Query gi|254780509|ref|YP_003064922.1| hypothetical protein CLIBASIA_01980 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 112 No_of_seqs 141 out of 240 Neff 5.0 Searched_HMMs 39220 Date Sun May 29 23:04:49 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780509.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK05684 flgJ peptidoglycan hy 99.9 1.1E-23 2.9E-28 149.6 8.3 84 22-106 5-90 (313) 2 PRK12709 flgJ peptidoglycan hy 99.9 2.1E-23 5.2E-28 148.2 8.3 82 23-106 12-93 (318) 3 TIGR02541 flagell_FlgJ flagell 99.9 2.5E-23 6.3E-28 147.8 6.9 79 27-106 3-87 (332) 4 PRK12712 flgJ peptidoglycan hy 99.9 1.2E-22 3.2E-27 143.9 8.8 92 8-106 5-96 (344) 5 PRK12710 flgJ peptidoglycan hy 99.9 1.5E-22 3.7E-27 143.5 8.2 82 24-106 6-90 (291) 6 PRK12713 flgJ peptidoglycan hy 99.9 3.3E-22 8.5E-27 141.6 8.5 84 22-106 12-96 (339) 7 PRK12711 flgJ peptidoglycan hy 99.8 2.2E-21 5.6E-26 137.1 6.9 65 41-106 14-78 (392) 8 PRK12790 chemotactic signal-re 99.8 1E-20 2.6E-25 133.5 7.6 68 39-106 31-99 (115) 9 COG3951 Rod binding protein [C 99.8 2.4E-20 6E-25 131.5 8.1 81 25-106 9-91 (166) 10 PRK12708 flgJ peptidoglycan hy 99.8 5.8E-19 1.5E-23 123.9 7.2 82 25-106 5-90 (134) 11 pfam10135 Rod-binding Rod bind 99.0 2.2E-10 5.6E-15 77.0 3.3 42 65-106 1-43 (49) 12 TIGR01371 met_syn_B12ind 5-met 51.0 18 0.00046 17.4 3.2 30 78-107 473-502 (778) 13 PRK05222 5-methyltetrahydropte 43.5 24 0.0006 16.8 2.8 31 78-108 450-480 (756) 14 TIGR02506 NrdE_NrdA ribonucleo 32.5 25 0.00065 16.6 1.6 20 91-110 100-119 (685) 15 COG0307 RibC Riboflavin syntha 23.0 5.6 0.00014 20.2 -3.2 29 79-107 113-141 (204) 16 PRK00448 polC DNA polymerase I 20.2 34 0.00086 16.0 0.3 37 53-89 1147-1186(1436) No 1 >PRK05684 flgJ peptidoglycan hydrolase; Validated Probab=99.90 E-value=1.1e-23 Score=149.58 Aligned_cols=84 Identities=18% Similarity=0.296 Sum_probs=75.3 Q ss_pred HHHHHHHHCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCC--CCCCCCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 544323120789999987022855479999999999999999999951021--123357533368999999999999998 Q gi|254780509|r 22 ISQDDSSFQSFLQLKDVQEACDKSKSVPEMTQKLQGIMFQYFIKSILPEET--VKSLGGGFNGDFWQEILAENISDVIVK 99 (112) Q Consensus 22 is~~~~s~q~~~~Lk~~~~~~~~~~~l~~~a~~fEa~fl~~~lksmr~~~~--~~~lggg~a~d~~~sMl~ee~a~~iAk 99 (112) .+....+++++++||. ++..|+.++|++||+|||++|+||||||||.+.+ +++++++.++++|++|+|+|+|+.|++ T Consensus 5 ~~~~a~D~~~L~~Lk~-~a~~d~~~al~~vA~QFEalF~q~mlKsMR~A~~~~~d~l~~s~~~~~y~~M~DqQla~~ls~ 83 (313) T PRK05684 5 LSGAALDLQSLNSLKA-KAGKDPAANLRKVAQQFEGIFVQMMLKSMRDANPVFKDGLMNSQQTKLYTSMYDQQIAQQLSA 83 (313) T ss_pred HHHHHCCHHHHHHHHH-HHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHC T ss_conf 0022218788999998-854292999999999999999999999998445523588878806779999999999999860 Q ss_pred CCCCCCC Q ss_conf 