Query 004805
Match_columns 729
No_of_seqs 316 out of 2015
Neff 6.3
Searched_HMMs 46136
Date Thu Mar 28 13:12:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004805.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004805hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2095 DNA polymerase iota/DN 100.0 1.2E-78 2.6E-83 675.5 31.7 359 1-364 5-375 (656)
2 PRK01216 DNA polymerase IV; Va 100.0 1.8E-69 3.9E-74 589.5 34.9 338 13-439 2-342 (351)
3 cd01701 PolY_Rev1 DNA polymera 100.0 2.4E-69 5.1E-74 600.1 36.5 350 9-436 44-404 (404)
4 PTZ00205 DNA polymerase kappa; 100.0 4.8E-69 1E-73 604.2 34.1 340 12-439 133-487 (571)
5 PRK14133 DNA polymerase IV; Pr 100.0 3.3E-68 7.2E-73 580.2 36.2 346 10-450 1-347 (347)
6 PRK01810 DNA polymerase IV; Va 100.0 3.8E-68 8.2E-73 591.4 36.5 353 10-451 3-358 (407)
7 cd01702 PolY_Pol_eta DNA Polym 100.0 1.7E-68 3.8E-73 583.7 31.2 339 15-435 1-359 (359)
8 PRK03103 DNA polymerase IV; Re 100.0 6.3E-68 1.4E-72 590.0 35.6 356 10-452 1-362 (409)
9 PRK03348 DNA polymerase IV; Pr 100.0 1.7E-67 3.8E-72 592.3 39.0 353 10-454 3-357 (454)
10 cd01703 PolY_Pol_iota DNA Poly 100.0 6.9E-68 1.5E-72 582.3 35.0 348 15-435 1-379 (379)
11 PRK03858 DNA polymerase IV; Va 100.0 1.3E-67 2.7E-72 585.1 36.0 349 11-451 3-353 (396)
12 PRK02794 DNA polymerase IV; Pr 100.0 1.2E-67 2.7E-72 589.2 36.1 357 4-452 29-386 (419)
13 cd00424 PolY Y-family of DNA p 100.0 3.3E-67 7.2E-72 571.4 35.4 340 15-434 1-343 (343)
14 PRK03352 DNA polymerase IV; Va 100.0 1.2E-66 2.7E-71 567.5 35.5 340 9-439 2-345 (346)
15 cd03586 PolY_Pol_IV_kappa DNA 100.0 1.9E-65 4.2E-70 554.6 34.1 333 15-436 1-334 (334)
16 PRK03609 umuC DNA polymerase V 100.0 2.9E-65 6.3E-70 570.7 33.1 353 13-452 1-363 (422)
17 cd01700 PolY_Pol_V_umuC umuC s 100.0 1.1E-64 2.3E-69 551.9 31.6 337 15-435 1-344 (344)
18 PRK02406 DNA polymerase IV; Va 100.0 9.6E-64 2.1E-68 544.2 34.2 331 19-439 1-334 (343)
19 COG0389 DinP Nucleotidyltransf 100.0 3.5E-60 7.5E-65 517.9 34.0 344 12-439 1-347 (354)
20 KOG2094 Predicted DNA damage i 100.0 4.4E-61 9.5E-66 499.4 21.9 346 8-440 99-447 (490)
21 cd03468 PolY_like DNA Polymera 100.0 3.7E-52 8E-57 450.8 32.5 327 15-434 1-334 (335)
22 KOG2093 Translesion DNA polyme 100.0 2.3E-52 5.1E-57 471.5 18.8 349 14-439 373-733 (1016)
23 PF00817 IMS: impB/mucB/samB f 100.0 3.4E-35 7.4E-40 283.6 15.7 147 17-223 1-149 (149)
24 PF11799 IMS_C: impB/mucB/samB 99.3 7.5E-12 1.6E-16 116.1 9.0 125 302-450 1-127 (127)
25 PF11798 IMS_HHH: IMS family H 98.3 3.1E-07 6.7E-12 66.0 1.3 32 235-267 1-32 (32)
26 PRK04301 radA DNA repair and r 97.7 3.8E-05 8.3E-10 83.5 4.8 80 241-321 2-88 (317)
27 TIGR02236 recomb_radA DNA repa 97.0 0.00098 2.1E-08 72.2 5.4 74 247-321 1-81 (310)
28 PF14520 HHH_5: Helix-hairpin- 96.2 0.0038 8.1E-08 51.2 3.1 50 247-297 7-58 (60)
29 PF11731 Cdd1: Pathogenicity l 95.7 0.012 2.6E-07 52.6 3.9 40 246-286 13-52 (93)
30 PRK12766 50S ribosomal protein 92.3 0.19 4.2E-06 52.1 5.0 56 246-302 4-61 (232)
31 PF08827 DUF1805: Domain of un 92.0 0.091 2E-06 43.1 1.7 27 50-76 32-58 (59)
32 COG3743 Uncharacterized conser 91.6 0.19 4.1E-06 47.6 3.6 37 246-283 68-104 (133)
33 PF10391 DNA_pol_lambd_f: Fing 91.2 0.14 3E-06 41.1 2.0 27 248-275 5-31 (52)
34 PF04994 TfoX_C: TfoX C-termin 90.9 0.28 6.1E-06 42.9 3.9 33 246-279 4-36 (81)
35 PF03118 RNA_pol_A_CTD: Bacter 89.4 0.61 1.3E-05 39.2 4.5 45 240-286 7-51 (66)
36 PRK02362 ski2-like helicase; P 88.0 0.49 1.1E-05 57.6 4.3 55 245-300 652-706 (737)
37 PF14229 DUF4332: Domain of un 84.8 0.58 1.3E-05 44.1 2.1 41 246-287 54-94 (122)
38 PF12826 HHH_2: Helix-hairpin- 82.9 0.98 2.1E-05 37.6 2.5 47 250-298 8-56 (64)
39 KOG2093 Translesion DNA polyme 80.3 0.41 8.8E-06 57.5 -1.0 31 14-44 330-360 (1016)
40 COG2251 Predicted nuclease (Re 80.1 1.5 3.4E-05 49.4 3.5 68 235-303 215-284 (474)
41 PF14229 DUF4332: Domain of un 79.9 3.2 6.9E-05 39.1 5.0 44 251-296 1-49 (122)
42 PRK01172 ski2-like helicase; P 78.5 2.5 5.4E-05 50.9 4.8 51 245-296 612-664 (674)
43 PRK00254 ski2-like helicase; P 77.5 2.2 4.8E-05 51.8 4.1 54 244-298 644-699 (720)
44 PF14377 DUF4414: Domain of un 72.1 1.7 3.7E-05 40.0 1.0 21 684-704 1-21 (108)
45 PRK08609 hypothetical protein; 71.2 2.9 6.3E-05 49.5 2.8 64 188-277 57-120 (570)
46 smart00483 POLXc DNA polymeras 70.5 2.3 5E-05 47.0 1.7 30 247-277 91-120 (334)
47 PF14377 DUF4414: Domain of un 69.7 2.8 6E-05 38.6 1.8 25 681-705 42-66 (108)
48 PF02961 BAF: Barrier to autoi 69.0 4.8 0.0001 35.9 3.0 35 239-274 13-47 (89)
49 TIGR03491 RecB family nuclease 68.9 3.8 8.3E-05 47.1 3.1 59 239-298 201-261 (457)
50 PRK07758 hypothetical protein; 67.2 10 0.00022 34.2 4.8 36 250-286 39-74 (95)
51 smart00611 SEC63 Domain of unk 65.7 13 0.00028 40.1 6.3 61 244-305 150-212 (312)
52 PF02889 Sec63: Sec63 Brl doma 65.6 8.5 0.00018 41.5 4.8 60 245-305 148-209 (314)
53 cd00141 NT_POLXc Nucleotidyltr 65.0 4.2 9.2E-05 44.3 2.3 29 247-276 87-115 (307)
54 PRK14667 uvrC excinuclease ABC 63.7 7.6 0.00016 45.9 4.2 54 244-299 513-567 (567)
55 PRK07956 ligA NAD-dependent DN 62.9 8.4 0.00018 46.5 4.5 49 248-296 448-498 (665)
56 PRK00116 ruvA Holliday junctio 62.4 7.6 0.00016 39.5 3.5 56 247-302 75-133 (192)
57 TIGR00596 rad1 DNA repair prot 61.8 8.2 0.00018 47.6 4.2 52 247-300 759-811 (814)
58 PTZ00035 Rad51 protein; Provis 59.7 11 0.00023 41.8 4.3 55 245-300 21-79 (337)
59 COG3377 Uncharacterized conser 59.3 3.1 6.7E-05 37.0 0.0 26 51-76 69-94 (95)
60 PLN03186 DNA repair protein RA 59.3 7.7 0.00017 43.0 3.1 44 244-288 25-70 (342)
61 PRK10917 ATP-dependent DNA hel 59.0 6.4 0.00014 47.6 2.6 31 245-276 9-39 (681)
62 TIGR00575 dnlj DNA ligase, NAD 56.1 13 0.00028 44.8 4.5 51 248-298 435-487 (652)
63 PRK14672 uvrC excinuclease ABC 56.0 20 0.00043 43.3 5.9 62 244-307 607-670 (691)
64 PRK12278 50S ribosomal protein 55.5 11 0.00025 39.2 3.4 36 246-282 159-194 (221)
65 TIGR02239 recomb_RAD51 DNA rep 55.3 13 0.00028 40.7 4.0 36 252-288 8-43 (316)
66 PRK14973 DNA topoisomerase I; 55.3 24 0.00053 44.3 6.8 80 215-298 849-931 (936)
67 PF00633 HHH: Helix-hairpin-he 55.1 8 0.00017 27.5 1.5 16 247-262 13-28 (30)
68 PRK14671 uvrC excinuclease ABC 54.6 15 0.00033 44.0 4.7 51 245-297 569-619 (621)
69 PRK14666 uvrC excinuclease ABC 54.2 14 0.00031 44.5 4.3 51 245-297 637-689 (694)
70 TIGR02238 recomb_DMC1 meiotic 53.1 15 0.00032 40.2 4.0 47 251-298 7-55 (313)
71 PRK12311 rpsB 30S ribosomal pr 53.0 10 0.00022 41.8 2.7 36 246-282 264-299 (326)
72 PLN03187 meiotic recombination 52.9 13 0.00029 41.2 3.7 56 244-300 28-87 (344)
73 PRK14670 uvrC excinuclease ABC 51.0 19 0.00041 42.8 4.7 53 244-298 513-567 (574)
74 COG1200 RecG RecG-like helicas 47.3 12 0.00026 44.7 2.3 31 245-276 10-40 (677)
75 PRK14351 ligA NAD-dependent DN 45.9 25 0.00054 42.7 4.7 50 248-297 465-516 (689)
76 TIGR01954 nusA_Cterm_rpt trans 44.9 28 0.00061 26.8 3.4 33 254-287 2-34 (50)
77 PRK12373 NADH dehydrogenase su 42.3 22 0.00048 40.2 3.3 36 246-282 324-359 (400)
78 PRK14669 uvrC excinuclease ABC 41.3 32 0.0007 41.3 4.6 54 244-299 551-604 (624)
79 COG5018 KapD Inhibitor of the 39.6 8.4 0.00018 38.4 -0.4 41 678-718 24-64 (210)
80 TIGR02027 rpoA DNA-directed RN 35.2 38 0.00082 36.9 3.6 54 242-297 232-287 (297)
81 PRK00558 uvrC excinuclease ABC 32.2 49 0.0011 39.6 4.3 53 244-298 542-596 (598)
82 TIGR00575 dnlj DNA ligase, NAD 32.2 49 0.0011 40.0 4.3 32 251-284 504-535 (652)
83 PRK05182 DNA-directed RNA poly 32.2 45 0.00097 36.6 3.6 51 243-295 247-299 (310)
84 KOG2534 DNA polymerase IV (fam 31.3 42 0.00092 36.7 3.2 29 248-277 100-128 (353)
85 PF07887 Calmodulin_bind: Calm 30.8 54 0.0012 35.7 3.9 48 249-297 166-218 (299)
86 smart00278 HhH1 Helix-hairpin- 30.5 34 0.00074 23.1 1.5 16 247-262 3-18 (26)
87 PF08004 DUF1699: Protein of u 30.5 84 0.0018 30.0 4.5 35 68-109 31-65 (131)
88 TIGR00084 ruvA Holliday juncti 28.9 53 0.0011 33.4 3.3 51 248-301 75-131 (191)
89 PRK13766 Hef nuclease; Provisi 28.5 60 0.0013 39.8 4.3 50 247-298 717-768 (773)
90 COG1796 POL4 DNA polymerase IV 27.8 37 0.00081 37.2 2.0 34 245-278 93-126 (326)
91 COG1948 MUS81 ERCC4-type nucle 27.3 76 0.0016 33.9 4.1 50 247-298 184-235 (254)
92 PF00416 Ribosomal_S13: Riboso 26.6 78 0.0017 29.1 3.7 35 247-281 17-51 (107)
93 PF07647 SAM_2: SAM domain (St 26.6 50 0.0011 26.8 2.2 47 233-288 4-50 (66)
94 PRK08097 ligB NAD-dependent DN 26.5 77 0.0017 37.7 4.4 47 249-296 429-478 (562)
95 COG0632 RuvA Holliday junction 25.8 31 0.00067 35.5 1.0 45 210-262 80-125 (201)
96 TIGR03631 bact_S13 30S ribosom 22.9 91 0.002 29.1 3.4 36 246-281 16-51 (113)
97 CHL00013 rpoA RNA polymerase a 21.9 87 0.0019 34.7 3.6 55 241-297 259-315 (327)
98 PTZ00134 40S ribosomal protein 21.9 97 0.0021 30.6 3.5 41 246-286 31-74 (154)
99 PRK14605 ruvA Holliday junctio 21.8 88 0.0019 31.9 3.3 53 248-300 76-131 (194)
100 PRK14351 ligA NAD-dependent DN 21.2 97 0.0021 37.8 4.0 53 239-296 525-579 (689)
101 PRK13844 recombination protein 20.8 83 0.0018 32.4 2.9 16 247-262 17-32 (200)
102 COG2199 c-di-GMP synthetase (d 20.6 2.3E+02 0.0051 27.3 6.0 29 100-128 77-109 (181)
103 cd00166 SAM Sterile alpha moti 20.3 1.1E+02 0.0025 24.0 3.1 46 234-289 3-48 (63)
No 1
>KOG2095 consensus DNA polymerase iota/DNA damage inducible protein [Replication, recombination and repair]
Probab=100.00 E-value=1.2e-78 Score=675.51 Aligned_cols=359 Identities=52% Similarity=0.769 Sum_probs=327.1
Q ss_pred CCCCCCCCCCCCEEEEEeCCchhHhhhchhCCCCCCCcEEEEeccCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCc
Q 004805 1 MPVARPDSSGARIIAHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQI 80 (729)
Q Consensus 1 ~~~~~~~~~~~rvI~HIDmD~FyASVE~~~~P~LrgkPvaV~q~~~~~~g~ViA~SYeARk~GVk~GM~~~eA~~LCP~L 80 (729)
|+|+++.-++.|||+||||||||||||++++|+|+++|+||+||+ +||||||+||++||+++|+++||+++||+|
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 578899889999999999999999999999999999999999997 599999999999999999999999999999
Q ss_pred EEEEccccCCCCChHHHHHHHHHHHHHHHhc-CCeeeeccceeEEecccchhHhhhcCCCCCcchhhHHHhhhhcccCc-
Q 004805 81 ELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLE- 158 (729)
Q Consensus 81 ~vv~Vp~~~~k~d~~~Yr~~S~~I~~iL~~~-~~vE~~SIDEafLDlT~~~~~~l~~~~~~~~~~~~~~~~~~~l~G~~- 158 (729)
+++|||++++|+|...||+++.+|+.+|..| +.||++++||+|+|+|.++++.+.+..........++....++++..
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 9999999999999999999999999999997 68999999999999999998765543321100011111123444432
Q ss_pred ----------cCCCCCchhhhhhhhhccCcchhhhhhhhHHHHHHHHHHHHHhHhCCceeEeecCCHHHHHHhccCCCCC
Q 004805 159 ----------SKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPA 228 (729)
Q Consensus 159 ----------~~~~~~~~~~~~~w~~~~~~~~~d~ll~~~~~la~~IR~~I~~etGlt~S~GIA~NklLAKLAS~~~KPn 228 (729)
.+++....+.+..|++.++.+|+|.+|.+|+.||++||++|+.+||||||+|||+||+|||||+.++|||
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 2344445567889999999999999999999999999999999999999999999999999999999999
Q ss_pred ceeeccCCchhcccccCcccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCCChHHHHHHHHhcCCCcccccc
Q 004805 229 QQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQAR 308 (729)
Q Consensus 229 gqtvv~~~~v~~fL~~LPI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~~~g~~L~~~arGiD~~~V~~~ 308 (729)
.||+|++..+++||..|||+++|++|+++++.|.+.|||.++|||+++++..|++.||.+.|.|||..|+|+|.++|.++
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 004805 309 LLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLH 364 (729)
Q Consensus 309 ~~pKSis~s~tF~~p~di~~~eel~~~L~~LaeeL~~RLr~~~~~~~~~artLtL~ 364 (729)
..||||+.+++|++...+.+.+++..||..|++++..||..+..++.+.+.++.++
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 99999999999998888999999999999999999999999888899999999998
No 2
>PRK01216 DNA polymerase IV; Validated
Probab=100.00 E-value=1.8e-69 Score=589.53 Aligned_cols=338 Identities=28% Similarity=0.425 Sum_probs=299.9
Q ss_pred EEEEEeCCchhHhhhchhCCCCCCCcEEEEeccC--CCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEEEccccCC
Q 004805 13 IIAHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNE--WKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVARG 90 (729)
Q Consensus 13 vI~HIDmD~FyASVE~~~~P~LrgkPvaV~q~~~--~~~g~ViA~SYeARk~GVk~GM~~~eA~~LCP~L~vv~Vp~~~~ 90 (729)
+|+||||||||||||++++|+|+|+||||+++.+ .++|+|++|||+||++||++||++.+|+++||++++++
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 6999999999999999999999999999986432 13578899999999999999999999999999998884
Q ss_pred CCChHHHHHHHHHHHHHHHhc-CCeeeeccceeEEecccchhHhhhcCCCCCcchhhHHHhhhhcccCccCCCCCchhhh
Q 004805 91 KADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKATV 169 (729)
Q Consensus 91 k~d~~~Yr~~S~~I~~iL~~~-~~vE~~SIDEafLDlT~~~~~~l~~~~~~~~~~~~~~~~~~~l~G~~~~~~~~~~~~~ 169 (729)
+|++.|+++|++|++++.+| |.||.+||||+|||+|++. ++||
T Consensus 76 -~d~~~y~~~s~~i~~~l~~~tp~ve~~siDE~~LDvt~~~----------------------~l~g------------- 119 (351)
T PRK01216 76 -MRKEVYQQVSNRIMKLLREYSEKIEIASIDEAYLDISDKV----------------------KNYQ------------- 119 (351)
T ss_pred -CCHHHHHHHHHHHHHHHHHhCCceEEccCCeEEEEcccch----------------------hccC-------------
Confidence 79999999999999999996 8999999999999999975 2333
Q ss_pred hhhhhccCcchhhhhhhhHHHHHHHHHHHHHhHhCCceeEeecCCHHHHHHhccCCCCCceeeccCCchhcccccCcccc
Q 004805 170 KEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKK 249 (729)
Q Consensus 170 ~~w~~~~~~~~~d~ll~~~~~la~~IR~~I~~etGlt~S~GIA~NklLAKLAS~~~KPngqtvv~~~~v~~fL~~LPI~~ 249 (729)
.+..++++||++|++++|||||+|||+||++|||||+++||+|+++++++++.+||++|||++
T Consensus 120 -----------------~~~~la~~ir~~I~~~~glt~siGia~nk~lAKlas~~~KP~g~~vi~~~~~~~~L~~LPi~~ 182 (351)
T PRK01216 120 -----------------DAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRFINELDIAD 182 (351)
T ss_pred -----------------CHHHHHHHHHHHHHHHHCCcEEEEecCCHHHHHHHHhccCCCCEEEeCHHHHHHHHhcCCccc
Confidence 345789999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCCChHHHHHHHHhcCCCcccccccCCcccccccccCCCCCCCcH
Q 004805 250 MKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTV 329 (729)
Q Consensus 250 L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~~~g~~L~~~arGiD~~~V~~~~~pKSis~s~tF~~p~di~~~ 329 (729)
|||||+++.++|+ ++||+|+|||+++|.+.|.++||...|.+||++++|+|.++|.+. .+|||+.+.+|+ .++.+.
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-VRKSIGRYVTLP--RNTRDL 258 (351)
T ss_pred ccCCCHHHHHHHH-HcCCCcHHHHhcCCHHHHHHHHCHHHHHHHHHHhCCCCCCCCCCC-CCCCCcCeEECC--CccCCH
Confidence 9999999999997 999999999999999999999997679999999999999999884 569999999998 579999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhcCceeEEEEEEEeeccCCCCCCCCCcCcccccCCCcchhHHHhHHHHHHHHHHHhh
Q 004805 330 ASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFL 409 (729)
Q Consensus 330 eel~~~L~~LaeeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~~~~srs~~L~~~t~~i~~~a~~L~~aal~l~~ 409 (729)
+++...|.+|+++++.||+. .+++++++++|.+ |. +.+++.+++.+|+ ...+++.+.++|.
T Consensus 259 ~~l~~~l~~L~~~~~~rl~~-------~~~~~~~~~~~~d---f~----~~t~~~tl~~~~~-----~~~~~~~a~~Ll~ 319 (351)
T PRK01216 259 EEIKPYLKRAIEEAYYKLDG-------IPKAIHVVAIMED---LD----IVSRGRTFTHGIS-----KETAYREAVRLLQ 319 (351)
T ss_pred HHHHHHHHHHHHHHHHHHHh-------CCCEEEEEEEcCC---CC----EEEEEEECCCCCC-----HHHHHHHHHHHHH
Confidence 99999999999999999984 4667888888643 32 3588889988873 2457888888886
Q ss_pred cccCccccCCCCCCcceeEEEEEccCcccc
Q 004805 410 GSFGVKTQGSHYSGWRITALSVSASKIVPV 439 (729)
Q Consensus 410 ~~~~~~~~~~~~~~~~IR~IGVsls~L~~~ 439 (729)
+.. .+.+.+||+|||++++|.+.
T Consensus 320 ~~~-------~~~~~~vRllGv~~~~l~~~ 342 (351)
T PRK01216 320 KIL-------EEDERKIRRIGVRFSKIIEA 342 (351)
T ss_pred hhh-------hcCCCCeeEEEEEEeccccc
Confidence 432 12245899999999999775
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=2.4e-69 Score=600.12 Aligned_cols=350 Identities=29% Similarity=0.394 Sum_probs=310.3
Q ss_pred CCCCEEEEEeCCchhHhhhchhCCCCCCCcEEEEeccCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEEEcccc
Q 004805 9 SGARIIAHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVA 88 (729)
Q Consensus 9 ~~~rvI~HIDmD~FyASVE~~~~P~LrgkPvaV~q~~~~~~g~ViA~SYeARk~GVk~GM~~~eA~~LCP~L~vv~Vp~~ 88 (729)
...|+|+||||||||||||++++|+|+|+||||++.+. ++|+|+||||+||++||++||++.+|+++||+|++++
T Consensus 44 ~~~r~i~hiD~d~FyasvE~~~~p~L~~kPv~V~~~~~-~~~~V~a~sy~AR~~GV~~gM~~~~A~~lcP~l~vv~---- 118 (404)
T cd01701 44 DLQRIIMHVDFDCFFVSVSIRNRPDLKGKPVAVCHGKG-PNSEIASCNYEARSYGIKNGMWVGQAKKLCPQLVTLP---- 118 (404)
T ss_pred CCCcEEEEEeCchHHHHHHhhhCccccCCCEEEecCCC-CCeEEEecCHHHHhcCCCCCCcHHHHHHHCCCcEEEC----
Confidence 45689999999999999999999999999999987643 3678999999999999999999999999999998884
Q ss_pred CCCCChHHHHHHHHHHHHHHHhc-CCeeeeccceeEEecccchhHhhhcCCCCCcchhhHHHhhhhcccCccCCCCCchh
Q 004805 89 RGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKA 167 (729)
Q Consensus 89 ~~k~d~~~Yr~~S~~I~~iL~~~-~~vE~~SIDEafLDlT~~~~~~l~~~~~~~~~~~~~~~~~~~l~G~~~~~~~~~~~ 167 (729)
+|++.|+++|++|+++|.+| +.||++||||+|||+|++.+. ++
T Consensus 119 ---~~~~~Y~~~s~~i~~il~~~s~~ve~~SiDE~~lDvt~~~~~---------------------~~------------ 162 (404)
T cd01701 119 ---YDFEAYEEVSLTFYEILASYTDNIEAVSCDEALIDITSLLEE---------------------TY------------ 162 (404)
T ss_pred ---CChHHHHHHHHHHHHHHHHhCCceEEcccceEEEEccccccc---------------------cc------------
Confidence 79999999999999999996 789999999999999987410 11
Q ss_pred hhhhhhhccCcchhhhhhhhHHHHHHHHHHHHHhHhCCceeEeecCCHHHHHHhccCCCCCceeeccCCchhcccccCcc
Q 004805 168 TVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPI 247 (729)
Q Consensus 168 ~~~~w~~~~~~~~~d~ll~~~~~la~~IR~~I~~etGlt~S~GIA~NklLAKLAS~~~KPngqtvv~~~~v~~fL~~LPI 247 (729)
+.+..++++||++|++++||+||||||+||++||||++.+||+|++++.++++.+||++|||
T Consensus 163 ------------------~~~~~la~~ir~~I~~~~gl~~siGia~nk~lAKlAs~~aKP~g~~~i~~~~~~~~L~~lPv 224 (404)
T cd01701 163 ------------------ELPEELAEAIRNEIRETTGCSASVGIGPNILLARLATRKAKPDGQYHLSAEKVEEFLSQLKV 224 (404)
T ss_pred ------------------CCHHHHHHHHHHHHHHHHCCCEEEEEcCCHHHHHHHhcccCCCcEEEECHHHHHHHhhcCCH
Confidence 22457899999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCcHHHHHHHHHHhCCcchhhhhcCC--HHHHHHhhCCChHHHHHHHHhcCCCcccccccCCcccccccccCCCCC
Q 004805 248 KKMKQLGGKLGTSLQNELGVTTVGDLLKFS--EDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRA 325 (729)
Q Consensus 248 ~~L~GIG~k~~~~L~~~lGI~TigDLa~l~--~~~L~~rFG~~~g~~L~~~arGiD~~~V~~~~~pKSis~s~tF~~p~d 325 (729)
++|||||++++++|. .+||+|++||+.++ ...|+++||...|.+||+.++|+|+++|.+..++|||+.+++|+ .+
T Consensus 225 ~~l~GIG~~~~~~L~-~~Gi~t~~dl~~~~~~~~~L~~~fG~~~g~~L~~~a~G~d~~~v~~~~~~ksi~~~~tf~--~~ 301 (404)
T cd01701 225 GDLPGVGSSLAEKLV-KLFGDTCGGLELRSKTKEKLQKVLGPKTGEKLYDYCRGIDDRPVTGEKERKSVSAEINYG--IR 301 (404)
T ss_pred hHhCCCCHHHHHHHH-HcCCcchHHHHhCcccHHHHHHHHCHHHHHHHHHHhCCcCCCCCCCCCCCccccceeeCC--CC
Confidence 999999999999997 99999999999999 99999999975799999999999999999888899999999998 56
Q ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHhhhcCceeEEEEEEEeeccCC-CCCC--C-----CCcCcccccCCCcchhHHHhH
Q 004805 326 LKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSS-DSDS--R-----KKFPSKSCPLRYGTAKIQEDT 397 (729)
Q Consensus 326 i~~~eel~~~L~~LaeeL~~RLr~~~~~~~~~artLtL~lr~~~~~-~~~s--~-----~~~~srs~~L~~~t~~i~~~a 397 (729)
+.+.+++..+|..|+++|+.||+. ++..+++|+|++++.... ++.. + .+..+++.+++.+|+ +.
