Query 007824
Match_columns 588
No_of_seqs 362 out of 1939
Neff 7.1
Searched_HMMs 46136
Date Thu Mar 28 15:50:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007824.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007824hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK03609 umuC DNA polymerase V 100.0 7.2E-77 1.6E-81 644.8 33.4 388 13-488 1-422 (422)
2 KOG2095 DNA polymerase iota/DN 100.0 8.4E-74 1.8E-78 615.1 23.9 359 1-364 5-375 (656)
3 cd01701 PolY_Rev1 DNA polymera 100.0 4.9E-71 1.1E-75 595.3 35.6 348 8-436 43-404 (404)
4 cd01702 PolY_Pol_eta DNA Polym 100.0 8.4E-71 1.8E-75 583.3 30.8 338 15-435 1-359 (359)
5 PTZ00205 DNA polymerase kappa; 100.0 2.4E-70 5.2E-75 594.2 34.7 350 12-452 133-508 (571)
6 PRK01216 DNA polymerase IV; Va 100.0 5.9E-70 1.3E-74 574.7 35.5 336 13-439 2-342 (351)
7 PRK01810 DNA polymerase IV; Va 100.0 4E-69 8.7E-74 582.2 35.0 340 9-439 2-347 (407)
8 cd00424 PolY Y-family of DNA p 100.0 6.6E-69 1.4E-73 568.0 35.5 338 15-434 1-343 (343)
9 cd01703 PolY_Pol_iota DNA Poly 100.0 4.7E-69 1E-73 572.9 34.2 341 15-435 1-379 (379)
10 PRK14133 DNA polymerase IV; Pr 100.0 1.7E-68 3.7E-73 565.7 34.6 340 11-445 2-345 (347)
11 PRK03858 DNA polymerase IV; Va 100.0 2.2E-68 4.7E-73 574.7 35.7 337 11-439 3-343 (396)
12 PRK03103 DNA polymerase IV; Re 100.0 2.5E-68 5.4E-73 576.3 34.8 343 11-440 2-353 (409)
13 PRK02794 DNA polymerase IV; Pr 100.0 8.8E-68 1.9E-72 573.3 34.9 339 10-440 34-376 (419)
14 PRK03348 DNA polymerase IV; Pr 100.0 1E-67 2.2E-72 576.2 35.4 347 10-448 3-354 (454)
15 PRK03352 DNA polymerase IV; Va 100.0 1.8E-67 4E-72 557.7 34.6 337 9-439 2-345 (346)
16 cd03586 PolY_Pol_IV_kappa DNA 100.0 3.4E-66 7.3E-71 545.3 33.1 330 15-436 1-334 (334)
17 cd01700 PolY_Pol_V_umuC umuC s 100.0 1.3E-65 2.9E-70 543.1 30.4 334 15-435 1-344 (344)
18 PRK02406 DNA polymerase IV; Va 100.0 4.1E-65 8.9E-70 539.2 32.5 334 19-445 1-340 (343)
19 COG0389 DinP Nucleotidyltransf 100.0 3.8E-61 8.2E-66 509.3 34.6 342 12-440 1-348 (354)
20 KOG2094 Predicted DNA damage i 100.0 8.1E-61 1.8E-65 479.2 21.6 341 9-439 100-446 (490)
21 cd03468 PolY_like DNA Polymera 100.0 1.3E-52 2.8E-57 442.1 31.6 323 15-433 1-333 (335)
22 KOG2093 Translesion DNA polyme 100.0 1.1E-49 2.4E-54 435.0 18.7 358 13-450 372-746 (1016)
23 PF00817 IMS: impB/mucB/samB f 100.0 5.6E-36 1.2E-40 279.9 16.7 147 17-223 1-149 (149)
24 PF11799 IMS_C: impB/mucB/samB 99.2 4.7E-11 1E-15 107.5 9.5 118 302-443 1-123 (127)
25 PF13438 DUF4113: Domain of un 98.9 1.6E-10 3.5E-15 88.1 -0.2 43 444-487 2-52 (52)
26 PF11798 IMS_HHH: IMS family H 98.4 8.2E-08 1.8E-12 65.7 1.7 32 235-267 1-32 (32)
27 PRK04301 radA DNA repair and r 97.7 2.6E-05 5.6E-10 82.1 4.4 79 241-320 2-87 (317)
28 TIGR02236 recomb_radA DNA repa 97.0 0.0007 1.5E-08 70.9 5.2 73 247-320 1-80 (310)
29 PF14520 HHH_5: Helix-hairpin- 96.5 0.0018 3.9E-08 50.9 2.3 49 248-297 8-58 (60)
30 PF11731 Cdd1: Pathogenicity l 95.9 0.008 1.7E-07 51.4 3.6 40 246-286 13-52 (93)
31 PF08827 DUF1805: Domain of un 93.6 0.042 9.2E-07 42.7 1.8 27 50-76 32-58 (59)
32 PRK12766 50S ribosomal protein 93.4 0.11 2.5E-06 51.5 4.9 55 246-301 4-60 (232)
33 PF10391 DNA_pol_lambd_f: Fing 93.1 0.068 1.5E-06 40.8 2.3 27 248-275 5-31 (52)
34 COG3743 Uncharacterized conser 92.6 0.12 2.5E-06 46.8 3.3 37 246-283 68-104 (133)
35 PF03118 RNA_pol_A_CTD: Bacter 90.0 0.44 9.5E-06 38.2 3.9 45 240-286 7-51 (66)
36 PF14229 DUF4332: Domain of un 89.8 0.24 5.2E-06 44.7 2.6 53 234-287 42-94 (122)
37 PF04994 TfoX_C: TfoX C-termin 89.5 0.23 5.1E-06 41.5 2.0 33 246-279 4-36 (81)
38 PRK02362 ski2-like helicase; P 89.2 0.33 7.1E-06 57.1 3.8 54 245-299 652-705 (737)
39 PF12826 HHH_2: Helix-hairpin- 84.4 0.77 1.7E-05 36.5 2.3 46 250-297 8-55 (64)
40 COG2251 Predicted nuclease (Re 83.3 1.2 2.6E-05 48.4 3.9 64 235-299 215-280 (474)
41 PF14229 DUF4332: Domain of un 82.3 2 4.4E-05 38.7 4.5 44 251-296 1-49 (122)
42 PRK01172 ski2-like helicase; P 81.7 1.6 3.5E-05 50.7 4.6 41 245-286 612-652 (674)
43 PRK07758 hypothetical protein; 80.5 2.9 6.2E-05 35.9 4.4 43 250-293 39-83 (95)
44 PRK00254 ski2-like helicase; P 79.6 1.7 3.6E-05 51.1 3.8 54 244-298 644-699 (720)
45 KOG2093 Translesion DNA polyme 77.3 0.56 1.2E-05 54.4 -1.0 31 14-44 330-360 (1016)
46 smart00483 POLXc DNA polymeras 75.7 1.3 2.8E-05 47.1 1.2 30 247-277 91-120 (334)
47 TIGR03491 RecB family nuclease 74.8 2.2 4.7E-05 47.4 2.8 59 239-298 201-261 (457)
48 PF02961 BAF: Barrier to autoi 74.0 2.3 5E-05 36.0 2.1 32 242-274 16-47 (89)
49 cd00141 NT_POLXc Nucleotidyltr 71.1 2.3 5E-05 44.6 1.8 27 249-276 89-115 (307)
50 smart00611 SEC63 Domain of unk 69.6 9.5 0.00021 39.7 6.1 62 244-306 150-213 (312)
51 COG3377 Uncharacterized conser 68.6 1.7 3.6E-05 36.7 0.1 26 51-76 69-94 (95)
52 PRK08609 hypothetical protein; 68.5 3 6.5E-05 47.6 2.1 28 249-276 92-119 (570)
53 PRK14667 uvrC excinuclease ABC 67.3 5.9 0.00013 45.1 4.1 54 244-299 513-567 (567)
54 PRK00116 ruvA Holliday junctio 67.1 5.2 0.00011 39.0 3.2 55 247-301 75-132 (192)
55 PF00633 HHH: Helix-hairpin-he 66.7 3.3 7.2E-05 27.8 1.2 14 249-262 15-28 (30)
56 PRK07956 ligA NAD-dependent DN 65.5 6.7 0.00014 45.6 4.2 48 248-295 448-497 (665)
57 PTZ00035 Rad51 protein; Provis 64.1 5.4 0.00012 42.5 2.9 54 245-299 21-78 (337)
58 PRK10917 ATP-dependent DNA hel 64.0 4.3 9.3E-05 47.4 2.3 31 245-276 9-39 (681)
59 PF02889 Sec63: Sec63 Brl doma 64.0 7.7 0.00017 40.3 4.0 60 245-305 148-209 (314)
60 PLN03186 DNA repair protein RA 62.9 4.6 9.9E-05 43.1 2.1 44 244-288 25-70 (342)
61 TIGR02239 recomb_RAD51 DNA rep 62.8 8 0.00017 40.8 3.9 36 252-288 8-43 (316)
62 PRK12278 50S ribosomal protein 62.6 6.8 0.00015 39.1 3.1 36 246-282 159-194 (221)
63 PLN03187 meiotic recombination 61.0 7.1 0.00015 41.7 3.1 54 244-298 28-85 (344)
64 TIGR02238 recomb_DMC1 meiotic 60.5 9.2 0.0002 40.3 3.8 47 251-298 7-55 (313)
65 PRK14671 uvrC excinuclease ABC 60.0 11 0.00024 43.5 4.6 51 245-297 569-619 (621)
66 PRK14669 uvrC excinuclease ABC 59.8 11 0.00023 43.5 4.5 53 244-298 551-603 (624)
67 TIGR00575 dnlj DNA ligase, NAD 59.1 10 0.00023 44.0 4.3 51 248-298 435-487 (652)
68 PRK12311 rpsB 30S ribosomal pr 57.4 7.2 0.00016 41.2 2.4 36 246-282 264-299 (326)
69 PRK14666 uvrC excinuclease ABC 57.4 11 0.00024 43.7 4.0 52 244-297 636-689 (694)
70 TIGR00596 rad1 DNA repair prot 57.0 10 0.00022 45.1 3.7 52 247-300 759-811 (814)
71 PRK14973 DNA topoisomerase I; 56.3 14 0.00029 44.8 4.7 69 216-288 850-919 (936)
72 COG1200 RecG RecG-like helicas 55.5 6.9 0.00015 44.9 1.9 31 245-276 10-40 (677)
73 PRK14670 uvrC excinuclease ABC 54.3 15 0.00033 41.9 4.5 53 244-298 513-567 (574)
74 PRK14672 uvrC excinuclease ABC 53.2 17 0.00038 42.0 4.7 62 244-307 607-670 (691)
75 TIGR01954 nusA_Cterm_rpt trans 50.0 18 0.0004 26.5 3.0 33 254-287 2-34 (50)
76 TIGR02027 rpoA DNA-directed RN 48.9 18 0.00039 37.8 3.7 55 242-298 232-288 (297)
77 PRK12373 NADH dehydrogenase su 47.9 16 0.00034 39.7 3.1 36 246-282 324-359 (400)
78 PRK05182 DNA-directed RNA poly 47.5 19 0.00041 37.9 3.6 52 243-296 247-300 (310)
79 smart00278 HhH1 Helix-hairpin- 46.9 14 0.00031 23.6 1.7 16 247-262 3-18 (26)
80 PRK14351 ligA NAD-dependent DN 46.8 22 0.00048 41.5 4.3 50 248-297 465-516 (689)
81 COG1796 POL4 DNA polymerase IV 43.4 12 0.00025 39.3 1.3 35 245-279 93-127 (326)
82 KOG2534 DNA polymerase IV (fam 43.0 22 0.00047 37.2 3.1 31 248-279 100-130 (353)
83 COG0632 RuvA Holliday junction 39.9 18 0.00039 35.6 1.9 43 210-262 80-125 (201)
84 PF08004 DUF1699: Protein of u 39.1 52 0.0011 29.8 4.5 35 68-109 31-65 (131)
85 PF00416 Ribosomal_S13: Riboso 38.6 40 0.00087 29.6 3.8 35 247-281 17-51 (107)
86 PRK02515 psbU photosystem II c 38.1 54 0.0012 30.0 4.5 54 213-277 39-93 (132)
87 PF07887 Calmodulin_bind: Calm 36.0 35 0.00076 35.6 3.4 47 249-296 166-217 (299)
88 PRK14606 ruvA Holliday junctio 32.7 22 0.00047 34.6 1.2 45 210-262 80-125 (188)
89 PRK00558 uvrC excinuclease ABC 32.5 48 0.001 38.2 4.1 52 244-297 542-595 (598)
90 TIGR03631 bact_S13 30S ribosom 32.3 52 0.0011 29.3 3.4 37 246-282 16-52 (113)
91 TIGR00575 dnlj DNA ligase, NAD 32.1 48 0.001 38.6 4.0 30 251-282 504-533 (652)
92 TIGR00084 ruvA Holliday juncti 31.3 40 0.00088 32.8 2.8 50 248-300 75-130 (191)
93 PTZ00134 40S ribosomal protein 31.2 58 0.0013 30.7 3.7 41 245-285 30-73 (154)
94 PRK14603 ruvA Holliday junctio 31.1 24 0.00052 34.6 1.2 43 210-262 79-124 (197)
95 TIGR00615 recR recombination p 30.9 39 0.00084 33.1 2.6 16 247-262 13-28 (195)
96 PRK08097 ligB NAD-dependent DN 29.5 62 0.0014 36.9 4.3 48 249-297 429-479 (562)
97 PRK14605 ruvA Holliday junctio 29.4 50 0.0011 32.3 3.1 52 249-300 77-131 (194)
98 TIGR00084 ruvA Holliday juncti 29.0 26 0.00057 34.2 1.1 43 210-262 79-124 (191)
99 COG2199 c-di-GMP synthetase (d 28.7 1.5E+02 0.0032 27.6 6.3 29 101-129 78-110 (181)
100 PRK13844 recombination protein 28.6 44 0.00095 32.9 2.5 16 247-262 17-32 (200)
101 COG1948 MUS81 ERCC4-type nucle 28.4 66 0.0014 32.8 3.8 50 247-298 184-235 (254)
102 PRK14601 ruvA Holliday junctio 27.7 32 0.00068 33.4 1.4 54 197-262 69-125 (183)
103 PF07647 SAM_2: SAM domain (St 27.3 70 0.0015 24.8 3.1 47 233-288 4-50 (66)
104 CHL00013 rpoA RNA polymerase a 27.1 59 0.0013 34.5 3.4 55 241-297 259-315 (327)
105 PRK13766 Hef nuclease; Provisi 25.8 67 0.0014 38.0 3.9 49 247-297 717-767 (773)
106 PRK00076 recR recombination pr 25.8 33 0.00072 33.6 1.1 16 247-262 13-28 (196)
107 PRK05179 rpsM 30S ribosomal pr 25.8 84 0.0018 28.4 3.6 37 245-281 17-53 (122)
108 CHL00137 rps13 ribosomal prote 25.6 87 0.0019 28.3 3.7 37 245-281 17-53 (122)
109 PF07237 DUF1428: Protein of u 25.4 1.4E+02 0.0029 26.3 4.7 37 82-125 7-43 (103)
110 smart00279 HhH2 Helix-hairpin- 24.3 70 0.0015 22.4 2.2 17 247-263 18-34 (36)
111 PRK13901 ruvA Holliday junctio 24.1 40 0.00086 33.1 1.3 58 195-262 66-124 (196)
112 PRK14604 ruvA Holliday junctio 22.9 44 0.00096 32.7 1.4 54 197-262 69-125 (195)
113 PRK14602 ruvA Holliday junctio 22.7 46 0.001 32.8 1.5 16 247-262 111-126 (203)
114 PF12836 HHH_3: Helix-hairpin- 22.6 76 0.0016 25.0 2.5 28 249-276 18-49 (65)
115 TIGR03629 arch_S13P archaeal r 22.3 1E+02 0.0022 28.7 3.6 31 245-275 21-54 (144)
116 TIGR01259 comE comEA protein. 22.3 68 0.0015 28.8 2.4 28 248-275 71-102 (120)
117 PRK07945 hypothetical protein; 22.1 1.5E+02 0.0033 31.5 5.3 49 246-299 50-98 (335)
118 cd00080 HhH2_motif Helix-hairp 21.9 77 0.0017 25.9 2.4 20 247-266 24-43 (75)
119 TIGR00426 competence protein C 21.9 57 0.0012 25.9 1.6 30 247-276 18-52 (69)
120 PRK04053 rps13p 30S ribosomal 21.5 1.2E+02 0.0025 28.6 3.8 41 245-285 25-68 (149)
121 COG0353 RecR Recombinational D 21.0 45 0.00099 32.6 1.0 16 247-262 14-29 (198)
122 PF14716 HHH_8: Helix-hairpin- 20.9 65 0.0014 25.6 1.8 17 247-263 49-65 (68)
123 PRK14668 uvrC excinuclease ABC 20.6 76 0.0016 36.4 2.9 41 244-286 524-564 (577)
124 COG1555 ComEA DNA uptake prote 20.4 1E+02 0.0022 28.9 3.2 28 248-275 100-131 (149)
No 1
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=100.00 E-value=7.2e-77 Score=644.85 Aligned_cols=388 Identities=22% Similarity=0.253 Sum_probs=333.1
Q ss_pred EEEEEeCChhHHHHhhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHhcCCCCCCcHHHHHhhCC--CcEEEEccCCCC
Q 007824 13 IIAHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCP--QIELVQVPVARG 90 (588)
Q Consensus 13 ~I~hiD~D~FyasvE~~~~P~L~~~PvaV~~~~~~~~g~Via~SyeAR~~GVk~gM~~~~A~~lcP--~L~~v~v~~~~~ 90 (588)
+|+||||||||||||+++||+|+|+||||++++ +|+|+|+||+||++||++|||+++|+++|| ++++++
T Consensus 1 ~~~hvD~d~FfaS~E~~~~p~l~g~Pv~V~~~~---~g~V~aasyeAr~~GV~~gmp~~~a~~l~~~~~l~~~~------ 71 (422)
T PRK03609 1 MFALCDVNSFYASCETVFRPDLRGKPVVVLSNN---DGCVIARSAEAKALGIKMGDPWFKQKDLFRRCGVVCFS------ 71 (422)
T ss_pred CEEEEecCcceeeeeeccCccccCCcEEEEECC---CcEEEEcCHHHHHhCCCCCCcHHHHHHHhccCCeEEeC------
Confidence 599999999999999999999999999999865 489999999999999999999999999994 377763
Q ss_pred CCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEeccchhHHhhhcCCCCCchhhhHHhhhhhcccCccCCCCCchhhh
Q 007824 91 KADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKATV 169 (588)
Q Consensus 91 ~~d~~~Y~~~S~~v~~iL~~~-~~vE~~SiDEafLDlt~~~~~~l~~~~~~~~~~~~~~~~~~~l~g~~~~~~~~~~~~~ 169 (588)
+|++.|.++|++|++++.+| |.||++||||+|||+|++.+ +++
T Consensus 72 -~d~~~y~~~s~~i~~~l~~~tp~ve~~siDE~~lDvt~~~~----------------------l~~------------- 115 (422)
T PRK03609 72 -SNYELYADMSNRVMSTLEELSPRVEIYSIDEAFCDLTGVRN----------------------CRD------------- 115 (422)
T ss_pred -CCHHHHHHHHHHHHHHHHHhCCCceEeccccceecCCCCcC----------------------CCC-------------
Confidence 89999999999999999998 89999999999999999752 111
Q ss_pred hhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEEecCcHHHHHHHhcCCCC-----CCcccc-CccCHHHhcc
Q 007824 170 KEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKP-----AQQTTV-PFSSVKGLLD 243 (588)
Q Consensus 170 ~~~~~~~~~~~~~~ll~~g~~la~~Ir~~I~~~~Glt~SvGIa~nk~LAKLAs~~~KP-----~g~~vv-~~~~~~~~L~ 243 (588)
...++++||++|++++||+||||||+||++|||||.++|| +|..++ .+++..+||+
T Consensus 116 ------------------~~~~a~~i~~~I~~~~gl~~siGia~n~~lAK~As~~~k~~~k~~~g~~~i~~~~~~~~~L~ 177 (422)
T PRK03609 116 ------------------LTDFGREIRATVLQRTHLTVGVGIAQTKTLAKLANHAAKKWQRQTGGVVDLSNLERQRKLLS 177 (422)
T ss_pred ------------------HHHHHHHHHHHHHHHHCCceEEEecCCHHHHHHHHHHhCCCCCCCCcEEEcCCHHHHHHHhh
Confidence 1357999999999999999999999999999999988776 566666 5778999999
Q ss_pred cCCCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCcchHHHHHHHHhcCCCcccccccCC-cccccccccCC
Q 007824 244 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLP-KSHGSGKSFPG 322 (588)
Q Consensus 244 ~lPI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~~~g~~l~~~a~G~d~~~v~~~~~p-Ksi~~s~sF~~ 322 (588)
++||++|||||+++.++|. .+||+|+|||+++|+..|+++||+ .|..+++.++|+++.++....++ |+|+.++||+.
T Consensus 178 ~lPv~~l~GiG~~~~~~L~-~lGi~TigdL~~~~~~~L~~~fG~-~~~~l~~~a~G~~~~~~~~~~~~~ksi~~~~tf~~ 255 (422)
T PRK03609 178 LQPVEEVWGVGRRISKKLN-AMGIKTALDLADTNIRFIRKHFNV-VLERTVRELRGEPCLSLEEFAPTKQEIVCSRSFGE 255 (422)
T ss_pred cCChhhcCCccHHHHHHHH-HcCCCcHHHHhcCCHHHHHHHHCH-HHHHHHHHhCCCCCCCccccCCCCceEEEeeECCC
Confidence 9999999999999999998 899999999999999999999997 59999999999999999876665 69999999985
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHhhhhhcCceeeEEEEEEEeccCCCCCCCcccCccccccCCCch---hHHHHHHH
Q 007824 323 PRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTA---KIQEDTFN 399 (588)
Q Consensus 323 ~~~i~~~e~l~~~L~~La~eL~~RLr~~l~~~~~~~~tltL~lr~~~~~~~~~~~~~~s~s~~L~~~T~---~i~~~A~~ 399 (588)
++.+.+++..++.+|+++|+.||+++ ++.|++|+|++++.+|... .+.|..+++.+++.||+ .|++.+.+
T Consensus 256 --~~~~~~~l~~~l~~l~~~l~~rLr~~----~~~~~~l~l~ir~~~~~~~-~~~~~~~~~~~l~~pt~d~~~l~~~a~~ 328 (422)
T PRK03609 256 --RITDYESMRQAICSYAARAAEKLRGE----HQYCRFISTFVKTSPFALN-EPYYGNSASVKLLTPTQDSRDIIAAATR 328 (422)
T ss_pred --CCCCHHHHHHHHHHHHHHHHHHHHHc----CCcccEEEEEEEcCCcccc-CCCcCceeEEeCCCCCCCHHHHHHHHHH
Confidence 49999999999999999999999987 9999999999999887531 22344567777887876 57888888
Q ss_pred HHHHHHHHhhccccccccCCCCCCCceeEEeeccCCcc----------cCC---ccchhhhhhh--------cCCCCCCC
Q 007824 400 LFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIV----------PVL---SGTCSIMKYF--------NGPDKFGS 458 (588)
Q Consensus 400 Ll~~i~r~~~~~~~y~kaGv~~~~~~Ir~lgvs~s~L~----------~~~---~~~~sLm~~f--------~~~~~~~~ 458 (588)
+|+++|+. +.+++.+||.+++|. +.. .+...|+.++ .+.+..|+
T Consensus 329 ll~~~~~~---------------~~~~r~~GV~~~~l~~~~~~q~~LF~~~~~~~~~~~l~~~iD~i~~r~G~~~i~~a~ 393 (422)
T PRK03609 329 ALDAIWRD---------------GHRYQKAGVMLGDFFSQGVAQLNLFDDNAPRPGSEQLMKVLDTLNAKSGKGTLYFAG 393 (422)
T ss_pred HHHHHhCC---------------CCceEEeeEEEEeeccCCCcCccCccccccccchHHHHHHHHHHHHhhCCCeEEECC
Confidence 98886543 125666666665554 321 1234566665 56788888
Q ss_pred CCCCCCCcccccCCCCCCcccccCcCcchh
Q 007824 459 TSEQLPDNFIDAAPLSPSGSESYSTLNSTE 488 (588)
Q Consensus 459 ~~~~~~~w~m~~~~~SP~ytT~w~~Lp~~~ 488 (588)
++..+ +|.|+++++||+|||+|+|||.++
T Consensus 394 ~~~~~-~w~~~~~~~s~~ytt~~~~l~~~~ 422 (422)
T PRK03609 394 QGIAQ-QWQMKREMLSPRYTTRWSDLLRVK 422 (422)
T ss_pred CCCCC-CccCchhhcCCCCCCCHHHcceeC
Confidence 88865 799999999999999999999874
No 2
>KOG2095 consensus DNA polymerase iota/DNA damage inducible protein [Replication, recombination and repair]
Probab=100.00 E-value=8.4e-74 Score=615.06 Aligned_cols=359 Identities=52% Similarity=0.769 Sum_probs=327.1
Q ss_pred CCCCCCCCCCCCEEEEEeCChhHHHHhhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHhcCCCCCCcHHHHHhhCCCc
Q 007824 1 MPVARPDSSGARIIAHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQI 80 (588)
Q Consensus 1 ~~~~~~~~~~~r~I~hiD~D~FyasvE~~~~P~L~~~PvaV~~~~~~~~g~Via~SyeAR~~GVk~gM~~~~A~~lcP~L 80 (588)
|+|.++..+..|||+||||||||||||++++|+|+++|+||+||| +|||||||||++||+++|++.||+++||+|
T Consensus 5 ~s~~~~~~s~~RVIahVDMDcFyaQVEq~r~P~lr~~PlaVvQ~n-----gIIAVsYeARa~GV~R~M~v~EAK~kCPqL 79 (656)
T KOG2095|consen 5 GSVLGTQNSSLRVIAHVDMDCFYAQVEQRRNPELRSKPLAVVQYN-----GIIAVSYEARAFGVKRLMTVDEAKKKCPQL 79 (656)
T ss_pred ccccCccccccceEEEecchhhHHHHHhhcCchhccCceEEEEee-----eEEEEehhhhhhCCchhhhHHHHHhhCCce
Confidence 689999999999999999999999999999999999999999998 499999999999999999999999999999
Q ss_pred EEEEccCCCCCCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEeccchhHHhhhcCCCCCchhhhHHhhhhhcccCcc
Q 007824 81 ELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLES 159 (588)
Q Consensus 81 ~~v~v~~~~~~~d~~~Y~~~S~~v~~iL~~~-~~vE~~SiDEafLDlt~~~~~~l~~~~~~~~~~~~~~~~~~~l~g~~~ 159 (588)
+++|||+.++++|...||+++.+|+.+|..| +.||++++||+|+|+|.++...+.+..........++....+.++.+.
T Consensus 80 vlv~v~~~~~ka~~~~YR~as~ev~~~L~~y~~viek~~~dea~ld~tasvder~q~L~s~~~~~~~~~~p~~~~~~~~s 159 (656)
T KOG2095|consen 80 VLVHVPVAREKADLPKYREASEEVKESLEPYRPVIEKASKDEAFLDLTASVDERLQDLQSDEFNMLLEEPPYGLIYGLPS 159 (656)
T ss_pred EEeecccccccchhhhhhhhHHHHHHHHhhhHHHHHHHhhhhhhhhHHHHHHHHHHHHhhhhhhhhhhccchhcccCCcc
Confidence 9999999999999999999999999999999 689999999999999999987665533111000011111123333321
Q ss_pred -----------CCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEEecCcHHHHHHHhcCCCCC
Q 007824 160 -----------KDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPA 228 (588)
Q Consensus 160 -----------~~~~~~~~~~~~~~~~~~~~~~~~ll~~g~~la~~Ir~~I~~~~Glt~SvGIa~nk~LAKLAs~~~KP~ 228 (588)
+.+...++.+..|++.++.+|+|++|.+|+.||.+||++|+.+||||||+|||+||+|||||+.++|||
T Consensus 160 ~~~~~~~~~~~e~~~~~ee~~~~~~~~~d~~~~d~~L~iGa~Iv~EiR~~i~~elg~tCSAGIa~NKmLAKLvsg~nKPn 239 (656)
T KOG2095|consen 160 ALPNTREATNSENPLMREEIVSLWIENDDFDWDDVRLLIGAQIVKEIRDAIKLELGYTCSAGIAHNKMLAKLVSGRNKPN 239 (656)
T ss_pred ccchhhhhhhhccccchhhHhhhhhhccccCchhhhhHHHHHHHHHHHHHHHHHhCceeeccccccHHHHHHHhccCCCC
Confidence 334455678889999999999999999999999999999999999999999999999999999999999
Q ss_pred CccccCccCHHHhcccCCCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCcchHHHHHHHHhcCCCcccccc
Q 007824 229 QQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQAR 308 (588)
Q Consensus 229 g~~vv~~~~~~~~L~~lPI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~~~g~~l~~~a~G~d~~~v~~~ 308 (588)
.||||++..+.+||..|||.++|++|+++++.|.+.+||.++|||.+++...|++.||.+.|.|||..++|+|.++|.++
T Consensus 240 qQTil~~~~v~~ll~slpi~k~~~lGGk~G~~lie~LGi~~vgdl~~fse~~L~~~fg~~~g~~l~~la~Gid~s~V~pr 319 (656)
T KOG2095|consen 240 QQTILPNTYVQDLLDSLPITKIRTLGGKLGEELIEVLGIDSVGDLQQFSETQLQKKFGEKNGTWLRNLARGIDNSPVRPR 319 (656)
T ss_pred cceecchHHHHHHHHhCCCceeeeccchHHHHHHHHhCCchHHHHHhcCHHHHHHhhCcchhHHHHHHhcccCCCccccC
Confidence 99999999999999999999999999999999999999999999999999999999998899999999999999999999
Q ss_pred cCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhhhhcCceeeEEEEE
Q 007824 309 LLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLH 364 (588)
Q Consensus 309 ~~pKsi~~s~sF~~~~~i~~~e~l~~~L~~La~eL~~RLr~~l~~~~~~~~tltL~ 364 (588)
..||+|+++++|++...+++.+++..||..+++++..||..+..++.+.+.++.++
T Consensus 320 ~~pkSig~~K~Fpg~~~~~~~~~l~~wl~~la~el~~Rl~~d~~en~r~as~l~~~ 375 (656)
T KOG2095|consen 320 GLPKSIGSEKNFPGKRSRKSLEELQRWLNQLAEELAERLGKDRNENKRRASTLVVS 375 (656)
T ss_pred CCCcchhhhhcCCCccccccHHHHHHHHHHHHHHHHHHHHhhhhhhccccceEEee
Confidence 99999999999998888999999999999999999999999988899999999998
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=4.9e-71 Score=595.33 Aligned_cols=348 Identities=30% Similarity=0.416 Sum_probs=308.1
Q ss_pred CCCCCEEEEEeCChhHHHHhhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHhcCCCCCCcHHHHHhhCCCcEEEEccC
Q 007824 8 SSGARIIAHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPV 87 (588)
Q Consensus 8 ~~~~r~I~hiD~D~FyasvE~~~~P~L~~~PvaV~~~~~~~~g~Via~SyeAR~~GVk~gM~~~~A~~lcP~L~~v~v~~ 87 (588)
....|+|+||||||||||||++++|+|+++||||+++++ ++|+|+||||+||++||++||++.+|+++||++++++
T Consensus 43 ~~~~r~i~hiD~d~FyasvE~~~~p~L~~kPv~V~~~~~-~~~~V~a~sy~AR~~GV~~gM~~~~A~~lcP~l~vv~--- 118 (404)
T cd01701 43 PDLQRIIMHVDFDCFFVSVSIRNRPDLKGKPVAVCHGKG-PNSEIASCNYEARSYGIKNGMWVGQAKKLCPQLVTLP--- 118 (404)
T ss_pred CCCCcEEEEEeCchHHHHHHhhhCccccCCCEEEecCCC-CCeEEEecCHHHHhcCCCCCCcHHHHHHHCCCcEEEC---
Confidence 356789999999999999999999999999999987653 4688999999999999999999999999999999884
Q ss_pred CCCCCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEeccchhHHhhhcCCCCCchhhhHHhhhhhcccCccCCCCCch
Q 007824 88 ARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSK 166 (588)
Q Consensus 88 ~~~~~d~~~Y~~~S~~v~~iL~~~-~~vE~~SiDEafLDlt~~~~~~l~~~~~~~~~~~~~~~~~~~l~g~~~~~~~~~~ 166 (588)
+|++.|+++|++|+++|.+| +.||++||||+|||+|++.+. +++.
