Query gi|254780237|ref|YP_003064650.1| DNA-directed RNA polymerase subunit alpha [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 340
No_of_seqs 142 out of 1377
Neff 5.5
Searched_HMMs 39220
Date Tue May 24 00:20:40 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780237.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR02027 rpoA DNA-directed RN 100.0 0 0 872.4 27.4 294 27-320 1-324 (324)
2 PRK05182 DNA-directed RNA poly 100.0 0 0 804.3 32.3 305 8-319 2-306 (306)
3 CHL00013 rpoA RNA polymerase a 100.0 0 0 773.6 31.2 303 13-322 11-333 (333)
4 COG0202 RpoA DNA-directed RNA 100.0 0 0 606.4 23.1 313 9-326 1-313 (317)
5 cd06928 RNAP_alpha_NTD N-termi 100.0 0 0 570.4 25.4 212 20-231 3-215 (215)
6 smart00662 RPOLD RNA polymeras 100.0 0 0 335.6 19.9 195 27-231 1-224 (224)
7 pfam01000 RNA_pol_A_bac RNA po 100.0 5.8E-37 1.5E-41 259.6 12.1 115 63-178 1-117 (117)
8 cd07030 RNAP_D D subunit of Ar 99.9 6.7E-22 1.7E-26 162.1 16.7 206 22-233 7-257 (259)
9 PRK00783 DNA-directed RNA poly 99.9 4.5E-21 1.2E-25 156.7 16.1 200 22-233 7-259 (265)
10 pfam01193 RNA_pol_L RNA polyme 99.9 1.2E-21 3.1E-26 160.3 9.1 91 32-233 1-91 (91)
11 cd07028 RNAP_RPB3_like RPB3 su 99.8 5.3E-17 1.4E-21 130.3 18.2 185 20-232 5-210 (212)
12 pfam03118 RNA_pol_A_CTD Bacter 99.8 7.2E-19 1.8E-23 142.4 5.6 60 253-312 3-62 (62)
13 cd00460 RNAP_RPB11_RPB3 RPB11 99.6 6.6E-16 1.7E-20 123.2 5.7 82 149-230 4-85 (86)
14 cd07031 RNAP_II_RPB3 RPB3 subu 99.5 6.2E-12 1.6E-16 97.5 17.5 190 20-232 5-259 (265)
15 cd07032 RNAP_I_II_AC40 AC40 su 99.5 2.2E-11 5.7E-16 93.9 19.2 197 22-233 7-290 (291)
16 KOG1522 consensus 98.9 5.4E-07 1.4E-11 65.5 16.6 203 18-232 8-262 (285)
17 PRK07758 hypothetical protein; 98.0 1E-05 2.6E-10 57.3 4.8 55 264-318 41-95 (95)
18 KOG1521 consensus 97.8 0.0024 6.1E-08 41.9 14.5 206 8-231 41-333 (338)
19 PRK03773 DNA-directed RNA poly 96.0 0.021 5.3E-07 35.8 5.8 51 180-234 38-88 (95)
20 PRK04301 radA DNA repair and r 96.0 0.02 5E-07 36.0 5.6 50 37-92 13-63 (318)
21 cd06927 RNAP_L L subunit of Ar 95.3 0.062 1.6E-06 32.7 6.1 48 179-232 35-82 (83)
22 PTZ00035 Rad51; Provisional 94.6 0.11 2.8E-06 31.1 5.9 55 259-313 34-91 (350)
23 cd07027 RNAP_RPB11_like RPB11 94.2 0.16 4E-06 30.2 5.9 46 180-231 36-81 (83)
24 cd00460 RNAP_RPB11_RPB3 RPB11 94.2 0.074 1.9E-06 32.3 4.2 40 22-67 5-44 (86)
25 cd06926 RNAP_II_RPB11 RPB11 su 93.6 0.23 5.8E-06 29.1 5.8 47 180-232 44-90 (93)
26 cd07027 RNAP_RPB11_like RPB11 93.1 0.15 3.9E-06 30.3 4.2 39 22-65 5-43 (83)
27 cd07029 RNAP_I_III_AC19 AC19 s 93.0 0.3 7.7E-06 28.3 5.6 48 180-233 36-83 (85)
28 PRK07956 ligA NAD-dependent DN 92.4 0.28 7.1E-06 28.5 4.8 73 264-336 452-531 (668)
29 COG1761 RPB11 DNA-directed RNA 92.4 0.32 8.3E-06 28.1 5.1 49 179-233 41-89 (99)
30 cd06927 RNAP_L L subunit of Ar 92.4 0.12 3E-06 30.9 2.9 39 22-65 5-43 (83)
31 cd07029 RNAP_I_III_AC19 AC19 s 91.9 0.23 5.8E-06 29.1 3.8 38 22-64 5-42 (85)
32 PRK03773 DNA-directed RNA poly 91.4 0.37 9.3E-06 27.8 4.5 39 22-65 7-45 (95)
33 PRK02406 DNA polymerase IV; Va 91.4 1.2 3.2E-05 24.3 7.9 53 255-310 177-230 (355)
34 cd06926 RNAP_II_RPB11 RPB11 su 90.5 0.56 1.4E-05 26.6 4.8 47 13-65 5-51 (93)
35 COG1948 MUS81 ERCC4-type nucle 87.4 1.3 3.2E-05 24.3 4.8 47 266-314 192-238 (254)
36 PRK08097 ligB NAD-dependent DN 87.1 0.89 2.3E-05 25.3 3.8 49 264-312 433-482 (563)
37 PRK00254 ski2-like helicase; P 86.8 0.88 2.3E-05 25.3 3.7 44 268-311 655-698 (717)
38 PRK03858 DNA polymerase IV; Va 86.2 2.8 7.2E-05 22.0 6.0 53 255-309 170-223 (398)
39 cd03468 Pol_Y_like Pol_Y_like: 86.2 0.88 2.2E-05 25.3 3.4 48 255-304 165-212 (330)
40 PRK01216 DNA polymerase IV; Va 85.9 1.3 3.4E-05 24.1 4.2 51 255-307 175-226 (351)
41 PRK01172 ski2-like helicase; P 85.7 1.8 4.6E-05 23.3 4.8 45 269-313 624-668 (674)
42 PRK13766 Hef nuclease; Provisi 84.7 2.1 5.4E-05 22.8 4.8 45 266-312 716-760 (764)
43 PRK03352 DNA polymerase IV; Va 84.1 2 5E-05 23.0 4.4 50 257-308 176-226 (345)
44 PRK05618 50S ribosomal protein 84.1 2.7 6.9E-05 22.2 5.1 29 112-140 154-183 (193)
45 pfam12482 DUF3701 Phage integr 83.2 1.4 3.7E-05 23.9 3.4 57 264-320 20-80 (96)
46 TIGR02238 recomb_DMC1 meiotic 82.5 2 5.1E-05 23.0 3.9 51 263-313 7-57 (314)
47 PRK02794 DNA polymerase IV; Pr 82.3 4.1 0.00011 21.0 7.4 52 256-310 207-259 (417)
48 PRK08609 hypothetical protein; 81.6 3.8 9.6E-05 21.2 5.1 53 266-322 448-500 (570)
49 PRK03348 DNA polymerase IV; Pr 81.1 4.6 0.00012 20.7 6.3 52 256-309 177-229 (456)
50 TIGR01954 nusA_Cterm_rpt trans 79.2 2.9 7.5E-05 21.9 3.9 40 270-309 6-47 (52)
51 PRK03609 umuC DNA polymerase V 78.3 2.5 6.4E-05 22.4 3.3 45 254-300 174-220 (422)
52 TIGR00575 dnlj DNA ligase, NAD 78.3 2.3 5.8E-05 22.6 3.1 40 273-312 469-511 (706)
53 cd01700 Pol_V Pol V was discov 76.7 3.5 9E-05 21.4 3.7 51 257-310 174-225 (344)
54 PTZ00298 mevalonate kinase; Pr 75.6 6.5 0.00017 19.7 4.8 73 265-339 226-309 (328)
55 PRK01810 DNA polymerase IV; Va 75.2 6.8 0.00017 19.6 6.4 52 257-311 178-230 (410)
56 COG0272 Lig NAD-dependent DNA 75.1 4.7 0.00012 20.6 3.9 72 265-336 453-531 (667)
57 PRK13209 L-xylulose 5-phosphat 75.1 2.6 6.7E-05 22.2 2.6 51 168-230 229-279 (283)
58 TIGR03491 RecB family nuclease 74.1 6.5 0.00017 19.7 4.5 48 259-306 208-256 (457)
59 cd00424 Pol_Y Y-family of DNA 74.0 6.3 0.00016 19.8 4.4 52 257-310 172-224 (341)
60 cd01684 Tet_like_IV EF-G_domai 73.1 1.8 4.5E-05 23.3 1.4 47 28-74 28-94 (115)
61 cd03586 Pol_IV_kappa Pol_IV_ka 72.0 4.9 0.00012 20.5 3.4 53 255-309 169-222 (337)
62 cd01701 Pol_zeta Pol_zeta, a m 71.5 6.5 0.00017 19.7 4.0 54 256-311 222-277 (405)
63 PRK13210 putative L-xylulose 5 70.6 4.1 0.00011 20.9 2.8 51 168-230 230-280 (284)
64 PRK03103 DNA polymerase IV; Re 70.5 5.7 0.00015 20.0 3.5 53 255-310 179-232 (410)
65 PRK12373 NADH dehydrogenase su 68.8 4.1 0.0001 21.0 2.5 46 288-337 324-369 (403)
66 PRK12278 50S ribosomal protein 68.3 3.3 8.3E-05 21.6 1.9 26 267-292 163-188 (216)
67 PRK12311 rpsB 30S ribosomal pr 67.5 4.3 0.00011 20.8 2.4 239 25-337 64-312 (332)
68 cd01434 EFG_mtEFG1_IV EFG_mtEF 60.0 14 0.00035 17.6 4.4 44 29-72 29-93 (116)
69 PRK03926 mevalonate kinase; Pr 53.3 18 0.00045 16.9 4.1 73 264-338 200-282 (302)
70 smart00611 SEC63 Domain of unk 53.1 18 0.00045 16.8 7.0 99 214-314 106-208 (312)
71 pfam02889 Sec63 Sec63 Brl doma 50.6 19 0.0005 16.6 4.8 96 214-313 103-205 (309)
72 pfam00633 HHH Helix-hairpin-he 50.3 10 0.00026 18.4 1.8 28 281-308 2-29 (30)
73 PRK02362 ski2-like helicase; P 50.2 19 0.00048 16.7 3.2 43 267-312 663-705 (736)
74 PRK10917 ATP-dependent DNA hel 48.2 18 0.00047 16.8 2.9 17 132-148 79-96 (677)
75 pfam04994 TfoX_C TfoX C-termin 47.2 22 0.00056 16.3 3.2 36 264-299 6-42 (77)
76 TIGR01259 comE comEA protein; 45.7 12 0.00029 18.1 1.5 23 288-310 100-122 (124)
77 TIGR00426 TIGR00426 competence 44.6 14 0.00035 17.6 1.8 24 288-311 46-69 (70)
78 smart00483 POLXc DNA polymeras 44.5 24 0.00061 16.0 3.3 19 70-88 48-66 (334)
79 KOG4392 consensus 41.0 27 0.0007 15.6 4.5 47 180-232 56-102 (117)
80 pfam08221 HTH_9 RNA polymerase 39.9 28 0.00072 15.5 3.3 39 264-313 13-51 (62)
81 cd01702 Pol_eta Pol eta is mem 38.1 25 0.00064 15.9 2.3 54 255-310 179-236 (358)
82 TIGR00368 TIGR00368 Mg chelata 36.7 27 0.00069 15.7 2.3 44 253-305 457-500 (505)
83 COG3743 Uncharacterized conser 36.4 18 0.00047 16.8 1.4 26 268-293 78-103 (133)
84 cd01703 Pol_iota Pol iota is m 36.0 33 0.00083 15.1 3.7 49 258-307 210-259 (394)
85 PTZ00144 dihydrolipoamide succ 35.4 33 0.00085 15.1 4.4 80 68-147 24-105 (430)
86 KOG1684 consensus 34.4 14 0.00036 17.5 0.5 37 296-334 271-307 (401)
87 PRK09202 nusA transcription el 34.3 35 0.00088 15.0 5.2 45 264-308 381-425 (428)
88 MTH00078 COX1 cytochrome c oxi 34.2 20 0.0005 16.5 1.2 16 40-55 4-19 (548)
89 PRK13397 3-deoxy-7-phosphohept 34.0 35 0.00089 14.9 3.7 57 29-91 17-76 (250)
90 TIGR01357 aroB 3-dehydroquinat 33.0 17 0.00042 17.1 0.7 28 274-301 212-241 (361)
91 pfam04106 APG5 Autophagy prote 32.3 36 0.00091 14.9 2.3 32 38-69 135-167 (195)
92 pfam11731 Cdd1 Pathogenicity l 32.1 38 0.00096 14.7 2.4 37 289-329 11-47 (92)
93 smart00278 HhH1 Helix-hairpin- 30.6 27 0.00069 15.7 1.4 22 290-311 1-22 (26)
94 TIGR02236 recomb_radA DNA repa 30.2 40 0.001 14.5 3.9 54 260-313 2-56 (333)
95 COG4277 Predicted DNA-binding 29.8 41 0.001 14.5 3.4 143 169-318 191-368 (404)
96 KOG3438 consensus 29.3 42 0.0011 14.4 4.4 48 179-232 42-89 (105)
97 COG0197 RplP Ribosomal protein 28.8 35 0.0009 14.9 1.8 88 99-225 30-129 (146)
98 COG2838 Icd Monomeric isocitra 28.4 43 0.0011 14.3 3.0 11 211-221 521-531 (744)
99 TIGR01088 aroQ 3-dehydroquinat 28.3 32 0.00082 15.2 1.5 36 297-332 20-61 (144)
100 PRK10880 adenine DNA glycosyla 26.7 32 0.00082 15.2 1.3 13 129-141 196-208 (350)
101 COG1400 SEC65 Signal recogniti 26.3 47 0.0012 14.1 2.3 22 294-318 28-49 (93)
102 cd00056 ENDO3c endonuclease II 26.1 48 0.0012 14.1 3.2 22 286-307 79-100 (158)
103 TIGR01083 nth endonuclease III 26.0 34 0.00087 15.0 1.3 58 253-310 60-127 (192)
104 cd00181 TarH Taxis toward Aspa 25.9 42 0.0011 14.4 1.7 67 268-337 25-91 (140)
105 KOG0980 consensus 25.6 41 0.001 14.5 1.6 50 72-121 218-272 (980)
106 COG0153 GalK Galactokinase [Ca 25.5 49 0.0012 14.0 6.9 157 172-338 198-369 (390)
107 COG0389 DinP Nucleotidyltransf 24.3 51 0.0013 13.9 2.6 44 257-302 175-219 (354)
108 cd01680 EFG_like_IV Elongation 24.3 51 0.0013 13.9 5.4 44 29-72 29-93 (116)
109 PRK10702 endonuclease III; Pro 23.7 29 0.00074 15.5 0.6 52 256-307 72-126 (211)
110 PRK00558 uvrC excinuclease ABC 23.1 54 0.0014 13.7 3.7 35 278-312 574-608 (609)
111 KOG0095 consensus 22.8 28 0.00072 15.5 0.4 29 28-67 25-53 (213)
112 COG1796 POL4 DNA polymerase IV 22.6 55 0.0014 13.7 2.8 19 72-90 55-73 (326)
113 TIGR02668 moaA_archaeal probab 22.5 56 0.0014 13.6 2.4 112 56-194 59-173 (324)
114 TIGR02683 upstrm_HI1419 probab 22.3 46 0.0012 14.2 1.4 14 144-157 47-60 (95)
115 pfam06569 DUF1128 Protein of u 21.9 57 0.0015 13.6 2.2 34 303-337 13-46 (71)
116 smart00478 ENDO3c endonuclease 20.6 61 0.0015 13.4 2.3 50 258-307 37-89 (149)
117 TIGR00607 rad52 recombination 20.4 30 0.00076 15.4 0.1 14 58-71 73-87 (164)
118 pfam02697 DUF217 Uncharacteriz 20.3 61 0.0016 13.4 1.7 23 289-312 11-33 (71)
119 TIGR01815 TrpE-clade3 anthrani 20.3 62 0.0016 13.4 2.0 121 34-163 531-685 (726)
120 KOG2534 consensus 20.2 62 0.0016 13.3 2.9 16 205-220 293-308 (353)
No 1
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit; InterPro: IPR011773 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. 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 , .; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription DNA-dependent.
Probab=100.00 E-value=0 Score=872.36 Aligned_cols=294 Identities=50% Similarity=0.821 Sum_probs=281.5
Q ss_pred EEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECC--------CCCCCCCCCCCHHHHHHHHHHHCCCE-----
Q ss_conf 58999961697566788899999874169830688999887--------14431466462444999998401141-----
Q gi|254780237|r 27 RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG--------VLHEISSIKGVHEDLTDIILNIKGIN----- 93 (340)
Q Consensus 27 ~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI~g--------v~HEfs~i~GV~EDV~eIiLNLK~I~----- 93 (340)
||||+++|||||||+||||||||||||||||+|||||||+| |.|||++|+||+|||++||||||+|+
T Consensus 1 ~g~F~~~PLErGfG~TlGNALRRvLLSSipG~Ait~~~I~G~~~D~~~~V~HEF~~i~GV~EDV~eIiLNlK~l~~k~~~ 80 (324)
T TIGR02027 1 YGKFVLEPLERGFGITLGNALRRVLLSSIPGAAITAIKIDGFDKDVAKVVLHEFSTIEGVKEDVTEIILNLKKLRLKIKE 80 (324)
T ss_pred CEEEEEECCCCCCCEECHHHHHHHHHHCCCCCEEEEEEEECCCCCEEEEEEECCCCCCCEEHHHHHHHHHCCCEEEEEEH
T ss_conf 94799932788832131057899986337454047889815776603478202033787020278998750403343200
Q ss_pred -EEECCCCC--EE----EEEEEECCEEEEEEEEE-CCCCEEEECCCEEEEEECCC-CEEEEEEEEECCCCCEECCCCCCC
Q ss_conf -77727982--79----99999447169963351-38985998888089997789-649999997468763203444465
Q gi|254780237|r 94 -LKMSGDSH--KR----VTIFKRGPGVVTAGDIQ-TVNDIEVLNPDHVICNLDVD-AVVRMELTVSKGHGYVPAKHHRTE 164 (340)
Q Consensus 94 -~k~~~~~~--~~----~~l~~~Gp~~vtA~Di~-~p~~veivNpd~~IaTl~~~-~~l~iel~ie~G~GY~~~e~~~~~ 164 (340)
|+++.+.+ .+ +++.++||++|||+||. .|++|||+|||||||||+++ +.|+||++|++||||||+++|+.+
T Consensus 81 l~~~~~~~~~~~~~WP~~~~~~~Gp~~~~A~Di~~~~~~~EvvNpdl~Iatl~~~Na~l~~e~~v~~GRGYVp~e~~~~~ 160 (324)
T TIGR02027 81 LVKSEGDEERQVTKWPIMTLSKKGPGVVTAGDIKAQPGGVEVVNPDLVIATLTEDNAKLEIELRVERGRGYVPAEENREE 160 (324)
T ss_pred HHCCCCCCCCCEEECCEEEEEEECCCEEEEEEEECCCCCEEEECCCCEEEEECCCCEEEEEEEEEEECCCEEECCCCCCC
T ss_conf 01035886552132560599986573145220013799646878885266740797279999999735612200134000
Q ss_pred CCCCCEECCCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC--
Q ss_conf 575430212431111442235776411688776218999999389617779999999999998887622444432210--
Q gi|254780237|r 165 NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVK-- 242 (340)
Q Consensus 165 ~~~ig~i~iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~~~~~~~~~~-- 242 (340)
..++|+|||||+||||+||+|.||++||||++|||||+|||||||||+|+||++.||+||.+||.+|+++++.....+
T Consensus 161 ~~~~g~I~~Ds~fsPV~kV~Y~VE~~Rvgq~~dyDkL~lei~T~G~i~P~dA~~~Aa~IL~~hl~~f~~~~~~~~~~~~~ 240 (324)
T TIGR02027 161 DSPVGVIAVDSIFSPVKKVNYEVENTRVGQRTDYDKLILEIETDGSIRPKDAIAEAAKILIEHLEPFVEIEEEIEELEES 240 (324)
T ss_pred CCCCCEEEECCCCCCEEEEEEEEEEEEECCCCCCEEEEEEEEECCEECHHHHHHHHHHHHHHHHHHHHCCCCHHHHCCHH
T ss_conf 37688577665258703421248887537987612788998657710789999999999999888851577104421211
Q ss_pred CHHHCCCC-----HHHHHHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHH-HCCC
Q ss_conf 00000000-----11233311122101105888989883983718887449888861889886449999999998-0831
Q gi|254780237|r 243 EDINVKSL-----PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT-MGLF 316 (340)
Q Consensus 243 ~~~~~~~~-----~~~~~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~-~gl~ 316 (340)
.....++. +..+.|.++||||||||||+||||||||+|||||+++|++||+++|||||||++||+++|++ |||.
T Consensus 241 ~~~~~ee~~~~~~~~~~~l~~~IeeLdLSVRs~NCLk~~gI~t~geL~~~~e~eLl~i~NfGkKSl~EI~ekL~~~lgL~ 320 (324)
T TIGR02027 241 QEEEKEEDFDIKLEKSKLLSIKIEELDLSVRSYNCLKRAGIHTLGELVSKSEEELLKIKNFGKKSLDEIKEKLAEKLGLE 320 (324)
T ss_pred HHHCCCCCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf 12058764456725778751780032454898864646035417888860389884178857333899999988761888
Q ss_pred CCCC
Q ss_conf 2676
Q gi|254780237|r 317 LGMN 320 (340)
Q Consensus 317 lg~~ 320 (340)
|||+
T Consensus 321 Lg~~ 324 (324)
T TIGR02027 321 LGMD 324 (324)
T ss_pred CCCC
T ss_conf 7889
No 2
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=100.00 E-value=0 Score=804.32 Aligned_cols=305 Identities=55% Similarity=0.899 Sum_probs=290.2
Q ss_pred HCCCCCCCEEEECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 51797420158636788815899996169756678889999987416983068899988714431466462444999998
Q gi|254780237|r 8 ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIIL 87 (340)
Q Consensus 8 ~~~~P~~i~~~~~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI~gv~HEfs~i~GV~EDV~eIiL 87 (340)
+|.+|+++++. +.+++||||+++||+||||+|+|||||||||||++|+|||+|||+||.||||+||||+|||+||+|
T Consensus 2 ~~~~p~~~~~~---~~~~~yg~F~i~Ple~G~G~TiGNaLRRvLLssi~G~aIt~vkI~Gv~HEfsti~GV~EdV~~IlL 78 (306)
T PRK05182 2 EFLKPKKIEVE---EESDNYGKFVLEPLERGFGTTLGNALRRVLLSSLPGAAVTSVKIDGVLHEFSTIPGVREDVTEIIL 78 (306)
T ss_pred CCCCCCEEEEE---ECCCCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCCCCCCHHHHHHHHHH
T ss_conf 77688676898---647977999996588874315789999999856985189999988964312348871666999997
Q ss_pred HHCCCEEEECCCCCEEEEEEEECCEEEEEEEEECCCCEEEECCCEEEEEECCCCEEEEEEEEECCCCCEECCCCCCCCCC
Q ss_conf 40114177727982799999944716996335138985998888089997789649999997468763203444465575
Q gi|254780237|r 88 NIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDP 167 (340)
Q Consensus 88 NLK~I~~k~~~~~~~~~~l~~~Gp~~vtA~Di~~p~~veivNpd~~IaTl~~~~~l~iel~ie~G~GY~~~e~~~~~~~~ 167 (340)
|||+|+|++..++++.++++++|||+|||+||++|++++|+||||||||+++++.|+|+++|++||||+++++++....+
T Consensus 79 NLK~i~~k~~~~~~~~~~l~~~Gp~~vtA~Di~~p~~veivnpd~~Iatl~~~~~l~~el~i~~G~GY~~~~~~~~~~~~ 158 (306)
T PRK05182 79 NLKGLALKLEGEEEKTLTLSKKGPGEVTAGDIETDSDVEIVNPDLVIATLNEGAKLEMELTVERGRGYVPAEENKKEDRP 158 (306)
T ss_pred HHHCCEEEECCCCCEEEEEEEECCCEEEHHHCCCCCCEEEECCCEEEEEECCCCEEEEEEEEECCCCCCCHHHCCCCCCC
T ss_conf 33042798348975899999946834887474898843996898899997788639999999888353112104555677
Q ss_pred CCEECCCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHC
Q ss_conf 43021243111144223577641168877621899999938961777999999999999888762244443221000000
Q gi|254780237|r 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINV 247 (340)
Q Consensus 168 ig~i~iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~~~~~~~~~~~~~~~ 247 (340)
+|+|++||+||||+||||.|+++||||+++||||+|||||||||+|++|+++||+||++||.+|+++++...... .
T Consensus 159 ig~i~iDa~FsPV~kVny~Ve~~rvg~~~d~ekL~leI~TnGsI~P~eAl~~Aa~il~~~~~~f~~~~~~~~~~~----~ 234 (306)
T PRK05182 159 IGRIPVDAIFSPVRKVNYTVENTRVGQRTDYDKLVLEIETNGSITPEEALALAAKILVEQLSVFVDLEEEEAEVE----E 234 (306)
T ss_pred CCCEECCCCCCCCEEEEEEEEECCCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC----C
T ss_conf 772786755567036889999645588775406999999599799999999999999999999748664554545----5
Q ss_pred CCCHHHHHHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCC
Q ss_conf 000112333111221011058889898839837188874498888618898864499999999980831267
Q gi|254780237|r 248 KSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGM 319 (340)
Q Consensus 248 ~~~~~~~~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~ 319 (340)
+..+.++.|.++||+||||+||+||||||||+|||||+++|++||+++||||+||++||+++|+++||+|||
T Consensus 235 ~~~~~~~~l~~~IeeLeLSvRs~NcLk~a~I~tI~dLv~~se~dLl~ikNfGkKSl~EI~~kL~~~gl~lgm 306 (306)
T PRK05182 235 EEPEFDPILLRPIEELELSVRSYNCLKRAGINTIGDLVQRTEEELLKTPNLGKKSLEEIKEKLAELGLSLGM 306 (306)
T ss_pred CCCCCCHHHCCCHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCCCCHHHHHHHHHHCCCCCCC
T ss_conf 665526464496988138688875587859936999874799999618997620399999999972987899
No 3
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=100.00 E-value=0 Score=773.64 Aligned_cols=303 Identities=32% Similarity=0.501 Sum_probs=274.1
Q ss_pred CCCEEEECC----CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 420158636----7888158999961697566788899999874169830688999887144314664624449999984
Q gi|254780237|r 13 NNIEYIVLG----QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88 (340)
Q Consensus 13 ~~i~~~~~~----~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI~gv~HEfs~i~GV~EDV~eIiLN 88 (340)
+.++|.|++ +.+.+||||+++||+||||+|+|||||||||||++|+|||+|||+||.|||||||||+|||+||+||
T Consensus 11 ~~~~~~Cie~~~~~~~~~YgrF~~~Ple~G~g~TlGNaLRRvLLssl~G~aIt~vkI~Gv~HEfsti~GV~EdV~eIiLN 90 (333)
T CHL00013 11 RTLQWKCVESRVDSKRLYYGRFILSPLMKGQADTIGIALRRALLGEIEGTCITRVKIEGVPHEYSTIVGIRESVHEILLN 90 (333)
T ss_pred CCCEEEEEEEEECCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCCCCCCCCCCHHHHHHC
T ss_conf 55248985027526876278999705888742146788988877458850789999889653105789864479999856
Q ss_pred HCCCEEEECCCCCEEEEEEEECCEEEEEEEEECCCCEEEECCCEEEEEECCCCEEEEEEEEECCCCCEECCCCCCCCCCC
Q ss_conf 01141777279827999999447169963351389859988880899977896499999974687632034444655754
Q gi|254780237|r 89 IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 168 (340)
Q Consensus 89 LK~I~~k~~~~~~~~~~l~~~Gp~~vtA~Di~~p~~veivNpd~~IaTl~~~~~l~iel~ie~G~GY~~~e~~~~~~~~i 168 (340)
||+|+|+.+.++++.++|+++|||+|||+||++|+++||+||||||||+++++.|+||++|++||||++++.++ .+.