T Consensus 302 ~~~~~~l~~~l~~L~~~l~~rLr~----~~~~~~~l~l~l~~~~~~~~~~~~~y~g~~~~~~~~~~~~l~~pT~----d~ 373 (404)
T cd01701 302 FTNVDDVEQFLQRLSEELSKRLEE----SNVTGRQITLKLMKRAPGAPIEPPKYMGHGICDSFSKSSTLGVATD----DS 373 (404)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHH----cCCceeeEEEEEEeccccCccccccccccCCCcEEeeeeECCCCCC----CH
Confidence 899999999999999999999997 599999999999973211 1100 1 124578899999984 67
Q ss_pred HHHHHHHHHHhhcccCccccCCCCCCcceeEEEEEccCc
Q 004805 398 FNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKI 436 (729)
Q Consensus 398 ~~L~~aal~l~~~~~~~~~~~~~~~~~~IR~IGVsls~L 436 (729)
..|+++++.+|.+.+ ..+.+||+|||++++|
T Consensus 374 ~~i~~~a~~ll~~~~--------~~~~~vR~lgv~~~~l 404 (404)
T cd01701 374 GVIGTEAKKLFRDLS--------IPPEELRGVGIQVTKL 404 (404)
T ss_pred HHHHHHHHHHHHhcc--------CCCCCeeEEEEEEecC
Confidence 789999998887543 1246899999999886
No 4
>PTZ00205 DNA polymerase kappa; Provisional
Probab=100.00 E-value=4.8e-69 Score=604.22 Aligned_cols=340 Identities=23% Similarity=0.310 Sum_probs=298.2
Q ss_pred CEEEEEeCCchhHhhhchhCCCCCCCcEEEEeccCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEEEccccCCC
Q 004805 12 RIIAHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVARGK 91 (729)
Q Consensus 12 rvI~HIDmD~FyASVE~~~~P~LrgkPvaV~q~~~~~~g~ViA~SYeARk~GVk~GM~~~eA~~LCP~L~vv~Vp~~~~k 91 (729)
++|+||||||||||||++++|+|+++||||++ +|+|+||||+||+|||++|||+++|+++||+|++|+
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 378999999999999999999999999999998884
Q ss_pred CChHHHHHHHHHHHHHHHhc-CCeeeeccceeEEecccchhHhhhcCCCCCcchhhHHHhhhhcccCccCCCCCchhhhh
Q 004805 92 ADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKATVK 170 (729)
Q Consensus 92 ~d~~~Yr~~S~~I~~iL~~~-~~vE~~SIDEafLDlT~~~~~~l~~~~~~~~~~~~~~~~~~~l~G~~~~~~~~~~~~~~ 170 (729)
+||+.|+++|.+|+++|.+| |.+|++||||+|||+|++... ++..
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 79999999999999999997 889999999999999997521 1100
Q ss_pred hhhhccCcchhhhhhhhHHHHHHHHHHHHHhHhCCceeEeecCCHHHHHHhccCCCCCceeec---cCCchhcccccCcc
Q 004805 171 EWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTV---PFSSVKGLLDSLPI 247 (729)
Q Consensus 171 ~w~~~~~~~~~d~ll~~~~~la~~IR~~I~~etGlt~S~GIA~NklLAKLAS~~~KPngqtvv---~~~~v~~fL~~LPI 247 (729)
..+..+|++||++|+++||||||||||+||+|||||++++||||++++ +++++..||++|||
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 014568999999999999999999999999999999999999999986 56789999999999
Q ss_pred cccCCCcHHHHHHHHHHhCCcchhhhhcCCHH--------HHHHhhCCChHHHHHHHHhcCCCcc-cc--cccCCccccc
Q 004805 248 KKMKQLGGKLGTSLQNELGVTTVGDLLKFSED--------KLQESYGFNTGTWLWNIARGISGEE-VQ--ARLLPKSHGS 316 (729)
Q Consensus 248 ~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~--------~L~~rFG~~~g~~L~~~arGiD~~~-V~--~~~~pKSis~ 316 (729)
++|||||++++++|. .+||+||+||++.+.. .|+..||...|.++|+.++|+|.++ +. ....+|||+.
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 9999999999998876 4788999767999999999999884 33 2446799999
Q ss_pred ccccCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHhhhcCceeEEEEEEEeeccCCCCCCCCCcCcccccCCCcchhHHHh
Q 004805 317 GKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQED 396 (729)
Q Consensus 317 s~tF~~p~di~~~eel~~~L~~LaeeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~~~~srs~~L~~~t~~i~~~ 396 (729)
++||.. +.+.+++...|..|+++|+.||++ .++.+++|+|++|+.+ |.. .+++.+++.+| ++
T Consensus 391 ErTF~~---~~d~~el~~~L~~L~~~v~~rLrk----~~l~artVtlKlK~~d---F~~----~trs~tL~~pT----~d 452 (571)
T PTZ00205 391 ERSFTT---PRTKEGLQEMVDTVFNGAYEEMRK----SELMCRQISLTIRWAS---YRY----QQYTKSLIQYS----DD 452 (571)
T ss_pred eEeCCC---CCCHHHHHHHHHHHHHHHHHHHHh----cCCCccEEEEEEEECC---CCc----eEEEEECCCCc----CC
Confidence 999973 579999999999999999999997 6999999999999854 322 37788898888 46
Q ss_pred HHHHHHHHHHHhhcccCccccCCCCCCcceeEEEEEccCcccc
Q 004805 397 TFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPV 439 (729)
Q Consensus 397 a~~L~~aal~l~~~~~~~~~~~~~~~~~~IR~IGVsls~L~~~ 439 (729)
...|++++..+|.... +.+.+||+|||++++|...
T Consensus 453 ~~~I~~aa~~Ll~~~~--------~~~~~vRLlGV~ls~L~~~ 487 (571)
T PTZ00205 453 SATLRRAVDGLLLPHA--------AKYSEMCLLGVRFLDLISA 487 (571)
T ss_pred HHHHHHHHHHHHHhcc--------ccCCCEEEEEEEEcccCcH
Confidence 7788998888876431 2346899999999999875
No 5
>PRK14133 DNA polymerase IV; Provisional
Probab=100.00 E-value=3.3e-68 Score=580.19 Aligned_cols=346 Identities=29% Similarity=0.403 Sum_probs=311.1
Q ss_pred CCCEEEEEeCCchhHhhhchhCCCCCCCcEEEEeccCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEEEccccC
Q 004805 10 GARIIAHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVAR 89 (729)
Q Consensus 10 ~~rvI~HIDmD~FyASVE~~~~P~LrgkPvaV~q~~~~~~g~ViA~SYeARk~GVk~GM~~~eA~~LCP~L~vv~Vp~~~ 89 (729)
+.|+|+||||||||||||+..+|+|+++||||.+.. ++|+|++|||+||++||++||++.+|+++||++++++
T Consensus 1 ~~r~i~hiD~d~F~as~e~~~~p~l~~~Pvvv~~~~--~~~~V~a~n~~Ar~~GV~~Gm~~~~A~~lcP~l~~~~----- 73 (347)
T PRK14133 1 MDRVIIHVDMDAFFASVEQMDNPKLKGKPVIVGGIS--ERGVVSTCSYEARKYGVHSAMPVFMAKKRCPHGIFLP----- 73 (347)
T ss_pred CCCEEEEEecChHHHHHHhhhCccccCCCEEEecCC--CCcEEEECCHHHHhcCCCCCChHHHHHHHCCCcEEEC-----
Confidence 358999999999999999999999999999987543 3578999999999999999999999999999998884
Q ss_pred CCCChHHHHHHHHHHHHHHHhc-CCeeeeccceeEEecccchhHhhhcCCCCCcchhhHHHhhhhcccCccCCCCCchhh
Q 004805 90 GKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKAT 168 (729)
Q Consensus 90 ~k~d~~~Yr~~S~~I~~iL~~~-~~vE~~SIDEafLDlT~~~~~~l~~~~~~~~~~~~~~~~~~~l~G~~~~~~~~~~~~ 168 (729)
+|++.|+++|++|++++.+| |.||++||||+|||+|++. |
T Consensus 74 --~d~~~y~~~s~~i~~~l~~~s~~ve~~siDe~~ldv~~~~-------------------------~------------ 114 (347)
T PRK14133 74 --VRHERYKEVSKNIFKILYEVTPIVEPVSIDEAYLDITNIK-------------------------E------------ 114 (347)
T ss_pred --CCHHHHHHHHHHHHHHHHHhCCceEEccCCeEEEEccCCC-------------------------C------------
Confidence 79999999999999999996 8999999999999999852 0
Q ss_pred hhhhhhccCcchhhhhhhhHHHHHHHHHHHHHhHhCCceeEeecCCHHHHHHhccCCCCCceeeccCCchhcccccCccc
Q 004805 169 VKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIK 248 (729)
Q Consensus 169 ~~~w~~~~~~~~~d~ll~~~~~la~~IR~~I~~etGlt~S~GIA~NklLAKLAS~~~KPngqtvv~~~~v~~fL~~LPI~ 248 (729)
.+..++++||++|++++||+||+|||+||++||||++++||+|+++++++++.+||++|||+
T Consensus 115 ------------------~~~~la~~i~~~i~~~~gl~~siGia~n~~~Aklas~~~kp~g~~~~~~~~~~~~L~~lpv~ 176 (347)
T PRK14133 115 ------------------EPIKIAKYIKKKVKKETGLTLSVGISYNKFLAKLASDWNKPDGIKIITEDMIPDILKPLPIS 176 (347)
T ss_pred ------------------CHHHHHHHHHHHHHHHHCCcEEEEEcCcHHHHHHHhccCCCCceEEECHHHHHHHHHhCCcc
Confidence 13468999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCCChHHHHHHHHhcCCCcccccccCCcccccccccCCCCCCCc
Q 004805 249 KMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKT 328 (729)
Q Consensus 249 ~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~~~g~~L~~~arGiD~~~V~~~~~pKSis~s~tF~~p~di~~ 328 (729)
+|||||+++.++|. .+||+|++||+++|...|.++||. .|.++|+.++|+|.+++.+..++|+|+.+++|. .++.+
T Consensus 177 ~l~gig~~~~~~L~-~~Gi~ti~dl~~l~~~~L~~rfG~-~g~~l~~~a~G~d~~~v~~~~~~ksi~~~~~~~--~~~~~ 252 (347)
T PRK14133 177 KVHGIGKKSVEKLN-NIGIYTIEDLLKLSREFLIEYFGK-FGVEIYERIRGIDYREVEVSRERKSIGKETTLK--KDTKD 252 (347)
T ss_pred ccCCCCHHHHHHHH-HcCCccHHHHhhCCHHHHHHHHhH-HHHHHHHHhCCCCCCCCCCCCCCcceEeeEEcC--CCCCC
Confidence 99999999999997 999999999999999999999997 699999999999999999888999999999998 56999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhcCceeEEEEEEEeeccCCCCCCCCCcCcccccCCCcchhHHHhHHHHHHHHHHHh
Q 004805 329 VASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLREF 408 (729)
Q Consensus 329 ~eel~~~L~~LaeeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~~~~srs~~L~~~t~~i~~~a~~L~~aal~l~ 408 (729)
.+++.++|.+|+++|+.||+. +++.+++|+|++++.+. . ..+++.+++.+|+ +...|++.+..+|
T Consensus 253 ~~~l~~~l~~L~~~l~~rL~~----~~~~~~~l~l~l~~~~~---~----~~~~~~~l~~~t~----~~~~l~~l~~~ll 317 (347)
T PRK14133 253 KEELKKYLKDFSNIISEELKK----RNLYGKTVTVKIKTSDF---Q----THTKSKTLNDYIR----DKEEIYNVACEIL 317 (347)
T ss_pred HHHHHHHHHHHHHHHHHHHHh----cCCCcceEEEEEEECCC---C----eeEEEEECCCCcC----CHHHHHHHHHHHH
Confidence 999999999999999999997 69999999999997432 2 2367788888884 6677888887777
Q ss_pred hcccCccccCCCCCCcceeEEEEEccCccccccccccccccc
Q 004805 409 LGSFGVKTQGSHYSGWRITALSVSASKIVPVLSGTCSIMKYF 450 (729)
Q Consensus 409 ~~~~~~~~~~~~~~~~~IR~IGVsls~L~~~~~~~~si~dlF 450 (729)
..+ +.+.+||.|||++++|.+. ...|.+||
T Consensus 318 e~~---------~~~~~vr~lgl~~~~l~~~---~~~q~~l~ 347 (347)
T PRK14133 318 EHI---------NIKEPIRLIGLSVSNLSEN---KIEQLSFL 347 (347)
T ss_pred Hhc---------cCCCCEEEEEEEEecCCCC---cccccCCC
Confidence 643 3467999999999999865 34567776
No 6
>PRK01810 DNA polymerase IV; Validated
Probab=100.00 E-value=3.8e-68 Score=591.36 Aligned_cols=353 Identities=29% Similarity=0.456 Sum_probs=313.8
Q ss_pred CCCEEEEEeCCchhHhhhchhCCCCCCCcEEEEeccCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEEEccccC
Q 004805 10 GARIIAHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVAR 89 (729)
Q Consensus 10 ~~rvI~HIDmD~FyASVE~~~~P~LrgkPvaV~q~~~~~~g~ViA~SYeARk~GVk~GM~~~eA~~LCP~L~vv~Vp~~~ 89 (729)
..|+|+||||||||||||++++|+|+++||||++.+..++|+|+||||+||++||++||++.+|+++||+|++++
T Consensus 3 ~~r~i~hiD~d~Fyasve~~~~p~l~~~Pv~V~~~~~~~~~~v~a~ny~Ar~~GV~~Gm~~~~A~~lcP~l~~~~----- 77 (407)
T PRK01810 3 KGRVIFHVDMNSFFASVEIAYDPSLQGKPLAVAGNEKERKGIIVTCSYEARAYGIRTTMPLWEAKRLCPQLIVRR----- 77 (407)
T ss_pred CCCEEEEEecCcHHHhHHhhhCccccCCcEEEeCCCCCCCeEEEEcCHHHHHhCCCCCChHHHHHHHCCCeEEEC-----
Confidence 569999999999999999999999999999998654334678999999999999999999999999999998885
Q ss_pred CCCChHHHHHHHHHHHHHHHhc-CCeeeeccceeEEecccchhHhhhcCCCCCcchhhHHHhhhhcccCccCCCCCchhh
Q 004805 90 GKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKAT 168 (729)
Q Consensus 90 ~k~d~~~Yr~~S~~I~~iL~~~-~~vE~~SIDEafLDlT~~~~~~l~~~~~~~~~~~~~~~~~~~l~G~~~~~~~~~~~~ 168 (729)
+|++.|+++|.+|++++.+| |.||.+||||+|||+|++. +++
T Consensus 78 --~d~~~y~~~s~~i~~~l~~~sp~ve~~siDe~~ldvt~~~----------------------~~~------------- 120 (407)
T PRK01810 78 --PNFDRYREASRQMFQILSEFTPLVQPVSIDEGYLDITDCY----------------------ALG------------- 120 (407)
T ss_pred --CChHHHHHHHHHHHHHHHHhCCceEEecCCeEEEeccCcc----------------------ccC-------------
Confidence 79999999999999999996 8999999999999999864 111
Q ss_pred hhhhhhccCcchhhhhhhhHHHHHHHHHHHHHhHhCCceeEeecCCHHHHHHhccCCCCCceeeccCCchhcccccCccc
Q 004805 169 VKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIK 248 (729)
Q Consensus 169 ~~~w~~~~~~~~~d~ll~~~~~la~~IR~~I~~etGlt~S~GIA~NklLAKLAS~~~KPngqtvv~~~~v~~fL~~LPI~ 248 (729)
.+..++++||++|++++|++||||||+||++||||++.+||+|++++.++++..||+++||+
T Consensus 121 ------------------~~~~~a~~i~~~i~~~~gl~~svGia~n~~lAklas~~~Kp~g~~vi~~~~~~~~L~~lpv~ 182 (407)
T PRK01810 121 ------------------SPLEIAKMIQQRLLTELQLPCSIGIAPNKFLAKMASDMKKPLGITVLRKRDVPEMLWPLPVG 182 (407)
T ss_pred ------------------CHHHHHHHHHHHHHHHHCCceEEEEcCCHHHHHHHhcCCCCCCEEEECHHHHHHHHHhCCHh
Confidence 13467999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCCChHHHHHHHHhcCCCcccccccC--CcccccccccCCCCCC
Q 004805 249 KMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLL--PKSHGSGKSFPGPRAL 326 (729)
Q Consensus 249 ~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~~~g~~L~~~arGiD~~~V~~~~~--pKSis~s~tF~~p~di 326 (729)
+|||||+++.++|. .+||+|+|||+++|...|.++||. .|.++|+.|+|+|+++|.+..+ +|||+.+++|+ .++
T Consensus 183 ~l~giG~~~~~~L~-~~Gi~tigdL~~~~~~~L~~rfG~-~g~~l~~~a~G~d~~~v~~~~~~~~ksi~~~~~~~--~~~ 258 (407)
T PRK01810 183 EMHGIGEKTAEKLK-DIGIQTIGDLAKADEHILRAKLGI-NGVRLQRRANGIDDRPVDPEAIYQFKSVGNSTTLS--HDM 258 (407)
T ss_pred hcCCcCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHHHhH-HHHHHHHHhcCCCCCCCCCCCCCCCceecceEECC--CCC
Confidence 99999999999997 999999999999999999999997 6999999999999999986553 58999999998 579
Q ss_pred CcHHHHHHHHHHHHHHHHHHHHHHhhhcCceeEEEEEEEeeccCCCCCCCCCcCcccccCCCcchhHHHhHHHHHHHHHH
Q 004805 327 KTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLR 406 (729)
Q Consensus 327 ~~~eel~~~L~~LaeeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~~~~srs~~L~~~t~~i~~~a~~L~~aal~ 406 (729)
.+.+++..+|.+|+++|+.||+. .++.+++|+|++++.+. . ..+++.+++.||+ +...|++.+..
T Consensus 259 ~~~~~l~~~l~~L~~~l~~rLr~----~~~~~~~l~l~lr~~~~---~----~~~~~~~l~~pt~----~~~~l~~~~~~ 323 (407)
T PRK01810 259 DEEKELLDVLRRLSKSVSKRLQK----KTVVSYNVQIMIRYHDR---R----TITRSKTLKNPIW----EKRDIFQAASR 323 (407)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHH----cCCccceeEEEEEECCC---C----ceEEEEECCCCCC----CHHHHHHHHHH
Confidence 99999999999999999999997 69999999999998532 1 2367788888884 66778888888
Q ss_pred HhhcccCccccCCCCCCcceeEEEEEccCcccccccccccccccc
Q 004805 407 EFLGSFGVKTQGSHYSGWRITALSVSASKIVPVLSGTCSIMKYFN 451 (729)
Q Consensus 407 l~~~~~~~~~~~~~~~~~~IR~IGVsls~L~~~~~~~~si~dlF~ 451 (729)
+|... +.+.+||+|||++++|.+.. ....|.+||+
T Consensus 324 ll~~~---------~~~~~vr~lgv~~~~l~~~~-~~~~q~~Lf~ 358 (407)
T PRK01810 324 LFKQH---------WNGDPVRLLGVTATDLEWKT-EAVKQLDLFS 358 (407)
T ss_pred HHHhc---------cCCCCEEEEEEEEecCcccc-cccccccccc
Confidence 88743 23568999999999998752 1245789996
No 7
>cd01702 PolY_Pol_eta DNA Polymerase eta. Pol eta, also called Rad30A, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Unlike other Y-family members, Pol eta can efficiently and accurately replicate DNA past UV-induced lesions. Its activity is initiated by two simultaneous interactions: the PIP box in pol eta interacting with PCNA, and the UBZ (ubiquitin-binding zinc finger) in pol eta interacting with monoubiquitin attached to PCNA. Pol eta is more efficient in copying damaged DNA than undamaged DNA and seems to recognize when a lesion has been passed, facilitating a lesion-dependent dissociation from the DNA.
Probab=100.00 E-value=1.7e-68 Score=583.74 Aligned_cols=339 Identities=45% Similarity=0.665 Sum_probs=296.4
Q ss_pred EEEeCCchhHhhhchhCCCCCCCcEEEEeccCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEEEcc--------
Q 004805 15 AHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVP-------- 86 (729)
Q Consensus 15 ~HIDmD~FyASVE~~~~P~LrgkPvaV~q~~~~~~g~ViA~SYeARk~GVk~GM~~~eA~~LCP~L~vv~Vp-------- 86 (729)
+||||||||||||++++|+|+|+||||++++ .|+||||+||++||++||++++|+++||++++++++
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 5999999999999999999999999998753 399999999999999999999999999999999765
Q ss_pred --------ccCCCCChHHHHHHHHHHHHHHHhc-CCeeeeccceeEEecccchhHhhhcCCCCCcchhhHHHhhhhcccC
Q 004805 87 --------VARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGL 157 (729)
Q Consensus 87 --------~~~~k~d~~~Yr~~S~~I~~iL~~~-~~vE~~SIDEafLDlT~~~~~~l~~~~~~~~~~~~~~~~~~~l~G~ 157 (729)
+++++++|+.|+++|++|++++.+| |.||++||||+|||+..
