Query gi|254780723|ref|YP_003065136.1| hypothetical protein CLIBASIA_03050 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 137 No_of_seqs 72 out of 74 Neff 4.5 Searched_HMMs 39220 Date Sun May 29 19:43:11 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780723.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 COG4965 TadB Flp pilus assembl 99.6 1.3E-14 3.3E-19 110.2 8.7 116 6-137 2-122 (309) 2 COG3167 PilO Tfp pilus assembl 95.4 0.16 4E-06 30.0 8.5 86 6-93 24-117 (211) 3 CHL00118 atpG ATP synthase CF0 90.3 1.3 3.4E-05 24.3 6.5 30 1-30 18-48 (156) 4 CHL00019 atpF ATP synthase CF0 89.8 1.3 3.2E-05 24.5 6.1 17 14-30 34-50 (184) 5 PRK13453 F0F1 ATP synthase sub 87.9 2.4 6E-05 22.8 6.7 28 3-30 17-44 (173) 6 PRK07353 F0F1 ATP synthase sub 87.3 1.9 4.8E-05 23.4 5.6 30 1-30 1-31 (140) 7 PRK08475 F0F1 ATP synthase sub 86.6 0.6 1.5E-05 26.5 2.8 38 51-88 51-88 (170) 8 PRK13461 F0F1 ATP synthase sub 84.6 3.5 9E-05 21.8 6.6 28 3-30 4-31 (159) 9 PRK07352 F0F1 ATP synthase sub 82.4 4.3 0.00011 21.2 6.1 28 3-30 18-45 (174) 10 PRK13460 F0F1 ATP synthase sub 81.9 4.5 0.00011 21.1 6.1 27 5-31 17-43 (173) 11 PRK05759 F0F1 ATP synthase sub 81.6 4.6 0.00012 21.0 6.7 25 6-30 6-30 (156) 12 pfam11239 DUF3040 Protein of u 80.4 5.1 0.00013 20.8 7.6 62 61-126 8-73 (82) 13 pfam04888 SseC Secretion syste 73.7 7.8 0.0002 19.6 9.5 22 55-76 33-54 (303) 14 PRK12705 hypothetical protein; 72.8 8.3 0.00021 19.5 8.3 26 4-29 7-32 (485) 15 COG4235 Cytochrome c biogenesi 66.5 11 0.00027 18.8 4.2 27 4-33 1-27 (287) 16 PRK10236 hypothetical protein; 64.3 7.4 0.00019 19.8 3.1 55 55-114 117-176 (237) 17 TIGR01495 ETRAMP early transcr 62.4 12 0.0003 18.6 3.8 42 62-120 45-88 (99) 18 pfam06738 DUF1212 Protein of u 60.5 15 0.00037 18.0 6.3 37 96-132 102-138 (193) 19 pfam04156 IncA IncA protein. C 60.2 15 0.00038 17.9 7.8 22 8-29 39-60 (186) 20 COG0711 AtpF F0F1-type ATP syn 59.4 15 0.00039 17.9 6.0 25 7-31 9-33 (161) 21 PRK13454 F0F1 ATP synthase sub 56.6 17 0.00043 17.6 5.8 11 20-30 47-57 (181) 22 COG2165 PulG Type II secretory 49.8 22 0.00056 16.9 5.8 52 8-59 12-63 (149) 23 TIGR00792 gph sugar (Glycoside 47.3 24 0.00061 16.7 5.0 44 91-134 304-349 (470) 24 PRK10361 DNA recombination pro 46.4 25 0.00063 16.6 8.2 25 6-30 4-28 (475) 25 COG4120 ABC-type uncharacteriz 45.8 22 0.00057 16.9 3.0 23 8-30 136-158 (293) 26 KOG2890 consensus 44.1 17 0.00042 17.6 2.1 40 49-91 285-324 (326) 27 pfam11382 DUF3186 Protein of u 44.0 27 0.00068 16.3 3.3 14 80-93 101-114 (307) 28 pfam08566 Pam17 Mitochondrial 43.9 20 0.0005 17.2 2.5 27 3-30 74-100 (174) 29 pfam10779 XhlA Haemolysin XhlA 43.6 27 0.00069 16.3 4.1 57 58-118 2-59 (60) 30 PRK06231 F0F1 ATP synthase sub 42.1 25 0.00064 16.5 2.8 22 17-38 61-83 (201) 31 KOG1830 consensus 40.3 19 0.00049 17.2 2.0 16 61-76 163-178 (518) 32 pfam00430 ATP-synt_B ATP synth 40.0 31 0.00079 16.0 5.7 24 7-30 2-25 (132) 33 TIGR00883 2A0106 MFS transport 37.8 34 0.00085 15.8 4.9 54 77-135 211-270 (413) 34 pfam06024 DUF912 Nucleopolyhed 37.5 34 0.00086 15.7 3.2 31 2-32 59-89 (101) 35 TIGR01144 ATP_synt_b ATP synth 36.4 33 0.00085 15.8 2.7 14 54-67 71-84 (147) 36 pfam07578 LAB_N Lipid A Biosyn 35.2 37 0.00094 15.5 3.9 36 87-122 22-57 (72) 37 COG2966 Uncharacterized conser 34.6 38 0.00096 15.4 5.6 42 91-132 119-160 (250) 38 pfam09340 NuA4 Histone acetylt 33.4 37 0.00095 15.5 2.5 20 51-70 5-24 (80) 39 cd01324 cbb3_Oxidase_CcoQ Cyto 32.6 36 0.00091 15.6 2.3 33 5-42 12-44 (48) 40 pfam07332 DUF1469 Protein of u 32.5 41 0.001 15.2 6.4 12 125-136 61-72 (121) 41 pfam11026 DUF2721 Protein of u 31.7 42 0.0011 15.2 4.6 16 56-71 44-59 (130) 42 TIGR02745 ccoG_rdxA_fixG cytoc 31.4 43 0.0011 15.1 3.3 21 3-23 53-73 (474) 43 pfam04678 DUF607 Protein of un 30.5 42 0.0011 15.1 2.4 44 54-97 54-97 (171) 44 COG1575 MenA 1,4-dihydroxy-2-n 29.9 45 0.0012 15.0 3.1 56 60-122 194-249 (303) 45 pfam04791 LMBR1 LMBR1-like mem 29.3 46 0.0012 14.9 8.5 29 94-122 264-292 (419) 46 PRK09174 F0F1 ATP synthase sub 28.9 47 0.0012 14.9 6.1 24 7-30 55-79 (204) 47 PRK11404 putative PTS transpor 28.7 47 0.0012 14.8 3.8 34 99-133 127-160 (482) 48 pfam11970 Git3_C G protein-cou 28.3 37 0.00094 15.5 1.8 14 55-68 2-15 (76) 49 PRK03814 oxaloacetate decarbox 27.8 49 0.0013 14.7 3.7 29 1-29 1-30 (85) 50 pfam05039 Agouti Agouti protei 27.6 49 0.0013 14.7 2.5 56 17-73 7-65 (121) 51 pfam06120 Phage_HK97_TLTM Tail 26.5 52 0.0013 14.6 7.5 85 10-98 29-125 (311) 52 pfam01237 Oxysterol_BP Oxyster 25.2 45 0.0011 15.0 1.8 25 66-97 289-313 (337) 53 pfam03245 Phage_lysis Bacterio 24.0 58 0.0015 14.3 8.1 55 15-73 14-68 (151) 54 TIGR00833 actII Transport prot 23.7 58 0.0015 14.3 3.2 50 80-129 277-329 (992) 55 pfam06504 RepC Replication pro 23.5 59 0.0015 14.2 2.6 19 50-68 242-260 (283) 56 PRK10947 global DNA-binding tr 23.0 61 0.0015 14.2 3.5 36 54-93 38-73 (135) 57 TIGR01410 tatB twin arginine-t 22.8 61 0.0016 14.2 6.1 45 12-65 8-54 (82) 58 KOG1262 consensus 22.8 52 0.0013 14.6 1.7 52 7-69 24-76 (543) 59 pfam11022 DUF2611 Protein of u 22.2 56 0.0014 14.4 1.8 51 14-71 18-68 (70) 60 pfam00862 Sucrose_synth Sucros 22.0 61 0.0015 14.2 1.9 32 59-90 199-232 (550) 61 KOG2210 consensus 21.9 64 0.0016 14.1 2.2 27 65-98 336-362 (392) 62 TIGR03488 cas_Cas5p CRISPR-ass 21.0 62 0.0016 14.1 1.8 23 53-75 61-83 (237) 63 pfam10112 Halogen_Hydrol 5-bro 21.0 67 0.0017 13.9 4.5 10 93-102 120-129 (199) 64 pfam00429 TLV_coat ENV polypro 20.9 67 0.0017 13.9 6.8 67 56-127 492-558 (560) 65 PRK01021 lpxB lipid-A-disaccha 20.9 67 0.0017 13.9 4.1 10 55-64 456-465 (607) 66 pfam05399 EVI2A Ectropic viral 20.3 69 0.0018 13.8 5.1 33 4-36 126-158 (227) 67 COG2818 Tag 3-methyladenine DN 20.1 44 0.0011 15.0 0.9 12 81-92 146-157 (188) No 1 >COG4965 TadB Flp pilus assembly protein TadB [Intracellular trafficking and secretion] Probab=99.57 E-value=1.3e-14 Score=110.21 Aligned_cols=116 Identities=18% Similarity=0.259 Sum_probs=98.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHH-----CCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 6999999999999999999996306047789999999775420-----12205899999999999999999962237989 Q gi|254780723|r 6 SWFLVGLITVSVFCFLYAIFYNVINPGDSKSQDNAKVVRADRV-----IPTANTKRRKELREAIQKIELNHKAKIGNTKS 80 (137) Q Consensus 6 ~l~~~gL~~vavg~laya~~yp~ls~~~~~aqrr~~~~~a~R~-----~~~~~~kRRksvq~sLKelE~rqk~~~k~~~s 80 (137) .+++..++..++++++||++++. +.+++..++..++..+.-+ ...+..+|+.+++|+||++|+||+. T Consensus 2 ~~~~~~~~~~~~~~~~~a~~~~~-~~~~r~~~~~~~i~~~~~~~~~~~~~~~~~~r~~~~~~~l~~~~~~~~~------- 73 (309) T COG4965 2 ILFYLVLAALSALLLAYAFLGWR-SKSKRARIRNRRIKAAATDLSSALALRDLSSRRLSAQDSLKRLDRKQPR------- 73 (309) T ss_pred HHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHCCCHHHHHCCCHHHCCCCCCHHHHHHHHCCC------- T ss_conf 12999999999999999998488-8788988877889997733401788547023046554046667652244------- Q ss_pred HHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCCC Q ss_conf 899999619997899999999999999999999957118999999999974887659 Q gi|254780723|r 81 IDSLISCSGLPISKQHYYIGSCVIGFICGVLSLTLSSSFFTFLCVSVSSALVFPRFF 137 (137) Q Consensus 81 l~~rL~QAGL~~s~~~F~i~S~v~g~v~~~i~~i~g~~~l~a~g~a~~~glGLPRw~ 137 (137) |+|+.|+..+||++|++.+++.+++. .++.++++++ ++++++.++|||+ T Consensus 74 ------q~G~~~~~~~~~~l~~~~~l~~~~v~-~~~~~l~v~~-~~~~~~~llp~~~ 122 (309) T COG4965 74 ------QAGLRVSLARLILLSAGAGLAVALVA-WLGLSLLVAL-VALIGAALLPRLV 122 (309) T ss_pred ------CCCCCCCHHHHHHHHHHHHHHHHHHH-HHHCCHHHHH-HHHHHHHHHHHHH T ss_conf ------56656647999999999999999999-9861389999-9999999999999 No 2 >COG3167 PilO Tfp pilus assembly protein PilO [Cell motility and secretion / Intracellular trafficking and secretion] Probab=95.43 E-value=0.16 Score=30.01 Aligned_cols=86 Identities=12% Similarity=0.146 Sum_probs=52.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH--HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHH--HH----CC Q ss_conf 699999999999999999999630604778999999--97754201220589999999999999999996--22----37 Q gi|254780723|r 6 SWFLVGLITVSVFCFLYAIFYNVINPGDSKSQDNAK--VVRADRVIPTANTKRRKELREAIQKIELNHKA--KI----GN 77 (137) Q Consensus 6 ~l~~~gL~~vavg~laya~~yp~ls~~~~~aqrr~~--~~~a~R~~~~~~~kRRksvq~sLKelE~rqk~--~~----k~ 77 (137) -+++..