHHhhccC
Confidence 35677888888999999999999999995 99999999999999888888888 44577777777765443
No 40
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=86.00 E-value=1.4 Score=40.04 Aligned_cols=44 Identities=27% Similarity=0.429 Sum_probs=32.8
Q ss_pred cCCcHHHHHHHHHhcCCCcHHHHhhcCHH-----HHHHHhccchHHHHHHH
Q 009729 55 KQLGGKLGTSLQNELGVTTVGDLLKFSED-----KLQESYGFNTGTWLWNI 100 (527)
Q Consensus 55 pGIG~k~~~kL~~~lGI~TigDLa~~~~~-----~L~~~FG~~~G~~L~~~ 100 (527)
||||++.+++| +..||+|++||...... .|....|. ....+..+
T Consensus 1 pgi~~~~~~~L-~~~GI~t~~~Ll~~~~~~~~r~~La~~~~i-~~~~l~~w 49 (122)
T PF14229_consen 1 PGIGPKEAAKL-KAAGIKTTGDLLEAGDTPLGRKALAKKLGI-SERNLLKW 49 (122)
T ss_pred CCCCHHHHHHH-HHcCCCcHHHHHHcCCCHHHHHHHHHhcCC-CHHHHHHH
Confidence 79999999999 59999999999987432 36666665 34444333
No 41
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=84.39 E-value=1.3 Score=50.27 Aligned_cols=54 Identities=17% Similarity=0.142 Sum_probs=45.9
Q ss_pred cCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH-hccchHHHHHHHHcC
Q 009729 48 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES-YGFNTGTWLWNIARG 103 (527)
Q Consensus 48 ~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~-FG~~~G~~L~~~arG 103 (527)
.-.+.+|||||++..++|. --+.++..|..++.++|.+. +|.+.++.++..++|
T Consensus 513 ~S~Ld~I~GiG~kr~~~Ll--~~Fgs~~~ik~As~eeL~~vgi~~~~A~~I~~~l~~ 567 (567)
T PRK14667 513 KDILDKIKGIGEVKKEIIY--RNFKTLYDFLKADDEELKKLGIPPSVKQEVKKYLSG 567 (567)
T ss_pred cCccccCCCCCHHHHHHHH--HHhCCHHHHHhCCHHHHHHcCCCHHHHHHHHHHhcC
Confidence 4567899999999999996 44559999999999999998 556678899988876
No 42
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=82.65 E-value=1.3 Score=43.20 Aligned_cols=56 Identities=13% Similarity=0.074 Sum_probs=44.2
Q ss_pred CCCcccCCcHHHHHHHHHhcCCCcHH-HHhhcCHHHHHHH--hccchHHHHHHHHcCCc
Q 009729 50 PIKKMKQLGGKLGTSLQNELGVTTVG-DLLKFSEDKLQES--YGFNTGTWLWNIARGIS 105 (527)
Q Consensus 50 PI~kLpGIG~k~~~kL~~~lGI~Tig-DLa~~~~~~L~~~--FG~~~G~~L~~~arGiD 105 (527)
.+..++|||++++.++.+.+|..++- .+...+++.|.+. +|.+.+++++..+++..
T Consensus 74 ~L~~i~GIGpk~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~~~l~~~~ 132 (192)
T PRK00116 74 LLISVSGVGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELKDKL 132 (192)
T ss_pred HHhcCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHHh
Confidence 45679999999999887778876653 4556688889887 77788999998888754
No 43
>PRK08609 hypothetical protein; Provisional
Probab=82.30 E-value=0.93 Score=51.32 Aligned_cols=31 Identities=35% Similarity=0.423 Sum_probs=27.3
Q ss_pred CCcccCCcHHHHHHHHHhcCCCcHHHHhhcC
Q 009729 51 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFS 81 (527)
Q Consensus 51 I~kLpGIG~k~~~kL~~~lGI~TigDLa~~~ 81 (527)
+.++||||++++.+|.+.+||.|+.||...-
T Consensus 90 l~~i~GiGpk~a~~l~~~lGi~tl~~L~~a~ 120 (570)
T PRK08609 90 LLKLPGLGGKKIAKLYKELGVVDKESLKEAC 120 (570)
T ss_pred HhcCCCCCHHHHHHHHHHhCCCCHHHHHHHH
Confidence 4589999999999998789999999999753
No 44
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=82.22 E-value=1.1 Score=47.36 Aligned_cols=30 Identities=20% Similarity=0.255 Sum_probs=26.8
Q ss_pred CCcccCCcHHHHHHHHHhcCCCcHHHHhhcC
Q 009729 51 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFS 81 (527)
Q Consensus 51 I~kLpGIG~k~~~kL~~~lGI~TigDLa~~~ 81 (527)
+..+||||++++++|. .+||.|+.||....
T Consensus 91 l~~i~GiGpk~a~~l~-~lGi~tl~eL~~a~ 120 (334)
T smart00483 91 FTNVFGVGPKTAAKWY-RKGIRTLEELKKNK 120 (334)
T ss_pred HHccCCcCHHHHHHHH-HhCCCCHHHHHhcc
Confidence 5689999999999997 59999999998754
No 45
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=81.71 E-value=1.6 Score=51.51 Aligned_cols=52 Identities=23% Similarity=0.314 Sum_probs=46.6
Q ss_pred CCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhc-cchHHHHHHHHcCC
Q 009729 51 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYG-FNTGTWLWNIARGI 104 (527)
Q Consensus 51 I~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~FG-~~~G~~L~~~arGi 104 (527)
+..|||||.+.+.+|. ..+.++.+|+.++.+.|....| .+.|..+|+.++.-
T Consensus 759 L~~lPgI~~~~a~~ll--~~f~si~~l~~as~eeL~~~iG~~~~A~~i~~fl~~~ 811 (814)
T TIGR00596 759 LLKLPGVTKKNYRNLR--KKVKSIRELAKLSQNELNELIGDEEAAKRLYDFLRTE 811 (814)
T ss_pred HHHCCCCCHHHHHHHH--HHcCCHHHHHhCCHHHHHHHhCCHHHHHHHHHHhccc
Confidence 4578999999999996 4689999999999999999999 88899999998863
No 46
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=80.30 E-value=4.2 Score=41.73 Aligned_cols=62 Identities=16% Similarity=0.364 Sum_probs=51.8
Q ss_pred cCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhcc--chHHHHHHHHcCCcCcccc
Q 009729 48 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF--NTGTWLWNIARGISGEEVQ 110 (527)
Q Consensus 48 ~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~FG~--~~G~~L~~~arGiD~~~V~ 110 (527)
..|+.-+|+||....++|. ..||.+++||..++.+.+...+|. ..|..++..++.+..-.|.
T Consensus 150 ~~~L~Qlp~i~~~~~~~l~-~~~i~s~~~l~~~~~~~~~~ll~~~~~~~~~i~~~~~~~P~l~v~ 213 (312)
T smart00611 150 DSPLLQLPHLPEEILKRLE-KKKVLSLEDLLELEDEERGELLGLLDAEGERVYKVLSRLPKLNIE 213 (312)
T ss_pred CCccccCCCCCHHHHHHHH-hCCCCCHHHHHhcCHHHHHHHHcCCHHHHHHHHHHHHhCCcceeE
Confidence 3688999999999999995 899999999999999988888774 2588888888877665543
No 47
>TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Probab=80.25 E-value=1.4 Score=48.30 Aligned_cols=60 Identities=23% Similarity=0.248 Sum_probs=43.9
Q ss_pred HHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHH--HhccchHHHHHHHHc
Q 009729 42 VKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQE--SYGFNTGTWLWNIAR 102 (527)
Q Consensus 42 v~~fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~--~FG~~~G~~L~~~ar 102 (527)
.......-+|..|+||+++....|. ..||.|+.||+..+...|.. .++...+.+|...|+
T Consensus 200 ~~~~~~~~~lslv~gi~~~~~~~L~-~~GI~ti~~La~~~~~~l~~~~~~~~~~~~~l~~qA~ 261 (457)
T TIGR03491 200 EAVAKEEGHLSLVPGIGPSRYRLLQ-ELGIHTLEDLAAADPNDLEDFGEQGLGVAEQLVQQAR 261 (457)
T ss_pred HHHHHhcCCeeecCCCCHHHHHHHH-HcCCCcHHHHhcCCccccccccccCHHHHHHHHHHHH
Confidence 3445557789999999999999995 99999999999987544444 344334555554444
No 48
>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=79.68 E-value=3.1 Score=42.67 Aligned_cols=60 Identities=23% Similarity=0.364 Sum_probs=44.7
Q ss_pred CCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhcc--chHHHHHHHHcCCcCccc
Q 009729 49 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF--NTGTWLWNIARGISGEEV 109 (527)
Q Consensus 49 LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~FG~--~~G~~L~~~arGiD~~~V 109 (527)
.|+..|||||....++|. ..||.|++||..++.+.+...++. ..|..+...++.+..-.|
T Consensus 148 ~~L~Qlp~i~~~~~~~l~-~~~i~~l~~l~~~~~~e~~~ll~~~~~~~~~i~~~~~~~P~~~i 209 (314)
T PF02889_consen 148 SPLLQLPHIGEESLKKLE-KRGIKTLQDLRDLSPEELEELLNRNPPFGKEILEVASRIPRLEI 209 (314)
T ss_dssp -GGGGSTT--HHHHHHHH-HTT--SHHHHHHS-HHHHHHHH-S-HHHHHHHHHHHCCS--EEE
T ss_pred ChhhcCCCCCHHHHHHHh-ccCCCcHHHHhhCCHHHHHHHHhhhhhhHHHHHHHHHHCCCEEE
Confidence 678999999999999995 899999999999999999988862 358889999998866555
No 49
>PF14377 DUF4414: Domain of unknown function (DUF4414)
Probab=78.77 E-value=1.3 Score=39.22 Aligned_cols=25 Identities=36% Similarity=0.627 Sum_probs=21.3
Q ss_pred cccCCccccccCChHHHHHHHHhhC
Q 009729 479 IEEIDPSVIDELPKEIQDEIQAWLR 503 (527)
Q Consensus 479 ~~~id~~~~~el~~ei~~e~~~~~~ 503 (527)
-.+|||.+++-||++||+||-+=.+
T Consensus 42 ~~~I~pefL~ALP~diR~EVl~qe~ 66 (108)
T PF14377_consen 42 PSQIDPEFLAALPPDIREEVLAQER 66 (108)
T ss_pred ccccCHHHHHhCCHHHHHHHHHHHH
Confidence 5689999999999999999865443
No 50
>PF14377 DUF4414: Domain of unknown function (DUF4414)
Probab=78.36 E-value=0.97 Score=40.13 Aligned_cols=21 Identities=38% Similarity=0.730 Sum_probs=18.4
Q ss_pred CCccccccCChHHHHHHHHhh
Q 009729 482 IDPSVIDELPKEIQDEIQAWL 502 (527)
Q Consensus 482 id~~~~~el~~ei~~e~~~~~ 502 (527)
|||+|+.+||.+|+.||-.=.
T Consensus 1 iDp~fLaaLPeDiR~Evl~~~ 21 (108)
T PF14377_consen 1 IDPEFLAALPEDIREEVLAQQ 21 (108)
T ss_pred CCHHHHHHCCHHHHHHHHHHH
Confidence 899999999999999994433
No 51
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=78.32 E-value=3.3 Score=47.50 Aligned_cols=51 Identities=20% Similarity=0.285 Sum_probs=43.4
Q ss_pred CCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhccchHHHHHHHH
Q 009729 49 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIA 101 (527)
Q Consensus 49 LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~FG~~~G~~L~~~a 101 (527)
..+..|+|||++++..|.+.+| |+.+|..++.+.|.+.+|.+.++.++...
T Consensus 569 s~L~~I~GIG~k~a~~Ll~~Fg--s~~~i~~As~eeL~~vig~k~A~~I~~~~ 619 (621)
T PRK14671 569 TELTDIAGIGEKTAEKLLEHFG--SVEKVAKASLEELAAVAGPKTAETIYRYY 619 (621)
T ss_pred hhhhcCCCcCHHHHHHHHHHcC--CHHHHHhCCHHHHHHHhCHHHHHHHHHHh
Confidence 4567899999999999965555 88999999999998889988899888765
No 52
>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=77.46 E-value=1.6 Score=45.52 Aligned_cols=29 Identities=34% Similarity=0.493 Sum_probs=26.6
Q ss_pred CCcccCCcHHHHHHHHHhcCCCcHHHHhhc
Q 009729 51 IKKMKQLGGKLGTSLQNELGVTTVGDLLKF 80 (527)
Q Consensus 51 I~kLpGIG~k~~~kL~~~lGI~TigDLa~~ 80 (527)
+.++||||++++++|. .+||.|+.||...
T Consensus 87 l~~i~GiGpk~a~~l~-~lGi~sl~dL~~a 115 (307)
T cd00141 87 LLRVPGVGPKTARKLY-ELGIRTLEDLRKA 115 (307)
T ss_pred HHcCCCCCHHHHHHHH-HcCCCCHHHHHHH
Confidence 4589999999999997 9999999999985
No 53
>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=76.93 E-value=2.2 Score=37.00 Aligned_cols=33 Identities=24% Similarity=0.434 Sum_probs=23.0
Q ss_pred cccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhh
Q 009729 46 LDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLK 79 (527)
Q Consensus 46 L~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~ 79 (527)
|..-||++|+|||+.++.+|. ..|+..+..|..
