Query 006218
Match_columns 656
No_of_seqs 283 out of 1840
Neff 5.9
Searched_HMMs 46136
Date Thu Mar 28 20:05:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006218.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006218hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2095 DNA polymerase iota/DN 100.0 2.7E-56 5.8E-61 492.3 26.3 297 1-297 67-375 (656)
2 PTZ00205 DNA polymerase kappa; 100.0 1.1E-53 2.4E-58 475.0 29.7 289 1-372 184-487 (571)
3 cd01703 PolY_Pol_iota DNA Poly 100.0 3.9E-52 8.4E-57 451.3 29.9 300 1-368 49-379 (379)
4 cd01701 PolY_Rev1 DNA polymera 100.0 7.1E-52 1.5E-56 453.4 30.8 292 1-369 102-404 (404)
5 cd01702 PolY_Pol_eta DNA Polym 100.0 3.7E-52 7.9E-57 448.9 27.6 288 1-368 49-359 (359)
6 cd00424 PolY Y-family of DNA p 100.0 1.4E-51 3E-56 441.8 30.8 288 1-367 53-343 (343)
7 PRK01216 DNA polymerase IV; Va 100.0 3.3E-51 7.1E-56 440.2 30.3 283 1-372 59-342 (351)
8 PRK03858 DNA polymerase IV; Va 100.0 9.1E-51 2E-55 443.0 31.3 298 1-384 54-353 (396)
9 PRK03348 DNA polymerase IV; Pr 100.0 3.6E-50 7.8E-55 445.6 33.1 296 1-386 59-356 (454)
10 PRK14133 DNA polymerase IV; Pr 100.0 2.6E-50 5.6E-55 432.6 30.9 290 1-383 57-347 (347)
11 PRK02794 DNA polymerase IV; Pr 100.0 2.8E-50 6.2E-55 442.6 30.6 297 1-385 89-386 (419)
12 PRK03103 DNA polymerase IV; Re 100.0 4.1E-50 8.9E-55 439.9 31.2 298 1-385 59-362 (409)
13 PRK01810 DNA polymerase IV; Va 100.0 4.2E-50 9.1E-55 439.6 31.0 295 1-384 61-358 (407)
14 PRK02406 DNA polymerase IV; Va 100.0 1.7E-49 3.7E-54 425.5 30.5 283 1-372 49-334 (343)
15 PRK03609 umuC DNA polymerase V 100.0 3E-49 6.5E-54 434.9 29.7 301 1-385 53-363 (422)
16 PRK03352 DNA polymerase IV; Va 100.0 4E-49 8.7E-54 423.1 29.6 281 1-372 63-345 (346)
17 cd03586 PolY_Pol_IV_kappa DNA 100.0 9.8E-49 2.1E-53 416.9 30.0 282 1-369 52-334 (334)
18 cd01700 PolY_Pol_V_umuC umuC s 100.0 3.7E-48 8.1E-53 415.3 28.0 285 1-368 51-344 (344)
19 KOG2094 Predicted DNA damage i 100.0 9.4E-48 2E-52 397.3 20.4 292 1-374 154-448 (490)
20 COG0389 DinP Nucleotidyltransf 100.0 1.2E-45 2.7E-50 397.7 29.4 290 1-372 55-347 (354)
21 KOG2093 Translesion DNA polyme 100.0 6.5E-45 1.4E-49 407.8 19.7 304 1-384 429-747 (1016)
22 cd03468 PolY_like DNA Polymera 100.0 8.7E-41 1.9E-45 355.8 27.6 276 1-367 52-334 (335)
23 PF00817 IMS: impB/mucB/samB f 99.8 1.5E-18 3.2E-23 165.3 10.8 97 1-156 51-149 (149)
24 PF11799 IMS_C: impB/mucB/samB 99.3 3E-12 6.4E-17 116.9 8.9 125 235-383 1-127 (127)
25 PF11798 IMS_HHH: IMS family H 98.5 4.8E-08 1E-12 69.7 1.9 32 168-200 1-32 (32)
26 PRK04301 radA DNA repair and r 97.9 7.9E-06 1.7E-10 87.5 4.0 80 174-254 2-88 (317)
27 TIGR02236 recomb_radA DNA repa 97.3 0.00024 5.1E-09 75.7 4.9 74 180-254 1-81 (310)
28 PF14520 HHH_5: Helix-hairpin- 96.8 0.00083 1.8E-08 54.5 2.4 50 181-231 8-59 (60)
29 PF11731 Cdd1: Pathogenicity l 96.4 0.0026 5.6E-08 56.5 3.2 44 179-223 13-56 (93)
30 PRK12766 50S ribosomal protein 94.5 0.042 9.2E-07 56.3 4.5 56 179-235 4-61 (232)
31 PF10391 DNA_pol_lambd_f: Fing 93.3 0.061 1.3E-06 42.8 2.4 27 181-208 5-31 (52)
32 PF04994 TfoX_C: TfoX C-termin 92.7 0.12 2.5E-06 44.9 3.4 32 179-211 4-35 (81)
33 COG3743 Uncharacterized conser 91.8 0.18 3.9E-06 47.4 3.7 37 179-216 68-104 (133)
34 PRK02362 ski2-like helicase; P 91.5 0.14 3.1E-06 61.2 3.5 55 178-233 652-706 (737)
35 PF03118 RNA_pol_A_CTD: Bacter 91.4 0.16 3.5E-06 42.3 2.7 45 173-219 7-51 (66)
36 PF14229 DUF4332: Domain of un 90.0 0.28 6.1E-06 45.7 3.3 54 166-220 41-94 (122)
37 PF12826 HHH_2: Helix-hairpin- 89.5 0.25 5.4E-06 40.7 2.3 47 183-231 8-56 (64)
38 PRK01172 ski2-like helicase; P 86.2 0.73 1.6E-05 54.6 4.3 52 178-230 612-665 (674)
39 PRK00254 ski2-like helicase; P 85.6 0.67 1.4E-05 55.4 3.6 53 178-231 645-699 (720)
40 PRK07758 hypothetical protein; 81.9 2 4.3E-05 38.4 4.1 38 183-221 39-78 (95)
41 COG2251 Predicted nuclease (Re 81.7 1.4 2.9E-05 49.4 3.7 68 168-236 215-284 (474)
42 PF14229 DUF4332: Domain of un 81.7 2 4.4E-05 40.0 4.4 44 184-229 1-49 (122)
43 PRK14667 uvrC excinuclease ABC 77.8 2 4.4E-05 50.0 3.7 54 177-232 513-567 (567)
44 PRK00116 ruvA Holliday junctio 76.9 2.1 4.5E-05 43.0 3.1 56 180-235 75-133 (192)
45 smart00483 POLXc DNA polymeras 75.9 1.7 3.6E-05 47.4 2.2 30 180-210 91-120 (334)
46 PF02961 BAF: Barrier to autoi 75.3 2.3 5.1E-05 37.5 2.5 33 175-208 16-48 (89)
47 TIGR00596 rad1 DNA repair prot 74.4 2.5 5.5E-05 51.2 3.4 52 180-233 759-811 (814)
48 PF14377 DUF4414: Domain of un 73.9 1.5 3.2E-05 40.0 1.0 21 611-631 1-21 (108)
49 smart00611 SEC63 Domain of unk 73.7 5.9 0.00013 42.1 5.7 62 177-239 150-213 (312)
50 TIGR03491 RecB family nuclease 73.2 2.3 5E-05 48.2 2.5 60 171-231 200-261 (457)
51 cd00141 NT_POLXc Nucleotidyltr 72.8 2.3 4.9E-05 45.8 2.2 28 181-209 88-115 (307)
52 PRK08609 hypothetical protein; 72.3 2.4 5.1E-05 49.6 2.4 29 181-209 91-119 (570)
53 PF14377 DUF4414: Domain of un 71.2 2.5 5.4E-05 38.5 1.8 25 608-632 42-66 (108)
54 PF02889 Sec63: Sec63 Brl doma 70.9 4.2 9.2E-05 43.1 3.8 60 178-238 148-209 (314)
55 PRK07956 ligA NAD-dependent DN 69.4 4.8 0.0001 47.9 4.1 51 179-229 446-498 (665)
56 PRK14671 uvrC excinuclease ABC 69.1 5.1 0.00011 47.3 4.2 51 178-230 569-619 (621)
57 PRK14672 uvrC excinuclease ABC 68.9 5.4 0.00012 47.3 4.3 62 177-240 607-670 (691)
58 PTZ00035 Rad51 protein; Provis 68.6 4.4 9.4E-05 44.2 3.3 55 178-233 21-79 (337)
59 TIGR00575 dnlj DNA ligase, NAD 68.4 5.2 0.00011 47.5 4.1 53 179-231 433-487 (652)
60 PRK10917 ATP-dependent DNA hel 67.3 3.7 8E-05 48.9 2.6 31 178-209 9-39 (681)
61 PRK14670 uvrC excinuclease ABC 66.9 6.1 0.00013 46.2 4.2 53 177-231 513-567 (574)
62 PF00633 HHH: Helix-hairpin-he 66.0 3.2 6.9E-05 29.3 1.1 15 181-195 14-28 (30)
63 PRK14666 uvrC excinuclease ABC 65.9 5.7 0.00012 47.2 3.8 51 178-230 637-689 (694)
64 TIGR02239 recomb_RAD51 DNA rep 65.7 6.8 0.00015 42.3 4.1 36 185-221 8-43 (316)
65 PLN03186 DNA repair protein RA 64.5 4.6 0.0001 44.2 2.5 43 178-221 26-70 (342)
66 TIGR02238 recomb_DMC1 meiotic 64.0 7.8 0.00017 41.9 4.1 48 184-232 7-56 (313)
67 PLN03187 meiotic recombination 63.6 6 0.00013 43.4 3.2 56 177-233 28-87 (344)
68 PRK14669 uvrC excinuclease ABC 62.2 7.8 0.00017 45.8 4.0 54 177-232 551-604 (624)
69 PRK12278 50S ribosomal protein 61.7 7.8 0.00017 39.9 3.4 36 179-215 159-194 (221)
70 PRK12311 rpsB 30S ribosomal pr 59.4 7 0.00015 42.6 2.7 35 180-215 265-299 (326)
71 PRK14351 ligA NAD-dependent DN 58.9 10 0.00022 45.4 4.2 52 179-230 463-516 (689)
72 COG0632 RuvA Holliday junction 58.8 6.5 0.00014 39.9 2.2 43 143-195 80-125 (201)
73 COG1200 RecG RecG-like helicas 58.6 6.4 0.00014 46.5 2.4 31 178-209 10-40 (677)
74 PRK14601 ruvA Holliday junctio 55.7 7.8 0.00017 38.8 2.2 57 127-195 66-125 (183)
75 PRK14973 DNA topoisomerase I; 55.4 19 0.0004 44.7 5.7 79 149-231 850-931 (936)
76 TIGR00084 ruvA Holliday juncti 52.5 11 0.00024 37.9 2.7 51 181-234 75-131 (191)
77 PRK14606 ruvA Holliday junctio 52.4 9 0.00019 38.5 2.0 55 129-195 68-125 (188)
78 TIGR01954 nusA_Cterm_rpt trans 52.3 19 0.00041 27.5 3.4 33 187-220 2-34 (50)
79 PRK12373 NADH dehydrogenase su 49.1 15 0.00033 41.0 3.3 35 180-215 325-359 (400)
80 TIGR02027 rpoA DNA-directed RN 48.2 19 0.0004 38.8 3.7 54 175-230 232-287 (297)
81 PRK14605 ruvA Holliday junctio 47.6 16 0.00035 36.8 3.0 52 182-233 77-131 (194)
82 PF08004 DUF1699: Protein of u 47.4 33 0.00071 32.4 4.6 34 3-43 33-66 (131)
83 PRK14604 ruvA Holliday junctio 47.2 13 0.00027 37.7 2.2 56 128-195 67-125 (195)
84 smart00278 HhH1 Helix-hairpin- 47.1 12 0.00027 25.1 1.4 16 180-195 3-18 (26)
85 PRK13901 ruvA Holliday junctio 46.8 12 0.00027 37.8 2.0 58 126-195 64-124 (196)
86 TIGR00575 dnlj DNA ligase, NAD 46.7 19 0.00041 42.9 3.9 15 49-63 268-282 (652)
87 COG1948 MUS81 ERCC4-type nucle 46.6 18 0.0004 38.0 3.3 50 180-231 184-235 (254)
88 PRK00558 uvrC excinuclease ABC 46.2 19 0.00042 42.4 3.8 53 177-231 542-596 (598)
89 PRK05182 DNA-directed RNA poly 46.2 21 0.00045 38.7 3.7 52 175-228 246-299 (310)
90 PF07887 Calmodulin_bind: Calm 46.0 24 0.00051 38.1 4.0 50 180-230 164-218 (299)
91 PRK14603 ruvA Holliday junctio 45.4 14 0.00031 37.4 2.2 56 128-195 66-124 (197)
92 TIGR00084 ruvA Holliday juncti 43.9 13 0.00027 37.5 1.6 55 129-195 67-124 (191)
93 PRK14602 ruvA Holliday junctio 43.5 16 0.00035 37.1 2.3 57 127-195 67-126 (203)
94 PRK13766 Hef nuclease; Provisi 40.1 26 0.00056 42.2 3.7 50 180-231 717-768 (773)
95 COG5018 KapD Inhibitor of the 39.9 8.4 0.00018 38.1 -0.4 41 605-645 24-64 (210)
96 PRK08097 ligB NAD-dependent DN 39.4 30 0.00065 40.5 3.9 48 181-229 428-478 (562)
97 COG2199 c-di-GMP synthetase (d 38.3 72 0.0016 30.5 5.9 29 34-62 78-110 (181)
98 PF00416 Ribosomal_S13: Riboso 38.3 31 0.00067 31.4 3.0 35 180-214 17-51 (107)
99 KOG2534 DNA polymerase IV (fam 38.1 25 0.00054 38.1 2.7 29 181-210 100-128 (353)
100 TIGR00615 recR recombination p 37.2 28 0.00061 35.3 2.8 16 180-195 13-28 (195)
101 PF07647 SAM_2: SAM domain (St 35.7 45 0.00097 26.8 3.4 47 166-221 4-50 (66)
102 PRK00076 recR recombination pr 35.6 31 0.00066 35.0 2.8 16 180-195 13-28 (196)
103 PRK02515 psbU photosystem II c 35.5 61 0.0013 30.9 4.5 53 147-210 40-93 (132)
104 PRK14600 ruvA Holliday junctio 35.3 27 0.00059 35.0 2.4 56 127-195 66-124 (186)
105 TIGR03631 bact_S13 30S ribosom 35.2 37 0.00081 31.4 3.1 37 179-215 16-52 (113)
106 PRK13844 recombination protein 34.7 32 0.0007 35.0 2.8 16 180-195 17-32 (200)
107 PTZ00134 40S ribosomal protein 31.9 45 0.00098 32.6 3.2 41 179-219 31-74 (154)
108 PF07237 DUF1428: Protein of u 31.5 84 0.0018 28.7 4.6 37 15-58 7-43 (103)
109 PRK14351 ligA NAD-dependent DN 30.9 54 0.0012 39.4 4.2 45 183-229 533-579 (689)
110 COG1796 POL4 DNA polymerase IV 30.2 27 0.00059 37.9 1.5 34 178-211 93-126 (326)
111 CHL00013 rpoA RNA polymerase a 29.6 47 0.001 36.3 3.2 55 174-230 259-315 (327)
112 cd07556 Nucleotidyl_cyc_III Cl 29.3 3.8E+02 0.0083 23.3 9.6 29 32-60 30-59 (133)
113 PRK14668 uvrC excinuclease ABC 28.7 40 0.00087 39.6 2.7 49 177-227 524-574 (577)
114 cd00166 SAM Sterile alpha moti 28.6 94 0.002 24.1 4.1 46 167-222 3-48 (63)
115 PRK05179 rpsM 30S ribosomal pr 27.5 62 0.0013 30.4 3.2 36 179-214 18-53 (122)
116 CHL00137 rps13 ribosomal prote 27.3 63 0.0014 30.3 3.2 36 179-214 18-53 (122)
117 PRK14350 ligA NAD-dependent DN 25.9 68 0.0015 38.5 3.9 49 180-229 438-489 (669)
118 COG0353 RecR Recombinational D 25.8 56 0.0012 33.1 2.7 16 180-195 14-29 (198)
119 PRK07956 ligA NAD-dependent DN 25.6 65 0.0014 38.6 3.7 14 49-62 280-293 (665)
120 cd00080 HhH2_motif Helix-hairp 25.5 60 0.0013 27.5 2.5 19 181-199 25-43 (75)
121 COG0322 UvrC Nuclease subunit 24.8 56 0.0012 38.5 2.9 51 175-228 527-579 (581)
122 PRK14604 ruvA Holliday junctio 24.7 59 0.0013 32.9 2.7 51 181-234 76-132 (195)
123 TIGR03629 arch_S13P archaeal r 24.4 73 0.0016 30.8 3.1 40 179-218 22-64 (144)
124 COG0177 Nth Predicted EndoIII- 24.2 1.3E+02 0.0028 31.0 5.0 88 111-219 59-149 (211)
125 PRK07945 hypothetical protein; 23.8 1.1E+02 0.0025 33.3 4.9 49 179-232 50-98 (335)
126 PRK13482 DNA integrity scannin 23.5 86 0.0019 34.7 3.8 38 180-219 289-326 (352)
127 PF14716 HHH_8: Helix-hairpin- 23.4 48 0.001 27.4 1.5 16 180-195 49-64 (68)
128 PRK04053 rps13p 30S ribosomal 23.1 83 0.0018 30.6 3.3 40 179-218 26-68 (149)
129 TIGR00426 competence protein C 22.7 69 0.0015 26.4 2.3 30 180-209 18-52 (69)
130 PRK14603 ruvA Holliday junctio 22.6 67 0.0015 32.5 2.7 50 182-234 76-131 (197)
131 COG4380 Uncharacterized protei 22.2 56 0.0012 32.3 1.9 31 190-221 76-106 (216)
132 COG0099 RpsM Ribosomal protein 21.4 1.1E+02 0.0024 28.8 3.5 39 178-216 17-55 (121)
133 PRK14601 ruvA Holliday junctio 21.4 77 0.0017 31.8 2.7 50 182-234 77-132 (183)
134 PRK13901 ruvA Holliday junctio 20.9 81 0.0018 32.0 2.8 50 182-234 76-131 (196)
135 TIGR01259 comE comEA protein. 20.8 80 0.0017 29.3 2.6 28 181-208 71-102 (120)
136 smart00279 HhH2 Helix-hairpin- 20.2 86 0.0019 23.0 2.1 16 180-195 18-33 (36)
No 1
>KOG2095 consensus DNA polymerase iota/DNA damage inducible protein [Replication, recombination and repair]
Probab=100.00 E-value=2.7e-56 Score=492.27 Aligned_cols=297 Identities=49% Similarity=0.718 Sum_probs=268.8
Q ss_pred CcHHHHHHhCCCcEEEeccCcCCCCChHHHHHHHHHHHHHHhhc-CCeEEecCceEEEEccchhHHHhccCCCCCcchhh
Q 006218 1 MRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVD 79 (656)
Q Consensus 1 Mp~~~AkklCP~LivV~vP~~~~k~d~~~Yr~~S~~V~~IL~~~-~~VE~~SIDEafLDlT~~~~~~L~~~~~~~l~~~~ 79 (656)
|++++||++||+|++||||+.++++|..+||++|.+|+.+|..| +.||++|+||+|||+|.++++++.+.......-..
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 89999999999999999999999999999999999999999999 69999999999999999998876543311100001
Q ss_pred HHhhhhhcccCc-----------cCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEeccCcH
Q 006218 80 EEALKSHILGLE-----------SKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNK 148 (656)
Q Consensus 80 ~e~~~s~l~g~~-----------~~~g~~~~~~v~~w~~~~~~~~~d~ll~~~~~iA~~IR~~I~~~tGlt~SiGIA~NK 148 (656)
++-..+|.++.. .++|...++.+..|++.++.+|+|.+|.+|+.||++||++|+.+||||||+|||+||
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 111223444333 255556677889999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhcCCCCCCeeecCcccHHhhcccCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhcccchhhHHH
Q 006218 149 MLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWN 228 (656)
Q Consensus 149 lLAKLAS~~~KP~G~~vl~~~~v~~fL~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~~~G~~L~~ 228 (656)
+|||||++++|||.||+|+...+.+||..|||+++|++|+++++.|.+.+||.++|||+++++..|++.||.+.|.|||+
T Consensus 227 mLAKLvsg~nKPnqQTil~~~~v~~ll~slpi~k~~~lGGk~G~~lie~LGi~~vgdl~~fse~~L~~~fg~~~g~~l~~ 306 (656)
T KOG2095|consen 227 MLAKLVSGRNKPNQQTILPNTYVQDLLDSLPITKIRTLGGKLGEELIEVLGIDSVGDLQQFSETQLQKKFGEKNGTWLRN 306 (656)
T ss_pred HHHHHHhccCCCCcceecchHHHHHHHHhCCCceeeeccchHHHHHHHHhCCchHHHHHhcCHHHHHHhhCcchhHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999889999999
Q ss_pred HHhcCCCcccccccCCCcccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEE
Q 006218 229 IARGISGEEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLH 297 (656)
Q Consensus 229 ~arGiD~~~V~~~~~~KSIs~~~tF~~~~~i~~~eel~~~L~~L~~eL~~RLr~~~~~~~~~a~tvtL~ 297 (656)
.|+|+|.++|.++..+|||+++++|++...+.+.+++..||..+++++..||..+...+.+.+.+++++
T Consensus 307 la~Gid~s~V~pr~~pkSig~~K~Fpg~~~~~~~~~l~~wl~~la~el~~Rl~~d~~en~r~as~l~~~ 375 (656)
T KOG2095|consen 307 LARGIDNSPVRPRGLPKSIGSEKNFPGKRSRKSLEELQRWLNQLAEELAERLGKDRNENKRRASTLVVS 375 (656)
T ss_pred HhcccCCCccccCCCCcchhhhhcCCCccccccHHHHHHHHHHHHHHHHHHHHhhhhhhccccceEEee
Confidence 999999999999999999999999998788999999999999999999999999988899999999999
No 2
>PTZ00205 DNA polymerase kappa; Provisional
Probab=100.00 E-value=1.1e-53 Score=475.02 Aligned_cols=289 Identities=22% Similarity=0.276 Sum_probs=251.0
Q ss_pred CcHHHHHHhCCCcEEEeccCcCCCCChHHHHHHHHHHHHHHhhc-CCeEEecCceEEEEccchhHHHhccCCCCCcchhh
Q 006218 1 MRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVD 79 (656)
Q Consensus 1 Mp~~~AkklCP~LivV~vP~~~~k~d~~~Yr~~S~~V~~IL~~~-~~VE~~SIDEafLDlT~~~~~~L~~~~~~~l~~~~ 79 (656)
||+++|+++||+|++| | +||+.|+++|++|++||.+| |.+|++||||+|||+|++...
T Consensus 184 Mp~~~AkkLCP~Liiv--p-----~d~~~Y~~~S~~I~~il~~ysp~ve~~SIDEafLDlT~~~~~-------------- 242 (571)
T PTZ00205 184 MPGFLALKICPNLLIL--P-----PDFDAYNEESNTVRRIVAEYDPNYISFGLDELTLEVSAYIER-------------- 242 (571)
T ss_pred CcHHHHHHhCCCCcEe--c-----CCHHHHHHHHHHHHHHHHhcCCcEEEeechhceeccCCchhh--------------
Confidence 9999999999999998 5 89999999999999999999 799999999999999997521
Q ss_pred HHhhhhhcccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEeccCcHHHHHHHhcCCC
Q 006218 80 EEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNK 159 (656)
Q Consensus 80 ~e~~~s~l~g~~~~~g~~~~~~v~~w~~~~~~~~~d~ll~~~~~iA~~IR~~I~~~tGlt~SiGIA~NKlLAKLAS~~~K 159 (656)
++. . ..+..+|++||++|+++||||||||||+||+||||||+++|
T Consensus 243 --------~~~-----~----------------------~~~~~iA~~IR~~I~~~tgLt~SiGIA~NklLAKiASd~~K 287 (571)
T PTZ00205 243 --------FEG-----T----------------------KTAEDVASELRVRVFGETKLTASAGIGPTAALAKIASNINK 287 (571)
T ss_pred --------ccC-----C----------------------CCHHHHHHHHHHHHHHHHCCcEEEEEcCCHHHHHHhhhccC
Confidence 100 0 01457899999999999999999999999999999999999
Q ss_pred CCCeeec---CcccHHhhcccCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHH--------HHHHhhcccchhhHHH
Q 006218 160 PAQQTTV---PFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSED--------KLQESYGFNTGTWLWN 228 (656)
Q Consensus 160 P~G~~vl---~~~~v~~fL~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~--------~L~~~FG~~~G~~L~~ 228 (656)
|||++++ +++++..||++|||++|||||++++.+|. .+||+||+||++.+.. .|+..||...|.++|+
T Consensus 288 PnG~~vl~l~~~~~v~~fL~~LpV~ki~GIG~~t~~~L~-~~GI~TigDLa~~~~~l~~~f~~k~l~~llG~~~G~~l~~ 366 (571)
T PTZ00205 288 PNGQHDLNLHTRGDVMTYVRDLGLRSVPGVGKVTEALLK-GLGITTLSDIYNRRVELCYILHNNLFRFLLGASIGIMQWP 366 (571)
T ss_pred CCCCeEEecCCHHHHHHHHhCCCcceeCCcCHHHHHHHH-HcCCCcHHHHhcCCHHHHHHhHHHHHHHHhCchhhHHHHH
Confidence 9999986 67899999999999999999999999997 9999999999998876 4778899767999999
Q ss_pred HHhcCCCcc-ccc--ccCCCcccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCC
Q 006218 229 IARGISGEE-VQA--RLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSD 305 (656)
Q Consensus 229 ~arGiD~~~-V~~--~~~~KSIs~~~tF~~~~~i~~~eel~~~L~~L~~eL~~RLr~~~~~~~~~a~tvtL~ir~~~~~~ 305 (656)
.++|+|.++ +.+ ...+||||+++||. .+.+.+++...|..||++|+.||++ .++.|++|+|++|+.+
T Consensus 367 ~a~G~d~~~~v~~~~~~~rKSIg~ErTF~---~~~d~~el~~~L~~L~~~v~~rLrk----~~l~artVtlKlK~~d--- 436 (571)
T PTZ00205 367 DAATAANTENCEGATGGQRKAISSERSFT---TPRTKEGLQEMVDTVFNGAYEEMRK----SELMCRQISLTIRWAS--- 436 (571)
T ss_pred HhcCCCCCCccCCCCCCCCceeEEeEeCC---CCCCHHHHHHHHHHHHHHHHHHHHh----cCCCccEEEEEEEECC---
Confidence 999999984 332 34689999999997 3679999999999999999999997 5999999999999854
Q ss_pred CCCCCCcCcceeeCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEecCCeec
Q 006218 306 SDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPV 372 (656)
Q Consensus 306 ~~s~~~~~sks~~l~~~t~~I~~da~~L~~~al~ll~~~~~~~l~~~~~~~~~ir~lgVsls~L~~~ 372 (656)
|.+ .+++.+|+.+|+ ++..|++++..+|...+ +.+.+||+|||++++|...
T Consensus 437 F~~----~trs~tL~~pT~----d~~~I~~aa~~Ll~~~~--------~~~~~vRLlGV~ls~L~~~ 487 (571)
T PTZ00205 437 YRY----QQYTKSLIQYSD----DSATLRRAVDGLLLPHA--------AKYSEMCLLGVRFLDLISA 487 (571)
T ss_pred CCc----eEEEEECCCCcC----CHHHHHHHHHHHHHhcc--------ccCCCEEEEEEEEcccCcH
Confidence 432 477888998885 67778888888776431 2346899999999999875
No 3
>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=3.9e-52 Score=451.31 Aligned_cols=300 Identities=28% Similarity=0.431 Sum_probs=254.7
Q ss_pred CcHHHHHHhCCCcEEEeccCcCCCCChHHHHHHHHHHHHHHhhc-C--CeEEecCceEEEEccchhHHHhccCCCCCcch
Q 006218 1 MRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-G--RCERASIDEVYLDLTDAAEAMLAETPPESLDE 77 (656)
Q Consensus 1 Mp~~~AkklCP~LivV~vP~~~~k~d~~~Yr~~S~~V~~IL~~~-~--~VE~~SIDEafLDlT~~~~~~L~~~~~~~l~~ 77 (656)
||+++|+++||+|++| | .+||+.|+++|++|++++.+| | .||++||||+|||+|+...
T Consensus 49 m~~~~A~~lcP~li~v--~----~~~~~~Y~~~S~~i~~~l~~~sp~~~ve~~SiDE~~lDvt~~~~------------- 109 (379)
T cd01703 49 MSIKDAKEICPDLVLV--N----GEDLTPFRDMSKKVYRLLRSYSWNDRVERLGFDENFMDVTEMRL------------- 109 (379)
T ss_pred CcHHHHHHhCCCeEEE--c----CCChHHHHHHHHHHHHHHHHcCCHhhEEecCCCcEEEEccCccc-------------
Confidence 9999999999999887 4 258999999999999999998 8 8999999999999998631
Q ss_pred hhHHhhhhhcccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEeccCcHHHHHHHhcC
Q 006218 78 VDEEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGM 157 (656)
Q Consensus 78 ~~~e~~~s~l~g~~~~~g~~~~~~v~~w~~~~~~~~~d~ll~~~~~iA~~IR~~I~~~tGlt~SiGIA~NKlLAKLAS~~ 157 (656)
+ .+..+|.+||++|+++||||||||||+||+|||||+++
T Consensus 110 ---------~--------------------------------~g~~la~~ir~~I~~~~Glt~siGIa~nk~lAKlas~~ 148 (379)
T cd01703 110 ---------L--------------------------------VASHIAYEMRERIENELGLTCCAGIASNKLLAKLVGSV 148 (379)
T ss_pred ---------h--------------------------------hHHHHHHHHHHHHHHHhCCeEEEEEcCCHHHHHHHhhh
Confidence 1 13578999999999999999999999999999999999
Q ss_pred CCCCCeeecCc---ccHHhhcccCCCccccCCchHHHHHHHHhcCCcchhhhhcCC---------------HHHHHHhhc
Q 006218 158 NKPAQQTTVPF---SSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFS---------------EDKLQESYG 219 (656)
Q Consensus 158 ~KP~G~~vl~~---~~v~~fL~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~---------------~~~L~~~FG 219 (656)
+||+|+++|.+ +++.+||+++||++|||||++++++|. .+||+|+|||++++ ...|++.||
T Consensus 149 ~KP~g~~~i~~~~~~~~~~fl~~lpv~~l~GiG~~~~~kL~-~~GI~tigdl~~~~~~~~~~~~~~~~~~s~~~L~~~fG 227 (379)
T cd01703 149 NKPNQQTTLLPPSCADLMDFMDLHDLRKIPGIGYKTAAKLE-AHGISSVRDLQEFSNRNRQTVGAAPSLLELLLMVKEFG 227 (379)
T ss_pred cCCCCeEEEcCCchHHHHHHhccCCccccCCcCHHHHHHHH-HcCCCcHHHHHhCCcccccccccccccccHHHHHHHHC
Confidence 99999999876 567789999999999999999999997 99999999999999 999999999
Q ss_pred ccchhhHHHHHhcCCCccc-ccccCCCcccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhh----cCceeeEE
Q 006218 220 FNTGTWLWNIARGISGEEV-QARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQ----NKRIAHTL 294 (656)
Q Consensus 220 ~~~G~~L~~~arGiD~~~V-~~~~~~KSIs~~~tF~~~~~i~~~eel~~~L~~L~~eL~~RLr~~~~~----~~~~a~tv 294 (656)
...|.+||+.|+|+|+++| .+...+|||+.++||.. .++.+.+++..+|..|+++|+.||++++.+ .+..++||
T Consensus 228 ~~~g~~l~~~a~G~d~~~V~~~~~~~ksis~e~tf~~-~~~~~~~~~~~~l~~l~~~l~~rl~~~l~~~~~~~~~~~~tv 306 (379)
T cd01703 228 EGIGQRIWKLLFGRDTSPVKPASDFPQQISIEDSYKK-CSLEEIREARNKIEELLASLLERMKQDLQEVKAGDGRRPHTL 306 (379)
T ss_pred HHHHHHHHHHHCCCCCCccCCCCCCCceeEEeeccCC-CCCCCHHHHHHHHHHHHHHHHHHHHhhhhccchhcCeeeeEE
Confidence 7569999999999999999 55566899999999984 389999999999999999999999985422 68899999
Q ss_pred EEEEeeccCCCCCCCCCcCcceeeCCCcchh-h---H-HhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEecC
Q 006218 295 TLHASAFKSSDSDSRKKFPSKSCPLRYGTAK-I---Q-EDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASK 368 (656)
Q Consensus 295 tL~ir~~~~~~~~s~~~~~sks~~l~~~t~~-I---~-~da~~L~~~al~ll~~~~~~~l~~~~~~~~~ir~lgVsls~ 368 (656)
+|++|+.+. ...+.++.+++++++.++++ + . .+...|++.++.+|...++. ....+.+||++||++++
T Consensus 307 ~l~vr~~~~--~~~~~~~~sr~~~l~~~~~~~~~~~~~~~~~~i~~~~~~L~~~~~~~----~~~~~~~irl~gv~~~~ 379 (379)
T cd01703 307 RLTLRRYTS--TKKHYNRESKQAPIPSHVFQKLTGGNEIAARPIEKILMRLFRELVPP----KNVKGFNLTLLNVCFTN 379 (379)
T ss_pred EEEEEECCC--CCCccceeeeccccCchhhccccccchhhHHHHHHHHHHHHHHhccc----ccCCCCceEEEEEEeeC
Confidence 999998642 11122446899999988751 1 1 13457888888888765421 01124589999999874
No 4
>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=7.1e-52 Score=453.41 Aligned_cols=292 Identities=26% Similarity=0.324 Sum_probs=257.9
Q ss_pred CcHHHHHHhCCCcEEEeccCcCCCCChHHHHHHHHHHHHHHhhc-CCeEEecCceEEEEccchhHHHhccCCCCCcchhh
Q 006218 1 MRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVD 79 (656)
Q Consensus 1 Mp~~~AkklCP~LivV~vP~~~~k~d~~~Yr~~S~~V~~IL~~~-~~VE~~SIDEafLDlT~~~~~~L~~~~~~~l~~~~ 79 (656)
||+++|+++||+|+++ | +|++.|+++|++|+++|.+| +.||++||||+|||+|+....
