Query 009922
Match_columns 522
No_of_seqs 172 out of 1423
Neff 6.4
Searched_HMMs 46136
Date Thu Mar 28 18:56:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009922.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009922hhsearch_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 3.2E-58 7E-63 496.1 36.4 311 1-312 184-513 (571)
2 PRK01216 DNA polymerase IV; Va 100.0 2.6E-55 5.7E-60 457.9 35.4 279 1-288 59-342 (351)
3 KOG2094 Predicted DNA damage i 100.0 7E-57 1.5E-61 451.3 22.1 298 1-302 154-457 (490)
4 cd00424 PolY Y-family of DNA p 100.0 1.3E-54 2.8E-59 451.8 33.8 277 1-283 53-343 (343)
5 PRK03858 DNA polymerase IV; Va 100.0 1.7E-54 3.7E-59 458.7 35.3 284 1-288 54-343 (396)
6 cd01701 PolY_Rev1 DNA polymera 100.0 1.3E-54 2.9E-59 461.0 34.5 281 1-285 102-404 (404)
7 PRK14133 DNA polymerase IV; Pr 100.0 4.1E-54 8.9E-59 448.6 35.2 280 1-288 57-339 (347)
8 PRK02406 DNA polymerase IV; Va 100.0 3.5E-54 7.6E-59 448.3 33.6 282 1-288 49-334 (343)
9 PRK02794 DNA polymerase IV; Pr 100.0 8.4E-54 1.8E-58 456.9 34.3 285 1-289 89-376 (419)
10 PRK03352 DNA polymerase IV; Va 100.0 1.5E-53 3.3E-58 444.0 35.1 279 1-288 63-345 (346)
11 PRK03348 DNA polymerase IV; Pr 100.0 4.6E-53 9.9E-58 454.9 35.4 284 1-287 59-346 (454)
12 PRK03103 DNA polymerase IV; Re 100.0 3.2E-53 6.8E-58 451.0 32.8 283 1-288 59-352 (409)
13 cd03586 PolY_Pol_IV_kappa DNA 100.0 7.7E-53 1.7E-57 435.6 34.3 280 1-285 52-334 (334)
14 PRK01810 DNA polymerase IV; Va 100.0 6.1E-53 1.3E-57 448.6 34.2 282 1-288 61-347 (407)
15 cd01703 PolY_Pol_iota DNA Poly 100.0 7.7E-53 1.7E-57 443.2 32.9 280 1-284 49-379 (379)
16 cd01702 PolY_Pol_eta DNA Polym 100.0 7.7E-52 1.7E-56 433.2 30.3 269 1-284 49-359 (359)
17 cd01700 PolY_Pol_V_umuC umuC s 100.0 3.5E-51 7.6E-56 426.0 30.0 279 1-284 51-344 (344)
18 PRK03609 umuC DNA polymerase V 100.0 8.6E-51 1.9E-55 434.1 32.7 283 1-288 53-353 (422)
19 COG0389 DinP Nucleotidyltransf 100.0 4.3E-47 9.4E-52 396.9 31.4 284 1-288 55-347 (354)
20 cd03468 PolY_like DNA Polymera 100.0 5.2E-46 1.1E-50 384.6 29.3 275 1-283 52-334 (335)
21 KOG2093 Translesion DNA polyme 100.0 1.3E-44 2.9E-49 393.8 18.0 305 1-312 429-753 (1016)
22 KOG2095 DNA polymerase iota/DN 100.0 1.3E-37 2.9E-42 334.2 12.1 232 1-234 67-375 (656)
23 PF00817 IMS: impB/mucB/samB f 99.9 6.9E-22 1.5E-26 182.5 9.4 98 1-99 51-149 (149)
24 PF11799 IMS_C: impB/mucB/samB 99.5 1.4E-13 3.1E-18 121.9 11.2 107 180-286 2-116 (127)
25 PF11798 IMS_HHH: IMS family H 98.5 1E-07 2.3E-12 65.5 3.0 30 115-145 3-32 (32)
26 PRK04301 radA DNA repair and r 97.6 3.5E-05 7.6E-10 79.9 3.2 79 119-198 2-88 (317)
27 TIGR02236 recomb_radA DNA repa 96.7 0.0014 3.1E-08 67.5 3.9 73 125-198 1-81 (310)
28 PF14520 HHH_5: Helix-hairpin- 96.3 0.0041 8.8E-08 48.7 3.6 47 126-173 8-57 (60)
29 PF11731 Cdd1: Pathogenicity l 95.6 0.012 2.6E-07 50.4 3.6 36 124-160 13-49 (93)
30 PF10391 DNA_pol_lambd_f: Fing 94.4 0.029 6.3E-07 43.0 2.3 28 126-154 5-32 (52)
31 PF04994 TfoX_C: TfoX C-termin 94.0 0.1 2.2E-06 43.6 5.0 32 123-155 3-34 (81)
32 PF03118 RNA_pol_A_CTD: Bacter 92.1 0.25 5.3E-06 39.7 4.3 51 118-170 7-60 (66)
33 PRK12766 50S ribosomal protein 92.0 0.27 5.9E-06 48.8 5.4 52 124-176 4-58 (232)
34 COG3743 Uncharacterized conser 91.4 0.21 4.6E-06 45.3 3.6 31 124-155 68-98 (133)
35 PRK02362 ski2-like helicase; P 89.0 0.47 1E-05 55.0 4.9 52 123-175 652-704 (737)
36 PF12826 HHH_2: Helix-hairpin- 83.1 1.2 2.6E-05 35.3 2.9 43 128-172 8-53 (64)
37 PRK14672 uvrC excinuclease ABC 82.0 8.2 0.00018 44.3 10.0 54 122-177 607-663 (691)
38 PF14229 DUF4332: Domain of un 82.0 1.5 3.3E-05 39.4 3.5 49 115-164 45-94 (122)
39 COG2251 Predicted nuclease (Re 81.8 1.8 3.9E-05 46.9 4.5 48 115-163 217-265 (474)
40 smart00483 POLXc DNA polymeras 81.4 1 2.3E-05 47.3 2.6 29 125-154 91-119 (334)
41 PRK08609 hypothetical protein; 80.7 1.4 3E-05 49.8 3.4 64 63-154 56-119 (570)
42 PRK01172 ski2-like helicase; P 80.7 2 4.3E-05 49.3 4.8 50 122-172 611-663 (674)
43 PF02961 BAF: Barrier to autoi 79.5 1.9 4.1E-05 36.7 3.0 33 120-153 16-48 (89)
44 cd00141 NT_POLXc Nucleotidyltr 79.1 1.5 3.2E-05 45.7 2.7 29 125-154 87-115 (307)
45 PF14229 DUF4332: Domain of un 78.9 1.8 4E-05 38.8 3.0 26 129-155 1-26 (122)
46 PRK07758 hypothetical protein; 77.6 4.1 8.8E-05 35.1 4.5 44 127-171 38-84 (95)
47 PRK00254 ski2-like helicase; P 77.3 2.7 6E-05 48.6 4.6 53 122-175 644-699 (720)
48 PF00633 HHH: Helix-hairpin-he 75.1 1.5 3.3E-05 29.6 1.1 16 125-140 13-28 (30)
49 PRK10917 ATP-dependent DNA hel 72.5 2.7 5.8E-05 48.4 2.9 30 123-153 9-38 (681)
50 PF13878 zf-C2H2_3: zinc-finge 70.6 1.8 3.9E-05 31.5 0.6 26 435-460 14-39 (41)
51 TIGR03491 RecB family nuclease 68.2 5.6 0.00012 43.6 4.1 38 117-155 201-238 (457)
52 PRK14667 uvrC excinuclease ABC 67.0 7.7 0.00017 43.8 4.9 53 122-176 513-567 (567)
53 COG0322 UvrC Nuclease subunit 66.1 48 0.001 37.7 10.9 131 9-171 443-578 (581)
54 COG1200 RecG RecG-like helicas 64.8 4.8 0.0001 45.9 2.7 32 123-155 10-42 (677)
55 PF02889 Sec63: Sec63 Brl doma 63.6 13 0.00028 38.1 5.5 54 122-176 147-203 (314)
56 cd07556 Nucleotidyl_cyc_III Cl 62.6 79 0.0017 26.8 9.6 61 27-90 32-97 (133)
57 PTZ00035 Rad51 protein; Provis 62.2 7.7 0.00017 40.9 3.6 52 122-174 20-76 (337)
58 PRK12278 50S ribosomal protein 59.8 8.9 0.00019 38.1 3.3 32 123-155 158-189 (221)
59 PLN03187 meiotic recombination 59.7 9.3 0.0002 40.5 3.7 42 122-164 28-72 (344)
60 PRK14669 uvrC excinuclease ABC 57.8 16 0.00035 41.8 5.3 52 122-175 551-603 (624)
61 TIGR00596 rad1 DNA repair prot 57.6 13 0.00028 43.9 4.6 49 125-175 759-809 (814)
62 PLN03186 DNA repair protein RA 56.4 11 0.00024 39.9 3.5 43 122-165 25-70 (342)
63 smart00278 HhH1 Helix-hairpin- 55.6 7.6 0.00017 25.0 1.4 17 125-141 3-19 (26)
64 COG2199 c-di-GMP synthetase (d 55.3 33 0.00072 31.7 6.3 63 25-90 76-148 (181)
65 TIGR02239 recomb_RAD51 DNA rep 55.2 14 0.00029 38.7 4.0 35 130-165 8-43 (316)
66 PRK12311 rpsB 30S ribosomal pr 54.7 9.7 0.00021 40.1 2.8 31 124-155 264-294 (326)
67 PRK00116 ruvA Holliday junctio 53.8 12 0.00026 36.2 3.1 53 124-176 74-130 (192)
68 PRK07956 ligA NAD-dependent DN 53.7 20 0.00042 41.4 5.2 51 121-171 443-496 (665)
69 TIGR01448 recD_rel helicase, p 53.1 21 0.00046 41.5 5.5 48 109-159 73-120 (720)
70 TIGR02238 recomb_DMC1 meiotic 52.0 17 0.00036 38.0 4.0 38 126-164 2-42 (313)
71 PRK14670 uvrC excinuclease ABC 50.9 22 0.00047 40.4 4.9 50 122-173 513-565 (574)
72 PRK14973 DNA topoisomerase I; 49.5 30 0.00065 41.5 6.0 76 93-174 851-930 (936)
73 PF04475 DUF555: Protein of un 49.4 6.8 0.00015 33.9 0.5 34 432-470 45-95 (102)
74 TIGR00575 dnlj DNA ligase, NAD 49.1 27 0.0006 40.2 5.5 51 121-171 430-483 (652)
75 PRK03922 hypothetical protein; 49.1 6.7 0.00015 34.6 0.5 43 432-479 47-106 (113)
76 smart00611 SEC63 Domain of unk 48.3 24 0.00051 36.2 4.4 52 122-174 150-204 (312)
77 KOG3014 Protein involved in es 47.3 7.6 0.00016 39.1 0.6 29 435-463 38-66 (257)
78 TIGR02027 rpoA DNA-directed RN 47.0 23 0.00051 36.7 4.1 51 120-172 232-285 (297)
79 PRK14671 uvrC excinuclease ABC 46.9 27 0.00058 40.0 4.9 49 123-173 569-618 (621)
80 PRK05182 DNA-directed RNA poly 46.9 23 0.00049 37.1 4.0 50 120-171 246-298 (310)
81 TIGR00426 competence protein C 45.6 25 0.00054 27.9 3.2 43 124-171 17-64 (69)
82 PRK12373 NADH dehydrogenase su 43.8 21 0.00045 38.6 3.3 31 124-155 324-354 (400)
83 PRK02515 psbU photosystem II c 43.3 20 0.00044 32.7 2.6 29 126-155 64-93 (132)
84 PF13894 zf-C2H2_4: C2H2-type 42.8 7.3 0.00016 23.5 -0.2 12 435-446 1-12 (24)
85 COG5540 RING-finger-containing 42.5 9.2 0.0002 39.5 0.3 17 430-446 355-373 (374)
86 PRK14666 uvrC excinuclease ABC 42.5 31 0.00068 39.8 4.6 49 122-172 636-687 (694)
87 KOG2534 DNA polymerase IV (fam 42.3 29 0.00062 36.4 3.8 32 125-157 99-130 (353)
88 TIGR00615 recR recombination p 41.8 13 0.00028 36.3 1.2 16 125-140 13-28 (195)
89 PRK00076 recR recombination pr 41.1 13 0.00029 36.2 1.2 16 125-140 13-28 (196)
90 PRK00558 uvrC excinuclease ABC 40.9 33 0.00072 39.1 4.5 50 122-173 542-594 (598)
91 PRK14601 ruvA Holliday junctio 40.8 14 0.00031 35.6 1.3 17 124-140 109-125 (183)
92 COG4071 Uncharacterized protei 40.6 57 0.0012 32.3 5.3 57 41-99 117-177 (278)
93 PRK14351 ligA NAD-dependent DN 39.1 45 0.00098 38.7 5.2 51 121-171 460-513 (689)
94 PF02591 DUF164: Putative zinc 39.1 10 0.00022 29.1 0.0 25 427-451 15-39 (56)
95 PRK13844 recombination protein 38.8 15 0.00033 36.0 1.2 16 125-140 17-32 (200)
96 PRK14606 ruvA Holliday junctio 37.0 18 0.00038 35.1 1.3 17 124-140 109-125 (188)
97 COG2062 SixA Phosphohistidine 36.5 1.8E+02 0.004 27.5 8.0 76 10-102 47-122 (163)
98 PRK13901 ruvA Holliday junctio 36.4 18 0.00039 35.3 1.3 17 124-140 108-124 (196)
99 COG0353 RecR Recombinational D 36.3 17 0.00037 35.4 1.1 16 125-140 14-29 (198)
100 PF14716 HHH_8: Helix-hairpin- 35.4 22 0.00048 28.3 1.5 18 124-141 48-65 (68)
101 TIGR01259 comE comEA protein. 35.3 44 0.00095 29.9 3.5 30 125-154 70-103 (120)
102 PRK14604 ruvA Holliday junctio 34.8 20 0.00043 34.9 1.3 17 124-140 109-125 (195)
103 PRK14602 ruvA Holliday junctio 34.1 21 0.00046 34.9 1.4 16 125-140 111-126 (203)
104 PRK14603 ruvA Holliday junctio 33.8 21 0.00046 34.8 1.3 17 124-140 108-124 (197)
105 TIGR01954 nusA_Cterm_rpt trans 32.7 58 0.0013 23.7 3.3 32 131-163 1-33 (50)
106 COG1885 Uncharacterized protei 32.2 18 0.00039 31.7 0.5 43 432-479 47-106 (115)
107 COG0632 RuvA Holliday junction 31.8 25 0.00054 34.5 1.4 43 86-140 80-125 (201)
108 PRK05752 uroporphyrinogen-III 31.5 1.2E+02 0.0026 30.1 6.4 79 64-146 11-103 (255)
109 PF01246 Ribosomal_L24e: Ribos 31.4 15 0.00033 30.0 -0.1 14 434-447 3-16 (71)
110 COG2075 RPL24A Ribosomal prote 31.2 22 0.00048 28.6 0.8 13 435-447 4-16 (66)
111 CHL00013 rpoA RNA polymerase a 30.3 58 0.0013 34.3 3.9 53 119-173 259-314 (327)
112 PRK14600 ruvA Holliday junctio 30.2 28 0.0006 33.7 1.4 15 125-140 110-124 (186)
113 PF13240 zinc_ribbon_2: zinc-r 29.5 27 0.00059 22.1 0.8 12 436-447 1-12 (23)
114 TIGR00194 uvrC excinuclease AB 28.2 2.3E+02 0.0049 32.3 8.4 117 20-153 425-569 (574)
115 TIGR01916 F420_cofE F420-0:gam 28.1 2E+02 0.0043 29.2 7.1 86 3-92 57-152 (243)
116 TIGR00575 dnlj DNA ligase, NAD 27.5 76 0.0016 36.6 4.6 16 125-140 468-483 (652)
117 PRK14668 uvrC excinuclease ABC 27.1 74 0.0016 36.2 4.3 48 122-171 524-574 (577)
118 COG1796 POL4 DNA polymerase IV 26.6 32 0.00069 36.1 1.2 33 123-155 93-125 (326)
119 PRK08097 ligB NAD-dependent DN 26.6 83 0.0018 35.7 4.6 47 124-171 426-476 (562)
120 COG1555 ComEA DNA uptake prote 25.9 43 0.00092 31.2 1.8 30 126-155 100-133 (149)
121 PRK02240 GTP cyclohydrolase II 25.5 4E+02 0.0087 27.2 8.7 58 30-94 38-97 (254)
122 smart00267 GGDEF diguanylate c 25.4 2.8E+02 0.0061 23.7 7.0 63 24-89 58-130 (163)
123 smart00279 HhH2 Helix-hairpin- 25.4 49 0.0011 23.3 1.6 16 125-140 18-33 (36)
124 PF06397 Desulfoferrod_N: Desu 25.2 24 0.00052 25.1 0.0 9 434-442 6-14 (36)
125 TIGR00084 ruvA Holliday juncti 24.5 87 0.0019 30.3 3.7 52 115-171 66-124 (191)
126 PRK00807 50S ribosomal protein 23.7 33 0.00071 26.2 0.5 14 435-448 2-15 (52)
127 PF13909 zf-H2C2_5: C2H2-type 23.6 29 0.00062 21.5 0.1 11 435-445 1-11 (24)
128 smart00483 POLXc DNA polymeras 22.9 1.2E+02 0.0025 32.0 4.7 53 125-179 50-112 (334)
129 PRK14891 50S ribosomal protein 22.3 38 0.00082 30.8 0.7 15 434-448 4-18 (131)
130 cd00472 Ribosomal_L24e_L24 Rib 21.8 37 0.0008 26.3 0.5 14 434-447 3-16 (54)
131 COG1948 MUS81 ERCC4-type nucle 21.6 1.1E+02 0.0024 31.1 4.0 47 125-173 184-233 (254)
132 PHA02768 hypothetical protein; 20.9 38 0.00081 26.4 0.3 27 432-460 3-29 (55)
133 COG0177 Nth Predicted EndoIII- 20.8 79 0.0017 31.3 2.7 53 84-147 78-134 (211)
134 PRK14605 ruvA Holliday junctio 20.7 48 0.001 32.2 1.1 15 125-139 110-124 (194)
135 smart00355 ZnF_C2H2 zinc finge 20.6 42 0.00091 20.1 0.5 11 435-445 1-11 (26)
136 TIGR00084 ruvA Holliday juncti 20.5 51 0.0011 31.9 1.3 18 123-140 107-124 (191)
137 KOG0633 Histidinol phosphate a 20.1 2.9E+02 0.0064 28.6 6.5 44 11-56 161-206 (375)
138 PF05715 zf-piccolo: Piccolo Z 20.0 48 0.001 26.2 0.7 29 415-451 19-47 (61)
No 1
>PTZ00205 DNA polymerase kappa; Provisional
Probab=100.00 E-value=3.2e-58 Score=496.09 Aligned_cols=311 Identities=30% Similarity=0.482 Sum_probs=281.3
Q ss_pred CcHHHHHHhCCCcEEECCChHHHHHHHHHHHHHHHhhCCCEEeecccEEEEEcCcchhhcC--CCHHHHHHHHHHHHHHH
Q 009922 1 MPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERG--ISGIEIAEELRTSVYEE 78 (522)
Q Consensus 1 Mpl~~A~kLCPdLvvvp~d~~~Y~~~s~~i~~il~~~tp~VE~~SiDEafLDvT~~~~l~g--~~~~~lA~~IR~~I~~e 78 (522)
||+++|+++||+|++||+||+.|..+|+++++++.+|+|.||++||||+|||||+....++ .++.++|++||++|+++
T Consensus 184 Mp~~~AkkLCP~Liivp~d~~~Y~~~S~~I~~il~~ysp~ve~~SIDEafLDlT~~~~~~~~~~~~~~iA~~IR~~I~~~ 263 (571)
T PTZ00205 184 MPGFLALKICPNLLILPPDFDAYNEESNTVRRIVAEYDPNYISFGLDELTLEVSAYIERFEGTKTAEDVASELRVRVFGE 263 (571)
T ss_pred CcHHHHHHhCCCCcEecCCHHHHHHHHHHHHHHHHhcCCcEEEeechhceeccCCchhhccCCCCHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999876652 26899999999999999
Q ss_pred hCCceEEeccCChhHHHHHhhcCCCCcEEEEc-CChHHHHHhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhchHH
Q 009922 79 AGLTCSAGVAPNRLLAKVCSDINKPNGQFVLP-NDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSL 157 (522)
Q Consensus 79 tGlt~S~GIA~NKllAKLAS~~~KP~G~~vI~-~~~~~~~~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~~~ 157 (522)
||||||||||+||++|||||+++||||+++++ ...+++.+||+++||++|||||++++++|+. +||+||+||++.+..
T Consensus 264 tgLt~SiGIA~NklLAKiASd~~KPnG~~vl~l~~~~~v~~fL~~LpV~ki~GIG~~t~~~L~~-~GI~TigDLa~~~~~ 342 (571)
T PTZ00205 264 TKLTASAGIGPTAALAKIASNINKPNGQHDLNLHTRGDVMTYVRDLGLRSVPGVGKVTEALLKG-LGITTLSDIYNRRVE 342 (571)
T ss_pred HCCcEEEEEcCCHHHHHHhhhccCCCCCeEEecCCHHHHHHHHhCCCcceeCCcCHHHHHHHHH-cCCCcHHHHhcCCHH
Confidence 99999999999999999999999999999874 2345899999999999999999999999997 999999999987733
Q ss_pred ---------HHHHcChhHHHHHHHhccCCCCCC-CC--CCCCCCcceeecccCCcCCHHHHHHHHHHHHHHHHHHHHHhC
Q 009922 158 ---------LCAVFSHSTADFFLSVGLGLGSTN-TP--QARFRKSISSERTFSVTEDKALLYRKLAEIAEMLSADMQKEG 225 (522)
Q Consensus 158 ---------L~~~FG~~~~~~l~~~a~G~d~~~-v~--~~~~~KSIs~e~tF~~~~~~e~L~~~L~~La~~L~~RLr~~g 225 (522)
+...||...|.++|..++|+|..+ +. ....+|||++++||+...+.+++...|..|+++|+.||++++
T Consensus 343 l~~~f~~k~l~~llG~~~G~~l~~~a~G~d~~~~v~~~~~~~rKSIg~ErTF~~~~d~~el~~~L~~L~~~v~~rLrk~~ 422 (571)
T PTZ00205 343 LCYILHNNLFRFLLGASIGIMQWPDAATAANTENCEGATGGQRKAISSERSFTTPRTKEGLQEMVDTVFNGAYEEMRKSE 422 (571)
T ss_pred HHHHhHHHHHHHHhCchhhHHHHHHhcCCCCCCccCCCCCCCCceeEEeEeCCCCCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 567788767888889999999874 32 245689999999999888999999999999999999999999
Q ss_pred CCccEEEEEEEecCCeeeEEEEEcCCCCCCHHHHHHHHHHHHHhh-C-CCCEEEEEEEeecCCcCCcc--CCCCcccchH
Q 009922 226 LRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAE-L-PVSLRLIGLRVTQFNEDKVR--APSDPTQKTL 301 (522)
Q Consensus 226 ~~artltLkL~~~d~~~~srs~~L~~pt~d~~~L~~~a~~LL~~~-l-~~~IR~lGV~vs~L~~~~~~--~~~~~~q~si 301 (522)
+.+++|+|++++.+|.+.+++.+++.||++...|++++..||+.. + ..+||+|||++++|.....- -.+++.|.+|
T Consensus 423 l~artVtlKlK~~dF~~~trs~tL~~pT~d~~~I~~aa~~Ll~~~~~~~~~vRLlGV~ls~L~~~~~~~~~~~~~~~~~~ 502 (571)
T PTZ00205 423 LMCRQISLTIRWASYRYQQYTKSLIQYSDDSATLRRAVDGLLLPHAAKYSEMCLLGVRFLDLISAKDFHMKRKGGNQLSI 502 (571)
T ss_pred CCccEEEEEEEECCCCceEEEEECCCCcCCHHHHHHHHHHHHHhccccCCCEEEEEEEEcccCcHHHHHHHhcCCceeeH
Confidence 999999999999999999999999999999999999999999876 3 36899999999999987521 2457899999
Q ss_pred HHhhccCcccc
Q 009922 302 TNFMTSGHASK 312 (522)
Q Consensus 302 ~~ff~~~~~~~ 312 (522)
..|..++.+..
T Consensus 503 ~~~~~~~~~~~ 513 (571)
T PTZ00205 503 SQFIRPKKPGE 513 (571)
T ss_pred HHHcCCCCCCc
Confidence 99999877553
No 2
>PRK01216 DNA polymerase IV; Validated
Probab=100.00 E-value=2.6e-55 Score=457.86 Aligned_cols=279 Identities=26% Similarity=0.401 Sum_probs=264.2
Q ss_pred CcHHHHHHhCCCcEEECCChHHHHHHHHHHHHHHHhhCCCEEeecccEEEEEcCcchhhcCCCHHHHHHHHHHHHHHHhC
Q 009922 1 MPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAG 80 (522)
Q Consensus 1 Mpl~~A~kLCPdLvvvp~d~~~Y~~~s~~i~~il~~~tp~VE~~SiDEafLDvT~~~~l~g~~~~~lA~~IR~~I~~etG 80 (522)
||+++|+++||+++++++|++.|+.+|++++.|+++|+|.||++|+||+|||||++.++|| ++.++|++||++|++++|
T Consensus 59 M~~~~A~~lcP~li~v~~d~~~y~~~s~~i~~~l~~~tp~ve~~siDE~~LDvt~~~~l~g-~~~~la~~ir~~I~~~~g 137 (351)
T PRK01216 59 MPIVEAKKILPNAVYLPMRKEVYQQVSNRIMKLLREYSEKIEIASIDEAYLDISDKVKNYQ-DAYNLGLEIKNKILEKEK 137 (351)
T ss_pred CcHHHHHHHCCCeEEECCCHHHHHHHHHHHHHHHHHhCCceEEccCCeEEEEcccchhccC-CHHHHHHHHHHHHHHHHC
Confidence 9999999999999999999999999999999999999999999999999999999999998 899999999999999999
Q ss_pred CceEEeccCChhHHHHHhhcCCCCcEEEEcCChHHHHHhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHH
Q 009922 81 LTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLC 159 (522)
Q Consensus 81 lt~S~GIA~NKllAKLAS~~~KP~G~~vI~~~~~~~~~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~ 159 (522)
+|||+|||+||++|||||+.+||+|+++++++ ++.+||+++||+++||||++++++|++ +||+|++||+++| ..|.
T Consensus 138 lt~siGia~nk~lAKlas~~~KP~g~~vi~~~--~~~~~L~~LPi~~l~giG~~~~~~L~~-~Gi~TigdL~~~~~~~L~ 214 (351)
T PRK01216 138 ITVTVGISKNKVFAKIAADMAKPNGIKVIDDE--EVKRFINELDIADIPGIGDITAEKLKK-LGVNKLVDTLRIEFDELK 214 (351)
T ss_pred CcEEEEecCCHHHHHHHHhccCCCCEEEeCHH--HHHHHHhcCCcccccCCCHHHHHHHHH-cCCCcHHHHhcCCHHHHH
Confidence 99999999999999999999999999999875 789999999999999999999999997 9999999999999 8999
Q ss_pred HHcChhHHHHHHHhccCCCCCCCCCCCCCCcceeecccCC-cCCHHHHHHHHHHHHHHHHHHHHHhCCCccEEEEEEEec
Q 009922 160 AVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV-TEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTA 238 (522)
Q Consensus 160 ~~FG~~~~~~l~~~a~G~d~~~v~~~~~~KSIs~e~tF~~-~~~~e~L~~~L~~La~~L~~RLr~~g~~artltLkL~~~ 238 (522)
++||...+.++|..++|++.+++.+. ++|||+.+.+|.. +.+.+++...|.+|+++++.||+. .++++++++++.
T Consensus 215 ~rfG~~~~~~L~~~a~G~d~~pv~~~-~~ksi~~~~tl~~di~~~~~l~~~l~~L~~~~~~rl~~---~~~~~~~~~~~~ 290 (351)
T PRK01216 215 GIIGEAKAKYLFSLARNEYNEPVRAR-VRKSIGRYVTLPRNTRDLEEIKPYLKRAIEEAYYKLDG---IPKAIHVVAIME 290 (351)
T ss_pred HHHCHHHHHHHHHHhCCCCCCCCCCC-CCCCCcCeEECCCccCCHHHHHHHHHHHHHHHHHHHHh---CCCEEEEEEEcC
Confidence 99998778899999999999998774 5699999999997 689999999999999999999996 678999999999
Q ss_pred CCeeeEEEEEcCCCCCCHHHHHHHHHHHHHhhC---CCCEEEEEEEeecCCcC
Q 009922 239 SFEVRTRAVTLQKYISSSEDILKHASVLLKAEL---PVSLRLIGLRVTQFNED 288 (522)
Q Consensus 239 d~~~~srs~~L~~pt~d~~~L~~~a~~LL~~~l---~~~IR~lGV~vs~L~~~ 288 (522)
+|.+.+++.+++.|++ .+.|++.+..||++.+ ..+||+|||++++|.+.