T Consensus 119 ----~~~~~Y~~~s~~i~~il~~~s~~ve~~SiDE~~lDvt~~~~~---------------------~~~~--------- 164 (404)
T cd01701 119 ----YDFEAYEEVSLTFYEILASYTDNIEAVSCDEALIDITSLLEE---------------------TYEL--------- 164 (404)
T ss_pred ----CChHHHHHHHHHHHHHHHHhCCceEEcccceEEEEccccccc---------------------ccCC---------
Confidence 79999999999999999998 689999999999999997520 2221
Q ss_pred hhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEEecCcHHHHHHHhcCCCCCCccccCccCHHHhcccCC
Q 007824 167 ATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLP 246 (588)
Q Consensus 167 ~~~~~~~~~~~~~~~~~ll~~g~~la~~Ir~~I~~~~Glt~SvGIa~nk~LAKLAs~~~KP~g~~vv~~~~~~~~L~~lP 246 (588)
+..++++||++|++++|||||||||+||++||||++.+||+|++++.++++.++|+++|
T Consensus 165 ---------------------~~~la~~ir~~I~~~~gl~~siGia~nk~lAKlAs~~aKP~g~~~i~~~~~~~~L~~lP 223 (404)
T cd01701 165 ---------------------PEELAEAIRNEIRETTGCSASVGIGPNILLARLATRKAKPDGQYHLSAEKVEEFLSQLK 223 (404)
T ss_pred ---------------------HHHHHHHHHHHHHHHHCCCEEEEEcCCHHHHHHHhcccCCCcEEEECHHHHHHHhhcCC
Confidence 24679999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCcHHHHHHHHHhhCCcchhhhccCC--HHHHHHHhCcchHHHHHHHHhcCCCcccccccCCcccccccccCCCC
Q 007824 247 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFS--EDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPR 324 (588)
Q Consensus 247 I~~l~GiG~k~~~~L~~~lGI~TigDLa~l~--~~~L~~rfG~~~g~~l~~~a~G~d~~~v~~~~~pKsi~~s~sF~~~~ 324 (588)
|++|||||++++++|. .+||+|++||+++| +..|.++||...|.+||+.++|+|+++|.+..++|||+.+++|+.
T Consensus 224 v~~l~GIG~~~~~~L~-~~Gi~t~~dl~~~~~~~~~L~~~fG~~~g~~L~~~a~G~d~~~v~~~~~~ksi~~~~tf~~-- 300 (404)
T cd01701 224 VGDLPGVGSSLAEKLV-KLFGDTCGGLELRSKTKEKLQKVLGPKTGEKLYDYCRGIDDRPVTGEKERKSVSAEINYGI-- 300 (404)
T ss_pred HhHhCCCCHHHHHHHH-HcCCcchHHHHhCcccHHHHHHHHCHHHHHHHHHHhCCcCCCCCCCCCCCccccceeeCCC--
Confidence 9999999999999998 89999999999999 999999999756999999999999999998888999999999985
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhhhcCceeeEEEEEEEeccCC-CCCCCc-------ccCccccccCCCch---hH
Q 007824 325 ALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSS-DSDSRK-------KFPSKSCPLRYGTA---KI 393 (588)
Q Consensus 325 ~i~~~e~l~~~L~~La~eL~~RLr~~l~~~~~~~~tltL~lr~~~~~-~~~~~~-------~~~s~s~~L~~~T~---~i 393 (588)
++.+.+++..+|..|+++|+.||+++ ++.|++|+|++++.... .+..++ +..+++.+|+.+|+ .|
T Consensus 301 ~~~~~~~l~~~l~~L~~~l~~rLr~~----~~~~~~l~l~l~~~~~~~~~~~~~y~g~~~~~~~~~~~~l~~pT~d~~~i 376 (404)
T cd01701 301 RFTNVDDVEQFLQRLSEELSKRLEES----NVTGRQITLKLMKRAPGAPIEPPKYMGHGICDSFSKSSTLGVATDDSGVI 376 (404)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHc----CCceeeEEEEEEeccccCccccccccccCCCcEEeeeeECCCCCCCHHHH
Confidence 48999999999999999999999987 99999999999973211 111111 24567888988886 58
Q ss_pred HHHHHHHHHHHHHHhhccccccccCCCCCCCceeEEeeccCCc
Q 007824 394 QEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKI 436 (588)
Q Consensus 394 ~~~A~~Ll~~i~r~~~~~~~y~kaGv~~~~~~Ir~lgvs~s~L 436 (588)
.+.|..||+.++. .+.+||.|||++++|
T Consensus 377 ~~~a~~ll~~~~~---------------~~~~vR~lgv~~~~l 404 (404)
T cd01701 377 GTEAKKLFRDLSI---------------PPEELRGVGIQVTKL 404 (404)
T ss_pred HHHHHHHHHhccC---------------CCCCeeEEEEEEecC
Confidence 8888888887421 124899999999876
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=8.4e-71 Score=583.25 Aligned_cols=338 Identities=49% Similarity=0.708 Sum_probs=301.0
Q ss_pred EEEeCChhHHHHhhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHhcCCCCCCcHHHHHhhCCCcEEEEcc--------
Q 007824 15 AHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVP-------- 86 (588)
Q Consensus 15 ~hiD~D~FyasvE~~~~P~L~~~PvaV~~~~~~~~g~Via~SyeAR~~GVk~gM~~~~A~~lcP~L~~v~v~-------- 86 (588)
+||||||||||||++++|+|+|+||||++++ .|+||||+||++||++||++.+|+++||++++++++
T Consensus 1 ~hiD~D~FfasvE~~~~p~l~~~PvvV~~~~-----~V~a~syeAR~~GV~~gm~~~~A~~lcP~l~~v~~~~~~~~~~~ 75 (359)
T cd01702 1 AHIDMDAFFAQVEQVRLGLLRNDPVAVVQWN-----SIIAVSYAARAFGVTRFMTIDEAKKKCPDLILAHVATYKKGEDE 75 (359)
T ss_pred CccccchHHHHHHhHhcccccCCcEEEecCC-----cEEEECHHHHhcCCCCCCcHHHHHHHCCCcEEECCccccccccc
Confidence 5999999999999999999999999999764 299999999999999999999999999999999765
Q ss_pred --------CCCCCCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEeccchhHHhhhcCCCCCchhhhHHhhhhhcccC
Q 007824 87 --------VARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGL 157 (588)
Q Consensus 87 --------~~~~~~d~~~Y~~~S~~v~~iL~~~-~~vE~~SiDEafLDlt~~~~~~l~~~~~~~~~~~~~~~~~~~l~g~ 157 (588)
+.+++++++.|+++|++|++++.++ |.||++||||+|||+.
T Consensus 76 ~~~~~~~~~~~~~~~~~~Y~~~S~~i~~~l~~~sp~vE~~SiDE~flDv~------------------------------ 125 (359)
T cd01702 76 ADYHENPSPARHKVSLDPYRRASRKILNILKRFGDVVEKASIDEAYLDLG------------------------------ 125 (359)
T ss_pred cccccccccccccccHHHHHHHHHHHHHHHHHcCCceEECcCCeeHHHHH------------------------------
Confidence 4456778999999999999999998 7999999999999992
Q ss_pred ccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEEecCcHHHHHHHhcCCCCCCccccCccC
Q 007824 158 ESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSS 237 (588)
Q Consensus 158 ~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~g~~la~~Ir~~I~~~~Glt~SvGIa~nk~LAKLAs~~~KP~g~~vv~~~~ 237 (588)
..+|.+||++|++++|||||||||+||++||||++++||+|++++.+++
T Consensus 126 -------------------------------~~la~~ir~~I~~~~glt~SiGIa~nk~lAKlAs~~~KP~g~~v~~~~~ 174 (359)
T cd01702 126 -------------------------------SRIVEEIRQQVYDELGYTCSAGIAHNKMLAKLASGMNKPNAQTILRNDA 174 (359)
T ss_pred -------------------------------HHHHHHHHHHHHHHhCccEEeeecCCHHHHHHHhcccCCCCeEEECHHH
Confidence 1358999999999999999999999999999999999999999999999
Q ss_pred HHHhcccCCCCCCCCCcHHHHHHHHHhhCCcchhhhccC--CHHHHHHHhCcchHHHHHHHHhcCCCcccccccCCcccc
Q 007824 238 VKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKF--SEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHG 315 (588)
Q Consensus 238 ~~~~L~~lPI~~l~GiG~k~~~~L~~~lGI~TigDLa~l--~~~~L~~rfG~~~g~~l~~~a~G~d~~~v~~~~~pKsi~ 315 (588)
+.+||+++||++|||||++++++|.+.+||+|++||+++ |...|.++||.+.|.++|+.++|+|+++|.+..++|||+
T Consensus 175 ~~~~L~~lpv~~l~GiG~~~~~~ll~~~Gi~ti~dl~~~~~~~~~L~~~fG~~~g~~l~~~a~G~d~~~v~~~~~~ksi~ 254 (359)
T cd01702 175 VASFLSSLPITSIRGLGGKLGEEIIDLLGLPTEGDVAGFRSSESDLQEHFGEKLGEWLYNLLRGIDHEPVKPRPLPKSMG 254 (359)
T ss_pred HHHHhhcCcHHHhCCcCHHHHHHHHHHcCCcCHHHHHhccCCHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCCceee
Confidence 999999999999999999998876448999999999999 999999999965799999999999999999888899999
Q ss_pred cccccCCCCCCCCH-HHHHHHHHHHHHHHHHHHHhhhhhcCceeeEEEEEEEeccCCCCCCCcccCccccccCCCch-hH
Q 007824 316 SGKSFPGPRALKTV-ASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTA-KI 393 (588)
Q Consensus 316 ~s~sF~~~~~i~~~-e~l~~~L~~La~eL~~RLr~~l~~~~~~~~tltL~lr~~~~~~~~~~~~~~s~s~~L~~~T~-~i 393 (588)
.+++|+.+ +.+. +++..+|..|+++|+.||++++..+++.+++|+|++++.+| ....+++.+++.+|. .|
T Consensus 255 ~~~tf~~~--~~~~~~~l~~~l~~L~~~l~~rL~~~~~~~~~~~~~v~v~lr~~~~------~~~~sr~~~~~~~~~~~i 326 (359)
T cd01702 255 SSKNFPGK--TALSTEDVQHWLLVLASELNSRLEDDRYENNRRPKTLVLSLRQRGD------GVRRSRSCALPRYDAQKI 326 (359)
T ss_pred eeeecCCC--CCChHHHHHHHHHHHHHHHHHHHHhhhhhcCceeeEEEEEEEECCC------cEEEEEEecCCCCCHHHH
Confidence 99999954 7777 99999999999999999998766679999999999999874 123467788876664 68
Q ss_pred HHHHHHHHHHHHHHhhccccccccCCCCCCCceeEEeeccCC
Q 007824 394 QEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASK 435 (588)
Q Consensus 394 ~~~A~~Ll~~i~r~~~~~~~y~kaGv~~~~~~Ir~lgvs~s~ 435 (588)
+..|.+||++++++..+ . + -+++||++||+++|
T Consensus 327 ~~~~~~l~~~~~~~~~~---~-~-----~~~~~rl~g~~~~~ 359 (359)
T cd01702 327 VKDAFKLIKAINEEGLG---L-A-----WNYPLTLLSLSFTK 359 (359)
T ss_pred HHHHHHHHHHhhhhccc---c-c-----cCCCeEEEEEEecC
Confidence 89999999987654110 0 0 03699999999875
No 5
>PTZ00205 DNA polymerase kappa; Provisional
Probab=100.00 E-value=2.4e-70 Score=594.19 Aligned_cols=350 Identities=22% Similarity=0.309 Sum_probs=302.4
Q ss_pred CEEEEEeCChhHHHHhhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHhcCCCCCCcHHHHHhhCCCcEEEEccCCCCC
Q 007824 12 RIIAHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVARGK 91 (588)
Q Consensus 12 r~I~hiD~D~FyasvE~~~~P~L~~~PvaV~~~~~~~~g~Via~SyeAR~~GVk~gM~~~~A~~lcP~L~~v~v~~~~~~ 91 (588)
++|+||||||||||||++++|+|+++||||++ +|+|+||||+||+|||++|||+++|+++||+|++++
T Consensus 133 ~~I~HVDmDaFYASVE~~~~PeLrgkPvaVg~-----~gvV~TaSYeARk~GVrsgMp~~~AkkLCP~Liivp------- 200 (571)
T PTZ00205 133 GTYIHLDMDMFYAAVEIKKHPEYAAIPLAIGT-----MTMLQTANYVARGRGIRQGMPGFLALKICPNLLILP------- 200 (571)
T ss_pred CeEEEEecCcHhhhhheccCccccCCcEEEcc-----CCEEEEcCHHHHhhCCCcCCcHHHHHHhCCCCcEec-------
Confidence 58999999999999999999999999999975 278999999999999999999999999999999984
Q ss_pred CChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEeccchhHHhhhcCCCCCchhhhHHhhhhhcccCccCCCCCchhhhh
Q 007824 92 ADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKATVK 170 (588)
Q Consensus 92 ~d~~~Y~~~S~~v~~iL~~~-~~vE~~SiDEafLDlt~~~~~~l~~~~~~~~~~~~~~~~~~~l~g~~~~~~~~~~~~~~ 170 (588)
+||+.|+++|.+|+++|.+| |.+|++||||+|||+|++... |+..
T Consensus 201 ~d~~~Y~~~S~~I~~il~~ysp~ve~~SIDEafLDlT~~~~~----------------------~~~~------------ 246 (571)
T PTZ00205 201 PDFDAYNEESNTVRRIVAEYDPNYISFGLDELTLEVSAYIER----------------------FEGT------------ 246 (571)
T ss_pred CCHHHHHHHHHHHHHHHHhcCCcEEEeechhceeccCCchhh----------------------ccCC------------
Confidence 89999999999999999999 799999999999999997531 1100
Q ss_pred hhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEEecCcHHHHHHHhcCCCCCCcccc---CccCHHHhcccCCC
Q 007824 171 EWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTV---PFSSVKGLLDSLPI 247 (588)
Q Consensus 171 ~~~~~~~~~~~~~ll~~g~~la~~Ir~~I~~~~Glt~SvGIa~nk~LAKLAs~~~KP~g~~vv---~~~~~~~~L~~lPI 247 (588)
..+..+|++||++|+++||||||||||+||+||||||+++||+|++++ +++++..||+++||
T Consensus 247 ---------------~~~~~iA~~IR~~I~~~tgLt~SiGIA~NklLAKiASd~~KPnG~~vl~l~~~~~v~~fL~~LpV 311 (571)
T PTZ00205 247 ---------------KTAEDVASELRVRVFGETKLTASAGIGPTAALAKIASNINKPNGQHDLNLHTRGDVMTYVRDLGL 311 (571)
T ss_pred ---------------CCHHHHHHHHHHHHHHHHCCcEEEEEcCCHHHHHHhhhccCCCCCeEEecCCHHHHHHHHhCCCc
Confidence 012467999999999999999999999999999999999999999986 56789999999999
Q ss_pred CCCCCCcHHHHHHHHHhhCCcchhhhccCCHH--------HHHHHhCcchHHHHHHHHhcCCCcc-ccc--ccCCccccc
Q 007824 248 KKMKQLGGKLGTSLQNELGVTTVGDLLKFSED--------KLQESYGFNTGTWLWNIARGISGEE-VQA--RLLPKSHGS 316 (588)
Q Consensus 248 ~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~--------~L~~rfG~~~g~~l~~~a~G~d~~~-v~~--~~~pKsi~~ 316 (588)
++|||||+++.++|. .+||+|++||++.+.. .++..||...|..+|+.++|+|..+ +.. ...+|||+.
T Consensus 312 ~ki~GIG~~t~~~L~-~~GI~TigDLa~~~~~l~~~f~~k~l~~llG~~~G~~l~~~a~G~d~~~~v~~~~~~~rKSIg~ 390 (571)
T PTZ00205 312 RSVPGVGKVTEALLK-GLGITTLSDIYNRRVELCYILHNNLFRFLLGASIGIMQWPDAATAANTENCEGATGGQRKAISS 390 (571)
T ss_pred ceeCCcCHHHHHHHH-HcCCCcHHHHhcCCHHHHHHhHHHHHHHHhCchhhHHHHHHhcCCCCCCccCCCCCCCCceeEE
Confidence 999999999999997 8999999999998876 4778899767999999999999884 332 345799999
Q ss_pred ccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhhhhcCceeeEEEEEEEeccCCCCCCCcccCccccccCCCch---hH
Q 007824 317 GKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTA---KI 393 (588)
Q Consensus 317 s~sF~~~~~i~~~e~l~~~L~~La~eL~~RLr~~l~~~~~~~~tltL~lr~~~~~~~~~~~~~~s~s~~L~~~T~---~i 393 (588)
++||.. +.+.+++...|..|+++++.||+++ ++.|++|+|++++.+|.. .+++.+|+.+|+ .|
T Consensus 391 ErTF~~---~~d~~el~~~L~~L~~~v~~rLrk~----~l~artVtlKlK~~dF~~-------~trs~tL~~pT~d~~~I 456 (571)
T PTZ00205 391 ERSFTT---PRTKEGLQEMVDTVFNGAYEEMRKS----ELMCRQISLTIRWASYRY-------QQYTKSLIQYSDDSATL 456 (571)
T ss_pred eEeCCC---CCCHHHHHHHHHHHHHHHHHHHHhc----CCCccEEEEEEEECCCCc-------eEEEEECCCCcCCHHHH
Confidence 999974 5799999999999999999999987 999999999999988753 255777887776 57
Q ss_pred HHHHHHHHHHHHHHhhccccccccCCCCCCCceeEEeeccCCcccCC--------ccchhhhhhhcC
Q 007824 394 QEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPVL--------SGTCSIMKYFNG 452 (588)
Q Consensus 394 ~~~A~~Ll~~i~r~~~~~~~y~kaGv~~~~~~Ir~lgvs~s~L~~~~--------~~~~sLm~~f~~ 452 (588)
.++|..||+..+ + .+.+||+|||++++|.... ..|.+|..|.+.
T Consensus 457 ~~aa~~Ll~~~~---~------------~~~~vRLlGV~ls~L~~~~~~~~~~~~~~~~~~~~~~~~ 508 (571)
T PTZ00205 457 RRAVDGLLLPHA---A------------KYSEMCLLGVRFLDLISAKDFHMKRKGGNQLSISQFIRP 508 (571)
T ss_pred HHHHHHHHHhcc---c------------cCCCEEEEEEEEcccCcHHHHHHHhcCCceeeHHHHcCC
Confidence 777777776521 1 1248999999999998732 346678888743
No 6
>PRK01216 DNA polymerase IV; Validated
Probab=100.00 E-value=5.9e-70 Score=574.74 Aligned_cols=336 Identities=28% Similarity=0.422 Sum_probs=299.0
Q ss_pred EEEEEeCChhHHHHhhhhCCCCCCCcEEEEecCC--CCCcEEEEcCHHHHhcCCCCCCcHHHHHhhCCCcEEEEccCCCC
Q 007824 13 IIAHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNE--WKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVARG 90 (588)
Q Consensus 13 ~I~hiD~D~FyasvE~~~~P~L~~~PvaV~~~~~--~~~g~Via~SyeAR~~GVk~gM~~~~A~~lcP~L~~v~v~~~~~ 90 (588)
+|+||||||||||||++++|+|+|+||||+++.. .++|+|++|||+||++||++||++.+|+++||++++++
T Consensus 2 ~i~hiD~daFfasve~~~~P~L~~kPv~V~~~~~~~~~~gvV~aasy~Ar~~GV~sgM~~~~A~~lcP~li~v~------ 75 (351)
T PRK01216 2 IILFVDFDYFFAQVEEVLNPSLKGKPVVVCVYSGRFEDSGAVATANYEARKLGIKAGMPIVEAKKILPNAVYLP------ 75 (351)
T ss_pred EEEEEecchHHHHHHhHhChhhcCCcEEEEecCCCCCCCeEEEECCHHHHHhCCCCCCcHHHHHHHCCCeEEEC------
Confidence 7999999999999999999999999999985422 24588999999999999999999999999999999984
Q ss_pred CCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEeccchhHHhhhcCCCCCchhhhHHhhhhhcccCccCCCCCchhhh
Q 007824 91 KADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKATV 169 (588)
Q Consensus 91 ~~d~~~Y~~~S~~v~~iL~~~-~~vE~~SiDEafLDlt~~~~~~l~~~~~~~~~~~~~~~~~~~l~g~~~~~~~~~~~~~ 169 (588)
+|++.|+.+|++|++++.+| |.||++||||+|||+|++. ++||.
T Consensus 76 -~d~~~y~~~s~~i~~~l~~~tp~ve~~siDE~~LDvt~~~----------------------~l~g~------------ 120 (351)
T PRK01216 76 -MRKEVYQQVSNRIMKLLREYSEKIEIASIDEAYLDISDKV----------------------KNYQD------------ 120 (351)
T ss_pred -CCHHHHHHHHHHHHHHHHHhCCceEEccCCeEEEEcccch----------------------hccCC------------
Confidence 79999999999999999998 7999999999999999976 34543
Q ss_pred hhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEEecCcHHHHHHHhcCCCCCCccccCccCHHHhcccCCCCC
Q 007824 170 KEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKK 249 (588)
Q Consensus 170 ~~~~~~~~~~~~~~ll~~g~~la~~Ir~~I~~~~Glt~SvGIa~nk~LAKLAs~~~KP~g~~vv~~~~~~~~L~~lPI~~ 249 (588)
+..++++||++|++++|||||||||+||++||||++++||+|++++.++++.++|+++||++
T Consensus 121 ------------------~~~la~~ir~~I~~~~glt~siGia~nk~lAKlas~~~KP~g~~vi~~~~~~~~L~~LPi~~ 182 (351)
T PRK01216 121 ------------------AYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRFINELDIAD 182 (351)
T ss_pred ------------------HHHHHHHHHHHHHHHHCCcEEEEecCCHHHHHHHHhccCCCCEEEeCHHHHHHHHhcCCccc
Confidence 24689999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCcchHHHHHHHHhcCCCcccccccCCcccccccccCCCCCCCCH
Q 007824 250 MKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTV 329 (588)
Q Consensus 250 l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~~~g~~l~~~a~G~d~~~v~~~~~pKsi~~s~sF~~~~~i~~~ 329 (588)
+||||+++.++|. ++||+|++||+++|.+.|.++||...|.+|++.++|++.+||.+. ++|||+.+.+|.. ++.+.
T Consensus 183 l~giG~~~~~~L~-~~Gi~TigdL~~~~~~~L~~rfG~~~~~~L~~~a~G~d~~pv~~~-~~ksi~~~~tl~~--di~~~ 258 (351)
T PRK01216 183 IPGIGDITAEKLK-KLGVNKLVDTLRIEFDELKGIIGEAKAKYLFSLARNEYNEPVRAR-VRKSIGRYVTLPR--NTRDL 258 (351)
T ss_pred ccCCCHHHHHHHH-HcCCCcHHHHhcCCHHHHHHHHCHHHHHHHHHHhCCCCCCCCCCC-CCCCCcCeEECCC--ccCCH
Confidence 9999999999998 899999999999999999999997668999999999999999884 4699999999984 59999
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhhcCceeeEEEEEEEeccCCCCCCCcccCccccccCCCch--hHHHHHHHHHHHHHHH
Q 007824 330 ASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTA--KIQEDTFNLFQAGLRE 407 (588)
Q Consensus 330 e~l~~~L~~La~eL~~RLr~~l~~~~~~~~tltL~lr~~~~~~~~~~~~~~s~s~~L~~~T~--~i~~~A~~Ll~~i~r~ 407 (588)
+++...|.+|+++++.||+. .+.++++++++.+|.+ .+++.+++.+|+ ++++.|..||++.+..
T Consensus 259 ~~l~~~l~~L~~~~~~rl~~-------~~~~~~~~~~~~df~~-------~t~~~tl~~~~~~~~~~~~a~~Ll~~~~~~ 324 (351)
T PRK01216 259 EEIKPYLKRAIEEAYYKLDG-------IPKAIHVVAIMEDLDI-------VSRGRTFTHGISKETAYREAVRLLQKILEE 324 (351)
T ss_pred HHHHHHHHHHHHHHHHHHHh-------CCCEEEEEEEcCCCCE-------EEEEEECCCCCCHHHHHHHHHHHHHhhhhc
Confidence 99999999999999999984 3678888888877642 467777776664 6788888888764211
Q ss_pred hhccccccccCCCCCCCceeEEeeccCCcccC
Q 007824 408 FLGSFGVKTQGSHYSGWRITALSVSASKIVPV 439 (588)
Q Consensus 408 ~~~~~~y~kaGv~~~~~~Ir~lgvs~s~L~~~ 439 (588)
.+.+||+|||++++|.+.
T Consensus 325 --------------~~~~vRllGv~~~~l~~~ 342 (351)
T PRK01216 325 --------------DERKIRRIGVRFSKIIEA 342 (351)
T ss_pred --------------CCCCeeEEEEEEeccccc
Confidence 123899999999999754
No 7
>PRK01810 DNA polymerase IV; Validated
Probab=100.00 E-value=4e-69 Score=582.15 Aligned_cols=340 Identities=30% Similarity=0.453 Sum_probs=304.5
Q ss_pred CCCCEEEEEeCChhHHHHhhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHhcCCCCCCcHHHHHhhCCCcEEEEccCC
Q 007824 9 SGARIIAHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVA 88 (588)
Q Consensus 9 ~~~r~I~hiD~D~FyasvE~~~~P~L~~~PvaV~~~~~~~~g~Via~SyeAR~~GVk~gM~~~~A~~lcP~L~~v~v~~~ 88 (588)
...|+|+||||||||||||++++|+|+|+||||++.+..++|+|+||||+||++||++||++.+|+++||++++++
T Consensus 2 ~~~r~i~hiD~d~Fyasve~~~~p~l~~~Pv~V~~~~~~~~~~v~a~ny~Ar~~GV~~Gm~~~~A~~lcP~l~~~~---- 77 (407)
T PRK01810 2 KKGRVIFHVDMNSFFASVEIAYDPSLQGKPLAVAGNEKERKGIIVTCSYEARAYGIRTTMPLWEAKRLCPQLIVRR---- 77 (407)
T ss_pred CCCCEEEEEecCcHHHhHHhhhCccccCCcEEEeCCCCCCCeEEEEcCHHHHHhCCCCCChHHHHHHHCCCeEEEC----
Confidence 4579999999999999999999999999999999765335689999999999999999999999999999999884
Q ss_pred CCCCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEeccchhHHhhhcCCCCCchhhhHHhhhhhcccCccCCCCCchh
Q 007824 89 RGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKA 167 (588)
Q Consensus 89 ~~~~d~~~Y~~~S~~v~~iL~~~-~~vE~~SiDEafLDlt~~~~~~l~~~~~~~~~~~~~~~~~~~l~g~~~~~~~~~~~ 167 (588)
+|++.|+++|.+|++++.+| |.||++||||+|||+|++.. +++
T Consensus 78 ---~d~~~y~~~s~~i~~~l~~~sp~ve~~siDe~~ldvt~~~~----------------------~~~----------- 121 (407)
T PRK01810 78 ---PNFDRYREASRQMFQILSEFTPLVQPVSIDEGYLDITDCYA----------------------LGS----------- 121 (407)
T ss_pred ---CChHHHHHHHHHHHHHHHHhCCceEEecCCeEEEeccCccc----------------------cCC-----------
Confidence 79999999999999999998 79999999999999998752 222
Q ss_pred hhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEEecCcHHHHHHHhcCCCCCCccccCccCHHHhcccCCC
Q 007824 168 TVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPI 247 (588)
Q Consensus 168 ~~~~~~~~~~~~~~~~ll~~g~~la~~Ir~~I~~~~Glt~SvGIa~nk~LAKLAs~~~KP~g~~vv~~~~~~~~L~~lPI 247 (588)
+..++++||++|++++|++||||||+||++||||++.+||+|+.++.++++..||+++||
T Consensus 122 --------------------~~~~a~~i~~~i~~~~gl~~svGia~n~~lAklas~~~Kp~g~~vi~~~~~~~~L~~lpv 181 (407)
T PRK01810 122 --------------------PLEIAKMIQQRLLTELQLPCSIGIAPNKFLAKMASDMKKPLGITVLRKRDVPEMLWPLPV 181 (407)
T ss_pred --------------------HHHHHHHHHHHHHHHHCCceEEEEcCCHHHHHHHhcCCCCCCEEEECHHHHHHHHHhCCH
Confidence 235799999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCcchHHHHHHHHhcCCCcccccccC--CcccccccccCCCCC
Q 007824 248 KKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLL--PKSHGSGKSFPGPRA 325 (588)
Q Consensus 248 ~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~~~g~~l~~~a~G~d~~~v~~~~~--pKsi~~s~sF~~~~~ 325 (588)
++|||||+++.++|. .+||+|++||+++|...|.++||+ .|.++|+.++|+++++|.+..+ .|||+.+++|+. +
T Consensus 182 ~~l~giG~~~~~~L~-~~Gi~tigdL~~~~~~~L~~rfG~-~g~~l~~~a~G~d~~~v~~~~~~~~ksi~~~~~~~~--~ 257 (407)
T PRK01810 182 GEMHGIGEKTAEKLK-DIGIQTIGDLAKADEHILRAKLGI-NGVRLQRRANGIDDRPVDPEAIYQFKSVGNSTTLSH--D 257 (407)
T ss_pred hhcCCcCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHHHhH-HHHHHHHHhcCCCCCCCCCCCCCCCceecceEECCC--C
Confidence 999999999999998 899999999999999999999997 5999999999999999986554 489999999995 4
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHhhhhhcCceeeEEEEEEEeccCCCCCCCcccCccccccCCCch---hHHHHHHHHHH
Q 007824 326 LKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTA---KIQEDTFNLFQ 402 (588)
Q Consensus 326 i~~~e~l~~~L~~La~eL~~RLr~~l~~~~~~~~tltL~lr~~~~~~~~~~~~~~s~s~~L~~~T~---~i~~~A~~Ll~ 402 (588)
+++.+++..+|..|+++|+.||+++ ++.|++|+|++++.++.. .+++.+++.||+ .|++.+..+|+
T Consensus 258 ~~~~~~l~~~l~~L~~~l~~rLr~~----~~~~~~l~l~lr~~~~~~-------~~~~~~l~~pt~~~~~l~~~~~~ll~ 326 (407)
T PRK01810 258 MDEEKELLDVLRRLSKSVSKRLQKK----TVVSYNVQIMIRYHDRRT-------ITRSKTLKNPIWEKRDIFQAASRLFK 326 (407)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHc----CCccceeEEEEEECCCCc-------eEEEEECCCCCCCHHHHHHHHHHHHH
Confidence 9999999999999999999999987 999999999999987642 245677777775 57777778877
Q ss_pred HHHHHhhccccccccCCCCCCCceeEEeeccCCcccC
Q 007824 403 AGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPV 439 (588)
Q Consensus 403 ~i~r~~~~~~~y~kaGv~~~~~~Ir~lgvs~s~L~~~ 439 (588)
+++ .+.+++.+||.+++|.+.