0798756 Q gi|254780509|r 100 QQRITLD 106 (112) Q Consensus 100 ~ggiGL~ 106 (112) +|||||- T Consensus 84 ~~glGla 90 (313) T PRK05684 84 GGGLGLA 90 (313) T ss_pred CCCCCHH T ss_conf 7998499 No 2 >PRK12709 flgJ peptidoglycan hydrolase; Provisional Probab=99.89 E-value=2.1e-23 Score=148.20 Aligned_cols=82 Identities=12% Similarity=0.216 Sum_probs=75.0 Q ss_pred HHHHHHHCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 44323120789999987022855479999999999999999999951021123357533368999999999999998079 Q gi|254780509|r 23 SQDDSSFQSFLQLKDVQEACDKSKSVPEMTQKLQGIMFQYFIKSILPEETVKSLGGGFNGDFWQEILAENISDVIVKQQR 102 (112) Q Consensus 23 s~~~~s~q~~~~Lk~~~~~~~~~~~l~~~a~~fEa~fl~~~lksmr~~~~~~~lggg~a~d~~~sMl~ee~a~~iAk~gg 102 (112) ++...+++++++||. .+..++.++|++||+|||++|+||||||||.+.++++++++.+.++|++|+|+|+|..|+++ | T Consensus 12 ~~~a~D~~~L~~Lk~-~a~~~~~~al~~vA~QFEalF~qmmlKsMR~a~~~~~l~~s~~~~~y~~M~DqQla~~ls~~-G 89 (318) T PRK12709 12 QRFALDVQGFDALRA-QAKASPQAGAKMVAGQFDAMFTQMMLKSMRDATPSDGLFDSHTSKMYTSMLDQQLAQQMSSK-G 89 (318) T ss_pred HHHHHHHHHHHHHHH-HHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHC-C T ss_conf 677745776999999-87419399999999999999999999999846767888787067899999999999998537-8 Q ss_pred CCCC Q ss_conf 8756 Q gi|254780509|r 103 ITLD 106 (112) Q Consensus 103 iGL~ 106 (112) |||- T Consensus 90 ~Gla 93 (318) T PRK12709 90 IGVA 93 (318) T ss_pred CCHH T ss_conf 7799 No 3 >TIGR02541 flagell_FlgJ flagellar rod assembly protein/muramidase FlgJ; InterPro: IPR013377 The N-terminal region of this protein acts directly in flagellar rod assembly, while the C-terminal region is a flagellum-specific muramidase (peptidoglycan hydrolase) required for formation of the outer membrane L ring .; GO: 0016798 hydrolase activity acting on glycosyl bonds, 0001539 ciliary or flagellar motility, 0009296 flagellum biogenesis, 0009288 flagellin-based flagellum. Probab=99.89 E-value=2.5e-23 Score=147.75 Aligned_cols=79 Identities=18% Similarity=0.307 Sum_probs=72.1 Q ss_pred HHHCCHHHHHHHHCCCCHH--HHHH--HHHHHHHHHHHHHHHHHHHHCCCCCCC--CCCCHHHHHHHHHHHHHHHHHHHC Q ss_conf 3120789999987022855--4799--999999999999999999510211233--575333689999999999999980 Q gi|254780509|r 27 SSFQSFLQLKDVQEACDKS--KSVP--EMTQKLQGIMFQYFIKSILPEETVKSL--GGGFNGDFWQEILAENISDVIVKQ 100 (112) Q Consensus 27 ~s~q~~~~Lk~~~~~~~~~--~~l~--~~a~~fEa~fl~~~lksmr~~~~~~~l--ggg~a~d~~~sMl~ee~a~~iAk~ 100 (112) .+.+++++||. ++..||. ++.+ +||+||||||++||||+||++.+++++ +.+..+++|++|+|||++++|+.