Query 009298
Match_columns 538
No_of_seqs 178 out of 1489
Neff 6.6
Searched_HMMs 46136
Date Thu Mar 28 22:51:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009298.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009298hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00205 DNA polymerase kappa; 100.0 5.5E-62 1.2E-66 526.1 37.9 328 3-331 170-516 (571)
2 PRK01216 DNA polymerase IV; Va 100.0 1.7E-59 3.7E-64 490.8 37.1 294 2-304 44-342 (351)
3 PRK03858 DNA polymerase IV; Va 100.0 1E-59 2.3E-64 501.0 33.9 299 2-304 39-343 (396)
4 cd00424 PolY Y-family of DNA p 100.0 8.2E-59 1.8E-63 485.4 35.6 292 2-299 38-343 (343)
5 PRK14133 DNA polymerase IV; Pr 100.0 1.3E-58 2.8E-63 484.7 36.6 296 2-305 42-340 (347)
6 PRK02406 DNA polymerase IV; Va 100.0 8.5E-59 1.8E-63 485.2 35.1 305 2-318 34-342 (343)
7 cd01701 PolY_Rev1 DNA polymera 100.0 1.5E-58 3.3E-63 493.1 36.2 295 3-301 88-404 (404)
8 KOG2094 Predicted DNA damage i 100.0 5.8E-60 1.2E-64 473.0 23.3 312 3-318 140-457 (490)
9 PRK02794 DNA polymerase IV; Pr 100.0 3.5E-58 7.7E-63 492.7 35.8 300 2-305 74-376 (419)
10 PRK03352 DNA polymerase IV; Va 100.0 1.1E-57 2.4E-62 477.3 36.7 294 2-304 48-345 (346)
11 cd03586 PolY_Pol_IV_kappa DNA 100.0 1.4E-57 3.1E-62 473.5 35.6 295 2-301 37-334 (334)
12 PRK03348 DNA polymerase IV; Pr 100.0 2.2E-57 4.8E-62 490.2 37.4 298 3-303 45-346 (454)
13 PRK01810 DNA polymerase IV; Va 100.0 1.6E-57 3.5E-62 485.9 35.8 297 2-304 46-347 (407)
14 PRK03103 DNA polymerase IV; Re 100.0 1.8E-57 3.9E-62 485.9 34.3 297 3-304 45-352 (409)
15 cd01703 PolY_Pol_iota DNA Poly 100.0 1.6E-56 3.4E-61 472.7 34.7 294 3-300 35-379 (379)
16 cd01702 PolY_Pol_eta DNA Polym 100.0 7.1E-56 1.5E-60 465.1 32.0 284 2-300 34-359 (359)
17 cd01700 PolY_Pol_V_umuC umuC s 100.0 9E-56 1.9E-60 462.6 31.2 294 2-300 36-344 (344)
18 PRK03609 umuC DNA polymerase V 100.0 6.2E-55 1.3E-59 468.0 34.1 297 3-304 39-353 (422)
19 COG0389 DinP Nucleotidyltransf 100.0 2.5E-50 5.3E-55 422.8 33.2 298 3-304 41-347 (354)
20 cd03468 PolY_like DNA Polymera 100.0 1.9E-50 4.2E-55 419.9 31.3 289 2-299 37-334 (335)
21 KOG2093 Translesion DNA polyme 100.0 6.7E-48 1.4E-52 419.7 19.0 319 3-328 415-753 (1016)
22 KOG2095 DNA polymerase iota/DN 100.0 3.1E-42 6.7E-47 370.0 13.4 247 2-250 52-375 (656)
23 PF00817 IMS: impB/mucB/samB f 99.9 2.8E-27 6.1E-32 219.2 9.6 113 2-115 36-149 (149)
24 PF11799 IMS_C: impB/mucB/samB 99.5 1.4E-13 3.1E-18 122.5 11.4 107 196-302 2-116 (127)
25 PF11798 IMS_HHH: IMS family H 98.4 2.5E-07 5.4E-12 63.5 2.9 31 130-161 2-32 (32)
26 PRK04301 radA DNA repair and r 97.4 0.0001 2.2E-09 76.8 3.5 79 135-214 2-88 (317)
27 TIGR02236 recomb_radA DNA repa 96.5 0.002 4.4E-08 66.7 3.8 73 141-214 1-81 (310)
28 PF14520 HHH_5: Helix-hairpin- 96.1 0.0059 1.3E-07 47.8 3.5 48 141-189 7-57 (60)
29 PF11731 Cdd1: Pathogenicity l 95.3 0.017 3.7E-07 49.4 3.5 36 140-176 13-49 (93)
30 PF10391 DNA_pol_lambd_f: Fing 93.8 0.045 9.7E-07 41.9 2.2 28 142-170 5-32 (52)
31 PF04994 TfoX_C: TfoX C-termin 93.4 0.15 3.4E-06 42.5 5.1 31 140-171 4-34 (81)
32 PF08827 DUF1805: Domain of un 92.8 0.075 1.6E-06 41.5 2.1 24 2-25 35-58 (59)
33 PF03118 RNA_pol_A_CTD: Bacter 91.9 0.24 5.2E-06 39.7 4.1 52 133-186 6-60 (66)
34 COG3743 Uncharacterized conser 91.6 0.2 4.4E-06 45.3 3.7 31 140-171 68-98 (133)
35 PRK12766 50S ribosomal protein 91.3 0.38 8.2E-06 47.8 5.6 52 140-192 4-58 (232)
36 PRK02362 ski2-like helicase; P 86.9 0.72 1.6E-05 53.7 4.7 52 139-191 652-704 (737)
37 COG2251 Predicted nuclease (Re 79.8 2.5 5.4E-05 45.9 4.7 48 131-179 217-265 (474)
38 PF14229 DUF4332: Domain of un 79.3 2.1 4.5E-05 38.5 3.5 48 131-179 45-93 (122)
39 PF14229 DUF4332: Domain of un 79.2 3.6 7.7E-05 37.0 5.0 36 145-181 1-42 (122)
40 smart00483 POLXc DNA polymeras 77.6 1.6 3.5E-05 46.0 2.6 29 141-170 91-119 (334)
41 PF12826 HHH_2: Helix-hairpin- 76.9 2.6 5.6E-05 33.4 3.0 44 144-189 8-54 (64)
42 PRK01172 ski2-like helicase; P 76.6 3.2 7E-05 47.8 4.9 49 139-188 612-663 (674)
43 PRK00254 ski2-like helicase; P 75.6 3.3 7.3E-05 48.1 4.7 52 139-191 645-699 (720)
44 cd00141 NT_POLXc Nucleotidyltr 75.5 2.1 4.5E-05 44.6 2.7 29 141-170 87-115 (307)
45 PF02961 BAF: Barrier to autoi 74.7 3.1 6.7E-05 35.3 3.0 32 136-168 16-47 (89)
46 PRK08609 hypothetical protein; 73.2 3.6 7.8E-05 46.6 4.1 80 76-184 54-137 (570)
47 PF13878 zf-C2H2_3: zinc-finge 71.4 1.7 3.6E-05 31.5 0.6 26 451-476 14-39 (41)
48 PRK07758 hypothetical protein; 69.0 9.9 0.00021 32.7 4.8 43 144-187 39-84 (95)
49 PRK10917 ATP-dependent DNA hel 67.3 4.1 8.8E-05 47.1 2.9 31 139-170 9-39 (681)
50 TIGR03491 RecB family nuclease 67.2 6.3 0.00014 43.4 4.2 54 132-186 200-256 (457)
51 PF00633 HHH: Helix-hairpin-he 65.8 3.4 7.4E-05 27.9 1.1 17 141-157 13-29 (30)
52 PRK14667 uvrC excinuclease ABC 64.5 9.6 0.00021 43.1 5.1 53 138-192 513-567 (567)
53 PF02889 Sec63: Sec63 Brl doma 63.8 12 0.00027 38.4 5.5 54 139-193 148-204 (314)
54 PTZ00035 Rad51 protein; Provis 62.1 10 0.00023 40.0 4.6 52 139-191 21-77 (337)
55 COG1200 RecG RecG-like helicas 58.4 7.2 0.00016 44.6 2.7 32 139-171 10-42 (677)
56 PLN03187 meiotic recombination 55.9 13 0.00029 39.4 4.1 43 138-181 28-73 (344)
57 cd07556 Nucleotidyl_cyc_III Cl 55.7 1.2E+02 0.0026 25.7 9.6 61 43-106 32-97 (133)
58 PRK12278 50S ribosomal protein 54.9 12 0.00025 37.3 3.2 31 140-171 159-189 (221)
59 PRK14669 uvrC excinuclease ABC 54.5 20 0.00043 41.1 5.4 53 138-192 551-604 (624)
60 PLN03186 DNA repair protein RA 51.6 14 0.00031 39.1 3.5 43 138-181 25-70 (342)
61 TIGR00596 rad1 DNA repair prot 51.5 19 0.0004 42.7 4.7 50 141-192 759-810 (814)
62 PRK07956 ligA NAD-dependent DN 50.9 20 0.00044 41.4 4.8 48 140-187 446-496 (665)
63 TIGR02239 recomb_RAD51 DNA rep 50.6 18 0.00038 37.9 4.0 35 146-181 8-43 (316)
64 PRK00116 ruvA Holliday junctio 50.5 17 0.00037 35.2 3.6 53 140-192 74-130 (192)
65 PF04475 DUF555: Protein of un 50.2 6.5 0.00014 34.0 0.5 34 448-486 45-95 (102)
66 KOG2534 DNA polymerase IV (fam 50.0 18 0.00038 37.8 3.7 31 141-172 99-129 (353)
67 PRK03922 hypothetical protein; 49.8 6.5 0.00014 34.6 0.5 43 448-495 47-106 (113)
68 PRK12311 rpsB 30S ribosomal pr 49.5 13 0.00027 39.3 2.6 31 140-171 264-294 (326)
69 TIGR02238 recomb_DMC1 meiotic 49.3 20 0.00043 37.5 4.1 35 145-180 7-42 (313)
70 COG0322 UvrC Nuclease subunit 48.3 1.4E+02 0.0031 34.0 10.9 130 25-187 443-578 (581)
71 smart00611 SEC63 Domain of unk 48.0 23 0.00051 36.4 4.4 53 138-191 150-205 (312)
72 KOG3014 Protein involved in es 47.7 7.4 0.00016 39.1 0.6 29 451-479 38-66 (257)
73 COG2199 c-di-GMP synthetase (d 47.1 55 0.0012 30.3 6.4 65 40-107 75-149 (181)
74 PF13894 zf-C2H2_4: C2H2-type 43.5 7.1 0.00015 23.5 -0.2 12 451-462 1-12 (24)
75 COG0632 RuvA Holliday junction 43.3 12 0.00027 36.6 1.3 43 102-156 80-125 (201)
76 smart00278 HhH1 Helix-hairpin- 43.2 16 0.00035 23.4 1.5 17 141-157 3-19 (26)
77 TIGR00575 dnlj DNA ligase, NAD 42.9 33 0.00071 39.6 4.9 48 140-187 433-483 (652)
78 COG5540 RING-finger-containing 42.8 9 0.0002 39.6 0.3 17 446-462 355-373 (374)
79 PRK14973 DNA topoisomerase I; 41.8 44 0.00095 40.3 5.8 77 109-191 851-931 (936)
80 TIGR01448 recD_rel helicase, p 41.6 46 0.001 38.9 5.9 49 125-176 73-121 (720)
81 PRK05182 DNA-directed RNA poly 40.9 32 0.00069 36.0 4.0 50 136-187 246-298 (310)
82 TIGR02027 rpoA DNA-directed RN 40.6 33 0.00071 35.7 4.1 52 135-188 231-285 (297)
83 PRK14672 uvrC excinuclease ABC 40.4 41 0.0009 38.9 5.1 53 138-192 607-662 (691)
84 PF02591 DUF164: Putative zinc 40.3 9.4 0.0002 29.3 0.0 25 443-467 15-39 (56)
85 PRK14666 uvrC excinuclease ABC 39.5 38 0.00082 39.2 4.6 50 138-189 636-688 (694)
86 PRK14670 uvrC excinuclease ABC 39.3 41 0.00089 38.2 4.9 50 138-189 513-565 (574)
87 PRK12373 NADH dehydrogenase su 38.7 27 0.00059 37.7 3.2 31 140-171 324-354 (400)
88 PRK14671 uvrC excinuclease ABC 38.6 44 0.00095 38.4 5.0 49 139-189 569-618 (621)
89 PRK00558 uvrC excinuclease ABC 35.0 48 0.001 37.9 4.6 50 138-189 542-594 (598)
90 PRK14351 ligA NAD-dependent DN 33.9 54 0.0012 38.2 4.8 48 140-187 463-513 (689)
91 COG1885 Uncharacterized protei 33.0 17 0.00037 31.7 0.5 43 448-495 47-106 (115)
92 COG2075 RPL24A Ribosomal prote 32.4 21 0.00044 28.7 0.8 13 451-463 4-16 (66)
93 PF01246 Ribosomal_L24e: Ribos 32.3 15 0.00032 30.1 -0.1 14 450-463 3-16 (71)
94 PF13240 zinc_ribbon_2: zinc-r 31.0 25 0.00054 22.2 0.8 12 452-463 1-12 (23)
95 COG2519 GCD14 tRNA(1-methylade 29.8 1.5E+02 0.0033 30.2 6.6 68 4-71 83-173 (256)
96 TIGR01954 nusA_Cterm_rpt trans 29.5 70 0.0015 23.2 3.3 32 147-179 1-33 (50)
97 PRK14601 ruvA Holliday junctio 29.3 28 0.00062 33.6 1.4 43 102-156 80-125 (183)
98 PRK02515 psbU photosystem II c 29.3 44 0.00096 30.5 2.5 30 141-171 63-93 (132)
99 PRK14606 ruvA Holliday junctio 26.9 33 0.00073 33.2 1.4 43 102-156 80-125 (188)
100 COG1796 POL4 DNA polymerase IV 26.7 31 0.00067 36.1 1.1 33 139-171 93-125 (326)
101 COG2062 SixA Phosphohistidine 26.5 3.5E+02 0.0076 25.6 8.1 74 27-117 48-121 (163)
102 PF06397 Desulfoferrod_N: Desu 25.8 23 0.0005 25.1 0.0 9 450-458 6-14 (36)
103 COG4071 Uncharacterized protei 25.6 1.2E+02 0.0027 30.0 4.9 54 63-116 121-178 (278)
104 PRK13901 ruvA Holliday junctio 25.5 36 0.00079 33.2 1.3 43 102-156 79-124 (196)
105 TIGR00426 competence protein C 25.4 52 0.0011 26.0 2.0 43 140-187 17-64 (69)
106 PF14716 HHH_8: Helix-hairpin- 24.9 46 0.001 26.4 1.6 17 141-157 49-65 (68)
107 TIGR00615 recR recombination p 24.8 36 0.00077 33.3 1.1 16 141-156 13-28 (195)
108 PRK00807 50S ribosomal protein 24.6 31 0.00067 26.3 0.5 14 451-464 2-15 (52)
109 PRK00076 recR recombination pr 24.1 37 0.00081 33.2 1.1 16 141-156 13-28 (196)
110 PF13909 zf-H2C2_5: C2H2-type 24.0 28 0.0006 21.5 0.1 11 451-461 1-11 (24)
111 PRK14668 uvrC excinuclease ABC 24.0 1E+02 0.0022 35.2 4.7 48 138-187 524-574 (577)
112 PRK14602 ruvA Holliday junctio 23.9 42 0.0009 32.9 1.4 43 102-156 81-126 (203)
113 PRK14604 ruvA Holliday junctio 23.8 41 0.00089 32.8 1.4 43 102-156 80-125 (195)
114 CHL00013 rpoA RNA polymerase a 23.5 86 0.0019 33.1 3.7 54 134-189 258-314 (327)
115 TIGR00084 ruvA Holliday juncti 23.4 32 0.0007 33.3 0.6 43 102-156 79-124 (191)
116 PRK14603 ruvA Holliday junctio 23.4 43 0.00092 32.7 1.4 43 102-156 79-124 (197)
117 PRK14891 50S ribosomal protein 23.0 36 0.00078 30.9 0.7 15 450-464 4-18 (131)
118 PRK13844 recombination protein 22.9 40 0.00087 33.0 1.1 16 141-156 17-32 (200)
119 cd00472 Ribosomal_L24e_L24 Rib 22.6 35 0.00075 26.4 0.5 14 450-463 3-16 (54)
120 PRK02240 GTP cyclohydrolase II 22.4 4.5E+02 0.0096 26.9 8.4 101 10-117 85-236 (254)
121 PRK05752 uroporphyrinogen-III 22.1 2.2E+02 0.0047 28.4 6.3 79 80-162 11-103 (255)
122 KOG0633 Histidinol phosphate a 21.9 1.5E+02 0.0032 30.6 4.8 43 27-71 161-205 (375)
123 smart00267 GGDEF diguanylate c 21.6 3.7E+02 0.0081 23.0 7.1 64 39-105 57-130 (163)
124 TIGR01916 F420_cofE F420-0:gam 21.4 2.7E+02 0.0058 28.2 6.6 36 75-110 119-154 (243)
125 PHA02768 hypothetical protein; 21.4 36 0.00078 26.4 0.3 27 448-476 3-29 (55)
126 PF05715 zf-piccolo: Piccolo Z 21.1 44 0.00095 26.3 0.7 30 430-467 18-47 (61)
127 smart00355 ZnF_C2H2 zinc finge 20.8 41 0.0009 20.1 0.5 12 451-462 1-12 (26)
128 TIGR01259 comE comEA protein. 20.8 80 0.0017 28.2 2.5 30 141-170 70-103 (120)
129 COG2888 Predicted Zn-ribbon RN 20.8 44 0.00095 26.3 0.7 13 449-461 49-61 (61)
130 PF09889 DUF2116: Uncharacteri 20.7 44 0.00096 26.3 0.7 12 452-463 5-16 (59)
131 PF13248 zf-ribbon_3: zinc-rib 20.1 51 0.0011 21.2 0.8 14 451-464 3-16 (26)
132 TIGR00575 dnlj DNA ligase, NAD 20.1 1.4E+02 0.0029 34.7 4.7 18 140-157 467-484 (652)
133 smart00782 PhnA_Zn_Ribbon PhnA 20.1 48 0.001 24.9 0.7 10 450-459 7-16 (47)
No 1
>PTZ00205 DNA polymerase kappa; Provisional
Probab=100.00 E-value=5.5e-62 Score=526.09 Aligned_cols=328 Identities=30% Similarity=0.473 Sum_probs=298.1
Q ss_pred ccCHHHHHcCCCCCCcHHHHHhhCCCeEEEcCChHHHHHHHHHHHHHHHhcCCCeEeeCccEEEEEcCccchhcC--CCH
Q 009298 3 FELLSARRFGVRAAMPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERG--ISG 80 (538)
Q Consensus 3 ~~syeAR~~GVr~GM~l~~A~~LCP~Lvvvp~d~~~Y~~~s~~l~~il~~~sp~Ve~~SiDEafLDlT~~~~l~g--~~~ 80 (538)
-|||+||+|||++|||+++|++|||+|+++|+|++.|+++|+++++++.+|+|.||++|+||+|||+|++...|+ .++
T Consensus 170 TaSYeARk~GVrsgMp~~~AkkLCP~Liivp~d~~~Y~~~S~~I~~il~~ysp~ve~~SIDEafLDlT~~~~~~~~~~~~ 249 (571)
T PTZ00205 170 TANYVARGRGIRQGMPGFLALKICPNLLILPPDFDAYNEESNTVRRIVAEYDPNYISFGLDELTLEVSAYIERFEGTKTA 249 (571)
T ss_pred EcCHHHHhhCCCcCCcHHHHHHhCCCCcEecCCHHHHHHHHHHHHHHHHhcCCcEEEeechhceeccCCchhhccCCCCH
Confidence 589999999999999999999999999999999999999999999999999999999999999999999876652 268
Q ss_pred HHHHHHHHHHHHHHhCCceEEEecCChhHHHHHhcccCCCCeEEec-CChHHHHHhhcCCCcccccCCCHHHHHHHHhhc
Q 009298 81 IEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLP-NDRMAVMTFISSLPIRKIGGIGKVTEHILRDVF 159 (538)
Q Consensus 81 ~~la~~IR~~I~~~~Glt~S~GIA~nk~lAKLAS~~aKP~G~~vl~-~~~~~~~~fL~~lPl~~L~GIG~kt~~kL~~~l 159 (538)
.++|++||.+|++++|+|||||||+||++|||||+++||||+++++ ...+++..||+++||++|||||+++.++|.. +
T Consensus 250 ~~iA~~IR~~I~~~tgLt~SiGIA~NklLAKiASd~~KPnG~~vl~l~~~~~v~~fL~~LpV~ki~GIG~~t~~~L~~-~ 328 (571)
T PTZ00205 250 EDVASELRVRVFGETKLTASAGIGPTAALAKIASNINKPNGQHDLNLHTRGDVMTYVRDLGLRSVPGVGKVTEALLKG-L 328 (571)
T ss_pred HHHHHHHHHHHHHHHCCcEEEEEcCCHHHHHHhhhccCCCCCeEEecCCHHHHHHHHhCCCcceeCCcCHHHHHHHHH-c
Confidence 9999999999999999999999999999999999999999999874 2345899999999999999999999999997 9
Q ss_pred CCCchHHHHhchH---------HHHHHcChhHHHHHHHhccCCCCCC-CC--CCCCCccceeeeccCccCCHHHHHHHHH
Q 009298 160 GINTCEEMLQKGS---------LLCAVFSHSTADFFLSVGLGLGSTN-TP--QARFRKSISSERTFSVTEDKALLYRKLA 227 (538)
Q Consensus 160 GI~TlgDL~~lp~---------~L~krFG~~~~~~L~~~a~Gid~~~-v~--~~~~pKSIs~e~tF~~~~d~e~L~~~L~ 227 (538)
||+||+||++.+. .+...||...+.++|..++|+|..+ +. ....+|||++++||+...+.+++...|.
T Consensus 329 GI~TigDLa~~~~~l~~~f~~k~l~~llG~~~G~~l~~~a~G~d~~~~v~~~~~~~rKSIg~ErTF~~~~d~~el~~~L~ 408 (571)
T PTZ00205 329 GITTLSDIYNRRVELCYILHNNLFRFLLGASIGIMQWPDAATAANTENCEGATGGQRKAISSERSFTTPRTKEGLQEMVD 408 (571)
T ss_pred CCCcHHHHhcCCHHHHHHhHHHHHHHHhCchhhHHHHHHhcCCCCCCccCCCCCCCCceeEEeEeCCCCCCHHHHHHHHH
Confidence 9999999999873 3567788766778888999999874 32 2456899999999998889999999999
Q ss_pred HHHHHHHHHHHHhCCCccEEEEEEEEcCCceeEEEEecCCCCCCHHHHHHHHHHHHHhh-C-CCCEEEEEEEecCCCcCc
Q 009298 228 EIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAE-L-PVSLRLIGLRVTQFNEDK 305 (538)
Q Consensus 228 ~Lae~L~~RLr~~gl~~rtLtL~Lr~~d~~~~srs~~L~~~t~~~~~L~~~a~~LL~~~-l-p~~VR~IGV~ls~L~~~~ 305 (538)
.|+++|+.+|+++++.+++|+|++++++|++.+++.+++.||++...|++++..||+.. + +.+||+|||++++|....
T Consensus 409 ~L~~~v~~rLrk~~l~artVtlKlK~~dF~~~trs~tL~~pT~d~~~I~~aa~~Ll~~~~~~~~~vRLlGV~ls~L~~~~ 488 (571)
T PTZ00205 409 TVFNGAYEEMRKSELMCRQISLTIRWASYRYQQYTKSLIQYSDDSATLRRAVDGLLLPHAAKYSEMCLLGVRFLDLISAK 488 (571)
T ss_pred HHHHHHHHHHHhcCCCccEEEEEEEECCCCceEEEEECCCCcCCHHHHHHHHHHHHHhccccCCCEEEEEEEEcccCcHH
Confidence 99999999999999999999999999999999999999999999999999999999876 3 368999999999999976
Q ss_pred cc--CCCCcccccHHHHhccCccccccc
Q 009298 306 VR--APSDPTQKTLTNFMTSGHASKKIV 331 (538)
Q Consensus 306 ~~--~~~~~~Q~tI~~ff~~~~~~~~~~ 331 (538)
.. -..++.|.+|..|..++.+...+.
T Consensus 489 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 516 (571)
T PTZ00205 489 DFHMKRKGGNQLSISQFIRPKKPGEVTA 516 (571)
T ss_pred HHHHHhcCCceeeHHHHcCCCCCCceee
Confidence 42 355799999999999888766443
No 2
>PRK01216 DNA polymerase IV; Validated
Probab=100.00 E-value=1.7e-59 Score=490.84 Aligned_cols=294 Identities=26% Similarity=0.405 Sum_probs=278.8
Q ss_pred CccCHHHHHcCCCCCCcHHHHHhhCCCeEEEcCChHHHHHHHHHHHHHHHhcCCCeEeeCccEEEEEcCccchhcCCCHH
Q 009298 2 RFELLSARRFGVRAAMPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGI 81 (538)
Q Consensus 2 ~~~syeAR~~GVr~GM~l~~A~~LCP~Lvvvp~d~~~Y~~~s~~l~~il~~~sp~Ve~~SiDEafLDlT~~~~l~g~~~~ 81 (538)
..|||+||++||++|||+++|++|||+++++++|++.|+.++++++.++++|+|.||++|+||+|||||++.++|| ++.
T Consensus 44 ~aasy~Ar~~GV~sgM~~~~A~~lcP~li~v~~d~~~y~~~s~~i~~~l~~~tp~ve~~siDE~~LDvt~~~~l~g-~~~ 122 (351)
T PRK01216 44 ATANYEARKLGIKAGMPIVEAKKILPNAVYLPMRKEVYQQVSNRIMKLLREYSEKIEIASIDEAYLDISDKVKNYQ-DAY 122 (351)
T ss_pred EECCHHHHHhCCCCCCcHHHHHHHCCCeEEECCCHHHHHHHHHHHHHHHHHhCCceEEccCCeEEEEcccchhccC-CHH
Confidence 3689999999999999999999999999999999999999999999999999999999999999999999999998 899
Q ss_pred HHHHHHHHHHHHHhCCceEEEecCChhHHHHHhcccCCCCeEEecCChHHHHHhhcCCCcccccCCCHHHHHHHHhhcCC
Q 009298 82 EIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGI 161 (538)
Q Consensus 82 ~la~~IR~~I~~~~Glt~S~GIA~nk~lAKLAS~~aKP~G~~vl~~~~~~~~~fL~~lPl~~L~GIG~kt~~kL~~~lGI 161 (538)
.+|++||++|++++|+|||+|||+||++|||||+.+||+|+++++++ ++.+||+++||++|||||+++.++|++ +||
T Consensus 123 ~la~~ir~~I~~~~glt~siGia~nk~lAKlas~~~KP~g~~vi~~~--~~~~~L~~LPi~~l~giG~~~~~~L~~-~Gi 199 (351)
T PRK01216 123 NLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDE--EVKRFINELDIADIPGIGDITAEKLKK-LGV 199 (351)
T ss_pred HHHHHHHHHHHHHHCCcEEEEecCCHHHHHHHHhccCCCCEEEeCHH--HHHHHHhcCCcccccCCCHHHHHHHHH-cCC
Confidence 99999999999999999999999999999999999999999999875 789999999999999999999999998 999
Q ss_pred CchHHHHhch-HHHHHHcChhHHHHHHHhccCCCCCCCCCCCCCccceeeeccCc-cCCHHHHHHHHHHHHHHHHHHHHH
Q 009298 162 NTCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV-TEDKALLYRKLAEIAEMLSADMQK 239 (538)
Q Consensus 162 ~TlgDL~~lp-~~L~krFG~~~~~~L~~~a~Gid~~~v~~~~~pKSIs~e~tF~~-~~d~e~L~~~L~~Lae~L~~RLr~ 239 (538)
+|++||+++| ..|.++||...+.+|+.+++|++++++.+. ++|||+.+.+|.. +.+.+++...|.+|+++++.||+.
T Consensus 200 ~TigdL~~~~~~~L~~rfG~~~~~~L~~~a~G~d~~pv~~~-~~ksi~~~~tl~~di~~~~~l~~~l~~L~~~~~~rl~~ 278 (351)
T PRK01216 200 NKLVDTLRIEFDELKGIIGEAKAKYLFSLARNEYNEPVRAR-VRKSIGRYVTLPRNTRDLEEIKPYLKRAIEEAYYKLDG 278 (351)
T ss_pred CcHHHHhcCCHHHHHHHHCHHHHHHHHHHhCCCCCCCCCCC-CCCCCcCeEECCCccCCHHHHHHHHHHHHHHHHHHHHh
Confidence 9999999999 899999998778889898999999998874 5699999999987 789999999999999999999996
Q ss_pred hCCCccEEEEEEEEcCCceeEEEEecCCCCCCHHHHHHHHHHHHHhhC---CCCEEEEEEEecCCCcC
Q 009298 240 EGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAEL---PVSLRLIGLRVTQFNED 304 (538)
Q Consensus 240 ~gl~~rtLtL~Lr~~d~~~~srs~~L~~~t~~~~~L~~~a~~LL~~~l---p~~VR~IGV~ls~L~~~ 304 (538)
.++++++++++.+|.+.+++.+++.|++ .+.|++.+..||++.+ ..+||+|||++++|.+.
T Consensus 279 ---~~~~~~~~~~~~df~~~t~~~tl~~~~~-~~~~~~~a~~Ll~~~~~~~~~~vRllGv~~~~l~~~ 342 (351)
T PRK01216 279 ---IPKAIHVVAIMEDLDIVSRGRTFTHGIS-KETAYREAVRLLQKILEEDERKIRRIGVRFSKIIEA 342 (351)
T ss_pred ---CCCEEEEEEEcCCCCEEEEEEECCCCCC-HHHHHHHHHHHHHhhhhcCCCCeeEEEEEEeccccc
Confidence 6789999999999999999999999997 6889999999999863 25899999999999876
No 3
>PRK03858 DNA polymerase IV; Validated
Probab=100.00 E-value=1e-59 Score=500.97 Aligned_cols=299 Identities=31% Similarity=0.508 Sum_probs=286.6
Q ss_pred CccCHHHHHcCCCCCCcHHHHHhhCCCeEEEcCChHHHHHHHHHHHHHHHhcCCCeEeeCccEEEEEcCccchhcCCCHH
Q 009298 2 RFELLSARRFGVRAAMPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGI 81 (538)
Q Consensus 2 ~~~syeAR~~GVr~GM~l~~A~~LCP~Lvvvp~d~~~Y~~~s~~l~~il~~~sp~Ve~~SiDEafLDlT~~~~l~g~~~~ 81 (538)
..|||+||++||++|||+++|+++||+|+++++|++.|+.++++++.++++|+|.||++|+||+|||||++.++|| ++.
T Consensus 39 ~a~sy~Ar~~GV~~gm~~~~A~~lcP~l~~~~~d~~~y~~~s~~i~~~l~~~s~~ve~~siDe~~ldvt~~~~~~~-~~~ 117 (396)
T PRK03858 39 LAASYEAKAYGVRTAMGGRQARRLCPQAVVVPPRMSAYSRASKAVFEVFRDTTPLVEGLSIDEAFLDVGGLRRISG-TPV 117 (396)
T ss_pred EEeCHHHHHhCCCCCChHHHHHHHCCCeEEECCCHHHHHHHHHHHHHHHHHhCCceEEecCCeEEEEccccccccC-CHH
Confidence 4699999999999999999999999999999999999999999999999999999999999999999999999998 899
Q ss_pred HHHHHHHHHHHHHhCCceEEEecCChhHHHHHhcccCCCCeEEecCChHHHHHhhcCCCcccccCCCHHHHHHHHhhcCC
Q 009298 82 EIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGI 161 (538)
Q Consensus 82 ~la~~IR~~I~~~~Glt~S~GIA~nk~lAKLAS~~aKP~G~~vl~~~~~~~~~fL~~lPl~~L~GIG~kt~~kL~~~lGI 161 (538)
++|++||++|++++|++||+|||+|+++||||++.+||+|+++++++ ++..||+++||++|||||+++.++|++ +||
T Consensus 118 ~la~~ir~~i~~~~gl~~svGia~n~~lAklas~~~Kp~g~~~i~~~--~~~~~L~~lpl~~l~Gig~~~~~~L~~-~Gi 194 (396)
T PRK03858 118 QIAARLRRRVREEVGLPITVGVARTKFLAKVASQVAKPDGLLVVPPD--RELAFLHPLPVRRLWGVGPVTAAKLRA-HGI 194 (396)
T ss_pred HHHHHHHHHHHHHHCCCeEEEEcCChHHHHHhhcccCCCceEEECcH--HHHHHHhcCChhhcCCCCHHHHHHHHH-hCC
Confidence 99999999999899999999999999999999999999999999886 678999999999999999999999998 999
Q ss_pred CchHHHHhch-HHHHHHcChhHHHHHHHhccCCCCCCCCCCCCCccceeeeccCc-cCCHHHHHHHHHHHHHHHHHHHHH
Q 009298 162 NTCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV-TEDKALLYRKLAEIAEMLSADMQK 239 (538)
Q Consensus 162 ~TlgDL~~lp-~~L~krFG~~~~~~L~~~a~Gid~~~v~~~~~pKSIs~e~tF~~-~~d~e~L~~~L~~Lae~L~~RLr~ 239 (538)
+|++||+++| ..|.++||...+.+|+.+++|++..++.+..++|||+.+.+|.. +.+.+++..+|++|+++|+.+|++
T Consensus 195 ~t~~dl~~l~~~~L~~~fG~~~~~~l~~~a~G~d~~~v~~~~~~ksi~~~~t~~~~~~~~~~l~~~l~~L~~~l~~rLr~ 274 (396)
T PRK03858 195 TTVGDVAELPESALVSLLGPAAGRHLHALAHNRDPRRVETGRRRRSVGAQRALGRGPNSPAEVDAVVVALVDRVARRMRA 274 (396)
T ss_pred CcHHHHhcCCHHHHHHHhCcHHHHHHHHHhCCCCCCCCCCCCCCccccceeEcCCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 9999999998 89999999887899998999999999988888999999999987 799999999999999999999999
Q ss_pred hCCCccEEEEEEEEcCCceeEEEEecCCCCCCHHHHHHHHHHHHHhhC----CCCEEEEEEEecCCCcC
Q 009298 240 EGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAEL----PVSLRLIGLRVTQFNED 304 (538)
Q Consensus 240 ~gl~~rtLtL~Lr~~d~~~~srs~~L~~~t~~~~~L~~~a~~LL~~~l----p~~VR~IGV~ls~L~~~ 304 (538)
+++.+++|+|++++.+++..+++++++.||++...|+++++.+|++.+ +.+||++||++++|.+.
