Query 006108
Match_columns 661
No_of_seqs 283 out of 1886
Neff 6.0
Searched_HMMs 46136
Date Thu Mar 28 18:27:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006108.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006108hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2095 DNA polymerase iota/DN 100.0 4E-57 8.7E-62 499.1 27.0 301 2-302 63-375 (656)
2 PTZ00205 DNA polymerase kappa; 100.0 5.2E-54 1.1E-58 478.0 31.3 293 2-377 180-487 (571)
3 cd01701 PolY_Rev1 DNA polymera 100.0 4.5E-53 9.8E-58 463.4 31.9 296 2-374 98-404 (404)
4 cd01702 PolY_Pol_eta DNA Polym 100.0 3.7E-53 8E-58 457.1 28.2 295 2-373 45-359 (359)
5 cd00424 PolY Y-family of DNA p 100.0 1.3E-52 2.7E-57 450.4 32.2 292 2-372 49-343 (343)
6 cd01703 PolY_Pol_iota DNA Poly 100.0 1.1E-52 2.3E-57 456.2 31.2 304 2-373 45-379 (379)
7 PRK01216 DNA polymerase IV; Va 100.0 3E-52 6.5E-57 448.7 31.4 287 2-377 55-342 (351)
8 PRK03858 DNA polymerase IV; Va 100.0 6E-52 1.3E-56 453.0 32.4 302 2-389 50-353 (396)
9 PRK14133 DNA polymerase IV; Pr 100.0 1.5E-51 3.1E-56 442.9 32.1 294 2-388 53-347 (347)
10 PRK03348 DNA polymerase IV; Pr 100.0 3.9E-51 8.4E-56 453.9 34.9 300 2-391 55-356 (454)
11 PRK02794 DNA polymerase IV; Pr 100.0 1.8E-51 4E-56 452.6 32.0 301 2-390 85-386 (419)
12 PRK03103 DNA polymerase IV; Re 100.0 2.5E-51 5.4E-56 450.1 32.7 302 2-390 55-362 (409)
13 PRK01810 DNA polymerase IV; Va 100.0 3.1E-51 6.7E-56 449.1 32.2 299 2-389 57-358 (407)
14 PRK02406 DNA polymerase IV; Va 100.0 9.3E-51 2E-55 435.8 31.6 287 2-377 45-334 (343)
15 PRK03609 umuC DNA polymerase V 100.0 2.3E-50 5.1E-55 444.3 30.9 303 2-390 49-363 (422)
16 PRK03352 DNA polymerase IV; Va 100.0 2.8E-50 6.2E-55 432.5 30.8 285 2-377 59-345 (346)
17 cd03586 PolY_Pol_IV_kappa DNA 100.0 4.3E-50 9.2E-55 428.0 31.3 286 2-374 48-334 (334)
18 cd01700 PolY_Pol_V_umuC umuC s 100.0 1.4E-49 3.1E-54 426.8 29.2 291 2-373 47-344 (344)
19 KOG2094 Predicted DNA damage i 100.0 2.3E-47 4.9E-52 394.6 21.0 295 2-378 150-447 (490)
20 COG0389 DinP Nucleotidyltransf 100.0 6.5E-46 1.4E-50 400.3 30.4 294 2-377 51-347 (354)
21 KOG2093 Translesion DNA polyme 100.0 4.5E-46 9.8E-51 417.3 20.1 308 2-389 425-747 (1016)
22 cd03468 PolY_like DNA Polymera 100.0 4.1E-42 8.8E-47 366.5 29.3 280 2-372 48-334 (335)
23 PF00817 IMS: impB/mucB/samB f 99.8 6.7E-20 1.5E-24 174.7 11.7 101 2-161 47-149 (149)
24 PF11799 IMS_C: impB/mucB/samB 99.3 3.1E-12 6.7E-17 117.0 8.3 125 240-388 1-127 (127)
25 PF11798 IMS_HHH: IMS family H 98.4 1E-07 2.2E-12 68.1 2.0 32 173-205 1-32 (32)
26 PRK04301 radA DNA repair and r 97.9 1.3E-05 2.8E-10 86.0 4.6 80 179-259 2-88 (317)
27 TIGR02236 recomb_radA DNA repa 97.3 0.00035 7.5E-09 74.6 5.4 74 185-259 1-81 (310)
28 PF14520 HHH_5: Helix-hairpin- 96.9 0.00084 1.8E-08 54.5 3.0 50 186-236 8-59 (60)
29 PF11731 Cdd1: Pathogenicity l 96.1 0.0034 7.3E-08 55.8 2.5 41 184-225 13-53 (93)
30 PRK12766 50S ribosomal protein 94.8 0.044 9.5E-07 56.2 5.4 56 184-240 4-61 (232)
31 PF10391 DNA_pol_lambd_f: Fing 93.7 0.057 1.2E-06 43.0 2.7 27 186-213 5-31 (52)
32 COG3743 Uncharacterized conser 92.3 0.16 3.6E-06 47.7 4.0 37 184-221 68-104 (133)
33 PF04994 TfoX_C: TfoX C-termin 92.2 0.18 3.8E-06 43.8 3.9 32 184-216 4-35 (81)
34 PRK02362 ski2-like helicase; P 92.1 0.13 2.9E-06 61.5 4.2 55 183-238 652-706 (737)
35 PF03118 RNA_pol_A_CTD: Bacter 91.8 0.19 4.1E-06 41.9 3.5 45 178-224 7-51 (66)
36 PF14229 DUF4332: Domain of un 90.8 0.25 5.5E-06 46.0 3.7 54 171-225 41-94 (122)
37 PF12826 HHH_2: Helix-hairpin- 89.7 0.27 5.9E-06 40.6 2.6 47 188-236 8-56 (64)
38 PRK01172 ski2-like helicase; P 87.6 0.68 1.5E-05 54.9 5.1 52 183-235 612-665 (674)
39 COG2251 Predicted nuclease (Re 87.5 0.66 1.4E-05 51.9 4.5 68 172-240 214-283 (474)
40 PRK00254 ski2-like helicase; P 86.9 0.63 1.4E-05 55.7 4.3 53 183-236 645-699 (720)
41 PRK07758 hypothetical protein; 83.9 2 4.3E-05 38.5 4.8 44 188-232 39-84 (95)
42 PF14229 DUF4332: Domain of un 82.0 2.6 5.7E-05 39.3 5.2 43 189-233 1-48 (122)
43 PRK14667 uvrC excinuclease ABC 79.9 2 4.4E-05 50.1 4.5 54 182-237 513-567 (567)
44 smart00483 POLXc DNA polymeras 79.3 1 2.2E-05 49.1 1.8 30 185-215 91-120 (334)
45 PRK00116 ruvA Holliday junctio 78.1 2.2 4.7E-05 42.9 3.6 56 185-240 75-133 (192)
46 TIGR03491 RecB family nuclease 77.2 1.9 4.1E-05 48.9 3.2 61 175-236 199-261 (457)
47 PRK08609 hypothetical protein; 76.5 1.8 3.8E-05 50.6 2.7 29 186-214 91-119 (570)
48 cd00141 NT_POLXc Nucleotidyltr 76.4 1.8 3.9E-05 46.7 2.6 29 185-214 87-115 (307)
49 TIGR00596 rad1 DNA repair prot 76.2 2.7 5.8E-05 51.1 4.2 52 185-238 759-811 (814)
50 smart00611 SEC63 Domain of unk 75.5 6.1 0.00013 42.0 6.3 61 182-243 150-212 (312)
51 PF02889 Sec63: Sec63 Brl doma 75.4 3.9 8.5E-05 43.4 4.8 60 183-243 148-209 (314)
52 PF14377 DUF4414: Domain of un 73.9 1.5 3.2E-05 40.0 1.0 21 616-636 1-21 (108)
53 PRK07956 ligA NAD-dependent DN 73.8 4 8.6E-05 48.6 4.8 52 184-235 446-499 (665)
54 PF02961 BAF: Barrier to autoi 73.5 2.9 6.4E-05 36.9 2.7 34 179-213 15-48 (89)
55 PRK14671 uvrC excinuclease ABC 72.1 5 0.00011 47.4 5.0 51 183-235 569-619 (621)
56 TIGR00575 dnlj DNA ligase, NAD 71.9 4.8 0.0001 47.9 4.8 53 184-236 433-487 (652)
57 PTZ00035 Rad51 protein; Provis 71.7 5.8 0.00012 43.4 5.1 55 183-238 21-79 (337)
58 PRK14670 uvrC excinuclease ABC 71.4 5.3 0.00011 46.8 4.9 54 182-237 513-568 (574)
59 PF14377 DUF4414: Domain of un 71.3 2.5 5.4E-05 38.6 1.8 25 613-637 42-66 (108)
60 PRK14666 uvrC excinuclease ABC 71.0 4.8 0.0001 47.9 4.5 51 183-235 637-689 (694)
61 PRK14672 uvrC excinuclease ABC 71.0 5.6 0.00012 47.2 5.0 62 182-245 607-670 (691)
62 PRK10917 ATP-dependent DNA hel 66.7 4.1 8.9E-05 48.6 2.9 31 183-214 9-39 (681)
63 PF00633 HHH: Helix-hairpin-he 66.6 3.1 6.6E-05 29.4 1.1 16 185-200 13-28 (30)
64 TIGR02239 recomb_RAD51 DNA rep 66.6 7 0.00015 42.3 4.4 36 190-226 8-43 (316)
65 PRK12278 50S ribosomal protein 65.7 6.3 0.00014 40.7 3.6 37 183-220 158-194 (221)
66 PLN03187 meiotic recombination 64.7 6.6 0.00014 43.1 3.8 56 182-238 28-87 (344)
67 PRK14351 ligA NAD-dependent DN 64.1 8.8 0.00019 45.9 4.9 53 184-236 463-517 (689)
68 TIGR02238 recomb_DMC1 meiotic 63.8 13 0.00029 40.2 5.8 51 186-237 2-56 (313)
69 PRK14669 uvrC excinuclease ABC 63.6 9.6 0.00021 45.1 5.0 54 182-237 551-604 (624)
70 PRK14973 DNA topoisomerase I; 63.3 11 0.00025 46.5 5.8 51 185-236 879-931 (936)
71 PLN03186 DNA repair protein RA 62.9 5.7 0.00012 43.5 2.9 44 182-226 25-70 (342)
72 PRK12311 rpsB 30S ribosomal pr 62.1 6.1 0.00013 43.0 2.9 36 184-220 264-299 (326)
73 COG1200 RecG RecG-like helicas 56.6 7.7 0.00017 45.8 2.6 31 183-214 10-40 (677)
74 COG0632 RuvA Holliday junction 56.3 7.6 0.00016 39.5 2.2 43 148-200 80-125 (201)
75 PRK14601 ruvA Holliday junctio 55.3 7.7 0.00017 38.8 2.1 55 134-200 68-125 (183)
76 TIGR02027 rpoA DNA-directed RN 53.2 17 0.00037 39.1 4.4 54 180-235 232-287 (297)
77 PRK12373 NADH dehydrogenase su 52.6 13 0.00029 41.5 3.5 36 184-220 324-359 (400)
78 TIGR01954 nusA_Cterm_rpt trans 52.4 20 0.00043 27.3 3.6 33 192-225 2-34 (50)
79 PRK14606 ruvA Holliday junctio 51.9 9.1 0.0002 38.5 2.0 54 135-200 69-125 (188)
80 TIGR00084 ruvA Holliday juncti 51.9 15 0.00032 37.0 3.4 51 186-239 75-131 (191)
81 PRK00558 uvrC excinuclease ABC 51.3 18 0.00038 42.7 4.5 53 182-236 542-596 (598)
82 PRK05182 DNA-directed RNA poly 50.4 20 0.00043 38.9 4.4 54 180-235 246-301 (310)
83 TIGR00575 dnlj DNA ligase, NAD 49.0 20 0.00044 42.7 4.5 33 188-222 503-535 (652)
84 COG1948 MUS81 ERCC4-type nucle 47.7 22 0.00048 37.5 4.0 49 186-236 185-235 (254)
85 PRK14605 ruvA Holliday junctio 47.0 19 0.00042 36.3 3.5 53 186-238 76-131 (194)
86 smart00278 HhH1 Helix-hairpin- 46.8 13 0.00027 25.1 1.4 16 185-200 3-18 (26)
87 PRK14604 ruvA Holliday junctio 46.1 13 0.00029 37.5 2.1 55 134-200 68-125 (195)
88 PRK13901 ruvA Holliday junctio 45.9 13 0.00027 37.8 1.9 57 132-200 65-124 (196)
89 PRK14603 ruvA Holliday junctio 45.5 14 0.0003 37.5 2.1 54 135-200 68-124 (197)
90 PRK13766 Hef nuclease; Provisi 44.9 24 0.00052 42.6 4.4 50 185-236 717-768 (773)
91 PRK08097 ligB NAD-dependent DN 44.1 28 0.0006 40.8 4.6 49 186-235 428-479 (562)
92 PF08004 DUF1699: Protein of u 43.8 40 0.00087 31.8 4.7 37 5-48 30-66 (131)
93 COG1796 POL4 DNA polymerase IV 43.8 15 0.00033 39.7 2.2 49 183-231 93-144 (326)
94 PRK14602 ruvA Holliday junctio 42.1 17 0.00037 36.9 2.2 56 133-200 68-126 (203)
95 PF07887 Calmodulin_bind: Calm 41.3 34 0.00073 36.9 4.3 50 185-235 164-218 (299)
96 COG5018 KapD Inhibitor of the 40.6 8.1 0.00018 38.3 -0.4 41 610-650 24-64 (210)
97 TIGR00084 ruvA Holliday juncti 40.4 14 0.00031 37.1 1.3 54 135-200 68-124 (191)
98 COG0322 UvrC Nuclease subunit 39.5 31 0.00067 40.6 4.0 50 181-233 528-579 (581)
99 TIGR00426 competence protein C 39.5 28 0.0006 28.7 2.7 30 185-214 18-52 (69)
100 TIGR00615 recR recombination p 39.3 26 0.00057 35.5 3.0 27 185-219 13-39 (195)
101 KOG2534 DNA polymerase IV (fam 39.1 27 0.00058 37.9 3.1 30 186-216 100-129 (353)
102 PRK14351 ligA NAD-dependent DN 38.2 44 0.00094 40.2 5.1 45 188-234 533-579 (689)
103 PF00416 Ribosomal_S13: Riboso 38.1 27 0.00058 31.8 2.6 35 185-219 17-51 (107)
104 COG2199 c-di-GMP synthetase (d 38.1 84 0.0018 30.1 6.3 28 40-67 79-110 (181)
105 TIGR03631 bact_S13 30S ribosom 37.8 30 0.00065 32.0 2.9 38 184-221 16-53 (113)
106 PRK00076 recR recombination pr 37.8 28 0.00062 35.3 3.0 16 185-200 13-28 (196)
107 PRK13844 recombination protein 37.3 29 0.00063 35.3 2.9 28 185-220 17-44 (200)
108 PF07647 SAM_2: SAM domain (St 36.9 56 0.0012 26.3 4.1 47 171-226 4-50 (66)
109 PF07237 DUF1428: Protein of u 36.2 62 0.0013 29.6 4.6 38 19-63 6-43 (103)
110 PTZ00134 40S ribosomal protein 34.4 35 0.00076 33.4 2.9 40 184-223 31-73 (154)
111 PRK14600 ruvA Holliday junctio 34.2 28 0.00061 34.9 2.3 55 133-200 67-124 (186)
112 CHL00013 rpoA RNA polymerase a 33.5 47 0.001 36.3 4.0 55 179-235 259-315 (327)
113 cd00166 SAM Sterile alpha moti 33.2 90 0.002 24.3 4.7 47 171-227 2-48 (63)
114 PRK14668 uvrC excinuclease ABC 31.3 39 0.00084 39.8 3.2 50 181-232 523-574 (577)
115 PRK05179 rpsM 30S ribosomal pr 30.6 48 0.001 31.1 3.0 37 184-220 18-54 (122)
116 CHL00137 rps13 ribosomal prote 30.2 48 0.001 31.1 3.0 38 183-220 17-54 (122)
117 PRK14350 ligA NAD-dependent DN 30.2 62 0.0013 38.8 4.6 51 185-235 438-490 (669)
118 cd00080 HhH2_motif Helix-hairp 29.6 52 0.0011 27.9 2.8 26 185-212 24-49 (75)
119 PRK13482 DNA integrity scannin 27.8 77 0.0017 35.0 4.5 38 185-224 289-326 (352)
120 PRK07956 ligA NAD-dependent DN 27.4 71 0.0015 38.3 4.5 15 185-199 481-495 (665)
121 PRK07945 hypothetical protein; 27.0 1.1E+02 0.0024 33.5 5.5 49 184-237 50-98 (335)
122 TIGR03629 arch_S13P archaeal r 26.5 58 0.0012 31.5 2.9 31 183-213 21-54 (144)
123 COG0353 RecR Recombinational D 26.2 57 0.0012 33.1 2.9 27 185-219 14-40 (198)
124 COG0099 RpsM Ribosomal protein 26.0 79 0.0017 29.7 3.5 39 183-221 17-55 (121)
125 PRK02515 psbU photosystem II c 25.4 55 0.0012 31.1 2.5 53 152-215 40-93 (132)
126 PRK04053 rps13p 30S ribosomal 25.0 66 0.0014 31.3 3.0 41 183-223 25-68 (149)
127 PRK14604 ruvA Holliday junctio 24.2 78 0.0017 32.0 3.5 51 186-239 76-132 (195)
128 TIGR01448 recD_rel helicase, p 23.7 84 0.0018 38.0 4.2 37 175-214 79-115 (720)
129 PRK14603 ruvA Holliday junctio 23.1 82 0.0018 31.9 3.4 50 187-239 76-131 (197)
130 cd07556 Nucleotidyl_cyc_III Cl 23.0 5E+02 0.011 22.5 10.0 30 36-65 29-59 (133)
131 TIGR01259 comE comEA protein. 22.8 74 0.0016 29.5 2.8 29 185-213 70-102 (120)
132 PRK14601 ruvA Holliday junctio 21.4 98 0.0021 31.1 3.5 50 187-239 77-132 (183)
133 PRK13901 ruvA Holliday junctio 21.0 1E+02 0.0022 31.3 3.6 50 187-239 76-131 (196)
134 PF01367 5_3_exonuc: 5'-3' exo 20.9 22 0.00047 32.3 -1.1 33 172-204 2-39 (101)
135 PF14716 HHH_8: Helix-hairpin- 20.9 59 0.0013 26.9 1.5 16 185-200 49-64 (68)
136 COG0272 Lig NAD-dependent DNA 20.8 1.3E+02 0.0027 36.1 4.7 47 187-233 449-497 (667)
137 PRK14602 ruvA Holliday junctio 20.6 87 0.0019 31.8 3.0 51 186-239 77-133 (203)
138 smart00279 HhH2 Helix-hairpin- 20.6 85 0.0018 23.1 2.1 16 185-200 18-33 (36)
No 1
>KOG2095 consensus DNA polymerase iota/DNA damage inducible protein [Replication, recombination and repair]
Probab=100.00 E-value=4e-57 Score=499.07 Aligned_cols=301 Identities=49% Similarity=0.708 Sum_probs=272.9
Q ss_pred CCCCCcHHHHHHhCCCcEEEeccccCCCCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEEcCchhhhhhhCCCCCCc
Q 006108 2 VVSSMRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESL 80 (661)
Q Consensus 2 Vk~GMp~~eAkklCP~L~iV~VP~~~~k~d~~~Yr~~S~~V~~iL~~~-~~VE~~SIDEayLDlT~~~~~~L~~~~~~~l 80 (661)
|+++|+++|||++||+|++||||+.++++|..+||++|.+|+.+|..| +.||++++||+|+|+|..+++++.+...+..
T Consensus 63 V~R~M~v~EAK~kCPqLvlv~v~~~~~ka~~~~YR~as~ev~~~L~~y~~viek~~~dea~ld~tasvder~q~L~s~~~ 142 (656)
T KOG2095|consen 63 VKRLMTVDEAKKKCPQLVLVHVPVAREKADLPKYREASEEVKESLEPYRPVIEKASKDEAFLDLTASVDERLQDLQSDEF 142 (656)
T ss_pred CchhhhHHHHHhhCCceEEeecccccccchhhhhhhhHHHHHHHHhhhHHHHHHHhhhhhhhhHHHHHHHHHHHHhhhhh
Confidence 899999999999999999999999999999999999999999999999 7999999999999999999877654331110
Q ss_pred chhhHHHhhhhhccCc-----------cCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHhhCCceeEEe
Q 006108 81 DEVDEEALKSHILGLE-----------SKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGI 149 (661)
Q Consensus 81 ~~~~~e~~~s~l~g~~-----------~~~g~d~~~~v~~w~~~~~~~~~d~ll~~~~~lA~~IR~~I~~etGlt~SiGI 149 (661)
.-..++-..+|.++.+ .+++...++.+..|++.++.+|+|.+|.+|+.||++||++|+.+|||||||||
T Consensus 143 ~~~~~~~p~~~~~~~~s~~~~~~~~~~~e~~~~~ee~~~~~~~~~d~~~~d~~L~iGa~Iv~EiR~~i~~elg~tCSAGI 222 (656)
T KOG2095|consen 143 NMLLEEPPYGLIYGLPSALPNTREATNSENPLMREEIVSLWIENDDFDWDDVRLLIGAQIVKEIRDAIKLELGYTCSAGI 222 (656)
T ss_pred hhhhhccchhcccCCccccchhhhhhhhccccchhhHhhhhhhccccCchhhhhHHHHHHHHHHHHHHHHHhCceeeccc
Confidence 0001111123344333 25555667788999999999999999999999999999999999999999999
Q ss_pred cCCHHHHHHHhcCCCCCcccccCcccHHHhcccCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCcCcHH
Q 006108 150 AHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGT 229 (661)
Q Consensus 150 A~NKlLAKLAS~~~KP~G~~vl~~~~v~~fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~~~G~ 229 (661)
|+||+||||||++||||.||+|+...+.+||..|||+++|++|+++++.|.+.|||.++|||+++++..|++.||.+.|.
T Consensus 223 a~NKmLAKLvsg~nKPnqQTil~~~~v~~ll~slpi~k~~~lGGk~G~~lie~LGi~~vgdl~~fse~~L~~~fg~~~g~ 302 (656)
T KOG2095|consen 223 AHNKMLAKLVSGRNKPNQQTILPNTYVQDLLDSLPITKIRTLGGKLGEELIEVLGIDSVGDLQQFSETQLQKKFGEKNGT 302 (656)
T ss_pred cccHHHHHHHhccCCCCcceecchHHHHHHHHhCCCceeeeccchHHHHHHHHhCCchHHHHHhcCHHHHHHhhCcchhH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999988999
Q ss_pred HHHHHHhCCCCCcccccCCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEE
Q 006108 230 WLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLH 302 (661)
Q Consensus 230 ~L~~~arGiD~~pV~~~~~~KSIs~e~tF~~~~~i~~~eel~~~L~~L~eeL~~RLr~~~~~~~~~artLtL~ 302 (661)
|||+.|+|+|.++|.++..+|||+++++|++...+.+.+++..||..+++++..||..+...+.+.+.+++++
T Consensus 303 ~l~~la~Gid~s~V~pr~~pkSig~~K~Fpg~~~~~~~~~l~~wl~~la~el~~Rl~~d~~en~r~as~l~~~ 375 (656)
T KOG2095|consen 303 WLRNLARGIDNSPVRPRGLPKSIGSEKNFPGKRSRKSLEELQRWLNQLAEELAERLGKDRNENKRRASTLVVS 375 (656)
T ss_pred HHHHHhcccCCCccccCCCCcchhhhhcCCCccccccHHHHHHHHHHHHHHHHHHHHhhhhhhccccceEEee
Confidence 9999999999999999999999999999998888999999999999999999999999988899999999999
No 2
>PTZ00205 DNA polymerase kappa; Provisional
Probab=100.00 E-value=5.2e-54 Score=477.95 Aligned_cols=293 Identities=22% Similarity=0.266 Sum_probs=255.1
Q ss_pred CCCCCcHHHHHHhCCCcEEEeccccCCCCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEEcCchhhhhhhCCCCCCc
Q 006108 2 VVSSMRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESL 80 (661)
Q Consensus 2 Vk~GMp~~eAkklCP~L~iV~VP~~~~k~d~~~Yr~~S~~V~~iL~~~-~~VE~~SIDEayLDlT~~~~~~L~~~~~~~l 80 (661)
||+|||+++|+++||+|++| | +||+.|+++|++|++||.+| |.+|++||||+|||||++...
T Consensus 180 VrsgMp~~~AkkLCP~Liiv--p-----~d~~~Y~~~S~~I~~il~~ysp~ve~~SIDEafLDlT~~~~~---------- 242 (571)
T PTZ00205 180 IRQGMPGFLALKICPNLLIL--P-----PDFDAYNEESNTVRRIVAEYDPNYISFGLDELTLEVSAYIER---------- 242 (571)
T ss_pred CCcCCcHHHHHHhCCCCcEe--c-----CCHHHHHHHHHHHHHHHHhcCCcEEEeechhceeccCCchhh----------
Confidence 89999999999999999887 5 89999999999999999999 899999999999999997521
Q ss_pred chhhHHHhhhhhccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHhhCCceeEEecCCHHHHHHHh
Q 006108 81 DEVDEEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLAS 160 (661)
Q Consensus 81 ~~~~~e~~~s~l~g~~~~~g~d~~~~v~~w~~~~~~~~~d~ll~~~~~lA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS 160 (661)
++. . ..+..+|++||++|+++||||||||||+||+||||||
T Consensus 243 ------------~~~---~------------------------~~~~~iA~~IR~~I~~~tgLt~SiGIA~NklLAKiAS 283 (571)
T PTZ00205 243 ------------FEG---T------------------------KTAEDVASELRVRVFGETKLTASAGIGPTAALAKIAS 283 (571)
T ss_pred ------------ccC---C------------------------CCHHHHHHHHHHHHHHHHCCcEEEEEcCCHHHHHHhh
Confidence 100 0 0145789999999999999999999999999999999
Q ss_pred cCCCCCccccc---CcccHHHhcccCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHH--------HHHHHhCcCcHH
Q 006108 161 GMNKPAQQTTV---PFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSED--------KLQESYGFNTGT 229 (661)
Q Consensus 161 ~~~KP~G~~vl---~~~~v~~fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~--------~L~~~FG~~~G~ 229 (661)
+++||||++++ +++++.+||++|||++|||||++++.+|. .+||+||+||++.+.. .|+..||...|.
T Consensus 284 d~~KPnG~~vl~l~~~~~v~~fL~~LpV~ki~GIG~~t~~~L~-~~GI~TigDLa~~~~~l~~~f~~k~l~~llG~~~G~ 362 (571)
T PTZ00205 284 NINKPNGQHDLNLHTRGDVMTYVRDLGLRSVPGVGKVTEALLK-GLGITTLSDIYNRRVELCYILHNNLFRFLLGASIGI 362 (571)
T ss_pred hccCCCCCeEEecCCHHHHHHHHhCCCcceeCCcCHHHHHHHH-HcCCCcHHHHhcCCHHHHHHhHHHHHHHHhCchhhH
Confidence 99999999986 67899999999999999999999999997 9999999999998866 477889976799
Q ss_pred HHHHHHhCCCCCcccc---cCCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeec
Q 006108 230 WLWNIARGISGEEVQA---RLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAF 306 (661)
Q Consensus 230 ~L~~~arGiD~~pV~~---~~~~KSIs~e~tF~~~~~i~~~eel~~~L~~L~eeL~~RLr~~~~~~~~~artLtL~lr~~ 306 (661)
++|+.++|+|.+++.. ...+|||++++||. .+.+.+++...|..|+++|+.||+++ ++.+++|+|++|+.
T Consensus 363 ~l~~~a~G~d~~~~v~~~~~~~rKSIg~ErTF~---~~~d~~el~~~L~~L~~~v~~rLrk~----~l~artVtlKlK~~ 435 (571)
T PTZ00205 363 MQWPDAATAANTENCEGATGGQRKAISSERSFT---TPRTKEGLQEMVDTVFNGAYEEMRKS----ELMCRQISLTIRWA 435 (571)
T ss_pred HHHHHhcCCCCCCccCCCCCCCCceeEEeEeCC---CCCCHHHHHHHHHHHHHHHHHHHHhc----CCCccEEEEEEEEC
Confidence 9999999999884332 34689999999997 36799999999999999999999985 99999999999975
Q ss_pred cCCCCCCCCCcCcceeeCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEccCCccc
Q 006108 307 KSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPV 377 (661)
Q Consensus 307 ~~~~~~s~~~~~srs~~L~~~t~~i~~da~~L~~aal~l~~~~~~~~l~~~~~~g~~ir~lgVsls~L~~~ 377 (661)
+ |.+ .+++.+|+.+|+ +...|++++..+|...+ +.+.+||+|||++++|...
T Consensus 436 d---F~~----~trs~tL~~pT~----d~~~I~~aa~~Ll~~~~--------~~~~~vRLlGV~ls~L~~~ 487 (571)
T PTZ00205 436 S---YRY----QQYTKSLIQYSD----DSATLRRAVDGLLLPHA--------AKYSEMCLLGVRFLDLISA 487 (571)
T ss_pred C---CCc----eEEEEECCCCcC----CHHHHHHHHHHHHHhcc--------ccCCCEEEEEEEEcccCcH
Confidence 3 432 477888998986 67788888888876431 2346899999999999875
No 3
>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=4.5e-53 Score=463.37 Aligned_cols=296 Identities=26% Similarity=0.323 Sum_probs=262.4
Q ss_pred CCCCCcHHHHHHhCCCcEEEeccccCCCCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEEcCchhhhhhhCCCCCCc
Q 006108 2 VVSSMRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESL 80 (661)
Q Consensus 2 Vk~GMp~~eAkklCP~L~iV~VP~~~~k~d~~~Yr~~S~~V~~iL~~~-~~VE~~SIDEayLDlT~~~~~~L~~~~~~~l 80 (661)
|++|||+++|+++||+|+++ | +|++.|+++|++|++++.+| |.||++||||+|||+|+....
