Query gi|254780440|ref|YP_003064853.1| transcription elongation factor GreA [Candidatus Liberibacter asiaticus str. psy62] Match_columns 158 No_of_seqs 135 out of 2199 Neff 6.5 Searched_HMMs 39220 Date Sun May 29 19:15:32 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780440.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 TIGR01462 greA transcription e 100.0 0 0 385.1 16.0 151 6-156 1-155 (155) 2 PRK00226 greA transcription el 100.0 0 0 361.3 18.6 157 1-157 1-157 (157) 3 PRK01885 greB transcription el 100.0 0 0 355.7 17.8 156 1-157 3-158 (159) 4 TIGR01461 greB transcription e 100.0 0 0 316.8 11.2 154 4-158 2-156 (157) 5 PRK05892 nucleoside diphosphat 100.0 4.3E-44 0 301.6 17.6 152 2-157 5-159 (161) 6 PRK06330 transcript cleavage f 100.0 5E-44 0 301.2 14.8 154 3-156 748-901 (906) 7 COG0782 Uncharacterized conser 100.0 2.4E-42 0 290.5 16.0 151 7-158 1-151 (151) 8 PRK06342 transcription elongat 100.0 3.2E-32 8.1E-37 226.1 14.7 134 3-156 27-160 (160) 9 PRK05753 nucleoside diphosphat 100.0 2.6E-30 6.7E-35 213.9 7.4 123 27-157 4-127 (135) 10 pfam01272 GreA_GreB Transcript 99.9 1.7E-22 4.3E-27 164.2 9.4 76 82-157 2-77 (77) 11 pfam03449 GreA_GreB_N domain. 99.8 8.3E-21 2.1E-25 153.4 8.3 71 5-75 1-71 (71) 12 PRK01490 tig trigger factor; P 91.5 1.3 3.3E-05 24.8 8.5 86 56-156 134-241 (435) 13 COG0544 Tig FKBP-type peptidyl 74.5 7.8 0.0002 19.9 7.3 34 123-156 195-241 (441) 14 cd06213 oxygenase_e_transfer_s 70.6 9.5 0.00024 19.3 5.1 65 86-150 28-96 (227) 15 PRK05431 seryl-tRNA synthetase 69.7 10 0.00025 19.2 7.9 79 10-90 35-115 (422) 16 pfam02359 CDC48_N Cell divisio 68.8 10 0.00027 19.1 5.1 69 70-143 14-83 (87) 17 COG1047 SlpA FKBP-type peptidy 68.7 7.1 0.00018 20.1 3.7 28 118-145 38-65 (174) 18 pfam11599 AviRa RRNA methyltra 68.1 8.4 0.00021 19.7 3.9 86 6-106 99-185 (249) 19 PRK02195 V-type ATP synthase s 67.2 11 0.00029 18.9 8.5 69 1-77 1-75 (201) 20 PRK04290 30S ribosomal protein 62.9 11 0.00027 19.0 3.7 27 119-145 18-44 (115) 21 cd06165 Sortase_A_1 Sortase A 57.5 17 0.00043 17.8 4.0 27 131-157 62-88 (127) 22 PRK10737 FKBP-type peptidyl-pr 57.4 17 0.00043 17.8 4.5 23 123-145 42-64 (196) 23 cd06166 Sortase_D_5 Sortase D 56.1 18 0.00045 17.6 3.8 28 130-157 62-89 (126) 24 COG5246 PRP11 Splicing factor 55.9 12 0.00031 18.6 3.0 73 44-117 94-167 (222) 25 cd05828 Sortase_D_4 Sortase D 55.5 18 0.00046 17.6 3.9 26 132-157 61-86 (127) 26 cd05830 Sortase_D_5 Sortase D 55.4 18 0.00046 17.5 4.1 36 121-157 55-90 (137) 27 pfam00970 FAD_binding_6 Oxidor 53.6 19 0.00049 17.4 5.3 65 86-150 30-99 (99) 28 COG3127 Predicted ABC-type tra 51.7 21 0.00053 17.2 4.7 38 119-157 598-635 (829) 29 cd00004 Sortase Sortases are c 51.2 21 0.00054 17.1 3.9 29 130-158 62-90 (128) 30 cd06210 MMO_FAD_NAD_binding Me 48.0 24 0.0006 16.8 5.5 64 87-150 36-103 (236) 31 TIGR03007 pepcterm_ChnLen poly 47.7 24 0.00061 16.8 4.4 21 86-110 393-413 (510) 32 cd06209 BenDO_FAD_NAD Benzoate 47.5 24 0.00061 16.8 5.4 64 86-149 31-97 (228) 33 COG3764 SrtA Sortase (surface 46.8 25 0.00063 16.7 4.2 33 122-158 128-160 (210) 34 pfam11160 DUF2945 Protein of u 45.5 26 0.00066 16.6 3.4 22 136-157 1-22 (62) 35 PRK12306 uvrC excinuclease ABC 44.2 27 0.00069 16.4 6.8 130 6-146 169-328 (519) 36 PTZ00066 pyruvate kinase; Prov 43.9 27 0.0007 16.4 6.0 87 60-156 83-175 (513) 37 COG1018 Hmp Flavodoxin reducta 43.8 27 0.0007 16.4 4.8 65 85-150 34-105 (266) 38 cd05827 Sortase_C_3 Sortase C 43.2 28 0.00072 16.3 4.0 29 128-156 62-90 (131) 39 pfam06940 DUF1287 Domain of un 43.1 28 0.00072 16.3 3.2 23 132-154 106-128 (164) 40 COG2960 Uncharacterized protei 42.4 29 0.00074 16.3 6.5 23 51-73 70-92 (103) 41 pfam07798 DUF1640 Protein of u 41.7 30 0.00075 16.2 6.9 60 9-72 79-138 (177) 42 COG3973 Superfamily I DNA and 41.1 30 0.00077 16.1 5.1 70 86-157 99-172 (747) 43 COG3738 Uncharacterized protei 40.4 17 0.00044 17.7 1.7 31 125-155 133-163 (200) 44 COG1188 Ribosome-associated he 39.8 30 0.00077 16.1 2.9 30 81-112 44-73 (100) 45 cd06189 flavin_oxioreductase N 38.4 33 0.00085 15.9 5.4 64 86-150 26-93 (224) 46 PRK09239 chorismate mutase; Pr 37.9 34 0.00086 15.8 5.3 54 1-57 1-60 (104) 47 cd00986 PDZ_LON_protease PDZ d 36.6 35 0.0009 15.7 3.3 33 119-151 38-70 (79) 48 COG2012 RPB5 DNA-directed RNA 35.2 30 0.00077 16.1 2.3 26 119-145 42-67 (80) 49 TIGR01801 CM_A chorismate muta 34.3 38 0.00098 15.5 4.7 45 11-59 6-58 (104) 50 cd02782 MopB_CT_1 The MopB_CT_ 34.3 39 0.00098 15.5 4.6 31 122-152 36-66 (129) 51 cd06193 siderophore_interactin 34.0 28 0.00071 16.4 2.0 61 86-149 27-115 (235) 52 PRK05802 hypothetical protein; 33.9 39 0.001 15.4 3.1 66 77-144 87-157 (328) 53 cd00508 MopB_CT_Fdh-Nap-like T 32.6 41 0.001 15.3 4.5 31 121-151 37-67 (120) 54 cd06183 cyt_b5_reduct_like Cyt 32.4 41 0.0011 15.3 5.2 65 86-150 29-98 (234) 55 PRK10465 hydrogenase 2-specifi 31.8 42 0.0011 15.2 3.1 83 58-154 15-98 (159) 56 KOG3206 consensus 31.5 43 0.0011 15.2 7.6 97 1-129 94-194 (234) 57 pfam11344 DUF3146 Protein of u 31.1 18 0.00047 17.5 0.7 41 114-154 35-79 (80) 58 pfam01191 RNA_pol_Rpb5_C RNA p 30.9 44 0.0011 15.1 3.3 29 118-147 35-63 (74) 59 pfam06152 Phage_min_cap2 Phage 30.4 45 0.0011 15.1 3.0 14 7-20 3-16 (361) 60 PRK09570 rpoH DNA-directed RNA 29.8 46 0.0012 15.0 3.1 28 118-146 38-65 (79) 61 COG2125 RPS6A Ribosomal protei 29.5 29 0.00074 16.2 1.4 18 123-140 22-39 (120) 62 cd02775 MopB_CT Molybdopterin- 29.3 47 0.0012 14.9 4.5 34 119-152 23-56 (101) 63 pfam10781 DSRB Dextransucrase 29.1 47 0.0012 14.9 3.1 23 134-156 2-25 (62) 64 COG2139 RPL21A Ribosomal prote 28.9 43 0.0011 15.2 2.2 15 101-115 79-93 (98) 65 TIGR01076 sortase_fam sortase 28.7 48 0.0012 14.9 3.9 31 128-158 59-89 (140) 66 PRK10708 hypothetical protein; 28.6 48 0.0012 14.9 2.8 23 134-156 2-25 (62) 67 PRK00558 uvrC excinuclease ABC 27.6 50 0.0013 14.7 11.0 135 6-146 183-348 (609) 68 COG0853 PanD Aspartate 1-decar 27.3 50 0.0013 14.7 4.7 71 66-143 5-88 (126) 69 pfam01092 Ribosomal_S6e Riboso 27.3 50 0.0013 14.7 4.2 20 126-145 23-42 (127) 70 TIGR02160 PA_CoA_Oxy5 phenylac 26.7 42 0.0011 15.2 1.9 64 86-150 33-103 (371) 71 KOG3129 consensus 26.2 53 0.0013 14.6 3.7 33 106-140 132-164 (231) 72 cd02788 MopB_CT_NDH-1_NuoG2-N7 25.8 54 0.0014 14.5 4.4 31 121-151 31-61 (96) 73 TIGR00875 talC transaldolase, 25.5 39 0.001 15.4 1.5 12 4-15 86-97 (216) 74 KOG3026 consensus 25.1 55 0.0014 14.5 7.0 34 36-73 16-49 (262) 75 pfam06273 eIF-4B Plant specifi 24.4 44 0.0011 15.1 1.6 38 61-104 341-378 (430) 76 cd06190 T4MO_e_transfer_like T 24.2 57 0.0015 14.3 5.5 63 86-148 24-90 (232) 77 cd06215 FNR_iron_sulfur_bindin 24.2 58 0.0015 14.3 4.4 64 86-149 28-97 (231) 78 cd02790 MopB_CT_Formate-Dh_H F 23.6 59 0.0015 14.3 4.5 33 120-152 36-68 (116) 79 PRK04778 septation ring format 22.7 62 0.0016 14.2 7.6 32 41-72 185-216 (569) 80 pfam11939 DUF3457 Protein of u 22.6 62 0.0016 14.1 3.1 44 106-155 48-92 (158) 81 KOG0534 consensus 22.5 62 0.0016 14.1 5.9 65 86-151 82-152 (286) 82 TIGR01439 lp_hng_hel_AbrB tran 22.5 62 0.0016 14.1 3.5 33 117-150 7-40 (44) 83 pfam02403 Seryl_tRNA_N Seryl-t 22.2 63 0.0016 14.1 7.7 58 10-73 36-93 (108) 84 cd02778 MopB_CT_Thiosulfate-R- 22.1 63 0.0016 14.1 4.6 26 123-148 34-59 (123) 85 KOG3227 consensus 21.1 66 0.0017 14.0 5.1 57 4-75 17-73 (231) 86 KOG0493 consensus 20.9 67 0.0017 13.9 3.5 29 7-35 253-284 (342) 87 cd06212 monooxygenase_like The 20.6 68 0.0017 13.9 5.2 65 86-150 30-98 (232) 88 pfam06160 EzrA Septation ring 20.0 70 0.0018 13.8 7.7 31 42-72 182-212 (559) No 1 >TIGR01462 greA transcription elongation factor GreA; InterPro: IPR006359 Bacterial GreA and GreB IPR006358 from INTERPRO promote transcription elongation by stimulating an endogenous, endonucleolytic transcript cleavage activity of the RNA polymerase (RNAP) , allowing RNA transcription to continue past template-encoded arresting sites. GreA and GreB are sequence homologues and have homologues in every known bacterial genome. GreA and GreB stimulate transcript cleavage in different ways; GreA induces cleavage of 3'-RNA fragments 23 nt in length and can only prevent the formation of arrested complexes, whereas GreB induces cleavage of fragments up to 18 nt in length and can rescue pre-existing arrested complexes. The 2.2 Å resolution crystal structure of Escherichia coli GreA comprises an N-terminal antiparallel alpha-helical coiled coil, and a C-terminal globular domain. While the C-terminal domain binds RNAP, the N-terminal coiled coil interacts with the transcript 3' end and is responsible for stimulating the transcript cleavage reaction . Functional differences between GreA and GreB correlate with the distribution of positively charged residues on one face of the N-terminal coiled coil. Because members of the family outside the Proteobacteria resemble GreA more closely than GreB, the GreB clade (IPR006358 from INTERPRO) forms a plausible outgroup and the remainder of the GreA/B family, included in this family, is designated GreA. In the Chlamydias and some spirochetes, the conserved region of these proteins is found as the C-terminal region of a much larger protein. ; GO: 0003677 DNA binding, 0003711 transcription elongation regulator activity, 0006355 regulation of transcription DNA-dependent. Probab=100.00 E-value=0 Score=385.14 Aligned_cols=151 Identities=50% Similarity=0.844 Sum_probs=149.5 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC- Q ss_conf 1488999999999999987248999999999975176222430489998876879999999974444210472101332- Q gi|254780440|r 6 PVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGD- 84 (158) Q Consensus 6 ~lT~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~~~~~- 84 (158) |||++||++|++||++|++++||+++++|++||+||||||||||||||++|+++++||.+|+++|+||+||+++..++| T Consensus 1 ~~T~~g~~kL~~EL~~Lk~v~RpeI~~~I~~AR~~GDLsENAEY~AAKe~Q~~~E~RI~~le~~l~~A~vi~~~~~~~~g 80 (155) T TIGR01462 1 PLTQEGYEKLKEELEYLKTVKRPEISEEIKEAREHGDLSENAEYHAAKEEQGFIEGRIAELEDLLANAEVIDDSKLSTDG 80 (155) T ss_pred CCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCEEECCHHHCCCCC T ss_conf 97888999999999885026118999999999851886556003899999999988999999887620623601004788 Q ss_pred -CCCCCCEEEEEECCCCCEEEEEEECHHHCCCCCC--EECCCCHHHHHHCCCCCCCEEEEECCCCEEEEEEEEEE Q ss_conf -1113657999534765235999963101334588--15013178998728888878999828971999999989 Q gi|254780440|r 85 -RIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSG--LVSISSPIARALIGKELGDIISVNAPGGEKTYEILQVL 156 (158) Q Consensus 85 -~V~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~~~~--~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~Il~I~ 156 (158) +|.|||+|+|.|.++|++.+|+|||++|+||+.| +||+.||||+|||||++||.|+|++|+|.+.|+|++|+ T Consensus 81 d~V~~G~~V~~~~~~~~e~~~y~IVG~~EaD~~~giekIS~~SPlg~aL~Gkk~GD~~~v~~P~g~~~~~Il~i~ 155 (155) T TIGR01462 81 DKVSFGSTVTIKDEDTGEEETYTIVGSWEADPKEGIEKISIESPLGKALIGKKVGDEVEVQVPKGEKEYEILKIE 155 (155) T ss_pred CEEECCCEEEEEECCCCCEEEEEEECCCCCCHHCCCEEEECCCHHHHHHCCCCCCCEEEEEECCCEEEEEEEEEC T ss_conf 377157589999838996489998345205533080782267702353337625877899858923799888737 No 2 >PRK00226 greA transcription elongation factor GreA; Reviewed Probab=100.00 E-value=0 Score=361.32 Aligned_cols=157 Identities=52% Similarity=0.839 Sum_probs=155.7 Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC Q ss_conf 99843148899999999999998724899999999997517622243048999887687999999997444421047210 Q gi|254780440|r 1 MVDKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDIST 80 (158) Q Consensus 1 M~~k~~lT~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~ 80 (158) |++++|||++||++|++||++|++++||+++++|++||++|||||||+|++||++|+++++||++|+.+|++|+||+++. T Consensus 1 m~~~~~lT~eg~~~L~~El~~L~~~~r~~i~~~i~~Ar~~GDlsENaeY~aAke~q~~~e~rI~~Le~~L~~A~iid~~~ 80 (157) T PRK00226 1 MMKKIPMTQEGYEKLEEELEELKTVERPEIIEAIAEAREHGDLSENAEYHAAKEEQGFIEGRIRELEDKLSNAEVIDPTK 80 (157) T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC T ss_conf 99773549999999999999998723689999999999869964057699999999999999999999998501458665 Q ss_pred CCCCCCCCCCEEEEEECCCCCEEEEEEECHHHCCCCCCEECCCCHHHHHHCCCCCCCEEEEECCCCEEEEEEEEEEE Q ss_conf 13321113657999534765235999963101334588150131789987288888789998289719999999897 Q gi|254780440|r 81 MSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAPGGEKTYEILQVLW 157 (158) Q Consensus 81 ~~~~~V~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~~~~~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~Il~I~y 157 (158) .++|+|+|||+|++.|.++|+..+|+||||+|+||..|+||+.||||+||+|+++||+|+|++|+|..+|+|++|+| T Consensus 81 ~~~~~V~~Gs~V~l~d~~~g~~~~y~iVG~~Ead~~~g~IS~~SPlg~ALlGk~~Gd~V~v~~P~G~~~~~I~~I~y 157 (157) T PRK00226 81 PSSGKVKFGATVTIYDLDTDEEETYQIVGDDEADIKEGKISVNSPIARALIGKKVGDTVTVKAPGGEYEVEIVSVEY 157 (157) T ss_pred CCCCCEECCCEEEEEECCCCCEEEEEEECCCCCCCCCCEECCCCHHHHHHHCCCCCCEEEEECCCCCEEEEEEEEEC T ss_conf 77884206758999985899679999913322456676524779899998289999989998499878999999889 No 3 >PRK01885 greB transcription elongation factor GreB; Reviewed Probab=100.00 E-value=0 Score=355.73 Aligned_cols=156 Identities=34% Similarity=0.572 Sum_probs=153.5 Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC Q ss_conf 99843148899999999999998724899999999997517622243048999887687999999997444421047210 Q gi|254780440|r 1 MVDKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDIST 80 (158) Q Consensus 1 M~~k~~lT~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~ 80 (158) +|.++|||++||++|++||++|.+++||+++++|++||++||||||||||+||++|+++++||++|+.