T Consensus 102 M~~~~A~~lcP~l~vv--~-----~~~~~Y~~~s~~i~~il~~~s~~ve~~SiDE~~lDvt~~~~~-------------- 160 (404)
T cd01701 102 MWVGQAKKLCPQLVTL--P-----YDFEAYEEVSLTFYEILASYTDNIEAVSCDEALIDITSLLEE-------------- 160 (404)
T ss_pred CcHHHHHHHCCCcEEE--C-----CChHHHHHHHHHHHHHHHHhCCceEEcccceEEEEccccccc--------------
Confidence 9999999999999988 5 89999999999999999998 799999999999999986410
Q ss_pred HHhhhhhcccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEeccCcHHHHHHHhcCCC
Q 006218 80 EEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNK 159 (656)
Q Consensus 80 ~e~~~s~l~g~~~~~g~~~~~~v~~w~~~~~~~~~d~ll~~~~~iA~~IR~~I~~~tGlt~SiGIA~NKlLAKLAS~~~K 159 (656)
+++ .+..+|.+||++|++++|||||||||+||++||||++.+|
T Consensus 161 -------~~~------------------------------~~~~la~~ir~~I~~~~gl~~siGia~nk~lAKlAs~~aK 203 (404)
T cd01701 161 -------TYE------------------------------LPEELAEAIRNEIRETTGCSASVGIGPNILLARLATRKAK 203 (404)
T ss_pred -------ccC------------------------------CHHHHHHHHHHHHHHHHCCCEEEEEcCCHHHHHHHhcccC
Confidence 111 1357899999999999999999999999999999999999
Q ss_pred CCCeeecCcccHHhhcccCCCccccCCchHHHHHHHHhcCCcchhhhhcCC--HHHHHHhhcccchhhHHHHHhcCCCcc
Q 006218 160 PAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFS--EDKLQESYGFNTGTWLWNIARGISGEE 237 (656)
Q Consensus 160 P~G~~vl~~~~v~~fL~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~--~~~L~~~FG~~~G~~L~~~arGiD~~~ 237 (656)
|+|++++.++++..||+++||++|||||++++++|. .+||+|++||++++ ...|+++||...|.+||+.++|+|+++
T Consensus 204 P~g~~~i~~~~~~~~L~~lPv~~l~GIG~~~~~~L~-~~Gi~t~~dl~~~~~~~~~L~~~fG~~~g~~L~~~a~G~d~~~ 282 (404)
T cd01701 204 PDGQYHLSAEKVEEFLSQLKVGDLPGVGSSLAEKLV-KLFGDTCGGLELRSKTKEKLQKVLGPKTGEKLYDYCRGIDDRP 282 (404)
T ss_pred CCcEEEECHHHHHHHhhcCCHhHhCCCCHHHHHHHH-HcCCcchHHHHhCcccHHHHHHHHCHHHHHHHHHHhCCcCCCC
Confidence 999999999999999999999999999999999997 99999999999999 999999999757999999999999999
Q ss_pred cccccCCCcccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccC-CCCCCC-------
Q 006218 238 VQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKS-SDSDSR------- 309 (656)
Q Consensus 238 V~~~~~~KSIs~~~tF~~~~~i~~~eel~~~L~~L~~eL~~RLr~~~~~~~~~a~tvtL~ir~~~~-~~~~s~------- 309 (656)
|.+..++|||+.++||+ .++.+.+++..+|..|+++|+.||+. .++.|++|+|++++... .++..+
T Consensus 283 v~~~~~~ksi~~~~tf~--~~~~~~~~l~~~l~~L~~~l~~rLr~----~~~~~~~l~l~l~~~~~~~~~~~~~y~g~~~ 356 (404)
T cd01701 283 VTGEKERKSVSAEINYG--IRFTNVDDVEQFLQRLSEELSKRLEE----SNVTGRQITLKLMKRAPGAPIEPPKYMGHGI 356 (404)
T ss_pred CCCCCCCccccceeeCC--CCCCCHHHHHHHHHHHHHHHHHHHHH----cCCceeeEEEEEEeccccCccccccccccCC
Confidence 99888899999999998 58999999999999999999999997 49999999999997221 111111
Q ss_pred CCcCcceeeCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEecCC
Q 006218 310 KKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKI 369 (656)
Q Consensus 310 ~~~~sks~~l~~~t~~I~~da~~L~~~al~ll~~~~~~~l~~~~~~~~~ir~lgVsls~L 369 (656)
.+..+++.+++.+|+ +...|+++++.+|...+ ..+.+||+|||++++|
T Consensus 357 ~~~~~~~~~l~~pT~----d~~~i~~~a~~ll~~~~--------~~~~~vR~lgv~~~~l 404 (404)
T cd01701 357 CDSFSKSSTLGVATD----DSGVIGTEAKKLFRDLS--------IPPEELRGVGIQVTKL 404 (404)
T ss_pred CcEEeeeeECCCCCC----CHHHHHHHHHHHHHhcc--------CCCCCeeEEEEEEecC
Confidence 124678899999996 67778888888887653 2346899999999986
No 5
>cd01702 PolY_Pol_eta DNA Polymerase eta. Pol eta, also called Rad30A, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Unlike other Y-family members, Pol eta can efficiently and accurately replicate DNA past UV-induced lesions. Its activity is initiated by two simultaneous interactions: the PIP box in pol eta interacting with PCNA, and the UBZ (ubiquitin-binding zinc finger) in pol eta interacting with monoubiquitin attached to PCNA. Pol eta is more efficient in copying damaged DNA than undamaged DNA and seems to recognize when a lesion has been passed, facilitating a lesion-dependent dissociation from the DNA.
Probab=100.00 E-value=3.7e-52 Score=448.88 Aligned_cols=288 Identities=44% Similarity=0.641 Sum_probs=249.9
Q ss_pred CcHHHHHHhCCCcEEEecc----------------CcCCCCChHHHHHHHHHHHHHHhhc-CCeEEecCceEEEEccchh
Q 006218 1 MRGDEAKEVCPQIELVQVP----------------VARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAA 63 (656)
Q Consensus 1 Mp~~~AkklCP~LivV~vP----------------~~~~k~d~~~Yr~~S~~V~~IL~~~-~~VE~~SIDEafLDlT~~~ 63 (656)
||+++|+++||++++|+++ ..+++++|+.|+++|++|++++.+| |.||++||||+|||+.
T Consensus 49 m~~~~A~~lcP~l~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Y~~~S~~i~~~l~~~sp~vE~~SiDE~flDv~--- 125 (359)
T cd01702 49 MTIDEAKKKCPDLILAHVATYKKGEDEADYHENPSPARHKVSLDPYRRASRKILNILKRFGDVVEKASIDEAYLDLG--- 125 (359)
T ss_pred CcHHHHHHHCCCcEEECCccccccccccccccccccccccccHHHHHHHHHHHHHHHHHcCCceEECcCCeeHHHHH---
Confidence 9999999999999999653 2355778999999999999999998 8999999999999992
Q ss_pred HHHhccCCCCCcchhhHHhhhhhcccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEe
Q 006218 64 EAMLAETPPESLDEVDEEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAG 143 (656)
Q Consensus 64 ~~~L~~~~~~~l~~~~~e~~~s~l~g~~~~~g~~~~~~v~~w~~~~~~~~~d~ll~~~~~iA~~IR~~I~~~tGlt~SiG 143 (656)
..+|.+||++|++++|||||||
T Consensus 126 ----------------------------------------------------------~~la~~ir~~I~~~~glt~SiG 147 (359)
T cd01702 126 ----------------------------------------------------------SRIVEEIRQQVYDELGYTCSAG 147 (359)
T ss_pred ----------------------------------------------------------HHHHHHHHHHHHHHhCccEEee
Confidence 1368899999999999999999
Q ss_pred ccCcHHHHHHHhcCCCCCCeeecCcccHHhhcccCCCccccCCchHHHHHHHHhcCCcchhhhhcC--CHHHHHHhhccc
Q 006218 144 IAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKF--SEDKLQESYGFN 221 (656)
Q Consensus 144 IA~NKlLAKLAS~~~KP~G~~vl~~~~v~~fL~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l--~~~~L~~~FG~~ 221 (656)
||+||++|||||+++||+|+++++++++.+||+++||++|||||++++.+|.+.+||+|++||+++ +...|.++||.+
T Consensus 148 Ia~nk~lAKlAs~~~KP~g~~v~~~~~~~~~L~~lpv~~l~GiG~~~~~~ll~~~Gi~ti~dl~~~~~~~~~L~~~fG~~ 227 (359)
T cd01702 148 IAHNKMLAKLASGMNKPNAQTILRNDAVASFLSSLPITSIRGLGGKLGEEIIDLLGLPTEGDVAGFRSSESDLQEHFGEK 227 (359)
T ss_pred ecCCHHHHHHHhcccCCCCeEEECHHHHHHHhhcCcHHHhCCcCHHHHHHHHHHcCCcCHHHHHhccCCHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999998875348999999999999 999999999965
Q ss_pred chhhHHHHHhcCCCcccccccCCCcccccccCCCCCCCCCH-HHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEee
Q 006218 222 TGTWLWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTV-ASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASA 300 (656)
Q Consensus 222 ~G~~L~~~arGiD~~~V~~~~~~KSIs~~~tF~~~~~i~~~-eel~~~L~~L~~eL~~RLr~~~~~~~~~a~tvtL~ir~ 300 (656)
.|.+||+.++|+|+++|.+...+|||+.++||. .++.+. +++..+|..|+++|+.||+.++..+++.|++|+|++++
T Consensus 228 ~g~~l~~~a~G~d~~~v~~~~~~ksi~~~~tf~--~~~~~~~~~l~~~l~~L~~~l~~rL~~~~~~~~~~~~~v~v~lr~ 305 (359)
T cd01702 228 LGEWLYNLLRGIDHEPVKPRPLPKSMGSSKNFP--GKTALSTEDVQHWLLVLASELNSRLEDDRYENNRRPKTLVLSLRQ 305 (359)
T ss_pred HHHHHHHHhCCCCCCCCCCCCCCceeeeeeecC--CCCCChHHHHHHHHHHHHHHHHHHHHhhhhhcCceeeEEEEEEEE
Confidence 799999999999999999888899999999998 578887 99999999999999999998655569999999999998
Q ss_pred ccCCCCCCCCCcCcceeeCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCC---CcceeEEEEEecC
Q 006218 301 FKSSDSDSRKKFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYS---GWRITALSVSASK 368 (656)
Q Consensus 301 ~~~~~~~s~~~~~sks~~l~~~t~~I~~da~~L~~~al~ll~~~~~~~l~~~~~~---~~~ir~lgVsls~ 368 (656)
..+ + ...+++++++.++ ...|+++++.+|..++.- ... +.+||+|||++++
T Consensus 306 ~~~--~----~~~sr~~~~~~~~------~~~i~~~~~~l~~~~~~~-----~~~~~~~~~~rl~g~~~~~ 359 (359)
T cd01702 306 RGD--G----VRRSRSCALPRYD------AQKIVKDAFKLIKAINEE-----GLGLAWNYPLTLLSLSFTK 359 (359)
T ss_pred CCC--c----EEEEEEecCCCCC------HHHHHHHHHHHHHHhhhh-----ccccccCCCeEEEEEEecC
Confidence 542 1 2357777777665 344666666666655421 111 4799999999875
No 6
>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=1.4e-51 Score=441.81 Aligned_cols=288 Identities=31% Similarity=0.450 Sum_probs=252.7
Q ss_pred CcHHHHHHhCCCcEEEeccCcCCCCChHHHHHHHHHHHHHHhhc-CCeEEecCceEEEEccchhHHHhccCCCCCcchhh
Q 006218 1 MRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVD 79 (656)
Q Consensus 1 Mp~~~AkklCP~LivV~vP~~~~k~d~~~Yr~~S~~V~~IL~~~-~~VE~~SIDEafLDlT~~~~~~L~~~~~~~l~~~~ 79 (656)
||+++|+++||+++++ | +|++.|+++|++|++++.+| |.||++||||+|||+|+...
T Consensus 53 m~~~~A~~lcP~l~~~--~-----~~~~~y~~~s~~i~~~l~~~sp~ve~~siDE~~ldvt~~~~--------------- 110 (343)
T cd00424 53 MPVREARKMCPNLILV--P-----ARLDLYRRLSERLLSELEEVAPLVEVASIDELFLDLTGSAR--------------- 110 (343)
T ss_pred CcHHHHHHhCCCeEEE--C-----CCcHHHHHHHHHHHHHHHHhCCcEEEccCCEEEEECCCchh---------------
Confidence 9999999999999888 4 89999999999999999998 89999999999999998651
Q ss_pred HHhhhhhcccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhC-CceeEeccCcHHHHHHHhcCC
Q 006218 80 EEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETE-FTCSAGIAHNKMLAKLASGMN 158 (656)
Q Consensus 80 ~e~~~s~l~g~~~~~g~~~~~~v~~w~~~~~~~~~d~ll~~~~~iA~~IR~~I~~~tG-lt~SiGIA~NKlLAKLAS~~~ 158 (656)
+|+ .+..+|++||++|++++| ||||||||+||++||||++++
T Consensus 111 -------~~~------------------------------~~~~la~~i~~~i~~~~ggl~~siGia~n~~lAKlAs~~~ 153 (343)
T cd00424 111 -------LLG------------------------------LGSEVALRIKRHIAEQLGGITASIGIASNKLLAKLAAKYA 153 (343)
T ss_pred -------ccC------------------------------CHHHHHHHHHHHHHHHhCCceEEEeecccHHHHHHHhccC
Confidence 122 245789999999999998 999999999999999999999
Q ss_pred CCCCeeecCcccHHhhcccCCCccccCCchHHHHHHHHhcCCcchhhhhcCC-HHHHHHhhcccchhhHHHHHhcCCCcc
Q 006218 159 KPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFS-EDKLQESYGFNTGTWLWNIARGISGEE 237 (656)
Q Consensus 159 KP~G~~vl~~~~v~~fL~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~-~~~L~~~FG~~~G~~L~~~arGiD~~~ 237 (656)
||+|+++++++++..||+++||+++||||++++++|. .+||+|++||++++ ...|+++||. .|.++|+.++|+|+++
T Consensus 154 KP~g~~v~~~~~~~~~L~~lpi~~l~giG~~~~~~L~-~~Gi~ti~dl~~~~~~~~l~~~fg~-~~~~l~~~a~G~d~~~ 231 (343)
T cd00424 154 KPDGLTILDPEDLPGFLSKLPLTDLPGIGAVTAKRLE-AVGINPIGDLLAASPDALLALWGGV-SGERLWYALRGIDDEP 231 (343)
T ss_pred CCCCEEEEcHHHHHHHHhcCChhhcCCCCHHHHHHHH-HcCCCcHHHHhcCCHHHHHHHHhhH-HHHHHHHHhCCcCCCC
Confidence 9999999999999999999999999999999999997 99999999999999 8889999997 6999999999999999
Q ss_pred cccccCCCcccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCCCCCCCcCccee
Q 006218 238 VQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSC 317 (656)
Q Consensus 238 V~~~~~~KSIs~~~tF~~~~~i~~~eel~~~L~~L~~eL~~RLr~~~~~~~~~a~tvtL~ir~~~~~~~~s~~~~~sks~ 317 (656)
|.+...+|||+.++||+ .++.+.+++..+|..|+++|+.||+. .++.+++|+|++++.+. ....+....+++.
T Consensus 232 v~~~~~~ksi~~~~tf~--~~~~~~~~l~~~l~~l~~~l~~rL~~----~~~~~~~l~l~lr~~~~-~~~~~~~~~~~~~ 304 (343)
T cd00424 232 LSPPRPRKSFSHERVLP--RDSRNAEDARPLLRLLLEKLARRLRR----DGRGATRLRLWLRTVDG-RWSGHADIPSRSA 304 (343)
T ss_pred CCCCCCCCceeeeEECC--CCCCCHHHHHHHHHHHHHHHHHHHHH----cCCceeEEEEEEEeCCC-cccccceeeeeee
Confidence 98888899999999998 58999999999999999999999997 49999999999997542 1001112467888
Q ss_pred eCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEec
Q 006218 318 PLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSAS 367 (656)
Q Consensus 318 ~l~~~t~~I~~da~~L~~~al~ll~~~~~~~l~~~~~~~~~ir~lgVsls 367 (656)
+++.+| +...|+++++.+|...+. ...+.+||++||+++
T Consensus 305 ~l~~~t-----~~~~l~~~~~~l~~~~~~------~~~~~~ir~~gv~~~ 343 (343)
T cd00424 305 PRPIST-----EDGELLHALDKLWRALLD------DKGPRRLRRLGVRLS 343 (343)
T ss_pred eCCCCC-----CHHHHHHHHHHHHHhhhh------ccCCCCeeEEEEEeC
Confidence 998887 345677777777765541 113568999999875
No 7
>PRK01216 DNA polymerase IV; Validated
Probab=100.00 E-value=3.3e-51 Score=440.17 Aligned_cols=283 Identities=25% Similarity=0.377 Sum_probs=250.7
Q ss_pred CcHHHHHHhCCCcEEEeccCcCCCCChHHHHHHHHHHHHHHhhc-CCeEEecCceEEEEccchhHHHhccCCCCCcchhh
Q 006218 1 MRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVD 79 (656)
Q Consensus 1 Mp~~~AkklCP~LivV~vP~~~~k~d~~~Yr~~S~~V~~IL~~~-~~VE~~SIDEafLDlT~~~~~~L~~~~~~~l~~~~ 79 (656)
||+++|+++||++++| | +|++.|+++|++|++++.+| |.||++||||+|||+|++.
T Consensus 59 M~~~~A~~lcP~li~v--~-----~d~~~y~~~s~~i~~~l~~~tp~ve~~siDE~~LDvt~~~---------------- 115 (351)
T PRK01216 59 MPIVEAKKILPNAVYL--P-----MRKEVYQQVSNRIMKLLREYSEKIEIASIDEAYLDISDKV---------------- 115 (351)
T ss_pred CcHHHHHHHCCCeEEE--C-----CCHHHHHHHHHHHHHHHHHhCCceEEccCCeEEEEcccch----------------
Confidence 9999999999999888 5 89999999999999999998 8999999999999999865
Q ss_pred HHhhhhhcccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEeccCcHHHHHHHhcCCC
Q 006218 80 EEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNK 159 (656)
Q Consensus 80 ~e~~~s~l~g~~~~~g~~~~~~v~~w~~~~~~~~~d~ll~~~~~iA~~IR~~I~~~tGlt~SiGIA~NKlLAKLAS~~~K 159 (656)
++|| .+..+|++||++|++++|||||||||+||++|||||+++|
T Consensus 116 ------~l~g------------------------------~~~~la~~ir~~I~~~~glt~siGia~nk~lAKlas~~~K 159 (351)
T PRK01216 116 ------KNYQ------------------------------DAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAK 159 (351)
T ss_pred ------hccC------------------------------CHHHHHHHHHHHHHHHHCCcEEEEecCCHHHHHHHHhccC
Confidence 2232 2457899999999999999999999999999999999999
Q ss_pred CCCeeecCcccHHhhcccCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhcccchhhHHHHHhcCCCcccc
Q 006218 160 PAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQ 239 (656)
Q Consensus 160 P~G~~vl~~~~v~~fL~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~~~G~~L~~~arGiD~~~V~ 239 (656)
|+|+++++++++.+||++|||+++||||++++++|. ++||+|+|||++++.+.|.++||...|.+||+.++|+|.++|.
T Consensus 160 P~g~~vi~~~~~~~~L~~LPi~~l~giG~~~~~~L~-~~Gi~TigdL~~~~~~~L~~rfG~~~~~~L~~~a~G~d~~pv~ 238 (351)
T PRK01216 160 PNGIKVIDDEEVKRFINELDIADIPGIGDITAEKLK-KLGVNKLVDTLRIEFDELKGIIGEAKAKYLFSLARNEYNEPVR 238 (351)
T ss_pred CCCEEEeCHHHHHHHHhcCCcccccCCCHHHHHHHH-HcCCCcHHHHhcCCHHHHHHHHCHHHHHHHHHHhCCCCCCCCC
Confidence 999999999999999999999999999999999997 9999999999999999999999975699999999999999998
Q ss_pred cccCCCcccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCCCCCCCcCcceeeC
Q 006218 240 ARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPL 319 (656)
Q Consensus 240 ~~~~~KSIs~~~tF~~~~~i~~~eel~~~L~~L~~eL~~RLr~~~~~~~~~a~tvtL~ir~~~~~~~~s~~~~~sks~~l 319 (656)
+ ..+|||+.++||. .++.+.+++...|.+|+++++.||+. .++++++++++. +|. +.+++.++
T Consensus 239 ~-~~~ksi~~~~tl~--~di~~~~~l~~~l~~L~~~~~~rl~~-------~~~~~~~~~~~~---df~----~~t~~~tl 301 (351)
T PRK01216 239 A-RVRKSIGRYVTLP--RNTRDLEEIKPYLKRAIEEAYYKLDG-------IPKAIHVVAIME---DLD----IVSRGRTF 301 (351)
T ss_pred C-CCCCCCcCeEECC--CccCCHHHHHHHHHHHHHHHHHHHHh-------CCCEEEEEEEcC---CCC----EEEEEEEC
Confidence 7 4569999999998 68999999999999999999999974 467889998864 343 35888999
Q ss_pred CCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEecCCeec
Q 006218 320 RYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPV 372 (656)
Q Consensus 320 ~~~t~~I~~da~~L~~~al~ll~~~~~~~l~~~~~~~~~ir~lgVsls~L~~~ 372 (656)
+.+++ ...+++.+.++|...+ .+.+.+||+|||++++|.+.
T Consensus 302 ~~~~~-----~~~~~~~a~~Ll~~~~-------~~~~~~vRllGv~~~~l~~~ 342 (351)
T PRK01216 302 THGIS-----KETAYREAVRLLQKIL-------EEDERKIRRIGVRFSKIIEA 342 (351)
T ss_pred CCCCC-----HHHHHHHHHHHHHhhh-------hcCCCCeeEEEEEEeccccc
Confidence 88874 2456777777776432 11235899999999999864
No 8
>PRK03858 DNA polymerase IV; Validated
Probab=100.00 E-value=9.1e-51 Score=443.04 Aligned_cols=298 Identities=26% Similarity=0.359 Sum_probs=263.6
Q ss_pred CcHHHHHHhCCCcEEEeccCcCCCCChHHHHHHHHHHHHHHhhc-CCeEEecCceEEEEccchhHHHhccCCCCCcchhh
Q 006218 1 MRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVD 79 (656)
Q Consensus 1 Mp~~~AkklCP~LivV~vP~~~~k~d~~~Yr~~S~~V~~IL~~~-~~VE~~SIDEafLDlT~~~~~~L~~~~~~~l~~~~ 79 (656)
||+++|+++||+|+++ | +|++.|+++|++|++++.+| |.||++||||+|||+|+..
T Consensus 54 m~~~~A~~lcP~l~~~--~-----~d~~~y~~~s~~i~~~l~~~s~~ve~~siDe~~ldvt~~~---------------- 110 (396)
T PRK03858 54 MGGRQARRLCPQAVVV--P-----PRMSAYSRASKAVFEVFRDTTPLVEGLSIDEAFLDVGGLR---------------- 110 (396)
T ss_pred ChHHHHHHHCCCeEEE--C-----CCHHHHHHHHHHHHHHHHHhCCceEEecCCeEEEEccccc----------------
Confidence 9999999999999888 5 89999999999999999998 8999999999999999864
Q ss_pred HHhhhhhcccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEeccCcHHHHHHHhcCCC
Q 006218 80 EEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNK 159 (656)
Q Consensus 80 ~e~~~s~l~g~~~~~g~~~~~~v~~w~~~~~~~~~d~ll~~~~~iA~~IR~~I~~~tGlt~SiGIA~NKlLAKLAS~~~K 159 (656)
++|| .+..+|.+||++|++++|||||||||+||++||||++.+|
T Consensus 111 ------~~~~------------------------------~~~~la~~ir~~i~~~~gl~~svGia~n~~lAklas~~~K 154 (396)
T PRK03858 111 ------RISG------------------------------TPVQIAARLRRRVREEVGLPITVGVARTKFLAKVASQVAK 154 (396)
T ss_pred ------cccC------------------------------CHHHHHHHHHHHHHHHHCCCeEEEEcCChHHHHHhhcccC
Confidence 2232 1357899999999999999999999999999999999999
Q ss_pred CCCeeecCcccHHhhcccCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhcccchhhHHHHHhcCCCcccc
Q 006218 160 PAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQ 239 (656)
Q Consensus 160 P~G~~vl~~~~v~~fL~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~~~G~~L~~~arGiD~~~V~ 239 (656)
|+|+++++++++..||+++||++|||||++++++|. ++||+|++||++++...|.++||...|++||+.++|+|+++|.
T Consensus 155 p~g~~~i~~~~~~~~L~~lpl~~l~Gig~~~~~~L~-~~Gi~t~~dl~~l~~~~L~~~fG~~~~~~l~~~a~G~d~~~v~ 233 (396)
T PRK03858 155 PDGLLVVPPDRELAFLHPLPVRRLWGVGPVTAAKLR-AHGITTVGDVAELPESALVSLLGPAAGRHLHALAHNRDPRRVE 233 (396)
T ss_pred CCceEEECcHHHHHHHhcCChhhcCCCCHHHHHHHH-HhCCCcHHHHhcCCHHHHHHHhCcHHHHHHHHHhCCCCCCCCC
Confidence 999999999999999999999999999999999997 9999999999999999999999986799999999999999998
Q ss_pred cccCCCcccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCCCCCCCcCcceeeC
Q 006218 240 ARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPL 319 (656)
Q Consensus 240 ~~~~~KSIs~~~tF~~~~~i~~~eel~~~L~~L~~eL~~RLr~~~~~~~~~a~tvtL~ir~~~~~~~~s~~~~~sks~~l 319 (656)
+..++|||+.+++|. .++.+.+++..+|..|+++|+.||++ .++.+++|+|++++.+ +. ..++++++
T Consensus 234 ~~~~~ksi~~~~t~~--~~~~~~~~l~~~l~~L~~~l~~rLr~----~~~~~~~l~l~l~~~~---~~----~~~~~~~l 300 (396)
T PRK03858 234 TGRRRRSVGAQRALG--RGPNSPAEVDAVVVALVDRVARRMRA----AGRTGRTVVLRLRFDD---FT----RATRSHTL 300 (396)
T ss_pred CCCCCccccceeEcC--CCCCCHHHHHHHHHHHHHHHHHHHHh----cCCCcceEEEEEEeCC---CC----EEEEEEEC
Confidence 878889999999998 58999999999999999999999997 4999999999999753 22 24678888
Q ss_pred CCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEecCCeeccCcccccccc-cc
Q 006218 320 RYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPVLSGTCSIMKY-FN 384 (656)
Q Consensus 320 ~~~t~~I~~da~~L~~~al~ll~~~~~~~l~~~~~~~~~ir~lgVsls~L~~~~~~~~sq~~l-F~ 384 (656)
+.+|+ +...|++.+..+|...+. ...+.+||++||.+++|.+. ...|.+| |+
T Consensus 301 ~~~t~----~~~~l~~l~~~ll~~~~~------~~~~~~irligv~~~~l~~~---~~~q~~L~f~ 353 (396)
T PRK03858 301 PRPTA----STATLLAAARDLVAAAAP------LIAERGLTLVGFAVSNLDDD---GAQQLELPFG 353 (396)
T ss_pred CCCcC----CHHHHHHHHHHHHHhhhh------ccCCCCeEEEEEEeecCCcc---cccccCCCcc
Confidence 88886 556677777777765331 11246899999999999864 3457788 75
No 9
>PRK03348 DNA polymerase IV; Provisional
Probab=100.00 E-value=3.6e-50 Score=445.64 Aligned_cols=296 Identities=26% Similarity=0.344 Sum_probs=263.0
Q ss_pred CcHHHHHHhCCC-cEEEeccCcCCCCChHHHHHHHHHHHHHHhhc-CCeEEecCceEEEEccchhHHHhccCCCCCcchh
Q 006218 1 MRGDEAKEVCPQ-IELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEV 78 (656)
Q Consensus 1 Mp~~~AkklCP~-LivV~vP~~~~k~d~~~Yr~~S~~V~~IL~~~-~~VE~~SIDEafLDlT~~~~~~L~~~~~~~l~~~ 78 (656)
||+.+|+++||+ ++++ | +|++.|+.+|++||+++.+| |.||++||||+|||+++..
