Query 537021.9.peg.788_1 Match_columns 270 No_of_seqs 139 out of 2893 Neff 9.1 Searched_HMMs 39220 Date Wed May 25 04:40:38 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i peg_788.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 TIGR02212 lolCE lipoprotein re 100.0 0 0 432.3 13.8 263 6-270 1-267 (414) 2 COG4591 LolE ABC-type transpor 100.0 0 0 363.0 17.6 264 3-270 1-267 (408) 3 PRK11146 outer membrane-specif 100.0 0 0 358.0 19.7 264 5-270 1-265 (412) 4 PRK10814 outer membrane-specif 100.0 0 0 346.0 18.8 260 3-270 1-262 (396) 5 TIGR02213 lolE_release lipopro 100.0 0 0 333.1 5.2 262 6-269 1-268 (416) 6 PRK10535 macrolide transporter 99.9 7.2E-22 1.8E-26 143.2 15.6 232 8-262 257-512 (648) 7 TIGR03434 ADOP Acidobacterial 99.3 8.5E-11 2.2E-15 80.4 11.3 212 8-246 4-236 (803) 8 COG3127 Predicted ABC-type tra 98.7 5.9E-06 1.5E-10 53.0 16.4 222 6-255 5-239 (829) 9 COG0577 SalY ABC-type antimicr 98.5 3.2E-05 8.1E-10 48.8 17.1 229 29-266 4-277 (419) 10 TIGR01185 devC DevC protein; I 98.4 3.1E-06 7.9E-11 54.6 9.3 221 11-260 3-244 (381) 11 COG3127 Predicted ABC-type tra 97.8 0.0012 3.1E-08 39.9 13.3 228 5-266 452-702 (829) 12 TIGR03434 ADOP Acidobacterial 97.8 0.0026 6.7E-08 38.0 16.4 169 80-267 478-673 (803) 13 PRK11026 ftsX cell division pr 94.8 0.11 2.8E-06 28.8 6.2 93 5-105 13-106 (309) 14 COG2177 FtsX Cell division pro 86.4 2.3 5.9E-05 21.3 7.0 89 5-101 6-95 (297) 15 TIGR01553 formate-DH-alph form 80.4 1.4 3.5E-05 22.6 2.5 42 152-193 948-990 (1043) 16 PRK10549 signal transduction h 77.4 5.1 0.00013 19.3 5.8 31 29-59 15-45 (467) 17 TIGR01462 greA transcription e 72.5 2.7 6.8E-05 20.9 2.2 90 81-177 52-147 (155) 18 pfam11688 DUF3285 Protein of u 71.5 7.3 0.00019 18.5 4.3 33 9-41 8-41 (45) 19 TIGR02609 doc_partner putative 67.4 2.7 6.9E-05 20.9 1.3 25 147-171 9-33 (77) 20 COG4771 FepA Outer membrane re 67.4 2 5.1E-05 21.6 0.6 60 51-125 41-101 (699) 21 TIGR01425 SRP54_euk signal rec 64.5 0.81 2.1E-05 23.9 -1.8 65 202-267 299-365 (453) 22 cd02792 MopB_CT_Formate-Dh-Na- 62.8 7.1 0.00018 18.5 2.7 54 148-216 35-88 (122) 23 TIGR01439 lp_hng_hel_AbrB tran 58.2 5.2 0.00013 19.3 1.4 26 147-172 7-32 (44) 24 cd02789 MopB_CT_FmdC-FwdD The 54.7 12 0.00031 17.2 2.8 57 149-220 32-89 (106) 25 PRK01885 greB transcription el 53.8 11 0.00027 17.6 2.4 47 137-194 109-156 (159) 26 PRK00226 greA transcription el 51.5 13 0.00033 17.1 2.5 47 137-194 108-155 (157) 27 cd00508 MopB_CT_Fdh-Nap-like T 50.0 9.6 0.00025 17.8 1.6 53 147-214 34-86 (120) 28 pfam04014 SpoVT_AbrB SpoVT / A 46.5 10 0.00027 17.6 1.4 26 147-172 6-31 (47) 29 TIGR01941 nqrF NADH:ubiquinone 45.7 9.4 0.00024 17.9 1.0 23 156-178 256-278 (425) 30 cd02775 MopB_CT Molybdopterin- 44.4 13 0.00033 17.1 1.6 54 148-216 23-76 (101) 31 cd02790 MopB_CT_Formate-Dh_H F 41.9 15 0.00038 16.7 1.6 52 148-214 35-86 (116) 32 TIGR01398 FlhA flagellar biosy 39.2 27 0.0007 15.2 5.8 67 25-93 201-278 (713) 33 PRK05892 nucleoside diphosphat 39.1 21 0.00054 15.8 2.0 28 150-177 122-150 (161) 34 TIGR03243 arg_catab_AOST argin 38.7 17 0.00043 16.4 1.5 15 203-217 308-322 (335) 35 cd02780 MopB_CT_Tetrathionate_ 38.1 20 0.0005 16.0 1.7 31 147-177 29-59 (143) 36 cd02778 MopB_CT_Thiosulfate-R- 38.0 20 0.00051 16.0 1.7 30 148-177 30-59 (123) 37 cd02781 MopB_CT_Acetylene-hydr 37.8 20 0.00052 16.0 1.8 31 147-177 32-62 (130) 38 cd02786 MopB_CT_3 The MopB_CT_ 37.6 21 0.00053 15.9 1.8 57 147-218 30-86 (116) 39 TIGR03245 arg_AOST_alph argini 37.6 18 0.00046 16.2 1.5 12 206-217 312-323 (336) 40 COG2336 MazE Growth regulator 37.6 18 0.00046 16.2 1.5 27 147-173 11-37 (82) 41 TIGR03244 arg_catab_AstA argin 37.2 18 0.00047 16.2 1.5 15 203-217 309-323 (336) 42 pfam11374 DUF3176 Protein of u 36.9 30 0.00076 15.0 3.8 18 29-47 24-41 (111) 43 cd02784 MopB_CT_PHLH The MopB_ 36.9 22 0.00055 15.8 1.8 28 147-174 37-64 (137) 44 cd02791 MopB_CT_Nitrate-R-NapA 36.4 20 0.00052 15.9 1.6 54 148-216 35-88 (122) 45 pfam01568 Molydop_binding Moly 36.0 21 0.00054 15.9 1.6 53 149-216 31-83 (110) 46 PRK10456 arginine succinyltran 34.9 21 0.00054 15.8 1.5 17 202-218 309-325 (344) 47 pfam01272 GreA_GreB Transcript 34.2 24 0.00062 15.5 1.7 28 149-176 39-67 (77) 48 PRK11347 antitoxin ChpS; Provi 32.6 28 0.00072 15.1 1.8 46 147-195 11-56 (83) 49 pfam04958 AstA Arginine N-succ 32.0 27 0.00069 15.2 1.6 12 206-217 314-325 (338) 50 COG2002 AbrB Regulators of sta 31.0 27 0.00069 15.2 1.5 27 146-172 12-38 (89) 51 PRK11465 hypothetical protein; 30.8 14 0.00036 16.8 0.0 75 162-248 574-653 (741) 52 cd02783 MopB_CT_2 The MopB_CT_ 30.3 32 0.00082 14.8 1.8 32 147-178 31-62 (156) 53 PRK13657 cyclic beta-1,2-gluca 29.9 39 0.001 14.3 3.8 19 159-177 355-373 (585) 54 TIGR00439 ftsX putative protei 29.9 39 0.001 14.3 6.3 75 28-105 34-110 (314) 55 TIGR02066 dsrB sulfite reducta 29.6 40 0.001 14.3 4.1 41 207-247 41-91 (366) 56 cd02782 MopB_CT_1 The MopB_CT_ 28.9 36 0.00091 14.6 1.8 32 147-178 32-63 (129) 57 TIGR00959 ffh signal recogniti 28.6 15 0.00037 16.8 -0.2 60 202-262 286-345 (439) 58 PRK08221 anaerobic sulfite red 28.4 41 0.001 14.2 2.1 30 151-180 67-96 (263) 59 cd02794 MopB_CT_DmsA-EC The Mo 28.3 36 0.00091 14.6 1.7 31 148-178 30-60 (121) 60 cd02785 MopB_CT_4 The MopB_CT_ 28.1 35 0.0009 14.6 1.7 31 147-177 31-61 (124) 61 PRK09798 antitoxin MazE; Provi 27.3 31 0.00079 14.9 1.3 29 147-175 12-40 (82) 62 cd02788 MopB_CT_NDH-1_NuoG2-N7 26.9 37 0.00095 14.4 1.6 30 148-177 29-58 (96) 63 cd02779 MopB_CT_Arsenite-Ox Th 26.8 38 0.00096 14.4 1.6 50 149-213 34-83 (115) 64 cd02777 MopB_CT_DMSOR-like The 25.8 44 0.0011 14.0 1.8 31 148-178 34-64 (127) 65 cd02793 MopB_CT_DMSOR-BSOR-TMA 25.0 47 0.0012 13.9 1.9 31 148-178 33-63 (129) 66 TIGR02160 PA_CoA_Oxy5 phenylac 23.9 36 0.00092 14.5 1.1 31 154-184 78-108 (371) 67 TIGR01393 lepA GTP-binding pro 23.8 30 0.00076 15.0 0.7 43 154-197 262-304 (598) 68 TIGR02624 rhamnu_1P_ald rhamnu 23.4 40 0.001 14.3 1.2 28 186-216 201-233 (273) 69 cd07047 BMC_PduB_repeat1 1,2-p 22.0 56 0.0014 13.5 3.9 89 161-249 5-108 (134) 70 PRK05753 nucleoside diphosphat 20.7 59 0.0015 13.3 2.4 37 149-194 88-125 (135) No 1 >TIGR02212 lolCE lipoprotein releasing system, transmembrane protein, LolC/E family; InterPro: IPR011925 This entry describes the LolC protein, and its paralog LolE found in some species. These proteins are homologous to permease proteins of ABC transporters. In some species, two paralogs occur, designated LolC and LolE. In others, a single form is found and tends to be designated LolC .; GO: 0006810 transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane. Probab=100.00 E-value=0 Score=432.26 Aligned_cols=263 Identities=35% Similarity=0.598 Sum_probs=251.5 Q ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCC-CCCCHHHHH Q ss_conf 4799999987522554546899999999999999999999999987699999631110245300000000-012136665 Q 537021.9.peg.7 6 RFEVIVAWRYLFSNRKNAFISIASFISFIGVMIGVMALIVVMSVMNGFREDMIKRVLGINGHVVIQQKYY-PLVDYQFIA 84 (270) Q Consensus 6 ~~~~~iA~R~l~~~k~r~~~~~is~ls~lgI~igv~~li~~lsv~~G~~~~i~~~i~~~~~~i~i~~~~~-~~~~~~~~~ 84 (270) ++|++||+||+|+|||.+|+++||.+|++||+||||+||++||||||||.++.++++++.||+.++.... +..+|+++. T Consensus 1 ~~~l~Ig~RY~RAk~~n~F~s~I~~~S~iGI~LGVaaLIvVlSVMNGFe~eL~~riLg~~PH~~~~~~~~~~~~~~~~~~ 80 (414) T TIGR02212 1 PLSLFIGLRYLRAKRRNRFVSFISLFSIIGIALGVAALIVVLSVMNGFERELRQRILGVIPHAIIESKQNAPISDWQELL 80 (414) T ss_pred CCHHHHHHHHHHHHHCCCCEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEECCCEEEECCCCCCCCCHHHHH T ss_conf 92367877777752058864511688999999988886666666666799882074101261888347898998989999 Q ss_pred HHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCC-CCCCCCHHHHHHHHHCC Q ss_conf 55422641034665420011111222332210111243100000120011002775421111-23421013454554213 Q 537021.9.peg.7 85 NRLDFIPDVIKVLPFVSGQAFVSGLSSGGSGVLVRGISNSDFSYLQNSFSRFYGNVSNDFDR-GKGVIIGKDLARNLGIS 163 (270) Q Consensus 85 ~~l~~~~~V~~~~p~i~~~~~i~~~~~~~~~v~i~Gv~~~~~~~~~~~~~~~~~~~~~~~~~-~~~iiiG~~lA~~L~l~ 163 (270) +.++++|+|.+++|++++++++.+ +...+++.++||+|+++++.....+....+.+..+.. .+.|+||+++|++||++ T Consensus 81 ~~~~~~pgv~~aaP~v~~~~lv~~-~~~~~~~~V~Gv~~~~~~~~~~~~~~~~~g~~~~f~~G~~~iiiG~~lA~~LgV~ 159 (414) T TIGR02212 81 ETIEKNPGVKAAAPIVSGQALVQS-AGKVSGVQVRGVDPSDEDKLSAISNNVKQGALKKFKPGEYNIIIGEQLAEKLGVS 159 (414) T ss_pred HHHHHCCCCEEEEEEEEEEEEEEE-CCCEEEEEEECCCCHHHHHHHHHHHHCCCCCCCCCCCCCCEEEEHHHHHHHCCCC T ss_conf 999728980688546641489982-7834599985566033454555320102455445568852788715889845899 Q ss_pred CCCEEEECCCC-CCCCCCCCCCCCCCCCCCEEEEEECCCCCCCEEEEEHHHHHHHCCCC-CCEEEEEEEECCHHHHHHHH Q ss_conf 33202311344-21000122110000122102331024455516898548899971899-87107999956988999999 Q 537021.9.peg.7 164 IGDKINILSPY-GDVTPMGMGIRSKSYTVLGMFRMRFPDYDNGMVYMSLQEAQLYFNLE-NAVSGIEVFVKDPDAIEKTH 241 (270) Q Consensus 164 vGD~i~l~~~~-~~~~~~~~~~~~~~f~V~GI~~sg~~~~D~~~v~~~l~~~q~l~~~~-~~~~~i~i~l~d~~~~~~~~ 241 (270) +||+|++++|+ .+.++.|..||.|+|+|+|+|++|++|+|.+.+++|+++||++++.+ +.++++++|++||++++++. T Consensus 160 ~GD~~~li~p~~~~~t~~G~~P~~k~f~V~giF~~gm~e~D~~~~l~p~~dA~~f~~~~~~~v~g~~lk~~Dp~~a~~l~ 239 (414) T TIGR02212 160 VGDKVTLISPENSNVTPFGEIPRQKRFTVIGIFSTGMGEVDGYLALMPLEDAQRFLRYGPDQVTGLRLKLDDPFQADALA 239 (414) T ss_pred CCCEEEEEECCCCCCCEEECCCEEEEEEEEEEEEECCHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCHHHHH T ss_conf 89779999828975210001450466899999970110320566750189999860899763306899823865315689 Q ss_pred HHHHHHCCCCEEEEEHHHHHHHHHHHHCC Q ss_conf 99998619985999689988989998609 Q 537021.9.peg.7 242 ENIVRILGNGVVVIDWQQRYQIFFSCYES 270 (270) Q Consensus 242 ~~i~~~l~~~~~v~~w~e~~~~lf~ai~~ 270 (270) +++.+.++ ...++||+++|++||+|+|. T Consensus 240 ~~~~~~~~-~~~~~dW~~~~g~~F~A~~~ 267 (414) T TIGR02212 240 QQVQPELG-ELYVRDWRDQNGELFSAIQM 267 (414) T ss_pred HHHHHHHC-CEEEECHHHHHHHHHHHHHH T ss_conf 99988604-24320056653558999999 No 2 >COG4591 LolE ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane] Probab=100.00 E-value=0 Score=363.04 Aligned_cols=264 Identities=36% Similarity=0.637 Sum_probs=238.5 Q ss_pred CCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCCCCCCHHH Q ss_conf 42347999999875225545468999999999999999999999999876999996311102453000000000121366 Q 537021.9.peg.7 3 IFSRFEVIVAWRYLFSNRKNAFISIASFISFIGVMIGVMALIVVMSVMNGFREDMIKRVLGINGHVVIQQKYYPLVDYQF 82 (270) Q Consensus 3 m~~~~~~~iA~R~l~~~k~r~~~~~is~ls~lgI~igv~~li~~lsv~~G~~~~i~~~i~~~~~~i~i~~~~~~~~~~~~ 82 (270) |+++++++|||||+|++|+ +++++++++|.+||++||++|++++|+||||++++.+++++..||+++++.+.+..+|++ T Consensus 1 m~~~~~~~ia~rylr~rk~-~~~s~i~~~s~~GI~lgV~~LIv~lsvmnGf~~el~~~il~~~pH~~i~~~~~~~~~~~~ 79 (408) T COG4591 1 MFMPLELFIALRYLRARKR-RFISIISALSLIGIALGVAVLIVVLSVMNGFQKELENRILGVNPHVQITPEDGPIDDYRE 79 (408) T ss_pred CCCCHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCHHH T ss_conf 9975589999999996221-177899999999999889999999998856799998434134676899558788743589 Q ss_pred HHHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCC-CCCCCCCHHHHHHHHH Q ss_conf 655542264103466542001111122233221011124310000012001100277542111-1234210134545542 Q 537021.9.peg.7 83 IANRLDFIPDVIKVLPFVSGQAFVSGLSSGGSGVLVRGISNSDFSYLQNSFSRFYGNVSNDFD-RGKGVIIGKDLARNLG 161 (270) Q Consensus 83 ~~~~l~~~~~V~~~~p~i~~~~~i~~~~~~~~~v~i~Gv~~~~~~~~~~~~~~~~~~~~~~~~-~~~~iiiG~~lA~~L~ 161 (270) ..+.+++.|+|.+++|++++++++.+ ++...++.++||+|+++++ .............++. ...+|+||+.+|++|| T Consensus 80 ~~~~i~~~~~v~~~~P~~~~~~l~~~-~~~~~~~~v~Gv~p~~~~~-~~i~~~~~~~~~~~~~~g~~~iilG~~LA~~Lg 157 (408) T COG4591 80 LIKLILKNPGVKAASPYIEGQALLQS-GNNSSGVLVRGVDPKDEDK-SAISSFLKDGSEDDLKPGEFGIILGSGLAEKLG 157 (408) T ss_pred HHHHHHCCCCCCEECCEEEEEEEEEC-CCCCCEEEEEEECCCCCHH-HHHHHHHHHCCCCCCCCCCCCEEECHHHHHHCC T ss_conf 99998438575023345778899974-8753205898645520005-678887420133445678972896089998719 Q ss_pred CCCCCEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCEEEEEHHHHHHHCCCC-CCEEEEEEEECCHHHHHHH Q ss_conf 133320231134421000122110000122102331024455516898548899971899-8710799995698899999 Q 537021.9.peg.7 162 ISIGDKINILSPYGDVTPMGMGIRSKSYTVLGMFRMRFPDYDNGMVYMSLQEAQLYFNLE-NAVSGIEVFVKDPDAIEKT 240 (270) Q Consensus 162 l~vGD~i~l~~~~~~~~~~~~~~~~~~f~V~GI~~sg~~~~D~~~v~~~l~~~q~l~~~~-~~~~~i~i~l~d~~~~~~~ 240 (270) +++||++++++|.++. +.+..|+.++|+|+|+|++|.+|+|+.++|+|++++|++++.+ +.++++.++++||++++++ T Consensus 158 v~~GD~v~li~p~~~~-~~g~~p~~~~f~V~Gif~tG~~e~D~~~~~~~L~~aq~l~~~~~~~v~~i~v~l~dp~~a~~~ 236 (408) T COG4591 158 VRVGDKVTLITPESNT-PFGRGPRQKRFTVVGIFSTGLSELDESLAYIPLEDAQNLFNLPKGVVTGIRLKLKDPFNAEEL 236 (408) T ss_pred CCCCCEEEEEEECCCC-CCCCCCCEEEEEEEEEEECCCHHHHHHHHHHCHHHHHHHHCCCCCCEEEEEEEECCCCHHHHH T ss_conf 9879889999516877-656675138999999996085555179888169989998558988446899991792243999 Q ss_pred HHHHHHH-CCCCEEEEEHHHHHHHHHHHHCC Q ss_conf 9999986-19985999689988989998609 Q 537021.9.peg.7 241 HENIVRI-LGNGVVVIDWQQRYQIFFSCYES 270 (270) Q Consensus 241 ~~~i~~~-l~~~~~v~~w~e~~~~lf~ai~~ 270 (270) ++.+.+. .++++.+.