T Consensus 91 LK~i~~k~~~~~~~~~~l~~~Gp~~VtA~Di~~p~~veivNpd~~IATl~~~~~l~mel~ie~G~GY~~~~~~~---~~~ 167 (333)
T CHL00013 91 LKEIVLRSNLYGTQIASICVQGPGYVTAQDIILPPSVEIVDPTQYIATLTEPIDLCIELKIERGRGYRLKNPNN---FQD 167 (333)
T ss_pred HHHEEEECCCCCCEEEEEEEECCCEEEEHHCCCCCCEEEECCCEEEEEECCCCEEEEEEEEECCCCCEECCCCC---CCC
T ss_conf 45438972479857999996078058803416888539977987999967997799999997686865177566---777
Q ss_pred CEECCCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHH--
Q ss_conf 302124311114422357764116887762189999993896177799999999999988876224444322100000--
Q gi|254780237|r 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDIN-- 246 (340)
Q Consensus 169 g~i~iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~~~~~~~~~~~~~~-- 246 (340)
|+|||||+||||+||||.|+++|+|+++ ||||+|||||||||+|++||++||+||++||.+|+++++..........
T Consensus 168 g~i~iDaiFsPV~kVny~Ve~~rvg~~~-~ekL~lEI~TnGsI~P~eAL~~AakIL~~~f~~~~~~~~~~~~~~~~~~~~ 246 (333)
T CHL00013 168 GSYPIDAVFMPVRNVNYSIHSYGNGNEK-QEILFLEIWTNGSLTPKEALHEASRNLIDLFIPFLHAEEENLHLENNQNKV 246 (333)
T ss_pred CEEECCCCCCCCCEEEEEEEECCCCCCC-CCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf 6077677667502378999975678755-626999999589789999999999999999998744432112333344434
Q ss_pred --------------CCCCHHHHHHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHH
Q ss_conf --------------000011233311122101105888989883983718887449888861889886449999999998
Q gi|254780237|r 247 --------------VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312 (340)
Q Consensus 247 --------------~~~~~~~~~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~ 312 (340)
.+.........++||+|||||||+||||||||+|||||+++|++||+++||||+||++||+++|++
T Consensus 247 ~~~~~~~~~~~~~~~~~~~~~~~~~~~IeeLeLSvRs~NCLKra~I~tvgdLv~~se~dLl~ikNfGkKSl~EI~ekL~e 326 (333)
T CHL00013 247 TLPLFTFHDRLANLRKNKKEIALKQIFIDQLELSVRAYNCLKRANIHTLLDLLNYSQEDLLKIKNFGQKSVKQVLDALEK 326 (333)
T ss_pred CCCCCCCCHHHHHHHHCCCCCCCCCCCHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHH
T ss_conf 45543320012110100111200277088821878877436373893799986389999941899863029999999988
Q ss_pred HCCCCCCCCC
Q ss_conf 0831267687
Q gi|254780237|r 313 MGLFLGMNLP 322 (340)
Q Consensus 313 ~gl~lg~~l~ 322 (340)
. |||+||
T Consensus 327 ~---~Gi~Lp 333 (333)
T CHL00013 327 R---FGIDLP 333 (333)
T ss_pred H---HCCCCC
T ss_conf 6---299798
No 4
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]
Probab=100.00 E-value=0 Score=606.44 Aligned_cols=313 Identities=47% Similarity=0.771 Sum_probs=291.0
Q ss_pred CCCCCCCEEEECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 17974201586367888158999961697566788899999874169830688999887144314664624449999984
Q gi|254780237|r 9 LIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILN 88 (340)
Q Consensus 9 ~~~P~~i~~~~~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI~gv~HEfs~i~GV~EDV~eIiLN 88 (340)
|.+|..+++.. .++.||+|.++||+||||+|+||||||+||||+||+||++|+|+||.|||++++||+|||++++||
T Consensus 1 ~~~p~~i~i~~---~~~~~~~~~ieplerG~g~tlgNALRRvLLSsiPg~Av~~V~I~~v~hef~s~~gv~Edvl~~~Ln 77 (317)
T COG0202 1 FLKPKKVKIEE---LSDTYAKFVIEPLERGFGVTLGNALRRVLLSSIPGAAVTAVEIDGVLHEFDSIEGVQEDVLAHRLN 77 (317)
T ss_pred CCCCCCEEEEE---CCCCCCCEEEEEEEECCCCHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCHHHHHHHHHC
T ss_conf 98665258997---146634089998540785035789999999748430479999961322334676747999999846
Q ss_pred HCCCEEEECCCCCEEEEEEEECCEEEEEEEEECCCCEEEECCCEEEEEECCCCEEEEEEEEECCCCCEECCCCCCCCCCC
Q ss_conf 01141777279827999999447169963351389859988880899977896499999974687632034444655754
Q gi|254780237|r 89 IKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPI 168 (340)
Q Consensus 89 LK~I~~k~~~~~~~~~~l~~~Gp~~vtA~Di~~p~~veivNpd~~IaTl~~~~~l~iel~ie~G~GY~~~e~~~~~~~~i 168 (340)
||.+.++.+....+++.+.++|||.++|+|+..|.++||+||++||||+++++.|.|+++|.+|+||+|++.++.+..++
T Consensus 78 Lk~L~~k~~~~~~~~~~~~~~g~g~v~a~d~~~~~~lEv~np~~~ia~~~~~~~l~~~~~V~~G~gyv~~~~~~~~~~~v 157 (317)
T COG0202 78 LKPLAVKLDGDEEVTLELDKEGPGEVTASDITVPLDLEVVNPDHVIATLTEDAKLEMELRVYSGDGYVPAEGNREDDPPV 157 (317)
T ss_pred CCEEEEECCCCCCEEEEEECCCCCCCCHHHCCCCEEEEEECCCCEEEECCCCCCEEEEEEEECCCCEECCCCCCCCCCCC
T ss_conf 83276203456640799850578622175646540489978985356506786047999998176176265454447874
Q ss_pred CEECCCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHCC
Q ss_conf 30212431111442235776411688776218999999389617779999999999998887622444432210000000
Q gi|254780237|r 169 GLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVK 248 (340)
Q Consensus 169 g~i~iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~~~~~~~~~~~~~~~~ 248 (340)
|.|++|+.|+||++|+|.|+++|++++++||+|.+++|||||+.|.+|+..|++||.+|+..|.++.+.......+..
T Consensus 158 ~~i~~D~~~spv~kvqy~ve~~r~~~~~~~Dhl~~~~~T~gsi~~~~a~~~aa~il~e~~~~~~~~~~~~~~~~~e~~-- 235 (317)
T COG0202 158 GPIAVDAPFSPVRKVQYIVEEARVGQGTDKDHLKWEPETNGSIRPEEALAIAAKILIEHLEVFVELCPKAVEIEEEKP-- 235 (317)
T ss_pred EEEECCCCEEEEEECEEEEEEEEEECCCCCEEEEEEEEECCEEEHHHHHHHHHHHHHHHHHHHHHHCCCCCCEECCCC--
T ss_conf 064079840366412079986798446774069999764637502799999999889999998753655440101565--
Q ss_pred CCHHHHHHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCH
Q ss_conf 001123331112210110588898988398371888744988886188988644999999999808312676878986
Q gi|254780237|r 249 SLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPP 326 (340)
Q Consensus 249 ~~~~~~~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~~~~~ 326 (340)
..+....+..+|++|+||+|++||||+++|++++||+++++.+|++++|||+||++||+++|+++||.|||+.++|++
T Consensus 236 ~~~~~~~~~~~I~~l~lsvrs~ncLk~~~i~~i~~L~~~se~~l~~v~n~G~ksleEi~~kl~~~~l~l~~~~e~~~~ 313 (317)
T COG0202 236 EFPILLVLEAPIDELDLSVRSYNCLKREGIETIGELVQRTEEELLKVENLGKKSLEEIKEKLAELGLELGMELENWPP 313 (317)
T ss_pred CCCCCCCCCCCCCCCCCCEEEEHHHCCCCCHHHHHHHHCCHHHHHCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHCCC
T ss_conf 442332334653412313335012311581146877745798885043656699999999999851332356400156
No 5
>cd06928 RNAP_alpha_NTD N-terminal domain of the Alpha subunit of Bacterial RNA polymerase. The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bac
Probab=100.00 E-value=0 Score=570.42 Aligned_cols=212 Identities=50% Similarity=0.813 Sum_probs=206.7
Q ss_pred CCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCEEEECC-
Q ss_conf 3678881589999616975667888999998741698306889998871443146646244499999840114177727-
Q gi|254780237|r 20 LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG- 98 (340)
Q Consensus 20 ~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI~gv~HEfs~i~GV~EDV~eIiLNLK~I~~k~~~- 98 (340)
+++.+.+||||+++||+||||+||||||||+||||++|+|||+|||+|+.|||++||||+|||+||+||||+|+|+...
T Consensus 3 ~~~~~~~yg~f~i~Pl~~G~g~TlGnaLRR~LLs~i~G~ait~vkI~gv~hEfs~i~GV~Edv~~IlLNLK~i~~~~~~~ 82 (215)
T cd06928 3 VENKRENYGRFVIEPLERGQGTTLGNALRRVLLSSLPGAAITAVKIEGVLHEFSTIPGVREDVLEILLNLKEIVFKSDSE 82 (215)
T ss_pred CCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHEEEEECCC
T ss_conf 01388857799996588972614678999988756984289999999942102348882340899997565049995279
Q ss_pred CCCEEEEEEEECCEEEEEEEEECCCCEEEECCCEEEEEECCCCEEEEEEEEECCCCCEECCCCCCCCCCCCEECCCCCHH
Q ss_conf 98279999994471699633513898599888808999778964999999746876320344446557543021243111
Q gi|254780237|r 99 DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS 178 (340)
Q Consensus 99 ~~~~~~~l~~~Gp~~vtA~Di~~p~~veivNpd~~IaTl~~~~~l~iel~ie~G~GY~~~e~~~~~~~~ig~i~iDa~Fs 178 (340)
++++.++++++||++|||+||++|++++|+||||||||+++++.|+||++|++|+||++++.++....++|+|++||+||
T Consensus 83 ~~~~~~~l~~~Gp~~vtA~Di~~p~~ieivNpdq~IaTl~~~~~l~~el~i~~G~GY~~~~~~~~~~~~~g~i~iDa~Fs 162 (215)
T cd06928 83 DEPQVLRLKVKGPGVVTAADIELPSGVEIVNPDQYIATLTEDASLEMELRIEKGRGYVPAEENKSEEKPIGFIPIDAIFS 162 (215)
T ss_pred CCCEEEEEEEECCEEEEEEHCCCCCCEEEECCCEEEEEECCCCEEEEEEEEECCEEEEEHHHCCCCCCCCCEEECCCCCC
T ss_conf 98489999970680599203058886699689979999778965999999989642467444466667675087687554
Q ss_pred EEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 14422357764116887762189999993896177799999999999988876
Q gi|254780237|r 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231 (340)
Q Consensus 179 PV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f 231 (340)
||+||||.|+++|++++++||+|+|||||||||+|++||++||++|++||.+|
T Consensus 163 PV~~Vny~Ve~~~~~~~~~~e~L~lEI~TnGsi~P~~Al~~Aa~iL~~~~~~f 215 (215)
T cd06928 163 PVRKVNYSVESTRVGQRTDYEKLILEIWTNGSISPEEALAQAAKILINHFSPF 215 (215)
T ss_pred CEEEEEEEEEEEECCCCCCCEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHCC
T ss_conf 64799999999405889874699999998998999999999999999986269
No 6
>smart00662 RPOLD RNA polymerases D. DNA-directed RNA polymerase subunit D and bacterial alpha chain
Probab=100.00 E-value=0 Score=335.61 Aligned_cols=195 Identities=40% Similarity=0.639 Sum_probs=179.3
Q ss_pred EEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCEEEECCC-------
Q ss_conf 5899996169756678889999987416983068899988714431466462444999998401141777279-------
Q gi|254780237|r 27 RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD------- 99 (340)
Q Consensus 27 ~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI~gv~HEfs~i~GV~EDV~eIiLNLK~I~~k~~~~------- 99 (340)
|+||+++| ||+|+||||||+|||++||+||++|+|+| +++|+.|+|+++.||||.|+++.+..
T Consensus 1 ~~kF~l~~----~~~tiaNALRR~lLseip~~AI~~V~I~~------n~s~l~eevl~~rL~Lipi~~~~~~~~~~~~~~ 70 (224)
T smart00662 1 RAKFVLEP----YGLTLANALRRVLLSSVPGMAVTEVEIEG------NTSGVQDEVLAHRLGLKPLASDPDGDEYQRDCE 70 (224)
T ss_pred CCEEEEEC----CCCHHHHHHHHHHHHCCCCEEEEEEEEEE------CCCCCHHHHHHHHHCCCEEEEECCCCCCCCCCC
T ss_conf 96899968----87157999999998659540579999980------898864679999846830687424444443322
Q ss_pred -------CCEEEEEEEECCEEEEEEEEECC--CCEEEECCCEEEEEECCCCEEEEEEEEECCCCCEECCCCCC---CCCC
Q ss_conf -------82799999944716996335138--98599888808999778964999999746876320344446---5575
Q gi|254780237|r 100 -------SHKRVTIFKRGPGVVTAGDIQTV--NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDP 167 (340)
Q Consensus 100 -------~~~~~~l~~~Gp~~vtA~Di~~p--~~veivNpd~~IaTl~~~~~l~iel~ie~G~GY~~~e~~~~---~~~~ 167 (340)
.....+|+++||++|||+||++| ++++++||++|||+|..+..|+|++++..|+||..+..+.. ....
T Consensus 71 ~~~~~~~~~v~~~L~~~gp~~V~a~Dl~~~~~~~v~~vn~~i~I~~L~~gq~l~~~~~~~~G~G~~hak~~p~~~~~~~~ 150 (224)
T smart00662 71 CEEGCEKCSVTLTLDVKGPGEVTAGDLKSDSDPDVEIVNPDIPIAKLREGQELELEARAEKGRGYVHAKWSPVSTVEYRY 150 (224)
T ss_pred CCCCCCCCEEEEEEEEECCCEEEHHHCCCCCCCCCEECCCCEEEEEECCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCC
T ss_conf 24578773699999985464468566104788971760899089996799759999999956721102106666433442
Q ss_pred CCEECCCCCHHEEEEEEEEEEEECCCCCCC----------CCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 430212431111442235776411688776----------2189999993896177799999999999988876
Q gi|254780237|r 168 IGLITIDALYSPIKKVSYTVESAREGQVLD----------YDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231 (340)
Q Consensus 168 ig~i~iDa~FsPV~~Vny~Ve~~rvg~~t~----------~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f 231 (340)
.+.|++|+.|+|+++|+|.++..|++++++ +|+++|+|||||+++|++|+.+|+++|++||..|
T Consensus 151 ~~~i~id~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~f~IeT~Gsi~p~~al~~A~~iL~~kl~~f 224 (224)
T smart00662 151 IPRIPVDASFSPVDRVAYQVECPRVVQRTDCCRECDEGEEYDKLIFDVETNGSLKPEEAVLEAAKILKEKLEAF 224 (224)
T ss_pred CCEEEECCCCCHHHEEEEEEECCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHCC
T ss_conf 20354025227012353244267553424443000135888779999995787499999999999999997539
No 7
>pfam01000 RNA_pol_A_bac RNA polymerase Rpb3/RpoA insert domain. Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal
Probab=100.00 E-value=5.8e-37 Score=259.57 Aligned_cols=115 Identities=40% Similarity=0.675 Sum_probs=108.7
Q ss_pred EEECCCCCCCCCCCCCHHHHHHHHHHHCCCEEEECCCC--CEEEEEEEECCEEEEEEEEECCCCEEEECCCEEEEEECCC
Q ss_conf 99887144314664624449999984011417772798--2799999944716996335138985998888089997789
Q gi|254780237|r 63 VQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDS--HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140 (340)
Q Consensus 63 vkI~gv~HEfs~i~GV~EDV~eIiLNLK~I~~k~~~~~--~~~~~l~~~Gp~~vtA~Di~~p~~veivNpd~~IaTl~~~ 140 (340)
|||+||.|||++||||+|||++|+||||+++|+++.++ +.+++|+++||++|||+||++|++++|+|||||||||+++
T Consensus 1 V~I~gv~HEf~~I~GV~Edv~~IilNlK~i~~~~~~~~~~~~~~~l~~~gp~~VtA~Di~~~~~veivnpd~~Iatl~~~ 80 (117)
T pfam01000 1 VYINGVAHEFGLIPGVSEDVLEIILNLKELVCKIEGCEECSVTLTLDVKGPGEVTAGDLESDPDVEIVNPDILIATLRKG 80 (117)
T ss_pred CEECCEEEEECCCCCCHHHHHHHHHCCCCCEEEECCCCCCEEEEEEEEECCCEEEEEEECCCCCEEECCCCEEEEEECCC
T ss_conf 93787675612589832609999736465399832688815999999745838994016168854864987599997899
Q ss_pred CEEEEEEEEECCCCCEECCCCCCCCCCCCEECCCCCHH
Q ss_conf 64999999746876320344446557543021243111
Q gi|254780237|r 141 AVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS 178 (340)
Q Consensus 141 ~~l~iel~ie~G~GY~~~e~~~~~~~~ig~i~iDa~Fs 178 (340)
..|+||+++++||||+++++|+.... +|+||+||+||
T Consensus 81 ~~l~~e~~i~~GrGY~~ae~~~~~~~-~g~i~iDa~fs 117 (117)
T pfam01000 81 QELELEAYAKKGRGYVHAKENKEDEE-EGRIPVDSIFS 117 (117)
T ss_pred CEEEEEEEEECCCCCCCHHHCCCCCC-CCEEEECCCCC
T ss_conf 78999999989897315544688899-99898263469
No 8
>cd07030 RNAP_D D subunit of Archaeal RNA polymerase. The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit w
Probab=99.89 E-value=6.7e-22 Score=162.06 Aligned_cols=206 Identities=20% Similarity=0.282 Sum_probs=153.7
Q ss_pred CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEE---------CCCCCCCCCCCCCHHHHHHHHHHHCCC
Q ss_conf 78881589999616975667888999998741698306889998---------871443146646244499999840114
Q gi|254780237|r 22 QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI---------DGVLHEISSIKGVHEDLTDIILNIKGI 92 (340)
Q Consensus 22 ~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI---------~gv~HEfs~i~GV~EDV~eIiLNLK~I 92 (340)
+.++++.+|.+. |....++|||||+|||++|..||..|.| +-+.|-.+.||-..+..... .....
T Consensus 7 ~~~~~~~~F~l~----~~~~s~aNalRRillsevPt~Aid~V~i~~NtS~l~DE~laHRLglIPi~~~~~~~~--~~~~~ 80 (259)
T cd07030 7 ELDDDRARFVLE----GVPPAFANAIRRAIISEVPTLAIDDVNIYENTSVLFDEMLAHRLGLIPLRTDLDLYK--YRSEC 80 (259)
T ss_pred ECCCCEEEEEEE----CCCHHHHHHHHHHHHHCCCEEEEEEEEEEECCCCCCCHHHHHHHCCCCCCCCHHHHH--CCCCC
T ss_conf 768987999997----898999999999998739844778999997885254278887632654323644420--34432
Q ss_pred EEEE--CCCCCEEEEEEEECCEEEEEEEEEC-CCCEEEECCCEEEEEECCCCEEEEEEEEECCCCC--------------
Q ss_conf 1777--2798279999994471699633513-8985998888089997789649999997468763--------------
Q gi|254780237|r 93 NLKM--SGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGY-------------- 155 (340)
Q Consensus 93 ~~k~--~~~~~~~~~l~~~Gp~~vtA~Di~~-p~~veivNpd~~IaTl~~~~~l~iel~ie~G~GY-------------- 155 (340)
.... .+....+.+|+++||+.|+|+|++. ++.++.++|+..||+|..|-.|+|+.+...|+|.
T Consensus 81 ~~~~~~~~~~~v~~~l~~~~~~~v~s~dl~~~d~~v~p~~~dI~I~kL~~GQ~l~l~~~a~~G~Gk~HaKw~pv~~~~y~ 160 (259)
T cd07030 81 SCGGAGCPLCTVTLTLSVEGPGTVYSGDLKSSDPDVKPVYDNIPIVKLGKGQKLVLEAYARLGRGKEHAKWQPTTACGYK 160 (259)
T ss_pred CCCCCCCCCCEEEEEEEEECCCEEECCCCCCCCCCCEECCCCEEEEEECCCCEEEEEEEEECCCCCCCCCCCCCEEEEEE
T ss_conf 23568998738999999864956880214337998256689827999579998999999951533205402651489984
Q ss_pred -EECCC---------CCCCCCCCCEECCCCCHHEEEEEEE---------EEEEECCCCCCCCCEEEEEEEECCCCCHHHH
Q ss_conf -20344---------4465575430212431111442235---------7764116887762189999993896177799
Q gi|254780237|r 156 -VPAKH---------HRTENDPIGLITIDALYSPIKKVSY---------TVESAREGQVLDYDKLSMTIDTDGSITGEDS 216 (340)
Q Consensus 156 -~~~e~---------~~~~~~~ig~i~iDa~FsPV~~Vny---------~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eA 216 (340)
.|.-. ...+..|.+.+.++.....+.+... ..+.-++....+.++.+|.|||+|+++|+++
T Consensus 161 ~~p~i~~~~~~~~~~~~~~~~p~~v~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~I~~~~~~d~F~F~VES~G~l~p~~i 240 (259)
T cd07030 161 YYPVIEIDEDCDGCGKCVEECPRGVLELEEGKVVVEDLEDCSLCKLCERACDAGAIRVGWDEDRFIFEVESDGSLPPKEI 240 (259)
T ss_pred CCCCEEEECCCHHHHHHHHHCCCCCCCCCCCCCEECCCCCCCHHHHHHHHCCCCCEEEEEECCEEEEEEEECCCCCHHHH
T ss_conf 04416861531577887765754421234575301354212077899864246834898508979999990387299999
Q ss_pred HHHHHHHHHHHHHHHHC
Q ss_conf 99999999998887622
Q gi|254780237|r 217 VALASRILQDQLGMFIN 233 (340)
Q Consensus 217 l~~Aa~iL~~~l~~f~~ 233 (340)
+.+|+++|++.+.-|.+
T Consensus 241 v~~A~~iL~~kl~~l~~ 257 (259)
T cd07030 241 LLEALRILKEKADELIE 257 (259)
T ss_pred HHHHHHHHHHHHHHHHH
T ss_conf 99999999999999996
No 9
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional
Probab=99.88 E-value=4.5e-21 Score=156.67 Aligned_cols=200 Identities=21% Similarity=0.331 Sum_probs=149.3
Q ss_pred CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEE---------CCCCCCCCCCCCCHHHHHHHHHHHCCC
Q ss_conf 78881589999616975667888999998741698306889998---------871443146646244499999840114
Q gi|254780237|r 22 QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI---------DGVLHEISSIKGVHEDLTDIILNIKGI 92 (340)
Q Consensus 22 ~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI---------~gv~HEfs~i~GV~EDV~eIiLNLK~I 92 (340)
+.++++.+|.+.. .-..++|||||+|||++|..||..|.| +-+.|-...|| |.-+++..
T Consensus 7 ~~~~~~~~F~l~~----~~~s~aNalRRillseVPt~AId~V~I~~NtS~l~DE~iaHRLgLIP--------l~~~~~~~ 74 (265)
T PRK00783 7 ELSDDSAKFVLSG----VTPAFANALRRAMIAEVPTLAIEDVNIYDNTSALFDEVLAHRLGLIP--------LKTDLDRF 74 (265)
T ss_pred ECCCCEEEEEEEC----CCHHHHHHHHHHHHHCCCEEEEEEEEEEECCCCCCCCHHHEEEEEEE--------ECCCHHHC
T ss_conf 8779889999978----98899889999998739702799999985873145533316861166--------01365441
Q ss_pred EEEEC--------CCCCEEEEEEEECCEEEEEEEEEC-CCCEEEECCCEEEEEECCCCEEEEEEEEECCCCCEECCCCC-
Q ss_conf 17772--------798279999994471699633513-89859988880899977896499999974687632034444-
Q gi|254780237|r 93 NLKMS--------GDSHKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHR- 162 (340)
Q Consensus 93 ~~k~~--------~~~~~~~~l~~~Gp~~vtA~Di~~-p~~veivNpd~~IaTl~~~~~l~iel~ie~G~GY~~~e~~~- 162 (340)
.+... ...+...+|+++||+.|+|+|++. .+.+..++|+-.||.|..|-.++++.+...|+|..-|..+.