T Consensus 275 ~~~~~~~l~l~l~~~~~~~~~~~~~l~~~t~~~~~l~~l~~~ll~~~~~~~~~~~irligv~~~~l~~~ 343 (396)
T PRK03858 275 AGRTGRTVVLRLRFDDFTRATRSHTLPRPTASTATLLAAARDLVAAAAPLIAERGLTLVGFAVSNLDDD 343 (396)
T ss_pred cCCCcceEEEEEEeCCCCEEEEEEECCCCcCCHHHHHHHHHHHHHhhhhccCCCCeEEEEEEeecCCcc
Confidence 999999999999999999999999999999999999999999999863 36899999999999975
No 4
>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=8.2e-59 Score=485.40 Aligned_cols=292 Identities=30% Similarity=0.445 Sum_probs=276.9
Q ss_pred CccCHHHHHcCCCCCCcHHHHHhhCCCeEEEcCChHHHHHHHHHHHHHHHhcCCCeEeeCccEEEEEcCccchhcCCCHH
Q 009298 2 RFELLSARRFGVRAAMPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGI 81 (538)
Q Consensus 2 ~~~syeAR~~GVr~GM~l~~A~~LCP~Lvvvp~d~~~Y~~~s~~l~~il~~~sp~Ve~~SiDEafLDlT~~~~l~g~~~~ 81 (538)
..|||+||++||++|||+++|+++||+++++++|++.|+++++++++++.+|+|.||++|+||+|||+|++.++|+ ++.
T Consensus 38 ~a~sy~Ar~~GV~~gm~~~~A~~lcP~l~~~~~~~~~y~~~s~~i~~~l~~~sp~ve~~siDE~~ldvt~~~~~~~-~~~ 116 (343)
T cd00424 38 IACSYEARKYGVKRGMPVREARKMCPNLILVPARLDLYRRLSERLLSELEEVAPLVEVASIDELFLDLTGSARLLG-LGS 116 (343)
T ss_pred EEeCHHHHHhCCCCCCcHHHHHHhCCCeEEECCCcHHHHHHHHHHHHHHHHhCCcEEEccCCEEEEECCCchhccC-CHH
Confidence 3699999999999999999999999999999999999999999999999999999999999999999999999888 799
Q ss_pred HHHHHHHHHHHHHhC-CceEEEecCChhHHHHHhcccCCCCeEEecCChHHHHHhhcCCCcccccCCCHHHHHHHHhhcC
Q 009298 82 EIAEELRTSVYEEAG-LTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFG 160 (538)
Q Consensus 82 ~la~~IR~~I~~~~G-lt~S~GIA~nk~lAKLAS~~aKP~G~~vl~~~~~~~~~fL~~lPl~~L~GIG~kt~~kL~~~lG 160 (538)
.+|++||++|++++| +|||+|||+|+++||||++.+||+|+++++++ ++.+||+++||++|||||+++.++|++ +|
T Consensus 117 ~la~~i~~~i~~~~ggl~~siGia~n~~lAKlAs~~~KP~g~~v~~~~--~~~~~L~~lpi~~l~giG~~~~~~L~~-~G 193 (343)
T cd00424 117 EVALRIKRHIAEQLGGITASIGIASNKLLAKLAAKYAKPDGLTILDPE--DLPGFLSKLPLTDLPGIGAVTAKRLEA-VG 193 (343)
T ss_pred HHHHHHHHHHHHHhCCceEEEeecccHHHHHHHhccCCCCCEEEEcHH--HHHHHHhcCChhhcCCCCHHHHHHHHH-cC
Confidence 999999999999998 99999999999999999999999999999875 688999999999999999999999997 99
Q ss_pred CCchHHHHhch--HHHHHHcChhHHHHHHHhccCCCCCCCCCCCCCccceeeeccCc-cCCHHHHHHHHHHHHHHHHHHH
Q 009298 161 INTCEEMLQKG--SLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV-TEDKALLYRKLAEIAEMLSADM 237 (538)
Q Consensus 161 I~TlgDL~~lp--~~L~krFG~~~~~~L~~~a~Gid~~~v~~~~~pKSIs~e~tF~~-~~d~e~L~~~L~~Lae~L~~RL 237 (538)
|+|++||+++| ..+.++||.. +.++|+.++|++..++.+..++|||+.+++|+. +.+.+++..+|++|+++|+.||
T Consensus 194 i~ti~dl~~~~~~~~l~~~fg~~-~~~l~~~a~G~d~~~v~~~~~~ksi~~~~tf~~~~~~~~~l~~~l~~l~~~l~~rL 272 (343)
T cd00424 194 INPIGDLLAASPDALLALWGGVS-GERLWYALRGIDDEPLSPPRPRKSFSHERVLPRDSRNAEDARPLLRLLLEKLARRL 272 (343)
T ss_pred CCcHHHHhcCCHHHHHHHHhhHH-HHHHHHHhCCcCCCCCCCCCCCCceeeeEECCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 99999999998 5778889976 677889999999999988888999999999987 7899999999999999999999
Q ss_pred HHhCCCccEEEEEEEEcC------CceeEEEEecCCCCCCHHHHHHHHHHHHHhhC----CCCEEEEEEEec
Q 009298 238 QKEGLRGRTLTLKLKTAS------FEVRTRAVTLQKYISSSEDILKHASVLLKAEL----PVSLRLIGLRVT 299 (538)
Q Consensus 238 r~~gl~~rtLtL~Lr~~d------~~~~srs~~L~~~t~~~~~L~~~a~~LL~~~l----p~~VR~IGV~ls 299 (538)
+++++.+++|+|++++.+ +...+++.+++.|| +...|++.+..||++++ +.+||++||+++
T Consensus 273 ~~~~~~~~~l~l~lr~~~~~~~~~~~~~~~~~~l~~~t-~~~~l~~~~~~l~~~~~~~~~~~~ir~~gv~~~ 343 (343)
T cd00424 273 RRDGRGATRLRLWLRTVDGRWSGHADIPSRSAPRPIST-EDGELLHALDKLWRALLDDKGPRRLRRLGVRLS 343 (343)
T ss_pred HHcCCceeEEEEEEEeCCCcccccceeeeeeeeCCCCC-CHHHHHHHHHHHHHhhhhccCCCCeeEEEEEeC
Confidence 999999999999999998 66889999999999 99999999999999985 368999999975
No 5
>PRK14133 DNA polymerase IV; Provisional
Probab=100.00 E-value=1.3e-58 Score=484.66 Aligned_cols=296 Identities=35% Similarity=0.550 Sum_probs=282.5
Q ss_pred CccCHHHHHcCCCCCCcHHHHHhhCCCeEEEcCChHHHHHHHHHHHHHHHhcCCCeEeeCccEEEEEcCccchhcCCCHH
Q 009298 2 RFELLSARRFGVRAAMPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGI 81 (538)
Q Consensus 2 ~~~syeAR~~GVr~GM~l~~A~~LCP~Lvvvp~d~~~Y~~~s~~l~~il~~~sp~Ve~~SiDEafLDlT~~~~l~g~~~~ 81 (538)
..|||+||++||++|||+++|+++||+++++++|++.|+.++++++.++++|+|.||++|+||+|||++++. + ++.
T Consensus 42 ~a~n~~Ar~~GV~~Gm~~~~A~~lcP~l~~~~~d~~~y~~~s~~i~~~l~~~s~~ve~~siDe~~ldv~~~~---~-~~~ 117 (347)
T PRK14133 42 STCSYEARKYGVHSAMPVFMAKKRCPHGIFLPVRHERYKEVSKNIFKILYEVTPIVEPVSIDEAYLDITNIK---E-EPI 117 (347)
T ss_pred EECCHHHHhcCCCCCChHHHHHHHCCCcEEECCCHHHHHHHHHHHHHHHHHhCCceEEccCCeEEEEccCCC---C-CHH
Confidence 359999999999999999999999999999999999999999999999999999999999999999999986 4 789
Q ss_pred HHHHHHHHHHHHHhCCceEEEecCChhHHHHHhcccCCCCeEEecCChHHHHHhhcCCCcccccCCCHHHHHHHHhhcCC
Q 009298 82 EIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGI 161 (538)
Q Consensus 82 ~la~~IR~~I~~~~Glt~S~GIA~nk~lAKLAS~~aKP~G~~vl~~~~~~~~~fL~~lPl~~L~GIG~kt~~kL~~~lGI 161 (538)
.+|++||++|++++|++||+|||+||++||||++.+||+|++++.++ ++..||+++||++|||||+++.++|++ +||
T Consensus 118 ~la~~i~~~i~~~~gl~~siGia~n~~~Aklas~~~kp~g~~~~~~~--~~~~~L~~lpv~~l~gig~~~~~~L~~-~Gi 194 (347)
T PRK14133 118 KIAKYIKKKVKKETGLTLSVGISYNKFLAKLASDWNKPDGIKIITED--MIPDILKPLPISKVHGIGKKSVEKLNN-IGI 194 (347)
T ss_pred HHHHHHHHHHHHHHCCcEEEEEcCcHHHHHHHhccCCCCceEEECHH--HHHHHHHhCCccccCCCCHHHHHHHHH-cCC
Confidence 99999999999999999999999999999999999999999999875 789999999999999999999999997 999
Q ss_pred CchHHHHhch-HHHHHHcChhHHHHHHHhccCCCCCCCCCCCCCccceeeeccCc-cCCHHHHHHHHHHHHHHHHHHHHH
Q 009298 162 NTCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV-TEDKALLYRKLAEIAEMLSADMQK 239 (538)
Q Consensus 162 ~TlgDL~~lp-~~L~krFG~~~~~~L~~~a~Gid~~~v~~~~~pKSIs~e~tF~~-~~d~e~L~~~L~~Lae~L~~RLr~ 239 (538)
+|++||+++| ..|.++||.. +.++|+.++|++..++.+..++|||+.+.+|.. +.+.+++..+|++|+++|+.+|++
T Consensus 195 ~ti~dl~~l~~~~L~~rfG~~-g~~l~~~a~G~d~~~v~~~~~~ksi~~~~~~~~~~~~~~~l~~~l~~L~~~l~~rL~~ 273 (347)
T PRK14133 195 YTIEDLLKLSREFLIEYFGKF-GVEIYERIRGIDYREVEVSRERKSIGKETTLKKDTKDKEELKKYLKDFSNIISEELKK 273 (347)
T ss_pred ccHHHHhhCCHHHHHHHHhHH-HHHHHHHhCCCCCCCCCCCCCCcceEeeEEcCCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 9999999999 8999999976 567779999999999988889999999999987 789999999999999999999999
Q ss_pred hCCCccEEEEEEEEcCCceeEEEEecCCCCCCHHHHHHHHHHHHHhhC-CCCEEEEEEEecCCCcCc
Q 009298 240 EGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAEL-PVSLRLIGLRVTQFNEDK 305 (538)
Q Consensus 240 ~gl~~rtLtL~Lr~~d~~~~srs~~L~~~t~~~~~L~~~a~~LL~~~l-p~~VR~IGV~ls~L~~~~ 305 (538)
+++.+++++|++++.++...+++++++.||++.+.|+++++.+|+++. +.+||.|||++++|.+..
T Consensus 274 ~~~~~~~l~l~l~~~~~~~~~~~~~l~~~t~~~~~l~~l~~~lle~~~~~~~vr~lgl~~~~l~~~~ 340 (347)
T PRK14133 274 RNLYGKTVTVKIKTSDFQTHTKSKTLNDYIRDKEEIYNVACEILEHINIKEPIRLIGLSVSNLSENK 340 (347)
T ss_pred cCCCcceEEEEEEECCCCeeEEEEECCCCcCCHHHHHHHHHHHHHhccCCCCEEEEEEEEecCCCCc
Confidence 999999999999999999999999999999999999999999999984 689999999999999763
No 6
>PRK02406 DNA polymerase IV; Validated
Probab=100.00 E-value=8.5e-59 Score=485.19 Aligned_cols=305 Identities=38% Similarity=0.538 Sum_probs=287.0
Q ss_pred CccCHHHHHcCCCCCCcHHHHHhhCCCeEEEcCChHHHHHHHHHHHHHHHhcCCCeEeeCccEEEEEcCccchhcCCCHH
Q 009298 2 RFELLSARRFGVRAAMPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGI 81 (538)
Q Consensus 2 ~~~syeAR~~GVr~GM~l~~A~~LCP~Lvvvp~d~~~Y~~~s~~l~~il~~~sp~Ve~~SiDEafLDlT~~~~l~g~~~~ 81 (538)
..|||+||++||++|||+++|+++||+|+++++|++.|+.++++++.++++|+|.||++|+||+|||+|++.++|| ++.
T Consensus 34 ~a~n~~Ar~~GV~~gm~~~~A~~lcP~l~~~~~d~~~y~~~s~~i~~~l~~~sp~ve~~siDe~~ldvt~~~~~~~-~~~ 112 (343)
T PRK02406 34 STCNYEARKFGVRSAMPTAQALKLCPDLIFVPGRFDVYKEVSRQIREIFRRYTDLIEPLSLDEAYLDVTDNKLCIG-SAT 112 (343)
T ss_pred EecCHHHHHhCCCCCCcHHHHHHHCCCeEEECCChHHHHHHHHHHHHHHHHhCCceEEccCCeEEEeccCccccCC-CHH
Confidence 3699999999999999999999999999999999999999999999999999999999999999999999999998 789
Q ss_pred HHHHHHHHHHHHHhCCceEEEecCChhHHHHHhcccCCCCeEEecCChHHHHHhhcCCCcccccCCCHHHHHHHHhhcCC
Q 009298 82 EIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGI 161 (538)
Q Consensus 82 ~la~~IR~~I~~~~Glt~S~GIA~nk~lAKLAS~~aKP~G~~vl~~~~~~~~~fL~~lPl~~L~GIG~kt~~kL~~~lGI 161 (538)
.+|+.||++|++++|++||+|||+|+++||||++.+||+|+++++++ ++..||+++||++|||||+++.++|++ +||
T Consensus 113 ~la~~i~~~i~~~~gl~~siGia~n~~lAklas~~~Kp~g~~~~~~~--~~~~~L~~lpi~~l~giG~~~~~~L~~-~Gi 189 (343)
T PRK02406 113 LIAQEIRQDIFEELGLTASAGVAPNKFLAKIASDWNKPNGLFVITPE--EVDAFLATLPVEKIPGVGKVTAEKLHA-LGI 189 (343)
T ss_pred HHHHHHHHHHHHHHCCCeEEEeccCHHHHHHHhcCCCCCCEEEECHH--HHHHHHHcCCcchhcCCCHHHHHHHHH-cCC
Confidence 99999999999999999999999999999999999999999999875 789999999999999999999999997 999
Q ss_pred CchHHHHhch-HHHHHHcChhHHHHHHHhccCCCCCCCCCCCCCccceeeeccCc-cCCHHHHHHHHHHHHHHHHHHHHH
Q 009298 162 NTCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV-TEDKALLYRKLAEIAEMLSADMQK 239 (538)
Q Consensus 162 ~TlgDL~~lp-~~L~krFG~~~~~~L~~~a~Gid~~~v~~~~~pKSIs~e~tF~~-~~d~e~L~~~L~~Lae~L~~RLr~ 239 (538)
+|++||+++| ..|.++||.. +.++|+.++|+++.++.+..++|+|+++++|+. +.+.+++..+|++|+++|+.||++
T Consensus 190 ~ti~dl~~l~~~~L~~~fG~~-~~~l~~~a~G~d~~~v~~~~~~ksi~~~~~~~~~~~~~~~l~~~l~~l~~~l~~rL~~ 268 (343)
T PRK02406 190 YTCADLQKYDLAELIRHFGKF-GRRLYERARGIDERPVKPDRERKSVGVERTFAEDLYDLEACLAELPRLAEKLERRLER 268 (343)
T ss_pred CcHHHHHhCCHHHHHHHHhHH-HHHHHHHhCCCCCCccccCCCCcceeeeeeCCCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 9999999998 8999999986 567889999999999988888999999999987 789999999999999999999999
Q ss_pred hC--CCccEEEEEEEEcCCceeEEEEecCCCCCCHHHHHHHHHHHHHhhCCCCEEEEEEEecCCCcCcccCCCCcccccH
Q 009298 240 EG--LRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAELPVSLRLIGLRVTQFNEDKVRAPSDPTQKTL 317 (538)
Q Consensus 240 ~g--l~~rtLtL~Lr~~d~~~~srs~~L~~~t~~~~~L~~~a~~LL~~~lp~~VR~IGV~ls~L~~~~~~~~~~~~Q~tI 317 (538)
++ +.+++|+|+++++++...+++.+ ..++++...+...+..|++..++.+||.|||++++|.+.. ..|.+|
T Consensus 269 ~~~~~~~~~l~l~l~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~L~~~~~~~~vr~lgv~~~~l~~~~------~~q~~~ 341 (343)
T PRK02406 269 AKPDKRIKTVGVKLKFADFQQTTKEHT-ADPLDKADLIELLAQALLRRLGGRGVRLLGVGVTLLEPQL------ERQLLL 341 (343)
T ss_pred cCCCccceeEEEEEEeCCCCeEEEecC-CCCCCcHHHHHHHHHHHHhhCcCCCEEEEEEEEecCCcCc------hhhhcc
Confidence 99 99999999999999998888888 7778888888899999998878889999999999999753 356555
Q ss_pred H
Q 009298 318 T 318 (538)
Q Consensus 318 ~ 318 (538)
+
T Consensus 342 ~ 342 (343)
T PRK02406 342 D 342 (343)
T ss_pred C
Confidence 4
No 7
>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=1.5e-58 Score=493.09 Aligned_cols=295 Identities=28% Similarity=0.403 Sum_probs=279.4
Q ss_pred ccCHHHHHcCCCCCCcHHHHHhhCCCeEEEcCChHHHHHHHHHHHHHHHhcCCCeEeeCccEEEEEcCccch-hcCCCHH
Q 009298 3 FELLSARRFGVRAAMPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCR-ERGISGI 81 (538)
Q Consensus 3 ~~syeAR~~GVr~GM~l~~A~~LCP~Lvvvp~d~~~Y~~~s~~l~~il~~~sp~Ve~~SiDEafLDlT~~~~-l~g~~~~ 81 (538)
.|||+||++||++|||+++|+++||+|+++++|++.|.++++++++++++|+|.||++||||+|||||++.+ +++ ++.
T Consensus 88 a~sy~AR~~GV~~gM~~~~A~~lcP~l~vv~~~~~~Y~~~s~~i~~il~~~s~~ve~~SiDE~~lDvt~~~~~~~~-~~~ 166 (404)
T cd01701 88 SCNYEARSYGIKNGMWVGQAKKLCPQLVTLPYDFEAYEEVSLTFYEILASYTDNIEAVSCDEALIDITSLLEETYE-LPE 166 (404)
T ss_pred ecCHHHHhcCCCCCCcHHHHHHHCCCcEEECCChHHHHHHHHHHHHHHHHhCCceEEcccceEEEEcccccccccC-CHH
Confidence 599999999999999999999999999999999999999999999999999999999999999999999985 777 799
Q ss_pred HHHHHHHHHHHHHhCCceEEEecCChhHHHHHhcccCCCCeEEecCChHHHHHhhcCCCcccccCCCHHHHHHHHhhcCC
Q 009298 82 EIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGI 161 (538)
Q Consensus 82 ~la~~IR~~I~~~~Glt~S~GIA~nk~lAKLAS~~aKP~G~~vl~~~~~~~~~fL~~lPl~~L~GIG~kt~~kL~~~lGI 161 (538)
.+|++||++|++++|+|||+|||+||++||||++.+||+|++++.++ ++..||+++||++|||||+++.++|.+ +||
T Consensus 167 ~la~~ir~~I~~~~gl~~siGia~nk~lAKlAs~~aKP~g~~~i~~~--~~~~~L~~lPv~~l~GIG~~~~~~L~~-~Gi 243 (404)
T cd01701 167 ELAEAIRNEIRETTGCSASVGIGPNILLARLATRKAKPDGQYHLSAE--KVEEFLSQLKVGDLPGVGSSLAEKLVK-LFG 243 (404)
T ss_pred HHHHHHHHHHHHHHCCCEEEEEcCCHHHHHHHhcccCCCcEEEECHH--HHHHHhhcCCHhHhCCCCHHHHHHHHH-cCC
Confidence 99999999999999999999999999999999999999999999875 789999999999999999999999997 999
Q ss_pred CchHHHHhch---HHHHHHcChhHHHHHHHhccCCCCCCCCCCCCCccceeeeccCc-cCCHHHHHHHHHHHHHHHHHHH
Q 009298 162 NTCEEMLQKG---SLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV-TEDKALLYRKLAEIAEMLSADM 237 (538)
Q Consensus 162 ~TlgDL~~lp---~~L~krFG~~~~~~L~~~a~Gid~~~v~~~~~pKSIs~e~tF~~-~~d~e~L~~~L~~Lae~L~~RL 237 (538)
+|++||+++| ..|.++||...+.+||+.++|++..++.+..++|||+.+++|+. +.+.+++..+|.+|+++|+.||
T Consensus 244 ~t~~dl~~~~~~~~~L~~~fG~~~g~~L~~~a~G~d~~~v~~~~~~ksi~~~~tf~~~~~~~~~l~~~l~~L~~~l~~rL 323 (404)
T cd01701 244 DTCGGLELRSKTKEKLQKVLGPKTGEKLYDYCRGIDDRPVTGEKERKSVSAEINYGIRFTNVDDVEQFLQRLSEELSKRL 323 (404)
T ss_pred cchHHHHhCcccHHHHHHHHCHHHHHHHHHHhCCcCCCCCCCCCCCccccceeeCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 9999999986 68999999877888999999999999988888999999999987 7899999999999999999999
Q ss_pred HHhCCCccEEEEEEEEc---------------CCceeEEEEecCCCCCCHHHHHHHHHHHHHhhC--CCCEEEEEEEecC
Q 009298 238 QKEGLRGRTLTLKLKTA---------------SFEVRTRAVTLQKYISSSEDILKHASVLLKAEL--PVSLRLIGLRVTQ 300 (538)
Q Consensus 238 r~~gl~~rtLtL~Lr~~---------------d~~~~srs~~L~~~t~~~~~L~~~a~~LL~~~l--p~~VR~IGV~ls~ 300 (538)
+++++.+++|+|++++. ++...+++++++.||++...|+..+..||++++ +.+||+|||++++
T Consensus 324 r~~~~~~~~l~l~l~~~~~~~~~~~~~y~g~~~~~~~~~~~~l~~pT~d~~~i~~~a~~ll~~~~~~~~~vR~lgv~~~~ 403 (404)
T cd01701 324 EESNVTGRQITLKLMKRAPGAPIEPPKYMGHGICDSFSKSSTLGVATDDSGVIGTEAKKLFRDLSIPPEELRGVGIQVTK 403 (404)
T ss_pred HHcCCceeeEEEEEEeccccCccccccccccCCCcEEeeeeECCCCCCCHHHHHHHHHHHHHhccCCCCCeeEEEEEEec
Confidence 99999999999999972 256788999999999999999999999999984 3699999999998
Q ss_pred C
Q 009298 301 F 301 (538)
Q Consensus 301 L 301 (538)
|
T Consensus 404 l 404 (404)
T cd01701 404 L 404 (404)
T ss_pred C
Confidence 6
No 8
>KOG2094 consensus Predicted DNA damage inducible protein [Replication, recombination and repair]
Probab=100.00 E-value=5.8e-60 Score=473.01 Aligned_cols=312 Identities=55% Similarity=0.862 Sum_probs=295.5
Q ss_pred ccCHHHHHcCCCCCCcHHHHHhhCCCeEEEcCChHHHHHHHHHHHHHHHhcCCCeEeeCccEEEEEcCccchhc--C---
Q 009298 3 FELLSARRFGVRAAMPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRER--G--- 77 (538)
Q Consensus 3 ~~syeAR~~GVr~GM~l~~A~~LCP~Lvvvp~d~~~Y~~~s~~l~~il~~~sp~Ve~~SiDEafLDlT~~~~l~--g--- 77 (538)
-+||.||+||||+|||.+.|++|||+|++||.|+.+|+.+|+++.++|..|.|.+.+.|+||+|||+|..++.. |
T Consensus 140 TaNY~ARkFGVRaaMPgFIarklCPdLiiVP~n~~kYt~~Ske~~~v~~~YDsn~~~~SlDEaylnlT~~l~~~~~g~l~ 219 (490)
T KOG2094|consen 140 TANYVARKFGVRAAMPGFIARKLCPDLIIVPLNFSKYTIVSKEIQNVLAQYDSNFCAMSLDEAYLNLTSHLRERELGFLV 219 (490)
T ss_pred hhhHHHHHhhhhhcCchHHHhccCCceEEeCCCcHHHHHHHHHHHHHHHHcCCccccchHHHHHHhHHHHHHHhhcchhh
Confidence 47999999999999999999999999999999999999999999999999999999999999999999998765 3
Q ss_pred -CCHHHHHHHHHHHHHHHhCCceEEEecCChhHHHHHhcccCCCCeEEecCChHHHHHhhcCCCcccccCCCHHHHHHHH
Q 009298 78 -ISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILR 156 (538)
Q Consensus 78 -~~~~~la~~IR~~I~~~~Glt~S~GIA~nk~lAKLAS~~aKP~G~~vl~~~~~~~~~fL~~lPl~~L~GIG~kt~~kL~ 156 (538)
.+..+++++||-+|+++||+|||+|||+|++|||++|+.+||||||++++++..+.+|+.+|||+++.|||+++.+.|.
T Consensus 220 ~nG~~evveeiR~rV~qeTglT~SaGIAaN~lLAKicSd~nKPNgQf~i~~dr~aim~F~kdLPvRkV~GIGrV~E~qLk 299 (490)
T KOG2094|consen 220 ENGITEVVEEIRFRVEQETGLTCSAGIAANKLLAKICSDKNKPNGQFVIPNDRIAIMKFMKDLPVRKVSGIGRVTEQQLK 299 (490)
T ss_pred hccHHHHHHHHHHHHHHhcCceeeccccHhHHHHHHhccccCCCCceEecccHHHHHHHHhcCCcccccchhHHHHHHHH
Confidence 1367999999999999999999999999999999999999999999999998899999999999999999999999999
Q ss_pred hhcCCCchHHHHhchHHHHHHcChhHHHHHHHhccCCCCCCCCCCCCCccceeeeccCccCCHHHHHHHHHHHHHHHHHH
Q 009298 157 DVFGINTCEEMLQKGSLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSVTEDKALLYRKLAEIAEMLSAD 236 (538)
Q Consensus 157 ~~lGI~TlgDL~~lp~~L~krFG~~~~~~L~~~a~Gid~~~v~~~~~pKSIs~e~tF~~~~d~e~L~~~L~~Lae~L~~R 236 (538)
. +||.||+|+.+.-..|...|.+...+.+.+.++|.+.++.+....+|||++|+||..+.+...+...+++||+.|...
T Consensus 300 a-l~IkTcgdm~~k~~ll~~lFsp~S~~~fLr~slG~g~t~~~~~~eRKsis~ErTFs~~sd~~il~~k~qel~~~lsed 378 (490)
T KOG2094|consen 300 A-LGIKTCGDMQQKLVLLSLLFSPKSFQNFLRCSLGLGTTILDEDGERKSISSERTFSSTSDPSILYSKLQELCQMLSED 378 (490)
T ss_pred h-cCceeHHHHHHhhhHHHHHhCchhHHHHHHHhhcCCCCcCccccccccccceeeecccCCHHHHHHHHHHHHHHHHHH
Confidence 5 999999999988888899999988888888899999998888888999999999999999999999999999999999
Q ss_pred HHHhCCCccEEEEEEEEcCCceeEEEEecCCCCCCHHHHHHHHHHHHHhhCCCCEEEEEEEecCCCcCcccCCCCccccc
Q 009298 237 MQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAELPVSLRLIGLRVTQFNEDKVRAPSDPTQKT 316 (538)
Q Consensus 237 Lr~~gl~~rtLtL~Lr~~d~~~~srs~~L~~~t~~~~~L~~~a~~LL~~~lp~~VR~IGV~ls~L~~~~~~~~~~~~Q~t 316 (538)
|+++|+.++||+|+++++.|+..+++.++.....+.++|+..|.+||++.+|..||++||+++.|.... +....|.+
T Consensus 379 lqK~glv~rtvtiKlK~ssFev~Tr~~t~s~vv~S~edi~k~aleLLk~e~~~~iRLlGvR~sqlv~ee---d~~~~~~t 455 (490)
T KOG2094|consen 379 LQKEGLVGRTVTIKLKTSSFEVHTRQKTISQVVHSEEDILKPALELLKQEYPMTIRLLGVRASQLVSEE---DRKLAQQT 455 (490)
T ss_pred HHhcCcccceEEEEEeccceeeeeccCchhhhhccHHHHHHHHHHHHHhhcCceEeeeeeeHhhccchh---ccchhhcc
Confidence 999999999999999999999999999999999999999999999999999999999999999999984 44566777
Q ss_pred HH
Q 009298 317 LT 318 (538)
Q Consensus 317 I~ 318 (538)
+.
T Consensus 456 v~ 457 (490)
T KOG2094|consen 456 VS 457 (490)
T ss_pred hh
Confidence 76
No 9
>PRK02794 DNA polymerase IV; Provisional
Probab=100.00 E-value=3.5e-58 Score=492.68 Aligned_cols=300 Identities=32% Similarity=0.458 Sum_probs=285.8
Q ss_pred CccCHHHHHcCCCCCCcHHHHHhhCCCeEEEcCChHHHHHHHHHHHHHHHhcCCCeEeeCccEEEEEcCccchhcCCCHH
Q 009298 2 RFELLSARRFGVRAAMPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGI 81 (538)
Q Consensus 2 ~~~syeAR~~GVr~GM~l~~A~~LCP~Lvvvp~d~~~Y~~~s~~l~~il~~~sp~Ve~~SiDEafLDlT~~~~l~g~~~~ 81 (538)
..|||+||++||++|||+++|+++||+++++++|++.|+++++++++++++|+|.||++|+||+|||||++.++||....