T Consensus 291 df~~~t~~~tl~~~~~-~~~~~~~a~~Ll~~~~~~~~~~vRllGv~~~~l~~~ 342 (351)
T PRK01216 291 DLDIVSRGRTFTHGIS-KETAYREAVRLLQKILEEDERKIRRIGVRFSKIIEA 342 (351)
T ss_pred CCCEEEEEEECCCCCC-HHHHHHHHHHHHHhhhhcCCCCeeEEEEEEeccccc
Confidence 9999999999999997 6889999999999863 25899999999999865
No 3
>KOG2094 consensus Predicted DNA damage inducible protein [Replication, recombination and repair]
Probab=100.00 E-value=7e-57 Score=451.26 Aligned_cols=298 Identities=55% Similarity=0.869 Sum_probs=281.7
Q ss_pred CcHHHHHHhCCCcEEECCChHHHHHHHHHHHHHHHhhCCCEEeecccEEEEEcCcchhhc--C----CCHHHHHHHHHHH
Q 009922 1 MPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRER--G----ISGIEIAEELRTS 74 (522)
Q Consensus 1 Mpl~~A~kLCPdLvvvp~d~~~Y~~~s~~i~~il~~~tp~VE~~SiDEafLDvT~~~~l~--g----~~~~~lA~~IR~~ 74 (522)
||.+.|++|||+|++||.||.+|+.+|+++.++|.+|+|++-+.|+||||||+|..+++. | .+..+++++||.+
T Consensus 154 MPgFIarklCPdLiiVP~n~~kYt~~Ske~~~v~~~YDsn~~~~SlDEaylnlT~~l~~~~~g~l~~nG~~evveeiR~r 233 (490)
T KOG2094|consen 154 MPGFIARKLCPDLIIVPLNFSKYTIVSKEIQNVLAQYDSNFCAMSLDEAYLNLTSHLRERELGFLVENGITEVVEEIRFR 233 (490)
T ss_pred CchHHHhccCCceEEeCCCcHHHHHHHHHHHHHHHHcCCccccchHHHHHHhHHHHHHHhhcchhhhccHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999998765 3 1267999999999
Q ss_pred HHHHhCCceEEeccCChhHHHHHhhcCCCCcEEEEcCChHHHHHhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhc
Q 009922 75 VYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQK 154 (522)
Q Consensus 75 I~~etGlt~S~GIA~NKllAKLAS~~~KP~G~~vI~~~~~~~~~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l 154 (522)
|+++||+|||+|||.|++|||+||+.+|||||++|++++..+.+|+.+|||+++.|||+.+.+.|.. +||.||||+.+.
T Consensus 234 V~qeTglT~SaGIAaN~lLAKicSd~nKPNgQf~i~~dr~aim~F~kdLPvRkV~GIGrV~E~qLka-l~IkTcgdm~~k 312 (490)
T KOG2094|consen 234 VEQETGLTCSAGIAANKLLAKICSDKNKPNGQFVIPNDRIAIMKFMKDLPVRKVSGIGRVTEQQLKA-LGIKTCGDMQQK 312 (490)
T ss_pred HHHhcCceeeccccHhHHHHHHhccccCCCCceEecccHHHHHHHHhcCCcccccchhHHHHHHHHh-cCceeHHHHHHh
Confidence 9999999999999999999999999999999999999999999999999999999999999999996 999999999888
Q ss_pred hHHHHHHcChhHHHHHHHhccCCCCCCCCCCCCCCcceeecccCCcCCHHHHHHHHHHHHHHHHHHHHHhCCCccEEEEE
Q 009922 155 GSLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSVTEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLK 234 (522)
Q Consensus 155 ~~~L~~~FG~~~~~~l~~~a~G~d~~~v~~~~~~KSIs~e~tF~~~~~~e~L~~~L~~La~~L~~RLr~~g~~artltLk 234 (522)
-..|...|.+..++.+.+.+.|.+.++.+....+|||++|+||..+.+...++..+++||+.|+..|+++|+.+++||++
T Consensus 313 ~~ll~~lFsp~S~~~fLr~slG~g~t~~~~~~eRKsis~ErTFs~~sd~~il~~k~qel~~~lsedlqK~glv~rtvtiK 392 (490)
T KOG2094|consen 313 LVLLSLLFSPKSFQNFLRCSLGLGTTILDEDGERKSISSERTFSSTSDPSILYSKLQELCQMLSEDLQKEGLVGRTVTIK 392 (490)
T ss_pred hhHHHHHhCchhHHHHHHHhhcCCCCcCccccccccccceeeecccCCHHHHHHHHHHHHHHHHHHHHhcCcccceEEEE
Confidence 78889999999888888889999998888888899999999999999999999999999999999999999999999999
Q ss_pred EEecCCeeeEEEEEcCCCCCCHHHHHHHHHHHHHhhCCCCEEEEEEEeecCCcCCccCCCCcccchHH
Q 009922 235 LKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAELPVSLRLIGLRVTQFNEDKVRAPSDPTQKTLT 302 (522)
Q Consensus 235 L~~~d~~~~srs~~L~~pt~d~~~L~~~a~~LL~~~l~~~IR~lGV~vs~L~~~~~~~~~~~~q~si~ 302 (522)
++++.|++.+++.+......+.++|+..|.+||++.+|..||++||+++.|.... .+...|+++.
T Consensus 393 lK~ssFev~Tr~~t~s~vv~S~edi~k~aleLLk~e~~~~iRLlGvR~sqlv~ee---d~~~~~~tv~ 457 (490)
T KOG2094|consen 393 LKTSSFEVHTRQKTISQVVHSEEDILKPALELLKQEYPMTIRLLGVRASQLVSEE---DRKLAQQTVS 457 (490)
T ss_pred EeccceeeeeccCchhhhhccHHHHHHHHHHHHHhhcCceEeeeeeeHhhccchh---ccchhhcchh
Confidence 9999999999999999999999999999999999999999999999999999874 3455666665
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=1.3e-54 Score=451.75 Aligned_cols=277 Identities=30% Similarity=0.448 Sum_probs=262.3
Q ss_pred CcHHHHHHhCCCcEEECCChHHHHHHHHHHHHHHHhhCCCEEeecccEEEEEcCcchhhcCCCHHHHHHHHHHHHHHHhC
Q 009922 1 MPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAG 80 (522)
Q Consensus 1 Mpl~~A~kLCPdLvvvp~d~~~Y~~~s~~i~~il~~~tp~VE~~SiDEafLDvT~~~~l~g~~~~~lA~~IR~~I~~etG 80 (522)
||+++|+++||+++++++|++.|.++|+++++++.+|+|.||++||||+|||+|++.++|+ ++.++|+.||++|++++|
T Consensus 53 m~~~~A~~lcP~l~~~~~~~~~y~~~s~~i~~~l~~~sp~ve~~siDE~~ldvt~~~~~~~-~~~~la~~i~~~i~~~~g 131 (343)
T cd00424 53 MPVREARKMCPNLILVPARLDLYRRLSERLLSELEEVAPLVEVASIDELFLDLTGSARLLG-LGSEVALRIKRHIAEQLG 131 (343)
T ss_pred CcHHHHHHhCCCeEEECCCcHHHHHHHHHHHHHHHHhCCcEEEccCCEEEEECCCchhccC-CHHHHHHHHHHHHHHHhC
Confidence 9999999999999999999999999999999999999999999999999999999999888 799999999999999998
Q ss_pred -CceEEeccCChhHHHHHhhcCCCCcEEEEcCChHHHHHhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhch--HH
Q 009922 81 -LTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG--SL 157 (522)
Q Consensus 81 -lt~S~GIA~NKllAKLAS~~~KP~G~~vI~~~~~~~~~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~--~~ 157 (522)
+|||||||+||++|||||+.+||+|+++++++ ++.+||+++||++|||||+++.++|++ +||+|++||+++| ..
T Consensus 132 gl~~siGia~n~~lAKlAs~~~KP~g~~v~~~~--~~~~~L~~lpi~~l~giG~~~~~~L~~-~Gi~ti~dl~~~~~~~~ 208 (343)
T cd00424 132 GITASIGIASNKLLAKLAAKYAKPDGLTILDPE--DLPGFLSKLPLTDLPGIGAVTAKRLEA-VGINPIGDLLAASPDAL 208 (343)
T ss_pred CceEEEeecccHHHHHHHhccCCCCCEEEEcHH--HHHHHHhcCChhhcCCCCHHHHHHHHH-cCCCcHHHHhcCCHHHH
Confidence 99999999999999999999999999999875 678999999999999999999999997 9999999999998 46
Q ss_pred HHHHcChhHHHHHHHhccCCCCCCCCCCCCCCcceeecccCC-cCCHHHHHHHHHHHHHHHHHHHHHhCCCccEEEEEEE
Q 009922 158 LCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV-TEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLK 236 (522)
Q Consensus 158 L~~~FG~~~~~~l~~~a~G~d~~~v~~~~~~KSIs~e~tF~~-~~~~e~L~~~L~~La~~L~~RLr~~g~~artltLkL~ 236 (522)
+.++||.. +.++|+.++|+|.+++.+..++|||+.+++|+. ..+.+++..+|..|+++|+.||+.+++.+++|+|+++
T Consensus 209 l~~~fg~~-~~~l~~~a~G~d~~~v~~~~~~ksi~~~~tf~~~~~~~~~l~~~l~~l~~~l~~rL~~~~~~~~~l~l~lr 287 (343)
T cd00424 209 LALWGGVS-GERLWYALRGIDDEPLSPPRPRKSFSHERVLPRDSRNAEDARPLLRLLLEKLARRLRRDGRGATRLRLWLR 287 (343)
T ss_pred HHHHhhHH-HHHHHHHhCCcCCCCCCCCCCCCceeeeEECCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCceeEEEEEEE
Confidence 77888865 778889999999999988888999999999987 6899999999999999999999999999999999999
Q ss_pred ecC------CeeeEEEEEcCCCCCCHHHHHHHHHHHHHhhC----CCCEEEEEEEee
Q 009922 237 TAS------FEVRTRAVTLQKYISSSEDILKHASVLLKAEL----PVSLRLIGLRVT 283 (522)
Q Consensus 237 ~~d------~~~~srs~~L~~pt~d~~~L~~~a~~LL~~~l----~~~IR~lGV~vs 283 (522)
+.+ |...+++.+++.|| +...|+..+..||++++ +.+||++||+++
T Consensus 288 ~~~~~~~~~~~~~~~~~~l~~~t-~~~~l~~~~~~l~~~~~~~~~~~~ir~~gv~~~ 343 (343)
T cd00424 288 TVDGRWSGHADIPSRSAPRPIST-EDGELLHALDKLWRALLDDKGPRRLRRLGVRLS 343 (343)
T ss_pred eCCCcccccceeeeeeeeCCCCC-CHHHHHHHHHHHHHhhhhccCCCCeeEEEEEeC
Confidence 998 67889999999999 99999999999999985 358999999875
No 5
>PRK03858 DNA polymerase IV; Validated
Probab=100.00 E-value=1.7e-54 Score=458.74 Aligned_cols=284 Identities=31% Similarity=0.510 Sum_probs=271.8
Q ss_pred CcHHHHHHhCCCcEEECCChHHHHHHHHHHHHHHHhhCCCEEeecccEEEEEcCcchhhcCCCHHHHHHHHHHHHHHHhC
Q 009922 1 MPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAG 80 (522)
Q Consensus 1 Mpl~~A~kLCPdLvvvp~d~~~Y~~~s~~i~~il~~~tp~VE~~SiDEafLDvT~~~~l~g~~~~~lA~~IR~~I~~etG 80 (522)
||+++|+++||+++++++|++.|..+|++++.++.+|+|.||++||||+|||||++.++|| ++.++|++||++|++++|
T Consensus 54 m~~~~A~~lcP~l~~~~~d~~~y~~~s~~i~~~l~~~s~~ve~~siDe~~ldvt~~~~~~~-~~~~la~~ir~~i~~~~g 132 (396)
T PRK03858 54 MGGRQARRLCPQAVVVPPRMSAYSRASKAVFEVFRDTTPLVEGLSIDEAFLDVGGLRRISG-TPVQIAARLRRRVREEVG 132 (396)
T ss_pred ChHHHHHHHCCCeEEECCCHHHHHHHHHHHHHHHHHhCCceEEecCCeEEEEccccccccC-CHHHHHHHHHHHHHHHHC
Confidence 9999999999999999999999999999999999999999999999999999999999898 899999999999999999
Q ss_pred CceEEeccCChhHHHHHhhcCCCCcEEEEcCChHHHHHhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHH
Q 009922 81 LTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLC 159 (522)
Q Consensus 81 lt~S~GIA~NKllAKLAS~~~KP~G~~vI~~~~~~~~~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~ 159 (522)
+|||||||+||++|||||+.+||+|+++++++ ++.+||+++||++|||||++++++|++ +||+|++||+++| ..|.
T Consensus 133 l~~svGia~n~~lAklas~~~Kp~g~~~i~~~--~~~~~L~~lpl~~l~Gig~~~~~~L~~-~Gi~t~~dl~~l~~~~L~ 209 (396)
T PRK03858 133 LPITVGVARTKFLAKVASQVAKPDGLLVVPPD--RELAFLHPLPVRRLWGVGPVTAAKLRA-HGITTVGDVAELPESALV 209 (396)
T ss_pred CCeEEEEcCChHHHHHhhcccCCCceEEECcH--HHHHHHhcCChhhcCCCCHHHHHHHHH-hCCCcHHHHhcCCHHHHH
Confidence 99999999999999999999999999999886 578999999999999999999999997 9999999999998 7899
Q ss_pred HHcChhHHHHHHHhccCCCCCCCCCCCCCCcceeecccCC-cCCHHHHHHHHHHHHHHHHHHHHHhCCCccEEEEEEEec
Q 009922 160 AVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV-TEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTA 238 (522)
Q Consensus 160 ~~FG~~~~~~l~~~a~G~d~~~v~~~~~~KSIs~e~tF~~-~~~~e~L~~~L~~La~~L~~RLr~~g~~artltLkL~~~ 238 (522)
++||...+.++|..++|+|..++.+..++|||+++++|+. +.+.+++..+|..|+++|+.||+++++.+++|+|++++.
T Consensus 210 ~~fG~~~~~~l~~~a~G~d~~~v~~~~~~ksi~~~~t~~~~~~~~~~l~~~l~~L~~~l~~rLr~~~~~~~~l~l~l~~~ 289 (396)
T PRK03858 210 SLLGPAAGRHLHALAHNRDPRRVETGRRRRSVGAQRALGRGPNSPAEVDAVVVALVDRVARRMRAAGRTGRTVVLRLRFD 289 (396)
T ss_pred HHhCcHHHHHHHHHhCCCCCCCCCCCCCCccccceeEcCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCcceEEEEEEeC
Confidence 9999888999999999999999987778899999999987 689999999999999999999999999999999999999
Q ss_pred CCeeeEEEEEcCCCCCCHHHHHHHHHHHHHhhC----CCCEEEEEEEeecCCcC
Q 009922 239 SFEVRTRAVTLQKYISSSEDILKHASVLLKAEL----PVSLRLIGLRVTQFNED 288 (522)
Q Consensus 239 d~~~~srs~~L~~pt~d~~~L~~~a~~LL~~~l----~~~IR~lGV~vs~L~~~ 288 (522)
+|.+.+++++++.||++...|+++++.+|+..+ +.+||++||++++|.+.
T Consensus 290 ~~~~~~~~~~l~~~t~~~~~l~~l~~~ll~~~~~~~~~~~irligv~~~~l~~~ 343 (396)
T PRK03858 290 DFTRATRSHTLPRPTASTATLLAAARDLVAAAAPLIAERGLTLVGFAVSNLDDD 343 (396)
T ss_pred CCCEEEEEEECCCCcCCHHHHHHHHHHHHHhhhhccCCCCeEEEEEEeecCCcc
Confidence 999999999999999999999999999998853 35899999999999864
No 6
>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=1.3e-54 Score=461.01 Aligned_cols=281 Identities=28% Similarity=0.404 Sum_probs=265.4
Q ss_pred CcHHHHHHhCCCcEEECCChHHHHHHHHHHHHHHHhhCCCEEeecccEEEEEcCcchh-hcCCCHHHHHHHHHHHHHHHh
Q 009922 1 MPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCR-ERGISGIEIAEELRTSVYEEA 79 (522)
Q Consensus 1 Mpl~~A~kLCPdLvvvp~d~~~Y~~~s~~i~~il~~~tp~VE~~SiDEafLDvT~~~~-l~g~~~~~lA~~IR~~I~~et 79 (522)
||+++|+++||+++++++|++.|.++|+++++++.+|+|.||++||||+|||||++.+ +++ ++.++|++||++|++++
T Consensus 102 M~~~~A~~lcP~l~vv~~~~~~Y~~~s~~i~~il~~~s~~ve~~SiDE~~lDvt~~~~~~~~-~~~~la~~ir~~I~~~~ 180 (404)
T cd01701 102 MWVGQAKKLCPQLVTLPYDFEAYEEVSLTFYEILASYTDNIEAVSCDEALIDITSLLEETYE-LPEELAEAIRNEIRETT 180 (404)
T ss_pred CcHHHHHHHCCCcEEECCChHHHHHHHHHHHHHHHHhCCceEEcccceEEEEcccccccccC-CHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999985 677 79999999999999999
Q ss_pred CCceEEeccCChhHHHHHhhcCCCCcEEEEcCChHHHHHhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhch---H
Q 009922 80 GLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG---S 156 (522)
Q Consensus 80 Glt~S~GIA~NKllAKLAS~~~KP~G~~vI~~~~~~~~~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~---~ 156 (522)
|+|||||||+||++|||||+.+||+|+++++++ ++.+||+++||++|||||++++++|++ +||+|++||+++| .
T Consensus 181 gl~~siGia~nk~lAKlAs~~aKP~g~~~i~~~--~~~~~L~~lPv~~l~GIG~~~~~~L~~-~Gi~t~~dl~~~~~~~~ 257 (404)
T cd01701 181 GCSASVGIGPNILLARLATRKAKPDGQYHLSAE--KVEEFLSQLKVGDLPGVGSSLAEKLVK-LFGDTCGGLELRSKTKE 257 (404)
T ss_pred CCCEEEEEcCCHHHHHHHhcccCCCcEEEECHH--HHHHHhhcCCHhHhCCCCHHHHHHHHH-cCCcchHHHHhCcccHH
Confidence 999999999999999999999999999999875 688999999999999999999999997 9999999999986 5
Q ss_pred HHHHHcChhHHHHHHHhccCCCCCCCCCCCCCCcceeecccCC-cCCHHHHHHHHHHHHHHHHHHHHHhCCCccEEEEEE
Q 009922 157 LLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV-TEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKL 235 (522)
Q Consensus 157 ~L~~~FG~~~~~~l~~~a~G~d~~~v~~~~~~KSIs~e~tF~~-~~~~e~L~~~L~~La~~L~~RLr~~g~~artltLkL 235 (522)
.|.++||...+.++|+.++|++.+++.+..++|||+.+++|+. ..+.+++..+|.+|+++|+.||+.+++.+++|+|++
T Consensus 258 ~L~~~fG~~~g~~L~~~a~G~d~~~v~~~~~~ksi~~~~tf~~~~~~~~~l~~~l~~L~~~l~~rLr~~~~~~~~l~l~l 337 (404)
T cd01701 258 KLQKVLGPKTGEKLYDYCRGIDDRPVTGEKERKSVSAEINYGIRFTNVDDVEQFLQRLSEELSKRLEESNVTGRQITLKL 337 (404)
T ss_pred HHHHHHCHHHHHHHHHHhCCcCCCCCCCCCCCccccceeeCCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCceeeEEEEE
Confidence 8999999877899999999999999988788999999999997 689999999999999999999999999999999999
Q ss_pred Eec---------------CCeeeEEEEEcCCCCCCHHHHHHHHHHHHHhhC--CCCEEEEEEEeecC
Q 009922 236 KTA---------------SFEVRTRAVTLQKYISSSEDILKHASVLLKAEL--PVSLRLIGLRVTQF 285 (522)
Q Consensus 236 ~~~---------------d~~~~srs~~L~~pt~d~~~L~~~a~~LL~~~l--~~~IR~lGV~vs~L 285 (522)
++. +|.+.+++++++.||++...|+..+..||++.+ ..+||+|||++++|
T Consensus 338 ~~~~~~~~~~~~~y~g~~~~~~~~~~~~l~~pT~d~~~i~~~a~~ll~~~~~~~~~vR~lgv~~~~l 404 (404)
T cd01701 338 MKRAPGAPIEPPKYMGHGICDSFSKSSTLGVATDDSGVIGTEAKKLFRDLSIPPEELRGVGIQVTKL 404 (404)
T ss_pred EeccccCccccccccccCCCcEEeeeeECCCCCCCHHHHHHHHHHHHHhccCCCCCeeEEEEEEecC
Confidence 972 256789999999999999999999999999874 36999999999986
No 7
>PRK14133 DNA polymerase IV; Provisional
Probab=100.00 E-value=4.1e-54 Score=448.60 Aligned_cols=280 Identities=35% Similarity=0.551 Sum_probs=267.7
Q ss_pred CcHHHHHHhCCCcEEECCChHHHHHHHHHHHHHHHhhCCCEEeecccEEEEEcCcchhhcCCCHHHHHHHHHHHHHHHhC
Q 009922 1 MPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAG 80 (522)
Q Consensus 1 Mpl~~A~kLCPdLvvvp~d~~~Y~~~s~~i~~il~~~tp~VE~~SiDEafLDvT~~~~l~g~~~~~lA~~IR~~I~~etG 80 (522)
||+++|+++||+++++++|++.|..++++++.|+++|+|.||++||||+|||+|++. + ++.++|++||++|++++|
T Consensus 57 m~~~~A~~lcP~l~~~~~d~~~y~~~s~~i~~~l~~~s~~ve~~siDe~~ldv~~~~---~-~~~~la~~i~~~i~~~~g 132 (347)
T PRK14133 57 MPVFMAKKRCPHGIFLPVRHERYKEVSKNIFKILYEVTPIVEPVSIDEAYLDITNIK---E-EPIKIAKYIKKKVKKETG 132 (347)
T ss_pred ChHHHHHHHCCCcEEECCCHHHHHHHHHHHHHHHHHhCCceEEccCCeEEEEccCCC---C-CHHHHHHHHHHHHHHHHC
Confidence 999999999999999999999999999999999999999999999999999999985 4 789999999999999999
Q ss_pred CceEEeccCChhHHHHHhhcCCCCcEEEEcCChHHHHHhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHH
Q 009922 81 LTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLC 159 (522)
Q Consensus 81 lt~S~GIA~NKllAKLAS~~~KP~G~~vI~~~~~~~~~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~ 159 (522)
++||+|||+||++||||++.+||+|+++++++ ++.+||+++||++|||||+++.++|++ +||+|++||+++| ..|.
T Consensus 133 l~~siGia~n~~~Aklas~~~kp~g~~~~~~~--~~~~~L~~lpv~~l~gig~~~~~~L~~-~Gi~ti~dl~~l~~~~L~ 209 (347)
T PRK14133 133 LTLSVGISYNKFLAKLASDWNKPDGIKIITED--MIPDILKPLPISKVHGIGKKSVEKLNN-IGIYTIEDLLKLSREFLI 209 (347)
T ss_pred CcEEEEEcCcHHHHHHHhccCCCCceEEECHH--HHHHHHHhCCccccCCCCHHHHHHHHH-cCCccHHHHhhCCHHHHH
Confidence 99999999999999999999999999999875 688999999999999999999999997 9999999999998 7899
Q ss_pred HHcChhHHHHHHHhccCCCCCCCCCCCCCCcceeecccCC-cCCHHHHHHHHHHHHHHHHHHHHHhCCCccEEEEEEEec
Q 009922 160 AVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV-TEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTA 238 (522)
Q Consensus 160 ~~FG~~~~~~l~~~a~G~d~~~v~~~~~~KSIs~e~tF~~-~~~~e~L~~~L~~La~~L~~RLr~~g~~artltLkL~~~ 238 (522)
++||.. +..+|+.++|+|..++.+..++|||+.+.+|.. +.+.+++..+|.+|+++|+.||+++++.+++++|++++.
T Consensus 210 ~rfG~~-g~~l~~~a~G~d~~~v~~~~~~ksi~~~~~~~~~~~~~~~l~~~l~~L~~~l~~rL~~~~~~~~~l~l~l~~~ 288 (347)
T PRK14133 210 EYFGKF-GVEIYERIRGIDYREVEVSRERKSIGKETTLKKDTKDKEELKKYLKDFSNIISEELKKRNLYGKTVTVKIKTS 288 (347)
T ss_pred HHHhHH-HHHHHHHhCCCCCCCCCCCCCCcceEeeEEcCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCcceEEEEEEEC
Confidence 999975 777889999999999988888999999999987 689999999999999999999999999999999999999
Q ss_pred CCeeeEEEEEcCCCCCCHHHHHHHHHHHHHhhC-CCCEEEEEEEeecCCcC
Q 009922 239 SFEVRTRAVTLQKYISSSEDILKHASVLLKAEL-PVSLRLIGLRVTQFNED 288 (522)
Q Consensus 239 d~~~~srs~~L~~pt~d~~~L~~~a~~LL~~~l-~~~IR~lGV~vs~L~~~ 288 (522)
++...+++++++.||++.+.|++.+..+|++++ +.+||.|||++++|.+.
T Consensus 289 ~~~~~~~~~~l~~~t~~~~~l~~l~~~lle~~~~~~~vr~lgl~~~~l~~~ 339 (347)
T PRK14133 289 DFQTHTKSKTLNDYIRDKEEIYNVACEILEHINIKEPIRLIGLSVSNLSEN 339 (347)
T ss_pred CCCeeEEEEECCCCcCCHHHHHHHHHHHHHhccCCCCEEEEEEEEecCCCC
Confidence 999999999999999999999999999999874 67999999999999975
No 8
>PRK02406 DNA polymerase IV; Validated
Probab=100.00 E-value=3.5e-54 Score=448.34 Aligned_cols=282 Identities=38% Similarity=0.550 Sum_probs=268.3
Q ss_pred CcHHHHHHhCCCcEEECCChHHHHHHHHHHHHHHHhhCCCEEeecccEEEEEcCcchhhcCCCHHHHHHHHHHHHHHHhC
Q 009922 1 MPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAG 80 (522)
Q Consensus 1 Mpl~~A~kLCPdLvvvp~d~~~Y~~~s~~i~~il~~~tp~VE~~SiDEafLDvT~~~~l~g~~~~~lA~~IR~~I~~etG 80 (522)
||+++|+++||+|+++++|++.|..++++++.++++|+|.||++||||+|||+|++.++|| ++.++|+.||++|++++|
T Consensus 49 m~~~~A~~lcP~l~~~~~d~~~y~~~s~~i~~~l~~~sp~ve~~siDe~~ldvt~~~~~~~-~~~~la~~i~~~i~~~~g 127 (343)
T PRK02406 49 MPTAQALKLCPDLIFVPGRFDVYKEVSRQIREIFRRYTDLIEPLSLDEAYLDVTDNKLCIG-SATLIAQEIRQDIFEELG 127 (343)
T ss_pred CcHHHHHHHCCCeEEECCChHHHHHHHHHHHHHHHHhCCceEEccCCeEEEeccCccccCC-CHHHHHHHHHHHHHHHHC
Confidence 9999999999999999999999999999999999999999999999999999999999998 789999999999999999
Q ss_pred CceEEeccCChhHHHHHhhcCCCCcEEEEcCChHHHHHhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHH
Q 009922 81 LTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLC 159 (522)
Q Consensus 81 lt~S~GIA~NKllAKLAS~~~KP~G~~vI~~~~~~~~~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~ 159 (522)
++||||||+||++|||||+.+||+|+++++++ ++.+||+++||++|||||+++.++|++ +||+|++||+++| ..|.
T Consensus 128 l~~siGia~n~~lAklas~~~Kp~g~~~~~~~--~~~~~L~~lpi~~l~giG~~~~~~L~~-~Gi~ti~dl~~l~~~~L~ 204 (343)
T PRK02406 128 LTASAGVAPNKFLAKIASDWNKPNGLFVITPE--EVDAFLATLPVEKIPGVGKVTAEKLHA-LGIYTCADLQKYDLAELI 204 (343)
T ss_pred CCeEEEeccCHHHHHHHhcCCCCCCEEEECHH--HHHHHHHcCCcchhcCCCHHHHHHHHH-cCCCcHHHHHhCCHHHHH
Confidence 99999999999999999999999999999875 689999999999999999999999997 9999999999998 7899
Q ss_pred HHcChhHHHHHHHhccCCCCCCCCCCCCCCcceeecccCC-cCCHHHHHHHHHHHHHHHHHHHHHhC--CCccEEEEEEE
Q 009922 160 AVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV-TEDKALLYRKLAEIAEMLSADMQKEG--LRGRTLTLKLK 236 (522)
Q Consensus 160 ~~FG~~~~~~l~~~a~G~d~~~v~~~~~~KSIs~e~tF~~-~~~~e~L~~~L~~La~~L~~RLr~~g--~~artltLkL~ 236 (522)
++||.. +.++|+.++|++.+++.+..++|||+++++|+. +.+.+++..+|.+|+++|+.||++++ +.+++|+|+++
T Consensus 205 ~~fG~~-~~~l~~~a~G~d~~~v~~~~~~ksi~~~~~~~~~~~~~~~l~~~l~~l~~~l~~rL~~~~~~~~~~~l~l~l~ 283 (343)
T PRK02406 205 RHFGKF-GRRLYERARGIDERPVKPDRERKSVGVERTFAEDLYDLEACLAELPRLAEKLERRLERAKPDKRIKTVGVKLK 283 (343)
T ss_pred HHHhHH-HHHHHHHhCCCCCCccccCCCCcceeeeeeCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCccceeEEEEEE
Confidence 999975 777889999999999988788999999999987 68999999999999999999999999 99999999999
Q ss_pred ecCCeeeEEEEEcCCCCCCHHHHHHHHHHHHHhhCCCCEEEEEEEeecCCcC
Q 009922 237 TASFEVRTRAVTLQKYISSSEDILKHASVLLKAELPVSLRLIGLRVTQFNED 288 (522)
Q Consensus 237 ~~d~~~~srs~~L~~pt~d~~~L~~~a~~LL~~~l~~~IR~lGV~vs~L~~~ 288 (522)
+.++.+.+++.+ ..++++...+...+..|++..++.+||.|||++++|.+.