|++++|.+++|.|+. .++-+..++.++. ..+..=+....+.---++++++|.|+|++=.. +. +- T Consensus 24 rlv~~lL~~~~V~~lGy~f~~--s~k~eel~~~~~eEe~LKs~~q~K~~~aanL~~lr~Ql~emee~~~~llrQLPs~tE 101 (211) T COG3167 24 RLVFCLLAVAAVLGLGYAFYL--SGKLEELEELEAEEEELKSTYQQKAIQAANLEALRAQLAEMEERFDILLRQLPSDTE 101 (211) T ss_pred HHHHHHHHHHHHHHHHHHHHH--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCCCCCC T ss_conf 999999999999999999985--407888999987799999999999998735599999999999999999985886210 Q ss_pred CCCHHHHHHHCCCCCC Q ss_conf 9898999996199978 Q gi|254780723|r 78 TKSIDSLISCSGLPIS 93 (137) Q Consensus 78 ~~sl~~rL~QAGL~~s 93 (137) -|+|-.-+.|+|++=. T Consensus 102 mp~Ll~dv~q~Gl~sg 117 (211) T COG3167 102 MPNLLADVNQAGLSSG 117 (211) T ss_pred HHHHHHHHHHHHHCCC T ss_conf 4679999987502247 No 3 >CHL00118 atpG ATP synthase CF0 B' subunit; Validated Probab=90.27 E-value=1.3 Score=24.31 Aligned_cols=30 Identities=30% Similarity=0.514 Sum_probs=18.5 Q ss_pred CCHHHHHHHHHHHHH-HHHHHHHHHHHHHCC Q ss_conf 970346999999999-999999999996306 Q gi|254780723|r 1 MFDVNSWFLVGLITV-SVFCFLYAIFYNVIN 30 (137) Q Consensus 1 m~~~~~l~~~gL~~v-avg~laya~~yp~ls 30 (137) |+|.|..++..++.. ...-+.+-|+||-+. T Consensus 18 ~~~~n~Tl~~q~i~FliL~~lL~kf~~~Pi~ 48 (156) T CHL00118 18 LFDFNATLPLMALQFLLLMVLLNAIFYKPIG 48 (156) T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 7086589999999999999999999898999 No 4 >CHL00019 atpF ATP synthase CF0 B subunit Probab=89.77 E-value=1.3 Score=24.48 Aligned_cols=17 Identities=18% Similarity=0.051 Sum_probs=9.1 Q ss_pred HHHHHHHHHHHHHHHCC Q ss_conf 99999999999996306 Q gi|254780723|r 14 TVSVFCFLYAIFYNVIN 30 (137) Q Consensus 14 ~vavg~laya~~yp~ls 30 (137) -+.+.|+.|-|.++.++ T Consensus 34 l~Ivi~iL~~f~~~~L~ 50 (184) T CHL00019 34 LSVVLGVLIYFGKGVLS 50 (184) T ss_pred HHHHHHHHHHHHHHHHH T ss_conf 99999999999599999 No 5 >PRK13453 F0F1 ATP synthase subunit B; Provisional Probab=87.92 E-value=2.4 Score=22.81 Aligned_cols=28 Identities=7% Similarity=0.163 Sum_probs=20.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 0346999999999999999999996306 Q gi|254780723|r 3 DVNSWFLVGLITVSVFCFLYAIFYNVIN 30 (137) Q Consensus 3 ~~~~l~~~gL~~vavg~laya~~yp~ls 30 (137) |..+++...+.-+....+.|-|+||-+. T Consensus 17 dw~t~~~q~I~F~il~~ll~kf~~~pi~ 44 (173) T PRK13453 17 EWGTVIVQVLTFIVLLALLKKFAWGPLK 44 (173) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 7899999999999999999999898999 No 6 >PRK07353 F0F1 ATP synthase subunit B'; Validated Probab=87.29 E-value=1.9 Score=23.40 Aligned_cols=30 Identities=20% Similarity=0.473 Sum_probs=17.1 Q ss_pred CCHHHHHHHHHHHHHHHH-HHHHHHHHHHCC Q ss_conf 970346999999999999-999999996306 Q gi|254780723|r 1 MFDVNSWFLVGLITVSVF-CFLYAIFYNVIN 30 (137) Q Consensus 1 m~~~~~l~~~gL~~vavg-~laya~~yp~ls 30 (137) |+|+|.-++.-++...+. -+.+-++||-+. T Consensus 1 m~~~n~Tl~~q~i~Flil~~il~k~l~~Pi~ 31 (140) T PRK07353 1 LFDFDATLPLMAVQFVLLTFILNALFYKPVG 31 (140) T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9151288999999999999999999888899 No 7 >PRK08475 F0F1 ATP synthase subunit B; Validated Probab=86.61 E-value=0.6 Score=26.46 Aligned_cols=38 Identities=11% Similarity=0.107 Sum_probs=19.1 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHC Q ss_conf 20589999999999999999996223798989999961 Q gi|254780723|r 51 TANTKRRKELREAIQKIELNHKAKIGNTKSIDSLISCS 88 (137) Q Consensus 51 ~~~~kRRksvq~sLKelE~rqk~~~k~~~sl~~rL~QA 88 (137) +.=..||++|.+.|.|+|+++++..+...-...+|++| T Consensus 51 ~~l~~R~~~I~~~L~eae~~~~eA~~~l~~~~~kLe~A 88 (170) T PRK08475 51 NFYKSRINSISKRLEEIQAKLKESKEKKKDALKKLEEA 88 (170) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99998999999999999999999999999999999999 No 8 >PRK13461 F0F1 ATP synthase subunit B; Provisional Probab=84.61 E-value=3.5 Score=21.76 Aligned_cols=28 Identities=11% Similarity=0.255 Sum_probs=20.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 0346999999999999999999996306 Q gi|254780723|r 3 DVNSWFLVGLITVSVFCFLYAIFYNVIN 30 (137) Q Consensus 3 ~~~~l~~~gL~~vavg~laya~~yp~ls 30 (137) |..+++...+.-+....+.+-|+||-+. T Consensus 4 n~~t~i~q~inF~il~~il~kf~~~pi~ 31 (159) T PRK13461 4 NIPTIIATIINFIILLLILKHFFFDKIK 31 (159) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 5999999999999999999999788899 No 9 >PRK07352 F0F1 ATP synthase subunit B; Validated Probab=82.36 E-value=4.3 Score=21.20 Aligned_cols=28 Identities=14% Similarity=0.110 Sum_probs=15.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 0346999999999999999999996306 Q gi|254780723|r 3 DVNSWFLVGLITVSVFCFLYAIFYNVIN 30 (137) Q Consensus 3 ~~~~l~~~gL~~vavg~laya~~yp~ls 30 (137) |.|.++.-.+.-+-..++.|-|+||-+. T Consensus 18 n~~~l~~~iInf~Il~~iL~~f~~~pi~ 45 (174) T PRK07352 18 NLNLLETNLINLAIVIGLLYYFLRGFLG 45 (174) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9128999999999999999999598999 No 10 >PRK13460 F0F1 ATP synthase subunit B; Provisional Probab=81.92 E-value=4.5 Score=21.10 Aligned_cols=27 Identities=15% Similarity=0.038 Sum_probs=16.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCH Q ss_conf 469999999999999999999963060 Q gi|254780723|r 5 NSWFLVGLITVSVFCFLYAIFYNVINP 31 (137) Q Consensus 5 ~~l~~~gL~~vavg~laya~~yp~ls~ 31 (137) ..++...+.-+....+.|-|+||.+.. T Consensus 17 ~~~iw~~i~F~il~~il~kf~~~pi~~ 43 (173) T PRK13460 17 GLVVWTLVTFLVVVLVLKKFAWDVILK 43 (173) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 799999999999999999996888999 No 11 >PRK05759 F0F1 ATP synthase subunit B; Validated Probab=81.65 E-value=4.6 Score=21.04 Aligned_cols=25 Identities=8% Similarity=0.021 Sum_probs=14.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 6999999999999999999996306 Q gi|254780723|r 6 SWFLVGLITVSVFCFLYAIFYNVIN 30 (137) Q Consensus 6 ~l~~~gL~~vavg~laya~~yp~ls 30 (137) |++...+..+-...+.|-|+||-+. T Consensus 6 T~~~~~I~F~il~~ll~~~~~~pi~ 30 (156) T PRK05759 6 TLIGQLIAFLILVWFCMKFVWPPIM 30 (156) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999999999999999999787899 No 12 >pfam11239 DUF3040 Protein of unknown function (DUF3040). Some members in this family of proteins with unknown function are annotated as membrane proteins however this cannot be confirmed. Probab=80.41 E-value=5.1 Score=20.78 Aligned_cols=62 Identities=11% Similarity=0.055 Sum_probs=31.6 Q ss_pred HHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHC----CHHHHHHHHH Q ss_conf 99999999999962237989899999619997899999999999999999999957----1189999999 Q gi|254780723|r 61 REAIQKIELNHKAKIGNTKSIDSLISCSGLPISKQHYYIGSCVIGFICGVLSLTLS----SSFFTFLCVS 126 (137) Q Consensus 61 q~sLKelE~rqk~~~k~~~sl~~rL~QAGL~~s~~~F~i~S~v~g~v~~~i~~i~g----~~~l~a~g~a 126 (137) |.-|+|+|+.=.+. .|.+...++..+..+....-. +-++++++..++.++.| ..++..+|+. T Consensus 8 qr~L~eiE~~L~~e---DP~fa~~~~~~~~~~~~~rr~-~~~~~~~v~Gl~~lv~Gv~~~~~~lgv~GFl 73 (82) T pfam11239 8 QRRLEEIERALYAE---DPKFAAAVRSGRPRRPSRRRI-VLGVLAAVLGVALLVAGVVLQQPPLGVAGFL 73 (82) T ss_pred HHHHHHHHHHHHHC---CHHHHHHHCCCCCCCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999843---979999751578888761269-9999999999999999999999999999999 No 13 >pfam04888 SseC Secretion system effector C (SseC) like family. SseC is a secreted protein that forms a complex together with SecB and SecD on the surface of Salmonella. All these proteins are secreted by the type III secretion system. Many mucosal pathogens use type III secretion systems for the injection of effector proteins into target cells. SecB, SseC and SecD are inserted into the target cell membrane. where they form a small pore or translocon. In addition to SseC, this family includes the bacterial secreted proteins PopB, PepB, YopB and EspD which are thought to be directly involved in pore formation, and type III secretion system translocon. Probab=73.74 E-value=7.8 Score=19.62 Aligned_cols=22 Identities=23% Similarity=0.229 Sum_probs=11.