T Consensus 74 ~a~ny~Ar~~GV~~GM~~~~A~~lcP~l~~v~~d~~~y~~~s~~i~~~l~~~sp~ve~~siDe~~ldvt~~~~l~g~~~~ 153 (419)
T PRK02794 74 STACYIARIHGVRSAMPMFKALKLCPDAVVIKPDMEKYVRVGREVRAMMQALTPLVEPLSIDEAFLDLSGTERLHGAPPA 153 (419)
T ss_pred EecCHHHHHhCCCcCCHHHHHHHHCCCcEEECCCHHHHHHHHHHHHHHHHHhCcceeeccCCeEEEeccchhhhcCCCHH
Confidence 36899999999999999999999999999999999999999999999999999999999999999999999999985566
Q ss_pred HHHHHHHHHHHHHhCCceEEEecCChhHHHHHhcccCCCCeEEecCChHHHHHhhcCCCcccccCCCHHHHHHHHhhcCC
Q 009298 82 EIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGI 161 (538)
Q Consensus 82 ~la~~IR~~I~~~~Glt~S~GIA~nk~lAKLAS~~aKP~G~~vl~~~~~~~~~fL~~lPl~~L~GIG~kt~~kL~~~lGI 161 (538)
.++++|+++|++++|++||+|||+|+++||||++.+||+|++++.++ ++.+||+++||++|||||+++.++|.+ +||
T Consensus 154 ~~~~~i~~~i~~~~gl~~svGIa~n~~lAKlas~~~KP~g~~ii~~~--~~~~~L~~lPl~~L~GiG~~~~~~L~~-~GI 230 (419)
T PRK02794 154 VVLARFARRVEREIGITVSVGLSYNKFLAKIASDLDKPRGFSVIGRA--EALAFLAPKPVGIIWGVGPATAARLAR-DGI 230 (419)
T ss_pred HHHHHHHHHHHHHHCCceEEEEcCCHHHHHHHHhhhCCCCeEecCHH--HHHHHHhcCChhhhCCCCHHHHHHHHH-hcc
Confidence 68999999999999999999999999999999999999999999875 789999999999999999999999997 999
Q ss_pred CchHHHHhch-HHHHHHcChhHHHHHHHhccCCCCCCCCCCCCCccceeeeccCc-cCCHHHHHHHHHHHHHHHHHHHHH
Q 009298 162 NTCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV-TEDKALLYRKLAEIAEMLSADMQK 239 (538)
Q Consensus 162 ~TlgDL~~lp-~~L~krFG~~~~~~L~~~a~Gid~~~v~~~~~pKSIs~e~tF~~-~~d~e~L~~~L~~Lae~L~~RLr~ 239 (538)
+|++||+++| ..|.++||.. +.++|+.++|+++.++.+..++|||+++.+|.. +.+.+++..+|++|+++|+.+|++
T Consensus 231 ~tigdL~~l~~~~L~~rfG~~-g~~l~~~a~G~d~~~v~~~~~~ksi~~~~tl~~~~~~~~~l~~~l~~L~~~l~~rL~~ 309 (419)
T PRK02794 231 RTIGDLQRADEADLMRRFGSM-GLRLWRLARGIDDRKVSPDREAKSVSAETTFETDLSDFEDLEPILWRLSEKVSRRLKA 309 (419)
T ss_pred chHHHHhhCCHHHHHHHHhHH-HHHHHHHhCCCCCCCCccCCCCceeeeeEECCCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 9999999999 8999999985 677889999999999988888999999999987 789999999999999999999999
Q ss_pred hCCCccEEEEEEEEcCCceeEEEEecCCCCCCHHHHHHHHHHHHHhhC-CCCEEEEEEEecCCCcCc
Q 009298 240 EGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAEL-PVSLRLIGLRVTQFNEDK 305 (538)
Q Consensus 240 ~gl~~rtLtL~Lr~~d~~~~srs~~L~~~t~~~~~L~~~a~~LL~~~l-p~~VR~IGV~ls~L~~~~ 305 (538)
+++.+++|+|++++.++...+++++++.||++...|+++++.+|++++ +.+||+|||++++|.+..
T Consensus 310 ~~~~~~~l~l~l~~~~~~~~~~~~~l~~pt~~~~~l~~~~~~ll~~~~~~~~vr~igv~~~~l~~~~ 376 (419)
T PRK02794 310 AGLAGRTVTLKLKTADFRLRTRRRTLEDPTQLADRIFRTARELLEKETDGTAFRLIGIGVSDLSPAD 376 (419)
T ss_pred cCCCcceEEEEEEECCCCceEEEEECCCCcCCHHHHHHHHHHHHHhcccCCCEEEEEEEEecCCCcc
Confidence 999999999999999999999999999999999999999999999985 589999999999999853
No 10
>PRK03352 DNA polymerase IV; Validated
Probab=100.00 E-value=1.1e-57 Score=477.29 Aligned_cols=294 Identities=29% Similarity=0.423 Sum_probs=279.6
Q ss_pred CccCHHHHHcCCCCCCcHHHHHhhCCCeEEEcCChHHHHHHHHHHHHHHHhcCCCeEeeCccEEEEEcCccchhcCCCHH
Q 009298 2 RFELLSARRFGVRAAMPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGI 81 (538)
Q Consensus 2 ~~~syeAR~~GVr~GM~l~~A~~LCP~Lvvvp~d~~~Y~~~s~~l~~il~~~sp~Ve~~SiDEafLDlT~~~~l~g~~~~ 81 (538)
..|||+||++||++||++++|+++||+++++++|++.|+.++++++.++++|+|.||++|+||+|||+|+. ++.
T Consensus 48 ~~~sy~Ar~~GV~~gM~~~~A~~lcP~l~~v~~~~~~y~~~s~~i~~~l~~~s~~ve~~siDe~~ld~t~~------~~~ 121 (346)
T PRK03352 48 TCASYEARAFGVRAGMPLRTAARRCPDAVFLPSDPAAYDAASEEVMATLRDLGVPVEVWGWDEAFLGVDTD------DPE 121 (346)
T ss_pred EECCHHHHHhCCCcCChHHHHHHHCCCeEEECCCcHHHHHHHHHHHHHHHHhCCceEEecCccEEEeCCCC------CHH
Confidence 36999999999999999999999999999999999999999999999999999999999999999999985 689
Q ss_pred HHHHHHHHHHHHHhCCceEEEecCChhHHHHHhcccCCCCeEEecCChHHHHHhhcCCCcccccCCCHHHHHHHHhhcCC
Q 009298 82 EIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGI 161 (538)
Q Consensus 82 ~la~~IR~~I~~~~Glt~S~GIA~nk~lAKLAS~~aKP~G~~vl~~~~~~~~~fL~~lPl~~L~GIG~kt~~kL~~~lGI 161 (538)
.+|+.||++|++++|++||+|||+||++||||++.+||+|++++.++ ++..||+++||++|||||+++.++|++ +||
T Consensus 122 ~la~~ir~~i~~~~gl~~siGia~nk~lAklaa~~~Kp~g~~~~~~~--~~~~~L~~lpl~~l~gig~~~~~~L~~-~Gi 198 (346)
T PRK03352 122 ALAEEIRAAVLERTGLSCSVGIGDNKLRAKIATGFAKPAGVFRLTDA--NWMAVMGDRPTDALWGVGPKTAKRLAA-LGI 198 (346)
T ss_pred HHHHHHHHHHHHHHCCCEEEeecCCHHHHHHHHhhcCCCcEEEECHH--HHHHHHhcCCHHHcCCCCHHHHHHHHH-cCC
Confidence 99999999999989999999999999999999999999999999875 688999999999999999999999998 999
Q ss_pred CchHHHHhch-HHHHHHcChhHHHHHHHhccCCCCCCCCCC-CCCccceeeeccCc-cCCHHHHHHHHHHHHHHHHHHHH
Q 009298 162 NTCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNTPQA-RFRKSISSERTFSV-TEDKALLYRKLAEIAEMLSADMQ 238 (538)
Q Consensus 162 ~TlgDL~~lp-~~L~krFG~~~~~~L~~~a~Gid~~~v~~~-~~pKSIs~e~tF~~-~~d~e~L~~~L~~Lae~L~~RLr 238 (538)
+|++||+++| ..|.++||...+.+|+..++|+|..+++.. ..|||++.+.+|.. +.+.+++..+|++|+++|+.+|+
T Consensus 199 ~ti~dl~~l~~~~L~~~fG~~~~~~l~~~a~G~d~~~~~~~~~~~ksi~~~~tf~~~~~~~~~l~~~l~~L~~~l~~rLr 278 (346)
T PRK03352 199 TTVADLAAADPAELAATFGPTTGPWLLLLARGGGDTEVSAEPWVPRSRSREVTFPQDLTDRAEVESAVRELARRVLDEVV 278 (346)
T ss_pred ccHHHHhcCCHHHHHHHhChHHHHHHHHHhCCCCCCCCCCCCCCCceEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 9999999998 899999998778899999999999988754 34799999999987 78999999999999999999999
Q ss_pred HhCCCccEEEEEEEEcCCceeEEEEecCCCCCCHHHHHHHHHHHHHhh-CCCCEEEEEEEecCCCcC
Q 009298 239 KEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAE-LPVSLRLIGLRVTQFNED 304 (538)
Q Consensus 239 ~~gl~~rtLtL~Lr~~d~~~~srs~~L~~~t~~~~~L~~~a~~LL~~~-lp~~VR~IGV~ls~L~~~ 304 (538)
++++.+++|+|+++++++...+++++++.||++...|++++..+|+++ ++.+||.|||++++|.+.
T Consensus 279 ~~~~~~~~l~l~l~~~~~~~~~~~~~l~~pt~d~~~l~~~~~~ll~~~~~~~~vr~igl~~~~~~~~ 345 (346)
T PRK03352 279 AEGRPVTRVAVKVRTATFYTRTKIRKLPEPTTDPDVIEAAALDVLDRFELDRPVRLLGVRLELAMPD 345 (346)
T ss_pred HcCCccceEEEEEEeCCCceeEEEEECCCCcCCHHHHHHHHHHHHHhccCCCCEEEEEEEEeccCCC
Confidence 999999999999999999888999999999999999999999999997 467999999999999875
No 11
>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=1.4e-57 Score=473.45 Aligned_cols=295 Identities=44% Similarity=0.686 Sum_probs=282.8
Q ss_pred CccCHHHHHcCCCCCCcHHHHHhhCCCeEEEcCChHHHHHHHHHHHHHHHhcCCCeEeeCccEEEEEcCccchhcCCCHH
Q 009298 2 RFELLSARRFGVRAAMPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGI 81 (538)
Q Consensus 2 ~~~syeAR~~GVr~GM~l~~A~~LCP~Lvvvp~d~~~Y~~~s~~l~~il~~~sp~Ve~~SiDEafLDlT~~~~l~g~~~~ 81 (538)
..|||+||++||++||++++|+++||+++++++|++.|+++++++++++++|+|.||++|+||+|+|+|++.++|| ++.
T Consensus 37 ~a~n~~Ar~~GV~~Gm~~~~A~~lcp~l~~~~~~~~~y~~~s~~i~~~l~~~~~~ve~~s~De~~ldv~~~~~~~~-~~~ 115 (334)
T cd03586 37 STASYEARKFGVRSAMPIFQAKKLCPNLIFVPPRFDKYREVSRQIMEILREYTPLVEPLSIDEAYLDVTDYVRLFG-SAT 115 (334)
T ss_pred EEcCHHHHhcCCCcCCcHHHHHHHCCCeEEECCCcHHHHHHHHHHHHHHHHcCCceEEecccceeEccccccccCC-CHH
Confidence 3699999999999999999999999999999999999999999999999999999999999999999999999998 899
Q ss_pred HHHHHHHHHHHHHhCCceEEEecCChhHHHHHhcccCCCCeEEecCChHHHHHhhcCCCcccccCCCHHHHHHHHhhcCC
Q 009298 82 EIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGI 161 (538)
Q Consensus 82 ~la~~IR~~I~~~~Glt~S~GIA~nk~lAKLAS~~aKP~G~~vl~~~~~~~~~fL~~lPl~~L~GIG~kt~~kL~~~lGI 161 (538)
.+|++||++|++++|++||+|||+|+++||||++.+||+|+++++++ ++..||+++||++|||||+++.++|.+ +||
T Consensus 116 ~la~~ir~~i~~~~g~~~siGia~n~~lAklaa~~~kp~g~~i~~~~--~~~~~L~~lpl~~l~gig~~~~~~L~~-~Gi 192 (334)
T cd03586 116 EIAKEIRARIREETGLTASAGIAPNKFLAKIASDLNKPNGLTVIPPE--DVEEFLAPLPVRKIPGVGKVTAEKLKE-LGI 192 (334)
T ss_pred HHHHHHHHHHHHHHCCceEEEEhhcHHHHHHHhcCCCCCcEEEECHH--HHHHHHhcCCchhhCCcCHHHHHHHHH-cCC
Confidence 99999999999999999999999999999999999999999999875 789999999999999999999999997 999
Q ss_pred CchHHHHhch-HHHHHHcChhHHHHHHHhccCCCCCCCCCCCCCccceeeeccCc-cCCHHHHHHHHHHHHHHHHHHHHH
Q 009298 162 NTCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV-TEDKALLYRKLAEIAEMLSADMQK 239 (538)
Q Consensus 162 ~TlgDL~~lp-~~L~krFG~~~~~~L~~~a~Gid~~~v~~~~~pKSIs~e~tF~~-~~d~e~L~~~L~~Lae~L~~RLr~ 239 (538)
+|++||+++| ..|.++||.. +.+++++++|++..++.+..++|+|+++.+|+. +.+.+++.++|..|+++|+.||+.
T Consensus 193 ~ti~dl~~~~~~~L~~~~g~~-~~~l~~~~~G~~~~~v~~~~~~ks~~~~~~~~~~~~~~~~l~~~l~~l~~~l~~rL~~ 271 (334)
T cd03586 193 KTIGDLAKLDVELLKKLFGKS-GRRLYELARGIDNRPVEPDRERKSIGVERTFSEDLTDPEELLEELLELAEELAERLRK 271 (334)
T ss_pred cCHHHHHcCCHHHHHHHHhHH-HHHHHHHhCCCCCCCCCCCCCCCeeeeeEECCCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 9999999999 8999999986 566779999999999988889999999999987 789999999999999999999999
Q ss_pred hCCCccEEEEEEEEcCCceeEEEEecCCCCCCHHHHHHHHHHHHHhhC-CCCEEEEEEEecCC
Q 009298 240 EGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAEL-PVSLRLIGLRVTQF 301 (538)
Q Consensus 240 ~gl~~rtLtL~Lr~~d~~~~srs~~L~~~t~~~~~L~~~a~~LL~~~l-p~~VR~IGV~ls~L 301 (538)
+++.+++++|++++.++...+++.+++.|+++...|++++..+|+++. +.+||.|||++++|
T Consensus 272 ~~~~~~~l~l~l~~~~~~~~~~~~~l~~~t~~~~~l~~~~~~~l~~~~~~~~vr~igv~~~~l 334 (334)
T cd03586 272 RGLKGRTVTVKLKYADFSTRTRSRTLPEPTDDAEDIYELALELLEELLDGRPIRLLGVRLSGL 334 (334)
T ss_pred CCCCeEEEEEEEEECCCCeEEEEEECCCCCCCHHHHHHHHHHHHHhccCCCCEEEEEEEeecC
Confidence 999999999999999999999999999999999999999999999984 57999999999876
No 12
>PRK03348 DNA polymerase IV; Provisional
Probab=100.00 E-value=2.2e-57 Score=490.19 Aligned_cols=298 Identities=28% Similarity=0.408 Sum_probs=282.7
Q ss_pred ccCHHHHHcCCCCCCcHHHHHhhCCC-eEEEcCChHHHHHHHHHHHHHHHhcCCCeEeeCccEEEEEcCccchhcCCCHH
Q 009298 3 FELLSARRFGVRAAMPGFIARKLCPE-LIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGI 81 (538)
Q Consensus 3 ~~syeAR~~GVr~GM~l~~A~~LCP~-Lvvvp~d~~~Y~~~s~~l~~il~~~sp~Ve~~SiDEafLDlT~~~~l~g~~~~ 81 (538)
-|||+||++||++|||+.+|++|||+ ++++++|++.|+.+++++++++++|+|.||++|+||+|||+++.......++.
T Consensus 45 aasyeAR~~GVrsgMp~~~A~~lcP~~lv~v~~d~~~Y~~~s~~i~~~l~~~sp~VE~~SiDE~flD~~~l~~~~~~~~~ 124 (454)
T PRK03348 45 GASYEARVFGARSAMPMHQARRLVGNGAVVLPPRFVVYRAASRRVFDTLRELSPVVEQLSFDEAFVEPAELAGASAEEVE 124 (454)
T ss_pred eCCHHHHhcCCCCCCcHHHHHHhCCCCEEEECCChHHHHHHHHHHHHHHHHhCCceEEecCCeEEEEccccccccCCCHH
Confidence 59999999999999999999999999 99999999999999999999999999999999999999998876432222688
Q ss_pred HHHHHHHHHHHHHhCCceEEEecCChhHHHHHhcccCCCCeEEecCChHHHHHhhcCCCcccccCCCHHHHHHHHhhcCC
Q 009298 82 EIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGI 161 (538)
Q Consensus 82 ~la~~IR~~I~~~~Glt~S~GIA~nk~lAKLAS~~aKP~G~~vl~~~~~~~~~fL~~lPl~~L~GIG~kt~~kL~~~lGI 161 (538)
.+|++||++|++++||+||+|||+||++||||++.+||+|+++++++ ++.+||+++||++|||||+++.++|++ +||
T Consensus 125 ~~a~~lr~~I~~~~Gl~~SvGIa~nk~lAKlAs~~aKP~G~~vi~~~--~~~~~L~~LPv~~L~GIG~~t~~~L~~-lGI 201 (454)
T PRK03348 125 AFAERLRARVREETGLPASVGAGSGKQIAKIASGLAKPDGIRVVPPG--EERELLAPLPVRRLWGIGPVTEEKLHR-LGI 201 (454)
T ss_pred HHHHHHHHHHHHHHCCCeEEEEcCCHHHHHHhhccCCCCcEEEEEch--HHHHHHHhCCccccCCCCHHHHHHHHH-cCC
Confidence 99999999999999999999999999999999999999999999886 688999999999999999999999998 999
Q ss_pred CchHHHHhch-HHHHHHcChhHHHHHHHhccCCCCCCCCCCCCCccceeeeccCc-cCCHHHHHHHHHHHHHHHHHHHHH
Q 009298 162 NTCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV-TEDKALLYRKLAEIAEMLSADMQK 239 (538)
Q Consensus 162 ~TlgDL~~lp-~~L~krFG~~~~~~L~~~a~Gid~~~v~~~~~pKSIs~e~tF~~-~~d~e~L~~~L~~Lae~L~~RLr~ 239 (538)
+|++||+++| ..|.++||...+.+||+.++|++.+++.+..++|+|+.+.+|+. +.+.+.+..+|++|+++|+.||++
T Consensus 202 ~TigDLa~l~~~~L~~~fG~~~g~~L~~~a~G~d~~pv~~~~~~ksis~e~tf~~~i~~~~~l~~~L~~L~~~l~~rL~~ 281 (454)
T PRK03348 202 ETIGDLAALSEAEVANLLGATVGPALHRLARGIDDRPVAERAEAKQISAESTFAVDLTTRAQLREAIERIAEHAHRRLLK 281 (454)
T ss_pred ccHHHHhcCCHHHHHHHHCHHHHHHHHHHHcCCCCCCcccCCCCceEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999 89999999877899999999999999998889999999999987 789999999999999999999999
Q ss_pred hCCCccEEEEEEEEcCCceeEEEEecCCCCCCHHHHHHHHHHHHHhhC-CCCEEEEEEEecCCCc
Q 009298 240 EGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAEL-PVSLRLIGLRVTQFNE 303 (538)
Q Consensus 240 ~gl~~rtLtL~Lr~~d~~~~srs~~L~~~t~~~~~L~~~a~~LL~~~l-p~~VR~IGV~ls~L~~ 303 (538)
+++.+++|+|++++.++...+++++++.||++...|+++++.+|++.. ..+||++||++++|.+
T Consensus 282 ~g~~~r~v~l~l~~~d~~~~srs~~l~~pt~d~~~L~~la~~ll~~~~~~~~vRllgV~~s~l~~ 346 (454)
T PRK03348 282 DGRGARTVTVKLRKSDFSTLTRSATLPYATDDAAVLAATARRLLLDPDEIGPIRLVGVGFSGLSD 346 (454)
T ss_pred cCCCccEEEEEEEeCCCCccEEEEECCCCCCCHHHHHHHHHHHHHhhccCCCeEEEEEEECCCCc
Confidence 999999999999999999999999999999999999999999999874 4789999999999975
No 13
>PRK01810 DNA polymerase IV; Validated
Probab=100.00 E-value=1.6e-57 Score=485.88 Aligned_cols=297 Identities=29% Similarity=0.443 Sum_probs=281.5
Q ss_pred CccCHHHHHcCCCCCCcHHHHHhhCCCeEEEcCChHHHHHHHHHHHHHHHhcCCCeEeeCccEEEEEcCccchhcCCCHH
Q 009298 2 RFELLSARRFGVRAAMPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGI 81 (538)
Q Consensus 2 ~~~syeAR~~GVr~GM~l~~A~~LCP~Lvvvp~d~~~Y~~~s~~l~~il~~~sp~Ve~~SiDEafLDlT~~~~l~g~~~~ 81 (538)
..|||+||++||++|||+++|+++||+|+++|+|++.|+++++++++++++|+|.||++|+||+|||||++.+++ ++.
T Consensus 46 ~a~ny~Ar~~GV~~Gm~~~~A~~lcP~l~~~~~d~~~y~~~s~~i~~~l~~~sp~ve~~siDe~~ldvt~~~~~~--~~~ 123 (407)
T PRK01810 46 VTCSYEARAYGIRTTMPLWEAKRLCPQLIVRRPNFDRYREASRQMFQILSEFTPLVQPVSIDEGYLDITDCYALG--SPL 123 (407)
T ss_pred EEcCHHHHHhCCCCCChHHHHHHHCCCeEEECCChHHHHHHHHHHHHHHHHhCCceEEecCCeEEEeccCccccC--CHH
Confidence 469999999999999999999999999999999999999999999999999999999999999999999998766 489
Q ss_pred HHHHHHHHHHHHHhCCceEEEecCChhHHHHHhcccCCCCeEEecCChHHHHHhhcCCCcccccCCCHHHHHHHHhhcCC
Q 009298 82 EIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGI 161 (538)
Q Consensus 82 ~la~~IR~~I~~~~Glt~S~GIA~nk~lAKLAS~~aKP~G~~vl~~~~~~~~~fL~~lPl~~L~GIG~kt~~kL~~~lGI 161 (538)
++|++||++|++++|++||+|||+|+++||||++.+||+|++++.++ ++..||+++||++|||||+++.++|++ +||
T Consensus 124 ~~a~~i~~~i~~~~gl~~svGia~n~~lAklas~~~Kp~g~~vi~~~--~~~~~L~~lpv~~l~giG~~~~~~L~~-~Gi 200 (407)
T PRK01810 124 EIAKMIQQRLLTELQLPCSIGIAPNKFLAKMASDMKKPLGITVLRKR--DVPEMLWPLPVGEMHGIGEKTAEKLKD-IGI 200 (407)
T ss_pred HHHHHHHHHHHHHHCCceEEEEcCCHHHHHHHhcCCCCCCEEEECHH--HHHHHHHhCCHhhcCCcCHHHHHHHHH-cCC
Confidence 99999999999999999999999999999999999999999999875 688999999999999999999999997 999
Q ss_pred CchHHHHhch-HHHHHHcChhHHHHHHHhccCCCCCCCCCCCC--CccceeeeccCc-cCCHHHHHHHHHHHHHHHHHHH
Q 009298 162 NTCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNTPQARF--RKSISSERTFSV-TEDKALLYRKLAEIAEMLSADM 237 (538)
Q Consensus 162 ~TlgDL~~lp-~~L~krFG~~~~~~L~~~a~Gid~~~v~~~~~--pKSIs~e~tF~~-~~d~e~L~~~L~~Lae~L~~RL 237 (538)
+|++||+++| ..|.++||.. +.++|+.++|+++.++.+..+ +|||+++++|+. +.+.+++..+|.+|+++|+.+|
T Consensus 201 ~tigdL~~~~~~~L~~rfG~~-g~~l~~~a~G~d~~~v~~~~~~~~ksi~~~~~~~~~~~~~~~l~~~l~~L~~~l~~rL 279 (407)
T PRK01810 201 QTIGDLAKADEHILRAKLGIN-GVRLQRRANGIDDRPVDPEAIYQFKSVGNSTTLSHDMDEEKELLDVLRRLSKSVSKRL 279 (407)
T ss_pred CcHHHHHhCCHHHHHHHHhHH-HHHHHHHhcCCCCCCCCCCCCCCCceecceEECCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 9999999999 8999999986 677889999999999876543 599999999998 7899999999999999999999
Q ss_pred HHhCCCccEEEEEEEEcCCceeEEEEecCCCCCCHHHHHHHHHHHHHhhC-CCCEEEEEEEecCCCcC
Q 009298 238 QKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAEL-PVSLRLIGLRVTQFNED 304 (538)
Q Consensus 238 r~~gl~~rtLtL~Lr~~d~~~~srs~~L~~~t~~~~~L~~~a~~LL~~~l-p~~VR~IGV~ls~L~~~ 304 (538)
+++++.+++|+|+++++++...+++++++.||++...|+++++.+|++.+ +.+||++||++++|.+.
T Consensus 280 r~~~~~~~~l~l~lr~~~~~~~~~~~~l~~pt~~~~~l~~~~~~ll~~~~~~~~vr~lgv~~~~l~~~ 347 (407)
T PRK01810 280 QKKTVVSYNVQIMIRYHDRRTITRSKTLKNPIWEKRDIFQAASRLFKQHWNGDPVRLLGVTATDLEWK 347 (407)
T ss_pred HHcCCccceeEEEEEECCCCceEEEEECCCCCCCHHHHHHHHHHHHHhccCCCCEEEEEEEEecCccc
Confidence 99999999999999999999999999999999999999999999999985 46899999999999975
No 14
>PRK03103 DNA polymerase IV; Reviewed
Probab=100.00 E-value=1.8e-57 Score=485.87 Aligned_cols=297 Identities=24% Similarity=0.398 Sum_probs=283.1
Q ss_pred ccCHHHHHcCCCCCCcHHHHHhhCCCeEEEcCChHHHHHHHHHHHHHHHhcCCCeEeeCccEEEEEcCccchhcCCCHHH
Q 009298 3 FELLSARRFGVRAAMPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIE 82 (538)
Q Consensus 3 ~~syeAR~~GVr~GM~l~~A~~LCP~Lvvvp~d~~~Y~~~s~~l~~il~~~sp~Ve~~SiDEafLDlT~~~~l~g~~~~~ 82 (538)
.|||+||++||++|||+++|+++||+|+++++|++.|+.+++++++++++|+|.||++|+||+|||+|++.++|| ++..
T Consensus 45 a~sy~Ar~~GV~~gm~~~~A~~lcP~l~~~~~d~~~y~~~s~~i~~~l~~~sp~ve~~siDe~~lDvt~~~~~~~-~~~~ 123 (409)
T PRK03103 45 AACPLAKAYGVKTAERLWEAQQKCPDLVVVKPRMQRYIDVSLQITRILEDFTDLVEPFSIDEQFLDVTGSQKLFG-SPLE 123 (409)
T ss_pred EcCHHHHHhCCCCCChHHHHHHHCCCeEEECCCHHHHHHHHHHHHHHHHHhCccceecCCCeeEeeccchhhcCC-CHHH
Confidence 689999999999999999999999999999999999999999999999999999999999999999999999998 8999
Q ss_pred HHHHHHHHHHHHhCCceEEEecCChhHHHHHhcc---cCCCCeEEecCChHHHHHhhcCCCcccccCCCHHHHHHHHhhc
Q 009298 83 IAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDI---NKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVF 159 (538)
Q Consensus 83 la~~IR~~I~~~~Glt~S~GIA~nk~lAKLAS~~---aKP~G~~vl~~~~~~~~~fL~~lPl~~L~GIG~kt~~kL~~~l 159 (538)
+|++||++|++++|++||+|||+|+++||||++. +||+|++++.++ ++..||+++||++|||||+++.++|++ +
T Consensus 124 la~~ir~~i~~~~gl~~svGia~n~~lAklas~~~~k~kp~g~~v~~~~--~~~~~L~~lpi~~l~gig~~~~~~L~~-~ 200 (409)
T PRK03103 124 IAQKIQQRIMRETGVYARVGIGPNKLLAKMACDNFAKKNPDGLFTLDKE--DVPADLWPLPVRKLFGVGSRMEKHLRR-M 200 (409)
T ss_pred HHHHHHHHHHHHHCceEEEeecCCHHHHHHHhcchhhcCCCcEEEECHH--HHHHHHHcCCHhhcCCccHHHHHHHHH-c
Confidence 9999999999999999999999999999999998 899999999874 789999999999999999999999997 9
Q ss_pred CCCchHHHHhch-HHHHHHcChhHHHHHHHhccCCCCCCCCCCCC--CccceeeeccCc-cCCHHHHHHHHHHHHHHHHH
Q 009298 160 GINTCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNTPQARF--RKSISSERTFSV-TEDKALLYRKLAEIAEMLSA 235 (538)
Q Consensus 160 GI~TlgDL~~lp-~~L~krFG~~~~~~L~~~a~Gid~~~v~~~~~--pKSIs~e~tF~~-~~d~e~L~~~L~~Lae~L~~ 235 (538)
||+|++||+++| ..|.++||.. +.++|+.++|++++++.+..+ +|||+.+.+|+. +.+.+++...|.+|+++|+.
T Consensus 201 Gi~tigdl~~~~~~~L~~~fG~~-~~~l~~~a~G~d~~~v~~~~~~~~ksi~~~~t~~~~~~~~~~l~~~l~~L~~~l~~ 279 (409)
T PRK03103 201 GIRTIGQLANTPLERLKKRWGIN-GEVLWRTANGIDYSPVTPHSLDRQKAIGHQMTLPRDYRGFEEIKVVLLELCEEVCR 279 (409)
T ss_pred CCCCHHHHhcCCHHHHHHHHCHH-HHHHHHHhcCCCCCcCCcccCCCCCccCCCeECCCCCCCHHHHHHHHHHHHHHHHH
Confidence 999999999999 8999999986 677889999999999977654 589999999987 78999999999999999999
Q ss_pred HHHHhCCCccEEEEEEEEcCCce---eEEEEecCCCCCCHHHHHHHHHHHHHhhC-CCCEEEEEEEecCCCcC
Q 009298 236 DMQKEGLRGRTLTLKLKTASFEV---RTRAVTLQKYISSSEDILKHASVLLKAEL-PVSLRLIGLRVTQFNED 304 (538)
Q Consensus 236 RLr~~gl~~rtLtL~Lr~~d~~~---~srs~~L~~~t~~~~~L~~~a~~LL~~~l-p~~VR~IGV~ls~L~~~ 304 (538)
||++.++.+++|+|++++.+++. .+++++++.||++...|+.+++.+|++++ +.+||+|||++++|.+.
T Consensus 280 rLr~~~~~~~~l~l~lr~~~~~~~~~~~~~~~l~~pt~~~~~l~~~~~~ll~~~~~~~~vr~lgv~~~~l~~~ 352 (409)
T PRK03103 280 RARAKGYMGRTVSVSLRGADFDWPTGFSRQMTLPEPTNLAMEVYEAACKLFHRHWDGKPVRRVGVTLSNLVSD 352 (409)
T ss_pred HHHHhCCceeEEEEEEEeCCCcCCCCcceeeecCCCCCCHHHHHHHHHHHHHhcccCCCceEEEEEEeCCCCC
Confidence 99999999999999999999988 99999999999999999999999999985 47999999999999975
No 15
>cd01703 PolY_Pol_iota DNA Polymerase iota. Pol iota, also called Rad30B, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol iota is thought to be one of the least efficient polymerases, particularly when opposite pyrimidines; it can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine, and prefers to insert guanosine instead of adenosine opposite thymidine. Pol iota is believed to use Hoogsteen rather than Watson-Crick base pairing, which may explain the varying efficiency for different template nucleotides.
Probab=100.00 E-value=1.6e-56 Score=472.72 Aligned_cols=294 Identities=28% Similarity=0.422 Sum_probs=272.3
Q ss_pred ccCHHHHHcCCCCCCcHHHHHhhCCCeEEEcC-ChHHHHHHHHHHHHHHHhcCC--CeEeeCccEEEEEcCccchhcCCC
Q 009298 3 FELLSARRFGVRAAMPGFIARKLCPELIFVPT-DFTKYTYYSDLTRKVFCKYDP--NFMAASLDEAYLDITEVCRERGIS 79 (538)
Q Consensus 3 ~~syeAR~~GVr~GM~l~~A~~LCP~Lvvvp~-d~~~Y~~~s~~l~~il~~~sp--~Ve~~SiDEafLDlT~~~~l~g~~ 79 (538)
.|||+||++||++|||+++|+++||+++++++ |++.|+++++++++++.+|+| .||++|+||+|||+|+...++
T Consensus 35 aasy~AR~~GV~~gm~~~~A~~lcP~li~v~~~~~~~Y~~~S~~i~~~l~~~sp~~~ve~~SiDE~~lDvt~~~~~~--- 111 (379)
T cd01703 35 TCNYEARRLGVKKLMSIKDAKEICPDLVLVNGEDLTPFRDMSKKVYRLLRSYSWNDRVERLGFDENFMDVTEMRLLV--- 111 (379)
T ss_pred EcCHHHHHhCCCCCCcHHHHHHhCCCeEEEcCCChHHHHHHHHHHHHHHHHcCCHhhEEecCCCcEEEEccCccchh---
Confidence 58999999999999999999999999999996 899999999999999999999 999999999999999986654
Q ss_pred HHHHHHHHHHHHHHHhCCceEEEecCChhHHHHHhcccCCCCeEEecC-ChHHHHHhhcCCCcccccCCCHHHHHHHHhh
Q 009298 80 GIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPN-DRMAVMTFISSLPIRKIGGIGKVTEHILRDV 158 (538)
Q Consensus 80 ~~~la~~IR~~I~~~~Glt~S~GIA~nk~lAKLAS~~aKP~G~~vl~~-~~~~~~~fL~~lPl~~L~GIG~kt~~kL~~~ 158 (538)
+..+|++||++|++++|+|||+|||+||++||||++.+||+|++++.+ +.+++.+||+++||++|||||+++.++|++
T Consensus 112 g~~la~~ir~~I~~~~Glt~siGIa~nk~lAKlas~~~KP~g~~~i~~~~~~~~~~fl~~lpv~~l~GiG~~~~~kL~~- 190 (379)
T cd01703 112 ASHIAYEMRERIENELGLTCCAGIASNKLLAKLVGSVNKPNQQTTLLPPSCADLMDFMDLHDLRKIPGIGYKTAAKLEA- 190 (379)
T ss_pred HHHHHHHHHHHHHHHhCCeEEEEEcCCHHHHHHHhhhcCCCCeEEEcCCchHHHHHHhccCCccccCCcCHHHHHHHHH-
Confidence 488999999999999999999999999999999999999999998865 323578899999999999999999999997
Q ss_pred cCCCchHHHHhch---------------H-HHHHHcChhHHHHHHHhccCCCCCCC-CCCCCCccceeeeccCc--cCCH
Q 009298 159 FGINTCEEMLQKG---------------S-LLCAVFSHSTADFFLSVGLGLGSTNT-PQARFRKSISSERTFSV--TEDK 219 (538)
Q Consensus 159 lGI~TlgDL~~lp---------------~-~L~krFG~~~~~~L~~~a~Gid~~~v-~~~~~pKSIs~e~tF~~--~~d~ 219 (538)
+||.|++||++.+ . .|.++||...+.+||+.++|+|.+++ .+...+|||+.+++|.. ..+.