||+|+|+++|+|++. T Consensus 237 ~~~~~~~~~~~~~~~~~W~e~n~~~~~al~~ 267 (408) T COG4591 237 KRKLEIELLPQGLKAKDWREQNGEFFSALRL 267 (408) T ss_pred HHHHHHHCCCCCEEEECHHHHHHHHHHHHHH T ss_conf 9998742368874895179970799999999 No 3 >PRK11146 outer membrane-specific lipoprotein transporter subunit LolE; Provisional Probab=100.00 E-value=0 Score=358.00 Aligned_cols=264 Identities=22% Similarity=0.385 Sum_probs=241.0 Q ss_pred HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCCCCCCHHHHH Q ss_conf 34799999987522554546899999999999999999999999987699999631110245300000000012136665 Q 537021.9.peg.7 5 SRFEVIVAWRYLFSNRKNAFISIASFISFIGVMIGVMALIVVMSVMNGFREDMIKRVLGINGHVVIQQKYYPLVDYQFIA 84 (270) Q Consensus 5 ~~~~~~iA~R~l~~~k~r~~~~~is~ls~lgI~igv~~li~~lsv~~G~~~~i~~~i~~~~~~i~i~~~~~~~~~~~~~~ 84 (270) +++||||||||++++|+.++++++|++|++||++||++|++++|+||||++++.+++++..||+.+++.+.++.+++++. T Consensus 1 M~~~~fIA~Ryl~~~k~~~~is~is~lS~lGIaigv~~livvlSv~nGf~~~l~~~i~~~~ph~~i~~~~~~~~~~~~~~ 80 (412) T PRK11146 1 MPLSLLIGLRFSRGRRRGGMVSLISVISTIGIALGVAVLIVGLSAMNGFERELNNRILAVVPHGEIEAVNQPWTNWQEAL 80 (412) T ss_pred CCHHHHHHHHHCCCCCCCCEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCHHHHH T ss_conf 96799999998332567972439999999999999999999999997589999999827157689982898876659999 Q ss_pred HHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCC-CCCCCCCCHHHHHHHHHCC Q ss_conf 554226410346654200111112223322101112431000001200110027754211-1123421013454554213 Q 537021.9.peg.7 85 NRLDFIPDVIKVLPFVSGQAFVSGLSSGGSGVLVRGISNSDFSYLQNSFSRFYGNVSNDF-DRGKGVIIGKDLARNLGIS 163 (270) Q Consensus 85 ~~l~~~~~V~~~~p~i~~~~~i~~~~~~~~~v~i~Gv~~~~~~~~~~~~~~~~~~~~~~~-~~~~~iiiG~~lA~~L~l~ 163 (270) +.+++.|+|.+++|++++++++.+ ++...++.++||||+++..+........++.+..+ ...++++||+.+|++|+++ T Consensus 81 ~~l~~~~~V~~~~p~i~~~~li~~-~~~~~~v~l~Gvd~~~~~~~~~~~~~i~~g~~~~~~~~~~~iiIG~~lA~~L~l~ 159 (412) T PRK11146 81 ARVQKVPGIAAAAPYVNFTGLVEN-GAKLKAVQVKGVDPQQEQQVSALPSFVQNDAWQNFKAGQQQIILGKGVADALKVK 159 (412) T ss_pred HHHHCCCCCEEEEEEEEEEEEEEC-CCCEEEEEEEEECHHHHHHHHHHHHHHHCCCHHHCCCCCCEEEECHHHHHHCCCC T ss_conf 998629995288766445578842-8713457997107677655546778763585433047897499748999875999 Q ss_pred CCCEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCEEEEEHHHHHHHCCCCCCEEEEEEEECCHHHHHHHHHH Q ss_conf 33202311344210001221100001221023310244555168985488999718998710799995698899999999 Q 537021.9.peg.7 164 IGDKINILSPYGDVTPMGMGIRSKSYTVLGMFRMRFPDYDNGMVYMSLQEAQLYFNLENAVSGIEVFVKDPDAIEKTHEN 243 (270) Q Consensus 164 vGD~i~l~~~~~~~~~~~~~~~~~~f~V~GI~~sg~~~~D~~~v~~~l~~~q~l~~~~~~~~~i~i~l~d~~~~~~~~~~ 243 (270) +||++++++|+.........|+.++|+|+|+|++| .++|++++|+|++++|++++.++.+++++++++|+.++++++++ T Consensus 160 ~Gd~v~l~~p~~~~~~~~~~p~~~~~~V~Gif~~~-~~~D~~~v~~~l~~aq~l~~~~~~~~~i~i~l~d~~~~~~~~~~ 238 (412) T PRK11146 160 QGDWVTLMIPNSNPDHKLLQPKRVRLQVAGILQLS-GQLDHSLALIPLADAQQYLDMGDSVTGIALKVTDVFNANKLVRD 238 (412) T ss_pred CCCEEEEEECCCCCCCCCCCCCEEEEEEEEEEECC-CCCCCCEEEEEHHHHHHHHCCCCCCCEEEEEECCHHHHHHHHHH T ss_conf 79878999227877765567613789999998247-75565158977999999857888862599993687568999999 Q ss_pred HHHHCCCCEEEEEHHHHHHHHHHHHCC Q ss_conf 998619985999689988989998609 Q 537021.9.peg.7 244 IVRILGNGVVVIDWQQRYQIFFSCYES 270 (270) Q Consensus 244 i~~~l~~~~~v~~w~e~~~~lf~ai~~ 270 (270) +.+.++..+.++||+|+|+.+|+|+++ T Consensus 239 ~~~~~~~~~~~~tw~~~~~~l~~~i~~ 265 (412) T PRK11146 239 AGEVTNSYVYIKSWIGTYGYMYRDIQM 265 (412) T ss_pred HHHHCCCCEEEEEHHHHHHHHHHHHHH T ss_conf 998648881896699989999999999 No 4 >PRK10814 outer membrane-specific lipoprotein transporter subunit LolC; Provisional Probab=100.00 E-value=0 Score=346.02 Aligned_cols=260 Identities=22% Similarity=0.423 Sum_probs=225.7 Q ss_pred CCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCCCCCCHHH Q ss_conf 42347999999875225545468999999999999999999999999876999996311102453000000000121366 Q 537021.9.peg.7 3 IFSRFEVIVAWRYLFSNRKNAFISIASFISFIGVMIGVMALIVVMSVMNGFREDMIKRVLGINGHVVIQQKYYPLVDYQF 82 (270) Q Consensus 3 m~~~~~~~iA~R~l~~~k~r~~~~~is~ls~lgI~igv~~li~~lsv~~G~~~~i~~~i~~~~~~i~i~~~~~~~~~~~~ 82 (270) ||++++||||+||+|++|+++|++++|++|++||++|||+|++++||||||++++.+++++++||+.+++.++. .+++. T Consensus 1 m~~~~~~fIA~RYl~~kk~~~~~~~is~iSilGI~iGvaaLivvlSV~nGf~~~i~~~i~~~~phi~i~~~~g~-~~~~~ 79 (396) T PRK10814 1 MYQPVALFIGLRYMRGRAADRFGRFVSWLSTIGITLGVMALVTVLSVMNGFERELQNNILGLMPQAILSSEHGS-LNPQQ 79 (396) T ss_pred CCCCHHHHHHHHHCCCCCCCCEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCC-CCHHH T ss_conf 98619999999975446778723799999999999999999999999972899999998585688899658998-89899 Q ss_pred HHHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHC Q ss_conf 65554226410346654200111112223322101112431000001200110027754211112342101345455421 Q 537021.9.peg.7 83 IANRLDFIPDVIKVLPFVSGQAFVSGLSSGGSGVLVRGISNSDFSYLQNSFSRFYGNVSNDFDRGKGVIIGKDLARNLGI 162 (270) Q Consensus 83 ~~~~l~~~~~V~~~~p~i~~~~~i~~~~~~~~~v~i~Gv~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiiG~~lA~~L~l 162 (270) ....+.+.++|..++|++++++++.+ ++...++.++|+||++.+.+.... ..+.......+.++++||+++|++|++ T Consensus 80 ~~~~~~~~~~v~~~sp~i~~~~~l~~-~~~~~~~~l~Gvd~~~~~~l~~~~--~~~~~~~~~~~~~~iiiG~~lA~~L~v 156 (396) T PRK10814 80 LPESAVKLDGVNRVAPLTTGDVVLQS-ARSVAVGVMLGIDPAQKDPLTPYL--VNVKQTDLEPGKYNVILGEQLAGQLGV 156 (396) T ss_pred HHHHHHHCCCCCEEEEEEECCCEEEC-CCCEEEEEEEEECHHHHHHHHHHH--HCCCHHHCCCCCCCEEECHHHHHHCCC T ss_conf 89998708786268666531301313-785147999987678765788988--507365403899728985899986399 Q ss_pred CCCCEEEECCCCCC-CCCCCCCCCCCCCCCCEEEEEECCCCCCCEEEEEHHHHHHHCCCC-CCEEEEEEEECCHHHHHHH Q ss_conf 33320231134421-000122110000122102331024455516898548899971899-8710799995698899999 Q 537021.9.peg.7 163 SIGDKINILSPYGD-VTPMGMGIRSKSYTVLGMFRMRFPDYDNGMVYMSLQEAQLYFNLE-NAVSGIEVFVKDPDAIEKT 240 (270) Q Consensus 163 ~vGD~i~l~~~~~~-~~~~~~~~~~~~f~V~GI~~sg~~~~D~~~v~~~l~~~q~l~~~~-~~~~~i~i~l~d~~~~~~~ 240 (270) ++||++++++|... .++.+..|+.+.|+|+|+|++| .|+|++++|+|++++|++++.+ +.+++++++++||.+++++ T Consensus 157 ~~Gd~i~l~~p~~~~~~~~g~~p~~~~f~V~GiF~~g-~e~D~~~v~~~l~~a~~ll~~~~~~is~i~i~l~d~~~~~~~ 235 (396) T PRK10814 157 NRGDQIRLMVPSASQFTPMGRIPSQRLFNVIGTFAAN-SEVDGYQMLVNIQDASRLMRYPAGNITGWRLWLDEPLKVDSL 235 (396) T ss_pred CCCCEEEEEECCCCCCCCCCCCCCEEEEEEEEEEECC-CCCCCEEEEECHHHHHHHHCCCCCCEEEEEEEECCHHHHHHH T ss_conf 8798899993688766756668633789999986226-633460799649999998466878714899995787668999 Q ss_pred HHHHHHHCCCCEEEEEHHHHHHHHHHHHCC Q ss_conf 999998619985999689988989998609 Q 537021.9.peg.7 241 HENIVRILGNGVVVIDWQQRYQIFFSCYES 270 (270) Q Consensus 241 ~~~i~~~l~~~~~v~~w~e~~~~lf~ai~~ 270 (270) .+ +.+++.+.++||+|+|++||+|+++ T Consensus 236 ~~---~~l~~~~~~~~w~e~n~~lf~al~~ 262 (396) T PRK10814 236 SQ---QTLPEGTKWQDWRERKGELFQAVRM 262 (396) T ss_pred HH---HHCCCCCEEEEHHHHHHHHHHHHHH T ss_conf 99---7544575474799989999999999 No 5 >TIGR02213 lolE_release lipoprotein releasing system, transmembrane protein LolE; InterPro: IPR011926 This protein is part of an unusual ABC transporter complex that releases lipoproteins from the periplasmic side of the bacterial inner membrane, rather than transport any substrate across the inner membrane. In some species, the permease-like transmembrane protein is represented by two paralogs, LolC and LolE, both in the LolCDE complex. This family consists of LolE, as found in Escherichia coli and related species.; GO: 0006810 transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane. Probab=100.00 E-value=0 Score=333.07 Aligned_cols=262 Identities=23% Similarity=0.387 Sum_probs=246.6 Q ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEECCC----CCCCCHH Q ss_conf 479999998752255454689999999999999999999999998769999963111024530000000----0012136 Q 537021.9.peg.7 6 RFEVIVAWRYLFSNRKNAFISIASFISFIGVMIGVMALIVVMSVMNGFREDMIKRVLGINGHVVIQQKY----YPLVDYQ 81 (270) Q Consensus 6 ~~~~~iA~R~l~~~k~r~~~~~is~ls~lgI~igv~~li~~lsv~~G~~~~i~~~i~~~~~~i~i~~~~----~~~~~~~ 81 (270) +++|+|.|||-+.++|...+++||.+|.+|||+|||+||+.||.|||||+|+.+|+++.-||-++++-. .|.++|+ T Consensus 1 ~l~llIg~Rfsrgkqrn~mVslIs~~StIGIAlGVAVlIvGLSAMNGFERELn~RiLaVvPHaEie~v~nate~p~~nWQ 80 (416) T TIGR02213 1 SLALLIGLRFSRGKQRNKMVSLISVISTIGIALGVAVLIVGLSAMNGFERELNSRILAVVPHAEIEAVDNATEAPVENWQ 80 (416) T ss_pred CCCCEEEHHHHHCHHCCCCCHHHHHHHHHHHHHHHHHHEEEHHCCCCHHHHHCCCCEEEECCHHHHCCCCCCCCCHHHHH T ss_conf 97501001244000128701024577676688743541220004560367764951576073453036533567567899 Q ss_pred HHHHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCC-CCCCCCHHHHHHHH Q ss_conf 66555422641034665420011111222332210111243100000120011002775421111-23421013454554 Q 537021.9.peg.7 82 FIANRLDFIPDVIKVLPFVSGQAFVSGLSSGGSGVLVRGISNSDFSYLQNSFSRFYGNVSNDFDR-GKGVIIGKDLARNL 160 (270) Q Consensus 82 ~~~~~l~~~~~V~~~~p~i~~~~~i~~~~~~~~~v~i~Gv~~~~~~~~~~~~~~~~~~~~~~~~~-~~~iiiG~~lA~~L 160 (270) ++.+++.++|+|.+++||++.+|++++ +++-+.+.++||+|+.|.+++...+...+..|..+.. .+++++|+.+|++| T Consensus 81 ~~~~~~~~nP~i~aaaPyv~FTgLVE~-G~kLkavqVkGVepq~Eq~vS~~~~Fvq~qaW~~F~~Ge~q~i~G~GvA~eL 159 (416) T TIGR02213 81 EVLKRVQKNPKIKAAAPYVKFTGLVER-GAKLKAVQVKGVEPQAEQKVSALSSFVQEQAWRKFKKGENQVIVGKGVADEL 159 (416) T ss_pred HHHHHHHHCCCEEEECCCCEEEEEEEC-CCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEHHHC T ss_conf 999999738952787272012134421-7722289974588102355520000233564674207797079833004320 Q ss_pred HCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCEEEEEHHHHHHHCCCC-CCEEEEEEEECCHHHHHH Q ss_conf 2133320231134421000122110000122102331024455516898548899971899-871079999569889999 Q 537021.9.peg.7 161 GISIGDKINILSPYGDVTPMGMGIRSKSYTVLGMFRMRFPDYDNGMVYMSLQEAQLYFNLE-NAVSGIEVFVKDPDAIEK 239 (270) Q Consensus 161 ~l~vGD~i~l~~~~~~~~~~~~~~~~~~f~V~GI~~sg~~~~D~~~v~~~l~~~q~l~~~~-~~~~~i~i~l~d~~~~~~ 239 (270) ++++||.|+|+.|+.+.+-.-..|+..+.+|+|+++-.+ .+|.+++++|+.+||.+++++ +.+|+|++|++|+.+++. T Consensus 160 ~VkvGDwvtllIpq~n~~~k~~qPkRvrv~VtgiL~L~G-QlDhs~allPlAdAQ~yl~~gP~~vtGiaLK~~DvfnA~~ 238 (416) T TIGR02213 160 DVKVGDWVTLLIPQSNEDEKLAQPKRVRVKVTGILRLDG-QLDHSYALLPLADAQQYLDLGPDSVTGIALKLDDVFNARK 238 (416) T ss_pred CCCCCCEEEEEECCCCCCCCCCCCCCEEEEEEEEEEECC-CHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCHHHHH T ss_conf 866265799971078974323588300378877875366-1226678712787655765489830147642478022789 Q ss_pred HHHHHHHHCCCCEEEEEHHHHHHHHHHHHC Q ss_conf 999999861998599968998898999860 Q 537021.9.peg.7 240 THENIVRILGNGVVVIDWQQRYQIFFSCYE 269 (270) Q Consensus 240 ~~~~i~~~l~~~~~v~~w~e~~~~lf~ai~ 269 (270) +.++.-+..+.-.++++|..+++-+|.-|| T Consensus 239 lvr~~g~~~~~yvY~~sWi~~fGymYRDIQ 268 (416) T TIGR02213 239 LVREVGEDIDSYVYLKSWISKFGYMYRDIQ 268 (416) T ss_pred HHHHHHCCCCCEEEEEEHHHCCCCEEHHHH T ss_conf 989873035634776301300682003699 No 6 >PRK10535 macrolide transporter ATP-binding /permease protein; Provisional Probab=99.89 E-value=7.2e-22 Score=143.22 Aligned_cols=232 Identities=16% Similarity=0.211 Sum_probs=160.6 Q ss_pred HHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-CEEECCCC-----CC---C Q ss_conf 999999875225545468999999999999999999999999876999996311102453-00000000-----01---2 Q 537021.9.peg.7 8 EVIVAWRYLFSNRKNAFISIASFISFIGVMIGVMALIVVMSVMNGFREDMIKRVLGINGH-VVIQQKYY-----PL---V 78 (270) Q Consensus 8 ~~~iA~R~l~~~k~r~~~~~is~ls~lgI~igv~~li~~lsv~~G~~~~i~~~i~~~~~~-i~i~~~~~-----~~---~ 78 (270) ++.+|||+++++|.| |+|++|||++||+++++++++.+|+++.+.+++-++.++ +.|.+... +. . T Consensus 257 alr~A~~sl~~~KlR------s~LT~LGI~IGI~sVi~~~slg~G~~~~i~~~~~~lg~n~i~V~p~~~~~~~~~~~~~~ 330 (648) T PRK10535 257 ALTMAWRAMAANKMR------TLLTMLGIIIGIASVVSIVVVGDAAKQMVLADIRAIGTNTIDIYPGKDFGDDDPQYQQA 330 (648) T ss_pred HHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCC T ss_conf 999999999885889------99999999999999999999988999999999986088779998367668888532356 Q ss_pred CHHHHHHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCC--C-CCCCCCCHHH Q ss_conf 136665554226410346654200111112223322101112431000001200110027754211--1-1234210134 Q 537021.9.peg.7 79 DYQFIANRLDFIPDVIKVLPFVSGQAFVSGLSSGGSGVLVRGISNSDFSYLQNSFSRFYGNVSNDF--D-RGKGVIIGKD 155 (270) Q Consensus 79 ~~~~~~~~l~~~~~V~~~~p~i~~~~~i~~~~~~~~~v~i~Gv~~~~~~~~~~~~~~~~~~~~~~~--~-~~~~iiiG~~ 155 (270) ...+..+.+++.|+|..++|.+..++.+.. ++......+.|+++++...... ....|...... + ..+.+++|+. T Consensus 331 l~~~d~~~i~~~~~v~~v~p~~~~~~~~~~-~~~~~~~~i~g~~~~~~~i~~~--~~~~Gr~f~~~d~~~~~~V~Vlg~~ 407 (648) T PRK10535 331 LKYDDLIAIQKQPWVASATPAVSQSLRLRY-GNIDVAASANGVSGDYFNVYGM--TFSEGNTFNQEQLNGRAQVVVLDSN 407 (648) T ss_pred CCHHHHHHHHCCCCCEEEEEEEEEEEEEEE-CCEEEEEEEEECCCCHHHHHCC--CHHCCCCCCHHHHHCCCCEEEECHH T ss_conf 999999998548986499679875489999-9898889999417137878196--5213876897787357958996479 Q ss_pred HHHHHHC---C-CCCEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEECCCC---CCCEEEEEHHHHHHHCCCCCCEEEEE Q ss_conf 5455421---3-332023113442100012211000012210233102445---55168985488999718998710799 Q 537021.9.peg.7 156 LARNLGI---S-IGDKINILSPYGDVTPMGMGIRSKSYTVLGMFRMRFPDY---DNGMVYMSLQEAQLYFNLENAVSGIE 228 (270) Q Consensus 156 lA~~L~l---~-vGD~i~l~~~~~~~~~~~~~~~~~~f~V~GI~~sg~~~~---D~~~v~~~l~~~q~l~~~~~~~~~i~ 228 (270) +|++|-- + +|+.