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHC Q ss_conf 9999999999999999996223 Q gi|254780723|r 55 KRRKELREAIQKIELNHKAKIG 76 (137) Q Consensus 55 kRRksvq~sLKelE~rqk~~~k 76 (137) ++-+..++.++|.|+++++.+| T Consensus 33 ~k~~e~~e~i~e~~~kaeea~K 54 (303) T pfam04888 33 KKAEEYQEQIKKAIEKAEEAKK 54 (303) T ss_pred HHHHHHHHHHHHHHHHHHHHHH T ss_conf 9899999999999999999986 No 14 >PRK12705 hypothetical protein; Provisional Probab=72.79 E-value=8.3 Score=19.48 Aligned_cols=26 Identities=19% Similarity=0.066 Sum_probs=13.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 34699999999999999999999630 Q gi|254780723|r 4 VNSWFLVGLITVSVFCFLYAIFYNVI 29 (137) Q Consensus 4 ~~~l~~~gL~~vavg~laya~~yp~l 29 (137) +++.++.+|+.+.+|-..+.+++-.. T Consensus 7 ~~~~~i~~l~~~~ig~~lg~~~~~~~ 32 (485) T PRK12705 7 VLTILVLFLILVLIGLVLGVFIRYLY 32 (485) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999999999999999999 No 15 >COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones] Probab=66.52 E-value=11 Score=18.80 Aligned_cols=27 Identities=11% Similarity=0.346 Sum_probs=18.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCHHH Q ss_conf 346999999999999999999996306047 Q gi|254780723|r 4 VNSWFLVGLITVSVFCFLYAIFYNVINPGD 33 (137) Q Consensus 4 ~~~l~~~gL~~vavg~laya~~yp~ls~~~ 33 (137) |+.|+++.+-+..+. +..+||+..+.+ T Consensus 1 m~fw~~~a~~~~~~~---~~l~~pL~~~~~ 27 (287) T COG4235 1 MAFWLAAALLTLAAA---ALLLLPLARARE 27 (287) T ss_pred CCHHHHHHHHHHHHH---HHHHHHHHHCCC T ss_conf 918999999999999---999899986130 No 16 >PRK10236 hypothetical protein; Provisional Probab=64.30 E-value=7.4 Score=19.77 Aligned_cols=55 Identities=18% Similarity=0.314 Sum_probs=24.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHH-----CCCCCHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999999999999622-----379898999996199978999999999999999999999 Q gi|254780723|r 55 KRRKELREAIQKIELNHKAKI-----GNTKSIDSLISCSGLPISKQHYYIGSCVIGFICGVLSLT 114 (137) Q Consensus 55 kRRksvq~sLKelE~rqk~~~-----k~~~sl~~rL~QAGL~~s~~~F~i~S~v~g~v~~~i~~i 114 (137) -=.|-++++|.++.+.+++.- .+.-.+... +++....+-+.+.+.++...-++.+ T Consensus 117 lL~Kil~~sl~kMs~ee~~el~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~s~~lt~i 176 (237) T PRK10236 117 LLEQFLRNTWKKMDEEHKQEFLHAVDARVNELEEL-----LPLLMKDKLLAKGVSHLLSSQLTRI 176 (237) T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999779999999999827764427888-----9999999999987778899999999 No 17 >TIGR01495 ETRAMP early transcribed membrane protein (ETRAMP) family; InterPro: IPR006389 These sequences represent a family of proteins from the malaria parasite Plasmodium falciparum, several of which have been shown to be expressed specifically in the ring stage as well as the rodent parasite Plasmodium yoelii . A homolog from Plasmodium chabaudi was localized to the parasitophorous vacuole membrane . Members have an initial hydrophobic, Phe/Tyr-rich stretch long enough to span the membrane, a highly charged region rich in Lys, a second putative transmembrane region, and a second highly charged, low complexity sequence region. Some members have up to 100 residues of additional C-terminal sequence. These genes have been shown to be found in the sub-telomeric regions of both Plasmodium falciparum and P. yoelii chromosomes.. Probab=62.38 E-value=12 Score=18.55 Aligned_cols=42 Identities=12% Similarity=0.206 Sum_probs=29.6 Q ss_pred HHHHHHHHHHHHH-HCCCCCHHHHHHHCCCCCCHHHHHHHH-HHHHHHHHHHHHHHCCHHH Q ss_conf 9999999999962-237989899999619997899999999-9999999999999571189 Q gi|254780723|r 62 EAIQKIELNHKAK-IGNTKSIDSLISCSGLPISKQHYYIGS-CVIGFICGVLSLTLSSSFF 120 (137) Q Consensus 62 ~sLKelE~rqk~~-~k~~~sl~~rL~QAGL~~s~~~F~i~S-~v~g~v~~~i~~i~g~~~l 120 (137) +.+|.+|+.+++| +++ ++-.++| ++...++.++...+|.+.. T Consensus 45 kn~kkl~~~~~~KkNr~-----------------~k~ilySl~~as~lAlL~g~~~GlG~y 88 (99) T TIGR01495 45 KNLKKLTKAEKKKKNRN-----------------KKIILYSLSIASGLALLVGAGVGLGYY 88 (99) T ss_pred HHHCCCCHHHHHHHHHH-----------------HHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 10024218999877775-----------------227999899999999999999999998 No 18 >pfam06738 DUF1212 Protein of unknown function (DUF1212). This family represents a conserved region within a number of hypothetical proteins of unknown function found in eukaryotes, bacteria and archaea. Some family members are membrane proteins. Probab=60.54 E-value=15 Score=17.98 Aligned_cols=37 Identities=11% Similarity=0.249 Sum_probs=30.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHC Q ss_conf 9999999999999999999571189999999999748 Q gi|254780723|r 96 HYYIGSCVIGFICGVLSLTLSSSFFTFLCVSVSSALV 132 (137) Q Consensus 96 ~F~i~S~v~g~v~~~i~~i~g~~~l~a~g~a~~~glG 132 (137) ..|......++.++..++++|+++.-.+..+++++++ T Consensus 102 ~~~~~~l~~~~~~~~fa~l~gG~~~~~~~a~i~g~~~ 138 (193) T pfam06738 102 PRWLVVLAAGLASAAFAVLFGGDWIDFLIAFLAGLLG 138 (193) T ss_pred CHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH T ss_conf 8799999999999999999879779999999999999 No 19 >pfam04156 IncA IncA protein. Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is non-fusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA, is functionally associated with the homotypic fusion of inclusions. This family probably includes members of the wider Inc family rather than just IncA. Probab=60.18 E-value=15 Score=17.94 Aligned_cols=22 Identities=18% Similarity=0.196 Sum_probs=11.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHC Q ss_conf 9999999999999999999630 Q gi|254780723|r 8 FLVGLITVSVFCFLYAIFYNVI 29 (137) Q Consensus 8 ~~~gL~~vavg~laya~~yp~l 29 (137) .+.|++.+++|++.+++.+-.+ T Consensus 39 ~~lg~~~la~g~vLl~~g~~~l 60 (186) T pfam04156 39 TLLGIALLALGLVLLALGLLCL 60 (186) T ss_pred HHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999999999999999999999 No 20 >COG0711 AtpF F0F1-type ATP synthase, subunit b [Energy production and conversion] Probab=59.39 E-value=15 Score=17.86 Aligned_cols=25 Identities=12% Similarity=0.081 Sum_probs=15.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCH Q ss_conf 9999999999999999999963060 Q gi|254780723|r 7 WFLVGLITVSVFCFLYAIFYNVINP 31 (137) Q Consensus 7 l~~~gL~~vavg~laya~~yp~ls~ 31 (137) ++...+.-+--..+.|-|+||-+.+ T Consensus 9 ~~~~~i~F~ill~ll~~~~~~pi~~ 33 (161) T COG0711 9 ILWQLIAFVILLWLLKKFVWKPILK 33 (161) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999999999999999996867999 No 21 >PRK13454 F0F1 ATP synthase subunit B'; Provisional Probab=56.59 E-value=17 Score=17.57 Aligned_cols=11 Identities=18% Similarity=0.120 Sum_probs=5.7 Q ss_pred HHHHHHHHHCC Q ss_conf 99999996306 Q gi|254780723|r 20 FLYAIFYNVIN 30 (137) Q Consensus 20 laya~~yp~ls 30 (137) +.+=|+.|.++ T Consensus 47 vl~k~~lPrI~ 57 (181) T PRK13454 47 VLTRVALPRIG 57 (181) T ss_pred HHHHHHHHHHH T ss_conf 99999998889 No 22 >COG2165 PulG Type II secretory pathway, pseudopilin PulG [Cell motility and secretion / Intracellular trafficking and secretion] Probab=49.80 E-value=22 Score=16.90 Aligned_cols=52 Identities=19% Similarity=0.181 Sum_probs=33.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHH Q ss_conf 9999999999999999999630604778999999977542012205899999 Q gi|254780723|r 8 FLVGLITVSVFCFLYAIFYNVINPGDSKSQDNAKVVRADRVIPTANTKRRKE 59 (137) Q Consensus 8 ~~~gL~~vavg~laya~~yp~ls~~~~~aqrr~~~~~a~R~~~~~~~kRRks 59 (137) ++-.|+++++.|++-++..|.+.....++++......+.+.........