T Consensus 75 ~~~~~~~~~~~~~~~~~v~~~l~~~~~~~V~s~dl~~~d~~v~pv~~~I~I~kL~~GQ~i~l~a~a~~G~Gk~HAKwsPv 154 (265)
T PRK00783 75 VPRSECSCGGAGCPLCTVTLSLSAEGPGVVYSGDLISSDPDVKPVDPNIPIVKLKEGQKLVLEAVAKLGRGKEHAKWQPT 154 (265)
T ss_pred EECCCCCCCCCCCCCEEEEEEEEEECCCEEEHHHCCCCCCCCEECCCCEEEEEECCCCEEEEEEEEECCCCCCCCEECCC
T ss_conf 52144666666898638999999623863777787147997152489903899079998999999982444316352662
Q ss_pred -----------------------CCCCCCCEECCCC-----------CHHEEEEEEEEEEEECCCCCCCCCEEEEEEEEC
Q ss_conf -----------------------6557543021243-----------111144223577641168877621899999938
Q gi|254780237|r 163 -----------------------TENDPIGLITIDA-----------LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTD 208 (340)
Q Consensus 163 -----------------------~~~~~ig~i~iDa-----------~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~Tn 208 (340)
....+.+.+.++. .+++.+.+.+..+.-++....+.++.+|.|+|+
T Consensus 155 ~~~~y~~~p~i~i~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~~~~~d~f~F~VES~ 234 (265)
T PRK00783 155 TVCGYKYYPEITISEDCDGCGECKEECPRSVLEVEENKVEVTEEDLEKCSLCRLCERACEGNAIRVGADENRFIFTVETD 234 (265)
T ss_pred EEEEEEECCEEEECCCCHHHHHHHHHCCCCCCCCCCCCEEEEECCHHHCCHHHHHEECCCCCCEEEEEECCEEEEEEECC
T ss_conf 58999744226863661078888765777622135882168744612254223420016667268996189799999767
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9617779999999999998887622
Q gi|254780237|r 209 GSITGEDSVALASRILQDQLGMFIN 233 (340)
Q Consensus 209 Gsi~P~eAl~~Aa~iL~~~l~~f~~ 233 (340)
|+++|++++.+|+++|++.+.-|.+
T Consensus 235 G~l~p~~i~~~A~~iL~~Kl~~l~~ 259 (265)
T PRK00783 235 GSLPVKEILLIALKILKDKADELIE 259 (265)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 8889999999999999999999999
No 10
>pfam01193 RNA_pol_L RNA polymerase Rpb3/Rpb11 dimerization domain. The two eukaryotic subunits Rpb3 and Rpb11 dimerize to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerization domain of the alpha subunit/Rpb3 is interrupted by an insert domain (pfam01000). Some of the alpha subunits also contain iron-sulphur binding domains (pfam00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp.
Probab=99.86 E-value=1.2e-21 Score=160.34 Aligned_cols=91 Identities=53% Similarity=0.776 Sum_probs=87.1
Q ss_pred EECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCEEEECCCCCEEEEEEEECC
Q ss_conf 96169756678889999987416983068899988714431466462444999998401141777279827999999447
Q gi|254780237|r 32 AEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGP 111 (340)
Q Consensus 32 ~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI~gv~HEfs~i~GV~EDV~eIiLNLK~I~~k~~~~~~~~~~l~~~Gp 111 (340)
++|+.+|+++|+||+|||+||+++||.||++
T Consensus 1 i~~~~~g~~~t~~NaLRr~Ll~evp~~ai~~------------------------------------------------- 31 (91)
T pfam01193 1 IEFLLEGEDHTLGNALRRILLSEVPGVAIAG------------------------------------------------- 31 (91)
T ss_pred CCCCCCCCCEEHHHHHHHHHHHCCCCCEEEE-------------------------------------------------
T ss_conf 9522155530067899999885188744785-------------------------------------------------
Q ss_pred EEEEEEEEECCCCEEEECCCEEEEEECCCCEEEEEEEEECCCCCEECCCCCCCCCCCCEECCCCCHHEEEEEEEEEEEEC
Q ss_conf 16996335138985998888089997789649999997468763203444465575430212431111442235776411
Q gi|254780237|r 112 GVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAR 191 (340)
Q Consensus 112 ~~vtA~Di~~p~~veivNpd~~IaTl~~~~~l~iel~ie~G~GY~~~e~~~~~~~~ig~i~iDa~FsPV~~Vny~Ve~~r 191 (340)
||.|+||.+|+|.+++.+
T Consensus 32 --------------------------------------------------------------~a~~~Pv~~v~y~~~~~~ 49 (91)
T pfam01193 32 --------------------------------------------------------------DAKFSPVKKVNYRVEPTR 49 (91)
T ss_pred --------------------------------------------------------------CCCCCCCEEEEEEEECCC
T ss_conf --------------------------------------------------------------166678147766883422
Q ss_pred CCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 688776218999999389617779999999999998887622
Q gi|254780237|r 192 EGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233 (340)
Q Consensus 192 vg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~ 233 (340)
++...++|+++|+|||||+++|++|+.+|+++|++++..|.+
T Consensus 50 ~~~~~~~~~~~~~IeT~Gsi~p~~~l~~A~~~L~~~~~~~~~ 91 (91)
T pfam01193 50 VGQNTDYDKLILEIETDGSITPEEALLEAAKILIDKLDELLE 91 (91)
T ss_pred CCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHCC
T ss_conf 067677505999999799889999999999999999987629
No 11
>cd07028 RNAP_RPB3_like RPB3 subunit of RNA polymerase. The eukaryotic RPB3 subunit of RNA polymerase (RNAP), as well as its archaeal (D subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar to the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and
Probab=99.78 E-value=5.3e-17 Score=130.31 Aligned_cols=185 Identities=18% Similarity=0.288 Sum_probs=142.9
Q ss_pred CCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEE---------CCCCCCCCCCCCCHHHHHHHHHHHC
Q ss_conf 3678881589999616975667888999998741698306889998---------8714431466462444999998401
Q gi|254780237|r 20 LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI---------DGVLHEISSIKGVHEDLTDIILNIK 90 (340)
Q Consensus 20 ~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI---------~gv~HEfs~i~GV~EDV~eIiLNLK 90 (340)
+-+.++++-+|.+.- .-..++|||||+|+|++|-.||..|.| +-..|-...||-..++..+...+-.
T Consensus 5 i~~~~~~~~~F~l~g----~d~s~aNaLRRi~iseVPt~AId~V~i~~NTSvl~DE~laHRLGLIPl~s~~~~~~~~~~~ 80 (212)
T cd07028 5 IREADKDNVDFILSG----VDLAMANALRRVMIAEVPTMAVDSVEVETNTSVLADEILAHRLGLIPLQSMDILQLYRSPE 80 (212)
T ss_pred EEECCCCEEEEEEEC----CCHHHHHHHHHHHHHCCCEEEEEEEEEEECCCCCCCHHHHHEECCCCCCCCCCHHHHCCCC
T ss_conf 997589779999968----9999999999999875974267799999788626546665130352013451023320733
Q ss_pred C-CEEEEC-CCCCEEEEEEEECCE----EEEEEEEECCC------CEEEECCCEEEEEECCCCEEEEEEEEECCCCCEEC
Q ss_conf 1-417772-798279999994471----69963351389------85998888089997789649999997468763203
Q gi|254780237|r 91 G-INLKMS-GDSHKRVTIFKRGPG----VVTAGDIQTVN------DIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158 (340)
Q Consensus 91 ~-I~~k~~-~~~~~~~~l~~~Gp~----~vtA~Di~~p~------~veivNpd~~IaTl~~~~~l~iel~ie~G~GY~~~ 158 (340)
. ...... ..-....++.++|++ .|+++|++..+ .+.-++++-.|+.|..|-.++++++..+|+|+..
T Consensus 81 ~~~~~~~~~~~~~v~~~l~~~~~~~~~~~V~s~dl~~~~~~~~~~~~~pv~~~I~I~kL~~gQ~I~l~a~a~kG~Gk~H- 159 (212)
T cd07028 81 EDCECEDHCDKCSVVLTLQAFAESESTTNVYSKDLVIVSNLMGRNIGHPIIQDILICKLRKGQEIKLTCVAKKGIGKEH- 159 (212)
T ss_pred CCCCCCCCCCCEEEEEEEECCCCCCCCCEEECHHCEECCCCCCCCCCCCCCCCCEEEEECCCCEEEEEEEEEECCCCCC-
T ss_conf 3775567776469999996458999874498400788477777887633699958999389998999999994405646-
Q ss_pred CCCCCCCCCCCEECCCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 44446557543021243111144223577641168877621899999938961777999999999999888762
Q gi|254780237|r 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232 (340)
Q Consensus 159 e~~~~~~~~ig~i~iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~ 232 (340)
|-||||..|.|..++.+ |+.+|.|+|.|++.|++.+.+|+++|++-+.-|+
T Consensus 160 ----------------AKwsPvs~~~y~~~p~~-------d~f~f~vES~G~l~p~~i~~~A~~iL~~K~~~~~ 210 (212)
T cd07028 160 ----------------AKFGPVAAIEFRYDPVA-------DTYIMNVESVGSLPPDQVVVEAIKTLQKKVASIL 210 (212)
T ss_pred ----------------EEECCCEEEEEEEEECC-------CEEEEEEEEECCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf ----------------08677168999984048-------6699999851799989999999999999999985
No 12
>pfam03118 RNA_pol_A_CTD Bacterial RNA polymerase, alpha chain C terminal domain. The alpha subunit of RNA polymerase consists of two independently folded domains, referred to as amino-terminal and carboxyl terminal domains. The amino terminal domain is involved in the interaction with the other subunits of the RNA polymerase. The carboxyl-terminal domain interacts with the DNA and activators. The amino acid sequence of the alpha subunit is conserved in prokaryotic and chloroplast RNA polymerases. There are three regions of particularly strong conservation, two in the amino-terminal and one in the carboxyl- terminal.
Probab=99.76 E-value=7.2e-19 Score=142.41 Aligned_cols=60 Identities=50% Similarity=0.734 Sum_probs=57.4
Q ss_pred HHHHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHH
Q ss_conf 233311122101105888989883983718887449888861889886449999999998
Q gi|254780237|r 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312 (340)
Q Consensus 253 ~~~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~ 312 (340)
...+.++|++|+||+|++|||+++||+|||||+++|++||+++||||+||++||+++|++
T Consensus 3 ~~~l~~~I~~L~LS~R~~N~Lk~~~I~tv~dL~~~s~~dLl~i~N~G~kSl~EI~~~L~~ 62 (62)
T pfam03118 3 LALLSIPIEELELSVRSYNCLKRAGINTVGDLLSKSEEDLLKIKNFGKKSLEEIKEKLEE 62 (62)
T ss_pred HHHHCCCHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCC
T ss_conf 888639899816868999999894996799998589999974889868579999999829
No 13
>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase. The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the
Probab=99.61 E-value=6.6e-16 Score=123.24 Aligned_cols=82 Identities=28% Similarity=0.303 Sum_probs=76.6
Q ss_pred EECCCCCEECCCCCCCCCCCCEECCCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHH
Q ss_conf 74687632034444655754302124311114422357764116887762189999993896177799999999999988
Q gi|254780237|r 149 VSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQL 228 (340)
Q Consensus 149 ie~G~GY~~~e~~~~~~~~ig~i~iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l 228 (340)
+++++||+++..++.+-...|.+..++.|+||.+|.|.|+..+++++|+|||++|+|||||+++|++||.+|+++|++++
T Consensus 4 i~~~~~~~tf~~~~EDHTlgN~Lr~~l~~~PV~~~~Y~v~hp~~~~~t~~dk~~l~IqT~g~i~p~eAl~~A~~~L~~~l 83 (86)
T cd00460 4 LEKEKNYVDFVLENEDHTLGNSLRRILLKSPVEFAAYYVEHPVKLQRTDEDKFILRIETVGSIPPEEALRRAVEILRKKL 83 (86)
T ss_pred EECCCCEEEEEEECCCCHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHH
T ss_conf 85289859999947885278899999801983789987588765543676617999998999999999999999999987
Q ss_pred HH
Q ss_conf 87
Q gi|254780237|r 229 GM 230 (340)
Q Consensus 229 ~~ 230 (340)
..
T Consensus 84 ~~ 85 (86)
T cd00460 84 EH 85 (86)
T ss_pred HC
T ss_conf 14
No 14
>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB3 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=99.50 E-value=6.2e-12 Score=97.54 Aligned_cols=190 Identities=18% Similarity=0.283 Sum_probs=123.3
Q ss_pred CCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECC---------CCCCCCCCCCCHHHHHHHHHHHC
Q ss_conf 367888158999961697566788899999874169830688999887---------14431466462444999998401
Q gi|254780237|r 20 LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIKGVHEDLTDIILNIK 90 (340)
Q Consensus 20 ~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI~g---------v~HEfs~i~GV~EDV~eIiLNLK 90 (340)
+-+.+++.-+|.+. |.-..++|||||+|||.+|-.||-.|.|.- ..|--..||=..+...+..-..+
T Consensus 5 i~~~~~~~l~F~l~----~~~~s~aNaLRR~~iseVPtlAId~V~I~~NTS~l~DE~laHRLgLIPi~~~~~~~~~~~~~ 80 (265)
T cd07031 5 ITELTDDKVKFILE----NTDLSVANSLRRVMIAEVPTLAIDLVEIEENTSVLHDEFIAHRLGLIPLTSDDVDEFLYYSR 80 (265)
T ss_pred EEECCCCEEEEEEE----CCCHHHHHHHHHHHHHCCCEEEEEEEEEEECCCCCCCHHHHHHHCCCCCCCCCCHHCCCCCC
T ss_conf 99757977999995----89899999999999865984589899999788635447888744363112563100023443
Q ss_pred CCEEEEC-CCCCEEEEEEE----ECCEEEEEEEEECCC-CE--------------EEECCCEEEEEECCCCEEEEEEEEE
Q ss_conf 1417772-79827999999----447169963351389-85--------------9988880899977896499999974
Q gi|254780237|r 91 GINLKMS-GDSHKRVTIFK----RGPGVVTAGDIQTVN-DI--------------EVLNPDHVICNLDVDAVVRMELTVS 150 (340)
Q Consensus 91 ~I~~k~~-~~~~~~~~l~~----~Gp~~vtA~Di~~p~-~v--------------eivNpd~~IaTl~~~~~l~iel~ie 150 (340)
...-... +......+|++ .||..||++||+..+ .. ...+++-.|+.|..|-.++++....
T Consensus 81 ~~~~~~~~~~~~v~~~L~v~~~~~~~~~V~s~Dl~~~~~~~~~~~~~~~~~~~~~~~~~~~I~I~kL~pGQ~i~l~a~a~ 160 (265)
T cd07031 81 DCDCDEFCDKCSVELTLDVKCTGDQTREVTSRDLVSSGPKVNDVVPVPIRNDSEDNGEEDGILIVKLRKGQELKLRCIAK 160 (265)
T ss_pred CCCCCCCCCCCEEEEEEEEEECCCCCEEEEHHHCEECCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCEEEEEEEEE
T ss_conf 47655689775799999989479997489925569857776654564422467776567996799957999899999997
Q ss_pred CCCCCEECCCCCCCCCCCCEECCCCCHHEEEEEEEEEEE------------------------------------ECCCC
Q ss_conf 687632034444655754302124311114422357764------------------------------------11688
Q gi|254780237|r 151 KGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVES------------------------------------AREGQ 194 (340)
Q Consensus 151 ~G~GY~~~e~~~~~~~~ig~i~iDa~FsPV~~Vny~Ve~------------------------------------~rvg~ 194 (340)
.|+|-.-| -|+||--+.|.-.+ .++++
T Consensus 161 ~G~Gk~HA-----------------KwsPV~~~~Y~~~p~i~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~ 223 (265)
T cd07031 161 KGIGKEHA-----------------KWSPTAAVTFEYDPDNALRHTDYWYLEDEDKEWPKSENACIEEPPEKDALFDIDA 223 (265)
T ss_pred ECCCCCCC-----------------CCCCCEEEEEEECCCEEECCHHHCCCCHHHHHCCCCHHHHHHCCCCCCCCEEEEE
T ss_conf 35612056-----------------0066247997525533660101123212344336406777533411267478874
Q ss_pred CCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 77621899999938961777999999999999888762
Q gi|254780237|r 195 VLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232 (340)
Q Consensus 195 ~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~ 232 (340)
.-++.+|.|+|.|+++|++.+.+|.++|++-+.-+.
T Consensus 224 --~~~~f~F~VES~G~l~p~~i~~~A~~iL~~K~~~l~ 259 (265)
T cd07031 224 --KPDKFYFNVESTGALPPEQIVLSGLEILKKKLADLQ 259 (265)
T ss_pred --ECCEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf --089799999654775999999999999999999999
No 15
>cd07032 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC40 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC40 subunit is the equivalent of the RPB3 subunit of RNAP II. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The RPB3 subun
Probab=99.48 E-value=2.2e-11 Score=93.93 Aligned_cols=197 Identities=22% Similarity=0.277 Sum_probs=121.3
Q ss_pred CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEEC---CC------CCCCCCCCCCHHHHHHHHHHHCCC
Q ss_conf 788815899996169756678889999987416983068899988---71------443146646244499999840114
Q gi|254780237|r 22 QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQID---GV------LHEISSIKGVHEDLTDIILNIKGI 92 (340)
Q Consensus 22 ~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI~---gv------~HEfs~i~GV~EDV~eIiLNLK~I 92 (340)
+.+++.-+|.+. |.-..++|||||++||++|-.||-.|.|. ++ .|--..||=-- | .+..
T Consensus 7 ~~~~~~~~F~L~----~~d~s~aNaLRR~~lseVPtlAId~V~i~eNtS~l~DE~iaHRLglIPl~~-d-------~~~~ 74 (291)
T cd07032 7 SLSDEELEFDLI----GVDASIANAFRRILLAEVPTMAIEKVYIYNNTSVIQDEVLAHRLGLIPIKA-D-------PRLF 74 (291)
T ss_pred ECCCCEEEEEEE----CCCHHHHHHHHHHHHHCCCEEEEEEEEEEECCCCCCHHHHHHHHCCCCCCC-C-------HHHC
T ss_conf 668977999995----798999999999998739857899999997786361489887643633233-8-------6661
Q ss_pred EEEEC------CCCCEEEEEEEECC------------------EEEEEEEEE-----------CCCCEEEECCCEEEEEE
Q ss_conf 17772------79827999999447------------------169963351-----------38985998888089997
Q gi|254780237|r 93 NLKMS------GDSHKRVTIFKRGP------------------GVVTAGDIQ-----------TVNDIEVLNPDHVICNL 137 (340)
Q Consensus 93 ~~k~~------~~~~~~~~l~~~Gp------------------~~vtA~Di~-----------~p~~veivNpd~~IaTl 137 (340)
.+... +.......|+++++ ..|+++|++ ....+..++++-.|+.|
T Consensus 75 ~~~~~~~~~~~~~~~v~~~l~v~~~~~~~~~~~~~~~~~~~~~~~V~s~dl~~~p~~~~~~~~~~~~~~~~~~~I~I~kL 154 (291)
T cd07032 75 EYREDSDDEPTEENTLVFELKVKCTRNPNAPKDSTDPDELYINHKVYSGDLKWVPIGSQEKRFADNPIRPVHPDILIAKL 154 (291)
T ss_pred CCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCCCEEECCCCEECCCCCCCCCCCCCCCCCCCCCCEEEEE
T ss_conf 35564023689875799999966367866555545654234675698000666467753434668886546899669993
Q ss_pred CCCCEEEEEEEEECCCCCEECCCCCC--------------------------CCCCCCEECCCCCHHEEEEEEEEEEEE-
Q ss_conf 78964999999746876320344446--------------------------557543021243111144223577641-
Q gi|254780237|r 138 DVDAVVRMELTVSKGHGYVPAKHHRT--------------------------ENDPIGLITIDALYSPIKKVSYTVESA- 190 (340)
Q Consensus 138 ~~~~~l~iel~ie~G~GY~~~e~~~~--------------------------~~~~ig~i~iDa~FsPV~~Vny~Ve~~- 190 (340)
..|-.|+++.+...|.|=.-|..+.. ...|.|.+-++.... .-...|.+.
T Consensus 155 ~~gQ~l~l~a~a~~G~GkeHAKw~Pv~~~~y~~~p~i~i~~~~~~~~~~~l~~~~p~~v~~~~~~~~---~~~~~v~~~~ 231 (291)
T cd07032 155 RPGQEIDLELHCVKGIGKDHAKFSPVATASYRLLPEITLLKPITGEDAEKLQKCFPPGVIDIEEVKG---KKKAVVANPR 231 (291)
T ss_pred CCCCEEEEEEEEEECCCCCCCCCCCCEEEEEEECCEEEECCCCCHHHHHHHHHHCCCCCEECCCCCC---CCEEEECCCH
T ss_conf 7999899999998555440562277168999642115773523477899999758787332146777---6527864711
Q ss_pred ---------CC-------CCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf ---------16-------88776218999999389617779999999999998887622
Q gi|254780237|r 191 ---------RE-------GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233 (340)
Q Consensus 191 ---------rv-------g~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~ 233 (340)
|. .-..+-++.+|.|+|+|+++|++.+..|..+|++.+.-|+.
T Consensus 232 ~c~~~~e~~~~~~~~~~i~~~~~~~~F~F~VES~G~l~p~~Iv~~A~~~L~~Kl~~l~~ 290 (291)
T cd07032 232 KDTLSREVLRHEEFKDKVELGRVRDHFIFSIESTGALPPDVLFLEAIKILKEKCRKLLE 290 (291)
T ss_pred HCCHHHHHHCCCCCCCCEEEEECCCEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 15412655103101565257764997999996647769999999999999999999964
No 16
>KOG1522 consensus
Probab=98.87 E-value=5.4e-07 Score=65.54 Aligned_cols=203 Identities=18% Similarity=0.259 Sum_probs=131.9
Q ss_pred EECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECC---------CCCCCCCCCCCHHHHHHHHHH
Q ss_conf 86367888158999961697566788899999874169830688999887---------144314664624449999984
Q gi|254780237|r 18 IVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG---------VLHEISSIKGVHEDLTDIILN 88 (340)
Q Consensus 18 ~~~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI~g---------v~HEfs~i~GV~EDV~eIiLN 88 (340)
+++.+.++.+.+|++.--. ..++||||||+++.+|-.||-.|.|+- +-|-...||=..+++.+
T Consensus 8 v~I~Elt~d~vkF~L~nTd----lsvANsLRRV~iaEvPTiAID~VeIe~NssVL~DEFiAHRLGLIPl~S~~~~~---- 79 (285)
T KOG1522 8 VKIRELTDDNVKFVLSNTD----LSVANSLRRVMIAEVPTIAIDLVEIEVNSSVLPDEFIAHRLGLIPLISDRIVE---- 79 (285)
T ss_pred EEEEECCCCCEEEEEECCH----HHHHHHHHHHHHHCCCEEEEEEEEEECCCCCCCHHHHHHHHCCEECCCHHHHH----
T ss_conf 5889637871689995370----88877888898751860278899983266425278888650650002003555----
Q ss_pred HCCCEEEECC-------CCCEEEEEEEEC----CEEEEEEEEEC-------------CCCEEEEC-CCEEEEEECCCCEE
Q ss_conf 0114177727-------982799999944----71699633513-------------89859988-88089997789649
Q gi|254780237|r 89 IKGINLKMSG-------DSHKRVTIFKRG----PGVVTAGDIQT-------------VNDIEVLN-PDHVICNLDVDAVV 143 (340)
Q Consensus 89 LK~I~~k~~~-------~~~~~~~l~~~G----p~~vtA~Di~~-------------p~~veivN-pd~~IaTl~~~~~l 143 (340)
+.+.-+- .-++..+|.+++ -..||+.|+.. .+..+..+ ..-.||.|-++-.|
T Consensus 80 ---l~ytrdC~C~~~C~eCSVef~L~~kc~~d~T~~VtsrDL~s~~~~v~pv~~~~~~~~~~~~e~~gilI~KLRkgQEL 156 (285)
T KOG1522 80 ---LQYTRDCECDEFCPECSVEFTLDVKCTDDQTRDVTSRDLVSLDPTVTPVDSNRGSEIDDDSESKGILIVKLRKGQEL 156 (285)
T ss_pred ---HHHCCCCCHHCCCCCCEEEEEEEEEECCCCEEEEEHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCE
T ss_conf ---34155674201487643799995065365415655676543688412344677986332334677389995068720
Q ss_pred EEEEEEECCCCCEECCCCCCC-----CCCCC--------EECCCCCH-HEEEEEEEEEEEECCCCCC----CCCEEEEEE
Q ss_conf 999997468763203444465-----57543--------02124311-1144223577641168877----621899999
Q gi|254780237|r 144 RMELTVSKGHGYVPAKHHRTE-----NDPIG--------LITIDALY-SPIKKVSYTVESAREGQVL----DYDKLSMTI 205 (340)
Q Consensus 144 ~iel~ie~G~GY~~~e~~~~~-----~~~ig--------~i~iDa~F-sPV~~Vny~Ve~~rvg~~t----~~dkL~lEI 205 (340)
++.....+|.|---|..+... .+|-+ +--.|..= .|.+...+. +..+-|..- .-|+..|.|
T Consensus 157 kLra~akKGigKeHAKWsPta~V~FeYDPdn~lrhT~y~~e~~~~~Ewp~sk~~e~~-~~~~e~~pyd~~~kpd~F~~~V 235 (285)
T KOG1522 157 KLRAIAKKGIGKEHAKWSPTAAVAFEYDPDNKLRHTLYWFEEDDLIEWPKSKNSELE-EDPEEGAPYDPEGKPDKFYFNV 235 (285)
T ss_pred EEEEEECCCCCCCCCCCCCCCEEEEEECCCHHHHCCCCCCCCCCHHHCCCCCCCCCC-CCCCCCCCCCCCCCCCEEEEEE
T ss_conf 124323025552235437761478887750765302787543313118864466778-8852358878457976699986
Q ss_pred EECCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 938961777999999999999888762
Q gi|254780237|r 206 DTDGSITGEDSVALASRILQDQLGMFI 232 (340)
Q Consensus 206 ~TnGsi~P~eAl~~Aa~iL~~~l~~f~ 232 (340)
+.-|++-|...+..+..||++-+..+.
T Consensus 236 Es~Gal~~~~iVl~gi~iLk~Kl~~l~ 262 (285)
T KOG1522 236 ESVGALPPSQIVLMGIDILKEKLAALR 262 (285)
T ss_pred EECCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 742787878979989999999999997
No 17
>PRK07758 hypothetical protein; Provisional
Probab=97.99 E-value=1e-05 Score=57.31 Aligned_cols=55 Identities=24% Similarity=0.365 Sum_probs=52.5
Q ss_pred CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf 1105888989883983718887449888861889886449999999998083126
Q gi|254780237|r 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG 318 (340)
Q Consensus 264 eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg 318 (340)
-||.-|.++|-.+||+|+.||.++|+.+|+++-++|.+|+.-+++.|++.||+|.