+|++|+||+++. T Consensus 3 ~~~~~ylT~eg~~kL~~El~~L~~~~r~~~~~~i~~Ar~~GDlsENaeY~aAke~q~~le~rI~~Le~~L~~A~iid~~~ 82 (159) T PRK01885 3 AMKTNYITREGYERLKQELDYLWREERPEVTQKVSWAASLGDRSENADYIYGKKRLREIDRRVRFLTKRLENLKVVDYSP 82 (159) T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC T ss_conf 98654539999999999999987453045899999999859943026389999999999999999999987330357666 Q ss_pred CCCCCCCCCCEEEEEECCCCCEEEEEEECHHHCCCCCCEECCCCHHHHHHCCCCCCCEEEEECCCCEEEEEEEEEEE Q ss_conf 13321113657999534765235999963101334588150131789987288888789998289719999999897 Q gi|254780440|r 81 MSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAPGGEKTYEILQVLW 157 (158) Q Consensus 81 ~~~~~V~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~~~~~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~Il~I~y 157 (158) .+.++|+|||+|+++| ++|++.+|+|||++|+||..|+||+.||||+||||+++||+|+|++|+|...|+|++|+| T Consensus 83 ~~~~~V~~Gs~V~l~~-~~g~~~~y~iVG~~Ead~~~g~IS~~SPlg~ALlGkk~Gd~V~v~~P~G~~~~~Il~I~y 158 (159) T PRK01885 83 QQEGKVFFGAWVEIEN-EDGEEKRFRIVGPDEIDGRKGYISIDSPMARALLKKEVGDEVTVNTPAGEAEWYVNEIEY 158 (159) T ss_pred CCCCEEECCCEEEEEE-CCCCEEEEEEECHHHCCCCCCCCCCCCHHHHHHHCCCCCCEEEEECCCCCEEEEEEEEEC T ss_conf 7788156240899986-689769999948244266678222469899998389999989998599978999999989 No 4 >TIGR01461 greB transcription elongation factor GreB; InterPro: IPR006358 Bacterial GreA IPR006359 from INTERPRO and GreB promote transcription elongation by stimulating an endogenous, endonucleolytic transcript cleavage activity of the RNA polymerase, allowing RNA transcription to continue past template-encoded arresting sites. GreA and GreB are sequence homologues and have homologues in every known bacterial genome. GreA and GreB stimulate transcript cleavage in different ways; GreA induces cleavage of 3'-RNA fragments 23 nt in length and can only prevent the formation of arrested complexes, whereas GreB induces cleavage of fragments up to 18 nt in length and can rescue preexisting arrested complexes . A 15 Å resolution helical reconstruction of the Escherichia coli core RNA polymerase (RNAP)/GreB complex that allows fitting of high-resolution RNAP and GreB structures. The model of the complex reveals a remarkable binding mode for GreB; the globular C-terminal domain binds RNAP at the edge of the active site channel, while the N-terminal coiled-coil domain extends 45 Å into a channel directly to the RNAP active site. The results point to a key role for conserved acidic residues at the tip of the Gre factor coiled coil in modifying the RNAP active site to catalyse the transcript cleavage reaction, and mutational studies confirm that these positions are critical for Gre factor function. Functional differences between GreA and GreB correlate with the distribution of positively charged residues on one face of the N-terminal coiled coil.; GO: 0003677 DNA binding, 0003711 transcription elongation regulator activity, 0006355 regulation of transcription DNA-dependent. Probab=100.00 E-value=0 Score=316.84 Aligned_cols=154 Identities=36% Similarity=0.563 Sum_probs=150.5 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC Q ss_conf 43148899999999999998724899999999997517622243048999887687999999997444421047210133 Q gi|254780440|r 4 KIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSG 83 (158) Q Consensus 4 k~~lT~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~~~~ 83 (158) +.|+|++|+++|++||.+|++++||++.+.+.+|+++||+||||||.+.|.+++.+|+||++|..+|.+++|||++.... T Consensus 2 ~pliTpeG~~~Lk~EL~~Lw~~eRPevtq~V~wAA~lGDRSENadY~YgKkrlREIDrRvRfLtKrLEnlkvVd~~p~~~ 81 (157) T TIGR01461 2 TPLITPEGYEKLKDELYELWRKERPEVTQIVSWAAALGDRSENADYLYGKKRLREIDRRVRFLTKRLENLKVVDEEPREA 81 (157) T ss_pred CCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCEECCCCCCCC T ss_conf 88717878999999999886232862113232442168712242100166000022112446555443001117653554 Q ss_pred -CCCCCCCEEEEEECCCCCEEEEEEECHHHCCCCCCEECCCCHHHHHHCCCCCCCEEEEECCCCEEEEEEEEEEEC Q ss_conf -211136579995347652359999631013345881501317899872888887899982897199999998979 Q gi|254780440|r 84 -DRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAPGGEKTYEILQVLWI 158 (158) Q Consensus 84 -~~V~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~~~~~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~Il~I~yi 158 (158) ++|.||+||+|.+ ++|.+.+|.|||++|.|..+++||+.|||++||+++++||+|.+.||.|...+.|++|+|| T Consensus 82 t~~VfFGAwV~le~-~DG~~~r~rIVG~DEid~r~n~ISidSPlARaL~kke~gdevvvnTPaGe~~~~v~~iEY~ 156 (157) T TIGR01461 82 TDKVFFGAWVELED-DDGREQRYRIVGIDEIDTRKNKISIDSPLARALIKKEVGDEVVVNTPAGEEEWYVLSIEYV 156 (157) T ss_pred CCCEEEEEEEEEEC-CCCCCCCEEEEECCCCCCCCCCEEEECHHHHHHHCCCCCCEEEEECCCCCCEEEEEEEEEC T ss_conf 57677225888653-8883202688605521235772014266788863012587778757888504788875206 No 5 >PRK05892 nucleoside diphosphate kinase regulator; Provisional Probab=100.00 E-value=4.3e-44 Score=301.55 Aligned_cols=152 Identities=18% Similarity=0.277 Sum_probs=139.6 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC Q ss_conf 98431488999999999999987248999999999975176222430489998876879999999974444210472101 Q gi|254780440|r 2 VDKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTM 81 (158) Q Consensus 2 ~~k~~lT~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~~ 81 (158) |+.-|||++||++|++||++|++++|+.+.+.+.+|+++|||||||||++||++|+++++||++|+.+|.+|.+ ... T Consensus 5 ~~~p~lTpeG~~~L~~EL~~Lk~~rr~~v~~~~~~a~~~GDlSENaEY~~aK~eq~~ie~RI~~Le~~L~~a~~---~~~ 81 (161) T PRK05892 5 VESPGLADAARDHLAAELARLRQRRDRLEVEVKNDRGMIGDHGDAAEAIQRADELAILGDRINELDRRLRTGPT---PWS 81 (161) T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC---CCC T ss_conf 57999799999999999999988263999999999997799456673999999999999999999999972888---778 Q ss_pred CCCCCCCCCEEEEEECCCCCEEEEEEECHHHCCC---CCCEECCCCHHHHHHCCCCCCCEEEEECCCCEEEEEEEEEEE Q ss_conf 3321113657999534765235999963101334---588150131789987288888789998289719999999897 Q gi|254780440|r 82 SGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADV---QSGLVSISSPIARALIGKELGDIISVNAPGGEKTYEILQVLW 157 (158) Q Consensus 82 ~~~~V~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~---~~~~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~Il~I~y 157 (158) ..+.|.||++|++.+ ++|+..+|+|||..++++ +.++||+.||||+|||||++||+|+|++|+|..+|+|++|+| T Consensus 82 ~~~~v~~G~~Vti~~-edg~~~~~~iVg~~ee~~~~~~~~~IS~~SPlgrALlGk~~GD~V~v~tP~G~~~~~Il~Ik~ 159 (161) T PRK05892 82 GSETLPGGTEVTLRF-PDGEVVTMHVISIVEETPVGREAETLTARSPLGQALAGHQPGDTVTYSTPQGPNQVQLLAVKL 159 (161) T ss_pred CCCEEECCEEEEEEE-CCCCEEEEEEECCCCCCCCCCCCCEECCCCHHHHHHHCCCCCCEEEEECCCCCEEEEEEEEEC T ss_conf 888784666999996-899889999973416574567676563679789998489899989997599757999999967 No 6 >PRK06330 transcript cleavage factor/unknown domain fusion protein; Validated Probab=100.00 E-value=5e-44 Score=301.21 Aligned_cols=154 Identities=33% Similarity=0.551 Sum_probs=151.5 Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC Q ss_conf 84314889999999999999872489999999999751762224304899988768799999999744442104721013 Q gi|254780440|r 3 DKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMS 82 (158) Q Consensus 3 ~k~~lT~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~~~ 82 (158) +.+++|+++|++.+.||++|+.++.|+++++|++||++|||+|||||+||+|+|+++.+++..|+..|.+|+|+|+.+.. T Consensus 748 ~~liVT~~sl~kKKkELe~Lv~veipENSKdIg~ArelGDLRENAEYKaAkEkQ~~L~~~i~rLe~Ei~rArIlD~~~v~ 827 (906) T PRK06330 748 IGFLVTRRALNKKKKELEHLKNVEIPENSKDIGEAQELGDLRENAEYKAAKEKQQQLQAALKRLEAEIKSAKILDLTDVK 827 (906) T ss_pred CEEEEEHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEECCCCCCC T ss_conf 52896189998889999998644555245779999863660120677889999999999999999985520622532032 Q ss_pred CCCCCCCCEEEEEECCCCCEEEEEEECHHHCCCCCCEECCCCHHHHHHCCCCCCCEEEEECCCCEEEEEEEEEE Q ss_conf 32111365799953476523599996310133458815013178998728888878999828971999999989 Q gi|254780440|r 83 GDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAPGGEKTYEILQVL 156 (158) Q Consensus 83 ~~~V~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~~~~~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~Il~I~ 156 (158) +++|+|||+|++.|..+|+..+|+|+||||+||++|.|||.||+|++|||++.||++++.+|+....|+|++|+ T Consensus 828 T~kVg~GTkV~l~n~~tg~~etYtILGpWDaDPek~IISY~SP~G~~LLgkKtGd~~~~~~~~~~~~y~v~~I~ 901 (906) T PRK06330 828 TSKVGFGTKVKLKNESTGEEESYSILGPWESDPEKGIISYQSPLGKSLLGKKEGDSADFVINDTETRYTVLDIE 901 (906) T ss_pred CCEECCCEEEEEEECCCCCEEEEEEECCCCCCCCCCCEECCCHHHHHHHCCCCCCEEEEEECCCEEEEEEEEEE T ss_conf 33440554899875577866789974476678212823401755476527876771699967846899998633 No 7 >COG0782 Uncharacterized conserved protein, YhbC family [Function unknown] Probab=100.00 E-value=2.4e-42 Score=290.52 Aligned_cols=151 Identities=46% Similarity=0.756 Sum_probs=147.4 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC Q ss_conf 48899999999999998724899999999997517622243048999887687999999997444421047210133211 Q gi|254780440|r 7 VTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGDRI 86 (158) Q Consensus 7 lT~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~~~~~~V 86 (158) ||.+|+++|+.||++|+.++||++.+.+.+|+++|||+|||+|++||++|+++++||.+|+.+|++|++++++..+. +| T Consensus 1 ~T~~g~~~l~~el~~l~~~~rp~i~~~i~~ar~~gdl~enaey~aak~~q~~~e~ri~~le~~l~~a~vi~~~~~~~-~V 79 (151) T COG0782 1 LTDEGFRKLKEELEYLKPVERPEIVEEIADARELGDLSENAEYRAAKEEQAFIERRIRLLEELLRNAQVIDDEKPPD-VV 79 (151) T ss_pred CCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCHHHCHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCCCCC-EE T ss_conf 96027789999999765535226999999999715501083547899875101779999998860754158777789-78 Q ss_pred CCCCEEEEEECCCCCEEEEEEECHHHCCCCCCEECCCCHHHHHHCCCCCCCEEEEECCCCEEEEEEEEEEEC Q ss_conf 136579995347652359999631013345881501317899872888887899982897199999998979 Q gi|254780440|r 87 AFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAPGGEKTYEILQVLWI 158 (158) Q Consensus 87 ~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~~~~~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~Il~I~yi 158 (158) .|||+|++.+.++|++.+|+||||+|+||++|+||+.||+|+||+|+++||+|.|.+|+|...|+|++|.|. T Consensus 80 ~~Gs~V~~~~~~~ge~~~~~iVg~~ead~~~~~IS~~SPig~aLlGk~vGd~v~v~~p~g~~~~~I~~I~~~ 151 (151) T COG0782 80 TFGSTVTLENLDDGEEVTYTIVGPDEADPAKGKISVDSPLGRALLGKKVGDTVEVNTPGGEKEVEILSIEYQ 151 (151) T ss_pred ECCCEEEEEECCCCCEEEEEEECCCCCCCCCCCEECCCHHHHHHHCCCCCCEEEEECCCCEEEEEEEEEECC T ss_conf 469889999879996899999824103601493304597789972899999899835996079999987129 No 8 >PRK06342 transcription elongation factor regulatory protein; Validated Probab=100.00 E-value=3.2e-32 Score=226.06 Aligned_cols=134 Identities=31% Similarity=0.510 Sum_probs=121.4 Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC Q ss_conf 84314889999999999999872489999999999751762224304899988768799999999744442104721013 Q gi|254780440|r 3 DKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMS 82 (158) Q Consensus 3 ~k~~lT~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~~~ 82 (158) .++|+|++||.+|++||..|. ..+.+|...||.++| |.+++.+++||++|..+|+.|+||++.. . T Consensus 27 ~~NYvTP~G~~~L~~el~~l~--------~~~~~a~~~~d~~~~------k~~l~~i~R~iRyl~~Rl~~A~vv~~~~-~ 91 (160) T PRK06342 27 HPNLVTEAGLKALEDQLQQAR--------AAYEAAQAIEDVNER------RRQMARPLRDLRYLAARVRTAQLMPDPP-S 91 (160) T ss_pred CCCEECHHHHHHHHHHHHHHH--------HHHHHHHHCCCHHHH------HHHHHHHHHHHHHHHHHHHCCEEECCCC-C T ss_conf 876108999999999999999--------999987516531576------8876326688999999872178848999-8 Q ss_pred CCCCCCCCEEEEEECCCCCEEEEEEECHHHCCCCCCEECCCCHHHHHHCCCCCCCEEEEECCCCEEEEEEEEEE Q ss_conf 32111365799953476523599996310133458815013178998728888878999828971999999989 Q gi|254780440|r 83 GDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAPGGEKTYEILQVL 156 (158) Q Consensus 83 ~~~V~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~~~~~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~Il~I~ 156 (158) .++|.||+||++.+ ++|++.+|+|||++|+|+.+|+|||.||||+||||+++||+|++ |...|+|++|. T Consensus 92 ~d~V~FGatVt~~~-e~g~~~t~~IVG~dEaD~~~g~IS~~SPlaraLlgk~vGD~V~v----G~~~~EI~~Is 160 (160) T PRK06342 92 TDVVAFGSTVTFSR-DDGRVQTYRIVGEDEADPKAGSISYVSPVARLLMGKAVGDVVGV----GGQELEIIAIA 160 (160) T ss_pred CCEEEEEEEEEEEE-CCCCEEEEEEECHHHCCCCCCEEECCCHHHHHHHCCCCCCEEEE----CCEEEEEEEEC T ss_conf 99899835999992-89999999996834447358967535989999838999998998----88279999859 No 9 >PRK05753 nucleoside diphosphate kinase regulator; Provisional Probab=99.96 E-value=2.6e-30 Score=213.87 Aligned_cols=123 Identities=28% Similarity=0.468 Sum_probs=109.8 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCEEEEE Q ss_conf 89999999999751762224304899988768799999999744442104721013321113657999534765235999 Q gi|254780440|r 27 RPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQ 106 (158) Q Consensus 27 r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~~~~~~V~~Gs~V~l~d~~~~~~~~~~ 106 (158) ||.+.-...+++.++||.||++|++++. ...|+..|++|+||+++.+|.|+|+|||+|+++|.++|++++|+ T Consensus 4 rP~I~it~~D~~rL~~L~e~a~~~~~~~--------a~~L~~eL~rA~Vvd~~~ip~dvV~~gS~V~~~d~~~g~~~~~~ 75 (135) T PRK05753 4 RPTIIINELDAERLDRLLEQPAYAGPPI--------AEALNAELDRAQVVPPAEMPADVVTMNSRVRFRDLSSGEERVVT 75 (135) T ss_pred CCCEEEEHHHHHHHHHHHHHHHHCCCHH--------HHHHHHHHCCCEEECHHHCCCCEEEECCEEEEEECCCCCEEEEE T ss_conf 8978977788999999986565418689--------99999987487895822079998998989999988999899999 Q ss_pred EECHHHCCCCCCEECCCCHHHHHHCCCCCCCEEEEECCCCE-EEEEEEEEEE Q ss_conf 96310133458815013178998728888878999828971-9999999897 Q gi|254780440|r 107 IVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAPGGE-KTYEILQVLW 157 (158) Q Consensus 107 lVg~~e~d~~~~~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~-~~~~Il~I~y 157 (158) ||||+|+|+..