T Consensus 191 ~GI~tigdl~~~~~~~~~~~~~~~~~~s~~~L~~~fG~~~g~~l~~~a~G~d~~~V~~~~~~~ksis~e~tf~~~~~~~~ 270 (379)
T cd01703 191 HGISSVRDLQEFSNRNRQTVGAAPSLLELLLMVKEFGEGIGQRIWKLLFGRDTSPVKPASDFPQQISIEDSYKKCSLEEI 270 (379)
T ss_pred cCCCcHHHHHhCCcccccccccccccccHHHHHHHHCHHHHHHHHHHHCCCCCCccCCCCCCCceeEEeeccCCCCCCCH
Confidence 9999999999877 3 79999998778899999999999999 65667899999999986 4688
Q ss_pred HHHHHHHHHHHHHHHHHHHH--------hCCCccEEEEEEEEcC-----CceeEEEEecCCCCC---------CHHHHHH
Q 009298 220 ALLYRKLAEIAEMLSADMQK--------EGLRGRTLTLKLKTAS-----FEVRTRAVTLQKYIS---------SSEDILK 277 (538)
Q Consensus 220 e~L~~~L~~Lae~L~~RLr~--------~gl~~rtLtL~Lr~~d-----~~~~srs~~L~~~t~---------~~~~L~~ 277 (538)
+++..+|.+|+++|+.||++ .+..++||+|++++.+ |.+.+++.+++.+++ +.+.|++
T Consensus 271 ~~~~~~l~~l~~~l~~rl~~~l~~~~~~~~~~~~tv~l~vr~~~~~~~~~~~~sr~~~l~~~~~~~~~~~~~~~~~~i~~ 350 (379)
T cd01703 271 REARNKIEELLASLLERMKQDLQEVKAGDGRRPHTLRLTLRRYTSTKKHYNRESKQAPIPSHVFQKLTGGNEIAARPIEK 350 (379)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhccchhcCeeeeEEEEEEEECCCCCCccceeeeccccCchhhccccccchhhHHHHHH
Confidence 99999999999999999999 9999999999999999 999999999999997 6789999
Q ss_pred HHHHHHHhhCC------CCEEEEEEEecC
Q 009298 278 HASVLLKAELP------VSLRLIGLRVTQ 300 (538)
Q Consensus 278 ~a~~LL~~~lp------~~VR~IGV~ls~ 300 (538)
.+..||+++++ .+||++||++++
T Consensus 351 ~~~~L~~~~~~~~~~~~~~irl~gv~~~~ 379 (379)
T cd01703 351 ILMRLFRELVPPKNVKGFNLTLLNVCFTN 379 (379)
T ss_pred HHHHHHHHhcccccCCCCceEEEEEEeeC
Confidence 99999998743 379999999975
No 16
>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=7.1e-56 Score=465.08 Aligned_cols=284 Identities=33% Similarity=0.462 Sum_probs=262.3
Q ss_pred CccCHHHHHcCCCCCCcHHHHHhhCCCeEEEcCC-----------------------hHHHHHHHHHHHHHHHhcCCCeE
Q 009298 2 RFELLSARRFGVRAAMPGFIARKLCPELIFVPTD-----------------------FTKYTYYSDLTRKVFCKYDPNFM 58 (538)
Q Consensus 2 ~~~syeAR~~GVr~GM~l~~A~~LCP~Lvvvp~d-----------------------~~~Y~~~s~~l~~il~~~sp~Ve 58 (538)
.-|||+||++||++|||+++|+++||++++++++ ++.|+++|+++++++.+|+|.||
T Consensus 34 ~a~syeAR~~GV~~gm~~~~A~~lcP~l~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Y~~~S~~i~~~l~~~sp~vE 113 (359)
T cd01702 34 IAVSYAARAFGVTRFMTIDEAKKKCPDLILAHVATYKKGEDEADYHENPSPARHKVSLDPYRRASRKILNILKRFGDVVE 113 (359)
T ss_pred EEECHHHHhcCCCCCCcHHHHHHHCCCcEEECCccccccccccccccccccccccccHHHHHHHHHHHHHHHHHcCCceE
Confidence 3589999999999999999999999999999875 99999999999999999999999
Q ss_pred eeCccEEEEEcCccchhcCCCHHHHHHHHHHHHHHHhCCceEEEecCChhHHHHHhcccCCCCeEEecCChHHHHHhhcC
Q 009298 59 AASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISS 138 (538)
Q Consensus 59 ~~SiDEafLDlT~~~~l~g~~~~~la~~IR~~I~~~~Glt~S~GIA~nk~lAKLAS~~aKP~G~~vl~~~~~~~~~fL~~ 138 (538)
++||||+|||+ +..+|++||++|++++|+|||+|||+||++||||++.+||+|+++++++ ++.+||++
T Consensus 114 ~~SiDE~flDv----------~~~la~~ir~~I~~~~glt~SiGIa~nk~lAKlAs~~~KP~g~~v~~~~--~~~~~L~~ 181 (359)
T cd01702 114 KASIDEAYLDL----------GSRIVEEIRQQVYDELGYTCSAGIAHNKMLAKLASGMNKPNAQTILRND--AVASFLSS 181 (359)
T ss_pred ECcCCeeHHHH----------HHHHHHHHHHHHHHHhCccEEeeecCCHHHHHHHhcccCCCCeEEECHH--HHHHHhhc
Confidence 99999999999 4679999999999999999999999999999999999999999999875 78999999
Q ss_pred CCcccccCCCHHHHHH-HHhhcCCCchHHHHhc--h-HHHHHHcChhHHHHHHHhccCCCCCCCCCCCCCccceeeeccC
Q 009298 139 LPIRKIGGIGKVTEHI-LRDVFGINTCEEMLQK--G-SLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFS 214 (538)
Q Consensus 139 lPl~~L~GIG~kt~~k-L~~~lGI~TlgDL~~l--p-~~L~krFG~~~~~~L~~~a~Gid~~~v~~~~~pKSIs~e~tF~ 214 (538)
+||++|||||+++.++ |+. +||+|++||+++ | ..|.++||...+.++|+.++|+|..++.+..++|||+.+++|.
T Consensus 182 lpv~~l~GiG~~~~~~ll~~-~Gi~ti~dl~~~~~~~~~L~~~fG~~~g~~l~~~a~G~d~~~v~~~~~~ksi~~~~tf~ 260 (359)
T cd01702 182 LPITSIRGLGGKLGEEIIDL-LGLPTEGDVAGFRSSESDLQEHFGEKLGEWLYNLLRGIDHEPVKPRPLPKSMGSSKNFP 260 (359)
T ss_pred CcHHHhCCcCHHHHHHHHHH-cCCcCHHHHHhccCCHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCCceeeeeeecC
Confidence 9999999999999776 576 999999999999 8 8899999977789999999999999998888899999999999
Q ss_pred c-cCCH-HHHHHHHHHHHHHHHHHHHHh----CCCccEEEEEEEEcC-CceeEEEEecCCCCCCHHHHHHHHHHHHHhhC
Q 009298 215 V-TEDK-ALLYRKLAEIAEMLSADMQKE----GLRGRTLTLKLKTAS-FEVRTRAVTLQKYISSSEDILKHASVLLKAEL 287 (538)
Q Consensus 215 ~-~~d~-e~L~~~L~~Lae~L~~RLr~~----gl~~rtLtL~Lr~~d-~~~~srs~~L~~~t~~~~~L~~~a~~LL~~~l 287 (538)
. +.+. +++..+|..|+++|+.||++. ++.+++|+|++++++ +.+.+++.+++.++ .+.|++.+..||++++
T Consensus 261 ~~~~~~~~~l~~~l~~L~~~l~~rL~~~~~~~~~~~~~v~v~lr~~~~~~~~sr~~~~~~~~--~~~i~~~~~~l~~~~~ 338 (359)
T cd01702 261 GKTALSTEDVQHWLLVLASELNSRLEDDRYENNRRPKTLVLSLRQRGDGVRRSRSCALPRYD--AQKIVKDAFKLIKAIN 338 (359)
T ss_pred CCCCChHHHHHHHHHHHHHHHHHHHHhhhhhcCceeeEEEEEEEECCCcEEEEEEecCCCCC--HHHHHHHHHHHHHHhh
Confidence 8 5666 999999999999999999997 999999999999999 56666776666555 9999999999999864
Q ss_pred --------CCCEEEEEEEecC
Q 009298 288 --------PVSLRLIGLRVTQ 300 (538)
Q Consensus 288 --------p~~VR~IGV~ls~ 300 (538)
..+||++||++++
T Consensus 339 ~~~~~~~~~~~~rl~g~~~~~ 359 (359)
T cd01702 339 EEGLGLAWNYPLTLLSLSFTK 359 (359)
T ss_pred hhccccccCCCeEEEEEEecC
Confidence 2789999999875
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=9e-56 Score=462.58 Aligned_cols=294 Identities=24% Similarity=0.371 Sum_probs=270.4
Q ss_pred CccCHHHHHcCCCCCCcHHHHHhhCCCe--EEEcCChHHHHHHHHHHHHHHHhcCCCeEeeCccEEEEEcCccchhcCCC
Q 009298 2 RFELLSARRFGVRAAMPGFIARKLCPEL--IFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGIS 79 (538)
Q Consensus 2 ~~~syeAR~~GVr~GM~l~~A~~LCP~L--vvvp~d~~~Y~~~s~~l~~il~~~sp~Ve~~SiDEafLDlT~~~~l~g~~ 79 (538)
..|||+||++||++||++.+|+++||++ +++++|++.|+++++++++++++|+|.||++|+||+|||+|++.+ || +
T Consensus 36 ~~~ny~Ar~~GV~~gm~~~~A~~lcP~l~~~~v~~~~~~y~~~s~~i~~~l~~~~~~ve~~s~De~~ldvt~~~~-~~-~ 113 (344)
T cd01700 36 IARSPEAKALGIKMGSPYFKVPDLLERHGVAVFSSNYALYGDMSRRIMSILERFSPDVEVYSIDESFLDLTGSLR-FG-D 113 (344)
T ss_pred EECCHHHHHhCCCCCCcHHHhHhhccccCeEEEcCchHHHHHHHHHHHHHHHhcCCcceEeecchhhccCcCCCC-CC-C
Confidence 4699999999999999999999999999 999999999999999999999999999999999999999999998 87 8
Q ss_pred HHHHHHHHHHHHHHHhCCceEEEecCChhHHHHHhcccCCC----CeEEecCChHHHHHhhcCCCcccccCCCHHHHHHH
Q 009298 80 GIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPN----GQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHIL 155 (538)
Q Consensus 80 ~~~la~~IR~~I~~~~Glt~S~GIA~nk~lAKLAS~~aKP~----G~~vl~~~~~~~~~fL~~lPl~~L~GIG~kt~~kL 155 (538)
+..+|++||++|++++|++||+|||+||++|||||+.+||+ |++++++.. ....||+++||.+|||||+++.++|
T Consensus 114 ~~~la~~i~~~i~~~~gl~~s~Gia~~~~lAklas~~~kp~~~~~g~~~~~~~~-~~~~~l~~lpl~~l~gig~~~~~~L 192 (344)
T cd01700 114 LEELARKIRRRILQETGIPVTVGIGPTKTLAKLANDLAKKKNPYGGVVDLTDEE-VRDKLLKILPVGDVWGIGRRTAKKL 192 (344)
T ss_pred HHHHHHHHHHHHHHHhCCceEEEecCCHHHHHHHHHHhcCCCCCCeEEEecChh-HHHHHhccCChhhcCccCHHHHHHH
Confidence 99999999999999999999999999999999999999984 787776641 2348999999999999999999999
Q ss_pred HhhcCCCchHHHHhch-HHHHHHcChhHHHHHHHhccCCCCCCCCCCCC-CccceeeeccCc-cCCHHHHHHHHHHHHHH
Q 009298 156 RDVFGINTCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNTPQARF-RKSISSERTFSV-TEDKALLYRKLAEIAEM 232 (538)
Q Consensus 156 ~~~lGI~TlgDL~~lp-~~L~krFG~~~~~~L~~~a~Gid~~~v~~~~~-pKSIs~e~tF~~-~~d~e~L~~~L~~Lae~ 232 (538)
++ +||+|++||+++| ..|.++||.. +.++|+.++|++..++.+..+ +|||+.+.+|.. +.+.+++..+|++|+++
T Consensus 193 ~~-~Gi~ti~dL~~~~~~~L~~rfG~~-~~~l~~~a~G~d~~~v~~~~~~~ks~~~~~~~~~~~~~~~~l~~~l~~L~~~ 270 (344)
T cd01700 193 NA-MGIHTAGDLAQADPDLLRKKFGVV-GERLVRELNGIDCLPLEEYPPPKKSIGSSRSFGRDVTDLDELKQALAEYAER 270 (344)
T ss_pred HH-cCCCcHHHHhcCCHHHHHHHHHHH-HHHHHHHhCCCCCCcCCCCCCCCcEEEEeeEcCCCCCCHHHHHHHHHHHHHH
Confidence 97 9999999999999 8999999986 567789999999999965544 599999999987 78999999999999999
Q ss_pred HHHHHHHhCCCccEEEEEEEEcCCceeEE----EEecCCCCCCHHHHHHHHHHHHHhhC--CCCEEEEEEEecC
Q 009298 233 LSADMQKEGLRGRTLTLKLKTASFEVRTR----AVTLQKYISSSEDILKHASVLLKAEL--PVSLRLIGLRVTQ 300 (538)
Q Consensus 233 L~~RLr~~gl~~rtLtL~Lr~~d~~~~sr----s~~L~~~t~~~~~L~~~a~~LL~~~l--p~~VR~IGV~ls~ 300 (538)
|+.+|+++++.+++|+|++++++|...+. +.+++.|+++...|++.+..+|++++ ..+||+|||++++
T Consensus 271 l~~~L~~~~~~~~~l~l~l~~~~~~~~~~~~~~~~~~~~~t~~~~~l~~~~~~ll~~~~~~~~~iR~iGV~~~~ 344 (344)
T cd01700 271 AAEKLRRQKSVARTISVFIGTSGFSRQPKYYSATNTLPYPTNDTREIVKAALRLLYAIYRPGYAYRKAGVMLSD 344 (344)
T ss_pred HHHHHHHcCCcccEEEEEEEcCCCCCCCCccccccccCCcchhHHHHHHHHHHHHHHHhCCCCcEEEEEEEeeC
Confidence 99999999999999999999998875443 35778899999999999999999985 3689999999975
No 18
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=100.00 E-value=6.2e-55 Score=468.04 Aligned_cols=297 Identities=20% Similarity=0.266 Sum_probs=273.2
Q ss_pred ccCHHHHHcCCCCCCcHHHHHhhCC--CeEEEcCChHHHHHHHHHHHHHHHhcCCCeEeeCccEEEEEcCccchhcCCCH
Q 009298 3 FELLSARRFGVRAAMPGFIARKLCP--ELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISG 80 (538)
Q Consensus 3 ~~syeAR~~GVr~GM~l~~A~~LCP--~Lvvvp~d~~~Y~~~s~~l~~il~~~sp~Ve~~SiDEafLDlT~~~~l~g~~~ 80 (538)
.|||+||++||++|||+++|+++|| +++++++|++.|..+++++++++.+|+|.||++||||+|||||++.++ + ++
T Consensus 39 aasyeAr~~GV~~gmp~~~a~~l~~~~~l~~~~~d~~~y~~~s~~i~~~l~~~tp~ve~~siDE~~lDvt~~~~l-~-~~ 116 (422)
T PRK03609 39 ARSAEAKALGIKMGDPWFKQKDLFRRCGVVCFSSNYELYADMSNRVMSTLEELSPRVEIYSIDEAFCDLTGVRNC-R-DL 116 (422)
T ss_pred EcCHHHHHhCCCCCCcHHHHHHHhccCCeEEeCCCHHHHHHHHHHHHHHHHHhCCCceEeccccceecCCCCcCC-C-CH
Confidence 5899999999999999999999994 399999999999999999999999999999999999999999999876 3 68
Q ss_pred HHHHHHHHHHHHHHhCCceEEEecCChhHHHHHhcccCC-----CCeEEecCChHHHHHhhcCCCcccccCCCHHHHHHH
Q 009298 81 IEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKP-----NGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHIL 155 (538)
Q Consensus 81 ~~la~~IR~~I~~~~Glt~S~GIA~nk~lAKLAS~~aKP-----~G~~vl~~~~~~~~~fL~~lPl~~L~GIG~kt~~kL 155 (538)
..+|++||++|++++|++||+|||+||++||||++.+|| +|++++.+. ++..+||+++||++|||||+++.++|
T Consensus 117 ~~~a~~i~~~I~~~~gl~~siGia~n~~lAK~As~~~k~~~k~~~g~~~i~~~-~~~~~~L~~lPv~~l~GiG~~~~~~L 195 (422)
T PRK03609 117 TDFGREIRATVLQRTHLTVGVGIAQTKTLAKLANHAAKKWQRQTGGVVDLSNL-ERQRKLLSLQPVEEVWGVGRRISKKL 195 (422)
T ss_pred HHHHHHHHHHHHHHHCCceEEEecCCHHHHHHHHHHhCCCCCCCCcEEEcCCH-HHHHHHhhcCChhhcCCccHHHHHHH
Confidence 999999999999999999999999999999999998876 688877422 37899999999999999999999999
Q ss_pred HhhcCCCchHHHHhch-HHHHHHcChhHHHHHHHhccCCCCCCCCCCCCC-ccceeeeccCc-cCCHHHHHHHHHHHHHH
Q 009298 156 RDVFGINTCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNTPQARFR-KSISSERTFSV-TEDKALLYRKLAEIAEM 232 (538)
Q Consensus 156 ~~~lGI~TlgDL~~lp-~~L~krFG~~~~~~L~~~a~Gid~~~v~~~~~p-KSIs~e~tF~~-~~d~e~L~~~L~~Lae~ 232 (538)
++ +||+|++||+++| ..|.++||..+ ..+++.++|++..++....++ |+|+.+++|+. +.+.+++...+.+|+++
T Consensus 196 ~~-lGi~TigdL~~~~~~~L~~~fG~~~-~~l~~~a~G~~~~~~~~~~~~~ksi~~~~tf~~~~~~~~~l~~~l~~l~~~ 273 (422)
T PRK03609 196 NA-MGIKTALDLADTNIRFIRKHFNVVL-ERTVRELRGEPCLSLEEFAPTKQEIVCSRSFGERITDYESMRQAICSYAAR 273 (422)
T ss_pred HH-cCCCcHHHHhcCCHHHHHHHHCHHH-HHHHHHhCCCCCCCccccCCCCceEEEeeECCCCCCCHHHHHHHHHHHHHH
Confidence 97 9999999999999 89999999874 556689999999888766654 79999999987 78999999999999999
Q ss_pred HHHHHHHhCCCccEEEEEEEEcCCc------eeEEEEecCCCCCCHHHHHHHHHHHHHhhCC--CCEEEEEEEecCCCcC
Q 009298 233 LSADMQKEGLRGRTLTLKLKTASFE------VRTRAVTLQKYISSSEDILKHASVLLKAELP--VSLRLIGLRVTQFNED 304 (538)
Q Consensus 233 L~~RLr~~gl~~rtLtL~Lr~~d~~------~~srs~~L~~~t~~~~~L~~~a~~LL~~~lp--~~VR~IGV~ls~L~~~ 304 (538)
|+.+|+++++.+++|+|++++++|. ..+++++++.||++...|++++..+|++++. .++|++||.+++|.+.
T Consensus 274 l~~rLr~~~~~~~~l~l~ir~~~~~~~~~~~~~~~~~~l~~pt~d~~~l~~~a~~ll~~~~~~~~~~r~~GV~~~~l~~~ 353 (422)
T PRK03609 274 AAEKLRGEHQYCRFISTFVKTSPFALNEPYYGNSASVKLLTPTQDSRDIIAAATRALDAIWRDGHRYQKAGVMLGDFFSQ 353 (422)
T ss_pred HHHHHHHcCCcccEEEEEEEcCCccccCCCcCceeEEeCCCCCCCHHHHHHHHHHHHHHHhCCCCceEEeeEEEEeeccC
Confidence 9999999999999999999999986 3578889999999999999999999999753 5799999999999975
No 19
>COG0389 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]
Probab=100.00 E-value=2.5e-50 Score=422.78 Aligned_cols=298 Identities=35% Similarity=0.530 Sum_probs=282.4
Q ss_pred ccCHHHHHcCCCCCCcHHHHHhhCCCeEEEcCChHHHHHHHHHHHHHHHhcCCCeEeeCccEEEEEcCccchhcCC-CHH
Q 009298 3 FELLSARRFGVRAAMPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGI-SGI 81 (538)
Q Consensus 3 ~~syeAR~~GVr~GM~l~~A~~LCP~Lvvvp~d~~~Y~~~s~~l~~il~~~sp~Ve~~SiDEafLDlT~~~~l~g~-~~~ 81 (538)
-|||+||+|||++|||+++|+++||+++++|++++.|..++..++.++.+|+|.||++|+||+|||+|+..+.+|. .+.
T Consensus 41 ~~sy~Ar~~Gv~sam~~~~A~~~cp~~~~~~~~~~~y~~~s~~i~~i~~~~~~~ve~lSIDE~~ldvt~~~~~~g~~~~~ 120 (354)
T COG0389 41 AASYEARAFGVRSAMPLFEALKLCPRAIVAPPNFAAYRLASAEIRAILERYTPLVEPLSIDEAFLDLTDALRLLGLADAP 120 (354)
T ss_pred ecCHHHHHhCCcccChHHHHHHHCCCCEEeCCcHHHHHHHHHHHHHHHHhccccceeeeccceeeecccccccCCcccHH
Confidence 4899999999999999999999999999999999999999999999999999999999999999999999888774 589
Q ss_pred HHHHHHHHHHHHHhCCceEEEecCChhHHHHHhcccCCCCeEEecCChHHHHHhhcCCCcccccCCCHHHHHHHHhhcCC
Q 009298 82 EIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGI 161 (538)
Q Consensus 82 ~la~~IR~~I~~~~Glt~S~GIA~nk~lAKLAS~~aKP~G~~vl~~~~~~~~~fL~~lPl~~L~GIG~kt~~kL~~~lGI 161 (538)
.+|++||..|+.++|+|+|+|||+||++||||++.+||+|++++.+. .+.+||+++|+.++||||+.+.++|+. +||
T Consensus 121 ~~a~~ir~~i~~~~~l~~s~Gi~~nk~laKiAs~~~kp~gi~~~~~~--~~~~~l~~Lpv~~~~GvG~~~~~~l~~-~Gi 197 (354)
T COG0389 121 RIALEIRFGILLELGLTASVGISDNKFLAKIASDLNKPDGITVIEPE--EVPALLWQLPVLEFWGVGKVTAEKLRR-LGI 197 (354)
T ss_pred HHHHHHHHHHHHhhCCEEEEEecCcHHHHHHHhcccCCCCEEEECHH--HHHHHHhcCChhhhCCCCHHHHHHHHH-cCC
Confidence 99999999999999999999999999999999999999999999954 799999999999999999999999997 999
Q ss_pred CchHHHHhch-HHHHHHcChhHHHHHHHhccCCCCCCCCCCCCC-ccceeeeccCc-cCCHHHHHHHHHH-HHHHHHHHH
Q 009298 162 NTCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNTPQARFR-KSISSERTFSV-TEDKALLYRKLAE-IAEMLSADM 237 (538)
Q Consensus 162 ~TlgDL~~lp-~~L~krFG~~~~~~L~~~a~Gid~~~v~~~~~p-KSIs~e~tF~~-~~d~e~L~~~L~~-Lae~L~~RL 237 (538)
.|++|+++.+ ..|.++||..+ .+||..++|+|.+++.....+ ||++.+.+|+. ..+.+.+...|.. |+++++.||
T Consensus 198 ~ti~dl~~~~~~~L~~~~g~~~-~~l~~~a~Gid~~~v~~~~~~~ksi~~~~t~~~d~~~~~~~~~~l~~~l~e~~~~rl 276 (354)
T COG0389 198 STIGDLAETDLDALKKRFGKLG-ERLYRLARGIDNRPVREQALRAKSIGAESTFEEDLTDAEELIERLRARLGEEVVSRL 276 (354)
T ss_pred hhHHHHHhcCHHHHHHHHhHhH-HHHHHHhcCCCccccccccccCccccceeeccccccCHHHHHHHHHHHHHHHHHHHH
Confidence 9999999976 89999999987 889899999999999888887 99999999998 6888877777777 999999999
Q ss_pred HHhCCCccEEEEEEEEcCCceeEEEEecCCCCCCHHHHHHHHHHHHHhhC----CCCEEEEEEEecCCCcC
Q 009298 238 QKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAEL----PVSLRLIGLRVTQFNED 304 (538)
Q Consensus 238 r~~gl~~rtLtL~Lr~~d~~~~srs~~L~~~t~~~~~L~~~a~~LL~~~l----p~~VR~IGV~ls~L~~~ 304 (538)
+..+..++++++++++++|...+++.+++.|+++..+++..+..+++..+ +..+|++||++++|.+.
T Consensus 277 ~~~~~~~r~v~~~~~~~df~~~t~~~~l~~p~~~~~~i~~~~~~l~~~~~~~~~~~~~rl~gv~~~~~~~~ 347 (354)
T COG0389 277 RKSGRHGRTVSVKLKTADFPTNTRSRKLAQPTSDPIEIYAAALPLLPPLLFRGRGRRIRLLGVSGPELIDS 347 (354)
T ss_pred HHhCCCceEEEEEEEecCCCcceeecccCCcCCCHHHHHHHHHHHHHHhhccCCCceEEEEEEEecCcccc
Confidence 99999999999999999999999999999999999999999999999875 35899999999999986
No 20
>cd03468 PolY_like DNA Polymerase Y-family. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in order to access the lesion. Because of their high error rates, TLS polymerases are potential targets for cancer treatment and prevention.
Probab=100.00 E-value=1.9e-50 Score=419.89 Aligned_cols=289 Identities=21% Similarity=0.189 Sum_probs=265.7
Q ss_pred CccCHHHHHcCCCCCCcHHHHHhhCCCeEEEcCChHHHHHHHHHHHHHHHhcCCCeEeeCccEEEEEcCccchhcCCCHH
Q 009298 2 RFELLSARRFGVRAAMPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGI 81 (538)
Q Consensus 2 ~~~syeAR~~GVr~GM~l~~A~~LCP~Lvvvp~d~~~Y~~~s~~l~~il~~~sp~Ve~~SiDEafLDlT~~~~l~g~~~~ 81 (538)
..|||+||++||++|||+++|+++||+++++++|++.|.++++++++++++|+|.|+++|+||+|||+|++.++|| ++.
T Consensus 37 ~~~s~~Ar~~GV~~Gm~~~~A~~lcP~l~~~~~~~~~y~~~s~~i~~~l~~~s~~ve~~s~de~~ldvs~~~~~~~-~~~ 115 (335)
T cd03468 37 LACNAAARAAGVRPGMPLAEALALCPNLQVVEYDPEADARALQELALWLLRFTPLVALDGPDGLLLDVTGCLHLFG-GED 115 (335)
T ss_pred EecCHHHHHcCCCCCCcHHHHHHhCCCCeeecCChHHHHHHHHHHHHHHHhcCCccccCCCCeEEEEcccchhhcC-CHH
Confidence 3699999999999999999999999999999999999999999999999999999999999999999999999998 799
Q ss_pred HHHHHHHHHHHHHhCCceEEEecCChhHHHHHhcccCCCCeEEecCChHHHH-HhhcCCCcccccCCCHHHHHHHHhhcC
Q 009298 82 EIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVM-TFISSLPIRKIGGIGKVTEHILRDVFG 160 (538)
Q Consensus 82 ~la~~IR~~I~~~~Glt~S~GIA~nk~lAKLAS~~aKP~G~~vl~~~~~~~~-~fL~~lPl~~L~GIG~kt~~kL~~~lG 160 (538)
.+|++|++.+ .++|++||+|||+|+++||||++.+||+|++..... ... .|++++|+ ++||||+++.++|++ +|
T Consensus 116 ~~a~~i~~~~-~~~gl~~siGia~n~~~Aklas~~~kp~~~~~~~~~--~~~~~~l~~lp~-~~~gig~~~~~~L~~-~G 190 (335)
T cd03468 116 ALAASLRAAL-ATLGLSARAGIADTPGAAWLLARAGGGRGVLRREAL--AAALVLLAPLPV-AALRLPPETVELLAR-LG 190 (335)
T ss_pred HHHHHHHHHH-HHcCCeEEEEecCCHHHHHHHhccCCCCccCCchHH--HHHhhccCCCCh-hHhCCCHHHHHHHHH-hC
Confidence 9999999999 478999999999999999999999999999876553 333 38899999 599999999999998 99
Q ss_pred CCchHHHHhch-HHHHHHcChhHHHHHHHhccCCCCCCC--CCCCCCccceeeeccCcc-CCHHHHHHHHHHHHHHHHHH
Q 009298 161 INTCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNT--PQARFRKSISSERTFSVT-EDKALLYRKLAEIAEMLSAD 236 (538)
Q Consensus 161 I~TlgDL~~lp-~~L~krFG~~~~~~L~~~a~Gid~~~v--~~~~~pKSIs~e~tF~~~-~d~e~L~~~L~~Lae~L~~R 236 (538)
|+|++||+++| ..|.++||.. +..+|..++|+++.++ .+...+++++.+.+|+.. .+.+ ...+.+|+++|+.+
T Consensus 191 i~t~~dl~~~~~~~l~~rfG~~-~~~l~~~~~G~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~l~~l~~~l~~~ 267 (335)
T cd03468 191 LRTLGDLAALPRAELARRFGLA-LLLRLDQAYGRDPEPLLFSPPPPAFDFRLELQLEEPIARGL--LFPLRRLLEQLCAF 267 (335)
T ss_pred cccHHHHHhCChHHHHhhcCHH-HHHHHHHHCCCCCCCCCCCCCCCChhhhhhcCCCCCcchhH--HHHHHHHHHHHHHH
Confidence 99999999999 8999999987 4556789999999998 455678999999999874 3333 89999999999999
Q ss_pred HHHhCCCccEEEEEEEEcCCceeEEEEecCCCCCCHHHHHHHHHHHHHhhC-C---CCEEEEEEEec
Q 009298 237 MQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAEL-P---VSLRLIGLRVT 299 (538)
Q Consensus 237 Lr~~gl~~rtLtL~Lr~~d~~~~srs~~L~~~t~~~~~L~~~a~~LL~~~l-p---~~VR~IGV~ls 299 (538)
|+++++.+++|+|++++.+++..+.++++..++++...|++.++.+|++.. . .+||+++|++.
T Consensus 268 L~~~~~~~~~l~l~l~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~l~~~~~~~~~~~v~~~~v~~~ 334 (335)
T cd03468 268 LALRGLGARRLSLTLFREDGRVTRVLVGLARPSRDDLPLLRLLRERLERLALPRGIAPVRLLALTAE 334 (335)
T ss_pred HHHcCCeeeEEEEEEEEECCceEEEEEeccCCccCHHHHHHHHHhhhhccCCCCCeeeEEEEEeecc
Confidence 999999999999999999999999999999999999999999999999875 3 68999999874
No 21
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=100.00 E-value=6.7e-48 Score=419.68 Aligned_cols=319 Identities=24% Similarity=0.369 Sum_probs=292.1
Q ss_pred ccCHHHHHcCCCCCCcHHHHHhhCCCeEEEcCChHHHHHHHHHHHHHHHhcCCCeEeeCccEEEEEcCccchhcCCCHHH
Q 009298 3 FELLSARRFGVRAAMPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIE 82 (538)
Q Consensus 3 ~~syeAR~~GVr~GM~l~~A~~LCP~Lvvvp~d~~~Y~~~s~~l~~il~~~sp~Ve~~SiDEafLDlT~~~~l~g~~~~~ 82 (538)
=|||+||++|||+||.+.+|++|||+|+++||||+.|.++++.+|++|.+|+-.|+++|+||+|+|++..+.....++..
