Query gi|254780894|ref|YP_003065307.1| hypothetical protein CLIBASIA_03955 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 103 No_of_seqs 46 out of 48 Neff 3.9 Searched_HMMs 39220 Date Mon May 30 00:36:08 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780894.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 TIGR02473 flagell_FliJ flagell 97.4 0.0065 1.6E-07 39.1 11.9 97 3-102 3-108 (141) 2 pfam02050 FliJ Flagellar FliJ 90.2 1.7 4.2E-05 23.9 13.4 100 2-101 4-109 (143) 3 COG4477 EzrA Negative regulato 88.7 2.1 5.4E-05 23.2 8.5 77 24-101 112-188 (570) 4 PRK06231 F0F1 ATP synthase sub 63.2 13 0.00033 18.3 6.4 42 56-97 66-107 (201) 5 PRK13453 F0F1 ATP synthase sub 61.0 14 0.00036 18.0 6.1 40 56-95 36-75 (173) 6 PRK13460 F0F1 ATP synthase sub 60.6 14 0.00037 18.0 6.1 41 55-95 33-73 (173) 7 PRK13461 F0F1 ATP synthase sub 59.9 15 0.00038 17.9 6.1 40 56-95 23-62 (159) 8 pfam00430 ATP-synt_B ATP synth 56.8 17 0.00043 17.6 6.1 39 56-94 17-55 (132) 9 pfam05983 Med7 MED7 protein. T 53.0 19 0.00049 17.2 5.0 34 3-36 127-160 (161) 10 PRK05759 F0F1 ATP synthase sub 50.2 21 0.00055 16.9 6.2 37 57-93 23-59 (156) 11 PRK07352 F0F1 ATP synthase sub 49.9 22 0.00055 16.9 6.2 40 56-95 37-76 (174) 12 PRK08476 F0F1 ATP synthase sub 49.5 22 0.00056 16.8 6.0 25 57-81 26-50 (141) 13 COG1071 AcoA Pyruvate/2-oxoglu 49.3 9.8 0.00025 19.1 1.6 69 1-74 284-356 (358) 14 CHL00019 atpF ATP synthase CF0 43.9 27 0.00068 16.3 6.2 40 56-95 42-81 (184) 15 TIGR01737 FGAM_synth_I phospho 37.2 34 0.00087 15.7 3.3 28 54-81 58-89 (264) 16 TIGR02044 CueR Cu(I)-responsiv 35.9 36 0.00091 15.5 3.9 24 14-37 87-110 (127) 17 PRK10636 putative ABC transpor 35.5 36 0.00092 15.5 11.4 74 19-94 555-630 (638) 18 TIGR01120 rpiB ribose 5-phosph 35.3 23 0.00058 16.8 1.7 20 51-70 32-51 (143) 19 pfam03962 Mnd1 Mnd1 family. Th 33.8 38 0.00098 15.3 9.4 66 13-93 62-127 (188) 20 CHL00118 atpG ATP synthase CF0 32.7 40 0.001 15.2 6.0 33 57-89 41-73 (156) 21 CHL00167 consensus 32.2 41 0.001 15.2 6.2 40 56-95 44-83 (182) 22 TIGR00689 rpiB_lacA_lacB sugar 32.1 32 0.00081 15.8 2.0 20 51-70 31-51 (146) 23 PRK10803 hypothetical protein; 30.4 44 0.0011 15.0 7.3 42 4-45 45-86 (262) 24 KOG2509 consensus 27.1 50 0.0013 14.6 7.4 69 11-94 46-114 (455) 25 COG0711 AtpF F0F1-type ATP syn 26.9 50 0.0013 14.6 6.2 30 57-86 25-54 (161) 26 TIGR01144 ATP_synt_b ATP synth 25.5 54 0.0014 14.4 6.3 44 57-100 14-57 (147) 27 pfam04652 DUF605 Vta1 like. Vt 25.4 54 0.0014 14.4 2.7 49 25-73 46-94 (312) 28 pfam03285 Paralemmin Paralemmi 24.7 55 0.0014 14.3 3.6 29 19-47 2-30 (270) 29 cd07624 BAR_SNX7_30 The Bin/Am 24.7 55 0.0014 14.3 9.3 74 28-101 75-159 (200) 30 COG2882 FliJ Flagellar biosynt 24.6 56 0.0014 14.3 13.1 97 2-99 5-108 (148) 31 pfam11180 DUF2968 Protein of u 24.5 56 0.0014 14.3 9.5 76 18-93 96-171 (192) 32 PRK08475 F0F1 ATP synthase sub 24.5 56 0.0014 14.3 6.2 39 57-95 43-81 (170) 33 COG4877 Uncharacterized protei 24.1 57 0.0014 14.3 2.7 38 8-45 19-56 (63) 34 PRK06986 fliA flagellar biosyn 24.1 57 0.0014 14.3 4.2 18 53-70 56-74 (234) 35 pfam12617 LdpA_C Iron-Sulfur b 23.5 42 0.0011 15.1 1.4 19 52-70 131-149 (182) 36 PRK07353 F0F1 ATP synthase sub 23.1 59 0.0015 14.1 6.0 25 57-81 24-48 (140) 37 pfam06160 EzrA Septation ring 21.0 65 0.0017 13.9 9.6 89 10-99 91-183 (559) 38 TIGR03007 pepcterm_ChnLen poly 20.9 66 0.0017 13.9 7.0 35 14-48 268-302 (510) 39 TIGR01256 modA molybdate ABC t 20.8 52 0.0013 14.5 1.4 24 47-70 105-128 (225) 40 pfam07321 YscO Type III secret 20.7 66 0.0017 13.8 10.9 92 4-95 2-93 (152) 41 TIGR00473 pssA CDP-diacylglyce 20.3 43 0.0011 15.0 0.9 12 6-17 104-115 (174) 42 TIGR01020 rpsE_arch ribosomal 20.1 47 0.0012 14.8 1.0 22 48-69 172-199 (220) 43 PRK04778 septation ring format 20.1 68 0.0017 13.7 9.7 89 10-99 95-187 (569) 44 COG4970 FimT Tfp pilus assembl 20.0 69 0.0017 13.7 4.2 34 56-91 26-59 (181) No 1 >TIGR02473 flagell_FliJ flagellar export protein FliJ; InterPro: IPR012823 Members of this family are the FliJ protein found, in nearly every case, in the midst of other flagellar biosynthesis genes in bacterial genomes. Typically the fliJ gene is found adjacent to the gene for the flagellum-specific ATPase FliI. Closely related sequences include both probable FliJ proteins and components of bacterial type III secretion systems.; GO: 0006935 chemotaxis, 0016020 membrane, 0044461 flagellin-based flagellum part. Probab=97.40 E-value=0.0065 Score=39.07 Aligned_cols=97 Identities=18% Similarity=0.181 Sum_probs=73.5 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHCCCCCCCCHHHHHHHHHHHHHH Q ss_conf 6788899999889999999999999999999999999999999---------9999715770014318999999999999 Q gi|254780894|r 3 LQEQRTRLKEFRLNDERRQLQQLRATILEFRRIVADLEKQIAI---------EERQVGIYDKDHFAYPILAKSARQRIDN 73 (103) Q Consensus 3 sretLIRLk~fqVdEkRR~laql~~m~~ef~~~~~~LE~qI~~---------Ee~~agi~d~~hFaY~tfAraa~~RRdn 73 (103) ++..|..|..++.| ....+|..++.+|..+...|..-+.. +...+|++.+.+..|+.|-...-.+++. T Consensus 3 ~L~~ll~lr~~~e~---~~~~~l~~~~~~~~~~~~~L~~l~~~~~~~~~~~~~~~~~g~s~~~~~~~~~f~~~l~~~i~~ 79 (141) T TIGR02473 3 RLQKLLDLREKEEE---QAKLELAKAQAEFERLETQLQQLIKYREEYEQQANEKVQSGTSAAELSNYQRFIRQLDEAIQQ 79 (141) T ss_pred CHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 07899999999999---999999999888888888888888888889999887631699999999898888888888888 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 99999999999999999999999997422 Q gi|254780894|r 74 LLLSIRDLLLRQESLESHLESESNSDKSV 102 (103) Q Consensus 74 L~~Si~~l~~Q~e~a~~~L~~a~~~~k~~ 102 (103) +...+..+..+.+.++..|.+++...|++ T Consensus 80 q~~~~~~~~~~~e~~r~~l~~~~~e~k~~ 108 (141) T TIGR02473 80 QQQELALLEKELEAKRERLLEAAKERKAL 108 (141) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 88888888888888888889999999999 No 2 >pfam02050 FliJ Flagellar FliJ protein. Probab=90.19 E-value=1.7 Score=23.90 Aligned_cols=100 Identities=15% Similarity=0.098 Sum_probs=80.2 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHCCCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 86788899999889999999999999999999999999999999999------971577001431899999999999999 Q gi|254780894|r 2 RLQEQRTRLKEFRLNDERRQLQQLRATILEFRRIVADLEKQIAIEER------QVGIYDKDHFAYPILAKSARQRIDNLL 75 (103) Q Consensus 2 KsretLIRLk~fqVdEkRR~laql~~m~~ef~~~~~~LE~qI~~Ee~------~agi~d~~hFaY~tfAraa~~RRdnL~ 75 (103) .