|+||+.||+|+||||+++||+|+|++|+|. ..|+|++|.| T Consensus 76 LV~p~ead~~~gkISv~SPiG~ALlG~~~Gd~i~~~~P~G~~~~l~I~~V~y 127 (135) T PRK05753 76 LVYPADADISNGQVSVLAPVGAALLGLSVGQSIDWPLPGGKETHLTVLEVEY 127 (135) T ss_pred EECHHHCCCCCCCCCCCCHHHHHHHCCCCCCEEEEECCCCCEEEEEEEEEEE T ss_conf 9490264944792010169999973899999999988999778999999988 No 10 >pfam01272 GreA_GreB Transcription elongation factor, GreA/GreB, C-term. This domain has a FKBP-like fold. Probab=99.88 E-value=1.7e-22 Score=164.18 Aligned_cols=76 Identities=46% Similarity=0.850 Sum_probs=74.2 Q ss_pred CCCCCCCCCEEEEEECCCCCEEEEEEECHHHCCCCCCEECCCCHHHHHHCCCCCCCEEEEECCCCEEEEEEEEEEE Q ss_conf 3321113657999534765235999963101334588150131789987288888789998289719999999897 Q gi|254780440|r 82 SGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAPGGEKTYEILQVLW 157 (158) Q Consensus 82 ~~~~V~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~~~~~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~Il~I~y 157 (158) |.|+|+|||+|+++|.+++++.+|+||||+|+|++.++||+.||||+||||+++||+|+|++|+|..+|+|++|+| T Consensus 2 ~~d~V~~Gs~V~i~~~~~~~~~~~~iVg~~ea~~~~~~IS~~SPlg~ALlG~~~Gd~v~~~~p~G~~~~~I~~I~~ 77 (77) T pfam01272 2 PADVVTFGSTVTLEDLDDGEEETYTIVGPDEADPSKGKISVLSPLGRALLGKKVGDEVEVTAPSGEKKYEILKIEY 77 (77) T ss_pred CCCEEEECCEEEEEECCCCCEEEEEEECHHHCCCCCCCCCCCCHHHHHHHCCCCCCEEEEECCCCCEEEEEEEEEC T ss_conf 9999999989999999999899999979689282579228889889997399999999999699879999999999 No 11 >pfam03449 GreA_GreB_N domain. This domain adopts a long alpha-hairpin structure. Probab=99.84 E-value=8.3e-21 Score=153.39 Aligned_cols=71 Identities=56% Similarity=0.797 Sum_probs=69.2 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 31488999999999999987248999999999975176222430489998876879999999974444210 Q gi|254780440|r 5 IPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEV 75 (158) Q Consensus 5 ~~lT~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~i 75 (158) +|||++||++|++||++|++++||+++++|++||++|||||||||++||++|+++++||.+|+.+|++|+| T Consensus 1 ~~lT~eg~~~L~~EL~~L~~v~rp~i~~~i~~Ar~~GDlsENaeY~aAke~q~~le~RI~eLe~~L~~A~I 71 (71) T pfam03449 1 NPITPEGYEKLQEELERLKNVERPEIIKAIAEAREHGDLSENAEYHAAKEEQREIEARIRELEDRLARAEI 71 (71) T ss_pred CCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC T ss_conf 99999999999999999987538999999999988599042067899999999999999999999961869 No 12 >PRK01490 tig trigger factor; Provisional Probab=91.53 E-value=1.3 Score=24.83 Aligned_cols=86 Identities=13% Similarity=0.264 Sum_probs=47.6 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEEC--------CCCCEEEEEE-ECHHHCCCCCCEECCCCHH Q ss_conf 768799999999744442104721013321113657999534--------7652359999-6310133458815013178 Q gi|254780440|r 56 QNLNEGRMAELENIITRAEVIDISTMSGDRIAFGATVSLVEK--------NSGDKKNYQI-VGDQEADVQSGLVSISSPI 126 (158) Q Consensus 56 q~~~~~ri~~L~~~L~~A~iv~~~~~~~~~V~~Gs~V~l~d~--------~~~~~~~~~l-Vg~~e~d~~~~~IS~~SPl 126 (158) ...++..|..|....+...-++. .+..|..|++-.. +.+....|.+ +|+. ++..-+ T Consensus 134 d~~Vd~~i~~l~~~~a~~~~~e~------~~~~gD~v~id~~~~~dg~~~~~~~~~~~~~~lg~~---------~~i~gf 198 (435) T PRK01490 134 DEDVDEMLENLRKQFATLVPVER------PAENGDRVTIDFVGSIDGEEFEGGKAEDFSLELGSG---------RMIPGF 198 (435) T ss_pred HHHHHHHHHHHHHHCCCCCCCCH------HHCCCCEEEEEEEEEECCCCCCCCCCCCEEEEECCC---------CCCHHH T ss_conf 89999999999975076556540------212698799998987668204677765069990588---------775559 Q ss_pred HHHHCCCCCCCEEEEEC--CC--------C---EEEEEEEEEE Q ss_conf 99872888887899982--89--------7---1999999989 Q gi|254780440|r 127 ARALIGKELGDIISVNA--PG--------G---EKTYEILQVL 156 (158) Q Consensus 127 G~ALlG~~~Gd~V~v~~--p~--------G---~~~~~Il~I~ 156 (158) ..+|+|.++||++++.+ |. | ..+++|.+|. T Consensus 199 ~~~LiG~k~Gd~~~~~v~fp~d~~~~~laGk~~~f~v~v~~I~ 241 (435) T PRK01490 199 EEQLVGMKAGEEKTIDVTFPEDYHAEDLAGKEATFKVTVKEVK 241 (435) T ss_pred HHHHCCCCCCCEEEEEECCCCCCCCHHHCCCCEEEEEEEEEEE T ss_conf 9985468778621122037642220243488527999875530 No 13 >COG0544 Tig FKBP-type peptidyl-prolyl cis-trans isomerase (trigger factor) [Posttranslational modification, protein turnover, chaperones] Probab=74.49 E-value=7.8 Score=19.88 Aligned_cols=34 Identities=24% Similarity=0.338 Sum_probs=22.3 Q ss_pred CCHHHHHHCCCCCCCEEE--EECCC--------C-E--EEEEEEEEE Q ss_conf 317899872888887899--98289--------7-1--999999989 Q gi|254780440|r 123 SSPIARALIGKELGDIIS--VNAPG--------G-E--KTYEILQVL 156 (158) Q Consensus 123 ~SPlG~ALlG~~~Gd~V~--v~~p~--------G-~--~~~~Il~I~ 156 (158) .--+-.+|+|.++||++. +..|. | . ..++|.+|. T Consensus 195 ipgFe~~LvG~k~Ge~k~i~vtFP~~y~a~~LaGK~a~F~V~vkeVk 241 (441) T COG0544 195 IPGFEDQLVGMKAGEEKDIKVTFPEDYHAEELAGKEATFKVKVKEVK 241 (441) T ss_pred HHHHHHHHCCCCCCCEEEEEEECCCCCCHHHHCCCCEEEEEEEEEEE T ss_conf 44288641368579756898871665306673899638999999985 No 14 >cd06213 oxygenase_e_transfer_subunit The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons. Electron transfer is from NADH via FAD (in the oxygenase reductase) and an [2FE-2S] ferredoxin center (fused to the FAD/NADH domain and/or discrete) to the oxygenase. Dioxygenases add both atoms of oxygen to the substrate while mono-oxygenases add one atom to the substrate and one atom to water. In dioxygenases, Class I enzymes are 2 component, containing a reductase with Rieske type [2Fe-2S] redox centers and an oxygenase. Class II are 3 component, having discrete flavin and ferredoxin proteins and an oxygenase. Class III have 2 [2Fe-2S] centers, one fused to the flavin domain and the other separate. Probab=70.62 E-value=9.5 Score=19.32 Aligned_cols=65 Identities=17% Similarity=0.200 Sum_probs=42.2 Q ss_pred CCCCCEEEEEECCCCCEEEEEEECHHHCCCCC-CEECC--CCHHHHHHCC-CCCCCEEEEECCCCEEEE Q ss_conf 11365799953476523599996310133458-81501--3178998728-888878999828971999 Q gi|254780440|r 86 IAFGATVSLVEKNSGDKKNYQIVGDQEADVQS-GLVSI--SSPIARALIG-KELGDIISVNAPGGEKTY 150 (158) Q Consensus 86 V~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~~~-~~IS~--~SPlG~ALlG-~~~Gd~V~v~~p~G~~~~ 150 (158) -..|-.|.+.-.+.+..+.|+|+.+...+..- -.|.. ...+...|.. .++||+|.+.-|.|...+ T Consensus 28 f~pGQ~v~l~~~g~~~~R~ySias~p~~~~~i~~~Vk~~~~G~~s~~l~~~l~~Gd~v~v~gP~G~f~l 96 (227) T cd06213 28 YKAGQYAELTLPGLPAARSYSFANAPQGDGQLSFHIRKVPGGAFSGWLFGADRTGERLTVRGPFGDFWL 96 (227) T ss_pred CCCCEEEEEEECCCCCCCEEEECCCCCCCCEEEEEEEEECCCCHHHHHHHCCCCCCEEEEECCCCCEEE T ss_conf 199858999989907520345536899888899999986799427899843899989999747336483 No 15 >PRK05431 seryl-tRNA synthetase; Provisional Probab=69.74 E-value=10 Score=19.20 Aligned_cols=79 Identities=28% Similarity=0.331 Sum_probs=47.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC Q ss_conf 9999999999999872489999999999751762224--30489998876879999999974444210472101332111 Q gi|254780440|r 10 KGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSEN--AEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGDRIA 87 (158) Q Consensus 10 ~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~EN--aeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~~~~~~V~ 87 (158) +-+.+++.+++.|+. +|-.++++|..+...|+-.+. .+-..-+++...++..+.+++..|...- ..-..++.+.|. T Consensus 35 ~~rr~l~~e~e~Lr~-erN~iSK~Ig~~kk~g~~~~~l~~~~~~lk~~i~~le~~~~~~~~~l~~~l-l~IPNi~~~~VP 112 (422) T PRK05431 35 EERRELQTETEELQA-ERNALSKEIGQAKAKGEDAEELIAEVKELKEEIKALEAELKELEAELEELL-LSIPNLPHDSVP 112 (422) T ss_pred HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHCCCCCCCCCC T ss_conf 999999999999999-999999999998748977999999999999999999999999999999999-848998886578 Q ss_pred CCC Q ss_conf 365 Q gi|254780440|r 88 FGA 90 (158) Q Consensus 88 ~Gs 90 (158) +|. T Consensus 113 ~G~ 115 (422) T PRK05431 113 VGK 115 (422) T ss_pred CCC T ss_conf 899 No 16 >pfam02359 CDC48_N Cell division protein 48 (CDC48), N-terminal domain. This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the N-terminus. The VAT-N domain found in AAA ATPases pfam00004 is a substrate 185-residue recognition domain. Probab=68.84 E-value=10 Score=19.08 Aligned_cols=69 Identities=17% Similarity=0.220 Sum_probs=51.5 Q ss_pred HHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCEEEEEEECHHHC-CCCCCEECCCCHHHHHHCCCCCCCEEEEEC Q ss_conf 44421047210133211136579995347652359999631013-345881501317899872888887899982 Q gi|254780440|r 70 ITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEA-DVQSGLVSISSPIARALIGKELGDIISVNA 143 (158) Q Consensus 70 L~~A~iv~~~~~~~~~V~~Gs~V~l~d~~~~~~~~~~lVg~~e~-d~~~~~IS~~SPlG~ALlG~~~Gd~V~v~~ 143 (158) ..+...++|..++.-.+.-|..|.+.. +..|.-+|.|... |...|.|.+..+. +.-+|-..||.|++.. T Consensus 14 g~~iarv~p~~m~~l~~~~GD~v~i~G----~r~t~a~v~~~~~~d~~~g~I~~d~~~-R~na~v~igd~V~V~~ 83 (87) T pfam02359 14 GRGIARLSPKDMDELGLFRGDIVEIKG----KRRTVAIVFPARPEDEGPGIIRMDGVQ-RKNAGVSIGDEVTVRP 83 (87) T ss_pred CCCEEEECHHHHHHCCCCCCCEEEEEE----CCEEEEEEECCCCCCCCCCEEEECHHH-HHHCCCCCCCEEEEEE T ss_conf 887799699999985999999999981----744899997178242679879977788-8666988999899997 No 17 >COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones] Probab=68.67 E-value=7.1 Score=20.14 Aligned_cols=28 Identities=32% Similarity=0.576 Sum_probs=22.6 Q ss_pred CEECCCCHHHHHHCCCCCCCEEEEECCC Q ss_conf 8150131789987288888789998289 Q gi|254780440|r 118 GLVSISSPIARALIGKELGDIISVNAPG 145 (158) Q Consensus 118 ~~IS~~SPlG~ALlG~~~Gd~V~v~~p~ 145 (158) |.=++..+|=+||+|+.+|+..++.+|- T Consensus 38 G~g~li~glE~al~g~~~Ge~~~V~IpP 65 (174) T COG1047 38 GAGQLIPGLEEALLGKEVGEEFTVEIPP 65 (174) T ss_pred CCCCCCHHHHHHHHCCCCCCEEEEEECC T ss_conf 6987206599987177789616898682 No 18 >pfam11599 AviRa RRNA methyltransferase AviRa. This family of proteins represents the methyltransferase AviRa from Streptomyces viridochromogenes. This protein mediates the resistance to the antibiotic avilamycin. AviRa methylates a specific guanine base within the peptidyl-transferase loop of the 23S ribosomal RNA. Probab=68.05 E-value=8.4 Score=19.67 Aligned_cols=86 Identities=16% Similarity=0.266 Sum_probs=52.9 Q ss_pred CCCHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC Q ss_conf 1488999999999999987-248999999999975176222430489998876879999999974444210472101332 Q gi|254780440|r 6 PVTSKGFDKIQQELRWRQQ-EERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGD 84 (158) Q Consensus 6 ~lT~~g~~~L~~El~~l~~-~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~~~~~ 84 (158) .+|++|+++-++||..+-. -.+|.-++.. ++|.+-.+.+.+.-..+-..+++|-|.|+.....- T Consensus 99 LLt~~GL~~R~~eL~e~~~~f~k~s~~~aa---------------~aA~Rl~~~l~a~gg~~p~~~~~ADvfdp~~l~~~ 163 (249) T pfam11599 99 LLSKAGINAREDELKALSERFGKASHIDAA---------------HAADRIEELLTAEGGALPCAIKTADLFDGNALEAC 163 (249) T ss_pred HHCHHHHHHHHHHHHHHHHHHCCCHHHHHH---------------HHHHHHHHHHHCCCCCCCCHHHEECCCCCCHHHHH T ss_conf 403201677899999999984882578899---------------88899999986038998612100023586036777 Q ss_pred CCCCCCEEEEEECCCCCEEEEE Q ss_conf 1113657999534765235999 Q gi|254780440|r 85 RIAFGATVSLVEKNSGDKKNYQ 106 (158) Q Consensus 85 ~V~~Gs~V~l~d~~~~~~~~~~ 106 (158) ...++.-|.+.|+.-|+..+++ T Consensus 164 ~~g~~pDiVvTDlPYGe~t~We 185 (249) T pfam11599 164 DAGFAPDIIITDLPYGEMTEWE 185 (249) T ss_pred HCCCCCCEEEECCCCCCEEEEC T ss_conf 4378888688437877400223 No 19 >PRK02195 V-type ATP synthase subunit D; Provisional Probab=67.19 E-value=11 Score=18.87 Aligned_cols=69 Identities=17% Similarity=0.287 Sum_probs=38.6 Q ss_pred CCCCCCCCHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99843148899999999999998------724899999999997517622243048999887687999999997444421 Q gi|254780440|r 1 MVDKIPVTSKGFDKIQQELRWRQ------QEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAE 74 (158) Q Consensus 1 M~~k~~lT~~g~~~L~~El~~l~------~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~ 74 (158) ||-++-.|+--+.+++..|.... .-+|..+..++..+.+ ++...++....+...+......++.+- T Consensus 1 mm~kv~pTr~eL~~lk~~Lk~a~rg~~lLk~Kr~~L~~e~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 (201) T PRK02195 1 MMSKVKLTKNSLRKQKQQLKMLERYLPTLKLKKAQLQAEVQRAKA--------EAAELELEREQLEERIYAFASLFSEPL 72 (201) T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 976658749999999999999986434799999999999999999--------999999999999999999999855400 Q ss_pred CCC Q ss_conf 047 Q gi|254780440|r 75 VID 77 (158) Q Consensus 75 iv~ 77 (158) .++ T Consensus 73 ~~~ 75 (201) T PRK02195 73 EFD 75 (201) T ss_pred HHH T ss_conf 333 No 20 >PRK04290 30S ribosomal protein S6e; Validated Probab=62.93 E-value=11 Score=18.99 Aligned_cols=27 Identities=37% Similarity=0.529 Sum_probs=18.5 Q ss_pred EECCCCHHHHHHCCCCCCCEEEEECCC Q ss_conf 150131789987288888789998289 Q gi|254780440|r 119 LVSISSPIARALIGKELGDIISVNAPG 145 (158) Q Consensus 119 ~IS~~SPlG~ALlG~~~Gd~V~v~~p~ 145 (158) .+.+...-..+|+|++.||+|.-..-+ T Consensus 18 ~~ei~~~~~~~~~gkkIGdevdg~~lG 44 (115) T PRK04290 18 QIEIDGAEANRLIGKKIGDEIDGSIVG 44 (115) T ss_pred EEEECCHHHHHHHCCCCCCEECCCEEC T ss_conf 999784787433045011477531807 No 21 >cd06165 Sortase_A_1 Sortase A (SrtA) or subfamily-1 sortases are cysteine transpeptidases found in gram-positive bacteria that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal (usually a pentapeptide motif), and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. This group contains a subset of Class A (subfamily-1) sortases, excluding SrtA from Staphylococcus aureus. Sortase A cleaves between threonine and glycine of the LPXTG motif in a wide range of protein substrates. It affects the ability of a pathogen to establish successful infection. Sortase A contains an N-terminal region that functions as both a signal peptide for secretion and a stop-tra Probab=57.49 E-value=17 Score=17.76 Aligned_cols=27 Identities=15% Similarity=0.175 Sum_probs=17.3 Q ss_pred CCCCCCCEEEEECCCCEEEEEEEEEEE Q ss_conf 288888789998289719999999897 Q gi|254780440|r 131 IGKELGDIISVNAPGGEKTYEILQVLW 157 (158) Q Consensus 131 lG~~~Gd~V~v~~p~G~~~~~Il~I~y 157 (158) --.