T Consensus 41 ~LsAPARRAL~~~GI~TLedLskytEkELL~LHGmGP~ai~~L~~aLke~GLsFK 95 (95)
T PRK07758 41 LLSAPARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSFK 95 (95)
T ss_pred HHCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCC
T ss_conf 8415889999982811499998851999999848688889999999998388779
No 18
>KOG1521 consensus
Probab=97.82 E-value=0.0024 Score=41.93 Aligned_cols=206 Identities=21% Similarity=0.294 Sum_probs=118.5
Q ss_pred HCCCCCCCEEEECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 51797420158636788815899996169756678889999987416983068899988714431466462444999998
Q gi|254780237|r 8 ELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIIL 87 (340)
Q Consensus 8 ~~~~P~~i~~~~~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI~gv~HEfs~i~GV~EDV~eIiL 87 (340)
.|.+--++.++.. ++..-.|-+ .|---.|+||+||+|++.+|..|+-.|-|..-. |.| +.-|+-==|
T Consensus 41 ~f~~~~~V~iv~~---~~~~leFDl----igIda~IANAfRRILiaEVPtmAiEkVyi~nNT---SVi---qDEvLaHRl 107 (338)
T KOG1521 41 NFKDNFKVDIVSL---DEETLEFDL----IGIDASIANAFRRILIAEVPTMAIEKVYIYNNT---SVI---QDEVLAHRL 107 (338)
T ss_pred HHHHCEEEEEEEC---CCCCEEEEE----EECCHHHHHHHHHHHHHHCCHHHEEEEEEECCC---CCC---HHHHHHHHH
T ss_conf 7623118888862---676406777----504588889999999863624400136775376---100---778888762
Q ss_pred HHCCCEE-------EECC---CC---CEEEEEEEECC------------------EEEEEEEEEC-----------CCCE
Q ss_conf 4011417-------7727---98---27999999447------------------1699633513-----------8985
Q gi|254780237|r 88 NIKGINL-------KMSG---DS---HKRVTIFKRGP------------------GVVTAGDIQT-----------VNDI 125 (340)
Q Consensus 88 NLK~I~~-------k~~~---~~---~~~~~l~~~Gp------------------~~vtA~Di~~-----------p~~v 125 (340)
-|=-|.. ..+. ++ +-..+|.++-+ ..|.++|+.+ ..-+
T Consensus 108 GLvPl~aDPrlFe~~~e~d~~~e~~ntlvF~L~VkC~~n~~a~~~~sdpk~Ly~ns~vyS~~~~w~P~g~Q~~~f~e~~i 187 (338)
T KOG1521 108 GLVPLRADPRLFEYRSENDEDDEKENTLVFKLNVKCTKNPNAKKDSSDPKELYNNSEVYSRDLTWKPKGYQAEIFAENPI 187 (338)
T ss_pred CCCCCCCCCCHHHCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCHHHHCCCCEEECCCCEECCCCCHHHHCCCCCC
T ss_conf 67211128206430566787667643489999700367888666778856715676786176343566526655146996
Q ss_pred EEECCCEEEEEECCCCEEEEEEEEECCCCCEECCCC--------------------------CCCCCCCCEECCCCCHHE
Q ss_conf 998888089997789649999997468763203444--------------------------465575430212431111
Q gi|254780237|r 126 EVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHH--------------------------RTENDPIGLITIDALYSP 179 (340)
Q Consensus 126 eivNpd~~IaTl~~~~~l~iel~ie~G~GY~~~e~~--------------------------~~~~~~ig~i~iDa~FsP 179 (340)
..+++|-.||.|..|-.++.++..-+|.|-.-|... -....+-|.|-|+-.=.
T Consensus 188 ~~~~~DILiAkLrPGQEI~le~havkGIGkdHAKfSPVaTAsYRLlP~I~l~~ei~ge~A~~lqkcfs~gVi~iee~~~- 266 (338)
T KOG1521 188 RPVHDDILIAKLRPGQEIELEAHAVKGIGKDHAKFSPVATASYRLLPTIVLLAEIEGEDAERLQKCFSPGVIDIEEMGG- 266 (338)
T ss_pred CCCCCCEEEEECCCCCEEEEEEEEECCCCCCCCCCCCCCCCEEECCCEEEECCCCCCHHHHHHHHHCCCCEEEEECCCC-
T ss_conf 5567646887327998722564030056755443057522020005305734745646599998518987076503797-
Q ss_pred EEEEEEEEEEECC-------------------CCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 4422357764116-------------------887762189999993896177799999999999988876
Q gi|254780237|r 180 IKKVSYTVESARE-------------------GQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231 (340)
Q Consensus 180 V~~Vny~Ve~~rv-------------------g~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f 231 (340)
++..|. .+.|. |+.. |--++.|.+-|++.|..-+.+|.++|..--...
T Consensus 267 -kk~A~V-ad~R~dT~sRe~~R~ee~~d~V~Lgrvr--dHfIFsvestgal~p~~lf~eavkvle~Kc~al 333 (338)
T KOG1521 267 -KKRAYV-ADPRKDTCSREVLRHEELKDKVQLGRVR--DHFIFSVESTGALKPEVLFEEAVKVLEEKCRAL 333 (338)
T ss_pred -CEEEEE-CCCCCCHHHHHHHCCHHHHHHEEECCCC--CEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf -047885-0742021447775267765430320012--238998612467880566999999999999987
No 19
>PRK03773 DNA-directed RNA polymerase subunit L; Provisional
Probab=95.98 E-value=0.021 Score=35.85 Aligned_cols=51 Identities=25% Similarity=0.306 Sum_probs=39.2
Q ss_pred EEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 4422357764116887762189999993896177799999999999988876224
Q gi|254780237|r 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234 (340)
Q Consensus 180 V~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~~ 234 (340)
|.-+.|+|...-+.. .+..+-|.|||+++|.+||.+|++-+++..+.|.+.
T Consensus 38 V~fAgY~ipHPl~~~----~~p~~rIqTdg~~~P~~aL~~A~~~li~~c~~~~e~ 88 (95)
T PRK03773 38 VKFAAYTIEHPITMA----RKPRFRVVTDGKITPEKALEEAAQKIFDRAKEVLEA 88 (95)
T ss_pred EEEEEECCCCCCCCC----CCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 599985389976556----864899983899898999999999999999999999
No 20
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=95.96 E-value=0.02 Score=35.97 Aligned_cols=50 Identities=22% Similarity=0.338 Sum_probs=23.8
Q ss_pred CCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCHHHH-HHHHHHHCCC
Q ss_conf 7566788899999874169830688999887144314664624449-9999840114
Q gi|254780237|r 37 RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDL-TDIILNIKGI 92 (340)
Q Consensus 37 ~G~g~TlGNaLRRvLLssi~G~ait~vkI~gv~HEfs~i~GV~EDV-~eIiLNLK~I 92 (340)
+|-|-+.-+.|+..=..++.+.+.+. ..|.+.+.|+.|.- ..|+-..+++
T Consensus 13 pGv~~~~~~kL~~aG~~tv~~l~~~~------~~~L~~~~gis~~~a~ki~~~a~~~ 63 (318)
T PRK04301 13 PGVGPATAEKLREAGYDTVEAIAVAS------PKELSEIAGISESTAAKIIEAAREA 63 (318)
T ss_pred CCCCHHHHHHHHHCCCCCHHHHHCCC------HHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf 99899999999986995499987489------9999985099999999999999985
No 21
>cd06927 RNAP_L L subunit of Archaeal RNA polymerase. The archaeal L subunit of RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer.
Probab=95.30 E-value=0.062 Score=32.75 Aligned_cols=48 Identities=25% Similarity=0.356 Sum_probs=38.1
Q ss_pred EEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 144223577641168877621899999938961777999999999999888762
Q gi|254780237|r 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232 (340)
Q Consensus 179 PV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~ 232 (340)
-|.-+.|.+... ..+...|-|.|+|+.+|.+||..|++-|++.+.-|.
T Consensus 35 ~V~fa~Y~i~HP------l~~~~~l~I~T~~~~~p~~al~~a~~~l~~~~~~~~ 82 (83)
T cd06927 35 GVKVASYDIEHP------LLSNPVLKIKTDGGVDPLEALKEAAKRLIDLCEEFL 82 (83)
T ss_pred CEEEEEEECCCC------CCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHC
T ss_conf 858996328999------889208999989999989999999999999998750
No 22
>PTZ00035 Rad51; Provisional
Probab=94.63 E-value=0.11 Score=31.12 Aligned_cols=55 Identities=11% Similarity=0.159 Sum_probs=32.9
Q ss_pred CHHHC---CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH
Q ss_conf 12210---11058889898839837188874498888618898864499999999980
Q gi|254780237|r 259 KVEEL---ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313 (340)
Q Consensus 259 ~IeeL---eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~ 313 (340)
+|+.| ..+..-.+-|+.||++||..+..-+..+|+.+|+++..-.+-|++.-.++
T Consensus 34 ~i~~l~~~Gi~~~di~kl~~aG~~tv~~v~~~~~k~L~~ikgise~k~~Ki~~~a~k~ 91 (350)
T PTZ00035 34 KIEQLLAKGFVKRDLELLKEGGLQTVECVAYAPMRTLCAIKGISEQKAEKLKKACKEL 91 (350)
T ss_pred CHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf 2999987799989999999849124899985099989773794699999999999975
No 23
>cd07027 RNAP_RPB11_like RPB11 subunit of RNA polymerase. The eukaryotic RPB11 subunit of RNA polymerase (RNAP), as well as its archaeal (L subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/
Probab=94.20 E-value=0.16 Score=30.18 Aligned_cols=46 Identities=20% Similarity=0.273 Sum_probs=35.6
Q ss_pred EEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 4422357764116887762189999993896177799999999999988876
Q gi|254780237|r 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF 231 (340)
Q Consensus 180 V~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f 231 (340)
|.-+.|.+.. ...++..|-|.|+|.++|.+||..|++-|.+.+..+
T Consensus 36 V~fA~Y~ipH------Pl~~~~~lrIqT~~~~~p~~al~~a~~~L~~~~~~l 81 (83)
T cd07027 36 VDFARYYIKH------PVIDKIQIRIQTKSGIKPKDALKRAVNKLSKLYEHL 81 (83)
T ss_pred EEEEEEECCC------CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 2798410889------988940899998999998999999999999998750
No 24
>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase. The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the
Probab=94.17 E-value=0.074 Score=32.26 Aligned_cols=40 Identities=35% Similarity=0.529 Sum_probs=29.6
Q ss_pred CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECC
Q ss_conf 7888158999961697566788899999874169830688999887
Q gi|254780237|r 22 QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67 (340)
Q Consensus 22 ~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI~g 67 (340)
+.+++|..|++. +..||+||+||+.|+.+ | ....+-+++-
T Consensus 5 ~~~~~~~tf~~~----~EDHTlgN~Lr~~l~~~-P-V~~~~Y~v~h 44 (86)
T cd00460 5 EKEKNYVDFVLE----NEDHTLGNSLRRILLKS-P-VEFAAYYVEH 44 (86)
T ss_pred ECCCCEEEEEEE----CCCCHHHHHHHHHHCCC-C-EEEEEEECCC
T ss_conf 528985999994----78852788999998019-8-3789987588
No 25
>cd06926 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB11 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=93.58 E-value=0.23 Score=29.08 Aligned_cols=47 Identities=28% Similarity=0.360 Sum_probs=35.1
Q ss_pred EEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 44223577641168877621899999938961777999999999999888762
Q gi|254780237|r 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232 (340)
Q Consensus 180 V~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~ 232 (340)
|.-+.|.|-... ..+..|-|.|+|+++|.+||..|.+-|++.+..+.
T Consensus 44 v~fagY~~pHPl------~~~i~lriqT~~~~~p~~aL~~al~~L~~~~~~l~ 90 (93)
T cd06926 44 VLFAGYKVPHPL------EHKIELRIQTDGSITPKEALKNAITDLISELSLLK 90 (93)
T ss_pred CEEEEECCCCCC------CCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 569775178998------77058999979999999999999999999999998
No 26
>cd07027 RNAP_RPB11_like RPB11 subunit of RNA polymerase. The eukaryotic RPB11 subunit of RNA polymerase (RNAP), as well as its archaeal (L subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/
Probab=93.10 E-value=0.15 Score=30.25 Aligned_cols=39 Identities=28% Similarity=0.346 Sum_probs=29.6
Q ss_pred CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEE
Q ss_conf 78881589999616975667888999998741698306889998
Q gi|254780237|r 22 QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65 (340)
Q Consensus 22 ~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI 65 (340)
+.++++..|.+ .|..||+||+||..|+.. |+.-..+-++
T Consensus 5 ~~~~n~~~f~i----~~EdHTlgN~Lr~~L~~~-~~V~fA~Y~i 43 (83)
T cd07027 5 SKEKNSVTVEM----ENEDHTLGNLLREELLKD-DQVDFARYYI 43 (83)
T ss_pred ECCCCEEEEEE----ECCCCHHHHHHHHHHHCC-CCEEEEEEEC
T ss_conf 53899899999----489815689999999579-9827984108
No 27
>cd07029 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC19 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC19 subunit is the equivalent of the RPB11 subunit of RNAP II. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC19 to RPB11 suggests a similar function. The AC19 subunit is likely to ass
Probab=92.95 E-value=0.3 Score=28.32 Aligned_cols=48 Identities=15% Similarity=0.251 Sum_probs=35.6
Q ss_pred EEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 442235776411688776218999999389617779999999999998887622
Q gi|254780237|r 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233 (340)
Q Consensus 180 V~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~ 233 (340)
|.-+.|.|-- .-..++.+-|.|+|+.+|.+|+..|.+-|.+.+..+.+
T Consensus 36 V~fagY~ipH------Pl~~~i~irIqT~~~~~~~~al~~al~dL~~~~~~i~~ 83 (85)
T cd07029 36 VEFCGYSIPH------PSENKINLRIQTKGGEPAVDVLKKGLEDLEQICDHILS 83 (85)
T ss_pred CEEEECCCCC------CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 5485326899------99871379999589999899999999999999999984
No 28
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=92.44 E-value=0.28 Score=28.54 Aligned_cols=73 Identities=21% Similarity=0.332 Sum_probs=49.8
Q ss_pred CCCHHHHHHHHHCC-CCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHC------CCCCCCCCCCCHHHHHHHHHHH
Q ss_conf 11058889898839-8371888744988886188988644999999999808------3126768789867799999877
Q gi|254780237|r 264 ELSVRSTNCLRGEN-IVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG------LFLGMNLPDWPPESIEELAKKY 336 (340)
Q Consensus 264 eLSvRs~NcLk~a~-I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~g------l~lg~~l~~~~~~~~~~~~~~~ 336 (340)
.|+.....-|-.+| |+++.||-.++.++|+++.+||.||.+-+.+.++.-- +-++..++.-.......|.+.|
T Consensus 452 GlG~~~i~~L~~~g~i~~~~Diy~L~~~~L~~l~gfgeKsa~nLl~aIe~SK~~~l~r~L~ALGI~~VG~~~Ak~La~~f 531 (668)
T PRK07956 452 GLGEKIIEQLFEKGLIHTPADLFKLTEEDLLQLEGFGEKSAQNLLDAIEKSKETPLARFLYALGIRHVGEKAAKALARHF 531 (668)
T ss_pred CCCHHHHHHHHHCCCCCCHHHHHCCCHHHHHCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCCCCHHHHHHHHHHH
T ss_conf 65999999998768766589997288545402123556699999999998547758889986278641299999999996
No 29
>COG1761 RPB11 DNA-directed RNA polymerase, subunit L [Transcription]
Probab=92.39 E-value=0.32 Score=28.12 Aligned_cols=49 Identities=16% Similarity=0.350 Sum_probs=39.8
Q ss_pred EEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 1442235776411688776218999999389617779999999999998887622
Q gi|254780237|r 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233 (340)
Q Consensus 179 PV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~ 233 (340)
-|.-+.|+|+..-. +...+-|.|+|.+.|++||..|++.+.+.+.-|.+
T Consensus 41 ~V~~a~Y~i~HP~~------~~~~i~Ikt~~~~dp~~aL~~A~~~i~~~~~~l~~ 89 (99)
T COG1761 41 DVEFAAYSIPHPLI------DNPKIRIKTKGGVDPKEALKRAARKILKDLEELLD 89 (99)
T ss_pred CEEEEEEECCCCCC------CCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 72699875789777------88428999779999799999999999999999999
No 30
>cd06927 RNAP_L L subunit of Archaeal RNA polymerase. The archaeal L subunit of RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer.
Probab=92.36 E-value=0.12 Score=30.92 Aligned_cols=39 Identities=28% Similarity=0.415 Sum_probs=29.2
Q ss_pred CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEE
Q ss_conf 78881589999616975667888999998741698306889998
Q gi|254780237|r 22 QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65 (340)
Q Consensus 22 ~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI 65 (340)
+.++++-+|.+ .|.+||+||+||..|+.. |+....+-++
T Consensus 5 ~~~~n~l~~~i----~gEdHTlgNlLr~~L~~~-~~V~fa~Y~i 43 (83)
T cd06927 5 EKEDNELELEI----EGEDHTLLNLLKEELLRD-PGVKVASYDI 43 (83)
T ss_pred ECCCCEEEEEE----ECCCCHHHHHHHHHHHCC-CCEEEEEEEC
T ss_conf 54898999999----489833899999999469-9858996328
No 31
>cd07029 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC19 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC19 subunit is the equivalent of the RPB11 subunit of RNAP II. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC19 to RPB11 suggests a similar function. The AC19 subunit is likely to ass
Probab=91.86 E-value=0.23 Score=29.09 Aligned_cols=38 Identities=29% Similarity=0.414 Sum_probs=27.8
Q ss_pred CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEE
Q ss_conf 7888158999961697566788899999874169830688999
Q gi|254780237|r 22 QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQ 64 (340)
Q Consensus 22 ~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vk 64 (340)
..+++-+.|++ .|..|||||+||.+|+.. ++....+-+
T Consensus 5 ~~~~~~~tf~~----~~EdHTlGN~Lr~~L~~~-~~V~fagY~ 42 (85)
T cd07029 5 GTDESCATFVF----YGEDHTLGNSLRYVIMKN-PEVEFCGYS 42 (85)
T ss_pred CCCCCEEEEEE----ECCCCHHHHHHHHHHHHC-CCCEEEECC
T ss_conf 69997258999----378853899999999779-995485326
No 32
>PRK03773 DNA-directed RNA polymerase subunit L; Provisional
Probab=91.42 E-value=0.37 Score=27.76 Aligned_cols=39 Identities=31% Similarity=0.331 Sum_probs=31.0
Q ss_pred CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEE
Q ss_conf 78881589999616975667888999998741698306889998
Q gi|254780237|r 22 QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65 (340)
Q Consensus 22 ~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI 65 (340)
+.++++-.|.+. |-.||+||+||-.||.. ||+...+-+|
T Consensus 7 ~~~~n~~ef~l~----~EDHTl~NlLr~~Ll~~-p~V~fAgY~i 45 (95)
T PRK03773 7 KKEENLLEFYLE----GEDHTFANLLTETLREN-PHVKFAAYTI 45 (95)
T ss_pred ECCCCEEEEEEE----CCCCHHHHHHHHHHHCC-CCEEEEEECC
T ss_conf 648988999992----78741789999998449-9859998538
No 33
>PRK02406 DNA polymerase IV; Validated
Probab=91.35 E-value=1.2 Score=24.33 Aligned_cols=53 Identities=21% Similarity=0.169 Sum_probs=42.5
Q ss_pred HHHCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf 331112210-11058889898839837188874498888618898864499999999
Q gi|254780237|r 255 ALLKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310 (340)
Q Consensus 255 ~L~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L 310 (340)
+-..+|.++ +..-|+..-|++.||+|++||...++..|.+. ||+ .-..+.+..
T Consensus 177 L~~lpv~~l~GIG~~~~~~L~~~GI~ti~DL~~~~~~~L~~~--fG~-~g~~l~~~a 230 (355)
T PRK02406 177 VATLPVEKIPGVGKVTAEKLHALGIRTCADLQKWDLATLLRR--FGK-FGRRLYERA 230 (355)
T ss_pred HHHCCCCCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHH--HCH-HHHHHHHHH
T ss_conf 961887405885889999999829817999760999999999--798-999999996
No 34
>cd06926 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB11 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=90.52 E-value=0.56 Score=26.58 Aligned_cols=47 Identities=21% Similarity=0.210 Sum_probs=33.5
Q ss_pred CCCEEEECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEE
Q ss_conf 42015863678881589999616975667888999998741698306889998
Q gi|254780237|r 13 NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI 65 (340)
Q Consensus 13 ~~i~~~~~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI 65 (340)
.+|++. .+...+|-+.|.+ .+..|||||+||..|+. -+++...+-++
T Consensus 5 ~Kv~~~-~dtk~pn~~~f~~----~~EDHTLGNlL~~~L~~-~~~v~fagY~~ 51 (93)
T cd06926 5 KKITEK-KDTKVPNAATFTI----NKEDHTLGNLLRMQLLK-DPNVLFAGYKV 51 (93)
T ss_pred CCEEEE-CCCCCCCEEEEEE----ECCCCCHHHHHHHHHHH-CCCCEEEEECC
T ss_conf 445984-1788985389999----17885089999999962-99956977517
No 35
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=87.43 E-value=1.3 Score=24.31 Aligned_cols=47 Identities=19% Similarity=0.265 Sum_probs=41.9
Q ss_pred CHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHC
Q ss_conf 0588898988398371888744988886188988644999999999808
Q gi|254780237|r 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMG 314 (340)
Q Consensus 266 SvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~g 314 (340)
+..++|||+. +-++++++.-|+.+|+++++.|.|...+|...|....
T Consensus 192 ~~~a~~ll~~--fgS~~~~~tas~~eL~~v~gig~k~A~~I~~~~~t~~ 238 (254)
T COG1948 192 PKLAERLLKK--FGSVEDVLTASEEELMKVKGIGEKKAREIYRFLRTEY 238 (254)
T ss_pred HHHHHHHHHH--HCCHHHHHHCCHHHHHHHCCCCHHHHHHHHHHHHCHH
T ss_conf 8999999998--5688877655999997744846889999999983444
No 36
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=87.08 E-value=0.89 Score=25.29 Aligned_cols=49 Identities=6% Similarity=0.062 Sum_probs=37.6
Q ss_pred CCCHHHHHHHH-HCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHH
Q ss_conf 11058889898-83983718887449888861889886449999999998
Q gi|254780237|r 264 ELSVRSTNCLR-GENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312 (340)
Q Consensus 264 eLSvRs~NcLk-~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~ 312 (340)
.|+......|- ..-|+.+.||-..+.++|+++++||+||.+-+.+.++.
T Consensus 433 GLGek~i~~L~~~gli~~~~Dly~L~~~~L~~l~g~geKsa~nLl~aIe~ 482 (563)
T PRK08097 433 GIGEGTWRALHQTGRFEHLFSWLALTPEQLANTPGIGKARAAQLWHQFNL 482 (563)
T ss_pred CCCHHHHHHHHHCCCCCCHHHHHHCCHHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf 76999999999758889979975089999855898578999999999999
No 37
>PRK00254 ski2-like helicase; Provisional
Probab=86.81 E-value=0.88 Score=25.29 Aligned_cols=44 Identities=18% Similarity=0.323 Sum_probs=37.4
Q ss_pred HHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHH
Q ss_conf 88898988398371888744988886188988644999999999
Q gi|254780237|r 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311 (340)
Q Consensus 268 Rs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~ 311 (340)
.-.-.|-+|||+|+.||..-+.++|..++++|.|-.+.|.+-+.
T Consensus 655 ~RAR~Ly~aGi~s~~~ia~A~p~~l~~i~g~g~~~a~~i~~~~~ 698 (717)
T PRK00254 655 KRARALYNAGFRDLEDIMNAKPSELLAVEGIGAKIVEGIFKHLG 698 (717)
T ss_pred HHHHHHHHCCCCCHHHHHCCCHHHEECCCCCCHHHHHHHHHHHC
T ss_conf 99999998699999999659999903023727899999999838
No 38
>PRK03858 DNA polymerase IV; Validated
Probab=86.24 E-value=2.8 Score=22.04 Aligned_cols=53 Identities=17% Similarity=0.187 Sum_probs=39.9
Q ss_pred HHHCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHH
Q ss_conf 331112210-1105888989883983718887449888861889886449999999
Q gi|254780237|r 255 ALLKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309 (340)
Q Consensus 255 ~L~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~ 309 (340)
+-..+|.++ ...-|+..-|++.||+|++||.+.++..|.+. ||...-..+.+.
T Consensus 170 L~~lpv~~iwGIG~~~~~~L~~~GI~T~~dLa~~~~~~l~~~--fG~~~g~~l~~~ 223 (398)
T PRK03858 170 LHPLPVRRLWGVGAVTAAKLRAHGIETVADVAELSESTLSSM--VGPAMGRQLYAL 223 (398)
T ss_pred HHHCCCCCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHH--HHHHHHHHHHHH
T ss_conf 864660121586879999999849968999760999999999--778987999998
No 39
>cd03468 Pol_Y_like Pol_Y_like: a group of putative Y-family DNA polymerases. Y-family polymerases can transverse normal replication-blocking DNA lesions, such as cyclobutane pyrimidine dimers resulting from UV damage, at higher error rate. The Y-family has no 3'-5' exonuclease activity. In addition to possessing a topology akin to a right hand, with "thumb", "fingers" and "palm" motifs, like polymerases from the A-, B-, C- and X-families, the Y-family has a unique "little finger" motif. Expression of Y-family polymerases is often induced by DNA damage. These polymerases are phylogenetically unrelated to classical DNA polymerases.
Probab=86.23 E-value=0.88 Score=25.30 Aligned_cols=48 Identities=25% Similarity=0.285 Sum_probs=41.4
Q ss_pred HHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHH
Q ss_conf 33111221011058889898839837188874498888618898864499
Q gi|254780237|r 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLV 304 (340)
Q Consensus 255 ~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~ 304 (340)
....++..|.++.++..-|.+.||+|+|||...+..+|. +-||.....
T Consensus 165 l~~lPv~~l~i~~~~~~~L~~lGi~tigdL~~lp~~~L~--~RfG~~~~~ 212 (330)
T cd03468 165 LAPLPVAALRLPPETVERLRRLGLRTLGDLAALPRAGLA--RRFGPELLR 212 (330)
T ss_pred HHCCCHHHHCCCHHHHHHHHHCCCCCHHHHHCCCHHHHH--HHHCHHHHH
T ss_conf 635986673889899999998599679998659999999--987979999
No 40
>PRK01216 DNA polymerase IV; Validated
Probab=85.87 E-value=1.3 Score=24.13 Aligned_cols=51 Identities=8% Similarity=0.089 Sum_probs=41.3
Q ss_pred HHHCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHH
Q ss_conf 331112210-11058889898839837188874498888618898864499999
Q gi|254780237|r 255 ALLKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307 (340)
Q Consensus 255 ~L~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~ 307 (340)
.-..+|.++ ...-++..-|.+.||+|++||.+++.+.|. +-||++.-.-+.