++++|..|+....|+....|+...............|......=.. ..|++...--.|..|-...-....... T Consensus 4 frL~~vl~l~~~~ee~a~~~la~a~~~~~~~~~~L~~L~~~~~~y~~~~~~~~~~g~~~~~l~~~~~fi~~L~~~i~~q~ 83 (143) T pfam02050 4 FRLQTLLDLAEKAEEEAARQLGEAQRELEQAEQQLEQLEQYRQEYRQQLQSKGQQGISAAQLRNYQAFIAQLDQAIAQQQ 83 (143) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 32599999999999999999999999999999999999999999999999764289999999999999999999999999 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999999999999742 Q gi|254780894|r 76 LSIRDLLLRQESLESHLESESNSDKS 101 (103) Q Consensus 76 ~Si~~l~~Q~e~a~~~L~~a~~~~k~ 101 (103) ..+..+..+++.++..|-++.-..|+ T Consensus 84 ~~l~~~~~~~e~~r~~~~~a~~~~k~ 109 (143) T pfam02050 84 QQVAQAEQQVEQAREAWQEAQQKRKA 109 (143) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999999999999999999 No 3 >COG4477 EzrA Negative regulator of septation ring formation [Cell division and chromosome partitioning] Probab=88.74 E-value=2.1 Score=23.22 Aligned_cols=77 Identities=19% Similarity=0.157 Sum_probs=65.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999999999999999999997157700143189999999999999999999999999999999999999742 Q gi|254780894|r 24 QLRATILEFRRIVADLEKQIAIEERQVGIYDKDHFAYPILAKSARQRIDNLLLSIRDLLLRQESLESHLESESNSDKS 101 (103) Q Consensus 24 ql~~m~~ef~~~~~~LE~qI~~Ee~~agi~d~~hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~~L~~a~~~~k~ 101 (103) +|..+..+...+..++-.=+..|++-++-.+..-=-|.-.-+-+..+++++..++..++.+++.....|+ .|++++. T Consensus 112 ~l~~iE~~i~~il~~l~~Lv~sEekN~~~i~~~~ely~elr~~vl~n~~~~Ge~~~~lEk~Le~i~~~l~-qf~~lt~ 188 (570) T COG4477 112 QLTLIEEDIEQILEDLNELVESEEKNSEEIDHVLELYEELRRDVLANRHQYGEAAPELEKKLENIEEELS-QFVELTS 188 (570) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHCC T ss_conf 9999999999999999999998873478899999999999999987245532125899999999999999-9998615 No 4 >PRK06231 F0F1 ATP synthase subunit B; Validated Probab=63.24 E-value=13 Score=18.28 Aligned_cols=42 Identities=10% Similarity=0.038 Sum_probs=33.7 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 014318999999999999999999999999999999999999 Q gi|254780894|r 56 DHFAYPILAKSARQRIDNLLLSIRDLLLRQESLESHLESESN 97 (103) Q Consensus 56 ~hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~~L~~a~~ 97 (103) ..|+|+++.+.--.|++.+..++.+-....++|+.-+++.-. T Consensus 66 ~k~awKPI~k~Ld~R~~kI~~~L~~Aekar~EAe~ll~e~e~ 107 (201) T PRK06231 66 IFLFWKPTQRFLNKRKELIEAEINQANELKQQAQQLLENAKQ 107 (201) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999787899999999999999999999999999999999999 No 5 >PRK13453 F0F1 ATP synthase subunit B; Provisional Probab=60.99 E-value=14 Score=18.03 Aligned_cols=40 Identities=18% Similarity=0.155 Sum_probs=29.5 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 0143189999999999999999999999999999999999 Q gi|254780894|r 56 DHFAYPILAKSARQRIDNLLLSIRDLLLRQESLESHLESE 95 (103) Q Consensus 56 ~hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~~L~~a 95 (103) ..|+||++-+.--.|++.+...+.+.......|...+++. T Consensus 36 ~kf~~~pi~~~L~~R~~~I~~~l~~Ae~~k~eA~~~~~e~ 75 (173) T PRK13453 36 KKFAWGPLKDVMDKRERDINRDIDDAEQAKLNAQKLEEEN 75 (173) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9998989999999999999988999999999999999999 No 6 >PRK13460 F0F1 ATP synthase subunit B; Provisional Probab=60.62 E-value=14 Score=17.99 Aligned_cols=41 Identities=17% Similarity=0.193 Sum_probs=32.9 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 00143189999999999999999999999999999999999 Q gi|254780894|r 55 KDHFAYPILAKSARQRIDNLLLSIRDLLLRQESLESHLESE 95 (103) Q Consensus 55 ~~hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~~L~~a 95 (103) ..+|+||.+.+.--.|++.+..++.+-+....+|...+.+. T Consensus 33 l~kf~~~pi~~~Ld~R~~~I~~~l~~Ae~~k~eA~~~~~e~ 73 (173) T PRK13460 33 LKKFAWDVILKALDERASGVQNDINKASELRLEAEALLKDY 73 (173) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99996888999999999999988999999999999999999 No 7 >PRK13461 F0F1 ATP synthase subunit B; Provisional Probab=59.89 E-value=15 Score=17.91 Aligned_cols=40 Identities=13% Similarity=0.066 Sum_probs=30.9 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 0143189999999999999999999999999999999999 Q gi|254780894|r 56 DHFAYPILAKSARQRIDNLLLSIRDLLLRQESLESHLESE 95 (103) Q Consensus 56 ~hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~~L~~a 95 (103) .+|.||++.+.--.|++.+..++.+.....+.|...+++. T Consensus 23 ~kf~~~pi~~~l~~R~~~I~~~l~~Ae~~~~ea~~~~~e~ 62 (159) T PRK13461 23 KHFFFDKIKAVIDSRQSEIDEKIEKADEDAEKARELKLKN 62 (159) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9997888999999999999999999999999999999999 No 8 >pfam00430 ATP-synt_B ATP synthase B/B' CF(0). Part of the CF(0) (base unit) of the ATP synthase. The base unit is thought to translocate protons through membrane (inner membrane in mitochondria, thylakoid membrane in plants, cytoplasmic membrane in bacteria). The B subunits are thought to interact with the stalk of the CF(1) subunits. This domain should not be confused with the ab CF(1) proteins (in the head of the ATP synthase) which are found in pfam00006 Probab=56.79 E-value=17 Score=17.58 Aligned_cols=39 Identities=21% Similarity=0.233 Sum_probs=28.6 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 014318999999999999999999999999999999999 Q gi|254780894|r 56 DHFAYPILAKSARQRIDNLLLSIRDLLLRQESLESHLES 94 (103) Q Consensus 56 ~hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~~L~~ 94 (103) ..|.||++.+.--.|++.+..++.+.......+...