T Consensus 16 MGeK~V~~laGIG~~lg~~L~-~~GfdKAy~vLG 48 (89)
T PF02961_consen 16 MGEKPVTELAGIGPVLGKRLE-EKGFDKAYVVLG 48 (89)
T ss_dssp -TT-BGGGSTT--HHHHHHHH-HTT--BHHHHHH
T ss_pred cCCCCccccCCcCHHHHHHHH-HCCCcHHHHHhh
Confidence 445789999999999999994 999998777654
No 54
>PRK07758 hypothetical protein; Provisional
Probab=76.25 E-value=4.9 Score=35.33 Aligned_cols=38 Identities=26% Similarity=0.405 Sum_probs=31.9
Q ss_pred ccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hccc
Q 009729 54 MKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFN 92 (527)
Q Consensus 54 LpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~--FG~~ 92 (527)
+++++-+....|. ..||.|++||..++.+.|.+. ||++
T Consensus 39 ~~~LSvRA~N~Lk-~AGI~TL~dLv~~te~ELl~iknlGkK 78 (95)
T PRK07758 39 LSLLSAPARRALE-HHGIHTVEELSKYSEKEILKLHGMGPA 78 (95)
T ss_pred CccccHHHHHHHH-HcCCCcHHHHHcCCHHHHHHccCCCHH
Confidence 4789999999995 999999999999999988655 4543
No 55
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=75.71 E-value=3.8 Score=47.36 Aligned_cols=54 Identities=20% Similarity=0.252 Sum_probs=43.0
Q ss_pred cCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHH--HhccchHHHHHHHH
Q 009729 48 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQE--SYGFNTGTWLWNIA 101 (527)
Q Consensus 48 ~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~--~FG~~~G~~L~~~a 101 (527)
+-..-+|+|+|+++.++|.+..+|.++.||..+..+.|.. .||.+.++.|++..
T Consensus 444 sr~al~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~ll~~I 499 (665)
T PRK07956 444 SRNAMDIDGLGEKIIEQLFEKGLIHDPADLFKLTAEDLLGLEGFGEKSAQNLLDAI 499 (665)
T ss_pred cccccCCCCcCHHHHHHHHHcCCCCCHHHHHhcCHHHHhcCcCcchHHHHHHHHHH
Confidence 3445689999999999998778899999999999888876 47776666655443
No 56
>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=75.23 E-value=4.1 Score=47.01 Aligned_cols=55 Identities=25% Similarity=0.296 Sum_probs=43.6
Q ss_pred cCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hccchHHHHHHHHc
Q 009729 48 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 102 (527)
Q Consensus 48 ~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~--FG~~~G~~L~~~ar 102 (527)
+-.--+|+|+|+++.++|.+..+|+++.||..+..+.|... ||.+.+..|++...
T Consensus 431 sr~al~I~GLG~k~i~~L~~~g~I~~~~Dl~~L~~~~L~~L~GfG~Ksa~nIl~~Ie 487 (652)
T TIGR00575 431 SRNAMDIEGLGDKVIEQLFEKKLVRSVADLYALKKEDLLELEGFGEKSAQNLLNAIE 487 (652)
T ss_pred cCCccCCCCcCHHHHHHHHHcCCcCCHHHHHhcCHHHHhhccCccHHHHHHHHHHHH
Confidence 34456799999999999987788999999999998888764 67666766665554
No 57
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=74.95 E-value=3.7 Score=47.53 Aligned_cols=51 Identities=14% Similarity=0.188 Sum_probs=42.8
Q ss_pred CCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hccchHHHHHHHH
Q 009729 49 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIA 101 (527)
Q Consensus 49 LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~--FG~~~G~~L~~~a 101 (527)
-.+..+||||++..++|.+.+| ++.+|...+.+.|.+. +|.+.++.++..+
T Consensus 637 s~L~~IPGIGpkr~k~LL~~FG--Sle~I~~AS~eELa~V~Gig~k~Ae~I~~~L 689 (694)
T PRK14666 637 GELQRVEGIGPATARLLWERFG--SLQAMAAAGEEGLAAVPGIGPARAAALHEHL 689 (694)
T ss_pred hHHhhCCCCCHHHHHHHHHHhC--CHHHHHhcCHHHHHhcCCcCHHHHHHHHHHH
Confidence 4577899999999999987788 9999999999999887 6766677776654
No 58
>PTZ00035 Rad51 protein; Provisional
Probab=74.44 E-value=4.6 Score=42.81 Aligned_cols=55 Identities=18% Similarity=0.177 Sum_probs=45.3
Q ss_pred CCCCcc--cCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhccc--hHHHHHHHHcCC
Q 009729 49 LPIKKM--KQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN--TGTWLWNIARGI 104 (527)
Q Consensus 49 LPI~kL--pGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~FG~~--~G~~L~~~arGi 104 (527)
.+|.++ +||+....++|. ..||+|+.||+..++..|.+..|.. .++.+...++-.
T Consensus 21 ~~~~~l~~~g~~~~~~~kL~-~~g~~t~~~~~~~~~~~L~~~~gis~~~~~~i~~~~~~~ 79 (337)
T PTZ00035 21 QEIEKLQSAGINAADIKKLK-EAGICTVESVAYATKKDLCNIKGISEAKVEKIKEAASKL 79 (337)
T ss_pred ccHHHHhcCCCCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHhhCCCHHHHHHHHHHHHHh
Confidence 478888 779999999995 9999999999999999999999963 245666666644
No 59
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=73.45 E-value=4.9 Score=46.15 Aligned_cols=55 Identities=11% Similarity=0.045 Sum_probs=47.1
Q ss_pred cCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhccchHHHHHHHHcCC
Q 009729 48 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGI 104 (527)
Q Consensus 48 ~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~FG~~~G~~L~~~arGi 104 (527)
.-.+.+|||||++..++|. --+.++..+..++.++|.+.+|.+.++.++..++..
T Consensus 551 ~S~L~~IpGIG~kr~~~LL--~~FgSi~~I~~As~eeL~~vi~~k~A~~I~~~l~~~ 605 (624)
T PRK14669 551 TSELLEIPGVGAKTVQRLL--KHFGSLERVRAATETQLAAVVGRAAAEAIIAHFTTE 605 (624)
T ss_pred HHHHhcCCCCCHHHHHHHH--HHcCCHHHHHhCCHHHHHHHhCHHHHHHHHHHhcCc
Confidence 3457799999999999996 445599999999999999999988899999998743
No 60
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=71.15 E-value=3.1 Score=48.09 Aligned_cols=31 Identities=39% Similarity=0.618 Sum_probs=28.4
Q ss_pred CCCCcccCCcHHHHHHHHHhcCCCcHHHHhhc
Q 009729 49 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKF 80 (527)
Q Consensus 49 LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~ 80 (527)
.||..|.|||++.++.|. ++||.|+.||...
T Consensus 9 ~~~~~l~gvg~~~~~~l~-~lgi~t~~dll~~ 39 (681)
T PRK10917 9 APLTSLKGVGPKTAEKLA-KLGIHTVQDLLLH 39 (681)
T ss_pred CChhhcCCCCHHHHHHHH-HcCCCCHHHHhhc
Confidence 489999999999999995 9999999999974
No 61
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=70.67 E-value=5.6 Score=46.06 Aligned_cols=62 Identities=10% Similarity=0.160 Sum_probs=52.2
Q ss_pred cCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hccchHHHHHHHHcCCcCccccc
Q 009729 48 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIARGISGEEVQA 111 (527)
Q Consensus 48 ~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~--FG~~~G~~L~~~arGiD~~~V~~ 111 (527)
...+.+|||||++..++|.+.| .++..|..++.++|.+. ++...+..+++.+.--...||..
T Consensus 607 ~s~L~~IpGiG~kr~~~LL~~F--gS~~~i~~As~eel~~v~gi~~~~A~~i~~~~~~~~~~~~~~ 670 (691)
T PRK14672 607 VLSFERLPHVGKVRAHRLLAHF--GSFRSLQSATPQDIATAIHIPLTQAHTILHAATRSTTAPVRE 670 (691)
T ss_pred ccccccCCCCCHHHHHHHHHHh--cCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHhhcccccchhH
Confidence 4578899999999999996444 59999999999999998 77778999999888777777754
No 62
>TIGR02239 recomb_RAD51 DNA repair protein RAD51. This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).
Probab=69.44 E-value=6 Score=41.54 Aligned_cols=36 Identities=25% Similarity=0.240 Sum_probs=33.4
Q ss_pred CCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhccc
Q 009729 56 QLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN 92 (527)
Q Consensus 56 GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~FG~~ 92 (527)
||+..+.++|. ..||.|+.||+..++..|.+.+|..
T Consensus 8 ~~~~~~~~~l~-~~g~~t~~~~~~~~~~~L~~i~~ls 43 (316)
T TIGR02239 8 GITAADIKKLQ-EAGLHTVESVAYAPKKQLLEIKGIS 43 (316)
T ss_pred CCCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHHhCCC
Confidence 59999999995 9999999999999999999999963
No 63
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=68.71 E-value=5 Score=42.78 Aligned_cols=56 Identities=18% Similarity=0.229 Sum_probs=44.9
Q ss_pred cCCCCcc--cCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhccc--hHHHHHHHHcCC
Q 009729 48 SLPIKKM--KQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN--TGTWLWNIARGI 104 (527)
Q Consensus 48 ~LPI~kL--pGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~FG~~--~G~~L~~~arGi 104 (527)
..+|.+| .||+..+.++|+ ..||+|+.||+..++..|.+..|.. .+..+...++..
T Consensus 28 ~~~~~~l~~~g~~~~~~~kL~-~~g~~tv~~~~~~~~~~L~~~~g~s~~~~~ki~~~a~~~ 87 (344)
T PLN03187 28 FESIDKLISQGINAGDVKKLQ-DAGIYTCNGLMMHTKKNLTGIKGLSEAKVDKICEAAEKL 87 (344)
T ss_pred ccCHHHHhhCCCCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHHh
Confidence 6778888 679999999995 9999999999999999999988853 244555555543
No 64
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=68.05 E-value=6.6 Score=44.70 Aligned_cols=53 Identities=23% Similarity=0.342 Sum_probs=44.5
Q ss_pred cCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hccchHHHHHHHHc
Q 009729 48 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 102 (527)
Q Consensus 48 ~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~--FG~~~G~~L~~~ar 102 (527)
...+.+|||||++..++|.+. ..++..+..++.++|.++ ++.+.+..++..++
T Consensus 513 ~s~L~~I~GiG~kr~~~LL~~--Fgs~~~I~~As~eeL~~v~gi~~~~A~~I~~~l~ 567 (574)
T PRK14670 513 KLNYTKIKGIGEKKAKKILKS--LGTYKDILLLNEDEIAEKMKINIKMAKKIKKFAE 567 (574)
T ss_pred ccccccCCCCCHHHHHHHHHH--hCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHH
Confidence 457889999999999999644 459999999999999999 66667888888765
No 65
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=67.90 E-value=2.2 Score=45.41 Aligned_cols=44 Identities=20% Similarity=0.332 Sum_probs=39.7
Q ss_pred cCCCCcc--cCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhccc
Q 009729 48 SLPIKKM--KQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN 92 (527)
Q Consensus 48 ~LPI~kL--pGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~FG~~ 92 (527)
..+|.+| .||+....++|+ ..||.|+.||+..++..|.+.+|..
T Consensus 25 ~~~~~~l~~~gi~~~~i~kL~-~~g~~T~~~~~~~~~~~L~~i~~is 70 (342)
T PLN03186 25 PFPIEQLQASGIAALDIKKLK-DAGIHTVESLAYAPKKDLLQIKGIS 70 (342)
T ss_pred CccHHHHHhCCCCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHhcCCC
Confidence 4578888 679999999995 9999999999999999999999974
No 66
>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=67.82 E-value=2.7 Score=29.18 Aligned_cols=16 Identities=19% Similarity=0.393 Sum_probs=12.3
Q ss_pred CCcccCCcHHHHHHHH
Q 009729 51 IKKMKQLGGKLGTSLQ 66 (527)
Q Consensus 51 I~kLpGIG~k~~~kL~ 66 (527)
+.+|||||++++..+.
T Consensus 13 L~~lpGIG~~tA~~I~ 28 (30)
T PF00633_consen 13 LMKLPGIGPKTANAIL 28 (30)
T ss_dssp HHTSTT-SHHHHHHHH
T ss_pred HHhCCCcCHHHHHHHH
Confidence 3479999999999874
No 67
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=66.98 E-value=5.9 Score=39.84 Aligned_cols=37 Identities=27% Similarity=0.460 Sum_probs=32.6
Q ss_pred CCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHH
Q 009729 49 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQ 86 (527)
Q Consensus 49 LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~ 86 (527)
=.+.++.|||+.++++| +..||.+..+|+.++.+.+.
T Consensus 158 DDL~~I~GIGp~~a~~L-~eaGi~tfaQIAa~t~a~ia 194 (221)
T PRK12278 158 DDLTKITGVGPALAKKL-NEAGVTTFAQIAALTDADIA 194 (221)
T ss_pred chheeccccChHHHHHH-HHcCCCCHHHhhCCChhhhh
Confidence 45788999999999999 59999999999999877554
No 68
>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1. This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.