+.+ ....|+|+||++.....+ ++..+++|+.+++..+..++..+.+. T Consensus 408 ~a~~Lf~~~~~~vG~~i~i--------------~~~~~~VIGV~~~~~~~~g~~~~~~v~iP~~t~~~~~~~~~~~~~i~ 473 (648) T PRK10535 408 TRRQLFPHKADVVGEVILV--------------GNMPATVIGVAEEKQSMFGSSKVLRVWLPYSTMSGRVMGQSWLNSIT 473 (648) T ss_pred HHHHHCCCCCCCCCCEEEE--------------CCEEEEEEEEECCCCCCCCCCCCCEEEEEHHHHHHHHCCCCCCEEEE T ss_conf 9998538987888988998--------------98779999997546666678877469988899998842777521799 Q ss_pred EEECCHHHHHHHHHHHHHHCC-----CCEEEEEHHHHHH Q ss_conf 995698899999999998619-----9859996899889 Q 537021.9.peg.7 229 VFVKDPDAIEKTHENIVRILG-----NGVVVIDWQQRYQ 262 (270) Q Consensus 229 i~l~d~~~~~~~~~~i~~~l~-----~~~~v~~w~e~~~ 262 (270) +++++..+.+++.+++.+.+. .++.+.++.+.-+ T Consensus 474 v~~~~~~~~~~~~~~i~~~l~~~~~~~d~~~~~~~~~~~ 512 (648) T PRK10535 474 VRVKEGYDSAEAEQQLTRLLTLRHGKKDFFTWNMDSVLK 512 (648) T ss_pred EEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHH T ss_conf 997788888999999999998735876530137999999 No 7 >TIGR03434 ADOP Acidobacterial duplicated orphan permease. Members of this protein family are found, so far, only in three species of Acidobacteria, namely Acidobacteria bacterium Ellin345, Acidobacterium capsulatum ATCC 51196, and Solibacter usitatus Ellin6076, where they form large paralogous families. Each protein contains two copies of a domain called the efflux ABC transporter permease protein (pfam02687). However, unlike other members of that family (including LolC, FtsX, and MacB), genes for these proteins are essentially never found fused or adjacent to ABC transporter ATP-binding protein (pfam00005) genes. We name this family ADOP, for Acidobacterial Duplicated Orphan Permease, to reflect the restricted lineage, internal duplication, lack of associated ATP-binding cassette proteins, and permease homology. The function is unknown. Probab=99.27 E-value=8.5e-11 Score=80.45 Aligned_cols=212 Identities=14% Similarity=0.134 Sum_probs=105.7 Q ss_pred HHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCC--CEEECCC------CCCC Q ss_conf 999999875225545468999999999999999999999999876999996311102-453--0000000------0012 Q 537021.9.peg.7 8 EVIVAWRYLFSNRKNAFISIASFISFIGVMIGVMALIVVMSVMNGFREDMIKRVLGI-NGH--VVIQQKY------YPLV 78 (270) Q Consensus 8 ~~~iA~R~l~~~k~r~~~~~is~ls~lgI~igv~~li~~lsv~~G~~~~i~~~i~~~-~~~--i~i~~~~------~~~~ 78 (270) .+++|||+|+++|..++ +.++|.++|+++.+++.++.+.+ +.. -+.+ +++ ..+.... .... T Consensus 4 dlK~A~R~L~k~k~~s~------inI~gLalGi~~~~~if~~v~~~---~~~-~l~y~~~dri~~v~~~~~~~~~~~~~~ 73 (803) T TIGR03434 4 DLRYALRTLRRSPGFTA------VAVLTLALGIGANTAIFSVVNAV---LLR-PLPYPDPDRLVALWERGPGAGSPGGNF 73 (803) T ss_pred HHHHHHHHHHHCHHHHH------HHHHHHHHHHHHHHHHHHHHHHH---HCC-CCCCCCCCEEEEEEEECCCCCCCCCCC T ss_conf 89999999987748899------99999999999999999999999---556-889898451899998778888788888 Q ss_pred CHHHHHHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCC----CCCCCCCCCCHH Q ss_conf 1366655542264103466542001111122233221011124310000012001100277542----111123421013 Q 537021.9.peg.7 79 DYQFIANRLDFIPDVIKVLPFVSGQAFVSGLSSGGSGVLVRGISNSDFSYLQNSFSRFYGNVSN----DFDRGKGVIIGK 154 (270) Q Consensus 79 ~~~~~~~~l~~~~~V~~~~p~i~~~~~i~~~~~~~~~v~i~Gv~~~~~~~~~~~~~~~~~~~~~----~~~~~~~iiiG~ 154 (270) ......+..++.++++.+..+......+.. ++........-+||++++.+.-. ...|+... .....+.++|++ T Consensus 74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~vd~~fF~~f~~~--~l~Gr~~~~~~~~~~~~~~vvlS~ 150 (803) T TIGR03434 74 SYPDYEDWRAQNRSFSSLAAYSGASFNLTG-GGEPERVRGALVSANFFPVLGVQ--PALGRLFTPEDDRPGAPPVVVLSY 150 (803) T ss_pred CHHHHHHHHHHCHHHHHHHEEECCEEEECC-CCCCEEEEEEEECCCHHHHCCCC--CCCCCCCCCCHHCCCCCCEEEECH T ss_conf 978999999846167776704132058606-88744877899985369775986--025888895001369999899829 Q ss_pred HHHHHH-H-CC--CCCEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEECCCC-CCCEEEEEHHHHHHHCCCCC---CEEE Q ss_conf 454554-2-13--332023113442100012211000012210233102445-55168985488999718998---7107 Q 537021.9.peg.7 155 DLARNL-G-IS--IGDKINILSPYGDVTPMGMGIRSKSYTVLGMFRMRFPDY-DNGMVYMSLQEAQLYFNLEN---AVSG 226 (270) Q Consensus 155 ~lA~~L-~-l~--vGD~i~l~~~~~~~~~~~~~~~~~~f~V~GI~~sg~~~~-D~~~v~~~l~~~q~l~~~~~---~~~~ 226 (270) .+|+++ + -. +|.++.+ ..+.|+|+||+......- ...-+++|+...+......+ .... T Consensus 151 ~~a~k~Fg~d~~~iGkti~~--------------~~~~~~V~GV~p~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~ 216 (803) T TIGR03434 151 ALWQRRFGGDPAVVGRTIRL--------------NGRPYTVVGVMPPGFRFPGRDPDVWVPLAMDPALLAGADRGSHWLR 216 (803) T ss_pred HHHHHHHCCCCCCCCCEEEE--------------CCEEEEEEEEECCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCEEE T ss_conf 99999838992004887999--------------9977899999779878889885499987444100245788870289 Q ss_pred EEEEECCHHHHHHHHHHHHH Q ss_conf 99995698899999999998 Q 537021.9.peg.7 227 IEVFVKDPDAIEKTHENIVR 246 (270) Q Consensus 227 i~i~l~d~~~~~~~~~~i~~ 246 (270) ..+++++..+.+++.++++. T Consensus 217 ~~~~L~~g~~~~~~~~~l~~ 236 (803) T TIGR03434 217 VIGRLKPGVTLAQAQAELDA 236 (803) T ss_pred EEEEECCCCCHHHHHHHHHH T ss_conf 99996899999999999999 No 8 >COG3127 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism] Probab=98.66 E-value=5.9e-06 Score=53.02 Aligned_cols=222 Identities=14% Similarity=0.170 Sum_probs=124.3 Q ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCCCEEECCCCCCCCHHHHH Q ss_conf 47999999875225545468999999999999999999999999876999996311102-45300000000012136665 Q 537021.9.peg.7 6 RFEVIVAWRYLFSNRKNAFISIASFISFIGVMIGVMALIVVMSVMNGFREDMIKRVLGI-NGHVVIQQKYYPLVDYQFIA 84 (270) Q Consensus 6 ~~~~~iA~R~l~~~k~r~~~~~is~ls~lgI~igv~~li~~lsv~~G~~~~i~~~i~~~-~~~i~i~~~~~~~~~~~~~~ 84 (270) ++.+..++|..|+. +.|.-+ .+.++++|+++..+-|+...|++.+.++--.+ .+|+.... +.+.. ++.. T Consensus 5 p~a~R~~~RE~R~G--~~l~i~-----~~al~L~vAaiaA~~sls~rm~~gl~~qare~L~gD~~f~~-~r~~~--~~~~ 74 (829) T COG3127 5 PLALRWALREWRSG--RGLLIF-----LAALALAVAAIAALGSLSDRMEKGLAQQAREFLAGDRVFVS-NRPVP--PAER 74 (829) T ss_pred HHHHHHHHHHHHCC--CCHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEC-CCCCC--HHHH T ss_conf 78899999986049--846999-----99999999999988799999987788889998525568754-89899--8999 Q ss_pred HHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC--CCCCHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHC Q ss_conf 5542264103466542001111122233221011124310000--01200110027754211112342101345455421 Q 537021.9.peg.7 85 NRLDFIPDVIKVLPFVSGQAFVSGLSSGGSGVLVRGISNSDFS--YLQNSFSRFYGNVSNDFDRGKGVIIGKDLARNLGI 162 (270) Q Consensus 85 ~~l~~~~~V~~~~p~i~~~~~i~~~~~~~~~v~i~Gv~~~~~~--~~~~~~~~~~~~~~~~~~~~~~iiiG~~lA~~L~l 162 (270) +...+. + ..++-..+..+++-. ++...-+.+++||..|-- ++....+..............++.+...+-+.||+ T Consensus 75 ~~~~~~-G-l~~s~~~rf~a~~~~-g~~~qLv~vKAVD~aYPL~G~L~t~p~~~~~~~~~~~~~~~~~~v~p~Ll~~Lgl 151 (829) T COG3127 75 EEAAKL-G-LAVSATLRFMAMLFA-GDGQQLVEVKAVDDAYPLYGTLETAPQASLAELLGGKPQAGGVWVAPRLLERLGL 151 (829) T ss_pred HHHHHH-H-HHHHHHHHHHHHCCC-CCCCCEEEEEECCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCEEECHHHHHHHCC T ss_conf 999862-1-168889899986418-9855001454115657766520467665314664468888864336679998299 Q ss_pred CCCCEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEE----CCCCC-CCEEEEEHHHHHHHCCC--CCCEEEEEEEE--CC Q ss_conf 333202311344210001221100001221023310----24455-51689854889997189--98710799995--69 Q 537021.9.peg.7 163 SIGDKINILSPYGDVTPMGMGIRSKSYTVLGMFRMR----FPDYD-NGMVYMSLQEAQLYFNL--ENAVSGIEVFV--KD 233 (270) Q Consensus 163 ~vGD~i~l~~~~~~~~~~~~~~~~~~f~V~GI~~sg----~~~~D-~~~v~~~l~~~q~l~~~--~~~~~~i~i~l--~d 233 (270) |+||+|.+ ++ ..|+|.|..... ...|. ...++++++++.+- |. +|.--....++ .| T Consensus 152 kvGd~i~v----G~----------~tlri~~~v~~EPD~~~~~F~~APR~mi~~adl~~T-GlvQpGSrV~~~y~v~g~p 216 (829) T COG3127 152 KVGDRIDV----GD----------ATLRIAGEVTQEPDAGSNGFQFAPRLMISLADLDAT-GLVQPGSRVTYRYKVAGPP 216 (829) T ss_pred CCCCEEEE----CC----------CEEEEEEEECCCCCCCCCCCCCCCCEEEEHHHHHHC-CCCCCCCEEEEEEEECCCH T ss_conf 85754763----47----------327998776068865677301375203427443012-7777786047898725884 Q ss_pred HHHHHHHHHHHHHHCCC-CEEEE Q ss_conf 88999999999986199-85999 Q 537021.9.peg.7 234 PDAIEKTHENIVRILGN-GVVVI 255 (270) Q Consensus 234 ~~~~~~~~~~i~~~l~~-~~~v~ 255 (270) +......+....+.+|+ .+++. T Consensus 217 ~a~~~~~~~~~~~~~p~~rw~~~ 239 (829) T COG3127 217 NALIAYIKWQAPQLFPEQRWYIR 239 (829) T ss_pred HHHHHHHHHHHHCCCCCCCCCHH T ss_conf 88899999876400861344010 No 9 >COG0577 SalY ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms] Probab=98.52 E-value=3.2e-05 Score=48.85 Aligned_cols=229 Identities=20% Similarity=0.240 Sum_probs=129.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCEEECCCC-------CC------CCHHHHHHHHHCCCCHH Q ss_conf 99999999999999999999987699999631110245-300000000-------01------21366655542264103 Q 537021.9.peg.7 29 SFISFIGVMIGVMALIVVMSVMNGFREDMIKRVLGING-HVVIQQKYY-------PL------VDYQFIANRLDFIPDVI 94 (270) Q Consensus 29 s~ls~lgI~igv~~li~~lsv~~G~~~~i~~~i~~~~~-~i~i~~~~~-------~~------~~~~~~~~~l~~~~~V~ 94 (270) ++++++||++|+++++.++++..|++......+....+ .+.+.+... +. ...+.....+...+.+. T Consensus 4 ~~l~~~~i~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 83 (419) T COG0577 4 TLLTILGIIIGVALVVALLALGLGFRLTVLASLSDLGANTILVLPKKNNAIFTPNPLSTETLLGLAEDVIKILAFIFIVY 83 (419) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 59999999999999999999877678999999863468708998435543123220001234435788998766556665 Q ss_pred HHHHHHHCC--CCCCCCCCCCCCCCCCCCCCCCCC---CCCCHHHHCCCCCCCCCC----CCCCCCCHHHHHHHHHCCCC Q ss_conf 466542001--111122233221011124310000---012001100277542111----12342101345455421333 Q 537021.9.peg.7 95 KVLPFVSGQ--AFVSGLSSGGSGVLVRGISNSDFS---YLQNSFSRFYGNVSNDFD----RGKGVIIGKDLARNLGISIG 165 (270) Q Consensus 95 ~~~p~i~~~--~~i~~~~~~~~~v~i~Gv~~~~~~---~~~~~~~~~~~~~~~~~~----~~~~iiiG~~lA~~L~l~vG 165 (270) .+.+..... ..+.. ........+.|+++.... ..........|....... .....+++..+|+++..+.+ T Consensus 84 ~~~~~~~~~~~~~~~~-~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~ 162 (419) T COG0577 84 SVSFLLSSREEFGLLL-LGGLSKAQIVGLLFLENFLISVLAILLGIIEGRLFSKLFVLTIIKKSVVIGLELAEELFKKGP 162 (419) T ss_pred HHHHHHCCCCCEEEEE-CCCCCCEEEEEECCCHHHHHHHHHCCCCEECCEECCCHHHHHCCCEEEEECHHHHHHHCCCCC T ss_conf 3102202442136886-055023379960320000014443031123150023013332022035723688876222455 Q ss_pred --CEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCC------CCEEEEEHHHHHHHCCCCC-----CEEEEEEEEC Q ss_conf --20231134421000122110000122102331024455------5168985488999718998-----7107999956 Q 537021.9.peg.7 166 --DKINILSPYGDVTPMGMGIRSKSYTVLGMFRMRFPDYD------NGMVYMSLQEAQLYFNLEN-----AVSGIEVFVK 232 (270) Q Consensus 166 --D~i~l~~~~~~~~~~~~~~~~~~f~V~GI~~sg~~~~D------~~~v~~~l~~~q~l~~~~~-----~~~~i~i~l~ 232 (270) +.+......... ...++|+|+++......+ .+.+++|....+....... ..+.+.+... T Consensus 163 ~~~~~~~~~~~~~~--------~~~~~vig~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 234 (419) T COG0577 163 LLDGLGYTISINGL--------GLLFKVIGILKLFGSSLSASFSKLNNLILIPLSAFRLLLNARILFTVSSLSAVTITVA 234 (419) T ss_pred CCCCCCEEEEECCC--------CCEEEEEEEEECCCCCCCCCCCCCCCEEEEEHHHHHHHHHCCCCCCCCCCCEEEEEEC T ss_conf 33443407874045--------3037999998226543321123456459951688987752134222244306999961 Q ss_pred CHHHHHH----HHHHHHHHCCCC-----EEEEEHHHHHHHHHH Q ss_conf 9889999----999999861998-----599968998898999 Q 537021.9.peg.7 233 DPDAIEK----THENIVRILGNG-----VVVIDWQQRYQIFFS 266 (270) Q Consensus 233 d~~~~~~----~~~~i~~~l~~~-----~~v~~w~e~~~~lf~ 266 (270) +..+.+. +.+.+++.++.. +.+.+.++.-++.-+ T Consensus 235 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 277 (419) T COG0577 235 GVASIQEVSKKVAELLAERLSNKKESKDYDVKDIQKVLENLKS 277 (419) T ss_pred CCCHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEHHHHHHHHHH T ss_conf 6411667789999999987234565443455107878988999 No 10 >TIGR01185 devC DevC protein; InterPro: IPR005891 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This family contains a predicted membrane subunit, DevC, of an ABC transporter known so far from two species of cyanobacteria. Some experimental data from mutational analysis { suggest that this protein, along with DevA and DevB encoded in the same operon, may be involved in the transport/export of glycolipids.; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane. Probab=98.39 E-value=3.1e-06 Score=54.59 Aligned_cols=221 Identities=16% Similarity=0.234 Sum_probs=126.2 Q ss_pred HHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHCCCCCEEECCCC-CC-----CCH Q ss_conf 999875225545468999999999999999999999999876999996311----10245300000000-01-----213 Q 537021.9.peg.7 11 VAWRYLFSNRKNAFISIASFISFIGVMIGVMALIVVMSVMNGFREDMIKRV----LGINGHVVIQQKYY-PL-----VDY 80 (270) Q Consensus 11 iA~R~l~~~k~r~~~~~is~ls~lgI~igv~~li~~lsv~~G~~~~i~~~i----~~~~~~i~i~~~~~-~~-----~~~ 80 (270) |||..|++.|.| -..++.|||++ =+++.|- -||++.+.++- .++.||+.