T Consensus 284 ~~~~~~~~~~~~-~~~~~~~~~l~~~~~~L~~~~~~~~vr~lgv~~~~l~~~ 334 (343)
T PRK02406 284 FADFQQTTKEHT-ADPLDKADLIELLAQALLRRLGGRGVRLLGVGVTLLEPQ 334 (343)
T ss_pred eCCCCeEEEecC-CCCCCcHHHHHHHHHHHHhhCcCCCEEEEEEEEecCCcC
Confidence 999998889888 777888888888899998887788999999999999975
No 9
>PRK02794 DNA polymerase IV; Provisional
Probab=100.00 E-value=8.4e-54 Score=456.90 Aligned_cols=285 Identities=32% Similarity=0.462 Sum_probs=271.5
Q ss_pred CcHHHHHHhCCCcEEECCChHHHHHHHHHHHHHHHhhCCCEEeecccEEEEEcCcchhhcCCCHHHHHHHHHHHHHHHhC
Q 009922 1 MPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAG 80 (522)
Q Consensus 1 Mpl~~A~kLCPdLvvvp~d~~~Y~~~s~~i~~il~~~tp~VE~~SiDEafLDvT~~~~l~g~~~~~lA~~IR~~I~~etG 80 (522)
||+++|+++||+++++++||+.|.++|+++++|+++|+|.||++||||+|||||++.++||..+..++++||++|++++|
T Consensus 89 M~~~~A~~lcP~l~~v~~d~~~y~~~s~~i~~~l~~~sp~ve~~siDe~~ldvt~~~~l~g~~~~~~~~~i~~~i~~~~g 168 (419)
T PRK02794 89 MPMFKALKLCPDAVVIKPDMEKYVRVGREVRAMMQALTPLVEPLSIDEAFLDLSGTERLHGAPPAVVLARFARRVEREIG 168 (419)
T ss_pred CHHHHHHHHCCCcEEECCCHHHHHHHHHHHHHHHHHhCcceeeccCCeEEEeccchhhhcCCCHHHHHHHHHHHHHHHHC
Confidence 99999999999999999999999999999999999999999999999999999999999986667789999999999999
Q ss_pred CceEEeccCChhHHHHHhhcCCCCcEEEEcCChHHHHHhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHH
Q 009922 81 LTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLC 159 (522)
Q Consensus 81 lt~S~GIA~NKllAKLAS~~~KP~G~~vI~~~~~~~~~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~ 159 (522)
++||+|||+||++|||||+.+||+|++++.++ ++.+||+++||++|||||+++.++|++ +||+|++||+++| ..|.
T Consensus 169 l~~svGIa~n~~lAKlas~~~KP~g~~ii~~~--~~~~~L~~lPl~~L~GiG~~~~~~L~~-~GI~tigdL~~l~~~~L~ 245 (419)
T PRK02794 169 ITVSVGLSYNKFLAKIASDLDKPRGFSVIGRA--EALAFLAPKPVGIIWGVGPATAARLAR-DGIRTIGDLQRADEADLM 245 (419)
T ss_pred CceEEEEcCCHHHHHHHHhhhCCCCeEecCHH--HHHHHHhcCChhhhCCCCHHHHHHHHH-hccchHHHHhhCCHHHHH
Confidence 99999999999999999999999999999875 689999999999999999999999997 9999999999998 7899
Q ss_pred HHcChhHHHHHHHhccCCCCCCCCCCCCCCcceeecccCC-cCCHHHHHHHHHHHHHHHHHHHHHhCCCccEEEEEEEec
Q 009922 160 AVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV-TEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTA 238 (522)
Q Consensus 160 ~~FG~~~~~~l~~~a~G~d~~~v~~~~~~KSIs~e~tF~~-~~~~e~L~~~L~~La~~L~~RLr~~g~~artltLkL~~~ 238 (522)
++||.. +.++|+.++|++..++.+..++|||+++.+|+. +.+.+++..+|..|+++|+.||+.+++.+++|+|++++.
T Consensus 246 ~rfG~~-g~~l~~~a~G~d~~~v~~~~~~ksi~~~~tl~~~~~~~~~l~~~l~~L~~~l~~rL~~~~~~~~~l~l~l~~~ 324 (419)
T PRK02794 246 RRFGSM-GLRLWRLARGIDDRKVSPDREAKSVSAETTFETDLSDFEDLEPILWRLSEKVSRRLKAAGLAGRTVTLKLKTA 324 (419)
T ss_pred HHHhHH-HHHHHHHhCCCCCCCCccCCCCceeeeeEECCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCcceEEEEEEEC
Confidence 999985 788899999999999988788999999999997 689999999999999999999999999999999999999
Q ss_pred CCeeeEEEEEcCCCCCCHHHHHHHHHHHHHhhC-CCCEEEEEEEeecCCcCC
Q 009922 239 SFEVRTRAVTLQKYISSSEDILKHASVLLKAEL-PVSLRLIGLRVTQFNEDK 289 (522)
Q Consensus 239 d~~~~srs~~L~~pt~d~~~L~~~a~~LL~~~l-~~~IR~lGV~vs~L~~~~ 289 (522)
+|...+++++++.||++.+.|++++..+|++.+ +.+||.|||++++|.+..
T Consensus 325 ~~~~~~~~~~l~~pt~~~~~l~~~~~~ll~~~~~~~~vr~igv~~~~l~~~~ 376 (419)
T PRK02794 325 DFRLRTRRRTLEDPTQLADRIFRTARELLEKETDGTAFRLIGIGVSDLSPAD 376 (419)
T ss_pred CCCceEEEEECCCCcCCHHHHHHHHHHHHHhcccCCCEEEEEEEEecCCCcc
Confidence 999999999999999999999999999999875 579999999999999753
No 10
>PRK03352 DNA polymerase IV; Validated
Probab=100.00 E-value=1.5e-53 Score=444.00 Aligned_cols=279 Identities=28% Similarity=0.404 Sum_probs=265.3
Q ss_pred CcHHHHHHhCCCcEEECCChHHHHHHHHHHHHHHHhhCCCEEeecccEEEEEcCcchhhcCCCHHHHHHHHHHHHHHHhC
Q 009922 1 MPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAG 80 (522)
Q Consensus 1 Mpl~~A~kLCPdLvvvp~d~~~Y~~~s~~i~~il~~~tp~VE~~SiDEafLDvT~~~~l~g~~~~~lA~~IR~~I~~etG 80 (522)
||+++|+++||+++++++|++.|..+|++++.++++|+|.||++|+||+|||+|+. ++..+|+.||++|++++|
T Consensus 63 M~~~~A~~lcP~l~~v~~~~~~y~~~s~~i~~~l~~~s~~ve~~siDe~~ld~t~~------~~~~la~~ir~~i~~~~g 136 (346)
T PRK03352 63 MPLRTAARRCPDAVFLPSDPAAYDAASEEVMATLRDLGVPVEVWGWDEAFLGVDTD------DPEALAEEIRAAVLERTG 136 (346)
T ss_pred ChHHHHHHHCCCeEEECCCcHHHHHHHHHHHHHHHHhCCceEEecCccEEEeCCCC------CHHHHHHHHHHHHHHHHC
Confidence 99999999999999999999999999999999999999999999999999999985 589999999999999999
Q ss_pred CceEEeccCChhHHHHHhhcCCCCcEEEEcCChHHHHHhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHH
Q 009922 81 LTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLC 159 (522)
Q Consensus 81 lt~S~GIA~NKllAKLAS~~~KP~G~~vI~~~~~~~~~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~ 159 (522)
+|||+|||+||++||||++.+||+|++++.++ ++.+||+++||++|||||+++.++|++ +||+|++||+++| ..|.
T Consensus 137 l~~siGia~nk~lAklaa~~~Kp~g~~~~~~~--~~~~~L~~lpl~~l~gig~~~~~~L~~-~Gi~ti~dl~~l~~~~L~ 213 (346)
T PRK03352 137 LSCSVGIGDNKLRAKIATGFAKPAGVFRLTDA--NWMAVMGDRPTDALWGVGPKTAKRLAA-LGITTVADLAAADPAELA 213 (346)
T ss_pred CCEEEeecCCHHHHHHHHhhcCCCcEEEECHH--HHHHHHhcCCHHHcCCCCHHHHHHHHH-cCCccHHHHhcCCHHHHH
Confidence 99999999999999999999999999999875 678999999999999999999999997 9999999999998 8999
Q ss_pred HHcChhHHHHHHHhccCCCCCCCCCC-CCCCcceeecccCC-cCCHHHHHHHHHHHHHHHHHHHHHhCCCccEEEEEEEe
Q 009922 160 AVFSHSTADFFLSVGLGLGSTNTPQA-RFRKSISSERTFSV-TEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKT 237 (522)
Q Consensus 160 ~~FG~~~~~~l~~~a~G~d~~~v~~~-~~~KSIs~e~tF~~-~~~~e~L~~~L~~La~~L~~RLr~~g~~artltLkL~~ 237 (522)
++||...+.++|..++|+|.++++.. ..+||++.+.+|+. +.+.+++..+|..|+++|+.||+.+++.+++|+|++++
T Consensus 214 ~~fG~~~~~~l~~~a~G~d~~~~~~~~~~~ksi~~~~tf~~~~~~~~~l~~~l~~L~~~l~~rLr~~~~~~~~l~l~l~~ 293 (346)
T PRK03352 214 ATFGPTTGPWLLLLARGGGDTEVSAEPWVPRSRSREVTFPQDLTDRAEVESAVRELARRVLDEVVAEGRPVTRVAVKVRT 293 (346)
T ss_pred HHhChHHHHHHHHHhCCCCCCCCCCCCCCCceEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCccceEEEEEEe
Confidence 99998778899999999999998754 34799999999987 68999999999999999999999999999999999999
Q ss_pred cCCeeeEEEEEcCCCCCCHHHHHHHHHHHHHhhC-CCCEEEEEEEeecCCcC
Q 009922 238 ASFEVRTRAVTLQKYISSSEDILKHASVLLKAEL-PVSLRLIGLRVTQFNED 288 (522)
Q Consensus 238 ~d~~~~srs~~L~~pt~d~~~L~~~a~~LL~~~l-~~~IR~lGV~vs~L~~~ 288 (522)
.+|.+.+++++++.||++.+.|++++..+|++.. +.+||+|||++++|.++
T Consensus 294 ~~~~~~~~~~~l~~pt~d~~~l~~~~~~ll~~~~~~~~vr~igl~~~~~~~~ 345 (346)
T PRK03352 294 ATFYTRTKIRKLPEPTTDPDVIEAAALDVLDRFELDRPVRLLGVRLELAMPD 345 (346)
T ss_pred CCCceeEEEEECCCCcCCHHHHHHHHHHHHHhccCCCCEEEEEEEEeccCCC
Confidence 9998889999999999999999999999999974 67999999999999875
No 11
>PRK03348 DNA polymerase IV; Provisional
Probab=100.00 E-value=4.6e-53 Score=454.95 Aligned_cols=284 Identities=27% Similarity=0.405 Sum_probs=268.8
Q ss_pred CcHHHHHHhCCC-cEEECCChHHHHHHHHHHHHHHHhhCCCEEeecccEEEEEcCcchhhcCCCHHHHHHHHHHHHHHHh
Q 009922 1 MPGFIARKLCPE-LIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEA 79 (522)
Q Consensus 1 Mpl~~A~kLCPd-Lvvvp~d~~~Y~~~s~~i~~il~~~tp~VE~~SiDEafLDvT~~~~l~g~~~~~lA~~IR~~I~~et 79 (522)
||+++|+++||+ ++++++|++.|..+|++++.++++|+|.||++||||+|||+++.......++..+|++||++|++++
T Consensus 59 Mp~~~A~~lcP~~lv~v~~d~~~Y~~~s~~i~~~l~~~sp~VE~~SiDE~flD~~~l~~~~~~~~~~~a~~lr~~I~~~~ 138 (454)
T PRK03348 59 MPMHQARRLVGNGAVVLPPRFVVYRAASRRVFDTLRELSPVVEQLSFDEAFVEPAELAGASAEEVEAFAERLRARVREET 138 (454)
T ss_pred CcHHHHHHhCCCCEEEECCChHHHHHHHHHHHHHHHHhCCceEEecCCeEEEEccccccccCCCHHHHHHHHHHHHHHHH
Confidence 999999999999 9999999999999999999999999999999999999999887654222268899999999999999
Q ss_pred CCceEEeccCChhHHHHHhhcCCCCcEEEEcCChHHHHHhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHH
Q 009922 80 GLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLL 158 (522)
Q Consensus 80 Glt~S~GIA~NKllAKLAS~~~KP~G~~vI~~~~~~~~~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L 158 (522)
||+||||||+||++|||||+.+||||+++++++ .+.+||+++||++|||||+++.++|++ +||+|++||++++ ..|
T Consensus 139 Gl~~SvGIa~nk~lAKlAs~~aKP~G~~vi~~~--~~~~~L~~LPv~~L~GIG~~t~~~L~~-lGI~TigDLa~l~~~~L 215 (454)
T PRK03348 139 GLPASVGAGSGKQIAKIASGLAKPDGIRVVPPG--EERELLAPLPVRRLWGIGPVTEEKLHR-LGIETIGDLAALSEAEV 215 (454)
T ss_pred CCCeEEEEcCCHHHHHHhhccCCCCcEEEEEch--HHHHHHHhCCccccCCCCHHHHHHHHH-cCCccHHHHhcCCHHHH
Confidence 999999999999999999999999999999886 678999999999999999999999997 9999999999998 899
Q ss_pred HHHcChhHHHHHHHhccCCCCCCCCCCCCCCcceeecccCC-cCCHHHHHHHHHHHHHHHHHHHHHhCCCccEEEEEEEe
Q 009922 159 CAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV-TEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKT 237 (522)
Q Consensus 159 ~~~FG~~~~~~l~~~a~G~d~~~v~~~~~~KSIs~e~tF~~-~~~~e~L~~~L~~La~~L~~RLr~~g~~artltLkL~~ 237 (522)
.++||...+.+||..++|++.+++.+..++|||+.+.+|+. +.+.+++..+|.+|+++|+.||+++++.+++|+|++++
T Consensus 216 ~~~fG~~~g~~L~~~a~G~d~~pv~~~~~~ksis~e~tf~~~i~~~~~l~~~L~~L~~~l~~rL~~~g~~~r~v~l~l~~ 295 (454)
T PRK03348 216 ANLLGATVGPALHRLARGIDDRPVAERAEAKQISAESTFAVDLTTRAQLREAIERIAEHAHRRLLKDGRGARTVTVKLRK 295 (454)
T ss_pred HHHHCHHHHHHHHHHHcCCCCCCcccCCCCceEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCCccEEEEEEEe
Confidence 99999878999999999999999988888999999999987 68999999999999999999999999999999999999
Q ss_pred cCCeeeEEEEEcCCCCCCHHHHHHHHHHHHHhhC-CCCEEEEEEEeecCCc
Q 009922 238 ASFEVRTRAVTLQKYISSSEDILKHASVLLKAEL-PVSLRLIGLRVTQFNE 287 (522)
Q Consensus 238 ~d~~~~srs~~L~~pt~d~~~L~~~a~~LL~~~l-~~~IR~lGV~vs~L~~ 287 (522)
.+|.+.+++++++.||++...|+++++.+|++.. ..+||++||++++|.+
T Consensus 296 ~d~~~~srs~~l~~pt~d~~~L~~la~~ll~~~~~~~~vRllgV~~s~l~~ 346 (454)
T PRK03348 296 SDFSTLTRSATLPYATDDAAVLAATARRLLLDPDEIGPIRLVGVGFSGLSD 346 (454)
T ss_pred CCCCccEEEEECCCCCCCHHHHHHHHHHHHHhhccCCCeEEEEEEECCCCc
Confidence 9999999999999999999999999999999864 4689999999999974
No 12
>PRK03103 DNA polymerase IV; Reviewed
Probab=100.00 E-value=3.2e-53 Score=451.02 Aligned_cols=283 Identities=24% Similarity=0.398 Sum_probs=268.9
Q ss_pred CcHHHHHHhCCCcEEECCChHHHHHHHHHHHHHHHhhCCCEEeecccEEEEEcCcchhhcCCCHHHHHHHHHHHHHHHhC
Q 009922 1 MPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAG 80 (522)
Q Consensus 1 Mpl~~A~kLCPdLvvvp~d~~~Y~~~s~~i~~il~~~tp~VE~~SiDEafLDvT~~~~l~g~~~~~lA~~IR~~I~~etG 80 (522)
||+++|+++||+++++++||+.|..+|+++++|+++|+|.||++|+||+|||+|++.++|| ++..+|++||++|++++|
T Consensus 59 m~~~~A~~lcP~l~~~~~d~~~y~~~s~~i~~~l~~~sp~ve~~siDe~~lDvt~~~~~~~-~~~~la~~ir~~i~~~~g 137 (409)
T PRK03103 59 ERLWEAQQKCPDLVVVKPRMQRYIDVSLQITRILEDFTDLVEPFSIDEQFLDVTGSQKLFG-SPLEIAQKIQQRIMRETG 137 (409)
T ss_pred ChHHHHHHHCCCeEEECCCHHHHHHHHHHHHHHHHHhCccceecCCCeeEeeccchhhcCC-CHHHHHHHHHHHHHHHHC
Confidence 9999999999999999999999999999999999999999999999999999999999998 899999999999999999
Q ss_pred CceEEeccCChhHHHHHhhc---CCCCcEEEEcCChHHHHHhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-H
Q 009922 81 LTCSAGVAPNRLLAKVCSDI---NKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-S 156 (522)
Q Consensus 81 lt~S~GIA~NKllAKLAS~~---~KP~G~~vI~~~~~~~~~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~ 156 (522)
+|||||||+|+++||||++. +||+|++++.++ ++.+||+++||++|||||+++.++|++ +||+|++||+++| .
T Consensus 138 l~~svGia~n~~lAklas~~~~k~kp~g~~v~~~~--~~~~~L~~lpi~~l~gig~~~~~~L~~-~Gi~tigdl~~~~~~ 214 (409)
T PRK03103 138 VYARVGIGPNKLLAKMACDNFAKKNPDGLFTLDKE--DVPADLWPLPVRKLFGVGSRMEKHLRR-MGIRTIGQLANTPLE 214 (409)
T ss_pred ceEEEeecCCHHHHHHHhcchhhcCCCcEEEECHH--HHHHHHHcCCHhhcCCccHHHHHHHHH-cCCCCHHHHhcCCHH
Confidence 99999999999999999998 999999999874 688999999999999999999999997 9999999999998 7
Q ss_pred HHHHHcChhHHHHHHHhccCCCCCCCCCCCC--CCcceeecccCC-cCCHHHHHHHHHHHHHHHHHHHHHhCCCccEEEE
Q 009922 157 LLCAVFSHSTADFFLSVGLGLGSTNTPQARF--RKSISSERTFSV-TEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTL 233 (522)
Q Consensus 157 ~L~~~FG~~~~~~l~~~a~G~d~~~v~~~~~--~KSIs~e~tF~~-~~~~e~L~~~L~~La~~L~~RLr~~g~~artltL 233 (522)
.|.++||.. +.++|+.++|++++++.+..+ +|||+.+.+|+. +.+.+++...|.+|+++|+.||++.++.+++|+|
T Consensus 215 ~L~~~fG~~-~~~l~~~a~G~d~~~v~~~~~~~~ksi~~~~t~~~~~~~~~~l~~~l~~L~~~l~~rLr~~~~~~~~l~l 293 (409)
T PRK03103 215 RLKKRWGIN-GEVLWRTANGIDYSPVTPHSLDRQKAIGHQMTLPRDYRGFEEIKVVLLELCEEVCRRARAKGYMGRTVSV 293 (409)
T ss_pred HHHHHHCHH-HHHHHHHhcCCCCCcCCcccCCCCCccCCCeECCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCceeEEEE
Confidence 899999975 788889999999999877644 589999999988 6899999999999999999999999999999999
Q ss_pred EEEecCCee---eEEEEEcCCCCCCHHHHHHHHHHHHHhhC-CCCEEEEEEEeecCCcC
Q 009922 234 KLKTASFEV---RTRAVTLQKYISSSEDILKHASVLLKAEL-PVSLRLIGLRVTQFNED 288 (522)
Q Consensus 234 kL~~~d~~~---~srs~~L~~pt~d~~~L~~~a~~LL~~~l-~~~IR~lGV~vs~L~~~ 288 (522)
++++.+++. .+++++++.||++...|+.++..+|++++ +.+||+|||++++|.+.
T Consensus 294 ~lr~~~~~~~~~~~~~~~l~~pt~~~~~l~~~~~~ll~~~~~~~~vr~lgv~~~~l~~~ 352 (409)
T PRK03103 294 SLRGADFDWPTGFSRQMTLPEPTNLAMEVYEAACKLFHRHWDGKPVRRVGVTLSNLVSD 352 (409)
T ss_pred EEEeCCCcCCCCcceeeecCCCCCCHHHHHHHHHHHHHhcccCCCceEEEEEEeCCCCC
Confidence 999999988 89999999999999999999999999975 47999999999999875
No 13
>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=7.7e-53 Score=435.61 Aligned_cols=280 Identities=44% Similarity=0.686 Sum_probs=268.2
Q ss_pred CcHHHHHHhCCCcEEECCChHHHHHHHHHHHHHHHhhCCCEEeecccEEEEEcCcchhhcCCCHHHHHHHHHHHHHHHhC
Q 009922 1 MPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAG 80 (522)
Q Consensus 1 Mpl~~A~kLCPdLvvvp~d~~~Y~~~s~~i~~il~~~tp~VE~~SiDEafLDvT~~~~l~g~~~~~lA~~IR~~I~~etG 80 (522)
||+++|+++||+++++++|++.|..+|++++.++++|+|.||++|+||+|||+|++.++++ ++..+|++||++|++++|
T Consensus 52 m~~~~A~~lcp~l~~~~~~~~~y~~~s~~i~~~l~~~~~~ve~~s~De~~ldv~~~~~~~~-~~~~la~~ir~~i~~~~g 130 (334)
T cd03586 52 MPIFQAKKLCPNLIFVPPRFDKYREVSRQIMEILREYTPLVEPLSIDEAYLDVTDYVRLFG-SATEIAKEIRARIREETG 130 (334)
T ss_pred CcHHHHHHHCCCeEEECCCcHHHHHHHHHHHHHHHHcCCceEEecccceeEccccccccCC-CHHHHHHHHHHHHHHHHC
Confidence 9999999999999999999999999999999999999999999999999999999999898 899999999999999999
Q ss_pred CceEEeccCChhHHHHHhhcCCCCcEEEEcCChHHHHHhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHH
Q 009922 81 LTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLC 159 (522)
Q Consensus 81 lt~S~GIA~NKllAKLAS~~~KP~G~~vI~~~~~~~~~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~ 159 (522)
++||+|||+|+++||||++.+||+|+++++++ ++.+||+++||++|||||+++.++|++ +||+|++||+++| ..|.
T Consensus 131 ~~~siGia~n~~lAklaa~~~kp~g~~i~~~~--~~~~~L~~lpl~~l~gig~~~~~~L~~-~Gi~ti~dl~~~~~~~L~ 207 (334)
T cd03586 131 LTASAGIAPNKFLAKIASDLNKPNGLTVIPPE--DVEEFLAPLPVRKIPGVGKVTAEKLKE-LGIKTIGDLAKLDVELLK 207 (334)
T ss_pred CceEEEEhhcHHHHHHHhcCCCCCcEEEECHH--HHHHHHhcCCchhhCCcCHHHHHHHHH-cCCcCHHHHHcCCHHHHH
Confidence 99999999999999999999999999999875 689999999999999999999999997 9999999999998 7899
Q ss_pred HHcChhHHHHHHHhccCCCCCCCCCCCCCCcceeecccCC-cCCHHHHHHHHHHHHHHHHHHHHHhCCCccEEEEEEEec
Q 009922 160 AVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV-TEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTA 238 (522)
Q Consensus 160 ~~FG~~~~~~l~~~a~G~d~~~v~~~~~~KSIs~e~tF~~-~~~~e~L~~~L~~La~~L~~RLr~~g~~artltLkL~~~ 238 (522)
++||.. +.++|+.++|++.+++.+..++|||+++.+|+. +.+.+++..+|..|+++|+.||+.+++.+++++|++++.
T Consensus 208 ~~~g~~-~~~l~~~~~G~~~~~v~~~~~~ks~~~~~~~~~~~~~~~~l~~~l~~l~~~l~~rL~~~~~~~~~l~l~l~~~ 286 (334)
T cd03586 208 KLFGKS-GRRLYELARGIDNRPVEPDRERKSIGVERTFSEDLTDPEELLEELLELAEELAERLRKRGLKGRTVTVKLKYA 286 (334)
T ss_pred HHHhHH-HHHHHHHhCCCCCCCCCCCCCCCeeeeeEECCCCCCCHHHHHHHHHHHHHHHHHHHHhCCCCeEEEEEEEEEC
Confidence 999975 777889999999999988788999999999987 688999999999999999999999999999999999999
Q ss_pred CCeeeEEEEEcCCCCCCHHHHHHHHHHHHHhhC-CCCEEEEEEEeecC
Q 009922 239 SFEVRTRAVTLQKYISSSEDILKHASVLLKAEL-PVSLRLIGLRVTQF 285 (522)
Q Consensus 239 d~~~~srs~~L~~pt~d~~~L~~~a~~LL~~~l-~~~IR~lGV~vs~L 285 (522)
++.+.+++++++.|+++...|++++..+|++.. +.+||+|||++++|
T Consensus 287 ~~~~~~~~~~l~~~t~~~~~l~~~~~~~l~~~~~~~~vr~igv~~~~l 334 (334)
T cd03586 287 DFSTRTRSRTLPEPTDDAEDIYELALELLEELLDGRPIRLLGVRLSGL 334 (334)
T ss_pred CCCeEEEEEECCCCCCCHHHHHHHHHHHHHhccCCCCEEEEEEEeecC
Confidence 999999999999999999999999999999974 57999999999886
No 14
>PRK01810 DNA polymerase IV; Validated
Probab=100.00 E-value=6.1e-53 Score=448.57 Aligned_cols=282 Identities=29% Similarity=0.445 Sum_probs=266.8
Q ss_pred CcHHHHHHhCCCcEEECCChHHHHHHHHHHHHHHHhhCCCEEeecccEEEEEcCcchhhcCCCHHHHHHHHHHHHHHHhC
Q 009922 1 MPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAG 80 (522)
Q Consensus 1 Mpl~~A~kLCPdLvvvp~d~~~Y~~~s~~i~~il~~~tp~VE~~SiDEafLDvT~~~~l~g~~~~~lA~~IR~~I~~etG 80 (522)
||+++|+++||+++++++||+.|..+|+++++++++|+|.||++|+||+|||||++.+++ ++.++|+.||++|++++|
T Consensus 61 m~~~~A~~lcP~l~~~~~d~~~y~~~s~~i~~~l~~~sp~ve~~siDe~~ldvt~~~~~~--~~~~~a~~i~~~i~~~~g 138 (407)
T PRK01810 61 MPLWEAKRLCPQLIVRRPNFDRYREASRQMFQILSEFTPLVQPVSIDEGYLDITDCYALG--SPLEIAKMIQQRLLTELQ 138 (407)
T ss_pred ChHHHHHHHCCCeEEECCChHHHHHHHHHHHHHHHHhCCceEEecCCeEEEeccCccccC--CHHHHHHHHHHHHHHHHC
Confidence 999999999999999999999999999999999999999999999999999999998765 589999999999999999
Q ss_pred CceEEeccCChhHHHHHhhcCCCCcEEEEcCChHHHHHhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHH
Q 009922 81 LTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLC 159 (522)
Q Consensus 81 lt~S~GIA~NKllAKLAS~~~KP~G~~vI~~~~~~~~~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~ 159 (522)
+|||||||+||++|||||+.+||+|++++.++ ++..||+++||++|||||+++.++|++ +||+|++||+++| ..|.