Probab=66.59 E-value=11 Score=39.70 Aligned_cols=50 Identities=16% Similarity=0.180 Sum_probs=39.7
Q ss_pred Ccc--cCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhccc--hHHHHHHHHc
Q 009729 52 KKM--KQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN--TGTWLWNIAR 102 (527)
Q Consensus 52 ~kL--pGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~FG~~--~G~~L~~~ar 102 (527)
.+| .|||..+.++|+ ..||+|+.||+.+++..|.+..|.. .+..+.+.++
T Consensus 2 ~~~~~~g~~~~~~~~L~-~~g~~t~~~~~~~~~~~L~~~~gls~~~~~~i~~~~~ 55 (313)
T TIGR02238 2 DKLQAHGINAADIKKLK-SAGICTVNGVIMTTRRALCKIKGLSEAKVDKIKEAAS 55 (313)
T ss_pred chhhcCCCCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHH
Confidence 455 469999999995 9999999999999999999998852 2444444444
No 69
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=66.32 E-value=8.6 Score=44.72 Aligned_cols=55 Identities=20% Similarity=0.182 Sum_probs=43.1
Q ss_pred cCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hccchHHHHHHHHc
Q 009729 48 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 102 (527)
Q Consensus 48 ~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~--FG~~~G~~L~~~ar 102 (527)
+-..-+|.|+|+++.++|.+..+|.++.||..+..+.|... ||.+.+..|++...
T Consensus 461 sr~al~I~GLG~k~i~~L~~~g~V~~~~Dl~~L~~~~L~~l~g~g~Ksa~~Ll~~Ie 517 (689)
T PRK14351 461 SRDALDIEGLGEERVQQLVDAGLVESLADLYDLTVADLAELEGWGETSAENLLAELE 517 (689)
T ss_pred cccccCCCCcCHHHHHHHHHcCCCCCHHHHHHcCHHHHhcCcCcchhHHHHHHHHHH
Confidence 34456799999999999986666899999999998888765 77766776655543
No 70
>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=66.32 E-value=13 Score=27.52 Aligned_cols=34 Identities=35% Similarity=0.422 Sum_probs=29.0
Q ss_pred CcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhcc
Q 009729 57 LGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF 91 (527)
Q Consensus 57 IG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~FG~ 91 (527)
|...++.+|. ..|+.|+.+|+.++++.|..+-|.
T Consensus 1 i~~~~~~~L~-~~G~~s~e~la~~~~~eL~~i~g~ 34 (50)
T TIGR01954 1 IDEEIAQLLV-EEGFTTVEDLAYVPIDELLSIEGF 34 (50)
T ss_pred CCHHHHHHHH-HcCCCCHHHHHccCHHHHhcCCCC
Confidence 3467788895 999999999999999999888664
No 71
>PRK14973 DNA topoisomerase I; Provisional
Probab=64.53 E-value=10 Score=45.59 Aligned_cols=79 Identities=19% Similarity=0.112 Sum_probs=53.3
Q ss_pred HHHHHh-cCCCCCCeEEeccCCHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhcc--chHHHH
Q 009729 21 LAKLAS-GMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF--NTGTWL 97 (527)
Q Consensus 21 LAKLAS-~~aKPnG~~vl~~e~v~~fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~FG~--~~G~~L 97 (527)
++++|. .+.+|+--.+.. ...--..-++..++|||.++.++| +.-||.++.||+..++..|.+.=|+ +....|
T Consensus 851 ~~~~~~~~~~~~~~~~~~~---~~~~~~~~el~~vkg~ge~t~~~l-~~ag~~~~e~l~~~d~~~la~~~~i~~k~~~~~ 926 (936)
T PRK14973 851 HAKLVCEKLGRPVPEKISK---AAFERGRAELLSVPGLGETTLEKL-YLAGVYDGDLLVSADPKKLAKVTGIDEKKLRNL 926 (936)
T ss_pred HHHHHHHHhcCCCchhhhh---hhhcccchhhhhccCCCHHHHHHH-HHcCCCCHHHhccCCHHHHhhhcCCCHHHHHHH
Confidence 456666 777776433221 000011112777899999999999 5999999999999999999888775 234455
Q ss_pred HHHHcC
Q 009729 98 WNIARG 103 (527)
Q Consensus 98 ~~~arG 103 (527)
...+++
T Consensus 927 ~~~~~~ 932 (936)
T PRK14973 927 QAYAKK 932 (936)
T ss_pred HHHHhh
Confidence 555543
No 72
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=64.15 E-value=8.6 Score=39.44 Aligned_cols=50 Identities=24% Similarity=0.387 Sum_probs=40.0
Q ss_pred CCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhcc--chHHHHHHHHc
Q 009729 51 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF--NTGTWLWNIAR 102 (527)
Q Consensus 51 I~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~FG~--~~G~~L~~~ar 102 (527)
+..+||||.+++.+|. .-+.+++++..++...|.+.-|+ +.+..+++..+
T Consensus 184 l~s~pgig~~~a~~ll--~~fgS~~~~~tas~~eL~~v~gig~k~A~~I~~~~~ 235 (254)
T COG1948 184 LESIPGIGPKLAERLL--KKFGSVEDVLTASEEELMKVKGIGEKKAREIYRFLR 235 (254)
T ss_pred HHcCCCccHHHHHHHH--HHhcCHHHHhhcCHHHHHHhcCccHHHHHHHHHHHh
Confidence 4567899999999996 45569999999999999999997 45666665554
No 73
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=63.04 E-value=5.2 Score=46.05 Aligned_cols=31 Identities=39% Similarity=0.727 Sum_probs=28.4
Q ss_pred CCCCcccCCcHHHHHHHHHhcCCCcHHHHhhc
Q 009729 49 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKF 80 (527)
Q Consensus 49 LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~ 80 (527)
.|+..+.|||.+++++| +++||+|+.||+-.
T Consensus 10 ~~l~~l~gig~~~a~~l-~~Lgi~tv~DLL~~ 40 (677)
T COG1200 10 VPLSTLKGIGPKTAEKL-KKLGIHTVQDLLLY 40 (677)
T ss_pred cchhhhcCcCHHHHHHH-HHcCCCcHHHHHHh
Confidence 38999999999999999 59999999999874
No 74
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=62.91 E-value=5.9 Score=42.02 Aligned_cols=36 Identities=22% Similarity=0.401 Sum_probs=31.3
Q ss_pred CCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHH
Q 009729 50 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQ 86 (527)
Q Consensus 50 PI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~ 86 (527)
.+.+|.|||++++++| +.+||++..||+.++.+.+.
T Consensus 264 dL~~I~GiGp~~e~~L-~~~Gi~~f~QiA~~t~~~~a 299 (326)
T PRK12311 264 DLKKLTGVSPQIEKKL-NDLGIFHFWQLAELDPDDAA 299 (326)
T ss_pred hhhhhccCChhhhhhh-hhcCCCCHHHhhCCChhhhh
Confidence 3678999999999999 59999999999999876443
No 75
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=62.09 E-value=4.2 Score=40.29 Aligned_cols=43 Identities=19% Similarity=0.264 Sum_probs=31.3
Q ss_pred EEcccHHHHHHHhcCCCCCCeEEeccCCHHhhcccCC---CCcccCCcHHHHHHHH
Q 009729 14 GIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLP---IKKMKQLGGKLGTSLQ 66 (527)
Q Consensus 14 GIA~NKlLAKLAS~~aKPnG~~vl~~e~v~~fL~~LP---I~kLpGIG~k~~~kL~ 66 (527)
||||---||=|++ ++++++...+..-. +.++||||+|++++|.
T Consensus 80 GIGpK~ALaiLs~----------~~~~~l~~aI~~~d~~~L~k~PGIGkKtAeriv 125 (201)
T COG0632 80 GIGPKLALAILSN----------LDPEELAQAIANEDVKALSKIPGIGKKTAERIV 125 (201)
T ss_pred CccHHHHHHHHcC----------CCHHHHHHHHHhcChHhhhcCCCCCHHHHHHHH
Confidence 8888888887764 24455555555433 5789999999999995
No 76
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=61.41 E-value=3.9 Score=39.87 Aligned_cols=43 Identities=26% Similarity=0.277 Sum_probs=24.7
Q ss_pred EEcccHHHHHHHhcCCCCCCeEEeccCCHHhhcccCC---CCcccCCcHHHHHHHH
Q 009729 14 GIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLP---IKKMKQLGGKLGTSLQ 66 (527)
Q Consensus 14 GIA~NKlLAKLAS~~aKPnG~~vl~~e~v~~fL~~LP---I~kLpGIG~k~~~kL~ 66 (527)
||||-.-||-|.+ ++++++...+..=. +.++||||+|+++++-
T Consensus 80 GIGpK~Al~ILs~----------~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIi 125 (183)
T PRK14601 80 GIGANTAMAVCSS----------LDVNSFYKALSLGDESVLKKVPGIGPKSAKRII 125 (183)
T ss_pred CccHHHHHHHHcC----------CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 6666555554432 23445544444433 4567888888887774
No 77
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=58.74 E-value=13 Score=42.48 Aligned_cols=53 Identities=9% Similarity=0.170 Sum_probs=43.5
Q ss_pred cCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hccchHHHHHHHHc
Q 009729 48 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 102 (527)
Q Consensus 48 ~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~--FG~~~G~~L~~~ar 102 (527)
..++..|||||.+..++|.+.+ .++..+..++.+.|.+. +|...+..++...+
T Consensus 542 ~s~L~~IpGIG~k~~k~Ll~~F--gS~~~i~~As~eeL~~v~Gig~~~A~~I~~~l~ 596 (598)
T PRK00558 542 TSALDDIPGIGPKRRKALLKHF--GSLKAIKEASVEELAKVPGISKKLAEAIYEALH 596 (598)
T ss_pred hhhHhhCCCcCHHHHHHHHHHc--CCHHHHHhCCHHHHhhcCCcCHHHHHHHHHHhc
Confidence 3667899999999999997555 57999999999999988 77777787777654
No 78
>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=58.46 E-value=13 Score=42.96 Aligned_cols=16 Identities=19% Similarity=0.368 Sum_probs=8.3
Q ss_pred CCcccCCcHHHHHHHH
Q 009729 51 IKKMKQLGGKLGTSLQ 66 (527)
Q Consensus 51 I~kLpGIG~k~~~kL~ 66 (527)
|..|+|+|.+++++|.
T Consensus 468 L~~L~GfG~Ksa~nIl 483 (652)
T TIGR00575 468 LLELEGFGEKSAQNLL 483 (652)
T ss_pred HhhccCccHHHHHHHH
Confidence 3445556655555543
No 79
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=58.16 E-value=4.6 Score=39.49 Aligned_cols=43 Identities=9% Similarity=0.169 Sum_probs=26.0
Q ss_pred EEcccHHHHHHHhcCCCCCCeEEeccCCHHhhcccCC---CCcccCCcHHHHHHHH
Q 009729 14 GIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLP---IKKMKQLGGKLGTSLQ 66 (527)
Q Consensus 14 GIA~NKlLAKLAS~~aKPnG~~vl~~e~v~~fL~~LP---I~kLpGIG~k~~~kL~ 66 (527)
||||-.-||=|.. ++++++...+..-. +.++||||+|+++++-
T Consensus 80 GIGpK~AL~iLs~----------~~~~el~~aI~~~D~~~L~~vpGIGkKtAerIi 125 (188)
T PRK14606 80 RLGPKTALKIISN----------EDAETLVTMIASQDVEGLSKLPGISKKTAERIV 125 (188)
T ss_pred CccHHHHHHHHcC----------CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 6776666665532 23444554444433 5677888888888874
No 80
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=54.93 E-value=12 Score=40.85 Aligned_cols=36 Identities=25% Similarity=0.455 Sum_probs=31.4
Q ss_pred CCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHH
Q 009729 50 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQ 86 (527)
Q Consensus 50 PI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~ 86 (527)
.+..|.|||++++++| +.+||++..+|+.++...+.
T Consensus 324 DLk~I~GIGpk~e~~L-n~~Gi~~f~QIA~wt~~eia 359 (400)
T PRK12373 324 DLKLISGVGPKIEATL-NELGIFTFDQVAAWKKAERA 359 (400)
T ss_pred hhhhccCCChHHHHHH-HhcCCCCHHHHhCCCHHHhH
Confidence 4678999999999999 59999999999999876443
No 81
>PF07887 Calmodulin_bind: Calmodulin binding protein-like; InterPro: IPR012416 The members of this family are putative or actual calmodulin binding proteins expressed by various plant species. Some members (for example, Q8H6T7 from SWISSPROT), are known to be involved in the induction of plant defence responses []. However, their precise function in this regard is as yet unknown.
Probab=53.87 E-value=16 Score=38.38 Aligned_cols=49 Identities=27% Similarity=0.550 Sum_probs=34.4
Q ss_pred CCcccCCcH--HHHHHHHHhcCCCcHHHHhhc---CHHHHHHHhccchHHHHHHH
Q 009729 51 IKKMKQLGG--KLGTSLQNELGVTTVGDLLKF---SEDKLQESYGFNTGTWLWNI 100 (527)
Q Consensus 51 I~kLpGIG~--k~~~kL~~~lGI~TigDLa~~---~~~~L~~~FG~~~G~~L~~~ 100 (527)
|..|-.||+ ..-++|. .-||.|++|++.+ ++..|+++||..+-...|..