T Consensus 59 Mp~~~A~~lcP~~lv~v--~-----~d~~~Y~~~s~~i~~~l~~~sp~VE~~SiDE~flD~~~l~--------------- 116 (454)
T PRK03348 59 MPMHQARRLVGNGAVVL--P-----PRFVVYRAASRRVFDTLRELSPVVEQLSFDEAFVEPAELA--------------- 116 (454)
T ss_pred CcHHHHHHhCCCCEEEE--C-----CChHHHHHHHHHHHHHHHHhCCceEEecCCeEEEEccccc---------------
Confidence 999999999999 8887 5 89999999999999999998 8999999999999987643
Q ss_pred hHHhhhhhcccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEeccCcHHHHHHHhcCC
Q 006218 79 DEEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMN 158 (656)
Q Consensus 79 ~~e~~~s~l~g~~~~~g~~~~~~v~~w~~~~~~~~~d~ll~~~~~iA~~IR~~I~~~tGlt~SiGIA~NKlLAKLAS~~~ 158 (656)
+.. ...+..+|.+||++|++++||+||||||+||+|||||++++
T Consensus 117 ----------~~~--------------------------~~~~~~~a~~lr~~I~~~~Gl~~SvGIa~nk~lAKlAs~~a 160 (454)
T PRK03348 117 ----------GAS--------------------------AEEVEAFAERLRARVREETGLPASVGAGSGKQIAKIASGLA 160 (454)
T ss_pred ----------ccc--------------------------CCCHHHHHHHHHHHHHHHHCCCeEEEEcCCHHHHHHhhccC
Confidence 100 00135689999999999999999999999999999999999
Q ss_pred CCCCeeecCcccHHhhcccCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhcccchhhHHHHHhcCCCccc
Q 006218 159 KPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEV 238 (656)
Q Consensus 159 KP~G~~vl~~~~v~~fL~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~~~G~~L~~~arGiD~~~V 238 (656)
||+|+++++++++..||++|||++|||||++++++|. ++||+||+||++++...|.++||...|.+||+.|+|+|+++|
T Consensus 161 KP~G~~vi~~~~~~~~L~~LPv~~L~GIG~~t~~~L~-~lGI~TigDLa~l~~~~L~~~fG~~~g~~L~~~a~G~d~~pv 239 (454)
T PRK03348 161 KPDGIRVVPPGEERELLAPLPVRRLWGIGPVTEEKLH-RLGIETIGDLAALSEAEVANLLGATVGPALHRLARGIDDRPV 239 (454)
T ss_pred CCCcEEEEEchHHHHHHHhCCccccCCCCHHHHHHHH-HcCCccHHHHhcCCHHHHHHHHCHHHHHHHHHHHcCCCCCCc
Confidence 9999999999999999999999999999999999997 999999999999999999999996579999999999999999
Q ss_pred ccccCCCcccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCCCCCCCcCcceee
Q 006218 239 QARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCP 318 (656)
Q Consensus 239 ~~~~~~KSIs~~~tF~~~~~i~~~eel~~~L~~L~~eL~~RLr~~~~~~~~~a~tvtL~ir~~~~~~~~s~~~~~sks~~ 318 (656)
.+...+|+|+.+++|. .++.+.+++..+|..|+++|+.||++ .++.|++|+|++++.+ +. ..+++.+
T Consensus 240 ~~~~~~ksis~e~tf~--~~i~~~~~l~~~L~~L~~~l~~rL~~----~g~~~r~v~l~l~~~d---~~----~~srs~~ 306 (454)
T PRK03348 240 AERAEAKQISAESTFA--VDLTTRAQLREAIERIAEHAHRRLLK----DGRGARTVTVKLRKSD---FS----TLTRSAT 306 (454)
T ss_pred ccCCCCceEEEEEECC--CCCCCHHHHHHHHHHHHHHHHHHHHH----cCCCccEEEEEEEeCC---CC----ccEEEEE
Confidence 9988899999999998 58999999999999999999999997 4999999999998753 22 2478899
Q ss_pred CCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEecCCeeccCccccccccccCC
Q 006218 319 LRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPVLSGTCSIMKYFNGP 386 (656)
Q Consensus 319 l~~~t~~I~~da~~L~~~al~ll~~~~~~~l~~~~~~~~~ir~lgVsls~L~~~~~~~~sq~~lF~~~ 386 (656)
++++|+ +...|++.+..+|...+ ...+||++||++++|.+ ..|.+||...
T Consensus 307 l~~pt~----d~~~L~~la~~ll~~~~---------~~~~vRllgV~~s~l~~-----~~q~~LF~~~ 356 (454)
T PRK03348 307 LPYATD----DAAVLAATARRLLLDPD---------EIGPIRLVGVGFSGLSD-----VRQESLFPEL 356 (454)
T ss_pred CCCCCC----CHHHHHHHHHHHHHhhc---------cCCCeEEEEEEECCCCc-----chhhccCCCc
Confidence 999886 56678888877776532 23489999999999974 2678999754
No 10
>PRK14133 DNA polymerase IV; Provisional
Probab=100.00 E-value=2.6e-50 Score=432.63 Aligned_cols=290 Identities=28% Similarity=0.353 Sum_probs=261.2
Q ss_pred CcHHHHHHhCCCcEEEeccCcCCCCChHHHHHHHHHHHHHHhhc-CCeEEecCceEEEEccchhHHHhccCCCCCcchhh
Q 006218 1 MRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVD 79 (656)
Q Consensus 1 Mp~~~AkklCP~LivV~vP~~~~k~d~~~Yr~~S~~V~~IL~~~-~~VE~~SIDEafLDlT~~~~~~L~~~~~~~l~~~~ 79 (656)
||+++|+++||+++++ | +|++.|+++|++|++++.+| |.||++||||+|||+|+...
T Consensus 57 m~~~~A~~lcP~l~~~--~-----~d~~~y~~~s~~i~~~l~~~s~~ve~~siDe~~ldv~~~~~--------------- 114 (347)
T PRK14133 57 MPVFMAKKRCPHGIFL--P-----VRHERYKEVSKNIFKILYEVTPIVEPVSIDEAYLDITNIKE--------------- 114 (347)
T ss_pred ChHHHHHHHCCCcEEE--C-----CCHHHHHHHHHHHHHHHHHhCCceEEccCCeEEEEccCCCC---------------
Confidence 9999999999999888 5 89999999999999999998 89999999999999998530
Q ss_pred HHhhhhhcccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEeccCcHHHHHHHhcCCC
Q 006218 80 EEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNK 159 (656)
Q Consensus 80 ~e~~~s~l~g~~~~~g~~~~~~v~~w~~~~~~~~~d~ll~~~~~iA~~IR~~I~~~tGlt~SiGIA~NKlLAKLAS~~~K 159 (656)
.+..+|++||++|++++|||||||||+||++||||++.+|
T Consensus 115 ----------------------------------------~~~~la~~i~~~i~~~~gl~~siGia~n~~~Aklas~~~k 154 (347)
T PRK14133 115 ----------------------------------------EPIKIAKYIKKKVKKETGLTLSVGISYNKFLAKLASDWNK 154 (347)
T ss_pred ----------------------------------------CHHHHHHHHHHHHHHHHCCcEEEEEcCcHHHHHHHhccCC
Confidence 1246899999999999999999999999999999999999
Q ss_pred CCCeeecCcccHHhhcccCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhcccchhhHHHHHhcCCCcccc
Q 006218 160 PAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQ 239 (656)
Q Consensus 160 P~G~~vl~~~~v~~fL~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~~~G~~L~~~arGiD~~~V~ 239 (656)
|+|+++++++++..||+++||+++||||+++.++|. .+||+|++||++++...|+++||. .|.++|+.++|+|..+|.
T Consensus 155 p~g~~~~~~~~~~~~L~~lpv~~l~gig~~~~~~L~-~~Gi~ti~dl~~l~~~~L~~rfG~-~g~~l~~~a~G~d~~~v~ 232 (347)
T PRK14133 155 PDGIKIITEDMIPDILKPLPISKVHGIGKKSVEKLN-NIGIYTIEDLLKLSREFLIEYFGK-FGVEIYERIRGIDYREVE 232 (347)
T ss_pred CCceEEECHHHHHHHHHhCCccccCCCCHHHHHHHH-HcCCccHHHHhhCCHHHHHHHHhH-HHHHHHHHhCCCCCCCCC
Confidence 999999999999999999999999999999999997 999999999999999999999997 699999999999999999
Q ss_pred cccCCCcccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCCCCCCCcCcceeeC
Q 006218 240 ARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPL 319 (656)
Q Consensus 240 ~~~~~KSIs~~~tF~~~~~i~~~eel~~~L~~L~~eL~~RLr~~~~~~~~~a~tvtL~ir~~~~~~~~s~~~~~sks~~l 319 (656)
+..++|||+.+++|. .++.+.+++..+|..|+++|+.||++ +++.+++|+|++++.+ +. ..+++.++
T Consensus 233 ~~~~~ksi~~~~~~~--~~~~~~~~l~~~l~~L~~~l~~rL~~----~~~~~~~l~l~l~~~~---~~----~~~~~~~l 299 (347)
T PRK14133 233 VSRERKSIGKETTLK--KDTKDKEELKKYLKDFSNIISEELKK----RNLYGKTVTVKIKTSD---FQ----THTKSKTL 299 (347)
T ss_pred CCCCCcceEeeEEcC--CCCCCHHHHHHHHHHHHHHHHHHHHh----cCCCcceEEEEEEECC---CC----eeEEEEEC
Confidence 888899999999998 58999999999999999999999997 5999999999999743 22 23678888
Q ss_pred CCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEecCCeeccCccccccccc
Q 006218 320 RYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPVLSGTCSIMKYF 383 (656)
Q Consensus 320 ~~~t~~I~~da~~L~~~al~ll~~~~~~~l~~~~~~~~~ir~lgVsls~L~~~~~~~~sq~~lF 383 (656)
+.+|+ +...|++.+..+|..++ .+.+||.|||++++|.+. ...|.+||
T Consensus 300 ~~~t~----~~~~l~~l~~~lle~~~---------~~~~vr~lgl~~~~l~~~---~~~q~~l~ 347 (347)
T PRK14133 300 NDYIR----DKEEIYNVACEILEHIN---------IKEPIRLIGLSVSNLSEN---KIEQLSFL 347 (347)
T ss_pred CCCcC----CHHHHHHHHHHHHHhcc---------CCCCEEEEEEEEecCCCC---cccccCCC
Confidence 88885 66778888777776532 357999999999999965 34567776
No 11
>PRK02794 DNA polymerase IV; Provisional
Probab=100.00 E-value=2.8e-50 Score=442.65 Aligned_cols=297 Identities=24% Similarity=0.358 Sum_probs=263.9
Q ss_pred CcHHHHHHhCCCcEEEeccCcCCCCChHHHHHHHHHHHHHHhhc-CCeEEecCceEEEEccchhHHHhccCCCCCcchhh
Q 006218 1 MRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVD 79 (656)
Q Consensus 1 Mp~~~AkklCP~LivV~vP~~~~k~d~~~Yr~~S~~V~~IL~~~-~~VE~~SIDEafLDlT~~~~~~L~~~~~~~l~~~~ 79 (656)
||+++|+++||+|+++ | +|++.|+++|++|++++.+| |.||++||||+|||+|+..
T Consensus 89 M~~~~A~~lcP~l~~v--~-----~d~~~y~~~s~~i~~~l~~~sp~ve~~siDe~~ldvt~~~---------------- 145 (419)
T PRK02794 89 MPMFKALKLCPDAVVI--K-----PDMEKYVRVGREVRAMMQALTPLVEPLSIDEAFLDLSGTE---------------- 145 (419)
T ss_pred CHHHHHHHHCCCcEEE--C-----CCHHHHHHHHHHHHHHHHHhCcceeeccCCeEEEeccchh----------------
Confidence 9999999999999888 5 89999999999999999998 8999999999999999864
Q ss_pred HHhhhhhcccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEeccCcHHHHHHHhcCCC
Q 006218 80 EEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNK 159 (656)
Q Consensus 80 ~e~~~s~l~g~~~~~g~~~~~~v~~w~~~~~~~~~d~ll~~~~~iA~~IR~~I~~~tGlt~SiGIA~NKlLAKLAS~~~K 159 (656)
++||.. +..++.+||++|++++|||||||||+||++||||++.+|
T Consensus 146 ------~l~g~~-----------------------------~~~~~~~i~~~i~~~~gl~~svGIa~n~~lAKlas~~~K 190 (419)
T PRK02794 146 ------RLHGAP-----------------------------PAVVLARFARRVEREIGITVSVGLSYNKFLAKIASDLDK 190 (419)
T ss_pred ------hhcCCC-----------------------------HHHHHHHHHHHHHHHHCCceEEEEcCCHHHHHHHHhhhC
Confidence 333321 234678999999999999999999999999999999999
Q ss_pred CCCeeecCcccHHhhcccCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhcccchhhHHHHHhcCCCcccc
Q 006218 160 PAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQ 239 (656)
Q Consensus 160 P~G~~vl~~~~v~~fL~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~~~G~~L~~~arGiD~~~V~ 239 (656)
|+|++++.++++.+||+++||++|||||++++++|. ++||+||+||++++...|+++||. .|.++|+.++|+|+++|.
T Consensus 191 P~g~~ii~~~~~~~~L~~lPl~~L~GiG~~~~~~L~-~~GI~tigdL~~l~~~~L~~rfG~-~g~~l~~~a~G~d~~~v~ 268 (419)
T PRK02794 191 PRGFSVIGRAEALAFLAPKPVGIIWGVGPATAARLA-RDGIRTIGDLQRADEADLMRRFGS-MGLRLWRLARGIDDRKVS 268 (419)
T ss_pred CCCeEecCHHHHHHHHhcCChhhhCCCCHHHHHHHH-HhccchHHHHhhCCHHHHHHHHhH-HHHHHHHHhCCCCCCCCc
Confidence 999999999999999999999999999999999997 999999999999999999999998 699999999999999999
Q ss_pred cccCCCcccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCCCCCCCcCcceeeC
Q 006218 240 ARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPL 319 (656)
Q Consensus 240 ~~~~~KSIs~~~tF~~~~~i~~~eel~~~L~~L~~eL~~RLr~~~~~~~~~a~tvtL~ir~~~~~~~~s~~~~~sks~~l 319 (656)
+..++|||+.+++|. .++.+.+++..+|..|+++|+.||+. .++.+++|+|++++.+ +. ..++++++
T Consensus 269 ~~~~~ksi~~~~tl~--~~~~~~~~l~~~l~~L~~~l~~rL~~----~~~~~~~l~l~l~~~~---~~----~~~~~~~l 335 (419)
T PRK02794 269 PDREAKSVSAETTFE--TDLSDFEDLEPILWRLSEKVSRRLKA----AGLAGRTVTLKLKTAD---FR----LRTRRRTL 335 (419)
T ss_pred cCCCCceeeeeEECC--CCCCCHHHHHHHHHHHHHHHHHHHHh----cCCCcceEEEEEEECC---CC----ceEEEEEC
Confidence 888899999999998 58999999999999999999999997 5999999999999643 22 24678888
Q ss_pred CCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEecCCeeccCccccccccccC
Q 006218 320 RYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPVLSGTCSIMKYFNG 385 (656)
Q Consensus 320 ~~~t~~I~~da~~L~~~al~ll~~~~~~~l~~~~~~~~~ir~lgVsls~L~~~~~~~~sq~~lF~~ 385 (656)
+.+|+ +...|++.+..+|... +.+.+||.|||++++|.+.. ...|.+||+.
T Consensus 336 ~~pt~----~~~~l~~~~~~ll~~~---------~~~~~vr~igv~~~~l~~~~--~~~q~~LF~~ 386 (419)
T PRK02794 336 EDPTQ----LADRIFRTARELLEKE---------TDGTAFRLIGIGVSDLSPAD--EADPPDLLDP 386 (419)
T ss_pred CCCcC----CHHHHHHHHHHHHHhc---------ccCCCEEEEEEEEecCCCcc--ccccccccCc
Confidence 88885 5667888777777643 24668999999999999752 2247899974
No 12
>PRK03103 DNA polymerase IV; Reviewed
Probab=100.00 E-value=4.1e-50 Score=439.88 Aligned_cols=298 Identities=25% Similarity=0.405 Sum_probs=265.0
Q ss_pred CcHHHHHHhCCCcEEEeccCcCCCCChHHHHHHHHHHHHHHhhc-CCeEEecCceEEEEccchhHHHhccCCCCCcchhh
Q 006218 1 MRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVD 79 (656)
Q Consensus 1 Mp~~~AkklCP~LivV~vP~~~~k~d~~~Yr~~S~~V~~IL~~~-~~VE~~SIDEafLDlT~~~~~~L~~~~~~~l~~~~ 79 (656)
||+++|+++||+|+++ | +|++.|+++|++|++++.+| |.||++||||+|||+|+..
T Consensus 59 m~~~~A~~lcP~l~~~--~-----~d~~~y~~~s~~i~~~l~~~sp~ve~~siDe~~lDvt~~~---------------- 115 (409)
T PRK03103 59 ERLWEAQQKCPDLVVV--K-----PRMQRYIDVSLQITRILEDFTDLVEPFSIDEQFLDVTGSQ---------------- 115 (409)
T ss_pred ChHHHHHHHCCCeEEE--C-----CCHHHHHHHHHHHHHHHHHhCccceecCCCeeEeeccchh----------------
Confidence 9999999999999888 5 89999999999999999998 8999999999999999875
Q ss_pred HHhhhhhcccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEeccCcHHHHHHHhcC--
Q 006218 80 EEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGM-- 157 (656)
Q Consensus 80 ~e~~~s~l~g~~~~~g~~~~~~v~~w~~~~~~~~~d~ll~~~~~iA~~IR~~I~~~tGlt~SiGIA~NKlLAKLAS~~-- 157 (656)
++|| .+..+|.+||++|++++|||||||||+||++||||++.
T Consensus 116 ------~~~~------------------------------~~~~la~~ir~~i~~~~gl~~svGia~n~~lAklas~~~~ 159 (409)
T PRK03103 116 ------KLFG------------------------------SPLEIAQKIQQRIMRETGVYARVGIGPNKLLAKMACDNFA 159 (409)
T ss_pred ------hcCC------------------------------CHHHHHHHHHHHHHHHHCceEEEeecCCHHHHHHHhcchh
Confidence 2232 13578999999999999999999999999999999998
Q ss_pred -CCCCCeeecCcccHHhhcccCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhcccchhhHHHHHhcCCCc
Q 006218 158 -NKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGE 236 (656)
Q Consensus 158 -~KP~G~~vl~~~~v~~fL~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~~~G~~L~~~arGiD~~ 236 (656)
+||+|+++++++++..||+++||++|||||+++.++|. .+||+|+|||++++...|+++||. .|.++|+.++|+|++
T Consensus 160 k~kp~g~~v~~~~~~~~~L~~lpi~~l~gig~~~~~~L~-~~Gi~tigdl~~~~~~~L~~~fG~-~~~~l~~~a~G~d~~ 237 (409)
T PRK03103 160 KKNPDGLFTLDKEDVPADLWPLPVRKLFGVGSRMEKHLR-RMGIRTIGQLANTPLERLKKRWGI-NGEVLWRTANGIDYS 237 (409)
T ss_pred hcCCCcEEEECHHHHHHHHHcCCHhhcCCccHHHHHHHH-HcCCCCHHHHhcCCHHHHHHHHCH-HHHHHHHHhcCCCCC
Confidence 99999999999999999999999999999999999997 999999999999999999999997 699999999999999
Q ss_pred ccccccC--CCcccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCCCCCCCcCc
Q 006218 237 EVQARLL--PKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPS 314 (656)
Q Consensus 237 ~V~~~~~--~KSIs~~~tF~~~~~i~~~eel~~~L~~L~~eL~~RLr~~~~~~~~~a~tvtL~ir~~~~~~~~s~~~~~s 314 (656)
+|.+... +|||+.+.+|+ .++.+.++|...|..|+++|+.||++ .+..+++|+|++++.++ .. .++.+
T Consensus 238 ~v~~~~~~~~ksi~~~~t~~--~~~~~~~~l~~~l~~L~~~l~~rLr~----~~~~~~~l~l~lr~~~~---~~-~~~~~ 307 (409)
T PRK03103 238 PVTPHSLDRQKAIGHQMTLP--RDYRGFEEIKVVLLELCEEVCRRARA----KGYMGRTVSVSLRGADF---DW-PTGFS 307 (409)
T ss_pred cCCcccCCCCCccCCCeECC--CCCCCHHHHHHHHHHHHHHHHHHHHH----hCCceeEEEEEEEeCCC---cC-CCCcc
Confidence 9988654 58999999998 68999999999999999999999997 49999999999987542 22 23357
Q ss_pred ceeeCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEecCCeeccCccccccccccC
Q 006218 315 KSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPVLSGTCSIMKYFNG 385 (656)
Q Consensus 315 ks~~l~~~t~~I~~da~~L~~~al~ll~~~~~~~l~~~~~~~~~ir~lgVsls~L~~~~~~~~sq~~lF~~ 385 (656)
++++++.||+ +...|++.+..+|..+ +.+.+||+|||++++|.+. ...|.+||+.
T Consensus 308 ~~~~l~~pt~----~~~~l~~~~~~ll~~~---------~~~~~vr~lgv~~~~l~~~---~~~q~~LF~~ 362 (409)
T PRK03103 308 RQMTLPEPTN----LAMEVYEAACKLFHRH---------WDGKPVRRVGVTLSNLVSD---DVWQLSLFGD 362 (409)
T ss_pred eeeecCCCCC----CHHHHHHHHHHHHHhc---------ccCCCceEEEEEEeCCCCC---cccCCCcccc
Confidence 8888988885 6677888888777653 2467899999999999975 4568899974
No 13
>PRK01810 DNA polymerase IV; Validated
Probab=100.00 E-value=4.2e-50 Score=439.56 Aligned_cols=295 Identities=28% Similarity=0.408 Sum_probs=262.3
Q ss_pred CcHHHHHHhCCCcEEEeccCcCCCCChHHHHHHHHHHHHHHhhc-CCeEEecCceEEEEccchhHHHhccCCCCCcchhh
Q 006218 1 MRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVD 79 (656)
Q Consensus 1 Mp~~~AkklCP~LivV~vP~~~~k~d~~~Yr~~S~~V~~IL~~~-~~VE~~SIDEafLDlT~~~~~~L~~~~~~~l~~~~ 79 (656)
||+++|+++||+|+++ | +|++.|+++|++|++++.+| |.||++||||+|||+|++..
T Consensus 61 m~~~~A~~lcP~l~~~--~-----~d~~~y~~~s~~i~~~l~~~sp~ve~~siDe~~ldvt~~~~--------------- 118 (407)
T PRK01810 61 MPLWEAKRLCPQLIVR--R-----PNFDRYREASRQMFQILSEFTPLVQPVSIDEGYLDITDCYA--------------- 118 (407)
T ss_pred ChHHHHHHHCCCeEEE--C-----CChHHHHHHHHHHHHHHHHhCCceEEecCCeEEEeccCccc---------------
Confidence 9999999999999888 5 89999999999999999998 89999999999999998641
Q ss_pred HHhhhhhcccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEeccCcHHHHHHHhcCCC
Q 006218 80 EEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNK 159 (656)
Q Consensus 80 ~e~~~s~l~g~~~~~g~~~~~~v~~w~~~~~~~~~d~ll~~~~~iA~~IR~~I~~~tGlt~SiGIA~NKlLAKLAS~~~K 159 (656)
+++ +..+|.+||++|++++|||||||||+||++||||++.+|
T Consensus 119 -------~~~-------------------------------~~~~a~~i~~~i~~~~gl~~svGia~n~~lAklas~~~K 160 (407)
T PRK01810 119 -------LGS-------------------------------PLEIAKMIQQRLLTELQLPCSIGIAPNKFLAKMASDMKK 160 (407)
T ss_pred -------cCC-------------------------------HHHHHHHHHHHHHHHHCCceEEEEcCCHHHHHHHhcCCC
Confidence 111 346899999999999999999999999999999999999
Q ss_pred CCCeeecCcccHHhhcccCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhcccchhhHHHHHhcCCCcccc
Q 006218 160 PAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQ 239 (656)
Q Consensus 160 P~G~~vl~~~~v~~fL~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~~~G~~L~~~arGiD~~~V~ 239 (656)
|+|++++.++++..||+++||++|||||+++.++|. .+||+|+|||++++...|+++||. .|.++|+.|+|+|+++|.
T Consensus 161 p~g~~vi~~~~~~~~L~~lpv~~l~giG~~~~~~L~-~~Gi~tigdL~~~~~~~L~~rfG~-~g~~l~~~a~G~d~~~v~ 238 (407)
T PRK01810 161 PLGITVLRKRDVPEMLWPLPVGEMHGIGEKTAEKLK-DIGIQTIGDLAKADEHILRAKLGI-NGVRLQRRANGIDDRPVD 238 (407)
T ss_pred CCCEEEECHHHHHHHHHhCCHhhcCCcCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHHHhH-HHHHHHHHhcCCCCCCCC
Confidence 999999999999999999999999999999999997 999999999999999999999997 699999999999999998
Q ss_pred cccC--CCcccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCCCCCCCcCccee
Q 006218 240 ARLL--PKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSC 317 (656)
Q Consensus 240 ~~~~--~KSIs~~~tF~~~~~i~~~eel~~~L~~L~~eL~~RLr~~~~~~~~~a~tvtL~ir~~~~~~~~s~~~~~sks~ 317 (656)
+... +|||+.+++|+ .++.+.+++..+|..|+++|+.||+. .++.|++|+|++++.++ . ..+++.
T Consensus 239 ~~~~~~~ksi~~~~~~~--~~~~~~~~l~~~l~~L~~~l~~rLr~----~~~~~~~l~l~lr~~~~---~----~~~~~~ 305 (407)
T PRK01810 239 PEAIYQFKSVGNSTTLS--HDMDEEKELLDVLRRLSKSVSKRLQK----KTVVSYNVQIMIRYHDR---R----TITRSK 305 (407)
T ss_pred CCCCCCCceecceEECC--CCCCCHHHHHHHHHHHHHHHHHHHHH----cCCccceeEEEEEECCC---C----ceEEEE
Confidence 6543 58999999998 58999999999999999999999997 59999999999997542 2 246788
Q ss_pred eCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEecCCeeccCcccccccccc
Q 006218 318 PLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPVLSGTCSIMKYFN 384 (656)
Q Consensus 318 ~l~~~t~~I~~da~~L~~~al~ll~~~~~~~l~~~~~~~~~ir~lgVsls~L~~~~~~~~sq~~lF~ 384 (656)
+++.||+ +...|++.+..+|...+ .+.+||++||++++|.+.. ....|.+||+
T Consensus 306 ~l~~pt~----~~~~l~~~~~~ll~~~~---------~~~~vr~lgv~~~~l~~~~-~~~~q~~Lf~ 358 (407)
T PRK01810 306 TLKNPIW----EKRDIFQAASRLFKQHW---------NGDPVRLLGVTATDLEWKT-EAVKQLDLFS 358 (407)
T ss_pred ECCCCCC----CHHHHHHHHHHHHHhcc---------CCCCEEEEEEEEecCcccc-cccccccccc
Confidence 8888885 66778888888776532 3568999999999998752 1345789997
No 14
>PRK02406 DNA polymerase IV; Validated
Probab=100.00 E-value=1.7e-49 Score=425.52 Aligned_cols=283 Identities=28% Similarity=0.396 Sum_probs=249.4
Q ss_pred CcHHHHHHhCCCcEEEeccCcCCCCChHHHHHHHHHHHHHHhhc-CCeEEecCceEEEEccchhHHHhccCCCCCcchhh
Q 006218 1 MRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVD 79 (656)
Q Consensus 1 Mp~~~AkklCP~LivV~vP~~~~k~d~~~Yr~~S~~V~~IL~~~-~~VE~~SIDEafLDlT~~~~~~L~~~~~~~l~~~~ 79 (656)
||+.+|+++||+|+++ | +|++.|+++|++|+.++.+| |.||++||||+|||+|+..
T Consensus 49 m~~~~A~~lcP~l~~~--~-----~d~~~y~~~s~~i~~~l~~~sp~ve~~siDe~~ldvt~~~---------------- 105 (343)
T PRK02406 49 MPTAQALKLCPDLIFV--P-----GRFDVYKEVSRQIREIFRRYTDLIEPLSLDEAYLDVTDNK---------------- 105 (343)
T ss_pred CcHHHHHHHCCCeEEE--C-----CChHHHHHHHHHHHHHHHHhCCceEEccCCeEEEeccCcc----------------
Confidence 9999999999999988 4 89999999999999999998 8999999999999999865
Q ss_pred HHhhhhhcccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEeccCcHHHHHHHhcCCC
Q 006218 80 EEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNK 159 (656)
Q Consensus 80 ~e~~~s~l~g~~~~~g~~~~~~v~~w~~~~~~~~~d~ll~~~~~iA~~IR~~I~~~tGlt~SiGIA~NKlLAKLAS~~~K 159 (656)
++|| .+..+|+.||++|++++|||||||||+||++||||++++|
T Consensus 106 ------~~~~------------------------------~~~~la~~i~~~i~~~~gl~~siGia~n~~lAklas~~~K 149 (343)
T PRK02406 106 ------LCIG------------------------------SATLIAQEIRQDIFEELGLTASAGVAPNKFLAKIASDWNK 149 (343)
T ss_pred ------ccCC------------------------------CHHHHHHHHHHHHHHHHCCCeEEEeccCHHHHHHHhcCCC
Confidence 2232 1357899999999999999999999999999999999999
Q ss_pred CCCeeecCcccHHhhcccCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhcccchhhHHHHHhcCCCcccc
Q 006218 160 PAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQ 239 (656)
Q Consensus 160 P~G~~vl~~~~v~~fL~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~~~G~~L~~~arGiD~~~V~ 239 (656)
|+|+++++++++..||+++||++|||||+++.++|. .+||+|+|||++++...|.++||. .|.++|+.++|+|+++|.
T Consensus 150 p~g~~~~~~~~~~~~L~~lpi~~l~giG~~~~~~L~-~~Gi~ti~dl~~l~~~~L~~~fG~-~~~~l~~~a~G~d~~~v~ 227 (343)
T PRK02406 150 PNGLFVITPEEVDAFLATLPVEKIPGVGKVTAEKLH-ALGIYTCADLQKYDLAELIRHFGK-FGRRLYERARGIDERPVK 227 (343)
T ss_pred CCCEEEECHHHHHHHHHcCCcchhcCCCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHHHhH-HHHHHHHHhCCCCCCccc
Confidence 999999999999999999999999999999999997 999999999999999999999997 699999999999999999
Q ss_pred cccCCCcccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcC--ceeeEEEEEEeeccCCCCCCCCCcCccee
Q 006218 240 ARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNK--RIAHTLTLHASAFKSSDSDSRKKFPSKSC 317 (656)
Q Consensus 240 ~~~~~KSIs~~~tF~~~~~i~~~eel~~~L~~L~~eL~~RLr~~~~~~~--~~a~tvtL~ir~~~~~~~~s~~~~~sks~ 317 (656)
+...+|||+.+++|+ .++.+.+++..+|..|+++|+.||++ .+ +.+++|+|++++.. +.. .+++.
T Consensus 228 ~~~~~ksi~~~~~~~--~~~~~~~~l~~~l~~l~~~l~~rL~~----~~~~~~~~~l~l~l~~~~---~~~----~~~~~ 294 (343)
T PRK02406 228 PDRERKSVGVERTFA--EDLYDLEACLAELPRLAEKLERRLER----AKPDKRIKTVGVKLKFAD---FQQ----TTKEH 294 (343)
T ss_pred cCCCCcceeeeeeCC--CCCCCHHHHHHHHHHHHHHHHHHHHh----cCCCccceeEEEEEEeCC---CCe----EEEec
Confidence 888899999999998 58999999999999999999999997 48 99999999999753 221 24444
Q ss_pred eCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEecCCeec
Q 006218 318 PLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPV 372 (656)
Q Consensus 318 ~l~~~t~~I~~da~~L~~~al~ll~~~~~~~l~~~~~~~~~ir~lgVsls~L~~~ 372 (656)
+ ..+++ +...|+..+.+++... + +.+||.|||++++|.+.
T Consensus 295 ~-~~~~~----~~~~l~~~~~~L~~~~---------~-~~~vr~lgv~~~~l~~~ 334 (343)
T PRK02406 295 T-ADPLD----KADLIELLAQALLRRL---------G-GRGVRLLGVGVTLLEPQ 334 (343)
T ss_pred C-CCCCC----cHHHHHHHHHHHHhhC---------c-CCCEEEEEEEEecCCcC
Confidence 4 44443 3444555566555432 2 67899999999999865
No 15
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=100.00 E-value=3e-49 Score=434.92 Aligned_cols=301 Identities=19% Similarity=0.204 Sum_probs=260.1
Q ss_pred CcHHHHHHhCC-C-cEEEeccCcCCCCChHHHHHHHHHHHHHHhhc-CCeEEecCceEEEEccchhHHHhccCCCCCcch
Q 006218 1 MRGDEAKEVCP-Q-IELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDE 77 (656)
Q Consensus 1 Mp~~~AkklCP-~-LivV~vP~~~~k~d~~~Yr~~S~~V~~IL~~~-~~VE~~SIDEafLDlT~~~~~~L~~~~~~~l~~ 77 (656)
||+++|+++|| + ++++ | +|++.|.++|++|+++|.+| |.||++||||+|||+|++..