T Consensus 139 l~~svGia~n~~lAklas~~~Kp~g~~vi~~~--~~~~~L~~lpv~~l~giG~~~~~~L~~-~Gi~tigdL~~~~~~~L~ 215 (407)
T PRK01810 139 LPCSIGIAPNKFLAKMASDMKKPLGITVLRKR--DVPEMLWPLPVGEMHGIGEKTAEKLKD-IGIQTIGDLAKADEHILR 215 (407)
T ss_pred CceEEEEcCCHHHHHHHhcCCCCCCEEEECHH--HHHHHHHhCCHhhcCCcCHHHHHHHHH-cCCCcHHHHHhCCHHHHH
Confidence 99999999999999999999999999999875 678999999999999999999999997 9999999999998 8899
Q ss_pred HHcChhHHHHHHHhccCCCCCCCCCCCC--CCcceeecccCC-cCCHHHHHHHHHHHHHHHHHHHHHhCCCccEEEEEEE
Q 009922 160 AVFSHSTADFFLSVGLGLGSTNTPQARF--RKSISSERTFSV-TEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLK 236 (522)
Q Consensus 160 ~~FG~~~~~~l~~~a~G~d~~~v~~~~~--~KSIs~e~tF~~-~~~~e~L~~~L~~La~~L~~RLr~~g~~artltLkL~ 236 (522)
++||.. +.++|+.++|++..++.+..+ +|||+++++|+. +.+.+++..+|.+|+++|+.||+++++.+++|+|+++
T Consensus 216 ~rfG~~-g~~l~~~a~G~d~~~v~~~~~~~~ksi~~~~~~~~~~~~~~~l~~~l~~L~~~l~~rLr~~~~~~~~l~l~lr 294 (407)
T PRK01810 216 AKLGIN-GVRLQRRANGIDDRPVDPEAIYQFKSVGNSTTLSHDMDEEKELLDVLRRLSKSVSKRLQKKTVVSYNVQIMIR 294 (407)
T ss_pred HHHhHH-HHHHHHHhcCCCCCCCCCCCCCCCceecceEECCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCccceeEEEEE
Confidence 999975 778889999999999865443 599999999998 6899999999999999999999999999999999999
Q ss_pred ecCCeeeEEEEEcCCCCCCHHHHHHHHHHHHHhhC-CCCEEEEEEEeecCCcC
Q 009922 237 TASFEVRTRAVTLQKYISSSEDILKHASVLLKAEL-PVSLRLIGLRVTQFNED 288 (522)
Q Consensus 237 ~~d~~~~srs~~L~~pt~d~~~L~~~a~~LL~~~l-~~~IR~lGV~vs~L~~~ 288 (522)
+.++.+.+++++++.||++...|+.++..+|++.+ +.+||++||++++|.+.
T Consensus 295 ~~~~~~~~~~~~l~~pt~~~~~l~~~~~~ll~~~~~~~~vr~lgv~~~~l~~~ 347 (407)
T PRK01810 295 YHDRRTITRSKTLKNPIWEKRDIFQAASRLFKQHWNGDPVRLLGVTATDLEWK 347 (407)
T ss_pred ECCCCceEEEEECCCCCCCHHHHHHHHHHHHHhccCCCCEEEEEEEEecCccc
Confidence 99999999999999999999999999999999875 46899999999999875
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=7.7e-53 Score=443.24 Aligned_cols=280 Identities=27% Similarity=0.423 Sum_probs=258.4
Q ss_pred CcHHHHHHhCCCcEEECC-ChHHHHHHHHHHHHHHHhhCC--CEEeecccEEEEEcCcchhhcCCCHHHHHHHHHHHHHH
Q 009922 1 MPGFIARKLCPELIFVPT-DFTKYTYYSDLTRKVFCKYDP--NFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYE 77 (522)
Q Consensus 1 Mpl~~A~kLCPdLvvvp~-d~~~Y~~~s~~i~~il~~~tp--~VE~~SiDEafLDvT~~~~l~g~~~~~lA~~IR~~I~~ 77 (522)
||+++|+++||+++++++ |++.|+++|++++.++.+|+| .||++||||+|||+|+...++ +.++|++||++|++
T Consensus 49 m~~~~A~~lcP~li~v~~~~~~~Y~~~S~~i~~~l~~~sp~~~ve~~SiDE~~lDvt~~~~~~---g~~la~~ir~~I~~ 125 (379)
T cd01703 49 MSIKDAKEICPDLVLVNGEDLTPFRDMSKKVYRLLRSYSWNDRVERLGFDENFMDVTEMRLLV---ASHIAYEMRERIEN 125 (379)
T ss_pred CcHHHHHHhCCCeEEEcCCChHHHHHHHHHHHHHHHHcCCHhhEEecCCCcEEEEccCccchh---HHHHHHHHHHHHHH
Confidence 999999999999999985 999999999999999999999 999999999999999986544 47899999999999
Q ss_pred HhCCceEEeccCChhHHHHHhhcCCCCcEEEEcC-ChHHHHHhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-
Q 009922 78 EAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPN-DRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG- 155 (522)
Q Consensus 78 etGlt~S~GIA~NKllAKLAS~~~KP~G~~vI~~-~~~~~~~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~- 155 (522)
+||||||||||+||++||||++.+||+|+++|.+ +.+++.+||+++||++|||||++++++|++ +||.|++||++.+
T Consensus 126 ~~Glt~siGIa~nk~lAKlas~~~KP~g~~~i~~~~~~~~~~fl~~lpv~~l~GiG~~~~~kL~~-~GI~tigdl~~~~~ 204 (379)
T cd01703 126 ELGLTCCAGIASNKLLAKLVGSVNKPNQQTTLLPPSCADLMDFMDLHDLRKIPGIGYKTAAKLEA-HGISSVRDLQEFSN 204 (379)
T ss_pred HhCCeEEEEEcCCHHHHHHHhhhcCCCCeEEEcCCchHHHHHHhccCCccccCCcCHHHHHHHHH-cCCCcHHHHHhCCc
Confidence 9999999999999999999999999999998865 333567899999999999999999999997 9999999999876
Q ss_pred --------------H-HHHHHcChhHHHHHHHhccCCCCCCC-CCCCCCCcceeecccCC--cCCHHHHHHHHHHHHHHH
Q 009922 156 --------------S-LLCAVFSHSTADFFLSVGLGLGSTNT-PQARFRKSISSERTFSV--TEDKALLYRKLAEIAEML 217 (522)
Q Consensus 156 --------------~-~L~~~FG~~~~~~l~~~a~G~d~~~v-~~~~~~KSIs~e~tF~~--~~~~e~L~~~L~~La~~L 217 (522)
. .|+++||...+.++|+.++|+|.+++ .+...+|||+.++||.. ..+.+++..+|..|+++|
T Consensus 205 ~~~~~~~~~~~~~s~~~L~~~fG~~~g~~l~~~a~G~d~~~V~~~~~~~ksis~e~tf~~~~~~~~~~~~~~l~~l~~~l 284 (379)
T cd01703 205 RNRQTVGAAPSLLELLLMVKEFGEGIGQRIWKLLFGRDTSPVKPASDFPQQISIEDSYKKCSLEEIREARNKIEELLASL 284 (379)
T ss_pred ccccccccccccccHHHHHHHHCHHHHHHHHHHHCCCCCCccCCCCCCCceeEEeeccCCCCCCCHHHHHHHHHHHHHHH
Confidence 3 79999998778999999999999999 65567899999999986 368899999999999999
Q ss_pred HHHHHH--------hCCCccEEEEEEEecC-----CeeeEEEEEcCCCCC---------CHHHHHHHHHHHHHhhCC---
Q 009922 218 SADMQK--------EGLRGRTLTLKLKTAS-----FEVRTRAVTLQKYIS---------SSEDILKHASVLLKAELP--- 272 (522)
Q Consensus 218 ~~RLr~--------~g~~artltLkL~~~d-----~~~~srs~~L~~pt~---------d~~~L~~~a~~LL~~~l~--- 272 (522)
+.||++ .+..++||+|++++.+ |.+.+++.+++.+++ +...|++.+..||+++++
T Consensus 285 ~~rl~~~l~~~~~~~~~~~~tv~l~vr~~~~~~~~~~~~sr~~~l~~~~~~~~~~~~~~~~~~i~~~~~~L~~~~~~~~~ 364 (379)
T cd01703 285 LERMKQDLQEVKAGDGRRPHTLRLTLRRYTSTKKHYNRESKQAPIPSHVFQKLTGGNEIAARPIEKILMRLFRELVPPKN 364 (379)
T ss_pred HHHHHhhhhccchhcCeeeeEEEEEEEECCCCCCccceeeeccccCchhhccccccchhhHHHHHHHHHHHHHHhccccc
Confidence 999999 9999999999999999 999999999999998 678999999999998742
Q ss_pred ---CCEEEEEEEeec
Q 009922 273 ---VSLRLIGLRVTQ 284 (522)
Q Consensus 273 ---~~IR~lGV~vs~ 284 (522)
.+||++||++++
T Consensus 365 ~~~~~irl~gv~~~~ 379 (379)
T cd01703 365 VKGFNLTLLNVCFTN 379 (379)
T ss_pred CCCCceEEEEEEeeC
Confidence 279999999975
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=7.7e-52 Score=433.17 Aligned_cols=269 Identities=33% Similarity=0.472 Sum_probs=247.8
Q ss_pred CcHHHHHHhCCCcEEECCC-----------------------hHHHHHHHHHHHHHHHhhCCCEEeecccEEEEEcCcch
Q 009922 1 MPGFIARKLCPELIFVPTD-----------------------FTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVC 57 (522)
Q Consensus 1 Mpl~~A~kLCPdLvvvp~d-----------------------~~~Y~~~s~~i~~il~~~tp~VE~~SiDEafLDvT~~~ 57 (522)
||+++|+++||++++++++ ++.|+.+|+++++++.+|+|.||++||||+|||+
T Consensus 49 m~~~~A~~lcP~l~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Y~~~S~~i~~~l~~~sp~vE~~SiDE~flDv---- 124 (359)
T cd01702 49 MTIDEAKKKCPDLILAHVATYKKGEDEADYHENPSPARHKVSLDPYRRASRKILNILKRFGDVVEKASIDEAYLDL---- 124 (359)
T ss_pred CcHHHHHHHCCCcEEECCccccccccccccccccccccccccHHHHHHHHHHHHHHHHHcCCceEECcCCeeHHHH----
Confidence 9999999999999999875 9999999999999999999999999999999999
Q ss_pred hhcCCCHHHHHHHHHHHHHHHhCCceEEeccCChhHHHHHhhcCCCCcEEEEcCChHHHHHhhcCCCcccccCCChHHHH
Q 009922 58 RERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEH 137 (522)
Q Consensus 58 ~l~g~~~~~lA~~IR~~I~~etGlt~S~GIA~NKllAKLAS~~~KP~G~~vI~~~~~~~~~fL~~LPI~~LpGIG~kt~~ 137 (522)
+..+|++||++|++++|+|||||||+||++|||||+.+||+|+++++++ ++.+||+++||++|||||+++++
T Consensus 125 ------~~~la~~ir~~I~~~~glt~SiGIa~nk~lAKlAs~~~KP~g~~v~~~~--~~~~~L~~lpv~~l~GiG~~~~~ 196 (359)
T cd01702 125 ------GSRIVEEIRQQVYDELGYTCSAGIAHNKMLAKLASGMNKPNAQTILRND--AVASFLSSLPITSIRGLGGKLGE 196 (359)
T ss_pred ------HHHHHHHHHHHHHHHhCccEEeeecCCHHHHHHHhcccCCCCeEEECHH--HHHHHhhcCcHHHhCCcCHHHHH
Confidence 3679999999999999999999999999999999999999999999875 78999999999999999999977
Q ss_pred H-HhhhcCCCCHHHHHhc--h-HHHHHHcChhHHHHHHHhccCCCCCCCCCCCCCCcceeecccCC-cCCH-HHHHHHHH
Q 009922 138 I-LRDVFGINTCEEMLQK--G-SLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV-TEDK-ALLYRKLA 211 (522)
Q Consensus 138 ~-L~~~lGI~T~gdL~~l--~-~~L~~~FG~~~~~~l~~~a~G~d~~~v~~~~~~KSIs~e~tF~~-~~~~-e~L~~~L~ 211 (522)
+ |+. +||+|++||+++ + ..|.++||...+.++|+.++|+|.+++.+..++|||+.+++|+. ..+. +++..+|.
T Consensus 197 ~ll~~-~Gi~ti~dl~~~~~~~~~L~~~fG~~~g~~l~~~a~G~d~~~v~~~~~~ksi~~~~tf~~~~~~~~~~l~~~l~ 275 (359)
T cd01702 197 EIIDL-LGLPTEGDVAGFRSSESDLQEHFGEKLGEWLYNLLRGIDHEPVKPRPLPKSMGSSKNFPGKTALSTEDVQHWLL 275 (359)
T ss_pred HHHHH-cCCcCHHHHHhccCCHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCCceeeeeeecCCCCCChHHHHHHHHH
Confidence 6 576 999999999999 7 78999999878999999999999999988778999999999998 5666 99999999
Q ss_pred HHHHHHHHHHHHh----CCCccEEEEEEEecC-CeeeEEEEEcCCCCCCHHHHHHHHHHHHHhhC--------CCCEEEE
Q 009922 212 EIAEMLSADMQKE----GLRGRTLTLKLKTAS-FEVRTRAVTLQKYISSSEDILKHASVLLKAEL--------PVSLRLI 278 (522)
Q Consensus 212 ~La~~L~~RLr~~----g~~artltLkL~~~d-~~~~srs~~L~~pt~d~~~L~~~a~~LL~~~l--------~~~IR~l 278 (522)
.|+++|+.||+++ ++.+++|+|++++.+ +.+.+++.+++.++ .+.|+..+..||++++ ..+||+|
T Consensus 276 ~L~~~l~~rL~~~~~~~~~~~~~v~v~lr~~~~~~~~sr~~~~~~~~--~~~i~~~~~~l~~~~~~~~~~~~~~~~~rl~ 353 (359)
T cd01702 276 VLASELNSRLEDDRYENNRRPKTLVLSLRQRGDGVRRSRSCALPRYD--AQKIVKDAFKLIKAINEEGLGLAWNYPLTLL 353 (359)
T ss_pred HHHHHHHHHHHhhhhhcCceeeEEEEEEEECCCcEEEEEEecCCCCC--HHHHHHHHHHHHHHhhhhccccccCCCeEEE
Confidence 9999999999997 999999999999999 56666766665554 9999999999998764 2789999
Q ss_pred EEEeec
Q 009922 279 GLRVTQ 284 (522)
Q Consensus 279 GV~vs~ 284 (522)
||++++
T Consensus 354 g~~~~~ 359 (359)
T cd01702 354 SLSFTK 359 (359)
T ss_pred EEEecC
Confidence 999875
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=3.5e-51 Score=425.98 Aligned_cols=279 Identities=25% Similarity=0.379 Sum_probs=256.3
Q ss_pred CcHHHHHHhCCCc--EEECCChHHHHHHHHHHHHHHHhhCCCEEeecccEEEEEcCcchhhcCCCHHHHHHHHHHHHHHH
Q 009922 1 MPGFIARKLCPEL--IFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEE 78 (522)
Q Consensus 1 Mpl~~A~kLCPdL--vvvp~d~~~Y~~~s~~i~~il~~~tp~VE~~SiDEafLDvT~~~~l~g~~~~~lA~~IR~~I~~e 78 (522)
||+++|+++||++ +++++|++.|..+|+++++++++|+|.||++||||+|||||++.+ |+ ++..+|++||++|+++
T Consensus 51 m~~~~A~~lcP~l~~~~v~~~~~~y~~~s~~i~~~l~~~~~~ve~~s~De~~ldvt~~~~-~~-~~~~la~~i~~~i~~~ 128 (344)
T cd01700 51 SPYFKVPDLLERHGVAVFSSNYALYGDMSRRIMSILERFSPDVEVYSIDESFLDLTGSLR-FG-DLEELARKIRRRILQE 128 (344)
T ss_pred CcHHHhHhhccccCeEEEcCchHHHHHHHHHHHHHHHhcCCcceEeecchhhccCcCCCC-CC-CHHHHHHHHHHHHHHH
Confidence 9999999999999 999999999999999999999999999999999999999999988 87 8999999999999999
Q ss_pred hCCceEEeccCChhHHHHHhhcCCCC----cEEEEcCChHHHHHhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhc
Q 009922 79 AGLTCSAGVAPNRLLAKVCSDINKPN----GQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQK 154 (522)
Q Consensus 79 tGlt~S~GIA~NKllAKLAS~~~KP~----G~~vI~~~~~~~~~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l 154 (522)
+|+|||+|||+||++|||||+.+||+ |++++++.. ...+||+++||++|||||+++.++|++ +||+|++||+++
T Consensus 129 ~gl~~s~Gia~~~~lAklas~~~kp~~~~~g~~~~~~~~-~~~~~l~~lpl~~l~gig~~~~~~L~~-~Gi~ti~dL~~~ 206 (344)
T cd01700 129 TGIPVTVGIGPTKTLAKLANDLAKKKNPYGGVVDLTDEE-VRDKLLKILPVGDVWGIGRRTAKKLNA-MGIHTAGDLAQA 206 (344)
T ss_pred hCCceEEEecCCHHHHHHHHHHhcCCCCCCeEEEecChh-HHHHHhccCChhhcCccCHHHHHHHHH-cCCCcHHHHhcC
Confidence 99999999999999999999999984 888886642 334899999999999999999999997 999999999999
Q ss_pred h-HHHHHHcChhHHHHHHHhccCCCCCCCCCCC-CCCcceeecccCC-cCCHHHHHHHHHHHHHHHHHHHHHhCCCccEE
Q 009922 155 G-SLLCAVFSHSTADFFLSVGLGLGSTNTPQAR-FRKSISSERTFSV-TEDKALLYRKLAEIAEMLSADMQKEGLRGRTL 231 (522)
Q Consensus 155 ~-~~L~~~FG~~~~~~l~~~a~G~d~~~v~~~~-~~KSIs~e~tF~~-~~~~e~L~~~L~~La~~L~~RLr~~g~~artl 231 (522)
| ..|.++||.. +.++|+.++|++.+++.... ++|||+.+.+|.. +.+.+++..+|++|+++|+.||+++++.+++|
T Consensus 207 ~~~~L~~rfG~~-~~~l~~~a~G~d~~~v~~~~~~~ks~~~~~~~~~~~~~~~~l~~~l~~L~~~l~~~L~~~~~~~~~l 285 (344)
T cd01700 207 DPDLLRKKFGVV-GERLVRELNGIDCLPLEEYPPPKKSIGSSRSFGRDVTDLDELKQALAEYAERAAEKLRRQKSVARTI 285 (344)
T ss_pred CHHHHHHHHHHH-HHHHHHHhCCCCCCcCCCCCCCCcEEEEeeEcCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCcccEE
Confidence 8 7899999975 77788999999999986544 4599999999988 68999999999999999999999999999999
Q ss_pred EEEEEecCCeeeEE----EEEcCCCCCCHHHHHHHHHHHHHhhC--CCCEEEEEEEeec
Q 009922 232 TLKLKTASFEVRTR----AVTLQKYISSSEDILKHASVLLKAEL--PVSLRLIGLRVTQ 284 (522)
Q Consensus 232 tLkL~~~d~~~~sr----s~~L~~pt~d~~~L~~~a~~LL~~~l--~~~IR~lGV~vs~ 284 (522)
+|++++.+|.+.++ +.+++.|+++...|++.+..+|++++ ..+||+|||++++
T Consensus 286 ~l~l~~~~~~~~~~~~~~~~~~~~~t~~~~~l~~~~~~ll~~~~~~~~~iR~iGV~~~~ 344 (344)
T cd01700 286 SVFIGTSGFSRQPKYYSATNTLPYPTNDTREIVKAALRLLYAIYRPGYAYRKAGVMLSD 344 (344)
T ss_pred EEEEEcCCCCCCCCccccccccCCcchhHHHHHHHHHHHHHHHhCCCCcEEEEEEEeeC
Confidence 99999999875443 35778999999999999999999885 3589999999875
No 18
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=100.00 E-value=8.6e-51 Score=434.13 Aligned_cols=283 Identities=20% Similarity=0.263 Sum_probs=259.4
Q ss_pred CcHHHHHHhCC--CcEEECCChHHHHHHHHHHHHHHHhhCCCEEeecccEEEEEcCcchhhcCCCHHHHHHHHHHHHHHH
Q 009922 1 MPGFIARKLCP--ELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEE 78 (522)
Q Consensus 1 Mpl~~A~kLCP--dLvvvp~d~~~Y~~~s~~i~~il~~~tp~VE~~SiDEafLDvT~~~~l~g~~~~~lA~~IR~~I~~e 78 (522)
||+++|+++|| +++++++||+.|..+|++++.++.+|+|.||++||||+|||||++.++ + ++.++|++||++|+++
T Consensus 53 mp~~~a~~l~~~~~l~~~~~d~~~y~~~s~~i~~~l~~~tp~ve~~siDE~~lDvt~~~~l-~-~~~~~a~~i~~~I~~~ 130 (422)
T PRK03609 53 DPWFKQKDLFRRCGVVCFSSNYELYADMSNRVMSTLEELSPRVEIYSIDEAFCDLTGVRNC-R-DLTDFGREIRATVLQR 130 (422)
T ss_pred CcHHHHHHHhccCCeEEeCCCHHHHHHHHHHHHHHHHHhCCCceEeccccceecCCCCcCC-C-CHHHHHHHHHHHHHHH
Confidence 99999999994 399999999999999999999999999999999999999999999876 3 6899999999999999
Q ss_pred hCCceEEeccCChhHHHHHhhcCCC-----CcEEEEcCChHHHHHhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHh
Q 009922 79 AGLTCSAGVAPNRLLAKVCSDINKP-----NGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQ 153 (522)
Q Consensus 79 tGlt~S~GIA~NKllAKLAS~~~KP-----~G~~vI~~~~~~~~~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~ 153 (522)
+|++||||||+||++|||||+.+|| +|++++.+. +...+||+++||++|||||+++.++|++ +||+|+|||++
T Consensus 131 ~gl~~siGia~n~~lAK~As~~~k~~~k~~~g~~~i~~~-~~~~~~L~~lPv~~l~GiG~~~~~~L~~-lGi~TigdL~~ 208 (422)
T PRK03609 131 THLTVGVGIAQTKTLAKLANHAAKKWQRQTGGVVDLSNL-ERQRKLLSLQPVEEVWGVGRRISKKLNA-MGIKTALDLAD 208 (422)
T ss_pred HCCceEEEecCCHHHHHHHHHHhCCCCCCCCcEEEcCCH-HHHHHHhhcCChhhcCCccHHHHHHHHH-cCCCcHHHHhc
Confidence 9999999999999999999998876 688877422 3688999999999999999999999997 99999999999
Q ss_pred ch-HHHHHHcChhHHHHHHHhccCCCCCCCCCCCCC-CcceeecccCC-cCCHHHHHHHHHHHHHHHHHHHHHhCCCccE
Q 009922 154 KG-SLLCAVFSHSTADFFLSVGLGLGSTNTPQARFR-KSISSERTFSV-TEDKALLYRKLAEIAEMLSADMQKEGLRGRT 230 (522)
Q Consensus 154 l~-~~L~~~FG~~~~~~l~~~a~G~d~~~v~~~~~~-KSIs~e~tF~~-~~~~e~L~~~L~~La~~L~~RLr~~g~~art 230 (522)
+| ..|+++||.. +..++..++|++..++....++ |+|+++++|+. ..+.+++...+.+|+++|+.||+++++.+++
T Consensus 209 ~~~~~L~~~fG~~-~~~l~~~a~G~~~~~~~~~~~~~ksi~~~~tf~~~~~~~~~l~~~l~~l~~~l~~rLr~~~~~~~~ 287 (422)
T PRK03609 209 TNIRFIRKHFNVV-LERTVRELRGEPCLSLEEFAPTKQEIVCSRSFGERITDYESMRQAICSYAARAAEKLRGEHQYCRF 287 (422)
T ss_pred CCHHHHHHHHCHH-HHHHHHHhCCCCCCCccccCCCCceEEEeeECCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCcccE
Confidence 98 7899999986 5667788999999887665554 79999999998 6899999999999999999999999999999
Q ss_pred EEEEEEecCCe------eeEEEEEcCCCCCCHHHHHHHHHHHHHhhCC--CCEEEEEEEeecCCcC
Q 009922 231 LTLKLKTASFE------VRTRAVTLQKYISSSEDILKHASVLLKAELP--VSLRLIGLRVTQFNED 288 (522)
Q Consensus 231 ltLkL~~~d~~------~~srs~~L~~pt~d~~~L~~~a~~LL~~~l~--~~IR~lGV~vs~L~~~ 288 (522)
|+|++++++|. ..+++++++.||++...|++.+..+|++++. .++|.+||.+++|.+.
T Consensus 288 l~l~ir~~~~~~~~~~~~~~~~~~l~~pt~d~~~l~~~a~~ll~~~~~~~~~~r~~GV~~~~l~~~ 353 (422)
T PRK03609 288 ISTFVKTSPFALNEPYYGNSASVKLLTPTQDSRDIIAAATRALDAIWRDGHRYQKAGVMLGDFFSQ 353 (422)
T ss_pred EEEEEEcCCccccCCCcCceeEEeCCCCCCCHHHHHHHHHHHHHHHhCCCCceEEeeEEEEeeccC
Confidence 99999999986 3578889999999999999999999999753 4799999999999864
No 19
>COG0389 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]
Probab=100.00 E-value=4.3e-47 Score=396.85 Aligned_cols=284 Identities=34% Similarity=0.524 Sum_probs=267.4
Q ss_pred CcHHHHHHhCCCcEEECCChHHHHHHHHHHHHHHHhhCCCEEeecccEEEEEcCcchhhcCC-CHHHHHHHHHHHHHHHh
Q 009922 1 MPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGI-SGIEIAEELRTSVYEEA 79 (522)
Q Consensus 1 Mpl~~A~kLCPdLvvvp~d~~~Y~~~s~~i~~il~~~tp~VE~~SiDEafLDvT~~~~l~g~-~~~~lA~~IR~~I~~et 79 (522)
||+++|+++||+++++|++|+.|..+|.+++.|+.+|+|.||++||||+|||+|+....+|. .+..+|.+||..|+.++
T Consensus 55 m~~~~A~~~cp~~~~~~~~~~~y~~~s~~i~~i~~~~~~~ve~lSIDE~~ldvt~~~~~~g~~~~~~~a~~ir~~i~~~~ 134 (354)
T COG0389 55 MPLFEALKLCPRAIVAPPNFAAYRLASAEIRAILERYTPLVEPLSIDEAFLDLTDALRLLGLADAPRIALEIRFGILLEL 134 (354)
T ss_pred ChHHHHHHHCCCCEEeCCcHHHHHHHHHHHHHHHHhccccceeeeccceeeecccccccCCcccHHHHHHHHHHHHHHhh
Confidence 89999999999999999999999999999999999999999999999999999998887764 68999999999999999
Q ss_pred CCceEEeccCChhHHHHHhhcCCCCcEEEEcCChHHHHHhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHH
Q 009922 80 GLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLL 158 (522)
Q Consensus 80 Glt~S~GIA~NKllAKLAS~~~KP~G~~vI~~~~~~~~~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L 158 (522)
|+|||+|||+||++||||++.+||+|++++.+. ++..||++|||.++||||+.++++|+. +||.|++|+++.+ ..|
T Consensus 135 ~l~~s~Gi~~nk~laKiAs~~~kp~gi~~~~~~--~~~~~l~~Lpv~~~~GvG~~~~~~l~~-~Gi~ti~dl~~~~~~~L 211 (354)
T COG0389 135 GLTASVGISDNKFLAKIASDLNKPDGITVIEPE--EVPALLWQLPVLEFWGVGKVTAEKLRR-LGISTIGDLAETDLDAL 211 (354)
T ss_pred CCEEEEEecCcHHHHHHHhcccCCCCEEEECHH--HHHHHHhcCChhhhCCCCHHHHHHHHH-cCChhHHHHHhcCHHHH
Confidence 999999999999999999999999999999964 799999999999999999999999997 9999999999976 789
Q ss_pred HHHcChhHHHHHHHhccCCCCCCCCCCCCC-CcceeecccCC-cCCHHHHHHHHHH-HHHHHHHHHHHhCCCccEEEEEE
Q 009922 159 CAVFSHSTADFFLSVGLGLGSTNTPQARFR-KSISSERTFSV-TEDKALLYRKLAE-IAEMLSADMQKEGLRGRTLTLKL 235 (522)
Q Consensus 159 ~~~FG~~~~~~l~~~a~G~d~~~v~~~~~~-KSIs~e~tF~~-~~~~e~L~~~L~~-La~~L~~RLr~~g~~artltLkL 235 (522)
.++||... .++|..++|+|.+++...... ||++.+.||+. ..+.+.+...|.. |++++..||+..+..++++++++
T Consensus 212 ~~~~g~~~-~~l~~~a~Gid~~~v~~~~~~~ksi~~~~t~~~d~~~~~~~~~~l~~~l~e~~~~rl~~~~~~~r~v~~~~ 290 (354)
T COG0389 212 KKRFGKLG-ERLYRLARGIDNRPVREQALRAKSIGAESTFEEDLTDAEELIERLRARLGEEVVSRLRKSGRHGRTVSVKL 290 (354)
T ss_pred HHHHhHhH-HHHHHHhcCCCccccccccccCccccceeeccccccCHHHHHHHHHHHHHHHHHHHHHHhCCCceEEEEEE
Confidence 99999886 899999999999999888777 99999999998 4778877777777 99999999999999999999999
Q ss_pred EecCCeeeEEEEEcCCCCCCHHHHHHHHHHHHHhhC----CCCEEEEEEEeecCCcC
Q 009922 236 KTASFEVRTRAVTLQKYISSSEDILKHASVLLKAEL----PVSLRLIGLRVTQFNED 288 (522)
Q Consensus 236 ~~~d~~~~srs~~L~~pt~d~~~L~~~a~~LL~~~l----~~~IR~lGV~vs~L~~~ 288 (522)
++++|.+.+++.+++.|+++..+++..+..+++..+ +..+|++||.+++|.+.