T Consensus 175 l~~lpv~~i~GIG~~t~~~L~~~GI~ti~dL~~~~~~~L~--~~fG~~~~~~l~ 226 (351)
T PRK01216 175 LNNLDIDDVPGIGKVLSERLNELGINKLRDILSKSFNKLK--SIIGEAKANYLY 226 (351)
T ss_pred HHCCCCCEECCCCHHHHHHHHHCCCCCHHHHHHCCHHHHH--HHHCHHHHHHHH
T ss_conf 7609943854857999999998599689997529999999--997779999999
No 41
>PRK01172 ski2-like helicase; Provisional
Probab=85.65 E-value=1.8 Score=23.26 Aligned_cols=45 Identities=9% Similarity=0.099 Sum_probs=39.2
Q ss_pred HHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH
Q ss_conf 889898839837188874498888618898864499999999980
Q gi|254780237|r 269 STNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313 (340)
Q Consensus 269 s~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~ 313 (340)
..-.|-+|||+|+.||..-+.++|.++.++|+|-.+.|.+.-+.+
T Consensus 624 RAR~Ly~aG~~s~~dia~a~~~~L~~i~g~~~~~A~~Ii~~A~~l 668 (674)
T PRK01172 624 RARRLYDAGFKTVDDIARSSPERIKKIYGFSDTLANAIVNRAMKI 668 (674)
T ss_pred HHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf 999999869999999970999898764198999999999999977
No 42
>PRK13766 Hef nuclease; Provisional
Probab=84.74 E-value=2.1 Score=22.82 Aligned_cols=45 Identities=18% Similarity=0.313 Sum_probs=38.9
Q ss_pred CHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHH
Q ss_conf 05888989883983718887449888861889886449999999998
Q gi|254780237|r 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312 (340)
Q Consensus 266 SvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~ 312 (340)
++++.+-|.+ ..+|.++..-|++||.+++++|+|...+|.+.|..
T Consensus 716 ~~~a~~ll~~--fgsi~~i~~a~~~eL~~v~giG~~~A~~i~~~~~~ 760 (764)
T PRK13766 716 PVLARNLLDH--FGSVENVMTASEEELKAVEGIGEKTAKKIREVVTS 760 (764)
T ss_pred HHHHHHHHHH--CCCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHCC
T ss_conf 9999999997--19999996599999954749699999999998525
No 43
>PRK03352 DNA polymerase IV; Validated
Probab=84.12 E-value=2 Score=23.02 Aligned_cols=50 Identities=18% Similarity=0.198 Sum_probs=40.6
Q ss_pred HCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHH
Q ss_conf 1112210-110588898988398371888744988886188988644999999
Q gi|254780237|r 257 LKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308 (340)
Q Consensus 257 ~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~ 308 (340)
..+|.++ +..-|+..-|+..||+|++||.+.+...|.+. ||.+.-..+.+
T Consensus 176 ~lpv~~i~GIG~~~~~kL~~~GI~Ti~DL~~~~~~~L~~~--fG~~~g~~l~~ 226 (345)
T PRK03352 176 DRPVDALWGVGPKTAKKLAALGITTVADLAATDPAVLTAT--FGPRTGLWLLL 226 (345)
T ss_pred CCCCHHCCCCCHHHHHHHHHCCCCCHHHHHCCCHHHHHHH--HCHHHHHHHHH
T ss_conf 2782112782899999999759971999866999999999--78899999999
No 44
>PRK05618 50S ribosomal protein L25/general stress protein Ctc; Reviewed
Probab=84.08 E-value=2.7 Score=22.16 Aligned_cols=29 Identities=21% Similarity=0.464 Sum_probs=22.6
Q ss_pred EEEEEEEEECCCCEEEE-CCCEEEEEECCC
Q ss_conf 16996335138985998-888089997789
Q gi|254780237|r 112 GVVTAGDIQTVNDIEVL-NPDHVICNLDVD 140 (340)
Q Consensus 112 ~~vtA~Di~~p~~veiv-Npd~~IaTl~~~ 140 (340)
..++.+||.+|.+++++ +||..||++...
T Consensus 154 d~i~v~Dl~lpegv~~~~d~~~~V~~V~~p 183 (193)
T PRK05618 154 DSIHVSDIKLPEGVKLLDDPDFVVVTVVAP 183 (193)
T ss_pred CEEEEEEECCCCCEEECCCCCCEEEEEECC
T ss_conf 868975005899808945999589999799
No 45
>pfam12482 DUF3701 Phage integrase protein. This domain family is found in bacteria, and is approximately 100 amino acids in length. The family is found in association with pfam00589.
Probab=83.19 E-value=1.4 Score=23.91 Aligned_cols=57 Identities=19% Similarity=0.193 Sum_probs=48.1
Q ss_pred CCCHHHHHHHHHCCCCCHHHHHHCCHH----HHHCCCCCCHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 110588898988398371888744988----886188988644999999999808312676
Q gi|254780237|r 264 ELSVRSTNCLRGENIVYMGDLIQRTEA----DMLRMANFGRKSLVEIKGVLGTMGLFLGMN 320 (340)
Q Consensus 264 eLSvRs~NcLk~a~I~tigdLv~~s~~----dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~ 320 (340)
=|..|..-.|..+||.|++||+.+-.. =-..++.+|..+..-|+.-|..+.-.+|..
T Consensus 20 W~~p~~a~~L~~~Gi~TLa~L~~~i~~rg~~Wwr~vp~lG~~~Ar~Iea~la~h~~~~~ra 80 (96)
T pfam12482 20 WLAPRVARRLAAAGITTLADLTVRINRRGRRWWRAVPGLGAAGARRIEAFLAAHPALTGRA 80 (96)
T ss_pred HCCHHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHCCCCCCHHHHHHHHHHHHHCHHHHHHH
T ss_conf 6178999999984863399999999722650244187610687999999999899999778
No 46
>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1; InterPro: IPR011940 This entry 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 (IPR011938 from INTERPRO) and RadB (IPR011939 from INTERPRO) and bacterial RecA. It has been characterised for human as a recombinase active only in meiosis .; GO: 0003677 DNA binding, 0005524 ATP binding, 0008094 DNA-dependent ATPase activity, 0007131 meiotic recombination, 0005634 nucleus.
Probab=82.54 E-value=2 Score=23.00 Aligned_cols=51 Identities=14% Similarity=0.285 Sum_probs=41.5
Q ss_pred CCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH
Q ss_conf 011058889898839837188874498888618898864499999999980
Q gi|254780237|r 263 LELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313 (340)
Q Consensus 263 LeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~ 313 (340)
....+.-.+-||.++|.||.-+...|+..|.++|+|-+--++-|+|+=.++
T Consensus 7 ~GIn~~Di~KLk~~g~~T~~~~~~~T~r~L~~iKGlSEaKVdKi~EaA~K~ 57 (314)
T TIGR02238 7 HGINAADIKKLKSAGICTVNGVIMTTKRELLKIKGLSEAKVDKIKEAASKI 57 (314)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf 388788999988636899999999888887403785167799999999876
No 47
>PRK02794 DNA polymerase IV; Provisional
Probab=82.31 E-value=4.1 Score=20.95 Aligned_cols=52 Identities=25% Similarity=0.318 Sum_probs=41.8
Q ss_pred HHCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf 31112210-11058889898839837188874498888618898864499999999
Q gi|254780237|r 256 LLKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310 (340)
Q Consensus 256 L~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L 310 (340)
-.++|.++ ...-|+..-|++.||+|++||.+.++..|.+ -||.. -..+...+
T Consensus 207 ~~lpv~diwGIG~rt~~kL~~~GI~Ti~DL~~~~~~~L~~--~fG~~-g~~l~~~a 259 (417)
T PRK02794 207 APKPVGFIWGVGPATAARLAADGIRTIGDLQRADEADLMR--RFGSM-GRRLWRLA 259 (417)
T ss_pred HCCCHHHHCCCCHHHHHHHHHCCCCCHHHHHCCCHHHHHH--HHCHH-HHHHHHHH
T ss_conf 5388455168468999999984990999986599989778--71978-99999996
No 48
>PRK08609 hypothetical protein; Provisional
Probab=81.63 E-value=3.8 Score=21.20 Aligned_cols=53 Identities=11% Similarity=0.102 Sum_probs=29.1
Q ss_pred CHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf 058889898839837188874498888618898864499999999980831267687
Q gi|254780237|r 266 SVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP 322 (340)
Q Consensus 266 SvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~ 322 (340)
+-|...++++-.++-+|--.-+ -|.+=+.+ .--+++|.++-++.|-.|-+|-.
T Consensus 448 t~r~~~Ai~np~v~ii~HptgR---~l~~r~~~-~~d~~~v~~~aa~~~~~lEINa~ 500 (570)
T PRK08609 448 MKRLETACRNPYVRLIAHPTGR---LIGRRDGY-DVNIDQLIELAKETNTVLELNAN 500 (570)
T ss_pred HHHHHHHHHCCCCCEEECCCCC---CCCCCCCC-CCCHHHHHHHHHHHCCEEEEECC
T ss_conf 9999999718998788488754---24777888-77999999999985979998099
No 49
>PRK03348 DNA polymerase IV; Provisional
Probab=81.11 E-value=4.6 Score=20.68 Aligned_cols=52 Identities=19% Similarity=0.177 Sum_probs=40.9
Q ss_pred HHCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHH
Q ss_conf 31112210-1105888989883983718887449888861889886449999999
Q gi|254780237|r 256 LLKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309 (340)
Q Consensus 256 L~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~ 309 (340)
-.++|.+| ...-|+..-|++.||+|++||.+.++..|. +-||++.-..+.+.
T Consensus 177 ~~lPV~~lwGIG~~t~~kL~~~GI~TigDLa~~~~~~L~--~~~G~~~G~~L~~~ 229 (456)
T PRK03348 177 APLPVRRLWGIGPVAEEKLHRLGIETIGDLAALSEAEVA--NLLGATIGPALHRL 229 (456)
T ss_pred HHCCHHHCCCCCHHHHHHHHHCCCHHHHHHHCCCHHHHH--HHHHHHHHHHHHHH
T ss_conf 756574338775999999998698146877609999999--99819999999999
No 50
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication; InterPro: IPR010214 NusA, or N utilisation substance protein A, is a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in Escherichia coli of phage lambda antitermination protein N with the N-utilisation substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and NusG . This entry 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 ; GO: 0030528 transcription regulator activity.
Probab=79.22 E-value=2.9 Score=21.91 Aligned_cols=40 Identities=15% Similarity=0.204 Sum_probs=36.1
Q ss_pred HHHHHHCCCCCHHHHHHCCHHHHHC--CCCCCHHHHHHHHHH
Q ss_conf 8989883983718887449888861--889886449999999
Q gi|254780237|r 270 TNCLRGENIVYMGDLIQRTEADMLR--MANFGRKSLVEIKGV 309 (340)
Q Consensus 270 ~NcLk~a~I~tigdLv~~s~~dLl~--ikNfG~KSl~EI~~~ 309 (340)
...|-..|+.|+-||...+-+||+. |.||-.....+++..
T Consensus 6 a~~Lv~eGf~t~EdlAy~~~~EL~~fGIeG~~Ee~A~~L~~~ 47 (52)
T TIGR01954 6 AQLLVEEGFTTVEDLAYVPVDELLSFGIEGLDEETAKELINR 47 (52)
T ss_pred HHHHHHHCCCHHHHHHCCCHHHHHHHCCCCCCHHHHHHHHHH
T ss_conf 999997367317887504556688635899887889999999
No 51
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=78.34 E-value=2.5 Score=22.36 Aligned_cols=45 Identities=24% Similarity=0.199 Sum_probs=37.1
Q ss_pred HHH-HCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCH
Q ss_conf 333-1112210-1105888989883983718887449888861889886
Q gi|254780237|r 254 PAL-LKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300 (340)
Q Consensus 254 ~~L-~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~ 300 (340)
..| ..+|.++ +..-|+..-|++.||+|++||.+.+...|.+ .||.
T Consensus 174 ~~l~~~pv~~lwGIG~~~~~kL~~~GI~Ti~dLa~~~~~~l~k--~fgv 220 (422)
T PRK03609 174 KLLSLLPVEEVWGVGRRISKKLNAMGIKTALDLADTDIRFIRK--HFNV 220 (422)
T ss_pred HHHCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHCCHHHHHH--HHHH
T ss_conf 8706587889861139999999987881089987299899998--8889
No 52
>TIGR00575 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase: one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC). This family is predominantly composed of NAD-dependent bacterial DNA ligases. They are proteins of about 75 to 85 Kd whose sequence is well conserved , . They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair.
Probab=78.33 E-value=2.3 Score=22.63 Aligned_cols=40 Identities=20% Similarity=0.335 Sum_probs=34.5
Q ss_pred HHHCCCCCHHHHHHCC--HHHHHCCCC-CCHHHHHHHHHHHHH
Q ss_conf 9883983718887449--888861889-886449999999998
Q gi|254780237|r 273 LRGENIVYMGDLIQRT--EADMLRMAN-FGRKSLVEIKGVLGT 312 (340)
Q Consensus 273 Lk~a~I~tigdLv~~s--~~dLl~ikN-fG~KSl~EI~~~L~~ 312 (340)
+.+.=|.+++||=.++ .++|++++. ||.||.+-+.+.++.
T Consensus 469 fE~~Lv~~~~DLY~L~~k~~~Ll~le~~~g~~sa~nLl~aIe~ 511 (706)
T TIGR00575 469 FEEKLVRSVADLYALKEKLEDLLELEGKFGEKSAQNLLSAIEK 511 (706)
T ss_pred HHCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 8726667856665778899998706403556889999999998
No 53
>cd01700 Pol_V Pol V was discovered in Escherichia coli as Umuc and UmuD proteins induced by UV. This branch of DNA polymerases is mostly found in bacteria. Pol V enables DNA replication to bypass covalently linked cys-sin T-T photo-dimers and 6-4 T-T or T-C photoproducts, which would otherwise stall the DNA replication fork.
Probab=76.71 E-value=3.5 Score=21.40 Aligned_cols=51 Identities=20% Similarity=0.093 Sum_probs=38.7
Q ss_pred HCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf 1112210-11058889898839837188874498888618898864499999999
Q gi|254780237|r 257 LKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310 (340)
Q Consensus 257 ~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L 310 (340)
..+|.++ +.--++..-|++.||+|++||.+.+++.|. +.||.. -..+...+
T Consensus 174 ~lpv~~i~GIG~~t~~kL~~~GI~Ti~dLa~~~~~~l~--~~fg~~-g~~l~~~~ 225 (344)
T cd01700 174 RTPVGDVWGIGRRLSKRLAAMGIHTALDLAQADPKWIR--KRFSVV-LERTVREL 225 (344)
T ss_pred HCCHHHCCCCCHHHHHHHHHCCCCCHHHHHCCCHHHHH--HHHHHH-HHHHHHHH
T ss_conf 28744427836999999998699789998709999999--997689-99999995
No 54
>PTZ00298 mevalonate kinase; Provisional
Probab=75.62 E-value=6.5 Score=19.68 Aligned_cols=73 Identities=16% Similarity=0.266 Sum_probs=54.6
Q ss_pred CCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCC-----------CHHHHHHHH
Q ss_conf 105888989883983718887449888861889886449999999998083126768789-----------867799999
Q gi|254780237|r 265 LSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDW-----------PPESIEELA 333 (340)
Q Consensus 265 LSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~~~-----------~~~~~~~~~ 333 (340)
+..++..+|++.++..+|+|+..+.. ||+--+..--.|+++.+....+| .||-++-+. +.+..+...
T Consensus 226 iv~~a~~aL~~~d~~~lG~Lm~~nh~-lL~~lgVS~p~Ld~lv~~a~~~G-AlGAKLTGAG~GGcvIaL~~~~~~a~~i~ 303 (328)
T PTZ00298 226 CVSEAKEALQKGNLFRVGELMNANHD-LCQKLTVSCRELDSIVQTCRTYG-ALGAKMSGTGRGGLVVALAASEDQRDAIA 303 (328)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHH-HHHHCCCCCHHHHHHHHHHHHCC-CCEEEECCCCCCCEEEEECCCHHHHHHHH
T ss_conf 99999999864899999999999999-89746889789999999999769-96557514688758999838666699999
Q ss_pred HHHHCC
Q ss_conf 877503
Q gi|254780237|r 334 KKYEDK 339 (340)
Q Consensus 334 ~~~~~~ 339 (340)
+.+.+.
T Consensus 304 ~al~~~ 309 (328)
T PTZ00298 304 KAVRAR 309 (328)
T ss_pred HHHHHH
T ss_conf 999974
No 55
>PRK01810 DNA polymerase IV; Validated
Probab=75.24 E-value=6.8 Score=19.57 Aligned_cols=52 Identities=21% Similarity=0.256 Sum_probs=40.6
Q ss_pred HCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHH
Q ss_conf 1112210-110588898988398371888744988886188988644999999999
Q gi|254780237|r 257 LKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311 (340)
Q Consensus 257 ~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~ 311 (340)
..+|.++ +..-|+...|++.||+|++||.+.+...|. +.||.. ...+...+.
T Consensus 178 ~lpv~~iwGIG~~~~~~L~~~GI~Ti~dl~~~~~~~l~--~~fG~~-g~~l~~~~~ 230 (410)
T PRK01810 178 PLPVEEMHGIGEKTAEKLKDIHIHTIGDLAKADEHILR--AKLGIN-GPRLQRRAN 230 (410)
T ss_pred CCCCCCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHH--HHHHHH-HHHHHHHHC
T ss_conf 48851205867789999998699689998749999999--876549-999999971
No 56
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=75.07 E-value=4.7 Score=20.60 Aligned_cols=72 Identities=21% Similarity=0.325 Sum_probs=45.4
Q ss_pred CCHHHHHHH-HHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH------CCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf 105888989-8839837188874498888618898864499999999980------83126768789867799999877
Q gi|254780237|r 265 LSVRSTNCL-RGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM------GLFLGMNLPDWPPESIEELAKKY 336 (340)
Q Consensus 265 LSvRs~NcL-k~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~------gl~lg~~l~~~~~~~~~~~~~~~ 336 (340)
|+.....-| ...-|+++.||-..+.++|+.++.||+||.+-+-+.++.- -+-+|+.++.-.......|.+.+
T Consensus 453 LG~k~i~~L~e~~lI~~~~Dly~Lt~~~l~~l~~~~~ks~~nLl~aIe~sK~~~l~r~l~aLGIr~VG~~~Ak~La~~f 531 (667)
T COG0272 453 LGEKIIEQLFEKGLIKDIADLYTLTEEDLLSLEGFGEKSAENLLNAIEKSKKQPLARFLYALGIRHVGETTAKSLARHF 531 (667)
T ss_pred CCHHHHHHHHHCCCCCCHHHHHHCCHHHHHHCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHHHHH
T ss_conf 6799999999737537879877378988841622446579999999998604989999998797114089999999876
No 57
>PRK13209 L-xylulose 5-phosphate 3-epimerase; Reviewed
Probab=75.06 E-value=2.6 Score=22.25 Aligned_cols=51 Identities=12% Similarity=0.238 Sum_probs=43.7
Q ss_pred CCEECCCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 430212431111442235776411688776218999999389617779999999999998887
Q gi|254780237|r 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230 (340)
Q Consensus 168 ig~i~iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~ 230 (340)
.|.+..+.+|.-.++.+|.. .+++|.|..++-.|..++.+|...+.++|.-
T Consensus 229 ~G~vdf~~vf~aLk~~gY~G------------~~~iE~w~~~~~~~~~~i~~a~~f~~~~~~~ 279 (283)
T PRK13209 229 EGVVDFERAFKTLKQSGYCG------------PYLIEMWSETAEDPAAEVAKARDFVKARMAE 279 (283)
T ss_pred CCCCCHHHHHHHHHHHCCCC------------CEEEEEECCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 88508899999999979976------------2899984189957899999999999999986
No 58
>TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Probab=74.11 E-value=6.5 Score=19.67 Aligned_cols=48 Identities=13% Similarity=0.126 Sum_probs=34.8
Q ss_pred CHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHH
Q ss_conf 12210-1105888989883983718887449888861889886449999
Q gi|254780237|r 259 KVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306 (340)
Q Consensus 259 ~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI 306 (340)
.+..+ +++-.-..-|+.+||+||.+|...+.+.|-+.+.++.+....+
T Consensus 208 ~LslVagi~~~q~~~L~~~GI~Ti~~LA~~~~~~l~~~~~~~~~~~~~l 256 (457)
T TIGR03491 208 HLSLVPGIGPSRYRLLQELGIHTLEDLAAADPNDLEDFGEQGLGVAEQL 256 (457)
T ss_pred CHHHHCCCCHHHHHHHHHCCCCCHHHHHCCCHHHCCCCCCCCHHHHHHH
T ss_conf 9766059999999999985998799986299433035666366999999
No 59
>cd00424 Pol_Y Y-family of DNA polymerases. Pol_Y's can transverse replication-blocking DNA lesions, such as cyclobutane pyrimidine dimers resulting from UV damage, at the cost of an elevated error rate. The Y-family has no 3'-5' exonuclease activity. In addition to possessing a topology akin to a right hand, with "thumb", "fingers" and "palm" motifs, like polymerases from the A-, B-, C- and X-families, the Y-family has a unique "little finger" motif. Expression of Y-family polymerases is often induced by DNA damage. These polymerases are phylogenetically unrelated to classical DNA polymerases.
Probab=73.98 E-value=6.3 Score=19.77 Aligned_cols=52 Identities=15% Similarity=0.181 Sum_probs=41.4
Q ss_pred HCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf 1112210-11058889898839837188874498888618898864499999999
Q gi|254780237|r 257 LKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310 (340)
Q Consensus 257 ~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L 310 (340)
..+|.++ .+.-++..-|++.||+|++||.+.+..+|++. +|.+....+.+.+
T Consensus 172 ~lpv~~l~GIG~~~~~~L~~~gi~ti~dl~~~~~~~l~~~--~~~~~g~~l~~~~ 224 (341)
T cd00424 172 KLPLSDIPGIGSVTASRLEALGIIRKCDLLALQPDQLLAS--LGGKLGERLWSAL 224 (341)
T ss_pred CCCHHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHH--HCCHHHHHHHHHH
T ss_conf 3887887487889999999849935999871899999999--7688999999996
No 60
>cd01684 Tet_like_IV EF-G_domain IV_RPP domain is a part of bacterial ribosomal protected proteins (RPP) family. RPPs such as tetracycline resistance proteins Tet(M) and Tet(O) mediate tetracycline resistance in both gram-positive and -negative species. Tetracyclines inhibit the accommodation of aminoacyl-tRNA into ribosomal A site and therefore prevent the addition of new amino acids to the growing polypeptide. RPPs Tet(M) confer tetracycline resistance by releasing tetracycline from the ribosome and thereby freeing the ribosome from inhibitory effects of the drug, such that aa-tRNA can bind to the A site and protein synthesis can continue.
Probab=73.12 E-value=1.8 Score=23.32 Aligned_cols=47 Identities=30% Similarity=0.419 Sum_probs=30.9
Q ss_pred EEEEEECCCCCHHHHHHH-----------------HHHHHHHCCCCCEEEEEEEE---CCCCCCCCC
Q ss_conf 899996169756678889-----------------99998741698306889998---871443146
Q gi|254780237|r 28 TLMIAEPLPRGFAHTLGN-----------------ALRRVLMSSLRGAAITAVQI---DGVLHEISS 74 (340)
Q Consensus 28 g~f~~~Ple~G~g~TlGN-----------------aLRRvLLssi~G~ait~vkI---~gv~HEfs~ 74 (340)
-.+.++|++||-|..+-| ..|-.|-+-+-|+.+|.+|+ +|..|+=.+
T Consensus 28 V~l~veP~~~g~G~~F~~~i~gg~iP~~f~~ave~Gv~eal~~Gv~Gypv~DvkVtL~dG~~h~vdS 94 (115)
T cd01684 28 VGLRVEPLPRGSGLQYESEVSLGSLPRSFQNAVEETVRETLQQGLYGWEVTDCKVTLTYGRYHSPVS 94 (115)
T ss_pred EEEEEEECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEEECCCCCCCC
T ss_conf 9999988999998889887608847988999999999999952988887745899998163048878
No 61
>cd03586 Pol_IV_kappa Pol_IV_kappa, a member of the Y-family of DNA polymerases. Pol_Y's can transverse replication-blocking DNA lesions, such as cyclobutane pyrimidine dimers resulting from UV damage, at the cost of an elevated error rate. The Y-family has no 3'-5' exonuclease activity. In addition to possessing a topology akin to a right hand, with "thumb", "fingers" and "palm" motifs, like polymerases from the A-, B-, C- and X-families, the Y-family has a unique "little finger" motif. Expression of Y-family polymerases is often induced by DNA damage. These polymerases are phylogenetically unrelated to classical DNA polymerases. Originally called the DinB family, they belong to the recently described Y-family of DNA polymerases. Pol IV is mostly found in bacteria and archaea. Although the structure of Pol IV is similar to that of Pol eta, it shows markedly differenct efficiencies and fidelities in bypassing various DNA lesions. All Pol IV-like polymerases studied to date are able to b
Probab=71.97 E-value=4.9 Score=20.48 Aligned_cols=53 Identities=13% Similarity=0.074 Sum_probs=39.1
Q ss_pred HHHCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHH
Q ss_conf 331112210-1105888989883983718887449888861889886449999999
Q gi|254780237|r 255 ALLKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309 (340)
Q Consensus 255 ~L~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~ 309 (340)
.-.++|.++ +..-|+..-|++.||+|++||.+++.+.|.+. ||.+.-..+.+.
T Consensus 169 L~~lpv~~l~GIG~~~~~~L~~~gI~t~~dl~~~~~~~l~~~--~~~~~g~~l~~~ 222 (337)
T cd03586 169 LAPLPVRKIWGIGKVTAEKLNRLGIRTIGDLAAADLELLKKR--FFGAWGIDLYRL 222 (337)
T ss_pred HCCCCCHHCCCCCHHHHHHHHHCCCCCHHHHHCCCHHHHHHH--CCCCHHHHHHHH
T ss_conf 612763020784689999999808968999864999999876--043189999998
No 62
>cd01701 Pol_zeta Pol_zeta, a member of the Y-family of DNA polymerases. Y-family polymerases can transverse normal replication-blocking DNA lesions, such as cyclobutane pyrimidine dimers resulting from UV damage, at higher error rate. The Y-family has no 3'-5' exonuclease activity. Pol zeta has also been named Rev1; this subfamily is mainly present in eukaryotes.
Probab=71.53 E-value=6.5 Score=19.69 Aligned_cols=54 Identities=19% Similarity=0.224 Sum_probs=41.1
Q ss_pred HHCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHH-HHHCCCCCCHHHHHHHHHHHH
Q ss_conf 31112210-110588898988398371888744988-886188988644999999999
Q gi|254780237|r 256 LLKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEA-DMLRMANFGRKSLVEIKGVLG 311 (340)
Q Consensus 256 L~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~-dLl~ikNfG~KSl~EI~~~L~ 311 (340)
-..+|.++ ...-++..-|.+.||+|++||...+.. .|.+. ||.|.-..+.....