T Consensus 53 mp~~~a~~l~~~~~l~~~--~-----~d~~~y~~~s~~i~~~l~~~tp~ve~~siDE~~lDvt~~~~------------- 112 (422)
T PRK03609 53 DPWFKQKDLFRRCGVVCF--S-----SNYELYADMSNRVMSTLEELSPRVEIYSIDEAFCDLTGVRN------------- 112 (422)
T ss_pred CcHHHHHHHhccCCeEEe--C-----CCHHHHHHHHHHHHHHHHHhCCCceEeccccceecCCCCcC-------------
Confidence 99999999994 3 6776 5 89999999999999999998 89999999999999998641
Q ss_pred hhHHhhhhhcccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEeccCcHHHHHHHhcC
Q 006218 78 VDEEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGM 157 (656)
Q Consensus 78 ~~~e~~~s~l~g~~~~~g~~~~~~v~~w~~~~~~~~~d~ll~~~~~iA~~IR~~I~~~tGlt~SiGIA~NKlLAKLAS~~ 157 (656)
+. ....+|++||++|++++|||||||||+||++|||||.+
T Consensus 113 ---------l~-------------------------------~~~~~a~~i~~~I~~~~gl~~siGia~n~~lAK~As~~ 152 (422)
T PRK03609 113 ---------CR-------------------------------DLTDFGREIRATVLQRTHLTVGVGIAQTKTLAKLANHA 152 (422)
T ss_pred ---------CC-------------------------------CHHHHHHHHHHHHHHHHCCceEEEecCCHHHHHHHHHH
Confidence 10 12468999999999999999999999999999999988
Q ss_pred CCC-----CCeeec-CcccHHhhcccCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhcccchhhHHHHHh
Q 006218 158 NKP-----AQQTTV-PFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIAR 231 (656)
Q Consensus 158 ~KP-----~G~~vl-~~~~v~~fL~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~~~G~~L~~~ar 231 (656)
+|| +|+++| .++++..||++|||++|||||+++.++|. .+||+|+|||+++++..|+++||. .|.++|+.++
T Consensus 153 ~k~~~k~~~g~~~i~~~~~~~~~L~~lPv~~l~GiG~~~~~~L~-~lGi~TigdL~~~~~~~L~~~fG~-~~~~l~~~a~ 230 (422)
T PRK03609 153 AKKWQRQTGGVVDLSNLERQRKLLSLQPVEEVWGVGRRISKKLN-AMGIKTALDLADTNIRFIRKHFNV-VLERTVRELR 230 (422)
T ss_pred hCCCCCCCCcEEEcCCHHHHHHHhhcCChhhcCCccHHHHHHHH-HcCCCcHHHHhcCCHHHHHHHHCH-HHHHHHHHhC
Confidence 776 688877 68899999999999999999999999997 999999999999999999999997 6999999999
Q ss_pred cCCCcccccccCC-CcccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCCCCCC
Q 006218 232 GISGEEVQARLLP-KSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRK 310 (656)
Q Consensus 232 GiD~~~V~~~~~~-KSIs~~~tF~~~~~i~~~eel~~~L~~L~~eL~~RLr~~~~~~~~~a~tvtL~ir~~~~~~~~s~~ 310 (656)
|+++.++....++ |+|+.++||+ .++.+.+++...+..|+++|+.||+. .++.|++|+|++|+.++.. ....
T Consensus 231 G~~~~~~~~~~~~~ksi~~~~tf~--~~~~~~~~l~~~l~~l~~~l~~rLr~----~~~~~~~l~l~ir~~~~~~-~~~~ 303 (422)
T PRK03609 231 GEPCLSLEEFAPTKQEIVCSRSFG--ERITDYESMRQAICSYAARAAEKLRG----EHQYCRFISTFVKTSPFAL-NEPY 303 (422)
T ss_pred CCCCCCccccCCCCceEEEeeECC--CCCCCHHHHHHHHHHHHHHHHHHHHH----cCCcccEEEEEEEcCCccc-cCCC
Confidence 9999999766554 7999999998 58999999999999999999999997 5999999999999864310 0012
Q ss_pred CcCcceeeCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEecCCeeccCccccccccccC
Q 006218 311 KFPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPVLSGTCSIMKYFNG 385 (656)
Q Consensus 311 ~~~sks~~l~~~t~~I~~da~~L~~~al~ll~~~~~~~l~~~~~~~~~ir~lgVsls~L~~~~~~~~sq~~lF~~ 385 (656)
+..+++.+++.+|+ ++..|++.++.+|..+| ..+.++|++||.+++|.+. ...|.+||+.
T Consensus 304 ~~~~~~~~l~~pt~----d~~~l~~~a~~ll~~~~--------~~~~~~r~~GV~~~~l~~~---~~~q~~LF~~ 363 (422)
T PRK03609 304 YGNSASVKLLTPTQ----DSRDIIAAATRALDAIW--------RDGHRYQKAGVMLGDFFSQ---GVAQLNLFDD 363 (422)
T ss_pred cCceeEEeCCCCCC----CHHHHHHHHHHHHHHHh--------CCCCceEEeeEEEEeeccC---CCcCccCccc
Confidence 33577788888885 67778888888887654 2356899999999999964 3458899974
No 16
>PRK03352 DNA polymerase IV; Validated
Probab=100.00 E-value=4e-49 Score=423.10 Aligned_cols=281 Identities=26% Similarity=0.360 Sum_probs=253.3
Q ss_pred CcHHHHHHhCCCcEEEeccCcCCCCChHHHHHHHHHHHHHHhhc-CCeEEecCceEEEEccchhHHHhccCCCCCcchhh
Q 006218 1 MRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVD 79 (656)
Q Consensus 1 Mp~~~AkklCP~LivV~vP~~~~k~d~~~Yr~~S~~V~~IL~~~-~~VE~~SIDEafLDlT~~~~~~L~~~~~~~l~~~~ 79 (656)
||+.+|+++||+|++| | +|++.|+++|++|+.++.+| |.||++||||+|||+|+..
T Consensus 63 M~~~~A~~lcP~l~~v--~-----~~~~~y~~~s~~i~~~l~~~s~~ve~~siDe~~ld~t~~~---------------- 119 (346)
T PRK03352 63 MPLRTAARRCPDAVFL--P-----SDPAAYDAASEEVMATLRDLGVPVEVWGWDEAFLGVDTDD---------------- 119 (346)
T ss_pred ChHHHHHHHCCCeEEE--C-----CCcHHHHHHHHHHHHHHHHhCCceEEecCccEEEeCCCCC----------------
Confidence 9999999999999988 5 89999999999999999998 8999999999999999741
Q ss_pred HHhhhhhcccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEeccCcHHHHHHHhcCCC
Q 006218 80 EEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNK 159 (656)
Q Consensus 80 ~e~~~s~l~g~~~~~g~~~~~~v~~w~~~~~~~~~d~ll~~~~~iA~~IR~~I~~~tGlt~SiGIA~NKlLAKLAS~~~K 159 (656)
+..+|+.||++|++++|||||||||+||++||||++.+|
T Consensus 120 -----------------------------------------~~~la~~ir~~i~~~~gl~~siGia~nk~lAklaa~~~K 158 (346)
T PRK03352 120 -----------------------------------------PEALAEEIRAAVLERTGLSCSVGIGDNKLRAKIATGFAK 158 (346)
T ss_pred -----------------------------------------HHHHHHHHHHHHHHHHCCCEEEeecCCHHHHHHHHhhcC
Confidence 236899999999999999999999999999999999999
Q ss_pred CCCeeecCcccHHhhcccCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhcccchhhHHHHHhcCCCcccc
Q 006218 160 PAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQ 239 (656)
Q Consensus 160 P~G~~vl~~~~v~~fL~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~~~G~~L~~~arGiD~~~V~ 239 (656)
|+|++++.++++..||+++||+++||||+++.++|. ++||+|+|||+.++...|.++||...|.+||+.++|+|.+++.
T Consensus 159 p~g~~~~~~~~~~~~L~~lpl~~l~gig~~~~~~L~-~~Gi~ti~dl~~l~~~~L~~~fG~~~~~~l~~~a~G~d~~~~~ 237 (346)
T PRK03352 159 PAGVFRLTDANWMAVMGDRPTDALWGVGPKTAKRLA-ALGITTVADLAAADPAELAATFGPTTGPWLLLLARGGGDTEVS 237 (346)
T ss_pred CCcEEEECHHHHHHHHhcCCHHHcCCCCHHHHHHHH-HcCCccHHHHhcCCHHHHHHHhChHHHHHHHHHhCCCCCCCCC
Confidence 999999999999999999999999999999999997 9999999999999999999999976799999999999999987
Q ss_pred cc-cCCCcccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCCCCCCCcCcceee
Q 006218 240 AR-LLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCP 318 (656)
Q Consensus 240 ~~-~~~KSIs~~~tF~~~~~i~~~eel~~~L~~L~~eL~~RLr~~~~~~~~~a~tvtL~ir~~~~~~~~s~~~~~sks~~ 318 (656)
.. ..+|||+.+.+|. .++.+.+++..+|..|+++|+.||++ +++.+++|+|++++.+ +. ..+++.+
T Consensus 238 ~~~~~~ksi~~~~tf~--~~~~~~~~l~~~l~~L~~~l~~rLr~----~~~~~~~l~l~l~~~~---~~----~~~~~~~ 304 (346)
T PRK03352 238 AEPWVPRSRSREVTFP--QDLTDRAEVESAVRELARRVLDEVVA----EGRPVTRVAVKVRTAT---FY----TRTKIRK 304 (346)
T ss_pred CCCCCCceEEEEEECC--CCCCCHHHHHHHHHHHHHHHHHHHHH----cCCccceEEEEEEeCC---Cc----eeEEEEE
Confidence 64 3579999999998 58999999999999999999999997 5999999999999753 22 2467888
Q ss_pred CCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEecCCeec
Q 006218 319 LRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPV 372 (656)
Q Consensus 319 l~~~t~~I~~da~~L~~~al~ll~~~~~~~l~~~~~~~~~ir~lgVsls~L~~~ 372 (656)
++.+|+ +...|++.+..+|... +.+.+||.|||++.+|.+.
T Consensus 305 l~~pt~----d~~~l~~~~~~ll~~~---------~~~~~vr~igl~~~~~~~~ 345 (346)
T PRK03352 305 LPEPTT----DPDVIEAAALDVLDRF---------ELDRPVRLLGVRLELAMPD 345 (346)
T ss_pred CCCCcC----CHHHHHHHHHHHHHhc---------cCCCCEEEEEEEEeccCCC
Confidence 888885 6677888777777643 2356899999999999863
No 17
>cd03586 PolY_Pol_IV_kappa DNA Polymerase IV/Kappa. Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Known primarily as Pol IV in prokaryotes and Pol kappa in eukaryotes, this polymerase has a propensity for generating frameshift mutations. The eukaryotic Pol kappa differs from Pol IV and Dpo4 by an N-terminal extension of ~75 residues known as the "N-clasp" region. The structure of Pol kappa shows DNA that is almost totally encircled by Pol kappa, with the N-clasp region augmenting the interactions between DNA and the polymerase. Pol kappa is more resistant than Pol eta and Pol iota to bulky guanine adducts and is efficient at catalyzing the incorporation of dCTP. Bacterial pol IV has a
Probab=100.00 E-value=9.8e-49 Score=416.90 Aligned_cols=282 Identities=33% Similarity=0.493 Sum_probs=255.6
Q ss_pred CcHHHHHHhCCCcEEEeccCcCCCCChHHHHHHHHHHHHHHhhc-CCeEEecCceEEEEccchhHHHhccCCCCCcchhh
Q 006218 1 MRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVD 79 (656)
Q Consensus 1 Mp~~~AkklCP~LivV~vP~~~~k~d~~~Yr~~S~~V~~IL~~~-~~VE~~SIDEafLDlT~~~~~~L~~~~~~~l~~~~ 79 (656)
|++++|+++||+|+++ | +|++.|+++|++|++++.+| |.||++||||+|||+|+..
T Consensus 52 m~~~~A~~lcp~l~~~--~-----~~~~~y~~~s~~i~~~l~~~~~~ve~~s~De~~ldv~~~~---------------- 108 (334)
T cd03586 52 MPIFQAKKLCPNLIFV--P-----PRFDKYREVSRQIMEILREYTPLVEPLSIDEAYLDVTDYV---------------- 108 (334)
T ss_pred CcHHHHHHHCCCeEEE--C-----CCcHHHHHHHHHHHHHHHHcCCceEEecccceeEcccccc----------------
Confidence 9999999999999988 4 89999999999999999998 8999999999999999864
Q ss_pred HHhhhhhcccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEeccCcHHHHHHHhcCCC
Q 006218 80 EEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNK 159 (656)
Q Consensus 80 ~e~~~s~l~g~~~~~g~~~~~~v~~w~~~~~~~~~d~ll~~~~~iA~~IR~~I~~~tGlt~SiGIA~NKlLAKLAS~~~K 159 (656)
+++| .+..+|.+||++|++++||+||||||+|+++||||++.+|
T Consensus 109 ------~~~~------------------------------~~~~la~~ir~~i~~~~g~~~siGia~n~~lAklaa~~~k 152 (334)
T cd03586 109 ------RLFG------------------------------SATEIAKEIRARIREETGLTASAGIAPNKFLAKIASDLNK 152 (334)
T ss_pred ------ccCC------------------------------CHHHHHHHHHHHHHHHHCCceEEEEhhcHHHHHHHhcCCC
Confidence 2222 2457899999999999999999999999999999999999
Q ss_pred CCCeeecCcccHHhhcccCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhcccchhhHHHHHhcCCCcccc
Q 006218 160 PAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQ 239 (656)
Q Consensus 160 P~G~~vl~~~~v~~fL~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~~~G~~L~~~arGiD~~~V~ 239 (656)
|+|+++++++++..||+++||+++||||++++++|. .+||+|++||++++...|.++||. .|.++|+.++|+|+.+|.
T Consensus 153 p~g~~i~~~~~~~~~L~~lpl~~l~gig~~~~~~L~-~~Gi~ti~dl~~~~~~~L~~~~g~-~~~~l~~~~~G~~~~~v~ 230 (334)
T cd03586 153 PNGLTVIPPEDVEEFLAPLPVRKIPGVGKVTAEKLK-ELGIKTIGDLAKLDVELLKKLFGK-SGRRLYELARGIDNRPVE 230 (334)
T ss_pred CCcEEEECHHHHHHHHhcCCchhhCCcCHHHHHHHH-HcCCcCHHHHHcCCHHHHHHHHhH-HHHHHHHHhCCCCCCCCC
Confidence 999999999999999999999999999999999997 999999999999999999999997 699999999999999999
Q ss_pred cccCCCcccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCCCCCCCcCcceeeC
Q 006218 240 ARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPL 319 (656)
Q Consensus 240 ~~~~~KSIs~~~tF~~~~~i~~~eel~~~L~~L~~eL~~RLr~~~~~~~~~a~tvtL~ir~~~~~~~~s~~~~~sks~~l 319 (656)
+..++|||+.+++|+ .++.+.+++..+|..|+++|+.||+. .++.|++|+|++++.+. ...+++.++
T Consensus 231 ~~~~~ks~~~~~~~~--~~~~~~~~l~~~l~~l~~~l~~rL~~----~~~~~~~l~l~l~~~~~-------~~~~~~~~l 297 (334)
T cd03586 231 PDRERKSIGVERTFS--EDLTDPEELLEELLELAEELAERLRK----RGLKGRTVTVKLKYADF-------STRTRSRTL 297 (334)
T ss_pred CCCCCCeeeeeEECC--CCCCCHHHHHHHHHHHHHHHHHHHHh----CCCCeEEEEEEEEECCC-------CeEEEEEEC
Confidence 888899999999998 58999999999999999999999997 49999999999987532 224788888
Q ss_pred CCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEecCC
Q 006218 320 RYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKI 369 (656)
Q Consensus 320 ~~~t~~I~~da~~L~~~al~ll~~~~~~~l~~~~~~~~~ir~lgVsls~L 369 (656)
+.+++ +...|++.+..+|..++ .+.+||+|||++++|
T Consensus 298 ~~~t~----~~~~l~~~~~~~l~~~~---------~~~~vr~igv~~~~l 334 (334)
T cd03586 298 PEPTD----DAEDIYELALELLEELL---------DGRPIRLLGVRLSGL 334 (334)
T ss_pred CCCCC----CHHHHHHHHHHHHHhcc---------CCCCEEEEEEEeecC
Confidence 88885 67778888887776543 247899999999886
No 18
>cd01700 PolY_Pol_V_umuC umuC subunit of DNA Polymerase V. umuC subunit of Pol V. Pol V is a bacterial translesion synthesis (TLS) polymerase that consists of the heterotrimer of one umuC and two umuD subunits. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol V, RecA, single stranded DNA-binding protein, beta sliding clamp, and gamma clamp loading complex are responsible for inducing the SOS response in bacteria to repair UV-induced DNA damage.
Probab=100.00 E-value=3.7e-48 Score=415.29 Aligned_cols=285 Identities=26% Similarity=0.369 Sum_probs=246.5
Q ss_pred CcHHHHHHhCCCc--EEEeccCcCCCCChHHHHHHHHHHHHHHhhc-CCeEEecCceEEEEccchhHHHhccCCCCCcch
Q 006218 1 MRGDEAKEVCPQI--ELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDE 77 (656)
Q Consensus 1 Mp~~~AkklCP~L--ivV~vP~~~~k~d~~~Yr~~S~~V~~IL~~~-~~VE~~SIDEafLDlT~~~~~~L~~~~~~~l~~ 77 (656)
||+.+|+++||+| +++ | +|++.|+++|++|++++.+| |.||.+||||+|||+|+...
T Consensus 51 m~~~~A~~lcP~l~~~~v--~-----~~~~~y~~~s~~i~~~l~~~~~~ve~~s~De~~ldvt~~~~------------- 110 (344)
T cd01700 51 SPYFKVPDLLERHGVAVF--S-----SNYALYGDMSRRIMSILERFSPDVEVYSIDESFLDLTGSLR------------- 110 (344)
T ss_pred CcHHHhHhhccccCeEEE--c-----CchHHHHHHHHHHHHHHHhcCCcceEeecchhhccCcCCCC-------------
Confidence 9999999999999 555 5 89999999999999999998 79999999999999998641
Q ss_pred hhHHhhhhhcccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEeccCcHHHHHHHhcC
Q 006218 78 VDEEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGM 157 (656)
Q Consensus 78 ~~~e~~~s~l~g~~~~~g~~~~~~v~~w~~~~~~~~~d~ll~~~~~iA~~IR~~I~~~tGlt~SiGIA~NKlLAKLAS~~ 157 (656)
|+ .+..+|++||++|++++|||||||||+||++|||||++
T Consensus 111 ----------~~------------------------------~~~~la~~i~~~i~~~~gl~~s~Gia~~~~lAklas~~ 150 (344)
T cd01700 111 ----------FG------------------------------DLEELARKIRRRILQETGIPVTVGIGPTKTLAKLANDL 150 (344)
T ss_pred ----------CC------------------------------CHHHHHHHHHHHHHHHhCCceEEEecCCHHHHHHHHHH
Confidence 11 13578999999999999999999999999999999999
Q ss_pred CCCC----CeeecCcccHH-hhcccCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhcccchhhHHHHHhc
Q 006218 158 NKPA----QQTTVPFSSVK-GLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARG 232 (656)
Q Consensus 158 ~KP~----G~~vl~~~~v~-~fL~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~~~G~~L~~~arG 232 (656)
+||+ |++++++++.. .||+++||+++||||+++.++|. .+||+|+|||++++.+.|.++||. .|.++|+.++|
T Consensus 151 ~kp~~~~~g~~~~~~~~~~~~~l~~lpl~~l~gig~~~~~~L~-~~Gi~ti~dL~~~~~~~L~~rfG~-~~~~l~~~a~G 228 (344)
T cd01700 151 AKKKNPYGGVVDLTDEEVRDKLLKILPVGDVWGIGRRTAKKLN-AMGIHTAGDLAQADPDLLRKKFGV-VGERLVRELNG 228 (344)
T ss_pred hcCCCCCCeEEEecChhHHHHHhccCChhhcCccCHHHHHHHH-HcCCCcHHHHhcCCHHHHHHHHHH-HHHHHHHHhCC
Confidence 9984 78888776665 89999999999999999999997 999999999999999999999997 69999999999
Q ss_pred CCCcccccccC-CCcccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCCCCCCC
Q 006218 233 ISGEEVQARLL-PKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKK 311 (656)
Q Consensus 233 iD~~~V~~~~~-~KSIs~~~tF~~~~~i~~~eel~~~L~~L~~eL~~RLr~~~~~~~~~a~tvtL~ir~~~~~~~~s~~~ 311 (656)
+|+++|.+... +|||+.+.+|. .++.+.+++..+|..|+++|+.||+. +++.|++|+|++++.. |....+
T Consensus 229 ~d~~~v~~~~~~~ks~~~~~~~~--~~~~~~~~l~~~l~~L~~~l~~~L~~----~~~~~~~l~l~l~~~~---~~~~~~ 299 (344)
T cd01700 229 IDCLPLEEYPPPKKSIGSSRSFG--RDVTDLDELKQALAEYAERAAEKLRR----QKSVARTISVFIGTSG---FSRQPK 299 (344)
T ss_pred CCCCcCCCCCCCCcEEEEeeEcC--CCCCCHHHHHHHHHHHHHHHHHHHHH----cCCcccEEEEEEEcCC---CCCCCC
Confidence 99999975544 58999999998 58999999999999999999999997 5999999999999754 222222
Q ss_pred cCcceeeCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEecC
Q 006218 312 FPSKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASK 368 (656)
Q Consensus 312 ~~sks~~l~~~t~~I~~da~~L~~~al~ll~~~~~~~l~~~~~~~~~ir~lgVsls~ 368 (656)
..+.+.+++.+|+ +...|++.++.+|..++ ..+.+||+|||++++
T Consensus 300 ~~~~~~~~~~~t~----~~~~l~~~~~~ll~~~~--------~~~~~iR~iGV~~~~ 344 (344)
T cd01700 300 YYSATNTLPYPTN----DTREIVKAALRLLYAIY--------RPGYAYRKAGVMLSD 344 (344)
T ss_pred ccccccccCCcch----hHHHHHHHHHHHHHHHh--------CCCCcEEEEEEEeeC
Confidence 2334456677775 66778888888887654 235689999999875
No 19
>KOG2094 consensus Predicted DNA damage inducible protein [Replication, recombination and repair]
Probab=100.00 E-value=9.4e-48 Score=397.30 Aligned_cols=292 Identities=27% Similarity=0.397 Sum_probs=246.6
Q ss_pred CcHHHHHHhCCCcEEEeccCcCCCCChHHHHHHHHHHHHHHhhc-CCeEEecCceEEEEccchhHHHhccCCCCCcchhh
Q 006218 1 MRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVD 79 (656)
Q Consensus 1 Mp~~~AkklCP~LivV~vP~~~~k~d~~~Yr~~S~~V~~IL~~~-~~VE~~SIDEafLDlT~~~~~~L~~~~~~~l~~~~ 79 (656)
||++.|+++||+|++| | .||..|+.+|++|.+||++| +.+..+|+||||||+|.++..+
T Consensus 154 MPgFIarklCPdLiiV--P-----~n~~kYt~~Ske~~~v~~~YDsn~~~~SlDEaylnlT~~l~~~------------- 213 (490)
T KOG2094|consen 154 MPGFIARKLCPDLIIV--P-----LNFSKYTIVSKEIQNVLAQYDSNFCAMSLDEAYLNLTSHLRER------------- 213 (490)
T ss_pred CchHHHhccCCceEEe--C-----CCcHHHHHHHHHHHHHHHHcCCccccchHHHHHHhHHHHHHHh-------------
Confidence 9999999999999998 7 79999999999999999999 6899999999999999987532
Q ss_pred HHhhhhhcccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEeccCcHHHHHHHhcCCC
Q 006218 80 EEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNK 159 (656)
Q Consensus 80 ~e~~~s~l~g~~~~~g~~~~~~v~~w~~~~~~~~~d~ll~~~~~iA~~IR~~I~~~tGlt~SiGIA~NKlLAKLAS~~~K 159 (656)
-||.-..+| ...++++||.+|+++||+|||+|||+|++|||+||+++|
T Consensus 214 -------~~g~l~~nG-------------------------~~evveeiR~rV~qeTglT~SaGIAaN~lLAKicSd~nK 261 (490)
T KOG2094|consen 214 -------ELGFLVENG-------------------------ITEVVEEIRFRVEQETGLTCSAGIAANKLLAKICSDKNK 261 (490)
T ss_pred -------hcchhhhcc-------------------------HHHHHHHHHHHHHHhcCceeeccccHhHHHHHHhccccC
Confidence 122110011 357899999999999999999999999999999999999
Q ss_pred CCCeeecCcc--cHHhhcccCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhcccchhhHHHHHhcCCCcc
Q 006218 160 PAQQTTVPFS--SVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEE 237 (656)
Q Consensus 160 P~G~~vl~~~--~v~~fL~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~~~G~~L~~~arGiD~~~ 237 (656)
||||++|+.+ .+.+||..|||+++-|||+.++..|. .+||.||||+.+- ...|.-.|.+...+.+.+.+.|...++
T Consensus 262 PNgQf~i~~dr~aim~F~kdLPvRkV~GIGrV~E~qLk-al~IkTcgdm~~k-~~ll~~lFsp~S~~~fLr~slG~g~t~ 339 (490)
T KOG2094|consen 262 PNGQFVIPNDRIAIMKFMKDLPVRKVSGIGRVTEQQLK-ALGIKTCGDMQQK-LVLLSLLFSPKSFQNFLRCSLGLGTTI 339 (490)
T ss_pred CCCceEecccHHHHHHHHhcCCcccccchhHHHHHHHH-hcCceeHHHHHHh-hhHHHHHhCchhHHHHHHHhhcCCCCc
Confidence 9999999865 57899999999999999999999997 9999999999874 456777899987888999999999999
Q ss_pred cccccCCCcccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCCCCCCCcCccee
Q 006218 238 VQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSC 317 (656)
Q Consensus 238 V~~~~~~KSIs~~~tF~~~~~i~~~eel~~~L~~L~~eL~~RLr~~~~~~~~~a~tvtL~ir~~~~~~~~s~~~~~sks~ 317 (656)
......+|||+.++||. .+.+...+...+.+||..|++-|+. .|++++||||+++... |.. .+++.
T Consensus 340 ~~~~~eRKsis~ErTFs---~~sd~~il~~k~qel~~~lsedlqK----~glv~rtvtiKlK~ss---Fev----~Tr~~ 405 (490)
T KOG2094|consen 340 LDEDGERKSISSERTFS---STSDPSILYSKLQELCQMLSEDLQK----EGLVGRTVTIKLKTSS---FEV----HTRQK 405 (490)
T ss_pred Cccccccccccceeeec---ccCCHHHHHHHHHHHHHHHHHHHHh----cCcccceEEEEEeccc---eee----eeccC
Confidence 88888899999999997 6899999999999999998888875 6999999999998754 333 23443
Q ss_pred eCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEecCCeeccC
Q 006218 318 PLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPVLS 374 (656)
Q Consensus 318 ~l~~~t~~I~~da~~L~~~al~ll~~~~~~~l~~~~~~~~~ir~lgVsls~L~~~~~ 374 (656)
++.. +-....+|+.-++++|...+ +..||++||.+++|+...+
T Consensus 406 t~s~----vv~S~edi~k~aleLLk~e~----------~~~iRLlGvR~sqlv~eed 448 (490)
T KOG2094|consen 406 TISQ----VVHSEEDILKPALELLKQEY----------PMTIRLLGVRASQLVSEED 448 (490)
T ss_pred chhh----hhccHHHHHHHHHHHHHhhc----------CceEeeeeeeHhhccchhc
Confidence 3322 11245567788888776443 5689999999999998643
No 20
>COG0389 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.2e-45 Score=397.67 Aligned_cols=290 Identities=33% Similarity=0.468 Sum_probs=256.0
Q ss_pred CcHHHHHHhCCCcEEEeccCcCCCCChHHHHHHHHHHHHHHhhc-CCeEEecCceEEEEccchhHHHhccCCCCCcchhh
Q 006218 1 MRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVD 79 (656)
Q Consensus 1 Mp~~~AkklCP~LivV~vP~~~~k~d~~~Yr~~S~~V~~IL~~~-~~VE~~SIDEafLDlT~~~~~~L~~~~~~~l~~~~ 79 (656)
||+++|+++||+++++ | ++|+.|+.+|.+|++|+.+| +.||++||||+|||+|+...
T Consensus 55 m~~~~A~~~cp~~~~~--~-----~~~~~y~~~s~~i~~i~~~~~~~ve~lSIDE~~ldvt~~~~--------------- 112 (354)
T COG0389 55 MPLFEALKLCPRAIVA--P-----PNFAAYRLASAEIRAILERYTPLVEPLSIDEAFLDLTDALR--------------- 112 (354)
T ss_pred ChHHHHHHHCCCCEEe--C-----CcHHHHHHHHHHHHHHHHhccccceeeeccceeeecccccc---------------
Confidence 8999999999999988 5 89999999999999999998 79999999999999997642
Q ss_pred HHhhhhhcccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEeccCcHHHHHHHhcCCC
Q 006218 80 EEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNK 159 (656)
Q Consensus 80 ~e~~~s~l~g~~~~~g~~~~~~v~~w~~~~~~~~~d~ll~~~~~iA~~IR~~I~~~tGlt~SiGIA~NKlLAKLAS~~~K 159 (656)
.+|. ..+..+|.+||..|+.++|||||+|||+||++|||||+++|
T Consensus 113 -------~~g~----------------------------~~~~~~a~~ir~~i~~~~~l~~s~Gi~~nk~laKiAs~~~k 157 (354)
T COG0389 113 -------LLGL----------------------------ADAPRIALEIRFGILLELGLTASVGISDNKFLAKIASDLNK 157 (354)
T ss_pred -------cCCc----------------------------ccHHHHHHHHHHHHHHhhCCEEEEEecCcHHHHHHHhcccC
Confidence 1221 12468999999999999999999999999999999999999
Q ss_pred CCCeeecCcccHHhhcccCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhcccchhhHHHHHhcCCCcccc
Q 006218 160 PAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQ 239 (656)
Q Consensus 160 P~G~~vl~~~~v~~fL~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~~~G~~L~~~arGiD~~~V~ 239 (656)
|+|++++.++++.+||++|||.++||||+.++.+|. .+||.||+||+..+...|.+.||. .|.+||+.++|+|.++|.
T Consensus 158 p~gi~~~~~~~~~~~l~~Lpv~~~~GvG~~~~~~l~-~~Gi~ti~dl~~~~~~~L~~~~g~-~~~~l~~~a~Gid~~~v~ 235 (354)
T COG0389 158 PDGITVIEPEEVPALLWQLPVLEFWGVGKVTAEKLR-RLGISTIGDLAETDLDALKKRFGK-LGERLYRLARGIDNRPVR 235 (354)
T ss_pred CCCEEEECHHHHHHHHhcCChhhhCCCCHHHHHHHH-HcCChhHHHHHhcCHHHHHHHHhH-hHHHHHHHhcCCCccccc
Confidence 999999999999999999999999999999999997 999999999999999999999998 689999999999999999
Q ss_pred cccCC-CcccccccCCCCCCCCCHHHHHHHHHH-HHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCCCCCCCcCccee
Q 006218 240 ARLLP-KSHGSGKSFPGPRALKTVASVQHWLNQ-LCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSC 317 (656)
Q Consensus 240 ~~~~~-KSIs~~~tF~~~~~i~~~eel~~~L~~-L~~eL~~RLr~~~~~~~~~a~tvtL~ir~~~~~~~~s~~~~~sks~ 317 (656)
+.... ||++.+.||. .++.+.+++...|.. |+++++.||+. .+..+++|++++++.+ | ++.+++.
T Consensus 236 ~~~~~~ksi~~~~t~~--~d~~~~~~~~~~l~~~l~e~~~~rl~~----~~~~~r~v~~~~~~~d---f----~~~t~~~ 302 (354)
T COG0389 236 EQALRAKSIGAESTFE--EDLTDAEELIERLRARLGEEVVSRLRK----SGRHGRTVSVKLKTAD---F----PTNTRSR 302 (354)
T ss_pred cccccCccccceeecc--ccccCHHHHHHHHHHHHHHHHHHHHHH----hCCCceEEEEEEEecC---C----Ccceeec
Confidence 98887 9999999998 689999988888887 99999999997 4888899999999854 3 2357888
Q ss_pred eCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEecCCeec
Q 006218 318 PLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPV 372 (656)
Q Consensus 318 ~l~~~t~~I~~da~~L~~~al~ll~~~~~~~l~~~~~~~~~ir~lgVsls~L~~~ 372 (656)
+++.|++ +..+++.++..+|...+. .+.+.++|.+||++++|.+.