+ T Consensus 3 ~D~~~L~~Lk~-kA~~dP~dG~~~~~~~~ArQFEalF~~mMLKsMReAt~k~glni~~S~~~~~y~~m~DqQ~a~~L~~~ 81 (332) T TIGR02541 3 IDAQSLDELKA-KAVKDPKDGEAAKLTEAARQFEALFLNMMLKSMREATPKDGLNIFDSQQTRFYQQMLDQQLAQQLSAR 81 (332) T ss_pred CCHHHHHHHHH-HHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCC T ss_conf 16467999998-85028810799886688889999998624455440478887653255316788635489999998458 Q ss_pred CCCCCC Q ss_conf 798756 Q gi|254780509|r 101 QRITLD 106 (112) Q Consensus 101 ggiGL~ 106 (112) +||||- T Consensus 82 ~GiGLA 87 (332) T TIGR02541 82 KGIGLA 87 (332) T ss_pred CCCCHH T ss_conf 997689 No 4 >PRK12712 flgJ peptidoglycan hydrolase; Provisional Probab=99.88 E-value=1.2e-22 Score=143.93 Aligned_cols=92 Identities=12% Similarity=0.209 Sum_probs=76.1 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHH Q ss_conf 61135543336887544323120789999987022855479999999999999999999951021123357533368999 Q gi|254780509|r 8 NISHSQSMGGNLAKISQDDSSFQSFLQLKDVQEACDKSKSVPEMTQKLQGIMFQYFIKSILPEETVKSLGGGFNGDFWQE 87 (112) Q Consensus 8 ~is~~~~M~gnla~is~~~~s~q~~~~Lk~~~~~~~~~~~l~~~a~~fEa~fl~~~lksmr~~~~~~~lggg~a~d~~~s 87 (112) +++....+++ +...++++++.||......++.++|++||+|||++|+||||||||.+.++++++++..+++|++ T Consensus 5 ~~~~~~dls~------~~a~D~~~l~~Lk~~a~~~~~~~al~~va~qFEalF~q~mlKsMR~a~~~~~~~~s~~~~~y~~ 78 (344) T PRK12712 5 TLSAQADLSQ------RFALDTQGFEALKHSARGGADAGTLQAAARQFEAVFTQMVLKSMRDATPQDGLFDNEQSKLYMS 78 (344) T ss_pred CCCCCCCHHH------HHHHCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHH T ss_conf 8786433034------5562677799999998539817899999999999999999999984677788878716789999 Q ss_pred HHHHHHHHHHHHCCCCCCC Q ss_conf 9999999999980798756 Q gi|254780509|r 88 ILAENISDVIVKQQRITLD 106 (112) Q Consensus 88 Ml~ee~a~~iAk~ggiGL~ 106 (112) |+|+|++..|+++ ||||- T Consensus 79 m~DqQla~~ls~~-G~GLa 96 (344) T PRK12712 79 MMDQQLAQQMSSR-GIGLA 96 (344) T ss_pred HHHHHHHHHHHHC-CCCHH T ss_conf 9999999998546-88899 No 5 >PRK12710 flgJ peptidoglycan hydrolase; Provisional Probab=99.88 E-value=1.5e-22 Score=143.53 Aligned_cols=82 Identities=27% Similarity=0.376 Sum_probs=72.7 Q ss_pred HHHHHHCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCC---CCCCCCCCCHHHHHHHHHHHHHHHHHHHC Q ss_conf 432312078999998702285547999999999999999999995102---11233575333689999999999999980 Q gi|254780509|r 24 QDDSSFQSFLQLKDVQEACDKSKSVPEMTQKLQGIMFQYFIKSILPEE---TVKSLGGGFNGDFWQEILAENISDVIVKQ 100 (112) Q Consensus 24 ~~~~s~q~~~~Lk~~~~~~~~~~~l~~~a~~fEa~fl~~~lksmr~~~---~~~~lggg~a~d~~~sMl~ee~a~~iAk~ 100 (112) ....+++++++||. .+..++.++|++||+|||++|+||||||||.+. .+++++.+..+++|++|+|+|+|..|+++ T Consensus 6 ~~~~D~~~L~~Lk~-~A~~~~~~al~~vA~QFEalF~qmmLKsMR~A~~~~~~~~~~~s~~~~~y~~M~DqQlA~~ls~~ 84 (291) T PRK12710 6 IATSDFQGLNELKI-QAKNNAKEALPEVAKQFEGIFLQSMLKSMRMGQHFLDESSPFSGKNEATFQEMLDAQYASTIAES 84 (291) T ss_pred HHHHCHHHHHHHHH-HHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCC T ss_conf 00415778999999-86229499999999999999999999998724466766898786167899999899999998428 Q ss_pred CCCCCC Q ss_conf 798756 Q gi|254780509|r 101 QRITLD 106 (112) Q Consensus 101 ggiGL~ 106 (112) +||||- T Consensus 85 ~g~GLA 90 (291) T