T Consensus 164 VwRLe~Igk~G~~hk~L~-~~~I~tV~dFl~l~~~d~~~Lr~ilg~~ms~k~We~ 217 (299)
T PF07887_consen 164 VWRLEKIGKDGAFHKRLK-KNGINTVEDFLKLLNKDPQKLREILGSGMSNKMWET 217 (299)
T ss_pred hhhhhhccccCHHHHHHH-HcCCccHHHHHHHHhcCHHHHHHHHhcCCChhhHHH
Confidence 445556665 3557884 8999999999874 78899999994333444443
No 82
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=52.52 E-value=6.8 Score=38.53 Aligned_cols=43 Identities=14% Similarity=0.186 Sum_probs=25.0
Q ss_pred EEcccHHHHHHHhcCCCCCCeEEeccCCHHhhcccCC---CCcccCCcHHHHHHHH
Q 009729 14 GIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLP---IKKMKQLGGKLGTSLQ 66 (527)
Q Consensus 14 GIA~NKlLAKLAS~~aKPnG~~vl~~e~v~~fL~~LP---I~kLpGIG~k~~~kL~ 66 (527)
||||-.-||=|.. ++++++...+..-. +.++||||+|+++++.
T Consensus 80 GIGpK~Al~iLs~----------~~~~el~~aI~~~D~~~L~kvpGIGkKtAerIi 125 (195)
T PRK14604 80 GVGPKAALNLLSS----------GTPDELQLAIAGGDVARLARVPGIGKKTAERIV 125 (195)
T ss_pred CcCHHHHHHHHcC----------CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 6666555554431 23444554444433 4567888888888874
No 83
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=52.48 E-value=6.9 Score=38.54 Aligned_cols=43 Identities=21% Similarity=0.275 Sum_probs=26.5
Q ss_pred EEcccHHHHHHHhcCCCCCCeEEeccCCHHhhcccCC---CCcccCCcHHHHHHHH
Q 009729 14 GIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLP---IKKMKQLGGKLGTSLQ 66 (527)
Q Consensus 14 GIA~NKlLAKLAS~~aKPnG~~vl~~e~v~~fL~~LP---I~kLpGIG~k~~~kL~ 66 (527)
||||-.-||=|.+ ++++++...+..-. +.++||||+|+++++.
T Consensus 79 GIGpK~AL~iLs~----------~~~~~l~~aI~~~D~~~L~kvpGIGkKtAerIi 124 (197)
T PRK14603 79 GVGPKLALALLSA----------LPPALLARALLEGDARLLTSASGVGKKLAERIA 124 (197)
T ss_pred CcCHHHHHHHHcC----------CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 6666555555432 24455555555433 5677888888888874
No 84
>PRK13766 Hef nuclease; Provisional
Probab=52.39 E-value=18 Score=42.17 Aligned_cols=50 Identities=22% Similarity=0.408 Sum_probs=41.6
Q ss_pred CCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hccchHHHHHHHHc
Q 009729 51 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 102 (527)
Q Consensus 51 I~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~--FG~~~G~~L~~~ar 102 (527)
+..+||||.+.+.+|.+.+| ++.++..++.+.|... +|.+.+..++...+
T Consensus 717 L~~ipgig~~~a~~Ll~~fg--s~~~i~~as~~~L~~i~Gig~~~a~~i~~~~~ 768 (773)
T PRK13766 717 VESLPDVGPVLARNLLEHFG--SVEAVMTASEEELMEVEGIGEKTAKRIREVVT 768 (773)
T ss_pred HhcCCCCCHHHHHHHHHHcC--CHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHh
Confidence 67899999999999975555 8999999999999988 78767888776554
No 85
>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=52.35 E-value=17 Score=35.55 Aligned_cols=51 Identities=20% Similarity=0.219 Sum_probs=38.0
Q ss_pred CCcccCCcHHHHHHHHHhcCCCcHHHHhhc----CHHHHHHH--hccchHHHHHHHHcCC
Q 009729 51 IKKMKQLGGKLGTSLQNELGVTTVGDLLKF----SEDKLQES--YGFNTGTWLWNIARGI 104 (527)
Q Consensus 51 I~kLpGIG~k~~~kL~~~lGI~TigDLa~~----~~~~L~~~--FG~~~G~~L~~~arGi 104 (527)
+-.++|||+|++..+ +++.++.+|..+ +...|.+. ||+++++++.-.+++.
T Consensus 74 L~~V~GIGpK~Al~i---L~~~~~~el~~aI~~~d~~~L~~ipGiGkKtAerIileLk~k 130 (191)
T TIGR00084 74 LIKVNGVGPKLALAI---LSNMSPEEFVYAIETEEVKALVKIPGVGKKTAERLLLELKGK 130 (191)
T ss_pred HhCCCCCCHHHHHHH---HhcCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHhh
Confidence 458999999999765 778888888864 45667664 5667888888776664
No 86
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=51.69 E-value=6.6 Score=38.78 Aligned_cols=16 Identities=31% Similarity=0.555 Sum_probs=11.3
Q ss_pred CCcccCCcHHHHHHHH
Q 009729 51 IKKMKQLGGKLGTSLQ 66 (527)
Q Consensus 51 I~kLpGIG~k~~~kL~ 66 (527)
+.++||||+|+++|+-
T Consensus 109 L~~vpGIGkKtAeRII 124 (196)
T PRK13901 109 ISKVKGIGNKMAGKIF 124 (196)
T ss_pred HhhCCCCCHHHHHHHH
Confidence 4567777777777774
No 87
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=51.36 E-value=10 Score=25.06 Aligned_cols=16 Identities=19% Similarity=0.320 Sum_probs=14.0
Q ss_pred CCcccCCcHHHHHHHH
Q 009729 51 IKKMKQLGGKLGTSLQ 66 (527)
Q Consensus 51 I~kLpGIG~k~~~kL~ 66 (527)
+.+++|||++++++|.
T Consensus 3 L~~i~GiG~k~A~~il 18 (26)
T smart00278 3 LLKVPGIGPKTAEKIL 18 (26)
T ss_pred hhhCCCCCHHHHHHHH
Confidence 4679999999999985
No 88
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=50.37 E-value=8.7 Score=37.99 Aligned_cols=28 Identities=11% Similarity=0.239 Sum_probs=16.1
Q ss_pred cCCHHhhcccCC---CCcccCCcHHHHHHHH
Q 009729 39 FSSVKGLLDSLP---IKKMKQLGGKLGTSLQ 66 (527)
Q Consensus 39 ~e~v~~fL~~LP---I~kLpGIG~k~~~kL~ 66 (527)
++++...+..-. +.++||||+|+++++.
T Consensus 96 ~~~l~~aI~~~D~~~L~~ipGIGkKtAerIi 126 (203)
T PRK14602 96 PDDLRRLVAEEDVAALTRVSGIGKKTAQHIF 126 (203)
T ss_pred HHHHHHHHHhCCHHHHhcCCCcCHHHHHHHH
Confidence 344444444332 4567777777777774
No 89
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=48.83 E-value=13 Score=35.35 Aligned_cols=40 Identities=18% Similarity=0.340 Sum_probs=31.5
Q ss_pred CCcccCCcHHHHHHHHHhcCCC---cHHHHhhcCHHHHHHHhc
Q 009729 51 IKKMKQLGGKLGTSLQNELGVT---TVGDLLKFSEDKLQESYG 90 (527)
Q Consensus 51 I~kLpGIG~k~~~kL~~~lGI~---TigDLa~~~~~~L~~~FG 90 (527)
++.|+|||.+++..+...+||. +++||-.-....|...+.
T Consensus 32 Lt~I~GIG~~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~ 74 (154)
T PTZ00134 32 LTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIA 74 (154)
T ss_pred ecccccccHHHHHHHHHHcCcCcCCCcccCCHHHHHHHHHHHh
Confidence 5789999999999999999995 677777665566666554
No 90
>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=46.33 E-value=22 Score=28.57 Aligned_cols=30 Identities=23% Similarity=0.325 Sum_probs=22.4
Q ss_pred CCc-ccCCcHHHHHHHHHh---c-CCCcHHHHhhc
Q 009729 51 IKK-MKQLGGKLGTSLQNE---L-GVTTVGDLLKF 80 (527)
Q Consensus 51 I~k-LpGIG~k~~~kL~~~---l-GI~TigDLa~~ 80 (527)
+.. +||||.+.+++|.+. + ++.++.||...
T Consensus 18 L~~~ipgig~~~a~~Il~~R~~~g~~~s~~dL~~v 52 (69)
T TIGR00426 18 LQRAMNGVGLKKAEAIVSYREEYGPFKTVEDLKQV 52 (69)
T ss_pred HHhHCCCCCHHHHHHHHHHHHHcCCcCCHHHHHcC
Confidence 445 899999999988744 3 47777777764
No 91
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=46.22 E-value=23 Score=37.62 Aligned_cols=32 Identities=25% Similarity=0.258 Sum_probs=26.6
Q ss_pred CcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHH
Q 009729 52 KKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKL 85 (527)
Q Consensus 52 ~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L 85 (527)
+.++|||.+++++. ...|++|+.|++.- ++.+
T Consensus 100 tnifGvG~ktA~~W-y~~GfrTled~Rk~-~~kf 131 (353)
T KOG2534|consen 100 TNIFGVGLKTAEKW-YREGFRTLEDVRKK-PDKF 131 (353)
T ss_pred HHHhccCHHHHHHH-HHhhhhHHHHHHhC-HHHH
Confidence 46899999999999 59999999999943 3444
No 92
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=45.44 E-value=17 Score=33.27 Aligned_cols=39 Identities=13% Similarity=0.152 Sum_probs=28.2
Q ss_pred CCCcccCCcHHHHHHHHHhcCCC---cHHHHhhcCHHHHHHH
Q 009729 50 PIKKMKQLGGKLGTSLQNELGVT---TVGDLLKFSEDKLQES 88 (527)
Q Consensus 50 PI~kLpGIG~k~~~kL~~~lGI~---TigDLa~~~~~~L~~~ 88 (527)
-++.+.|||.+++..+.+.+||. .+++|-+...+.|...
T Consensus 18 aLt~i~GIG~~~A~~ic~~lgi~~~~~~~~Lt~~qi~~l~~~ 59 (122)
T CHL00137 18 ALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQISALREI 59 (122)
T ss_pred eecccccccHHHHHHHHHHcCcCcCcCcccCCHHHHHHHHHH
Confidence 35789999999999999999996 5566554444444433
No 93
>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=44.95 E-value=17 Score=32.26 Aligned_cols=29 Identities=28% Similarity=0.565 Sum_probs=22.4
Q ss_pred CCcccCCcHHHHHHHHHhcCCCc---HHHHhh
Q 009729 51 IKKMKQLGGKLGTSLQNELGVTT---VGDLLK 79 (527)
Q Consensus 51 I~kLpGIG~k~~~kL~~~lGI~T---igDLa~ 79 (527)
+..++|||..++..+...+||.. +++|-+
T Consensus 17 Lt~IyGIG~~~A~~Ic~~lgi~~~~~~~~Ls~ 48 (107)
T PF00416_consen 17 LTKIYGIGRRKAKQICKKLGINPNKKVGDLSD 48 (107)
T ss_dssp HTTSTTBCHHHHHHHHHHTTS-SSSBTTTSTH
T ss_pred HhhhhccCHHHHHHHHHHcCCChhhhcccCCH
Confidence 46899999999999988999964 444444
No 94
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type. This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins.
Probab=44.94 E-value=23 Score=37.09 Aligned_cols=54 Identities=26% Similarity=0.364 Sum_probs=41.1
Q ss_pred cccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHH--HhccchHHHHHHHH
Q 009729 46 LDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQE--SYGFNTGTWLWNIA 101 (527)
Q Consensus 46 L~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~--~FG~~~G~~L~~~a 101 (527)
+..++|.+| ++--+....|. +.||+|++||..++.+.|.+ -||.+.-+.+.+.+
T Consensus 232 ~~~~~I~~L-~LSvR~~n~Lk-~~~I~ti~dL~~~~~~~l~~~~n~G~ksl~ei~~~l 287 (297)
T TIGR02027 232 LLSIKIEEL-DLSVRSYNCLK-RAGIHTLGELVSKSEEELLKIKNFGKKSLTEIKEKL 287 (297)
T ss_pred hccccHHHh-CccHHHHhHHH-HcCCcCHHHHHhCCHHHHhhCCCCChhhHHHHHHHH
Confidence 456788888 68889999995 99999999999999988744 46665544444443
No 95
>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=44.89 E-value=20 Score=32.30 Aligned_cols=37 Identities=16% Similarity=0.295 Sum_probs=26.6
Q ss_pred CCcccCCcHHHHHHHHHhcCCC---cHHHHhhcCHHHHHH
Q 009729 51 IKKMKQLGGKLGTSLQNELGVT---TVGDLLKFSEDKLQE 87 (527)
Q Consensus 51 I~kLpGIG~k~~~kL~~~lGI~---TigDLa~~~~~~L~~ 87 (527)
++.++|||.+++..+...+||. .+++|-....+.|..