+++ T Consensus 17 ~~~~~~pi~~~l~~R~~~I~~~l~~a~~~~~ea~~~~~~ 55 (132) T pfam00430 17 IYFGYKPLGKILDERKEKIANNIKEAEERLKQAAALLAE 55 (132) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999798899999999999999999999999999999999 No 9 >pfam05983 Med7 MED7 protein. This family consists of several eukaryotic proteins which are homologues of the yeast MED7 protein. Activation of gene transcription in metazoans is a multi-step process that is triggered by factors that recognize transcriptional enhancer sites in DNA. These factors work with co-activators such as MED7 to direct transcriptional initiation by the RNA polymerase II apparatus. Probab=52.98 E-value=19 Score=17.20 Aligned_cols=34 Identities=24% Similarity=0.446 Sum_probs=24.7 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 6788899999889999999999999999999999 Q gi|254780894|r 3 LQEQRTRLKEFRLNDERRQLQQLRATILEFRRIV 36 (103) Q Consensus 3 sretLIRLk~fqVdEkRR~laql~~m~~ef~~~~ 36 (103) +|+|||-+=+-|+++||-.+.++..+.++...++ T Consensus 127 AResLi~~me~Ql~~kr~~i~~i~~~~~~v~~~l 160 (161) T pfam05983 127 ARESLIMLMEEQLDEKREEIEAIRKVLEEVREVL 160 (161) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999999999999999999999999999999862 No 10 >PRK05759 F0F1 ATP synthase subunit B; Validated Probab=50.19 E-value=21 Score=16.92 Aligned_cols=37 Identities=16% Similarity=0.276 Sum_probs=18.4 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 1431899999999999999999999999999999999 Q gi|254780894|r 57 HFAYPILAKSARQRIDNLLLSIRDLLLRQESLESHLE 93 (103) Q Consensus 57 hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~~L~ 93 (103) .|.||.+.+.--.|++.+...+.+.+.....|...++ T Consensus 23 ~~~~~pi~~~l~~R~~~I~~~l~~Ae~~~~~a~~~~~ 59 (156) T PRK05759 23 KFVWPPIMKALEERQKKIADGLAAAERAKKELEAAQA 59 (156) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9978789999999999999899999999999999999 No 11 >PRK07352 F0F1 ATP synthase subunit B; Validated Probab=49.85 E-value=22 Score=16.89 Aligned_cols=40 Identities=18% Similarity=0.197 Sum_probs=31.0 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 0143189999999999999999999999999999999999 Q gi|254780894|r 56 DHFAYPILAKSARQRIDNLLLSIRDLLLRQESLESHLESE 95 (103) Q Consensus 56 ~hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~~L~~a 95 (103) .+|.||+..+.--.|++.+..++.+-..-..+|...|.+. T Consensus 37 ~~f~~~pi~~~L~~R~~~I~~~l~~Ae~~k~eA~~~l~e~ 76 (174) T PRK07352 37 YYFLRGFLGKILERRREAILQALKEAEERLRKAAQALAEA 76 (174) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9995989999999999999999999999999999999999 No 12 >PRK08476 F0F1 ATP synthase subunit B'; Validated Probab=49.47 E-value=22 Score=16.85 Aligned_cols=25 Identities=16% Similarity=0.214 Sum_probs=11.1 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 1431899999999999999999999 Q gi|254780894|r 57 HFAYPILAKSARQRIDNLLLSIRDL 81 (103) Q Consensus 57 hFaY~tfAraa~~RRdnL~~Si~~l 81 (103) +|.||+.-+..-.|.+.+..++... T Consensus 26 kflykPi~k~ld~R~~~I~~~l~~A 50 (141) T PRK08476 26 SWLYKPLLKFMDNRNASIKNDLEKV 50 (141) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9958789999999999999889999 No 13 >COG1071 AcoA Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion] Probab=49.30 E-value=9.8 Score=19.06 Aligned_cols=69 Identities=13% Similarity=0.142 Sum_probs=34.7 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----CCCCCCCCHHHHHHHHHHHHHHH Q ss_conf 986788899999889999999999999999999999999999999999971----57700143189999999999999 Q gi|254780894|r 1 MRLQEQRTRLKEFRLNDERRQLQQLRATILEFRRIVADLEKQIAIEERQVG----IYDKDHFAYPILAKSARQRIDNL 74 (103) Q Consensus 1 MKsretLIRLk~fqVdEkRR~laql~~m~~ef~~~~~~LE~qI~~Ee~~ag----i~d~~hFaY~tfAraa~~RRdnL 74 (103) ++++++|+||++|=++.--=-=.+++.+.++...++.+- .|...+. .++..+.-|..+....+.++..+ T Consensus 284 ~~~~DPi~r~~~~L~~~g~~see~~~~i~~e~~~~V~ea-----~e~a~~~p~P~~~~~~~~Vy~~~~~~l~~q~~~~ 356 (358) T COG1071 284 WKKRDPIVRLRKYLIEAGILSEEELEAIEAEAKAEVDEA-----VEFAEASPYPDVSELFEDVYAEGPPHLEEQREEL 356 (358) T ss_pred HHCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHH-----HHHHHHCCCCCHHHHHHCCCCCCCHHHHHHHHHH T ss_conf 750694999999999768989999999999999999999-----9999708999846765132147885089988763 No 14 >CHL00019 atpF ATP synthase CF0 B subunit Probab=43.87 E-value=27 Score=16.31 Aligned_cols=40 Identities=25% Similarity=0.256 Sum_probs=30.2 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 0143189999999999999999999999999999999999 Q gi|254780894|r 56 DHFAYPILAKSARQRIDNLLLSIRDLLLRQESLESHLESE 95 (103) Q Consensus 56 ~hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~~L~~a 95 (103) .+|.|+.+...--.|+++...+|.+-+....+|...|+++ T Consensus 42 ~~f~~~~L~~~L~~R~~~I~~~I~eAE~~~~eA~~~L~e~ 81 (184) T CHL00019 42 IYFGKGVLSDLLDNRKQRILNTIRNSEERREEAIEKLEKA 81 (184) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9995999999999999999999999999999999999999 No 15 >TIGR01737 FGAM_synth_I phosphoribosylformylglycinamidine synthase I; InterPro: IPR010075 In some species, phosphoribosylformylglycinamidine synthase is composed of a single polypeptide chain. This entry describes the PurQ protein of Bacillus subtilis (where PurL, PurQ, and PurS are required for phosphoribosylformylglycinamidine synthase activity) and functionally equivalent proteins from other bacteria and archaea.; GO: 0004642 phosphoribosylformylglycinamidine synthase activity, 0006189 'de novo' IMP biosynthetic process, 0005737 cytoplasm. Probab=37.21 E-value=34 Score=15.66 Aligned_cols=28 Identities=14% Similarity=0.305 Sum_probs=19.6 Q ss_pred CCCCCCHHHHHHH-HHHHH---HHHHHHHHHH Q ss_conf 7001431899999-99999---9999999999 Q gi|254780894|r 54 DKDHFAYPILAKS-ARQRI---DNLLLSIRDL 81 (103) Q Consensus 54 d~~hFaY~tfAra-a~~RR---dnL~~Si~~l 81 (103) -||+|.|+.|=|| ||..+ --+..-|.++ T Consensus 58 lPGGFSyGDYLRaGAIAa~rvk~p~~~~V~~~ 89 (264) T TIGR01737 58 LPGGFSYGDYLRAGAIAALRVKSPIMQEVREF 89 (264) T ss_pred ECCCCCHHHHHHHHHHHHHHCCHHHHHHHHHH T ss_conf 66877723577799999875030889999999 No 16 >TIGR02044 CueR Cu(I)-responsive transcriptional regulator; InterPro: IPR011789 This entry represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system . This protein is a member of the MerR family of transcriptional activators and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue .; GO: 0003677 DNA binding, 0005507 copper ion binding, 0016563 transcription activator activity, 0045941 positive regulation of transcription. Probab=35.91 E-value=36 Score=15.53 Aligned_cols=24 Identities=8% Similarity=0.302 Sum_probs=13.