T Consensus 327 ~~~----------------~~~~vr~lgv~~~~l~~~ 347 (407)
T PRK01810 327 QHW----------------NGDPVRLLGVTATDLEWK 347 (407)
T ss_pred hcc----------------CCCCEEEEEEEEecCccc
Confidence 632 124899999999999864
No 8
>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=6.6e-69 Score=568.03 Aligned_cols=338 Identities=34% Similarity=0.518 Sum_probs=301.9
Q ss_pred EEEeCChhHHHHhhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHhcCCCCCCcHHHHHhhCCCcEEEEccCCCCCCCh
Q 007824 15 AHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVARGKADL 94 (588)
Q Consensus 15 ~hiD~D~FyasvE~~~~P~L~~~PvaV~~~~~~~~g~Via~SyeAR~~GVk~gM~~~~A~~lcP~L~~v~v~~~~~~~d~ 94 (588)
+||||||||||||++++|+|+++||||+++++ ++|+|+||||+||++||++||++.+|+++||++++++ +|+
T Consensus 1 ~hiD~d~F~as~e~~~~p~l~~~Pv~V~~~~~-~~~~V~a~sy~Ar~~GV~~gm~~~~A~~lcP~l~~~~-------~~~ 72 (343)
T cd00424 1 LHIDFDNFFASVEQLARPELKGRPVVVVPFNS-DSTCVIACSYEARKYGVKRGMPVREARKMCPNLILVP-------ARL 72 (343)
T ss_pred CeEecchHHHHHHhhhCccccCCCEEEecCCC-CCeEEEEeCHHHHHhCCCCCCcHHHHHHhCCCeEEEC-------CCc
Confidence 59999999999999999999999999998764 4588999999999999999999999999999998884 799
Q ss_pred HHHHHHHHHHHHHHhhc-CCeEEeccceEEEeccchhHHhhhcCCCCCchhhhHHhhhhhcccCccCCCCCchhhhhhhh
Q 007824 95 SSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKATVKEWL 173 (588)
Q Consensus 95 ~~Y~~~S~~v~~iL~~~-~~vE~~SiDEafLDlt~~~~~~l~~~~~~~~~~~~~~~~~~~l~g~~~~~~~~~~~~~~~~~ 173 (588)
+.|+++|++|++++.+| |.||++||||+|||+|++.. +|+.
T Consensus 73 ~~y~~~s~~i~~~l~~~sp~ve~~siDE~~ldvt~~~~----------------------~~~~---------------- 114 (343)
T cd00424 73 DLYRRLSERLLSELEEVAPLVEVASIDELFLDLTGSAR----------------------LLGL---------------- 114 (343)
T ss_pred HHHHHHHHHHHHHHHHhCCcEEEccCCEEEEECCCchh----------------------ccCC----------------
Confidence 99999999999999998 79999999999999999752 3332
Q ss_pred hccCccchhhhhhhHHHHHHHHHHHHHHHhC-CceeEEecCcHHHHHHHhcCCCCCCccccCccCHHHhcccCCCCCCCC
Q 007824 174 CRCDADHRDKLLACGVLIVTELRMQVLKETE-FTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQ 252 (588)
Q Consensus 174 ~~~~~~~~~~ll~~g~~la~~Ir~~I~~~~G-lt~SvGIa~nk~LAKLAs~~~KP~g~~vv~~~~~~~~L~~lPI~~l~G 252 (588)
+..+|++||++|++++| +|||||||+||++||||++++||+|++++.++++.+||+++||++|||
T Consensus 115 --------------~~~la~~i~~~i~~~~ggl~~siGia~n~~lAKlAs~~~KP~g~~v~~~~~~~~~L~~lpi~~l~g 180 (343)
T cd00424 115 --------------GSEVALRIKRHIAEQLGGITASIGIASNKLLAKLAAKYAKPDGLTILDPEDLPGFLSKLPLTDLPG 180 (343)
T ss_pred --------------HHHHHHHHHHHHHHHhCCceEEEeecccHHHHHHHhccCCCCCEEEEcHHHHHHHHhcCChhhcCC
Confidence 24679999999999998 999999999999999999999999999999999999999999999999
Q ss_pred CcHHHHHHHHHhhCCcchhhhccCC-HHHHHHHhCcchHHHHHHHHhcCCCcccccccCCcccccccccCCCCCCCCHHH
Q 007824 253 LGGKLGTSLQNELGVTTVGDLLKFS-EDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTVAS 331 (588)
Q Consensus 253 iG~k~~~~L~~~lGI~TigDLa~l~-~~~L~~rfG~~~g~~l~~~a~G~d~~~v~~~~~pKsi~~s~sF~~~~~i~~~e~ 331 (588)
||+++.++|. .+||+|++||+++| ...|+++||+ .|.++|+.++|+|++++.+..++|||+.+++|+. ++++.++
T Consensus 181 iG~~~~~~L~-~~Gi~ti~dl~~~~~~~~l~~~fg~-~~~~l~~~a~G~d~~~v~~~~~~ksi~~~~tf~~--~~~~~~~ 256 (343)
T cd00424 181 IGAVTAKRLE-AVGINPIGDLLAASPDALLALWGGV-SGERLWYALRGIDDEPLSPPRPRKSFSHERVLPR--DSRNAED 256 (343)
T ss_pred CCHHHHHHHH-HcCCCcHHHHhcCCHHHHHHHHhhH-HHHHHHHHhCCcCCCCCCCCCCCCceeeeEECCC--CCCCHHH
Confidence 9999999998 89999999999999 8899999997 5999999999999999988888999999999985 5999999
Q ss_pred HHHHHHHHHHHHHHHHHhhhhhcCceeeEEEEEEEeccCCCCCCCcccCccccccCCCch--hHHHHHHHHHHHHHHHhh
Q 007824 332 VQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTA--KIQEDTFNLFQAGLREFL 409 (588)
Q Consensus 332 l~~~L~~La~eL~~RLr~~l~~~~~~~~tltL~lr~~~~~~~~~~~~~~s~s~~L~~~T~--~i~~~A~~Ll~~i~r~~~ 409 (588)
+..+|..|+++|+.||+++ +..+++|+|++++.+..+. ......+++.+++.+|+ +|++.+.+||+++++.
T Consensus 257 l~~~l~~l~~~l~~rL~~~----~~~~~~l~l~lr~~~~~~~-~~~~~~~~~~~l~~~t~~~~l~~~~~~l~~~~~~~-- 329 (343)
T cd00424 257 ARPLLRLLLEKLARRLRRD----GRGATRLRLWLRTVDGRWS-GHADIPSRSAPRPISTEDGELLHALDKLWRALLDD-- 329 (343)
T ss_pred HHHHHHHHHHHHHHHHHHc----CCceeEEEEEEEeCCCccc-ccceeeeeeeeCCCCCCHHHHHHHHHHHHHhhhhc--
Confidence 9999999999999999987 9999999999998875431 11234567788887773 6888889998885432
Q ss_pred ccccccccCCCCCCCceeEEeeccC
Q 007824 410 GSFGVKTQGSHYSGWRITALSVSAS 434 (588)
Q Consensus 410 ~~~~y~kaGv~~~~~~Ir~lgvs~s 434 (588)
..+.+||.+||+++
T Consensus 330 -----------~~~~~ir~~gv~~~ 343 (343)
T cd00424 330 -----------KGPRRLRRLGVRLS 343 (343)
T ss_pred -----------cCCCCeeEEEEEeC
Confidence 01348999999764
No 9
>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=4.7e-69 Score=572.94 Aligned_cols=341 Identities=31% Similarity=0.507 Sum_probs=294.8
Q ss_pred EEEeCChhHHHHhhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHhcCCCCCCcHHHHHhhCCCcEEEEccCCCCCCCh
Q 007824 15 AHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVARGKADL 94 (588)
Q Consensus 15 ~hiD~D~FyasvE~~~~P~L~~~PvaV~~~~~~~~g~Via~SyeAR~~GVk~gM~~~~A~~lcP~L~~v~v~~~~~~~d~ 94 (588)
+||||||||||||++++|+|+|+||||.+ +|+|+||||+||++||++|||+.+|+++||++++++ .+|+
T Consensus 1 ~HiD~DaFyasve~~~~P~L~~kPv~V~~-----~~~V~aasy~AR~~GV~~gm~~~~A~~lcP~li~v~------~~~~ 69 (379)
T cd01703 1 IHLDLDCFYAQVEEIRDPSLKSKPLGIQQ-----KYIVVTCNYEARRLGVKKLMSIKDAKEICPDLVLVN------GEDL 69 (379)
T ss_pred CeeecccHHHHHHhhhccccCCCcEEECC-----CCEEEEcCHHHHHhCCCCCCcHHHHHHhCCCeEEEc------CCCh
Confidence 59999999999999999999999999964 378999999999999999999999999999998874 2489
Q ss_pred HHHHHHHHHHHHHHhhc-C--CeEEeccceEEEeccchhHHhhhcCCCCCchhhhHHhhhhhcccCccCCCCCchhhhhh
Q 007824 95 SSYRNAGSEVVSILARK-G--RCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKATVKE 171 (588)
Q Consensus 95 ~~Y~~~S~~v~~iL~~~-~--~vE~~SiDEafLDlt~~~~~~l~~~~~~~~~~~~~~~~~~~l~g~~~~~~~~~~~~~~~ 171 (588)
+.|+++|++|++++.+| | .||++||||+|||+|++.. ++
T Consensus 70 ~~Y~~~S~~i~~~l~~~sp~~~ve~~SiDE~~lDvt~~~~----------------------~~---------------- 111 (379)
T cd01703 70 TPFRDMSKKVYRLLRSYSWNDRVERLGFDENFMDVTEMRL----------------------LV---------------- 111 (379)
T ss_pred HHHHHHHHHHHHHHHHcCCHhhEEecCCCcEEEEccCccc----------------------hh----------------
Confidence 99999999999999998 7 8999999999999998731 11
Q ss_pred hhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEEecCcHHHHHHHhcCCCCCCccccCc---cCHHHhcccCCCC
Q 007824 172 WLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPF---SSVKGLLDSLPIK 248 (588)
Q Consensus 172 ~~~~~~~~~~~~ll~~g~~la~~Ir~~I~~~~Glt~SvGIa~nk~LAKLAs~~~KP~g~~vv~~---~~~~~~L~~lPI~ 248 (588)
|..+|++||++|++++|||||||||+||++||||++.+||+|++++.+ +++.+||+++||+
T Consensus 112 ----------------g~~la~~ir~~I~~~~Glt~siGIa~nk~lAKlas~~~KP~g~~~i~~~~~~~~~~fl~~lpv~ 175 (379)
T cd01703 112 ----------------ASHIAYEMRERIENELGLTCCAGIASNKLLAKLVGSVNKPNQQTTLLPPSCADLMDFMDLHDLR 175 (379)
T ss_pred ----------------HHHHHHHHHHHHHHHhCCeEEEEEcCCHHHHHHHhhhcCCCCeEEEcCCchHHHHHHhccCCcc
Confidence 356899999999999999999999999999999999999999999877 4567899999999
Q ss_pred CCCCCcHHHHHHHHHhhCCcchhhhccCC---------------HHHHHHHhCcchHHHHHHHHhcCCCccc-ccccCCc
Q 007824 249 KMKQLGGKLGTSLQNELGVTTVGDLLKFS---------------EDKLQESYGFNTGTWLWNIARGISGEEV-QARLLPK 312 (588)
Q Consensus 249 ~l~GiG~k~~~~L~~~lGI~TigDLa~l~---------------~~~L~~rfG~~~g~~l~~~a~G~d~~~v-~~~~~pK 312 (588)
+|||||++++++|. .+||.|++||++++ ...|+++||...|.++|+.++|+|+++| .+...+|
T Consensus 176 ~l~GiG~~~~~kL~-~~GI~tigdl~~~~~~~~~~~~~~~~~~s~~~L~~~fG~~~g~~l~~~a~G~d~~~V~~~~~~~k 254 (379)
T cd01703 176 KIPGIGYKTAAKLE-AHGISSVRDLQEFSNRNRQTVGAAPSLLELLLMVKEFGEGIGQRIWKLLFGRDTSPVKPASDFPQ 254 (379)
T ss_pred ccCCcCHHHHHHHH-HcCCCcHHHHHhCCcccccccccccccccHHHHHHHHCHHHHHHHHHHHCCCCCCccCCCCCCCc
Confidence 99999999999998 79999999999999 9999999996569999999999999999 5566689
Q ss_pred ccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhhhh----cCceeeEEEEEEEeccCCCCCCCcccCccccccCC
Q 007824 313 SHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQ----NKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRY 388 (588)
Q Consensus 313 si~~s~sF~~~~~i~~~e~l~~~L~~La~eL~~RLr~~l~~----~~~~~~tltL~lr~~~~~~~~~~~~~~s~s~~L~~ 388 (588)
+|+.++||+.+ ++.+.+++..+|..|+++|+.||++++.+ .+..++||+|++++.+.. ..+.+..|++++++.
T Consensus 255 sis~e~tf~~~-~~~~~~~~~~~l~~l~~~l~~rl~~~l~~~~~~~~~~~~tv~l~vr~~~~~--~~~~~~~sr~~~l~~ 331 (379)
T cd01703 255 QISIEDSYKKC-SLEEIREARNKIEELLASLLERMKQDLQEVKAGDGRRPHTLRLTLRRYTST--KKHYNRESKQAPIPS 331 (379)
T ss_pred eeEEeeccCCC-CCCCHHHHHHHHHHHHHHHHHHHHhhhhccchhcCeeeeEEEEEEEECCCC--CCccceeeeccccCc
Confidence 99999999863 78999999999999999999999984433 588999999999998721 011234578888887
Q ss_pred Cch------------hHHHHHHHHHHHHHHHhhccccccccCCCCCCCceeEEeeccCC
Q 007824 389 GTA------------KIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASK 435 (588)
Q Consensus 389 ~T~------------~i~~~A~~Ll~~i~r~~~~~~~y~kaGv~~~~~~Ir~lgvs~s~ 435 (588)
+|+ .|++.+..||++.+.. .. ..+.+||++||+++|
T Consensus 332 ~~~~~~~~~~~~~~~~i~~~~~~L~~~~~~~-------~~----~~~~~irl~gv~~~~ 379 (379)
T cd01703 332 HVFQKLTGGNEIAARPIEKILMRLFRELVPP-------KN----VKGFNLTLLNVCFTN 379 (379)
T ss_pred hhhccccccchhhHHHHHHHHHHHHHHhccc-------cc----CCCCceEEEEEEeeC
Confidence 663 5667777777763311 00 023589999998864
No 10
>PRK14133 DNA polymerase IV; Provisional
Probab=100.00 E-value=1.7e-68 Score=565.71 Aligned_cols=340 Identities=30% Similarity=0.399 Sum_probs=304.9
Q ss_pred CCEEEEEeCChhHHHHhhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHhcCCCCCCcHHHHHhhCCCcEEEEccCCCC
Q 007824 11 ARIIAHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVARG 90 (588)
Q Consensus 11 ~r~I~hiD~D~FyasvE~~~~P~L~~~PvaV~~~~~~~~g~Via~SyeAR~~GVk~gM~~~~A~~lcP~L~~v~v~~~~~ 90 (588)
.|+|+||||||||||||+.++|+|+++||||.+.. ++|+|++|||+||++||++||++.+|+++||++++++
T Consensus 2 ~r~i~hiD~d~F~as~e~~~~p~l~~~Pvvv~~~~--~~~~V~a~n~~Ar~~GV~~Gm~~~~A~~lcP~l~~~~------ 73 (347)
T PRK14133 2 DRVIIHVDMDAFFASVEQMDNPKLKGKPVIVGGIS--ERGVVSTCSYEARKYGVHSAMPVFMAKKRCPHGIFLP------ 73 (347)
T ss_pred CCEEEEEecChHHHHHHhhhCccccCCCEEEecCC--CCcEEEECCHHHHhcCCCCCChHHHHHHHCCCcEEEC------
Confidence 58999999999999999999999999999987543 3588999999999999999999999999999999984
Q ss_pred CCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEeccchhHHhhhcCCCCCchhhhHHhhhhhcccCccCCCCCchhhh
Q 007824 91 KADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKATV 169 (588)
Q Consensus 91 ~~d~~~Y~~~S~~v~~iL~~~-~~vE~~SiDEafLDlt~~~~~~l~~~~~~~~~~~~~~~~~~~l~g~~~~~~~~~~~~~ 169 (588)
+|++.|+++|++|++++.+| |.||++||||+|||+|++. +.
T Consensus 74 -~d~~~y~~~s~~i~~~l~~~s~~ve~~siDe~~ldv~~~~-------------------------~~------------ 115 (347)
T PRK14133 74 -VRHERYKEVSKNIFKILYEVTPIVEPVSIDEAYLDITNIK-------------------------EE------------ 115 (347)
T ss_pred -CCHHHHHHHHHHHHHHHHHhCCceEEccCCeEEEEccCCC-------------------------CC------------
Confidence 89999999999999999998 7999999999999999863 00
Q ss_pred hhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEEecCcHHHHHHHhcCCCCCCccccCccCHHHhcccCCCCC
Q 007824 170 KEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKK 249 (588)
Q Consensus 170 ~~~~~~~~~~~~~~ll~~g~~la~~Ir~~I~~~~Glt~SvGIa~nk~LAKLAs~~~KP~g~~vv~~~~~~~~L~~lPI~~ 249 (588)
...++++||++|++++||+||||||+||++||||++.+||+|++++.++++.+||+++||++
T Consensus 116 ------------------~~~la~~i~~~i~~~~gl~~siGia~n~~~Aklas~~~kp~g~~~~~~~~~~~~L~~lpv~~ 177 (347)
T PRK14133 116 ------------------PIKIAKYIKKKVKKETGLTLSVGISYNKFLAKLASDWNKPDGIKIITEDMIPDILKPLPISK 177 (347)
T ss_pred ------------------HHHHHHHHHHHHHHHHCCcEEEEEcCcHHHHHHHhccCCCCceEEECHHHHHHHHHhCCccc
Confidence 14579999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCcchHHHHHHHHhcCCCcccccccCCcccccccccCCCCCCCCH
Q 007824 250 MKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTV 329 (588)
Q Consensus 250 l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~~~g~~l~~~a~G~d~~~v~~~~~pKsi~~s~sF~~~~~i~~~ 329 (588)
|||||+++.++|. .+||+|++||+++|+..|.++||. .|.++|+.++|+|+.++.+..++|+|+.+.+|+. ++++.
T Consensus 178 l~gig~~~~~~L~-~~Gi~ti~dl~~l~~~~L~~rfG~-~g~~l~~~a~G~d~~~v~~~~~~ksi~~~~~~~~--~~~~~ 253 (347)
T PRK14133 178 VHGIGKKSVEKLN-NIGIYTIEDLLKLSREFLIEYFGK-FGVEIYERIRGIDYREVEVSRERKSIGKETTLKK--DTKDK 253 (347)
T ss_pred cCCCCHHHHHHHH-HcCCccHHHHhhCCHHHHHHHHhH-HHHHHHHHhCCCCCCCCCCCCCCcceEeeEEcCC--CCCCH
Confidence 9999999999998 899999999999999999999997 6999999999999999998888999999999985 49999
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhhcCceeeEEEEEEEeccCCCCCCCcccCccccccCCCch---hHHHHHHHHHHHHHH
Q 007824 330 ASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTA---KIQEDTFNLFQAGLR 406 (588)
Q Consensus 330 e~l~~~L~~La~eL~~RLr~~l~~~~~~~~tltL~lr~~~~~~~~~~~~~~s~s~~L~~~T~---~i~~~A~~Ll~~i~r 406 (588)
+++.++|.+|+++|+.||+++ ++.+++|+|++++.++.. .+++.+++.+|+ .+.+.+..+|+.++
T Consensus 254 ~~l~~~l~~L~~~l~~rL~~~----~~~~~~l~l~l~~~~~~~-------~~~~~~l~~~t~~~~~l~~l~~~lle~~~- 321 (347)
T PRK14133 254 EELKKYLKDFSNIISEELKKR----NLYGKTVTVKIKTSDFQT-------HTKSKTLNDYIRDKEEIYNVACEILEHIN- 321 (347)
T ss_pred HHHHHHHHHHHHHHHHHHHhc----CCCcceEEEEEEECCCCe-------eEEEEECCCCcCCHHHHHHHHHHHHHhcc-
Confidence 999999999999999999987 999999999999876542 255677777775 57777777776631
Q ss_pred HhhccccccccCCCCCCCceeEEeeccCCcccCCccchh
Q 007824 407 EFLGSFGVKTQGSHYSGWRITALSVSASKIVPVLSGTCS 445 (588)
Q Consensus 407 ~~~~~~~y~kaGv~~~~~~Ir~lgvs~s~L~~~~~~~~s 445 (588)
.+.+|+.|||++++|.+....|.+
T Consensus 322 ---------------~~~~vr~lgl~~~~l~~~~~~q~~ 345 (347)
T PRK14133 322 ---------------IKEPIRLIGLSVSNLSENKIEQLS 345 (347)
T ss_pred ---------------CCCCEEEEEEEEecCCCCcccccC
Confidence 135899999999999865433433
No 11
>PRK03858 DNA polymerase IV; Validated
Probab=100.00 E-value=2.2e-68 Score=574.65 Aligned_cols=337 Identities=29% Similarity=0.435 Sum_probs=302.9
Q ss_pred CCEEEEEeCChhHHHHhhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHhcCCCCCCcHHHHHhhCCCcEEEEccCCCC
Q 007824 11 ARIIAHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVARG 90 (588)
Q Consensus 11 ~r~I~hiD~D~FyasvE~~~~P~L~~~PvaV~~~~~~~~g~Via~SyeAR~~GVk~gM~~~~A~~lcP~L~~v~v~~~~~ 90 (588)
.++|+||||||||||||++++|+|+|+||||+ +|+|+||||+||++||++||++.+|+++||++++++
T Consensus 3 ~~~i~hiD~d~Fyas~e~~~~p~l~~~Pv~V~------~~~V~a~sy~Ar~~GV~~gm~~~~A~~lcP~l~~~~------ 70 (396)
T PRK03858 3 DASILHADLDSFYASVEQRDDPALRGRPVIVG------GGVVLAASYEAKAYGVRTAMGGRQARRLCPQAVVVP------ 70 (396)
T ss_pred CCEEEEEccChHHHHHHhhhCccccCCcEEEe------CCEEEEeCHHHHHhCCCCCChHHHHHHHCCCeEEEC------
Confidence 47899999999999999999999999999996 378999999999999999999999999999998884
Q ss_pred CCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEeccchhHHhhhcCCCCCchhhhHHhhhhhcccCccCCCCCchhhh
Q 007824 91 KADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKATV 169 (588)
Q Consensus 91 ~~d~~~Y~~~S~~v~~iL~~~-~~vE~~SiDEafLDlt~~~~~~l~~~~~~~~~~~~~~~~~~~l~g~~~~~~~~~~~~~ 169 (588)
+|++.|+++|++|++++.+| +.||++||||+|||+|++. ++||.
T Consensus 71 -~d~~~y~~~s~~i~~~l~~~s~~ve~~siDe~~ldvt~~~----------------------~~~~~------------ 115 (396)
T PRK03858 71 -PRMSAYSRASKAVFEVFRDTTPLVEGLSIDEAFLDVGGLR----------------------RISGT------------ 115 (396)
T ss_pred -CCHHHHHHHHHHHHHHHHHhCCceEEecCCeEEEEccccc----------------------cccCC------------
Confidence 79999999999999999998 7999999999999999975 34442
Q ss_pred hhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEEecCcHHHHHHHhcCCCCCCccccCccCHHHhcccCCCCC
Q 007824 170 KEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKK 249 (588)
Q Consensus 170 ~~~~~~~~~~~~~~ll~~g~~la~~Ir~~I~~~~Glt~SvGIa~nk~LAKLAs~~~KP~g~~vv~~~~~~~~L~~lPI~~ 249 (588)
...++++||++|++++|+|||||||+||++||||++.+||+|++++.++++..||+++||++
T Consensus 116 ------------------~~~la~~ir~~i~~~~gl~~svGia~n~~lAklas~~~Kp~g~~~i~~~~~~~~L~~lpl~~ 177 (396)
T PRK03858 116 ------------------PVQIAARLRRRVREEVGLPITVGVARTKFLAKVASQVAKPDGLLVVPPDRELAFLHPLPVRR 177 (396)
T ss_pred ------------------HHHHHHHHHHHHHHHHCCCeEEEEcCChHHHHHhhcccCCCceEEECcHHHHHHHhcCChhh
Confidence 24679999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCcchHHHHHHHHhcCCCcccccccCCcccccccccCCCCCCCCH
Q 007824 250 MKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTV 329 (588)
Q Consensus 250 l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~~~g~~l~~~a~G~d~~~v~~~~~pKsi~~s~sF~~~~~i~~~ 329 (588)
|||||+++.++|. ++||+|++||+++|+..|.++||...|.++|+.++|+|+.++.+..++|+|+.+++|+. ++.+.
T Consensus 178 l~Gig~~~~~~L~-~~Gi~t~~dl~~l~~~~L~~~fG~~~~~~l~~~a~G~d~~~v~~~~~~ksi~~~~t~~~--~~~~~ 254 (396)
T PRK03858 178 LWGVGPVTAAKLR-AHGITTVGDVAELPESALVSLLGPAAGRHLHALAHNRDPRRVETGRRRRSVGAQRALGR--GPNSP 254 (396)
T ss_pred cCCCCHHHHHHHH-HhCCCcHHHHhcCCHHHHHHHhCcHHHHHHHHHhCCCCCCCCCCCCCCccccceeEcCC--CCCCH
Confidence 9999999999998 89999999999999999999999867999999999999999988888899999999985 49999
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhhcCceeeEEEEEEEeccCCCCCCCcccCccccccCCCch---hHHHHHHHHHHHHHH
Q 007824 330 ASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTA---KIQEDTFNLFQAGLR 406 (588)
Q Consensus 330 e~l~~~L~~La~eL~~RLr~~l~~~~~~~~tltL~lr~~~~~~~~~~~~~~s~s~~L~~~T~---~i~~~A~~Ll~~i~r 406 (588)
+++..+|..|+++|+.||+++ ++.|++|+|++++.++.. .+++.+++.+|+ .|.+.+..+|+.++.
T Consensus 255 ~~l~~~l~~L~~~l~~rLr~~----~~~~~~l~l~l~~~~~~~-------~~~~~~l~~~t~~~~~l~~l~~~ll~~~~~ 323 (396)
T PRK03858 255 AEVDAVVVALVDRVARRMRAA----GRTGRTVVLRLRFDDFTR-------ATRSHTLPRPTASTATLLAAARDLVAAAAP 323 (396)
T ss_pred HHHHHHHHHHHHHHHHHHHhc----CCCcceEEEEEEeCCCCE-------EEEEEECCCCcCCHHHHHHHHHHHHHhhhh
Confidence 999999999999999999987 999999999999876542 355677777776 567777777776432
Q ss_pred HhhccccccccCCCCCCCceeEEeeccCCcccC
Q 007824 407 EFLGSFGVKTQGSHYSGWRITALSVSASKIVPV 439 (588)
Q Consensus 407 ~~~~~~~y~kaGv~~~~~~Ir~lgvs~s~L~~~ 439 (588)
. + .+.+|+.+||.+++|.+.
T Consensus 324 ~----~---------~~~~irligv~~~~l~~~ 343 (396)
T PRK03858 324 L----I---------AERGLTLVGFAVSNLDDD 343 (396)
T ss_pred c----c---------CCCCeEEEEEEeecCCcc
Confidence 1 0 124799999999988754
No 12
>PRK03103 DNA polymerase IV; Reviewed
Probab=100.00 E-value=2.5e-68 Score=576.34 Aligned_cols=343 Identities=27% Similarity=0.430 Sum_probs=306.2
Q ss_pred CCEEEEEeCChhHHHHhhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHhcCCCCCCcHHHHHhhCCCcEEEEccCCCC
Q 007824 11 ARIIAHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVARG 90 (588)
Q Consensus 11 ~r~I~hiD~D~FyasvE~~~~P~L~~~PvaV~~~~~~~~g~Via~SyeAR~~GVk~gM~~~~A~~lcP~L~~v~v~~~~~ 90 (588)
.|+|+||||||||||||+..+|+|+|+||||+++...++|+|+||||+||++||++||++.+|+++||++++++
T Consensus 2 ~r~i~hiD~d~Ffasve~~~~P~l~~~Pv~V~~~~~~~~~~v~a~sy~Ar~~GV~~gm~~~~A~~lcP~l~~~~------ 75 (409)
T PRK03103 2 ERVILLVDMQSFYASVEKAANPELKGRPVIVSGDPERRSGVVLAACPLAKAYGVKTAERLWEAQQKCPDLVVVK------ 75 (409)
T ss_pred CCEEEEEecchHHHhHhcccChhhcCCcEEEeccCCCCCEEEEEcCHHHHHhCCCCCChHHHHHHHCCCeEEEC------
Confidence 58999999999999999999999999999998764334688999999999999999999999999999999884
Q ss_pred CCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEeccchhHHhhhcCCCCCchhhhHHhhhhhcccCccCCCCCchhhh
Q 007824 91 KADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKATV 169 (588)
Q Consensus 91 ~~d~~~Y~~~S~~v~~iL~~~-~~vE~~SiDEafLDlt~~~~~~l~~~~~~~~~~~~~~~~~~~l~g~~~~~~~~~~~~~ 169 (588)
+|++.|+++|++|++++.+| |.||++||||+|||+|++. ++||.
T Consensus 76 -~d~~~y~~~s~~i~~~l~~~sp~ve~~siDe~~lDvt~~~----------------------~~~~~------------ 120 (409)
T PRK03103 76 -PRMQRYIDVSLQITRILEDFTDLVEPFSIDEQFLDVTGSQ----------------------KLFGS------------ 120 (409)
T ss_pred -CCHHHHHHHHHHHHHHHHHhCccceecCCCeeEeeccchh----------------------hcCCC------------
Confidence 79999999999999999998 7999999999999999985 34442
Q ss_pred hhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEEecCcHHHHHHHhcC---CCCCCccccCccCHHHhcccCC
Q 007824 170 KEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGM---NKPAQQTTVPFSSVKGLLDSLP 246 (588)
Q Consensus 170 ~~~~~~~~~~~~~~ll~~g~~la~~Ir~~I~~~~Glt~SvGIa~nk~LAKLAs~~---~KP~g~~vv~~~~~~~~L~~lP 246 (588)
...++++||++|++++|+|||||||+||++||||++. +||+|+.++.++++.+||+++|
T Consensus 121 ------------------~~~la~~ir~~i~~~~gl~~svGia~n~~lAklas~~~~k~kp~g~~v~~~~~~~~~L~~lp 182 (409)
T PRK03103 121 ------------------PLEIAQKIQQRIMRETGVYARVGIGPNKLLAKMACDNFAKKNPDGLFTLDKEDVPADLWPLP 182 (409)
T ss_pred ------------------HHHHHHHHHHHHHHHHCceEEEeecCCHHHHHHHhcchhhcCCCcEEEECHHHHHHHHHcCC
Confidence 2457999999999999999999999999999999998 9999999999999999999999
Q ss_pred CCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCcchHHHHHHHHhcCCCcccccccC--CcccccccccCCCC
Q 007824 247 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLL--PKSHGSGKSFPGPR 324 (588)
Q Consensus 247 I~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~~~g~~l~~~a~G~d~~~v~~~~~--pKsi~~s~sF~~~~ 324 (588)
|++|||||+++.++|. .+||+|++||+++|+..|.++||. .|.++|+.++|+++++|.+..+ +|||+.+.+|+.