T Consensus 222 ~~lpv~~i~GIG~~t~~kL~~~gi~t~~dl~~~~~~~~L~~~--fG~k~G~~l~~~a~ 277 (405)
T cd01701 222 DTLPVKDLPGVGSSTKEKLKSLGIDTCGDLQLISTKEKLQKV--FGKKTGEKLYNYCR 277 (405)
T ss_pred HHCCCCCCCCCCHHHHHHHHHCCCCCHHHHHCCCHHHHHHHH--HHHHHHHHHHHHHC
T ss_conf 855211158717899999998499168998627879999999--77899999999967
No 63
>PRK13210 putative L-xylulose 5-phosphate 3-epimerase; Reviewed
Probab=70.61 E-value=4.1 Score=20.95 Aligned_cols=51 Identities=12% Similarity=0.251 Sum_probs=41.0
Q ss_pred CCEECCCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 430212431111442235776411688776218999999389617779999999999998887
Q gi|254780237|r 168 IGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM 230 (340)
Q Consensus 168 ig~i~iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~ 230 (340)
.|.+...++|.-.++.+|.- .+++|.|+.++-.|.+++.+|.+.|.+.+.-
T Consensus 230 ~G~vDf~~~~~~L~~~gY~G------------~~~iE~w~~~~~~~~~~i~~a~~~~~~~~~~ 280 (284)
T PRK13210 230 EGCVDFVGIFKTLKELNYRG------------PFLIEMWTEKAEEPVAEIIQARRFIEPKMEE 280 (284)
T ss_pred CCCCCHHHHHHHHHHHCCCC------------CEEEEEECCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 87658899999999819963------------2799992489978799999999999999986
No 64
>PRK03103 DNA polymerase IV; Reviewed
Probab=70.49 E-value=5.7 Score=20.04 Aligned_cols=53 Identities=17% Similarity=0.138 Sum_probs=39.3
Q ss_pred HHHCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf 331112210-11058889898839837188874498888618898864499999999
Q gi|254780237|r 255 ALLKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVL 310 (340)
Q Consensus 255 ~L~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L 310 (340)
+-..+|.++ ..--|..--|++.||+|++||.+.+.+.|.+ .||.. -..+...+
T Consensus 179 l~~lpv~~iwGIG~~~~~kL~~~GI~t~~dL~~~~~~~l~~--~fGv~-G~~l~~~~ 232 (410)
T PRK03103 179 LWPLPIGKLFGVGRRMEHHLRRMGISTIGQLAQTPLERLKK--RWGIN-GHVLWMTA 232 (410)
T ss_pred HHCCCHHHCCCCCHHHHHHHHHCCCCCHHHHHCCCHHHHHH--HHCHH-HHHHHHHH
T ss_conf 72588133068788999999985897499986599999999--83959-99999997
No 65
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=68.84 E-value=4.1 Score=20.98 Aligned_cols=46 Identities=20% Similarity=0.361 Sum_probs=39.3
Q ss_pred CHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf 98888618898864499999999980831267687898677999998775
Q gi|254780237|r 288 TEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYE 337 (340)
Q Consensus 288 s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~~~~~~~~~~~~~~~~ 337 (340)
..+||.+|++.|.| ++..|..+|+.-=..+..|-++.+.|....++
T Consensus 324 ~~DDLk~ikGvGPk----le~~ln~lG~~hfdQiA~W~~~evaWvd~~l~ 369 (403)
T PRK12373 324 GADDLKLISGVGPK----IEGTLNELGIFTFDQVASWKKAERAWVDGYLN 369 (403)
T ss_pred CCCHHHHHCCCCHH----HHHHHHHHCCEEHHHHHCCCHHHHHHHHHHCC
T ss_conf 96355664175878----99998862626489865268999999874236
No 66
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=68.29 E-value=3.3 Score=21.62 Aligned_cols=26 Identities=15% Similarity=0.196 Sum_probs=15.0
Q ss_pred HHHHHHHHHCCCCCHHHHHHCCHHHH
Q ss_conf 58889898839837188874498888
Q gi|254780237|r 267 VRSTNCLRGENIVYMGDLIQRTEADM 292 (340)
Q Consensus 267 vRs~NcLk~a~I~tigdLv~~s~~dL 292 (340)
...---|..+||+|..++...|++|.
T Consensus 163 P~~e~~Ln~~GI~~F~QIA~~t~~di 188 (216)
T PRK12278 163 PALAKKLNEAGITTFAQIAALTDEDI 188 (216)
T ss_pred HHHHHHHHHHCCCHHHHHHCCCHHHH
T ss_conf 89999999818723999855999999
No 67
>PRK12311 rpsB 30S ribosomal protein S2; Provisional
Probab=67.52 E-value=4.3 Score=20.82 Aligned_cols=239 Identities=14% Similarity=0.181 Sum_probs=114.4
Q ss_pred CCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCEEEECCC-C---
Q ss_conf 815899996169756678889999987416983068899988714431466462444999998401141777279-8---
Q gi|254780237|r 25 ENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD-S--- 100 (340)
Q Consensus 25 ~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI~gv~HEfs~i~GV~EDV~eIiLNLK~I~~k~~~~-~--- 100 (340)
..-|++.+=.-.+.....+..+-+|. ..+-|+.==+-|...-|.||.+-..-.-++---++.-.+..... +
T Consensus 64 ~~Gg~ILFVGTK~qa~~~V~~~A~r~-----~~~YVn~RWLGGtLTN~~TI~~sI~rL~~le~~~~~g~~~~ltKKE~l~ 138 (332)
T PRK12311 64 AKGGRVLFVGTKRQAQDAVADAAKRS-----AQYFVNSRWLGGTLTNWKTISGSIKRLRKLDEVLSSGDAGAYTKKERLT 138 (332)
T ss_pred HCCCEEEEEECCHHHHHHHHHHHHHC-----CCCEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH
T ss_conf 66997999868788999999999983-----9965734002763555999999999999999986126523358788999
Q ss_pred ----CEEEEEEEECCEEEEEEEEECCCCEEEECCCEEEEEECCCCEEEEEEEEECCCCCEECCCCCCCCCCCCEECCCCC
Q ss_conf ----2799999944716996335138985998888089997789649999997468763203444465575430212431
Q gi|254780237|r 101 ----HKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDAL 176 (340)
Q Consensus 101 ----~~~~~l~~~Gp~~vtA~Di~~p~~veivNpd~~IaTl~~~~~l~iel~ie~G~GY~~~e~~~~~~~~ig~i~iDa~ 176 (340)
..++.-...|-... =.+|.-+-|+||....--+. |-++ -+-|+ .=-+|++
T Consensus 139 l~Re~~KL~k~lgGIk~M----~~lPDlvfViD~~kE~iAV~--------------------EA~k-LgIPv-IaIvDTN 192 (332)
T PRK12311 139 LQRERDKLDRSLGGIKDM----GGLPDLIFVIDTNKEDIAIQ--------------------EAQR-LGIPV-AAIVDTN 192 (332)
T ss_pred HHHHHHHHHHHHHHHHHH----CCCCCEEEEECCCCCHHHHH--------------------HHHH-CCCCE-EEEEECC
T ss_conf 987999999854625420----55999899968973389999--------------------9998-09798-9997389
Q ss_pred HHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHH--HHCCCCCCCCCCCHHHCCCCHHHH
Q ss_conf 111442235776411688776218999999389617779999999999998887--622444432210000000001123
Q gi|254780237|r 177 YSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGM--FINFEEPKKEVKEDINVKSLPFNP 254 (340)
Q Consensus 177 FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~--f~~~~~~~~~~~~~~~~~~~~~~~ 254 (340)
..| ..|.|-|-. + .||+ .|.+...+.+.- +-++.........+....+.+..+
T Consensus 193 ~dP-~~IdYpIPg-N----------------------DDai-rsI~L~c~lia~A~l~G~~~~~~~~g~d~g~~~~~~~~ 247 (332)
T PRK12311 193 CDP-KGITYLVPG-N----------------------DDAG-RAIALYCDLIARAAIDGISRAQGDLGIDIGASEAPLAE 247 (332)
T ss_pred CCC-CCCCCCCCC-C----------------------CCHH-HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHH
T ss_conf 998-657756848-6----------------------5589-99999999999999999987520026675543467311
Q ss_pred HHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 33111221011058889898839837188874498888618898864499999999980831267687898677999998
Q gi|254780237|r 255 ALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334 (340)
Q Consensus 255 ~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~~~~~~~~~~~~~ 334 (340)
.| +-.+.+ ..+--| .=-+--.+||.+|++.|.+ ++.+|...|+.-=-.+.+|.++++.+...
T Consensus 248 ~~--~~~~~~---~~~~~l---------~~p~g~~ddl~ki~gvgp~----~~~~ln~~g~~h~~qia~~t~~~~~~~d~ 309 (332)
T PRK12311 248 EL--PAAQAP---EGFQGL---------AGPRGAPDDLKKLTGVSGA----IEKKLNDLGIFHYWQLAELDPDTAHKIGE 309 (332)
T ss_pred HC--CCCCCH---HHHHCC---------CCCCCCCCHHHHHCCCCHH----HHHHHHHCCCEEHHHHHCCCHHHHHHHHH
T ss_conf 25--643333---454212---------4788984257771576788----99985012412189886279999998888
Q ss_pred HHH
Q ss_conf 775
Q gi|254780237|r 335 KYE 337 (340)
Q Consensus 335 ~~~ 337 (340)
++.
T Consensus 310 ~l~ 312 (332)
T PRK12311 310 EVG 312 (332)
T ss_pred HCC
T ss_conf 718
No 68
>cd01434 EFG_mtEFG1_IV EFG_mtEFG1_IV: domains similar to domain IV of the bacterial translational elongation factor (EF) EF-G. Included in this group is a domain of mitochondrial Elongation factor G1 (mtEFG1) proteins homologous to domain IV of EF-G. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provi
Probab=59.96 E-value=14 Score=17.57 Aligned_cols=44 Identities=34% Similarity=0.655 Sum_probs=23.7
Q ss_pred EEEEECCCCCHHHHHHH-----------------HHHHHHHC-CCCCEEEEEEEE---CCCCCCC
Q ss_conf 99996169756678889-----------------99998741-698306889998---8714431
Q gi|254780237|r 29 LMIAEPLPRGFAHTLGN-----------------ALRRVLMS-SLRGAAITAVQI---DGVLHEI 72 (340)
Q Consensus 29 ~f~~~Ple~G~g~TlGN-----------------aLRRvLLs-si~G~ait~vkI---~gv~HEf 72 (340)
.+.++|+++|.|..+-| .+|..+-+ -+-|+.++.||+ +|..|+=
T Consensus 29 ~l~ieP~~~g~g~~F~~~i~gg~iP~e~i~avekGv~ea~~~G~l~G~pv~dvkv~L~dG~~H~v 93 (116)
T cd01434 29 VLEIEPLPRGSGFEFVNKIVGGAIPKEYIPAVEKGFREALEKGPLAGYPVVDVKVTLYDGSYHDV 93 (116)
T ss_pred EEEEEECCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEEECCCCCCC
T ss_conf 99999888999748986326996999999999999999982687447527899999971551238
No 69
>PRK03926 mevalonate kinase; Provisional
Probab=53.30 E-value=18 Score=16.87 Aligned_cols=73 Identities=21% Similarity=0.305 Sum_probs=52.5
Q ss_pred CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCC----------CCHHHHHHHH
Q ss_conf 110588898988398371888744988886188988644999999999808312676878----------9867799999
Q gi|254780237|r 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPD----------WPPESIEELA 333 (340)
Q Consensus 264 eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~~----------~~~~~~~~~~ 333 (340)
+++.++..+|++.+...+|+|+..+. .|+.--+.--..|+++.+.....| .+|-++.+ .+|+..++..
T Consensus 200 ~i~~~a~~~l~~~d~~~lG~Lm~~~h-~ll~~lgVS~peld~lv~~a~~~G-alGAKltGaG~GGc~iaL~~~d~~~~v~ 277 (302)
T PRK03926 200 KLSEKAEELVLSGDYVSIGELMNINQ-GLLDALGVSTKELSELVYAARTAG-AFGAKITGAGGGGCMVALTAPDKCREVA 277 (302)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHH-HHHHHCCCCCHHHHHHHHHHHHCC-CCEEEECCCCCCCEEEEEECCCCHHHHH
T ss_conf 99999998776564999999999968-878731689889999999999679-8288805898762899994613199999
Q ss_pred HHHHC
Q ss_conf 87750
Q gi|254780237|r 334 KKYED 338 (340)
Q Consensus 334 ~~~~~ 338 (340)
+.++.
T Consensus 278 ~al~~ 282 (302)
T PRK03926 278 TAIGI 282 (302)
T ss_pred HHHHH
T ss_conf 99997
No 70
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=53.09 E-value=18 Score=16.85 Aligned_cols=99 Identities=11% Similarity=0.043 Sum_probs=61.5
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCH---HHCCCCHHHHHHHCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCH
Q ss_conf 7999999999999888762244443221000---0000001123331112210-11058889898839837188874498
Q gi|254780237|r 214 EDSVALASRILQDQLGMFINFEEPKKEVKED---INVKSLPFNPALLKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTE 289 (340)
Q Consensus 214 ~eAl~~Aa~iL~~~l~~f~~~~~~~~~~~~~---~~~~~~~~~~~L~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~ 289 (340)
.-.+..|.+++..++.......-........ .-..+.- -.-..++-+| .++.....-|++.++.++.+|...++
T Consensus 106 ~~Vl~~~~Ril~am~di~~~~~~~~~~~~~l~l~q~i~q~~--w~~~~pL~Qlp~~~~~~~~~l~~~~i~~l~~l~~~~~ 183 (312)
T smart00611 106 VYVLQNAGRLLQAMVDIALERGWLSTALNALNLSQMIIQAL--WPTDSPLLQLPHLPEEILKRLEKKKVLSLEDLLELED 183 (312)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC--CCCCCCHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCH
T ss_conf 99999889999999999972696999999999999988454--8999901248999999999999669998999973899
Q ss_pred HHHHCCCCCCHHHHHHHHHHHHHHC
Q ss_conf 8886188988644999999999808
Q gi|254780237|r 290 ADMLRMANFGRKSLVEIKGVLGTMG 314 (340)
Q Consensus 290 ~dLl~ikNfG~KSl~EI~~~L~~~g 314 (340)
+++..+-++-.+-..+|.+.+..+-
T Consensus 184 ~e~~~ll~~~~~~~~~i~~~~~~~P 208 (312)
T smart00611 184 EERGELLGLLDAEGERVYKVLSRLP 208 (312)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCC
T ss_conf 9999997899999999999999789
No 71
>pfam02889 Sec63 Sec63 Brl domain. This domain (also known as the Brl domain) is required for assembly of functional endoplasmic reticulum translocons.
Probab=50.57 E-value=19 Score=16.59 Aligned_cols=96 Identities=13% Similarity=0.125 Sum_probs=57.0
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCCC-----CHHHCCCCHHHHHHHCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHC
Q ss_conf 79999999999998887622444432210-----000000001123331112210-110588898988398371888744
Q gi|254780237|r 214 EDSVALASRILQDQLGMFINFEEPKKEVK-----EDINVKSLPFNPALLKKVEEL-ELSVRSTNCLRGENIVYMGDLIQR 287 (340)
Q Consensus 214 ~eAl~~Aa~iL~~~l~~f~~~~~~~~~~~-----~~~~~~~~~~~~~L~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~ 287 (340)
...+..|.++++.++.....-.-...... ......--+. .-+.-+| .++.....-|.+.||.++.+|...
T Consensus 103 ~~I~~~~~Ri~~am~ei~~~~~~~~~~~~~l~l~q~i~q~~w~~----~~pL~Qlp~~~~~~i~~l~~~~i~sl~~l~~~ 178 (309)
T pfam02889 103 NYILQNAGRLLRALFEIALSKGWLSPALNALELSKMIEQRLWPS----DSPLRQLPHIPPEVIKKLEKKGISSLEDLMDL 178 (309)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCC----CCHHHCCCCCCHHHHHHHHHCCCCCHHHHHHC
T ss_conf 99999899999999999986897999999999999998335999----98545179999999999997799989999609
Q ss_pred CHHHHHCCCCC-CHHHHHHHHHHHHHH
Q ss_conf 98888618898-864499999999980
Q gi|254780237|r 288 TEADMLRMANF-GRKSLVEIKGVLGTM 313 (340)
Q Consensus 288 s~~dLl~ikNf-G~KSl~EI~~~L~~~ 313 (340)
+.+++..+-+. -.+-..+|.+.+..+
T Consensus 179 ~~~el~~ll~~~~~~~~~~i~~~~~~~ 205 (309)
T pfam02889 179 DPEELGELLGRNPPKQGKDIAEFVNRF 205 (309)
T ss_pred CHHHHHHHHCCCCHHHHHHHHHHHHHC
T ss_conf 999999997027989999999999857
No 72
>pfam00633 HHH Helix-hairpin-helix motif. The helix-hairpin-helix DNA-binding motif is found to be duplicated in the central domain of RuvA. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain.
Probab=50.28 E-value=10 Score=18.40 Aligned_cols=28 Identities=21% Similarity=0.398 Sum_probs=22.8
Q ss_pred HHHHHHCCHHHHHCCCCCCHHHHHHHHH
Q ss_conf 1888744988886188988644999999
Q gi|254780237|r 281 MGDLIQRTEADMLRMANFGRKSLVEIKG 308 (340)
Q Consensus 281 igdLv~~s~~dLl~ikNfG~KSl~EI~~ 308 (340)
...+..-|.++|+++++.|+|..+.|.+
T Consensus 2 ~~~~~~as~eeL~~lpGVG~~tA~~I~~ 29 (30)
T pfam00633 2 LEGLIPASREELLALPGVGPKTAEAILS 29 (30)
T ss_pred CCCCCCCCHHHHHHCCCCCHHHHHHHHC
T ss_conf 6443523599997288977688998853
No 73
>PRK02362 ski2-like helicase; Provisional
Probab=50.24 E-value=19 Score=16.66 Aligned_cols=43 Identities=23% Similarity=0.256 Sum_probs=32.3
Q ss_pred HHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHH
Q ss_conf 5888989883983718887449888861889886449999999998
Q gi|254780237|r 267 VRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312 (340)
Q Consensus 267 vRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~ 312 (340)
+|| -.|-+|||+|+.||..-+.++|.++ +|+|-.+-|.+-+..
T Consensus 663 ~RA-R~Ly~aGi~s~~dla~A~p~~l~~i--lg~~~a~~i~~~~~~ 705 (736)
T PRK02362 663 VRA-RRLYNAGITSRADLRAADKEVVAAI--LGPKIAERVLEQLGR 705 (736)
T ss_pred HHH-HHHHHCCCCCHHHHHHCCHHHHHHH--HHHHHHHHHHHHHCC
T ss_conf 999-9999879999999970999999999--777899999998388
No 74
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=48.24 E-value=18 Score=16.76 Aligned_cols=17 Identities=12% Similarity=0.169 Sum_probs=7.2
Q ss_pred EEEEEECCCC-EEEEEEE
Q ss_conf 0899977896-4999999
Q gi|254780237|r 132 HVICNLDVDA-VVRMELT 148 (340)
Q Consensus 132 ~~IaTl~~~~-~l~iel~ 148 (340)
.+.++++++. .+.+.++
T Consensus 79 ~l~v~v~D~tG~I~lvfF 96 (677)
T PRK10917 79 RLRVTLSDGTGVLTLVFF 96 (677)
T ss_pred EEEEEEEECCEEEEEEEE
T ss_conf 499999989879999998
No 75
>pfam04994 TfoX_C TfoX C-terminal domain. 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 associated with pfam00383 in a cytidine and deoxycytidylate deaminase family protein from Neisseria meningitidis serogroup B. It is also found as an isolated domain in some proteins suggesting this is an autonomous domain.
Probab=47.16 E-value=22 Score=16.26 Aligned_cols=36 Identities=19% Similarity=0.320 Sum_probs=25.8
Q ss_pred CCCHHHHHHHHHCCCCCHHHHHHCCHHH-HHCCCCCC
Q ss_conf 1105888989883983718887449888-86188988
Q gi|254780237|r 264 ELSVRSTNCLRGENIVYMGDLIQRTEAD-MLRMANFG 299 (340)
Q Consensus 264 eLSvRs~NcLk~a~I~tigdLv~~s~~d-Ll~ikNfG 299 (340)
+|+..+-.-|+++||+|+.||-.....+ -++++-.|
T Consensus 6 Nlg~~~er~L~~vGI~t~~~L~~~Ga~~ay~kl~~~g 42 (77)
T pfam04994 6 NLGLKLERMLKKAGIHTVEDLRELGAVEAYLKLKRSG 42 (77)
T ss_pred CCCHHHHHHHHHCCCCCHHHHHHHCHHHHHHHHHHHC
T ss_conf 9899999999994999899999818999999999878
No 76
>TIGR01259 comE comEA protein; InterPro: IPR004787 The comE locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. comEA and comEC are required for transformability, whereas the products of comEB and of the overlapping comER, which is transcribed in the reverse direction, are dispensable . ComEA has been shown to be an integral membrane protein, as predicted from hydropathy analysis, with its C-terminal domain outside the cytoplasmic membrane. This C-terminal domain possesses a sequence with similarity to those of several proteins known to be involved in nucleic acid transactions including UvrC and a human protein that binds to the replication origin of the Human herpesvirus 4 (Epstein-Barr virus) ..
Probab=45.66 E-value=12 Score=18.06 Aligned_cols=23 Identities=26% Similarity=0.505 Sum_probs=14.0
Q ss_pred CHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf 98888618898864499999999
Q gi|254780237|r 288 TEADMLRMANFGRKSLVEIKGVL 310 (340)
Q Consensus 288 s~~dLl~ikNfG~KSl~EI~~~L 310 (340)
|=+||+++.+.|.||++=+++.+
T Consensus 100 SvddL~kVsGIG~k~~eKLk~~~ 122 (124)
T TIGR01259 100 SVDDLTKVSGIGEKSLEKLKDYV 122 (124)
T ss_pred CHHHHHCCCCCCHHHHHHHHHCC
T ss_conf 75550035788546687420003
No 77
>TIGR00426 TIGR00426 competence protein ComEA helix-hairpin-helix repeat region; InterPro: IPR004509 This domain is found in 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 domain represents a region of two tandem copies of a helix-hairpin-helix domain, each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to this domain..
Probab=44.64 E-value=14 Score=17.55 Aligned_cols=24 Identities=25% Similarity=0.360 Sum_probs=19.7
Q ss_pred CHHHHHCCCCCCHHHHHHHHHHHH
Q ss_conf 988886188988644999999999
Q gi|254780237|r 288 TEADMLRMANFGRKSLVEIKGVLG 311 (340)
Q Consensus 288 s~~dLl~ikNfG~KSl~EI~~~L~ 311 (340)
+-+||++++++|+++++-+++.|.
T Consensus 46 t~Edl~~V~GiG~~~~Ek~~~~i~ 69 (70)
T TIGR00426 46 TVEDLKKVSGIGEKLLEKNKASIT 69 (70)
T ss_pred CHHHHHHCCCCCHHHHHHHHHHHC
T ss_conf 622232147876245555644306
No 78
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=44.48 E-value=24 Score=15.99 Aligned_cols=19 Identities=11% Similarity=0.417 Sum_probs=10.8
Q ss_pred CCCCCCCCCHHHHHHHHHH
Q ss_conf 4314664624449999984
Q gi|254780237|r 70 HEISSIKGVHEDLTDIILN 88 (340)
Q Consensus 70 HEfs~i~GV~EDV~eIiLN 88 (340)
-+...||||=+.+.+-|--
T Consensus 48 ~~l~~ipGIG~~ia~kI~E 66 (334)
T smart00483 48 KDLKGLPGIGDKIKKKIEE 66 (334)
T ss_pred HHHCCCCCCCHHHHHHHHH
T ss_conf 9972799987899999999
No 79
>KOG4392 consensus
Probab=40.98 E-value=27 Score=15.65 Aligned_cols=47 Identities=17% Similarity=0.210 Sum_probs=36.1
Q ss_pred EEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 44223577641168877621899999938961777999999999999888762
Q gi|254780237|r 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232 (340)
Q Consensus 180 V~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~ 232 (340)
|.-..|.|+.. -.-+.+|-|.|.--.+|++|+..|++-+...+..+.
T Consensus 56 vLFagYkvpHP------l~~~~~LRiqtt~d~~p~~al~~a~~~l~~el~~l~ 102 (117)
T KOG4392 56 VLFAGYKVPHP------LEHKIILRVQTTEDCSPADALTNAITDLIEELSLLE 102 (117)
T ss_pred CEEEEECCCCC------CCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 16765048995------426679987406789989999999999997788889
No 80
>pfam08221 HTH_9 RNA polymerase III subunit RPC82 helix-turn-helix domain. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In Saccharomyces cerevisiae, the enzyme is composed of 15 subunits, ranging from 160 to about 10 kDa. This region is a probably DNA-binding helix-turn-helix.
Probab=39.93 E-value=28 Score=15.54 Aligned_cols=39 Identities=18% Similarity=0.262 Sum_probs=31.8
Q ss_pred CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH
Q ss_conf 11058889898839837188874498888618898864499999999980
Q gi|254780237|r 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313 (340)
Q Consensus 264 eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~ 313 (340)
|+..+...||-+.|-.|+.++++.++ -|.++|+..|..+
T Consensus 13 ei~~~V~~~Ll~~g~~tl~~i~~~t~-----------L~~~~Vk~aL~vL 51 (62)
T pfam08221 13 EVVAKVVSTLLRKGRLTLREIVKLTK-----------LSLDQVKKSLVVL 51 (62)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHCC-----------CCHHHHHHHHHHH
T ss_conf 38999999999858816999997828-----------9999999999999
No 81
>cd01702 Pol_eta Pol eta is member of the DNA polimerase Y-family. Unlike other Y-family members, Pol eta can efficiently and accurately replicate DNA past UV-induced cis-syn cyclobutane thymine-thumine (T-T) lesions. It synthesizes AA opposite a TT dimer. Pol eta is able to replicate through a variety of other distorting DNA lesion as well.