++||.|.+....+.+.|+|.+++- T Consensus 62 ~~l~~GD~I~v~~~~~~~~Y~V~~~~i 88 (127) T cd06165 62 YKVKVGDKIYLTDKDNVYEYKVTSKKI 88 (127) T ss_pred HHCCCCCEEEEEECCCEEEEEEEEEEE T ss_conf 568999999999899399999948999 No 22 >PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional Probab=57.42 E-value=17 Score=17.75 Aligned_cols=23 Identities=35% Similarity=0.443 Sum_probs=11.0 Q ss_pred CCHHHHHHCCCCCCCEEEEECCC Q ss_conf 31789987288888789998289 Q gi|254780440|r 123 SSPIARALIGKELGDIISVNAPG 145 (158) Q Consensus 123 ~SPlG~ALlG~~~Gd~V~v~~p~ 145 (158) ..-|=+||+|+++||.++|.+|. T Consensus 42 ipglE~aL~G~~~Gd~~~vtl~p 64 (196) T PRK10737 42 ISGLETALEGHEVGDKFDVAVGA 64 (196) T ss_pred CHHHHHHHCCCCCCCEEEEEECH T ss_conf 67899985799999778999787 No 23 >cd06166 Sortase_D_5 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-5, represented by Clostridium perfringens CPE2315. Subfamily-5 sortases recognize a nonstandard sorting signal (LAXTG) and have replaced Sortase A in some gram-postive bacteria. They may play a housekeeping role in the cell. Probab=56.14 E-value=18 Score=17.62 Aligned_cols=28 Identities=32% Similarity=0.419 Sum_probs=16.3 Q ss_pred HCCCCCCCEEEEECCCCEEEEEEEEEEE Q ss_conf 7288888789998289719999999897 Q gi|254780440|r 130 LIGKELGDIISVNAPGGEKTYEILQVLW 157 (158) Q Consensus 130 LlG~~~Gd~V~v~~p~G~~~~~Il~I~y 157 (158) |--.+.||.|.+...++.+.|+|.+++. T Consensus 62 L~~l~~GD~I~l~~~~~~y~Y~V~~~~i 89 (126) T cd06166 62 LDEVEKGDEIKVTTKNGTYKYKITSIFV 89 (126) T ss_pred HHHCCCCCEEEEEECCEEEEEEEEEEEE T ss_conf 5518589999999999899999977999 No 24 >COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification] Probab=55.88 E-value=12 Score=18.64 Aligned_cols=73 Identities=22% Similarity=0.333 Sum_probs=50.0 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHH-HHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCEEEEEEECHHHCCCCC Q ss_conf 22430489998876879999999974-444210472101332111365799953476523599996310133458 Q gi|254780440|r 44 SENAEYQAAKELQNLNEGRMAELENI-ITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQS 117 (158) Q Consensus 44 ~ENaeY~aAke~q~~~~~ri~~L~~~-L~~A~iv~~~~~~~~~V~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~~~ 117 (158) +||+.-|.-+..|..++++ +-|... +-.+.|-..-....+++++|-.|.+.|..-+..-.|+||..-|-+... T Consensus 94 rEnqtthdfrqqQkiieaK-qSlk~~GiP~ykv~~~~epk~G~~Gl~iqvnY~Dd~a~~~P~yRivs~lEq~ve~ 167 (222) T COG5246 94 RENQTTHDFRQQQKIIEAK-QSLKRSGIPSYKVRSLVEPKGGRRGLGIQVNYEDDLAEEMPQYRIVSSLEQNVEE 167 (222) T ss_pred CCCCCHHHHHHHHHHHHHH-HHHHHCCCCCEEEEEEECCCCCCEEEEEEEECCCHHHCCCCCEEHHHHHHHCCHH T ss_conf 3588404556677889998-8787549973367776637788400478972550221258614304466652010 No 25 >cd05828 Sortase_D_4 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-4. These sortases recognize a unique sorting signal (LPXTA) and they constitute a specialized sorting pathway found in bacilli. Their substrates are predicted to be predominantly enzymes such as 5'-nucleotidases, glycosyl hydrolase, and subtilase. Probab=55.54 E-value=18 Score=17.56 Aligned_cols=26 Identities=35% Similarity=0.510 Sum_probs=16.2 Q ss_pred CCCCCCEEEEECCCCEEEEEEEEEEE Q ss_conf 88888789998289719999999897 Q gi|254780440|r 132 GKELGDIISVNAPGGEKTYEILQVLW 157 (158) Q Consensus 132 G~~~Gd~V~v~~p~G~~~~~Il~I~y 157 (158) -.+.||.|.+...++.+.|+|.+++- T Consensus 61 ~l~~GD~I~l~~~~~~y~Y~V~~~~v 86 (127) T cd05828 61 ELEPGDIITLQTLGGTYTYRVTSTRI 86 (127) T ss_pred HCCCCCEEEEEECCEEEEEEEEEEEE T ss_conf 57479999999788399999977999 No 26 >cd05830 Sortase_D_5 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-5 represented by Streptomyces avermitilis SAV4337. Subfamily-5 sortases recognize a nonstandard sorting signal (LAXTG) and have replaced Sortase A in some gram-postive bacteria. They may play a housekeeping role in the cell. Probab=55.41 E-value=18 Score=17.54 Aligned_cols=36 Identities=25% Similarity=0.252 Sum_probs=26.3 Q ss_pred CCCCHHHHHHCCCCCCCEEEEECCCCEEEEEEEEEEE Q ss_conf 0131789987288888789998289719999999897 Q gi|254780440|r 121 SISSPIARALIGKELGDIISVNAPGGEKTYEILQVLW 157 (158) Q Consensus 121 S~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~Il~I~y 157 (158) ++.+|+. -|-..++||.|.+...++.+.|+|.+++- T Consensus 55 ~~~~~F~-~L~~l~~GD~I~v~~~~~~~~Y~V~~~~i 90 (137) T cd05830 55 TYGAPFN-DLDKLRPGDKIVVETADGWYTYVVRSSEI 90 (137) T ss_pred CCCCCCC-CHHCCCCCCEEEEEECCEEEEEEEEEEEE T ss_conf 9775560-13538999999999999899999974999 No 27 >pfam00970 FAD_binding_6 Oxidoreductase FAD-binding domain. Probab=53.65 E-value=19 Score=17.36 Aligned_cols=65 Identities=20% Similarity=0.244 Sum_probs=42.1 Q ss_pred CCCCCEEEEEECCCC--CEEEEEEECHHHCC-CCCCEEC--CCCHHHHHHCCCCCCCEEEEECCCCEEEE Q ss_conf 113657999534765--23599996310133-4588150--13178998728888878999828971999 Q gi|254780440|r 86 IAFGATVSLVEKNSG--DKKNYQIVGDQEAD-VQSGLVS--ISSPIARALIGKELGDIISVNAPGGEKTY 150 (158) Q Consensus 86 V~~Gs~V~l~d~~~~--~~~~~~lVg~~e~d-~~~~~IS--~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~ 150 (158) ...|..|.+.-...| ....|+++.+...+ ...=.|- ..-++-..|-..++||+|.+.-|-|...| T Consensus 30 f~pGQ~v~l~~~~~g~~~~R~YS~~s~p~~~~~~e~~Vk~~~~G~~S~~l~~l~~Gd~v~i~gP~G~F~~ 99 (99) T pfam00970 30 LPPGQHIFLRLPIDGKLVVRAYSPASSPDDVGELELLVKVYPGGKMSQYLDSLKVGDTVEVKGPLGHFEY 99 (99) T ss_pred CCCCEEEEEEEEECCEEEEEEEECCCCCCCCCEEEEEEEEECCCCHHHHHHCCCCCCEEEEECCCEEEEC T ss_conf 8996099999765998998772215665789859999999707966778752899999999843586679 No 28 >COG3127 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism] Probab=51.66 E-value=21 Score=17.16 Aligned_cols=38 Identities=26% Similarity=0.302 Sum_probs=29.4 Q ss_pred EECCCCHHHHHHCCCCCCCEEEEECCCCEEEEEEEEEEE Q ss_conf 150131789987288888789998289719999999897 Q gi|254780440|r 119 LVSISSPIARALIGKELGDIISVNAPGGEKTYEILQVLW 157 (158) Q Consensus 119 ~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~Il~I~y 157 (158) .+|+.--+++. +|-|.||+|++..-+-+..-+|.+++- T Consensus 598 ~VS~e~~~A~~-LglKLGDtvTf~v~gq~i~A~I~slR~ 635 (829) T COG3127 598 EVSMEEGEAKR-LGLKLGDTVTFMVLGQNITAKITSLRK 635 (829) T ss_pred CCCHHHHHHHH-HCCCCCCEEEEEECCCEEEEEECEEEE T ss_conf 44020867987-097627779998426267765110223 No 29 >cd00004 Sortase Sortases are cysteine transpeptidases, found in gram-positive bacteria, that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The different classes are called Sortase A or SrtA (subfamily 1), B or SrtB (subfamily 2), C or SrtC (subfamily3), D or SrtD (subfamilies 4 and 5), and E or SrtE. In two different sortase subfamilies, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one s Probab=51.23 E-value=21 Score=17.12 Aligned_cols=29 Identities=24% Similarity=0.350 Sum_probs=20.4 Q ss_pred HCCCCCCCEEEEECCCCEEEEEEEEEEEC Q ss_conf 72888887899982897199999998979 Q gi|254780440|r 130 LIGKELGDIISVNAPGGEKTYEILQVLWI 158 (158) Q Consensus 130 LlG~~~Gd~V~v~~p~G~~~~~Il~I~yi 158 (158) |--.+.||.|.+...++.+.|+|.+++.+ T Consensus 62 L~~l~~GD~i~i~~~~~~y~Y~V~~~~iv 90 (128) T cd00004 62 LDNLKKGDKIYLTDGGKTYVYKVTSILTV 90 (128) T ss_pred HHHCCCCCEEEEEECCEEEEEEEEEEEEE T ss_conf 54576899899999998999999889998 No 30 >cd06210 MMO_FAD_NAD_binding Methane monooxygenase (MMO) reductase of methanotrophs catalyzes the NADH-dependent hydroxylation of methane to methanol. This multicomponent enzyme mediates electron transfer via a hydroxylase (MMOH), a coupling protein, and a reductase which is comprised of an N-terminal [2Fe-2S] ferredoxin domain, an FAD binding subdomain, and an NADH binding subdomain. Oxygenases oxidize hydrocarbons using dioxygen as the oxidant. Dioxygenases add both atom of oxygen to the substrate, while mono-oxygenases add one atom to the substrate and one atom to water. Probab=48.01 E-value=24 Score=16.81 Aligned_cols=64 Identities=14% Similarity=0.215 Sum_probs=41.7 Q ss_pred CCCCEEEEEECCCCCEEEEEEECHHHCCCC-CCEEC--CCCHHHHHHCC-CCCCCEEEEECCCCEEEE Q ss_conf 136579995347652359999631013345-88150--13178998728-888878999828971999 Q gi|254780440|r 87 AFGATVSLVEKNSGDKKNYQIVGDQEADVQ-SGLVS--ISSPIARALIG-KELGDIISVNAPGGEKTY 150 (158) Q Consensus 87 ~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~~-~~~IS--~~SPlG~ALlG-~~~Gd~V~v~~p~G~~~~ 150 (158) ..|--|++.-.+.+....|+|+++...+.. .=.|. ....+...|.. .++||.|.+.-|.|...+ T Consensus 36 ~pGQ~v~l~~~g~~~~R~ySi~s~p~~~~~l~~~vk~~~~G~~S~~l~~~l~~Gd~v~v~gP~G~f~l 103 (236) T cd06210 36 VPGQFVEIEIPGTDTRRSYSLANTPNWDGRLEFLIRLLPGGAFSTYLETRAKVGQRLNLRGPLGAFGL 103 (236) T ss_pred CCCCEEEEEECCCCEEEEEEEEECCCCCCEEEEEEEEECCCCHHHHHHHCCCCCCEEEEEECCCCCCC T ss_conf 89960899989988089887602799999899999998499467799855999999999706457501 No 31 >TIGR03007 pepcterm_ChnLen polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; InterPro: IPR014345 Members of this entry belong to the family of polysaccharide chain length determinant proteins. They are found in species that encode the PEP-CTERM/exosortase system and are predicted to act in protein sorting in a number of Gram-negative bacteria, they are also found near the epsH homologue that is the putative exosortase gene.. Probab=47.73 E-value=24 Score=16.78 Aligned_cols=21 Identities=0% Similarity=0.208 Sum_probs=10.6 Q ss_pred CCCCCEEEEEECCCCCEEEEEEECH Q ss_conf 1136579995347652359999631 Q gi|254780440|r 86 IAFGATVSLVEKNSGDKKNYQIVGD 110 (158) Q Consensus 86 V~~Gs~V~l~d~~~~~~~~~~lVg~ 110 (158) +.+.-.+++. ++..+|+||=| T Consensus 393 A~~S~~~e~~----~~~v~FRviDP 413 (510) T TIGR03007 393 AEVSKQMEVQ----DKAVSFRVIDP 413 (510) T ss_pred HHHHHHEEEE----CCCEEEEEECC T ss_conf 5553303320----67024677567 No 32 >cd06209 BenDO_FAD_NAD Benzoate dioxygenase reductase (BenDO) FAD/NAD binding domain. Oxygenases oxidize hydrocarbons using dioxygen as the oxidant. As a Class I bacterial dioxygenases, benzoate dioxygenase like proteins combine an [2Fe-2S] cluster containing N-terminal ferredoxin at the end fused to an FAD/NADP(P) domain. In dioxygenase FAD/NAD(P) binding domain, the reductase transfers 2 electrons from NAD(P)H to the oxygenase which insert into an aromatic substrate, an initial step in microbial aerobic degradation of aromatic rings. Flavin oxidoreductases use flavins as substrates, unlike flavoenzymes which have a flavin prosthetic group. Probab=47.48 E-value=24 Score=16.75 Aligned_cols=64 Identities=16% Similarity=0.248 Sum_probs=41.3 Q ss_pred CCCCCEEEEEECCCCCEEEEEEECHHHCCCCCCEECC--CCHHHHHHCCC-CCCCEEEEECCCCEEE Q ss_conf 1136579995347652359999631013345881501--31789987288-8887899982897199 Q gi|254780440|r 86 IAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSI--SSPIARALIGK-ELGDIISVNAPGGEKT 149 (158) Q Consensus 86 V~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~~~~~IS~--~SPlG~ALlG~-~~Gd~V~v~~p~G~~~ 149 (158) -..|..|.+.-.+.+....|+|..+.+...-.-.|-. .-+....|... ++||.|.+.-|-|.-. T Consensus 31 f~pGQ~v~l~~~g~~~~R~ySias~p~~~~l~~~Ik~~~~G~~s~~l~~~~~~Gd~v~i~gP~G~f~ 97 (228) T cd06209 31 FLPGQYVNLQVPGTDETRSYSFSSAPGDPRLEFLIRLLPGGAMSSYLRDRAQPGDRLTLTGPLGSFY 97 (228) T ss_pred CCCCCEEEEEECCCCCEEEEEEECCCCCCEEEEEEEECCCCCHHHHHHHCCCCCCEEEEECCCCCCC T ss_conf 4899759999899284689987008997989999999079956789985589999999970354742 No 33 >COG3764 SrtA Sortase (surface protein transpeptidase) [Cell envelope biogenesis, outer membrane] Probab=46.84 E-value=25 Score=16.69 Aligned_cols=33 Identities=18% Similarity=0.414 Sum_probs=27.0 Q ss_pred CCCHHHHHHCCCCCCCEEEEECCCCEEEEEEEEEEEC Q ss_conf 1317899872888887899982897199999998979 Q gi|254780440|r 122 ISSPIARALIGKELGDIISVNAPGGEKTYEILQVLWI 158 (158) Q Consensus 122 ~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~Il~I~yi 158 (158) ..+||++ .++||.|-+..+++...|+|.+|.-| T Consensus 128 ~F~~L~~----lk~GD~iyv~~~~~~~~Y~v~~~~~V 160 (210) T COG3764 128 LFRPLGK----LKVGDKIYVTTKNETYVYKVTDISIV 160 (210) T ss_pred CCCCHHH----HCCCCEEEEEECCCEEEEEEEEEEEE T ss_conf 5565556----03798899995795799999987885 No 34 >pfam11160 DUF2945 Protein of unknown function (DUF2945). This family of proteins has no known function. Probab=45.48 E-value=26 Score=16.56 Aligned_cols=22 Identities=32% Similarity=0.407 Sum_probs=17.5 Q ss_pred CCEEEEECCCCEEEEEEEEEEE Q ss_conf 8789998289719999999897 Q gi|254780440|r 136 GDIISVNAPGGEKTYEILQVLW 157 (158) Q Consensus 136 Gd~V~v~~p~G~~~~~Il~I~y 157 (158) ||.|.|..+.|...=+|+++.+ T Consensus 1 GD~V~WnS~~g~~~G~V~~~~T 22 (62) T pfam11160 1 GDHVRWNSEAGEVSGKIVKVHT 22 (62) T ss_pred CCCEEECCCCCEEEEEEEEEEC T ss_conf 9822772899668689999983 No 35 >PRK12306 uvrC excinuclease ABC subunit C; Reviewed Probab=44.25 E-value=27 Score=16.44 Aligned_cols=130 Identities=13% Similarity=0.195 Sum_probs=72.2 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC Q ss_conf 14889999999999999872489999999999751762224304899988768799999999744442104721013321 Q gi|254780440|r 6 PVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGDR 85 (158) Q Consensus 6 ~lT~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~~~~~~ 85 (158) .+|++.|.+.-++....-.=+-.++...+..... ..|+|-+|..|. .+-.+|..|+...+.-.|+.....+.