T Consensus 415 SCsY~AR~~GIKNGMfV~~A~klCPqL~~lPY~FE~Ykevs~tlYetlasytl~I~aVSCDEa~vd~s~~~~~~~~tp~~ 494 (1016)
T KOG2093|consen 415 SCSYEARAYGIKNGMFVRHAKKLCPQLVILPYDFEAYKEVSETLYETLASYTLNIEAVSCDEAFVDVSDLSDEENETPAV 494 (1016)
T ss_pred ccccHHHHhCcccceeHHHHHHhCcccEeecccHHHHHHHHHHHHHHHHhhccceeeecchhhhhhhhhhhhhhccCHHH
Confidence 49999999999999999999999999999999999999999999999999999999999999999999999888878999
Q ss_pred HHHHHHHHHHHHhCCceEEEecCChhHHHHHhcccCCCCeEEecCChHHHHHhhcCCCcccccCCCHHHHHHHHhhcCCC
Q 009298 83 IAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGIN 162 (538)
Q Consensus 83 la~~IR~~I~~~~Glt~S~GIA~nk~lAKLAS~~aKP~G~~vl~~~~~~~~~fL~~lPl~~L~GIG~kt~~kL~~~lGI~ 162 (538)
+|..||++|++.||++||+|||.|++||+||++.||||||+++.+. .+.+||..++|.+|||+|..+..+|.. +||+
T Consensus 495 la~~IRqEI~e~TgC~aS~Gig~t~LLARlATr~AKP~Gq~~l~a~--~veeFis~~~v~~LPGVG~sm~~kL~s-~~i~ 571 (1016)
T KOG2093|consen 495 LAEHIRQEILEKTGCPASAGIGGTMLLARLATRVAKPNGQFYLSAE--KVEEFISQLKVDDLPGVGSSMKSKLVS-QFIQ 571 (1016)
T ss_pred HHHHHHHHHHhccCCceeeccchHHHHHHHHHhhcCCCceeeecHH--HHHHHhhhcccccCCCccHHHHHHHHH-hccc
Confidence 9999999999999999999999999999999999999999999986 799999999999999999999999997 9999
Q ss_pred chHHHHhch-HHHHHHcChhHHHHHHHhccCCCCCCCCCCCCCccceeeeccCc-cCCHHHHHHHHHHHHHHHHHHHHHh
Q 009298 163 TCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV-TEDKALLYRKLAEIAEMLSADMQKE 240 (538)
Q Consensus 163 TlgDL~~lp-~~L~krFG~~~~~~L~~~a~Gid~~~v~~~~~pKSIs~e~tF~~-~~d~e~L~~~L~~Lae~L~~RLr~~ 240 (538)
|||||+-.. ..|++.||+..+..+|..|+|+|+.|....+.|||++.+.+|.- ..+.-++...|..++++|-.+|..-
T Consensus 572 tCgdLq~~T~~kl~k~~G~Klgq~i~~~CrG~Dd~P~~~~~~RKSvS~dIN~GIRFtn~~ev~~fl~~~~eEl~rkL~ei 651 (1016)
T KOG2093|consen 572 TCGDLQLITLIKLRKVFGPKLGQKIYRGCRGIDDDPRSIEQVRKSVSADINYGIRFTNIKEVEQFLCLLSEELRRKLLEI 651 (1016)
T ss_pred hhHHHHHHHHHHHHhhhcccHHHHHHHhcCCCcCChHHHhhhhcceeeeeecceeeccHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999887 89999999999999999999999999887778999999999996 6888899999999999999999999
Q ss_pred CCCccEEEEEEEEcC---------------CceeEEEEecCCCCCCHHHHHHHHHHHHHhh-C-CCCEEEEEEEec-CCC
Q 009298 241 GLRGRTLTLKLKTAS---------------FEVRTRAVTLQKYISSSEDILKHASVLLKAE-L-PVSLRLIGLRVT-QFN 302 (538)
Q Consensus 241 gl~~rtLtL~Lr~~d---------------~~~~srs~~L~~~t~~~~~L~~~a~~LL~~~-l-p~~VR~IGV~ls-~L~ 302 (538)
++.+++++|++..+. ++..+++.++..||+....|...+..|++.. . +..+|.+||.+. +|.
T Consensus 652 ~k~~~sitLKlMvR~~~APietaK~mGhGiCD~~~rs~~l~~~Td~~~iItt~~~~L~~t~~~~~~elRG~gi~~ntkL~ 731 (1016)
T KOG2093|consen 652 SKTASSITLKLMVRTAKAPIETAKYMGHGICDDFVRSSKLREPTDCNRIITTEVLRLYETNSEPPSELRGLGIHSNTKLM 731 (1016)
T ss_pred hccccchhHHHHhhcCCCCCccccccceeeccchhhhhhccCccccccchHHHHHHHHHhcCCChHHhccchhhcccccc
Confidence 999999999885432 3447889999999999999999999999987 3 367999999995 888
Q ss_pred cCcccCCCCcccccHHHHhccCcccc
Q 009298 303 EDKVRAPSDPTQKTLTNFMTSGHASK 328 (538)
Q Consensus 303 ~~~~~~~~~~~Q~tI~~ff~~~~~~~ 328 (538)
+.. . ...+.-|..+|......+
T Consensus 732 ~~~--~--~~~~~~l~e~Fgt~s~~~ 753 (1016)
T KOG2093|consen 732 DVL--E--NLPPELLSEMFGTYSGKR 753 (1016)
T ss_pred ccc--c--CCcHHHHHhhcccccccc
Confidence 764 1 234667777887766554
No 22
>KOG2095 consensus DNA polymerase iota/DNA damage inducible protein [Replication, recombination and repair]
Probab=100.00 E-value=3.1e-42 Score=370.03 Aligned_cols=247 Identities=35% Similarity=0.512 Sum_probs=225.4
Q ss_pred CccCHHHHHcCCCCCCcHHHHHhhCCCeEEEcC-------ChHHHHHHHHHHHHHHHhcCCCeEeeCccEEEEEcCccch
Q 009298 2 RFELLSARRFGVRAAMPGFIARKLCPELIFVPT-------DFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCR 74 (538)
Q Consensus 2 ~~~syeAR~~GVr~GM~l~~A~~LCP~Lvvvp~-------d~~~Y~~~s~~l~~il~~~sp~Ve~~SiDEafLDlT~~~~ 74 (538)
..|||+||++||+++|++.+|+++||+|++++. |...|+.++..++.+|..|+|.||.+++||+|+|+|.+..
T Consensus 52 IAVsYeARa~GV~R~M~v~EAK~kCPqLvlv~v~~~~~ka~~~~YR~as~ev~~~L~~y~~viek~~~dea~ld~tasvd 131 (656)
T KOG2095|consen 52 IAVSYEARAFGVKRLMTVDEAKKKCPQLVLVHVPVAREKADLPKYREASEEVKESLEPYRPVIEKASKDEAFLDLTASVD 131 (656)
T ss_pred EEEehhhhhhCCchhhhHHHHHhhCCceEEeecccccccchhhhhhhhHHHHHHHHhhhHHHHHHHhhhhhhhhHHHHHH
Confidence 469999999999999999999999999988764 4456999999999999999999999999999999987743
Q ss_pred hc----------------------C----------------------------------------CCHHHHHHHHHHHHH
Q 009298 75 ER----------------------G----------------------------------------ISGIEIAEELRTSVY 92 (538)
Q Consensus 75 l~----------------------g----------------------------------------~~~~~la~~IR~~I~ 92 (538)
.. + .-+..+|++||++|+
T Consensus 132 er~q~L~s~~~~~~~~~~p~~~~~~~~s~~~~~~~~~~~e~~~~~ee~~~~~~~~~d~~~~d~~L~iGa~Iv~EiR~~i~ 211 (656)
T KOG2095|consen 132 ERLQDLQSDEFNMLLEEPPYGLIYGLPSALPNTREATNSENPLMREEIVSLWIENDDFDWDDVRLLIGAQIVKEIRDAIK 211 (656)
T ss_pred HHHHHHhhhhhhhhhhccchhcccCCccccchhhhhhhhccccchhhHhhhhhhccccCchhhhhHHHHHHHHHHHHHHH
Confidence 10 0 014679999999999
Q ss_pred HHhCCceEEEecCChhHHHHHhcccCCCCeEEecCChHHHHHhhcCCCcccccCCCHHHHHHHHhhcCCCchHHHHhch-
Q 009298 93 EEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG- 171 (538)
Q Consensus 93 ~~~Glt~S~GIA~nk~lAKLAS~~aKP~G~~vl~~~~~~~~~fL~~lPl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp- 171 (538)
.+||||||+|||+||+|||||+.++|||.|++++.+ .+.+||..|||.++|++|.+..+.|...+||.+++||++.+
T Consensus 212 ~elg~tCSAGIa~NKmLAKLvsg~nKPnqQTil~~~--~v~~ll~slpi~k~~~lGGk~G~~lie~LGi~~vgdl~~fse 289 (656)
T KOG2095|consen 212 LELGYTCSAGIAHNKMLAKLVSGRNKPNQQTILPNT--YVQDLLDSLPITKIRTLGGKLGEELIEVLGIDSVGDLQQFSE 289 (656)
T ss_pred HHhCceeeccccccHHHHHHHhccCCCCcceecchH--HHHHHHHhCCCceeeeccchHHHHHHHHhCCchHHHHHhcCH
Confidence 999999999999999999999999999999999987 79999999999999999988888888889999999999998
Q ss_pred HHHHHHcChhHHHHHHHhccCCCCCCCCCCCCCccceeeeccCc---cCCHHHHHHHHHHHHHHHHHHHHHh----CCCc
Q 009298 172 SLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV---TEDKALLYRKLAEIAEMLSADMQKE----GLRG 244 (538)
Q Consensus 172 ~~L~krFG~~~~~~L~~~a~Gid~~~v~~~~~pKSIs~e~tF~~---~~d~e~L~~~L~~Lae~L~~RLr~~----gl~~ 244 (538)
..|.+.||...+.|||..++|+|.++|.+...||||+++++|+. ..+.+.+..||..|++++..||-.. ...+
T Consensus 290 ~~L~~~fg~~~g~~l~~la~Gid~s~V~pr~~pkSig~~K~Fpg~~~~~~~~~l~~wl~~la~el~~Rl~~d~~en~r~a 369 (656)
T KOG2095|consen 290 TQLQKKFGEKNGTWLRNLARGIDNSPVRPRGLPKSIGSEKNFPGKRSRKSLEELQRWLNQLAEELAERLGKDRNENKRRA 369 (656)
T ss_pred HHHHHhhCcchhHHHHHHhcccCCCccccCCCCcchhhhhcCCCccccccHHHHHHHHHHHHHHHHHHHHhhhhhhcccc
Confidence 89999999999999999999999999999999999999999996 5788999999999999999998665 4678
Q ss_pred cEEEEE
Q 009298 245 RTLTLK 250 (538)
Q Consensus 245 rtLtL~ 250 (538)
.++.++
T Consensus 370 s~l~~~ 375 (656)
T KOG2095|consen 370 STLVVS 375 (656)
T ss_pred ceEEee
Confidence 888888
No 23
>PF00817 IMS: impB/mucB/samB family; InterPro: IPR001126 In Escherichia coli, UV and many chemicals appear to cause mutagenesis by a process of translesion synthesis that requires DNA polymerase III and the SOS-regulated proteins UmuD, UmuC and RecA. This machinery allows the replication to continue through DNA lesion, and therefore avoid lethal interruption of DNA replication after DNA damage []. UmuC is a well conserved protein in prokaryotes, with a homologue in yeast species. Proteins currently known to belong to this family are listed below: E. coli MucB protein. Plasmid-born analogue of the UmuC protein. Saccharomyces cerevisiae (Baker's yeast) Rev1 protein. Homologue of UmuC also required for normal induction of mutations by physical and chemical agents. Salmonella typhimurium ImpB protein. Plasmid-born analogue of the UmuC protein. Bacterial UmuC protein. E. coli DNA-damage-inducible protein P (DinP). S. typhimurium SamB homologue of UmuC plasmid associated. ; GO: 0003684 damaged DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006281 DNA repair; PDB: 3BJY_A 2AQ4_A 3OSP_A 4DL7_A 4DL6_A 3TQ1_A 3MR2_A 4EEY_A 3MR3_A 4DL4_A ....
Probab=99.94 E-value=2.8e-27 Score=219.17 Aligned_cols=113 Identities=39% Similarity=0.569 Sum_probs=106.6
Q ss_pred CccCHHHHHcCCCCCCcHHHHHhhCCCeEEEcCChHHHHHHHHHHHHHHHhc-CCCeEeeCccEEEEEcCccchhcCCCH
Q 009298 2 RFELLSARRFGVRAAMPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKY-DPNFMAASLDEAYLDITEVCRERGISG 80 (538)
Q Consensus 2 ~~~syeAR~~GVr~GM~l~~A~~LCP~Lvvvp~d~~~Y~~~s~~l~~il~~~-sp~Ve~~SiDEafLDlT~~~~l~g~~~ 80 (538)
..|||+||++||++||++.+|+++||+++++++|++.|++++++++.++++| +|.||.+|+||+|+|+|++.++|| +.
T Consensus 36 ~a~n~~Ar~~GV~~Gm~~~~A~~lcp~l~~~~~d~~~~~~~~~~l~~~l~~~~sp~ve~~s~de~~ldv~~~~~l~~-~~ 114 (149)
T PF00817_consen 36 IAANYEARAAGVRPGMPLAEALALCPDLVVVPPDPERYREASERLAEILYRFSSPRVEVYSPDELFLDVTGSLRLFG-GE 114 (149)
T ss_dssp EEE-HHHHTTTSTTTSBHHHHHHHSTTSEEEEEEHHHHHHHHHHHHHHHHTTTCSEEEEEETTEEEEEEHHHHHHHH-HH
T ss_pred hhhHHHHHhhccccchhhhhHhhhccceeeccccHHHHHHHHHHHHHHHHhcccccceecccccccccCCcchhhcc-hH
Confidence 4799999999999999999999999999999999999999999999999999 789999999999999999999998 78
Q ss_pred HHHHHHHHHHHHHHhCCceEEEecCChhHHHHHhc
Q 009298 81 IEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSD 115 (538)
Q Consensus 81 ~~la~~IR~~I~~~~Glt~S~GIA~nk~lAKLAS~ 115 (538)
..++++|+++|.+++|++||+|||+|+++||||++
T Consensus 115 ~~~~~~l~~~i~~~~gl~~s~Gia~~~~~Aklaa~ 149 (149)
T PF00817_consen 115 EALARRLRQAIAEETGLTASIGIAPNPLLAKLAAD 149 (149)
T ss_dssp HHHHHHHHHHHHHHHS--EEEEEESSHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhCCEEEEEEeCCHHHHHHhcC
Confidence 99999999999999999999999999999999985
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=99.50 E-value=1.4e-13 Score=122.48 Aligned_cols=107 Identities=33% Similarity=0.457 Sum_probs=96.3
Q ss_pred CCCC-CCCCCccceeeeccCc-cCCHHHHHHHHHHHHHHHHHHHHHhCCCccEEEEEEEEcCCc---eeEEEEecCCCCC
Q 009298 196 TNTP-QARFRKSISSERTFSV-TEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFE---VRTRAVTLQKYIS 270 (538)
Q Consensus 196 ~~v~-~~~~pKSIs~e~tF~~-~~d~e~L~~~L~~Lae~L~~RLr~~gl~~rtLtL~Lr~~d~~---~~srs~~L~~~t~ 270 (538)
+||. +..++|||+++++|+. +.+.+.+..+|..|+++|+.||++.++.+++|+|++++.+++ ..+++.+++.|++
T Consensus 2 ~pV~~~~~~~ksi~~~~t~~~~~~~~~~i~~~l~~l~~~l~~rL~~~~~~~~~i~l~l~~~~~~~~~~~~~~~~l~~p~~ 81 (127)
T PF11799_consen 2 EPVQQPRPPPKSIGSERTFPEPISDREEIEEWLRELAEELAERLRERGLAARTITLKLRYSDFGRCSSRSRSIRLPFPTN 81 (127)
T ss_dssp -----SCSS-SEEEEEEEECEEESSHHHHHHHHHHHHHHHHHHHHHCTEEEEEEEEEEEETTSCSCEEEEEEEEECCCEH
T ss_pred CCCCCCCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHhhCcCCceEEEEEEecCCcccceeeEEEeccCCcC
Confidence 4666 7788999999999987 789999999999999999999999999999999999999998 8899999999999
Q ss_pred CHHHHHHHHHHHHHhh-C--CCCEEEEEEEecCCC
Q 009298 271 SSEDILKHASVLLKAE-L--PVSLRLIGLRVTQFN 302 (538)
Q Consensus 271 ~~~~L~~~a~~LL~~~-l--p~~VR~IGV~ls~L~ 302 (538)
+...|+..+..+|++. + ..+||+|||++++|.
T Consensus 82 ~~~~l~~~~~~l~~~~~~~~~~~vr~igv~~~~l~ 116 (127)
T PF11799_consen 82 DADELLKAARELLERLLYDPGFPVRLIGVSASDLI 116 (127)
T ss_dssp CHHHHHHHHHHHHHHHHHHTTCGEEEEEEEEEEEE
T ss_pred CHHHHHHHHHHHHHHHhcCCCCCEEEEEEEECCCc
Confidence 9999999999999665 4 478999999999999
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=98.38 E-value=2.5e-07 Score=63.49 Aligned_cols=31 Identities=48% Similarity=0.679 Sum_probs=27.3
Q ss_pred HHHHHhhcCCCcccccCCCHHHHHHHHhhcCC
Q 009298 130 MAVMTFISSLPIRKIGGIGKVTEHILRDVFGI 161 (538)
Q Consensus 130 ~~~~~fL~~lPl~~L~GIG~kt~~kL~~~lGI 161 (538)
+++.+||+++||+++||||++|+++|++ +||
T Consensus 2 e~v~~~l~~lpi~~~~GIG~kt~~kL~~-~GI 32 (32)
T PF11798_consen 2 EDVPEFLWPLPIRKFWGIGKKTAKKLNK-LGI 32 (32)
T ss_dssp HHHHHHHHCSBGGGSTTS-HHHHHHHHC-TT-
T ss_pred hHHHHHHhcCCHHhhCCccHHHHHHHHH-ccC
Confidence 3789999999999999999999999997 996
No 26
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=97.41 E-value=0.0001 Score=76.76 Aligned_cols=79 Identities=23% Similarity=0.244 Sum_probs=60.5
Q ss_pred hhcCCCcccccCCCHHHHHHHHhhcCCCchHHHHhch-HHHHHHcCh--hHHHHHHHhccC---CC--CCCCCCCCCCcc
Q 009298 135 FISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSH--STADFFLSVGLG---LG--STNTPQARFRKS 206 (538)
Q Consensus 135 fL~~lPl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~krFG~--~~~~~L~~~a~G---id--~~~v~~~~~pKS 206 (538)
.|.++||.++||||++++++|.+ .||.|++||+..+ ..|.+.+|. ..+..++..+.| .+ .+.+.....+++
T Consensus 2 ~~~~~~l~~l~gIg~~~a~~L~~-~Gi~t~~dl~~~~~~~L~~~~g~~~~~a~~l~~~a~~~~~~~~~~t~~~l~~~~ks 80 (317)
T PRK04301 2 KMKEKDLEDLPGVGPATAEKLRE-AGYDTVEAIAVASPKELSEAAGIGESTAAKIIEAAREAADIGGFETALEVLERRKN 80 (317)
T ss_pred CcccccHhhcCCCCHHHHHHHHH-cCCCCHHHHHcCCHHHHHHhcCCCHHHHHHHHHHHHHhhccccCccHHHHHHhhcc
Confidence 47889999999999999999998 9999999999998 799999994 467778888877 32 222222234566
Q ss_pred ceeeeccC
Q 009298 207 ISSERTFS 214 (538)
Q Consensus 207 Is~e~tF~ 214 (538)
++...|+.
T Consensus 81 ~~~~~Tg~ 88 (317)
T PRK04301 81 VGKITTGS 88 (317)
T ss_pred CCccCCCC
Confidence 66555554
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=96.52 E-value=0.002 Score=66.73 Aligned_cols=73 Identities=27% Similarity=0.310 Sum_probs=54.8
Q ss_pred cccccCCCHHHHHHHHhhcCCCchHHHHhch-HHHHHHcChh--HHHHHHHhcc---CCC--CCCCCCCCCCccceeeec
Q 009298 141 IRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHS--TADFFLSVGL---GLG--STNTPQARFRKSISSERT 212 (538)
Q Consensus 141 l~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~krFG~~--~~~~L~~~a~---Gid--~~~v~~~~~pKSIs~e~t 212 (538)
|.++||||++++++|.+ .||.|++||+..+ ..|.+.+|.. .+..++..+. |.+ ...+.....+++++...|
T Consensus 1 l~~i~gig~~~~~~L~~-~Gi~ti~dl~~~~~~~L~~~~g~~~~~a~~l~~~~~~~~~~~~~~t~~~~~~~~~s~~~~~T 79 (310)
T TIGR02236 1 LEDLPGVGPATAEKLRE-AGYDTFEAIAVASPKELSEIAGISEGTAAKIIQAARKAADLGGFETADDVLERRKTIGKITT 79 (310)
T ss_pred CcccCCCCHHHHHHHHH-cCCCCHHHHHcCCHHHHHhccCCCHHHHHHHHHHHHHHhhccCCCCHHHHHHhhccCCeecC
Confidence 46899999999999998 9999999999998 8999999953 5677776666 655 333333344567666665
Q ss_pred cC
Q 009298 213 FS 214 (538)
Q Consensus 213 F~ 214 (538)
+.
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=96.12 E-value=0.0059 Score=47.78 Aligned_cols=48 Identities=25% Similarity=0.381 Sum_probs=39.5
Q ss_pred cccccCCCHHHHHHHHhhcCCCchHHHHhch-HHHHHH--cChhHHHHHHHh
Q 009298 141 IRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFLSV 189 (538)
Q Consensus 141 l~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~kr--FG~~~~~~L~~~ 189 (538)
+..|+|||++++++|.+ .|+.|+.||+..+ ..|.+. +|+..++.+...
T Consensus 7 L~~I~Gig~~~a~~L~~-~G~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~ 57 (60)
T PF14520_consen 7 LLSIPGIGPKRAEKLYE-AGIKTLEDLANADPEELAEIPGIGEKTAEKIIEA 57 (60)
T ss_dssp HHTSTTCHHHHHHHHHH-TTCSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHH
T ss_pred hccCCCCCHHHHHHHHh-cCCCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHH
Confidence 34689999999999998 8999999999987 777775 677777766544
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=95.32 E-value=0.017 Score=49.39 Aligned_cols=36 Identities=28% Similarity=0.374 Sum_probs=30.7
Q ss_pred CcccccCCCHHHHHHHHhhcCCCchHHHHhch-HHHHH
Q 009298 140 PIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCA 176 (538)
Q Consensus 140 Pl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~k 176 (538)
.+++||+||+++++-|.. +||+++.||+..+ ..|..
T Consensus 13 ~L~~iP~IG~a~a~DL~~-LGi~s~~~L~g~dP~~Ly~ 49 (93)
T PF11731_consen 13 DLTDIPNIGKATAEDLRL-LGIRSPADLKGRDPEELYE 49 (93)
T ss_pred HHhcCCCccHHHHHHHHH-cCCCCHHHHhCCCHHHHHH
Confidence 478999999999999997 9999999999875 44443
No 30
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. This entry represents the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone []. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1KDH_A 1KEJ_A 1JMS_A 2IHM_A 3OGU_A 1MQ2_A 2P66_A 7ICI_A 1ZQN_A 1ZQK_A ....
Probab=93.78 E-value=0.045 Score=41.86 Aligned_cols=28 Identities=29% Similarity=0.335 Sum_probs=21.2
Q ss_pred ccccCCCHHHHHHHHhhcCCCchHHHHhc
Q 009298 142 RKIGGIGKVTEHILRDVFGINTCEEMLQK 170 (538)
Q Consensus 142 ~~L~GIG~kt~~kL~~~lGI~TlgDL~~l 170 (538)
..|||||++|++++-. .|++|+.||...
T Consensus 5 ~~I~GVG~~tA~~w~~-~G~rtl~Dl~~~ 32 (52)
T PF10391_consen 5 TGIWGVGPKTARKWYA-KGIRTLEDLRKS 32 (52)
T ss_dssp HTSTT--HHHHHHHHH-TT--SHHHHHHG
T ss_pred hhcccccHHHHHHHHH-hCCCCHHHHhhh
Confidence 5689999999999997 999999999653
No 31
>PF04994 TfoX_C: TfoX C-terminal domain; InterPro: IPR007077 This domain is found in a number of bacterial proteins including the TfoX gene product of Haemophilus influenzae. TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes []. This family corresponds to the C-terminal presumed domain of TfoX. The domain is found in association with the N-terminal domain in some, but not all members of this group, suggesting this is an autonomous and functionally unrelated domain. For example it is found associated with Q9JZR1 from SWISSPROT in IPR002125 from INTERPRO.; PDB: 3BQT_A 3MAB_A.
Probab=93.42 E-value=0.15 Score=42.51 Aligned_cols=31 Identities=29% Similarity=0.588 Sum_probs=24.4
Q ss_pred CcccccCCCHHHHHHHHhhcCCCchHHHHhch
Q 009298 140 PIRKIGGIGKVTEHILRDVFGINTCEEMLQKG 171 (538)
Q Consensus 140 Pl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp 171 (538)
.|++||+||+++++.|.+ .||+|+.||.++-
T Consensus 4 ~l~~LpNig~~~e~~L~~-vGI~t~~~L~~~G 34 (81)
T PF04994_consen 4 RLKDLPNIGPKSERMLAK-VGIHTVEDLRELG 34 (81)
T ss_dssp -GCGSTT--HHHHHHHHH-TT--SHHHHHHHH
T ss_pred chhhCCCCCHHHHHHHHH-cCCCCHHHHHHhC
Confidence 589999999999999998 8999999999884
No 32
>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=92.84 E-value=0.075 Score=41.53 Aligned_cols=24 Identities=21% Similarity=0.227 Sum_probs=17.6
Q ss_pred CccCHHHHHcCCCCCCcHHHHHhh
Q 009298 2 RFELLSARRFGVRAAMPGFIARKL 25 (538)
Q Consensus 2 ~~~syeAR~~GVr~GM~l~~A~~L 25 (538)
..+|+.|+++||++||+..+|+.+
T Consensus 35 ~~vt~~A~~lGI~~Gm~g~eAL~~ 58 (59)
T PF08827_consen 35 ESVTSAAEELGIKPGMTGREALEK 58 (59)
T ss_dssp SEE-HHHHHTT--TT-BHHHHGGG
T ss_pred HHHHHHHHHhCCCCCCCHHHHHHh
Confidence 357999999999999999999864
No 33
>PF03118 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha chain C terminal domain; InterPro: IPR011260 The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals. The alpha subunit (RpoA) initiates RNAP assembly by dimerising to form a platform on which the beta subunits can interact. The alpha subunit consists of a N-terminal domain (NTD) and a C-terminal domain (CTD), connected by a short linker. The NTD is essential for RNAP assembly, while the CTD is necessary for transcription regulation, interacting with transcription factors and promoter upstream elements. In Escherichia coli, the catabolite activator protein (CAP or CRP) was shown to exert its effect through its interactions with the CTD, where CAP binding to CTD promotes RNAP binding to promoter DNA, thereby stimulating transcription initiation at class I CAP-dependent promoters. At class II CAP-dependent promoters, the interaction of CAP with CTD is one of multiple interactions involved in activation []. The CTD has a compact structure of four helices and two long arms enclosing its hydrophobic core, making its folding topology distinct from most other binding proteins. The upstream promoter element-binding site is formed from helices 1 and 4 [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3N97_B 1XS9_D 3K4G_A 3N4M_B 1COO_A 1LB2_E 3IYD_A 1Z3E_B 3GFK_B 3IHQ_B ....
Probab=91.89 E-value=0.24 Score=39.71 Aligned_cols=52 Identities=17% Similarity=0.273 Sum_probs=38.7
Q ss_pred HHhhcCCCcccccCCCHHHHHHHHhhcCCCchHHHHhch-HHHHH--HcChhHHHHH
Q 009298 133 MTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCA--VFSHSTADFF 186 (538)
Q Consensus 133 ~~fL~~lPl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~k--rFG~~~~~~L 186 (538)
...+...||..| ++...+...|++ .||+|++||..++ ..|.+ -||......+
T Consensus 6 ~~~~~~~~I~~L-~LS~Ra~n~L~~-~~I~tv~dL~~~s~~~L~~i~n~G~ksl~EI 60 (66)
T PF03118_consen 6 EEELLDTPIEDL-GLSVRAYNCLKR-AGIHTVGDLVKYSEEDLLKIKNFGKKSLEEI 60 (66)
T ss_dssp -HHHHCSBGGGS-TSBHHHHHHHHC-TT--BHHHHHCS-HHHHHTSTTSHHHHHHHH
T ss_pred hHHHhcCcHHHh-CCCHHHHHHHHH-hCCcCHHHHHhCCHHHHHhCCCCCHhHHHHH
Confidence 356778899999 899999999998 9999999999998 55554 5666655544
No 34
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=91.57 E-value=0.2 Score=45.31 Aligned_cols=31 Identities=29% Similarity=0.499 Sum_probs=28.9
Q ss_pred CcccccCCCHHHHHHHHhhcCCCchHHHHhch
Q 009298 140 PIRKIGGIGKVTEHILRDVFGINTCEEMLQKG 171 (538)
Q Consensus 140 Pl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp 171 (538)
.|+.|-|||++....|+. +||+|..||+.+.
T Consensus 68 DLt~I~GIGPk~e~~Ln~-~GI~tfaQIAAwt 98 (133)
T COG3743 68 DLTRISGIGPKLEKVLNE-LGIFTFAQIAAWT 98 (133)
T ss_pred cchhhcccCHHHHHHHHH-cCCccHHHHHhcC
Confidence 478899999999999998 9999999999986
No 35
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=91.26 E-value=0.38 Score=47.80 Aligned_cols=52 Identities=23% Similarity=0.328 Sum_probs=45.0
Q ss_pred CcccccCCCHHHHHHHHhhcCCCchHHHHhch-HHHHHH--cChhHHHHHHHhccC
Q 009298 140 PIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFLSVGLG 192 (538)
Q Consensus 140 Pl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~kr--FG~~~~~~L~~~a~G 192 (538)
+|.+|+|||++++++|.. .|+.|+.+|...+ ..|.+. +|...+..++..+.+
T Consensus 4 ~L~~IpGIG~krakkLl~-~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l~~ 58 (232)
T PRK12766 4 ELEDISGVGPSKAEALRE-AGFESVEDVRAADQSELAEVDGIGNALAARIKADVGG 58 (232)
T ss_pred ccccCCCcCHHHHHHHHH-cCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHHhcc
Confidence 578899999999999997 9999999999987 888888 888888888766553
No 36
>PRK02362 ski2-like helicase; Provisional
Probab=86.89 E-value=0.72 Score=53.72 Aligned_cols=52 Identities=21% Similarity=0.353 Sum_probs=45.7
Q ss_pred CCcccccCCCHHHHHHHHhhcCCCchHHHHhch-HHHHHHcChhHHHHHHHhcc
Q 009298 139 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHSTADFFLSVGL 191 (538)
Q Consensus 139 lPl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~krFG~~~~~~L~~~a~ 191 (538)
+||..|||||++.+++|.+ +||+|+.||++.. ..|.+.||...+..+...+.