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 899999999999999999999999 Q gi|254780894|r 14 RLNDERRQLQQLRATILEFRRIVA 37 (103) Q Consensus 14 qVdEkRR~laql~~m~~ef~~~~~ 37 (103) +|+|--|++++|+.|...+..+++ T Consensus 87 k~~E~~~kI~eL~~m~~qL~~la~ 110 (127) T TIGR02044 87 KVAELERKISELQEMKDQLEELAE 110 (127) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 899999999999889999999998 No 17 >PRK10636 putative ABC transporter ATP-binding protein; Provisional Probab=35.47 E-value=36 Score=15.48 Aligned_cols=74 Identities=20% Similarity=0.230 Sum_probs=41.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999999999999999999999715770014318999--999999999999999999999999999999 Q gi|254780894|r 19 RRQLQQLRATILEFRRIVADLEKQIAIEERQVGIYDKDHFAYPILA--KSARQRIDNLLLSIRDLLLRQESLESHLES 94 (103) Q Consensus 19 RR~laql~~m~~ef~~~~~~LE~qI~~Ee~~agi~d~~hFaY~tfA--raa~~RRdnL~~Si~~l~~Q~e~a~~~L~~ 94 (103) +.+...++..++.++..+..||.+|..=+..- .||.-|..+..+ ..+.++.+.+...+.++..+-+++...|++ T Consensus 555 ~~~~~~~~~~~~~~e~~i~~le~~~~~l~~~l--~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~W~el~e~lE~ 630 (638) T PRK10636 555 RTQTQPLRKEIARLEKEMEKLNAQLAQAEEKL--GDSELYDQSRKAELTACLQQQASAKSGLEECEMAWLEAQEQLEQ 630 (638) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 87647999999999999999999999999984--39202356578999999999999999999999999999999999 No 18 >TIGR01120 rpiB ribose 5-phosphate isomerase B; InterPro: IPR004785 Ribose 5-phosphate isomerase (5.3.1.6 from EC) forms a homodimer and catalyses the interconversion of D-ribose 5-phosphate and D-ribulose 5-phosphate in the non-oxidative branch of the pentose phosphate pathway. This reaction permits the synthesis of ribose from other sugars, as well as the recycling of sugars from nucleotide breakdown. Two unrelated enzymes can catalyse this reaction: RpiA (found in most organisms) and RpiB (found in some bacteria and eukaryotes). RpiB is also involved in metabolism of the rare sugar, allose, in addition to ribose sugars. The structures of RpiA and RpiB are distinct, RpiB having a Rossmann-type alpha/beta/alpha sandwich topology . This entry represents the RpiB enzyme.; GO: 0004751 ribose-5-phosphate isomerase activity, 0006098 pentose-phosphate shunt. Probab=35.27 E-value=23 Score=16.75 Aligned_cols=20 Identities=25% Similarity=0.385 Sum_probs=14.3 Q ss_pred HCCCCCCCCHHHHHHHHHHH Q ss_conf 15770014318999999999 Q gi|254780894|r 51 GIYDKDHFAYPILAKSARQR 70 (103) Q Consensus 51 gi~d~~hFaY~tfAraa~~R 70 (103) |.-+...-.||.||+-+.+. T Consensus 32 GT~~~ertdYP~YAk~V~~a 51 (143) T TIGR01120 32 GTLASERTDYPDYAKEVVRA 51 (143) T ss_pred CCCCCCCCCCCHHHHHHHHH T ss_conf 37886763660689999999 No 19 >pfam03962 Mnd1 Mnd1 family. This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair. Probab=33.82 E-value=38 Score=15.32 Aligned_cols=66 Identities=24% Similarity=0.362 Sum_probs=46.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 88999999999999999999999999999999999997157700143189999999999999999999999999999999 Q gi|254780894|r 13 FRLNDERRQLQQLRATILEFRRIVADLEKQIAIEERQVGIYDKDHFAYPILAKSARQRIDNLLLSIRDLLLRQESLESHL 92 (103) Q Consensus 13 fqVdEkRR~laql~~m~~ef~~~~~~LE~qI~~Ee~~agi~d~~hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~~L 92 (103) .....+++.+..|..-+.+....+..|+.+|..+ +.|-.+. ..|..|..-+.+|..+....+.+| T Consensus 62 ~~~~~~~~~~~~L~~~~~~~~~~i~~l~~~i~~~--k~~r~~~-------------~er~~ll~~l~~l~~~~~~L~~el 126 (188) T pfam03962 62 QAKNKLKTRLEKLKKELEELKQRIAELQAQIEKL--KVGREET-------------EERTELLEELKQLEKELKKLKAEL 126 (188) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHCCCCC-------------HHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999999999999999999999999999999999--8658551-------------669999999999999999999999 Q ss_pred H Q ss_conf 9 Q gi|254780894|r 93 E 93 (103) Q Consensus 93 ~ 93 (103) + T Consensus 127 ~ 127 (188) T pfam03962 127 E 127 (188) T ss_pred H T ss_conf 9 No 20 >CHL00118 atpG ATP synthase CF0 B' subunit; Validated Probab=32.68 E-value=40 Score=15.20 Aligned_cols=33 Identities=9% Similarity=0.086 Sum_probs=14.3 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 143189999999999999999999999999999 Q gi|254780894|r 57 HFAYPILAKSARQRIDNLLLSIRDLLLRQESLE 89 (103) Q Consensus 57 hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~ 89 (103) .|.||++-+.--.|++.+..++.+.+.-.+.|. T Consensus 41 kf~~~Pi~~~ld~R~~~I~~~l~~Ae~~~~ea~ 73 (156) T CHL00118 41 AIFYKPIGKILDEREEYIRSNLAKASSKLAKAN 73 (156) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 998989999999999999988999999999999 No 21 >CHL00167 consensus Probab=32.22 E-value=41 Score=15.15 Aligned_cols=40 Identities=23% Similarity=0.213 Sum_probs=25.2 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 0143189999999999999999999999999999999999 Q gi|254780894|r 56 DHFAYPILAKSARQRIDNLLLSIRDLLLRQESLESHLESE 95 (103) Q Consensus 56 ~hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~~L~~a 95 (103) ..|.++.+-..--.|+++...+|.+-+.....|...|.