T Consensus 98 V~~gM~~~~A~~lcP~l~vv--~-----~~~~~Y~~~s~~i~~il~~~s~~ve~~SiDE~~lDvt~~~~~---------- 160 (404)
T cd01701 98 IKNGMWVGQAKKLCPQLVTL--P-----YDFEAYEEVSLTFYEILASYTDNIEAVSCDEALIDITSLLEE---------- 160 (404)
T ss_pred CCCCCcHHHHHHHCCCcEEE--C-----CChHHHHHHHHHHHHHHHHhCCceEEcccceEEEEccccccc----------
Confidence 89999999999999999887 4 89999999999999999998 799999999999999986410
Q ss_pred chhhHHHhhhhhccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHhhCCceeEEecCCHHHHHHHh
Q 006108 81 DEVDEEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLAS 160 (661)
Q Consensus 81 ~~~~~e~~~s~l~g~~~~~g~d~~~~v~~w~~~~~~~~~d~ll~~~~~lA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS 160 (661)
+++ .+..+|++||++|++++|||||||||+||++|||||
T Consensus 161 -----------~~~------------------------------~~~~la~~ir~~I~~~~gl~~siGia~nk~lAKlAs 199 (404)
T cd01701 161 -----------TYE------------------------------LPEELAEAIRNEIRETTGCSASVGIGPNILLARLAT 199 (404)
T ss_pred -----------ccC------------------------------CHHHHHHHHHHHHHHHHCCCEEEEEcCCHHHHHHHh
Confidence 111 135789999999999999999999999999999999
Q ss_pred cCCCCCcccccCcccHHHhcccCCCccccCCchHHHHHHHHhcCCccHHHHhhCC--HHHHHHHhCcCcHHHHHHHHhCC
Q 006108 161 GMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFS--EDKLQESYGFNTGTWLWNIARGI 238 (661)
Q Consensus 161 ~~~KP~G~~vl~~~~v~~fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~--~~~L~~~FG~~~G~~L~~~arGi 238 (661)
+.+||+|++++.++++..||++|||++|||||++++++|. .+||+|++||++++ ...|+++||...|.+||+.++|+
T Consensus 200 ~~aKP~g~~~i~~~~~~~~L~~lPv~~l~GIG~~~~~~L~-~~Gi~t~~dl~~~~~~~~~L~~~fG~~~g~~L~~~a~G~ 278 (404)
T cd01701 200 RKAKPDGQYHLSAEKVEEFLSQLKVGDLPGVGSSLAEKLV-KLFGDTCGGLELRSKTKEKLQKVLGPKTGEKLYDYCRGI 278 (404)
T ss_pred cccCCCcEEEECHHHHHHHhhcCCHhHhCCCCHHHHHHHH-HcCCcchHHHHhCcccHHHHHHHHCHHHHHHHHHHhCCc
Confidence 9999999999999999999999999999999999999997 99999999999999 99999999975799999999999
Q ss_pred CCCcccccCCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccC-CCCCCC---
Q 006108 239 SGEEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKS-SDSDSR--- 314 (661)
Q Consensus 239 D~~pV~~~~~~KSIs~e~tF~~~~~i~~~eel~~~L~~L~eeL~~RLr~~~~~~~~~artLtL~lr~~~~-~~~~s~--- 314 (661)
|+++|.+..++|||+.+++|+ .++.+.+++..+|..|+++|+.||+.+ +..+++|+|++++... .++..+
T Consensus 279 d~~~v~~~~~~ksi~~~~tf~--~~~~~~~~l~~~l~~L~~~l~~rLr~~----~~~~~~l~l~l~~~~~~~~~~~~~y~ 352 (404)
T cd01701 279 DDRPVTGEKERKSVSAEINYG--IRFTNVDDVEQFLQRLSEELSKRLEES----NVTGRQITLKLMKRAPGAPIEPPKYM 352 (404)
T ss_pred CCCCCCCCCCCccccceeeCC--CCCCCHHHHHHHHHHHHHHHHHHHHHc----CCceeeEEEEEEeccccCcccccccc
Confidence 999999888899999999998 689999999999999999999999985 9999999999996321 111111
Q ss_pred ----CCcCcceeeCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEccCC
Q 006108 315 ----KKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKI 374 (661)
Q Consensus 315 ----~~~~srs~~L~~~t~~i~~da~~L~~aal~l~~~~~~~~l~~~~~~g~~ir~lgVsls~L 374 (661)
.+..+++.+|+.+|+ +...|++++..+|.+++ ..+.+||+|||++++|
T Consensus 353 g~~~~~~~~~~~~l~~pT~----d~~~i~~~a~~ll~~~~--------~~~~~vR~lgv~~~~l 404 (404)
T cd01701 353 GHGICDSFSKSSTLGVATD----DSGVIGTEAKKLFRDLS--------IPPEELRGVGIQVTKL 404 (404)
T ss_pred ccCCCcEEeeeeECCCCCC----CHHHHHHHHHHHHHhcc--------CCCCCeeEEEEEEecC
Confidence 124678899999996 67788999998887653 2346899999999876
No 4
>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=3.7e-53 Score=457.10 Aligned_cols=295 Identities=44% Similarity=0.614 Sum_probs=254.5
Q ss_pred CCCCCcHHHHHHhCCCcEEEecc----------------ccCCCCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEEc
Q 006108 2 VVSSMRGDEAKEVCPQIELVQVP----------------VARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDL 64 (661)
Q Consensus 2 Vk~GMp~~eAkklCP~L~iV~VP----------------~~~~k~d~~~Yr~~S~~V~~iL~~~-~~VE~~SIDEayLDl 64 (661)
||+|||+++|+++||++++|+++ ..+++++|+.|+++|++|++++.+| |.||++||||+|||+
T Consensus 45 V~~gm~~~~A~~lcP~l~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Y~~~S~~i~~~l~~~sp~vE~~SiDE~flDv 124 (359)
T cd01702 45 VTRFMTIDEAKKKCPDLILAHVATYKKGEDEADYHENPSPARHKVSLDPYRRASRKILNILKRFGDVVEKASIDEAYLDL 124 (359)
T ss_pred CCCCCcHHHHHHHCCCcEEECCccccccccccccccccccccccccHHHHHHHHHHHHHHHHHcCCceEECcCCeeHHHH
Confidence 89999999999999999998654 3456789999999999999999998 899999999999998
Q ss_pred CchhhhhhhCCCCCCcchhhHHHhhhhhccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHhhCCc
Q 006108 65 TDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFT 144 (661)
Q Consensus 65 T~~~~~~L~~~~~~~l~~~~~e~~~s~l~g~~~~~g~d~~~~v~~w~~~~~~~~~d~ll~~~~~lA~~IR~~I~~etGlt 144 (661)
. ..+|.+||++|++++|||
T Consensus 125 ~-------------------------------------------------------------~~la~~ir~~I~~~~glt 143 (359)
T cd01702 125 G-------------------------------------------------------------SRIVEEIRQQVYDELGYT 143 (359)
T ss_pred H-------------------------------------------------------------HHHHHHHHHHHHHHhCcc
Confidence 2 136889999999999999
Q ss_pred eeEEecCCHHHHHHHhcCCCCCcccccCcccHHHhcccCCCccccCCchHHHHHHHHhcCCccHHHHhhC--CHHHHHHH
Q 006108 145 CSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKF--SEDKLQES 222 (661)
Q Consensus 145 ~SiGIA~NKlLAKLAS~~~KP~G~~vl~~~~v~~fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l--~~~~L~~~ 222 (661)
||||||+||+||||||+++||+|+++++++++.+||++|||++|||||++++.+|.+.+||+|++||+++ +...|.++
T Consensus 144 ~SiGIa~nk~lAKlAs~~~KP~g~~v~~~~~~~~~L~~lpv~~l~GiG~~~~~~ll~~~Gi~ti~dl~~~~~~~~~L~~~ 223 (359)
T cd01702 144 CSAGIAHNKMLAKLASGMNKPNAQTILRNDAVASFLSSLPITSIRGLGGKLGEEIIDLLGLPTEGDVAGFRSSESDLQEH 223 (359)
T ss_pred EEeeecCCHHHHHHHhcccCCCCeEEECHHHHHHHhhcCcHHHhCCcCHHHHHHHHHHcCCcCHHHHHhccCCHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999998775348999999999999 99999999
Q ss_pred hCcCcHHHHHHHHhCCCCCcccccCCCccccccccCCCCCCCCCH-HHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEE
Q 006108 223 YGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTV-ASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTL 301 (661)
Q Consensus 223 FG~~~G~~L~~~arGiD~~pV~~~~~~KSIs~e~tF~~~~~i~~~-eel~~~L~~L~eeL~~RLr~~~~~~~~~artLtL 301 (661)
||.+.|.+||+.++|+|+++|.+..++|||+.+++|. .++.+. +++..+|..|+++|+.||+.++..+++.+++|+|
T Consensus 224 fG~~~g~~l~~~a~G~d~~~v~~~~~~ksi~~~~tf~--~~~~~~~~~l~~~l~~L~~~l~~rL~~~~~~~~~~~~~v~v 301 (359)
T cd01702 224 FGEKLGEWLYNLLRGIDHEPVKPRPLPKSMGSSKNFP--GKTALSTEDVQHWLLVLASELNSRLEDDRYENNRRPKTLVL 301 (359)
T ss_pred HHHHHHHHHHHHhCCCCCCCCCCCCCCceeeeeeecC--CCCCChHHHHHHHHHHHHHHHHHHHHhhhhhcCceeeEEEE
Confidence 9965799999999999999999888899999999998 578887 9999999999999999999866556999999999
Q ss_pred EEeeccCCCCCCCCCcCcceeeCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEccC
Q 006108 302 HASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASK 373 (661)
Q Consensus 302 ~lr~~~~~~~~s~~~~~srs~~L~~~t~~i~~da~~L~~aal~l~~~~~~~~l~~~~~~g~~ir~lgVsls~ 373 (661)
++++.+ | ....+++.+++.++ ...|+++++.+|.+++.-... ..-+.+||++||++++
T Consensus 302 ~lr~~~---~---~~~~sr~~~~~~~~------~~~i~~~~~~l~~~~~~~~~~--~~~~~~~rl~g~~~~~ 359 (359)
T cd01702 302 SLRQRG---D---GVRRSRSCALPRYD------AQKIVKDAFKLIKAINEEGLG--LAWNYPLTLLSLSFTK 359 (359)
T ss_pred EEEECC---C---cEEEEEEecCCCCC------HHHHHHHHHHHHHHhhhhccc--cccCCCeEEEEEEecC
Confidence 999753 2 12357777777665 345666777777655421000 0014799999999875
No 5
>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=1.3e-52 Score=450.41 Aligned_cols=292 Identities=31% Similarity=0.449 Sum_probs=257.3
Q ss_pred CCCCCcHHHHHHhCCCcEEEeccccCCCCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEEcCchhhhhhhCCCCCCc
Q 006108 2 VVSSMRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESL 80 (661)
Q Consensus 2 Vk~GMp~~eAkklCP~L~iV~VP~~~~k~d~~~Yr~~S~~V~~iL~~~-~~VE~~SIDEayLDlT~~~~~~L~~~~~~~l 80 (661)
|++|||+++|+++||+|+++ | +|++.|+++|++|++++.+| |.||++||||+|||+|+...
T Consensus 49 V~~gm~~~~A~~lcP~l~~~--~-----~~~~~y~~~s~~i~~~l~~~sp~ve~~siDE~~ldvt~~~~----------- 110 (343)
T cd00424 49 VKRGMPVREARKMCPNLILV--P-----ARLDLYRRLSERLLSELEEVAPLVEVASIDELFLDLTGSAR----------- 110 (343)
T ss_pred CCCCCcHHHHHHhCCCeEEE--C-----CCcHHHHHHHHHHHHHHHHhCCcEEEccCCEEEEECCCchh-----------
Confidence 89999999999999999887 4 89999999999999999998 89999999999999999752
Q ss_pred chhhHHHhhhhhccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHhhC-CceeEEecCCHHHHHHH
Q 006108 81 DEVDEEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETE-FTCSAGIAHNKMLAKLA 159 (661)
Q Consensus 81 ~~~~~e~~~s~l~g~~~~~g~d~~~~v~~w~~~~~~~~~d~ll~~~~~lA~~IR~~I~~etG-lt~SiGIA~NKlLAKLA 159 (661)
+|| .+..+|+.||++|++++| ||||||||+||++||||
T Consensus 111 -----------~~~------------------------------~~~~la~~i~~~i~~~~ggl~~siGia~n~~lAKlA 149 (343)
T cd00424 111 -----------LLG------------------------------LGSEVALRIKRHIAEQLGGITASIGIASNKLLAKLA 149 (343)
T ss_pred -----------ccC------------------------------CHHHHHHHHHHHHHHHhCCceEEEeecccHHHHHHH
Confidence 222 135789999999999998 99999999999999999
Q ss_pred hcCCCCCcccccCcccHHHhcccCCCccccCCchHHHHHHHHhcCCccHHHHhhCC-HHHHHHHhCcCcHHHHHHHHhCC
Q 006108 160 SGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFS-EDKLQESYGFNTGTWLWNIARGI 238 (661)
Q Consensus 160 S~~~KP~G~~vl~~~~v~~fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~-~~~L~~~FG~~~G~~L~~~arGi 238 (661)
++++||+|+++++++++.+||+++||++|||||+++.++|. .+||+|++||++++ ...|+++||. .|.++|+.++|+
T Consensus 150 s~~~KP~g~~v~~~~~~~~~L~~lpi~~l~giG~~~~~~L~-~~Gi~ti~dl~~~~~~~~l~~~fg~-~~~~l~~~a~G~ 227 (343)
T cd00424 150 AKYAKPDGLTILDPEDLPGFLSKLPLTDLPGIGAVTAKRLE-AVGINPIGDLLAASPDALLALWGGV-SGERLWYALRGI 227 (343)
T ss_pred hccCCCCCEEEEcHHHHHHHHhcCChhhcCCCCHHHHHHHH-HcCCCcHHHHhcCCHHHHHHHHhhH-HHHHHHHHhCCc
Confidence 99999999999999999999999999999999999999997 99999999999999 8889999997 699999999999
Q ss_pred CCCcccccCCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCCCCCCCcC
Q 006108 239 SGEEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFP 318 (661)
Q Consensus 239 D~~pV~~~~~~KSIs~e~tF~~~~~i~~~eel~~~L~~L~eeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~~~~ 318 (661)
|+++|.+..++|||+.+++|. .++.+.+++..+|..|+++|+.||+.+ ++.+++|+|++++.+.. ...+....
T Consensus 228 d~~~v~~~~~~ksi~~~~tf~--~~~~~~~~l~~~l~~l~~~l~~rL~~~----~~~~~~l~l~lr~~~~~-~~~~~~~~ 300 (343)
T cd00424 228 DDEPLSPPRPRKSFSHERVLP--RDSRNAEDARPLLRLLLEKLARRLRRD----GRGATRLRLWLRTVDGR-WSGHADIP 300 (343)
T ss_pred CCCCCCCCCCCCceeeeEECC--CCCCCHHHHHHHHHHHHHHHHHHHHHc----CCceeEEEEEEEeCCCc-ccccceee
Confidence 999998888899999999998 689999999999999999999999985 99999999999975421 00111246
Q ss_pred cceeeCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEcc
Q 006108 319 SKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSAS 372 (661)
Q Consensus 319 srs~~L~~~t~~i~~da~~L~~aal~l~~~~~~~~l~~~~~~g~~ir~lgVsls 372 (661)
+++++++.+| +...|+++++.+|.+++. ...+.+||++||+++
T Consensus 301 ~~~~~l~~~t-----~~~~l~~~~~~l~~~~~~------~~~~~~ir~~gv~~~ 343 (343)
T cd00424 301 SRSAPRPIST-----EDGELLHALDKLWRALLD------DKGPRRLRRLGVRLS 343 (343)
T ss_pred eeeeeCCCCC-----CHHHHHHHHHHHHHhhhh------ccCCCCeeEEEEEeC
Confidence 7888998887 345678888888876541 113568999999874
No 6
>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=1.1e-52 Score=456.18 Aligned_cols=304 Identities=28% Similarity=0.425 Sum_probs=258.9
Q ss_pred CCCCCcHHHHHHhCCCcEEEeccccCCCCChHHHHHHHHHHHHHHhhc-C--CeEEeccceEEEEcCchhhhhhhCCCCC
Q 006108 2 VVSSMRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-G--RCERASIDEVYLDLTDAAEAMLAETPPE 78 (661)
Q Consensus 2 Vk~GMp~~eAkklCP~L~iV~VP~~~~k~d~~~Yr~~S~~V~~iL~~~-~--~VE~~SIDEayLDlT~~~~~~L~~~~~~ 78 (661)
|++|||+++|+++||+|+++ | .+|++.|+++|++|++++.+| | .||++||||+|||+|+...
T Consensus 45 V~~gm~~~~A~~lcP~li~v--~----~~~~~~Y~~~S~~i~~~l~~~sp~~~ve~~SiDE~~lDvt~~~~--------- 109 (379)
T cd01703 45 VKKLMSIKDAKEICPDLVLV--N----GEDLTPFRDMSKKVYRLLRSYSWNDRVERLGFDENFMDVTEMRL--------- 109 (379)
T ss_pred CCCCCcHHHHHHhCCCeEEE--c----CCChHHHHHHHHHHHHHHHHcCCHhhEEecCCCcEEEEccCccc---------
Confidence 89999999999999999887 4 258999999999999999998 8 8999999999999998631
Q ss_pred CcchhhHHHhhhhhccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHhhCCceeEEecCCHHHHHH
Q 006108 79 SLDEVDEEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKL 158 (661)
Q Consensus 79 ~l~~~~~e~~~s~l~g~~~~~g~d~~~~v~~w~~~~~~~~~d~ll~~~~~lA~~IR~~I~~etGlt~SiGIA~NKlLAKL 158 (661)
+ .+..+|++||++|+++||||||||||+||+||||
T Consensus 110 -------------~--------------------------------~g~~la~~ir~~I~~~~Glt~siGIa~nk~lAKl 144 (379)
T cd01703 110 -------------L--------------------------------VASHIAYEMRERIENELGLTCCAGIASNKLLAKL 144 (379)
T ss_pred -------------h--------------------------------hHHHHHHHHHHHHHHHhCCeEEEEEcCCHHHHHH
Confidence 1 1357899999999999999999999999999999
Q ss_pred HhcCCCCCcccccCc---ccHHHhcccCCCccccCCchHHHHHHHHhcCCccHHHHhhCC---------------HHHHH
Q 006108 159 ASGMNKPAQQTTVPF---SSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFS---------------EDKLQ 220 (661)
Q Consensus 159 AS~~~KP~G~~vl~~---~~v~~fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~---------------~~~L~ 220 (661)
|++++||+|++++.+ +++.+||+++||++|||||++++++|. .+||.|++||++++ ...|+
T Consensus 145 as~~~KP~g~~~i~~~~~~~~~~fl~~lpv~~l~GiG~~~~~kL~-~~GI~tigdl~~~~~~~~~~~~~~~~~~s~~~L~ 223 (379)
T cd01703 145 VGSVNKPNQQTTLLPPSCADLMDFMDLHDLRKIPGIGYKTAAKLE-AHGISSVRDLQEFSNRNRQTVGAAPSLLELLLMV 223 (379)
T ss_pred HhhhcCCCCeEEEcCCchHHHHHHhccCCccccCCcCHHHHHHHH-HcCCCcHHHHHhCCcccccccccccccccHHHHH
Confidence 999999999998876 467789999999999999999999997 99999999999999 99999
Q ss_pred HHhCcCcHHHHHHHHhCCCCCcc-cccCCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhh----cCce
Q 006108 221 ESYGFNTGTWLWNIARGISGEEV-QARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQ----NKRI 295 (661)
Q Consensus 221 ~~FG~~~G~~L~~~arGiD~~pV-~~~~~~KSIs~e~tF~~~~~i~~~eel~~~L~~L~eeL~~RLr~~~~~----~~~~ 295 (661)
++||...|.+||+.|+|+|+++| .+...+|||+.++||.. .++.+.+++..+|..|+++|+.||++++.+ .+..
T Consensus 224 ~~fG~~~g~~l~~~a~G~d~~~V~~~~~~~ksis~e~tf~~-~~~~~~~~~~~~l~~l~~~l~~rl~~~l~~~~~~~~~~ 302 (379)
T cd01703 224 KEFGEGIGQRIWKLLFGRDTSPVKPASDFPQQISIEDSYKK-CSLEEIREARNKIEELLASLLERMKQDLQEVKAGDGRR 302 (379)
T ss_pred HHHCHHHHHHHHHHHCCCCCCccCCCCCCCceeEEeeccCC-CCCCCHHHHHHHHHHHHHHHHHHHHhhhhccchhcCee
Confidence 99997569999999999999999 55567899999999984 388999999999999999999999985422 5889
Q ss_pred eeEEEEEEeeccCCCCCCCCCcCcceeeCCCcchh-h---H-HhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEE
Q 006108 296 AHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAK-I---Q-EDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVS 370 (661)
Q Consensus 296 artLtL~lr~~~~~~~~s~~~~~srs~~L~~~t~~-i---~-~da~~L~~aal~l~~~~~~~~l~~~~~~g~~ir~lgVs 370 (661)
++||+|++|+.+. ...+.++.+++++++.+|++ + . .+...|++.++.+|.+.++. ....+.+||++||+
T Consensus 303 ~~tv~l~vr~~~~--~~~~~~~~sr~~~l~~~~~~~~~~~~~~~~~~i~~~~~~L~~~~~~~----~~~~~~~irl~gv~ 376 (379)
T cd01703 303 PHTLRLTLRRYTS--TKKHYNRESKQAPIPSHVFQKLTGGNEIAARPIEKILMRLFRELVPP----KNVKGFNLTLLNVC 376 (379)
T ss_pred eeEEEEEEEECCC--CCCccceeeeccccCchhhccccccchhhHHHHHHHHHHHHHHhccc----ccCCCCceEEEEEE
Confidence 9999999998642 11122346899999988851 1 1 13467888888888765421 01125589999999
Q ss_pred ccC
Q 006108 371 ASK 373 (661)
Q Consensus 371 ls~ 373 (661)
+++
T Consensus 377 ~~~ 379 (379)
T cd01703 377 FTN 379 (379)
T ss_pred eeC
Confidence 874
No 7
>PRK01216 DNA polymerase IV; Validated
Probab=100.00 E-value=3e-52 Score=448.67 Aligned_cols=287 Identities=25% Similarity=0.375 Sum_probs=254.8
Q ss_pred CCCCCcHHHHHHhCCCcEEEeccccCCCCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEEcCchhhhhhhCCCCCCc
Q 006108 2 VVSSMRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESL 80 (661)
Q Consensus 2 Vk~GMp~~eAkklCP~L~iV~VP~~~~k~d~~~Yr~~S~~V~~iL~~~-~~VE~~SIDEayLDlT~~~~~~L~~~~~~~l 80 (661)
||+|||+++|+++||+++++ | +|++.|+++|++|++++.+| |.||++||||+|||+|++.
T Consensus 55 V~sgM~~~~A~~lcP~li~v--~-----~d~~~y~~~s~~i~~~l~~~tp~ve~~siDE~~LDvt~~~------------ 115 (351)
T PRK01216 55 IKAGMPIVEAKKILPNAVYL--P-----MRKEVYQQVSNRIMKLLREYSEKIEIASIDEAYLDISDKV------------ 115 (351)
T ss_pred CCCCCcHHHHHHHCCCeEEE--C-----CCHHHHHHHHHHHHHHHHHhCCceEEccCCeEEEEcccch------------
Confidence 89999999999999999887 5 89999999999999999998 8999999999999999975
Q ss_pred chhhHHHhhhhhccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHhhCCceeEEecCCHHHHHHHh
Q 006108 81 DEVDEEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLAS 160 (661)
Q Consensus 81 ~~~~~e~~~s~l~g~~~~~g~d~~~~v~~w~~~~~~~~~d~ll~~~~~lA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS 160 (661)
++|| .+..+|++||++|++++|||||||||+||++|||||
T Consensus 116 ----------~l~g------------------------------~~~~la~~ir~~I~~~~glt~siGia~nk~lAKlas 155 (351)
T PRK01216 116 ----------KNYQ------------------------------DAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAA 155 (351)
T ss_pred ----------hccC------------------------------CHHHHHHHHHHHHHHHHCCcEEEEecCCHHHHHHHH
Confidence 2333 135789999999999999999999999999999999
Q ss_pred cCCCCCcccccCcccHHHhcccCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCcCcHHHHHHHHhCCCC
Q 006108 161 GMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISG 240 (661)
Q Consensus 161 ~~~KP~G~~vl~~~~v~~fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~~~G~~L~~~arGiD~ 240 (661)
+++||+|+++++++++.+||++|||+++||||++++++|. ++||+|+|||+++|...|.++||...|.+||+.++|+|.
T Consensus 156 ~~~KP~g~~vi~~~~~~~~L~~LPi~~l~giG~~~~~~L~-~~Gi~TigdL~~~~~~~L~~rfG~~~~~~L~~~a~G~d~ 234 (351)
T PRK01216 156 DMAKPNGIKVIDDEEVKRFINELDIADIPGIGDITAEKLK-KLGVNKLVDTLRIEFDELKGIIGEAKAKYLFSLARNEYN 234 (351)
T ss_pred hccCCCCEEEeCHHHHHHHHhcCCcccccCCCHHHHHHHH-HcCCCcHHHHhcCCHHHHHHHHCHHHHHHHHHHhCCCCC
Confidence 9999999999999999999999999999999999999997 999999999999999999999997669999999999999
Q ss_pred CcccccCCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCCCCCCCcCcc
Q 006108 241 EEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSK 320 (661)
Q Consensus 241 ~pV~~~~~~KSIs~e~tF~~~~~i~~~eel~~~L~~L~eeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~~~~sr 320 (661)
+||.+ ..+|||+.+++|. .++.+.+++...|.+|+++++.||+. .++++++++++. +|. +.++
T Consensus 235 ~pv~~-~~~ksi~~~~tl~--~di~~~~~l~~~l~~L~~~~~~rl~~-------~~~~~~~~~~~~---df~----~~t~ 297 (351)
T PRK01216 235 EPVRA-RVRKSIGRYVTLP--RNTRDLEEIKPYLKRAIEEAYYKLDG-------IPKAIHVVAIME---DLD----IVSR 297 (351)
T ss_pred CCCCC-CCCCCCcCeEECC--CccCCHHHHHHHHHHHHHHHHHHHHh-------CCCEEEEEEEcC---CCC----EEEE
Confidence 99987 4569999999998 68999999999999999999999984 467888888853 443 3588
Q ss_pred eeeCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEccCCccc
Q 006108 321 SCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPV 377 (661)
Q Consensus 321 s~~L~~~t~~i~~da~~L~~aal~l~~~~~~~~l~~~~~~g~~ir~lgVsls~L~~~ 377 (661)
+.+++.+|+ ...+++.+.++|.+.+ .+.+.+||+|||++++|.+.
T Consensus 298 ~~tl~~~~~-----~~~~~~~a~~Ll~~~~-------~~~~~~vRllGv~~~~l~~~ 342 (351)
T PRK01216 298 GRTFTHGIS-----KETAYREAVRLLQKIL-------EEDERKIRRIGVRFSKIIEA 342 (351)
T ss_pred EEECCCCCC-----HHHHHHHHHHHHHhhh-------hcCCCCeeEEEEEEeccccc
Confidence 899988874 2457888888876532 11235899999999999864
No 8
>PRK03858 DNA polymerase IV; Validated
Probab=100.00 E-value=6e-52 Score=452.95 Aligned_cols=302 Identities=26% Similarity=0.359 Sum_probs=268.3
Q ss_pred CCCCCcHHHHHHhCCCcEEEeccccCCCCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEEcCchhhhhhhCCCCCCc
Q 006108 2 VVSSMRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESL 80 (661)
Q Consensus 2 Vk~GMp~~eAkklCP~L~iV~VP~~~~k~d~~~Yr~~S~~V~~iL~~~-~~VE~~SIDEayLDlT~~~~~~L~~~~~~~l 80 (661)
|++|||+++|+++||+|+++ | +|++.|+++|++|++++.+| |.||++||||+|||+|+..