T Consensus 291 ~~~df~~~t~~~~l~~p~~~~~~i~~~~~~l~~~~~~~~~~~~~rl~gv~~~~~~~~ 347 (354)
T COG0389 291 KTADFPTNTRSRKLAQPTSDPIEIYAAALPLLPPLLFRGRGRRIRLLGVSGPELIDS 347 (354)
T ss_pred EecCCCcceeecccCCcCCCHHHHHHHHHHHHHHhhccCCCceEEEEEEEecCcccc
Confidence 999999999999999999999999999999999875 35899999999999875
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=5.2e-46 Score=384.56 Aligned_cols=275 Identities=21% Similarity=0.193 Sum_probs=252.0
Q ss_pred CcHHHHHHhCCCcEEECCChHHHHHHHHHHHHHHHhhCCCEEeecccEEEEEcCcchhhcCCCHHHHHHHHHHHHHHHhC
Q 009922 1 MPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAG 80 (522)
Q Consensus 1 Mpl~~A~kLCPdLvvvp~d~~~Y~~~s~~i~~il~~~tp~VE~~SiDEafLDvT~~~~l~g~~~~~lA~~IR~~I~~etG 80 (522)
||+++|+++||+++++++|++.|..+++++++++++|+|.|+++|+||+|||+|++.++|| ++..+|+.|++.+. ++|
T Consensus 52 m~~~~A~~lcP~l~~~~~~~~~y~~~s~~i~~~l~~~s~~ve~~s~de~~ldvs~~~~~~~-~~~~~a~~i~~~~~-~~g 129 (335)
T cd03468 52 MPLAEALALCPNLQVVEYDPEADARALQELALWLLRFTPLVALDGPDGLLLDVTGCLHLFG-GEDALAASLRAALA-TLG 129 (335)
T ss_pred CcHHHHHHhCCCCeeecCChHHHHHHHHHHHHHHHhcCCccccCCCCeEEEEcccchhhcC-CHHHHHHHHHHHHH-HcC
Confidence 9999999999999999999999999999999999999999999999999999999999998 79999999999995 789
Q ss_pred CceEEeccCChhHHHHHhhcCCCCcEEEEcCChHHHH-HhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHH
Q 009922 81 LTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVM-TFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLL 158 (522)
Q Consensus 81 lt~S~GIA~NKllAKLAS~~~KP~G~~vI~~~~~~~~-~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L 158 (522)
++||+|||+|+++||||++.+||+|++.+.+. ... .|++++|+. +||||+++.++|++ +||+|++||+++| ..|
T Consensus 130 l~~siGia~n~~~Aklas~~~kp~~~~~~~~~--~~~~~~l~~lp~~-~~gig~~~~~~L~~-~Gi~t~~dl~~~~~~~l 205 (335)
T cd03468 130 LSARAGIADTPGAAWLLARAGGGRGVLRREAL--AAALVLLAPLPVA-ALRLPPETVELLAR-LGLRTLGDLAALPRAEL 205 (335)
T ss_pred CeEEEEecCCHHHHHHHhccCCCCccCCchHH--HHHhhccCCCChh-HhCCCHHHHHHHHH-hCcccHHHHHhCChHHH
Confidence 99999999999999999999999999876653 233 388999995 99999999999997 9999999999998 789
Q ss_pred HHHcChhHHHHHHHhccCCCCCCC--CCCCCCCcceeecccCCcCCHHHHHHHHHHHHHHHHHHHHHhCCCccEEEEEEE
Q 009922 159 CAVFSHSTADFFLSVGLGLGSTNT--PQARFRKSISSERTFSVTEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLK 236 (522)
Q Consensus 159 ~~~FG~~~~~~l~~~a~G~d~~~v--~~~~~~KSIs~e~tF~~~~~~e~L~~~L~~La~~L~~RLr~~g~~artltLkL~ 236 (522)
.++||.. +..+|..++|++..++ .+...+++++.+.+|+....... ...+..|+++++.+|+.++..+++|+|+++
T Consensus 206 ~~rfG~~-~~~l~~~~~G~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~l~~l~~~l~~~L~~~~~~~~~l~l~l~ 283 (335)
T cd03468 206 ARRFGLA-LLLRLDQAYGRDPEPLLFSPPPPAFDFRLELQLEEPIARGL-LFPLRRLLEQLCAFLALRGLGARRLSLTLF 283 (335)
T ss_pred HhhcCHH-HHHHHHHHCCCCCCCCCCCCCCCChhhhhhcCCCCCcchhH-HHHHHHHHHHHHHHHHHcCCeeeEEEEEEE
Confidence 9999987 5667789999999998 44566899999999998543333 899999999999999999999999999999
Q ss_pred ecCCeeeEEEEEcCCCCCCHHHHHHHHHHHHHhhC-C---CCEEEEEEEee
Q 009922 237 TASFEVRTRAVTLQKYISSSEDILKHASVLLKAEL-P---VSLRLIGLRVT 283 (522)
Q Consensus 237 ~~d~~~~srs~~L~~pt~d~~~L~~~a~~LL~~~l-~---~~IR~lGV~vs 283 (522)
+.++.+.++++++..|+++...|++.++.+|++.. . .+||.+||++.
T Consensus 284 ~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~l~~~~~~~~~~~v~~~~v~~~ 334 (335)
T cd03468 284 REDGRVTRVLVGLARPSRDDLPLLRLLRERLERLALPRGIAPVRLLALTAE 334 (335)
T ss_pred EECCceEEEEEeccCCccCHHHHHHHHHhhhhccCCCCCeeeEEEEEeecc
Confidence 99999999999999999999999999999999875 3 58999999864
No 21
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=100.00 E-value=1.3e-44 Score=393.81 Aligned_cols=305 Identities=24% Similarity=0.366 Sum_probs=277.0
Q ss_pred CcHHHHHHhCCCcEEECCChHHHHHHHHHHHHHHHhhCCCEEeecccEEEEEcCcchhhcCCCHHHHHHHHHHHHHHHhC
Q 009922 1 MPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAG 80 (522)
Q Consensus 1 Mpl~~A~kLCPdLvvvp~d~~~Y~~~s~~i~~il~~~tp~VE~~SiDEafLDvT~~~~l~g~~~~~lA~~IR~~I~~etG 80 (522)
|-+.+|++|||+|+.|||||+.|..+++.+|+.|.+|+-.|+++|+||||+|+|..+..+..++..+|..||++|++.||
T Consensus 429 MfV~~A~klCPqL~~lPY~FE~Ykevs~tlYetlasytl~I~aVSCDEa~vd~s~~~~~~~~tp~~la~~IRqEI~e~Tg 508 (1016)
T KOG2093|consen 429 MFVRHAKKLCPQLVILPYDFEAYKEVSETLYETLASYTLNIEAVSCDEAFVDVSDLSDEENETPAVLAEHIRQEILEKTG 508 (1016)
T ss_pred eeHHHHHHhCcccEeecccHHHHHHHHHHHHHHHHhhccceeeecchhhhhhhhhhhhhhccCHHHHHHHHHHHHHhccC
Confidence 78999999999999999999999999999999999999999999999999999999988877899999999999999999
Q ss_pred CceEEeccCChhHHHHHhhcCCCCcEEEEcCChHHHHHhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHH
Q 009922 81 LTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLC 159 (522)
Q Consensus 81 lt~S~GIA~NKllAKLAS~~~KP~G~~vI~~~~~~~~~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~ 159 (522)
|+||||||.|++||+||++.||||||+++.+. .+.+||++++|++|||||..+..+|.+ +||+|||||+... ..|+
T Consensus 509 C~aS~Gig~t~LLARlATr~AKP~Gq~~l~a~--~veeFis~~~v~~LPGVG~sm~~kL~s-~~i~tCgdLq~~T~~kl~ 585 (1016)
T KOG2093|consen 509 CPASAGIGGTMLLARLATRVAKPNGQFYLSAE--KVEEFISQLKVDDLPGVGSSMKSKLVS-QFIQTCGDLQLITLIKLR 585 (1016)
T ss_pred CceeeccchHHHHHHHHHhhcCCCceeeecHH--HHHHHhhhcccccCCCccHHHHHHHHH-hccchhHHHHHHHHHHHH
Confidence 99999999999999999999999999999886 789999999999999999999999997 9999999998877 8899
Q ss_pred HHcChhHHHHHHHhccCCCCCCCCCCCCCCcceeecccCC-cCCHHHHHHHHHHHHHHHHHHHHHhCCCccEEEEEEEec
Q 009922 160 AVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV-TEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTA 238 (522)
Q Consensus 160 ~~FG~~~~~~l~~~a~G~d~~~v~~~~~~KSIs~e~tF~~-~~~~e~L~~~L~~La~~L~~RLr~~g~~artltLkL~~~ 238 (522)
+.||++.|..+|..|+|+|++|......+||++++.+|+. ..+.-++...|-.++++|-.+|-+-++.++.+||++.-+
T Consensus 586 k~~G~Klgq~i~~~CrG~Dd~P~~~~~~RKSvS~dIN~GIRFtn~~ev~~fl~~~~eEl~rkL~ei~k~~~sitLKlMvR 665 (1016)
T KOG2093|consen 586 KVFGPKLGQKIYRGCRGIDDDPRSIEQVRKSVSADINYGIRFTNIKEVEQFLCLLSEELRRKLLEISKTASSITLKLMVR 665 (1016)
T ss_pred hhhcccHHHHHHHhcCCCcCChHHHhhhhcceeeeeecceeeccHHHHHHHHHHHHHHHHHHHHHhhccccchhHHHHhh
Confidence 9999999999999999999999877667999999999997 578889999999999999999999999999999988643
Q ss_pred C---------------CeeeEEEEEcCCCCCCHHHHHHHHHHHHHhhC--CCCEEEEEEEee-cCCcCCccCCCCcccch
Q 009922 239 S---------------FEVRTRAVTLQKYISSSEDILKHASVLLKAEL--PVSLRLIGLRVT-QFNEDKVRAPSDPTQKT 300 (522)
Q Consensus 239 d---------------~~~~srs~~L~~pt~d~~~L~~~a~~LL~~~l--~~~IR~lGV~vs-~L~~~~~~~~~~~~q~s 300 (522)
. ++..+++.++..||+....|...+..|++..- +..+|++||.+. +|.+... .-.+.-
T Consensus 666 ~~~APietaK~mGhGiCD~~~rs~~l~~~Td~~~iItt~~~~L~~t~~~~~~elRG~gi~~ntkL~~~~~----~~~~~~ 741 (1016)
T KOG2093|consen 666 TAKAPIETAKYMGHGICDDFVRSSKLREPTDCNRIITTEVLRLYETNSEPPSELRGLGIHSNTKLMDVLE----NLPPEL 741 (1016)
T ss_pred cCCCCCccccccceeeccchhhhhhccCccccccchHHHHHHHHHhcCCChHHhccchhhcccccccccc----CCcHHH
Confidence 2 34578899999999999999999999999863 357999999995 8887641 223556
Q ss_pred HHHhhccCcccc
Q 009922 301 LTNFMTSGHASK 312 (522)
Q Consensus 301 i~~ff~~~~~~~ 312 (522)
+..+|......+
T Consensus 742 l~e~Fgt~s~~~ 753 (1016)
T KOG2093|consen 742 LSEMFGTYSGKR 753 (1016)
T ss_pred HHhhcccccccc
Confidence 677777666444
No 22
>KOG2095 consensus DNA polymerase iota/DNA damage inducible protein [Replication, recombination and repair]
Probab=100.00 E-value=1.3e-37 Score=334.19 Aligned_cols=232 Identities=35% Similarity=0.523 Sum_probs=210.9
Q ss_pred CcHHHHHHhCCCcEEEC-------CChHHHHHHHHHHHHHHHhhCCCEEeecccEEEEEcCcchhhc-------------
Q 009922 1 MPGFIARKLCPELIFVP-------TDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRER------------- 60 (522)
Q Consensus 1 Mpl~~A~kLCPdLvvvp-------~d~~~Y~~~s~~i~~il~~~tp~VE~~SiDEafLDvT~~~~l~------------- 60 (522)
|.+.+|+++||+|+++. +|..+|+.++.+++.+|..|+|.||..++||+|+|+|.+..+.
T Consensus 67 M~v~EAK~kCPqLvlv~v~~~~~ka~~~~YR~as~ev~~~L~~y~~viek~~~dea~ld~tasvder~q~L~s~~~~~~~ 146 (656)
T KOG2095|consen 67 MTVDEAKKKCPQLVLVHVPVAREKADLPKYREASEEVKESLEPYRPVIEKASKDEAFLDLTASVDERLQDLQSDEFNMLL 146 (656)
T ss_pred hhHHHHHhhCCceEEeecccccccchhhhhhhhHHHHHHHHhhhHHHHHHHhhhhhhhhHHHHHHHHHHHHhhhhhhhhh
Confidence 89999999999998875 3555699999999999999999999999999999999886532
Q ss_pred ---------CC----------------------------------------CHHHHHHHHHHHHHHHhCCceEEeccCCh
Q 009922 61 ---------GI----------------------------------------SGIEIAEELRTSVYEEAGLTCSAGVAPNR 91 (522)
Q Consensus 61 ---------g~----------------------------------------~~~~lA~~IR~~I~~etGlt~S~GIA~NK 91 (522)
+. -+..+|++||++|+.+||||||+|||+||
T Consensus 147 ~~~p~~~~~~~~s~~~~~~~~~~~e~~~~~ee~~~~~~~~~d~~~~d~~L~iGa~Iv~EiR~~i~~elg~tCSAGIa~NK 226 (656)
T KOG2095|consen 147 EEPPYGLIYGLPSALPNTREATNSENPLMREEIVSLWIENDDFDWDDVRLLIGAQIVKEIRDAIKLELGYTCSAGIAHNK 226 (656)
T ss_pred hccchhcccCCccccchhhhhhhhccccchhhHhhhhhhccccCchhhhhHHHHHHHHHHHHHHHHHhCceeeccccccH
Confidence 00 14579999999999999999999999999
Q ss_pred hHHHHHhhcCCCCcEEEEcCChHHHHHhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHHcChhHHHHH
Q 009922 92 LLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHSTADFF 170 (522)
Q Consensus 92 llAKLAS~~~KP~G~~vI~~~~~~~~~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~FG~~~~~~l 170 (522)
+||||||.++|||.||+|++. .+.+||..|||+++|++|+++.+.|...+||.++|||++.+ ..|.+.||.+.+.|+
T Consensus 227 mLAKLvsg~nKPnqQTil~~~--~v~~ll~slpi~k~~~lGGk~G~~lie~LGi~~vgdl~~fse~~L~~~fg~~~g~~l 304 (656)
T KOG2095|consen 227 MLAKLVSGRNKPNQQTILPNT--YVQDLLDSLPITKIRTLGGKLGEELIEVLGIDSVGDLQQFSETQLQKKFGEKNGTWL 304 (656)
T ss_pred HHHHHHhccCCCCcceecchH--HHHHHHHhCCCceeeeccchHHHHHHHHhCCchHHHHHhcCHHHHHHhhCcchhHHH
Confidence 999999999999999999986 79999999999999999988888887789999999999998 899999999999999
Q ss_pred HHhccCCCCCCCCCCCCCCcceeecccCC---cCCHHHHHHHHHHHHHHHHHHHHHh----CCCccEEEEE
Q 009922 171 LSVGLGLGSTNTPQARFRKSISSERTFSV---TEDKALLYRKLAEIAEMLSADMQKE----GLRGRTLTLK 234 (522)
Q Consensus 171 ~~~a~G~d~~~v~~~~~~KSIs~e~tF~~---~~~~e~L~~~L~~La~~L~~RLr~~----g~~artltLk 234 (522)
|..|+|+|.++|.++..+|||+++++|+. ..+.+++..||..|++++..||-.. .+.+.+++++
T Consensus 305 ~~la~Gid~s~V~pr~~pkSig~~K~Fpg~~~~~~~~~l~~wl~~la~el~~Rl~~d~~en~r~as~l~~~ 375 (656)
T KOG2095|consen 305 RNLARGIDNSPVRPRGLPKSIGSEKNFPGKRSRKSLEELQRWLNQLAEELAERLGKDRNENKRRASTLVVS 375 (656)
T ss_pred HHHhcccCCCccccCCCCcchhhhhcCCCccccccHHHHHHHHHHHHHHHHHHHHhhhhhhccccceEEee
Confidence 99999999999999999999999999996 5788899999999999999998665 5678888888
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=99.86 E-value=6.9e-22 Score=182.51 Aligned_cols=98 Identities=40% Similarity=0.614 Sum_probs=93.4
Q ss_pred CcHHHHHHhCCCcEEECCChHHHHHHHHHHHHHHHhh-CCCEEeecccEEEEEcCcchhhcCCCHHHHHHHHHHHHHHHh
Q 009922 1 MPGFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKY-DPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEA 79 (522)
Q Consensus 1 Mpl~~A~kLCPdLvvvp~d~~~Y~~~s~~i~~il~~~-tp~VE~~SiDEafLDvT~~~~l~g~~~~~lA~~IR~~I~~et 79 (522)
||+.+|+++||+++++++|++.|.+++++++.++++| +|.|+.+|+||+|||+|++.++|| +..+++++|+++|.+++
T Consensus 51 m~~~~A~~lcp~l~~~~~d~~~~~~~~~~l~~~l~~~~sp~ve~~s~de~~ldv~~~~~l~~-~~~~~~~~l~~~i~~~~ 129 (149)
T PF00817_consen 51 MPLAEALALCPDLVVVPPDPERYREASERLAEILYRFSSPRVEVYSPDELFLDVTGSLRLFG-GEEALARRLRQAIAEET 129 (149)
T ss_dssp SBHHHHHHHSTTSEEEEEEHHHHHHHHHHHHHHHHTTTCSEEEEEETTEEEEEEHHHHHHHH-HHHHHHHHHHHHHHHHH
T ss_pred hhhhhHhhhccceeeccccHHHHHHHHHHHHHHHHhcccccceecccccccccCCcchhhcc-hHHHHHHHHHHHHHHHh
Confidence 8999999999999999999999999999999999999 789999999999999999999998 78999999999999999
Q ss_pred CCceEEeccCChhHHHHHhh
Q 009922 80 GLTCSAGVAPNRLLAKVCSD 99 (522)
Q Consensus 80 Glt~S~GIA~NKllAKLAS~ 99 (522)
|++||+|||+|+++||||++
T Consensus 130 gl~~s~Gia~~~~~Aklaa~ 149 (149)
T PF00817_consen 130 GLTASIGIAPNPLLAKLAAD 149 (149)
T ss_dssp S--EEEEEESSHHHHHHHHH
T ss_pred CCEEEEEEeCCHHHHHHhcC
Confidence 99999999999999999985
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=121.91 Aligned_cols=107 Identities=33% Similarity=0.457 Sum_probs=95.9
Q ss_pred CCCC-CCCCCCcceeecccCC-cCCHHHHHHHHHHHHHHHHHHHHHhCCCccEEEEEEEecCCe---eeEEEEEcCCCCC
Q 009922 180 TNTP-QARFRKSISSERTFSV-TEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFE---VRTRAVTLQKYIS 254 (522)
Q Consensus 180 ~~v~-~~~~~KSIs~e~tF~~-~~~~e~L~~~L~~La~~L~~RLr~~g~~artltLkL~~~d~~---~~srs~~L~~pt~ 254 (522)
+||. +..++|||+++++|+. +.+.+.+..+|..|+++|+.||+++++.+++|+|++++.++. +.+++.+++.|++
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 6788999999999997 689999999999999999999999999999999999999998 8899999999999
Q ss_pred CHHHHHHHHHHHHHhh-C--CCCEEEEEEEeecCC
Q 009922 255 SSEDILKHASVLLKAE-L--PVSLRLIGLRVTQFN 286 (522)
Q Consensus 255 d~~~L~~~a~~LL~~~-l--~~~IR~lGV~vs~L~ 286 (522)
+...|+..+..+|++. + ..+||+|||++++|.
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 468999999999999
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=98.48 E-value=1e-07 Score=65.55 Aligned_cols=30 Identities=50% Similarity=0.723 Sum_probs=26.8
Q ss_pred HHHHhhcCCCcccccCCChHHHHHHhhhcCC
Q 009922 115 AVMTFISSLPIRKIGGIGKVTEHILRDVFGI 145 (522)
Q Consensus 115 ~~~~fL~~LPI~~LpGIG~kt~~~L~~~lGI 145 (522)
++.+||+++||+++||||++|+++|++ +||
T Consensus 3 ~v~~~l~~lpi~~~~GIG~kt~~kL~~-~GI 32 (32)
T PF11798_consen 3 DVPEFLWPLPIRKFWGIGKKTAKKLNK-LGI 32 (32)
T ss_dssp HHHHHHHCSBGGGSTTS-HHHHHHHHC-TT-
T ss_pred HHHHHHhcCCHHhhCCccHHHHHHHHH-ccC
Confidence 689999999999999999999999997 997
No 26
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=97.61 E-value=3.5e-05 Score=79.93 Aligned_cols=79 Identities=23% Similarity=0.244 Sum_probs=61.0
Q ss_pred hhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHHcCh--hHHHHHHHhccC---CC--CCCCCCCCCCCc
Q 009922 119 FISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSH--STADFFLSVGLG---LG--STNTPQARFRKS 190 (522)
Q Consensus 119 fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~FG~--~~~~~l~~~a~G---~d--~~~v~~~~~~KS 190 (522)
.|.++||.++||||++++++|.+ .||.|++||++.+ ..|.+.+|. +.+..++..+.| .+ .+.+.....+++
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 47899999999999999999997 9999999999987 789999985 467888888877 42 222222234577
Q ss_pred ceeecccC
Q 009922 191 ISSERTFS 198 (522)
Q Consensus 191 Is~e~tF~ 198 (522)
++...|+.
T Consensus 81 ~~~~~Tg~ 88 (317)
T PRK04301 81 VGKITTGS 88 (317)
T ss_pred CCccCCCC
Confidence 76666554
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=96.67 E-value=0.0014 Score=67.53 Aligned_cols=73 Identities=27% Similarity=0.310 Sum_probs=54.9
Q ss_pred cccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHHcChh--HHHHHHHhcc---CCC--CCCCCCCCCCCcceeecc
Q 009922 125 IRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHS--TADFFLSVGL---GLG--STNTPQARFRKSISSERT 196 (522)
Q Consensus 125 I~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~FG~~--~~~~l~~~a~---G~d--~~~v~~~~~~KSIs~e~t 196 (522)
|.++||||++++++|.+ .||.|++||+..+ ..|.+.+|.. .+..++..+. |.+ .+.+.....+++++...|
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 56899999999999997 9999999999987 7899998853 5677776665 665 322332234677776666
Q ss_pred cC
Q 009922 197 FS 198 (522)
Q Consensus 197 F~ 198 (522)
+.
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=96.34 E-value=0.0041 Score=48.67 Aligned_cols=47 Identities=26% Similarity=0.369 Sum_probs=38.7
Q ss_pred ccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHH--cChhHHHHHHHh
Q 009922 126 RKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFLSV 173 (522)
Q Consensus 126 ~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~--FG~~~~~~l~~~ 173 (522)
..|+|||++++.+|.+ .|+.|+.||+..+ ..|.+. +|+..++.+...
T Consensus 8 ~~I~Gig~~~a~~L~~-~G~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~ 57 (60)
T PF14520_consen 8 LSIPGIGPKRAEKLYE-AGIKTLEDLANADPEELAEIPGIGEKTAEKIIEA 57 (60)
T ss_dssp HTSTTCHHHHHHHHHH-TTCSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHH
T ss_pred ccCCCCCHHHHHHHHh-cCCCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHH
Confidence 4689999999999997 8999999999986 677776 677777666543
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=95.63 E-value=0.012 Score=50.42 Aligned_cols=36 Identities=28% Similarity=0.374 Sum_probs=30.4
Q ss_pred CcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHH
Q 009922 124 PIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCA 160 (522)
Q Consensus 124 PI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~ 160 (522)
.+.+|||||+++++-|.. +||+++.||+... ..|..
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 478899999999999997 9999999999875 44433
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=94.39 E-value=0.029 Score=42.96 Aligned_cols=28 Identities=29% Similarity=0.335 Sum_probs=21.1
Q ss_pred ccccCCChHHHHHHhhhcCCCCHHHHHhc
Q 009922 126 RKIGGIGKVTEHILRDVFGINTCEEMLQK 154 (522)
Q Consensus 126 ~~LpGIG~kt~~~L~~~lGI~T~gdL~~l 154 (522)
..|||||+++|+++-. .|++|+.||...
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 4689999999999997 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=93.99 E-value=0.1 Score=43.61 Aligned_cols=32 Identities=28% Similarity=0.538 Sum_probs=24.3
Q ss_pred CCcccccCCChHHHHHHhhhcCCCCHHHHHhch
Q 009922 123 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG 155 (522)
Q Consensus 123 LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~ 155 (522)
-.|+++|+||+++++.|.+ .||+|+.||.+..
T Consensus 3 ~~l~~LpNig~~~e~~L~~-vGI~t~~~L~~~G 34 (81)
T PF04994_consen 3 NRLKDLPNIGPKSERMLAK-VGIHTVEDLRELG 34 (81)
T ss_dssp --GCGSTT--HHHHHHHHH-TT--SHHHHHHHH
T ss_pred cchhhCCCCCHHHHHHHHH-cCCCCHHHHHHhC
Confidence 4689999999999999997 8999999999874
No 32
>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=92.06 E-value=0.25 Score=39.67 Aligned_cols=51 Identities=18% Similarity=0.326 Sum_probs=38.0
Q ss_pred HhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHH--cChhHHHHH
Q 009922 118 TFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFF 170 (522)
Q Consensus 118 ~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~--FG~~~~~~l 170 (522)
..+...||..| |+...+...|++ .||+|++||..++ ..|.+. ||..+...+
T Consensus 7 ~~~~~~~I~~L-~LS~Ra~n~L~~-~~I~tv~dL~~~s~~~L~~i~n~G~ksl~EI 60 (66)
T PF03118_consen 7 EELLDTPIEDL-GLSVRAYNCLKR-AGIHTVGDLVKYSEEDLLKIKNFGKKSLEEI 60 (66)
T ss_dssp HHHHCSBGGGS-TSBHHHHHHHHC-TT--BHHHHHCS-HHHHHTSTTSHHHHHHHH
T ss_pred HHHhcCcHHHh-CCCHHHHHHHHH-hCCcCHHHHHhCCHHHHHhCCCCCHhHHHHH
Confidence 45678999999 899999999997 9999999999997 555543 666655444
No 33
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=91.98 E-value=0.27 Score=48.79 Aligned_cols=52 Identities=23% Similarity=0.328 Sum_probs=44.8
Q ss_pred CcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHH--cChhHHHHHHHhccC
Q 009922 124 PIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFLSVGLG 176 (522)
Q Consensus 124 PI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~--FG~~~~~~l~~~a~G 176 (522)
+|.+|+|||++++++|-. .|+.|+.+|...+ ..|.+. +|...+..++..+.+
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 8999999999886 788888 888888888776553
No 34
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=91.43 E-value=0.21 Score=45.27 Aligned_cols=31 Identities=29% Similarity=0.499 Sum_probs=28.8
Q ss_pred CcccccCCChHHHHHHhhhcCCCCHHHHHhch
Q 009922 124 PIRKIGGIGKVTEHILRDVFGINTCEEMLQKG 155 (522)
Q Consensus 124 PI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~ 155 (522)
.|+.|-|||++.+..|+. +||+|..||+.+.
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 578899999999999998 9999999999986
No 35
>PRK02362 ski2-like helicase; Provisional
Probab=89.03 E-value=0.47 Score=55.02 Aligned_cols=52 Identities=21% Similarity=0.353 Sum_probs=45.5
Q ss_pred CCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHHcChhHHHHHHHhcc
Q 009922 123 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHSTADFFLSVGL 175 (522)
Q Consensus 123 LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~FG~~~~~~l~~~a~ 175 (522)
+|+..|||||++.+++|.+ +||+|+.||+... ..|.+.||.+.+..+...+.
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 5777899999999999997 9999999999875 78888899999888876544
No 36
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=83.10 E-value=1.2 Score=35.32 Aligned_cols=43 Identities=26% Similarity=0.451 Sum_probs=26.8
Q ss_pred ccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHH--cChhHHHHHHH
Q 009922 128 IGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFLS 172 (522)
Q Consensus 128 LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~--FG~~~~~~l~~ 172 (522)
|||||.++++.|.+.+| |+..|.+.+ ..|.+. +|+..+..++.