+.. T Consensus 12 LiElLVvl~Iigil~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 (149) T COG2165 12 LIELLVVLAIIGILAALALPSLQGSIDKAKRLEAAQQALRVIRLALEEYRLD 63 (149) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999999999999999999999998899999999999999999999999980 No 23 >TIGR00792 gph sugar (Glycoside-Pentoside-Hexuronide) transporter; InterPro: IPR001927 It has been shown that integral membrane proteins that mediate the intake of a wide variety of molecules with the concomitant uptake of sodium ions (sodium symporters) can be grouped, on the basis of sequence and functional similarities into a number of distinct families. This collection of sequences represents the sodium: galactoside symporter family (SGF). Like sugar transport proteins, these integral membrane proteins are predicted to comprise twelve membrane spanning domains. ; GO: 0005215 transporter activity, 0006814 sodium ion transport, 0016020 membrane. Probab=47.30 E-value=24 Score=16.66 Aligned_cols=44 Identities=5% Similarity=0.104 Sum_probs=37.8 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHC--CHHHHHHHHHHHHHHCCC Q ss_conf 97899999999999999999999957--118999999999974887 Q gi|254780723|r 91 PISKQHYYIGSCVIGFICGVLSLTLS--SSFFTFLCVSVSSALVFP 134 (137) Q Consensus 91 ~~s~~~F~i~S~v~g~v~~~i~~i~g--~~~l~a~g~a~~~glGLP 134 (137) .+++++.|..+.++.++..++.++.+ .+.....-..+++++|.+ T Consensus 304 ~~grk~~~~~~~~~~~~g~l~~~~~~~A~~~~~~~~~~~~~~~~~~ 349 (470) T TIGR00792 304 KFGRKRLFLIGILLMVLGLLILFFVGKASNLPLILVLIIIAGFGQN 349 (470) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 6125999999999999999999873167799999999999988776 No 24 >PRK10361 DNA recombination protein RmuC; Provisional Probab=46.40 E-value=25 Score=16.58 Aligned_cols=25 Identities=8% Similarity=-0.016 Sum_probs=16.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 6999999999999999999996306 Q gi|254780723|r 6 SWFLVGLITVSVFCFLYAIFYNVIN 30 (137) Q Consensus 6 ~l~~~gL~~vavg~laya~~yp~ls 30 (137) |+|++.++++....++|-+.+...+ T Consensus 4 ~~~i~~i~al~G~~igwl~~~~~~~ 28 (475) T PRK10361 4 SIMVYAVIALVGVAIGWLFASYQHA 28 (475) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 7999999999999999999998734 No 25 >COG4120 ABC-type uncharacterized transport system, permease component [General function prediction only] Probab=45.81 E-value=22 Score=16.85 Aligned_cols=23 Identities=0% Similarity=0.128 Sum_probs=9.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 99999999999999999996306 Q gi|254780723|r 8 FLVGLITVSVFCFLYAIFYNVIN 30 (137) Q Consensus 8 ~~~gL~~vavg~laya~~yp~ls 30 (137) ++.+..++.+.-+.|-|+...++ T Consensus 136 li~~vlvii~~~~v~~fl~t~~G 158 (293) T COG4120 136 LILVVLVIIAKLLVIRFLKTDLG 158 (293) T ss_pred HHHHHHHHHHHHHHHHHHHCCCC T ss_conf 99999999999999999734536 No 26 >KOG2890 consensus Probab=44.09 E-value=17 Score=17.64 Aligned_cols=40 Identities=15% Similarity=0.082 Sum_probs=22.4 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCC Q ss_conf 1220589999999999999999996223798989999961999 Q gi|254780723|r 49 IPTANTKRRKELREAIQKIELNHKAKIGNTKSIDSLISCSGLP 91 (137) Q Consensus 49 ~~~~~~kRRksvq~sLKelE~rqk~~~k~~~sl~~rL~QAGL~ 91 (137) .+..++.||+| ..||++|+|=|+-+-. |..+..=.++|++ T Consensus 285 ~d~~d~eRRRQ--~alkaL~eRl~~~~~~-p~~~~~~~~~~~d 324 (326) T KOG2890 285 LDPKDAERRRQ--LALKALEERLKKTRTA-PVASYDEWDDGDD 324 (326) T ss_pred CCHHHHHHHHH--HHHHHHHHHHCCCCCC-CCCCCCCHHHCCC T ss_conf 98127889999--9999999985685547-5556652210699 No 27 >pfam11382 DUF3186 Protein of unknown function (DUF3186). This bacterial family of proteins has no known function. Probab=44.01 E-value=27 Score=16.35 Aligned_cols=14 Identities=7% Similarity=0.342 Sum_probs=9.6 Q ss_pred CHHHHHHHCCCCCC Q ss_conf 98999996199978 Q gi|254780723|r 80 SIDSLISCSGLPIS 93 (137) Q Consensus 80 sl~~rL~QAGL~~s 93 (137) .+...|++||=+.+ T Consensus 101 ~v~~~l~~AGa~V~ 114 (307) T pfam11382 101 AVSEALTQAGATVV 114 (307) T ss_pred HHHHHHHHCCCEEE T ss_conf 99999998699146 No 28 >pfam08566 Pam17 Mitochondrial import protein Pam17. The presequence translocase-associated motor (PAM) drives the completion of preprotein translocation into the mitochondrial matrix. The Pam17 subunit is required for formation of a stable complex between cochaperones Pam16 and Pam18 and promotes the association of Pam16-Pam18 with the presequence translocase. Mitochondria lacking Pam17 are selectively impaired in the import of matrix proteins. Probab=43.93 E-value=20 Score=17.19 Aligned_cols=27 Identities=15% Similarity=0.332 Sum_probs=21.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 0346999999999999999999996306 Q gi|254780723|r 3 DVNSWFLVGLITVSVFCFLYAIFYNVIN 30 (137) Q Consensus 3 ~~~~l~~~gL~~vavg~laya~~yp~ls 30 (137) -+|-+++.|+++++++++.|-+. |.++ T Consensus 74 GlDP~~~~g~~~~a~~~~G~L~G-P~iG 100 (174) T pfam08566 74 GLDPFMVLGLATIACGALGWLLG-PFIG 100 (174) T ss_pred CCCHHHHHHHHHHHHHHHHHHHC-CHHH T ss_conf 85889999999999742557516-3678 No 29 >pfam10779 XhlA Haemolysin XhlA. XhlA is a cell-surface associated haemolysin that lyses the two most prevalent types of insect immune cells (granulocytes and plasmatocytes) as well as rabbit and horse erythrocytes. Probab=43.60 E-value=27 Score=16.31 Aligned_cols=57 Identities=25% Similarity=0.392 Sum_probs=32.5 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCHHHHHHHHHHHH-HHHHHHHHHHCCH Q ss_conf 999999999999999622379898999996199978999999999999-9999999995711 Q gi|254780723|r 58 KELREAIQKIELNHKAKIGNTKSIDSLISCSGLPISKQHYYIGSCVIG-FICGVLSLTLSSS 118 (137) Q Consensus 58 ksvq~sLKelE~rqk~~~k~~~sl~~rL~QAGL~~s~~~F~i~S~v~g-~v~~~i~~i~g~~ 118 (137) |.++.-++.+|.|---..++-.+++.+|+- ++-..-||.-.+.| ++.+++++++.++ T Consensus 2 k~l~~di~~LE~r~~v~ekdI~~in~~L~k----I~~NTtWIlRlIigaii~avl~~iikGg 59 (60) T pfam10779 2 KELERRIRDLETRTAVNEKDIKNINKRLGK----IEDNTTWILRLIIGAIITAVLTFIIKGG 59 (60) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHCCC T ss_conf 278999999988744249999999989988----8401289999999999999999997077 No 30 >PRK06231 F0F1 ATP synthase subunit B; Validated Probab=42.05 E-value=25 Score=16.54 Aligned_cols=22 Identities=5% Similarity=0.072 Sum_probs=7.8 Q ss_pred HHHHHHHHHHH-HCCHHHHHHHH Q ss_conf 99999999996-30604778999 Q gi|254780723|r 17 VFCFLYAIFYN-VINPGDSKSQD 38 (137) Q Consensus 17 vg~laya~~yp-~ls~~~~~aqr 38 (137) ..-+.+-+.|+ ...-=+.|.++ T Consensus 61 Ll~lL~k~awKPI~k~Ld~R~~k 83 (201) T PRK06231 61 LLLLGIFLFWKPTQRFLNKRKEL 83 (201) T ss_pred HHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999787899999999999 No 31 >KOG1830 consensus Probab=40.28 E-value=19 Score=17.25 Aligned_cols=16 Identities=25% Similarity=0.175 Sum_probs=8.0 Q ss_pred HHHHHHHHHHHHHHHC Q ss_conf 9999999999996223 Q gi|254780723|r 61 REAIQKIELNHKAKIG 76 (137) Q Consensus 61 q~sLKelE~rqk~~~k 76 (137) |+.|||.|++-|+|+| T Consensus 163 ekmLqdted~~kekrk 178 (518) T KOG1830 163 EKMLQDTEDKMKEKRK 178 (518) T ss_pred HHHHHHHHHHHHHHHH T ss_conf 9998889998753444 No 32 >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=39.98 E-value=31 Score=15.97 Aligned_cols=24 Identities=8% Similarity=-0.079 Sum_probs=12.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 999999999999999999996306 Q gi|254780723|r 7 WFLVGLITVSVFCFLYAIFYNVIN 30 (137) Q Consensus 7 l~~~gL~~vavg~laya~~yp~ls 30 (137) ++.-.+.-+....+.+-|+||-+. T Consensus 2 l~~qlI~F~il~~il~~~~~~pi~ 25 (132) T pfam00430 2 LETNLINFLILVGLLIYFGYKPLG 25 (132) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 888999999999999999798899 No 33 >TIGR00883 2A0106 MFS transporter, metabolite:H+ symporter (MHS) family protein; InterPro: IPR004736 Recent genome-sequencing data and a wealth of biochemical and molecular genetic investigations have revealed the occurrence of dozens of families of primary and secondary transporters. Two such families have been found to occur ubiquitously in all classifications of living organisms. These are the ATP-binding cassette (ABC) superfamily and the major facilitator superfamily (MFS), also called the uniporter-symporter-antiporter family. While ABC family permeases are in general multicomponent primary active transporters, capable of transporting both small molecules and macromolecules in response to ATP hydrolysis the MFS transporters are single-polypeptide secondary carriers capable only of transporting small solutes in response to chemiosmotic ion gradients. Although well over 100 families of transporters have now been recognized and classified, the ABC superfamily and MFS account for nearly half of the solute transporters encoded within the genomes of microorganisms. They are also prevalent in higher organisms. The importance of these two families of transport systems to living organisms can therefore not be overestimated . The MFS was originally believed to function primarily in the uptake of sugars but subsequent studies revealed that drug efflux systems, Krebs cycle metabolites, organophosphate:phosphate exchangers, oligosaccharide:H1 symport permeases, and bacterial aromatic acid permeases were all members of the MFS. These observations led to the probability that the MFS is far more widespread in nature and far more diverse in function than had been thought previously. 