PRK12710 85 KGIGLA 90 (291) T ss_pred CCCCHH T ss_conf 998599 No 6 >PRK12713 flgJ peptidoglycan hydrolase; Provisional Probab=99.87 E-value=3.3e-22 Score=141.58 Aligned_cols=84 Identities=14% Similarity=0.209 Sum_probs=73.2 Q ss_pred HHHHHHHHCCHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHC Q ss_conf 5443231207899999870-228554799999999999999999999510211233575333689999999999999980 Q gi|254780509|r 22 ISQDDSSFQSFLQLKDVQE-ACDKSKSVPEMTQKLQGIMFQYFIKSILPEETVKSLGGGFNGDFWQEILAENISDVIVKQ 100 (112) Q Consensus 22 is~~~~s~q~~~~Lk~~~~-~~~~~~~l~~~a~~fEa~fl~~~lksmr~~~~~~~lggg~a~d~~~sMl~ee~a~~iAk~ 100 (112) ++.+..++++++.||.... .++...++++||+|||++|+||||||||.+.++++++++..+++|++|+|+|+|..|+++ T Consensus 12 ~q~~a~D~~~L~~Lk~~A~~~~~~~~~~r~vA~QFEalF~q~mlKsMR~a~~~~~l~~s~~~~~y~~m~DqQla~~ls~~ 91 (339) T PRK12713 12 VQESVFDLGRLADLKRDAVKAPDGQRQQTEVARQFEALFLQMMLKRMREATPKEGLFDSQQTEMLQGMADEQLALQLASP 91 (339) T ss_pred CCHHHHCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHC T ss_conf 31323066569999999851952567799999999999999999999846777888887177899999999999998346 Q ss_pred CCCCCC Q ss_conf 798756 Q gi|254780509|r 101 QRITLD 106 (112) Q Consensus 101 ggiGL~ 106 (112) ||||- T Consensus 92 -G~Gla 96 (339) T PRK12713 92 -GIGLA 96 (339) T ss_pred -CCCHH T ss_conf -87799 No 7 >PRK12711 flgJ peptidoglycan hydrolase; Reviewed Probab=99.84 E-value=2.2e-21 Score=137.12 Aligned_cols=65 Identities=12% Similarity=0.296 Sum_probs=59.0 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCC Q ss_conf 228554799999999999999999999510211233575333689999999999999980798756 Q gi|254780509|r 41 ACDKSKSVPEMTQKLQGIMFQYFIKSILPEETVKSLGGGFNGDFWQEILAENISDVIVKQQRITLD 106 (112) Q Consensus 41 ~~~~~~~l~~~a~~fEa~fl~~~lksmr~~~~~~~lggg~a~d~~~sMl~ee~a~~iAk~ggiGL~ 106 (112) .++..++||+||+|||++|+||||||||++.++++++.+. .++|++|+|||+|..|++.|||||- T Consensus 14 ~kndpaaLr~VAqQFEslFvqMMLKSMRdAt~~d~l~ss~-sk~Y~~M~DQQLA~~LS~~gGiGLA 78 (392) T PRK12711 14 TKADPAKIDKVSRQLEGQFAQMLVKSMRDASSGDPMFPGE-NQMFREMYDQQMAKALTDGKGLGLS 78 (392) T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHH-HHHHHHHHHHHHHHHHHCCCCCCHH T ss_conf 3299899999999999999999999997178889998624-4788889999999998658997199 No 8 >PRK12790 chemotactic signal-response protein CheL; Provisional Probab=99.83 E-value=1e-20 Score=133.46 Aligned_cols=68 Identities=9% Similarity=0.243 Sum_probs=62.1 Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC-CCCCCHHHHHHHHHHHHHHHHHHHCCCCCCC Q ss_conf 7022855479999999999999999999951021123-3575333689999999999999980798756 Q gi|254780509|r 39 QEACDKSKSVPEMTQKLQGIMFQYFIKSILPEETVKS-LGGGFNGDFWQEILAENISDVIVKQQRITLD 106 (112) Q Consensus 39 ~~~~~~~~~l~~~a~~fEa~fl~~~lksmr~~~~~~~-lggg~a~d~~~sMl~ee~a~~iAk~ggiGL~ 106 (112) +..+++.+.+|++|++|||+||++||++||.+...++ ||+|.++++|||||++|||+.