T Consensus 652 ~~L~~ip~i~~~~a~~l~~-~gi~s~~dl~~~~~~~l~~~~g~~~~~~i~~~~~ 704 (737)
T PRK02362 652 LDLVGLRGVGRVRARRLYN-AGIESRADLRAADKSVVLAILGEKIAENILEQAG 704 (737)
T ss_pred HHHhCCCCCCHHHHHHHHH-cCCCCHHHHHhCCHHHHHHHHCHHHHHHHHHHhC
Confidence 5788899999999999998 9999999999886 78888899998888876544
No 37
>COG2251 Predicted nuclease (RecB family) [General function prediction only]
Probab=79.81 E-value=2.5 Score=45.85 Aligned_cols=48 Identities=19% Similarity=0.257 Sum_probs=42.2
Q ss_pred HHHHhhcCCCcccccCCCHHHHHHHHhhcCCCchHHHHhch-HHHHHHcC
Q 009298 131 AVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFS 179 (538)
Q Consensus 131 ~~~~fL~~lPl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~krFG 179 (538)
....+...-.|.-++||++...+.|.. +||+|+.||++.. ..+...+|
T Consensus 217 C~~~a~e~~~L~Lv~Gi~~~r~~~l~~-~GI~Ti~~LA~~~~~~~~~~~g 265 (474)
T COG2251 217 CESEALEEDDLSLVPGITPSRYDVLEE-VGITTIEDLADASLPILELVAG 265 (474)
T ss_pred hhHHHhhccceeccCCCCHHHHHHHHH-cCcchHHHHHhccccchhhhhh
Confidence 567888889999999999999999998 9999999999976 56666666
No 38
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=79.31 E-value=2.1 Score=38.50 Aligned_cols=48 Identities=23% Similarity=0.451 Sum_probs=39.2
Q ss_pred HHHHhhcCCCcccccCCCHHHHHHHHhhcCCCchHHHHhch-HHHHHHcC
Q 009298 131 AVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFS 179 (538)
Q Consensus 131 ~~~~fL~~lPl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~krFG 179 (538)
.+..+...-.+..++|||+..+..|.. .||.|+.+|+..+ ..|....+
T Consensus 45 ~l~~w~~~AdL~ri~gi~~~~a~LL~~-AGv~Tv~~LA~~~p~~L~~~l~ 93 (122)
T PF14229_consen 45 NLLKWVNQADLMRIPGIGPQYAELLEH-AGVDTVEELAQRNPQNLHQKLG 93 (122)
T ss_pred HHHHHHhHHHhhhcCCCCHHHHHHHHH-hCcCcHHHHHhCCHHHHHHHHH
Confidence 456666666677899999999999997 8999999999986 66666654
No 39
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=79.22 E-value=3.6 Score=36.99 Aligned_cols=36 Identities=31% Similarity=0.449 Sum_probs=29.6
Q ss_pred cCCCHHHHHHHHhhcCCCchHHHHhch----H--HHHHHcChh
Q 009298 145 GGIGKVTEHILRDVFGINTCEEMLQKG----S--LLCAVFSHS 181 (538)
Q Consensus 145 ~GIG~kt~~kL~~~lGI~TlgDL~~lp----~--~L~krFG~~ 181 (538)
||||+++..+|.+ .||+|.+||.... . .|....|..
T Consensus 1 pgi~~~~~~~L~~-~GI~t~~~Ll~~~~~~~~r~~La~~~~i~ 42 (122)
T PF14229_consen 1 PGIGPKEAAKLKA-AGIKTTGDLLEAGDTPLGRKALAKKLGIS 42 (122)
T ss_pred CCCCHHHHHHHHH-cCCCcHHHHHHcCCCHHHHHHHHHhcCCC
Confidence 7999999999997 9999999998873 2 366666655
No 40
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=77.65 E-value=1.6 Score=46.04 Aligned_cols=29 Identities=28% Similarity=0.336 Sum_probs=26.3
Q ss_pred cccccCCCHHHHHHHHhhcCCCchHHHHhc
Q 009298 141 IRKIGGIGKVTEHILRDVFGINTCEEMLQK 170 (538)
Q Consensus 141 l~~L~GIG~kt~~kL~~~lGI~TlgDL~~l 170 (538)
+..|||||++++.+|-+ +||+|+.||...
T Consensus 91 l~~i~GiGpk~a~~l~~-lGi~tl~eL~~a 119 (334)
T smart00483 91 FTNVFGVGPKTAAKWYR-KGIRTLEELKKN 119 (334)
T ss_pred HHccCCcCHHHHHHHHH-hCCCCHHHHHhc
Confidence 57789999999999998 999999999654
No 41
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=76.85 E-value=2.6 Score=33.39 Aligned_cols=44 Identities=25% Similarity=0.441 Sum_probs=27.1
Q ss_pred ccCCCHHHHHHHHhhcCCCchHHHHhch-HHHHHH--cChhHHHHHHHh
Q 009298 144 IGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFLSV 189 (538)
Q Consensus 144 L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~kr--FG~~~~~~L~~~ 189 (538)
|||||.++++.|.+.+| |+..|.+.+ ..|.+. +|+..++.++++
T Consensus 8 I~~VG~~~ak~L~~~f~--sl~~l~~a~~e~L~~i~gIG~~~A~si~~f 54 (64)
T PF12826_consen 8 IPGVGEKTAKLLAKHFG--SLEALMNASVEELSAIPGIGPKIAQSIYEF 54 (64)
T ss_dssp STT--HHHHHHHHHCCS--CHHHHCC--HHHHCTSTT--HHHHHHHHHH
T ss_pred CCCccHHHHHHHHHHcC--CHHHHHHcCHHHHhccCCcCHHHHHHHHHH
Confidence 58899999999987455 888887766 566654 666666655443
No 42
>PRK01172 ski2-like helicase; Provisional
Probab=76.56 E-value=3.2 Score=47.78 Aligned_cols=49 Identities=20% Similarity=0.386 Sum_probs=40.4
Q ss_pred CCcccccCCCHHHHHHHHhhcCCCchHHHHhch-HHHHHH--cChhHHHHHHH
Q 009298 139 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFLS 188 (538)
Q Consensus 139 lPl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~kr--FG~~~~~~L~~ 188 (538)
+||..|||+|+..+++|.+ .|++|+.||+.+. ..+.+. +|...++.+..
T Consensus 612 ~~L~~ip~~~~~~a~~l~~-~g~~~~~di~~~~~~~~~~i~~~~~~~~~~i~~ 663 (674)
T PRK01172 612 IDLVLIPKVGRVRARRLYD-AGFKTVDDIARSSPERIKKIYGFSDTLANAIVN 663 (674)
T ss_pred HhhcCCCCCCHHHHHHHHH-cCCCCHHHHHhCCHHHHHHHhccCHHHHHHHHH
Confidence 6889999999999999998 9999999999986 667766 56655555543
No 43
>PRK00254 ski2-like helicase; Provisional
Probab=75.57 E-value=3.3 Score=48.09 Aligned_cols=52 Identities=17% Similarity=0.202 Sum_probs=45.4
Q ss_pred CCcccccCCCHHHHHHHHhhcCCCchHHHHhch-HHHHHH--cChhHHHHHHHhcc
Q 009298 139 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFLSVGL 191 (538)
Q Consensus 139 lPl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~kr--FG~~~~~~L~~~a~ 191 (538)
+|+..|||||++.+++|.+ .|+.|+.|+...+ ..|.+. +|...++.++..+.
T Consensus 645 ~~L~~ipgig~~~~~~l~~-~g~~s~~~i~~a~~~el~~~~gi~~~~a~~i~~~~~ 699 (720)
T PRK00254 645 LELMRLPMIGRKRARALYN-AGFRSIEDIVNAKPSELLKVEGIGAKIVEGIFKHLG 699 (720)
T ss_pred hhhhcCCCCCHHHHHHHHH-ccCCCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHhc
Confidence 6888999999999999997 9999999999987 888888 77888888876643
No 44
>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=75.55 E-value=2.1 Score=44.62 Aligned_cols=29 Identities=28% Similarity=0.536 Sum_probs=25.6
Q ss_pred cccccCCCHHHHHHHHhhcCCCchHHHHhc
Q 009298 141 IRKIGGIGKVTEHILRDVFGINTCEEMLQK 170 (538)
Q Consensus 141 l~~L~GIG~kt~~kL~~~lGI~TlgDL~~l 170 (538)
+..|||||++++++|-+ +||.|+.||...
T Consensus 87 l~~i~GiGpk~a~~l~~-lGi~sl~dL~~a 115 (307)
T cd00141 87 LLRVPGVGPKTARKLYE-LGIRTLEDLRKA 115 (307)
T ss_pred HHcCCCCCHHHHHHHHH-cCCCCHHHHHHH
Confidence 46789999999999996 999999999653
No 45
>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=74.72 E-value=3.1 Score=35.27 Aligned_cols=32 Identities=25% Similarity=0.494 Sum_probs=22.6
Q ss_pred hcCCCcccccCCCHHHHHHHHhhcCCCchHHHH
Q 009298 136 ISSLPIRKIGGIGKVTEHILRDVFGINTCEEML 168 (538)
Q Consensus 136 L~~lPl~~L~GIG~kt~~kL~~~lGI~TlgDL~ 168 (538)
|..-||+.|+|||+.++.+|.. -|+.....|.
T Consensus 16 MGeK~V~~laGIG~~lg~~L~~-~GfdKAy~vL 47 (89)
T PF02961_consen 16 MGEKPVTELAGIGPVLGKRLEE-KGFDKAYVVL 47 (89)
T ss_dssp -TT-BGGGSTT--HHHHHHHHH-TT--BHHHHH
T ss_pred cCCCCccccCCcCHHHHHHHHH-CCCcHHHHHh
Confidence 4456999999999999999997 9998877664
No 46
>PRK08609 hypothetical protein; Provisional
Probab=73.24 E-value=3.6 Score=46.59 Aligned_cols=80 Identities=21% Similarity=0.352 Sum_probs=49.9
Q ss_pred cCCCHHHHHHHHHHHHHHHhCCceEEEecCChhHHHHHhcccCCCCeEEecCChHHHHHhhcCCCcccccCCCHHHHHHH
Q 009298 76 RGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHIL 155 (538)
Q Consensus 76 ~g~~~~~la~~IR~~I~~~~Glt~S~GIA~nk~lAKLAS~~aKP~G~~vl~~~~~~~~~fL~~lPl~~L~GIG~kt~~kL 155 (538)
.| -+..+|..|++-+ +|| .-..+-.|... +++ .+.+ +..|||||++++.+|
T Consensus 54 pg-IG~~ia~kI~Eil--~tG--------~~~~le~l~~~---------~p~---~~~~------l~~i~GiGpk~a~~l 104 (570)
T PRK08609 54 KG-IGKGTAEVIQEYR--ETG--------ESSVLQELKKE---------VPE---GLLP------LLKLPGLGGKKIAKL 104 (570)
T ss_pred CC-cCHHHHHHHHHHH--HhC--------ChHHHHHHHhh---------CcH---HHHH------HhcCCCCCHHHHHHH
Confidence 45 3677898888777 344 23344444432 111 1222 457899999999999
Q ss_pred HhhcCCCchHHHHhch--HHHH--HHcChhHHH
Q 009298 156 RDVFGINTCEEMLQKG--SLLC--AVFSHSTAD 184 (538)
Q Consensus 156 ~~~lGI~TlgDL~~lp--~~L~--krFG~~~~~ 184 (538)
.+.+||+|+.||.... ..+. ..||....+
T Consensus 105 ~~~lGi~tl~~L~~a~~~~~~~~~~gfg~k~~~ 137 (570)
T PRK08609 105 YKELGVVDKESLKEACENGKVQALAGFGKKTEE 137 (570)
T ss_pred HHHhCCCCHHHHHHHHHhCChhhccCcchhHHH
Confidence 8559999999997643 1122 346755433
No 47
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=71.36 E-value=1.7 Score=31.52 Aligned_cols=26 Identities=27% Similarity=0.583 Sum_probs=24.2
Q ss_pred ccccccccCCCCCcHhhhhccccchH
Q 009298 451 YKCSLCGTEMPPSFIEERQEHSDFHL 476 (538)
Q Consensus 451 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 476 (538)
-+|+.||..--|+=.|.+..|.-||=
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 48999999999999999999999983
No 48
>PRK07758 hypothetical protein; Provisional
Probab=68.96 E-value=9.9 Score=32.72 Aligned_cols=43 Identities=14% Similarity=0.159 Sum_probs=34.0
Q ss_pred ccCCCHHHHHHHHhhcCCCchHHHHhch-HHHHH--HcChhHHHHHH
Q 009298 144 IGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCA--VFSHSTADFFL 187 (538)
Q Consensus 144 L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~k--rFG~~~~~~L~ 187 (538)
+++++-....-|.+ .||+|++||..++ ..|.+ -||+...+.|.
T Consensus 39 ~~~LSvRA~N~Lk~-AGI~TL~dLv~~te~ELl~iknlGkKSL~EIk 84 (95)
T PRK07758 39 LSLLSAPARRALEH-HGIHTVEELSKYSEKEILKLHGMGPASLPKLR 84 (95)
T ss_pred CccccHHHHHHHHH-cCCCcHHHHHcCCHHHHHHccCCCHHHHHHHH
Confidence 46888888999997 8999999999998 55553 57877666654
No 49
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=67.27 E-value=4.1 Score=47.14 Aligned_cols=31 Identities=29% Similarity=0.603 Sum_probs=28.4
Q ss_pred CCcccccCCCHHHHHHHHhhcCCCchHHHHhc
Q 009298 139 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQK 170 (538)
Q Consensus 139 lPl~~L~GIG~kt~~kL~~~lGI~TlgDL~~l 170 (538)
.||+.|.|||+++++.|.+ +||.|+.||+..
T Consensus 9 ~~~~~l~gvg~~~~~~l~~-lgi~t~~dll~~ 39 (681)
T PRK10917 9 APLTSLKGVGPKTAEKLAK-LGIHTVQDLLLH 39 (681)
T ss_pred CChhhcCCCCHHHHHHHHH-cCCCCHHHHhhc
Confidence 4899999999999999998 999999999753
No 50
>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=67.16 E-value=6.3 Score=43.35 Aligned_cols=54 Identities=19% Similarity=0.205 Sum_probs=40.4
Q ss_pred HHHhhcCCCcccccCCCHHHHHHHHhhcCCCchHHHHhch-HHHHH--HcChhHHHHH
Q 009298 132 VMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCA--VFSHSTADFF 186 (538)
Q Consensus 132 ~~~fL~~lPl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~k--rFG~~~~~~L 186 (538)
.......-+|..|+||+++....|++ .||+|+.||++.. ..|.. .++...+..|
T Consensus 200 ~~~~~~~~~lslv~gi~~~~~~~L~~-~GI~ti~~La~~~~~~l~~~~~~~~~~~~~l 256 (457)
T TIGR03491 200 EAVAKEEGHLSLVPGIGPSRYRLLQE-LGIHTLEDLAAADPNDLEDFGEQGLGVAEQL 256 (457)
T ss_pred HHHHHhcCCeeecCCCCHHHHHHHHH-cCCCcHHHHhcCCccccccccccCHHHHHHH
Confidence 44555577999999999999999997 9999999999885 33444 3454444444
No 51
>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=65.76 E-value=3.4 Score=27.85 Aligned_cols=17 Identities=29% Similarity=0.479 Sum_probs=13.1
Q ss_pred cccccCCCHHHHHHHHh
Q 009298 141 IRKIGGIGKVTEHILRD 157 (538)
Q Consensus 141 l~~L~GIG~kt~~kL~~ 157 (538)
|.+|||||++++..+..
T Consensus 13 L~~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 13 LMKLPGIGPKTANAILS 29 (30)
T ss_dssp HHTSTT-SHHHHHHHHH
T ss_pred HHhCCCcCHHHHHHHHh
Confidence 57889999999988753
No 52
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=64.47 E-value=9.6 Score=43.14 Aligned_cols=53 Identities=23% Similarity=0.231 Sum_probs=42.2
Q ss_pred CCCcccccCCCHHHHHHHHhhcCCCchHHHHhch-HHHHHH-cChhHHHHHHHhccC
Q 009298 138 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV-FSHSTADFFLSVGLG 192 (538)
Q Consensus 138 ~lPl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~kr-FG~~~~~~L~~~a~G 192 (538)
.-+|.+|||||+++.++|-+ -..|+..+.+.+ ..|.+. +|...+..++....|
T Consensus 513 ~S~Ld~I~GiG~kr~~~Ll~--~Fgs~~~ik~As~eeL~~vgi~~~~A~~I~~~l~~ 567 (567)
T PRK14667 513 KDILDKIKGIGEVKKEIIYR--NFKTLYDFLKADDEELKKLGIPPSVKQEVKKYLSG 567 (567)
T ss_pred cCccccCCCCCHHHHHHHHH--HhCCHHHHHhCCHHHHHHcCCCHHHHHHHHHHhcC
Confidence 35789999999999999876 455899998887 888888 556778877766554
No 53
>PF02889 Sec63: Sec63 Brl domain; InterPro: IPR004179 This domain was named after the yeast Sec63 (or NPL1) (also known as the Brl domain) protein in which it was found. This protein is required for assembly of functional endoplasmic reticulum translocons [, ]. Other yeast proteins containing this domain include pre-mRNA splicing helicase BRR2, HFM1 protein and putative helicases. ; PDB: 3IM2_A 3IM1_A 3HIB_A 2Q0Z_X.
Probab=63.75 E-value=12 Score=38.37 Aligned_cols=54 Identities=19% Similarity=0.242 Sum_probs=37.0
Q ss_pred CCcccccCCCHHHHHHHHhhcCCCchHHHHhch-HHHHHHcC--hhHHHHHHHhccCC
Q 009298 139 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFS--HSTADFFLSVGLGL 193 (538)
Q Consensus 139 lPl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~krFG--~~~~~~L~~~a~Gi 193 (538)
.|+..||+||....++|.+ .||.|++||.+++ ..+...++ ...+..+...+..+
T Consensus 148 ~~L~Qlp~i~~~~~~~l~~-~~i~~l~~l~~~~~~e~~~ll~~~~~~~~~i~~~~~~~ 204 (314)
T PF02889_consen 148 SPLLQLPHIGEESLKKLEK-RGIKTLQDLRDLSPEELEELLNRNPPFGKEILEVASRI 204 (314)
T ss_dssp -GGGGSTT--HHHHHHHHH-TT--SHHHHHHS-HHHHHHHH-S-HHHHHHHHHHHCCS
T ss_pred ChhhcCCCCCHHHHHHHhc-cCCCcHHHHhhCCHHHHHHHHhhhhhhHHHHHHHHHHC
Confidence 5899999999999999998 9999999999997 67777765 33455555555543
No 54
>PTZ00035 Rad51 protein; Provisional
Probab=62.10 E-value=10 Score=39.98 Aligned_cols=52 Identities=23% Similarity=0.280 Sum_probs=40.7
Q ss_pred CCcccc--cCCCHHHHHHHHhhcCCCchHHHHhch-HHHHHHcChh--HHHHHHHhcc
Q 009298 139 LPIRKI--GGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHS--TADFFLSVGL 191 (538)
Q Consensus 139 lPl~~L--~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~krFG~~--~~~~L~~~a~ 191 (538)
++|.+| +||++.+.++|+. -||.|+.||+..+ ..|.+..|.. .++.+...++
T Consensus 21 ~~~~~l~~~g~~~~~~~kL~~-~g~~t~~~~~~~~~~~L~~~~gis~~~~~~i~~~~~ 77 (337)
T PTZ00035 21 QEIEKLQSAGINAADIKKLKE-AGICTVESVAYATKKDLCNIKGISEAKVEKIKEAAS 77 (337)
T ss_pred ccHHHHhcCCCCHHHHHHHHH-cCCCcHHHHHhCCHHHHHHhhCCCHHHHHHHHHHHH
Confidence 478888 6799999999997 9999999999987 7888888843 3444444333
No 55
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=58.44 E-value=7.2 Score=44.57 Aligned_cols=32 Identities=31% Similarity=0.614 Sum_probs=28.9
Q ss_pred CCcccccCCCHHHHHHHHhhcCCCchHHHHhc-h
Q 009298 139 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQK-G 171 (538)
Q Consensus 139 lPl~~L~GIG~kt~~kL~~~lGI~TlgDL~~l-p 171 (538)
.|+..+.|||++++++|++ +||+|+.||+-. |
T Consensus 10 ~~l~~l~gig~~~a~~l~~-Lgi~tv~DLL~~~P 42 (677)
T COG1200 10 VPLSTLKGIGPKTAEKLKK-LGIHTVQDLLLYLP 42 (677)
T ss_pred cchhhhcCcCHHHHHHHHH-cCCCcHHHHHHhCc
Confidence 3899999999999999997 999999999764 5
No 56
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=55.87 E-value=13 Score=39.40 Aligned_cols=43 Identities=28% Similarity=0.345 Sum_probs=37.0
Q ss_pred CCCcccc--cCCCHHHHHHHHhhcCCCchHHHHhch-HHHHHHcChh
Q 009298 138 SLPIRKI--GGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHS 181 (538)
Q Consensus 138 ~lPl~~L--~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~krFG~~ 181 (538)
..+|.+| .||++.+.++|+. -||+|+.||+..+ ..|.+.-|..
T Consensus 28 ~~~~~~l~~~g~~~~~~~kL~~-~g~~tv~~~~~~~~~~L~~~~g~s 73 (344)
T PLN03187 28 FESIDKLISQGINAGDVKKLQD-AGIYTCNGLMMHTKKNLTGIKGLS 73 (344)
T ss_pred ccCHHHHhhCCCCHHHHHHHHH-cCCCcHHHHHhCCHHHHHHhcCCC
Confidence 6678888 5799999999997 9999999999987 7888877743
No 57
>cd07556 Nucleotidyl_cyc_III Class III nucleotidyl cyclases. Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's). The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways.
Probab=55.66 E-value=1.2e+02 Score=25.72 Aligned_cols=61 Identities=11% Similarity=0.060 Sum_probs=36.7
Q ss_pred HHHHHHHHHhcCCCeEeeCccEEEEEcCccchhcCCCHHHHHHHHHHHHHHHh-----CCceEEEecCC
Q 009298 43 SDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEA-----GLTCSAGVAPN 106 (538)
Q Consensus 43 s~~l~~il~~~sp~Ve~~SiDEafLDlT~~~~l~g~~~~~la~~IR~~I~~~~-----Glt~S~GIA~n 106 (538)
.+.+..++..+...+..++-|+.++=+.+... . ....++.+|++.+.... ++++++|++..
T Consensus 32 ~~~l~~~~~~~~~~~~r~~~d~f~~l~~~~~~-~--~~~~~~~~i~~~~~~~~~~~~~~~~~~ig~~~g 97 (133)
T cd07556 32 AGRFDSLIRRSGDLKIKTIGDEFMVVSGLDHP-A--AAVAFAEDMREAVSALNQSEGNPVRVRIGIHTG 97 (133)
T ss_pred HHHHHHHHHHcCcEEEEeecceEEEEECchHH-H--HHHHHHHHHHHHHHHHHhccCCceEEEEEEecc
Confidence 44444555554555677788887766654211 1 35677888888874322 56777776643
No 58
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=54.95 E-value=12 Score=37.35 Aligned_cols=31 Identities=23% Similarity=0.401 Sum_probs=28.8
Q ss_pred CcccccCCCHHHHHHHHhhcCCCchHHHHhch
Q 009298 140 PIRKIGGIGKVTEHILRDVFGINTCEEMLQKG 171 (538)
Q Consensus 140 Pl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp 171 (538)
.++.|.|||++..++|.. .||++..|++.+.
T Consensus 159 DL~~I~GIGp~~a~~L~e-aGi~tfaQIAa~t 189 (221)
T PRK12278 159 DLTKITGVGPALAKKLNE-AGVTTFAQIAALT 189 (221)
T ss_pred hheeccccChHHHHHHHH-cCCCCHHHhhCCC
Confidence 478899999999999997 9999999999986
No 59
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=54.46 E-value=20 Score=41.12 Aligned_cols=53 Identities=19% Similarity=0.202 Sum_probs=42.5
Q ss_pred CCCcccccCCCHHHHHHHHhhcCCCchHHHHhch-HHHHHHcChhHHHHHHHhccC
Q 009298 138 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHSTADFFLSVGLG 192 (538)
Q Consensus 138 ~lPl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~krFG~~~~~~L~~~a~G 192 (538)
.-.|..|||||+++.++|-+ -..++..+...+ ..|.+.+|...+..++.....
T Consensus 551 ~S~L~~IpGIG~kr~~~LL~--~FgSi~~I~~As~eeL~~vi~~k~A~~I~~~l~~ 604 (624)
T PRK14669 551 TSELLEIPGVGAKTVQRLLK--HFGSLERVRAATETQLAAVVGRAAAEAIIAHFTT 604 (624)
T ss_pred HHHHhcCCCCCHHHHHHHHH--HcCCHHHHHhCCHHHHHHHhCHHHHHHHHHHhcC
Confidence 35688999999999999876 455888888887 788888998888888766543
No 60
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=51.55 E-value=14 Score=39.07 Aligned_cols=43 Identities=28% Similarity=0.397 Sum_probs=37.6
Q ss_pred CCCcccc--cCCCHHHHHHHHhhcCCCchHHHHhch-HHHHHHcChh
Q 009298 138 SLPIRKI--GGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHS 181 (538)
Q Consensus 138 ~lPl~~L--~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~krFG~~ 181 (538)
..+|++| .||++....+|++ -|+.|+.|++..+ ..|.+.+|..
T Consensus 25 ~~~~~~l~~~gi~~~~i~kL~~-~g~~T~~~~~~~~~~~L~~i~~is 70 (342)
T PLN03186 25 PFPIEQLQASGIAALDIKKLKD-AGIHTVESLAYAPKKDLLQIKGIS 70 (342)
T ss_pred CccHHHHHhCCCCHHHHHHHHH-cCCCcHHHHHhCCHHHHHHhcCCC
Confidence 3578888 5799999999997 8999999999997 7899988854
No 61
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=51.54 E-value=19 Score=42.66 Aligned_cols=50 Identities=16% Similarity=0.187 Sum_probs=42.8
Q ss_pred cccccCCCHHHHHHHHhhcCCCchHHHHhch-HHHHHHcC-hhHHHHHHHhccC
Q 009298 141 IRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFS-HSTADFFLSVGLG 192 (538)
Q Consensus 141 l~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~krFG-~~~~~~L~~~a~G 192 (538)
|..|||||++.+..|.. .+.++.+|++.+ ..|....| ...+..+|+..+.
T Consensus 759 L~~lPgI~~~~a~~ll~--~f~si~~l~~as~eeL~~~iG~~~~A~~i~~fl~~ 810 (814)
T TIGR00596 759 LLKLPGVTKKNYRNLRK--KVKSIRELAKLSQNELNELIGDEEAAKRLYDFLRT 810 (814)
T ss_pred HHHCCCCCHHHHHHHHH--HcCCHHHHHhCCHHHHHHHhCCHHHHHHHHHHhcc
Confidence 55789999999999986 788999999998 78999899 8888888876543
No 62
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=50.92 E-value=20 Score=41.43 Aligned_cols=48 Identities=19% Similarity=0.165 Sum_probs=37.5
Q ss_pred CcccccCCCHHHHHHHHhhcCCCchHHHHhch-HHHHH--HcChhHHHHHH
Q 009298 140 PIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCA--VFSHSTADFFL 187 (538)
Q Consensus 140 Pl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~k--rFG~~~~~~L~ 187 (538)
..=+|+|+|+++.++|-+..+|.++.||..+. ..|.+ .||...++.|+
T Consensus 446 ~al~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~ll 496 (665)
T PRK07956 446 NAMDIDGLGEKIIEQLFEKGLIHDPADLFKLTAEDLLGLEGFGEKSAQNLL 496 (665)
T ss_pred cccCCCCcCHHHHHHHHHcCCCCCHHHHHhcCHHHHhcCcCcchHHHHHHH
Confidence 45678999999999999866789999999886 55554 68877666553
No 63
>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=50.62 E-value=18 Score=37.88 Aligned_cols=35 Identities=23% Similarity=0.246 Sum_probs=31.3
Q ss_pred CCCHHHHHHHHhhcCCCchHHHHhch-HHHHHHcChh
Q 009298 146 GIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHS 181 (538)
Q Consensus 146 GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~krFG~~ 181 (538)
||++.+..+|+. -||.|+.||+..+ ..|.+.+|-.
T Consensus 8 ~~~~~~~~~l~~-~g~~t~~~~~~~~~~~L~~i~~ls 43 (316)
T TIGR02239 8 GITAADIKKLQE-AGLHTVESVAYAPKKQLLEIKGIS 43 (316)
T ss_pred CCCHHHHHHHHH-cCCCcHHHHHhCCHHHHHHHhCCC
Confidence 599999999997 9999999999987 7888888854
No 64
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=50.48 E-value=17 Score=35.16 Aligned_cols=53 Identities=11% Similarity=0.068 Sum_probs=35.9
Q ss_pred CcccccCCCHHHHHHHHhhcCCCchHHH-Hhch-HHHHHH--cChhHHHHHHHhccC
Q 009298 140 PIRKIGGIGKVTEHILRDVFGINTCEEM-LQKG-SLLCAV--FSHSTADFFLSVGLG 192 (538)
Q Consensus 140 Pl~~L~GIG~kt~~kL~~~lGI~TlgDL-~~lp-~~L~kr--FG~~~~~~L~~~a~G 192 (538)
.+..++|||++++.++-+.+|..++.+. .+-+ ..|.+. +|+..++.+.....+
T Consensus 74 ~L~~i~GIGpk~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~~~l~~ 130 (192)
T PRK00116 74 LLISVSGVGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELKD 130 (192)
T ss_pred HHhcCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 4567999999999987666887666533 3333 567665 677777777544443
No 65
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=50.22 E-value=6.5 Score=33.96 Aligned_cols=34 Identities=44% Similarity=0.858 Sum_probs=25.2
Q ss_pred ecCccccccccCCCCCcH-----------------hhhhccccchHHHHhhhhhcc
Q 009298 448 LDDYKCSLCGTEMPPSFI-----------------EERQEHSDFHLAERLQKEESG 486 (538)
Q Consensus 448 ~~~~~~~~~~~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~~~ 486 (538)
+....|.-||.||+|-|+ .|.-|| |+|+-|-|-+
T Consensus 45 vG~~~cP~Cge~~~~a~vva~taLVgL~l~mkVfnAes~EH-----A~RIAKs~iG 95 (102)
T PF04475_consen 45 VGDTICPKCGEELDSAFVVADTALVGLILEMKVFNAESEEH-----AERIAKSEIG 95 (102)
T ss_pred cCcccCCCCCCccCceEEEeccceEEEEEEEEEeecCCHHH-----HHHHHHHHHh
Confidence 346789999999999875 567777 5666665544
No 66
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=49.95 E-value=18 Score=37.83 Aligned_cols=31 Identities=26% Similarity=0.273 Sum_probs=27.0
Q ss_pred cccccCCCHHHHHHHHhhcCCCchHHHHhchH
Q 009298 141 IRKIGGIGKVTEHILRDVFGINTCEEMLQKGS 172 (538)
Q Consensus 141 l~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp~ 172 (538)
.+.++|||.+++++--+ .|++|+.|++..|.
T Consensus 99 FtnifGvG~ktA~~Wy~-~GfrTled~Rk~~~ 129 (353)
T KOG2534|consen 99 FTNIFGVGLKTAEKWYR-EGFRTLEDVRKKPD 129 (353)
T ss_pred HHHHhccCHHHHHHHHH-hhhhHHHHHHhCHH
Confidence 35679999999999997 99999999997763
No 67
>PRK03922 hypothetical protein; Provisional
Probab=49.77 E-value=6.5 Score=34.58 Aligned_cols=43 Identities=33% Similarity=0.591 Sum_probs=32.9
Q ss_pred ecCccccccccCCCCCcH-----------------hhhhccccchHHHHhhhhhccCcccccccc
Q 009298 448 LDDYKCSLCGTEMPPSFI-----------------EERQEHSDFHLAERLQKEESGSDLRILTHR 495 (538)
Q Consensus 448 ~~~~~~~~~~~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 (538)
+....|.-||.+++|-|+ .|+-|| |+|+-|-|-+-..+.+|-+
T Consensus 47 vG~~~cP~cge~~~~afvvA~taLVgL~lemkVFnAes~EH-----A~RIAK~eIG~aL~dvPL~ 106 (113)
T PRK03922 47 VGLTICPKCGEPFDSAFVVADTALVGLLLEMKVFNAESEEH-----ASRIAKSEIGKALRDIPLE 106 (113)
T ss_pred cCcccCCCCCCcCCcEEEEeccceEEEEEEEEEeecCCHHH-----HHHHHHHHHhhHHhcCCce
Confidence 346789999999999864 678888 7888888777666666654
No 68
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=49.46 E-value=13 Score=39.27 Aligned_cols=31 Identities=23% Similarity=0.381 Sum_probs=28.6
Q ss_pred CcccccCCCHHHHHHHHhhcCCCchHHHHhch
Q 009298 140 PIRKIGGIGKVTEHILRDVFGINTCEEMLQKG 171 (538)
Q Consensus 140 Pl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp 171 (538)
.++.|.|||++.+++|.. +||++..|++++.