+-+... .. +.. T Consensus 3 L~W~QL~~E~~R------L~~A~AGIAFA--D~L~FMQ--~GF~~ALy~S~VR~~~SLQGD~~~l~~Q~~~~~~~~PF~~ 72 (381) T TIGR01185 3 LAWLQLTREKTR------LLVALAGIAFA--DVLIFMQ--LGFKDALYDSAVRLHKSLQGDLVLLSKQSDAVLAMKPFAA 72 (381) T ss_pred CHHHHHHHHHHH------HHHHHHHHHHH--HHHHHHH--HHHHHHHHHCCCCCCCCCCCCEEEEECCCCCCCCCCCHHH T ss_conf 415688888999------99998768999--9999986--3045654311245453345567888335342005896346 Q ss_pred HHHHHHHHCCCCHHHHHHHHHCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCHH----- Q ss_conf 66655542264103466542001111122-233221011124310000012001100277542111123421013----- Q 537021.9.peg.7 81 QFIANRLDFIPDVIKVLPFVSGQAFVSGL-SSGGSGVLVRGISNSDFSYLQNSFSRFYGNVSNDFDRGKGVIIGK----- 154 (270) Q Consensus 81 ~~~~~~l~~~~~V~~~~p~i~~~~~i~~~-~~~~~~v~i~Gv~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiiG~----- 154 (270) ..+ -+-.+++.|.+++|.+-.-..=++. -+-++.+.++|++|+.--- +. ....++.+. .+..+.++--. T Consensus 73 RRL-Y~~l~~~SV~~~~~~Y~D~~~WKNP~T~~~R~I~~~G~NP~~N~~--NL-~GV~ENLD~-~K~PD~~LFD~~SR~E 147 (381) T TIGR01185 73 RRL-YKALELASVKDVTSLYLDISIWKNPETKLSRSILVFGINPVTNII--NL-AGVAENLDK-LKLPDVVLFDRDSREE 147 (381) T ss_pred HHH-HHHHCCCCCCCCCEEEEECCCCCCCCCCCEEEEEEEEECCCCCCC--CC-CCHHHHHHH-HCCCCEEEECCCCCCC T ss_conf 789-998368742356327873234548887650378987106765664--56-633443443-1589667730677743 Q ss_pred --HHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEECC-CCCCCEEEEEHHHHHHHCCCC-CCEEEEEEE Q ss_conf --4545542133320231134421000122110000122102331024-455516898548899971899-871079999 Q 537021.9.peg.7 155 --DLARNLGISIGDKINILSPYGDVTPMGMGIRSKSYTVLGMFRMRFP-DYDNGMVYMSLQEAQLYFNLE-NAVSGIEVF 230 (270) Q Consensus 155 --~lA~~L~l~vGD~i~l~~~~~~~~~~~~~~~~~~f~V~GI~~sg~~-~~D~~~v~~~l~~~q~l~~~~-~~~~~i~i~ 230 (270) .+|+.+ .-|..|. ...+.+..+|.|+|.-|.+ .-|.+.+--++..++-+=.+. +.+..=.++ T Consensus 148 yGP~~~~l--E~~~~~~------------~EV~~RRI~V~GLFTLG~SFGADG~L~TSD~NFlRLFP~R~~~~ID~G~~~ 213 (381) T TIGR01185 148 YGPVAKLL--EADQSVS------------AEVRRRRINVVGLFTLGASFGADGNLVTSDLNFLRLFPLRDRSLIDIGLLR 213 (381) T ss_pred CCCCHHHH--CCCCCEE------------EEECCEEEEEEEEEEECCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEEEE T ss_conf 47524663--2889466------------623253788887653064415787403432466742777565541034454 Q ss_pred ECCHHHHHHHHHHHHHHCCC-CEEEEEHHHH Q ss_conf 56988999999999986199-8599968998 Q 537021.9.peg.7 231 VKDPDAIEKTHENIVRILGN-GVVVIDWQQR 260 (270) Q Consensus 231 l~d~~~~~~~~~~i~~~l~~-~~~v~~w~e~ 260 (270) +|...+.+.++++|++.+++ +..|.|-++. T Consensus 214 LKPG~~P~~~~~E~R~~L~~GD~~VlTK~~l 244 (381) T TIGR01185 214 LKPGVDPEKVVEELRSELTDGDVNVLTKEKL 244 (381) T ss_pred CCCCCCHHHHHHHHHHHCCCCCCEEHHHHHH T ss_conf 0698888899999986468764020205788 No 11 >COG3127 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism] Probab=97.84 E-value=0.0012 Score=39.86 Aligned_cols=228 Identities=12% Similarity=0.144 Sum_probs=106.4 Q ss_pred HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHCCCCC---EEECCCCCCCCH Q ss_conf 347999999875225545468999999999999999999999999876-9999963111024530---000000001213 Q 537021.9.peg.7 5 SRFEVIVAWRYLFSNRKNAFISIASFISFIGVMIGVMALIVVMSVMNG-FREDMIKRVLGINGHV---VIQQKYYPLVDY 80 (270) Q Consensus 5 ~~~~~~iA~R~l~~~k~r~~~~~is~ls~lgI~igv~~li~~lsv~~G-~~~~i~~~i~~~~~~i---~i~~~~~~~~~~ 80 (270) ++.+|.+|.-++.|.+.-+. .-.+...+|.|.|.+ +.+..| ..+..++++=.-.|+. .|++.+ . T Consensus 452 ~s~~lRLal~~l~R~~~~t~------sq~~algLgl~LLa~-l~lirgdLl~~wq~~lP~~APN~F~vnI~~~q-----v 519 (829) T COG3127 452 TSLALRLALGNLLRPGAATP------SQVLALGLGLMLLAL-LALIRGDLLRQWQQQLPPDAPNFFFVNIQPSQ-----V 519 (829) T ss_pred CCHHHHHHHHHHCCCCCCCH------HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHCCCCCCCEEEEECCHHH-----H T ss_conf 63668999887427875527------889998999999999-99973179999987589878774787268655-----1 Q ss_pred HHHHHHHHC-CCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC------------CCCCCCCCHHHHCCCCCCCCCC-C Q ss_conf 666555422-6410346654200111112223322101112431------------0000012001100277542111-1 Q 537021.9.peg.7 81 QFIANRLDF-IPDVIKVLPFVSGQAFVSGLSSGGSGVLVRGISN------------SDFSYLQNSFSRFYGNVSNDFD-R 146 (270) Q Consensus 81 ~~~~~~l~~-~~~V~~~~p~i~~~~~i~~~~~~~~~v~i~Gv~~------------~~~~~~~~~~~~~~~~~~~~~~-~ 146 (270) ......+.+ .++=....|.+.+.-+-.+.+... =++++| .+..+.........|..+.... . T Consensus 520 a~f~a~l~~~~~~~~~~~PmvrGRl~aiNGq~v~----~~~~~~~~~~al~rd~~LT~~~~~P~~n~l~aG~Ww~~~~~g 595 (829) T COG3127 520 APFSALLAGASPEGETFYPMVRGRLTAINGQPVT----EMSVPPSARWALRRDLNLTWAEKRPENNPLTAGRWWPKNDSG 595 (829) T ss_pred HHHHHHHHHCCCCCCCCCCEEEEEEEEECCCCCC----CCCCCCHHHHHHHCCCCCCHHHCCCCCCCCCCCCCCCCCCCC T ss_conf 5799997424887655565022057776584675----246892578888234476003008998863556588988889 Q ss_pred CCCCCCHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEECCCC--CCCEEEEEHHHHHHHCCCCCCE Q ss_conf 23421013454554213332023113442100012211000012210233102445--5516898548899971899871 Q 537021.9.peg.7 147 GKGVIIGKDLARNLGISIGDKINILSPYGDVTPMGMGIRSKSYTVLGMFRMRFPDY--DNGMVYMSLQEAQLYFNLENAV 224 (270) Q Consensus 147 ~~~iiiG~~lA~~L~l~vGD~i~l~~~~~~~~~~~~~~~~~~f~V~GI~~sg~~~~--D~~~v~~~l~~~q~l~~~~~~~ 224 (270) .+++-...++|++||+|+||++|+..-..+.+ -+|..+=+....++ |-.++|-| .+++ +.+- T Consensus 596 ~P~VS~e~~~A~~LglKLGDtvTf~v~gq~i~----------A~I~slR~VeWesl~pNF~~IF~P-~tl~---g~P~-- 659 (829) T COG3127 596 EPEVSMEEGEAKRLGLKLGDTVTFMVLGQNIT----------AKITSLRKVEWESLRPNFYMIFSP-GTLD---GAPQ-- 659 (829) T ss_pred CCCCCHHHHHHHHHCCCCCCEEEEEECCCEEE----------EEECEEEEECCCCCCCCEEEEECC-HHHC---CCCH-- T ss_conf 97440208679870976277799984262677----------651102232000256557999682-1104---7744-- Q ss_pred EEEEEEECCHHHHHHHHHHHHHHCCCCEEEEEHHH---HHHHHHH Q ss_conf 07999956988999999999986199859996899---8898999 Q 537021.9.peg.7 225 SGIEVFVKDPDAIEKTHENIVRILGNGVVVIDWQQ---RYQIFFS 266 (270) Q Consensus 225 ~~i~i~l~d~~~~~~~~~~i~~~l~~~~~v~~w~e---~~~~lf~ 266 (270) +.+ .....|...+.+-.++.+.+|. ..+.+-++ +-..+++ T Consensus 660 twl-tsfr~~~~~~~~l~ql~r~fPt-vt~v~v~~~L~~v~~ll~ 702 (829) T COG3127 660 TWL-TSFRIPNGQAALLRQLTRAFPT-VTLVDVGAALDQVNQLLD 702 (829) T ss_pred HHH-EEEECCCCCHHHHHHHHHHCCC-EEEEEHHHHHHHHHHHHH T ss_conf 053-1255678516799999872896-178669999999999999 No 12 >TIGR03434 ADOP Acidobacterial duplicated orphan permease. Members of this protein family are found, so far, only in three species of Acidobacteria, namely Acidobacteria bacterium Ellin345, Acidobacterium capsulatum ATCC 51196, and Solibacter usitatus Ellin6076, where they form large paralogous families. Each protein contains two copies of a domain called the efflux ABC transporter permease protein (pfam02687). However, unlike other members of that family (including LolC, FtsX, and MacB), genes for these proteins are essentially never found fused or adjacent to ABC transporter ATP-binding protein (pfam00005) genes. We name this family ADOP, for Acidobacterial Duplicated Orphan Permease, to reflect the restricted lineage, internal duplication, lack of associated ATP-binding cassette proteins, and permease homology. The function is unknown. Probab=97.76 E-value=0.0026 Score=38.00 Aligned_cols=169 Identities=18% Similarity=0.154 Sum_probs=86.2 Q ss_pred HHHHHHHHHCCCCHHHHHHHHHCC--------C-CCCC----CCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCC--CC Q ss_conf 366655542264103466542001--------1-1112----2233221011124310000012001100277542--11 Q 537021.9.peg.7 80 YQFIANRLDFIPDVIKVLPFVSGQ--------A-FVSG----LSSGGSGVLVRGISNSDFSYLQNSFSRFYGNVSN--DF 144 (270) Q Consensus 80 ~~~~~~~l~~~~~V~~~~p~i~~~--------~-~i~~----~~~~~~~v~i~Gv~~~~~~~~~~~~~~~~~~~~~--~~ 144 (270) .+.+.+++++.|+|++++..-... . .+.+ ..+....+....+|+++++..... ...|.... +. T Consensus 478 ~~~l~~~l~~~pgV~~vs~s~~~p~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~v~~~y~~~~gi~--ll~Gr~f~~~d~ 555 (803) T TIGR03434 478 YRRLLERLRALPGVESAALASSLPLGGNGWSTGVTIEGRPPPPPGEEPLALYRRVSPGYFETMGIP--LLRGRDFTERDT 555 (803) T ss_pred HHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCEEEECCCCCCCCCCCCEEEEEEECHHHHHHHCCE--EECCCCCCCHHC T ss_conf 999999985589843898762577668888851687782478877561256665478489880980--524888980012 Q ss_pred CC-CCCCCCHHHHHHHH---HCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCEEEEE---EC-CCCCCCEEEEEHHHHHH Q ss_conf 11-23421013454554---2133320231134421000122110000122102331---02-44555168985488999 Q 537021.9.peg.7 145 DR-GKGVIIGKDLARNL---GISIGDKINILSPYGDVTPMGMGIRSKSYTVLGMFRM---RF-PDYDNGMVYMSLQEAQL 216 (270) Q Consensus 145 ~~-~~~iiiG~~lA~~L---~l~vGD~i~l~~~~~~~~~~~~~~~~~~f~V~GI~~s---g~-~~~D~~~v~~~l~~~q~ 216 (270) .. .+.+++.+.+|+++ +-.+|.++.+-.. ....++|+||++- +. .+--...+|+|.. T Consensus 556 ~~~~~~~iine~~a~~l~~~~~~iG~~~~~~~~-----------~~~~~~IvGVv~D~~~~s~~~~~~p~v~~~~~---- 620 (803) T TIGR03434 556 AGSPPVAIVNEAFARRYFPGEDPIGKRIRLGGD-----------DGPWYEIVGVVGDVRYAGLDEPPRPEVYLPYA---- 620 (803) T ss_pred CCCCCEEEECHHHHHHHCCCCCCCCCEEEECCC-----------CCCEEEEEEEECCCCCCCCCCCCCCEEEEECC---- T ss_conf 689837998799999747988988778985588-----------99705999998875246777888866999713---- Q ss_pred HCCCCCCEEEEEEEEC-CHHH-HHHHHHHHHHHCCC-C-EEEEEHHHHHHHHHHH Q ss_conf 7189987107999956-9889-99999999986199-8-5999689988989998 Q 537021.9.peg.7 217 YFNLENAVSGIEVFVK-DPDA-IEKTHENIVRILGN-G-VVVIDWQQRYQIFFSC 267 (270) Q Consensus 217 l~~~~~~~~~i~i~l~-d~~~-~~~~~~~i~~~l~~-~-~~v~~w~e~~~~lf~a 267 (270) ........+.++.. |+.. .+.+.+.+++..|+ . +.+.+..|.....|.. T Consensus 621 --~~~~~~~~i~v~~~~~~~~~~~~i~~~~~~~~p~~~~~~~~~l~~~~~~~~~~ 673 (803) T TIGR03434 621 --QSPSRGMTLVVRTAGDPAALAAAVRRAVRAIDPNLPVYNVRTMEEQVDDSLAQ 673 (803) T ss_pred --CCCCCCEEEEEECCCCHHHHHHHHHHHHHHHCCCCCCEEEECHHHHHHHHHHH T ss_conf --58888659999858999999999999999868999840103099999999887 No 13 >PRK11026 ftsX cell division protein FtsX; Provisional Probab=94.78 E-value=0.11 Score=28.78 Aligned_cols=93 Identities=12% Similarity=0.060 Sum_probs=46.2 Q ss_pred HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCC-CCCCHHHH Q ss_conf 34799999987522554546899999999999999999999999987699999631110245300000000-01213666 Q 537021.9.peg.7 5 SRFEVIVAWRYLFSNRKNAFISIASFISFIGVMIGVMALIVVMSVMNGFREDMIKRVLGINGHVVIQQKYY-PLVDYQFI 83 (270) Q Consensus 5 ~~~~~~iA~R~l~~~k~r~~~~~is~ls~lgI~igv~~li~~lsv~~G~~~~i~~~i~~~~~~i~i~~~~~-~~~~~~~~ 83 (270) +++.+.=|+++++|++--++. |+++ ++|++........ +....+ .+.++. .-..++.|.-..+ +..+.+.+ T Consensus 13 ~ry~l~eal~~l~Rn~~~sl~---ti~~-iaisL~l~g~~~l--~~~Nv~-~~~~~~-~~~~~IsvfL~~~~~~~~~~~l 84 (309) T PRK11026 13 VRYAWHGALADLKRKPFATFL---TVMV-IAISLTLPSVCYL--VWKNVN-QAATQF-YPSPQLTVYLHKTLDDDAANAV 84 (309) T ss_pred HHHHHHHHHHHHHCCHHHHHH---HHHH-HHHHHHHHHHHHH--HHHHHH-HHHHHH-CCCCEEEEEECCCCCHHHHHHH T ss_conf 999999999998706999999---9999-9999999999999--999999-999963-6684599987899899999999 Q ss_pred HHHHHCCCCHHHHHHHHHCCCC Q ss_conf 5554226410346654200111 Q 537021.9.peg.7 84 ANRLDFIPDVIKVLPFVSGQAF 105 (270) Q Consensus 84 ~~~l~~~~~V~~~~p~i~~~~~ 105 (270) .+++++.|+|+.+.-.-..+|+ T Consensus 85 ~~~l~~~~~V~~v~~vskeeAl 106 (309) T PRK11026 85 VEQLRAEQGVEKVNYLSREEAL 106 (309) T ss_pred HHHHHCCCCCCEEEEECHHHHH T ss_conf 9998657884379886799999 No 14 >COG2177 FtsX Cell division protein [Cell division and chromosome partitioning] Probab=86.39 E-value=2.3 Score=21.30 Aligned_cols=89 Identities=15% Similarity=0.089 Sum_probs=39.0 Q ss_pred HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCCC-CCCHHHH Q ss_conf 347999999875225545468999999999999999999999999876999996311102453000000000-1213666 Q 537021.9.peg.7 5 SRFEVIVAWRYLFSNRKNAFISIASFISFIGVMIGVMALIVVMSVMNGFREDMIKRVLGINGHVVIQQKYYP-LVDYQFI 83 (270) Q Consensus 5 ~~~~~~iA~R~l~~~k~r~~~~~is~ls~lgI~igv~~li~~lsv~~G~~~~i~~~i~~~~~~i~i~~~~~~-~~~~~~~ 83 (270) +.+.+.=+++.++++... ++.++..|++..+...+.+.+..-.++ ..+.. ..+.+++++-.... ..+.+.+ T Consensus 6 ~~~~~~~~l~~l~r~~~~------t~a~v~~vaitl~L~~~~~l~~~nv~~-~a~~~-~~~v~i~vyL~~~~~~~~~~~v 77 (297) T COG2177 6 FGYHLREALKGLPRNPWM------TFATVSVVAITLFLPGVFLLVVLNVNS-LATQW-ESQVEITVYLQIDADQDDAALV 77 (297) T ss_pred HHHHHHHHHHHCCCCCHH------HHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHH-HCCCEEEEEEECCCCHHHHHHH T ss_conf 999999998644556568------899999999999999999999999999-99863-2162589997368786889999 Q ss_pred HHHHHCCCCHHHHHHHHH Q ss_conf 555422641034665420 Q 537021.9.peg.7 84 ANRLDFIPDVIKVLPFVS 101 (270) Q Consensus 84 ~~~l~~~~~V~~~~p~i~ 101 (270) .++++..|+|+++.-.-+ T Consensus 78 ~~~i~~~~gV~~v~~~sr 95 (297) T COG2177 78 REKIEGIPGVKSVRFISR 95 (297) T ss_pred HHHHHCCCCCCEEEEECH T ss_conf 999846899644787679 No 15 >TIGR01553 formate-DH-alph formate dehydrogenase, alpha subunit; InterPro: IPR006443 This family of sequences describe a subset of formate dehydrogenase alpha chains found mainly in proteobacteria but also in Aquifex aeolicus. The alpha chain contains domains for molybdopterin dinucleotide binding and molybdopterin oxidoreductase. The holo-enzyme also contains beta and gamma subunits of 32 and 20 kDa. The enzyme catalyzes the oxidation of formate (produced from pyruvate during anaerobic growth) to carbon dioxide with the concomitant release of two electrons and two protons. The electrons are utilised mainly in the nitrate respiration by nitrate reductase . In Escherichia coli and Salmonella typhi, there are two forms of the formate dehydrogenase, one induced by nitrate which is strictly anaerobic (fdn), and one incuced during the transition from aerobic to anaerobic growth (fdo). This subunit is one of only three proteins in Escherichia coli which contain selenocysteine .; GO: 0008863 formate dehydrogenase activity, 0045333 cellular respiration, 0005737 cytoplasm. Probab=80.42 E-value=1.4 Score=22.59 Aligned_cols=42 Identities=29% Similarity=0.468 Sum_probs=18.4 Q ss_pred CHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCC-CCCCCCCCE Q ss_conf 013454554213332023113442100012211-000012210 Q 537021.9.peg.7 152 IGKDLARNLGISIGDKINILSPYGDVTPMGMGI-RSKSYTVLG 193 (270) Q Consensus 152 iG~~lA~~L~l~vGD~i~l~~~~~~~~~~~~~~-~~~~f~V~G 193 (270) ||++||..