|||+|||||- T Consensus 31 kv~p~~~ak~k~tAqdFEA~FLn~Ml~~M~~gl~~dGpfG~g~ge~iwRSML~eeyak~iAkaGGIGIA 99 (115) T PRK12790 31 KVSPQAQAKAKATATDFEAMFLNSMFSQMTSGLKGEGPFGDTVGTGVWRSMLTEQYSKSFAKAGGVGIS 99 (115) T ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCHH T ss_conf 279367899999999999999999999998237778887898426689999999999999873886479 No 9 >COG3951 Rod binding protein [Cell envelope biogenesis, outer membrane / Cell motility and secretion / Posttranslational modification, protein turnover, chaperones] Probab=99.82 E-value=2.4e-20 Score=131.49 Aligned_cols=81 Identities=15% Similarity=0.272 Sum_probs=73.6 Q ss_pred HHHHHCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCCCHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 323120789999987022855479999999999999999999951021123--357533368999999999999998079 Q gi|254780509|r 25 DDSSFQSFLQLKDVQEACDKSKSVPEMTQKLQGIMFQYFIKSILPEETVKS--LGGGFNGDFWQEILAENISDVIVKQQR 102 (112) Q Consensus 25 ~~~s~q~~~~Lk~~~~~~~~~~~l~~~a~~fEa~fl~~~lksmr~~~~~~~--lggg~a~d~~~sMl~ee~a~~iAk~gg 102 (112) .....+.++.|+. .+..++.++|+.||+|||++|+++||||||++.++.+ ++.+..+++|++||||++|.++++++| T Consensus 9 ~~~daq~l~~lk~-~a~~d~~~~l~~~ArqfE~vFv~mMLKSMR~Al~~~~~dl~~S~q~rlY~dmyDqqlaqqlss~~g 87 (166) T COG3951 9 SAWDAQSLNELKQ-GARRDPAANLRQVARQFEGVFVQMMLKSMREALPKDGADLFNSQQTRLYTDMYDQQLAQQLSSQKG 87 (166) T ss_pred HHHHHHHHHHHHH-HHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCCCHHHHHHHHHHHHHHHHHHHHCCC T ss_conf 7999987788764-110181778999999999999999999999872530300104226889999999999999972588 Q ss_pred CCCC Q ss_conf 8756 Q gi|254780509|r 103 ITLD 106 (112) Q Consensus 103 iGL~ 106 (112) |||- T Consensus 88 ~GLA 91 (166) T COG3951 88 LGLA 91 (166) T ss_pred CCHH T ss_conf 5489 No 10 >PRK12708 flgJ peptidoglycan hydrolase; Reviewed Probab=99.77 E-value=5.8e-19 Score=123.90 Aligned_cols=82 Identities=11% Similarity=0.161 Sum_probs=70.6 Q ss_pred HHHHHCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCC----CCCCCCCCCHHHHHHHHHHHHHHHHHHHC Q ss_conf 32312078999998702285547999999999999999999995102----11233575333689999999999999980 Q gi|254780509|r 25 DDSSFQSFLQLKDVQEACDKSKSVPEMTQKLQGIMFQYFIKSILPEE----TVKSLGGGFNGDFWQEILAENISDVIVKQ 100 (112) Q Consensus 25 ~~~s~q~~~~Lk~~~~~~~~~~~l~~~a~~fEa~fl~~~lksmr~~~----~~~~lggg~a~d~~~sMl~ee~a~~iAk~ 100 (112) +.+.|.......++........+|++||+|||++|+|+|||+||.+. .++..+.+...++||+|+|+|+|..