T Consensus 76 ~~~~~~~~~~~~~~~~~~Y~~~S~~i~~~l~~~sp~vE~~SiDE~flDv~~----------------------------- 126 (359)
T cd01702 76 ADYHENPSPARHKVSLDPYRRASRKILNILKRFGDVVEKASIDEAYLDLGS----------------------------- 126 (359)
T ss_pred cccccccccccccccHHHHHHHHHHHHHHHHHcCCceEECcCCeeHHHHHH-----------------------------
Confidence 4566789999999999999999996 89999999999999821
Q ss_pred ccCCCCCchhhhhhhhhccCcchhhhhhhhHHHHHHHHHHHHHhHhCCceeEeecCCHHHHHHhccCCCCCceeeccCCc
Q 004805 158 ESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSS 237 (729)
Q Consensus 158 ~~~~~~~~~~~~~~w~~~~~~~~~d~ll~~~~~la~~IR~~I~~etGlt~S~GIA~NklLAKLAS~~~KPngqtvv~~~~ 237 (729)
.+|++||++|++++|||||||||+||++||||++++||+|++++++++
T Consensus 127 --------------------------------~la~~ir~~I~~~~glt~SiGIa~nk~lAKlAs~~~KP~g~~v~~~~~ 174 (359)
T cd01702 127 --------------------------------RIVEEIRQQVYDELGYTCSAGIAHNKMLAKLASGMNKPNAQTILRNDA 174 (359)
T ss_pred --------------------------------HHHHHHHHHHHHHhCccEEeeecCCHHHHHHHhcccCCCCeEEECHHH
Confidence 368899999999999999999999999999999999999999999999
Q ss_pred hhcccccCcccccCCCcHHHHHHHHHHhCCcchhhhhcC--CHHHHHHhhCCChHHHHHHHHhcCCCcccccccCCcccc
Q 004805 238 VKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKF--SEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHG 315 (729)
Q Consensus 238 v~~fL~~LPI~~L~GIG~k~~~~L~~~lGI~TigDLa~l--~~~~L~~rFG~~~g~~L~~~arGiD~~~V~~~~~pKSis 315 (729)
+.+||+++||++|||||++++.+|.+.+||+|++||+++ +...|.++||.+.|.+||+.|+|+|+++|.+..++|||+
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 999999999999999999998775348999999999999 999999999966799999999999999999888899999
Q ss_pred cccccCCCCCCCcH-HHHHHHHHHHHHHHHHHHHHHhhhcCceeEEEEEEEeeccCCCCCCCCCcCcccccCCCcchhHH
Q 004805 316 SGKSFPGPRALKTV-ASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQ 394 (729)
Q Consensus 316 ~s~tF~~p~di~~~-eel~~~L~~LaeeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~~~~srs~~L~~~t~~i~ 394 (729)
.+++|. .++.+. +++..+|..|+++|+.||+.++..+++.+++|+|++++.++ + ...+++.+++.++
T Consensus 255 ~~~tf~--~~~~~~~~~l~~~l~~L~~~l~~rL~~~~~~~~~~~~~v~v~lr~~~~--~----~~~sr~~~~~~~~---- 322 (359)
T cd01702 255 SSKNFP--GKTALSTEDVQHWLLVLASELNSRLEDDRYENNRRPKTLVLSLRQRGD--G----VRRSRSCALPRYD---- 322 (359)
T ss_pred eeeecC--CCCCChHHHHHHHHHHHHHHHHHHHHhhhhhcCceeeEEEEEEEECCC--c----EEEEEEecCCCCC----
Confidence 999998 467777 99999999999999999998655568999999999998532 1 2357777777655
Q ss_pred HhHHHHHHHHHHHhhcccCccccCCCCCCcceeEEEEEccC
Q 004805 395 EDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASK 435 (729)
Q Consensus 395 ~~a~~L~~aal~l~~~~~~~~~~~~~~~~~~IR~IGVsls~ 435 (729)
...|+++++.+|.+++..... ..| +++||+|||+++|
T Consensus 323 --~~~i~~~~~~l~~~~~~~~~~-~~~-~~~~rl~g~~~~~ 359 (359)
T cd01702 323 --AQKIVKDAFKLIKAINEEGLG-LAW-NYPLTLLSLSFTK 359 (359)
T ss_pred --HHHHHHHHHHHHHHhhhhccc-ccc-CCCeEEEEEEecC
Confidence 345777777777655421100 001 4799999999875
No 8
>PRK03103 DNA polymerase IV; Reviewed
Probab=100.00 E-value=6.3e-68 Score=589.96 Aligned_cols=356 Identities=27% Similarity=0.434 Sum_probs=316.4
Q ss_pred CCCEEEEEeCCchhHhhhchhCCCCCCCcEEEEeccCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEEEccccC
Q 004805 10 GARIIAHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVAR 89 (729)
Q Consensus 10 ~~rvI~HIDmD~FyASVE~~~~P~LrgkPvaV~q~~~~~~g~ViA~SYeARk~GVk~GM~~~eA~~LCP~L~vv~Vp~~~ 89 (729)
+.|+|+||||||||||||+..+|+|+|+||||++....++|+|+||||+||++||++||++.+|+++||+|++++
T Consensus 1 m~r~i~hiD~d~Ffasve~~~~P~l~~~Pv~V~~~~~~~~~~v~a~sy~Ar~~GV~~gm~~~~A~~lcP~l~~~~----- 75 (409)
T PRK03103 1 MERVILLVDMQSFYASVEKAANPELKGRPVIVSGDPERRSGVVLAACPLAKAYGVKTAERLWEAQQKCPDLVVVK----- 75 (409)
T ss_pred CCCEEEEEecchHHHhHhcccChhhcCCcEEEeccCCCCCEEEEEcCHHHHHhCCCCCChHHHHHHHCCCeEEEC-----
Confidence 468999999999999999999999999999998754334578999999999999999999999999999998884
Q ss_pred CCCChHHHHHHHHHHHHHHHhc-CCeeeeccceeEEecccchhHhhhcCCCCCcchhhHHHhhhhcccCccCCCCCchhh
Q 004805 90 GKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKAT 168 (729)
Q Consensus 90 ~k~d~~~Yr~~S~~I~~iL~~~-~~vE~~SIDEafLDlT~~~~~~l~~~~~~~~~~~~~~~~~~~l~G~~~~~~~~~~~~ 168 (729)
+|++.|+++|++|++++.+| |.||++||||+|||+|++. ++||
T Consensus 76 --~d~~~y~~~s~~i~~~l~~~sp~ve~~siDe~~lDvt~~~----------------------~~~~------------ 119 (409)
T PRK03103 76 --PRMQRYIDVSLQITRILEDFTDLVEPFSIDEQFLDVTGSQ----------------------KLFG------------ 119 (409)
T ss_pred --CCHHHHHHHHHHHHHHHHHhCccceecCCCeeEeeccchh----------------------hcCC------------
Confidence 79999999999999999996 8999999999999999975 2333
Q ss_pred hhhhhhccCcchhhhhhhhHHHHHHHHHHHHHhHhCCceeEeecCCHHHHHHhccC---CCCCceeeccCCchhcccccC
Q 004805 169 VKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGM---NKPAQQTTVPFSSVKGLLDSL 245 (729)
Q Consensus 169 ~~~w~~~~~~~~~d~ll~~~~~la~~IR~~I~~etGlt~S~GIA~NklLAKLAS~~---~KPngqtvv~~~~v~~fL~~L 245 (729)
.+..++++||++|++++||+||||||+||++||||++. +||+|++++.++++.+||++|
T Consensus 120 ------------------~~~~la~~ir~~i~~~~gl~~svGia~n~~lAklas~~~~k~kp~g~~v~~~~~~~~~L~~l 181 (409)
T PRK03103 120 ------------------SPLEIAQKIQQRIMRETGVYARVGIGPNKLLAKMACDNFAKKNPDGLFTLDKEDVPADLWPL 181 (409)
T ss_pred ------------------CHHHHHHHHHHHHHHHHCceEEEeecCCHHHHHHHhcchhhcCCCcEEEECHHHHHHHHHcC
Confidence 24578999999999999999999999999999999998 999999999999999999999
Q ss_pred cccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCCChHHHHHHHHhcCCCcccccccC--CcccccccccCCC
Q 004805 246 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLL--PKSHGSGKSFPGP 323 (729)
Q Consensus 246 PI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~~~g~~L~~~arGiD~~~V~~~~~--pKSis~s~tF~~p 323 (729)
||++|||||+++.++|. .+||+|+|||+++|...|+++||. .|.++|+.++|+|+++|.+..+ +|||+.+.+|+
T Consensus 182 pi~~l~gig~~~~~~L~-~~Gi~tigdl~~~~~~~L~~~fG~-~~~~l~~~a~G~d~~~v~~~~~~~~ksi~~~~t~~-- 257 (409)
T PRK03103 182 PVRKLFGVGSRMEKHLR-RMGIRTIGQLANTPLERLKKRWGI-NGEVLWRTANGIDYSPVTPHSLDRQKAIGHQMTLP-- 257 (409)
T ss_pred CHhhcCCccHHHHHHHH-HcCCCCHHHHhcCCHHHHHHHHCH-HHHHHHHHhcCCCCCcCCcccCCCCCccCCCeECC--
Confidence 99999999999999997 999999999999999999999997 5999999999999999988754 57999999998
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHHHHHHhhhcCceeEEEEEEEeeccCCCCCCCCCcCcccccCCCcchhHHHhHHHHHHH
Q 004805 324 RALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQA 403 (729)
Q Consensus 324 ~di~~~eel~~~L~~LaeeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~~~~srs~~L~~~t~~i~~~a~~L~~a 403 (729)
.++.+.+++...|..|+++|+.||+. .+..+++|+|++++.+. +. .+..+++++++.+|+ +...|++.
T Consensus 258 ~~~~~~~~l~~~l~~L~~~l~~rLr~----~~~~~~~l~l~lr~~~~---~~-~~~~~~~~~l~~pt~----~~~~l~~~ 325 (409)
T PRK03103 258 RDYRGFEEIKVVLLELCEEVCRRARA----KGYMGRTVSVSLRGADF---DW-PTGFSRQMTLPEPTN----LAMEVYEA 325 (409)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHH----hCCceeEEEEEEEeCCC---cC-CCCcceeeecCCCCC----CHHHHHHH
Confidence 57999999999999999999999997 58899999999987542 21 123577888888884 66778888
Q ss_pred HHHHhhcccCccccCCCCCCcceeEEEEEccCccccccccccccccccc
Q 004805 404 GLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPVLSGTCSIMKYFNG 452 (729)
Q Consensus 404 al~l~~~~~~~~~~~~~~~~~~IR~IGVsls~L~~~~~~~~si~dlF~~ 452 (729)
+..+|... +.+.+||+|||++++|.+. ...|.+||+.
T Consensus 326 ~~~ll~~~---------~~~~~vr~lgv~~~~l~~~---~~~q~~LF~~ 362 (409)
T PRK03103 326 ACKLFHRH---------WDGKPVRRVGVTLSNLVSD---DVWQLSLFGD 362 (409)
T ss_pred HHHHHHhc---------ccCCCceEEEEEEeCCCCC---cccCCCcccc
Confidence 88877643 3467999999999999875 3567899974
No 9
>PRK03348 DNA polymerase IV; Provisional
Probab=100.00 E-value=1.7e-67 Score=592.34 Aligned_cols=353 Identities=28% Similarity=0.391 Sum_probs=313.7
Q ss_pred CCCEEEEEeCCchhHhhhchhCCCCCCCcEEEEeccCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCC-cEEEEcccc
Q 004805 10 GARIIAHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQ-IELVQVPVA 88 (729)
Q Consensus 10 ~~rvI~HIDmD~FyASVE~~~~P~LrgkPvaV~q~~~~~~g~ViA~SYeARk~GVk~GM~~~eA~~LCP~-L~vv~Vp~~ 88 (729)
..|+|+||||||||||||++.+|+|+|+||+|.+.. ++|+|++|||+||++||++||++.+|+++||+ +++++
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 468999999999999999999999999999987643 36788899999999999999999999999999 88874
Q ss_pred CCCCChHHHHHHHHHHHHHHHhc-CCeeeeccceeEEecccchhHhhhcCCCCCcchhhHHHhhhhcccCccCCCCCchh
Q 004805 89 RGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKA 167 (729)
Q Consensus 89 ~~k~d~~~Yr~~S~~I~~iL~~~-~~vE~~SIDEafLDlT~~~~~~l~~~~~~~~~~~~~~~~~~~l~G~~~~~~~~~~~ 167 (729)
+|++.|+++|++|++++.+| +.||++||||+|||+++.. |..
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 79999999999999999996 8999999999999977542 110
Q ss_pred hhhhhhhccCcchhhhhhhhHHHHHHHHHHHHHhHhCCceeEeecCCHHHHHHhccCCCCCceeeccCCchhcccccCcc
Q 004805 168 TVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPI 247 (729)
Q Consensus 168 ~~~~w~~~~~~~~~d~ll~~~~~la~~IR~~I~~etGlt~S~GIA~NklLAKLAS~~~KPngqtvv~~~~v~~fL~~LPI 247 (729)
......++++||++|++++||+||||||+||++||||++++||+|+++++++++.+||++|||
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 011346899999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCCChHHHHHHHHhcCCCcccccccCCcccccccccCCCCCCC
Q 004805 248 KKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALK 327 (729)
Q Consensus 248 ~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~~~g~~L~~~arGiD~~~V~~~~~pKSis~s~tF~~p~di~ 327 (729)
++|||||+++.++|+ ++||+|++||++++...|.++||...|.+||++|+|+|.++|.+..++|+|+.+++|+ .++.
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-RLGIETIGDLAALSEAEVANLLGATVGPALHRLARGIDDRPVAERAEAKQISAESTFA--VDLT 259 (454)
T ss_pred cccCCCCHHHHHHHH-HcCCccHHHHhcCCHHHHHHHHCHHHHHHHHHHHcCCCCCCcccCCCCceEEEEEECC--CCCC
Confidence 999999999999997 9999999999999999999999966799999999999999999988999999999998 5799
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHhhhcCceeEEEEEEEeeccCCCCCCCCCcCcccccCCCcchhHHHhHHHHHHHHHHH
Q 004805 328 TVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLRE 407 (729)
Q Consensus 328 ~~eel~~~L~~LaeeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~~~~srs~~L~~~t~~i~~~a~~L~~aal~l 407 (729)
+.+++..+|.+|+++|+.||++ .++.+++|+|++++.+. . ..+++.+++++|+ +...|++.+..+
T Consensus 260 ~~~~l~~~L~~L~~~l~~rL~~----~g~~~r~v~l~l~~~d~---~----~~srs~~l~~pt~----d~~~L~~la~~l 324 (454)
T PRK03348 260 TRAQLREAIERIAEHAHRRLLK----DGRGARTVTVKLRKSDF---S----TLTRSATLPYATD----DAAVLAATARRL 324 (454)
T ss_pred CHHHHHHHHHHHHHHHHHHHHH----cCCCccEEEEEEEeCCC---C----ccEEEEECCCCCC----CHHHHHHHHHHH
Confidence 9999999999999999999997 59999999999987532 2 2478888998884 667788888888
Q ss_pred hhcccCccccCCCCCCcceeEEEEEccCccccccccccccccccccC
Q 004805 408 FLGSFGVKTQGSHYSGWRITALSVSASKIVPVLSGTCSIMKYFNGPD 454 (729)
Q Consensus 408 ~~~~~~~~~~~~~~~~~~IR~IGVsls~L~~~~~~~~si~dlF~~~~ 454 (729)
|...+ ...+||++||++++|.+. .|.+||...+
T Consensus 325 l~~~~---------~~~~vRllgV~~s~l~~~-----~q~~LF~~~~ 357 (454)
T PRK03348 325 LLDPD---------EIGPIRLVGVGFSGLSDV-----RQESLFPELD 357 (454)
T ss_pred HHhhc---------cCCCeEEEEEEECCCCcc-----hhhccCCCcc
Confidence 76432 234899999999999752 5789997544
No 10
>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=6.9e-68 Score=582.25 Aligned_cols=348 Identities=30% Similarity=0.483 Sum_probs=300.0
Q ss_pred EEEeCCchhHhhhchhCCCCCCCcEEEEeccCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEEEccccCCCCCh
Q 004805 15 AHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVARGKADL 94 (729)
Q Consensus 15 ~HIDmD~FyASVE~~~~P~LrgkPvaV~q~~~~~~g~ViA~SYeARk~GVk~GM~~~eA~~LCP~L~vv~Vp~~~~k~d~ 94 (729)
+||||||||||||++++|+|+|+||||++ +|+|+||||+||++||++||++.+|+++||++++++ + .|+
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--G----EDL 69 (379)
T ss_pred CeeecccHHHHHHhhhccccCCCcEEECC-----CCEEEEcCHHHHHhCCCCCCcHHHHHHhCCCeEEEc--C----CCh
Confidence 59999999999999999999999999964 478999999999999999999999999999998774 1 489
Q ss_pred HHHHHHHHHHHHHHHhc-C--CeeeeccceeEEecccchhHhhhcCCCCCcchhhHHHhhhhcccCccCCCCCchhhhhh
Q 004805 95 SSYRNAGSEVVSILARK-G--RCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKATVKE 171 (729)
Q Consensus 95 ~~Yr~~S~~I~~iL~~~-~--~vE~~SIDEafLDlT~~~~~~l~~~~~~~~~~~~~~~~~~~l~G~~~~~~~~~~~~~~~ 171 (729)
+.|+++|++|++++.+| | .||++||||+|||+|++. ++
T Consensus 70 ~~Y~~~S~~i~~~l~~~sp~~~ve~~SiDE~~lDvt~~~----------------------~~----------------- 110 (379)
T cd01703 70 TPFRDMSKKVYRLLRSYSWNDRVERLGFDENFMDVTEMR----------------------LL----------------- 110 (379)
T ss_pred HHHHHHHHHHHHHHHHcCCHhhEEecCCCcEEEEccCcc----------------------ch-----------------
Confidence 99999999999999996 7 899999999999999863 11
Q ss_pred hhhccCcchhhhhhhhHHHHHHHHHHHHHhHhCCceeEeecCCHHHHHHhccCCCCCceeeccC---CchhcccccCccc
Q 004805 172 WLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPF---SSVKGLLDSLPIK 248 (729)
Q Consensus 172 w~~~~~~~~~d~ll~~~~~la~~IR~~I~~etGlt~S~GIA~NklLAKLAS~~~KPngqtvv~~---~~v~~fL~~LPI~ 248 (729)
.+..+|++||++|+++|||+||||||+||++||||++++||+|+++|.+ +++.+||+++||+
T Consensus 111 ---------------~g~~la~~ir~~I~~~~Glt~siGIa~nk~lAKlas~~~KP~g~~~i~~~~~~~~~~fl~~lpv~ 175 (379)
T cd01703 111 ---------------VASHIAYEMRERIENELGLTCCAGIASNKLLAKLVGSVNKPNQQTTLLPPSCADLMDFMDLHDLR 175 (379)
T ss_pred ---------------hHHHHHHHHHHHHHHHhCCeEEEEEcCCHHHHHHHhhhcCCCCeEEEcCCchHHHHHHhccCCcc
Confidence 1356899999999999999999999999999999999999999999877 4567899999999
Q ss_pred ccCCCcHHHHHHHHHHhCCcchhhhhcCC---------------HHHHHHhhCCChHHHHHHHHhcCCCccc-ccccCCc
Q 004805 249 KMKQLGGKLGTSLQNELGVTTVGDLLKFS---------------EDKLQESYGFNTGTWLWNIARGISGEEV-QARLLPK 312 (729)
Q Consensus 249 ~L~GIG~k~~~~L~~~lGI~TigDLa~l~---------------~~~L~~rFG~~~g~~L~~~arGiD~~~V-~~~~~pK 312 (729)
+|||||+++.++|. .+||.|+|||+.++ ...|+++||...|.+||+.|+|+|+++| .+...+|
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 99999999999997 99999999999999 9999999996569999999999999999 5566789
Q ss_pred ccccccccCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHhhh----cCceeEEEEEEEeeccCCCCCCCCCcCcccccCCC
Q 004805 313 SHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQ----NKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRY 388 (729)
Q Consensus 313 Sis~s~tF~~p~di~~~eel~~~L~~LaeeL~~RLr~~~~~----~~~~artLtL~lr~~~~~~~~s~~~~~srs~~L~~ 388 (729)
||+.++||.. .++.+.+++..+|..|+++|+.||++++.+ .+..++||+|++|+.+. ...+.++.|++++++.
T Consensus 255 sis~e~tf~~-~~~~~~~~~~~~l~~l~~~l~~rl~~~l~~~~~~~~~~~~tv~l~vr~~~~--~~~~~~~~sr~~~l~~ 331 (379)
T cd01703 255 QISIEDSYKK-CSLEEIREARNKIEELLASLLERMKQDLQEVKAGDGRRPHTLRLTLRRYTS--TKKHYNRESKQAPIPS 331 (379)
T ss_pred eeEEeeccCC-CCCCCHHHHHHHHHHHHHHHHHHHHhhhhccchhcCeeeeEEEEEEEECCC--CCCccceeeeccccCc
Confidence 9999999985 378999999999999999999999985533 68899999999998641 1111244689999998
Q ss_pred cchh-H----HHhHHHHHHHHHHHhhcccCccccCCCCCCcceeEEEEEccC
Q 004805 389 GTAK-I----QEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASK 435 (729)
Q Consensus 389 ~t~~-i----~~~a~~L~~aal~l~~~~~~~~~~~~~~~~~~IR~IGVsls~ 435 (729)
+++. + ..+...|++.++.+|.+.++.+ ...+.+||+|||++++
T Consensus 332 ~~~~~~~~~~~~~~~~i~~~~~~L~~~~~~~~----~~~~~~irl~gv~~~~ 379 (379)
T cd01703 332 HVFQKLTGGNEIAARPIEKILMRLFRELVPPK----NVKGFNLTLLNVCFTN 379 (379)
T ss_pred hhhccccccchhhHHHHHHHHHHHHHHhcccc----cCCCCceEEEEEEeeC
Confidence 8741 1 0145678888988887654210 1124589999999875
No 11
>PRK03858 DNA polymerase IV; Validated
Probab=100.00 E-value=1.3e-67 Score=585.07 Aligned_cols=349 Identities=29% Similarity=0.426 Sum_probs=311.1
Q ss_pred CCEEEEEeCCchhHhhhchhCCCCCCCcEEEEeccCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEEEccccCC
Q 004805 11 ARIIAHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVARG 90 (729)
Q Consensus 11 ~rvI~HIDmD~FyASVE~~~~P~LrgkPvaV~q~~~~~~g~ViA~SYeARk~GVk~GM~~~eA~~LCP~L~vv~Vp~~~~ 90 (729)
.++|+||||||||||||++.+|+|+|+||||+ +|+|+||||+||++||++||++.+|+++||+|++++
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 57899999999999999999999999999996 368999999999999999999999999999998874
Q ss_pred CCChHHHHHHHHHHHHHHHhc-CCeeeeccceeEEecccchhHhhhcCCCCCcchhhHHHhhhhcccCccCCCCCchhhh
Q 004805 91 KADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKATV 169 (729)
Q Consensus 91 k~d~~~Yr~~S~~I~~iL~~~-~~vE~~SIDEafLDlT~~~~~~l~~~~~~~~~~~~~~~~~~~l~G~~~~~~~~~~~~~ 169 (729)
+|++.|+++|++|++++.+| +.||++||||+|||+|++. ++||
T Consensus 71 -~d~~~y~~~s~~i~~~l~~~s~~ve~~siDe~~ldvt~~~----------------------~~~~------------- 114 (396)
T PRK03858 71 -PRMSAYSRASKAVFEVFRDTTPLVEGLSIDEAFLDVGGLR----------------------RISG------------- 114 (396)
T ss_pred -CCHHHHHHHHHHHHHHHHHhCCceEEecCCeEEEEccccc----------------------cccC-------------
Confidence 79999999999999999996 8899999999999999974 2333
Q ss_pred hhhhhccCcchhhhhhhhHHHHHHHHHHHHHhHhCCceeEeecCCHHHHHHhccCCCCCceeeccCCchhcccccCcccc
Q 004805 170 KEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKK 249 (729)
Q Consensus 170 ~~w~~~~~~~~~d~ll~~~~~la~~IR~~I~~etGlt~S~GIA~NklLAKLAS~~~KPngqtvv~~~~v~~fL~~LPI~~ 249 (729)
.+..++++||++|++++|++||||||+||++||||++.+||+|+++++++++..||+++||++
T Consensus 115 -----------------~~~~la~~ir~~i~~~~gl~~svGia~n~~lAklas~~~Kp~g~~~i~~~~~~~~L~~lpl~~ 177 (396)
T PRK03858 115 -----------------TPVQIAARLRRRVREEVGLPITVGVARTKFLAKVASQVAKPDGLLVVPPDRELAFLHPLPVRR 177 (396)
T ss_pred -----------------CHHHHHHHHHHHHHHHHCCCeEEEEcCChHHHHHhhcccCCCceEEECcHHHHHHHhcCChhh
Confidence 345789999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCCChHHHHHHHHhcCCCcccccccCCcccccccccCCCCCCCcH
Q 004805 250 MKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTV 329 (729)
Q Consensus 250 L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~~~g~~L~~~arGiD~~~V~~~~~pKSis~s~tF~~p~di~~~ 329 (729)
|||||+++.++|. .+||+|++||++++...|.++||...|.+||++++|+|+++|.+..++|||+.+++|. .++.+.
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-AHGITTVGDVAELPESALVSLLGPAAGRHLHALAHNRDPRRVETGRRRRSVGAQRALG--RGPNSP 254 (396)
T ss_pred cCCCCHHHHHHHH-HhCCCcHHHHhcCCHHHHHHHhCcHHHHHHHHHhCCCCCCCCCCCCCCccccceeEcC--CCCCCH
Confidence 9999999999997 9999999999999999999999987799999999999999998888889999999998 579999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhcCceeEEEEEEEeeccCCCCCCCCCcCcccccCCCcchhHHHhHHHHHHHHHHHhh
Q 004805 330 ASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFL 409 (729)
Q Consensus 330 eel~~~L~~LaeeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~~~~srs~~L~~~t~~i~~~a~~L~~aal~l~~ 409 (729)
+++..+|.+|+++|+.||++ .++.+++|+|++++.+ +. ..+++.+++.+|+ +...|++.+..+|.
T Consensus 255 ~~l~~~l~~L~~~l~~rLr~----~~~~~~~l~l~l~~~~---~~----~~~~~~~l~~~t~----~~~~l~~l~~~ll~ 319 (396)
T PRK03858 255 AEVDAVVVALVDRVARRMRA----AGRTGRTVVLRLRFDD---FT----RATRSHTLPRPTA----STATLLAAARDLVA 319 (396)
T ss_pred HHHHHHHHHHHHHHHHHHHh----cCCCcceEEEEEEeCC---CC----EEEEEEECCCCcC----CHHHHHHHHHHHHH
Confidence 99999999999999999997 5899999999999743 22 2467888888884 55678887777776
Q ss_pred cccCccccCCCCCCcceeEEEEEccCcccccccccccccc-cc
Q 004805 410 GSFGVKTQGSHYSGWRITALSVSASKIVPVLSGTCSIMKY-FN 451 (729)
Q Consensus 410 ~~~~~~~~~~~~~~~~IR~IGVsls~L~~~~~~~~si~dl-F~ 451 (729)
..+. ...+.+||++||.+++|.+. ...|.+| |+
T Consensus 320 ~~~~------~~~~~~irligv~~~~l~~~---~~~q~~L~f~ 353 (396)
T PRK03858 320 AAAP------LIAERGLTLVGFAVSNLDDD---GAQQLELPFG 353 (396)
T ss_pred hhhh------ccCCCCeEEEEEEeecCCcc---cccccCCCcc
Confidence 5321 11246899999999999865 3446777 74
No 12
>PRK02794 DNA polymerase IV; Provisional
Probab=100.00 E-value=1.2e-67 Score=589.21 Aligned_cols=357 Identities=26% Similarity=0.390 Sum_probs=316.0
Q ss_pred CCCCCCCCCEEEEEeCCchhHhhhchhCCCCCCCcEEEEeccCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEE
Q 004805 4 ARPDSSGARIIAHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELV 83 (729)
Q Consensus 4 ~~~~~~~~rvI~HIDmD~FyASVE~~~~P~LrgkPvaV~q~~~~~~g~ViA~SYeARk~GVk~GM~~~eA~~LCP~L~vv 83 (729)
.+++ ...|+|+||||||||||||++.+|+|+|+||||+.. ++++|++|||+||++||++||++.+|+++||+++++
T Consensus 29 ~~~~-~~~~~i~hiD~d~Fyasve~~~~p~l~~~Pv~v~~~---~~~~V~a~ny~Ar~~GV~~GM~~~~A~~lcP~l~~v 104 (419)
T PRK02794 29 RHPE-LYTLSIAHIDCDAFYASVEKRDNPELRDKPVIIGGG---KRGVVSTACYIARIHGVRSAMPMFKALKLCPDAVVI 104 (419)
T ss_pred cCcc-ccCCEEEEEcCCcHHHHHHhhhCccccCCcEEEecC---CCeEEEecCHHHHHhCCCcCCHHHHHHHHCCCcEEE
Confidence 3444 235899999999999999999999999999999753 357899999999999999999999999999999888
Q ss_pred EccccCCCCChHHHHHHHHHHHHHHHhc-CCeeeeccceeEEecccchhHhhhcCCCCCcchhhHHHhhhhcccCccCCC
Q 004805 84 QVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDG 162 (729)
Q Consensus 84 ~Vp~~~~k~d~~~Yr~~S~~I~~iL~~~-~~vE~~SIDEafLDlT~~~~~~l~~~~~~~~~~~~~~~~~~~l~G~~~~~~ 162 (729)
+ +|++.|+++|++|++++.+| |.||++||||+|||+|++. ++||..
T Consensus 105 ~-------~d~~~y~~~s~~i~~~l~~~sp~ve~~siDe~~ldvt~~~----------------------~l~g~~---- 151 (419)
T PRK02794 105 K-------PDMEKYVRVGREVRAMMQALTPLVEPLSIDEAFLDLSGTE----------------------RLHGAP---- 151 (419)
T ss_pred C-------CCHHHHHHHHHHHHHHHHHhCcceeeccCCeEEEeccchh----------------------hhcCCC----
Confidence 4 79999999999999999996 8999999999999999875 344431
Q ss_pred CCchhhhhhhhhccCcchhhhhhhhHHHHHHHHHHHHHhHhCCceeEeecCCHHHHHHhccCCCCCceeeccCCchhccc
Q 004805 163 NDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLL 242 (729)
Q Consensus 163 ~~~~~~~~~w~~~~~~~~~d~ll~~~~~la~~IR~~I~~etGlt~S~GIA~NklLAKLAS~~~KPngqtvv~~~~v~~fL 242 (729)
...++++||++|++++||+||||||+||++||||++++||+|++++.++++.+||
T Consensus 152 -------------------------~~~~~~~i~~~i~~~~gl~~svGIa~n~~lAKlas~~~KP~g~~ii~~~~~~~~L 206 (419)
T PRK02794 152 -------------------------PAVVLARFARRVEREIGITVSVGLSYNKFLAKIASDLDKPRGFSVIGRAEALAFL 206 (419)
T ss_pred -------------------------HHHHHHHHHHHHHHHHCCceEEEEcCCHHHHHHHHhhhCCCCeEecCHHHHHHHH
Confidence 2346789999999999999999999999999999999999999999999999999
Q ss_pred ccCcccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCCChHHHHHHHHhcCCCcccccccCCcccccccccCC
Q 004805 243 DSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPG 322 (729)
Q Consensus 243 ~~LPI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~~~g~~L~~~arGiD~~~V~~~~~pKSis~s~tF~~ 322 (729)
+++||++|||||+++.++|. .+||+|++||+++|...|.++||. .|.++|++++|+|+++|.+..++|||+.+++|.