T Consensus 303 ~l~~p~~----~~~~i~~~~~~l~~~~~~------~~~~~~~rl~gv~~~~~~~~ 347 (354)
T COG0389 303 KLAQPTS----DPIEIYAAALPLLPPLLF------RGRGRRIRLLGVSGPELIDS 347 (354)
T ss_pred ccCCcCC----CHHHHHHHHHHHHHHhhc------cCCCceEEEEEEEecCcccc
Confidence 8888875 456677777777765431 12367899999999999875
No 21
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=100.00 E-value=6.5e-45 Score=407.80 Aligned_cols=304 Identities=23% Similarity=0.354 Sum_probs=258.4
Q ss_pred CcHHHHHHhCCCcEEEeccCcCCCCChHHHHHHHHHHHHHHhhcC-CeEEecCceEEEEccchhHHHhccCCCCCcchhh
Q 006218 1 MRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARKG-RCERASIDEVYLDLTDAAEAMLAETPPESLDEVD 79 (656)
Q Consensus 1 Mp~~~AkklCP~LivV~vP~~~~k~d~~~Yr~~S~~V~~IL~~~~-~VE~~SIDEafLDlT~~~~~~L~~~~~~~l~~~~ 79 (656)
|.+.+|++|||+|++| | |||+.|.++|+.+|++|++|. .||.+||||||+|+|......
T Consensus 429 MfV~~A~klCPqL~~l--P-----Y~FE~Ykevs~tlYetlasytl~I~aVSCDEa~vd~s~~~~~~------------- 488 (1016)
T KOG2093|consen 429 MFVRHAKKLCPQLVIL--P-----YDFEAYKEVSETLYETLASYTLNIEAVSCDEAFVDVSDLSDEE------------- 488 (1016)
T ss_pred eeHHHHHHhCcccEee--c-----ccHHHHHHHHHHHHHHHHhhccceeeecchhhhhhhhhhhhhh-------------
Confidence 8999999999999988 7 999999999999999999994 799999999999999865321
Q ss_pred HHhhhhhcccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEeccCcHHHHHHHhcCCC
Q 006218 80 EEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNK 159 (656)
Q Consensus 80 ~e~~~s~l~g~~~~~g~~~~~~v~~w~~~~~~~~~d~ll~~~~~iA~~IR~~I~~~tGlt~SiGIA~NKlLAKLAS~~~K 159 (656)
. ..++.+|..||++|++.|||+||||||.|++||+||++.||
T Consensus 489 ---------~-----------------------------~tp~~la~~IRqEI~e~TgC~aS~Gig~t~LLARlATr~AK 530 (1016)
T KOG2093|consen 489 ---------N-----------------------------ETPAVLAEHIRQEILEKTGCPASAGIGGTMLLARLATRVAK 530 (1016)
T ss_pred ---------c-----------------------------cCHHHHHHHHHHHHHhccCCceeeccchHHHHHHHHHhhcC
Confidence 0 01367999999999999999999999999999999999999
Q ss_pred CCCeeecCcccHHhhcccCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhcccchhhHHHHHhcCCCcccc
Q 006218 160 PAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQ 239 (656)
Q Consensus 160 P~G~~vl~~~~v~~fL~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~~~G~~L~~~arGiD~~~V~ 239 (656)
||||+++.++.+.+||.+++|.+|||||..|..+|. .+||+|||||+.++...|++.||++.|..+|+.|||+|++|+.
T Consensus 531 P~Gq~~l~a~~veeFis~~~v~~LPGVG~sm~~kL~-s~~i~tCgdLq~~T~~kl~k~~G~Klgq~i~~~CrG~Dd~P~~ 609 (1016)
T KOG2093|consen 531 PNGQFYLSAEKVEEFISQLKVDDLPGVGSSMKSKLV-SQFIQTCGDLQLITLIKLRKVFGPKLGQKIYRGCRGIDDDPRS 609 (1016)
T ss_pred CCceeeecHHHHHHHhhhcccccCCCccHHHHHHHH-HhccchhHHHHHHHHHHHHhhhcccHHHHHHHhcCCCcCChHH
Confidence 999999999999999999999999999999999997 9999999999999999999999999999999999999999988
Q ss_pred cccCCCcccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccC------CCCCCCC--C
Q 006218 240 ARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKS------SDSDSRK--K 311 (656)
Q Consensus 240 ~~~~~KSIs~~~tF~~~~~i~~~eel~~~L~~L~~eL~~RLr~~~~~~~~~a~tvtL~ir~~~~------~~~~s~~--~ 311 (656)
....+||++.+.+|+ .+++...+++.+|..++++|-+||.+ -++.++.++|++..... ..|..|. .
T Consensus 610 ~~~~RKSvS~dIN~G--IRFtn~~ev~~fl~~~~eEl~rkL~e----i~k~~~sitLKlMvR~~~APietaK~mGhGiCD 683 (1016)
T KOG2093|consen 610 IEQVRKSVSADINYG--IRFTNIKEVEQFLCLLSEELRRKLLE----ISKTASSITLKLMVRTAKAPIETAKYMGHGICD 683 (1016)
T ss_pred Hhhhhcceeeeeecc--eeeccHHHHHHHHHHHHHHHHHHHHH----hhccccchhHHHHhhcCCCCCccccccceeecc
Confidence 777899999999999 69999999999999999999999986 48899999999853211 1222221 3
Q ss_pred cCcceeeCCCcchh---hHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEec-CCeecc--Ccccccccccc
Q 006218 312 FPSKSCPLRYGTAK---IQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSAS-KIVPVL--SGTCSIMKYFN 384 (656)
Q Consensus 312 ~~sks~~l~~~t~~---I~~da~~L~~~al~ll~~~~~~~l~~~~~~~~~ir~lgVsls-~L~~~~--~~~~sq~~lF~ 384 (656)
.+++++.|.++|+. |+..++.||+.+. .++-.+|++|+.+. +|.+.. .....+..+|.
T Consensus 684 ~~~rs~~l~~~Td~~~iItt~~~~L~~t~~---------------~~~~elRG~gi~~ntkL~~~~~~~~~~~l~e~Fg 747 (1016)
T KOG2093|consen 684 DFVRSSKLREPTDCNRIITTEVLRLYETNS---------------EPPSELRGLGIHSNTKLMDVLENLPPELLSEMFG 747 (1016)
T ss_pred chhhhhhccCccccccchHHHHHHHHHhcC---------------CChHHhccchhhccccccccccCCcHHHHHhhcc
Confidence 46889999999864 4555555555431 34557899999995 777642 22334445554
No 22
>cd03468 PolY_like DNA Polymerase Y-family. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in order to access the lesion. Because of their high error rates, TLS polymerases are potential targets for cancer treatment and prevention.
Probab=100.00 E-value=8.7e-41 Score=355.78 Aligned_cols=276 Identities=20% Similarity=0.159 Sum_probs=233.2
Q ss_pred CcHHHHHHhCCCcEEEeccCcCCCCChHHHHHHHHHHHHHHhhc-CCeEEecCceEEEEccchhHHHhccCCCCCcchhh
Q 006218 1 MRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-GRCERASIDEVYLDLTDAAEAMLAETPPESLDEVD 79 (656)
Q Consensus 1 Mp~~~AkklCP~LivV~vP~~~~k~d~~~Yr~~S~~V~~IL~~~-~~VE~~SIDEafLDlT~~~~~~L~~~~~~~l~~~~ 79 (656)
||+++|+++||+++++ | +|++.|.++|++|++++.+| |.||.+||||+|||+|+..
T Consensus 52 m~~~~A~~lcP~l~~~--~-----~~~~~y~~~s~~i~~~l~~~s~~ve~~s~de~~ldvs~~~---------------- 108 (335)
T cd03468 52 MPLAEALALCPNLQVV--E-----YDPEADARALQELALWLLRFTPLVALDGPDGLLLDVTGCL---------------- 108 (335)
T ss_pred CcHHHHHHhCCCCeee--c-----CChHHHHHHHHHHHHHHHhcCCccccCCCCeEEEEcccch----------------
Confidence 9999999999999988 5 89999999999999999998 8999999999999999864
Q ss_pred HHhhhhhcccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEeccCcHHHHHHHhcCCC
Q 006218 80 EEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNK 159 (656)
Q Consensus 80 ~e~~~s~l~g~~~~~g~~~~~~v~~w~~~~~~~~~d~ll~~~~~iA~~IR~~I~~~tGlt~SiGIA~NKlLAKLAS~~~K 159 (656)
++|| .+..+|..|++.+. ++|++||||||+||++||||++.+|
T Consensus 109 ------~~~~------------------------------~~~~~a~~i~~~~~-~~gl~~siGia~n~~~Aklas~~~k 151 (335)
T cd03468 109 ------HLFG------------------------------GEDALAASLRAALA-TLGLSARAGIADTPGAAWLLARAGG 151 (335)
T ss_pred ------hhcC------------------------------CHHHHHHHHHHHHH-HcCCeEEEEecCCHHHHHHHhccCC
Confidence 2222 13468999999995 7899999999999999999999999
Q ss_pred CCCeeecCcccHHh-hcccCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhcccchhhHHHHHhcCCCccc
Q 006218 160 PAQQTTVPFSSVKG-LLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEV 238 (656)
Q Consensus 160 P~G~~vl~~~~v~~-fL~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~~~G~~L~~~arGiD~~~V 238 (656)
|+|++.+....... ||+++|+ ++||||+++.++|. ++||+|++||++++...|.++||. .|.++|+.++|+|+.++
T Consensus 152 p~~~~~~~~~~~~~~~l~~lp~-~~~gig~~~~~~L~-~~Gi~t~~dl~~~~~~~l~~rfG~-~~~~l~~~~~G~d~~~~ 228 (335)
T cd03468 152 GRGVLRREALAAALVLLAPLPV-AALRLPPETVELLA-RLGLRTLGDLAALPRAELARRFGL-ALLLRLDQAYGRDPEPL 228 (335)
T ss_pred CCccCCchHHHHHhhccCCCCh-hHhCCCHHHHHHHH-HhCcccHHHHHhCChHHHHhhcCH-HHHHHHHHHCCCCCCCC
Confidence 99998877666654 8999999 59999999999997 999999999999999999999998 59999999999999999
Q ss_pred --ccccCCCcccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCCCCCCCcCcce
Q 006218 239 --QARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKS 316 (656)
Q Consensus 239 --~~~~~~KSIs~~~tF~~~~~i~~~eel~~~L~~L~~eL~~RLr~~~~~~~~~a~tvtL~ir~~~~~~~~s~~~~~sks 316 (656)
.....+|+++.+.+|+ .+..+.+ ...+..|+++++.||+. ++..+++|+|++++.+ +. ..+.+
T Consensus 229 ~~~~~~~~~~~~~~~~~~--~~~~~~~--~~~l~~l~~~l~~~L~~----~~~~~~~l~l~l~~~~---~~----~~~~~ 293 (335)
T cd03468 229 LFSPPPPAFDFRLELQLE--EPIARGL--LFPLRRLLEQLCAFLAL----RGLGARRLSLTLFRED---GR----VTRVL 293 (335)
T ss_pred CCCCCCCChhhhhhcCCC--CCcchhH--HHHHHHHHHHHHHHHHH----cCCeeeEEEEEEEEEC---Cc----eEEEE
Confidence 4555679999999998 4665554 88999999999999997 5999999999998753 22 23566
Q ss_pred eeCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCC---cceeEEEEEec
Q 006218 317 CPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSG---WRITALSVSAS 367 (656)
Q Consensus 317 ~~l~~~t~~I~~da~~L~~~al~ll~~~~~~~l~~~~~~~---~~ir~lgVsls 367 (656)
.++..+++ +...|++.+...|.+. ..+ .+++.++|++.
T Consensus 294 ~~~~~~~~----~~~~l~~l~~~~l~~~---------~~~~~~~~v~~~~v~~~ 334 (335)
T cd03468 294 VGLARPSR----DDLPLLRLLRERLERL---------ALPRGIAPVRLLALTAE 334 (335)
T ss_pred EeccCCcc----CHHHHHHHHHhhhhcc---------CCCCCeeeEEEEEeecc
Confidence 77777774 4445666666555432 234 68999999764
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=99.77 E-value=1.5e-18 Score=165.31 Aligned_cols=97 Identities=39% Similarity=0.570 Sum_probs=85.1
Q ss_pred CcHHHHHHhCCCcEEEeccCcCCCCChHHHHHHHHHHHHHHhhc-C-CeEEecCceEEEEccchhHHHhccCCCCCcchh
Q 006218 1 MRGDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILARK-G-RCERASIDEVYLDLTDAAEAMLAETPPESLDEV 78 (656)
Q Consensus 1 Mp~~~AkklCP~LivV~vP~~~~k~d~~~Yr~~S~~V~~IL~~~-~-~VE~~SIDEafLDlT~~~~~~L~~~~~~~l~~~ 78 (656)
|++.+|+++||+++++ + +|++.|+++|++|+.++.+| + .||.+|+||+|||+|+...
T Consensus 51 m~~~~A~~lcp~l~~~--~-----~d~~~~~~~~~~l~~~l~~~~sp~ve~~s~de~~ldv~~~~~-------------- 109 (149)
T PF00817_consen 51 MPLAEALALCPDLVVV--P-----PDPERYREASERLAEILYRFSSPRVEVYSPDELFLDVTGSLR-------------- 109 (149)
T ss_dssp SBHHHHHHHSTTSEEE--E-----EEHHHHHHHHHHHHHHHHTTTCSEEEEEETTEEEEEEHHHHH--------------
T ss_pred hhhhhHhhhccceeec--c-----ccHHHHHHHHHHHHHHHHhcccccceecccccccccCCcchh--------------
Confidence 8999999999999988 3 89999999999999999998 4 7999999999999999652
Q ss_pred hHHhhhhhcccCccCCCCCchhhhhhhhhccCccchhhhhhhHHHHHHHHHHHHHHHhCCceeEeccCcHHHHHHHhc
Q 006218 79 DEEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASG 156 (656)
Q Consensus 79 ~~e~~~s~l~g~~~~~g~~~~~~v~~w~~~~~~~~~d~ll~~~~~iA~~IR~~I~~~tGlt~SiGIA~NKlLAKLAS~ 156 (656)
+|| ....++++||++|++++||+||+|||+||++||||++
T Consensus 110 --------l~~------------------------------~~~~~~~~l~~~i~~~~gl~~s~Gia~~~~~Aklaa~ 149 (149)
T PF00817_consen 110 --------LFG------------------------------GEEALARRLRQAIAEETGLTASIGIAPNPLLAKLAAD 149 (149)
T ss_dssp --------HHH------------------------------HHHHHHHHHHHHHHHHHS--EEEEEESSHHHHHHHHH
T ss_pred --------hcc------------------------------hHHHHHHHHHHHHHHHhCCEEEEEEeCCHHHHHHhcC
Confidence 222 2357899999999999999999999999999999985
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=99.34 E-value=3e-12 Score=116.92 Aligned_cols=125 Identities=31% Similarity=0.430 Sum_probs=89.3
Q ss_pred Ccccc-cccCCCcccccccCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccCCCCCCCCCcC
Q 006218 235 GEEVQ-ARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFP 313 (656)
Q Consensus 235 ~~~V~-~~~~~KSIs~~~tF~~~~~i~~~eel~~~L~~L~~eL~~RLr~~~~~~~~~a~tvtL~ir~~~~~~~~s~~~~~ 313 (656)
++||. +...+|||+++++|+ .++.+.+++..+|..|+++|+.||++ +++.|++|+|++++.++ . .....
T Consensus 1 ~~pV~~~~~~~ksi~~~~t~~--~~~~~~~~i~~~l~~l~~~l~~rL~~----~~~~~~~i~l~l~~~~~---~-~~~~~ 70 (127)
T PF11799_consen 1 DEPVQQPRPPPKSIGSERTFP--EPISDREEIEEWLRELAEELAERLRE----RGLAARTITLKLRYSDF---G-RCSSR 70 (127)
T ss_dssp ------SCSS-SEEEEEEEEC--EEESSHHHHHHHHHHHHHHHHHHHHH----CTEEEEEEEEEEEETTS---C-SCEEE
T ss_pred CCCCCCCCCCCCEEEEEEECC--CCCCCHHHHHHHHHHHHHHHHHHHHh----hCcCCceEEEEEEecCC---c-cccee
Confidence 46787 778899999999998 57999999999999999999999996 69999999999997543 2 11235
Q ss_pred cceeeCCCcchhhHHhHHHHHHHHHHHHhcccCccccCCCCCCcceeEEEEEecCCe-eccCccccccccc
Q 006218 314 SKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIV-PVLSGTCSIMKYF 383 (656)
Q Consensus 314 sks~~l~~~t~~I~~da~~L~~~al~ll~~~~~~~l~~~~~~~~~ir~lgVsls~L~-~~~~~~~sq~~lF 383 (656)
+++++++.|++ +...|+.++..+|.... ...+.+||+|||++++|. +. ...|.+||
T Consensus 71 ~~~~~l~~p~~----~~~~l~~~~~~l~~~~~-------~~~~~~vr~igv~~~~l~~~~---~~~q~~lF 127 (127)
T PF11799_consen 71 SRSIRLPFPTN----DADELLKAARELLERLL-------YDPGFPVRLIGVSASDLIEPA---GQRQLDLF 127 (127)
T ss_dssp EEEEEECCCEH----CHHHHHHHHHHHHHHHH-------HHTTCGEEEEEEEEEEEEEC-------B----
T ss_pred eEEEeccCCcC----CHHHHHHHHHHHHHHHh-------cCCCCCEEEEEEEECCCcCCC---CCcccccC
Confidence 77888988886 45667777777774331 012678999999999999 43 57788888
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=98.50 E-value=4.8e-08 Score=69.74 Aligned_cols=32 Identities=34% Similarity=0.513 Sum_probs=28.2
Q ss_pred cccHHhhcccCCCccccCCchHHHHHHHHhcCC
Q 006218 168 FSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGV 200 (656)
Q Consensus 168 ~~~v~~fL~~LPI~kL~GIG~kt~~kL~~~lGI 200 (656)
|+++.+||++|||+++||||++|+++|+ .+||
T Consensus 1 pe~v~~~l~~lpi~~~~GIG~kt~~kL~-~~GI 32 (32)
T PF11798_consen 1 PEDVPEFLWPLPIRKFWGIGKKTAKKLN-KLGI 32 (32)
T ss_dssp CHHHHHHHHCSBGGGSTTS-HHHHHHHH-CTT-
T ss_pred ChHHHHHHhcCCHHhhCCccHHHHHHHH-HccC
Confidence 4688999999999999999999999997 9997
No 26
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=97.91 E-value=7.9e-06 Score=87.48 Aligned_cols=80 Identities=20% Similarity=0.218 Sum_probs=66.6
Q ss_pred hcccCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhcc--cchhhHHHHHhc---CC--CcccccccCCCc
Q 006218 174 LLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF--NTGTWLWNIARG---IS--GEEVQARLLPKS 246 (656)
Q Consensus 174 fL~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~--~~G~~L~~~arG---iD--~~~V~~~~~~KS 246 (656)
.|.++||.++||||++++++|. ..||+|++||+.++++.|.+.+|. +.+..+|..++| .+ .+.+.....+++
T Consensus 2 ~~~~~~l~~l~gIg~~~a~~L~-~~Gi~t~~dl~~~~~~~L~~~~g~~~~~a~~l~~~a~~~~~~~~~~t~~~l~~~~ks 80 (317)
T PRK04301 2 KMKEKDLEDLPGVGPATAEKLR-EAGYDTVEAIAVASPKELSEAAGIGESTAAKIIEAAREAADIGGFETALEVLERRKN 80 (317)
T ss_pred CcccccHhhcCCCCHHHHHHHH-HcCCCCHHHHHcCCHHHHHHhcCCCHHHHHHHHHHHHHhhccccCccHHHHHHhhcc
Confidence 4789999999999999999997 999999999999999999999995 368999999998 53 444444345677
Q ss_pred ccccccCC
Q 006218 247 HGSGKSFP 254 (656)
Q Consensus 247 Is~~~tF~ 254 (656)
++...|+.
T Consensus 81 ~~~~~Tg~ 88 (317)
T PRK04301 81 VGKITTGS 88 (317)
T ss_pred CCccCCCC
Confidence 87776664
No 27
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=97.30 E-value=0.00024 Score=75.74 Aligned_cols=74 Identities=19% Similarity=0.189 Sum_probs=61.4
Q ss_pred CccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhccc--chhhHHHHHh---cCC--CcccccccCCCccccccc
Q 006218 180 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN--TGTWLWNIAR---GIS--GEEVQARLLPKSHGSGKS 252 (656)
Q Consensus 180 I~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~~--~G~~L~~~ar---GiD--~~~V~~~~~~KSIs~~~t 252 (656)
|.++||||++++++|. ..||.|++||+.++.+.|.+.+|.. .+..++..++ |.+ .+.+.....+++++...|
T Consensus 1 l~~i~gig~~~~~~L~-~~Gi~ti~dl~~~~~~~L~~~~g~~~~~a~~l~~~~~~~~~~~~~~t~~~~~~~~~s~~~~~T 79 (310)
T TIGR02236 1 LEDLPGVGPATAEKLR-EAGYDTFEAIAVASPKELSEIAGISEGTAAKIIQAARKAADLGGFETADDVLERRKTIGKITT 79 (310)
T ss_pred CcccCCCCHHHHHHHH-HcCCCCHHHHHcCCHHHHHhccCCCHHHHHHHHHHHHHHhhccCCCCHHHHHHhhccCCeecC
Confidence 4689999999999997 9999999999999999999999963 4888999988 877 555554445678777776
Q ss_pred CC
Q 006218 253 FP 254 (656)
Q Consensus 253 F~ 254 (656)
+.
T Consensus 80 g~ 81 (310)
T TIGR02236 80 GS 81 (310)
T ss_pred CC
Confidence 64
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=96.78 E-value=0.00083 Score=54.51 Aligned_cols=50 Identities=28% Similarity=0.349 Sum_probs=41.8
Q ss_pred ccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHh--hcccchhhHHHHHh
Q 006218 181 KKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 231 (656)
Q Consensus 181 ~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~--FG~~~G~~L~~~ar 231 (656)
.+|+|||++++.+|. ..|+.|+.||+..+.+.|.+. +|.+.++.+...++
T Consensus 8 ~~I~Gig~~~a~~L~-~~G~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 8 LSIPGIGPKRAEKLY-EAGIKTLEDLANADPEELAEIPGIGEKTAEKIIEAAR 59 (60)
T ss_dssp HTSTTCHHHHHHHHH-HTTCSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHHHH
T ss_pred ccCCCCCHHHHHHHH-hcCCCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHHHh
Confidence 368999999999997 889999999999999999988 55555666665553
No 29
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=96.42 E-value=0.0026 Score=56.46 Aligned_cols=44 Identities=23% Similarity=0.326 Sum_probs=37.4
Q ss_pred CCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhcccch
Q 006218 179 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTG 223 (656)
Q Consensus 179 PI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~~~G 223 (656)
.+.+|||||+++++-|. .+||+++.||+..++..|..++-...|
T Consensus 13 ~L~~iP~IG~a~a~DL~-~LGi~s~~~L~g~dP~~Ly~~lc~~~G 56 (93)
T PF11731_consen 13 DLTDIPNIGKATAEDLR-LLGIRSPADLKGRDPEELYERLCALTG 56 (93)
T ss_pred HHhcCCCccHHHHHHHH-HcCCCCHHHHhCCCHHHHHHHHHHHcC
Confidence 35689999999999997 999999999999999888777654334
No 30
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=94.55 E-value=0.042 Score=56.34 Aligned_cols=56 Identities=18% Similarity=0.262 Sum_probs=50.0
Q ss_pred CCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHh--hcccchhhHHHHHhcCCC
Q 006218 179 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIARGISG 235 (656)
Q Consensus 179 PI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~--FG~~~G~~L~~~arGiD~ 235 (656)
.+.+|+|||++.+.+|. ..|+.|+.+|...+.+.|.+. +|...+..++..+.+.+.
T Consensus 4 ~L~~IpGIG~krakkLl-~~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l~~~~~ 61 (232)
T PRK12766 4 ELEDISGVGPSKAEALR-EAGFESVEDVRAADQSELAEVDGIGNALAARIKADVGGLEV 61 (232)
T ss_pred ccccCCCcCHHHHHHHH-HcCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHHhccccc
Confidence 46789999999999998 999999999999999999999 787788999999886544
No 31
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. This entry represents the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone []. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1KDH_A 1KEJ_A 1JMS_A 2IHM_A 3OGU_A 1MQ2_A 2P66_A 7ICI_A 1ZQN_A 1ZQK_A ....
Probab=93.35 E-value=0.061 Score=42.80 Aligned_cols=27 Identities=26% Similarity=0.302 Sum_probs=20.8
Q ss_pred ccccCCchHHHHHHHHhcCCcchhhhhc
Q 006218 181 KKMKQLGGKLGTSLQNELGVTTVGDLLK 208 (656)
Q Consensus 181 ~kL~GIG~kt~~kL~~~lGI~TigDLa~ 208 (656)
..|||||+++|+++. ..|++|+.||..
T Consensus 5 ~~I~GVG~~tA~~w~-~~G~rtl~Dl~~ 31 (52)
T PF10391_consen 5 TGIWGVGPKTARKWY-AKGIRTLEDLRK 31 (52)
T ss_dssp HTSTT--HHHHHHHH-HTT--SHHHHHH
T ss_pred hhcccccHHHHHHHH-HhCCCCHHHHhh
Confidence 468999999999998 899999999965
No 32
>PF04994 TfoX_C: TfoX C-terminal domain; InterPro: IPR007077 This domain is found in a number of bacterial proteins including the TfoX gene product of Haemophilus influenzae. TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes []. This family corresponds to the C-terminal presumed domain of TfoX. The domain is found in association with the N-terminal domain in some, but not all members of this group, suggesting this is an autonomous and functionally unrelated domain. For example it is found associated with Q9JZR1 from SWISSPROT in IPR002125 from INTERPRO.; PDB: 3BQT_A 3MAB_A.
Probab=92.70 E-value=0.12 Score=44.94 Aligned_cols=32 Identities=28% Similarity=0.484 Sum_probs=24.7
Q ss_pred CCccccCCchHHHHHHHHhcCCcchhhhhcCCH
Q 006218 179 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSE 211 (656)
Q Consensus 179 PI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~ 211 (656)
.|+++|+||+++++.|. +.||+|+.||..+..
T Consensus 4 ~l~~LpNig~~~e~~L~-~vGI~t~~~L~~~Ga 35 (81)
T PF04994_consen 4 RLKDLPNIGPKSERMLA-KVGIHTVEDLRELGA 35 (81)
T ss_dssp -GCGSTT--HHHHHHHH-HTT--SHHHHHHHHH
T ss_pred chhhCCCCCHHHHHHHH-HcCCCCHHHHHHhCH
Confidence 57899999999999997 999999999998754
No 33
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=91.76 E-value=0.18 Score=47.42 Aligned_cols=37 Identities=22% Similarity=0.441 Sum_probs=31.9
Q ss_pred CCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHH
Q 006218 179 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQE 216 (656)
Q Consensus 179 PI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~ 216 (656)
.++.|-|||++++..|+ .+||+|..||+.++...+..
T Consensus 68 DLt~I~GIGPk~e~~Ln-~~GI~tfaQIAAwt~~di~~ 104 (133)
T COG3743 68 DLTRISGIGPKLEKVLN-ELGIFTFAQIAAWTRADIAW 104 (133)
T ss_pred cchhhcccCHHHHHHHH-HcCCccHHHHHhcCHHHHHH
Confidence 36678999999999997 99999999999998765443
No 34
>PRK02362 ski2-like helicase; Provisional
Probab=91.51 E-value=0.14 Score=61.23 Aligned_cols=55 Identities=15% Similarity=0.151 Sum_probs=49.8
Q ss_pred CCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhcccchhhHHHHHhcC
Q 006218 178 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGI 233 (656)
Q Consensus 178 LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~~~G~~L~~~arGi 233 (656)
+|+..|||||++.+++|. .+||+|+.||+.+..+.|.+.||.+.++.++..++..
T Consensus 652 ~~L~~ip~i~~~~a~~l~-~~gi~s~~dl~~~~~~~l~~~~g~~~~~~i~~~~~~~ 706 (737)
T PRK02362 652 LDLVGLRGVGRVRARRLY-NAGIESRADLRAADKSVVLAILGEKIAENILEQAGRR 706 (737)
T ss_pred HHHhCCCCCCHHHHHHHH-HcCCCCHHHHHhCCHHHHHHHHCHHHHHHHHHHhCcc
Confidence 467789999999999997 8999999999999999999999999999998887744
No 35
>PF03118 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha chain C terminal domain; InterPro: IPR011260 The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals. The alpha subunit (RpoA) initiates RNAP assembly by dimerising to form a platform on which the beta subunits can interact. The alpha subunit consists of a N-terminal domain (NTD) and a C-terminal domain (CTD), connected by a short linker. The NTD is essential for RNAP assembly, while the CTD is necessary for transcription regulation, interacting with transcription factors and promoter upstream elements. In Escherichia coli, the catabolite activator protein (CAP or CRP) was shown to exert its effect through its interactions with the CTD, where CAP binding to CTD promotes RNAP binding to promoter DNA, thereby stimulating transcription initiation at class I CAP-dependent promoters. At class II CAP-dependent promoters, the interaction of CAP with CTD is one of multiple interactions involved in activation []. The CTD has a compact structure of four helices and two long arms enclosing its hydrophobic core, making its folding topology distinct from most other binding proteins. The upstream promoter element-binding site is formed from helices 1 and 4 [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3N97_B 1XS9_D 3K4G_A 3N4M_B 1COO_A 1LB2_E 3IYD_A 1Z3E_B 3GFK_B 3IHQ_B ....
Probab=91.39 E-value=0.16 Score=42.33 Aligned_cols=45 Identities=33% Similarity=0.478 Sum_probs=36.1
Q ss_pred hhcccCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhc
Q 006218 173 GLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYG 219 (656)
Q Consensus 173 ~fL~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG 219 (656)
..+...||.++ |+..++...|. +.||+|++||..++...|.+.=|
T Consensus 7 ~~~~~~~I~~L-~LS~Ra~n~L~-~~~I~tv~dL~~~s~~~L~~i~n 51 (66)
T PF03118_consen 7 EELLDTPIEDL-GLSVRAYNCLK-RAGIHTVGDLVKYSEEDLLKIKN 51 (66)
T ss_dssp HHHHCSBGGGS-TSBHHHHHHHH-CTT--BHHHHHCS-HHHHHTSTT
T ss_pred HHHhcCcHHHh-CCCHHHHHHHH-HhCCcCHHHHHhCCHHHHHhCCC
Confidence 45567899888 79999999997 99999999999999999887644
No 36
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=90.05 E-value=0.28 Score=45.70 Aligned_cols=54 Identities=17% Similarity=0.306 Sum_probs=44.4
Q ss_pred cCcccHHhhcccCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhcc
Q 006218 166 VPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF 220 (656)
Q Consensus 166 l~~~~v~~fL~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~ 220 (656)
++...+..+...-.+..++|||+..+..|. ..||.|+.+|+..++..|...++.
T Consensus 41 i~~~~l~~w~~~AdL~ri~gi~~~~a~LL~-~AGv~Tv~~LA~~~p~~L~~~l~~ 94 (122)
T PF14229_consen 41 ISERNLLKWVNQADLMRIPGIGPQYAELLE-HAGVDTVEELAQRNPQNLHQKLGR 94 (122)
T ss_pred CCHHHHHHHHhHHHhhhcCCCCHHHHHHHH-HhCcCcHHHHHhCCHHHHHHHHHH
Confidence 344556666555556689999999999997 999999999999999999888774
No 37
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=89.53 E-value=0.25 Score=40.74 Aligned_cols=47 Identities=17% Similarity=0.314 Sum_probs=33.2
Q ss_pred ccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHh--hcccchhhHHHHHh
Q 006218 183 MKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 231 (656)
Q Consensus 183 L~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~--FG~~~G~~L~~~ar 231 (656)
|||||.++++.|.+.+| ++..|.+.+.+.|.+. +|+..++.++++..