++ T Consensus 44 ~~fg~~~L~~~L~~Rke~I~~~I~eAE~r~~eA~~~L~ea 83 (182) T CHL00167 44 IYLGKNFLGSSLEERQQKVLEAIQESEERLEQANSRLSES 83 (182) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9984676898999999999999999999999999999999 No 22 >TIGR00689 rpiB_lacA_lacB sugar-phosphate isomerases, RpiB/LacA/LacB family; InterPro: IPR003500 This entry represents the sugar isomerase enzymes ribose 5-phosphate isomerase B (rpiB), galactose isomerase subunit A (LacA) and galactose isomerase subunit B (LacB). Galactose-6-phosphate isomerase (5.3.1.26 from EC) is a heteromultimeric protein consisting of subunits LacA and LacB, and catalyses the conversion of D-galactose 6-phosphate to D-tagatose and 6-phosphate in the tagatose 6-phosphate pathway of lactose catabolism . Galactose-6-phosphate isomerase is induced by galactose or lactose. This entry represents the LacB subunit. Ribose 5-phosphate isomerase (5.3.1.6 from EC) forms a homodimer and catalyses the interconversion of D-ribose 5-phosphate and D-ribulose 5-phosphate in the non-oxidative branch of the pentose phosphate pathway. This reaction permits the synthesis of ribose from other sugars, as well as the recycling of sugars from nucleotide breakdown. Two unrelated enzymes can catalyse this reaction: RpiA (found in most organisms) and RpiB (found in some bacteria and eukaryotes). RpiB is also involved in metabolism of the rare sugar, allose, in addition to ribose sugars. The structures of RpiA and RpiB are distinct, RpiB having a Rossmann-type alpha/beta/alpha sandwich topology .; GO: 0005975 carbohydrate metabolic process. Probab=32.13 E-value=32 Score=15.84 Aligned_cols=20 Identities=30% Similarity=0.526 Sum_probs=15.0 Q ss_pred HCCC-CCCCCHHHHHHHHHHH Q ss_conf 1577-0014318999999999 Q gi|254780894|r 51 GIYD-KDHFAYPILAKSARQR 70 (103) Q Consensus 51 gi~d-~~hFaY~tfAraa~~R 70 (103) |..+ ...-.||.||..+.++ T Consensus 31 G~~~~~~~~DYPdYA~~Va~~ 51 (146) T TIGR00689 31 GTLEYDESVDYPDYAKLVAQK 51 (146) T ss_pred CCCCCCCCCCCHHHHHHHHHH T ss_conf 676788998874789999999 No 23 >PRK10803 hypothetical protein; Provisional Probab=30.37 E-value=44 Score=14.96 Aligned_cols=42 Identities=17% Similarity=0.162 Sum_probs=28.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 788899999889999999999999999999999999999999 Q gi|254780894|r 4 QEQRTRLKEFRLNDERRQLQQLRATILEFRRIVADLEKQIAI 45 (103) Q Consensus 4 retLIRLk~fqVdEkRR~laql~~m~~ef~~~~~~LE~qI~~ 45 (103) +|-++......+.+.++||.+++.-+.++.+.+.++..+|.. T Consensus 45 LEr~~~~~~~~~~qlq~Ql~~LQ~EV~~LRGqiEe~~~~l~q 86 (262) T PRK10803 45 LERISNAHSQLLTQLQQQLSDNQSDIDSLRGQIQENQYQLNQ 86 (262) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999999742799999999999999999998799999999999 No 24 >KOG2509 consensus Probab=27.14 E-value=50 Score=14.61 Aligned_cols=69 Identities=17% Similarity=0.163 Sum_probs=47.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99889999999999999999999999999999999999971577001431899999999999999999999999999999 Q gi|254780894|r 11 KEFRLNDERRQLQQLRATILEFRRIVADLEKQIAIEERQVGIYDKDHFAYPILAKSARQRIDNLLLSIRDLLLRQESLES 90 (103) Q Consensus 11 k~fqVdEkRR~laql~~m~~ef~~~~~~LE~qI~~Ee~~agi~d~~hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~ 90 (103) -+|++|+.+++-+.+...|.. ..|.. =|.....++.++.++.- .++-+|.....++......+++ T Consensus 46 ~~~~ldeln~~~n~l~k~i~~-~k~kk-ke~~~~l~~~~~~~~~~-------------~~~~~l~e~~~~~~~~~~~l~~ 110 (455) T KOG2509 46 TRFELDELNKEKNKLNKEIGD-LKLKK-KEDIGQLEESKAKNTEG-------------AERKLLKEEAVELEEDESKLED 110 (455) T ss_pred HHHHHHHHHHHHHHHHHHHHH-HHHHH-CCHHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHHHHHHHH T ss_conf 668788888888776667667-88764-02125777766676556-------------6655457887766789999999 Q ss_pred HHHH Q ss_conf 9999 Q gi|254780894|r 91 HLES 94 (103) Q Consensus 91 ~L~~ 94 (103) +|-+ T Consensus 111 el~~ 114 (455) T KOG2509 111 ELYE 114 (455) T ss_pred HHHH T ss_conf 9999 No 25 >COG0711 AtpF F0F1-type ATP synthase, subunit b [Energy production and conversion] Probab=26.95 E-value=50 Score=14.59 Aligned_cols=30 Identities=13% Similarity=0.199 Sum_probs=11.3 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 143189999999999999999999999999 Q gi|254780894|r 57 HFAYPILAKSARQRIDNLLLSIRDLLLRQE 86 (103) Q Consensus 57 hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e 86 (103) .|.||++-++--.|.+++...+.+-+.... T Consensus 25 ~~~~~pi~~~l~~R~~~I~~~l~~A~~~~~ 54 (161) T COG0711 25 KFVWKPILKALDERQAKIADDLAEAERLKE 54 (161) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 996867999999999999988999999899 No 26 >TIGR01144 ATP_synt_b ATP synthase F0, B subunit; InterPro: IPR005864 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (F-, V- and A-ATPases contain rotary motors) and in the type of ions they transport , . F-ATPases (F1F0-ATPases) in mitochondria, chloroplasts and bacterial plasma membranes are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases) are primarily found in eukaryotic vacuoles, catalysing ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases) are found in Archaea and function like F-ATPases. P-ATPases (E1E2-ATPases) are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis . These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunit B from the F0 complex in F-ATPases found in bacterial plasma membranes. The B subunits are part of the peripheral stalk that links the F1 and F0 complexes together, and which acts as a stator to prevent certain subunits from rotating with the central rotary element. The peripheral stalk differs in subunit composition between mitochondrial, chloroplast and bacterial F-ATPases. In bacterial F-ATPases, the peripheral stalk is composed of one copy of the delta subunit (homologous to OSCP in mitochondria), and two copies of subunit B . More information about this protein can be found at Protein of the Month: ATP Synthases .; GO: 0046933 hydrogen ion transporting ATP synthase activity rotational mechanism, 0046961 hydrogen ion transporting ATPase activity rotational mechanism, 0015986 ATP synthesis coupled proton transport, 0016469 proton-transporting two-sector ATPase complex. Probab=25.46 E-value=54 Score=14.42 Aligned_cols=44 Identities=14% Similarity=0.131 Sum_probs=31.0 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 14318999999999999999999999999999999999999974 Q gi|254780894|r 57 HFAYPILAKSARQRIDNLLLSIRDLLLRQESLESHLESESNSDK 100 (103) Q Consensus 57 hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~~L~~a~~~~k 100 (103) =|.||+.+++-=+|++++-+++.......+++...=..+-..