T Consensus 207 ~~lPl~~L~GiG~~~~~~L~-~~GI~tigdL~~l~~~~L~~rfG~-~g~~l~~~a~G~d~~~v~~~~~~ksi~~~~tl~- 283 (419)
T PRK02794 207 APKPVGIIWGVGPATAARLA-RDGIRTIGDLQRADEADLMRRFGS-MGLRLWRLARGIDDRKVSPDREAKSVSAETTFE- 283 (419)
T ss_pred hcCChhhhCCCCHHHHHHHH-HhccchHHHHhhCCHHHHHHHHhH-HHHHHHHHhCCCCCCCCccCCCCceeeeeEECC-
Confidence 99999999999999999997 999999999999999999999998 699999999999999999888899999999998
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHhhhcCceeEEEEEEEeeccCCCCCCCCCcCcccccCCCcchhHHHhHHHHHH
Q 004805 323 PRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQ 402 (729)
Q Consensus 323 p~di~~~eel~~~L~~LaeeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~~~~srs~~L~~~t~~i~~~a~~L~~ 402 (729)
.++.+.+++..+|..|+++|+.||+. +++.+++|+|++++.+. . ..+++.+++.+|+ +...|++
T Consensus 284 -~~~~~~~~l~~~l~~L~~~l~~rL~~----~~~~~~~l~l~l~~~~~---~----~~~~~~~l~~pt~----~~~~l~~ 347 (419)
T PRK02794 284 -TDLSDFEDLEPILWRLSEKVSRRLKA----AGLAGRTVTLKLKTADF---R----LRTRRRTLEDPTQ----LADRIFR 347 (419)
T ss_pred -CCCCCHHHHHHHHHHHHHHHHHHHHh----cCCCcceEEEEEEECCC---C----ceEEEEECCCCcC----CHHHHHH
Confidence 56999999999999999999999997 69999999999997432 2 2367888888884 6667888
Q ss_pred HHHHHhhcccCccccCCCCCCcceeEEEEEccCccccccccccccccccc
Q 004805 403 AGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPVLSGTCSIMKYFNG 452 (729)
Q Consensus 403 aal~l~~~~~~~~~~~~~~~~~~IR~IGVsls~L~~~~~~~~si~dlF~~ 452 (729)
.+..+|.+. +.+.+||+|||++++|.+.. ...|.+||+.
T Consensus 348 ~~~~ll~~~---------~~~~~vr~igv~~~~l~~~~--~~~q~~LF~~ 386 (419)
T PRK02794 348 TARELLEKE---------TDGTAFRLIGIGVSDLSPAD--EADPPDLLDP 386 (419)
T ss_pred HHHHHHHhc---------ccCCCEEEEEEEEecCCCcc--ccccccccCc
Confidence 877777643 34678999999999998753 2247899974
No 13
>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=3.3e-67 Score=571.45 Aligned_cols=340 Identities=33% Similarity=0.497 Sum_probs=301.2
Q ss_pred EEEeCCchhHhhhchhCCCCCCCcEEEEeccCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEEEccccCCCCCh
Q 004805 15 AHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVARGKADL 94 (729)
Q Consensus 15 ~HIDmD~FyASVE~~~~P~LrgkPvaV~q~~~~~~g~ViA~SYeARk~GVk~GM~~~eA~~LCP~L~vv~Vp~~~~k~d~ 94 (729)
+||||||||||||++++|+|+++||||++++. ++|+|+||||+||++||++||++.+|+++||++++++ +|+
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 69999999999999999999999999998754 3578999999999999999999999999999998875 799
Q ss_pred HHHHHHHHHHHHHHHhc-CCeeeeccceeEEecccchhHhhhcCCCCCcchhhHHHhhhhcccCccCCCCCchhhhhhhh
Q 004805 95 SSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKATVKEWL 173 (729)
Q Consensus 95 ~~Yr~~S~~I~~iL~~~-~~vE~~SIDEafLDlT~~~~~~l~~~~~~~~~~~~~~~~~~~l~G~~~~~~~~~~~~~~~w~ 173 (729)
+.|+++|++|++++.+| |.||++||||+|||+|++. ++|
T Consensus 73 ~~y~~~s~~i~~~l~~~sp~ve~~siDE~~ldvt~~~----------------------~~~------------------ 112 (343)
T cd00424 73 DLYRRLSERLLSELEEVAPLVEVASIDELFLDLTGSA----------------------RLL------------------ 112 (343)
T ss_pred HHHHHHHHHHHHHHHHhCCcEEEccCCEEEEECCCch----------------------hcc------------------
Confidence 99999999999999996 8999999999999999975 222
Q ss_pred hccCcchhhhhhhhHHHHHHHHHHHHHhHhC-CceeEeecCCHHHHHHhccCCCCCceeeccCCchhcccccCcccccCC
Q 004805 174 CRCDADHRDKLLACGVLIVTELRMQVLKETE-FTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQ 252 (729)
Q Consensus 174 ~~~~~~~~d~ll~~~~~la~~IR~~I~~etG-lt~S~GIA~NklLAKLAS~~~KPngqtvv~~~~v~~fL~~LPI~~L~G 252 (729)
+.+..+|++||++|++++| +|||||||+||++||||++++||+|+++++++++.+||+++||++|||
T Consensus 113 ------------~~~~~la~~i~~~i~~~~ggl~~siGia~n~~lAKlAs~~~KP~g~~v~~~~~~~~~L~~lpi~~l~g 180 (343)
T cd00424 113 ------------GLGSEVALRIKRHIAEQLGGITASIGIASNKLLAKLAAKYAKPDGLTILDPEDLPGFLSKLPLTDLPG 180 (343)
T ss_pred ------------CCHHHHHHHHHHHHHHHhCCceEEEeecccHHHHHHHhccCCCCCEEEEcHHHHHHHHhcCChhhcCC
Confidence 2345789999999999998 999999999999999999999999999999999999999999999999
Q ss_pred CcHHHHHHHHHHhCCcchhhhhcCC-HHHHHHhhCCChHHHHHHHHhcCCCcccccccCCcccccccccCCCCCCCcHHH
Q 004805 253 LGGKLGTSLQNELGVTTVGDLLKFS-EDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTVAS 331 (729)
Q Consensus 253 IG~k~~~~L~~~lGI~TigDLa~l~-~~~L~~rFG~~~g~~L~~~arGiD~~~V~~~~~pKSis~s~tF~~p~di~~~ee 331 (729)
||+++.++|. .+||+|++||+++| ...|.++||+ .|.++|+.|+|+|+++|.+..++|||+.+++|+ .++.+.++
T Consensus 181 iG~~~~~~L~-~~Gi~ti~dl~~~~~~~~l~~~fg~-~~~~l~~~a~G~d~~~v~~~~~~ksi~~~~tf~--~~~~~~~~ 256 (343)
T cd00424 181 IGAVTAKRLE-AVGINPIGDLLAASPDALLALWGGV-SGERLWYALRGIDDEPLSPPRPRKSFSHERVLP--RDSRNAED 256 (343)
T ss_pred CCHHHHHHHH-HcCCCcHHHHhcCCHHHHHHHHhhH-HHHHHHHHhCCcCCCCCCCCCCCCceeeeEECC--CCCCCHHH
Confidence 9999999997 99999999999999 8999999997 599999999999999998888899999999998 57999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhcCceeEEEEEEEeeccCCCCCCCCCcCcccccCCCcchhHHHhHHHHHHHHHHHhhcc
Q 004805 332 VQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGS 411 (729)
Q Consensus 332 l~~~L~~LaeeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~~~~srs~~L~~~t~~i~~~a~~L~~aal~l~~~~ 411 (729)
+..+|..|+++|+.||+. .++.+++|+|++++.+... .......+++.+++.+| +...|+++++.+|...
T Consensus 257 l~~~l~~l~~~l~~rL~~----~~~~~~~l~l~lr~~~~~~-~~~~~~~~~~~~l~~~t-----~~~~l~~~~~~l~~~~ 326 (343)
T cd00424 257 ARPLLRLLLEKLARRLRR----DGRGATRLRLWLRTVDGRW-SGHADIPSRSAPRPIST-----EDGELLHALDKLWRAL 326 (343)
T ss_pred HHHHHHHHHHHHHHHHHH----cCCceeEEEEEEEeCCCcc-cccceeeeeeeeCCCCC-----CHHHHHHHHHHHHHhh
Confidence 999999999999999997 5999999999999754211 01112357888888877 3456888888888754
Q ss_pred cCccccCCCCCCcceeEEEEEcc
Q 004805 412 FGVKTQGSHYSGWRITALSVSAS 434 (729)
Q Consensus 412 ~~~~~~~~~~~~~~IR~IGVsls 434 (729)
++ ...+.+||+|||+++
T Consensus 327 ~~------~~~~~~ir~~gv~~~ 343 (343)
T cd00424 327 LD------DKGPRRLRRLGVRLS 343 (343)
T ss_pred hh------ccCCCCeeEEEEEeC
Confidence 32 112568999999874
No 14
>PRK03352 DNA polymerase IV; Validated
Probab=100.00 E-value=1.2e-66 Score=567.53 Aligned_cols=340 Identities=28% Similarity=0.382 Sum_probs=304.3
Q ss_pred CCCCEEEEEeCCchhHhhhchhCCCCCCCcEEEEeccC--CCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEEEcc
Q 004805 9 SGARIIAHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNE--WKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVP 86 (729)
Q Consensus 9 ~~~rvI~HIDmD~FyASVE~~~~P~LrgkPvaV~q~~~--~~~g~ViA~SYeARk~GVk~GM~~~eA~~LCP~L~vv~Vp 86 (729)
.+.|+|+||||||||||||++.+|+|+++||||++.+. .++|+|++|||+||++||++||++.+|+++||++++++
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 36799999999999999999999999999999985432 12578889999999999999999999999999998885
Q ss_pred ccCCCCChHHHHHHHHHHHHHHHhc-CCeeeeccceeEEecccchhHhhhcCCCCCcchhhHHHhhhhcccCccCCCCCc
Q 004805 87 VARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDS 165 (729)
Q Consensus 87 ~~~~k~d~~~Yr~~S~~I~~iL~~~-~~vE~~SIDEafLDlT~~~~~~l~~~~~~~~~~~~~~~~~~~l~G~~~~~~~~~ 165 (729)
+|++.|+++|++|++++.+| +.||.+||||+|||+|+.-
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 79999999999999999996 8999999999999999741
Q ss_pred hhhhhhhhhccCcchhhhhhhhHHHHHHHHHHHHHhHhCCceeEeecCCHHHHHHhccCCCCCceeeccCCchhcccccC
Q 004805 166 KATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSL 245 (729)
Q Consensus 166 ~~~~~~w~~~~~~~~~d~ll~~~~~la~~IR~~I~~etGlt~S~GIA~NklLAKLAS~~~KPngqtvv~~~~v~~fL~~L 245 (729)
...+++.||++|++++||+||+|||+||++||||++.+||+|++++.++++.+||+++
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 2357899999999999999999999999999999999999999999999999999999
Q ss_pred cccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCCChHHHHHHHHhcCCCcccccc-cCCcccccccccCCCC
Q 004805 246 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQAR-LLPKSHGSGKSFPGPR 324 (729)
Q Consensus 246 PI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~~~g~~L~~~arGiD~~~V~~~-~~pKSis~s~tF~~p~ 324 (729)
||++|||||+++.++|. ++||+|+|||+++|...|.++||...|.+||+.++|+|.+++... ..|||++.+.+|+ .
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-ALGITTVADLAAADPAELAATFGPTTGPWLLLLARGGGDTEVSAEPWVPRSRSREVTFP--Q 254 (346)
T ss_pred CHHHcCCCCHHHHHHHH-HcCCccHHHHhcCCHHHHHHHhChHHHHHHHHHhCCCCCCCCCCCCCCCceEEEEEECC--C
Confidence 99999999999999997 999999999999999999999997679999999999999999764 3579999999998 5
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHhhhcCceeEEEEEEEeeccCCCCCCCCCcCcccccCCCcchhHHHhHHHHHHHH
Q 004805 325 ALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAG 404 (729)
Q Consensus 325 di~~~eel~~~L~~LaeeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~~~~srs~~L~~~t~~i~~~a~~L~~aa 404 (729)
++.+.+++..+|..|+++|+.||+. +++.+++|+|++++.+. . ..+++.+++.+| ++...|++.+
T Consensus 255 ~~~~~~~l~~~l~~L~~~l~~rLr~----~~~~~~~l~l~l~~~~~---~----~~~~~~~l~~pt----~d~~~l~~~~ 319 (346)
T PRK03352 255 DLTDRAEVESAVRELARRVLDEVVA----EGRPVTRVAVKVRTATF---Y----TRTKIRKLPEPT----TDPDVIEAAA 319 (346)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHH----cCCccceEEEEEEeCCC---c----eeEEEEECCCCc----CCHHHHHHHH
Confidence 7999999999999999999999997 69999999999997532 1 236778888888 4667788887
Q ss_pred HHHhhcccCccccCCCCCCcceeEEEEEccCcccc
Q 004805 405 LREFLGSFGVKTQGSHYSGWRITALSVSASKIVPV 439 (729)
Q Consensus 405 l~l~~~~~~~~~~~~~~~~~~IR~IGVsls~L~~~ 439 (729)
..+|.+. +.+.+||.|||++++|.+.
T Consensus 320 ~~ll~~~---------~~~~~vr~igl~~~~~~~~ 345 (346)
T PRK03352 320 LDVLDRF---------ELDRPVRLLGVRLELAMPD 345 (346)
T ss_pred HHHHHhc---------cCCCCEEEEEEEEeccCCC
Confidence 7777642 3356899999999999764
No 15
>cd03586 PolY_Pol_IV_kappa DNA Polymerase IV/Kappa. Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Known primarily as Pol IV in prokaryotes and Pol kappa in eukaryotes, this polymerase has a propensity for generating frameshift mutations. The eukaryotic Pol kappa differs from Pol IV and Dpo4 by an N-terminal extension of ~75 residues known as the "N-clasp" region. The structure of Pol kappa shows DNA that is almost totally encircled by Pol kappa, with the N-clasp region augmenting the interactions between DNA and the polymerase. Pol kappa is more resistant than Pol eta and Pol iota to bulky guanine adducts and is efficient at catalyzing the incorporation of dCTP. Bacterial pol IV has a
Probab=100.00 E-value=1.9e-65 Score=554.56 Aligned_cols=333 Identities=35% Similarity=0.534 Sum_probs=302.8
Q ss_pred EEEeCCchhHhhhchhCCCCCCCcEEEEeccCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEEEccccCCCCCh
Q 004805 15 AHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVARGKADL 94 (729)
Q Consensus 15 ~HIDmD~FyASVE~~~~P~LrgkPvaV~q~~~~~~g~ViA~SYeARk~GVk~GM~~~eA~~LCP~L~vv~Vp~~~~k~d~ 94 (729)
+||||||||||||++++|+|+++||||+++++ +|+|+||||+||++||++||++.+|+++||+|++++ +|+
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 69999999999999999999999999998653 679999999999999999999999999999998885 799
Q ss_pred HHHHHHHHHHHHHHHhc-CCeeeeccceeEEecccchhHhhhcCCCCCcchhhHHHhhhhcccCccCCCCCchhhhhhhh
Q 004805 95 SSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKATVKEWL 173 (729)
Q Consensus 95 ~~Yr~~S~~I~~iL~~~-~~vE~~SIDEafLDlT~~~~~~l~~~~~~~~~~~~~~~~~~~l~G~~~~~~~~~~~~~~~w~ 173 (729)
+.|+++|++|++++.+| |.||++|+||+|||+|++. ++||
T Consensus 72 ~~y~~~s~~i~~~l~~~~~~ve~~s~De~~ldv~~~~----------------------~~~~----------------- 112 (334)
T cd03586 72 DKYREVSRQIMEILREYTPLVEPLSIDEAYLDVTDYV----------------------RLFG----------------- 112 (334)
T ss_pred HHHHHHHHHHHHHHHHcCCceEEecccceeEcccccc----------------------ccCC-----------------
Confidence 99999999999999996 8999999999999999874 2232
Q ss_pred hccCcchhhhhhhhHHHHHHHHHHHHHhHhCCceeEeecCCHHHHHHhccCCCCCceeeccCCchhcccccCcccccCCC
Q 004805 174 CRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQL 253 (729)
Q Consensus 174 ~~~~~~~~d~ll~~~~~la~~IR~~I~~etGlt~S~GIA~NklLAKLAS~~~KPngqtvv~~~~v~~fL~~LPI~~L~GI 253 (729)
.+..++++||++|++++||+||+|||+|+++||||++.+||+|+++++++++.+||+++||++||||
T Consensus 113 -------------~~~~la~~ir~~i~~~~g~~~siGia~n~~lAklaa~~~kp~g~~i~~~~~~~~~L~~lpl~~l~gi 179 (334)
T cd03586 113 -------------SATEIAKEIRARIREETGLTASAGIAPNKFLAKIASDLNKPNGLTVIPPEDVEEFLAPLPVRKIPGV 179 (334)
T ss_pred -------------CHHHHHHHHHHHHHHHHCCceEEEEhhcHHHHHHHhcCCCCCcEEEECHHHHHHHHhcCCchhhCCc
Confidence 3567899999999999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCCChHHHHHHHHhcCCCcccccccCCcccccccccCCCCCCCcHHHHH
Q 004805 254 GGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTVASVQ 333 (729)
Q Consensus 254 G~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~~~g~~L~~~arGiD~~~V~~~~~pKSis~s~tF~~p~di~~~eel~ 333 (729)
|+++.++|. .+||+|++||+++|...|.++||. .|.++|++++|+|++++.+..++|+|+.+++|+ .++.+.+++.
T Consensus 180 g~~~~~~L~-~~Gi~ti~dl~~~~~~~L~~~~g~-~~~~l~~~~~G~~~~~v~~~~~~ks~~~~~~~~--~~~~~~~~l~ 255 (334)
T cd03586 180 GKVTAEKLK-ELGIKTIGDLAKLDVELLKKLFGK-SGRRLYELARGIDNRPVEPDRERKSIGVERTFS--EDLTDPEELL 255 (334)
T ss_pred CHHHHHHHH-HcCCcCHHHHHcCCHHHHHHHHhH-HHHHHHHHhCCCCCCCCCCCCCCCeeeeeEECC--CCCCCHHHHH
Confidence 999999997 999999999999999999999997 699999999999999999888999999999998 5689999999
Q ss_pred HHHHHHHHHHHHHHHHHhhhcCceeEEEEEEEeeccCCCCCCCCCcCcccccCCCcchhHHHhHHHHHHHHHHHhhcccC
Q 004805 334 HWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFG 413 (729)
Q Consensus 334 ~~L~~LaeeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~~~~srs~~L~~~t~~i~~~a~~L~~aal~l~~~~~~ 413 (729)
++|..|+++|+.||+. .++.+++|+|++++.+. ...+++.+++.+++ ++..|++.+..+|.+++
T Consensus 256 ~~l~~l~~~l~~rL~~----~~~~~~~l~l~l~~~~~-------~~~~~~~~l~~~t~----~~~~l~~~~~~~l~~~~- 319 (334)
T cd03586 256 EELLELAEELAERLRK----RGLKGRTVTVKLKYADF-------STRTRSRTLPEPTD----DAEDIYELALELLEELL- 319 (334)
T ss_pred HHHHHHHHHHHHHHHh----CCCCeEEEEEEEEECCC-------CeEEEEEECCCCCC----CHHHHHHHHHHHHHhcc-
Confidence 9999999999999997 59999999999987532 22467888888884 67778888887777542
Q ss_pred ccccCCCCCCcceeEEEEEccCc
Q 004805 414 VKTQGSHYSGWRITALSVSASKI 436 (729)
Q Consensus 414 ~~~~~~~~~~~~IR~IGVsls~L 436 (729)
.+.+||+|||++++|
T Consensus 320 --------~~~~vr~igv~~~~l 334 (334)
T cd03586 320 --------DGRPIRLLGVRLSGL 334 (334)
T ss_pred --------CCCCEEEEEEEeecC
Confidence 347899999999875
No 16
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=100.00 E-value=2.9e-65 Score=570.67 Aligned_cols=353 Identities=22% Similarity=0.263 Sum_probs=306.3
Q ss_pred EEEEEeCCchhHhhhchhCCCCCCCcEEEEeccCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCC-C-cEEEEccccCC
Q 004805 13 IIAHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCP-Q-IELVQVPVARG 90 (729)
Q Consensus 13 vI~HIDmD~FyASVE~~~~P~LrgkPvaV~q~~~~~~g~ViA~SYeARk~GVk~GM~~~eA~~LCP-~-L~vv~Vp~~~~ 90 (729)
+|+||||||||||||++.+|+|+|+||||++.+ +|+|+||||+||++||++||++++|+++|| + +++++
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 499999999999999999999999999998743 589999999999999999999999999994 3 77764
Q ss_pred CCChHHHHHHHHHHHHHHHhc-CCeeeeccceeEEecccchhHhhhcCCCCCcchhhHHHhhhhcccCccCCCCCchhhh
Q 004805 91 KADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKATV 169 (729)
Q Consensus 91 k~d~~~Yr~~S~~I~~iL~~~-~~vE~~SIDEafLDlT~~~~~~l~~~~~~~~~~~~~~~~~~~l~G~~~~~~~~~~~~~ 169 (729)
+|++.|.++|++|+++|.+| |.||++||||+|||+|++.+ +.
T Consensus 72 -~d~~~y~~~s~~i~~~l~~~tp~ve~~siDE~~lDvt~~~~----------------------l~-------------- 114 (422)
T PRK03609 72 -SNYELYADMSNRVMSTLEELSPRVEIYSIDEAFCDLTGVRN----------------------CR-------------- 114 (422)
T ss_pred -CCHHHHHHHHHHHHHHHHHhCCCceEeccccceecCCCCcC----------------------CC--------------
Confidence 79999999999999999996 89999999999999999741 11
Q ss_pred hhhhhccCcchhhhhhhhHHHHHHHHHHHHHhHhCCceeEeecCCHHHHHHhccCCCC-----Cceeec-cCCchhcccc
Q 004805 170 KEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKP-----AQQTTV-PFSSVKGLLD 243 (729)
Q Consensus 170 ~~w~~~~~~~~~d~ll~~~~~la~~IR~~I~~etGlt~S~GIA~NklLAKLAS~~~KP-----ngqtvv-~~~~v~~fL~ 243 (729)
....++++||++|++++||+||||||+||++||||+.++|| +|+++| .++++.+||+
T Consensus 115 -----------------~~~~~a~~i~~~I~~~~gl~~siGia~n~~lAK~As~~~k~~~k~~~g~~~i~~~~~~~~~L~ 177 (422)
T PRK03609 115 -----------------DLTDFGREIRATVLQRTHLTVGVGIAQTKTLAKLANHAAKKWQRQTGGVVDLSNLERQRKLLS 177 (422)
T ss_pred -----------------CHHHHHHHHHHHHHHHHCCceEEEecCCHHHHHHHHHHhCCCCCCCCcEEEcCCHHHHHHHhh
Confidence 13467899999999999999999999999999999987776 578777 5788999999
Q ss_pred cCcccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCCChHHHHHHHHhcCCCcccccccCC-cccccccccCC
Q 004805 244 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLP-KSHGSGKSFPG 322 (729)
Q Consensus 244 ~LPI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~~~g~~L~~~arGiD~~~V~~~~~p-KSis~s~tF~~ 322 (729)
+|||++|||||+++.++|. .+||+|+|||+++|+..|+++||. .|..+|+.++|+++.++....++ |+|+.+++|.
T Consensus 178 ~lPv~~l~GiG~~~~~~L~-~lGi~TigdL~~~~~~~L~~~fG~-~~~~l~~~a~G~~~~~~~~~~~~~ksi~~~~tf~- 254 (422)
T PRK03609 178 LQPVEEVWGVGRRISKKLN-AMGIKTALDLADTNIRFIRKHFNV-VLERTVRELRGEPCLSLEEFAPTKQEIVCSRSFG- 254 (422)
T ss_pred cCChhhcCCccHHHHHHHH-HcCCCcHHHHhcCCHHHHHHHHCH-HHHHHHHHhCCCCCCCccccCCCCceEEEeeECC-
Confidence 9999999999999999997 999999999999999999999997 59999999999999999776665 6999999998
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHhhhcCceeEEEEEEEeeccCCCCCCCCCcCcccccCCCcchhHHHhHHHHHH
Q 004805 323 PRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQ 402 (729)
Q Consensus 323 p~di~~~eel~~~L~~LaeeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~~~~srs~~L~~~t~~i~~~a~~L~~ 402 (729)
.++.+.+++..++.+|+++|+.||+. +++.+++|+|+++|.++.. ....+..+++.+++.+|+ +...|++
T Consensus 255 -~~~~~~~~l~~~l~~l~~~l~~rLr~----~~~~~~~l~l~ir~~~~~~-~~~~~~~~~~~~l~~pt~----d~~~l~~ 324 (422)
T PRK03609 255 -ERITDYESMRQAICSYAARAAEKLRG----EHQYCRFISTFVKTSPFAL-NEPYYGNSASVKLLTPTQ----DSRDIIA 324 (422)
T ss_pred -CCCCCHHHHHHHHHHHHHHHHHHHHH----cCCcccEEEEEEEcCCccc-cCCCcCceeEEeCCCCCC----CHHHHHH
Confidence 56999999999999999999999997 6999999999999854311 000123467777888884 6777888
Q ss_pred HHHHHhhcccCccccCCCCCCcceeEEEEEccCccccccccccccccccc
Q 004805 403 AGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPVLSGTCSIMKYFNG 452 (729)
Q Consensus 403 aal~l~~~~~~~~~~~~~~~~~~IR~IGVsls~L~~~~~~~~si~dlF~~ 452 (729)
.++.+|...+. .+.++|++||.+++|.+. ...|.+||+.