T Consensus 17 L~~i~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~ 56 (113)
T TIGR03631 17 LTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAIRE 56 (113)
T ss_pred eeeeecccHHHHHHHHHHhCcCcccccccCCHHHHHHHHH
Confidence 5789999999999999999996 445554433333333
No 96
>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=44.24 E-value=8.8 Score=37.55 Aligned_cols=43 Identities=19% Similarity=0.242 Sum_probs=29.1
Q ss_pred EEcccHHHHHHHhcCCCCCCeEEeccCCHHhhccc---CCCCcccCCcHHHHHHHH
Q 009729 14 GIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDS---LPIKKMKQLGGKLGTSLQ 66 (527)
Q Consensus 14 GIA~NKlLAKLAS~~aKPnG~~vl~~e~v~~fL~~---LPI~kLpGIG~k~~~kL~ 66 (527)
||||-.-+|=|. ...++++...+.. --+..+||||+|+++++.
T Consensus 79 GIGpK~Al~iL~----------~~~~~el~~aI~~~d~~~L~~ipGiGkKtAerIi 124 (191)
T TIGR00084 79 GVGPKLALAILS----------NMSPEEFVYAIETEEVKALVKIPGVGKKTAERLL 124 (191)
T ss_pred CCCHHHHHHHHh----------cCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHH
Confidence 777766555432 2245556555554 447889999999999984
No 97
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=43.94 E-value=25 Score=34.47 Aligned_cols=53 Identities=13% Similarity=0.183 Sum_probs=39.6
Q ss_pred CcccCCcHHHHHHHHHhcCCCc-HHHHhhcCHHHHHHHhc--cchHHHHHHHHcCC
Q 009729 52 KKMKQLGGKLGTSLQNELGVTT-VGDLLKFSEDKLQESYG--FNTGTWLWNIARGI 104 (527)
Q Consensus 52 ~kLpGIG~k~~~kL~~~lGI~T-igDLa~~~~~~L~~~FG--~~~G~~L~~~arGi 104 (527)
-.++|||++++-.+...++... +..++.-+...|.+.-| +++++++.-.++|.
T Consensus 76 i~V~GIGpK~Al~ILs~~~~~~l~~aI~~~D~~~L~~vpGIGkKtAerIilELk~K 131 (194)
T PRK14605 76 IDVSGIGPKLGLAMLSAMNAEALASAIISGNAELLSTIPGIGKKTASRIVLELKDK 131 (194)
T ss_pred hCCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHH
Confidence 5899999999988876677766 44455668888888655 46788877777764
No 98
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=43.42 E-value=6.9 Score=38.07 Aligned_cols=39 Identities=26% Similarity=0.541 Sum_probs=35.0
Q ss_pred ccccccCCccccccCChHHHHHHHHhhCCCCCCCcccCC
Q 009729 476 KLRIEEIDPSVIDELPKEIQDEIQAWLRPSKRPHRVKQG 514 (527)
Q Consensus 476 ~~~~~~id~~~~~el~~ei~~e~~~~~~~~~~~~~~~~~ 514 (527)
.|.|.||..-+|+-.-.||-++++.++||.|.|.--++-
T Consensus 24 e~eiiei~a~lv~~id~~vvd~F~syVRP~~~P~Lt~~C 62 (210)
T COG5018 24 EFEIIEIEAGLVKSIDDEVVDTFSSYVRPKKFPKLTKRC 62 (210)
T ss_pred hceeeeehhhHHHHhhHHHHHHHHHhcCcccCchHHHHH
Confidence 466999999999999999999999999999999766553
No 99
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=41.80 E-value=14 Score=36.13 Aligned_cols=14 Identities=29% Similarity=0.408 Sum_probs=11.5
Q ss_pred cccCCcHHHHHHHH
Q 009729 53 KMKQLGGKLGTSLQ 66 (527)
Q Consensus 53 kLpGIG~k~~~kL~ 66 (527)
++||||+|+++++.
T Consensus 111 ~vpGIGkKtAerIi 124 (186)
T PRK14600 111 KVNGIGEKLINRII 124 (186)
T ss_pred ECCCCcHHHHHHHH
Confidence 67888888888885
No 100
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=41.04 E-value=20 Score=33.91 Aligned_cols=41 Identities=20% Similarity=0.412 Sum_probs=32.0
Q ss_pred CCCcccCCcHHHHHHHHHhcCCC---cHHHHhhcCHHHHHHHhc
Q 009729 50 PIKKMKQLGGKLGTSLQNELGVT---TVGDLLKFSEDKLQESYG 90 (527)
Q Consensus 50 PI~kLpGIG~k~~~kL~~~lGI~---TigDLa~~~~~~L~~~FG 90 (527)
-++.|.|||.+++..+.+.+||. .++||-.--...|...+.
T Consensus 26 aLt~IyGIG~~~a~~Ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~ 69 (149)
T PRK04053 26 ALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEALE 69 (149)
T ss_pred eccccccccHHHHHHHHHHcCcCCCCccCcCCHHHHHHHHHHHH
Confidence 36789999999999999999996 677777665566666553
No 101
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=40.92 E-value=39 Score=38.59 Aligned_cols=50 Identities=16% Similarity=0.255 Sum_probs=39.7
Q ss_pred CCcccCCcHHHHHHHHHhcC-CCcHHHHhhcCHHHHHHH--hccchHHHHHHHH
Q 009729 51 IKKMKQLGGKLGTSLQNELG-VTTVGDLLKFSEDKLQES--YGFNTGTWLWNIA 101 (527)
Q Consensus 51 I~kLpGIG~k~~~kL~~~lG-I~TigDLa~~~~~~L~~~--FG~~~G~~L~~~a 101 (527)
-=+|-|+|.++.++|. ..| |.++.||..+..+.|... ||.+.+..|++..
T Consensus 427 amdI~GlGe~~i~~L~-~~G~i~~~~Diy~L~~~~l~~l~gfgeks~~nll~aI 479 (562)
T PRK08097 427 GLGLDGIGEGTWRALH-QTGLFEHLFSWLALTPEQLANTPGIGKARAEQLWHQF 479 (562)
T ss_pred ccCCCCcCHHHHHHHH-HcCCcCCHHHHhcCCHHHHhcCcCccHHHHHHHHHHH
Confidence 3468899999999997 666 699999999998887664 7876677666543
No 102
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=40.09 E-value=25 Score=34.77 Aligned_cols=16 Identities=31% Similarity=0.488 Sum_probs=14.2
Q ss_pred CCcccCCcHHHHHHHH
Q 009729 51 IKKMKQLGGKLGTSLQ 66 (527)
Q Consensus 51 I~kLpGIG~k~~~kL~ 66 (527)
+.+|||||+|+++||.
T Consensus 13 l~~LPGIG~KsA~RlA 28 (195)
T TIGR00615 13 LKKLPGIGPKSAQRLA 28 (195)
T ss_pred HHHCCCCCHHHHHHHH
Confidence 5679999999999995
No 103
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=39.98 E-value=40 Score=39.40 Aligned_cols=45 Identities=16% Similarity=0.273 Sum_probs=27.1
Q ss_pred ccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hccchHHHHHHH
Q 009729 54 MKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNI 100 (527)
Q Consensus 54 LpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~--FG~~~G~~L~~~ 100 (527)
|||||.+++++|.+.+ .++.+|..++.+.|... +|.+.+..++..
T Consensus 533 IpgIG~~~ak~L~~~F--~si~~L~~As~eeL~~i~GIG~k~A~sI~~f 579 (689)
T PRK14351 533 IPEVGPTTARNLAREF--GTFEAIMDADEEALRAVDDVGPTVAEEIREF 579 (689)
T ss_pred CCCcCHHHHHHHHHHh--CCHHHHHhCCHHHHhccCCcCHHHHHHHHHH
Confidence 5667777766664333 55666766666666665 555555555444
No 104
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=39.53 E-value=32 Score=36.25 Aligned_cols=51 Identities=24% Similarity=0.377 Sum_probs=39.6
Q ss_pred cccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hccchHHHHH
Q 009729 46 LDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLW 98 (527)
Q Consensus 46 L~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~--FG~~~G~~L~ 98 (527)
+..++|.+| ++--+....|. +.||+|++||.+++.+.|.+. ||.+.-+.+.
T Consensus 246 ~l~~~I~~L-~LS~R~~n~Lk-~~~I~ti~dL~~~~~~~l~~~~n~G~ksl~ei~ 298 (310)
T PRK05182 246 ILLRPIEEL-ELSVRSYNCLK-RAGINTIGDLVQRTEEELLKTRNLGKKSLEEIK 298 (310)
T ss_pred cccccHHHh-ccchHHHHHHH-HcCCcCHHHHHhCCHHHHhcCCCCChhhHHHHH
Confidence 346788888 78899999995 999999999999999887544 5654444443
No 105
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=38.52 E-value=29 Score=39.70 Aligned_cols=49 Identities=16% Similarity=0.186 Sum_probs=38.9
Q ss_pred cCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hccchHHHHH
Q 009729 48 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLW 98 (527)
Q Consensus 48 ~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~--FG~~~G~~L~ 98 (527)
.+.+..+||||.+...+|.+. +.++.++..++.+.|.+. +|.+.+..++
T Consensus 524 ~~~L~~IpGIG~kr~~~LL~~--FGS~~~I~~As~eeL~~vpGi~~~~A~~I~ 574 (577)
T PRK14668 524 STVLDDVPGVGPETRKRLLRR--FGSVEGVREASVEDLRDVPGVGEKTAETIR 574 (577)
T ss_pred HhHHhcCCCCCHHHHHHHHHH--cCCHHHHHhCCHHHHHhCCCCCHHHHHHHH
Confidence 467889999999999999644 469999999999999888 5554455554
No 106
>PRK00076 recR recombination protein RecR; Reviewed
Probab=38.45 E-value=27 Score=34.53 Aligned_cols=16 Identities=25% Similarity=0.478 Sum_probs=14.2
Q ss_pred CCcccCCcHHHHHHHH
Q 009729 51 IKKMKQLGGKLGTSLQ 66 (527)
Q Consensus 51 I~kLpGIG~k~~~kL~ 66 (527)
+.+|||||+|+++||.
T Consensus 13 l~~LPGIG~KsA~Rla 28 (196)
T PRK00076 13 LRKLPGIGPKSAQRLA 28 (196)
T ss_pred HHHCCCCCHHHHHHHH
Confidence 5679999999999995
No 107
>PRK13844 recombination protein RecR; Provisional
Probab=37.88 E-value=28 Score=34.58 Aligned_cols=16 Identities=25% Similarity=0.507 Sum_probs=14.2
Q ss_pred CCcccCCcHHHHHHHH
Q 009729 51 IKKMKQLGGKLGTSLQ 66 (527)
Q Consensus 51 I~kLpGIG~k~~~kL~ 66 (527)
+.+|||||+|+++||.
T Consensus 17 l~~LPGIG~KsA~Rla 32 (200)
T PRK13844 17 LRKLPTIGKKSSQRLA 32 (200)
T ss_pred HHHCCCCCHHHHHHHH
Confidence 5679999999999995
No 108
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=37.15 E-value=48 Score=35.66 Aligned_cols=39 Identities=26% Similarity=0.388 Sum_probs=33.9
Q ss_pred CCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhcc
Q 009729 51 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF 91 (527)
Q Consensus 51 I~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~FG~ 91 (527)
+.++|+|++.++++|.+.|| ++..+..++.+.|.+.=|+
T Consensus 289 Ls~IPrl~k~iAk~Ll~~FG--SL~~Il~As~eeL~~VeGI 327 (352)
T PRK13482 289 LSKIPRLPSAVIENLVEHFG--SLQGLLAASIEDLDEVEGI 327 (352)
T ss_pred HhcCCCCCHHHHHHHHHHcC--CHHHHHcCCHHHHhhCCCc
Confidence 56799999999999988888 9999999999999886553
No 109
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=36.62 E-value=34 Score=31.27 Aligned_cols=39 Identities=21% Similarity=0.314 Sum_probs=28.1
Q ss_pred CCCcccCCcHHHHHHHHHhcCCC---cHHHHhhcCHHHHHHH
Q 009729 50 PIKKMKQLGGKLGTSLQNELGVT---TVGDLLKFSEDKLQES 88 (527)
Q Consensus 50 PI~kLpGIG~k~~~kL~~~lGI~---TigDLa~~~~~~L~~~ 88 (527)
-++.|.|||..++..+...+||. +++||-.-..+.|...
T Consensus 18 aL~~I~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~ 59 (122)
T PRK05179 18 ALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREE 59 (122)
T ss_pred eecccccccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHH
Confidence 35789999999999999999996 4555554444444443
No 110
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=36.48 E-value=35 Score=39.10 Aligned_cols=50 Identities=12% Similarity=0.201 Sum_probs=39.1
Q ss_pred ccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhcc--chHHHHHH
Q 009729 47 DSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF--NTGTWLWN 99 (527)
Q Consensus 47 ~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~FG~--~~G~~L~~ 99 (527)
-.-++.+|+|||++..++|.+ ...++.++..++.++|.+. |+ ..++.+|.