17 subgroups of the MFS have been identified . Evidence suggests that the MFS permeases arose by a tandem intragenic duplication event in the early prokaryotes. This event generated a 2-transmembrane-spanner (TMS) protein topology from a primordial 6-TMS unit. Surprisingly, all currently recognized MFS permeases retain the two six-TMS units within a single polypeptide chain, although in 3 of the 17 MFS families, an additional two TMSs are found . Moreover, the well-conserved MFS specific motif between TMS2 and TMS3 and the related but less well conserved motif between TMS8 and TMS9 prove to be a characteristic of virtually all of the more than 300 MFS proteins identified. This entry represents the metabolite-H(+) symport (MHS) subfamily of the MFS. Members include citrate-proton symporters , alpha-ketoglutarate permease , shikimate transporters , and the proline/betaine transporter ProP .; GO: 0005215 transporter activity, 0006810 transport, 0016021 integral to membrane. Probab=37.82 E-value=34 Score=15.76 Aligned_cols=54 Identities=9% Similarity=0.086 Sum_probs=23.3 Q ss_pred CCCCHHHHHHHCCCCCCHHHHHHH--HHHHHHHHHHHHHHHCCHHHHHHH----HHHHHHHCCCC Q ss_conf 798989999961999789999999--999999999999995711899999----99999748876 Q gi|254780723|r 77 NTKSIDSLISCSGLPISKQHYYIG--SCVIGFICGVLSLTLSSSFFTFLC----VSVSSALVFPR 135 (137) Q Consensus 77 ~~~sl~~rL~QAGL~~s~~~F~i~--S~v~g~v~~~i~~i~g~~~l~a~g----~a~~~glGLPR 135 (137) ++.++..-+++ .++.|+++ ..++..+++-+.-+.-++-..... .+.+-|||+|+ T Consensus 211 ~~~p~~~~~~~-----~~~~~~~~~~~~~~~~~~fY~~t~y~~~Y~~~~~~vsEAGYA~GLg~~~ 270 (413) T TIGR00883 211 KRIPLAELLTK-----HRKAFLLVLGLVIATTTTFYLITTYLPTYLTTTLGVSEAGYALGLGLSA 270 (413) T ss_pred CCCCHHHHHHH-----CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCH T ss_conf 67409999872-----2299999999999989999999999999886516751456877326876 No 34 >pfam06024 DUF912 Nucleopolyhedrovirus protein of unknown function (DUF912). This family consists of several Nucleopolyhedrovirus proteins of unknown function. Probab=37.55 E-value=34 Score=15.73 Aligned_cols=31 Identities=32% Similarity=0.323 Sum_probs=19.5 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHCCHH Q ss_conf 7034699999999999999999999630604 Q gi|254780723|r 2 FDVNSWFLVGLITVSVFCFLYAIFYNVINPG 32 (137) Q Consensus 2 ~~~~~l~~~gL~~vavg~laya~~yp~ls~~ 32 (137) +.+|.+++..++.+++.-+.|+.+|=.+.-+ T Consensus 59 ~~~~~ili~ll~~~~ilvlly~IyYFVILRe 89 (101) T pfam06024 59 NAGNIILIGLLAFFCVLVLLYAIYYFVILRE 89 (101) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHEEEE T ss_conf 0024589999999999999999998623641 No 35 >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=36.42 E-value=33 Score=15.77 Aligned_cols=14 Identities=36% Similarity=0.423 Sum_probs=7.1 Q ss_pred HHHHHHHHHHHHHH Q ss_conf 89999999999999 Q gi|254780723|r 54 TKRRKELREAIQKI 67 (137) Q Consensus 54 ~kRRksvq~sLKel 67 (137) .+|+.++.+..+.- T Consensus 71 ~k~~~~~~ee~~~~ 84 (147) T TIGR01144 71 NKRGSEILEEIKAE 84 (147) T ss_pred HHHHHHHHHHHHHH T ss_conf 78888869999999 No 36 >pfam07578 LAB_N Lipid A Biosynthesis N-terminal domain. This family is found at the N-terminus of a group of Chlamydial Lipid A biosynthesis proteins. It is also found by itself in a family of proteins of unknown function. Probab=35.19 E-value=37 Score=15.50 Aligned_cols=36 Identities=11% Similarity=0.085 Sum_probs=26.7 Q ss_pred HCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCHHHHH Q ss_conf 619997899999999999999999999957118999 Q gi|254780723|r 87 CSGLPISKQHYYIGSCVIGFICGVLSLTLSSSFFTF 122 (137) Q Consensus 87 QAGL~~s~~~F~i~S~v~g~v~~~i~~i~g~~~l~a 122 (137) .++-+..|.-||..|..=++..+.-++.-..+.++. T Consensus 22 k~k~sviP~~FW~lSl~Gs~lll~Y~i~r~Dpv~il 57 (72) T pfam07578 22 KAKRSVVPRLFWYLSVLGGLLMLVYFIIQSDPVNIL 57 (72) T ss_pred HCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCHHEE T ss_conf 459974868999999999999999999973844024 No 37 >COG2966 Uncharacterized conserved protein [Function unknown] Probab=34.58 E-value=38 Score=15.44 Aligned_cols=42 Identities=12% Similarity=0.214 Sum_probs=32.3 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHC Q ss_conf 978999999999999999999999571189999999999748 Q gi|254780723|r 91 PISKQHYYIGSCVIGFICGVLSLTLSSSFFTFLCVSVSSALV 132 (137) Q Consensus 91 ~~s~~~F~i~S~v~g~v~~~i~~i~g~~~l~a~g~a~~~glG 132 (137) .-.+-.+|..-...|+.+..+++++|+++..++-..|++.++ T Consensus 119 ~~~~y~~~l~~~~~g~~~~~f~~l~gG~w~d~~iaf~~~~~~ 160 (250) T COG2966 119 QPLRYSRWLVLLMAGLAAAAFALLFGGGWLDFLIAFFAGLLG 160 (250) T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHH T ss_conf 865566689999999999999999089538889999999999 No 38 >pfam09340 NuA4 Histone acetyltransferase subunit NuA4. The NuA4 histone acetyltransferase (HAT) multisubunit complex is responsible for acetylation of histone H4 and H2A N-terminal tails in yeast. NuA4 complexes are highly conserved in eukaryotes and play primary roles in transcription, cellular response to DNA damage, and cell cycle control. Probab=33.41 E-value=37 Score=15.48 Aligned_cols=20 Identities=15% Similarity=0.331 Sum_probs=16.2 Q ss_pred CCHHHHHHHHHHHHHHHHHH Q ss_conf 20589999999999999999 Q gi|254780723|r 51 TANTKRRKELREAIQKIELN 70 (137) Q Consensus 51 ~~~~kRRksvq~sLKelE~r 70 (137) .+.-++|+.++++|+.+|+. T Consensus 5 ~~ll~kK~~Le~~L~~lE~q 24 (80) T pfam09340 5 KELLQKKKKLEKELAALERQ 24 (80) T ss_pred HHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999999999999 No 39 >cd01324 cbb3_Oxidase_CcoQ Cytochrome cbb oxidase CcoQ. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. Found exclusively in proteobacteria, cbb3 is believed to be a modern enzyme that has evolved independently to perform a specialized function in microaerobic energy metabolism. The cbb3 operon contains four genes (ccoNOQP or fixNOQP), with ccoN coding for subunit I. Instead of a CuA-containing subunit II analogous to other cytochrome oxidases, cbb3 utilizes subunits ccoO and ccoP, which contain one and two hemes, respectively, to transfer electrons to the binuclear center. ccoQ, the fourth subunit, is a single transmembrane helix protein. It has been shown to protect the core complex from proteolytic degradation by serine proteases. See cd00919, cd01322 Probab=32.65 E-value=36 Score=15.58 Aligned_cols=33 Identities=30% Similarity=0.388 Sum_probs=23.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH Q ss_conf 46999999999999999999996306047789999999 Q gi|254780723|r 5 NSWFLVGLITVSVFCFLYAIFYNVINPGDSKSQDNAKV 42 (137) Q Consensus 5 ~~l~~~gL~~vavg~laya~~yp~ls~~~~~aqrr~~~ 42 (137) ++|.+..+...-+|.+.||+- |+.++.-+++.. T Consensus 12 dsWgLl~~~~~Figvv~wa~~-----Pg~k~~~deaA~ 44 (48) T cd01324 12 DSWGLLYLALFFLGVVVWAFR-----PGRKKAFDEAAN 44 (48) T ss_pred HHHHHHHHHHHHHHHHHHHCC-----CCCCHHHHHHHC T ss_conf 999999999999999875058-----876235788754 No 40 >pfam07332 DUF1469 Protein of unknown function (DUF1469). This family consists of several hypothetical bacterial proteins of around 140 residues in length. The function of this family is unknown. Probab=32.46 E-value=41 Score=15.23 Aligned_cols=12 Identities=25% Similarity=0.470 Sum_probs=4.7 Q ss_pred HHHHHHHCCCCC Q ss_conf 999997488765 Q gi|254780723|r 125 VSVSSALVFPRF 136 (137) Q Consensus 125 ~a~~~glGLPRw 136 (137) .++....++|.