T Consensus 325 ~a~~ll~~~~~--------~~~~~r~~GV~~~~l~~~---~~~q~~LF~~ 363 (422)
T PRK03609 325 AATRALDAIWR--------DGHRYQKAGVMLGDFFSQ---GVAQLNLFDD 363 (422)
T ss_pred HHHHHHHHHhC--------CCCceEEeeEEEEeeccC---CCcCccCccc
Confidence 88888876542 256899999999999864 2457899964
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=1.1e-64 Score=551.88 Aligned_cols=337 Identities=28% Similarity=0.392 Sum_probs=292.2
Q ss_pred EEEeCCchhHhhhchhCCCCCCCcEEEEeccCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEEEccccCCCCCh
Q 004805 15 AHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVARGKADL 94 (729)
Q Consensus 15 ~HIDmD~FyASVE~~~~P~LrgkPvaV~q~~~~~~g~ViA~SYeARk~GVk~GM~~~eA~~LCP~L~vv~Vp~~~~k~d~ 94 (729)
+||||||||||||++++|+|+++||||++.. ++.|++|||+||++||++||++.+|+++||++.++.+| +|+
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 6999999999999999999999999998754 46799999999999999999999999999999333334 799
Q ss_pred HHHHHHHHHHHHHHHhc-CCeeeeccceeEEecccchhHhhhcCCCCCcchhhHHHhhhhcccCccCCCCCchhhhhhhh
Q 004805 95 SSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKATVKEWL 173 (729)
Q Consensus 95 ~~Yr~~S~~I~~iL~~~-~~vE~~SIDEafLDlT~~~~~~l~~~~~~~~~~~~~~~~~~~l~G~~~~~~~~~~~~~~~w~ 173 (729)
+.|+++|++|++++.+| |.||.+||||+|||+|++. + ||
T Consensus 73 ~~y~~~s~~i~~~l~~~~~~ve~~s~De~~ldvt~~~----------------------~-~~----------------- 112 (344)
T cd01700 73 ALYGDMSRRIMSILERFSPDVEVYSIDESFLDLTGSL----------------------R-FG----------------- 112 (344)
T ss_pred HHHHHHHHHHHHHHHhcCCcceEeecchhhccCcCCC----------------------C-CC-----------------
Confidence 99999999999999996 7899999999999999875 1 12
Q ss_pred hccCcchhhhhhhhHHHHHHHHHHHHHhHhCCceeEeecCCHHHHHHhccCCCCC----ceeeccCCchh-cccccCccc
Q 004805 174 CRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPA----QQTTVPFSSVK-GLLDSLPIK 248 (729)
Q Consensus 174 ~~~~~~~~d~ll~~~~~la~~IR~~I~~etGlt~S~GIA~NklLAKLAS~~~KPn----gqtvv~~~~v~-~fL~~LPI~ 248 (729)
.+..+|++||++|++++|++||+|||+||++||||++++||+ |++++++.+.. +||+++||+
T Consensus 113 -------------~~~~la~~i~~~i~~~~gl~~s~Gia~~~~lAklas~~~kp~~~~~g~~~~~~~~~~~~~l~~lpl~ 179 (344)
T cd01700 113 -------------DLEELARKIRRRILQETGIPVTVGIGPTKTLAKLANDLAKKKNPYGGVVDLTDEEVRDKLLKILPVG 179 (344)
T ss_pred -------------CHHHHHHHHHHHHHHHhCCceEEEecCCHHHHHHHHHHhcCCCCCCeEEEecChhHHHHHhccCChh
Confidence 245789999999999999999999999999999999999984 77777766664 899999999
Q ss_pred ccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCCChHHHHHHHHhcCCCcccccccC-CcccccccccCCCCCCC
Q 004805 249 KMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLL-PKSHGSGKSFPGPRALK 327 (729)
Q Consensus 249 ~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~~~g~~L~~~arGiD~~~V~~~~~-pKSis~s~tF~~p~di~ 327 (729)
+|||||+++.++|+ .+||+|+|||+++|.+.|.++||. .|.++|+.++|+|+++|.+..+ +|+|+.+.+|. .++.
T Consensus 180 ~l~gig~~~~~~L~-~~Gi~ti~dL~~~~~~~L~~rfG~-~~~~l~~~a~G~d~~~v~~~~~~~ks~~~~~~~~--~~~~ 255 (344)
T cd01700 180 DVWGIGRRTAKKLN-AMGIHTAGDLAQADPDLLRKKFGV-VGERLVRELNGIDCLPLEEYPPPKKSIGSSRSFG--RDVT 255 (344)
T ss_pred hcCccCHHHHHHHH-HcCCCcHHHHhcCCHHHHHHHHHH-HHHHHHHHhCCCCCCcCCCCCCCCcEEEEeeEcC--CCCC
Confidence 99999999999997 999999999999999999999997 6999999999999999976554 58999999998 5799
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHhhhcCceeEEEEEEEeeccCCCCCCCCCcCcccccCCCcchhHHHhHHHHHHHHHHH
Q 004805 328 TVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLRE 407 (729)
Q Consensus 328 ~~eel~~~L~~LaeeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~~~~srs~~L~~~t~~i~~~a~~L~~aal~l 407 (729)
+.+++..+|++|+++|+.||+. +++.+++|+|++++.++ .......+.+.++..+| ++...|++.++.+
T Consensus 256 ~~~~l~~~l~~L~~~l~~~L~~----~~~~~~~l~l~l~~~~~---~~~~~~~~~~~~~~~~t----~~~~~l~~~~~~l 324 (344)
T cd01700 256 DLDELKQALAEYAERAAEKLRR----QKSVARTISVFIGTSGF---SRQPKYYSATNTLPYPT----NDTREIVKAALRL 324 (344)
T ss_pred CHHHHHHHHHHHHHHHHHHHHH----cCCcccEEEEEEEcCCC---CCCCCccccccccCCcc----hhHHHHHHHHHHH
Confidence 9999999999999999999997 69999999999997532 22112223345666777 4667788888888
Q ss_pred hhcccCccccCCCCCCcceeEEEEEccC
Q 004805 408 FLGSFGVKTQGSHYSGWRITALSVSASK 435 (729)
Q Consensus 408 ~~~~~~~~~~~~~~~~~~IR~IGVsls~ 435 (729)
|..++. .+.+||+|||++++
T Consensus 325 l~~~~~--------~~~~iR~iGV~~~~ 344 (344)
T cd01700 325 LYAIYR--------PGYAYRKAGVMLSD 344 (344)
T ss_pred HHHHhC--------CCCcEEEEEEEeeC
Confidence 875432 35689999999875
No 18
>PRK02406 DNA polymerase IV; Validated
Probab=100.00 E-value=9.6e-64 Score=544.24 Aligned_cols=331 Identities=30% Similarity=0.453 Sum_probs=293.5
Q ss_pred CCchhHhhhchhCCCCCCCcEEEEeccCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEEEccccCCCCChHHHH
Q 004805 19 LDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVARGKADLSSYR 98 (729)
Q Consensus 19 mD~FyASVE~~~~P~LrgkPvaV~q~~~~~~g~ViA~SYeARk~GVk~GM~~~eA~~LCP~L~vv~Vp~~~~k~d~~~Yr 98 (729)
|||||||||++.+|+|+++||||++... ++++|++|||+||++|||+||++.+|+++||+|++++ +|++.|+
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 8999999999999999999999987532 4678999999999999999999999999999999885 7999999
Q ss_pred HHHHHHHHHHHhc-CCeeeeccceeEEecccchhHhhhcCCCCCcchhhHHHhhhhcccCccCCCCCchhhhhhhhhccC
Q 004805 99 NAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKATVKEWLCRCD 177 (729)
Q Consensus 99 ~~S~~I~~iL~~~-~~vE~~SIDEafLDlT~~~~~~l~~~~~~~~~~~~~~~~~~~l~G~~~~~~~~~~~~~~~w~~~~~ 177 (729)
++|++|++++.+| |.||.+||||+|||+|++. ++||
T Consensus 73 ~~s~~i~~~l~~~sp~ve~~siDe~~ldvt~~~----------------------~~~~--------------------- 109 (343)
T PRK02406 73 EVSRQIREIFRRYTDLIEPLSLDEAYLDVTDNK----------------------LCIG--------------------- 109 (343)
T ss_pred HHHHHHHHHHHHhCCceEEccCCeEEEeccCcc----------------------ccCC---------------------
Confidence 9999999999996 8999999999999999975 2333
Q ss_pred cchhhhhhhhHHHHHHHHHHHHHhHhCCceeEeecCCHHHHHHhccCCCCCceeeccCCchhcccccCcccccCCCcHHH
Q 004805 178 ADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKL 257 (729)
Q Consensus 178 ~~~~d~ll~~~~~la~~IR~~I~~etGlt~S~GIA~NklLAKLAS~~~KPngqtvv~~~~v~~fL~~LPI~~L~GIG~k~ 257 (729)
.+..++++||++|++++|++||||||+||++||||++++||+|+++++++++.+||+++||++|||||+++
T Consensus 110 ---------~~~~la~~i~~~i~~~~gl~~siGia~n~~lAklas~~~Kp~g~~~~~~~~~~~~L~~lpi~~l~giG~~~ 180 (343)
T PRK02406 110 ---------SATLIAQEIRQDIFEELGLTASAGVAPNKFLAKIASDWNKPNGLFVITPEEVDAFLATLPVEKIPGVGKVT 180 (343)
T ss_pred ---------CHHHHHHHHHHHHHHHHCCCeEEEeccCHHHHHHHhcCCCCCCEEEECHHHHHHHHHcCCcchhcCCCHHH
Confidence 24578999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhCCcchhhhhcCCHHHHHHhhCCChHHHHHHHHhcCCCcccccccCCcccccccccCCCCCCCcHHHHHHHHH
Q 004805 258 GTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLN 337 (729)
Q Consensus 258 ~~~L~~~lGI~TigDLa~l~~~~L~~rFG~~~g~~L~~~arGiD~~~V~~~~~pKSis~s~tF~~p~di~~~eel~~~L~ 337 (729)
.++|. .+||+|+|||+++|...|.++||. .|.++|++++|+|+++|.+..++|+|+.+++|+ .++.+.+++..+|.
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-FGRRLYERARGIDERPVKPDRERKSVGVERTFA--EDLYDLEACLAELP 256 (343)
T ss_pred HHHHH-HcCCCcHHHHHhCCHHHHHHHHhH-HHHHHHHHhCCCCCCccccCCCCcceeeeeeCC--CCCCCHHHHHHHHH
Confidence 99997 999999999999999999999997 699999999999999999888899999999998 57999999999999
Q ss_pred HHHHHHHHHHHHHhhhcC--ceeEEEEEEEeeccCCCCCCCCCcCcccccCCCcchhHHHhHHHHHHHHHHHhhcccCcc
Q 004805 338 QLCEELSERLCSDLEQNK--RIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVK 415 (729)
Q Consensus 338 ~LaeeL~~RLr~~~~~~~--~~artLtL~lr~~~~~~~~s~~~~~srs~~L~~~t~~i~~~a~~L~~aal~l~~~~~~~~ 415 (729)
+|+++|+.||++ .+ +.+++|+|++++.+ +.. .+++.+ ..++ ++...|+..+.+++..
T Consensus 257 ~l~~~l~~rL~~----~~~~~~~~~l~l~l~~~~---~~~----~~~~~~-~~~~----~~~~~l~~~~~~L~~~----- 315 (343)
T PRK02406 257 RLAEKLERRLER----AKPDKRIKTVGVKLKFAD---FQQ----TTKEHT-ADPL----DKADLIELLAQALLRR----- 315 (343)
T ss_pred HHHHHHHHHHHh----cCCCccceeEEEEEEeCC---CCe----EEEecC-CCCC----CcHHHHHHHHHHHHhh-----
Confidence 999999999997 58 99999999999743 221 234444 3344 2444556666666552
Q ss_pred ccCCCCCCcceeEEEEEccCcccc
Q 004805 416 TQGSHYSGWRITALSVSASKIVPV 439 (729)
Q Consensus 416 ~~~~~~~~~~IR~IGVsls~L~~~ 439 (729)
.+ +.+||.|||++++|.+.
T Consensus 316 ----~~-~~~vr~lgv~~~~l~~~ 334 (343)
T PRK02406 316 ----LG-GRGVRLLGVGVTLLEPQ 334 (343)
T ss_pred ----Cc-CCCEEEEEEEEecCCcC
Confidence 23 67999999999999865
No 19
>COG0389 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]
Probab=100.00 E-value=3.5e-60 Score=517.90 Aligned_cols=344 Identities=35% Similarity=0.509 Sum_probs=305.9
Q ss_pred CEEEEEeCCchhHhhhchhCCCCCCCcEEEEeccCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEEEccccCCC
Q 004805 12 RIIAHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVARGK 91 (729)
Q Consensus 12 rvI~HIDmD~FyASVE~~~~P~LrgkPvaV~q~~~~~~g~ViA~SYeARk~GVk~GM~~~eA~~LCP~L~vv~Vp~~~~k 91 (729)
|+|+||||||||||||++.+|+|+++||||++. . .+|+|++|||+||+|||++||++.+|+++||++.+++
T Consensus 1 ~~i~hvD~Daf~Asve~~~~p~l~~~Pvvv~~~-~-~~gvV~~~sy~Ar~~Gv~sam~~~~A~~~cp~~~~~~------- 71 (354)
T COG0389 1 RKILHVDMDAFYASVEERDNPELKGKPVVVGGG-A-PRGVVLAASYEARAFGVRSAMPLFEALKLCPRAIVAP------- 71 (354)
T ss_pred CeEEEEeccchhhhhhhhcCccccCCCeEEEec-C-CCCEEEecCHHHHHhCCcccChHHHHHHHCCCCEEeC-------
Confidence 589999999999999999999999999999985 2 3689999999999999999999999999999998874
Q ss_pred CChHHHHHHHHHHHHHHHhc-CCeeeeccceeEEecccchhHhhhcCCCCCcchhhHHHhhhhcccCccCCCCCchhhhh
Q 004805 92 ADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKATVK 170 (729)
Q Consensus 92 ~d~~~Yr~~S~~I~~iL~~~-~~vE~~SIDEafLDlT~~~~~~l~~~~~~~~~~~~~~~~~~~l~G~~~~~~~~~~~~~~ 170 (729)
++|+.|+.+|.+|++++.+| +.||++||||+|||+|+..+ .+|.
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 79999999999999999996 88999999999999998652 2221
Q ss_pred hhhhccCcchhhhhhhhHHHHHHHHHHHHHhHhCCceeEeecCCHHHHHHhccCCCCCceeeccCCchhcccccCccccc
Q 004805 171 EWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKM 250 (729)
Q Consensus 171 ~w~~~~~~~~~d~ll~~~~~la~~IR~~I~~etGlt~S~GIA~NklLAKLAS~~~KPngqtvv~~~~v~~fL~~LPI~~L 250 (729)
..+..++.+||..|+.++|+|||+|||+||++||||++++||+|++++.+..+.+||++|||.++
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 12457899999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCCChHHHHHHHHhcCCCcccccccCC-cccccccccCCCCCCCcH
Q 004805 251 KQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLP-KSHGSGKSFPGPRALKTV 329 (729)
Q Consensus 251 ~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~~~g~~L~~~arGiD~~~V~~~~~p-KSis~s~tF~~p~di~~~ 329 (729)
||||+.++.+|+ .+||.|++||+..+.+.|.++||. .|.+||+.++|+|.++|...... ||++.+.+|. .++.+.
T Consensus 182 ~GvG~~~~~~l~-~~Gi~ti~dl~~~~~~~L~~~~g~-~~~~l~~~a~Gid~~~v~~~~~~~ksi~~~~t~~--~d~~~~ 257 (354)
T COG0389 182 WGVGKVTAEKLR-RLGISTIGDLAETDLDALKKRFGK-LGERLYRLARGIDNRPVREQALRAKSIGAESTFE--EDLTDA 257 (354)
T ss_pred CCCCHHHHHHHH-HcCChhHHHHHhcCHHHHHHHHhH-hHHHHHHHhcCCCccccccccccCccccceeecc--ccccCH
Confidence 999999999997 999999999999999999999997 58999999999999999998888 9999999998 689999
Q ss_pred HHHHHHHHH-HHHHHHHHHHHHhhhcCceeEEEEEEEeeccCCCCCCCCCcCcccccCCCcchhHHHhHHHHHHHHHHHh
Q 004805 330 ASVQHWLNQ-LCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLREF 408 (729)
Q Consensus 330 eel~~~L~~-LaeeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~~~~srs~~L~~~t~~i~~~a~~L~~aal~l~ 408 (729)
+++...|.. |+++++.||+. .+..++++++++++.++ ...+++.+++.+++ +..+++..+..+|
T Consensus 258 ~~~~~~l~~~l~e~~~~rl~~----~~~~~r~v~~~~~~~df-------~~~t~~~~l~~p~~----~~~~i~~~~~~l~ 322 (354)
T COG0389 258 EELIERLRARLGEEVVSRLRK----SGRHGRTVSVKLKTADF-------PTNTRSRKLAQPTS----DPIEIYAAALPLL 322 (354)
T ss_pred HHHHHHHHHHHHHHHHHHHHH----hCCCceEEEEEEEecCC-------CcceeecccCCcCC----CHHHHHHHHHHHH
Confidence 988888877 99999999997 57788999999998543 23577888888874 4566777777777
Q ss_pred hcccCccccCCCCCCcceeEEEEEccCcccc
Q 004805 409 LGSFGVKTQGSHYSGWRITALSVSASKIVPV 439 (729)
Q Consensus 409 ~~~~~~~~~~~~~~~~~IR~IGVsls~L~~~ 439 (729)
...+. .|.+.++|++||+++++.+.
T Consensus 323 ~~~~~------~~~~~~~rl~gv~~~~~~~~ 347 (354)
T COG0389 323 PPLLF------RGRGRRIRLLGVSGPELIDS 347 (354)
T ss_pred HHhhc------cCCCceEEEEEEEecCcccc
Confidence 65431 23367999999999999775
No 20
>KOG2094 consensus Predicted DNA damage inducible protein [Replication, recombination and repair]
Probab=100.00 E-value=4.4e-61 Score=499.38 Aligned_cols=346 Identities=29% Similarity=0.420 Sum_probs=296.0
Q ss_pred CCCCCEEEEEeCCchhHhhhchhCCCCCCCcEEEEeccCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEEEccc
Q 004805 8 SSGARIIAHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPV 87 (729)
Q Consensus 8 ~~~~rvI~HIDmD~FyASVE~~~~P~LrgkPvaV~q~~~~~~g~ViA~SYeARk~GVk~GM~~~eA~~LCP~L~vv~Vp~ 87 (729)
+.-.|+|+|||||+|||+||+++||.|+++|+||++. ..+.++||.||+||||.+||.+.|+++||+|++|+
T Consensus 99 RdLsr~~vhvDmDAfyAaVE~~dnP~lk~~PmAVGs~-----smlsTaNY~ARkFGVRaaMPgFIarklCPdLiiVP--- 170 (490)
T KOG2094|consen 99 RDLSRIIVHVDMDAFYAAVEMLDNPKLKSKPMAVGSK-----SMLSTANYVARKFGVRAAMPGFIARKLCPDLIIVP--- 170 (490)
T ss_pred ccccceEEEechHHHHHHHHhccCcccccCCccccch-----hhhhhhhHHHHHhhhhhcCchHHHhccCCceEEeC---
Confidence 3467999999999999999999999999999999864 35779999999999999999999999999999884
Q ss_pred cCCCCChHHHHHHHHHHHHHHHhc-CCeeeeccceeEEecccchhHhhhcCCCCCcchhhHHHhhhhcccCccCCCCCch
Q 004805 88 ARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSK 166 (729)
Q Consensus 88 ~~~k~d~~~Yr~~S~~I~~iL~~~-~~vE~~SIDEafLDlT~~~~~~l~~~~~~~~~~~~~~~~~~~l~G~~~~~~~~~~ 166 (729)
.+|..|+.+|.++.++|++| +.+-..|+||+|||+|..++. +-+|....
T Consensus 171 ----~n~~kYt~~Ske~~~v~~~YDsn~~~~SlDEaylnlT~~l~~--------------------~~~g~l~~------ 220 (490)
T KOG2094|consen 171 ----LNFSKYTIVSKEIQNVLAQYDSNFCAMSLDEAYLNLTSHLRE--------------------RELGFLVE------ 220 (490)
T ss_pred ----CCcHHHHHHHHHHHHHHHHcCCccccchHHHHHHhHHHHHHH--------------------hhcchhhh------
Confidence 69999999999999999998 689999999999999987643 12231100
Q ss_pred hhhhhhhhccCcchhhhhhhhHHHHHHHHHHHHHhHhCCceeEeecCCHHHHHHhccCCCCCceeeccCC--chhccccc
Q 004805 167 ATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFS--SVKGLLDS 244 (729)
Q Consensus 167 ~~~~~w~~~~~~~~~d~ll~~~~~la~~IR~~I~~etGlt~S~GIA~NklLAKLAS~~~KPngqtvv~~~--~v~~fL~~ 244 (729)
.+...++++||.+|.++||+|||+|||.|++|||++|+.+|||||++++++ .+.+||.+
T Consensus 221 -------------------nG~~evveeiR~rV~qeTglT~SaGIAaN~lLAKicSd~nKPNgQf~i~~dr~aim~F~kd 281 (490)
T KOG2094|consen 221 -------------------NGITEVVEEIRFRVEQETGLTCSAGIAANKLLAKICSDKNKPNGQFVIPNDRIAIMKFMKD 281 (490)
T ss_pred -------------------ccHHHHHHHHHHHHHHhcCceeeccccHhHHHHHHhccccCCCCceEecccHHHHHHHHhc
Confidence 113578999999999999999999999999999999999999999999886 57899999
Q ss_pred CcccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCCChHHHHHHHHhcCCCcccccccCCcccccccccCCCC
Q 004805 245 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPR 324 (729)
Q Consensus 245 LPI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~~~g~~L~~~arGiD~~~V~~~~~pKSis~s~tF~~p~ 324 (729)
|||+++-|||+.++..|. .|||.||||+.. ....|--.|.+...+.+++.+.|...++......+|||++++||.
T Consensus 282 LPvRkV~GIGrV~E~qLk-al~IkTcgdm~~-k~~ll~~lFsp~S~~~fLr~slG~g~t~~~~~~eRKsis~ErTFs--- 356 (490)
T KOG2094|consen 282 LPVRKVSGIGRVTEQQLK-ALGIKTCGDMQQ-KLVLLSLLFSPKSFQNFLRCSLGLGTTILDEDGERKSISSERTFS--- 356 (490)
T ss_pred CCcccccchhHHHHHHHH-hcCceeHHHHHH-hhhHHHHHhCchhHHHHHHHhhcCCCCcCccccccccccceeeec---
Confidence 999999999999999997 999999999975 345677889987788899999999999998888899999999997
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHhhhcCceeEEEEEEEeeccCCCCCCCCCcCcccccCCCcchhHHHhHHHHHHHH
Q 004805 325 ALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAG 404 (729)
Q Consensus 325 di~~~eel~~~L~~LaeeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~~~~srs~~L~~~t~~i~~~a~~L~~aa 404 (729)
.+.+...+...+.+||+.|++-|+. .|++++||||+++... |.- .+|+.++..-+ ....+|+..+
T Consensus 357 ~~sd~~il~~k~qel~~~lsedlqK----~glv~rtvtiKlK~ss---Fev----~Tr~~t~s~vv----~S~edi~k~a 421 (490)
T KOG2094|consen 357 STSDPSILYSKLQELCQMLSEDLQK----EGLVGRTVTIKLKTSS---FEV----HTRQKTISQVV----HSEEDILKPA 421 (490)
T ss_pred ccCCHHHHHHHHHHHHHHHHHHHHh----cCcccceEEEEEeccc---eee----eeccCchhhhh----ccHHHHHHHH
Confidence 3788888888888888888888876 6999999999988643 332 24555443222 4567788999
Q ss_pred HHHhhcccCccccCCCCCCcceeEEEEEccCccccc
Q 004805 405 LREFLGSFGVKTQGSHYSGWRITALSVSASKIVPVL 440 (729)
Q Consensus 405 l~l~~~~~~~~~~~~~~~~~~IR~IGVsls~L~~~~ 440 (729)
++|+...+ +..||++||.++.|+...
T Consensus 422 leLLk~e~----------~~~iRLlGvR~sqlv~ee 447 (490)
T KOG2094|consen 422 LELLKQEY----------PMTIRLLGVRASQLVSEE 447 (490)
T ss_pred HHHHHhhc----------CceEeeeeeeHhhccchh
Confidence 99887543 568999999999998864
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=3.7e-52 Score=450.80 Aligned_cols=327 Identities=20% Similarity=0.183 Sum_probs=278.3
Q ss_pred EEEeCCchhHhhhchhCCCCCCCcEEEEeccCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEEEccccCCCCCh
Q 004805 15 AHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVARGKADL 94 (729)
Q Consensus 15 ~HIDmD~FyASVE~~~~P~LrgkPvaV~q~~~~~~g~ViA~SYeARk~GVk~GM~~~eA~~LCP~L~vv~Vp~~~~k~d~ 94 (729)
+.|+|++||++++.+.+|+|+++||||++.+. +|+|++|||+||++||++||++.+|+++||++++++ +|+
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 36899999999999999999999999987543 689999999999999999999999999999999885 799
Q ss_pred HHHHHHHHHHHHHHHhc-CCeeeeccceeEEecccchhHhhhcCCCCCcchhhHHHhhhhcccCccCCCCCchhhhhhhh
Q 004805 95 SSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKATVKEWL 173 (729)
Q Consensus 95 ~~Yr~~S~~I~~iL~~~-~~vE~~SIDEafLDlT~~~~~~l~~~~~~~~~~~~~~~~~~~l~G~~~~~~~~~~~~~~~w~ 173 (729)
+.|.+++.+|+++|.+| |.||.+||||+|||+|++. ++||
T Consensus 72 ~~y~~~s~~i~~~l~~~s~~ve~~s~de~~ldvs~~~----------------------~~~~----------------- 112 (335)
T cd03468 72 EADARALQELALWLLRFTPLVALDGPDGLLLDVTGCL----------------------HLFG----------------- 112 (335)
T ss_pred HHHHHHHHHHHHHHHhcCCccccCCCCeEEEEcccch----------------------hhcC-----------------
Confidence 99999999999999996 8899999999999999874 2233
Q ss_pred hccCcchhhhhhhhHHHHHHHHHHHHHhHhCCceeEeecCCHHHHHHhccCCCCCceeeccCCchhc-ccccCcccccCC
Q 004805 174 CRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKG-LLDSLPIKKMKQ 252 (729)
Q Consensus 174 ~~~~~~~~d~ll~~~~~la~~IR~~I~~etGlt~S~GIA~NklLAKLAS~~~KPngqtvv~~~~v~~-fL~~LPI~~L~G 252 (729)
....++++|++.+. ++|++||+|||+||++||||++++||+|++.+....... |++++|+ ++||
T Consensus 113 -------------~~~~~a~~i~~~~~-~~gl~~siGia~n~~~Aklas~~~kp~~~~~~~~~~~~~~~l~~lp~-~~~g 177 (335)
T cd03468 113 -------------GEDALAASLRAALA-TLGLSARAGIADTPGAAWLLARAGGGRGVLRREALAAALVLLAPLPV-AALR 177 (335)
T ss_pred -------------CHHHHHHHHHHHHH-HcCCeEEEEecCCHHHHHHHhccCCCCccCCchHHHHHhhccCCCCh-hHhC
Confidence 23467899999995 689999999999999999999999999998776665554 8999999 5999
Q ss_pred CcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCCChHHHHHHHHhcCCCccc--ccccCCcccccccccCCCCCCCcHH
Q 004805 253 LGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEV--QARLLPKSHGSGKSFPGPRALKTVA 330 (729)
Q Consensus 253 IG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~~~g~~L~~~arGiD~~~V--~~~~~pKSis~s~tF~~p~di~~~e 330 (729)
||+++.++|. .+||+|++||+++|...|.++||. .|.++|+.++|+|+.++ .....+|+++.+.+|+ .+..+.+
T Consensus 178 ig~~~~~~L~-~~Gi~t~~dl~~~~~~~l~~rfG~-~~~~l~~~~~G~d~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~ 253 (335)
T cd03468 178 LPPETVELLA-RLGLRTLGDLAALPRAELARRFGL-ALLLRLDQAYGRDPEPLLFSPPPPAFDFRLELQLE--EPIARGL 253 (335)
T ss_pred CCHHHHHHHH-HhCcccHHHHHhCChHHHHhhcCH-HHHHHHHHHCCCCCCCCCCCCCCCChhhhhhcCCC--CCcchhH
Confidence 9999999997 999999999999999999999997 49999999999999999 4455679999999998 3455544
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhcCceeEEEEEEEeeccCCCCCCCCCcCcccccCCCcchhHHHhHHHHHHHHHHHhhc
Q 004805 331 SVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLG 410 (729)
Q Consensus 331 el~~~L~~LaeeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~~~~srs~~L~~~t~~i~~~a~~L~~aal~l~~~ 410 (729)
...+.+|+++++.||+. ++..+++|+|++++.+. . ..+++.++..+++ +...|++.+..+|.+
T Consensus 254 --~~~l~~l~~~l~~~L~~----~~~~~~~l~l~l~~~~~---~----~~~~~~~~~~~~~----~~~~l~~l~~~~l~~ 316 (335)
T cd03468 254 --LFPLRRLLEQLCAFLAL----RGLGARRLSLTLFREDG---R----VTRVLVGLARPSR----DDLPLLRLLRERLER 316 (335)
T ss_pred --HHHHHHHHHHHHHHHHH----cCCeeeEEEEEEEEECC---c----eEEEEEeccCCcc----CHHHHHHHHHhhhhc
Confidence 88999999999999997 69999999999987532 1 1245666666663 444466665555543
Q ss_pred ccCccccCCCCCC---cceeEEEEEcc
Q 004805 411 SFGVKTQGSHYSG---WRITALSVSAS 434 (729)
Q Consensus 411 ~~~~~~~~~~~~~---~~IR~IGVsls 434 (729)
. +.+ .+||.++|++.