|+ T Consensus 169 ~is~e~Y~~~V~~~~~fL~Gk~~~~~~~L~~~M~--~aS~~l~FE~AA----~~RD~I~aL~~i~~~Q~v~~~~~~d~Dv 242 (519) T PRK12306 169 NISSDEYLEQVKKAEEVLKGNIQELIEKLEEEMA--EKAKNQQFERAL----VIRDEINAIENLQERQNVERQKKYDEDI 242 (519) T ss_pred CCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHH--HHHHHHHHHHHH----HHHHHHHHHHHHHHCCCCCCCCCCCCCE T ss_conf 6899999999999999981796899999999999--999744089999----9999999999997505111577655415 Q ss_pred CCCC-----CEEEEEECCCCCEEEEEEECHHHC--------------------C-CCCCEECC----CCHHHHHHCCCCC Q ss_conf 1136-----579995347652359999631013--------------------3-45881501----3178998728888 Q gi|254780440|r 86 IAFG-----ATVSLVEKNSGDKKNYQIVGDQEA--------------------D-VQSGLVSI----SSPIARALIGKEL 135 (158) Q Consensus 86 V~~G-----s~V~l~d~~~~~~~~~~lVg~~e~--------------------d-~~~~~IS~----~SPlG~ALlG~~~ 135 (158) +++- +.|.+...-.|. |+|.... . |..=.++. ...+=...|..+. T Consensus 243 i~~~~~~~~~~i~v~~vR~G~-----l~g~~~~~~~~~e~il~~fl~qyY~~~~~P~~Iil~~~~~~~~~~l~~~L~~~~ 317 (519) T PRK12306 243 INYIVKDGTVYLMVFNVLKGT-----LFDKKEFVFDYGENFFEEFLIQYYSENEPPSEIILSELPENLEEALLEYLSHKK 317 (519) T ss_pred EEEEECCCEEEEEEEEEECCE-----EECCCCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHH T ss_conf 789862882999999998999-----835752215764057999999997437998403425788766899999998860 Q ss_pred CCEEEEECCCC Q ss_conf 87899982897 Q gi|254780440|r 136 GDIISVNAPGG 146 (158) Q Consensus 136 Gd~V~v~~p~G 146 (158) |..|.+.+|.. T Consensus 318 ~~kv~i~~P~r 328 (519) T PRK12306 318 GSKVKITVPKQ 328 (519) T ss_pred CCCEEEECCCC T ss_conf 99569975896 No 36 >PTZ00066 pyruvate kinase; Provisional Probab=43.90 E-value=27 Score=16.40 Aligned_cols=87 Identities=21% Similarity=0.268 Sum_probs=47.7 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC-----EEEEEECCCCCEEEEEEECHHHCCCCCCEECCCCH-HHHHHCCC Q ss_conf 9999999974444210472101332111365-----79995347652359999631013345881501317-89987288 Q gi|254780440|r 60 EGRMAELENIITRAEVIDISTMSGDRIAFGA-----TVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSP-IARALIGK 133 (158) Q Consensus 60 ~~ri~~L~~~L~~A~iv~~~~~~~~~V~~Gs-----~V~l~d~~~~~~~~~~lVg~~e~d~~~~~IS~~SP-lG~ALlG~ 133 (158) -..+++......+..+-=--+.++.+++.|. .+.+ ..|+.. +|....+...+...|++..| |-+ .. T Consensus 83 i~~iR~a~~~~~~~~v~Il~Dl~GPkIR~G~l~~~~~i~l---~~G~~v--~i~~~~~~~g~~~~I~v~~~~l~~---~v 154 (513) T PTZ00066 83 LNNVREAQKSRPNANIGLMLDTKGPEIRTGFLKNHKPITL---KEGSTL--KITTDYTILGDETCISCSYKKLPQ---SV 154 (513) T ss_pred HHHHHHHHHHCCCCCEEEEEECCCCEEEEEECCCCCEEEE---CCCCEE--EEECCCCCCCCCCEEEECCCCCHH---HC T ss_conf 9999999986599966999988898258887489964785---389999--997488657987879725865775---67 Q ss_pred CCCCEEEEECCCCEEEEEEEEEE Q ss_conf 88878999828971999999989 Q gi|254780440|r 134 ELGDIISVNAPGGEKTYEILQVL 156 (158) Q Consensus 134 ~~Gd~V~v~~p~G~~~~~Il~I~ 156 (158) ++||.+.+. +|...++|+++. T Consensus 155 ~~Gd~Ilid--DG~I~l~V~~v~ 175 (513) T PTZ00066 155 KVGNIILIA--DGSLSCEVLEVH 175 (513) T ss_pred CCCCEEEEE--CCEEEEEEEEEC T ss_conf 889889997--997999999822 No 37 >COG1018 Hmp Flavodoxin reductases (ferredoxin-NADPH reductases) family 1 [Energy production and conversion] Probab=43.79 E-value=27 Score=16.39 Aligned_cols=65 Identities=18% Similarity=0.235 Sum_probs=44.5 Q ss_pred CCCCCCEEEEEECCC--CCEEEEEEECHHHCCCCCCEECCC----CHHHHHHC-CCCCCCEEEEECCCCEEEE Q ss_conf 111365799953476--523599996310133458815013----17899872-8888878999828971999 Q gi|254780440|r 85 RIAFGATVSLVEKNS--GDKKNYQIVGDQEADVQSGLVSIS----SPIARALI-GKELGDIISVNAPGGEKTY 150 (158) Q Consensus 85 ~V~~Gs~V~l~d~~~--~~~~~~~lVg~~e~d~~~~~IS~~----SPlG~ALl-G~~~Gd~V~v~~p~G~~~~ 150 (158) ....|.-|+|.-... .....|+|+.+-..+ ..-.||+. .++-.-|- ..++||++.+..|.|.-.+ T Consensus 34 ~f~pGQ~i~v~l~~~~~~~~R~YSl~s~p~~~-~~~~isVk~~~~G~~S~~Lh~~lk~Gd~l~v~~P~G~F~l 105 (266) T COG1018 34 DFEPGQYITVGLPNGGEPLLRAYSLSSAPDED-SLYRISVKREDGGGGSNWLHDHLKVGDTLEVSAPAGDFVL 105 (266) T ss_pred CCCCCCEEEEEEECCCCEEEEEEEECCCCCCC-CEEEEEEEECCCCCCCHHHHHCCCCCCEEEEECCCCCCCC T ss_conf 25799738998655994378888833799998-3499999973899746788845999999999668877636 No 38 >cd05827 Sortase_C_3 Sortase C (SrtC) or subfamily-3 sortases are membrane cysteine transpeptidases found in Gram-positive bacteria that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Sortase C cleaves surface proteins at the LPXTG motif between Thr and Gly and catalyzes the formation of an amide bond between the carboxyl group of Thr and the amino group of cell-wall cross bridges. It is a narrow-range enzyme required for anchoring a few substrates. It plays a role in Streptococcus pneumoniae pathogenesis and is required in the assembly of pili on the surface of Corynebacterium diphtheriae. Sortase C is Probab=43.16 E-value=28 Score=16.33 Aligned_cols=29 Identities=21% Similarity=0.252 Sum_probs=17.1 Q ss_pred HHHCCCCCCCEEEEECCCCEEEEEEEEEE Q ss_conf 98728888878999828971999999989 Q gi|254780440|r 128 RALIGKELGDIISVNAPGGEKTYEILQVL 156 (158) Q Consensus 128 ~ALlG~~~Gd~V~v~~p~G~~~~~Il~I~ 156 (158) ..|--.+.||.|.+...++.+.|+|.+++ T Consensus 62 ~~L~~l~~GD~I~l~~~~~~y~Y~V~~~~ 90 (131) T cd05827 62 TDLDKLKKGDKFYIHVLGETLAYQVDQIE 90 (131) T ss_pred CHHHCCCCCCEEEEEECCEEEEEEEEEEE T ss_conf 10343878999999979909999998899 No 39 >pfam06940 DUF1287 Domain of unknown function (DUF1287). This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown. This family is related to pfam00877. Probab=43.08 E-value=28 Score=16.32 Aligned_cols=23 Identities=26% Similarity=0.388 Sum_probs=15.1 Q ss_pred CCCCCCEEEEECCCCEEEEEEEE Q ss_conf 88888789998289719999999 Q gi|254780440|r 132 GKELGDIISVNAPGGEKTYEILQ 154 (158) Q Consensus 132 G~~~Gd~V~v~~p~G~~~~~Il~ 154 (158) --+.||.|+|.+|+|..+.-|++ T Consensus 106 ~yqpGDIV~w~l~~~~~HIgIVs 128 (164) T pfam06940 106 DYQPGDIVTWMLPGNLPHIGIVS 128 (164) T ss_pred HCCCCCEEEEECCCCCCEEEEEE T ss_conf 66897879997799974589983 No 40 >COG2960 Uncharacterized protein conserved in bacteria [Function unknown] Probab=42.39 E-value=29 Score=16.26 Aligned_cols=23 Identities=30% Similarity=0.342 Sum_probs=19.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99988768799999999744442 Q gi|254780440|r 51 AAKELQNLNEGRMAELENIITRA 73 (158) Q Consensus 51 aAke~q~~~~~ri~~L~~~L~~A 73 (158) -+|++...+++||.+|+.+|..+ T Consensus 70 rtR~kl~~Leari~~LEarl~~~ 92 (103) T COG2960 70 RTREKLAALEARIEELEARLASA 92 (103) T ss_pred HHHHHHHHHHHHHHHHHHHHCCC T ss_conf 99999999999999999874246 No 41 >pfam07798 DUF1640 Protein of unknown function (DUF1640). This family consists of sequences derived from hypothetical eukaryotic proteins. A region approximately 100 residues in length is featured. Probab=41.65 E-value=30 Score=16.19 Aligned_cols=60 Identities=23% Similarity=0.178 Sum_probs=35.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 8999999999999987248999999999975176222430489998876879999999974444 Q gi|254780440|r 9 SKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITR 72 (158) Q Consensus 9 ~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~ 72 (158) +...++|+.|++.|+..-+.++.+-- |--.+|+ |-|=-.-|++++..+.+|.++..++.. T Consensus 79 r~e~e~L~~dve~L~~~L~~ei~k~~--a~~klDl--NleK~riree~~~~e~ki~e~~~kId~ 138 (177) T pfam07798 79 QAENEKLKNDLEKLKNRLRDEIDKVT--AGVRLDL--NLEKGRIREELAEQELKIKETDTKIDT 138 (177) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999999999999999861--5257654--555207789998799999999989999 No 42 >COG3973 Superfamily I DNA and RNA helicases [General function prediction only] Probab=41.06 E-value=30 Score=16.13 Aligned_cols=70 Identities=23% Similarity=0.253 Sum_probs=45.6 Q ss_pred CCCCCEEEEEECCCCCEEEEEEE--CHH-HCCCCCCEECCCCHHHHHHCCCCCCCEEEEECCCCEEEEE-EEEEEE Q ss_conf 11365799953476523599996--310-1334588150131789987288888789998289719999-999897 Q gi|254780440|r 86 IAFGATVSLVEKNSGDKKNYQIV--GDQ-EADVQSGLVSISSPIARALIGKELGDIISVNAPGGEKTYE-ILQVLW 157 (158) Q Consensus 86 V~~Gs~V~l~d~~~~~~~~~~lV--g~~-e~d~~~~~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~-Il~I~y 157 (158) --||.. .+.....++.+++.|- |-. +.+...-.++|.||+|.-......| ...+..|+|...-+ +++.+| T Consensus 99 PYFGrI-Df~e~g~~~~eriYIGk~g~~de~~~~~lvvDWRaPIasLfYs~t~g-k~~y~~~~~~v~gel~~krk~ 172 (747) T COG3973 99 PYFGRI-DFREGGHGREERIYIGKFGLRDEVGGEHLVVDWRAPIASLFYSDTLG-KRRYKKPQIRVRGELVLKRKF 172 (747) T ss_pred CCEEEE-EEEECCCCCCEEEEEEECCCCCCCCCCEEEEECCCCCCCHHCCCCCC-CCCEECCCCEEEEEEEEEEEE T ss_conf 730157-67745877603688730023456797237886567421000368877-632013661488788752220 No 43 >COG3738 Uncharacterized protein conserved in bacteria [Function unknown] Probab=40.37 E-value=17 Score=17.67 Aligned_cols=31 Identities=19% Similarity=0.312 Sum_probs=22.7 Q ss_pred HHHHHHCCCCCCCEEEEECCCCEEEEEEEEE Q ss_conf 7899872888887899982897199999998 Q gi|254780440|r 125 PIARALIGKELGDIISVNAPGGEKTYEILQV 155 (158) Q Consensus 125 PlG~ALlG~~~Gd~V~v~~p~G~~~~~Il~I 155 (158) |+-+..--.+.||.|+|.+++|.-..-|++- T Consensus 133 p~~~~~s~y~aGDIvsWRLdngl~HiGv~sd 163 (200) T COG3738 133 PLSKDPSDYQAGDIVSWRLDNGLAHIGVVSD 163 (200) T ss_pred CCCCCCCCCCCCCEEEEECCCCCCEEEEEEC T ss_conf 9987800037876589872799743678633 No 44 >COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis] Probab=39.80 E-value=30 Score=16.12 Aligned_cols=30 Identities=7% Similarity=0.148 Sum_probs=19.7 Q ss_pred CCCCCCCCCCEEEEEECCCCCEEEEEEECHHH Q ss_conf 13321113657999534765235999963101 Q gi|254780440|r 81 MSGDRIAFGATVSLVEKNSGDKKNYQIVGDQE 112 (158) Q Consensus 81 ~~~~~V~~Gs~V~l~d~~~~~~~~~~lVg~~e 112 (158) -|...|-+|..++|.. . ....+|.+++..+ T Consensus 44 KpS~~VK~GD~l~i~~-~-~~~~~v~Vl~~~~ 73 (100) T COG1188 44 KPSKEVKVGDILTIRF-G-NKEFTVKVLALGE 73 (100) T ss_pred CCCCCCCCCCEEEEEE-C-CCEEEEEEEECCC T ss_conf 6556147798999995-7-8189999973543 No 45 >cd06189 flavin_oxioreductase NAD(P)H dependent flavin oxidoreductases use flavin as a substrate in mediating electron transfer from iron complexes or iron proteins. Structurally similar to ferredoxin reductases, but with only 15% sequence identity, flavin reductases reduce FAD, FMN, or riboflavin via NAD(P)H. Flavin is used as a substrate, rather than a tightly bound prosthetic group as in flavoenzymes; weaker binding is due to the absence of a binding site for the AMP moeity of FAD. Probab=38.36 E-value=33 Score=15.86 Aligned_cols=64 Identities=14% Similarity=0.247 Sum_probs=42.4 Q ss_pred CCCCCEEEEEECCCCCEEEEEEECHHHCC-CCCCEE--CCCCHHHHHHCC-CCCCCEEEEECCCCEEEE Q ss_conf 11365799953476523599996310133-458815--013178998728-888878999828971999 Q gi|254780440|r 86 IAFGATVSLVEKNSGDKKNYQIVGDQEAD-VQSGLV--SISSPIARALIG-KELGDIISVNAPGGEKTY 150 (158) Q Consensus 86 V~~Gs~V~l~d~~~~~~~~~~lVg~~e~d-~~~~~I--S~~SPlG~ALlG-~~~Gd~V~v~~p~G~~~~ 150 (158) -..|-.|.+.- +.+....|+|+++...+ ...=.| .....+...|+. .++||++.+.-|.|...+ T Consensus 26 f~pGQ~v~v~~-~~~~~R~ySi~s~p~~~~~l~l~ik~~~~G~~s~~l~~~l~~Gd~v~v~gP~G~f~l 93 (224) T cd06189 26 FLAGQYLDLLL-DDGDKRPFSIASAPHEDGEIELHIRAVPGGSFSDYVFEELKENGLVRIEGPLGDFFL 93 (224) T ss_pred CCCCCEEEEEE-CCCCEEEEEECCCCCCCCEEEEEEEEECCCCHHHHHHHCCCCCCEEEEECCCCCCCC T ss_conf 78997489995-998789986165899998399999996798158899854999998999706757411 No 46 >PRK09239 chorismate mutase; Provisional Probab=37.85 E-value=34 Score=15.81 Aligned_cols=54 Identities=19% Similarity=0.215 Sum_probs=34.7 Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHH Q ss_conf 9984314889999999999999872------48999999999975176222430489998876 Q gi|254780440|r 1 MVDKIPVTSKGFDKIQQELRWRQQE------ERPRIIKAISEARAYGDLSENAEYQAAKELQN 57 (158) Q Consensus 1 M~~k~~lT~~g~~~L~~El~~l~~~------~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~ 57 (158) |++...=+++.+..|+.+++.+-.. +|-.++.+|..-....++ .-|+..|+++- T Consensus 1 ~~~~~~~~~~~L~~lR~~ID~iD~~iv~LLa~R~~~~~~Ig~~K~~~~~---pv~dp~RE~~v 60 (104) T PRK09239 1 MSDEQARAPAELAALRQSIDNIDAALIHMLAERFKCTQAVGVLKAEHGL---PPADPAREARQ 60 (104) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC---CCCCHHHHHHH T ss_conf 9847887689999999999999999999999999999999999987598---98888999999 No 47 >cd00986 PDZ_LON_protease PDZ domain of ATP-dependent LON serine proteases. Most PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this bacterial subfamily of protease-associated PDZ domains a C-terminal beta-strand is thought to form the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins. Probab=36.56 E-value=35 Score=15.68 Aligned_cols=33 Identities=15% Similarity=0.192 Sum_probs=25.9 Q ss_pred EECCCCHHHHHHCCCCCCCEEEEECCCCEEEEE Q ss_conf 150131789987288888789998289719999 Q gi|254780440|r 119 LVSISSPIARALIGKELGDIISVNAPGGEKTYE 151 (158) Q Consensus 119 ~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~ 151 (158) .|+-.+-|-..+-++++||+|++..-++-...+ T Consensus 38 ~v~~~~~l~~~i~~~~~Gd~V~l~v~R~gk~~~ 70 (79) T cd00986 38 PFKEAEELIDYIQSKKEGDTVKLKVKREEKELP 70 (79) T ss_pred ECCCHHHHHHHHHCCCCCCEEEEEEEECCEEEE T ss_conf 957999999999659999989999999999999 No 48 >COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription] Probab=35.17 E-value=30 Score=16.13 Aligned_cols=26 Identities=27% Similarity=0.600 Sum_probs=20.8 Q ss_pred EECCCCHHHHHHCCCCCCCEEEEECCC Q ss_conf 150131789987288888789998289 Q gi|254780440|r 119 LVSISSPIARALIGKELGDIISVNAPG 145 (158) Q Consensus 119 ~IS~~SPlG~ALlG~~~Gd~V~v~~p~ 145 (158) +|+..-|++++ +|.+.||.|.+.