Probab=38.08 E-value=25 Score=15.86 Aligned_cols=54 Identities=15% Similarity=0.159 Sum_probs=31.3
Q ss_pred HHHCCHHHC-CCCHHHHHHHHHC-CCCCHHHHHHCC--HHHHHCCCCCCHHHHHHHHHHH
Q ss_conf 331112210-1105888989883-983718887449--8888618898864499999999
Q gi|254780237|r 255 ALLKKVEEL-ELSVRSTNCLRGE-NIVYMGDLIQRT--EADMLRMANFGRKSLVEIKGVL 310 (340)
Q Consensus 255 ~L~~~IeeL-eLSvRs~NcLk~a-~I~tigdLv~~s--~~dLl~ikNfG~KSl~EI~~~L 310 (340)
+..++|.++ ...-++..-|.+. ||+|++||..+. +..|+. -+|.+.-..+.+.+
T Consensus 179 l~~lpI~~i~GvG~k~~~~L~~~lgi~ti~dl~~~~~~~~~l~~--~~~~~~g~~l~~~a 236 (358)
T cd01702 179 LSSLPITKIRGLGGKLGESIIEVLGVPTEGDLLWFRSSEAQLQE--KLGDKTGTWLYNLV 236 (358)
T ss_pred HHCCCCCEECCCCHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHH--HHHHHHHHHHHHHH
T ss_conf 85599766278678999999998399658989875148599999--98279999999997
No 82
>TIGR00368 TIGR00368 Mg chelatase homolog; InterPro: IPR004482 This family of bacterial proteins are variously described as 'hypothetical protein yifB', 'competence protein', 'hypothetical protein' or 'Mg chelatase-related protein'. These proteins are a subset of the magnesium chelatase, ChlI subunit family and either belong to or show significant homology to the non-peptidase homologs of the MEROPS peptidase family S16 (lon protease family, clan SF), IPR001984 from INTERPRO. .
Probab=36.71 E-value=27 Score=15.67 Aligned_cols=44 Identities=27% Similarity=0.302 Sum_probs=28.5
Q ss_pred HHHHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHH
Q ss_conf 23331112210110588898988398371888744988886188988644999
Q gi|254780237|r 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVE 305 (340)
Q Consensus 253 ~~~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~E 305 (340)
...|...+.-|+||+||+..+-+- =.||.| |..=++.-+..|.|
T Consensus 457 ~~~Le~~L~kLglS~RA~~riLKv-aRTIaD--------L~~~~~I~~~hL~E 500 (505)
T TIGR00368 457 ANLLEGALNKLGLSVRATHRILKV-ARTIAD--------LKEEENISREHLAE 500 (505)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHHH-HHHHHH--------HHHHHHHHHHHHHH
T ss_conf 999999998708516688768878-864663--------20003578999999
No 83
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=36.43 E-value=18 Score=16.76 Aligned_cols=26 Identities=19% Similarity=0.247 Sum_probs=13.6
Q ss_pred HHHHHHHHCCCCCHHHHHHCCHHHHH
Q ss_conf 88898988398371888744988886
Q gi|254780237|r 268 RSTNCLRGENIVYMGDLIQRTEADML 293 (340)
Q Consensus 268 Rs~NcLk~a~I~tigdLv~~s~~dLl 293 (340)
..-..|...||+|..++...|..|+-
T Consensus 78 k~e~~Ln~~GI~tfaQIAAwt~~di~ 103 (133)
T COG3743 78 KLEKVLNELGIFTFAQIAAWTRADIA 103 (133)
T ss_pred HHHHHHHHCCCCCHHHHHHCCHHHHH
T ss_conf 89989987477639999744899999
No 84
>cd01703 Pol_iota Pol iota is member of the DNA polymerase Y-family, and has also been called Rad30 homolog B. Unlike classic DNA polymerases,Y-family polymerases are induced by DNA damage. They can transverse normal replication-blocking DNA lesions. Unlike Pol eta, Pol iota is unable to replicate through a cis-syn T-T dimer. In human Pol iota, the base-pairing mode in the active site at the replicative end mat bee Hoogsteen instead of Watson-Click. Human Pol iota can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine. Pol iota prefers to insert Guanosine instead of Adenosine opposite Thymidine.
Probab=35.96 E-value=33 Score=15.15 Aligned_cols=49 Identities=18% Similarity=0.283 Sum_probs=36.8
Q ss_pred CCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHH
Q ss_conf 112210-11058889898839837188874498888618898864499999
Q gi|254780237|r 258 KKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIK 307 (340)
Q Consensus 258 ~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~ 307 (340)
.+|.++ .+.-++..-|.+.||.|++||.++++-+++. +.||++.-..+.
T Consensus 210 ~~i~ki~GIG~kt~~~L~~~gi~ti~dl~~~~~~~~l~-~~fG~~~g~~l~ 259 (394)
T cd01703 210 GSLRKIPGIGYKTAKKLEDHGISSVRDLQECSELLLLE-KGFGKGIAQRIW 259 (394)
T ss_pred CCHHHHCCCCHHHHHHHHHCCCEEHHHHHCCCHHHHHH-HHHHHHHHHHHH
T ss_conf 88055278179999999983892679876588799999-987889999999
No 85
>PTZ00144 dihydrolipoamide succinyltransferase; Provisional
Probab=35.36 E-value=33 Score=15.08 Aligned_cols=80 Identities=11% Similarity=0.048 Sum_probs=57.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHCCCEEEECCCCCEEEEEEEECCEEEEEEEEEC-CCCEEEECCCEEEEEEC-CCCEEEE
Q ss_conf 144314664624449999984011417772798279999994471699633513-89859988880899977-8964999
Q gi|254780237|r 68 VLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLD-VDAVVRM 145 (340)
Q Consensus 68 v~HEfs~i~GV~EDV~eIiLNLK~I~~k~~~~~~~~~~l~~~Gp~~vtA~Di~~-p~~veivNpd~~IaTl~-~~~~l~i 145 (340)
..|.|+.+|+..-..-.+.--||-+-.++...+.+++++-.=|++.--+.=.+| -..=.-|..++.||.+. +.+..++
T Consensus 24 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~ikMP~LGetm~EG~Iv~WlvkeGD~V~~gd~L~EVETDKA~~EV 103 (430)
T PTZ00144 24 LNRFYSVLPNCKSTLKRDFNPLKLIGNRYFSKDIKTIKVPRLGDSISEGTLSEWKKKVGDYVKVDETIAIVETDKVSVDI 103 (430)
T ss_pred HHHHHHHCCCCCCHHHHHCCHHHHHCCCCCCCCCEEEECCCCCCCCEEEEEEEEECCCCCEECCCCCEEEEECCCCCEEE
T ss_conf 88888658874002665513223101001467864987988999820699979981899986899908999858841796
Q ss_pred EE
Q ss_conf 99
Q gi|254780237|r 146 EL 147 (340)
Q Consensus 146 el 147 (340)
+-
T Consensus 104 eS 105 (430)
T PTZ00144 104 NS 105 (430)
T ss_pred CC
T ss_conf 57
No 86
>KOG1684 consensus
Probab=34.42 E-value=14 Score=17.47 Aligned_cols=37 Identities=22% Similarity=0.384 Sum_probs=20.4
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 898864499999999980831267687898677999998
Q gi|254780237|r 296 ANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAK 334 (340)
Q Consensus 296 kNfG~KSl~EI~~~L~~~gl~lg~~l~~~~~~~~~~~~~ 334 (340)
+.|+.+|++||.+.|+++.- --+...|-.+.+..|++
T Consensus 271 ~~Fs~~tVeeIie~lk~~q~--~~~~~ewak~tlk~L~k 307 (401)
T KOG1684 271 KCFSANTVEEIIEALKNYQQ--SADGSEWAKETLKTLKK 307 (401)
T ss_pred HHHCCCCHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHH
T ss_conf 76121659999999998764--40588999999998860
No 87
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=34.29 E-value=35 Score=14.98 Aligned_cols=45 Identities=11% Similarity=0.132 Sum_probs=39.7
Q ss_pred CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHH
Q ss_conf 110588898988398371888744988886188988644999999
Q gi|254780237|r 264 ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKG 308 (340)
Q Consensus 264 eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~ 308 (340)
+++.....-|..+|+.++.||...+.++|..+.+++....+++..
T Consensus 381 ~~~~~~~~~l~~~g~~~~edl~~~~~del~~~~~~~~e~a~~li~ 425 (428)
T PRK09202 381 GLDPELAFKLAEKGVKTLEDLAELAVDELIDIEGLDEEEAGELIM 425 (428)
T ss_pred CCCHHHHHHHHHCCCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHH
T ss_conf 999999999998699879999657988896377989999999998
No 88
>MTH00078 COX1 cytochrome c oxidase subunit I; Provisional
Probab=34.20 E-value=20 Score=16.55 Aligned_cols=16 Identities=19% Similarity=0.640 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHHHCCC
Q ss_conf 6788899999874169
Q gi|254780237|r 40 AHTLGNALRRVLMSSL 55 (340)
Q Consensus 40 g~TlGNaLRRvLLssi 55 (340)
|.|.||+|||-+|++.
T Consensus 4 ~~~~~~~~~~~~lttt 19 (548)
T MTH00078 4 GMTFGNSMKQSIINTV 19 (548)
T ss_pred CCCHHHHHHHHHHCCC
T ss_conf 4405678888883056
No 89
>PRK13397 3-deoxy-7-phosphoheptulonate synthase; Provisional
Probab=34.03 E-value=35 Score=14.95 Aligned_cols=57 Identities=9% Similarity=0.032 Sum_probs=26.2
Q ss_pred EEEEECCC---CCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCC
Q ss_conf 99996169---7566788899999874169830688999887144314664624449999984011
Q gi|254780237|r 29 LMIAEPLP---RGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKG 91 (340)
Q Consensus 29 ~f~~~Ple---~G~g~TlGNaLRRvLLssi~G~ait~vkI~gv~HEfs~i~GV~EDV~eIiLNLK~ 91 (340)
.|+.+|=- +-+...++-.++.. |..+..--+.....--.+-.|+-+.-++++-++|+
T Consensus 17 ~lIAGPC~iES~e~~~~~A~~lk~~------g~~~~r~~~~K~RTs~~sfrG~G~egL~~L~~vk~ 76 (250)
T PRK13397 17 NFIVGPCSIESYDHIRLAASSAKKL------GYNYFRGGAYKPRTSAASFQGLGLQGIRYLHEVCQ 76 (250)
T ss_pred CEEECCCHHCCHHHHHHHHHHHHHC------CCCEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf 7885587330999999999999984------98857536268889997767888889999999999
No 90
>TIGR01357 aroB 3-dehydroquinate synthase; InterPro: IPR016037 The 3-dehydroquinate synthase (4.2.3.4 from EC) domain is present in isolation in various bacterial 3-dehydroquinate synthases and also present as a domain in the pentafunctional AROM polypeptide (P07547 from SWISSPROT) . 3-dehydroquinate (DHQ) synthase catalyses the formation of dehydroquinate (DHQ) and orthophosphate from 3-deoxy-D-arabino heptulosonic 7 phosphate . This reaction is part of the shikimate pathway which is involved in the biosynthesis of aromatic amino acids.; GO: 0003856 3-dehydroquinate synthase activity, 0009073 aromatic amino acid family biosynthetic process.
Probab=32.99 E-value=17 Score=17.06 Aligned_cols=28 Identities=18% Similarity=0.356 Sum_probs=13.1
Q ss_pred HHCCCCCHHHHHHCCHHH--HHCCCCCCHH
Q ss_conf 883983718887449888--8618898864
Q gi|254780237|r 274 RGENIVYMGDLIQRTEAD--MLRMANFGRK 301 (340)
Q Consensus 274 k~a~I~tigdLv~~s~~d--Ll~ikNfG~K 301 (340)
-.-+|..=.+.|...+.| |.++=|||=.
T Consensus 212 i~~S~~~Ka~iV~~De~E~GlR~~LNfGHT 241 (361)
T TIGR01357 212 IKRSIEVKASIVAEDEKESGLRAILNFGHT 241 (361)
T ss_pred HHHHHHHHHHHHCCCCCCCHHHHHHHCCCH
T ss_conf 998868889983128120024766522545
No 91
>pfam04106 APG5 Autophagy protein Apg5. Apg5 is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway.
Probab=32.28 E-value=36 Score=14.90 Aligned_cols=32 Identities=28% Similarity=0.428 Sum_probs=12.3
Q ss_pred CHHHHHHHHHHHHHHCCCCC-EEEEEEEECCCC
Q ss_conf 56678889999987416983-068899988714
Q gi|254780237|r 38 GFAHTLGNALRRVLMSSLRG-AAITAVQIDGVL 69 (340)
Q Consensus 38 G~g~TlGNaLRRvLLssi~G-~ait~vkI~gv~ 69 (340)
|...|||.+|+..|-...+. ..+..+.|.|+.
T Consensus 135 g~~~TLg~~L~~~lP~lf~s~~~~~~viihGI~ 167 (195)
T pfam04106 135 GQPQTLGDALSELLPELFPSSEELAKPIIHGIE 167 (195)
T ss_pred CCCCCHHHHHHHHCHHHCCCCCCCCEEEEECCC
T ss_conf 730319999998685435876555579981761
No 92
>pfam11731 Cdd1 Pathogenicity locus. 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=32.11 E-value=38 Score=14.75 Aligned_cols=37 Identities=16% Similarity=0.268 Sum_probs=21.5
Q ss_pred HHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHH
Q ss_conf 88886188988644999999999808312676878986779
Q gi|254780237|r 289 EADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESI 329 (340)
Q Consensus 289 ~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~~~~~~~~ 329 (340)
-.+|..|||.|++ +.+-|..+|++-=.+|.+.+|...
T Consensus 11 l~~L~~lPnIG~a----~a~DL~~LGi~~~~~L~g~dp~el 47 (92)
T pfam11731 11 LKELTDLPNIGKA----TAKDLRLLGINSPAQLAGRDPLEL 47 (92)
T ss_pred HHHHHCCCCCCHH----HHHHHHHHCCCCHHHHHCCCHHHH
T ss_conf 9987418974699----999999918998999917999999
No 93
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=30.64 E-value=27 Score=15.67 Aligned_cols=22 Identities=18% Similarity=0.383 Sum_probs=17.6
Q ss_pred HHHHCCCCCCHHHHHHHHHHHH
Q ss_conf 8886188988644999999999
Q gi|254780237|r 290 ADMLRMANFGRKSLVEIKGVLG 311 (340)
Q Consensus 290 ~dLl~ikNfG~KSl~EI~~~L~ 311 (340)
++|++++++|+|+.+-|.+...
T Consensus 1 ~~L~~v~GIG~k~A~~ll~~~~ 22 (26)
T smart00278 1 EELLKVPGIGPKTAEKILEAXX 22 (26)
T ss_pred CCCCCCCCCCCHHHHHHHHHHH
T ss_conf 9210179988115999999762
No 94
>TIGR02236 recomb_radA DNA repair and recombination protein RadA; InterPro: IPR011938 This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA, eukaryotic RAD51 (IPR011941 from INTERPRO), and archaeal RadB (IPR011939 from INTERPRO). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0008094 DNA-dependent ATPase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=30.16 E-value=40 Score=14.54 Aligned_cols=54 Identities=13% Similarity=0.200 Sum_probs=39.6
Q ss_pred HHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHH
Q ss_conf 2210-11058889898839837188874498888618898864499999999980
Q gi|254780237|r 260 VEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTM 313 (340)
Q Consensus 260 IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~ 313 (340)
|+|| .--..+..=|+-||..|+..+..=|..||-.+.+.|.+....|.++=-+.
T Consensus 2 ledLPGVGp~TA~KL~EaGy~t~~~iA~A~~~EL~~~~gI~E~~A~kiI~AAR~a 56 (333)
T TIGR02236 2 LEDLPGVGPATAEKLREAGYDTLEAIAVASPKELSEIAGIGEGTAAKIIQAARKA 56 (333)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHHHHHH
T ss_conf 6657897576889988610788999844585795320378777899999999998
No 95
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=29.82 E-value=41 Score=14.50 Aligned_cols=143 Identities=19% Similarity=0.200 Sum_probs=75.1
Q ss_pred CEE--CCCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHH------HHHHHHCCCCCCCC
Q ss_conf 302--1243111144223577641168877621899999938961777999999999999------88876224444322
Q gi|254780237|r 169 GLI--TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQD------QLGMFINFEEPKKE 240 (340)
Q Consensus 169 g~i--~iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~------~l~~f~~~~~~~~~ 240 (340)
|+| .|+-+-.|.++-..+-+-++.||.|. ++ |-.+|. +-.+.|+.++++-.. +|+.|.-+......
T Consensus 191 g~ir~~i~e~~e~~~r~r~tp~fapaGQSTQ---mi--vGA~~~-tD~~Ilsrs~~ly~~y~lkRVyySaf~Pv~~s~~l 264 (404)
T COG4277 191 GWIRLKILENAEDKRRKRHTPEFAPAGQSTQ---MI--VGADGE-TDEDILSRSENLYGRYSLKRVYYSAFSPVPSSPLL 264 (404)
T ss_pred HHHHHHHHHCCCCHHHHCCCCCCCCCCCCEE---EE--EECCCC-CHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCC
T ss_conf 9999877651550222104723367787327---88--715887-44889988887753243148986213336889888
Q ss_pred CCCHHHCCCC---------------HHHHHHHCCHH--HCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHH
Q ss_conf 1000000000---------------11233311122--101105888989883983718887449888861889886449
Q gi|254780237|r 241 VKEDINVKSL---------------PFNPALLKKVE--ELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSL 303 (340)
Q Consensus 241 ~~~~~~~~~~---------------~~~~~L~~~Ie--eLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl 303 (340)
.......-.+ ..++++...=+ ++++-....-+|+...+.-| |+-.-+..+|+++|++|.||.
T Consensus 265 p~~~pplmRehRLYQADwLlrfYgF~~~Ei~~~g~~~ld~~lDPK~~wAl~~~d~FPV-dvn~A~~~~llRVPGiG~ksa 343 (404)
T COG4277 265 PDDKPPLMREHRLYQADWLLRFYGFSADEILASGGDFLDPDLDPKTAWALKHMDRFPV-DVNKAPYKELLRVPGIGVKSA 343 (404)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHCCCCCCCCCCCHHHHHHHHCCCCCCC-CCCCCCHHHHCCCCCCCHHHH
T ss_conf 6667853677777777789997088878887448975578878345777733553651-334567778211688773788
Q ss_pred HHHHH----------HHHHHCCCCC
Q ss_conf 99999----------9998083126
Q gi|254780237|r 304 VEIKG----------VLGTMGLFLG 318 (340)
Q Consensus 304 ~EI~~----------~L~~~gl~lg 318 (340)
.-|.. -|+.+|..+.
T Consensus 344 ~rIv~~Rr~~rl~~e~Lkk~Gvvlk 368 (404)
T COG4277 344 RRIVMTRRRTRLTLEDLKKLGVVLK 368 (404)
T ss_pred HHHHHHHHHCCCCHHHHHHHCEEEE
T ss_conf 9998874230267989865330322
No 96
>KOG3438 consensus
Probab=29.33 E-value=42 Score=14.45 Aligned_cols=48 Identities=15% Similarity=0.140 Sum_probs=32.6
Q ss_pred EEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 144223577641168877621899999938961777999999999999888762
Q gi|254780237|r 179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232 (340)
Q Consensus 179 PV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~ 232 (340)
-|.-+.|+|-. ..-+++-+-|.|-|+....++|..+..=|++.++...
T Consensus 42 eVefcGYtIPH------Pse~k~niRIQt~~~~~A~evl~kgl~el~~~c~~v~ 89 (105)
T KOG3438 42 EVEFCGYTIPH------PSEDKINIRIQTRDGDPAVEVLKKGLEELMQLCDHVR 89 (105)
T ss_pred CEEEEECCCCC------CCHHHHEEEEEECCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 44787515899------7555603788805898606899999999999999999
No 97
>COG0197 RplP Ribosomal protein L16/L10E [Translation, ribosomal structure and biogenesis]
Probab=28.78 E-value=35 Score=14.91 Aligned_cols=88 Identities=19% Similarity=0.225 Sum_probs=55.2
Q ss_pred CCCEEEEEEEECCEEEEEEEEEC-----------CCCEEE-ECCCEEEEEECCCCEEEEEEEEECCCCCEECCCCCCCCC
Q ss_conf 98279999994471699633513-----------898599-888808999778964999999746876320344446557
Q gi|254780237|r 99 DSHKRVTIFKRGPGVVTAGDIQT-----------VNDIEV-LNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTEND 166 (340)
Q Consensus 99 ~~~~~~~l~~~Gp~~vtA~Di~~-----------p~~vei-vNpd~~IaTl~~~~~l~iel~ie~G~GY~~~e~~~~~~~ 166 (340)
..+....|....|+.|||..|+. -.++.| +-||+.++.=- .+.+..+|+| .
T Consensus 30 ~~fg~~gL~a~e~~~It~~qiEAARia~~R~lkr~g~~wIRvfP~~~~~~kp------~e~Rmg~GkG-----------~ 92 (146)
T COG0197 30 VFFGEYGLVALEPGQITARQIEAARIAANRYLKRGGGLWIRVFPDKPLTEKP------GEDRMGKGKG-----------K 92 (146)
T ss_pred CCCEEEEEEECCCCEECHHHHHHHHHHHHHHHHHCCCEEEEECCCCEEEECC------CCCCCCCCCC-----------C
T ss_conf 5515889998553105188999999999998265287799985995045278------8510048989-----------8
Q ss_pred CCCEECCCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHH
Q ss_conf 54302124311114422357764116887762189999993896177799999999999
Q gi|254780237|r 167 PIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQ 225 (340)
Q Consensus 167 ~ig~i~iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~ 225 (340)
+.||.+ - |. -.+..||||++..=..+|||..|+..|-
T Consensus 93 pegwaA------------r-Vk---------pG~vlfei~g~~e~~A~EAlr~Aa~KLP 129 (146)
T COG0197 93 PEGWAA------------R-VK---------PGRVLFEIAGVPEELAREALRRAAAKLP 129 (146)
T ss_pred CCEEEE------------E-EC---------CCCEEEEEECCCHHHHHHHHHHHHHCCC
T ss_conf 647899------------9-66---------9968999945868999999999861199
No 98
>COG2838 Icd Monomeric isocitrate dehydrogenase [Energy production and conversion]
Probab=28.36 E-value=43 Score=14.34 Aligned_cols=11 Identities=0% Similarity=0.141 Sum_probs=4.7
Q ss_pred CCHHHHHHHHH
Q ss_conf 17779999999
Q gi|254780237|r 211 ITGEDSVALAS 221 (340)
Q Consensus 211 i~P~eAl~~Aa 221 (340)
++|.+|...+.
T Consensus 521 lsp~ea~~~sl 531 (744)
T COG2838 521 LSPVEAMRYSL 531 (744)
T ss_pred ECHHHHHHHHH
T ss_conf 46899999999
No 99
>TIGR01088 aroQ 3-dehydroquinate dehydratase, type II; InterPro: IPR001874 3-dehydroquinate dehydratase (4.2.1.10 from EC), or dehydroquinase, catalyzes the conversion of 3-dehydroquinate into 3-dehydroshikimate. It is the third step in the shikimate pathway for the biosynthesis of aromatic amino acids from chorismate. Two classes of dehydroquinases exist, known as types I and II. Class-II enzymes are homododecameric enzymes of about 17 kDa. They are found in some bacteria such as actinomycetales , and some fungi where they act in a catabolic pathway that allows the use of quinic acid as a carbon source.; GO: 0003855 3-dehydroquinate dehydratase activity, 0009073 aromatic amino acid family biosynthetic process.
Probab=28.28 E-value=32 Score=15.18 Aligned_cols=36 Identities=25% Similarity=0.433 Sum_probs=27.6
Q ss_pred CCCHHHHHHHHHHHHHHCCCCC--CCCC----CCCHHHHHHH
Q ss_conf 9886449999999998083126--7687----8986779999
Q gi|254780237|r 297 NFGRKSLVEIKGVLGTMGLFLG--MNLP----DWPPESIEEL 332 (340)
Q Consensus 297 NfG~KSl~EI~~~L~~~gl~lg--~~l~----~~~~~~~~~~ 332 (340)
=+|.-|++||.+.|+..+-.++ +.++ |+.=+-+++.
T Consensus 20 ~YG~~tle~i~~~~~~~a~~~~ld~e~~~fQSN~EG~L~d~I 61 (144)
T TIGR01088 20 VYGSQTLEEIEEILETFAAQLNLDVEVEFFQSNSEGELIDKI 61 (144)
T ss_pred CCCCCCHHHHHHHHHHHHHHCCCEEEEEEECCCCHHHHHHHH
T ss_conf 247868789999999999853982789873044357899999
No 100
>PRK10880 adenine DNA glycosylase; Provisional
Probab=26.69 E-value=32 Score=15.18 Aligned_cols=13 Identities=23% Similarity=0.575 Sum_probs=7.3
Q ss_pred CCCEEEEEECCCC
Q ss_conf 8880899977896
Q gi|254780237|r 129 NPDHVICNLDVDA 141 (340)
Q Consensus 129 Npd~~IaTl~~~~ 141 (340)
||...+|-+...|
T Consensus 196 ~P~C~~CPl~~~C 208 (350)
T PRK10880 196 KPKCELCPLQNGC 208 (350)
T ss_pred CCCCCCCCCCCCC
T ss_conf 9987889882206
No 101
>COG1400 SEC65 Signal recognition particle 19 kDa protein [Intracellular trafficking and secretion]
Probab=26.30 E-value=47 Score=14.11 Aligned_cols=22 Identities=36% Similarity=0.326 Sum_probs=17.3
Q ss_pred CCCCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf 1889886449999999998083126
Q gi|254780237|r 294 RMANFGRKSLVEIKGVLGTMGLFLG 318 (340)
Q Consensus 294 ~ikNfG~KSl~EI~~~L~~~gl~lg 318 (340)
.+.|+ |++||.+++.++|+..-
T Consensus 28 aV~~P---~~~ei~~a~~~LGl~~~ 49 (93)
T COG1400 28 AVENP---SLEEIAEALRELGLKPK 49 (93)
T ss_pred CCCCC---CHHHHHHHHHHCCCCEE
T ss_conf 14599---98999999998499746
No 102
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=26.05 E-value=48 Score=14.08 Aligned_cols=22 Identities=18% Similarity=0.376 Sum_probs=17.4
Q ss_pred HCCHHHHHCCCCCCHHHHHHHH
Q ss_conf 4498888618898864499999
Q gi|254780237|r 286 QRTEADMLRMANFGRKSLVEIK 307 (340)
Q Consensus 286 ~~s~~dLl~ikNfG~KSl~EI~ 307 (340)
....++|+++|+.|+|+.+-+-
T Consensus 79 ~~~~~~L~~l~GIG~~TA~~vl 100 (158)
T cd00056 79 PDAREELLALPGVGRKTANVVL 100 (158)
T ss_pred HHHHHHHHCCCCCCHHHHHHHH
T ss_conf 8899998758982899999999
No 103
>TIGR01083 nth endonuclease III; InterPro: IPR005759 The spectrum of DNA damage caused by reactive oxygen species includes a wide variety of modifications of purine and pyrimidine bases. Among these modified bases, 7,8-dihydro-8-oxoguanine (8-oxoG) is an important mutagenic lesion. Base excision repair is a critical mechanism for preventing mutations by removing the oxidative lesion from the DNA. Escherichia coli Nth protein (endonuclease III) has an 8-oxoG DNA glycosylase/AP lyase activity which removes 8-oxoG preferentially from 8-oxoG/G mispairs. Human hNTH1 protein, a homolog of E. coli Nth protein, has similar DNA glycosylase/AP lyase activity that removes 8-oxoG from 8-oxoG/G mispairs . ; GO: 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0006284 base-excision repair, 0005622 intracellular.