T Consensus 50 V~~gm~~~~A~~lcP~l~~~--~-----~d~~~y~~~s~~i~~~l~~~s~~ve~~siDe~~ldvt~~~------------ 110 (396)
T PRK03858 50 VRTAMGGRQARRLCPQAVVV--P-----PRMSAYSRASKAVFEVFRDTTPLVEGLSIDEAFLDVGGLR------------ 110 (396)
T ss_pred CCCCChHHHHHHHCCCeEEE--C-----CCHHHHHHHHHHHHHHHHHhCCceEEecCCeEEEEccccc------------
Confidence 89999999999999999887 5 89999999999999999998 8999999999999999964
Q ss_pred chhhHHHhhhhhccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHhhCCceeEEecCCHHHHHHHh
Q 006108 81 DEVDEEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLAS 160 (661)
Q Consensus 81 ~~~~~e~~~s~l~g~~~~~g~d~~~~v~~w~~~~~~~~~d~ll~~~~~lA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS 160 (661)
++|| .+..+|++||++|++++|||||||||+||++||||+
T Consensus 111 ----------~~~~------------------------------~~~~la~~ir~~i~~~~gl~~svGia~n~~lAklas 150 (396)
T PRK03858 111 ----------RISG------------------------------TPVQIAARLRRRVREEVGLPITVGVARTKFLAKVAS 150 (396)
T ss_pred ----------cccC------------------------------CHHHHHHHHHHHHHHHHCCCeEEEEcCChHHHHHhh
Confidence 2333 135789999999999999999999999999999999
Q ss_pred cCCCCCcccccCcccHHHhcccCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCcCcHHHHHHHHhCCCC
Q 006108 161 GMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISG 240 (661)
Q Consensus 161 ~~~KP~G~~vl~~~~v~~fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~~~G~~L~~~arGiD~ 240 (661)
+.+||+|+++++++++..||+++||++|||||+++.++|. ++||+|++||++++...|.++||...|.+||+.++|+|+
T Consensus 151 ~~~Kp~g~~~i~~~~~~~~L~~lpl~~l~Gig~~~~~~L~-~~Gi~t~~dl~~l~~~~L~~~fG~~~~~~l~~~a~G~d~ 229 (396)
T PRK03858 151 QVAKPDGLLVVPPDRELAFLHPLPVRRLWGVGPVTAAKLR-AHGITTVGDVAELPESALVSLLGPAAGRHLHALAHNRDP 229 (396)
T ss_pred cccCCCceEEECcHHHHHHHhcCChhhcCCCCHHHHHHHH-HhCCCcHHHHhcCCHHHHHHHhCcHHHHHHHHHhCCCCC
Confidence 9999999999999999999999999999999999999997 999999999999999999999998679999999999999
Q ss_pred CcccccCCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCCCCCCCcCcc
Q 006108 241 EEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSK 320 (661)
Q Consensus 241 ~pV~~~~~~KSIs~e~tF~~~~~i~~~eel~~~L~~L~eeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~~~~sr 320 (661)
.+|.+..++|||+.+++|. .++.+.++++.+|..|+++|+.||+++ ++.+++|+|++++.+ |. ..++
T Consensus 230 ~~v~~~~~~ksi~~~~t~~--~~~~~~~~l~~~l~~L~~~l~~rLr~~----~~~~~~l~l~l~~~~---~~----~~~~ 296 (396)
T PRK03858 230 RRVETGRRRRSVGAQRALG--RGPNSPAEVDAVVVALVDRVARRMRAA----GRTGRTVVLRLRFDD---FT----RATR 296 (396)
T ss_pred CCCCCCCCCccccceeEcC--CCCCCHHHHHHHHHHHHHHHHHHHHhc----CCCcceEEEEEEeCC---CC----EEEE
Confidence 9998877889999999998 689999999999999999999999985 999999999999743 22 2467
Q ss_pred eeeCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEccCCccccccccccccc-cc
Q 006108 321 SCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPVLSGTCSIMKY-FN 389 (661)
Q Consensus 321 s~~L~~~t~~i~~da~~L~~aal~l~~~~~~~~l~~~~~~g~~ir~lgVsls~L~~~~~~~~sq~~l-F~ 389 (661)
+.+++.+|+ +...|++.+..+|...+. ...+.+|+++||.+++|.+. +..|.+| |+
T Consensus 297 ~~~l~~~t~----~~~~l~~l~~~ll~~~~~------~~~~~~irligv~~~~l~~~---~~~q~~L~f~ 353 (396)
T PRK03858 297 SHTLPRPTA----STATLLAAARDLVAAAAP------LIAERGLTLVGFAVSNLDDD---GAQQLELPFG 353 (396)
T ss_pred EEECCCCcC----CHHHHHHHHHHHHHhhhh------ccCCCCeEEEEEEeecCCcc---cccccCCCcc
Confidence 888888886 566788877777765431 11246899999999999875 3457788 75
No 9
>PRK14133 DNA polymerase IV; Provisional
Probab=100.00 E-value=1.5e-51 Score=442.85 Aligned_cols=294 Identities=28% Similarity=0.359 Sum_probs=265.9
Q ss_pred CCCCCcHHHHHHhCCCcEEEeccccCCCCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEEcCchhhhhhhCCCCCCc
Q 006108 2 VVSSMRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESL 80 (661)
Q Consensus 2 Vk~GMp~~eAkklCP~L~iV~VP~~~~k~d~~~Yr~~S~~V~~iL~~~-~~VE~~SIDEayLDlT~~~~~~L~~~~~~~l 80 (661)
||+|||+++|+++||+++++ | +|++.|+++|++|++++.+| |.||++||||+|||+|+...
T Consensus 53 V~~Gm~~~~A~~lcP~l~~~--~-----~d~~~y~~~s~~i~~~l~~~s~~ve~~siDe~~ldv~~~~~----------- 114 (347)
T PRK14133 53 VHSAMPVFMAKKRCPHGIFL--P-----VRHERYKEVSKNIFKILYEVTPIVEPVSIDEAYLDITNIKE----------- 114 (347)
T ss_pred CCCCChHHHHHHHCCCcEEE--C-----CCHHHHHHHHHHHHHHHHHhCCceEEccCCeEEEEccCCCC-----------
Confidence 89999999999999999887 5 89999999999999999998 89999999999999998531
Q ss_pred chhhHHHhhhhhccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHhhCCceeEEecCCHHHHHHHh
Q 006108 81 DEVDEEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLAS 160 (661)
Q Consensus 81 ~~~~~e~~~s~l~g~~~~~g~d~~~~v~~w~~~~~~~~~d~ll~~~~~lA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS 160 (661)
.+..+|++||++|++++|||||||||+||++||||+
T Consensus 115 --------------------------------------------~~~~la~~i~~~i~~~~gl~~siGia~n~~~Aklas 150 (347)
T PRK14133 115 --------------------------------------------EPIKIAKYIKKKVKKETGLTLSVGISYNKFLAKLAS 150 (347)
T ss_pred --------------------------------------------CHHHHHHHHHHHHHHHHCCcEEEEEcCcHHHHHHHh
Confidence 024689999999999999999999999999999999
Q ss_pred cCCCCCcccccCcccHHHhcccCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCcCcHHHHHHHHhCCCC
Q 006108 161 GMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISG 240 (661)
Q Consensus 161 ~~~KP~G~~vl~~~~v~~fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~~~G~~L~~~arGiD~ 240 (661)
+++||+|+++++++++..||++|||++|||||+++.++|. .+||+|++||++++...|+++||. .|.++|+.++|+|.
T Consensus 151 ~~~kp~g~~~~~~~~~~~~L~~lpv~~l~gig~~~~~~L~-~~Gi~ti~dl~~l~~~~L~~rfG~-~g~~l~~~a~G~d~ 228 (347)
T PRK14133 151 DWNKPDGIKIITEDMIPDILKPLPISKVHGIGKKSVEKLN-NIGIYTIEDLLKLSREFLIEYFGK-FGVEIYERIRGIDY 228 (347)
T ss_pred ccCCCCceEEECHHHHHHHHHhCCccccCCCCHHHHHHHH-HcCCccHHHHhhCCHHHHHHHHhH-HHHHHHHHhCCCCC
Confidence 9999999999999999999999999999999999999997 999999999999999999999997 69999999999999
Q ss_pred CcccccCCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCCCCCCCcCcc
Q 006108 241 EEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSK 320 (661)
Q Consensus 241 ~pV~~~~~~KSIs~e~tF~~~~~i~~~eel~~~L~~L~eeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~~~~sr 320 (661)
.++.+..++|||+.+++|. .++.+.+++..+|..|+++|+.||+++ ++.+++|+|++++.+ +.. .++
T Consensus 229 ~~v~~~~~~ksi~~~~~~~--~~~~~~~~l~~~l~~L~~~l~~rL~~~----~~~~~~l~l~l~~~~---~~~----~~~ 295 (347)
T PRK14133 229 REVEVSRERKSIGKETTLK--KDTKDKEELKKYLKDFSNIISEELKKR----NLYGKTVTVKIKTSD---FQT----HTK 295 (347)
T ss_pred CCCCCCCCCcceEeeEEcC--CCCCCHHHHHHHHHHHHHHHHHHHHhc----CCCcceEEEEEEECC---CCe----eEE
Confidence 9999888899999999998 689999999999999999999999985 999999999999643 222 367
Q ss_pred eeeCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEccCCcccccccccccccc
Q 006108 321 SCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPVLSGTCSIMKYF 388 (661)
Q Consensus 321 s~~L~~~t~~i~~da~~L~~aal~l~~~~~~~~l~~~~~~g~~ir~lgVsls~L~~~~~~~~sq~~lF 388 (661)
+.+++.+|+ +...|++.+..+|.++ +.+.+|+.|||.+++|.+. ...|.+||
T Consensus 296 ~~~l~~~t~----~~~~l~~l~~~lle~~---------~~~~~vr~lgl~~~~l~~~---~~~q~~l~ 347 (347)
T PRK14133 296 SKTLNDYIR----DKEEIYNVACEILEHI---------NIKEPIRLIGLSVSNLSEN---KIEQLSFL 347 (347)
T ss_pred EEECCCCcC----CHHHHHHHHHHHHHhc---------cCCCCEEEEEEEEecCCCC---cccccCCC
Confidence 888988886 6677888888877654 2357999999999999965 34567776
No 10
>PRK03348 DNA polymerase IV; Provisional
Probab=100.00 E-value=3.9e-51 Score=453.87 Aligned_cols=300 Identities=26% Similarity=0.338 Sum_probs=267.4
Q ss_pred CCCCCcHHHHHHhCCC-cEEEeccccCCCCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEEcCchhhhhhhCCCCCC
Q 006108 2 VVSSMRGDEAKEVCPQ-IELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPES 79 (661)
Q Consensus 2 Vk~GMp~~eAkklCP~-L~iV~VP~~~~k~d~~~Yr~~S~~V~~iL~~~-~~VE~~SIDEayLDlT~~~~~~L~~~~~~~ 79 (661)
||+|||+++|+++||+ ++++ | +|++.|+++|++||+++.+| |.||++||||+|||+++...
T Consensus 55 VrsgMp~~~A~~lcP~~lv~v--~-----~d~~~Y~~~s~~i~~~l~~~sp~VE~~SiDE~flD~~~l~~---------- 117 (454)
T PRK03348 55 ARSAMPMHQARRLVGNGAVVL--P-----PRFVVYRAASRRVFDTLRELSPVVEQLSFDEAFVEPAELAG---------- 117 (454)
T ss_pred CCCCCcHHHHHHhCCCCEEEE--C-----CChHHHHHHHHHHHHHHHHhCCceEEecCCeEEEEcccccc----------
Confidence 8999999999999999 8877 4 89999999999999999998 89999999999999776431
Q ss_pred cchhhHHHhhhhhccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHhhCCceeEEecCCHHHHHHH
Q 006108 80 LDEVDEEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLA 159 (661)
Q Consensus 80 l~~~~~e~~~s~l~g~~~~~g~d~~~~v~~w~~~~~~~~~d~ll~~~~~lA~~IR~~I~~etGlt~SiGIA~NKlLAKLA 159 (661)
... ..+..+|++||++|++++||+||||||+||+|||||
T Consensus 118 ---------------~~~--------------------------~~~~~~a~~lr~~I~~~~Gl~~SvGIa~nk~lAKlA 156 (454)
T PRK03348 118 ---------------ASA--------------------------EEVEAFAERLRARVREETGLPASVGAGSGKQIAKIA 156 (454)
T ss_pred ---------------ccC--------------------------CCHHHHHHHHHHHHHHHHCCCeEEEEcCCHHHHHHh
Confidence 000 013568999999999999999999999999999999
Q ss_pred hcCCCCCcccccCcccHHHhcccCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCcCcHHHHHHHHhCCC
Q 006108 160 SGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGIS 239 (661)
Q Consensus 160 S~~~KP~G~~vl~~~~v~~fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~~~G~~L~~~arGiD 239 (661)
|+++||+|+++++++++..||++|||++|||||+++.++|. ++||+||+||++++...|.++||...|.+||+.|+|+|
T Consensus 157 s~~aKP~G~~vi~~~~~~~~L~~LPv~~L~GIG~~t~~~L~-~lGI~TigDLa~l~~~~L~~~fG~~~g~~L~~~a~G~d 235 (454)
T PRK03348 157 SGLAKPDGIRVVPPGEERELLAPLPVRRLWGIGPVTEEKLH-RLGIETIGDLAALSEAEVANLLGATVGPALHRLARGID 235 (454)
T ss_pred hccCCCCcEEEEEchHHHHHHHhCCccccCCCCHHHHHHHH-HcCCccHHHHhcCCHHHHHHHHCHHHHHHHHHHHcCCC
Confidence 99999999999999999999999999999999999999997 99999999999999999999999657999999999999
Q ss_pred CCcccccCCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCCCCCCCcCc
Q 006108 240 GEEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPS 319 (661)
Q Consensus 240 ~~pV~~~~~~KSIs~e~tF~~~~~i~~~eel~~~L~~L~eeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~~~~s 319 (661)
+++|.+..++|+|+.+++|. .++.+.++++.+|..|+++|+.||+++ ++.+++|+|++++.+ +. ..+
T Consensus 236 ~~pv~~~~~~ksis~e~tf~--~~i~~~~~l~~~L~~L~~~l~~rL~~~----g~~~r~v~l~l~~~d---~~----~~s 302 (454)
T PRK03348 236 DRPVAERAEAKQISAESTFA--VDLTTRAQLREAIERIAEHAHRRLLKD----GRGARTVTVKLRKSD---FS----TLT 302 (454)
T ss_pred CCCcccCCCCceEEEEEECC--CCCCCHHHHHHHHHHHHHHHHHHHHHc----CCCccEEEEEEEeCC---CC----ccE
Confidence 99999988899999999998 689999999999999999999999985 999999999998743 32 247
Q ss_pred ceeeCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEccCCcccccccccccccccCC
Q 006108 320 KSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPVLSGTCSIMKYFNGP 391 (661)
Q Consensus 320 rs~~L~~~t~~i~~da~~L~~aal~l~~~~~~~~l~~~~~~g~~ir~lgVsls~L~~~~~~~~sq~~lF~~~ 391 (661)
++.+++++|+ +...|++.+..+|...+ ...+||++||.+++|.+ ..|.+||...
T Consensus 303 rs~~l~~pt~----d~~~L~~la~~ll~~~~---------~~~~vRllgV~~s~l~~-----~~q~~LF~~~ 356 (454)
T PRK03348 303 RSATLPYATD----DAAVLAATARRLLLDPD---------EIGPIRLVGVGFSGLSD-----VRQESLFPEL 356 (454)
T ss_pred EEEECCCCCC----CHHHHHHHHHHHHHhhc---------cCCCeEEEEEEECCCCc-----chhhccCCCc
Confidence 8899999986 56778888888876542 23489999999999974 2678999754
No 11
>PRK02794 DNA polymerase IV; Provisional
Probab=100.00 E-value=1.8e-51 Score=452.65 Aligned_cols=301 Identities=24% Similarity=0.359 Sum_probs=268.6
Q ss_pred CCCCCcHHHHHHhCCCcEEEeccccCCCCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEEcCchhhhhhhCCCCCCc
Q 006108 2 VVSSMRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESL 80 (661)
Q Consensus 2 Vk~GMp~~eAkklCP~L~iV~VP~~~~k~d~~~Yr~~S~~V~~iL~~~-~~VE~~SIDEayLDlT~~~~~~L~~~~~~~l 80 (661)
|++|||+++|+++||+|+++ | +|++.|+++|++|++++.+| |.||++||||+|||+|+..
T Consensus 85 V~~GM~~~~A~~lcP~l~~v--~-----~d~~~y~~~s~~i~~~l~~~sp~ve~~siDe~~ldvt~~~------------ 145 (419)
T PRK02794 85 VRSAMPMFKALKLCPDAVVI--K-----PDMEKYVRVGREVRAMMQALTPLVEPLSIDEAFLDLSGTE------------ 145 (419)
T ss_pred CCcCCHHHHHHHHCCCcEEE--C-----CCHHHHHHHHHHHHHHHHHhCcceeeccCCeEEEeccchh------------
Confidence 89999999999999999887 4 89999999999999999998 8999999999999999864
Q ss_pred chhhHHHhhhhhccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHhhCCceeEEecCCHHHHHHHh
Q 006108 81 DEVDEEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLAS 160 (661)
Q Consensus 81 ~~~~~e~~~s~l~g~~~~~g~d~~~~v~~w~~~~~~~~~d~ll~~~~~lA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS 160 (661)
++||.. ...++.+||++|++++|||||||||+||++|||||
T Consensus 146 ----------~l~g~~-----------------------------~~~~~~~i~~~i~~~~gl~~svGIa~n~~lAKlas 186 (419)
T PRK02794 146 ----------RLHGAP-----------------------------PAVVLARFARRVEREIGITVSVGLSYNKFLAKIAS 186 (419)
T ss_pred ----------hhcCCC-----------------------------HHHHHHHHHHHHHHHHCCceEEEEcCCHHHHHHHH
Confidence 334421 23467899999999999999999999999999999
Q ss_pred cCCCCCcccccCcccHHHhcccCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCcCcHHHHHHHHhCCCC
Q 006108 161 GMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISG 240 (661)
Q Consensus 161 ~~~KP~G~~vl~~~~v~~fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~~~G~~L~~~arGiD~ 240 (661)
+.+||+|++++.++++.+||+++||++|||||+++.++|. ++||+||+||++++...|+++||. .|.++|+.++|+|+
T Consensus 187 ~~~KP~g~~ii~~~~~~~~L~~lPl~~L~GiG~~~~~~L~-~~GI~tigdL~~l~~~~L~~rfG~-~g~~l~~~a~G~d~ 264 (419)
T PRK02794 187 DLDKPRGFSVIGRAEALAFLAPKPVGIIWGVGPATAARLA-RDGIRTIGDLQRADEADLMRRFGS-MGLRLWRLARGIDD 264 (419)
T ss_pred hhhCCCCeEecCHHHHHHHHhcCChhhhCCCCHHHHHHHH-HhccchHHHHhhCCHHHHHHHHhH-HHHHHHHHhCCCCC
Confidence 9999999999999999999999999999999999999997 999999999999999999999998 69999999999999
Q ss_pred CcccccCCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCCCCCCCcCcc
Q 006108 241 EEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSK 320 (661)
Q Consensus 241 ~pV~~~~~~KSIs~e~tF~~~~~i~~~eel~~~L~~L~eeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~~~~sr 320 (661)
++|.+..++|||+.+++|. .++.+.+++..+|..|+++|+.||+.+ ++.+++|+|++++.+ |. ..++
T Consensus 265 ~~v~~~~~~ksi~~~~tl~--~~~~~~~~l~~~l~~L~~~l~~rL~~~----~~~~~~l~l~l~~~~---~~----~~~~ 331 (419)
T PRK02794 265 RKVSPDREAKSVSAETTFE--TDLSDFEDLEPILWRLSEKVSRRLKAA----GLAGRTVTLKLKTAD---FR----LRTR 331 (419)
T ss_pred CCCccCCCCceeeeeEECC--CCCCCHHHHHHHHHHHHHHHHHHHHhc----CCCcceEEEEEEECC---CC----ceEE
Confidence 9999888899999999998 689999999999999999999999985 999999999999643 22 2467
Q ss_pred eeeCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEccCCcccccccccccccccC
Q 006108 321 SCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPVLSGTCSIMKYFNG 390 (661)
Q Consensus 321 s~~L~~~t~~i~~da~~L~~aal~l~~~~~~~~l~~~~~~g~~ir~lgVsls~L~~~~~~~~sq~~lF~~ 390 (661)
+++++.+|+ +...|++.+..+|.+. +.+.+||.|||.+++|.+.. ...|.+||+.
T Consensus 332 ~~~l~~pt~----~~~~l~~~~~~ll~~~---------~~~~~vr~igv~~~~l~~~~--~~~q~~LF~~ 386 (419)
T PRK02794 332 RRTLEDPTQ----LADRIFRTARELLEKE---------TDGTAFRLIGIGVSDLSPAD--EADPPDLLDP 386 (419)
T ss_pred EEECCCCcC----CHHHHHHHHHHHHHhc---------ccCCCEEEEEEEEecCCCcc--ccccccccCc
Confidence 888888886 6677888888777653 24668999999999999752 2247899974
No 12
>PRK03103 DNA polymerase IV; Reviewed
Probab=100.00 E-value=2.5e-51 Score=450.07 Aligned_cols=302 Identities=25% Similarity=0.401 Sum_probs=269.8
Q ss_pred CCCCCcHHHHHHhCCCcEEEeccccCCCCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEEcCchhhhhhhCCCCCCc
Q 006108 2 VVSSMRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESL 80 (661)
Q Consensus 2 Vk~GMp~~eAkklCP~L~iV~VP~~~~k~d~~~Yr~~S~~V~~iL~~~-~~VE~~SIDEayLDlT~~~~~~L~~~~~~~l 80 (661)
||+|||+++|+++||+|+++ | +|++.|+++|++|++++.+| |.||++||||+|||+|++.
T Consensus 55 V~~gm~~~~A~~lcP~l~~~--~-----~d~~~y~~~s~~i~~~l~~~sp~ve~~siDe~~lDvt~~~------------ 115 (409)
T PRK03103 55 VKTAERLWEAQQKCPDLVVV--K-----PRMQRYIDVSLQITRILEDFTDLVEPFSIDEQFLDVTGSQ------------ 115 (409)
T ss_pred CCCCChHHHHHHHCCCeEEE--C-----CCHHHHHHHHHHHHHHHHHhCccceecCCCeeEeeccchh------------
Confidence 89999999999999999887 4 89999999999999999998 8999999999999999975
Q ss_pred chhhHHHhhhhhccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHhhCCceeEEecCCHHHHHHHh
Q 006108 81 DEVDEEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLAS 160 (661)
Q Consensus 81 ~~~~~e~~~s~l~g~~~~~g~d~~~~v~~w~~~~~~~~~d~ll~~~~~lA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS 160 (661)
++||. ...+|++||++|++++|||||||||+||++||||+
T Consensus 116 ----------~~~~~------------------------------~~~la~~ir~~i~~~~gl~~svGia~n~~lAklas 155 (409)
T PRK03103 116 ----------KLFGS------------------------------PLEIAQKIQQRIMRETGVYARVGIGPNKLLAKMAC 155 (409)
T ss_pred ----------hcCCC------------------------------HHHHHHHHHHHHHHHHCceEEEeecCCHHHHHHHh
Confidence 23331 35689999999999999999999999999999999
Q ss_pred cC---CCCCcccccCcccHHHhcccCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCcCcHHHHHHHHhC
Q 006108 161 GM---NKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARG 237 (661)
Q Consensus 161 ~~---~KP~G~~vl~~~~v~~fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~~~G~~L~~~arG 237 (661)
+. +||+|+++++++++..||++|||++|||||+++.++|. .+||+|++||++++...|+++||. .|.++|+.++|
T Consensus 156 ~~~~k~kp~g~~v~~~~~~~~~L~~lpi~~l~gig~~~~~~L~-~~Gi~tigdl~~~~~~~L~~~fG~-~~~~l~~~a~G 233 (409)
T PRK03103 156 DNFAKKNPDGLFTLDKEDVPADLWPLPVRKLFGVGSRMEKHLR-RMGIRTIGQLANTPLERLKKRWGI-NGEVLWRTANG 233 (409)
T ss_pred cchhhcCCCcEEEECHHHHHHHHHcCCHhhcCCccHHHHHHHH-HcCCCCHHHHhcCCHHHHHHHHCH-HHHHHHHHhcC
Confidence 98 99999999999999999999999999999999999997 999999999999999999999998 69999999999
Q ss_pred CCCCcccccCC--CccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCCCCCC
Q 006108 238 ISGEEVQARLL--PKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRK 315 (661)
Q Consensus 238 iD~~pV~~~~~--~KSIs~e~tF~~~~~i~~~eel~~~L~~L~eeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~ 315 (661)
+|+++|.+..+ +|||+.+++|+ .++.+.++|+..|..|+++|+.||+.. +..+++|+|++++.+ +.. .
T Consensus 234 ~d~~~v~~~~~~~~ksi~~~~t~~--~~~~~~~~l~~~l~~L~~~l~~rLr~~----~~~~~~l~l~lr~~~---~~~-~ 303 (409)
T PRK03103 234 IDYSPVTPHSLDRQKAIGHQMTLP--RDYRGFEEIKVVLLELCEEVCRRARAK----GYMGRTVSVSLRGAD---FDW-P 303 (409)
T ss_pred CCCCcCCcccCCCCCccCCCeECC--CCCCCHHHHHHHHHHHHHHHHHHHHHh----CCceeEEEEEEEeCC---CcC-C
Confidence 99999988654 58999999998 689999999999999999999999975 999999999998753 222 2
Q ss_pred CcCcceeeCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEccCCcccccccccccccccC
Q 006108 316 KFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPVLSGTCSIMKYFNG 390 (661)
Q Consensus 316 ~~~srs~~L~~~t~~i~~da~~L~~aal~l~~~~~~~~l~~~~~~g~~ir~lgVsls~L~~~~~~~~sq~~lF~~ 390 (661)
+..+++++++.||+ +...|++.+..+|.++ +.+.+|++|||.+++|.+. ...|.+||+.
T Consensus 304 ~~~~~~~~l~~pt~----~~~~l~~~~~~ll~~~---------~~~~~vr~lgv~~~~l~~~---~~~q~~LF~~ 362 (409)
T PRK03103 304 TGFSRQMTLPEPTN----LAMEVYEAACKLFHRH---------WDGKPVRRVGVTLSNLVSD---DVWQLSLFGD 362 (409)
T ss_pred CCcceeeecCCCCC----CHHHHHHHHHHHHHhc---------ccCCCceEEEEEEeCCCCC---cccCCCcccc
Confidence 33578889988886 6677888888888754 2467899999999999975 4568899974
No 13
>PRK01810 DNA polymerase IV; Validated
Probab=100.00 E-value=3.1e-51 Score=449.09 Aligned_cols=299 Identities=28% Similarity=0.407 Sum_probs=266.8
Q ss_pred CCCCCcHHHHHHhCCCcEEEeccccCCCCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEEcCchhhhhhhCCCCCCc
Q 006108 2 VVSSMRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESL 80 (661)
Q Consensus 2 Vk~GMp~~eAkklCP~L~iV~VP~~~~k~d~~~Yr~~S~~V~~iL~~~-~~VE~~SIDEayLDlT~~~~~~L~~~~~~~l 80 (661)
|++|||+++|+++||+|+++ | +|++.|+++|++|++++.+| |.||++||||+|||+|++..
T Consensus 57 V~~Gm~~~~A~~lcP~l~~~--~-----~d~~~y~~~s~~i~~~l~~~sp~ve~~siDe~~ldvt~~~~----------- 118 (407)
T PRK01810 57 IRTTMPLWEAKRLCPQLIVR--R-----PNFDRYREASRQMFQILSEFTPLVQPVSIDEGYLDITDCYA----------- 118 (407)
T ss_pred CCCCChHHHHHHHCCCeEEE--C-----CChHHHHHHHHHHHHHHHHhCCceEEecCCeEEEeccCccc-----------
Confidence 89999999999999999887 5 89999999999999999998 89999999999999998641
Q ss_pred chhhHHHhhhhhccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHhhCCceeEEecCCHHHHHHHh
Q 006108 81 DEVDEEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLAS 160 (661)
Q Consensus 81 ~~~~~e~~~s~l~g~~~~~g~d~~~~v~~w~~~~~~~~~d~ll~~~~~lA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS 160 (661)
+++ +..+|++||++|++++|||||||||+||++|||||
T Consensus 119 -----------~~~-------------------------------~~~~a~~i~~~i~~~~gl~~svGia~n~~lAklas 156 (407)
T PRK01810 119 -----------LGS-------------------------------PLEIAKMIQQRLLTELQLPCSIGIAPNKFLAKMAS 156 (407)
T ss_pred -----------cCC-------------------------------HHHHHHHHHHHHHHHHCCceEEEEcCCHHHHHHHh
Confidence 111 34689999999999999999999999999999999
Q ss_pred cCCCCCcccccCcccHHHhcccCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCcCcHHHHHHHHhCCCC
Q 006108 161 GMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISG 240 (661)
Q Consensus 161 ~~~KP~G~~vl~~~~v~~fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~~~G~~L~~~arGiD~ 240 (661)
+.+||+|++++.++++..||+++||++|||||+++.++|. .+||+|++||+++|...|+++||. .|.++|+.|+|+|+
T Consensus 157 ~~~Kp~g~~vi~~~~~~~~L~~lpv~~l~giG~~~~~~L~-~~Gi~tigdL~~~~~~~L~~rfG~-~g~~l~~~a~G~d~ 234 (407)
T PRK01810 157 DMKKPLGITVLRKRDVPEMLWPLPVGEMHGIGEKTAEKLK-DIGIQTIGDLAKADEHILRAKLGI-NGVRLQRRANGIDD 234 (407)
T ss_pred cCCCCCCEEEECHHHHHHHHHhCCHhhcCCcCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHHHhH-HHHHHHHHhcCCCC
Confidence 9999999999999999999999999999999999999997 999999999999999999999998 69999999999999
Q ss_pred CcccccCC--CccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCCCCCCCcC
Q 006108 241 EEVQARLL--PKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFP 318 (661)
Q Consensus 241 ~pV~~~~~--~KSIs~e~tF~~~~~i~~~eel~~~L~~L~eeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~~~~ 318 (661)
++|.+..+ +|||+.+++|+ .++.+.+++..+|..|+++|+.||+.+ ++.|++|+|++++.+ +. ..
T Consensus 235 ~~v~~~~~~~~ksi~~~~~~~--~~~~~~~~l~~~l~~L~~~l~~rLr~~----~~~~~~l~l~lr~~~---~~----~~ 301 (407)
T PRK01810 235 RPVDPEAIYQFKSVGNSTTLS--HDMDEEKELLDVLRRLSKSVSKRLQKK----TVVSYNVQIMIRYHD---RR----TI 301 (407)
T ss_pred CCCCCCCCCCCceecceEECC--CCCCCHHHHHHHHHHHHHHHHHHHHHc----CCccceeEEEEEECC---CC----ce
Confidence 99987543 58999999998 689999999999999999999999974 999999999999753 22 24
Q ss_pred cceeeCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEccCCccccccccccccccc
Q 006108 319 SKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPVLSGTCSIMKYFN 389 (661)
Q Consensus 319 srs~~L~~~t~~i~~da~~L~~aal~l~~~~~~~~l~~~~~~g~~ir~lgVsls~L~~~~~~~~sq~~lF~ 389 (661)
+++.+++.||+ +...|++.+..+|.+.+ .+.+||.+||.+++|.+.. ....|.+||+
T Consensus 302 ~~~~~l~~pt~----~~~~l~~~~~~ll~~~~---------~~~~vr~lgv~~~~l~~~~-~~~~q~~Lf~ 358 (407)
T PRK01810 302 TRSKTLKNPIW----EKRDIFQAASRLFKQHW---------NGDPVRLLGVTATDLEWKT-EAVKQLDLFS 358 (407)
T ss_pred EEEEECCCCCC----CHHHHHHHHHHHHHhcc---------CCCCEEEEEEEEecCcccc-cccccccccc
Confidence 67888888886 66778888888887542 3568999999999998752 1345789997
No 14
>PRK02406 DNA polymerase IV; Validated
Probab=100.00 E-value=9.3e-51 Score=435.81 Aligned_cols=287 Identities=28% Similarity=0.396 Sum_probs=254.3
Q ss_pred CCCCCcHHHHHHhCCCcEEEeccccCCCCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEEcCchhhhhhhCCCCCCc
Q 006108 2 VVSSMRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESL 80 (661)
Q Consensus 2 Vk~GMp~~eAkklCP~L~iV~VP~~~~k~d~~~Yr~~S~~V~~iL~~~-~~VE~~SIDEayLDlT~~~~~~L~~~~~~~l 80 (661)
||+||++++|+++||+|+++ | +|++.|+++|++|++++.+| |.||++||||+|||+|+..