T Consensus 528 ~~s~Ld~I~GiG~~r~~~LL~--~Fgs~~~i~~As~eel~~v-gi~~~~a~~i~~ 579 (581)
T COG0322 528 LQSSLDDIPGIGPKRRKALLK--HFGSLKGIKSASVEELAKV-GISKKLAEKIYE 579 (581)
T ss_pred hcCccccCCCcCHHHHHHHHH--HhhCHHHHHhcCHHHHHHc-CCCHHHHHHHHh
Confidence 345778999999999999964 4558999999999999999 65 34555554
No 111
>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=36.46 E-value=34 Score=30.99 Aligned_cols=30 Identities=17% Similarity=0.284 Sum_probs=21.2
Q ss_pred CCcccCCcHHHHHHHHHhc----CCCcHHHHhhc
Q 009729 51 IKKMKQLGGKLGTSLQNEL----GVTTVGDLLKF 80 (527)
Q Consensus 51 I~kLpGIG~k~~~kL~~~l----GI~TigDLa~~ 80 (527)
+..+||||.+.++++.... ++.++.||..+
T Consensus 70 L~~lpGIG~~~A~~Ii~~R~~~g~f~s~eeL~~V 103 (120)
T TIGR01259 70 LQALPGIGPAKAKAIIEYREENGAFKSVDDLTKV 103 (120)
T ss_pred HhcCCCCCHHHHHHHHHHHHhcCCcCCHHHHHcC
Confidence 4468999999999987443 45666666543
No 112
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=36.21 E-value=47 Score=38.63 Aligned_cols=16 Identities=19% Similarity=0.320 Sum_probs=10.4
Q ss_pred CCcccCCcHHHHHHHH
Q 009729 51 IKKMKQLGGKLGTSLQ 66 (527)
Q Consensus 51 I~kLpGIG~k~~~kL~ 66 (527)
|..|+|+|.|++++|.
T Consensus 481 L~~l~gfG~Ksa~~ll 496 (665)
T PRK07956 481 LLGLEGFGEKSAQNLL 496 (665)
T ss_pred HhcCcCcchHHHHHHH
Confidence 5566777777766654
No 113
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=34.49 E-value=42 Score=35.73 Aligned_cols=55 Identities=20% Similarity=0.355 Sum_probs=43.3
Q ss_pred hcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHH--HHHhccchHHHHHHHH
Q 009729 45 LLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKL--QESYGFNTGTWLWNIA 101 (527)
Q Consensus 45 fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L--~~~FG~~~G~~L~~~a 101 (527)
.+..++|.+| .+--+...-|. +.||+|+|||.+.+.+.| .+-||.+..+.+...+
T Consensus 259 ~~~~~~Ie~L-~LSvRs~NcLk-~a~I~ti~dL~~~s~~dLl~ikN~GkKSl~EI~~~L 315 (327)
T CHL00013 259 ALKQIFIEQL-ELSVRAYNCLK-RANIHTLLDLLNYSQEDLLKIKNFGQKSAKEVLEAL 315 (327)
T ss_pred hhhceeHHhc-cCchhhhhhhh-hcCccCHHHHHhcCHHHHhhhhccCHhHHHHHHHHH
Confidence 4556778888 57778888894 999999999999998886 4568877666666655
No 114
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=33.55 E-value=59 Score=37.93 Aligned_cols=52 Identities=17% Similarity=0.029 Sum_probs=40.2
Q ss_pred CCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hccchHHHHHHHH
Q 009729 50 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIA 101 (527)
Q Consensus 50 PI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~--FG~~~G~~L~~~a 101 (527)
.--+|-|+|.++.++|.+.--|.++.||..+..+.|... ||.+.+..|++..
T Consensus 437 ~aldI~GlG~~~i~~L~~~G~i~~~~Dly~L~~~~l~~l~g~geksa~nl~~~I 490 (669)
T PRK14350 437 KCMNIVGLSDKTIEFLFEKKFISSEIDLYTFNFDRLINLKGFKDKRINNLKRSI 490 (669)
T ss_pred CcccccCcCHHHHHHHHHcCCcCCHHHHhhCCHHHHhhccCccHHHHHHHHHHH
Confidence 345789999999999974455689999999998887654 6766677776643
No 115
>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=33.05 E-value=38 Score=31.93 Aligned_cols=40 Identities=25% Similarity=0.454 Sum_probs=29.7
Q ss_pred CCCcccCCcHHHHHHHHHhcCCC---cHHHHhhcCHHHHHHHh
Q 009729 50 PIKKMKQLGGKLGTSLQNELGVT---TVGDLLKFSEDKLQESY 89 (527)
Q Consensus 50 PI~kLpGIG~k~~~kL~~~lGI~---TigDLa~~~~~~L~~~F 89 (527)
-+..|.|||.+++..+...+||. .++||-.--...|...+
T Consensus 22 aLt~I~GIG~~~a~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i 64 (144)
T TIGR03629 22 ALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKLEEAV 64 (144)
T ss_pred eecceeccCHHHHHHHHHHcCcCCCCCcccCCHHHHHHHHHHH
Confidence 36789999999999999999996 56666655444454443
No 116
>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=32.53 E-value=58 Score=38.15 Aligned_cols=42 Identities=21% Similarity=0.305 Sum_probs=31.0
Q ss_pred CHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHH
Q 009729 41 SVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQ 86 (527)
Q Consensus 41 ~v~~fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~ 86 (527)
.+..||. =..++|||+++++++.+.||..++.-|.+- ++.|.
T Consensus 79 ~i~~yL~---s~~~~GIG~~~A~~iv~~fg~~~~~~i~~~-~~~L~ 120 (720)
T TIGR01448 79 GIVAYLS---SRSIKGVGKKLAQRIVKTFGEAAFDVLDDD-PEKLL 120 (720)
T ss_pred HHHHHHh---cCCCCCcCHHHHHHHHHHhCHhHHHHHHhC-HHHHh
Confidence 3456665 346999999999999989999887777654 33344
No 117
>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=32.43 E-value=49 Score=32.27 Aligned_cols=57 Identities=21% Similarity=0.306 Sum_probs=35.3
Q ss_pred CCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhccchHHHHHHHHcCCcCccccccCCCccccccccCCCCCCC
Q 009729 51 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRAL 130 (527)
Q Consensus 51 I~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~FG~~~G~~L~~~arGiD~~~V~~~~~~KSIs~erTF~~~~di 130 (527)
+..|||||++++.-+. ..|.+.|++. -.=|+.+-|--. +|.|+ ++. .++
T Consensus 117 Ll~LpGVG~KTAnvVL----------------~~l~~~~~~~--~~~~~~~~~~~~-------~~~~~---~~~---~~~ 165 (177)
T TIGR03252 117 LKALPGFGKQKAKIFL----------------ALLGKQLGVT--PEGWREAAGPYG-------EPGSF---RSV---ADI 165 (177)
T ss_pred HHcCCCCCHHHHHHHH----------------HHHHHHhCCC--CcchHHhccccC-------CCCcc---cch---hhc
Confidence 5678999999998875 4667778863 234667766322 22222 223 367
Q ss_pred CCHHHHHH
Q 009729 131 KTVASVQH 138 (527)
Q Consensus 131 ~~~eel~~ 138 (527)
.+++.+.+
T Consensus 166 ~~~~~~~~ 173 (177)
T TIGR03252 166 TDPESLTQ 173 (177)
T ss_pred CCHHHHHH
Confidence 77776654
No 118
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=31.04 E-value=61 Score=29.78 Aligned_cols=39 Identities=8% Similarity=0.252 Sum_probs=29.0
Q ss_pred CCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH
Q 009729 50 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES 88 (527)
Q Consensus 50 PI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~ 88 (527)
-++.|+|||..++..+.+.+||.--.-+-+++.+++.+.
T Consensus 18 ALt~IyGIG~~~a~~I~~~~gi~~~~r~~eLteeei~~i 56 (121)
T COG0099 18 ALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERL 56 (121)
T ss_pred hhhhhccccHHHHHHHHHHcCCCHhHhhccCCHHHHHHH
Confidence 366799999999999988999976555555666655443
No 119
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=30.40 E-value=40 Score=31.39 Aligned_cols=53 Identities=21% Similarity=0.243 Sum_probs=36.9
Q ss_pred cHHHHHHHhcCCCCCCeEEeccCCHHhhcccCCCCcccCCcHHHHHHHHHhcC-CCcHHHHhhcC
Q 009729 18 NKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELG-VTTVGDLLKFS 81 (527)
Q Consensus 18 NKlLAKLAS~~aKPnG~~vl~~e~v~~fL~~LPI~kLpGIG~k~~~kL~~~lG-I~TigDLa~~~ 81 (527)
|..=|||+ .... -.-|....+.+|. .+||||+.+++++- ..| ..++.||.+.+
T Consensus 40 N~~d~kl~-~~~~---kIdiN~A~~~el~------~lpGigP~~A~~IV-~nGpf~sveDL~~V~ 93 (132)
T PRK02515 40 NVADAKLG-EFGE---KIDLNNSSVRAFR------QFPGMYPTLAGKIV-KNAPYDSVEDVLNLP 93 (132)
T ss_pred ChhhHHHH-hcCC---cccCCccCHHHHH------HCCCCCHHHHHHHH-HCCCCCCHHHHHcCC
Confidence 66667777 3322 1234556666653 48999999999997 555 88999999864
No 120
>PRK07945 hypothetical protein; Provisional
Probab=29.93 E-value=90 Score=33.06 Aligned_cols=57 Identities=14% Similarity=0.060 Sum_probs=36.1
Q ss_pred HHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhccchHHHHHHHHcC
Q 009729 42 VKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARG 103 (527)
Q Consensus 42 v~~fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~FG~~~G~~L~~~arG 103 (527)
+..+...-.+++|||||+.++.++.+-+-=-++.- .+.|+...++..|.-|....+|
T Consensus 42 ~~~~~~~g~l~~~~giG~~~a~~i~e~~~tg~~~~-----l~~l~~~~~~~~g~~l~~~~~~ 98 (335)
T PRK07945 42 RARRARAGSLTSLPGIGPKTAKVIAQALAGRVPDY-----LAELRADAEPLGGGALRAALRG 98 (335)
T ss_pred HHHHHhcCCcccCCCcCHHHHHHHHHHHhcCCHHH-----HHHHHHhhcCCccHHHHHHHhh
Confidence 55544444788999999999998863222222222 2455666666557777777776
No 121
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=28.96 E-value=56 Score=30.81 Aligned_cols=30 Identities=20% Similarity=0.276 Sum_probs=22.7
Q ss_pred CcccCCcHHHHHHHHHh---c-CCCcHHHHhhcC
Q 009729 52 KKMKQLGGKLGTSLQNE---L-GVTTVGDLLKFS 81 (527)
Q Consensus 52 ~kLpGIG~k~~~kL~~~---l-GI~TigDLa~~~ 81 (527)
..|||||++.++++... . ...+++||+..+
T Consensus 100 ~~lpgIG~~kA~aIi~yRe~~G~f~sv~dL~~v~ 133 (149)
T COG1555 100 QALPGIGPKKAQAIIDYREENGPFKSVDDLAKVK 133 (149)
T ss_pred HHCCCCCHHHHHHHHHHHHHcCCCCcHHHHHhcc
Confidence 56899999999988622 2 478888888753
No 122
>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=28.47 E-value=36 Score=27.44 Aligned_cols=16 Identities=19% Similarity=0.542 Sum_probs=14.3
Q ss_pred CCcccCCcHHHHHHHH
Q 009729 51 IKKMKQLGGKLGTSLQ 66 (527)
Q Consensus 51 I~kLpGIG~k~~~kL~ 66 (527)
+..|||||++++.++.
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 6789999999999885
No 123
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=27.17 E-value=81 Score=31.07 Aligned_cols=50 Identities=20% Similarity=0.143 Sum_probs=38.3
Q ss_pred CcccCCcHHHHHHHHHhcCCCcHHHHhhc----CHHHHHHHhc--cchHHHHHHHHcCC
Q 009729 52 KKMKQLGGKLGTSLQNELGVTTVGDLLKF----SEDKLQESYG--FNTGTWLWNIARGI 104 (527)
Q Consensus 52 ~kLpGIG~k~~~kL~~~lGI~TigDLa~~----~~~~L~~~FG--~~~G~~L~~~arGi 104 (527)
..+.|||+|++-.+ |+-.+..+|+.+ +...|.+.-| +++++++.-.++|.
T Consensus 76 i~V~GIGpK~Al~i---Ls~~~~~el~~aI~~~D~~~L~kvpGIGkKtAerIilELk~K 131 (195)
T PRK14604 76 IGVSGVGPKAALNL---LSSGTPDELQLAIAGGDVARLARVPGIGKKTAERIVLELKGK 131 (195)
T ss_pred hCcCCcCHHHHHHH---HcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHH
Confidence 46899999998554 566677787764 6777877765 56899999888875
No 124
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=26.40 E-value=56 Score=32.44 Aligned_cols=16 Identities=31% Similarity=0.468 Sum_probs=14.2
Q ss_pred CCcccCCcHHHHHHHH
Q 009729 51 IKKMKQLGGKLGTSLQ 66 (527)
Q Consensus 51 I~kLpGIG~k~~~kL~ 66 (527)
+.+|||||.|++.++.
T Consensus 14 l~kLPGvG~KsA~R~A 29 (198)
T COG0353 14 LKKLPGVGPKSAQRLA 29 (198)
T ss_pred HhhCCCCChhHHHHHH
Confidence 4679999999999995
No 125
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=25.71 E-value=78 Score=31.32 Aligned_cols=50 Identities=16% Similarity=0.187 Sum_probs=37.3
Q ss_pred CcccCCcHHHHHHHHHhcCCCcHHHHhhc----CHHHHHHHhc--cchHHHHHHHHcCC
Q 009729 52 KKMKQLGGKLGTSLQNELGVTTVGDLLKF----SEDKLQESYG--FNTGTWLWNIARGI 104 (527)
Q Consensus 52 ~kLpGIG~k~~~kL~~~lGI~TigDLa~~----~~~~L~~~FG--~~~G~~L~~~arGi 104 (527)
..+.|||+|++-.+ |+-.++.+|+.+ +...|.+.-| +++++++.-.+++.