Probab=25.98 E-value=34 Score=15.03 Aligned_cols=58 Identities=19% Similarity=0.313 Sum_probs=37.1
Q ss_pred HHHHHCCHHHCCCCHHHHHH--HHHCCCCCHHHH--------HHCCHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf 23331112210110588898--988398371888--------74498888618898864499999999
Q gi|254780237|r 253 NPALLKKVEELELSVRSTNC--LRGENIVYMGDL--------IQRTEADMLRMANFGRKSLVEIKGVL 310 (340)
Q Consensus 253 ~~~L~~~IeeLeLSvRs~Nc--Lk~a~I~tigdL--------v~~s~~dLl~ikNfG~KSl~EI~~~L 310 (340)
+..+....|+|+==.|+.+- =|+.+|.-++.. |-.+.++|+++||-|+|..+=|-..-
T Consensus 60 ~~~a~a~~eel~~~Ik~iGlYr~KAk~I~~~~~~LvE~y~GeVP~~~~eL~~LPGVGRKTANVVL~~a 127 (192)
T TIGR01083 60 QALAAAGLEELEEYIKSIGLYRNKAKNIIALCRKLVERYGGEVPEDREELVKLPGVGRKTANVVLNVA 127 (192)
T ss_pred HHHHCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCCCHHHHHHHHHH
T ss_conf 89960893134776422586456899999999999998189877553766178998711456243344
No 104
>cd00181 TarH Taxis toward Aspartate and Related amino acids and Homologs (TarH). The Tar chemoreceptor of Escherichia coli mediates attractant responses to aspartate, maltose, and phenol, repellent responses to Ni2+ and Co2+, and thermoresponses. These transmembrane signalers monitor the chemical environment by means of specific ligand-binding sites arrayed on the periplasmic side of the membrane, and in turn control cytoplasmic signals that modulate the flagellar rotational machinery. Aspartate is detected through direct binding to Tar molecules, whereas maltose is detected indirectly when complexed with the periplasmic maltose-binding protein.
Probab=25.89 E-value=42 Score=14.43 Aligned_cols=67 Identities=15% Similarity=0.112 Sum_probs=33.9
Q ss_pred HHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf 8889898839837188874498888618898864499999999980831267687898677999998775
Q gi|254780237|r 268 RSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYE 337 (340)
Q Consensus 268 Rs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~~~~~~~~~~~~~~~~ 337 (340)
-+.|-|-|+||....|--..++.....+-..-++||..=....+.+... +..+. ++....+++++|.
T Consensus 25 qAR~~LNRag~r~~~~~~~~~~~~~~~L~~~A~~~L~~a~~~f~~~~~~--~~~~~-~~~~~~~l~~~Y~ 91 (140)
T cd00181 25 QARINLNRAGERGMMDQNKIGEKAKMALLAYASESLTQAIVHYKNYSAM--TAQPV-EVQASAELKEKFK 91 (140)
T ss_pred HHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC--CCCCC-CHHHHHHHHHHHH
T ss_conf 9998888999999872678995328999999999999999999999736--68988-7589999999999
No 105
>KOG0980 consensus
Probab=25.64 E-value=41 Score=14.51 Aligned_cols=50 Identities=12% Similarity=0.185 Sum_probs=34.4
Q ss_pred CCCCCCCHHHHHHHHHHHCCCEEEECCC-----CCEEEEEEEECCEEEEEEEEEC
Q ss_conf 1466462444999998401141777279-----8279999994471699633513
Q gi|254780237|r 72 ISSIKGVHEDLTDIILNIKGINLKMSGD-----SHKRVTIFKRGPGVVTAGDIQT 121 (340)
Q Consensus 72 fs~i~GV~EDV~eIiLNLK~I~~k~~~~-----~~~~~~l~~~Gp~~vtA~Di~~ 121 (340)
+.++.|-|+-...+..-||+.--.+.+- -...-+|...-|-...++|+.-
T Consensus 218 ~dtLeghRdRf~~qf~rLk~FY~~~S~lqYfk~LI~IP~LP~~~Pnf~~~sdl~~ 272 (980)
T KOG0980 218 PDTLEGHRDRFHTQFERLKQFYADCSNLQYFKRLIQIPTLPEDAPNFLRQSDLES 272 (980)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHH
T ss_conf 7774027899999999999999865434899999507778999954202232334
No 106
>COG0153 GalK Galactokinase [Carbohydrate transport and metabolism]
Probab=25.53 E-value=49 Score=14.02 Aligned_cols=157 Identities=13% Similarity=0.185 Sum_probs=84.6
Q ss_pred CCCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHH-HHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHCCCC
Q ss_conf 12431111442235776411688776218999999389617779-99999999999888762244443221000000000
Q gi|254780237|r 172 TIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGED-SVALASRILQDQLGMFINFEEPKKEVKEDINVKSL 250 (340)
Q Consensus 172 ~iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~e-Al~~Aa~iL~~~l~~f~~~~~~~~~~~~~~~~~~~ 250 (340)
-....-+|+.++.+.|-++++-+.+ +++...-+- -...|++.|......+-++....-+.-...-....
T Consensus 198 ~~~~~~~p~~~~~ivI~ns~vkr~l----------a~seYn~Rr~ece~A~~~l~~~~~~L~d~~~~~~~~~~~~i~~~~ 267 (390)
T COG0153 198 EYEPVPFPVGGVSIVIVNSNVKREL----------ADSEYNERRAECEEAAEFLGVSIKSLRDVTDEEFAALQAEIEVDP 267 (390)
T ss_pred CEEEECCCCCCEEEEEECCCCCCCC----------CHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCH
T ss_conf 2687304766459999637976654----------234789999999999999987550354337999996452414466
Q ss_pred HHHHHHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCC--CC----
Q ss_conf 112333111221011058889898839837188874498888618898864499999999980831267687--89----
Q gi|254780237|r 251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLP--DW---- 324 (340)
Q Consensus 251 ~~~~~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg~~l~--~~---- 324 (340)
..-.-...-+.|-.=..++.++|+..++.++|.|+..|...|...=..--.-++.+.+.....+=.+|.++- +|
T Consensus 268 ~~~rRa~hvv~En~Rvl~a~~Al~~~dl~~fG~Lm~~SH~slrddyevt~pElD~lve~a~~~~G~~GaRmTGaGfGGc~ 347 (390)
T COG0153 268 KIARRARHVVTENQRVLEAAKALRSGDLTEFGELMNESHESLRDDYEVTCPELDTLVEIALAAGGAYGARMTGAGFGGCV 347 (390)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCCCCEECCCCCCCEE
T ss_conf 88899999986777899999998718899999999998998874356656628999999987278650120378878559
Q ss_pred ----CHHHHH----HHHHHHHC
Q ss_conf ----867799----99987750
Q gi|254780237|r 325 ----PPESIE----ELAKKYED 338 (340)
Q Consensus 325 ----~~~~~~----~~~~~~~~ 338 (340)
|.+.++ .+.++|+.
T Consensus 348 IaLv~~~~v~~~~e~v~~~y~~ 369 (390)
T COG0153 348 IALVPNDDVEAVAEAVAEEYEK 369 (390)
T ss_pred EEEECHHHHHHHHHHHHHHHHH
T ss_conf 9993220279999999876776
No 107
>COG0389 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]
Probab=24.31 E-value=51 Score=13.87 Aligned_cols=44 Identities=23% Similarity=0.302 Sum_probs=33.1
Q ss_pred HCCHHHC-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHH
Q ss_conf 1112210-110588898988398371888744988886188988644
Q gi|254780237|r 257 LKKVEEL-ELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKS 302 (340)
Q Consensus 257 ~~~IeeL-eLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KS 302 (340)
..++.++ +.--++.--|++.||.|++||...+.+.|++ -||+.-
T Consensus 175 ~Lpv~~~~GvG~~~~~~l~~~Gi~ti~dl~~~~~~~L~~--~~g~~~ 219 (354)
T COG0389 175 QLPVLEFWGVGKVTAEKLRRLGISTIGDLAETDLDALKK--RFGKLG 219 (354)
T ss_pred CCCHHHHCCCCHHHHHHHHHCCCHHHHHHHHCCHHHHHH--HHHHHH
T ss_conf 095677268458999999972848899987358999999--999989
No 108
>cd01680 EFG_like_IV Elongation Factor G-like domain IV. This family includes the translational elongation factor termed EF-2 (for Archaea and Eukarya) and EF-G (for Bacteria), ribosomal protection proteins that mediate tetracycline resistance and, an evolutionarily conserved U5 snRNP-specific protein (U5-116kD). In complex with GTP, EF-G/EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site of the small subunit of ribosome and the mRNA is shifted one codon relative to the ribosome. It has been shown that EF-G/EF-2_IV domain mimics the shape of anticodon arm of the tRNA in the structurally homologous ternary complex of Petra, EF-Tu (another transcriptional elongation factor) and GTP analog. The tip portion of this domain is found in a position that overlaps the anticodon arm of the A-site tRNA, implying that EF-G/EF-2 displaces the A-site tRNA to the P-site by physical interaction with the anticodon arm.
Probab=24.27 E-value=51 Score=13.86 Aligned_cols=44 Identities=32% Similarity=0.433 Sum_probs=25.2
Q ss_pred EEEEECCCCCHHHHH-----------------HHHHHHHHHCC-CCCEEEEEEEE---CCCCCCC
Q ss_conf 999961697566788-----------------89999987416-98306889998---8714431
Q gi|254780237|r 29 LMIAEPLPRGFAHTL-----------------GNALRRVLMSS-LRGAAITAVQI---DGVLHEI 72 (340)
Q Consensus 29 ~f~~~Ple~G~g~Tl-----------------GNaLRRvLLss-i~G~ait~vkI---~gv~HEf 72 (340)
.+.++|++||.|.++ -..+|-.+.+- +-|+.++.||+ +|..|+=
T Consensus 29 ~l~veP~~~g~g~~f~~~~~~~~ip~~~~~ave~gv~~~~~~G~l~G~Pv~dvkV~L~~g~~h~~ 93 (116)
T cd01680 29 TLRVEPLERGSGVRVVDPVDEELLPAELKEAVEEGIRDACASGPLTGYPLTDVRVTVLDVPYHEG 93 (116)
T ss_pred EEEEEECCCCCCCEEEECCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEECCCCCC
T ss_conf 99999898898748961477884799999999999999997598158826607999994588789
No 109
>PRK10702 endonuclease III; Provisional
Probab=23.69 E-value=29 Score=15.46 Aligned_cols=52 Identities=13% Similarity=0.225 Sum_probs=35.2
Q ss_pred HHCCHHHCCCC-HHHHHHHHHCCCC--CHHHHHHCCHHHHHCCCCCCHHHHHHHH
Q ss_conf 31112210110-5888989883983--7188874498888618898864499999
Q gi|254780237|r 256 LLKKVEELELS-VRSTNCLRGENIV--YMGDLIQRTEADMLRMANFGRKSLVEIK 307 (340)
Q Consensus 256 L~~~IeeLeLS-vRs~NcLk~a~I~--tigdLv~~s~~dLl~ikNfG~KSl~EI~ 307 (340)
+..-|.-++|- .||.|-.+.+.+- .-+.-+..+.++|+++|+.|+|+..-|-
T Consensus 72 l~~~i~~~G~y~~KA~~L~~~a~~i~~~~~G~vP~~~~~L~~LpGIG~kTA~aIl 126 (211)
T PRK10702 72 VKTYIKTIGLYNSKAENVIKTCRILLEKHNGEVPEDRAALEALPGVGRKTANVVL 126 (211)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHH
T ss_conf 9999998635999999999999999999099876669999987663588999999
No 110
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=23.06 E-value=54 Score=13.72 Aligned_cols=35 Identities=9% Similarity=0.146 Sum_probs=24.8
Q ss_pred CCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHH
Q ss_conf 83718887449888861889886449999999998
Q gi|254780237|r 278 IVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312 (340)
Q Consensus 278 I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~ 312 (340)
..++..+..-|.+||.++++.|++..+.|.+.|.+
T Consensus 574 Fgs~~~i~~As~eeL~~v~Gi~~~~A~~I~~~l~~ 608 (609)
T PRK00558 574 FGSLKAIKEASVEELAKVPGISKKLAEKIYEALHK 608 (609)
T ss_pred CCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHC
T ss_conf 07999997389999964899899999999999705
No 111
>KOG0095 consensus
Probab=22.84 E-value=28 Score=15.55 Aligned_cols=29 Identities=24% Similarity=0.417 Sum_probs=15.4
Q ss_pred EEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECC
Q ss_conf 8999961697566788899999874169830688999887
Q gi|254780237|r 28 TLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDG 67 (340)
Q Consensus 28 g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI~g 67 (340)
-||.-+-|.+|||-|+|- +.-|-.|++.|
T Consensus 25 rrftqglfppgqgatigv-----------dfmiktvev~g 53 (213)
T KOG0095 25 RRFTQGLFPPGQGATIGV-----------DFMIKTVEVNG 53 (213)
T ss_pred HHHHCCCCCCCCCCEEEE-----------EEEEEEEEECC
T ss_conf 455226789998766423-----------37999999878
No 112
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=22.60 E-value=55 Score=13.66 Aligned_cols=19 Identities=11% Similarity=0.357 Sum_probs=10.5
Q ss_pred CCCCCCCHHHHHHHHHHHC
Q ss_conf 1466462444999998401
Q gi|254780237|r 72 ISSIKGVHEDLTDIILNIK 90 (340)
Q Consensus 72 fs~i~GV~EDV~eIiLNLK 90 (340)
++.||||-..+.+.|--++
T Consensus 55 ~t~l~gIGk~ia~~I~e~l 73 (326)
T COG1796 55 LTELPGIGKGIAEKISEYL 73 (326)
T ss_pred CCCCCCCCHHHHHHHHHHH
T ss_conf 4778875688999999999
No 113
>TIGR02668 moaA_archaeal probable molybdenum cofactor biosynthesis protein A; InterPro: IPR013485 This entry consists of archaeal proteins which are predicted to be functionally equivalent to MoaA (molybdenum cofactor biosynthesis protein A) from bacteria (see IPR013483 from INTERPRO).; GO: 0046872 metal ion binding, 0006777 Mo-molybdopterin cofactor biosynthetic process.
Probab=22.50 E-value=56 Score=13.64 Aligned_cols=112 Identities=20% Similarity=0.248 Sum_probs=67.5
Q ss_pred CCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCEEEECCCCCEEEEEEEECCE-EEEEEEEECCCCEEEECCCEEE
Q ss_conf 830688999887144314664624449999984011417772798279999994471-6996335138985998888089
Q gi|254780237|r 56 RGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG-VVTAGDIQTVNDIEVLNPDHVI 134 (340)
Q Consensus 56 ~G~ait~vkI~gv~HEfs~i~GV~EDV~eIiLNLK~I~~k~~~~~~~~~~l~~~Gp~-~vtA~Di~~p~~veivNpd~~I 134 (340)
.-..|-.|||-|=. |=+|.|+.+||.|||+..++- +++..+|-- .-.|++++ ..|+.=||=.+|
T Consensus 59 ~~fGV~kvKlTGGE------PlLR~D~~~Ii~~~~~~~~~~-------vSmTTNG~LL~~~A~~Lk-~AGLdRVNVSLd- 123 (324)
T TIGR02668 59 SEFGVRKVKLTGGE------PLLRKDLIEIIRRIKDYGIKD-------VSMTTNGILLEKLAKKLK-EAGLDRVNVSLD- 123 (324)
T ss_pred HHCCCCEEEECCCC------CCHHHHHHHHHHHHCCCCCEE-------EECCCCHHHHHHHHHHHH-HHCCCEEEECCC-
T ss_conf 87088327751787------434566999998614675034-------420303144898999999-828561312026-
Q ss_pred EEECCCCEEEEEEEEECCCCCEECCCCCCCCCCCCE-ECCCCCHHEEEEEEEEEEE-ECCCC
Q ss_conf 997789649999997468763203444465575430-2124311114422357764-11688
Q gi|254780237|r 135 CNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGL-ITIDALYSPIKKVSYTVES-AREGQ 194 (340)
Q Consensus 135 aTl~~~~~l~iel~ie~G~GY~~~e~~~~~~~~ig~-i~iDa~FsPV~~Vny~Ve~-~rvg~ 194 (340)
|++....-.| += ..+++.. ... -|. =|+|+=.+|| |||+.|-. .++++
T Consensus 124 -tld~e~Y~kI--TG-~~~~~~~-----~Vi--~GI~~A~~~GL~PV-KlN~Vvl~G~N~~~ 173 (324)
T TIGR02668 124 -TLDPEKYKKI--TG-QSRDALD-----RVI--EGIESAVDAGLTPV-KLNMVVLKGINDNE 173 (324)
T ss_pred -CCCHHHHHHH--CC-CCCCHHH-----HHH--HHHHHHHHCCCCCE-EEEEEEECCCCCCC
T ss_conf -7886788864--48-9986078-----999--99999997289813-78888754778850
No 114
>TIGR02683 upstrm_HI1419 probable addiction module killer protein; InterPro: IPR014056 Members of this strictly bacterial protein family are small, at roughly 100 amino acids. The gene is almost invariably the upstream member of a gene pair, where the downstream member is a predicted DNA-binding protein from a clade within Pfam helix-turn-helix family IPR001387 from INTERPRO. These gene pairs, when found on the bacterial chromosome, often are located with prophage regions, but also in both integrated plasmid regions and near housekeeping genes. Analysis suggests that the gene pair may serve as an addiction module..
Probab=22.31 E-value=46 Score=14.16 Aligned_cols=14 Identities=36% Similarity=0.515 Sum_probs=11.3
Q ss_pred EEEEEEECCCCCEE
Q ss_conf 99999746876320
Q gi|254780237|r 144 RMELTVSKGHGYVP 157 (340)
Q Consensus 144 ~iel~ie~G~GY~~ 157 (340)
-.||+|..|.||+-
T Consensus 47 V~ElRId~GpGYRv 60 (95)
T TIGR02683 47 VSELRIDYGPGYRV 60 (95)
T ss_pred EEEEEECCCCCEEE
T ss_conf 03543226996468
No 115
>pfam06569 DUF1128 Protein of unknown function (DUF1128). This family consists of several short, hypothetical bacterial proteins of unknown function.
Probab=21.91 E-value=57 Score=13.57 Aligned_cols=34 Identities=26% Similarity=0.369 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf 99999999980831267687898677999998775
Q gi|254780237|r 303 LVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYE 337 (340)
Q Consensus 303 l~EI~~~L~~~gl~lg~~l~~~~~~~~~~~~~~~~ 337 (340)
+++|++||.-.+-.. |+.+.|.....++++.-|+
T Consensus 13 Ie~Ik~KL~mvN~~~-i~~~~f~~~~yedl~diy~ 46 (71)
T pfam06569 13 IEEIKEKLNMVNQGV-IKPEDFKSAKYEDLRDIYE 46 (71)
T ss_pred HHHHHHHHHHHHHHH-CCHHHCCCCCHHHHHHHHH
T ss_conf 999999997774974-8997668323899999999
No 116
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=20.57 E-value=61 Score=13.39 Aligned_cols=50 Identities=14% Similarity=0.262 Sum_probs=30.8
Q ss_pred CCHHHCCCCH-HHHHHHHHCCC--CCHHHHHHCCHHHHHCCCCCCHHHHHHHH
Q ss_conf 1122101105-88898988398--37188874498888618898864499999
Q gi|254780237|r 258 KKVEELELSV-RSTNCLRGENI--VYMGDLIQRTEADMLRMANFGRKSLVEIK 307 (340)
Q Consensus 258 ~~IeeLeLSv-Rs~NcLk~a~I--~tigdLv~~s~~dLl~ikNfG~KSl~EI~ 307 (340)
.-|..+.++. |+.+....+.+ ..-+.-+..+.++|+++|+.|.|+.+-|-
T Consensus 37 ~~i~~~g~~~~ka~~i~~~a~~i~~~~~~~~p~~~~~L~~lpGVG~~tA~~vl 89 (149)
T smart00478 37 ELIRPLGFYRRKAKYLIELARILVEEYGGEVPDDREELLKLPGVGRKTANAVL 89 (149)
T ss_pred HHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHCCCCCCHHHHHHHH
T ss_conf 99998688999999999999999986655588559998758986599999999
No 117
>TIGR00607 rad52 recombination protein rad52; InterPro: IPR004585 Rad52 was identified in Saccharomyces cerevisiae as a component of the homologous recombination repair pathway and to play an important role in both meiotic and mitotic recombination. The human protein is highly homologous in both structure and function. In the presence of absence of DNA, Rad52 forms ring-shaped oligomers which bind both single and double stranded DNA, stimulating annealing of complimentary DNA strands and promoting ligation of both cohesive and blunt-end fragments. Rad52 may act as a recombination mediator, optimising catalysis of strand exchange by the Rad51 protein. A C-terminal self-association domain has been identified that mediates formation of higher order oligomers of Rad52 rings. Formation of these oligomers may be important for interaction with more than one DNA molecule . ; GO: 0006281 DNA repair, 0006310 DNA recombination.
Probab=20.41 E-value=30 Score=15.38 Aligned_cols=14 Identities=50% Similarity=0.786 Sum_probs=5.6
Q ss_pred EEEEEEEE-CCCCCC
Q ss_conf 06889998-871443
Q gi|254780237|r 58 AAITAVQI-DGVLHE 71 (340)
Q Consensus 58 ~ait~vkI-~gv~HE 71 (340)
+||+.|.+ +|.-||
T Consensus 73 ~aiVrV~LkdG~yhE 87 (164)
T TIGR00607 73 SAIVRVTLKDGSYHE 87 (164)
T ss_pred EEEEEEEECCCCEEE
T ss_conf 999999735886621
No 118
>pfam02697 DUF217 Uncharacterized ACR, COG1753.
Probab=20.32 E-value=61 Score=13.36 Aligned_cols=23 Identities=26% Similarity=0.336 Sum_probs=18.8
Q ss_pred HHHHHCCCCCCHHHHHHHHHHHHH
Q ss_conf 888861889886449999999998
Q gi|254780237|r 289 EADMLRMANFGRKSLVEIKGVLGT 312 (340)
Q Consensus 289 ~~dLl~ikNfG~KSl~EI~~~L~~ 312 (340)
.+.|+++|+ |.+|..|+...|-.
T Consensus 11 Y~~L~k~K~-~~~SFSeVI~~L~~ 33 (71)
T pfam02697 11 YEKLLKLKR-GGKSFSEVIRELIE 33 (71)
T ss_pred HHHHHHHHC-CCCCHHHHHHHHHH
T ss_conf 999999863-78769999999998
No 119
>TIGR01815 TrpE-clade3 anthranilate synthase; InterPro: IPR010112 This entry represents a small clade of anthranilate synthases from alpha proteobacteria and Nostoc (a cyanobacterium). This enzyme is the first step in the pathway for the biosynthesis of tryprophan from chorismate.; GO: 0004049 anthranilate synthase activity, 0000162 tryptophan biosynthetic process.
Probab=20.29 E-value=62 Score=13.35 Aligned_cols=121 Identities=19% Similarity=0.246 Sum_probs=59.6
Q ss_pred CCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCC--------------------CCCCCCCCCHHH------HHHHHH
Q ss_conf 169756678889999987416983068899988714--------------------431466462444------999998
Q gi|254780237|r 34 PLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVL--------------------HEISSIKGVHED------LTDIIL 87 (340)
Q Consensus 34 Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI~gv~--------------------HEfs~i~GV~ED------V~eIiL 87 (340)
==|-.|=|||+|=||.| |+.||.+|-.=+. .||..-.-|.-- |+-+.|
T Consensus 531 DHeDSFVHTLAnY~RqT------GAsVTTlRh~~ae~~fd~~rPDLVVLSPGPGrP~dFdv~~Ti~aa~ar~lP~FGVCL 604 (726)
T TIGR01815 531 DHEDSFVHTLANYLRQT------GASVTTLRHSFAEELFDEERPDLVVLSPGPGRPKDFDVKETIKAALARDLPVFGVCL 604 (726)
T ss_pred ECCCCHHHHHHHHHHHC------CCEEEECCCHHHHHHHHCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCEEEEHH
T ss_conf 54754377778887634------875530430478999732799889868731238754478899999972898577413
Q ss_pred HHCCCEEEECCC-----CCE---EEEEEEECCEEEEEEEEECCCCEEEECCCEEEEEECCCCEEEEEEEEECCCCCEECC
Q ss_conf 401141777279-----827---999999447169963351389859988880899977896499999974687632034
Q gi|254780237|r 88 NIKGINLKMSGD-----SHK---RVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAK 159 (340)
Q Consensus 88 NLK~I~~k~~~~-----~~~---~~~l~~~Gp~~vtA~Di~~p~~veivNpd~~IaTl~~~~~l~iel~ie~G~GY~~~e 159 (340)
=|..++=..-.+ .|+ --++.+-+|+.|.-+| +|..+.|- -=|-|.-..+.-+-++.++.+.-=|-+.+-
T Consensus 605 GLQg~vEafGG~L~vL~~P~HGK~srirVl~p~s~~F~g--Lpe~~TVG-RYHSlfA~~~rLP~el~vTA~s~Dg~iMai 681 (726)
T TIGR01815 605 GLQGLVEAFGGELDVLAIPVHGKASRIRVLEPDSVLFAG--LPEELTVG-RYHSLFARSDRLPKELKVTAESEDGVIMAI 681 (726)
T ss_pred HHHHHHHHHCCCCCCCCCCCCCCCCEEEEECCCEEEECC--CCCCEEEE-EEEEEEECCCCCCCCCEEEEEECCCEEEEE
T ss_conf 468999874672135788878863368883687578727--89703430-037675564568742378785068717320
Q ss_pred CCCC
Q ss_conf 4446
Q gi|254780237|r 160 HHRT 163 (340)
Q Consensus 160 ~~~~ 163 (340)
+|++
T Consensus 682 EH~~ 685 (726)
T TIGR01815 682 EHRK 685 (726)
T ss_pred ECCC
T ss_conf 2476
No 120
>KOG2534 consensus
Probab=20.20 E-value=62 Score=13.34 Aligned_cols=16 Identities=19% Similarity=-0.170 Sum_probs=5.9
Q ss_pred EEECCCCCHHHHHHHH
Q ss_conf 9938961777999999
Q gi|254780237|r 205 IDTDGSITGEDSVALA 220 (340)
Q Consensus 205 I~TnGsi~P~eAl~~A 220 (340)
=||-+-..-++-=..|
T Consensus 293 gwTGS~~FnR~lR~~A 308 (353)
T KOG2534 293 GWTGSKEFNRDLRRYA 308 (353)
T ss_pred EECCHHHHHHHHHHHH
T ss_conf 4142388889999999
Done!