=|++-||.|.|.+-++...+....- |.|.|+|.| T Consensus 948 i~EeLA~ekGI~nGD~V~~~s~Rg~i~A~A~vTKRiKpl~i~G 990 (1043) T TIGR01553 948 ISEELAKEKGIQNGDLVKVESVRGKIKAVAVVTKRIKPLKIDG 990 (1043) T ss_pred CCHHHHHHCCCCCCCEEEEEECCEEEEEEEEEEECCCCCEECC T ss_conf 3358885448654786899722514899999730467513268 No 16 >PRK10549 signal transduction histidine-protein kinase BaeS; Provisional Probab=77.43 E-value=5.1 Score=19.33 Aligned_cols=31 Identities=19% Similarity=0.211 Sum_probs=18.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999999999998769999963 Q 537021.9.peg.7 29 SFISFIGVMIGVMALIVVMSVMNGFREDMIK 59 (270) Q Consensus 29 s~ls~lgI~igv~~li~~lsv~~G~~~~i~~ 59 (270) +++++..+++..+.+.+-+++-.||.+.+.+ T Consensus 15 ~~~~~~~~~~~~~~~~~~~~f~~~f~~y~~~ 45 (467) T PRK10549 15 AIFATCIVLLITMHWAVRISFERGFIDYIKH 45 (467) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999999999999999999999989999999 No 17 >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=72.47 E-value=2.7 Score=20.94 Aligned_cols=90 Identities=19% Similarity=0.348 Sum_probs=53.8 Q ss_pred HHHHHHHHCCCCHHHHHHHHHCCCCCCCCC--CCCCC--CCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCC-CCCCCHHH Q ss_conf 666555422641034665420011111222--33221--01112431000001200110027754211112-34210134 Q 537021.9.peg.7 81 QFIANRLDFIPDVIKVLPFVSGQAFVSGLS--SGGSG--VLVRGISNSDFSYLQNSFSRFYGNVSNDFDRG-KGVIIGKD 155 (270) Q Consensus 81 ~~~~~~l~~~~~V~~~~p~i~~~~~i~~~~--~~~~~--v~i~Gv~~~~~~~~~~~~~~~~~~~~~~~~~~-~~iiiG~~ 155 (270) ..+..+|.++.+...-+-.++...+- + + .-.-| |.|.-.+.+.... -.+.|....++..+ .-|=+.+. T Consensus 52 ~~~E~RI~~le~~l~~A~vi~~~~~~-~-~gd~V~~G~~V~~~~~~~~e~~~-----y~IVG~~EaD~~~giekIS~~SP 124 (155) T TIGR01462 52 GFIEGRIAELEDLLANAEVIDDSKLS-T-DGDKVSFGSTVTIKDEDTGEEET-----YTIVGSWEADPKEGIEKISIESP 124 (155) T ss_pred HHHHHHHHHHHHHHHCEEECCHHHCC-C-CCCEEECCCEEEEEECCCCCEEE-----EEEECCCCCCHHCCCEEEECCCH T ss_conf 99988999999887620623601004-7-88377157589999838996489-----99834520553308078226770 Q ss_pred HHHHH-HCCCCCEEEECCCCCCC Q ss_conf 54554-21333202311344210 Q 537021.9.peg.7 156 LARNL-GISIGDKINILSPYGDV 177 (270) Q Consensus 156 lA~~L-~l~vGD~i~l~~~~~~~ 177 (270) ||+.| |-++||.+.+-.|.+.. T Consensus 125 lg~aL~Gkk~GD~~~v~~P~g~~ 147 (155) T TIGR01462 125 LGKALIGKKVGDEVEVQVPKGEK 147 (155) T ss_pred HHHHHCCCCCCCEEEEEECCCEE T ss_conf 23533376258778998589237 No 18 >pfam11688 DUF3285 Protein of unknown function (DUF3285). This family of proteins with unknown function appears to be restricted to Cyanobacteria. Probab=71.51 E-value=7.3 Score=18.46 Aligned_cols=33 Identities=12% Similarity=0.338 Sum_probs=21.3 Q ss_pred HHHHHHHHHCCCCCCHHHH-HHHHHHHHHHHHHH Q ss_conf 9999987522554546899-99999999999999 Q 537021.9.peg.7 9 VIVAWRYLFSNRKNAFISI-ASFISFIGVMIGVM 41 (270) Q Consensus 9 ~~iA~R~l~~~k~r~~~~~-is~ls~lgI~igv~ 41 (270) .++|-||.-|+.+.++.-| ++.+..+|..+|++ T Consensus 8 vKLAMRNMVRKg~~SL~HF~LT~~gll~~lv~la 41 (45) T pfam11688 8 VKLAMRNMVRKGGKSLLHFGLTALGLLGFLVLIA 41 (45) T ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH T ss_conf 9999999998068400568999999999999999 No 19 >TIGR02609 doc_partner putative addiction module antidote; InterPro: IPR013432 This entry contains putative addiction module antidote proteins encoded by genes that appear recurrently in two-gene operons where the other gene encodes a Doc (death-on-curing) protein IPR006440 from INTERPRO. Note that these proteins tend to be found on bacterial chromosomes, not on plasmids.. Probab=67.44 E-value=2.7 Score=20.90 Aligned_cols=25 Identities=28% Similarity=0.490 Sum_probs=21.1 Q ss_pred CCCCCCHHHHHHHHHCCCCCEEEEC Q ss_conf 2342101345455421333202311 Q 537021.9.peg.7 147 GKGVIIGKDLARNLGISIGDKINIL 171 (270) Q Consensus 147 ~~~iiiG~~lA~~L~l~vGD~i~l~ 171 (270) +-++.|.+++.+.||++-||++.++ T Consensus 9 S~vv~lpKE~l~~L~~~~GDtl~i~ 33 (77) T TIGR02609 9 SLVVTLPKEVLESLGLKEGDTLEIY 33 (77) T ss_pred CEEEEECHHHHHHCCCCCCCEEEEE T ss_conf 1226747488974689999827899 No 20 >COG4771 FepA Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism] Probab=67.36 E-value=2 Score=21.65 Aligned_cols=60 Identities=18% Similarity=0.266 Sum_probs=31.1 Q ss_pred HHHHHHHHHHHHHCCCCCE-EECCCCCCCCHHHHHHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 7699999631110245300-00000001213666555422641034665420011111222332210111243100 Q 537021.9.peg.7 51 NGFREDMIKRVLGINGHVV-IQQKYYPLVDYQFIANRLDFIPDVIKVLPFVSGQAFVSGLSSGGSGVLVRGISNSD 125 (270) Q Consensus 51 ~G~~~~i~~~i~~~~~~i~-i~~~~~~~~~~~~~~~~l~~~~~V~~~~p~i~~~~~i~~~~~~~~~v~i~Gv~~~~ 125 (270) .|+++.+.+.= +-|. |...+-.-..+.++.+.|+.+|+|.-. +.......+.|+|+.|++ T Consensus 41 s~~eQ~lk~AP----aSVSvIT~edlqk~p~rDl~ealr~vpGV~lt-----------g~~G~nr~IsIRGM~~~y 101 (699) T COG4771 41 SGAEQNLKDAP----ASVSVITAEDLQKRPYRDLAEALRTVPGVNLT-----------GNRGNNRQISIRGMGPEY 101 (699) T ss_pred HHHHHHHHCCC----CEEEEEEHHHHHHCCHHHHHHHHHCCCCEEEE-----------CCCCCCCCEEEECCCCCC T ss_conf 24556765188----43789729985226411399998428964776-----------667875635771168753 No 21 >TIGR01425 SRP54_euk signal recognition particle protein SRP54; InterPro: IPR006325 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes , . SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor . In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. This entry represents the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species.; GO: 0005525 GTP binding, 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle. Probab=64.52 E-value=0.81 Score=23.87 Aligned_cols=65 Identities=12% Similarity=0.157 Sum_probs=44.3 Q ss_pred CCCCEEEEEHHHHHHHCCCCCCEEEEEEEECCHHHHHHHH--HHHHHHCCCCEEEEEHHHHHHHHHHH Q ss_conf 5551689854889997189987107999956988999999--99998619985999689988989998 Q 537021.9.peg.7 202 YDNGMVYMSLQEAQLYFNLENAVSGIEVFVKDPDAIEKTH--ENIVRILGNGVVVIDWQQRYQIFFSC 267 (270) Q Consensus 202 ~D~~~v~~~l~~~q~l~~~~~~~~~i~i~l~d~~~~~~~~--~~i~~~l~~~~~v~~w~e~~~~lf~a 267 (270) +|+--.|=+-....+|||+.| +.++.=+++|....++-. .-|+++-.-.+-+++|+||.+||.+. T Consensus 299 v~d~E~F~~~~FvskLLGmGD-l~GL~~~v~~l~~~~~~~hk~li~~L~eG~fTlRd~~eQ~~NllKM 365 (453) T TIGR01425 299 VDDFEIFDAEPFVSKLLGMGD-LKGLIDKVQDLKLDDEEKHKELIEKLKEGTFTLRDLYEQFQNLLKM 365 (453) T ss_pred CCCCCCCCCCCHHHHHCCCCC-HHHHHHHHHHHCHHCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHC T ss_conf 276057899714775402021-8899999975142103107999999835961068899999876311 No 22 >cd02792 MopB_CT_Formate-Dh-Na-like Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the major electron donor to the nitrate respiratory chain. Also included in this CD is the Desulfovibrio gigas tungsten formate dehydrogenase, DgW-FDH. In contrast to Fdh-N, which is a functional heterotrimer, DgW-FDH is a heterodimer. The DgW-FDH complex is composed of a large subunit carrying the W active site and one [4Fe-4S] center, and a small subunit that harbors a series of three [4Fe-4S] clusters as well as a putative vacant binding site for a fourth cluster. The smaller subunit is not included in this alignment. This CD (MopB_CT_Formate-Dh-Na-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=62.77 E-value=7.1 Score=18.55 Aligned_cols=54 Identities=24% Similarity=0.213 Sum_probs=35.9 Q ss_pred CCCCCHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCEEEEEHHHHHH Q ss_conf 342101345455421333202311344210001221100001221023310244555168985488999 Q 537021.9.peg.7 148 KGVIIGKDLARNLGISIGDKINILSPYGDVTPMGMGIRSKSYTVLGMFRMRFPDYDNGMVYMSLQEAQL 216 (270) Q Consensus 148 ~~iiiG~~lA~~L~l~vGD~i~l~~~~~~~~~~~~~~~~~~f~V~GI~~sg~~~~D~~~v~~~l~~~q~ 216 (270) +-+-|....|++||++-||.|.+.++.+.... +.+|. ..+....+|+|.-+... T Consensus 35 ~~v~i~p~dA~~lgi~dGd~V~v~s~~G~i~~--------~a~vt-------~~v~~g~vf~p~h~~~~ 88 (122) T cd02792 35 MFVEISPELAAERGIKNGDMVWVSSPRGKIKV--------KALVT-------DRVKPHEVGIPYHWGGM 88 (122) T ss_pred CEEEECHHHHHHCCCCCCCEEEEECCCEEEEE--------EEEEC-------CCCCCCEEEEECCCCCC T ss_conf 89999999998749988988999889989999--------99988-------99789979996202765 No 23 >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=58.17 E-value=5.2 Score=19.28 Aligned_cols=26 Identities=27% Similarity=0.634 Sum_probs=22.8 Q ss_pred CCCCCCHHHHHHHHHCCCCCEEEECC Q ss_conf 23421013454554213332023113 Q 537021.9.peg.7 147 GKGVIIGKDLARNLGISIGDKINILS 172 (270) Q Consensus 147 ~~~iiiG~~lA~~L~l~vGD~i~l~~ 172 (270) ...|+|-+.+-++||++-||.+.+.. T Consensus 7 kG~i~IPK~iR~~lgl~eGd~l~~~~ 32 (44) T TIGR01439 7 KGQIVIPKEIREKLGLKEGDKLEVIR 32 (44) T ss_pred CCEEEECHHHHHHCCCCCCCEEEEEE T ss_conf 76299273896406999998788988 No 24 >cd02789 MopB_CT_FmdC-FwdD The MopB_FmdC-FwdD CD includes the C-terminus of subunit C of molybdenum formylmethanofuran dehydrogenase (FmdC) and subunit D of tungsten formylmethanofuran dehydrogenase (FwdD), and other related proteins. Formylmethanofuran dehydrogenase catalyzes the first step in methane formation from CO2 in methanogenic archaea and some eubacteria. Members of this CD belong to the molybdopterin_binding superfamily of proteins. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=54.75 E-value=12 Score=17.18 Aligned_cols=57 Identities=25% Similarity=0.366 Sum_probs=36.5 Q ss_pred CCCCHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCEEEEEHH-HHHHHCCC Q ss_conf 4210134545542133320231134421000122110000122102331024455516898548-89997189 Q 537021.9.peg.7 149 GVIIGKDLARNLGISIGDKINILSPYGDVTPMGMGIRSKSYTVLGMFRMRFPDYDNGMVYMSLQ-EAQLYFNL 220 (270) Q Consensus 149 ~iiiG~~lA~~L~l~vGD~i~l~~~~~~~~~~~~~~~~~~f~V~GI~~sg~~~~D~~~v~~~l~-~~q~l~~~ 220 (270) -+-|.-.=|++||++-||.|.+.+..+.. .+..... .+.-...+|||.. ++..+.+- T Consensus 32 ~~~i~P~D~~~lGi~~Gd~V~v~s~~G~v------------v~~a~~~---~~v~~G~vFmP~g~waN~lv~~ 89 (106) T cd02789 32 YCEINPEDYKLLGKPEGDKVKVTSEFGEV------------VVFAKEN---EGVPEGMVFIPMGPWANVVVDP 89 (106) T ss_pred EEEECHHHHHHCCCCCCCEEEEECCCEEE------------EEEEEEC---CCCCCCEEEEECCHHHHEEECC T ss_conf 99989999998098999999998798789------------9999989---9988996997566676020186 No 25 >PRK01885 greB transcription elongation factor GreB; Reviewed Probab=53.84 E-value=11 Score=17.56 Aligned_cols=47 Identities=23% Similarity=0.366 Sum_probs=31.2 Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHH-HCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCEE Q ss_conf 277542111123421013454554-2133320231134421000122110000122102 Q 537021.9.peg.7 137 YGNVSNDFDRGKGVIIGKDLARNL-GISIGDKINILSPYGDVTPMGMGIRSKSYTVLGM 194 (270) Q Consensus 137 ~~~~~~~~~~~~~iiiG~~lA~~L-~l~vGD~i~l~~~~~~~~~~~~~~~~~~f~V~GI 194 (270) .|....++.. +.|-..+.+++.| |-++||+|++-.|.+.. +|+|..| T Consensus 109 VG~~Ead~~~-g~IS~~SPlg~ALlGkk~Gd~V~v~~P~G~~----------~~~Il~I 156 (159) T PRK01885 109 VGPDEIDGRK-GYISIDSPMARALLKKEVGDEVTVNTPAGEA----------EWYVNEI 156 (159) T ss_pred ECHHHCCCCC-CCCCCCCHHHHHHHCCCCCCEEEEECCCCCE----------EEEEEEE T ss_conf 4824426667-8222469899998389999989998599978----------9999999 No 26 >PRK00226 greA transcription elongation factor GreA; Reviewed Probab=51.48 E-value=13 Score=17.07 Aligned_cols=47 Identities=23% Similarity=0.548 Sum_probs=30.1 Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHH-HCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCEE Q ss_conf 277542111123421013454554-2133320231134421000122110000122102 Q 537021.9.peg.7 137 YGNVSNDFDRGKGVIIGKDLARNL-GISIGDKINILSPYGDVTPMGMGIRSKSYTVLGM 194 (270) Q Consensus 137 ~~~~~~~~~~~~~iiiG~~lA~~L-~l~vGD~i~l~~~~~~~~~~~~~~~~~~f~V~GI 194 (270) .|....++..+ .|-+-+.+++.| |-++||.|.+-.|.+.. +|+|..| T Consensus 108 VG~~Ead~~~g-~IS~~SPlg~ALlGk~~Gd~V~v~~P~G~~----------~~~I~~I 155 (157) T PRK00226 108 VGDDEADIKEG-KISVNSPIARALIGKKVGDTVTVKAPGGEY----------EVEIVSV 155 (157) T ss_pred ECCCCCCCCCC-EECCCCHHHHHHHCCCCCCEEEEECCCCCE----------EEEEEEE T ss_conf 13322456676-524779899998289999989998499878----------9999998 No 27 >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=49.97 E-value=9.6 Score=17.79 Aligned_cols=53 Identities=26% Similarity=0.276 Sum_probs=35.7 Q ss_pred CCCCCCHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCEEEEEHHHH Q ss_conf 23421013454554213332023113442100012211000012210233102445551689854889 Q 537021.9.peg.7 147 GKGVIIGKDLARNLGISIGDKINILSPYGDVTPMGMGIRSKSYTVLGMFRMRFPDYDNGMVYMSLQEA 214 (270) Q Consensus 147 ~~~iiiG~~lA~~L~l~vGD~i~l~~~~~~~~~~~~~~~~~~f~V~GI~~sg~~~~D~~~v~~~l~~~ 214 (270) .