T Consensus 45 V~~gm~~~~A~~lcP~l~~~--~-----~d~~~y~~~s~~i~~~l~~~sp~ve~~siDe~~ldvt~~~------------ 105 (343)
T PRK02406 45 VRSAMPTAQALKLCPDLIFV--P-----GRFDVYKEVSRQIREIFRRYTDLIEPLSLDEAYLDVTDNK------------ 105 (343)
T ss_pred CCCCCcHHHHHHHCCCeEEE--C-----CChHHHHHHHHHHHHHHHHhCCceEEccCCeEEEeccCcc------------
Confidence 89999999999999999888 4 89999999999999999998 8999999999999999975
Q ss_pred chhhHHHhhhhhccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHhhCCceeEEecCCHHHHHHHh
Q 006108 81 DEVDEEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLAS 160 (661)
Q Consensus 81 ~~~~~e~~~s~l~g~~~~~g~d~~~~v~~w~~~~~~~~~d~ll~~~~~lA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS 160 (661)
++|| .+..+|+.||++|++++|||||||||+||++||||+
T Consensus 106 ----------~~~~------------------------------~~~~la~~i~~~i~~~~gl~~siGia~n~~lAklas 145 (343)
T PRK02406 106 ----------LCIG------------------------------SATLIAQEIRQDIFEELGLTASAGVAPNKFLAKIAS 145 (343)
T ss_pred ----------ccCC------------------------------CHHHHHHHHHHHHHHHHCCCeEEEeccCHHHHHHHh
Confidence 2333 135789999999999999999999999999999999
Q ss_pred cCCCCCcccccCcccHHHhcccCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCcCcHHHHHHHHhCCCC
Q 006108 161 GMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISG 240 (661)
Q Consensus 161 ~~~KP~G~~vl~~~~v~~fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~~~G~~L~~~arGiD~ 240 (661)
+++||+|+++++++++..||+++||++|||||+++.++|. .+||+|++||++++...|.++||. .|.++|+.++|+|+
T Consensus 146 ~~~Kp~g~~~~~~~~~~~~L~~lpi~~l~giG~~~~~~L~-~~Gi~ti~dl~~l~~~~L~~~fG~-~~~~l~~~a~G~d~ 223 (343)
T PRK02406 146 DWNKPNGLFVITPEEVDAFLATLPVEKIPGVGKVTAEKLH-ALGIYTCADLQKYDLAELIRHFGK-FGRRLYERARGIDE 223 (343)
T ss_pred cCCCCCCEEEECHHHHHHHHHcCCcchhcCCCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHHHhH-HHHHHHHHhCCCCC
Confidence 9999999999999999999999999999999999999997 999999999999999999999997 69999999999999
Q ss_pred CcccccCCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcC--ceeeEEEEEEeeccCCCCCCCCCcC
Q 006108 241 EEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNK--RIAHTLTLHASAFKSSDSDSRKKFP 318 (661)
Q Consensus 241 ~pV~~~~~~KSIs~e~tF~~~~~i~~~eel~~~L~~L~eeL~~RLr~~~~~~~--~~artLtL~lr~~~~~~~~s~~~~~ 318 (661)
.+|.+..++|||+.+++|. .++.+.+++..+|.+|+++|+.||+++ + +.+++|+|++++.+ +.+ .
T Consensus 224 ~~v~~~~~~ksi~~~~~~~--~~~~~~~~l~~~l~~l~~~l~~rL~~~----~~~~~~~~l~l~l~~~~---~~~----~ 290 (343)
T PRK02406 224 RPVKPDRERKSVGVERTFA--EDLYDLEACLAELPRLAEKLERRLERA----KPDKRIKTVGVKLKFAD---FQQ----T 290 (343)
T ss_pred CccccCCCCcceeeeeeCC--CCCCCHHHHHHHHHHHHHHHHHHHHhc----CCCccceeEEEEEEeCC---CCe----E
Confidence 9999888899999999998 689999999999999999999999985 8 99999999999743 222 2
Q ss_pred cceeeCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEccCCccc
Q 006108 319 SKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPV 377 (661)
Q Consensus 319 srs~~L~~~t~~i~~da~~L~~aal~l~~~~~~~~l~~~~~~g~~ir~lgVsls~L~~~ 377 (661)
+++.+ ..+++ +...|+..+.+++... + +.+||.|||++++|.+.
T Consensus 291 ~~~~~-~~~~~----~~~~l~~~~~~L~~~~---------~-~~~vr~lgv~~~~l~~~ 334 (343)
T PRK02406 291 TKEHT-ADPLD----KADLIELLAQALLRRL---------G-GRGVRLLGVGVTLLEPQ 334 (343)
T ss_pred EEecC-CCCCC----cHHHHHHHHHHHHhhC---------c-CCCEEEEEEEEecCCcC
Confidence 44444 44443 4445666666666532 2 67899999999999865
No 15
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=100.00 E-value=2.3e-50 Score=444.26 Aligned_cols=303 Identities=19% Similarity=0.204 Sum_probs=264.5
Q ss_pred CCCCCcHHHHHHhCC-C-cEEEeccccCCCCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEEcCchhhhhhhCCCCC
Q 006108 2 VVSSMRGDEAKEVCP-Q-IELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPE 78 (661)
Q Consensus 2 Vk~GMp~~eAkklCP-~-L~iV~VP~~~~k~d~~~Yr~~S~~V~~iL~~~-~~VE~~SIDEayLDlT~~~~~~L~~~~~~ 78 (661)
||+|||+++|+++|| + ++++ | +|++.|.++|++|++++.+| |.||++||||+|||+|++..
T Consensus 49 V~~gmp~~~a~~l~~~~~l~~~--~-----~d~~~y~~~s~~i~~~l~~~tp~ve~~siDE~~lDvt~~~~--------- 112 (422)
T PRK03609 49 IKMGDPWFKQKDLFRRCGVVCF--S-----SNYELYADMSNRVMSTLEELSPRVEIYSIDEAFCDLTGVRN--------- 112 (422)
T ss_pred CCCCCcHHHHHHHhccCCeEEe--C-----CCHHHHHHHHHHHHHHHHHhCCCceEeccccceecCCCCcC---------
Confidence 899999999999995 3 6666 5 89999999999999999998 89999999999999999741
Q ss_pred CcchhhHHHhhhhhccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHhhCCceeEEecCCHHHHHH
Q 006108 79 SLDEVDEEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKL 158 (661)
Q Consensus 79 ~l~~~~~e~~~s~l~g~~~~~g~d~~~~v~~w~~~~~~~~~d~ll~~~~~lA~~IR~~I~~etGlt~SiGIA~NKlLAKL 158 (661)
+. ....+|++||++|++++|||||||||+||++|||
T Consensus 113 -------------l~-------------------------------~~~~~a~~i~~~I~~~~gl~~siGia~n~~lAK~ 148 (422)
T PRK03609 113 -------------CR-------------------------------DLTDFGREIRATVLQRTHLTVGVGIAQTKTLAKL 148 (422)
T ss_pred -------------CC-------------------------------CHHHHHHHHHHHHHHHHCCceEEEecCCHHHHHH
Confidence 11 1246899999999999999999999999999999
Q ss_pred HhcCCCC-----Cccccc-CcccHHHhcccCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCcCcHHHHH
Q 006108 159 ASGMNKP-----AQQTTV-PFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLW 232 (661)
Q Consensus 159 AS~~~KP-----~G~~vl-~~~~v~~fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~~~G~~L~ 232 (661)
||.++|| +|+++| +++++..||++|||++|||||+++.++|. .+||+|+|||++++...|+++||. .|.++|
T Consensus 149 As~~~k~~~k~~~g~~~i~~~~~~~~~L~~lPv~~l~GiG~~~~~~L~-~lGi~TigdL~~~~~~~L~~~fG~-~~~~l~ 226 (422)
T PRK03609 149 ANHAAKKWQRQTGGVVDLSNLERQRKLLSLQPVEEVWGVGRRISKKLN-AMGIKTALDLADTNIRFIRKHFNV-VLERTV 226 (422)
T ss_pred HHHHhCCCCCCCCcEEEcCCHHHHHHHhhcCChhhcCCccHHHHHHHH-HcCCCcHHHHhcCCHHHHHHHHCH-HHHHHH
Confidence 9998776 688877 68899999999999999999999999997 999999999999999999999998 699999
Q ss_pred HHHhCCCCCcccccCCC-ccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCC
Q 006108 233 NIARGISGEEVQARLLP-KSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDS 311 (661)
Q Consensus 233 ~~arGiD~~pV~~~~~~-KSIs~e~tF~~~~~i~~~eel~~~L~~L~eeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~ 311 (661)
+.++|+++.++....++ |+|+.++||+ .++.+.+++..+|..|+++|+.||+.+ ++.+++|+|++|+.+ |
T Consensus 227 ~~a~G~~~~~~~~~~~~~ksi~~~~tf~--~~~~~~~~l~~~l~~l~~~l~~rLr~~----~~~~~~l~l~ir~~~---~ 297 (422)
T PRK03609 227 RELRGEPCLSLEEFAPTKQEIVCSRSFG--ERITDYESMRQAICSYAARAAEKLRGE----HQYCRFISTFVKTSP---F 297 (422)
T ss_pred HHhCCCCCCCccccCCCCceEEEeeECC--CCCCCHHHHHHHHHHHHHHHHHHHHHc----CCcccEEEEEEEcCC---c
Confidence 99999999998766654 7999999998 689999999999999999999999985 999999999999854 3
Q ss_pred CCC--CCcCcceeeCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEccCCccccccccccccccc
Q 006108 312 DSR--KKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPVLSGTCSIMKYFN 389 (661)
Q Consensus 312 ~s~--~~~~srs~~L~~~t~~i~~da~~L~~aal~l~~~~~~~~l~~~~~~g~~ir~lgVsls~L~~~~~~~~sq~~lF~ 389 (661)
... .+..+++.+++.+|+ +...|++.+..+|.+++ ..+.++|++||.+++|.+. ...|.+||+
T Consensus 298 ~~~~~~~~~~~~~~l~~pt~----d~~~l~~~a~~ll~~~~--------~~~~~~r~~GV~~~~l~~~---~~~q~~LF~ 362 (422)
T PRK03609 298 ALNEPYYGNSASVKLLTPTQ----DSRDIIAAATRALDAIW--------RDGHRYQKAGVMLGDFFSQ---GVAQLNLFD 362 (422)
T ss_pred cccCCCcCceeEEeCCCCCC----CHHHHHHHHHHHHHHHh--------CCCCceEEeeEEEEeeccC---CCcCccCcc
Confidence 221 234577788988886 67788888888887654 2356899999999999974 346889997
Q ss_pred C
Q 006108 390 G 390 (661)
Q Consensus 390 ~ 390 (661)
.
T Consensus 363 ~ 363 (422)
T PRK03609 363 D 363 (422)
T ss_pred c
Confidence 4
No 16
>PRK03352 DNA polymerase IV; Validated
Probab=100.00 E-value=2.8e-50 Score=432.55 Aligned_cols=285 Identities=26% Similarity=0.360 Sum_probs=257.9
Q ss_pred CCCCCcHHHHHHhCCCcEEEeccccCCCCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEEcCchhhhhhhCCCCCCc
Q 006108 2 VVSSMRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESL 80 (661)
Q Consensus 2 Vk~GMp~~eAkklCP~L~iV~VP~~~~k~d~~~Yr~~S~~V~~iL~~~-~~VE~~SIDEayLDlT~~~~~~L~~~~~~~l 80 (661)
|++||++++|+++||+|+++ | +|++.|+++|++|++++.+| |.||++||||+|||+|+..
T Consensus 59 V~~gM~~~~A~~lcP~l~~v--~-----~~~~~y~~~s~~i~~~l~~~s~~ve~~siDe~~ld~t~~~------------ 119 (346)
T PRK03352 59 VRAGMPLRTAARRCPDAVFL--P-----SDPAAYDAASEEVMATLRDLGVPVEVWGWDEAFLGVDTDD------------ 119 (346)
T ss_pred CCcCChHHHHHHHCCCeEEE--C-----CCcHHHHHHHHHHHHHHHHhCCceEEecCccEEEeCCCCC------------
Confidence 89999999999999999887 5 89999999999999999998 8999999999999999741
Q ss_pred chhhHHHhhhhhccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHhhCCceeEEecCCHHHHHHHh
Q 006108 81 DEVDEEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLAS 160 (661)
Q Consensus 81 ~~~~~e~~~s~l~g~~~~~g~d~~~~v~~w~~~~~~~~~d~ll~~~~~lA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS 160 (661)
...+|+.||++|++++|||||||||+||++||||+
T Consensus 120 ---------------------------------------------~~~la~~ir~~i~~~~gl~~siGia~nk~lAklaa 154 (346)
T PRK03352 120 ---------------------------------------------PEALAEEIRAAVLERTGLSCSVGIGDNKLRAKIAT 154 (346)
T ss_pred ---------------------------------------------HHHHHHHHHHHHHHHHCCCEEEeecCCHHHHHHHH
Confidence 23579999999999999999999999999999999
Q ss_pred cCCCCCcccccCcccHHHhcccCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCcCcHHHHHHHHhCCCC
Q 006108 161 GMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISG 240 (661)
Q Consensus 161 ~~~KP~G~~vl~~~~v~~fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~~~G~~L~~~arGiD~ 240 (661)
+.+||+|++++.++++..||+++||++|||||+++.++|. ++||+|++||++++...|.++||...|.+||+.++|+|.
T Consensus 155 ~~~Kp~g~~~~~~~~~~~~L~~lpl~~l~gig~~~~~~L~-~~Gi~ti~dl~~l~~~~L~~~fG~~~~~~l~~~a~G~d~ 233 (346)
T PRK03352 155 GFAKPAGVFRLTDANWMAVMGDRPTDALWGVGPKTAKRLA-ALGITTVADLAAADPAELAATFGPTTGPWLLLLARGGGD 233 (346)
T ss_pred hhcCCCcEEEECHHHHHHHHhcCCHHHcCCCCHHHHHHHH-HcCCccHHHHhcCCHHHHHHHhChHHHHHHHHHhCCCCC
Confidence 9999999999999999999999999999999999999997 999999999999999999999997679999999999999
Q ss_pred Cccccc-CCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCCCCCCCcCc
Q 006108 241 EEVQAR-LLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPS 319 (661)
Q Consensus 241 ~pV~~~-~~~KSIs~e~tF~~~~~i~~~eel~~~L~~L~eeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~~~~s 319 (661)
+++... ..+||++.+++|. .++.+.+++..+|..|+++|+.||+.+ ++.+++|+|++++.+ +. ..+
T Consensus 234 ~~~~~~~~~~ksi~~~~tf~--~~~~~~~~l~~~l~~L~~~l~~rLr~~----~~~~~~l~l~l~~~~---~~----~~~ 300 (346)
T PRK03352 234 TEVSAEPWVPRSRSREVTFP--QDLTDRAEVESAVRELARRVLDEVVAE----GRPVTRVAVKVRTAT---FY----TRT 300 (346)
T ss_pred CCCCCCCCCCceEEEEEECC--CCCCCHHHHHHHHHHHHHHHHHHHHHc----CCccceEEEEEEeCC---Cc----eeE
Confidence 998764 3579999999998 689999999999999999999999985 999999999999753 22 236
Q ss_pred ceeeCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEccCCccc
Q 006108 320 KSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPV 377 (661)
Q Consensus 320 rs~~L~~~t~~i~~da~~L~~aal~l~~~~~~~~l~~~~~~g~~ir~lgVsls~L~~~ 377 (661)
++.+++.+|+ +...|++.+..+|.++ +.+.+||.|||++.+|.+.
T Consensus 301 ~~~~l~~pt~----d~~~l~~~~~~ll~~~---------~~~~~vr~igl~~~~~~~~ 345 (346)
T PRK03352 301 KIRKLPEPTT----DPDVIEAAALDVLDRF---------ELDRPVRLLGVRLELAMPD 345 (346)
T ss_pred EEEECCCCcC----CHHHHHHHHHHHHHhc---------cCCCCEEEEEEEEeccCCC
Confidence 7888888886 6777888888877653 2356899999999999864
No 17
>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=4.3e-50 Score=427.97 Aligned_cols=286 Identities=34% Similarity=0.491 Sum_probs=260.2
Q ss_pred CCCCCcHHHHHHhCCCcEEEeccccCCCCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEEcCchhhhhhhCCCCCCc
Q 006108 2 VVSSMRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESL 80 (661)
Q Consensus 2 Vk~GMp~~eAkklCP~L~iV~VP~~~~k~d~~~Yr~~S~~V~~iL~~~-~~VE~~SIDEayLDlT~~~~~~L~~~~~~~l 80 (661)
||+||++++|+++||+|+++ | +|++.|+++|++|++++.+| |.||++||||+|||+|+..
T Consensus 48 V~~Gm~~~~A~~lcp~l~~~--~-----~~~~~y~~~s~~i~~~l~~~~~~ve~~s~De~~ldv~~~~------------ 108 (334)
T cd03586 48 VRSAMPIFQAKKLCPNLIFV--P-----PRFDKYREVSRQIMEILREYTPLVEPLSIDEAYLDVTDYV------------ 108 (334)
T ss_pred CCcCCcHHHHHHHCCCeEEE--C-----CCcHHHHHHHHHHHHHHHHcCCceEEecccceeEcccccc------------
Confidence 89999999999999999888 4 89999999999999999998 8999999999999999864
Q ss_pred chhhHHHhhhhhccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHhhCCceeEEecCCHHHHHHHh
Q 006108 81 DEVDEEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLAS 160 (661)
Q Consensus 81 ~~~~~e~~~s~l~g~~~~~g~d~~~~v~~w~~~~~~~~~d~ll~~~~~lA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS 160 (661)
++|| .+..+|++||++|++++||+||+|||+|+++||||+
T Consensus 109 ----------~~~~------------------------------~~~~la~~ir~~i~~~~g~~~siGia~n~~lAklaa 148 (334)
T cd03586 109 ----------RLFG------------------------------SATEIAKEIRARIREETGLTASAGIAPNKFLAKIAS 148 (334)
T ss_pred ----------ccCC------------------------------CHHHHHHHHHHHHHHHHCCceEEEEhhcHHHHHHHh
Confidence 2232 145789999999999999999999999999999999
Q ss_pred cCCCCCcccccCcccHHHhcccCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCcCcHHHHHHHHhCCCC
Q 006108 161 GMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISG 240 (661)
Q Consensus 161 ~~~KP~G~~vl~~~~v~~fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~~~G~~L~~~arGiD~ 240 (661)
+.+||+|+++++++++..||+++||+++||||+++.++|. .+||+|++||++++...|.++||. .|.++|+.++|+|+
T Consensus 149 ~~~kp~g~~i~~~~~~~~~L~~lpl~~l~gig~~~~~~L~-~~Gi~ti~dl~~~~~~~L~~~~g~-~~~~l~~~~~G~~~ 226 (334)
T cd03586 149 DLNKPNGLTVIPPEDVEEFLAPLPVRKIPGVGKVTAEKLK-ELGIKTIGDLAKLDVELLKKLFGK-SGRRLYELARGIDN 226 (334)
T ss_pred cCCCCCcEEEECHHHHHHHHhcCCchhhCCcCHHHHHHHH-HcCCcCHHHHHcCCHHHHHHHHhH-HHHHHHHHhCCCCC
Confidence 9999999999999999999999999999999999999997 999999999999999999999997 69999999999999
Q ss_pred CcccccCCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCCCCCCCcCcc
Q 006108 241 EEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSK 320 (661)
Q Consensus 241 ~pV~~~~~~KSIs~e~tF~~~~~i~~~eel~~~L~~L~eeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~~~~sr 320 (661)
+++.+..++|||+.+++|+ .++.+.+++..+|..|+++|+.||+.+ ++.+++|+|++++.+. ...++
T Consensus 227 ~~v~~~~~~ks~~~~~~~~--~~~~~~~~l~~~l~~l~~~l~~rL~~~----~~~~~~l~l~l~~~~~-------~~~~~ 293 (334)
T cd03586 227 RPVEPDRERKSIGVERTFS--EDLTDPEELLEELLELAEELAERLRKR----GLKGRTVTVKLKYADF-------STRTR 293 (334)
T ss_pred CCCCCCCCCCeeeeeEECC--CCCCCHHHHHHHHHHHHHHHHHHHHhC----CCCeEEEEEEEEECCC-------CeEEE
Confidence 9999888899999999998 689999999999999999999999985 9999999999987532 12478
Q ss_pred eeeCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEccCC
Q 006108 321 SCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKI 374 (661)
Q Consensus 321 s~~L~~~t~~i~~da~~L~~aal~l~~~~~~~~l~~~~~~g~~ir~lgVsls~L 374 (661)
+.+++.+|+ +...|++.+..+|.+++ .+.+||++||++++|
T Consensus 294 ~~~l~~~t~----~~~~l~~~~~~~l~~~~---------~~~~vr~igv~~~~l 334 (334)
T cd03586 294 SRTLPEPTD----DAEDIYELALELLEELL---------DGRPIRLLGVRLSGL 334 (334)
T ss_pred EEECCCCCC----CHHHHHHHHHHHHHhcc---------CCCCEEEEEEEeecC
Confidence 888888886 67788888888887543 347899999999875
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=1.4e-49 Score=426.81 Aligned_cols=291 Identities=25% Similarity=0.360 Sum_probs=251.3
Q ss_pred CCCCCcHHHHHHhCCCcEEEeccccCCCCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEEcCchhhhhhhCCCCCCc
Q 006108 2 VVSSMRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESL 80 (661)
Q Consensus 2 Vk~GMp~~eAkklCP~L~iV~VP~~~~k~d~~~Yr~~S~~V~~iL~~~-~~VE~~SIDEayLDlT~~~~~~L~~~~~~~l 80 (661)
|++||++.+|+++||+|.++.|| +|++.|+++|++|++++.+| |.||.+||||+|||+|+...
T Consensus 47 V~~gm~~~~A~~lcP~l~~~~v~-----~~~~~y~~~s~~i~~~l~~~~~~ve~~s~De~~ldvt~~~~----------- 110 (344)
T cd01700 47 IKMGSPYFKVPDLLERHGVAVFS-----SNYALYGDMSRRIMSILERFSPDVEVYSIDESFLDLTGSLR----------- 110 (344)
T ss_pred CCCCCcHHHhHhhccccCeEEEc-----CchHHHHHHHHHHHHHHHhcCCcceEeecchhhccCcCCCC-----------
Confidence 89999999999999999333335 89999999999999999998 89999999999999998641
Q ss_pred chhhHHHhhhhhccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHhhCCceeEEecCCHHHHHHHh
Q 006108 81 DEVDEEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLAS 160 (661)
Q Consensus 81 ~~~~~e~~~s~l~g~~~~~g~d~~~~v~~w~~~~~~~~~d~ll~~~~~lA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS 160 (661)
|| .+..+|++||++|++++|||||+|||+||++|||||
T Consensus 111 ------------~~------------------------------~~~~la~~i~~~i~~~~gl~~s~Gia~~~~lAklas 148 (344)
T cd01700 111 ------------FG------------------------------DLEELARKIRRRILQETGIPVTVGIGPTKTLAKLAN 148 (344)
T ss_pred ------------CC------------------------------CHHHHHHHHHHHHHHHhCCceEEEecCCHHHHHHHH
Confidence 11 135789999999999999999999999999999999
Q ss_pred cCCCCC----cccccCcccHH-HhcccCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCcCcHHHHHHHH
Q 006108 161 GMNKPA----QQTTVPFSSVK-GLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIA 235 (661)
Q Consensus 161 ~~~KP~----G~~vl~~~~v~-~fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~~~G~~L~~~a 235 (661)
+++||+ |++++.+++.. .||+++||++|||||+++.++|. ++||+|++||+++|...|.++||. .|.++|+.+
T Consensus 149 ~~~kp~~~~~g~~~~~~~~~~~~~l~~lpl~~l~gig~~~~~~L~-~~Gi~ti~dL~~~~~~~L~~rfG~-~~~~l~~~a 226 (344)
T cd01700 149 DLAKKKNPYGGVVDLTDEEVRDKLLKILPVGDVWGIGRRTAKKLN-AMGIHTAGDLAQADPDLLRKKFGV-VGERLVREL 226 (344)
T ss_pred HHhcCCCCCCeEEEecChhHHHHHhccCChhhcCccCHHHHHHHH-HcCCCcHHHHhcCCHHHHHHHHHH-HHHHHHHHh
Confidence 999984 77787766664 89999999999999999999997 999999999999999999999997 699999999
Q ss_pred hCCCCCcccccCC-CccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCCCCC
Q 006108 236 RGISGEEVQARLL-PKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSR 314 (661)
Q Consensus 236 rGiD~~pV~~~~~-~KSIs~e~tF~~~~~i~~~eel~~~L~~L~eeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~ 314 (661)
+|+|+++|.+..+ +|||+.+.+|. .++.+.+++..+|..|+++|+.||+.+ ++.+++|+|++++.+ |...
T Consensus 227 ~G~d~~~v~~~~~~~ks~~~~~~~~--~~~~~~~~l~~~l~~L~~~l~~~L~~~----~~~~~~l~l~l~~~~---~~~~ 297 (344)
T cd01700 227 NGIDCLPLEEYPPPKKSIGSSRSFG--RDVTDLDELKQALAEYAERAAEKLRRQ----KSVARTISVFIGTSG---FSRQ 297 (344)
T ss_pred CCCCCCcCCCCCCCCcEEEEeeEcC--CCCCCHHHHHHHHHHHHHHHHHHHHHc----CCcccEEEEEEEcCC---CCCC
Confidence 9999999975544 58999999998 689999999999999999999999985 999999999999753 2222
Q ss_pred CCcCcceeeCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEccC
Q 006108 315 KKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASK 373 (661)
Q Consensus 315 ~~~~srs~~L~~~t~~i~~da~~L~~aal~l~~~~~~~~l~~~~~~g~~ir~lgVsls~ 373 (661)
.+..+.+.++..+|+ +...|++.++.+|..++ ..+.+||+|||++++
T Consensus 298 ~~~~~~~~~~~~~t~----~~~~l~~~~~~ll~~~~--------~~~~~iR~iGV~~~~ 344 (344)
T cd01700 298 PKYYSATNTLPYPTN----DTREIVKAALRLLYAIY--------RPGYAYRKAGVMLSD 344 (344)
T ss_pred CCccccccccCCcch----hHHHHHHHHHHHHHHHh--------CCCCcEEEEEEEeeC
Confidence 222334456677775 66778888888887654 235689999999875
No 19
>KOG2094 consensus Predicted DNA damage inducible protein [Replication, recombination and repair]
Probab=100.00 E-value=2.3e-47 Score=394.61 Aligned_cols=295 Identities=27% Similarity=0.393 Sum_probs=248.7
Q ss_pred CCCCCcHHHHHHhCCCcEEEeccccCCCCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEEcCchhhhhhhCCCCCCc
Q 006108 2 VVSSMRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESL 80 (661)
Q Consensus 2 Vk~GMp~~eAkklCP~L~iV~VP~~~~k~d~~~Yr~~S~~V~~iL~~~-~~VE~~SIDEayLDlT~~~~~~L~~~~~~~l 80 (661)
||+|||.|.|+++||+|++| | .||..|+.+|+++-+||++| |.+-.+|+||||||+|.+++.+
T Consensus 150 VRaaMPgFIarklCPdLiiV--P-----~n~~kYt~~Ske~~~v~~~YDsn~~~~SlDEaylnlT~~l~~~--------- 213 (490)
T KOG2094|consen 150 VRAAMPGFIARKLCPDLIIV--P-----LNFSKYTIVSKEIQNVLAQYDSNFCAMSLDEAYLNLTSHLRER--------- 213 (490)
T ss_pred hhhcCchHHHhccCCceEEe--C-----CCcHHHHHHHHHHHHHHHHcCCccccchHHHHHHhHHHHHHHh---------
Confidence 89999999999999999987 6 79999999999999999999 7899999999999999987532
Q ss_pred chhhHHHhhhhhccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHhhCCceeEEecCCHHHHHHHh
Q 006108 81 DEVDEEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLAS 160 (661)
Q Consensus 81 ~~~~~e~~~s~l~g~~~~~g~d~~~~v~~w~~~~~~~~~d~ll~~~~~lA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS 160 (661)
-+|.-..+| ...++++||.+|+++||+|||+|||+|++|||++|
T Consensus 214 -----------~~g~l~~nG-------------------------~~evveeiR~rV~qeTglT~SaGIAaN~lLAKicS 257 (490)
T KOG2094|consen 214 -----------ELGFLVENG-------------------------ITEVVEEIRFRVEQETGLTCSAGIAANKLLAKICS 257 (490)
T ss_pred -----------hcchhhhcc-------------------------HHHHHHHHHHHHHHhcCceeeccccHhHHHHHHhc
Confidence 122100111 35789999999999999999999999999999999
Q ss_pred cCCCCCcccccCcc--cHHHhcccCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCcCcHHHHHHHHhCC
Q 006108 161 GMNKPAQQTTVPFS--SVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGI 238 (661)
Q Consensus 161 ~~~KP~G~~vl~~~--~v~~fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~~~G~~L~~~arGi 238 (661)
+++|||||++++++ .+..||..|||+++-|||+.++..|. .+||.||||+.+- ...|--.|.+...+.+.+.+.|.
T Consensus 258 d~nKPNgQf~i~~dr~aim~F~kdLPvRkV~GIGrV~E~qLk-al~IkTcgdm~~k-~~ll~~lFsp~S~~~fLr~slG~ 335 (490)
T KOG2094|consen 258 DKNKPNGQFVIPNDRIAIMKFMKDLPVRKVSGIGRVTEQQLK-ALGIKTCGDMQQK-LVLLSLLFSPKSFQNFLRCSLGL 335 (490)
T ss_pred cccCCCCceEecccHHHHHHHHhcCCcccccchhHHHHHHHH-hcCceeHHHHHHh-hhHHHHHhCchhHHHHHHHhhcC
Confidence 99999999999765 58899999999999999999999997 9999999999874 45677789987788899999999
Q ss_pred CCCcccccCCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCCCCCCCcC
Q 006108 239 SGEEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFP 318 (661)
Q Consensus 239 D~~pV~~~~~~KSIs~e~tF~~~~~i~~~eel~~~L~~L~eeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~~~~ 318 (661)
...++.....+|||+.++||. ++.+...+...+.+||..|.+-|+. .|++++||+|+++... |+.+
T Consensus 336 g~t~~~~~~eRKsis~ErTFs---~~sd~~il~~k~qel~~~lsedlqK----~glv~rtvtiKlK~ss---Fev~---- 401 (490)
T KOG2094|consen 336 GTTILDEDGERKSISSERTFS---STSDPSILYSKLQELCQMLSEDLQK----EGLVGRTVTIKLKTSS---FEVH---- 401 (490)
T ss_pred CCCcCccccccccccceeeec---ccCCHHHHHHHHHHHHHHHHHHHHh----cCcccceEEEEEeccc---eeee----
Confidence 999988888899999999997 6899999998888888888777776 5999999999998754 4332
Q ss_pred cceeeCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEccCCcccc
Q 006108 319 SKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPVL 378 (661)
Q Consensus 319 srs~~L~~~t~~i~~da~~L~~aal~l~~~~~~~~l~~~~~~g~~ir~lgVsls~L~~~~ 378 (661)
+++.++..-. ....+|+..+++|+...+ +..||++||.+++|+...