T Consensus 183 i~~l~gig~~~~~~L~-~~Gi~tigdl~~~~~~~L~~~fG~-~~~~l~~~a~G~d~~~v~~~~~~~~ksi~~~~t~~~-- 258 (409)
T PRK03103 183 VRKLFGVGSRMEKHLR-RMGIRTIGQLANTPLERLKKRWGI-NGEVLWRTANGIDYSPVTPHSLDRQKAIGHQMTLPR-- 258 (409)
T ss_pred HhhcCCccHHHHHHHH-HcCCCCHHHHhcCCHHHHHHHHCH-HHHHHHHHhcCCCCCcCCcccCCCCCccCCCeECCC--
Confidence 9999999999999998 899999999999999999999997 5999999999999999988754 479999999985
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhhhcCceeeEEEEEEEeccCCCCCCCcccCccccccCCCch---hHHHHHHHHH
Q 007824 325 ALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTA---KIQEDTFNLF 401 (588)
Q Consensus 325 ~i~~~e~l~~~L~~La~eL~~RLr~~l~~~~~~~~tltL~lr~~~~~~~~~~~~~~s~s~~L~~~T~---~i~~~A~~Ll 401 (588)
++.+.++|...|.+|+++|+.||+++ +..+++|+|++++.++.. .+..+++.+++.||+ .|.+.+..+|
T Consensus 259 ~~~~~~~l~~~l~~L~~~l~~rLr~~----~~~~~~l~l~lr~~~~~~----~~~~~~~~~l~~pt~~~~~l~~~~~~ll 330 (409)
T PRK03103 259 DYRGFEEIKVVLLELCEEVCRRARAK----GYMGRTVSVSLRGADFDW----PTGFSRQMTLPEPTNLAMEVYEAACKLF 330 (409)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHh----CCceeEEEEEEEeCCCcC----CCCcceeeecCCCCCCHHHHHHHHHHHH
Confidence 59999999999999999999999986 999999999999887642 133567788887776 5677777777
Q ss_pred HHHHHHhhccccccccCCCCCCCceeEEeeccCCcccCC
Q 007824 402 QAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPVL 440 (588)
Q Consensus 402 ~~i~r~~~~~~~y~kaGv~~~~~~Ir~lgvs~s~L~~~~ 440 (588)
++++ .+.+|+.+||.+++|.+..
T Consensus 331 ~~~~----------------~~~~vr~lgv~~~~l~~~~ 353 (409)
T PRK03103 331 HRHW----------------DGKPVRRVGVTLSNLVSDD 353 (409)
T ss_pred Hhcc----------------cCCCceEEEEEEeCCCCCc
Confidence 7632 2358999999999988643
No 13
>PRK02794 DNA polymerase IV; Provisional
Probab=100.00 E-value=8.8e-68 Score=573.28 Aligned_cols=339 Identities=27% Similarity=0.408 Sum_probs=304.1
Q ss_pred CCCEEEEEeCChhHHHHhhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHhcCCCCCCcHHHHHhhCCCcEEEEccCCC
Q 007824 10 GARIIAHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVAR 89 (588)
Q Consensus 10 ~~r~I~hiD~D~FyasvE~~~~P~L~~~PvaV~~~~~~~~g~Via~SyeAR~~GVk~gM~~~~A~~lcP~L~~v~v~~~~ 89 (588)
..|+|+||||||||||||++.+|+|+|+||||... ++|+|++|||+||++||++||++.+|+++||++++++
T Consensus 34 ~~~~i~hiD~d~Fyasve~~~~p~l~~~Pv~v~~~---~~~~V~a~ny~Ar~~GV~~GM~~~~A~~lcP~l~~v~----- 105 (419)
T PRK02794 34 YTLSIAHIDCDAFYASVEKRDNPELRDKPVIIGGG---KRGVVSTACYIARIHGVRSAMPMFKALKLCPDAVVIK----- 105 (419)
T ss_pred cCCEEEEEcCCcHHHHHHhhhCccccCCcEEEecC---CCeEEEecCHHHHHhCCCcCCHHHHHHHHCCCcEEEC-----
Confidence 35799999999999999999999999999999753 2589999999999999999999999999999999884
Q ss_pred CCCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEeccchhHHhhhcCCCCCchhhhHHhhhhhcccCccCCCCCchhh
Q 007824 90 GKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKAT 168 (588)
Q Consensus 90 ~~~d~~~Y~~~S~~v~~iL~~~-~~vE~~SiDEafLDlt~~~~~~l~~~~~~~~~~~~~~~~~~~l~g~~~~~~~~~~~~ 168 (588)
+|++.|+++|++|++++.+| |.||++||||+|||+|++. ++||.+
T Consensus 106 --~d~~~y~~~s~~i~~~l~~~sp~ve~~siDe~~ldvt~~~----------------------~l~g~~---------- 151 (419)
T PRK02794 106 --PDMEKYVRVGREVRAMMQALTPLVEPLSIDEAFLDLSGTE----------------------RLHGAP---------- 151 (419)
T ss_pred --CCHHHHHHHHHHHHHHHHHhCcceeeccCCeEEEeccchh----------------------hhcCCC----------
Confidence 79999999999999999998 7999999999999999975 355532
Q ss_pred hhhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEEecCcHHHHHHHhcCCCCCCccccCccCHHHhcccCCCC
Q 007824 169 VKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIK 248 (588)
Q Consensus 169 ~~~~~~~~~~~~~~~ll~~g~~la~~Ir~~I~~~~Glt~SvGIa~nk~LAKLAs~~~KP~g~~vv~~~~~~~~L~~lPI~ 248 (588)
.+.++.+||++|++++||+||||||+||++||||++.+||+|++++.++++.+||+++||+
T Consensus 152 -------------------~~~~~~~i~~~i~~~~gl~~svGIa~n~~lAKlas~~~KP~g~~ii~~~~~~~~L~~lPl~ 212 (419)
T PRK02794 152 -------------------PAVVLARFARRVEREIGITVSVGLSYNKFLAKIASDLDKPRGFSVIGRAEALAFLAPKPVG 212 (419)
T ss_pred -------------------HHHHHHHHHHHHHHHHCCceEEEEcCCHHHHHHHHhhhCCCCeEecCHHHHHHHHhcCChh
Confidence 1235789999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCcchHHHHHHHHhcCCCcccccccCCcccccccccCCCCCCCC
Q 007824 249 KMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKT 328 (588)
Q Consensus 249 ~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~~~g~~l~~~a~G~d~~~v~~~~~pKsi~~s~sF~~~~~i~~ 328 (588)
+|||||+++.++|. .+||+|++||+++|...|.++||. .|.++|+.++|+|+.++.+..++|+|+.+++|+. ++.+
T Consensus 213 ~L~GiG~~~~~~L~-~~GI~tigdL~~l~~~~L~~rfG~-~g~~l~~~a~G~d~~~v~~~~~~ksi~~~~tl~~--~~~~ 288 (419)
T PRK02794 213 IIWGVGPATAARLA-RDGIRTIGDLQRADEADLMRRFGS-MGLRLWRLARGIDDRKVSPDREAKSVSAETTFET--DLSD 288 (419)
T ss_pred hhCCCCHHHHHHHH-HhccchHHHHhhCCHHHHHHHHhH-HHHHHHHHhCCCCCCCCccCCCCceeeeeEECCC--CCCC
Confidence 99999999999998 899999999999999999999998 5999999999999999998888999999999985 4999
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhcCceeeEEEEEEEeccCCCCCCCcccCccccccCCCch---hHHHHHHHHHHHHH
Q 007824 329 VASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTA---KIQEDTFNLFQAGL 405 (588)
Q Consensus 329 ~e~l~~~L~~La~eL~~RLr~~l~~~~~~~~tltL~lr~~~~~~~~~~~~~~s~s~~L~~~T~---~i~~~A~~Ll~~i~ 405 (588)
.+++..+|..|+++|+.||+++ ++.+++|+|++++.++.. .+++.+++.+|+ .|++.+..+|++++
T Consensus 289 ~~~l~~~l~~L~~~l~~rL~~~----~~~~~~l~l~l~~~~~~~-------~~~~~~l~~pt~~~~~l~~~~~~ll~~~~ 357 (419)
T PRK02794 289 FEDLEPILWRLSEKVSRRLKAA----GLAGRTVTLKLKTADFRL-------RTRRRTLEDPTQLADRIFRTARELLEKET 357 (419)
T ss_pred HHHHHHHHHHHHHHHHHHHHhc----CCCcceEEEEEEECCCCc-------eEEEEECCCCcCCHHHHHHHHHHHHHhcc
Confidence 9999999999999999999987 999999999999876532 356677777775 56667777776531
Q ss_pred HHhhccccccccCCCCCCCceeEEeeccCCcccCC
Q 007824 406 REFLGSFGVKTQGSHYSGWRITALSVSASKIVPVL 440 (588)
Q Consensus 406 r~~~~~~~y~kaGv~~~~~~Ir~lgvs~s~L~~~~ 440 (588)
.+.+|+.+||.+++|.+..
T Consensus 358 ----------------~~~~vr~igv~~~~l~~~~ 376 (419)
T PRK02794 358 ----------------DGTAFRLIGIGVSDLSPAD 376 (419)
T ss_pred ----------------cCCCEEEEEEEEecCCCcc
Confidence 2348999999999998643
No 14
>PRK03348 DNA polymerase IV; Provisional
Probab=100.00 E-value=1e-67 Score=576.18 Aligned_cols=347 Identities=28% Similarity=0.392 Sum_probs=306.5
Q ss_pred CCCEEEEEeCChhHHHHhhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHhcCCCCCCcHHHHHhhCCC-cEEEEccCC
Q 007824 10 GARIIAHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQ-IELVQVPVA 88 (588)
Q Consensus 10 ~~r~I~hiD~D~FyasvE~~~~P~L~~~PvaV~~~~~~~~g~Via~SyeAR~~GVk~gM~~~~A~~lcP~-L~~v~v~~~ 88 (588)
..|+|+||||||||||||++.+|+|+|+||+|.+.. .+|+|++|||+||++||++||++.+|+++||+ +++++
T Consensus 3 ~~r~I~hiDmDaFfasvE~~~~P~L~g~PvvV~~~~--~~gvV~aasyeAR~~GVrsgMp~~~A~~lcP~~lv~v~---- 76 (454)
T PRK03348 3 AQRWVLHLDMDAFFASVEQLTRPTLRGRPVLVGGLG--GRGVVAGASYEARVFGARSAMPMHQARRLVGNGAVVLP---- 76 (454)
T ss_pred CCCEEEEEecChHHHhhhhhhCccccCCcEEEEcCC--CCeEEEeCCHHHHhcCCCCCCcHHHHHHhCCCCEEEEC----
Confidence 458999999999999999999999999999987643 36888999999999999999999999999999 88873
Q ss_pred CCCCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEeccchhHHhhhcCCCCCchhhhHHhhhhhcccCccCCCCCchh
Q 007824 89 RGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKA 167 (588)
Q Consensus 89 ~~~~d~~~Y~~~S~~v~~iL~~~-~~vE~~SiDEafLDlt~~~~~~l~~~~~~~~~~~~~~~~~~~l~g~~~~~~~~~~~ 167 (588)
+|++.|+.+|++|++++.+| +.||++||||+|||+++.. +..
T Consensus 77 ---~d~~~Y~~~s~~i~~~l~~~sp~VE~~SiDE~flD~~~l~-------------------------~~~--------- 119 (454)
T PRK03348 77 ---PRFVVYRAASRRVFDTLRELSPVVEQLSFDEAFVEPAELA-------------------------GAS--------- 119 (454)
T ss_pred ---CChHHHHHHHHHHHHHHHHhCCceEEecCCeEEEEccccc-------------------------ccc---------
Confidence 89999999999999999999 7999999999999987643 110
Q ss_pred hhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEEecCcHHHHHHHhcCCCCCCccccCccCHHHhcccCCC
Q 007824 168 TVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPI 247 (588)
Q Consensus 168 ~~~~~~~~~~~~~~~~ll~~g~~la~~Ir~~I~~~~Glt~SvGIa~nk~LAKLAs~~~KP~g~~vv~~~~~~~~L~~lPI 247 (588)
......++++||++|++++||+||||||+||++||||++++||+|+++++++.+.+||+++||
T Consensus 120 -----------------~~~~~~~a~~lr~~I~~~~Gl~~SvGIa~nk~lAKlAs~~aKP~G~~vi~~~~~~~~L~~LPv 182 (454)
T PRK03348 120 -----------------AEEVEAFAERLRARVREETGLPASVGAGSGKQIAKIASGLAKPDGIRVVPPGEERELLAPLPV 182 (454)
T ss_pred -----------------CCCHHHHHHHHHHHHHHHHCCCeEEEEcCCHHHHHHhhccCCCCcEEEEEchHHHHHHHhCCc
Confidence 001245799999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCcchHHHHHHHHhcCCCcccccccCCcccccccccCCCCCCC
Q 007824 248 KKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALK 327 (588)
Q Consensus 248 ~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~~~g~~l~~~a~G~d~~~v~~~~~pKsi~~s~sF~~~~~i~ 327 (588)
++|||||+++.++|. ++||+|++||+++|...|.++||...|.+||+.++|+|+++|.+..++|+|+.+++|+. ++.
T Consensus 183 ~~L~GIG~~t~~~L~-~lGI~TigDLa~l~~~~L~~~fG~~~g~~L~~~a~G~d~~pv~~~~~~ksis~e~tf~~--~i~ 259 (454)
T PRK03348 183 RRLWGIGPVTEEKLH-RLGIETIGDLAALSEAEVANLLGATVGPALHRLARGIDDRPVAERAEAKQISAESTFAV--DLT 259 (454)
T ss_pred cccCCCCHHHHHHHH-HcCCccHHHHhcCCHHHHHHHHCHHHHHHHHHHHcCCCCCCcccCCCCceEEEEEECCC--CCC
Confidence 999999999999998 89999999999999999999999657999999999999999999889999999999985 599
Q ss_pred CHHHHHHHHHHHHHHHHHHHHhhhhhcCceeeEEEEEEEeccCCCCCCCcccCccccccCCCch---hHHHHHHHHHHHH
Q 007824 328 TVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTA---KIQEDTFNLFQAG 404 (588)
Q Consensus 328 ~~e~l~~~L~~La~eL~~RLr~~l~~~~~~~~tltL~lr~~~~~~~~~~~~~~s~s~~L~~~T~---~i~~~A~~Ll~~i 404 (588)
+.+++..+|.+|+++|+.||+++ ++.|++|+|++++.++. ..+++.+++.+|+ .|.+.+..+|+.+
T Consensus 260 ~~~~l~~~L~~L~~~l~~rL~~~----g~~~r~v~l~l~~~d~~-------~~srs~~l~~pt~d~~~L~~la~~ll~~~ 328 (454)
T PRK03348 260 TRAQLREAIERIAEHAHRRLLKD----GRGARTVTVKLRKSDFS-------TLTRSATLPYATDDAAVLAATARRLLLDP 328 (454)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHc----CCCccEEEEEEEeCCCC-------ccEEEEECCCCCCCHHHHHHHHHHHHHhh
Confidence 99999999999999999999987 99999999999987654 2367788888886 4667777777652
Q ss_pred HHHhhccccccccCCCCCCCceeEEeeccCCcccCCccchhhhh
Q 007824 405 LREFLGSFGVKTQGSHYSGWRITALSVSASKIVPVLSGTCSIMK 448 (588)
Q Consensus 405 ~r~~~~~~~y~kaGv~~~~~~Ir~lgvs~s~L~~~~~~~~sLm~ 448 (588)
+ ...+||++||++++|.+. .|.+|..
T Consensus 329 ~----------------~~~~vRllgV~~s~l~~~--~q~~LF~ 354 (454)
T PRK03348 329 D----------------EIGPIRLVGVGFSGLSDV--RQESLFP 354 (454)
T ss_pred c----------------cCCCeEEEEEEECCCCcc--hhhccCC
Confidence 1 113899999999999743 4555543
No 15
>PRK03352 DNA polymerase IV; Validated
Probab=100.00 E-value=1.8e-67 Score=557.71 Aligned_cols=337 Identities=27% Similarity=0.398 Sum_probs=301.0
Q ss_pred CCCCEEEEEeCChhHHHHhhhhCCCCCCCcEEEEecCC--CCCcEEEEcCHHHHhcCCCCCCcHHHHHhhCCCcEEEEcc
Q 007824 9 SGARIIAHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNE--WKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVP 86 (588)
Q Consensus 9 ~~~r~I~hiD~D~FyasvE~~~~P~L~~~PvaV~~~~~--~~~g~Via~SyeAR~~GVk~gM~~~~A~~lcP~L~~v~v~ 86 (588)
...|+|+||||||||||||++.+|+|+++||||++.++ .++|+|++|||+||++||++||++.+|+++||++++++
T Consensus 2 ~~~r~i~hiD~d~F~as~e~~~~p~l~~~Pvvv~~~~~~~~~~~~V~~~sy~Ar~~GV~~gM~~~~A~~lcP~l~~v~-- 79 (346)
T PRK03352 2 AMPRWVLHVDLDQFIAAVELLRRPELAGLPVIVGGNGDPTEPRKVVTCASYEARAFGVRAGMPLRTAARRCPDAVFLP-- 79 (346)
T ss_pred CCCcEEEEEccchHHHHHHhhhCccccCCCEEEecCCCCCCCceEEEECCHHHHHhCCCcCChHHHHHHHCCCeEEEC--
Confidence 45799999999999999999999999999999986543 13588999999999999999999999999999999984
Q ss_pred CCCCCCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEeccchhHHhhhcCCCCCchhhhHHhhhhhcccCccCCCCCc
Q 007824 87 VARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDS 165 (588)
Q Consensus 87 ~~~~~~d~~~Y~~~S~~v~~iL~~~-~~vE~~SiDEafLDlt~~~~~~l~~~~~~~~~~~~~~~~~~~l~g~~~~~~~~~ 165 (588)
+|++.|+++|++|+.++.+| +.||++||||+|||+|+..
T Consensus 80 -----~~~~~y~~~s~~i~~~l~~~s~~ve~~siDe~~ld~t~~~----------------------------------- 119 (346)
T PRK03352 80 -----SDPAAYDAASEEVMATLRDLGVPVEVWGWDEAFLGVDTDD----------------------------------- 119 (346)
T ss_pred -----CCcHHHHHHHHHHHHHHHHhCCceEEecCccEEEeCCCCC-----------------------------------
Confidence 79999999999999999998 7999999999999999851
Q ss_pred hhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEEecCcHHHHHHHhcCCCCCCccccCccCHHHhcccC
Q 007824 166 KATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSL 245 (588)
Q Consensus 166 ~~~~~~~~~~~~~~~~~~ll~~g~~la~~Ir~~I~~~~Glt~SvGIa~nk~LAKLAs~~~KP~g~~vv~~~~~~~~L~~l 245 (588)
...++++||++|++++|||||||||+||++||||++.+||+|++++.++++.+||+++
T Consensus 120 ----------------------~~~la~~ir~~i~~~~gl~~siGia~nk~lAklaa~~~Kp~g~~~~~~~~~~~~L~~l 177 (346)
T PRK03352 120 ----------------------PEALAEEIRAAVLERTGLSCSVGIGDNKLRAKIATGFAKPAGVFRLTDANWMAVMGDR 177 (346)
T ss_pred ----------------------HHHHHHHHHHHHHHHHCCCEEEeecCCHHHHHHHHhhcCCCcEEEECHHHHHHHHhcC
Confidence 1356899999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCcchHHHHHHHHhcCCCccccccc-CCcccccccccCCCC
Q 007824 246 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARL-LPKSHGSGKSFPGPR 324 (588)
Q Consensus 246 PI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~~~g~~l~~~a~G~d~~~v~~~~-~pKsi~~s~sF~~~~ 324 (588)
||++|||||+++.++|. ++||+|++||+++|+..|.++||...|.++|+.++|+|+.++.... .||+++.+.+|+.
T Consensus 178 pl~~l~gig~~~~~~L~-~~Gi~ti~dl~~l~~~~L~~~fG~~~~~~l~~~a~G~d~~~~~~~~~~~ksi~~~~tf~~-- 254 (346)
T PRK03352 178 PTDALWGVGPKTAKRLA-ALGITTVADLAAADPAELAATFGPTTGPWLLLLARGGGDTEVSAEPWVPRSRSREVTFPQ-- 254 (346)
T ss_pred CHHHcCCCCHHHHHHHH-HcCCccHHHHhcCCHHHHHHHhChHHHHHHHHHhCCCCCCCCCCCCCCCceEEEEEECCC--
Confidence 99999999999999998 8999999999999999999999976699999999999999987643 4799999999984
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhhhcCceeeEEEEEEEeccCCCCCCCcccCccccccCCCch---hHHHHHHHHH
Q 007824 325 ALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTA---KIQEDTFNLF 401 (588)
Q Consensus 325 ~i~~~e~l~~~L~~La~eL~~RLr~~l~~~~~~~~tltL~lr~~~~~~~~~~~~~~s~s~~L~~~T~---~i~~~A~~Ll 401 (588)
++.+.+++..+|..|+++|+.||+++ ++.|++|+|++++.++.. .+++.+++.+|+ .+.+.+..+|
T Consensus 255 ~~~~~~~l~~~l~~L~~~l~~rLr~~----~~~~~~l~l~l~~~~~~~-------~~~~~~l~~pt~d~~~l~~~~~~ll 323 (346)
T PRK03352 255 DLTDRAEVESAVRELARRVLDEVVAE----GRPVTRVAVKVRTATFYT-------RTKIRKLPEPTTDPDVIEAAALDVL 323 (346)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHc----CCccceEEEEEEeCCCce-------eEEEEECCCCcCCHHHHHHHHHHHH
Confidence 59999999999999999999999987 999999999999887532 256677777776 4667777777
Q ss_pred HHHHHHhhccccccccCCCCCCCceeEEeeccCCcccC
Q 007824 402 QAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPV 439 (588)
Q Consensus 402 ~~i~r~~~~~~~y~kaGv~~~~~~Ir~lgvs~s~L~~~ 439 (588)
++++ .+.+|+.||+++.+|.+.
T Consensus 324 ~~~~----------------~~~~vr~igl~~~~~~~~ 345 (346)
T PRK03352 324 DRFE----------------LDRPVRLLGVRLELAMPD 345 (346)
T ss_pred Hhcc----------------CCCCEEEEEEEEeccCCC
Confidence 6521 124899999999998753
No 16
>cd03586 PolY_Pol_IV_kappa DNA Polymerase IV/Kappa. Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Known primarily as Pol IV in prokaryotes and Pol kappa in eukaryotes, this polymerase has a propensity for generating frameshift mutations. The eukaryotic Pol kappa differs from Pol IV and Dpo4 by an N-terminal extension of ~75 residues known as the "N-clasp" region. The structure of Pol kappa shows DNA that is almost totally encircled by Pol kappa, with the N-clasp region augmenting the interactions between DNA and the polymerase. Pol kappa is more resistant than Pol eta and Pol iota to bulky guanine adducts and is efficient at catalyzing the incorporation of dCTP. Bacterial pol IV has a
Probab=100.00 E-value=3.4e-66 Score=545.34 Aligned_cols=330 Identities=36% Similarity=0.538 Sum_probs=298.6
Q ss_pred EEEeCChhHHHHhhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHhcCCCCCCcHHHHHhhCCCcEEEEccCCCCCCCh
Q 007824 15 AHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVARGKADL 94 (588)
Q Consensus 15 ~hiD~D~FyasvE~~~~P~L~~~PvaV~~~~~~~~g~Via~SyeAR~~GVk~gM~~~~A~~lcP~L~~v~v~~~~~~~d~ 94 (588)
+||||||||||||++++|+|+++||||+++++ +|+|+||||+||++||++||++.+|+++||++++++ +|+
T Consensus 1 ~hiD~d~Ffas~e~~~~p~l~~~Pv~V~~~~~--~~~v~a~n~~Ar~~GV~~Gm~~~~A~~lcp~l~~~~-------~~~ 71 (334)
T cd03586 1 IHIDMDAFYASVEQRDNPELKGKPVAVGGSSD--RGVVSTASYEARKFGVRSAMPIFQAKKLCPNLIFVP-------PRF 71 (334)
T ss_pred CeeccchHHHHHHhhhCccccCCCEEEEeCCC--CeEEEEcCHHHHhcCCCcCCcHHHHHHHCCCeEEEC-------CCc
Confidence 59999999999999999999999999998764 689999999999999999999999999999999984 899
Q ss_pred HHHHHHHHHHHHHHhhc-CCeEEeccceEEEeccchhHHhhhcCCCCCchhhhHHhhhhhcccCccCCCCCchhhhhhhh
Q 007824 95 SSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKATVKEWL 173 (588)
Q Consensus 95 ~~Y~~~S~~v~~iL~~~-~~vE~~SiDEafLDlt~~~~~~l~~~~~~~~~~~~~~~~~~~l~g~~~~~~~~~~~~~~~~~ 173 (588)
+.|+++|++|++++.+| |.||++||||+|||+|++. ++|+.
T Consensus 72 ~~y~~~s~~i~~~l~~~~~~ve~~s~De~~ldv~~~~----------------------~~~~~---------------- 113 (334)
T cd03586 72 DKYREVSRQIMEILREYTPLVEPLSIDEAYLDVTDYV----------------------RLFGS---------------- 113 (334)
T ss_pred HHHHHHHHHHHHHHHHcCCceEEecccceeEcccccc----------------------ccCCC----------------
Confidence 99999999999999998 7999999999999999975 23442
Q ss_pred hccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEEecCcHHHHHHHhcCCCCCCccccCccCHHHhcccCCCCCCCCC
Q 007824 174 CRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQL 253 (588)
Q Consensus 174 ~~~~~~~~~~ll~~g~~la~~Ir~~I~~~~Glt~SvGIa~nk~LAKLAs~~~KP~g~~vv~~~~~~~~L~~lPI~~l~Gi 253 (588)
+..++++||++|++++|++||+|||+||++||||++.+||+|+++++++++.+||+++||+++|||
T Consensus 114 --------------~~~la~~ir~~i~~~~g~~~siGia~n~~lAklaa~~~kp~g~~i~~~~~~~~~L~~lpl~~l~gi 179 (334)
T cd03586 114 --------------ATEIAKEIRARIREETGLTASAGIAPNKFLAKIASDLNKPNGLTVIPPEDVEEFLAPLPVRKIPGV 179 (334)
T ss_pred --------------HHHHHHHHHHHHHHHHCCceEEEEhhcHHHHHHHhcCCCCCcEEEECHHHHHHHHhcCCchhhCCc
Confidence 256899999999999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCcchHHHHHHHHhcCCCcccccccCCcccccccccCCCCCCCCHHHHH
Q 007824 254 GGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTVASVQ 333 (588)
Q Consensus 254 G~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~~~g~~l~~~a~G~d~~~v~~~~~pKsi~~s~sF~~~~~i~~~e~l~ 333 (588)
|+++.++|. .+||+|++||+++|+..|.++||. .|.++|+.++|+++.++.+..++|+|+.+++|+. ++.+.+++.
T Consensus 180 g~~~~~~L~-~~Gi~ti~dl~~~~~~~L~~~~g~-~~~~l~~~~~G~~~~~v~~~~~~ks~~~~~~~~~--~~~~~~~l~ 255 (334)
T cd03586 180 GKVTAEKLK-ELGIKTIGDLAKLDVELLKKLFGK-SGRRLYELARGIDNRPVEPDRERKSIGVERTFSE--DLTDPEELL 255 (334)
T ss_pred CHHHHHHHH-HcCCcCHHHHHcCCHHHHHHHHhH-HHHHHHHHhCCCCCCCCCCCCCCCeeeeeEECCC--CCCCHHHHH
Confidence 999999998 899999999999999999999997 5999999999999999998888999999999985 489999999
Q ss_pred HHHHHHHHHHHHHHHhhhhhcCceeeEEEEEEEeccCCCCCCCcccCccccccCCCch---hHHHHHHHHHHHHHHHhhc
Q 007824 334 HWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTA---KIQEDTFNLFQAGLREFLG 410 (588)
Q Consensus 334 ~~L~~La~eL~~RLr~~l~~~~~~~~tltL~lr~~~~~~~~~~~~~~s~s~~L~~~T~---~i~~~A~~Ll~~i~r~~~~ 410 (588)
++|..|+++|+.||+++ ++.|++|+|++++.++. ..+++.+++.+|+ .|.+.+..+|++++
T Consensus 256 ~~l~~l~~~l~~rL~~~----~~~~~~l~l~l~~~~~~-------~~~~~~~l~~~t~~~~~l~~~~~~~l~~~~----- 319 (334)
T cd03586 256 EELLELAEELAERLRKR----GLKGRTVTVKLKYADFS-------TRTRSRTLPEPTDDAEDIYELALELLEELL----- 319 (334)
T ss_pred HHHHHHHHHHHHHHHhC----CCCeEEEEEEEEECCCC-------eEEEEEECCCCCCCHHHHHHHHHHHHHhcc-----
Confidence 99999999999999987 99999999999987643 2356677777765 46666666666531
Q ss_pred cccccccCCCCCCCceeEEeeccCCc
Q 007824 411 SFGVKTQGSHYSGWRITALSVSASKI 436 (588)
Q Consensus 411 ~~~y~kaGv~~~~~~Ir~lgvs~s~L 436 (588)
.+.+|+.+||++++|
T Consensus 320 -----------~~~~vr~igv~~~~l 334 (334)
T cd03586 320 -----------DGRPIRLLGVRLSGL 334 (334)
T ss_pred -----------CCCCEEEEEEEeecC
Confidence 124899999998875
No 17
>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=1.3e-65 Score=543.10 Aligned_cols=334 Identities=28% Similarity=0.379 Sum_probs=288.4
Q ss_pred EEEeCChhHHHHhhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHhcCCCCCCcHHHHHhhCCCcEEEEccCCCCCCCh
Q 007824 15 AHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVARGKADL 94 (588)
Q Consensus 15 ~hiD~D~FyasvE~~~~P~L~~~PvaV~~~~~~~~g~Via~SyeAR~~GVk~gM~~~~A~~lcP~L~~v~v~~~~~~~d~ 94 (588)
+||||||||||||++.+|+|+++||||++.+ +|.|++|||+||++||++||++.+|+++||++.++.++ +|+
T Consensus 1 ~hiD~d~Ffasve~~~~p~l~~~Pv~V~~~~---~~~i~~~ny~Ar~~GV~~gm~~~~A~~lcP~l~~~~v~-----~~~ 72 (344)
T cd01700 1 ALVDCNSFYASCERVFRPLLLGRPLVVLSNN---DGCVIARSPEAKALGIKMGSPYFKVPDLLERHGVAVFS-----SNY 72 (344)
T ss_pred CccccccceeeehhhhCCCcCCCeEEEEECC---CCEEEECCHHHHHhCCCCCCcHHHhHhhccccCeEEEc-----Cch
Confidence 5999999999999999999999999998764 36799999999999999999999999999999322233 799
Q ss_pred HHHHHHHHHHHHHHhhc-CCeEEeccceEEEeccchhHHhhhcCCCCCchhhhHHhhhhhcccCccCCCCCchhhhhhhh
Q 007824 95 SSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKATVKEWL 173 (588)
Q Consensus 95 ~~Y~~~S~~v~~iL~~~-~~vE~~SiDEafLDlt~~~~~~l~~~~~~~~~~~~~~~~~~~l~g~~~~~~~~~~~~~~~~~ 173 (588)
+.|+++|++|++++.+| +.||++||||+|||+|++.+ |+.
T Consensus 73 ~~y~~~s~~i~~~l~~~~~~ve~~s~De~~ldvt~~~~-----------------------~~~---------------- 113 (344)
T cd01700 73 ALYGDMSRRIMSILERFSPDVEVYSIDESFLDLTGSLR-----------------------FGD---------------- 113 (344)
T ss_pred HHHHHHHHHHHHHHHhcCCcceEeecchhhccCcCCCC-----------------------CCC----------------
Confidence 99999999999999999 79999999999999999752 221
Q ss_pred hccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEEecCcHHHHHHHhcCCCCC----CccccCccCHH-HhcccCCCC
Q 007824 174 CRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPA----QQTTVPFSSVK-GLLDSLPIK 248 (588)
Q Consensus 174 ~~~~~~~~~~ll~~g~~la~~Ir~~I~~~~Glt~SvGIa~nk~LAKLAs~~~KP~----g~~vv~~~~~~-~~L~~lPI~ 248 (588)
...++++||++|++++|++||+|||+||++||||++++||+ |+.++.+++.. +||+++||+
T Consensus 114 --------------~~~la~~i~~~i~~~~gl~~s~Gia~~~~lAklas~~~kp~~~~~g~~~~~~~~~~~~~l~~lpl~ 179 (344)
T cd01700 114 --------------LEELARKIRRRILQETGIPVTVGIGPTKTLAKLANDLAKKKNPYGGVVDLTDEEVRDKLLKILPVG 179 (344)
T ss_pred --------------HHHHHHHHHHHHHHHhCCceEEEecCCHHHHHHHHHHhcCCCCCCeEEEecChhHHHHHhccCChh
Confidence 24679999999999999999999999999999999999985 56666666654 899999999
Q ss_pred CCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCcchHHHHHHHHhcCCCcccccccC-CcccccccccCCCCCCC
Q 007824 249 KMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLL-PKSHGSGKSFPGPRALK 327 (588)
Q Consensus 249 ~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~~~g~~l~~~a~G~d~~~v~~~~~-pKsi~~s~sF~~~~~i~ 327 (588)
+|||||+++.++|. .+||+|++||+++|...|.++||. .|.++|+.++|++++++....+ +|+|+.+.+|.. ++.