+.+.|....|++||++-||.|.|.++.+... .+| ... ..+-...+|+|.-+. T Consensus 34 ep~v~~~p~dA~~lgi~~Gd~V~v~s~~G~~~----------~~v--~v~---~~i~~g~v~~p~~~~ 86 (120) T cd00508 34 EPFVEIHPEDAARLGIKDGDLVRVSSRRGSVV----------VRA--RVT---DRVRPGTVFMPFHWG 86 (120) T ss_pred CCEEEECHHHHHHCCCCCCCEEEEECCCEEEE----------EEE--EEC---CCCCCCEEEEECCCC T ss_conf 98899999999885999999999981773899----------999--987---996899799967008 No 28 >pfam04014 SpoVT_AbrB SpoVT / AbrB like domain. One member of this family is AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator or the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation. AbrB is thought to interact directly with the transcription initiation regions of genes under its control. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins. The product of the Bacillus subtilis gene spoVT is another member of this family and is also a transcriptional regulator. DNA binding activity in the Bacillus 0 AbrB homologue requires hexamerisation. Another family member has been isolated from the archaeon Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The E.coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as Probab=46.49 E-value=10 Score=17.58 Aligned_cols=26 Identities=31% Similarity=0.539 Sum_probs=22.6 Q ss_pred CCCCCCHHHHHHHHHCCCCCEEEECC Q ss_conf 23421013454554213332023113 Q 537021.9.peg.7 147 GKGVIIGKDLARNLGISIGDKINILS 172 (270) Q Consensus 147 ~~~iiiG~~lA~~L~l~vGD~i~l~~ 172 (270) +..|.|-+.+++.++++.||++.+.. T Consensus 6 s~~V~IPk~~r~~l~l~~Gd~v~~~~ 31 (47) T pfam04014 6 SGAVTIPKEVRKALGIKEGDEVELEV 31 (47) T ss_pred CCEEECCHHHHHHCCCCCCCCEEEEE T ss_conf 64697459999970999899579997 No 29 >TIGR01941 nqrF NADH:ubiquinone oxidoreductase, Na(+)-translocating, F subunit; InterPro: IPR010205 This entry represents the NqrF subunit of the six-protein, Na(+)-pumping NADH-quinone reductase of a number of marine and pathogenic Gram-negative bacteria.; GO: 0016655 oxidoreductase activity acting on NADH or NADPH quinone or similar compound as acceptor, 0051537 2 iron 2 sulfur cluster binding, 0006814 sodium ion transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane. Probab=45.71 E-value=9.4 Score=17.85 Aligned_cols=23 Identities=22% Similarity=0.530 Sum_probs=14.1 Q ss_pred HHHHHHCCCCCEEEECCCCCCCC Q ss_conf 54554213332023113442100 Q 537021.9.peg.7 156 LARNLGISIGDKINILSPYGDVT 178 (270) Q Consensus 156 lA~~L~l~vGD~i~l~~~~~~~~ 178 (270) =+.-.+||.||+|++..|+|+.- T Consensus 256 SSYifsLKpGDKv~~sGPfGefF 278 (425) T TIGR01941 256 SSYIFSLKPGDKVTVSGPFGEFF 278 (425) T ss_pred EEEEEECCCCCEEEEECCCCCCE T ss_conf 33377447987779977888530 No 30 >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=44.37 E-value=13 Score=17.08 Aligned_cols=54 Identities=24% Similarity=0.247 Sum_probs=35.6 Q ss_pred CCCCCHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCEEEEEHHHHHH Q ss_conf 342101345455421333202311344210001221100001221023310244555168985488999 Q 537021.9.peg.7 148 KGVIIGKDLARNLGISIGDKINILSPYGDVTPMGMGIRSKSYTVLGMFRMRFPDYDNGMVYMSLQEAQL 216 (270) Q Consensus 148 ~~iiiG~~lA~~L~l~vGD~i~l~~~~~~~~~~~~~~~~~~f~V~GI~~sg~~~~D~~~v~~~l~~~q~ 216 (270) +.+.+...-|+++|++-||.|.|.++.+... +.-.+.. .+-...+++|..+... T Consensus 23 ~~v~~np~dA~~~Gi~~Gd~v~v~~~~g~~~------------~~~~~~~---~v~~g~v~~~~g~~~~ 76 (101) T cd02775 23 PVVEINPEDAAALGIKDGDLVRVESRRGSVV------------LRAKVTD---GVPPGVVFLPHGWGHR 76 (101) T ss_pred CEEEECHHHHHHCCCCCCCEEEEEECCEEEE------------EEEEECC---CCCCCEEEEECCCCCC T ss_conf 9899999999986998899999996985899------------9999889---9689989997860666 No 31 >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=41.88 E-value=15 Score=16.70 Aligned_cols=52 Identities=29% Similarity=0.397 Sum_probs=35.8 Q ss_pred CCCCCHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCEEEEEHHHH Q ss_conf 3421013454554213332023113442100012211000012210233102445551689854889 Q 537021.9.peg.7 148 KGVIIGKDLARNLGISIGDKINILSPYGDVTPMGMGIRSKSYTVLGMFRMRFPDYDNGMVYMSLQEA 214 (270) Q Consensus 148 ~~iiiG~~lA~~L~l~vGD~i~l~~~~~~~~~~~~~~~~~~f~V~GI~~sg~~~~D~~~v~~~l~~~ 214 (270) +-+.|....|++||++-||.|.|.++.+... .++ ... ..+-...+|+|.-+. T Consensus 35 p~v~i~p~dA~~lGi~~Gd~V~v~s~~G~i~----------~~a--~v~---~~i~~G~v~~p~h~~ 86 (116) T cd02790 35 EYVEINPEDAKRLGIEDGEKVRVSSRRGSVE----------VRA--RVT---DRVPEGVVFMPFHFA 86 (116) T ss_pred CEEEECHHHHHHCCCCCCCEEEEECCCEEEE----------EEE--EEC---CCCCCCEEEECCCCC T ss_conf 8899899999885998899899987998999----------999--986---998899799727768 No 32 >TIGR01398 FlhA flagellar biosynthesis protein FlhA; InterPro: IPR006301 These sequences describe the flagellar biosynthesis protein FlhA, one of a large number of genes associated with the biosynthesis of functional bacterial flagella. Homologs of many such proteins, including FlhA, function in type III protein secretion systems. ; GO: 0015031 protein transport, 0016021 integral to membrane, 0019861 flagellum. Probab=39.21 E-value=27 Score=15.21 Aligned_cols=67 Identities=15% Similarity=0.274 Sum_probs=39.9 Q ss_pred HHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCC-CCCCHHHHHHHHHCCCCH Q ss_conf 89999999999999999----------9999999987699999631110245300000000-012136665554226410 Q 537021.9.peg.7 25 ISIASFISFIGVMIGVM----------ALIVVMSVMNGFREDMIKRVLGINGHVVIQQKYY-PLVDYQFIANRLDFIPDV 93 (270) Q Consensus 25 ~~~is~ls~lgI~igv~----------~li~~lsv~~G~~~~i~~~i~~~~~~i~i~~~~~-~~~~~~~~~~~l~~~~~V 93 (270) ++++.+ +-|+.+||. ...+.|+|++|+-..+=.-+++...=+.|+.... ...-.+.+..++.+.|-+ T Consensus 201 It~iNI--igGliiGv~~h~M~~~~Aa~~YT~LTiGDGLVaQIPaL~iS~AtG~~VTR~~~~~~~~~~~~~~QL~~~p~~ 278 (713) T TIGR01398 201 ITLINI--IGGLIIGVVQHGMSLSEAASTYTILTIGDGLVAQIPALIISTATGIIVTRASSDEGNLGKAIVTQLTANPRV 278 (713) T ss_pred HHHHHH--HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCHHH T ss_conf 999999--887876566317638999988677768778999878999999876632225664012478999998622189 No 33 >PRK05892 nucleoside diphosphate kinase regulator; Provisional Probab=39.14 E-value=21 Score=15.82 Aligned_cols=28 Identities=25% Similarity=0.404 Sum_probs=22.6 Q ss_pred CCCHHHHHHHH-HCCCCCEEEECCCCCCC Q ss_conf 21013454554-21333202311344210 Q 537021.9.peg.7 150 VIIGKDLARNL-GISIGDKINILSPYGDV 177 (270) Q Consensus 150 iiiG~~lA~~L-~l~vGD~i~l~~~~~~~ 177 (270) |-..+.|++.| |-++||+|++.+|.|.. T Consensus 122 IS~~SPlgrALlGk~~GD~V~v~tP~G~~ 150 (161) T PRK05892 122 LTARSPLGQALAGHQPGDTVTYSTPQGPN 150 (161) T ss_pred ECCCCHHHHHHHCCCCCCEEEEECCCCCE T ss_conf 63679789998489899989997599757 No 34 >TIGR03243 arg_catab_AOST arginine and ornithine succinyltransferase subunits. In many bacteria, the sole member of this protein family is arginine N-succinyltransferase (EC 2.3.1.109), the AstA protein of the arginine succinyltransferase (ast) pathway. However, in Pseudomonas aeruginosa and several other species, a tandem gene pair encodes alpha and beta subunits of a heterodimer that is designated arginine and ornithine succinyltransferase (AOST). Probab=38.68 E-value=17 Score=16.40 Aligned_cols=15 Identities=27% Similarity=0.408 Sum_probs=7.4 Q ss_pred CCCEEEEEHHHHHHH Q ss_conf 551689854889997 Q 537021.9.peg.7 203 DNGMVYMSLQEAQLY 217 (270) Q Consensus 203 D~~~v~~~l~~~q~l 217 (270) +...+.++-++++.| T Consensus 308 ~~~~~~l~~~~a~aL 322 (335) T TIGR03243 308 DAGTLILSADAADAL 322 (335) T ss_pred CCCEEEECHHHHHHC T ss_conf 699799589999775 No 35 >cd02780 MopB_CT_Tetrathionate_Arsenate-R This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of tetrathionate reductase, subunit A, (TtrA); respiratory arsenate As(V) reductase, catalytic subunit (ArrA); and other related proteins. Probab=38.05 E-value=20 Score=16.03 Aligned_cols=31 Identities=35% Similarity=0.614 Sum_probs=26.4 Q ss_pred CCCCCCHHHHHHHHHCCCCCEEEECCCCCCC Q ss_conf 2342101345455421333202311344210 Q 537021.9.peg.7 147 GKGVIIGKDLARNLGISIGDKINILSPYGDV 177 (270) Q Consensus 147 ~~~iiiG~~lA~~L~l~vGD~i~l~~~~~~~ 177 (270) .+.+.|...-|++++++-||.|.+.++.+.. T Consensus 29 en~v~inp~dA~~~Gi~~Gd~V~v~s~~G~i 59 (143) T cd02780 29 ENPVWINPEDAAKLGIKTGDRVRVVTPGGSV 59 (143) T ss_pred CCEEEECHHHHHHCCCCCCCEEEEECCCEEE T ss_conf 9859999999998699989999998798579 No 36 >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=37.99 E-value=20 Score=15.99 Aligned_cols=30 Identities=33% Similarity=0.535 Sum_probs=25.5 Q ss_pred CCCCCHHHHHHHHHCCCCCEEEECCCCCCC Q ss_conf 342101345455421333202311344210 Q 537021.9.peg.7 148 KGVIIGKDLARNLGISIGDKINILSPYGDV 177 (270) Q Consensus 148 ~~iiiG~~lA~~L~l~vGD~i~l~~~~~~~ 177 (270) +.+-|...-|++||++-||.|.|.++.+.. T Consensus 30 ~~v~inp~dA~~~Gi~dGd~V~v~s~~G~~ 59 (123) T cd02778 30 NTLWINPETAARLGIKDGDRVEVSSARGKV 59 (123) T ss_pred CEEEECHHHHHHCCCCCCCEEEEECCCEEE T ss_conf 889999999998499999999998899689 No 37 >cd02781 MopB_CT_Acetylene-hydratase The MopB_CT_Acetylene-hydratase CD contains acetylene hydratase (Ahy) and other related proteins. The acetylene hydratase of Pelobacter acetylenicus is a tungsten iron-sulfur protein involved in the fermentation of acetylene to ethanol and acetate. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=37.83 E-value=20 Score=15.95 Aligned_cols=31 Identities=29% Similarity=0.373 Sum_probs=26.2 Q ss_pred CCCCCCHHHHHHHHHCCCCCEEEECCCCCCC Q ss_conf 2342101345455421333202311344210 Q 537021.9.peg.7 147 GKGVIIGKDLARNLGISIGDKINILSPYGDV 177 (270) Q Consensus 147 ~~~iiiG~~lA~~L~l~vGD~i~l~~~~~~~ 177 (270) .+.+-|....|+++|++-||.|.+.++.+.. T Consensus 32 ~p~v~i~p~dA~~~Gi~~Gd~V~v~s~~G~i 62 (130) T cd02781 32 DPVAEINPETAAKLGIADGDWVWVETPRGRA 62 (130) T ss_pred CCEEEECHHHHHHCCCCCCCEEEEECCCEEE T ss_conf 9989999999998499999999998489789 No 38 >cd02786 MopB_CT_3 The MopB_CT_3 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=37.59 E-value=21 Score=15.90 Aligned_cols=57 Identities=21% Similarity=0.128 Sum_probs=36.5 Q ss_pred CCCCCCHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCEEEEEHHHHHHHC Q ss_conf 234210134545542133320231134421000122110000122102331024455516898548899971 Q 537021.9.peg.7 147 GKGVIIGKDLARNLGISIGDKINILSPYGDVTPMGMGIRSKSYTVLGMFRMRFPDYDNGMVYMSLQEAQLYF 218 (270) Q Consensus 147 ~~~iiiG~~lA~~L~l~vGD~i~l~~~~~~~~~~~~~~~~~~f~V~GI~~sg~~~~D~~~v~~~l~~~q~l~ 218 (270) .+.+.|...-|+++|++-||.|.+.++.+... +.-.+.. .+-...+++|-.+-.+.+ T Consensus 30 ~p~v~i~p~DA~~~GI~dGd~V~v~n~~G~v~------------~~a~v~~---~i~~gvv~~~~gww~~~~ 86 (116) T cd02786 30 EPTLLIHPADAAARGIADGDLVVVFNDRGSVT------------LRAKVTD---DVPPGVVVAEGGWWREHS 86 (116) T ss_pred CCEEEECHHHHHHCCCCCCCEEEEECCCEEEE------------EEEEECC---CCCCCEEEECCCCCCCCC T ss_conf 98699999999885999999999978998999------------9999779---828998997564457768 No 39 >TIGR03245 arg_AOST_alph arginine/ornithine succinyltransferase, alpha subunit. In some bacteria, including Pseudomonas aeruginosa, the astB gene (arginine N-succinyltransferase) is replaced by tandem paralogs that form a heterodimer. This heterodimer from P. aeruginosa is characterized as arginine and ornithine N-2 succinyltransferase (AOST). Members of this protein family represent the less widespread paralog, designated AruI, or arginine/ornithine succinyltransferase, alpha subunit. Probab=37.57 E-value=18 Score=16.23 Aligned_cols=12 Identities=8% Similarity=0.205 Sum_probs=4.9 Q ss_pred EEEEEHHHHHHH Q ss_conf 689854889997 Q 537021.9.peg.7 206 MVYMSLQEAQLY 217 (270) Q Consensus 206 ~v~~~l~~~q~l 217 (270) .+.++-++++.| T Consensus 312 ~v~l~~~~a~aL 323 (336) T TIGR03245 312 LLRLKRDAAEAL 323 (336) T ss_pred EEEECHHHHHHC T ss_conf 798599999774 No 40 >COG2336 MazE Growth regulator [Signal transduction mechanisms] Probab=37.56 E-value=18 Score=16.22 Aligned_cols=27 Identities=26% Similarity=0.449 Sum_probs=22.9 Q ss_pred CCCCCCHHHHHHHHHCCCCCEEEECCC Q ss_conf 234210134545542133320231134 Q 537021.9.peg.7 147 GKGVIIGKDLARNLGISIGDKINILSP 173 (270) Q Consensus 147 ~~~iiiG~~lA~~L~l~vGD~i~l~~~ 173 (270) +-.+.|...+++.||+..||.|++... T Consensus 11 S~avrIP~~l~kql~l~~g~~v~v~v~ 37 (82) T COG2336 11 SAAVRIPAALLKQLNLTIGDEVEVEVG 37 (82) T ss_pred CCEEECCHHHHHHHCCCCCCEEEEEEC T ss_conf 632661699998709975860899975 No 41 >TIGR03244 arg_catab_AstA arginine N-succinyltransferase. In many bacteria, the arginine succinyltransferase (ast) pathway operon consists of five genes, including this protein, arginine N-succinyltransferase (EC 2.3.1.109). In a few species, such as Pseudomonas aeruginosa, the member of this family is encoded adjacent to a paralog, and the two polypeptides form a heterodimeric enzyme, active on both arginine and ornithine. In such species, this polypeptide may be treated as the beta subunit of an enzyme that may be named either arginine N-succinyltransferase (AST) or arginine and orthithine N-succinyltransferase (AOST). Probab=37.18 E-value=18 Score=16.19 Aligned_cols=15 Identities=20% Similarity=0.366 Sum_probs=7.3 Q ss_pred CCCEEEEEHHHHHHH Q ss_conf 551689854889997 Q 537021.9.peg.7 203 DNGMVYMSLQEAQLY 217 (270) Q Consensus 203 D~~~v~~~l~~~q~l 217 (270) |...