T Consensus 8 I~~VG~~~ak~L~~~f~--sl~~l~~a~~e~L~~i~gIG~~~A~si~~ 53 (64)
T PF12826_consen 8 IPGVGEKTAKLLAKHFG--SLEALMNASVEELSAIPGIGPKIAQSIYE 53 (64)
T ss_dssp STT--HHHHHHHHHCCS--CHHHHCC--HHHHCTSTT--HHHHHHHHH
T ss_pred CCCccHHHHHHHHHHcC--CHHHHHHcCHHHHhccCCcCHHHHHHHHH
Confidence 68999999999987455 888887765 556655 66666655543
No 37
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=82.01 E-value=8.2 Score=44.33 Aligned_cols=54 Identities=19% Similarity=0.274 Sum_probs=41.9
Q ss_pred CCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHH--cChhHHHHHHHhccCC
Q 009922 122 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFLSVGLGL 177 (522)
Q Consensus 122 ~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~--FG~~~~~~l~~~a~G~ 177 (522)
...+.+|||||++..++|-+.|| ++..|.+.+ ..|.+. ++...+..++..+..-
T Consensus 607 ~s~L~~IpGiG~kr~~~LL~~Fg--S~~~i~~As~eel~~v~gi~~~~A~~i~~~~~~~ 663 (691)
T PRK14672 607 VLSFERLPHVGKVRAHRLLAHFG--SFRSLQSATPQDIATAIHIPLTQAHTILHAATRS 663 (691)
T ss_pred ccccccCCCCCHHHHHHHHHHhc--CHHHHHhCCHHHHHhCCCCCHHHHHHHHHHhhcc
Confidence 46788999999999999865354 888888876 788887 7777888887665543
No 38
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=81.99 E-value=1.5 Score=39.38 Aligned_cols=49 Identities=22% Similarity=0.446 Sum_probs=38.3
Q ss_pred HHHHhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHHcCh
Q 009922 115 AVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSH 164 (522)
Q Consensus 115 ~~~~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~FG~ 164 (522)
.+..+...-.+..++|||+..+..|.. .||.|+.+|+..+ ..|...++.
T Consensus 45 ~l~~w~~~AdL~ri~gi~~~~a~LL~~-AGv~Tv~~LA~~~p~~L~~~l~~ 94 (122)
T PF14229_consen 45 NLLKWVNQADLMRIPGIGPQYAELLEH-AGVDTVEELAQRNPQNLHQKLGR 94 (122)
T ss_pred HHHHHHhHHHhhhcCCCCHHHHHHHHH-hCcCcHHHHHhCCHHHHHHHHHH
Confidence 455555555566899999999999997 9999999999976 666665543
No 39
>COG2251 Predicted nuclease (RecB family) [General function prediction only]
Probab=81.83 E-value=1.8 Score=46.89 Aligned_cols=48 Identities=19% Similarity=0.257 Sum_probs=40.8
Q ss_pred HHHHhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHHcC
Q 009922 115 AVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFS 163 (522)
Q Consensus 115 ~~~~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~FG 163 (522)
-..++++.-.|..+|||++...+.|.. .||+|+.+|++.. ..+...+|
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 456788899999999999999999997 9999999999965 55555555
No 40
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=81.39 E-value=1 Score=47.32 Aligned_cols=29 Identities=28% Similarity=0.336 Sum_probs=26.1
Q ss_pred cccccCCChHHHHHHhhhcCCCCHHHHHhc
Q 009922 125 IRKIGGIGKVTEHILRDVFGINTCEEMLQK 154 (522)
Q Consensus 125 I~~LpGIG~kt~~~L~~~lGI~T~gdL~~l 154 (522)
+..|||||++++++|-+ +||+|+.||...
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 56799999999999998 999999999654
No 41
>PRK08609 hypothetical protein; Provisional
Probab=80.72 E-value=1.4 Score=49.78 Aligned_cols=64 Identities=20% Similarity=0.349 Sum_probs=42.7
Q ss_pred CHHHHHHHHHHHHHHHhCCceEEeccCChhHHHHHhhcCCCCcEEEEcCChHHHHHhhcCCCcccccCCChHHHHHHhhh
Q 009922 63 SGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDV 142 (522)
Q Consensus 63 ~~~~lA~~IR~~I~~etGlt~S~GIA~NKllAKLAS~~~KP~G~~vI~~~~~~~~~fL~~LPI~~LpGIG~kt~~~L~~~ 142 (522)
-+..+|..|+.-+ +|| .-..+-+|... +++ .+.+ +..|||||++++.+|-+.
T Consensus 56 IG~~ia~kI~Eil--~tG--------~~~~le~l~~~---------~p~---~~~~------l~~i~GiGpk~a~~l~~~ 107 (570)
T PRK08609 56 IGKGTAEVIQEYR--ETG--------ESSVLQELKKE---------VPE---GLLP------LLKLPGLGGKKIAKLYKE 107 (570)
T ss_pred cCHHHHHHHHHHH--HhC--------ChHHHHHHHhh---------CcH---HHHH------HhcCCCCCHHHHHHHHHH
Confidence 3577888888777 343 23344444442 222 1223 347999999999999755
Q ss_pred cCCCCHHHHHhc
Q 009922 143 FGINTCEEMLQK 154 (522)
Q Consensus 143 lGI~T~gdL~~l 154 (522)
+||+|+.||...
T Consensus 108 lGi~tl~~L~~a 119 (570)
T PRK08609 108 LGVVDKESLKEA 119 (570)
T ss_pred hCCCCHHHHHHH
Confidence 999999999764
No 42
>PRK01172 ski2-like helicase; Provisional
Probab=80.70 E-value=2 Score=49.26 Aligned_cols=50 Identities=20% Similarity=0.365 Sum_probs=40.6
Q ss_pred CCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHH--cChhHHHHHHH
Q 009922 122 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFLS 172 (522)
Q Consensus 122 ~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~--FG~~~~~~l~~ 172 (522)
.+|+..|||+|+..+++|.+ .||+|+.||+... ..+.+. +|...+..+..
T Consensus 611 ~~~L~~ip~~~~~~a~~l~~-~g~~~~~di~~~~~~~~~~i~~~~~~~~~~i~~ 663 (674)
T PRK01172 611 LIDLVLIPKVGRVRARRLYD-AGFKTVDDIARSSPERIKKIYGFSDTLANAIVN 663 (674)
T ss_pred HHhhcCCCCCCHHHHHHHHH-cCCCCHHHHHhCCHHHHHHHhccCHHHHHHHHH
Confidence 46888999999999999997 9999999999986 666666 66665555543
No 43
>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=79.55 E-value=1.9 Score=36.66 Aligned_cols=33 Identities=24% Similarity=0.469 Sum_probs=23.2
Q ss_pred hcCCCcccccCCChHHHHHHhhhcCCCCHHHHHh
Q 009922 120 ISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQ 153 (522)
Q Consensus 120 L~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~ 153 (522)
|..-||+.|+|||+..+.+|.+ -|+.....++.
T Consensus 16 MGeK~V~~laGIG~~lg~~L~~-~GfdKAy~vLG 48 (89)
T PF02961_consen 16 MGEKPVTELAGIGPVLGKRLEE-KGFDKAYVVLG 48 (89)
T ss_dssp -TT-BGGGSTT--HHHHHHHHH-TT--BHHHHHH
T ss_pred cCCCCccccCCcCHHHHHHHHH-CCCcHHHHHhh
Confidence 4567999999999999999997 89999777643
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=79.08 E-value=1.5 Score=45.66 Aligned_cols=29 Identities=28% Similarity=0.536 Sum_probs=25.5
Q ss_pred cccccCCChHHHHHHhhhcCCCCHHHHHhc
Q 009922 125 IRKIGGIGKVTEHILRDVFGINTCEEMLQK 154 (522)
Q Consensus 125 I~~LpGIG~kt~~~L~~~lGI~T~gdL~~l 154 (522)
+..|||||++++++|-+ +||+|+.||...
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 45699999999999995 999999999653
No 45
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=78.93 E-value=1.8 Score=38.83 Aligned_cols=26 Identities=35% Similarity=0.570 Sum_probs=24.0
Q ss_pred cCCChHHHHHHhhhcCCCCHHHHHhch
Q 009922 129 GGIGKVTEHILRDVFGINTCEEMLQKG 155 (522)
Q Consensus 129 pGIG~kt~~~L~~~lGI~T~gdL~~l~ 155 (522)
||||++++.+|++ .||+|.+||+...
T Consensus 1 pgi~~~~~~~L~~-~GI~t~~~Ll~~~ 26 (122)
T PF14229_consen 1 PGIGPKEAAKLKA-AGIKTTGDLLEAG 26 (122)
T ss_pred CCCCHHHHHHHHH-cCCCcHHHHHHcC
Confidence 7999999999997 9999999998863
No 46
>PRK07758 hypothetical protein; Provisional
Probab=77.60 E-value=4.1 Score=35.11 Aligned_cols=44 Identities=14% Similarity=0.169 Sum_probs=34.3
Q ss_pred cccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHH--cChhHHHHHH
Q 009922 127 KIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFL 171 (522)
Q Consensus 127 ~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~--FG~~~~~~l~ 171 (522)
-+|+++-....-|.+ .||+|++||..++ ..|.+. ||++....+.
T Consensus 38 ~~~~LSvRA~N~Lk~-AGI~TL~dLv~~te~ELl~iknlGkKSL~EIk 84 (95)
T PRK07758 38 FLSLLSAPARRALEH-HGIHTVEELSKYSEKEILKLHGMGPASLPKLR 84 (95)
T ss_pred CCccccHHHHHHHHH-cCCCcHHHHHcCCHHHHHHccCCCHHHHHHHH
Confidence 356888888899997 8999999999987 555544 7887766653
No 47
>PRK00254 ski2-like helicase; Provisional
Probab=77.33 E-value=2.7 Score=48.61 Aligned_cols=53 Identities=17% Similarity=0.186 Sum_probs=45.4
Q ss_pred CCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHH--cChhHHHHHHHhcc
Q 009922 122 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFLSVGL 175 (522)
Q Consensus 122 ~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~--FG~~~~~~l~~~a~ 175 (522)
.+|+..|||||++.+++|-+ .|+.|+.|+...+ ..|.+. +|.+.+..++..+.
T Consensus 644 ~~~L~~ipgig~~~~~~l~~-~g~~s~~~i~~a~~~el~~~~gi~~~~a~~i~~~~~ 699 (720)
T PRK00254 644 LLELMRLPMIGRKRARALYN-AGFRSIEDIVNAKPSELLKVEGIGAKIVEGIFKHLG 699 (720)
T ss_pred HhhhhcCCCCCHHHHHHHHH-ccCCCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHhc
Confidence 46788999999999999997 9999999999986 788888 78888888876533
No 48
>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=75.11 E-value=1.5 Score=29.65 Aligned_cols=16 Identities=31% Similarity=0.499 Sum_probs=12.6
Q ss_pred cccccCCChHHHHHHh
Q 009922 125 IRKIGGIGKVTEHILR 140 (522)
Q Consensus 125 I~~LpGIG~kt~~~L~ 140 (522)
+.+|||||++++..+.
T Consensus 13 L~~lpGIG~~tA~~I~ 28 (30)
T PF00633_consen 13 LMKLPGIGPKTANAIL 28 (30)
T ss_dssp HHTSTT-SHHHHHHHH
T ss_pred HHhCCCcCHHHHHHHH
Confidence 5679999999998875
No 49
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=72.54 E-value=2.7 Score=48.43 Aligned_cols=30 Identities=30% Similarity=0.616 Sum_probs=28.0
Q ss_pred CCcccccCCChHHHHHHhhhcCCCCHHHHHh
Q 009922 123 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQ 153 (522)
Q Consensus 123 LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~ 153 (522)
.||..|.|||+++++.|++ +||.|+.||+.
T Consensus 9 ~~~~~l~gvg~~~~~~l~~-lgi~t~~dll~ 38 (681)
T PRK10917 9 APLTSLKGVGPKTAEKLAK-LGIHTVQDLLL 38 (681)
T ss_pred CChhhcCCCCHHHHHHHHH-cCCCCHHHHhh
Confidence 5899999999999999997 99999999976
No 50
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=70.57 E-value=1.8 Score=31.46 Aligned_cols=26 Identities=27% Similarity=0.583 Sum_probs=24.2
Q ss_pred ccccccccCCCCCcHhhhhccccchH
Q 009922 435 YKCSLCGTEMPPSFIEERQEHSDFHL 460 (522)
Q Consensus 435 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 460 (522)
-+|+.||..--|+=.|.+..|.-||=
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 58999999999999999999999993
No 51
>TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Probab=68.18 E-value=5.6 Score=43.61 Aligned_cols=38 Identities=21% Similarity=0.337 Sum_probs=33.1
Q ss_pred HHhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhch
Q 009922 117 MTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG 155 (522)
Q Consensus 117 ~~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~ 155 (522)
......-+|..|+||+++....|++ .||+|+.||++..
T Consensus 201 ~~~~~~~~lslv~gi~~~~~~~L~~-~GI~ti~~La~~~ 238 (457)
T TIGR03491 201 AVAKEEGHLSLVPGIGPSRYRLLQE-LGIHTLEDLAAAD 238 (457)
T ss_pred HHHHhcCCeeecCCCCHHHHHHHHH-cCCCcHHHHhcCC
Confidence 3445577999999999999999997 9999999999875
No 52
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=66.99 E-value=7.7 Score=43.83 Aligned_cols=53 Identities=23% Similarity=0.231 Sum_probs=41.9
Q ss_pred CCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHH-cChhHHHHHHHhccC
Q 009922 122 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV-FSHSTADFFLSVGLG 176 (522)
Q Consensus 122 ~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~-FG~~~~~~l~~~a~G 176 (522)
.-++.+|||||+++.+.|-+ ...|+..+.+.+ ..|.+. +|...+..++....|
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 45789999999999999865 445999998887 788888 667778777766544
No 53
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=66.08 E-value=48 Score=37.69 Aligned_cols=131 Identities=15% Similarity=0.103 Sum_probs=76.0
Q ss_pred hCCCcEEECCChHHHHHHHHHHHHHHHhhCCCEEeeccc-EEEEEcCc-chhh-cCCCHHHHHHHHHHHHHHHhCCceEE
Q 009922 9 LCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLD-EAYLDITE-VCRE-RGISGIEIAEELRTSVYEEAGLTCSA 85 (522)
Q Consensus 9 LCPdLvvvp~d~~~Y~~~s~~i~~il~~~tp~VE~~SiD-EafLDvT~-~~~l-~g~~~~~lA~~IR~~I~~etGlt~S~ 85 (522)
..|||+++..--.....+.+.+ +-+.--.|.|...=-+ +.|+.-.+ ...+ .+..+-.+.++||++++. +
T Consensus 443 ~~Pdli~iDGGkgQl~~a~~vl-~~l~~~~~viglaK~~~~~~~~~~~~~~~l~~~~p~l~~lq~irDEaHr-f------ 514 (581)
T COG0322 443 ELPDLILIDGGKGQLNAAKEVL-KELGLDIPVIGLAKGEEELLLPGPGEEFDLPPNSPALYLLQRIRDEAHR-F------ 514 (581)
T ss_pred CCCCEEEEeCCHHHHHHHHHHH-HHcCCCccEEEEEecCceeEecCCCceecCCCCCHHHHHHHHHHHHHHH-H------
Confidence 4689999887666555544333 2222223544443333 36654331 1111 122356899999999975 2
Q ss_pred eccCChhHHHHHhhcCCCCcEEEEcCChHHHHHhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHH-cC
Q 009922 86 GVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV-FS 163 (522)
Q Consensus 86 GIA~NKllAKLAS~~~KP~G~~vI~~~~~~~~~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~-FG 163 (522)
+|+.++.. -..-+-.-++.+|+|||++..++|=. ...|+..+...+ ..|.+. .+
T Consensus 515 Ai~~hR~~----------------------R~k~~~~s~Ld~I~GiG~~r~~~LL~--~Fgs~~~i~~As~eel~~vgi~ 570 (581)
T COG0322 515 AITYHRKK----------------------RSKAMLQSSLDDIPGIGPKRRKALLK--HFGSLKGIKSASVEELAKVGIS 570 (581)
T ss_pred HHHHHHHH----------------------hhhhhhcCccccCCCcCHHHHHHHHH--HhhCHHHHHhcCHHHHHHcCCC
Confidence 44444431 01123355788999999999998865 444888887766 677777 33
Q ss_pred hhHHHHHH
Q 009922 164 HSTADFFL 171 (522)
Q Consensus 164 ~~~~~~l~ 171 (522)
...+..++
T Consensus 571 ~~~a~~i~ 578 (581)
T COG0322 571 KKLAEKIY 578 (581)
T ss_pred HHHHHHHH
Confidence 34455554
No 54
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=64.75 E-value=4.8 Score=45.92 Aligned_cols=32 Identities=31% Similarity=0.614 Sum_probs=28.9
Q ss_pred CCcccccCCChHHHHHHhhhcCCCCHHHHHh-ch
Q 009922 123 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQ-KG 155 (522)
Q Consensus 123 LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~-l~ 155 (522)
.|+..+.|||++++++|++ +||+|+.||+- +|
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 4899999999999999997 99999999976 35
No 55
>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=63.60 E-value=13 Score=38.09 Aligned_cols=54 Identities=19% Similarity=0.228 Sum_probs=36.3
Q ss_pred CCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHHcC--hhHHHHHHHhccC
Q 009922 122 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFS--HSTADFFLSVGLG 176 (522)
Q Consensus 122 ~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~FG--~~~~~~l~~~a~G 176 (522)
+.|+.-|||||+..+++|.. .||.|+++|.+++ ..+...++ ...+..+...+..
T Consensus 147 ~~~L~Qlp~i~~~~~~~l~~-~~i~~l~~l~~~~~~e~~~ll~~~~~~~~~i~~~~~~ 203 (314)
T PF02889_consen 147 DSPLLQLPHIGEESLKKLEK-RGIKTLQDLRDLSPEELEELLNRNPPFGKEILEVASR 203 (314)
T ss_dssp S-GGGGSTT--HHHHHHHHH-TT--SHHHHHHS-HHHHHHHH-S-HHHHHHHHHHHCC
T ss_pred CChhhcCCCCCHHHHHHHhc-cCCCcHHHHhhCCHHHHHHHHhhhhhhHHHHHHHHHH
Confidence 36899999999999999997 9999999999987 67777765 2345555555444
No 56
>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=62.62 E-value=79 Score=26.80 Aligned_cols=61 Identities=11% Similarity=0.060 Sum_probs=36.4
Q ss_pred HHHHHHHHHhhCCCEEeecccEEEEEcCcchhhcCCCHHHHHHHHHHHHHHHh-----CCceEEeccCC
Q 009922 27 SDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEA-----GLTCSAGVAPN 90 (522)
Q Consensus 27 s~~i~~il~~~tp~VE~~SiDEafLDvT~~~~l~g~~~~~lA~~IR~~I~~et-----Glt~S~GIA~N 90 (522)
.+.+..++..+...+-.++-|++.+=+.+... . ....++.+|++.+.... ++++++|++..
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 33344444454445667788887766664211 1 35678888888875422 56777776644
No 57
>PTZ00035 Rad51 protein; Provisional
Probab=62.20 E-value=7.7 Score=40.91 Aligned_cols=52 Identities=23% Similarity=0.275 Sum_probs=39.8
Q ss_pred CCCcccc--cCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHHcChh--HHHHHHHhc
Q 009922 122 SLPIRKI--GGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHS--TADFFLSVG 174 (522)
Q Consensus 122 ~LPI~~L--pGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~FG~~--~~~~l~~~a 174 (522)
..+|.+| +||++.+.++|++ .||+|+.||+..+ ..|.+..|-. .++.+...+
T Consensus 20 ~~~~~~l~~~g~~~~~~~kL~~-~g~~t~~~~~~~~~~~L~~~~gis~~~~~~i~~~~ 76 (337)
T PTZ00035 20 FQEIEKLQSAGINAADIKKLKE-AGICTVESVAYATKKDLCNIKGISEAKVEKIKEAA 76 (337)
T ss_pred CccHHHHhcCCCCHHHHHHHHH-cCCCcHHHHHhCCHHHHHHhhCCCHHHHHHHHHHH
Confidence 3478888 6799999999997 9999999999987 7788777643 344443333
No 58
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=59.76 E-value=8.9 Score=38.13 Aligned_cols=32 Identities=22% Similarity=0.347 Sum_probs=29.2
Q ss_pred CCcccccCCChHHHHHHhhhcCCCCHHHHHhch
Q 009922 123 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG 155 (522)
Q Consensus 123 LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~ 155 (522)
=.+..|.|||+..+++|+. .||.+..||+.+.
T Consensus 158 DDL~~I~GIGp~~a~~L~e-aGi~tfaQIAa~t 189 (221)
T PRK12278 158 DDLTKITGVGPALAKKLNE-AGVTTFAQIAALT 189 (221)
T ss_pred chheeccccChHHHHHHHH-cCCCCHHHhhCCC
Confidence 3578899999999999997 9999999999986
No 59
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=59.71 E-value=9.3 Score=40.46 Aligned_cols=42 Identities=26% Similarity=0.336 Sum_probs=35.9
Q ss_pred CCCcccc--cCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHHcCh
Q 009922 122 SLPIRKI--GGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSH 164 (522)
Q Consensus 122 ~LPI~~L--pGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~FG~ 164 (522)
..+|.+| .||++.+.++|+. .||+|+.||+..+ ..|.+.-|-
T Consensus 28 ~~~~~~l~~~g~~~~~~~kL~~-~g~~tv~~~~~~~~~~L~~~~g~ 72 (344)
T PLN03187 28 FESIDKLISQGINAGDVKKLQD-AGIYTCNGLMMHTKKNLTGIKGL 72 (344)
T ss_pred ccCHHHHhhCCCCHHHHHHHHH-cCCCcHHHHHhCCHHHHHHhcCC
Confidence 6678888 5799999999997 9999999999887 677777664
No 60
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=57.77 E-value=16 Score=41.80 Aligned_cols=52 Identities=19% Similarity=0.213 Sum_probs=41.9
Q ss_pred CCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHHcChhHHHHHHHhcc
Q 009922 122 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHSTADFFLSVGL 175 (522)
Q Consensus 122 ~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~FG~~~~~~l~~~a~ 175 (522)
.-.+..|||||++++++|-+ -..++..+.+.+ ..|.+.+|.+.+..++....
T Consensus 551 ~S~L~~IpGIG~kr~~~LL~--~FgSi~~I~~As~eeL~~vi~~k~A~~I~~~l~ 603 (624)
T PRK14669 551 TSELLEIPGVGAKTVQRLLK--HFGSLERVRAATETQLAAVVGRAAAEAIIAHFT 603 (624)
T ss_pred HHHHhcCCCCCHHHHHHHHH--HcCCHHHHHhCCHHHHHHHhCHHHHHHHHHHhc
Confidence 35788999999999999865 445899998877 77888899888888876654
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=57.63 E-value=13 Score=43.92 Aligned_cols=49 Identities=16% Similarity=0.198 Sum_probs=41.8
Q ss_pred cccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHHcC-hhHHHHHHHhcc
Q 009922 125 IRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFS-HSTADFFLSVGL 175 (522)
Q Consensus 125 I~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~FG-~~~~~~l~~~a~ 175 (522)
|..|||||++.+.+|-. .+.++.+|++.+ ..|....| .+.|..+|....
T Consensus 759 L~~lPgI~~~~a~~ll~--~f~si~~l~~as~eeL~~~iG~~~~A~~i~~fl~ 809 (814)
T TIGR00596 759 LLKLPGVTKKNYRNLRK--KVKSIRELAKLSQNELNELIGDEEAAKRLYDFLR 809 (814)
T ss_pred HHHCCCCCHHHHHHHHH--HcCCHHHHHhCCHHHHHHHhCCHHHHHHHHHHhc
Confidence 45789999999999975 688999999998 78898899 888888887644
No 62
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=56.39 E-value=11 Score=39.92 Aligned_cols=43 Identities=28% Similarity=0.397 Sum_probs=37.0
Q ss_pred CCCcccc--cCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHHcChh
Q 009922 122 SLPIRKI--GGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHS 165 (522)
Q Consensus 122 ~LPI~~L--pGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~FG~~ 165 (522)
..+|.+| .||++...++|++ .||.|+.|++..+ ..|.+.+|-.
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 4578898 5799999999997 9999999999987 7888888754
No 63
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=55.63 E-value=7.6 Score=25.04 Aligned_cols=17 Identities=29% Similarity=0.477 Sum_probs=14.5
Q ss_pred cccccCCChHHHHHHhh
Q 009922 125 IRKIGGIGKVTEHILRD 141 (522)
Q Consensus 125 I~~LpGIG~kt~~~L~~ 141 (522)
+..+||||++++++|..
T Consensus 3 L~~i~GiG~k~A~~il~ 19 (26)
T smart00278 3 LLKVPGIGPKTAEKILE 19 (26)
T ss_pred hhhCCCCCHHHHHHHHH
Confidence 56799999999999864
No 64
>COG2199 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]
Probab=55.25 E-value=33 Score=31.68 Aligned_cols=63 Identities=17% Similarity=0.035 Sum_probs=45.3
Q ss_pred HHHHHHHHHHHhhCC---CEEeecccEEEEEcCcchhhcCCCHHHHHHHHHHHHHHHh-------CCceEEeccCC
Q 009922 25 YYSDLTRKVFCKYDP---NFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEA-------GLTCSAGVAPN 90 (522)
Q Consensus 25 ~~s~~i~~il~~~tp---~VE~~SiDEafLDvT~~~~l~g~~~~~lA~~IR~~I~~et-------Glt~S~GIA~N 90 (522)
.+...+.+++....+ .+-.++-||+-+=+.+... .....+|++|+..|.... .+++|+||+..
T Consensus 76 ~vL~~va~~L~~~~~~~~~~~R~gGdEF~i~l~~~~~---~~~~~~~~~l~~~~~~~~~~~~~~~~~t~siGi~~~ 148 (181)
T COG2199 76 EVLREVARRLRSNLREGDLVARLGGDEFAVLLPGTSL---EEAARLAERIRAALEEPFFLGGEELRVTVSIGVALY 148 (181)
T ss_pred HHHHHHHHHHHHhcCCCCEEEEeccceeEEEeCCCCH---HHHHHHHHHHHHHHHcccccCCceEEEEEEEEEEec
Confidence 345667777777664 4677888998877776642 147889999988886644 37999998844
No 65
>TIGR02239 recomb_RAD51 DNA repair protein RAD51. This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).
Probab=55.23 E-value=14 Score=38.66 Aligned_cols=35 Identities=23% Similarity=0.246 Sum_probs=30.6
Q ss_pred CCChHHHHHHhhhcCCCCHHHHHhch-HHHHHHcChh
Q 009922 130 GIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHS 165 (522)
Q Consensus 130 GIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~FG~~ 165 (522)
||++.+..+|++ .||.|+.|++..+ ..|.+.+|-.
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 9999999999986 7888888754
No 66
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=54.69 E-value=9.7 Score=40.05 Aligned_cols=31 Identities=23% Similarity=0.381 Sum_probs=28.6
Q ss_pred CcccccCCChHHHHHHhhhcCCCCHHHHHhch
Q 009922 124 PIRKIGGIGKVTEHILRDVFGINTCEEMLQKG 155 (522)
Q Consensus 124 PI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~ 155 (522)
.+++|-|||++.+++|+. +||++..|++.+.
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 478899999999999997 9999999999885
No 67
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=53.80 E-value=12 Score=36.22 Aligned_cols=53 Identities=11% Similarity=0.068 Sum_probs=35.0
Q ss_pred CcccccCCChHHHHHHhhhcCCCCHHHH-Hhch-HHHHHH--cChhHHHHHHHhccC
Q 009922 124 PIRKIGGIGKVTEHILRDVFGINTCEEM-LQKG-SLLCAV--FSHSTADFFLSVGLG 176 (522)
Q Consensus 124 PI~~LpGIG~kt~~~L~~~lGI~T~gdL-~~l~-~~L~~~--FG~~~~~~l~~~a~G 176 (522)
.+..++|||++++.++-+.+|..++.+. .+-+ ..|.+. +|.+.++.+.....+
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 4567999999999987655787665432 2333 567666 677777776544333
No 68
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=53.71 E-value=20 Score=41.44 Aligned_cols=51 Identities=20% Similarity=0.149 Sum_probs=39.0
Q ss_pred cCCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHH--HcChhHHHHHH
Q 009922 121 SSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCA--VFSHSTADFFL 171 (522)
Q Consensus 121 ~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~--~FG~~~~~~l~ 171 (522)
.+-..-+|+|+|+++.++|-+..+|+++.||..+. ..|.. .||.+.+..++
T Consensus 443 ~sr~al~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~ll 496 (665)
T PRK07956 443 VSRNAMDIDGLGEKIIEQLFEKGLIHDPADLFKLTAEDLLGLEGFGEKSAQNLL 496 (665)
T ss_pred hcccccCCCCcCHHHHHHHHHcCCCCCHHHHHhcCHHHHhcCcCcchHHHHHHH
Confidence 34445678999999999998767899999999876 55554 48887766553
No 69
>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=53.11 E-value=21 Score=41.50 Aligned_cols=48 Identities=21% Similarity=0.396 Sum_probs=35.1
Q ss_pred EcCChHHHHHhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhchHHHH
Q 009922 109 LPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLC 159 (522)
Q Consensus 109 I~~~~~~~~~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~~~L~ 159 (522)
+|+..+.+..||+ =+.++|||++++++|-+.||..++.-|.+-|..|.