||++ T Consensus 5 ~~~~yl~~~~~~~l~k~n~e~~al~~va~QFE~~F~q~mlksMR~A~dal~~eD~p~nS~~~~~YrdM~DqQLA~~LS~~ 84 (134) T PRK12708 5 NSSPYLPGLNAGDLIPQNLEQGALKLAAQQFEAQFLQTVLKQMRSASDVMADEDDPFNSKNQGMYRDFYDAELASRLSSQ 84 (134) T ss_pred CCCCHHCCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHC T ss_conf 77520102777778660453779999999999999999999999865430456885430578899999999999999866 Q ss_pred CCCCCC Q ss_conf 798756 Q gi|254780509|r 101 QRITLD 106 (112) Q Consensus 101 ggiGL~ 106 (112) ||+||- T Consensus 85 gg~GLA 90 (134) T PRK12708 85 RSMGLA 90 (134) T ss_pred CCCCHH T ss_conf 896499 No 11 >pfam10135 Rod-binding Rod binding protein. Members of this family are involved in the assembly of the prokaryotic flagellar rod. Probab=99.00 E-value=2.2e-10 Score=77.04 Aligned_cols=42 Identities=24% Similarity=0.394 Sum_probs=37.1 Q ss_pred HHHHHCCCCCCCC-CCCHHHHHHHHHHHHHHHHHHHCCCCCCC Q ss_conf 9995102112335-75333689999999999999980798756 Q gi|254780509|r 65 KSILPEETVKSLG-GGFNGDFWQEILAENISDVIVKQQRITLD 106 (112) Q Consensus 65 ksmr~~~~~~~lg-gg~a~d~~~sMl~ee~a~~iAk~ggiGL~ 106 (112) |+||++.++++++ +++++++|++|||+|+|+.||++|||||- T Consensus 1 ksMr~t~~~~~~~~~~~~~~~~~~m~d~q~a~~~a~~ggiGLA 43 (49) T pfam10135 1 KSMRKAVPKDGLFGSGFAEDMFRSMLDQQLAKQLAKRGGIGLA 43 (49) T ss_pred CCHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCHH T ss_conf 9455358776887885399999999999999999876998699 No 12 >TIGR01371 met_syn_B12ind 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; InterPro: IPR006276 This group represents cobalamin-independent methionine synthase. A family of uncharacterised archaeal proteins having substantial homology to the C-terminal region of this family, are not included in this group, though they are contained in a larger family of vitamin-B12 independent methionine synthase.; GO: 0003871 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity, 0009086 methionine biosynthetic process. Probab=51.01 E-value=18 Score=17.44 Aligned_cols=30 Identities=27% Similarity=0.510 Sum_probs=27.6 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHCCCCCCCC Q ss_conf 753336899999999999999807987564 Q gi|254780509|r 78 GGFNGDFWQEILAENISDVIVKQQRITLDL 107 (112) Q Consensus 78 gg~a~d~~~sMl~ee~a~~iAk~ggiGL~~ 107 (112) |.-.++-|+..+-+|+.+.|..|.-||||. T Consensus 473 g~iS~e~Ye~~~k~eI~~~I~~QEelGLDV 502 (778) T TIGR01371 473 GEISEEEYEKFIKEEIKKVIKIQEELGLDV 502 (778) T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHCCCCE T ss_conf 587789999999988999998742327860 No 13 >PRK05222 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional Probab=43.55 E-value=24 Score=16.83 Aligned_cols=31 Identities=23% Similarity=0.444 Sum_probs=27.4 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHCCCCCCCCH Q ss_conf 7533368999999999999998079875640 Q gi|254780509|r 78 GGFNGDFWQEILAENISDVIVKQQRITLDLP 108 (112) Q Consensus 78 gg~a~d~~~sMl~ee~a~~iAk~ggiGL~~~ 108 (112) |-...+-|+.++.++++..|..|..||||.