T Consensus 8 I~~VG~~~ak~L~~~f~--sl~~l~~a~~e~L~~i~gIG~~~A~si~~ff~ 56 (64)
T PF12826_consen 8 IPGVGEKTAKLLAKHFG--SLEALMNASVEELSAIPGIGPKIAQSIYEFFQ 56 (64)
T ss_dssp STT--HHHHHHHHHCCS--CHHHHCC--HHHHCTSTT--HHHHHHHHHHHH
T ss_pred CCCccHHHHHHHHHHcC--CHHHHHHcCHHHHhccCCcCHHHHHHHHHHHC
Confidence 68999999999986666 8999999999999887 77766777766544
No 38
>PRK01172 ski2-like helicase; Provisional
Probab=86.20 E-value=0.73 Score=54.59 Aligned_cols=52 Identities=17% Similarity=0.279 Sum_probs=42.9
Q ss_pred CCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHh--hcccchhhHHHHH
Q 006218 178 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIA 230 (656)
Q Consensus 178 LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~--FG~~~G~~L~~~a 230 (656)
+|+..|||||+..+++|. ..||+|+.||+.++.+.+.+. ||.+.+..++..+
T Consensus 612 ~~L~~ip~~~~~~a~~l~-~~g~~~~~di~~~~~~~~~~i~~~~~~~~~~i~~~~ 665 (674)
T PRK01172 612 IDLVLIPKVGRVRARRLY-DAGFKTVDDIARSSPERIKKIYGFSDTLANAIVNRA 665 (674)
T ss_pred HhhcCCCCCCHHHHHHHH-HcCCCCHHHHHhCCHHHHHHHhccCHHHHHHHHHHH
Confidence 588889999999999997 999999999999999999888 4544455555443
No 39
>PRK00254 ski2-like helicase; Provisional
Probab=85.55 E-value=0.67 Score=55.40 Aligned_cols=53 Identities=15% Similarity=0.271 Sum_probs=47.9
Q ss_pred CCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHh--hcccchhhHHHHHh
Q 006218 178 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 231 (656)
Q Consensus 178 LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~--FG~~~G~~L~~~ar 231 (656)
+|+..+||||++.+++|. ..|+.|+.||..++.+.|.+. +|.+.++.++..++
T Consensus 645 ~~L~~ipgig~~~~~~l~-~~g~~s~~~i~~a~~~el~~~~gi~~~~a~~i~~~~~ 699 (720)
T PRK00254 645 LELMRLPMIGRKRARALY-NAGFRSIEDIVNAKPSELLKVEGIGAKIVEGIFKHLG 699 (720)
T ss_pred hhhhcCCCCCHHHHHHHH-HccCCCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHhc
Confidence 577789999999999997 999999999999999999998 77777888888766
No 40
>PRK07758 hypothetical protein; Provisional
Probab=81.88 E-value=2 Score=38.43 Aligned_cols=38 Identities=26% Similarity=0.405 Sum_probs=32.4
Q ss_pred ccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHh--hccc
Q 006218 183 MKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFN 221 (656)
Q Consensus 183 L~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~--FG~~ 221 (656)
+++++-+...-|. ..||.|++||..++.+.|.+. ||++
T Consensus 39 ~~~LSvRA~N~Lk-~AGI~TL~dLv~~te~ELl~iknlGkK 78 (95)
T PRK07758 39 LSLLSAPARRALE-HHGIHTVEELSKYSEKEILKLHGMGPA 78 (95)
T ss_pred CccccHHHHHHHH-HcCCCcHHHHHcCCHHHHHHccCCCHH
Confidence 4678889999996 999999999999999998776 5554
No 41
>COG2251 Predicted nuclease (RecB family) [General function prediction only]
Probab=81.69 E-value=1.4 Score=49.44 Aligned_cols=68 Identities=21% Similarity=0.096 Sum_probs=55.9
Q ss_pred cccHHhhcccCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhc--ccchhhHHHHHhcCCCc
Q 006218 168 FSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYG--FNTGTWLWNIARGISGE 236 (656)
Q Consensus 168 ~~~v~~fL~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG--~~~G~~L~~~arGiD~~ 236 (656)
+.....++..-.+.-++||++.....|. .+||+|+.||++.+...+...+| ...+..+...++-....
T Consensus 215 p~C~~~a~e~~~L~Lv~Gi~~~r~~~l~-~~GI~Ti~~LA~~~~~~~~~~~ga~~~~~~~l~~qa~~~~e~ 284 (474)
T COG2251 215 PQCESEALEEDDLSLVPGITPSRYDVLE-EVGITTIEDLADASLPILELVAGALTALAAQLVLQARARVEG 284 (474)
T ss_pred hhhhHHHhhccceeccCCCCHHHHHHHH-HcCcchHHHHHhccccchhhhhhhHHHHHHHHHHHHHhhccC
Confidence 5566778888888889999999999997 99999999999999888888888 44566777777765443
No 42
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=81.68 E-value=2 Score=39.97 Aligned_cols=44 Identities=27% Similarity=0.438 Sum_probs=33.0
Q ss_pred cCCchHHHHHHHHhcCCcchhhhhcCCH-----HHHHHhhcccchhhHHHH
Q 006218 184 KQLGGKLGTSLQNELGVTTVGDLLKFSE-----DKLQESYGFNTGTWLWNI 229 (656)
Q Consensus 184 ~GIG~kt~~kL~~~lGI~TigDLa~l~~-----~~L~~~FG~~~G~~L~~~ 229 (656)
||||++.+.+|. ..||+|.+||..... ..|....|. ....+..+
T Consensus 1 pgi~~~~~~~L~-~~GI~t~~~Ll~~~~~~~~r~~La~~~~i-~~~~l~~w 49 (122)
T PF14229_consen 1 PGIGPKEAAKLK-AAGIKTTGDLLEAGDTPLGRKALAKKLGI-SERNLLKW 49 (122)
T ss_pred CCCCHHHHHHHH-HcCCCcHHHHHHcCCCHHHHHHHHHhcCC-CHHHHHHH
Confidence 799999999996 999999999998643 236666665 34444443
No 43
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=77.82 E-value=2 Score=50.00 Aligned_cols=54 Identities=17% Similarity=0.157 Sum_probs=45.1
Q ss_pred cCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHh-hcccchhhHHHHHhc
Q 006218 177 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES-YGFNTGTWLWNIARG 232 (656)
Q Consensus 177 ~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~-FG~~~G~~L~~~arG 232 (656)
.-.+.+|||||++...+|.+ -..++..+...+.++|.+. +|.+.++.++..++|
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 45678999999999999974 4559999999999999998 556678888888776
No 44
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=76.90 E-value=2.1 Score=42.96 Aligned_cols=56 Identities=13% Similarity=0.091 Sum_probs=43.3
Q ss_pred CccccCCchHHHHHHHHhcCCcchh-hhhcCCHHHHHHh--hcccchhhHHHHHhcCCC
Q 006218 180 IKKMKQLGGKLGTSLQNELGVTTVG-DLLKFSEDKLQES--YGFNTGTWLWNIARGISG 235 (656)
Q Consensus 180 I~kL~GIG~kt~~kL~~~lGI~Tig-DLa~l~~~~L~~~--FG~~~G~~L~~~arGiD~ 235 (656)
+..++|||++++.++.+.+|..++- .+..-+.+.|.+. +|.+.+++++...++...
T Consensus 75 L~~i~GIGpk~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~~~l~~~~~ 133 (192)
T PRK00116 75 LISVSGVGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELKDKLA 133 (192)
T ss_pred HhcCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHHhh
Confidence 3468999999999887678876653 4556688889887 777788999888887553
No 45
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=75.86 E-value=1.7 Score=47.39 Aligned_cols=30 Identities=20% Similarity=0.255 Sum_probs=26.2
Q ss_pred CccccCCchHHHHHHHHhcCCcchhhhhcCC
Q 006218 180 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFS 210 (656)
Q Consensus 180 I~kL~GIG~kt~~kL~~~lGI~TigDLa~l~ 210 (656)
+.+|||||++++.+|. .+||+|+.||....
T Consensus 91 l~~i~GiGpk~a~~l~-~lGi~tl~eL~~a~ 120 (334)
T smart00483 91 FTNVFGVGPKTAAKWY-RKGIRTLEELKKNK 120 (334)
T ss_pred HHccCCcCHHHHHHHH-HhCCCCHHHHHhcc
Confidence 3479999999999998 69999999998643
No 46
>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=75.28 E-value=2.3 Score=37.52 Aligned_cols=33 Identities=24% Similarity=0.434 Sum_probs=23.1
Q ss_pred cccCCCccccCCchHHHHHHHHhcCCcchhhhhc
Q 006218 175 LDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLK 208 (656)
Q Consensus 175 L~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~ 208 (656)
|..-||++|+|||+.++.+|. ..|+..+..|..
T Consensus 16 MGeK~V~~laGIG~~lg~~L~-~~GfdKAy~vLG 48 (89)
T PF02961_consen 16 MGEKPVTELAGIGPVLGKRLE-EKGFDKAYVVLG 48 (89)
T ss_dssp -TT-BGGGSTT--HHHHHHHH-HTT--BHHHHHH
T ss_pred cCCCCccccCCcCHHHHHHHH-HCCCcHHHHHhh
Confidence 445689999999999999996 999998877653
No 47
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=74.38 E-value=2.5 Score=51.25 Aligned_cols=52 Identities=23% Similarity=0.314 Sum_probs=46.0
Q ss_pred CccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhc-ccchhhHHHHHhcC
Q 006218 180 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYG-FNTGTWLWNIARGI 233 (656)
Q Consensus 180 I~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG-~~~G~~L~~~arGi 233 (656)
+..|||||++.+.+|. ..+.++.+|.+++.+.|....| .+.|..+|++.+.-
T Consensus 759 L~~lPgI~~~~a~~ll--~~f~si~~l~~as~eeL~~~iG~~~~A~~i~~fl~~~ 811 (814)
T TIGR00596 759 LLKLPGVTKKNYRNLR--KKVKSIRELAKLSQNELNELIGDEEAAKRLYDFLRTE 811 (814)
T ss_pred HHHCCCCCHHHHHHHH--HHcCCHHHHHhCCHHHHHHHhCCHHHHHHHHHHhccc
Confidence 4478899999999996 4688999999999999999999 88899999988753
No 48
>PF14377 DUF4414: Domain of unknown function (DUF4414)
Probab=73.85 E-value=1.5 Score=39.97 Aligned_cols=21 Identities=38% Similarity=0.730 Sum_probs=18.4
Q ss_pred CCccccccCChHHHHHHHHhh
Q 006218 611 IDPSVIDELPKEIQDEIQAWL 631 (656)
Q Consensus 611 ~~~~~~~~~~~~~~~~~~~~~ 631 (656)
|||+|+.+||.+|+.||-.=.
T Consensus 1 iDp~fLaaLPeDiR~Evl~~~ 21 (108)
T PF14377_consen 1 IDPEFLAALPEDIREEVLAQQ 21 (108)
T ss_pred CCHHHHHHCCHHHHHHHHHHH
Confidence 899999999999999994433
No 49
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=73.67 E-value=5.9 Score=42.08 Aligned_cols=62 Identities=16% Similarity=0.364 Sum_probs=50.7
Q ss_pred cCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhcc--cchhhHHHHHhcCCCcccc
Q 006218 177 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF--NTGTWLWNIARGISGEEVQ 239 (656)
Q Consensus 177 ~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~--~~G~~L~~~arGiD~~~V~ 239 (656)
..|+..+||||.....+|. ..||.+++||..++.+.+...+|. ..|..+++.++....-.|.
T Consensus 150 ~~~L~Qlp~i~~~~~~~l~-~~~i~s~~~l~~~~~~~~~~ll~~~~~~~~~i~~~~~~~P~l~v~ 213 (312)
T smart00611 150 DSPLLQLPHLPEEILKRLE-KKKVLSLEDLLELEDEERGELLGLLDAEGERVYKVLSRLPKLNIE 213 (312)
T ss_pred CCccccCCCCCHHHHHHHH-hCCCCCHHHHHhcCHHHHHHHHcCCHHHHHHHHHHHHhCCcceeE
Confidence 4688899999999999996 899999999999999988888774 2477788887766555443
No 50
>TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Probab=73.18 E-value=2.3 Score=48.18 Aligned_cols=60 Identities=23% Similarity=0.248 Sum_probs=42.7
Q ss_pred HHhhcccCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHH--hhcccchhhHHHHHh
Q 006218 171 VKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQE--SYGFNTGTWLWNIAR 231 (656)
Q Consensus 171 v~~fL~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~--~FG~~~G~~L~~~ar 231 (656)
.......-+|..|+|||++...+|. ..||.|+.||+..+...|.. .+|...+.+|...|+
T Consensus 200 ~~~~~~~~~lslv~gi~~~~~~~L~-~~GI~ti~~La~~~~~~l~~~~~~~~~~~~~l~~qA~ 261 (457)
T TIGR03491 200 EAVAKEEGHLSLVPGIGPSRYRLLQ-ELGIHTLEDLAAADPNDLEDFGEQGLGVAEQLVQQAR 261 (457)
T ss_pred HHHHHhcCCeeecCCCCHHHHHHHH-HcCCCcHHHHhcCCccccccccccCHHHHHHHHHHHH
Confidence 3445556789999999999999997 99999999999987543433 234333444444443
No 51
>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=72.76 E-value=2.3 Score=45.79 Aligned_cols=28 Identities=36% Similarity=0.477 Sum_probs=25.7
Q ss_pred ccccCCchHHHHHHHHhcCCcchhhhhcC
Q 006218 181 KKMKQLGGKLGTSLQNELGVTTVGDLLKF 209 (656)
Q Consensus 181 ~kL~GIG~kt~~kL~~~lGI~TigDLa~l 209 (656)
.++||||++++++|. .+||.|+.||...
T Consensus 88 ~~i~GiGpk~a~~l~-~lGi~sl~dL~~a 115 (307)
T cd00141 88 LRVPGVGPKTARKLY-ELGIRTLEDLRKA 115 (307)
T ss_pred HcCCCCCHHHHHHHH-HcCCCCHHHHHHH
Confidence 379999999999998 9999999999874
No 52
>PRK08609 hypothetical protein; Provisional
Probab=72.30 E-value=2.4 Score=49.57 Aligned_cols=29 Identities=38% Similarity=0.418 Sum_probs=26.2
Q ss_pred ccccCCchHHHHHHHHhcCCcchhhhhcC
Q 006218 181 KKMKQLGGKLGTSLQNELGVTTVGDLLKF 209 (656)
Q Consensus 181 ~kL~GIG~kt~~kL~~~lGI~TigDLa~l 209 (656)
.++||||++++.+|.+.+||.|+.||...
T Consensus 91 ~~i~GiGpk~a~~l~~~lGi~tl~~L~~a 119 (570)
T PRK08609 91 LKLPGLGGKKIAKLYKELGVVDKESLKEA 119 (570)
T ss_pred hcCCCCCHHHHHHHHHHhCCCCHHHHHHH
Confidence 37999999999999877999999999964
No 53
>PF14377 DUF4414: Domain of unknown function (DUF4414)
Probab=71.19 E-value=2.5 Score=38.51 Aligned_cols=25 Identities=36% Similarity=0.627 Sum_probs=21.2
Q ss_pred cccCCccccccCChHHHHHHHHhhC
Q 006218 608 IEEIDPSVIDELPKEIQDEIQAWLR 632 (656)
Q Consensus 608 ~~~~~~~~~~~~~~~~~~~~~~~~~ 632 (656)
-.+|||.+++-||++||+||-+=.+
T Consensus 42 ~~~I~pefL~ALP~diR~EVl~qe~ 66 (108)
T PF14377_consen 42 PSQIDPEFLAALPPDIREEVLAQER 66 (108)
T ss_pred ccccCHHHHHhCCHHHHHHHHHHHH
Confidence 5689999999999999999865443
No 54
>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=70.94 E-value=4.2 Score=43.09 Aligned_cols=60 Identities=23% Similarity=0.364 Sum_probs=43.1
Q ss_pred CCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhcc--cchhhHHHHHhcCCCccc
Q 006218 178 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF--NTGTWLWNIARGISGEEV 238 (656)
Q Consensus 178 LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~--~~G~~L~~~arGiD~~~V 238 (656)
.|+..|||||.....+|. ..||.|++||..++...+...++. ..|..+.+.++.+..-.|
T Consensus 148 ~~L~Qlp~i~~~~~~~l~-~~~i~~l~~l~~~~~~e~~~ll~~~~~~~~~i~~~~~~~P~~~i 209 (314)
T PF02889_consen 148 SPLLQLPHIGEESLKKLE-KRGIKTLQDLRDLSPEELEELLNRNPPFGKEILEVASRIPRLEI 209 (314)
T ss_dssp -GGGGSTT--HHHHHHHH-HTT--SHHHHHHS-HHHHHHHH-S-HHHHHHHHHHHCCS--EEE
T ss_pred ChhhcCCCCCHHHHHHHh-ccCCCcHHHHhhCCHHHHHHHHhhhhhhHHHHHHHHHHCCCEEE
Confidence 578899999999999997 899999999999999999888863 247778888887755444
No 55
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=69.37 E-value=4.8 Score=47.94 Aligned_cols=51 Identities=20% Similarity=0.255 Sum_probs=41.3
Q ss_pred CCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHh--hcccchhhHHHH
Q 006218 179 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNI 229 (656)
Q Consensus 179 PI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~--FG~~~G~~L~~~ 229 (656)
..-+|+|+|+++.++|.+..+|.++.||..+..+.|... ||.+.++.|++.
T Consensus 446 ~al~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~ll~~ 498 (665)
T PRK07956 446 NAMDIDGLGEKIIEQLFEKGLIHDPADLFKLTAEDLLGLEGFGEKSAQNLLDA 498 (665)
T ss_pred cccCCCCcCHHHHHHHHHcCCCCCHHHHHhcCHHHHhcCcCcchHHHHHHHHH
Confidence 345789999999999987788999999999998888764 777666655543
No 56
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=69.12 E-value=5.1 Score=47.32 Aligned_cols=51 Identities=20% Similarity=0.285 Sum_probs=42.8
Q ss_pred CCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhcccchhhHHHHH
Q 006218 178 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIA 230 (656)
Q Consensus 178 LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~~~G~~L~~~a 230 (656)
..+..|+|||++++..|.+.+| |+.+|...+.+.|.+.+|.+.++.++.+.
T Consensus 569 s~L~~I~GIG~k~a~~Ll~~Fg--s~~~i~~As~eeL~~vig~k~A~~I~~~~ 619 (621)
T PRK14671 569 TELTDIAGIGEKTAEKLLEHFG--SVEKVAKASLEELAAVAGPKTAETIYRYY 619 (621)
T ss_pred hhhhcCCCcCHHHHHHHHHHcC--CHHHHHhCCHHHHHHHhCHHHHHHHHHHh
Confidence 3567899999999999975555 88999999999999889988888887764
No 57
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=68.88 E-value=5.4 Score=47.33 Aligned_cols=62 Identities=11% Similarity=0.201 Sum_probs=51.6
Q ss_pred cCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHh--hcccchhhHHHHHhcCCCccccc
Q 006218 177 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIARGISGEEVQA 240 (656)
Q Consensus 177 ~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~--FG~~~G~~L~~~arGiD~~~V~~ 240 (656)
...+.+|||||++...+|.+.+| ++.+|...+.+.|.+. +|.+.+..+++.+.--...||..
T Consensus 607 ~s~L~~IpGiG~kr~~~LL~~Fg--S~~~i~~As~eel~~v~gi~~~~A~~i~~~~~~~~~~~~~~ 670 (691)
T PRK14672 607 VLSFERLPHVGKVRAHRLLAHFG--SFRSLQSATPQDIATAIHIPLTQAHTILHAATRSTTAPVRE 670 (691)
T ss_pred ccccccCCCCCHHHHHHHHHHhc--CHHHHHhCCHHHHHhCCCCCHHHHHHHHHHhhcccccchhH
Confidence 45788999999999999975554 8999999999999998 67777888998887777777754
No 58
>PTZ00035 Rad51 protein; Provisional
Probab=68.61 E-value=4.4 Score=44.25 Aligned_cols=55 Identities=18% Similarity=0.177 Sum_probs=45.4
Q ss_pred CCCccc--cCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhccc--chhhHHHHHhcC
Q 006218 178 LPIKKM--KQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN--TGTWLWNIARGI 233 (656)
Q Consensus 178 LPI~kL--~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~~--~G~~L~~~arGi 233 (656)
++|.++ +||+..+..+|. ..||+|+.||+..++..|.+..|.. .++.+...++-.
T Consensus 21 ~~~~~l~~~g~~~~~~~kL~-~~g~~t~~~~~~~~~~~L~~~~gis~~~~~~i~~~~~~~ 79 (337)
T PTZ00035 21 QEIEKLQSAGINAADIKKLK-EAGICTVESVAYATKKDLCNIKGISEAKVEKIKEAASKL 79 (337)
T ss_pred ccHHHHhcCCCCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHhhCCCHHHHHHHHHHHHHh
Confidence 367778 779999999997 9999999999999999999998862 245666666654
No 59
>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=68.36 E-value=5.2 Score=47.50 Aligned_cols=53 Identities=25% Similarity=0.307 Sum_probs=42.3
Q ss_pred CCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHh--hcccchhhHHHHHh
Q 006218 179 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 231 (656)
Q Consensus 179 PI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~--FG~~~G~~L~~~ar 231 (656)
.--+|+|+|+++..+|.+..+|+++.||..+..+.|... ||.+.+..|++...
T Consensus 433 ~al~I~GLG~k~i~~L~~~g~I~~~~Dl~~L~~~~L~~L~GfG~Ksa~nIl~~Ie 487 (652)
T TIGR00575 433 NAMDIEGLGDKVIEQLFEKKLVRSVADLYALKKEDLLELEGFGEKSAQNLLNAIE 487 (652)
T ss_pred CccCCCCcCHHHHHHHHHcCCcCCHHHHHhcCHHHHhhccCccHHHHHHHHHHHH
Confidence 345789999999999986678999999999998888765 67666666665544
No 60
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=67.34 E-value=3.7 Score=48.95 Aligned_cols=31 Identities=39% Similarity=0.618 Sum_probs=28.4
Q ss_pred CCCccccCCchHHHHHHHHhcCCcchhhhhcC
Q 006218 178 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKF 209 (656)
Q Consensus 178 LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l 209 (656)
.||..+.|||++.++.|. ++||.|+.||...
T Consensus 9 ~~~~~l~gvg~~~~~~l~-~lgi~t~~dll~~ 39 (681)
T PRK10917 9 APLTSLKGVGPKTAEKLA-KLGIHTVQDLLLH 39 (681)
T ss_pred CChhhcCCCCHHHHHHHH-HcCCCCHHHHhhc
Confidence 489999999999999997 9999999999863
No 61
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=66.86 E-value=6.1 Score=46.19 Aligned_cols=53 Identities=25% Similarity=0.356 Sum_probs=43.6
Q ss_pred cCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHh--hcccchhhHHHHHh
Q 006218 177 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 231 (656)
Q Consensus 177 ~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~--FG~~~G~~L~~~ar 231 (656)
...+.+|||||++...+|.+.+ .++..+...+.++|.+. ++.+.+..++...+
T Consensus 513 ~s~L~~I~GiG~kr~~~LL~~F--gs~~~I~~As~eeL~~v~gi~~~~A~~I~~~l~ 567 (574)
T PRK14670 513 KLNYTKIKGIGEKKAKKILKSL--GTYKDILLLNEDEIAEKMKINIKMAKKIKKFAE 567 (574)
T ss_pred ccccccCCCCCHHHHHHHHHHh--CCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHH
Confidence 4578899999999999997555 48999999999999998 66557888877664
No 62
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=66.01 E-value=3.2 Score=29.31 Aligned_cols=15 Identities=20% Similarity=0.357 Sum_probs=11.9
Q ss_pred ccccCCchHHHHHHH
Q 006218 181 KKMKQLGGKLGTSLQ 195 (656)
Q Consensus 181 ~kL~GIG~kt~~kL~ 195 (656)
.+|||||++++..+.
T Consensus 14 ~~lpGIG~~tA~~I~ 28 (30)
T PF00633_consen 14 MKLPGIGPKTANAIL 28 (30)
T ss_dssp HTSTT-SHHHHHHHH
T ss_pred HhCCCcCHHHHHHHH
Confidence 479999999998875
No 63
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=65.86 E-value=5.7 Score=47.21 Aligned_cols=51 Identities=14% Similarity=0.188 Sum_probs=41.9
Q ss_pred CCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHh--hcccchhhHHHHH
Q 006218 178 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIA 230 (656)
Q Consensus 178 LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~--FG~~~G~~L~~~a 230 (656)
-.+..+||||++...+|.+.+| ++.+|...+.+.|.+. +|.+.++.+++.+
T Consensus 637 s~L~~IPGIGpkr~k~LL~~FG--Sle~I~~AS~eELa~V~Gig~k~Ae~I~~~L 689 (694)
T PRK14666 637 GELQRVEGIGPATARLLWERFG--SLQAMAAAGEEGLAAVPGIGPARAAALHEHL 689 (694)
T ss_pred hHHhhCCCCCHHHHHHHHHHhC--CHHHHHhcCHHHHHhcCCcCHHHHHHHHHHH
Confidence 4577899999999999987778 9999999999999887 6666666666554
No 64
>TIGR02239 recomb_RAD51 DNA repair protein RAD51. This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).
Probab=65.72 E-value=6.8 Score=42.33 Aligned_cols=36 Identities=25% Similarity=0.240 Sum_probs=33.5
Q ss_pred CCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhccc
Q 006218 185 QLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN 221 (656)
Q Consensus 185 GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~~ 221 (656)
||+..+..+|. ..||.|+.||+..++..|.+.+|..
T Consensus 8 ~~~~~~~~~l~-~~g~~t~~~~~~~~~~~L~~i~~ls 43 (316)
T TIGR02239 8 GITAADIKKLQ-EAGLHTVESVAYAPKKQLLEIKGIS 43 (316)
T ss_pred CCCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHHhCCC
Confidence 59999999997 9999999999999999999999963
No 65
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=64.48 E-value=4.6 Score=44.22 Aligned_cols=43 Identities=21% Similarity=0.337 Sum_probs=39.1
Q ss_pred CCCccc--cCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhccc
Q 006218 178 LPIKKM--KQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN 221 (656)
Q Consensus 178 LPI~kL--~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~~ 221 (656)
.+|.++ .||+.....+|+ ..||.|+.||+..++..|.+.+|..
T Consensus 26 ~~~~~l~~~gi~~~~i~kL~-~~g~~T~~~~~~~~~~~L~~i~~is 70 (342)
T PLN03186 26 FPIEQLQASGIAALDIKKLK-DAGIHTVESLAYAPKKDLLQIKGIS 70 (342)
T ss_pred ccHHHHHhCCCCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHhcCCC
Confidence 478888 679999999997 9999999999999999999999974
No 66
>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1. This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.
Probab=63.97 E-value=7.8 Score=41.89 Aligned_cols=48 Identities=15% Similarity=0.135 Sum_probs=38.9
Q ss_pred cCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhccc--chhhHHHHHhc
Q 006218 184 KQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN--TGTWLWNIARG 232 (656)
Q Consensus 184 ~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~~--~G~~L~~~arG 232 (656)
.|||..+.++|+ ..||+|+.||+..++..|.+..|.. .+..+.+.++-
T Consensus 7 ~g~~~~~~~~L~-~~g~~t~~~~~~~~~~~L~~~~gls~~~~~~i~~~~~~ 56 (313)
T TIGR02238 7 HGINAADIKKLK-SAGICTVNGVIMTTRRALCKIKGLSEAKVDKIKEAASK 56 (313)
T ss_pred CCCCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHh
Confidence 479999999997 9999999999999999999998852 24445554443
No 67
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=63.62 E-value=6 Score=43.38 Aligned_cols=56 Identities=18% Similarity=0.229 Sum_probs=45.0
Q ss_pred cCCCccc--cCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhccc--chhhHHHHHhcC
Q 006218 177 SLPIKKM--KQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN--TGTWLWNIARGI 233 (656)
Q Consensus 177 ~LPI~kL--~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~~--~G~~L~~~arGi 233 (656)
..+|.++ .||++.+.++|. ..||+|+.||+..++..|.+..|.. .+..+...++..
T Consensus 28 ~~~~~~l~~~g~~~~~~~kL~-~~g~~tv~~~~~~~~~~L~~~~g~s~~~~~ki~~~a~~~ 87 (344)
T PLN03187 28 FESIDKLISQGINAGDVKKLQ-DAGIYTCNGLMMHTKKNLTGIKGLSEAKVDKICEAAEKL 87 (344)
T ss_pred ccCHHHHhhCCCCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHHh
Confidence 5667888 679999999997 9999999999999999999988852 245555555544
No 68
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=62.20 E-value=7.8 Score=45.78 Aligned_cols=54 Identities=11% Similarity=0.091 Sum_probs=45.8
Q ss_pred cCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhcccchhhHHHHHhc
Q 006218 177 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARG 232 (656)
Q Consensus 177 ~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~~~G~~L~~~arG 232 (656)
.-.+.+|||||++...+|.+. ..++..+...+.+.|.+.+|.+.++.++..++.
T Consensus 551 ~S~L~~IpGIG~kr~~~LL~~--FgSi~~I~~As~eeL~~vi~~k~A~~I~~~l~~ 604 (624)
T PRK14669 551 TSELLEIPGVGAKTVQRLLKH--FGSLERVRAATETQLAAVVGRAAAEAIIAHFTT 604 (624)
T ss_pred HHHHhcCCCCCHHHHHHHHHH--cCCHHHHHhCCHHHHHHHhCHHHHHHHHHHhcC
Confidence 346779999999999999744 458999999999999999998889999988764
No 69
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=61.69 E-value=7.8 Score=39.94 Aligned_cols=36 Identities=25% Similarity=0.481 Sum_probs=32.1
Q ss_pred CCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHH
Q 006218 179 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQ 215 (656)
Q Consensus 179 PI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~ 215 (656)
.+.+|.|||+.++.+|. ..||++..+|+.++.+.+.
T Consensus 159 DL~~I~GIGp~~a~~L~-eaGi~tfaQIAa~t~a~ia 194 (221)
T PRK12278 159 DLTKITGVGPALAKKLN-EAGVTTFAQIAALTDADIA 194 (221)
T ss_pred hheeccccChHHHHHHH-HcCCCCHHHhhCCChhhhh
Confidence 46789999999999997 9999999999999887554
No 70
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=59.36 E-value=7 Score=42.57 Aligned_cols=35 Identities=20% Similarity=0.390 Sum_probs=31.2
Q ss_pred CccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHH
Q 006218 180 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQ 215 (656)
Q Consensus 180 I~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~ 215 (656)
+.+|.|||++++++|. .+||++..|++.++.+.+.
T Consensus 265 L~~I~GiGp~~e~~L~-~~Gi~~f~QiA~~t~~~~a 299 (326)
T PRK12311 265 LKKLTGVSPQIEKKLN-DLGIFHFWQLAELDPDDAA 299 (326)
T ss_pred hhhhccCChhhhhhhh-hcCCCCHHHhhCCChhhhh
Confidence 6789999999999997 9999999999999877443
No 71
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=58.93 E-value=10 Score=45.38 Aligned_cols=52 Identities=19% Similarity=0.190 Sum_probs=41.0
Q ss_pred CCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHh--hcccchhhHHHHH
Q 006218 179 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIA 230 (656)
Q Consensus 179 PI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~--FG~~~G~~L~~~a 230 (656)
..-+|.|+|+++..+|.+..+|+++.||..+..+.|... ||.+.+..|++..