T Consensus 73 ~p~~~~~i~~yL~---s~~~~GIG~~~A~~iv~~fg~~~~~~i~~~~~~L~ 120 (720)
T TIGR01448 73 APTSKEGIVAYLS---SRSIKGVGKKLAQRIVKTFGEAAFDVLDDDPEKLL 120 (720)
T ss_pred CCCCHHHHHHHHh---cCCCCCcCHHHHHHHHHHhCHhHHHHHHhCHHHHh
Confidence 4455456777887 34689999999999987799888877765554444
No 70
>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1. This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.
Probab=52.00 E-value=17 Score=37.97 Aligned_cols=38 Identities=24% Similarity=0.365 Sum_probs=31.6
Q ss_pred ccc--cCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHHcCh
Q 009922 126 RKI--GGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSH 164 (522)
Q Consensus 126 ~~L--pGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~FG~ 164 (522)
.+| .||++.+.++|++ .||.|+.|++..+ ..|.+..|-
T Consensus 2 ~~~~~~g~~~~~~~~L~~-~g~~t~~~~~~~~~~~L~~~~gl 42 (313)
T TIGR02238 2 DKLQAHGINAADIKKLKS-AGICTVNGVIMTTRRALCKIKGL 42 (313)
T ss_pred chhhcCCCCHHHHHHHHH-cCCCcHHHHHhCCHHHHHHhcCC
Confidence 445 4699999999997 9999999999986 678877663
No 71
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=50.88 E-value=22 Score=40.36 Aligned_cols=50 Identities=20% Similarity=0.260 Sum_probs=38.7
Q ss_pred CCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHH--cChhHHHHHHHh
Q 009922 122 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFLSV 173 (522)
Q Consensus 122 ~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~--FG~~~~~~l~~~ 173 (522)
...+.+|||||+++.+.|=+.|| |+..+.+.+ ..|.+. ++...+..++..
T Consensus 513 ~s~L~~I~GiG~kr~~~LL~~Fg--s~~~I~~As~eeL~~v~gi~~~~A~~I~~~ 565 (574)
T PRK14670 513 KLNYTKIKGIGEKKAKKILKSLG--TYKDILLLNEDEIAEKMKINIKMAKKIKKF 565 (574)
T ss_pred ccccccCCCCCHHHHHHHHHHhC--CHHHHHhCCHHHHHhCCCCCHHHHHHHHHH
Confidence 45889999999999998865354 888888877 788887 666677766544
No 72
>PRK14973 DNA topoisomerase I; Provisional
Probab=49.49 E-value=30 Score=41.55 Aligned_cols=76 Identities=13% Similarity=0.126 Sum_probs=48.6
Q ss_pred HHHHHh-hcCCCCcEEEEcCChHHHHHhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHHcC--hhHHH
Q 009922 93 LAKVCS-DINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFS--HSTAD 168 (522)
Q Consensus 93 lAKLAS-~~~KP~G~~vI~~~~~~~~~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~FG--~~~~~ 168 (522)
++.+|+ ++.+|+-..+..- +.--..-++..|+|+|++|.++|.. .||.++.||++.+ ..|.+.=| .+..+
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 345666 7777765433210 0011222377889999999999997 9999999999886 66666544 33444
Q ss_pred HHHHhc
Q 009922 169 FFLSVG 174 (522)
Q Consensus 169 ~l~~~a 174 (522)
.+..++
T Consensus 925 ~~~~~~ 930 (936)
T PRK14973 925 NLQAYA 930 (936)
T ss_pred HHHHHH
Confidence 444443
No 73
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=49.41 E-value=6.8 Score=33.93 Aligned_cols=34 Identities=44% Similarity=0.858 Sum_probs=25.2
Q ss_pred ecCccccccccCCCCCcH-----------------hhhhccccchHHHHhhhhhcc
Q 009922 432 LDDYKCSLCGTEMPPSFI-----------------EERQEHSDFHLAERLQKEESG 470 (522)
Q Consensus 432 ~~~~~~~~~~~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~~~ 470 (522)
+....|.-||.||+|-|+ .|.-|| |+|+-|-|-+
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 74
>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=49.06 E-value=27 Score=40.17 Aligned_cols=51 Identities=18% Similarity=0.160 Sum_probs=38.5
Q ss_pred cCCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHH--HcChhHHHHHH
Q 009922 121 SSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCA--VFSHSTADFFL 171 (522)
Q Consensus 121 ~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~--~FG~~~~~~l~ 171 (522)
.+-.--+|+|+|+++.++|-+..+|+++.||..+. ..|.. .||.+.+..++
T Consensus 430 ~sr~al~I~GLG~k~i~~L~~~g~I~~~~Dl~~L~~~~L~~L~GfG~Ksa~nIl 483 (652)
T TIGR00575 430 ASRNAMDIEGLGDKVIEQLFEKKLVRSVADLYALKKEDLLELEGFGEKSAQNLL 483 (652)
T ss_pred hcCCccCCCCcCHHHHHHHHHcCCcCCHHHHHhcCHHHHhhccCccHHHHHHHH
Confidence 34455678999999999998756789999999876 55554 37877766554
No 75
>PRK03922 hypothetical protein; Provisional
Probab=49.05 E-value=6.7 Score=34.56 Aligned_cols=43 Identities=33% Similarity=0.591 Sum_probs=32.9
Q ss_pred ecCccccccccCCCCCcH-----------------hhhhccccchHHHHhhhhhccCcccccccc
Q 009922 432 LDDYKCSLCGTEMPPSFI-----------------EERQEHSDFHLAERLQKEESGSDLRILTHR 479 (522)
Q Consensus 432 ~~~~~~~~~~~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 479 (522)
+....|.-||.+++|-|+ .|+-|| |+|+-|-|-+-..+.+|-+
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 7888888776666666654
No 76
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=48.29 E-value=24 Score=36.21 Aligned_cols=52 Identities=10% Similarity=0.075 Sum_probs=39.6
Q ss_pred CCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHHcCh--hHHHHHHHhc
Q 009922 122 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSH--STADFFLSVG 174 (522)
Q Consensus 122 ~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~FG~--~~~~~l~~~a 174 (522)
..|+.-||+||+..+++|.+ .|+.+++||...+ ..+...+|. ..+..+...+
T Consensus 150 ~~~L~Qlp~i~~~~~~~l~~-~~i~s~~~l~~~~~~~~~~ll~~~~~~~~~i~~~~ 204 (312)
T smart00611 150 DSPLLQLPHLPEEILKRLEK-KKVLSLEDLLELEDEERGELLGLLDAEGERVYKVL 204 (312)
T ss_pred CCccccCCCCCHHHHHHHHh-CCCCCHHHHHhcCHHHHHHHHcCCHHHHHHHHHHH
Confidence 46899999999999999997 8999999999987 556655543 3344444443
No 77
>KOG3014 consensus Protein involved in establishing cohesion between sister chromatids during DNA replication [Replication, recombination and repair]
Probab=47.26 E-value=7.6 Score=39.10 Aligned_cols=29 Identities=28% Similarity=0.432 Sum_probs=26.3
Q ss_pred ccccccccCCCCCcHhhhhccccchHHHH
Q 009922 435 YKCSLCGTEMPPSFIEERQEHSDFHLAER 463 (522)
Q Consensus 435 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 463 (522)
-+|.-||-.--++=+|++.+|..||=+.+
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 78
>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=47.03 E-value=23 Score=36.71 Aligned_cols=51 Identities=20% Similarity=0.270 Sum_probs=40.4
Q ss_pred hcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHH--HHcChhHHHHHHH
Q 009922 120 ISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLC--AVFSHSTADFFLS 172 (522)
Q Consensus 120 L~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~--~~FG~~~~~~l~~ 172 (522)
+..+||.+| ++.-++..-|++ .||.|++||.+++ ..|. +-||++..+.+.+
T Consensus 232 ~~~~~I~~L-~LSvR~~n~Lk~-~~I~ti~dL~~~~~~~l~~~~n~G~ksl~ei~~ 285 (297)
T TIGR02027 232 LLSIKIEEL-DLSVRSYNCLKR-AGIHTLGELVSKSEEELLKIKNFGKKSLTEIKE 285 (297)
T ss_pred hccccHHHh-CccHHHHhHHHH-cCCcCHHHHHhCCHHHHhhCCCCChhhHHHHHH
Confidence 567899999 799999999997 9999999999987 4444 3388877665543
No 79
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=46.88 E-value=27 Score=40.02 Aligned_cols=49 Identities=24% Similarity=0.314 Sum_probs=39.5
Q ss_pred CCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHHcChhHHHHHHHh
Q 009922 123 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHSTADFFLSV 173 (522)
Q Consensus 123 LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~FG~~~~~~l~~~ 173 (522)
..+..|+|||++++..|-+ .+.|+.+|.+.+ ..|.+.+|...+..++..
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 4678899999999999976 455889998877 677777999888877543
No 80
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=46.87 E-value=23 Score=37.05 Aligned_cols=50 Identities=20% Similarity=0.270 Sum_probs=39.8
Q ss_pred hcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHH--HcChhHHHHHH
Q 009922 120 ISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCA--VFSHSTADFFL 171 (522)
Q Consensus 120 L~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~--~FG~~~~~~l~ 171 (522)
+..+||.+| ++.-++..-|++ .||+|++||.+++ ..|.+ -||.+..+.+.
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 347899999 899999999997 9999999999987 55543 37877665553
No 81
>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=45.65 E-value=25 Score=27.90 Aligned_cols=43 Identities=16% Similarity=0.285 Sum_probs=28.6
Q ss_pred Cccc-ccCCChHHHHHHhhh---c-CCCCHHHHHhchHHHHHHcChhHHHHHH
Q 009922 124 PIRK-IGGIGKVTEHILRDV---F-GINTCEEMLQKGSLLCAVFSHSTADFFL 171 (522)
Q Consensus 124 PI~~-LpGIG~kt~~~L~~~---l-GI~T~gdL~~l~~~L~~~FG~~~~~~l~ 171 (522)
++.. +||||.+.+++|-+. . ++.+..||.+.+ -||.+.++.+.
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 4556 899999998888652 3 488888886653 14455555443
No 82
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=43.83 E-value=21 Score=38.56 Aligned_cols=31 Identities=26% Similarity=0.441 Sum_probs=28.6
Q ss_pred CcccccCCChHHHHHHhhhcCCCCHHHHHhch
Q 009922 124 PIRKIGGIGKVTEHILRDVFGINTCEEMLQKG 155 (522)
Q Consensus 124 PI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~ 155 (522)
.++.|.|||++++++|+. +||.+..|++.+.
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 83
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=43.33 E-value=20 Score=32.75 Aligned_cols=29 Identities=14% Similarity=0.185 Sum_probs=24.8
Q ss_pred ccccCCChHHHHHHhhhcC-CCCHHHHHhch
Q 009922 126 RKIGGIGKVTEHILRDVFG-INTCEEMLQKG 155 (522)
Q Consensus 126 ~~LpGIG~kt~~~L~~~lG-I~T~gdL~~l~ 155 (522)
..+||||++.++++-. .| ..++.||.+.+
T Consensus 64 ~~lpGigP~~A~~IV~-nGpf~sveDL~~V~ 93 (132)
T PRK02515 64 RQFPGMYPTLAGKIVK-NAPYDSVEDVLNLP 93 (132)
T ss_pred HHCCCCCHHHHHHHHH-CCCCCCHHHHHcCC
Confidence 4589999999999986 55 89999998876
No 84
>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=42.84 E-value=7.3 Score=23.46 Aligned_cols=12 Identities=25% Similarity=1.132 Sum_probs=8.1
Q ss_pred ccccccccCCCC
Q 009922 435 YKCSLCGTEMPP 446 (522)
Q Consensus 435 ~~~~~~~~~~~~ 446 (522)
|+|.+||...+-
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 85
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=42.52 E-value=9.2 Score=39.55 Aligned_cols=17 Identities=53% Similarity=1.323 Sum_probs=15.8
Q ss_pred eeecCc--cccccccCCCC
Q 009922 430 IWLDDY--KCSLCGTEMPP 446 (522)
Q Consensus 430 ~~~~~~--~~~~~~~~~~~ 446 (522)
-|++|| +|..|-.++||
T Consensus 355 kW~~~y~~~CPvCrt~iPP 373 (374)
T COG5540 355 KWLLGYSNKCPVCRTAIPP 373 (374)
T ss_pred HHHhhhcccCCccCCCCCC
Confidence 599999 59999999999
No 86
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=42.51 E-value=31 Score=39.84 Aligned_cols=49 Identities=27% Similarity=0.432 Sum_probs=37.9
Q ss_pred CCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHH--cChhHHHHHHH
Q 009922 122 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFLS 172 (522)
Q Consensus 122 ~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~--FG~~~~~~l~~ 172 (522)
.-.+..|||||++++++|-+.|| ++.++.+.+ ..|.+. +|...+..++.
T Consensus 636 ~s~L~~IPGIGpkr~k~LL~~FG--Sle~I~~AS~eELa~V~Gig~k~Ae~I~~ 687 (694)
T PRK14666 636 TGELQRVEGIGPATARLLWERFG--SLQAMAAAGEEGLAAVPGIGPARAAALHE 687 (694)
T ss_pred HhHHhhCCCCCHHHHHHHHHHhC--CHHHHHhcCHHHHHhcCCcCHHHHHHHHH
Confidence 35788999999999999876567 999998876 677776 67776666654
No 87
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=42.34 E-value=29 Score=36.36 Aligned_cols=32 Identities=25% Similarity=0.242 Sum_probs=27.3
Q ss_pred cccccCCChHHHHHHhhhcCCCCHHHHHhchHH
Q 009922 125 IRKIGGIGKVTEHILRDVFGINTCEEMLQKGSL 157 (522)
Q Consensus 125 I~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~~~ 157 (522)
.+.++|||.+++++--+ .|++|+.|++.-|..
T Consensus 99 FtnifGvG~ktA~~Wy~-~GfrTled~Rk~~~k 130 (353)
T KOG2534|consen 99 FTNIFGVGLKTAEKWYR-EGFRTLEDVRKKPDK 130 (353)
T ss_pred HHHHhccCHHHHHHHHH-hhhhHHHHHHhCHHH
Confidence 35689999999999997 999999999966643
No 88
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=41.81 E-value=13 Score=36.31 Aligned_cols=16 Identities=31% Similarity=0.594 Sum_probs=14.8
Q ss_pred cccccCCChHHHHHHh
Q 009922 125 IRKIGGIGKVTEHILR 140 (522)
Q Consensus 125 I~~LpGIG~kt~~~L~ 140 (522)
+++|||||+++++||.
T Consensus 13 l~~LPGIG~KsA~RlA 28 (195)
T TIGR00615 13 LKKLPGIGPKSAQRLA 28 (195)
T ss_pred HHHCCCCCHHHHHHHH
Confidence 6789999999999996
No 89
>PRK00076 recR recombination protein RecR; Reviewed
Probab=41.13 E-value=13 Score=36.24 Aligned_cols=16 Identities=38% Similarity=0.636 Sum_probs=14.8
Q ss_pred cccccCCChHHHHHHh
Q 009922 125 IRKIGGIGKVTEHILR 140 (522)
Q Consensus 125 I~~LpGIG~kt~~~L~ 140 (522)
++.|||||+++|+||.
T Consensus 13 l~~LPGIG~KsA~Rla 28 (196)
T PRK00076 13 LRKLPGIGPKSAQRLA 28 (196)
T ss_pred HHHCCCCCHHHHHHHH
Confidence 6789999999999997
No 90
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=40.86 E-value=33 Score=39.08 Aligned_cols=50 Identities=18% Similarity=0.250 Sum_probs=39.2
Q ss_pred CCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHH--cChhHHHHHHHh
Q 009922 122 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFLSV 173 (522)
Q Consensus 122 ~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~--FG~~~~~~l~~~ 173 (522)
..++..|||||++++++|-+ ...++..+.+.+ ..|.+. +|...+..++.+
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 46789999999999999976 445788988877 678877 777777766544
No 91
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=40.81 E-value=14 Score=35.64 Aligned_cols=17 Identities=24% Similarity=0.460 Sum_probs=14.4
Q ss_pred CcccccCCChHHHHHHh
Q 009922 124 PIRKIGGIGKVTEHILR 140 (522)
Q Consensus 124 PI~~LpGIG~kt~~~L~ 140 (522)
-+.++||||+||++|+-
T Consensus 109 ~L~~vpGIGkKtAeRIi 125 (183)
T PRK14601 109 VLKKVPGIGPKSAKRII 125 (183)
T ss_pred HHhhCCCCCHHHHHHHH
Confidence 36778999999999974
No 92
>COG4071 Uncharacterized protein conserved in archaea [Function unknown]
Probab=40.64 E-value=57 Score=32.35 Aligned_cols=57 Identities=23% Similarity=0.176 Sum_probs=42.0
Q ss_pred EEeecccEEEEEcCcchhhcC----CCHHHHHHHHHHHHHHHhCCceEEeccCChhHHHHHhh
Q 009922 41 FMAASLDEAYLDITEVCRERG----ISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSD 99 (522)
Q Consensus 41 VE~~SiDEafLDvT~~~~l~g----~~~~~lA~~IR~~I~~etGlt~S~GIA~NKllAKLAS~ 99 (522)
.+++| |+=+|+|.....+. -++..+|++|+.+|++++|..+++=|+++--.=.+...
T Consensus 117 LkP~s--EaG~Dl~NVPGtya~plPenp~~vA~el~~Ei~rr~GvDV~v~v~DTDaTY~iLg~ 177 (278)
T COG4071 117 LKPYS--EAGVDLTNVPGTYACPLPENPKKVAEELYKEIKRRLGVDVVVMVADTDATYRILGF 177 (278)
T ss_pred cCchh--hcCccccCCCcceeccCCCChHHHHHHHHHHHHHHhCCceEEEEecCchHHHHHHH
Confidence 34455 67778887644331 15899999999999999999999999998655444433
No 93
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=39.12 E-value=45 Score=38.71 Aligned_cols=51 Identities=18% Similarity=0.242 Sum_probs=38.1
Q ss_pred cCCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHH--cChhHHHHHH
Q 009922 121 SSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFL 171 (522)
Q Consensus 121 ~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~--FG~~~~~~l~ 171 (522)
..-..-+|.|+|+++.++|-+..+|+++.||..+. ..|... ||.+.+..++
T Consensus 460 ~sr~al~I~GLG~k~i~~L~~~g~V~~~~Dl~~L~~~~L~~l~g~g~Ksa~~Ll 513 (689)
T PRK14351 460 ASRDALDIEGLGEERVQQLVDAGLVESLADLYDLTVADLAELEGWGETSAENLL 513 (689)
T ss_pred hcccccCCCCcCHHHHHHHHHcCCCCCHHHHHHcCHHHHhcCcCcchhHHHHHH
Confidence 34455678999999999998744579999999986 556553 7887766553
No 94
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=39.10 E-value=10 Score=29.13 Aligned_cols=25 Identities=28% Similarity=0.525 Sum_probs=19.6
Q ss_pred CcceeecCccccccccCCCCCcHhh
Q 009922 427 DQFIWLDDYKCSLCGTEMPPSFIEE 451 (522)
Q Consensus 427 ~~~~~~~~~~~~~~~~~~~~~~~~~ 451 (522)
..+-=|++-.|+-|+.+|||....+
T Consensus 15 ~~va~v~~~~C~gC~~~l~~~~~~~ 39 (56)
T PF02591_consen 15 VAVARVEGGTCSGCHMELPPQELNE 39 (56)
T ss_pred cEEEEeeCCccCCCCEEcCHHHHHH
Confidence 3445577889999999999987654
No 95
>PRK13844 recombination protein RecR; Provisional
Probab=38.82 E-value=15 Score=35.96 Aligned_cols=16 Identities=38% Similarity=0.559 Sum_probs=14.8
Q ss_pred cccccCCChHHHHHHh
Q 009922 125 IRKIGGIGKVTEHILR 140 (522)
Q Consensus 125 I~~LpGIG~kt~~~L~ 140 (522)
++.|||||+++++||.
T Consensus 17 l~~LPGIG~KsA~Rla 32 (200)
T PRK13844 17 LRKLPTIGKKSSQRLA 32 (200)
T ss_pred HHHCCCCCHHHHHHHH
Confidence 6789999999999997
No 96
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=36.99 E-value=18 Score=35.08 Aligned_cols=17 Identities=29% Similarity=0.378 Sum_probs=14.6
Q ss_pred CcccccCCChHHHHHHh
Q 009922 124 PIRKIGGIGKVTEHILR 140 (522)
Q Consensus 124 PI~~LpGIG~kt~~~L~ 140 (522)
-+..+||||++|+++|-
T Consensus 109 ~L~~vpGIGkKtAerIi 125 (188)
T PRK14606 109 GLSKLPGISKKTAERIV 125 (188)
T ss_pred HHhhCCCCCHHHHHHHH
Confidence 36778999999999974
No 97
>COG2062 SixA Phosphohistidine phosphatase SixA [Signal transduction mechanisms]
Probab=36.47 E-value=1.8e+02 Score=27.53 Aligned_cols=76 Identities=14% Similarity=0.104 Sum_probs=52.1
Q ss_pred CCCcEEECCChHHHHHHHHHHHHHHHhhCCCEEeecccEEEEEcCcchhhcCCCHHHHHHHHHHHHHHHhCCceEEeccC
Q 009922 10 CPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAP 89 (522)
Q Consensus 10 CPdLvvvp~d~~~Y~~~s~~i~~il~~~tp~VE~~SiDEafLDvT~~~~l~g~~~~~lA~~IR~~I~~etGlt~S~GIA~ 89 (522)
-||++++.+ |.++.+....+...+.+ ...+.|-+++- +.++..+...|+... + ++.+-.=||+
T Consensus 47 ~~D~VL~Sp----a~Ra~QTae~v~~~~~~-----~~~~~~~~l~p-----~~d~~~~l~~l~~~~-d--~v~~vllVgH 109 (163)
T COG2062 47 EPDLVLVSP----AVRARQTAEIVAEHLGE-----KKVEVFEELLP-----NGDPGTVLDYLEALG-D--GVGSVLLVGH 109 (163)
T ss_pred CCCEEEeCh----hHHHHHHHHHHHHhhCc-----ccceeccccCC-----CCCHHHHHHHHHHhc-c--cCceEEEECC
Confidence 378888874 55655544445555542 23466666663 337888888887765 3 6888888999
Q ss_pred ChhHHHHHhhcCC
Q 009922 90 NRLLAKVCSDINK 102 (522)
Q Consensus 90 NKllAKLAS~~~K 102 (522)
|+.++-||..++-
T Consensus 110 ~P~l~~l~~~L~~ 122 (163)
T COG2062 110 NPLLEELALLLAG 122 (163)
T ss_pred CccHHHHHHHHcc
Confidence 9999999988643
No 98
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=36.37 E-value=18 Score=35.31 Aligned_cols=17 Identities=29% Similarity=0.364 Sum_probs=14.6
Q ss_pred CcccccCCChHHHHHHh
Q 009922 124 PIRKIGGIGKVTEHILR 140 (522)
Q Consensus 124 PI~~LpGIG~kt~~~L~ 140 (522)
.+..+||||++||+|+-
T Consensus 108 ~L~~vpGIGkKtAeRII 124 (196)
T PRK13901 108 LISKVKGIGNKMAGKIF 124 (196)
T ss_pred HHhhCCCCCHHHHHHHH
Confidence 36788999999999974
No 99
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=36.33 E-value=17 Score=35.41 Aligned_cols=16 Identities=25% Similarity=0.576 Sum_probs=14.7
Q ss_pred cccccCCChHHHHHHh
Q 009922 125 IRKIGGIGKVTEHILR 140 (522)
Q Consensus 125 I~~LpGIG~kt~~~L~ 140 (522)
+++|||||+++|+|++
T Consensus 14 l~kLPGvG~KsA~R~A 29 (198)
T COG0353 14 LKKLPGVGPKSAQRLA 29 (198)
T ss_pred HhhCCCCChhHHHHHH
Confidence 6789999999999996
No 100
>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=35.42 E-value=22 Score=28.27 Aligned_cols=18 Identities=28% Similarity=0.588 Sum_probs=15.5
Q ss_pred CcccccCCChHHHHHHhh
Q 009922 124 PIRKIGGIGKVTEHILRD 141 (522)
Q Consensus 124 PI~~LpGIG~kt~~~L~~ 141 (522)
-+..|||||++++.++.+
T Consensus 48 ~~~~l~gIG~~ia~kI~E 65 (68)
T PF14716_consen 48 DLKKLPGIGKSIAKKIDE 65 (68)
T ss_dssp HHCTSTTTTHHHHHHHHH
T ss_pred HHhhCCCCCHHHHHHHHH
Confidence 368899999999999875
No 101
>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=35.27 E-value=44 Score=29.88 Aligned_cols=30 Identities=10% Similarity=0.346 Sum_probs=22.2
Q ss_pred cccccCCChHHHHHHhhhc----CCCCHHHHHhc
Q 009922 125 IRKIGGIGKVTEHILRDVF----GINTCEEMLQK 154 (522)
Q Consensus 125 I~~LpGIG~kt~~~L~~~l----GI~T~gdL~~l 154 (522)
+..|||||+++++++-+.. ++.++.||.+.
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 4568999999999886522 46777787655
No 102
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=34.81 E-value=20 Score=34.91 Aligned_cols=17 Identities=29% Similarity=0.501 Sum_probs=14.6
Q ss_pred CcccccCCChHHHHHHh
Q 009922 124 PIRKIGGIGKVTEHILR 140 (522)
Q Consensus 124 PI~~LpGIG~kt~~~L~ 140 (522)
-+.++||||++|++|+-
T Consensus 109 ~L~kvpGIGkKtAerIi 125 (195)
T PRK14604 109 RLARVPGIGKKTAERIV 125 (195)
T ss_pred HHhhCCCCCHHHHHHHH
Confidence 36778999999999985
No 103
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=34.14 E-value=21 Score=34.92 Aligned_cols=16 Identities=31% Similarity=0.596 Sum_probs=14.3
Q ss_pred cccccCCChHHHHHHh
Q 009922 125 IRKIGGIGKVTEHILR 140 (522)
Q Consensus 125 I~~LpGIG~kt~~~L~ 140 (522)
+..+||||++|++++-
T Consensus 111 L~~ipGIGkKtAerIi 126 (203)
T PRK14602 111 LTRVSGIGKKTAQHIF 126 (203)
T ss_pred HhcCCCcCHHHHHHHH
Confidence 6788999999999985
No 104
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=33.84 E-value=21 Score=34.77 Aligned_cols=17 Identities=18% Similarity=0.329 Sum_probs=14.7
Q ss_pred CcccccCCChHHHHHHh
Q 009922 124 PIRKIGGIGKVTEHILR 140 (522)
Q Consensus 124 PI~~LpGIG~kt~~~L~ 140 (522)
-+.++||||++|++++-
T Consensus 108 ~L~kvpGIGkKtAerIi 124 (197)
T PRK14603 108 LLTSASGVGKKLAERIA 124 (197)
T ss_pred HHhhCCCCCHHHHHHHH
Confidence 36788999999999985
No 105
>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=32.73 E-value=58 Score=23.69 Aligned_cols=32 Identities=19% Similarity=0.231 Sum_probs=25.5
Q ss_pred CChHHHHHHhhhcCCCCHHHHHhch-HHHHHHcC
Q 009922 131 IGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFS 163 (522)
Q Consensus 131 IG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~FG 163 (522)
|...++.+|.. .|+.|+.+|+..+ ..|...-|
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 35678889987 8999999999986 66776644
No 106
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=32.20 E-value=18 Score=31.67 Aligned_cols=43 Identities=33% Similarity=0.648 Sum_probs=33.8
Q ss_pred ecCccccccccCCCCCcH-----------------hhhhccccchHHHHhhhhhccCcccccccc
Q 009922 432 LDDYKCSLCGTEMPPSFI-----------------EERQEHSDFHLAERLQKEESGSDLRILTHR 479 (522)
Q Consensus 432 ~~~~~~~~~~~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 479 (522)
+-.++|.-||..+-+-|+ .|+.|| |+|+-|-|-+-..+.+|-+
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 107
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=31.80 E-value=25 Score=34.50 Aligned_cols=43 Identities=30% Similarity=0.416 Sum_probs=27.6
Q ss_pred eccCChhHHHHHhhcCCCCcEEEEcCChHHHHHhhcCC---CcccccCCChHHHHHHh
Q 009922 86 GVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSL---PIRKIGGIGKVTEHILR 140 (522)
Q Consensus 86 GIA~NKllAKLAS~~~KP~G~~vI~~~~~~~~~fL~~L---PI~~LpGIG~kt~~~L~ 140 (522)
|||+.--||=|++.- |+ +..+.+..- -+.++||||++++++|-
T Consensus 80 GIGpK~ALaiLs~~~--~~----------~l~~aI~~~d~~~L~k~PGIGkKtAeriv 125 (201)
T COG0632 80 GIGPKLALAILSNLD--PE----------ELAQAIANEDVKALSKIPGIGKKTAERIV 125 (201)
T ss_pred CccHHHHHHHHcCCC--HH----------HHHHHHHhcChHhhhcCCCCCHHHHHHHH
Confidence 888877777666521 11 233333332 36789999999999985
No 108
>PRK05752 uroporphyrinogen-III synthase; Validated
Probab=31.47 E-value=1.2e+02 Score=30.14 Aligned_cols=79 Identities=22% Similarity=0.290 Sum_probs=46.1
Q ss_pred HHHHHHHHHHHHHHHhCCceEE-------eccCChhHHHHHhhcCCCCcEEEEcCChHHHHHhhcCC-------Cccccc
Q 009922 64 GIEIAEELRTSVYEEAGLTCSA-------GVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSL-------PIRKIG 129 (522)
Q Consensus 64 ~~~lA~~IR~~I~~etGlt~S~-------GIA~NKllAKLAS~~~KP~G~~vI~~~~~~~~~fL~~L-------PI~~Lp 129 (522)
+..-+.++.+.+ ++.|..+-. -...+.-+.....++..-+.+.+..+. .++.|+..+ +-..+.