T Consensus 180 ~l~gig~~~~~~L~-~~Gi~ti~dL~~~~~~~L~~rfG~-~~~~l~~~a~G~d~~~v~~~~~~~ks~~~~~~~~~--~~~ 255 (344)
T cd01700 180 DVWGIGRRTAKKLN-AMGIHTAGDLAQADPDLLRKKFGV-VGERLVRELNGIDCLPLEEYPPPKKSIGSSRSFGR--DVT 255 (344)
T ss_pred hcCccCHHHHHHHH-HcCCCcHHHHhcCCHHHHHHHHHH-HHHHHHHHhCCCCCCcCCCCCCCCcEEEEeeEcCC--CCC
Confidence 99999999999998 899999999999999999999997 5999999999999999976555 489999999985 599
Q ss_pred CHHHHHHHHHHHHHHHHHHHHhhhhhcCceeeEEEEEEEeccCCCCCCCcccCccccccCCCch---hHHHHHHHHHHHH
Q 007824 328 TVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTA---KIQEDTFNLFQAG 404 (588)
Q Consensus 328 ~~e~l~~~L~~La~eL~~RLr~~l~~~~~~~~tltL~lr~~~~~~~~~~~~~~s~s~~L~~~T~---~i~~~A~~Ll~~i 404 (588)
+.+++..+|.+|+++|+.||+++ ++.|++|+|++++.++... ....+.+.+++.+|+ .|.+.+..+|+++
T Consensus 256 ~~~~l~~~l~~L~~~l~~~L~~~----~~~~~~l~l~l~~~~~~~~---~~~~~~~~~~~~~t~~~~~l~~~~~~ll~~~ 328 (344)
T cd01700 256 DLDELKQALAEYAERAAEKLRRQ----KSVARTISVFIGTSGFSRQ---PKYYSATNTLPYPTNDTREIVKAALRLLYAI 328 (344)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHc----CCcccEEEEEEEcCCCCCC---CCccccccccCCcchhHHHHHHHHHHHHHHH
Confidence 99999999999999999999987 9999999999999876531 122233455666775 4666777777764
Q ss_pred HHHhhccccccccCCCCCCCceeEEeeccCC
Q 007824 405 LREFLGSFGVKTQGSHYSGWRITALSVSASK 435 (588)
Q Consensus 405 ~r~~~~~~~y~kaGv~~~~~~Ir~lgvs~s~ 435 (588)
+. .+.+||.|||+++|
T Consensus 329 ~~---------------~~~~iR~iGV~~~~ 344 (344)
T cd01700 329 YR---------------PGYAYRKAGVMLSD 344 (344)
T ss_pred hC---------------CCCcEEEEEEEeeC
Confidence 32 13489999998864
No 18
>PRK02406 DNA polymerase IV; Validated
Probab=100.00 E-value=4.1e-65 Score=539.15 Aligned_cols=334 Identities=31% Similarity=0.457 Sum_probs=294.6
Q ss_pred CChhHHHHhhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHhcCCCCCCcHHHHHhhCCCcEEEEccCCCCCCChHHHH
Q 007824 19 LDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVARGKADLSSYR 98 (588)
Q Consensus 19 ~D~FyasvE~~~~P~L~~~PvaV~~~~~~~~g~Via~SyeAR~~GVk~gM~~~~A~~lcP~L~~v~v~~~~~~~d~~~Y~ 98 (588)
|||||||||++.+|+|+++||||++... ++|+|++|||+||++|||+||++.+|+++||++++++ +|++.|+
T Consensus 1 ~d~Ffasve~~~~p~l~~~Pv~v~~~~~-~~~~v~a~n~~Ar~~GV~~gm~~~~A~~lcP~l~~~~-------~d~~~y~ 72 (343)
T PRK02406 1 MDCFYAAVEMRDNPELRGKPVAVGGSPG-RRGVISTCNYEARKFGVRSAMPTAQALKLCPDLIFVP-------GRFDVYK 72 (343)
T ss_pred CCchHHHHHhhhCccccCCCEEEecCCC-CCeEEEecCHHHHHhCCCCCCcHHHHHHHCCCeEEEC-------CChHHHH
Confidence 8999999999999999999999987642 4689999999999999999999999999999999984 7999999
Q ss_pred HHHHHHHHHHhhc-CCeEEeccceEEEeccchhHHhhhcCCCCCchhhhHHhhhhhcccCccCCCCCchhhhhhhhhccC
Q 007824 99 NAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKATVKEWLCRCD 177 (588)
Q Consensus 99 ~~S~~v~~iL~~~-~~vE~~SiDEafLDlt~~~~~~l~~~~~~~~~~~~~~~~~~~l~g~~~~~~~~~~~~~~~~~~~~~ 177 (588)
++|++|+.++.+| |.||++||||+|||+|++. ++||.
T Consensus 73 ~~s~~i~~~l~~~sp~ve~~siDe~~ldvt~~~----------------------~~~~~-------------------- 110 (343)
T PRK02406 73 EVSRQIREIFRRYTDLIEPLSLDEAYLDVTDNK----------------------LCIGS-------------------- 110 (343)
T ss_pred HHHHHHHHHHHHhCCceEEccCCeEEEeccCcc----------------------ccCCC--------------------
Confidence 9999999999998 7999999999999999976 34442
Q ss_pred ccchhhhhhhHHHHHHHHHHHHHHHhCCceeEEecCcHHHHHHHhcCCCCCCccccCccCHHHhcccCCCCCCCCCcHHH
Q 007824 178 ADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKL 257 (588)
Q Consensus 178 ~~~~~~ll~~g~~la~~Ir~~I~~~~Glt~SvGIa~nk~LAKLAs~~~KP~g~~vv~~~~~~~~L~~lPI~~l~GiG~k~ 257 (588)
+..++++||++|++++|++||||||+||++||||++++||+|++++.++++.+||+++||++|||||+++
T Consensus 111 ----------~~~la~~i~~~i~~~~gl~~siGia~n~~lAklas~~~Kp~g~~~~~~~~~~~~L~~lpi~~l~giG~~~ 180 (343)
T PRK02406 111 ----------ATLIAQEIRQDIFEELGLTASAGVAPNKFLAKIASDWNKPNGLFVITPEEVDAFLATLPVEKIPGVGKVT 180 (343)
T ss_pred ----------HHHHHHHHHHHHHHHHCCCeEEEeccCHHHHHHHhcCCCCCCEEEECHHHHHHHHHcCCcchhcCCCHHH
Confidence 2467999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhCCcchhhhccCCHHHHHHHhCcchHHHHHHHHhcCCCcccccccCCcccccccccCCCCCCCCHHHHHHHHH
Q 007824 258 GTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLN 337 (588)
Q Consensus 258 ~~~L~~~lGI~TigDLa~l~~~~L~~rfG~~~g~~l~~~a~G~d~~~v~~~~~pKsi~~s~sF~~~~~i~~~e~l~~~L~ 337 (588)
.++|. .+||+|++||+++|...|.++||. .|.++|+.++|+|+.+|.+..++|+|+.+++|+. ++.+.+++..+|.
T Consensus 181 ~~~L~-~~Gi~ti~dl~~l~~~~L~~~fG~-~~~~l~~~a~G~d~~~v~~~~~~ksi~~~~~~~~--~~~~~~~l~~~l~ 256 (343)
T PRK02406 181 AEKLH-ALGIYTCADLQKYDLAELIRHFGK-FGRRLYERARGIDERPVKPDRERKSVGVERTFAE--DLYDLEACLAELP 256 (343)
T ss_pred HHHHH-HcCCCcHHHHHhCCHHHHHHHHhH-HHHHHHHHhCCCCCCccccCCCCcceeeeeeCCC--CCCCHHHHHHHHH
Confidence 99998 899999999999999999999997 5999999999999999998888999999999985 5999999999999
Q ss_pred HHHHHHHHHHHhhhhhcC--ceeeEEEEEEEeccCCCCCCCcccCccccccCCCch---hHHHHHHHHHHHHHHHhhccc
Q 007824 338 QLCEELSERLCSDLEQNK--RIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTA---KIQEDTFNLFQAGLREFLGSF 412 (588)
Q Consensus 338 ~La~eL~~RLr~~l~~~~--~~~~tltL~lr~~~~~~~~~~~~~~s~s~~L~~~T~---~i~~~A~~Ll~~i~r~~~~~~ 412 (588)
+|+++|+.||+++ + +.+++|+|++++.++.. .+++.+ ..+|+ .+...+..|++..+
T Consensus 257 ~l~~~l~~rL~~~----~~~~~~~~l~l~l~~~~~~~-------~~~~~~-~~~~~~~~~l~~~~~~L~~~~~------- 317 (343)
T PRK02406 257 RLAEKLERRLERA----KPDKRIKTVGVKLKFADFQQ-------TTKEHT-ADPLDKADLIELLAQALLRRLG------- 317 (343)
T ss_pred HHHHHHHHHHHhc----CCCccceeEEEEEEeCCCCe-------EEEecC-CCCCCcHHHHHHHHHHHHhhCc-------
Confidence 9999999999987 8 99999999999877542 122222 33343 34555566655421
Q ss_pred cccccCCCCCCCceeEEeeccCCcccCCccchh
Q 007824 413 GVKTQGSHYSGWRITALSVSASKIVPVLSGTCS 445 (588)
Q Consensus 413 ~y~kaGv~~~~~~Ir~lgvs~s~L~~~~~~~~s 445 (588)
+.+|+.+||++++|.+....|.+
T Consensus 318 ----------~~~vr~lgv~~~~l~~~~~~q~~ 340 (343)
T PRK02406 318 ----------GRGVRLLGVGVTLLEPQLERQLL 340 (343)
T ss_pred ----------CCCEEEEEEEEecCCcCchhhhc
Confidence 24899999999999865444444
No 19
>COG0389 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]
Probab=100.00 E-value=3.8e-61 Score=509.32 Aligned_cols=342 Identities=35% Similarity=0.508 Sum_probs=305.1
Q ss_pred CEEEEEeCChhHHHHhhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHhcCCCCCCcHHHHHhhCCCcEEEEccCCCCC
Q 007824 12 RIIAHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVARGK 91 (588)
Q Consensus 12 r~I~hiD~D~FyasvE~~~~P~L~~~PvaV~~~~~~~~g~Via~SyeAR~~GVk~gM~~~~A~~lcP~L~~v~v~~~~~~ 91 (588)
|+|+||||||||||||++++|+|+++||||++++ .+|+|++|||+||+|||++|||+.+|+++||++.+++
T Consensus 1 ~~i~hvD~Daf~Asve~~~~p~l~~~Pvvv~~~~--~~gvV~~~sy~Ar~~Gv~sam~~~~A~~~cp~~~~~~------- 71 (354)
T COG0389 1 RKILHVDMDAFYASVEERDNPELKGKPVVVGGGA--PRGVVLAASYEARAFGVRSAMPLFEALKLCPRAIVAP------- 71 (354)
T ss_pred CeEEEEeccchhhhhhhhcCccccCCCeEEEecC--CCCEEEecCHHHHHhCCcccChHHHHHHHCCCCEEeC-------
Confidence 5799999999999999999999999999999862 4699999999999999999999999999999999884
Q ss_pred CChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEeccchhHHhhhcCCCCCchhhhHHhhhhhcccCccCCCCCchhhhh
Q 007824 92 ADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKATVK 170 (588)
Q Consensus 92 ~d~~~Y~~~S~~v~~iL~~~-~~vE~~SiDEafLDlt~~~~~~l~~~~~~~~~~~~~~~~~~~l~g~~~~~~~~~~~~~~ 170 (588)
++++.|+.+|.+++.|+.++ +.||++||||+|||+|+..+ .+|.
T Consensus 72 ~~~~~y~~~s~~i~~i~~~~~~~ve~lSIDE~~ldvt~~~~----------------------~~g~------------- 116 (354)
T COG0389 72 PNFAAYRLASAEIRAILERYTPLVEPLSIDEAFLDLTDALR----------------------LLGL------------- 116 (354)
T ss_pred CcHHHHHHHHHHHHHHHHhccccceeeeccceeeecccccc----------------------cCCc-------------
Confidence 79999999999999999998 78999999999999998753 2221
Q ss_pred hhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEEecCcHHHHHHHhcCCCCCCccccCccCHHHhcccCCCCCC
Q 007824 171 EWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKM 250 (588)
Q Consensus 171 ~~~~~~~~~~~~~ll~~g~~la~~Ir~~I~~~~Glt~SvGIa~nk~LAKLAs~~~KP~g~~vv~~~~~~~~L~~lPI~~l 250 (588)
..+..+|.+||..|++++|+|||+|||+||++||||++++||+|++++.+..+.+||++|||.++
T Consensus 117 ---------------~~~~~~a~~ir~~i~~~~~l~~s~Gi~~nk~laKiAs~~~kp~gi~~~~~~~~~~~l~~Lpv~~~ 181 (354)
T COG0389 117 ---------------ADAPRIALEIRFGILLELGLTASVGISDNKFLAKIASDLNKPDGITVIEPEEVPALLWQLPVLEF 181 (354)
T ss_pred ---------------ccHHHHHHHHHHHHHHhhCCEEEEEecCcHHHHHHHhcccCCCCEEEECHHHHHHHHhcCChhhh
Confidence 11357899999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCcchHHHHHHHHhcCCCcccccccCC-cccccccccCCCCCCCCH
Q 007824 251 KQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLP-KSHGSGKSFPGPRALKTV 329 (588)
Q Consensus 251 ~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~~~g~~l~~~a~G~d~~~v~~~~~p-Ksi~~s~sF~~~~~i~~~ 329 (588)
||||+.+.++|. .+||+|++||++.+...|.++||. .+.+||+.++|+|.++|...... ||++.+.+|+. ++++.
T Consensus 182 ~GvG~~~~~~l~-~~Gi~ti~dl~~~~~~~L~~~~g~-~~~~l~~~a~Gid~~~v~~~~~~~ksi~~~~t~~~--d~~~~ 257 (354)
T COG0389 182 WGVGKVTAEKLR-RLGISTIGDLAETDLDALKKRFGK-LGERLYRLARGIDNRPVREQALRAKSIGAESTFEE--DLTDA 257 (354)
T ss_pred CCCCHHHHHHHH-HcCChhHHHHHhcCHHHHHHHHhH-hHHHHHHHhcCCCccccccccccCccccceeeccc--cccCH
Confidence 999999999998 899999999999999999999998 57999999999999999998887 99999999994 68999
Q ss_pred HHHHHHHHH-HHHHHHHHHHhhhhhcCceeeEEEEEEEeccCCCCCCCcccCccccccCCCch---hHHHHHHHHHHHHH
Q 007824 330 ASVQHWLNQ-LCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTA---KIQEDTFNLFQAGL 405 (588)
Q Consensus 330 e~l~~~L~~-La~eL~~RLr~~l~~~~~~~~tltL~lr~~~~~~~~~~~~~~s~s~~L~~~T~---~i~~~A~~Ll~~i~ 405 (588)
+++...|.. |+++++.||+.. +..++++++++++.+|.+ .+++..|+.||+ +++..+..+|+..+
T Consensus 258 ~~~~~~l~~~l~e~~~~rl~~~----~~~~r~v~~~~~~~df~~-------~t~~~~l~~p~~~~~~i~~~~~~l~~~~~ 326 (354)
T COG0389 258 EELIERLRARLGEEVVSRLRKS----GRHGRTVSVKLKTADFPT-------NTRSRKLAQPTSDPIEIYAAALPLLPPLL 326 (354)
T ss_pred HHHHHHHHHHHHHHHHHHHHHh----CCCceEEEEEEEecCCCc-------ceeecccCCcCCCHHHHHHHHHHHHHHhh
Confidence 988888887 999999999986 888999999999998743 456667777664 67777888888744
Q ss_pred HHhhccccccccCCCCCCCceeEEeeccCCcccCC
Q 007824 406 REFLGSFGVKTQGSHYSGWRITALSVSASKIVPVL 440 (588)
Q Consensus 406 r~~~~~~~y~kaGv~~~~~~Ir~lgvs~s~L~~~~ 440 (588)
.. +.+..+|.+|++++++.+..
T Consensus 327 ~~-------------~~~~~~rl~gv~~~~~~~~~ 348 (354)
T COG0389 327 FR-------------GRGRRIRLLGVSGPELIDSE 348 (354)
T ss_pred cc-------------CCCceEEEEEEEecCccccc
Confidence 22 11358999999999988654
No 20
>KOG2094 consensus Predicted DNA damage inducible protein [Replication, recombination and repair]
Probab=100.00 E-value=8.1e-61 Score=479.24 Aligned_cols=341 Identities=30% Similarity=0.437 Sum_probs=293.0
Q ss_pred CCCCEEEEEeCChhHHHHhhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHhcCCCCCCcHHHHHhhCCCcEEEEccCC
Q 007824 9 SGARIIAHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVA 88 (588)
Q Consensus 9 ~~~r~I~hiD~D~FyasvE~~~~P~L~~~PvaV~~~~~~~~g~Via~SyeAR~~GVk~gM~~~~A~~lcP~L~~v~v~~~ 88 (588)
+-.|+|+|||||+|||+||.++||.|+++|+||++.. .+.++||.||++||+.+||++.|+++||+|++|+
T Consensus 100 dLsr~~vhvDmDAfyAaVE~~dnP~lk~~PmAVGs~s-----mlsTaNY~ARkFGVRaaMPgFIarklCPdLiiVP---- 170 (490)
T KOG2094|consen 100 DLSRIIVHVDMDAFYAAVEMLDNPKLKSKPMAVGSKS-----MLSTANYVARKFGVRAAMPGFIARKLCPDLIIVP---- 170 (490)
T ss_pred cccceEEEechHHHHHHHHhccCcccccCCccccchh-----hhhhhhHHHHHhhhhhcCchHHHhccCCceEEeC----
Confidence 5579999999999999999999999999999998653 5778999999999999999999999999999984
Q ss_pred CCCCChHHHHHHHHHHHHHHhhc-CCeEEeccceEEEeccchhHHhhhcCCCCCchhhhHHhhhhhcccCccCCCCCchh
Q 007824 89 RGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKA 167 (588)
Q Consensus 89 ~~~~d~~~Y~~~S~~v~~iL~~~-~~vE~~SiDEafLDlt~~~~~~l~~~~~~~~~~~~~~~~~~~l~g~~~~~~~~~~~ 167 (588)
.||..|+.+|.++-+||.+| +.+-..|+||+|||+|..++.. -+|...++|
T Consensus 171 ---~n~~kYt~~Ske~~~v~~~YDsn~~~~SlDEaylnlT~~l~~~--------------------~~g~l~~nG----- 222 (490)
T KOG2094|consen 171 ---LNFSKYTIVSKEIQNVLAQYDSNFCAMSLDEAYLNLTSHLRER--------------------ELGFLVENG----- 222 (490)
T ss_pred ---CCcHHHHHHHHHHHHHHHHcCCccccchHHHHHHhHHHHHHHh--------------------hcchhhhcc-----
Confidence 79999999999999999999 7899999999999999987531 123110000
Q ss_pred hhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEEecCcHHHHHHHhcCCCCCCccccCcc--CHHHhcccC
Q 007824 168 TVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFS--SVKGLLDSL 245 (588)
Q Consensus 168 ~~~~~~~~~~~~~~~~ll~~g~~la~~Ir~~I~~~~Glt~SvGIa~nk~LAKLAs~~~KP~g~~vv~~~--~~~~~L~~l 245 (588)
...++++||.+|.++||+|||+|||+|++|||++|+.+|||||++++++ .+..|+.+|
T Consensus 223 --------------------~~evveeiR~rV~qeTglT~SaGIAaN~lLAKicSd~nKPNgQf~i~~dr~aim~F~kdL 282 (490)
T KOG2094|consen 223 --------------------ITEVVEEIRFRVEQETGLTCSAGIAANKLLAKICSDKNKPNGQFVIPNDRIAIMKFMKDL 282 (490)
T ss_pred --------------------HHHHHHHHHHHHHHhcCceeeccccHhHHHHHHhccccCCCCceEecccHHHHHHHHhcC
Confidence 2467999999999999999999999999999999999999999999886 578999999
Q ss_pred CCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCcchHHHHHHHHhcCCCcccccccCCcccccccccCCCCC
Q 007824 246 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRA 325 (588)
Q Consensus 246 PI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~~~g~~l~~~a~G~d~~~v~~~~~pKsi~~s~sF~~~~~ 325 (588)
||+++-|||+.+...|. .+||.||||+.. ....|--.|.+...+.+++.+.|....++.....+|||++++||..
T Consensus 283 PvRkV~GIGrV~E~qLk-al~IkTcgdm~~-k~~ll~~lFsp~S~~~fLr~slG~g~t~~~~~~eRKsis~ErTFs~--- 357 (490)
T KOG2094|consen 283 PVRKVSGIGRVTEQQLK-ALGIKTCGDMQQ-KLVLLSLLFSPKSFQNFLRCSLGLGTTILDEDGERKSISSERTFSS--- 357 (490)
T ss_pred CcccccchhHHHHHHHH-hcCceeHHHHHH-hhhHHHHHhCchhHHHHHHHhhcCCCCcCccccccccccceeeecc---
Confidence 99999999999999997 899999999976 3456777898877788999999999998888888999999999974
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHhhhhhcCceeeEEEEEEEeccCCCCCCCcccCcccccc---CCCchhHHHHHHHHHH
Q 007824 326 LKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPL---RYGTAKIQEDTFNLFQ 402 (588)
Q Consensus 326 i~~~e~l~~~L~~La~eL~~RLr~~l~~~~~~~~tltL~lr~~~~~~~~~~~~~~s~s~~L---~~~T~~i~~~A~~Ll~ 402 (588)
+.+...+...+.+||+.|++-|+++ |++++||+|+++.+.|... +++.++ .....+|.+.|++|++
T Consensus 358 ~sd~~il~~k~qel~~~lsedlqK~----glv~rtvtiKlK~ssFev~-------Tr~~t~s~vv~S~edi~k~aleLLk 426 (490)
T KOG2094|consen 358 TSDPSILYSKLQELCQMLSEDLQKE----GLVGRTVTIKLKTSSFEVH-------TRQKTISQVVHSEEDILKPALELLK 426 (490)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHhc----CcccceEEEEEeccceeee-------eccCchhhhhccHHHHHHHHHHHHH
Confidence 7888889988999999988888876 9999999999999887632 222221 1233589999999988
Q ss_pred HHHHHhhccccccccCCCCCCCceeEEeeccCCcccC
Q 007824 403 AGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPV 439 (588)
Q Consensus 403 ~i~r~~~~~~~y~kaGv~~~~~~Ir~lgvs~s~L~~~ 439 (588)
+- -+..||++||.++.|...
T Consensus 427 ~e-----------------~~~~iRLlGvR~sqlv~e 446 (490)
T KOG2094|consen 427 QE-----------------YPMTIRLLGVRASQLVSE 446 (490)
T ss_pred hh-----------------cCceEeeeeeeHhhccch
Confidence 71 135899999999999875
No 21
>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=1.3e-52 Score=442.09 Aligned_cols=323 Identities=20% Similarity=0.172 Sum_probs=273.5
Q ss_pred EEEeCChhHHHHhhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHhcCCCCCCcHHHHHhhCCCcEEEEccCCCCCCCh
Q 007824 15 AHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVARGKADL 94 (588)
Q Consensus 15 ~hiD~D~FyasvE~~~~P~L~~~PvaV~~~~~~~~g~Via~SyeAR~~GVk~gM~~~~A~~lcP~L~~v~v~~~~~~~d~ 94 (588)
+.|+|+.||++|+.+.+|+|+++||||++.+. +|+|++|||+||++||++||++.+|+++||++++++ +|+
T Consensus 1 l~~~~p~~~l~~~~~~~p~l~~~Pv~V~~~~~--~~~V~~~s~~Ar~~GV~~Gm~~~~A~~lcP~l~~~~-------~~~ 71 (335)
T cd03468 1 LALWFPRLPLDALLRNRPADDEAPLAVVERKK--AGRILACNAAARAAGVRPGMPLAEALALCPNLQVVE-------YDP 71 (335)
T ss_pred CeeeCCcCHHHHHhhcCCcccCCCeEEEEeCC--CCEEEecCHHHHHcCCCCCCcHHHHHHhCCCCeeec-------CCh
Confidence 36899999999999999999999999997653 689999999999999999999999999999999884 799
Q ss_pred HHHHHHHHHHHHHHhhc-CCeEEeccceEEEeccchhHHhhhcCCCCCchhhhHHhhhhhcccCccCCCCCchhhhhhhh
Q 007824 95 SSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKATVKEWL 173 (588)
Q Consensus 95 ~~Y~~~S~~v~~iL~~~-~~vE~~SiDEafLDlt~~~~~~l~~~~~~~~~~~~~~~~~~~l~g~~~~~~~~~~~~~~~~~ 173 (588)
+.|.++|++|++++.+| |.||++||||+|||+|++. ++||.
T Consensus 72 ~~y~~~s~~i~~~l~~~s~~ve~~s~de~~ldvs~~~----------------------~~~~~---------------- 113 (335)
T cd03468 72 EADARALQELALWLLRFTPLVALDGPDGLLLDVTGCL----------------------HLFGG---------------- 113 (335)
T ss_pred HHHHHHHHHHHHHHHhcCCccccCCCCeEEEEcccch----------------------hhcCC----------------
Confidence 99999999999999998 7899999999999999975 23442
Q ss_pred hccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEEecCcHHHHHHHhcCCCCCCccccCccCHHH-hcccCCCCCCCC
Q 007824 174 CRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKG-LLDSLPIKKMKQ 252 (588)
Q Consensus 174 ~~~~~~~~~~ll~~g~~la~~Ir~~I~~~~Glt~SvGIa~nk~LAKLAs~~~KP~g~~vv~~~~~~~-~L~~lPI~~l~G 252 (588)
...++..|++.+ .++|++||||||+||++||||++.+||+|.+......... |++++|+ ++||
T Consensus 114 --------------~~~~a~~i~~~~-~~~gl~~siGia~n~~~Aklas~~~kp~~~~~~~~~~~~~~~l~~lp~-~~~g 177 (335)
T cd03468 114 --------------EDALAASLRAAL-ATLGLSARAGIADTPGAAWLLARAGGGRGVLRREALAAALVLLAPLPV-AALR 177 (335)
T ss_pred --------------HHHHHHHHHHHH-HHcCCeEEEEecCCHHHHHHHhccCCCCccCCchHHHHHhhccCCCCh-hHhC
Confidence 135789999998 5789999999999999999999999999987766655544 8899999 5999
Q ss_pred CcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCcchHHHHHHHHhcCCCcccc--cccCCcccccccccCCCCCCCCHH
Q 007824 253 LGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQ--ARLLPKSHGSGKSFPGPRALKTVA 330 (588)
Q Consensus 253 iG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~~~g~~l~~~a~G~d~~~v~--~~~~pKsi~~s~sF~~~~~i~~~e 330 (588)
||+++.++|. .+||+|++||+++|...|.++||.. |.++|+.++|+|+.++. ....+++++.+.+|+.+ ..+.+
T Consensus 178 ig~~~~~~L~-~~Gi~t~~dl~~~~~~~l~~rfG~~-~~~l~~~~~G~d~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~ 253 (335)
T cd03468 178 LPPETVELLA-RLGLRTLGDLAALPRAELARRFGLA-LLLRLDQAYGRDPEPLLFSPPPPAFDFRLELQLEEP--IARGL 253 (335)
T ss_pred CCHHHHHHHH-HhCcccHHHHHhCChHHHHhhcCHH-HHHHHHHHCCCCCCCCCCCCCCCChhhhhhcCCCCC--cchhH
Confidence 9999999998 8999999999999999999999974 99999999999999994 44556899999999853 55544
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhhcCceeeEEEEEEEeccCCCCCCCcccCccccccCCCch---hHHHHHHHHHHHHHHH
Q 007824 331 SVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTA---KIQEDTFNLFQAGLRE 407 (588)
Q Consensus 331 ~l~~~L~~La~eL~~RLr~~l~~~~~~~~tltL~lr~~~~~~~~~~~~~~s~s~~L~~~T~---~i~~~A~~Ll~~i~r~ 407 (588)
.+.+.+|+++++.||+.+ +..|++|+|++++.++.. .+.+.++..+|+ .+.+.+..+|+..
T Consensus 254 --~~~l~~l~~~l~~~L~~~----~~~~~~l~l~l~~~~~~~-------~~~~~~~~~~~~~~~~l~~l~~~~l~~~--- 317 (335)
T cd03468 254 --LFPLRRLLEQLCAFLALR----GLGARRLSLTLFREDGRV-------TRVLVGLARPSRDDLPLLRLLRERLERL--- 317 (335)
T ss_pred --HHHHHHHHHHHHHHHHHc----CCeeeEEEEEEEEECCce-------EEEEEeccCCccCHHHHHHHHHhhhhcc---
Confidence 889999999999999987 999999999999877642 234555555664 3444444444431
Q ss_pred hhccccccccCCCCCC---CceeEEeecc
Q 007824 408 FLGSFGVKTQGSHYSG---WRITALSVSA 433 (588)
Q Consensus 408 ~~~~~~y~kaGv~~~~---~~Ir~lgvs~ 433 (588)
. .+ .+++.+++++
T Consensus 318 -~------------~~~~~~~v~~~~v~~ 333 (335)
T cd03468 318 -A------------LPRGIAPVRLLALTA 333 (335)
T ss_pred -C------------CCCCeeeEEEEEeec
Confidence 0 12 4788888875
No 22
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=100.00 E-value=1.1e-49 Score=435.00 Aligned_cols=358 Identities=24% Similarity=0.379 Sum_probs=301.5
Q ss_pred EEEEEeCChhHHHHhhhhCCCCCCCcEEEEecCCC--CCcEEEEcCHHHHhcCCCCCCcHHHHHhhCCCcEEEEccCCCC
Q 007824 13 IIAHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEW--KGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVARG 90 (588)
Q Consensus 13 ~I~hiD~D~FyasvE~~~~P~L~~~PvaV~~~~~~--~~g~Via~SyeAR~~GVk~gM~~~~A~~lcP~L~~v~v~~~~~ 90 (588)
..+|+++||||.|++...+++++++|++|....+. ...-|.+|||+||+||||.||-+.+|+++||+|+.++
T Consensus 372 ~~~~v~~dcf~~sv~~~n~~D~k~kpvav~hg~d~~~s~sEIASCsY~AR~~GIKNGMfV~~A~klCPqL~~lP------ 445 (1016)
T KOG2093|consen 372 ASVKVELDCFFVSVVIKNRLDLKDKPVAVCHGSDNPKSTSEIASCSYEARAYGIKNGMFVRHAKKLCPQLVILP------ 445 (1016)
T ss_pred chhHHHHHHhhhhheeccccccccCcceeeccCCCCcchhhhhccccHHHHhCcccceeHHHHHHhCcccEeec------
Confidence 34566778888888888899999999999873332 1234778999999999999999999999999999884
Q ss_pred CCChHHHHHHHHHHHHHHhhcC-CeEEeccceEEEeccchhHHhhhcCCCCCchhhhHHhhhhhcccCccCCCCCchhhh
Q 007824 91 KADLSSYRNAGSEVVSILARKG-RCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKATV 169 (588)
Q Consensus 91 ~~d~~~Y~~~S~~v~~iL~~~~-~vE~~SiDEafLDlt~~~~~~l~~~~~~~~~~~~~~~~~~~l~g~~~~~~~~~~~~~ 169 (588)
++|+.|.++|+.++++|++|. .||.+|+||+|+|+|...... .