T Consensus 317 ~---------~~~~~~~~v~~~~v~~~ 334 (335)
T cd03468 317 L---------ALPRGIAPVRLLALTAE 334 (335)
T ss_pred c---------CCCCCeeeEEEEEeecc
Confidence 2 234 68999999864
No 22
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=100.00 E-value=2.3e-52 Score=471.54 Aligned_cols=349 Identities=24% Similarity=0.368 Sum_probs=292.9
Q ss_pred EEEEeCCchhHhhhchhCCCCCCCcEEEEeccCC--CCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEEEccccCCC
Q 004805 14 IAHVDLDCFYVQVEQRKQPKLRGLPTAVVQYNEW--KGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVARGK 91 (729)
Q Consensus 14 I~HIDmD~FyASVE~~~~P~LrgkPvaV~q~~~~--~~g~ViA~SYeARk~GVk~GM~~~eA~~LCP~L~vv~Vp~~~~k 91 (729)
.+|+++||||.+|+....++++++|++|...... ...-|.+|||+||+||||+||.+.+|+++||+|++++
T Consensus 373 ~~~v~~dcf~~sv~~~n~~D~k~kpvav~hg~d~~~s~sEIASCsY~AR~~GIKNGMfV~~A~klCPqL~~lP------- 445 (1016)
T KOG2093|consen 373 SVKVELDCFFVSVVIKNRLDLKDKPVAVCHGSDNPKSTSEIASCSYEARAYGIKNGMFVRHAKKLCPQLVILP------- 445 (1016)
T ss_pred hhHHHHHHhhhhheeccccccccCcceeeccCCCCcchhhhhccccHHHHhCcccceeHHHHHHhCcccEeec-------
Confidence 4566778888888888999999999999872211 1245778999999999999999999999999998884
Q ss_pred CChHHHHHHHHHHHHHHHhc-CCeeeeccceeEEecccchhHhhhcCCCCCcchhhHHHhhhhcccCccCCCCCchhhhh
Q 004805 92 ADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKATVK 170 (729)
Q Consensus 92 ~d~~~Yr~~S~~I~~iL~~~-~~vE~~SIDEafLDlT~~~~~~l~~~~~~~~~~~~~~~~~~~l~G~~~~~~~~~~~~~~ 170 (729)
|||+.|.++|+.++++|++| -.||.+|+||+|+|+|...... ..
T Consensus 446 Y~FE~Ykevs~tlYetlasytl~I~aVSCDEa~vd~s~~~~~~----------------------~~------------- 490 (1016)
T KOG2093|consen 446 YDFEAYKEVSETLYETLASYTLNIEAVSCDEAFVDVSDLSDEE----------------------NE------------- 490 (1016)
T ss_pred ccHHHHHHHHHHHHHHHHhhccceeeecchhhhhhhhhhhhhh----------------------cc-------------
Confidence 89999999999999999997 5699999999999999865210 00
Q ss_pred hhhhccCcchhhhhhhhHHHHHHHHHHHHHhHhCCceeEeecCCHHHHHHhccCCCCCceeeccCCchhcccccCccccc
Q 004805 171 EWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKM 250 (729)
Q Consensus 171 ~w~~~~~~~~~d~ll~~~~~la~~IR~~I~~etGlt~S~GIA~NklLAKLAS~~~KPngqtvv~~~~v~~fL~~LPI~~L 250 (729)
.++.+|..||++|++.||++||||||.|++||+||++.+|||||+++.++.+.+||+.++|.+|
T Consensus 491 ----------------tp~~la~~IRqEI~e~TgC~aS~Gig~t~LLARlATr~AKP~Gq~~l~a~~veeFis~~~v~~L 554 (1016)
T KOG2093|consen 491 ----------------TPAVLAEHIRQEILEKTGCPASAGIGGTMLLARLATRVAKPNGQFYLSAEKVEEFISQLKVDDL 554 (1016)
T ss_pred ----------------CHHHHHHHHHHHHHhccCCceeeccchHHHHHHHHHhhcCCCceeeecHHHHHHHhhhcccccC
Confidence 1357899999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCCChHHHHHHHHhcCCCcccccccCCcccccccccCCCCCCCcHH
Q 004805 251 KQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTVA 330 (729)
Q Consensus 251 ~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~~~g~~L~~~arGiD~~~V~~~~~pKSis~s~tF~~p~di~~~e 330 (729)
||+|..+..+|. .+||+|||||+..+...|++.||++.|..+|+.|+|+|++|+.....+||++...+|. .++++.-
T Consensus 555 PGVG~sm~~kL~-s~~i~tCgdLq~~T~~kl~k~~G~Klgq~i~~~CrG~Dd~P~~~~~~RKSvS~dIN~G--IRFtn~~ 631 (1016)
T KOG2093|consen 555 PGVGSSMKSKLV-SQFIQTCGDLQLITLIKLRKVFGPKLGQKIYRGCRGIDDDPRSIEQVRKSVSADINYG--IRFTNIK 631 (1016)
T ss_pred CCccHHHHHHHH-HhccchhHHHHHHHHHHHHhhhcccHHHHHHHhcCCCcCChHHHhhhhcceeeeeecc--eeeccHH
Confidence 999999999997 9999999999999999999999999999999999999999998877899999999998 6899999
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhcCceeEEEEEEEeeccCCCC------CCCC--CcCcccccCCCcchhHHHhHHHHHH
Q 004805 331 SVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDS------DSRK--KFPSKSCPLRYGTAKIQEDTFNLFQ 402 (729)
Q Consensus 331 el~~~L~~LaeeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~------~s~~--~~~srs~~L~~~t~~i~~~a~~L~~ 402 (729)
++..+|-.++++|-+||.+ -++.++.|||++.....+.+ ..|. -..+|++.|.++|+. ..-|.-
T Consensus 632 ev~~fl~~~~eEl~rkL~e----i~k~~~sitLKlMvR~~~APietaK~mGhGiCD~~~rs~~l~~~Td~----~~iItt 703 (1016)
T KOG2093|consen 632 EVEQFLCLLSEELRRKLLE----ISKTASSITLKLMVRTAKAPIETAKYMGHGICDDFVRSSKLREPTDC----NRIITT 703 (1016)
T ss_pred HHHHHHHHHHHHHHHHHHH----hhccccchhHHHHhhcCCCCCccccccceeeccchhhhhhccCcccc----ccchHH
Confidence 9999999999999999986 58889999998654322211 1111 124789999999862 223333
Q ss_pred HHHHHhhcccCccccCCCCCCcceeEEEEEcc-Ccccc
Q 004805 403 AGLREFLGSFGVKTQGSHYSGWRITALSVSAS-KIVPV 439 (729)
Q Consensus 403 aal~l~~~~~~~~~~~~~~~~~~IR~IGVsls-~L~~~ 439 (729)
.+++|+..+ ......+|++||++. +|.+.
T Consensus 704 ~~~~L~~t~--------~~~~~elRG~gi~~ntkL~~~ 733 (1016)
T KOG2093|consen 704 EVLRLYETN--------SEPPSELRGLGIHSNTKLMDV 733 (1016)
T ss_pred HHHHHHHhc--------CCChHHhccchhhcccccccc
Confidence 444444322 123557899999995 77764
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=3.4e-35 Score=283.61 Aligned_cols=147 Identities=40% Similarity=0.622 Sum_probs=131.3
Q ss_pred EeCCchhHhhhchhCCCCCCCcEEEEeccCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEEEccccCCCCChHH
Q 004805 17 VDLDCFYVQVEQRKQPKLRGLPTAVVQYNEWKGGGLIAVGYEARNYGVKRSMRGDEAKEVCPQIELVQVPVARGKADLSS 96 (729)
Q Consensus 17 IDmD~FyASVE~~~~P~LrgkPvaV~q~~~~~~g~ViA~SYeARk~GVk~GM~~~eA~~LCP~L~vv~Vp~~~~k~d~~~ 96 (729)
|||||||||||++++|+|+++||||++.+. ++++|++|||+||++||++||++.+|+++||++++++ +|++.
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 799999999999999999999999998753 3589999999999999999999999999999999886 79999
Q ss_pred HHHHHHHHHHHHHhc-C-CeeeeccceeEEecccchhHhhhcCCCCCcchhhHHHhhhhcccCccCCCCCchhhhhhhhh
Q 004805 97 YRNAGSEVVSILARK-G-RCERASIDEVYLDLTDAAEAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKATVKEWLC 174 (729)
Q Consensus 97 Yr~~S~~I~~iL~~~-~-~vE~~SIDEafLDlT~~~~~~l~~~~~~~~~~~~~~~~~~~l~G~~~~~~~~~~~~~~~w~~ 174 (729)
|++++++|+.++.+| + .+|.+|+||+|||+|++. ++
T Consensus 73 ~~~~~~~l~~~l~~~~sp~ve~~s~de~~ldv~~~~----------------------~l-------------------- 110 (149)
T PF00817_consen 73 YREASERLAEILYRFSSPRVEVYSPDELFLDVTGSL----------------------RL-------------------- 110 (149)
T ss_dssp HHHHHHHHHHHHHTTTCSEEEEEETTEEEEEEHHHH----------------------HH--------------------
T ss_pred HHHHHHHHHHHHHhcccccceecccccccccCCcch----------------------hh--------------------
Confidence 999999999999997 4 799999999999999965 22
Q ss_pred ccCcchhhhhhhhHHHHHHHHHHHHHhHhCCceeEeecCCHHHHHHhcc
Q 004805 175 RCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASG 223 (729)
Q Consensus 175 ~~~~~~~d~ll~~~~~la~~IR~~I~~etGlt~S~GIA~NklLAKLAS~ 223 (729)
|+....++++||++|.+++|++||+|||+||++||||++
T Consensus 111 ----------~~~~~~~~~~l~~~i~~~~gl~~s~Gia~~~~~Aklaa~ 149 (149)
T PF00817_consen 111 ----------FGGEEALARRLRQAIAEETGLTASIGIAPNPLLAKLAAD 149 (149)
T ss_dssp ----------HHHHHHHHHHHHHHHHHHHS--EEEEEESSHHHHHHHHH
T ss_pred ----------cchHHHHHHHHHHHHHHHhCCEEEEEEeCCHHHHHHhcC
Confidence 233457899999999999999999999999999999974
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=99.30 E-value=7.5e-12 Score=116.15 Aligned_cols=125 Identities=30% Similarity=0.413 Sum_probs=89.1
Q ss_pred Ccccc-cccCCcccccccccCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHhhhcCceeEEEEEEEeeccCCCCCCCCCcC
Q 004805 302 GEEVQ-ARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFP 380 (729)
Q Consensus 302 ~~~V~-~~~~pKSis~s~tF~~p~di~~~eel~~~L~~LaeeL~~RLr~~~~~~~~~artLtL~lr~~~~~~~~s~~~~~ 380 (729)
++||. ++.++|||+.+++|+ .++.+.+++..+|..|+++|+.||++ +++.+++|+|+++|.+. .. ....
T Consensus 1 ~~pV~~~~~~~ksi~~~~t~~--~~~~~~~~i~~~l~~l~~~l~~rL~~----~~~~~~~i~l~l~~~~~---~~-~~~~ 70 (127)
T PF11799_consen 1 DEPVQQPRPPPKSIGSERTFP--EPISDREEIEEWLRELAEELAERLRE----RGLAARTITLKLRYSDF---GR-CSSR 70 (127)
T ss_dssp ------SCSS-SEEEEEEEEC--EEESSHHHHHHHHHHHHHHHHHHHHH----CTEEEEEEEEEEEETTS---CS-CEEE
T ss_pred CCCCCCCCCCCCEEEEEEECC--CCCCCHHHHHHHHHHHHHHHHHHHHh----hCcCCceEEEEEEecCC---cc-ccee
Confidence 36787 788999999999997 46899999999999999999999996 79999999999997532 11 1134
Q ss_pred cccccCCCcchhHHHhHHHHHHHHHHHhhcccCccccCCCCCCcceeEEEEEccCcc-ccccccccccccc
Q 004805 381 SKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIV-PVLSGTCSIMKYF 450 (729)
Q Consensus 381 srs~~L~~~t~~i~~~a~~L~~aal~l~~~~~~~~~~~~~~~~~~IR~IGVsls~L~-~~~~~~~si~dlF 450 (729)
+++.+++.|++ +...|++.+..+|.+... ..+.+||+|||++++|. +. ...|++||
T Consensus 71 ~~~~~l~~p~~----~~~~l~~~~~~l~~~~~~-------~~~~~vr~igv~~~~l~~~~---~~~q~~lF 127 (127)
T PF11799_consen 71 SRSIRLPFPTN----DADELLKAARELLERLLY-------DPGFPVRLIGVSASDLIEPA---GQRQLDLF 127 (127)
T ss_dssp EEEEEECCCEH----CHHHHHHHHHHHHHHHHH-------HTTCGEEEEEEEEEEEEEC-------B----
T ss_pred eEEEeccCCcC----CHHHHHHHHHHHHHHHhc-------CCCCCEEEEEEEECCCcCCC---CCcccccC
Confidence 67888888884 566688888887743310 12678999999999998 43 56788887
No 25
>PF11798 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 This helix-hairpin-helix motif is found in proteins belonging to the type-Y family of DNA polymerases []. This type of polymerases are thought to be involved in UV protection and mutation [, ]. ; PDB: 3PZP_B 2OH2_B 2W7O_B 3IN5_B 1T94_A 2W7P_B 2W8K_A 2AGQ_A 1RYR_A 3RAX_A ....
Probab=98.27 E-value=3.1e-07 Score=65.99 Aligned_cols=32 Identities=34% Similarity=0.513 Sum_probs=27.9
Q ss_pred CCchhcccccCcccccCCCcHHHHHHHHHHhCC
Q 004805 235 FSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGV 267 (729)
Q Consensus 235 ~~~v~~fL~~LPI~~L~GIG~k~~~~L~~~lGI 267 (729)
|+++.+||++|||+++||||++++++|+ .+||
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 4678999999999999999999999997 9997
No 26
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=97.68 E-value=3.8e-05 Score=83.47 Aligned_cols=80 Identities=20% Similarity=0.218 Sum_probs=65.3
Q ss_pred ccccCcccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCC--ChHHHHHHHHhc---CC--CcccccccCCcc
Q 004805 241 LLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF--NTGTWLWNIARG---IS--GEEVQARLLPKS 313 (729)
Q Consensus 241 fL~~LPI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~--~~g~~L~~~arG---iD--~~~V~~~~~pKS 313 (729)
.|.++||.++||||++++++|. ..||+|++||+.+++..|.+.||. +.+..+++.++| .+ .+.+.....+++
T Consensus 2 ~~~~~~l~~l~gIg~~~a~~L~-~~Gi~t~~dl~~~~~~~L~~~~g~~~~~a~~l~~~a~~~~~~~~~~t~~~l~~~~ks 80 (317)
T PRK04301 2 KMKEKDLEDLPGVGPATAEKLR-EAGYDTVEAIAVASPKELSEAAGIGESTAAKIIEAAREAADIGGFETALEVLERRKN 80 (317)
T ss_pred CcccccHhhcCCCCHHHHHHHH-HcCCCCHHHHHcCCHHHHHHhcCCCHHHHHHHHHHHHHhhccccCccHHHHHHhhcc
Confidence 4789999999999999999997 999999999999999999999996 368999999998 53 333433334566
Q ss_pred cccccccC
Q 004805 314 HGSGKSFP 321 (729)
Q Consensus 314 is~s~tF~ 321 (729)
++...|+.
T Consensus 81 ~~~~~Tg~ 88 (317)
T PRK04301 81 VGKITTGS 88 (317)
T ss_pred CCccCCCC
Confidence 66655553
No 27
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=96.95 E-value=0.00098 Score=72.16 Aligned_cols=74 Identities=19% Similarity=0.189 Sum_probs=60.1
Q ss_pred ccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCCC--hHHHHHHHHh---cCC--CcccccccCCcccccccc
Q 004805 247 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN--TGTWLWNIAR---GIS--GEEVQARLLPKSHGSGKS 319 (729)
Q Consensus 247 I~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~~--~g~~L~~~ar---GiD--~~~V~~~~~pKSis~s~t 319 (729)
|.++||||++++++|. ..||.|++||+.++.+.|.+.+|.. .+..++..++ |.+ .+.+.....+++++...|
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 4689999999999997 9999999999999999999999963 4888999888 877 555544444567766665
Q ss_pred cC
Q 004805 320 FP 321 (729)
Q Consensus 320 F~ 321 (729)
+.
T Consensus 80 g~ 81 (310)
T TIGR02236 80 GS 81 (310)
T ss_pred CC
Confidence 54
No 28
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=96.24 E-value=0.0038 Score=51.21 Aligned_cols=50 Identities=26% Similarity=0.320 Sum_probs=41.0
Q ss_pred ccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhh--CCChHHHHHHHH
Q 004805 247 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESY--GFNTGTWLWNIA 297 (729)
Q Consensus 247 I~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rF--G~~~g~~L~~~a 297 (729)
+..++|||++++.+|. ..|+.|+.||+..+.+.|.+.- |...+..+...+
T Consensus 7 L~~I~Gig~~~a~~L~-~~G~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~ 58 (60)
T PF14520_consen 7 LLSIPGIGPKRAEKLY-EAGIKTLEDLANADPEELAEIPGIGEKTAEKIIEAA 58 (60)
T ss_dssp HHTSTTCHHHHHHHHH-HTTCSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHHH
T ss_pred hccCCCCCHHHHHHHH-hcCCCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHHH
Confidence 3478999999999998 8899999999999999999884 444555555544
No 29
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=95.66 E-value=0.012 Score=52.64 Aligned_cols=40 Identities=20% Similarity=0.327 Sum_probs=35.8
Q ss_pred cccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhC
Q 004805 246 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYG 286 (729)
Q Consensus 246 PI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG 286 (729)
.+++|||||+++++-|. .+||+++.||+..++..|..++-
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 46789999999999998 99999999999999988876664
No 30
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=92.31 E-value=0.19 Score=52.10 Aligned_cols=56 Identities=18% Similarity=0.262 Sum_probs=49.6
Q ss_pred cccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHh--hCCChHHHHHHHHhcCCC
Q 004805 246 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIARGISG 302 (729)
Q Consensus 246 PI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~r--FG~~~g~~L~~~arGiD~ 302 (729)
.|.+|+|||++...+|. ..|+.|+.+|...+.+.|.+. +|...+..++..+.+.+.
T Consensus 4 ~L~~IpGIG~krakkLl-~~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l~~~~~ 61 (232)
T PRK12766 4 ELEDISGVGPSKAEALR-EAGFESVEDVRAADQSELAEVDGIGNALAARIKADVGGLEV 61 (232)
T ss_pred ccccCCCcCHHHHHHHH-HcCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHHhccccc
Confidence 46788999999999998 899999999999999999999 777778889998876544
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=91.97 E-value=0.091 Score=43.07 Aligned_cols=27 Identities=33% Similarity=0.394 Sum_probs=19.4
Q ss_pred cEEEEcCHHHHHcCCCCCCCHHHHHhh
Q 004805 50 GGLIAVGYEARNYGVKRSMRGDEAKEV 76 (729)
Q Consensus 50 g~ViA~SYeARk~GVk~GM~~~eA~~L 76 (729)
+-|..+|+.|++.||+.||++.+|+.+
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 357899999999999999999999864
No 32
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=91.55 E-value=0.19 Score=47.63 Aligned_cols=37 Identities=22% Similarity=0.441 Sum_probs=32.3
Q ss_pred cccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHH
Q 004805 246 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQE 283 (729)
Q Consensus 246 PI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~ 283 (729)
.|+.|-|||++++..|+ .+||+|..||+.++...+..
T Consensus 68 DLt~I~GIGPk~e~~Ln-~~GI~tfaQIAAwt~~di~~ 104 (133)
T COG3743 68 DLTRISGIGPKLEKVLN-ELGIFTFAQIAAWTRADIAW 104 (133)
T ss_pred cchhhcccCHHHHHHHH-HcCCccHHHHHhcCHHHHHH
Confidence 46778999999999997 99999999999998776543
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=91.18 E-value=0.14 Score=41.10 Aligned_cols=27 Identities=26% Similarity=0.302 Sum_probs=20.6
Q ss_pred cccCCCcHHHHHHHHHHhCCcchhhhhc
Q 004805 248 KKMKQLGGKLGTSLQNELGVTTVGDLLK 275 (729)
Q Consensus 248 ~~L~GIG~k~~~~L~~~lGI~TigDLa~ 275 (729)
..+||||+++++++. ..|++|+.||..
T Consensus 5 ~~I~GVG~~tA~~w~-~~G~rtl~Dl~~ 31 (52)
T PF10391_consen 5 TGIWGVGPKTARKWY-AKGIRTLEDLRK 31 (52)
T ss_dssp HTSTT--HHHHHHHH-HTT--SHHHHHH
T ss_pred hhcccccHHHHHHHH-HhCCCCHHHHhh
Confidence 468999999999998 899999999964
No 34
>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=90.94 E-value=0.28 Score=42.93 Aligned_cols=33 Identities=27% Similarity=0.440 Sum_probs=25.0
Q ss_pred cccccCCCcHHHHHHHHHHhCCcchhhhhcCCHH
Q 004805 246 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSED 279 (729)
Q Consensus 246 PI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~ 279 (729)
.|++||+||+++++.|. +.||+|+.||..+...
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 57899999999999997 9999999999987543
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=89.41 E-value=0.61 Score=39.20 Aligned_cols=45 Identities=33% Similarity=0.478 Sum_probs=36.3
Q ss_pred cccccCcccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhC
Q 004805 240 GLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYG 286 (729)
Q Consensus 240 ~fL~~LPI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG 286 (729)
..+...||..| |+..++...|. +.||+|++||..++...|.+.=|
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 44567899998 89999999997 99999999999999999877655
No 36
>PRK02362 ski2-like helicase; Provisional
Probab=88.02 E-value=0.49 Score=57.58 Aligned_cols=55 Identities=15% Similarity=0.151 Sum_probs=49.6
Q ss_pred CcccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCCChHHHHHHHHhcC
Q 004805 245 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGI 300 (729)
Q Consensus 245 LPI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~~~g~~L~~~arGi 300 (729)
+|+..|||||++.+.+|. .+||+|+.||+++....|.+.||.+.+..++..++..
T Consensus 652 ~~L~~ip~i~~~~a~~l~-~~gi~s~~dl~~~~~~~l~~~~g~~~~~~i~~~~~~~ 706 (737)
T PRK02362 652 LDLVGLRGVGRVRARRLY-NAGIESRADLRAADKSVVLAILGEKIAENILEQAGRR 706 (737)
T ss_pred HHHhCCCCCCHHHHHHHH-HcCCCCHHHHHhCCHHHHHHHHCHHHHHHHHHHhCcc
Confidence 577789999999999997 8999999999999999999999998888888877644
No 37
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=84.84 E-value=0.58 Score=44.10 Aligned_cols=41 Identities=22% Similarity=0.393 Sum_probs=36.6
Q ss_pred cccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCC
Q 004805 246 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF 287 (729)
Q Consensus 246 PI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~ 287 (729)
.+-.++|||+..+..|. ..||.|+.+|+..++..|....+.
T Consensus 54 dL~ri~gi~~~~a~LL~-~AGv~Tv~~LA~~~p~~L~~~l~~ 94 (122)
T PF14229_consen 54 DLMRIPGIGPQYAELLE-HAGVDTVEELAQRNPQNLHQKLGR 94 (122)
T ss_pred HhhhcCCCCHHHHHHHH-HhCcCcHHHHHhCCHHHHHHHHHH
Confidence 34478999999999997 999999999999999999988874
No 38
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=82.95 E-value=0.98 Score=37.59 Aligned_cols=47 Identities=17% Similarity=0.314 Sum_probs=32.3
Q ss_pred cCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHh--hCCChHHHHHHHHh
Q 004805 250 MKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 298 (729)
Q Consensus 250 L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~r--FG~~~g~~L~~~ar 298 (729)
+||||.++++.|.+.+| ++..|...+.+.|... +|+..+..++++..
T Consensus 8 I~~VG~~~ak~L~~~f~--sl~~l~~a~~e~L~~i~gIG~~~A~si~~ff~ 56 (64)
T PF12826_consen 8 IPGVGEKTAKLLAKHFG--SLEALMNASVEELSAIPGIGPKIAQSIYEFFQ 56 (64)
T ss_dssp STT--HHHHHHHHHCCS--CHHHHCC--HHHHCTSTT--HHHHHHHHHHHH
T ss_pred CCCccHHHHHHHHHHcC--CHHHHHHcCHHHHhccCCcCHHHHHHHHHHHC
Confidence 48999999999986666 8999999999999887 66666666666543
No 39
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=80.25 E-value=0.41 Score=57.50 Aligned_cols=31 Identities=39% Similarity=0.562 Sum_probs=29.2
Q ss_pred EEEEeCCchhHhhhchhCCCCCCCcEEEEec
Q 004805 14 IAHVDLDCFYVQVEQRKQPKLRGLPTAVVQY 44 (729)
Q Consensus 14 I~HIDmD~FyASVE~~~~P~LrgkPvaV~q~ 44 (729)
++|+||||||++|-.+..|.++|.|.|+...