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 456866544 233333333444445555666556553 566664322 112455
Q ss_pred CCChHHHHHHhhhcCCC
Q 009922 130 GIGKVTEHILRDVFGIN 146 (522)
Q Consensus 130 GIG~kt~~~L~~~lGI~ 146 (522)
.||++|++.|++ +|+.
T Consensus 88 aVG~~Ta~al~~-~G~~ 103 (255)
T PRK05752 88 SVGAATAAILQD-YGLD 103 (255)
T ss_pred EECHHHHHHHHH-cCCC
Confidence 899999999997 8985
No 109
>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=31.38 E-value=15 Score=29.97 Aligned_cols=14 Identities=36% Similarity=0.705 Sum_probs=9.6
Q ss_pred CccccccccCCCCC
Q 009922 434 DYKCSLCGTEMPPS 447 (522)
Q Consensus 434 ~~~~~~~~~~~~~~ 447 (522)
-++|+.||.+++|+
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 110
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=31.22 E-value=22 Score=28.60 Aligned_cols=13 Identities=38% Similarity=1.065 Sum_probs=12.0
Q ss_pred ccccccccCCCCC
Q 009922 435 YKCSLCGTEMPPS 447 (522)
Q Consensus 435 ~~~~~~~~~~~~~ 447 (522)
..||-||.+++|+
T Consensus 4 ~~CsFcG~~I~PG 16 (66)
T COG2075 4 RVCSFCGKKIEPG 16 (66)
T ss_pred eEecCcCCccCCC
Confidence 5799999999998
No 111
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=30.27 E-value=58 Score=34.34 Aligned_cols=53 Identities=17% Similarity=0.199 Sum_probs=41.4
Q ss_pred hhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHH--HHcChhHHHHHHHh
Q 009922 119 FISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLC--AVFSHSTADFFLSV 173 (522)
Q Consensus 119 fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~--~~FG~~~~~~l~~~ 173 (522)
.+..++|.+| .+.-+...-|++ .||.|++||.+.. ..|. +-||.+..+.+.+.
T Consensus 259 ~~~~~~Ie~L-~LSvRs~NcLk~-a~I~ti~dL~~~s~~dLl~ikN~GkKSl~EI~~~ 314 (327)
T CHL00013 259 ALKQIFIEQL-ELSVRAYNCLKR-ANIHTLLDLLNYSQEDLLKIKNFGQKSAKEVLEA 314 (327)
T ss_pred hhhceeHHhc-cCchhhhhhhhh-cCccCHHHHHhcCHHHHhhhhccCHhHHHHHHHH
Confidence 4667889999 788888889997 9999999999987 4443 44899876665443
No 112
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=30.23 E-value=28 Score=33.70 Aligned_cols=15 Identities=27% Similarity=0.476 Sum_probs=13.2
Q ss_pred cccccCCChHHHHHHh
Q 009922 125 IRKIGGIGKVTEHILR 140 (522)
Q Consensus 125 I~~LpGIG~kt~~~L~ 140 (522)
+ ++||||++|++++-
T Consensus 110 L-~vpGIGkKtAerIi 124 (186)
T PRK14600 110 L-KVNGIGEKLINRII 124 (186)
T ss_pred e-ECCCCcHHHHHHHH
Confidence 5 68999999999974
No 113
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=29.50 E-value=27 Score=22.11 Aligned_cols=12 Identities=33% Similarity=0.858 Sum_probs=9.8
Q ss_pred cccccccCCCCC
Q 009922 436 KCSLCGTEMPPS 447 (522)
Q Consensus 436 ~~~~~~~~~~~~ 447 (522)
+|.-||.|+++.
T Consensus 1 ~Cp~CG~~~~~~ 12 (23)
T PF13240_consen 1 YCPNCGAEIEDD 12 (23)
T ss_pred CCcccCCCCCCc
Confidence 588999999874
No 114
>TIGR00194 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.
Probab=28.19 E-value=2.3e+02 Score=32.31 Aligned_cols=117 Identities=15% Similarity=0.194 Sum_probs=64.0
Q ss_pred hHHHHHHHHHHHHHHHhhCCCEEeecccEEEEEcCcchhhcCCCHHHHHHHHHHHHHHHhCCc---eEEeccCChhHHHH
Q 009922 20 FTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLT---CSAGVAPNRLLAKV 96 (522)
Q Consensus 20 ~~~Y~~~s~~i~~il~~~tp~VE~~SiDEafLDvT~~~~l~g~~~~~lA~~IR~~I~~etGlt---~S~GIA~NKllAKL 96 (522)
.+.|..+.+-+.+-+.++...-+..-+|=+.+|=.- .. .....+.+ +++|+. .-+|+|-++ +-
T Consensus 425 ~dDya~m~Evl~RR~~r~~~~~~~~~PDLiliDGGk---------gQ-l~aa~~~l-~~lg~~~~i~viglaK~~---~~ 490 (574)
T TIGR00194 425 GDDYAAMREVLRRRYSSIQKKNNLPLPDLILIDGGK---------GQ-LNAALEVL-KSLGVVNKPIVIGLAKAK---RH 490 (574)
T ss_pred CCHHHHHHHHHHHHHhhhccccCCCCCCEEEEeCCH---------HH-HHHHHHHH-HHcCCCCCCcEEEEEecC---CC
Confidence 357777777666666655431000135767666332 11 12223333 678882 468998865 22
Q ss_pred HhhcCCCC--cEEEEcCChHHHHHhh-----------------------cCCCcccccCCChHHHHHHhhhcCCCCHHHH
Q 009922 97 CSDINKPN--GQFVLPNDRMAVMTFI-----------------------SSLPIRKIGGIGKVTEHILRDVFGINTCEEM 151 (522)
Q Consensus 97 AS~~~KP~--G~~vI~~~~~~~~~fL-----------------------~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL 151 (522)
...+-.|+ ....+++.. .+-.|| -.-++.+|||||+++.+.|=+.|| |+..+
T Consensus 491 ~~~i~~~~~~~~i~l~~~s-~~l~lLq~irDEaHRFAi~~hR~~r~k~~~~S~Ld~I~GIG~kr~~~LL~~Fg--s~~~i 567 (574)
T TIGR00194 491 ETDIFLIGDKQGINIDLNS-PALQLLQHIRDEAHRFAISFHRKKRLKASLQSPLLKIPGVGEKRVQKLLKYFG--SLKGI 567 (574)
T ss_pred ceEEEeCCCCceeecCCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcC--CHHHH
Confidence 23444454 233455442 111222 234788999999999988865354 77776
Q ss_pred Hh
Q 009922 152 LQ 153 (522)
Q Consensus 152 ~~ 153 (522)
.+
T Consensus 568 ~~ 569 (574)
T TIGR00194 568 KK 569 (574)
T ss_pred Hh
Confidence 54
No 115
>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=28.06 E-value=2e+02 Score=29.16 Aligned_cols=86 Identities=15% Similarity=0.034 Sum_probs=52.4
Q ss_pred HHHHHHhCCCcEEECCChHHHHHHHHHHHHHHHhhCCCEE----------eecccEEEEEcCcchhhcCCCHHHHHHHHH
Q 009922 3 GFIARKLCPELIFVPTDFTKYTYYSDLTRKVFCKYDPNFM----------AASLDEAYLDITEVCRERGISGIEIAEELR 72 (522)
Q Consensus 3 l~~A~kLCPdLvvvp~d~~~Y~~~s~~i~~il~~~tp~VE----------~~SiDEafLDvT~~~~l~g~~~~~lA~~IR 72 (522)
...|+.+|-. +.-|+..-+...++..+++....+.+- -.+||+.=.+= +...++-.++.+.|++||
T Consensus 57 s~~A~~La~~---~~kDpr~~e~il~Es~~vv~~~~~~~i~~~~~G~v~anAGID~SN~~~-g~v~LLP~DPd~sA~~ir 132 (243)
T TIGR01916 57 SPEALEIAAR---TGKDPRFVQAILDEAVEVVAVGTPFLITETRHGHVCANAGIDESNVGN-GELLLLPEDPDASAEKIR 132 (243)
T ss_pred CHHHHHHHHH---hCCChHHHHHHHHHHHHHHhccCCeEEEEecCceEEeccccccccCCC-CeEEecCCChHHHHHHHH
Confidence 3445555433 345665566666677777754333221 13444332211 122233347999999999
Q ss_pred HHHHHHhCCceEEeccCChh
Q 009922 73 TSVYEEAGLTCSAGVAPNRL 92 (522)
Q Consensus 73 ~~I~~etGlt~S~GIA~NKl 92 (522)
++|.+.+|..+.|=|..+..
T Consensus 133 ~~l~~~~g~~v~VIItDt~g 152 (243)
T TIGR01916 133 RGLRELTGVDVGVIITDTNG 152 (243)
T ss_pred HHHHHHHCCCEEEEEECCCC
Confidence 99999999999888887755
No 116
>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=27.54 E-value=76 Score=36.65 Aligned_cols=16 Identities=19% Similarity=0.401 Sum_probs=8.1
Q ss_pred cccccCCChHHHHHHh
Q 009922 125 IRKIGGIGKVTEHILR 140 (522)
Q Consensus 125 I~~LpGIG~kt~~~L~ 140 (522)
|..|+|+|.+++++|.
T Consensus 468 L~~L~GfG~Ksa~nIl 483 (652)
T TIGR00575 468 LLELEGFGEKSAQNLL 483 (652)
T ss_pred HhhccCccHHHHHHHH
Confidence 3345555555555443
No 117
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=27.08 E-value=74 Score=36.17 Aligned_cols=48 Identities=21% Similarity=0.225 Sum_probs=36.9
Q ss_pred CCCcccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHH--cChhHHHHHH
Q 009922 122 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFL 171 (522)
Q Consensus 122 ~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~--FG~~~~~~l~ 171 (522)
.+.+..|||||++++.+|-+ ...++.++.+.+ ..|.+. +|...+..+.
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 47788999999999999865 445899998887 677777 5666565553
No 118
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=26.61 E-value=32 Score=36.06 Aligned_cols=33 Identities=27% Similarity=0.359 Sum_probs=26.4
Q ss_pred CCcccccCCChHHHHHHhhhcCCCCHHHHHhch
Q 009922 123 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG 155 (522)
Q Consensus 123 LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~ 155 (522)
.|+-++||+||+...+|=..+||+++.+|+.-.
T Consensus 93 ~~Ll~v~GlGpkKi~~Ly~elgi~~~e~l~~a~ 125 (326)
T COG1796 93 EPLLKVPGLGPKKIVSLYKELGIKDLEELQEAL 125 (326)
T ss_pred HHHhhCCCCCcHHHHHHHHHHCcccHHHHHHHH
Confidence 466788999997777775559999999997754
No 119
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=26.61 E-value=83 Score=35.67 Aligned_cols=47 Identities=19% Similarity=0.145 Sum_probs=35.8
Q ss_pred CcccccCCChHHHHHHhhhcC-CCCHHHHHhch-HHHHH--HcChhHHHHHH
Q 009922 124 PIRKIGGIGKVTEHILRDVFG-INTCEEMLQKG-SLLCA--VFSHSTADFFL 171 (522)
Q Consensus 124 PI~~LpGIG~kt~~~L~~~lG-I~T~gdL~~l~-~~L~~--~FG~~~~~~l~ 171 (522)
.--+|-|+|.++.++|-+ .| |+++.||..+. ..|.. .||.+.+..++
T Consensus 426 ~amdI~GlGe~~i~~L~~-~G~i~~~~Diy~L~~~~l~~l~gfgeks~~nll 476 (562)
T PRK08097 426 QGLGLDGIGEGTWRALHQ-TGLFEHLFSWLALTPEQLANTPGIGKARAEQLW 476 (562)
T ss_pred cccCCCCcCHHHHHHHHH-cCCcCCHHHHhcCCHHHHhcCcCccHHHHHHHH
Confidence 334577999999999987 77 69999999987 45554 48887766553
No 120
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=25.88 E-value=43 Score=31.21 Aligned_cols=30 Identities=17% Similarity=0.372 Sum_probs=23.7
Q ss_pred ccccCCChHHHHHHhh---hcC-CCCHHHHHhch
Q 009922 126 RKIGGIGKVTEHILRD---VFG-INTCEEMLQKG 155 (522)
Q Consensus 126 ~~LpGIG~kt~~~L~~---~lG-I~T~gdL~~l~ 155 (522)
..|||||++.++.+.. ..| .++++||++.+
T Consensus 100 ~~lpgIG~~kA~aIi~yRe~~G~f~sv~dL~~v~ 133 (149)
T COG1555 100 QALPGIGPKKAQAIIDYREENGPFKSVDDLAKVK 133 (149)
T ss_pred HHCCCCCHHHHHHHHHHHHHcCCCCcHHHHHhcc
Confidence 6789999999998854 133 78999998764
No 121
>PRK02240 GTP cyclohydrolase III; Provisional
Probab=25.47 E-value=4e+02 Score=27.16 Aligned_cols=58 Identities=12% Similarity=0.102 Sum_probs=35.4
Q ss_pred HHHHHHhhCCCEEeecccEEEEEcCcchhhcCCCHHHHHHHHHHHHHHHhCC--ceEEeccCChhHH
Q 009922 30 TRKVFCKYDPNFMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGL--TCSAGVAPNRLLA 94 (522)
Q Consensus 30 i~~il~~~tp~VE~~SiDEafLDvT~~~~l~g~~~~~lA~~IR~~I~~etGl--t~S~GIA~NKllA 94 (522)
+.+.+..+-..+-...-|..+.=..|. +.+. ..+|.+.|....++ .+.+|+|.|+.-|
T Consensus 38 L~~~~~~~ggl~Ff~RgDN~iavtNGI------~~~~-~~~i~e~I~n~~PV~ls~GIG~g~TP~eA 97 (254)
T PRK02240 38 LAQQFGARDGYVFFTRFDNMIAVTNGI------DLED-HARIQESIRNRYPVTVSMGIGTAETPYEA 97 (254)
T ss_pred HHHHHHhCCCEEEeccCceEEEEcCCC------CHHH-HHHHHHHHHhcCCCceEEEEEecCCHHHH
Confidence 334444555566667778776554443 3333 35578888888666 5666666676666
No 122
>smart00267 GGDEF diguanylate cyclase. Diguanylate cyclase, present in a variety of bacteria
Probab=25.38 E-value=2.8e+02 Score=23.72 Aligned_cols=63 Identities=22% Similarity=0.130 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHHhhCCC---EEeecccEEEEEcCcchhhcCCCHHHHHHHHHHHHHHHhC-------CceEEeccC
Q 009922 24 TYYSDLTRKVFCKYDPN---FMAASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAG-------LTCSAGVAP 89 (522)
Q Consensus 24 ~~~s~~i~~il~~~tp~---VE~~SiDEafLDvT~~~~l~g~~~~~lA~~IR~~I~~etG-------lt~S~GIA~ 89 (522)
......+..++....+. +-.++-|++.+=+.+... . ....++.+|.+.+..... +++++|++.
T Consensus 58 ~~~l~~i~~~l~~~~~~~~~~~r~~~~~f~ii~~~~~~-~--~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~g~~~ 130 (163)
T smart00267 58 DELLQEVAQRLSSCLRPGDLLARLGGDEFALLLPETSL-E--EAIALAERILQQLREPIIIHGIPLYLTISIGVAA 130 (163)
T ss_pred HHHHHHHHHHHHHhcCCCCEEEEecCceEEEEecCCCH-H--HHHHHHHHHHHHHhCccccCCcEEEEEEEEEEEe
Confidence 34455566666666653 445666776655554421 1 356778888888865544 788899875
No 123
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=25.38 E-value=49 Score=23.29 Aligned_cols=16 Identities=38% Similarity=0.401 Sum_probs=13.1
Q ss_pred cccccCCChHHHHHHh
Q 009922 125 IRKIGGIGKVTEHILR 140 (522)
Q Consensus 125 I~~LpGIG~kt~~~L~ 140 (522)
|.-+||||++++.+|-
T Consensus 18 i~Gv~giG~ktA~~ll 33 (36)
T smart00279 18 IPGVKGIGPKTALKLL 33 (36)
T ss_pred CCCCCcccHHHHHHHH
Confidence 5568999999998774
No 124
>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=25.19 E-value=24 Score=25.07 Aligned_cols=9 Identities=56% Similarity=1.291 Sum_probs=5.3
Q ss_pred Ccccccccc
Q 009922 434 DYKCSLCGT 442 (522)
Q Consensus 434 ~~~~~~~~~ 442 (522)
=|||..||-
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 125
>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=24.46 E-value=87 Score=30.35 Aligned_cols=52 Identities=17% Similarity=0.259 Sum_probs=35.5
Q ss_pred HHHHhhcCCCcccccCCChHHHHHHhhhcCCCCHHHHHhc----h-HHHHHH--cChhHHHHHH
Q 009922 115 AVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQK----G-SLLCAV--FSHSTADFFL 171 (522)
Q Consensus 115 ~~~~fL~~LPI~~LpGIG~kt~~~L~~~lGI~T~gdL~~l----~-~~L~~~--FG~~~~~~l~ 171 (522)
+.++++.. +-.++||||+++..+ ++..+..+|.+. + ..|.+. ||+++++.+.
T Consensus 66 ~Er~lF~~--L~~V~GIGpK~Al~i---L~~~~~~el~~aI~~~d~~~L~~ipGiGkKtAerIi 124 (191)
T TIGR00084 66 EERELFKE--LIKVNGVGPKLALAI---LSNMSPEEFVYAIETEEVKALVKIPGVGKKTAERLL 124 (191)
T ss_pred HHHHHHHH--HhCCCCCCHHHHHHH---HhcCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHH
Confidence 44555555 357899999999666 677788887653 1 455554 6777877764
No 126
>PRK00807 50S ribosomal protein L24e; Validated
Probab=23.70 E-value=33 Score=26.25 Aligned_cols=14 Identities=43% Similarity=1.037 Sum_probs=12.1
Q ss_pred ccccccccCCCCCc
Q 009922 435 YKCSLCGTEMPPSF 448 (522)
Q Consensus 435 ~~~~~~~~~~~~~~ 448 (522)
++|+-||.++.|+-
T Consensus 2 ~~C~fcG~~I~pg~ 15 (52)
T PRK00807 2 RTCSFCGKEIEPGT 15 (52)
T ss_pred cccCCCCCeEcCCC
Confidence 57999999999874
No 127
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=23.59 E-value=29 Score=21.53 Aligned_cols=11 Identities=36% Similarity=0.939 Sum_probs=7.1
Q ss_pred ccccccccCCC
Q 009922 435 YKCSLCGTEMP 445 (522)
Q Consensus 435 ~~~~~~~~~~~ 445 (522)
|+|+.|.+.-.
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 128
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=22.87 E-value=1.2e+02 Score=32.00 Aligned_cols=53 Identities=21% Similarity=0.396 Sum_probs=32.8
Q ss_pred cccccCCChHHHHHHhhhcCCCCHH---HHHh--chH---HHHHHc--ChhHHHHHHHhccCCCC
Q 009922 125 IRKIGGIGKVTEHILRDVFGINTCE---EMLQ--KGS---LLCAVF--SHSTADFFLSVGLGLGS 179 (522)
Q Consensus 125 I~~LpGIG~kt~~~L~~~lGI~T~g---dL~~--l~~---~L~~~F--G~~~~~~l~~~a~G~d~ 179 (522)
+.+|||||+++++++.+.+-=.++. +.+. .|. .|.+.. |++.+..||. .|+..
T Consensus 50 l~~lpgIG~~ia~kI~Eil~tG~~~~~~e~l~~~~p~~l~~l~~i~GiGpk~a~~l~~--lGi~t 112 (334)
T smart00483 50 LKGLPGIGDKIKKKIEEIIETGKSSKVLEILNDEVYKSLKLFTNVFGVGPKTAAKWYR--KGIRT 112 (334)
T ss_pred HhcCCCccHHHHHHHHHHHHhCcHHHHHHHhcCcHHHHHHHHHccCCcCHHHHHHHHH--hCCCC
Confidence 6689999999999998633323344 2222 132 344554 5667777776 67654
No 129
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=22.29 E-value=38 Score=30.83 Aligned_cols=15 Identities=27% Similarity=0.616 Sum_probs=13.1
Q ss_pred CccccccccCCCCCc
Q 009922 434 DYKCSLCGTEMPPSF 448 (522)
Q Consensus 434 ~~~~~~~~~~~~~~~ 448 (522)
-++|+.||..+.|+-
T Consensus 4 ~e~CsFcG~kIyPG~ 18 (131)
T PRK14891 4 TRTCDYTGEEIEPGT 18 (131)
T ss_pred eeeecCcCCcccCCC
Confidence 468999999999983
No 130
>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=21.80 E-value=37 Score=26.28 Aligned_cols=14 Identities=43% Similarity=0.975 Sum_probs=12.4
Q ss_pred CccccccccCCCCC
Q 009922 434 DYKCSLCGTEMPPS 447 (522)
Q Consensus 434 ~~~~~~~~~~~~~~ 447 (522)
-..|+-||..++|+
T Consensus 3 ~~~C~f~g~~I~PG 16 (54)
T cd00472 3 TEKCSFCGYKIYPG 16 (54)
T ss_pred EEEecCcCCeecCC
Confidence 35899999999998
No 131
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=21.62 E-value=1.1e+02 Score=31.10 Aligned_cols=47 Identities=21% Similarity=0.222 Sum_probs=34.6
Q ss_pred cccccCCChHHHHHHhhhcCCCCHHHHHhch-HHHHHHcCh--hHHHHHHHh
Q 009922 125 IRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSH--STADFFLSV 173 (522)
Q Consensus 125 I~~LpGIG~kt~~~L~~~lGI~T~gdL~~l~-~~L~~~FG~--~~~~~l~~~ 173 (522)
+..+||||+.++.+|-. -+.++++++... ..|.+.-|. +.+..++..
T Consensus 184 l~s~pgig~~~a~~ll~--~fgS~~~~~tas~~eL~~v~gig~k~A~~I~~~ 233 (254)
T COG1948 184 LESIPGIGPKLAERLLK--KFGSVEDVLTASEEELMKVKGIGEKKAREIYRF 233 (254)
T ss_pred HHcCCCccHHHHHHHHH--HhcCHHHHhhcCHHHHHHhcCccHHHHHHHHHH
Confidence 45577999999999975 455999998886 677777665 556555543
No 132
>PHA02768 hypothetical protein; Provisional
Probab=20.88 E-value=38 Score=26.39 Aligned_cols=27 Identities=26% Similarity=0.452 Sum_probs=17.1
Q ss_pred ecCccccccccCCCCCcHhhhhccccchH
Q 009922 432 LDDYKCSLCGTEMPPSFIEERQEHSDFHL 460 (522)
Q Consensus 432 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 460 (522)
+-||.|+.||....-+ ..-+.|...|.
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 4589999999876432 23345555544
No 133
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=20.82 E-value=79 Score=31.29 Aligned_cols=53 Identities=23% Similarity=0.453 Sum_probs=29.1
Q ss_pred EEeccCChhHH--HHHhh-cCCCCcEEEEcCChHHHHHhhcCCCcccccCCChHHHHHHhh-hcCCCC
Q 009922 84 SAGVAPNRLLA--KVCSD-INKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRD-VFGINT 147 (522)
Q Consensus 84 S~GIA~NKllA--KLAS~-~~KP~G~~vI~~~~~~~~~fL~~LPI~~LpGIG~kt~~~L~~-~lGI~T 147 (522)
++|.-.||--. ++|-. ..+.+|. +|.. ..+ +-+|||||+||+.-.-. .+|+.+
T Consensus 78 ~iGlyr~KAk~I~~~~~~l~e~~~g~--vP~~---~~e------L~~LPGVGrKTAnvVL~~a~g~p~ 134 (211)
T COG0177 78 SIGLYRNKAKNIKELARILLEKFGGE--VPDT---REE------LLSLPGVGRKTANVVLSFAFGIPA 134 (211)
T ss_pred hcCCcHHHHHHHHHHHHHHHHHcCCC--CCch---HHH------HHhCCCcchHHHHHHHHhhcCCCc
Confidence 46777777533 12211 2456663 4432 222 44689999999987432 255543
No 134
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=20.67 E-value=48 Score=32.18 Aligned_cols=15 Identities=40% Similarity=0.589 Sum_probs=13.4
Q ss_pred cccccCCChHHHHHH
Q 009922 125 IRKIGGIGKVTEHIL 139 (522)
Q Consensus 125 I~~LpGIG~kt~~~L 139 (522)
+..+||||+++++++
T Consensus 110 L~~vpGIGkKtAerI 124 (194)
T PRK14605 110 LSTIPGIGKKTASRI 124 (194)
T ss_pred HHhCCCCCHHHHHHH
Confidence 677999999999994
No 135
>smart00355 ZnF_C2H2 zinc finger.
Probab=20.63 E-value=42 Score=20.07 Aligned_cols=11 Identities=36% Similarity=1.117 Sum_probs=9.2
Q ss_pred ccccccccCCC
Q 009922 435 YKCSLCGTEMP 445 (522)
Q Consensus 435 ~~~~~~~~~~~ 445 (522)
|+|..||...+
T Consensus 1 ~~C~~C~~~f~ 11 (26)
T smart00355 1 YRCPECGKVFK 11 (26)
T ss_pred CCCCCCcchhC
Confidence 78999998775
No 136
>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=20.54 E-value=51 Score=31.95 Aligned_cols=18 Identities=39% Similarity=0.458 Sum_probs=15.3
Q ss_pred CCcccccCCChHHHHHHh
Q 009922 123 LPIRKIGGIGKVTEHILR 140 (522)
Q Consensus 123 LPI~~LpGIG~kt~~~L~ 140 (522)
--+..+||||++|++++-
T Consensus 107 ~~L~~ipGiGkKtAerIi 124 (191)
T TIGR00084 107 KALVKIPGVGKKTAERLL 124 (191)
T ss_pred HHHHhCCCCCHHHHHHHH
Confidence 347889999999999974
No 137
>KOG0633 consensus Histidinol phosphate aminotransferase [Amino acid transport and metabolism]
Probab=20.15 E-value=2.9e+02 Score=28.58 Aligned_cols=44 Identities=30% Similarity=0.365 Sum_probs=29.0
Q ss_pred CCcEEE--CCChHHHHHHHHHHHHHHHhhCCCEEeecccEEEEEcCcc
Q 009922 11 PELIFV--PTDFTKYTYYSDLTRKVFCKYDPNFMAASLDEAYLDITEV 56 (522)
Q Consensus 11 PdLvvv--p~d~~~Y~~~s~~i~~il~~~tp~VE~~SiDEafLDvT~~ 56 (522)
|.++|+ |.+|..-.--.+-+.+|++..+..+ +=+||||+|.++.
T Consensus 161 iK~~F~tSPgNPtg~~ik~~di~KiLe~p~ngl--VVvDEAYidFsg~ 206 (375)
T KOG0633|consen 161 IKCIFLTSPGNPTGSIIKEDDILKILEMPDNGL--VVVDEAYIDFSGV 206 (375)
T ss_pred ceEEEEcCCCCCCcccccHHHHHHHHhCCCCcE--EEEeeeeEeeccc
Confidence 344554 4555544444556778888887543 4579999999983
No 138
>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=20.02 E-value=48 Score=26.22 Aligned_cols=29 Identities=28% Similarity=0.510 Sum_probs=19.3
Q ss_pred CCCCCccccCcCCcceeecCccccccccCCCCCcHhh
Q 009922 415 PDNKVGTSSNQKDQFIWLDDYKCSLCGTEMPPSFIEE 451 (522)
Q Consensus 415 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 451 (522)
..|-+.=+.|+. --|++|||-=.|...|-
T Consensus 19 ~pNyntCT~Ck~--------~VCnlCGFNP~Phl~E~ 47 (61)
T PF05715_consen 19 PPNYNTCTECKS--------QVCNLCGFNPTPHLTEV 47 (61)
T ss_pred CCCccHHHHHhh--------hhhcccCCCCCcccccc
Confidence 444444445554 36999999988877763
Done!