| T Consensus 61 ~~l~~~~~l~~w 72 (121) T pfam07332 61 AALWEALRLPAW 72 (121) T ss_pred HHHHHHHHHHHH T ss_conf 999997621689 No 41 >pfam11026 DUF2721 Protein of unknown function (DUF2721). This family is conserved in bacteria. The function is not known. Probab=31.73 E-value=42 Score=15.15 Aligned_cols=16 Identities=19% Similarity=0.409 Sum_probs=8.0 Q ss_pred HHHHHHHHHHHHHHHH Q ss_conf 9999999999999999 Q gi|254780723|r 56 RRKELREAIQKIELNH 71 (137) Q Consensus 56 RRksvq~sLKelE~rq 71 (137) .++....+++.+++|- T Consensus 44 ~~~~~~~ql~~L~~R~ 59 (130) T pfam11026 44 ERARIRRQIRNLRRRA 59 (130) T ss_pred CHHHHHHHHHHHHHHH T ss_conf 0678999999999999 No 42 >TIGR02745 ccoG_rdxA_fixG cytochrome c oxidase accessory protein CcoG; InterPro: IPR014116 Member of this ferredoxin-like protein family, include FixG, CcoG and RdxA,. They are found exclusively in species with an operon encoding the cbb3 type of cytochrome c oxidase (cco-cbb3), and near the cco-cbb3 operon in about half the cases. The cco-cbb3 is found in a variety of proteobacteria and almost nowhere else; it is associated with oxygen use under microaerobic conditions. Some (but not all) of these proteobacteria are also nitrogen-fixing, hence the gene symbol fixG. FixG was shown essential for functional cco-cbb3 expression in Bradyrhizobium japonicum.. Probab=31.37 E-value=43 Score=15.12 Aligned_cols=21 Identities=14% Similarity=0.501 Sum_probs=16.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHH Q ss_conf 034699999999999999999 Q gi|254780723|r 3 DVNSWFLVGLITVSVFCFLYA 23 (137) Q Consensus 3 ~~~~l~~~gL~~vavg~laya 23 (137) -|+..++++|..++..||.+. T Consensus 53 pqe~~Ll~~lLi~aalgLFfi 73 (474) T TIGR02745 53 PQEFYLLAGLLIIAALGLFFI 73 (474) T ss_pred HHHHHHHHHHHHHHHHHHHHH T ss_conf 036889999999999999999 No 43 >pfam04678 DUF607 Protein of unknown function, DUF607. This family represents a conserved region found in several uncharacterized eukaryotic proteins. Probab=30.51 E-value=42 Score=15.14 Aligned_cols=44 Identities=18% Similarity=0.166 Sum_probs=24.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCHHHH Q ss_conf 89999999999999999996223798989999961999789999 Q gi|254780723|r 54 TKRRKELREAIQKIELNHKAKIGNTKSIDSLISCSGLPISKQHY 97 (137) Q Consensus 54 ~kRRksvq~sLKelE~rqk~~~k~~~sl~~rL~QAGL~~s~~~F 97 (137) .+|-+.+++.|..+|+.+++-+++-..-..|+..+||..-.-|+ T Consensus 54 ~~~l~~~~~~l~~le~~k~e~d~~A~~~~~r~~w~Gl~~l~~Q~ 97 (171) T pfam04678 54 RKRLEALSEELAPLEEIKKEIDRLAHRRARRLLWGGLGLLSAQW 97 (171) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 66478999999999999999999999998999999999999999 No 44 >COG1575 MenA 1,4-dihydroxy-2-naphthoate octaprenyltransferase [Coenzyme metabolism] Probab=29.88 E-value=45 Score=14.96 Aligned_cols=56 Identities=13% Similarity=0.121 Sum_probs=38.7 Q ss_pred HHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCHHHHH Q ss_conf 999999999999962237989899999619997899999999999999999999957118999 Q gi|254780723|r 60 LREAIQKIELNHKAKIGNTKSIDSLISCSGLPISKQHYYIGSCVIGFICGVLSLTLSSSFFTF 122 (137) Q Consensus 60 vq~sLKelE~rqk~~~k~~~sl~~rL~QAGL~~s~~~F~i~S~v~g~v~~~i~~i~g~~~l~a 122 (137) .-.+++|+|+-.|. + |.|+-.||.+.. -+++|....+...++.++..+++..++.. T Consensus 194 ~aNNirDie~D~~~-g--k~TLavrLG~~~----~~~l~~~l~~~a~l~~~~~~i~~~~~~~~ 249 (303) T COG1575 194 LANNLRDIEEDIRN-G--KYTLAVRLGRKN----ARKLYAALLVVAYLAIVIFVILGLFPVWG 249 (303) T ss_pred HHCCCCCCHHHHHC-C--CCCEEEEECCHH----HHHHHHHHHHHHHHHHHHHHHHHHCCHHH T ss_conf 86213345017866-9--601134625475----89999999999999999999996221799 No 45 >pfam04791 LMBR1 LMBR1-like membrane protein. Members of this family are integral membrane proteins that are around 500 residues in length. LMBR1 is not involved in preaxial polydactyly, as originally thought. Vertebrate members of this family may play a role in limb development. A member of this family has been shown to be a lipocalin membrane receptor Probab=29.34 E-value=46 Score=14.90 Aligned_cols=29 Identities=21% Similarity=0.264 Sum_probs=18.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHH Q ss_conf 99999999999999999999957118999 Q gi|254780723|r 94 KQHYYIGSCVIGFICGVLSLTLSSSFFTF 122 (137) Q Consensus 94 ~~~F~i~S~v~g~v~~~i~~i~g~~~l~a 122 (137) ..-.+.+..++|++...+.++...+.+.. T Consensus 264 ~~l~~~~~~vl~Vv~~ilSll~~~~~~~~ 292 (419) T pfam04791 264 TLLVLTFCSILGVVTNTLSLLVVESELPF 292 (419) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999999999999999999986 No 46 >PRK09174 F0F1 ATP synthase subunit B'; Validated Probab=28.94 E-value=47 Score=14.86 Aligned_cols=24 Identities=21% Similarity=0.271 Sum_probs=10.1 Q ss_pred HHHHHHHHHHHHHHHH-HHHHHHCC Q ss_conf 9999999999999999-99996306 Q gi|254780723|r 7 WFLVGLITVSVFCFLY-AIFYNVIN 30 (137) Q Consensus 7 l~~~gL~~vavg~lay-a~~yp~ls 30 (137) -++=.+++-.++-+.. =++.|.++ T Consensus 55 QifWL~I~F~~lY~~~sk~~lPrI~ 79 (204) T PRK09174 55 QLLWLAITFGLFYLFLSRVILPRIG 79 (204) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999999999999999999760377 No 47 >PRK11404 putative PTS transporter components IIBC; Provisional Probab=28.72 E-value=47 Score=14.84 Aligned_cols=34 Identities=9% Similarity=0.171 Sum_probs=26.1 Q ss_pred HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCC Q ss_conf 99999999999999995711899999999997488 Q gi|254780723|r 99 IGSCVIGFICGVLSLTLSSSFFTFLCVSVSSALVF 133 (137) Q Consensus 99 i~S~v~g~v~~~i~~i~g~~~l~a~g~a~~~glGL 133 (137) +++..+--+...+.|+..++++++++..+. ++|. T Consensus 127 ~ykhLMtGVSyMlPfVVaGGiliAia~l~~-~~g~ 160 (482) T PRK11404 127 VMSHLMAGVSAALPFVIGGGILVALANMLV-QFGL 160 (482) T ss_pred HHHHHHCCCCHHHHHHHHHHHHHHHHHHHH-HCCC T ss_conf 999998062355569999789999999987-5288 No 48 >pfam11970 Git3_C G protein-coupled glucose receptor regulating Gpa2 C-term. Git3 is one of six proteins required for glucose-triggered adenylate cyclase activation, and is a G protein-coupled receptor responsible for the activation of adenylate cyclase through Gpa2 - heterotrimeric G protein alpha subunit, part of the glucose-detection pathway. Git3 contains seven predicted transmembrane domains, a third cytoplasmic loop and a cytoplasmic tail. This family is the conserved C-terminal domain of the member proteins. Probab=28.26 E-value=37 Score=15.52 Aligned_cols=14 Identities=43% Similarity=0.726 Sum_probs=11.0 Q ss_pred HHHHHHHHHHHHHH Q ss_conf 99999999999999 Q gi|254780723|r 55 KRRKELREAIQKIE 68 (137) Q Consensus 55 kRRksvq~sLKelE 68 (137) +||++||+++|-+= T Consensus 2 krr~~I~rq~r~iF 15 (76) T pfam11970 2 KRRKQIRKQLKSIF 15 (76) T ss_pred CHHHHHHHHHHHHH T ss_conf 36899999998999 No 49 >PRK03814 oxaloacetate decarboxylase subunit gamma; Provisional Probab=27.84 E-value=49 Score=14.74 Aligned_cols=29 Identities=10% Similarity=0.221 Sum_probs=17.0 Q ss_pred CCHHHHHHHHHHHH-HHHHHHHHHHHHHHC Q ss_conf 97034699999999-999999999999630 Q gi|254780723|r 1 MFDVNSWFLVGLIT-VSVFCFLYAIFYNVI 29 (137) Q Consensus 1 m~~~~~l~~~gL~~-vavg~laya~~yp~l 29 (137) |+|++.|+.-|+-- +..=|+-|.|+--++ T Consensus 1 M~~~~ell~ea~~LM~~GMg~VFvFL~lLI 30 (85) T PRK03814 1 MTDIGSLLVDAATLMLTGMGVVFIFLTILV 30 (85) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 976899999999999986699999999999 No 50 >pfam05039 Agouti Agouti protein. The agouti protein regulates pigmentation in the mouse hair follicle producing a black hair with a subapical yellow band. A highly homologous protein agouti signal protein (ASIP)is present in humans and is expressed at highest levels in adipose tissue where it may play a role in energy homeostasis and possibly human pigmentation. Probab=27.64 E-value=49 Score=14.72 Aligned_cols=56 Identities=14% Similarity=0.105 Sum_probs=24.9 Q ss_pred HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHH---CCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999996306047789999999775420---1220589999999999999999996 Q gi|254780723|r 17 VFCFLYAIFYNVINPGDSKSQDNAKVVRADRV---IPTANTKRRKELREAIQKIELNHKA 73 (137) Q Consensus 17 vg~laya~~yp~ls~~~~~aqrr~~~~~a~R~---~~~~~~kRRksvq~sLKelE~rqk~ 73 (137) .+.+.+-.+|.-++++.+.+-.+.. -+.+.. ......-++++=.-+.+|.