--. T Consensus 42 kI~~~DPva~~-lgak~GdvVkIvRkS 67 (80) T COG2012 42 KIKASDPVAKA-LGAKPGDVVKIVRKS 67 (80) T ss_pred CCCCCCHHHHH-HCCCCCCEEEEEECC T ss_conf 50246766777-067878679998638 No 49 >TIGR01801 CM_A chorismate mutase; InterPro: IPR010954 This entry represents chorismate mutase (CM) domains N-terminally fused to the first enzyme in the chorismate pathway, 2-dehydro-3-deoxyphosphoheptanoate aldolase (DAHP synthetase, AroA) which are found in some Gram-positive species and Deinococcus. Only in Deinococcus, where this domain is the sole CM domain in the genome can a trusted assignment of function be made. In the other species there is at least one other CM domain present. The similarity between the Deinococcus gene and the others in this clade is sufficiently strong (~44 0dentity), that the whole clade can be trusted to be functional. The possibility exists, however, that in the Gram-positive species the fusion to the first enzyme in the pathway has evolved a separate, regulatory role.. Probab=34.33 E-value=38 Score=15.46 Aligned_cols=45 Identities=27% Similarity=0.463 Sum_probs=31.0 Q ss_pred HHHHHHHHHH-------HHHHHHHHHHHHHHHHHH-HHCCCCCCCCHHHHHHHHHHH Q ss_conf 9999999999-------998724899999999997-517622243048999887687 Q gi|254780440|r 11 GFDKIQQELR-------WRQQEERPRIIKAISEAR-AYGDLSENAEYQAAKELQNLN 59 (158) Q Consensus 11 g~~~L~~El~-------~l~~~~r~~~~~~i~~A~-~~GDl~ENaeY~aAke~q~~~ 59 (158) -++.|++|.+ .|.+ +|-++++.|+.|. ++|-- --|+-+||++.+. T Consensus 6 ~le~lR~e~d~lN~qiL~Lis-~RGevv~~IG~aK~a~Gr~---n~yDP~RE~~~L~ 58 (104) T TIGR01801 6 ELEDLRAEVDELNRQILKLIS-KRGEVVKKIGKAKEAQGRV---NRYDPAREKEMLN 58 (104) T ss_pred HHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHCCCC---CCCCCHHHHHHHH T ss_conf 188899999998799999985-3118999975777617899---8889853799999 No 50 >cd02782 MopB_CT_1 The MopB_CT_1 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=34.31 E-value=39 Score=15.46 Aligned_cols=31 Identities=26% Similarity=0.328 Sum_probs=17.5 Q ss_pred CCCHHHHHHCCCCCCCEEEEECCCCEEEEEE Q ss_conf 1317899872888887899982897199999 Q gi|254780440|r 122 ISSPIARALIGKELGDIISVNAPGGEKTYEI 152 (158) Q Consensus 122 ~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~I 152 (158) ..+|--.+=+|-+-||.|.+..+.|.....+ T Consensus 36 ~i~p~dA~~lgi~~Gd~V~v~s~~G~~~~~~ 66 (129) T cd02782 36 RIHPDDAAALGLADGDKVRVTSAAGSVEAEV 66 (129) T ss_pred EECHHHHHHCCCCCCCEEEEECCCEEEEEEE T ss_conf 9999999886998999999986984799999 No 51 >cd06193 siderophore_interacting Siderophore interacting proteins share the domain structure of the ferredoxin reductase like family. Siderophores are produced in various bacteria (and some plants) to extract iron from hosts. Binding constants are high, so iron can be pilfered from transferrin and lactoferrin for bacterial uptake, contributing to pathogen virulence. Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hy Probab=33.96 E-value=28 Score=16.36 Aligned_cols=61 Identities=23% Similarity=0.377 Sum_probs=41.0 Q ss_pred CCCCCEEEEEECCCC---------------------CEEEEEEECHHHCCCCCCEECC-------CCHHHHHHCCCCCCC Q ss_conf 113657999534765---------------------2359999631013345881501-------317899872888887 Q gi|254780440|r 86 IAFGATVSLVEKNSG---------------------DKKNYQIVGDQEADVQSGLVSI-------SSPIARALIGKELGD 137 (158) Q Consensus 86 V~~Gs~V~l~d~~~~---------------------~~~~~~lVg~~e~d~~~~~IS~-------~SPlG~ALlG~~~Gd 137 (158) -..|..|+|.....+ ...+||+. ..|+..+.+.+ ..|-+.=....++|| T Consensus 27 ~~~~~~vkl~~p~~~~~~~~~~~~~~~~~~~~~~~p~~R~YTvR---~~d~~~~~l~iDfvlH~~~Gpas~WA~~a~~GD 103 (235) T cd06193 27 DGPDQHVKLLFPDPGQAPPVLPVLGRRRWPPEEPRPVMRTYTVR---RFDPEAGELDIDFVLHGDEGPASRWAASAQPGD 103 (235) T ss_pred CCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEE---EECCCCCEEEEEEEECCCCCCHHHHHHHCCCCC T ss_conf 99988799984799987777876664235787888878777401---177878979999996799985799998589999 Q ss_pred EEEEECCCCEEE Q ss_conf 899982897199 Q gi|254780440|r 138 IISVNAPGGEKT 149 (158) Q Consensus 138 ~V~v~~p~G~~~ 149 (158) .+.+.-|+|... T Consensus 104 ~i~i~gP~g~~~ 115 (235) T cd06193 104 TLGIAGPGGSFL 115 (235) T ss_pred EEEEECCCCCCC T ss_conf 778886898878 No 52 >PRK05802 hypothetical protein; Provisional Probab=33.85 E-value=39 Score=15.41 Aligned_cols=66 Identities=18% Similarity=0.312 Sum_probs=48.2 Q ss_pred CCCCCCCCCCCCCCEEEEEECCCCCEEEEEE-ECHHHCCCCCCEECC----CCHHHHHHCCCCCCCEEEEECC Q ss_conf 7210133211136579995347652359999-631013345881501----3178998728888878999828 Q gi|254780440|r 77 DISTMSGDRIAFGATVSLVEKNSGDKKNYQI-VGDQEADVQSGLVSI----SSPIARALIGKELGDIISVNAP 144 (158) Q Consensus 77 ~~~~~~~~~V~~Gs~V~l~d~~~~~~~~~~l-Vg~~e~d~~~~~IS~----~SPlG~ALlG~~~Gd~V~v~~p 144 (158) -|.....+-+.+||.|=+++.++.. -|.. .+-.++|.+.+.|.+ .-|=-+.|...+.||.+.+.-| T Consensus 87 vp~kLa~~L~~PGSfVFlR~~~~~~--yfd~PISIM~~d~~~~ii~vaiei~G~KTk~i~~~~~~~~i~iRGP 157 (328) T PRK05802 87 VPHKLARDLVYPGSFVFLRNKNSNP--FFDVPISIMESDTEENIIKVAIEVRGIKTKKILNLNKGEEILIRGP 157 (328) T ss_pred CCHHHHHHHCCCCCEEEEECCCCCC--CCCCCEEEEECCCCCCEEEEEEEEECCCCHHHHHCCCCCEEEEECC T ss_conf 8689999706897589985798887--5246548876155567599999971234030331246876999677 No 53 >cd00508 MopB_CT_Fdh-Nap-like This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex and catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. Formate dehydrogenase N (alpha subunit) is the major electron donor to the bacterial nitrate respiratory chain and nitrate reductases, Nap and Nas, catalyze the reduction of nitrate to nitrite. This CD (MopB_CT_Fdh-Nap-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=32.62 E-value=41 Score=15.28 Aligned_cols=31 Identities=23% Similarity=0.302 Sum_probs=15.6 Q ss_pred CCCCHHHHHHCCCCCCCEEEEECCCCEEEEE Q ss_conf 0131789987288888789998289719999 Q gi|254780440|r 121 SISSPIARALIGKELGDIISVNAPGGEKTYE 151 (158) Q Consensus 121 S~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~ 151 (158) -..+|--.+-+|-+.||.|.+..+.|..... T Consensus 37 v~~~p~dA~~lgi~~Gd~V~v~s~~G~~~~~ 67 (120) T cd00508 37 VEIHPEDAARLGIKDGDLVRVSSRRGSVVVR 67 (120) T ss_pred EEECHHHHHHCCCCCCCEEEEECCCEEEEEE T ss_conf 9999999988599999999998177389999 No 54 >cd06183 cyt_b5_reduct_like Cytochrome b5 reductase catalyzes the reduction of 2 molecules of cytochrome b5 using NADH as an electron donor. Like ferredoxin reductases, these proteins have an N-terminal FAD binding subdomain and a C-terminal NADH binding subdomain, separated by a cleft, which accepts FAD. The NADH-binding moiety interacts with part of the FAD and resembles a Rossmann fold. However, NAD is bound differently than in canonical Rossmann fold proteins. Nitrate reductases, flavoproteins similar to pyridine nucleotide cytochrome reductases, catalyze the reduction of nitrate to nitrite. The enzyme can be divided into three functional fragments that bind the cofactors molybdopterin, heme-iron, and FAD/NADH. Probab=32.37 E-value=41 Score=15.26 Aligned_cols=65 Identities=18% Similarity=0.349 Sum_probs=41.9 Q ss_pred CCCCCEEEEEECCCCC--EEEEEEECHHHC-CCCCCEE--CCCCHHHHHHCCCCCCCEEEEECCCCEEEE Q ss_conf 1136579995347652--359999631013-3458815--013178998728888878999828971999 Q gi|254780440|r 86 IAFGATVSLVEKNSGD--KKNYQIVGDQEA-DVQSGLV--SISSPIARALIGKELGDIISVNAPGGEKTY 150 (158) Q Consensus 86 V~~Gs~V~l~d~~~~~--~~~~~lVg~~e~-d~~~~~I--S~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~ 150 (158) ...|-.|.+.-...|+ .+.|+++.+... +...-.| -...++...|-..++||.+.+.-|.|...+ T Consensus 29 ~~~GQ~v~l~~~~~g~~~~R~YS~~s~~~~~~~~~~~Vk~~~~G~~s~~L~~~~~Gd~l~v~gP~G~f~~ 98 (234) T cd06183 29 LPVGQHVELKAPDDGEQVVRPYTPISPDDDKGYFDLLIKIYPGGKMSQYLHSLKPGDTVEIRGPFGKFEY 98 (234) T ss_pred CCCCEEEEEEEEECCEEEEEEEEECCCCCCCCEEEEEEEEEECCCCCHHHHCCCCCCEEEEECCCCCEEE T ss_conf 8999789998341994899767889779999989999999809997223532899999998778053676 No 55 >PRK10465 hydrogenase 2-specific chaperone; Provisional Probab=31.84 E-value=42 Score=15.20 Aligned_cols=83 Identities=11% Similarity=0.099 Sum_probs=44.6 Q ss_pred HHHHHHHHHHH-HHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCEEEEEEECHHHCCCCCCEECCCCHHHHHHCCCCCC Q ss_conf 87999999997-44442104721013321113657999534765235999963101334588150131789987288888 Q gi|254780440|r 58 LNEGRMAELEN-IITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELG 136 (158) Q Consensus 58 ~~~~ri~~L~~-~L~~A~iv~~~~~~~~~V~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~~~~~IS~~SPlG~ALlG~~~G 136 (158) ++++.-+++-+ ++..--++. ..++-..|+|-.+ + |. -.=.+|.||=.|.-. .-.-++..-++++| T Consensus 15 ~Lea~f~~I~~~~M~dLP~~N-paL~VeAvGF~~~------e-g~-wlGvliTPWfmnLv~-----lPg~~q~w~~~~~G 80 (159) T PRK10465 15 LVQAAFEEIARRSMHDLPFLH-PSMPVYVSDFTLF------E-GQ-WTGCVLTPWMLSAVI-----FPGPDQLWPLRTVG 80 (159) T ss_pred HHHHHHHHHHHHHHCCCCCCC-CCCCEEEECCEEE------C-CE-EEEEEECHHHHHEEE-----CCCCCCCCCCCCCC T ss_conf 999999999997743587458-8874676067898------7-87-899880432354254-----56886666667887 Q ss_pred CEEEEECCCCEEEEEEEE Q ss_conf 789998289719999999 Q gi|254780440|r 137 DIISVNAPGGEKTYEILQ 154 (158) Q Consensus 137 d~V~v~~p~G~~~~~Il~ 154 (158) +.+.+..|.|.+.|.+-. T Consensus 81 ~k~~~~lP~G~~~F~~~~ 98 (159) T PRK10465 81 EKLGLQLPYGTMTFTVGE 98 (159) T ss_pred CEEEEECCCCCEEEEECC T ss_conf 667886477757887316 No 56 >KOG3206 consensus Probab=31.47 E-value=43 Score=15.16 Aligned_cols=97 Identities=23% Similarity=0.367 Sum_probs=49.7 Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC Q ss_conf 99843148899999999999998724899999999997517622243048999887687999999997444421047210 Q gi|254780440|r 1 MVDKIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDIST 80 (158) Q Consensus 1 M~~k~~lT~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~ 80 (158) |.+|.-|+++.|.+-.+-...-+ .++-.| +=|++-. .|+..+++ ..+....+.+. T Consensus 94 ~veky~iSee~Y~qRtdSvr~~k------------k~~~~g--ryn~~~~----~q~ea~~~-~~~~e~~~~~~------ 148 (234) T KOG3206 94 IVEKYEISEEDYLQRTDSVRRFK------------KKHGYG--RYNAEEQ----AQAEAEAK-QDLAEERAQAT------ 148 (234) T ss_pred CCEEEECCHHHHHHHHHHHHHHH------------HHHCCC--CCCHHHH----HHHHHHHH-HHHHHHHHHHC------ T ss_conf 30014427888866558999999------------985115--4341326----58988867-77999987300------ Q ss_pred CCCCCCCCCCEEEEE-ECCCCCEEEEEEECHHHCCCCCC-E--ECCCCHHHHH Q ss_conf 133211136579995-34765235999963101334588-1--5013178998 Q gi|254780440|r 81 MSGDRIAFGATVSLV-EKNSGDKKNYQIVGDQEADVQSG-L--VSISSPIARA 129 (158) Q Consensus 81 ~~~~~V~~Gs~V~l~-d~~~~~~~~~~lVg~~e~d~~~~-~--IS~~SPlG~A 129 (158) +.+|....+. .......-++.-|||.+ ...| + |-+.-|+|+- T Consensus 149 -----i~vG~rCeVtv~G~~~Rrg~vrYvG~~~--~k~G~wiGVeydEplGKn 194 (234) T KOG3206 149 -----IAVGRRCEVTVPGQAPRRGTVRYVGPLE--FKPGYWIGVEYDEPLGKN 194 (234) T ss_pred -----CCCCCEEEEECCCCCCCCEEEEEECCCC--CCCCEEEEEECCCCCCCC T ss_conf -----5137806895389787514788832468--888428877547766667 No 57 >pfam11344 DUF3146 Protein of unknown function (DUF3146). This family of proteins with unknown function appear to be restricted to Cyanobacteria. Probab=31.14 E-value=18 Score=17.49 Aligned_cols=41 Identities=22% Similarity=0.408 Sum_probs=26.5 Q ss_pred CCCCCEECCCCHHHHHHCCCCCCC---EEEEEC-CCCEEEEEEEE Q ss_conf 345881501317899872888887---899982-89719999999 Q gi|254780440|r 114 DVQSGLVSISSPIARALIGKELGD---IISVNA-PGGEKTYEILQ 154 (158) Q Consensus 114 d~~~~~IS~~SPlG~ALlG~~~Gd---~V~v~~-p~G~~~~~Il~ 154 (158) ....|.+++.-|||+||+--..+- .-.+++ |+|.+.|+|-+ T Consensus 35 ~F~~G~L~V~PsLGRALI~d~L~RFL~k~DY~LE~GgdY~Ftira 79 (80) T pfam11344 35 HFRRGELLVEPSLGRALIKDALLRFLEKSDYQLEPGGDYSFTVRA 79 (80) T ss_pred EECCCEEEECCCCCHHHHHHHHHHHHHHCCEEECCCCCEEEEEEC T ss_conf 976982998686027888879997886514060589947899965 No 58 >pfam01191 RNA_pol_Rpb5_C RNA polymerase Rpb5, C-terminal domain. The assembly domain of Rpb5. The archaeal equivalent to this domain is subunit H. Subunit H lacks the N-terminal domain. Probab=30.87 E-value=44 Score=15.10 Aligned_cols=29 Identities=24% Similarity=0.471 Sum_probs=23.7 Q ss_pred CEECCCCHHHHHHCCCCCCCEEEEECCCCE Q ss_conf 815013178998728888878999828971 Q gi|254780440|r 118 GLVSISSPIARALIGKELGDIISVNAPGGE 147 (158) Q Consensus 118 ~~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~ 147 (158) =+|+..-|+++.+ |.+.||.+.+.-++.+ T Consensus 35 P~I~~~DPv~~~~-g~~~GdiikI~R~s~t 63 (74) T pfam01191 35 PRILATDPVARYL-GLKPGDVVKITRKSET 63 (74) T ss_pred CEECCCCHHHHHH-CCCCCCEEEEEECCCC T ss_conf 8163619988982-9999978999974887 No 59 >pfam06152 Phage_min_cap2 Phage minor capsid protein 2. Family of related phage minor capsid proteins. Probab=30.43 E-value=45 Score=15.05 Aligned_cols=14 Identities=21% Similarity=0.347 Sum_probs=6.6 Q ss_pred CCHHHHHHHHHHHH Q ss_conf 48899999999999 Q gi|254780440|r 7 VTSKGFDKIQQELR 20 (158) Q Consensus 7 lT~~g~~~L~~El~ 20 (158) |||+-+.++-+.+. T Consensus 3 LtPe~l~~~~~~vv 16 (361) T pfam06152 3 LTPEQLDLLSQPVV 16 (361) T ss_pred CCHHHHHHCCHHHH T ss_conf 98799987007899 No 60 >PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed Probab=29.78 E-value=46 Score=14.98 Aligned_cols=28 Identities=21% Similarity=0.493 Sum_probs=22.7 Q ss_pred CEECCCCHHHHHHCCCCCCCEEEEECCCC Q ss_conf 81501317899872888887899982897 Q gi|254780440|r 118 GLVSISSPIARALIGKELGDIISVNAPGG 146 (158) Q Consensus 118 ~~IS~~SPlG~ALlG~~~Gd~V~v~~p~G 146 (158) =+|+..-|+++.+ |.+.||.|.+.-++. T Consensus 38 P~I~~~DPva~~l-g~~~GdvvkI~R~S~ 65 (79) T PRK09570 38 PKIKASDPVVKAI-GAKPGDVVKIVRKSP 65 (79) T ss_pred CCCCCCCHHHHHH-CCCCCCEEEEEECCC T ss_conf 9213519888984-999996899997577 No 61 >COG2125 RPS6A Ribosomal protein S6E (S10) [Translation, ribosomal structure and biogenesis] Probab=29.47 E-value=29 Score=16.25 Aligned_cols=18 Identities=44% Similarity=0.724 Sum_probs=10.7 Q ss_pred CCHHHHHHCCCCCCCEEE Q ss_conf 317899872888887899 Q gi|254780440|r 123 SSPIARALIGKELGDIIS 140 (158) Q Consensus 123 ~SPlG~ALlG~~~Gd~V~ 140 (158) ..+-+..|+|++.