T Consensus 463 ~al~I~GLG~k~i~~L~~~g~V~~~~Dl~~L~~~~L~~l~g~g~Ksa~~Ll~~I 516 (689)
T PRK14351 463 DALDIEGLGEERVQQLVDAGLVESLADLYDLTVADLAELEGWGETSAENLLAEL 516 (689)
T ss_pred cccCCCCcCHHHHHHHHHcCCCCCHHHHHHcCHHHHhcCcCcchhHHHHHHHHH
Confidence 344789999999999985556899999999998888765 7776666665543
No 72
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=58.81 E-value=6.5 Score=39.93 Aligned_cols=43 Identities=19% Similarity=0.264 Sum_probs=30.7
Q ss_pred eccCcHHHHHHHhcCCCCCCeeecCcccHHhhcccCC---CccccCCchHHHHHHH
Q 006218 143 GIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLP---IKKMKQLGGKLGTSLQ 195 (656)
Q Consensus 143 GIA~NKlLAKLAS~~~KP~G~~vl~~~~v~~fL~~LP---I~kL~GIG~kt~~kL~ 195 (656)
|||+---||-|++ ++++++...+..-. +.++||||+|++++|-
T Consensus 80 GIGpK~ALaiLs~----------~~~~~l~~aI~~~d~~~L~k~PGIGkKtAeriv 125 (201)
T COG0632 80 GIGPKLALAILSN----------LDPEELAQAIANEDVKALSKIPGIGKKTAERIV 125 (201)
T ss_pred CccHHHHHHHHcC----------CCHHHHHHHHHhcChHhhhcCCCCCHHHHHHHH
Confidence 8999888887763 23444444444432 5789999999999985
No 73
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=58.63 E-value=6.4 Score=46.47 Aligned_cols=31 Identities=39% Similarity=0.734 Sum_probs=28.3
Q ss_pred CCCccccCCchHHHHHHHHhcCCcchhhhhcC
Q 006218 178 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKF 209 (656)
Q Consensus 178 LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l 209 (656)
.|+..+.|||++++++|. ++||+|+.||+-.
T Consensus 10 ~~l~~l~gig~~~a~~l~-~Lgi~tv~DLL~~ 40 (677)
T COG1200 10 VPLSTLKGIGPKTAEKLK-KLGIHTVQDLLLY 40 (677)
T ss_pred cchhhhcCcCHHHHHHHH-HcCCCcHHHHHHh
Confidence 389999999999999996 9999999999864
No 74
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=55.73 E-value=7.8 Score=38.80 Aligned_cols=57 Identities=19% Similarity=0.225 Sum_probs=36.9
Q ss_pred HHHHHHHHHhCCceeEeccCcHHHHHHHhcCCCCCCeeecCcccHHhhcccCC---CccccCCchHHHHHHH
Q 006218 127 ELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLP---IKKMKQLGGKLGTSLQ 195 (656)
Q Consensus 127 ~IR~~I~~~tGlt~SiGIA~NKlLAKLAS~~~KP~G~~vl~~~~v~~fL~~LP---I~kL~GIG~kt~~kL~ 195 (656)
.--+++|+.+ +.+| ||||-.-||-|.+ ++++++...+..=. +.++||||+|+++++-
T Consensus 66 ~~Er~lF~~L-i~Vs-GIGpK~Al~ILs~----------~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIi 125 (183)
T PRK14601 66 KDEQKMFEML-LKVN-GIGANTAMAVCSS----------LDVNSFYKALSLGDESVLKKVPGIGPKSAKRII 125 (183)
T ss_pred HHHHHHHHHH-hccC-CccHHHHHHHHcC----------CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 3444455554 4555 8998777776632 24555555554432 5688999999999984
No 75
>PRK14973 DNA topoisomerase I; Provisional
Probab=55.40 E-value=19 Score=44.72 Aligned_cols=79 Identities=19% Similarity=0.104 Sum_probs=52.0
Q ss_pred HHHHHHh-cCCCCCCeeecCcccHHhhcccCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhcc--cchhh
Q 006218 149 MLAKLAS-GMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF--NTGTW 225 (656)
Q Consensus 149 lLAKLAS-~~~KP~G~~vl~~~~v~~fL~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~--~~G~~ 225 (656)
-++++|. .+.+|+-..+.... .--..-.+..++|||.+|.++|. .-||.++.||++.+++.|.+.=|. +..+.
T Consensus 850 ~~~~~~~~~~~~~~~~~~~~~~---~~~~~~el~~vkg~ge~t~~~l~-~ag~~~~e~l~~~d~~~la~~~~i~~k~~~~ 925 (936)
T PRK14973 850 RHAKLVCEKLGRPVPEKISKAA---FERGRAELLSVPGLGETTLEKLY-LAGVYDGDLLVSADPKKLAKVTGIDEKKLRN 925 (936)
T ss_pred HHHHHHHHHhcCCCchhhhhhh---hcccchhhhhccCCCHHHHHHHH-HcCCCCHHHhccCCHHHHhhhcCCCHHHHHH
Confidence 3445666 67777654433100 00011116678999999999996 999999999999999999987665 22344
Q ss_pred HHHHHh
Q 006218 226 LWNIAR 231 (656)
Q Consensus 226 L~~~ar 231 (656)
|...++
T Consensus 926 ~~~~~~ 931 (936)
T PRK14973 926 LQAYAK 931 (936)
T ss_pred HHHHHh
Confidence 444443
No 76
>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=52.48 E-value=11 Score=37.90 Aligned_cols=51 Identities=20% Similarity=0.187 Sum_probs=37.3
Q ss_pred ccccCCchHHHHHHHHhcCCcchhhhhcC----CHHHHHHh--hcccchhhHHHHHhcCC
Q 006218 181 KKMKQLGGKLGTSLQNELGVTTVGDLLKF----SEDKLQES--YGFNTGTWLWNIARGIS 234 (656)
Q Consensus 181 ~kL~GIG~kt~~kL~~~lGI~TigDLa~l----~~~~L~~~--FG~~~G~~L~~~arGiD 234 (656)
-.++|||+|++..+ +++.+..+|... +...|.+. ||+++++++.-.++|.-
T Consensus 75 ~~V~GIGpK~Al~i---L~~~~~~el~~aI~~~d~~~L~~ipGiGkKtAerIileLk~k~ 131 (191)
T TIGR00084 75 IKVNGVGPKLALAI---LSNMSPEEFVYAIETEEVKALVKIPGVGKKTAERLLLELKGKL 131 (191)
T ss_pred hCCCCCCHHHHHHH---HhcCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHhhh
Confidence 47899999999776 677777777753 45667764 67778888887766643
No 77
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=52.42 E-value=9 Score=38.48 Aligned_cols=55 Identities=9% Similarity=0.149 Sum_probs=35.5
Q ss_pred HHHHHHHhCCceeEeccCcHHHHHHHhcCCCCCCeeecCcccHHhhcccC---CCccccCCchHHHHHHH
Q 006218 129 RMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSL---PIKKMKQLGGKLGTSLQ 195 (656)
Q Consensus 129 R~~I~~~tGlt~SiGIA~NKlLAKLAS~~~KP~G~~vl~~~~v~~fL~~L---PI~kL~GIG~kt~~kL~ 195 (656)
-+++|+.+ +.++ ||||-.-||=|.+ ++++++...+..= -++++||||+|+++++-
T Consensus 68 Er~lF~~L-i~V~-GIGpK~AL~iLs~----------~~~~el~~aI~~~D~~~L~~vpGIGkKtAerIi 125 (188)
T PRK14606 68 KKELFLSL-TKVS-RLGPKTALKIISN----------EDAETLVTMIASQDVEGLSKLPGISKKTAERIV 125 (188)
T ss_pred HHHHHHHH-hccC-CccHHHHHHHHcC----------CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 34444444 4555 8998877776632 2445555554443 25688999999999984
No 78
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication. NusA is a bacterial transcription termination factor. It is named for its interaction with phage lambda protein N, as part of the N utilization substance. Some members of the NusA family have a long C-terminal extension. This model represents an acidic 50-residue region found in two copies toward the C-terminus of most Proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic.
Probab=52.32 E-value=19 Score=27.46 Aligned_cols=33 Identities=36% Similarity=0.406 Sum_probs=28.5
Q ss_pred chHHHHHHHHhcCCcchhhhhcCCHHHHHHhhcc
Q 006218 187 GGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF 220 (656)
Q Consensus 187 G~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~ 220 (656)
...++.+|. ..|+.|+.+|+.++.+.|...-|.
T Consensus 2 ~~~~~~~L~-~~G~~s~e~la~~~~~eL~~i~g~ 34 (50)
T TIGR01954 2 DEEIAQLLV-EEGFTTVEDLAYVPIDELLSIEGF 34 (50)
T ss_pred CHHHHHHHH-HcCCCCHHHHHccCHHHHhcCCCC
Confidence 456788997 999999999999999999887663
No 79
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=49.10 E-value=15 Score=40.96 Aligned_cols=35 Identities=23% Similarity=0.445 Sum_probs=31.2
Q ss_pred CccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHH
Q 006218 180 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQ 215 (656)
Q Consensus 180 I~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~ 215 (656)
+.+|.|||++++.+|+ .+||++..+|+.++.+.+.
T Consensus 325 Lk~I~GIGpk~e~~Ln-~~Gi~~f~QIA~wt~~eia 359 (400)
T PRK12373 325 LKLISGVGPKIEATLN-ELGIFTFDQVAAWKKAERA 359 (400)
T ss_pred hhhccCCChHHHHHHH-hcCCCCHHHHhCCCHHHhH
Confidence 6789999999999997 9999999999999877543
No 80
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type. This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins.
Probab=48.24 E-value=19 Score=38.79 Aligned_cols=54 Identities=26% Similarity=0.347 Sum_probs=41.1
Q ss_pred cccCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHh--hcccchhhHHHHH
Q 006218 175 LDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIA 230 (656)
Q Consensus 175 L~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~--FG~~~G~~L~~~a 230 (656)
+..+||.+| ++--++..-|. +.||+|++||..++.+.|.+. ||.+..+.+.+.+
T Consensus 232 ~~~~~I~~L-~LSvR~~n~Lk-~~~I~ti~dL~~~~~~~l~~~~n~G~ksl~ei~~~l 287 (297)
T TIGR02027 232 LLSIKIEEL-DLSVRSYNCLK-RAGIHTLGELVSKSEEELLKIKNFGKKSLTEIKEKL 287 (297)
T ss_pred hccccHHHh-CccHHHHhHHH-HcCCcCHHHHHhCCHHHHhhCCCCChhhHHHHHHHH
Confidence 455678777 57778889996 999999999999999987665 6765555444443
No 81
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=47.61 E-value=16 Score=36.83 Aligned_cols=52 Identities=13% Similarity=0.215 Sum_probs=38.7
Q ss_pred cccCCchHHHHHHHHhcCCcc-hhhhhcCCHHHHHHh--hcccchhhHHHHHhcC
Q 006218 182 KMKQLGGKLGTSLQNELGVTT-VGDLLKFSEDKLQES--YGFNTGTWLWNIARGI 233 (656)
Q Consensus 182 kL~GIG~kt~~kL~~~lGI~T-igDLa~l~~~~L~~~--FG~~~G~~L~~~arGi 233 (656)
.++|||++++-.+...++... +..++.-+...|.+. .|+++++++.-.++|.
T Consensus 77 ~V~GIGpK~Al~ILs~~~~~~l~~aI~~~D~~~L~~vpGIGkKtAerIilELk~K 131 (194)
T PRK14605 77 DVSGIGPKLGLAMLSAMNAEALASAIISGNAELLSTIPGIGKKTASRIVLELKDK 131 (194)
T ss_pred CCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHH
Confidence 688999999988776688777 455556678888886 4456788877777664
No 82
>PF08004 DUF1699: Protein of unknown function (DUF1699); InterPro: IPR012546 This family contains many archaeal proteins which have very conserved sequences.
Probab=47.41 E-value=33 Score=32.41 Aligned_cols=34 Identities=24% Similarity=0.401 Sum_probs=28.0
Q ss_pred HHHHHHhCCCcEEEeccCcCCCCChHHHHHHHHHHHHHHhh
Q 006218 3 GDEAKEVCPQIELVQVPVARGKADLSSYRNAGSEVVSILAR 43 (656)
Q Consensus 3 ~~~AkklCP~LivV~vP~~~~k~d~~~Yr~~S~~V~~IL~~ 43 (656)
++...+.||+|.++|+| -..|+.+|+.+-..|.-
T Consensus 33 if~Lv~~CP~lk~iqiP-------~SY~~t~Sksi~mfL~m 66 (131)
T PF08004_consen 33 IFSLVERCPNLKAIQIP-------PSYYKTLSKSIKMFLEM 66 (131)
T ss_pred HHHHHHhCCCCeEEeCC-------hHHHHHHhHHHHHHHHh
Confidence 45678899999999999 36688999888888774
No 83
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=47.24 E-value=13 Score=37.65 Aligned_cols=56 Identities=14% Similarity=0.169 Sum_probs=36.2
Q ss_pred HHHHHHHHhCCceeEeccCcHHHHHHHhcCCCCCCeeecCcccHHhhcccCC---CccccCCchHHHHHHH
Q 006218 128 LRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLP---IKKMKQLGGKLGTSLQ 195 (656)
Q Consensus 128 IR~~I~~~tGlt~SiGIA~NKlLAKLAS~~~KP~G~~vl~~~~v~~fL~~LP---I~kL~GIG~kt~~kL~ 195 (656)
--+++|+.+ +.++ |||+-.-||=|.+ ++++++...+..=. ++++||||+|+++++-
T Consensus 67 ~Er~lF~~L-i~V~-GIGpK~Al~iLs~----------~~~~el~~aI~~~D~~~L~kvpGIGkKtAerIi 125 (195)
T PRK14604 67 AQRQLFELL-IGVS-GVGPKAALNLLSS----------GTPDELQLAIAGGDVARLARVPGIGKKTAERIV 125 (195)
T ss_pred HHHHHHHHH-hCcC-CcCHHHHHHHHcC----------CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 344445554 4555 8888777776632 24455555554432 5688999999999985
No 84
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=47.10 E-value=12 Score=25.10 Aligned_cols=16 Identities=19% Similarity=0.320 Sum_probs=13.9
Q ss_pred CccccCCchHHHHHHH
Q 006218 180 IKKMKQLGGKLGTSLQ 195 (656)
Q Consensus 180 I~kL~GIG~kt~~kL~ 195 (656)
+.+++|||++++.+|.
T Consensus 3 L~~i~GiG~k~A~~il 18 (26)
T smart00278 3 LLKVPGIGPKTAEKIL 18 (26)
T ss_pred hhhCCCCCHHHHHHHH
Confidence 4579999999999986
No 85
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=46.77 E-value=12 Score=37.78 Aligned_cols=58 Identities=21% Similarity=0.369 Sum_probs=37.2
Q ss_pred HHHHHHHHHHhCCceeEeccCcHHHHHHHhcCCCCCCeeecCcccHHhhcccC---CCccccCCchHHHHHHH
Q 006218 126 TELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSL---PIKKMKQLGGKLGTSLQ 195 (656)
Q Consensus 126 ~~IR~~I~~~tGlt~SiGIA~NKlLAKLAS~~~KP~G~~vl~~~~v~~fL~~L---PI~kL~GIG~kt~~kL~ 195 (656)
..--+++|+.+ +.+| ||||-.-||=|.+ ++++++...+..= .+.++||||+|+++|+-
T Consensus 64 t~~Er~lF~~L-isVs-GIGPK~ALaILs~----------~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRII 124 (196)
T PRK13901 64 NSSEREVFEEL-IGVD-GIGPRAALRVLSG----------IKYNEFRDAIDREDIELISKVKGIGNKMAGKIF 124 (196)
T ss_pred CHHHHHHHHHH-hCcC-CcCHHHHHHHHcC----------CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 34445555555 5666 8988777776632 2344444444433 35688999999999984
No 86
>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=46.71 E-value=19 Score=42.87 Aligned_cols=15 Identities=33% Similarity=0.386 Sum_probs=8.3
Q ss_pred EecCceEEEEccchh
Q 006218 49 RASIDEVYLDLTDAA 63 (656)
Q Consensus 49 ~~SIDEafLDlT~~~ 63 (656)
.|-||-+-+-+....
T Consensus 268 ~y~iDGiViKvn~~~ 282 (652)
T TIGR00575 268 PYEIDGVVVKVDDLA 282 (652)
T ss_pred CCCCCcEEEEecCHH
Confidence 355666666555443
No 87
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=46.64 E-value=18 Score=38.00 Aligned_cols=50 Identities=24% Similarity=0.387 Sum_probs=38.8
Q ss_pred CccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhcc--cchhhHHHHHh
Q 006218 180 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF--NTGTWLWNIAR 231 (656)
Q Consensus 180 I~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~--~~G~~L~~~ar 231 (656)
+..+||||.+++.+|. .-+.+++++..++...|.+.-|. +.+..++...+
T Consensus 184 l~s~pgig~~~a~~ll--~~fgS~~~~~tas~~eL~~v~gig~k~A~~I~~~~~ 235 (254)
T COG1948 184 LESIPGIGPKLAERLL--KKFGSVEDVLTASEEELMKVKGIGEKKAREIYRFLR 235 (254)
T ss_pred HHcCCCccHHHHHHHH--HHhcCHHHHhhcCHHHHHHhcCccHHHHHHHHHHHh
Confidence 3456799999999996 44569999999999999999886 44555555544
No 88
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=46.20 E-value=19 Score=42.41 Aligned_cols=53 Identities=9% Similarity=0.170 Sum_probs=42.4
Q ss_pred cCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHh--hcccchhhHHHHHh
Q 006218 177 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 231 (656)
Q Consensus 177 ~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~--FG~~~G~~L~~~ar 231 (656)
..++..|||||+++..+|.+.+ .++..+...+.+.|.+. +|...+..++...+
T Consensus 542 ~s~L~~IpGIG~k~~k~Ll~~F--gS~~~i~~As~eeL~~v~Gig~~~A~~I~~~l~ 596 (598)
T PRK00558 542 TSALDDIPGIGPKRRKALLKHF--GSLKAIKEASVEELAKVPGISKKLAEAIYEALH 596 (598)
T ss_pred hhhHhhCCCcCHHHHHHHHHHc--CCHHHHHhCCHHHHhhcCCcCHHHHHHHHHHhc
Confidence 4667899999999999997555 56999999999999988 67766777766543
No 89
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=46.17 E-value=21 Score=38.66 Aligned_cols=52 Identities=23% Similarity=0.375 Sum_probs=40.6
Q ss_pred cccCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHh--hcccchhhHHH
Q 006218 175 LDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWN 228 (656)
Q Consensus 175 L~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~--FG~~~G~~L~~ 228 (656)
+..++|.++ ++--++..-|. +.||+|++||.+++.+.|.+. ||.+.-+.+.+
T Consensus 246 ~l~~~I~~L-~LS~R~~n~Lk-~~~I~ti~dL~~~~~~~l~~~~n~G~ksl~ei~~ 299 (310)
T PRK05182 246 ILLRPIEEL-ELSVRSYNCLK-RAGINTIGDLVQRTEEELLKTRNLGKKSLEEIKE 299 (310)
T ss_pred cccccHHHh-ccchHHHHHHH-HcCCcCHHHHHhCCHHHHhcCCCCChhhHHHHHH
Confidence 346788888 78889999996 999999999999999988765 66554444443
No 90
>PF07887 Calmodulin_bind: Calmodulin binding protein-like; InterPro: IPR012416 The members of this family are putative or actual calmodulin binding proteins expressed by various plant species. Some members (for example, Q8H6T7 from SWISSPROT), are known to be involved in the induction of plant defence responses []. However, their precise function in this regard is as yet unknown.
Probab=46.01 E-value=24 Score=38.06 Aligned_cols=50 Identities=26% Similarity=0.543 Sum_probs=35.7
Q ss_pred CccccCCch--HHHHHHHHhcCCcchhhhhcC---CHHHHHHhhcccchhhHHHHH
Q 006218 180 IKKMKQLGG--KLGTSLQNELGVTTVGDLLKF---SEDKLQESYGFNTGTWLWNIA 230 (656)
Q Consensus 180 I~kL~GIG~--kt~~kL~~~lGI~TigDLa~l---~~~~L~~~FG~~~G~~L~~~a 230 (656)
|..|-.||+ ..-++|. .-||.|++|++.+ ++..|++.||..+-...|...
T Consensus 164 VwRLe~Igk~G~~hk~L~-~~~I~tV~dFl~l~~~d~~~Lr~ilg~~ms~k~We~~ 218 (299)
T PF07887_consen 164 VWRLEKIGKDGAFHKRLK-KNGINTVEDFLKLLNKDPQKLREILGSGMSNKMWETT 218 (299)
T ss_pred hhhhhhccccCHHHHHHH-HcCCccHHHHHHHHhcCHHHHHHHHhcCCChhhHHHH
Confidence 444556665 3557886 8999999999874 788999999954445555443
No 91
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=45.35 E-value=14 Score=37.35 Aligned_cols=56 Identities=18% Similarity=0.237 Sum_probs=36.5
Q ss_pred HHHHHHHHhCCceeEeccCcHHHHHHHhcCCCCCCeeecCcccHHhhcccCC---CccccCCchHHHHHHH
Q 006218 128 LRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLP---IKKMKQLGGKLGTSLQ 195 (656)
Q Consensus 128 IR~~I~~~tGlt~SiGIA~NKlLAKLAS~~~KP~G~~vl~~~~v~~fL~~LP---I~kL~GIG~kt~~kL~ 195 (656)
--+++|+.+ ++++ ||||-.-||=|.+ ++++++...+..=. +.++||||+|+++++-
T Consensus 66 ~Er~lF~~L-~~V~-GIGpK~AL~iLs~----------~~~~~l~~aI~~~D~~~L~kvpGIGkKtAerIi 124 (197)
T PRK14603 66 DSLELFELL-LGVS-GVGPKLALALLSA----------LPPALLARALLEGDARLLTSASGVGKKLAERIA 124 (197)
T ss_pred HHHHHHHHH-hCcC-CcCHHHHHHHHcC----------CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 334445554 4566 8888777776632 24555555555432 5789999999999984
No 92
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=43.88 E-value=13 Score=37.48 Aligned_cols=55 Identities=18% Similarity=0.260 Sum_probs=35.0
Q ss_pred HHHHHHHhCCceeEeccCcHHHHHHHhcCCCCCCeeecCcccHHhhccc---CCCccccCCchHHHHHHH
Q 006218 129 RMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDS---LPIKKMKQLGGKLGTSLQ 195 (656)
Q Consensus 129 R~~I~~~tGlt~SiGIA~NKlLAKLAS~~~KP~G~~vl~~~~v~~fL~~---LPI~kL~GIG~kt~~kL~ 195 (656)
-+++|..+ +.++ |||+-.-+|-|. .++++++...+.. --+.++||||+|+++++.
T Consensus 67 Er~lF~~L-~~V~-GIGpK~Al~iL~----------~~~~~el~~aI~~~d~~~L~~ipGiGkKtAerIi 124 (191)
T TIGR00084 67 ERELFKEL-IKVN-GVGPKLALAILS----------NMSPEEFVYAIETEEVKALVKIPGVGKKTAERLL 124 (191)
T ss_pred HHHHHHHH-hCCC-CCCHHHHHHHHh----------cCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHH
Confidence 33444444 3444 888877766542 2345555555554 347789999999999984
No 93
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=43.49 E-value=16 Score=37.05 Aligned_cols=57 Identities=14% Similarity=0.148 Sum_probs=35.9
Q ss_pred HHHHHHHHHhCCceeEeccCcHHHHHHHhcCCCCCCeeecCcccHHhhcccC---CCccccCCchHHHHHHH
Q 006218 127 ELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSL---PIKKMKQLGGKLGTSLQ 195 (656)
Q Consensus 127 ~IR~~I~~~tGlt~SiGIA~NKlLAKLAS~~~KP~G~~vl~~~~v~~fL~~L---PI~kL~GIG~kt~~kL~ 195 (656)
.--+++|..+ +.++ |||+-.-|+=|.+ ++++++...+..= -+.++||||+||++++-
T Consensus 67 ~~Er~lF~~L-i~V~-GIGpK~Al~iLs~----------~~~~~l~~aI~~~D~~~L~~ipGIGkKtAerIi 126 (203)
T PRK14602 67 WDERQTFIVL-ISIS-KVGAKTALAILSQ----------FRPDDLRRLVAEEDVAALTRVSGIGKKTAQHIF 126 (203)
T ss_pred HHHHHHHHHH-hCCC-CcCHHHHHHHHhh----------CCHHHHHHHHHhCCHHHHhcCCCcCHHHHHHHH
Confidence 3444555554 4555 8888777666542 2444554444433 25689999999999984
No 94
>PRK13766 Hef nuclease; Provisional
Probab=40.09 E-value=26 Score=42.23 Aligned_cols=50 Identities=22% Similarity=0.408 Sum_probs=40.6
Q ss_pred CccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHh--hcccchhhHHHHHh
Q 006218 180 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 231 (656)
Q Consensus 180 I~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~--FG~~~G~~L~~~ar 231 (656)
+..+||||++++.+|.+.+| ++.++...+.+.|... +|.+.+..++....
T Consensus 717 L~~ipgig~~~a~~Ll~~fg--s~~~i~~as~~~L~~i~Gig~~~a~~i~~~~~ 768 (773)
T PRK13766 717 VESLPDVGPVLARNLLEHFG--SVEAVMTASEEELMEVEGIGEKTAKRIREVVT 768 (773)
T ss_pred HhcCCCCCHHHHHHHHHHcC--CHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHh
Confidence 66789999999999975555 7999999999999987 77766777766543
No 95
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=39.86 E-value=8.4 Score=38.15 Aligned_cols=41 Identities=24% Similarity=0.500 Sum_probs=35.7
Q ss_pred ccccccCCccccccCChHHHHHHHHhhCCCCCCCcccCCcc
Q 006218 605 KLRIEEIDPSVIDELPKEIQDEIQAWLRPSKRPHRVKQGFT 645 (656)
Q Consensus 605 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 645 (656)
.|.|.||..-+|+-.-.||-++++.++||.|.|.--++--|
T Consensus 24 e~eiiei~a~lv~~id~~vvd~F~syVRP~~~P~Lt~~Cks 64 (210)
T COG5018 24 EFEIIEIEAGLVKSIDDEVVDTFSSYVRPKKFPKLTKRCKS 64 (210)
T ss_pred hceeeeehhhHHHHhhHHHHHHHHHhcCcccCchHHHHHHH
Confidence 46699999999999999999999999999999976665333
No 96
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=39.44 E-value=30 Score=40.48 Aligned_cols=48 Identities=17% Similarity=0.313 Sum_probs=38.8
Q ss_pred ccccCCchHHHHHHHHhcC-CcchhhhhcCCHHHHHHh--hcccchhhHHHH
Q 006218 181 KKMKQLGGKLGTSLQNELG-VTTVGDLLKFSEDKLQES--YGFNTGTWLWNI 229 (656)
Q Consensus 181 ~kL~GIG~kt~~kL~~~lG-I~TigDLa~l~~~~L~~~--FG~~~G~~L~~~ 229 (656)
-+|-|+|.++.++|. ..| |+++.||..++.+.|.+. ||.+.+..|++.
T Consensus 428 mdI~GlGe~~i~~L~-~~G~i~~~~Diy~L~~~~l~~l~gfgeks~~nll~a 478 (562)
T PRK08097 428 LGLDGIGEGTWRALH-QTGLFEHLFSWLALTPEQLANTPGIGKARAEQLWHQ 478 (562)
T ss_pred cCCCCcCHHHHHHHH-HcCCcCCHHHHhcCCHHHHhcCcCccHHHHHHHHHH
Confidence 357799999999998 677 699999999998888764 777666666554
No 97
>COG2199 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]
Probab=38.31 E-value=72 Score=30.52 Aligned_cols=29 Identities=24% Similarity=0.117 Sum_probs=19.0
Q ss_pred HHHHHHHHhhc----CCeEEecCceEEEEccch
Q 006218 34 GSEVVSILARK----GRCERASIDEVYLDLTDA 62 (656)
Q Consensus 34 S~~V~~IL~~~----~~VE~~SIDEafLDlT~~ 62 (656)
-..|..+|+.. ..+-+++=||.-+=+.+.
T Consensus 78 L~~va~~L~~~~~~~~~~~R~gGdEF~i~l~~~ 110 (181)
T COG2199 78 LREVARRLRSNLREGDLVARLGGDEFAVLLPGT 110 (181)
T ss_pred HHHHHHHHHHhcCCCCEEEEeccceeEEEeCCC
Confidence 34455555553 358899999988766653
No 98
>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a beta-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [, ].; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBN_M 2QBB_M 3I1M_M 3OFP_M 3OFX_M 3OFO_M 1VS5_M 3OAQ_M 2QAL_M 3J18_M ....
Probab=38.27 E-value=31 Score=31.36 Aligned_cols=35 Identities=14% Similarity=0.392 Sum_probs=24.7
Q ss_pred CccccCCchHHHHHHHHhcCCcchhhhhcCCHHHH
Q 006218 180 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKL 214 (656)
Q Consensus 180 I~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L 214 (656)
+.+|+|||+.++..+...+||..-.-+-.++.+.+
T Consensus 17 Lt~IyGIG~~~A~~Ic~~lgi~~~~~~~~Ls~~~i 51 (107)
T PF00416_consen 17 LTKIYGIGRRKAKQICKKLGINPNKKVGDLSDEQI 51 (107)
T ss_dssp HTTSTTBCHHHHHHHHHHTTS-SSSBTTTSTHHHH
T ss_pred HhhhhccCHHHHHHHHHHcCCChhhhcccCCHHHH
Confidence 45899999999999888999965444444444443
No 99
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=38.10 E-value=25 Score=38.10 Aligned_cols=29 Identities=21% Similarity=0.178 Sum_probs=25.8
Q ss_pred ccccCCchHHHHHHHHhcCCcchhhhhcCC
Q 006218 181 KKMKQLGGKLGTSLQNELGVTTVGDLLKFS 210 (656)
Q Consensus 181 ~kL~GIG~kt~~kL~~~lGI~TigDLa~l~ 210 (656)
+.++|||.+++++-. ..|++|+.|++.-+
T Consensus 100 tnifGvG~ktA~~Wy-~~GfrTled~Rk~~ 128 (353)
T KOG2534|consen 100 TNIFGVGLKTAEKWY-REGFRTLEDVRKKP 128 (353)
T ss_pred HHHhccCHHHHHHHH-HhhhhHHHHHHhCH
Confidence 578999999999996 99999999999443
No 100
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=37.23 E-value=28 Score=35.27 Aligned_cols=16 Identities=31% Similarity=0.488 Sum_probs=14.0
Q ss_pred CccccCCchHHHHHHH
Q 006218 180 IKKMKQLGGKLGTSLQ 195 (656)
Q Consensus 180 I~kL~GIG~kt~~kL~ 195 (656)
+++|||||+|++.||.
T Consensus 13 l~~LPGIG~KsA~RlA 28 (195)
T TIGR00615 13 LKKLPGIGPKSAQRLA 28 (195)
T ss_pred HHHCCCCCHHHHHHHH
Confidence 4578999999999995
No 101
>PF07647 SAM_2: SAM domain (Sterile alpha motif); InterPro: IPR011510 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents a second domain related to the SAM domain. ; GO: 0005515 protein binding; PDB: 1B0X_A 1X9X_B 1OW5_A 1V38_A 3BS7_A 3BS5_A 3TAD_A 3TAC_B 2K60_A 2DL0_A ....
Probab=35.72 E-value=45 Score=26.82 Aligned_cols=47 Identities=28% Similarity=0.455 Sum_probs=38.9
Q ss_pred cCcccHHhhcccCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhccc
Q 006218 166 VPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN 221 (656)
Q Consensus 166 l~~~~v~~fL~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~~ 221 (656)
++++++..||..+ |+ ......+. ..||..+..|..++.+.|. .+|..
T Consensus 4 w~~~~v~~WL~~~------gl-~~y~~~f~-~~~i~g~~~L~~l~~~~L~-~lGI~ 50 (66)
T PF07647_consen 4 WSPEDVAEWLKSL------GL-EQYADNFR-ENGIDGLEDLLQLTEEDLK-ELGIT 50 (66)
T ss_dssp HCHHHHHHHHHHT------TC-GGGHHHHH-HTTCSHHHHHTTSCHHHHH-HTTTT
T ss_pred CCHHHHHHHHHHC------Cc-HHHHHHHH-HcCCcHHHHHhhCCHHHHH-HcCCC
Confidence 4677888999876 55 46677886 8999999999999999997 78974
No 102
>PRK00076 recR recombination protein RecR; Reviewed
Probab=35.65 E-value=31 Score=35.03 Aligned_cols=16 Identities=25% Similarity=0.478 Sum_probs=14.0
Q ss_pred CccccCCchHHHHHHH
Q 006218 180 IKKMKQLGGKLGTSLQ 195 (656)
Q Consensus 180 I~kL~GIG~kt~~kL~ 195 (656)
+.+|||||+|++.||.