|++++. T Consensus 7 L~~~~~l~~~shL~~ee~~~~~~~l-r~~d~~~~P~vsiv~L~k~~kk~s~~eaE~kk~~ 65 (121) T pfam05039 7 LSVLLLLTLAAHLSPEEDLSPDRGI-RRSDNALDPEVSIVGLPKGLKKFNKNEAEEKKKS 65 (121) T ss_pred HHHHHHHHHHHHHCHHCCCCCCCCC-CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHH T ss_conf 9999998888731112156752234-5665434755563213737899889999988886 No 51 >pfam06120 Phage_HK97_TLTM Tail length tape measure protein. This family consists of the tail length tape measure protein from bacteriophage HK97 and related sequences from Escherichia coli O157:H7. Probab=26.49 E-value=52 Score=14.59 Aligned_cols=85 Identities=15% Similarity=0.234 Sum_probs=42.7 Q ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHH---------CCCCHHHHHHHHHHHHHHHHHHHHHHHCCCC- Q ss_conf 999999999999999996306047789999999775420---------1220589999999999999999996223798- Q gi|254780723|r 10 VGLITVSVFCFLYAIFYNVINPGDSKSQDNAKVVRADRV---------IPTANTKRRKELREAIQKIELNHKAKIGNTK- 79 (137) Q Consensus 10 ~gL~~vavg~laya~~yp~ls~~~~~aqrr~~~~~a~R~---------~~~~~~kRRksvq~sLKelE~rqk~~~k~~~- 79 (137) .||+++++|+. |.+ |..-.-.+.-++..+..+-..|. ...+..+-++++..+.++|++.+.+-..-+- T Consensus 29 pGlvmlaAGA~-Y~~-YQ~qeQAresA~~yA~~ideIr~kl~~Ms~~el~~n~~k~~~sL~~Qn~~i~~qeqkI~~lk~~ 106 (311) T pfam06120 29 PGILMLGAGAW-YAL-YQNQEQARESAIDYADTIEEIRDKLKEMSLPEASANEGKANEALDAQNRAIEDQEQKIAEIKDA 106 (311) T ss_pred HHHHHHHHHHH-HHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 78999998899-999-9989999999999997699999987737817655327789998999998899899899999999 Q ss_pred --CHHHHHHHCCCCCCHHHHH Q ss_conf --9899999619997899999 Q gi|254780723|r 80 --SIDSLISCSGLPISKQHYY 98 (137) Q Consensus 80 --sl~~rL~QAGL~~s~~~F~ 98 (137) -+...+.+-| ||..-|. T Consensus 107 i~~yq~~l~~~~--~s~~~~~ 125 (311) T pfam06120 107 ISGYNAKLAANG--ASEGGWL 125 (311) T ss_pred HHHHHHHHHCCC--CCCCHHH T ss_conf 999999983788--7742245 No 52 >pfam01237 Oxysterol_BP Oxysterol-binding protein. Probab=25.16 E-value=45 Score=14.98 Aligned_cols=25 Identities=8% Similarity=0.173 Sum_probs=16.1 Q ss_pred HHHHHHHHHHCCCCCHHHHHHHCCCCCCHHHH Q ss_conf 99999996223798989999961999789999 Q gi|254780723|r 66 KIELNHKAKIGNTKSIDSLISCSGLPISKQHY 97 (137) Q Consensus 66 elE~rqk~~~k~~~sl~~rL~QAGL~~s~~~F 97 (137) .+|++|++++|. -...|-.|.|+-| T Consensus 289 ~lEe~QR~~rk~-------r~~~g~~w~P~~F 313 (337) T pfam01237 289 RLEEKQRERRKE-------REEKGEEWKPRWF 313 (337) T ss_pred HHHHHHHHHHHH-------HHHCCCCCCCCCE T ss_conf 999999999998-------8765998056707 No 53 >pfam03245 Phage_lysis Bacteriophage lysis protein. This protein is involved in host lysis. This family is not considered to be a peptidase according to the MEROPs database. Probab=24.02 E-value=58 Score=14.31 Aligned_cols=55 Identities=7% Similarity=0.189 Sum_probs=19.5 Q ss_pred HHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999963060477899999997754201220589999999999999999996 Q gi|254780723|r 15 VSVFCFLYAIFYNVINPGDSKSQDNAKVVRADRVIPTANTKRRKELREAIQKIELNHKA 73 (137) Q Consensus 15 vavg~laya~~yp~ls~~~~~aqrr~~~~~a~R~~~~~~~kRRksvq~sLKelE~rqk~ 73 (137) +...++.|+ .| -+......+.+.++...-+....+. .....-|..+-+++.|.-+ T Consensus 14 ~l~~al~w~-hy--~~~a~~~k~q~~~~~~~l~~~~a~i-~~~q~r~r~la~LD~k~tk 68 (151) T pfam03245 14 ALLLALAWA-TY--RDNADTAERQRDQATAELALANATI-EDMQTRQRDLAALDAKHTK 68 (151) T ss_pred HHHHHHHHH-HH--HHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHH T ss_conf 999999999-99--8779999999999999999999799-9999999999999789999 No 54 >TIGR00833 actII Transport protein; InterPro: IPR004707 Characterised members of the Resistance-Nodulation-Cell Division (RND) superfamily all probably catalyze substrate efflux via an H+ antiport mechanism. These proteins are found ubiquitously in bacteria, archaea and eukaryotes. This group includes the Streptomyces coelicolor ActII3 protein, which may play a role in drug resistance, and the Mycobacterium tuberculosis MmpL7 protein, which catalyzes export of an outer membrane lipid, phthiocerol dimycocerosate.; GO: 0016021 integral to membrane. Probab=23.74 E-value=58 Score=14.28 Aligned_cols=50 Identities=10% Similarity=0.070 Sum_probs=35.5 Q ss_pred CHHHHHHHCCCCCCHHHHHHH---HHHHHHHHHHHHHHHCCHHHHHHHHHHHH Q ss_conf 989999961999789999999---99999999999999571189999999999 Q gi|254780723|r 80 SIDSLISCSGLPISKQHYYIG---SCVIGFICGVLSLTLSSSFFTFLCVSVSS 129 (137) Q Consensus 80 sl~~rL~QAGL~~s~~~F~i~---S~v~g~v~~~i~~i~g~~~l~a~g~a~~~ 129 (137) .++.=+..+|--+.-.-+-+. -+.+.+.+.-+.++-+.++..+.|+.++. T Consensus 277 A~~~A~r~~g~aI~gsa~tv~tsl~~~l~Ls~a~l~~f~~lG~~~avG~l~~~ 329 (992) T TIGR00833 277 ALAEALRGTGKAILGSALTVATSLVAFLALSLARLPSFKTLGVVCAVGVLVAL 329 (992) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999998889999889999999999999999875443223699999999999 No 55 >pfam06504 RepC Replication protein C (RepC). This family consists of several bacterial replication protein C (RepC) sequences. Probab=23.49 E-value=59 Score=14.25 Aligned_cols=19 Identities=32% Similarity=0.463 Sum_probs=13.9 Q ss_pred CCCHHHHHHHHHHHHHHHH Q ss_conf 2205899999999999999 Q gi|254780723|r 50 PTANTKRRKELREAIQKIE 68 (137) Q Consensus 50 ~~~~~kRRksvq~sLKelE 68 (137) +.+.++||..+.+.|.|++ T Consensus 242 ~~~~rkRr~~vR~AL~el~ 260 (283) T pfam06504 242 GEAMKKRRQTARKALPELA 260 (283) T ss_pred HHHHHHHHHHHHHHHHHHH T ss_conf 1788999999999999999 No 56 >PRK10947 global DNA-binding transcriptional dual regulator H-NS; Provisional Probab=22.99 E-value=61 Score=14.19 Aligned_cols=36 Identities=17% Similarity=0.269 Sum_probs=24.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCC Q ss_conf 8999999999999999999622379898999996199978 Q gi|254780723|r 54 TKRRKELREAIQKIELNHKAKIGNTKSIDSLISCSGLPIS 93 (137) Q Consensus 54 ~kRRksvq~sLKelE~rqk~~~k~~~sl~~rL~QAGL~~s 93 (137) ..||+..+...++.++|+.+-. .+...|.++|++.+ T Consensus 38 ~Erreee~~~~~e~~er~~Kl~----~~~e~l~~~Gid~~ 73 (135) T PRK10947 38 NERREEESAAAAEVEERTRKLQ----QYREMLIADGIDPN 73 (135) T ss_pred HHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHCCCCHH T ss_conf 9999999999999999999999----99999998599999 No 57 >TIGR01410 tatB twin arginine-targeting protein translocase TatB; InterPro: IPR003998 Translocation of proteins across the two membranes of Gram-negative bacteria can be carried out via a number of routes. Most proteins marked for export carry a secretion signal at their N-terminus, and are secreted by the general secretory pathway. The signal peptide is cleaved as they pass through the outer membrane. Other secretion systems include the type III system found in a select group of Gram-negative plant and animal pathogens, and the CagA system of Helicobacter pylori . In some bacterial species, however, there exists a system that operates independently of the Sec pathway . It selectively translocates periplasmic-bound molecules that are synthesised with, or are in close association with, "partner" proteins bearing an (S/T)RRXFLK twin arginine motif at the N-terminus. The pathway is therefore termed the Twin-Arginine Translocation or TAT system. Surprisingly, the four components that make up the TAT system are structurally and mechanistically related to a pH-dependent import system in plant chloroplast thylakoid membranes . The gene products responsible for the Sec-independent pathway are called TatA, TatB, TatC and TatE. TatB is essential for the secretion of these specific proteins, and forms a scaffold upon which TatC assembles in the membrane. Deletion studies have shown that it is crucial in the forming of the TAT complex, and is therefore necessary for the correct working of the system.; GO: 0015450 P-P-bond-hydrolysis-driven protein transmembrane transporter activity, 0009306 protein secretion, 0016020 membrane. Probab=22.85 E-value=61 Score=14.17 Aligned_cols=45 Identities=24% Similarity=0.414 Sum_probs=21.8 Q ss_pred HHHHHHHHHHHHHHHHHCCHHH--HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH Q ss_conf 9999999999999996306047--78999999977542012205899999999999 Q gi|254780723|r 12 LITVSVFCFLYAIFYNVINPGD--SKSQDNAKVVRADRVIPTANTKRRKELREAIQ 65 (137) Q Consensus 12 L~~vavg~laya~~yp~ls~~~--~~aqrr~~~~~a~R~~~~~~~kRRksvq~sLK 65 (137) |..