+.++-++++.| T Consensus 309 ~~~~~~l~~~~a~aL 323 (336) T TIGR03244 309 DAGELVLTAAQADAL 323 (336) T ss_pred CCCEEEECHHHHHHC T ss_conf 799898589999775 No 42 >pfam11374 DUF3176 Protein of unknown function (DUF3176). This eukaryotic family of proteins has no known function. Probab=36.93 E-value=30 Score=15.00 Aligned_cols=18 Identities=28% Similarity=0.447 Sum_probs=6.6 Q ss_pred HHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999999999 Q 537021.9.peg.7 29 SFISFIGVMIGVMALIVVM 47 (270) Q Consensus 29 s~ls~lgI~igv~~li~~l 47 (270) +++|+++ +++-++++..+ T Consensus 24 a~iSils-ti~~a~l~~~v 41 (111) T pfam11374 24 ALISILS-TIAKAALLFPV 41 (111) T ss_pred HHHHHHH-HHHHHHHHHHH T ss_conf 9999999-99999999999 No 43 >cd02784 MopB_CT_PHLH The MopB_CT_PHLH CD includes a group of related uncharacterized putative hydrogenase-like homologs (PHLH) of molybdopterin binding proteins. This CD is of the PHLH region homologous to the conserved molybdopterin-binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=36.87 E-value=22 Score=15.78 Aligned_cols=28 Identities=21% Similarity=0.317 Sum_probs=23.8 Q ss_pred CCCCCCHHHHHHHHHCCCCCEEEECCCC Q ss_conf 2342101345455421333202311344 Q 537021.9.peg.7 147 GKGVIIGKDLARNLGISIGDKINILSPY 174 (270) Q Consensus 147 ~~~iiiG~~lA~~L~l~vGD~i~l~~~~ 174 (270) .+.+.|+...|++|+++-||.++|.... T Consensus 37 DN~~~isp~~A~~lgi~~gd~v~l~~~~ 64 (137) T cd02784 37 DNAALVSPRTAEALGLLQGDVVRIRRGG 64 (137) T ss_pred CCCEEECHHHHHHHCCCCCCEEEEEECC T ss_conf 4604589999998479778889999689 No 44 >cd02791 MopB_CT_Nitrate-R-NapA-like Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol oxidation via a membrane-anchored tetraheme cytochrome. This CD (MopB_CT_Nitrate-R-Nap) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs Probab=36.43 E-value=20 Score=15.93 Aligned_cols=54 Identities=22% Similarity=0.262 Sum_probs=36.6 Q ss_pred CCCCCHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCEEEEEHHHHHH Q ss_conf 342101345455421333202311344210001221100001221023310244555168985488999 Q 537021.9.peg.7 148 KGVIIGKDLARNLGISIGDKINILSPYGDVTPMGMGIRSKSYTVLGMFRMRFPDYDNGMVYMSLQEAQL 216 (270) Q Consensus 148 ~~iiiG~~lA~~L~l~vGD~i~l~~~~~~~~~~~~~~~~~~f~V~GI~~sg~~~~D~~~v~~~l~~~q~ 216 (270) +-+-|...-|+++|++-||.|.+.++.+... +.-... ..+-...+|+|.-+... T Consensus 35 ~~v~inp~dA~~~gi~dgd~V~v~s~~G~~~------------~~a~i~---~~v~~G~v~~p~~~~~~ 88 (122) T cd02791 35 PYVEIHPEDAARLGLKEGDLVRVTSRRGEVV------------LRVRVT---DRVRPGEVFVPMHWGDQ 88 (122) T ss_pred CEEEECHHHHHHCCCCCCCEEEEECCCEEEE------------EEEEEC---CCCCCCEEEEECCCCCC T ss_conf 7899999999886998999999984880899------------999987---99789989985621654 No 45 >pfam01568 Molydop_binding Molydopterin dinucleotide binding domain. This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entire subunit. The formylmethanofuran dehydrogenase catalyses the first step in methane formation from CO2 in methanogenic archaea and has a molybdopterin dinucleotide cofactor. This domain corresponds to the C-terminal domain IV in dimethyl sulfoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules. Probab=36.02 E-value=21 Score=15.85 Aligned_cols=53 Identities=28% Similarity=0.273 Sum_probs=36.2 Q ss_pred CCCCHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCEEEEEHHHHHH Q ss_conf 42101345455421333202311344210001221100001221023310244555168985488999 Q 537021.9.peg.7 149 GVIIGKDLARNLGISIGDKINILSPYGDVTPMGMGIRSKSYTVLGMFRMRFPDYDNGMVYMSLQEAQL 216 (270) Q Consensus 149 ~iiiG~~lA~~L~l~vGD~i~l~~~~~~~~~~~~~~~~~~f~V~GI~~sg~~~~D~~~v~~~l~~~q~ 216 (270) .+.|....|++||++-||.|.+.++.+... +.-.+.. .+-...+|+|.-+-.. T Consensus 31 ~v~i~p~dA~~lgi~~Gd~V~v~s~~G~~~------------~~a~i~~---~v~~g~v~~p~~~~~~ 83 (110) T pfam01568 31 FVEINPEDAAALGIKDGDLVEVTSRRGSVV------------VRAKVTD---RVRPGVVFMPFGWWAA 83 (110) T ss_pred EEEECHHHHHHCCCCCCCEEEEECCCEEEE------------EEEEECC---CCCCCEEEEECCCCCC T ss_conf 799999999983998899999976898999------------9999899---8379989996765566 No 46 >PRK10456 arginine succinyltransferase; Provisional Probab=34.93 E-value=21 Score=15.83 Aligned_cols=17 Identities=0% Similarity=-0.085 Sum_probs=9.0 Q ss_pred CCCCEEEEEHHHHHHHC Q ss_conf 55516898548899971 Q 537021.9.peg.7 202 YDNGMVYMSLQEAQLYF 218 (270) Q Consensus 202 ~D~~~v~~~l~~~q~l~ 218 (270) .++..+.++-++++.|- T Consensus 309 ~~~~~v~l~~~~a~aL~ 325 (344) T PRK10456 309 PATERLILTAAQLDALK 325 (344) T ss_pred CCCCEEEECHHHHHHCC T ss_conf 66997986899998749 No 47 >pfam01272 GreA_GreB Transcription elongation factor, GreA/GreB, C-term. This domain has a FKBP-like fold. Probab=34.22 E-value=24 Score=15.49 Aligned_cols=28 Identities=29% Similarity=0.635 Sum_probs=20.9 Q ss_pred CCCCHHHHHHHH-HCCCCCEEEECCCCCC Q ss_conf 421013454554-2133320231134421 Q 537021.9.peg.7 149 GVIIGKDLARNL-GISIGDKINILSPYGD 176 (270) Q Consensus 149 ~iiiG~~lA~~L-~l~vGD~i~l~~~~~~ 176 (270) .|-+-+.+++.| |.++||++.+-.|.+. T Consensus 39 ~IS~~SPlg~ALlG~~~Gd~v~~~~p~G~ 67 (77) T pfam01272 39 KISVLSPLGRALLGKKVGDEVEVTAPSGE 67 (77) T ss_pred CCCCCCHHHHHHHCCCCCCEEEEECCCCC T ss_conf 22888988999739999999999969987 No 48 >PRK11347 antitoxin ChpS; Provisional Probab=32.59 E-value=28 Score=15.14 Aligned_cols=46 Identities=13% Similarity=0.309 Sum_probs=29.4 Q ss_pred CCCCCCHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCEEE Q ss_conf 2342101345455421333202311344210001221100001221023 Q 537021.9.peg.7 147 GKGVIIGKDLARNLGISIGDKINILSPYGDVTPMGMGIRSKSYTVLGMF 195 (270) Q Consensus 147 ~~~iiiG~~lA~~L~l~vGD~i~l~~~~~~~~~~~~~~~~~~f~V~GI~ 195 (270) +-++.|-..+.+.|++++|+++.+...++..- ..|..++|+..-.+ T Consensus 11 S~~~~iP~alL~~l~l~~G~~v~~~v~~g~lv---i~P~~~kYtL~eLl 56 (83) T PRK11347 11 SAGMVIPNIVMKELNLQPGQSVEAQVSNNQLI---LTPISRRYSLDELL 56 (83) T ss_pred EEEEEECHHHHHHHCCCCCCEEEEEEECCEEE---EEECCCCCCHHHHH T ss_conf 03687189999980999999988999899699---96478777899999 No 49 >pfam04958 AstA Arginine N-succinyltransferase beta subunit. Arginine N-succinyltransferase EC:2.3.1.109 catalyses the transfer of succinyl-CoA to arginine to produce succinylarginine. This is the first step in arginine catabolism by the arginine succinyltransferase pathway. Probab=31.98 E-value=27 Score=15.23 Aligned_cols=12 Identities=25% Similarity=0.260 Sum_probs=5.3 Q ss_pred EEEEEHHHHHHH Q ss_conf 689854889997 Q 537021.9.peg.7 206 MVYMSLQEAQLY 217 (270) Q Consensus 206 ~v~~~l~~~q~l 217 (270) .+.++-++++.| T Consensus 314 ~l~l~~~~a~~L 325 (338) T pfam04958 314 TVVLSAEAADAL 325 (338) T ss_pred EEEECHHHHHHC T ss_conf 599789999763 No 50 >COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription] Probab=30.99 E-value=27 Score=15.25 Aligned_cols=27 Identities=33% Similarity=0.610 Sum_probs=22.9 Q ss_pred CCCCCCCHHHHHHHHHCCCCCEEEECC Q ss_conf 123421013454554213332023113 Q 537021.9.peg.7 146 RGKGVIIGKDLARNLGISIGDKINILS 172 (270) Q Consensus 146 ~~~~iiiG~~lA~~L~l~vGD~i~l~~ 172 (270) ....|+|.+.+-+.||++.||.+.++. T Consensus 12 ~~GqIvIPkeiR~~lgi~~Gd~lei~~ 38 (89) T COG2002 12 RKGQIVIPKEIREALGIKEGDVLEIIV 38 (89) T ss_pred CCCEEEEEHHHHHHCCCCCCCEEEEEE T ss_conf 796599559999983999899899999 No 51 >PRK11465 hypothetical protein; Provisional Probab=30.75 E-value=14 Score=16.81 Aligned_cols=75 Identities=15% Similarity=0.175 Sum_probs=40.5 Q ss_pred CCCCCEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCEEEEEHHHHHHHCCCCCCE--EEEEEEE---CCHHH Q ss_conf 133320231134421000122110000122102331024455516898548899971899871--0799995---69889 Q 537021.9.peg.7 162 ISIGDKINILSPYGDVTPMGMGIRSKSYTVLGMFRMRFPDYDNGMVYMSLQEAQLYFNLENAV--SGIEVFV---KDPDA 236 (270) Q Consensus 162 l~vGD~i~l~~~~~~~~~~~~~~~~~~f~V~GI~~sg~~~~D~~~v~~~l~~~q~l~~~~~~~--~~i~i~l---~d~~~ 236 (270) .++||.|++-.-.| + ..++. +=.+..-+.|...-++|-+.....-|..... ..+++.+ .|.++ T Consensus 574 ~~vGD~V~vgg~~G--t-------VE~is---lRs~~LRd~~G~~h~IP~s~I~~V~N~sr~~~~~~~~v~VaY~eDid~ 641 (741) T PRK11465 574 MNTGDLVTIGPLTG--T-------VERMS---IRSVGVRQDTGAYHIIPWSSITTFANFVRGIGSVVANYDVDRHEDADK 641 (741) T ss_pred CCCCCEEEECCCEE--E-------EEEEE---EEEEEEECCCCCEEEEECCCCCEEEECCCCCEEEEEEECCCCCCCHHH T ss_conf 37799899889358--9-------99997---489999879987899748865345774776558999953478689999 Q ss_pred HHHHHHHHHHHC Q ss_conf 999999999861 Q 537021.9.peg.7 237 IEKTHENIVRIL 248 (270) Q Consensus 237 ~~~~~~~i~~~l 248 (270) +.++.+++-+.+ T Consensus 642 v~~vl~~~~~~l 653 (741) T PRK11465 642 ANQALKDAVAEL 653 (741) T ss_pred HHHHHHHHHHHH T ss_conf 999999999998 No 52 >cd02783 MopB_CT_2 The MopB_CT_2 CD includes a group of related uncharacterized bacterial and archaeal 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=30.34 E-value=32 Score=14.80 Aligned_cols=32 Identities=28% Similarity=0.313 Sum_probs=26.2 Q ss_pred CCCCCCHHHHHHHHHCCCCCEEEECCCCCCCC Q ss_conf 23421013454554213332023113442100 Q 537021.9.peg.7 147 GKGVIIGKDLARNLGISIGDKINILSPYGDVT 178 (270) Q Consensus 147 ~~~iiiG~~lA~~L~l~vGD~i~l~~~~~~~~ 178 (270) .+.+-|....|+++|++-||.|.+.++.+... T Consensus 31 ~N~L~i~p~~A~~~GI~dGDwV~VeS~~G~i~ 62 (156) T cd02783 31 RNYLYMHPKTAKELGIKDGDWVWVESVNGRVK 62 (156) T ss_pred CCEEEECHHHHHHCCCCCCCEEEEECCCCCEE T ss_conf 98289899999985998698899975797499 No 53 >PRK13657 cyclic beta-1,2-glucan ABC transporter; Provisional Probab=29.95 E-value=39 Score=14.33 Aligned_cols=19 Identities=21% Similarity=0.424 Sum_probs=11.5 Q ss_pred HHHCCCCCEEEECCCCCCC Q ss_conf 5421333202311344210 Q 537021.9.peg.7 159 NLGISIGDKINILSPYGDV 177 (270) Q Consensus 159 ~L~l~vGD~i~l~~~~~~~ 177 (270) ++.++.|+++.+..|.|.+ T Consensus 355 sl~i~~Ge~vaiVG~SGsG 373 (585) T PRK13657 355 SFEAKPGQTVAIVGPTGAG 373 (585) T ss_pred EEEECCCCEEEEECCCCCC T ss_conf 3897599889998898986 No 54 >TIGR00439 ftsX putative protein insertion permease FtsX; InterPro: IPR004513 FtsX is an integral membrane protein encoded in the same operon as signal recognition particle docking protein FtsY and FtsE. FtsE is a hydrophilic nucleotide-binding protein that associates with the inner membrane by means of association with FtsX; FtsE mutants are viable only in high salt, supporting possible roles in cell division, as previously indicated, or in transport.; GO: 0007049 cell cycle, 0016021 integral to membrane. Probab=29.88 E-value=39 Score=14.33 Aligned_cols=75 Identities=9% Similarity=0.131 Sum_probs=37.0 Q ss_pred HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCC-CCCCHHHHHHHHHCCCCHHHHHHHHHCCCC Q ss_conf 999999999999999-999999987699999631110245300000000-012136665554226410346654200111 Q 537021.9.peg.7 28 ASFISFIGVMIGVMA-LIVVMSVMNGFREDMIKRVLGINGHVVIQQKYY-PLVDYQFIANRLDFIPDVIKVLPFVSGQAF 105 (270) Q Consensus 28 is~ls~lgI~igv~~-li~~lsv~~G~~~~i~~~i~~~~~~i~i~~~~~-~~~~~~~~~~~l~~~~~V~~~~p~i~~~~~ 105 (270) -|+||++-||++.+. .+.=|.+-|+ +....++. -.|+++|+-... ...+.+.+.++|++..+|+.+...-+..++ T Consensus 34 gTlLT~~viAvslTlP~v~Yl~~kn~--~~a~t~~y-pspqiTvYl~k~l~~~~a~~Vv~~l~~~kgve~~~y~sred~L 110 (314) T TIGR00439 34 GTLLTVLVIAVSLTLPLVSYLVYKNV--QSALTQLY-PSPQITVYLEKALAEEDADTVVSKLRRDKGVEKINYISREDAL 110 (314) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHCC-CCCCHHHHHHHHHCHHHHHHHHHHHHHHCCCCHHHCCCHHHHH T ss_conf 47999999999986579999998857--77742017-8840357877501344689999999874062021011356677 No 55 >TIGR02066 dsrB sulfite reductase, dissimilatory-type beta subunit; InterPro: IPR011808 Dissimilatory sulphite reductase catalyzes the six-electron reduction of sulphite to sulphide, as the terminal reaction in dissimilatory sulphate reduction. It remains unclear however, whether trithionate and thiosulphate serve as intermediate compounds to sulphide, or as end products of sulphite reduction . Sulphite reductase is a multisubunit enzyme composed of dimers of either alpha/beta or alpha/beta/gamma subunits, each containing a siroheme and iron sulphur cluster prosthetic centre . Found in sulphate-reducing bacteria, these genes are commonly located in a unidirectional gene cluster . This entry describes the beta subunit of sulphite reductase.; GO: 0018551 hydrogensulfite reductase activity, 0051539 4 iron 4 sulfur cluster binding, 0006118 electron transport. Probab=29.59 E-value=40 Score=14.30 Aligned_cols=41 Identities=10% Similarity=0.270 Sum_probs=25.7 Q ss_pred EEEEHHHHHHHCCCCCCE----------EEEEEEECCHHHHHHHHHHHHHH Q ss_conf 898548899971899871----------07999956988999999999986 Q 537021.9.peg.7 207 VYMSLQEAQLYFNLENAV----------SGIEVFVKDPDAIEKTHENIVRI 247 (270) Q Consensus 207 v~~~l~~~q~l~~~~~~~----------~~i~i~l~d~~~~~~~~~~i~~~ 247 (270) ++++..+++++-+..|++ ++|+..++|.+.++.