T Consensus 77 i~V~GIGpK~Al~i---Ls~~~~~~l~~aI~~~D~~~L~~ipGIGkKtAerIilELkdK 132 (203)
T PRK14602 77 ISISKVGAKTALAI---LSQFRPDDLRRLVAEEDVAALTRVSGIGKKTAQHIFLELKYK 132 (203)
T ss_pred hCCCCcCHHHHHHH---HhhCCHHHHHHHHHhCCHHHHhcCCCcCHHHHHHHHHHHHHh
Confidence 56899999998655 455566666653 6777877765 56899999888875
No 126
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=25.67 E-value=91 Score=33.04 Aligned_cols=55 Identities=15% Similarity=0.286 Sum_probs=32.4
Q ss_pred CCcccCCcHHHHHHHHHhcCCCcHH---HHhhc--C--HHHHHHHhc--cchHHHHHHHHcCCcCc
Q 009729 51 IKKMKQLGGKLGTSLQNELGVTTVG---DLLKF--S--EDKLQESYG--FNTGTWLWNIARGISGE 107 (527)
Q Consensus 51 I~kLpGIG~k~~~kL~~~lGI~Tig---DLa~~--~--~~~L~~~FG--~~~G~~L~~~arGiD~~ 107 (527)
+.+|||||+++++++.+-+-=-++. ++..- + ...|.+++| ++.+..||+ .|+..-
T Consensus 50 l~~lpgIG~~ia~kI~Eil~tG~~~~~~e~l~~~~p~~l~~l~~i~GiGpk~a~~l~~--lGi~tl 113 (334)
T smart00483 50 LKGLPGIGDKIKKKIEEIIETGKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKWYR--KGIRTL 113 (334)
T ss_pred HhcCCCccHHHHHHHHHHHHhCcHHHHHHHhcCcHHHHHHHHHccCCcCHHHHHHHHH--hCCCCH
Confidence 6689999999999996333222333 22221 1 224455554 456677766 788654
No 127
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=25.63 E-value=41 Score=35.71 Aligned_cols=34 Identities=35% Similarity=0.428 Sum_probs=27.7
Q ss_pred CCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCH
Q 009729 49 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSE 82 (527)
Q Consensus 49 LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~ 82 (527)
.|+-++||+|++...+|-+.+||+++.+|+....
T Consensus 93 ~~Ll~v~GlGpkKi~~Ly~elgi~~~e~l~~a~~ 126 (326)
T COG1796 93 EPLLKVPGLGPKKIVSLYKELGIKDLEELQEALE 126 (326)
T ss_pred HHHhhCCCCCcHHHHHHHHHHCcccHHHHHHHHH
Confidence 3566899999977777777999999999997643
No 128
>cd00166 SAM Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
Probab=25.27 E-value=1.1e+02 Score=23.12 Aligned_cols=46 Identities=28% Similarity=0.432 Sum_probs=34.9
Q ss_pred ccCCHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhccch
Q 009729 38 PFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNT 93 (527)
Q Consensus 38 ~~e~v~~fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~FG~~~ 93 (527)
..+++..||..+ |+ ......+. ..|| +..+|..++.+.|. .+|+..
T Consensus 3 ~~~~V~~wL~~~------~~-~~y~~~f~-~~~i-~g~~L~~l~~~dL~-~lgi~~ 48 (63)
T cd00166 3 SPEDVAEWLESL------GL-GQYADNFR-ENGI-DGDLLLLLTEEDLK-ELGITL 48 (63)
T ss_pred CHHHHHHHHHHc------Ch-HHHHHHHH-HcCC-CHHHHhHCCHHHHH-HcCCCC
Confidence 345677777654 33 56777784 8999 99999999999998 889854
No 129
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=25.23 E-value=65 Score=23.21 Aligned_cols=16 Identities=31% Similarity=0.366 Sum_probs=13.2
Q ss_pred CCcccCCcHHHHHHHH
Q 009729 51 IKKMKQLGGKLGTSLQ 66 (527)
Q Consensus 51 I~kLpGIG~k~~~kL~ 66 (527)
|.-+||||.+++.+|.
T Consensus 18 i~Gv~giG~ktA~~ll 33 (36)
T smart00279 18 IPGVKGIGPKTALKLL 33 (36)
T ss_pred CCCCCcccHHHHHHHH
Confidence 4468999999998885
No 130
>COG4380 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.04 E-value=82 Score=30.65 Aligned_cols=31 Identities=23% Similarity=0.498 Sum_probs=27.0
Q ss_pred HHHHHHHhcCCCcHHHHhhcCHHHHHHHhccc
Q 009729 61 LGTSLQNELGVTTVGDLLKFSEDKLQESYGFN 92 (527)
Q Consensus 61 ~~~kL~~~lGI~TigDLa~~~~~~L~~~FG~~ 92 (527)
..+.+ +.-|+++.||+-..++..|+.+||.+
T Consensus 76 veETF-kQNGlT~AgDih~v~paKL~qIfGaD 106 (216)
T COG4380 76 VEETF-KQNGLTNAGDIHAVRPAKLHQIFGAD 106 (216)
T ss_pred hHHHH-HHcCCCcccccccCCHHHHHHHhCcc
Confidence 44566 48899999999999999999999974
No 131
>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=24.35 E-value=64 Score=26.66 Aligned_cols=24 Identities=29% Similarity=0.473 Sum_probs=16.8
Q ss_pred cccCCcHHHHHHHHHhcCCCcHHHHh
Q 009729 53 KMKQLGGKLGTSLQNELGVTTVGDLL 78 (527)
Q Consensus 53 kLpGIG~k~~~kL~~~lGI~TigDLa 78 (527)
-+||||.+++.+|.+.+| ++..+.
T Consensus 26 gv~giG~k~A~~ll~~~~--~~~~~~ 49 (75)
T cd00080 26 GVPGIGPKTALKLLKEYG--SLENLL 49 (75)
T ss_pred CCCcccHHHHHHHHHHhC--CHHHHH
Confidence 589999999999864443 444443
No 132
>PF00730 HhH-GPD: HhH-GPD superfamily base excision DNA repair protein This entry corresponds to Endonuclease III This entry corresponds to Alkylbase DNA glycosidase; InterPro: IPR003265 Endonuclease III (4.2.99.18 from EC) is a DNA repair enzyme which removes a number of damaged pyrimidines from DNA via its glycosylase activity and also cleaves the phosphodiester backbone at apurinic / apyrimidinic sites via a beta-elimination mechanism [, ]. The structurally related DNA glycosylase MutY recognises and excises the mutational intermediate 8-oxoguanine-adenine mispair []. The 3-D structures of Escherichia coli endonuclease III [] and catalytic domain of MutY [] have been determined. The structures contain two all-alpha domains: a sequence-continuous, six-helix domain (residues 22-132) and a Greek-key, four-helix domain formed by one N-terminal and three C-terminal helices (residues 1-21 and 133-211) together with the [Fe4S4] cluster. The cluster is bound entirely within the C-terminal loop by four cysteine residues with a ligation pattern Cys-(Xaa)6-Cys-(Xaa)2-Cys-(Xaa)5-Cys which is distinct from all other known Fe4S4 proteins. This structural motif is referred to as a [Fe4S4] cluster loop (FCL) []. Two DNA-binding motifs have been proposed, one at either end of the interdomain groove: the helix-hairpin-helix (HhH) and FCL motifs (see IPR003651 from INTERPRO). The primary role of the iron-sulphur cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone by forming the loop of the FCL motif [, ]. The HhH-GPD domain gets its name from its hallmark helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This domain is found in a diverse range of structurally related DNA repair proteins that include: endonuclease III, 4.2.99.18 from EC and DNA glycosylase MutY, an A/G-specific adenine glycosylase. Both of these enzymes have a C-terminal iron-sulphur cluster loop (FCL). The methyl-CPG binding protein (MBD4) also contain a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II 3.2.2.21 from EC, 8-oxoguanine DNA glycosylases and other members of the AlkA family.; GO: 0006284 base-excision repair; PDB: 3F0Z_A 3I0X_A 3F10_A 3I0W_A 3S6I_D 3N5N_Y 1PU7_A 1PU8_B 1PU6_B 1NGN_A ....
Probab=23.93 E-value=1.2e+02 Score=26.00 Aligned_cols=47 Identities=26% Similarity=0.354 Sum_probs=35.7
Q ss_pred HHHHHHHHHhcCCCcHHHHhhcCHHHHHHH-----hccchHHHHHHHHcCCc
Q 009729 59 GKLGTSLQNELGVTTVGDLLKFSEDKLQES-----YGFNTGTWLWNIARGIS 105 (527)
Q Consensus 59 ~k~~~kL~~~lGI~TigDLa~~~~~~L~~~-----FG~~~G~~L~~~arGiD 105 (527)
.++..+|.+.+|.-|..+|+.++.+.|... |+...+.+|...++-+-
T Consensus 15 ~~~~~~l~~~~g~pt~~~l~~~~~~el~~~i~~~G~~~~ka~~i~~~a~~~~ 66 (108)
T PF00730_consen 15 RKIYRRLFERYGFPTPEALAEASEEELRELIRPLGFSRRKAKYIIELARAIL 66 (108)
T ss_dssp HHHHHHHHHHHSCSSHHHHHCSHHHHHHHHHTTSTSHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCHHHHHhCCHHHHHHHhhccCCCHHHHHHHHHHHHHhh
Confidence 456667777889999999999999999887 55335777777776443
No 133
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=23.56 E-value=1e+02 Score=30.43 Aligned_cols=51 Identities=16% Similarity=0.079 Sum_probs=38.5
Q ss_pred CcccCCcHHHHHHHHHhcCCCcHHHHhhc----CHHHHHHHhc--cchHHHHHHHHcCCc
Q 009729 52 KKMKQLGGKLGTSLQNELGVTTVGDLLKF----SEDKLQESYG--FNTGTWLWNIARGIS 105 (527)
Q Consensus 52 ~kLpGIG~k~~~kL~~~lGI~TigDLa~~----~~~~L~~~FG--~~~G~~L~~~arGiD 105 (527)
..+.|||+|++-. -|+-.+..+|+.+ +...|.+.-| +++++++.-.++|.-
T Consensus 75 ~~V~GIGpK~AL~---iLs~~~~~~l~~aI~~~D~~~L~kvpGIGkKtAerIilELkdK~ 131 (197)
T PRK14603 75 LGVSGVGPKLALA---LLSALPPALLARALLEGDARLLTSASGVGKKLAERIALELKGKV 131 (197)
T ss_pred hCcCCcCHHHHHH---HHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHHh
Confidence 4689999999854 4566677777764 6777877765 568999998888753
No 134
>PF07647 SAM_2: SAM domain (Sterile alpha motif); InterPro: IPR011510 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents a second domain related to the SAM domain. ; GO: 0005515 protein binding; PDB: 1B0X_A 1X9X_B 1OW5_A 1V38_A 3BS7_A 3BS5_A 3TAD_A 3TAC_B 2K60_A 2DL0_A ....
Probab=23.23 E-value=52 Score=25.69 Aligned_cols=46 Identities=28% Similarity=0.484 Sum_probs=37.4
Q ss_pred ccCCHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhccc
Q 009729 38 PFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN 92 (527)
Q Consensus 38 ~~e~v~~fL~~LPI~kLpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~FG~~ 92 (527)
+++++.+||..+ |+ ......+. ..||..+..|..++.+.|. .+|+.
T Consensus 5 ~~~~v~~WL~~~------gl-~~y~~~f~-~~~i~g~~~L~~l~~~~L~-~lGI~ 50 (66)
T PF07647_consen 5 SPEDVAEWLKSL------GL-EQYADNFR-ENGIDGLEDLLQLTEEDLK-ELGIT 50 (66)
T ss_dssp CHHHHHHHHHHT------TC-GGGHHHHH-HTTCSHHHHHTTSCHHHHH-HTTTT
T ss_pred CHHHHHHHHHHC------Cc-HHHHHHHH-HcCCcHHHHHhhCCHHHHH-HcCCC
Confidence 467788888766 56 46677784 9999999999999999997 88973
No 135
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=23.16 E-value=1.1e+02 Score=30.30 Aligned_cols=50 Identities=10% Similarity=0.116 Sum_probs=38.0
Q ss_pred CcccCCcHHHHHHHHHhcCCCcHHHHhhc----CHHHHHHHhc--cchHHHHHHHHcCC
Q 009729 52 KKMKQLGGKLGTSLQNELGVTTVGDLLKF----SEDKLQESYG--FNTGTWLWNIARGI 104 (527)
Q Consensus 52 ~kLpGIG~k~~~kL~~~lGI~TigDLa~~----~~~~L~~~FG--~~~G~~L~~~arGi 104 (527)
-.+.|||+|++-.+ |.-.++.+|+.+ +...|.+.-| +++++++.-.++|.
T Consensus 75 isVsGIGPK~ALaI---Ls~~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIIlELkdK 130 (196)
T PRK13901 75 IGVDGIGPRAALRV---LSGIKYNEFRDAIDREDIELISKVKGIGNKMAGKIFLKLRGK 130 (196)
T ss_pred hCcCCcCHHHHHHH---HcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHh
Confidence 46899999998544 666777887764 6677877765 56899999888875
No 136
>PF12937 F-box-like: F-box-like; PDB: 1P22_A 2OVP_B 2OVR_B 2OVQ_B 1FS1_A 1FS2_C 1FQV_I 1LDK_E 2AST_B 2ASS_B.