T Consensus 402 Tr~~t~s~vv----~S~edi~k~aleLLk~e~----------~~~iRLlGvR~sqlv~ee 447 (490)
T KOG2094|consen 402 TRQKTISQVV----HSEEDILKPALELLKQEY----------PMTIRLLGVRASQLVSEE 447 (490)
T ss_pred eccCchhhhh----ccHHHHHHHHHHHHHhhc----------CceEeeeeeeHhhccchh
Confidence 3433332211 235568888888887543 669999999999998764
No 20
>COG0389 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]
Probab=100.00 E-value=6.5e-46 Score=400.27 Aligned_cols=294 Identities=34% Similarity=0.467 Sum_probs=260.4
Q ss_pred CCCCCcHHHHHHhCCCcEEEeccccCCCCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEEcCchhhhhhhCCCCCCc
Q 006108 2 VVSSMRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESL 80 (661)
Q Consensus 2 Vk~GMp~~eAkklCP~L~iV~VP~~~~k~d~~~Yr~~S~~V~~iL~~~-~~VE~~SIDEayLDlT~~~~~~L~~~~~~~l 80 (661)
|++|||+++|+++||+++++ | ++|+.|+.+|.+|++|+.+| +.||++||||+|||+|+...
T Consensus 51 v~sam~~~~A~~~cp~~~~~--~-----~~~~~y~~~s~~i~~i~~~~~~~ve~lSIDE~~ldvt~~~~----------- 112 (354)
T COG0389 51 VRSAMPLFEALKLCPRAIVA--P-----PNFAAYRLASAEIRAILERYTPLVEPLSIDEAFLDLTDALR----------- 112 (354)
T ss_pred CcccChHHHHHHHCCCCEEe--C-----CcHHHHHHHHHHHHHHHHhccccceeeeccceeeecccccc-----------
Confidence 78999999999999999887 5 79999999999999999998 89999999999999997642
Q ss_pred chhhHHHhhhhhccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHhhCCceeEEecCCHHHHHHHh
Q 006108 81 DEVDEEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLAS 160 (661)
Q Consensus 81 ~~~~~e~~~s~l~g~~~~~g~d~~~~v~~w~~~~~~~~~d~ll~~~~~lA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS 160 (661)
.+|. ..+..+|.+||..|+.++|+|||+|||+||++|||||
T Consensus 113 -----------~~g~----------------------------~~~~~~a~~ir~~i~~~~~l~~s~Gi~~nk~laKiAs 153 (354)
T COG0389 113 -----------LLGL----------------------------ADAPRIALEIRFGILLELGLTASVGISDNKFLAKIAS 153 (354)
T ss_pred -----------cCCc----------------------------ccHHHHHHHHHHHHHHhhCCEEEEEecCcHHHHHHHh
Confidence 1221 1256789999999999999999999999999999999
Q ss_pred cCCCCCcccccCcccHHHhcccCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCcCcHHHHHHHHhCCCC
Q 006108 161 GMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISG 240 (661)
Q Consensus 161 ~~~KP~G~~vl~~~~v~~fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~~~G~~L~~~arGiD~ 240 (661)
+++||+|++++.+.++.+||++|||.++||||++++.+|. .+||.||+||+..+...|.+.||. .|.+||+.++|+|.
T Consensus 154 ~~~kp~gi~~~~~~~~~~~l~~Lpv~~~~GvG~~~~~~l~-~~Gi~ti~dl~~~~~~~L~~~~g~-~~~~l~~~a~Gid~ 231 (354)
T COG0389 154 DLNKPDGITVIEPEEVPALLWQLPVLEFWGVGKVTAEKLR-RLGISTIGDLAETDLDALKKRFGK-LGERLYRLARGIDN 231 (354)
T ss_pred cccCCCCEEEECHHHHHHHHhcCChhhhCCCCHHHHHHHH-HcCChhHHHHHhcCHHHHHHHHhH-hHHHHHHHhcCCCc
Confidence 9999999999999999999999999999999999999997 999999999999999999999998 68999999999999
Q ss_pred CcccccCCC-ccccccccCCCCCCCCCHHHHHHHHHH-HHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCCCCCCCcC
Q 006108 241 EEVQARLLP-KSHGSGKSFPGPRALKTVASVQHWLNQ-LCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFP 318 (661)
Q Consensus 241 ~pV~~~~~~-KSIs~e~tF~~~~~i~~~eel~~~L~~-L~eeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~~~~ 318 (661)
++|.+...+ ||++.+.||. .++.+.+++...|.. |+++++.||+.. +..++++++++++.+ | ++.
T Consensus 232 ~~v~~~~~~~ksi~~~~t~~--~d~~~~~~~~~~l~~~l~e~~~~rl~~~----~~~~r~v~~~~~~~d---f----~~~ 298 (354)
T COG0389 232 RPVREQALRAKSIGAESTFE--EDLTDAEELIERLRARLGEEVVSRLRKS----GRHGRTVSVKLKTAD---F----PTN 298 (354)
T ss_pred cccccccccCccccceeecc--ccccCHHHHHHHHHHHHHHHHHHHHHHh----CCCceEEEEEEEecC---C----Ccc
Confidence 999998887 9999999998 688999988888887 999999999985 888899999999754 3 235
Q ss_pred cceeeCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEccCCccc
Q 006108 319 SKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPV 377 (661)
Q Consensus 319 srs~~L~~~t~~i~~da~~L~~aal~l~~~~~~~~l~~~~~~g~~ir~lgVsls~L~~~ 377 (661)
+++.+|+.|++ +..+++.++..+|...+. .+.+.++|.+||+++++.+.
T Consensus 299 t~~~~l~~p~~----~~~~i~~~~~~l~~~~~~------~~~~~~~rl~gv~~~~~~~~ 347 (354)
T COG0389 299 TRSRKLAQPTS----DPIEIYAAALPLLPPLLF------RGRGRRIRLLGVSGPELIDS 347 (354)
T ss_pred eeecccCCcCC----CHHHHHHHHHHHHHHhhc------cCCCceEEEEEEEecCcccc
Confidence 78888888885 456677777777765441 12367899999999999875
No 21
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=100.00 E-value=4.5e-46 Score=417.28 Aligned_cols=308 Identities=22% Similarity=0.346 Sum_probs=262.4
Q ss_pred CCCCCcHHHHHHhCCCcEEEeccccCCCCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEEcCchhhhhhhCCCCCCc
Q 006108 2 VVSSMRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESL 80 (661)
Q Consensus 2 Vk~GMp~~eAkklCP~L~iV~VP~~~~k~d~~~Yr~~S~~V~~iL~~~-~~VE~~SIDEayLDlT~~~~~~L~~~~~~~l 80 (661)
||+||.+.+|+++||+|++| | +||+.|.++|+.+|++|++| -.||.+||||+|+|+|......
T Consensus 425 IKNGMfV~~A~klCPqL~~l--P-----Y~FE~Ykevs~tlYetlasytl~I~aVSCDEa~vd~s~~~~~~--------- 488 (1016)
T KOG2093|consen 425 IKNGMFVRHAKKLCPQLVIL--P-----YDFEAYKEVSETLYETLASYTLNIEAVSCDEAFVDVSDLSDEE--------- 488 (1016)
T ss_pred cccceeHHHHHHhCcccEee--c-----ccHHHHHHHHHHHHHHHHhhccceeeecchhhhhhhhhhhhhh---------
Confidence 89999999999999999987 7 99999999999999999999 4799999999999999876321
Q ss_pred chhhHHHhhhhhccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHhhCCceeEEecCCHHHHHHHh
Q 006108 81 DEVDEEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLAS 160 (661)
Q Consensus 81 ~~~~~e~~~s~l~g~~~~~g~d~~~~v~~w~~~~~~~~~d~ll~~~~~lA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS 160 (661)
.. .++.+|..||++|++.|||+||||||.|++||+||+
T Consensus 489 -------------~~-----------------------------tp~~la~~IRqEI~e~TgC~aS~Gig~t~LLARlAT 526 (1016)
T KOG2093|consen 489 -------------NE-----------------------------TPAVLAEHIRQEILEKTGCPASAGIGGTMLLARLAT 526 (1016)
T ss_pred -------------cc-----------------------------CHHHHHHHHHHHHHhccCCceeeccchHHHHHHHHH
Confidence 00 136789999999999999999999999999999999
Q ss_pred cCCCCCcccccCcccHHHhcccCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCcCcHHHHHHHHhCCCC
Q 006108 161 GMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISG 240 (661)
Q Consensus 161 ~~~KP~G~~vl~~~~v~~fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~~~G~~L~~~arGiD~ 240 (661)
++||||||+++.++.+.+||.+++|.+|||||..+..+|. .+||+|||||+..+...|++.||++.|..+|+.|||+|+
T Consensus 527 r~AKP~Gq~~l~a~~veeFis~~~v~~LPGVG~sm~~kL~-s~~i~tCgdLq~~T~~kl~k~~G~Klgq~i~~~CrG~Dd 605 (1016)
T KOG2093|consen 527 RVAKPNGQFYLSAEKVEEFISQLKVDDLPGVGSSMKSKLV-SQFIQTCGDLQLITLIKLRKVFGPKLGQKIYRGCRGIDD 605 (1016)
T ss_pred hhcCCCceeeecHHHHHHHhhhcccccCCCccHHHHHHHH-HhccchhHHHHHHHHHHHHhhhcccHHHHHHHhcCCCcC
Confidence 9999999999999999999999999999999999999997 999999999999999999999999999999999999999
Q ss_pred CcccccCCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccC------CCCCCC
Q 006108 241 EEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKS------SDSDSR 314 (661)
Q Consensus 241 ~pV~~~~~~KSIs~e~tF~~~~~i~~~eel~~~L~~L~eeL~~RLr~~~~~~~~~artLtL~lr~~~~------~~~~s~ 314 (661)
+|+.....+||++.+.+|+ ..+++..++..+|..++++|.+||.+- ++.++.++|++..... ..|.+|
T Consensus 606 ~P~~~~~~RKSvS~dIN~G--IRFtn~~ev~~fl~~~~eEl~rkL~ei----~k~~~sitLKlMvR~~~APietaK~mGh 679 (1016)
T KOG2093|consen 606 DPRSIEQVRKSVSADINYG--IRFTNIKEVEQFLCLLSEELRRKLLEI----SKTASSITLKLMVRTAKAPIETAKYMGH 679 (1016)
T ss_pred ChHHHhhhhcceeeeeecc--eeeccHHHHHHHHHHHHHHHHHHHHHh----hccccchhHHHHhhcCCCCCccccccce
Confidence 9988777899999999999 789999999999999999999999874 8899999999853221 223333
Q ss_pred C--CcCcceeeCCCcchh---hHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEcc-CCcccc--cccccccc
Q 006108 315 K--KFPSKSCPLRYGTAK---IQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSAS-KIVPVL--SGTCSIMK 386 (661)
Q Consensus 315 ~--~~~srs~~L~~~t~~---i~~da~~L~~aal~l~~~~~~~~l~~~~~~g~~ir~lgVsls-~L~~~~--~~~~sq~~ 386 (661)
+ ..+++++.|.++|+. |+..+..||+.+ -.....+|++||.+. +|.+.. .....+..
T Consensus 680 GiCD~~~rs~~l~~~Td~~~iItt~~~~L~~t~---------------~~~~~elRG~gi~~ntkL~~~~~~~~~~~l~e 744 (1016)
T KOG2093|consen 680 GICDDFVRSSKLREPTDCNRIITTEVLRLYETN---------------SEPPSELRGLGIHSNTKLMDVLENLPPELLSE 744 (1016)
T ss_pred eeccchhhhhhccCccccccchHHHHHHHHHhc---------------CCChHHhccchhhccccccccccCCcHHHHHh
Confidence 2 346899999999873 444444554443 134557899999995 777743 22334445
Q ss_pred ccc
Q 006108 387 YFN 389 (661)
Q Consensus 387 lF~ 389 (661)
+|+
T Consensus 745 ~Fg 747 (1016)
T KOG2093|consen 745 MFG 747 (1016)
T ss_pred hcc
Confidence 554
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=100.00 E-value=4.1e-42 Score=366.52 Aligned_cols=280 Identities=20% Similarity=0.156 Sum_probs=237.2
Q ss_pred CCCCCcHHHHHHhCCCcEEEeccccCCCCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEEcCchhhhhhhCCCCCCc
Q 006108 2 VVSSMRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESL 80 (661)
Q Consensus 2 Vk~GMp~~eAkklCP~L~iV~VP~~~~k~d~~~Yr~~S~~V~~iL~~~-~~VE~~SIDEayLDlT~~~~~~L~~~~~~~l 80 (661)
||+|||+++|+++||+++++ | +|++.|.++|++|++++.+| |.||.+||||+|||+|+..
T Consensus 48 V~~Gm~~~~A~~lcP~l~~~--~-----~~~~~y~~~s~~i~~~l~~~s~~ve~~s~de~~ldvs~~~------------ 108 (335)
T cd03468 48 VRPGMPLAEALALCPNLQVV--E-----YDPEADARALQELALWLLRFTPLVALDGPDGLLLDVTGCL------------ 108 (335)
T ss_pred CCCCCcHHHHHHhCCCCeee--c-----CChHHHHHHHHHHHHHHHhcCCccccCCCCeEEEEcccch------------
Confidence 89999999999999999887 4 89999999999999999998 8999999999999999864
Q ss_pred chhhHHHhhhhhccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHhhCCceeEEecCCHHHHHHHh
Q 006108 81 DEVDEEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLAS 160 (661)
Q Consensus 81 ~~~~~e~~~s~l~g~~~~~g~d~~~~v~~w~~~~~~~~~d~ll~~~~~lA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS 160 (661)
++||. ...++..|++.|. ++|++||||||+||++||||+
T Consensus 109 ----------~~~~~------------------------------~~~~a~~i~~~~~-~~gl~~siGia~n~~~Aklas 147 (335)
T cd03468 109 ----------HLFGG------------------------------EDALAASLRAALA-TLGLSARAGIADTPGAAWLLA 147 (335)
T ss_pred ----------hhcCC------------------------------HHHHHHHHHHHHH-HcCCeEEEEecCCHHHHHHHh
Confidence 22321 2467899999995 789999999999999999999
Q ss_pred cCCCCCcccccCcccHHH-hcccCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCcCcHHHHHHHHhCCC
Q 006108 161 GMNKPAQQTTVPFSSVKG-LLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGIS 239 (661)
Q Consensus 161 ~~~KP~G~~vl~~~~v~~-fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~~~G~~L~~~arGiD 239 (661)
+++||+|++.+....... ||+++|+ ++||||+++.++|. ++||+|++||++++...|.++||. .|.++|+.++|+|
T Consensus 148 ~~~kp~~~~~~~~~~~~~~~l~~lp~-~~~gig~~~~~~L~-~~Gi~t~~dl~~~~~~~l~~rfG~-~~~~l~~~~~G~d 224 (335)
T cd03468 148 RAGGGRGVLRREALAAALVLLAPLPV-AALRLPPETVELLA-RLGLRTLGDLAALPRAELARRFGL-ALLLRLDQAYGRD 224 (335)
T ss_pred ccCCCCccCCchHHHHHhhccCCCCh-hHhCCCHHHHHHHH-HhCcccHHHHHhCChHHHHhhcCH-HHHHHHHHHCCCC
Confidence 999999998877666554 8999999 59999999999997 999999999999999999999998 5999999999999
Q ss_pred CCcc--cccCCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCCCCCCCc
Q 006108 240 GEEV--QARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKF 317 (661)
Q Consensus 240 ~~pV--~~~~~~KSIs~e~tF~~~~~i~~~eel~~~L~~L~eeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~~~ 317 (661)
+.++ .....+++++.+.+|. .+..+.+ ...+..|+++++.||+.+ +..+++|+|++++.+ +. .
T Consensus 225 ~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~--~~~l~~l~~~l~~~L~~~----~~~~~~l~l~l~~~~---~~----~ 289 (335)
T cd03468 225 PEPLLFSPPPPAFDFRLELQLE--EPIARGL--LFPLRRLLEQLCAFLALR----GLGARRLSLTLFRED---GR----V 289 (335)
T ss_pred CCCCCCCCCCCChhhhhhcCCC--CCcchhH--HHHHHHHHHHHHHHHHHc----CCeeeEEEEEEEEEC---Cc----e
Confidence 9999 4455679999999998 4555554 889999999999999984 999999999998743 22 2
Q ss_pred CcceeeCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCC---cceeEEEEEcc
Q 006108 318 PSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSG---WRITALSVSAS 372 (661)
Q Consensus 318 ~srs~~L~~~t~~i~~da~~L~~aal~l~~~~~~~~l~~~~~~g---~~ir~lgVsls 372 (661)
.+.+.++..+++ +...|++.+..+|.+. ..+ .+++.++|++.
T Consensus 290 ~~~~~~~~~~~~----~~~~l~~l~~~~l~~~---------~~~~~~~~v~~~~v~~~ 334 (335)
T cd03468 290 TRVLVGLARPSR----DDLPLLRLLRERLERL---------ALPRGIAPVRLLALTAE 334 (335)
T ss_pred EEEEEeccCCcc----CHHHHHHHHHhhhhcc---------CCCCCeeeEEEEEeecc
Confidence 356677777775 4445776666666532 234 67999998764
No 23
>PF00817 IMS: impB/mucB/samB family; InterPro: IPR001126 In Escherichia coli, UV and many chemicals appear to cause mutagenesis by a process of translesion synthesis that requires DNA polymerase III and the SOS-regulated proteins UmuD, UmuC and RecA. This machinery allows the replication to continue through DNA lesion, and therefore avoid lethal interruption of DNA replication after DNA damage []. UmuC is a well conserved protein in prokaryotes, with a homologue in yeast species. Proteins currently known to belong to this family are listed below: E. coli MucB protein. Plasmid-born analogue of the UmuC protein. Saccharomyces cerevisiae (Baker's yeast) Rev1 protein. Homologue of UmuC also required for normal induction of mutations by physical and chemical agents. Salmonella typhimurium ImpB protein. Plasmid-born analogue of the UmuC protein. Bacterial UmuC protein. E. coli DNA-damage-inducible protein P (DinP). S. typhimurium SamB homologue of UmuC plasmid associated. ; GO: 0003684 damaged DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006281 DNA repair; PDB: 3BJY_A 2AQ4_A 3OSP_A 4DL7_A 4DL6_A 3TQ1_A 3MR2_A 4EEY_A 3MR3_A 4DL4_A ....
Probab=99.82 E-value=6.7e-20 Score=174.74 Aligned_cols=101 Identities=38% Similarity=0.529 Sum_probs=88.9
Q ss_pred CCCCCcHHHHHHhCCCcEEEeccccCCCCChHHHHHHHHHHHHHHhhc-C-CeEEeccceEEEEcCchhhhhhhCCCCCC
Q 006108 2 VVSSMRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-G-RCERASIDEVYLDLTDAAEAMLAETPPES 79 (661)
Q Consensus 2 Vk~GMp~~eAkklCP~L~iV~VP~~~~k~d~~~Yr~~S~~V~~iL~~~-~-~VE~~SIDEayLDlT~~~~~~L~~~~~~~ 79 (661)
|++||++.+|+++||++++++ +|++.|+++|++|+.++.+| + .||.+|+||+|||+|+...
T Consensus 47 V~~Gm~~~~A~~lcp~l~~~~-------~d~~~~~~~~~~l~~~l~~~~sp~ve~~s~de~~ldv~~~~~---------- 109 (149)
T PF00817_consen 47 VRPGMPLAEALALCPDLVVVP-------PDPERYREASERLAEILYRFSSPRVEVYSPDELFLDVTGSLR---------- 109 (149)
T ss_dssp STTTSBHHHHHHHSTTSEEEE-------EEHHHHHHHHHHHHHHHHTTTCSEEEEEETTEEEEEEHHHHH----------
T ss_pred cccchhhhhHhhhccceeecc-------ccHHHHHHHHHHHHHHHHhcccccceecccccccccCCcchh----------
Confidence 899999999999999998883 79999999999999999998 4 7999999999999999652
Q ss_pred cchhhHHHhhhhhccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHhhCCceeEEecCCHHHHHHH
Q 006108 80 LDEVDEEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLA 159 (661)
Q Consensus 80 l~~~~~e~~~s~l~g~~~~~g~d~~~~v~~w~~~~~~~~~d~ll~~~~~lA~~IR~~I~~etGlt~SiGIA~NKlLAKLA 159 (661)
+|| ....++++||++|++++||+||+|||+||++||||
T Consensus 110 ------------l~~------------------------------~~~~~~~~l~~~i~~~~gl~~s~Gia~~~~~Akla 147 (149)
T PF00817_consen 110 ------------LFG------------------------------GEEALARRLRQAIAEETGLTASIGIAPNPLLAKLA 147 (149)
T ss_dssp ------------HHH------------------------------HHHHHHHHHHHHHHHHHS--EEEEEESSHHHHHHH
T ss_pred ------------hcc------------------------------hHHHHHHHHHHHHHHHhCCEEEEEEeCCHHHHHHh
Confidence 232 12578999999999999999999999999999999
Q ss_pred hc
Q 006108 160 SG 161 (661)
Q Consensus 160 S~ 161 (661)
++
T Consensus 148 a~ 149 (149)
T PF00817_consen 148 AD 149 (149)
T ss_dssp HH
T ss_pred cC
Confidence 84
No 24
>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=99.33 E-value=3.1e-12 Score=116.98 Aligned_cols=125 Identities=31% Similarity=0.430 Sum_probs=89.9
Q ss_pred CCccc-ccCCCccccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCCCCCCCcC
Q 006108 240 GEEVQ-ARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFP 318 (661)
Q Consensus 240 ~~pV~-~~~~~KSIs~e~tF~~~~~i~~~eel~~~L~~L~eeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~~~~ 318 (661)
++||. +...+|||+++++|+ .++.+.+++..+|..|+++|+.||++ +++.|++|+|++++.++ . .....
T Consensus 1 ~~pV~~~~~~~ksi~~~~t~~--~~~~~~~~i~~~l~~l~~~l~~rL~~----~~~~~~~i~l~l~~~~~---~-~~~~~ 70 (127)
T PF11799_consen 1 DEPVQQPRPPPKSIGSERTFP--EPISDREEIEEWLRELAEELAERLRE----RGLAARTITLKLRYSDF---G-RCSSR 70 (127)
T ss_dssp ------SCSS-SEEEEEEEEC--EEESSHHHHHHHHHHHHHHHHHHHHH----CTEEEEEEEEEEEETTS---C-SCEEE
T ss_pred CCCCCCCCCCCCEEEEEEECC--CCCCCHHHHHHHHHHHHHHHHHHHHh----hCcCCceEEEEEEecCC---c-cccee
Confidence 46787 778899999999998 57999999999999999999999997 59999999999997542 2 11235
Q ss_pred cceeeCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEccCCc-ccccccccccccc
Q 006108 319 SKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIV-PVLSGTCSIMKYF 388 (661)
Q Consensus 319 srs~~L~~~t~~i~~da~~L~~aal~l~~~~~~~~l~~~~~~g~~ir~lgVsls~L~-~~~~~~~sq~~lF 388 (661)
+++++++.|++ +...|++++..+|.+.. ...+.+|++|||.+++|. +. ...|.+||
T Consensus 71 ~~~~~l~~p~~----~~~~l~~~~~~l~~~~~-------~~~~~~vr~igv~~~~l~~~~---~~~q~~lF 127 (127)
T PF11799_consen 71 SRSIRLPFPTN----DADELLKAARELLERLL-------YDPGFPVRLIGVSASDLIEPA---GQRQLDLF 127 (127)
T ss_dssp EEEEEECCCEH----CHHHHHHHHHHHHHHHH-------HHTTCGEEEEEEEEEEEEEC-------B----
T ss_pred eEEEeccCCcC----CHHHHHHHHHHHHHHHh-------cCCCCCEEEEEEEECCCcCCC---CCcccccC
Confidence 77888988886 45668888887774432 012678999999999999 44 57788887
No 25
>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=98.43 E-value=1e-07 Score=68.14 Aligned_cols=32 Identities=34% Similarity=0.513 Sum_probs=28.2
Q ss_pred cccHHHhcccCCCccccCCchHHHHHHHHhcCC
Q 006108 173 FSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGV 205 (661)
Q Consensus 173 ~~~v~~fL~~LPI~kLpGIG~k~~~rL~~~lGI 205 (661)
|+++.+||++|||+++||||++++++|. .+||
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 4688999999999999999999999997 9997
No 26
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=97.86 E-value=1.3e-05 Score=85.96 Aligned_cols=80 Identities=20% Similarity=0.218 Sum_probs=65.7
Q ss_pred hcccCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCc--CcHHHHHHHHhC---CC--CCcccccCCCcc
Q 006108 179 LLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF--NTGTWLWNIARG---IS--GEEVQARLLPKS 251 (661)
Q Consensus 179 fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~--~~G~~L~~~arG---iD--~~pV~~~~~~KS 251 (661)
.|.++||.++||||++++++|. ..||.|++||+.+++..|.+.+|. +.+..+++.++| .+ .+.+.....+++
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 4789999999999999999997 999999999999999999999995 368999999998 43 333333344577
Q ss_pred ccccccCC
Q 006108 252 HGSGKSFP 259 (661)
Q Consensus 252 Is~e~tF~ 259 (661)
++...|+.
T Consensus 81 ~~~~~Tg~ 88 (317)
T PRK04301 81 VGKITTGS 88 (317)
T ss_pred CCccCCCC
Confidence 77666654
No 27
>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=97.25 E-value=0.00035 Score=74.57 Aligned_cols=74 Identities=19% Similarity=0.189 Sum_probs=60.3
Q ss_pred CccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCcC--cHHHHHHHHh---CCC--CCcccccCCCcccccccc
Q 006108 185 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN--TGTWLWNIAR---GIS--GEEVQARLLPKSHGSGKS 257 (661)
Q Consensus 185 I~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~~--~G~~L~~~ar---GiD--~~pV~~~~~~KSIs~e~t 257 (661)
|.++||||++++++|. ..||.|++||+.++.+.|.+.+|.. .+..++..++ |.+ ...+.....+++++...|
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 5689999999999998 9999999999999999999999963 4888999888 877 444444344677777666
Q ss_pred CC
Q 006108 258 FP 259 (661)
Q Consensus 258 F~ 259 (661)
+.
T Consensus 80 g~ 81 (310)
T TIGR02236 80 GS 81 (310)
T ss_pred CC
Confidence 54
No 28
>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=96.86 E-value=0.00084 Score=54.54 Aligned_cols=50 Identities=28% Similarity=0.349 Sum_probs=42.0
Q ss_pred ccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHH--hCcCcHHHHHHHHh
Q 006108 186 KKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 236 (661)
Q Consensus 186 ~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~--FG~~~G~~L~~~ar 236 (661)
.+|+|||++++.+|. ..|+.|+.||+..+.+.|.+. +|.+.++.+...++
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 468999999999998 889999999999999999988 55556666666553
No 29
>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=96.15 E-value=0.0034 Score=55.75 Aligned_cols=41 Identities=20% Similarity=0.301 Sum_probs=35.5
Q ss_pred CCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCc
Q 006108 184 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF 225 (661)
Q Consensus 184 PI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~ 225 (661)
.+.+|||||+++++-|. .+||+++.||+..++..|..++-.
T Consensus 13 ~L~~iP~IG~a~a~DL~-~LGi~s~~~L~g~dP~~Ly~~lc~ 53 (93)
T PF11731_consen 13 DLTDIPNIGKATAEDLR-LLGIRSPADLKGRDPEELYERLCA 53 (93)
T ss_pred HHhcCCCccHHHHHHHH-HcCCCCHHHHhCCCHHHHHHHHHH
Confidence 35789999999999998 999999999999998877666543
No 30
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=94.80 E-value=0.044 Score=56.25 Aligned_cols=56 Identities=18% Similarity=0.262 Sum_probs=50.3
Q ss_pred CCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHH--hCcCcHHHHHHHHhCCCC
Q 006108 184 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIARGISG 240 (661)
Q Consensus 184 PI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~--FG~~~G~~L~~~arGiD~ 240 (661)
.|.+|+|||++.+.+|. ..|+.|+.+|...+.+.|.+. +|...+..++..+.+.+.
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 57789999999999998 899999999999999999999 787789999999886554
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=93.68 E-value=0.057 Score=42.99 Aligned_cols=27 Identities=26% Similarity=0.302 Sum_probs=20.9
Q ss_pred ccccCCchHHHHHHHHhcCCccHHHHhh
Q 006108 186 KKMKQLGGKLGTSLQNELGVTTVGDLLK 213 (661)
Q Consensus 186 ~kLpGIG~k~~~rL~~~lGI~TigDL~~ 213 (661)
..|||||+++++++. ..|++|+.||..
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 468999999999998 899999999975
No 32
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=92.26 E-value=0.16 Score=47.69 Aligned_cols=37 Identities=22% Similarity=0.441 Sum_probs=32.5
Q ss_pred CCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHH
Q 006108 184 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQE 221 (661)
Q Consensus 184 PI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~ 221 (661)
.|+.|-|||++++..|+ .+||+|..||+.++...+..
T Consensus 68 DLt~I~GIGPk~e~~Ln-~~GI~tfaQIAAwt~~di~~ 104 (133)
T COG3743 68 DLTRISGIGPKLEKVLN-ELGIFTFAQIAAWTRADIAW 104 (133)
T ss_pred cchhhcccCHHHHHHHH-HcCCccHHHHHhcCHHHHHH
Confidence 46778999999999997 99999999999998876544
No 33
>PF04994 TfoX_C: TfoX C-terminal domain; InterPro: IPR007077 This domain is found in a number of bacterial proteins including the TfoX gene product of Haemophilus influenzae. TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes []. This family corresponds to the C-terminal presumed domain of TfoX. The domain is found in association with the N-terminal domain in some, but not all members of this group, suggesting this is an autonomous and functionally unrelated domain. For example it is found associated with Q9JZR1 from SWISSPROT in IPR002125 from INTERPRO.; PDB: 3BQT_A 3MAB_A.