T Consensus 446 -Y~FE~Ykevs~tlYetlasytl~I~aVSCDEa~vd~s~~~~~~----------------------~------------- 489 (1016)
T KOG2093|consen 446 -YDFEAYKEVSETLYETLASYTLNIEAVSCDEAFVDVSDLSDEE----------------------N------------- 489 (1016)
T ss_pred -ccHHHHHHHHHHHHHHHHhhccceeeecchhhhhhhhhhhhhh----------------------c-------------
Confidence 899999999999999999995 799999999999999876321 0
Q ss_pred hhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEEecCcHHHHHHHhcCCCCCCccccCccCHHHhcccCCCCC
Q 007824 170 KEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKK 249 (588)
Q Consensus 170 ~~~~~~~~~~~~~~ll~~g~~la~~Ir~~I~~~~Glt~SvGIa~nk~LAKLAs~~~KP~g~~vv~~~~~~~~L~~lPI~~ 249 (588)
. -.+.+|..||++|++.||++||||||.|.+||+||++.||||||..+.++.+.+|+.+++|.+
T Consensus 490 --------------~--tp~~la~~IRqEI~e~TgC~aS~Gig~t~LLARlATr~AKP~Gq~~l~a~~veeFis~~~v~~ 553 (1016)
T KOG2093|consen 490 --------------E--TPAVLAEHIRQEILEKTGCPASAGIGGTMLLARLATRVAKPNGQFYLSAEKVEEFISQLKVDD 553 (1016)
T ss_pred --------------c--CHHHHHHHHHHHHHhccCCceeeccchHHHHHHHHHhhcCCCceeeecHHHHHHHhhhccccc
Confidence 0 125679999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCcchHHHHHHHHhcCCCcccccccCCcccccccccCCCCCCCCH
Q 007824 250 MKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTV 329 (588)
Q Consensus 250 l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~~~g~~l~~~a~G~d~~~v~~~~~pKsi~~s~sF~~~~~i~~~ 329 (588)
|||+|..+..+|. .+||+|||||+......|++.||++.|..+|+.|+|+|++|+.....+|++++...|+. ++++.
T Consensus 554 LPGVG~sm~~kL~-s~~i~tCgdLq~~T~~kl~k~~G~Klgq~i~~~CrG~Dd~P~~~~~~RKSvS~dIN~GI--RFtn~ 630 (1016)
T KOG2093|consen 554 LPGVGSSMKSKLV-SQFIQTCGDLQLITLIKLRKVFGPKLGQKIYRGCRGIDDDPRSIEQVRKSVSADINYGI--RFTNI 630 (1016)
T ss_pred CCCccHHHHHHHH-HhccchhHHHHHHHHHHHHhhhcccHHHHHHHhcCCCcCChHHHhhhhcceeeeeecce--eeccH
Confidence 9999999999998 79999999999999999999999999999999999999999887778999999999994 58999
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhhcCceeeEEEEEEEeccCCCCCCC-c-------ccCccccccCCCch---hHHHHHH
Q 007824 330 ASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSR-K-------KFPSKSCPLRYGTA---KIQEDTF 398 (588)
Q Consensus 330 e~l~~~L~~La~eL~~RLr~~l~~~~~~~~tltL~lr~~~~~~~~~~-~-------~~~s~s~~L~~~T~---~i~~~A~ 398 (588)
.++...|..++++|-+||.+- ++.++.|+|++.....+...++ + -..++++.|.++|+ .|...++
T Consensus 631 ~ev~~fl~~~~eEl~rkL~ei----~k~~~sitLKlMvR~~~APietaK~mGhGiCD~~~rs~~l~~~Td~~~iItt~~~ 706 (1016)
T KOG2093|consen 631 KEVEQFLCLLSEELRRKLLEI----SKTASSITLKLMVRTAKAPIETAKYMGHGICDDFVRSSKLREPTDCNRIITTEVL 706 (1016)
T ss_pred HHHHHHHHHHHHHHHHHHHHh----hccccchhHHHHhhcCCCCCccccccceeeccchhhhhhccCccccccchHHHHH
Confidence 999999999999999998875 8899999998755433322121 1 12467888999987 3556666
Q ss_pred HHHHHHHHHhhccccccccCCCCCCCceeEEeeccC-CcccC--Cccchhhhhhh
Q 007824 399 NLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSAS-KIVPV--LSGTCSIMKYF 450 (588)
Q Consensus 399 ~Ll~~i~r~~~~~~~y~kaGv~~~~~~Ir~lgvs~s-~L~~~--~~~~~sLm~~f 450 (588)
.|++.. + .+...+|++|+... +|.+. +.....|-.+|
T Consensus 707 ~L~~t~-----~----------~~~~elRG~gi~~ntkL~~~~~~~~~~~l~e~F 746 (1016)
T KOG2093|consen 707 RLYETN-----S----------EPPSELRGLGIHSNTKLMDVLENLPPELLSEMF 746 (1016)
T ss_pred HHHHhc-----C----------CChHHhccchhhccccccccccCCcHHHHHhhc
Confidence 776651 1 13457999999995 88773 34445666666
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=100.00 E-value=5.6e-36 Score=279.95 Aligned_cols=147 Identities=41% Similarity=0.630 Sum_probs=131.6
Q ss_pred EeCChhHHHHhhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHhcCCCCCCcHHHHHhhCCCcEEEEccCCCCCCChHH
Q 007824 17 VDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVARGKADLSS 96 (588)
Q Consensus 17 iD~D~FyasvE~~~~P~L~~~PvaV~~~~~~~~g~Via~SyeAR~~GVk~gM~~~~A~~lcP~L~~v~v~~~~~~~d~~~ 96 (588)
||||+||||||++++|+|+++|+||++.+. ++++|++|||+||++||++||++.+|+++||++++++ +|++.
T Consensus 1 iD~~~F~as~e~~~~p~L~~~PvaV~~~~~-~~~~V~a~n~~Ar~~GV~~Gm~~~~A~~lcp~l~~~~-------~d~~~ 72 (149)
T PF00817_consen 1 IDMDAFFASVERRRDPELRGRPVAVVSGQG-NRGRVIAANYEARAAGVRPGMPLAEALALCPDLVVVP-------PDPER 72 (149)
T ss_dssp EEETTHHHHHHHHHSGGGTTSSEEEEECTS-STCEEEEE-HHHHTTTSTTTSBHHHHHHHSTTSEEEE-------EEHHH
T ss_pred CccccHHHHHHhhhCccccCCCEEEEeccc-ccchhhhhHHHHHhhccccchhhhhHhhhccceeecc-------ccHHH
Confidence 799999999999999999999999998764 3589999999999999999999999999999999985 79999
Q ss_pred HHHHHHHHHHHHhhc-C-CeEEeccceEEEeccchhHHhhhcCCCCCchhhhHHhhhhhcccCccCCCCCchhhhhhhhh
Q 007824 97 YRNAGSEVVSILARK-G-RCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKATVKEWLC 174 (588)
Q Consensus 97 Y~~~S~~v~~iL~~~-~-~vE~~SiDEafLDlt~~~~~~l~~~~~~~~~~~~~~~~~~~l~g~~~~~~~~~~~~~~~~~~ 174 (588)
|++++++|+.++.+| + .||.+|+||+|+|+|++.+ +||.
T Consensus 73 ~~~~~~~l~~~l~~~~sp~ve~~s~de~~ldv~~~~~----------------------l~~~----------------- 113 (149)
T PF00817_consen 73 YREASERLAEILYRFSSPRVEVYSPDELFLDVTGSLR----------------------LFGG----------------- 113 (149)
T ss_dssp HHHHHHHHHHHHHTTTCSEEEEEETTEEEEEEHHHHH----------------------HHHH-----------------
T ss_pred HHHHHHHHHHHHHhcccccceecccccccccCCcchh----------------------hcch-----------------
Confidence 999999999999998 4 7999999999999999763 3332
Q ss_pred ccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEEecCcHHHHHHHhc
Q 007824 175 RCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASG 223 (588)
Q Consensus 175 ~~~~~~~~~ll~~g~~la~~Ir~~I~~~~Glt~SvGIa~nk~LAKLAs~ 223 (588)
...++++||++|.+++|++||+|||+||++||||++
T Consensus 114 -------------~~~~~~~l~~~i~~~~gl~~s~Gia~~~~~Aklaa~ 149 (149)
T PF00817_consen 114 -------------EEALARRLRQAIAEETGLTASIGIAPNPLLAKLAAD 149 (149)
T ss_dssp -------------HHHHHHHHHHHHHHHHS--EEEEEESSHHHHHHHHH
T ss_pred -------------HHHHHHHHHHHHHHHhCCEEEEEEeCCHHHHHHhcC
Confidence 146799999999999999999999999999999984
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=99.22 E-value=4.7e-11 Score=107.51 Aligned_cols=118 Identities=31% Similarity=0.434 Sum_probs=86.5
Q ss_pred Ccccc-cccCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhhhhcCceeeEEEEEEEeccCCCCCCCcccC
Q 007824 302 GEEVQ-ARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFP 380 (588)
Q Consensus 302 ~~~v~-~~~~pKsi~~s~sF~~~~~i~~~e~l~~~L~~La~eL~~RLr~~l~~~~~~~~tltL~lr~~~~~~~~~~~~~~ 380 (588)
++||. +..++|||+++++|+. ++.+.+++..+|..|+++|+.||++. ++.|++|+|++++.+++. ....
T Consensus 1 ~~pV~~~~~~~ksi~~~~t~~~--~~~~~~~i~~~l~~l~~~l~~rL~~~----~~~~~~i~l~l~~~~~~~----~~~~ 70 (127)
T PF11799_consen 1 DEPVQQPRPPPKSIGSERTFPE--PISDREEIEEWLRELAEELAERLRER----GLAARTITLKLRYSDFGR----CSSR 70 (127)
T ss_dssp ------SCSS-SEEEEEEEECE--EESSHHHHHHHHHHHHHHHHHHHHHC----TEEEEEEEEEEEETTSCS----CEEE
T ss_pred CCCCCCCCCCCCEEEEEEECCC--CCCCHHHHHHHHHHHHHHHHHHHHhh----CcCCceEEEEEEecCCcc----ccee
Confidence 46787 7888999999999985 48999999999999999999999976 999999999999876541 1234
Q ss_pred ccccccCCCch---hHHHHHHHHHHHHHHHhhccccccccCCCCCCCceeEEeeccCCcc-cCCccc
Q 007824 381 SKSCPLRYGTA---KIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIV-PVLSGT 443 (588)
Q Consensus 381 s~s~~L~~~T~---~i~~~A~~Ll~~i~r~~~~~~~y~kaGv~~~~~~Ir~lgvs~s~L~-~~~~~~ 443 (588)
+++.+++.||+ .|.+.+..||+++... .+.+++.|||++++|. +....|
T Consensus 71 ~~~~~l~~p~~~~~~l~~~~~~l~~~~~~~--------------~~~~vr~igv~~~~l~~~~~~~q 123 (127)
T PF11799_consen 71 SRSIRLPFPTNDADELLKAARELLERLLYD--------------PGFPVRLIGVSASDLIEPAGQRQ 123 (127)
T ss_dssp EEEEEECCCEHCHHHHHHHHHHHHHHHHHH--------------TTCGEEEEEEEEEEEEEC----B
T ss_pred eEEEeccCCcCCHHHHHHHHHHHHHHHhcC--------------CCCCEEEEEEEECCCcCCCCCcc
Confidence 56778877775 5777777787553211 1358999999999999 444433
No 25
>PF13438 DUF4113: Domain of unknown function (DUF4113)
Probab=98.92 E-value=1.6e-10 Score=88.13 Aligned_cols=43 Identities=16% Similarity=0.168 Sum_probs=38.2
Q ss_pred hhhhhhh--------cCCCCCCCCCCCCCCcccccCCCCCCcccccCcCcch
Q 007824 444 CSIMKYF--------NGPDKFGSTSEQLPDNFIDAAPLSPSGSESYSTLNST 487 (588)
Q Consensus 444 ~sLm~~f--------~~~~~~~~~~~~~~~w~m~~~~~SP~ytT~w~~Lp~~ 487 (588)
..||.++ ++++.+|+++..+ +|.|+++++||+|||+|+|||.+
T Consensus 2 ~~LM~~iD~iN~r~G~~~i~~a~~g~~~-~W~mr~~~~Sp~yTT~w~el~~v 52 (52)
T PF13438_consen 2 QRLMQAIDAINRRFGRGTIRLASQGFRR-SWKMRREMLSPRYTTRWDELPVV 52 (52)
T ss_pred hHHHHHHHHHHHhcCCCEEEEeECCCCc-chHHHHHhcCCCCcCCHHHcccC
Confidence 4677777 7889999999876 89999999999999999999975
No 26
>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=98.44 E-value=8.2e-08 Score=65.66 Aligned_cols=32 Identities=34% Similarity=0.513 Sum_probs=27.9
Q ss_pred ccCHHHhcccCCCCCCCCCcHHHHHHHHHhhCC
Q 007824 235 FSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGV 267 (588)
Q Consensus 235 ~~~~~~~L~~lPI~~l~GiG~k~~~~L~~~lGI 267 (588)
|+++.+||+++||+++||||++++++|+ .+||
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 4678999999999999999999999998 7997
No 27
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=97.73 E-value=2.6e-05 Score=82.05 Aligned_cols=79 Identities=20% Similarity=0.219 Sum_probs=64.1
Q ss_pred hcccCCCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCc--chHHHHHHHHhc---CC--CcccccccCCcc
Q 007824 241 LLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF--NTGTWLWNIARG---IS--GEEVQARLLPKS 313 (588)
Q Consensus 241 ~L~~lPI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~--~~g~~l~~~a~G---~d--~~~v~~~~~pKs 313 (588)
.|.++||.++||||++++++|. ..||+|++||+.+++..|.+.+|. ..+..+++.++| .+ +.++.....+++
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 4789999999999999999998 899999999999999999999995 368899999998 43 333433333466
Q ss_pred ccccccc
Q 007824 314 HGSGKSF 320 (588)
Q Consensus 314 i~~s~sF 320 (588)
++...|+
T Consensus 81 ~~~~~Tg 87 (317)
T PRK04301 81 VGKITTG 87 (317)
T ss_pred CCccCCC
Confidence 6666555
No 28
>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=97.04 E-value=0.0007 Score=70.92 Aligned_cols=73 Identities=19% Similarity=0.190 Sum_probs=58.9
Q ss_pred CCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCcc--hHHHHHHHHh---cCC--CcccccccCCcccccccc
Q 007824 247 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN--TGTWLWNIAR---GIS--GEEVQARLLPKSHGSGKS 319 (588)
Q Consensus 247 I~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~~--~g~~l~~~a~---G~d--~~~v~~~~~pKsi~~s~s 319 (588)
|.++||||+++.++|. ..||.|++||+.+++..|.+.+|.. .+..++..++ |.+ +..+.....+++++...|
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 4689999999999998 7999999999999999999999963 4788888888 777 555544344566666655
Q ss_pred c
Q 007824 320 F 320 (588)
Q Consensus 320 F 320 (588)
+
T Consensus 80 g 80 (310)
T TIGR02236 80 G 80 (310)
T ss_pred C
Confidence 5
No 29
>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=96.47 E-value=0.0018 Score=50.86 Aligned_cols=49 Identities=27% Similarity=0.308 Sum_probs=39.9
Q ss_pred CCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHh--CcchHHHHHHHH
Q 007824 248 KKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESY--GFNTGTWLWNIA 297 (588)
Q Consensus 248 ~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rf--G~~~g~~l~~~a 297 (588)
.+|+|||++++.+|. ..|+.|+.||+..+++.|.+.- |...+..+...+
T Consensus 8 ~~I~Gig~~~a~~L~-~~G~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~ 58 (60)
T PF14520_consen 8 LSIPGIGPKRAEKLY-EAGIKTLEDLANADPEELAEIPGIGEKTAEKIIEAA 58 (60)
T ss_dssp HTSTTCHHHHHHHHH-HTTCSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHHH
T ss_pred ccCCCCCHHHHHHHH-hcCCCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHHH
Confidence 368999999999998 6899999999999999998884 444455555444
No 30
>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=95.92 E-value=0.008 Score=51.37 Aligned_cols=40 Identities=20% Similarity=0.327 Sum_probs=35.4
Q ss_pred CCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhC
Q 007824 246 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYG 286 (588)
Q Consensus 246 PI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG 286 (588)
.+.+|||||+++++-|. .+||+++.||+..++..|-.++-
T Consensus 13 ~L~~iP~IG~a~a~DL~-~LGi~s~~~L~g~dP~~Ly~~lc 52 (93)
T PF11731_consen 13 DLTDIPNIGKATAEDLR-LLGIRSPADLKGRDPEELYERLC 52 (93)
T ss_pred HHhcCCCccHHHHHHHH-HcCCCCHHHHhCCCHHHHHHHHH
Confidence 35689999999999998 89999999999999988876654
No 31
>PF08827 DUF1805: Domain of unknown function (DUF1805); InterPro: IPR014931 This protein is found in bacteria and archaea and has an N-terminal tetramerisation region that is composed of beta sheets. ; PDB: 1QW2_A.
Probab=93.59 E-value=0.042 Score=42.73 Aligned_cols=27 Identities=33% Similarity=0.394 Sum_probs=19.2
Q ss_pred cEEEEcCHHHHhcCCCCCCcHHHHHhh
Q 007824 50 GGLIAVGYEARNYGVKRSMRGDEAKEV 76 (588)
Q Consensus 50 g~Via~SyeAR~~GVk~gM~~~~A~~l 76 (588)
+-|..+|+.|+++||+.||++.+|+.+
T Consensus 32 a~v~~vt~~A~~lGI~~Gm~g~eAL~~ 58 (59)
T PF08827_consen 32 APVESVTSAAEELGIKPGMTGREALEK 58 (59)
T ss_dssp SB-SEE-HHHHHTT--TT-BHHHHGGG
T ss_pred ChHHHHHHHHHHhCCCCCCCHHHHHHh
Confidence 347899999999999999999999864
No 32
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=93.38 E-value=0.11 Score=51.54 Aligned_cols=55 Identities=18% Similarity=0.287 Sum_probs=48.4
Q ss_pred CCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHH--hCcchHHHHHHHHhcCC
Q 007824 246 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIARGIS 301 (588)
Q Consensus 246 PI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~r--fG~~~g~~l~~~a~G~d 301 (588)
++.+|+|||++...+|. ..|+.|+.+|..++...|.+. +|...+..++..+.+.+
T Consensus 4 ~L~~IpGIG~krakkLl-~~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l~~~~ 60 (232)
T PRK12766 4 ELEDISGVGPSKAEALR-EAGFESVEDVRAADQSELAEVDGIGNALAARIKADVGGLE 60 (232)
T ss_pred ccccCCCcCHHHHHHHH-HcCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHHhcccc
Confidence 57789999999999998 799999999999999999999 77767888888877544
No 33
>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=93.14 E-value=0.068 Score=40.79 Aligned_cols=27 Identities=26% Similarity=0.302 Sum_probs=20.6
Q ss_pred CCCCCCcHHHHHHHHHhhCCcchhhhcc
Q 007824 248 KKMKQLGGKLGTSLQNELGVTTVGDLLK 275 (588)
Q Consensus 248 ~~l~GiG~k~~~~L~~~lGI~TigDLa~ 275 (588)
..|||||+++++++- ..|++|+.||..
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 378999999999998 799999999964
No 34
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=92.57 E-value=0.12 Score=46.79 Aligned_cols=37 Identities=22% Similarity=0.441 Sum_probs=32.6
Q ss_pred CCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHH
Q 007824 246 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQE 283 (588)
Q Consensus 246 PI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~ 283 (588)
.|+.|-|||+++...|+ .+||+|..||+.+++..+..
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 46778999999999998 79999999999998877654
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=89.97 E-value=0.44 Score=38.24 Aligned_cols=45 Identities=33% Similarity=0.478 Sum_probs=35.8
Q ss_pred HhcccCCCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhC
Q 007824 240 GLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYG 286 (588)
Q Consensus 240 ~~L~~lPI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG 286 (588)
..+...||.++ |+..++...|. +.||+|++||..++...|.+.=|
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 34557899999 89999999998 89999999999999999876644
No 36
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=89.80 E-value=0.24 Score=44.73 Aligned_cols=53 Identities=17% Similarity=0.293 Sum_probs=42.7
Q ss_pred CccCHHHhcccCCCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCc
Q 007824 234 PFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF 287 (588)
Q Consensus 234 ~~~~~~~~L~~lPI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~ 287 (588)
+...+..+...-.+-.++|||+..+..|. ..||.|+.+|+..++..|.+..+.
T Consensus 42 ~~~~l~~w~~~AdL~ri~gi~~~~a~LL~-~AGv~Tv~~LA~~~p~~L~~~l~~ 94 (122)
T PF14229_consen 42 SERNLLKWVNQADLMRIPGIGPQYAELLE-HAGVDTVEELAQRNPQNLHQKLGR 94 (122)
T ss_pred CHHHHHHHHhHHHhhhcCCCCHHHHHHHH-HhCcCcHHHHHhCCHHHHHHHHHH
Confidence 34445555544455588999999999998 799999999999999999888773
No 37
>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=89.45 E-value=0.23 Score=41.51 Aligned_cols=33 Identities=27% Similarity=0.440 Sum_probs=24.8
Q ss_pred CCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHH
Q 007824 246 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSED 279 (588)
Q Consensus 246 PI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~ 279 (588)
.|+++|+||+++.+.|. +.||+|+.||..+...
T Consensus 4 ~l~~LpNig~~~e~~L~-~vGI~t~~~L~~~Ga~ 36 (81)
T PF04994_consen 4 RLKDLPNIGPKSERMLA-KVGIHTVEDLRELGAV 36 (81)
T ss_dssp -GCGSTT--HHHHHHHH-HTT--SHHHHHHHHHH
T ss_pred chhhCCCCCHHHHHHHH-HcCCCCHHHHHHhCHH
Confidence 57899999999999998 8999999999987543
No 38
>PRK02362 ski2-like helicase; Provisional
Probab=89.20 E-value=0.33 Score=57.12 Aligned_cols=54 Identities=15% Similarity=0.168 Sum_probs=48.5
Q ss_pred CCCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCcchHHHHHHHHhc
Q 007824 245 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARG 299 (588)
Q Consensus 245 lPI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~~~g~~l~~~a~G 299 (588)
+|+-.|||||++.+.+|. .+||+|+.||+++....|.+.||.+.+..+...+..
T Consensus 652 ~~L~~ip~i~~~~a~~l~-~~gi~s~~dl~~~~~~~l~~~~g~~~~~~i~~~~~~ 705 (737)
T PRK02362 652 LDLVGLRGVGRVRARRLY-NAGIESRADLRAADKSVVLAILGEKIAENILEQAGR 705 (737)
T ss_pred HHHhCCCCCCHHHHHHHH-HcCCCCHHHHHhCCHHHHHHHHCHHHHHHHHHHhCc
Confidence 567789999999999998 699999999999999999999999888888877663
No 39
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=84.40 E-value=0.77 Score=36.48 Aligned_cols=46 Identities=17% Similarity=0.310 Sum_probs=30.4
Q ss_pred CCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHH--hCcchHHHHHHHH
Q 007824 250 MKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIA 297 (588)
Q Consensus 250 l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~r--fG~~~g~~l~~~a 297 (588)
|+|||.++++.|.+.+| |+..|.+.+.+.|.+. +|...+..+++..
T Consensus 8 I~~VG~~~ak~L~~~f~--sl~~l~~a~~e~L~~i~gIG~~~A~si~~ff 55 (64)
T PF12826_consen 8 IPGVGEKTAKLLAKHFG--SLEALMNASVEELSAIPGIGPKIAQSIYEFF 55 (64)
T ss_dssp STT--HHHHHHHHHCCS--CHHHHCC--HHHHCTSTT--HHHHHHHHHHH
T ss_pred CCCccHHHHHHHHHHcC--CHHHHHHcCHHHHhccCCcCHHHHHHHHHHH
Confidence 58999999999986555 8999999999988876 5655555555543
No 40
>COG2251 Predicted nuclease (RecB family) [General function prediction only]
Probab=83.35 E-value=1.2 Score=48.35 Aligned_cols=64 Identities=22% Similarity=0.128 Sum_probs=52.1
Q ss_pred ccCHHHhcccCCCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhC--cchHHHHHHHHhc
Q 007824 235 FSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYG--FNTGTWLWNIARG 299 (588)
Q Consensus 235 ~~~~~~~L~~lPI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG--~~~g~~l~~~a~G 299 (588)
+.....++..-.|.-++||++...+.|+ .+||+|+.||++.+...+...+| ...+.++...++-
T Consensus 215 p~C~~~a~e~~~L~Lv~Gi~~~r~~~l~-~~GI~Ti~~LA~~~~~~~~~~~ga~~~~~~~l~~qa~~ 280 (474)
T COG2251 215 PQCESEALEEDDLSLVPGITPSRYDVLE-EVGITTIEDLADASLPILELVAGALTALAAQLVLQARA 280 (474)
T ss_pred hhhhHHHhhccceeccCCCCHHHHHHHH-HcCcchHHHHHhccccchhhhhhhHHHHHHHHHHHHHh
Confidence 4456677888888889999999999998 79999999999999988888888 3345566666663
No 41
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=82.31 E-value=2 Score=38.74 Aligned_cols=44 Identities=27% Similarity=0.430 Sum_probs=33.1
Q ss_pred CCCcHHHHHHHHHhhCCcchhhhccCCHH-----HHHHHhCcchHHHHHHH
Q 007824 251 KQLGGKLGTSLQNELGVTTVGDLLKFSED-----KLQESYGFNTGTWLWNI 296 (588)
Q Consensus 251 ~GiG~k~~~~L~~~lGI~TigDLa~l~~~-----~L~~rfG~~~g~~l~~~ 296 (588)
||||++...+|. ..||+|.+||...... .|....|.. ...+.++
T Consensus 1 pgi~~~~~~~L~-~~GI~t~~~Ll~~~~~~~~r~~La~~~~i~-~~~l~~w 49 (122)
T PF14229_consen 1 PGIGPKEAAKLK-AAGIKTTGDLLEAGDTPLGRKALAKKLGIS-ERNLLKW 49 (122)
T ss_pred CCCCHHHHHHHH-HcCCCcHHHHHHcCCCHHHHHHHHHhcCCC-HHHHHHH
Confidence 799999999997 8999999999986432 366667763 4444443
No 42
>PRK01172 ski2-like helicase; Provisional
Probab=81.73 E-value=1.6 Score=50.74 Aligned_cols=41 Identities=22% Similarity=0.457 Sum_probs=37.6
Q ss_pred CCCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhC
Q 007824 245 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYG 286 (588)
Q Consensus 245 lPI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG 286 (588)
+|+-.|||+|+..+++|. ..||+|+.||+.++++.+.+..|
T Consensus 612 ~~L~~ip~~~~~~a~~l~-~~g~~~~~di~~~~~~~~~~i~~ 652 (674)
T PRK01172 612 IDLVLIPKVGRVRARRLY-DAGFKTVDDIARSSPERIKKIYG 652 (674)
T ss_pred HhhcCCCCCCHHHHHHHH-HcCCCCHHHHHhCCHHHHHHHhc
Confidence 688889999999999998 79999999999999999988844
No 43
>PRK07758 hypothetical protein; Provisional
Probab=80.45 E-value=2.9 Score=35.90 Aligned_cols=43 Identities=26% Similarity=0.340 Sum_probs=33.9
Q ss_pred CCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHH--hCcchHHHH
Q 007824 250 MKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWL 293 (588)
Q Consensus 250 l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~r--fG~~~g~~l 293 (588)
+++++-+...-|. ..||+|++||...+.+.|.+. ||+.....|
T Consensus 39 ~~~LSvRA~N~Lk-~AGI~TL~dLv~~te~ELl~iknlGkKSL~EI 83 (95)
T PRK07758 39 LSLLSAPARRALE-HHGIHTVEELSKYSEKEILKLHGMGPASLPKL 83 (95)
T ss_pred CccccHHHHHHHH-HcCCCcHHHHHcCCHHHHHHccCCCHHHHHHH
Confidence 4678888888897 799999999999999998765 565433333
No 44
>PRK00254 ski2-like helicase; Provisional
Probab=79.55 E-value=1.7 Score=51.09 Aligned_cols=54 Identities=15% Similarity=0.253 Sum_probs=47.1
Q ss_pred cCCCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHH--hCcchHHHHHHHHh
Q 007824 244 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 298 (588)
Q Consensus 244 ~lPI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~r--fG~~~g~~l~~~a~ 298 (588)
.+|+..|+|||++.+++|. ..|+.|+.|+..++.+.|.+. +|.+.+..++..++
T Consensus 644 ~~~L~~ipgig~~~~~~l~-~~g~~s~~~i~~a~~~el~~~~gi~~~~a~~i~~~~~ 699 (720)
T PRK00254 644 LLELMRLPMIGRKRARALY-NAGFRSIEDIVNAKPSELLKVEGIGAKIVEGIFKHLG 699 (720)
T ss_pred HhhhhcCCCCCHHHHHHHH-HccCCCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHhc
Confidence 3678889999999999998 799999999999999999998 66666777777655
No 45
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=77.35 E-value=0.56 Score=54.36 Aligned_cols=31 Identities=39% Similarity=0.562 Sum_probs=29.1
Q ss_pred EEEEeCChhHHHHhhhhCCCCCCCcEEEEec
Q 007824 14 IAHVDLDCFYVQVEQRKQPKLRGLPTAVVQY 44 (588)
Q Consensus 14 I~hiD~D~FyasvE~~~~P~L~~~PvaV~~~ 44 (588)
++|+||+|||++|-.+..|.++|.|.|+...
T Consensus 330 ~~~~dmk~fF~nv~l~~k~~~kg~~~a~~~d 360 (1016)
T KOG2093|consen 330 TWHNDMKDFFVNVGLRLKPALKGQPTAETAD 360 (1016)
T ss_pred HHHHhhhhhhhcccccCCccccCCceeeecc
Confidence 7899999999999999999999999999754
No 46
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=75.72 E-value=1.3 Score=47.12 Aligned_cols=30 Identities=20% Similarity=0.254 Sum_probs=26.3
Q ss_pred CCCCCCCcHHHHHHHHHhhCCcchhhhccCC
Q 007824 247 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFS 277 (588)
Q Consensus 247 I~~l~GiG~k~~~~L~~~lGI~TigDLa~l~ 277 (588)
+.+|||||++++.+|-+ +||+|+.||....
T Consensus 91 l~~i~GiGpk~a~~l~~-lGi~tl~eL~~a~ 120 (334)
T smart00483 91 FTNVFGVGPKTAAKWYR-KGIRTLEELKKNK 120 (334)
T ss_pred HHccCCcCHHHHHHHHH-hCCCCHHHHHhcc
Confidence 33899999999999995 9999999998754
No 47
>TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Probab=74.81 E-value=2.2 Score=47.39 Aligned_cols=59 Identities=24% Similarity=0.263 Sum_probs=42.3
Q ss_pred HHhcccCCCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHH--HhCcchHHHHHHHHh
Q 007824 239 KGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQE--SYGFNTGTWLWNIAR 298 (588)
Q Consensus 239 ~~~L~~lPI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~--rfG~~~g~~l~~~a~ 298 (588)
+.....-+|..|+||+++....|+ ..||+|+.||+..++..|.. .++...+.+|...++
T Consensus 201 ~~~~~~~~lslv~gi~~~~~~~L~-~~GI~ti~~La~~~~~~l~~~~~~~~~~~~~l~~qA~ 261 (457)
T TIGR03491 201 AVAKEEGHLSLVPGIGPSRYRLLQ-ELGIHTLEDLAAADPNDLEDFGEQGLGVAEQLVQQAR 261 (457)
T ss_pred HHHHhcCCeeecCCCCHHHHHHHH-HcCCCcHHHHhcCCccccccccccCHHHHHHHHHHHH
Confidence 344446688999999999999998 79999999999997654444 344333444444444
No 48
>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=73.98 E-value=2.3 Score=35.96 Aligned_cols=32 Identities=25% Similarity=0.459 Sum_probs=22.3
Q ss_pred cccCCCCCCCCCcHHHHHHHHHhhCCcchhhhc
Q 007824 242 LDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLL 274 (588)
Q Consensus 242 L~~lPI~~l~GiG~k~~~~L~~~lGI~TigDLa 274 (588)
|..-||++|+|||+.++.+|. ..|+..+..|.