||++. T Consensus 22 ~~~~a~~ligkkIGd~~d 39 (120) T COG2125 22 DEARARRLIGKKIGDEVD 39 (120) T ss_pred CHHHHHHHHHHEECCCCC T ss_conf 646655443210044137 No 62 >cd02775 MopB_CT Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-containing enzymes, including formate dehydrogenase-H (Fdh-H) and -N (Fdh-N), several forms of nitrate reductase (Nap, Nas, NarG), dimethylsulfoxide reductase (DMSOR), thiosulfate reductase, formylmethanofuran dehydrogenase, and arsenite oxidase. Molybdenum is present in most of these enzymes in the form of molybdopterin, a modified pterin ring with a dithiolene side chain, which is responsible for ligating the Mo. In many bacterial and archaeal species, molybdopterin is in the form of a dinucleotide, with two molybdopterin dinucleotide units per molybdenum. These proteins can function as monomers, heterodimers, or heterotrimers, depending on the protein and organism. Also included in the MopB superfamily is Probab=29.34 E-value=47 Score=14.93 Aligned_cols=34 Identities=24% Similarity=0.309 Sum_probs=23.6 Q ss_pred EECCCCHHHHHHCCCCCCCEEEEECCCCEEEEEE Q ss_conf 1501317899872888887899982897199999 Q gi|254780440|r 119 LVSISSPIARALIGKELGDIISVNAPGGEKTYEI 152 (158) Q Consensus 119 ~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~I 152 (158) -.-+.+|--.+-+|-+.||.|.+..+.|.....+ T Consensus 23 ~~v~~np~dA~~~Gi~~Gd~v~v~~~~g~~~~~~ 56 (101) T cd02775 23 PVVEINPEDAAALGIKDGDLVRVESRRGSVVLRA 56 (101) T ss_pred CEEEECHHHHHHCCCCCCCEEEEEECCEEEEEEE T ss_conf 9899999999986998899999996985899999 No 63 >pfam10781 DSRB Dextransucrase DSRB. DSRB is a novel dextransucrase which produces a dextran different from the typical dextran, as it contains (1-6) and (1-2) linkages, when this strain is grown in the presence of sucrose. Probab=29.13 E-value=47 Score=14.91 Aligned_cols=23 Identities=30% Similarity=0.468 Sum_probs=12.8 Q ss_pred CCCCEEEEECCCCEE-EEEEEEEE Q ss_conf 888789998289719-99999989 Q gi|254780440|r 134 ELGDIISVNAPGGEK-TYEILQVL 156 (158) Q Consensus 134 ~~Gd~V~v~~p~G~~-~~~Il~I~ 156 (158) +++|.|++++-+|++ .=.|+.|+ T Consensus 2 ~vnD~VtVKTDG~~rReG~il~vE 25 (62) T pfam10781 2 KVNDRVTVKTDGGPRREGVILAVE 25 (62) T ss_pred CCCCEEEEECCCCCCCCEEEEEEE T ss_conf 335679995489755440699983 No 64 >COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis] Probab=28.87 E-value=43 Score=15.16 Aligned_cols=15 Identities=20% Similarity=0.206 Sum_probs=6.6 Q ss_pred CEEEEEEECHHHCCC Q ss_conf 235999963101334 Q gi|254780440|r 101 DKKNYQIVGDQEADV 115 (158) Q Consensus 101 ~~~~~~lVg~~e~d~ 115 (158) .....-||.|...-| T Consensus 79 ~k~K~liv~peHLk~ 93 (98) T COG2139 79 NKEKTLIVRPEHLKP 93 (98) T ss_pred CCEEEEEECHHHCCC T ss_conf 945899867788544 No 65 >TIGR01076 sortase_fam sortase family protein; InterPro: IPR005754 Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad . This group of cysteine peptidases belong to MEROPS peptidase family C60 (clan C-) and include the members of both subfamilies of sortases. The Staphylococcus aureus sortase is a transpeptidase that attaches surface proteins to the cell wall; it cleaves between the Gly and Thr of the LPXTG motif and catalyses the formation of an amide bond between the carboxyl-group of threonine and the amino-group of the cell-wall peptidoglycan . Sortase homologues are found in almost all Gram-positives, a single Gram-negative (Shewanella putrefaciens) and an archaean (Methanobacterium thermoautotrophicum), where cell wall LPXTG-mediated decoration has not been reported , . Surface proteins not only promote interaction between the invading pathogen and animal tissues, but also provide ingenious strategies for bacterial escape from the host's immune response. In the case of S. aureus protein A, immunoglobulins are captured on the microbial surface and camouflage bacteria during the invasion of host tissues. S. aureus mutants lacking the srtA gene fail to anchor and display some surface proteins and are impaired in the ability to cause animal infections. Sortase acts on surface proteins that are initiated into the secretion (Sec) pathway and have their signal peptide removed by signal peptidase. The S. aureus genome encodes two sets of sortase and secretion genes. It is conceivable that S. aureus has evolved more than one pathway for the transport of 20 surface proteins to the cell wall envelope. . Probab=28.72 E-value=48 Score=14.87 Aligned_cols=31 Identities=16% Similarity=0.184 Sum_probs=21.9 Q ss_pred HHHCCCCCCCEEEEECCCCEEEEEEEEEEEC Q ss_conf 9872888887899982897199999998979 Q gi|254780440|r 128 RALIGKELGDIISVNAPGGEKTYEILQVLWI 158 (158) Q Consensus 128 ~ALlG~~~Gd~V~v~~p~G~~~~~Il~I~yi 158 (158) +.|=-.|+||.+-+..-.+...|+|.+|+-| T Consensus 59 ~~L~~~K~GD~ly~~~~~e~~~Y~~~~~~~v 89 (140) T TIGR01076 59 TNLDKLKKGDALYLKVGNEVLTYQVTSTKIV 89 (140) T ss_pred CCCCCCCCCCEEEEEECCCEEEEEEEEEEEE T ss_conf 2221001375889984251898887888984 No 66 >PRK10708 hypothetical protein; Provisional Probab=28.64 E-value=48 Score=14.86 Aligned_cols=23 Identities=26% Similarity=0.458 Sum_probs=10.7 Q ss_pred CCCCEEEEECCCCEE-EEEEEEEE Q ss_conf 888789998289719-99999989 Q gi|254780440|r 134 ELGDIISVNAPGGEK-TYEILQVL 156 (158) Q Consensus 134 ~~Gd~V~v~~p~G~~-~~~Il~I~ 156 (158) +++|.|++++-+|++ .=.|+.|+ T Consensus 2 kvnd~VtVKTDG~~rR~G~ilavE 25 (62) T PRK10708 2 KVNDRVTVKTDGGPRRPGVVLAVE 25 (62) T ss_pred CCCCEEEEECCCCCCCCCEEEEEE T ss_conf 435549995489856664699983 No 67 >PRK00558 uvrC excinuclease ABC subunit C; Validated Probab=27.58 E-value=50 Score=14.74 Aligned_cols=135 Identities=17% Similarity=0.247 Sum_probs=76.1 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC Q ss_conf 14889999999999999872489999999999751762224304899988768799999999744442104721013321 Q gi|254780440|r 6 PVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSGDR 85 (158) Q Consensus 6 ~lT~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~~~~~~ 85 (158) .+|++.|.+.-+++...-.=.-.++...+...+.. .|+|-+|..|.+ +-.+|..|+.....-.|+.+...+.|+ T Consensus 183 ~Is~~~Y~~~V~~~~~fL~G~~~~l~~~L~~~M~~--aS~~l~FE~Aa~----~RD~i~aL~~i~~~Q~v~~~~~~d~DV 256 (609) T PRK00558 183 LVSKEEYAELVDEAKLFLQGKSDEVIKELEEKMEK--ASENLEFERAAR----LRDQIQALRRVQEKQKVSLADLEDADV 256 (609) T ss_pred CCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH--HHHHHHHHHHHH----HHHHHHHHHHHHHCCEEECCCCCCCEE T ss_conf 57999999999999999827949999999999999--997320667899----999999999986356532588765407 Q ss_pred CCCC-----CEEEEEECCCCC---EEEEEEECHHHCC-------------------CCCCEECC----CCHHHHHHCCCC Q ss_conf 1136-----579995347652---3599996310133-------------------45881501----317899872888 Q gi|254780440|r 86 IAFG-----ATVSLVEKNSGD---KKNYQIVGDQEAD-------------------VQSGLVSI----SSPIARALIGKE 134 (158) Q Consensus 86 V~~G-----s~V~l~d~~~~~---~~~~~lVg~~e~d-------------------~~~~~IS~----~SPlG~ALlG~~ 134 (158) +++- +.|.+...-.|. ..+|.+=...+.+ |..=.++. ...+=...|..+ T Consensus 257 i~i~~~~~~~~i~v~~vR~G~i~g~~~~~~~~~~~~~~~eil~~fl~q~Y~~~~~~P~eIlv~~~~~~d~~~l~~~L~~~ 336 (609) T PRK00558 257 IAIAVDKGWACVQVFFIRGGKLLGRRSFFPKVPGDTELEEVLEAFIGQFYLDNRPIPKEILVPHELEIDKELLEEALSEK 336 (609) T ss_pred EEEEECCCEEEEEEEEEECCEEEEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCHHHHHHHHHHH T ss_conf 99997198589999998788996005677046677998999999999998417899976883576785689999999853 Q ss_pred CCCEEEEECCCC Q ss_conf 887899982897 Q gi|254780440|r 135 LGDIISVNAPGG 146 (158) Q Consensus 135 ~Gd~V~v~~p~G 146 (158) -|..|.+..|.. T Consensus 337 ~~~kv~i~~Pkr 348 (609) T PRK00558 337 AGRKVKIRVPQR 348 (609) T ss_pred CCCCEEEECCCC T ss_conf 599469961885 No 68 >COG0853 PanD Aspartate 1-decarboxylase [Coenzyme metabolism] Probab=27.34 E-value=50 Score=14.71 Aligned_cols=71 Identities=24% Similarity=0.412 Sum_probs=47.1 Q ss_pred HHHHHHHHHCCC------------CCCCCCCCCCCCCEEEEEECCCCCE-EEEEEECHHHCCCCCCEECCCCHHHHHHCC Q ss_conf 997444421047------------2101332111365799953476523-599996310133458815013178998728 Q gi|254780440|r 66 LENIITRAEVID------------ISTMSGDRIAFGATVSLVEKNSGDK-KNYQIVGDQEADVQSGLVSISSPIARALIG 132 (158) Q Consensus 66 L~~~L~~A~iv~------------~~~~~~~~V~~Gs~V~l~d~~~~~~-~~~~lVg~~e~d~~~~~IS~~SPlG~ALlG 132 (158) |..+|.+|.|.+ +.-.+..-+..+-.|.+.|..+|.. .||-|.|+.-+ |.|+. =|.|--- T Consensus 5 l~aKiHratVT~A~L~Y~GSitID~dlldaagile~EkV~I~N~nNGaRf~TYvI~g~rGS----g~I~l---NGAAArl 77 (126) T COG0853 5 LKAKIHRATVTEADLNYVGSITIDEDLLDAAGILENEKVDIVNVNNGARFSTYVIAGERGS----GVICL---NGAAARL 77 (126) T ss_pred HHHHHHEEEEEECCCCEEEEEEECHHHHHHCCCCCCCEEEEEECCCCCEEEEEEEECCCCC----CEEEE---CHHHHHH T ss_conf 4312102688502330477688899999653898776689998888837899998726878----67975---6698852 Q ss_pred CCCCCEEEEEC Q ss_conf 88887899982 Q gi|254780440|r 133 KELGDIISVNA 143 (158) Q Consensus 133 ~~~Gd~V~v~~ 143 (158) .++||.|-+-. T Consensus 78 ~~~GD~VII~s 88 (126) T COG0853 78 VQVGDLVIIMS 88 (126) T ss_pred CCCCCEEEEEE T ss_conf 68899899998 No 69 >pfam01092 Ribosomal_S6e Ribosomal protein S6e. Probab=27.32 E-value=50 Score=14.71 Aligned_cols=20 Identities=25% Similarity=0.378 Sum_probs=12.9 Q ss_pred HHHHHCCCCCCCEEEEECCC Q ss_conf 89987288888789998289 Q gi|254780440|r 126 IARALIGKELGDIISVNAPG 145 (158) Q Consensus 126 lG~ALlG~~~Gd~V~v~~p~ 145 (158) --++++|++.||+|.-..-+ T Consensus 23 ~~~~f~gkrIGdevdg~~lG 42 (127) T pfam01092 23 RLRVFYEKRMGQEVDGDAVG 42 (127) T ss_pred HHHHHHCCCCCCEECHHCCC T ss_conf 74343156021477502028 No 70 >TIGR02160 PA_CoA_Oxy5 phenylacetate-CoA oxygenase/reductase, PaaK subunit; InterPro: IPR011884 Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation , . Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA . . Probab=26.70 E-value=42 Score=15.21 Aligned_cols=64 Identities=23% Similarity=0.409 Sum_probs=37.8 Q ss_pred CCCCCEEEEEECCCCCE--EEEEEE-CHHHCCCCCCE--E--CCCCHHHHHHCCCCCCCEEEEECCCCEEEE Q ss_conf 11365799953476523--599996-31013345881--5--013178998728888878999828971999 Q gi|254780440|r 86 IAFGATVSLVEKNSGDK--KNYQIV-GDQEADVQSGL--V--SISSPIARALIGKELGDIISVNAPGGEKTY 150 (158) Q Consensus 86 V~~Gs~V~l~d~~~~~~--~~~~lV-g~~e~d~~~~~--I--S~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~ 150 (158) -..|=.++|+-.=+|++ ++|.|+ ++....+.-+. | -.-|--+.- =|-|.||+++|-+|.|...+ T Consensus 33 F~pGQ~l~Lk~~~dG~e~RRSYSIC~~~~~~~~rvAvk~~~GG~FS~wa~d-~Gir~GdtlEVM~P~G~F~~ 103 (371) T TIGR02160 33 FEPGQHLTLKAEVDGEELRRSYSICDAPAPGEIRVAVKKIEGGLFSTWAND-EGIRAGDTLEVMAPQGRFTS 103 (371) T ss_pred CCCCCEEEEEEEECCCCCCEEEEECCCCCCCCCEEEEEECCCCCEEHHHHC-CCCCCCCEEEEECCCCCCCC T ss_conf 688934554200077411302222167798963388997289711321111-87044887887167897788 No 71 >KOG3129 consensus Probab=26.24 E-value=53 Score=14.59 Aligned_cols=33 Identities=27% Similarity=0.226 Sum_probs=21.8 Q ss_pred EEECHHHCCCCCCEECCCCHHHHHHCCCCCCCEEE Q ss_conf 99631013345881501317899872888887899 Q gi|254780440|r 106 QIVGDQEADVQSGLVSISSPIARALIGKELGDIIS 140 (158) Q Consensus 106 ~lVg~~e~d~~~~~IS~~SPlG~ALlG~~~Gd~V~ 140 (158) +..||.-+=..-+.|+..||-..| |.++||.+. T Consensus 132 ~~~gP~~~Fa~V~sV~~~SPA~~a--Gl~~gD~il 164 (231) T KOG3129 132 TSLGPMRPFAVVDSVVPGSPADEA--GLCVGDEIL 164 (231) T ss_pred CCCCCCCCEEEEEECCCCCHHHHH--CCCCCCEEE T ss_conf 005786524887522789834540--754376578 No 72 >cd02788 MopB_CT_NDH-1_NuoG2-N7 MopB_CT_NDH-1_NuoG2-N7: C-terminal region of the NuoG-like subunit (of the variant with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy production. In Escherichia coli NDH-1, the largest subunit is encoded by the nuoG gene, and is part of the 14 distinct subunits constituting the functional enzyme. The NuoG subunit is made of two domains: the first contains three binding sites for FeS clusters (the fer2 domain), the second domain, is of unknown function or, as postulated, has lost an ancestral formate dehydrogenase activity that became redundant during the evolution of the complex I enzyme. Unique to this group, compared to the other prokaryotic and eukaryotic groups Probab=25.77 E-value=54 Score=14.53 Aligned_cols=31 Identities=26% Similarity=0.327 Sum_probs=16.5 Q ss_pred CCCCHHHHHHCCCCCCCEEEEECCCCEEEEE Q ss_conf 0131789987288888789998289719999 Q gi|254780440|r 121 SISSPIARALIGKELGDIISVNAPGGEKTYE 151 (158) Q Consensus 121 S~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~ 151 (158) -..||--.+-||-+.||.|++..++|...+- T Consensus 31 ~~l~~~dA~~Lgl~~G~~v~v~~~~g~~~LP 61 (96) T cd02788 31 ARLSPADAARLGLADGDLVEFSLGDGTLTLP 61 (96) T ss_pred EEECHHHHHHHCCCCCCEEEEEECCEEEEEE T ss_conf 9999989998199999989999899689999 No 73 >TIGR00875 talC transaldolase, putative; InterPro: IPR004731 Transaldolase (2.2.1.2 from EC) catalyzes the reversible transfer of a three-carbon ketol unit from sedoheptulose 7-phosphate to glyceraldehyde 3-phosphate to form erythrose 4-phosphate and fructose 6-phosphate. This enzyme, together with transketolase, provides a link between the glycolytic and pentose-phosphate pathways. Transaldolase is an enzyme of about 34 Kd whose sequence has been well conserved throughout evolution. A lysine has been implicated in the catalytic mechanism of the enzyme; it acts as a nucleophilic group that attacks the carbonyl group of fructose-6-phosphate. Transaldolase is evolutionary related to a bacterial protein of about 20 Kd (known as talC in Escherichia coli), whose exact function is not yet known.; GO: 0005975 carbohydrate metabolic process. Probab=25.47 E-value=39 Score=15.42 Aligned_cols=12 Identities=50% Similarity=0.947 Sum_probs=5.3 Q ss_pred CCCCCHHHHHHH Q ss_conf 431488999999 Q gi|254780440|r 4 KIPVTSKGFDKI 15 (158) Q Consensus 4 k~~lT~~g~~~L 15 (158) |||||++|++.. T Consensus 86 KIP~T~~GLkAv 97 (216) T TIGR00875 86 KIPMTSEGLKAV 97 (216) T ss_pred EECCCHHHHHHH T ss_conf 614785379999 No 74 >KOG3026 consensus Probab=25.13 E-value=55 Score=14.46 Aligned_cols=34 Identities=24% Similarity=0.248 Sum_probs=18.3 Q ss_pred HHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99751762224304899988768799999999744442 Q gi|254780440|r 36 EARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRA 73 (158) Q Consensus 36 ~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A 73 (158) +|+-+|| .