T Consensus 264 dL~~I~GiGp~~e~~L~~-~Gi~~f~QiA~~t 294 (326)
T PRK12311 264 DLKKLTGVSPQIEKKLND-LGIFHFWQLAELD 294 (326)
T ss_pred hhhhhccCChhhhhhhhh-cCCCCHHHhhCCC
Confidence 378899999999999997 9999999999986
No 69
>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=49.33 E-value=20 Score=37.53 Aligned_cols=35 Identities=23% Similarity=0.342 Sum_probs=31.1
Q ss_pred cCCCHHHHHHHHhhcCCCchHHHHhch-HHHHHHcCh
Q 009298 145 GGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSH 180 (538)
Q Consensus 145 ~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~krFG~ 180 (538)
.||++.+.++|++ -|+.|+.|++..+ ..|.+..|-
T Consensus 7 ~g~~~~~~~~L~~-~g~~t~~~~~~~~~~~L~~~~gl 42 (313)
T TIGR02238 7 HGINAADIKKLKS-AGICTVNGVIMTTRRALCKIKGL 42 (313)
T ss_pred CCCCHHHHHHHHH-cCCCcHHHHHhCCHHHHHHhcCC
Confidence 4799999999997 9999999999987 788888874
No 70
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=48.27 E-value=1.4e+02 Score=33.98 Aligned_cols=130 Identities=15% Similarity=0.101 Sum_probs=73.4
Q ss_pred hCCCeEEEcCChHHHHHHHHHHHHHHHhcCCCeEeeCccE-EEEEcC-ccchh-cCCCHHHHHHHHHHHHHHHhCCceEE
Q 009298 25 LCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDE-AYLDIT-EVCRE-RGISGIEIAEELRTSVYEEAGLTCSA 101 (538)
Q Consensus 25 LCP~Lvvvp~d~~~Y~~~s~~l~~il~~~sp~Ve~~SiDE-afLDlT-~~~~l-~g~~~~~la~~IR~~I~~~~Glt~S~ 101 (538)
..|||+++.---.....+.+.+ +-+.--.|.|..+--++ .|+.-. ....+ .+..+-.+.++||+++. .+
T Consensus 443 ~~Pdli~iDGGkgQl~~a~~vl-~~l~~~~~viglaK~~~~~~~~~~~~~~~l~~~~p~l~~lq~irDEaH-rf------ 514 (581)
T COG0322 443 ELPDLILIDGGKGQLNAAKEVL-KELGLDIPVIGLAKGEEELLLPGPGEEFDLPPNSPALYLLQRIRDEAH-RF------ 514 (581)
T ss_pred CCCCEEEEeCCHHHHHHHHHHH-HHcCCCccEEEEEecCceeEecCCCceecCCCCCHHHHHHHHHHHHHH-HH------
Confidence 3689999886544443333332 33333345555443333 555432 11111 12235678888998883 33
Q ss_pred EecCChhHHHHHhcccCCCCeEEecCChHHHHHhhcCCCcccccCCCHHHHHHHHhhcCCCchHHHHhch-HHHHHHcCh
Q 009298 102 GVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSH 180 (538)
Q Consensus 102 GIA~nk~lAKLAS~~aKP~G~~vl~~~~~~~~~fL~~lPl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~krFG~ 180 (538)
+|+.++.. -..-.-.-++.+|+|||++..++|-. -..|+..+...+ ..|.+. |.
T Consensus 515 Ai~~hR~~----------------------R~k~~~~s~Ld~I~GiG~~r~~~LL~--~Fgs~~~i~~As~eel~~v-gi 569 (581)
T COG0322 515 AITYHRKK----------------------RSKAMLQSSLDDIPGIGPKRRKALLK--HFGSLKGIKSASVEELAKV-GI 569 (581)
T ss_pred HHHHHHHH----------------------hhhhhhcCccccCCCcCHHHHHHHHH--HhhCHHHHHhcCHHHHHHc-CC
Confidence 22222210 11223344688999999999998876 445788887776 777877 54
Q ss_pred --hHHHHHH
Q 009298 181 --STADFFL 187 (538)
Q Consensus 181 --~~~~~L~ 187 (538)
..+..++
T Consensus 570 ~~~~a~~i~ 578 (581)
T COG0322 570 SKKLAEKIY 578 (581)
T ss_pred CHHHHHHHH
Confidence 4455554
No 71
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=47.99 E-value=23 Score=36.37 Aligned_cols=53 Identities=9% Similarity=0.061 Sum_probs=40.6
Q ss_pred CCCcccccCCCHHHHHHHHhhcCCCchHHHHhch-HHHHHHcCh--hHHHHHHHhcc
Q 009298 138 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSH--STADFFLSVGL 191 (538)
Q Consensus 138 ~lPl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~krFG~--~~~~~L~~~a~ 191 (538)
..|+..||++|....++|.+ .|+.+++||..++ ..+...+|. ..+..+...+.
T Consensus 150 ~~~L~Qlp~i~~~~~~~l~~-~~i~s~~~l~~~~~~~~~~ll~~~~~~~~~i~~~~~ 205 (312)
T smart00611 150 DSPLLQLPHLPEEILKRLEK-KKVLSLEDLLELEDEERGELLGLLDAEGERVYKVLS 205 (312)
T ss_pred CCccccCCCCCHHHHHHHHh-CCCCCHHHHHhcCHHHHHHHHcCCHHHHHHHHHHHH
Confidence 36899999999999999997 8999999999997 666655552 34455544443
No 72
>KOG3014 consensus Protein involved in establishing cohesion between sister chromatids during DNA replication [Replication, recombination and repair]
Probab=47.65 E-value=7.4 Score=39.14 Aligned_cols=29 Identities=28% Similarity=0.432 Sum_probs=26.3
Q ss_pred ccccccccCCCCCcHhhhhccccchHHHH
Q 009298 451 YKCSLCGTEMPPSFIEERQEHSDFHLAER 479 (538)
Q Consensus 451 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 479 (538)
-+|.-||-.--++=+|++.+|+.||=+.+
T Consensus 38 ~~C~~Cgm~Yt~~s~EDe~~H~~fH~~~l 66 (257)
T KOG3014|consen 38 VKCKECGMKYTVTSPEDEALHEKFHNRFL 66 (257)
T ss_pred eehhhcCceecCCCHHHHHHHHHHHHhhc
Confidence 47999999999999999999999997654
No 73
>COG2199 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]
Probab=47.05 E-value=55 Score=30.32 Aligned_cols=65 Identities=18% Similarity=0.062 Sum_probs=46.5
Q ss_pred HHHHHHHHHHHHhcCC---CeEeeCccEEEEEcCccchhcCCCHHHHHHHHHHHHHHHh-------CCceEEEecCCh
Q 009298 40 TYYSDLTRKVFCKYDP---NFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEA-------GLTCSAGVAPNR 107 (538)
Q Consensus 40 ~~~s~~l~~il~~~sp---~Ve~~SiDEafLDlT~~~~l~g~~~~~la~~IR~~I~~~~-------Glt~S~GIA~nk 107 (538)
..+...+..++....+ .+-.++-||.-+=+.+.... ....++++|+..+.... .+++|+||+..+
T Consensus 75 D~vL~~va~~L~~~~~~~~~~~R~gGdEF~i~l~~~~~~---~~~~~~~~l~~~~~~~~~~~~~~~~~t~siGi~~~~ 149 (181)
T COG2199 75 DEVLREVARRLRSNLREGDLVARLGGDEFAVLLPGTSLE---EAARLAERIRAALEEPFFLGGEELRVTVSIGVALYP 149 (181)
T ss_pred HHHHHHHHHHHHHhcCCCCEEEEeccceeEEEeCCCCHH---HHHHHHHHHHHHHHcccccCCceEEEEEEEEEEecC
Confidence 4566777888887765 46778889987777665421 57889999988886543 379999988543
No 74
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=43.45 E-value=7.1 Score=23.50 Aligned_cols=12 Identities=25% Similarity=1.132 Sum_probs=8.1
Q ss_pred ccccccccCCCC
Q 009298 451 YKCSLCGTEMPP 462 (538)
Q Consensus 451 ~~~~~~~~~~~~ 462 (538)
|+|.+||...+-
T Consensus 1 ~~C~~C~~~~~~ 12 (24)
T PF13894_consen 1 FQCPICGKSFRS 12 (24)
T ss_dssp EE-SSTS-EESS
T ss_pred CCCcCCCCcCCc
Confidence 789999988764
No 75
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=43.28 E-value=12 Score=36.62 Aligned_cols=43 Identities=28% Similarity=0.328 Sum_probs=29.7
Q ss_pred EecCChhHHHHHhcccCCCCeEEecCChHHHHHhhcCC---CcccccCCCHHHHHHHH
Q 009298 102 GVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSL---PIRKIGGIGKVTEHILR 156 (538)
Q Consensus 102 GIA~nk~lAKLAS~~aKP~G~~vl~~~~~~~~~fL~~l---Pl~~L~GIG~kt~~kL~ 156 (538)
|||+.--||-|.+.- + +++...+..- -|.++||||+|+++++-
T Consensus 80 GIGpK~ALaiLs~~~----------~--~~l~~aI~~~d~~~L~k~PGIGkKtAeriv 125 (201)
T COG0632 80 GIGPKLALAILSNLD----------P--EELAQAIANEDVKALSKIPGIGKKTAERIV 125 (201)
T ss_pred CccHHHHHHHHcCCC----------H--HHHHHHHHhcChHhhhcCCCCCHHHHHHHH
Confidence 899988888776622 1 1334444432 26788999999999985
No 76
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=43.23 E-value=16 Score=23.41 Aligned_cols=17 Identities=29% Similarity=0.477 Sum_probs=14.4
Q ss_pred cccccCCCHHHHHHHHh
Q 009298 141 IRKIGGIGKVTEHILRD 157 (538)
Q Consensus 141 l~~L~GIG~kt~~kL~~ 157 (538)
+..++|||++++++|..
T Consensus 3 L~~i~GiG~k~A~~il~ 19 (26)
T smart00278 3 LLKVPGIGPKTAEKILE 19 (26)
T ss_pred hhhCCCCCHHHHHHHHH
Confidence 56789999999999874
No 77
>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=42.87 E-value=33 Score=39.64 Aligned_cols=48 Identities=17% Similarity=0.162 Sum_probs=36.8
Q ss_pred CcccccCCCHHHHHHHHhhcCCCchHHHHhch-HHHHH--HcChhHHHHHH
Q 009298 140 PIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCA--VFSHSTADFFL 187 (538)
Q Consensus 140 Pl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~k--rFG~~~~~~L~ 187 (538)
.--+|+|+|+++.++|-+..+|+++.||..+. ..|.. .||...+..|+
T Consensus 433 ~al~I~GLG~k~i~~L~~~g~I~~~~Dl~~L~~~~L~~L~GfG~Ksa~nIl 483 (652)
T TIGR00575 433 NAMDIEGLGDKVIEQLFEKKLVRSVADLYALKKEDLLELEGFGEKSAQNLL 483 (652)
T ss_pred CccCCCCcCHHHHHHHHHcCCcCCHHHHHhcCHHHHhhccCccHHHHHHHH
Confidence 44568999999999998756689999999886 45554 57877666554
No 78
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=42.82 E-value=9 Score=39.55 Aligned_cols=17 Identities=53% Similarity=1.323 Sum_probs=15.8
Q ss_pred eeecCc--cccccccCCCC
Q 009298 446 IWLDDY--KCSLCGTEMPP 462 (538)
Q Consensus 446 ~~~~~~--~~~~~~~~~~~ 462 (538)
-|++|| +|..|-.++||
T Consensus 355 kW~~~y~~~CPvCrt~iPP 373 (374)
T COG5540 355 KWLLGYSNKCPVCRTAIPP 373 (374)
T ss_pred HHHhhhcccCCccCCCCCC
Confidence 599999 59999999999
No 79
>PRK14973 DNA topoisomerase I; Provisional
Probab=41.84 E-value=44 Score=40.28 Aligned_cols=77 Identities=13% Similarity=0.104 Sum_probs=49.9
Q ss_pred HHHHHh-cccCCCCeEEecCChHHHHHhhcCCCcccccCCCHHHHHHHHhhcCCCchHHHHhch-HHHHHHcCh--hHHH
Q 009298 109 LAKVCS-DINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSH--STAD 184 (538)
Q Consensus 109 lAKLAS-~~aKP~G~~vl~~~~~~~~~fL~~lPl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~krFG~--~~~~ 184 (538)
++.+|+ .+.+|+...+... +.--..-++..++|+|++|.++|.+ -||.+..||++.+ ..|.+.=|. ....
T Consensus 851 ~~~~~~~~~~~~~~~~~~~~-----~~~~~~~el~~vkg~ge~t~~~l~~-ag~~~~e~l~~~d~~~la~~~~i~~k~~~ 924 (936)
T PRK14973 851 HAKLVCEKLGRPVPEKISKA-----AFERGRAELLSVPGLGETTLEKLYL-AGVYDGDLLVSADPKKLAKVTGIDEKKLR 924 (936)
T ss_pred HHHHHHHHhcCCCchhhhhh-----hhcccchhhhhccCCCHHHHHHHHH-cCCCCHHHhccCCHHHHhhhcCCCHHHHH
Confidence 345566 6666654433211 0111122378889999999999998 8999999999987 777776654 3344
Q ss_pred HHHHhcc
Q 009298 185 FFLSVGL 191 (538)
Q Consensus 185 ~L~~~a~ 191 (538)
.|..++.
T Consensus 925 ~~~~~~~ 931 (936)
T PRK14973 925 NLQAYAK 931 (936)
T ss_pred HHHHHHh
Confidence 4544443
No 80
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=41.64 E-value=46 Score=38.91 Aligned_cols=49 Identities=22% Similarity=0.415 Sum_probs=35.3
Q ss_pred ecCChHHHHHhhcCCCcccccCCCHHHHHHHHhhcCCCchHHHHhchHHHHH
Q 009298 125 LPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCA 176 (538)
Q Consensus 125 l~~~~~~~~~fL~~lPl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp~~L~k 176 (538)
.+++.+.+..||.. ..++|||+++++++-+.||..++.-|.+-|..|..
T Consensus 73 ~p~~~~~i~~yL~s---~~~~GIG~~~A~~iv~~fg~~~~~~i~~~~~~L~~ 121 (720)
T TIGR01448 73 APTSKEGIVAYLSS---RSIKGVGKKLAQRIVKTFGEAAFDVLDDDPEKLLE 121 (720)
T ss_pred CCCCHHHHHHHHhc---CCCCCcCHHHHHHHHHHhCHhHHHHHHhCHHHHhc
Confidence 44444456777773 46899999999999888998888777665544443
No 81
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=40.94 E-value=32 Score=36.03 Aligned_cols=50 Identities=20% Similarity=0.269 Sum_probs=40.2
Q ss_pred hcCCCcccccCCCHHHHHHHHhhcCCCchHHHHhch-HHHH--HHcChhHHHHHH
Q 009298 136 ISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLC--AVFSHSTADFFL 187 (538)
Q Consensus 136 L~~lPl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~--krFG~~~~~~L~ 187 (538)
+..+||.+| ++.-++..-|++ .||+|++||.+++ ..|. +-||+...+.+.
T Consensus 246 ~l~~~I~~L-~LS~R~~n~Lk~-~~I~ti~dL~~~~~~~l~~~~n~G~ksl~ei~ 298 (310)
T PRK05182 246 ILLRPIEEL-ELSVRSYNCLKR-AGINTIGDLVQRTEEELLKTRNLGKKSLEEIK 298 (310)
T ss_pred cccccHHHh-ccchHHHHHHHH-cCCcCHHHHHhCCHHHHhcCCCCChhhHHHHH
Confidence 447789999 899999999998 8999999999998 5554 457877655553
No 82
>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=40.61 E-value=33 Score=35.68 Aligned_cols=52 Identities=19% Similarity=0.243 Sum_probs=41.2
Q ss_pred hhcCCCcccccCCCHHHHHHHHhhcCCCchHHHHhch-HHHH--HHcChhHHHHHHH
Q 009298 135 FISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLC--AVFSHSTADFFLS 188 (538)
Q Consensus 135 fL~~lPl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~--krFG~~~~~~L~~ 188 (538)
-+..+||.+| ++.-++..-|++ .||+|++||.+++ ..|. +-||+...+-+.+
T Consensus 231 ~~~~~~I~~L-~LSvR~~n~Lk~-~~I~ti~dL~~~~~~~l~~~~n~G~ksl~ei~~ 285 (297)
T TIGR02027 231 KLLSIKIEEL-DLSVRSYNCLKR-AGIHTLGELVSKSEEELLKIKNFGKKSLTEIKE 285 (297)
T ss_pred hhccccHHHh-CccHHHHhHHHH-cCCcCHHHHHhCCHHHHhhCCCCChhhHHHHHH
Confidence 3566789999 799999999998 8999999999987 5544 4688776655543
No 83
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=40.42 E-value=41 Score=38.86 Aligned_cols=53 Identities=15% Similarity=0.219 Sum_probs=41.6
Q ss_pred CCCcccccCCCHHHHHHHHhhcCCCchHHHHhch-HHHHHH--cChhHHHHHHHhccC
Q 009298 138 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFLSVGLG 192 (538)
Q Consensus 138 ~lPl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~kr--FG~~~~~~L~~~a~G 192 (538)
...+..|||||++..++|-+ -..++.+|.+.+ ..|.+. +|...+..++..+..
T Consensus 607 ~s~L~~IpGiG~kr~~~LL~--~FgS~~~i~~As~eel~~v~gi~~~~A~~i~~~~~~ 662 (691)
T PRK14672 607 VLSFERLPHVGKVRAHRLLA--HFGSFRSLQSATPQDIATAIHIPLTQAHTILHAATR 662 (691)
T ss_pred ccccccCCCCCHHHHHHHHH--HhcCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHhhc
Confidence 45899999999999998876 444888888877 788887 677778888766543
No 84
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=40.33 E-value=9.4 Score=29.28 Aligned_cols=25 Identities=28% Similarity=0.525 Sum_probs=19.6
Q ss_pred CcceeecCccccccccCCCCCcHhh
Q 009298 443 DQFIWLDDYKCSLCGTEMPPSFIEE 467 (538)
Q Consensus 443 ~~~~~~~~~~~~~~~~~~~~~~~~~ 467 (538)
..+-=|++-.|+-|+.+|||....+
T Consensus 15 ~~va~v~~~~C~gC~~~l~~~~~~~ 39 (56)
T PF02591_consen 15 VAVARVEGGTCSGCHMELPPQELNE 39 (56)
T ss_pred cEEEEeeCCccCCCCEEcCHHHHHH
Confidence 3445577889999999999987654
No 85
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=39.53 E-value=38 Score=39.24 Aligned_cols=50 Identities=26% Similarity=0.411 Sum_probs=38.6
Q ss_pred CCCcccccCCCHHHHHHHHhhcCCCchHHHHhch-HHHHHH--cChhHHHHHHHh
Q 009298 138 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFLSV 189 (538)
Q Consensus 138 ~lPl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~kr--FG~~~~~~L~~~ 189 (538)
.-.|..+||||+++.++|-+.+| ++.++.+.+ ..|.+. +|...++.+++.
T Consensus 636 ~s~L~~IPGIGpkr~k~LL~~FG--Sle~I~~AS~eELa~V~Gig~k~Ae~I~~~ 688 (694)
T PRK14666 636 TGELQRVEGIGPATARLLWERFG--SLQAMAAAGEEGLAAVPGIGPARAAALHEH 688 (694)
T ss_pred HhHHhhCCCCCHHHHHHHHHHhC--CHHHHHhcCHHHHHhcCCcCHHHHHHHHHH
Confidence 34688999999999988877577 999998877 678776 777766666543
No 86
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=39.33 E-value=41 Score=38.22 Aligned_cols=50 Identities=18% Similarity=0.233 Sum_probs=38.9
Q ss_pred CCCcccccCCCHHHHHHHHhhcCCCchHHHHhch-HHHHHH--cChhHHHHHHHh
Q 009298 138 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFLSV 189 (538)
Q Consensus 138 ~lPl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~kr--FG~~~~~~L~~~ 189 (538)
...|.+|||||+++.++|-+ -..++..+.+.+ ..|.+. ++...+..++..
T Consensus 513 ~s~L~~I~GiG~kr~~~LL~--~Fgs~~~I~~As~eeL~~v~gi~~~~A~~I~~~ 565 (574)
T PRK14670 513 KLNYTKIKGIGEKKAKKILK--SLGTYKDILLLNEDEIAEKMKINIKMAKKIKKF 565 (574)
T ss_pred ccccccCCCCCHHHHHHHHH--HhCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHH
Confidence 45799999999999999876 444888888887 788887 666667766554
No 87
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=38.68 E-value=27 Score=37.73 Aligned_cols=31 Identities=26% Similarity=0.441 Sum_probs=28.6
Q ss_pred CcccccCCCHHHHHHHHhhcCCCchHHHHhch
Q 009298 140 PIRKIGGIGKVTEHILRDVFGINTCEEMLQKG 171 (538)
Q Consensus 140 Pl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp 171 (538)
.++.|.|||++..++|+. +||++..|++.+.
T Consensus 324 DLk~I~GIGpk~e~~Ln~-~Gi~~f~QIA~wt 354 (400)
T PRK12373 324 DLKLISGVGPKIEATLNE-LGIFTFDQVAAWK 354 (400)
T ss_pred hhhhccCCChHHHHHHHh-cCCCCHHHHhCCC
Confidence 478899999999999997 9999999999886
No 88
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=38.62 E-value=44 Score=38.39 Aligned_cols=49 Identities=24% Similarity=0.314 Sum_probs=39.7
Q ss_pred CCcccccCCCHHHHHHHHhhcCCCchHHHHhch-HHHHHHcChhHHHHHHHh
Q 009298 139 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHSTADFFLSV 189 (538)
Q Consensus 139 lPl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~krFG~~~~~~L~~~ 189 (538)
..|..|+|||++++..|-+ .+.|+.+|...+ ..|.+.+|...++.++.+
T Consensus 569 s~L~~I~GIG~k~a~~Ll~--~Fgs~~~i~~As~eeL~~vig~k~A~~I~~~ 618 (621)
T PRK14671 569 TELTDIAGIGEKTAEKLLE--HFGSVEKVAKASLEELAAVAGPKTAETIYRY 618 (621)
T ss_pred hhhhcCCCcCHHHHHHHHH--HcCCHHHHHhCCHHHHHHHhCHHHHHHHHHH
Confidence 4578999999999999876 455889998887 778777998888877654
No 89
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=34.99 E-value=48 Score=37.88 Aligned_cols=50 Identities=18% Similarity=0.250 Sum_probs=39.3
Q ss_pred CCCcccccCCCHHHHHHHHhhcCCCchHHHHhch-HHHHHH--cChhHHHHHHHh
Q 009298 138 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFLSV 189 (538)
Q Consensus 138 ~lPl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~kr--FG~~~~~~L~~~ 189 (538)
..+|..|||||+++.++|-+ -..++.++...+ ..|.+. +|...+..++.+
T Consensus 542 ~s~L~~IpGIG~k~~k~Ll~--~FgS~~~i~~As~eeL~~v~Gig~~~A~~I~~~ 594 (598)
T PRK00558 542 TSALDDIPGIGPKRRKALLK--HFGSLKAIKEASVEELAKVPGISKKLAEAIYEA 594 (598)
T ss_pred hhhHhhCCCcCHHHHHHHHH--HcCCHHHHHhCCHHHHhhcCCcCHHHHHHHHHH
Confidence 46788999999999999987 445788888877 778877 677777777554
No 90
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=33.90 E-value=54 Score=38.16 Aligned_cols=48 Identities=17% Similarity=0.214 Sum_probs=36.3
Q ss_pred CcccccCCCHHHHHHHHhhcCCCchHHHHhch-HHHHH--HcChhHHHHHH
Q 009298 140 PIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCA--VFSHSTADFFL 187 (538)
Q Consensus 140 Pl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~k--rFG~~~~~~L~ 187 (538)
..=+|.|+|+++.++|-+.-+|+++.||..+. ..|.. .||...+..|+
T Consensus 463 ~al~I~GLG~k~i~~L~~~g~V~~~~Dl~~L~~~~L~~l~g~g~Ksa~~Ll 513 (689)
T PRK14351 463 DALDIEGLGEERVQQLVDAGLVESLADLYDLTVADLAELEGWGETSAENLL 513 (689)
T ss_pred cccCCCCcCHHHHHHHHHcCCCCCHHHHHHcCHHHHhcCcCcchhHHHHHH
Confidence 45578999999999999833479999999987 55654 47877665543
No 91
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=32.99 E-value=17 Score=31.70 Aligned_cols=43 Identities=33% Similarity=0.648 Sum_probs=33.8
Q ss_pred ecCccccccccCCCCCcH-----------------hhhhccccchHHHHhhhhhccCcccccccc
Q 009298 448 LDDYKCSLCGTEMPPSFI-----------------EERQEHSDFHLAERLQKEESGSDLRILTHR 495 (538)
Q Consensus 448 ~~~~~~~~~~~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 495 (538)
+-.++|.-||..+-+-|+ .|+.|| |+|+-|-|-+-..+.+|-+
T Consensus 47 ~G~t~CP~Cg~~~e~~fvva~~aLVgl~l~mkVFNaes~EH-----A~RIAK~eIGk~L~~iPL~ 106 (115)
T COG1885 47 VGSTSCPKCGEPFESAFVVANTALVGLILSMKVFNAESDEH-----AERIAKAEIGKALKDIPLE 106 (115)
T ss_pred cccccCCCCCCccceeEEEecceeEEEEEEEEEecCCCHHH-----HHHHHHHHHhhHhhcCCce
Confidence 346899999999998765 577777 8899998877777776655
No 92
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=32.38 E-value=21 Score=28.68 Aligned_cols=13 Identities=38% Similarity=1.065 Sum_probs=12.0
Q ss_pred ccccccccCCCCC
Q 009298 451 YKCSLCGTEMPPS 463 (538)
Q Consensus 451 ~~~~~~~~~~~~~ 463 (538)
..||-||.+++|+
T Consensus 4 ~~CsFcG~~I~PG 16 (66)
T COG2075 4 RVCSFCGKKIEPG 16 (66)
T ss_pred eEecCcCCccCCC
Confidence 5799999999998
No 93
>PF01246 Ribosomal_L24e: Ribosomal protein L24e; InterPro: IPR000988 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 [, ]. A number of eukaryotic and archaeabacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families [] consists of mammalian ribosomal protein L24; yeast ribosomal protein L30A/B (Rp29) (YL21); Kluyveromyces lactis ribosomal protein L30; Arabidopsis thaliana ribosomal protein L24 homolog; Haloarcula marismortui ribosomal protein HL21/HL22; and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ1201. These proteins have 60 to 160 amino-acid residues. This entry represents proteins related to the L24e ribosomal proteins.; PDB: 2ZKR_u 1VQ9_U 1VQL_U 1KD1_V 1VQP_U 3CCM_U 3CD6_U 3CCL_U 3CCR_U 1Q86_V ....
Probab=32.30 E-value=15 Score=30.05 Aligned_cols=14 Identities=36% Similarity=0.705 Sum_probs=9.6
Q ss_pred CccccccccCCCCC
Q 009298 450 DYKCSLCGTEMPPS 463 (538)
Q Consensus 450 ~~~~~~~~~~~~~~ 463 (538)
-++|+.||.+++|+
T Consensus 3 ~~~C~Fsg~~I~PG 16 (71)
T PF01246_consen 3 TEKCSFSGYKIYPG 16 (71)
T ss_dssp SEE-TTT-SEE-SS
T ss_pred eEEecccCCccCCC
Confidence 36899999999998
No 94
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=31.03 E-value=25 Score=22.20 Aligned_cols=12 Identities=33% Similarity=0.858 Sum_probs=9.9
Q ss_pred cccccccCCCCC
Q 009298 452 KCSLCGTEMPPS 463 (538)
Q Consensus 452 ~~~~~~~~~~~~ 463 (538)
+|.-||.|+++.
T Consensus 1 ~Cp~CG~~~~~~ 12 (23)
T PF13240_consen 1 YCPNCGAEIEDD 12 (23)
T ss_pred CCcccCCCCCCc
Confidence 588999999874
No 95
>COG2519 GCD14 tRNA(1-methyladenosine) methyltransferase and related methyltransferases [Translation, ribosomal structure and biogenesis]
Probab=29.77 E-value=1.5e+02 Score=30.16 Aligned_cols=68 Identities=13% Similarity=0.137 Sum_probs=46.6
Q ss_pred cCHHHHHcCCCCCCcHHHH------------HhhCCC--eEEEcCChHHHHHHHHHHHHH-HHh--------cCCCeEee
Q 009298 4 ELLSARRFGVRAAMPGFIA------------RKLCPE--LIFVPTDFTKYTYYSDLTRKV-FCK--------YDPNFMAA 60 (538)
Q Consensus 4 ~syeAR~~GVr~GM~l~~A------------~~LCP~--Lvvvp~d~~~Y~~~s~~l~~i-l~~--------~sp~Ve~~ 60 (538)
+.|.+.+.||.+|+++-+| +..+|. ++.++.+.+.|+.+.+.+.++ +.. .+..+...
T Consensus 83 ~~~I~~~~gi~pg~rVlEAGtGSG~lt~~La~~vg~~G~v~tyE~r~d~~k~A~~Nl~~~~l~d~v~~~~~Dv~~~~~~~ 162 (256)
T COG2519 83 AGYIVARLGISPGSRVLEAGTGSGALTAYLARAVGPEGHVTTYEIREDFAKTARENLSEFGLGDRVTLKLGDVREGIDEE 162 (256)
T ss_pred HHHHHHHcCCCCCCEEEEcccCchHHHHHHHHhhCCCceEEEEEecHHHHHHHHHHHHHhccccceEEEecccccccccc
Confidence 3578889999999876554 567885 666778888898888877774 111 11112223
Q ss_pred CccEEEEEcCc
Q 009298 61 SLDEAYLDITE 71 (538)
Q Consensus 61 SiDEafLDlT~ 71 (538)
..|-+|||+-.
T Consensus 163 ~vDav~LDmp~ 173 (256)
T COG2519 163 DVDAVFLDLPD 173 (256)
T ss_pred ccCEEEEcCCC
Confidence 67889999874
No 96
>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=29.50 E-value=70 Score=23.22 Aligned_cols=32 Identities=19% Similarity=0.231 Sum_probs=25.9
Q ss_pred CCHHHHHHHHhhcCCCchHHHHhch-HHHHHHcC
Q 009298 147 IGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFS 179 (538)
Q Consensus 147 IG~kt~~kL~~~lGI~TlgDL~~lp-~~L~krFG 179 (538)
|+..+..+|.. -|+.|+.+|+..+ ..|...-|
T Consensus 1 i~~~~~~~L~~-~G~~s~e~la~~~~~eL~~i~g 33 (50)
T TIGR01954 1 IDEEIAQLLVE-EGFTTVEDLAYVPIDELLSIEG 33 (50)
T ss_pred CCHHHHHHHHH-cCCCCHHHHHccCHHHHhcCCC
Confidence 35677888987 8999999999986 77777655
No 97
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=29.31 E-value=28 Score=33.57 Aligned_cols=43 Identities=21% Similarity=0.271 Sum_probs=28.3
Q ss_pred EecCChhHHHHHhcccCCCCeEEecCChHHHHHhhcCC---CcccccCCCHHHHHHHH
Q 009298 102 GVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSL---PIRKIGGIGKVTEHILR 156 (538)
Q Consensus 102 GIA~nk~lAKLAS~~aKP~G~~vl~~~~~~~~~fL~~l---Pl~~L~GIG~kt~~kL~ 156 (538)
||||-..+|-|.+- +++ ++...+..= -++.+||||+||++++-
T Consensus 80 GIGpK~Al~ILs~~----------~~~--el~~aI~~~D~~~L~~vpGIGkKtAeRIi 125 (183)
T PRK14601 80 GIGANTAMAVCSSL----------DVN--SFYKALSLGDESVLKKVPGIGPKSAKRII 125 (183)
T ss_pred CccHHHHHHHHcCC----------CHH--HHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 88887777755442 121 344444432 36788999999999974
No 98
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=29.31 E-value=44 Score=30.51 Aligned_cols=30 Identities=13% Similarity=0.190 Sum_probs=25.3
Q ss_pred cccccCCCHHHHHHHHhhcC-CCchHHHHhch
Q 009298 141 IRKIGGIGKVTEHILRDVFG-INTCEEMLQKG 171 (538)
Q Consensus 141 l~~L~GIG~kt~~kL~~~lG-I~TlgDL~~lp 171 (538)
+..+||||++.++++-. -| ..++.||.+.+
T Consensus 63 l~~lpGigP~~A~~IV~-nGpf~sveDL~~V~ 93 (132)
T PRK02515 63 FRQFPGMYPTLAGKIVK-NAPYDSVEDVLNLP 93 (132)
T ss_pred HHHCCCCCHHHHHHHHH-CCCCCCHHHHHcCC
Confidence 35579999999999886 66 88999998876
No 99
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=26.86 E-value=33 Score=33.19 Aligned_cols=43 Identities=23% Similarity=0.399 Sum_probs=28.0
Q ss_pred EecCChhHHHHHhcccCCCCeEEecCChHHHHHhhcCC---CcccccCCCHHHHHHHH
Q 009298 102 GVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSL---PIRKIGGIGKVTEHILR 156 (538)
Q Consensus 102 GIA~nk~lAKLAS~~aKP~G~~vl~~~~~~~~~fL~~l---Pl~~L~GIG~kt~~kL~ 156 (538)
||||-..+|-|... +++ ++...+..- -|+.+||||++|++++-
T Consensus 80 GIGpK~AL~iLs~~----------~~~--el~~aI~~~D~~~L~~vpGIGkKtAerIi 125 (188)
T PRK14606 80 RLGPKTALKIISNE----------DAE--TLVTMIASQDVEGLSKLPGISKKTAERIV 125 (188)
T ss_pred CccHHHHHHHHcCC----------CHH--HHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 88887777755431 111 344444432 37788999999999975
No 100
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=26.73 E-value=31 Score=36.14 Aligned_cols=33 Identities=27% Similarity=0.359 Sum_probs=27.4
Q ss_pred CCcccccCCCHHHHHHHHhhcCCCchHHHHhch
Q 009298 139 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG 171 (538)
Q Consensus 139 lPl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp 171 (538)
.|+-++||+|++...+|-..+||.++.+|....