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 7899999999999999999999999999864
No 40
>COG2251 Predicted nuclease (RecB family) [General function prediction only]
Probab=80.11 E-value=1.5 Score=49.44 Aligned_cols=68 Identities=21% Similarity=0.096 Sum_probs=56.2
Q ss_pred CCchhcccccCcccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhC--CChHHHHHHHHhcCCCc
Q 004805 235 FSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYG--FNTGTWLWNIARGISGE 303 (729)
Q Consensus 235 ~~~v~~fL~~LPI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG--~~~g~~L~~~arGiD~~ 303 (729)
+.....++..-.|.-++||++.....|+ .+||+|+.||++.+...+...+| ...+.++...|+-....
T Consensus 215 p~C~~~a~e~~~L~Lv~Gi~~~r~~~l~-~~GI~Ti~~LA~~~~~~~~~~~ga~~~~~~~l~~qa~~~~e~ 284 (474)
T COG2251 215 PQCESEALEEDDLSLVPGITPSRYDVLE-EVGITTIEDLADASLPILELVAGALTALAAQLVLQARARVEG 284 (474)
T ss_pred hhhhHHHhhccceeccCCCCHHHHHHHH-HcCcchHHHHHhccccchhhhhhhHHHHHHHHHHHHHhhccC
Confidence 5566777888888899999999999997 99999999999999999998888 34566777777765543
No 41
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=79.85 E-value=3.2 Score=39.13 Aligned_cols=44 Identities=27% Similarity=0.416 Sum_probs=33.5
Q ss_pred CCCcHHHHHHHHHHhCCcchhhhhcCC-----HHHHHHhhCCChHHHHHHH
Q 004805 251 KQLGGKLGTSLQNELGVTTVGDLLKFS-----EDKLQESYGFNTGTWLWNI 296 (729)
Q Consensus 251 ~GIG~k~~~~L~~~lGI~TigDLa~l~-----~~~L~~rFG~~~g~~L~~~ 296 (729)
||||++...+|. ..||+|.+||.... +..|....|.. ...+..+
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 99999999999864 33366677763 4444443
No 42
>PRK01172 ski2-like helicase; Provisional
Probab=78.47 E-value=2.5 Score=50.94 Aligned_cols=51 Identities=20% Similarity=0.327 Sum_probs=41.8
Q ss_pred CcccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhC--CChHHHHHHH
Q 004805 245 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYG--FNTGTWLWNI 296 (729)
Q Consensus 245 LPI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG--~~~g~~L~~~ 296 (729)
+|+..|||+|+..+++|. ..||+|+.||+.++.+.|.+..| ...+..++..
T Consensus 612 ~~L~~ip~~~~~~a~~l~-~~g~~~~~di~~~~~~~~~~i~~~~~~~~~~i~~~ 664 (674)
T PRK01172 612 IDLVLIPKVGRVRARRLY-DAGFKTVDDIARSSPERIKKIYGFSDTLANAIVNR 664 (674)
T ss_pred HhhcCCCCCCHHHHHHHH-HcCCCCHHHHHhCCHHHHHHHhccCHHHHHHHHHH
Confidence 588889999999999997 99999999999999999988844 4334444443
No 43
>PRK00254 ski2-like helicase; Provisional
Probab=77.45 E-value=2.2 Score=51.79 Aligned_cols=54 Identities=15% Similarity=0.253 Sum_probs=48.0
Q ss_pred cCcccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHh--hCCChHHHHHHHHh
Q 004805 244 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 298 (729)
Q Consensus 244 ~LPI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~r--FG~~~g~~L~~~ar 298 (729)
.+|+..+||+|++.+.+|. ..|+.|+.||..++.+.|.+. +|.+.+..++..++
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 3578889999999999998 999999999999999999998 77777888888765
No 44
>PF14377 DUF4414: Domain of unknown function (DUF4414)
Probab=72.06 E-value=1.7 Score=40.00 Aligned_cols=21 Identities=38% Similarity=0.730 Sum_probs=18.3
Q ss_pred CCccccccCChHHHHHHHHhh
Q 004805 684 IDPSVIDELPKEIQDEIQAWL 704 (729)
Q Consensus 684 ~~~~~~~~~~~~~~~~~~~~~ 704 (729)
|||+|+.|||.+|+.||-.=.
T Consensus 1 iDp~fLaaLPeDiR~Evl~~~ 21 (108)
T PF14377_consen 1 IDPEFLAALPEDIREEVLAQQ 21 (108)
T ss_pred CCHHHHHHCCHHHHHHHHHHH
Confidence 899999999999999994433
No 45
>PRK08609 hypothetical protein; Provisional
Probab=71.16 E-value=2.9 Score=49.51 Aligned_cols=64 Identities=25% Similarity=0.237 Sum_probs=43.3
Q ss_pred HHHHHHHHHHHHHhHhCCceeEeecCCHHHHHHhccCCCCCceeeccCCchhcccccCcccccCCCcHHHHHHHHHHhCC
Q 004805 188 GVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGV 267 (729)
Q Consensus 188 ~~~la~~IR~~I~~etGlt~S~GIA~NklLAKLAS~~~KPngqtvv~~~~v~~fL~~LPI~~L~GIG~k~~~~L~~~lGI 267 (729)
|..+|..|++-+ +|| .-..+-+|... - |..+.+ +.++||||++++.+|.+.+||
T Consensus 57 G~~ia~kI~Eil--~tG--------~~~~le~l~~~--~--------p~~~~~------l~~i~GiGpk~a~~l~~~lGi 110 (570)
T PRK08609 57 GKGTAEVIQEYR--ETG--------ESSVLQELKKE--V--------PEGLLP------LLKLPGLGGKKIAKLYKELGV 110 (570)
T ss_pred CHHHHHHHHHHH--HhC--------ChHHHHHHHhh--C--------cHHHHH------HhcCCCCCHHHHHHHHHHhCC
Confidence 456778887777 355 22345555432 1 222323 337899999999999868999
Q ss_pred cchhhhhcCC
Q 004805 268 TTVGDLLKFS 277 (729)
Q Consensus 268 ~TigDLa~l~ 277 (729)
+|+.||...-
T Consensus 111 ~tl~~L~~a~ 120 (570)
T PRK08609 111 VDKESLKEAC 120 (570)
T ss_pred CCHHHHHHHH
Confidence 9999998643
No 46
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=70.50 E-value=2.3 Score=46.96 Aligned_cols=30 Identities=20% Similarity=0.255 Sum_probs=26.3
Q ss_pred ccccCCCcHHHHHHHHHHhCCcchhhhhcCC
Q 004805 247 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFS 277 (729)
Q Consensus 247 I~~L~GIG~k~~~~L~~~lGI~TigDLa~l~ 277 (729)
+..+||||++++.+|. .+||+|+.||....
T Consensus 91 l~~i~GiGpk~a~~l~-~lGi~tl~eL~~a~ 120 (334)
T smart00483 91 FTNVFGVGPKTAAKWY-RKGIRTLEELKKNK 120 (334)
T ss_pred HHccCCcCHHHHHHHH-HhCCCCHHHHHhcc
Confidence 4478999999999998 59999999998654
No 47
>PF14377 DUF4414: Domain of unknown function (DUF4414)
Probab=69.68 E-value=2.8 Score=38.63 Aligned_cols=25 Identities=36% Similarity=0.627 Sum_probs=21.2
Q ss_pred cccCCccccccCChHHHHHHHHhhC
Q 004805 681 IEEIDPSVIDELPKEIQDEIQAWLR 705 (729)
Q Consensus 681 ~~~~~~~~~~~~~~~~~~~~~~~~~ 705 (729)
-.+|||.+++-||++||+||-+=.+
T Consensus 42 ~~~I~pefL~ALP~diR~EVl~qe~ 66 (108)
T PF14377_consen 42 PSQIDPEFLAALPPDIREEVLAQER 66 (108)
T ss_pred ccccCHHHHHhCCHHHHHHHHHHHH
Confidence 5689999999999999999865443
No 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=68.99 E-value=4.8 Score=35.86 Aligned_cols=35 Identities=23% Similarity=0.392 Sum_probs=23.4
Q ss_pred hcccccCcccccCCCcHHHHHHHHHHhCCcchhhhh
Q 004805 239 KGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLL 274 (729)
Q Consensus 239 ~~fL~~LPI~~L~GIG~k~~~~L~~~lGI~TigDLa 274 (729)
.+-|..-||+.|+|||+.++.+|. ..|+.....|.
T Consensus 13 ~EPMGeK~V~~laGIG~~lg~~L~-~~GfdKAy~vL 47 (89)
T PF02961_consen 13 SEPMGEKPVTELAGIGPVLGKRLE-EKGFDKAYVVL 47 (89)
T ss_dssp TS--TT-BGGGSTT--HHHHHHHH-HTT--BHHHHH
T ss_pred cCccCCCCccccCCcCHHHHHHHH-HCCCcHHHHHh
Confidence 344667799999999999999997 99998866654
No 49
>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=68.95 E-value=3.8 Score=47.12 Aligned_cols=59 Identities=24% Similarity=0.263 Sum_probs=42.4
Q ss_pred hcccccCcccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHH--hhCCChHHHHHHHHh
Q 004805 239 KGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQE--SYGFNTGTWLWNIAR 298 (729)
Q Consensus 239 ~~fL~~LPI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~--rFG~~~g~~L~~~ar 298 (729)
+.....-+|..++||+++....|+ ..||.|+.||+..+...|.. .+|...+..|...|+
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 334445688899999999999997 99999999999997654544 344334444444443
No 50
>PRK07758 hypothetical protein; Provisional
Probab=67.17 E-value=10 Score=34.22 Aligned_cols=36 Identities=28% Similarity=0.446 Sum_probs=30.4
Q ss_pred cCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhC
Q 004805 250 MKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYG 286 (729)
Q Consensus 250 L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG 286 (729)
+++++-+....|. +.||+|++||..++.+.|.+.=|
T Consensus 39 ~~~LSvRA~N~Lk-~AGI~TL~dLv~~te~ELl~ikn 74 (95)
T PRK07758 39 LSLLSAPARRALE-HHGIHTVEELSKYSEKEILKLHG 74 (95)
T ss_pred CccccHHHHHHHH-HcCCCcHHHHHcCCHHHHHHccC
Confidence 4677888888997 99999999999999999866543
No 51
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=65.71 E-value=13 Score=40.05 Aligned_cols=61 Identities=16% Similarity=0.346 Sum_probs=49.4
Q ss_pred cCcccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCCC--hHHHHHHHHhcCCCccc
Q 004805 244 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN--TGTWLWNIARGISGEEV 305 (729)
Q Consensus 244 ~LPI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~~--~g~~L~~~arGiD~~~V 305 (729)
..|+..||++|.....+|. ..||.+++||..++.+.+...+|.. .|..+++.++....-.|
T Consensus 150 ~~~L~Qlp~i~~~~~~~l~-~~~i~s~~~l~~~~~~~~~~ll~~~~~~~~~i~~~~~~~P~l~v 212 (312)
T smart00611 150 DSPLLQLPHLPEEILKRLE-KKKVLSLEDLLELEDEERGELLGLLDAEGERVYKVLSRLPKLNI 212 (312)
T ss_pred CCccccCCCCCHHHHHHHH-hCCCCCHHHHHhcCHHHHHHHHcCCHHHHHHHHHHHHhCCccee
Confidence 4688899999999999997 8899999999999999998887742 46777777766544333
No 52
>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=65.59 E-value=8.5 Score=41.46 Aligned_cols=60 Identities=23% Similarity=0.364 Sum_probs=42.7
Q ss_pred CcccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCC--ChHHHHHHHHhcCCCccc
Q 004805 245 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF--NTGTWLWNIARGISGEEV 305 (729)
Q Consensus 245 LPI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~--~~g~~L~~~arGiD~~~V 305 (729)
.|+..||++|.+...+|. ..||.|++||.+++...+...++. ..|..+.+.++.+..-.+
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 688899999999999997 899999999999999999998873 247777887776654333
No 53
>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=64.97 E-value=4.2 Score=44.32 Aligned_cols=29 Identities=34% Similarity=0.493 Sum_probs=26.0
Q ss_pred ccccCCCcHHHHHHHHHHhCCcchhhhhcC
Q 004805 247 IKKMKQLGGKLGTSLQNELGVTTVGDLLKF 276 (729)
Q Consensus 247 I~~L~GIG~k~~~~L~~~lGI~TigDLa~l 276 (729)
+..+||||++++++|. .+||+|+.||...
T Consensus 87 l~~i~GiGpk~a~~l~-~lGi~sl~dL~~a 115 (307)
T cd00141 87 LLRVPGVGPKTARKLY-ELGIRTLEDLRKA 115 (307)
T ss_pred HHcCCCCCHHHHHHHH-HcCCCCHHHHHHH
Confidence 3478999999999998 9999999999874
No 54
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=63.67 E-value=7.6 Score=45.94 Aligned_cols=54 Identities=17% Similarity=0.172 Sum_probs=44.5
Q ss_pred cCcccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHh-hCCChHHHHHHHHhc
Q 004805 244 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES-YGFNTGTWLWNIARG 299 (729)
Q Consensus 244 ~LPI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~r-FG~~~g~~L~~~arG 299 (729)
.-.+.+++|||++..+.|...+ .|+..+..++.++|.+. +|.+.+..++..++|
T Consensus 513 ~S~Ld~I~GiG~kr~~~Ll~~F--gs~~~ik~As~eeL~~vgi~~~~A~~I~~~l~~ 567 (567)
T PRK14667 513 KDILDKIKGIGEVKKEIIYRNF--KTLYDFLKADDEELKKLGIPPSVKQEVKKYLSG 567 (567)
T ss_pred cCccccCCCCCHHHHHHHHHHh--CCHHHHHhCCHHHHHHcCCCHHHHHHHHHHhcC
Confidence 4567899999999999997444 58999999999999998 445567888888776
No 55
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=62.88 E-value=8.4 Score=46.50 Aligned_cols=49 Identities=20% Similarity=0.294 Sum_probs=40.2
Q ss_pred cccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHH--hhCCChHHHHHHH
Q 004805 248 KKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQE--SYGFNTGTWLWNI 296 (729)
Q Consensus 248 ~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~--rFG~~~g~~L~~~ 296 (729)
-+++|+|+++.++|-+..+|.++.||..+....|.. .||.+.+..|++.
T Consensus 448 l~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~ll~~ 498 (665)
T PRK07956 448 MDIDGLGEKIIEQLFEKGLIHDPADLFKLTAEDLLGLEGFGEKSAQNLLDA 498 (665)
T ss_pred cCCCCcCHHHHHHHHHcCCCCCHHHHHhcCHHHHhcCcCcchHHHHHHHHH
Confidence 467999999999998778899999999999888876 5787666655543
No 56
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=62.41 E-value=7.6 Score=39.46 Aligned_cols=56 Identities=13% Similarity=0.091 Sum_probs=43.1
Q ss_pred ccccCCCcHHHHHHHHHHhCCcchh-hhhcCCHHHHHHh--hCCChHHHHHHHHhcCCC
Q 004805 247 IKKMKQLGGKLGTSLQNELGVTTVG-DLLKFSEDKLQES--YGFNTGTWLWNIARGISG 302 (729)
Q Consensus 247 I~~L~GIG~k~~~~L~~~lGI~Tig-DLa~l~~~~L~~r--FG~~~g~~L~~~arGiD~ 302 (729)
+..++|||++++.++.+.+|..++- .+...+...|.+. +|.+.+..++..+++...
T Consensus 75 L~~i~GIGpk~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~~~l~~~~~ 133 (192)
T PRK00116 75 LISVSGVGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELKDKLA 133 (192)
T ss_pred HhcCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHHhh
Confidence 4468999999999887678887664 3556688889887 667778888888877653
No 57
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=61.80 E-value=8.2 Score=47.61 Aligned_cols=52 Identities=23% Similarity=0.314 Sum_probs=46.3
Q ss_pred ccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhC-CChHHHHHHHHhcC
Q 004805 247 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYG-FNTGTWLWNIARGI 300 (729)
Q Consensus 247 I~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG-~~~g~~L~~~arGi 300 (729)
|..|||||++.+.+|. -.+.++.+|+.++.+.|....| .+.|..+|++.+..
T Consensus 759 L~~lPgI~~~~a~~ll--~~f~si~~l~~as~eeL~~~iG~~~~A~~i~~fl~~~ 811 (814)
T TIGR00596 759 LLKLPGVTKKNYRNLR--KKVKSIRELAKLSQNELNELIGDEEAAKRLYDFLRTE 811 (814)
T ss_pred HHHCCCCCHHHHHHHH--HHcCCHHHHHhCCHHHHHHHhCCHHHHHHHHHHhccc
Confidence 5588999999999997 4588999999999999999999 88899999988754
No 58
>PTZ00035 Rad51 protein; Provisional
Probab=59.66 E-value=11 Score=41.84 Aligned_cols=55 Identities=18% Similarity=0.176 Sum_probs=45.0
Q ss_pred Cccccc--CCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCCCh--HHHHHHHHhcC
Q 004805 245 LPIKKM--KQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNT--GTWLWNIARGI 300 (729)
Q Consensus 245 LPI~~L--~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~~~--g~~L~~~arGi 300 (729)
.+|.+| +||++.+.++|. .-||+|+.||+..++..|.+..|... +..+...++-.
T Consensus 21 ~~~~~l~~~g~~~~~~~kL~-~~g~~t~~~~~~~~~~~L~~~~gis~~~~~~i~~~~~~~ 79 (337)
T PTZ00035 21 QEIEKLQSAGINAADIKKLK-EAGICTVESVAYATKKDLCNIKGISEAKVEKIKEAASKL 79 (337)
T ss_pred ccHHHHhcCCCCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHhhCCCHHHHHHHHHHHHHh
Confidence 367777 779999999997 99999999999999999999999642 34566655544
No 59
>COG3377 Uncharacterized conserved protein [Function unknown]
Probab=59.35 E-value=3.1 Score=37.01 Aligned_cols=26 Identities=38% Similarity=0.584 Sum_probs=22.9
Q ss_pred EEEEcCHHHHHcCCCCCCCHHHHHhh
Q 004805 51 GLIAVGYEARNYGVKRSMRGDEAKEV 76 (729)
Q Consensus 51 ~ViA~SYeARk~GVk~GM~~~eA~~L 76 (729)
-|+.++++|-+.||++||.+.+|+..
T Consensus 69 ~i~evT~~Ae~lGI~~Gm~~r~aL~k 94 (95)
T COG3377 69 PIVEVTSAAEELGIKRGMKGREALEK 94 (95)
T ss_pred hHHHHHHHHHHhCCCccchHHHHHhc
Confidence 46679999999999999999999853
No 60
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=59.28 E-value=7.7 Score=43.02 Aligned_cols=44 Identities=20% Similarity=0.332 Sum_probs=39.6
Q ss_pred cCccccc--CCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCCC
Q 004805 244 SLPIKKM--KQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN 288 (729)
Q Consensus 244 ~LPI~~L--~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~~ 288 (729)
..+|.+| .||+.....+|+ .-||.|+.||+..++..|.+.+|..
T Consensus 25 ~~~~~~l~~~gi~~~~i~kL~-~~g~~T~~~~~~~~~~~L~~i~~is 70 (342)
T PLN03186 25 PFPIEQLQASGIAALDIKKLK-DAGIHTVESLAYAPKKDLLQIKGIS 70 (342)
T ss_pred CccHHHHHhCCCCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHhcCCC
Confidence 3478888 679999999997 9999999999999999999999975
No 61
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=58.96 E-value=6.4 Score=47.63 Aligned_cols=31 Identities=39% Similarity=0.618 Sum_probs=28.0
Q ss_pred CcccccCCCcHHHHHHHHHHhCCcchhhhhcC
Q 004805 245 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKF 276 (729)
Q Consensus 245 LPI~~L~GIG~k~~~~L~~~lGI~TigDLa~l 276 (729)
.||+.|.|||++.++.|. ++||.|+.||...
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 9999999998753
No 62
>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=56.11 E-value=13 Score=44.79 Aligned_cols=51 Identities=25% Similarity=0.347 Sum_probs=40.8
Q ss_pred cccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHH--hhCCChHHHHHHHHh
Q 004805 248 KKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQE--SYGFNTGTWLWNIAR 298 (729)
Q Consensus 248 ~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~--rFG~~~g~~L~~~ar 298 (729)
-+++|+|+++..+|-+..+|+++.||..+....|.. .||.+.+..|++...
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 367999999999998667799999999999888876 467666666665444
No 63
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=55.96 E-value=20 Score=43.25 Aligned_cols=62 Identities=11% Similarity=0.201 Sum_probs=50.7
Q ss_pred cCcccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHh--hCCChHHHHHHHHhcCCCccccc
Q 004805 244 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIARGISGEEVQA 307 (729)
Q Consensus 244 ~LPI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~r--FG~~~g~~L~~~arGiD~~~V~~ 307 (729)
...+.+|+|||++...+|.+.+| ++.+|..++.+.|.+. +|...+..+++.+.--...||..
T Consensus 607 ~s~L~~IpGiG~kr~~~LL~~Fg--S~~~i~~As~eel~~v~gi~~~~A~~i~~~~~~~~~~~~~~ 670 (691)
T PRK14672 607 VLSFERLPHVGKVRAHRLLAHFG--SFRSLQSATPQDIATAIHIPLTQAHTILHAATRSTTAPVRE 670 (691)
T ss_pred ccccccCCCCCHHHHHHHHHHhc--CHHHHHhCCHHHHHhCCCCCHHHHHHHHHHhhcccccchhH
Confidence 45788999999999999875555 8899999999999998 66667888888877666667754
No 64
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=55.54 E-value=11 Score=39.18 Aligned_cols=36 Identities=25% Similarity=0.481 Sum_probs=32.1
Q ss_pred cccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHH
Q 004805 246 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQ 282 (729)
Q Consensus 246 PI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~ 282 (729)
.+..+.|||++++.+|. ..||.+..+|+.++.+.+.
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 46789999999999997 9999999999999887554
No 65
>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=55.27 E-value=13 Score=40.74 Aligned_cols=36 Identities=25% Similarity=0.240 Sum_probs=33.8
Q ss_pred CCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCCC
Q 004805 252 QLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN 288 (729)
Q Consensus 252 GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~~ 288 (729)
||++.+.++|. .-||.|+.||+..++..|.+.+|..
T Consensus 8 ~~~~~~~~~l~-~~g~~t~~~~~~~~~~~L~~i~~ls 43 (316)
T TIGR02239 8 GITAADIKKLQ-EAGLHTVESVAYAPKKQLLEIKGIS 43 (316)
T ss_pred CCCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHHhCCC
Confidence 59999999997 9999999999999999999999964
No 66
>PRK14973 DNA topoisomerase I; Provisional
Probab=55.26 E-value=24 Score=44.26 Aligned_cols=80 Identities=19% Similarity=0.097 Sum_probs=53.4
Q ss_pred HHHHHHhc-cCCCCCceeeccCCchhcccccCcccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCCC--hHH
Q 004805 215 KMLAKLAS-GMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN--TGT 291 (729)
Q Consensus 215 klLAKLAS-~~~KPngqtvv~~~~v~~fL~~LPI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~~--~g~ 291 (729)
.-++++|+ ++.+|+...+.... .--..-++..++|+|+++.++|. .-||.++.||+..+.+.|.++=|.. ...
T Consensus 849 ~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~el~~vkg~ge~t~~~l~-~ag~~~~e~l~~~d~~~la~~~~i~~k~~~ 924 (936)
T PRK14973 849 CRHAKLVCEKLGRPVPEKISKAA---FERGRAELLSVPGLGETTLEKLY-LAGVYDGDLLVSADPKKLAKVTGIDEKKLR 924 (936)
T ss_pred HHHHHHHHHHhcCCCchhhhhhh---hcccchhhhhccCCCHHHHHHHH-HcCCCCHHHhccCCHHHHhhhcCCCHHHHH
Confidence 34556666 77777654433110 00011115678999999999996 9999999999999999999988863 233
Q ss_pred HHHHHHh
Q 004805 292 WLWNIAR 298 (729)
Q Consensus 292 ~L~~~ar 298 (729)
.+..+++
T Consensus 925 ~~~~~~~ 931 (936)
T PRK14973 925 NLQAYAK 931 (936)
T ss_pred HHHHHHh
Confidence 4444443
No 67
>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=55.15 E-value=8 Score=27.48 Aligned_cols=16 Identities=19% Similarity=0.393 Sum_probs=12.4
Q ss_pred ccccCCCcHHHHHHHH
Q 004805 247 IKKMKQLGGKLGTSLQ 262 (729)
Q Consensus 247 I~~L~GIG~k~~~~L~ 262 (729)
+.+|||||++++..+.
T Consensus 13 L~~lpGIG~~tA~~I~ 28 (30)
T PF00633_consen 13 LMKLPGIGPKTANAIL 28 (30)
T ss_dssp HHTSTT-SHHHHHHHH
T ss_pred HHhCCCcCHHHHHHHH
Confidence 4479999999998875
No 68
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=54.63 E-value=15 Score=44.03 Aligned_cols=51 Identities=20% Similarity=0.285 Sum_probs=42.5
Q ss_pred CcccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCCChHHHHHHHH
Q 004805 245 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIA 297 (729)
Q Consensus 245 LPI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~~~g~~L~~~a 297 (729)
..+..++|||++++..|.+.+| |+.+|...+.+.|.+.+|.+.+..++.+.
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 3457889999999999975555 88999999999999889988888887764
No 69
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=54.23 E-value=14 Score=44.53 Aligned_cols=51 Identities=14% Similarity=0.188 Sum_probs=41.6
Q ss_pred CcccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHh--hCCChHHHHHHHH
Q 004805 245 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIA 297 (729)
Q Consensus 245 LPI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~r--FG~~~g~~L~~~a 297 (729)
-.+..+||||++...+|.+.+| ++.++...+.+.|.+. +|...+..+++.+
T Consensus 637 s~L~~IPGIGpkr~k~LL~~FG--Sle~I~~AS~eELa~V~Gig~k~Ae~I~~~L 689 (694)
T PRK14666 637 GELQRVEGIGPATARLLWERFG--SLQAMAAAGEEGLAAVPGIGPARAAALHEHL 689 (694)
T ss_pred hHHhhCCCCCHHHHHHHHHHhC--CHHHHHhcCHHHHHhcCCcCHHHHHHHHHHH
Confidence 4577889999999999987888 9999999999999887 6665566666544
No 70
>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=53.07 E-value=15 Score=40.23 Aligned_cols=47 Identities=15% Similarity=0.144 Sum_probs=38.2
Q ss_pred CCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCCCh--HHHHHHHHh
Q 004805 251 KQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNT--GTWLWNIAR 298 (729)
Q Consensus 251 ~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~~~--g~~L~~~ar 298 (729)
.||+..+.++|+ .-||+|+.||+..++..|.+..|... ...+.+.++
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 479999999997 99999999999999999999999632 334444443
No 71
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=53.00 E-value=10 Score=41.82 Aligned_cols=36 Identities=19% Similarity=0.373 Sum_probs=31.5
Q ss_pred cccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHH
Q 004805 246 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQ 282 (729)
Q Consensus 246 PI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~ 282 (729)
.++++.|||++++++|+ .+||++..|++.++.+...