+|.||.--++.+..+ |.--++.|..+ T Consensus 16 eaaL~~d-P~NeEllkLe~DLkEv---IsLTedLlqT~ 49 (262) T KOG3026 16 EAALQGD-PENEELLKLEKDLKEV---ISLTEDLLQTQ 49 (262) T ss_pred HHHHCCC-CCCHHHHHHHHHHHHH---HHHHHHHHHHH T ss_conf 9997069-8538999999889999---99999998750 No 75 >pfam06273 eIF-4B Plant specific eukaryotic initiation factor 4B. This family consists of several plant specific eukaryotic initiation factor 4B proteins. Probab=24.42 E-value=44 Score=15.11 Aligned_cols=38 Identities=18% Similarity=0.268 Sum_probs=19.9 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCEEE Q ss_conf 99999997444421047210133211136579995347652359 Q gi|254780440|r 61 GRMAELENIITRAEVIDISTMSGDRIAFGATVSLVEKNSGDKKN 104 (158) Q Consensus 61 ~ri~~L~~~L~~A~iv~~~~~~~~~V~~Gs~V~l~d~~~~~~~~ 104 (158) -.|.+.+..|..... + -.|+|+||-....+ ..++--.+ T Consensus 341 e~i~~kEk~Le~L~r----~-lDdKvRFgqk~~eR-PgSgAgR~ 378 (430) T pfam06273 341 ELIRQKEKELERLTR----E-LDDKVRFGQKAVER-PGSGAGRT 378 (430) T ss_pred HHHHHHHHHHHHHHH----H-HCCCCCCCCCCCCC-CCCCCCCC T ss_conf 998877888999998----7-33531235111448-77666753 No 76 >cd06190 T4MO_e_transfer_like Toluene-4-monoxygenase electron transfer component of Pseudomonas mendocina hydroxylates toluene and forms p-cresol as part of a three component toluene-4-monoxygenase system. Electron transfer is from NADH to an NADH:ferredoxin oxidoreductase (TmoF in P. mendocina) to ferredoxin to an iron-containing oxygenase. TmoF is homologous to other mono- and dioxygenase systems within the ferredoxin reductase family. Probab=24.21 E-value=57 Score=14.35 Aligned_cols=63 Identities=16% Similarity=0.179 Sum_probs=40.3 Q ss_pred CCCCCEEEEEECCCCCEEEEEEECHH-HCCCCCCEE--CCCCHHHHHHC-CCCCCCEEEEECCCCEE Q ss_conf 11365799953476523599996310-133458815--01317899872-88888789998289719 Q gi|254780440|r 86 IAFGATVSLVEKNSGDKKNYQIVGDQ-EADVQSGLV--SISSPIARALI-GKELGDIISVNAPGGEK 148 (158) Q Consensus 86 V~~Gs~V~l~d~~~~~~~~~~lVg~~-e~d~~~~~I--S~~SPlG~ALl-G~~~Gd~V~v~~p~G~~ 148 (158) ...|-.|.+.-...+....|+|+.+. +.+.-.-.| .....+..+|. ..++||.|.+.-|.|.. T Consensus 24 f~pGQ~v~l~i~~~~~~R~ySi~s~p~~~~~l~~~i~~~~~G~~S~~L~~~l~~Gd~v~v~gP~G~f 90 (232) T cd06190 24 FLPGQYALLALPGVEGARAYSMANLANASGEWEFIIKRKPGGAASNALFDNLEPGDELELDGPYGLA 90 (232) T ss_pred CCCCEEEEEEECCCCEEEEEEECCCCCCCCEEEEEEEEEECCHHHHHHHHCCCCCCEEEEEECCCCC T ss_conf 0898069999899012688886528999987999999943992688998648999999999545674 No 77 >cd06215 FNR_iron_sulfur_binding_1 Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal portion of the FAD/NAD binding domain contains most of the NADP(H) binding residues and the N-terminal sub-domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. In this ferredoxin like sub-group, the FAD/NAD sub-domains is typically fused to a C-terminal iron-sulfur binding domain. Iron-sulfur pr Probab=24.18 E-value=58 Score=14.34 Aligned_cols=64 Identities=22% Similarity=0.267 Sum_probs=38.7 Q ss_pred CCCCCEEEEEECCCCC--EEEEEEECH-HHCCCCCCEECC--CCHHHHHHC-CCCCCCEEEEECCCCEEE Q ss_conf 1136579995347652--359999631-013345881501--317899872-888887899982897199 Q gi|254780440|r 86 IAFGATVSLVEKNSGD--KKNYQIVGD-QEADVQSGLVSI--SSPIARALI-GKELGDIISVNAPGGEKT 149 (158) Q Consensus 86 V~~Gs~V~l~d~~~~~--~~~~~lVg~-~e~d~~~~~IS~--~SPlG~ALl-G~~~Gd~V~v~~p~G~~~ 149 (158) -..|-.|.+.-...|+ ...|+|+.. .+.+...=.|.. ...+-..|. ..++||.|.+.-|.|... T Consensus 28 f~aGQ~v~l~~~~~g~~~~R~ySias~p~~~~~~~~~Vk~~~~G~~S~~l~~~l~~G~~v~v~gP~G~f~ 97 (231) T cd06215 28 YKPGQFLTLELEIDGETVYRAYTLSSSPSRPDSLSITVKRVPGGLVSNWLHDNLKVGDELWASGPAGEFT 97 (231) T ss_pred CCCCEEEEEEEEECCEEEEEEEECCCCCCCCCEEEEEEEEECCCCHHHHHHHCCCCCCEEEEEECCCCCC T ss_conf 5898779999766993787666335579999989999999559806789996188999999970344874 No 78 >cd02790 MopB_CT_Formate-Dh_H Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is a monomer composed of a single polypeptide chain with a Mo active site region and a [4Fe-4S] center. This CD (MopB_CT_Formate-Dh_H) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=23.59 E-value=59 Score=14.27 Aligned_cols=33 Identities=18% Similarity=0.201 Sum_probs=21.7 Q ss_pred ECCCCHHHHHHCCCCCCCEEEEECCCCEEEEEE Q ss_conf 501317899872888887899982897199999 Q gi|254780440|r 120 VSISSPIARALIGKELGDIISVNAPGGEKTYEI 152 (158) Q Consensus 120 IS~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~I 152 (158) +-..+|--.+=+|-+.||.|.+..+.|.....+ T Consensus 36 ~v~i~p~dA~~lGi~~Gd~V~v~s~~G~i~~~a 68 (116) T cd02790 36 YVEINPEDAKRLGIEDGEKVRVSSRRGSVEVRA 68 (116) T ss_pred EEEECHHHHHHCCCCCCCEEEEECCCEEEEEEE T ss_conf 899899999885998899899987998999999 No 79 >PRK04778 septation ring formation regulator EzrA; Provisional Probab=22.68 E-value=62 Score=14.16 Aligned_cols=32 Identities=31% Similarity=0.505 Sum_probs=18.9 Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 76222430489998876879999999974444 Q gi|254780440|r 41 GDLSENAEYQAAKELQNLNEGRMAELENIITR 72 (158) Q Consensus 41 GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~ 72 (158) -.|.++++|..|++-...+...+..|+..+.. T Consensus 185 ~~lt~~Gd~~~A~evl~~l~~~~~~L~~~me~ 216 (569) T PRK04778 185 VELTESGDYVEAREVLDKLEEELAALEQIMEE 216 (569) T ss_pred HHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99986889899999999999999999999988 No 80 >pfam11939 DUF3457 Protein of unknown function (DUF3457). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 162 to 197 amino acids in length. This protein has a conserved CSL sequence motif. Probab=22.58 E-value=62 Score=14.15 Aligned_cols=44 Identities=14% Similarity=0.209 Sum_probs=31.3 Q ss_pred EEECHHHCCCCCCEECCCCH-HHHHHCCCCCCCEEEEECCCCEEEEEEEEE Q ss_conf 99631013345881501317-899872888887899982897199999998 Q gi|254780440|r 106 QIVGDQEADVQSGLVSISSP-IARALIGKELGDIISVNAPGGEKTYEILQV 155 (158) Q Consensus 106 ~lVg~~e~d~~~~~IS~~SP-lG~ALlG~~~Gd~V~v~~p~G~~~~~Il~I 155 (158) -+|.||=.|.-. =| =+...-++++|+...+.+|.|.+.|.+-.+ T Consensus 48 vliTPWfmnLv~------lPg~~~~w~~~~~G~k~~~~lP~G~~eF~~~~~ 92 (158) T pfam11939 48 VLVTPWFMNLVL------LPGPDQDWSALPVGDKLALALPSGTYEFIVGEL 92 (158) T ss_pred EEECHHHHHHEE------CCCCCCCCCCCCCCCEEEEECCCCCEEEEEECC T ss_conf 980445575502------448855666689886778763775279885247 No 81 >KOG0534 consensus Probab=22.55 E-value=62 Score=14.14 Aligned_cols=65 Identities=22% Similarity=0.292 Sum_probs=41.4 Q ss_pred CCCCCEEEEEECCCCCEEEEEEECHHHCCCCCCEE------CCCCHHHHHHCCCCCCCEEEEECCCCEEEEE Q ss_conf 11365799953476523599996310133458815------0131789987288888789998289719999 Q gi|254780440|r 86 IAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLV------SISSPIARALIGKELGDIISVNAPGGEKTYE 151 (158) Q Consensus 86 V~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~~~~~I------S~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~ 151 (158) ...|..|.+.-.- +....++=-.|--.|...|.+ -..-|+.+-|-..+.||+|+|.-|-|...|. T Consensus 82 lp~g~hv~~~~~i-~g~~vvRpYTPvs~~~~~g~~~l~VK~Y~~G~mS~~l~~LkiGd~ve~rGP~G~~~~~ 152 (286) T KOG0534 82 LPIGQHVVLKAPI-GGKLVVRPYTPVSLDDDKGYFDLVVKVYPKGKMSQHLDSLKIGDTVEFRGPIGEFKYD 152 (286) T ss_pred CCCCEEEEEEECC-CCCEEEEECCCCCCCCCCCEEEEEEEECCCCCCCHHHHCCCCCCEEEEECCCCCEEEC T ss_conf 6552589999628-9868997068746713465089999952688653788659999989996684335767 No 82 >TIGR01439 lp_hng_hel_AbrB transcriptional regulator, AbrB family; InterPro: IPR006339 This DNA-binding domain is found in proteins like AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. . Probab=22.51 E-value=62 Score=14.14 Aligned_cols=33 Identities=30% Similarity=0.441 Sum_probs=23.0 Q ss_pred CCEECCCCHHHHHHCCCCCCCEEEEE-CCCCEEEE Q ss_conf 88150131789987288888789998-28971999 Q gi|254780440|r 117 SGLVSISSPIARALIGKELGDIISVN-APGGEKTY 150 (158) Q Consensus 117 ~~~IS~~SPlG~ALlG~~~Gd~V~v~-~p~G~~~~ 150 (158) +|.|.+=..+ +..||-+.||.+.+. ..+|...+ T Consensus 7 kG~i~IPK~i-R~~lgl~eGd~l~~~~~~d~~i~l 40 (44) T TIGR01439 7 KGQIVIPKEI-REKLGLKEGDKLEVIRVEDGEIIL 40 (44) T ss_pred CCEEEECHHH-HHHCCCCCCCEEEEEEECCCEEEE T ss_conf 7629927389-640699999878898827987989 No 83 >pfam02403 Seryl_tRNA_N Seryl-tRNA synthetase N-terminal domain. This domain is found associated with the Pfam tRNA synthetase class II domain (pfam00587) and represents the N-terminal domain of seryl-tRNA synthetase. Probab=22.25 E-value=63 Score=14.11 Aligned_cols=58 Identities=21% Similarity=0.177 Sum_probs=39.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999872489999999999751762224304899988768799999999744442 Q gi|254780440|r 10 KGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRA 73 (158) Q Consensus 10 ~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A 73 (158) .-+..+..+++.|.. +|-.+++.|+.+...|+ +-..-+++...+...|..++..+... T Consensus 36 ~~~r~~~~~~e~L~~-~~N~~sk~ig~~~~~~~-----~~~~l~~~~~~lk~~i~~le~~~~~~ 93 (108) T pfam02403 36 EERRELQVELEELQA-ERNELSKEIGKAKKKKE-----DAEALIAEVKELKDELKALEAELREL 93 (108) T ss_pred HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHCCC-----CHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999999999999999-98598999999875774-----16889999999999999999999999 No 84 >cd02778 MopB_CT_Thiosulfate-R-like The MopB_CT_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme that catalyzes the reduction of polysulfide using either hydrogen or formate as the electron donor. Also included in this CD is the phenylacetyl-CoA:acceptor oxidoreductase, large subunit (PadB2), which has been characterized as a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. The MopB_CT_Thiosulfate-R-like CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=22.14 E-value=63 Score=14.09 Aligned_cols=26 Identities=27% Similarity=0.408 Sum_probs=10.4 Q ss_pred CCHHHHHHCCCCCCCEEEEECCCCEE Q ss_conf 31789987288888789998289719 Q gi|254780440|r 123 SSPIARALIGKELGDIISVNAPGGEK 148 (158) Q Consensus 123 ~SPlG~ALlG~~~Gd~V~v~~p~G~~ 148 (158) .+|--.+=+|-+-||.|.+..+.|.. T Consensus 34 inp~dA~~~Gi~dGd~V~v~s~~G~~ 59 (123) T cd02778 34 INPETAARLGIKDGDRVEVSSARGKV 59 (123) T ss_pred ECHHHHHHCCCCCCCEEEEECCCEEE T ss_conf 99999998499999999998899689 No 85 >KOG3227 consensus Probab=21.12 E-value=66 Score=13.96 Aligned_cols=57 Identities=33% Similarity=0.342 Sum_probs=39.9 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 431488999999999999987248999999999975176222430489998876879999999974444210 Q gi|254780440|r 4 KIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEV 75 (158) Q Consensus 4 k~~lT~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~i 75 (158) +--+|.+.-.|+.+|=.+|.. .|-+--..|-++|-+.|++. |.+-+.+|- .|+.+.- T Consensus 17 ~~~vt~~~IQk~LdEN~~LI~--------~I~e~Qn~Gk~~EC~qyq~~------LhrNL~YLA-~iAD~qp 73 (231) T KOG3227 17 KGEVTSEQIQKMLDENKHLIQ--------CIVESQNKGKLSECAQYQAL------LHRNLVYLA-TIADSQP 73 (231) T ss_pred CCCCCHHHHHHHHHHHHHHHH--------HHHHHHCCCHHHHHHHHHHH------HHHHHHHHH-HHHHCCC T ss_conf 776689999999975047999--------99986314307889999999------987489999-9861488 No 86 >KOG0493 consensus Probab=20.88 E-value=67 Score=13.93 Aligned_cols=29 Identities=10% Similarity=0.438 Sum_probs=21.3 Q ss_pred CCHHHHHHHHHHHH---HHHHHHHHHHHHHHH Q ss_conf 48899999999999---998724899999999 Q gi|254780440|r 7 VTSKGFDKIQQELR---WRQQEERPRIIKAIS 35 (158) Q Consensus 7 lT~~g~~~L~~El~---~l~~~~r~~~~~~i~ 35 (158) .|.+.+.||+.|+. +|...+|++++.++. T Consensus 253 FtaeQL~RLK~EF~enRYlTEqRRQ~La~ELg 284 (342) T KOG0493 253 FTAEQLQRLKAEFQENRYLTEQRRQELAQELG 284 (342) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 14999999999986603578999999998737 No 87 >cd06212 monooxygenase_like The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons. These flavoprotein monooxygenases use molecular oxygen as a substrate and require reduced FAD. One atom of oxygen is incorportated into the aromatic compond, while the other is used to form a molecule of water. In contrast dioxygenases add both atoms of oxygen to the substrate. Probab=20.61 E-value=68 Score=13.89 Aligned_cols=65 Identities=14% Similarity=0.231 Sum_probs=42.2 Q ss_pred CCCCCEEEEEECCCCCEEEEEEECHH-HCCCCCCEECC--CCHHHHHHCC-CCCCCEEEEECCCCEEEE Q ss_conf 11365799953476523599996310-13345881501--3178998728-888878999828971999 Q gi|254780440|r 86 IAFGATVSLVEKNSGDKKNYQIVGDQ-EADVQSGLVSI--SSPIARALIG-KELGDIISVNAPGGEKTY 150 (158) Q Consensus 86 V~~Gs~V~l~d~~~~~~~~~~lVg~~-e~d~~~~~IS~--~SPlG~ALlG-~~~Gd~V~v~~p~G~~~~ 150 (158) ...|-.|++.-.+.+....|+|..+. +.+.-.=.|.. ...+...|.. .++||.|.+.-|-|.-.+ T Consensus 30 f~~GQ~v~~~~~g~~~~R~ySi~s~p~~~~~~~l~Vk~~~~G~~s~~l~~~l~~Gd~v~v~gP~G~f~l 98 (232) T cd06212 30 FFAGQYVDITVPGTEETRSFSMANTPADPGRLEFIIKKYPGGLFSSFLDDGLAVGDPVTVTGPYGTCTL 98 (232) T ss_pred CCCCEEEEEEECCCCCEEEEEECCCCCCCCEEEEEEEEECCCCHHHHHHHCCCCCCEEEEECCCCCCEE T ss_conf 189855999989988178997462799998899999997799558899855899989999737567510 No 88 >pfam06160 EzrA Septation ring formation regulator, EzrA. During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation. Probab=20.02 E-value=70 Score=13.81 Aligned_cols=31 Identities=26% Similarity=0.369 Sum_probs=17.2 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 6222430489998876879999999974444 Q gi|254780440|r 42 DLSENAEYQAAKELQNLNEGRMAELENIITR 72 (158) Q Consensus 42 Dl~ENaeY~aAke~q~~~~~ri~~L~~~L~~ 72 (158) .|.++++|..|++-...++..+..|+..+.. T Consensus 182 ~lt~~Gd~~~A~e~l~~l~~~~~~L~~~me~ 212 (559) T pfam06160 182 ELTESGDYLEAREVLLKLEEETDALEQKMEE 212 (559) T ss_pred HHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9986899899999999999999999999998 Done!