+| T Consensus 14 KY~w~Pl~~~~~~R~~~IA~~L~~AE~~~~~~~~~~~~~~~~l~ 57 (147) T TIGR01144 14 KYVWPPLAKAIETRQKKIADDLASAERAKKEAALAQKEAQVLLK 57 (147) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 86237999999988998598899999988889999989889999 No 27 >pfam04652 DUF605 Vta1 like. Vta1 (VPS20-associated protein 1) is a positive regulator of Vps4. Vps4 is an ATPase that is required in the multivesicular body (MVB) sorting pathway to dissociate the endosomal sorting complex required for transport (ESCRT). Vta1 promotes correct assembly of Vps4 and stimulates its ATPase activity through its conserved Vta1/SBP1/LIP5 region. Probab=25.40 E-value=54 Score=14.41 Aligned_cols=49 Identities=14% Similarity=0.206 Sum_probs=34.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHH Q ss_conf 9999999999999999999999999715770014318999999999999 Q gi|254780894|r 25 LRATILEFRRIVADLEKQIAIEERQVGIYDKDHFAYPILAKSARQRIDN 73 (103) Q Consensus 25 l~~m~~ef~~~~~~LE~qI~~Ee~~agi~d~~hFaY~tfAraa~~RRdn 73 (103) +-.+++.++.+...+...-+...+.+|..-+-.||+-.|.+|-.+-|.+ T Consensus 46 l~~Lmd~LE~~K~~~~d~~ai~d~~~~~a~ve~FAl~lF~~AD~~dRag 94 (312) T pfam04652 46 LTKLLDQLEAFKKELGDNDAITDEVAAQAYVENFALKLFNRADKQDRAG 94 (312) T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 9999999999987567336564089999999999999999999998606 No 28 >pfam03285 Paralemmin Paralemmin. Probab=24.69 E-value=55 Score=14.32 Aligned_cols=29 Identities=24% Similarity=0.377 Sum_probs=18.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999999999999999999 Q gi|254780894|r 19 RRQLQQLRATILEFRRIVADLEKQIAIEE 47 (103) Q Consensus 19 RR~laql~~m~~ef~~~~~~LE~qI~~Ee 47 (103) |||+.+=+...-.|+.-|.+||++|..=+ T Consensus 2 rrQ~qEDE~k~k~LEe~I~RLE~Eie~LE 30 (270) T pfam03285 2 KKQMQEDEAKTRELEETIQRLERELEELE 30 (270) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 11677789999889999999999999885 No 29 >cd07624 BAR_SNX7_30 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexins 7 and 30. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. This subfamily consists of SNX7, SNX30, and similar proteins. The specific functions of SNX7 and SNX30 have not been elucidated. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. Probab=24.67 E-value=55 Score=14.32 Aligned_cols=74 Identities=22% Similarity=0.142 Sum_probs=42.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999999999999999971577001431899999999999999-----------999999999999999999999 Q gi|254780894|r 28 TILEFRRIVADLEKQIAIEERQVGIYDKDHFAYPILAKSARQRIDNLL-----------LSIRDLLLRQESLESHLESES 96 (103) Q Consensus 28 m~~ef~~~~~~LE~qI~~Ee~~agi~d~~hFaY~tfAraa~~RRdnL~-----------~Si~~l~~Q~e~a~~~L~~a~ 96 (103) +-.-++.-+.-++..+..+...-...---...|+.--+++..+||+.+ ....+|..+++.+++.++.+- T Consensus 75 ~~~~~d~~s~~l~~l~~~~~~~~~~~Lkeyv~y~~slk~vlk~Rdq~Q~~~E~~~e~L~~k~~eL~~~ve~~~~~~E~~~ 154 (200) T cd07624 75 VSSAVERCTAALEVLLSDHEFVFLPPLREYLLYSDAVKDVLKRRDQFQIEYELSVEELNKKRLELLKEVEKLQDKLECAN 154 (200) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99889999999999998537776788999999999999999989999987999999999879999988999888999988 Q ss_pred HHHHH Q ss_conf 99742 Q gi|254780894|r 97 NSDKS 101 (103) Q Consensus 97 ~~~k~ 101 (103) +..|+ T Consensus 155 ~~~k~ 159 (200) T cd07624 155 ADLKA 159 (200) T ss_pred HHHHH T ss_conf 99999 No 30 >COG2882 FliJ Flagellar biosynthesis chaperone [Cell motility and secretion / Intracellular trafficking and secretion / Posttranslational modification, protein turnover, chaperones] Probab=24.60 E-value=56 Score=14.32 Aligned_cols=97 Identities=11% Similarity=0.076 Sum_probs=64.7 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHH Q ss_conf 867888999998899999999999999999999999999-------9999999997157700143189999999999999 Q gi|254780894|r 2 RLQEQRTRLKEFRLNDERRQLQQLRATILEFRRIVADLE-------KQIAIEERQVGIYDKDHFAYPILAKSARQRIDNL 74 (103) Q Consensus 2 KsretLIRLk~fqVdEkRR~laql~~m~~ef~~~~~~LE-------~qI~~Ee~~agi~d~~hFaY~tfAraa~~RRdnL 74 (103) +++++|..|+++++++.-..|..+..-.......+..|. +++ ++.-.+|++...--+|-.|--..=...+.. T Consensus 5 ~~L~~l~dl~~k~~e~a~~el~k~~~~~~~~~~qL~~l~~y~~ey~q~~-~~k~~~G~s~~q~~nyq~fI~~Le~~I~q~ 83 (148) T COG2882 5 FALQKLLDLAKKEEEEAAIELSKIRSEKENAEEQLKMLSGYRNEYEQNL-NEKLKSGVSAAQWQNYQQFISQLEVAIDQQ 83 (148) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHCCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 4789999999977889999999999999999999999999999999888-998863450999999999999999999999 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999999999999997 Q gi|254780894|r 75 LLSIRDLLLRQESLESHLESESNSD 99 (103) Q Consensus 75 ~~Si~~l~~Q~e~a~~~L~~a~~~~ 99 (103) ...+..++-+++.++..+.+.--.. T Consensus 84 ~~~~~~~~~~ve~~r~~w~ek~~~~ 108 (148) T COG2882 84 QSQLSKLRKQVEQKREIWQEKQIEL 108 (148) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9889999999999999999999999 No 31 >pfam11180 DUF2968 Protein of unknown function (DUF2968). This family of proteins has no known function. Probab=24.52 E-value=56 Score=14.30 Aligned_cols=76 Identities=17% Similarity=0.153 Sum_probs=39.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999999999999999999999971577001431899999999999999999999999999999999 Q gi|254780894|r 18 ERRQLQQLRATILEFRRIVADLEKQIAIEERQVGIYDKDHFAYPILAKSARQRIDNLLLSIRDLLLRQESLESHLE 93 (103) Q Consensus 18 kRR~laql~~m~~ef~~~~~~LE~qI~~Ee~~agi~d~~hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~~L~ 93 (103) --.+|++.+.....++.....+|++|..-+.++.---..-=.-.+=-.++..|....+.-...|..|..++...|. T Consensus 96 Qt~~LA~~eirr~~LeAQka~~eR~ia~~q~ra~~Lqadl~~a~~Q~~~va~rQ~q~r~ea~aL~aqr~~aq~QL~ 171 (192) T pfam11180 96 QTAQLADVEIRRAQLEAQKAQLERQIAASEARAERLQADLQLAQAQEQQVAARQQQARQEAVALEAQRQAAQAQLR 171 (192) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999878999999999899999999999999999999779999999999999999999999999999999999999 No 32 >PRK08475 F0F1 ATP synthase subunit B; Validated Probab=24.46 E-value=56 Score=14.30 Aligned_cols=39 Identities=10% Similarity=0.181 Sum_probs=27.4 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 143189999999999999999999999999999999999 Q gi|254780894|r 57 HFAYPILAKSARQRIDNLLLSIRDLLLRQESLESHLESE 95 (103) Q Consensus 57 hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~~L~~a 95 (103) +|..