T Consensus 16 MGeK~V~~laGIG~~lg~~L~-~~GfdKAy~vL 47 (89)
T PF02961_consen 16 MGEKPVTELAGIGPVLGKRLE-EKGFDKAYVVL 47 (89)
T ss_dssp -TT-BGGGSTT--HHHHHHHH-HTT--BHHHHH
T ss_pred cCCCCccccCCcCHHHHHHHH-HCCCcHHHHHh
Confidence 455689999999999999998 79998876664
No 49
>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=71.14 E-value=2.3 Score=44.61 Aligned_cols=27 Identities=37% Similarity=0.520 Sum_probs=25.4
Q ss_pred CCCCCcHHHHHHHHHhhCCcchhhhccC
Q 007824 249 KMKQLGGKLGTSLQNELGVTTVGDLLKF 276 (588)
Q Consensus 249 ~l~GiG~k~~~~L~~~lGI~TigDLa~l 276 (588)
+|||||++++++|- .+||.|+.||...
T Consensus 89 ~i~GiGpk~a~~l~-~lGi~sl~dL~~a 115 (307)
T cd00141 89 RVPGVGPKTARKLY-ELGIRTLEDLRKA 115 (307)
T ss_pred cCCCCCHHHHHHHH-HcCCCCHHHHHHH
Confidence 89999999999999 8999999999874
No 50
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=69.60 E-value=9.5 Score=39.70 Aligned_cols=62 Identities=16% Similarity=0.350 Sum_probs=50.6
Q ss_pred cCCCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCcc--hHHHHHHHHhcCCCcccc
Q 007824 244 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN--TGTWLWNIARGISGEEVQ 306 (588)
Q Consensus 244 ~lPI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~~--~g~~l~~~a~G~d~~~v~ 306 (588)
..|+..+|++|....++|. ..||.+++||..++...+...+|.. .|..+++.++....-.|.
T Consensus 150 ~~~L~Qlp~i~~~~~~~l~-~~~i~s~~~l~~~~~~~~~~ll~~~~~~~~~i~~~~~~~P~l~v~ 213 (312)
T smart00611 150 DSPLLQLPHLPEEILKRLE-KKKVLSLEDLLELEDEERGELLGLLDAEGERVYKVLSRLPKLNIE 213 (312)
T ss_pred CCccccCCCCCHHHHHHHH-hCCCCCHHHHHhcCHHHHHHHHcCCHHHHHHHHHHHHhCCcceeE
Confidence 4688899999999999997 7899999999999999998887742 477777777766655543
No 51
>COG3377 Uncharacterized conserved protein [Function unknown]
Probab=68.62 E-value=1.7 Score=36.73 Aligned_cols=26 Identities=38% Similarity=0.584 Sum_probs=22.6
Q ss_pred EEEEcCHHHHhcCCCCCCcHHHHHhh
Q 007824 51 GLIAVGYEARNYGVKRSMRGDEAKEV 76 (588)
Q Consensus 51 ~Via~SyeAR~~GVk~gM~~~~A~~l 76 (588)
-|+.++++|-++||+.||.+.+|+..
T Consensus 69 ~i~evT~~Ae~lGI~~Gm~~r~aL~k 94 (95)
T COG3377 69 PIVEVTSAAEELGIKRGMKGREALEK 94 (95)
T ss_pred hHHHHHHHHHHhCCCccchHHHHHhc
Confidence 36678999999999999999999753
No 52
>PRK08609 hypothetical protein; Provisional
Probab=68.53 E-value=3 Score=47.61 Aligned_cols=28 Identities=39% Similarity=0.458 Sum_probs=25.9
Q ss_pred CCCCCcHHHHHHHHHhhCCcchhhhccC
Q 007824 249 KMKQLGGKLGTSLQNELGVTTVGDLLKF 276 (588)
Q Consensus 249 ~l~GiG~k~~~~L~~~lGI~TigDLa~l 276 (588)
+|||||+|++.+|-+.+||+|+.||...
T Consensus 92 ~i~GiGpk~a~~l~~~lGi~tl~~L~~a 119 (570)
T PRK08609 92 KLPGLGGKKIAKLYKELGVVDKESLKEA 119 (570)
T ss_pred cCCCCCHHHHHHHHHHhCCCCHHHHHHH
Confidence 8999999999999877999999999974
No 53
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=67.29 E-value=5.9 Score=45.13 Aligned_cols=54 Identities=17% Similarity=0.157 Sum_probs=44.3
Q ss_pred cCCCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHH-hCcchHHHHHHHHhc
Q 007824 244 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES-YGFNTGTWLWNIARG 299 (588)
Q Consensus 244 ~lPI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~r-fG~~~g~~l~~~a~G 299 (588)
.-++.+|+|||++..+.|.+ -..|+..+.+++.++|.+. .|...+..++..++|
T Consensus 513 ~S~Ld~I~GiG~kr~~~Ll~--~Fgs~~~ik~As~eeL~~vgi~~~~A~~I~~~l~~ 567 (567)
T PRK14667 513 KDILDKIKGIGEVKKEIIYR--NFKTLYDFLKADDEELKKLGIPPSVKQEVKKYLSG 567 (567)
T ss_pred cCccccCCCCCHHHHHHHHH--HhCCHHHHHhCCHHHHHHcCCCHHHHHHHHHHhcC
Confidence 45788999999999999985 5568999999999999998 445567778877765
No 54
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=67.14 E-value=5.2 Score=39.02 Aligned_cols=55 Identities=13% Similarity=0.090 Sum_probs=41.7
Q ss_pred CCCCCCCcHHHHHHHHHhhCCcchh-hhccCCHHHHHHH--hCcchHHHHHHHHhcCC
Q 007824 247 IKKMKQLGGKLGTSLQNELGVTTVG-DLLKFSEDKLQES--YGFNTGTWLWNIARGIS 301 (588)
Q Consensus 247 I~~l~GiG~k~~~~L~~~lGI~Tig-DLa~l~~~~L~~r--fG~~~g~~l~~~a~G~d 301 (588)
+..++|||+|++.++.+.+|..++. .+...++..|.+. +|.+.+.+++..+++..
T Consensus 75 L~~i~GIGpk~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~~~l~~~~ 132 (192)
T PRK00116 75 LISVSGVGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELKDKL 132 (192)
T ss_pred HhcCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHHh
Confidence 3468999999999998778886654 3556688888876 66667788887777654
No 55
>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=66.75 E-value=3.3 Score=27.81 Aligned_cols=14 Identities=21% Similarity=0.415 Sum_probs=11.7
Q ss_pred CCCCCcHHHHHHHH
Q 007824 249 KMKQLGGKLGTSLQ 262 (588)
Q Consensus 249 ~l~GiG~k~~~~L~ 262 (588)
+|||||++++..+.
T Consensus 15 ~lpGIG~~tA~~I~ 28 (30)
T PF00633_consen 15 KLPGIGPKTANAIL 28 (30)
T ss_dssp TSTT-SHHHHHHHH
T ss_pred hCCCcCHHHHHHHH
Confidence 89999999998875
No 56
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=65.53 E-value=6.7 Score=45.63 Aligned_cols=48 Identities=21% Similarity=0.306 Sum_probs=39.5
Q ss_pred CCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHH--HhCcchHHHHHH
Q 007824 248 KKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQE--SYGFNTGTWLWN 295 (588)
Q Consensus 248 ~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~--rfG~~~g~~l~~ 295 (588)
-+|+|+|+++.++|-+..+|+++.||.++....|.. .||.+.+..+++
T Consensus 448 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~ll~ 497 (665)
T PRK07956 448 MDIDGLGEKIIEQLFEKGLIHDPADLFKLTAEDLLGLEGFGEKSAQNLLD 497 (665)
T ss_pred cCCCCcCHHHHHHHHHcCCCCCHHHHHhcCHHHHhcCcCcchHHHHHHHH
Confidence 478999999999999778899999999999888876 578765555544
No 57
>PTZ00035 Rad51 protein; Provisional
Probab=64.12 E-value=5.4 Score=42.46 Aligned_cols=54 Identities=19% Similarity=0.162 Sum_probs=43.8
Q ss_pred CCCCCC--CCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCcch--HHHHHHHHhc
Q 007824 245 LPIKKM--KQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNT--GTWLWNIARG 299 (588)
Q Consensus 245 lPI~~l--~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~~~--g~~l~~~a~G 299 (588)
.+|.++ +||++.+.++|. .-||+|+.||+..++..|.+..|... +..+...++-
T Consensus 21 ~~~~~l~~~g~~~~~~~kL~-~~g~~t~~~~~~~~~~~L~~~~gis~~~~~~i~~~~~~ 78 (337)
T PTZ00035 21 QEIEKLQSAGINAADIKKLK-EAGICTVESVAYATKKDLCNIKGISEAKVEKIKEAASK 78 (337)
T ss_pred ccHHHHhcCCCCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHhhCCCHHHHHHHHHHHHH
Confidence 467777 679999999998 79999999999999999999998632 3455555553
No 58
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=64.04 E-value=4.3 Score=47.41 Aligned_cols=31 Identities=39% Similarity=0.618 Sum_probs=28.2
Q ss_pred CCCCCCCCCcHHHHHHHHHhhCCcchhhhccC
Q 007824 245 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKF 276 (588)
Q Consensus 245 lPI~~l~GiG~k~~~~L~~~lGI~TigDLa~l 276 (588)
.||..|.|||++.++.|. ++||.|+.||...
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 8999999999864
No 59
>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=63.99 E-value=7.7 Score=40.34 Aligned_cols=60 Identities=23% Similarity=0.364 Sum_probs=42.3
Q ss_pred CCCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCc--chHHHHHHHHhcCCCccc
Q 007824 245 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF--NTGTWLWNIARGISGEEV 305 (588)
Q Consensus 245 lPI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~--~~g~~l~~~a~G~d~~~v 305 (588)
.|+..|||||.+..++|. ..||.|++||..++...+...++. ..|..+.+.++.+..-.+
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 678889999999999998 799999999999999999998873 246777777776654444
No 60
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=62.86 E-value=4.6 Score=43.09 Aligned_cols=44 Identities=20% Similarity=0.332 Sum_probs=39.3
Q ss_pred cCCCCCC--CCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCcc
Q 007824 244 SLPIKKM--KQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN 288 (588)
Q Consensus 244 ~lPI~~l--~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~~ 288 (588)
..+|.+| .||+....++|+ .-||.|+.||+..++..|.+.+|..
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 3477788 579999999998 7999999999999999999999975
No 61
>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=62.83 E-value=8 Score=40.76 Aligned_cols=36 Identities=25% Similarity=0.240 Sum_probs=33.5
Q ss_pred CCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCcc
Q 007824 252 QLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN 288 (588)
Q Consensus 252 GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~~ 288 (588)
||++.+.++|. .-||.|+.||+..++..|.+.+|..
T Consensus 8 ~~~~~~~~~l~-~~g~~t~~~~~~~~~~~L~~i~~ls 43 (316)
T TIGR02239 8 GITAADIKKLQ-EAGLHTVESVAYAPKKQLLEIKGIS 43 (316)
T ss_pred CCCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHHhCCC
Confidence 59999999998 7999999999999999999999864
No 62
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=62.61 E-value=6.8 Score=39.10 Aligned_cols=36 Identities=25% Similarity=0.481 Sum_probs=32.2
Q ss_pred CCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHH
Q 007824 246 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQ 282 (588)
Q Consensus 246 PI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~ 282 (588)
.+.+|.|||+.+.++|. ..||.|..+|+.++.+.+.
T Consensus 159 DL~~I~GIGp~~a~~L~-eaGi~tfaQIAa~t~a~ia 194 (221)
T PRK12278 159 DLTKITGVGPALAKKLN-EAGVTTFAQIAALTDADIA 194 (221)
T ss_pred hheeccccChHHHHHHH-HcCCCCHHHhhCCChhhhh
Confidence 47789999999999998 7999999999999887655
No 63
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=60.95 E-value=7.1 Score=41.68 Aligned_cols=54 Identities=19% Similarity=0.225 Sum_probs=43.1
Q ss_pred cCCCCCC--CCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCcch--HHHHHHHHh
Q 007824 244 SLPIKKM--KQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNT--GTWLWNIAR 298 (588)
Q Consensus 244 ~lPI~~l--~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~~~--g~~l~~~a~ 298 (588)
..+|.+| .||++.+.++|. ..||+|+.||+..++..|.+..|... +..+...++
T Consensus 28 ~~~~~~l~~~g~~~~~~~kL~-~~g~~tv~~~~~~~~~~L~~~~g~s~~~~~ki~~~a~ 85 (344)
T PLN03187 28 FESIDKLISQGINAGDVKKLQ-DAGIYTCNGLMMHTKKNLTGIKGLSEAKVDKICEAAE 85 (344)
T ss_pred ccCHHHHhhCCCCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHH
Confidence 5567777 579999999998 79999999999999999999888532 344444444
No 64
>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=60.46 E-value=9.2 Score=40.29 Aligned_cols=47 Identities=15% Similarity=0.145 Sum_probs=37.8
Q ss_pred CCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCcc--hHHHHHHHHh
Q 007824 251 KQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN--TGTWLWNIAR 298 (588)
Q Consensus 251 ~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~~--~g~~l~~~a~ 298 (588)
.|||..+.++|+ .-||.|+.||+..++..|.+..|.. .+..+.+.+.
T Consensus 7 ~g~~~~~~~~L~-~~g~~t~~~~~~~~~~~L~~~~gls~~~~~~i~~~~~ 55 (313)
T TIGR02238 7 HGINAADIKKLK-SAGICTVNGVIMTTRRALCKIKGLSEAKVDKIKEAAS 55 (313)
T ss_pred CCCCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHH
Confidence 479999999998 7999999999999999999998853 2334444443
No 65
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=60.02 E-value=11 Score=43.50 Aligned_cols=51 Identities=20% Similarity=0.285 Sum_probs=41.8
Q ss_pred CCCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCcchHHHHHHHH
Q 007824 245 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIA 297 (588)
Q Consensus 245 lPI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~~~g~~l~~~a 297 (588)
..+..|+|||++++..|.+.+| |+.+|..++.+.|.+.+|...+..++...
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 3567899999999999986444 88999999999998888987777776653
No 66
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=59.80 E-value=11 Score=43.52 Aligned_cols=53 Identities=11% Similarity=0.088 Sum_probs=45.3
Q ss_pred cCCCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCcchHHHHHHHHh
Q 007824 244 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIAR 298 (588)
Q Consensus 244 ~lPI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~~~g~~l~~~a~ 298 (588)
.-.+.+|+|||++...+|.+ -..++.++..++.+.|.+.+|.+.+..++..++
T Consensus 551 ~S~L~~IpGIG~kr~~~LL~--~FgSi~~I~~As~eeL~~vi~~k~A~~I~~~l~ 603 (624)
T PRK14669 551 TSELLEIPGVGAKTVQRLLK--HFGSLERVRAATETQLAAVVGRAAAEAIIAHFT 603 (624)
T ss_pred HHHHhcCCCCCHHHHHHHHH--HcCCHHHHHhCCHHHHHHHhCHHHHHHHHHHhc
Confidence 35677999999999999985 556889999999999998899878888888876
No 67
>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=59.13 E-value=10 Score=43.96 Aligned_cols=51 Identities=25% Similarity=0.330 Sum_probs=40.7
Q ss_pred CCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHH--hCcchHHHHHHHHh
Q 007824 248 KKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 298 (588)
Q Consensus 248 ~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~r--fG~~~g~~l~~~a~ 298 (588)
-+|+|+|+++.++|-+..+|+++.||..+....|... ||...+..+++...
T Consensus 435 l~I~GLG~k~i~~L~~~g~I~~~~Dl~~L~~~~L~~L~GfG~Ksa~nIl~~Ie 487 (652)
T TIGR00575 435 MDIEGLGDKVIEQLFEKKLVRSVADLYALKKEDLLELEGFGEKSAQNLLNAIE 487 (652)
T ss_pred cCCCCcCHHHHHHHHHcCCcCCHHHHHhcCHHHHhhccCccHHHHHHHHHHHH
Confidence 4689999999999997677999999999998888764 67665665655444
No 68
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=57.41 E-value=7.2 Score=41.24 Aligned_cols=36 Identities=19% Similarity=0.373 Sum_probs=31.7
Q ss_pred CCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHH
Q 007824 246 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQ 282 (588)
Q Consensus 246 PI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~ 282 (588)
.+.+|.|||+++.++|. .+||.+..|+++++.+.+.
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 37789999999999998 7999999999999877554
No 69
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=57.35 E-value=11 Score=43.73 Aligned_cols=52 Identities=13% Similarity=0.194 Sum_probs=41.3
Q ss_pred cCCCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHH--hCcchHHHHHHHH
Q 007824 244 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIA 297 (588)
Q Consensus 244 ~lPI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~r--fG~~~g~~l~~~a 297 (588)
.-.+..++|||++...+|.+.+| ++.++...+.+.|.+. +|...+..+++.+
T Consensus 636 ~s~L~~IPGIGpkr~k~LL~~FG--Sle~I~~AS~eELa~V~Gig~k~Ae~I~~~L 689 (694)
T PRK14666 636 TGELQRVEGIGPATARLLWERFG--SLQAMAAAGEEGLAAVPGIGPARAAALHEHL 689 (694)
T ss_pred HhHHhhCCCCCHHHHHHHHHHhC--CHHHHHhcCHHHHHhcCCcCHHHHHHHHHHH
Confidence 34677899999999999997778 9999999999999887 5655555555543
No 70
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=56.98 E-value=10 Score=45.14 Aligned_cols=52 Identities=23% Similarity=0.332 Sum_probs=45.8
Q ss_pred CCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhC-cchHHHHHHHHhcC
Q 007824 247 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYG-FNTGTWLWNIARGI 300 (588)
Q Consensus 247 I~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG-~~~g~~l~~~a~G~ 300 (588)
|..|||||++.+.+|.. .+.++.+|++++.+.|....| .+.|..+|+.++..
T Consensus 759 L~~lPgI~~~~a~~ll~--~f~si~~l~~as~eeL~~~iG~~~~A~~i~~fl~~~ 811 (814)
T TIGR00596 759 LLKLPGVTKKNYRNLRK--KVKSIRELAKLSQNELNELIGDEEAAKRLYDFLRTE 811 (814)
T ss_pred HHHCCCCCHHHHHHHHH--HcCCHHHHHhCCHHHHHHHhCCHHHHHHHHHHhccc
Confidence 45789999999999984 699999999999999999999 87899999887753
No 71
>PRK14973 DNA topoisomerase I; Provisional
Probab=56.35 E-value=14 Score=44.80 Aligned_cols=69 Identities=19% Similarity=0.139 Sum_probs=48.1
Q ss_pred HHHHHHh-cCCCCCCccccCccCHHHhcccCCCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCcc
Q 007824 216 MLAKLAS-GMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN 288 (588)
Q Consensus 216 ~LAKLAs-~~~KP~g~~vv~~~~~~~~L~~lPI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~~ 288 (588)
-++++|+ ++.+|+...+..-. .--..-++..+.|+|+++.++|. .-||.++.||++.+...|.+.=|+.
T Consensus 850 ~~~~~~~~~~~~~~~~~~~~~~---~~~~~~el~~vkg~ge~t~~~l~-~ag~~~~e~l~~~d~~~la~~~~i~ 919 (936)
T PRK14973 850 RHAKLVCEKLGRPVPEKISKAA---FERGRAELLSVPGLGETTLEKLY-LAGVYDGDLLVSADPKKLAKVTGID 919 (936)
T ss_pred HHHHHHHHHhcCCCchhhhhhh---hcccchhhhhccCCCHHHHHHHH-HcCCCCHHHhccCCHHHHhhhcCCC
Confidence 3455566 66666544332100 00011126688999999999997 8999999999999999999988763
No 72
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=55.52 E-value=6.9 Score=44.92 Aligned_cols=31 Identities=39% Similarity=0.734 Sum_probs=28.3
Q ss_pred CCCCCCCCCcHHHHHHHHHhhCCcchhhhccC
Q 007824 245 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKF 276 (588)
Q Consensus 245 lPI~~l~GiG~k~~~~L~~~lGI~TigDLa~l 276 (588)
.|+..+.|||++++++|. ++||+|+.||.-.
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 8999999998864
No 73
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=54.29 E-value=15 Score=41.87 Aligned_cols=53 Identities=23% Similarity=0.343 Sum_probs=42.5
Q ss_pred cCCCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHH--hCcchHHHHHHHHh
Q 007824 244 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 298 (588)
Q Consensus 244 ~lPI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~r--fG~~~g~~l~~~a~ 298 (588)
...+.+|+|||++..+.|.+ -..++.++.+++.++|.+. ++...+..++..+.
T Consensus 513 ~s~L~~I~GiG~kr~~~LL~--~Fgs~~~I~~As~eeL~~v~gi~~~~A~~I~~~l~ 567 (574)
T PRK14670 513 KLNYTKIKGIGEKKAKKILK--SLGTYKDILLLNEDEIAEKMKINIKMAKKIKKFAE 567 (574)
T ss_pred ccccccCCCCCHHHHHHHHH--HhCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHH
Confidence 45788999999999999986 4558899999999999988 55446777776654
No 74
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=53.21 E-value=17 Score=42.04 Aligned_cols=62 Identities=10% Similarity=0.150 Sum_probs=48.6
Q ss_pred cCCCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHH--hCcchHHHHHHHHhcCCCccccc
Q 007824 244 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIARGISGEEVQA 307 (588)
Q Consensus 244 ~lPI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~r--fG~~~g~~l~~~a~G~d~~~v~~ 307 (588)
...+.+|+|||++...+|.+. ..++.++..++.++|.+. +|...+..++..+.--...||..
T Consensus 607 ~s~L~~IpGiG~kr~~~LL~~--FgS~~~i~~As~eel~~v~gi~~~~A~~i~~~~~~~~~~~~~~ 670 (691)
T PRK14672 607 VLSFERLPHVGKVRAHRLLAH--FGSFRSLQSATPQDIATAIHIPLTQAHTILHAATRSTTAPVRE 670 (691)
T ss_pred ccccccCCCCCHHHHHHHHHH--hcCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHhhcccccchhH
Confidence 457889999999999999864 458899999999999988 66666777887776555555543
No 75
>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=50.04 E-value=18 Score=26.50 Aligned_cols=33 Identities=36% Similarity=0.406 Sum_probs=28.2
Q ss_pred cHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCc
Q 007824 254 GGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF 287 (588)
Q Consensus 254 G~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~ 287 (588)
+..+..+|. .-|+.|+.+|+.+++..|...-|.
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 456788887 799999999999999999887664
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=48.89 E-value=18 Score=37.80 Aligned_cols=55 Identities=25% Similarity=0.337 Sum_probs=42.1
Q ss_pred cccCCCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHH--hCcchHHHHHHHHh
Q 007824 242 LDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 298 (588)
Q Consensus 242 L~~lPI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~r--fG~~~g~~l~~~a~ 298 (588)
+-.+||.+| ++--++..-|. +.||+|++||...+...|.+. ||.+....+.+.+.
T Consensus 232 ~~~~~I~~L-~LSvR~~n~Lk-~~~I~ti~dL~~~~~~~l~~~~n~G~ksl~ei~~~l~ 288 (297)
T TIGR02027 232 LLSIKIEEL-DLSVRSYNCLK-RAGIHTLGELVSKSEEELLKIKNFGKKSLTEIKEKLA 288 (297)
T ss_pred hccccHHHh-CccHHHHhHHH-HcCCcCHHHHHhCCHHHHhhCCCCChhhHHHHHHHHH
Confidence 445788888 68888889997 899999999999999987654 77765555554443
No 77
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=47.91 E-value=16 Score=39.71 Aligned_cols=36 Identities=22% Similarity=0.426 Sum_probs=31.8
Q ss_pred CCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHH
Q 007824 246 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQ 282 (588)
Q Consensus 246 PI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~ 282 (588)
.+.+|.|||+++.++|+ .+||.+..+++.++...+.
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 36789999999999998 7999999999999887554
No 78
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=47.49 E-value=19 Score=37.91 Aligned_cols=52 Identities=23% Similarity=0.344 Sum_probs=40.9
Q ss_pred ccCCCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHH--hCcchHHHHHHH
Q 007824 243 DSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNI 296 (588)
Q Consensus 243 ~~lPI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~r--fG~~~g~~l~~~ 296 (588)
-.+||.+| ++--++..-|. +.||+|++||.+++...|.+. ||.+....+.+.
T Consensus 247 l~~~I~~L-~LS~R~~n~Lk-~~~I~ti~dL~~~~~~~l~~~~n~G~ksl~ei~~~ 300 (310)
T PRK05182 247 LLRPIEEL-ELSVRSYNCLK-RAGINTIGDLVQRTEEELLKTRNLGKKSLEEIKEK 300 (310)
T ss_pred ccccHHHh-ccchHHHHHHH-HcCCcCHHHHHhCCHHHHhcCCCCChhhHHHHHHH
Confidence 36788888 78889999997 899999999999999998654 676544444443
No 79
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=46.90 E-value=14 Score=23.58 Aligned_cols=16 Identities=19% Similarity=0.320 Sum_probs=14.0
Q ss_pred CCCCCCCcHHHHHHHH
Q 007824 247 IKKMKQLGGKLGTSLQ 262 (588)
Q Consensus 247 I~~l~GiG~k~~~~L~ 262 (588)
+.+++|||++++++|.
T Consensus 3 L~~i~GiG~k~A~~il 18 (26)
T smart00278 3 LLKVPGIGPKTAEKIL 18 (26)
T ss_pred hhhCCCCCHHHHHHHH
Confidence 4578999999999987
No 80
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=46.75 E-value=22 Score=41.53 Aligned_cols=50 Identities=20% Similarity=0.207 Sum_probs=39.4
Q ss_pred CCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHH--hCcchHHHHHHHH
Q 007824 248 KKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIA 297 (588)
Q Consensus 248 ~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~r--fG~~~g~~l~~~a 297 (588)
=+|.|+|+++.++|-+..+|+++.||..+....|... ||.+.+..|++..
T Consensus 465 l~I~GLG~k~i~~L~~~g~V~~~~Dl~~L~~~~L~~l~g~g~Ksa~~Ll~~I 516 (689)
T PRK14351 465 LDIEGLGEERVQQLVDAGLVESLADLYDLTVADLAELEGWGETSAENLLAEL 516 (689)
T ss_pred cCCCCcCHHHHHHHHHcCCCCCHHHHHHcCHHHHhcCcCcchhHHHHHHHHH
Confidence 3688999999999996556899999999998888764 7776665555443
No 81
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=43.43 E-value=12 Score=39.27 Aligned_cols=35 Identities=34% Similarity=0.436 Sum_probs=28.7
Q ss_pred CCCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHH
Q 007824 245 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSED 279 (588)
Q Consensus 245 lPI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~ 279 (588)
.|+-+++|+|+|...+|-+.+||+++.+|......
T Consensus 93 ~~Ll~v~GlGpkKi~~Ly~elgi~~~e~l~~a~~~ 127 (326)
T COG1796 93 EPLLKVPGLGPKKIVSLYKELGIKDLEELQEALEN 127 (326)
T ss_pred HHHhhCCCCCcHHHHHHHHHHCcccHHHHHHHHHh
Confidence 35668999999877788878999999999876553
No 82
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=42.97 E-value=22 Score=37.22 Aligned_cols=31 Identities=19% Similarity=0.201 Sum_probs=26.6
Q ss_pred CCCCCCcHHHHHHHHHhhCCcchhhhccCCHH
Q 007824 248 KKMKQLGGKLGTSLQNELGVTTVGDLLKFSED 279 (588)
Q Consensus 248 ~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~ 279 (588)
+.++|||.+++++-. ..|++|+.|++.-+..
T Consensus 100 tnifGvG~ktA~~Wy-~~GfrTled~Rk~~~k 130 (353)
T KOG2534|consen 100 TNIFGVGLKTAEKWY-REGFRTLEDVRKKPDK 130 (353)
T ss_pred HHHhccCHHHHHHHH-HhhhhHHHHHHhCHHH
Confidence 468999999999998 8999999999954433
No 83
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=39.92 E-value=18 Score=35.58 Aligned_cols=43 Identities=19% Similarity=0.224 Sum_probs=28.4
Q ss_pred EecCcHHHHHHHhcCCCCCCccccCccCHHHhcccC---CCCCCCCCcHHHHHHHH
Q 007824 210 GIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSL---PIKKMKQLGGKLGTSLQ 262 (588)
Q Consensus 210 GIa~nk~LAKLAs~~~KP~g~~vv~~~~~~~~L~~l---PI~~l~GiG~k~~~~L~ 262 (588)
||||.--||-|.+. +++.+.+.+..= -+.++||||+|+++++-
T Consensus 80 GIGpK~ALaiLs~~----------~~~~l~~aI~~~d~~~L~k~PGIGkKtAeriv 125 (201)
T COG0632 80 GIGPKLALAILSNL----------DPEELAQAIANEDVKALSKIPGIGKKTAERIV 125 (201)
T ss_pred CccHHHHHHHHcCC----------CHHHHHHHHHhcChHhhhcCCCCCHHHHHHHH
Confidence 88888888877652 222222323221 25689999999999986
No 84
>PF08004 DUF1699: Protein of unknown function (DUF1699); InterPro: IPR012546 This family contains many archaeal proteins which have very conserved sequences.
Probab=39.08 E-value=52 Score=29.78 Aligned_cols=35 Identities=23% Similarity=0.394 Sum_probs=28.5
Q ss_pred CcHHHHHhhCCCcEEEEccCCCCCCChHHHHHHHHHHHHHHh
Q 007824 68 MRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILA 109 (588)
Q Consensus 68 M~~~~A~~lcP~L~~v~v~~~~~~~d~~~Y~~~S~~v~~iL~ 109 (588)
.-+....+.||++.++++|+ ..|+.+|..+-.+|.
T Consensus 31 ~Dif~Lv~~CP~lk~iqiP~-------SY~~t~Sksi~mfL~ 65 (131)
T PF08004_consen 31 KDIFSLVERCPNLKAIQIPP-------SYYKTLSKSIKMFLE 65 (131)
T ss_pred hHHHHHHHhCCCCeEEeCCh-------HHHHHHhHHHHHHHH
Confidence 34677788999999999884 578888888887775
No 85
>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=38.59 E-value=40 Score=29.57 Aligned_cols=35 Identities=14% Similarity=0.392 Sum_probs=25.2
Q ss_pred CCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHH
Q 007824 247 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKL 281 (588)
Q Consensus 247 I~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L 281 (588)
+.++.|||+.++..+.+.+||..-.-+-.++.+.+
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 46899999999999888999975444444454444
No 86
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=38.06 E-value=54 Score=29.97 Aligned_cols=54 Identities=20% Similarity=0.233 Sum_probs=36.9
Q ss_pred CcHHHHHHHhcCCCCCCccccCccCHHHhcccCCCCCCCCCcHHHHHHHHHhhC-CcchhhhccCC
Q 007824 213 HNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELG-VTTVGDLLKFS 277 (588)
Q Consensus 213 ~nk~LAKLAs~~~KP~g~~vv~~~~~~~~L~~lPI~~l~GiG~k~~~~L~~~lG-I~TigDLa~l~ 277 (588)
.|+.=|||+ ....+ .-+...++.+|. .+||||+.+++++- ..| ..++.||.+.+
T Consensus 39 ~N~~d~kl~-~~~~k---IdiN~A~~~el~------~lpGigP~~A~~IV-~nGpf~sveDL~~V~ 93 (132)
T PRK02515 39 QNVADAKLG-EFGEK---IDLNNSSVRAFR------QFPGMYPTLAGKIV-KNAPYDSVEDVLNLP 93 (132)
T ss_pred cChhhHHHH-hcCCc---ccCCccCHHHHH------HCCCCCHHHHHHHH-HCCCCCCHHHHHcCC
Confidence 377778887 33222 123344566554 68999999999998 455 88999998763
No 87
>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=35.95 E-value=35 Score=35.59 Aligned_cols=47 Identities=28% Similarity=0.577 Sum_probs=32.6
Q ss_pred CCCCCcH--HHHHHHHHhhCCcchhhhccC---CHHHHHHHhCcchHHHHHHH
Q 007824 249 KMKQLGG--KLGTSLQNELGVTTVGDLLKF---SEDKLQESYGFNTGTWLWNI 296 (588)
Q Consensus 249 ~l~GiG~--k~~~~L~~~lGI~TigDLa~l---~~~~L~~rfG~~~g~~l~~~ 296 (588)
.|-.||. ...++|. .-||+|++|+.++ ++..|++.||...-...|+.