Probab=92.23 E-value=0.18 Score=43.83 Aligned_cols=32 Identities=28% Similarity=0.484 Sum_probs=24.8
Q ss_pred CCccccCCchHHHHHHHHhcCCccHHHHhhCCH
Q 006108 184 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSE 216 (661)
Q Consensus 184 PI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~ 216 (661)
.|+++|+||++++..|. +.||+|+.||..+..
T Consensus 4 ~l~~LpNig~~~e~~L~-~vGI~t~~~L~~~Ga 35 (81)
T PF04994_consen 4 RLKDLPNIGPKSERMLA-KVGIHTVEDLRELGA 35 (81)
T ss_dssp -GCGSTT--HHHHHHHH-HTT--SHHHHHHHHH
T ss_pred chhhCCCCCHHHHHHHH-HcCCCCHHHHHHhCH
Confidence 58899999999999997 999999999998754
No 34
>PRK02362 ski2-like helicase; Provisional
Probab=92.14 E-value=0.13 Score=61.48 Aligned_cols=55 Identities=15% Similarity=0.151 Sum_probs=49.7
Q ss_pred CCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCcCcHHHHHHHHhCC
Q 006108 183 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGI 238 (661)
Q Consensus 183 LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~~~G~~L~~~arGi 238 (661)
+|+..|||||++.+.+|. .+||+|+.||..+..+.|.+.||.+.++.++..++..
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 467789999999999998 8999999999999999999999998899888887744
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=91.84 E-value=0.19 Score=41.92 Aligned_cols=45 Identities=33% Similarity=0.478 Sum_probs=36.4
Q ss_pred HhcccCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhC
Q 006108 178 GLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYG 224 (661)
Q Consensus 178 ~fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG 224 (661)
..+...||.++ |+..++...|. +.||+|++||..++...|.+.=|
T Consensus 7 ~~~~~~~I~~L-~LS~Ra~n~L~-~~~I~tv~dL~~~s~~~L~~i~n 51 (66)
T PF03118_consen 7 EELLDTPIEDL-GLSVRAYNCLK-RAGIHTVGDLVKYSEEDLLKIKN 51 (66)
T ss_dssp HHHHCSBGGGS-TSBHHHHHHHH-CTT--BHHHHHCS-HHHHHTSTT
T ss_pred HHHhcCcHHHh-CCCHHHHHHHH-HhCCcCHHHHHhCCHHHHHhCCC
Confidence 45667899999 89999999997 99999999999999999887644
No 36
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=90.81 E-value=0.25 Score=46.04 Aligned_cols=54 Identities=17% Similarity=0.306 Sum_probs=44.4
Q ss_pred cCcccHHHhcccCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCc
Q 006108 171 VPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF 225 (661)
Q Consensus 171 l~~~~v~~fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~ 225 (661)
++...+..+...-.+..++|||+..+..|. ..||.|+.+|+..++..|...++.
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 345555666555566679999999999997 999999999999999999887764
No 37
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=89.66 E-value=0.27 Score=40.55 Aligned_cols=47 Identities=17% Similarity=0.314 Sum_probs=33.4
Q ss_pred ccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHH--hCcCcHHHHHHHHh
Q 006108 188 MKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 236 (661)
Q Consensus 188 LpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~--FG~~~G~~L~~~ar 236 (661)
|||||.++++.|.+.+| |+..|.+.+.+.|... +|+..++.++++.+
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 67999999999986666 8999999999999887 77766777766554
No 38
>PRK01172 ski2-like helicase; Provisional
Probab=87.57 E-value=0.68 Score=54.88 Aligned_cols=52 Identities=17% Similarity=0.279 Sum_probs=43.2
Q ss_pred CCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHH--hCcCcHHHHHHHH
Q 006108 183 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIA 235 (661)
Q Consensus 183 LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~--FG~~~G~~L~~~a 235 (661)
+|+..|||||+..+.+|. ..||+|+.||+.++.+.+.+. ||...+..++..+
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 588889999999999998 999999999999999999888 5544455555443
No 39
>COG2251 Predicted nuclease (RecB family) [General function prediction only]
Probab=87.52 E-value=0.66 Score=51.88 Aligned_cols=68 Identities=21% Similarity=0.097 Sum_probs=56.8
Q ss_pred CcccHHHhcccCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhC--cCcHHHHHHHHhCCCC
Q 006108 172 PFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYG--FNTGTWLWNIARGISG 240 (661)
Q Consensus 172 ~~~~v~~fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG--~~~G~~L~~~arGiD~ 240 (661)
.+.....++..-.|.-++||++.....|. .+||+|+.||++.+...+...+| ...+..+...++-...
T Consensus 214 ~p~C~~~a~e~~~L~Lv~Gi~~~r~~~l~-~~GI~Ti~~LA~~~~~~~~~~~ga~~~~~~~l~~qa~~~~e 283 (474)
T COG2251 214 EPQCESEALEEDDLSLVPGITPSRYDVLE-EVGITTIEDLADASLPILELVAGALTALAAQLVLQARARVE 283 (474)
T ss_pred chhhhHHHhhccceeccCCCCHHHHHHHH-HcCcchHHHHHhccccchhhhhhhHHHHHHHHHHHHHhhcc
Confidence 45667788888899999999999999998 99999999999999888888888 4456677777776544
No 40
>PRK00254 ski2-like helicase; Provisional
Probab=86.90 E-value=0.63 Score=55.67 Aligned_cols=53 Identities=15% Similarity=0.271 Sum_probs=48.0
Q ss_pred CCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHH--hCcCcHHHHHHHHh
Q 006108 183 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 236 (661)
Q Consensus 183 LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~--FG~~~G~~L~~~ar 236 (661)
+|+..|||||++.+.+|. ..|+.|+.||..++.+.|.+. +|.+.++.++..++
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 578889999999999998 999999999999999999998 77777888888766
No 41
>PRK07758 hypothetical protein; Provisional
Probab=83.91 E-value=2 Score=38.46 Aligned_cols=44 Identities=25% Similarity=0.321 Sum_probs=35.1
Q ss_pred ccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHH--hCcCcHHHHH
Q 006108 188 MKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLW 232 (661)
Q Consensus 188 LpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~--FG~~~G~~L~ 232 (661)
+++++-+...-|. +.||.|++||..++.++|.++ ||++....|.
T Consensus 39 ~~~LSvRA~N~Lk-~AGI~TL~dLv~~te~ELl~iknlGkKSL~EIk 84 (95)
T PRK07758 39 LSLLSAPARRALE-HHGIHTVEELSKYSEKEILKLHGMGPASLPKLR 84 (95)
T ss_pred CccccHHHHHHHH-HcCCCcHHHHHcCCHHHHHHccCCCHHHHHHHH
Confidence 5688889999997 999999999999999998776 6654444333
No 42
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=82.00 E-value=2.6 Score=39.26 Aligned_cols=43 Identities=28% Similarity=0.458 Sum_probs=32.8
Q ss_pred cCCchHHHHHHHHhcCCccHHHHhhCCH-----HHHHHHhCcCcHHHHHH
Q 006108 189 KQLGGKLGTSLQNELGVTTVGDLLKFSE-----DKLQESYGFNTGTWLWN 233 (661)
Q Consensus 189 pGIG~k~~~rL~~~lGI~TigDL~~l~~-----~~L~~~FG~~~G~~L~~ 233 (661)
||||++.+.+|. ..||+|.+||..... ..|....|.. ...+..
T Consensus 1 pgi~~~~~~~L~-~~GI~t~~~Ll~~~~~~~~r~~La~~~~i~-~~~l~~ 48 (122)
T PF14229_consen 1 PGIGPKEAAKLK-AAGIKTTGDLLEAGDTPLGRKALAKKLGIS-ERNLLK 48 (122)
T ss_pred CCCCHHHHHHHH-HcCCCcHHHHHHcCCCHHHHHHHHHhcCCC-HHHHHH
Confidence 799999999997 999999999998743 2366667763 444443
No 43
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=79.89 E-value=2 Score=50.06 Aligned_cols=54 Identities=17% Similarity=0.172 Sum_probs=45.5
Q ss_pred cCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHH-hCcCcHHHHHHHHhC
Q 006108 182 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES-YGFNTGTWLWNIARG 237 (661)
Q Consensus 182 ~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~-FG~~~G~~L~~~arG 237 (661)
.-.+.+|||||++...+|.+.+ .++..+...+.++|.+. +|.+.++.++..++|
T Consensus 513 ~S~Ld~I~GiG~kr~~~Ll~~F--gs~~~ik~As~eeL~~vgi~~~~A~~I~~~l~~ 567 (567)
T PRK14667 513 KDILDKIKGIGEVKKEIIYRNF--KTLYDFLKADDEELKKLGIPPSVKQEVKKYLSG 567 (567)
T ss_pred cCccccCCCCCHHHHHHHHHHh--CCHHHHHhCCHHHHHHcCCCHHHHHHHHHHhcC
Confidence 4578899999999999997555 48999999999999998 556678888888876
No 44
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=79.34 E-value=1 Score=49.09 Aligned_cols=30 Identities=20% Similarity=0.255 Sum_probs=26.4
Q ss_pred CccccCCchHHHHHHHHhcCCccHHHHhhCC
Q 006108 185 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFS 215 (661)
Q Consensus 185 I~kLpGIG~k~~~rL~~~lGI~TigDL~~l~ 215 (661)
+.+|||||++++.+|. .+||+|+.||....
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 4569999999999998 59999999998753
No 45
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=78.08 E-value=2.2 Score=42.88 Aligned_cols=56 Identities=13% Similarity=0.091 Sum_probs=43.3
Q ss_pred CccccCCchHHHHHHHHhcCCccHH-HHhhCCHHHHHHH--hCcCcHHHHHHHHhCCCC
Q 006108 185 IKKMKQLGGKLGTSLQNELGVTTVG-DLLKFSEDKLQES--YGFNTGTWLWNIARGISG 240 (661)
Q Consensus 185 I~kLpGIG~k~~~rL~~~lGI~Tig-DL~~l~~~~L~~~--FG~~~G~~L~~~arGiD~ 240 (661)
+..++|||++++.++.+.+|..++. .+..-+...|.+. +|.+.+++++..+++...
T Consensus 75 L~~i~GIGpk~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~~~l~~~~~ 133 (192)
T PRK00116 75 LISVSGVGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELKDKLA 133 (192)
T ss_pred HhcCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHHhh
Confidence 4559999999999888678886654 3556678888887 677788989888887653
No 46
>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=77.21 E-value=1.9 Score=48.93 Aligned_cols=61 Identities=23% Similarity=0.244 Sum_probs=43.9
Q ss_pred cHHHhcccCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHH--HhCcCcHHHHHHHHh
Q 006108 175 SVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQE--SYGFNTGTWLWNIAR 236 (661)
Q Consensus 175 ~v~~fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~--~FG~~~G~~L~~~ar 236 (661)
........-+|..|+||+++...+|. ..||.|+.||+..+...|.. .++...+.+|...|+
T Consensus 199 C~~~~~~~~~lslv~gi~~~~~~~L~-~~GI~ti~~La~~~~~~l~~~~~~~~~~~~~l~~qA~ 261 (457)
T TIGR03491 199 CEAVAKEEGHLSLVPGIGPSRYRLLQ-ELGIHTLEDLAAADPNDLEDFGEQGLGVAEQLVQQAR 261 (457)
T ss_pred HHHHHHhcCCeeecCCCCHHHHHHHH-HcCCCcHHHHhcCCccccccccccCHHHHHHHHHHHH
Confidence 34445556789999999999999998 99999999999987544444 344334455444443
No 47
>PRK08609 hypothetical protein; Provisional
Probab=76.50 E-value=1.8 Score=50.63 Aligned_cols=29 Identities=38% Similarity=0.418 Sum_probs=26.3
Q ss_pred ccccCCchHHHHHHHHhcCCccHHHHhhC
Q 006108 186 KKMKQLGGKLGTSLQNELGVTTVGDLLKF 214 (661)
Q Consensus 186 ~kLpGIG~k~~~rL~~~lGI~TigDL~~l 214 (661)
.+|||||++++.+|.+.+||+|+.||...
T Consensus 91 ~~i~GiGpk~a~~l~~~lGi~tl~~L~~a 119 (570)
T PRK08609 91 LKLPGLGGKKIAKLYKELGVVDKESLKEA 119 (570)
T ss_pred hcCCCCCHHHHHHHHHHhCCCCHHHHHHH
Confidence 46999999999999877999999999974
No 48
>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=76.41 E-value=1.8 Score=46.65 Aligned_cols=29 Identities=34% Similarity=0.493 Sum_probs=26.2
Q ss_pred CccccCCchHHHHHHHHhcCCccHHHHhhC
Q 006108 185 IKKMKQLGGKLGTSLQNELGVTTVGDLLKF 214 (661)
Q Consensus 185 I~kLpGIG~k~~~rL~~~lGI~TigDL~~l 214 (661)
+.+|||||++++.+|. .+||+|+.||...
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 3469999999999999 9999999999874
No 49
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=76.16 E-value=2.7 Score=51.09 Aligned_cols=52 Identities=23% Similarity=0.314 Sum_probs=46.1
Q ss_pred CccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhC-cCcHHHHHHHHhCC
Q 006108 185 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYG-FNTGTWLWNIARGI 238 (661)
Q Consensus 185 I~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG-~~~G~~L~~~arGi 238 (661)
|..|||||++.+.+|. ..+.++.+|.+++.+.|....| .+.|..+|++++..
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 4468899999999997 4588999999999999999999 88899999988764
No 50
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=75.48 E-value=6.1 Score=42.00 Aligned_cols=61 Identities=16% Similarity=0.346 Sum_probs=50.5
Q ss_pred cCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCcC--cHHHHHHHHhCCCCCcc
Q 006108 182 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN--TGTWLWNIARGISGEEV 243 (661)
Q Consensus 182 ~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~~--~G~~L~~~arGiD~~pV 243 (661)
..|+..+|+||.....+|. ..||.+++||..++.+.+...+|.. .|..+++.++....-.|
T Consensus 150 ~~~L~Qlp~i~~~~~~~l~-~~~i~s~~~l~~~~~~~~~~ll~~~~~~~~~i~~~~~~~P~l~v 212 (312)
T smart00611 150 DSPLLQLPHLPEEILKRLE-KKKVLSLEDLLELEDEERGELLGLLDAEGERVYKVLSRLPKLNI 212 (312)
T ss_pred CCccccCCCCCHHHHHHHH-hCCCCCHHHHHhcCHHHHHHHHcCCHHHHHHHHHHHHhCCccee
Confidence 4688899999999999997 8999999999999999988887742 47778888776655444
No 51
>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=75.37 E-value=3.9 Score=43.41 Aligned_cols=60 Identities=23% Similarity=0.364 Sum_probs=43.4
Q ss_pred CCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCc--CcHHHHHHHHhCCCCCcc
Q 006108 183 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF--NTGTWLWNIARGISGEEV 243 (661)
Q Consensus 183 LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~--~~G~~L~~~arGiD~~pV 243 (661)
.|+..|||||.....+|. ..||.|++||.+++..++...++. ..|..+.+.++.+..-.+
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 578899999999999997 899999999999999999998873 347778888887654444
No 52
>PF14377 DUF4414: Domain of unknown function (DUF4414)
Probab=73.88 E-value=1.5 Score=40.00 Aligned_cols=21 Identities=38% Similarity=0.730 Sum_probs=18.4
Q ss_pred CCccccccCChHHHHHHHHhh
Q 006108 616 IDPSVIDELPKEIQDEIQAWL 636 (661)
Q Consensus 616 ~~~~~~~~~~~~~~~~~~~~~ 636 (661)
|||+|+.+||.+|+.||-.=.
T Consensus 1 iDp~fLaaLPeDiR~Evl~~~ 21 (108)
T PF14377_consen 1 IDPEFLAALPEDIREEVLAQQ 21 (108)
T ss_pred CCHHHHHHCCHHHHHHHHHHH
Confidence 899999999999999994433
No 53
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=73.80 E-value=4 Score=48.62 Aligned_cols=52 Identities=19% Similarity=0.261 Sum_probs=42.0
Q ss_pred CCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHH--HhCcCcHHHHHHHH
Q 006108 184 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQE--SYGFNTGTWLWNIA 235 (661)
Q Consensus 184 PI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~--~FG~~~G~~L~~~a 235 (661)
..-+|+|+|+++.++|.+..+|.++.||..+..+.|.. .||.+.++.|++..
T Consensus 446 ~al~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~ll~~I 499 (665)
T PRK07956 446 NAMDIDGLGEKIIEQLFEKGLIHDPADLFKLTAEDLLGLEGFGEKSAQNLLDAI 499 (665)
T ss_pred cccCCCCcCHHHHHHHHHcCCCCCHHHHHhcCHHHHhcCcCcchHHHHHHHHHH
Confidence 34568999999999999778899999999999888876 47776666665443
No 54
>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=73.55 E-value=2.9 Score=36.90 Aligned_cols=34 Identities=24% Similarity=0.399 Sum_probs=23.0
Q ss_pred hcccCCCccccCCchHHHHHHHHhcCCccHHHHhh
Q 006108 179 LLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLK 213 (661)
Q Consensus 179 fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~ 213 (661)
-|..-||++|+|||+.++.+|. ..|+..+..|..
T Consensus 15 PMGeK~V~~laGIG~~lg~~L~-~~GfdKAy~vLG 48 (89)
T PF02961_consen 15 PMGEKPVTELAGIGPVLGKRLE-EKGFDKAYVVLG 48 (89)
T ss_dssp --TT-BGGGSTT--HHHHHHHH-HTT--BHHHHHH
T ss_pred ccCCCCccccCCcCHHHHHHHH-HCCCcHHHHHhh
Confidence 3445689999999999999997 999998776653
No 55
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=72.08 E-value=5 Score=47.42 Aligned_cols=51 Identities=20% Similarity=0.285 Sum_probs=43.2
Q ss_pred CCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCcCcHHHHHHHH
Q 006108 183 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIA 235 (661)
Q Consensus 183 LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~~~G~~L~~~a 235 (661)
..+..|+|||++++..|...+| |+.+|...+.+.|.+.+|.+.++.++.+.
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 3567899999999999975555 88999999999999889988888887764
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=71.93 E-value=4.8 Score=47.87 Aligned_cols=53 Identities=25% Similarity=0.307 Sum_probs=42.6
Q ss_pred CCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHH--hCcCcHHHHHHHHh
Q 006108 184 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 236 (661)
Q Consensus 184 PI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~--FG~~~G~~L~~~ar 236 (661)
.--+|+|+|+++..+|.+..+|+++.||..+..+.|... ||.+.+..|++...
T Consensus 433 ~al~I~GLG~k~i~~L~~~g~I~~~~Dl~~L~~~~L~~L~GfG~Ksa~nIl~~Ie 487 (652)
T TIGR00575 433 NAMDIEGLGDKVIEQLFEKKLVRSVADLYALKKEDLLELEGFGEKSAQNLLNAIE 487 (652)
T ss_pred CccCCCCcCHHHHHHHHHcCCcCCHHHHHhcCHHHHhhccCccHHHHHHHHHHHH
Confidence 345689999999999996778999999999998888765 67766766665554
No 57
>PTZ00035 Rad51 protein; Provisional
Probab=71.72 E-value=5.8 Score=43.35 Aligned_cols=55 Identities=18% Similarity=0.177 Sum_probs=45.5
Q ss_pred CCCccc--cCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCcC--cHHHHHHHHhCC
Q 006108 183 LPIKKM--KQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN--TGTWLWNIARGI 238 (661)
Q Consensus 183 LPI~kL--pGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~~--~G~~L~~~arGi 238 (661)
++|.++ +||++....+|+ ..||+|+.||+..++..|.+..|.. .++.+...++-.
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 467778 789999999997 9999999999999999999999863 245666666654
No 58
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=71.44 E-value=5.3 Score=46.76 Aligned_cols=54 Identities=26% Similarity=0.390 Sum_probs=44.7
Q ss_pred cCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHH--hCcCcHHHHHHHHhC
Q 006108 182 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIARG 237 (661)
Q Consensus 182 ~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~--FG~~~G~~L~~~arG 237 (661)
...+.+|||||++...+|.+.+| ++..+...+.++|.+. ++.+.+..++..++-
T Consensus 513 ~s~L~~I~GiG~kr~~~LL~~Fg--s~~~I~~As~eeL~~v~gi~~~~A~~I~~~l~~ 568 (574)
T PRK14670 513 KLNYTKIKGIGEKKAKKILKSLG--TYKDILLLNEDEIAEKMKINIKMAKKIKKFAEK 568 (574)
T ss_pred ccccccCCCCCHHHHHHHHHHhC--CHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 45788999999999999975555 8999999999999998 565578888877653
No 59
>PF14377 DUF4414: Domain of unknown function (DUF4414)
Probab=71.33 E-value=2.5 Score=38.55 Aligned_cols=25 Identities=36% Similarity=0.627 Sum_probs=21.2
Q ss_pred cccCCccccccCChHHHHHHHHhhC
Q 006108 613 IEEIDPSVIDELPKEIQDEIQAWLR 637 (661)
Q Consensus 613 ~~~~~~~~~~~~~~~~~~~~~~~~~ 637 (661)
-.+|||.+++-||++||+||-+=.+
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 60
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=71.02 E-value=4.8 Score=47.90 Aligned_cols=51 Identities=14% Similarity=0.188 Sum_probs=42.5
Q ss_pred CCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHH--hCcCcHHHHHHHH
Q 006108 183 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIA 235 (661)
Q Consensus 183 LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~--FG~~~G~~L~~~a 235 (661)
-.+..+||||++...+|.+.+| ++.+|...+.+.|.+. +|.+.++.+++.+
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 4677899999999999987788 9999999999999887 6666677666654
No 61
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=70.96 E-value=5.6 Score=47.21 Aligned_cols=62 Identities=11% Similarity=0.201 Sum_probs=51.1
Q ss_pred cCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHH--hCcCcHHHHHHHHhCCCCCcccc
Q 006108 182 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIARGISGEEVQA 245 (661)
Q Consensus 182 ~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~--FG~~~G~~L~~~arGiD~~pV~~ 245 (661)
...+.+|||||++...+|.+.|| ++.+|...+.++|.+. +|...+..+++.+.--...||..
T Consensus 607 ~s~L~~IpGiG~kr~~~LL~~Fg--S~~~i~~As~eel~~v~gi~~~~A~~i~~~~~~~~~~~~~~ 670 (691)
T PRK14672 607 VLSFERLPHVGKVRAHRLLAHFG--SFRSLQSATPQDIATAIHIPLTQAHTILHAATRSTTAPVRE 670 (691)
T ss_pred ccccccCCCCCHHHHHHHHHHhc--CHHHHHhCCHHHHHhCCCCCHHHHHHHHHHhhcccccchhH
Confidence 45788999999999999975555 8999999999999998 67777888888887666667654
No 62
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=66.65 E-value=4.1 Score=48.60 Aligned_cols=31 Identities=39% Similarity=0.618 Sum_probs=28.5
Q ss_pred CCCccccCCchHHHHHHHHhcCCccHHHHhhC
Q 006108 183 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKF 214 (661)
Q Consensus 183 LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l 214 (661)
.||+.|.|||++.++.|. ++||.|+.||...
T Consensus 9 ~~~~~l~gvg~~~~~~l~-~lgi~t~~dll~~ 39 (681)
T PRK10917 9 APLTSLKGVGPKTAEKLA-KLGIHTVQDLLLH 39 (681)
T ss_pred CChhhcCCCCHHHHHHHH-HcCCCCHHHHhhc
Confidence 489999999999999997 9999999999864
No 63
>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=66.62 E-value=3.1 Score=29.41 Aligned_cols=16 Identities=19% Similarity=0.393 Sum_probs=12.4
Q ss_pred CccccCCchHHHHHHH
Q 006108 185 IKKMKQLGGKLGTSLQ 200 (661)
Q Consensus 185 I~kLpGIG~k~~~rL~ 200 (661)
|.+|||||++++..+.
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 4568999999998875
No 64
>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=66.57 E-value=7 Score=42.30 Aligned_cols=36 Identities=25% Similarity=0.240 Sum_probs=33.7
Q ss_pred CCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCcC
Q 006108 190 QLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN 226 (661)
Q Consensus 190 GIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~~ 226 (661)
||++.+..+|. ..||.|+.||+..++..|.+.+|..
T Consensus 8 ~~~~~~~~~l~-~~g~~t~~~~~~~~~~~L~~i~~ls 43 (316)
T TIGR02239 8 GITAADIKKLQ-EAGLHTVESVAYAPKKQLLEIKGIS 43 (316)
T ss_pred CCCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHHhCCC
Confidence 59999999997 9999999999999999999999963
No 65
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=65.68 E-value=6.3 Score=40.65 Aligned_cols=37 Identities=24% Similarity=0.433 Sum_probs=32.8
Q ss_pred CCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHH
Q 006108 183 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQ 220 (661)
Q Consensus 183 LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~ 220 (661)
=.+.+|.|||+.++.+|. ..||.+..+|+.++.+.+.
T Consensus 158 DDL~~I~GIGp~~a~~L~-eaGi~tfaQIAa~t~a~ia 194 (221)
T PRK12278 158 DDLTKITGVGPALAKKLN-EAGVTTFAQIAALTDADIA 194 (221)
T ss_pred chheeccccChHHHHHHH-HcCCCCHHHhhCCChhhhh
Confidence 347889999999999997 9999999999999887554
No 66
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=64.70 E-value=6.6 Score=43.10 Aligned_cols=56 Identities=18% Similarity=0.229 Sum_probs=45.3
Q ss_pred cCCCccc--cCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCcC--cHHHHHHHHhCC
Q 006108 182 SLPIKKM--KQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN--TGTWLWNIARGI 238 (661)
Q Consensus 182 ~LPI~kL--pGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~~--~G~~L~~~arGi 238 (661)
..+|.++ .||++.+.++|+ ..||+|+.||+..++..|.+..|.. .+..+...++..
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 6678888 679999999997 9999999999999999999998853 244555555543
No 67
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=64.12 E-value=8.8 Score=45.94 Aligned_cols=53 Identities=19% Similarity=0.189 Sum_probs=41.8
Q ss_pred CCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHH--hCcCcHHHHHHHHh
Q 006108 184 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 236 (661)
Q Consensus 184 PI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~--FG~~~G~~L~~~ar 236 (661)
..=+|.|+|+++.++|.+..+|+++.||..+..+.|... ||.+.+..|++...
T Consensus 463 ~al~I~GLG~k~i~~L~~~g~V~~~~Dl~~L~~~~L~~l~g~g~Ksa~~Ll~~Ie 517 (689)
T PRK14351 463 DALDIEGLGEERVQQLVDAGLVESLADLYDLTVADLAELEGWGETSAENLLAELE 517 (689)
T ss_pred cccCCCCcCHHHHHHHHHcCCCCCHHHHHHcCHHHHhcCcCcchhHHHHHHHHHH
Confidence 345688999999999985556899999999999888765 78776766665543
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=63.84 E-value=13 Score=40.18 Aligned_cols=51 Identities=16% Similarity=0.169 Sum_probs=40.6
Q ss_pred ccc--cCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCcC--cHHHHHHHHhC
Q 006108 186 KKM--KQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN--TGTWLWNIARG 237 (661)
Q Consensus 186 ~kL--pGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~~--~G~~L~~~arG 237 (661)
.++ .|||..+.++|+ ..||.|+.||+..++..|.+..|.. .+..+.+.++-
T Consensus 2 ~~~~~~g~~~~~~~~L~-~~g~~t~~~~~~~~~~~L~~~~gls~~~~~~i~~~~~~ 56 (313)
T TIGR02238 2 DKLQAHGINAADIKKLK-SAGICTVNGVIMTTRRALCKIKGLSEAKVDKIKEAASK 56 (313)
T ss_pred chhhcCCCCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHh
Confidence 345 479999999997 9999999999999999999998853 24445555443
No 69
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=63.62 E-value=9.6 Score=45.10 Aligned_cols=54 Identities=11% Similarity=0.103 Sum_probs=46.1
Q ss_pred cCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCcCcHHHHHHHHhC
Q 006108 182 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARG 237 (661)
Q Consensus 182 ~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~~~G~~L~~~arG 237 (661)
.-.+.+|||||++...+|.+.+ .++..+...+.++|.+.+|.+.++.++..++.
T Consensus 551 ~S~L~~IpGIG~kr~~~LL~~F--gSi~~I~~As~eeL~~vi~~k~A~~I~~~l~~ 604 (624)
T PRK14669 551 TSELLEIPGVGAKTVQRLLKHF--GSLERVRAATETQLAAVVGRAAAEAIIAHFTT 604 (624)
T ss_pred HHHHhcCCCCCHHHHHHHHHHc--CCHHHHHhCCHHHHHHHhCHHHHHHHHHHhcC
Confidence 3467789999999999997555 48999999999999999998889999988864
No 70
>PRK14973 DNA topoisomerase I; Provisional
Probab=63.25 E-value=11 Score=46.52 Aligned_cols=51 Identities=22% Similarity=0.137 Sum_probs=41.7
Q ss_pred CccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCcC--cHHHHHHHHh
Q 006108 185 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN--TGTWLWNIAR 236 (661)
Q Consensus 185 I~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~~--~G~~L~~~ar 236 (661)
+..++|+|.++.++|. .-||.++.||++.+++.|.+.-|.. ....+...++
T Consensus 879 l~~vkg~ge~t~~~l~-~ag~~~~e~l~~~d~~~la~~~~i~~k~~~~~~~~~~ 931 (936)
T PRK14973 879 LLSVPGLGETTLEKLY-LAGVYDGDLLVSADPKKLAKVTGIDEKKLRNLQAYAK 931 (936)
T ss_pred hhhccCCCHHHHHHHH-HcCCCCHHHhccCCHHHHhhhcCCCHHHHHHHHHHHh
Confidence 6678999999999997 9999999999999999999987752 3444544444
No 71
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=62.93 E-value=5.7 Score=43.54 Aligned_cols=44 Identities=20% Similarity=0.332 Sum_probs=39.6
Q ss_pred cCCCccc--cCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCcC
Q 006108 182 SLPIKKM--KQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN 226 (661)
Q Consensus 182 ~LPI~kL--pGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~~ 226 (661)
..+|.+| .||+.....+|+ ..||.|+.||+..++..|.+.+|..