+.....-..|++++..++.+.+....+|...|.++ T Consensus 43 yf~~kpi~~~l~~R~~~I~~~L~eae~~~~eA~~~l~~~ 81 (170) T PRK08475 43 YFAAKPIKNFYKSRINSISKRLEEIQAKLKESKEKKKDA 81 (170) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 992878999999899999999999999999999999999 No 33 >COG4877 Uncharacterized protein conserved in bacteria [Function unknown] Probab=24.10 E-value=57 Score=14.26 Aligned_cols=38 Identities=13% Similarity=0.058 Sum_probs=30.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999889999999999999999999999999999999 Q gi|254780894|r 8 TRLKEFRLNDERRQLQQLRATILEFRRIVADLEKQIAI 45 (103) Q Consensus 8 IRLk~fqVdEkRR~laql~~m~~ef~~~~~~LE~qI~~ 45 (103) --|.+|--||.|-.-+||+.|..|-.+...++-.++.. T Consensus 19 ~Aia~wA~de~RSiNaQIE~lL~E~lrq~gr~~~~~~d 56 (63) T COG4877 19 AAIAQWAEDEFRSINAQIEILLKEALRQRGRATADAAD 56 (63) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHCC T ss_conf 99999977777656689999999999982665033325 No 34 >PRK06986 fliA flagellar biosynthesis sigma factor; Validated Probab=24.06 E-value=57 Score=14.25 Aligned_cols=18 Identities=17% Similarity=0.270 Sum_probs=14.1 Q ss_pred CCCC-CCCHHHHHHHHHHH Q ss_conf 7700-14318999999999 Q gi|254780894|r 53 YDKD-HFAYPILAKSARQR 70 (103) Q Consensus 53 ~d~~-hFaY~tfAraa~~R 70 (103) .||. +|..+|||.-|+.. T Consensus 56 FDp~~G~rFsTYA~~~Ir~ 74 (234) T PRK06986 56 YDGEQGASFETYAGQRIRG 74 (234) T ss_pred HCCCCCCCHHHHHHHHHHH T ss_conf 1886699969999999999 No 35 >pfam12617 LdpA_C Iron-Sulfur binding protein C terminal. This domain family is found in bacteria and eukaryotes, and is typically between 179 and 201 amino acids in length. The family is found in association with pfam00037. LdpA (light-dependent period) plays a role in controlling the redox state in cyanobacteria to modulate its. circadian clock. LdpA is a protein with Iron-Sulfur cluster-binding motifs. Probab=23.50 E-value=42 Score=15.09 Aligned_cols=19 Identities=21% Similarity=-0.010 Sum_probs=15.1 Q ss_pred CCCCCCCCHHHHHHHHHHH Q ss_conf 5770014318999999999 Q gi|254780894|r 52 IYDKDHFAYPILAKSARQR 70 (103) Q Consensus 52 i~d~~hFaY~tfAraa~~R 70 (103) ...+.+.||++|||.-.+. T Consensus 131 ~~~~aGVAfGs~ARkll~p 149 (182) T pfam12617 131 SVFIAGVAYGSYARKLLQP 149 (182) T ss_pred CCCCCEEEECHHHHHHHHH T ss_conf 7788767761999999899 No 36 >PRK07353 F0F1 ATP synthase subunit B'; Validated Probab=23.06 E-value=59 Score=14.13 Aligned_cols=25 Identities=16% Similarity=0.191 Sum_probs=9.8 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 1431899999999999999999999 Q gi|254780894|r 57 HFAYPILAKSARQRIDNLLLSIRDL 81 (103) Q Consensus 57 hFaY~tfAraa~~RRdnL~~Si~~l 81 (103) .|.||++-+.--.|++.+..++.+. T Consensus 24 k~l~~Pi~~~ld~R~~~I~~~l~~A 48 (140) T PRK07353 24 ALFYKPVGKVVEEREDYIRTNRAEA 48 (140) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9988889999999999998889999 No 37 >pfam06160 EzrA Septation ring formation regulator, EzrA. During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation. Probab=21.02 E-value=65 Score=13.87 Aligned_cols=89 Identities=12% Similarity=0.156 Sum_probs=66.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9998899999999999999999999999999999----999999715770014318999999999999999999999999 Q gi|254780894|r 10 LKEFRLNDERRQLQQLRATILEFRRIVADLEKQI----AIEERQVGIYDKDHFAYPILAKSARQRIDNLLLSIRDLLLRQ 85 (103) Q Consensus 10 Lk~fqVdEkRR~laql~~m~~ef~~~~~~LE~qI----~~Ee~~agi~d~~hFaY~tfAraa~~RRdnL~~Si~~l~~Q~ 85 (103) +.+|.+-.-++.+.+++.++...+..+..+-.++ ..|++-...-+...=-|-.+-+.....+..+..++..|..|+ T Consensus 91 ~~~~rf~ka~~~i~~~~~~i~~~e~~i~~i~~~l~~L~~~e~~nr~~v~~lk~~y~~lrk~ll~~~~~yG~a~~~LE~~L 170 (559) T pfam06160 91 NDKFRFLKAKKAIKEIEELLDTIEEDIEQILEELNELKESEEKNRKEVEELKDKYRELRKTLLAKSFSYGPALDELEKQL 170 (559) T ss_pred HHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH T ss_conf 86062899999999999999999999999999999999878988999999999999999999985222013689999999 Q ss_pred HHHHHHHHHHHHHH Q ss_conf 99999999999997 Q gi|254780894|r 86 ESLESHLESESNSD 99 (103) Q Consensus 86 e~a~~~L~~a~~~~ 99 (103) +..+..+. .|+++ T Consensus 171 ~~ie~~F~-~f~~l 183 (559) T pfam06160 171 DELEEEFE-QFVEL 183 (559) T ss_pred HHHHHHHH-HHHHH T ss_conf 99999899-99999 No 38 >TIGR03007 pepcterm_ChnLen polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; InterPro: IPR014345 Members of this entry belong to the family of polysaccharide chain length determinant proteins. They are found in species that encode the PEP-CTERM/exosortase system and are predicted to act in protein sorting in a number of Gram-negative bacteria, they are also found near the epsH homologue that is the putative exosortase gene.. Probab=20.87 E-value=66 Score=13.85 Aligned_cols=35 Identities=23% Similarity=0.297 Sum_probs=16.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 89999999999999999999999999999999999 Q gi|254780894|r 14 RLNDERRQLQQLRATILEFRRIVADLEKQIAIEER 48 (103) Q Consensus 14 qVdEkRR~laql~~m~~ef~~~~~~LE~qI~~Ee~ 48 (103) ++|+.+=+-++-+--+-+.-+.+..|+.+-..|-+ T Consensus 268 ~Ld~L~l~YTd~HPdv~~~k~~Ia~L~~~~~~e~~ 302 (510) T TIGR03007 268 QLDALRLRYTDKHPDVIATKREIAQLEEQKEEELE 302 (510) T ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99986336301155899999999999999889998 No 39 >TIGR01256 modA molybdate ABC transporter, periplasmic molybdate-binding protein; InterPro: IPR005950 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 entry describes the molybdate ABC transporter periplasmic binding protein in bacteria and archae. Several of the periplasmic receptors constitute a diverse class of binding proteins that differ widely in size, sequence and ligand specificity. It has been shown experimentally by radioactive labeling that ModA represents a hydrophylioc periplasmic-binding protein in Gram-negative organisms and its counterpart in Gram-positive organisms is a lipoprotein. The other components of the system include ModB, an integral membrane protein and ModC, the ATP-binding subunit. Almost all of them display a common beta/alpha folding motif and have similar tertiary structures consisting of two globular domains.; GO: 0015412 molybdate transmembrane-transporting ATPase activity, 0015689 molybdate ion transport, 0030288 outer membrane-bounded periplasmic space. Probab=20.79 E-value=52 Score=14.50 Aligned_cols=24 Identities=33% Similarity=0.434 Sum_probs=20.7 Q ss_pred HHHHHCCCCCCCCHHHHHHHHHHH Q ss_conf 999715770014318999999999 Q gi|254780894|r 47 ERQVGIYDKDHFAYPILAKSARQR 70 (103) Q Consensus 47 e~~agi~d~~hFaY~tfAraa~~R 70 (103) -++.