Probab=22.73 E-value=44 Score=24.53 Aligned_cols=18 Identities=50% Similarity=0.746 Sum_probs=13.6
Q ss_pred cccCChHHHHHHHHhhCC
Q 009729 487 IDELPKEIQDEIQAWLRP 504 (527)
Q Consensus 487 ~~el~~ei~~e~~~~~~~ 504 (527)
|..||+||..+|=.+|.|
T Consensus 1 i~~LP~Eil~~If~~L~~ 18 (47)
T PF12937_consen 1 ISSLPDEILLEIFSYLDP 18 (47)
T ss_dssp CCCS-HHHHHHHHTTS-H
T ss_pred ChHhHHHHHHHHHhcCCH
Confidence 568999999999988744
No 137
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=22.67 E-value=1.1e+02 Score=29.83 Aligned_cols=50 Identities=14% Similarity=0.137 Sum_probs=37.9
Q ss_pred CcccCCcHHHHHHHHHhcCCCcHHHHhhc----CHHHHHHHhc--cchHHHHHHHHcCC
Q 009729 52 KKMKQLGGKLGTSLQNELGVTTVGDLLKF----SEDKLQESYG--FNTGTWLWNIARGI 104 (527)
Q Consensus 52 ~kLpGIG~k~~~kL~~~lGI~TigDLa~~----~~~~L~~~FG--~~~G~~L~~~arGi 104 (527)
..+.|||+|++-. -|.-.++.+|+.+ +...|.+.-| +++++++.-.++|.
T Consensus 76 i~VsGIGpK~Al~---ILs~~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIilELkdK 131 (183)
T PRK14601 76 LKVNGIGANTAMA---VCSSLDVNSFYKALSLGDESVLKKVPGIGPKSAKRIIAELSDA 131 (183)
T ss_pred hccCCccHHHHHH---HHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHH
Confidence 4689999999854 4566678887764 6677877655 57899999888875
No 138
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=22.16 E-value=58 Score=26.00 Aligned_cols=29 Identities=14% Similarity=0.228 Sum_probs=19.4
Q ss_pred CcccCCcHHHHHHHHHhc----CCCcHHHHhhc
Q 009729 52 KKMKQLGGKLGTSLQNEL----GVTTVGDLLKF 80 (527)
Q Consensus 52 ~kLpGIG~k~~~kL~~~l----GI~TigDLa~~ 80 (527)
..+||||.++++++.+.- ++.++.||...
T Consensus 17 ~~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL~~v 49 (65)
T PF12836_consen 17 QALPGIGPKQAKAIVEYREKNGPFKSLEDLKEV 49 (65)
T ss_dssp HTSTT--HHHHHHHHHHHHHH-S-SSGGGGGGS
T ss_pred HHcCCCCHHHHHHHHHHHHhCcCCCCHHHHhhC
Confidence 357999999998886332 77888888875
No 139
>PF05643 DUF799: Putative bacterial lipoprotein (DUF799); InterPro: IPR008517 This family consists of several bacterial proteins of unknown function. Some of the family members are described as putative lipoproteins.
Probab=22.15 E-value=1.4e+02 Score=30.10 Aligned_cols=63 Identities=19% Similarity=0.354 Sum_probs=43.5
Q ss_pred cCCCCCCeEEeccCC-------HHhhccc--CCCCc-----ccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhccc
Q 009729 27 GMNKPAQQTTVPFSS-------VKGLLDS--LPIKK-----MKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN 92 (527)
Q Consensus 27 ~~aKPnG~~vl~~e~-------v~~fL~~--LPI~k-----LpGIG~k~~~kL~~~lGI~TigDLa~~~~~~L~~~FG~~ 92 (527)
...||.-+.|+++-+ -..|+.. .|+.. +| ++ .+.+.| +..||...+|+...++..|+++||.+
T Consensus 31 ~~~kPrSILVlPp~N~S~dV~A~~~~ls~~~~PLAe~GYYV~P-v~-~vde~f-kqnGlt~~~~i~~v~~~kL~eiFGAD 107 (215)
T PF05643_consen 31 KESKPRSILVLPPVNESPDVKAAYYVLSTVTYPLAEKGYYVFP-VA-LVDETF-KQNGLTDAEDIHAVPPAKLREIFGAD 107 (215)
T ss_pred hcCCCceEEEeCCCCCCcccchHHHHHHHHHHHHHhCCceecC-HH-HHHHHH-HHcCCCCHHHhccCCHHHHHHHhCCC
Confidence 446888899987521 1223332 24433 22 32 455666 59999999999999999999999975
No 140
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=21.73 E-value=1.2e+02 Score=29.69 Aligned_cols=50 Identities=16% Similarity=0.183 Sum_probs=37.2
Q ss_pred CcccCCcHHHHHHHHHhcCCCcHHHHhhc----CHHHHHHHhc--cchHHHHHHHHcCC
Q 009729 52 KKMKQLGGKLGTSLQNELGVTTVGDLLKF----SEDKLQESYG--FNTGTWLWNIARGI 104 (527)
Q Consensus 52 ~kLpGIG~k~~~kL~~~lGI~TigDLa~~----~~~~L~~~FG--~~~G~~L~~~arGi 104 (527)
-.+.|||+|++-.+ ++-.++.+|+.+ +...|.+.-| +++++++.-.+++.
T Consensus 76 i~V~GIGpK~AL~i---Ls~~~~~el~~aI~~~D~~~L~~vpGIGkKtAerIilELkdK 131 (188)
T PRK14606 76 TKVSRLGPKTALKI---ISNEDAETLVTMIASQDVEGLSKLPGISKKTAERIVMELKDE 131 (188)
T ss_pred hccCCccHHHHHHH---HcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHh
Confidence 47899999998544 555677777663 6777877755 56899998888875
No 141
>PRK08609 hypothetical protein; Provisional
Probab=21.22 E-value=2.1e+02 Score=32.70 Aligned_cols=56 Identities=21% Similarity=0.279 Sum_probs=31.7
Q ss_pred CCCcccCCcHHHHHHHHHhc--C-CCcHHHHhh-cCH--HHHHHHhcc--chHHHHHHHHcCCcC
Q 009729 50 PIKKMKQLGGKLGTSLQNEL--G-VTTVGDLLK-FSE--DKLQESYGF--NTGTWLWNIARGISG 106 (527)
Q Consensus 50 PI~kLpGIG~k~~~kL~~~l--G-I~TigDLa~-~~~--~~L~~~FG~--~~G~~L~~~arGiD~ 106 (527)
.+.+|||||+++++++.+-+ | +....+|.. .+. ..|.+++|. +++.++|. -.|+..
T Consensus 49 ~l~~ipgIG~~ia~kI~Eil~tG~~~~le~l~~~~p~~~~~l~~i~GiGpk~a~~l~~-~lGi~t 112 (570)
T PRK08609 49 DFTKLKGIGKGTAEVIQEYRETGESSVLQELKKEVPEGLLPLLKLPGLGGKKIAKLYK-ELGVVD 112 (570)
T ss_pred hhccCCCcCHHHHHHHHHHHHhCChHHHHHHHhhCcHHHHHHhcCCCCCHHHHHHHHH-HhCCCC
Confidence 47899999999999886333 3 344455553 232 234556664 33444443 236643
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=21.08 E-value=1.6e+02 Score=30.89 Aligned_cols=54 Identities=22% Similarity=0.278 Sum_probs=30.6
Q ss_pred CCcccCCcHHHHHHHHHhcCCCcHHHHhhc---CHH---HHHHHhc--cchHHHHHHHHcCCcC
Q 009729 51 IKKMKQLGGKLGTSLQNELGVTTVGDLLKF---SED---KLQESYG--FNTGTWLWNIARGISG 106 (527)
Q Consensus 51 I~kLpGIG~k~~~kL~~~lGI~TigDLa~~---~~~---~L~~~FG--~~~G~~L~~~arGiD~ 106 (527)
+.+|||||+++++++.+-+---++..|..+ .+. .|.+++| ++.+..+| ..|+..
T Consensus 47 ~~~ipgiG~~ia~kI~E~~~tG~~~~le~l~~~~~~~l~~l~~i~GiGpk~a~~l~--~lGi~s 108 (307)
T cd00141 47 AKKLPGIGKKIAEKIEEILETGKLRKLEELREDVPPGLLLLLRVPGVGPKTARKLY--ELGIRT 108 (307)
T ss_pred hcCCCCccHHHHHHHHHHHHcCCHHHHHHHhccchHHHHHHHcCCCCCHHHHHHHH--HcCCCC
Confidence 478999999999999633222233333322 122 3444544 34566666 567754
No 143
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=20.96 E-value=1.1e+02 Score=30.82 Aligned_cols=50 Identities=22% Similarity=0.172 Sum_probs=31.2
Q ss_pred ccchHHHHHHHHcCCcCccccccCCCccccccccCCCCCCCCCHHHHHHHHHHHH
Q 009729 90 GFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLC 144 (527)
Q Consensus 90 G~~~G~~L~~~arGiD~~~V~~~~~~KSIs~erTF~~~~di~~~eel~~~L~~La 144 (527)
|.++|.-+...+.|+...+|..+..+ ++....+. +-.+.++++.+|..+.
T Consensus 118 GrKTAnvVL~~a~g~p~i~VDTHV~R--vs~R~gl~---~~~~p~~ve~~L~~~i 167 (211)
T COG0177 118 GRKTANVVLSFAFGIPAIAVDTHVHR--VSNRLGLV---PGKTPEEVEEALMKLI 167 (211)
T ss_pred chHHHHHHHHhhcCCCcccccchHHH--HHHHhCCC---CCCCHHHHHHHHHHHC
Confidence 44667777778888886677654322 22222233 3467888888887777
No 144
>KOG3285 consensus Spindle assembly checkpoint protein [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]
Probab=20.69 E-value=46 Score=32.63 Aligned_cols=32 Identities=13% Similarity=0.239 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHHhcCceeeEEEEEEE
Q 009729 133 VASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHAS 170 (527)
Q Consensus 133 ~eel~~~L~~LaeeLa~RLr~dl~~~~~~a~tLtL~iR 170 (527)
.+++...++.+..++.+-|.. ...+.|.+.|.
T Consensus 57 D~elk~f~~~ilsQ~~~WL~~------~kiqklvlvI~ 88 (203)
T KOG3285|consen 57 DEELKTFIRNILSQVHEWLSK------GKIQKLVLVIT 88 (203)
T ss_pred CHHHHHHHHHHHHHHHHHHHh------CCcceEEEEEE
Confidence 345666666666666666642 33455555554
No 145
>PF03538 VRP1: Salmonella virulence plasmid 28.1kDa A protein; InterPro: IPR018003 This entry included insecticidal toxin complex proteins (TcaA, TccA, TcbA, TcdA) from Photorhabdus luminescens subsp. laumondii and Xenorhabdus nematophilus (Achromobacter nematophilus) [], and virulence proteins from Salmonella typhimurium that are encoded on a 90kb plasmid. P. luminescens and X. nematophilus are Gram-negative bacteria that form entomopathogenic symbioses with soil nematodes. The bacteria are found in the gut of entomopathogenic nematodes that invade and kill insects. When the nematode invades an insect host the bacteria are released into the insect haemocoel (the open circulatory system), both the bacteria and the nematode undergo multiple rounds of replication which kills the insect host. Mapping of the insecticidal toxin loci and studies on knockout mutants in P. luminescens showed that deletion of either tca or tcd loci dramatically reduced toxicity, while the double mutant tca/tcd abolished toxicity []. However the biology of toxin action is unclear as is the species range of insects the toxins are active against. S. typhimurium contains a 90kb plasmid that is associated with virulence. This plasmid encodes at least 6 genes needed by the bacterium for invading host macrophages during infection. These include the 70kDa mkaA protein [], a recognised virulence factor, and more recently described, four spv genes under the control of a regulator []. Deletion studies on the virulence plasmid have shown that an open reading frame encoding a 28kDa protein was needed for successful invasion of the host. This protein, designated mkfA [], VRP4 [] or VirA [] by different groups, is utilised by the microbe upon entry into macrophages, although the exact mechanism is unclear.
Probab=20.51 E-value=1.4e+02 Score=31.89 Aligned_cols=46 Identities=26% Similarity=0.327 Sum_probs=34.1
Q ss_pred HHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhccc---hHHHHHHHHcCC
Q 009729 59 GKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN---TGTWLWNIARGI 104 (527)
Q Consensus 59 ~k~~~kL~~~lGI~TigDLa~~~~~~L~~~FG~~---~G~~L~~~arGi 104 (527)
..+...|.+.+|++++-||.+.+....++.++.. .++.+|+.|++.
T Consensus 15 ~~~~~~L~~~~G~~SvfDI~~~S~~~Fi~~~~~~l~~~a~~ly~~A~~~ 63 (325)
T PF03538_consen 15 YRLTDKLQNQLGYHSVFDIARLSRNEFIEKHPEHLSWDAEQLYDRAQQY 63 (325)
T ss_pred HHHHHHHHHhcCCchHHHHHHhCHHHHHHHhhcccchhHHHHHHHHHHH
Confidence 4566778533599999999999998887777632 466677777663
Done!