T Consensus 13 l~~LPGIG~KsA~Rla 28 (196)
T PRK00076 13 LRKLPGIGPKSAQRLA 28 (196)
T ss_pred HHHCCCCCHHHHHHHH
Confidence 4578999999999995
No 103
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=35.45 E-value=61 Score=30.86 Aligned_cols=53 Identities=21% Similarity=0.243 Sum_probs=37.0
Q ss_pred cHHHHHHHhcCCCCCCeeecCcccHHhhcccCCCccccCCchHHHHHHHHhcC-CcchhhhhcCC
Q 006218 147 NKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELG-VTTVGDLLKFS 210 (656)
Q Consensus 147 NKlLAKLAS~~~KP~G~~vl~~~~v~~fL~~LPI~kL~GIG~kt~~kL~~~lG-I~TigDLa~l~ 210 (656)
|+.=|||+ .... ..-|....+.+|. .+||||+.+++++- ..| ..++.||.+++
T Consensus 40 N~~d~kl~-~~~~---kIdiN~A~~~el~------~lpGigP~~A~~IV-~nGpf~sveDL~~V~ 93 (132)
T PRK02515 40 NVADAKLG-EFGE---KIDLNNSSVRAFR------QFPGMYPTLAGKIV-KNAPYDSVEDVLNLP 93 (132)
T ss_pred ChhhHHHH-hcCC---cccCCccCHHHHH------HCCCCCHHHHHHHH-HCCCCCCHHHHHcCC
Confidence 77778887 3322 2234455555553 58899999999997 555 88999998763
No 104
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=35.26 E-value=27 Score=35.04 Aligned_cols=56 Identities=14% Similarity=0.195 Sum_probs=33.3
Q ss_pred HHHHHHHHHhCCceeEeccCcHHHHHHHhcCCCCCCeeecCcccHHhhcccC---CCccccCCchHHHHHHH
Q 006218 127 ELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSL---PIKKMKQLGGKLGTSLQ 195 (656)
Q Consensus 127 ~IR~~I~~~tGlt~SiGIA~NKlLAKLAS~~~KP~G~~vl~~~~v~~fL~~L---PI~kL~GIG~kt~~kL~ 195 (656)
.--+++|+.+ +.++ |||+-.-||=|.+ +.++++...+..= -+ ++||||+|+++++-
T Consensus 66 ~~Er~lF~~L-isV~-GIGpK~Al~iLs~----------~~~~~l~~aI~~~D~~~L-~vpGIGkKtAerIi 124 (186)
T PRK14600 66 REEQDCLRML-VKVS-GVNYKTAMSILSK----------LTPEQLFSAIVNEDKAAL-KVNGIGEKLINRII 124 (186)
T ss_pred HHHHHHHHHH-hCcC-CcCHHHHHHHHcc----------CCHHHHHHHHHcCCHhhe-ECCCCcHHHHHHHH
Confidence 3444555555 4555 8888776665532 1233333333321 24 68999999999984
No 105
>TIGR03631 bact_S13 30S ribosomal protein S13. This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type.
Probab=35.18 E-value=37 Score=31.37 Aligned_cols=37 Identities=11% Similarity=0.278 Sum_probs=26.5
Q ss_pred CCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHH
Q 006218 179 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQ 215 (656)
Q Consensus 179 PI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~ 215 (656)
-++.|.|||..++..+...+||..-.=+-.++.+++.
T Consensus 16 aL~~i~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~ 52 (113)
T TIGR03631 16 ALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELN 52 (113)
T ss_pred eeeeeecccHHHHHHHHHHhCcCcccccccCCHHHHH
Confidence 3578999999999999889999644334444444443
No 106
>PRK13844 recombination protein RecR; Provisional
Probab=34.71 E-value=32 Score=34.99 Aligned_cols=16 Identities=25% Similarity=0.507 Sum_probs=13.9
Q ss_pred CccccCCchHHHHHHH
Q 006218 180 IKKMKQLGGKLGTSLQ 195 (656)
Q Consensus 180 I~kL~GIG~kt~~kL~ 195 (656)
+.+|||||+|+++||.
T Consensus 17 l~~LPGIG~KsA~Rla 32 (200)
T PRK13844 17 LRKLPTIGKKSSQRLA 32 (200)
T ss_pred HHHCCCCCHHHHHHHH
Confidence 4578999999999995
No 107
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=31.87 E-value=45 Score=32.59 Aligned_cols=41 Identities=17% Similarity=0.334 Sum_probs=30.6
Q ss_pred CCccccCCchHHHHHHHHhcCCc---chhhhhcCCHHHHHHhhc
Q 006218 179 PIKKMKQLGGKLGTSLQNELGVT---TVGDLLKFSEDKLQESYG 219 (656)
Q Consensus 179 PI~kL~GIG~kt~~kL~~~lGI~---TigDLa~l~~~~L~~~FG 219 (656)
-++.|.|||..++..+...+||. +++||-.-....|...+.
T Consensus 31 aLt~I~GIG~~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~ 74 (154)
T PTZ00134 31 ALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIA 74 (154)
T ss_pred eecccccccHHHHHHHHHHcCcCcCCCcccCCHHHHHHHHHHHh
Confidence 35789999999999988899995 566666554555555554
No 108
>PF07237 DUF1428: Protein of unknown function (DUF1428); InterPro: IPR009874 This family consists of several hypothetical bacterial and one archaeal sequence of around 120 residues in length. The function of this family is unknown.; PDB: 2OKQ_A.
Probab=31.48 E-value=84 Score=28.74 Aligned_cols=37 Identities=22% Similarity=0.443 Sum_probs=28.9
Q ss_pred EEeccCcCCCCChHHHHHHHHHHHHHHhhcCCeEEecCceEEEE
Q 006218 15 LVQVPVARGKADLSSYRNAGSEVVSILARKGRCERASIDEVYLD 58 (656)
Q Consensus 15 vV~vP~~~~k~d~~~Yr~~S~~V~~IL~~~~~VE~~SIDEafLD 58 (656)
++-|| ..+.+.|++++++.-.++++|.-++.. |++-|
T Consensus 7 v~~VP----~~nk~aY~~~A~~a~~vf~e~GAl~~v---E~wgd 43 (103)
T PF07237_consen 7 VLPVP----TANKDAYRAMAEKAAEVFKEHGALRVV---ECWGD 43 (103)
T ss_dssp EEEEE----GGGHHHHHHHHHHHHHHHHHTT-SEEE---EEEEE
T ss_pred EEECc----HHHHHHHHHHHHHHHHHHHHhCCEEEE---EeecC
Confidence 45568 489999999999999999999765544 66664
No 109
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=30.90 E-value=54 Score=39.44 Aligned_cols=45 Identities=16% Similarity=0.273 Sum_probs=29.3
Q ss_pred ccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHh--hcccchhhHHHH
Q 006218 183 MKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNI 229 (656)
Q Consensus 183 L~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~--FG~~~G~~L~~~ 229 (656)
|||||.+++.+|.+.+ .++.+|...+.+.|.+. +|...+..++.+
T Consensus 533 IpgIG~~~ak~L~~~F--~si~~L~~As~eeL~~i~GIG~k~A~sI~~f 579 (689)
T PRK14351 533 IPEVGPTTARNLAREF--GTFEAIMDADEEALRAVDDVGPTVAEEIREF 579 (689)
T ss_pred CCCcCHHHHHHHHHHh--CCHHHHHhCCHHHHhccCCcCHHHHHHHHHH
Confidence 5778887777775333 56777777777777666 565555555444
No 110
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=30.18 E-value=27 Score=37.87 Aligned_cols=34 Identities=35% Similarity=0.428 Sum_probs=28.2
Q ss_pred CCCccccCCchHHHHHHHHhcCCcchhhhhcCCH
Q 006218 178 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSE 211 (656)
Q Consensus 178 LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~ 211 (656)
.|+-++||+|++...+|-..+||+++.+|+....
T Consensus 93 ~~Ll~v~GlGpkKi~~Ly~elgi~~~e~l~~a~~ 126 (326)
T COG1796 93 EPLLKVPGLGPKKIVSLYKELGIKDLEELQEALE 126 (326)
T ss_pred HHHhhCCCCCcHHHHHHHHHHCcccHHHHHHHHH
Confidence 3566899999988888877999999999987543
No 111
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=29.62 E-value=47 Score=36.30 Aligned_cols=55 Identities=20% Similarity=0.340 Sum_probs=41.8
Q ss_pred hcccCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHh--hcccchhhHHHHH
Q 006218 174 LLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIA 230 (656)
Q Consensus 174 fL~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~--FG~~~G~~L~~~a 230 (656)
.+..++|.+| .+--+...-|. +.||+|+|||.+.+.+.|.+. ||.+....+...+
T Consensus 259 ~~~~~~Ie~L-~LSvRs~NcLk-~a~I~ti~dL~~~s~~dLl~ikN~GkKSl~EI~~~L 315 (327)
T CHL00013 259 ALKQIFIEQL-ELSVRAYNCLK-RANIHTLLDLLNYSQEDLLKIKNFGQKSAKEVLEAL 315 (327)
T ss_pred hhhceeHHhc-cCchhhhhhhh-hcCccCHHHHHhcCHHHHhhhhccCHhHHHHHHHHH
Confidence 4556677777 46667778886 999999999999999887654 8877666665555
No 112
>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=29.28 E-value=3.8e+02 Score=23.28 Aligned_cols=29 Identities=14% Similarity=0.043 Sum_probs=17.8
Q ss_pred HHHHHHHHHHhhc-CCeEEecCceEEEEcc
Q 006218 32 NAGSEVVSILARK-GRCERASIDEVYLDLT 60 (656)
Q Consensus 32 ~~S~~V~~IL~~~-~~VE~~SIDEafLDlT 60 (656)
.+.+++..++..+ ..+-+.+=||..+=++
T Consensus 30 ~~~~~l~~~~~~~~~~~~r~~~d~f~~l~~ 59 (133)
T cd07556 30 ELAGRFDSLIRRSGDLKIKTIGDEFMVVSG 59 (133)
T ss_pred HHHHHHHHHHHHcCcEEEEeecceEEEEEC
Confidence 3355555555554 3567778888776554
No 113
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=28.66 E-value=40 Score=39.63 Aligned_cols=49 Identities=16% Similarity=0.199 Sum_probs=38.0
Q ss_pred cCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHh--hcccchhhHH
Q 006218 177 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLW 227 (656)
Q Consensus 177 ~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~--FG~~~G~~L~ 227 (656)
.+.+..+||||+++..+|.+.+ .++.++...+.+.|.+. +|.+.+..++
T Consensus 524 ~~~L~~IpGIG~kr~~~LL~~F--GS~~~I~~As~eeL~~vpGi~~~~A~~I~ 574 (577)
T PRK14668 524 STVLDDVPGVGPETRKRLLRRF--GSVEGVREASVEDLRDVPGVGEKTAETIR 574 (577)
T ss_pred HhHHhcCCCCCHHHHHHHHHHc--CCHHHHHhCCHHHHHhCCCCCHHHHHHHH
Confidence 4678899999999999997444 68999999999999887 4444444443
No 114
>cd00166 SAM Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
Probab=28.65 E-value=94 Score=24.13 Aligned_cols=46 Identities=28% Similarity=0.428 Sum_probs=36.0
Q ss_pred CcccHHhhcccCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhcccc
Q 006218 167 PFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNT 222 (656)
Q Consensus 167 ~~~~v~~fL~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~~~ 222 (656)
+.+++..||..+- + ......+. ..|| +..+|..++.+.|. .+|...
T Consensus 3 ~~~~V~~wL~~~~------~-~~y~~~f~-~~~i-~g~~L~~l~~~dL~-~lgi~~ 48 (63)
T cd00166 3 SPEDVAEWLESLG------L-GQYADNFR-ENGI-DGDLLLLLTEEDLK-ELGITL 48 (63)
T ss_pred CHHHHHHHHHHcC------h-HHHHHHHH-HcCC-CHHHHhHCCHHHHH-HcCCCC
Confidence 4567778886654 3 46677886 8999 99999999999998 889864
No 115
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=27.54 E-value=62 Score=30.35 Aligned_cols=36 Identities=8% Similarity=0.253 Sum_probs=25.6
Q ss_pred CCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHH
Q 006218 179 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKL 214 (656)
Q Consensus 179 PI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L 214 (656)
-++.|.|||..++..+...+||..-.-+-.++.+++
T Consensus 18 aL~~I~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi 53 (122)
T PRK05179 18 ALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEEL 53 (122)
T ss_pred eecccccccHHHHHHHHHHhCcCcccccccCCHHHH
Confidence 457899999999999888999964333333444443
No 116
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=27.34 E-value=63 Score=30.30 Aligned_cols=36 Identities=3% Similarity=0.119 Sum_probs=25.5
Q ss_pred CCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHH
Q 006218 179 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKL 214 (656)
Q Consensus 179 PI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L 214 (656)
-++.|.|||..++..+.+.+||..-.-+-.++.+++
T Consensus 18 aLt~i~GIG~~~A~~ic~~lgi~~~~~~~~Lt~~qi 53 (122)
T CHL00137 18 ALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQI 53 (122)
T ss_pred eecccccccHHHHHHHHHHcCcCcCcCcccCCHHHH
Confidence 467899999999999988999964333333444443
No 117
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=25.89 E-value=68 Score=38.46 Aligned_cols=49 Identities=20% Similarity=0.079 Sum_probs=38.8
Q ss_pred CccccCCchHHHHHHHHhcC-CcchhhhhcCCHHHHHHh--hcccchhhHHHH
Q 006218 180 IKKMKQLGGKLGTSLQNELG-VTTVGDLLKFSEDKLQES--YGFNTGTWLWNI 229 (656)
Q Consensus 180 I~kL~GIG~kt~~kL~~~lG-I~TigDLa~l~~~~L~~~--FG~~~G~~L~~~ 229 (656)
--+|-|+|.++..+|. ..| |.++.||..++.+.|.+. ||.+.+..|++.
T Consensus 438 aldI~GlG~~~i~~L~-~~G~i~~~~Dly~L~~~~l~~l~g~geksa~nl~~~ 489 (669)
T PRK14350 438 CMNIVGLSDKTIEFLF-EKKFISSEIDLYTFNFDRLINLKGFKDKRINNLKRS 489 (669)
T ss_pred cccccCcCHHHHHHHH-HcCCcCCHHHHhhCCHHHHhhccCccHHHHHHHHHH
Confidence 3478899999999998 555 789999999998888765 676666666654
No 118
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=25.76 E-value=56 Score=33.13 Aligned_cols=16 Identities=31% Similarity=0.468 Sum_probs=13.9
Q ss_pred CccccCCchHHHHHHH
Q 006218 180 IKKMKQLGGKLGTSLQ 195 (656)
Q Consensus 180 I~kL~GIG~kt~~kL~ 195 (656)
+++|||||+|++.|++
T Consensus 14 l~kLPGvG~KsA~R~A 29 (198)
T COG0353 14 LKKLPGVGPKSAQRLA 29 (198)
T ss_pred HhhCCCCChhHHHHHH
Confidence 4578999999999995
No 119
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=25.65 E-value=65 Score=38.56 Aligned_cols=14 Identities=29% Similarity=0.387 Sum_probs=7.6
Q ss_pred EecCceEEEEccch
Q 006218 49 RASIDEVYLDLTDA 62 (656)
Q Consensus 49 ~~SIDEafLDlT~~ 62 (656)
.|-||-+-+-+...
T Consensus 280 ~y~iDGiViKvn~~ 293 (665)
T PRK07956 280 PYDIDGVVIKVDDL 293 (665)
T ss_pred CCCCCcEEEEecCH
Confidence 35566666655543
No 120
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=25.47 E-value=60 Score=27.52 Aligned_cols=19 Identities=26% Similarity=0.364 Sum_probs=14.8
Q ss_pred ccccCCchHHHHHHHHhcC
Q 006218 181 KKMKQLGGKLGTSLQNELG 199 (656)
Q Consensus 181 ~kL~GIG~kt~~kL~~~lG 199 (656)
.-+||||++++.+|...+|
T Consensus 25 ~gv~giG~k~A~~ll~~~~ 43 (75)
T cd00080 25 PGVPGIGPKTALKLLKEYG 43 (75)
T ss_pred CCCCcccHHHHHHHHHHhC
Confidence 3589999999999874444
No 121
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=24.84 E-value=56 Score=38.46 Aligned_cols=51 Identities=12% Similarity=0.239 Sum_probs=38.7
Q ss_pred cccCCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhcc--cchhhHHH
Q 006218 175 LDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF--NTGTWLWN 228 (656)
Q Consensus 175 L~~LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~--~~G~~L~~ 228 (656)
+-.-++.+|+|||++..++|.+.+ .++.++...+.+.|.+. |. ..++.++.
T Consensus 527 ~~~s~Ld~I~GiG~~r~~~LL~~F--gs~~~i~~As~eel~~v-gi~~~~a~~i~~ 579 (581)
T COG0322 527 MLQSSLDDIPGIGPKRRKALLKHF--GSLKGIKSASVEELAKV-GISKKLAEKIYE 579 (581)
T ss_pred hhcCccccCCCcCHHHHHHHHHHh--hCHHHHHhcCHHHHHHc-CCCHHHHHHHHh
Confidence 334577899999999999997444 48889999999999998 65 33454443
No 122
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=24.68 E-value=59 Score=32.87 Aligned_cols=51 Identities=18% Similarity=0.074 Sum_probs=36.9
Q ss_pred ccccCCchHHHHHHHHhcCCcchhhhhc----CCHHHHHHhh--cccchhhHHHHHhcCC
Q 006218 181 KKMKQLGGKLGTSLQNELGVTTVGDLLK----FSEDKLQESY--GFNTGTWLWNIARGIS 234 (656)
Q Consensus 181 ~kL~GIG~kt~~kL~~~lGI~TigDLa~----l~~~~L~~~F--G~~~G~~L~~~arGiD 234 (656)
..+.|||+|++-.+. +-.+..+|+. -+...|.+.- |+++++++.-.++|.-
T Consensus 76 i~V~GIGpK~Al~iL---s~~~~~el~~aI~~~D~~~L~kvpGIGkKtAerIilELk~K~ 132 (195)
T PRK14604 76 IGVSGVGPKAALNLL---SSGTPDELQLAIAGGDVARLARVPGIGKKTAERIVLELKGKI 132 (195)
T ss_pred hCcCCcCHHHHHHHH---cCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHHh
Confidence 358899999986654 4456666665 3677788774 5578899998888763
No 123
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=24.38 E-value=73 Score=30.77 Aligned_cols=40 Identities=25% Similarity=0.454 Sum_probs=28.2
Q ss_pred CCccccCCchHHHHHHHHhcCCc---chhhhhcCCHHHHHHhh
Q 006218 179 PIKKMKQLGGKLGTSLQNELGVT---TVGDLLKFSEDKLQESY 218 (656)
Q Consensus 179 PI~kL~GIG~kt~~kL~~~lGI~---TigDLa~l~~~~L~~~F 218 (656)
-++.|.|||++++..+...+||. .++||-.--...|...+
T Consensus 22 aLt~I~GIG~~~a~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i 64 (144)
T TIGR03629 22 ALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKLEEAV 64 (144)
T ss_pred eecceeccCHHHHHHHHHHcCcCCCCCcccCCHHHHHHHHHHH
Confidence 46789999999999888899996 55665543333444433
No 124
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=24.23 E-value=1.3e+02 Score=30.97 Aligned_cols=88 Identities=15% Similarity=0.088 Sum_probs=0.0
Q ss_pred ccchhhhhhhHHHHHHHHHHHHHHHhCCceeEeccCcHHHHHHHhcC---CCCCCeeecCcccHHhhcccCCCccccCCc
Q 006218 111 ADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGM---NKPAQQTTVPFSSVKGLLDSLPIKKMKQLG 187 (656)
Q Consensus 111 ~~~~d~ll~~~~~iA~~IR~~I~~~tGlt~SiGIA~NKlLAKLAS~~---~KP~G~~vl~~~~v~~fL~~LPI~kL~GIG 187 (656)
.++++.+...-..+...|+ ++|.-.||--.-++... .+.+| -.|++..+.+ +|||||
T Consensus 59 ~t~e~l~~a~~~~l~~~I~-----------~iGlyr~KAk~I~~~~~~l~e~~~g---~vP~~~~eL~------~LPGVG 118 (211)
T COG0177 59 PTPEDLLNADEEELEELIK-----------SIGLYRNKAKNIKELARILLEKFGG---EVPDTREELL------SLPGVG 118 (211)
T ss_pred CCHHHHHcCCHHHHHHHHH-----------hcCCcHHHHHHHHHHHHHHHHHcCC---CCCchHHHHH------hCCCcc
Q ss_pred hHHHHHHHHhcCCcchhhhhcCCHHHHHHhhc
Q 006218 188 GKLGTSLQNELGVTTVGDLLKFSEDKLQESYG 219 (656)
Q Consensus 188 ~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG 219 (656)
+||+.-.. ..+..-.+=--+.-...+.+++|
T Consensus 119 rKTAnvVL-~~a~g~p~i~VDTHV~Rvs~R~g 149 (211)
T COG0177 119 RKTANVVL-SFAFGIPAIAVDTHVHRVSNRLG 149 (211)
T ss_pred hHHHHHHH-HhhcCCCcccccchHHHHHHHhC
No 125
>PRK07945 hypothetical protein; Provisional
Probab=23.77 E-value=1.1e+02 Score=33.25 Aligned_cols=49 Identities=16% Similarity=0.140 Sum_probs=31.2
Q ss_pred CCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhcccchhhHHHHHhc
Q 006218 179 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARG 232 (656)
Q Consensus 179 PI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG~~~G~~L~~~arG 232 (656)
.+++|||||+.++.++.+-+---++.- .+.|+...|+..|.-|....+|
T Consensus 50 ~l~~~~giG~~~a~~i~e~~~tg~~~~-----l~~l~~~~~~~~g~~l~~~~~~ 98 (335)
T PRK07945 50 SLTSLPGIGPKTAKVIAQALAGRVPDY-----LAELRADAEPLGGGALRAALRG 98 (335)
T ss_pred CcccCCCcCHHHHHHHHHHHhcCCHHH-----HHHHHHhhcCCccHHHHHHHhh
Confidence 577899999999998863222222222 2456666676556666666664
No 126
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=23.51 E-value=86 Score=34.65 Aligned_cols=38 Identities=26% Similarity=0.389 Sum_probs=32.7
Q ss_pred CccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHHhhc
Q 006218 180 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYG 219 (656)
Q Consensus 180 I~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~~FG 219 (656)
+..+|+||+.++++|.+.|| ++..+...+.+.|.+.=|
T Consensus 289 Ls~IPrl~k~iAk~Ll~~FG--SL~~Il~As~eeL~~VeG 326 (352)
T PRK13482 289 LSKIPRLPSAVIENLVEHFG--SLQGLLAASIEDLDEVEG 326 (352)
T ss_pred HhcCCCCCHHHHHHHHHHcC--CHHHHHcCCHHHHhhCCC
Confidence 45789999999999987888 999999999999988655
No 127
>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=23.36 E-value=48 Score=27.43 Aligned_cols=16 Identities=19% Similarity=0.542 Sum_probs=13.9
Q ss_pred CccccCCchHHHHHHH
Q 006218 180 IKKMKQLGGKLGTSLQ 195 (656)
Q Consensus 180 I~kL~GIG~kt~~kL~ 195 (656)
+..|||||++++.++.
T Consensus 49 ~~~l~gIG~~ia~kI~ 64 (68)
T PF14716_consen 49 LKKLPGIGKSIAKKID 64 (68)
T ss_dssp HCTSTTTTHHHHHHHH
T ss_pred HhhCCCCCHHHHHHHH
Confidence 4689999999999885
No 128
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=23.15 E-value=83 Score=30.60 Aligned_cols=40 Identities=20% Similarity=0.429 Sum_probs=30.0
Q ss_pred CCccccCCchHHHHHHHHhcCCc---chhhhhcCCHHHHHHhh
Q 006218 179 PIKKMKQLGGKLGTSLQNELGVT---TVGDLLKFSEDKLQESY 218 (656)
Q Consensus 179 PI~kL~GIG~kt~~kL~~~lGI~---TigDLa~l~~~~L~~~F 218 (656)
-++.|.|||..++..+.+.+||. +++||-.--...|...+
T Consensus 26 aLt~IyGIG~~~a~~Ic~~lgi~~~~~~~~Lt~~qi~~l~~~i 68 (149)
T PRK04053 26 ALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEAL 68 (149)
T ss_pred eccccccccHHHHHHHHHHcCcCCCCccCcCCHHHHHHHHHHH
Confidence 46789999999999988899996 56666654445555555
No 129
>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=22.75 E-value=69 Score=26.35 Aligned_cols=30 Identities=23% Similarity=0.325 Sum_probs=21.5
Q ss_pred Ccc-ccCCchHHHHHHHHh---c-CCcchhhhhcC
Q 006218 180 IKK-MKQLGGKLGTSLQNE---L-GVTTVGDLLKF 209 (656)
Q Consensus 180 I~k-L~GIG~kt~~kL~~~---l-GI~TigDLa~l 209 (656)
+.. ++|||.+.+.+|-.. . ++.+..||..+
T Consensus 18 L~~~ipgig~~~a~~Il~~R~~~g~~~s~~dL~~v 52 (69)
T TIGR00426 18 LQRAMNGVGLKKAEAIVSYREEYGPFKTVEDLKQV 52 (69)
T ss_pred HHhHCCCCCHHHHHHHHHHHHHcCCcCCHHHHHcC
Confidence 445 899999999888733 3 47777777654
No 130
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=22.58 E-value=67 Score=32.49 Aligned_cols=50 Identities=18% Similarity=0.121 Sum_probs=36.5
Q ss_pred cccCCchHHHHHHHHhcCCcchhhhhc----CCHHHHHHhh--cccchhhHHHHHhcCC
Q 006218 182 KMKQLGGKLGTSLQNELGVTTVGDLLK----FSEDKLQESY--GFNTGTWLWNIARGIS 234 (656)
Q Consensus 182 kL~GIG~kt~~kL~~~lGI~TigDLa~----l~~~~L~~~F--G~~~G~~L~~~arGiD 234 (656)
.+.|||+|++-.+ ++-.+..+|+. -+...|.+.- |+++++++.-.++|.-
T Consensus 76 ~V~GIGpK~AL~i---Ls~~~~~~l~~aI~~~D~~~L~kvpGIGkKtAerIilELkdK~ 131 (197)
T PRK14603 76 GVSGVGPKLALAL---LSALPPALLARALLEGDARLLTSASGVGKKLAERIALELKGKV 131 (197)
T ss_pred CcCCcCHHHHHHH---HcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHHh
Confidence 5889999998665 44446666654 3677788874 5578899998888864
No 131
>COG4380 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.22 E-value=56 Score=32.26 Aligned_cols=31 Identities=23% Similarity=0.505 Sum_probs=27.3
Q ss_pred HHHHHHHhcCCcchhhhhcCCHHHHHHhhccc
Q 006218 190 LGTSLQNELGVTTVGDLLKFSEDKLQESYGFN 221 (656)
Q Consensus 190 t~~kL~~~lGI~TigDLa~l~~~~L~~~FG~~ 221 (656)
..+.++ .-|+++.||+-..+++.|+++||..
T Consensus 76 veETFk-QNGlT~AgDih~v~paKL~qIfGaD 106 (216)
T COG4380 76 VEETFK-QNGLTNAGDIHAVRPAKLHQIFGAD 106 (216)
T ss_pred hHHHHH-HcCCCcccccccCCHHHHHHHhCcc
Confidence 456665 8999999999999999999999975
No 132
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=21.36 E-value=1.1e+02 Score=28.78 Aligned_cols=39 Identities=8% Similarity=0.294 Sum_probs=28.6
Q ss_pred CCCccccCCchHHHHHHHHhcCCcchhhhhcCCHHHHHH
Q 006218 178 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQE 216 (656)
Q Consensus 178 LPI~kL~GIG~kt~~kL~~~lGI~TigDLa~l~~~~L~~ 216 (656)
+.++.|.|||..++....+.+||.--.-+-.++.+++.+
T Consensus 17 iALt~IyGIG~~~a~~I~~~~gi~~~~r~~eLteeei~~ 55 (121)
T COG0099 17 IALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIER 55 (121)
T ss_pred ehhhhhccccHHHHHHHHHHcCCCHhHhhccCCHHHHHH
Confidence 346779999999999887799997655555566665543
No 133
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=21.35 E-value=77 Score=31.79 Aligned_cols=50 Identities=14% Similarity=0.193 Sum_probs=35.9
Q ss_pred cccCCchHHHHHHHHhcCCcchhhhhcC----CHHHHHHh--hcccchhhHHHHHhcCC
Q 006218 182 KMKQLGGKLGTSLQNELGVTTVGDLLKF----SEDKLQES--YGFNTGTWLWNIARGIS 234 (656)
Q Consensus 182 kL~GIG~kt~~kL~~~lGI~TigDLa~l----~~~~L~~~--FG~~~G~~L~~~arGiD 234 (656)
.+.|||+|++-.+ +.-.++.+|... +...|.+. .|+++++++.-.++|.-
T Consensus 77 ~VsGIGpK~Al~I---Ls~~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIilELkdK~ 132 (183)
T PRK14601 77 KVNGIGANTAMAV---CSSLDVNSFYKALSLGDESVLKKVPGIGPKSAKRIIAELSDAK 132 (183)
T ss_pred ccCCccHHHHHHH---HcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHHh
Confidence 5789999998654 444566666653 66778776 45678899998888763
No 134
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=20.87 E-value=81 Score=32.02 Aligned_cols=50 Identities=10% Similarity=0.105 Sum_probs=36.2
Q ss_pred cccCCchHHHHHHHHhcCCcchhhhhc----CCHHHHHHhh--cccchhhHHHHHhcCC
Q 006218 182 KMKQLGGKLGTSLQNELGVTTVGDLLK----FSEDKLQESY--GFNTGTWLWNIARGIS 234 (656)
Q Consensus 182 kL~GIG~kt~~kL~~~lGI~TigDLa~----l~~~~L~~~F--G~~~G~~L~~~arGiD 234 (656)
.+.|||+|++-.+ +.-.++.+|+. -+...|.+.- |+++++++.-.++|.=
T Consensus 76 sVsGIGPK~ALaI---Ls~~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIIlELkdKl 131 (196)
T PRK13901 76 GVDGIGPRAALRV---LSGIKYNEFRDAIDREDIELISKVKGIGNKMAGKIFLKLRGKL 131 (196)
T ss_pred CcCCcCHHHHHHH---HcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHhh
Confidence 5789999998655 44456666665 3667787774 5578899998888753
No 135
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=20.84 E-value=80 Score=29.29 Aligned_cols=28 Identities=18% Similarity=0.269 Sum_probs=19.5
Q ss_pred ccccCCchHHHHHHHHhc----CCcchhhhhc
Q 006218 181 KKMKQLGGKLGTSLQNEL----GVTTVGDLLK 208 (656)
Q Consensus 181 ~kL~GIG~kt~~kL~~~l----GI~TigDLa~ 208 (656)
..+||||.+.+.++-... ++.++.||..
T Consensus 71 ~~lpGIG~~~A~~Ii~~R~~~g~f~s~eeL~~ 102 (120)
T TIGR01259 71 QALPGIGPAKAKAIIEYREENGAFKSVDDLTK 102 (120)
T ss_pred hcCCCCCHHHHHHHHHHHHhcCCcCCHHHHHc
Confidence 468999999999887333 3555555544
No 136
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=20.21 E-value=86 Score=23.03 Aligned_cols=16 Identities=31% Similarity=0.366 Sum_probs=13.0
Q ss_pred CccccCCchHHHHHHH
Q 006218 180 IKKMKQLGGKLGTSLQ 195 (656)
Q Consensus 180 I~kL~GIG~kt~~kL~ 195 (656)
|.-+||||.+++.+|.
T Consensus 18 i~Gv~giG~ktA~~ll 33 (36)
T smart00279 18 IPGVKGIGPKTALKLL 33 (36)
T ss_pred CCCCCcccHHHHHHHH
Confidence 3458899999998875
Done!