+|-||.|--||.||..|.+- T Consensus 105 ~~~vaigdP~~~P~G~~A~E~L~~ 128 (225) T TIGR01256 105 DKTVAIGDPKHAPYGAAAKEVLQK 128 (225) T ss_pred CCCCCCCCCCCCHHHHHHHHHHHH T ss_conf 370234682444357999999970 No 40 >pfam07321 YscO Type III secretion protein YscO. This family contains the bacterial type III secretion protein YscO, which is approximately 150 residues long. YscO has been shown to be required for high-level expression and secretion of the anti-host proteins V antigen and Yops in Yersinia pestis. Probab=20.74 E-value=66 Score=13.83 Aligned_cols=92 Identities=12% Similarity=0.107 Sum_probs=71.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 78889999988999999999999999999999999999999999997157700143189999999999999999999999 Q gi|254780894|r 4 QEQRTRLKEFRLNDERRQLQQLRATILEFRRIVADLEKQIAIEERQVGIYDKDHFAYPILAKSARQRIDNLLLSIRDLLL 83 (103) Q Consensus 4 retLIRLk~fqVdEkRR~laql~~m~~ef~~~~~~LE~qI~~Ee~~agi~d~~hFaY~tfAraa~~RRdnL~~Si~~l~~ 83 (103) ..+|.+++.|.+|.-.+.|.--+.....-......-..++..-..|-..-...-|+-+.-+--....-|.++..|+-|+. T Consensus 2 i~~Ll~Ik~~R~~~A~~a~~~qe~~l~~a~~~~~~a~~~~~dyr~Wr~~EE~Rl~~~~~~~~~~~kele~~q~~ia~Lr~ 81 (152) T pfam07321 2 IARLLEIKKLRAERAEKAVKRQEQALVQARARHREAQQSLQDYRQWRQQEENRLFAELQGATVLLKELEKWQQQVGLLRE 81 (152) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH T ss_conf 37789989998889999999999999999999999999898899988888998999985135107769999999899998 Q ss_pred HHHHHHHHHHHH Q ss_conf 999999999999 Q gi|254780894|r 84 RQESLESHLESE 95 (103) Q Consensus 84 Q~e~a~~~L~~a 95 (103) .-......+.++ T Consensus 82 ~e~~le~~~~ea 93 (152) T pfam07321 82 NEASLEQQLAEA 93 (152) T ss_pred HHHHHHHHHHHH T ss_conf 787899999999 No 41 >TIGR00473 pssA CDP-diacylglycerol--serine O-phosphatidyltransferase; InterPro: IPR004533 This enzyme, CDP-diacylglycerol--serine O-phosphatidyltransferase, is involved in phospholipid biosynthesis catalyzing the reaction CDP-diacylglycerol + L-serine = CMP + L-1-phosphatidylserine. Members of this family do not bear any significant sequence similarity to the corresponding Escherichia coli protein.; GO: 0003882 CDP-diacylglycerol-serine O-phosphatidyltransferase activity, 0008654 phospholipid biosynthetic process, 0046341 CDP-diacylglycerol metabolic process, 0016020 membrane. Probab=20.29 E-value=43 Score=15.03 Aligned_cols=12 Identities=25% Similarity=0.282 Sum_probs=8.7 Q ss_pred HHHHHHHHHHHH Q ss_conf 889999988999 Q gi|254780894|r 6 QRTRLKEFRLND 17 (103) Q Consensus 6 tLIRLk~fqVdE 17 (103) .++||+||+|.. T Consensus 104 G~lRLaRFNv~~ 115 (174) T TIGR00473 104 GILRLARFNVLT 115 (174) T ss_pred HHHHHHHHCCCC T ss_conf 999888733335 No 42 >TIGR01020 rpsE_arch ribosomal protein S5; InterPro: IPR005711 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . This model finds eukaryotic ribosomal protein S2 as well as archaeal ribosomal protein S5.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit. Probab=20.11 E-value=47 Score=14.78 Aligned_cols=22 Identities=27% Similarity=0.133 Sum_probs=15.6 Q ss_pred HHHHCCCCCCCCH------HHHHHHHHH Q ss_conf 9971577001431------899999999 Q gi|254780894|r 48 RQVGIYDKDHFAY------PILAKSARQ 69 (103) Q Consensus 48 ~~agi~d~~hFaY------~tfAraa~~ 69 (103) +-|||+|+=.|+- .+||||.=. T Consensus 172 ~LAGI~DVWt~T~G~T~Tt~NFAkAtF~ 199 (220) T TIGR01020 172 RLAGIKDVWTQTRGETRTTVNFAKATFE 199 (220) T ss_pred HHCCCCEEEECCCCCCCCCCHHHHHHHH T ss_conf 7459623540455602233038899999 No 43 >PRK04778 septation ring formation regulator EzrA; Provisional Probab=20.10 E-value=68 Score=13.75 Aligned_cols=89 Identities=15% Similarity=0.166 Sum_probs=66.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9998899999999999999999999999999999----999999715770014318999999999999999999999999 Q gi|254780894|r 10 LKEFRLNDERRQLQQLRATILEFRRIVADLEKQI----AIEERQVGIYDKDHFAYPILAKSARQRIDNLLLSIRDLLLRQ 85 (103) Q Consensus 10 Lk~fqVdEkRR~laql~~m~~ef~~~~~~LE~qI----~~Ee~~agi~d~~hFaY~tfAraa~~RRdnL~~Si~~l~~Q~ 85 (103) +.+|.+-.-++.+.+++.++...+..+..+-..+ ..|++-...-+...=-|-.+-+.....+..+..++..|..++ T Consensus 95 ~~~~rf~kak~~l~~~~~~l~~~e~~i~~i~~~l~~L~~~e~~nr~~v~~lk~~y~~lrk~ll~~~~~yG~a~~~LE~~L 174 (569) T PRK04778 95 NDKFRFFKAKHEINEIESLLDEIEEDIEQILEELQELLESEEKNREEVEQLKDKYRELRKSLLANSFSFGPALDELEKQL 174 (569) T ss_pred HHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH T ss_conf 87252899999999999999999999999999999999868998999999999999999999985221033699999999 Q ss_pred HHHHHHHHHHHHHH Q ss_conf 99999999999997 Q gi|254780894|r 86 ESLESHLESESNSD 99 (103) Q Consensus 86 e~a~~~L~~a~~~~ 99 (103) ...+..++ .|+++ T Consensus 175 ~~le~~f~-~f~~l 187 (569) T PRK04778 175 ENLEEEFS-QFVEL 187 (569) T ss_pred HHHHHHHH-HHHHH T ss_conf 99999899-99999 No 44 >COG4970 FimT Tfp pilus assembly protein FimT [Cell motility and secretion / Intracellular trafficking and secretion] Probab=20.03 E-value=69 Score=13.74 Aligned_cols=34 Identities=15% Similarity=0.108 Sum_probs=27.4 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 014318999999999999999999999999999999 Q gi|254780894|r 56 DHFAYPILAKSARQRIDNLLLSIRDLLLRQESLESH 91 (103) Q Consensus 56 ~hFaY~tfAraa~~RRdnL~~Si~~l~~Q~e~a~~~ 91 (103) ..||+|.|..-.. +..|.++..+|-..+--||.+ T Consensus 26 a~~A~P~fs~~i~--~~rl~s~a~eL~a~l~lARte 59 (181) T COG4970 26 AVIAAPNFSQWIR--SQRLRSAADELAAALQLARTE 59 (181) T ss_pred HHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHH T ss_conf 9985100888877--878988999999999999999 Done!