T Consensus 93 ~~Ll~v~GlGpkKi~~Ly~elgi~~~e~l~~a~ 125 (326)
T COG1796 93 EPLLKVPGLGPKKIVSLYKELGIKDLEELQEAL 125 (326)
T ss_pred HHHhhCCCCCcHHHHHHHHHHCcccHHHHHHHH
Confidence 467888999997777776679999999998765
No 101
>COG2062 SixA Phosphohistidine phosphatase SixA [Signal transduction mechanisms]
Probab=26.53 E-value=3.5e+02 Score=25.64 Aligned_cols=74 Identities=15% Similarity=0.123 Sum_probs=48.0
Q ss_pred CCeEEEcCChHHHHHHHHHHHHHHHhcCCCeEeeCccEEEEEcCccchhcCCCHHHHHHHHHHHHHHHhCCceEEEecCC
Q 009298 27 PELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPN 106 (538)
Q Consensus 27 P~Lvvvp~d~~~Y~~~s~~l~~il~~~sp~Ve~~SiDEafLDlT~~~~l~g~~~~~la~~IR~~I~~~~Glt~S~GIA~n 106 (538)
||++++.+ |.++.+....+...+.+ ...+.|-+++ ++.++..+...|+..- + ++.+-+=||||
T Consensus 48 ~D~VL~Sp----a~Ra~QTae~v~~~~~~-----~~~~~~~~l~-----p~~d~~~~l~~l~~~~-d--~v~~vllVgH~ 110 (163)
T COG2062 48 PDLVLVSP----AVRARQTAEIVAEHLGE-----KKVEVFEELL-----PNGDPGTVLDYLEALG-D--GVGSVLLVGHN 110 (163)
T ss_pred CCEEEeCh----hHHHHHHHHHHHHhhCc-----ccceeccccC-----CCCCHHHHHHHHHHhc-c--cCceEEEECCC
Confidence 78888775 34443333333333432 2335666665 3337888888877555 3 78888999999
Q ss_pred hhHHHHHhccc
Q 009298 107 RLLAKVCSDIN 117 (538)
Q Consensus 107 k~lAKLAS~~a 117 (538)
+.++-++....
T Consensus 111 P~l~~l~~~L~ 121 (163)
T COG2062 111 PLLEELALLLA 121 (163)
T ss_pred ccHHHHHHHHc
Confidence 99999988753
No 102
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=25.83 E-value=23 Score=25.07 Aligned_cols=9 Identities=56% Similarity=1.291 Sum_probs=5.3
Q ss_pred Ccccccccc
Q 009298 450 DYKCSLCGT 458 (538)
Q Consensus 450 ~~~~~~~~~ 458 (538)
=|||..||-
T Consensus 6 ~YkC~~CGn 14 (36)
T PF06397_consen 6 FYKCEHCGN 14 (36)
T ss_dssp EEE-TTT--
T ss_pred EEEccCCCC
Confidence 499999995
No 103
>COG4071 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.65 E-value=1.2e+02 Score=29.98 Aligned_cols=54 Identities=22% Similarity=0.179 Sum_probs=41.6
Q ss_pred cEEEEEcCccchhcC----CCHHHHHHHHHHHHHHHhCCceEEEecCChhHHHHHhcc
Q 009298 63 DEAYLDITEVCRERG----ISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDI 116 (538)
Q Consensus 63 DEafLDlT~~~~l~g----~~~~~la~~IR~~I~~~~Glt~S~GIA~nk~lAKLAS~~ 116 (538)
.|+=+|++.....+. -++..+|+.|+.+|++++|..+++=|++|-..=.+....
T Consensus 121 sEaG~Dl~NVPGtya~plPenp~~vA~el~~Ei~rr~GvDV~v~v~DTDaTY~iLg~y 178 (278)
T COG4071 121 SEAGVDLTNVPGTYACPLPENPKKVAEELYKEIKRRLGVDVVVMVADTDATYRILGFY 178 (278)
T ss_pred hhcCccccCCCcceeccCCCChHHHHHHHHHHHHHHhCCceEEEEecCchHHHHHHHH
Confidence 366778876643321 158899999999999999999999999997766665543
No 104
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=25.50 E-value=36 Score=33.24 Aligned_cols=43 Identities=21% Similarity=0.256 Sum_probs=27.5
Q ss_pred EecCChhHHHHHhcccCCCCeEEecCChHHHHHhhcCC---CcccccCCCHHHHHHHH
Q 009298 102 GVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSL---PIRKIGGIGKVTEHILR 156 (538)
Q Consensus 102 GIA~nk~lAKLAS~~aKP~G~~vl~~~~~~~~~fL~~l---Pl~~L~GIG~kt~~kL~ 156 (538)
||||-..+|-|.+. +++ ++...+..= .|+.+||||+||++++-
T Consensus 79 GIGPK~ALaILs~~----------~~~--el~~aI~~~D~~~L~~vpGIGkKtAeRII 124 (196)
T PRK13901 79 GIGPRAALRVLSGI----------KYN--EFRDAIDREDIELISKVKGIGNKMAGKIF 124 (196)
T ss_pred CcCHHHHHHHHcCC----------CHH--HHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 88887777755442 111 333334332 37788999999999974
No 105
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=25.43 E-value=52 Score=26.03 Aligned_cols=43 Identities=16% Similarity=0.285 Sum_probs=28.5
Q ss_pred Cccc-ccCCCHHHHHHHHhh---c-CCCchHHHHhchHHHHHHcChhHHHHHH
Q 009298 140 PIRK-IGGIGKVTEHILRDV---F-GINTCEEMLQKGSLLCAVFSHSTADFFL 187 (538)
Q Consensus 140 Pl~~-L~GIG~kt~~kL~~~---l-GI~TlgDL~~lp~~L~krFG~~~~~~L~ 187 (538)
+|.. +||||.+.+++|-.. . ++.+..||...+ -||...++.+.
T Consensus 17 ~L~~~ipgig~~~a~~Il~~R~~~g~~~s~~dL~~v~-----gi~~~~~~~i~ 64 (69)
T TIGR00426 17 ELQRAMNGVGLKKAEAIVSYREEYGPFKTVEDLKQVP-----GIGNSLVEKNL 64 (69)
T ss_pred HHHhHCCCCCHHHHHHHHHHHHHcCCcCCHHHHHcCC-----CCCHHHHHHHH
Confidence 3556 899999998888762 2 477888876653 24455555553
No 106
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=24.91 E-value=46 Score=26.44 Aligned_cols=17 Identities=29% Similarity=0.636 Sum_probs=15.0
Q ss_pred cccccCCCHHHHHHHHh
Q 009298 141 IRKIGGIGKVTEHILRD 157 (538)
Q Consensus 141 l~~L~GIG~kt~~kL~~ 157 (538)
+..|||||++++.++.+
T Consensus 49 ~~~l~gIG~~ia~kI~E 65 (68)
T PF14716_consen 49 LKKLPGIGKSIAKKIDE 65 (68)
T ss_dssp HCTSTTTTHHHHHHHHH
T ss_pred HhhCCCCCHHHHHHHHH
Confidence 68899999999999875
No 107
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.76 E-value=36 Score=33.27 Aligned_cols=16 Identities=31% Similarity=0.594 Sum_probs=14.5
Q ss_pred cccccCCCHHHHHHHH
Q 009298 141 IRKIGGIGKVTEHILR 156 (538)
Q Consensus 141 l~~L~GIG~kt~~kL~ 156 (538)
+.+|||||+|++++|.
T Consensus 13 l~~LPGIG~KsA~RlA 28 (195)
T TIGR00615 13 LKKLPGIGPKSAQRLA 28 (195)
T ss_pred HHHCCCCCHHHHHHHH
Confidence 6788999999999996
No 108
>PRK00807 50S ribosomal protein L24e; Validated
Probab=24.59 E-value=31 Score=26.34 Aligned_cols=14 Identities=43% Similarity=1.037 Sum_probs=12.1
Q ss_pred ccccccccCCCCCc
Q 009298 451 YKCSLCGTEMPPSF 464 (538)
Q Consensus 451 ~~~~~~~~~~~~~~ 464 (538)
++|+-||.++.|+-
T Consensus 2 ~~C~fcG~~I~pg~ 15 (52)
T PRK00807 2 RTCSFCGKEIEPGT 15 (52)
T ss_pred cccCCCCCeEcCCC
Confidence 57999999999874
No 109
>PRK00076 recR recombination protein RecR; Reviewed
Probab=24.09 E-value=37 Score=33.17 Aligned_cols=16 Identities=38% Similarity=0.636 Sum_probs=14.5
Q ss_pred cccccCCCHHHHHHHH
Q 009298 141 IRKIGGIGKVTEHILR 156 (538)
Q Consensus 141 l~~L~GIG~kt~~kL~ 156 (538)
+..|||||+|++++|.
T Consensus 13 l~~LPGIG~KsA~Rla 28 (196)
T PRK00076 13 LRKLPGIGPKSAQRLA 28 (196)
T ss_pred HHHCCCCCHHHHHHHH
Confidence 6788999999999996
No 110
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=23.97 E-value=28 Score=21.53 Aligned_cols=11 Identities=36% Similarity=0.939 Sum_probs=7.1
Q ss_pred ccccccccCCC
Q 009298 451 YKCSLCGTEMP 461 (538)
Q Consensus 451 ~~~~~~~~~~~ 461 (538)
|+|+.|.+.-.
T Consensus 1 y~C~~C~y~t~ 11 (24)
T PF13909_consen 1 YKCPHCSYSTS 11 (24)
T ss_dssp EE-SSSS-EES
T ss_pred CCCCCCCCcCC
Confidence 79999987653
No 111
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=23.97 E-value=1e+02 Score=35.18 Aligned_cols=48 Identities=21% Similarity=0.225 Sum_probs=37.3
Q ss_pred CCCcccccCCCHHHHHHHHhhcCCCchHHHHhch-HHHHHH--cChhHHHHHH
Q 009298 138 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFL 187 (538)
Q Consensus 138 ~lPl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~kr--FG~~~~~~L~ 187 (538)
.+.+..|||||+++.++|-+ -..++.++...+ ..|.+. +|...+..+.
T Consensus 524 ~~~L~~IpGIG~kr~~~LL~--~FGS~~~I~~As~eeL~~vpGi~~~~A~~I~ 574 (577)
T PRK14668 524 STVLDDVPGVGPETRKRLLR--RFGSVEGVREASVEDLRDVPGVGEKTAETIR 574 (577)
T ss_pred HhHHhcCCCCCHHHHHHHHH--HcCCHHHHHhCCHHHHHhCCCCCHHHHHHHH
Confidence 46788999999999999876 456888998887 778777 5566666553
No 112
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=23.89 E-value=42 Score=32.91 Aligned_cols=43 Identities=21% Similarity=0.307 Sum_probs=27.7
Q ss_pred EecCChhHHHHHhcccCCCCeEEecCChHHHHHhhcCC---CcccccCCCHHHHHHHH
Q 009298 102 GVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSL---PIRKIGGIGKVTEHILR 156 (538)
Q Consensus 102 GIA~nk~lAKLAS~~aKP~G~~vl~~~~~~~~~fL~~l---Pl~~L~GIG~kt~~kL~ 156 (538)
||||-..++-|.+- +++ ++...+..= -|+.+||||++|++++-
T Consensus 81 GIGpK~Al~iLs~~----------~~~--~l~~aI~~~D~~~L~~ipGIGkKtAerIi 126 (203)
T PRK14602 81 KVGAKTALAILSQF----------RPD--DLRRLVAEEDVAALTRVSGIGKKTAQHIF 126 (203)
T ss_pred CcCHHHHHHHHhhC----------CHH--HHHHHHHhCCHHHHhcCCCcCHHHHHHHH
Confidence 88887777655542 111 333344432 37788999999999975
No 113
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=23.81 E-value=41 Score=32.77 Aligned_cols=43 Identities=26% Similarity=0.334 Sum_probs=27.8
Q ss_pred EecCChhHHHHHhcccCCCCeEEecCChHHHHHhhcCC---CcccccCCCHHHHHHHH
Q 009298 102 GVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSL---PIRKIGGIGKVTEHILR 156 (538)
Q Consensus 102 GIA~nk~lAKLAS~~aKP~G~~vl~~~~~~~~~fL~~l---Pl~~L~GIG~kt~~kL~ 156 (538)
||||-..+|-|... ++ +++...+..= -++++||||++|++++-
T Consensus 80 GIGpK~Al~iLs~~----------~~--~el~~aI~~~D~~~L~kvpGIGkKtAerIi 125 (195)
T PRK14604 80 GVGPKAALNLLSSG----------TP--DELQLAIAGGDVARLARVPGIGKKTAERIV 125 (195)
T ss_pred CcCHHHHHHHHcCC----------CH--HHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 88887777655431 11 1344444443 36788999999999975
No 114
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=23.48 E-value=86 Score=33.12 Aligned_cols=54 Identities=17% Similarity=0.191 Sum_probs=42.0
Q ss_pred HhhcCCCcccccCCCHHHHHHHHhhcCCCchHHHHhch-HHHH--HHcChhHHHHHHHh
Q 009298 134 TFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLC--AVFSHSTADFFLSV 189 (538)
Q Consensus 134 ~fL~~lPl~~L~GIG~kt~~kL~~~lGI~TlgDL~~lp-~~L~--krFG~~~~~~L~~~ 189 (538)
..+..++|.+| .+.-+...-|++ .||+|++||.+.. ..|. +-||+...+-+.+.
T Consensus 258 ~~~~~~~Ie~L-~LSvRs~NcLk~-a~I~ti~dL~~~s~~dLl~ikN~GkKSl~EI~~~ 314 (327)
T CHL00013 258 IALKQIFIEQL-ELSVRAYNCLKR-ANIHTLLDLLNYSQEDLLKIKNFGQKSAKEVLEA 314 (327)
T ss_pred hhhhceeHHhc-cCchhhhhhhhh-cCccCHHHHHhcCHHHHhhhhccCHhHHHHHHHH
Confidence 35677789998 788888899998 8999999999987 4443 57898766655443
No 115
>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=23.44 E-value=32 Score=33.34 Aligned_cols=43 Identities=30% Similarity=0.393 Sum_probs=26.6
Q ss_pred EecCChhHHHHHhcccCCCCeEEecCChHHHHHhhcC---CCcccccCCCHHHHHHHH
Q 009298 102 GVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISS---LPIRKIGGIGKVTEHILR 156 (538)
Q Consensus 102 GIA~nk~lAKLAS~~aKP~G~~vl~~~~~~~~~fL~~---lPl~~L~GIG~kt~~kL~ 156 (538)
||||-..+|-|.. . .+ ++....+.. --|..+||||++|++++-
T Consensus 79 GIGpK~Al~iL~~-~---------~~--~el~~aI~~~d~~~L~~ipGiGkKtAerIi 124 (191)
T TIGR00084 79 GVGPKLALAILSN-M---------SP--EEFVYAIETEEVKALVKIPGVGKKTAERLL 124 (191)
T ss_pred CCCHHHHHHHHhc-C---------CH--HHHHHHHHhCCHHHHHhCCCCCHHHHHHHH
Confidence 7887766654322 1 11 134444443 347889999999998874
No 116
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=23.37 E-value=43 Score=32.71 Aligned_cols=43 Identities=21% Similarity=0.276 Sum_probs=28.3
Q ss_pred EecCChhHHHHHhcccCCCCeEEecCChHHHHHhhcCC---CcccccCCCHHHHHHHH
Q 009298 102 GVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSL---PIRKIGGIGKVTEHILR 156 (538)
Q Consensus 102 GIA~nk~lAKLAS~~aKP~G~~vl~~~~~~~~~fL~~l---Pl~~L~GIG~kt~~kL~ 156 (538)
||||-..+|-|.+- ++ +++...+..= -|+++||||+||++++-
T Consensus 79 GIGpK~AL~iLs~~----------~~--~~l~~aI~~~D~~~L~kvpGIGkKtAerIi 124 (197)
T PRK14603 79 GVGPKLALALLSAL----------PP--ALLARALLEGDARLLTSASGVGKKLAERIA 124 (197)
T ss_pred CcCHHHHHHHHcCC----------CH--HHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 88887777755442 11 1344444442 37788999999999985
No 117
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=22.95 E-value=36 Score=30.90 Aligned_cols=15 Identities=27% Similarity=0.616 Sum_probs=13.1
Q ss_pred CccccccccCCCCCc
Q 009298 450 DYKCSLCGTEMPPSF 464 (538)
Q Consensus 450 ~~~~~~~~~~~~~~~ 464 (538)
-++||.||..+.|+-
T Consensus 4 ~e~CsFcG~kIyPG~ 18 (131)
T PRK14891 4 TRTCDYTGEEIEPGT 18 (131)
T ss_pred eeeecCcCCcccCCC
Confidence 468999999999983
No 118
>PRK13844 recombination protein RecR; Provisional
Probab=22.90 E-value=40 Score=33.03 Aligned_cols=16 Identities=38% Similarity=0.559 Sum_probs=14.5
Q ss_pred cccccCCCHHHHHHHH
Q 009298 141 IRKIGGIGKVTEHILR 156 (538)
Q Consensus 141 l~~L~GIG~kt~~kL~ 156 (538)
+..|||||++++++|.
T Consensus 17 l~~LPGIG~KsA~Rla 32 (200)
T PRK13844 17 LRKLPTIGKKSSQRLA 32 (200)
T ss_pred HHHCCCCCHHHHHHHH
Confidence 6788999999999996
No 119
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=22.64 E-value=35 Score=26.36 Aligned_cols=14 Identities=43% Similarity=0.975 Sum_probs=12.4
Q ss_pred CccccccccCCCCC
Q 009298 450 DYKCSLCGTEMPPS 463 (538)
Q Consensus 450 ~~~~~~~~~~~~~~ 463 (538)
-..|+-||..++|+
T Consensus 3 ~~~C~f~g~~I~PG 16 (54)
T cd00472 3 TEKCSFCGYKIYPG 16 (54)
T ss_pred EEEecCcCCeecCC
Confidence 35899999999998
No 120
>PRK02240 GTP cyclohydrolase III; Provisional
Probab=22.38 E-value=4.5e+02 Score=26.85 Aligned_cols=101 Identities=16% Similarity=0.042 Sum_probs=0.0
Q ss_pred HcCCCCCCcHHHHHhhC------------------------------CC-eEEEcCC-----------------hHHHHH
Q 009298 10 RFGVRAAMPGFIARKLC------------------------------PE-LIFVPTD-----------------FTKYTY 41 (538)
Q Consensus 10 ~~GVr~GM~l~~A~~LC------------------------------P~-Lvvvp~d-----------------~~~Y~~ 41 (538)
+.||-.|-+..+|..+| ++ +++.|.| +-.-.+
T Consensus 85 s~GIG~g~TP~eA~~~At~~Le~~g~aq~~~r~e~l~~~~~~~~~~~~~~v~iaH~Di~~~T~~~td~~~~~dt~~~i~~ 164 (254)
T PRK02240 85 SMGIGTAETPYEAQKLATEALQEAGSAQDENRKEVLAGDDVANEDRTDGYVQIAHFDINDITGTYTDIENAFDTFLEIEQ 164 (254)
T ss_pred EEEEEecCCHHHHHHHHHHHHHHhcccccccchhhhcccCccccccCCCceEEEEEeeecccceeeccCchhHHHHHHHH
Q ss_pred HHHHHHHHHHh-cCCCeEeeCccEEEEEcCccchhcCCCHHHHHHHHHHHHHHHhCC--ceEEEecCChhHHHHHhccc
Q 009298 42 YSDLTRKVFCK-YDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGL--TCSAGVAPNRLLAKVCSDIN 117 (538)
Q Consensus 42 ~s~~l~~il~~-~sp~Ve~~SiDEafLDlT~~~~l~g~~~~~la~~IR~~I~~~~Gl--t~S~GIA~nk~lAKLAS~~a 117 (538)
....+++.++. +...--..+=|...+=..+. .++-...+-..|..+.|+ .|-||+|.|+--|-..+..+
T Consensus 165 ~~~~l~~~~~~~~g~l~ff~GGDN~~~~~~~l-------~~~~~~~~i~~i~~~~~v~lkvGIG~g~~a~~A~~~A~~a 236 (254)
T PRK02240 165 AYLALMRELRKAHDALSFFVGGDNFMAPCPGL-------SEGDFLDAIEHVREEVGVELKVGIGRGKTAEDAGNLAKHA 236 (254)
T ss_pred HHHHHHHHHHHhcCcEEEEecCceEEEECCCC-------CHHHHHHHHHHHhhccCeeEEeeeccCCCHHHHHHHHHHH
No 121
>PRK05752 uroporphyrinogen-III synthase; Validated
Probab=22.09 E-value=2.2e+02 Score=28.38 Aligned_cols=79 Identities=22% Similarity=0.278 Sum_probs=43.9
Q ss_pred HHHHHHHHHHHHHHHhCCceEEE-------ecCChhHHHHHhcccCCCCeEEecCChHHHHHhhcCC-------Cccccc
Q 009298 80 GIEIAEELRTSVYEEAGLTCSAG-------VAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSL-------PIRKIG 145 (538)
Q Consensus 80 ~~~la~~IR~~I~~~~Glt~S~G-------IA~nk~lAKLAS~~aKP~G~~vl~~~~~~~~~fL~~l-------Pl~~L~ 145 (538)
+..-+..+.+.+ ++.|..+..- ...+..+.........-+.+...++. .++.|+..+ +-..+.
T Consensus 11 p~~~~~~l~~~l-~~~G~~~~~~P~i~i~p~~~~~~~~~~l~~l~~~d~iifTS~n--aV~~~~~~l~~~~~~~~~~~~~ 87 (255)
T PRK05752 11 PAEECAALAASL-AEAGIFSSSLPLLAIEPLPETPEQRALLLELDRYCAVIVVSKP--AARLGLELLDRYWPQPPQQPWF 87 (255)
T ss_pred cHHHHHHHHHHH-HHcCCCEEEcCcEEEeeCCCCHHHHHHHhcCCCCCEEEEECHH--HHHHHHHHHHhhCCCCcCCEEE
Confidence 344556666666 4678665442 23333333333444443444444432 555554332 123455
Q ss_pred CCCHHHHHHHHhhcCCC
Q 009298 146 GIGKVTEHILRDVFGIN 162 (538)
Q Consensus 146 GIG~kt~~kL~~~lGI~ 162 (538)
.||++|++.|++ +|+.
T Consensus 88 aVG~~Ta~al~~-~G~~ 103 (255)
T PRK05752 88 SVGAATAAILQD-YGLD 103 (255)
T ss_pred EECHHHHHHHHH-cCCC
Confidence 889999999997 9984
No 122
>KOG0633 consensus Histidinol phosphate aminotransferase [Amino acid transport and metabolism]
Probab=21.85 E-value=1.5e+02 Score=30.58 Aligned_cols=43 Identities=28% Similarity=0.359 Sum_probs=27.7
Q ss_pred CCeEEE--cCChHHHHHHHHHHHHHHHhcCCCeEeeCccEEEEEcCc
Q 009298 27 PELIFV--PTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITE 71 (538)
Q Consensus 27 P~Lvvv--p~d~~~Y~~~s~~l~~il~~~sp~Ve~~SiDEafLDlT~ 71 (538)
+.++++ |-||..-.--.+.+.+||+..+.-+. =+||||+|.++
T Consensus 161 iK~~F~tSPgNPtg~~ik~~di~KiLe~p~nglV--VvDEAYidFsg 205 (375)
T KOG0633|consen 161 IKCIFLTSPGNPTGSIIKEDDILKILEMPDNGLV--VVDEAYIDFSG 205 (375)
T ss_pred ceEEEEcCCCCCCcccccHHHHHHHHhCCCCcEE--EEeeeeEeecc
Confidence 344554 34554444445667788888775333 37999999998
No 123
>smart00267 GGDEF diguanylate cyclase. Diguanylate cyclase, present in a variety of bacteria
Probab=21.61 E-value=3.7e+02 Score=23.02 Aligned_cols=64 Identities=22% Similarity=0.107 Sum_probs=39.9
Q ss_pred HHHHHHHHHHHHHhcCCC---eEeeCccEEEEEcCccchhcCCCHHHHHHHHHHHHHHHhC-------CceEEEecC
Q 009298 39 YTYYSDLTRKVFCKYDPN---FMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAG-------LTCSAGVAP 105 (538)
Q Consensus 39 Y~~~s~~l~~il~~~sp~---Ve~~SiDEafLDlT~~~~l~g~~~~~la~~IR~~I~~~~G-------lt~S~GIA~ 105 (538)
.......+..++....+. +..++-|+..+=+.+... . ....++.+|.+.+..... +++++|++.
T Consensus 57 ~~~~l~~i~~~l~~~~~~~~~~~r~~~~~f~ii~~~~~~-~--~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~ 130 (163)
T smart00267 57 GDELLQEVAQRLSSCLRPGDLLARLGGDEFALLLPETSL-E--EAIALAERILQQLREPIIIHGIPLYLTISIGVAA 130 (163)
T ss_pred HHHHHHHHHHHHHHhcCCCCEEEEecCceEEEEecCCCH-H--HHHHHHHHHHHHHhCccccCCcEEEEEEEEEEEe
Confidence 345566667777776653 555666776655544321 1 356778888887754443 788888875
No 124
>TIGR01916 F420_cofE F420-0:gamma-glutamyl ligase. This model represents an enzyme of coenzyme F(420) biosynthesis, as catalyzed by MJ0768 of Methanococcus jannaschii and by the N-terminal half of FbiB of Mycobacterium bovis strain BCG. Note that only two glutamates are ligated in M. jannaschii, but five to six in the Mycobacterium lineage. In M. jannaschii, CofE catalyzes the GTP-dependent addition of two L-glutamates.
Probab=21.42 E-value=2.7e+02 Score=28.23 Aligned_cols=36 Identities=14% Similarity=0.023 Sum_probs=30.2
Q ss_pred hcCCCHHHHHHHHHHHHHHHhCCceEEEecCChhHH
Q 009298 75 ERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLA 110 (538)
Q Consensus 75 l~g~~~~~la~~IR~~I~~~~Glt~S~GIA~nk~lA 110 (538)
++-.++...|++||++|.+.+|..+.+=|..+..-+
T Consensus 119 LLP~DPd~sA~~ir~~l~~~~g~~v~VIItDt~gr~ 154 (243)
T TIGR01916 119 LLPEDPDASAEKIRRGLRELTGVDVGVIITDTNGRP 154 (243)
T ss_pred ecCCChHHHHHHHHHHHHHHHCCCEEEEEECCCCCc
Confidence 344489999999999999999999999998876544
No 125
>PHA02768 hypothetical protein; Provisional
Probab=21.37 E-value=36 Score=26.40 Aligned_cols=27 Identities=26% Similarity=0.452 Sum_probs=17.1
Q ss_pred ecCccccccccCCCCCcHhhhhccccchH
Q 009298 448 LDDYKCSLCGTEMPPSFIEERQEHSDFHL 476 (538)
Q Consensus 448 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 476 (538)
+-||.|+.||....-+ ..-+.|...|.
T Consensus 3 ~~~y~C~~CGK~Fs~~--~~L~~H~r~H~ 29 (55)
T PHA02768 3 LLGYECPICGEIYIKR--KSMITHLRKHN 29 (55)
T ss_pred ccccCcchhCCeeccH--HHHHHHHHhcC
Confidence 4589999999876532 23345555544
No 126
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=21.07 E-value=44 Score=26.31 Aligned_cols=30 Identities=27% Similarity=0.493 Sum_probs=19.8
Q ss_pred CCCCCCccccCcCCcceeecCccccccccCCCCCcHhh
Q 009298 430 TPDNKVGTSSNQKDQFIWLDDYKCSLCGTEMPPSFIEE 467 (538)
Q Consensus 430 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 467 (538)
...|-+.=+.|+. --|++|||-=.|...|-
T Consensus 18 ~~pNyntCT~Ck~--------~VCnlCGFNP~Phl~E~ 47 (61)
T PF05715_consen 18 DPPNYNTCTECKS--------QVCNLCGFNPTPHLTEV 47 (61)
T ss_pred CCCCccHHHHHhh--------hhhcccCCCCCcccccc
Confidence 3444444455554 36999999988877763
No 127
>smart00355 ZnF_C2H2 zinc finger.
Probab=20.85 E-value=41 Score=20.09 Aligned_cols=12 Identities=33% Similarity=1.035 Sum_probs=9.6
Q ss_pred ccccccccCCCC
Q 009298 451 YKCSLCGTEMPP 462 (538)
Q Consensus 451 ~~~~~~~~~~~~ 462 (538)
|+|..||...+-
T Consensus 1 ~~C~~C~~~f~~ 12 (26)
T smart00355 1 YRCPECGKVFKS 12 (26)
T ss_pred CCCCCCcchhCC
Confidence 789999987753
No 128
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=20.83 E-value=80 Score=28.20 Aligned_cols=30 Identities=10% Similarity=0.346 Sum_probs=21.8
Q ss_pred cccccCCCHHHHHHHHhhc----CCCchHHHHhc
Q 009298 141 IRKIGGIGKVTEHILRDVF----GINTCEEMLQK 170 (538)
Q Consensus 141 l~~L~GIG~kt~~kL~~~l----GI~TlgDL~~l 170 (538)
|..|||||++.++++-+.. ++.++.||.+.
T Consensus 70 L~~lpGIG~~~A~~Ii~~R~~~g~f~s~eeL~~V 103 (120)
T TIGR01259 70 LQALPGIGPAKAKAIIEYREENGAFKSVDDLTKV 103 (120)
T ss_pred HhcCCCCCHHHHHHHHHHHHhcCCcCCHHHHHcC
Confidence 5668999999998887622 46677777554
No 129
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=20.77 E-value=44 Score=26.34 Aligned_cols=13 Identities=46% Similarity=1.163 Sum_probs=11.1
Q ss_pred cCccccccccCCC
Q 009298 449 DDYKCSLCGTEMP 461 (538)
Q Consensus 449 ~~~~~~~~~~~~~ 461 (538)
+-|+|.-||||=|
T Consensus 49 ~~Y~Cp~CGF~GP 61 (61)
T COG2888 49 NPYRCPKCGFEGP 61 (61)
T ss_pred CceECCCcCccCC
Confidence 5799999999865
No 130
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=20.66 E-value=44 Score=26.29 Aligned_cols=12 Identities=42% Similarity=1.392 Sum_probs=10.6
Q ss_pred cccccccCCCCC
Q 009298 452 KCSLCGTEMPPS 463 (538)
Q Consensus 452 ~~~~~~~~~~~~ 463 (538)
.|..||..+||+
T Consensus 5 HC~~CG~~Ip~~ 16 (59)
T PF09889_consen 5 HCPVCGKPIPPD 16 (59)
T ss_pred cCCcCCCcCCcc
Confidence 599999999984
No 131
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=20.12 E-value=51 Score=21.20 Aligned_cols=14 Identities=36% Similarity=0.840 Sum_probs=11.3
Q ss_pred ccccccccCCCCCc
Q 009298 451 YKCSLCGTEMPPSF 464 (538)
Q Consensus 451 ~~~~~~~~~~~~~~ 464 (538)
..|.-||.++++++
T Consensus 3 ~~Cp~Cg~~~~~~~ 16 (26)
T PF13248_consen 3 MFCPNCGAEIDPDA 16 (26)
T ss_pred CCCcccCCcCCccc
Confidence 46999999988764
No 132
>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=20.10 E-value=1.4e+02 Score=34.71 Aligned_cols=18 Identities=17% Similarity=0.385 Sum_probs=11.5
Q ss_pred CcccccCCCHHHHHHHHh
Q 009298 140 PIRKIGGIGKVTEHILRD 157 (538)
Q Consensus 140 Pl~~L~GIG~kt~~kL~~ 157 (538)
.|..|+|+|.+++++|.+
T Consensus 467 ~L~~L~GfG~Ksa~nIl~ 484 (652)
T TIGR00575 467 DLLELEGFGEKSAQNLLN 484 (652)
T ss_pred HHhhccCccHHHHHHHHH
Confidence 355667777777666654
No 133
>smart00782 PhnA_Zn_Ribbon PhnA Zinc-Ribbon. This protein family includes an uncharacterised member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterised phosphonoacetate hydrolase designated PhnA.
Probab=20.09 E-value=48 Score=24.86 Aligned_cols=10 Identities=50% Similarity=1.398 Sum_probs=7.8
Q ss_pred CccccccccC
Q 009298 450 DYKCSLCGTE 459 (538)
Q Consensus 450 ~~~~~~~~~~ 459 (538)
|-||-|||.+
T Consensus 7 ~~kCELC~a~ 16 (47)
T smart00782 7 ESKCELCGSD 16 (47)
T ss_pred CCcccCcCCC
Confidence 5689999953
Done!