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 36788999999999997 9999999999999876443
No 72
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=52.91 E-value=13 Score=41.21 Aligned_cols=56 Identities=18% Similarity=0.227 Sum_probs=44.3
Q ss_pred cCccccc--CCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCCCh--HHHHHHHHhcC
Q 004805 244 SLPIKKM--KQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNT--GTWLWNIARGI 300 (729)
Q Consensus 244 ~LPI~~L--~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~~~--g~~L~~~arGi 300 (729)
..+|.+| .||++.+.++|+ .-||+|+.||+..++..|.+..|... ...+...++..
T Consensus 28 ~~~~~~l~~~g~~~~~~~kL~-~~g~~tv~~~~~~~~~~L~~~~g~s~~~~~ki~~~a~~~ 87 (344)
T PLN03187 28 FESIDKLISQGINAGDVKKLQ-DAGIYTCNGLMMHTKKNLTGIKGLSEAKVDKICEAAEKL 87 (344)
T ss_pred ccCHHHHhhCCCCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHHh
Confidence 4567777 579999999997 99999999999999999999998642 34455455543
No 73
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=50.99 E-value=19 Score=42.75 Aligned_cols=53 Identities=26% Similarity=0.404 Sum_probs=43.1
Q ss_pred cCcccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHh--hCCChHHHHHHHHh
Q 004805 244 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 298 (729)
Q Consensus 244 ~LPI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~r--FG~~~g~~L~~~ar 298 (729)
...+.+++|||++..+.|.+.+| ++..+..++.++|.+. ++.+.+..++..++
T Consensus 513 ~s~L~~I~GiG~kr~~~LL~~Fg--s~~~I~~As~eeL~~v~gi~~~~A~~I~~~l~ 567 (574)
T PRK14670 513 KLNYTKIKGIGEKKAKKILKSLG--TYKDILLLNEDEIAEKMKINIKMAKKIKKFAE 567 (574)
T ss_pred ccccccCCCCCHHHHHHHHHHhC--CHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHH
Confidence 35788999999999999975555 8999999999999999 55556777877664
No 74
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=47.25 E-value=12 Score=44.66 Aligned_cols=31 Identities=39% Similarity=0.734 Sum_probs=28.0
Q ss_pred CcccccCCCcHHHHHHHHHHhCCcchhhhhcC
Q 004805 245 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKF 276 (729)
Q Consensus 245 LPI~~L~GIG~k~~~~L~~~lGI~TigDLa~l 276 (729)
.|+..+.|||++++++|. ++||+|+.||+-.
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 389999999999999996 9999999998753
No 75
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=45.89 E-value=25 Score=42.74 Aligned_cols=50 Identities=20% Similarity=0.207 Sum_probs=39.7
Q ss_pred cccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHh--hCCChHHHHHHHH
Q 004805 248 KKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIA 297 (729)
Q Consensus 248 ~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~r--FG~~~g~~L~~~a 297 (729)
-++.|+|+++.++|.+..+|+++.||..+..+.|... ||.+.+..|++..
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 3679999999999985555899999999999888764 7876666666544
No 76
>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=44.89 E-value=28 Score=26.76 Aligned_cols=33 Identities=36% Similarity=0.406 Sum_probs=28.6
Q ss_pred cHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCC
Q 004805 254 GGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF 287 (729)
Q Consensus 254 G~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~ 287 (729)
+..+..+|. .-|+.|+.+|+.++...|...-|.
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 456788897 899999999999999999888774
No 77
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=42.30 E-value=22 Score=40.16 Aligned_cols=36 Identities=22% Similarity=0.426 Sum_probs=31.7
Q ss_pred cccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHH
Q 004805 246 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQ 282 (729)
Q Consensus 246 PI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~ 282 (729)
.++.|.|||++++.+|+ .+||++..+++.++.+.+.
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 36788999999999997 9999999999999877543
No 78
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=41.27 E-value=32 Score=41.25 Aligned_cols=54 Identities=11% Similarity=0.103 Sum_probs=45.4
Q ss_pred cCcccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCCChHHHHHHHHhc
Q 004805 244 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARG 299 (729)
Q Consensus 244 ~LPI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~~~g~~L~~~arG 299 (729)
.-.+..|||||++...+|.+.+ .++.++..++.+.|.+.+|.+.+..++..++.
T Consensus 551 ~S~L~~IpGIG~kr~~~LL~~F--gSi~~I~~As~eeL~~vi~~k~A~~I~~~l~~ 604 (624)
T PRK14669 551 TSELLEIPGVGAKTVQRLLKHF--GSLERVRAATETQLAAVVGRAAAEAIIAHFTT 604 (624)
T ss_pred HHHHhcCCCCCHHHHHHHHHHc--CCHHHHHhCCHHHHHHHhCHHHHHHHHHHhcC
Confidence 3467789999999999997444 48899999999999999998888889888764
No 79
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=39.62 E-value=8.4 Score=38.39 Aligned_cols=41 Identities=24% Similarity=0.500 Sum_probs=35.8
Q ss_pred ccccccCCccccccCChHHHHHHHHhhCCCCCCCcccCCcc
Q 004805 678 KLRIEEIDPSVIDELPKEIQDEIQAWLRPSKRPHRVKQGFT 718 (729)
Q Consensus 678 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 718 (729)
.|.|.||..-+|+-.-.||-++++.++||.|.|.--++--|
T Consensus 24 e~eiiei~a~lv~~id~~vvd~F~syVRP~~~P~Lt~~Cks 64 (210)
T COG5018 24 EFEIIEIEAGLVKSIDDEVVDTFSSYVRPKKFPKLTKRCKS 64 (210)
T ss_pred hceeeeehhhHHHHhhHHHHHHHHHhcCcccCchHHHHHHH
Confidence 46699999999999999999999999999999987665333
No 80
>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=35.22 E-value=38 Score=36.92 Aligned_cols=54 Identities=26% Similarity=0.364 Sum_probs=41.1
Q ss_pred cccCcccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHH--hhCCChHHHHHHHH
Q 004805 242 LDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQE--SYGFNTGTWLWNIA 297 (729)
Q Consensus 242 L~~LPI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~--rFG~~~g~~L~~~a 297 (729)
+-.++|..| ++.-+...-|. +.||+|++||..++.+.|.+ -||.+....+.+.+
T Consensus 232 ~~~~~I~~L-~LSvR~~n~Lk-~~~I~ti~dL~~~~~~~l~~~~n~G~ksl~ei~~~l 287 (297)
T TIGR02027 232 LLSIKIEEL-DLSVRSYNCLK-RAGIHTLGELVSKSEEELLKIKNFGKKSLTEIKEKL 287 (297)
T ss_pred hccccHHHh-CccHHHHhHHH-HcCCcCHHHHHhCCHHHHhhCCCCChhhHHHHHHHH
Confidence 455688888 68888999996 99999999999999998754 46765544444443
No 81
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=32.24 E-value=49 Score=39.57 Aligned_cols=53 Identities=11% Similarity=0.218 Sum_probs=42.1
Q ss_pred cCcccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHh--hCCChHHHHHHHHh
Q 004805 244 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 298 (729)
Q Consensus 244 ~LPI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~r--FG~~~g~~L~~~ar 298 (729)
..++..+||||++...+|.+.+| ++.++...+.+.|.+. +|...+..++.+.+
T Consensus 542 ~s~L~~IpGIG~k~~k~Ll~~Fg--S~~~i~~As~eeL~~v~Gig~~~A~~I~~~l~ 596 (598)
T PRK00558 542 TSALDDIPGIGPKRRKALLKHFG--SLKAIKEASVEELAKVPGISKKLAEAIYEALH 596 (598)
T ss_pred hhhHhhCCCcCHHHHHHHHHHcC--CHHHHHhCCHHHHhhcCCcCHHHHHHHHHHhc
Confidence 46778999999999999975554 6899999999999888 66666666766543
No 82
>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=32.23 E-value=49 Score=40.00 Aligned_cols=32 Identities=22% Similarity=0.341 Sum_probs=17.8
Q ss_pred CCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHh
Q 004805 251 KQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES 284 (729)
Q Consensus 251 ~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~r 284 (729)
||||.+++++|.+.+| ++.+|..++.+.|.+.
T Consensus 504 pgVG~~~ak~L~~~f~--sl~~l~~As~eeL~~i 535 (652)
T TIGR00575 504 RHVGEVTAKNLAKHFG--TLDKLKAASLEELLSV 535 (652)
T ss_pred CCcCHHHHHHHHHHhC--CHHHHHhCCHHHHhcC
Confidence 5666666665554444 5555555555555444
No 83
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=32.21 E-value=45 Score=36.59 Aligned_cols=51 Identities=24% Similarity=0.364 Sum_probs=39.7
Q ss_pred ccCcccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHh--hCCChHHHHHH
Q 004805 243 DSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWN 295 (729)
Q Consensus 243 ~~LPI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~r--FG~~~g~~L~~ 295 (729)
-.++|..| ++.-++..-|. +.||+|++||.+++.+.|.+. ||.+....+.+
T Consensus 247 l~~~I~~L-~LS~R~~n~Lk-~~~I~ti~dL~~~~~~~l~~~~n~G~ksl~ei~~ 299 (310)
T PRK05182 247 LLRPIEEL-ELSVRSYNCLK-RAGINTIGDLVQRTEEELLKTRNLGKKSLEEIKE 299 (310)
T ss_pred ccccHHHh-ccchHHHHHHH-HcCCcCHHHHHhCCHHHHhcCCCCChhhHHHHHH
Confidence 36788888 78889999997 999999999999999988654 56544443333
No 84
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=31.35 E-value=42 Score=36.72 Aligned_cols=29 Identities=21% Similarity=0.178 Sum_probs=25.8
Q ss_pred cccCCCcHHHHHHHHHHhCCcchhhhhcCC
Q 004805 248 KKMKQLGGKLGTSLQNELGVTTVGDLLKFS 277 (729)
Q Consensus 248 ~~L~GIG~k~~~~L~~~lGI~TigDLa~l~ 277 (729)
+.++|||.+++++.. ++|++|+.|++.-+
T Consensus 100 tnifGvG~ktA~~Wy-~~GfrTled~Rk~~ 128 (353)
T KOG2534|consen 100 TNIFGVGLKTAEKWY-REGFRTLEDVRKKP 128 (353)
T ss_pred HHHhccCHHHHHHHH-HhhhhHHHHHHhCH
Confidence 578999999999997 99999999999543
No 85
>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=30.78 E-value=54 Score=35.74 Aligned_cols=48 Identities=27% Similarity=0.569 Sum_probs=34.1
Q ss_pred ccCCCcH--HHHHHHHHHhCCcchhhhhcC---CHHHHHHhhCCChHHHHHHHH
Q 004805 249 KMKQLGG--KLGTSLQNELGVTTVGDLLKF---SEDKLQESYGFNTGTWLWNIA 297 (729)
Q Consensus 249 ~L~GIG~--k~~~~L~~~lGI~TigDLa~l---~~~~L~~rFG~~~g~~L~~~a 297 (729)
.|-.||+ ..-++|. .-||+|++|++++ ++..|++.||..+-...|...
T Consensus 166 RLe~Igk~G~~hk~L~-~~~I~tV~dFl~l~~~d~~~Lr~ilg~~ms~k~We~~ 218 (299)
T PF07887_consen 166 RLEKIGKDGAFHKRLK-KNGINTVEDFLKLLNKDPQKLREILGSGMSNKMWETT 218 (299)
T ss_pred hhhhccccCHHHHHHH-HcCCccHHHHHHHHhcCHHHHHHHHhcCCChhhHHHH
Confidence 4444443 4557886 8999999998874 788999999954444555544
No 86
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=30.52 E-value=34 Score=23.10 Aligned_cols=16 Identities=19% Similarity=0.320 Sum_probs=13.8
Q ss_pred ccccCCCcHHHHHHHH
Q 004805 247 IKKMKQLGGKLGTSLQ 262 (729)
Q Consensus 247 I~~L~GIG~k~~~~L~ 262 (729)
+..++|||++++.+|.
T Consensus 3 L~~i~GiG~k~A~~il 18 (26)
T smart00278 3 LLKVPGIGPKTAEKIL 18 (26)
T ss_pred hhhCCCCCHHHHHHHH
Confidence 4578999999999886
No 87
>PF08004 DUF1699: Protein of unknown function (DUF1699); InterPro: IPR012546 This family contains many archaeal proteins which have very conserved sequences.
Probab=30.50 E-value=84 Score=29.97 Aligned_cols=35 Identities=23% Similarity=0.394 Sum_probs=27.6
Q ss_pred CCHHHHHhhCCCcEEEEccccCCCCChHHHHHHHHHHHHHHH
Q 004805 68 MRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILA 109 (729)
Q Consensus 68 M~~~eA~~LCP~L~vv~Vp~~~~k~d~~~Yr~~S~~I~~iL~ 109 (729)
.-+....+.||+|.++++|+ ..|+..|..+-..|.
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 34677888999999999984 577888887776664
No 88
>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=28.88 E-value=53 Score=33.45 Aligned_cols=51 Identities=20% Similarity=0.187 Sum_probs=36.0
Q ss_pred cccCCCcHHHHHHHHHHhCCcchhhhhcC----CHHHHHHh--hCCChHHHHHHHHhcCC
Q 004805 248 KKMKQLGGKLGTSLQNELGVTTVGDLLKF----SEDKLQES--YGFNTGTWLWNIARGIS 301 (729)
Q Consensus 248 ~~L~GIG~k~~~~L~~~lGI~TigDLa~l----~~~~L~~r--FG~~~g~~L~~~arGiD 301 (729)
-.++|||+|++..+ +++.++.+|... +...|.+. ||+++++++.-.+++.-
T Consensus 75 ~~V~GIGpK~Al~i---L~~~~~~el~~aI~~~d~~~L~~ipGiGkKtAerIileLk~k~ 131 (191)
T TIGR00084 75 IKVNGVGPKLALAI---LSNMSPEEFVYAIETEEVKALVKIPGVGKKTAERLLLELKGKL 131 (191)
T ss_pred hCCCCCCHHHHHHH---HhcCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHhhh
Confidence 47799999998655 677778777753 45677664 55667777776666553
No 89
>PRK13766 Hef nuclease; Provisional
Probab=28.51 E-value=60 Score=39.77 Aligned_cols=50 Identities=22% Similarity=0.408 Sum_probs=40.5
Q ss_pred ccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHh--hCCChHHHHHHHHh
Q 004805 247 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 298 (729)
Q Consensus 247 I~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~r--FG~~~g~~L~~~ar 298 (729)
+..+||||++.+.+|.+.+| ++.++..++.+.|... +|.+.+..++...+
T Consensus 717 L~~ipgig~~~a~~Ll~~fg--s~~~i~~as~~~L~~i~Gig~~~a~~i~~~~~ 768 (773)
T PRK13766 717 VESLPDVGPVLARNLLEHFG--SVEAVMTASEEELMEVEGIGEKTAKRIREVVT 768 (773)
T ss_pred HhcCCCCCHHHHHHHHHHcC--CHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHh
Confidence 67889999999999876665 7999999999999887 77666776766543
No 90
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=27.83 E-value=37 Score=37.20 Aligned_cols=34 Identities=35% Similarity=0.428 Sum_probs=28.3
Q ss_pred CcccccCCCcHHHHHHHHHHhCCcchhhhhcCCH
Q 004805 245 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSE 278 (729)
Q Consensus 245 LPI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~ 278 (729)
.|+-+++|+|+|...+|-+.+||+++.+|.....
T Consensus 93 ~~Ll~v~GlGpkKi~~Ly~elgi~~~e~l~~a~~ 126 (326)
T COG1796 93 EPLLKVPGLGPKKIVSLYKELGIKDLEELQEALE 126 (326)
T ss_pred HHHhhCCCCCcHHHHHHHHHHCcccHHHHHHHHH
Confidence 3666899999977777877999999999987654
No 91
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=27.29 E-value=76 Score=33.86 Aligned_cols=50 Identities=24% Similarity=0.387 Sum_probs=38.4
Q ss_pred ccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCC--ChHHHHHHHHh
Q 004805 247 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF--NTGTWLWNIAR 298 (729)
Q Consensus 247 I~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~--~~g~~L~~~ar 298 (729)
+..+||||.+++.+|. .-+.++++++.++...|.+.-|. +.+..++...+
T Consensus 184 l~s~pgig~~~a~~ll--~~fgS~~~~~tas~~eL~~v~gig~k~A~~I~~~~~ 235 (254)
T COG1948 184 LESIPGIGPKLAERLL--KKFGSVEDVLTASEEELMKVKGIGEKKAREIYRFLR 235 (254)
T ss_pred HHcCCCccHHHHHHHH--HHhcCHHHHhhcCHHHHHHhcCccHHHHHHHHHHHh
Confidence 3466799999999996 44559999999999999999996 34555555443
No 92
>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=26.59 E-value=78 Score=29.06 Aligned_cols=35 Identities=14% Similarity=0.392 Sum_probs=25.0
Q ss_pred ccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHH
Q 004805 247 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKL 281 (729)
Q Consensus 247 I~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L 281 (729)
++.+.|||..++..+...+||..-.-+-.++.+++
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 56899999999999888999975444444444443
No 93
>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=26.57 E-value=50 Score=26.84 Aligned_cols=47 Identities=28% Similarity=0.455 Sum_probs=37.9
Q ss_pred ccCCchhcccccCcccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCCC
Q 004805 233 VPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN 288 (729)
Q Consensus 233 v~~~~v~~fL~~LPI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~~ 288 (729)
++++++.+||..+ |+ .+....+. ..||..+..|..++.+.|. .+|+.
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 4556778888755 55 46777786 8999999999999999997 89984
No 94
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=26.46 E-value=77 Score=37.66 Aligned_cols=47 Identities=17% Similarity=0.326 Sum_probs=38.2
Q ss_pred ccCCCcHHHHHHHHHHhC-CcchhhhhcCCHHHHHH--hhCCChHHHHHHH
Q 004805 249 KMKQLGGKLGTSLQNELG-VTTVGDLLKFSEDKLQE--SYGFNTGTWLWNI 296 (729)
Q Consensus 249 ~L~GIG~k~~~~L~~~lG-I~TigDLa~l~~~~L~~--rFG~~~g~~L~~~ 296 (729)
++-|+|.++.++|- ..| |+++.||..+....|.. .||.+....|++.
T Consensus 429 dI~GlGe~~i~~L~-~~G~i~~~~Diy~L~~~~l~~l~gfgeks~~nll~a 478 (562)
T PRK08097 429 GLDGIGEGTWRALH-QTGLFEHLFSWLALTPEQLANTPGIGKARAEQLWHQ 478 (562)
T ss_pred CCCCcCHHHHHHHH-HcCCcCCHHHHhcCCHHHHhcCcCccHHHHHHHHHH
Confidence 56799999999998 677 69999999999888876 4787666666654
No 95
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=25.82 E-value=31 Score=35.48 Aligned_cols=45 Identities=24% Similarity=0.341 Sum_probs=28.4
Q ss_pred eecCCHHHHHHhccCCCCCce-eeccCCchhcccccCcccccCCCcHHHHHHHH
Q 004805 210 GIAHNKMLAKLASGMNKPAQQ-TTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQ 262 (729)
Q Consensus 210 GIA~NklLAKLAS~~~KPngq-tvv~~~~v~~fL~~LPI~~L~GIG~k~~~~L~ 262 (729)
|||+---||-|.+.- |+.. ..|..+++. -+.++||||+|++++|.
T Consensus 80 GIGpK~ALaiLs~~~--~~~l~~aI~~~d~~------~L~k~PGIGkKtAeriv 125 (201)
T COG0632 80 GIGPKLALAILSNLD--PEELAQAIANEDVK------ALSKIPGIGKKTAERIV 125 (201)
T ss_pred CccHHHHHHHHcCCC--HHHHHHHHHhcChH------hhhcCCCCCHHHHHHHH
Confidence 899888888776521 1111 122223332 35688999999999986
No 96
>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=22.92 E-value=91 Score=29.12 Aligned_cols=36 Identities=11% Similarity=0.279 Sum_probs=25.9
Q ss_pred cccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHH
Q 004805 246 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKL 281 (729)
Q Consensus 246 PI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L 281 (729)
.++.+.|||..++..+...+||..-.-+-.++.+++
T Consensus 16 aL~~i~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi 51 (113)
T TIGR03631 16 ALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEEL 51 (113)
T ss_pred eeeeeecccHHHHHHHHHHhCcCcccccccCCHHHH
Confidence 457899999999999988999974333444444444
No 97
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=21.92 E-value=87 Score=34.66 Aligned_cols=55 Identities=20% Similarity=0.355 Sum_probs=42.4
Q ss_pred ccccCcccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHH--HHhhCCChHHHHHHHH
Q 004805 241 LLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKL--QESYGFNTGTWLWNIA 297 (729)
Q Consensus 241 fL~~LPI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L--~~rFG~~~g~~L~~~a 297 (729)
.+..++|.+| .+.-+...-|. +.||+|+|||.+.+.+.| .+-||.+....+.+.+
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 4556678877 57777888896 999999999999999887 4568877666565555
No 98
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=21.86 E-value=97 Score=30.59 Aligned_cols=41 Identities=17% Similarity=0.334 Sum_probs=30.5
Q ss_pred cccccCCCcHHHHHHHHHHhCCc---chhhhhcCCHHHHHHhhC
Q 004805 246 PIKKMKQLGGKLGTSLQNELGVT---TVGDLLKFSEDKLQESYG 286 (729)
Q Consensus 246 PI~~L~GIG~k~~~~L~~~lGI~---TigDLa~l~~~~L~~rFG 286 (729)
.|+.+.|||..++..+...+||. +++||-.-....|...+.
T Consensus 31 aLt~I~GIG~~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~ 74 (154)
T PTZ00134 31 ALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIA 74 (154)
T ss_pred eecccccccHHHHHHHHHHcCcCcCCCcccCCHHHHHHHHHHHh
Confidence 46789999999999998899996 566666555555555553
No 99
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=21.81 E-value=88 Score=31.93 Aligned_cols=53 Identities=13% Similarity=0.210 Sum_probs=37.0
Q ss_pred cccCCCcHHHHHHHHHHhCCcc-hhhhhcCCHHHHHHhhCC--ChHHHHHHHHhcC
Q 004805 248 KKMKQLGGKLGTSLQNELGVTT-VGDLLKFSEDKLQESYGF--NTGTWLWNIARGI 300 (729)
Q Consensus 248 ~~L~GIG~k~~~~L~~~lGI~T-igDLa~l~~~~L~~rFG~--~~g~~L~~~arGi 300 (729)
-.++|||+|++-.+.+.++... +..++.-+...|.+.-|+ ++++++.-.++|.
T Consensus 76 i~V~GIGpK~Al~ILs~~~~~~l~~aI~~~D~~~L~~vpGIGkKtAerIilELk~K 131 (194)
T PRK14605 76 IDVSGIGPKLGLAMLSAMNAEALASAIISGNAELLSTIPGIGKKTASRIVLELKDK 131 (194)
T ss_pred hCCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHH
Confidence 3678999999987776677776 444556688888886553 4667766555554
No 100
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=21.21 E-value=97 Score=37.80 Aligned_cols=53 Identities=19% Similarity=0.281 Sum_probs=32.4
Q ss_pred hcccccCcccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHh--hCCChHHHHHHH
Q 004805 239 KGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNI 296 (729)
Q Consensus 239 ~~fL~~LPI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~r--FG~~~g~~L~~~ 296 (729)
..||..|.| ||||.+++++|...+ .++.+|..++.+.|.+. +|...+..++.+
T Consensus 525 ~r~l~ALgI---pgIG~~~ak~L~~~F--~si~~L~~As~eeL~~i~GIG~k~A~sI~~f 579 (689)
T PRK14351 525 ADFLVALGI---PEVGPTTARNLAREF--GTFEAIMDADEEALRAVDDVGPTVAEEIREF 579 (689)
T ss_pred HHHHHHcCC---CCcCHHHHHHHHHHh--CCHHHHHhCCHHHHhccCCcCHHHHHHHHHH
Confidence 345555444 778887777775444 56677777777777666 555445444443
No 101
>PRK13844 recombination protein RecR; Provisional
Probab=20.84 E-value=83 Score=32.39 Aligned_cols=16 Identities=25% Similarity=0.507 Sum_probs=14.4
Q ss_pred ccccCCCcHHHHHHHH
Q 004805 247 IKKMKQLGGKLGTSLQ 262 (729)
Q Consensus 247 I~~L~GIG~k~~~~L~ 262 (729)
+.+|||||+|+++||.
T Consensus 17 l~~LPGIG~KsA~Rla 32 (200)
T PRK13844 17 LRKLPTIGKKSSQRLA 32 (200)
T ss_pred HHHCCCCCHHHHHHHH
Confidence 5689999999999996
No 102
>COG2199 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]
Probab=20.57 E-value=2.3e+02 Score=27.33 Aligned_cols=29 Identities=24% Similarity=0.111 Sum_probs=18.4
Q ss_pred HHHHHHHHHHhc----CCeeeeccceeEEeccc
Q 004805 100 AGSEVVSILARK----GRCERASIDEVYLDLTD 128 (729)
Q Consensus 100 ~S~~I~~iL~~~----~~vE~~SIDEafLDlT~ 128 (729)
+...+.++|+.. ..+.+++=||+-+=+.+
T Consensus 77 vL~~va~~L~~~~~~~~~~~R~gGdEF~i~l~~ 109 (181)
T COG2199 77 VLREVARRLRSNLREGDLVARLGGDEFAVLLPG 109 (181)
T ss_pred HHHHHHHHHHHhcCCCCEEEEeccceeEEEeCC
Confidence 345556666652 34788888988775544
No 103
>cd00166 SAM Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
Probab=20.32 E-value=1.1e+02 Score=23.96 Aligned_cols=46 Identities=28% Similarity=0.432 Sum_probs=34.7
Q ss_pred cCCchhcccccCcccccCCCcHHHHHHHHHHhCCcchhhhhcCCHHHHHHhhCCCh
Q 004805 234 PFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNT 289 (729)
Q Consensus 234 ~~~~v~~fL~~LPI~~L~GIG~k~~~~L~~~lGI~TigDLa~l~~~~L~~rFG~~~ 289 (729)
...++.+||..+ |+ ......+. ..|| +..+|..++.+.|. .+|+..
T Consensus 3 ~~~~V~~wL~~~------~~-~~y~~~f~-~~~i-~g~~L~~l~~~dL~-~lgi~~ 48 (63)
T cd00166 3 SPEDVAEWLESL------GL-GQYADNFR-ENGI-DGDLLLLLTEEDLK-ELGITL 48 (63)
T ss_pred CHHHHHHHHHHc------Ch-HHHHHHHH-HcCC-CHHHHhHCCHHHHH-HcCCCC
Confidence 345566677644 34 46777786 8899 99999999999998 899864
Done!