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 3478888 679999999997 9999999999999999999999974
No 72
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=62.06 E-value=6.1 Score=43.03 Aligned_cols=36 Identities=19% Similarity=0.373 Sum_probs=31.9
Q ss_pred CCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHH
Q 006108 184 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQ 220 (661)
Q Consensus 184 PI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~ 220 (661)
.+++|.|||++++++|. .+||++..|++.++.+.+.
T Consensus 264 dL~~I~GiGp~~e~~L~-~~Gi~~f~QiA~~t~~~~a 299 (326)
T PRK12311 264 DLKKLTGVSPQIEKKLN-DLGIFHFWQLAELDPDDAA 299 (326)
T ss_pred hhhhhccCChhhhhhhh-hcCCCCHHHhhCCChhhhh
Confidence 37789999999999997 9999999999999877543
No 73
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=56.64 E-value=7.7 Score=45.85 Aligned_cols=31 Identities=39% Similarity=0.734 Sum_probs=28.4
Q ss_pred CCCccccCCchHHHHHHHHhcCCccHHHHhhC
Q 006108 183 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKF 214 (661)
Q Consensus 183 LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l 214 (661)
.|+..+.|||++++++|. ++||+|+.||.-.
T Consensus 10 ~~l~~l~gig~~~a~~l~-~Lgi~tv~DLL~~ 40 (677)
T COG1200 10 VPLSTLKGIGPKTAEKLK-KLGIHTVQDLLLY 40 (677)
T ss_pred cchhhhcCcCHHHHHHHH-HcCCCcHHHHHHh
Confidence 489999999999999997 9999999999864
No 74
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=56.27 E-value=7.6 Score=39.51 Aligned_cols=43 Identities=19% Similarity=0.264 Sum_probs=30.7
Q ss_pred EecCCHHHHHHHhcCCCCCcccccCcccHHHhcccCC---CccccCCchHHHHHHH
Q 006108 148 GIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLP---IKKMKQLGGKLGTSLQ 200 (661)
Q Consensus 148 GIA~NKlLAKLAS~~~KP~G~~vl~~~~v~~fL~~LP---I~kLpGIG~k~~~rL~ 200 (661)
|||+---||=|++ ++++++...+..=. +.++||||+|++++|.
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 8998888887764 23444444444432 6788999999999985
No 75
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=55.34 E-value=7.7 Score=38.84 Aligned_cols=55 Identities=20% Similarity=0.250 Sum_probs=35.3
Q ss_pred HHHHHHhhCCceeEEecCCHHHHHHHhcCCCCCcccccCcccHHHhcccCC---CccccCCchHHHHHHH
Q 006108 134 RMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLP---IKKMKQLGGKLGTSLQ 200 (661)
Q Consensus 134 R~~I~~etGlt~SiGIA~NKlLAKLAS~~~KP~G~~vl~~~~v~~fL~~LP---I~kLpGIG~k~~~rL~ 200 (661)
-++++..+ +.+| ||||-.-||=|.+ ++++++...+..=. ++++||||+|+++|+-
T Consensus 68 Er~lF~~L-i~Vs-GIGpK~Al~ILs~----------~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIi 125 (183)
T PRK14601 68 EQKMFEML-LKVN-GIGANTAMAVCSS----------LDVNSFYKALSLGDESVLKKVPGIGPKSAKRII 125 (183)
T ss_pred HHHHHHHH-hccC-CccHHHHHHHHcC----------CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 34444444 4555 8888777776542 34555555544432 5778999999999985
No 76
>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=53.23 E-value=17 Score=39.12 Aligned_cols=54 Identities=26% Similarity=0.347 Sum_probs=42.2
Q ss_pred cccCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHH--hCcCcHHHHHHHH
Q 006108 180 LDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIA 235 (661)
Q Consensus 180 L~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~--FG~~~G~~L~~~a 235 (661)
+..++|.+| ++--+...-|. +.||.|++||..++.+.|.+. ||.+..+.+.+.+
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 456678887 57788889997 999999999999999987664 7776555555444
No 77
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=52.63 E-value=13 Score=41.50 Aligned_cols=36 Identities=22% Similarity=0.426 Sum_probs=32.0
Q ss_pred CCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHH
Q 006108 184 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQ 220 (661)
Q Consensus 184 PI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~ 220 (661)
.+++|.|||++++.+|. .+||++..+|+.++.+.+.
T Consensus 324 DLk~I~GIGpk~e~~Ln-~~Gi~~f~QIA~wt~~eia 359 (400)
T PRK12373 324 DLKLISGVGPKIEATLN-ELGIFTFDQVAAWKKAERA 359 (400)
T ss_pred hhhhccCCChHHHHHHH-hcCCCCHHHHhCCCHHHhH
Confidence 47789999999999997 9999999999999877544
No 78
>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=52.43 E-value=20 Score=27.32 Aligned_cols=33 Identities=36% Similarity=0.406 Sum_probs=28.6
Q ss_pred chHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCc
Q 006108 192 GGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF 225 (661)
Q Consensus 192 G~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~ 225 (661)
...++.+|. ..|+.|+.+|+.++++.|...-|.
T Consensus 2 ~~~~~~~L~-~~G~~s~e~la~~~~~eL~~i~g~ 34 (50)
T TIGR01954 2 DEEIAQLLV-EEGFTTVEDLAYVPIDELLSIEGF 34 (50)
T ss_pred CHHHHHHHH-HcCCCCHHHHHccCHHHHhcCCCC
Confidence 456788997 999999999999999999888664
No 79
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=51.94 E-value=9.1 Score=38.48 Aligned_cols=54 Identities=9% Similarity=0.135 Sum_probs=34.3
Q ss_pred HHHHHhhCCceeEEecCCHHHHHHHhcCCCCCcccccCcccHHHhcccC---CCccccCCchHHHHHHH
Q 006108 135 MQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSL---PIKKMKQLGGKLGTSLQ 200 (661)
Q Consensus 135 ~~I~~etGlt~SiGIA~NKlLAKLAS~~~KP~G~~vl~~~~v~~fL~~L---PI~kLpGIG~k~~~rL~ 200 (661)
+++++.+ +.++ ||||-.-||=|.+ ++++++...+..= -++++||||+|+++|+-
T Consensus 69 r~lF~~L-i~V~-GIGpK~AL~iLs~----------~~~~el~~aI~~~D~~~L~~vpGIGkKtAerIi 125 (188)
T PRK14606 69 KELFLSL-TKVS-RLGPKTALKIISN----------EDAETLVTMIASQDVEGLSKLPGISKKTAERIV 125 (188)
T ss_pred HHHHHHH-hccC-CccHHHHHHHHcC----------CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 3344444 3555 8888777776542 2444554444443 36778999999999985
No 80
>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=51.89 E-value=15 Score=37.04 Aligned_cols=51 Identities=20% Similarity=0.187 Sum_probs=37.1
Q ss_pred ccccCCchHHHHHHHHhcCCccHHHHhhC----CHHHHHHH--hCcCcHHHHHHHHhCCC
Q 006108 186 KKMKQLGGKLGTSLQNELGVTTVGDLLKF----SEDKLQES--YGFNTGTWLWNIARGIS 239 (661)
Q Consensus 186 ~kLpGIG~k~~~rL~~~lGI~TigDL~~l----~~~~L~~~--FG~~~G~~L~~~arGiD 239 (661)
-.++|||+|++..+ +++.+..+|... +...|.+. ||.++++++.-.+++.-
T Consensus 75 ~~V~GIGpK~Al~i---L~~~~~~el~~aI~~~d~~~L~~ipGiGkKtAerIileLk~k~ 131 (191)
T TIGR00084 75 IKVNGVGPKLALAI---LSNMSPEEFVYAIETEEVKALVKIPGVGKKTAERLLLELKGKL 131 (191)
T ss_pred hCCCCCCHHHHHHH---HhcCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHhhh
Confidence 46889999999776 677777777753 44667764 66777888887776653
No 81
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=51.27 E-value=18 Score=42.73 Aligned_cols=53 Identities=9% Similarity=0.170 Sum_probs=43.1
Q ss_pred cCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHH--hCcCcHHHHHHHHh
Q 006108 182 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 236 (661)
Q Consensus 182 ~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~--FG~~~G~~L~~~ar 236 (661)
...+..|||||+++..+|.+.+ .++..+...+.+.|.+. +|...+..++...+
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 4577899999999999997555 46999999999999988 77766777776654
No 82
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=50.44 E-value=20 Score=38.87 Aligned_cols=54 Identities=22% Similarity=0.341 Sum_probs=42.2
Q ss_pred cccCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHH--hCcCcHHHHHHHH
Q 006108 180 LDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIA 235 (661)
Q Consensus 180 L~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~--FG~~~G~~L~~~a 235 (661)
+..++|.+| ++--+...-|. +.||+|++||.+++.+.|.+. ||.+..+.+.+.+
T Consensus 246 ~l~~~I~~L-~LS~R~~n~Lk-~~~I~ti~dL~~~~~~~l~~~~n~G~ksl~ei~~~L 301 (310)
T PRK05182 246 ILLRPIEEL-ELSVRSYNCLK-RAGINTIGDLVQRTEEELLKTRNLGKKSLEEIKEKL 301 (310)
T ss_pred cccccHHHh-ccchHHHHHHH-HcCCcCHHHHHhCCHHHHhcCCCCChhhHHHHHHHH
Confidence 346788888 78889999997 999999999999999988765 6765555444433
No 83
>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=48.95 E-value=20 Score=42.69 Aligned_cols=33 Identities=21% Similarity=0.356 Sum_probs=16.6
Q ss_pred ccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHH
Q 006108 188 MKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES 222 (661)
Q Consensus 188 LpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~ 222 (661)
|||||.+++++|.+.+| ++.+|...+.+.|.+.
T Consensus 503 IpgVG~~~ak~L~~~f~--sl~~l~~As~eeL~~i 535 (652)
T TIGR00575 503 IRHVGEVTAKNLAKHFG--TLDKLKAASLEELLSV 535 (652)
T ss_pred CCCcCHHHHHHHHHHhC--CHHHHHhCCHHHHhcC
Confidence 35555555555543343 4555555555555444
No 84
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=47.69 E-value=22 Score=37.45 Aligned_cols=49 Identities=24% Similarity=0.375 Sum_probs=38.7
Q ss_pred ccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCc--CcHHHHHHHHh
Q 006108 186 KKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF--NTGTWLWNIAR 236 (661)
Q Consensus 186 ~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~--~~G~~L~~~ar 236 (661)
..+||||.+++.+|. .-..++++++.++...|.+.-|. +.+..++...+
T Consensus 185 ~s~pgig~~~a~~ll--~~fgS~~~~~tas~~eL~~v~gig~k~A~~I~~~~~ 235 (254)
T COG1948 185 ESIPGIGPKLAERLL--KKFGSVEDVLTASEEELMKVKGIGEKKAREIYRFLR 235 (254)
T ss_pred HcCCCccHHHHHHHH--HHhcCHHHHhhcCHHHHHHhcCccHHHHHHHHHHHh
Confidence 446699999999996 44559999999999999999886 45666666554
No 85
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=47.04 E-value=19 Score=36.25 Aligned_cols=53 Identities=13% Similarity=0.183 Sum_probs=38.5
Q ss_pred ccccCCchHHHHHHHHhcCCcc-HHHHhhCCHHHHHHHh--CcCcHHHHHHHHhCC
Q 006108 186 KKMKQLGGKLGTSLQNELGVTT-VGDLLKFSEDKLQESY--GFNTGTWLWNIARGI 238 (661)
Q Consensus 186 ~kLpGIG~k~~~rL~~~lGI~T-igDL~~l~~~~L~~~F--G~~~G~~L~~~arGi 238 (661)
-.++|||++++-.+...++... +..++.-+...|.+.- |.++++++.-.++|.
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 3588999999988876688777 4445566788888864 456778877666664
No 86
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=46.83 E-value=13 Score=25.07 Aligned_cols=16 Identities=19% Similarity=0.320 Sum_probs=14.0
Q ss_pred CccccCCchHHHHHHH
Q 006108 185 IKKMKQLGGKLGTSLQ 200 (661)
Q Consensus 185 I~kLpGIG~k~~~rL~ 200 (661)
+.+++|||++++.+|.
T Consensus 3 L~~i~GiG~k~A~~il 18 (26)
T smart00278 3 LLKVPGIGPKTAEKIL 18 (26)
T ss_pred hhhCCCCCHHHHHHHH
Confidence 4679999999999986
No 87
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=46.09 E-value=13 Score=37.52 Aligned_cols=55 Identities=15% Similarity=0.179 Sum_probs=34.7
Q ss_pred HHHHHHhhCCceeEEecCCHHHHHHHhcCCCCCcccccCcccHHHhcccCC---CccccCCchHHHHHHH
Q 006108 134 RMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLP---IKKMKQLGGKLGTSLQ 200 (661)
Q Consensus 134 R~~I~~etGlt~SiGIA~NKlLAKLAS~~~KP~G~~vl~~~~v~~fL~~LP---I~kLpGIG~k~~~rL~ 200 (661)
-+.++..+ +.++ ||||-.-||=|.+ ++++++...+..=. ++++||||+|+++|+-
T Consensus 68 Er~lF~~L-i~V~-GIGpK~Al~iLs~----------~~~~el~~aI~~~D~~~L~kvpGIGkKtAerIi 125 (195)
T PRK14604 68 QRQLFELL-IGVS-GVGPKAALNLLSS----------GTPDELQLAIAGGDVARLARVPGIGKKTAERIV 125 (195)
T ss_pred HHHHHHHH-hCcC-CcCHHHHHHHHcC----------CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 33444444 4555 8888777665542 24445555444432 6778999999999995
No 88
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=45.87 E-value=13 Score=37.79 Aligned_cols=57 Identities=21% Similarity=0.372 Sum_probs=35.8
Q ss_pred HHHHHHHHhhCCceeEEecCCHHHHHHHhcCCCCCcccccCcccHHHhcccC---CCccccCCchHHHHHHH
Q 006108 132 ELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSL---PIKKMKQLGGKLGTSLQ 200 (661)
Q Consensus 132 ~IR~~I~~etGlt~SiGIA~NKlLAKLAS~~~KP~G~~vl~~~~v~~fL~~L---PI~kLpGIG~k~~~rL~ 200 (661)
.--+++++.+ +.+| ||||-.-||=|.+ ++++++...+..= .+.++||||+|+++|+-
T Consensus 65 ~~Er~lF~~L-isVs-GIGPK~ALaILs~----------~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRII 124 (196)
T PRK13901 65 SSEREVFEEL-IGVD-GIGPRAALRVLSG----------IKYNEFRDAIDREDIELISKVKGIGNKMAGKIF 124 (196)
T ss_pred HHHHHHHHHH-hCcC-CcCHHHHHHHHcC----------CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 3444555555 4566 8888777765542 2344444444433 36778999999999985
No 89
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=45.53 E-value=14 Score=37.45 Aligned_cols=54 Identities=19% Similarity=0.262 Sum_probs=35.0
Q ss_pred HHHHHhhCCceeEEecCCHHHHHHHhcCCCCCcccccCcccHHHhcccC---CCccccCCchHHHHHHH
Q 006108 135 MQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSL---PIKKMKQLGGKLGTSLQ 200 (661)
Q Consensus 135 ~~I~~etGlt~SiGIA~NKlLAKLAS~~~KP~G~~vl~~~~v~~fL~~L---PI~kLpGIG~k~~~rL~ 200 (661)
+.++..+ +++| ||||-.-||=|.+ +.++++...+..= -++++||||+|+++|+-
T Consensus 68 r~lF~~L-~~V~-GIGpK~AL~iLs~----------~~~~~l~~aI~~~D~~~L~kvpGIGkKtAerIi 124 (197)
T PRK14603 68 LELFELL-LGVS-GVGPKLALALLSA----------LPPALLARALLEGDARLLTSASGVGKKLAERIA 124 (197)
T ss_pred HHHHHHH-hCcC-CcCHHHHHHHHcC----------CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 3444444 4555 8888777665542 2445555555543 26788999999999985
No 90
>PRK13766 Hef nuclease; Provisional
Probab=44.91 E-value=24 Score=42.60 Aligned_cols=50 Identities=22% Similarity=0.408 Sum_probs=41.3
Q ss_pred CccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHH--hCcCcHHHHHHHHh
Q 006108 185 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 236 (661)
Q Consensus 185 I~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~--FG~~~G~~L~~~ar 236 (661)
+..+||||++.+.+|.+.+| ++.++..++.+.|... +|.+.+..++...+
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 67789999999999976665 7999999999999987 77767777776544
No 91
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=44.14 E-value=28 Score=40.80 Aligned_cols=49 Identities=16% Similarity=0.291 Sum_probs=39.5
Q ss_pred ccccCCchHHHHHHHHhcC-CccHHHHhhCCHHHHHHH--hCcCcHHHHHHHH
Q 006108 186 KKMKQLGGKLGTSLQNELG-VTTVGDLLKFSEDKLQES--YGFNTGTWLWNIA 235 (661)
Q Consensus 186 ~kLpGIG~k~~~rL~~~lG-I~TigDL~~l~~~~L~~~--FG~~~G~~L~~~a 235 (661)
-+|-|+|.++.++|. ..| |+++.||..|+.+.|.+. ||.+.+..|++..
T Consensus 428 mdI~GlGe~~i~~L~-~~G~i~~~~Diy~L~~~~l~~l~gfgeks~~nll~aI 479 (562)
T PRK08097 428 LGLDGIGEGTWRALH-QTGLFEHLFSWLALTPEQLANTPGIGKARAEQLWHQF 479 (562)
T ss_pred cCCCCcCHHHHHHHH-HcCCcCCHHHHhcCCHHHHhcCcCccHHHHHHHHHHH
Confidence 346799999999998 677 699999999998888764 7877677666543
No 92
>PF08004 DUF1699: Protein of unknown function (DUF1699); InterPro: IPR012546 This family contains many archaeal proteins which have very conserved sequences.
Probab=43.85 E-value=40 Score=31.82 Aligned_cols=37 Identities=22% Similarity=0.385 Sum_probs=30.3
Q ss_pred CCcHHHHHHhCCCcEEEeccccCCCCChHHHHHHHHHHHHHHhh
Q 006108 5 SMRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILAR 48 (661)
Q Consensus 5 GMp~~eAkklCP~L~iV~VP~~~~k~d~~~Yr~~S~~V~~iL~~ 48 (661)
.+-++...+.||+|.++++| + ..|+.+|+.+-.+|.-
T Consensus 30 N~Dif~Lv~~CP~lk~iqiP-----~--SY~~t~Sksi~mfL~m 66 (131)
T PF08004_consen 30 NKDIFSLVERCPNLKAIQIP-----P--SYYKTLSKSIKMFLEM 66 (131)
T ss_pred chHHHHHHHhCCCCeEEeCC-----h--HHHHHHhHHHHHHHHh
Confidence 34467788999999999999 3 6789999998888874
No 93
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=43.82 E-value=15 Score=39.75 Aligned_cols=49 Identities=29% Similarity=0.410 Sum_probs=35.1
Q ss_pred CCCccccCCchHHHHHHHHhcCCccHHHHhhCCHH-HHHHH--hCcCcHHHH
Q 006108 183 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSED-KLQES--YGFNTGTWL 231 (661)
Q Consensus 183 LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~-~L~~~--FG~~~G~~L 231 (661)
.|+-++||+|++...+|.+.+||+++.+|+..... .++.. ||.+....+
T Consensus 93 ~~Ll~v~GlGpkKi~~Ly~elgi~~~e~l~~a~~~~~~~~l~GfG~kse~~i 144 (326)
T COG1796 93 EPLLKVPGLGPKKIVSLYKELGIKDLEELQEALENGKIRGLRGFGKKSEAKI 144 (326)
T ss_pred HHHhhCCCCCcHHHHHHHHHHCcccHHHHHHHHHhCCccccCCccchhHHHH
Confidence 46678999999888888889999999999975443 34444 444433333
No 94
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=42.10 E-value=17 Score=36.94 Aligned_cols=56 Identities=14% Similarity=0.176 Sum_probs=34.5
Q ss_pred HHHHHHHhhCCceeEEecCCHHHHHHHhcCCCCCcccccCcccHHHhcccC---CCccccCCchHHHHHHH
Q 006108 133 LRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSL---PIKKMKQLGGKLGTSLQ 200 (661)
Q Consensus 133 IR~~I~~etGlt~SiGIA~NKlLAKLAS~~~KP~G~~vl~~~~v~~fL~~L---PI~kLpGIG~k~~~rL~ 200 (661)
--+.+|..+ +.++ ||||-.-|+=|.+ ++++++...+..= -+.++||||+|+++|+-
T Consensus 68 ~Er~lF~~L-i~V~-GIGpK~Al~iLs~----------~~~~~l~~aI~~~D~~~L~~ipGIGkKtAerIi 126 (203)
T PRK14602 68 DERQTFIVL-ISIS-KVGAKTALAILSQ----------FRPDDLRRLVAEEDVAALTRVSGIGKKTAQHIF 126 (203)
T ss_pred HHHHHHHHH-hCCC-CcCHHHHHHHHhh----------CCHHHHHHHHHhCCHHHHhcCCCcCHHHHHHHH
Confidence 334444444 3555 8887766665542 2444444444433 26788999999999985
No 95
>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=41.29 E-value=34 Score=36.92 Aligned_cols=50 Identities=26% Similarity=0.543 Sum_probs=35.0
Q ss_pred CccccCCch--HHHHHHHHhcCCccHHHHhhC---CHHHHHHHhCcCcHHHHHHHH
Q 006108 185 IKKMKQLGG--KLGTSLQNELGVTTVGDLLKF---SEDKLQESYGFNTGTWLWNIA 235 (661)
Q Consensus 185 I~kLpGIG~--k~~~rL~~~lGI~TigDL~~l---~~~~L~~~FG~~~G~~L~~~a 235 (661)
|..|-.||+ ..-.+|. .-||.|++|++.+ ++..|+++||..+-...|...
T Consensus 164 VwRLe~Igk~G~~hk~L~-~~~I~tV~dFl~l~~~d~~~Lr~ilg~~ms~k~We~~ 218 (299)
T PF07887_consen 164 VWRLEKIGKDGAFHKRLK-KNGINTVEDFLKLLNKDPQKLREILGSGMSNKMWETT 218 (299)
T ss_pred hhhhhhccccCHHHHHHH-HcCCccHHHHHHHHhcCHHHHHHHHhcCCChhhHHHH
Confidence 444445665 3567886 8999999999874 778899999954444445433
No 96
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=40.56 E-value=8.1 Score=38.26 Aligned_cols=41 Identities=24% Similarity=0.500 Sum_probs=35.7
Q ss_pred ccccccCCccccccCChHHHHHHHHhhCCCCCCCcccCCcc
Q 006108 610 KLRIEEIDPSVIDELPKEIQDEIQAWLRPSKRPHRVKQGFT 650 (661)
Q Consensus 610 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 650 (661)
.|.|.||..-+|+-.-.||-++++.++||.|.|.--++--|
T Consensus 24 e~eiiei~a~lv~~id~~vvd~F~syVRP~~~P~Lt~~Cks 64 (210)
T COG5018 24 EFEIIEIEAGLVKSIDDEVVDTFSSYVRPKKFPKLTKRCKS 64 (210)
T ss_pred hceeeeehhhHHHHhhHHHHHHHHHhcCcccCchHHHHHHH
Confidence 46699999999999999999999999999999976665333
No 97
>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=40.39 E-value=14 Score=37.13 Aligned_cols=54 Identities=19% Similarity=0.263 Sum_probs=34.0
Q ss_pred HHHHHhhCCceeEEecCCHHHHHHHhcCCCCCcccccCcccHHHhccc---CCCccccCCchHHHHHHH
Q 006108 135 MQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDS---LPIKKMKQLGGKLGTSLQ 200 (661)
Q Consensus 135 ~~I~~etGlt~SiGIA~NKlLAKLAS~~~KP~G~~vl~~~~v~~fL~~---LPI~kLpGIG~k~~~rL~ 200 (661)
+.++..+ +.++ ||||-.-+|=|. .+.++++...+.. --|.++||||+|+++++.
T Consensus 68 r~lF~~L-~~V~-GIGpK~Al~iL~----------~~~~~el~~aI~~~d~~~L~~ipGiGkKtAerIi 124 (191)
T TIGR00084 68 RELFKEL-IKVN-GVGPKLALAILS----------NMSPEEFVYAIETEEVKALVKIPGVGKKTAERLL 124 (191)
T ss_pred HHHHHHH-hCCC-CCCHHHHHHHHh----------cCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHH
Confidence 3344444 3444 888876665533 2345555555554 347789999999999984
No 98
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=39.50 E-value=31 Score=40.60 Aligned_cols=50 Identities=14% Similarity=0.276 Sum_probs=38.8
Q ss_pred ccCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCc--CcHHHHHH
Q 006108 181 DSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF--NTGTWLWN 233 (661)
Q Consensus 181 ~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~--~~G~~L~~ 233 (661)
-.-++.+|+|||++...+|.+.+| |+.++...+.++|.+. |. ..++.++.
T Consensus 528 ~~s~Ld~I~GiG~~r~~~LL~~Fg--s~~~i~~As~eel~~v-gi~~~~a~~i~~ 579 (581)
T COG0322 528 LQSSLDDIPGIGPKRRKALLKHFG--SLKGIKSASVEELAKV-GISKKLAEKIYE 579 (581)
T ss_pred hcCccccCCCcCHHHHHHHHHHhh--CHHHHHhcCHHHHHHc-CCCHHHHHHHHh
Confidence 345788999999999999975554 8889999999999998 65 33454443
No 99
>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=39.46 E-value=28 Score=28.74 Aligned_cols=30 Identities=23% Similarity=0.325 Sum_probs=22.1
Q ss_pred Ccc-ccCCchHHHHHHHHh---c-CCccHHHHhhC
Q 006108 185 IKK-MKQLGGKLGTSLQNE---L-GVTTVGDLLKF 214 (661)
Q Consensus 185 I~k-LpGIG~k~~~rL~~~---l-GI~TigDL~~l 214 (661)
+.. +||||.+.+.+|.+. . ++.+..||..+
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 899999999888743 3 47777777664
No 100
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=39.31 E-value=26 Score=35.50 Aligned_cols=27 Identities=30% Similarity=0.373 Sum_probs=19.4
Q ss_pred CccccCCchHHHHHHHHhcCCccHHHHhhCCHHHH
Q 006108 185 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKL 219 (661)
Q Consensus 185 I~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L 219 (661)
+++|||||+|+++||. -.|...+.+.+
T Consensus 13 l~~LPGIG~KsA~RlA--------~~ll~~~~~~~ 39 (195)
T TIGR00615 13 LKKLPGIGPKSAQRLA--------FHLLKRDPSEV 39 (195)
T ss_pred HHHCCCCCHHHHHHHH--------HHHHcCCHHHH
Confidence 4678999999999995 34555555443
No 101
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=39.06 E-value=27 Score=37.88 Aligned_cols=30 Identities=20% Similarity=0.202 Sum_probs=26.2
Q ss_pred ccccCCchHHHHHHHHhcCCccHHHHhhCCH
Q 006108 186 KKMKQLGGKLGTSLQNELGVTTVGDLLKFSE 216 (661)
Q Consensus 186 ~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~ 216 (661)
+.++|||.+++++-. ..|++|+.|++.-+.
T Consensus 100 tnifGvG~ktA~~Wy-~~GfrTled~Rk~~~ 129 (353)
T KOG2534|consen 100 TNIFGVGLKTAEKWY-REGFRTLEDVRKKPD 129 (353)
T ss_pred HHHhccCHHHHHHHH-HhhhhHHHHHHhCHH
Confidence 568999999999997 999999999995443
No 102
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=38.16 E-value=44 Score=40.22 Aligned_cols=45 Identities=16% Similarity=0.273 Sum_probs=29.5
Q ss_pred ccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHH--hCcCcHHHHHHH
Q 006108 188 MKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNI 234 (661)
Q Consensus 188 LpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~--FG~~~G~~L~~~ 234 (661)
|||||.+++.+|...+ .++.+|..++.+.|.+. +|...+..++.+
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 5678888877776344 56777777777777666 565555555444
No 103
>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=38.12 E-value=27 Score=31.81 Aligned_cols=35 Identities=14% Similarity=0.392 Sum_probs=25.0
Q ss_pred CccccCCchHHHHHHHHhcCCccHHHHhhCCHHHH
Q 006108 185 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKL 219 (661)
Q Consensus 185 I~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L 219 (661)
+..|+|||+.++..+...+||..-.-+-.++.+++
T Consensus 17 Lt~IyGIG~~~A~~Ic~~lgi~~~~~~~~Ls~~~i 51 (107)
T PF00416_consen 17 LTKIYGIGRRKAKQICKKLGINPNKKVGDLSDEQI 51 (107)
T ss_dssp HTTSTTBCHHHHHHHHHHTTS-SSSBTTTSTHHHH
T ss_pred HhhhhccCHHHHHHHHHHcCCChhhhcccCCHHHH
Confidence 46799999999999888999965444444444443
No 104
>COG2199 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]
Probab=38.08 E-value=84 Score=30.09 Aligned_cols=28 Identities=25% Similarity=0.173 Sum_probs=18.0
Q ss_pred HHHHHHHhhc----CCeEEeccceEEEEcCch
Q 006108 40 SEVVSILARK----GRCERASIDEVYLDLTDA 67 (661)
Q Consensus 40 ~~V~~iL~~~----~~VE~~SIDEayLDlT~~ 67 (661)
..|..+|+.. ..+-+++=||.-+=+.+.
T Consensus 79 ~~va~~L~~~~~~~~~~~R~gGdEF~i~l~~~ 110 (181)
T COG2199 79 REVARRLRSNLREGDLVARLGGDEFAVLLPGT 110 (181)
T ss_pred HHHHHHHHHhcCCCCEEEEeccceeEEEeCCC
Confidence 4455555553 257888989977765553
No 105
>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=37.83 E-value=30 Score=31.99 Aligned_cols=38 Identities=11% Similarity=0.271 Sum_probs=28.0
Q ss_pred CCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHH
Q 006108 184 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQE 221 (661)
Q Consensus 184 PI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~ 221 (661)
.++.|.|||.+++..+...+||..-.-+-.++.+++.+
T Consensus 16 aL~~i~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~ 53 (113)
T TIGR03631 16 ALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNA 53 (113)
T ss_pred eeeeeecccHHHHHHHHHHhCcCcccccccCCHHHHHH
Confidence 46889999999999998899997544445555555443
No 106
>PRK00076 recR recombination protein RecR; Reviewed
Probab=37.80 E-value=28 Score=35.28 Aligned_cols=16 Identities=25% Similarity=0.478 Sum_probs=14.2
Q ss_pred CccccCCchHHHHHHH
Q 006108 185 IKKMKQLGGKLGTSLQ 200 (661)
Q Consensus 185 I~kLpGIG~k~~~rL~ 200 (661)
+++|||||+|+++||.