|+|.+|- .+||++ ...+...+.+++.|...++ =|.+..+-|| T Consensus 8 LLli~vVaLv------VLGPerLP~a~R~v~~~~~~~r~~a~~---~~~~l~~el~ 54 (82) T TIGR01410 8 LLLIAVVALV------VLGPERLPVAIRAVGKFVRRLRGMASD---VKNELDEELK 54 (82) T ss_pred HHHHHHHHHH------HHCCHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHC T ss_conf 9999999998------726253278999999999999998989---9999999845 No 58 >KOG1262 consensus Probab=22.81 E-value=52 Score=14.57 Aligned_cols=52 Identities=19% Similarity=0.378 Sum_probs=24.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHH-HHH Q ss_conf 999999999999999999996306047789999999775420122058999999999999-999 Q gi|254780723|r 7 WFLVGLITVSVFCFLYAIFYNVINPGDSKSQDNAKVVRADRVIPTANTKRRKELREAIQK-IEL 69 (137) Q Consensus 7 l~~~gL~~vavg~laya~~yp~ls~~~~~aqrr~~~~~a~R~~~~~~~kRRksvq~sLKe-lE~ 69 (137) |+++.+..+-..-+.+-++|-.. ...+.-.-.+++-.+|-|.||++||| .++ T Consensus 24 wv~Vv~f~LP~S~lF~~~i~~r~-----------~~~~~~ssa~~~H~qrVkkIqkqlkew~d~ 76 (543) T KOG1262 24 WVFVVLFLLPLSFLFDLFIYFRI-----------WLVRKLSSAPREHQQRVKKIQKQLKEWLDD 76 (543) T ss_pred EEEEEHHHHHHHHHHHHHHHHHH-----------HHHHHHCCCCHHHHHHHHHHHHHHHHHCCC T ss_conf 47876535359999999999999-----------999874148367899999999998751135 No 59 >pfam11022 DUF2611 Protein of unknown function (DUF2611). This family is conserved in the Dikarya of Fungi. The function is not known. Probab=22.23 E-value=56 Score=14.41 Aligned_cols=51 Identities=10% Similarity=0.112 Sum_probs=23.9 Q ss_pred HHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999630604778999999977542012205899999999999999999 Q gi|254780723|r 14 TVSVFCFLYAIFYNVINPGDSKSQDNAKVVRADRVIPTANTKRRKELREAIQKIELNH 71 (137) Q Consensus 14 ~vavg~laya~~yp~ls~~~~~aqrr~~~~~a~R~~~~~~~kRRksvq~sLKelE~rq 71 (137) +++..+..+.+.|+..++.+...+ .+.. .......--+-|++-|++.|..+ T Consensus 18 Ai~tLgs~~~~~~~~~~g~~~~k~----~tpp---i~asS~DEEkFI~~fl~~~~~~~ 68 (70) T pfam11022 18 AIGTLGSLFGGVALATGGKKAPKP----ATPP---INASSKDEEKFIKEFLKKHSKEE 68 (70) T ss_pred HHHHHHHHHHHEEECCCCCCCCCC----CCCC---CCCCCHHHHHHHHHHHHHHHHHC T ss_conf 599999888751346778878888----9998---66788779999999999866540 No 60 >pfam00862 Sucrose_synth Sucrose synthase. Sucrose synthases catalyse the synthesis of sucrose from UDP-glucose and fructose. This family includes the bulk of the sucrose synthase protein. However the carboxyl terminal region of the sucrose synthases belongs to the glycosyl transferase family pfam00534. Probab=21.96 E-value=61 Score=14.18 Aligned_cols=32 Identities=19% Similarity=0.171 Sum_probs=12.1 Q ss_pred HHHHHHHHHHHHHHHHHCCCC--CHHHHHHHCCC Q ss_conf 999999999999996223798--98999996199 Q gi|254780723|r 59 ELREAIQKIELNHKAKIGNTK--SIDSLISCSGL 90 (137) Q Consensus 59 svq~sLKelE~rqk~~~k~~~--sl~~rL~QAGL 90 (137) +.+.+|+..|+-=.+..+.+| .++.++.--|+ T Consensus 199 ~L~~~l~~A~~~l~~~p~dtpy~~f~~~lq~lGf 232 (550) T pfam00862 199 ALQSALRKAEDYLSTLPPDTPYSEFEHKFQEIGF 232 (550) T ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCC T ss_conf 9999999999999649999986999999998378 No 61 >KOG2210 consensus Probab=21.93 E-value=64 Score=14.05 Aligned_cols=27 Identities=11% Similarity=0.056 Sum_probs=17.7 Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHCCCCCCHHHHH Q ss_conf 9999999962237989899999619997899999 Q gi|254780723|r 65 QKIELNHKAKIGNTKSIDSLISCSGLPISKQHYY 98 (137) Q Consensus 65 KelE~rqk~~~k~~~sl~~rL~QAGL~~s~~~F~ 98 (137) .+||++|++..|+ =+.-|..|.++.|- T Consensus 336 ~~iEe~QR~~ak~-------ree~g~~W~pk~F~ 362 (392) T KOG2210 336 FELEEKQRELAKK-------REESGEEWKPKLFK 362 (392) T ss_pred HHHHHHHHHHHHH-------HHHHCCCCEECCEE T ss_conf 6889999999987-------88718951320045 No 62 >TIGR03488 cas_Cas5p CRISPR-associated protein, Cas5p family. CC Members of this protein family are cas, or CRISPR-associated, proteins. The two sequences in the alignment seed are found within cas gene clusters that are adjacent to CRISPR DNA repeats in two members of the order Bacteroidales, Porphyromonas gingivalis W83 and Bacteroides forsythus ATCC 43037. This cas protein family is unique to the Pgingi (Porphyromonas gingivalis) subtype, but shows some sequence similarity to genes of the Cas5 type (see TIGR02593). Probab=21.02 E-value=62 Score=14.12 Aligned_cols=23 Identities=26% Similarity=0.417 Sum_probs=17.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 58999999999999999999622 Q gi|254780723|r 53 NTKRRKELREAIQKIELNHKAKI 75 (137) Q Consensus 53 ~~kRRksvq~sLKelE~rqk~~~ 75 (137) ..|.|+.||+-++.+.+|||+-+ T Consensus 61 ~~kdr~~i~kdie~irkk~k~~~ 83 (237) T TIGR03488 61 DRKDREAIQKDIEKIRKKQKKGH 83 (237) T ss_pred CCCHHHHHHHHHHHHHHHHCCCC T ss_conf 52108999999999987500788 No 63 >pfam10112 Halogen_Hydrol 5-bromo-4-chloroindolyl phosphate hydrolysis protein. Members of this family of prokaryotic proteins mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds. Probab=20.96 E-value=67 Score=13.93 Aligned_cols=10 Identities=10% Similarity=0.368 Sum_probs=4.7 Q ss_pred CHHHHHHHHH Q ss_conf 8999999999 Q gi|254780723|r 93 SKQHYYIGSC 102 (137) Q Consensus 93 s~~~F~i~S~ 102 (137) .|++|+.++- T Consensus 120 ~P~~~~~a~~ 129 (199) T pfam10112 120 EPKRFYKAER 129 (199) T ss_pred CHHHHHHHHH T ss_conf 9798888899 No 64 >pfam00429 TLV_coat ENV polyprotein (coat polyprotein). Probab=20.94 E-value=67 Score=13.93 Aligned_cols=67 Identities=12% Similarity=0.024 Sum_probs=32.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHH Q ss_conf 999999999999999996223798989999961999789999999999999999999995711899999999 Q gi|254780723|r 56 RRKELREAIQKIELNHKAKIGNTKSIDSLISCSGLPISKQHYYIGSCVIGFICGVLSLTLSSSFFTFLCVSV 127 (137) Q Consensus 56 RRksvq~sLKelE~rqk~~~k~~~sl~~rL~QAGL~~s~~~F~i~S~v~g~v~~~i~~i~g~~~l~a~g~a~ 127 (137) -|++|.+-=+++|+|||+......- -+..+.+++=--=.+|.++|.+..++.++.=++-++--.+.| T Consensus 492 vrd~~~klre~l~~r~r~~~~~~~w-----~~~~~~~spw~~~llstl~gpl~~lll~l~fgpci~n~l~~f 558 (560) T pfam00429 492 VRDSIAKLQERLPQRQRLLTDNQLW-----FEGLFGLSPWFTTLLSTIMGPLLLLLLILLFGPCILNRLVQF 558 (560) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCH-----HHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 8899999999999988776614650-----013556781699998888889999999998667999988875 No 65 >PRK01021 lpxB lipid-A-disaccharide synthase; Reviewed Probab=20.91 E-value=67 Score=13.93 Aligned_cols=10 Identities=10% Similarity=0.172 Sum_probs=3.5 Q ss_pred HHHHHHHHHH Q ss_conf 9999999999 Q gi|254780723|r 55 KRRKELREAI 64 (137) Q Consensus 55 kRRksvq~sL 64 (137) +.++.+++.+ T Consensus 456 ~~~~~i~e~l 465 (607) T PRK01021 456 KYDHLILDVL 465 (607) T ss_pred HHHHHHHHHH T ss_conf 6889999999 No 66 >pfam05399 EVI2A Ectropic viral integration site 2A protein (EVI2A). This family contains several mammalian ectropic viral integration site 2A (EVI2A) proteins. The function of this protein is unknown although it is thought to be a membrane protein and may function as an oncogene in retrovirus induced myeloid tumours. Probab=20.33 E-value=69 Score=13.85 Aligned_cols=33 Identities=15% Similarity=0.192 Sum_probs=22.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHH Q ss_conf 346999999999999999999996306047789 Q gi|254780723|r 4 VNSWFLVGLITVSVFCFLYAIFYNVINPGDSKS 36 (137) Q Consensus 4 ~~~l~~~gL~~vavg~laya~~yp~ls~~~~~a 36 (137) -|++|+.-|+.||+.-|.-.|+|...---.-+. T Consensus 126 s~~amLIClIiIAvLfLICtfLFLSTVVlANKv 158 (227) T pfam05399 126 SNFAMLICLIIIAALFLICTFLFLSTVVLANKV 158 (227) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 631689999999999999999999999998688 No 67 >COG2818 Tag 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair] Probab=20.07 E-value=44 Score=15.02 Aligned_cols=12 Identities=8% Similarity=0.301 Sum_probs=5.1 Q ss_pred HHHHHHHCCCCC Q ss_conf 899999619997 Q gi|254780723|r 81 IDSLISCSGLPI 92 (137) Q Consensus 81 l~~rL~QAGL~~ 92 (137) |..-|...|... T Consensus 146 mskaLKkrGf~f 157 (188) T COG2818 146 MSKALKKRGFKF 157 (188) T ss_pred HHHHHHHCCCEE T ss_conf 999999866943 Done!