T Consensus 166 RLe~Igk~G~~hk~L~-~~~I~tV~dFl~l~~~d~~~Lr~ilg~~ms~k~We~ 217 (299)
T PF07887_consen 166 RLEKIGKDGAFHKRLK-KNGINTVEDFLKLLNKDPQKLREILGSGMSNKMWET 217 (299)
T ss_pred hhhhccccCHHHHHHH-HcCCccHHHHHHHHhcCHHHHHHHHhcCCChhhHHH
Confidence 3334443 4667887 7899999998874 78899999994333444443
No 88
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=32.65 E-value=22 Score=34.65 Aligned_cols=45 Identities=11% Similarity=0.180 Sum_probs=26.2
Q ss_pred EecCcHHHHHHHhcCCCCCC-ccccCccCHHHhcccCCCCCCCCCcHHHHHHHH
Q 007824 210 GIAHNKMLAKLASGMNKPAQ-QTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQ 262 (588)
Q Consensus 210 GIa~nk~LAKLAs~~~KP~g-~~vv~~~~~~~~L~~lPI~~l~GiG~k~~~~L~ 262 (588)
||||-.-||-|.+ + .|+. ...+..+++. -+.++||||+|++++|-
T Consensus 80 GIGpK~AL~iLs~-~-~~~el~~aI~~~D~~------~L~~vpGIGkKtAerIi 125 (188)
T PRK14606 80 RLGPKTALKIISN-E-DAETLVTMIASQDVE------GLSKLPGISKKTAERIV 125 (188)
T ss_pred CccHHHHHHHHcC-C-CHHHHHHHHHhCCHH------HHhhCCCCCHHHHHHHH
Confidence 7888766665532 1 1111 1122223332 25688999999999986
No 89
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=32.46 E-value=48 Score=38.17 Aligned_cols=52 Identities=10% Similarity=0.169 Sum_probs=40.4
Q ss_pred cCCCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHH--hCcchHHHHHHHH
Q 007824 244 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIA 297 (588)
Q Consensus 244 ~lPI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~r--fG~~~g~~l~~~a 297 (588)
..++..|+|||++...+|.+.+ .++.++..++.+.|.+. +|...+..+++..
T Consensus 542 ~s~L~~IpGIG~k~~k~Ll~~F--gS~~~i~~As~eeL~~v~Gig~~~A~~I~~~l 595 (598)
T PRK00558 542 TSALDDIPGIGPKRRKALLKHF--GSLKAIKEASVEELAKVPGISKKLAEAIYEAL 595 (598)
T ss_pred hhhHhhCCCcCHHHHHHHHHHc--CCHHHHHhCCHHHHhhcCCcCHHHHHHHHHHh
Confidence 4678899999999999998644 56889999999999887 5655555565543
No 90
>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=32.28 E-value=52 Score=29.29 Aligned_cols=37 Identities=11% Similarity=0.278 Sum_probs=26.5
Q ss_pred CCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHH
Q 007824 246 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQ 282 (588)
Q Consensus 246 PI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~ 282 (588)
.++.+.|||.+++..+.+.+||..-.-+-.++.+.+.
T Consensus 16 aL~~i~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~ 52 (113)
T TIGR03631 16 ALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELN 52 (113)
T ss_pred eeeeeecccHHHHHHHHHHhCcCcccccccCCHHHHH
Confidence 4678999999999999989999743333344444443
No 91
>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=32.08 E-value=48 Score=38.62 Aligned_cols=30 Identities=23% Similarity=0.372 Sum_probs=12.7
Q ss_pred CCCcHHHHHHHHHhhCCcchhhhccCCHHHHH
Q 007824 251 KQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQ 282 (588)
Q Consensus 251 ~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~ 282 (588)
+|||.++++.|.+.+| ++.+|..++.+.|.
T Consensus 504 pgVG~~~ak~L~~~f~--sl~~l~~As~eeL~ 533 (652)
T TIGR00575 504 RHVGEVTAKNLAKHFG--TLDKLKAASLEELL 533 (652)
T ss_pred CCcCHHHHHHHHHHhC--CHHHHHhCCHHHHh
Confidence 4444444444443333 34444444444333
No 92
>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=31.27 E-value=40 Score=32.84 Aligned_cols=50 Identities=20% Similarity=0.205 Sum_probs=34.0
Q ss_pred CCCCCCcHHHHHHHHHhhCCcchhhhccC----CHHHHHHH--hCcchHHHHHHHHhcC
Q 007824 248 KKMKQLGGKLGTSLQNELGVTTVGDLLKF----SEDKLQES--YGFNTGTWLWNIARGI 300 (588)
Q Consensus 248 ~~l~GiG~k~~~~L~~~lGI~TigDLa~l----~~~~L~~r--fG~~~g~~l~~~a~G~ 300 (588)
-.++|||+|++..+ +++.+..+|..+ +...|.+. ||.+.++++.-.+++.
T Consensus 75 ~~V~GIGpK~Al~i---L~~~~~~el~~aI~~~d~~~L~~ipGiGkKtAerIileLk~k 130 (191)
T TIGR00084 75 IKVNGVGPKLALAI---LSNMSPEEFVYAIETEEVKALVKIPGVGKKTAERLLLELKGK 130 (191)
T ss_pred hCCCCCCHHHHHHH---HhcCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHhh
Confidence 47899999999766 567777777653 45667664 5556667666555544
No 93
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=31.22 E-value=58 Score=30.71 Aligned_cols=41 Identities=17% Similarity=0.330 Sum_probs=28.9
Q ss_pred CCCCCCCCCcHHHHHHHHHhhCCc---chhhhccCCHHHHHHHh
Q 007824 245 LPIKKMKQLGGKLGTSLQNELGVT---TVGDLLKFSEDKLQESY 285 (588)
Q Consensus 245 lPI~~l~GiG~k~~~~L~~~lGI~---TigDLa~l~~~~L~~rf 285 (588)
..++.|.|||..++..+.+.+||. +++||-.-....|...+
T Consensus 30 ~aLt~I~GIG~~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i 73 (154)
T PTZ00134 30 YALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEII 73 (154)
T ss_pred EeecccccccHHHHHHHHHHcCcCcCCCcccCCHHHHHHHHHHH
Confidence 346789999999999999899996 56666544334444433
No 94
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=31.10 E-value=24 Score=34.63 Aligned_cols=43 Identities=21% Similarity=0.214 Sum_probs=26.3
Q ss_pred EecCcHHHHHHHhcCCCCCCccccCccCHHHhcccC---CCCCCCCCcHHHHHHHH
Q 007824 210 GIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSL---PIKKMKQLGGKLGTSLQ 262 (588)
Q Consensus 210 GIa~nk~LAKLAs~~~KP~g~~vv~~~~~~~~L~~l---PI~~l~GiG~k~~~~L~ 262 (588)
||||-.-||-|.+- .++++.+.+..= -+.++||||+|+++++-
T Consensus 79 GIGpK~AL~iLs~~----------~~~~l~~aI~~~D~~~L~kvpGIGkKtAerIi 124 (197)
T PRK14603 79 GVGPKLALALLSAL----------PPALLARALLEGDARLLTSASGVGKKLAERIA 124 (197)
T ss_pred CcCHHHHHHHHcCC----------CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 78876666655421 223333333221 25689999999999986
No 95
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=30.92 E-value=39 Score=33.11 Aligned_cols=16 Identities=31% Similarity=0.488 Sum_probs=14.3
Q ss_pred CCCCCCCcHHHHHHHH
Q 007824 247 IKKMKQLGGKLGTSLQ 262 (588)
Q Consensus 247 I~~l~GiG~k~~~~L~ 262 (588)
+++|||||+|++++|.
T Consensus 13 l~~LPGIG~KsA~RlA 28 (195)
T TIGR00615 13 LKKLPGIGPKSAQRLA 28 (195)
T ss_pred HHHCCCCCHHHHHHHH
Confidence 5689999999999996
No 96
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=29.49 E-value=62 Score=36.92 Aligned_cols=48 Identities=17% Similarity=0.304 Sum_probs=38.2
Q ss_pred CCCCCcHHHHHHHHHhhC-CcchhhhccCCHHHHHH--HhCcchHHHHHHHH
Q 007824 249 KMKQLGGKLGTSLQNELG-VTTVGDLLKFSEDKLQE--SYGFNTGTWLWNIA 297 (588)
Q Consensus 249 ~l~GiG~k~~~~L~~~lG-I~TigDLa~l~~~~L~~--rfG~~~g~~l~~~a 297 (588)
+|-|+|.++.++|- ..| |+++.||..+....|.. .||.+.+..|++..
T Consensus 429 dI~GlGe~~i~~L~-~~G~i~~~~Diy~L~~~~l~~l~gfgeks~~nll~aI 479 (562)
T PRK08097 429 GLDGIGEGTWRALH-QTGLFEHLFSWLALTPEQLANTPGIGKARAEQLWHQF 479 (562)
T ss_pred CCCCcCHHHHHHHH-HcCCcCCHHHHhcCCHHHHhcCcCccHHHHHHHHHHH
Confidence 57799999999998 577 69999999999888765 47876666665543
No 97
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=29.42 E-value=50 Score=32.26 Aligned_cols=52 Identities=13% Similarity=0.200 Sum_probs=36.2
Q ss_pred CCCCCcHHHHHHHHHhhCCcc-hhhhccCCHHHHHHHhC--cchHHHHHHHHhcC
Q 007824 249 KMKQLGGKLGTSLQNELGVTT-VGDLLKFSEDKLQESYG--FNTGTWLWNIARGI 300 (588)
Q Consensus 249 ~l~GiG~k~~~~L~~~lGI~T-igDLa~l~~~~L~~rfG--~~~g~~l~~~a~G~ 300 (588)
.++|||+|++-.+.+.++... +..++.-+...|.+.-| .+.++++.-.++|.
T Consensus 77 ~V~GIGpK~Al~ILs~~~~~~l~~aI~~~D~~~L~~vpGIGkKtAerIilELk~K 131 (194)
T PRK14605 77 DVSGIGPKLGLAMLSAMNAEALASAIISGNAELLSTIPGIGKKTASRIVLELKDK 131 (194)
T ss_pred CCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHH
Confidence 678999999988886678777 44455667888887655 34566655555543
No 98
>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=29.01 E-value=26 Score=34.16 Aligned_cols=43 Identities=21% Similarity=0.262 Sum_probs=26.6
Q ss_pred EecCcHHHHHHHhcCCCCCCccccCccCHHHhccc---CCCCCCCCCcHHHHHHHH
Q 007824 210 GIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDS---LPIKKMKQLGGKLGTSLQ 262 (588)
Q Consensus 210 GIa~nk~LAKLAs~~~KP~g~~vv~~~~~~~~L~~---lPI~~l~GiG~k~~~~L~ 262 (588)
||||-.-+|-|. .+ +++++.+.+.. --+.++||||+|+++++.
T Consensus 79 GIGpK~Al~iL~-~~---------~~~el~~aI~~~d~~~L~~ipGiGkKtAerIi 124 (191)
T TIGR00084 79 GVGPKLALAILS-NM---------SPEEFVYAIETEEVKALVKIPGVGKKTAERLL 124 (191)
T ss_pred CCCHHHHHHHHh-cC---------CHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHH
Confidence 788876655432 22 23333333332 236789999999999985
No 99
>COG2199 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]
Probab=28.74 E-value=1.5e+02 Score=27.63 Aligned_cols=29 Identities=24% Similarity=0.117 Sum_probs=18.9
Q ss_pred HHHHHHHHhhc----CCeEEeccceEEEeccch
Q 007824 101 GSEVVSILARK----GRCERASIDEVYLDLTDA 129 (588)
Q Consensus 101 S~~v~~iL~~~----~~vE~~SiDEafLDlt~~ 129 (588)
...|..+|... ..+-+++-||+-+=+.+.
T Consensus 78 L~~va~~L~~~~~~~~~~~R~gGdEF~i~l~~~ 110 (181)
T COG2199 78 LREVARRLRSNLREGDLVARLGGDEFAVLLPGT 110 (181)
T ss_pred HHHHHHHHHHhcCCCCEEEEeccceeEEEeCCC
Confidence 44555556543 358889999987766554
No 100
>PRK13844 recombination protein RecR; Provisional
Probab=28.65 E-value=44 Score=32.87 Aligned_cols=16 Identities=25% Similarity=0.507 Sum_probs=14.3
Q ss_pred CCCCCCCcHHHHHHHH
Q 007824 247 IKKMKQLGGKLGTSLQ 262 (588)
Q Consensus 247 I~~l~GiG~k~~~~L~ 262 (588)
+.+|||||+|++++|.
T Consensus 17 l~~LPGIG~KsA~Rla 32 (200)
T PRK13844 17 LRKLPTIGKKSSQRLA 32 (200)
T ss_pred HHHCCCCCHHHHHHHH
Confidence 4678999999999996
No 101
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=28.40 E-value=66 Score=32.84 Aligned_cols=50 Identities=24% Similarity=0.406 Sum_probs=38.3
Q ss_pred CCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCc--chHHHHHHHHh
Q 007824 247 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF--NTGTWLWNIAR 298 (588)
Q Consensus 247 I~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~--~~g~~l~~~a~ 298 (588)
+..+||||.+++.+|.. -+.+++++..++...|.+.-|+ +.+..+++..+
T Consensus 184 l~s~pgig~~~a~~ll~--~fgS~~~~~tas~~eL~~v~gig~k~A~~I~~~~~ 235 (254)
T COG1948 184 LESIPGIGPKLAERLLK--KFGSVEDVLTASEEELMKVKGIGEKKAREIYRFLR 235 (254)
T ss_pred HHcCCCccHHHHHHHHH--HhcCHHHHhhcCHHHHHHhcCccHHHHHHHHHHHh
Confidence 34566999999999974 5668999999999999999886 34555555444
No 102
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=27.69 E-value=32 Score=33.40 Aligned_cols=54 Identities=20% Similarity=0.251 Sum_probs=30.8
Q ss_pred HHHHHHhCCceeEEecCcHHHHHHHhcCCCCCCccccCccCHHHhcccC---CCCCCCCCcHHHHHHHH
Q 007824 197 MQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSL---PIKKMKQLGGKLGTSLQ 262 (588)
Q Consensus 197 ~~I~~~~Glt~SvGIa~nk~LAKLAs~~~KP~g~~vv~~~~~~~~L~~l---PI~~l~GiG~k~~~~L~ 262 (588)
+++++.+ +.++ ||||-.-||-|.+ + +++++...+..= -+.++||||+|+++++-
T Consensus 69 r~lF~~L-i~Vs-GIGpK~Al~ILs~-~---------~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIi 125 (183)
T PRK14601 69 QKMFEML-LKVN-GIGANTAMAVCSS-L---------DVNSFYKALSLGDESVLKKVPGIGPKSAKRII 125 (183)
T ss_pred HHHHHHH-hccC-CccHHHHHHHHcC-C---------CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 3444444 2333 7888766665543 1 223322222221 25688999999999986
No 103
>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=27.27 E-value=70 Score=24.79 Aligned_cols=47 Identities=28% Similarity=0.455 Sum_probs=38.5
Q ss_pred cCccCHHHhcccCCCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCcc
Q 007824 233 VPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN 288 (588)
Q Consensus 233 v~~~~~~~~L~~lPI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~~ 288 (588)
++++++.++|..+ |+ .+....+. ..||..+..|..++.+.|. .+|+.
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 4566788888766 66 47778887 7999999999999999997 89984
No 104
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=27.09 E-value=59 Score=34.49 Aligned_cols=55 Identities=20% Similarity=0.357 Sum_probs=42.6
Q ss_pred hcccCCCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHH--HHhCcchHHHHHHHH
Q 007824 241 LLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQ--ESYGFNTGTWLWNIA 297 (588)
Q Consensus 241 ~L~~lPI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~--~rfG~~~g~~l~~~a 297 (588)
.+-.++|.+| .+--+...-|. +.||+|++||...+...|. +-||.+....+.+.+
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 4556788888 57677788887 8999999999999998875 458887666666555
No 105
>PRK13766 Hef nuclease; Provisional
Probab=25.80 E-value=67 Score=38.05 Aligned_cols=49 Identities=22% Similarity=0.418 Sum_probs=38.8
Q ss_pred CCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHH--hCcchHHHHHHHH
Q 007824 247 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIA 297 (588)
Q Consensus 247 I~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~r--fG~~~g~~l~~~a 297 (588)
+..++|||++.+.+|.+.+| ++.++..++...|... +|...+..++...
T Consensus 717 L~~ipgig~~~a~~Ll~~fg--s~~~i~~as~~~L~~i~Gig~~~a~~i~~~~ 767 (773)
T PRK13766 717 VESLPDVGPVLARNLLEHFG--SVEAVMTASEEELMEVEGIGEKTAKRIREVV 767 (773)
T ss_pred HhcCCCCCHHHHHHHHHHcC--CHHHHHhCCHHHHHhCCCCCHHHHHHHHHHH
Confidence 67789999999999986555 7999999999999887 6765566665543
No 106
>PRK00076 recR recombination protein RecR; Reviewed
Probab=25.77 E-value=33 Score=33.64 Aligned_cols=16 Identities=25% Similarity=0.478 Sum_probs=14.3
Q ss_pred CCCCCCCcHHHHHHHH
Q 007824 247 IKKMKQLGGKLGTSLQ 262 (588)
Q Consensus 247 I~~l~GiG~k~~~~L~ 262 (588)
+.+|||||+|+++||.
T Consensus 13 l~~LPGIG~KsA~Rla 28 (196)
T PRK00076 13 LRKLPGIGPKSAQRLA 28 (196)
T ss_pred HHHCCCCCHHHHHHHH
Confidence 4679999999999996
No 107
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=25.75 E-value=84 Score=28.39 Aligned_cols=37 Identities=8% Similarity=0.271 Sum_probs=26.0
Q ss_pred CCCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHH
Q 007824 245 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKL 281 (588)
Q Consensus 245 lPI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L 281 (588)
..+..|.|||..++..+.+.+||..-.-+-.++.+.+
T Consensus 17 ~aL~~I~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi 53 (122)
T PRK05179 17 IALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEEL 53 (122)
T ss_pred eeecccccccHHHHHHHHHHhCcCcccccccCCHHHH
Confidence 3467899999999999998999974333333344443
No 108
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=25.60 E-value=87 Score=28.32 Aligned_cols=37 Identities=3% Similarity=0.116 Sum_probs=26.1
Q ss_pred CCCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHH
Q 007824 245 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKL 281 (588)
Q Consensus 245 lPI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L 281 (588)
..++.+.|||.+++..+.+.+||.--.-+-.++.+.+
T Consensus 17 ~aLt~i~GIG~~~A~~ic~~lgi~~~~~~~~Lt~~qi 53 (122)
T CHL00137 17 YALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQI 53 (122)
T ss_pred eeecccccccHHHHHHHHHHcCcCcCcCcccCCHHHH
Confidence 3467899999999999998999964333333344444
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=25.45 E-value=1.4e+02 Score=26.30 Aligned_cols=37 Identities=22% Similarity=0.443 Sum_probs=27.8
Q ss_pred EEEccCCCCCCChHHHHHHHHHHHHHHhhcCCeEEeccceEEEe
Q 007824 82 LVQVPVARGKADLSSYRNAGSEVVSILARKGRCERASIDEVYLD 125 (588)
Q Consensus 82 ~v~v~~~~~~~d~~~Y~~~S~~v~~iL~~~~~vE~~SiDEafLD 125 (588)
++.||. .+.+.|++++++...++.++..++.. ||+-|
T Consensus 7 v~~VP~----~nk~aY~~~A~~a~~vf~e~GAl~~v---E~wgd 43 (103)
T PF07237_consen 7 VLPVPT----ANKDAYRAMAEKAAEVFKEHGALRVV---ECWGD 43 (103)
T ss_dssp EEEEEG----GGHHHHHHHHHHHHHHHHHTT-SEEE---EEEEE
T ss_pred EEECcH----HHHHHHHHHHHHHHHHHHHhCCEEEE---EeecC
Confidence 566774 79999999999999999998654433 55554
No 110
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=24.31 E-value=70 Score=22.37 Aligned_cols=17 Identities=29% Similarity=0.350 Sum_probs=13.5
Q ss_pred CCCCCCCcHHHHHHHHH
Q 007824 247 IKKMKQLGGKLGTSLQN 263 (588)
Q Consensus 247 I~~l~GiG~k~~~~L~~ 263 (588)
|.-++|||.|++.+|.+
T Consensus 18 i~Gv~giG~ktA~~ll~ 34 (36)
T smart00279 18 IPGVKGIGPKTALKLLR 34 (36)
T ss_pred CCCCCcccHHHHHHHHH
Confidence 44688999999988863
No 111
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=24.14 E-value=40 Score=33.09 Aligned_cols=58 Identities=21% Similarity=0.315 Sum_probs=32.0
Q ss_pred HHHHHHHHhCCceeEEecCcHHHHHHHhcCCCCCCc-cccCccCHHHhcccCCCCCCCCCcHHHHHHHH
Q 007824 195 LRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQ-TTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQ 262 (588)
Q Consensus 195 Ir~~I~~~~Glt~SvGIa~nk~LAKLAs~~~KP~g~-~vv~~~~~~~~L~~lPI~~l~GiG~k~~~~L~ 262 (588)
-.+++++.+ +.++ ||||-.-+|-|.+ + .|+.. ..+..+++. .+.++||||+|+++++-
T Consensus 66 ~Er~lF~~L-isVs-GIGPK~ALaILs~-~-~~~el~~aI~~~D~~------~L~~vpGIGkKtAeRII 124 (196)
T PRK13901 66 SEREVFEEL-IGVD-GIGPRAALRVLSG-I-KYNEFRDAIDREDIE------LISKVKGIGNKMAGKIF 124 (196)
T ss_pred HHHHHHHHH-hCcC-CcCHHHHHHHHcC-C-CHHHHHHHHHhCCHH------HHhhCCCCCHHHHHHHH
Confidence 334445554 3333 7887766665543 1 12111 122223333 25689999999999986
No 112
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=22.89 E-value=44 Score=32.73 Aligned_cols=54 Identities=15% Similarity=0.171 Sum_probs=30.3
Q ss_pred HHHHHHhCCceeEEecCcHHHHHHHhcCCCCCCccccCccCHHHhcccC---CCCCCCCCcHHHHHHHH
Q 007824 197 MQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSL---PIKKMKQLGGKLGTSLQ 262 (588)
Q Consensus 197 ~~I~~~~Glt~SvGIa~nk~LAKLAs~~~KP~g~~vv~~~~~~~~L~~l---PI~~l~GiG~k~~~~L~ 262 (588)
++++..+ +.++ ||||-.-|+-|.. + +++++...+..= -+.++||||+|+++++-
T Consensus 69 r~lF~~L-i~V~-GIGpK~Al~iLs~-~---------~~~el~~aI~~~D~~~L~kvpGIGkKtAerIi 125 (195)
T PRK14604 69 RQLFELL-IGVS-GVGPKAALNLLSS-G---------TPDELQLAIAGGDVARLARVPGIGKKTAERIV 125 (195)
T ss_pred HHHHHHH-hCcC-CcCHHHHHHHHcC-C---------CHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 3344444 2333 7887766665542 1 222222222221 25689999999999996
No 113
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=22.68 E-value=46 Score=32.79 Aligned_cols=16 Identities=13% Similarity=0.356 Sum_probs=14.3
Q ss_pred CCCCCCCcHHHHHHHH
Q 007824 247 IKKMKQLGGKLGTSLQ 262 (588)
Q Consensus 247 I~~l~GiG~k~~~~L~ 262 (588)
+.++||||+|+++++-
T Consensus 111 L~~ipGIGkKtAerIi 126 (203)
T PRK14602 111 LTRVSGIGKKTAQHIF 126 (203)
T ss_pred HhcCCCcCHHHHHHHH
Confidence 5689999999999986
No 114
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=22.60 E-value=76 Score=24.99 Aligned_cols=28 Identities=14% Similarity=0.218 Sum_probs=19.3
Q ss_pred CCCCCcHHHHHHHHHhh----CCcchhhhccC
Q 007824 249 KMKQLGGKLGTSLQNEL----GVTTVGDLLKF 276 (588)
Q Consensus 249 ~l~GiG~k~~~~L~~~l----GI~TigDLa~l 276 (588)
.+||||.+.++++-+.- ++.++.||...
T Consensus 18 ~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL~~v 49 (65)
T PF12836_consen 18 ALPGIGPKQAKAIVEYREKNGPFKSLEDLKEV 49 (65)
T ss_dssp TSTT--HHHHHHHHHHHHHH-S-SSGGGGGGS
T ss_pred HcCCCCHHHHHHHHHHHHhCcCCCCHHHHhhC
Confidence 67899999998887322 67889998874
No 115
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=22.29 E-value=1e+02 Score=28.71 Aligned_cols=31 Identities=23% Similarity=0.491 Sum_probs=24.6
Q ss_pred CCCCCCCCCcHHHHHHHHHhhCCc---chhhhcc
Q 007824 245 LPIKKMKQLGGKLGTSLQNELGVT---TVGDLLK 275 (588)
Q Consensus 245 lPI~~l~GiG~k~~~~L~~~lGI~---TigDLa~ 275 (588)
..+..|.|||++++..+.+.+||. +++||-.
T Consensus 21 ~aLt~I~GIG~~~a~~I~~~lgi~~~~~~~~Lt~ 54 (144)
T TIGR03629 21 YALTGIKGIGRRFARAIARKLGVDPNAKLGYLDD 54 (144)
T ss_pred EeecceeccCHHHHHHHHHHcCcCCCCCcccCCH
Confidence 346789999999999998899996 4555554
No 116
>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=22.26 E-value=68 Score=28.75 Aligned_cols=28 Identities=18% Similarity=0.269 Sum_probs=20.2
Q ss_pred CCCCCCcHHHHHHHHHhh----CCcchhhhcc
Q 007824 248 KKMKQLGGKLGTSLQNEL----GVTTVGDLLK 275 (588)
Q Consensus 248 ~~l~GiG~k~~~~L~~~l----GI~TigDLa~ 275 (588)
..+||||++.++++.+.. ++.++.||..
T Consensus 71 ~~lpGIG~~~A~~Ii~~R~~~g~f~s~eeL~~ 102 (120)
T TIGR01259 71 QALPGIGPAKAKAIIEYREENGAFKSVDDLTK 102 (120)
T ss_pred hcCCCCCHHHHHHHHHHHHhcCCcCCHHHHHc
Confidence 478999999999998543 3566666654
No 117
>PRK07945 hypothetical protein; Provisional
Probab=22.09 E-value=1.5e+02 Score=31.48 Aligned_cols=49 Identities=18% Similarity=0.186 Sum_probs=31.2
Q ss_pred CCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhCcchHHHHHHHHhc
Q 007824 246 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARG 299 (588)
Q Consensus 246 PI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG~~~g~~l~~~a~G 299 (588)
.+++|||||+.++.++.+-+-=-++.-| +.|+...|+..|..|..+.+|
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 5779999999999998743322222222 345555565556667766665
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=21.94 E-value=77 Score=25.85 Aligned_cols=20 Identities=30% Similarity=0.413 Sum_probs=15.3
Q ss_pred CCCCCCCcHHHHHHHHHhhC
Q 007824 247 IKKMKQLGGKLGTSLQNELG 266 (588)
Q Consensus 247 I~~l~GiG~k~~~~L~~~lG 266 (588)
+.-++|||++++.+|.+.+|
T Consensus 24 i~gv~giG~k~A~~ll~~~~ 43 (75)
T cd00080 24 IPGVPGIGPKTALKLLKEYG 43 (75)
T ss_pred CCCCCcccHHHHHHHHHHhC
Confidence 33689999999999985443
No 119
>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=21.89 E-value=57 Score=25.86 Aligned_cols=30 Identities=27% Similarity=0.416 Sum_probs=21.7
Q ss_pred CCC-CCCCcHHHHHHHHHh---hC-CcchhhhccC
Q 007824 247 IKK-MKQLGGKLGTSLQNE---LG-VTTVGDLLKF 276 (588)
Q Consensus 247 I~~-l~GiG~k~~~~L~~~---lG-I~TigDLa~l 276 (588)
+.. ++|||.+.+.+|.+. .| +.+..||...
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 899999999988843 34 7777777654
No 120
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=21.49 E-value=1.2e+02 Score=28.56 Aligned_cols=41 Identities=20% Similarity=0.418 Sum_probs=29.5
Q ss_pred CCCCCCCCCcHHHHHHHHHhhCCc---chhhhccCCHHHHHHHh
Q 007824 245 LPIKKMKQLGGKLGTSLQNELGVT---TVGDLLKFSEDKLQESY 285 (588)
Q Consensus 245 lPI~~l~GiG~k~~~~L~~~lGI~---TigDLa~l~~~~L~~rf 285 (588)
..+..|.|||.+++..+.+.+||. +++||-.-....|...+
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 346789999999999999899997 56666554444444443
No 121
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=21.02 E-value=45 Score=32.56 Aligned_cols=16 Identities=31% Similarity=0.468 Sum_probs=14.3
Q ss_pred CCCCCCCcHHHHHHHH
Q 007824 247 IKKMKQLGGKLGTSLQ 262 (588)
Q Consensus 247 I~~l~GiG~k~~~~L~ 262 (588)
+.+|||||+|++.++.
T Consensus 14 l~kLPGvG~KsA~R~A 29 (198)
T COG0353 14 LKKLPGVGPKSAQRLA 29 (198)
T ss_pred HhhCCCCChhHHHHHH
Confidence 4689999999999996
No 122
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=20.94 E-value=65 Score=25.63 Aligned_cols=17 Identities=18% Similarity=0.528 Sum_probs=14.4
Q ss_pred CCCCCCCcHHHHHHHHH
Q 007824 247 IKKMKQLGGKLGTSLQN 263 (588)
Q Consensus 247 I~~l~GiG~k~~~~L~~ 263 (588)
+.+|||||.+++.++.+
T Consensus 49 ~~~l~gIG~~ia~kI~E 65 (68)
T PF14716_consen 49 LKKLPGIGKSIAKKIDE 65 (68)
T ss_dssp HCTSTTTTHHHHHHHHH
T ss_pred HhhCCCCCHHHHHHHHH
Confidence 46899999999998863
No 123
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=20.64 E-value=76 Score=36.43 Aligned_cols=41 Identities=17% Similarity=0.214 Sum_probs=34.6
Q ss_pred cCCCCCCCCCcHHHHHHHHHhhCCcchhhhccCCHHHHHHHhC
Q 007824 244 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYG 286 (588)
Q Consensus 244 ~lPI~~l~GiG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rfG 286 (588)
.+.+..++|||++...+|.+ -..++.++..++.+.|.+.-|
T Consensus 524 ~~~L~~IpGIG~kr~~~LL~--~FGS~~~I~~As~eeL~~vpG 564 (577)
T PRK14668 524 STVLDDVPGVGPETRKRLLR--RFGSVEGVREASVEDLRDVPG 564 (577)
T ss_pred HhHHhcCCCCCHHHHHHHHH--HcCCHHHHHhCCHHHHHhCCC
Confidence 57788999999999999985 456889999999999988734
No 124
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=20.43 E-value=1e+02 Score=28.86 Aligned_cols=28 Identities=29% Similarity=0.465 Sum_probs=21.4
Q ss_pred CCCCCCcHHHHHHHHH---hhC-Ccchhhhcc
Q 007824 248 KKMKQLGGKLGTSLQN---ELG-VTTVGDLLK 275 (588)
Q Consensus 248 ~~l~GiG~k~~~~L~~---~lG-I~TigDLa~ 275 (588)
..|||||++.++.+.+ ..| .+++.||..
T Consensus 100 ~~lpgIG~~kA~aIi~yRe~~G~f~sv~dL~~ 131 (149)
T COG1555 100 QALPGIGPKKAQAIIDYREENGPFKSVDDLAK 131 (149)
T ss_pred HHCCCCCHHHHHHHHHHHHHcCCCCcHHHHHh
Confidence 5789999999998873 233 678888875
Done!