T Consensus 13 l~~LPGIG~KsA~Rla 28 (196)
T PRK00076 13 LRKLPGIGPKSAQRLA 28 (196)
T ss_pred HHHCCCCCHHHHHHHH
Confidence 4678999999999995
No 107
>PRK13844 recombination protein RecR; Provisional
Probab=37.33 E-value=29 Score=35.32 Aligned_cols=28 Identities=25% Similarity=0.284 Sum_probs=20.0
Q ss_pred CccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHH
Q 006108 185 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQ 220 (661)
Q Consensus 185 I~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~ 220 (661)
+++|||||+|+++||. -.|...+...+.
T Consensus 17 l~~LPGIG~KsA~Rla--------~~lL~~~~~~~~ 44 (200)
T PRK13844 17 LRKLPTIGKKSSQRLA--------LYLLDKSPETAI 44 (200)
T ss_pred HHHCCCCCHHHHHHHH--------HHHHcCCHHHHH
Confidence 4678999999999995 345555555443
No 108
>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=36.94 E-value=56 Score=26.27 Aligned_cols=47 Identities=28% Similarity=0.455 Sum_probs=39.6
Q ss_pred cCcccHHHhcccCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCcC
Q 006108 171 VPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN 226 (661)
Q Consensus 171 l~~~~v~~fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~~ 226 (661)
++++++..||..+ |+ ......+. ..||..+..|..++.+.|. .+|+.
T Consensus 4 w~~~~v~~WL~~~------gl-~~y~~~f~-~~~i~g~~~L~~l~~~~L~-~lGI~ 50 (66)
T PF07647_consen 4 WSPEDVAEWLKSL------GL-EQYADNFR-ENGIDGLEDLLQLTEEDLK-ELGIT 50 (66)
T ss_dssp HCHHHHHHHHHHT------TC-GGGHHHHH-HTTCSHHHHHTTSCHHHHH-HTTTT
T ss_pred CCHHHHHHHHHHC------Cc-HHHHHHHH-HcCCcHHHHHhhCCHHHHH-HcCCC
Confidence 4677888999877 55 57778886 9999999999999999997 78974
No 109
>PF07237 DUF1428: Protein of unknown function (DUF1428); InterPro: IPR009874 This family consists of several hypothetical bacterial and one archaeal sequence of around 120 residues in length. The function of this family is unknown.; PDB: 2OKQ_A.
Probab=36.19 E-value=62 Score=29.59 Aligned_cols=38 Identities=21% Similarity=0.398 Sum_probs=29.6
Q ss_pred EEEeccccCCCCChHHHHHHHHHHHHHHhhcCCeEEeccceEEEE
Q 006108 19 ELVQVPVARGKADLSSYRNAGSEVVSILARKGRCERASIDEVYLD 63 (661)
Q Consensus 19 ~iV~VP~~~~k~d~~~Yr~~S~~V~~iL~~~~~VE~~SIDEayLD 63 (661)
-++.|| ..+.+.|++++++.-.++.+|..++.. |||-|
T Consensus 6 fv~~VP----~~nk~aY~~~A~~a~~vf~e~GAl~~v---E~wgd 43 (103)
T PF07237_consen 6 FVLPVP----TANKDAYRAMAEKAAEVFKEHGALRVV---ECWGD 43 (103)
T ss_dssp EEEEEE----GGGHHHHHHHHHHHHHHHHHTT-SEEE---EEEEE
T ss_pred EEEECc----HHHHHHHHHHHHHHHHHHHHhCCEEEE---EeecC
Confidence 355678 489999999999999999999755544 66665
No 110
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=34.39 E-value=35 Score=33.35 Aligned_cols=40 Identities=18% Similarity=0.338 Sum_probs=28.9
Q ss_pred CCccccCCchHHHHHHHHhcCCc---cHHHHhhCCHHHHHHHh
Q 006108 184 PIKKMKQLGGKLGTSLQNELGVT---TVGDLLKFSEDKLQESY 223 (661)
Q Consensus 184 PI~kLpGIG~k~~~rL~~~lGI~---TigDL~~l~~~~L~~~F 223 (661)
.|+.|.|||..++..+...+||. +++||-.-....|...+
T Consensus 31 aLt~I~GIG~~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i 73 (154)
T PTZ00134 31 ALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEII 73 (154)
T ss_pred eecccccccHHHHHHHHHHcCcCcCCCcccCCHHHHHHHHHHH
Confidence 46789999999999998899995 55555544444454444
No 111
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=34.20 E-value=28 Score=34.94 Aligned_cols=55 Identities=15% Similarity=0.196 Sum_probs=31.9
Q ss_pred HHHHHHHhhCCceeEEecCCHHHHHHHhcCCCCCcccccCcccHHHhcccC---CCccccCCchHHHHHHH
Q 006108 133 LRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSL---PIKKMKQLGGKLGTSLQ 200 (661)
Q Consensus 133 IR~~I~~etGlt~SiGIA~NKlLAKLAS~~~KP~G~~vl~~~~v~~fL~~L---PI~kLpGIG~k~~~rL~ 200 (661)
--+.+++.+ +.++ ||||-.-||=|.+ +.++++...+..= -+ ++||||+|+++|+-
T Consensus 67 ~Er~lF~~L-isV~-GIGpK~Al~iLs~----------~~~~~l~~aI~~~D~~~L-~vpGIGkKtAerIi 124 (186)
T PRK14600 67 EEQDCLRML-VKVS-GVNYKTAMSILSK----------LTPEQLFSAIVNEDKAAL-KVNGIGEKLINRII 124 (186)
T ss_pred HHHHHHHHH-hCcC-CcCHHHHHHHHcc----------CCHHHHHHHHHcCCHhhe-ECCCCcHHHHHHHH
Confidence 334445554 4555 8887666665542 1233333333221 24 68999999999985
No 112
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=33.46 E-value=47 Score=36.34 Aligned_cols=55 Identities=20% Similarity=0.340 Sum_probs=42.8
Q ss_pred hcccCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHH--hCcCcHHHHHHHH
Q 006108 179 LLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIA 235 (661)
Q Consensus 179 fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~--FG~~~G~~L~~~a 235 (661)
.+..++|.+| .+--+...-|. +.||.|++||.+.+.+.|.+. ||.+....+...+
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 4566677777 46667778886 999999999999999887654 8887666666655
No 113
>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=33.18 E-value=90 Score=24.27 Aligned_cols=47 Identities=28% Similarity=0.400 Sum_probs=37.1
Q ss_pred cCcccHHHhcccCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCcCc
Q 006108 171 VPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNT 227 (661)
Q Consensus 171 l~~~~v~~fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~~~ 227 (661)
+..+++..||..+- + ......+. ..|| +..+|..++...|. .+|...
T Consensus 2 w~~~~V~~wL~~~~------~-~~y~~~f~-~~~i-~g~~L~~l~~~dL~-~lgi~~ 48 (63)
T cd00166 2 WSPEDVAEWLESLG------L-GQYADNFR-ENGI-DGDLLLLLTEEDLK-ELGITL 48 (63)
T ss_pred CCHHHHHHHHHHcC------h-HHHHHHHH-HcCC-CHHHHhHCCHHHHH-HcCCCC
Confidence 34567778887664 3 57788886 8999 99999999999998 789865
No 114
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=31.32 E-value=39 Score=39.77 Aligned_cols=50 Identities=16% Similarity=0.175 Sum_probs=39.1
Q ss_pred ccCCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHH--hCcCcHHHHH
Q 006108 181 DSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLW 232 (661)
Q Consensus 181 ~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~--FG~~~G~~L~ 232 (661)
..+.+..+||||++...+|.+.+ .++.++...+.+.|.+. +|...+..++
T Consensus 523 ~~~~L~~IpGIG~kr~~~LL~~F--GS~~~I~~As~eeL~~vpGi~~~~A~~I~ 574 (577)
T PRK14668 523 VSTVLDDVPGVGPETRKRLLRRF--GSVEGVREASVEDLRDVPGVGEKTAETIR 574 (577)
T ss_pred HHhHHhcCCCCCHHHHHHHHHHc--CCHHHHHhCCHHHHHhCCCCCHHHHHHHH
Confidence 35678899999999999997555 68999999999999888 4444455443
No 115
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=30.64 E-value=48 Score=31.10 Aligned_cols=37 Identities=8% Similarity=0.254 Sum_probs=27.3
Q ss_pred CCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHH
Q 006108 184 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQ 220 (661)
Q Consensus 184 PI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~ 220 (661)
.++.|.|||..++..+...+||..-.-+-.++.+++.
T Consensus 18 aL~~I~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~ 54 (122)
T PRK05179 18 ALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELD 54 (122)
T ss_pred eecccccccHHHHHHHHHHhCcCcccccccCCHHHHH
Confidence 4678999999999999889999754444444555443
No 116
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=30.24 E-value=48 Score=31.09 Aligned_cols=38 Identities=3% Similarity=0.114 Sum_probs=27.4
Q ss_pred CCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHH
Q 006108 183 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQ 220 (661)
Q Consensus 183 LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~ 220 (661)
..++.|.|||..++..+.+.+||.--.-+-.++.+++.
T Consensus 17 ~aLt~i~GIG~~~A~~ic~~lgi~~~~~~~~Lt~~qi~ 54 (122)
T CHL00137 17 YALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQIS 54 (122)
T ss_pred eeecccccccHHHHHHHHHHcCcCcCcCcccCCHHHHH
Confidence 34678999999999999889999644444444455443
No 117
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=30.19 E-value=62 Score=38.83 Aligned_cols=51 Identities=18% Similarity=0.034 Sum_probs=39.6
Q ss_pred CccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHH--hCcCcHHHHHHHH
Q 006108 185 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIA 235 (661)
Q Consensus 185 I~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~--FG~~~G~~L~~~a 235 (661)
--+|-|+|.++.++|.+.--|.++.||..++.+.|.+. ||.+.+..|++..
T Consensus 438 aldI~GlG~~~i~~L~~~G~i~~~~Dly~L~~~~l~~l~g~geksa~nl~~~I 490 (669)
T PRK14350 438 CMNIVGLSDKTIEFLFEKKFISSEIDLYTFNFDRLINLKGFKDKRINNLKRSI 490 (669)
T ss_pred cccccCcCHHHHHHHHHcCCcCCHHHHhhCCHHHHhhccCccHHHHHHHHHHH
Confidence 34688999999999984344789999999998888755 7766677676644
No 118
>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=29.59 E-value=52 Score=27.93 Aligned_cols=26 Identities=31% Similarity=0.480 Sum_probs=17.9
Q ss_pred CccccCCchHHHHHHHHhcCCccHHHHh
Q 006108 185 IKKMKQLGGKLGTSLQNELGVTTVGDLL 212 (661)
Q Consensus 185 I~kLpGIG~k~~~rL~~~lGI~TigDL~ 212 (661)
+.-+||||++++.+|...+| ++..+.
T Consensus 24 i~gv~giG~k~A~~ll~~~~--~~~~~~ 49 (75)
T cd00080 24 IPGVPGIGPKTALKLLKEYG--SLENLL 49 (75)
T ss_pred CCCCCcccHHHHHHHHHHhC--CHHHHH
Confidence 34689999999999874444 444443
No 119
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=27.81 E-value=77 Score=35.02 Aligned_cols=38 Identities=26% Similarity=0.389 Sum_probs=33.0
Q ss_pred CccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhC
Q 006108 185 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYG 224 (661)
Q Consensus 185 I~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG 224 (661)
+.++|+|++.++++|.+.|| ++..+...+.+.|.+.=|
T Consensus 289 Ls~IPrl~k~iAk~Ll~~FG--SL~~Il~As~eeL~~VeG 326 (352)
T PRK13482 289 LSKIPRLPSAVIENLVEHFG--SLQGLLAASIEDLDEVEG 326 (352)
T ss_pred HhcCCCCCHHHHHHHHHHcC--CHHHHHcCCHHHHhhCCC
Confidence 45689999999999988888 999999999999988644
No 120
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=27.36 E-value=71 Score=38.28 Aligned_cols=15 Identities=20% Similarity=0.377 Sum_probs=7.9
Q ss_pred CccccCCchHHHHHH
Q 006108 185 IKKMKQLGGKLGTSL 199 (661)
Q Consensus 185 I~kLpGIG~k~~~rL 199 (661)
|..++|+|.|++.+|
T Consensus 481 L~~l~gfG~Ksa~~l 495 (665)
T PRK07956 481 LLGLEGFGEKSAQNL 495 (665)
T ss_pred HhcCcCcchHHHHHH
Confidence 444555665555444
No 121
>PRK07945 hypothetical protein; Provisional
Probab=26.99 E-value=1.1e+02 Score=33.46 Aligned_cols=49 Identities=18% Similarity=0.186 Sum_probs=32.3
Q ss_pred CCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHHhCcCcHHHHHHHHhC
Q 006108 184 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARG 237 (661)
Q Consensus 184 PI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~FG~~~G~~L~~~arG 237 (661)
.+++|||||+.++.++.+-+--.++.-| +.|+...|+..|..|....+|
T Consensus 50 ~l~~~~giG~~~a~~i~e~~~tg~~~~l-----~~l~~~~~~~~g~~l~~~~~~ 98 (335)
T PRK07945 50 SLTSLPGIGPKTAKVIAQALAGRVPDYL-----AELRADAEPLGGGALRAALRG 98 (335)
T ss_pred CcccCCCcCHHHHHHHHHHHhcCCHHHH-----HHHHHhhcCCccHHHHHHHhh
Confidence 5778999999999998743332333322 445556666557777777776
No 122
>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=26.47 E-value=58 Score=31.48 Aligned_cols=31 Identities=23% Similarity=0.491 Sum_probs=24.2
Q ss_pred CCCccccCCchHHHHHHHHhcCCc---cHHHHhh
Q 006108 183 LPIKKMKQLGGKLGTSLQNELGVT---TVGDLLK 213 (661)
Q Consensus 183 LPI~kLpGIG~k~~~rL~~~lGI~---TigDL~~ 213 (661)
..|+.|.|||++++..+...+||. .++||-.
T Consensus 21 ~aLt~I~GIG~~~a~~I~~~lgi~~~~~~~~Lt~ 54 (144)
T TIGR03629 21 YALTGIKGIGRRFARAIARKLGVDPNAKLGYLDD 54 (144)
T ss_pred EeecceeccCHHHHHHHHHHcCcCCCCCcccCCH
Confidence 346789999999999998899996 4555443
No 123
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=26.22 E-value=57 Score=33.09 Aligned_cols=27 Identities=26% Similarity=0.369 Sum_probs=19.5
Q ss_pred CccccCCchHHHHHHHHhcCCccHHHHhhCCHHHH
Q 006108 185 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKL 219 (661)
Q Consensus 185 I~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L 219 (661)
+.+|||||+|++.|+. -.|.+.++..+
T Consensus 14 l~kLPGvG~KsA~R~A--------fhLL~~~~~~~ 40 (198)
T COG0353 14 LKKLPGVGPKSAQRLA--------FHLLQRDREDV 40 (198)
T ss_pred HhhCCCCChhHHHHHH--------HHHHccCHHHH
Confidence 4678999999999995 34555555444
No 124
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=26.02 E-value=79 Score=29.67 Aligned_cols=39 Identities=8% Similarity=0.294 Sum_probs=30.1
Q ss_pred CCCccccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHH
Q 006108 183 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQE 221 (661)
Q Consensus 183 LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~ 221 (661)
+.++.|.|||..++....+.+||.--.-+-+|+.+++.+
T Consensus 17 iALt~IyGIG~~~a~~I~~~~gi~~~~r~~eLteeei~~ 55 (121)
T COG0099 17 IALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIER 55 (121)
T ss_pred ehhhhhccccHHHHHHHHHHcCCCHhHhhccCCHHHHHH
Confidence 346779999999999888899997666666666666654
No 125
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=25.42 E-value=55 Score=31.15 Aligned_cols=53 Identities=21% Similarity=0.277 Sum_probs=36.5
Q ss_pred CHHHHHHHhcCCCCCcccccCcccHHHhcccCCCccccCCchHHHHHHHHhcC-CccHHHHhhCC
Q 006108 152 NKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELG-VTTVGDLLKFS 215 (661)
Q Consensus 152 NKlLAKLAS~~~KP~G~~vl~~~~v~~fL~~LPI~kLpGIG~k~~~rL~~~lG-I~TigDL~~l~ 215 (661)
|..=|||+ ... +..-++...+.+| ..+||||+.+++++- ..| ..++.||.+++
T Consensus 40 N~~d~kl~-~~~---~kIdiN~A~~~el------~~lpGigP~~A~~IV-~nGpf~sveDL~~V~ 93 (132)
T PRK02515 40 NVADAKLG-EFG---EKIDLNNSSVRAF------RQFPGMYPTLAGKIV-KNAPYDSVEDVLNLP 93 (132)
T ss_pred ChhhHHHH-hcC---CcccCCccCHHHH------HHCCCCCHHHHHHHH-HCCCCCCHHHHHcCC
Confidence 77778887 322 2223444555554 348899999999998 565 88999998764
No 126
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=25.01 E-value=66 Score=31.27 Aligned_cols=41 Identities=20% Similarity=0.418 Sum_probs=29.2
Q ss_pred CCCccccCCchHHHHHHHHhcCCc---cHHHHhhCCHHHHHHHh
Q 006108 183 LPIKKMKQLGGKLGTSLQNELGVT---TVGDLLKFSEDKLQESY 223 (661)
Q Consensus 183 LPI~kLpGIG~k~~~rL~~~lGI~---TigDL~~l~~~~L~~~F 223 (661)
..|+.|.|||.+++..+.+.+||. .++||-.--...|...+
T Consensus 25 ~aLt~IyGIG~~~a~~Ic~~lgi~~~~~~~~Lt~~qi~~l~~~i 68 (149)
T PRK04053 25 YALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEAL 68 (149)
T ss_pred eeccccccccHHHHHHHHHHcCcCCCCccCcCCHHHHHHHHHHH
Confidence 346789999999999998899996 55655544334444444
No 127
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=24.19 E-value=78 Score=32.02 Aligned_cols=51 Identities=18% Similarity=0.074 Sum_probs=36.5
Q ss_pred ccccCCchHHHHHHHHhcCCccHHHHhh----CCHHHHHHHhC--cCcHHHHHHHHhCCC
Q 006108 186 KKMKQLGGKLGTSLQNELGVTTVGDLLK----FSEDKLQESYG--FNTGTWLWNIARGIS 239 (661)
Q Consensus 186 ~kLpGIG~k~~~rL~~~lGI~TigDL~~----l~~~~L~~~FG--~~~G~~L~~~arGiD 239 (661)
..+.|||+|++-.+. +-.+..+|.. -+...|.+.-| +++++++.-.++|.-
T Consensus 76 i~V~GIGpK~Al~iL---s~~~~~el~~aI~~~D~~~L~kvpGIGkKtAerIilELk~K~ 132 (195)
T PRK14604 76 IGVSGVGPKAALNLL---SSGTPDELQLAIAGGDVARLARVPGIGKKTAERIVLELKGKI 132 (195)
T ss_pred hCcCCcCHHHHHHHH---cCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHHh
Confidence 357899999987764 4446666655 36677887744 567899988888753
No 128
>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=23.72 E-value=84 Score=38.00 Aligned_cols=37 Identities=19% Similarity=0.276 Sum_probs=25.8
Q ss_pred cHHHhcccCCCccccCCchHHHHHHHHhcCCccHHHHhhC
Q 006108 175 SVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKF 214 (661)
Q Consensus 175 ~v~~fL~~LPI~kLpGIG~k~~~rL~~~lGI~TigDL~~l 214 (661)
.+..||. =..++|||+++++++.+.||..++.-|.+-
T Consensus 79 ~i~~yL~---s~~~~GIG~~~A~~iv~~fg~~~~~~i~~~ 115 (720)
T TIGR01448 79 GIVAYLS---SRSIKGVGKKLAQRIVKTFGEAAFDVLDDD 115 (720)
T ss_pred HHHHHHh---cCCCCCcCHHHHHHHHHHhCHhHHHHHHhC
Confidence 4445665 234788888888888878888777666553
No 129
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=23.08 E-value=82 Score=31.89 Aligned_cols=50 Identities=16% Similarity=0.084 Sum_probs=36.1
Q ss_pred cccCCchHHHHHHHHhcCCccHHHHhh----CCHHHHHHHh--CcCcHHHHHHHHhCCC
Q 006108 187 KMKQLGGKLGTSLQNELGVTTVGDLLK----FSEDKLQESY--GFNTGTWLWNIARGIS 239 (661)
Q Consensus 187 kLpGIG~k~~~rL~~~lGI~TigDL~~----l~~~~L~~~F--G~~~G~~L~~~arGiD 239 (661)
.+.|||+|++-.+. +-.+..+|.+ -+...|.+.- |+++++++.-.++|.-
T Consensus 76 ~V~GIGpK~AL~iL---s~~~~~~l~~aI~~~D~~~L~kvpGIGkKtAerIilELkdK~ 131 (197)
T PRK14603 76 GVSGVGPKLALALL---SALPPALLARALLEGDARLLTSASGVGKKLAERIALELKGKV 131 (197)
T ss_pred CcCCcCHHHHHHHH---cCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHHh
Confidence 57899999986664 4446666654 3677788774 4577899988888763
No 130
>cd07556 Nucleotidyl_cyc_III Class III nucleotidyl cyclases. Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's). The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways.
Probab=22.98 E-value=5e+02 Score=22.52 Aligned_cols=30 Identities=13% Similarity=0.045 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHhhc-CCeEEeccceEEEEcC
Q 006108 36 RNAGSEVVSILARK-GRCERASIDEVYLDLT 65 (661)
Q Consensus 36 r~~S~~V~~iL~~~-~~VE~~SIDEayLDlT 65 (661)
+.+..++.+++..+ ..+-+++=|+..+=++
T Consensus 29 ~~~~~~l~~~~~~~~~~~~r~~~d~f~~l~~ 59 (133)
T cd07556 29 NELAGRFDSLIRRSGDLKIKTIGDEFMVVSG 59 (133)
T ss_pred HHHHHHHHHHHHHcCcEEEEeecceEEEEEC
Confidence 33455555555553 3466777787666544
No 131
>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=22.84 E-value=74 Score=29.55 Aligned_cols=29 Identities=17% Similarity=0.292 Sum_probs=20.4
Q ss_pred CccccCCchHHHHHHHHhc----CCccHHHHhh
Q 006108 185 IKKMKQLGGKLGTSLQNEL----GVTTVGDLLK 213 (661)
Q Consensus 185 I~kLpGIG~k~~~rL~~~l----GI~TigDL~~ 213 (661)
+..+||||++.+.++.+.. +..++.||..
T Consensus 70 L~~lpGIG~~~A~~Ii~~R~~~g~f~s~eeL~~ 102 (120)
T TIGR01259 70 LQALPGIGPAKAKAIIEYREENGAFKSVDDLTK 102 (120)
T ss_pred HhcCCCCCHHHHHHHHHHHHhcCCcCCHHHHHc
Confidence 3468999999999887433 3566666654
No 132
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=21.45 E-value=98 Score=31.07 Aligned_cols=50 Identities=14% Similarity=0.177 Sum_probs=35.6
Q ss_pred cccCCchHHHHHHHHhcCCccHHHHhhC----CHHHHHHHh--CcCcHHHHHHHHhCCC
Q 006108 187 KMKQLGGKLGTSLQNELGVTTVGDLLKF----SEDKLQESY--GFNTGTWLWNIARGIS 239 (661)
Q Consensus 187 kLpGIG~k~~~rL~~~lGI~TigDL~~l----~~~~L~~~F--G~~~G~~L~~~arGiD 239 (661)
.+.|||+|++-.+ +.-.++.+|..+ +...|.+.- |+++++++.-.++|.-
T Consensus 77 ~VsGIGpK~Al~I---Ls~~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIilELkdK~ 132 (183)
T PRK14601 77 KVNGIGANTAMAV---CSSLDVNSFYKALSLGDESVLKKVPGIGPKSAKRIIAELSDAK 132 (183)
T ss_pred ccCCccHHHHHHH---HcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHHh
Confidence 4779999998655 344566666653 567787764 4577899988888763
No 133
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=21.00 E-value=1e+02 Score=31.30 Aligned_cols=50 Identities=8% Similarity=0.078 Sum_probs=35.8
Q ss_pred cccCCchHHHHHHHHhcCCccHHHHhhC----CHHHHHHHh--CcCcHHHHHHHHhCCC
Q 006108 187 KMKQLGGKLGTSLQNELGVTTVGDLLKF----SEDKLQESY--GFNTGTWLWNIARGIS 239 (661)
Q Consensus 187 kLpGIG~k~~~rL~~~lGI~TigDL~~l----~~~~L~~~F--G~~~G~~L~~~arGiD 239 (661)
.+.|||+|++-.+. .-.++.+|+.+ +...|.+.- |+++++++.-.++|.=
T Consensus 76 sVsGIGPK~ALaIL---s~~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIIlELkdKl 131 (196)
T PRK13901 76 GVDGIGPRAALRVL---SGIKYNEFRDAIDREDIELISKVKGIGNKMAGKIFLKLRGKL 131 (196)
T ss_pred CcCCcCHHHHHHHH---cCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHhh
Confidence 47899999986654 44566666653 667787774 4577899988888753
No 134
>PF01367 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases. The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include: Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins []. 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [, ]. Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases []. Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair []. ; GO: 0003677 DNA binding, 0003824 catalytic activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B.
Probab=20.92 E-value=22 Score=32.26 Aligned_cols=33 Identities=21% Similarity=0.304 Sum_probs=19.2
Q ss_pred CcccHHHhcccC-----CCccccCCchHHHHHHHHhcC
Q 006108 172 PFSSVKGLLDSL-----PIKKMKQLGGKLGTSLQNELG 204 (661)
Q Consensus 172 ~~~~v~~fL~~L-----PI~kLpGIG~k~~~rL~~~lG 204 (661)
+|+.+.+|++=+ .|--++|||+|++.+|.+.+|
T Consensus 2 ~P~q~~D~~aL~GD~sDNIPGV~GIG~KtA~~LL~~yg 39 (101)
T PF01367_consen 2 PPEQIADYKALVGDSSDNIPGVPGIGPKTAAKLLQEYG 39 (101)
T ss_dssp -GHHHHHHCCCC-CCCCTB---TTSTCHCCCCCHHHHT
T ss_pred CHHHHHHHHHHcCCcccCCCCCCCCCHHHHHHHHHHcC
Confidence 455566665533 244467899999888765555
No 135
>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=20.87 E-value=59 Score=26.91 Aligned_cols=16 Identities=19% Similarity=0.542 Sum_probs=14.0
Q ss_pred CccccCCchHHHHHHH
Q 006108 185 IKKMKQLGGKLGTSLQ 200 (661)
Q Consensus 185 I~kLpGIG~k~~~rL~ 200 (661)
+..|||||++++.++.
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 4779999999999886
No 136
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=20.81 E-value=1.3e+02 Score=36.06 Aligned_cols=47 Identities=23% Similarity=0.349 Sum_probs=35.8
Q ss_pred cccCCchHHHHHHHHhcCCccHHHHhhCCHHHHHHH--hCcCcHHHHHH
Q 006108 187 KMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWN 233 (661)
Q Consensus 187 kLpGIG~k~~~rL~~~lGI~TigDL~~l~~~~L~~~--FG~~~G~~L~~ 233 (661)
+|-|+|.++.++|.+.--|+++.||..+..+.|... ||.+.+..|++
T Consensus 449 dI~GLG~k~i~~L~e~~lI~~~~Dly~Lt~~~l~~l~~~~~ks~~nLl~ 497 (667)
T COG0272 449 DIDGLGEKIIEQLFEKGLIKDIADLYTLTEEDLLSLEGFGEKSAENLLN 497 (667)
T ss_pred CCCCcCHHHHHHHHHcCccCCHHHHHhCCHHHHhhccchhhhHHHHHHH
Confidence 467999999999995566899999999998877654 44444554544
No 137
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=20.62 E-value=87 Score=31.84 Aligned_cols=51 Identities=14% Similarity=0.146 Sum_probs=35.8
Q ss_pred ccccCCchHHHHHHHHhcCCccHHHHhh----CCHHHHHHHh--CcCcHHHHHHHHhCCC
Q 006108 186 KKMKQLGGKLGTSLQNELGVTTVGDLLK----FSEDKLQESY--GFNTGTWLWNIARGIS 239 (661)
Q Consensus 186 ~kLpGIG~k~~~rL~~~lGI~TigDL~~----l~~~~L~~~F--G~~~G~~L~~~arGiD 239 (661)
..+.|||+|++-.+...+ +..+|.. -+...|.+.- |.++++++.-.++|.-
T Consensus 77 i~V~GIGpK~Al~iLs~~---~~~~l~~aI~~~D~~~L~~ipGIGkKtAerIilELkdK~ 133 (203)
T PRK14602 77 ISISKVGAKTALAILSQF---RPDDLRRLVAEEDVAALTRVSGIGKKTAQHIFLELKYKL 133 (203)
T ss_pred hCCCCcCHHHHHHHHhhC---CHHHHHHHHHhCCHHHHhcCCCcCHHHHHHHHHHHHHhh
Confidence 357899999987765334 4555544 3677787774 4567899988888763
No 138
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=20.59 E-value=85 Score=23.05 Aligned_cols=16 Identities=31% Similarity=0.366 Sum_probs=13.2
Q ss_pred CccccCCchHHHHHHH
Q 006108 185 IKKMKQLGGKLGTSLQ 200 (661)
Q Consensus 185 I~kLpGIG~k~~~rL~ 200 (661)
|.-+||||.+++.+|.
T Consensus 18 i~Gv~giG~ktA~~ll 33 (36)
T smart00279 18 IPGVKGIGPKTALKLL 33 (36)
T ss_pred CCCCCcccHHHHHHHH
Confidence 4468999999998885
Done!