++++|+++ T Consensus 41 a~vsV~tlr~lcDIADk~~dGylr~T~r~NvEFlv~d~~K~~~li~~L~~R 91 (366) T TIGR02066 41 ALVSVDTLRKLCDIADKYGDGYLRWTIRNNVEFLVSDESKVQPLIDELEKR 91 (366) T ss_pred CEEEHHHHHHHHHHCHHHCCCCEEEEECCCEEEEECCHHHHHHHHHHHHHC T ss_conf 256154565563001111576078741166568745878877999999718 No 56 >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=28.90 E-value=36 Score=14.55 Aligned_cols=32 Identities=34% Similarity=0.416 Sum_probs=26.6 Q ss_pred CCCCCCHHHHHHHHHCCCCCEEEECCCCCCCC Q ss_conf 23421013454554213332023113442100 Q 537021.9.peg.7 147 GKGVIIGKDLARNLGISIGDKINILSPYGDVT 178 (270) Q Consensus 147 ~~~iiiG~~lA~~L~l~vGD~i~l~~~~~~~~ 178 (270) .+.+.|.-.-|++||++-||.|.|.++.+... T Consensus 32 ~~~~~i~p~dA~~lgi~~Gd~V~v~s~~G~~~ 63 (129) T cd02782 32 RCTLRIHPDDAAALGLADGDKVRVTSAAGSVE 63 (129) T ss_pred CCEEEECHHHHHHCCCCCCCEEEEECCCEEEE T ss_conf 97799999999886998999999986984799 No 57 >TIGR00959 ffh signal recognition particle protein; InterPro: IPR004780 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes , . SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor . In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. This entry represents various SRP subunits.; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle. Probab=28.65 E-value=15 Score=16.77 Aligned_cols=60 Identities=10% Similarity=0.104 Sum_probs=43.9 Q ss_pred CCCCEEEEEHHHHHHHCCCCCCEEEEEEEECCHHHHHHHHHHHHHHCCCCEEEEEHHHHHH Q ss_conf 5551689854889997189987107999956988999999999986199859996899889 Q 537021.9.peg.7 202 YDNGMVYMSLQEAQLYFNLENAVSGIEVFVKDPDAIEKTHENIVRILGNGVVVIDWQQRYQ 262 (270) Q Consensus 202 ~D~~~v~~~l~~~q~l~~~~~~~~~i~i~l~d~~~~~~~~~~i~~~l~~~~~v~~w~e~~~ 262 (270) +++--.|-|-.-|.++||+.|-+|=++ |.....|.+++++--++.....|...|..++-. T Consensus 286 ~~dLe~FhP~R~A~RILGMGDv~SLvE-KA~~~~D~~~a~~~~~K~~~~~FdleDfl~Ql~ 345 (439) T TIGR00959 286 IEDLEPFHPDRMASRILGMGDVLSLVE-KAQEVVDEEEAKKLAEKMLKGQFDLEDFLEQLR 345 (439) T ss_pred CCCCCCCCHHHHHHHHCCCCCHHHHHH-HHHHHCCHHHHHHHHHHHHCCCCCHHHHHHHHH T ss_conf 233124674789863236552236999-999851889999999986305889899999999 No 58 >PRK08221 anaerobic sulfite reductase subunit B; Provisional Probab=28.37 E-value=41 Score=14.21 Aligned_cols=30 Identities=30% Similarity=0.535 Sum_probs=23.5 Q ss_pred CCHHHHHHHHHCCCCCEEEECCCCCCCCCC Q ss_conf 101345455421333202311344210001 Q 537021.9.peg.7 151 IIGKDLARNLGISIGDKINILSPYGDVTPM 180 (270) Q Consensus 151 iiG~~lA~~L~l~vGD~i~l~~~~~~~~~~ 180 (270) ++|+....-.+++.||.+.+..|.++..+. T Consensus 67 ~vG~gT~~L~~lk~Gd~l~v~GPlGngF~~ 96 (263) T PRK08221 67 RVGKVTDEIFTLKEGDKVFLRGPYGNGFPV 96 (263) T ss_pred EECHHHHHHHCCCCCCEEEEEECCCCCCCC T ss_conf 488789999729998999997014897056 No 59 >cd02794 MopB_CT_DmsA-EC The MopB_CT_DmsA-EC CD includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted N-terminal iron-sulfur [4Fe-4S] cluster binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=28.34 E-value=36 Score=14.56 Aligned_cols=31 Identities=29% Similarity=0.343 Sum_probs=25.9 Q ss_pred CCCCCHHHHHHHHHCCCCCEEEECCCCCCCC Q ss_conf 3421013454554213332023113442100 Q 537021.9.peg.7 148 KGVIIGKDLARNLGISIGDKINILSPYGDVT 178 (270) Q Consensus 148 ~~iiiG~~lA~~L~l~vGD~i~l~~~~~~~~ 178 (270) +.+.|-..-|+++|++-||.|.+.++.+... T Consensus 30 ~~v~i~p~DA~~~gi~dGd~V~v~n~~G~i~ 60 (121) T cd02794 30 QEVWINPLDAAARGIKDGDRVLVFNDRGKVI 60 (121) T ss_pred CEEEECHHHHHHCCCCCCCEEEEECCCCEEE T ss_conf 6089899999983998999999981990699 No 60 >cd02785 MopB_CT_4 The MopB_CT_4 CD includes a group of related uncharacterized bacterial and archaeal 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=28.08 E-value=35 Score=14.58 Aligned_cols=31 Identities=29% Similarity=0.312 Sum_probs=25.9 Q ss_pred CCCCCCHHHHHHHHHCCCCCEEEECCCCCCC Q ss_conf 2342101345455421333202311344210 Q 537021.9.peg.7 147 GKGVIIGKDLARNLGISIGDKINILSPYGDV 177 (270) Q Consensus 147 ~~~iiiG~~lA~~L~l~vGD~i~l~~~~~~~ 177 (270) .+.+-|...-|+++|++-||.|.+++..+.. T Consensus 31 ~p~v~i~p~dA~~~GI~dgd~V~v~n~rG~~ 61 (124) T cd02785 31 EPRVKINPIDAAARGIAHGDLVEVYNDRGSV 61 (124) T ss_pred CCEEEECHHHHHHCCCCCCCEEEEECCCEEE T ss_conf 9879999999988499999999998599999 No 61 >PRK09798 antitoxin MazE; Provisional Probab=27.32 E-value=31 Score=14.89 Aligned_cols=29 Identities=28% Similarity=0.343 Sum_probs=23.2 Q ss_pred CCCCCCHHHHHHHHHCCCCCEEEECCCCC Q ss_conf 23421013454554213332023113442 Q 537021.9.peg.7 147 GKGVIIGKDLARNLGISIGDKINILSPYG 175 (270) Q Consensus 147 ~~~iiiG~~lA~~L~l~vGD~i~l~~~~~ 175 (270) +.+|=|.+.+++.+++..||.|.+....+ T Consensus 12 S~avRIP~~i~~~l~l~~~~~v~i~v~~g 40 (82) T PRK09798 12 SPAVRIPATLMQALNLNIDDEVKIDLVDG 40 (82) T ss_pred CHHHHCCHHHHHHCCCCCCCEEEEEEECC T ss_conf 68563479999984999999588999899 No 62 >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=26.86 E-value=37 Score=14.45 Aligned_cols=30 Identities=20% Similarity=0.204 Sum_probs=24.7 Q ss_pred CCCCCHHHHHHHHHCCCCCEEEECCCCCCC Q ss_conf 342101345455421333202311344210 Q 537021.9.peg.7 148 KGVIIGKDLARNLGISIGDKINILSPYGDV 177 (270) Q Consensus 148 ~~iiiG~~lA~~L~l~vGD~i~l~~~~~~~ 177 (270) ..+.|+..-|.+||++-||.+++....+.. T Consensus 29 p~~~l~~~dA~~Lgl~~G~~v~v~~~~g~~ 58 (96) T cd02788 29 PYARLSPADAARLGLADGDLVEFSLGDGTL 58 (96) T ss_pred CEEEECHHHHHHHCCCCCCEEEEEECCEEE T ss_conf 579999989998199999989999899689 No 63 >cd02779 MopB_CT_Arsenite-Ox This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of Arsenite oxidase (Arsenite-Ox) and related proteins. Arsenite oxidase oxidizes arsenite to the less toxic arsenate; it transfers the electrons obtained from the oxidation of arsenite towards the soluble periplasmic electron carriers cytochrome c and/or amicyanin. Probab=26.81 E-value=38 Score=14.43 Aligned_cols=50 Identities=22% Similarity=0.383 Sum_probs=33.1 Q ss_pred CCCCHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCEEEEEHHH Q ss_conf 42101345455421333202311344210001221100001221023310244555168985488 Q 537021.9.peg.7 149 GVIIGKDLARNLGISIGDKINILSPYGDVTPMGMGIRSKSYTVLGMFRMRFPDYDNGMVYMSLQE 213 (270) Q Consensus 149 ~iiiG~~lA~~L~l~vGD~i~l~~~~~~~~~~~~~~~~~~f~V~GI~~sg~~~~D~~~v~~~l~~ 213 (270) -+-|.-.-|+++|++-||.|.+.+..+..... ..|. ...-...+|+|.-+ T Consensus 34 ~veinP~DA~~lgI~~Gd~V~v~s~rG~i~~~--------a~vt-------~~v~~G~vF~p~h~ 83 (115) T cd02779 34 YIEVNPEDAKREGLKNGDLVEVYNDYGSTTAM--------AYVT-------NTVKPGQTFMLMAH 83 (115) T ss_pred EEEECHHHHHHCCCCCCCEEEEECCCEEEEEE--------EEEC-------CCCCCCCEEEECCC T ss_conf 99999999988599998999998799079999--------9988-------99799819997676 No 64 >cd02777 MopB_CT_DMSOR-like The MopB_CT_DMSOR-like CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO. Also included in this group is the pyrogallol-phloroglucinol transhydroxylase from Pelobacter acidigallici. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB hom Probab=25.76 E-value=44 Score=14.04 Aligned_cols=31 Identities=29% Similarity=0.299 Sum_probs=26.1 Q ss_pred CCCCCHHHHHHHHHCCCCCEEEECCCCCCCC Q ss_conf 3421013454554213332023113442100 Q 537021.9.peg.7 148 KGVIIGKDLARNLGISIGDKINILSPYGDVT 178 (270) Q Consensus 148 ~~iiiG~~lA~~L~l~vGD~i~l~~~~~~~~ 178 (270) +.+.|...-|++++++-||.|.++++.+... T Consensus 34 ~~v~inp~DA~~~gI~dGd~V~v~n~~G~i~ 64 (127) T cd02777 34 EPVWINPLDAAARGIKDGDIVRVFNDRGAVL 64 (127) T ss_pred CEEEECHHHHHHCCCCCCCEEEEECCCCEEE T ss_conf 8599899999885998989999987896499 No 65 >cd02793 MopB_CT_DMSOR-BSOR-TMAOR The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO.This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. Probab=24.96 E-value=47 Score=13.86 Aligned_cols=31 Identities=23% Similarity=0.304 Sum_probs=26.4 Q ss_pred CCCCCHHHHHHHHHCCCCCEEEECCCCCCCC Q ss_conf 3421013454554213332023113442100 Q 537021.9.peg.7 148 KGVIIGKDLARNLGISIGDKINILSPYGDVT 178 (270) Q Consensus 148 ~~iiiG~~lA~~L~l~vGD~i~l~~~~~~~~ 178 (270) +.+.|...-|+++|++-||.|.++...+... T Consensus 33 ~~v~i~p~DA~~~GI~dGd~V~V~n~rG~v~ 63 (129) T cd02793 33 EPIRINPADAAARGIADGDIVRVFNDRGACL 63 (129) T ss_pred CEEEECHHHHHHCCCCCCCEEEEECCCCEEE T ss_conf 7599999999885998989999988895699 No 66 >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=23.88 E-value=36 Score=14.52 Aligned_cols=31 Identities=26% Similarity=0.403 Sum_probs=22.4 Q ss_pred HHHHHHHHCCCCCEEEECCCCCCCCCCCCCC Q ss_conf 3454554213332023113442100012211 Q 537021.9.peg.7 154 KDLARNLGISIGDKINILSPYGDVTPMGMGI 184 (270) Q Consensus 154 ~~lA~~L~l~vGD~i~l~~~~~~~~~~~~~~ 184 (270) +.-|+.-|++.||++.++.|+|..+.....+ T Consensus 78 S~wa~d~Gir~GdtlEVM~P~G~F~~~~~~~ 108 (371) T TIGR02160 78 STWANDEGIRAGDTLEVMAPQGRFTSKLDAE 108 (371) T ss_pred EHHHHCCCCCCCCEEEEECCCCCCCCCCCCC T ss_conf 3211118704488788716789778888722 No 67 >TIGR01393 lepA GTP-binding protein LepA; InterPro: IPR006297 LepA (GUF1 in Saccaromyces) is a GTP-binding membrane protein related to EF-G and EF-Tu. Two types of phylogenetic tree, rooted by other GTP-binding proteins, suggest that eukaryotic homologs (including GUF1 of yeast) originated within the bacterial LepA family. The function of the proteins in this family are unknown. ; GO: 0005525 GTP binding. Probab=23.78 E-value=30 Score=14.99 Aligned_cols=43 Identities=14% Similarity=0.231 Sum_probs=22.1 Q ss_pred HHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCEEEEE Q ss_conf 34545542133320231134421000122110000122102331 Q 537021.9.peg.7 154 KDLARNLGISIGDKINILSPYGDVTPMGMGIRSKSYTVLGMFRM 197 (270) Q Consensus 154 ~~lA~~L~l~vGD~i~l~~~~~~~~~~~~~~~~~~f~V~GI~~s 197 (270) ..+=+--+++||||||..--. -..|..-+=+.+.+.-+|+|-. T Consensus 262 AgIK~v~D~~VGDTiT~~~~P-a~eplpGF~~~KP~VFaGlYPi 304 (598) T TIGR01393 262 AGIKDVSDVKVGDTITSVKNP-AKEPLPGFKEVKPMVFAGLYPI 304 (598) T ss_pred EEEEECCCEECCCEEECCCCC-CCCCCCCCCCCCCEEEECCCCC T ss_conf 865310411205445256787-3767888612576586012588 No 68 >TIGR02624 rhamnu_1P_ald rhamnulose-1-phosphate aldolase; InterPro: IPR013447 Proteins in this entry match the enzyme RhaD, rhamnulose-1-phosphate aldolase (4.1.2.19 from EC).; GO: 0008994 rhamnulose-1-phosphate aldolase activity. Probab=23.40 E-value=40 Score=14.28 Aligned_cols=28 Identities=25% Similarity=0.499 Sum_probs=18.8 Q ss_pred CCCCCCC-----EEEEEECCCCCCCEEEEEHHHHHH Q ss_conf 0001221-----023310244555168985488999 Q 537021.9.peg.7 186 SKSYTVL-----GMFRMRFPDYDNGMVYMSLQEAQL 216 (270) Q Consensus 186 ~~~f~V~-----GI~~sg~~~~D~~~v~~~l~~~q~ 216 (270) .++..++ |||.+| ..+|+.+- =++||+| T Consensus 201 M~e~rLv~WP~HGifGaG-~~lDe~FG--LIeTaEK 233 (273) T TIGR02624 201 MKEYRLVLWPHHGIFGAG-PSLDETFG--LIETAEK 233 (273) T ss_pred HHHCCEEEECCCCEECCC-CCHHHHCC--HHHHHHH T ss_conf 731878884487730378-76334406--0778889 No 69 >cd07047 BMC_PduB_repeat1 1,2-propanediol utilization protein B (PduB), Bacterial Micro-Compartment (BMC) domain repeat 1. PduB proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduB might form hexamers and further assemble into the flat facets of the polyhedral outer shell of pdu organelles at present no experimental evidence directly supports this view. PduB proteins contain two tandem BMC domains repeats. This CD contains repeat 1 (the first BMC domain of PduB). Probab=21.96 E-value=56 Score=13.47 Aligned_cols=89 Identities=19% Similarity=0.207 Sum_probs=49.9 Q ss_pred HCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEEC---CC---CCC-----CEEEEEHHHHHHHCCCCCCEEEEEE Q ss_conf 213332023113442100012211000012210233102---44---555-----1689854889997189987107999 Q 537021.9.peg.7 161 GISIGDKINILSPYGDVTPMGMGIRSKSYTVLGMFRMRF---PD---YDN-----GMVYMSLQEAQLYFNLENAVSGIEV 229 (270) Q Consensus 161 ~l~vGD~i~l~~~~~~~~~~~~~~~~~~f~V~GI~~sg~---~~---~D~-----~~v~~~l~~~q~l~~~~~~~~~i~i 229 (270) +..+||+|-+..|+-+.......--.++|+..||+.+.. +. .|+ |.=+++++..+.--+..+.-+-|.+ T Consensus 5 Gta~gdTIGlvI~nvd~~l~~~m~~~k~yrsiGIis~RtGAgpqimA~DEAVKatNtEvi~iElpRDTkGgaGHG~lii~ 84 (134) T cd07047 5 GTAIGDTIGLVIANVDPLLLEKMKLDKKYRSIGILGARTGAGPQIMAADEAVKATNTEVISIELPRDTKGGAGHGSLILF 84 (134) T ss_pred ECCCCCEEEEEECCCCHHHHHHHCCCCCEEEEEEEECCCCCCCHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCEEEEE T ss_conf 10247646899448898999972899641478887136686513211667774147468999803237898765049998 Q ss_pred EECCHHHHHHHH----HHHHHHCC Q ss_conf 956988999999----99998619 Q 537021.9.peg.7 230 FVKDPDAIEKTH----ENIVRILG 249 (270) Q Consensus 230 ~l~d~~~~~~~~----~~i~~~l~ 249 (270) -..|+.++.... +++.+.++ T Consensus 85 Ga~dvsD~rravevaL~~~~~~fg 108 (134) T cd07047 85 GAEDVSDVRRAVEVALSETEKTFG 108 (134) T ss_pred ECCCHHHHHHHHHHHHHHHHHHHH T ss_conf 068678999999999998787765 No 70 >PRK05753 nucleoside diphosphate kinase regulator; Provisional Probab=20.70 E-value=59 Score=13.31 Aligned_cols=37 Identities=30% Similarity=0.428 Sum_probs=25.4 Q ss_pred CCCCHHHHHHHH-HCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCEE Q ss_conf 421013454554-2133320231134421000122110000122102 Q 537021.9.peg.7 149 GVIIGKDLARNL-GISIGDKINILSPYGDVTPMGMGIRSKSYTVLGM 194 (270) Q Consensus 149 ~iiiG~~lA~~L-~l~vGD~i~l~~~~~~~~~~~~~~~~~~f~V~GI 194 (270) .|-+-+.++.-| |+++||.+..-.|.|. .++++|..| T Consensus 88 kISv~SPiG~ALlG~~~Gd~i~~~~P~G~---------~~~l~I~~V 125 (135) T PRK05753 88 QVSVLAPVGAALLGLSVGQSIDWPLPGGK---------ETHLTVLEV 125 (135) T ss_pred CCCCCCHHHHHHHCCCCCCEEEEECCCCC---------EEEEEEEEE T ss_conf 20101699999738999999999889997---------789999999 Done!