- T Consensus 450 G~is~~~Y~~~i~~~I~~~I~~QE~igLDVL 480 (756) T PRK05222 450 GELSAEEYEAFIKEEIARAIRLQEELGLDVL 480 (756) T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHCCCCEE T ss_conf 9989999999999999999999997299777 No 14 >TIGR02506 NrdE_NrdA ribonucleoside-diphosphate reductase, alpha subunit; InterPro: IPR013346 This entry represents the alpha (large) chain of the class I ribonucleotide reductase (RNR). RNR's are responsible for the conversion of the ribose sugar of RNA into the deoxyribose sugar of DNA. This is the rate-limiting step of DNA biosynthesis. Class I RNR's generate the required radical (on tyrosine) via a "non-heme" iron cofactor which resides in the beta (small) subunit. The alpha subunit contains the catalytic and allosteric regulatory sites. The mechanism of this enzyme requires molecular oxygen . E. coli contains two versions of this enzyme which are regulated independently (NrdAB and NrdEF, where NrdA and NrdE are the large chains , ). Most organisms contain only one, but the application of the gene symbols NrdA and NrdE are somewhat arbitrary. This model identifies RNR's in diverse clades of bacteria, eukaryotes as well as numerous DNA viruses and phage.; GO: 0005971 ribonucleoside-diphosphate reductase complex. Probab=32.47 E-value=25 Score=16.64 Aligned_cols=20 Identities=15% Similarity=0.391 Sum_probs=10.1 Q ss_pred HHHHHHHHHCCCCCCCCHHH Q ss_conf 99999999807987564010 Q gi|254780509|r 91 ENISDVIVKQQRITLDLPEI 110 (112) Q Consensus 91 ee~a~~iAk~ggiGL~~~~~ 110 (112) .+.++.++.+||||+++-++ T Consensus 100 ~~~~~l~~~~GGiG~~~~~~ 119 (685) T TIGR02506 100 DDVAQLSKHGGGIGLNLSKL 119 (685) T ss_pred HHHHHHHHCCCCEEEECCCC T ss_conf 99999986179768642340 No 15 >COG0307 RibC Riboflavin synthase alpha chain [Coenzyme metabolism] Probab=23.01 E-value=5.6 Score=20.24 Aligned_cols=29 Identities=28% Similarity=0.461 Sum_probs=24.8 Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCCC Q ss_conf 53336899999999999999807987564 Q gi|254780509|r 79 GFNGDFWQEILAENISDVIVKQQRITLDL 107 (112) Q Consensus 79 g~a~d~~~sMl~ee~a~~iAk~ggiGL~~ 107 (112) +.+-++|..+..+++++-|+.+|+|++|= T Consensus 113 ~na~~~~~~~~~~~l~kyiv~KGsIavDG 141 (204) T COG0307 113 GNAVRFWFKAPPEELAKYIVEKGSIAVDG 141 (204) T ss_pred CCEEEEEEECCCHHHHHHHCCCCEEEEEE T ss_conf 87099999759989985520464499831 No 16 >PRK00448 polC DNA polymerase III PolC; Validated Probab=20.17 E-value=34 Score=15.97 Aligned_cols=37 Identities=11% Similarity=0.230 Sum_probs=27.4 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCC---CCCCHHHHHHHHH Q ss_conf 999999999999999510211233---5753336899999 Q gi|254780509|r 53 QKLQGIMFQYFIKSILPEETVKSL---GGGFNGDFWQEIL 89 (112) Q Consensus 53 ~~fEa~fl~~~lksmr~~~~~~~l---ggg~a~d~~~sMl 89 (112) -+|+.-|+++||+.++|+...+.. |=++++|+|..+- T Consensus 1147 pEFgT~fvR~mL~~~kP~~F~DLi~IsgLsHGtdVwl~Na 1186 (1436) T PRK00448 1147 PEFGTKFVRQMLEETKPKTFAELVQISGLSHGTDVWLGNA 1186 (1436) T ss_pred CCCCCHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCCCCCH T ss_conf 4346588999999769997999999970457864443357 Done!